Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 135709677
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: 135709677
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 350 characters in sequence are not A, C, G, or T
File 1 of 438
Found at i:7425 original size:31 final size:31
Alignment explanation
Indices: 7387--7449 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
7377 AGTACGAGAA
7387 GGGAGGAAGAGAGAATAATGAAAACAAAAAG
1 GGGAGGAAGAGAGAATAATGAAAACAAAAAG
7418 GGGAGGAAGAGAGAATAATGAAAACAAAAAG
1 GGGAGGAAGAGAGAATAATGAAAACAAAAAG
7449 G
1 G
7450 AAATAAGGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.57, C:0.03, G:0.33, T:0.06
Consensus pattern (31 bp):
GGGAGGAAGAGAGAATAATGAAAACAAAAAG
Found at i:14446 original size:21 final size:22
Alignment explanation
Indices: 14407--14447 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
14397 ATCCATTCAT
*
14407 CAATTTTATTAGGCATAACACA
1 CAATTTTATTAGCCATAACACA
14429 CAATTTTATTA-CCATAACA
1 CAATTTTATTAGCCATAACA
14448 AATTGTACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.41, C:0.20, G:0.05, T:0.34
Consensus pattern (22 bp):
CAATTTTATTAGCCATAACACA
Found at i:14626 original size:21 final size:22
Alignment explanation
Indices: 14587--14627 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
14577 ATCCATTCAT
*
14587 CAATTTTATTAGGCATAACACA
1 CAATTTTATTAGCCATAACACA
14609 CAATTTTATTA-CCATAACA
1 CAATTTTATTAGCCATAACA
14628 AATTGTACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.41, C:0.20, G:0.05, T:0.34
Consensus pattern (22 bp):
CAATTTTATTAGCCATAACACA
Found at i:14682 original size:180 final size:180
Alignment explanation
Indices: 14374--14736 Score: 717
Period size: 180 Copynumber: 2.0 Consensus size: 180
14364 GGCAAAATAT
14374 GGAGACAACATAATTGGAGGGATATCCATTCATCAATTTTATTAGGCATAACACACAATTTTATT
1 GGAGACAACATAATTGGAGGGATATCCATTCATCAATTTTATTAGGCATAACACACAATTTTATT
14439 ACCATAACAAATTGTACAAAAGAAAAAAAATCAAAGTCATTCACCATTATAGAGCCCCAAACCCG
66 ACCATAACAAATTGTACAAAAGAAAAAAAATCAAAGTCATTCACCATTATAGAGCCCCAAACCCG
14504 AGCCAGATTTCACTGTGTCGATGGGGTTGGAGGTTTCCATGTGGTAGTCA
131 AGCCAGATTTCACTGTGTCGATGGGGTTGGAGGTTTCCATGTGGTAGTCA
*
14554 GGAGATAACATAATTGGAGGGATATCCATTCATCAATTTTATTAGGCATAACACACAATTTTATT
1 GGAGACAACATAATTGGAGGGATATCCATTCATCAATTTTATTAGGCATAACACACAATTTTATT
14619 ACCATAACAAATTGTACAAAAGAAAAAAAATCAAAGTCATTCACCATTATAGAGCCCCAAACCCG
66 ACCATAACAAATTGTACAAAAGAAAAAAAATCAAAGTCATTCACCATTATAGAGCCCCAAACCCG
14684 AGCCAGATTTCACTGTGTCGATGGGGTTGGAGGTTTCCATGTGGTAGTCA
131 AGCCAGATTTCACTGTGTCGATGGGGTTGGAGGTTTCCATGTGGTAGTCA
14734 GGA
1 GGA
14737 AAACCATCTA
Statistics
Matches: 182, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
180 182 1.00
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.27
Consensus pattern (180 bp):
GGAGACAACATAATTGGAGGGATATCCATTCATCAATTTTATTAGGCATAACACACAATTTTATT
ACCATAACAAATTGTACAAAAGAAAAAAAATCAAAGTCATTCACCATTATAGAGCCCCAAACCCG
AGCCAGATTTCACTGTGTCGATGGGGTTGGAGGTTTCCATGTGGTAGTCA
Found at i:21312 original size:26 final size:26
Alignment explanation
Indices: 21283--21334 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
21273 ATTTCTATAT
*
21283 ATTTCT-TTAACATTTTTGTTACTTAA
1 ATTTCTATTAACA-TTTTGGTACTTAA
* *
21309 ATTTTTATTCACATTTTGGTACTTAA
1 ATTTCTATTAACATTTTGGTACTTAA
21335 TTATCAATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 17 0.77
27 5 0.23
ACGTcount: A:0.27, C:0.12, G:0.06, T:0.56
Consensus pattern (26 bp):
ATTTCTATTAACATTTTGGTACTTAA
Found at i:22602 original size:14 final size:14
Alignment explanation
Indices: 22583--22609 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
22573 AAAAAATAAG
22583 TTGAAGGGAGAAAA
1 TTGAAGGGAGAAAA
22597 TTGAAGGGAGAAA
1 TTGAAGGGAGAAA
22610 GTGACAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.37, T:0.15
Consensus pattern (14 bp):
TTGAAGGGAGAAAA
Found at i:26946 original size:21 final size:21
Alignment explanation
Indices: 26922--26984 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
26912 ACCGAATGCC
26922 AAAACAGCTGAACCGGGGACT
1 AAAACAGCTGAACCGGGGACT
* *
26943 AAAA-ATACTGAACC-AGGA-T
1 AAAACA-GCTGAACCGGGGACT
26962 --AACAGCTGAACCGGGGACT
1 AAAACAGCTGAACCGGGGACT
26981 AAAA
1 AAAA
26985 ATACTGAACC
Statistics
Matches: 32, Mismatches: 4, Indels: 12
0.67 0.08 0.25
Matches are distributed among these distances:
17 9 0.28
18 4 0.12
19 2 0.06
20 4 0.12
21 13 0.41
ACGTcount: A:0.44, C:0.21, G:0.24, T:0.11
Consensus pattern (21 bp):
AAAACAGCTGAACCGGGGACT
Found at i:26974 original size:38 final size:38
Alignment explanation
Indices: 26924--26999 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
26914 CGAATGCCAA
26924 AACAGCTGAACCGGGGACTAAAAATACTGAACCAGGAT
1 AACAGCTGAACCGGGGACTAAAAATACTGAACCAGGAT
26962 AACAGCTGAACCGGGGACTAAAAATACTGAACCAGGAT
1 AACAGCTGAACCGGGGACTAAAAATACTGAACCAGGAT
27000 GGGATATGAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.42, C:0.21, G:0.24, T:0.13
Consensus pattern (38 bp):
AACAGCTGAACCGGGGACTAAAAATACTGAACCAGGAT
Found at i:26993 original size:21 final size:21
Alignment explanation
Indices: 26929--26994 Score: 77
Period size: 21 Copynumber: 3.3 Consensus size: 21
26919 GCCAAAACAG
26929 CTGAACCGGGGACTAAAAATA
1 CTGAACCGGGGACTAAAAATA
* * *
26950 CTGAACC-AGGA-T-AACA-G
1 CTGAACCGGGGACTAAAAATA
26967 CTGAACCGGGGACTAAAAATA
1 CTGAACCGGGGACTAAAAATA
26988 CTGAACC
1 CTGAACC
26995 AGGATGGGAT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
17 7 0.20
18 6 0.17
19 2 0.06
20 6 0.17
21 14 0.40
ACGTcount: A:0.41, C:0.23, G:0.23, T:0.14
Consensus pattern (21 bp):
CTGAACCGGGGACTAAAAATA
Found at i:27136 original size:27 final size:27
Alignment explanation
Indices: 27098--27171 Score: 139
Period size: 27 Copynumber: 2.7 Consensus size: 27
27088 CCCAATGCTT
*
27098 ATTGTTATGCACGCTTTGATTACGGTA
1 ATTGTTACGCACGCTTTGATTACGGTA
27125 ATTGTTACGCACGCTTTGATTACGGTA
1 ATTGTTACGCACGCTTTGATTACGGTA
27152 ATTGTTACGCACGCTTTGAT
1 ATTGTTACGCACGCTTTGAT
27172 CACAAATCTT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 46 1.00
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.39
Consensus pattern (27 bp):
ATTGTTACGCACGCTTTGATTACGGTA
Found at i:29603 original size:25 final size:26
Alignment explanation
Indices: 29541--29623 Score: 73
Period size: 25 Copynumber: 3.1 Consensus size: 26
29531 TAATACATAA
29541 AAATTATTTTATTTT-AATTAGGTAAC-T
1 AAATTATTTT-TTTTAAATTA-GT-ACTT
*
29568 AAACTTGTTTTTTTTAAATTAGTACTT
1 AAA-TTATTTTTTTTAAATTAGTACTT
* *
29595 AAATT-TTTTTTCTAAATTAGGACTAT
1 AAATTATTTTTTTTAAATTAGTACT-T
29621 AAA
1 AAA
29624 ACTAAGTTCA
Statistics
Matches: 49, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
25 17 0.35
26 8 0.16
27 13 0.27
28 11 0.22
ACGTcount: A:0.36, C:0.06, G:0.07, T:0.51
Consensus pattern (26 bp):
AAATTATTTTTTTTAAATTAGTACTT
Found at i:38393 original size:205 final size:206
Alignment explanation
Indices: 37864--38491 Score: 913
Period size: 211 Copynumber: 3.0 Consensus size: 206
37854 TAAAGCACAT
* * * *
37864 GTTGAGGTTTGAGTCCATAAGTAGCTTCAAAAGGTATCTTCATAATTGTTCTAATCCAAGGGTTG
1 GTTGAGGTTTGAGTCCATAAGTAGCTTCAAAAGGTGTCTTCTTAATTGTTCT-ATTCAAGAGTTG
*
37929 TATGTAAACTCATCTTGAGGAATAACCAAATCCTAACTCTTCACATGATTCCAAA-CAGGACACC
65 AATGTAAACTCATCTTGAGGAATAACCAAATCCTAACTCTTCACATGATTCCAAACCA-GACACC
* *
37993 TACGCATATTTCCTAAACTTTGGTTAACAGCCTCTATTTGCCCATCTGTTTGTGGATGAAAAGTG
129 TAAGCATATTTCCTAAAC--T--TTAACAGCCTCTATTTGCCCATCTATTTGTGGATGAAAAGTG
*
38058 CTAGAAAATTTCAATTG
190 CTAGAAAATTTCAATCG
* * *
38075 GTTGAGGTTTGAGTCCGTAAGTAGCTTTAAAAGGTGTCTTCTTAATTGTTCTATTTACAGAGTTG
1 GTTGAGGTTTGAGTCCATAAGTAGCTTCAAAAGGTGTCTTCTTAATTGTTCTATTCA-AGAGTTG
* *
38140 AATGTAAACTCATCTTGAGGACTAACCAAATCCTAACTCTTTACATGATTCCAAACCAGACACCT
65 AATGTAAACTCATCTTGAGGAATAACCAAATCCTAACTCTTCACATGATTCCAAACCAGACACCT
* * * *
38205 AAGCATATTTCCTAAAC-TTAACATCCTCTATTTTCCCATTTATTTCTGGATGAAAAGTGCTAGA
130 AAGCATATTTCCTAAACTTTAACAGCCTCTATTTGCCCATCTATTTGTGGATGAAAAGTGCTAGA
38269 AAATTTCAATCG
195 AAATTTCAATCG
* *
38281 GTTGAGGTTTAAGTCCATAAGTAGCTTCAAAAGGTGTATT-TTAATTGTTCTATTCATAGAGTTG
1 GTTGAGGTTTGAGTCCATAAGTAGCTTCAAAAGGTGTCTTCTTAATTGTTCTATTCA-AGAGTTG
* *
38345 CATGTAAACTCATCTTGAGGAATAACCAAATCCTAACTCTTCACATGATTCCAAACAAGACACCT
65 AATGTAAACTCATCTTGAGGAATAACCAAATCCTAACTCTTCACATGATTCCAAACCAGACACCT
38410 AAGTC-TATTTCCTAAACTTTGGTTAACAGCCTCTATTTGCCCATCTATTTGTGGATGAAAAGTG
130 AAG-CATATTTCCTAAAC--T--TTAACAGCCTCTATTTGCCCATCTATTTGTGGATGAAAAGTG
*
38474 CTAGGAAATTTCAATCG
190 CTAGAAAATTTCAATCG
38491 G
1 G
38492 GTTCCCATTT
Statistics
Matches: 377, Mismatches: 32, Indels: 17
0.88 0.08 0.04
Matches are distributed among these distances:
205 98 0.26
206 90 0.24
210 58 0.15
211 129 0.34
212 2 0.01
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (206 bp):
GTTGAGGTTTGAGTCCATAAGTAGCTTCAAAAGGTGTCTTCTTAATTGTTCTATTCAAGAGTTGA
ATGTAAACTCATCTTGAGGAATAACCAAATCCTAACTCTTCACATGATTCCAAACCAGACACCTA
AGCATATTTCCTAAACTTTAACAGCCTCTATTTGCCCATCTATTTGTGGATGAAAAGTGCTAGAA
AATTTCAATCG
Found at i:43014 original size:95 final size:95
Alignment explanation
Indices: 42903--43093 Score: 267
Period size: 95 Copynumber: 2.0 Consensus size: 95
42893 AATTGAATAA
* * * **
42903 ATAATTATAATTATTTAAATGTTCCTAGCTCTTATTACCATTGTAAAAGTTTTGCTTGTGTTTTA
1 ATAATTATAATTATTTAAATGCTCCTAGATCTTATTACCATTGTAAAAGTTTTACTTGTGTTAAA
*
42968 AAGTTATATATATAATT-TTTTTTCCAAAAT
66 AACTTATATATA-AATTATTTTTTCCAAAAT
* * * *
42998 ATAATTTTAGTTATTTAAATGCTCCTAGATTTTATTACCATTGTAATAGTTTTACTTGTGTTAAA
1 ATAATTATAATTATTTAAATGCTCCTAGATCTTATTACCATTGTAAAAGTTTTACTTGTGTTAAA
*
43063 AACTTATATATAATTTATTTTTTCCAAAAT
66 AACTTATATATAAATTATTTTTTCCAAAAT
43093 A
1 A
43094 AGTTTTTTAA
Statistics
Matches: 84, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
94 3 0.04
95 81 0.96
ACGTcount: A:0.34, C:0.09, G:0.08, T:0.49
Consensus pattern (95 bp):
ATAATTATAATTATTTAAATGCTCCTAGATCTTATTACCATTGTAAAAGTTTTACTTGTGTTAAA
AACTTATATATAAATTATTTTTTCCAAAAT
Found at i:56756 original size:15 final size:14
Alignment explanation
Indices: 56721--56760 Score: 53
Period size: 15 Copynumber: 2.8 Consensus size: 14
56711 TAATAGTAAA
*
56721 ATAATACTTAGAAT
1 ATAATATTTAGAAT
56735 ATAATATTTAGAAAT
1 ATAATATTTAG-AAT
*
56750 TTAATATTTAG
1 ATAATATTTAG
56761 GATTTAGGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 10 0.43
15 13 0.57
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (14 bp):
ATAATATTTAGAAT
Found at i:56765 original size:14 final size:14
Alignment explanation
Indices: 56722--56766 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
56712 AATAGTAAAA
* *
56722 TAATACTTAGAATA
1 TAATATTTAGAATT
56736 TAATATTTAGAAATT
1 TAATATTTAG-AATT
*
56751 TAATATTTAGGATT
1 TAATATTTAGAATT
56765 TA
1 TA
56767 GGATTAGAGT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
14 14 0.52
15 13 0.48
ACGTcount: A:0.44, C:0.02, G:0.09, T:0.44
Consensus pattern (14 bp):
TAATATTTAGAATT
Found at i:56868 original size:21 final size:22
Alignment explanation
Indices: 56814--56868 Score: 53
Period size: 21 Copynumber: 2.6 Consensus size: 22
56804 TAAAATTTAA
56814 AAGTTTAGA-ATTTGAGGATTT
1 AAGTTTAGATATTTGAGGATTT
** *
56835 -AGTTTTATTTATTT-AGGGTTT
1 AAG-TTTAGATATTTGAGGATTT
56856 AAGTTTAGATATT
1 AAGTTTAGATATT
56869 ACGATTTTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 6
0.70 0.14 0.16
Matches are distributed among these distances:
20 2 0.08
21 18 0.69
22 6 0.23
ACGTcount: A:0.29, C:0.00, G:0.20, T:0.51
Consensus pattern (22 bp):
AAGTTTAGATATTTGAGGATTT
Found at i:56918 original size:15 final size:16
Alignment explanation
Indices: 56900--56929 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
56890 GTTAAAAAAA
56900 TAGTATAAAT-TAATT
1 TAGTATAAATATAATT
56915 TAGTATAAATATAAT
1 TAGTATAAATATAAT
56930 GTGACATATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (16 bp):
TAGTATAAATATAATT
Found at i:59797 original size:2 final size:2
Alignment explanation
Indices: 59790--59823 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
59780 GAAACAAACA
59790 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
59824 GAGGAGAGCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:62652 original size:29 final size:29
Alignment explanation
Indices: 62619--62676 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
62609 TAATATCAAA
62619 CTTAAAATTAAAATAAAATATTTATATTC
1 CTTAAAATTAAAATAAAATATTTATATTC
62648 CTTAAAATTAAAATAAAATATTTATATTC
1 CTTAAAATTAAAATAAAATATTTATATTC
62677 TTACCTTATC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (29 bp):
CTTAAAATTAAAATAAAATATTTATATTC
Found at i:64353 original size:6 final size:6
Alignment explanation
Indices: 64342--64435 Score: 161
Period size: 6 Copynumber: 15.7 Consensus size: 6
64332 CAGAAAGGTA
64342 CGGGTG CGGGTG CGGGTG CGGGTG CGGGTG CGGGTG CGGGTG CGGGTG
1 CGGGTG CGGGTG CGGGTG CGGGTG CGGGTG CGGGTG CGGGTG CGGGTG
* * *
64390 CGGGTG CGGGTG CAGGTG TGGGTG CCGGTG CGGGTG CGGGTG CGGG
1 CGGGTG CGGGTG CGGGTG CGGGTG CGGGTG CGGGTG CGGGTG CGGG
64436 CGGAAAAGAA
Statistics
Matches: 82, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 82 1.00
ACGTcount: A:0.01, C:0.17, G:0.65, T:0.17
Consensus pattern (6 bp):
CGGGTG
Found at i:75943 original size:6 final size:6
Alignment explanation
Indices: 75932--75966 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
75922 CTAAGATACG
75932 ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA ATCAG
1 ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA ATCAG
75967 GGAAGCTTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.49, C:0.17, G:0.17, T:0.17
Consensus pattern (6 bp):
ATCAGA
Found at i:77051 original size:30 final size:30
Alignment explanation
Indices: 77015--77221 Score: 198
Period size: 30 Copynumber: 6.3 Consensus size: 30
77005 GCGGCATGAG
77015 CTGGGGCTGCGAATTCGAGGCTGACTTGGA
1 CTGGGGCTGCGAATTCGAGGCTGACTTGGA
77045 CTGGGGCTGCGAATTCGAGGCTGACTTGGA
1 CTGGGGCTGCGAATTCGAGGCTGACTTGGA
*
77075 CTGGGGCTGCGAATTCGAGGCTGACTTAGA
1 CTGGGGCTGCGAATTCGAGGCTGACTTGGA
* *
77105 CTTGGGCTCGGGCTACGAATTCGAGGCTGACTTAGA
1 C-T--G---GGGCTGCGAATTCGAGGCTGACTTGGA
* *
77141 CTTGGGCTCGGGCTGCGAATTCGAGGCCGACTTAGACTGGGG
1 C-T--G---GGGCTGCGAATTCGA-G--G-C-T-GACTTGGA
*
77183 CTGGGGCTGCGAATTCGAGGCTGACTTGGG
1 CTGGGGCTGCGAATTCGAGGCTGACTTGGA
77213 CTGGGGCTG
1 CTGGGGCTG
77222 GGGCTGCGAA
Statistics
Matches: 158, Mismatches: 7, Indels: 24
0.84 0.04 0.13
Matches are distributed among these distances:
30 76 0.48
31 2 0.01
32 1 0.01
33 2 0.01
35 1 0.01
36 64 0.41
37 1 0.01
39 2 0.01
40 1 0.01
41 2 0.01
42 6 0.04
ACGTcount: A:0.16, C:0.21, G:0.40, T:0.23
Consensus pattern (30 bp):
CTGGGGCTGCGAATTCGAGGCTGACTTGGA
Found at i:77118 original size:36 final size:35
Alignment explanation
Indices: 77018--77240 Score: 268
Period size: 36 Copynumber: 6.5 Consensus size: 35
77008 GCATGAGCTG
*
77018 GGGCTGCGAATTCGAGGCTGACTTGGAC-T--G--
1 GGGCTGCGAATTCGAGGCTGACTTAGACTTGGGCT
*
77048 GGGCTGCGAATTCGAGGCTGACTTGGAC-T--G--
1 GGGCTGCGAATTCGAGGCTGACTTAGACTTGGGCT
77078 GGGCTGCGAATTCGAGGCTGACTTAGACTTGGGCT
1 GGGCTGCGAATTCGAGGCTGACTTAGACTTGGGCT
*
77113 CGGGCTACGAATTCGAGGCTGACTTAGACTTGGGCT
1 -GGGCTGCGAATTCGAGGCTGACTTAGACTTGGGCT
* *
77149 CGGGCTGCGAATTCGAGGCCGACTTAGACTGGGGCT
1 -GGGCTGCGAATTCGAGGCTGACTTAGACTTGGGCT
* * *
77185 GGGGCTGCGAATTCGAGGCTGACTTGGGCTGGGGCT
1 -GGGCTGCGAATTCGAGGCTGACTTAGACTTGGGCT
77221 GGGGCTGCGAATTCGAGGCT
1 -GGGCTGCGAATTCGAGGCT
77241 TACTCGGACA
Statistics
Matches: 178, Mismatches: 9, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
30 57 0.32
31 1 0.01
33 1 0.01
36 119 0.67
ACGTcount: A:0.16, C:0.21, G:0.40, T:0.23
Consensus pattern (35 bp):
GGGCTGCGAATTCGAGGCTGACTTAGACTTGGGCT
Found at i:79679 original size:23 final size:23
Alignment explanation
Indices: 79652--79704 Score: 70
Period size: 25 Copynumber: 2.2 Consensus size: 23
79642 AAATAAGTAA
*
79652 ATTAATCTGTATATATTTCTATT
1 ATTAATCTATATATATTTCTATT
*
79675 ATTAAAATTTATATATATTTCTATT
1 ATT--AATCTATATATATTTCTATT
79700 ATTAA
1 ATTAA
79705 AAATTGATTC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
23 5 0.19
25 21 0.81
ACGTcount: A:0.38, C:0.06, G:0.02, T:0.55
Consensus pattern (23 bp):
ATTAATCTATATATATTTCTATT
Found at i:81700 original size:2 final size:2
Alignment explanation
Indices: 81688--81725 Score: 58
Period size: 2 Copynumber: 18.5 Consensus size: 2
81678 TCAAATATGA
*
81688 AT AT CAT AT AT AT GT 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
81726 AATTGACCAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
2 31 0.94
3 2 0.06
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:84637 original size:18 final size:18
Alignment explanation
Indices: 84613--84655 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
84603 GGATGAACCA
84613 GAAGAAGATGATGAAGGG
1 GAAGAAGATGATGAAGGG
* * *
84631 GATGAAGATGGTGAATGG
1 GAAGAAGATGATGAAGGG
84649 GAAGAAG
1 GAAGAAG
84656 CGGATGCTGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.44, T:0.14
Consensus pattern (18 bp):
GAAGAAGATGATGAAGGG
Found at i:87835 original size:4 final size:4
Alignment explanation
Indices: 87826--87928 Score: 98
Period size: 4 Copynumber: 25.2 Consensus size: 4
87816 TTCTTAATAG
* *
87826 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATG CATG
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * * * * * *
87874 CATG CATG CATGCA CACA CACA CACA CATG CACA GATA CATA CATA CATA
1 CATA CATA CAT--A CATA CATA CATA CATA CATA CATA CATA CATA CATA
87924 CATA C
1 CATA C
87929 CCACTGTCCA
Statistics
Matches: 87, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
4 85 0.98
6 2 0.02
ACGTcount: A:0.44, C:0.29, G:0.07, T:0.20
Consensus pattern (4 bp):
CATA
Found at i:88746 original size:21 final size:18
Alignment explanation
Indices: 88720--88764 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
88710 TTGTCCTCCA
88720 GCTGCTGCTGCGGTGGTC
1 GCTGCTGCTGCGGTGGTC
88738 GCTGCTGCTGCGGTGGTC
1 GCTGCTGCTGCGGTGGTC
*
88756 GCCGCTGCT
1 GCTGCTGCT
88765 ACAACAGCTG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.00, C:0.31, G:0.42, T:0.27
Consensus pattern (18 bp):
GCTGCTGCTGCGGTGGTC
Found at i:90088 original size:3 final size:3
Alignment explanation
Indices: 90080--90116 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
90070 TATATTAGGG
90080 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
90117 GAAATACGTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:95341 original size:24 final size:24
Alignment explanation
Indices: 95314--95360 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
95304 AGCCCACCCT
95314 TCCTTTTCTTTCACCTCTCACCAA
1 TCCTTTTCTTTCACCTCTCACCAA
95338 TCCTTTTCTTTCACCTCTCACCA
1 TCCTTTTCTTTCACCTCTCACCA
95361 CCACTCAGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.15, C:0.43, G:0.00, T:0.43
Consensus pattern (24 bp):
TCCTTTTCTTTCACCTCTCACCAA
Found at i:104987 original size:21 final size:22
Alignment explanation
Indices: 104948--104990 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
104938 CAAAGGAAAG
*
104948 AATTAGAAGTAAGAATGCAAAA
1 AATTAGAAGTAAAAATGCAAAA
104970 AATTAGAA-TAAAAATGCAAAA
1 AATTAGAAGTAAAAATGCAAAA
104991 GCTTAATCCG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.63, C:0.05, G:0.14, T:0.19
Consensus pattern (22 bp):
AATTAGAAGTAAAAATGCAAAA
Found at i:115288 original size:3 final size:3
Alignment explanation
Indices: 115280--115310 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
115270 AATGCATCTT
115280 TAA TAA TAA TAA TAA -AA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
115311 TACAATATGA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:115300 original size:14 final size:14
Alignment explanation
Indices: 115281--115308 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
115271 ATGCATCTTT
115281 AATAATAATAATAA
1 AATAATAATAATAA
115295 AATAATAATAATAA
1 AATAATAATAATAA
115309 TATACAATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (14 bp):
AATAATAATAATAA
Found at i:119037 original size:122 final size:124
Alignment explanation
Indices: 118833--119301 Score: 687
Period size: 122 Copynumber: 3.7 Consensus size: 124
118823 AATATCATAC
118833 TCAATCAAGATGAGCTAGCATGAAAAAGTGTTGATATAAACAT-ATATACATATAATTCATGGTG
1 TCAATCAAGATGAGCTAGCATGAAAAAGTGTTGATATAAACATAATATACATATAATTCATGGTG
118897 TGAACAA-TAGGAACCTTAAAGATGGAGCTTTAGATCAATTTGGGGTGTAATATAACAT
66 TGAACAACTAGGAACCTTAAAGATGGAGCTTTAGATCAATTTGGGGTGTAATATAACAT
*
118955 TCAATCAAGATGAGCTAGCATGAAAAAGTGTTGATATAAACAT-TTATACATATAATTCATGGTG
1 TCAATCAAGATGAGCTAGCATGAAAAAGTGTTGATATAAACATAATATACATATAATTCATGGTG
*
119019 TGAACAA-TAGGAACCTTAAAGATGGAGCTTTAGATCTATTTGGGGTGTAATATAACAT
66 TGAACAACTAGGAACCTTAAAGATGGAGCTTTAGATCAATTTGGGGTGTAATATAACAT
* *
119077 TCAATCAAGATGAGCTAGCATGAAAAAGTGTAGATATAGACACACATACATAAACATATAATTCA
1 TCAATCAAGATGAGCTAGCATGAAAAAGTGTTGATAT--A-A-ACATA-ATATACATATAATTCA
* * ** * *
119142 TGGTTTGAACAACTAAGAATGTTAAAGATGTAGCTTTAGGTCAATTTGGGGTGTAATATAACAT
61 TGGTGTGAACAACTAGGAACCTTAAAGATGGAGCTTTAGATCAATTTGGGGTGTAATATAACAT
* * *
119206 TCAATCAAGATGAGCTAGCATGAAAAAGTGTTG-TGATAGACATATACAAATACACATAATTCAT
1 TCAATCAAGATGAGCTAGCATGAAAAAGTGTTGAT-ATA-A-ACATA-ATATACATATAATTCAT
*
119270 GGTGTGAACAACTAGGAATCTTAAAAGATGGA
62 GGTGTGAACAACTAGGAACCTT-AAAGATGGA
119302 AAATTAGGAG
Statistics
Matches: 316, Mismatches: 22, Indels: 12
0.90 0.06 0.03
Matches are distributed among these distances:
122 156 0.49
124 1 0.00
125 1 0.00
126 4 0.01
127 41 0.13
128 34 0.11
129 79 0.25
ACGTcount: A:0.41, C:0.11, G:0.19, T:0.29
Consensus pattern (124 bp):
TCAATCAAGATGAGCTAGCATGAAAAAGTGTTGATATAAACATAATATACATATAATTCATGGTG
TGAACAACTAGGAACCTTAAAGATGGAGCTTTAGATCAATTTGGGGTGTAATATAACAT
Found at i:122033 original size:147 final size:147
Alignment explanation
Indices: 121761--122059 Score: 535
Period size: 147 Copynumber: 2.0 Consensus size: 147
121751 TAATTTCCTA
* *
121761 ATGTCCCAATCCTCTTGGAAACCCAAGGAAAAGTCTAATGCATGCCTTATGACAAACAATTTAGA
1 ATGTCCCAATCCTCTTGGAAACCCAAAGAAAAGTCTAATGCATGCCTTACGACAAACAATTTAGA
* * * *
121826 TCATATCGTGAAAGAAAAACACTACACATAATAATGGAAACCACAGCCAAATTTGTATGCCCCTT
66 TCATATCATGAAAGAAAAACACGACACATAATAATGGAAACCACAACCAAATTTGCATGCCCCTT
121891 ATCACAAATTCATCTCC
131 ATCACAAATTCATCTCC
121908 ATGTCCCAATCCTCTTGGAAACCCAAAGAAAAGTCTAATGCATGCCTTACGACAAACAATTTAGA
1 ATGTCCCAATCCTCTTGGAAACCCAAAGAAAAGTCTAATGCATGCCTTACGACAAACAATTTAGA
*
121973 TCATATCATGAAAGAAAAACACGACACATAATGATGGAAACCACAACCAAATTTGCATGCCCCTT
66 TCATATCATGAAAGAAAAACACGACACATAATAATGGAAACCACAACCAAATTTGCATGCCCCTT
122038 ATCACAAATTCATCTCC
131 ATCACAAATTCATCTCC
122055 ATGTC
1 ATGTC
122060 TCCTTAGAGT
Statistics
Matches: 145, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
147 145 1.00
ACGTcount: A:0.39, C:0.25, G:0.12, T:0.24
Consensus pattern (147 bp):
ATGTCCCAATCCTCTTGGAAACCCAAAGAAAAGTCTAATGCATGCCTTACGACAAACAATTTAGA
TCATATCATGAAAGAAAAACACGACACATAATAATGGAAACCACAACCAAATTTGCATGCCCCTT
ATCACAAATTCATCTCC
Found at i:122624 original size:9 final size:9
Alignment explanation
Indices: 122610--122682 Score: 64
Period size: 9 Copynumber: 8.3 Consensus size: 9
122600 TTCATTAAAA
*
122610 TTTTATGAT
1 TTTTATAAT
122619 TTTTATAA-
1 TTTTATAAT
*
122627 ATTTATAAAT
1 TTTTAT-AAT
122637 TTTTAATAAT
1 TTTT-ATAAT
122647 TTTTATAAT
1 TTTTATAAT
122656 TTTT-T-AT
1 TTTTATAAT
*
122663 TTTT-TTAT
1 TTTTATAAT
*
122671 TTTTATAGT
1 TTTTATAAT
122680 TTT
1 TTT
122683 AGAATTAATC
Statistics
Matches: 54, Mismatches: 5, Indels: 10
0.78 0.07 0.14
Matches are distributed among these distances:
7 7 0.13
8 12 0.22
9 23 0.43
10 10 0.19
11 2 0.04
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (9 bp):
TTTTATAAT
Found at i:122630 original size:18 final size:19
Alignment explanation
Indices: 122607--122659 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
122597 TATTTCATTA
*
122607 AAATTTTATGATTTTT-AT
1 AAATTTTATAATTTTTAAT
122625 AAA-TTTATAAATTTTTAAT
1 AAATTTTAT-AATTTTTAAT
*
122644 AATTTTTATAATTTTT
1 AAATTTTATAATTTTT
122660 TATTTTTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
17 5 0.17
18 9 0.30
19 11 0.37
20 5 0.17
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (19 bp):
AAATTTTATAATTTTTAAT
Found at i:122641 original size:10 final size:10
Alignment explanation
Indices: 122617--122662 Score: 53
Period size: 10 Copynumber: 4.8 Consensus size: 10
122607 AAATTTTATG
122617 ATTTTTATAA
1 ATTTTTATAA
122627 A--TTTATAA
1 ATTTTTATAA
122635 ATTTTTA-ATA
1 ATTTTTATA-A
122645 ATTTTTATAA
1 ATTTTTATAA
*
122655 TTTTTTAT
1 ATTTTTAT
122663 TTTTTTATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
8 8 0.26
9 1 0.03
10 21 0.68
11 1 0.03
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (10 bp):
ATTTTTATAA
Found at i:122666 original size:16 final size:17
Alignment explanation
Indices: 122610--122688 Score: 63
Period size: 16 Copynumber: 4.6 Consensus size: 17
122600 TTCATTAAAA
* *
122610 TTTTATGATTTTTATAA
1 TTTTATAATTTTTATAT
*
122627 ATTTATAAATTTTTAATAAT
1 TTTTAT-AATTTTT-AT-AT
122647 TTTTATAATTTTT-TAT
1 TTTTATAATTTTTATAT
* *
122663 TTTT-TTATTTTTATAG
1 TTTTATAATTTTTATAT
*
122679 TTTTAGAATT
1 TTTTATAATT
122689 AATCTGGACA
Statistics
Matches: 49, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
15 7 0.14
16 12 0.24
17 9 0.18
18 6 0.12
19 9 0.18
20 6 0.12
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (17 bp):
TTTTATAATTTTTATAT
Found at i:122682 original size:8 final size:8
Alignment explanation
Indices: 122610--122683 Score: 51
Period size: 8 Copynumber: 8.6 Consensus size: 8
122600 TTCATTAAAA
122610 TTTTATGAT
1 TTTTAT-AT
122619 TTTTATAAAT
1 TTTTAT--AT
* *
122629 TTATAAAT
1 TTTTATAT
122637 TTTTAATAAT
1 TTTT-AT-AT
122647 TTTTATAAT
1 TTTTAT-AT
122656 TTTT-TAT
1 TTTTATAT
*
122663 TTTTTTAT
1 TTTTATAT
*
122671 TTTTATAG
1 TTTTATAT
122679 TTTTA
1 TTTTA
122684 GAATTAATCT
Statistics
Matches: 54, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
7 6 0.11
8 20 0.37
9 16 0.30
10 12 0.22
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (8 bp):
TTTTATAT
Found at i:122789 original size:25 final size:25
Alignment explanation
Indices: 122761--122812 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 25
122751 CCAAATTTCA
*
122761 ATTTTTAAAATATTTTATTTTCTTG
1 ATTTTTAAAAGATTTTATTTTCTTG
** *
122786 ATTTTTTGAAGATTTTATTTTGTTG
1 ATTTTTAAAAGATTTTATTTTCTTG
122811 AT
1 AT
122813 GTGGCAATGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.25, C:0.02, G:0.10, T:0.63
Consensus pattern (25 bp):
ATTTTTAAAAGATTTTATTTTCTTG
Found at i:123917 original size:3 final size:3
Alignment explanation
Indices: 123909--123934 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
123899 ATTGTATTTG
123909 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
123935 GATTTTACAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:128907 original size:3 final size:3
Alignment explanation
Indices: 128899--128940 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
128889 AAAATGAGGA
128899 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
128941 AGAAGCAGCT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:139927 original size:14 final size:14
Alignment explanation
Indices: 139896--139929 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
139886 ATTAAAATCA
139896 AAATTTCATATATC
1 AAATTTCATATATC
139910 AAATTATCATATAT-
1 AAATT-TCATATATC
139924 AAATTT
1 AAATTT
139930 AAAATGTATC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 1 0.05
14 10 0.53
15 8 0.42
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.44
Consensus pattern (14 bp):
AAATTTCATATATC
Found at i:141145 original size:23 final size:23
Alignment explanation
Indices: 141101--141145 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
141091 ACCTGAATCT
*
141101 AATTTTAAAAATTATTTGTATAC
1 AATTTTAAAAATTATATGTATAC
141124 AATTTATAAAAATTATAT-TATA
1 AATTT-TAAAAATTATATGTATA
141146 AGAATCAACA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (23 bp):
AATTTTAAAAATTATATGTATAC
Found at i:143219 original size:8 final size:7
Alignment explanation
Indices: 143192--143218 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
143182 TTTAAAAAGA
143192 AAAAAAC
1 AAAAAAC
143199 AAAAAAC
1 AAAAAAC
143206 AAAAAAC
1 AAAAAAC
143213 AAAAAA
1 AAAAAA
143219 AACCAAAGAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (7 bp):
AAAAAAC
Found at i:145059 original size:36 final size:36
Alignment explanation
Indices: 145007--145077 Score: 115
Period size: 36 Copynumber: 2.0 Consensus size: 36
144997 AGCTTCTGTG
*
145007 TCATCTTATACAAGACCATCCTCTCCCATTACTCGA
1 TCATCTAATACAAGACCATCCTCTCCCATTACTCGA
* *
145043 TCATCTAATACCAGACCATCCTCTCCTATTACTCG
1 TCATCTAATACAAGACCATCCTCTCCCATTACTCG
145078 CTCGCCATCT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.27, C:0.37, G:0.06, T:0.31
Consensus pattern (36 bp):
TCATCTAATACAAGACCATCCTCTCCCATTACTCGA
Found at i:161931 original size:17 final size:16
Alignment explanation
Indices: 161894--161931 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
161884 TTATTCTATT
*
161894 TTTACTCTTTAATTGA
1 TTTACTCTTTAATTAA
161910 TTTACTCTTTAATTTAA
1 TTTACTCTTTAA-TTAA
161927 TTTAC
1 TTTAC
161932 AGGGACTAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 12 0.60
17 8 0.40
ACGTcount: A:0.26, C:0.13, G:0.03, T:0.58
Consensus pattern (16 bp):
TTTACTCTTTAATTAA
Found at i:164533 original size:13 final size:13
Alignment explanation
Indices: 164515--164567 Score: 70
Period size: 13 Copynumber: 4.1 Consensus size: 13
164505 AGTTCTTCAT
164515 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
*
164528 TGCTTTTGAGAAG
1 TGCTTTTGAAAAG
* *
164541 TGCTGTGGAAAAG
1 TGCTTTTGAAAAG
*
164554 TGCTTTTAAAAAG
1 TGCTTTTGAAAAG
164567 T
1 T
164568 TTAGTTTAAA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
13 33 1.00
ACGTcount: A:0.30, C:0.08, G:0.26, T:0.36
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:168616 original size:119 final size:119
Alignment explanation
Indices: 168405--168642 Score: 476
Period size: 119 Copynumber: 2.0 Consensus size: 119
168395 GCGCTTCCTT
168405 AACCTTTATGGTTTCCGTACTGGAGATCTTTTCAGCCTTCAGAGCACTCAACCTCTGAATTTTCT
1 AACCTTTATGGTTTCCGTACTGGAGATCTTTTCAGCCTTCAGAGCACTCAACCTCTGAATTTTCT
168470 CAACCTTGACAGCACTAGCAGTGCCATTTTTCTCACTCTTGGAAGGCTCTTCAA
66 CAACCTTGACAGCACTAGCAGTGCCATTTTTCTCACTCTTGGAAGGCTCTTCAA
168524 AACCTTTATGGTTTCCGTACTGGAGATCTTTTCAGCCTTCAGAGCACTCAACCTCTGAATTTTCT
1 AACCTTTATGGTTTCCGTACTGGAGATCTTTTCAGCCTTCAGAGCACTCAACCTCTGAATTTTCT
168589 CAACCTTGACAGCACTAGCAGTGCCATTTTTCTCACTCTTGGAAGGCTCTTCAA
66 CAACCTTGACAGCACTAGCAGTGCCATTTTTCTCACTCTTGGAAGGCTCTTCAA
168643 TAACAATTTT
Statistics
Matches: 119, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
119 119 1.00
ACGTcount: A:0.23, C:0.28, G:0.16, T:0.34
Consensus pattern (119 bp):
AACCTTTATGGTTTCCGTACTGGAGATCTTTTCAGCCTTCAGAGCACTCAACCTCTGAATTTTCT
CAACCTTGACAGCACTAGCAGTGCCATTTTTCTCACTCTTGGAAGGCTCTTCAA
Found at i:169584 original size:12 final size:12
Alignment explanation
Indices: 169564--169612 Score: 53
Period size: 12 Copynumber: 4.1 Consensus size: 12
169554 CACTGCTAGC
169564 ACATACATGCAT
1 ACATACATGCAT
* *
169576 ACATCCATGTAT
1 ACATACATGCAT
* *
169588 CCATGCATGCAT
1 ACATACATGCAT
*
169600 GCATACATGCAT
1 ACATACATGCAT
169612 A
1 A
169613 TAGTTAAATT
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.35, C:0.27, G:0.12, T:0.27
Consensus pattern (12 bp):
ACATACATGCAT
Found at i:173551 original size:27 final size:27
Alignment explanation
Indices: 173513--173564 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
173503 TTCACTCAGT
* *
173513 GATTGGTTTCATTTTATAATCAATCAC
1 GATTGGTTTCATTTTAAAACCAATCAC
173540 GATTGGTTTCATTTTAAAACCAATC
1 GATTGGTTTCATTTTAAAACCAATC
173565 CAACCACCTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.42
Consensus pattern (27 bp):
GATTGGTTTCATTTTAAAACCAATCAC
Found at i:179895 original size:43 final size:43
Alignment explanation
Indices: 179834--179920 Score: 174
Period size: 43 Copynumber: 2.0 Consensus size: 43
179824 GTGTTCGTTA
179834 TTCGTTTTTAGCTGAATTAACTGACCAAATTCGGTTTGTTGGT
1 TTCGTTTTTAGCTGAATTAACTGACCAAATTCGGTTTGTTGGT
179877 TTCGTTTTTAGCTGAATTAACTGACCAAATTCGGTTTGTTGGT
1 TTCGTTTTTAGCTGAATTAACTGACCAAATTCGGTTTGTTGGT
179920 T
1 T
179921 AACCATAAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.21, C:0.14, G:0.21, T:0.45
Consensus pattern (43 bp):
TTCGTTTTTAGCTGAATTAACTGACCAAATTCGGTTTGTTGGT
Found at i:184305 original size:2 final size:2
Alignment explanation
Indices: 184292--184342 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
184282 GGTAAATCTC
*
184292 AT AT AG 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
184334 AT AT AT AT A
1 AT AT AT AT A
184343 ATAAGAAACT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:184780 original size:50 final size:51
Alignment explanation
Indices: 184726--184827 Score: 197
Period size: 50 Copynumber: 2.0 Consensus size: 51
184716 TCACTTTTTT
184726 TTTTATTATCATAATAATTAATAATAATGATGTCAA-TTGAAATAATATTC
1 TTTTATTATCATAATAATTAATAATAATGATGTCAATTTGAAATAATATTC
184776 TTTTATTATCATAATAATTAATAATAATGATGTCAATTTGAAATAATATTC
1 TTTTATTATCATAATAATTAATAATAATGATGTCAATTTGAAATAATATTC
184827 T
1 T
184828 ATCAAAATTG
Statistics
Matches: 51, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
50 36 0.71
51 15 0.29
ACGTcount: A:0.43, C:0.06, G:0.06, T:0.45
Consensus pattern (51 bp):
TTTTATTATCATAATAATTAATAATAATGATGTCAATTTGAAATAATATTC
Found at i:187345 original size:46 final size:46
Alignment explanation
Indices: 187164--187347 Score: 244
Period size: 46 Copynumber: 4.0 Consensus size: 46
187154 TTTGACATGA
* * * * * *
187164 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGT
*** **
187210 TGCCATGGTATCTTTCAACCATGGTCTTGTTCATTTCATATCACAT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
187256 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
*
187302 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
187348 GGTCTTACAC
Statistics
Matches: 123, Mismatches: 14, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
45 4 0.03
46 119 0.97
ACGTcount: A:0.22, C:0.23, G:0.15, T:0.41
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
Found at i:187355 original size:24 final size:24
Alignment explanation
Indices: 187323--187371 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
187313 CTTTCAACCA
187323 TGGTCTTACACATTTTATATCAGG
1 TGGTCTTACACATTTTATATCAGG
187347 TGGTCTTACACATTTTATATCAGG
1 TGGTCTTACACATTTTATATCAGG
187371 T
1 T
187372 TGCCATGGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.24, C:0.16, G:0.16, T:0.43
Consensus pattern (24 bp):
TGGTCTTACACATTTTATATCAGG
Found at i:187358 original size:70 final size:70
Alignment explanation
Indices: 187277--187417 Score: 273
Period size: 70 Copynumber: 2.0 Consensus size: 70
187267 CTTTCAACCA
187277 TGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTTATA
1 TGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTTATA
187342 TCAGG
66 TCAGG
*
187347 TGGTCTTACACATTTTATATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTTATA
1 TGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTTATA
187412 TCAGG
66 TCAGG
187417 T
1 T
187418 TGCCATGGTA
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
70 70 1.00
ACGTcount: A:0.24, C:0.21, G:0.16, T:0.40
Consensus pattern (70 bp):
TGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTTATA
TCAGG
Found at i:187379 original size:162 final size:154
Alignment explanation
Indices: 187185--187499 Score: 459
Period size: 162 Copynumber: 2.0 Consensus size: 154
187175 CTTTCAACTA
* * * * ***
187185 TGGTCTTACTCATTTTCTGTCATGTTGCCATGGTATCTTTCAACCATGGTCTTGTTCATTTCATA
1 TGGTCTTACACATTTTATATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATA
187250 TCACATTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCT
66 TCACATTGCCATGGTATCTTTCAACCATGGTCTT--ACA---C---TCAGGTTGCCATGGTATCT
*
187315 TTCAACCATGGTCTTACACATTTTATATCAGG
123 TTCAACCATGGTCTTACACATTTCATATCAGG
*
187347 TGGTCTTACACATTTTATATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTTATA
1 TGGTCTTACACATTTTATATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATA
**
187412 TCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACTCAGGTTGCCATGGTATCTTTCAACCA
66 TCACATTGCCATGGTATCTTTCAACCATGGTCTTACACTCAGGTTGCCATGGTATCTTTCAACCA
187477 TGGTCTTACACATTTCATATCAG
131 TGGTCTTACACATTTCATATCAG
187500 AGAGCACACT
Statistics
Matches: 142, Mismatches: 11, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
154 49 0.35
157 1 0.01
160 3 0.02
162 89 0.63
ACGTcount: A:0.23, C:0.23, G:0.15, T:0.39
Consensus pattern (154 bp):
TGGTCTTACACATTTTATATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATA
TCACATTGCCATGGTATCTTTCAACCATGGTCTTACACTCAGGTTGCCATGGTATCTTTCAACCA
TGGTCTTACACATTTCATATCAGG
Found at i:187414 original size:46 final size:46
Alignment explanation
Indices: 187347--187499 Score: 241
Period size: 46 Copynumber: 3.5 Consensus size: 46
187337 TTATATCAGG
187347 TGGTCTTACACATTTTATATCAGGTTGCCATGGTATCTTTCAACCA
1 TGGTCTTACACATTTTATATCAGGTTGCCATGGTATCTTTCAACCA
187393 TGGTCTTACACATTTTATATCAGGTTGCCATGGTATCTTTCAACCA
1 TGGTCTTACACATTTTATATCAGGTTGCCATGGTATCTTTCAACCA
187439 TGGTCTTACAC--------TCAGGTTGCCATGGTATCTTTCAACCA
1 TGGTCTTACACATTTTATATCAGGTTGCCATGGTATCTTTCAACCA
*
187477 TGGTCTTACACATTTCATATCAG
1 TGGTCTTACACATTTTATATCAG
187500 AGAGCACACT
Statistics
Matches: 99, Mismatches: 0, Indels: 16
0.86 0.00 0.14
Matches are distributed among these distances:
38 38 0.38
46 61 0.62
ACGTcount: A:0.24, C:0.23, G:0.16, T:0.38
Consensus pattern (46 bp):
TGGTCTTACACATTTTATATCAGGTTGCCATGGTATCTTTCAACCA
Found at i:187435 original size:116 final size:116
Alignment explanation
Indices: 187241--187449 Score: 382
Period size: 116 Copynumber: 1.8 Consensus size: 116
187231 TGGTCTTGTT
187241 CATTTCATATCACATTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCC
1 CATTTCATATCACATTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCC
187306 ATGGTATCTTTCAACCATGGTCTTACACATTTTATATCAGGTGGTCTTACA
66 ATGGTATCTTTCAACCATGGTCTTACACATTTTATATCAGGTGGTCTTACA
* ** *
187357 CATTTTATATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTTATATCAGGTTGCC
1 CATTTCATATCACATTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCC
187422 ATGGTATCTTTCAACCATGGTCTTACAC
66 ATGGTATCTTTCAACCATGGTCTTACAC
187450 TCAGGTTGCC
Statistics
Matches: 89, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
116 89 1.00
ACGTcount: A:0.24, C:0.23, G:0.14, T:0.38
Consensus pattern (116 bp):
CATTTCATATCACATTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCC
ATGGTATCTTTCAACCATGGTCTTACACATTTTATATCAGGTGGTCTTACA
Found at i:187463 original size:38 final size:38
Alignment explanation
Indices: 187412--187487 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
187402 ACATTTTATA
187412 TCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
1 TCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
187450 TCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
1 TCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
187488 ATTTCATATC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.21, C:0.26, G:0.18, T:0.34
Consensus pattern (38 bp):
TCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
Found at i:189653 original size:11 final size:11
Alignment explanation
Indices: 189637--189688 Score: 52
Period size: 11 Copynumber: 4.7 Consensus size: 11
189627 TATACTAAAT
189637 AAATAATAATA
1 AAATAATAATA
*
189648 AAATAAT-ATT
1 AAATAATAATA
* *
189658 AAATATCTCATA
1 AAATA-ATAATA
*
189670 AAATATTAATA
1 AAATAATAATA
189681 AAATAATA
1 AAATAATA
189689 TTTATCTAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
10 7 0.21
11 19 0.58
12 7 0.21
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (11 bp):
AAATAATAATA
Found at i:190473 original size:6 final size:6
Alignment explanation
Indices: 190462--190493 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
190452 AGGTTTAATT
*
190462 TATAAA TATAAA TATAAA TATAAA TATGAA TA
1 TATAAA TATAAA TATAAA TATAAA TATAAA TA
190494 CAATATTATC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (6 bp):
TATAAA
Found at i:193996 original size:29 final size:30
Alignment explanation
Indices: 193928--193997 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 30
193918 TTATTTTTGA
* *
193928 GATATATGAGTTTTTATTTAATGTGTAATTT
1 GATATATGAATTTTAATTTAA-GTGTAATTT
*
193959 GATACATGAATTTTAATTTAA-TGTAATTAT
1 GATATATGAATTTTAATTTAAGTGTAATT-T
193989 -ATATATGAA
1 GATATATGAA
193998 ACTGTAACTT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
29 15 0.44
30 1 0.03
31 18 0.53
ACGTcount: A:0.37, C:0.01, G:0.13, T:0.49
Consensus pattern (30 bp):
GATATATGAATTTTAATTTAAGTGTAATTT
Found at i:196224 original size:2 final size:2
Alignment explanation
Indices: 196217--196248 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
196207 AAAATTTTAT
196217 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
196249 AATTACGTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:213985 original size:2 final size:2
Alignment explanation
Indices: 213978--214018 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
213968 ATCATTCCCT
* *
213978 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
214019 GTGATTTTTG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (2 bp):
TA
Found at i:222929 original size:15 final size:17
Alignment explanation
Indices: 222909--222941 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
222899 ACAGATGGAA
222909 AGATAA-TC-AAACACC
1 AGATAACTCAAAACACC
222924 AGATAACTCAAAACACC
1 AGATAACTCAAAACACC
222941 A
1 A
222942 AGATTTGCCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 2 0.12
17 8 0.50
ACGTcount: A:0.55, C:0.27, G:0.06, T:0.12
Consensus pattern (17 bp):
AGATAACTCAAAACACC
Found at i:229399 original size:19 final size:19
Alignment explanation
Indices: 229363--229459 Score: 65
Period size: 20 Copynumber: 5.0 Consensus size: 19
229353 ATTTTAACTT
* *
229363 TTTTTTACATATTCTTTATAA
1 TTTTTTAGA-ATT-TTTAAAA
*
229384 TTTTTTAGAATTTTT-AAT
1 TTTTTTAGAATTTTTAAAA
* *
229402 TTTTTTTG-TTTATTTAAAAA
1 TTTTTTAGAATT-TTT-AAAA
*
229422 TATTTTAGAATTTTTAAAAA
1 TTTTTTAGAATTTTT-AAAA
*
229442 TATTTT-GAATTTTTAAAA
1 TTTTTTAGAATTTTTAAAA
229460 ATCATTTTGA
Statistics
Matches: 63, Mismatches: 9, Indels: 11
0.76 0.11 0.13
Matches are distributed among these distances:
17 2 0.03
18 15 0.24
19 11 0.17
20 25 0.40
21 10 0.16
ACGTcount: A:0.34, C:0.02, G:0.04, T:0.60
Consensus pattern (19 bp):
TTTTTTAGAATTTTTAAAA
Found at i:229460 original size:19 final size:19
Alignment explanation
Indices: 229414--229476 Score: 99
Period size: 20 Copynumber: 3.2 Consensus size: 19
229404 TTTTTGTTTA
229414 TTTAAAAATATTTTAGAATT
1 TTTAAAAATATTTT-GAATT
229434 TTTAAAAATATTTTGAATT
1 TTTAAAAATATTTTGAATT
229453 TTTAAAAATCATTTTGAATAT
1 TTTAAAAAT-ATTTTGAAT-T
229474 TTT
1 TTT
229477 TTTTGTAATT
Statistics
Matches: 41, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
19 14 0.34
20 23 0.56
21 4 0.10
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.52
Consensus pattern (19 bp):
TTTAAAAATATTTTGAATT
Found at i:235192 original size:2 final size:2
Alignment explanation
Indices: 235185--235212 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
235175 AACTTGGATT
235185 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
235213 CACAAAATAT
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:236899 original size:22 final size:22
Alignment explanation
Indices: 236871--236914 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
236861 ATCACAAAGT
236871 ATGATATATAAAACAAGTGGTG
1 ATGATATATAAAACAAGTGGTG
236893 ATGATATATAAAACAAGTGGTG
1 ATGATATATAAAACAAGTGGTG
236915 TTGGAATGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.45, C:0.05, G:0.23, T:0.27
Consensus pattern (22 bp):
ATGATATATAAAACAAGTGGTG
Found at i:240194 original size:31 final size:29
Alignment explanation
Indices: 240156--240283 Score: 100
Period size: 29 Copynumber: 4.3 Consensus size: 29
240146 CATATGAGAA
240156 GCCCTTATTTGAGTGCTTTTGAAAAGGTTTG
1 GCCCTTATTTGA-T-CTTTTGAAAAGGTTTG
*
240187 GCCCTTATTTGACCATTTTGAAAA-GTTT-
1 GCCCTTATTTGATC-TTTTGAAAAGGTTTG
* * **
240215 GACCTTCATTTGATCACTTTTGTAAAGGTTAA
1 GCCCTT-ATTTGAT--CTTTTGAAAAGGTTTG
* * *
240247 GCCCTTATATGA-CTATTTTAAAAAGTTTG
1 GCCCTTATTTGATCT-TTTGAAAAGGTTTG
240276 GCCCTTAT
1 GCCCTTAT
240284 ATGAGCTACC
Statistics
Matches: 78, Mismatches: 12, Indels: 16
0.74 0.11 0.15
Matches are distributed among these distances:
28 7 0.09
29 28 0.36
30 17 0.22
31 21 0.27
32 5 0.06
ACGTcount: A:0.25, C:0.16, G:0.17, T:0.41
Consensus pattern (29 bp):
GCCCTTATTTGATCTTTTGAAAAGGTTTG
Found at i:240208 original size:30 final size:30
Alignment explanation
Indices: 240172--240283 Score: 113
Period size: 29 Copynumber: 3.8 Consensus size: 30
240162 ATTTGAGTGC
240172 TTTTGAAAAGGTTTGGCCCTTATTTGACCA
1 TTTTGAAAAGGTTTGGCCCTTATTTGACCA
* *
240202 TTTTGAAAA-GTTT-GACCTTCATTTGATCA
1 TTTTGAAAAGGTTTGGCCCTT-ATTTGACCA
* ** * *
240231 CTTTTGTAAAGGTTAAGCCCTTATATGACTA
1 -TTTTGAAAAGGTTTGGCCCTTATTTGACCA
*
240262 TTTT-AAAAAGTTTGGCCCTTAT
1 TTTTGAAAAGGTTTGGCCCTTAT
240284 ATGAGCTACC
Statistics
Matches: 66, Mismatches: 12, Indels: 9
0.76 0.14 0.10
Matches are distributed among these distances:
28 5 0.08
29 26 0.39
30 21 0.32
31 9 0.14
32 5 0.08
ACGTcount: A:0.27, C:0.15, G:0.16, T:0.42
Consensus pattern (30 bp):
TTTTGAAAAGGTTTGGCCCTTATTTGACCA
Found at i:251996 original size:5 final size:5
Alignment explanation
Indices: 251983--252012 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
251973 GGCCTTAATA
*
251983 CTTTG CTTTT CTTTT CTTTT CTTTT CTTTT
1 CTTTT CTTTT CTTTT CTTTT CTTTT CTTTT
252013 TTACGGATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.00, C:0.20, G:0.03, T:0.77
Consensus pattern (5 bp):
CTTTT
Found at i:262251 original size:23 final size:23
Alignment explanation
Indices: 262221--262268 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
262211 TTCATTGGCT
262221 AACTTATGTGAAATATTAAAGAA
1 AACTTATGTGAAATATTAAAGAA
262244 AACTTATGTGAAATATTAAAGAA
1 AACTTATGTGAAATATTAAAGAA
262267 AA
1 AA
262269 GAGTATCCTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.54, C:0.04, G:0.12, T:0.29
Consensus pattern (23 bp):
AACTTATGTGAAATATTAAAGAA
Found at i:263182 original size:6 final size:6
Alignment explanation
Indices: 263173--263220 Score: 96
Period size: 6 Copynumber: 8.0 Consensus size: 6
263163 TATTTTAATG
263173 ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT
1 ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT
263221 TTATTTTTTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (6 bp):
ATAAAT
Found at i:265013 original size:49 final size:49
Alignment explanation
Indices: 264941--265038 Score: 169
Period size: 49 Copynumber: 2.0 Consensus size: 49
264931 TTGTCGTTTT
**
264941 GCTGTCTTGGTTTTCATAGCTATCGGTTGGTGTGATCATCAACCTAAGA
1 GCTGTCTTGGTTTTCATAGCTATCAATTGGTGTGATCATCAACCTAAGA
*
264990 GCTGTCTTGGTTTTCATAGCTATCAATTGGTGTGATCATGAACCTAAGA
1 GCTGTCTTGGTTTTCATAGCTATCAATTGGTGTGATCATCAACCTAAGA
265039 TCATTCATTT
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 46 1.00
ACGTcount: A:0.22, C:0.17, G:0.23, T:0.37
Consensus pattern (49 bp):
GCTGTCTTGGTTTTCATAGCTATCAATTGGTGTGATCATCAACCTAAGA
Found at i:272079 original size:18 final size:18
Alignment explanation
Indices: 272056--272184 Score: 159
Period size: 18 Copynumber: 7.2 Consensus size: 18
272046 ACCATTTACG
* *
272056 GTACTATTCACATATACG
1 GTACTATTCACGTATACA
* *
272074 GCACTATTTACGTATACA
1 GTACTATTCACGTATACA
272092 GTACTATTCACGTATACA
1 GTACTATTCACGTATACA
*
272110 GCACTATTCACGTATACA
1 GTACTATTCACGTATACA
* * *
272128 ATACTGTTCACGTATACT
1 GTACTATTCACGTATACA
* *
272146 GCACTATTCACGTATACG
1 GTACTATTCACGTATACA
*
272164 GTACTGTTCACGTATACA
1 GTACTATTCACGTATACA
272182 GTA
1 GTA
272185 ATTGGGATTG
Statistics
Matches: 93, Mismatches: 18, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 93 1.00
ACGTcount: A:0.31, C:0.23, G:0.13, T:0.33
Consensus pattern (18 bp):
GTACTATTCACGTATACA
Found at i:272108 original size:36 final size:36
Alignment explanation
Indices: 272056--272182 Score: 182
Period size: 36 Copynumber: 3.5 Consensus size: 36
272046 ACCATTTACG
* * *
272056 GTACTATTCACATATACGGCACTATTTACGTATACA
1 GTACTATTCACGTATACAGCACTATTCACGTATACA
272092 GTACTATTCACGTATACAGCACTATTCACGTATACA
1 GTACTATTCACGTATACAGCACTATTCACGTATACA
* * * *
272128 ATACTGTTCACGTATACTGCACTATTCACGTATACG
1 GTACTATTCACGTATACAGCACTATTCACGTATACA
*
272164 GTACTGTTCACGTATACAG
1 GTACTATTCACGTATACAG
272183 TAATTGGGAT
Statistics
Matches: 82, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 82 1.00
ACGTcount: A:0.31, C:0.24, G:0.13, T:0.32
Consensus pattern (36 bp):
GTACTATTCACGTATACAGCACTATTCACGTATACA
Found at i:288381 original size:17 final size:18
Alignment explanation
Indices: 288350--288383 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
288340 CCCACAAACA
*
288350 TTTCTCTTTTTTTTTTTT
1 TTTCTCTTTTGTTTTTTT
288368 TTTC-CTTTTGTTTTTT
1 TTTCTCTTTTGTTTTTT
288384 GCCTACAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.00, C:0.12, G:0.03, T:0.85
Consensus pattern (18 bp):
TTTCTCTTTTGTTTTTTT
Found at i:289727 original size:13 final size:13
Alignment explanation
Indices: 289709--289734 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
289699 CCTCAAATCG
289709 ACTTAATTTTAAT
1 ACTTAATTTTAAT
289722 ACTTAATTTTAAT
1 ACTTAATTTTAAT
289735 GTATATTATT
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:0.08, G:0.00, T:0.54
Consensus pattern (13 bp):
ACTTAATTTTAAT
Found at i:298322 original size:9 final size:8
Alignment explanation
Indices: 298296--298366 Score: 54
Period size: 8 Copynumber: 8.6 Consensus size: 8
298286 AAAACTTAAT
298296 AAATAATTA
1 AAAT-ATTA
298305 AAATATTA
1 AAATATTA
298313 AAATATTTA
1 AAATA-TTA
*
298322 AGATATT-
1 AAATATTA
*
298329 ATATATTA
1 AAATATTA
* *
298337 AATTAATA
1 AAATATTA
*
298345 AAATTATTT
1 AAA-TATTA
*
298354 AAATATTT
1 AAATATTA
298362 AAATA
1 AAATA
298367 AAAATATAAA
Statistics
Matches: 51, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
7 6 0.12
8 28 0.55
9 17 0.33
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.42
Consensus pattern (8 bp):
AAATATTA
Found at i:298374 original size:41 final size:40
Alignment explanation
Indices: 298295--298378 Score: 95
Period size: 41 Copynumber: 2.1 Consensus size: 40
298285 GAAAACTTAA
**
298295 TAAATAATTAAAATATTAAAATATTTAAGATATTATATAT
1 TAAATAATTAAAATATTAAAATATTTAAGATAAAATATAT
*
298335 TAAATTAA-TAAAATTATTTAAATATTTAA-ATAAAA-ATA-
1 TAAA-TAATTAAAA-TATTAAAATATTTAAGATAAAATATAT
298373 TAAATA
1 TAAATA
298379 GTAAATTTCA
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
37 2 0.05
38 4 0.10
39 3 0.08
40 13 0.33
41 17 0.44
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.40
Consensus pattern (40 bp):
TAAATAATTAAAATATTAAAATATTTAAGATAAAATATAT
Found at i:299073 original size:13 final size:13
Alignment explanation
Indices: 299055--299080 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
299045 ATTGGAGGAG
299055 AATATGTATATAT
1 AATATGTATATAT
299068 AATATGTATATAT
1 AATATGTATATAT
299081 CATTTGTCCA
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:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (13 bp):
AATATGTATATAT
Found at i:299587 original size:18 final size:18
Alignment explanation
Indices: 299564--299598 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
299554 CATCACGTCA
*
299564 ATAAATATTTTAAAAATT
1 ATAAATATTTAAAAAATT
299582 ATAAATATTTAAAAAAT
1 ATAAATATTTAAAAAAT
299599 AAAAATTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
ATAAATATTTAAAAAATT
Found at i:299604 original size:17 final size:18
Alignment explanation
Indices: 299566--299604 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
299556 TCACGTCAAT
* *
299566 AAATATTTTAAAAATTAT
1 AAATATTTTAAAAAATAA
299584 AAATA-TTTAAAAAATAA
1 AAATATTTTAAAAAATAA
299601 AAAT
1 AAAT
299605 TTCATAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
AAATATTTTAAAAAATAA
Found at i:301788 original size:16 final size:16
Alignment explanation
Indices: 301767--301797 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
301757 TCTTATCTTA
301767 AACTATATATATATAT
1 AACTATATATATATAT
301783 AACTATATATATATA
1 AACTATATATATATA
301798 GTTTGATGTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (16 bp):
AACTATATATATATAT
Found at i:302681 original size:24 final size:24
Alignment explanation
Indices: 302654--302699 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
302644 CATTCCCATG
*
302654 TAAATATTAAAATATAAATTAGTA
1 TAAATATTAAAATAAAAATTAGTA
*
302678 TAAATATTAATATAAAAATTAG
1 TAAATATTAAAATAAAAATTAG
302700 GTATGATGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (24 bp):
TAAATATTAAAATAAAAATTAGTA
Found at i:302797 original size:19 final size:17
Alignment explanation
Indices: 302761--302801 Score: 55
Period size: 19 Copynumber: 2.3 Consensus size: 17
302751 ATTATTTTTT
302761 AATTTAAATTTATTTAA
1 AATTTAAATTTATTTAA
*
302778 AATTTATAATTTTTTTTAA
1 AATTTA-AA-TTTATTTAA
302797 AATTT
1 AATTT
302802 GAGTTATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 6 0.29
18 2 0.10
19 13 0.62
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
AATTTAAATTTATTTAA
Found at i:302841 original size:29 final size:28
Alignment explanation
Indices: 302773--302843 Score: 72
Period size: 29 Copynumber: 2.5 Consensus size: 28
302763 TTTAAATTTA
* *
302773 TTTA-AAATTTATAATTTTTTTTAAAAT
1 TTTATAAATTTATTATTATTTTTAAAAT
* * *
302800 TTGAGTTATTTTATTATTATTTTTAATAAT
1 TTTA-TAAATTTATTATTATTTTTAA-AAT
302830 TTTATAAATTTATT
1 TTTATAAATTTATT
302844 TATTGATGTG
Statistics
Matches: 33, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
27 3 0.09
29 24 0.73
30 6 0.18
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (28 bp):
TTTATAAATTTATTATTATTTTTAAAAT
Found at i:303451 original size:9 final size:9
Alignment explanation
Indices: 303437--303466 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
303427 TCCCCACCAG
303437 AAAAAAGAA
1 AAAAAAGAA
303446 AAAAAAGAA
1 AAAAAAGAA
303455 AAAAAA-AA
1 AAAAAAGAA
303463 AAAA
1 AAAA
303467 CCTTGAGTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 6 0.29
9 15 0.71
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (9 bp):
AAAAAAGAA
Found at i:303456 original size:16 final size:15
Alignment explanation
Indices: 303435--303466 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
303425 CTTCCCCACC
303435 AGAAAAAAGAAAAAAA
1 AGAAAAAA-AAAAAAA
303451 AGAAAAAAAAAAAAA
1 AGAAAAAAAAAAAAA
303466 A
1 A
303467 CCTTGAGTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (15 bp):
AGAAAAAAAAAAAAA
Found at i:307208 original size:9 final size:9
Alignment explanation
Indices: 307186--307238 Score: 56
Period size: 9 Copynumber: 5.8 Consensus size: 9
307176 TGTCATGTCA
307186 ATAAATAATT
1 ATAAA-AATT
307196 -TAAAAATT
1 ATAAAAATT
307204 ATAAAATATT
1 ATAAAA-ATT
307214 -TAAAAATT
1 ATAAAAATT
*
307222 ATAAAAGTT
1 ATAAAAATT
307231 CATAAAAA
1 -ATAAAAA
307239 AAAAAGATAT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
8 7 0.19
9 21 0.57
10 9 0.24
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (9 bp):
ATAAAAATT
Found at i:307214 original size:18 final size:19
Alignment explanation
Indices: 307188--307227 Score: 73
Period size: 18 Copynumber: 2.2 Consensus size: 19
307178 TCATGTCAAT
307188 AAATAATTTAAAAATTATA
1 AAATAATTTAAAAATTATA
307207 AAAT-ATTTAAAAATTATA
1 AAATAATTTAAAAATTATA
307225 AAA
1 AAA
307228 GTTCATAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 17 0.81
19 4 0.19
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
AAATAATTTAAAAATTATA
Found at i:307887 original size:22 final size:21
Alignment explanation
Indices: 307859--307909 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 21
307849 TTTTTATAAC
307859 TTTTAAATATTATTTGATAAA-A
1 TTTTAAAT-TT-TTTGATAAATA
*
307881 TTTTAAATTTTTTTATAAATA
1 TTTTAAATTTTTTGATAAATA
307902 TTTATAAA
1 TTT-TAAA
307910 AAATTAATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 8 0.31
21 6 0.23
22 12 0.46
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (21 bp):
TTTTAAATTTTTTGATAAATA
Found at i:308280 original size:30 final size:30
Alignment explanation
Indices: 308246--308325 Score: 76
Period size: 29 Copynumber: 2.6 Consensus size: 30
308236 TCTAGTGGAA
**
308246 TTAATTAAAAACTTTTAAAA-TTTA-AAGAGT
1 TTAATTAAAAA-TTTTAAAACTTTAGAA-AAC
*
308276 TTAA-TAAAAAGTTTCAAAACTTTATGAAAAC
1 TTAATTAAAAA-TTTTAAAACTTTA-GAAAAC
308307 TTAATTAAAAATTTTAAAA
1 TTAATTAAAAATTTTAAAA
308326 AGGAATAATA
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
29 13 0.32
30 8 0.20
31 12 0.29
32 8 0.20
ACGTcount: A:0.53, C:0.05, G:0.05, T:0.38
Consensus pattern (30 bp):
TTAATTAAAAATTTTAAAACTTTAGAAAAC
Found at i:308584 original size:21 final size:19
Alignment explanation
Indices: 308550--308593 Score: 70
Period size: 21 Copynumber: 2.2 Consensus size: 19
308540 ATTGATTCGG
308550 AAATTAATAAAAATTAATT
1 AAATTAATAAAAATTAATT
308569 AAATTAAATGAAAAATTAATT
1 AAATT-AAT-AAAAATTAATT
308590 AAAT
1 AAAT
308594 CGATTAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 5 0.22
20 3 0.13
21 15 0.65
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (19 bp):
AAATTAATAAAAATTAATT
Found at i:308676 original size:15 final size:15
Alignment explanation
Indices: 308656--308686 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
308646 AATCGAATTT
308656 ACTGATCTGTTTTTC
1 ACTGATCTGTTTTTC
308671 ACTGATCTGTTTTTC
1 ACTGATCTGTTTTTC
308686 A
1 A
308687 ACATGTTGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.16, C:0.19, G:0.13, T:0.52
Consensus pattern (15 bp):
ACTGATCTGTTTTTC
Found at i:317740 original size:31 final size:28
Alignment explanation
Indices: 317705--317769 Score: 76
Period size: 28 Copynumber: 2.2 Consensus size: 28
317695 TGTTTTTGTT
*
317705 ACTAAACTATTTAAAATTTTTCGTTTAAGTC
1 ACTAAACTATTTAAAA-GTTT--TTTAAGTC
* *
317736 ACTAAATTATTTGAAAGTTTTTTAAGTC
1 ACTAAACTATTTAAAAGTTTTTTAAGTC
317764 ACTAAA
1 ACTAAA
317770 TTGTTATTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
28 14 0.45
30 3 0.10
31 14 0.45
ACGTcount: A:0.38, C:0.11, G:0.08, T:0.43
Consensus pattern (28 bp):
ACTAAACTATTTAAAAGTTTTTTAAGTC
Found at i:320318 original size:8 final size:8
Alignment explanation
Indices: 320305--320332 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
320295 TCAACCACAA
320305 AAAAAAAG
1 AAAAAAAG
320313 AAAAAAAG
1 AAAAAAAG
320321 AAAAAAAG
1 AAAAAAAG
320329 AAAA
1 AAAA
320333 CCCAAATCGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (8 bp):
AAAAAAAG
Found at i:327646 original size:29 final size:30
Alignment explanation
Indices: 327590--327652 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 30
327580 AGTTTATATA
** * *
327590 TTTATAATTTTTAAAAAATTAAATTAAATT
1 TTTATAATTTTTAAAAAAGCAAAGTAAAAT
*
327620 TTTATAA-TTTTAAAGAAGCAAAGTAAAAT
1 TTTATAATTTTTAAAAAAGCAAAGTAAAAT
327649 TTTA
1 TTTA
327653 CCTTTAATAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
29 21 0.75
30 7 0.25
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (30 bp):
TTTATAATTTTTAAAAAAGCAAAGTAAAAT
Found at i:338657 original size:12 final size:12
Alignment explanation
Indices: 338637--338669 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
338627 CAATGATACA
*
338637 TATGTATGTTTG
1 TATGCATGTTTG
338649 TATGCATGTTTG
1 TATGCATGTTTG
338661 TATGCATGT
1 TATGCATGT
338670 ATATATGTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.18, C:0.06, G:0.24, T:0.52
Consensus pattern (12 bp):
TATGCATGTTTG
Found at i:342525 original size:4 final size:4
Alignment explanation
Indices: 342509--342560 Score: 58
Period size: 4 Copynumber: 13.8 Consensus size: 4
342499 TTATTTAAAT
*
342509 TTAA TTAA -T-A TTAA TTAA TTAA TTATA TTTA TT-A TTAA TT-A TTAA
1 TTAA TTAA TTAA TTAA TTAA TTAA TTA-A TTAA TTAA TTAA TTAA TTAA
342554 TTAA TTA
1 TTAA TTA
342561 TATTTAAATA
Statistics
Matches: 42, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
2 1 0.02
3 8 0.19
4 30 0.71
5 3 0.07
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (4 bp):
TTAA
Found at i:342532 original size:23 final size:22
Alignment explanation
Indices: 342506--342564 Score: 68
Period size: 24 Copynumber: 2.7 Consensus size: 22
342496 TTCTTATTTA
342506 AATTTAATTAATATTAATTAATT
1 AATTTAATTAATATTAATT-ATT
* *
342529 AATTATATTTATTATTAATTATT
1 AATT-TAATTAATATTAATTATT
342552 AA-TTAATT-ATATT
1 AATTTAATTAATATT
342565 TAAATAAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
20 4 0.13
21 4 0.13
22 1 0.03
23 9 0.29
24 13 0.42
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
AATTTAATTAATATTAATTATT
Found at i:342567 original size:14 final size:14
Alignment explanation
Indices: 342507--342567 Score: 58
Period size: 14 Copynumber: 4.4 Consensus size: 14
342497 TCTTATTTAA
342507 ATTTAATTAA-TATT
1 ATTTAATTAATTA-T
*
342521 AATTAATTAATTAT
1 ATTTAATTAATTAT
342535 ATTT-ATT-ATTA-
1 ATTTAATTAATTAT
342546 ATTATTAATTAATTAT
1 A-T-TTAATTAATTAT
342562 ATTTAA
1 ATTTAA
342568 ATAAAATTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
11 1 0.03
12 5 0.13
13 5 0.13
14 20 0.51
15 7 0.18
16 1 0.03
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
ATTTAATTAATTAT
Found at i:342575 original size:27 final size:27
Alignment explanation
Indices: 342507--342581 Score: 98
Period size: 27 Copynumber: 2.7 Consensus size: 27
342497 TCTTATTTAA
*
342507 ATTTAATTAATATTAATTAATTAATTAT
1 ATTTAATTAAAATT-ATTAATTAATTAT
*
342535 ATTT-ATTATTAATTATTAATTAATTAT
1 ATTTAATTA-AAATTATTAATTAATTAT
*
342562 ATTTAAATAAAATTATTAAT
1 ATTTAATTAAAATTATTAAT
342582 ATTTATTTAT
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
27 31 0.76
28 10 0.24
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (27 bp):
ATTTAATTAAAATTATTAATTAATTAT
Found at i:344301 original size:31 final size:32
Alignment explanation
Indices: 344263--344330 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 32
344253 TTTTTAAGCT
** * *
344263 AAATTTAATCTTCAACCTTTTAGAAAT-AGTG
1 AAATTTAATCACCAACCTTTTAAAAATGAGTC
*
344294 AAATTTAATCACCAATCTTTTAAAAATGAGTC
1 AAATTTAATCACCAACCTTTTAAAAATGAGTC
344326 AAATT
1 AAATT
344331 GATTTTTTTA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
31 23 0.74
32 8 0.26
ACGTcount: A:0.43, C:0.13, G:0.07, T:0.37
Consensus pattern (32 bp):
AAATTTAATCACCAACCTTTTAAAAATGAGTC
Found at i:348829 original size:23 final size:23
Alignment explanation
Indices: 348803--348867 Score: 62
Period size: 23 Copynumber: 2.9 Consensus size: 23
348793 ATAAGAATAA
348803 ATTTAATAGAGTTAAC-TTTGACT
1 ATTTAATAGAGTTAACATTT-ACT
* * *
348826 ATTTAA-AAAGATATCATTTACT
1 ATTTAATAGAGTTAACATTTACT
* *
348848 ATTTAATCGAGTTAATATTT
1 ATTTAATAGAGTTAACATTT
348868 TTTTTAAAAT
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
22 15 0.47
23 17 0.53
ACGTcount: A:0.38, C:0.08, G:0.09, T:0.45
Consensus pattern (23 bp):
ATTTAATAGAGTTAACATTTACT
Found at i:349648 original size:6 final size:6
Alignment explanation
Indices: 349639--349687 Score: 62
Period size: 6 Copynumber: 7.8 Consensus size: 6
349629 ACATTCACAA
* *
349639 ATATAC ATATAC ATGTAC ATACATAT ATATAC ATATAC ATATAC ATATA
1 ATATAC ATATAC ATATAC AT--ATAC ATATAC ATATAC ATATAC ATATA
349688 GACTTACTTC
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
6 33 0.89
8 4 0.11
ACGTcount: A:0.49, C:0.14, G:0.02, T:0.35
Consensus pattern (6 bp):
ATATAC
Found at i:349657 original size:26 final size:26
Alignment explanation
Indices: 349621--349685 Score: 85
Period size: 26 Copynumber: 2.5 Consensus size: 26
349611 TAGGGTTCAC
* *
349621 ATACACATACATTCACAAATATACAT
1 ATACATATACATACACAAATATACAT
* * *
349647 ATACATGTACATACATATATATACAT
1 ATACATATACATACACAAATATACAT
349673 ATACATATACATA
1 ATACATATACATA
349686 TAGACTTACT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.49, C:0.18, G:0.02, T:0.31
Consensus pattern (26 bp):
ATACATATACATACACAAATATACAT
Found at i:349662 original size:16 final size:16
Alignment explanation
Indices: 349619--349685 Score: 59
Period size: 16 Copynumber: 4.3 Consensus size: 16
349609 AGTAGGGTTC
349619 ACATACACATACAT-T
1 ACATACACATACATAT
*
349634 CACA-A-ATATACATAT
1 -ACATACACATACATAT
**
349649 ACATGTACATACATAT
1 ACATACACATACATAT
* *
349665 ATATACATATACATAT
1 ACATACACATACATAT
349681 ACATA
1 ACATA
349686 TAGACTTACT
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
14 10 0.25
15 2 0.05
16 28 0.70
ACGTcount: A:0.49, C:0.19, G:0.01, T:0.30
Consensus pattern (16 bp):
ACATACACATACATAT
Found at i:349687 original size:20 final size:19
Alignment explanation
Indices: 349621--349681 Score: 59
Period size: 20 Copynumber: 3.1 Consensus size: 19
349611 TAGGGTTCAC
* *
349621 ATACACATACATTCACAAAT
1 ATACATATACATT-ACATAT
*
349641 ATACATATACATGTACATAC
1 ATACATATACAT-TACATAT
*
349661 ATATATATACATATACATAT
1 ATACATATACAT-TACATAT
349681 A
1 A
349682 CATATAGACT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
20 33 0.97
21 1 0.03
ACGTcount: A:0.49, C:0.18, G:0.02, T:0.31
Consensus pattern (19 bp):
ATACATATACATTACATAT
Found at i:349911 original size:2 final size:2
Alignment explanation
Indices: 349906--349934 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
349896 CACTGTATAT
349906 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
349935 TATATGTGTA
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:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:350141 original size:2 final size:2
Alignment explanation
Indices: 350134--350169 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
350124 TTTTAAGGCA
350134 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
350170 TTATCTAATA
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:351683 original size:2 final size:2
Alignment explanation
Indices: 351676--351719 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
351666 CCTTTAAACC
351676 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
351718 AT
1 AT
351720 GCACAACACA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:352720 original size:2 final size:2
Alignment explanation
Indices: 352715--352739 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
352705 AATCAATAAT
352715 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 T
352740 CTAATATTCT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:356346 original size:31 final size:32
Alignment explanation
Indices: 356309--356372 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 32
356299 TTATTATTAT
*
356309 TTTCATTTACA-ATTCAA-TTTTAAATAAAATA
1 TTTCATTTACAGATACAACTTTTAAA-AAAATA
*
356340 TTTCATTTACAGATACAACTTTTTAAAAAATA
1 TTTCATTTACAGATACAACTTTTAAAAAAATA
356372 T
1 T
356373 ATACTCTATC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 11 0.38
32 12 0.41
33 6 0.21
ACGTcount: A:0.44, C:0.11, G:0.02, T:0.44
Consensus pattern (32 bp):
TTTCATTTACAGATACAACTTTTAAAAAAATA
Found at i:359163 original size:21 final size:23
Alignment explanation
Indices: 359139--359181 Score: 63
Period size: 21 Copynumber: 1.9 Consensus size: 23
359129 GGGCATGCAT
359139 TTAATTCA-AATATT-ATGGAAA
1 TTAATTCATAATATTAATGGAAA
359160 TTAATTCATTAATATTAATGGA
1 TTAATTCA-TAATATTAATGGA
359182 TTGTTTGATG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 8 0.42
23 6 0.32
24 5 0.26
ACGTcount: A:0.44, C:0.05, G:0.09, T:0.42
Consensus pattern (23 bp):
TTAATTCATAATATTAATGGAAA
Found at i:360061 original size:2 final size:2
Alignment explanation
Indices: 360054--360086 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
360044 GTAAAGTAAG
360054 AT AT AT AT AT AT AT AT AT AT -T AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
360087 ATACAGACAA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 27 0.93
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Done.