Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold423
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: 617052
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
File 2 of 6
Found at i:122695 original size:8 final size:8
Alignment explanation
Indices: 122670--122795 Score: 60
Period size: 8 Copynumber: 14.6 Consensus size: 8
122660 AATGTGATGA
122670 TATATATTT
1 TATATA-TT
122679 ATATCATATT
1 -TAT-ATATT
122689 TATATATTTT
1 TATATA--TT
*
122699 TATAAATT
1 TATATATT
*
122707 TATTTAAATT
1 TA--TATATT
*
122717 TAAAT-TAT
1 TATATAT-T
122725 TATATATT
1 TATATATT
122733 TATATATTT
1 TATATA-TT
122742 TAATATATT
1 T-ATATATT
*
122751 AATA-ATT
1 TATATATT
*
122758 TATATTATA
1 TATA-TATT
*
122767 TAAATATT
1 TATATATT
*
122775 AATATTATT
1 TATA-TATT
122784 T-TATATT
1 TATATATT
122791 TATAT
1 TATAT
122796 CATATTATTT
Statistics
Matches: 91, Mismatches: 12, Indels: 28
0.69 0.09 0.21
Matches are distributed among these distances:
7 12 0.13
8 33 0.36
9 18 0.20
10 25 0.27
11 3 0.03
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (8 bp):
TATATATT
Found at i:122777 original size:24 final size:25
Alignment explanation
Indices: 122746--122817 Score: 69
Period size: 27 Copynumber: 2.9 Consensus size: 25
122736 ATATTTTAAT
122746 ATATTAATAATTTATATTATATA-A
1 ATATTAATAATTTATATTATATATA
*
122770 ATATTAATATTATTTTATATT-TATATC
1 ATATTAATA--A-TTTATATTATATATA
**
122797 ATATT-ATTTTTTATATTATAT
1 ATATTAATAATTTATATTATAT
122818 TTTAATTATT
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
23 8 0.20
24 12 0.30
26 7 0.17
27 13 0.32
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.58
Consensus pattern (25 bp):
ATATTAATAATTTATATTATATATA
Found at i:122795 original size:16 final size:16
Alignment explanation
Indices: 122684--122833 Score: 69
Period size: 16 Copynumber: 10.2 Consensus size: 16
122674 TATTTATATC
122684 ATATTTATA-TATTTT
1 ATATTTATATTATTTT
**
122699 -TATAAAT-TTA-TTT
1 ATATTTATATTATTTT
* * *
122712 AAATTTAAATTATTAT
1 ATATTTATATTATTTT
122728 ATATTTATA-TATTTT
1 ATATTTATATTATTTT
*
122743 A-A--TATATTA--AT
1 ATATTTATATTATTTT
**
122754 A-ATTTATATTATATAA
1 ATATTTATATTAT-TTT
*
122770 ATATTAATATTATTTT
1 ATATTTATATTATTTT
* *
122786 ATATTTATATCATATT
1 ATATTTATATTATTTT
* *
122802 AT-TTTTTA-TATTAT
1 ATATTTATATTATTTT
122816 AT-TTTA-ATTATTTT
1 ATATTTATATTATTTT
122830 ATAT
1 ATAT
122834 CATGATTAAA
Statistics
Matches: 98, Mismatches: 24, Indels: 26
0.66 0.16 0.18
Matches are distributed among these distances:
11 3 0.03
12 4 0.04
13 13 0.13
14 26 0.27
15 15 0.15
16 27 0.28
17 10 0.10
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (16 bp):
ATATTTATATTATTTT
Found at i:122802 original size:21 final size:22
Alignment explanation
Indices: 122737--122833 Score: 76
Period size: 21 Copynumber: 4.5 Consensus size: 22
122727 TATATTTATA
*
122737 TATTTTAATATATTA-ATAAT-T
1 TATTTT-ATATATTATATCATAT
* * *
122758 TATATTATATA-AATATTAATAT
1 TATTTTATATATTATA-TCATAT
122780 TATTTTATAT-TTATATCATAT
1 TATTTTATATATTATATCATAT
* **
122801 TATTTTTTATATTATATTTTAAT
1 TATTTTATATATTATATCAT-AT
122824 TATTTTATAT
1 TATTTTATAT
122834 CATGATTAAA
Statistics
Matches: 61, Mismatches: 9, Indels: 10
0.76 0.11 0.12
Matches are distributed among these distances:
19 1 0.02
20 6 0.10
21 23 0.38
22 20 0.33
23 11 0.18
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (22 bp):
TATTTTATATATTATATCATAT
Found at i:122814 original size:12 final size:12
Alignment explanation
Indices: 122797--122829 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
122787 TATTTATATC
122797 ATATTATTTTTT
1 ATATTATTTTTT
*
122809 ATATTATATTTT
1 ATATTATTTTTT
122821 A-ATTATTTT
1 ATATTATTTT
122830 ATATCATGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 7 0.37
12 12 0.63
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (12 bp):
ATATTATTTTTT
Found at i:122825 original size:23 final size:22
Alignment explanation
Indices: 122745--122829 Score: 73
Period size: 23 Copynumber: 3.7 Consensus size: 22
122735 TATATTTTAA
* *
122745 TATATTAATAATTTATATTATATA
1 TATATTAATTATTT-T-TTATATT
*
122769 AATATTAA-TATTATTTTATATT
1 TATATTAATTATT-TTTTATATT
*
122791 TATATCATATTATTTTTTATATT
1 TATATTA-ATTATTTTTTATATT
*
122814 ATATTTTAATTATTTT
1 -TATATTAATTATTTT
122830 ATATCATGAT
Statistics
Matches: 50, Mismatches: 7, Indels: 9
0.76 0.11 0.14
Matches are distributed among these distances:
22 11 0.22
23 22 0.44
24 17 0.34
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (22 bp):
TATATTAATTATTTTTTATATT
Found at i:125392 original size:14 final size:15
Alignment explanation
Indices: 125369--125405 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
125359 TTATATCTTT
125369 TTTAAATAAAT-AAA
1 TTTAAATAAATGAAA
*
125383 TTTAATTAAATGAAA
1 TTTAAATAAATGAAA
125398 -TTAAATAA
1 TTTAAATAA
125406 TTTAATTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 17 0.85
15 3 0.15
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (15 bp):
TTTAAATAAATGAAA
Found at i:125427 original size:21 final size:22
Alignment explanation
Indices: 125398--125438 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
125388 TTAAATGAAA
*
125398 TTAAATAAT-TTAATTTTTATC
1 TTAAATAATCTTAAATTTTATC
*
125419 TTAATTAATCTTAAATTTTA
1 TTAAATAATCTTAAATTTTA
125439 AAATTAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.56
Consensus pattern (22 bp):
TTAAATAATCTTAAATTTTATC
Found at i:125452 original size:7 final size:7
Alignment explanation
Indices: 125429--125500 Score: 55
Period size: 7 Copynumber: 10.7 Consensus size: 7
125419 TTAATTAATC
*
125429 TTAAATT
1 TTAAAAT
125436 TTAAAA-
1 TTAAAAT
125442 TTAAAAT
1 TTAAAAT
*
125449 TTAATTAT
1 TTAA-AAT
125457 GTTAAAA-
1 -TTAAAAT
*
125464 TTAAATT
1 TTAAAAT
*
125471 TTAAATT
1 TTAAAAT
125478 TTAAAA-
1 TTAAAAT
125484 TT-AAAT
1 TTAAAAT
125490 TT-AAAT
1 TTAAAAT
125496 TTAAA
1 TTAAA
125501 TTTTTTATAA
Statistics
Matches: 54, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
5 3 0.06
6 21 0.39
7 23 0.43
8 3 0.06
9 4 0.07
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (7 bp):
TTAAAAT
Found at i:125501 original size:6 final size:6
Alignment explanation
Indices: 125429--125521 Score: 66
Period size: 6 Copynumber: 14.7 Consensus size: 6
125419 TTAATTAATC
* *
125429 TTAAATT TTAAAAT TAAAAT TTAATTAT GTTAAAA TTAAATT TTAAATT
1 TTAAA-T TT-AAAT TTAAAT TTAA--AT -TTAAAT TTAAA-T TTAAA-T
*
125478 TTAAAA TTAAAT TTAAAT TTAAAT TT---T TTATAAT TTAAAT TTAA
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTA-AAT TTAAAT TTAA
125522 GCCGAGTGGA
Statistics
Matches: 71, Mismatches: 6, Indels: 19
0.74 0.06 0.20
Matches are distributed among these distances:
3 3 0.04
6 38 0.54
7 21 0.30
8 5 0.07
9 4 0.06
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (6 bp):
TTAAAT
Found at i:125513 original size:42 final size:42
Alignment explanation
Indices: 125424--125500 Score: 108
Period size: 42 Copynumber: 1.9 Consensus size: 42
125414 TTATCTTAAT
*
125424 TAATCTTAAATTTTAAAATTAAAATTTAATTATGTTAAAATTA
1 TAATTTTAAATTTTAAAATTAAAATTTAA-TATGTTAAAATTA
125467 -AATTTTAAATTTTAAAATT-AAATTTAA-AT-TTAAA
1 TAATTTTAAATTTTAAAATTAAAATTTAATATGTTAAA
125501 TTTTTTATAA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
38 5 0.15
39 2 0.06
41 8 0.24
42 18 0.55
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (42 bp):
TAATTTTAAATTTTAAAATTAAAATTTAATATGTTAAAATTA
Found at i:125514 original size:16 final size:15
Alignment explanation
Indices: 125489--125519 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
125479 TAAAATTAAA
125489 TTTAAATTTAAATTT
1 TTTAAATTTAAATTT
125504 TTTATAATTTAAATTT
1 TTTA-AATTTAAATTT
125520 AAGCCGAGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
TTTAAATTTAAATTT
Found at i:131296 original size:18 final size:19
Alignment explanation
Indices: 131266--131307 Score: 77
Period size: 18 Copynumber: 2.3 Consensus size: 19
131256 ACCCATGTCC
131266 GACATATTTTTCAGATATG
1 GACATATTTTTCAGATATG
131285 GACATA-TTTTCAGATATG
1 GACATATTTTTCAGATATG
131303 GACAT
1 GACAT
131308 GGGGATATGG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 17 0.74
19 6 0.26
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.38
Consensus pattern (19 bp):
GACATATTTTTCAGATATG
Found at i:137414 original size:22 final size:20
Alignment explanation
Indices: 137365--137414 Score: 50
Period size: 19 Copynumber: 2.5 Consensus size: 20
137355 ACATGAATAA
* *
137365 AATATAAAATATAATAATTG
1 AATATAAAATAAAATAAATG
137385 AAT-T-AAATAAATATAAATG
1 AATATAAAATAAA-ATAAATG
137404 ATATATAAAAT
1 A-ATATAAAAT
137415 TACGAAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
18 6 0.25
19 8 0.33
20 5 0.21
21 1 0.04
22 4 0.17
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (20 bp):
AATATAAAATAAAATAAATG
Found at i:138818 original size:15 final size:14
Alignment explanation
Indices: 138791--138825 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
138781 TATATGATTT
138791 ATTTTTATTTTTAA
1 ATTTTTATTTTTAA
*
138805 ATTTTTATATTTTAT
1 ATTTTTAT-TTTTAA
138820 ATTTTT
1 ATTTTT
138826 CTTATTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.42
15 11 0.58
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (14 bp):
ATTTTTATTTTTAA
Found at i:141841 original size:11 final size:10
Alignment explanation
Indices: 141827--141892 Score: 61
Period size: 9 Copynumber: 6.9 Consensus size: 10
141817 TAAATAGATC
141827 TATAATACTAA
1 TATAATA-TAA
141838 TATAATAT-A
1 TATAATATAA
141847 TA-AATATAA
1 TATAATATAA
*
141856 TAT-ATTTAAA
1 TATAATAT-AA
141866 TATAAT-TAA
1 TATAATATAA
141875 TATAATAT-A
1 TATAATATAA
*
141884 TTTAATATA
1 TATAATATA
141893 CGTATCATAT
Statistics
Matches: 47, Mismatches: 2, Indels: 13
0.76 0.03 0.21
Matches are distributed among these distances:
8 5 0.11
9 25 0.53
10 8 0.17
11 9 0.19
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (10 bp):
TATAATATAA
Found at i:141854 original size:13 final size:14
Alignment explanation
Indices: 141836--141892 Score: 61
Period size: 13 Copynumber: 4.4 Consensus size: 14
141826 CTATAATACT
141836 AATATAATATA-TA
1 AATATAATATATTA
*
141849 AATATAATATATTT
1 AATATAATATATTA
141863 AA-AT-ATA-ATT-
1 AATATAATATATTA
*
141873 AATATAATATATTT
1 AATATAATATATTA
141887 AATATA
1 AATATA
141893 CGTATCATAT
Statistics
Matches: 38, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
10 2 0.05
11 5 0.13
12 6 0.16
13 16 0.42
14 9 0.24
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
AATATAATATATTA
Found at i:141854 original size:24 final size:21
Alignment explanation
Indices: 141828--141883 Score: 62
Period size: 20 Copynumber: 2.6 Consensus size: 21
141818 AAATAGATCT
141828 ATAATACTAATATAATATATAAAT
1 ATAATA-TAATATAA-ATAT-AAT
*
141852 ATAATAT-ATTTAAATATAAT
1 ATAATATAATATAAATATAAT
141872 -TAATATAATATA
1 ATAATATAATATA
141884 TTTAATATAC
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
19 6 0.21
20 7 0.24
21 4 0.14
22 5 0.17
23 1 0.03
24 6 0.21
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (21 bp):
ATAATATAATATAAATATAAT
Found at i:141926 original size:16 final size:16
Alignment explanation
Indices: 141905--141939 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
141895 TATCATATTT
141905 ATATTTAAAAATTTAC
1 ATATTTAAAAATTTAC
*
141921 ATATTTAATAATTTAC
1 ATATTTAAAAATTTAC
141937 ATA
1 ATA
141940 ATATTATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.46
Consensus pattern (16 bp):
ATATTTAAAAATTTAC
Found at i:143045 original size:22 final size:22
Alignment explanation
Indices: 143010--143079 Score: 61
Period size: 22 Copynumber: 3.1 Consensus size: 22
143000 TTATTATTTT
*
143010 ATAATTTTAATTTTTTATAATTA
1 ATAA-TTTATTTTTTTATAATTA
*
143033 ATAATTTATTTTTATTATATTTA
1 ATAATTTATTTTT-TTATAATTA
* * *
143056 A-AATTAATATTTATAATAATTA
1 ATAATTTAT-TTTTTTATAATTA
143078 AT
1 AT
143080 TATGTTAATA
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
22 22 0.58
23 16 0.42
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
ATAATTTATTTTTTTATAATTA
Found at i:143078 original size:16 final size:16
Alignment explanation
Indices: 143057--143122 Score: 57
Period size: 16 Copynumber: 4.1 Consensus size: 16
143047 TTATATTTAA
143057 AATTAATATTTATAAT
1 AATTAATATTTATAAT
*
143073 AATTAATTATGT-TAAT
1 AATTAA-TATTTATAAT
*
143089 ATTTATTATATTTATAAT
1 AATTA--ATATTTATAAT
*
143107 TA-TAA-ATTTATAAT
1 AATTAATATTTATAAT
143121 AA
1 AA
143123 AAATAATTAA
Statistics
Matches: 40, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
14 10 0.25
15 1 0.03
16 14 0.35
17 10 0.25
18 5 0.12
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
AATTAATATTTATAAT
Found at i:143095 original size:47 final size:46
Alignment explanation
Indices: 143000--143130 Score: 135
Period size: 47 Copynumber: 2.9 Consensus size: 46
142990 ATTATTGTAA
* * * * *
143000 TTATTAT-TTTATAATT-TTAATTTTTTATAATTAATAATTTATTT
1 TTATTATATTTAAAATTATAAATTTATAATAATTAATAATTTATAT
* *
143044 TTATTATATTTAAAATTA-ATATTTATAATAATTAATTATGTTAATAT
1 TTATTATATTTAAAATTATAAATTTATAATAATTAATAAT-TT-ATAT
* *
143091 TTATTATATTTATAATTATAAATTTATAATAA-AAATAATT
1 TTATTATATTTAAAATTATAAATTTATAATAATTAATAATT
143131 AAAAAATACG
Statistics
Matches: 71, Mismatches: 11, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
44 7 0.10
45 24 0.34
46 3 0.04
47 25 0.35
48 12 0.17
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (46 bp):
TTATTATATTTAAAATTATAAATTTATAATAATTAATAATTTATAT
Found at i:143388 original size:5 final size:5
Alignment explanation
Indices: 143378--143443 Score: 57
Period size: 5 Copynumber: 13.2 Consensus size: 5
143368 AAAGATGTTA
* * *
143378 AATAT AATAT AA-A- AATAA AATTAT AATAT AATAT TATAT AAAAAT AATAT
1 AATAT AATAT AATAT AATAT AA-TAT AATAT AATAT AATAT -AATAT AATAT
143428 AAATAT AATAT -ATAT A
1 -AATAT AATAT AATAT A
143444 GATCAAATTT
Statistics
Matches: 50, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
3 2 0.04
4 6 0.12
5 30 0.60
6 12 0.24
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (5 bp):
AATAT
Found at i:143416 original size:29 final size:27
Alignment explanation
Indices: 143378--143443 Score: 89
Period size: 29 Copynumber: 2.4 Consensus size: 27
143368 AAAGATGTTA
*
143378 AATATAATATAAAAATAAAATTATAATAT
1 AATATTATATAAAAATAAAA-TA-AATAT
*
143407 AATATTATATAAAAATAATATAAATAT
1 AATATTATATAAAAATAAAATAAATAT
143434 AATA-TATATA
1 AATATTATATA
143444 GATCAAATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
26 6 0.17
27 9 0.26
28 2 0.06
29 18 0.51
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (27 bp):
AATATTATATAAAAATAAAATAAATAT
Found at i:145910 original size:11 final size:11
Alignment explanation
Indices: 145891--145925 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
145881 GAGGTGCTTA
145891 TAAATATTAAT
1 TAAATATTAAT
*
145902 TAAAAATTAAT
1 TAAATATTAAT
*
145913 TAATTATTAAT
1 TAAATATTAAT
145924 TA
1 TA
145926 TTTTTTTTAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (11 bp):
TAAATATTAAT
Found at i:146969 original size:182 final size:181
Alignment explanation
Indices: 146598--147106 Score: 955
Period size: 182 Copynumber: 2.8 Consensus size: 181
146588 ACCCCTCTCT
146598 TTTGCAGGTTTACTAACCCTTCAAGCCAATCTTCATGCTCGCCGAGCCTCTGATGTTGGCGTTCG
1 TTTGCAGGTTTACTAACCCTTCAAGCCAATCTTCATGCTCGCCGAGCCTCTGATGTTGGCGTTCG
*
146663 CGTTCTTCTTTTTCGTGGCGTGTGGGCTTACCAACACATCGACGTAAGTGAAACATTGCAGTGTT
66 CGTTCTTCTTTTTCGTGGCGTGTGGGCTTACCAACACATCGACGTAAGTGAAACATTGCAGTATT
*
146728 TGCAGTTGAAAAATTAGGAAATAGTTCCAAATTCGTCACTCTTTAGATTGC
131 TGCAATTGAAAAATTAGGAAATAGTTCCAAATTCGTCACTCTTTAGATTGC
146779 TTTGCAGGTTTACTAACCCTTCAAGCCAATCTTCATGCTCGCCGAGCCTCTGATGTTGGCGTTCG
1 TTTGCAGGTTTACTAACCCTTCAAGCCAATCTTCATGCTCGCCGAGCCTCTGATGTTGGCGTTCG
* * *
146844 CGTTCTTCTTTTTCGTGGCGTGTGTAGCTTACCTACACATCGACGTAACTGAAACATTGCAGTAT
66 CGTTCTTCTTTTTCGTGGCGTGTG-GGCTTACCAACACATCGACGTAAGTGAAACATTGCAGTAT
*
146909 TTGCAATTGAAAAATTAGGAAATATTTCCAAATTCGTCACTCTTTAGATTGC
130 TTGCAATTGAAAAATTAGGAAATAGTTCCAAATTCGTCACTCTTTAGATTGC
146961 TTTGCAGGTTTACTAACCCTTCAAGCCAATCTTCATGCTCGCCGAGCCTCTGATGTTGGCGTTCG
1 TTTGCAGGTTTACTAACCCTTCAAGCCAATCTTCATGCTCGCCGAGCCTCTGATGTTGGCGTTCG
147026 CGTTCTTCTTTTTCGTGGCGTGTGGGCTTACCAACACATCGACGTAAGTGAAACATTGCAGTATT
66 CGTTCTTCTTTTTCGTGGCGTGTGGGCTTACCAACACATCGACGTAAGTGAAACATTGCAGTATT
147091 TGCAATTGAAAAATTA
131 TGCAATTGAAAAATTA
147107 CCTACTCCTT
Statistics
Matches: 318, Mismatches: 9, Indels: 2
0.97 0.03 0.01
Matches are distributed among these distances:
181 143 0.45
182 175 0.55
ACGTcount: A:0.23, C:0.23, G:0.20, T:0.34
Consensus pattern (181 bp):
TTTGCAGGTTTACTAACCCTTCAAGCCAATCTTCATGCTCGCCGAGCCTCTGATGTTGGCGTTCG
CGTTCTTCTTTTTCGTGGCGTGTGGGCTTACCAACACATCGACGTAAGTGAAACATTGCAGTATT
TGCAATTGAAAAATTAGGAAATAGTTCCAAATTCGTCACTCTTTAGATTGC
Found at i:150126 original size:23 final size:23
Alignment explanation
Indices: 150086--150142 Score: 68
Period size: 23 Copynumber: 2.6 Consensus size: 23
150076 ATTTTTGTCA
150086 TATT-ATTTTTAT-TGTAT-TTTG
1 TATTAATTTTTATAT-TATATTTG
150107 -ATTAATTTTTATATTATATTTG
1 TATTAATTTTTATATTATATTTG
*
150129 TATTATTTTTTATA
1 TATTAATTTTTATA
150143 CACAAATTGA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
20 3 0.10
21 11 0.35
22 5 0.16
23 12 0.39
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.68
Consensus pattern (23 bp):
TATTAATTTTTATATTATATTTG
Found at i:151682 original size:8 final size:7
Alignment explanation
Indices: 151645--151683 Score: 51
Period size: 7 Copynumber: 5.3 Consensus size: 7
151635 ATAATTACTC
*
151645 TTAAAAT
1 TTAAATT
151652 TTAAATT
1 TTAAATT
151659 TTAAATT
1 TTAAATT
151666 TTAATATT
1 TTAA-ATT
151674 TATAAATT
1 T-TAAATT
151682 TT
1 TT
151684 TTTGATTATC
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
7 18 0.62
8 8 0.28
9 3 0.10
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
TTAAATT
Found at i:152167 original size:25 final size:26
Alignment explanation
Indices: 152125--152188 Score: 69
Period size: 25 Copynumber: 2.5 Consensus size: 26
152115 TAAAATATTT
*
152125 TATAAAATATGATATAAAAATAATA-AA
1 TATAAAAT-T-ATTTAAAAATAATATAA
* *
152152 TATAAAATTATTTAAAATTTATATAA
1 TATAAAATTATTTAAAAATAATATAA
152178 TAT-AAATTATT
1 TATAAAATTATT
152189 AATATGTTGA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
25 19 0.58
26 6 0.18
27 8 0.24
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.41
Consensus pattern (26 bp):
TATAAAATTATTTAAAAATAATATAA
Found at i:152183 original size:32 final size:32
Alignment explanation
Indices: 152147--152209 Score: 76
Period size: 32 Copynumber: 2.0 Consensus size: 32
152137 TATAAAAATA
152147 ATAAA-TATAAAATTAT-TTAAAATTTATATAAT
1 ATAAATTAT-AAA-TATGTTAAAATTTATATAAT
* *
152179 ATAAATTATTAATATGTTGAAATTTATATAA
1 ATAAATTATAAATATGTTAAAATTTATATAA
152210 AAATAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
31 3 0.11
32 21 0.78
33 3 0.11
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.44
Consensus pattern (32 bp):
ATAAATTATAAATATGTTAAAATTTATATAAT
Found at i:152799 original size:16 final size:16
Alignment explanation
Indices: 152775--152805 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
152765 AATATATTTT
152775 TATTAATTATTTATTA
1 TATTAATTATTTATTA
*
152791 TATTTATTATTTATT
1 TATTAATTATTTATT
152806 TAATGTTTAA
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TATTAATTATTTATTA
Found at i:153376 original size:179 final size:172
Alignment explanation
Indices: 153130--153689 Score: 420
Period size: 179 Copynumber: 3.3 Consensus size: 172
153120 GAAGTAGTTA
* * * * * * *
153130 AAATTTAAATTTAACTAAATTTAAAATGACAT-AAATTTATTTGATTCGTAAATAAATTTATGTA
1 AAATTTAAATTTAACTAAATTCAAAATGAC-TCAAATCTATCTAATTCGTAAACAAATGTACGTA
* ** * *
153194 AATCTATCATATCTGTTATTATCCCATAAAAAAAATTTGACATAAAGA-TTGATGACCGAAATTA
65 AATCTATCACATCTACTATTATCCCAT--AAAAAATTTGACATAAAAATTTG-TGACCAAAATTA
** ** *
153258 TCATTGATTTAA-TTTCTAATCTC-ATTTTTTCAATTTTATCTTAAATAACT
127 TCACCGATTTAACTTTC-AAT-TCAATTTTTTCAATCATAT-GT-AA-AA-T
* * *
153308 CAAATTTAAATTTAACTAAATCCAAAATAACTCAAATCTATCTAATAT-GTGAACAAATGTACGT
1 -AAATTTAAATTTAACTAAATTCAAAATGACTCAAATCTATCTAAT-TCGTAAACAAATGTACGT
* *
153372 AAATCTATCACATCTACTATTATCTCATAAAAAATTTGACATAAAAATTTGTGATCAAAATTATC
64 AAATCTATCACATCTACTATTATCCCATAAAAAATTTGACATAAAAATTTGTGACCAAAATTATC
*
153437 ACCGATTTAACTTTCAATTCAATTTTTTTAATCATATGTAAAAT
129 ACCGATTTAACTTTCAATTCAATTTTTTCAATCATATGTAAAAT
* * ** *
153481 -AATTCAAATCTAACTAAATTCAAAATGACTC-AA---ATCT-A-TC-TAAACAAATCCACTTAA
1 AAATTTAAATTTAACTAAATTCAAAATGACTCAAATCTATCTAATTCGTAAACAAATGTACGTAA
* * * * **
153538 ATCTA-CTACATCTACTACTATCTCATAAAAAATTTGAC-----AATTGGTGATCAAAATTATTG
66 ATCTATC-ACATCTACTATTATCCCATAAAAAATTTGACATAAAAATTTGTGACCAAAATTATCA
* * * * ** *
153597 TCTATTTAACTTTAAATCCAATTTTTTCAATTTTATTTAAGATAATT
130 CCGATTTAACTTTCAATTCAATTTTTTCAATCATATGT-A-A-AA-T
* * *
153644 CAAATTTAAAATTTAATTAAATTTAAAATAACTCAAATCTATCTAA
1 -AAATTT-AAATTTAACTAAATTCAAAATGACTCAAATCTATCTAA
153690 CTCTTAAATA
Statistics
Matches: 314, Mismatches: 48, Indels: 46
0.77 0.12 0.11
Matches are distributed among these distances:
159 48 0.15
160 1 0.00
161 1 0.00
162 2 0.01
163 2 0.01
164 49 0.16
165 4 0.01
166 23 0.07
167 6 0.02
170 6 0.02
171 28 0.09
173 1 0.00
174 2 0.01
175 2 0.01
176 3 0.01
177 54 0.17
178 8 0.03
179 73 0.23
180 1 0.00
ACGTcount: A:0.43, C:0.14, G:0.05, T:0.39
Consensus pattern (172 bp):
AAATTTAAATTTAACTAAATTCAAAATGACTCAAATCTATCTAATTCGTAAACAAATGTACGTAA
ATCTATCACATCTACTATTATCCCATAAAAAATTTGACATAAAAATTTGTGACCAAAATTATCAC
CGATTTAACTTTCAATTCAATTTTTTCAATCATATGTAAAAT
Found at i:153652 original size:16 final size:16
Alignment explanation
Indices: 153631--153681 Score: 59
Period size: 16 Copynumber: 3.1 Consensus size: 16
153621 TTTCAATTTT
*
153631 ATTTAAGATAATTCAA
1 ATTTAAAATAATTCAA
153647 ATTTAAAATTTAATT-AA
1 ATTTAAAA--TAATTCAA
*
153664 ATTTAAAATAACTCAA
1 ATTTAAAATAATTCAA
153680 AT
1 AT
153682 CTATCTAACT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
15 4 0.13
16 11 0.37
17 10 0.33
18 5 0.17
ACGTcount: A:0.53, C:0.06, G:0.02, T:0.39
Consensus pattern (16 bp):
ATTTAAAATAATTCAA
Found at i:153667 original size:17 final size:18
Alignment explanation
Indices: 153639--153672 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
153629 TTATTTAAGA
153639 TAATTCAAATTTAAAATT
1 TAATTCAAATTTAAAATT
153657 TAATT-AAATTTAAAAT
1 TAATTCAAATTTAAAAT
153673 AACTCAAATC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (18 bp):
TAATTCAAATTTAAAATT
Found at i:154012 original size:23 final size:24
Alignment explanation
Indices: 153985--154034 Score: 66
Period size: 25 Copynumber: 2.1 Consensus size: 24
153975 TATTATGATA
153985 AAATTAAA-AATAAAAATATTTAT
1 AAATTAAATAATAAAAATATTTAT
* *
154008 AAATTAAATTAATTAAAATTTTTAT
1 AAATTAAA-TAATAAAAATATTTAT
154033 AA
1 AA
154035 TTTTGAATCT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 8 0.35
25 15 0.65
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (24 bp):
AAATTAAATAATAAAAATATTTAT
Found at i:154435 original size:12 final size:13
Alignment explanation
Indices: 154420--154449 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
154410 TAATTTTTAT
154420 TTTAAAATATA-A
1 TTTAAAATATATA
154432 TTTAAAATATATA
1 TTTAAAATATATA
154445 TTTAA
1 TTTAA
154450 TTGTAAACTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.65
13 6 0.35
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
TTTAAAATATATA
Found at i:155417 original size:30 final size:32
Alignment explanation
Indices: 155381--155452 Score: 80
Period size: 31 Copynumber: 2.3 Consensus size: 32
155371 ATGATAAAAT
155381 TTTTTAAAAGTTTA-TGAAT-AA-AAAATATAA
1 TTTTTAAAAGTTTATTG-ATGAATAAAATATAA
* *
155411 TTTTTAAACG-TTATTGATGAATAAAATGTAA
1 TTTTTAAAAGTTTATTGATGAATAAAATATAA
*
155442 ATTTTAAAAGT
1 TTTTTAAAAGT
155453 CATAAATGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
29 5 0.15
30 13 0.38
31 16 0.47
ACGTcount: A:0.47, C:0.01, G:0.10, T:0.42
Consensus pattern (32 bp):
TTTTTAAAAGTTTATTGATGAATAAAATATAA
Found at i:156861 original size:2 final size:2
Alignment explanation
Indices: 156856--156882 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
156846 TGTGCGTGTA
156856 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
156883 AACCGCCAAA
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:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:159221 original size:19 final size:19
Alignment explanation
Indices: 159197--159273 Score: 77
Period size: 19 Copynumber: 4.0 Consensus size: 19
159187 ATTATTTATT
159197 TTTATTTTTAAATTTTTTA
1 TTTATTTTTAAATTTTTTA
**
159216 TTTATTTTTTTATTTTTCT-
1 TTTATTTTTAAATTTTT-TA
*
159235 TTTTTTTTTGAAATTTTGTTA
1 TTTATTTTT-AAATTTT-TTA
*
159256 ATTATTTTT-AATTTTTTA
1 TTTATTTTTAAATTTTTTA
159274 AATTTTGTGA
Statistics
Matches: 47, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
18 3 0.06
19 29 0.62
20 7 0.15
21 8 0.17
ACGTcount: A:0.21, C:0.01, G:0.03, T:0.75
Consensus pattern (19 bp):
TTTATTTTTAAATTTTTTA
Found at i:159224 original size:12 final size:12
Alignment explanation
Indices: 159188--159230 Score: 52
Period size: 12 Copynumber: 3.5 Consensus size: 12
159178 GTTACTTATA
159188 TTATTTATTTTT
1 TTATTTATTTTT
*
159200 ATT-TTTAAATTTT
1 -TTATTT-ATTTTT
159213 TTATTTATTTTT
1 TTATTTATTTTT
159225 TTATTT
1 TTATTT
159231 TTCTTTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
12 16 0.62
13 10 0.38
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (12 bp):
TTATTTATTTTT
Found at i:159272 original size:40 final size:39
Alignment explanation
Indices: 159183--159271 Score: 110
Period size: 39 Copynumber: 2.3 Consensus size: 39
159173 TTCATGTTAC
* *
159183 TTATATTATTTATTTTTATTTTTAAATTTTTTATTTATTT
1 TTATATT-TTTCTTTTTATTTTTAAATTTTTTAATTATTT
*
159223 TTTTATTTTTCTTTTT-TTTTTGAAATTTTGTTAATTATTT
1 TTATATTTTTCTTTTTATTTTT-AAATTTT-TTAATTATTT
159263 TTA-ATTTTT
1 TTATATTTTT
159272 TAAATTTTGT
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
38 5 0.12
39 21 0.49
40 17 0.40
ACGTcount: A:0.21, C:0.01, G:0.02, T:0.75
Consensus pattern (39 bp):
TTATATTTTTCTTTTTATTTTTAAATTTTTTAATTATTT
Found at i:161438 original size:123 final size:121
Alignment explanation
Indices: 161051--161443 Score: 385
Period size: 123 Copynumber: 3.2 Consensus size: 121
161041 AACACAACCA
* * * * * * *
161051 AAGGGATATGTTAGAGCTAATTTGGGTTGATGATGTGTTTACTGATTTTTATTGGGATTTCACGC
1 AAGGGATGTGTTGGGGCTAATTTGGGTTAATGATGTATTTATTGAGTTTTATT-GGATTTCACGC
* *
161116 TTAGGTTGCCTACTAAGCAATGTTATTAGCCATGTATTTTAGAGGTTAGTCTATGGCTC
65 TTAGGTTGCCTACTAAGCAATGTTATTAGCCAT-T-TTTTGGGGGTTAGTCTATGGCTC
* * * * * * *
161175 AAAGGATGCGTTGGGGCTAACTTTGAGTTAATGATGTATTAATTGGGTTTTATTAGGATTTTACA
1 AAGGGATGTGTTGGGGCTAA-TTTGGGTTAATGATGTATTTATTGAGTTTTATT-GGATTTCACG
* * * * * * * * *
161240 CTTACGTTGCCTATTAAGCAATGTCATTCGCTATGTTTTGAGGGTTAATCCATGGCTC
64 CTTAGGTTGCCTACTAAGCAATGTTATTAGCCATTTTTTGGGGGTTAGTCTATGGCTC
* *
161298 AAGAGATGTGTTGGGGCTAATATTGGGTTAATGATGTATTTATTAAGTTTTATTGGTATTTCACG
1 AAGGGATGTGTTGGGGCTAAT-TTGGGTTAATGATGTATTTATTGAGTTTTATTGG-ATTTCACG
** * * **
161363 CTTAGGTTGCCTACTAAATAGTGTTAGTAGCCATTTTTTGGGGGGTTAG-CTTATGATTC
64 CTTAGGTTGCCTACTAAGCAATGTTATTAGCCATTTTTT-GGGGGTTAGTC-TATGGCTC
*
161422 AAGGGATGTGGT-GGGCTAATTT
1 AAGGGATGTGTTGGGGCTAATTT
161444 TGAACTAATG
Statistics
Matches: 212, Mismatches: 52, Indels: 12
0.77 0.19 0.04
Matches are distributed among these distances:
122 5 0.02
123 107 0.50
124 37 0.17
125 63 0.30
ACGTcount: A:0.24, C:0.11, G:0.26, T:0.40
Consensus pattern (121 bp):
AAGGGATGTGTTGGGGCTAATTTGGGTTAATGATGTATTTATTGAGTTTTATTGGATTTCACGCT
TAGGTTGCCTACTAAGCAATGTTATTAGCCATTTTTTGGGGGTTAGTCTATGGCTC
Found at i:162072 original size:22 final size:19
Alignment explanation
Indices: 162005--162072 Score: 59
Period size: 22 Copynumber: 3.3 Consensus size: 19
161995 TGAGTTTTTA
162005 TATATTAT-TTTA-TAATT
1 TATATTATATTTAGTAATT
162022 TATATTTATATTTATGTAATT
1 TATA-TTATATTTA-GTAATT
162043 TGATTATTATATTTACGTAGATT
1 T-A-TATTATATTTA-GTA-ATT
162066 ATATATT
1 -TATATT
162073 TTAAATTTTA
Statistics
Matches: 42, Mismatches: 1, Indels: 11
0.78 0.02 0.20
Matches are distributed among these distances:
17 4 0.10
18 4 0.10
19 4 0.10
21 6 0.14
22 17 0.40
23 6 0.14
24 1 0.02
ACGTcount: A:0.34, C:0.01, G:0.06, T:0.59
Consensus pattern (19 bp):
TATATTATATTTAGTAATT
Found at i:162137 original size:24 final size:23
Alignment explanation
Indices: 162090--162136 Score: 78
Period size: 22 Copynumber: 2.1 Consensus size: 23
162080 TTAAATAAAT
162090 TAAAAATATTTAATTATTTGATA
1 TAAAAATATTTAATTATTTGATA
*
162113 TAAAAA-ATTTAATTATTTAATA
1 TAAAAATATTTAATTATTTGATA
162135 TA
1 TA
162137 TTAAAATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 17 0.74
23 6 0.26
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (23 bp):
TAAAAATATTTAATTATTTGATA
Found at i:162161 original size:29 final size:30
Alignment explanation
Indices: 162112--162174 Score: 76
Period size: 29 Copynumber: 2.1 Consensus size: 30
162102 ATTATTTGAT
* *
162112 ATAAAAAATTTAATTATTTAATATATTA-AA
1 ATAAAAAATTT-ATTAATTAATATAATATAA
162142 ATAAAAATATTT-TTAATTAATATAATATAA
1 ATAAAAA-ATTTATTAATTAATATAATATAA
162172 ATA
1 ATA
162175 TCAAATCAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 13 0.45
30 12 0.41
31 4 0.14
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (30 bp):
ATAAAAAATTTATTAATTAATATAATATAA
Found at i:162415 original size:14 final size:15
Alignment explanation
Indices: 162385--162417 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
162375 ATATGTTTTT
*
162385 ATAAATATCACTTAA
1 ATAAAGATCACTTAA
162400 ATAAAGATCA-TTAA
1 ATAAAGATCACTTAA
162414 ATAA
1 ATAA
162418 TAATTAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.58, C:0.09, G:0.03, T:0.30
Consensus pattern (15 bp):
ATAAAGATCACTTAA
Found at i:164383 original size:18 final size:19
Alignment explanation
Indices: 164362--164401 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
164352 TTATTTTTAT
164362 ATATTTTAATATTAAA-AA
1 ATATTTTAATATTAAATAA
*
164380 ATATTTTTATATTAAATAA
1 ATATTTTAATATTAAATAA
164399 ATA
1 ATA
164402 GGTAATTTAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
ATATTTTAATATTAAATAA
Found at i:164401 original size:29 final size:29
Alignment explanation
Indices: 164344--164401 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
164334 GTTTATTAAT
** *
164344 TTAAAAAATTATTTTTATATATTTTAATA
1 TTAAAAAATTATTTTTATATAAATAAATA
164373 TTAAAAAA-TATTTTTATATTAAATAAATA
1 TTAAAAAATTATTTTTATA-TAAATAAATA
164402 GGTAATTTAG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 10 0.40
29 15 0.60
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (29 bp):
TTAAAAAATTATTTTTATATAAATAAATA
Found at i:165642 original size:3 final size:3
Alignment explanation
Indices: 165634--165708 Score: 123
Period size: 3 Copynumber: 25.0 Consensus size: 3
165624 TTTTCCTATC
* * *
165634 TTA TTA TTA TTA TTA TTG TTA TTG TTG TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
165682 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
165709 CTTTGATTTA
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 68 1.00
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:168327 original size:4 final size:4
Alignment explanation
Indices: 168320--168362 Score: 59
Period size: 4 Copynumber: 10.8 Consensus size: 4
168310 TATATATATA
* * *
168320 TATG TATG TATG TATG TACG TAGG TATG TATA TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
168363 TGTGCCTGTT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.28, C:0.02, G:0.23, T:0.47
Consensus pattern (4 bp):
TATG
Found at i:170973 original size:16 final size:16
Alignment explanation
Indices: 170946--170992 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
170936 TGATTGATTC
*
170946 AAAATAAAAATAATTT
1 AAAATTAAAATAATTT
* * *
170962 GAATTTAAAATATTTT
1 AAAATTAAAATAATTT
170978 AAAATTAAAATAATT
1 AAAATTAAAATAATT
170993 CAAACTCAAA
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (16 bp):
AAAATTAAAATAATTT
Found at i:171176 original size:14 final size:14
Alignment explanation
Indices: 171157--171207 Score: 57
Period size: 14 Copynumber: 3.4 Consensus size: 14
171147 ATTTTTAAAA
171157 AATAAAAATTTTAG
1 AATAAAAATTTTAG
* *
171171 AATAAATAGTTTTAAAA
1 AATAAA-AATTTT--AG
171188 AATAAAAATTTTAG
1 AATAAAAATTTTAG
171202 AATAAA
1 AATAAA
171208 TAGTTGTATC
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
14 13 0.43
15 5 0.17
16 5 0.17
17 7 0.23
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (14 bp):
AATAAAAATTTTAG
Found at i:171184 original size:31 final size:31
Alignment explanation
Indices: 171149--171212 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
171139 ACAAGTATAT
171149 TTTTAAAAAATAAAAATTTTAGAATAAATAG
1 TTTTAAAAAATAAAAATTTTAGAATAAATAG
171180 TTTTAAAAAATAAAAATTTTAGAATAAATAG
1 TTTTAAAAAATAAAAATTTTAGAATAAATAG
171211 TT
1 TT
171213 GTATCCAAGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (31 bp):
TTTTAAAAAATAAAAATTTTAGAATAAATAG
Found at i:171329 original size:25 final size:25
Alignment explanation
Indices: 171295--171344 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
171285 CGAGTCCCCT
*
171295 TTTTTTCCTCATTATGGTCTAGAAG
1 TTTTTCCCTCATTATGGTCTAGAAG
*
171320 TTTTTCCCTCATTGTGGTCTAGAAG
1 TTTTTCCCTCATTATGGTCTAGAAG
171345 ATGAAACAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.18, C:0.18, G:0.18, T:0.46
Consensus pattern (25 bp):
TTTTTCCCTCATTATGGTCTAGAAG
Found at i:171445 original size:18 final size:16
Alignment explanation
Indices: 171422--171457 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 16
171412 TGTTTTTAAA
171422 AATTTTTTATGTTATTTT
1 AATTTTTTAT-TT-TTTT
171440 AATTTTTTATTTTTTT
1 AATTTTTTATTTTTTT
171456 AA
1 AA
171458 AATATTCGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 6 0.33
17 2 0.11
18 10 0.56
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.72
Consensus pattern (16 bp):
AATTTTTTATTTTTTT
Found at i:171751 original size:16 final size:16
Alignment explanation
Indices: 171730--171775 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 16
171720 TGATAATTTT
171730 AAAAATAAATATATAA
1 AAAAATAAATATATAA
*
171746 AAAAATATAATATGATAT
1 AAAAATA-AATAT-ATAA
171764 AAAAAT-AATATA
1 AAAAATAAATATA
171776 AATATAGTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
15 1 0.04
16 12 0.44
17 5 0.19
18 9 0.33
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (16 bp):
AAAAATAAATATATAA
Found at i:171767 original size:18 final size:16
Alignment explanation
Indices: 171729--171781 Score: 61
Period size: 18 Copynumber: 3.1 Consensus size: 16
171719 TTGATAATTT
171729 TAAAAATAAATATATA
1 TAAAAATAAATATATA
*
171745 AAAAAATATAATATGATA
1 TAAAAATA-AATAT-ATA
*
171763 TAAAAATAATATAAATA
1 TAAAAATAA-ATATATA
171780 TA
1 TA
171782 GTATAATATA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
16 7 0.23
17 11 0.35
18 13 0.42
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (16 bp):
TAAAAATAAATATATA
Found at i:171848 original size:18 final size:18
Alignment explanation
Indices: 171825--171886 Score: 54
Period size: 18 Copynumber: 3.4 Consensus size: 18
171815 AAAGATGATT
171825 AAAATATCAAAATTTATA
1 AAAATATCAAAATTTATA
*
171843 AAAATAT-AAAATATTTTA
1 AAAATATCAAAAT-TTATA
* ** *
171861 AATATGATCATGATATATA
1 AAAAT-ATCAAAATTTATA
171880 AAAATAT
1 AAAATAT
171887 ATAAATTATC
Statistics
Matches: 34, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
17 5 0.15
18 17 0.50
19 9 0.26
20 3 0.09
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.35
Consensus pattern (18 bp):
AAAATATCAAAATTTATA
Found at i:172065 original size:21 final size:20
Alignment explanation
Indices: 172036--172074 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
172026 TATATAAATA
172036 TTAATATAAAAATAATTTTT
1 TTAATATAAAAATAATTTTT
*
172056 TTAATAATAATAATAATTT
1 TTAAT-ATAAAAATAATTT
172075 AAGGCATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TTAATATAAAAATAATTTTT
Found at i:173166 original size:22 final size:22
Alignment explanation
Indices: 173138--173210 Score: 65
Period size: 22 Copynumber: 3.1 Consensus size: 22
173128 GTTATAATAA
173138 AAAAATAATTAAAATATTATAT
1 AAAAATAATTAAAATATTATAT
*
173160 AAAAATAATATAACATAATATAAATAT
1 AAAAATAAT-T-A-A-AATAT-TATAT
* * *
173187 AAAAATATTTTAAATTTTATAT
1 AAAAATAATTAAAATATTATAT
173209 AA
1 AA
173211 TATACATTAT
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
22 15 0.37
23 5 0.12
24 2 0.05
25 1 0.02
26 6 0.15
27 12 0.29
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (22 bp):
AAAAATAATTAAAATATTATAT
Found at i:173170 original size:11 final size:11
Alignment explanation
Indices: 173131--173188 Score: 57
Period size: 11 Copynumber: 5.4 Consensus size: 11
173121 CGAAAATGTT
*
173131 ATAATAAAAAA
1 ATAATATAAAA
173142 ATAAT-TAAAA
1 ATAATATAAAA
*
173152 TATTATATAAAA
1 -ATAATATAAAA
*
173164 ATAATAT-AAC
1 ATAATATAAAA
*
173174 ATAATATAAAT
1 ATAATATAAAA
173185 ATAA
1 ATAA
173189 AAATATTTTA
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
10 13 0.33
11 21 0.54
12 5 0.13
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (11 bp):
ATAATATAAAA
Found at i:173212 original size:33 final size:32
Alignment explanation
Indices: 173174--173249 Score: 89
Period size: 32 Copynumber: 2.3 Consensus size: 32
173164 ATAATATAAC
* *
173174 ATAATATAAATATAAAAATATTTTAAATTTTAT
1 ATAATATAAAT-TAAAAATATATTAAAATTTAT
* **
173207 ATAATATACATTATTAATATATTAAAATTTAT
1 ATAATATAAATTAAAAATATATTAAAATTTAT
173239 ATAAATATAAA
1 AT-AATATAAA
173250 ATATTTTAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
32 19 0.53
33 17 0.47
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.43
Consensus pattern (32 bp):
ATAATATAAATTAAAAATATATTAAAATTTAT
Found at i:173253 original size:40 final size:42
Alignment explanation
Indices: 173141--173253 Score: 105
Period size: 40 Copynumber: 2.8 Consensus size: 42
173131 ATAATAAAAA
* *
173141 AATA-ATTAAAATATTATATAAAAATAATATA-ACATAATAT
1 AATATATTAAAATATTATATAAATATAAAATATACATAATAT
* * *
173181 AA-ATATAAAAATATT-T-TAAATTTTATATAATATACATTAT-T
1 AATATATTAAAATATTATATAAA---TATAAAATATACATAATAT
173222 AATATATTAAAAT-TTATATAAATATAAAATAT
1 AATATATTAAAATATTATATAAATATAAAATAT
173254 TTTAAATATA
Statistics
Matches: 58, Mismatches: 7, Indels: 16
0.72 0.09 0.20
Matches are distributed among these distances:
38 4 0.07
39 2 0.03
40 21 0.36
41 11 0.19
42 16 0.28
43 4 0.07
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.41
Consensus pattern (42 bp):
AATATATTAAAATATTATATAAATATAAAATATACATAATAT
Found at i:174289 original size:176 final size:173
Alignment explanation
Indices: 173884--174365 Score: 460
Period size: 176 Copynumber: 2.8 Consensus size: 173
173874 CTGATCCAAA
* * * *
173884 TGGTGATAGAAATTATCACCTATTTAATCTCTTATCATATTGTTTCAATGTTATCTGAAATAATT
1 TGGTGATAGAAATTATCACCGATTTAATCT-TAATCA-ATTTTTTCAATTTTATCT-AAATAATT
* * * * * * * **
173949 CAAAGCCGATTTAATTAAATTCAAAATGATTTAAATTTATTTAACTCATGAATAAATTTATGTAA
63 CAAATCCAATATAACTAAATTCAAAATCATTCAAATTTATCTAACTCATGAATAAATTTACATAA
174014 ATCTACAATATCTACTACTATCCCATACAAAAATTGACATAAAGAT
128 ATCTACAATATCTACTACTATCCCATACAAAAATTGACATAAAGAT
* * * * ** * * *
174060 TGATTATCGAAATTATTATTGATTTGACCTTCAATCTAATTTTTTTAATTTTATCTAATATAATT
1 TGGTGATAGAAATTATCACCGATTTAATCTT-AATC-AATTTTTTCAATTTTATCTAA-ATAATT
* *
174125 CAAATCCAAATATAGCTAAATTCAGAATCATTCAAATTTATCTAACTCAT-ATATAAATTTACAT
63 CAAATCC-AATATAACTAAATTCAAAATCATTCAAATTTATCTAACTCATGA-ATAAATTTACAT
* * *
174189 AAATCTA-ACATATCTGCTACTATCTCATA-AAAAATTGACATAAATAT
126 AAATCTACA-ATATCTACTACTATCCCATACAAAAATTGACATAAAGAT
*
174236 TGGTGATAGAAATTATCACCGACTTAATCTTAGATTCAATTTTTTCAATTTTATCTAAAATAATT
1 TGGTGATAGAAATTATCACCGATTTAATCTTA-A-TCAATTTTTTCAATTTTATCT-AAATAATT
* * * * ** * *
174301 TAAAT-C----TAATTAAA-TCTAAAATAATTCAAATCTATCCGACTGATGAACAAATTTACATA
63 CAAATCCAATATAACTAAATTC-AAAATCATTCAAATTTATCTAACTCATGAATAAATTTACATA
174360 AATCTA
127 AATCTA
174366 TTACATCTCA
Statistics
Matches: 248, Mismatches: 47, Indels: 28
0.77 0.15 0.09
Matches are distributed among these distances:
169 2 0.01
170 45 0.18
171 1 0.00
175 5 0.02
176 121 0.49
177 74 0.30
ACGTcount: A:0.41, C:0.14, G:0.06, T:0.39
Consensus pattern (173 bp):
TGGTGATAGAAATTATCACCGATTTAATCTTAATCAATTTTTTCAATTTTATCTAAATAATTCAA
ATCCAATATAACTAAATTCAAAATCATTCAAATTTATCTAACTCATGAATAAATTTACATAAATC
TACAATATCTACTACTATCCCATACAAAAATTGACATAAAGAT
Found at i:174923 original size:26 final size:25
Alignment explanation
Indices: 174885--174949 Score: 60
Period size: 28 Copynumber: 2.5 Consensus size: 25
174875 TTATTAAAAT
* *
174885 AATTTTATATTAATAT-TTTTAATA
1 AATTTAATTTTAATATATTTTAATA
* *
174909 TATTATAAATTTTAAATTTATTTTAATA
1 AATT-T-AATTTT-AATATATTTTAATA
174937 AATTTAATTTTAA
1 AATTTAATTTTAA
174950 AATACATACT
Statistics
Matches: 32, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
24 3 0.09
25 3 0.09
26 10 0.31
27 5 0.16
28 11 0.34
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (25 bp):
AATTTAATTTTAATATATTTTAATA
Found at i:174940 original size:14 final size:15
Alignment explanation
Indices: 174921--174949 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
174911 TTATAAATTT
174921 TAAATTT-ATTTTAA
1 TAAATTTAATTTTAA
174935 TAAATTTAATTTTAA
1 TAAATTTAATTTTAA
174950 AATACATACT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TAAATTTAATTTTAA
Found at i:175218 original size:6 final size:6
Alignment explanation
Indices: 175201--175233 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
175191 TTTTTTATTT
175201 TATAAA TA-AAA TATAAA TATAAA TATAAA TATA
1 TATAAA TATAAA TATAAA TATAAA TATAAA TATA
175234 TATTTTATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (6 bp):
TATAAA
Found at i:175310 original size:25 final size:26
Alignment explanation
Indices: 175269--175319 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 26
175259 TTTAAAATAT
*
175269 ATTTAAAAATATATATTAATTATAAA
1 ATTTAAAAATATATATTAATAATAAA
*
175295 ATTTAAAAAT-TTTATTAATAATAAA
1 ATTTAAAAATATATATTAATAATAAA
175320 TGAGATAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 13 0.57
26 10 0.43
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (26 bp):
ATTTAAAAATATATATTAATAATAAA
Found at i:178628 original size:28 final size:27
Alignment explanation
Indices: 178575--178628 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
178565 TTTAATTAAT
* *
178575 TTTTATTTTTATATTATAAAATAAATA
1 TTTTATTTTTAAATTATAAAACAAATA
*
178602 TTTTATTTTTAAATTATTGAAACAAAT
1 TTTTATTTTTAAATTA-TAAAACAAAT
178629 TAAAATATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 15 0.65
28 8 0.35
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (27 bp):
TTTTATTTTTAAATTATAAAACAAATA
Found at i:179043 original size:14 final size:14
Alignment explanation
Indices: 179026--179071 Score: 65
Period size: 14 Copynumber: 3.2 Consensus size: 14
179016 TATTCACATC
*
179026 TATATATATATAGG
1 TATATATGTATAGG
*
179040 TATATATGTATATG
1 TATATATGTATAGG
179054 TATATATGTATATGG
1 TATATATGTATA-GG
179069 TAT
1 TAT
179072 TAGGAAGATG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
14 24 0.86
15 4 0.14
ACGTcount: A:0.37, C:0.00, G:0.15, T:0.48
Consensus pattern (14 bp):
TATATATGTATAGG
Found at i:181010 original size:22 final size:24
Alignment explanation
Indices: 180984--181028 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
180974 GTTCACGAAG
180984 AATAAGA-TTTTAAA-ATAAAAAT
1 AATAAGATTTTTAAATATAAAAAT
*
181006 AATAATATTTTTAAATATAAAAA
1 AATAAGATTTTTAAATATAAAAA
181029 AAATTTGGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 6 0.30
23 7 0.35
24 7 0.35
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (24 bp):
AATAAGATTTTTAAATATAAAAAT
Found at i:181915 original size:12 final size:12
Alignment explanation
Indices: 181898--181922 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
181888 CGTACATATA
181898 TCTGTGTGTGTG
1 TCTGTGTGTGTG
181910 TCTGTGTGTGTG
1 TCTGTGTGTGTG
181922 T
1 T
181923 GTCTATGATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.08, G:0.40, T:0.52
Consensus pattern (12 bp):
TCTGTGTGTGTG
Found at i:181919 original size:14 final size:14
Alignment explanation
Indices: 181900--181926 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
181890 TACATATATC
181900 TGTGTGTGTGTCTG
1 TGTGTGTGTGTCTG
181914 TGTGTGTGTGTCT
1 TGTGTGTGTGTCT
181927 ATGATATTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.00, C:0.07, G:0.41, T:0.52
Consensus pattern (14 bp):
TGTGTGTGTGTCTG
Found at i:182684 original size:2 final size:2
Alignment explanation
Indices: 182677--182718 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
182667 TATAAACGTG
*
182677 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CG CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
182719 ACTGGCAAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.48, C:0.50, G:0.02, T:0.00
Consensus pattern (2 bp):
CA
Found at i:182841 original size:12 final size:12
Alignment explanation
Indices: 182824--182851 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
182814 TCTTGTGTAG
182824 GACACATATTCA
1 GACACATATTCA
182836 GACACATATTCA
1 GACACATATTCA
182848 GACA
1 GACA
182852 TTGGTATAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.43, C:0.25, G:0.11, T:0.21
Consensus pattern (12 bp):
GACACATATTCA
Found at i:188784 original size:70 final size:70
Alignment explanation
Indices: 188696--188839 Score: 252
Period size: 70 Copynumber: 2.1 Consensus size: 70
188686 TATACGTCTA
* * *
188696 ACATGGGGTATGTTATTAAACTTTTTACATGTTTTTGAGAGATCATATTTTCATATTTATGTCCA
1 ACATGGGGTATGTTATTAAACTTTTTACATATATTTGAAAGATCATATTTTCATATTTATGTCCA
188761 AATAT
66 AATAT
*
188766 ACATTGGGTATGTTATTAAACTTTTTACATATATTTGAAAGATCATATTTTCATATTTATGTCCA
1 ACATGGGGTATGTTATTAAACTTTTTACATATATTTGAAAGATCATATTTTCATATTTATGTCCA
188831 AATAT
66 AATAT
188836 ACAT
1 ACAT
188840 CGGATACAGA
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
70 70 1.00
ACGTcount: A:0.33, C:0.10, G:0.12, T:0.45
Consensus pattern (70 bp):
ACATGGGGTATGTTATTAAACTTTTTACATATATTTGAAAGATCATATTTTCATATTTATGTCCA
AATAT
Found at i:190128 original size:21 final size:19
Alignment explanation
Indices: 190097--190137 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
190087 TTATTTTTTA
190097 ATATTTACTTTATAATATT
1 ATATTTACTTTATAATATT
*
190116 ATATATTATCTTTATATTATT
1 ATAT-TTA-CTTTATAATATT
190137 A
1 A
190138 AAATTACGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 4 0.21
20 3 0.16
21 12 0.63
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.59
Consensus pattern (19 bp):
ATATTTACTTTATAATATT
Found at i:193835 original size:21 final size:21
Alignment explanation
Indices: 193809--193852 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
193799 CGGCAGTTTA
*
193809 TTTTATTATTTAAAAAATTAT
1 TTTTATTATATAAAAAATTAT
* *
193830 TTTTATTATATGAATAATTAT
1 TTTTATTATATAAAAAATTAT
193851 TT
1 TT
193853 GTACTTTAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (21 bp):
TTTTATTATATAAAAAATTAT
Found at i:195027 original size:3 final size:3
Alignment explanation
Indices: 195019--195048 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
195009 TAATATATTT
195019 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
195049 TTGTATTAAA
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:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:195515 original size:14 final size:14
Alignment explanation
Indices: 195476--195516 Score: 55
Period size: 15 Copynumber: 2.8 Consensus size: 14
195466 AAACTACTTA
195476 ATTTAAATATTATAT
1 ATTTAAAT-TTATAT
*
195491 ATTTAAAATTTATTT
1 ATTT-AAATTTATAT
195506 ATTTAAATTTA
1 ATTTAAATTTA
195517 CTTCGATAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 7 0.29
15 13 0.54
16 4 0.17
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
ATTTAAATTTATAT
Found at i:196676 original size:15 final size:15
Alignment explanation
Indices: 196636--196684 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
196626 GCGATTTGAT
*
196636 TTAATTTATTAAAAAA
1 TTAATTTATT-TAAAA
*
196652 TTAA-TAATTTAAAA
1 TTAATTTATTTAAAA
*
196666 TTAATTTATTTAAAT
1 TTAATTTATTTAAAA
196681 TTAA
1 TTAA
196685 AATAATTTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
14 8 0.29
15 16 0.57
16 4 0.14
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
TTAATTTATTTAAAA
Found at i:196694 original size:16 final size:16
Alignment explanation
Indices: 196654--196726 Score: 76
Period size: 16 Copynumber: 4.6 Consensus size: 16
196644 TTAAAAAATT
196654 AATAATTTAAAATT-A
1 AATAATTTAAAATTAA
* * *
196669 ATTTATTTAAATTTAA
1 AATAATTTAAAATTAA
*
196685 AATAATTTAAAAATAA
1 AATAATTTAAAATTAA
* *
196701 AATAATTTACACTTAA
1 AATAATTTAAAATTAA
*
196717 AATAAATTAA
1 AATAATTTAA
196727 GCTTAAATTA
Statistics
Matches: 45, Mismatches: 12, Indels: 1
0.78 0.21 0.02
Matches are distributed among these distances:
15 11 0.24
16 34 0.76
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.40
Consensus pattern (16 bp):
AATAATTTAAAATTAA
Found at i:196709 original size:32 final size:32
Alignment explanation
Indices: 196654--196726 Score: 85
Period size: 32 Copynumber: 2.3 Consensus size: 32
196644 TTAAAAAATT
* * * *
196654 AATAATTT-AAAATTAATTTATTTAAATTTAA
1 AATAATTTAAAAATAAAATAATTTAAACTTAA
*
196685 AATAATTTAAAAATAAAATAATTTACACTTAA
1 AATAATTTAAAAATAAAATAATTTAAACTTAA
*
196717 AATAAATTAA
1 AATAATTTAA
196727 GCTTAAATTA
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
31 8 0.23
32 27 0.77
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.40
Consensus pattern (32 bp):
AATAATTTAAAAATAAAATAATTTAAACTTAA
Found at i:197779 original size:36 final size:36
Alignment explanation
Indices: 197737--197811 Score: 132
Period size: 36 Copynumber: 2.1 Consensus size: 36
197727 TTAATAGTTA
* *
197737 TAATAAACAATAATTATATCAAATGGAAATTAATAT
1 TAATAAACAATAATTATATCAAAGGGAAATAAATAT
197773 TAATAAACAATAATTATATCAAAGGGAAATAAATAT
1 TAATAAACAATAATTATATCAAAGGGAAATAAATAT
197809 TAA
1 TAA
197812 AAGTCATGAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.57, C:0.05, G:0.07, T:0.31
Consensus pattern (36 bp):
TAATAAACAATAATTATATCAAAGGGAAATAAATAT
Found at i:199495 original size:6 final size:6
Alignment explanation
Indices: 199484--199517 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
199474 AATCTATTCC
* *
199484 AAACAT AAACAT AAATAT AAATAT AAACAT AAAC
1 AAACAT AAACAT AAACAT AAACAT AAACAT AAAC
199518 TTATATATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.68, C:0.12, G:0.00, T:0.21
Consensus pattern (6 bp):
AAACAT
Found at i:199712 original size:25 final size:27
Alignment explanation
Indices: 199682--199754 Score: 80
Period size: 28 Copynumber: 2.7 Consensus size: 27
199672 TAACATCAAC
199682 ATAATAAAAA-AT-TA-AAATATATTAA
1 ATAATAAAAATATATATAAATATA-TAA
199707 ATAATAAAAATATAATATAAATATATAA
1 ATAATAAAAATAT-ATATAAATATATAA
* *
199735 ATAATTTAAAATTTATATAA
1 ATAA-TAAAAATATATATAA
199755 TATTAATTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
25 10 0.24
26 2 0.05
28 15 0.37
29 14 0.34
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (27 bp):
ATAATAAAAATATATATAAATATATAA
Found at i:199726 original size:16 final size:17
Alignment explanation
Indices: 199694--199739 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 17
199684 AATAAAAAAT
199694 TAAAATATATTAAATAA
1 TAAAATATATTAAATAA
199711 TAAAA-ATA-T-AAT-A
1 TAAAATATATTAAATAA
199724 T-AAATATA-TAAATAA
1 TAAAATATATTAAATAA
199739 T
1 T
199740 TTAAAATTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
12 3 0.12
13 6 0.23
14 6 0.23
15 3 0.12
16 3 0.12
17 5 0.19
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
TAAAATATATTAAATAA
Found at i:199744 original size:47 final size:50
Alignment explanation
Indices: 199639--199746 Score: 118
Period size: 47 Copynumber: 2.2 Consensus size: 50
199629 AATTTCACTT
* * *
199639 ATAATTTATAATAAAATTAAGTAATATTAAATATAACATCAACATAATAA
1 ATAATTTAAAATAAAATTAAATAATATAAAATATAACATCAACATAATAA
* * *
199689 A-AAATTAAAAT-ATATTAAATAATA-AAAATATAATAT-AA-ATATATAA
1 ATAATTTAAAATAAAATTAAATAATATAAAATATAACATCAACATA-ATAA
199735 ATAATTTAAAAT
1 ATAATTTAAAAT
199747 TTATATAATA
Statistics
Matches: 49, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
45 3 0.06
46 7 0.14
47 19 0.39
48 11 0.22
49 8 0.16
50 1 0.02
ACGTcount: A:0.62, C:0.03, G:0.01, T:0.34
Consensus pattern (50 bp):
ATAATTTAAAATAAAATTAAATAATATAAAATATAACATCAACATAATAA
Found at i:199781 original size:31 final size:33
Alignment explanation
Indices: 199716--199794 Score: 92
Period size: 33 Copynumber: 2.4 Consensus size: 33
199706 AATAATAAAA
199716 ATATAATATAAATATATAAATAATTTAAAATTT
1 ATATAATATAAATATATAAATAATTTAAAATTT
* *
199749 ATATAATATTAAT-TATTAATAGA-TT-AAATTT
1 ATATAATATAAATATATAAATA-ATTTAAAATTT
199780 ATATAAAATATAAAT
1 ATAT--AATATAAAT
199795 TTTATATAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
31 10 0.25
32 9 0.22
33 21 0.52
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (33 bp):
ATATAATATAAATATATAAATAATTTAAAATTT
Found at i:199800 original size:18 final size:17
Alignment explanation
Indices: 199720--199807 Score: 62
Period size: 18 Copynumber: 5.2 Consensus size: 17
199710 ATAAAAATAT
*
199720 AATATAAATATATA-AA
1 AATATAAATTTATATAA
*
199736 TAATTTAAAATTTATAT--
1 -AATAT-AAATTTATATAA
*
199753 AATATTAA-TTAT-TAA
1 AATATAAATTTATATAA
199768 TAGAT-TAAATTTATATAA
1 -A-ATATAAATTTATATAA
199786 AATATAAATTTTATATAA
1 AATATAAA-TTTATATAA
199804 AATA
1 AATA
199808 ATATATTAAA
Statistics
Matches: 56, Mismatches: 5, Indels: 19
0.70 0.06 0.24
Matches are distributed among these distances:
13 1 0.02
14 4 0.07
15 2 0.04
16 10 0.18
17 15 0.27
18 24 0.43
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (17 bp):
AATATAAATTTATATAA
Found at i:200410 original size:5 final size:5
Alignment explanation
Indices: 200396--200487 Score: 67
Period size: 5 Copynumber: 20.2 Consensus size: 5
200386 GTGAAATAAA
* *
200396 AATA- AATAT AATAT AATAT AATAT AATA- AA-A- AATAA AAAAT AATAT
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT
* * * *
200442 AA-AT AA-AT AA-AT ATTTT AATAT TATAT AATAT AA-A- ACTAT AATAT
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT
200487 A
1 A
200488 TTAAAATTTA
Statistics
Matches: 71, Mismatches: 11, Indels: 11
0.76 0.12 0.12
Matches are distributed among these distances:
3 4 0.06
4 20 0.28
5 47 0.66
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.35
Consensus pattern (5 bp):
AATAT
Found at i:200429 original size:27 final size:27
Alignment explanation
Indices: 200391--200475 Score: 84
Period size: 27 Copynumber: 3.1 Consensus size: 27
200381 TTTATGTGAA
200391 ATAA-AAATAAATATAATATAATATAAT
1 ATAATAAA-AAATATAATATAATATAAT
* *
200418 ATAATAAAAAATAAAAAATAATATAA-
1 ATAATAAAAAATATAATATAATATAAT
* * * *
200444 ATAAATAAATATTTTAATATTATATAAT
1 AT-AATAAAAAATATAATATAATATAAT
200472 ATAA
1 ATAA
200476 AACTATAATA
Statistics
Matches: 47, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
26 2 0.04
27 40 0.85
28 5 0.11
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (27 bp):
ATAATAAAAAATATAATATAATATAAT
Found at i:200501 original size:59 final size:56
Alignment explanation
Indices: 200438--200550 Score: 138
Period size: 58 Copynumber: 2.0 Consensus size: 56
200428 ATAAAAAATA
* * *
200438 ATATAAATAAATAA-ATATTTTAATATTATATAATATAAAACTATAATATATTAAAATTT
1 ATATAAATAAA-AATAT-TTTTAAAATTATATAATAAAAAAATATAA-ATA-TAAAATTT
* *
200497 ATATAAATAAAAATATTTTTAAAATTTTATTATAAAAAAATATAAATATAAAAT
1 ATATAAATAAAAATATTTTTAAAATTATATAATAAAAAAATATAAATATAAAAT
200551 AAATACACAA
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
56 6 0.12
57 3 0.06
58 26 0.54
59 13 0.27
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (56 bp):
ATATAAATAAAAATATTTTTAAAATTATATAATAAAAAAATATAAATATAAAATTT
Found at i:200518 original size:27 final size:28
Alignment explanation
Indices: 200438--200540 Score: 90
Period size: 27 Copynumber: 3.6 Consensus size: 28
200428 ATAAAAAATA
*
200438 ATATAAATAAATAA-ATATTTTAATA-TT
1 ATATAAATAAA-AATATATTTTAAAATTT
*
200465 ATATAATATAAAACTATAATATATTAAAATTT
1 ATATAA-ATAAAA--AT-ATATTTTAAAATTT
200497 ATATAAATAAAAATAT-TTTTAAAATTT
1 ATATAAATAAAAATATATTTTAAAATTT
200524 -TATTATAA-AAAAATATA
1 ATA-TA-AATAAAAATATA
200541 AATATAAAAT
Statistics
Matches: 64, Mismatches: 3, Indels: 17
0.76 0.04 0.20
Matches are distributed among these distances:
26 2 0.03
27 27 0.42
28 9 0.14
29 3 0.05
31 15 0.23
32 8 0.12
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (28 bp):
ATATAAATAAAAATATATTTTAAAATTT
Found at i:200600 original size:24 final size:24
Alignment explanation
Indices: 200573--200687 Score: 111
Period size: 24 Copynumber: 5.0 Consensus size: 24
200563 TTTAAGTTTA
200573 ATAATATAAATATATAAAATAAAT
1 ATAATATAAATATATAAAATAAAT
* *
200597 ATAATATAAAAATATATAATTAAA-
1 ATAATATAAATATATA-AAATAAAT
200621 ATAATAT--ATA-A-AAAATTAAAT
1 ATAATATAAATATATAAAA-TAAAT
*
200642 ATAATATAAATATTTTAAAAT--AT
1 ATAATATAAATA-TATAAAATAAAT
200665 ATAATATAAAT-TATTAAAATAAA
1 ATAATATAAATATA-TAAAATAAA
200688 AAAATTATAA
Statistics
Matches: 74, Mismatches: 6, Indels: 22
0.73 0.06 0.22
Matches are distributed among these distances:
19 2 0.03
20 5 0.07
21 9 0.12
22 8 0.11
23 16 0.22
24 23 0.31
25 7 0.09
26 4 0.05
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (24 bp):
ATAATATAAATATATAAAATAAAT
Found at i:200605 original size:16 final size:16
Alignment explanation
Indices: 200584--200651 Score: 81
Period size: 16 Copynumber: 4.4 Consensus size: 16
200574 TAATATAAAT
200584 ATATAAAATAAATATA
1 ATATAAAATAAATATA
*
200600 ATATAAAA-ATATATA
1 ATATAAAATAAATATA
200615 AT-TAAAATAATATATA
1 ATATAAAATAA-ATATA
*
200631 A-A-AAATTAAATATA
1 ATATAAAATAAATATA
200645 ATATAAA
1 ATATAAA
200652 TATTTTAAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
14 11 0.25
15 16 0.36
16 17 0.39
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
ATATAAAATAAATATA
Found at i:200652 original size:16 final size:17
Alignment explanation
Indices: 200572--200651 Score: 84
Period size: 15 Copynumber: 5.1 Consensus size: 17
200562 TTTTAAGTTT
*
200572 AATAATATAAATATATAA
1 AATAATATATA-ATATAA
200590 AATAA-ATATAATAT-A
1 AATAATATATAATATAA
200605 AA-AATATATAAT-TAA
1 AATAATATATAATATAA
200620 AATAATATATAA-A-AA
1 AATAATATATAATATAA
*
200635 ATTAA-ATATAATATAA
1 AATAATATATAATATAA
200651 A
1 A
200652 TATTTTAAAA
Statistics
Matches: 54, Mismatches: 2, Indels: 14
0.77 0.03 0.20
Matches are distributed among these distances:
14 9 0.17
15 20 0.37
16 16 0.30
17 4 0.07
18 5 0.09
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
AATAATATATAATATAA
Found at i:200670 original size:23 final size:22
Alignment explanation
Indices: 200640--200685 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 22
200630 AAAAAATTAA
*
200640 ATATAATATAAATATTTTAAAAT
1 ATATAATATAAAT-TATTAAAAT
200663 ATATAATATAAATTATTAAAAT
1 ATATAATATAAATTATTAAAAT
200685 A
1 A
200686 AAAAAATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 9 0.41
23 13 0.59
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (22 bp):
ATATAATATAAATTATTAAAAT
Found at i:200901 original size:2 final size:2
Alignment explanation
Indices: 200896--200920 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
200886 GCAAAAAAAA
200896 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 A
200921 AATTTTCGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:202588 original size:18 final size:18
Alignment explanation
Indices: 202544--202591 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
202534 TATTTATAAG
* *
202544 ATTTGTATTTATTATATT
1 ATTTATATTTATTAAATT
*
202562 ATTTTTATTTATTAAA-T
1 ATTTATATTTATTAAATT
202579 ATATTATATTTAT
1 AT-TTATATTTAT
202592 ATTATATTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
17 3 0.12
18 23 0.88
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (18 bp):
ATTTATATTTATTAAATT
Found at i:204741 original size:32 final size:31
Alignment explanation
Indices: 204688--204793 Score: 99
Period size: 32 Copynumber: 3.4 Consensus size: 31
204678 TAAATTTTAC
* *
204688 AATTTAAA--AATATTAAGATATTAAAAATT
1 AATTTAAATTAATATTTATATATTAAAAATT
* * *
204717 ATTTTAATATTAATATTTATATATTTATAATT
1 AATTTAA-ATTAATATTTATATATTAAAAATT
* * *
204749 AAATTTAAATAAATATTTTTATTATTAAATATT
1 -AATTTAAATTAATATTTATA-TATTAAAAATT
204782 AATTTAAATTAA
1 AATTTAAATTAA
204794 ATCAAAATTA
Statistics
Matches: 60, Mismatches: 12, Indels: 7
0.76 0.15 0.09
Matches are distributed among these distances:
29 6 0.10
30 1 0.02
32 39 0.65
33 14 0.23
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (31 bp):
AATTTAAATTAATATTTATATATTAAAAATT
Found at i:207250 original size:60 final size:59
Alignment explanation
Indices: 207134--207267 Score: 162
Period size: 60 Copynumber: 2.2 Consensus size: 59
207124 TCAAAATTTT
* * *
207134 GATTTCAATAGTTAGATCTATTCATAATCGAGTAATTTGCCCGATCAACATGTATTAAATGA
1 GATTTCAATA--TAGATCTATTCATAATCGAGTAATCTACCCGATCAACATCTATTAAAT-A
* *
207196 GATTTCAATATAGATCTATTCATAATCGAGTAATCTACTCGATCAGTC-TCTATTAAATA
1 GATTTCAATATAGATCTATTCATAATCGAGTAATCTACCCGATCA-ACATCTATTAAATA
*
207255 GAATTTCAGTATA
1 G-ATTTCAATATA
207268 AATTTTTTTA
Statistics
Matches: 64, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
59 2 0.03
60 51 0.80
61 1 0.02
62 10 0.16
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.37
Consensus pattern (59 bp):
GATTTCAATATAGATCTATTCATAATCGAGTAATCTACCCGATCAACATCTATTAAATA
Found at i:208302 original size:21 final size:20
Alignment explanation
Indices: 208262--208307 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 20
208252 AAGTAATTAC
208262 AAATTTTTAAATTTAAATTTT
1 AAATTTTTAAATTT-AATTTT
*
208283 AAATTTATTAAATATTATTTTT
1 AAATTT-TTAAAT-TTAATTTT
208305 AAA
1 AAA
208308 AAATAATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 6 0.27
22 14 0.64
23 2 0.09
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
AAATTTTTAAATTTAATTTT
Found at i:208556 original size:3 final size:3
Alignment explanation
Indices: 208548--208579 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
208538 TAATCAAGAT
208548 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
208580 TTTAAATTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:208921 original size:16 final size:15
Alignment explanation
Indices: 208895--208950 Score: 53
Period size: 15 Copynumber: 3.7 Consensus size: 15
208885 ATAATTTTTA
*
208895 TTAAATATTATAATTT
1 TTAAATTTTAT-ATTT
208911 TTAAA-TTT-TATTT
1 TTAAATTTTATATTT
*
208924 TTAGTAATTTAATATTT
1 TTA--AATTTTATATTT
208941 TTAAATTTTA
1 TTAAATTTTA
208951 AAATATAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
13 7 0.21
14 1 0.03
15 10 0.30
16 7 0.21
17 8 0.24
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (15 bp):
TTAAATTTTATATTT
Found at i:209567 original size:2 final size:2
Alignment explanation
Indices: 209560--209598 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
209550 TTTGAATCAG
209560 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
209599 GCTAACAGAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:209793 original size:2 final size:2
Alignment explanation
Indices: 209786--209815 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
209776 TTAAGTGGGG
209786 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
209816 GAGAATTTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:210425 original size:11 final size:11
Alignment explanation
Indices: 210409--210435 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
210399 AAAAAAGTTA
210409 AAATTAAAAAT
1 AAATTAAAAAT
210420 AAATTAAAAAT
1 AAATTAAAAAT
210431 AAATT
1 AAATT
210436 TCGAATATGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (11 bp):
AAATTAAAAAT
Found at i:210767 original size:48 final size:47
Alignment explanation
Indices: 210683--210792 Score: 109
Period size: 48 Copynumber: 2.3 Consensus size: 47
210673 TGAGTTTTAA
* **
210683 AATAATAATTTATAAATTTAAATTTATTTATTATATA-ATAATAATAA-T
1 AATAATAATTT-T-TATTTAAATTTATTTAAAATATATA-AATAATAATT
*
210731 AATAATAATTTTTATTTAAATTTAATTATAAAATATATAAATATTAATT
1 AATAATAATTTTTATTTAAATTT-ATT-TAAAATATATAAATAATAATT
*
210780 AAAAAT-ATTTTTA
1 AATAATAATTTTTA
210793 ATATTAACGT
Statistics
Matches: 53, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
46 10 0.19
47 4 0.08
48 32 0.60
49 7 0.13
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (47 bp):
AATAATAATTTTTATTTAAATTTATTTAAAATATATAAATAATAATT
Found at i:210799 original size:22 final size:22
Alignment explanation
Indices: 210747--210787 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
210737 AATTTTTATT
210747 TAAAT-TTAATTATAAAATATA
1 TAAATATTAATTATAAAATATA
210768 TAAATATTAATTA-AAAATAT
1 TAAATATTAATTATAAAATAT
210788 TTTTAATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (22 bp):
TAAATATTAATTATAAAATATA
Found at i:211177 original size:11 final size:10
Alignment explanation
Indices: 211155--211184 Score: 51
Period size: 11 Copynumber: 2.9 Consensus size: 10
211145 TCATCATCCA
211155 TTATAGCCCT
1 TTATAGCCCT
211165 TTATAGTCCCT
1 TTATAG-CCCT
211176 TTATAGCCC
1 TTATAGCCC
211185 CAGAATCAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.20, C:0.30, G:0.10, T:0.40
Consensus pattern (10 bp):
TTATAGCCCT
Found at i:218289 original size:19 final size:19
Alignment explanation
Indices: 218250--218289 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
218240 ATTTGAGTAT
*
218250 TTTAATAATTATAATTTTA
1 TTTAATAATTATAATTATA
218269 TTTAATAATT-TATATTATA
1 TTTAATAATTATA-ATTATA
218288 TT
1 TT
218290 AATTTTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 2 0.11
19 17 0.89
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
TTTAATAATTATAATTATA
Found at i:219961 original size:2 final size:2
Alignment explanation
Indices: 219954--219997 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
219944 TTAGGTGAGG
219954 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
219996 AT
1 AT
219998 GAGAATTTAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:220523 original size:23 final size:23
Alignment explanation
Indices: 220488--220531 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
220478 TTTAGTTATT
220488 TTTAATATGTGAA-ATTTAATAAA
1 TTTAATATGTGAATA-TTAATAAA
* *
220511 TTTAATGTTTGAATATTAATA
1 TTTAATATGTGAATATTAATA
220532 TTTATTATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 17 0.94
24 1 0.06
ACGTcount: A:0.43, C:0.00, G:0.09, T:0.48
Consensus pattern (23 bp):
TTTAATATGTGAATATTAATAAA
Found at i:220946 original size:22 final size:19
Alignment explanation
Indices: 220916--220957 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 19
220906 AATATTTATT
220916 TAAATTTAATTATAAAATATA
1 TAAATTTAA-TA-AAAATATA
220937 TAAATATTAATAAAAATATA
1 TAAAT-TTAATAAAAATATA
220957 T
1 T
220958 TTTTAATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 9 0.45
21 7 0.35
22 4 0.20
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
TAAATTTAATAAAAATATA
Found at i:221471 original size:17 final size:19
Alignment explanation
Indices: 221449--221490 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
221439 ATAATTTATA
221449 TTATATAAAT-TA-AATAT
1 TTATATAAATGTATAATAT
*
221466 TTATATATATGTATAATAT
1 TTATATAAATGTATAATAT
221485 TTATAT
1 TTATAT
221491 TATTTTTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 9 0.41
18 2 0.09
19 11 0.50
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (19 bp):
TTATATAAATGTATAATAT
Found at i:222163 original size:8 final size:8
Alignment explanation
Indices: 222150--222175 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
222140 TAAATGTTAA
222150 AAAAAATT
1 AAAAAATT
222158 AAAAAATT
1 AAAAAATT
222166 AAAAAATT
1 AAAAAATT
222174 AA
1 AA
222176 CTAAACAGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (8 bp):
AAAAAATT
Found at i:223557 original size:20 final size:20
Alignment explanation
Indices: 223532--223575 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
223522 AAGAATTGAA
223532 GAGGGATACAAGAGAGGGAC
1 GAGGGATACAAGAGAGGGAC
** *
223552 GAGGGATACTTGAGAGGGAG
1 GAGGGATACAAGAGAGGGAC
223572 GAGG
1 GAGG
223576 AAGCCTCTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.34, C:0.07, G:0.50, T:0.09
Consensus pattern (20 bp):
GAGGGATACAAGAGAGGGAC
Found at i:225631 original size:21 final size:21
Alignment explanation
Indices: 225620--225673 Score: 90
Period size: 21 Copynumber: 2.5 Consensus size: 21
225610 CCACCTGTTT
225620 TGGAGTATACTCCACCTGCCG
1 TGGAGTATACTCCACCTGCCG
225641 TGGAGTATACTCCACCTGCCG
1 TGGAGTATACTCCACCTGCCG
*
225662 CGGAGTACTACT
1 TGGAGTA-TACT
225674 TGTCTGAACA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 27 0.87
22 4 0.13
ACGTcount: A:0.20, C:0.31, G:0.24, T:0.24
Consensus pattern (21 bp):
TGGAGTATACTCCACCTGCCG
Found at i:228151 original size:20 final size:20
Alignment explanation
Indices: 228126--228169 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
228116 AAGAATTGAA
*
228126 GAGGGATACAAGAGAGGGAT
1 GAGGGATACAAGAGAGGGAG
**
228146 GAGGGATACTTGAGAGGGAG
1 GAGGGATACAAGAGAGGGAG
228166 GAGG
1 GAGG
228170 AAGCCTCTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.34, C:0.05, G:0.50, T:0.11
Consensus pattern (20 bp):
GAGGGATACAAGAGAGGGAG
Done.