Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr1
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: 35726063
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1821929 characters in sequence are not A, C, G, or T
File 37 of 109
Found at i:11984279 original size:80 final size:80
Alignment explanation
Indices: 11984145--11984294 Score: 219
Period size: 80 Copynumber: 1.9 Consensus size: 80
11984135 AGTTACTGAG
* * *
11984145 GTACAAACAGGGGCACATATATGCATTTAGGGGTACCAAAGTACAAACAGGGGCACGTATGTGCA
1 GTACAAACAGGGACACATATATGCAATTAGGGGTACCAAAGTACAAACAAGGGCACGTATGTGCA
11984210 TTCAAGGGTACCGAA
66 TTCAAGGGTACCGAA
* * * * * *
11984225 GTACAATCAGGGACACGTATGTGCAATTAGGGGTACCAAAGTACAATCAAGGGCACGTGTGTGTA
1 GTACAAACAGGGACACATATATGCAATTAGGGGTACCAAAGTACAAACAAGGGCACGTATGTGCA
11984290 TTCAA
66 TTCAA
11984295 ACAATAATTA
Statistics
Matches: 61, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
80 61 1.00
ACGTcount: A:0.34, C:0.18, G:0.27, T:0.21
Consensus pattern (80 bp):
GTACAAACAGGGACACATATATGCAATTAGGGGTACCAAAGTACAAACAAGGGCACGTATGTGCA
TTCAAGGGTACCGAA
Found at i:11987330 original size:49 final size:49
Alignment explanation
Indices: 11987241--11987335 Score: 136
Period size: 49 Copynumber: 1.9 Consensus size: 49
11987231 ATATTTATAG
* * * * *
11987241 GTTGAAAAACCTTATTCTAATCAATGTCAAATAGATGAAGTGTAGTAAT
1 GTTGAAAAACATTATTCTAATCAATGTAAAATAAAAGAAGTATAGTAAT
*
11987290 GTTGAAAAATATTATTCTAATCAATGTAAAATAAAAGAAGTATAGT
1 GTTGAAAAACATTATTCTAATCAATGTAAAATAAAAGAAGTATAGT
11987336 TCTATATGAA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
49 40 1.00
ACGTcount: A:0.45, C:0.07, G:0.15, T:0.33
Consensus pattern (49 bp):
GTTGAAAAACATTATTCTAATCAATGTAAAATAAAAGAAGTATAGTAAT
Found at i:11999237 original size:24 final size:25
Alignment explanation
Indices: 11999210--11999406 Score: 126
Period size: 25 Copynumber: 7.6 Consensus size: 25
11999200 TTGTGCAACA
*
11999210 CGCCACAAAGACTTTACA-ATAACT
1 CGCCACAAAGGCTTTACAGATAACT
* *
11999234 CGCCACAAAGGCTTTTCAGATAATT
1 CGCCACAAAGGCTTTACAGATAACT
* * *
11999259 CACCGCAAAGGCTTTATAGATAACT
1 CGCCACAAAGGCTTTACAGATAACT
* * *
11999284 TGTCACAAAGGCTTTATAGATAACT
1 CGCCACAAAGGCTTTACAGATAACT
* * * *
11999309 CACCACAAAAGGATTTTCTGATAATTTTCCAACT
1 CGCCAC-AAAGGCTTTAC--A-GA---T--AACT
* ** *
11999343 CACCACAAAGGCTTTTTAGATAATT
1 CGCCACAAAGGCTTTACAGATAACT
* *
11999368 CGCCACAACGGCTTTAAAGATAACT
1 CGCCACAAAGGCTTTACAGATAACT
*
11999393 CGCCACAAATGCTT
1 CGCCACAAAGGCTT
11999407 GGTTTTACTT
Statistics
Matches: 133, Mismatches: 30, Indels: 19
0.73 0.16 0.10
Matches are distributed among these distances:
24 16 0.12
25 84 0.63
26 8 0.06
27 1 0.01
28 1 0.01
29 1 0.01
30 1 0.01
31 1 0.01
32 1 0.01
33 9 0.07
34 10 0.08
ACGTcount: A:0.36, C:0.24, G:0.13, T:0.27
Consensus pattern (25 bp):
CGCCACAAAGGCTTTACAGATAACT
Found at i:12003378 original size:32 final size:32
Alignment explanation
Indices: 12003336--12003399 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
12003326 ATATGAGTGA
*
12003336 GAAAGTTATGATAGTCTTGTGCAATAAAAGCC
1 GAAAGGTATGATAGTCTTGTGCAATAAAAGCC
12003368 GAAAGGTATGATAGTCTTGTGCAATAAAAGCC
1 GAAAGGTATGATAGTCTTGTGCAATAAAAGCC
12003400 TTTTCAAATA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.38, C:0.12, G:0.23, T:0.27
Consensus pattern (32 bp):
GAAAGGTATGATAGTCTTGTGCAATAAAAGCC
Found at i:12004699 original size:44 final size:44
Alignment explanation
Indices: 12004641--12004729 Score: 151
Period size: 44 Copynumber: 2.0 Consensus size: 44
12004631 TAAAGAAGAG
*
12004641 ATGAAATCGCTTCAAAAGAACGAGACTTGGAGGCTAGTTAAACC
1 ATGAAATCGCTTCAAAAGAACGAGACTTGAAGGCTAGTTAAACC
* *
12004685 ATGAAATCGTTTCAAAAGAATGAGACTTGAAGGCTAGTTAAACC
1 ATGAAATCGCTTCAAAAGAACGAGACTTGAAGGCTAGTTAAACC
12004729 A
1 A
12004730 CCCATCGGTA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.40, C:0.16, G:0.21, T:0.22
Consensus pattern (44 bp):
ATGAAATCGCTTCAAAAGAACGAGACTTGAAGGCTAGTTAAACC
Found at i:12008761 original size:10 final size:11
Alignment explanation
Indices: 12008745--12008782 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
12008735 CGATTGAATC
12008745 AATTTTTTAAT
1 AATTTTTTAAT
12008756 -A-TTTTT-AT
1 AATTTTTTAAT
12008764 AATTTTTTAAT
1 AATTTTTTAAT
12008775 AATTTTTT
1 AATTTTTT
12008783 TAATTAAACT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
8 2 0.08
9 6 0.25
10 6 0.25
11 10 0.42
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
AATTTTTTAAT
Found at i:12008769 original size:19 final size:20
Alignment explanation
Indices: 12008745--12008787 Score: 70
Period size: 19 Copynumber: 2.2 Consensus size: 20
12008735 CGATTGAATC
12008745 AATTTTTTAAT-ATTTTTAT
1 AATTTTTTAATAATTTTTAT
*
12008764 AATTTTTTAATAATTTTTTT
1 AATTTTTTAATAATTTTTAT
12008784 AATT
1 AATT
12008788 AAACTGATCA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 11 0.50
20 11 0.50
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (20 bp):
AATTTTTTAATAATTTTTAT
Found at i:12008786 original size:9 final size:10
Alignment explanation
Indices: 12008747--12008787 Score: 50
Period size: 11 Copynumber: 4.1 Consensus size: 10
12008737 ATTGAATCAA
12008747 TTTTT-TAAT
1 TTTTTATAAT
12008756 ATTTTTATAAT
1 -TTTTTATAAT
12008767 TTTTTAATAAT
1 TTTTT-ATAAT
12008778 TTTTT-TAAT
1 TTTTTATAAT
12008787 T
1 T
12008788 AAACTGATCA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
9 5 0.17
10 10 0.34
11 14 0.48
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (10 bp):
TTTTTATAAT
Found at i:12027861 original size:16 final size:16
Alignment explanation
Indices: 12027840--12027870 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
12027830 CTTTTCATGC
*
12027840 AAAATATAAAAGACAG
1 AAAATACAAAAGACAG
12027856 AAAATACAAAAGACA
1 AAAATACAAAAGACA
12027871 TAATAATGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.71, C:0.10, G:0.10, T:0.10
Consensus pattern (16 bp):
AAAATACAAAAGACAG
Found at i:12031712 original size:104 final size:102
Alignment explanation
Indices: 12031576--12031771 Score: 261
Period size: 104 Copynumber: 1.9 Consensus size: 102
12031566 CGATAGTGAG
* * * *
12031576 TTACACAGCCTGGCACATGGTCGTGTGACCCACACAGCCTGGACACAG-AGGCGTGTCCTTGGCC
1 TTACACAGCCTGGCACATGGCCATGTGACCCACACAGCCTGGACAC-GCAGGAGTGTCCTAGGCC
*
12031640 GTGTGAATACTTGGA-CTTAAATTTTCAAAAATTCAACGA
65 GTGTGAA-ACCTGGAGC-TAAATTTTCAAAAATTCAACGA
* * *
12031679 TTACACGGCCTGGCGACATGGCCATGTGACCCACACGGCCTGGACACGCGGGAGTGTCCTAGGCC
1 TTACACAGCCTGGC-ACATGGCCATGTGACCCACACAGCCTGGACACGCAGGAGTGTCCTAGGCC
*
12031744 GTGTGAAACCTGGAGCTAATTTTTCAAA
65 GTGTGAAACCTGGAGCTAAATTTTCAAA
12031772 GTCAGAGCGT
Statistics
Matches: 81, Mismatches: 9, Indels: 6
0.84 0.09 0.06
Matches are distributed among these distances:
103 31 0.38
104 50 0.62
ACGTcount: A:0.25, C:0.27, G:0.26, T:0.22
Consensus pattern (102 bp):
TTACACAGCCTGGCACATGGCCATGTGACCCACACAGCCTGGACACGCAGGAGTGTCCTAGGCCG
TGTGAAACCTGGAGCTAAATTTTCAAAAATTCAACGA
Found at i:12032047 original size:19 final size:19
Alignment explanation
Indices: 12032023--12032091 Score: 74
Period size: 19 Copynumber: 3.7 Consensus size: 19
12032013 GCCACCCCCT
*
12032023 TTTATTTTATTTTATTTTA
1 TTTATTTTATTTTATATTA
12032042 TTTATTATT-TTTTATATTA
1 TTTATT-TTATTTTATATTA
12032061 TTTATTTTTATTTTACTA--A
1 TTTA-TTTTATTTTA-TATTA
12032080 TTT-TTTTATTTT
1 TTTATTTTATTTT
12032092 TTAATTCTTA
Statistics
Matches: 45, Mismatches: 1, Indels: 10
0.80 0.02 0.18
Matches are distributed among these distances:
17 9 0.20
19 25 0.56
20 9 0.20
21 2 0.04
ACGTcount: A:0.22, C:0.01, G:0.00, T:0.77
Consensus pattern (19 bp):
TTTATTTTATTTTATATTA
Found at i:12032082 original size:15 final size:15
Alignment explanation
Indices: 12032022--12032102 Score: 60
Period size: 15 Copynumber: 5.4 Consensus size: 15
12032012 GGCCACCCCC
*
12032022 TTTTATTTTATT-TT
1 TTTTATTTTATTAAT
*
12032036 ATTTTA-TTTATTATT
1 -TTTTATTTTATTAAT
* *
12032051 TTTTATATTATTTAT
1 TTTTATTTTATTAAT
*
12032066 TTTTATTTTACTAATTT
1 TTTTATTTTATTAA--T
12032083 TTTTATTTT-TTAAT
1 TTTTATTTTATTAAT
*
12032097 TCTTAT
1 TTTTAT
12032103 ACTTAGATTT
Statistics
Matches: 54, Mismatches: 8, Indels: 9
0.76 0.11 0.13
Matches are distributed among these distances:
14 17 0.31
15 24 0.44
16 3 0.06
17 10 0.19
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.75
Consensus pattern (15 bp):
TTTTATTTTATTAAT
Found at i:12032091 original size:5 final size:5
Alignment explanation
Indices: 12032022--12032075 Score: 60
Period size: 5 Copynumber: 11.0 Consensus size: 5
12032012 GGCCACCCCC
*
12032022 TTTTA TTTTA TTTTA TTTTA -TTTA TTATT- TTTTA TATTA -TTTA TTTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TT-TTA TTTTA TTTTA TTTTA -TTTTA
12032071 TTTTA
1 TTTTA
12032076 CTAATTTTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
4 9 0.21
5 27 0.64
6 6 0.14
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (5 bp):
TTTTA
Found at i:12032093 original size:10 final size:10
Alignment explanation
Indices: 12032022--12032074 Score: 52
Period size: 12 Copynumber: 4.9 Consensus size: 10
12032012 GGCCACCCCC
*
12032022 TTTTATTTTA
1 TTTTATTTTT
12032032 TTTTATTTTAT
1 TTTTATTTT-T
12032043 TTATTATTTTT
1 TT-TTATTTTT
*
12032054 TATATTATTTAT
1 T-T-TTATTTTT
12032066 TTTTATTTT
1 TTTTATTTT
12032075 ACTAATTTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
10 15 0.41
11 5 0.14
12 17 0.46
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (10 bp):
TTTTATTTTT
Found at i:12037689 original size:12 final size:12
Alignment explanation
Indices: 12037664--12037721 Score: 59
Period size: 12 Copynumber: 4.9 Consensus size: 12
12037654 TTTATCAAGA
*
12037664 TAAATATTAGAT
1 TAAATATTAAAT
12037676 TAAAT-TTAATAT
1 TAAATATTAA-AT
*
12037688 TAAATCTTAAGA-
1 TAAATATTAA-AT
12037700 TAAATATTAAAT
1 TAAATATTAAAT
12037712 TAAA-ATTAAA
1 TAAATATTAAA
12037722 ATAATCGCAT
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
11 10 0.25
12 25 0.62
13 5 0.12
ACGTcount: A:0.55, C:0.02, G:0.03, T:0.40
Consensus pattern (12 bp):
TAAATATTAAAT
Found at i:12043817 original size:16 final size:16
Alignment explanation
Indices: 12043796--12043828 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
12043786 AAGACAATGG
12043796 GATGATAATTTGATTC
1 GATGATAATTTGATTC
12043812 GATGATAATTTGATTC
1 GATGATAATTTGATTC
12043828 G
1 G
12043829 TCCCTTCTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.06, G:0.21, T:0.42
Consensus pattern (16 bp):
GATGATAATTTGATTC
Found at i:12045694 original size:22 final size:22
Alignment explanation
Indices: 12045669--12045713 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
12045659 CCTAAAAAAA
12045669 AGAAGAATATTTATGGTAGAAG
1 AGAAGAATATTTATGGTAGAAG
12045691 AGAAGAATATTTATGGTAGAAG
1 AGAAGAATATTTATGGTAGAAG
12045713 A
1 A
12045714 CCTTGAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.47, C:0.00, G:0.27, T:0.27
Consensus pattern (22 bp):
AGAAGAATATTTATGGTAGAAG
Found at i:12049849 original size:5 final size:5
Alignment explanation
Indices: 12049839--12049868 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
12049829 TTATATTAAA
12049839 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT
12049869 GAGTTTTGGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTAT
Found at i:12056792 original size:29 final size:26
Alignment explanation
Indices: 12056752--12056810 Score: 73
Period size: 29 Copynumber: 2.2 Consensus size: 26
12056742 AAACCCTTTT
12056752 TTTTTTAAATTTACCGAAATAGGCCG
1 TTTTTTAAATTTACCGAAATAGGCCG
* *
12056778 ATTTTTTAATTATTTACCGGAATGGGCCG
1 -TTTTTTAA--ATTTACCGAAATAGGCCG
12056807 TTTT
1 TTTT
12056811 CCCCGAAATC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 8 0.29
28 4 0.14
29 16 0.57
ACGTcount: A:0.25, C:0.14, G:0.17, T:0.44
Consensus pattern (26 bp):
TTTTTTAAATTTACCGAAATAGGCCG
Found at i:12057093 original size:22 final size:22
Alignment explanation
Indices: 12057068--12057136 Score: 102
Period size: 22 Copynumber: 3.1 Consensus size: 22
12057058 ACAAATCCTA
*
12057068 TCTCAATTTCATTCAAAAATTC
1 TCTCAATTTCCTTCAAAAATTC
**
12057090 TCTCAAAGTCCTTCAAAAATTC
1 TCTCAATTTCCTTCAAAAATTC
*
12057112 TCTCAATTTCCTTCCAAAATTC
1 TCTCAATTTCCTTCAAAAATTC
12057134 TCT
1 TCT
12057137 TAAACTCTCG
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.32, C:0.28, G:0.01, T:0.39
Consensus pattern (22 bp):
TCTCAATTTCCTTCAAAAATTC
Found at i:12057171 original size:52 final size:51
Alignment explanation
Indices: 12057089--12057193 Score: 138
Period size: 52 Copynumber: 2.0 Consensus size: 51
12057079 TTCAAAAATT
* * * *
12057089 CTCTCAAAGTCCTTCAAAAATTCTCTCAATTTCCTTCCAAAATTCTCTTAAA
1 CTCTCAAAGTCCTTCAAAAATCCTCACAATTTCCTTCAAAAAATCTC-TAAA
* * *
12057141 CTCTCGAATTCCTTCCAAAATCCTCACAATTTCCTTCAAAAAATCTCTAAA
1 CTCTCAAAGTCCTTCAAAAATCCTCACAATTTCCTTCAAAAAATCTCTAAA
12057192 CT
1 CT
12057194 GTGCTGAAAT
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
51 6 0.13
52 40 0.87
ACGTcount: A:0.33, C:0.30, G:0.02, T:0.34
Consensus pattern (51 bp):
CTCTCAAAGTCCTTCAAAAATCCTCACAATTTCCTTCAAAAAATCTCTAAA
Found at i:12057399 original size:52 final size:51
Alignment explanation
Indices: 12057293--12057444 Score: 215
Period size: 52 Copynumber: 3.0 Consensus size: 51
12057283 AACGTCAACT
*
12057293 CGAAATAAATTTTTTCGGGACCCCTAAACCCT-----AGCCTGCACCCTAAA
1 CGAAATAATTTTTTTC-GGACCCCTAAACCCTAAAAAAGCCTGCACCCTAAA
12057340 CGAAATAATTTTTTTCGGCACCCCTAAACCCTAAAAAAGCCTGCACCCTAAA
1 CGAAATAATTTTTTTCGG-ACCCCTAAACCCTAAAAAAGCCTGCACCCTAAA
* *
12057392 CGAAATAATTTTTTTCGAGACCCCTAAACCCTAAAAAAGCTTGCACCCAAAA
1 CGAAATAATTTTTTTCG-GACCCCTAAACCCTAAAAAAGCCTGCACCCTAAA
12057444 C
1 C
12057445 CCTAAACTTT
Statistics
Matches: 95, Mismatches: 3, Indels: 9
0.89 0.03 0.08
Matches are distributed among these distances:
46 2 0.02
47 28 0.29
52 64 0.67
53 1 0.01
ACGTcount: A:0.36, C:0.30, G:0.11, T:0.23
Consensus pattern (51 bp):
CGAAATAATTTTTTTCGGACCCCTAAACCCTAAAAAAGCCTGCACCCTAAA
Found at i:12064440 original size:12 final size:12
Alignment explanation
Indices: 12064416--12064464 Score: 50
Period size: 12 Copynumber: 4.3 Consensus size: 12
12064406 TAAATAAAGC
12064416 TAATA-ATA-AA
1 TAATATATATAA
*
12064426 TAATATATATTA
1 TAATATATATAA
*
12064438 TAATAGATATAA
1 TAATATATATAA
*
12064450 TTATATAT-TAA
1 TAATATATATAA
12064461 TAAT
1 TAAT
12064465 TATCATCTTT
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
10 5 0.16
11 9 0.29
12 17 0.55
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (12 bp):
TAATATATATAA
Found at i:12073380 original size:4 final size:4
Alignment explanation
Indices: 12073371--12073400 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
12073361 AATAAACTTC
12073371 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
12073401 TTTTATTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:12073870 original size:15 final size:15
Alignment explanation
Indices: 12073850--12073881 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
12073840 ACCCCAGTCA
12073850 CAGATATAGAAATAT
1 CAGATATAGAAATAT
*
12073865 CAGATATAGTAATAT
1 CAGATATAGAAATAT
12073880 CA
1 CA
12073882 TGCATAACAT
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:0.50, C:0.09, G:0.12, T:0.28
Consensus pattern (15 bp):
CAGATATAGAAATAT
Found at i:12082198 original size:16 final size:16
Alignment explanation
Indices: 12082177--12082207 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
12082167 CTATGCATAC
*
12082177 AAAATATAAAAGACAA
1 AAAATACAAAAGACAA
12082193 AAAATACAAAAGACA
1 AAAATACAAAAGACA
12082208 TAAAGTGAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.74, C:0.10, G:0.06, T:0.10
Consensus pattern (16 bp):
AAAATACAAAAGACAA
Found at i:12082641 original size:61 final size:61
Alignment explanation
Indices: 12082541--12082708 Score: 185
Period size: 61 Copynumber: 2.8 Consensus size: 61
12082531 CTGAGTTTTT
* * * * ** * * *
12082541 CCACAAAGGC-ATCCTTTATATCTAGTGCTCCCCACAAAGGTTTTGTTGTCTAGAGTTGTG
1 CCACAAAGGCTATCCTTTATATCCAGTACTCACCACAAAGGCTTTCCTGTCCAAAGTTATG
* * *
12082601 TCACAAAGGCTATCCTTTATATCCAATACTCACCATAAAGGCTTTCCTGTCCAAAGTTATG
1 CCACAAAGGCTATCCTTTATATCCAGTACTCACCACAAAGGCTTTCCTGTCCAAAGTTATG
* * * *
12082662 CCACAAAAGCTGTCATTTATAACCAGTACTCACCACAAAGGCTTTCC
1 CCACAAAGGCTATCCTTTATATCCAGTACTCACCACAAAGGCTTTCC
12082709 CTTCAAAAAT
Statistics
Matches: 88, Mismatches: 19, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
60 9 0.10
61 79 0.90
ACGTcount: A:0.29, C:0.27, G:0.14, T:0.30
Consensus pattern (61 bp):
CCACAAAGGCTATCCTTTATATCCAGTACTCACCACAAAGGCTTTCCTGTCCAAAGTTATG
Found at i:12089889 original size:482 final size:483
Alignment explanation
Indices: 12088975--12089939 Score: 1923
Period size: 482 Copynumber: 2.0 Consensus size: 483
12088965 GGAATTTTTT
12088975 TAATACTATTTTTAATTAATATTAACATAAATAATTTAAAATAAAATTTTAATTTTAATTTTTCT
1 TAATACTATTTTTAATTAATATTAACATAAATAATTTAAAATAAAATTTTAATTTTAATTTTTCT
12089040 ATTTTTTTAAATTATTTTATACAAATAATGAGGTGGTTTGCTTATTTGCCTTTTTTGCCACATGT
66 ATTTTTTTAAATTATTTTATACAAATAATGAGGTGGTTTGCTTATTTGCCTTTTTTGCCACATGT
12089105 CGATTGATGATTAGTCATGTCATCATTGACCAAGGTTGACTATTGGTTGACTAACAAAGGTACCA
131 CGATTGATGATTAGTCATGTCATCATTGACCAAGGTTGACTATTGGTTGACTAACAAAGGTACCA
12089170 ATGTGAAAGTAAAACTTTTTAGATACTCAATTTGACCAAAAAAAAGTTTAGTTATGGGAAAACGA
196 ATGTGAAAGTAAAACTTTTTAGATACTCAATTTGACCAAAAAAAAGTTTAGTTATGGGAAAACGA
12089235 GTATAATTTAAGGTGCATTTTTTATATTAAGCCTGAAAATATACATGTTAAACAATTAGATATAA
261 GTATAATTTAAGGTGCATTTTTTATATTAAGCCTGAAAATATACATGTTAAACAATTAGATATAA
12089300 ATATCTTTAAAGATTTATATAAATAATAAAATATGAATAAATAATTACCATAAATTTATTTTTCT
326 ATATCTTTAAAGATTTATATAAATAATAAAATATGAATAAATAATTACCATAAATTTATTTTTCT
12089365 TATTTAATAAAAATAATTTAAAATAGTTATTATCAATTAATTTTATTTAAAAGTCCGACTAAAAT
391 TATTTAATAAAAATAATTTAAAATAGTTATTATCAATTAATTTTATTTAAAAGTCCGACTAAAAT
12089430 ATAAGAATTCTACTTAGTGCTTCTATAA
456 ATAAGAATTCTACTTAGTGCTTCTATAA
12089458 TAATACTA-TTTTAATTAATATTAACATAAATAATTTAAAATAAAATTTTAATTTTAATTTTTCT
1 TAATACTATTTTTAATTAATATTAACATAAATAATTTAAAATAAAATTTTAATTTTAATTTTTCT
12089522 ATTTTTTTAAATTATTTTATACAAATAATGAGGTGGTTTGCTTATTTGCCTTTTTTGCCACATGT
66 ATTTTTTTAAATTATTTTATACAAATAATGAGGTGGTTTGCTTATTTGCCTTTTTTGCCACATGT
12089587 CGATTGATGATTAGTCATGTCATCATTGACCAAGGTTGACTATTGGTTGACTAACAAAGGTACCA
131 CGATTGATGATTAGTCATGTCATCATTGACCAAGGTTGACTATTGGTTGACTAACAAAGGTACCA
12089652 ATGTGAAAGTAAAACTTTTTAGATACTCAATTTGACCAAAAAAAAGTTTAGTTATGGGAAAACGA
196 ATGTGAAAGTAAAACTTTTTAGATACTCAATTTGACCAAAAAAAAGTTTAGTTATGGGAAAACGA
12089717 GTATAATTTAAGGTGCATTTTTTATATTAAGCCTGAAAATATACATGTTAAACAATTAGATATAA
261 GTATAATTTAAGGTGCATTTTTTATATTAAGCCTGAAAATATACATGTTAAACAATTAGATATAA
12089782 ATATCTTTAAAGATTTATATAAATAATAAAATATGAATAAATAATTACCATAAATTTATTTTTCT
326 ATATCTTTAAAGATTTATATAAATAATAAAATATGAATAAATAATTACCATAAATTTATTTTTCT
12089847 TATTTAATAAAAATAATTTAAAATAGTTATTATCAATTAATTTTATTTAAAAGTCCGACTAAAAT
391 TATTTAATAAAAATAATTTAAAATAGTTATTATCAATTAATTTTATTTAAAAGTCCGACTAAAAT
12089912 ATAAGAATTCTACTTAGTGCTTCTATAA
456 ATAAGAATTCTACTTAGTGCTTCTATAA
12089940 AAAAATGTAA
Statistics
Matches: 482, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
482 474 0.98
483 8 0.02
ACGTcount: A:0.40, C:0.09, G:0.10, T:0.41
Consensus pattern (483 bp):
TAATACTATTTTTAATTAATATTAACATAAATAATTTAAAATAAAATTTTAATTTTAATTTTTCT
ATTTTTTTAAATTATTTTATACAAATAATGAGGTGGTTTGCTTATTTGCCTTTTTTGCCACATGT
CGATTGATGATTAGTCATGTCATCATTGACCAAGGTTGACTATTGGTTGACTAACAAAGGTACCA
ATGTGAAAGTAAAACTTTTTAGATACTCAATTTGACCAAAAAAAAGTTTAGTTATGGGAAAACGA
GTATAATTTAAGGTGCATTTTTTATATTAAGCCTGAAAATATACATGTTAAACAATTAGATATAA
ATATCTTTAAAGATTTATATAAATAATAAAATATGAATAAATAATTACCATAAATTTATTTTTCT
TATTTAATAAAAATAATTTAAAATAGTTATTATCAATTAATTTTATTTAAAAGTCCGACTAAAAT
ATAAGAATTCTACTTAGTGCTTCTATAA
Found at i:12090059 original size:11 final size:11
Alignment explanation
Indices: 12090043--12090067 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
12090033 ATTTAAAAAA
12090043 ATATTTTAAAT
1 ATATTTTAAAT
12090054 ATATTTTAAAT
1 ATATTTTAAAT
12090065 ATA
1 ATA
12090068 AAATTTTATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (11 bp):
ATATTTTAAAT
Found at i:12101888 original size:19 final size:19
Alignment explanation
Indices: 12101864--12101910 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
12101854 TCTCTTTCTT
12101864 TTTGCATT-CATTCCATGCA
1 TTTGCATTACATTCCAT-CA
*
12101883 TTTGCATTACATTGCATCA
1 TTTGCATTACATTCCATCA
12101902 TTTGCATTA
1 TTTGCATTA
12101911 GATTTTCACA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 19 0.73
20 7 0.27
ACGTcount: A:0.23, C:0.21, G:0.11, T:0.45
Consensus pattern (19 bp):
TTTGCATTACATTCCATCA
Found at i:12105184 original size:10 final size:10
Alignment explanation
Indices: 12105169--12105201 Score: 66
Period size: 10 Copynumber: 3.3 Consensus size: 10
12105159 GTTCCTTGAG
12105169 AAAAAAATAA
1 AAAAAAATAA
12105179 AAAAAAATAA
1 AAAAAAATAA
12105189 AAAAAAATAA
1 AAAAAAATAA
12105199 AAA
1 AAA
12105202 GAGGAGAGGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.91, C:0.00, G:0.00, T:0.09
Consensus pattern (10 bp):
AAAAAAATAA
Found at i:12106758 original size:177 final size:177
Alignment explanation
Indices: 12106462--12106965 Score: 749
Period size: 177 Copynumber: 2.8 Consensus size: 177
12106452 ATGTATTGAA
* * *
12106462 GAAGATGGCAAATCTTATCTCCATGAAGTTGCAGTGGAGCAGATTAAAGCCAATAATTCTATCTC
1 GAAGATGGCAAATCTTATCTCCCTAAAGTTGAAGTGGAGCAGATTAAAGCCAATAATTCTATCTC
* * **
12106527 CCTGAAGTTACAGTGGAGCAGATTAAAGCCA-ATAATCCTATCTCCCTGAAGTTGCAGTGGAGCG
66 CCTGAAGTTGCAGTGGAGCGGATTAAAGTTACA-AATCCTATCTCCCTGAAGTTGCAGTGGAGCG
*
12106591 GATTAAAGTTACAAGTCTTATCTACCTGAAGTTACAATGGAGCAGACT
130 GATTAAAGTTACAAGTCTTATCTACCTGAAGTTACAATGGAGCAAACT
* * *
12106639 GAAGATGACAACTCTTATCTCCCTAAAGTTGAAGTGGAGCAGATTAAAGCCAGTAATTCTATCTC
1 GAAGATGGCAAATCTTATCTCCCTAAAGTTGAAGTGGAGCAGATTAAAGCCAATAATTCTATCTC
* * *
12106704 CCTGAAGTTGTAGTGGAGCGGATTAAAGTTACAAATCCTATCTCCCTGAAGTTGCAATTGAGCGG
66 CCTGAAGTTGCAGTGGAGCGGATTAAAGTTACAAATCCTATCTCCCTGAAGTTGCAGTGGAGCGG
* * *
12106769 ATTAAAGTTACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAAACT
131 ATTAAAGTTACAAGTCTTATCTACCTGAAGTTACAATGGAGCAAACT
* * * *
12106816 GAAGATGGTAAATCTTAACTCCCTAAAGTTGTAGTGGAGCAGATTAAAGCCAATAATCCTATCTC
1 GAAGATGGCAAATCTTATCTCCCTAAAGTTGAAGTGGAGCAGATTAAAGCCAATAATTCTATCTC
* * * * * *
12106881 TCTAAAGTTGCAGTGGAGAGGATTAAATTTACAAATCCTATCTCCTTGAAGTTACAGTGGAGCGG
66 CCTGAAGTTGCAGTGGAGCGGATTAAAGTTACAAATCCTATCTCCCTGAAGTTGCAGTGGAGCGG
12106946 ATTAAAGTTACAAGTCTTAT
131 ATTAAAGTTACAAGTCTTAT
12106966 TGAAGAAAGT
Statistics
Matches: 293, Mismatches: 33, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
177 292 1.00
178 1 0.00
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (177 bp):
GAAGATGGCAAATCTTATCTCCCTAAAGTTGAAGTGGAGCAGATTAAAGCCAATAATTCTATCTC
CCTGAAGTTGCAGTGGAGCGGATTAAAGTTACAAATCCTATCTCCCTGAAGTTGCAGTGGAGCGG
ATTAAAGTTACAAGTCTTATCTACCTGAAGTTACAATGGAGCAAACT
Found at i:12106838 original size:133 final size:133
Alignment explanation
Indices: 12106470--12106952 Score: 494
Period size: 133 Copynumber: 3.6 Consensus size: 133
12106460 AAGAAGATGG
* * * *** * *
12106470 CAAATCTTATCTCCATGAAGTTGCAGTGGAGCAGATTAAAGCCAATAATTC-TATCTCCCTGAAG
1 CAAATCCTATCTCCCTGAAGTTGCAATGGAGCAGATTAAAGATTACAAATCTTATCTCCCTGAAG
* *
12106534 TTACAGTGGAGCAGATTAAAGCCAAT-AATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAA
66 TTACAGTGGAGCAGATTAAAGCCAGTAAAT-CTATCTCCCTGAAGTTGTAGTGGAGCGGATTAAA
12106598 GTTA
130 GTTA
* * * * * * * * *
12106602 CAAGTCTTATCTACCTGAAGTTACAATGGAGCAGACTGAAGATGACAACTCTTATCTCCCTAAAG
1 CAAATCCTATCTCCCTGAAGTTGCAATGGAGCAGATTAAAGATTACAAATCTTATCTCCCTGAAG
*
12106667 TTGA-AGTGGAGCAGATTAAAGCCAGTAATTCTATCTCCCTGAAGTTGTAGTGGAGCGGATTAAA
66 TT-ACAGTGGAGCAGATTAAAGCCAGTAAATCTATCTCCCTGAAGTTGTAGTGGAGCGGATTAAA
12106731 GTTA
130 GTTA
* * *
12106735 CAAATCCTATCTCCCTGAAGTTGCAATTGAGCGGATTAAAG-TTACAAGTCTTATCTCCCTGAAG
1 CAAATCCTATCTCCCTGAAGTTGCAATGGAGCAGATTAAAGATTACAAATCTTATCTCCCTGAAG
* * * * *** * * *
12106799 TTGCAGTGGAGCAAACTGAAGATGGTAAATCTTAACTCCCTAAAGTTGTAGTGGAGCAGATTAAA
66 TTACAGTGGAGCAGATTAAAGCCAGTAAATC-TATCTCCCTGAAGTTGTAGTGGAGCGGATTAAA
**
12106864 GCCA
130 GTTA
* * * * * *
12106868 -ATAATCCTATCTCTCTAAAGTTGCAGTGGAG-AGGATTAAA-TTTACAAATCCTATCTCCTTGA
1 CA-AATCCTATCTCCCTGAAGTTGCAATGGAGCA-GATTAAAGATTACAAATCTTATCTCCCTGA
*
12106930 AGTTACAGTGGAGCGGATTAAAG
64 AGTTACAGTGGAGCAGATTAAAG
12106953 TTACAAGTCT
Statistics
Matches: 290, Mismatches: 53, Indels: 15
0.81 0.15 0.04
Matches are distributed among these distances:
132 82 0.28
133 205 0.71
134 3 0.01
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.28
Consensus pattern (133 bp):
CAAATCCTATCTCCCTGAAGTTGCAATGGAGCAGATTAAAGATTACAAATCTTATCTCCCTGAAG
TTACAGTGGAGCAGATTAAAGCCAGTAAATCTATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAG
TTA
Found at i:12106957 original size:44 final size:44
Alignment explanation
Indices: 12106470--12106958 Score: 437
Period size: 44 Copynumber: 11.1 Consensus size: 44
12106460 AAGAAGATGG
* * **
12106470 CAAATCTTATCTCCATGAAGTTGCAGTGGAGCAGATTAAAGCCA
1 CAAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTTA
* * **
12106514 -ATAATTCTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAGCCA
1 CA-AATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTTA
*
12106558 -ATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAGTTA
1 CA-AATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTTA
* * * * * * * *
12106602 CAAGTCTTATCTACCTGAAGTTACAATGGAGCAGACTGAAGATGA
1 CAAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG-TTA
* * * * **
12106647 CAACTCTTATCTCCCTAAAGTTGAAGTGGAGCAGATTAAAGCCA
1 CAAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTTA
** * * *
12106691 GTAATTCTATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAGTTA
1 CAAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTTA
* * *
12106735 CAAATCCTATCTCCCTGAAGTTGCAATTGAGCGGATTAAAGTTA
1 CAAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTTA
* * * * * **
12106779 CAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAAACTGAAGATGG
1 CAAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG-TTA
* * * * * **
12106824 TAAATCTTAACTCCCTAAAGTTGTAGTGGAGCAGATTAAAGCCA
1 CAAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTTA
* * *
12106868 -ATAATCCTATCTCTCTAAAGTTGCAGTGGAG-AGGATTAAATTTA
1 CA-AATCCTATCTCCCTGAAGTTGCAGTGGAGCA-GATTAAAGTTA
* * *
12106912 CAAATCCTATCTCCTTGAAGTTACAGTGGAGCGGATTAAAGTTA
1 CAAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTTA
12106956 CAA
1 CAA
12106959 GTCTTATTGA
Statistics
Matches: 359, Mismatches: 78, Indels: 16
0.79 0.17 0.04
Matches are distributed among these distances:
43 3 0.01
44 285 0.79
45 71 0.20
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.28
Consensus pattern (44 bp):
CAAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTTA
Found at i:12107121 original size:196 final size:196
Alignment explanation
Indices: 12106780--12107139 Score: 479
Period size: 196 Copynumber: 1.8 Consensus size: 196
12106770 TTAAAGTTAC
* *
12106780 AAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAAACTGAAGATGGTAAATCTTAACTCCCTAAAGT
1 AAGTCTTATCCCCCTGAAGTTGCAGTGGAGCAAACTGAAGATGGCAAATCTTAACTCCCTAAAGT
* * * * * **
12106845 TGTAGTGGAGCAGATTAAAGCCAATAATCCTATCTCTCTAAAGTTGCAGTGGAGAGGATTAAATT
66 TGCAGCGGAGCAGATTAAAGCCAATAATCCTATCTCTCTAAAGTTACAGTGGAGAGAACTAAAGA
* * *
12106910 TACAAATCCTATCTCCTTGAAGTTACAGTGGAGCGGATTAAAGTTACAAGTCTTATTGAAGAAAG
131 GACAAATCCTATCTCCCTGAAGTTACAGTAGAGCGGATTAAAGTTACAAGTCTTATTGAAGAAAG
12106975 T
196 T
* * * *
12106976 AAGTCTTATCCCCCTGAAGTTGTAGTGGGGCAGACTGAAGATGGCAAATCTTATCTCCC-AGAAG
1 AAGTCTTATCCCCCTGAAGTTGCAGTGGAGCAAACTGAAGATGGCAAATCTTAACTCCCTA-AAG
* * * * *
12107040 TTGCAGCGGAGTAGATTAAAGCTAATAATCCTATCTCTCTGAAGTTACAGTGGAGCGAACTGAAG
65 TTGCAGCGGAGCAGATTAAAGCCAATAATCCTATCTCTCTAAAGTTACAGTGGAGAGAACTAAAG
* * * *
12107105 AGACCAGTCTTATCTCCCTGAAGTTCCAGTAGAGC
130 AGACAAATCCTATCTCCCTGAAGTTACAGTAGAGC
12107140 AAACTGAAGA
Statistics
Matches: 138, Mismatches: 25, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
195 1 0.01
196 137 0.99
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.28
Consensus pattern (196 bp):
AAGTCTTATCCCCCTGAAGTTGCAGTGGAGCAAACTGAAGATGGCAAATCTTAACTCCCTAAAGT
TGCAGCGGAGCAGATTAAAGCCAATAATCCTATCTCTCTAAAGTTACAGTGGAGAGAACTAAAGA
GACAAATCCTATCTCCCTGAAGTTACAGTAGAGCGGATTAAAGTTACAAGTCTTATTGAAGAAAG
T
Found at i:12107355 original size:42 final size:44
Alignment explanation
Indices: 12107247--12107371 Score: 155
Period size: 44 Copynumber: 2.9 Consensus size: 44
12107237 GATCATGGAA
*
12107247 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCAAT
* * * **
12107291 AATCCTATCTCCCTGAAGTTGCAATGGAGCGGATTGAAG-TGA-
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCAAT
* * *
12107333 AGTCTTATCTCCTTGAAGTTGCAGTGGAGCAGACTGAAG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAG
12107372 ATAGTAAATC
Statistics
Matches: 69, Mismatches: 12, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
42 33 0.48
43 1 0.01
44 35 0.51
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.27
Consensus pattern (44 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCAAT
Found at i:12107618 original size:131 final size:130
Alignment explanation
Indices: 12107425--12107746 Score: 439
Period size: 131 Copynumber: 2.4 Consensus size: 130
12107415 AAGACAGTGA
* *
12107425 ATCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCACCAGTCCTATCTCCCTGAGCAGTA
1 ATCTTATCTTCCCGAGGTAGTAGGGAAGCAGATTTAAGCCACCA-TCCTATCTCCCTAAGCAGTA
* * * *
12107490 GTGGAGTAGGTTGAAGATTGTAGATCCTGTCTCCCTAAGCAATAGTGGAGCAGATCGAAGACGAC
65 GTGGAGTAGGTTAAAGATTGTAGATCCTGTCTCCCTAAGCAATAGTGGAACAAATCAAAGACGAC
12107555 GG
130 -G
* *
12107557 ATCTTATCTTCCCGAGATAGTA-GGAAGCAGATTTAAGCCATCATTCCTATCTCCCTAAGCAGTA
1 ATCTTATCTTCCCGAGGTAGTAGGGAAGCAGATTTAAGCCACCA-TCCTATCTCCCTAAGCAGTA
* * * * * ** *
12107621 GTGGAGTAGGTTAAAGATTGTATATCTTGTCTCTCTAAGCAGTAGTGTAACAAATCAAAGTTGGC
65 GTGGAGTAGGTTAAAGATTGTAGATCCTGTCTCCCTAAGCAATAGTGGAACAAATCAAAGACGAC
12107686 G
130 G
*
12107687 AGTCTTATCTTCCCGAGGTAGTAGGGAAGCAGATTTAAGCCACCAGCCTTATCTCCCTAA
1 A-TCTTATCTTCCCGAGGTAGTAGGGAAGCAGATTTAAGCCACCATCC-TATCTCCCTAA
12107747 AGTTGCAGTG
Statistics
Matches: 167, Mismatches: 20, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
130 2 0.01
131 114 0.68
132 51 0.31
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (130 bp):
ATCTTATCTTCCCGAGGTAGTAGGGAAGCAGATTTAAGCCACCATCCTATCTCCCTAAGCAGTAG
TGGAGTAGGTTAAAGATTGTAGATCCTGTCTCCCTAAGCAATAGTGGAACAAATCAAAGACGACG
Found at i:12108255 original size:22 final size:22
Alignment explanation
Indices: 12108195--12108252 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 22
12108185 AATTTTCAAG
12108195 GATATGCAATCTT---AGATAT
1 GATATGCAATCTTAGAAGATAT
12108214 GATATGCAATCTTAGAAGATAT
1 GATATGCAATCTTAGAAGATAT
* *
12108236 GATTTTGTAATCTTAGA
1 GA-TATGCAATCTTAGA
12108253 GATTTAATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 13 0.39
22 8 0.24
23 12 0.36
ACGTcount: A:0.36, C:0.09, G:0.17, T:0.38
Consensus pattern (22 bp):
GATATGCAATCTTAGAAGATAT
Found at i:12114566 original size:21 final size:20
Alignment explanation
Indices: 12114529--12114568 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
12114519 ACTAACCAAA
* *
12114529 AAAAAATAGAAAGAAGAAAC
1 AAAAAATAAAAAAAAGAAAC
12114549 AAAAAATAAAAAAAAAGAAA
1 AAAAAAT-AAAAAAAAGAAA
12114569 GGAATACATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.82, C:0.03, G:0.10, T:0.05
Consensus pattern (20 bp):
AAAAAATAAAAAAAAGAAAC
Found at i:12116253 original size:29 final size:29
Alignment explanation
Indices: 12116221--12116357 Score: 131
Period size: 29 Copynumber: 4.8 Consensus size: 29
12116211 TTTAAGGACA
* *
12116221 CCTTTGTGGAAAAACTCTACAAAGGTAAG
1 CCTTTGTGGCAAACCTCTACAAAGGTAAG
* * *
12116250 CCTTTGTGGCAAACCTGTTC-AA-GTACAA
1 CCTTTGTGGCAAACCTCTACAAAGGTA-AG
* * * *
12116278 CCCTTGTGGTAAAACTCTAGAAAGGTAAG
1 CCTTTGTGGCAAACCTCTACAAAGGTAAG
*
12116307 CCTTTGTGGCAAACCTATTA-AAAGGT-AG
1 CCTTTGTGGCAAACCT-CTACAAAGGTAAG
12116335 CCTTTGTGGCAAACCTCT-CAAAG
1 CCTTTGTGGCAAACCTCTACAAAG
12116358 AATGACTTTG
Statistics
Matches: 86, Mismatches: 17, Indels: 12
0.75 0.15 0.10
Matches are distributed among these distances:
27 8 0.09
28 35 0.41
29 38 0.44
30 5 0.06
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.26
Consensus pattern (29 bp):
CCTTTGTGGCAAACCTCTACAAAGGTAAG
Found at i:12116343 original size:57 final size:56
Alignment explanation
Indices: 12116192--12116328 Score: 166
Period size: 57 Copynumber: 2.4 Consensus size: 56
12116182 AGAGAAGAAT
* * * * *
12116192 GCCTTTGTAGCAATCTCTATTTAAGGACACCTTTGTGGAAAAACTCTACAAAGGTAA
1 GCCTTTGTGGCAAAC-CTATTAAAGTAAACCTTTGTGGAAAAACTCTACAAAGGTAA
* * * * *
12116249 GCCTTTGTGGCAAACCTGTTCAAGTACAACCCTTGTGGTAAAACTCTAGAAAGGTAA
1 GCCTTTGTGGCAAACCTATTAAAGTA-AACCTTTGTGGAAAAACTCTACAAAGGTAA
12116306 GCCTTTGTGGCAAACCTATTAAA
1 GCCTTTGTGGCAAACCTATTAAA
12116329 AGGTAGCCTT
Statistics
Matches: 68, Mismatches: 11, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
56 8 0.12
57 60 0.88
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.28
Consensus pattern (56 bp):
GCCTTTGTGGCAAACCTATTAAAGTAAACCTTTGTGGAAAAACTCTACAAAGGTAA
Found at i:12116427 original size:29 final size:29
Alignment explanation
Indices: 12116366--12116428 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
12116356 AGAATGACTT
* *
12116366 TGTGGCAGATATCTGAAAGGAAAATCCTT
1 TGTGGCAGATATCTGAAAGGAAAAGCCTA
12116395 TGTGGCA-ATATCTGTCAAAGG-AAAGCCTA
1 TGTGGCAGATATCTG--AAAGGAAAAGCCTA
12116424 TGTGG
1 TGTGG
12116429 TGAACTCTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 7 0.23
29 18 0.60
30 5 0.17
ACGTcount: A:0.32, C:0.14, G:0.27, T:0.27
Consensus pattern (29 bp):
TGTGGCAGATATCTGAAAGGAAAAGCCTA
Found at i:12119251 original size:19 final size:19
Alignment explanation
Indices: 12119215--12119253 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
12119205 TCAGCCTCTA
*
12119215 ATCAATTAAATCCCTAATT
1 ATCAATTAAATCACTAATT
* *
12119234 ATCAATTAAGTCATTAATT
1 ATCAATTAAATCACTAATT
12119253 A
1 A
12119254 CCCTTAATTG
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:0.44, C:0.15, G:0.03, T:0.38
Consensus pattern (19 bp):
ATCAATTAAATCACTAATT
Found at i:12120694 original size:7 final size:8
Alignment explanation
Indices: 12120672--12120701 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
12120662 AAATGAGTAT
12120672 TTTTCTTTA
1 TTTT-TTTA
12120681 TTTTTTTA
1 TTTTTTTA
12120689 TTTTTTTA
1 TTTTTTTA
12120697 TTTTT
1 TTTTT
12120702 CTACTCACTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 17 0.81
9 4 0.19
ACGTcount: A:0.10, C:0.03, G:0.00, T:0.87
Consensus pattern (8 bp):
TTTTTTTA
Found at i:12122353 original size:17 final size:17
Alignment explanation
Indices: 12122331--12122366 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
12122321 AAAATAAATC
12122331 AATTAAA-ATAAATTTAA
1 AATTAAACA-AAATTTAA
12122348 AATTAAACAAAATTTAA
1 AATTAAACAAAATTTAA
12122365 AA
1 AA
12122367 GAGAAACCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 17 0.94
18 1 0.06
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (17 bp):
AATTAAACAAAATTTAA
Found at i:12124085 original size:19 final size:19
Alignment explanation
Indices: 12124049--12124087 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
12124039 TTAGCCTCTA
*
12124049 ATCAATTAAATCCCTAATT
1 ATCAATTAAATCACTAATT
* *
12124068 ATCAATTAAGTCATTAATT
1 ATCAATTAAATCACTAATT
12124087 A
1 A
12124088 CCCTTAATTG
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:0.44, C:0.15, G:0.03, T:0.38
Consensus pattern (19 bp):
ATCAATTAAATCACTAATT
Found at i:12129367 original size:11 final size:11
Alignment explanation
Indices: 12129342--12129381 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
12129332 ATAAATCCTT
12129342 TCTCTAATTTCC
1 TCTC-AATTTCC
*
12129354 TCTCAATTTGC
1 TCTCAATTTCC
*
12129365 TCTCAATTTTC
1 TCTCAATTTCC
12129376 TCTCAA
1 TCTCAA
12129382 AGTTCTCTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
11 22 0.85
12 4 0.15
ACGTcount: A:0.20, C:0.30, G:0.03, T:0.47
Consensus pattern (11 bp):
TCTCAATTTCC
Found at i:12129389 original size:22 final size:21
Alignment explanation
Indices: 12129341--12129392 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 21
12129331 AATAAATCCT
*
12129341 TTCTCT-AATTTCCTCTCAAT
1 TTCTCTCAATTTCCTCTCAAG
*
12129361 TTGCTCTCAATTTTCTCTCAAAG
1 TT-CTCTCAATTTCCTCTC-AAG
12129384 TTCTCTCAA
1 TTCTCTCAA
12129393 ATCCCTATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 2 0.07
21 4 0.15
22 17 0.63
23 4 0.15
ACGTcount: A:0.21, C:0.29, G:0.04, T:0.46
Consensus pattern (21 bp):
TTCTCTCAATTTCCTCTCAAG
Found at i:12129414 original size:51 final size:51
Alignment explanation
Indices: 12129354--12129455 Score: 170
Period size: 51 Copynumber: 2.0 Consensus size: 51
12129344 TCTAATTTCC
12129354 TCTCAATTTGCTCTCAATTTTCTCTCAAAGTT-CTCTCAAATCCCTATTTAA
1 TCTCAATTTGCTCTCAATTTTCTCTCAAA-TTCCTCTCAAATCCCTATTTAA
* *
12129405 TCTCCATTTGCTCTCTATTTTCTCTCAAATTCCTCTCAAATCCCTATTTAA
1 TCTCAATTTGCTCTCAATTTTCTCTCAAATTCCTCTCAAATCCCTATTTAA
12129456 AAGAGCTTTA
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
50 2 0.04
51 46 0.96
ACGTcount: A:0.24, C:0.29, G:0.03, T:0.44
Consensus pattern (51 bp):
TCTCAATTTGCTCTCAATTTTCTCTCAAATTCCTCTCAAATCCCTATTTAA
Found at i:12129641 original size:18 final size:18
Alignment explanation
Indices: 12129618--12129679 Score: 58
Period size: 18 Copynumber: 3.5 Consensus size: 18
12129608 TAAGTGTTAA
12129618 ATTTAATTTTTAAATATT
1 ATTTAATTTTTAAATATT
**
12129636 ATTTAATATTTTTTAT-TT
1 ATTTAAT-TTTTAAATATT
*
12129654 ATGTAA-TTTTAAATAATT
1 ATTTAATTTTTAAAT-ATT
12129672 A-TTAATTT
1 ATTTAATTT
12129680 ATTATTTGTT
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
16 6 0.18
17 3 0.09
18 19 0.56
19 6 0.18
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (18 bp):
ATTTAATTTTTAAATATT
Found at i:12131333 original size:18 final size:18
Alignment explanation
Indices: 12131292--12131326 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
12131282 GCCAGGTGCG
*
12131292 TATCCTAACCCTTTTATA
1 TATCCTAACCCTTATATA
12131310 TATCCTAACCCTTATAT
1 TATCCTAACCCTTATAT
12131327 GTTTCCTTTT
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:0.29, C:0.29, G:0.00, T:0.43
Consensus pattern (18 bp):
TATCCTAACCCTTATATA
Found at i:12135167 original size:126 final size:126
Alignment explanation
Indices: 12134941--12135357 Score: 597
Period size: 126 Copynumber: 3.3 Consensus size: 126
12134931 ACGTGGGAGC
* * * * * *
12134941 TTTTTTCAGGAGTTACTGTAGCAAAAGTGCGTCTATGTGGGAGCTTCTTTCAGTACTTCTGCTAA
1 TTTTTTCAGGAGCTACTGTAGCAAAAGCGCGTCTACGTGGAAGCTTTTTTCAGTACTTCTGCTGA
* * *
12135006 CAAAGCATCCTGCTTAAAGTGTTTTTGACATTGTTTGCTCAGAAACGTCTACTCGAAATTA
66 CAAAGCATCCTACTTAAAGCGTTTTTGACACTGTTTGCTCAGAAACGTCTACTCGAAATTA
** *
12135067 TTTTTTCAATAGCTACTATAGCAAAAGCGCGT-TCACGTGGAAGCTTTTTTCAGTACTTCTGCTG
1 TTTTTTCAGGAGCTACTGTAGCAAAAGCGCGTCT-ACGTGGAAGCTTTTTTCAGTACTTCTGCTG
** * * *
12135131 ACAAAGCATTTTTCTTAAAGCGTTTTTGACACTGTTTGCTCAAAAACGTCTACTCGAAATCA
65 ACAAAGCATCCTACTTAAAGCGTTTTTGACACTGTTTGCTCAGAAACGTCTACTCGAAATTA
12135193 TTTTTT-AGGAGCTACTGTAGCAAAAGCGCGTCTACGT-GAGAGCTTTTTTCAGTACTTCTGCTG
1 TTTTTTCAGGAGCTACTGTAGCAAAAGCGCGTCTACGTGGA-AGCTTTTTTCAGTACTTCTGCTG
* *
12135256 ACAAAGTATCCTACTTAAAGCGTTTTTGACACTGTTTGCTCAGAAATGTCTACTCGAAATTA
65 ACAAAGCATCCTACTTAAAGCGTTTTTGACACTGTTTGCTCAGAAACGTCTACTCGAAATTA
* * *
12135318 TTTTCTCAGGAGCCACTGTAGCAAAAGCGCGTCCACGTGG
1 TTTTTTCAGGAGCTACTGTAGCAAAAGCGCGTCTACGTGG
12135358 GAGTGTCTTT
Statistics
Matches: 257, Mismatches: 29, Indels: 9
0.87 0.10 0.03
Matches are distributed among these distances:
124 2 0.01
125 110 0.43
126 144 0.56
127 1 0.00
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.35
Consensus pattern (126 bp):
TTTTTTCAGGAGCTACTGTAGCAAAAGCGCGTCTACGTGGAAGCTTTTTTCAGTACTTCTGCTGA
CAAAGCATCCTACTTAAAGCGTTTTTGACACTGTTTGCTCAGAAACGTCTACTCGAAATTA
Found at i:12135611 original size:95 final size:97
Alignment explanation
Indices: 12135400--12135640 Score: 267
Period size: 96 Copynumber: 2.5 Consensus size: 97
12135390 AGTAATTGTA
* *
12135400 AACCCCAAACCCTAATTTATTTGAGTTTTTAC-TTAAAAACCCTAAACACTAAACCCTAAACTAA
1 AACCCTAAACCCTAATTTATTTGAATTTTT-CTTTAAAAACCCTAAACACTAAACCCTAAACTAA
* *
12135464 TTTATTATAAATTTATAATTTATTTACTCAAGT
65 TTTATTATAAATTTATAATTAAATTACTCAAGT
* * * * * * *
12135497 AACCATGAACTCC-AATTTATTT-AATTTTTCTTTAAAAACCCTTAACTCTAAATCCTAATCTGA
1 AACCCTAAAC-CCTAATTTATTTGAATTTTTCTTTAAAAACCCTAAACACTAAACCCTAAACTAA
* *
12135560 TTT-TTA-AATTTTTTTAATTAAATTACTCAAGT
65 TTTATTATAA-ATTTATAATTAAATTACTCAAGT
* * **
12135592 AACCCTAAACCCTAATTTATTTGATTTTTTCTTAAAAAACAATAAACAC
1 AACCCTAAACCCTAATTTATTTGAATTTTTCTTTAAAAACCCTAAACAC
12135641 GAAAACTAAT
Statistics
Matches: 118, Mismatches: 21, Indels: 11
0.79 0.14 0.07
Matches are distributed among these distances:
94 4 0.03
95 40 0.34
96 56 0.47
97 16 0.14
98 2 0.02
ACGTcount: A:0.39, C:0.19, G:0.03, T:0.39
Consensus pattern (97 bp):
AACCCTAAACCCTAATTTATTTGAATTTTTCTTTAAAAACCCTAAACACTAAACCCTAAACTAAT
TTATTATAAATTTATAATTAAATTACTCAAGT
Found at i:12135651 original size:95 final size:96
Alignment explanation
Indices: 12135400--12135629 Score: 270
Period size: 95 Copynumber: 2.4 Consensus size: 96
12135390 AGTAATTGTA
* * *
12135400 AACCCCAAACCCTAATTTATTTGAGTTTTTACTTAAAAACCCTAAACACTAAACCCTAAACTAAT
1 AACCCTAAACCCTAATTTATTTGA-TTTTTTCTTAAAAACCCTAAACACTAAACCCTAATCTAAT
* *
12135465 TTATTATAAATTTATAATTTATTTACTCAAGT
65 TTATTATAAATTTATAATTAAATTACTCAAGT
* * * * * * *
12135497 AACCATGAACTCC-AATTTATTT-AATTTTTCTTTAAAAACCCTTAACTCTAAATCCTAATCTGA
1 AACCCTAAAC-CCTAATTTATTTGATTTTTTC-TTAAAAACCCTAAACACTAAACCCTAATCTAA
* *
12135560 TTT-TTA-AATTTTTTTAATTAAATTACTCAAGT
64 TTTATTATAA-ATTTATAATTAAATTACTCAAGT
12135592 AACCCTAAACCCTAATTTATTTGATTTTTTCTTAAAAA
1 AACCCTAAACCCTAATTTATTTGATTTTTTCTTAAAAA
12135630 ACAATAAACA
Statistics
Matches: 111, Mismatches: 17, Indels: 12
0.79 0.12 0.09
Matches are distributed among these distances:
94 4 0.04
95 51 0.46
96 38 0.34
97 16 0.14
98 2 0.02
ACGTcount: A:0.38, C:0.18, G:0.03, T:0.41
Consensus pattern (96 bp):
AACCCTAAACCCTAATTTATTTGATTTTTTCTTAAAAACCCTAAACACTAAACCCTAATCTAATT
TATTATAAATTTATAATTAAATTACTCAAGT
Found at i:12142109 original size:15 final size:15
Alignment explanation
Indices: 12142089--12142119 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
12142079 ATGTATCAGT
12142089 AATGAATCAGAGCAC
1 AATGAATCAGAGCAC
12142104 AATGAATCAGAGCAC
1 AATGAATCAGAGCAC
12142119 A
1 A
12142120 CGGAACCGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.48, C:0.19, G:0.19, T:0.13
Consensus pattern (15 bp):
AATGAATCAGAGCAC
Found at i:12143135 original size:151 final size:151
Alignment explanation
Indices: 12142861--12143162 Score: 586
Period size: 151 Copynumber: 2.0 Consensus size: 151
12142851 CCTTTTATTT
12142861 AGAAAAATCCGAAATGAAGTGAAAACGAAAAAGTATTACTTGTTTTGGATTTGTATAGTATTATA
1 AGAAAAATCCGAAATGAAGTGAAAACGAAAAAGTATTACTTGTTTTGGATTTGTATAGTATTATA
*
12142926 CTATATATAGTATAAATATATATTTATACTAGTACTATACAAATTAGTACTATATCGAAATGAAA
66 CTATATATAGTAGAAATATATATTTATACTAGTACTATACAAATTAGTACTATATCGAAATGAAA
12142991 TCGAAATAAGTGGAATGTAAA
131 TCGAAATAAGTGGAATGTAAA
*
12143012 AGAAAAATCTGAAATGAAGTGAAAACGAAAAAGTATTACTTGTTTTGGATTTGTATAGTATTATA
1 AGAAAAATCCGAAATGAAGTGAAAACGAAAAAGTATTACTTGTTTTGGATTTGTATAGTATTATA
12143077 CTATATATAGTAGAAATATATATTTATACTAGTACTATACAAATTAGTACTATATCGAAATGAAA
66 CTATATATAGTAGAAATATATATTTATACTAGTACTATACAAATTAGTACTATATCGAAATGAAA
12143142 TCGAAATAAGTGGAATGTAAA
131 TCGAAATAAGTGGAATGTAAA
12143163 TAAAATAGGA
Statistics
Matches: 149, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
151 149 1.00
ACGTcount: A:0.45, C:0.07, G:0.15, T:0.33
Consensus pattern (151 bp):
AGAAAAATCCGAAATGAAGTGAAAACGAAAAAGTATTACTTGTTTTGGATTTGTATAGTATTATA
CTATATATAGTAGAAATATATATTTATACTAGTACTATACAAATTAGTACTATATCGAAATGAAA
TCGAAATAAGTGGAATGTAAA
Found at i:12146689 original size:18 final size:17
Alignment explanation
Indices: 12146663--12146697 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
12146653 TATCTGAATT
12146663 TTTAACCAACTCATATAA
1 TTTAACCAACTCA-ATAA
*
12146681 TTTATCCAACTCAATAA
1 TTTAACCAACTCAATAA
12146698 CCAATTTTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.43, C:0.23, G:0.00, T:0.34
Consensus pattern (17 bp):
TTTAACCAACTCAATAA
Found at i:12147585 original size:35 final size:35
Alignment explanation
Indices: 12147539--12147609 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
12147529 AGAAAAGTCC
12147539 ATGGCAACTGAATTATTTATTAACTTAGAATCTTT
1 ATGGCAACTGAATTATTTATTAACTTAGAATCTTT
12147574 ATGGCAACTGAATTATTTATTAACTTAGAATCTTT
1 ATGGCAACTGAATTATTTATTAACTTAGAATCTTT
12147609 A
1 A
12147610 GTCATAAGCT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.35, C:0.11, G:0.11, T:0.42
Consensus pattern (35 bp):
ATGGCAACTGAATTATTTATTAACTTAGAATCTTT
Found at i:12147604 original size:18 final size:18
Alignment explanation
Indices: 12147548--12147604 Score: 57
Period size: 18 Copynumber: 3.2 Consensus size: 18
12147538 CATGGCAACT
12147548 GAATTATTTATTAACTTA
1 GAATTATTTATTAACTTA
* *
12147566 GAA-TCTTTATGGCAAC-T-
1 GAATTATTTAT--TAACTTA
12147583 GAATTATTTATTAACTTA
1 GAATTATTTATTAACTTA
12147601 GAAT
1 GAAT
12147605 CTTTAGTCAT
Statistics
Matches: 30, Mismatches: 4, Indels: 10
0.68 0.09 0.23
Matches are distributed among these distances:
16 3 0.10
17 10 0.33
18 14 0.47
19 3 0.10
ACGTcount: A:0.37, C:0.09, G:0.11, T:0.44
Consensus pattern (18 bp):
GAATTATTTATTAACTTA
Found at i:12156106 original size:13 final size:13
Alignment explanation
Indices: 12156088--12156126 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
12156078 AACAGGCTTT
12156088 TAGCGGCGCTAAA
1 TAGCGGCGCTAAA
12156101 TAGCGGCGCTAAA
1 TAGCGGCGCTAAA
*
12156114 TAACGGCGCTAAA
1 TAGCGGCGCTAAA
12156127 AGCATTTGCG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.33, C:0.23, G:0.28, T:0.15
Consensus pattern (13 bp):
TAGCGGCGCTAAA
Found at i:12156351 original size:43 final size:42
Alignment explanation
Indices: 12156253--12156562 Score: 325
Period size: 43 Copynumber: 7.2 Consensus size: 42
12156243 TTTGGGAATG
* * * *
12156253 CGCCGCTAAAGACCATGACCTTTACCGGCGCTTTTACAAAAA
1 CGCCGCTAAAGACCCTGACCTTTAGCGGCGCTTTTTCACAAA
* *
12156295 CGCAGCTAAAGACCCTGATCTTTAGCGGCGCTTTTTCGACAAA
1 CGCCGCTAAAGACCCTGACCTTTAGCGGCGCTTTTTC-ACAAA
* * * * *
12156338 CGCCTCTAAAGACCTTGATCTTTAGCGGCGCTTTTCCTACAAT
1 CGCCGCTAAAGACCCTGACCTTTAGCGGCGCTTTTTC-ACAAA
*
12156381 CGCCGCTAAAGACTCTGACCTTTAGCGGCGCTTTTTCCACAAA
1 CGCCGCTAAAGACCCTGACCTTTAGCGGCGCTTTTT-CACAAA
* *
12156424 CGCCGCTAAAGACCCTGAACTTTAGCGGCGATGTTTTCACAAA
1 CGCCGCTAAAGACCCTGACCTTTAGCGGCGCT-TTTTCACAAA
* * *** *
12156467 CGCCAC-AATGACAAGGACCTTTAGCGGCGCTTTTGCCACAAA
1 CGCCGCTAAAGACCCTGACCTTTAGCGGCGCTTTT-TCACAAA
* * * *
12156509 CACCGCTAAAGACCCTGACCTTTAACGGTGATTTTTTTCCACAAA
1 CGCCGCTAAAGACCCTGACCTTTAGCGGCG--CTTTTT-CACAAA
12156554 CGCCGCTAA
1 CGCCGCTAA
12156563 TTTTGGCGGA
Statistics
Matches: 220, Mismatches: 40, Indels: 13
0.81 0.15 0.05
Matches are distributed among these distances:
41 3 0.01
42 61 0.28
43 133 0.60
44 5 0.02
45 18 0.08
ACGTcount: A:0.26, C:0.30, G:0.18, T:0.25
Consensus pattern (42 bp):
CGCCGCTAAAGACCCTGACCTTTAGCGGCGCTTTTTCACAAA
Found at i:12156367 original size:85 final size:85
Alignment explanation
Indices: 12156253--12156532 Score: 330
Period size: 85 Copynumber: 3.3 Consensus size: 85
12156243 TTTGGGAATG
* * * * *
12156253 CGCCGCTAAAGACCATGACCTTTACCGGCGCTTTTACAAAAACGCAGCTAAAGACCCTGATCTTT
1 CGCCGCTAAAGACCCTGACCTTTAGCGGCGCTTTTACACAAACGCAGCTAAAGACACTGACCTTT
*
12156318 AGCGGCGCTTTTTCGACAAA
66 AGCGGCGCTTTTTCCACAAA
* * * * * * *
12156338 CGCCTCTAAAGACCTTGATCTTTAGCGGCGCTTTTCCTACAATCGCCGCTAAAGACTCTGACCTT
1 CGCCGCTAAAGACCCTGACCTTTAGCGGCGCTTTTAC-ACAAACGCAGCTAAAGACACTGACCTT
12156403 TAGCGGCGCTTTTTCCACAAA
65 TAGCGGCGCTTTTTCCACAAA
* * * * **
12156424 CGCCGCTAAAGACCCTGAACTTTAGCGGCGATGTTTTCACAAACGCCA-C-AATGACAAGGACCT
1 CGCCGCTAAAGACCCTGACCTTTAGCGGCGCT-TTTACACAAACG-CAGCTAAAGACACTGACCT
*
12156487 TTAGCGGCGCTTTTGCCACAAA
64 TTAGCGGCGCTTTTTCCACAAA
*
12156509 CACCGCTAAAGACCCTGACCTTTA
1 CGCCGCTAAAGACCCTGACCTTTA
12156533 ACGGTGATTT
Statistics
Matches: 167, Mismatches: 25, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
85 85 0.51
86 77 0.46
87 5 0.03
ACGTcount: A:0.26, C:0.31, G:0.19, T:0.24
Consensus pattern (85 bp):
CGCCGCTAAAGACCCTGACCTTTAGCGGCGCTTTTACACAAACGCAGCTAAAGACACTGACCTTT
AGCGGCGCTTTTTCCACAAA
Found at i:12156544 original size:128 final size:128
Alignment explanation
Indices: 12156255--12156562 Score: 370
Period size: 128 Copynumber: 2.4 Consensus size: 128
12156245 TGGGAATGCG
* * * * * * *
12156255 CCGCTAAAGACCATGACCTTTACCGGCGCTTTTACAAAAACGCAGCTAAAGACCCTGATCTTTAG
1 CCGCTAAAGACCCTGACCTTTAACGGCGTTTTTCCACAAACGCCGCTAAAGACCCTGAACTTTAG
* * *** * * *
12156320 CGGCGCTTTTTCGACAAACGCCTCTAAAGACCTTGATCTTTAGCGGCGCTTTTCCTACAATCG
66 CGGCGATTTTTCGACAAACGCCACTAAAGACAAGGACCTTTAGCGGCGCTTTTCCTACAAACA
* *
12156383 CCGCTAAAGACTCTGACCTTTAGCGGCGCTTTTTCCACAAACGCCGCTAAAGACCCTGAACTTTA
1 CCGCTAAAGACCCTGACCTTTAACGGCG-TTTTTCCACAAACGCCGCTAAAGACCCTGAACTTTA
*
12156448 GCGGCGATGTTTTC-ACAAACGCCAC-AATGACAAGGACCTTTAGCGGCGCTTTTGCC-ACAAAC
65 GCGGCGAT-TTTTCGACAAACGCCACTAAAGACAAGGACCTTTAGCGGCGCTTTT-CCTACAAAC
12156510 A
128 A
*
12156511 CCGCTAAAGACCCTGACCTTTAACGGTGATTTTTTTCCACAAACGCCGCTAA
1 CCGCTAAAGACCCTGACCTTTAACGGCG---TTTTTCCACAAACGCCGCTAA
12156563 TTTTGGCGGA
Statistics
Matches: 154, Mismatches: 21, Indels: 8
0.84 0.11 0.04
Matches are distributed among these distances:
128 78 0.51
129 50 0.32
130 26 0.17
ACGTcount: A:0.27, C:0.30, G:0.18, T:0.25
Consensus pattern (128 bp):
CCGCTAAAGACCCTGACCTTTAACGGCGTTTTTCCACAAACGCCGCTAAAGACCCTGAACTTTAG
CGGCGATTTTTCGACAAACGCCACTAAAGACAAGGACCTTTAGCGGCGCTTTTCCTACAAACA
Found at i:12156776 original size:18 final size:18
Alignment explanation
Indices: 12156753--12156815 Score: 108
Period size: 18 Copynumber: 3.5 Consensus size: 18
12156743 ATAAAAGTTA
12156753 AAATGATAATTAAAAGTG
1 AAATGATAATTAAAAGTG
* *
12156771 AAATGATAAATAAAAGTT
1 AAATGATAATTAAAAGTG
12156789 AAATGATAATTAAAAGTG
1 AAATGATAATTAAAAGTG
12156807 AAATGATAA
1 AAATGATAA
12156816 AAATATTTAC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 41 1.00
ACGTcount: A:0.59, C:0.00, G:0.14, T:0.27
Consensus pattern (18 bp):
AAATGATAATTAAAAGTG
Found at i:12156800 original size:36 final size:37
Alignment explanation
Indices: 12156743--12156816 Score: 141
Period size: 36 Copynumber: 2.0 Consensus size: 37
12156733 TACAAAAATG
12156743 ATAAAAGTTAAAATGATAATTAAAAGTGAAATGATAA
1 ATAAAAGTTAAAATGATAATTAAAAGTGAAATGATAA
12156780 ATAAAAGTT-AAATGATAATTAAAAGTGAAATGATAA
1 ATAAAAGTTAAAATGATAATTAAAAGTGAAATGATAA
12156816 A
1 A
12156817 AATATTTACA
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
36 28 0.76
37 9 0.24
ACGTcount: A:0.59, C:0.00, G:0.14, T:0.27
Consensus pattern (37 bp):
ATAAAAGTTAAAATGATAATTAAAAGTGAAATGATAA
Found at i:12162465 original size:19 final size:19
Alignment explanation
Indices: 12162441--12162479 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
12162431 TTGTTCAGTG
12162441 GTAAGTATAAATGAGTTAT
1 GTAAGTATAAATGAGTTAT
12162460 GTAAGTATAAATGAGTTAT
1 GTAAGTATAAATGAGTTAT
12162479 G
1 G
12162480 ATATGATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.23, T:0.36
Consensus pattern (19 bp):
GTAAGTATAAATGAGTTAT
Found at i:12164755 original size:27 final size:27
Alignment explanation
Indices: 12164704--12164755 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
12164694 TCTTACATTT
* * *
12164704 AAATAATTAATTACCTATTTCTTTAAC
1 AAATAAATAATTACCTACTTATTTAAC
12164731 AAATAAATAATTACCTACTTATTTA
1 AAATAAATAATTACCTACTTATTTA
12164756 TTTGTTTATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.44, C:0.13, G:0.00, T:0.42
Consensus pattern (27 bp):
AAATAAATAATTACCTACTTATTTAAC
Found at i:12166115 original size:27 final size:27
Alignment explanation
Indices: 12166083--12166134 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
12166073 TCTTACATTT
* *
12166083 AAATAATTAATTACCTATTTATTTAAC
1 AAATAAATAATTACCTACTTATTTAAC
12166110 AAATAAATAATTACCTACTTATTTA
1 AAATAAATAATTACCTACTTATTTA
12166135 TTTCTTTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.42
Consensus pattern (27 bp):
AAATAAATAATTACCTACTTATTTAAC
Found at i:12167342 original size:28 final size:28
Alignment explanation
Indices: 12167291--12167345 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
12167281 TATCTTACAT
*
12167291 TTAAATAATTAATGACCTATTTATTTAC
1 TTAAATAATTAATGACCTAATTATTTAC
*
12167319 TTAAATAATTAATTG-CGTAATTATTTA
1 TTAAATAATTAA-TGACCTAATTATTTA
12167346 TTTATTTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 22 0.92
29 2 0.08
ACGTcount: A:0.40, C:0.07, G:0.05, T:0.47
Consensus pattern (28 bp):
TTAAATAATTAATGACCTAATTATTTAC
Found at i:12167449 original size:15 final size:16
Alignment explanation
Indices: 12167429--12167466 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
12167419 ACTGTTGAAA
12167429 CCCTAAATCC-CAAAC
1 CCCTAAATCCTCAAAC
*
12167444 CCCTAAA-CCTCTAAC
1 CCCTAAATCCTCAAAC
12167459 CCCTAAAT
1 CCCTAAAT
12167467 TAACCTTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 2 0.10
15 18 0.90
ACGTcount: A:0.37, C:0.45, G:0.00, T:0.18
Consensus pattern (16 bp):
CCCTAAATCCTCAAAC
Found at i:12168093 original size:41 final size:41
Alignment explanation
Indices: 12168021--12168194 Score: 231
Period size: 41 Copynumber: 4.2 Consensus size: 41
12168011 TTTTGTTACT
*** * * **
12168021 ATTAGCGGCGCTTAGTAAAAAACACCGCTAAAGGTAAGAGC
1 ATTAGCGGCGCTTAACCAAAAACGCCACTAAAGGCCAGAGC
** * *
12168062 ATTAGCGGCGCTTTCCCAAAAGCGCCTCTAAAGGCCAGAGC
1 ATTAGCGGCGCTTAACCAAAAACGCCACTAAAGGCCAGAGC
*
12168103 ATTAGCGGCGCTTAACCAAAAACGCCACTAAAGGCCCGAGC
1 ATTAGCGGCGCTTAACCAAAAACGCCACTAAAGGCCAGAGC
*
12168144 ATTAGCGGCGCTTAAACAAAAACGCCACTAAAGGCCAGAGC
1 ATTAGCGGCGCTTAACCAAAAACGCCACTAAAGGCCAGAGC
12168185 ATTAGCGGCG
1 ATTAGCGGCG
12168195 TTTTTGATAA
Statistics
Matches: 117, Mismatches: 16, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 117 1.00
ACGTcount: A:0.34, C:0.27, G:0.24, T:0.15
Consensus pattern (41 bp):
ATTAGCGGCGCTTAACCAAAAACGCCACTAAAGGCCAGAGC
Found at i:12168372 original size:40 final size:40
Alignment explanation
Indices: 12168299--12168428 Score: 124
Period size: 40 Copynumber: 3.2 Consensus size: 40
12168289 CGCTTTATAA
* * *
12168299 AAAATGCCGCTAATGC-CTATTTTTAGCGGCGCTTTTGG-
1 AAAACGCCGCTAATGCTCGATCTTTAGCGGCGCTTTTGGC
* *
12168337 AAATCCGCCGCTGATGCTCGATCTTTAGCGGCGC-TTTGGTC
1 AAA-ACGCCGCTAATGCTCGATCTTTAGCGGCGCTTTTGG-C
* * *
12168378 AAAACGCCGCTAATGCTCGATTTTTAGTGGCACTTTTGTTG-
1 AAAACGCCGCTAATGCTCGATCTTTAGCGGCGCTTTTG--GC
12168419 AAAACGCCGC
1 AAAACGCCGC
12168429 GTAAAGTGCC
Statistics
Matches: 75, Mismatches: 10, Indels: 11
0.78 0.10 0.11
Matches are distributed among these distances:
38 3 0.04
39 15 0.20
40 39 0.52
41 17 0.23
43 1 0.01
ACGTcount: A:0.21, C:0.25, G:0.24, T:0.31
Consensus pattern (40 bp):
AAAACGCCGCTAATGCTCGATCTTTAGCGGCGCTTTTGGC
Found at i:12176079 original size:53 final size:53
Alignment explanation
Indices: 12175999--12176153 Score: 229
Period size: 53 Copynumber: 2.9 Consensus size: 53
12175989 TCCTTGAATT
* * * *
12175999 TTTCCATATGATGCCATAAGCCACCAGTTATGGTCTTACACGATATGGTTTTA
1 TTTCCATATGATACCATAACCCACCAGTTACGGTCTTACACGATATGGTATTA
* *
12176052 TTTCCATATGATATCATAACCCACCAGTTACGGTCTTACACGATATGGTATTC
1 TTTCCATATGATACCATAACCCACCAGTTACGGTCTTACACGATATGGTATTA
* * *
12176105 TTTCCATATGATCCCATAACCCACCAATTACAGTCTTACACGATATGGT
1 TTTCCATATGATACCATAACCCACCAGTTACGGTCTTACACGATATGGT
12176154 CCCTTAGCGT
Statistics
Matches: 92, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
53 92 1.00
ACGTcount: A:0.28, C:0.25, G:0.14, T:0.34
Consensus pattern (53 bp):
TTTCCATATGATACCATAACCCACCAGTTACGGTCTTACACGATATGGTATTA
Found at i:12177810 original size:28 final size:28
Alignment explanation
Indices: 12177778--12177834 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
12177768 AGACTAGTAA
12177778 GAAAGTATGAATAGTCACTGACAATCCT
1 GAAAGTATGAATAGTCACTGACAATCCT
12177806 GAAAGTATGAATAGTCACTGACAATCCT
1 GAAAGTATGAATAGTCACTGACAATCCT
12177834 G
1 G
12177835 TTCAAAATGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.39, C:0.18, G:0.19, T:0.25
Consensus pattern (28 bp):
GAAAGTATGAATAGTCACTGACAATCCT
Found at i:12186569 original size:12 final size:12
Alignment explanation
Indices: 12186552--12186584 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
12186542 AGCGCCACAC
12186552 GGTCGTGTGGTA
1 GGTCGTGTGGTA
12186564 GGTCGTGTGGTA
1 GGTCGTGTGGTA
*
12186576 GATCGTGTG
1 GGTCGTGTG
12186585 CACCACACGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.09, C:0.09, G:0.48, T:0.33
Consensus pattern (12 bp):
GGTCGTGTGGTA
Found at i:12187129 original size:22 final size:23
Alignment explanation
Indices: 12187101--12187173 Score: 80
Period size: 22 Copynumber: 3.3 Consensus size: 23
12187091 GGGTAGGATT
12187101 TGATATGCTATGATATGTGATAA
1 TGATATGCTATGATATGTGATAA
* * **
12187124 T-ATATGTTTTGATATGAAAT-A
1 TGATATGCTATGATATGTGATAA
*
12187145 TGATATGCTATGACATGTGAT-A
1 TGATATGCTATGATATGTGATAA
12187167 TGATATG
1 TGATATG
12187174 TTCCGACATG
Statistics
Matches: 40, Mismatches: 9, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
21 2 0.05
22 37 0.93
23 1 0.03
ACGTcount: A:0.34, C:0.04, G:0.21, T:0.41
Consensus pattern (23 bp):
TGATATGCTATGATATGTGATAA
Found at i:12187150 original size:44 final size:44
Alignment explanation
Indices: 12187101--12187206 Score: 135
Period size: 44 Copynumber: 2.4 Consensus size: 44
12187091 GGGTAGGATT
* ** *
12187101 TGATATGCTATGATATGTGATAAT-ATATGTTTTGATATGA-AATA
1 TGATATGCTATGAAATGTGAT-ATGATATGTTCCGACATGATAA-A
*
12187145 TGATATGCTATGACATGTGATATGATATGTTCCGACATGATAAA
1 TGATATGCTATGAAATGTGATATGATATGTTCCGACATGATAAA
12187189 TGATATGCTATGAAATGT
1 TGATATGCTATGAAATGT
12187207 TACTTAATAT
Statistics
Matches: 55, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
43 2 0.04
44 51 0.93
45 2 0.04
ACGTcount: A:0.35, C:0.07, G:0.20, T:0.39
Consensus pattern (44 bp):
TGATATGCTATGAAATGTGATATGATATGTTCCGACATGATAAA
Found at i:12187156 original size:17 final size:17
Alignment explanation
Indices: 12187133--12187173 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
12187123 ATATATGTTT
12187133 TGATATGAAATATGATA
1 TGATATGAAATATGATA
* * *
12187150 TGCTATGACATGTGATA
1 TGATATGAAATATGATA
12187167 TGATATG
1 TGATATG
12187174 TTCCGACATG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.37, C:0.05, G:0.22, T:0.37
Consensus pattern (17 bp):
TGATATGAAATATGATA
Found at i:12187181 original size:22 final size:22
Alignment explanation
Indices: 12187142--12187198 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
12187132 TTGATATGAA
*
12187142 ATATGATATGCTATGACATGTG
1 ATATGATATGCTACGACATGTG
* *
12187164 ATATGATATGTTCCGACATGAT-
1 ATATGATATGCTACGACATG-TG
*
12187186 AAATGATATGCTA
1 ATATGATATGCTA
12187199 TGAAATGTTA
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
22 27 0.96
23 1 0.04
ACGTcount: A:0.35, C:0.11, G:0.19, T:0.35
Consensus pattern (22 bp):
ATATGATATGCTACGACATGTG
Found at i:12187237 original size:44 final size:43
Alignment explanation
Indices: 12187101--12187239 Score: 129
Period size: 44 Copynumber: 3.2 Consensus size: 43
12187091 GGGTAGGATT
* *
12187101 TGATATGCTATGATATGTGA-TAATATATGTTTTGATATGAAATA
1 TGATATGCTATGAAATGTGATTAATATA--TTCTGATATGAAATA
* * * * *
12187145 TGATATGCTATGACATGTGATATGATATGTTCCGACATGATAA-A
1 TGATATGCTATGAAATGTGAT-TAATATATTCTGATATGA-AATA
* * *
12187189 TGATATGCTATGAAATGTTACTTAATATATTCTAATATGAAATT
1 TGATATGCTATGAAATGTGA-TTAATATATTCTGATATGAAATA
12187233 TGATATG
1 TGATATG
12187240 AAATGATATA
Statistics
Matches: 76, Mismatches: 14, Indels: 10
0.76 0.14 0.10
Matches are distributed among these distances:
43 2 0.03
44 66 0.87
45 3 0.04
46 5 0.07
ACGTcount: A:0.36, C:0.06, G:0.17, T:0.40
Consensus pattern (43 bp):
TGATATGCTATGAAATGTGATTAATATATTCTGATATGAAATA
Found at i:12188766 original size:16 final size:16
Alignment explanation
Indices: 12188745--12188775 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
12188735 AAAATATTTT
12188745 TTATAAATGTTATATG
1 TTATAAATGTTATATG
*
12188761 TTATAAATTTTATAT
1 TTATAAATGTTATAT
12188776 TATTTTTACT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (16 bp):
TTATAAATGTTATATG
Found at i:12188871 original size:24 final size:25
Alignment explanation
Indices: 12188821--12188871 Score: 59
Period size: 24 Copynumber: 2.0 Consensus size: 25
12188811 ATAACCTAAC
**
12188821 ATAATTTTTTCCAAAATTAAATTTAT
1 ATAATTTTTT-CAAAATTAAAGCTAT
*
12188847 ATAATTTTTT-ATAATTAAAGCTAT
1 ATAATTTTTTCAAAATTAAAGCTAT
12188871 A
1 A
12188872 GACTATTTAG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
24 12 0.55
26 10 0.45
ACGTcount: A:0.43, C:0.06, G:0.02, T:0.49
Consensus pattern (25 bp):
ATAATTTTTTCAAAATTAAAGCTAT
Found at i:12189525 original size:24 final size:24
Alignment explanation
Indices: 12189510--12189585 Score: 116
Period size: 24 Copynumber: 3.2 Consensus size: 24
12189500 AATCAAAGTC
12189510 AAATATATTATGCTAATAAATGCT
1 AAATATATTATGCTAATAAATGCT
* *
12189534 AAATATATTATACTCATAAATGCT
1 AAATATATTATGCTAATAAATGCT
* *
12189558 AAATATATTATTCTCATAAATGCT
1 AAATATATTATGCTAATAAATGCT
12189582 AAAT
1 AAAT
12189586 CTTCTAGGAA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 49 1.00
ACGTcount: A:0.46, C:0.11, G:0.05, T:0.38
Consensus pattern (24 bp):
AAATATATTATGCTAATAAATGCT
Found at i:12190089 original size:17 final size:17
Alignment explanation
Indices: 12190056--12190101 Score: 74
Period size: 17 Copynumber: 2.6 Consensus size: 17
12190046 TAGTGGTAGA
*
12190056 CAAAGTGACTGTAGTTTG
1 CAAAGTGGCT-TAGTTTG
12190074 CAAAGTGGCTTAGTTTG
1 CAAAGTGGCTTAGTTTG
12190091 CAAAGTGGCTT
1 CAAAGTGGCTT
12190102 TCCAACTGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
17 18 0.67
18 9 0.33
ACGTcount: A:0.26, C:0.13, G:0.28, T:0.33
Consensus pattern (17 bp):
CAAAGTGGCTTAGTTTG
Found at i:12194007 original size:24 final size:24
Alignment explanation
Indices: 12193992--12194043 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
12193982 AATCAAAGTC
12193992 AAATATATTATGCTAATAAATGCT
1 AAATATATTATGCTAATAAATGCT
* * *
12194016 AAATATATTATACTCATAAATACT
1 AAATATATTATGCTAATAAATGCT
12194040 AAAT
1 AAAT
12194044 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.50, C:0.10, G:0.04, T:0.37
Consensus pattern (24 bp):
AAATATATTATGCTAATAAATGCT
Found at i:12194676 original size:24 final size:25
Alignment explanation
Indices: 12194629--12194676 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
12194619 GTTGACAACC
*
12194629 AATTTTTAATAGTAAAAATGAATTG
1 AATTTTTAATAGTAAAAATCAATTG
*
12194654 AATTTTTAATAG-AAAGATCAATT
1 AATTTTTAATAGTAAAAATCAATT
12194677 TATTCTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 9 0.43
25 12 0.57
ACGTcount: A:0.48, C:0.02, G:0.10, T:0.40
Consensus pattern (25 bp):
AATTTTTAATAGTAAAAATCAATTG
Found at i:12195102 original size:18 final size:18
Alignment explanation
Indices: 12195075--12195109 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
12195065 CAATAATTAA
*
12195075 ATAAATATTAAAAAAATC
1 ATAAAAATTAAAAAAATC
*
12195093 ATAAAAATTAATAAAAT
1 ATAAAAATTAAAAAAAT
12195110 TTTGAATATA
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:0.69, C:0.03, G:0.00, T:0.29
Consensus pattern (18 bp):
ATAAAAATTAAAAAAATC
Found at i:12195702 original size:9 final size:9
Alignment explanation
Indices: 12195688--12195721 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
12195678 TCTTTATTCT
*
12195688 ATTAATTTA
1 ATTAATTAA
12195697 ATTAATTAA
1 ATTAATTAA
*
12195706 ATTAACTAA
1 ATTAATTAA
12195715 ATTAATT
1 ATTAATT
12195722 TCTAATTAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (9 bp):
ATTAATTAA
Found at i:12203719 original size:47 final size:49
Alignment explanation
Indices: 12203596--12203719 Score: 119
Period size: 47 Copynumber: 2.6 Consensus size: 49
12203586 ACAATATATA
* * * * *
12203596 ACCATCCCAGATAGCCCAACAATGATGGTTTACTCTATTCCAATATTCT
1 ACCATCTCAGATGGCCCAAAAATGATGGTTTACTCTAATCAAATATTCT
** * *
12203645 ATTATCTCAGATTGCCCGATAAA-GATGG-TT-CTCTAATCAAATATTCT
1 ACCATCTCAGATGGCCC-AAAAATGATGGTTTACTCTAATCAAATATTCT
**
12203692 ACCATCTTGGATGGCCCAAAAATGATGG
1 ACCATCTCAGATGGCCCAAAAATGATGG
12203720 CTTTCACGAT
Statistics
Matches: 59, Mismatches: 14, Indels: 6
0.75 0.18 0.08
Matches are distributed among these distances:
46 4 0.07
47 32 0.54
48 2 0.03
49 18 0.31
50 3 0.05
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (49 bp):
ACCATCTCAGATGGCCCAAAAATGATGGTTTACTCTAATCAAATATTCT
Found at i:12206339 original size:32 final size:32
Alignment explanation
Indices: 12206299--12206359 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
12206289 TGATTATAAG
*
12206299 TTAATTAATCTTTATTAACTTTTAATTAACCA
1 TTAATTAATCTTTATCAACTTTTAATTAACCA
*
12206331 TTAATTAATCTTTATCAATTTTTAATTAA
1 TTAATTAATCTTTATCAACTTTTAATTAA
12206360 TAATTTTCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.52
Consensus pattern (32 bp):
TTAATTAATCTTTATCAACTTTTAATTAACCA
Found at i:12214750 original size:16 final size:16
Alignment explanation
Indices: 12214731--12214761 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
12214721 AACTTTATGT
12214731 TTTTAATAATTTTTTA
1 TTTTAATAATTTTTTA
*
12214747 TTTTATTAATTTTTT
1 TTTTAATAATTTTTT
12214762 CTGAATTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTTAATAATTTTTTA
Found at i:12218112 original size:40 final size:39
Alignment explanation
Indices: 12218064--12218197 Score: 155
Period size: 40 Copynumber: 3.4 Consensus size: 39
12218054 GTTTGGACAA
*
12218064 AAAACGCCGCTAAAAATCGAGCATTAGCGGCGCTTTAT-GG
1 AAAACGCCGCTAAAAAT-GAGCATTAGCGGCGCTTT-TCAG
** *
12218104 AAAACGCCGCTAAAGGTTGAGCATTTGCGGCGCTTTTCAG
1 AAAACGCCGCTAAA-AATGAGCATTAGCGGCGCTTTTCAG
* * *
12218144 AACACGCCGCTGAAAATGAGCATTAGCGGCGTTTTTCCAG
1 AAAACGCCGCTAAAAATGAGCATTAGCGGCGCTTTT-CAG
12218184 AAAACGCCGC-AAAA
1 AAAACGCCGCTAAAA
12218198 GACCTAAGCC
Statistics
Matches: 79, Mismatches: 12, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
39 22 0.28
40 56 0.71
41 1 0.01
ACGTcount: A:0.31, C:0.24, G:0.25, T:0.20
Consensus pattern (39 bp):
AAAACGCCGCTAAAAATGAGCATTAGCGGCGCTTTTCAG
Found at i:12218327 original size:41 final size:41
Alignment explanation
Indices: 12218219--12218416 Score: 231
Period size: 41 Copynumber: 4.9 Consensus size: 41
12218209 AACCGACCTT
* *
12218219 TCGGGGCTTTAGCGGCGTTTTTGAAAAAGCGCCACTAATGC
1 TCGGTGCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGC
* * * *
12218260 TCGGGGC-TTAG-GTGCATTTTTGAAAAAGTGCCGCTAATGT
1 TCGGTGCTTTAGCG-GCGTTTTTGAAAAAGCGCCGCTAATGC
* *
12218300 TTGGTGCTTTAGCGGCGTTTCTGAAAAAGCGCCGCTAATGC
1 TCGGTGCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGC
* * *
12218341 TCGGTGCTTTAACGGCGTTTTTGAAAAAGCGCCGTTAGTGC
1 TCGGTGCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGC
* * *
12218382 TCGAG-GATTTAGCGACATTTTTGAAAAAGCGCCGC
1 TCG-GTGCTTTAGCGGCGTTTTTGAAAAAGCGCCGC
12218417 AAAAAACATT
Statistics
Matches: 133, Mismatches: 20, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
39 1 0.01
40 32 0.24
41 98 0.74
42 2 0.02
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (41 bp):
TCGGTGCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGC
Found at i:12218776 original size:15 final size:14
Alignment explanation
Indices: 12218758--12218795 Score: 58
Period size: 15 Copynumber: 2.6 Consensus size: 14
12218748 ACTATTTTAA
12218758 GGTTTATGGATTAT
1 GGTTTATGGATTAT
*
12218772 GGGTTTAGGGATTAT
1 -GGTTTATGGATTAT
12218787 GGTTTATGG
1 GGTTTATGG
12218796 TTTAAGGATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 8 0.38
15 13 0.62
ACGTcount: A:0.18, C:0.00, G:0.37, T:0.45
Consensus pattern (14 bp):
GGTTTATGGATTAT
Found at i:12218778 original size:22 final size:21
Alignment explanation
Indices: 12218753--12218805 Score: 70
Period size: 22 Copynumber: 2.5 Consensus size: 21
12218743 GAGTTACTAT
*
12218753 TTTAAGGTTTATGGATTATGGG
1 TTTAAGGATTATGGATTAT-GG
* *
12218775 TTTAGGGATTATGGTTTATGG
1 TTTAAGGATTATGGATTATGG
12218796 TTTAAGGATT
1 TTTAAGGATT
12218806 GTCATTATAG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
21 11 0.41
22 16 0.59
ACGTcount: A:0.23, C:0.00, G:0.30, T:0.47
Consensus pattern (21 bp):
TTTAAGGATTATGGATTATGG
Found at i:12218898 original size:21 final size:22
Alignment explanation
Indices: 12218874--12218937 Score: 67
Period size: 21 Copynumber: 2.9 Consensus size: 22
12218864 TAGGTATTAT
*
12218874 GGTTTATGGTTTAAGGGTT-GG
1 GGTTTAAGGTTTAAGGGTTAGG
* *
12218895 GGTTTAAAGTTTAGGGGTTAGG
1 GGTTTAAGGTTTAAGGGTTAGG
*
12218917 GGTACTTAAGGGTTAAGGGTT
1 GGT--TTAAGGTTTAAGGGTT
12218938 TATGATTTAG
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
21 16 0.47
22 5 0.15
24 13 0.38
ACGTcount: A:0.20, C:0.02, G:0.41, T:0.38
Consensus pattern (22 bp):
GGTTTAAGGTTTAAGGGTTAGG
Found at i:12219137 original size:15 final size:15
Alignment explanation
Indices: 12219117--12219164 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
12219107 ACTATCTTAA
12219117 GGTTTATGGATTATG
1 GGTTTATGGATTATG
*
12219132 GGTTTAGGGATTAT-
1 GGTTTATGGATTATG
* *
12219146 GGTTTATGGTTTAAG
1 GGTTTATGGATTATG
12219161 GGTT
1 GGTT
12219165 GAGGTTTAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
14 11 0.39
15 17 0.61
ACGTcount: A:0.19, C:0.00, G:0.35, T:0.46
Consensus pattern (15 bp):
GGTTTATGGATTATG
Found at i:12219201 original size:38 final size:39
Alignment explanation
Indices: 12219156--12219229 Score: 98
Period size: 39 Copynumber: 1.9 Consensus size: 39
12219146 GGTTTATGGT
12219156 TTAAGGGTT-GAGGTTTAA-AGTTTAGGGGTTAGGGGTAC
1 TTAAGGGTTAGAGGTTTAAGA-TTTAGGGGTTAGGGGTAC
* * *
12219194 TTAAGGGTTAGGGGTTTATGATTTAGGGTTTAGGGG
1 TTAAGGGTTAGAGGTTTAAGATTTAGGGGTTAGGGG
12219230 ATAGAGGTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
38 9 0.29
39 21 0.68
40 1 0.03
ACGTcount: A:0.22, C:0.01, G:0.41, T:0.36
Consensus pattern (39 bp):
TTAAGGGTTAGAGGTTTAAGATTTAGGGGTTAGGGGTAC
Found at i:12219225 original size:7 final size:7
Alignment explanation
Indices: 12219117--12219248 Score: 61
Period size: 7 Copynumber: 18.0 Consensus size: 7
12219107 ACTATCTTAA
*
12219117 GGTTTAT
1 GGTTTAG
*
12219124 GGATTATG
1 GGTTTA-G
12219132 GGTTTAG
1 GGTTTAG
* *
12219139 GGATTAT
1 GGTTTAG
*
12219146 GGTTTAT
1 GGTTTAG
12219153 GGTTTAAG
1 GGTTT-AG
*
12219161 GGTTGA-
1 GGTTTAG
*
12219167 GGTTTAA
1 GGTTTAG
*
12219174 AGTTTAG
1 GGTTTAG
*
12219181 GGGTTAGG
1 GGTTTA-G
12219189 GGTACTTAAG
1 GGT--TT-AG
12219199 GG-TTAGG
1 GGTTTA-G
*
12219206 GGTTTAT
1 GGTTTAG
*
12219213 GATTTAG
1 GGTTTAG
12219220 GGTTTAG
1 GGTTTAG
**
12219227 GGGATAG
1 GGTTTAG
12219234 AGGTTTAG
1 -GGTTTAG
12219242 GGTTTAG
1 GGTTTAG
12219249 ATTAATTAGT
Statistics
Matches: 93, Mismatches: 22, Indels: 20
0.69 0.16 0.15
Matches are distributed among these distances:
6 6 0.06
7 60 0.65
8 21 0.23
10 5 0.05
11 1 0.01
ACGTcount: A:0.21, C:0.01, G:0.39, T:0.39
Consensus pattern (7 bp):
GGTTTAG
Found at i:12219332 original size:272 final size:263
Alignment explanation
Indices: 12218817--12219330 Score: 748
Period size: 272 Copynumber: 1.9 Consensus size: 263
12218807 TCATTATAGT
* *
12218817 TTAGGGTTTAAGATTTAGGAGTTCCTATCTTAAGATTTATGGATTTTTAGGTATTATGGTTTATG
1 TTAGGGTTTAAGATTTAGGAGTTACTATCTTAAGATTTATGGATTTTTAGGGATTATGGTTTATG
*
12218882 GTTTAAGGGTTGGGGTTTAAAGTTTAGGGGTTAGGGGTACTTAAGGGTTAAGGGTTTATGATTTA
66 GTTTAAGGGTTGAGGTTTAAAGTTTAGGGGTTAGGGGTACTTAAGGGTTAAGGGTTTATGATTTA
* * *
12218947 GGGTTTAAGAGATAGGAGATAGGGGTTTAGGATTTAGATTAATTAGTGTTTTTTAATTAATATAT
131 GGGTTT-A-AG--AGGAGATAGAGGTTTAGGATTTAGATTAATTAGTATTTTTTAATTAACATAT
* * *
12219012 TAAATAATTTCTTATATAATCGTAAAAGAGATAGTATTAATTTTAAAATATTAAATTAATTATTA
192 TAAATAATTTCTGATATAATCGTAAAAGAAATAATATTAATTTTAAAATATTAAATTAATTATTA
12219077 ATTATCA
257 ATTATCA
* *
12219084 TTAGGGTTTAAGGTTTAGGAGTTACTATCTTAAGGTTTATGGATTATGGGTTTAGGGATTATGGT
1 TTAGGGTTTAAGATTTAGGAGTTACTATCTTAAGATTTATGGA-T-T---TTTAGGGATTATGGT
*
12219149 TTATGGTTTAAGGGTTGAGGTTTAAAGTTTAGGGGTTAGGGGTACTTAAGGGTTAGGGGTTTATG
61 TTATGGTTTAAGGGTTGAGGTTTAAAGTTTAGGGGTTAGGGGTACTTAAGGGTTAAGGGTTTATG
* * *
12219214 ATTTAGGGTTT-AG-GG-GATAGAGGTTTAGGGTTTAGATTAATTAGTATTTTTTAATTTACGTA
126 ATTTAGGGTTTAAGAGGAGATAGAGGTTTAGGATTTAGATTAATTAGTATTTTTTAATTAACATA
* * * *
12219276 TTAAATAATTTCTGATGTAATTGTAAAAGAAATAATATTTATTTT-ATATATTAAA
191 TTAAATAATTTCTGATATAATCGTAAAAGAAATAATATTAATTTTAAAATATTAAA
12219331 ATTATGACTA
Statistics
Matches: 223, Mismatches: 19, Indels: 13
0.87 0.07 0.05
Matches are distributed among these distances:
264 9 0.04
265 80 0.36
266 2 0.01
267 40 0.18
268 1 0.00
269 3 0.01
272 88 0.39
ACGTcount: A:0.31, C:0.02, G:0.24, T:0.43
Consensus pattern (263 bp):
TTAGGGTTTAAGATTTAGGAGTTACTATCTTAAGATTTATGGATTTTTAGGGATTATGGTTTATG
GTTTAAGGGTTGAGGTTTAAAGTTTAGGGGTTAGGGGTACTTAAGGGTTAAGGGTTTATGATTTA
GGGTTTAAGAGGAGATAGAGGTTTAGGATTTAGATTAATTAGTATTTTTTAATTAACATATTAAA
TAATTTCTGATATAATCGTAAAAGAAATAATATTAATTTTAAAATATTAAATTAATTATTAATTA
TCA
Found at i:12220418 original size:46 final size:46
Alignment explanation
Indices: 12220363--12220459 Score: 176
Period size: 46 Copynumber: 2.1 Consensus size: 46
12220353 TTTAGCATTA
*
12220363 AAGTATTGGGTGTTTTCAGATTAGGGTTTAGCATTGGCGAAGTCAG
1 AAGTATTGGGTGTTTCCAGATTAGGGTTTAGCATTGGCGAAGTCAG
*
12220409 AAGTATTGGGTGTTTCCAGATTAGGGTTTAGCATTGGTGAAGTCAG
1 AAGTATTGGGTGTTTCCAGATTAGGGTTTAGCATTGGCGAAGTCAG
12220455 AAGTA
1 AAGTA
12220460 GAGTTGTCAA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 49 1.00
ACGTcount: A:0.26, C:0.08, G:0.32, T:0.34
Consensus pattern (46 bp):
AAGTATTGGGTGTTTCCAGATTAGGGTTTAGCATTGGCGAAGTCAG
Found at i:12224188 original size:43 final size:43
Alignment explanation
Indices: 12224141--12224318 Score: 173
Period size: 43 Copynumber: 4.1 Consensus size: 43
12224131 GAACGGTACT
* *
12224141 TTTAGCGATGGTTGT-GATAAAAGCGCCGCTAAAGGTCATGTTC
1 TTTAGCGATGTTTGTGGAT-AAAGCGCCGCTAAAGATCATGTTC
*** *
12224184 TTTAGCGGCATTTGTGGGTAAAGCGCCGCTAAAGATCATGTTC
1 TTTAGCGATGTTTGTGGATAAAGCGCCGCTAAAGATCATGTTC
** * * ***
12224227 TTTAGCGGCGTTTGT-GATAAAAGTGCCCCTAAAGATCATAACC
1 TTTAGCGATGTTTGTGGAT-AAAGCGCCGCTAAAGATCATGTTC
* *
12224270 TTTAGC-AGTGTTTGTGGGTAAAGCGTCGCTAAAGATCATGTTC
1 TTTAGCGA-TGTTTGTGGATAAAGCGCCGCTAAAGATCATGTTC
12224313 TTTAGC
1 TTTAGC
12224319 AGTGTTTTTT
Statistics
Matches: 109, Mismatches: 22, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
42 2 0.02
43 103 0.94
44 4 0.04
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.31
Consensus pattern (43 bp):
TTTAGCGATGTTTGTGGATAAAGCGCCGCTAAAGATCATGTTC
Found at i:12224273 original size:86 final size:86
Alignment explanation
Indices: 12224152--12224318 Score: 244
Period size: 86 Copynumber: 1.9 Consensus size: 86
12224142 TTAGCGATGG
* * *** *
12224152 TTGTGATAAAAGCGCCGCTAAAGGTCATGTTCTTTAGCGGCATTTGTGGGTAAAGCGCCGCTAAA
1 TTGTGATAAAAGCGCCCCTAAAGATCATAACCTTTAGCAGCATTTGTGGGTAAAGCGCCGCTAAA
12224217 GATCATGTTCTTTAGCGGCGT
66 GATCATGTTCTTTAGCGGCGT
* ** *
12224238 TTGTGATAAAAGTGCCCCTAAAGATCATAACCTTTAGCAGTGTTTGTGGGTAAAGCGTCGCTAAA
1 TTGTGATAAAAGCGCCCCTAAAGATCATAACCTTTAGCAGCATTTGTGGGTAAAGCGCCGCTAAA
12224303 GATCATGTTCTTTAGC
66 GATCATGTTCTTTAGC
12224319 AGTGTTTTTT
Statistics
Matches: 71, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
86 71 1.00
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.31
Consensus pattern (86 bp):
TTGTGATAAAAGCGCCCCTAAAGATCATAACCTTTAGCAGCATTTGTGGGTAAAGCGCCGCTAAA
GATCATGTTCTTTAGCGGCGT
Found at i:12224319 original size:43 final size:43
Alignment explanation
Indices: 12224160--12224325 Score: 199
Period size: 43 Copynumber: 3.9 Consensus size: 43
12224150 GGTTGTGATA
* * *
12224160 AAAGCGCCGCTAAAGGTCATGTTCTTTAGCGGCATTTGTGGGT
1 AAAGCGCCGCTAAAGATCATGTTCTTTAGCAGCGTTTGTGGGT
* *
12224203 AAAGCGCCGCTAAAGATCATGTTCTTTAGCGGCGTTTGT-GAT
1 AAAGCGCCGCTAAAGATCATGTTCTTTAGCAGCGTTTGTGGGT
* * *** *
12224245 AAAAGTGCCCCTAAAGATCATAACCTTTAGCAGTGTTTGTGGGT
1 -AAAGCGCCGCTAAAGATCATGTTCTTTAGCAGCGTTTGTGGGT
* *
12224289 AAAGCGTCGCTAAAGATCATGTTCTTTAGCAGTGTTT
1 AAAGCGCCGCTAAAGATCATGTTCTTTAGCAGCGTTT
12224326 TTTTACATAA
Statistics
Matches: 104, Mismatches: 17, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
42 2 0.02
43 100 0.96
44 2 0.02
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.31
Consensus pattern (43 bp):
AAAGCGCCGCTAAAGATCATGTTCTTTAGCAGCGTTTGTGGGT
Found at i:12236546 original size:27 final size:26
Alignment explanation
Indices: 12236524--12236940 Score: 364
Period size: 27 Copynumber: 15.5 Consensus size: 26
12236514 AGGGGTATAA
12236524 TAGTCATTTTACCCTATGAGGGTATTT
1 TAGTCATTTTACCCTATGAGGGTA-TT
* * *
12236551 TGGTCATTTTAACCTATGGGGGTATT
1 TAGTCATTTTACCCTATGAGGGTATT
12236577 TCAGTCATTTTACCCTAT-AGGGGTATT
1 T-AGTCATTTTACCCTATGA-GGGTATT
12236604 TCAGTCATTTTACCCTATGAGGGTATT
1 T-AGTCATTTTACCCTATGAGGGTATT
*
12236631 TCGATCATTTTACCCTATGAGGGTATTT
1 TAG-TCATTTTACCCTATGAGGGTA-TT
* * *
12236659 TGGTCATTTTAACCTATGGGGGTATT
1 TAGTCATTTTACCCTATGAGGGTATT
12236685 TCAGTCATTTTACCCTAT-AGGGGTATT
1 T-AGTCATTTTACCCTATGA-GGGTATT
12236712 TCAGTCATTTTACCCTATGAGGGTAATT
1 T-AGTCATTTTACCCTATGAGGGT-ATT
*
12236740 TCGATCA-TTTACCCTATGAGGGTATTT
1 TAG-TCATTTTACCCTATGAGGGTA-TT
* *
12236767 TGGTCATTTTACCCTA-CAGGGGTATTT
1 TAGTCATTTTACCCTATGA-GGGTA-TT
*
12236794 TGGTCATTTTACCCTATG-GGGTATTT
1 TAGTCATTTTACCCTATGAGGGTA-TT
* *
12236820 CTA-TCATTCTACCCTATGGGGGTATT
1 -TAGTCATTTTACCCTATGAGGGTATT
* * *
12236846 TCGATCATTCTACGCTATG-GGGTTATT
1 TAG-TCATTTTACCCTATGAGGG-TATT
* * *
12236873 TCGGTC-TTTCTATCCTATGGGGGTATT
1 T-AGTCATTT-TACCCTATGAGGGTATT
* * * *
12236900 TCGGTCATTCTATCCTATGGGGGTATT
1 T-AGTCATTTTACCCTATGAGGGTATT
*
12236927 TCGGTCATTTTACC
1 T-AGTCATTTTACC
12236941 TATTTTAGGG
Statistics
Matches: 339, Mismatches: 28, Indels: 46
0.82 0.07 0.11
Matches are distributed among these distances:
25 1 0.00
26 41 0.12
27 278 0.82
28 19 0.06
ACGTcount: A:0.19, C:0.18, G:0.21, T:0.42
Consensus pattern (26 bp):
TAGTCATTTTACCCTATGAGGGTATT
Found at i:12236601 original size:54 final size:52
Alignment explanation
Indices: 12236526--12236940 Score: 492
Period size: 54 Copynumber: 7.7 Consensus size: 52
12236516 GGGTATAATA
* *
12236526 GTCATTTTACCCTATGAGGGTATTTTGGTCATTTTAACCTATGGGGGTATTTC
1 GTCATTTTACCCTATG-GGGTATTTCGGTCATTTTACCCTATGGGGGTATTTC
* *
12236579 AGTCATTTTACCCTATAGGGGTATTTCAGTCATTTTACCCTATGAGGGTATTTC
1 -GTCATTTTACCCTAT-GGGGTATTTCGGTCATTTTACCCTATGGGGGTATTTC
* *
12236633 GATCATTTTACCCTATGAGGGTATTTTGGTCATTTTAACCTATGGGGGTATTTC
1 G-TCATTTTACCCTATG-GGGTATTTCGGTCATTTTACCCTATGGGGGTATTTC
* *
12236687 AGTCATTTTACCCTATAGGGGTATTTCAGTCATTTTACCCTATGAGGGTAATTTC
1 -GTCATTTTACCCTAT-GGGGTATTTCGGTCATTTTACCCTATGGGGGT-ATTTC
* ** *
12236742 GATCA-TTTACCCTATGAGGGTATTTTGGTCATTTTACCCTACAGGGGTATTTTG
1 G-TCATTTTACCCTATG-GGGTATTTCGGTCATTTTACCCTATGGGGGTA-TTTC
** *
12236796 GTCATTTTACCCTATGGGGTATTTCTATCATTCTACCCTATGGGGGTATTTC
1 GTCATTTTACCCTATGGGGTATTTCGGTCATTTTACCCTATGGGGGTATTTC
* * *
12236848 GATCATTCTACGCTATGGGGTTATTTCGGTC-TTTCTATCCTATGGGGGTATTTC
1 G-TCATTTTACCCTATGGGG-TATTTCGGTCATTT-TACCCTATGGGGGTATTTC
* *
12236902 GGTCATTCTATCCTATGGGGGTATTTCGGTCATTTTACC
1 -GTCATTTTACCCTAT-GGGGTATTTCGGTCATTTTACC
12236941 TATTTTAGGG
Statistics
Matches: 311, Mismatches: 34, Indels: 32
0.82 0.09 0.08
Matches are distributed among these distances:
52 4 0.01
53 51 0.16
54 237 0.76
55 19 0.06
ACGTcount: A:0.19, C:0.18, G:0.21, T:0.42
Consensus pattern (52 bp):
GTCATTTTACCCTATGGGGTATTTCGGTCATTTTACCCTATGGGGGTATTTC
Found at i:12236648 original size:81 final size:81
Alignment explanation
Indices: 12236525--12236940 Score: 490
Period size: 81 Copynumber: 5.1 Consensus size: 81
12236515 GGGGTATAAT
* *
12236525 AGTCATTTTACCCTATGAGGGTATTTTGGTCATTTTAACCTATGGGGGTATTTCAGTCATTTTAC
1 AGTCATTTTACCCTATGAGGGTATTTCGGTCATTTTACCCTATGGGGGTATTTCAGTCATTTTAC
*
12236590 CCTATAGGGGTATTTC
66 CCTATGGGGGTATTTC
* * ** *
12236606 AGTCATTTTACCCTATGAGGGTATTTCGATCATTTTACCCTATGAGGGTATTTTGGTCATTTTAA
1 AGTCATTTTACCCTATGAGGGTATTTCGGTCATTTTACCCTATGGGGGTATTTCAGTCATTTTAC
12236671 CCTATGGGGGTATTTC
66 CCTATGGGGGTATTTC
* *
12236687 AGTCATTTTACCCTAT-AGGGGTATTTCAGTCATTTTACCCTATGAGGGTAATTTC-GATCA-TT
1 AGTCATTTTACCCTATGA-GGGTATTTCGGTCATTTTACCCTATGGGGGT-ATTTCAG-TCATTT
* *
12236749 TACCCTATGAGGGTATTTT
63 TACCCTATGGGGGTATTTC
* * * *
12236768 GGTCATTTTACCCTA-CAGGGGTATTTTGGTCATTTTACCCTAT-GGGGTATTTCTA-TCATTCT
1 AGTCATTTTACCCTATGA-GGGTATTTCGGTCATTTTACCCTATGGGGGTATTTC-AGTCATTTT
12236830 ACCCTATGGGGGTATTTC
64 ACCCTATGGGGGTATTTC
* * * * *
12236848 -GATCATTCTACGCTATG-GGGTTATTTCGGTC-TTTCTATCCTATGGGGGTATTTCGGTCATTC
1 AG-TCATTTTACCCTATGAGGG-TATTTCGGTCATTT-TACCCTATGGGGGTATTTCAGTCATTT
*
12236910 TATCCTATGGGGGTATTTC
63 TACCCTATGGGGGTATTTC
*
12236929 GGTCATTTTACC
1 AGTCATTTTACC
12236941 TATTTTAGGG
Statistics
Matches: 291, Mismatches: 30, Indels: 28
0.83 0.09 0.08
Matches are distributed among these distances:
79 15 0.05
80 50 0.17
81 218 0.75
82 8 0.03
ACGTcount: A:0.19, C:0.18, G:0.21, T:0.42
Consensus pattern (81 bp):
AGTCATTTTACCCTATGAGGGTATTTCGGTCATTTTACCCTATGGGGGTATTTCAGTCATTTTAC
CCTATGGGGGTATTTC
Found at i:12240932 original size:16 final size:17
Alignment explanation
Indices: 12240906--12240939 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
12240896 TTCGTTTAAA
12240906 TAAATTAATTTTCCCAT
1 TAAATTAATTTTCCCAT
*
12240923 TAAA-TAATTTTCTCAT
1 TAAATTAATTTTCCCAT
12240939 T
1 T
12240940 CTAACTTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.35, C:0.15, G:0.00, T:0.50
Consensus pattern (17 bp):
TAAATTAATTTTCCCAT
Found at i:12244134 original size:18 final size:18
Alignment explanation
Indices: 12244108--12244142 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
12244098 CATTGCTTCT
12244108 AAAAAAACTTTT-GGGAC
1 AAAAAAACTTTTAGGGAC
12244125 AAAAAGAACTTTTAGGGA
1 AAAAA-AACTTTTAGGGA
12244143 GAAGCTAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 7 0.44
19 4 0.25
ACGTcount: A:0.49, C:0.09, G:0.20, T:0.23
Consensus pattern (18 bp):
AAAAAAACTTTTAGGGAC
Found at i:12249036 original size:23 final size:23
Alignment explanation
Indices: 12249009--12249057 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
12248999 CCATATCAAC
12249009 AATAATTAAAATTTTATGTATAT
1 AATAATTAAAATTTTATGTATAT
12249032 AATAATTAAAATTTTATGTATAT
1 AATAATTAAAATTTTATGTATAT
12249055 AAT
1 AAT
12249058 TAAACCGCTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (23 bp):
AATAATTAAAATTTTATGTATAT
Found at i:12256569 original size:22 final size:22
Alignment explanation
Indices: 12256516--12256569 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
12256506 GCCAGTGATT
*
12256516 AGAATGGCTAAGAGCCGTAAAC
1 AGAATGGCTAAGAGCCATAAAC
* * *
12256538 AGGATAGCTATA-AGCTATAAAC
1 AGAATGGCTA-AGAGCCATAAAC
12256560 AGAATGGCTA
1 AGAATGGCTA
12256570 CTAGCCACAA
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
22 24 0.96
23 1 0.04
ACGTcount: A:0.43, C:0.15, G:0.24, T:0.19
Consensus pattern (22 bp):
AGAATGGCTAAGAGCCATAAAC
Found at i:12256657 original size:26 final size:26
Alignment explanation
Indices: 12256628--12256683 Score: 85
Period size: 26 Copynumber: 2.2 Consensus size: 26
12256618 CGCAGTAAAC
*
12256628 CTGCCAGCAACAGTACCGCAACAAAG
1 CTGCAAGCAACAGTACCGCAACAAAG
* *
12256654 CTGCAAGTAATAGTACCGCAACAAAG
1 CTGCAAGCAACAGTACCGCAACAAAG
12256680 CTGC
1 CTGC
12256684 TAGTAATAGT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.38, C:0.30, G:0.20, T:0.12
Consensus pattern (26 bp):
CTGCAAGCAACAGTACCGCAACAAAG
Found at i:12256688 original size:26 final size:26
Alignment explanation
Indices: 12256639--12256694 Score: 103
Period size: 26 Copynumber: 2.2 Consensus size: 26
12256629 TGCCAGCAAC
12256639 AGTACCGCAACAAAGCTGCAAGTAAT
1 AGTACCGCAACAAAGCTGCAAGTAAT
*
12256665 AGTACCGCAACAAAGCTGCTAGTAAT
1 AGTACCGCAACAAAGCTGCAAGTAAT
12256691 AGTA
1 AGTA
12256695 TGTGTGGCCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.41, C:0.21, G:0.20, T:0.18
Consensus pattern (26 bp):
AGTACCGCAACAAAGCTGCAAGTAAT
Found at i:12256727 original size:27 final size:27
Alignment explanation
Indices: 12256697--12256773 Score: 113
Period size: 27 Copynumber: 2.9 Consensus size: 27
12256687 TAATAGTATG
12256697 TGTGGCCAAGCCACCAATAACAGTGAT
1 TGTGGCCAAGCCACCAATAACAGTGAT
12256724 TGTGG-CAGAGCCACCAATAACAGTGAT
1 TGTGGCCA-AGCCACCAATAACAGTGAT
**
12256751 TGTGGCGGAGCCACCAAT-ACAGT
1 TGTGGCCAAGCCACCAATAACAGT
12256774 ACTTCATCCA
Statistics
Matches: 46, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
26 7 0.15
27 39 0.85
ACGTcount: A:0.31, C:0.25, G:0.26, T:0.18
Consensus pattern (27 bp):
TGTGGCCAAGCCACCAATAACAGTGAT
Found at i:12256866 original size:24 final size:24
Alignment explanation
Indices: 12256838--12256895 Score: 82
Period size: 24 Copynumber: 2.4 Consensus size: 24
12256828 CCATGCTCAG
12256838 AATCAGTCATA-CAATTCACAGAAA
1 AATCAGTCATACCAA-TCACAGAAA
* *
12256862 AATCAGTTATACCAATCACAGACA
1 AATCAGTCATACCAATCACAGAAA
12256886 AATCAGTCAT
1 AATCAGTCAT
12256896 TTAAACTTGA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
24 27 0.90
25 3 0.10
ACGTcount: A:0.47, C:0.22, G:0.09, T:0.22
Consensus pattern (24 bp):
AATCAGTCATACCAATCACAGAAA
Found at i:12257017 original size:27 final size:27
Alignment explanation
Indices: 12256971--12257032 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
12256961 GGTATTACAA
* * *
12256971 TCATTTTA-CCTATAGGGGCATCACGG
1 TCATTTTACCCTACAAGGGCATCACAG
*
12256997 TCATTTTACCCTACAAGGGCATTACAG
1 TCATTTTACCCTACAAGGGCATCACAG
*
12257024 TTATTTTAC
1 TCATTTTAC
12257033 AAATTGTGGG
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
26 8 0.27
27 22 0.73
ACGTcount: A:0.26, C:0.23, G:0.16, T:0.35
Consensus pattern (27 bp):
TCATTTTACCCTACAAGGGCATCACAG
Found at i:12261073 original size:28 final size:28
Alignment explanation
Indices: 12261004--12261132 Score: 89
Period size: 28 Copynumber: 4.6 Consensus size: 28
12260994 AGTCTTCGGT
* * *
12261004 GGACTTTCCACATAAGATAGTTCTTGGC
1 GGACTTTCCACATAAGATAATCCTTAGC
* * * *
12261032 GGAGTTCCCGCATATGATAATCCTTAGC
1 GGACTTTCCACATAAGATAATCCTTAGC
* * *
12261060 GGACTTTCCACATAAGACAATCATT-GAT
1 GGACTTTCCACATAAGATAATCCTTAG-C
* * * **
12261088 GGACTTTTCGCATAAGATAGTCCTTAAT
1 GGACTTTCCACATAAGATAATCCTTAGC
* *
12261116 AGACCTTCCACATAAGA
1 GGACTTTCCACATAAGA
12261133 CAACCTTTGA
Statistics
Matches: 75, Mismatches: 24, Indels: 4
0.73 0.23 0.04
Matches are distributed among these distances:
27 1 0.01
28 74 0.99
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.29
Consensus pattern (28 bp):
GGACTTTCCACATAAGATAATCCTTAGC
Found at i:12263706 original size:19 final size:18
Alignment explanation
Indices: 12263659--12263706 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
12263649 ATAAACAAAT
12263659 CAAAACCCAAAAACAGAAC
1 CAAAA-CCAAAAACAGAAC
** *
12263678 CAAATTCAAAAACATGATC
1 CAAAACCAAAAACA-GAAC
12263697 CAAAACCAAA
1 CAAAACCAAA
12263707 TGCCCAAAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
18 8 0.35
19 15 0.65
ACGTcount: A:0.60, C:0.27, G:0.04, T:0.08
Consensus pattern (18 bp):
CAAAACCAAAAACAGAAC
Found at i:12268762 original size:22 final size:20
Alignment explanation
Indices: 12268721--12268762 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
12268711 CCATTGTTGA
*
12268721 GAAATTGATGAATTAGGCTT
1 GAAATTGATGAATTAAGCTT
12268741 GAAATTGATAGAACTTAAGCTT
1 GAAATTGAT-GAA-TTAAGCTT
12268763 AGATTATGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 9 0.47
21 3 0.16
22 7 0.37
ACGTcount: A:0.38, C:0.07, G:0.21, T:0.33
Consensus pattern (20 bp):
GAAATTGATGAATTAAGCTT
Found at i:12269193 original size:18 final size:18
Alignment explanation
Indices: 12269167--12269204 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
12269157 TTCGAGATCA
*
12269167 ATATACATGTTTATTTGC
1 ATATACATGTTAATTTGC
*
12269185 ATATTCATGTTAATTTGC
1 ATATACATGTTAATTTGC
12269203 AT
1 AT
12269205 GATTAAGTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.29, C:0.11, G:0.11, T:0.50
Consensus pattern (18 bp):
ATATACATGTTAATTTGC
Done.