Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2326
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: 94483
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:3066 original size:38 final size:38
Alignment explanation
Indices: 3011--3097 Score: 120
Period size: 38 Copynumber: 2.3 Consensus size: 38
3001 AACACCAACC
* * * *
3011 ACTATTTTAAACTGGTGGTACGGTTTGAAACGAAAACT
1 ACTATTTTAAACCGGTGGCACGATTCGAAACGAAAACT
*
3049 ACTATTTTAAACCGGTGGCACGATTCGAAACGAAAATT
1 ACTATTTTAAACCGGTGGCACGATTCGAAACGAAAACT
3087 ACTATTCTTAA
1 ACTATT-TTAA
3098 TCGGTGACAC
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
38 39 0.91
39 4 0.09
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.31
Consensus pattern (38 bp):
ACTATTTTAAACCGGTGGCACGATTCGAAACGAAAACT
Found at i:4612 original size:20 final size:20
Alignment explanation
Indices: 4584--4658 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
4574 TTTTACCTAG
4584 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
4604 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
4624 ATGTATTGATATATTCTTCA
1 ATGTATCGATACATTTTTCA
4644 ATGTATCGATACATT
1 ATGTATCGATACATT
4659 ATGTCTTTTT
Statistics
Matches: 42, Mismatches: 13, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.43
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:4644 original size:40 final size:39
Alignment explanation
Indices: 4584--4661 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
4574 TTTTACCTAG
*
4584 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTTCAATATATCGATACAT-TATGA
* * *
4624 ATGTATTGATATATTCTTCAATGTATCGATACATTATG
1 ATGTATCGATACATTCTTCAATATATCGATACATTATG
4662 TCTTTTTACC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.33, C:0.12, G:0.13, T:0.42
Consensus pattern (39 bp):
ATGTATCGATACATTCTTCAATATATCGATACATTATGA
Found at i:6873 original size:10 final size:10
Alignment explanation
Indices: 6858--6889 Score: 64
Period size: 10 Copynumber: 3.2 Consensus size: 10
6848 ATTTTATTTA
6858 TCGGGGATAC
1 TCGGGGATAC
6868 TCGGGGATAC
1 TCGGGGATAC
6878 TCGGGGATAC
1 TCGGGGATAC
6888 TC
1 TC
6890 CAACCCCATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.19, C:0.22, G:0.38, T:0.22
Consensus pattern (10 bp):
TCGGGGATAC
Found at i:18683 original size:11 final size:11
Alignment explanation
Indices: 18669--18695 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
18659 AAAAAATTAA
18669 AAAAACAAAAC
1 AAAAACAAAAC
18680 AAAAACAAAAC
1 AAAAACAAAAC
18691 AAAAA
1 AAAAA
18696 ATAAAAAACT
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:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAACAAAAC
Found at i:19984 original size:29 final size:29
Alignment explanation
Indices: 19944--22283 Score: 2599
Period size: 29 Copynumber: 80.9 Consensus size: 29
19934 TGTTCATCCC
19944 TTTCAAAGCCCACAAGTCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
19973 TTTCAAAGCCCACAAATCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
20002 TTTCAAAGCCAACAAGTCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* * *
20031 TTTCAAAGCCCATAAATCAGTGGCACCCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
20060 TTTCAAAGCCCACGAGTCAGTGGCAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
20088 TTTCAAAGCCCACAAGTCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* * * *
20117 TTTCAAAGCTCATAAATCAGTGGCATTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
20146 TTTCAAAGCCCACGAGTCAGTGGCAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
20174 TTTCAAAGCCCACAAGTCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
20203 TTTCAAAGCCTACAAGTTAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
20232 TTTCAAAGCCCACGAGTCAGTGGCACCCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* * *
20261 TTCCAAAGCCCACAAGTTAGTGGCACCCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
20290 TTCCAAAGCCCACAAGTCAATGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
20319 TTTCAAAGCCCACAAATCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
20348 TTTCAAAGCCCACAAGTCGGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
20377 TTTCAAAGCCCATAAATCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
20406 TTTCAAAGCCCACAAGTCAGTGACACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
20435 TTTCAAAGCCCACAAGTCAGTGGCAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
20463 TTTCAAAGCCCACAAGTCAGTGGCACCCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* * * *
20492 TTCCAAAACCCACAAGTGAGTGGCAC-CA
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* * * * * **
20520 CTGCGGAAGCCTTGGCA-AAG--ACT-TCAAGCT
1 TTTC-AAAGCC----CACAAGTCAGTGGCACTCT
* ** * * * *
20550 CTAGAAA-CCCTGCATCATTCGGGTAAG-ACTCT
1 TTTCAAAGCCC-ACA--AGTC-AGT-GGCACTCT
** ** ** * * *
20582 TTTC--TTCTTATCATCTTAG-GCCAAGACCCT
1 TTTCAAAGCCCA-CAAGTCAGTGGC---ACTCT
*** * ** * *
20612 TTT----G-CCATTTGTCA-AGAAATTACC
1 TTTCAAAGCCCACAAGTCAGTGGCACT-CT
* * ** * * *
20636 GTT--AAGAACTTC-TGTCTAGAATGTTCA-TCCC
1 TTTCAAAG-CCCACAAGTC-AG--TG-GCACT-CT
20667 TTTCAAAGCCCACAAGTCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
20696 TTTCAAAGCCCACAAATCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
20725 TTTCAAAGCCCACAAGTCAGTGGTACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
20754 TTTCAAAGCCCACAAGTCAGTGGCACCCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
20783 TTTCAAAGCCCACGAGTCAGTGGCAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
20811 TTTCAAAGCCCACAAGTCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
20840 TTTCAAAGCCCATAAATCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
20869 TTTCAAAGCTCA-AGAGTCAGTGGCAC-CC
1 TTTCAAAGCCCACA-AGTCAGTGGCACTCT
*
20897 TTTCAAAGCCCACAAGTTAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
20926 TTTCAAAGCCTACAAGTTAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
20955 TTTCAAAGCCCACGAGTCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
20984 TTTCAAAGCCCACAAATCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
21013 TTTCAAAGCCCACAAGTCAATGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
21042 TTTCAAAGCCTACAAATCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
21071 TTTCAAAGCCCACAAGTCGGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
21100 TTTCAAAGCCCATAAATCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
21129 TTTCAAAGCCCACAAGTCAGTGACACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
21158 TTTCAAAGCTCACAAGTCAGTGGCAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
21186 TTTCAAAGCCCACAAGTCAGTGGCACCCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* * *
21215 TTCCAAAACCCACAAGTGAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
21244 TTTCAAAGCCCACGAGTCAGTGGCACCCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
21273 TTCCAAAGCCCACAAGTCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
21302 TTTCAAAGCCCACAAATCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
21331 TTTCAAAGCCCACAAGTCAGTGGTACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
21360 TTTCAAAGCCCACAAATCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
21389 TTTTAAAGCCCACAAATCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
21418 TTTCAAAGCCCACAAGTCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* * *
21447 TTTCAAAGCCCACGAGTCAGTGACAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
21475 TTTCAAAGCCCAGAAGTCAGTGGCA-TCCT
1 TTTCAAAGCCCACAAGTCAGTGGCACT-CT
* *
21504 TTCCAAAGCCCACAAGTTAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
21533 TCTCAAAGCCCACAAATCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
21562 TTTCAAAGCCCACAAGTCAATGACACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
**
21591 TTTCAAAGCCCACACGAGTTGGTGGCAACTCT
1 TTTCAAAGCCCACA--AGTCAGTGGC-ACTCT
*
21623 TTCCAAAGCCCACAAGTCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
21652 TTTCAAAGCTCACAAGTCAGTGGCAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
21680 TTTAAAAGCCCACAAGTCAGTGGCA-TCC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
21708 TTTCAAAGCCCACAAGTCAGTGGCAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* * *
21736 TTTCAAAGACCATGCAAGTTAGTGGCAC-CC
1 TTTCAAAGCCCA--CAAGTCAGTGGCACTCT
*
21766 TTTCAAAGCCCACAAATCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
21795 TTTCAAAGCCCACAAGTCAGTGGCAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
21823 TTTCAAAGCCAACAAGTTAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
21852 TTTCAAAGCCCACAAGTTAGTGGCA-TCC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
21880 TTTCAAAGCCCACAAGTCAGTGGCA-TCC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
21908 TTTCAAAGCCCACAAGTCAGTGGCAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
21936 TTTCAAAGCCCATGCAAGTCAGTGGCAC-CC
1 TTTCAAAGCCCA--CAAGTCAGTGGCACTCT
* * *
21966 TTTCAAAGCTCATAAATCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
21995 TTTCAAAGCCCACAAGTCAGTGGCACTTT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* * * *
22024 TTTCGAAGCCCAAAAGTTAGTGGCA-TCC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* * *
22052 TTTCAATGCCCACAAGTTAGTGGCAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
**
22080 TTTCAAAGCCCACGTAAGTTGGTGGCACTC-
1 TTTCAAAGCCCAC--AAGTCAGTGGCACTCT
* *
22110 TTTCAAAACCCACAAGTTAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* * *
22139 TTTCAAAGCCCATAAGTCAATGGCAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
22167 TTTCAAAGCCCACAAGTCAGTGGCAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
22195 TTTCAAAGCCCATAAGGT-AGTGGCACTCT
1 TTTCAAAGCCCACAA-GTCAGTGGCACTCT
**
22224 TTTCAAAGCCCACACGAGTTGGTGGCAACTCT
1 TTTCAAAGCCCACA--AGTCAGTGGC-ACTCT
*
22256 TTTCAAAGCCCACACAAGTTAGTGGCAC
1 TTTCAAAG-CC-CACAAGTCAGTGGCAC
22284 CATTTTTTTT
Statistics
Matches: 1984, Mismatches: 254, Indels: 144
0.83 0.11 0.06
Matches are distributed among these distances:
23 1 0.00
24 4 0.00
26 6 0.00
27 5 0.00
28 467 0.24
29 1307 0.66
30 103 0.05
31 25 0.01
32 52 0.03
33 10 0.01
34 4 0.00
ACGTcount: A:0.29, C:0.30, G:0.17, T:0.24
Consensus pattern (29 bp):
TTTCAAAGCCCACAAGTCAGTGGCACTCT
Found at i:21179 original size:723 final size:722
Alignment explanation
Indices: 19793--21934 Score: 2990
Period size: 723 Copynumber: 3.0 Consensus size: 722
19783 GGTCTGCTGA
*
19793 ACCACTGCGGAAGCCTTGGCAAAGACTTCAAGCTCTAGAAACCCTGCGTCATTCGGGTAAGACTC
1 ACCACTGCGGAAGCCTTGGCAAAGACTTCAAGCTCTAGAAACCCTGCATCATTCGGGTAAGACTC
19858 TTTTCTTCTTATCATCTTAGGCCAAGACCCTTTTGCCATTTGTCAAGAAATTACCGTTAAGAACT
66 TTTTCTTCTTATCATCTTAGGCCAAGACCCTTTTGCCATTTGTCAAGAAATTACCGTTAAGAACT
19923 TCTGTCTAGAATGTTCATCCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAA
131 TCTGTCTAGAATGTTCATCCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAA
* * *
19988 ATCAGTGGCACTCTTTTCAAAGCCAACAAGTCAGTGGCACTCTTTTCAAAGCCCATAAATCAGTG
196 ATCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTG
20053 GCACCCTTTTCAAAGCCCACGAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTT
261 GCACCCTTTTCAAAGCCCACGAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTT
* * *
20118 TTCAAAGCTCATAAATCAGTGGCATTCTTTTCAAAGCCCACGAGTCAGTGGCACCCTTTCAAAGC
326 TTCAAAGCCCATAAATCAGTGGCACTCTTTTCAAAGCCCAAGAGTCAGTGGCACCCTTTCAAAGC
*
20183 CCACAAGTCAGTGGCACTCTTTTCAAAGCCTACAAGTTAGTGGCACTCTTTTCAAAGCCCACGAG
391 CCACAAGTTAGTGGCACTCTTTTCAAAGCCTACAAGTTAGTGGCACTCTTTTCAAAGCCCACGAG
* * * *
20248 TCAGTGGCACCCTTTCCAAAGCCCACAAGTTAGTGGCACCCTTTCCAAAGCCCACAAGTCAATGG
456 TCAGTGGCA-CCTTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAATGG
*
20313 CACTCTTTTCAAAGCCCACAAATCAGTGGCACTCTTTTCAAAGCCCACAAGTCGGTGGCACTCTT
520 CACTCTTTTCAAAGCCTACAAATCAGTGGCACTCTTTTCAAAGCCCACAAGTCGGTGGCACTCTT
20378 TTCAAAGCCCATAAATCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGACACTCTTTTCAAAG
585 TTCAAAGCCCATAAATCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGACACTCTTTTCAAAG
20443 CCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCCAAAACCCACAAG
650 CCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCCAAAACCCACAAG
20508 TGAGTGGC
715 TGAGTGGC
20516 ACCACTGCGGAAGCCTTGGCAAAGACTTCAAGCTCTAGAAACCCTGCATCATTCGGGTAAGACTC
1 ACCACTGCGGAAGCCTTGGCAAAGACTTCAAGCTCTAGAAACCCTGCATCATTCGGGTAAGACTC
20581 TTTTCTTCTTATCATCTTAGGCCAAGACCCTTTTGCCATTTGTCAAGAAATTACCGTTAAGAACT
66 TTTTCTTCTTATCATCTTAGGCCAAGACCCTTTTGCCATTTGTCAAGAAATTACCGTTAAGAACT
20646 TCTGTCTAGAATGTTCATCCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAA
131 TCTGTCTAGAATGTTCATCCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAA
*
20711 ATCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGTACTCTTTTCAAAGCCCACAAGTCAGTG
196 ATCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTG
20776 GCACCCTTTTCAAAGCCCACGAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTT
261 GCACCCTTTTCAAAGCCCACGAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTT
*
20841 TTCAAAGCCCATAAATCAGTGGCACTCTTTTCAAAGCTCAAGAGTCAGTGGCACCCTTTCAAAGC
326 TTCAAAGCCCATAAATCAGTGGCACTCTTTTCAAAGCCCAAGAGTCAGTGGCACCCTTTCAAAGC
20906 CCACAAGTTAGTGGCACTCTTTTCAAAGCCTACAAGTTAGTGGCACTCTTTTCAAAGCCCACGAG
391 CCACAAGTTAGTGGCACTCTTTTCAAAGCCTACAAGTTAGTGGCACTCTTTTCAAAGCCCACGAG
*
20971 TCAGTGGCACTCTTTTCAAAGCCCACAAATCAGTGGCACTCTTTTCAAAGCCCACAAGTCAATGG
456 TCAGTGGCAC-CTTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAATGG
21036 CACTCTTTTCAAAGCCTACAAATCAGTGGCACTCTTTTCAAAGCCCACAAGTCGGTGGCACTCTT
520 CACTCTTTTCAAAGCCTACAAATCAGTGGCACTCTTTTCAAAGCCCACAAGTCGGTGGCACTCTT
21101 TTCAAAGCCCATAAATCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGACACTCTTTTCAAAG
585 TTCAAAGCCCATAAATCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGACACTCTTTTCAAAG
*
21166 CTCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCCAAAACCCACAAG
650 CCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCCAAAACCCACAAG
21231 TGAGTGGC
715 TGAGTGGC
** * * *** *** * * ** * ** * * * *
21239 ACTCTTTTC-AAAGCCCACG-AGTCAGTGGCACCCTTTCCAAAGCC--CA-CAAGTC-AGT-GGC
1 AC-CACTGCGGAAGCCTTGGCAAAGACT-TCAAGCTCTAGAAACCCTGCATC-ATTCGGGTAAG-
* ** ** * * *
21297 ACTC--TT-TTC--A--A----AGCCCACA-AATC-AGTGGCACTCTTTTC---AAA--GCC---
62 ACTCTTTTCTTCTTATCATCTTAGGCCA-AGACCCTTTTGCCA-T-TTGTCAAGAAATTACCGTT
* * * * * *
21341 CACAA-----GTC-AG--TGGT-A-CTCTTTTCAAAGCCCACAAATCAGTGGCACTCTTTTTAAA
124 AAGAACTTCTGTCTAGAATGTTCATC-CCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAA
*
21396 GCCCACAAATCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACG
188 GCCCACAAATCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACA
* * *
21461 AGTCAGTGACACCC-TTTCAAAGCCCA-GAAGTCAGTGGCATCCTTTCCAAAGCCCACAAGTTAG
253 AGTCAGTGGCACCCTTTTCAAAGCCCACG-AGTCAGTGGCACCCTTT-CAAAGCCCACAAGTCAG
* * * *
21524 TGGCACTCTTCTCAAAGCCCACAAATCAGTGGCACTCTTTTCAAAGCCCACA-AGTCAATGACAC
316 TGGCACTCTTTTCAAAGCCCATAAATCAGTGGCACTCTTTTCAAAGCCCA-AGAGTCAGTGGCAC
* * * * *
21588 TCTTTTCAAAGCCCACACGAGTTGGTGGCAACTCTTTCCAAAGCCCACAAGTCAGTGGCACTCTT
380 -CCTTTCAAAGCCCACA--AGTTAGTGGC-ACTCTTTTCAAAGCCTACAAGTTAGTGGCACTCTT
* * * * *
21653 TTCAAAGCTCACAAGTCAGTGGCACCCTTTAAAAGCCCACAAGTCAGTGGCA-TCCTTTCAAAGC
441 TTCAAAGCCCACGAGTCAGTGGCACCTTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGC
* * * * * *
21717 CCACAAGTCAGTGGCAC-CCTTTCAAAGACCATGCAAGTTAGTGGCAC-CCTTTCAAAGCCCACA
506 CCACAAGTCAATGGCACTCTTTTCAAAG-CC-TACAAATCAGTGGCACTCTTTTCAAAGCCCACA
* * * * * * *
21780 AATCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCAACAAGTTAGT
569 AGTCGGTGGCACTCTTTTCAAAGCCCATAAATCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGT
* * * *
21844 GGCACTCTTTTCAAAGCCCACAAGTTAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCCT
634 GACACTCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCT
* *
21909 TT-CAAAGCCCACAAGTCAGTGGC
699 TTCCAAAACCCACAAGTGAGTGGC
21932 ACC
1 ACC
21935 CTTTCAAAGC
Statistics
Matches: 1308, Mismatches: 93, Indels: 67
0.89 0.06 0.05
Matches are distributed among these distances:
691 1 0.00
692 30 0.02
693 206 0.16
694 110 0.08
695 81 0.06
696 48 0.04
697 58 0.04
702 3 0.00
705 2 0.00
707 3 0.00
708 4 0.00
709 8 0.01
710 5 0.00
713 1 0.00
715 1 0.00
717 3 0.00
718 2 0.00
719 1 0.00
720 7 0.01
721 5 0.00
722 4 0.00
723 722 0.55
724 3 0.00
ACGTcount: A:0.28, C:0.30, G:0.17, T:0.24
Consensus pattern (722 bp):
ACCACTGCGGAAGCCTTGGCAAAGACTTCAAGCTCTAGAAACCCTGCATCATTCGGGTAAGACTC
TTTTCTTCTTATCATCTTAGGCCAAGACCCTTTTGCCATTTGTCAAGAAATTACCGTTAAGAACT
TCTGTCTAGAATGTTCATCCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAA
ATCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTG
GCACCCTTTTCAAAGCCCACGAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTT
TTCAAAGCCCATAAATCAGTGGCACTCTTTTCAAAGCCCAAGAGTCAGTGGCACCCTTTCAAAGC
CCACAAGTTAGTGGCACTCTTTTCAAAGCCTACAAGTTAGTGGCACTCTTTTCAAAGCCCACGAG
TCAGTGGCACCTTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAATGGC
ACTCTTTTCAAAGCCTACAAATCAGTGGCACTCTTTTCAAAGCCCACAAGTCGGTGGCACTCTTT
TCAAAGCCCATAAATCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGACACTCTTTTCAAAGC
CCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCCAAAACCCACAAGT
GAGTGGC
Found at i:22874 original size:20 final size:20
Alignment explanation
Indices: 22846--22920 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
22836 TTTTACCTAG
22846 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
22866 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
22886 ATGTATTGATATATTCTTCA
1 ATGTATCGATACATTTTTCA
22906 ATGTATCGATACATT
1 ATGTATCGATACATT
22921 ATATCTTTTT
Statistics
Matches: 42, Mismatches: 13, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.43
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:26441 original size:20 final size:20
Alignment explanation
Indices: 26403--26446 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
26393 AAAAGTCACC
*
26403 AAAAAAATCATCAAAATTTTA
1 AAAAAAATCA-CAAAATTTCA
26424 AAAAAAATCA-AAATATTTCA
1 AAAAAAATCACAAA-ATTTCA
26444 AAA
1 AAA
26447 TAAGACATGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 3 0.14
20 8 0.38
21 10 0.48
ACGTcount: A:0.66, C:0.09, G:0.00, T:0.25
Consensus pattern (20 bp):
AAAAAAATCACAAAATTTCA
Found at i:29475 original size:210 final size:208
Alignment explanation
Indices: 29107--29493 Score: 603
Period size: 210 Copynumber: 1.9 Consensus size: 208
29097 ATTACTAACC
*
29107 TGGCTGTTGATTGTATGGACAGATTGCAATACCATTATGTTTTCTTATCGTAACCTGGAAAGTAT
1 TGGCTGTTGATTGTATGGACAGATTGCAATACCATTATGGTTTCTTATCGTAACCTGGAAAGTAT
29172 TGAATTTCATTTTTGGGACTTGGAGCTTCATTCCTTAACCCAAAAGAATAGACCAGAATTTCACA
66 TGAATTTCATTTTTGGGACTTGGAGCTTCATTCCTTAACCCAAAAGAATAGACCAGAATTTCACA
*
29237 TCCACTTTAAATCTTATGAGAATAAACAACTAAACAAATTGTTTATGTTCTAAAGATGTCTTAAT
131 TCCACTTTAAATCTTATCAGAATAAACAACTAAACAAATTGTTTATGTTCTAAAGATGTCTTAAT
29302 GATTGGATTGTCT
196 GATTGGATTGTCT
* * **
29315 TGGCTGTTGATTGTATGGACAGATTGCAATACTATTATGGTTTCTTATCGTAACCTAAGTATTGT
1 TGGCTGTTGATTGTATGGACAGATTGCAATACCATTATGGTTTCTTATCGTAACCT--GGAAAGT
* ** * * *
29380 GTTTCATTTCATTTTTGGGAGTTGGAGCTTTATTCCTTAACCCAAAAGAATAGACCATAATTTCA
64 ATTGAATTTCATTTTTGGGACTTGGAGCTTCATTCCTTAACCCAAAAGAATAGACCAGAATTTCA
* * * * *
29445 CTTCCACTTTGAATCTTATCCGAGTAAACAACTAAGCAAATTGTTTATG
129 CATCCACTTTAAATCTTATCAGAATAAACAACTAAACAAATTGTTTATG
29494 AGCATTTATA
Statistics
Matches: 160, Mismatches: 17, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
208 54 0.34
210 106 0.66
ACGTcount: A:0.30, C:0.16, G:0.17, T:0.37
Consensus pattern (208 bp):
TGGCTGTTGATTGTATGGACAGATTGCAATACCATTATGGTTTCTTATCGTAACCTGGAAAGTAT
TGAATTTCATTTTTGGGACTTGGAGCTTCATTCCTTAACCCAAAAGAATAGACCAGAATTTCACA
TCCACTTTAAATCTTATCAGAATAAACAACTAAACAAATTGTTTATGTTCTAAAGATGTCTTAAT
GATTGGATTGTCT
Found at i:30519 original size:17 final size:18
Alignment explanation
Indices: 30493--30526 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
30483 TTTCTTATTC
30493 ATGCATTTTTCCCCTCTG
1 ATGCATTTTTCCCCTCTG
30511 ATGCA-TTTTCCCCTCT
1 ATGCATTTTTCCCCTCT
30527 TTTGCGTCTG
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:0.12, C:0.35, G:0.09, T:0.44
Consensus pattern (18 bp):
ATGCATTTTTCCCCTCTG
Found at i:31935 original size:5 final size:5
Alignment explanation
Indices: 31925--31950 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
31915 ATGCAATGGT
31925 TCCTC TCCTC TCCTC TCCTC TCCTC T
1 TCCTC TCCTC TCCTC TCCTC TCCTC T
31951 TAAGATTAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.58, G:0.00, T:0.42
Consensus pattern (5 bp):
TCCTC
Found at i:33083 original size:23 final size:22
Alignment explanation
Indices: 33055--33100 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
33045 AATAAGAATT
33055 TCATATCAAAATCTTTTAATATA
1 TCATATCAAAAT-TTTTAATATA
* *
33078 TCATATTATAATTTTTAATATA
1 TCATATCAAAATTTTTAATATA
33100 T
1 T
33101 TAAATTACAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 11 0.52
23 10 0.48
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (22 bp):
TCATATCAAAATTTTTAATATA
Found at i:33922 original size:23 final size:23
Alignment explanation
Indices: 33892--33935 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
33882 TAAGTCAAAT
33892 TATTATATTTAATATAATAATAA
1 TATTATATTTAATATAATAATAA
* *
33915 TATTATATTTAGTATATTAAT
1 TATTATATTTAATATAATAAT
33936 TAATTTAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (23 bp):
TATTATATTTAATATAATAATAA
Found at i:34904 original size:6 final size:6
Alignment explanation
Indices: 34893--34947 Score: 53
Period size: 6 Copynumber: 9.2 Consensus size: 6
34883 TTATGATTAC
*
34893 TAATTT TAATTT TAATTT T-CTTT TAATTT TGAATTTTT TAATTT T-ATTT
1 TAATTT TAATTT TAATTT TAATTT TAATTT T-AA--TTT TAATTT TAATTT
34942 T-ATTT T
1 TAATTT T
34948 TTACTAGTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 9
0.80 0.04 0.17
Matches are distributed among these distances:
5 14 0.33
6 21 0.49
7 2 0.05
8 2 0.05
9 4 0.09
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.71
Consensus pattern (6 bp):
TAATTT
Found at i:34918 original size:17 final size:18
Alignment explanation
Indices: 34896--34929 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
34886 TGATTACTAA
34896 TTTTAATTTT-AATTTTC
1 TTTTAATTTTGAATTTTC
34913 TTTTAATTTTGAATTTT
1 TTTTAATTTTGAATTTT
34930 TTAATTTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.24, C:0.03, G:0.03, T:0.71
Consensus pattern (18 bp):
TTTTAATTTTGAATTTTC
Found at i:35499 original size:20 final size:21
Alignment explanation
Indices: 35467--35505 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
35457 TAGATGTTAT
35467 ATTTAATTTTTCTTAATAATA
1 ATTTAATTTTTCTTAATAATA
*
35488 ATTTAA-TTTTCTTCATAA
1 ATTTAATTTTTCTTAATAA
35506 AAATATGTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (21 bp):
ATTTAATTTTTCTTAATAATA
Found at i:35533 original size:18 final size:20
Alignment explanation
Indices: 35510--35549 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
35500 TCATAAAAAT
35510 ATGTTA-TTTGT-TGATATG
1 ATGTTAGTTTGTGTGATATG
*
35528 ATGTTAGTTTTTGTGATATG
1 ATGTTAGTTTGTGTGATATG
35548 AT
1 AT
35550 TTTGATTTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 6 0.32
19 4 0.21
20 9 0.47
ACGTcount: A:0.23, C:0.00, G:0.23, T:0.55
Consensus pattern (20 bp):
ATGTTAGTTTGTGTGATATG
Found at i:35558 original size:20 final size:21
Alignment explanation
Indices: 35516--35565 Score: 61
Period size: 19 Copynumber: 2.5 Consensus size: 21
35506 AAATATGTTA
35516 TTTGTTGATATGATGTTAGTT
1 TTTGTTGATATGATGTTAGTT
* *
35537 TTTG-TGATATGAT-TTTGAT
1 TTTGTTGATATGATGTTAGTT
35556 TTTGTT-ATAT
1 TTTGTTGATAT
35566 ATAAATATTC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
19 12 0.46
20 10 0.38
21 4 0.15
ACGTcount: A:0.20, C:0.00, G:0.20, T:0.60
Consensus pattern (21 bp):
TTTGTTGATATGATGTTAGTT
Found at i:44602 original size:10 final size:10
Alignment explanation
Indices: 44587--44634 Score: 51
Period size: 11 Copynumber: 4.5 Consensus size: 10
44577 AAATAAAATT
44587 AAAAAAAGAA
1 AAAAAAAGAA
*
44597 AAAAAATGAAA
1 AAAAAAAG-AA
44608 AAAAAAATGAA
1 AAAAAAA-GAA
*
44619 AAAAAGAGAA
1 AAAAAAAGAA
44629 AGAAAA
1 A-AAAA
44635 GTAAAAAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
10 11 0.34
11 20 0.62
12 1 0.03
ACGTcount: A:0.83, C:0.00, G:0.12, T:0.04
Consensus pattern (10 bp):
AAAAAAAGAA
Found at i:44605 original size:31 final size:33
Alignment explanation
Indices: 44570--44643 Score: 102
Period size: 30 Copynumber: 2.3 Consensus size: 33
44560 GCTTTGATTC
*
44570 AATGAAAAAATAAAATTAAAAAAAGA-AAA-AA
1 AATGAAAAAATAAAATGAAAAAAAGAGAAAGAA
44601 AATGAAAAAA-AAAATGAAAAAAAGAGAAAGAA
1 AATGAAAAAATAAAATGAAAAAAAGAGAAAGAA
44633 AA-GTAAAAAAT
1 AATG-AAAAAAT
44644 TGAAATTTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
30 14 0.37
31 14 0.37
32 10 0.26
ACGTcount: A:0.78, C:0.00, G:0.11, T:0.11
Consensus pattern (33 bp):
AATGAAAAAATAAAATGAAAAAAAGAGAAAGAA
Found at i:44615 original size:30 final size:32
Alignment explanation
Indices: 44570--44642 Score: 98
Period size: 31 Copynumber: 2.3 Consensus size: 32
44560 GCTTTGATTC
*
44570 AATGAAAAAATAAAATTAAAAAAAGA-AAA-AA
1 AATGAAAAAA-AAAATGAAAAAAAGAGAAAGAA
44601 AATGAAAAAAAAAATGAAAAAAAGAGAAAGAA
1 AATGAAAAAAAAAATGAAAAAAAGAGAAAGAA
*
44633 AA-GTAAAAAA
1 AATGAAAAAAA
44643 TTGAAATTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
30 14 0.37
31 20 0.53
32 4 0.11
ACGTcount: A:0.79, C:0.00, G:0.11, T:0.10
Consensus pattern (32 bp):
AATGAAAAAAAAAATGAAAAAAAGAGAAAGAA
Found at i:44620 original size:18 final size:17
Alignment explanation
Indices: 44574--44620 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 17
44564 TGATTCAATG
*
44574 AAAAAATAAAATTAAAA
1 AAAAAATAAAATGAAAA
*
44591 AAAGAAAAAAAATGAAAA
1 AAA-AAATAAAATGAAAA
44609 AAAAAATGAAAA
1 AAAAAAT-AAAA
44621 AAAGAGAAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
17 6 0.24
18 19 0.76
ACGTcount: A:0.83, C:0.00, G:0.06, T:0.11
Consensus pattern (17 bp):
AAAAAATAAAATGAAAA
Found at i:44629 original size:22 final size:21
Alignment explanation
Indices: 44587--44648 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
44577 AAATAAAATT
44587 AAAAAAAGAAAAAAAATGAAA
1 AAAAAAAGAAAAAAAATGAAA
*
44608 AAAAAAATG-AAAAAAA-GAGA
1 AAAAAAA-GAAAAAAAATGAAA
* * *
44628 AAGAAAAGTAAAAAATTGAAA
1 AAAAAAAGAAAAAAAATGAAA
44649 TTTTTTTCAA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
19 1 0.03
20 15 0.44
21 17 0.50
22 1 0.03
ACGTcount: A:0.79, C:0.00, G:0.13, T:0.08
Consensus pattern (21 bp):
AAAAAAAGAAAAAAAATGAAA
Found at i:44640 original size:20 final size:20
Alignment explanation
Indices: 44587--44648 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
44577 AAATAAAATT
*
44587 AAAAAAAGAAAAAAAATGAA
1 AAAAAAAGTAAAAAAATGAA
*
44607 AAAAAAAATGAAAAAAA-GAGA
1 AAAAAAAGT-AAAAAAATGA-A
* *
44628 AAGAAAAGTAAAAAATTGAA
1 AAAAAAAGTAAAAAAATGAA
44648 A
1 A
44649 TTTTTTTCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
20 17 0.50
21 17 0.50
ACGTcount: A:0.79, C:0.00, G:0.13, T:0.08
Consensus pattern (20 bp):
AAAAAAAGTAAAAAAATGAA
Found at i:48865 original size:11 final size:11
Alignment explanation
Indices: 48849--48942 Score: 57
Period size: 11 Copynumber: 8.0 Consensus size: 11
48839 AACCTAGGCC
*
48849 CTTTTTTTTTT
1 CTTTCTTTTTT
48860 CTTT-TTTCTTT
1 CTTTCTTT-TTT
48871 CTTTCTCTATTTT
1 CTTTCT-T-TTTT
*
48884 CCTTTCCTTATTT
1 -CTTT-CTTTTTT
48897 CTTTCTTTTTT
1 CTTTCTTTTTT
* *
48908 -TTCTACCTTTCT
1 CTT-T-CTTTTTT
*
48920 CTTTTTTTTTGT
1 CTTTCTTTTT-T
48932 CTTTCTTTTTT
1 CTTTCTTTTTT
48943 GGTCCATTAT
Statistics
Matches: 65, Mismatches: 8, Indels: 20
0.70 0.09 0.22
Matches are distributed among these distances:
10 5 0.08
11 22 0.34
12 21 0.32
13 9 0.14
14 6 0.09
15 2 0.03
ACGTcount: A:0.03, C:0.20, G:0.01, T:0.76
Consensus pattern (11 bp):
CTTTCTTTTTT
Found at i:48909 original size:26 final size:25
Alignment explanation
Indices: 48851--48910 Score: 66
Period size: 26 Copynumber: 2.4 Consensus size: 25
48841 CCTAGGCCCT
* * *
48851 TTTTTTTTTCTTTTTTCTTTCTTTC
1 TTTTTTTTCCTTTCTTATTTCTTTC
* *
48876 TCTATTTTCCTTTCCTTATTTCTTTC
1 TTTTTTTTCCTTT-CTTATTTCTTTC
48902 TTTTTTTTC
1 TTTTTTTTC
48911 TACCTTTCTC
Statistics
Matches: 27, Mismatches: 7, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
25 10 0.37
26 17 0.63
ACGTcount: A:0.03, C:0.20, G:0.00, T:0.77
Consensus pattern (25 bp):
TTTTTTTTCCTTTCTTATTTCTTTC
Found at i:48917 original size:17 final size:17
Alignment explanation
Indices: 48897--48942 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
48887 TTCCTTATTT
48897 CTTTCTTTTTTTTCTAC
1 CTTTCTTTTTTTTCTAC
* **
48914 CTTTCTCTTTTTTTTTGT
1 CTTTCT-TTTTTTTCTAC
48932 CTTTCTTTTTT
1 CTTTCTTTTTT
48943 GGTCCATTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 11 0.44
18 14 0.56
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.76
Consensus pattern (17 bp):
CTTTCTTTTTTTTCTAC
Found at i:48935 original size:18 final size:17
Alignment explanation
Indices: 48852--48942 Score: 60
Period size: 17 Copynumber: 5.4 Consensus size: 17
48842 CTAGGCCCTT
*
48852 TTTTTTTTCT-TTTTTC
1 TTTTTTTTCTATCTTTC
*
48868 TTTCTTTCTCTAT-TTTC
1 TTT-TTTTTCTATCTTTC
* ** * *
48885 CTTTCCTTATTTCTTTC
1 TTTTTTTTCTATCTTTC
*
48902 TTTTTTTTCTACCTTTC
1 TTTTTTTTCTATCTTTC
* *
48919 TCTTTTTTTTTGTCTTTC
1 T-TTTTTTTCTATCTTTC
48937 TTTTTT
1 TTTTTT
48943 GGTCCATTAT
Statistics
Matches: 55, Mismatches: 16, Indels: 7
0.71 0.21 0.09
Matches are distributed among these distances:
16 7 0.13
17 33 0.60
18 15 0.27
ACGTcount: A:0.03, C:0.20, G:0.01, T:0.76
Consensus pattern (17 bp):
TTTTTTTTCTATCTTTC
Found at i:50215 original size:19 final size:20
Alignment explanation
Indices: 50191--50232 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
50181 AGCCTGATCC
*
50191 AAAATAGTA-ATTTTTAATT
1 AAAATAATATATTTTTAATT
*
50210 AAAATAATATATTTTTATTT
1 AAAATAATATATTTTTAATT
50230 AAA
1 AAA
50233 TTTAATTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (20 bp):
AAAATAATATATTTTTAATT
Found at i:50929 original size:40 final size:40
Alignment explanation
Indices: 50868--50944 Score: 104
Period size: 40 Copynumber: 1.9 Consensus size: 40
50858 CAATGGTCCG
*
50868 AAGATAAGAGATCTAGAAGGAAGCATA-AAGGAAAAAAGAA
1 AAGAAAAGAGATCTAGAAGGAAGCA-AGAAGGAAAAAAGAA
*
50908 AAGAAAAGAGATTTA-AGAGGAAGCAAGAAGGAAAAAA
1 AAGAAAAGAGATCTAGA-AGGAAGCAAGAAGGAAAAAA
50945 AAGGAAAGAG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
39 2 0.06
40 31 0.94
ACGTcount: A:0.61, C:0.04, G:0.26, T:0.09
Consensus pattern (40 bp):
AAGAAAAGAGATCTAGAAGGAAGCAAGAAGGAAAAAAGAA
Found at i:51622 original size:20 final size:22
Alignment explanation
Indices: 51582--51633 Score: 83
Period size: 20 Copynumber: 2.5 Consensus size: 22
51572 CTACAATTTA
51582 TATCGATACA-ACAAGTGAATG
1 TATCGATACATACAAGTGAATG
51603 TATCGATACATA-AA-TGAATG
1 TATCGATACATACAAGTGAATG
51623 TATCGATACAT
1 TATCGATACAT
51634 GTCTAAAATG
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
20 17 0.57
21 12 0.40
22 1 0.03
ACGTcount: A:0.42, C:0.13, G:0.15, T:0.29
Consensus pattern (22 bp):
TATCGATACATACAAGTGAATG
Found at i:51892 original size:51 final size:50
Alignment explanation
Indices: 51744--51911 Score: 203
Period size: 52 Copynumber: 3.3 Consensus size: 50
51734 TTGATCCAAA
* * *
51744 TGTATTGATACATTTTCTGGG-TTTGATCCAAATGTATCGATACATTTTTCAT
1 TGTATCGATACA--TTCTGGGTTTTGA-CCAAATGTATTGATACATTATTCAT
* *
51796 TGTATAGATACATTCTGGGTTTTTGACCCAAATGTATTAATACATTATTCAT
1 TGTATCGATACATTCTGGG-TTTTGA-CCAAATGTATTGATACATTATTCAT
* * *
51848 TGTATCGATACATTCTGGGTTTTGACCTAAATATATTGATACATTCTTCAA
1 TGTATCGATACATTCTGGGTTTTGACC-AAATGTATTGATACATTATTCAT
51899 TGTATCGATACAT
1 TGTATCGATACAT
51912 CCAGTTAAAT
Statistics
Matches: 103, Mismatches: 10, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
50 9 0.09
51 38 0.37
52 56 0.54
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.43
Consensus pattern (50 bp):
TGTATCGATACATTCTGGGTTTTGACCAAATGTATTGATACATTATTCAT
Found at i:54313 original size:27 final size:27
Alignment explanation
Indices: 54281--54343 Score: 108
Period size: 27 Copynumber: 2.3 Consensus size: 27
54271 TAATGAGGAC
54281 ACTCCAACCTCATTCTTTCGAAGGAAT
1 ACTCCAACCTCATTCTTTCGAAGGAAT
* *
54308 ACTCCAACCTCATTCTTTCGAGGGGAT
1 ACTCCAACCTCATTCTTTCGAAGGAAT
54335 ACTCCAACC
1 ACTCCAACC
54344 CTGTTTTTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.27, C:0.33, G:0.13, T:0.27
Consensus pattern (27 bp):
ACTCCAACCTCATTCTTTCGAAGGAAT
Found at i:58076 original size:13 final size:13
Alignment explanation
Indices: 58058--58120 Score: 66
Period size: 13 Copynumber: 5.3 Consensus size: 13
58048 ACAATTCTTC
58058 ATGTATCGATACA
1 ATGTATCGATACA
*
58071 ATGTATCAATACA
1 ATGTATCGATACA
58084 ATG--T-G-T-C-
1 ATGTATCGATACA
58091 ATGTATCGATACA
1 ATGTATCGATACA
*
58104 ATGTATCAATACA
1 ATGTATCGATACA
58117 ATGT
1 ATGT
58121 GCCATGTATT
Statistics
Matches: 41, Mismatches: 3, Indels: 12
0.73 0.05 0.21
Matches are distributed among these distances:
7 3 0.07
8 1 0.02
9 2 0.05
10 1 0.02
11 2 0.05
12 1 0.02
13 31 0.76
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.33
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:58077 original size:33 final size:33
Alignment explanation
Indices: 58035--58137 Score: 154
Period size: 33 Copynumber: 3.1 Consensus size: 33
58025 GCCATTTAGG
* *
58035 ACAATGTATCGATACAAT-TCTTCATGTATCGAT
1 ACAATGTATCAATACAATGT-GTCATGTATCGAT
58068 ACAATGTATCAATACAATGTGTCATGTATCGAT
1 ACAATGTATCAATACAATGTGTCATGTATCGAT
* *
58101 ACAATGTATCAATACAATGTGCCATGTATTGAT
1 ACAATGTATCAATACAATGTGTCATGTATCGAT
58134 ACAA
1 ACAA
58138 ACAATGGTAG
Statistics
Matches: 65, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
33 64 0.98
34 1 0.02
ACGTcount: A:0.37, C:0.17, G:0.14, T:0.33
Consensus pattern (33 bp):
ACAATGTATCAATACAATGTGTCATGTATCGAT
Found at i:60701 original size:13 final size:13
Alignment explanation
Indices: 60682--60721 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
60672 ATAGTAACCC
*
60682 ATGTATCGATACA
1 ATGTATCAATACA
* *
60695 TTGTATCAATATA
1 ATGTATCAATACA
60708 ATGTATCAATACA
1 ATGTATCAATACA
60721 A
1 A
60722 AGAACATTGT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.42, C:0.12, G:0.10, T:0.35
Consensus pattern (13 bp):
ATGTATCAATACA
Found at i:60781 original size:20 final size:21
Alignment explanation
Indices: 60750--60789 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
60740 ATCTAGGTTT
60750 TTTCAGATGTATCGATACATC
1 TTTCAGATGTATCGATACATC
60771 TTTCA-ATGTATCGATACAT
1 TTTCAGATGTATCGATACAT
60790 TCTGAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.40
Consensus pattern (21 bp):
TTTCAGATGTATCGATACATC
Found at i:62158 original size:16 final size:16
Alignment explanation
Indices: 62137--62167 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
62127 TCAATATTCC
*
62137 TCTATTAAAACTTTTT
1 TCTATTAAAAATTTTT
62153 TCTATTAAAAATTTT
1 TCTATTAAAAATTTT
62168 GAAAGCCTTT
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:0.35, C:0.10, G:0.00, T:0.55
Consensus pattern (16 bp):
TCTATTAAAAATTTTT
Found at i:67038 original size:19 final size:20
Alignment explanation
Indices: 66994--67044 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
66984 CTGCTAGTTT
**
66994 CATGTATCGATACAATCGTG
1 CATGTATCGATACAATCGAA
67014 CATGTATCGATACAAT-GAA
1 CATGTATCGATACAATCGAA
67033 CATGTATCGATA
1 CATGTATCGATA
67045 AAATATATCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 13 0.45
20 16 0.55
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (20 bp):
CATGTATCGATACAATCGAA
Found at i:69958 original size:79 final size:79
Alignment explanation
Indices: 69791--69994 Score: 223
Period size: 79 Copynumber: 2.6 Consensus size: 79
69781 GAGATAATAA
* * * * ** *
69791 CAGGGTTGGAGTGTCCCCTTGAAAATAACGGGGCTGGAGTATCCCCGGTTGTGAGAAATCAATGA
1 CAGGGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATGA
69856 TTAGAAAAAAAAAT
66 TTAGAAAAAAAAAT
*
69870 CAGGATTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAAT-A
1 CAGGGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATGA
* ** * *
69934 TTTTG-GGAATAAAG
66 -TTAGAAAAAAAAAT
* ** *
69948 CTGGGGTTGGAGTATCCCCTCGGAGGTAACAGGGTTGGAGTATCCCC
1 C-AGGGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCC
69995 GATGAAATAA
Statistics
Matches: 105, Mismatches: 18, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
78 7 0.07
79 98 0.93
ACGTcount: A:0.30, C:0.17, G:0.29, T:0.24
Consensus pattern (79 bp):
CAGGGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATGA
TTAGAAAAAAAAAT
Found at i:70072 original size:52 final size:51
Alignment explanation
Indices: 70013--70396 Score: 235
Period size: 52 Copynumber: 7.3 Consensus size: 51
70003 AATGAGGTTA
*
70013 GAGTATCCTCGATTGTGAAAAATTGGTGTTTTTGGAAATAAAATCGGAGTTG
1 GAGTATCCCCGATTGTGAAAAATTGGTG-TTTTGGAAATAAAATCGGAGTTG
** * * *
70065 GAGTATCCCCGATTAAAGGAAAATTGGTGTTTTGAAAATAAAA-CCGAGGTTG
1 GAGTATCCCCGATT-GTGAAAAATTGGTGTTTTGGAAATAAAATCGGA-GTTG
* * * *
70117 GAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATAAAATCGGGGTTG
1 GAGTATCCCCGATTGT-GAAAAATTGGTGTTTTGGAAATAAAATCGGAGTTG
* * * *** * *
70169 GAGTATCCCCGATTATTAGAAATCAATATTTTGGAAATAAAGTCAGG-GTTG
1 GAGTATCCCCGATTGTGAAAAATTGGTGTTTTGGAAATAAAATC-GGAGTTG
* * * * *** * * *
70220 GAATATCCCCTCGGA-GGT-AACAAGGTTGGAGTATCCCCGATGAT-TAA-CGGGGTTG
1 GAGTAT-CCC-C-GATTGTGAA-AA-ATTGGTGT-T-TTGGA-AATAAAATCGGAGTTG
* * *
70275 GAGTATCCCCGATTGTGAAAAATTGGTGTTTTTTTAGAAACAAAATCAGAGTTG
1 GAGTATCCCCGATTGTGAAAAATTGGTG---TTTTGGAAATAAAATCGGAGTTG
* * * *
70329 GAGTATCCCCGATTAT-AGAAAATTAGTGTCTTGAAAATAAAATCGGAGTTG
1 GAGTATCCCCGATTGTGA-AAAATTGGTGTTTTGGAAATAAAATCGGAGTTG
70380 G-GATATCCCCGATTGTG
1 GAG-TATCCCCGATTGTG
70397 GAGAATTGAG
Statistics
Matches: 248, Mismatches: 60, Indels: 48
0.70 0.17 0.13
Matches are distributed among these distances:
50 1 0.00
51 63 0.25
52 98 0.40
53 27 0.11
54 42 0.17
55 12 0.05
56 3 0.01
57 2 0.01
ACGTcount: A:0.32, C:0.13, G:0.25, T:0.30
Consensus pattern (51 bp):
GAGTATCCCCGATTGTGAAAAATTGGTGTTTTGGAAATAAAATCGGAGTTG
Found at i:70333 original size:54 final size:52
Alignment explanation
Indices: 70271--70401 Score: 142
Period size: 51 Copynumber: 2.5 Consensus size: 52
70261 GATTAACGGG
* * *
70271 GTTGGAGTATCCCCGATTGTGA-AAAATTGGTGTTTTTTTAGAAACAAAATCAGA
1 GTTGGAGTATCCCCGATTGTGAGAAAATTAGTG--TCTTGA-AAACAAAATCAGA
* * *
70325 GTTGGAGTATCCCCGATTAT-AGAAAATTAGTGTCTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGAGAAAATTAGTGTCTTGAAAACAAAATCAGA
70376 GTTGG-GATATCCCCGATTGTGGAGAA
1 GTTGGAG-TATCCCCGATTGT-GAGAA
70402 TTGAGAAAAC
Statistics
Matches: 66, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
50 1 0.02
51 28 0.42
52 4 0.06
53 5 0.08
54 28 0.42
ACGTcount: A:0.33, C:0.12, G:0.24, T:0.31
Consensus pattern (52 bp):
GTTGGAGTATCCCCGATTGTGAGAAAATTAGTGTCTTGAAAACAAAATCAGA
Found at i:70365 original size:263 final size:263
Alignment explanation
Indices: 69898--70398 Score: 760
Period size: 263 Copynumber: 1.9 Consensus size: 263
69888 TCGGAAATAA
* * *
69898 CGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGGGAATAAAGCTGGGGTTGGAGTAT
1 CGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGGAAATAAAGCTAGGGTTGGAATAT
* * *
69963 CCCCTCGGAGGTAACAGGGTTGGAGTATCCCCGATGAAATAATGAGGTTAGAGTATCCTCGATTG
66 CCCCTCGGAGGTAACAAGGTTGGAGTATCCCCGATGAAATAACGAGGTTAGAGTATCCCCGATTG
* * * *
70028 TGAAAAATTGGTGTTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGGAAAATTGGT
131 TGAAAAATTGGTGTTTTTAGAAACAAAATCAGAGTTGGAGTATCCCCGATTAAAGGAAAATTAGT
*
70093 GTTTTGAAAATAAAACC-GAGGTT-GGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAAT
196 GTCTTGAAAATAAAACCGGA-GTTGGGA-TATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAAT
70156 AAAAT
259 AAAAT
* *
70161 CGGGGTTGGAGTATCCCCGATTATTAGAAATCAATATTTTGGAAATAAAG-TCAGGGTTGGAATA
1 CGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGGAAATAAAGCT-AGGGTTGGAATA
* * *
70225 TCCCCTCGGAGGTAACAAGGTTGGAGTATCCCCGATG-ATTAACGGGGTTGGAGTATCCCCGATT
65 TCCCCTCGGAGGTAACAAGGTTGGAGTATCCCCGATGAAATAACGAGGTTAGAGTATCCCCGATT
*
70289 GTGAAAAATTGGTGTTTTTTTAGAAACAAAATCAGAGTTGGAGTATCCCCGATTATA-GAAAATT
130 GTGAAAAATTGGTG--TTTTTAGAAACAAAATCAGAGTTGGAGTATCCCCGATTAAAGGAAAATT
*
70353 AGTGTCTTGAAAATAAAATCGGAGTTGGGATATCCCCGATTGTGGA
193 AGTGTCTTGAAAATAAAACCGGAGTTGGGATATCCCCGATTGTGGA
70399 GAATTGAGAA
Statistics
Matches: 215, Mismatches: 18, Indels: 10
0.88 0.07 0.04
Matches are distributed among these distances:
262 37 0.17
263 136 0.63
264 42 0.20
ACGTcount: A:0.31, C:0.13, G:0.27, T:0.29
Consensus pattern (263 bp):
CGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGGAAATAAAGCTAGGGTTGGAATAT
CCCCTCGGAGGTAACAAGGTTGGAGTATCCCCGATGAAATAACGAGGTTAGAGTATCCCCGATTG
TGAAAAATTGGTGTTTTTAGAAACAAAATCAGAGTTGGAGTATCCCCGATTAAAGGAAAATTAGT
GTCTTGAAAATAAAACCGGAGTTGGGATATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATAA
AAT
Found at i:72778 original size:13 final size:13
Alignment explanation
Indices: 72760--72785 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
72750 ACAAAGATCC
72760 ATGTATCGATACA
1 ATGTATCGATACA
72773 ATGTATCGATACA
1 ATGTATCGATACA
72786 TGGAATAATG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:72845 original size:13 final size:13
Alignment explanation
Indices: 72823--72880 Score: 53
Period size: 13 Copynumber: 4.0 Consensus size: 13
72813 GGCAGTAGCT
*
72823 TTGTAGCGATACA
1 TTGTATCGATACA
72836 TTGTATCGATACATCA
1 TTGTATCGAT--A-CA
72852 CTTGTGTATCGATACA
1 --T-TGTATCGATACA
72868 TTGTATCGATACA
1 TTGTATCGATACA
72881 ACACTTATGT
Statistics
Matches: 38, Mismatches: 1, Indels: 12
0.75 0.02 0.24
Matches are distributed among these distances:
13 21 0.55
14 1 0.03
15 1 0.03
16 4 0.11
17 1 0.03
18 1 0.03
19 9 0.24
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:72870 original size:32 final size:32
Alignment explanation
Indices: 72824--72899 Score: 125
Period size: 32 Copynumber: 2.4 Consensus size: 32
72814 GCAGTAGCTT
* * *
72824 TGTAGCGATACATTGTATCGATACATCACTTG
1 TGTATCGATACATTGTATCGATACAACACTTA
72856 TGTATCGATACATTGTATCGATACAACACTTA
1 TGTATCGATACATTGTATCGATACAACACTTA
72888 TGTATCGATACA
1 TGTATCGATACA
72900 AATCGCTGAA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 41 1.00
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Consensus pattern (32 bp):
TGTATCGATACATTGTATCGATACAACACTTA
Found at i:72900 original size:19 final size:18
Alignment explanation
Indices: 72836--72900 Score: 68
Period size: 19 Copynumber: 3.8 Consensus size: 18
72826 TAGCGATACA
*
72836 TTGTATCGATACATCACT
1 TTGTATCGATACAACACT
72854 TGTGTATCGAT---ACA--
1 T-TGTATCGATACAACACT
72868 TTGTATCGATACAACACT
1 TTGTATCGATACAACACT
72886 TATGTATCGATACAA
1 T-TGTATCGATACAA
72901 ATCGCTGAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 13
0.74 0.02 0.25
Matches are distributed among these distances:
13 9 0.23
14 1 0.03
16 5 0.13
18 2 0.05
19 22 0.56
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.35
Consensus pattern (18 bp):
TTGTATCGATACAACACT
Found at i:72963 original size:21 final size:22
Alignment explanation
Indices: 72937--72994 Score: 75
Period size: 21 Copynumber: 2.7 Consensus size: 22
72927 GTTGGGACCT
* *
72937 TGTATCGATACATTTGTA-GAA
1 TGTATCGATACATTTGCACAAA
*
72958 TGTATCGATACA-TTCCACAAA
1 TGTATCGATACATTTGCACAAA
72979 TGTATCGATACATTTG
1 TGTATCGATACATTTG
72995 GATAAAAGTG
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
20 3 0.10
21 26 0.84
22 2 0.06
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.36
Consensus pattern (22 bp):
TGTATCGATACATTTGCACAAA
Found at i:75520 original size:25 final size:27
Alignment explanation
Indices: 75463--75523 Score: 83
Period size: 25 Copynumber: 2.4 Consensus size: 27
75453 CGATTTTAAA
75463 ATTT-TTATAATAAAATTATAATCAAT
1 ATTTATTATAATAAAATTATAATCAAT
* *
75489 ATTTATTATAATTAACTT-TAAT-AAT
1 ATTTATTATAATAAAATTATAATCAAT
75514 ATTTATTATA
1 ATTTATTATA
75524 TTTATAATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
25 13 0.41
26 8 0.25
27 11 0.34
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (27 bp):
ATTTATTATAATAAAATTATAATCAAT
Found at i:77977 original size:3 final size:3
Alignment explanation
Indices: 77969--78001 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
77959 TTTTGCTGTT
77969 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
78002 AAAAACACCA
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:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:78507 original size:5 final size:5
Alignment explanation
Indices: 78488--78553 Score: 56
Period size: 5 Copynumber: 14.2 Consensus size: 5
78478 TAATTTGCCG
78488 ATAAT ATAAT -T-AT ATAAT ATAA- A-AAT -TAAT -TAAGCT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAA--T ATAAT ATAAT
*
78534 ATTAT A-AAT ATAAT ATAAT A
1 ATAAT ATAAT ATAAT ATAAT A
78554 ATAAAAAGAT
Statistics
Matches: 51, Mismatches: 2, Indels: 16
0.74 0.03 0.23
Matches are distributed among these distances:
3 4 0.08
4 12 0.24
5 31 0.61
6 1 0.02
7 3 0.06
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (5 bp):
ATAAT
Found at i:78545 original size:14 final size:14
Alignment explanation
Indices: 78488--78554 Score: 61
Period size: 14 Copynumber: 4.9 Consensus size: 14
78478 TAATTTGCCG
*
78488 ATAATATAAT-TAT
1 ATAATATAATAAAT
78501 ATAATATAA-AAAT
1 ATAATATAATAAAT
78514 -TAAT-TAAGCTATAAT
1 ATAATATAA--TA-AAT
*
78529 ATAATATTATAAAT
1 ATAATATAATAAAT
78543 ATAATATAATAA
1 ATAATATAATAA
78555 TAAAAAGATA
Statistics
Matches: 44, Mismatches: 3, Indels: 13
0.73 0.05 0.22
Matches are distributed among these distances:
11 3 0.07
12 4 0.09
13 11 0.25
14 15 0.34
15 5 0.11
16 4 0.09
17 2 0.05
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.39
Consensus pattern (14 bp):
ATAATATAATAAAT
Found at i:78565 original size:19 final size:19
Alignment explanation
Indices: 78524--78569 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
78514 TAATTAAGCT
* * *
78524 ATAATATAATATTATAAAT
1 ATAATATAATAATAAAAAG
78543 ATAATATAATAATAAAAAG
1 ATAATATAATAATAAAAAG
78562 ATAA-ATAA
1 ATAATATAA
78570 ATATGATACG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
18 4 0.17
19 20 0.83
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (19 bp):
ATAATATAATAATAAAAAG
Found at i:79268 original size:38 final size:36
Alignment explanation
Indices: 79176--79269 Score: 100
Period size: 37 Copynumber: 2.5 Consensus size: 36
79166 TATATATAAT
*
79176 AAATAATTAAAAATTATA-TTAATGTTAAATAATAAA
1 AAATAATT-AAAATTATATTTAATGTTAAATAAAAAA
* * *
79212 ATATATGTTAAAATTATATTTTATGTTAAATAAAAATGA
1 AAATA-ATTAAAATTATATTTAATGTTAAATAAAAA--A
*
79251 AAATAATTAAAGTTATATT
1 AAATAATTAAAATTATATT
79270 AAATTAAAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
36 13 0.28
37 17 0.36
38 12 0.26
39 5 0.11
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.40
Consensus pattern (36 bp):
AAATAATTAAAATTATATTTAATGTTAAATAAAAAA
Found at i:79286 original size:12 final size:13
Alignment explanation
Indices: 79269--79297 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
79259 AAAGTTATAT
79269 TAAATTAA-AAAA
1 TAAATTAATAAAA
79281 TAAATTAATAAAA
1 TAAATTAATAAAA
79294 TAAA
1 TAAA
79298 ACTAAAAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.50
13 8 0.50
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (13 bp):
TAAATTAATAAAA
Found at i:79442 original size:23 final size:21
Alignment explanation
Indices: 79416--79464 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 21
79406 ACAATAAACT
*
79416 TTATTAATTATATTAAATAAAAG
1 TTATTAATT-T-TTAAATAAAAA
*
79439 TTATTTCATTTTTAAATAAAAA
1 TTA-TTAATTTTTAAATAAAAA
79461 TTAT
1 TTAT
79465 AATAAAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
21 1 0.04
22 13 0.57
23 4 0.17
24 5 0.22
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (21 bp):
TTATTAATTTTTAAATAAAAA
Found at i:79723 original size:2 final size:2
Alignment explanation
Indices: 79716--79762 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
79706 TTAAAAGTTC
*
79716 AT AT AT AT AT AT AT AC 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
79758 AT AT A
1 AT AT A
79763 CACACGGGTC
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:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:80944 original size:11 final size:11
Alignment explanation
Indices: 80918--80952 Score: 52
Period size: 12 Copynumber: 3.0 Consensus size: 11
80908 AGCCTCTTTG
80918 ATTTTATTTATT
1 ATTTTATTT-TT
80930 ATTTTATTTTT
1 ATTTTATTTTT
80941 ATTTTAATTTTT
1 ATTTT-ATTTTT
80953 TAATAATTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 7 0.32
12 15 0.68
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (11 bp):
ATTTTATTTTT
Found at i:81270 original size:21 final size:22
Alignment explanation
Indices: 81227--81270 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
81217 ATTTTATATT
* * *
81227 TTTTTTAAAAATAATTAATAAA
1 TTTTTAAAAAATAATAAAAAAA
81249 TTTTTAAAAAATAA-AAAAAAA
1 TTTTTAAAAAATAATAAAAAAA
81270 T
1 T
81271 AAAATAATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (22 bp):
TTTTTAAAAAATAATAAAAAAA
Found at i:82109 original size:13 final size:13
Alignment explanation
Indices: 82091--82180 Score: 57
Period size: 13 Copynumber: 6.9 Consensus size: 13
82081 TGCCACTGTT
82091 TGTATCGATACAA
1 TGTATCGATACAA
82104 TGTATCGATACATAGACA
1 TGTATCGATAC----A-A
*
82122 TTATATCGATACAA
1 -TGTATCGATACAA
82136 TGTATCGATAC-A
1 TGTATCGATACAA
* *
82148 TG-A---AGA-AT
1 TGTATCGATACAA
82156 TGTATCGATACAA
1 TGTATCGATACAA
82169 TGTATCGATACA
1 TGTATCGATACA
82181 TGAAGAATTG
Statistics
Matches: 59, Mismatches: 6, Indels: 24
0.66 0.07 0.27
Matches are distributed among these distances:
8 4 0.07
9 1 0.02
11 1 0.02
12 5 0.08
13 34 0.58
14 1 0.02
15 1 0.02
17 1 0.02
18 1 0.02
19 10 0.17
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:82161 original size:20 final size:20
Alignment explanation
Indices: 82136--82201 Score: 83
Period size: 20 Copynumber: 3.6 Consensus size: 20
82126 ATCGATACAA
82136 TGTATCGATACATGAAGAAT
1 TGTATCGATACATGAAGAAT
82156 TGTATCGATAC------AA-
1 TGTATCGATACATGAAGAAT
82169 TGTATCGATACATGAAGAAT
1 TGTATCGATACATGAAGAAT
82189 TGTATCGATACAT
1 TGTATCGATACAT
82202 TGTTCCAAAC
Statistics
Matches: 39, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
13 11 0.28
14 2 0.05
19 2 0.05
20 24 0.62
ACGTcount: A:0.38, C:0.12, G:0.18, T:0.32
Consensus pattern (20 bp):
TGTATCGATACATGAAGAAT
Found at i:82167 original size:33 final size:33
Alignment explanation
Indices: 82090--82200 Score: 190
Period size: 33 Copynumber: 3.4 Consensus size: 33
82080 CTGCCACTGT
82090 TTGTATCGATACAATGTATCGATACAT--AGACA
1 TTGTATCGATACAATGTATCGATACATGAAGA-A
*
82122 TTATATCGATACAATGTATCGATACATGAAGAA
1 TTGTATCGATACAATGTATCGATACATGAAGAA
82155 TTGTATCGATACAATGTATCGATACATGAAGAA
1 TTGTATCGATACAATGTATCGATACATGAAGAA
82188 TTGTATCGATACA
1 TTGTATCGATACA
82201 TTGTTCCAAA
Statistics
Matches: 75, Mismatches: 2, Indels: 3
0.94 0.03 0.04
Matches are distributed among these distances:
32 26 0.35
33 46 0.61
34 3 0.04
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.32
Consensus pattern (33 bp):
TTGTATCGATACAATGTATCGATACATGAAGAA
Found at i:88368 original size:13 final size:13
Alignment explanation
Indices: 88350--88386 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
88340 ACAATGTTAT
88350 TTGTATCGATACA
1 TTGTATCGATACA
*
88363 TTGTATTGATACA
1 TTGTATCGATACA
*
88376 ATGTATCGATA
1 TTGTATCGATA
88387 TATGGGTTAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:90947 original size:20 final size:19
Alignment explanation
Indices: 90903--90957 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
90893 GTATCGATAT
* **
90903 ATTGTATCAGTACATGTTC
1 ATTGTATCAATACATGCAC
90922 ATTGTATCAATACATGCAC
1 ATTGTATCAATACATGCAC
*
90941 AATTGTATCGATACATG
1 -ATTGTATCAATACATG
90958 AAATTGGCAG
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 16 0.52
20 15 0.48
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36
Consensus pattern (19 bp):
ATTGTATCAATACATGCAC
Done.