Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold4
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: 5986281
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.33
Warning! 213817 characters in sequence are not A, C, G, or T
File 1 of 31
Found at i:5546 original size:2 final size:2
Alignment explanation
Indices: 5539--5565 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5529 TCACAGAACA
5539 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
5566 TTATACAATA
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:5781 original size:4 final size:4
Alignment explanation
Indices: 5774--5806 Score: 66
Period size: 4 Copynumber: 8.2 Consensus size: 4
5764 ATATACATAG
5774 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
5807 TACACACATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:7885 original size:2 final size:2
Alignment explanation
Indices: 7878--7906 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
7868 TTAAGCAAAC
7878 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 T
7907 TATTGAACCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:8021 original size:2 final size:2
Alignment explanation
Indices: 8014--8039 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
8004 TTATAAACTG
8014 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
8040 GTTATGAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:8942 original size:3 final size:3
Alignment explanation
Indices: 8934--8964 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
8924 AGTCATTATC
8934 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
8965 AACCTCTCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:9698 original size:20 final size:20
Alignment explanation
Indices: 9673--9725 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
9663 TAAACTGATT
*
9673 GATCTAATATAATAATCACA
1 GATCTAATAAAATAATCACA
*
9693 GATCTACTAAAATAATCACA
1 GATCTAATAAAATAATCACA
*
9713 GATCTACTAAAAT
1 GATCTAATAAAAT
9726 CCCTTGTGCT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.49, C:0.17, G:0.06, T:0.28
Consensus pattern (20 bp):
GATCTAATAAAATAATCACA
Found at i:10809 original size:4 final size:4
Alignment explanation
Indices: 10800--10835 Score: 72
Period size: 4 Copynumber: 9.0 Consensus size: 4
10790 CCCTTAGTGG
10800 CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA
10836 TATATATATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
CATA
Found at i:11196 original size:2 final size:2
Alignment explanation
Indices: 11189--11226 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
11179 TTTAAACACG
11189 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
11227 AATCCATATG
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13427 original size:7 final size:7
Alignment explanation
Indices: 13393--13594 Score: 109
Period size: 7 Copynumber: 28.4 Consensus size: 7
13383 TTTTTATCCG
*
13393 AACCCCG
1 AACCCCA
*
13400 AACCCCG
1 AACCCCA
13407 AACCCCA
1 AACCCCA
*
13414 TACCCCA
1 AACCCCA
13421 AACCCCA
1 AACCCCA
* *
13428 GACCCTTA
1 AACCC-CA
*
13436 AACCCTA
1 AACCCCA
*
13443 AACCCTTA
1 AACCC-CA
*
13451 AACCCTA
1 AACCCCA
13458 AACCCCA
1 AACCCCA
*
13465 AACCTCA
1 AACCCCA
13472 AACCCCA
1 AACCCCA
* *
13479 AACTCAA
1 AACCCCA
*
13486 AACCCGA
1 AACCCCA
* **
13493 TACCCGG
1 AACCCCA
13500 AACCCCA
1 AACCCCA
***
13507 AACTTTA
1 AACCCCA
* *
13514 AACCTCG
1 AACCCCA
*
13521 AACCCTA
1 AACCCCA
13528 AACCCCA
1 AACCCCA
**
13535 AACCTTA
1 AACCCCA
**
13542 AACTTCA
1 AACCCCA
13549 AACCCCA
1 AACCCCA
*
13556 AACCCTTA
1 AACCC-CA
13564 AACCCCA
1 AACCCCA
*
13571 AA-CCCT
1 AACCCCA
13577 AACTCCCA
1 AAC-CCCA
*
13585 AACCCTA
1 AACCCCA
13592 AAC
1 AAC
13595 TCTAGCCTCG
Statistics
Matches: 151, Mismatches: 39, Indels: 10
0.75 0.19 0.05
Matches are distributed among these distances:
6 5 0.03
7 122 0.81
8 24 0.16
ACGTcount: A:0.39, C:0.46, G:0.03, T:0.12
Consensus pattern (7 bp):
AACCCCA
Found at i:13552 original size:28 final size:28
Alignment explanation
Indices: 13500--13620 Score: 86
Period size: 28 Copynumber: 4.3 Consensus size: 28
13490 CGATACCCGG
* * *
13500 AACCCCAAACTTTAAACCTCGAACCCTA
1 AACCCCAAACCTTAAACCTCAAACCCCA
*
13528 AACCCCAAACCTTAAACTTCAAACCCCA
1 AACCCCAAACCTTAAACCTCAAACCCCA
* ** *
13556 AACCCTTAAACCCCAAACC-CTAACTCCCA
1 AACCC-CAAACCTTAAACCTCAAAC-CCCA
* * *
13585 AACCCTAAA-CTCT-AGCCTCGAACCCCTA
1 AACCCCAAACCT-TAAACCTCAAACCCC-A
13613 AACCCCAA
1 AACCCCAA
13621 CCTCAAATCT
Statistics
Matches: 74, Mismatches: 14, Indels: 10
0.76 0.14 0.10
Matches are distributed among these distances:
27 7 0.09
28 49 0.66
29 18 0.24
ACGTcount: A:0.39, C:0.44, G:0.02, T:0.15
Consensus pattern (28 bp):
AACCCCAAACCTTAAACCTCAAACCCCA
Found at i:14062 original size:20 final size:20
Alignment explanation
Indices: 14026--14088 Score: 58
Period size: 20 Copynumber: 3.1 Consensus size: 20
14016 AAGAAAAATA
*
14026 AAATATAAATAATTAAATTG
1 AAATACAAATAATTAAATTG
*
14046 AAATACAAA-AATATAAA-TC
1 AAATACAAATAAT-TAAATTG
* *
14065 AAGTATAAATAAATTAAATTG
1 AAATACAAAT-AATTAAATTG
14086 AAA
1 AAA
14089 AATAAAATAA
Statistics
Matches: 33, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
19 11 0.33
20 16 0.48
21 6 0.18
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (20 bp):
AAATACAAATAATTAAATTG
Found at i:17453 original size:23 final size:23
Alignment explanation
Indices: 17427--17471 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
17417 TGTGTTTGTG
17427 TGTATTTGCATGTTCAAAACTGC
1 TGTATTTGCATGTTCAAAACTGC
*
17450 TGTATTTGCATGTTCAATACTG
1 TGTATTTGCATGTTCAAAACTG
17472 TAATGGTTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.24, C:0.16, G:0.18, T:0.42
Consensus pattern (23 bp):
TGTATTTGCATGTTCAAAACTGC
Found at i:17960 original size:87 final size:87
Alignment explanation
Indices: 17845--18096 Score: 312
Period size: 87 Copynumber: 2.9 Consensus size: 87
17835 TGCTCTCATT
* * * *
17845 TGTTTCATTTTTATTGTC-TTTCATTTTAGTTTTAAACTTTTTCTTTATTTACCAATATCTTTAA
1 TGTTTCATTTTTATTTTCTTTTCA-TTTAGTTTTAAACTTTTTCTTTATTCACCAAAATCTATAA
*
17909 AATGCATAATTTTAACTCTAATA
65 AATGCATAATTTCAACTCTAATA
**
17932 TGTTTCATTTTTATTTTCTTTTCATTTAGTTTTAATTTTTTTCTTTATTCACCAAAATCTATAAA
1 TGTTTCATTTTTATTTTCTTTTCATTTAGTTTTAAACTTTTTCTTTATTCACCAAAATCTATAAA
* * * *
17997 AGGCATAATGTCAATTCTAATT
66 ATGCATAATTTCAACTCTAATA
* * * *
18019 TGTCTCATTTTTATTTTCTCTTCGTTTTAGTTTT-AACTTTTT-TCTTATTGACCAAAATCTATA
1 TGTTTCATTTTTATTTTCTTTTC-ATTTAGTTTTAAACTTTTTCT-TTATTCACCAAAATCTATA
*
18082 GAATGCATAATTTCA
64 AAATGCATAATTTCA
18097 TGCTAAAAAT
Statistics
Matches: 142, Mismatches: 20, Indels: 6
0.85 0.12 0.04
Matches are distributed among these distances:
86 1 0.01
87 127 0.89
88 14 0.10
ACGTcount: A:0.27, C:0.13, G:0.06, T:0.54
Consensus pattern (87 bp):
TGTTTCATTTTTATTTTCTTTTCATTTAGTTTTAAACTTTTTCTTTATTCACCAAAATCTATAAA
ATGCATAATTTCAACTCTAATA
Found at i:19420 original size:6 final size:7
Alignment explanation
Indices: 19390--19505 Score: 80
Period size: 7 Copynumber: 16.6 Consensus size: 7
19380 CACCCCACTA
19390 TAAACCT
1 TAAACCT
19397 TAAACCT
1 TAAACCT
19404 TAAACCT
1 TAAACCT
19411 TAAA-CT
1 TAAACCT
*
19417 TAAAACCC
1 T-AAACCT
19425 TAAA-CT
1 TAAACCT
*
19431 CAAAACCT
1 -TAAACCT
*
19439 TAAACCG
1 TAAACCT
19446 TAAA-CT
1 TAAACCT
*
19452 TAAAACTT
1 T-AAACCT
* *
19460 TAATCCC
1 TAAACCT
19467 TAAA-CT
1 TAAACCT
19473 TAAATCAC-
1 TAAA-C-CT
19481 TAAACCT
1 TAAACCT
* *
19488 AAAAACT
1 TAAACCT
19495 TAAACCT
1 TAAACCT
19502 TAAA
1 TAAA
19506 AACCCTAAAC
Statistics
Matches: 83, Mismatches: 16, Indels: 20
0.70 0.13 0.17
Matches are distributed among these distances:
6 12 0.14
7 60 0.72
8 10 0.12
9 1 0.01
ACGTcount: A:0.48, C:0.25, G:0.01, T:0.26
Consensus pattern (7 bp):
TAAACCT
Found at i:19565 original size:25 final size:25
Alignment explanation
Indices: 19496--19557 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 25
19486 CTAAAAACTT
* *
19496 AAACCTTAAAAACCCTAAACCCTTAAA
1 AAACCTT--AAACCATAAACCCTAAAA
**
19523 AAATTTTAAACCATAAACCCTAAAA
1 AAACCTTAAACCATAAACCCTAAAA
19548 AAACCTTAAA
1 AAACCTTAAA
19558 TCTTAAACTT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
25 24 0.83
27 5 0.17
ACGTcount: A:0.55, C:0.24, G:0.00, T:0.21
Consensus pattern (25 bp):
AAACCTTAAACCATAAACCCTAAAA
Found at i:19583 original size:21 final size:19
Alignment explanation
Indices: 19559--19612 Score: 54
Period size: 21 Copynumber: 2.7 Consensus size: 19
19549 AACCTTAAAT
*
19559 CTTAAACTTTAACTTTAGACC
1 CTTAAACTTAAAC-TTA-ACC
19580 CTTAAACCTTAAACTTAACC
1 CTTAAA-CTTAAACTTAACC
* *
19600 CTAAAACTCAAAC
1 CTTAAACTTAAAC
19613 CCTAAACCCC
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 6 0.21
20 8 0.28
21 9 0.31
22 6 0.21
ACGTcount: A:0.41, C:0.28, G:0.02, T:0.30
Consensus pattern (19 bp):
CTTAAACTTAAACTTAACC
Found at i:19633 original size:14 final size:13
Alignment explanation
Indices: 19610--19686 Score: 73
Period size: 14 Copynumber: 5.6 Consensus size: 13
19600 CTAAAACTCA
*
19610 AACCCTAAACCCC
1 AACCCCAAACCCC
19623 AAGCCCCAAACCCC
1 AA-CCCCAAACCCC
*
19637 AACCTCTAAACCCC
1 AACC-CCAAACCCC
* *
19651 AAACCCAAAACCCGA
1 -AACCCCAAACCC-C
*
19666 AACCCCCAACCCC
1 AACCCCAAACCCC
19679 AACCCCAA
1 AACCCCAA
19687 CTTAAATTTC
Statistics
Matches: 52, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
13 11 0.21
14 37 0.71
15 4 0.08
ACGTcount: A:0.40, C:0.53, G:0.03, T:0.04
Consensus pattern (13 bp):
AACCCCAAACCCC
Found at i:19649 original size:28 final size:27
Alignment explanation
Indices: 19596--19686 Score: 83
Period size: 28 Copynumber: 3.3 Consensus size: 27
19586 CCTTAAACTT
* *
19596 AACCCTAAAACTCAAACCCTAAACCCCA
1 AACCC-AAAACCCCAACCCTAAACCCCA
* *
19624 AGCCCCAAACCCCAACCTCTAAACCCCA
1 AACCCAAAACCCCAACC-CTAAACCCCA
* **
19652 AACCCAAAACCCGAAACCCCCAACCCCA
1 AACCCAAAACCC-CAACCCTAAACCCCA
*
19680 ACCCCAA
1 AACCCAA
19687 CTTAAATTTC
Statistics
Matches: 51, Mismatches: 10, Indels: 4
0.78 0.15 0.06
Matches are distributed among these distances:
27 9 0.18
28 38 0.75
29 4 0.08
ACGTcount: A:0.42, C:0.51, G:0.02, T:0.05
Consensus pattern (27 bp):
AACCCAAAACCCCAACCCTAAACCCCA
Found at i:20256 original size:76 final size:76
Alignment explanation
Indices: 20174--20398 Score: 265
Period size: 76 Copynumber: 3.0 Consensus size: 76
20164 GATTTTTGTA
** * * * *
20174 TTGAACCATATCGTCAGTTTAAAATAATGATTTCCGTTTCTAACCGTG-CTATCAGTTTAGAAA-
1 TTGAACCATATCACCGGTTTAAAATAGTGATTTTCGTTTCGAACCGTGTC-ATCAGTTTA-AAAT
20237 AGTAGTTTTTATT
64 AGTAGTTTTTATT
* * * * *
20250 TTGAACCATACCACCGGTTTAAAATAGTGGTTTTTGTTTCGAACCGTGTCACCGGTTTAAAATAG
1 TTGAACCATATCACCGGTTTAAAATAGTGATTTTCGTTTCGAACCGTGTCATCAGTTTAAAATAG
20315 TAGTTTTTATT
66 TAGTTTTTATT
** ** * *
20326 TCAAACTGTATCACCGGTTTAAAATAGTAATTTTCGTTTCGAACCATGTCATCAGTTTAAAATAG
1 TTGAACCATATCACCGGTTTAAAATAGTGATTTTCGTTTCGAACCGTGTCATCAGTTTAAAATAG
20391 TAGTTTTT
66 TAGTTTTT
20399 GTTCATAGCT
Statistics
Matches: 125, Mismatches: 22, Indels: 4
0.83 0.15 0.03
Matches are distributed among these distances:
75 3 0.02
76 121 0.97
77 1 0.01
ACGTcount: A:0.29, C:0.15, G:0.16, T:0.40
Consensus pattern (76 bp):
TTGAACCATATCACCGGTTTAAAATAGTGATTTTCGTTTCGAACCGTGTCATCAGTTTAAAATAG
TAGTTTTTATT
Found at i:20283 original size:38 final size:38
Alignment explanation
Indices: 20228--20398 Score: 191
Period size: 38 Copynumber: 4.5 Consensus size: 38
20218 CGTGCTATCA
* *
20228 GTTTAGAAA-AGTAGTTTTTATTTTGAACCATACCACCG
1 GTTTA-AAATAGTAGTTTTTATTTCGAACCATATCACCG
* * * *
20266 GTTTAAAATAGTGGTTTTTGTTTCGAACCGTGTCACCG
1 GTTTAAAATAGTAGTTTTTATTTCGAACCATATCACCG
* **
20304 GTTTAAAATAGTAGTTTTTATTTCAAACTGTATCACCG
1 GTTTAAAATAGTAGTTTTTATTTCGAACCATATCACCG
* ** * * *
20342 GTTTAAAATAGTAATTTTCGTTTCGAACCATGTCATCA
1 GTTTAAAATAGTAGTTTTTATTTCGAACCATATCACCG
20380 GTTTAAAATAGTAGTTTTT
1 GTTTAAAATAGTAGTTTTT
20399 GTTCATAGCT
Statistics
Matches: 110, Mismatches: 22, Indels: 2
0.82 0.16 0.01
Matches are distributed among these distances:
37 3 0.03
38 107 0.97
ACGTcount: A:0.29, C:0.13, G:0.16, T:0.41
Consensus pattern (38 bp):
GTTTAAAATAGTAGTTTTTATTTCGAACCATATCACCG
Found at i:27295 original size:2 final size:2
Alignment explanation
Indices: 27288--27314 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
27278 TCACAGAACA
27288 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
27315 TTATACAATA
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:27530 original size:4 final size:4
Alignment explanation
Indices: 27523--27555 Score: 66
Period size: 4 Copynumber: 8.2 Consensus size: 4
27513 ATATACATAG
27523 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
27556 TACACACATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:29634 original size:2 final size:2
Alignment explanation
Indices: 29627--29655 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
29617 TTAAGCAAAC
29627 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 T
29656 TATTGAACCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:29770 original size:2 final size:2
Alignment explanation
Indices: 29763--29790 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
29753 TTATAAACTG
29763 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
29791 GTTATGAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:30693 original size:3 final size:3
Alignment explanation
Indices: 30685--30715 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
30675 AGTCATTATC
30685 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
30716 AACCTCTCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:32539 original size:4 final size:4
Alignment explanation
Indices: 32530--32579 Score: 73
Period size: 4 Copynumber: 12.5 Consensus size: 4
32520 CCCTTAGTGG
* * *
32530 CATA CATA CATA CATA CATA CATA CATA CATA CATA TATA TATA TATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
32578 CA
1 CA
32580 CACACACACA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 44 1.00
ACGTcount: A:0.50, C:0.20, G:0.00, T:0.30
Consensus pattern (4 bp):
CATA
Found at i:32924 original size:2 final size:2
Alignment explanation
Indices: 32917--32956 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
32907 TTTAAACACG
32917 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
32957 AATCCATATG
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40569 original size:45 final size:45
Alignment explanation
Indices: 40505--40594 Score: 171
Period size: 45 Copynumber: 2.0 Consensus size: 45
40495 AAGTCTGAAT
40505 ATTATTTATGTCCCTAAGACCTTATCTAAAGCATTATCCAAAGAA
1 ATTATTTATGTCCCTAAGACCTTATCTAAAGCATTATCCAAAGAA
*
40550 ATTATTTATGTCCCTAAGACCTTATCTAAAGTATTATCCAAAGAA
1 ATTATTTATGTCCCTAAGACCTTATCTAAAGCATTATCCAAAGAA
40595 GAATGCAACG
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.38, C:0.19, G:0.09, T:0.34
Consensus pattern (45 bp):
ATTATTTATGTCCCTAAGACCTTATCTAAAGCATTATCCAAAGAA
Found at i:44491 original size:12 final size:13
Alignment explanation
Indices: 44465--44497 Score: 59
Period size: 12 Copynumber: 2.6 Consensus size: 13
44455 AGAATACAAG
44465 TATTATTATCTAT
1 TATTATTATCTAT
44478 TATTATTA-CTAT
1 TATTATTATCTAT
44490 TATTATTA
1 TATTATTA
44498 GAAAAGGGTG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 12 0.60
13 8 0.40
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (13 bp):
TATTATTATCTAT
Found at i:45245 original size:4 final size:4
Alignment explanation
Indices: 45229--45261 Score: 50
Period size: 4 Copynumber: 8.5 Consensus size: 4
45219 ATCTGCTCAG
*
45229 AACA AAC- ACCA AACA AACA AACA AACA AACA AA
1 AACA AACA AACA AACA AACA AACA AACA AACA AA
45262 AGGAATCAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
3 2 0.08
4 24 0.92
ACGTcount: A:0.73, C:0.27, G:0.00, T:0.00
Consensus pattern (4 bp):
AACA
Found at i:46114 original size:21 final size:21
Alignment explanation
Indices: 46090--46169 Score: 65
Period size: 21 Copynumber: 3.8 Consensus size: 21
46080 AAAAATTACT
46090 AATTACATCAAAAGTTATCAA
1 AATTACATCAAAAGTTATCAA
* * **
46111 AATTATAACAAAAACTATCAA
1 AATTACATCAAAAGTTATCAA
***
46132 AATCGTATC-AAAGATTATCAA
1 AATTACATCAAAAG-TTATCAA
46153 ACA-TACATCAAAAGTTA
1 A-ATTACATCAAAAGTTA
46170 CTAAAAATGA
Statistics
Matches: 44, Mismatches: 12, Indels: 6
0.71 0.19 0.10
Matches are distributed among these distances:
20 3 0.07
21 36 0.82
22 5 0.11
ACGTcount: A:0.54, C:0.15, G:0.05, T:0.26
Consensus pattern (21 bp):
AATTACATCAAAAGTTATCAA
Found at i:47507 original size:26 final size:26
Alignment explanation
Indices: 47484--47536 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
47474 CTAGAATCTC
* *
47484 AGATAAAGTTGAACTTTATTAATCCT
1 AGATAAAGTTAAACTTTATGAATCCT
47510 AGATAAAGTTAAACTTTATGAATCCT
1 AGATAAAGTTAAACTTTATGAATCCT
47536 A
1 A
47537 TCTCTATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.36
Consensus pattern (26 bp):
AGATAAAGTTAAACTTTATGAATCCT
Found at i:55746 original size:6 final size:6
Alignment explanation
Indices: 55735--55762 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
55725 TTACCACCAT
55735 TTCATA TTCATA TTCATA TTCATA TTCA
1 TTCATA TTCATA TTCATA TTCATA TTCA
55763 GACTGATGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.32, C:0.18, G:0.00, T:0.50
Consensus pattern (6 bp):
TTCATA
Found at i:55914 original size:2 final size:2
Alignment explanation
Indices: 55907--55953 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
55897 ACTGTCAAGG
*
55907 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TG
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
55949 TC TC T
1 TC TC T
55954 GTTCCTTGTT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.00, C:0.47, G:0.02, T:0.51
Consensus pattern (2 bp):
TC
Found at i:60614 original size:2 final size:2
Alignment explanation
Indices: 60607--60661 Score: 101
Period size: 2 Copynumber: 27.5 Consensus size: 2
60597 AAGCTATCGC
60607 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
*
60649 AT AT AT AT GT AT A
1 AT AT AT AT AT AT A
60662 CCTGCTGCAC
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:61445 original size:2 final size:2
Alignment explanation
Indices: 61438--61470 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
61428 AAAATGGATG
61438 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 T
61471 TTTATGAACT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:61550 original size:59 final size:58
Alignment explanation
Indices: 61446--61575 Score: 183
Period size: 59 Copynumber: 2.2 Consensus size: 58
61436 TGTATATATA
** *
61446 TATATATATATATATATATATATATTTTATGAACTAGATTAAATTACAGATAATAAGAT
1 TATA-ATATATATATATATATATATTACATGAACTAGATTAAATTACAGATAAAAAGAT
*
61505 TATGAATATATATATATATATATA-TACATGAACTAGATTTGAATTACAGATAAAAAGAT
1 TAT-AATATATATATATATATATATTACATGAACTAGA-TTAAATTACAGATAAAAAGAT
61564 TATAAT-TATATA
1 TATAATATATATA
61576 GTGTGCGTGA
Statistics
Matches: 65, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
57 6 0.09
58 14 0.22
59 44 0.68
60 1 0.02
ACGTcount: A:0.48, C:0.04, G:0.08, T:0.40
Consensus pattern (58 bp):
TATAATATATATATATATATATATTACATGAACTAGATTAAATTACAGATAAAAAGAT
Found at i:62028 original size:3 final size:3
Alignment explanation
Indices: 62020--62047 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
62010 AGGTGGCCCT
62020 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
62048 AATCTACAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:62272 original size:1 final size:1
Alignment explanation
Indices: 62266--62294 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
62256 CGGCGTCAAA
62266 CCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCC
62295 AAAAAAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:63547 original size:2 final size:2
Alignment explanation
Indices: 63535--63575 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
63525 TACACCATCA
*
63535 AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
63576 GATAAATTCA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:67413 original size:5 final size:5
Alignment explanation
Indices: 67403--67438 Score: 63
Period size: 5 Copynumber: 7.2 Consensus size: 5
67393 AGTGCAGATT
*
67403 TGGTA TGGTA TGGTA TGGTC TGGTA TGGTA TGGTA T
1 TGGTA TGGTA TGGTA TGGTA TGGTA TGGTA TGGTA T
67439 AGTAGAGAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.17, C:0.03, G:0.39, T:0.42
Consensus pattern (5 bp):
TGGTA
Found at i:67524 original size:5 final size:5
Alignment explanation
Indices: 67503--67537 Score: 54
Period size: 5 Copynumber: 7.0 Consensus size: 5
67493 AAAGCGCTGC
67503 TCCTA TCCTA -CCTTA TCCTA TCCTA TCCTA TCCTA
1 TCCTA TCCTA TCC-TA TCCTA TCCTA TCCTA TCCTA
67538 AGTTAACAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
4 2 0.07
5 24 0.86
6 2 0.07
ACGTcount: A:0.20, C:0.40, G:0.00, T:0.40
Consensus pattern (5 bp):
TCCTA
Found at i:72270 original size:49 final size:49
Alignment explanation
Indices: 72198--72296 Score: 189
Period size: 49 Copynumber: 2.0 Consensus size: 49
72188 ATTTATGTGA
*
72198 ACCATAAATTGTACAGAGAATGATCTCTTTGTTAAGCTTAGAGAATGGG
1 ACCATAAATTATACAGAGAATGATCTCTTTGTTAAGCTTAGAGAATGGG
72247 ACCATAAATTATACAGAGAATGATCTCTTTGTTAAGCTTAGAGAATGGG
1 ACCATAAATTATACAGAGAATGATCTCTTTGTTAAGCTTAGAGAATGGG
72296 A
1 A
72297 TGCACCATCA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.36, C:0.12, G:0.21, T:0.30
Consensus pattern (49 bp):
ACCATAAATTATACAGAGAATGATCTCTTTGTTAAGCTTAGAGAATGGG
Found at i:76294 original size:155 final size:154
Alignment explanation
Indices: 76002--76313 Score: 588
Period size: 155 Copynumber: 2.0 Consensus size: 154
75992 CTTCATGATC
76002 TTGCCCCATAATCTCTTGGCAGCTTCAACATCCAGAAAATTATGAGTGCGAACAGAGGCCATTAA
1 TTGCCCCATAATCTCTTGGCAGCTTCAACATCCAGAAAATTATGAGTGCGAACAGAGGCCATTAA
*
76067 TTGTAAAATGGTTTTTTCTTGACACACGAAGTGAGTTCCCTAGTTTTGCGGCTTTTGATTGCAAC
66 TTGTAAAATGATTTTTTCTTGACACACGAAGTGAGTTCCCTAGTTTTGCGGCTTTTGATTGCAAC
76132 ACCACTCTTGTCATGTACTGAGAT
131 ACCACTCTTGTCATGTACTGAGAT
*
76156 TTGCCCCATAATCTCTTGGCAGCTTCAATATCCAGAAAATTATGAGTGCGAACAGAGGCCATTAA
1 TTGCCCCATAATCTCTTGGCAGCTTCAACATCCAGAAAATTATGAGTGCGAACAGAGGCCATTAA
*
76221 TATGTAAAATGATTTTTTCTTGACACACGAAGTGAGTTCCCTCGTTTTGCGGCTTTTGATTGCAA
66 T-TGTAAAATGATTTTTTCTTGACACACGAAGTGAGTTCCCTAGTTTTGCGGCTTTTGATTGCAA
76286 CACCACTCTTGTCATGTACTGAGAT
130 CACCACTCTTGTCATGTACTGAGAT
76311 TTG
1 TTG
76314 GAGATTTTCT
Statistics
Matches: 154, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
154 65 0.42
155 89 0.58
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (154 bp):
TTGCCCCATAATCTCTTGGCAGCTTCAACATCCAGAAAATTATGAGTGCGAACAGAGGCCATTAA
TTGTAAAATGATTTTTTCTTGACACACGAAGTGAGTTCCCTAGTTTTGCGGCTTTTGATTGCAAC
ACCACTCTTGTCATGTACTGAGAT
Found at i:77293 original size:405 final size:405
Alignment explanation
Indices: 76544--77758 Score: 2263
Period size: 405 Copynumber: 3.0 Consensus size: 405
76534 GTGTTAGCTG
76544 TGGAGGAGTTTGGGCTAGGCAGTGAGGATTGATTTCTTGGAATGGTTTTGGAGTTGGTGTGAGAA
1 TGGAGGAGTTTGGGCTAGGCAGTGAGGATTGATTTCTTGGAATGGTTTTGGAGTTGGTGTGAGAA
76609 TAGGCAGTAAAGGTGGTTCTTTAAAGGTGGTAGTGAGTTCTCACTGTAGTGTTTCTAAGGTTGAT
66 TAGGCAGTAAAGGTGGTTCTTTAAAGGTGGTAGTGAGTTCTCACTGTAGTGTTTCTAAGGTTGAT
76674 TCTTGAAGATGAGCCATAAGAAAAGCAGTTTC-A-AGTTTTTGGGACGAATATTTTGACAGACTT
131 TCTTGAAGATGAGCCATAAGAAAAGCAGTTTCAAGAGTTTTTGGGACGAATATTTTGACAGACTT
*
76737 TTGTATAGCATTCTTGAGCCTATTCAAGAACAAATTTGTTGTGTAATCCTCATGTAAATCTACAT
196 TTGTATAGCATTCTTGAGCCTATTCAAGAACAAATTTGTTGCGTAATCCTCATGTAAATCTACAT
*
76802 TCCCCAACAAACATACAAAATGATCATAGCATTAATCAACAATAACTGTTTGCTTGAAGCTTATC
261 TCCCCAACAAACATACAAAATGATCATAGCATTAATCAACAATACCTGTTTGCTTGAAGCTTATC
76867 AACTCTGTCAAGGGATCTTGCTTTTGAAGTTTGACCTTAATTTCTGTTAGAAACTCTTCCATTGT
326 AACTCTGTCAAGGGATCTTGCTTTTGAAGTTTGACCTTAATTTCTGTTAGAAACTCTTCCATTGT
*
76932 TTTCTATCGTTCTTT
391 TTTCTATCATTCTTT
*
76947 TGGAGGAGTTTGGGCTAGGCAGTGAGGATTGATTTCTTGGAATGGTTTCGGAGTTGGTGTGAGAA
1 TGGAGGAGTTTGGGCTAGGCAGTGAGGATTGATTTCTTGGAATGGTTTTGGAGTTGGTGTGAGAA
*
77012 TAGGCGGTAAAGGTGGTTCTTTAAAGGTGGTAGTGAGTTCTCACTGTAGTGTTTCTAAGGTTGAT
66 TAGGCAGTAAAGGTGGTTCTTTAAAGGTGGTAGTGAGTTCTCACTGTAGTGTTTCTAAGGTTGAT
77077 TCTTGAAGATGAGCCATAAGAAAAGCAGTTTCAAGAGTTTTTGGGACGAATATTTTGACAGACTT
131 TCTTGAAGATGAGCCATAAGAAAAGCAGTTTCAAGAGTTTTTGGGACGAATATTTTGACAGACTT
77142 TTGTATAGCATTCTTGAGCCTATTCAAGAACAAATTTGTTGCGTAATCCTCATGTAAATCTACAT
196 TTGTATAGCATTCTTGAGCCTATTCAAGAACAAATTTGTTGCGTAATCCTCATGTAAATCTACAT
*
77207 TCTCCAACAAACATACAAAATGATCATAGCATTAATCAACAATACCTGTTTGCTTGAAGCTTATC
261 TCCCCAACAAACATACAAAATGATCATAGCATTAATCAACAATACCTGTTTGCTTGAAGCTTATC
77272 AACTCTGTCAAGGGATCTTGCTTTTGAAGTTTGACCTTAATTTCTGTTAGAAACTCTTCCATTGT
326 AACTCTGTCAAGGGATCTTGCTTTTGAAGTTTGACCTTAATTTCTGTTAGAAACTCTTCCATTGT
77337 TTTCTATCATTCTTT
391 TTTCTATCATTCTTT
77352 TGGAGGAGTTTGGGCTAGGCAGTGAGGATTGATTTCTTGGAATGGTTTTGGAGTTGGTGTGAGAA
1 TGGAGGAGTTTGGGCTAGGCAGTGAGGATTGATTTCTTGGAATGGTTTTGGAGTTGGTGTGAGAA
* ** *
77417 TAGGCTGTAAAGGTGGTTCTTTAAAGGTGGTAGTGAGTTCTCGTTGTTGTGTTTCTAAGGTTGAT
66 TAGGCAGTAAAGGTGGTTCTTTAAAGGTGGTAGTGAGTTCTCACTGTAGTGTTTCTAAGGTTGAT
* * *
77482 TCTTGCAGATGAGCCATAAGAAAAGCAATTTCAAGAGTTTGTGGGACGAATATTTTGACAGACTT
131 TCTTGAAGATGAGCCATAAGAAAAGCAGTTTCAAGAGTTTTTGGGACGAATATTTTGACAGACTT
77547 TTGTATAGCATTCTTGAGCCTATTCAAGAACAAATTTGTTGCGTAATCCTCATGTAAATCTACAT
196 TTGTATAGCATTCTTGAGCCTATTCAAGAACAAATTTGTTGCGTAATCCTCATGTAAATCTACAT
* * *
77612 TCCCCAACAAACATACAAAATGATTATAGCATTCATCAACAATACATGTTTGCTTGAAGCTTATC
261 TCCCCAACAAACATACAAAATGATCATAGCATTAATCAACAATACCTGTTTGCTTGAAGCTTATC
*
77677 AACTCTGTCAAGGGATCTTGCTTTTGAAGTTTGACCTTAATTTCTGTTAGAAACTCCTCCATTGT
326 AACTCTGTCAAGGGATCTTGCTTTTGAAGTTTGACCTTAATTTCTGTTAGAAACTCTTCCATTGT
77742 TTTCTATCATTCTTT
391 TTTCTATCATTCTTT
77757 TG
1 TG
77759 AAGTCTTGAG
Statistics
Matches: 791, Mismatches: 19, Indels: 2
0.97 0.02 0.00
Matches are distributed among these distances:
403 160 0.20
404 1 0.00
405 630 0.80
ACGTcount: A:0.27, C:0.15, G:0.22, T:0.36
Consensus pattern (405 bp):
TGGAGGAGTTTGGGCTAGGCAGTGAGGATTGATTTCTTGGAATGGTTTTGGAGTTGGTGTGAGAA
TAGGCAGTAAAGGTGGTTCTTTAAAGGTGGTAGTGAGTTCTCACTGTAGTGTTTCTAAGGTTGAT
TCTTGAAGATGAGCCATAAGAAAAGCAGTTTCAAGAGTTTTTGGGACGAATATTTTGACAGACTT
TTGTATAGCATTCTTGAGCCTATTCAAGAACAAATTTGTTGCGTAATCCTCATGTAAATCTACAT
TCCCCAACAAACATACAAAATGATCATAGCATTAATCAACAATACCTGTTTGCTTGAAGCTTATC
AACTCTGTCAAGGGATCTTGCTTTTGAAGTTTGACCTTAATTTCTGTTAGAAACTCTTCCATTGT
TTTCTATCATTCTTT
Found at i:82315 original size:34 final size:34
Alignment explanation
Indices: 82269--82339 Score: 106
Period size: 34 Copynumber: 2.1 Consensus size: 34
82259 CCATTCTCCC
* * *
82269 CTGTAATGCACTGTATTTATAGCTTTGGGTATTA
1 CTGTAATACACTGCATTTATAGCTTTGGATATTA
*
82303 CTGTAATACACTGCATTTATAGCTTTTGATATTA
1 CTGTAATACACTGCATTTATAGCTTTGGATATTA
82337 CTG
1 CTG
82340 ACAGTTATTA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.25, C:0.14, G:0.17, T:0.44
Consensus pattern (34 bp):
CTGTAATACACTGCATTTATAGCTTTGGATATTA
Found at i:84678 original size:5 final size:5
Alignment explanation
Indices: 84668--84700 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
84658 TTCCAAGGTC
*
84668 TGGTT TGGTT TGGTT TGGTT TGGTT TAGTT TGG
1 TGGTT TGGTT TGGTT TGGTT TGGTT TGGTT TGG
84701 ATGGAATCGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.03, C:0.00, G:0.39, T:0.58
Consensus pattern (5 bp):
TGGTT
Found at i:91425 original size:2 final size:2
Alignment explanation
Indices: 91414--91454 Score: 57
Period size: 2 Copynumber: 21.0 Consensus size: 2
91404 AAAATTGATA
* *
91414 AT AT -T AT AT AT AT AT AT AC AT AT AC 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
91455 CAAACTCTGC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:92850 original size:3 final size:3
Alignment explanation
Indices: 92844--92877 Score: 50
Period size: 3 Copynumber: 11.0 Consensus size: 3
92834 AATATTATTG
*
92844 TAT TAT TACA TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT
92878 ATATAATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 26 0.93
4 2 0.07
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:93382 original size:2 final size:2
Alignment explanation
Indices: 93375--93405 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
93365 ATGGGTTGAA
93375 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
93406 AATTGAGATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:94825 original size:2 final size:2
Alignment explanation
Indices: 94818--94857 Score: 50
Period size: 2 Copynumber: 21.0 Consensus size: 2
94808 GAGCTAGGAG
94818 TA TA TA TA TA TA -A TA TA TA -A TA TA TGA TA TA TA -A TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA
94858 GAACAATGCT
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
1 3 0.09
2 29 0.85
3 2 0.06
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (2 bp):
TA
Found at i:94833 original size:7 final size:7
Alignment explanation
Indices: 94818--94857 Score: 64
Period size: 7 Copynumber: 5.9 Consensus size: 7
94808 GAGCTAGGAG
94818 TATAT-A
1 TATATAA
94824 TATATAA
1 TATATAA
94831 TATATAA
1 TATATAA
*
94838 TATATGA
1 TATATAA
94845 TATATAA
1 TATATAA
94852 TATATA
1 TATATA
94858 GAACAATGCT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
6 5 0.16
7 26 0.84
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (7 bp):
TATATAA
Found at i:99802 original size:2 final size:2
Alignment explanation
Indices: 99795--99834 Score: 53
Period size: 2 Copynumber: 19.5 Consensus size: 2
99785 CTCACTGCTC
* *
99795 TA TA TA TA TA TA TA TA TA TA TA TG TA CA TA TA TCA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA T
99835 GGTGTCAATT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
2 31 0.94
3 2 0.06
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:100727 original size:11 final size:11
Alignment explanation
Indices: 100707--100739 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
100697 TCATTGCGAT
100707 AAAAAA-AAAA
1 AAAAAAGAAAA
100717 AAAAAAGAAAA
1 AAAAAAGAAAA
*
100728 GAAAAAGAAAA
1 AAAAAAGAAAA
100739 A
1 A
100740 GCTGAACATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
10 6 0.30
11 14 0.70
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (11 bp):
AAAAAAGAAAA
Found at i:104709 original size:3 final size:3
Alignment explanation
Indices: 104703--104735 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
104693 AATAATAATA
104703 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
104736 TTGATTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
ATC
Found at i:105590 original size:2 final size:2
Alignment explanation
Indices: 105583--105610 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
105573 TCGGTCGGAC
105583 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
105611 TCTGATTTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:113777 original size:2 final size:2
Alignment explanation
Indices: 113770--113795 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
113760 TCGGTCGGAC
113770 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
113796 TCTGATTTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:119232 original size:2 final size:2
Alignment explanation
Indices: 119225--119249 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
119215 AGTGTATATC
119225 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
119250 AGAAAAGCAT
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:120471 original size:3 final size:3
Alignment explanation
Indices: 120463--120490 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
120453 GGCTTCTGTT
120463 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
120491 GTGAGTTCGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:124006 original size:2 final size:2
Alignment explanation
Indices: 124001--124033 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
123991 ACACATATTT
*
124001 TA TA TA TA TA TA TA TA TA TG TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
124034 CTTAAATTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:136044 original size:25 final size:25
Alignment explanation
Indices: 136016--136065 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
136006 AAACTGATTC
136016 TCCTAATCTATTTACAGCTCATCTA
1 TCCTAATCTATTTACAGCTCATCTA
*
136041 TCCTAATCTATTTACAGCTCGTCTA
1 TCCTAATCTATTTACAGCTCATCTA
136066 CATCTCGACA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.26, C:0.28, G:0.06, T:0.40
Consensus pattern (25 bp):
TCCTAATCTATTTACAGCTCATCTA
Found at i:141798 original size:36 final size:36
Alignment explanation
Indices: 141751--141822 Score: 117
Period size: 36 Copynumber: 2.0 Consensus size: 36
141741 ACATTTTCCA
*
141751 ATGAAGATCCAGATCTACTCATGGTCAAGGAAACAC
1 ATGAAGATCCAGATATACTCATGGTCAAGGAAACAC
* *
141787 ATGAAGATCCAGATATATTCGTGGTCAAGGAAACAC
1 ATGAAGATCCAGATATACTCATGGTCAAGGAAACAC
141823 CATTTGTGGA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.39, C:0.19, G:0.21, T:0.21
Consensus pattern (36 bp):
ATGAAGATCCAGATATACTCATGGTCAAGGAAACAC
Found at i:143955 original size:2 final size:2
Alignment explanation
Indices: 143948--143978 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
143938 ACTACTTTAT
143948 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
143979 GATGGATGCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:144349 original size:28 final size:28
Alignment explanation
Indices: 144296--144348 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
144286 TAAACAATGG
* * *
144296 AACAAATGAAGAGAGAAGAAACAAAAGA
1 AACAAATGAAAAGAGAAAAAAAAAAAGA
144324 AACAAATGAAAA-AGAAAAAAAAAAA
1 AACAAATGAAAAGAGAAAAAAAAAAA
144349 AAAGAAAGGC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 11 0.50
28 11 0.50
ACGTcount: A:0.75, C:0.06, G:0.15, T:0.04
Consensus pattern (28 bp):
AACAAATGAAAAGAGAAAAAAAAAAAGA
Found at i:144881 original size:15 final size:15
Alignment explanation
Indices: 144861--144906 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
144851 ATCATTTTTT
*
144861 TAAAAAATTTTTAAA
1 TAAAAAATTTTAAAA
*
144876 TAAAAAA-TTAAATAA
1 TAAAAAATTTTAA-AA
144891 TAAAAAATTTTAAAA
1 TAAAAAATTTTAAAA
144906 T
1 T
144907 GTTGTATCAC
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 3 0.12
15 19 0.73
16 4 0.15
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
TAAAAAATTTTAAAA
Found at i:145211 original size:6 final size:6
Alignment explanation
Indices: 145197--145226 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
145187 AATATCTCCG
*
145197 CCTTCC CCTTTC CCTTTC CCTTTC CCTTTC
1 CCTTTC CCTTTC CCTTTC CCTTTC CCTTTC
145227 GGCGTCTCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (6 bp):
CCTTTC
Found at i:145386 original size:20 final size:21
Alignment explanation
Indices: 145332--145386 Score: 51
Period size: 21 Copynumber: 2.7 Consensus size: 21
145322 CAACCAGGTA
* *
145332 TTTCCTTTCGATTTTCATCGT
1 TTTCCTATCGATTTTCACCGT
* *
145353 TTTCC-AACGAATTTTC-CCTT
1 TTTCCTATCG-ATTTTCACCGT
145373 TTTCCTATCGATTT
1 TTTCCTATCGATTT
145387 CTGCGGTATT
Statistics
Matches: 27, Mismatches: 5, Indels: 5
0.73 0.14 0.14
Matches are distributed among these distances:
20 13 0.48
21 14 0.52
ACGTcount: A:0.15, C:0.25, G:0.07, T:0.53
Consensus pattern (21 bp):
TTTCCTATCGATTTTCACCGT
Found at i:187396 original size:3 final size:3
Alignment explanation
Indices: 187388--187415 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
187378 ATTTAGTTTC
187388 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
187416 GTTCTATTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:188732 original size:2 final size:2
Alignment explanation
Indices: 188725--188761 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
188715 GACTTTTCAT
*
188725 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
188762 GGGATTGCAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:188974 original size:5 final size:5
Alignment explanation
Indices: 188964--188998 Score: 70
Period size: 5 Copynumber: 7.0 Consensus size: 5
188954 TAATAAAAAA
188964 TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT
188999 AAAACCAAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TATAT
Found at i:192919 original size:2 final size:2
Alignment explanation
Indices: 192912--192944 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
192902 ACTTGTGTAG
*
192912 AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
192945 CATTGCCGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:193274 original size:2 final size:2
Alignment explanation
Indices: 193267--193294 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
193257 TTATCTGCGC
193267 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
193295 GTTATTTCTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:193502 original size:3 final size:3
Alignment explanation
Indices: 193482--193529 Score: 69
Period size: 3 Copynumber: 15.7 Consensus size: 3
193472 TAAAATAAAC
* *
193482 AAT AAC AAT AAC AAT AAT AAT AAT ATAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT
193528 AA
1 AA
193530 ACAAAAAGAA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
3 37 0.93
4 3 0.08
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:194646 original size:2 final size:2
Alignment explanation
Indices: 194641--194678 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
194631 TTTTGGGAGT
194641 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
194679 CTGTAATTGA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:202651 original size:2 final size:2
Alignment explanation
Indices: 202646--202671 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
202636 GTGGTGTGTG
202646 TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC
202672 CCAGTATTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:214710 original size:2 final size:2
Alignment explanation
Indices: 214703--214738 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
214693 TTTAACACGA
214703 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
214739 GAAACAGAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:216716 original size:17 final size:15
Alignment explanation
Indices: 216678--216720 Score: 54
Period size: 13 Copynumber: 2.9 Consensus size: 15
216668 ATTATTAATT
216678 TAATTAATAAA-AAA
1 TAATTAATAAATAAA
216692 TAA-TAATAAATTAAA
1 TAATTAATAAA-TAAA
216707 TAATTAAATAAATA
1 TAATT-AATAAATA
216721 TTTTTTTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
13 7 0.28
14 3 0.12
15 6 0.24
16 3 0.12
17 6 0.24
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
TAATTAATAAATAAA
Found at i:219503 original size:6 final size:6
Alignment explanation
Indices: 219494--219526 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
219484 AAGAGTGAGT
219494 GAGTTG GAGTTG GAGTTG GAGTTG GAGTTG GAG
1 GAGTTG GAGTTG GAGTTG GAGTTG GAGTTG GAG
219527 AGAGAAGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.18, C:0.00, G:0.52, T:0.30
Consensus pattern (6 bp):
GAGTTG
Found at i:221628 original size:11 final size:11
Alignment explanation
Indices: 221614--221640 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
221604 TTTATCTCGT
221614 TTTTTTTTTTA
1 TTTTTTTTTTA
221625 TTTTTTTTTTA
1 TTTTTTTTTTA
221636 TTTTT
1 TTTTT
221641 AATCTTACTG
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:0.07, C:0.00, G:0.00, T:0.93
Consensus pattern (11 bp):
TTTTTTTTTTA
Found at i:225349 original size:31 final size:32
Alignment explanation
Indices: 225314--225376 Score: 110
Period size: 31 Copynumber: 2.0 Consensus size: 32
225304 TACGAAAATT
*
225314 TTTCATAAGATCTTCATAATAATTTTT-TTTA
1 TTTCATAAGAGCTTCATAATAATTTTTCTTTA
225345 TTTCATAAGAGCTTCATAATAATTTTTCTTTA
1 TTTCATAAGAGCTTCATAATAATTTTTCTTTA
225377 AAAAAAGCCA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 26 0.87
32 4 0.13
ACGTcount: A:0.32, C:0.11, G:0.05, T:0.52
Consensus pattern (32 bp):
TTTCATAAGAGCTTCATAATAATTTTTCTTTA
Found at i:227560 original size:2 final size:2
Alignment explanation
Indices: 227553--227589 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
227543 ATATACGTAC
227553 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
227590 AAACTCTGCT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:228598 original size:12 final size:12
Alignment explanation
Indices: 228581--228698 Score: 52
Period size: 12 Copynumber: 9.5 Consensus size: 12
228571 ACTAAAAATA
228581 AAATATAATTAT
1 AAATATAATTAT
228593 AAATATATATATATT
1 AAATATA-AT-TA-T
228608 AAA-AT--TTAT
1 AAATATAATTAT
*
228617 GTAATATAAATT-T
1 -AAATAT-AATTAT
* *
228630 ATATAAAATT-T
1 AAATATAATTAT
228641 AAA-AT-ATTATT
1 AAATATAATTA-T
228652 AAATATAATTAT
1 AAATATAATTAT
228664 AATATAATAAAATATAT
1 AA-AT-AT--AAT-TAT
*
228681 AAATATAAGTAT
1 AAATATAATTAT
228693 AAATAT
1 AAATAT
228699 GAAAACACCG
Statistics
Matches: 82, Mismatches: 7, Indels: 34
0.67 0.06 0.28
Matches are distributed among these distances:
9 4 0.05
10 5 0.06
11 14 0.17
12 24 0.29
13 11 0.13
14 8 0.10
15 6 0.07
16 5 0.06
17 5 0.06
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.42
Consensus pattern (12 bp):
AAATATAATTAT
Found at i:228655 original size:10 final size:10
Alignment explanation
Indices: 228642--228698 Score: 55
Period size: 10 Copynumber: 5.6 Consensus size: 10
228632 ATAAAATTTA
*
228642 AAATATTATT
1 AAATATAATT
228652 AAATATAATT
1 AAATATAATT
*
228662 ATAATATAATA
1 A-AATATAATT
228673 AAATAT-A-T
1 AAATATAATT
228681 AAATATAAGTAT
1 AAATATAA-T-T
228693 AAATAT
1 AAATAT
228699 GAAAACACCG
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
8 6 0.15
9 2 0.05
10 15 0.38
11 9 0.23
12 7 0.18
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.39
Consensus pattern (10 bp):
AAATATAATT
Found at i:233038 original size:14 final size:14
Alignment explanation
Indices: 232994--233030 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
232984 ACTTATGCCA
* *
232994 AAAGTATCCCTATC
1 AAAGTATCTCTATT
233008 AAAGTATCTCTATT
1 AAAGTATCTCTATT
233022 AAAGTATCT
1 AAAGTATCT
233031 TTGTTAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.38, C:0.19, G:0.08, T:0.35
Consensus pattern (14 bp):
AAAGTATCTCTATT
Found at i:236947 original size:25 final size:25
Alignment explanation
Indices: 236914--236971 Score: 77
Period size: 25 Copynumber: 2.4 Consensus size: 25
236904 AATTAAATAA
236914 AAAAT-ATT-AATAATATATAAAATT
1 AAAATAATTAAAT-ATATATAAAATT
*
236938 AAAATAATTAAATATATTTAAAATT
1 AAAATAATTAAATATATATAAAATT
236963 AAAA-AATTA
1 AAAATAATTA
236972 TTCACTAATC
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
24 10 0.32
25 18 0.58
26 3 0.10
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (25 bp):
AAAATAATTAAATATATATAAAATT
Found at i:243182 original size:40 final size:40
Alignment explanation
Indices: 243127--243209 Score: 166
Period size: 40 Copynumber: 2.1 Consensus size: 40
243117 GTGTAATTAG
243127 GTTAGAGGATTGATTCGATTGAATAATTGGCTAAATACTA
1 GTTAGAGGATTGATTCGATTGAATAATTGGCTAAATACTA
243167 GTTAGAGGATTGATTCGATTGAATAATTGGCTAAATACTA
1 GTTAGAGGATTGATTCGATTGAATAATTGGCTAAATACTA
243207 GTT
1 GTT
243210 TCATCCCTAG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.34, C:0.07, G:0.23, T:0.36
Consensus pattern (40 bp):
GTTAGAGGATTGATTCGATTGAATAATTGGCTAAATACTA
Found at i:250968 original size:18 final size:19
Alignment explanation
Indices: 250941--250976 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
250931 AATCAAGATG
*
250941 CTTTTGAATTTT-CTTTAC
1 CTTTTAAATTTTGCTTTAC
250959 CTTTTAAATTTTGCTTTA
1 CTTTTAAATTTTGCTTTA
250977 TAATTCATGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.19, C:0.14, G:0.06, T:0.61
Consensus pattern (19 bp):
CTTTTAAATTTTGCTTTAC
Found at i:252540 original size:2 final size:2
Alignment explanation
Indices: 252533--252584 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
252523 ATTAGATGAT
252533 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
252575 TC TC TC TC TC
1 TC TC TC TC TC
252585 ATATTGCTAT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:254327 original size:34 final size:34
Alignment explanation
Indices: 254272--254488 Score: 276
Period size: 34 Copynumber: 6.4 Consensus size: 34
254262 TCCTAAGTCC
*
254272 TGTTGATTAAAT-GGTGATTTGGTAGTTTACCAT
1 TGTTGATTAAATGGGTGATTTGGTAGCTTACCAT
* * * *
254305 TATTGATTAAATGGGTGATTTGGTGGTTTGCCAT
1 TGTTGATTAAATGGGTGATTTGGTAGCTTACCAT
* *
254339 TGTTGACTAAATGGGAGATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGTGATTTGGTAGCTTACCAT
* **
254373 TGTTGATTAAATGAGAAATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGTGATTTGGTAGCTTACCAT
* *
254407 TATTGATTAAATGGGTGATTTGGTGGCTTACCAT
1 TGTTGATTAAATGGGTGATTTGGTAGCTTACCAT
* * *
254441 TGTTGACTAAAT-GGTAGATTTGGTAGGTTGCCAT
1 TGTTGATTAAATGGGT-GATTTGGTAGCTTACCAT
254475 TGTTGATTAAATGG
1 TGTTGATTAAATGG
254489 TGGTTTTTAC
Statistics
Matches: 158, Mismatches: 23, Indels: 4
0.85 0.12 0.02
Matches are distributed among these distances:
33 14 0.09
34 143 0.91
35 1 0.01
ACGTcount: A:0.25, C:0.08, G:0.26, T:0.41
Consensus pattern (34 bp):
TGTTGATTAAATGGGTGATTTGGTAGCTTACCAT
Found at i:254464 original size:102 final size:101
Alignment explanation
Indices: 254272--254488 Score: 353
Period size: 102 Copynumber: 2.1 Consensus size: 101
254262 TCCTAAGTCC
** * * *
254272 TGTTGATTAAATGGTGATTTGGTAGTTTACCATTATTGATTAAATGGGTGATTTGGTGGTTTGCC
1 TGTTGATTAAATGGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTACC
254337 ATTGTTGACTAAATGGGAGATTTGGTAGCTTACCAT
66 ATTGTTGACTAAATGGGAGATTTGGTAGCTTACCAT
254373 TGTTGATTAAATGAGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTAC
1 TGTTGATTAAATG-GAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTAC
* * *
254438 CATTGTTGACTAAATGGTAGATTTGGTAGGTTGCCAT
65 CATTGTTGACTAAATGGGAGATTTGGTAGCTTACCAT
254475 TGTTGATTAAATGG
1 TGTTGATTAAATGG
254489 TGGTTTTTAC
Statistics
Matches: 107, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
101 14 0.13
102 93 0.87
ACGTcount: A:0.25, C:0.08, G:0.26, T:0.41
Consensus pattern (101 bp):
TGTTGATTAAATGGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTACC
ATTGTTGACTAAATGGGAGATTTGGTAGCTTACCAT
Found at i:254849 original size:19 final size:19
Alignment explanation
Indices: 254793--254855 Score: 90
Period size: 19 Copynumber: 3.3 Consensus size: 19
254783 TGGTTGTCGA
**
254793 GGTACTATTCACGTATATA
1 GGTACTATTCACGTATACG
254812 GGTACTATTCACGTATACG
1 GGTACTATTCACGTATACG
*
254831 GGTACTATTCAAGTATACG
1 GGTACTATTCACGTATACG
*
254850 GTTACT
1 GGTACT
254856 GTACACGTGA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (19 bp):
GGTACTATTCACGTATACG
Found at i:258978 original size:34 final size:34
Alignment explanation
Indices: 258921--259139 Score: 280
Period size: 34 Copynumber: 6.5 Consensus size: 34
258911 AAGTGGGAGA
*
258921 ATTGTTGATTAAAT-GGTGATTTGGTAGTTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* * * *
258954 ATTATTGATTAAATGGGTGATTTGGTGGTTTGCC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* *
258988 ATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* **
259022 ATTGTTGATTAAATGAGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* *
259056 ATTATTGATTAAATGGGTGATTTGGTGGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* * *
259090 ATTGTTGACTAAAT-GGTAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGT-GATTTGGTAGCTTACC
259124 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
259140 TGGTTTTTAC
Statistics
Matches: 160, Mismatches: 23, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
33 16 0.10
34 143 0.89
35 1 0.01
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.41
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
Found at i:259061 original size:102 final size:101
Alignment explanation
Indices: 258921--259139 Score: 357
Period size: 102 Copynumber: 2.2 Consensus size: 101
258911 AAGTGGGAGA
** * * *
258921 ATTGTTGATTAAATGGTGATTTGGTAGTTTACCATTATTGATTAAATGGGTGATTTGGTGGTTTG
1 ATTGTTGATTAAATGGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTA
258986 CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
66 CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
259022 ATTGTTGATTAAATGAGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTT
1 ATTGTTGATTAAATG-GAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTT
* * *
259087 ACCATTGTTGACTAAATGGTAGATTTGGTAGGTTGCC
65 ACCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
259124 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
259140 TGGTTTTTAC
Statistics
Matches: 109, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
101 16 0.15
102 93 0.85
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.41
Consensus pattern (101 bp):
ATTGTTGATTAAATGGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTA
CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
Found at i:271259 original size:13 final size:13
Alignment explanation
Indices: 271241--271266 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
271231 TGTCTCTAAA
271241 TTTTATTTTTATT
1 TTTTATTTTTATT
271254 TTTTATTTTTATT
1 TTTTATTTTTATT
271267 CACTAATTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (13 bp):
TTTTATTTTTATT
Found at i:275945 original size:12 final size:12
Alignment explanation
Indices: 275924--275956 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
275914 CTTGAGCATA
275924 AAATTAAAATTC
1 AAATTAAAATTC
*
275936 AAATTCAAATTC
1 AAATTAAAATTC
275948 AAATTAAAA
1 AAATTAAAA
275957 CCCAAGGAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.61, C:0.09, G:0.00, T:0.30
Consensus pattern (12 bp):
AAATTAAAATTC
Found at i:278117 original size:2 final size:2
Alignment explanation
Indices: 278110--278137 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
278100 ATGCCAAGCT
278110 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
278138 ATAAGACGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:280147 original size:2 final size:2
Alignment explanation
Indices: 280134--280166 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
280124 CATAAACTAT
*
280134 TA TA TC 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 T
280167 GTGTGTGTGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:280964 original size:27 final size:28
Alignment explanation
Indices: 280925--280993 Score: 79
Period size: 27 Copynumber: 2.5 Consensus size: 28
280915 ATTTAATTTA
* *
280925 TTTAAATTAAAAATTAATTTA-TTT-AAT
1 TTTAAA-TCAAAATTAATTAATTTTAAAT
280952 TTTAATATCAAAATTAATTAATTTTAAAT
1 TTTAA-ATCAAAATTAATTAATTTTAAAT
*
280981 TTTAAATTAAAAT
1 TTTAAATCAAAAT
280994 ACTTAAATCG
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
27 17 0.47
28 11 0.31
29 8 0.22
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (28 bp):
TTTAAATCAAAATTAATTAATTTTAAAT
Found at i:280999 original size:27 final size:28
Alignment explanation
Indices: 280925--280999 Score: 75
Period size: 28 Copynumber: 2.6 Consensus size: 28
280915 ATTTAATTTA
*
280925 TTTAAATTAAAA-ATTAATTTATTTAAT
1 TTTAAATTAAAATATTAATTTATTAAAT
*
280952 TTTAATATCAAAATTAATTAA-TT-TTAAAT
1 TTTAA-ATTAAAA-T-ATTAATTTATTAAAT
280981 TTTAAATTAAAATACTTAA
1 TTTAAATTAAAATA-TTAA
281000 ATCGTTATTA
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
26 1 0.03
27 10 0.25
28 12 0.30
29 10 0.25
30 2 0.05
31 5 0.12
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (28 bp):
TTTAAATTAAAATATTAATTTATTAAAT
Found at i:281105 original size:23 final size:22
Alignment explanation
Indices: 281070--281141 Score: 76
Period size: 23 Copynumber: 3.2 Consensus size: 22
281060 TATCTTCTTT
*
281070 TTTAATTAGATTTTTAGTTTAA
1 TTTAATTAGATTTTTAATTTAA
281092 GTTTATATTA-ATTTTTAATTTAAA
1 -TTTA-ATTAGATTTTTAATTT-AA
*
281116 TTTAAATAGA-TTTTAATTTTAA
1 TTTAATTAGATTTTTAA-TTTAA
281138 TTTA
1 TTTA
281142 TATTTTATTA
Statistics
Matches: 43, Mismatches: 2, Indels: 9
0.80 0.04 0.17
Matches are distributed among these distances:
22 15 0.35
23 22 0.51
24 6 0.14
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (22 bp):
TTTAATTAGATTTTTAATTTAA
Found at i:281874 original size:3 final size:3
Alignment explanation
Indices: 281866--281899 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
281856 ATATATACGT
281866 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
281900 AAAAATCTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:307405 original size:24 final size:23
Alignment explanation
Indices: 307374--307418 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 23
307364 TCAAGAATTT
*
307374 TAAAAAAATTATTTTT-ATTTTGA
1 TAAAAAAA-AATTTTTGATTTTGA
307397 TAAACAAAAAATTTTTGATTTT
1 TAAA-AAAAAATTTTTGATTTT
307419 AAAATTTTGG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.49
Consensus pattern (23 bp):
TAAAAAAAAATTTTTGATTTTGA
Found at i:308343 original size:2 final size:2
Alignment explanation
Indices: 308331--308361 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
308321 CCTCAACCCC
*
308331 TA TA TA CA 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 T
308362 GACATAACGC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:308545 original size:21 final size:21
Alignment explanation
Indices: 308521--308614 Score: 70
Period size: 21 Copynumber: 4.5 Consensus size: 21
308511 TATTTATTAT
*
308521 ATATTTTTATATAAATATAAA
1 ATATATTTATATAAATATAAA
308542 ATATTATTT-T-TAAATATATAA
1 ATA-TATTTATATAAATATA-AA
* * * *
308563 A-ATAATTACATAAAAATTAA
1 ATATATTTATATAAATATAAA
308583 ATATATTTATATAAA-ATAGATA
1 ATATATTTATATAAATATA-A-A
*
308605 TTATATTTAT
1 ATATATTTAT
308615 TATTCTCAAA
Statistics
Matches: 57, Mismatches: 9, Indels: 13
0.72 0.11 0.16
Matches are distributed among these distances:
19 4 0.07
20 14 0.25
21 25 0.44
22 14 0.25
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (21 bp):
ATATATTTATATAAATATAAA
Found at i:311249 original size:30 final size:30
Alignment explanation
Indices: 311208--311278 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 30
311198 TATTATTTAT
*
311208 AATAATATTATTATTAA-ATGTAATAAATAAA
1 AATATTATTATTATTAATATGT--TAAATAAA
* *
311239 AAT-TTATTATTTTTAATATGTTAGATAAA
1 AATATTATTATTATTAATATGTTAAATAAA
311268 AATATTATTAT
1 AATATTATTAT
311279 ATATGATAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
29 10 0.29
30 18 0.51
31 7 0.20
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.46
Consensus pattern (30 bp):
AATATTATTATTATTAATATGTTAAATAAA
Found at i:311578 original size:7 final size:7
Alignment explanation
Indices: 311568--311598 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
311558 TTTAACTTTT
*
311568 CTTTCGC
1 CTTTCTC
311575 CTTTCTC
1 CTTTCTC
311582 CTTTCTC
1 CTTTCTC
311589 CTTTCTC
1 CTTTCTC
311596 CTT
1 CTT
311599 CTTCCTCCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.00, C:0.42, G:0.03, T:0.55
Consensus pattern (7 bp):
CTTTCTC
Found at i:320984 original size:14 final size:14
Alignment explanation
Indices: 320965--320993 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
320955 AGAAAAGGCA
320965 TTAACTTACAGATT
1 TTAACTTACAGATT
320979 TTAACTTACAGATT
1 TTAACTTACAGATT
320993 T
1 T
320994 GTTTGAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.14, G:0.07, T:0.45
Consensus pattern (14 bp):
TTAACTTACAGATT
Found at i:323303 original size:99 final size:99
Alignment explanation
Indices: 323132--323323 Score: 314
Period size: 99 Copynumber: 1.9 Consensus size: 99
323122 TTAGAAACTT
* * *
323132 TGTTAGTAACATGCAGGGAGAGAACCAGGTTGCAGCAGGTAGCTGGCAATTAATTGTTTTGAGAT
1 TGTTAGTAACACGCAGGGAGAGAACCAAGTTGCAGCAGCTAGCTGGCAATTAATTGTTTTGAGAT
323197 GCTAATAACCACAATGTTACTTGTTCATTTGGCA
66 GCTAATAACCACAATGTTACTTGTTCATTTGGCA
*
323231 TGTTAGTAACACGCAGGGAGAGAACCAAGTTGCATCAGCTAG-TAGGCAATTAATTGTTTTGAGA
1 TGTTAGTAACACGCAGGGAGAGAACCAAGTTGCAGCAGCTAGCT-GGCAATTAATTGTTTTGAGA
* *
323295 TGCTAATAACCACGATGTTGCTTGTTCAT
65 TGCTAATAACCACAATGTTACTTGTTCAT
323324 ATGGTATCTC
Statistics
Matches: 86, Mismatches: 6, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
98 1 0.01
99 85 0.99
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.30
Consensus pattern (99 bp):
TGTTAGTAACACGCAGGGAGAGAACCAAGTTGCAGCAGCTAGCTGGCAATTAATTGTTTTGAGAT
GCTAATAACCACAATGTTACTTGTTCATTTGGCA
Found at i:325484 original size:2 final size:2
Alignment explanation
Indices: 325473--325510 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
325463 GTATTTGTTT
325473 TA TA -A 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
325511 TTTATTTTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:327190 original size:87 final size:86
Alignment explanation
Indices: 327069--327236 Score: 291
Period size: 87 Copynumber: 1.9 Consensus size: 86
327059 ATTAGATAGA
*
327069 TTTTTTTTGTTGTTTCTTCCCTGCTAACTGTTTCAAGCTGTCTGCTTTGATTATTTTGAAACTTT
1 TTTTTTTTGTTGTTTCTTCCCTGCTAACTATTTCAAGCTGTCTGCTTTGATTATTTTGAAACTTT
*
327134 TCCTCTCATTTTTCTGCAGAT
66 TCATCTCATTTTTCTGCAGAT
* *
327155 TTTTTTTTGTTGTTTCTTTCCCTGCTAACTATTTCAAGCTGTTTGCTTTGATTATTTTGGAACTT
1 TTTTTTTTGTTGTTTC-TTCCCTGCTAACTATTTCAAGCTGTCTGCTTTGATTATTTTGAAACTT
327220 TTCATCTCATTTTTCTG
65 TTCATCTCATTTTTCTG
327237 ATGTATGATT
Statistics
Matches: 77, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
86 16 0.21
87 61 0.79
ACGTcount: A:0.14, C:0.18, G:0.12, T:0.55
Consensus pattern (86 bp):
TTTTTTTTGTTGTTTCTTCCCTGCTAACTATTTCAAGCTGTCTGCTTTGATTATTTTGAAACTTT
TCATCTCATTTTTCTGCAGAT
Found at i:331792 original size:3 final size:3
Alignment explanation
Indices: 331784--331819 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
331774 TACTATATGT
331784 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
331820 CTAGGATTGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:337171 original size:24 final size:24
Alignment explanation
Indices: 337144--337190 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
337134 GAGTTCGACG
*
337144 ATAATGTTAGTATAAATGGTTTTA
1 ATAATGCTAGTATAAATGGTTTTA
337168 ATAATGCTAGTATAAATGGTTTT
1 ATAATGCTAGTATAAATGGTTTT
337191 GATATGTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.36, C:0.02, G:0.17, T:0.45
Consensus pattern (24 bp):
ATAATGCTAGTATAAATGGTTTTA
Found at i:337310 original size:2 final size:2
Alignment explanation
Indices: 337305--337331 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
337295 TGCGTATGTC
337305 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
337332 GTTTAACTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:338074 original size:26 final size:25
Alignment explanation
Indices: 338036--338092 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 25
338026 ATGTATTTCG
*
338036 TTTTTGTTGTTGA-CCGAAGTTTTTT
1 TTTTTTTTGTTGATCC-AAGTTTTTT
* *
338061 TTTTTTTTGCTTGATTCAGGTTTTTT
1 TTTTTTTTG-TTGATCCAAGTTTTTT
338087 TTTTTT
1 TTTTTT
338093 CTGTGCACTG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 8 0.30
26 18 0.67
27 1 0.04
ACGTcount: A:0.09, C:0.07, G:0.16, T:0.68
Consensus pattern (25 bp):
TTTTTTTTGTTGATCCAAGTTTTTT
Found at i:345655 original size:3 final size:3
Alignment explanation
Indices: 345647--345685 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
345637 CAAAGTCAAG
345647 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
345686 TATAGAATTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:353640 original size:4 final size:4
Alignment explanation
Indices: 353631--353690 Score: 84
Period size: 4 Copynumber: 15.0 Consensus size: 4
353621 CAATGTCCTA
* *
353631 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATGT ATGT ATAT ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
* *
353679 ATGT ATGT ATAT
1 ATAT ATAT ATAT
353691 TTTTTTAATA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 52 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (4 bp):
ATAT
Found at i:354943 original size:2 final size:2
Alignment explanation
Indices: 354936--354982 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
354926 GATCGAATCT
354936 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
354978 TA TA T
1 TA TA T
354983 TCCTTTATTG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:355406 original size:21 final size:21
Alignment explanation
Indices: 355380--355420 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
355370 TTCAATTTAA
355380 AAAAAAAAAGAAACGAAAAAC
1 AAAAAAAAAGAAACGAAAAAC
*
355401 AAAAAAAGAGAAACGAAAAA
1 AAAAAAAAAGAAACGAAAAA
355421 ACATTCGACT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.80, C:0.07, G:0.12, T:0.00
Consensus pattern (21 bp):
AAAAAAAAAGAAACGAAAAAC
Found at i:358174 original size:11 final size:12
Alignment explanation
Indices: 358130--358173 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
358120 GAGTGGGCGG
*
358130 GGGGCTGGGGCT
1 GGGGCTGGGGAT
358142 GGGGCTGGGGAT
1 GGGGCTGGGGAT
**
358154 GGGTAT-GGGAT
1 GGGGCTGGGGAT
358165 GGGGCTGGG
1 GGGGCTGGG
358174 ACTGGAGAGA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
11 9 0.35
12 17 0.65
ACGTcount: A:0.07, C:0.09, G:0.66, T:0.18
Consensus pattern (12 bp):
GGGGCTGGGGAT
Found at i:358522 original size:2 final size:2
Alignment explanation
Indices: 358515--358544 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
358505 CACCAACGCA
358515 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
358545 ATATATATAT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Done.