Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013923.1 Kokia drynarioides strain JFW-HI SEQ_128953, whole genome shotgun sequence
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: 73429
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.35
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:739 original size:6 final size:6
Alignment explanation
Indices: 728--766 Score: 53
Period size: 6 Copynumber: 6.5 Consensus size: 6
718 TATTTATTTC
*
728 ATTTTA ATTTTA ATTTTA ATTTTTA GTTTT- ATTTTA ATT
1 ATTTTA ATTTTA ATTTTA A-TTTTA ATTTTA ATTTTA ATT
767 ATGCAATATT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
5 4 0.14
6 20 0.69
7 5 0.17
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (6 bp):
ATTTTA
Found at i:745 original size:12 final size:12
Alignment explanation
Indices: 728--766 Score: 53
Period size: 13 Copynumber: 3.2 Consensus size: 12
718 TATTTATTTC
728 ATTTTAATTTTA
1 ATTTTAATTTTA
740 ATTTTAATTTTTA
1 ATTTTAA-TTTTA
*
753 GTTTT-ATTTTA
1 ATTTTAATTTTA
764 ATT
1 ATT
767 ATGCAATATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
11 7 0.29
12 8 0.33
13 9 0.38
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (12 bp):
ATTTTAATTTTA
Found at i:761 original size:18 final size:19
Alignment explanation
Indices: 729--766 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
719 ATTTATTTCA
729 TTTTAATTTTAATTTTAAT
1 TTTTAATTTTAATTTTAAT
*
748 TTTTAGTTTT-ATTTTAAT
1 TTTTAATTTTAATTTTAAT
766 T
1 T
767 ATGCAATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (19 bp):
TTTTAATTTTAATTTTAAT
Found at i:1585 original size:11 final size:10
Alignment explanation
Indices: 1559--1616 Score: 50
Period size: 10 Copynumber: 5.8 Consensus size: 10
1549 TTATTATTTA
1559 GAAAAAAAAT
1 GAAAAAAAAT
*
1569 GTAAAAAAAT
1 GAAAAAAAAT
*
1579 CGAAAAAAATT
1 -GAAAAAAAAT
1590 GAGAAAAAAA-
1 GA-AAAAAAAT
1600 -AAAGAAAAA-
1 GAAA-AAAAAT
1609 GAAAAAAA
1 GAAAAAAA
1617 GAGACAAAAG
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
8 2 0.05
9 10 0.25
10 14 0.35
11 14 0.35
ACGTcount: A:0.78, C:0.02, G:0.12, T:0.09
Consensus pattern (10 bp):
GAAAAAAAAT
Found at i:1613 original size:16 final size:17
Alignment explanation
Indices: 1594--1626 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1584 AAAATTGAGA
1594 AAAAAAAAAGA-AAAAG
1 AAAAAAAAAGACAAAAG
*
1610 AAAAAAAGAGACAAAAG
1 AAAAAAAAAGACAAAAG
1627 TGTGTTTGAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.82, C:0.03, G:0.15, T:0.00
Consensus pattern (17 bp):
AAAAAAAAAGACAAAAG
Found at i:1964 original size:9 final size:9
Alignment explanation
Indices: 1952--1987 Score: 63
Period size: 9 Copynumber: 4.0 Consensus size: 9
1942 ACCTTGAACA
1952 CTTTGAGTG
1 CTTTGAGTG
1961 CTTTGAGTG
1 CTTTGAGTG
*
1970 CTTTTAGTG
1 CTTTGAGTG
1979 CTTTGAGTG
1 CTTTGAGTG
1988 AATCTTTAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.11, C:0.11, G:0.31, T:0.47
Consensus pattern (9 bp):
CTTTGAGTG
Found at i:2695 original size:23 final size:25
Alignment explanation
Indices: 2669--2714 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
2659 CCAATTAGGG
2669 AATTAT-TGTTTAG-ATTTAATTCA
1 AATTATCTGTTTAGAATTTAATTCA
*
2692 AATTATCTTTTTAGAATTTAATT
1 AATTATCTGTTTAGAATTTAATT
2715 TGCATCCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.35, C:0.04, G:0.07, T:0.54
Consensus pattern (25 bp):
AATTATCTGTTTAGAATTTAATTCA
Found at i:5306 original size:30 final size:30
Alignment explanation
Indices: 5271--5327 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
5261 CCTTTCCCCC
*
5271 TAGTTTTTATGGCTAAACTAGAACCCTTCT
1 TAGTTTTTATGGCTAAACTAAAACCCTTCT
* *
5301 TAGTTTTTGTGGCTCAACTAAAACCCT
1 TAGTTTTTATGGCTAAACTAAAACCCT
5328 CCCAATTTAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.26, C:0.21, G:0.14, T:0.39
Consensus pattern (30 bp):
TAGTTTTTATGGCTAAACTAAAACCCTTCT
Found at i:8713 original size:23 final size:23
Alignment explanation
Indices: 8708--8751 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
8698 TAATATGCTT
*
8708 TATGCTTTATGATTAAATATTAA
1 TATGATTTATGATTAAATATTAA
* *
8731 TATGATTTGTGCTTAAATATT
1 TATGATTTATGATTAAATATT
8752 TGTGCTCAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.34, C:0.05, G:0.11, T:0.50
Consensus pattern (23 bp):
TATGATTTATGATTAAATATTAA
Found at i:8754 original size:14 final size:14
Alignment explanation
Indices: 8735--8764 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
8725 TATTAATATG
*
8735 ATTTGTGCTTAAAT
1 ATTTGTGCTCAAAT
8749 ATTTGTGCTCAAAT
1 ATTTGTGCTCAAAT
8763 AT
1 AT
8765 AAAAGTAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.30, C:0.10, G:0.13, T:0.47
Consensus pattern (14 bp):
ATTTGTGCTCAAAT
Found at i:9706 original size:30 final size:29
Alignment explanation
Indices: 9672--9931 Score: 256
Period size: 30 Copynumber: 8.7 Consensus size: 29
9662 TTTCAAAGAA
* * *
9672 TTAGGGTTAAAACGTAATTTTAAGAAAAAT
1 TTAGGGTCAAAATGTAATTTT-AGAAAAGT
* *
9702 TTAGGGATCAAAATGTGATTTTAGGAAAGT
1 TTAGGG-TCAAAATGTAATTTTAGAAAAGT
* *
9732 TTGGGAGTCAAAATGTAATTTTGGAAAAAGT
1 TTAGG-GTCAAAATGTAATTTTAG-AAAAGT
*
9763 TTGAGGGTCAAAATATAATTTT-GAAAAGT
1 TT-AGGGTCAAAATGTAATTTTAGAAAAGT
9792 TTGAGGGTCAAAATGTAATTTT-GAAAAGT
1 TT-AGGGTCAAAATGTAATTTTAGAAAAGT
* * *
9821 TCAGGCAAT-AAAATATAATTTTAGAAAAGT
1 TTAGG--GTCAAAATGTAATTTTAGAAAAGT
*
9851 TTAGGGTTAAAATGTAATTTTAGAAAAGT
1 TTAGGGTCAAAATGTAATTTTAGAAAAGT
* * *
9880 TTAGGAGCCAAAATGTAAATTTATAAAAGT
1 TTAGG-GTCAAAATGTAATTTTAGAAAAGT
* *
9910 TCGAAGGTCAAAATGTAATTTT
1 T-TAGGGTCAAAATGTAATTTT
9932 TAAAGAAAAT
Statistics
Matches: 194, Mismatches: 26, Indels: 20
0.81 0.11 0.08
Matches are distributed among these distances:
28 4 0.02
29 72 0.37
30 79 0.41
31 37 0.19
32 2 0.01
ACGTcount: A:0.42, C:0.04, G:0.20, T:0.33
Consensus pattern (29 bp):
TTAGGGTCAAAATGTAATTTTAGAAAAGT
Found at i:9758 original size:29 final size:29
Alignment explanation
Indices: 9680--9931 Score: 194
Period size: 29 Copynumber: 8.4 Consensus size: 29
9670 AATTAGGGTT
* *
9680 AAAACGTAATTTTAAGAAAAATTTAGGGA-TC
1 AAAATGTAATTTT--GAAAAGTTT-GGGAGTC
* *
9711 AAAATGTGATTTTAGGAAAGTTTGGGAGTC
1 AAAATGTAATTTT-GAAAAGTTTGGGAGTC
9741 AAAATGTAATTTTGGAAAAAGTTTGAGG-GTC
1 AAAATGTAATTTT-G-AAAAGTTTG-GGAGTC
*
9772 AAAATATAATTTTGAAAAGTTTGAGG-GTC
1 AAAATGTAATTTTGAAAAGTTTG-GGAGTC
* * *
9801 AAAATGTAATTTTGAAAAGTTCAGGCAAT-
1 AAAATGTAATTTTGAAAAGTT-TGGGAGTC
* * *
9830 AAAATATAATTTTAGAAAAGTTTAGG-GTT
1 AAAATGTAATTTT-GAAAAGTTTGGGAGTC
* *
9859 AAAATGTAATTTTAGAAAAGTTTAGGAGCC
1 AAAATGTAATTTT-GAAAAGTTTGGGAGTC
* *
9889 AAAATGTAAATTTAT-AAAAG-TTCGAAGGTC
1 AAAATGT-AATTT-TGAAAAGTTTGGGA-GTC
9919 AAAATGTAATTTT
1 AAAATGTAATTTT
9932 TAAAGAAAAT
Statistics
Matches: 187, Mismatches: 23, Indels: 25
0.80 0.10 0.11
Matches are distributed among these distances:
28 2 0.01
29 87 0.47
30 56 0.30
31 39 0.21
32 3 0.02
ACGTcount: A:0.43, C:0.04, G:0.20, T:0.33
Consensus pattern (29 bp):
AAAATGTAATTTTGAAAAGTTTGGGAGTC
Found at i:12862 original size:38 final size:37
Alignment explanation
Indices: 12820--12897 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 37
12810 ATATGTAGAA
*
12820 TTTTCAATAAGAACTCATAGGCGTTCTAGTATTTCTGG
1 TTTTCAAT-AGAACTCATAGGCGTTCTAGCATTTCTGG
* * * *
12858 TTTTCACTAGAGCTCATAGGTGTTCTAGCATTTTTGG
1 TTTTCAATAGAACTCATAGGCGTTCTAGCATTTCTGG
12895 TTT
1 TTT
12898 GTTCAAGATC
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
37 28 0.80
38 7 0.20
ACGTcount: A:0.22, C:0.15, G:0.19, T:0.44
Consensus pattern (37 bp):
TTTTCAATAGAACTCATAGGCGTTCTAGCATTTCTGG
Found at i:16590 original size:63 final size:63
Alignment explanation
Indices: 16523--16736 Score: 177
Period size: 63 Copynumber: 3.4 Consensus size: 63
16513 ACACATACAA
* ** * *
16523 CACCAGTTTATTTTACACTATTACCACAT-CACTCGCAATCATTCCATGCACCAACATATTCAT
1 CACCAGTTTATTTTACACAAGCACCA-ATACACGCGCAATCACTCCATGCACCAACATATTCAT
* * * * *
16586 CACCACTTTATTTTACACAAGCACCATTACACGCGCAATCGCTCCTTGCACCGACATATTCAT
1 CACCAGTTTATTTTACACAAGCACCAATACACGCGCAATCACTCCATGCACCAACATATTCAT
* * * * * * * *
16649 CAACAGTTTATTTCACACAAGCATC-ATAGCA-GATGCAATCATTCCCTACACCAACACAATT-A
1 CACCAGTTTATTTTACACAAGCACCAATA-CACG-CGCAATCACTCCATGCACCAACA-TATTCA
16711 T
63 T
*
16712 CACC-GATTTATTTTTCACAAGCACC
1 CACCAG-TTTATTTTACACAAGCACC
16737 TCAACACTTG
Statistics
Matches: 120, Mismatches: 26, Indels: 10
0.77 0.17 0.06
Matches are distributed among these distances:
62 5 0.04
63 112 0.93
64 3 0.03
ACGTcount: A:0.32, C:0.32, G:0.07, T:0.29
Consensus pattern (63 bp):
CACCAGTTTATTTTACACAAGCACCAATACACGCGCAATCACTCCATGCACCAACATATTCAT
Found at i:21600 original size:39 final size:39
Alignment explanation
Indices: 21545--21666 Score: 185
Period size: 39 Copynumber: 3.1 Consensus size: 39
21535 TCAAAATCTA
*
21545 AAATATTTTGAAAATGGGAGAAGACTGTTGGAACATTTTC
1 AAATA-TTTGAAAATGGGAGAAGATTGTTGGAACATTTTC
21585 AAATATTTGAAAAT-GGAGGAAGATTGTTGGAACATTTTC
1 AAATATTTGAAAATGGGA-GAAGATTGTTGGAACATTTTC
*
21624 AAATATTTGAAAATGAGGAG-AGATTGTTAGAACATTTTC
1 AAATATTTGAAAATG-GGAGAAGATTGTTGGAACATTTTC
21663 AAAT
1 AAAT
21667 GTTTATAGTG
Statistics
Matches: 77, Mismatches: 2, Indels: 7
0.90 0.02 0.08
Matches are distributed among these distances:
38 3 0.04
39 65 0.84
40 6 0.08
41 3 0.04
ACGTcount: A:0.40, C:0.06, G:0.21, T:0.33
Consensus pattern (39 bp):
AAATATTTGAAAATGGGAGAAGATTGTTGGAACATTTTC
Found at i:25033 original size:51 final size:51
Alignment explanation
Indices: 24930--25336 Score: 128
Period size: 51 Copynumber: 8.0 Consensus size: 51
24920 TTTTTTAATG
** * *
24930 AAAATCACTACTTTACTT-AAAAATCTAAACTTTTAT-TTTGAAATAA-TTAAA
1 AAAATCAAAACTTT-CTTAAAAAAT-TAAACTTTT-TCTTTAAAATAACTAAAA
*
24981 AAAATCAAAACTTTGTTAAAAAATTAAACTTTTTCTTTAAAATAACT--AA
1 AAAATCAAAACTTTCTTAAAAAATTAAACTTTTTCTTTAAAATAACTAAAA
** * * * **** *** *
25030 AAAA-CAAATTTTTAATTTTAAAAATATAAACTTTCTCTTTTTTTTTTTTAAAG
1 AAAATCAAAACTTT--CTTAAAAAAT-TAAACTTTTTCTTTAAAATAACTAAAA
** * * * * ** *
25083 AAAATCACTATTTTACCT-AAAAATTCAAA-TTTTTATTTTGAAATAGTTAAGA
1 AAAATCAAAACTTT-CTTAAAAAATT-AAACTTTTT-CTTTAAAATAACTAAAA
* *
25135 AAAATCAAAACTTTGTTAAAAATTTAAA-TATTTTCTTTAAAATAACTAAAA
1 AAAATCAAAACTTTCTTAAAAAATTAAACT-TTTTCTTTAAAATAACTAAAA
**** * ** *
25186 AAATATTTTTA-TTT-TT-AAAAATATAAACTTTCTCTTT----TTTCTAAAG
1 AAA-ATCAAAACTTTCTTAAAAAAT-TAAACTTTTTCTTTAAAATAACTAAAA
** * * * * ** *
25232 AAAATCACTATTTTACTTAAAAAATCAAA-TTTTTATTTCGAAATAGTTAAGA
1 AAAATCAAAACTTT-CTTAAAAAATTAAACTTTTTCTTT-AAAATAACTAAAA
* * *
25284 AAAACCAAAACTTTATTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAA
1 AAAATCAAAACTTTCTTAAAAAATTAAACTTTTTCTTTAAAATAACTAAAA
25335 AA
1 AA
25337 TAGATTTTTA
Statistics
Matches: 255, Mismatches: 75, Indels: 52
0.67 0.20 0.14
Matches are distributed among these distances:
45 4 0.02
46 12 0.05
47 7 0.03
48 12 0.05
49 18 0.07
50 41 0.16
51 85 0.33
52 63 0.25
53 7 0.03
54 6 0.02
ACGTcount: A:0.47, C:0.10, G:0.03, T:0.41
Consensus pattern (51 bp):
AAAATCAAAACTTTCTTAAAAAATTAAACTTTTTCTTTAAAATAACTAAAA
Found at i:25280 original size:149 final size:148
Alignment explanation
Indices: 24767--25400 Score: 822
Period size: 149 Copynumber: 4.3 Consensus size: 148
24757 AATTCAAAAG
* * * *
24767 TTTTCTTTTGATTAAAACAAAATCACTACTTTACTT-CAAAATCAAAACTTTTATTTCGAAATAG
1 TTTTCTTTT--TTTAAAGAAAATCACTATTTTACTTAAAAAATCAAAACTTTTATTTCGAAATAG
*
24831 TTAAAAAAATCAAAACTTTGTTTAAAAATTTAAACTTTTTCTTTAAAATCACTAAAAAA-ATATT
64 TTAAAAAAATCAAAACTTTG-TTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAACATATT
* *
24895 TTTATTTTTTACAAATGTAAAC
128 TTTA-TTTTTAAAAATATAAAC
* * * * *
24917 --TT-TTTTTTTAATGAAAATCACTACTTTACTT-AAAAATCTAAACTTTTATTTTGAAATAATT
1 TTTTCTTTTTTTAAAGAAAATCACTATTTTACTTAAAAAATCAAAACTTTTATTTCGAAATAGTT
* *
24978 AAAAAAATCAAAACTTTGTTAAAAAATTAAACTTTTTCTTTAAAATAACTAAAAAACAAATTTTT
66 AAAAAAATCAAAACTTTGTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAACATATTTTT
*
25043 AATTTTAAAAATATAAAC
131 ATTTTTAAAAATATAAAC
* * * *
25061 TTTCTCTTTTTTTTTTTTAAAGAAAATCACTATTTTACCTAAAAATTC-AAATTTTTATTTTGAA
1 TTT-TC-----TTTTTTTAAAGAAAATCACTATTTTACTTAAAAAATCAAAACTTTTATTTCGAA
25125 ATAGTTAAGAAAAATCAAAACTTTGTTAAAAATTTAAA-TATTTTCTTTAAAATAACTAAAAAA-
60 ATAGTTAA-AAAAATCAAAACTTTGTTAAAAATTTAAACT-TTTTCTTTAAAATAACTAAAAAAC
25188 ATATTTTTATTTTTAAAAATATAAAC
123 ATATTTTTATTTTTAAAAATATAAAC
*
25214 TTTCTCTTTTTTCTAAAGAAAATCACTATTTTACTTAAAAAATC-AAATTTTTATTTCGAAATAG
1 TTT-TCTTTTTT-TAAAGAAAATCACTATTTTACTTAAAAAATCAAAACTTTTATTTCGAAATAG
* * * *
25278 TTAAGAAAAACCAAAACTTTATTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAATAGATT
64 TTAA-AAAAATCAAAACTTTGTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAACATATT
25343 TTTATTTTTAAAAATATAAA-
128 TTTATTTTTAAAAATATAAAC
* *
25363 TTTTCTCTTTTTAAAGAAAATCACTATTTTACCTAAAA
1 TTTTCTTTTTTTAAAGAAAATCACTATTTTACTTAAAA
25401 TTTTATTTGA
Statistics
Matches: 438, Mismatches: 30, Indels: 35
0.87 0.06 0.07
Matches are distributed among these distances:
144 50 0.11
145 74 0.17
146 1 0.00
147 31 0.07
148 15 0.03
149 106 0.24
150 25 0.06
153 79 0.18
154 57 0.13
ACGTcount: A:0.45, C:0.10, G:0.03, T:0.42
Consensus pattern (148 bp):
TTTTCTTTTTTTAAAGAAAATCACTATTTTACTTAAAAAATCAAAACTTTTATTTCGAAATAGTT
AAAAAAATCAAAACTTTGTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAACATATTTTT
ATTTTTAAAAATATAAAC
Found at i:25365 original size:22 final size:22
Alignment explanation
Indices: 25330--25377 Score: 62
Period size: 23 Copynumber: 2.2 Consensus size: 22
25320 TTAAAATAAC
*
25330 TAAAAAATAGATTTT-TATTTT
1 TAAAAAATAAATTTTCTATTTT
*
25351 TAAAAATATAAATTTTCTCTTTT
1 TAAAAA-ATAAATTTTCTATTTT
25374 TAAA
1 TAAA
25378 GAAAATCACT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 6 0.26
22 8 0.35
23 9 0.39
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.50
Consensus pattern (22 bp):
TAAAAAATAAATTTTCTATTTT
Found at i:25832 original size:3 final size:3
Alignment explanation
Indices: 25824--25849 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
25814 AAAAAATTAA
25824 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
25850 GAAGAAGAAG
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:25854 original size:3 final size:3
Alignment explanation
Indices: 25848--25894 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
25838 TAATAATAAT
25848 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
25895 TGGTGATGAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:25953 original size:11 final size:11
Alignment explanation
Indices: 25939--25963 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
25929 CCCAAAAAGG
25939 AAAGAAAAATA
1 AAAGAAAAATA
25950 AAAGAAAAATA
1 AAAGAAAAATA
25961 AAA
1 AAA
25964 ACCTCTATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.84, C:0.00, G:0.08, T:0.08
Consensus pattern (11 bp):
AAAGAAAAATA
Found at i:27631 original size:15 final size:15
Alignment explanation
Indices: 27611--27639 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
27601 ATGCCTCACA
27611 CACCGTGTTATCAAT
1 CACCGTGTTATCAAT
27626 CACCGTGTTATCAA
1 CACCGTGTTATCAA
27640 GCAACAATAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.31
Consensus pattern (15 bp):
CACCGTGTTATCAAT
Found at i:29476 original size:30 final size:29
Alignment explanation
Indices: 29441--29550 Score: 82
Period size: 30 Copynumber: 3.7 Consensus size: 29
29431 AAGGGGAAAA
29441 TGGGGTCAACAA-TGAAATTTTAGAAAGTT
1 TGGGGTCAA-AATTGAAATTTTAGAAAGTT
* *
29470 TAGGGGT-AAAATTTGAATTTTTTGAAAGTT
1 T-GGGGTCAAAA-TTGAAATTTTAGAAAGTT
* * *
29500 TGGGGTC-AAATTAAAAATTTTGGAAAATT
1 TGGGGTCAAAATT-GAAATTTTAGAAAGTT
* * *
29529 TGAGGGTGAAATTTGAATTTTT
1 TG-GGGTCAAAATTGAAATTTT
29551 GGAAGTTAAG
Statistics
Matches: 64, Mismatches: 10, Indels: 13
0.74 0.11 0.15
Matches are distributed among these distances:
28 4 0.06
29 25 0.39
30 31 0.48
31 4 0.06
ACGTcount: A:0.35, C:0.03, G:0.24, T:0.38
Consensus pattern (29 bp):
TGGGGTCAAAATTGAAATTTTAGAAAGTT
Found at i:29489 original size:29 final size:28
Alignment explanation
Indices: 29456--29549 Score: 89
Period size: 29 Copynumber: 3.2 Consensus size: 28
29446 TCAACAATGA
29456 AATTTTAGAAAGTTTAGGGGTAAAATTTG
1 AATTTTAGAAAGTTT-GGGGTAAAATTTG
* * **
29485 AATTTTTTGAAAGTTTGGGGTCAAATTAAA
1 AA-TTTTAGAAAGTTTGGGGTAAAATT-TG
* * *
29515 AATTTTGGAAAATTTGAGGGTGAAATTTG
1 AATTTTAGAAAGTTTG-GGGTAAAATTTG
29544 AATTTT
1 AATTTT
29550 TGGAAGTTAA
Statistics
Matches: 53, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
29 30 0.57
30 23 0.43
ACGTcount: A:0.36, C:0.01, G:0.22, T:0.40
Consensus pattern (28 bp):
AATTTTAGAAAGTTTGGGGTAAAATTTG
Found at i:29551 original size:30 final size:29
Alignment explanation
Indices: 29453--29554 Score: 96
Period size: 30 Copynumber: 3.4 Consensus size: 29
29443 GGGTCAACAA
* * *
29453 TGAAATTTTAGAAAGTTTAGGGGTAAAATT
1 TGAATTTTTGGAAAATTT-GGGGTAAAATT
* * *
29483 TGAATTTTTTGAAAGTTTGGGGTCAAATT
1 TGAATTTTTGGAAAATTTGGGGTAAAATT
** * *
29512 AAAAATTTTGGAAAATTTGAGGGTGAAATT
1 TGAATTTTTGGAAAATTTG-GGGTAAAATT
29542 TGAATTTTTGGAA
1 TGAATTTTTGGAA
29555 GTTAAGAGGC
Statistics
Matches: 59, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
29 24 0.41
30 35 0.59
ACGTcount: A:0.36, C:0.01, G:0.24, T:0.39
Consensus pattern (29 bp):
TGAATTTTTGGAAAATTTGGGGTAAAATT
Found at i:31416 original size:46 final size:46
Alignment explanation
Indices: 31252--31568 Score: 344
Period size: 46 Copynumber: 6.9 Consensus size: 46
31242 TAGTAGTTTA
*
31252 AATCTGCCCCTC-TAGA-TTAGGGGTAAAAGATTGGATGATGGCTTT
1 AATCTGCCCCTCTTA-ACTTAGGGGTAAAAGATTGGATGATGGCTTC
* * * *
31297 AATCTG-CCC-CATGA--TCGGGGTAAGAA-ATTGGATAGTGATGTCGTT-
1 AATCTGCCCCTCTTAACTTAGGGGTAA-AAGATTGG--A-TGATGGC-TTC
* * * * *
31342 AATCTGCTCGTCTTGACTTAGGGGTAAAAGATTGGATGGTGACTTC
1 AATCTGCCCCTCTTAACTTAGGGGTAAAAGATTGGATGATGGCTTC
* *
31388 AATTTGGCCCTCTTAACTTAGGGGTAAAAGATTGGATGATGGCTTC
1 AATCTGCCCCTCTTAACTTAGGGGTAAAAGATTGGATGATGGCTTC
* * *
31434 AATCTGCCCCTCTTGACTTAGGGGTAAAAGATTGGGTGATGGCTTT
1 AATCTGCCCCTCTTAACTTAGGGGTAAAAGATTGGATGATGGCTTC
* *
31480 AATCTGCCCCTTTTAACTTAGGGGTAAAAGATTGGATGGTGGCTTC
1 AATCTGCCCCTCTTAACTTAGGGGTAAAAGATTGGATGATGGCTTC
*
31526 AATCTGCCCCTCTTTACTTAGGGGTAAAAGATTGAAGATGATG
1 AATCTGCCCCTCTTAACTTAGGGGTAAAAGATTG--GATGATG
31569 TAATTTCACT
Statistics
Matches: 229, Mismatches: 29, Indels: 25
0.81 0.10 0.09
Matches are distributed among these distances:
42 13 0.06
43 4 0.02
44 5 0.02
45 20 0.09
46 161 0.70
47 5 0.02
48 8 0.03
49 13 0.06
ACGTcount: A:0.26, C:0.16, G:0.27, T:0.32
Consensus pattern (46 bp):
AATCTGCCCCTCTTAACTTAGGGGTAAAAGATTGGATGATGGCTTC
Found at i:31517 original size:138 final size:135
Alignment explanation
Indices: 31252--31568 Score: 399
Period size: 138 Copynumber: 2.3 Consensus size: 135
31242 TAGTAGTTTA
* *
31252 AATCTGCCCCTC-TAGA-TTAGGGGTAAAAGATTGGATGATGGCTTTAATCTGCCCCATGATCGG
1 AATCTGCCCCTCTTA-ACTTAGGGGTAAAAGATTGGATGATGGCTTCAATCTGCCCCATGATAGG
* * * *
31315 GGTAAGAAATTGGATAGTGATGTCGTTAATCTGCTCGTCTTGACTTAGGGGTAAAAGATTGGATG
65 GGTAAGAAATTGG--AGTGATGGCGTTAATCTGCCCCTCTTAACTTAGGGGTAAAAGATTGGATG
31380 GTGACTTC
128 GTGACTTC
* * *
31388 AATTTGGCCCTCTTAACTTAGGGGTAAAAGATTGGATGATGGCTTCAATCTGCCCCTCTTGACTT
1 AATCTGCCCCTCTTAACTTAGGGGTAAAAGATTGGATGATGGCTTCAATCTG-CCC-CATGA--T
* *
31453 AGGGGTAA-AAGATTGG-GTGATGGCTTTAATCTGCCCCTTTTAACTTAGGGGTAAAAGATTGGA
62 AGGGGTAAGAA-ATTGGAGTGATGGCGTTAATCTGCCCCTCTTAACTTAGGGGTAAAAGATTGGA
*
31516 TGGTGGCTTC
126 TGGTGACTTC
*
31526 AATCTGCCCCTCTTTACTTAGGGGTAAAAGATTGAAGATGATG
1 AATCTGCCCCTCTTAACTTAGGGGTAAAAGATTG--GATGATG
31569 TAATTTCACT
Statistics
Matches: 157, Mismatches: 15, Indels: 14
0.84 0.08 0.08
Matches are distributed among these distances:
136 11 0.07
137 36 0.23
138 84 0.54
139 4 0.03
140 9 0.06
141 13 0.08
ACGTcount: A:0.26, C:0.16, G:0.27, T:0.32
Consensus pattern (135 bp):
AATCTGCCCCTCTTAACTTAGGGGTAAAAGATTGGATGATGGCTTCAATCTGCCCCATGATAGGG
GTAAGAAATTGGAGTGATGGCGTTAATCTGCCCCTCTTAACTTAGGGGTAAAAGATTGGATGGTG
ACTTC
Found at i:31903 original size:96 final size:95
Alignment explanation
Indices: 31632--32147 Score: 708
Period size: 96 Copynumber: 5.4 Consensus size: 95
31622 TTTGACTTAG
* * *
31632 TTCTCTGTATCTCATCAGGAAGATGGGTTTGAAGTTCCGCTCCACTCCATTGTAACCTCAGGGAC
1 TTCTCTGTATCTCATCAGGAAGATGGGTTTGAAGTTTCGCTCCACTCCACTGTAACCTCAGGGAT
* * *
31697 ATTGAGCTCTGGTTCATTATTTTGATCTAC
66 ATTGAGCTCTGCTTCATTGTTTTGATCCAC
*
31727 TTCTTTGTATCTCATCAGGAAGATGGGTTTGAAGTTTCGCTCCACTCCACTGTAACCTCAGGGAT
1 TTCTCTGTATCTCATCAGGAAGATGGGTTTGAAGTTTCGCTCCACTCCACTGTAACCTCAGGGAT
*
31792 ACTGAGCTCTGCTTCATTGTTTTGATCCAC
66 ATTGAGCTCTGCTTCATTGTTTTGATCCAC
* * * * * *
31822 TTCTCTGTATCTAATCTGGAAGATGGAGTTTGAATTTTCACTCTACTCCACTATAACCTCAGGGA
1 TTCTCTGTATCTCATCAGGAAGATGG-GTTTGAAGTTTCGCTCCACTCCACTGTAACCTCAGGGA
* * *
31887 TGTTAAGCTCTACTTCATTGTTTTGATCCAC
65 TATTGAGCTCTGCTTCATTGTTTTGATCCAC
* * *
31918 TTCTCTGTATCTTATCAAGAAGATGAGGTTTAAAGTTTCGCTCCACTCCACTGTAACCTCAGGGA
1 TTCTCTGTATCTCATCAGGAAGATG-GGTTTGAAGTTTCGCTCCACTCCACTGTAACCTCAGGGA
* * *
31983 TATTGAGTTCTACTTTATTGTTTTGATCCAC
65 TATTGAGCTCTGCTTCATTGTTTTGATCCAC
* ** *
32014 TTCTCTGTATCTCATCAGGAAGATGGGCTTTGAAGTTTCACTTTACTCCATTGTAACCTCAGGGA
1 TTCTCTGTATCTCATCAGGAAGATGGG-TTTGAAGTTTCGCTCCACTCCACTGTAACCTCAGGGA
**
32079 CGTTGAGCTCTGCTTCATTGTTTTGATCCAC
65 TATTGAGCTCTGCTTCATTGTTTTGATCCAC
* * *
32110 TTCTTTGTATCTCATTAGAAAGATGGGGTTTGAAGTTT
1 TTCTCTGTATCTCATCAGGAAGAT-GGGTTTGAAGTTT
32148 TGCTGTAATT
Statistics
Matches: 371, Mismatches: 46, Indels: 7
0.88 0.11 0.02
Matches are distributed among these distances:
95 112 0.30
96 255 0.69
97 4 0.01
ACGTcount: A:0.22, C:0.22, G:0.19, T:0.38
Consensus pattern (95 bp):
TTCTCTGTATCTCATCAGGAAGATGGGTTTGAAGTTTCGCTCCACTCCACTGTAACCTCAGGGAT
ATTGAGCTCTGCTTCATTGTTTTGATCCAC
Found at i:33155 original size:6 final size:6
Alignment explanation
Indices: 33144--33189 Score: 51
Period size: 6 Copynumber: 7.8 Consensus size: 6
33134 TTGACCTCTC
* *
33144 CTTTTT CTTTTT CTTCTT C-TTTT -TTTTT CTTTTCC CTTTTT CTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTT-T CTTTTT CTTTT
33190 CTCTCTCCTC
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
5 7 0.21
6 21 0.64
7 5 0.15
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (6 bp):
CTTTTT
Found at i:33183 original size:13 final size:12
Alignment explanation
Indices: 33142--33190 Score: 57
Period size: 12 Copynumber: 4.2 Consensus size: 12
33132 TCTTGACCTC
33142 TCCTTTTTCTTT
1 TCCTTTTTCTTT
* *
33154 TTCTTCTTCTTT
1 TCCTTTTTCTTT
33166 T--TTTTTCTTT
1 TCCTTTTTCTTT
33176 TCCCTTTTTCTTT
1 T-CCTTTTTCTTT
33189 TC
1 TC
33191 TCTCTCCTCT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
10 9 0.29
12 12 0.39
13 10 0.32
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (12 bp):
TCCTTTTTCTTT
Found at i:33204 original size:22 final size:20
Alignment explanation
Indices: 33139--33206 Score: 65
Period size: 18 Copynumber: 3.5 Consensus size: 20
33129 TCATCTTGAC
33139 CTCTCCTTTTTCTTTT-TCTT
1 CTCT-CTTTTTCTTTTCTCTT
33159 CT-TCTTTTT-TTTTCT-TT
1 CTCTCTTTTTCTTTTCTCTT
*
33176 -TCCCTTTTTCTTTTCTCTCT
1 CTCTCTTTTTCTTTTCTCT-T
33196 CCTCTCTTTTT
1 -CTCTCTTTTT
33207 TTTAGGTAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
16 1 0.03
17 12 0.31
18 13 0.33
19 2 0.05
20 3 0.08
22 8 0.21
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (20 bp):
CTCTCTTTTTCTTTTCTCTT
Found at i:34073 original size:24 final size:23
Alignment explanation
Indices: 34027--34073 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
34017 TCATCTTGAC
*
34027 TTTTTCTTCTTTTCTTTGCTTTT
1 TTTTTCTTCTTTTCTTGGCTTTT
* *
34050 TTTTTTTTCCTTTTCTTGGGTTTT
1 TTTTTCTT-CTTTTCTTGGCTTTT
34074 AAGATGCCCC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.00, C:0.15, G:0.09, T:0.77
Consensus pattern (23 bp):
TTTTTCTTCTTTTCTTGGCTTTT
Found at i:34162 original size:15 final size:16
Alignment explanation
Indices: 34129--34168 Score: 55
Period size: 15 Copynumber: 2.5 Consensus size: 16
34119 TTTCTTTCTT
*
34129 TCTTTCTTTCTTTTTCC
1 TCTTT-TTTCTTTTACC
34146 TCTTTTTT-TTTTACC
1 TCTTTTTTCTTTTACC
34161 TCTTTTTT
1 TCTTTTTT
34169 GATACAGTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 14 0.64
16 3 0.14
17 5 0.23
ACGTcount: A:0.03, C:0.23, G:0.00, T:0.75
Consensus pattern (16 bp):
TCTTTTTTCTTTTACC
Found at i:40134 original size:29 final size:30
Alignment explanation
Indices: 40049--40158 Score: 168
Period size: 30 Copynumber: 3.7 Consensus size: 30
40039 GTTATATTTG
* *
40049 AATTTTTGGAAAGTTTGAGAGTTAAAACAT
1 AATTTTTGGAAAGTTTGAGGGCTAAAACAT
*
40079 AATTTTTGGAAAGTTTGAGGGCCAAAACAT
1 AATTTTTGGAAAGTTTGAGGGCTAAAACAT
40109 AATTTTTGGAAAGTTTG-GGGCTAAAACAT
1 AATTTTTGGAAAGTTTGAGGGCTAAAACAT
*
40138 AATTTTTAGAAAGTTTCGAGG
1 AATTTTTGGAAAGTTT-GAGG
40159 TCAAAAATAG
Statistics
Matches: 73, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
29 26 0.36
30 45 0.62
31 2 0.03
ACGTcount: A:0.36, C:0.06, G:0.23, T:0.35
Consensus pattern (30 bp):
AATTTTTGGAAAGTTTGAGGGCTAAAACAT
Found at i:40173 original size:60 final size:60
Alignment explanation
Indices: 40048--40174 Score: 175
Period size: 60 Copynumber: 2.1 Consensus size: 60
40038 GGTTATATTT
* * *
40048 GAATTTTTGGAAAGTTTGAGAGTTAAAACATAATTTTTGGAAAGTTTGAGGGCCAAAACA
1 GAATTTTTGGAAAGTTTGAGAGCTAAAACATAATTTTTAGAAAGTTTGAGGGCAAAAACA
* * * *
40108 TAATTTTTGGAAAGTTTG-GGGCTAAAACATAATTTTTAGAAAGTTTCGAGGTCAAAAATA
1 GAATTTTTGGAAAGTTTGAGAGCTAAAACATAATTTTTAGAAAGTTT-GAGGGCAAAAACA
40168 GAATTTT
1 GAATTTT
40175 GAAGAGTTCA
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
59 25 0.43
60 33 0.57
ACGTcount: A:0.38, C:0.06, G:0.21, T:0.35
Consensus pattern (60 bp):
GAATTTTTGGAAAGTTTGAGAGCTAAAACATAATTTTTAGAAAGTTTGAGGGCAAAAACA
Found at i:40175 original size:59 final size:60
Alignment explanation
Indices: 40052--40175 Score: 164
Period size: 59 Copynumber: 2.1 Consensus size: 60
40042 ATATTTGAAT
* * *
40052 TTTTGGAAAGTTTGAGAGTTAAAACATAATTTTTGGAAAGTTTGAGGGCCAAAACATAAT
1 TTTTGGAAAGTTTGAGAGCTAAAACATAATTTTTAGAAAGTTTGAGGGCCAAAACATAAA
* *
40112 TTTTGGAAAGTTTG-GGGCTAAAACATAATTTTTAGAAAGTTTCGA-GGTCAAAA-ATAGAA
1 TTTTGGAAAGTTTGAGAGCTAAAACATAATTTTTAGAAAGTTT-GAGGGCCAAAACATA-AA
40171 TTTTG
1 TTTTG
40176 AAGAGTTCAA
Statistics
Matches: 57, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
58 3 0.05
59 38 0.67
60 16 0.28
ACGTcount: A:0.37, C:0.06, G:0.22, T:0.35
Consensus pattern (60 bp):
TTTTGGAAAGTTTGAGAGCTAAAACATAATTTTTAGAAAGTTTGAGGGCCAAAACATAAA
Found at i:44600 original size:21 final size:22
Alignment explanation
Indices: 44562--44602 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
44552 TTTTAACAAA
44562 TTTTAATGATTTTTATAATTTC
1 TTTTAATGATTTTTATAATTTC
44584 TTTT-ATG-TTTTCTATAATT
1 TTTTAATGATTTT-TATAATT
44603 CTAAAAAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.22
21 10 0.56
22 4 0.22
ACGTcount: A:0.24, C:0.05, G:0.05, T:0.66
Consensus pattern (22 bp):
TTTTAATGATTTTTATAATTTC
Found at i:48246 original size:52 final size:51
Alignment explanation
Indices: 48162--48710 Score: 767
Period size: 52 Copynumber: 10.6 Consensus size: 51
48152 TAAATGAGAA
* *
48162 AGGTCCGATGACTACGTGTCATCGTGAGTATATGAATCTTGTACCGATTATA
1 AGGTCCGATGACTACGTGTCATCGTGAGTATATGAATCTT-TACGGATTATG
* * * *
48214 AGATCTGATGACTACGTATCATCGTGAGTATATGAATCCTTTACGGATTACG
1 AGGTCCGATGACTACGTGTCATCGTGAGTATATGAAT-CTTTACGGATTATG
* * *
48266 AGGTCCAATGACTATGTGTCATCGTGAGTATATGAATCTTTTACGGATTACG
1 AGGTCCGATGACTACGTGTCATCGTGAGTATATGAATC-TTTACGGATTATG
**
48318 AGGTTTGAT-ACTACGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
1 AGGTCCGATGACTACGTGTCATCGTGAGTATATGAAT-CTTTACGGATTATG
**
48369 AGGTCCGATGACTACGTGTCATCGTGAGTATATGAATCCTTTACGGATTACA
1 AGGTCCGATGACTACGTGTCATCGTGAGTATATGAAT-CTTTACGGATTATG
* *
48421 AGGTCCAATGACTACGTGTCATTGTGAGTATATGAATCTTTTACGGATTATG
1 AGGTCCGATGACTACGTGTCATCGTGAGTATATGAATC-TTTACGGATTATG
*
48473 AGGTCCGATGACTACGTGTCATCGTGAGTATATGAATCTTTTACGGATTATA
1 AGGTCCGATGACTACGTGTCATCGTGAGTATATGAATC-TTTACGGATTATG
* *
48525 AGGTCCGATGACTACGTGTCATCGTGAGTGTATGATTCCTTTACGGATTATG
1 AGGTCCGATGACTACGTGTCATCGTGAGTATATGAAT-CTTTACGGATTATG
*
48577 AGGTCCGATGACTACGTGTCATCGTGAGTATATGAATCTTTACGGATTATA
1 AGGTCCGATGACTACGTGTCATCGTGAGTATATGAATCTTTACGGATTATG
* ** * ** *
48628 AGGTCAGATGACTACGTGTCATCGTGAGTGGATGATTCCTTTACGGAACAAG
1 AGGTCCGATGACTACGTGTCATCGTGAGTATATGAAT-CTTTACGGATTATG
*
48680 AGGTCCGATGACTATGTGTCATCGTGAGTAT
1 AGGTCCGATGACTACGTGTCATCGTGAGTAT
48711 TAAATATGCA
Statistics
Matches: 445, Mismatches: 45, Indels: 14
0.88 0.09 0.03
Matches are distributed among these distances:
51 93 0.21
52 348 0.78
53 4 0.01
ACGTcount: A:0.26, C:0.16, G:0.24, T:0.33
Consensus pattern (51 bp):
AGGTCCGATGACTACGTGTCATCGTGAGTATATGAATCTTTACGGATTATG
Found at i:48454 original size:155 final size:156
Alignment explanation
Indices: 48162--48710 Score: 827
Period size: 155 Copynumber: 3.5 Consensus size: 156
48152 TAAATGAGAA
* * * *
48162 AGGTCCGATGACTACGTGTCATCGTGAGTATATGAAT-CTTGTACCGATTATAAGATCTGATGAC
1 AGGTCAGATGACTACGTGTCATCGTGAGTATATGAATCCTT-TACGGATTATAAGGTCCGATGAC
* *
48226 TACGTATCATCGTGAGTATATGAATCCTTTACGGATTACGAGGTCCAATGACTATGTGTCATCGT
65 TACGTGTCATCGTGAGTATATGAATCCTTTACGGATTACGAGGTCCAATGACTACGTGTCATCGT
*
48291 GAGTATATGAATCTTTTACGGATTACG
130 GAGTATATGAATCTTTTACGGATTATG
** *
48318 AGGTTTGAT-ACTACGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCCGATGACT
1 AGGTCAGATGACTACGTGTCATCGTGAGTATATGAATCCTTTACGGATTATAAGGTCCGATGACT
* *
48382 ACGTGTCATCGTGAGTATATGAATCCTTTACGGATTACAAGGTCCAATGACTACGTGTCATTGTG
66 ACGTGTCATCGTGAGTATATGAATCCTTTACGGATTACGAGGTCCAATGACTACGTGTCATCGTG
48447 AGTATATGAATCTTTTACGGATTATG
131 AGTATATGAATCTTTTACGGATTATG
* *
48473 AGGTCCGATGACTACGTGTCATCGTGAGTATATGAATCTTTTACGGATTATAAGGTCCGATGACT
1 AGGTCAGATGACTACGTGTCATCGTGAGTATATGAATCCTTTACGGATTATAAGGTCCGATGACT
* * * *
48538 ACGTGTCATCGTGAGTGTATGATTCCTTTACGGATTATGAGGTCCGATGACTACGTGTCATCGTG
66 ACGTGTCATCGTGAGTATATGAATCCTTTACGGATTACGAGGTCCAATGACTACGTGTCATCGTG
*
48603 AGTATATGAATC-TTTACGGATTATA
131 AGTATATGAATCTTTTACGGATTATG
** * **
48628 AGGTCAGATGACTACGTGTCATCGTGAGTGGATGATTCCTTTACGGAACA-AGAGGTCCGATGAC
1 AGGTCAGATGACTACGTGTCATCGTGAGTATATGAATCCTTTACGGATTATA-AGGTCCGATGAC
*
48692 TATGTGTCATCGTGAGTAT
65 TACGTGTCATCGTGAGTAT
48711 TAAATATGCA
Statistics
Matches: 359, Mismatches: 31, Indels: 7
0.90 0.08 0.02
Matches are distributed among these distances:
154 1 0.00
155 224 0.62
156 134 0.37
ACGTcount: A:0.26, C:0.16, G:0.24, T:0.33
Consensus pattern (156 bp):
AGGTCAGATGACTACGTGTCATCGTGAGTATATGAATCCTTTACGGATTATAAGGTCCGATGACT
ACGTGTCATCGTGAGTATATGAATCCTTTACGGATTACGAGGTCCAATGACTACGTGTCATCGTG
AGTATATGAATCTTTTACGGATTATG
Found at i:48517 original size:207 final size:207
Alignment explanation
Indices: 48162--48710 Score: 850
Period size: 207 Copynumber: 2.6 Consensus size: 207
48152 TAAATGAGAA
* * **
48162 AGGTCCGATGACTACGTGTCATCGTGAGTATATGAATCTTGTACCGATTATAAGATCTGATGACT
1 AGGTCCGATGACTACGTGTCATCGTGAGTATATGAATCTT-TACGGATTATAAGGTCCAATGACT
* * *
48227 ACGTATCATCGTGAGTATATGAATCCTTTACGGATTACGAGGTCCAATGACTATGTGTCATCGTG
65 ACGTGTCATCGTGAGTATATGAATCCTTTACGGATTAAGAGGTCCGATGACTATGTGTCATCGTG
* **
48292 AGTATATGAATCTTTTACGGATTACGAGGTTTGAT-ACTACGTGTCATCGTGAGTATATGAATCC
130 AGTATATGAATCTTTTACGGATTACAAGGTCCGATGACTACGTGTCATCGTGAGTATATGAATCC
48356 TTTACGGATTATG
195 TTTACGGATTATG
*
48369 AGGTCCGATGACTACGTGTCATCGTGAGTATATGAATCCTTTACGGATTACAAGGTCCAATGACT
1 AGGTCCGATGACTACGTGTCATCGTGAGTATATGAAT-CTTTACGGATTATAAGGTCCAATGACT
* * * *
48434 ACGTGTCATTGTGAGTATATGAATCTTTTACGGATTATGAGGTCCGATGACTACGTGTCATCGTG
65 ACGTGTCATCGTGAGTATATGAATCCTTTACGGATTAAGAGGTCCGATGACTATGTGTCATCGTG
* * *
48499 AGTATATGAATCTTTTACGGATTATAAGGTCCGATGACTACGTGTCATCGTGAGTGTATGATTCC
130 AGTATATGAATCTTTTACGGATTACAAGGTCCGATGACTACGTGTCATCGTGAGTATATGAATCC
48564 TTTACGGATTATG
195 TTTACGGATTATG
48577 AGGTCCGATGACTACGTGTCATCGTGAGTATATGAATCTTTACGGATTATAAGGT-CAGATGACT
1 AGGTCCGATGACTACGTGTCATCGTGAGTATATGAATCTTTACGGATTATAAGGTCCA-ATGACT
** * **
48641 ACGTGTCATCGTGAGTGGATGATTCCTTTACGGAACAAGAGGTCCGATGACTATGTGTCATCGTG
65 ACGTGTCATCGTGAGTATATGAATCCTTTACGGATTAAGAGGTCCGATGACTATGTGTCATCGTG
48706 AGTAT
130 AGTAT
48711 TAAATATGCA
Statistics
Matches: 312, Mismatches: 27, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
206 2 0.01
207 230 0.74
208 80 0.26
ACGTcount: A:0.26, C:0.16, G:0.24, T:0.33
Consensus pattern (207 bp):
AGGTCCGATGACTACGTGTCATCGTGAGTATATGAATCTTTACGGATTATAAGGTCCAATGACTA
CGTGTCATCGTGAGTATATGAATCCTTTACGGATTAAGAGGTCCGATGACTATGTGTCATCGTGA
GTATATGAATCTTTTACGGATTACAAGGTCCGATGACTACGTGTCATCGTGAGTATATGAATCCT
TTACGGATTATG
Found at i:49662 original size:14 final size:14
Alignment explanation
Indices: 49630--49668 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
49620 TGATTGAATG
*
49630 AGATGAA-AATAAA
1 AGATGAATAGTAAA
*
49643 AGATGAATAGTAAT
1 AGATGAATAGTAAA
49657 AGATGAATAGTA
1 AGATGAATAGTA
49669 GGACACCGGG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 7 0.30
14 16 0.70
ACGTcount: A:0.56, C:0.00, G:0.21, T:0.23
Consensus pattern (14 bp):
AGATGAATAGTAAA
Found at i:55874 original size:16 final size:16
Alignment explanation
Indices: 55853--55883 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
55843 TATCATAATT
*
55853 TTTTTTTCTTTTTTCA
1 TTTTTTCCTTTTTTCA
55869 TTTTTTCCTTTTTTC
1 TTTTTTCCTTTTTTC
55884 TCAATTTTCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.81
Consensus pattern (16 bp):
TTTTTTCCTTTTTTCA
Found at i:56572 original size:14 final size:13
Alignment explanation
Indices: 56549--56579 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
56539 ACTGAGTGCT
56549 AAAAAATAAAATA
1 AAAAAATAAAATA
56562 AAAATAATAAAATA
1 AAAA-AATAAAATA
56576 AAAA
1 AAAA
56580 CTAACTCAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.24
14 13 0.76
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (13 bp):
AAAAAATAAAATA
Found at i:56742 original size:21 final size:21
Alignment explanation
Indices: 56718--56757 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
56708 TTTTATATGG
56718 AATT-TTGAATTAAAGATTTTT
1 AATTATTGAATTAAA-ATTTTT
56739 AATTATTGAATTAAAATTT
1 AATTATTGAATTAAAATTT
56758 AGTATAAGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.50
Consensus pattern (21 bp):
AATTATTGAATTAAAATTTTT
Found at i:59612 original size:21 final size:21
Alignment explanation
Indices: 59588--59639 Score: 104
Period size: 21 Copynumber: 2.5 Consensus size: 21
59578 GTTTTTAGTA
59588 TCGGTAGAAGCATGACATGTT
1 TCGGTAGAAGCATGACATGTT
59609 TCGGTAGAAGCATGACATGTT
1 TCGGTAGAAGCATGACATGTT
59630 TCGGTAGAAG
1 TCGGTAGAAG
59640 TCATACTTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.29, C:0.13, G:0.31, T:0.27
Consensus pattern (21 bp):
TCGGTAGAAGCATGACATGTT
Found at i:59657 original size:21 final size:21
Alignment explanation
Indices: 59585--59657 Score: 94
Period size: 21 Copynumber: 3.5 Consensus size: 21
59575 AGAGTTTTTA
59585 GTATCGGTAGAAGCATGACAT
1 GTATCGGTAGAAGCATGACAT
*
59606 GTTTCGGTAGAAGCATGACAT
1 GTATCGGTAGAAGCATGACAT
* *
59627 GTTTCGGTAGAAGTCAT-ACTT
1 GTATCGGTAGAAG-CATGACAT
*
59648 GTATCAGTAG
1 GTATCGGTAG
59658 TATTGTCTCA
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
21 44 0.94
22 3 0.06
ACGTcount: A:0.29, C:0.14, G:0.27, T:0.30
Consensus pattern (21 bp):
GTATCGGTAGAAGCATGACAT
Found at i:60639 original size:12 final size:12
Alignment explanation
Indices: 60622--60651 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
60612 GGGCATTGTA
60622 TTGCTTTTCCTC
1 TTGCTTTTCCTC
60634 TTGCTTTTCCTC
1 TTGCTTTTCCTC
60646 TTGCTT
1 TTGCTT
60652 CTTTGCAAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.00, C:0.30, G:0.10, T:0.60
Consensus pattern (12 bp):
TTGCTTTTCCTC
Found at i:67416 original size:17 final size:18
Alignment explanation
Indices: 67397--67431 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
67387 AAATAGCAAT
*
67397 AAACTTTTTCAAATAGTA
1 AAACTTATTCAAATAGTA
*
67415 AAAGTTATTCAAATAGT
1 AAACTTATTCAAATAGT
67432 TTACCTTAAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.46, C:0.09, G:0.09, T:0.37
Consensus pattern (18 bp):
AAACTTATTCAAATAGTA
Found at i:68276 original size:20 final size:21
Alignment explanation
Indices: 68242--68302 Score: 67
Period size: 19 Copynumber: 3.0 Consensus size: 21
68232 CTTTTTTAAA
68242 AAAAATTAAATTTTGTAATTTTT
1 AAAAATT--ATTTTGTAATTTTT
*
68265 ATAAA-TATTTTG-AA-TTTT
1 AAAAATTATTTTGTAATTTTT
68283 AAAAATTATTTT-TAATTTTT
1 AAAAATTATTTTGTAATTTTT
68303 TTTAATTTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
18 8 0.24
19 10 0.30
20 10 0.30
22 1 0.03
23 4 0.12
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (21 bp):
AAAAATTATTTTGTAATTTTT
Found at i:69647 original size:22 final size:22
Alignment explanation
Indices: 69619--69665 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
69609 CAATGATTTA
69619 AGAAAAAAACAAAATACATTGG
1 AGAAAAAAACAAAATACATTGG
69641 AGAAAAAAACAAAATACATTGG
1 AGAAAAAAACAAAATACATTGG
69663 AGA
1 AGA
69666 CTTGTAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.64, C:0.09, G:0.15, T:0.13
Consensus pattern (22 bp):
AGAAAAAAACAAAATACATTGG
Found at i:71359 original size:24 final size:22
Alignment explanation
Indices: 71332--71376 Score: 72
Period size: 24 Copynumber: 2.0 Consensus size: 22
71322 ATTTAACTCT
71332 TTAAAATAATAAAGATATATATTA
1 TTAAAATAATAAA-AT-TATATTA
71356 TTAAAATAATAAAATTATATT
1 TTAAAATAATAAAATTATATT
71377 TGTACTATCG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 6 0.29
23 2 0.10
24 13 0.62
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (22 bp):
TTAAAATAATAAAATTATATTA
Found at i:72802 original size:21 final size:22
Alignment explanation
Indices: 72776--72818 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
72766 ACTTTATTCA
72776 AAACCCAATT-TAAATAAAAAT
1 AAACCCAATTCTAAATAAAAAT
* *
72797 AAACCCATTTCTAATTAAAAAT
1 AAACCCAATTCTAAATAAAAAT
72819 TTAATATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.56, C:0.16, G:0.00, T:0.28
Consensus pattern (22 bp):
AAACCCAATTCTAAATAAAAAT
Found at i:73271 original size:11 final size:11
Alignment explanation
Indices: 73257--73282 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
73247 TATTACATAA
73257 TAATTAATGTT
1 TAATTAATGTT
73268 TAATTAATGTT
1 TAATTAATGTT
73279 TAAT
1 TAAT
73283 CATTTGTGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (11 bp):
TAATTAATGTT
Done.