Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold486
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: 154153
ACGTcount: A:0.30, C:0.14, G:0.15, T:0.32
Warning! 14007 characters in sequence are not A, C, G, or T
Found at i:1803 original size:41 final size:41
Alignment explanation
Indices: 1692--2012 Score: 231
Period size: 41 Copynumber: 7.8 Consensus size: 41
1682 TTTTGTTACT
* * * *
1692 ATTAGCGGCGCTTCGGA-AAAAACGCCGCTAAAGG---TAGC
1 ATTAGTGGCGC-TCAGATAAAAACGCCGCTAAAGGCCAGAGA
* * * *
1730 ATTAGCGGCGCTTACATATAAAACGCCGCTAAAGGCCAGAGT
1 ATTAGTGGCGCTCAGATA-AAAACGCCGCTAAAGGCCAGAGA
* * ** * * *
1772 ATTAGTGGCTCTCAGATAAAAACGCCACTAAAAACAAAAAA
1 ATTAGTGGCGCTCAGATAAAAACGCCGCTAAAGGCCAGAGA
* * * **
1813 ACTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGAACAGAGA
1 A--TTAGTGGCGCTCAGATAAAAACGCCGCTAAAGGCCAGAGA
* * * * * ** *
1856 ATTACTGGCGCTCAGACAATAACGCCACT-AATGATACGAGC
1 ATTAGTGGCGCTCAGATAAAAACGCCGCTAAAGGCCA-GAGA
* *
1897 ATTAGCGGCGCTTAGATAAAAACGCCGCTAAAGGCCAGA-A
1 ATTAGTGGCGCTCAGATAAAAACGCCGCTAAAGGCCAGAGA
** *
1937 CATTAGTGGCGCTCAGATAAAAACGCCGCTAAAGATCGGAGA
1 -ATTAGTGGCGCTCAGATAAAAACGCCGCTAAAGGCCAGAGA
* *
1979 ATTAGTGGCGCTAAAATAAAAACGCCGCTAAAGG
1 ATTAGTGGCGCTCAGATAAAAACGCCGCTAAAGG
2013 TTTAAAAATC
Statistics
Matches: 218, Mismatches: 54, Indels: 19
0.75 0.19 0.07
Matches are distributed among these distances:
37 2 0.01
38 12 0.06
39 16 0.07
40 4 0.02
41 132 0.61
42 21 0.10
43 31 0.14
ACGTcount: A:0.38, C:0.22, G:0.23, T:0.17
Consensus pattern (41 bp):
ATTAGTGGCGCTCAGATAAAAACGCCGCTAAAGGCCAGAGA
Found at i:1947 original size:82 final size:81
Alignment explanation
Indices: 1727--2012 Score: 313
Period size: 82 Copynumber: 3.5 Consensus size: 81
1717 CGCTAAAGGT
* * *
1727 AGCATTAGCGGCGCTTACATATAAAACGCCGCTAAAGGCCAGAGTATTAGTGGCTCTCAGATAAA
1 AGCATTAGCGGCGCTTAGATA-AAAACGCCGCTAAAGGCCAGA-AATTAGTGGCGCTCAGATAAA
* * **
1792 AACGCCACTAAAAACAAAAA
64 AACGCCACT--AAAGATACG
* * * ** * * *
1812 AACTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGAACAGAGAATTACTGGCGCTCAGACAATA
1 AGCATTAGCGGCGCTTAGATAAAAACGCCGCTAAAGGCCAGA-AATTAGTGGCGCTCAGATAAAA
*
1877 ACGCCACTAATGATACG
65 ACGCCACTAAAGATACG
1894 AGCATTAGCGGCGCTTAGATAAAAACGCCGCTAAAGGCCAGAACATTAGTGGCGCTCAGATAAAA
1 AGCATTAGCGGCGCTTAGATAAAAACGCCGCTAAAGGCCAGAA-ATTAGTGGCGCTCAGATAAAA
*
1959 ACGCCGCTAAAGAT-CGG
65 ACGCCACTAAAGATAC-G
* * * *
1976 AGAATTAGTGGCGCTAAAATAAAAACGCCGCTAAAGG
1 AGCATTAGCGGCGCTTAGATAAAAACGCCGCTAAAGG
2013 TTTAAAAATC
Statistics
Matches: 169, Mismatches: 30, Indels: 7
0.82 0.15 0.03
Matches are distributed among these distances:
81 2 0.01
82 105 0.62
84 45 0.27
85 17 0.10
ACGTcount: A:0.39, C:0.22, G:0.22, T:0.17
Consensus pattern (81 bp):
AGCATTAGCGGCGCTTAGATAAAAACGCCGCTAAAGGCCAGAAATTAGTGGCGCTCAGATAAAAA
CGCCACTAAAGATACG
Found at i:4423 original size:19 final size:19
Alignment explanation
Indices: 4386--4423 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
4376 GGAGTGGTAA
*
4386 TTAAATGGCATGTTAAATG
1 TTAAATGGCATATTAAATG
*
4405 TTAAATGGCATATTTAATG
1 TTAAATGGCATATTAAATG
4424 ATGATATGGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.37, C:0.05, G:0.18, T:0.39
Consensus pattern (19 bp):
TTAAATGGCATATTAAATG
Found at i:4596 original size:54 final size:54
Alignment explanation
Indices: 4532--4695 Score: 319
Period size: 54 Copynumber: 3.0 Consensus size: 54
4522 TTTGGTAATG
4532 GTTATATGCAATGTTTGGGATGCAATTTGGTGTATCTTTTATGCAGGTTATGTT
1 GTTATATGCAATGTTTGGGATGCAATTTGGTGTATCTTTTATGCAGGTTATGTT
4586 GTTATATGCAATGTTTGGGATGCAATTTGGTGTATCTTTTATGCAGGTTATGTT
1 GTTATATGCAATGTTTGGGATGCAATTTGGTGTATCTTTTATGCAGGTTATGTT
*
4640 GTTATATGCAATGTTTGGGATGCAATTTGGTGTATCTTTTATGCGGGTTATGTT
1 GTTATATGCAATGTTTGGGATGCAATTTGGTGTATCTTTTATGCAGGTTATGTT
4694 GT
1 GT
4696 GCATTTATGT
Statistics
Matches: 109, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
54 109 1.00
ACGTcount: A:0.20, C:0.07, G:0.27, T:0.46
Consensus pattern (54 bp):
GTTATATGCAATGTTTGGGATGCAATTTGGTGTATCTTTTATGCAGGTTATGTT
Found at i:27533 original size:1 final size:1
Alignment explanation
Indices: 27529--27558 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
27519 CTTTGTGTAG
27529 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
27559 GTTTCTAGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:35211 original size:39 final size:39
Alignment explanation
Indices: 35168--35343 Score: 237
Period size: 39 Copynumber: 4.5 Consensus size: 39
35158 AACATGTTTT
*
35168 TGAGTATTGCGACATATGCTTGAATGTTATGTGATTATA
1 TGAGTATTGCGATATATGCTTGAATGTTATGTGATTATA
* *
35207 TGAGTATTACGATATATGCTTGAATGTTATGTGATCATA
1 TGAGTATTGCGATATATGCTTGAATGTTATGTGATTATA
* * * *
35246 TGAATATTGCGATATGTGCTTGAACGTTATGTAATTATA
1 TGAGTATTGCGATATATGCTTGAATGTTATGTGATTATA
*
35285 TGAGTATTGTGATATATGCTT-AAGTGTTATGTGATTATA
1 TGAGTATTGCGATATATGCTTGAA-TGTTATGTGATTATA
* * *
35324 TGTGTAATGTGATATATGCT
1 TGAGTATTGCGATATATGCT
35344 CAAAAGTGGA
Statistics
Matches: 120, Mismatches: 16, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
38 2 0.02
39 118 0.98
ACGTcount: A:0.29, C:0.06, G:0.22, T:0.43
Consensus pattern (39 bp):
TGAGTATTGCGATATATGCTTGAATGTTATGTGATTATA
Found at i:35333 original size:17 final size:16
Alignment explanation
Indices: 35308--35341 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
35298 ATATGCTTAA
*
35308 GTGTTATGTGATTATAT
1 GTGTAATGTGA-TATAT
35325 GTGTAATGTGATATAT
1 GTGTAATGTGATATAT
35341 G
1 G
35342 CTCAAAAGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.47
Consensus pattern (16 bp):
GTGTAATGTGATATAT
Found at i:43777 original size:16 final size:15
Alignment explanation
Indices: 43751--43790 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
43741 ATTATATTTT
43751 TTTTAAAAAAATTAA
1 TTTTAAAAAAATTAA
43766 TTTTAAATAAAATTAA
1 TTTTAAA-AAAATTAA
43782 -TTTAAAAAA
1 TTTTAAAAAA
43791 TAAAAAATGG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
14 3 0.12
15 13 0.54
16 8 0.33
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
TTTTAAAAAAATTAA
Found at i:44634 original size:24 final size:24
Alignment explanation
Indices: 44601--44655 Score: 101
Period size: 24 Copynumber: 2.3 Consensus size: 24
44591 ATTTGTTTTG
*
44601 ATTAATCGATTGCTAACATGATAC
1 ATTAACCGATTGCTAACATGATAC
44625 ATTAACCGATTGCTAACATGATAC
1 ATTAACCGATTGCTAACATGATAC
44649 ATTAACC
1 ATTAACC
44656 AATTAGTCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.38, C:0.20, G:0.11, T:0.31
Consensus pattern (24 bp):
ATTAACCGATTGCTAACATGATAC
Found at i:44693 original size:13 final size:13
Alignment explanation
Indices: 44675--44705 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
44665 AAACTATTTT
44675 TTAACATGATACA
1 TTAACATGATACA
44688 TTAACATGATACA
1 TTAACATGATACA
44701 TTAAC
1 TTAAC
44706 CGATTGAGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.45, C:0.16, G:0.06, T:0.32
Consensus pattern (13 bp):
TTAACATGATACA
Found at i:55108 original size:62 final size:63
Alignment explanation
Indices: 55008--55128 Score: 183
Period size: 62 Copynumber: 1.9 Consensus size: 63
54998 TGACAGGCTA
* ** *
55008 TGTAACTCACTGTTTGTGAATTAGGTTTACACGGGCCAGGGACATGGGCGTGTGTCCAGGTCG
1 TGTAACTCACTGTTTGTGAATTAGGTTCACACAAGCCAGAGACATGGGCGTGTGTCCAGGTCG
55071 TGTAACTCACTGTTTG-GAATTAGAG-TCACACAAGCCAGAGACATGGGCGTGTGTCCAG
1 TGTAACTCACTGTTTGTGAATTAG-GTTCACACAAGCCAGAGACATGGGCGTGTGTCCAG
55129 TCCATGTGGG
Statistics
Matches: 53, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
62 36 0.68
63 17 0.32
ACGTcount: A:0.23, C:0.20, G:0.31, T:0.26
Consensus pattern (63 bp):
TGTAACTCACTGTTTGTGAATTAGGTTCACACAAGCCAGAGACATGGGCGTGTGTCCAGGTCG
Found at i:61286 original size:90 final size:90
Alignment explanation
Indices: 61133--61302 Score: 313
Period size: 90 Copynumber: 1.9 Consensus size: 90
61123 ATGATATATC
*
61133 ATCTCTCCATCCACCAATTTCACTTTTATACTAAGATTAGTTTGTTAATTAACCTTAATTTACTT
1 ATCTCTCCATCCACAAATTTCACTTTTATACTAAGATTAGTTTGTTAATTAACCTTAATTTACTT
61198 ATTTAACTATGTTTTGGTAACTTGG
66 ATTTAACTATGTTTTGGTAACTTGG
* *
61223 ATCTCTCTATCCACAAATTTCACTTTTATACTAAGATTAGTTTGTTAATTAACTTTAATTTACTT
1 ATCTCTCCATCCACAAATTTCACTTTTATACTAAGATTAGTTTGTTAATTAACCTTAATTTACTT
61288 ATTTAACTATGTTTT
66 ATTTAACTATGTTTT
61303 AATCAAATTA
Statistics
Matches: 77, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
90 77 1.00
ACGTcount: A:0.29, C:0.16, G:0.07, T:0.48
Consensus pattern (90 bp):
ATCTCTCCATCCACAAATTTCACTTTTATACTAAGATTAGTTTGTTAATTAACCTTAATTTACTT
ATTTAACTATGTTTTGGTAACTTGG
Found at i:73673 original size:13 final size:13
Alignment explanation
Indices: 73657--73722 Score: 63
Period size: 13 Copynumber: 5.5 Consensus size: 13
73647 ATTTTTAAAT
73657 TATTTAGTGATAA
1 TATTTAGTGATAA
*
73670 TATTTA--GA-AT
1 TATTTAGTGATAA
*
73680 TATTTATTGATAA
1 TATTTAGTGATAA
73693 TATTTAG-GAT--
1 TATTTAGTGATAA
*
73703 TATTTTGTGATAA
1 TATTTAGTGATAA
73716 TATTTAG
1 TATTTAG
73723 GAAAAATCTA
Statistics
Matches: 42, Mismatches: 5, Indels: 12
0.71 0.08 0.20
Matches are distributed among these distances:
10 13 0.31
11 5 0.12
12 5 0.12
13 19 0.45
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.52
Consensus pattern (13 bp):
TATTTAGTGATAA
Found at i:73684 original size:23 final size:23
Alignment explanation
Indices: 73650--73722 Score: 112
Period size: 23 Copynumber: 3.2 Consensus size: 23
73640 AAATTTGATT
73650 TTTA-AATTATTTAGTGATAATA
1 TTTAGAATTATTTAGTGATAATA
*
73672 TTTAGAATTATTTATTGATAATA
1 TTTAGAATTATTTAGTGATAATA
* *
73695 TTTAGGATTATTTTGTGATAATA
1 TTTAGAATTATTTAGTGATAATA
73718 TTTAG
1 TTTAG
73723 GAAAAATCTA
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
22 4 0.09
23 42 0.91
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.52
Consensus pattern (23 bp):
TTTAGAATTATTTAGTGATAATA
Found at i:76987 original size:92 final size:91
Alignment explanation
Indices: 76830--77038 Score: 278
Period size: 92 Copynumber: 2.3 Consensus size: 91
76820 TTGATTTTAG
* * *
76830 TAAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATCACTATTAAATTAT
1 TAAATTCATATAAGAA-AATTTATTATCAAGAATTTTATGAAATTATATATAACTATTAAATTAT
* *
76895 ATTTAAT-ATTAATTATTTTAAATTGTA
65 ATGTAATAATT-ATTATTTTAAATTATA
*
76922 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATT-TAATATTAATTATTAAATTA
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTAT-ATA-TAACTATTAAATTA
76986 TATGTAATAATTATTATTTTAAATTATA
64 TATGTAATAATTATTATTTTAAATTATA
* * * *
77014 CAAATTCATAAAATATAATTTATTA
1 TAAATTCATATAAGAAAATTTATTA
77039 GTTATAATTA
Statistics
Matches: 104, Mismatches: 10, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
90 1 0.01
91 29 0.28
92 71 0.68
93 3 0.03
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (91 bp):
TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATAACTATTAAATTATA
TGTAATAATTATTATTTTAAATTATA
Found at i:77001 original size:24 final size:25
Alignment explanation
Indices: 76966--77013 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
76956 TTATGAAATT
76966 TAATATTAATTA-TTAAATTATATG
1 TAATATTAATTATTTAAATTATATG
76990 TAATAATT-ATTATTTTAAATTATA
1 TAAT-ATTAATTA-TTTAAATTATA
77014 CAAATTCATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 8 0.38
25 3 0.14
26 10 0.48
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (25 bp):
TAATATTAATTATTTAAATTATATG
Found at i:77209 original size:16 final size:16
Alignment explanation
Indices: 77188--77229 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
77178 TTATTAAATT
*
77188 ATATATTTTAATTATA
1 ATATATTTTAATAATA
77204 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
77219 AT-TATGTTTAA
1 ATATAT-TTTAA
77230 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:77214 original size:15 final size:15
Alignment explanation
Indices: 77179--77220 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
77169 TTAAGAATTT
*
77179 TATTAAATTAT-ATA
1 TATTTAATTATAATA
77193 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
77207 TATTTAATAATAAT
1 TATTTAATTATAAT
77221 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:77464 original size:16 final size:16
Alignment explanation
Indices: 77445--77496 Score: 86
Period size: 16 Copynumber: 3.2 Consensus size: 16
77435 GATTTGCTAT
* *
77445 TACACCTCTATTCCAT
1 TACACCTCTAATCCAA
77461 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
77477 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
77493 TACA
1 TACA
77497 GCGAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.35, C:0.37, G:0.00, T:0.29
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:84975 original size:41 final size:40
Alignment explanation
Indices: 84928--85142 Score: 154
Period size: 33 Copynumber: 5.6 Consensus size: 40
84918 ATTGAATATA
84928 AAGGGGTTGCTAAGTGCTGATTCCACCGTATTTAAATGTG
1 AAGGGGTTGCTAAGTGCTGATTCCACCGTATTTAAATGTG
* *
84968 AACGGGGTTGCTAAGTGCTGATTCC-CCG-A-AT-CAT-TG
1 AA-GGGGTTGCTAAGTGCTGATTCCACCGTATTTAAATGTG
* * *
85004 --GTGGTTGCTAAGTGCTGATCCCACCGTATCTTAAAAGTG
1 AAGGGGTTGCTAAGTGCTGATTCCACCGTAT-TTAAATGTG
* * *
85043 AAAGGGGTTGCTAAGTGTTGATTCC-CTG-A-TT-CAT-TG
1 -AAGGGGTTGCTAAGTGCTGATTCCACCGTATTTAAATGTG
* * * *
85079 --GTGGTTGCT-AGTGCTGATTCTACCGTATTTTTGACTGTG
1 AAGGGGTTGCTAAGTGCTGATTCCACCGTA--TTTAAATGTG
*
85118 AAAAGGGTTGCTAAGTGCTGATTCC
1 -AAGGGGTTGCTAAGTGCTGATTCC
85143 CCGAATCACT
Statistics
Matches: 132, Mismatches: 22, Indels: 39
0.68 0.11 0.20
Matches are distributed among these distances:
32 10 0.08
33 30 0.23
34 4 0.03
35 1 0.01
36 4 0.03
37 6 0.05
38 5 0.04
39 5 0.04
40 6 0.05
41 24 0.18
42 26 0.20
43 11 0.08
ACGTcount: A:0.22, C:0.17, G:0.27, T:0.33
Consensus pattern (40 bp):
AAGGGGTTGCTAAGTGCTGATTCCACCGTATTTAAATGTG
Found at i:85015 original size:33 final size:33
Alignment explanation
Indices: 84973--85180 Score: 112
Period size: 33 Copynumber: 5.7 Consensus size: 33
84963 ATGTGAACGG
84973 GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
* * * *
85006 GGTTGCTAAGTGCTGATCCCACCGTATCTTAAAAGTGAAAGG
1 GGTTGCTAAGTGCTGATTCC-CCGAATC-----ATTG---GT
* * *
85048 GGTTGCTAAGTGTTGATTCCCTGATTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
* * **
85081 GGTTGCT-AGTGCTGATTCTACCGTATTTTTGACTGT
1 GGTTGCTAAGTGCTGATTC-CCCGAATCATTG---GT
*
85117 GAAAAGGGTTGCTAAGTGCTGATTCCCCGAATCACTGGT
1 ------GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
*
85156 GGTTGCTAAGTGCTGAATCCACCGA
1 GGTTGCTAAGTGCTGATTCC-CCGA
85181 TAACGGATAA
Statistics
Matches: 130, Mismatches: 24, Indels: 41
0.67 0.12 0.21
Matches are distributed among these distances:
32 10 0.08
33 52 0.40
34 10 0.08
36 5 0.04
39 5 0.04
41 4 0.03
42 33 0.25
43 11 0.08
ACGTcount: A:0.21, C:0.19, G:0.27, T:0.33
Consensus pattern (33 bp):
GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
Found at i:85065 original size:75 final size:74
Alignment explanation
Indices: 84932--85179 Score: 354
Period size: 75 Copynumber: 3.3 Consensus size: 74
84922 AATATAAAGG
*
84932 GGTTGCTAAGTGCTGATTCCACCGTATTTAAATGTGAACGGGGTTGCTAAGTGCTGATTCCCCGA
1 GGTTGCTAAGTGCTGATTCCACCGTATTTAAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCGA
84997 ATCATTGGT
66 ATCATTGGT
* * * *
85006 GGTTGCTAAGTGCTGATCCCACCGTATCTTAAAAGTGAAAGGGGTTGCTAAGTGTTGATTCCCTG
1 GGTTGCTAAGTGCTGATTCCACCGTAT-TTAAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCG
*
85071 ATTCATTGGT
65 AATCATTGGT
* * * *
85081 GGTTGCT-AGTGCTGATTCTACCGTATTTTTGACTGTGAAAAGGGTTGCTAAGTGCTGATTCCCC
1 GGTTGCTAAGTGCTGATTCCACCGTA--TTTAAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCC
*
85145 GAATCACTGGT
64 GAATCATTGGT
*
85156 GGTTGCTAAGTGCTGAATCCACCG
1 GGTTGCTAAGTGCTGATTCCACCG
85180 ATAACGGATA
Statistics
Matches: 152, Mismatches: 18, Indels: 6
0.86 0.10 0.03
Matches are distributed among these distances:
74 42 0.28
75 95 0.62
76 15 0.10
ACGTcount: A:0.21, C:0.19, G:0.27, T:0.33
Consensus pattern (74 bp):
GGTTGCTAAGTGCTGATTCCACCGTATTTAAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCGA
ATCATTGGT
Found at i:87596 original size:19 final size:19
Alignment explanation
Indices: 87528--87602 Score: 68
Period size: 19 Copynumber: 4.0 Consensus size: 19
87518 AATCAATACA
87528 CAATTCACATATTCACATAT
1 CAATTCACA-ATTCACATAT
* *
87548 C--TTCA-AATCTCATATCT
1 CAATTCACAAT-TCACATAT
*
87565 CGATTTC-CAATTCACATAT
1 C-AATTCACAATTCACATAT
87584 CAATTCACAATTCACATAT
1 CAATTCACAATTCACATAT
87603 TCACACATAA
Statistics
Matches: 44, Mismatches: 5, Indels: 13
0.71 0.08 0.21
Matches are distributed among these distances:
16 2 0.05
17 8 0.18
18 8 0.18
19 19 0.43
20 7 0.16
ACGTcount: A:0.36, C:0.27, G:0.01, T:0.36
Consensus pattern (19 bp):
CAATTCACAATTCACATAT
Found at i:88420 original size:13 final size:13
Alignment explanation
Indices: 88402--88441 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
88392 TCAATTTCCC
88402 CTTTTCTTTCTTT
1 CTTTTCTTTCTTT
*
88415 CTTTTCTTCCTTT
1 CTTTTCTTTCTTT
*
88428 C-TTTCTTTCCTT
1 CTTTTCTTTCTTT
88440 CT
1 CT
88442 CTGTTTCGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
12 10 0.43
13 13 0.57
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (13 bp):
CTTTTCTTTCTTT
Found at i:88427 original size:17 final size:17
Alignment explanation
Indices: 88407--88440 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
88397 TTCCCCTTTT
*
88407 CTTTCTTTCTTTTCTTC
1 CTTTCTTTCTTTCCTTC
88424 CTTTCTTTCTTTCCTTC
1 CTTTCTTTCTTTCCTTC
88441 TCTGTTTCGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (17 bp):
CTTTCTTTCTTTCCTTC
Found at i:88512 original size:5 final size:5
Alignment explanation
Indices: 88496--88546 Score: 70
Period size: 5 Copynumber: 10.2 Consensus size: 5
88486 CTCTTTTGTT
88496 ATATA TATATA ATATA ATATA ATATA ATAT- AT-TA ATAATA ATATA ATATA
1 ATATA -ATATA ATATA ATATA ATATA ATATA ATATA AT-ATA ATATA ATATA
88546 A
1 A
88547 AAACATAATC
Statistics
Matches: 42, Mismatches: 0, Indels: 7
0.86 0.00 0.14
Matches are distributed among these distances:
3 1 0.02
4 4 0.10
5 28 0.67
6 9 0.21
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
ATATA
Found at i:88526 original size:24 final size:24
Alignment explanation
Indices: 88498--88546 Score: 82
Period size: 24 Copynumber: 2.0 Consensus size: 24
88488 CTTTTGTTAT
88498 ATATATATAAT-ATAATATAATATA
1 ATATAT-TAATAATAATATAATATA
88522 ATATATTAATAATAATATAATATA
1 ATATATTAATAATAATATAATATA
88546 A
1 A
88547 AAACATAATC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 4 0.17
24 20 0.83
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (24 bp):
ATATATTAATAATAATATAATATA
Found at i:88536 original size:19 final size:19
Alignment explanation
Indices: 88496--88545 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 19
88486 CTCTTTTGTT
88496 ATATATATATAATATAATATA
1 ATATA-ATAT-ATATAATATA
88517 ATATAATATAT-TAATAATA
1 ATATAATATATATAAT-ATA
88536 ATATAATATA
1 ATATAATATA
88546 AAAACATAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
18 4 0.14
19 15 0.54
20 4 0.14
21 5 0.18
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
ATATAATATATATAATATA
Found at i:88776 original size:107 final size:108
Alignment explanation
Indices: 88641--88854 Score: 351
Period size: 108 Copynumber: 2.0 Consensus size: 108
88631 CAGCTTTAGA
*
88641 AAAAGGCATAATTGCCTATTTGGTCCTTTTAACTTTT-TTT-ATCTACAATTAAACTTTTATCTC
1 AAAAGGCATAATTACCTATTTGGTCCTTTTAACTTTTCTTTAATCTACAATTAAA-TTTTATCTC
* *
88704 TATTGCAATTTAATTCTTTTTCATAATTAACCACGATTTAGACG
65 TATTGCAATTTAATCCTTTTTCATAATTAACCACAATTTAGACG
* * *
88748 AAAATGCATAATTACTTATTTGGTCCTTTTAACTTTTCTTTAATCTATAATTAAATTTTATCTCT
1 AAAAGGCATAATTACCTATTTGGTCCTTTTAACTTTTCTTTAATCTACAATTAAATTTTATCTCT
88813 ATTGCAATTTAATCCTTTTTCATAATTAACCACAATTTAGAC
66 ATTGCAATTTAATCCTTTTTCATAATTAACCACAATTTAGAC
88855 AAATTCCCTT
Statistics
Matches: 99, Mismatches: 6, Indels: 3
0.92 0.06 0.03
Matches are distributed among these distances:
107 34 0.34
108 53 0.54
109 12 0.12
ACGTcount: A:0.31, C:0.16, G:0.07, T:0.46
Consensus pattern (108 bp):
AAAAGGCATAATTACCTATTTGGTCCTTTTAACTTTTCTTTAATCTACAATTAAATTTTATCTCT
ATTGCAATTTAATCCTTTTTCATAATTAACCACAATTTAGACG
Found at i:97555 original size:105 final size:105
Alignment explanation
Indices: 97362--97591 Score: 251
Period size: 105 Copynumber: 2.2 Consensus size: 105
97352 AATGTTTAAA
* * **
97362 TGTAAGACCATAGCTGGGGTATGGCATTTTAATGAAATGACCATAACTGGGTTATGACAACTTGA
1 TGTAAGACCATAGCTGGGCTATGGCATTCTAATGAAATGACCATAACTGGGTTATGACAACTCAA
**
97427 ACGTAAAACCATGGTTGGACTATGGCAGTATAGATACATG
66 ACGTAAAACCATGGCAGGACTATGGCAGTATAGATACATG
* * *
97467 TGTAAGATCATAGCTGGGCTATGGCATTCTGATGATAA-GACCATAATTGGGTTATGAC-ACTAC
1 TGTAAGACCATAGCTGGGCTATGGCATTCTAATGA-AATGACCATAACTGGGTTATGACAACT-C
* * * *
97530 AAATGTAAGACCATGGCAGGGCTATGACA--AT-G---CATG
64 AAACGTAAAACCATGGCAGGACTATGGCAGTATAGATACATG
* *
97566 TGTAAGACCATAGTTGGACTATGGCA
1 TGTAAGACCATAGCTGGGCTATGGCA
97592 CAAAAAGAAC
Statistics
Matches: 107, Mismatches: 16, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
99 27 0.25
102 1 0.01
103 2 0.02
104 3 0.03
105 72 0.67
106 2 0.02
ACGTcount: A:0.33, C:0.15, G:0.25, T:0.27
Consensus pattern (105 bp):
TGTAAGACCATAGCTGGGCTATGGCATTCTAATGAAATGACCATAACTGGGTTATGACAACTCAA
ACGTAAAACCATGGCAGGACTATGGCAGTATAGATACATG
Found at i:97588 original size:33 final size:33
Alignment explanation
Indices: 97460--97588 Score: 100
Period size: 33 Copynumber: 3.9 Consensus size: 33
97450 GGCAGTATAG
* *
97460 ATACATGTGTAAGATCATAGCTGGGCTATGGC-
1 ATACATGTGTAAGACCATAGCTGGGCTATGACA
* ** *
97492 ATTC-TGATGATAAGACCATAATTGGGTTATGACA
1 ATACATG-TG-TAAGACCATAGCTGGGCTATGACA
* ** * *
97526 CTACAAATGTAAGACCATGGCAGGGCTATGACA
1 ATACATGTGTAAGACCATAGCTGGGCTATGACA
* * *
97559 ATGCATGTGTAAGACCATAGTTGGACTATG
1 ATACATGTGTAAGACCATAGCTGGGCTATG
97589 GCACAAAAAG
Statistics
Matches: 70, Mismatches: 23, Indels: 7
0.70 0.23 0.07
Matches are distributed among these distances:
31 2 0.03
32 5 0.07
33 59 0.84
34 4 0.06
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.27
Consensus pattern (33 bp):
ATACATGTGTAAGACCATAGCTGGGCTATGACA
Found at i:102574 original size:24 final size:24
Alignment explanation
Indices: 102547--102592 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
102537 GTTGAGTGTG
102547 GAATG-ATGTAAATTAGCATTTCTT
1 GAATGTAT-TAAATTAGCATTTCTT
* *
102571 GAATGTATTATATTATCATTTC
1 GAATGTATTAAATTAGCATTTC
102593 CCTACTCTCT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 17 0.89
25 2 0.11
ACGTcount: A:0.33, C:0.09, G:0.13, T:0.46
Consensus pattern (24 bp):
GAATGTATTAAATTAGCATTTCTT
Found at i:103436 original size:19 final size:19
Alignment explanation
Indices: 103408--103451 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
103398 AATTTTCGAG
103408 GATATACAATCTTAGATAT
1 GATATACAATCTTAGATAT
*
103427 GATATGCAATCTTAGATAT
1 GATATACAATCTTAGATAT
103446 GATATA
1 GATATA
103452 TACAATATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.41, C:0.09, G:0.14, T:0.36
Consensus pattern (19 bp):
GATATACAATCTTAGATAT
Found at i:103469 original size:19 final size:19
Alignment explanation
Indices: 103409--103469 Score: 70
Period size: 19 Copynumber: 3.1 Consensus size: 19
103399 ATTTTCGAGG
103409 ATATACAATCTTAG-ATAT
1 ATATACAATCTTAGAATAT
*
103427 GATATGCAATCTTAGATATGAT
1 -ATATACAATCTTAGA-AT-AT
*
103449 ATATACAATATTAGAATAT
1 ATATACAATCTTAGAATAT
103468 AT
1 AT
103470 GATTTTGTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
19 17 0.47
20 2 0.06
21 15 0.42
22 2 0.06
ACGTcount: A:0.44, C:0.08, G:0.10, T:0.38
Consensus pattern (19 bp):
ATATACAATCTTAGAATAT
Found at i:104271 original size:13 final size:13
Alignment explanation
Indices: 104255--104282 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
104245 ATTTTGTACC
104255 TTTTTTTCTTTAT
1 TTTTTTTCTTTAT
104268 TTTTTTTCTTTAT
1 TTTTTTTCTTTAT
104281 TT
1 TT
104283 CCTTCATTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.07, C:0.07, G:0.00, T:0.86
Consensus pattern (13 bp):
TTTTTTTCTTTAT
Found at i:107811 original size:36 final size:36
Alignment explanation
Indices: 107764--107837 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
107754 TTCTCCTAGG
107764 TCCATTGCGGTATTGCCTATTAAAGACAAGATTCTT
1 TCCATTGCGGTATTGCCTATTAAAGACAAGATTCTT
107800 TCCATTGCGGTATTGCCTATTAAAGACAAGATTCTT
1 TCCATTGCGGTATTGCCTATTAAAGACAAGATTCTT
107836 TC
1 TC
107838 TCTCTGAGTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.27, C:0.20, G:0.16, T:0.36
Consensus pattern (36 bp):
TCCATTGCGGTATTGCCTATTAAAGACAAGATTCTT
Found at i:108170 original size:15 final size:15
Alignment explanation
Indices: 108130--108185 Score: 60
Period size: 15 Copynumber: 3.5 Consensus size: 15
108120 TTTTAAAAAA
108130 AAAAAGAGAAAGAAAG
1 AAAAAG-GAAAGAAAG
108146 AAAATA-GAAAGAAAG
1 AAAA-AGGAAAGAAAG
108161 AAAAAGGAAAAGAAAAG
1 AAAAAGG-AAAG-AAAG
*
108178 CAAAAGGA
1 AAAAAGGA
108186 GAGGCCAAGG
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
14 1 0.03
15 14 0.40
16 9 0.26
17 11 0.31
ACGTcount: A:0.73, C:0.02, G:0.23, T:0.02
Consensus pattern (15 bp):
AAAAAGGAAAGAAAG
Found at i:109654 original size:44 final size:44
Alignment explanation
Indices: 109449--109657 Score: 135
Period size: 44 Copynumber: 4.8 Consensus size: 44
109439 AAGATTGTAT
*
109449 ATCTTATCTCTCTAAGCAGTAGTA-GAGCAGATTGAAGACGGCAA
1 ATCTTATCTCTCCAAG-AGTAGTAGGAGCAGATTGAAGACGGCAA
* * * ** *
109493 ATCTTATCTTTCCAAGA-TAGTGGGAAGCAGATTTAAG-CCACCA
1 ATCTTATCTCTCCAAGAGTAGTAGG-AGCAGATTGAAGACGGCAA
* * * * * * ** * *
109536 AGCATTGTCTC-CC-TGAGTAGCAGCGGAGTAGGTTGAAGATTGTAT
1 ATC-TTATCTCTCCAAGAGTAGTA--GGAGCAGATTGAAGACGGCAA
*
109581 ATCTTATCTCTCTAAGCAGTAGTA-GAGCAGATTGAAGACGGCAA
1 ATCTTATCTCTCCAAG-AGTAGTAGGAGCAGATTGAAGACGGCAA
*
109625 ATCTTATCTTTCCAAGA-TAGTAGGAAGCAGATT
1 ATCTTATCTCTCCAAGAGTAGTAGG-AGCAGATT
109658 TAAGCCACAA
Statistics
Matches: 118, Mismatches: 35, Indels: 24
0.67 0.20 0.14
Matches are distributed among these distances:
42 11 0.09
43 14 0.12
44 81 0.69
45 5 0.04
46 1 0.01
47 6 0.05
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.28
Consensus pattern (44 bp):
ATCTTATCTCTCCAAGAGTAGTAGGAGCAGATTGAAGACGGCAA
Found at i:109916 original size:257 final size:257
Alignment explanation
Indices: 109443--110373 Score: 1477
Period size: 257 Copynumber: 3.6 Consensus size: 257
109433 AGGTTGAAGA
* * * * *
109443 TTGTATATCTTATCTCTCTAAGCAGTAGTAGAGCAGATTGAAGACGGCAAATCTTATCTTTCCAA
1 TTGTAGATCCTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAA
* *
109508 GATAGTGGGAAGCAGATTTAAGCCACCAAGCATTGTCTCCCTGAGTAGCAGCGGAGTAGGTTGAA
66 GATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAA
* * **
109573 GATTGTATATCTTATCTCTCTAAGCAGTAGT-AGAGCAGATTGAAGACGGCAAATCTTATCTTTC
131 GATTGTAGATCTTATCTCCCTAAGCAGTAGTGA-AGCAGATCAAAGACGGCAAATCTTATCTTTC
* * *
109637 CAAGATAGTAGGAAGCAGATTTAAGCCACAAAGCCTTGTCTCCCTAAGCAGCAGTGGAGTAGG
195 CAAGATAGTGGGAAGCAGATTTAAGCCACAAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGG
* * *
109700 TTGTAGATCCTATCTCCCTAAGCAGTAGTGGAGTAGATTGAAGACGGCAAATCTTATCTTCCCAA
1 TTGTAGATCCTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAA
109765 GATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAA
66 GATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAA
* *
109830 GATTGTAGATCTTATCTCCCTAAGCAGTAATGAAGCAGATCAAAGACGGTAAATCTTATCTTTCC
131 GATTGTAGATCTTATCTCCCTAAGCAGTAGTGAAGCAGATCAAAGACGGCAAATCTTATCTTTCC
*
109895 AAGATAGTGGGAAGTAGATTTAAGCCACAAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGG
196 AAGATAGTGGGAAGCAGATTTAAGCCACAAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGG
* *
109957 TTGTAGATCCTATCTCCCTAAGCAGTAGAGGAGCAGATCGAAGACGGTAAATCTTATCTTTCCAA
1 TTGTAGATCCTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAA
*
110022 GATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGTAGCGGAGTAGGTTGAA
66 GATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAA
* *
110087 GATTGTAGATCTTATCTCCCTAAGAAGTAGTGGAGCAGATCAAAGACGGCAAATCTTATCTTTCC
131 GATTGTAGATCTTATCTCCCTAAGCAGTAGTGAAGCAGATCAAAGACGGCAAATCTTATCTTTCC
*
110152 AAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAATGTTG
196 AAGATAGTGGGAAGCAGATTTAAGCCACAAAGCCTTGTCTCCCTGAGCAGCAGC-G-G-A-G-T-
*
110217 AAGA
255 -AGG
* *
110221 TTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGGCAAATCTTATCTTTCCAA
1 TTGTAGATCCTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAA
* *
110286 GATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTATCTCCCTAAGCAGCAGCGGAGTAGGTTGAA
66 GATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAA
* * *
110351 GATGGAAAATCTTATCTCCCTAA
131 GATTGTAGATCTTATCTCCCTAA
110374 AGTTGCAGTG
Statistics
Matches: 625, Mismatches: 41, Indels: 9
0.93 0.06 0.01
Matches are distributed among these distances:
257 474 0.76
258 2 0.00
259 1 0.00
260 1 0.00
261 1 0.00
262 1 0.00
264 145 0.23
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.25
Consensus pattern (257 bp):
TTGTAGATCCTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAA
GATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAA
GATTGTAGATCTTATCTCCCTAAGCAGTAGTGAAGCAGATCAAAGACGGCAAATCTTATCTTTCC
AAGATAGTGGGAAGCAGATTTAAGCCACAAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGG
Found at i:110118 original size:389 final size:382
Alignment explanation
Indices: 109399--110353 Score: 1455
Period size: 389 Copynumber: 2.5 Consensus size: 382
109389 ACCGGTGAAA
* * *
109399 CACCAAGCCTTGTCTCCCTAAGCAGCAGCGGAGAAGGTTGAAGATTGTATATCTTATCTCTCTAA
1 CACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAA
**
109464 GCAGTAGT-AGAGCAGATTGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTA
66 GCAGTAGTGA-AGCAGATCAAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTA
* * * * *
109528 AGCCACCAAGCATTGTCTCCCTGAGTAGCAGCGGAGTAGGTTGAAGATTGTATATCTTATCTCTC
130 AGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTA----G--G-TTGTAGATCCTATCTCCC
*
109593 TAAGCAGTAGTAGAGCAGATTGAAGACGGCAAATCTTATCTTTCCAAGATAGTAGGAAGCAGATT
188 TAAGCAGTAGTAGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTAGGAAGCAGATT
* *
109658 TAAGCCACAAAGCCTTGTCTCCCTAAGCAGCAGTGGAGTAGGTTGTAGATCCTATCTCCCTAAGC
253 TAAGCCACAAAGCCTTGTCTCCCTAAGCAGCAGCGGAGTAGGTTGTAGATCCTATCTCCCTAAGA
* **
109723 AGTAGTGGAGTAGATTGAAGACGGCAAATCTTATCTTCCCAAGATAGTGGGAAGCAGATTTAAGC
318 AGTAGTGGAGCAGATCAAAGACGGCAAATCTTATCTTCCCAAGATAGTGGGAAGCAGATTTAAGC
*
109788 CACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAA
1 CACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAA
* * *
109853 GCAGTAATGAAGCAGATCAAAGACGGTAAATCTTATCTTTCCAAGATAGTGGGAAGTAGATTTAA
66 GCAGTAGTGAAGCAGATCAAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
*
109918 GCCACAAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGTAGATCCTATCTCCCTAAGCAGT
131 GCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGTAGATCCTATCTCCCTAAGCAGT
* *
109983 AG-AGGAGCAGATCGAAGACGGTAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCA
196 AGTA-GAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTAGGAAGCAGATTTAAGCCA
* * * *
110047 CCAAGCCTTGTCTCCCTGAGCAGTAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGA
260 CAAAGCCTTGTCTCCCTAAGCAGCAGCGGAGTA----G--G-TTGTAGATCCTATCTCCCTAAGA
*
110112 AGTAGTGGAGCAGATCAAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGC
318 AGTAGTGGAGCAGATCAAAGACGGCAAATCTTATCTTCCCAAGATAGTGGGAAGCAGATTTAAGC
*
110177 CACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAATGTTGAAGATTGTAGATCTTATCTCCCTAA
1 CACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAA
*
110242 GCAGTAGTGGAGCAGATCAAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
66 GCAGTAGTGAAGCAGATCAAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
* * *
110307 GCCACCAAGCCTTATCTCCCTAAGCAGCAGCGGAGTAGGTTGAAGAT
131 GCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGTAGAT
110354 GGAAAATCTT
Statistics
Matches: 519, Mismatches: 38, Indels: 18
0.90 0.07 0.03
Matches are distributed among these distances:
381 1 0.00
382 111 0.21
383 1 0.00
385 1 0.00
386 1 0.00
388 1 0.00
389 402 0.77
390 1 0.00
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.25
Consensus pattern (382 bp):
CACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAA
GCAGTAGTGAAGCAGATCAAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
GCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGTAGATCCTATCTCCCTAAGCAGT
AGTAGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTAGGAAGCAGATTTAAGCCAC
AAAGCCTTGTCTCCCTAAGCAGCAGCGGAGTAGGTTGTAGATCCTATCTCCCTAAGAAGTAGTGG
AGCAGATCAAAGACGGCAAATCTTATCTTCCCAAGATAGTGGGAAGCAGATTTAAGC
Found at i:110143 original size:44 final size:44
Alignment explanation
Indices: 109967--110279 Score: 136
Period size: 44 Copynumber: 7.1 Consensus size: 44
109957 TTGTAGATCC
* * *
109967 TATCTCCCTAAGCAGTAGAGGAGCAGATCGAAGACGGTAAATCT
1 TATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGGCAAATCT
* ** * ** **
110011 TATCTTTCC-AAG-A-TAGTGGGAAGCAGATTTAAGCCACCAAGCCT
1 TATC-TCCCTAAGCAGTAGT-GG-AGCAGATCAAAGACGGCAAATCT
* * * * * ** ** * *
110055 TGTCTCCCTGAGCAGTAGCGGAGTAGGTTGAAGATTGTAGATCT
1 TATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGGCAAATCT
*
110099 TATCTCCCTAAGAAGTAGTGGAGCAGATCAAAGACGGCAAATCT
1 TATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGGCAAATCT
* ** * ** **
110143 TATCTTTCC-AAG-A-TAGTGGGAAGCAGATTTAAGCCACCAAGCCT
1 TATC-TCCCTAAGCAGTAGT-GG-AGCAGATCAAAGACGGCAAATCT
* * * * * ** ** * *
110187 TGTCTCCCTGAGCAGCAGCGGAGAATG-TTGAAGATTGTAGATCT
1 TATCTCCCTAAGCAGTAGTGGAGCA-GATCAAAGACGGCAAATCT
110231 TATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGGCAAATCT
1 TATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGGCAAATCT
110275 TATCT
1 TATCT
110280 TTCCAAGATA
Statistics
Matches: 184, Mismatches: 71, Indels: 28
0.65 0.25 0.10
Matches are distributed among these distances:
42 7 0.04
43 13 0.07
44 146 0.79
45 13 0.07
46 5 0.03
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.25
Consensus pattern (44 bp):
TATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGGCAAATCT
Found at i:110411 original size:44 final size:43
Alignment explanation
Indices: 110358--110648 Score: 168
Period size: 44 Copynumber: 6.7 Consensus size: 43
110348 GAAGATGGAA
110358 AATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCCGAT
1 AATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCC-AT
* * * * * *
110402 AATCCTATCTCCTTGAAGTTGCAGTGGAGCGGATTAAAACCTT
1 AATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCCAT
* ** * ** *** *
110445 GGATCTTATCTCTTTGAAGTTGCAG-AAAGCAGATCGCA-TC-T
1 -AATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCCAT
* * *
110486 AGTCTTATCTCCCTAAAGTTGTAGTGGAGCAGACTCAGCAAG-CA-
1 AATCTTATCTCCCTAAAGTTGCAGTGGAGCAGA-TTA--AAGCCAT
* * * * *
110530 AGTCTTATC-CTCCTGAAGTTGCAGT-GAGGTAGACTGAAGATGGCA-
1 AATCTTATCTC-CCTAAAGTTGCAGTGGA-GCAGA-TTAA-A-GCCAT
* *
110575 AATCTTATCTTCCC-AAAGTTGCAGTGGAGAAGATTAGAGCCGAT
1 AATCTTATC-TCCCTAAAGTTGCAGTGGAGCAGATTAAAGCC-AT
*
110619 AATCCTATCTCCCTAAAGTTGCAGTGGAGC
1 AATCTTATCTCCCTAAAGTTGCAGTGGAGC
110649 GGATCAAAAC
Statistics
Matches: 191, Mismatches: 38, Indels: 36
0.72 0.14 0.14
Matches are distributed among these distances:
40 18 0.09
41 7 0.04
42 6 0.03
43 18 0.09
44 113 0.59
45 24 0.13
46 4 0.02
47 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.28
Consensus pattern (43 bp):
AATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCCAT
Found at i:110411 original size:132 final size:132
Alignment explanation
Indices: 109399--110396 Score: 1484
Period size: 132 Copynumber: 7.7 Consensus size: 132
109389 ACCGGTGAAA
* * * *
109399 CACCAAGCCTTGTCTCCCTAAGCAGCAGCGGAGAAGGTTGAAGATTGTATATCTTATCTCTCTAA
1 CACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAA
* **
109464 GCAGTAGTAGAGCAGATTGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
66 GCAGTAGTGGAGCAGATCAAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
109529 GC
131 GC
* * * *
109531 CACCAAGCATTGTCTCCCTGAGTAGCAGCGGAGTAGGTTGAAGATTGTATATCTTATCTCTCTAA
1 CACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAA
* ** *
109596 GCAGTAGTAGAGCAGATTGAAGACGGCAAATCTTATCTTTCCAAGATAGTAGGAAGCAGATTTAA
66 GCAGTAGTGGAGCAGATCAAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
109661 GC
131 GC
* * * *
109663 CACAAAGCCTTGTCTCCCTAAGCAGCAGTGGAGTA----G--G-TTGTAGATCCTATCTCCCTAA
1 CACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAA
* ** *
109721 GCAGTAGTGGAGTAGATTGAAGACGGCAAATCTTATCTTCCCAAGATAGTGGGAAGCAGATTTAA
66 GCAGTAGTGGAGCAGATCAAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
109786 GC
131 GC
109788 CACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAA
1 CACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAA
* * * *
109853 GCAGTAATGAAGCAGATCAAAGACGGTAAATCTTATCTTTCCAAGATAGTGGGAAGTAGATTTAA
66 GCAGTAGTGGAGCAGATCAAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
109918 GC
131 GC
* *
109920 CACAAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTA----G--G-TTGTAGATCCTATCTCCCTAA
1 CACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAA
* * *
109978 GCAGTAGAGGAGCAGATCGAAGACGGTAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
66 GCAGTAGTGGAGCAGATCAAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
110043 GC
131 GC
*
110045 CACCAAGCCTTGTCTCCCTGAGCAGTAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAA
1 CACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAA
*
110110 GAAGTAGTGGAGCAGATCAAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
66 GCAGTAGTGGAGCAGATCAAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
110175 GC
131 GC
* *
110177 CACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAATGTTGAAGATTGTAGATCTTATCTCCCTAA
1 CACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAA
110242 GCAGTAGTGGAGCAGATCAAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
66 GCAGTAGTGGAGCAGATCAAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
110307 GC
131 GC
* * * * *
110309 CACCAAGCCTTATCTCCCTAAGCAGCAGCGGAGTAGGTTGAAGATGGAAAATCTTATCTCCCTAA
1 CACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCT-A
** * *
110374 AGTTGCAGTGGAGCAGATTAAAG
65 AGCAGTAGTGGAGCAGATCAAAG
110397 CCGATAATCC
Statistics
Matches: 793, Mismatches: 58, Indels: 29
0.90 0.07 0.03
Matches are distributed among these distances:
125 228 0.29
126 2 0.00
128 2 0.00
129 2 0.00
131 2 0.00
132 537 0.68
133 20 0.03
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.25
Consensus pattern (132 bp):
CACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAA
GCAGTAGTGGAGCAGATCAAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
GC
Found at i:110618 original size:217 final size:217
Alignment explanation
Indices: 110347--110781 Score: 721
Period size: 217 Copynumber: 2.0 Consensus size: 217
110337 CGGAGTAGGT
*
110347 TGAAGATGGAAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCCGATAATCCTATCT
1 TGAAGATGGAAAATCTTATCTCCCTAAAGTTGCAGTGGAGAAGATTAAAGCCGATAATCCTATCT
* * *
110412 CCTTGAAGTTGCAGTGGAGCGGATTAAAACCTTGGATCTTATCTCTTTGAAGTTGCAGAA-AGCA
66 CCCTAAAGTTGCAGTGGAGCGGATCAAAACCTTGGATCTTATCTCTTTGAAGTTGCA-AAGAGCA
* *
110476 GATCGCATCTAGTCTTATCTCCCTAAAGTTGTAGTGGAGCAGACTCAGCAAGCAAGTCTTATCCT
130 GATCGCATCTAGTCTTATCTCCCTAAAGTTGTAGTGGAGCAGACTAAGCAAACAAGTCTTATCCT
* *
110541 CCTGAAGTTGCAGTGAGGTAGAC
195 ACTGAAGTTGCAGTGAGGCAGAC
* *
110564 TGAAGATGGCAAATCTTATCTTCCC-AAAGTTGCAGTGGAGAAGATTAGAGCCGATAATCCTATC
1 TGAAGATGGAAAATCTTATC-TCCCTAAAGTTGCAGTGGAGAAGATTAAAGCCGATAATCCTATC
110628 TCCCTAAAGTTGCAGTGGAGCGGATCAAAACCTTGGATCTTATCTCTTTGAAGTTGCAAAGAGCA
65 TCCCTAAAGTTGCAGTGGAGCGGATCAAAACCTTGGATCTTATCTCTTTGAAGTTGCAAAGAGCA
* * *
110693 GATCGCGTCTAGTCTTATCTCCCTGAAGTTGTAGTGGAGCAGACTAAGTAAACAAGTCTTATCCT
130 GATCGCATCTAGTCTTATCTCCCTAAAGTTGTAGTGGAGCAGACTAAGCAAACAAGTCTTATCCT
110758 ACTGAAGTTGCAGTGAGGCAGAC
195 ACTGAAGTTGCAGTGAGGCAGAC
110781 T
1 T
110782 AAATAAACAA
Statistics
Matches: 203, Mismatches: 13, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
216 2 0.01
217 197 0.97
218 4 0.02
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.28
Consensus pattern (217 bp):
TGAAGATGGAAAATCTTATCTCCCTAAAGTTGCAGTGGAGAAGATTAAAGCCGATAATCCTATCT
CCCTAAAGTTGCAGTGGAGCGGATCAAAACCTTGGATCTTATCTCTTTGAAGTTGCAAAGAGCAG
ATCGCATCTAGTCTTATCTCCCTAAAGTTGTAGTGGAGCAGACTAAGCAAACAAGTCTTATCCTA
CTGAAGTTGCAGTGAGGCAGAC
Found at i:110754 original size:44 final size:44
Alignment explanation
Indices: 110703--110818 Score: 139
Period size: 44 Copynumber: 2.7 Consensus size: 44
110693 GATCGCGTCT
*
110703 AGTCTTATCTCCCTGAAGTTGTAGTGGAGCAGACTAAGTAAACA
1 AGTCTTATCTCCCTGAAGTTGTAGTGGAGCAGACTAAATAAACA
* *
110747 AGTCTTATC-CTACTGAAGTTGCAGT-GAGGCAGACTAAATAAACA
1 AGTCTTATCTC-CCTGAAGTTGTAGTGGA-GCAGACTAAATAAACA
* * *
110791 AATCCTGTCTCCCT-AAGTTGTAGTGGAG
1 AGTCTTATCTCCCTGAAGTTGTAGTGGAG
110819 TGGATTAGAG
Statistics
Matches: 60, Mismatches: 8, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
43 13 0.22
44 46 0.77
45 1 0.02
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (44 bp):
AGTCTTATCTCCCTGAAGTTGTAGTGGAGCAGACTAAATAAACA
Found at i:118853 original size:24 final size:24
Alignment explanation
Indices: 118821--118868 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
118811 TATCACTAGG
118821 GTAGCTTGGATAGTCATCCAGTAA
1 GTAGCTTGGATAGTCATCCAGTAA
*
118845 GTAGCTTGGATGGTCATCCAGTAA
1 GTAGCTTGGATAGTCATCCAGTAA
118869 ATGCTGTGGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.29
Consensus pattern (24 bp):
GTAGCTTGGATAGTCATCCAGTAA
Found at i:118878 original size:24 final size:24
Alignment explanation
Indices: 118822--118878 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 24
118812 ATCACTAGGG
*
118822 TAGCTTGGATAGTCATCCAGTAAG
1 TAGCTTGGATAGTCATCCAGTAAA
*
118846 TAGCTTGGATGGTCATCCAGTAAA
1 TAGCTTGGATAGTCATCCAGTAAA
118870 T-GCTGTGGA
1 TAGCT-TGGA
118879 AGATTTCTGA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 3 0.10
24 27 0.90
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (24 bp):
TAGCTTGGATAGTCATCCAGTAAA
Found at i:120820 original size:17 final size:17
Alignment explanation
Indices: 120779--120820 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
120769 AATAAATGCT
*
120779 TAAATAATTGTAAAACC
1 TAAATAATTGTAAAACA
*
120796 TAAGTAATTGTAAAACA
1 TAAATAATTGTAAAACA
120813 TAAATAAT
1 TAAATAAT
120821 CCTAAAATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.55, C:0.07, G:0.07, T:0.31
Consensus pattern (17 bp):
TAAATAATTGTAAAACA
Found at i:120844 original size:13 final size:13
Alignment explanation
Indices: 120826--120850 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
120816 ATAATCCTAA
120826 AATATTAAAAATG
1 AATATTAAAAATG
120839 AATATTAAAAAT
1 AATATTAAAAAT
120851 TGAGAGTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (13 bp):
AATATTAAAAATG
Found at i:130155 original size:72 final size:72
Alignment explanation
Indices: 130036--130176 Score: 201
Period size: 72 Copynumber: 2.0 Consensus size: 72
130026 TATATATTGG
* * * *
130036 TAAAGAATGATTCAATGTTACTCACACAAGCTTTAGAGAATCCAAAACACGTGTTGGATCTCAAG
1 TAAAGAATGATTCAATGTTACTCACACAAGCTTCAAAGAATCAAAAACACGTATTGGATCTCAAG
130101 CCATCGA
66 CCATCGA
* ** * *
130108 TAAAGAATGATTCGATGTTGTTCACACAAGCTTCAAATAATCAAAAACATGTATTGGATCTCAAG
1 TAAAGAATGATTCAATGTTACTCACACAAGCTTCAAAGAATCAAAAACACGTATTGGATCTCAAG
130173 CCAT
66 CCAT
130177 AGATCATTAA
Statistics
Matches: 60, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
72 60 1.00
ACGTcount: A:0.38, C:0.19, G:0.16, T:0.27
Consensus pattern (72 bp):
TAAAGAATGATTCAATGTTACTCACACAAGCTTCAAAGAATCAAAAACACGTATTGGATCTCAAG
CCATCGA
Found at i:132656 original size:3 final size:3
Alignment explanation
Indices: 132648--132705 Score: 80
Period size: 3 Copynumber: 18.3 Consensus size: 3
132638 TAAATAGTTG
*
132648 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TACT TACCT TAT CAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TA--T TAT TAT
132696 TAT TAT TAT T
1 TAT TAT TAT T
132706 TACCCATTTA
Statistics
Matches: 51, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
3 44 0.86
4 3 0.06
5 4 0.08
ACGTcount: A:0.31, C:0.07, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:145404 original size:34 final size:34
Alignment explanation
Indices: 145352--145452 Score: 132
Period size: 34 Copynumber: 3.0 Consensus size: 34
145342 GGAGGTTACA
* * *
145352 AATTGCTACCGTATTGATCTGTCATAAGCATATT
1 AATTTCTATCGTATTGATCTGTTATAAGCATATT
* *
145386 AATTTCTATCGTATTGATCTATTATAAGCATTTT
1 AATTTCTATCGTATTGATCTGTTATAAGCATATT
*
145420 AATTGT-TATTGTATTGATCTGTTATAAGCATAT
1 AATT-TCTATCGTATTGATCTGTTATAAGCATAT
145453 CATATTACAT
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
34 57 0.98
35 1 0.02
ACGTcount: A:0.30, C:0.12, G:0.13, T:0.46
Consensus pattern (34 bp):
AATTTCTATCGTATTGATCTGTTATAAGCATATT
Found at i:145465 original size:34 final size:33
Alignment explanation
Indices: 145362--145467 Score: 122
Period size: 34 Copynumber: 3.1 Consensus size: 33
145352 AATTGCTACC
* *
145362 GTATTGATCTGTCATAAGCATATTAATTTCTATC
1 GTATTGATCTGTTATAAGCATATTAATTTC-ATT
* * *
145396 GTATTGATCTATTATAAGCATTTTAATTGTTATT
1 GTATTGATCTGTTATAAGCATATTAATT-TCATT
* *
145430 GTATTGATCTGTTATAAGCATATCATATTACATT
1 GTATTGATCTGTTATAAGCATATTA-ATTTCATT
145464 GTAT
1 GTAT
145468 GAGGTGGGAA
Statistics
Matches: 60, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
34 56 0.93
35 4 0.07
ACGTcount: A:0.30, C:0.10, G:0.12, T:0.47
Consensus pattern (33 bp):
GTATTGATCTGTTATAAGCATATTAATTTCATT
Found at i:145606 original size:45 final size:45
Alignment explanation
Indices: 145557--145711 Score: 152
Period size: 45 Copynumber: 3.5 Consensus size: 45
145547 TATTTGCAAA
* * *
145557 TTTGTTGTGTATCCACAGCCAGAGGCAGATTCTATCTGCGAGATT
1 TTTGTTGTGTATCCACAGCCAAAGGCAAATTCTATATGCGAGATT
* * ** * *
145602 TTTGTTGTGTATTCACAGCTAAAGATAAATTTTATATGCAAGATT
1 TTTGTTGTGTATCCACAGCCAAAGGCAAATTCTATATGCGAGATT
** * * *
145647 TTTACTATGTATCCACAGCCATAA-GCATATTCTATTTGCGAGA-T
1 TTTGTTGTGTATCCACAGCCA-AAGGCAAATTCTATATGCGAGATT
*
145691 TTTGTTGTGTTTCCACAGCCA
1 TTTGTTGTGTATCCACAGCCA
145712 TTGGTAGTTT
Statistics
Matches: 85, Mismatches: 24, Indels: 3
0.76 0.21 0.03
Matches are distributed among these distances:
44 18 0.21
45 65 0.76
46 2 0.02
ACGTcount: A:0.26, C:0.17, G:0.18, T:0.38
Consensus pattern (45 bp):
TTTGTTGTGTATCCACAGCCAAAGGCAAATTCTATATGCGAGATT
Found at i:147791 original size:20 final size:19
Alignment explanation
Indices: 147757--147814 Score: 55
Period size: 20 Copynumber: 3.0 Consensus size: 19
147747 ACTGCTTTTA
* *
147757 TTAAAAATGAGAAAAAATAT
1 TTAAAAATCATAAAAAAT-T
147777 TTAAAAATCAT-AAAAATT
1 TTAAAAATCATAAAAAATT
* *
147795 GTAAAAATATATAAAAAATT
1 TTAAAAAT-CATAAAAAATT
147815 GTGAAATTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
18 8 0.25
19 8 0.25
20 16 0.50
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.29
Consensus pattern (19 bp):
TTAAAAATCATAAAAAATT
Found at i:147815 original size:20 final size:20
Alignment explanation
Indices: 147788--147879 Score: 73
Period size: 20 Copynumber: 4.7 Consensus size: 20
147778 TAAAAATCAT
147788 AAAAATTGTAAAAATATATA
1 AAAAATTGTAAAAATATATA
* * *
147808 AAAAATTGTGAAATTTTAT-
1 AAAAATTGTAAAAATATATA
*
147827 AAAAATCGTAAAAAGTAT-TA
1 AAAAATTGTAAAAA-TATATA
* * *
147847 TAAAATATATAGAAATATA-A
1 AAAAAT-TGTAAAAATATATA
*
147867 AAAAATTATAAAA
1 AAAAATTGTAAAA
147880 TTTTATAAAG
Statistics
Matches: 55, Mismatches: 13, Indels: 9
0.71 0.17 0.12
Matches are distributed among these distances:
19 18 0.33
20 32 0.58
21 5 0.09
ACGTcount: A:0.62, C:0.01, G:0.07, T:0.30
Consensus pattern (20 bp):
AAAAATTGTAAAAATATATA
Found at i:147855 original size:28 final size:29
Alignment explanation
Indices: 147807--147903 Score: 90
Period size: 29 Copynumber: 3.3 Consensus size: 29
147797 AAAAATATAT
* * *
147807 AAAAAATTGTGAAATTTTATAAAAATCGTA
1 AAAAAATTATAAAATTATAT-AAAATCGTA
* *
147837 AAAAGTATTATAAAA-TATATAGAAAT-ATA
1 AAAA-AATTATAAAATTATATA-AAATCGTA
* *
147866 AAAAAATTATAAAATTTTATAAAGTCGTA
1 AAAAAATTATAAAATTATATAAAATCGTA
147895 AAAAAATTA
1 AAAAAATTA
147904 CACAAAATGT
Statistics
Matches: 54, Mismatches: 9, Indels: 9
0.75 0.12 0.12
Matches are distributed among these distances:
28 12 0.22
29 23 0.43
30 12 0.22
31 7 0.13
ACGTcount: A:0.59, C:0.02, G:0.07, T:0.32
Consensus pattern (29 bp):
AAAAAATTATAAAATTATATAAAATCGTA
Found at i:147911 original size:59 final size:60
Alignment explanation
Indices: 147799--147924 Score: 143
Period size: 59 Copynumber: 2.1 Consensus size: 60
147789 AAAATTGTAA
* * * *
147799 AAATATATAAAAAATTGTGAAATTTTATAAAAATCGTAAAAAGTATTATAAAATATATA-G
1 AAATATATAAAAAATTATAAAATTTTATAAAAATCGTAAAAAGAATTACAAAATATA-ACG
* *
147859 AAATATA-AAAAAATTATAAAATTTTAT-AAAGTCGTAAAAA-AATTACACAAAATGTAACG
1 AAATATATAAAAAATTATAAAATTTTATAAAAATCGTAAAAAGAATT--ACAAAATATAACG
147918 AAATATA
1 AAATATA
147925 GATTTCGTAA
Statistics
Matches: 57, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
57 3 0.05
58 13 0.23
59 34 0.60
60 7 0.12
ACGTcount: A:0.59, C:0.04, G:0.07, T:0.30
Consensus pattern (60 bp):
AAATATATAAAAAATTATAAAATTTTATAAAAATCGTAAAAAGAATTACAAAATATAACG
Found at i:148169 original size:18 final size:17
Alignment explanation
Indices: 148148--148190 Score: 50
Period size: 19 Copynumber: 2.4 Consensus size: 17
148138 TTTAAATTTT
*
148148 TTTATATTTTTATTAAAA
1 TTTATATTTTT-CTAAAA
148166 TTTAATAATTTTTCTAAAA
1 TTT-AT-ATTTTTCTAAAA
148185 TTTATA
1 TTTATA
148191 ACTTTTATTG
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
17 1 0.05
18 5 0.23
19 10 0.45
20 6 0.27
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (17 bp):
TTTATATTTTTCTAAAA
Found at i:148196 original size:18 final size:19
Alignment explanation
Indices: 148161--148196 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
148151 ATATTTTTAT
*
148161 TAAAATTTAATAATTTTTC
1 TAAAATTTAATAACTTTTC
148180 TAAAATTT-ATAACTTTT
1 TAAAATTTAATAACTTTT
148197 ATTGATTTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.53
Consensus pattern (19 bp):
TAAAATTTAATAACTTTTC
Found at i:149352 original size:21 final size:21
Alignment explanation
Indices: 149306--149352 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 21
149296 CACACGCTTG
*
149306 ATTAATTTAAAATCAATTTTAT
1 ATTAATTTAAAAT-AATTTGAT
149328 -TTAATTTTAAAAT-ATTTGAT
1 ATTAA-TTTAAAATAATTTGAT
149348 ATTAA
1 ATTAA
149353 AAATATATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
20 6 0.27
21 8 0.36
22 8 0.36
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (21 bp):
ATTAATTTAAAATAATTTGAT
Found at i:150362 original size:38 final size:39
Alignment explanation
Indices: 150310--150397 Score: 124
Period size: 38 Copynumber: 2.3 Consensus size: 39
150300 ATAAATTACA
* * *
150310 TTTAATACAGTAAAATATTCATTATATTTAT-TTGTGTT
1 TTTAATATAATAAAATATTCATTATATTTATGTAGTGTT
*
150348 TTTAATATAATAAAATATTTATTATATTTATGGTAGTGTT
1 TTTAATATAATAAAATATTCATTATATTTAT-GTAGTGTT
150388 TTTAATATAA
1 TTTAATATAA
150398 ATAATTTTTA
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
38 28 0.64
40 16 0.36
ACGTcount: A:0.38, C:0.02, G:0.08, T:0.52
Consensus pattern (39 bp):
TTTAATATAATAAAATATTCATTATATTTATGTAGTGTT
Done.