Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold173
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: 2040036
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
File 1 of 16
Found at i:643 original size:19 final size:19
Alignment explanation
Indices: 619--686 Score: 76
Period size: 19 Copynumber: 3.9 Consensus size: 19
609 AATTCAACGA
619 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
638 TTTGTATCAATAC--AA--
1 TTTGTATCGATACATAAGT
653 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
670 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
687 TTAGCTACTG
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
13 10 0.24
15 2 0.05
17 2 0.05
19 27 0.66
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:657 original size:32 final size:32
Alignment explanation
Indices: 621--683 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
611 TTCAACGATT
*
621 TGTATCGATACATAAGTTTTGTATCAATACAA
1 TGTATCGATACATAAGTATTGTATCAATACAA
*
653 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCAATACA
684 TAATTAGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCAATACAA
Found at i:744 original size:13 final size:13
Alignment explanation
Indices: 726--751 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
716 CATTTTTCTG
726 TGTATCGATACAT
1 TGTATCGATACAT
739 TGTATCGATACAT
1 TGTATCGATACAT
752 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:748 original size:33 final size:33
Alignment explanation
Indices: 706--772 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
696 GCCAAGGAAA
***
706 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
739 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
772 T
1 T
773 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:3199 original size:51 final size:53
Alignment explanation
Indices: 3115--3245 Score: 169
Period size: 51 Copynumber: 2.5 Consensus size: 53
3105 GAGTTATCAA
* * * *
3115 TTCTCCACAATCGGGGATATTCCAACTCCGATTTTATTTTC-AAAACACTAA-
1 TTCTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAT
* *
3166 TT-TTCTATAATCGGGGATACTCTAACTCCGATTTTATTTCCAAAAAACACCAAT
1 TTCTTC-ACAATCGGGGATACTCCAACTCCGATTTTATTTCC-AAAAACACCAAT
3220 TTCTTCACAATCGGGGATACTCCAAC
1 TTCTTCACAATCGGGGATACTCCAAC
3246 CCCGTTAATC
Statistics
Matches: 67, Mismatches: 8, Indels: 7
0.82 0.10 0.09
Matches are distributed among these distances:
50 2 0.03
51 33 0.49
53 9 0.13
54 20 0.30
55 3 0.04
ACGTcount: A:0.31, C:0.25, G:0.11, T:0.33
Consensus pattern (53 bp):
TTCTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAT
Found at i:3259 original size:27 final size:28
Alignment explanation
Indices: 3229--3331 Score: 129
Period size: 27 Copynumber: 3.8 Consensus size: 28
3219 TTTCTTCACA
*
3229 ATCGGGGATACTCCAACCCCGTTA-ATC
1 ATCGGGGATACTCCAACCCCGTTACTTC
* * *
3256 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
3284 ATC-GGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
***
3311 CGAGGGGATACTCCAACCCCG
1 ATCGGGGATACTCCAACCCCG
3332 GCTTTATTCC
Statistics
Matches: 65, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
27 43 0.66
28 22 0.34
ACGTcount: A:0.24, C:0.34, G:0.18, T:0.23
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTACTTC
Found at i:3434 original size:79 final size:79
Alignment explanation
Indices: 3287--3487 Score: 228
Period size: 79 Copynumber: 2.5 Consensus size: 79
3277 TTATTTCATC
* * * * *
3287 GGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTTATTCCCAAAATATTG
1 GGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCCGACTTTATTCCCAAAATATCG
* *
3352 ATTTCTCATAA-TG
66 ATTTCTCACAACCG
* * * ** *
3365 GGAGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAATCCCGATTTTTTTTTC-TAATCAT
1 GG-GATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCCGACTTTATTCCCAAAAT-AT
3429 CGATTTCTCACAACCG
64 CGATTTCTCACAACCG
*
3445 GGGATACTCCAGCCCCGTTATTTTC-AAGGGAATACTCCAACCC
1 GGGATACTCCAACCCCGTTATTTTCGAAGGG-ATACTCCAACCC
3488 TGTTATTATC
Statistics
Matches: 104, Mismatches: 15, Indels: 7
0.83 0.12 0.06
Matches are distributed among these distances:
78 10 0.10
79 91 0.88
80 3 0.03
ACGTcount: A:0.25, C:0.29, G:0.16, T:0.29
Consensus pattern (79 bp):
GGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCCGACTTTATTCCCAAAATATCG
ATTTCTCACAACCG
Found at i:3514 original size:79 final size:79
Alignment explanation
Indices: 3287--3517 Score: 197
Period size: 79 Copynumber: 2.9 Consensus size: 79
3277 TTATTTCATC
* * * * **
3287 GGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCT-TTAT-TCCCAAA-ATA
1 GGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAATCCCGATTATTATCT-CCAAACATA
* * *
3349 TTGATTTCTCATAA-TG
65 --AATTTCTCACAACCG
* * * * * *
3365 GGAGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAATCCCGATTTTTTTTTCTAATCATC
1 GG-GATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAATCCCGATTATTATCTCCAAACATA
*
3430 GATTTCTCACAACCG
65 AATTTCTCACAACCG
*
3445 GGGATACTCCAGCCCCGTTATTTTC-AAGGGAATACTCCAA-CCCTG-TTATTATCTCCAAACAT
1 GGGATACTCCAACCCCGTTATTTTCGAAGGG-ATACTCCAATCCC-GATTATTATCTCCAAACA-
3507 TAAATTTCTCA
63 TAAATTTCTCA
3518 TCGGGAAATA
Statistics
Matches: 125, Mismatches: 20, Indels: 15
0.78 0.12 0.09
Matches are distributed among these distances:
78 21 0.17
79 92 0.74
80 9 0.07
81 3 0.02
ACGTcount: A:0.26, C:0.28, G:0.14, T:0.31
Consensus pattern (79 bp):
GGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAATCCCGATTATTATCTCCAAACATAA
ATTTCTCACAACCG
Found at i:7397 original size:21 final size:21
Alignment explanation
Indices: 7371--7413 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
7361 ATAAGCACCG
*
7371 AGGTGCACAATTGAGGCTTAC
1 AGGTGCACAAGTGAGGCTTAC
*
7392 AGGTGCACAAGTGAGGTTTAC
1 AGGTGCACAAGTGAGGCTTAC
7413 A
1 A
7414 CCTTAATGGC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.30, C:0.16, G:0.30, T:0.23
Consensus pattern (21 bp):
AGGTGCACAAGTGAGGCTTAC
Found at i:12251 original size:21 final size:22
Alignment explanation
Indices: 12227--12270 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
12217 TTTTTGCATG
*
12227 AAAATTTTATTTTAATT-CTTT
1 AAAATTTTATTTCAATTCCTTT
12248 AAAATTTTATTTCAATTCCTTT
1 AAAATTTTATTTCAATTCCTTT
12270 A
1 A
12271 TCACTAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.34, C:0.09, G:0.00, T:0.57
Consensus pattern (22 bp):
AAAATTTTATTTCAATTCCTTT
Found at i:17757 original size:17 final size:17
Alignment explanation
Indices: 17724--17775 Score: 68
Period size: 18 Copynumber: 2.9 Consensus size: 17
17714 TTTATTTATC
17724 TAATTTTATAATTATTAGA
1 TAATTTTAT--TTATTAGA
17743 TAATTTTATTTATTAGA
1 TAATTTTATTTATTAGA
*
17760 TGAATATTATTTATTA
1 T-AATTTTATTTATTA
17776 AAATAAGTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
17 9 0.29
18 13 0.42
19 9 0.29
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (17 bp):
TAATTTTATTTATTAGA
Found at i:20157 original size:120 final size:120
Alignment explanation
Indices: 19984--20214 Score: 356
Period size: 120 Copynumber: 1.9 Consensus size: 120
19974 AGTTAGTATG
* * * *
19984 AAAAGAGGTGGTAAGTCAAATTGATATAAGAGTTGATTCTTGAATCAAGGAGAGAGATTTGTTTT
1 AAAAGAGATGGTAAGTCAAATTGATATAAGAGTTGATTATTGAATCAAGGAGAGAGATTTATTTG
* * *
20049 GTGAGAAAATAAGTTCTTTAAAGTTCTCTATAGCTATTGCTTAAAGGAGCATATA
66 GTAAGAAAATAAGTTCTTTAAAGTTCTCTATAACTATTGCTCAAAGGAGCATATA
* *
20104 AAAAGAGATGGTTAGTCAAATTGATATAAGAGTTGATTATT-ACATCAATGAGAGAGATTTATTT
1 AAAAGAGATGGTAAGTCAAATTGATATAAGAGTTGATTATTGA-ATCAAGGAGAGAGATTTATTT
*
20168 GGTAAGAAAATAAGTTCTTTAAAGTTCTCTATAACTGTTGCTCAAAG
65 GGTAAGAAAATAAGTTCTTTAAAGTTCTCTATAACTATTGCTCAAAG
20215 AGTAAAATTA
Statistics
Matches: 100, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
119 1 0.01
120 99 0.99
ACGTcount: A:0.38, C:0.08, G:0.21, T:0.34
Consensus pattern (120 bp):
AAAAGAGATGGTAAGTCAAATTGATATAAGAGTTGATTATTGAATCAAGGAGAGAGATTTATTTG
GTAAGAAAATAAGTTCTTTAAAGTTCTCTATAACTATTGCTCAAAGGAGCATATA
Found at i:21326 original size:14 final size:15
Alignment explanation
Indices: 21297--21329 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
21287 GCACCTGCAC
*
21297 GTGCCAGGTGGCCAA
1 GTGCCAAGTGGCCAA
21312 GTGCCAAGT-GCCAA
1 GTGCCAAGTGGCCAA
21326 GTGC
1 GTGC
21330 TATATAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.21, C:0.27, G:0.36, T:0.15
Consensus pattern (15 bp):
GTGCCAAGTGGCCAA
Found at i:26648 original size:14 final size:15
Alignment explanation
Indices: 26619--26651 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
26609 GCACCTGCAC
*
26619 GTGCCACGTGGCCAA
1 GTGCCAAGTGGCCAA
26634 GTGCCAAGT-GCCAA
1 GTGCCAAGTGGCCAA
26648 GTGC
1 GTGC
26652 TATATAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.21, C:0.30, G:0.33, T:0.15
Consensus pattern (15 bp):
GTGCCAAGTGGCCAA
Found at i:32997 original size:20 final size:20
Alignment explanation
Indices: 32960--32998 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
32950 CTATTCACTT
*
32960 TTCACTTATTCATGCACTCG
1 TTCACTTATTAATGCACTCG
32980 TTCACTTACTTAAT-CACTC
1 TTCACTTA-TTAATGCACTC
32999 ACACAGAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.23, C:0.31, G:0.05, T:0.41
Consensus pattern (20 bp):
TTCACTTATTAATGCACTCG
Found at i:44851 original size:165 final size:165
Alignment explanation
Indices: 44579--45021 Score: 482
Period size: 165 Copynumber: 2.7 Consensus size: 165
44569 GGTTACAATT
* * * * **
44579 AAAAATATGACAAATGCATAGATTTTATTTTTTAATAAATATGATAAATGCATAGATTATTAAT-
1 AAAAATAAGACTAATGCATGGATTTTATTTTTGAATAAATATGATAAATATATAGATTATTAATA
* * * *
44643 GAAAATCAGATTTTTCTAATATAAAAGAAGTTGATAAGACTAATGCATACATTGTAAATGTCAA-
66 G-GAATCAGATTTTTCTTATATGAAAGAAGTTGATAAGACTAATGCATACATTGTAAATG-AAAG
* * *
44707 ACTACAAGGAATAAACAAATGCATGGATT-AGAGTTCG
129 ACTACAAGGAATAAACAAATGAATGAATTGA-AATTCG
* *
44744 AAAAATAAGATTAATGCATGGATTTTATTTTTGAATAAATATGATAAATATATAGATTTTTAATA
1 AAAAATAAGACTAATGCATGGATTTTATTTTTGAATAAATATGATAAATATATAGATTATTAATA
* ** *
44809 GGAATCAGATTTTTTTTATATGAAAGAAGTTGATAAGACTAATGCATGGATTGTAAATGAAAGAT
66 GGAATCAGATTTTTCTTATATGAAAGAAGTTGATAAGACTAATGCATACATTGTAAATGAAAGAC
* *
44874 TGCAAGGAATAAACTAATGAATGAATTGAAATTCG
131 TACAAGGAATAAACAAATGAATGAATTGAAATTCG
* ** * * * * * * *
44909 AAAGATGGGACTAATGTATGGATTCT-GTTTTGAAATAAATATAATTAATGCT-TAGATTACTAA
1 AAAAATAAGACTAATGCATGGATTTTATTTTTG-AATAAATATGATAAAT-ATATAGATTATTAA
* * * *
44972 TAAGAATTAGATTCCTTCTTATATGAAAAAAGTTGATAAGACTAATGCAT
64 TAGGAATCAGATT-TTTCTTATATGAAAGAAGTTGATAAGACTAATGCAT
45022 GATGCATACC
Statistics
Matches: 234, Mismatches: 38, Indels: 11
0.83 0.13 0.04
Matches are distributed among these distances:
164 7 0.03
165 191 0.82
166 36 0.15
ACGTcount: A:0.44, C:0.07, G:0.16, T:0.34
Consensus pattern (165 bp):
AAAAATAAGACTAATGCATGGATTTTATTTTTGAATAAATATGATAAATATATAGATTATTAATA
GGAATCAGATTTTTCTTATATGAAAGAAGTTGATAAGACTAATGCATACATTGTAAATGAAAGAC
TACAAGGAATAAACAAATGAATGAATTGAAATTCG
Found at i:48301 original size:18 final size:18
Alignment explanation
Indices: 48280--48316 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
48270 TTATTAAGTA
48280 TTGATTAATTGGTTAGTC
1 TTGATTAATTGGTTAGTC
48298 TTGATTAATTGGTTAGTC
1 TTGATTAATTGGTTAGTC
48316 T
1 T
48317 ATTTAATACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.22, C:0.05, G:0.22, T:0.51
Consensus pattern (18 bp):
TTGATTAATTGGTTAGTC
Found at i:50497 original size:22 final size:23
Alignment explanation
Indices: 50453--50498 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
50443 ACCGTAATCT
***
50453 TTTTTTATTTTTTTAATTTAATA
1 TTTTTTATTTTTTTAAAAAAATA
50476 TTTTTTA-TTTTTTAAAAAAATA
1 TTTTTTATTTTTTTAAAAAAATA
50498 T
1 T
50499 AGTAATTAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (23 bp):
TTTTTTATTTTTTTAAAAAAATA
Found at i:51462 original size:3 final size:3
Alignment explanation
Indices: 51454--51483 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
51444 TAACGAGATA
51454 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
51484 TTAAAAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:51692 original size:30 final size:31
Alignment explanation
Indices: 51631--51689 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
51621 TTATGTTATT
* *
51631 TAAAAAAATTTTAATAAAAATATTATATTTA
1 TAAAAAAATTTAAATAAAAATATAATATTTA
*
51662 TAAATAAATTTAAATAAAAA-ATAA-ATTT
1 TAAAAAAATTTAAATAAAAATATAATATTT
51690 TATTTAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 4 0.16
30 3 0.12
31 18 0.72
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (31 bp):
TAAAAAAATTTAAATAAAAATATAATATTTA
Found at i:51698 original size:17 final size:17
Alignment explanation
Indices: 51626--51699 Score: 59
Period size: 17 Copynumber: 4.6 Consensus size: 17
51616 GATTTTTATG
51626 TTATTT-AAAA-AAATT
1 TTATTTAAAAATAAATT
*
51641 TTA-ATAAAAAT--ATT
1 TTATTTAAAAATAAATT
* *
51655 ATATTTATAAATAAATT
1 TTATTTAAAAATAAATT
* * *
51672 TAAATAAAAAATAAATT
1 TTATTTAAAAATAAATT
51689 TTATTTAAAAA
1 TTATTTAAAAA
51700 CGAGTCATGC
Statistics
Matches: 42, Mismatches: 12, Indels: 8
0.68 0.19 0.13
Matches are distributed among these distances:
14 6 0.14
15 13 0.31
17 23 0.55
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
TTATTTAAAAATAAATT
Found at i:51969 original size:20 final size:20
Alignment explanation
Indices: 51941--51978 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
51931 ATAAAACAAA
*
51941 GAAAGATTAATTATTTATAG
1 GAAAAATTAATTATTTATAG
*
51961 GAAAAATTAATTTTTTAT
1 GAAAAATTAATTATTTAT
51979 CCAAATTTAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.45, C:0.00, G:0.11, T:0.45
Consensus pattern (20 bp):
GAAAAATTAATTATTTATAG
Found at i:52040 original size:6 final size:6
Alignment explanation
Indices: 52029--52069 Score: 50
Period size: 6 Copynumber: 7.0 Consensus size: 6
52019 TTTGTCACAA
*
52029 TAAATT TAAATT TATATTT TAAA-T TAAA-T TAAATT TAAATT
1 TAAATT TAAATT TA-AATT TAAATT TAAATT TAAATT TAAATT
52070 AACATATACT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
5 10 0.32
6 16 0.52
7 5 0.16
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (6 bp):
TAAATT
Found at i:54255 original size:2 final size:2
Alignment explanation
Indices: 54250--54281 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
54240 TATATATATA
54250 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
54282 CCACGCCTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:55480 original size:17 final size:18
Alignment explanation
Indices: 55449--55484 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
55439 TAAATTAATT
*
55449 AAATTAATTTTTTATTTA
1 AAATTAATTTATTATTTA
55467 AAATTAA-TTATTATTTA
1 AAATTAATTTATTATTTA
55484 A
1 A
55485 TGTCTATGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
AAATTAATTTATTATTTA
Found at i:55547 original size:24 final size:23
Alignment explanation
Indices: 55520--55572 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 23
55510 AGATAGTTTT
* *
55520 TTTATTAATTTTATAATTTTTAAA
1 TTTATTAATTTGA-AATTTATAAA
*
55544 TTTATTTTATTTGAAATTTATAAA
1 TTTA-TTAATTTGAAATTTATAAA
55568 TTTAT
1 TTTAT
55573 CAAAAAAATC
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
23 1 0.04
24 17 0.68
25 7 0.28
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (23 bp):
TTTATTAATTTGAAATTTATAAA
Found at i:55708 original size:11 final size:11
Alignment explanation
Indices: 55692--55723 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
55682 TTTAAGAAAA
55692 AATAAAAAATT
1 AATAAAAAATT
55703 AATAAAAAATT
1 AATAAAAAATT
55714 -ATAAAAAATT
1 AATAAAAAATT
55724 TAAAATTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 10 0.48
11 11 0.52
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (11 bp):
AATAAAAAATT
Found at i:55717 original size:10 final size:10
Alignment explanation
Indices: 55693--55728 Score: 56
Period size: 10 Copynumber: 3.6 Consensus size: 10
55683 TTAAGAAAAA
55693 ATAAAAAATT
1 ATAAAAAATT
55703 AATAAAAAATT
1 -ATAAAAAATT
55714 ATAAAAAATT
1 ATAAAAAATT
55724 -TAAAA
1 ATAAAA
55729 TTTAATTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
9 5 0.20
10 10 0.40
11 10 0.40
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (10 bp):
ATAAAAAATT
Found at i:55811 original size:24 final size:24
Alignment explanation
Indices: 55743--55812 Score: 63
Period size: 23 Copynumber: 2.9 Consensus size: 24
55733 ATTTAATTAA
* * *
55743 TTTATATATATATAAGTTTTAAAAT
1 TTTA-ATATTTATAATTTTTTAAAT
**
55768 AATAATATTTAT--TTTATTTAAAT
1 TTTAATATTTATAATTT-TTTAAAT
55791 TTTAATATTTATAATTTTTTAA
1 TTTAATATTTATAATTTTTTAA
55813 TTATTCGTGG
Statistics
Matches: 35, Mismatches: 7, Indels: 7
0.71 0.14 0.14
Matches are distributed among these distances:
22 2 0.06
23 16 0.46
24 12 0.34
25 5 0.14
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.57
Consensus pattern (24 bp):
TTTAATATTTATAATTTTTTAAAT
Found at i:60669 original size:1 final size:1
Alignment explanation
Indices: 60663--60687 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
60653 AGGGTAGTTC
60663 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
60688 CAGTAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:60849 original size:17 final size:17
Alignment explanation
Indices: 60824--60861 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
60814 ATTTATCAAT
*
60824 TATTAAATATAAGTATA
1 TATTAAATATAAATATA
*
60841 TATTTAATATAAATATA
1 TATTAAATATAAATATA
60858 -ATTA
1 TATTA
60862 TTTTTTTAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
16 3 0.17
17 15 0.83
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (17 bp):
TATTAAATATAAATATA
Found at i:62925 original size:22 final size:22
Alignment explanation
Indices: 62900--62967 Score: 61
Period size: 22 Copynumber: 3.1 Consensus size: 22
62890 AATTTTAATA
62900 AATTAATAATTTATATTATATT
1 AATTAATAATTTATATTATATT
*
62922 AATT-TTAATGTTATA-TATATTT
1 AATTAATAAT-TTATATTATA-TT
* *
62944 AAATAAT-TTTTATTATTATATT
1 AATTAATAATTTA-TATTATATT
62966 AA
1 AA
62968 ATTTTAATTA
Statistics
Matches: 37, Mismatches: 4, Indels: 10
0.73 0.08 0.20
Matches are distributed among these distances:
21 11 0.30
22 21 0.57
23 5 0.14
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (22 bp):
AATTAATAATTTATATTATATT
Found at i:63437 original size:18 final size:17
Alignment explanation
Indices: 63414--63447 Score: 59
Period size: 17 Copynumber: 1.9 Consensus size: 17
63404 AATTATATAA
63414 TAAAAATTATTAAATATG
1 TAAAAATT-TTAAATATG
63432 TAAAAATTTTAAATAT
1 TAAAAATTTTAAATAT
63448 AAATTTAAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (17 bp):
TAAAAATTTTAAATATG
Found at i:65023 original size:157 final size:150
Alignment explanation
Indices: 64803--65134 Score: 357
Period size: 151 Copynumber: 2.2 Consensus size: 150
64793 TTAGTAACTT
* * * * * *
64803 TAAAAGACTCGAT-ATAACATGAAATGACTAACCTATCCTTAAAGCACACCTTTAATATTAAAGT
1 TAAAAGACTTGATAATAATATGAAATAACTAACCTATCCGTAAAGCACACCTTTAACATGAAAGT
** *
64867 ATCTTAGTGATCTTAAAAGACTCAATTCTAAGGTGAAATTATTAAAAT-ATCTCCTAAAATATA-
66 ATCCAAGT-A----AAAA-ACTCAATTCTAAGGTGAAATTATTAAAATGCTCT-CTAAAATATAC
* *
64930 TATTTGACATAAAAGTATTTTGATAACCC
124 T-TTAGACATAAAAGTATTTTGAT-ACCA
* *
64959 T-AAAGAACTTGATAATAATATGAAATAACTAACCTATCCGTACAGCACACCTTTGACATGAAAG
1 TAAAAG-ACTTGATAATAATATGAAATAACTAACCTATCCGTAAAGCACACCTTTAACATGAAAG
* * * * *
65023 TATCCAAGTAAAGAACTCGATTCTAAGGTGAAATTATTGAAATGCTCTTTAAAGTATACTTTAGA
65 TATCCAAGTAAAAAACTCAATTCTAAGGTGAAATTATTAAAATGCTCTCTAAAATATACTTTAGA
* * *
65088 TATAAAAGTATTTTGGTATCA
130 CATAAAAGTATTTTGATACCA
65109 TAAAAGACTTGATAATAATATGAAAT
1 TAAAAGACTTGATAATAATATGAAAT
65135 GATAATTATA
Statistics
Matches: 150, Mismatches: 21, Indels: 16
0.80 0.11 0.09
Matches are distributed among these distances:
150 23 0.15
151 58 0.39
152 7 0.05
155 4 0.03
156 8 0.05
157 50 0.33
ACGTcount: A:0.42, C:0.14, G:0.12, T:0.32
Consensus pattern (150 bp):
TAAAAGACTTGATAATAATATGAAATAACTAACCTATCCGTAAAGCACACCTTTAACATGAAAGT
ATCCAAGTAAAAAACTCAATTCTAAGGTGAAATTATTAAAATGCTCTCTAAAATATACTTTAGAC
ATAAAAGTATTTTGATACCA
Found at i:67348 original size:29 final size:30
Alignment explanation
Indices: 67316--67380 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
67306 AAATGTTGGA
*
67316 AATTAGAAAAATTT-ATGTAT-AAAA-ATCTT
1 AATTA-AAAAATTTCATATATGAAAATAT-TT
67345 AATTAAAAAATTTCATATATGAAAATATTT
1 AATTAAAAAATTTCATATATGAAAATATTT
67375 AATTAA
1 AATTAA
67381 GACATCAAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
28 8 0.25
29 10 0.31
30 12 0.38
31 2 0.06
ACGTcount: A:0.54, C:0.03, G:0.05, T:0.38
Consensus pattern (30 bp):
AATTAAAAAATTTCATATATGAAAATATTT
Found at i:67991 original size:31 final size:31
Alignment explanation
Indices: 67947--68039 Score: 116
Period size: 31 Copynumber: 2.9 Consensus size: 31
67937 GTATTTAAGG
* *
67947 TATTATATGTTTATATAAATTTTATCATGTTAA
1 TATT-TAT-TTTATATAAATTTTATAATATTAA
*
67980 TATTTATTTTATATAAATTTTAAAATATTAA
1 TATTTATTTTATATAAATTTTATAATATTAA
*
68011 TAATTTATTTTATTTAAATTTTAT-ATATT
1 T-ATTTATTTTATATAAATTTTATAATATT
68040 TGTTTATTCA
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
31 27 0.50
32 23 0.43
33 4 0.07
ACGTcount: A:0.39, C:0.01, G:0.02, T:0.58
Consensus pattern (31 bp):
TATTTATTTTATATAAATTTTATAATATTAA
Found at i:68022 original size:32 final size:31
Alignment explanation
Indices: 67947--68033 Score: 111
Period size: 32 Copynumber: 2.7 Consensus size: 31
67937 GTATTTAAGG
** *
67947 TATTATATGTTTATATAAATTTTATCATGTTAA
1 TATT-TAT-TTTATATAAATTTTAAAATATTAA
67980 TATTTATTTTATATAAATTTTAAAATATTAA
1 TATTTATTTTATATAAATTTTAAAATATTAA
*
68011 TAATTTATTTTATTTAAATTTTA
1 T-ATTTATTTTATATAAATTTTA
68034 TATATTTGTT
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
31 22 0.45
32 23 0.47
33 4 0.08
ACGTcount: A:0.39, C:0.01, G:0.02, T:0.57
Consensus pattern (31 bp):
TATTTATTTTATATAAATTTTAAAATATTAA
Found at i:68336 original size:2 final size:2
Alignment explanation
Indices: 68329--68359 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
68319 TTAGTTTTGA
68329 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
68360 ATTTAATTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:71021 original size:69 final size:68
Alignment explanation
Indices: 70911--71044 Score: 205
Period size: 69 Copynumber: 2.0 Consensus size: 68
70901 TAGTGAGATT
70911 AAGTAGAGACATAAACAGGTAATGACATTTTAATGAGGAAACTATGTTATAAACTCCAGTTTCAA
1 AAGTAGAGACATAAACAGGTAATGACATTTTAATGAGGAAACTATGTTATAAACTCCAGTTTCAA
70976 ATG
66 ATG
* * * * * *
70979 AAGTAGAGACATGAAGAGGCTGATGGCATTTTAATGAGGAAACTATGTTATGAACTCCCGTTTCA
1 AAGTAGAGACATAAACAGG-TAATGACATTTTAATGAGGAAACTATGTTATAAACTCCAGTTTCA
71044 A
65 A
71045 TGTTTCATTA
Statistics
Matches: 59, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
68 17 0.29
69 42 0.71
ACGTcount: A:0.39, C:0.13, G:0.21, T:0.28
Consensus pattern (68 bp):
AAGTAGAGACATAAACAGGTAATGACATTTTAATGAGGAAACTATGTTATAAACTCCAGTTTCAA
ATG
Found at i:71482 original size:22 final size:20
Alignment explanation
Indices: 71452--71493 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 20
71442 AAATCGATTG
71452 ATTTATTTAAATAGTATTTTAA
1 ATTTATTTAAATA--ATTTTAA
*
71474 ATTTTTTTAAATAATTTTAA
1 ATTTATTTAAATAATTTTAA
71494 TATTAAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 7 0.37
22 12 0.63
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (20 bp):
ATTTATTTAAATAATTTTAA
Found at i:77687 original size:18 final size:18
Alignment explanation
Indices: 77661--77696 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
77651 CATGTTAACT
*
77661 ATTTTGTGATCGCATAAG
1 ATTTGGTGATCGCATAAG
*
77679 ATTTGGTGATTGCATAAG
1 ATTTGGTGATCGCATAAG
77697 GGTCAATAGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.28, C:0.08, G:0.25, T:0.39
Consensus pattern (18 bp):
ATTTGGTGATCGCATAAG
Found at i:79823 original size:17 final size:17
Alignment explanation
Indices: 79803--79839 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
79793 TTATTTTTTA
79803 TTTTTAACT-TAAAATAT
1 TTTTTAACTATAAAAT-T
79820 TTTTTAACTATAAAATT
1 TTTTTAACTATAAAATT
79837 TTT
1 TTT
79840 AATTACTATC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (17 bp):
TTTTTAACTATAAAATT
Found at i:80452 original size:16 final size:16
Alignment explanation
Indices: 80431--80466 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
80421 CTTGAATTAG
*
80431 AATTTAATTTAATAAT
1 AATTTAATTTAACAAT
80447 AATTTAATTTAACAAT
1 AATTTAATTTAACAAT
80463 AATT
1 AATT
80467 AAAGATATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (16 bp):
AATTTAATTTAACAAT
Found at i:82079 original size:58 final size:58
Alignment explanation
Indices: 81845--82172 Score: 213
Period size: 58 Copynumber: 5.7 Consensus size: 58
81835 GAAATTGTAC
* * * * * * **
81845 CAAAGTCCTTAAATCAT-AGAAAATGATCTAAATAACATCAAAATTTATAAAATTATGT
1 CAAAGTCCCTAGATCATGA-AAAATGACCTAAATGACATCAAAATTAACAAAATTACAT
* * * * * * * *
81903 AAAAGTTCCTAGATCATG-AATATGACTTAAATGACATTAAAA-T-ATAAAACTGCAT
1 CAAAGTCCCTAGATCATGAAAAATGACCTAAATGACATCAAAATTAACAAAATTACAT
* *** * * * * * *
81958 AAAAGTTTTTATATCAT-AAAAATAACCTAAATAACCTCAATA-T-ACATAAATATGCAT
1 CAAAGTCCCTAGATCATGAAAAATGACCTAAATGACATCAAAATTAACA-AAAT-TACAT
* * * *
82015 AAAAGTCCCTAGATCATGAAAAATGATCTAAATGGCATCAAAATTCACAAAATTACAT
1 CAAAGTCCCTAGATCATGAAAAATGACCTAAATGACATCAAAATTAACAAAATTACAT
* * * ** * ** *
82073 CTAAGTCCTTAGATAATGGCAAATGACCTAGATGACATTTAAATTAATAAAATTACAT
1 CAAAGTCCCTAGATCATGAAAAATGACCTAAATGACATCAAAATTAACAAAATTACAT
82131 CAAAG-CCTCTAGATCATGAAAAATGACCTAAATGACATCAAA
1 CAAAGTCC-CTAGATCATGAAAAATGACCTAAATGACATCAAA
82173 TTACATAGGA
Statistics
Matches: 205, Mismatches: 57, Indels: 16
0.74 0.21 0.06
Matches are distributed among these distances:
55 42 0.20
56 4 0.02
57 39 0.19
58 112 0.55
59 5 0.02
60 3 0.01
ACGTcount: A:0.48, C:0.15, G:0.09, T:0.28
Consensus pattern (58 bp):
CAAAGTCCCTAGATCATGAAAAATGACCTAAATGACATCAAAATTAACAAAATTACAT
Found at i:82803 original size:22 final size:21
Alignment explanation
Indices: 82752--82802 Score: 86
Period size: 21 Copynumber: 2.4 Consensus size: 21
82742 TATTCCTTTA
82752 TCTCTTTTTCTTTTTTTTTTC
1 TCTCTTTTTCTTTTTTTTTTC
82773 TCTCTTTTTCTTTTCTTTTTTC
1 TCTCTTTTTCTTTT-TTTTTTC
82795 TC-CTTTTT
1 TCTCTTTTT
82803 TTTGCTCTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
21 20 0.69
22 9 0.31
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (21 bp):
TCTCTTTTTCTTTTTTTTTTC
Found at i:84400 original size:24 final size:23
Alignment explanation
Indices: 84365--84422 Score: 55
Period size: 24 Copynumber: 2.4 Consensus size: 23
84355 TTTAATTAAT
84365 TTTA-ATTAATTAAAAAATAAATTA
1 TTTATATT-ATTAAAAAA-AAATTA
* **
84389 TTTATATTATTATATCAAAATTA
1 TTTATATTATTAAAAAAAAATTA
84412 TTGTATATTAT
1 TT-TATATTAT
84423 ATAACATAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
23 8 0.28
24 18 0.62
25 3 0.10
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (23 bp):
TTTATATTATTAAAAAAAAATTA
Found at i:84638 original size:25 final size:25
Alignment explanation
Indices: 84574--84638 Score: 73
Period size: 25 Copynumber: 2.7 Consensus size: 25
84564 TCAATTAAAC
*
84574 TAATTAAATA-GATT-AAATCAAAT
1 TAATTAAATATGATTAAAATCAAAA
* *
84597 TAATTAATTAAT-TTTAAAATCAAAA
1 TAATTAAAT-ATGATTAAAATCAAAA
84622 TAATTAAATATGATTAA
1 TAATTAAATATGATTAA
84639 TTTAATTTAT
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
23 8 0.24
24 5 0.15
25 20 0.61
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.38
Consensus pattern (25 bp):
TAATTAAATATGATTAAAATCAAAA
Found at i:84777 original size:2 final size:2
Alignment explanation
Indices: 84764--84808 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
84754 TTTTGATCAA
*
84764 AT AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
84806 AT A
1 AT A
84809 AAATGTGGAT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:86004 original size:20 final size:20
Alignment explanation
Indices: 85979--86019 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
85969 TTCATTCACA
85979 AAATTCAAACATGAAACTTT
1 AAATTCAAACATGAAACTTT
*
85999 AAATTCAAACTTGAAACTTT
1 AAATTCAAACATGAAACTTT
86019 A
1 A
86020 CTTAAAGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.49, C:0.15, G:0.05, T:0.32
Consensus pattern (20 bp):
AAATTCAAACATGAAACTTT
Found at i:87330 original size:54 final size:54
Alignment explanation
Indices: 87266--87376 Score: 186
Period size: 54 Copynumber: 2.1 Consensus size: 54
87256 AAATTTATAG
* * *
87266 TTTAGATAGTATGATAAATTATTTTAGATATACATGAATTTTCATGGTAATTCT
1 TTTAGATAGTATGATAAATTATTTTAGATATAAACGAATTTTCATGATAATTCT
*
87320 TTTAGATAGTATGATAAATTATTTTAGATATAAACGAATTTTCATGATAATTTT
1 TTTAGATAGTATGATAAATTATTTTAGATATAAACGAATTTTCATGATAATTCT
87374 TTT
1 TTT
87377 TATCATACAT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.36, C:0.05, G:0.12, T:0.48
Consensus pattern (54 bp):
TTTAGATAGTATGATAAATTATTTTAGATATAAACGAATTTTCATGATAATTCT
Found at i:93981 original size:166 final size:165
Alignment explanation
Indices: 93782--94885 Score: 937
Period size: 166 Copynumber: 6.7 Consensus size: 165
93772 CTCTTCTCCA
* ** * *
93782 TAATTTTTTCGAGA-AGATTTTTTTTAATTTTTAATTTTTAAAATTTATCAAATATTAAT-ATTT
1 TAATTTTTTCGAGAGA-ATTTTTCTTGGTTTTTAATTTTTAAAATTCATCAAATA-TCATCATTT
* * * * *
93845 ATTTCACATTAAATCAGTTTGTAAAAATTAATTCATTTTTATGAGTTTTTAAATTTCTCCTTGAA
64 ATTTCATATTAATTCAGTTT-TAAAAATTCATTCATTTTCATGAGTTTTTAAATTTTTCCTTGAA
* *
93910 ATTCTTATTTTTTTCGAAATACGGTGTTTTTTACTTCG
128 ATTCTTATTTTTTTCGAAATACGATATTTTTTACTTCG
* * *
93948 TAATTTTTTCGAGAGAATTTTTCTTGGTTTTTAATTTTTAAAATTCATAAAATACCATAATTTAT
1 TAATTTTTTCGAGAGAATTTTTCTTGGTTTTTAATTTTTAAAATTCATCAAATATCATCATTTAT
*
94013 TTCATATTAATTAAGTTTTCAAAAATTCATTCATTTTCATGAGTTTTT-AATTTTTCCTTTTCTG
66 TTCATATTAATTCAGTTTT-AAAAATTCATTCATTTTCATGAGTTTTTAAATTTTTCC---T-TG
* * * * * *
94077 AAATAC--AGTATTTTC-TACTTCG-TATTTTTT--TTC-
126 AAATTCTTATTTTTTTCGAAATACGATATTTTTTACTTCG
** *** *
94110 -AA-----GGGA-ATTT---TTCTTAGTTTTTAATTTTTAAAATTCATCAAATATCATCATTTAT
1 TAATTTTTTCGAGAGAATTTTTCTTGGTTTTTAATTTTTAAAATTCATCAAATATCATCATTTAT
* * * * *
94165 TTCACATTAATTCAGTTTTTAAAAATTCATTCATTTTCATTCA-TTTTTGATTTTTTTCTTGAAA
66 TTCATATTAATTCAG-TTTTAAAAATTCATTCATTTTCA-TGAGTTTTTAAATTTTTCCTTGAAA
** *
94229 TTCTT-TTTTTTTCGAAATACGACGTTTTCTACTTCG
129 TTCTTATTTTTTTCGAAATACGATATTTTTTACTTCG
* * *
94265 TAATTTTTTTCGAGGGGATTTTTCTTGGTTTTTAATTTTTAAAATTCATAAAATATCATCATTTA
1 TAA-TTTTTTCGAGAGAATTTTTCTTGGTTTTTAATTTTTAAAATTCATCAAATATCATCATTTA
* * ** ** *
94330 TTTCATATTAATTCAATTCTCAAAAATTCATTCATGCTCATGAGTTTTTGATTTTTTTCCTTGGA
65 TTTCATATTAATTCAGTT-TTAAAAATTCATTCATTTTCATGAGTTTTT-AAATTTTTCCTTGAA
* * * *
94395 ACTC-CA-TTTTTTCAAAATACGATATTTTCTA-TTCCG
128 ATTCTTATTTTTTTCGAAATACGATATTTTTTACTT-CG
* * * * * *
94431 TAAATTTTTTTGA-AGGGATTTTTCTCGGTTTTCAATTTTTAAAATTCATCAAATATTTATTATT
1 T-AATTTTTTCGAGA-GAATTTTTCTTGGTTTTTAATTTTTAAAATTCATCAAATA-TCATCATT
* * **
94495 TATTTCTTATCAATTCAGTTTTCAAAAATTCATTCATTTTCATGAGTTTTT-GTTATTTTCCTTG
63 TATTTCATATTAATTCAGTTTT-AAAAATTCATTCATTTTCATGAGTTTTTAAAT-TTTTCCTTG
* *
94559 AAATTCTT-TTTTTTT-GAAATA-TAGTATTTTTTACTCCG
126 AAATTCTTATTTTTTTCGAAATACGA-TATTTTTTACTTCG
* * *
94597 TAATTTTTTTGAGGGGATTTTTCTTGGTTTTTAATTTTTAAAATTCATCAAATATCATCATTTAT
1 TAATTTTTTCGAGAGAATTTTTCTTGGTTTTTAATTTTTAAAATTCATCAAATATCATCATTTAT
* * * * ** *
94662 TCCATATTAATTCAATTTTTTAAAATTCATTCATTTTCATAAGTTTTTGATTTTTTTACTTGAAA
66 TTCATATTAATTC-AGTTTTAAAAATTCATTCATTTTCATGAGTTTTT-AAATTTTTCCTTGAAA
* *
94727 CTCCTTTTTTTTTTCGAAATACGATATTTTTTAC-TCGG
129 -TTCTTATTTTTTTCGAAATACGATATTTTTTACTTC-G
* ** * * * *
94765 TAAATTGTTTCGA-AGAGATTTTTCTCAGTTTTCAATTTTTATAATTCATTAAACATCATCATTT
1 T-AATTTTTTCGAGAGA-ATTTTTCTTGGTTTTTAATTTTTAAAATTCATCAAATATCATCATTT
* * * *
94829 GA-TTCATATTAAATT-AATTTGAAAAAATTAATTCATTTTCATGAG-TTATAAATTTTT
64 -ATTTCATATT-AATTCAGTTT-TAAAAATTCATTCATTTTCATGAGTTTTTAAATTTTT
94886 TTATATGTAT
Statistics
Matches: 760, Mismatches: 122, Indels: 111
0.77 0.12 0.11
Matches are distributed among these distances:
149 7 0.01
150 7 0.01
151 4 0.01
152 83 0.11
153 13 0.02
154 3 0.00
155 1 0.00
156 4 0.01
161 2 0.00
162 2 0.00
163 3 0.00
164 45 0.06
165 92 0.12
166 283 0.37
167 94 0.12
168 27 0.04
169 85 0.11
170 5 0.01
ACGTcount: A:0.29, C:0.11, G:0.08, T:0.52
Consensus pattern (165 bp):
TAATTTTTTCGAGAGAATTTTTCTTGGTTTTTAATTTTTAAAATTCATCAAATATCATCATTTAT
TTCATATTAATTCAGTTTTAAAAATTCATTCATTTTCATGAGTTTTTAAATTTTTCCTTGAAATT
CTTATTTTTTTCGAAATACGATATTTTTTACTTCG
Found at i:94080 original size:151 final size:151
Alignment explanation
Indices: 93920--94204 Score: 437
Period size: 152 Copynumber: 1.9 Consensus size: 151
93910 ATTCTTATTT
* * * * *
93920 TTTTCGAAATACGGTGTTTTTTACTTCGTA-ATTTTTTCGAGAGAATTTTTCTTGGTTTTTAATT
1 TTTTCGAAATACAGTATTTTCTACTTCGTATATTTTTTCAAGAGAATTTTTCTTAGTTTTTAATT
*
93984 TTTAAAATTCATAAAATACCATAATTTATTTCATATTAATTAAGTTTTCAAAAATTCATTCATTT
66 TTTAAAATTCATAAAATACCATAATTTATTTCACATTAATTAAGTTTTCAAAAATTCATTCATTT
94049 TCATGAGTTTTTAATTTTTCC
131 TCATGAGTTTTTAATTTTTCC
* *
94070 TTTTCTGAAATACAGTATTTTCTACTTCGTATTTTTTTTCAAGGGAATTTTTCTTAGTTTTTAAT
1 TTTTC-GAAATACAGTATTTTCTACTTCGTATATTTTTTCAAGAGAATTTTTCTTAGTTTTTAAT
* * * * *
94135 TTTTAAAATTCATCAAATATCATCATTTATTTCACATTAATTCAGTTTTTAAAAATTCATTCATT
65 TTTTAAAATTCATAAAATACCATAATTTATTTCACATTAATTAAGTTTTCAAAAATTCATTCATT
94200 TTCAT
130 TTCAT
94205 TCATTTTTGA
Statistics
Matches: 120, Mismatches: 13, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
150 5 0.04
151 22 0.18
152 93 0.77
ACGTcount: A:0.29, C:0.12, G:0.07, T:0.52
Consensus pattern (151 bp):
TTTTCGAAATACAGTATTTTCTACTTCGTATATTTTTTCAAGAGAATTTTTCTTAGTTTTTAATT
TTTAAAATTCATAAAATACCATAATTTATTTCACATTAATTAAGTTTTCAAAAATTCATTCATTT
TCATGAGTTTTTAATTTTTCC
Found at i:94362 original size:318 final size:319
Alignment explanation
Indices: 93797--94716 Score: 1137
Period size: 318 Copynumber: 2.8 Consensus size: 319
93787 TTTTCGAGAA
* * * *
93797 GATTTTTTTTAATTTTTAATTTTTAAAATTTATCAAATATTAATATTTATTTCACATTAAATCAG
1 GATTTTTCTTAGTTTTTAATTTTTAAAATTCATCAAATATTAATATTTATTTCACATTAATTCAG
* * * * * *
93862 TTTGTAAAAATTAATTCATTTTTATGAGTTTTTAAATTTCTCCTTGAAATTCTTATTTTTTTCGA
66 TTTTTAAAAATTCATTCATTTTCATGAGTTTTTGATTTTTTCCTTGAAATTCTT-TTTTTTTCGA
* * *
93927 AATACGGTGTTTTTTACTTCGTAA-TTTTTTCGAGAGAATTTTTCTTGGTTTTTAATTTTTAAAA
130 AATAC-GAGTTTTTTACTTCGTAATTTTTTTCGAGGGGATTTTTCTTGGTTTTTAATTTTTAAAA
* *
93991 TTCATAAAATACCATAATTTATTTCATATTAATT-AAGTTTTCAAAAATTCATTCATTTTCATGA
194 TTCATAAAATATCATCATTTATTTCATATTAATTCAA-TTTTCAAAAATTCATTCATTTTCATGA
* *
94055 GTTTTTAATTTTTCC-TTTTCT-GAAATAC-AGTATTTTCTACTT-CGT-ATTTTTTTTCAAGG
258 GTTTTTAATTTTTCCATTTTCTCAAAATACGA-TATTTTCTA-TTCCGTAAATTTTTTTCAAGG
*
94114 GAATTTTTCTTAGTTTTTAATTTTTAAAATTCATCAAATA-TCATCATTTATTTCACATTAATTC
1 G-ATTTTTCTTAGTTTTTAATTTTTAAAATTCATCAAATATTAAT-ATTTATTTCACATTAATTC
* *
94178 AGTTTTTAAAAATTCATTCATTTTCATTCA-TTTTTGATTTTTTTCTTGAAATTCTTTTTTTTTC
64 AGTTTTTAAAAATTCATTCATTTTCA-TGAGTTTTTGATTTTTTCCTTGAAATTCTTTTTTTTTC
*
94242 GAAATACGACGTTTTCTACTTCGTAATTTTTTTCGAGGGGATTTTTCTTGGTTTTTAATTTTTAA
128 GAAATACGA-GTTTTTTACTTCGTAATTTTTTTCGAGGGGATTTTTCTTGGTTTTTAATTTTTAA
* **
94307 AATTCATAAAATATCATCATTTATTTCATATTAATTCAATTCTCAAAAATTCATTCATGCTCATG
192 AATTCATAAAATATCATCATTTATTTCATATTAATTCAATTTTCAAAAATTCATTCATTTTCATG
* *
94372 AGTTTTTGATTTTTTTCCTTGGAACTCCATTTTTTCAAAATACGATATTTTCTATTCCGTAAATT
257 AGTTTTT-A----ATT--TT-----TCCATTTTCTCAAAATACGATATTTTCTATTCCGTAAATT
*
94437 TTTTTGAAGG
310 TTTTTCAAGG
** * * ** *
94447 GATTTTTCTCGGTTTTCAATTTTTAAAATTCATCAAATATTTATTATTTATTTCTTATCAATTCA
1 GATTTTTCTTAGTTTTTAATTTTTAAAATTCATCAAATA-TTAATATTTATTTCACATTAATTCA
*
94512 GTTTTCAAAAATTCATTCATTTTCATGAGTTTTTG-TTATTTTCCTTGAAATTCTTTTTTTTT-G
65 GTTTTTAAAAATTCATTCATTTTCATGAGTTTTTGATT-TTTTCCTTGAAATTCTTTTTTTTTCG
* *
94575 AAATA-TAGTATTTTTTACTCCGTAATTTTTTT-GAGGGGATTTTTCTTGGTTTTTAATTTTTAA
129 AAATACGAG--TTTTTTACTTCGTAATTTTTTTCGAGGGGATTTTTCTTGGTTTTTAATTTTTAA
* * ** *
94638 AATTCATCAAATATCATCATTTATTCCATATTAATTCAATTTTTTAAAATTCATTCATTTTCATA
192 AATTCATAAAATATCATCATTTATTTCATATTAATTCAATTTTCAAAAATTCATTCATTTTCATG
*
94703 AGTTTTTGATTTTT
257 AGTTTTTAATTTTT
94717 TTACTTGAAA
Statistics
Matches: 523, Mismatches: 51, Indels: 56
0.83 0.08 0.09
Matches are distributed among these distances:
316 1 0.00
317 34 0.07
318 198 0.38
319 6 0.01
323 2 0.00
324 2 0.00
325 2 0.00
326 2 0.00
330 4 0.01
331 103 0.20
332 83 0.16
333 84 0.16
334 2 0.00
ACGTcount: A:0.28, C:0.11, G:0.08, T:0.53
Consensus pattern (319 bp):
GATTTTTCTTAGTTTTTAATTTTTAAAATTCATCAAATATTAATATTTATTTCACATTAATTCAG
TTTTTAAAAATTCATTCATTTTCATGAGTTTTTGATTTTTTCCTTGAAATTCTTTTTTTTTCGAA
ATACGAGTTTTTTACTTCGTAATTTTTTTCGAGGGGATTTTTCTTGGTTTTTAATTTTTAAAATT
CATAAAATATCATCATTTATTTCATATTAATTCAATTTTCAAAAATTCATTCATTTTCATGAGTT
TTTAATTTTTCCATTTTCTCAAAATACGATATTTTCTATTCCGTAAATTTTTTTCAAGG
Found at i:95258 original size:24 final size:24
Alignment explanation
Indices: 95205--95278 Score: 78
Period size: 24 Copynumber: 3.0 Consensus size: 24
95195 TGGCTGCTGG
* *
95205 AAAAAGAAGAGAGAAAAGAGAGAAA
1 AAAAAG-AGAGAGAAAATAGAAAAA
*
95230 GAAAAGCA-AGAGAAAATAGAAAAA
1 AAAAAG-AGAGAGAAAATAGAAAAA
95254 AAAAAGAGAGAGAAAAATTAGAAAA
1 AAAAAGAGAGAG-AAAA-TAGAAAA
95279 CACTAGCCAA
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
23 1 0.02
24 23 0.56
25 10 0.24
26 7 0.17
ACGTcount: A:0.72, C:0.01, G:0.23, T:0.04
Consensus pattern (24 bp):
AAAAAGAGAGAGAAAATAGAAAAA
Found at i:95269 original size:13 final size:12
Alignment explanation
Indices: 95205--95270 Score: 55
Period size: 13 Copynumber: 5.3 Consensus size: 12
95195 TGGCTGCTGG
95205 AAAAAGAAGAGA
1 AAAAAGAAGAGA
*
95217 GAAAAG-AGAGAA
1 AAAAAGAAGAG-A
95229 AGAAAAGCAAGAGA
1 A-AAAAG-AAGAGA
* *
95243 AAATAGAA-AAA
1 AAAAAGAAGAGA
95254 AAAAAGAGAGAGA
1 AAAAAGA-AGAGA
95267 AAAA
1 AAAA
95271 TTAGAAAACA
Statistics
Matches: 42, Mismatches: 6, Indels: 11
0.71 0.10 0.19
Matches are distributed among these distances:
11 12 0.29
12 9 0.21
13 15 0.36
14 2 0.05
15 4 0.10
ACGTcount: A:0.73, C:0.02, G:0.24, T:0.02
Consensus pattern (12 bp):
AAAAAGAAGAGA
Found at i:101029 original size:16 final size:16
Alignment explanation
Indices: 100987--101030 Score: 63
Period size: 15 Copynumber: 2.8 Consensus size: 16
100977 CTTTTTCTCC
*
100987 TCCTTCTTTTCATCTT
1 TCCTTCTTTTCTTCTT
*
101003 TCCTT-TTTTCTTTTT
1 TCCTTCTTTTCTTCTT
101018 TCCTTCTTTTCTT
1 TCCTTCTTTTCTT
101031 ATTCAAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 13 0.52
16 12 0.48
ACGTcount: A:0.02, C:0.27, G:0.00, T:0.70
Consensus pattern (16 bp):
TCCTTCTTTTCTTCTT
Found at i:101252 original size:75 final size:75
Alignment explanation
Indices: 101107--101252 Score: 161
Period size: 75 Copynumber: 1.9 Consensus size: 75
101097 AAAATAAATC
* * * ** ** *
101107 TTAAATTTTTATAAATAAAAATAAATTATATCATTAAAAATTTAAACTCATATCATACCCAAGAA
1 TTAAATTTTTACAAATAAAAATAAATTATATCATTAAAAATTTAAACCCACAAAATACAAAAAAA
101172 AAAATTATGT
66 AAAATTATGT
* * *
101182 TTAAATTTTTACAAATCAAAATAAATTATA-CTTTAAAATTTTAAACCCACAAAAT-CAAATAAA
1 TTAAATTTTTACAAATAAAAATAAATTATATCATTAAAAATTTAAACCCACAAAATACAAA-AAA
101245 AATAAATT
65 AA-AAATT
101253 TAAACTTCTA
Statistics
Matches: 58, Mismatches: 11, Indels: 4
0.79 0.15 0.05
Matches are distributed among these distances:
73 2 0.03
74 23 0.40
75 33 0.57
ACGTcount: A:0.53, C:0.10, G:0.01, T:0.35
Consensus pattern (75 bp):
TTAAATTTTTACAAATAAAAATAAATTATATCATTAAAAATTTAAACCCACAAAATACAAAAAAA
AAAATTATGT
Found at i:101940 original size:3 final size:3
Alignment explanation
Indices: 101932--101957 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
101922 GGAATAAAAA
101932 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
101958 AAAAAATCGA
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:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:105390 original size:19 final size:20
Alignment explanation
Indices: 105367--105410 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 20
105357 TTTTTTTTCG
105367 ATTTTTCATTT-TTTC-ATA
1 ATTTTTCATTTATTTCTATA
*
105385 ACTTTTTCTTTTATTTCTATA
1 A-TTTTTCATTTATTTCTATA
105406 ATTTT
1 ATTTT
105411 AAAATTGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 1 0.05
19 9 0.41
20 8 0.36
21 4 0.18
ACGTcount: A:0.20, C:0.11, G:0.00, T:0.68
Consensus pattern (20 bp):
ATTTTTCATTTATTTCTATA
Found at i:105520 original size:11 final size:11
Alignment explanation
Indices: 105501--105531 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
105491 TTCACTATTT
105501 TTTTCTTTTTTA
1 TTTT-TTTTTTA
105513 TTTTTTTTTTA
1 TTTTTTTTTTA
105524 TTTTTTTT
1 TTTTTTTT
105532 AATTTATGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 15 0.79
12 4 0.21
ACGTcount: A:0.06, C:0.03, G:0.00, T:0.90
Consensus pattern (11 bp):
TTTTTTTTTTA
Found at i:109894 original size:296 final size:301
Alignment explanation
Indices: 109530--110120 Score: 872
Period size: 296 Copynumber: 1.9 Consensus size: 301
109520 AAAAAAAAAA
* *
109530 TCCTTCAAACCTTTAACCCCCAAAATCTAAACTTTAGACAATCTTAACATGAAAATAGTTAAAGG
1 TCCTTCAAACCTTAAACCCCCAAAATCTAAACTTTAGACAATCTTAACATGAAAATAGCTAAAGG
* * *
109595 GCTTGCTTAATTATTAAGAAAATGTAACGCACAAATTATAAAATAAAAAAAAAATCAAGTTCATA
66 GCTTGCTTAACTAGTAAGAAAATGTAACGCACAAATTATAAAAAAAAAAAAAAATCAAGTTCATA
* *
109660 AAGCCAGCTGC-GCTAAACCTAGATCCTAAATACTTCAATTTCAAAATCAGAAACAA-ACACAGA
131 AAGCCAGCTGCGGCTAAACCTAGATCCTAAATACTTAAATTT-AAAATCAGAAACAAGAAACAGA
** *
109723 ATTATAACAAAA-T-T-AAAAAAAA-AATTAATAATTCCCTTTGCTTACAGTTCTTAGTGAGCCG
195 ATTATAACAAAATTATAAAAAAAAAGAAAAAATAATTCCCTTTGCTTACAGTTCCTAGTGAGCCG
109784 AAATAGACGAGATCACGTAAATGGGACAGGAAAACCCCCAAT
260 AAATAGACGAGATCACGTAAATGGGACAGGAAAACCCCCAAT
* *
109826 TCCTTCAAACCTTAAAACCCCCAATATCTAAGCTTT-GACAATCTTAACATGAAAATAGCTAAAG
1 TCCTTCAAACCTT-AAACCCCCAAAATCTAAACTTTAGACAATCTTAACATGAAAATAGCTAAAG
109890 GGCTTGCTTAACTAGTAAGAAAATGTAACGCACAAATTATAAAAAAAAAAAAAAATCAAGTTCAT
65 GGCTTGCTTAACTAGTAAGAAAATGTAACGCACAAATTATAAAAAAAAAAAAAAATCAAGTTCAT
*
109955 AAAGCCAGCTGCTGGGTTAGCTAAACCTAGATCCTAAATACTTAAATTTTAAATCAGAAACAAGA
130 AAAGCCAGCTGC---G---GCTAAACCTAGATCCTAAATACTTAAATTTAAAATCAGAAACAAGA
110020 AACAGAATTATAACAAAATTATAAAAAAAAAAAAAAAAAGAAAAAATAATTCCCTTTGCTTACAG
189 AACAGAATTATAACAAAATTAT--------AAAAAAAAAGAAAAAATAATTCCCTTTGCTTACAG
110085 TTCCTAGTGAGCCGAAATAGACGAGATCACGTAAAT
246 TTCCTAGTGAGCCGAAATAGACGAGATCACGTAAAT
110121 TTGAAAGAAA
Statistics
Matches: 261, Mismatches: 13, Indels: 23
0.88 0.04 0.08
Matches are distributed among these distances:
296 114 0.44
297 19 0.07
302 13 0.05
303 47 0.18
304 1 0.00
305 1 0.00
314 8 0.03
315 58 0.22
ACGTcount: A:0.46, C:0.18, G:0.12, T:0.24
Consensus pattern (301 bp):
TCCTTCAAACCTTAAACCCCCAAAATCTAAACTTTAGACAATCTTAACATGAAAATAGCTAAAGG
GCTTGCTTAACTAGTAAGAAAATGTAACGCACAAATTATAAAAAAAAAAAAAAATCAAGTTCATA
AAGCCAGCTGCGGCTAAACCTAGATCCTAAATACTTAAATTTAAAATCAGAAACAAGAAACAGAA
TTATAACAAAATTATAAAAAAAAAGAAAAAATAATTCCCTTTGCTTACAGTTCCTAGTGAGCCGA
AATAGACGAGATCACGTAAATGGGACAGGAAAACCCCCAAT
Found at i:110419 original size:40 final size:37
Alignment explanation
Indices: 110371--110477 Score: 103
Period size: 40 Copynumber: 2.8 Consensus size: 37
110361 TATATAATTT
* **
110371 AAATATAATATAATTACATAAATTATTAAAATATTTTAA
1 AAATATAATATAATTAAATAAATTATTAAAA-A-AATAA
110410 AATATATAATAT-ATTAAATAAAATTA-TAACAAAAATAA
1 AA-ATATAATATAATTAAAT-AAATTATTAA-AAAAATAA
*
110448 AAATATAATATTAA-TATATAAATTATTAAA
1 AAATATAATA-TAATTAAATAAATTATTAAA
110478 TTTTATTAAA
Statistics
Matches: 58, Mismatches: 4, Indels: 14
0.76 0.05 0.18
Matches are distributed among these distances:
37 15 0.26
38 13 0.22
39 13 0.22
40 17 0.29
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (37 bp):
AAATATAATATAATTAAATAAATTATTAAAAAAATAA
Found at i:111352 original size:14 final size:14
Alignment explanation
Indices: 111329--111358 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
111319 CTCCTTGTAT
*
111329 CAAGCTGATATAAA
1 CAAGCAGATATAAA
111343 CAAGCAGATATAAA
1 CAAGCAGATATAAA
111357 CA
1 CA
111359 CCTTATTTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.53, C:0.17, G:0.13, T:0.17
Consensus pattern (14 bp):
CAAGCAGATATAAA
Found at i:115615 original size:28 final size:28
Alignment explanation
Indices: 115583--115639 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
115573 GTCTCTTTCA
115583 AGCAAATCATGCTTAATCCACTTTAGAT
1 AGCAAATCATGCTTAATCCACTTTAGAT
*
115611 AGCAAATCATGCTTAATCCATTTTAGAT
1 AGCAAATCATGCTTAATCCACTTTAGAT
115639 A
1 A
115640 AAATGCATGC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (28 bp):
AGCAAATCATGCTTAATCCACTTTAGAT
Found at i:116586 original size:14 final size:15
Alignment explanation
Indices: 116564--116604 Score: 57
Period size: 14 Copynumber: 2.8 Consensus size: 15
116554 AAAAAACTAG
*
116564 AGAAGAAAAGGAGAA
1 AGAAGAAAAAGAGAA
116579 AGAA-AAAAAGAGAA
1 AGAAGAAAAAGAGAA
*
116593 AAAAGAAAAAGA
1 AGAAGAAAAAGA
116605 AAATGAGAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (15 bp):
AGAAGAAAAAGAGAA
Found at i:116613 original size:23 final size:25
Alignment explanation
Indices: 116552--116607 Score: 71
Period size: 23 Copynumber: 2.2 Consensus size: 25
116542 GGTTTTCAAT
*
116552 AGAAAAAACTAGAGAAGAAAAGGAGAA
1 AGAAAAAA--AGAGAAGAAAAGGAAAA
116579 AGAAAAAAAGAGAA-AAAA-GAAAA
1 AGAAAAAAAGAGAAGAAAAGGAAAA
116602 AGAAAA
1 AGAAAA
116608 TGAGAGTTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
23 10 0.36
24 4 0.14
25 6 0.21
27 8 0.29
ACGTcount: A:0.75, C:0.02, G:0.21, T:0.02
Consensus pattern (25 bp):
AGAAAAAAAGAGAAGAAAAGGAAAA
Found at i:118873 original size:32 final size:33
Alignment explanation
Indices: 118818--118879 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 33
118808 CAAGCCAATG
*
118818 TATCAATACATTTTGGGATGTATCGATACATTA
1 TATCAATACATCTTGGGATGTATCGATACATTA
* *
118851 TATCGATACATCTTGTG-TGTATCGATACA
1 TATCAATACATCTTGGGATGTATCGATACA
118880 AACAGTTAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 12 0.46
33 14 0.54
ACGTcount: A:0.31, C:0.15, G:0.16, T:0.39
Consensus pattern (33 bp):
TATCAATACATCTTGGGATGTATCGATACATTA
Found at i:127106 original size:157 final size:157
Alignment explanation
Indices: 126923--127265 Score: 374
Period size: 157 Copynumber: 2.2 Consensus size: 157
126913 CATTCTGCAA
* * * *
126923 TGAAAAATTTAATATTTTGCAGATAAAAATGGAG-TTAGAGTATTCTCTCGAAAATAACGGAGTT
1 TGAAAAA-TCAATATTTTGAAGATAAAAATCGAGATTAGAGTA-TCCCTCGAAAATAACGGAGTT
* * * *
126987 AGAGTATC-CTCGA-GAT-AAATTTTAATATTTTAAAAATAAAAACA-GGTTTGAAGTATCCCCT
64 AGAATATCTC-CAATGATAAAAATTTAATATTTTAAAAATAAAAACAGGGTTAG-AGTATCCCCT
127048 CAGAAGATAACGGGGTTGGAATATCCCTAACAG
127 CAGAA-ATAA-GGGGTTGGAATATCCCTAACAG
* *
127081 TGAAAAATCAATATTTTGGAGAT-AAAATCGAGATTAGAGTATCCCTCGAAAATAACGGAGTTGG
1 TGAAAAATCAATATTTTGAAGATAAAAATCGAGATTAGAGTATCCCTCGAAAATAACGGAGTTAG
* ** **
127145 AATATCTCCAATGGTGAAAAATTTAATATTTTGGAAATAAAAATGGGGTTAGAGTATCCCCTCAG
66 AATATCTCCAATGAT-AAAAATTTAATATTTTAAAAATAAAAACAGGGTTAGAGTATCCCCTCAG
* * * * **
127210 AAATAATGGGTTGGAGTATTCTTAATGG
130 AAATAAGGGGTTGGAATATCCCTAACAG
* *
127238 TGAAAAATCGATATTTTGAAAATAAAAA
1 TGAAAAATCAATATTTTGAAGATAAAAA
127266 CCGGGTTGGA
Statistics
Matches: 155, Mismatches: 23, Indels: 14
0.81 0.12 0.07
Matches are distributed among these distances:
156 36 0.23
157 61 0.39
158 15 0.10
159 38 0.25
160 5 0.03
ACGTcount: A:0.41, C:0.10, G:0.19, T:0.30
Consensus pattern (157 bp):
TGAAAAATCAATATTTTGAAGATAAAAATCGAGATTAGAGTATCCCTCGAAAATAACGGAGTTAG
AATATCTCCAATGATAAAAATTTAATATTTTAAAAATAAAAACAGGGTTAGAGTATCCCCTCAGA
AATAAGGGGTTGGAATATCCCTAACAG
Found at i:127149 original size:78 final size:77
Alignment explanation
Indices: 127038--127264 Score: 244
Period size: 79 Copynumber: 2.9 Consensus size: 77
127028 ACAGGTTTGA
* ** *
127038 AGTATCCCCTCAGAAGATAACGGGGTTGGAATATCCCTAACAGTGAAAAATCAATATTTTGGAGA
1 AGTATCCCCTC-GAAAATAAC-GGGTTGGAATATCCCTAATGGTGAAAAATCAATATTTTGGAAA
127103 TAAAATCGAGATTAG
64 TAAAAT-GAGATTAG
*
127118 AGTAT-CCCTCGAAAATAACGGAGTTGGAATATCTCC-AATGGTGAAAAATTTAATATTTTGGAA
1 AGTATCCCCTCGAAAATAACGG-GTTGGAATATC-CCTAATGGTGAAAAA-TCAATATTTTGGAA
* *
127181 ATAAAAATGGGGTTAG
63 AT-AAAATGAGATTAG
* * * * * *
127197 AGTATCCCCTC-AGAAATAATGGGTTGGAGTATTCTTAATGGTGAAAAATCGATATTTTGAAAAT
1 AGTATCCCCTCGA-AAATAACGGGTTGGAATATCCCTAATGGTGAAAAATCAATATTTTGGAAAT
127261 AAAA
65 AAAA
127265 ACCGGGTTGG
Statistics
Matches: 126, Mismatches: 14, Indels: 17
0.80 0.09 0.11
Matches are distributed among these distances:
77 6 0.05
78 43 0.34
79 54 0.43
80 23 0.18
ACGTcount: A:0.39, C:0.12, G:0.21, T:0.28
Consensus pattern (77 bp):
AGTATCCCCTCGAAAATAACGGGTTGGAATATCCCTAATGGTGAAAAATCAATATTTTGGAAATA
AAATGAGATTAG
Found at i:127479 original size:79 final size:78
Alignment explanation
Indices: 126922--127502 Score: 330
Period size: 78 Copynumber: 7.4 Consensus size: 78
126912 ACATTCTGCA
* * * * * * *
126922 ATGAAAAATTTAATATTTTGCAGATAAAAATG-GAGTTAGAGTAT-TCTCTCGAAAATAACGGAG
1 ATGAAAAATTTAATATTTTGGAAATAAAAACGAG-GTTGGAGTATCCCT-TCAAAAATAACGGGG
*
126985 TTAGAGTATCCTC-G
64 TTGGAGTATCCTCAG
* ** * * *
126999 A-GATAAATTTTAATATTTTAAAAATAAAAAC-AGGTTTGAAGTATCCCCTCAGAAGATAACGGG
1 ATGA-AAAATTTAATATTTTGGAAATAAAAACGAGG-TTGGAGTATCCCTTCA-AAAATAACGGG
*
127062 GTTGGAATATCCCTAACAG
63 GTTGGAGTAT-CCT--CAG
* * * * * * *
127081 -TGAAAAA-TCAATATTTTGGAGATAAAATCGAGATTAGAGTATCCC-TCGAAAATAACGGAGTT
1 ATGAAAAATTTAATATTTTGGAAATAAAAACGAGGTTGGAGTATCCCTTCAAAAATAACGGGGTT
*
127143 GGAATAT-CTCCAATG
66 GGAGTATCCT-C-A-G
* * * * * * *
127158 GTGAAAAATTTAATATTTTGGAAATAAAAATGGGGTTAGAGTATCCCCTCAGAAATAA-TGGGTT
1 ATGAAAAATTTAATATTTTGGAAATAAAAACGAGGTTGGAGTATCCCTTCAAAAATAACGGGGTT
* *
127222 GGAGTATTCTTAATG
66 GGAGTA-TCCTCA-G
* ** * * * * * **
127237 GTGAAAAA-TCGATATTTTGAAAATAAAAACCG-GGTTGGAGTATCCTTTCAGAATTGATAGGGT
1 ATGAAAAATTTAATATTTTGGAAATAAAAA-CGAGGTTGGAGTATCCCTTCAAAAATAACGGGGT
127300 TGGAGTATCCTCGAG
65 TGGAGTATCCTC-AG
** * * * * * * * * **
127315 ATGAAAAA-TCGATATTTTGGAAGTAAAAATGGGGTTGGAATAT-CTTCTCAGAATTGATAGGGT
1 ATGAAAAATTTAATATTTTGGAAATAAAAACGAGGTTGGAGTATCCCT-TCAAAAATAACGGGGT
** * *
127378 TTAAGTATCCCTGAA
65 TGGAGTAT-CCTCAG
* *
127393 ATGAAAATTTTAATATTTTTGAAATAAAAACGAGGTTGGAGTATCCCTTCAAAAATAACGGGGTT
1 ATGAAAAATTTAATATTTTGGAAATAAAAACGAGGTTGGAGTATCCCTTCAAAAATAACGGGGTT
127458 GGAGTATCCTCAG
66 GGAGTATCCTCAG
**
127471 ATGAAAAA-TCGATATTTT-GAAAGTAAAAACGA
1 ATGAAAAATTTAATATTTTGGAAA-TAAAAACGA
127503 AAATTTGACA
Statistics
Matches: 395, Mismatches: 82, Indels: 54
0.74 0.15 0.10
Matches are distributed among these distances:
75 1 0.00
76 10 0.03
77 55 0.14
78 163 0.41
79 118 0.30
80 38 0.10
81 7 0.02
82 3 0.01
ACGTcount: A:0.39, C:0.11, G:0.21, T:0.30
Consensus pattern (78 bp):
ATGAAAAATTTAATATTTTGGAAATAAAAACGAGGTTGGAGTATCCCTTCAAAAATAACGGGGTT
GGAGTATCCTCAG
Found at i:128698 original size:14 final size:14
Alignment explanation
Indices: 128679--128711 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
128669 ACATTTTTAT
128679 GAAAAGAAATGAAA
1 GAAAAGAAATGAAA
128693 GAAAAGAAATGAAA
1 GAAAAGAAATGAAA
128707 -AAAAG
1 GAAAAG
128712 TGCATGGTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 5 0.26
14 14 0.74
ACGTcount: A:0.73, C:0.00, G:0.21, T:0.06
Consensus pattern (14 bp):
GAAAAGAAATGAAA
Found at i:130791 original size:29 final size:29
Alignment explanation
Indices: 130749--130811 Score: 92
Period size: 29 Copynumber: 2.2 Consensus size: 29
130739 GATGACGATG
130749 AGTGGGGATAGGGGTGGATTTGGGTAAAT
1 AGTGGGGATAGGGGTGGATTTGGGTAAAT
* *
130778 AGTGAGGG-TAGGGGTGGGTTTGGGTAAGT
1 AGTG-GGGATAGGGGTGGATTTGGGTAAAT
130807 AGTGG
1 AGTGG
130812 TAAGTAGGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
28 1 0.03
29 27 0.87
30 3 0.10
ACGTcount: A:0.21, C:0.00, G:0.52, T:0.27
Consensus pattern (29 bp):
AGTGGGGATAGGGGTGGATTTGGGTAAAT
Found at i:130860 original size:15 final size:14
Alignment explanation
Indices: 130836--130865 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
130826 TAATAAAATA
130836 TATATTTATTAATT
1 TATATTTATTAATT
130850 TATAGTTTATTAATT
1 TATA-TTTATTAATT
130865 T
1 T
130866 TTTATAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.63
Consensus pattern (14 bp):
TATATTTATTAATT
Found at i:131344 original size:3 final size:3
Alignment explanation
Indices: 131336--131375 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
131326 ATATTAGATT
*
131336 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TAA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
131376 ATAATACATA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:131380 original size:8 final size:9
Alignment explanation
Indices: 131336--131380 Score: 56
Period size: 9 Copynumber: 5.1 Consensus size: 9
131326 ATATTAGATT
*
131336 TTATTATTA
1 TTATTATAA
*
131345 TTATTATTA
1 TTATTATAA
*
131354 TTATTATTA
1 TTATTATAA
131363 TTATTATAA
1 TTATTATAA
131372 TTA-TATAA
1 TTATTATAA
131380 T
1 T
131381 ACATAAATAA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
8 6 0.17
9 29 0.83
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (9 bp):
TTATTATAA
Found at i:138470 original size:15 final size:15
Alignment explanation
Indices: 138450--138481 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
138440 GTATCCCCTA
138450 CCTCAAATATATCAT
1 CCTCAAATATATCAT
*
138465 CCTCAAATATATTAT
1 CCTCAAATATATCAT
138480 CC
1 CC
138482 ACCTCTAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.38, C:0.28, G:0.00, T:0.34
Consensus pattern (15 bp):
CCTCAAATATATCAT
Found at i:139179 original size:11 final size:11
Alignment explanation
Indices: 139149--139195 Score: 53
Period size: 11 Copynumber: 4.4 Consensus size: 11
139139 TTCATTTATC
*
139149 TATATTATATT
1 TATATTATTTT
*
139160 CATATTATTTT
1 TATATTATTTT
139171 TATATTATTTT
1 TATATTATTTT
139182 TA-ATT-TTTCT
1 TATATTATTT-T
139192 TATA
1 TATA
139196 AAATATTAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
9 3 0.10
10 6 0.19
11 22 0.71
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.66
Consensus pattern (11 bp):
TATATTATTTT
Found at i:140090 original size:14 final size:14
Alignment explanation
Indices: 140073--140112 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
140063 GTTTTTAATG
140073 TATTTTTTTATTAA
1 TATTTTTTTATTAA
*
140087 TATTATTTTATTAA
1 TATTTTTTTATTAA
140101 T-TTTTTGTTATT
1 TATTTTT-TTATT
140113 TTAATAATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
13 4 0.17
14 19 0.83
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.72
Consensus pattern (14 bp):
TATTTTTTTATTAA
Found at i:140265 original size:10 final size:12
Alignment explanation
Indices: 140241--140276 Score: 56
Period size: 11 Copynumber: 3.1 Consensus size: 12
140231 TAATCAAATA
*
140241 TTTTATTTTATT
1 TTTTATTATATT
140253 TTTTATTA-ATT
1 TTTTATTATATT
140264 TTTTATTATATT
1 TTTTATTATATT
140276 T
1 T
140277 AAGCTAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 11 0.50
12 11 0.50
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (12 bp):
TTTTATTATATT
Found at i:140481 original size:2 final size:2
Alignment explanation
Indices: 140476--140507 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
140466 AAATATACAA
140476 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
140508 TGTTCACATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:140672 original size:16 final size:16
Alignment explanation
Indices: 140651--140691 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
140641 AAATCAAAAA
*
140651 TCTGAACTCGAAATAG
1 TCTGAACCCGAAATAG
140667 TCTGAACCCGAAATAG
1 TCTGAACCCGAAATAG
140683 TCTGAACCC
1 TCTGAACCC
140692 AAGAAAGCTC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.34, C:0.27, G:0.17, T:0.22
Consensus pattern (16 bp):
TCTGAACCCGAAATAG
Found at i:141588 original size:24 final size:23
Alignment explanation
Indices: 141560--141609 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
141550 TTTAGTTAAG
* *
141560 ATTAAATGGGTTTTTAAATATTTA
1 ATTAAATAGATTTTTAAATA-TTA
*
141584 ATTAAATATATTTTTAAATATTA
1 ATTAAATAGATTTTTAAATATTA
141607 ATT
1 ATT
141610 TAGTTAATTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 6 0.26
24 17 0.74
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (23 bp):
ATTAAATAGATTTTTAAATATTA
Found at i:141781 original size:16 final size:16
Alignment explanation
Indices: 141740--141782 Score: 50
Period size: 18 Copynumber: 2.6 Consensus size: 16
141730 TGTAATAATA
*
141740 AATTATTTAAAAAATT
1 AATTATATAAAAAATT
*
141756 AATTTTATATAACAAATT
1 AA--TTATATAAAAAATT
141774 AATTATATA
1 AATTATATA
141783 TATAAATATA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
16 9 0.39
18 14 0.61
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (16 bp):
AATTATATAAAAAATT
Found at i:142034 original size:17 final size:16
Alignment explanation
Indices: 142004--142087 Score: 71
Period size: 16 Copynumber: 5.1 Consensus size: 16
141994 AACTTAAACC
*
142004 AATTCAAACCTAAAAA
1 AATTTAAACCTAAAAA
142020 AATTTAAACCCT-AAAA
1 AATTTAAA-CCTAAAAA
** *
142036 AGCTTAAATTCTAAAAA
1 AATTTAAA-CCTAAAAA
*
142053 AATTATAAACTTAAAAA
1 AATT-TAAACCTAAAAA
**
142070 AATTTAAATTTAAAAA
1 AATTTAAACCTAAAAA
142086 AA
1 AA
142088 ATAAATTTAA
Statistics
Matches: 55, Mismatches: 10, Indels: 6
0.77 0.14 0.08
Matches are distributed among these distances:
16 32 0.58
17 19 0.35
18 4 0.07
ACGTcount: A:0.61, C:0.11, G:0.01, T:0.27
Consensus pattern (16 bp):
AATTTAAACCTAAAAA
Found at i:142050 original size:33 final size:34
Alignment explanation
Indices: 142013--142087 Score: 93
Period size: 33 Copynumber: 2.3 Consensus size: 34
142003 CAATTCAAAC
*
142013 CTAAAAAAATT-TAAACCCT-AAAAAGCTTAAATT
1 CTAAAAAAATTATAAA-CCTAAAAAAACTTAAATT
* *
142046 CTAAAAAAATTATAAACTTAAAAAAATTTAAATT
1 CTAAAAAAATTATAAACCTAAAAAAACTTAAATT
142080 -TAAAAAAA
1 CTAAAAAAA
142088 ATAAATTTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
33 21 0.57
34 16 0.43
ACGTcount: A:0.61, C:0.09, G:0.01, T:0.28
Consensus pattern (34 bp):
CTAAAAAAATTATAAACCTAAAAAAACTTAAATT
Found at i:149009 original size:2 final size:2
Alignment explanation
Indices: 149002--149039 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
148992 TATGTTTTAA
*
149002 AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
149040 TTTGAAATGT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:150513 original size:12 final size:12
Alignment explanation
Indices: 150486--150533 Score: 53
Period size: 13 Copynumber: 3.9 Consensus size: 12
150476 AATTATTTAA
150486 TAATGTTTCTTTT
1 TAATGTTTC-TTT
150499 TAATGTTTCTTT
1 TAATGTTTCTTT
*
150511 TAATGAATTCTTT
1 TAATG-TTTCTTT
*
150524 TGAT-TTTCTT
1 TAATGTTTCTT
150534 AATCATTGTA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
11 5 0.16
12 8 0.26
13 18 0.58
ACGTcount: A:0.19, C:0.08, G:0.08, T:0.65
Consensus pattern (12 bp):
TAATGTTTCTTT
Found at i:150947 original size:21 final size:23
Alignment explanation
Indices: 150905--150948 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
150895 TATTAGGTTT
*
150905 TTCTTGATCTTGAACAATGTTTTG
1 TTCTTGATC-TGAACAAAGTTTTG
150929 TTCTTGATC-GAA-AAAGTTTT
1 TTCTTGATCTGAACAAAGTTTT
150949 TTTTTGAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 7 0.37
22 3 0.16
24 9 0.47
ACGTcount: A:0.25, C:0.11, G:0.16, T:0.48
Consensus pattern (23 bp):
TTCTTGATCTGAACAAAGTTTTG
Found at i:152853 original size:17 final size:17
Alignment explanation
Indices: 152822--152879 Score: 55
Period size: 18 Copynumber: 3.2 Consensus size: 17
152812 TTTATTTATC
152822 TAATTATATAATTATTAAA
1 TAATTATAT--TTATTAAA
*
152841 TAATTATATTTATTAGA
1 TAATTATATTTATTAAA
152858 TGAA-TATTATTTATTGAAA
1 T-AATTA-TATTTATT-AAA
152877 TAA
1 TAA
152880 ATATGGAGTT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
17 10 0.29
18 12 0.35
19 12 0.35
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.48
Consensus pattern (17 bp):
TAATTATATTTATTAAA
Found at i:152870 original size:18 final size:18
Alignment explanation
Indices: 152847--152929 Score: 64
Period size: 18 Copynumber: 4.5 Consensus size: 18
152837 TAAATAATTA
152847 TATTTATTAGATGAATAT
1 TATTTATTAGATGAATAT
* *
152865 TATTTATTGAAATAAATAT
1 TATTTATT-AGATGAATAT
* *
152884 GGAGTTTAAATTA-A--AAAAT
1 -TA-TTT--ATTAGATGAATAT
152903 TATTTATTAGATGAATAT
1 TATTTATTAGATGAATAT
152921 TATTTATTA
1 TATTTATTA
152930 AGTGAGGCGC
Statistics
Matches: 51, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
15 4 0.08
16 1 0.02
17 3 0.06
18 22 0.43
19 12 0.24
20 1 0.02
21 4 0.08
22 1 0.02
23 3 0.06
ACGTcount: A:0.43, C:0.00, G:0.10, T:0.47
Consensus pattern (18 bp):
TATTTATTAGATGAATAT
Found at i:157851 original size:3 final size:3
Alignment explanation
Indices: 157843--157885 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
157833 AGAACAATAT
157843 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
157886 CTCTTTTTTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:159248 original size:20 final size:18
Alignment explanation
Indices: 159203--159239 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
159193 TATTAAGTTG
*
159203 AAATTATTTAAATATTAA
1 AAATAATTTAAATATTAA
*
159221 AAATAATTTTAATATTAA
1 AAATAATTTAAATATTAA
159239 A
1 A
159240 TAAATAATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
AAATAATTTAAATATTAA
Found at i:159267 original size:17 final size:16
Alignment explanation
Indices: 159218--159269 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 16
159208 ATTTAAATAT
159218 TAAAAATAAT-TTTAA
1 TAAAAATAATATTTAA
* *
159233 TATTAAATAAATAATTAA
1 TA-AAAAT-AATATTTAA
159251 TAAAAATATATATTTAA
1 TAAAAATA-ATATTTAA
159268 TA
1 TA
159270 TTTAATTTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
15 2 0.07
16 5 0.17
17 16 0.55
18 6 0.21
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
TAAAAATAATATTTAA
Found at i:159281 original size:33 final size:31
Alignment explanation
Indices: 159208--159288 Score: 81
Period size: 33 Copynumber: 2.5 Consensus size: 31
159198 AGTTGAAATT
* *
159208 ATTTAAATATTAAAAATAATTTTAATATTAA
1 ATTTAATTAATAAAAATAATTTTAATATTAA
* *
159239 ATAAATAATTAATAAAAATATATATTTAATATTTA
1 AT--TTAATTAATAAAAATA-AT-TTTAATATTAA
159274 ATTTAATTATATAAA
1 ATTTAATTA-ATAAA
159289 TTTTAATATA
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
31 2 0.05
33 19 0.47
34 7 0.17
35 12 0.30
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (31 bp):
ATTTAATTAATAAAAATAATTTTAATATTAA
Found at i:161507 original size:2 final size:2
Alignment explanation
Indices: 161500--161531 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
161490 ATTGATAATC
*
161500 AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
161532 GCTGTGTACA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:162028 original size:2 final size:2
Alignment explanation
Indices: 162021--162047 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
162011 GACTATGATT
162021 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
162048 GATTTATTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:162163 original size:28 final size:29
Alignment explanation
Indices: 162109--162173 Score: 73
Period size: 30 Copynumber: 2.3 Consensus size: 29
162099 AAATTTTATT
*
162109 TATATATATGATTATAAGAATAAAAATTCA
1 TATATATATGATTATAAGAAT-AAAATTAA
*
162139 TATATATATGATT-TATATAAT-AAATTAA
1 TATATATATGATTATA-AGAATAAAATTAA
162167 TA-ATATA
1 TATATATA
162174 AAAATAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
27 5 0.16
28 8 0.25
29 2 0.06
30 17 0.53
ACGTcount: A:0.52, C:0.02, G:0.05, T:0.42
Consensus pattern (29 bp):
TATATATATGATTATAAGAATAAAATTAA
Found at i:165776 original size:57 final size:57
Alignment explanation
Indices: 165688--165801 Score: 183
Period size: 57 Copynumber: 2.0 Consensus size: 57
165678 CTGAATATTG
* * *
165688 CTCAGTCTCTCAGGCTTCTGGTGCTGGTCTGTCTGCTCCAAAAATTTCTAGGCAGGA
1 CTCAGTCTCTCAGGCCTCTGGTGCTGATCTGTCTGCTCCAAAAACTTCTAGGCAGGA
* *
165745 CTCAGTCTCTCAGGCCTCTGGTGCTGATCTGTCTGCTCCAAGAACTTCTAGGGAGGA
1 CTCAGTCTCTCAGGCCTCTGGTGCTGATCTGTCTGCTCCAAAAACTTCTAGGCAGGA
165802 GGTATATAAA
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
57 52 1.00
ACGTcount: A:0.18, C:0.27, G:0.25, T:0.30
Consensus pattern (57 bp):
CTCAGTCTCTCAGGCCTCTGGTGCTGATCTGTCTGCTCCAAAAACTTCTAGGCAGGA
Found at i:166330 original size:276 final size:276
Alignment explanation
Indices: 165828--166386 Score: 985
Period size: 276 Copynumber: 2.0 Consensus size: 276
165818 AAGTTGAAAG
* * * *
165828 CTGCAATTGAGGCGGCTATCCGTTTGAGGCCTGGATTATGTGAAAGAAAATCCCAAGATCCATCA
1 CTGCCATTGAGGCAGCTATCCATTTGAGGCCTGGATTATGTGAAAGAAAATCCCAAGATCAATCA
165893 TCGGTTTCCAATAAGGCTAAGAATATGATTTCTGTTGAAGGTACACGTGAAGGGCAAACAAATCT
66 TCGGTTTCCAATAAGGCTAAGAATATGATTTCTGTTGAAGGTACACGTGAAGGGCAAACAAATCT
*
165958 TTGTAATCAGGCTTCCATTGGTAATATTAAGCTACTTAATGCACATGCCACTGATGCTGTCTCCG
131 TTGTAATCAGGCTTCCATTGGTAATATCAAGCTACTTAATGCACATGCCACTGATGCTGTCTCCG
*
166023 TAGTTTCTTCTGTTGGCAATCCTTCAATGAGAGATATTTCCATCCCTCCTTTAGCCTCAGTGTCT
196 TAGTTTCTTCTGTTGGCAATCCTTCAATGAGAGATATCTCCATCCCTCCTTTAGCCTCAGTGTCT
*
166088 GCTGTCTGTCAGATTT
261 GCTGTCTATCAGATTT
166104 CTGCCATTGAGGCAGCTATCCATTTGAGGCCTGGATTATGTGAAAGAAAATCCCAAGATCAATCA
1 CTGCCATTGAGGCAGCTATCCATTTGAGGCCTGGATTATGTGAAAGAAAATCCCAAGATCAATCA
* *
166169 TCGTTTTCCAATGAGGCTAAGAATATGATTTCTGTTGAAGGTACACAG-GAAGGGCAAACAAATC
66 TCGGTTTCCAATAAGGCTAAGAATATGATTTCTGTTGAAGGTACAC-GTGAAGGGCAAACAAATC
* *
166233 TTTGTAATCAGGCTTCCATTGGTGATATCAAGCTACTTAATGCACATTCCACTGATGCTGTCTCC
130 TTTGTAATCAGGCTTCCATTGGTAATATCAAGCTACTTAATGCACATGCCACTGATGCTGTCTCC
* *
166298 GTAGTTTCTTCTGTTGGCAATCCTTTAATGAGAGATATCTCCGTCCCTCCTTTAGCCTCAGTGTC
195 GTAGTTTCTTCTGTTGGCAATCCTTCAATGAGAGATATCTCCATCCCTCCTTTAGCCTCAGTGTC
166363 TGCTGTCTATCAGATTT
260 TGCTGTCTATCAGATTT
166380 CTGCCAT
1 CTGCCAT
166387 CCCAGAACAT
Statistics
Matches: 269, Mismatches: 13, Indels: 2
0.95 0.05 0.01
Matches are distributed among these distances:
276 268 1.00
277 1 0.00
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.32
Consensus pattern (276 bp):
CTGCCATTGAGGCAGCTATCCATTTGAGGCCTGGATTATGTGAAAGAAAATCCCAAGATCAATCA
TCGGTTTCCAATAAGGCTAAGAATATGATTTCTGTTGAAGGTACACGTGAAGGGCAAACAAATCT
TTGTAATCAGGCTTCCATTGGTAATATCAAGCTACTTAATGCACATGCCACTGATGCTGTCTCCG
TAGTTTCTTCTGTTGGCAATCCTTCAATGAGAGATATCTCCATCCCTCCTTTAGCCTCAGTGTCT
GCTGTCTATCAGATTT
Found at i:172026 original size:20 final size:20
Alignment explanation
Indices: 172001--172040 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
171991 TCTTATAGTT
*
172001 TTTAATATTTCAAATTTTGA
1 TTTAATATTTCAAATATTGA
* *
172021 TTTAATTTTTGAAATATTGA
1 TTTAATATTTCAAATATTGA
172041 AAGCTTATTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.35, C:0.03, G:0.07, T:0.55
Consensus pattern (20 bp):
TTTAATATTTCAAATATTGA
Found at i:172160 original size:30 final size:29
Alignment explanation
Indices: 172124--172232 Score: 109
Period size: 30 Copynumber: 3.8 Consensus size: 29
172114 TGTAATATAT
*
172124 TTTATTAATGTAATATTGAAAAGTGTAATA
1 TTTATTAATATAATATT-AAAAGTGTAATA
* *
172154 TTTATTAGA-ATAATATTAAAA-T-TTATT
1 TTTATTA-ATATAATATTAAAAGTGTAATA
* *
172181 TTTATTAATATAATATTAAAAGGAGTGATA
1 TTTATTAATATAATATTAAAA-GTGTAATA
172211 TTTATTAGA-ATAATATTAAAAG
1 TTTATTA-ATATAATATTAAAAG
172233 ATATATATTA
Statistics
Matches: 67, Mismatches: 6, Indels: 13
0.78 0.07 0.15
Matches are distributed among these distances:
26 1 0.01
27 22 0.33
28 1 0.01
29 5 0.07
30 36 0.54
31 2 0.03
ACGTcount: A:0.46, C:0.00, G:0.10, T:0.44
Consensus pattern (29 bp):
TTTATTAATATAATATTAAAAGTGTAATA
Found at i:172195 original size:57 final size:57
Alignment explanation
Indices: 172123--172231 Score: 175
Period size: 57 Copynumber: 1.9 Consensus size: 57
172113 CTGTAATATA
* *
172123 TTTTATTAATGTAATATTGAAAA-GTGTAATATTTATTAGAATAATATTAAAATTTAT
1 TTTTATTAATATAATATT-AAAAGGAGTAATATTTATTAGAATAATATTAAAATTTAT
*
172180 TTTTATTAATATAATATTAAAAGGAGTGATATTTATTAGAATAATATTAAAA
1 TTTTATTAATATAATATTAAAAGGAGTAATATTTATTAGAATAATATTAAAA
172232 GATATATATT
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
56 4 0.08
57 44 0.92
ACGTcount: A:0.46, C:0.00, G:0.09, T:0.45
Consensus pattern (57 bp):
TTTTATTAATATAATATTAAAAGGAGTAATATTTATTAGAATAATATTAAAATTTAT
Found at i:172238 original size:27 final size:27
Alignment explanation
Indices: 172151--172238 Score: 106
Period size: 27 Copynumber: 3.1 Consensus size: 27
172141 GAAAAGTGTA
**
172151 ATATTTATTAGAATAATATTAAAATTT
1 ATATTTATTAGAATAATATTAAAAGAT
*
172178 ATTTTTATTA-ATATAATATTAAAAGGAGT
1 ATATTTATTAGA-ATAATATTAAAA-GA-T
172207 GATATTTATTAGAATAATATTAAAAGAT
1 -ATATTTATTAGAATAATATTAAAAGAT
172235 ATAT
1 ATAT
172239 ATTAAAGTAA
Statistics
Matches: 52, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
26 1 0.02
27 25 0.48
28 1 0.02
29 3 0.06
30 21 0.40
31 1 0.02
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (27 bp):
ATATTTATTAGAATAATATTAAAAGAT
Found at i:172531 original size:38 final size:38
Alignment explanation
Indices: 172475--172548 Score: 103
Period size: 38 Copynumber: 1.9 Consensus size: 38
172465 TGATAGACTT
* * * *
172475 TAATTAAACCTATGCTACTTGAACCAAATGTTATGACA
1 TAATTAAACCCATCCTACTTAAACCAAATATTATGACA
*
172513 TAATTAAACCCATCCTACTTAAATCAAATATTATGA
1 TAATTAAACCCATCCTACTTAAACCAAATATTATGA
172549 TTTATAATTA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 31 1.00
ACGTcount: A:0.42, C:0.19, G:0.07, T:0.32
Consensus pattern (38 bp):
TAATTAAACCCATCCTACTTAAACCAAATATTATGACA
Found at i:172632 original size:25 final size:26
Alignment explanation
Indices: 172585--172650 Score: 75
Period size: 25 Copynumber: 2.6 Consensus size: 26
172575 CTCAAAAAAT
* *
172585 AAAATTAAATA-TGAATATATTTTT-
1 AAAATTATATATTTAATATATTTTTA
*
172609 AATATTAATATATTTAATAT-TTTTTA
1 AAAATT-ATATATTTAATATATTTTTA
172635 AAAATTATATATTTAA
1 AAAATTATATATTTAA
172651 AAAATCATAT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
24 5 0.14
25 19 0.54
26 11 0.31
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (26 bp):
AAAATTATATATTTAATATATTTTTA
Found at i:172653 original size:16 final size:16
Alignment explanation
Indices: 172634--172688 Score: 62
Period size: 16 Copynumber: 3.5 Consensus size: 16
172624 AATATTTTTT
172634 AAAAATTATATATTTA
1 AAAAATTATATATTTA
*
172650 AAAAATCATATATTTA
1 AAAAATTATATATTTA
172666 AATATAA--ATAT-TTTA
1 AA-A-AATTATATATTTA
172681 AAAAATTA
1 AAAAATTA
172689 ACAAAAATCG
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
13 2 0.06
14 1 0.03
15 7 0.21
16 21 0.62
17 1 0.03
18 2 0.06
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (16 bp):
AAAAATTATATATTTA
Found at i:173003 original size:36 final size:35
Alignment explanation
Indices: 172962--173038 Score: 95
Period size: 36 Copynumber: 2.2 Consensus size: 35
172952 TTTTTATTAA
172962 AAATAAATA-TTAA-AAAATAATTTTAAATTTTAAAT
1 AAATAAATATTTAATAAAAT-A-TTTAAATTTTAAAT
* *
172997 ATAATAAATATTTAATAAAATATTTATATTTTAATT
1 A-AATAAATATTTAATAAAATATTTAAATTTTAAAT
173033 AAATAA
1 AAATAA
173039 TATAATATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
35 6 0.16
36 21 0.57
37 5 0.14
38 5 0.14
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (35 bp):
AAATAAATATTTAATAAAATATTTAAATTTTAAAT
Found at i:173013 original size:16 final size:17
Alignment explanation
Indices: 172994--173055 Score: 54
Period size: 16 Copynumber: 3.4 Consensus size: 17
172984 TTAAATTTTA
172994 AATATAATA-AATATTT
1 AATATAATATAATATTT
* *
173010 AATAAAATATTTATATTTT
1 AATATAATA-TAATA-TTT
173029 AATTAAATAATATAATATTT
1 AA-T--ATAATATAATATTT
173049 AATATAA
1 AATATAA
173056 ATCTAAAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 11
0.71 0.08 0.22
Matches are distributed among these distances:
16 8 0.22
17 4 0.11
18 3 0.08
19 6 0.17
20 6 0.17
21 4 0.11
22 5 0.14
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
AATATAATATAATATTT
Found at i:173062 original size:27 final size:27
Alignment explanation
Indices: 173009--173072 Score: 67
Period size: 27 Copynumber: 2.3 Consensus size: 27
172999 AATAAATATT
* *
173009 TAATAAAATATTTATATTTTAATTAAA
1 TAATAAAATATTTATATATAAATTAAA
*
173036 TAATATAATATTTA-ATATAAATCTAAA
1 TAATAAAATATTTATATATAAAT-TAAA
*
173063 AAATTAAAAT
1 TAA-TAAAAT
173073 TTCTTATTAC
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
26 6 0.20
27 19 0.63
28 5 0.17
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (27 bp):
TAATAAAATATTTATATATAAATTAAA
Found at i:173247 original size:18 final size:18
Alignment explanation
Indices: 173224--173260 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
173214 TCTCTAATTT
173224 TCAATTAAATTAATTTAA
1 TCAATTAAATTAATTTAA
*
173242 TCAATTAATTTAATTTAA
1 TCAATTAAATTAATTTAA
173260 T
1 T
173261 TTTTTAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (18 bp):
TCAATTAAATTAATTTAA
Found at i:173249 original size:13 final size:13
Alignment explanation
Indices: 173231--173255 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
173221 TTTTCAATTA
173231 AATTAATTTAATC
1 AATTAATTTAATC
173244 AATTAATTTAAT
1 AATTAATTTAAT
173256 TTAATTTTTT
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:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (13 bp):
AATTAATTTAATC
Found at i:173893 original size:19 final size:19
Alignment explanation
Indices: 173871--173907 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
173861 TAAAATTAAA
173871 AAATAAAAAAGTATTTTTT
1 AAATAAAAAAGTATTTTTT
* *
173890 AAATAAATAATTATTTTT
1 AAATAAAAAAGTATTTTT
173908 AGTGACTAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (19 bp):
AAATAAAAAAGTATTTTTT
Found at i:174101 original size:22 final size:22
Alignment explanation
Indices: 174050--174107 Score: 55
Period size: 22 Copynumber: 2.6 Consensus size: 22
174040 TTTATAAAAA
**
174050 AATACTAATAAAATTAATGATATC
1 AATA-TAATAAAA-TAAAAATATC
*
174074 AA-ATAATAAAATAAAAATATG
1 AATATAATAAAATAAAAATATC
*
174095 AATATAATTAAAT
1 AATATAATAAAAT
174108 TTTTTTAATT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
21 9 0.31
22 17 0.59
23 1 0.03
24 2 0.07
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.31
Consensus pattern (22 bp):
AATATAATAAAATAAAAATATC
Found at i:178753 original size:2 final size:2
Alignment explanation
Indices: 178748--178790 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
178738 ACTCTCTCTC
178748 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
178790 T
1 T
178791 GTATCCATTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:183944 original size:53 final size:54
Alignment explanation
Indices: 183825--183951 Score: 134
Period size: 53 Copynumber: 2.4 Consensus size: 54
183815 ACTTAAAGTT
* *
183825 AAATCTAAAATGATTTGAACACGATTTAACTCGAATGTTAAATCTAATTAACTC
1 AAATCTAAAATGATCTGAACACGATTTAACTCCAATGTTAAATCTAATTAACTC
* * * * *
183879 GAATCCAGAATGATCTGAACACGA-TTAAC-CCAAGTGTTAAATCTGATTGA-TCC
1 AAATCTAAAATGATCTGAACACGATTTAACTCCAA-TGTTAAATCTAATTAACT-C
* *
183932 AAATCTGAAATGATCCGAAC
1 AAATCTAAAATGATCTGAAC
183952 CCGCAGTGAC
Statistics
Matches: 59, Mismatches: 12, Indels: 5
0.78 0.16 0.07
Matches are distributed among these distances:
52 4 0.07
53 35 0.59
54 20 0.34
ACGTcount: A:0.40, C:0.18, G:0.13, T:0.28
Consensus pattern (54 bp):
AAATCTAAAATGATCTGAACACGATTTAACTCCAATGTTAAATCTAATTAACTC
Found at i:184025 original size:15 final size:16
Alignment explanation
Indices: 184007--184037 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
183997 GAAAATTTTA
184007 AAACTCGAAA-TAACC
1 AAACTCGAAACTAACC
184022 AAACTCGAAACTAACC
1 AAACTCGAAACTAACC
184038 CGACCTACCC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.52, C:0.29, G:0.06, T:0.13
Consensus pattern (16 bp):
AAACTCGAAACTAACC
Found at i:184353 original size:29 final size:29
Alignment explanation
Indices: 184285--184357 Score: 89
Period size: 29 Copynumber: 2.6 Consensus size: 29
184275 GTAAGAAATA
184285 AAAATTA-TTTT-AAAATATAAAATATCT
1 AAAATTATTTTTAAAAATATAAAATATCT
* *
184312 AAAATTATATTTAAAAATATAAAA-ATTT
1 AAAATTATTTTTAAAAATATAAAATATCT
*
184340 TAAATTATTTTTTAAAAA
1 AAAATTA-TTTTTAAAAA
184358 ATTAATATAT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
27 7 0.18
28 12 0.31
29 20 0.51
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.42
Consensus pattern (29 bp):
AAAATTATTTTTAAAAATATAAAATATCT
Found at i:184356 original size:28 final size:29
Alignment explanation
Indices: 184290--184356 Score: 91
Period size: 28 Copynumber: 2.3 Consensus size: 29
184280 AAATAAAAAT
184290 TATTTTAAAATATAAAATATCTAAAATTA
1 TATTTTAAAATATAAAATATCTAAAATTA
* * *
184319 TATTTAAAAATATAAAA-ATTTTAAATTA
1 TATTTTAAAATATAAAATATCTAAAATTA
*
184347 TTTTTTAAAA
1 TATTTTAAAA
184357 AATTAATATA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
28 17 0.52
29 16 0.48
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (29 bp):
TATTTTAAAATATAAAATATCTAAAATTA
Found at i:184669 original size:18 final size:18
Alignment explanation
Indices: 184629--184669 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
184619 TTTATTTATC
* *
184629 ATTTAATTTTTTAAAATT
1 ATTTAATTATTTAAAAAT
*
184647 TTTTAATTATTTAAAAAT
1 ATTTAATTATTTAAAAAT
184665 ATTTA
1 ATTTA
184670 TAAGTTTTTC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
ATTTAATTATTTAAAAAT
Found at i:186757 original size:29 final size:27
Alignment explanation
Indices: 186648--186775 Score: 98
Period size: 29 Copynumber: 5.0 Consensus size: 27
186638 CAGCTATTAA
**
186648 TAAAATTATATTTACGTTAAATAATAAT
1 TAAAATTATATTTATATTAAA-AATAAT
186676 T-AAA--A-ATTTATA-TATAAAAT-A-
1 TAAAATTATATTTATATTA-AAAATAAT
*
186697 TAACA-TATATTTATATT--AAATAAT
1 TAAAATTATATTTATATTAAAAATAAT
186721 TAAAATTATATTTATATTAAAAATATTAT
1 TAAAATTATATTTATATTAAAAATA--AT
*
186750 TAAAATTACATTTAT-TTAACAAATAA
1 TAAAATTATATTTATATTAA-AAATAA
186776 AAAAGAAATT
Statistics
Matches: 82, Mismatches: 5, Indels: 27
0.72 0.04 0.24
Matches are distributed among these distances:
21 1 0.01
22 7 0.09
23 7 0.09
24 18 0.22
25 14 0.17
27 9 0.11
28 5 0.06
29 21 0.26
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (27 bp):
TAAAATTATATTTATATTAAAAATAAT
Done.