Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2554
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: 63803
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:7609 original size:157 final size:158
Alignment explanation
Indices: 7443--7804 Score: 681
Period size: 158 Copynumber: 2.3 Consensus size: 158
7433 GAGATAATAA
* *
7443 CGGGGTTGGAGTGTTCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGGTTGTGAGAAATCGATGA
1 CGGGGTTGGAGTATCCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGGTTGTGAGAAATCGATGA
*
7508 TTAG-AAAAAAAATCGGGATTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCAATTA
66 TTAGAAAAAAAAATCGGGATTGGAGTATCCCCTCAAAAATAACGGGGTTGGAGTATCCCCAATTA
7572 TGAGAAATCAATATTTTGGGAATAAAGC
131 TGAGAAATCAATATTTTGGGAATAAAGC
*
7600 CGGGGTTGGAGTATCCCCTCGGAAGTAACGGGGTTTGAGTATCCCCGGTTGTGAGAAATCGATGA
1 CGGGGTTGGAGTATCCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGGTTGTGAGAAATCGATGA
7665 TTAGAAAAAAAAATCGGGATTGGAGTATCCCCTCAAAAATAACGGGGTTGGAGTATCCCCAATTA
66 TTAGAAAAAAAAATCGGGATTGGAGTATCCCCTCAAAAATAACGGGGTTGGAGTATCCCCAATTA
7730 TGAGAAATCAATATTTTGGGAATAAAGC
131 TGAGAAATCAATATTTTGGGAATAAAGC
7758 CGGGGTTGGAGTATCCCCTCGGAAGTAACGGGGTTGGAGTATCCCCG
1 CGGGGTTGGAGTATCCCCTCGGAAGTAACGGGGTTGGAGTATCCCCG
7805 ATAAAATAAC
Statistics
Matches: 199, Mismatches: 5, Indels: 1
0.97 0.02 0.00
Matches are distributed among these distances:
157 66 0.33
158 133 0.67
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.24
Consensus pattern (158 bp):
CGGGGTTGGAGTATCCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGGTTGTGAGAAATCGATGA
TTAGAAAAAAAAATCGGGATTGGAGTATCCCCTCAAAAATAACGGGGTTGGAGTATCCCCAATTA
TGAGAAATCAATATTTTGGGAATAAAGC
Found at i:7640 original size:79 final size:79
Alignment explanation
Indices: 7443--7803 Score: 422
Period size: 79 Copynumber: 4.6 Consensus size: 79
7433 GAGATAATAA
* * ** * *
7443 CGGGGTTGGAGTGTTCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGGTTGTGAGAAATCGATGA
1 CGGGGTTGGAGTATCCCCTCGGAAGTAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATGA
* *
7508 -TTAGAAAAAAAAT
66 TTTGGAAAAAAAAC
* * *
7521 CGGGATTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAAT-A
1 CGGGGTTGGAGTATCCCCTCGGAAGTAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATGA
* * *
7585 TTTTGGGAATAAAGC
66 -TTTGGAAAAAAAAC
* ** * *
7600 CGGGGTTGGAGTATCCCCTCGGAAGTAACGGGGTTTGAGTATCCCCGGTTGTGAGAAATCGATGA
1 CGGGGTTGGAGTATCCCCTCGGAAGTAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATGA
* * *
7665 TTAGAAAAAAAAAT
66 TTTGGAAAAAAAAC
* ** *
7679 CGGGATTGGAGTATCCCCTCAAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAAT-A
1 CGGGGTTGGAGTATCCCCTCGGAAGTAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATGA
* * *
7743 TTTTGGGAATAAAGC
66 -TTTGGAAAAAAAAC
7758 CGGGGTTGGAGTATCCCCTCGGAAGTAACGGGGTTGGAGTATCCCC
1 CGGGGTTGGAGTATCCCCTCGGAAGTAACGGGGTTGGAGTATCCCC
7804 GATAAAATAA
Statistics
Matches: 232, Mismatches: 47, Indels: 7
0.81 0.16 0.02
Matches are distributed among these distances:
77 1 0.00
78 55 0.24
79 175 0.75
80 1 0.00
ACGTcount: A:0.30, C:0.17, G:0.29, T:0.24
Consensus pattern (79 bp):
CGGGGTTGGAGTATCCCCTCGGAAGTAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATGA
TTTGGAAAAAAAAC
Found at i:7715 original size:28 final size:29
Alignment explanation
Indices: 7670--7724 Score: 85
Period size: 28 Copynumber: 1.9 Consensus size: 29
7660 GATGATTAGA
7670 AAAAAAAATCGGGATTGGAGTATCCCCTC
1 AAAAAAAATCGGGATTGGAGTATCCCCTC
* *
7699 AAAAATAA-CGGGGTTGGAGTATCCCC
1 AAAAAAAATCGGGATTGGAGTATCCCC
7725 AATTATGAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 17 0.71
29 7 0.29
ACGTcount: A:0.36, C:0.20, G:0.24, T:0.20
Consensus pattern (29 bp):
AAAAAAAATCGGGATTGGAGTATCCCCTC
Found at i:7812 original size:107 final size:108
Alignment explanation
Indices: 7679--7883 Score: 261
Period size: 107 Copynumber: 1.9 Consensus size: 108
7669 AAAAAAAAAT
* *
7679 CGGGATTGGAGTATCCCCTCAAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATA-
1 CGGGATTGGAGTATCCCCTCAAAAATAACGAGGTTGGAGTATCCCCAATTATGAAAAATCAATAT
* * *
7743 TTTTGGGAATAAAGCCGGGGTTGGAGTATCCCCTCGGAAGTAA
66 TTTTGGAAATAAAACCGGAGTTGGAGTATCCCCTCGGAAGTAA
* * * * * ***
7786 CGGGGTTGGAGTATCCCC-GATAAAATAACGAGGTTGGAGTATCCTCGATTGTGAAAAATTGGTA
1 CGGGATTGGAGTATCCCCTCA-AAAATAACGAGGTTGGAGTATCCCCAATTATGAAAAATCAATA
*
7850 TTTTTGGAAATAAAATCGGAGTTGGAGTATCCCC
65 TTTTTGGAAATAAAACCGGAGTTGGAGTATCCCC
7884 GATTAAAGGT
Statistics
Matches: 82, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
106 1 0.01
107 52 0.63
108 29 0.35
ACGTcount: A:0.30, C:0.16, G:0.27, T:0.26
Consensus pattern (108 bp):
CGGGATTGGAGTATCCCCTCAAAAATAACGAGGTTGGAGTATCCCCAATTATGAAAAATCAATAT
TTTTGGAAATAAAACCGGAGTTGGAGTATCCCCTCGGAAGTAA
Found at i:7814 original size:28 final size:28
Alignment explanation
Indices: 7758--7834 Score: 91
Period size: 28 Copynumber: 2.8 Consensus size: 28
7748 GGAATAAAGC
**** *
7758 CGGGGTTGGAGTATCCCCTCGGAAGTAA
1 CGGGGTTGGAGTATCCCCGATAAAATAA
7786 CGGGGTTGGAGTATCCCCGATAAAATAA
1 CGGGGTTGGAGTATCCCCGATAAAATAA
* *
7814 CGAGGTTGGAGTATCCTCGAT
1 CGGGGTTGGAGTATCCCCGAT
7835 TGTGAAAAAT
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 42 1.00
ACGTcount: A:0.25, C:0.19, G:0.32, T:0.23
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATAAAATAA
Found at i:7938 original size:51 final size:52
Alignment explanation
Indices: 7817--7991 Score: 173
Period size: 52 Copynumber: 3.4 Consensus size: 52
7807 AAAATAACGA
* * * *
7817 GGTTGGAGTATCCTCGATT---GTGAAAAATTGGTATTTTTGGAAATAAAATCG
1 GGTTGGAGTATCCCCGATTAAAG-GAAAAATTGGT-GTTTTGAAAATAAAACCG
*
7868 GAGTTGGAGTATCCCCGATTAAAGG-TAAATTGGTGTTTTGAAAATAAAACCG
1 G-GTTGGAGTATCCCCGATTAAAGGAAAAATTGGTGTTTTGAAAATAAAACCG
** * * *
7920 GGTTGGAGTATCCCCGATT-GTGGAAAAATTAGTGTTTT-AGCAATAAAATCGG
1 GGTTGGAGTATCCCCGATTAAAGGAAAAATTGGTGTTTTGA-AAATAAAA-CCG
7972 GGTTGGAGTATCCCCGATTA
1 GGTTGGAGTATCCCCGATTA
7992 CGAAAAATCA
Statistics
Matches: 105, Mismatches: 11, Indels: 14
0.81 0.08 0.11
Matches are distributed among these distances:
50 3 0.03
51 38 0.36
52 54 0.51
53 8 0.08
54 1 0.01
55 1 0.01
ACGTcount: A:0.31, C:0.11, G:0.26, T:0.31
Consensus pattern (52 bp):
GGTTGGAGTATCCCCGATTAAAGGAAAAATTGGTGTTTTGAAAATAAAACCG
Found at i:8018 original size:262 final size:265
Alignment explanation
Indices: 7707--8208 Score: 773
Period size: 262 Copynumber: 1.9 Consensus size: 265
7697 TCAAAAATAA
* * *
7707 CGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGGGAATAAAGCCGGGGTTGGAGTAT
1 CGGGGTTGGAGTATCCCCAATTACGAAAAATCAATATTTTGGAAATAAAGCCGGGGTTGGAGTAT
** * *
7772 CCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGATAAAATAAC-GAGGTTGGAGTATCCTCGATT
66 CCCCTCAAAAATAACGGGGTTGGAGTATCCCCGAT-AAATAACTG-GGTTGGAGTATCCCCGATT
*
7836 GTGAA-AAATT-G-G-TATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGGTAAA
129 GTGAAGAAATTGGTGTTATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAA-GAAAA
* * *
7897 TTGGTGTTTTGAAAATAAAACCGG-GTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGC
193 TTAGTGTTTTGAAAATAAAACCGGAGTTGGAATATCCCAGATTGTGGAAAAATTAGTGTTTTAGC
7961 AATAAAAT
258 AATAAAAT
* *
7969 CGGGGTTGGAGTATCCCCGATTACGAAAAATCAATATTTTGGAAATAAAGTCGGGGTTGGAGTAT
1 CGGGGTTGGAGTATCCCCAATTACGAAAAATCAATATTTTGGAAATAAAGCCGGGGTTGGAGTAT
* *
8034 CCCCTCAAAAATAACGGGGTTGGAGTATCCCCGATGATTAACTGGGTTGGAGTATCCCCGATTGT
66 CCCCTCAAAAATAACGGGGTTGGAGTATCCCCGATAAATAACTGGGTTGGAGTATCCCCGATTGT
* *
8099 GAAGAAATTGGTGTTTTTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTATAGAAAATTA
131 GAAGAAATTGGTGTTATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGAAAATTA
*
8164 GTGTTTTGAAAATAAAATCGGAGTTGGAATATCCCAGATTGTGGA
196 GTGTTTTGAAAATAAAACCGGAGTTGGAATATCCCAGATTGTGGA
8209 GAATTGGGAA
Statistics
Matches: 216, Mismatches: 18, Indels: 9
0.89 0.07 0.04
Matches are distributed among these distances:
261 28 0.13
262 98 0.45
263 1 0.00
264 27 0.12
265 62 0.29
ACGTcount: A:0.31, C:0.13, G:0.26, T:0.29
Consensus pattern (265 bp):
CGGGGTTGGAGTATCCCCAATTACGAAAAATCAATATTTTGGAAATAAAGCCGGGGTTGGAGTAT
CCCCTCAAAAATAACGGGGTTGGAGTATCCCCGATAAATAACTGGGTTGGAGTATCCCCGATTGT
GAAGAAATTGGTGTTATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGAAAATTA
GTGTTTTGAAAATAAAACCGGAGTTGGAATATCCCAGATTGTGGAAAAATTAGTGTTTTAGCAAT
AAAAT
Found at i:8026 original size:103 final size:103
Alignment explanation
Indices: 7817--8037 Score: 266
Period size: 103 Copynumber: 2.1 Consensus size: 103
7807 AAAATAACGA
* * * *
7817 GGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAGTATCC
1 GGTTGGAGTATCCCCGATTGTGAAAAATTAGTAGTTTTAGAAATAAAATCGGAGTTGGAGTATCC
** *** *
7882 CCGATTAAAGGTAAATTGGTGTTTTGAAAATAAAACCG
66 CCGATTAAAGAAAAATCAATATTTTGAAAATAAAACCG
* *
7920 GGTTGGAGTATCCCCGATTGTGGAAAAATTAGT-GTTTTAGCAATAAAATCGGGGTTGGAGTATC
1 GGTTGGAGTATCCCCGATTGT-GAAAAATTAGTAGTTTTAGAAATAAAATCGGAGTTGGAGTATC
* * * *
7984 CCCGATT-ACGAAAAATCAATATTTTGGAAATAAAGTCGG
65 CCCGATTAAAGAAAAATCAATATTTTGAAAATAAA-ACCG
8023 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
8038 TCAAAAATAA
Statistics
Matches: 100, Mismatches: 16, Indels: 4
0.83 0.13 0.03
Matches are distributed among these distances:
102 19 0.19
103 71 0.71
104 10 0.10
ACGTcount: A:0.32, C:0.12, G:0.26, T:0.30
Consensus pattern (103 bp):
GGTTGGAGTATCCCCGATTGTGAAAAATTAGTAGTTTTAGAAATAAAATCGGAGTTGGAGTATCC
CCGATTAAAGAAAAATCAATATTTTGAAAATAAAACCG
Found at i:8083 original size:27 final size:27
Alignment explanation
Indices: 8020--8095 Score: 98
Period size: 27 Copynumber: 2.8 Consensus size: 27
8010 GAAATAAAGT
* *
8020 CGGGGTTGGAGTATCCCCTCAAAAATAA
1 CGGGGTTGGAGTATCCCC-GATAAATAA
* *
8048 CGGGGTTGGAGTATCCCCGATGATTAA
1 CGGGGTTGGAGTATCCCCGATAAATAA
*
8075 CTGGGTTGGAGTATCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
8096 TGTGAAGAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
27 25 0.58
28 18 0.42
ACGTcount: A:0.24, C:0.21, G:0.30, T:0.25
Consensus pattern (27 bp):
CGGGGTTGGAGTATCCCCGATAAATAA
Found at i:8185 original size:51 final size:52
Alignment explanation
Indices: 7818--8203 Score: 229
Period size: 51 Copynumber: 7.3 Consensus size: 52
7808 AAATAACGAG
* * * * *
7818 GTTGGAGTATCCTCGATTGT-GAAAAATTGGTATTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATAGAAAAATTAGT-GTTTTGAAAATAAAATCGGA
* ** * *
7870 GTTGGAGTATCCCCGATTAAAGGTAAATTGGTGTTTTGAAAATAAAACCGG-
1 GTTGGAGTATCCCCGATTATAGAAAAATTAGTGTTTTGAAAATAAAATCGGA
* * * *
7921 GTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTT-AGCAATAAAATCGGG
1 GTTGGAGTATCCCCGATTATAGAAAAATTAGTGTTTTGA-AAATAAAATCGGA
* * * * * * *
7973 GTTGGAGTATCCCCGATTA-CGAAAAATCAATATTTTGGAAATAAAGTCGGG
1 GTTGGAGTATCCCCGATTATAGAAAAATTAGTGTTTTGAAAATAAAATCGGA
* * *** ** * *
8024 GTTGGAGTATCCCC--TCA-A-AAATAACGGGGTTGGAGTATCCCCGATGATTAACT-GG-
1 GTTGGAGTATCCCCGATTATAGAAA-AA-----TT--AGTGT-TTTGAAAATAAAATCGGA
* * *
8079 GTTGGAGTATCCCCGATTGT-GAAGAAATTGGTGTTTTTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATAGAA-AAATTAGTG----TTTTGAAAATAAAATCGGA
8135 GTTGGAGTATCCCCGATTATAG-AAAATTAGTGTTTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATAGAAAAATTAGTGTTTTGAAAATAAAATCGGA
* *
8186 GTTGGAATATCCCAGATT
1 GTTGGAGTATCCCCGATT
8204 GTGGAGAATT
Statistics
Matches: 256, Mismatches: 53, Indels: 51
0.71 0.15 0.14
Matches are distributed among these distances:
48 3 0.01
49 4 0.02
50 1 0.00
51 115 0.45
52 51 0.20
53 11 0.04
54 7 0.03
55 25 0.10
56 26 0.10
57 8 0.03
58 4 0.02
59 1 0.00
ACGTcount: A:0.32, C:0.12, G:0.25, T:0.31
Consensus pattern (52 bp):
GTTGGAGTATCCCCGATTATAGAAAAATTAGTGTTTTGAAAATAAAATCGGA
Found at i:10772 original size:13 final size:13
Alignment explanation
Indices: 10754--10779 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
10744 ACATTGATCC
10754 ATGTATCGATACA
1 ATGTATCGATACA
10767 ATGTATCGATACA
1 ATGTATCGATACA
10780 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:10843 original size:19 final size:18
Alignment explanation
Indices: 10819--10886 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
10809 CAGTAGCTAA
10819 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
10838 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
10853 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
10870 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
10887 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:10859 original size:13 final size:13
Alignment explanation
Indices: 10841--10865 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
10831 ACAATACTTA
10841 TGTATCGATACAT
1 TGTATCGATACAT
10854 TGTATCGATACA
1 TGTATCGATACA
10866 AAACTTATGT
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:10863 original size:32 final size:32
Alignment explanation
Indices: 10822--10884 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
10812 TAGCTAATTA
*
10822 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
10854 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
10885 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:10948 original size:21 final size:21
Alignment explanation
Indices: 10922--11040 Score: 177
Period size: 21 Copynumber: 5.7 Consensus size: 21
10912 GTTGGGACCC
* *
10922 TGTATCGATACATTTGTA-GAA
1 TGTATCGATACA-TTCTACAAA
*
10943 TGTATCGATACATTCCACAAA
1 TGTATCGATACATTCTACAAA
*
10964 TGTATCGATATATTCTACAAA
1 TGTATCGATACATTCTACAAA
*
10985 TGTATCGATACATTCCACAAA
1 TGTATCGATACATTCTACAAA
11006 TGTATCGATACATTCTACAAA
1 TGTATCGATACATTCTACAAA
11027 TGTATCGATACATT
1 TGTATCGATACATT
11041 TAAAATTTTT
Statistics
Matches: 89, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
20 3 0.03
21 86 0.97
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.34
Consensus pattern (21 bp):
TGTATCGATACATTCTACAAA
Found at i:10987 original size:42 final size:42
Alignment explanation
Indices: 10922--11040 Score: 195
Period size: 42 Copynumber: 2.8 Consensus size: 42
10912 GTTGGGACCC
* *
10922 TGTATCGATACATTTGTA-GAATGTATCGATACATTCCACAAA
1 TGTATCGATACA-TTCTACAAATGTATCGATACATTCCACAAA
*
10964 TGTATCGATATATTCTACAAATGTATCGATACATTCCACAAA
1 TGTATCGATACATTCTACAAATGTATCGATACATTCCACAAA
11006 TGTATCGATACATTCTACAAATGTATCGATACATT
1 TGTATCGATACATTCTACAAATGTATCGATACATT
11041 TAAAATTTTT
Statistics
Matches: 72, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
41 4 0.06
42 68 0.94
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.34
Consensus pattern (42 bp):
TGTATCGATACATTCTACAAATGTATCGATACATTCCACAAA
Found at i:27865 original size:52 final size:52
Alignment explanation
Indices: 27782--27930 Score: 237
Period size: 52 Copynumber: 2.9 Consensus size: 52
27772 CGAAATATGA
*
27782 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATATCATAGTGTATCGATACATCTGGGC
*
27834 AAATTTGCCTGTATGTATCGATACATATCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATATCATAGTGTATCGATACATCTGGGC
* * *
27886 AAATTTGCATGCATGTATCGATACACA-GATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATATCAT-AGTGTATCGATACA
27931 AAGATCAGTG
Statistics
Matches: 90, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
51 2 0.02
52 88 0.98
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATATCATAGTGTATCGATACATCTGGGC
Found at i:27924 original size:20 final size:20
Alignment explanation
Indices: 27899--27970 Score: 135
Period size: 20 Copynumber: 3.6 Consensus size: 20
27889 TTTGCATGCA
*
27899 TGTATCGATACACAGATCAG
1 TGTATCGATACAAAGATCAG
27919 TGTATCGATACAAAGATCAG
1 TGTATCGATACAAAGATCAG
27939 TGTATCGATACAAAGATCAG
1 TGTATCGATACAAAGATCAG
27959 TGTATCGATACA
1 TGTATCGATACA
27971 TTTAAGTAAT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 51 1.00
ACGTcount: A:0.38, C:0.17, G:0.19, T:0.26
Consensus pattern (20 bp):
TGTATCGATACAAAGATCAG
Found at i:28047 original size:19 final size:18
Alignment explanation
Indices: 28023--28085 Score: 64
Period size: 19 Copynumber: 3.7 Consensus size: 18
28013 AGCGATACGT
28023 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
28042 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
*
28055 TGTATTGATACAACACTTA
1 TGTATCGATACAA-ACTTA
28074 TGTATCGATACA
1 TGTATCGATACA
28086 TTGTATCGAT
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
13 10 0.28
14 1 0.03
16 2 0.06
18 1 0.03
19 22 0.61
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:28058 original size:32 final size:32
Alignment explanation
Indices: 28015--28096 Score: 137
Period size: 32 Copynumber: 2.6 Consensus size: 32
28005 AGCTTCGTAG
*
28015 CGATACGTTGTATCGATACAAAACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
* *
28047 CGATACATTGTATTGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
28079 CGATACATTGTATCGATA
1 CGATACATTGTATCGATA
28097 TAAATCGTTG
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 46 1.00
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Consensus pattern (32 bp):
CGATACATTGTATCGATACAAAACTTATGTAT
Found at i:28971 original size:49 final size:49
Alignment explanation
Indices: 28803--29660 Score: 813
Period size: 49 Copynumber: 17.8 Consensus size: 49
28793 AAAAGGATGT
* * * * * * *
28803 CAATATGCTGATTCACGGTCAGCAACATTTAGACTTGAAGATGAGAAGAATGC
1 CAATATGCTGATTCAAGGCCAGCGATA-TTGGACTTAAAGAT--GAAG-GTGC
* * * ** *
28856 CAATGTGCTGATTCAAGGCCAACGACATTGGGTTTTAAAGATGATGAAGGCGC
1 CAATATGCTGATTCAAGGCCAGCGATATT-GGACTT-AA-A-GATGAAGGTGC
* * * *
28909 CAATATGCAGATTCAAGGCCAGCAATACTGGTCTTAAAGATGAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGC
* * **
28958 CAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGACAAAGGCAC
1 CAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG---AAGGTGC
*
29010 CAATATGCTGATTCAAGGCCAGCGATATTGGAATTAAAGATGAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGC
* *
29059 CAATATACTGATTCAAGGCCAGCGATATTGGACTTAAAGATAAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGC
29108 CAATATGCTGATTCAAGGCCAGCGATATTGGACTT----A--AAGGTGC
1 CAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGC
* * * *
29151 CAATGTGCTGATTCAAGGCCAGCGACATTAGACTTAAAGATGACGAAGGCGC
1 CAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGAT---GAAGGTGC
*
29203 CAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATGACAAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG---AAGGTGC
*
29255 CAATATGCTGATTCAAGGCTAGCGATATTGGACTT----A--AAGGTGC
1 CAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGC
* * * * * **
29298 CAATGTGTTGATTCAAGGCCAGCGACATTGGTCTGAAAGACAAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGC
*
29347 CAATATGCTGATTCAAGGCCAGCGATATTAGACTT----A--AAGGTGC
1 CAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGC
* * * **
29390 CAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGC
29439 CAATATGCTGATTCAAGGCCAGCGATATTGGACTT----A--AAGGTGC
1 CAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGC
* * * * ** *
29482 CAATGTGTTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAATGTGC
1 CAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGC
* *
29531 CAATATGCTAATTCAAGGCCAGCTATATTGGACTT----A--AAGGTGC
1 CAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGC
* * * * * **
29574 CAATGTGTTGATTCAAGGCCAGCAACATTGGTCTTAAAGACAAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGC
*
29623 CAATATGCTGATTCAAGGCCAGCGATATTGGGCTTAAA
1 CAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAA
29661 AGAAAACGCC
Statistics
Matches: 673, Mismatches: 89, Indels: 90
0.79 0.10 0.11
Matches are distributed among these distances:
43 186 0.28
45 4 0.01
47 5 0.01
48 1 0.00
49 282 0.42
50 1 0.00
51 2 0.00
52 133 0.20
53 50 0.07
54 5 0.01
55 1 0.00
56 3 0.00
ACGTcount: A:0.33, C:0.18, G:0.25, T:0.24
Consensus pattern (49 bp):
CAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGC
Found at i:29371 original size:92 final size:92
Alignment explanation
Indices: 29196--29660 Score: 768
Period size: 92 Copynumber: 5.0 Consensus size: 92
29186 AAAGATGACG
* * * * * *
29196 AAGGCGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATGACAAAGGTGCCAATAT
1 AAGGTGCCAATGTGTTGATTCAAGGCCAGCGACATTGGTCTT-AA-A-GACAAAGGTGCCAATAT
*
29261 GCTGATTCAAGGCTAGCGATATTGGACTTA
63 GCTGATTCAAGGCCAGCGATATTGGACTTA
*
29291 AAGGTGCCAATGTGTTGATTCAAGGCCAGCGACATTGGTCTGAAAGACAAAGGTGCCAATATGCT
1 AAGGTGCCAATGTGTTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAAGGTGCCAATATGCT
*
29356 GATTCAAGGCCAGCGATATTAGACTTA
66 GATTCAAGGCCAGCGATATTGGACTTA
*
29383 AAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAAGGTGCCAATATGCT
1 AAGGTGCCAATGTGTTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAAGGTGCCAATATGCT
29448 GATTCAAGGCCAGCGATATTGGACTTA
66 GATTCAAGGCCAGCGATATTGGACTTA
*
29475 AAGGTGCCAATGTGTTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAATGTGCCAATATGCT
1 AAGGTGCCAATGTGTTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAAGGTGCCAATATGCT
* *
29540 AATTCAAGGCCAGCTATATTGGACTTA
66 GATTCAAGGCCAGCGATATTGGACTTA
*
29567 AAGGTGCCAATGTGTTGATTCAAGGCCAGCAACATTGGTCTTAAAGACAAAGGTGCCAATATGCT
1 AAGGTGCCAATGTGTTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAAGGTGCCAATATGCT
*
29632 GATTCAAGGCCAGCGATATTGGGCTTA
66 GATTCAAGGCCAGCGATATTGGACTTA
29659 AA
1 AA
29661 AGAAAACGCC
Statistics
Matches: 349, Mismatches: 21, Indels: 3
0.94 0.06 0.01
Matches are distributed among these distances:
92 311 0.89
93 1 0.00
94 2 0.01
95 35 0.10
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.25
Consensus pattern (92 bp):
AAGGTGCCAATGTGTTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAAGGTGCCAATATGCT
GATTCAAGGCCAGCGATATTGGACTTA
Found at i:29457 original size:184 final size:184
Alignment explanation
Indices: 28918--29660 Score: 877
Period size: 184 Copynumber: 3.9 Consensus size: 184
28908 CCAATATGCA
* * * ** *
28918 GATTCAAGGCCAGCAATACTGGTCTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCGA
1 GATTCAAGGCCAGCGACATTGGTCTTAAAGACAAAGGTGCCAATATGCTGATTCAAGGCCAGCGA
* * * * *
28983 CATTGGACTTAAAGATGACAAAGGCACCAATATGCTGATTCAAGGCCAGCGATATTGGAATTAAA
66 CATTAGACTTAAAG--G-----TG--CCAATATGCTGATTCAAGGCCAGCAACATTGGACTTAAA
** * *
29048 GATGAAGGTGCCAATATACTGATTCAAGGCCAGCGATATTGGACTTAAAGATAAAGGTGCCAATA
122 GACAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC-T-----TAAAGGTGCCAATG
*
29113 TGCT
181 TGTT
* * *
29117 GATTCAAGGCCAGCGATATTGGACTT------AAAGGTGCCAATGTGCTGATTCAAGGCCAGCGA
1 GATTCAAGGCCAGCGACATTGGTCTTAAAGACAAAGGTGCCAATATGCTGATTCAAGGCCAGCGA
* *
29176 CATTAGACTTAAAGATGACGAAGGCGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAA
66 CATTAGAC-T-----T-A--AAGGTGCCAATATGCTGATTCAAGGCCAGCAACATTGGACTT-AA
*
29241 GATGACAAAGGTGCCAATATGCTGATTCAAGGCTAGCGATATTGGACTTAAAGGTGCCAATGTGT
121 -A-GACAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGT
29306 T
184 T
*
29307 GATTCAAGGCCAGCGACATTGGTCTGAAAGACAAAGGTGCCAATATGCTGATTCAAGGCCAGCGA
1 GATTCAAGGCCAGCGACATTGGTCTTAAAGACAAAGGTGCCAATATGCTGATTCAAGGCCAGCGA
* * * *
29372 TATTAGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAAGGT
66 CATTAGACTTAAAGGTGCCAATATGCTGATTCAAGGCCAGCAACATTGGACTTAAAGACAAAGGT
29437 GCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGTT
131 GCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGTT
* * *
29491 GATTCAAGGCCAGCGACATTGGTCTTAAAGACAAATGTGCCAATATGCTAATTCAAGGCCAGCTA
1 GATTCAAGGCCAGCGACATTGGTCTTAAAGACAAAGGTGCCAATATGCTGATTCAAGGCCAGCGA
* * * * *
29556 TATTGGACTTAAAGGTGCCAATGTGTTGATTCAAGGCCAGCAACATTGGTCTTAAAGACAAAGGT
66 CATTAGACTTAAAGGTGCCAATATGCTGATTCAAGGCCAGCAACATTGGACTTAAAGACAAAGGT
*
29621 GCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTTAAA
131 GCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAA
29661 AGAAAACGCC
Statistics
Matches: 493, Mismatches: 33, Indels: 51
0.85 0.06 0.09
Matches are distributed among these distances:
184 224 0.45
185 1 0.00
186 2 0.00
187 37 0.08
189 1 0.00
190 40 0.08
193 73 0.15
194 3 0.01
195 4 0.01
196 79 0.16
199 24 0.05
200 2 0.00
202 3 0.01
ACGTcount: A:0.33, C:0.18, G:0.25, T:0.24
Consensus pattern (184 bp):
GATTCAAGGCCAGCGACATTGGTCTTAAAGACAAAGGTGCCAATATGCTGATTCAAGGCCAGCGA
CATTAGACTTAAAGGTGCCAATATGCTGATTCAAGGCCAGCAACATTGGACTTAAAGACAAAGGT
GCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGTT
Found at i:29767 original size:27 final size:27
Alignment explanation
Indices: 29729--29784 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 27
29719 TAAAAAGGAG
* *
29729 AAAGATGCCACGGAGTTGTGGACTTAA
1 AAAGATGCCACGAAATTGTGGACTTAA
*
29756 AAAGGTGCCACGAAATTGTGGACTTAA
1 AAAGATGCCACGAAATTGTGGACTTAA
29783 AA
1 AA
29785 GGGAAAAAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.38, C:0.14, G:0.27, T:0.21
Consensus pattern (27 bp):
AAAGATGCCACGAAATTGTGGACTTAA
Found at i:29800 original size:35 final size:33
Alignment explanation
Indices: 29754--29901 Score: 133
Period size: 35 Copynumber: 4.4 Consensus size: 33
29744 TTGTGGACTT
*
29754 AAAAAGGTGCCACGAAATTGTGGAC-TTAAAAGGG
1 AAAAAGGTGCCACGAAATTGTGGGCTTTAAAA--G
* *
29788 AAAAAGAGTGCCA-TAGAGTTGTGGGCTTTAAAAAG
1 AAAAAG-GTGCCACGA-AATTGTGGGCTTT-AAAAG
*
29823 AAAAAGGGTGCCACGGAATTGTGGGCTTTGAAAAG
1 AAAAA-GGTGCCACGAAATTGTGGGCTTT-AAAAG
* * *
29858 AAAAAGGTGCCACGGAGTTGTGGGCTTT-GAAG
1 AAAAAGGTGCCACGAAATTGTGGGCTTTAAAAG
*
29890 -AAAAGATGCCAC
1 AAAAAGGTGCCAC
29902 TGAGTCGTGG
Statistics
Matches: 98, Mismatches: 10, Indels: 15
0.80 0.08 0.12
Matches are distributed among these distances:
31 11 0.11
32 3 0.03
34 29 0.30
35 48 0.49
36 3 0.03
37 4 0.04
ACGTcount: A:0.37, C:0.12, G:0.31, T:0.20
Consensus pattern (33 bp):
AAAAAGGTGCCACGAAATTGTGGGCTTTAAAAG
Found at i:29843 original size:70 final size:68
Alignment explanation
Indices: 29754--29923 Score: 181
Period size: 69 Copynumber: 2.5 Consensus size: 68
29744 TTGTGGACTT
*
29754 AAAAAGGTGCCACGAAATTGTGGAC-TT-AAAAGGGAAAAAGAGTGCCATAGAGTTGTGGGCTTT
1 AAAAAGGTGCCACGAAATTGTGGACTTTGAAAA--GAAAAAG-GTGCCACAGAGTTGTGGGCTTT
29817 AAAAAG
63 AAAAAG
* * *
29823 AAAAAGGGTGCCACGGAATTGTGGGCTTTGAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTT--
1 AAAAA-GGTGCCACGAAATTGTGGACTTTGAAAAGAAAAAGGTGCCACAGAGTTGTGGGCTTTAA
*
29886 GAAG
65 AAAG
* * *
29890 -AAAAGATGCCACTG-AGTCGTGGACTTTGAAAAGA
1 AAAAAGGTGCCAC-GAAATTGTGGACTTTGAAAAGA
29924 GATTGCCACT
Statistics
Matches: 88, Mismatches: 9, Indels: 12
0.81 0.08 0.11
Matches are distributed among these distances:
65 24 0.27
66 5 0.06
67 3 0.03
69 25 0.28
70 25 0.28
71 2 0.02
72 4 0.05
ACGTcount: A:0.36, C:0.12, G:0.31, T:0.21
Consensus pattern (68 bp):
AAAAAGGTGCCACGAAATTGTGGACTTTGAAAAGAAAAAGGTGCCACAGAGTTGTGGGCTTTAAA
AAG
Found at i:29900 original size:31 final size:31
Alignment explanation
Indices: 29729--30046 Score: 206
Period size: 31 Copynumber: 10.0 Consensus size: 31
29719 TAAAAAGGAG
*
29729 AAAGATGCCACGGAGTTGTGGAC-TT--A-A
1 AAAGATGCCACTGAGTTGTGGACTTTGAAGA
* * **
29756 AAAGGTGCCAC-GAAATTGTGGACTTAAAAGGGAA
1 AAAGATGCCACTG-AGTTGTGGACTTTGAA--G-A
* *
29790 AAAGAGTGCCA-TAGAGTTGTGGGCTTTAAAAAGAA
1 AAAGA-TGCCACT-GAGTTGTGGACTTT--GAAG-A
* * * *
29825 AAAGGGTGCCACGGAATTGTGGGCTTTGAAAAGAA
1 AAA-GATGCCACTGAGTTGTGGACTTTG--AAG-A
* * *
29860 AAAGGTGCCACGGAGTTGTGGGCTTTGAAGA
1 AAAGATGCCACTGAGTTGTGGACTTTGAAGA
*
29891 AAAGATGCCACTGAGTCGTGGACTTTGAA-A
1 AAAGATGCCACTGAGTTGTGGACTTTGAAGA
* *
29921 AGAGATTGCCACTGAGTTGTGGACTTTGGAGA
1 AAAGA-TGCCACTGAGTTGTGGACTTTGAAGA
* * *
29953 AAAAATGCCACTGAGTCGTGGACTTTG-GGA
1 AAAGATGCCACTGAGTTGTGGACTTTGAAGA
* *
29983 AGAGATGCCACTGAGTCGTGGACTTTG-AGA
1 AAAGATGCCACTGAGTTGTGGACTTTGAAGA
*
30013 AGAGAGATTGCCACTGAGTCGTGGACTTT-AAGA
1 A-A-AGA-TGCCACTGAGTTGTGGACTTTGAAGA
30046 A
1 A
30047 GGTATTTGAA
Statistics
Matches: 241, Mismatches: 27, Indels: 40
0.78 0.09 0.13
Matches are distributed among these distances:
26 1 0.00
27 19 0.08
28 1 0.00
30 36 0.15
31 69 0.29
32 10 0.04
33 25 0.10
34 28 0.12
35 47 0.20
36 2 0.01
37 3 0.01
ACGTcount: A:0.32, C:0.14, G:0.31, T:0.23
Consensus pattern (31 bp):
AAAGATGCCACTGAGTTGTGGACTTTGAAGA
Found at i:29948 original size:62 final size:60
Alignment explanation
Indices: 29857--30041 Score: 246
Period size: 62 Copynumber: 3.0 Consensus size: 60
29847 GCTTTGAAAA
* * *
29857 GAAAA-AGGTGCCACGGAGTTGTGGGCTTTGAAGAAAAGATGCCACTGAGTCGTGGACTTT
1 GAAAAGAGATGCCACTGAGTTGTGGACTTTG-AGAAAAGATGCCACTGAGTCGTGGACTTT
*
29917 GAAAAGAGATTGCCACTGAGTTGTGGACTTTGGAGAAAAAATGCCACTGAGTCGTGGACTTT
1 GAAAAGAGA-TGCCACTGAGTTGTGGACTTT-GAGAAAAGATGCCACTGAGTCGTGGACTTT
** *
29979 GGGAAGAGATGCCACTGAGTCGTGGACTTTGAGAAGAGAGATTGCCACTGAGTCGTGGACTTT
1 GAAAAGAGATGCCACTGAGTTGTGGACTTTGAGAA-A-AGA-TGCCACTGAGTCGTGGACTTT
30042 AAGAAGGTAT
Statistics
Matches: 111, Mismatches: 8, Indels: 9
0.87 0.06 0.07
Matches are distributed among these distances:
60 10 0.09
61 23 0.21
62 56 0.50
63 22 0.20
ACGTcount: A:0.28, C:0.15, G:0.32, T:0.24
Consensus pattern (60 bp):
GAAAAGAGATGCCACTGAGTTGTGGACTTTGAGAAAAGATGCCACTGAGTCGTGGACTTT
Found at i:30001 original size:92 final size:96
Alignment explanation
Indices: 29856--30041 Score: 281
Period size: 94 Copynumber: 2.0 Consensus size: 96
29846 GGCTTTGAAA
* * *
29856 AGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAGAAAAGATGCCACTGAGTCGTGGACTTTGA-A
1 AGAAAAAGATGCCACGGAGTCGTGGACTTTGAAGAAAAGATGCCACTGAGTCGTGGACTTTGAGA
*
29920 A-AGAGATTGCCACTGAGTTGTGGACTTTGG
66 AGAGAGATTGCCACTGAGTCGTGGACTTTGG
* * *
29950 AGAAAAA-ATGCCACTGAGTCGTGGACTTTG-GGAAGAGATGCCACTGAGTCGTGGACTTTGAGA
1 AGAAAAAGATGCCACGGAGTCGTGGACTTTGAAGAAAAGATGCCACTGAGTCGTGGACTTTGAGA
30013 AGAGAGATTGCCACTGAGTCGTGGACTTT
66 AGAGAGATTGCCACTGAGTCGTGGACTTT
30042 AAGAAGGTAT
Statistics
Matches: 83, Mismatches: 7, Indels: 4
0.88 0.07 0.04
Matches are distributed among these distances:
92 29 0.35
93 21 0.25
94 33 0.40
ACGTcount: A:0.28, C:0.15, G:0.32, T:0.24
Consensus pattern (96 bp):
AGAAAAAGATGCCACGGAGTCGTGGACTTTGAAGAAAAGATGCCACTGAGTCGTGGACTTTGAGA
AGAGAGATTGCCACTGAGTCGTGGACTTTGG
Found at i:31306 original size:14 final size:14
Alignment explanation
Indices: 31268--31306 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
31258 CCTTTGCATT
*
31268 TTTTTTGTG-TGTG
1 TTTTTTGTGTTTTG
*
31281 TTTTTTTTGTTTTG
1 TTTTTTGTGTTTTG
31295 TTTTTTGTGTTT
1 TTTTTTGTGTTT
31307 ACTTTTGACT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
13 8 0.36
14 14 0.64
ACGTcount: A:0.00, C:0.00, G:0.21, T:0.79
Consensus pattern (14 bp):
TTTTTTGTGTTTTG
Found at i:31312 original size:14 final size:13
Alignment explanation
Indices: 31268--31306 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
31258 CCTTTGCATT
*
31268 TTTTTTGTGTGTG
1 TTTTTTGTGTTTG
*
31281 TTTTTTTTGTTTTG
1 TTTTTTGTG-TTTG
31295 TTTTTTGTGTTT
1 TTTTTTGTGTTT
31307 ACTTTTGACT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
13 11 0.50
14 11 0.50
ACGTcount: A:0.00, C:0.00, G:0.21, T:0.79
Consensus pattern (13 bp):
TTTTTTGTGTTTG
Found at i:38348 original size:52 final size:51
Alignment explanation
Indices: 38210--38357 Score: 206
Period size: 52 Copynumber: 2.9 Consensus size: 51
38200 CGAAATATGA
38210 AAATTTGCCTGCATGTATCGATACATTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTCATAGTGTATCGATACATCTGGGC
* * *
38261 AAATTTGCCTGTATGTATCAATACATTTCATAGTGTATCAATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TTCATAGTGTATCGATACATCTGGGC
* * ***
38313 AAATTTGCCTACATGTATTGATACAAAGATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTCAT-AGTGTATCGATACA
38358 ATGTATCGAT
Statistics
Matches: 84, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
51 25 0.30
52 59 0.70
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.34
Consensus pattern (51 bp):
AAATTTGCCTGCATGTATCGATACATTCATAGTGTATCGATACATCTGGGC
Found at i:38364 original size:13 final size:13
Alignment explanation
Indices: 38346--38370 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
38336 CAAAGATCAG
38346 TGTATCGATACAA
1 TGTATCGATACAA
38359 TGTATCGATACA
1 TGTATCGATACA
38371 TTTGAATAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:38433 original size:13 final size:13
Alignment explanation
Indices: 38415--38466 Score: 50
Period size: 13 Copynumber: 3.5 Consensus size: 13
38405 AGCTTCGTAG
38415 CGATACATTGTAT
1 CGATACATTGTAT
38428 CGATACAAAACTTATGTAT
1 CGATAC---A-TT--GTAT
38447 CGATACATTGTAT
1 CGATACATTGTAT
38460 CGATACA
1 CGATACA
38467 ACACTTATGT
Statistics
Matches: 33, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
13 17 0.52
15 2 0.06
16 2 0.06
17 2 0.06
19 10 0.30
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (13 bp):
CGATACATTGTAT
Found at i:38447 original size:19 final size:18
Alignment explanation
Indices: 38423--38485 Score: 73
Period size: 19 Copynumber: 3.7 Consensus size: 18
38413 AGCGATACAT
38423 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
38442 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
38455 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
38474 TGTATCGATACA
1 TGTATCGATACA
38486 TTATATCGAT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 11 0.29
14 1 0.03
16 2 0.05
18 1 0.03
19 23 0.61
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:38456 original size:32 final size:32
Alignment explanation
Indices: 38415--38496 Score: 146
Period size: 32 Copynumber: 2.6 Consensus size: 32
38405 AGCTTCGTAG
38415 CGATACATTGTATCGATACAAAACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
*
38447 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
*
38479 CGATACATTATATCGATA
1 CGATACATTGTATCGATA
38497 TAAATCGTTG
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 48 1.00
ACGTcount: A:0.37, C:0.17, G:0.12, T:0.34
Consensus pattern (32 bp):
CGATACATTGTATCGATACAAAACTTATGTAT
Found at i:42077 original size:22 final size:22
Alignment explanation
Indices: 42052--42093 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
42042 TTTTTTAAGA
42052 TTTGACAAAGGGGGAGAAATGC
1 TTTGACAAAGGGGGAGAAATGC
*
42074 TTTGATAAAGGGGGAGAAAT
1 TTTGACAAAGGGGGAGAAAT
42094 ATGTTTATCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.38, C:0.05, G:0.36, T:0.21
Consensus pattern (22 bp):
TTTGACAAAGGGGGAGAAATGC
Found at i:42705 original size:13 final size:13
Alignment explanation
Indices: 42687--42713 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
42677 ACATTATGCT
42687 TTGTATCGATACA
1 TTGTATCGATACA
42700 TTGTATCGATACA
1 TTGTATCGATACA
42713 T
1 T
42714 GGACAATTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:42789 original size:20 final size:20
Alignment explanation
Indices: 42764--42834 Score: 84
Period size: 20 Copynumber: 3.9 Consensus size: 20
42754 TACCATTGTT
42764 TGTATCGATACATGGTATAA
1 TGTATCGATACATGGTATAA
42784 TGTATCGATAC-----AT--
1 TGTATCGATACATGGTATAA
42797 TGTATCGATACATGGTATAA
1 TGTATCGATACATGGTATAA
*
42817 TGTATCGATACATTGTAT
1 TGTATCGATACATGGTAT
42835 CGATACATGA
Statistics
Matches: 43, Mismatches: 1, Indels: 14
0.74 0.02 0.24
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
18 2 0.05
20 28 0.65
ACGTcount: A:0.32, C:0.11, G:0.18, T:0.38
Consensus pattern (20 bp):
TGTATCGATACATGGTATAA
Found at i:42800 original size:13 final size:13
Alignment explanation
Indices: 42784--42864 Score: 69
Period size: 13 Copynumber: 7.2 Consensus size: 13
42774 CATGGTATAA
42784 TGTATCGATACAT
1 TGTATCGATACAT
42797 TGTATCGATACA-
1 TGTATCGATACAT
*
42809 TG-GT--ATA-A-
1 TGTATCGATACAT
42817 TGTATCGATACAT
1 TGTATCGATACAT
42830 TGTATCGATACA-
1 TGTATCGATACAT
42842 TG-AT-G--A-AT
1 TGTATCGATACAT
42850 TGTATCGATACAT
1 TGTATCGATACAT
42863 TG
1 TG
42865 CTTGTAACGG
Statistics
Matches: 55, Mismatches: 2, Indels: 22
0.70 0.03 0.28
Matches are distributed among these distances:
7 1 0.02
8 6 0.11
9 6 0.11
10 2 0.04
11 6 0.11
12 6 0.11
13 28 0.51
ACGTcount: A:0.32, C:0.12, G:0.19, T:0.37
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:42803 original size:33 final size:33
Alignment explanation
Indices: 42763--42864 Score: 172
Period size: 33 Copynumber: 3.1 Consensus size: 33
42753 CTACCATTGT
42763 TTGTATCGATACATGGTATAATGTATCGATACA
1 TTGTATCGATACATGGTATAATGTATCGATACA
42796 TTGTATCGATACATGGTATAATGTATCGATACA
1 TTGTATCGATACATGGTATAATGTATCGATACA
42829 TTGTATCGATACAT-G-ATGAATTGTATCGATACA
1 TTGTATCGATACATGGTAT-AA-TGTATCGATACA
42862 TTG
1 TTG
42865 CTTGTAACGG
Statistics
Matches: 67, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
31 2 0.03
32 3 0.04
33 62 0.93
ACGTcount: A:0.32, C:0.12, G:0.19, T:0.37
Consensus pattern (33 bp):
TTGTATCGATACATGGTATAATGTATCGATACA
Found at i:43955 original size:17 final size:17
Alignment explanation
Indices: 43933--43967 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
43923 TGATTACAAA
43933 TGGAAAAAATTATCACT
1 TGGAAAAAATTATCACT
43950 TGGAAAAAATTATCACT
1 TGGAAAAAATTATCACT
43967 T
1 T
43968 TTAAGATACC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.31
Consensus pattern (17 bp):
TGGAAAAAATTATCACT
Found at i:45974 original size:51 final size:52
Alignment explanation
Indices: 45898--46024 Score: 175
Period size: 52 Copynumber: 2.5 Consensus size: 52
45888 ATATATCAAT
* * * *
45898 ACATTTTTCATCGTATCGATACATTCTGGGTTTTTGA-CCAAATGTATCGAA
1 ACATTATTCATTGTATCGATACATTCTGGATTTTCGACCCAAATGTATCGAA
*
45949 ACATTATTCATTGTATCGATACATTCTGGATTTTCGACCCAAATGTATCGAT
1 ACATTATTCATTGTATCGATACATTCTGGATTTTCGACCCAAATGTATCGAA
* * *
46001 ACATTCTTCAATGTATCAATACAT
1 ACATTATTCATTGTATCGATACAT
46025 CCAGTTAAAT
Statistics
Matches: 67, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
51 33 0.49
52 34 0.51
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.39
Consensus pattern (52 bp):
ACATTATTCATTGTATCGATACATTCTGGATTTTCGACCCAAATGTATCGAA
Found at i:46016 original size:52 final size:51
Alignment explanation
Indices: 45886--46024 Score: 172
Period size: 51 Copynumber: 2.7 Consensus size: 51
45876 TATGAAAAGA
* * * * *
45886 AAATATATCAATACATTTTTC-ATCGTATCGATACATTCTGGGTTTTTGACC
1 AAATGTATCGATACATTATTCAAT-GTATCGATACATTCTGGATTTTCGACC
* *
45937 AAATGTATCGAAACATTATTCATTGTATCGATACATTCTGGATTTTCGACCC
1 AAATGTATCGATACATTATTCAATGTATCGATACATTCTGGATTTTCGA-CC
* *
45989 AAATGTATCGATACATTCTTCAATGTATCAATACAT
1 AAATGTATCGATACATTATTCAATGTATCGATACAT
46025 CCAGTTAAAT
Statistics
Matches: 75, Mismatches: 11, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
51 40 0.53
52 35 0.47
ACGTcount: A:0.32, C:0.18, G:0.12, T:0.38
Consensus pattern (51 bp):
AAATGTATCGATACATTATTCAATGTATCGATACATTCTGGATTTTCGACC
Found at i:49878 original size:20 final size:18
Alignment explanation
Indices: 49839--49874 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
49829 AAATTATTTG
49839 AAAAATTAATTTTATATA
1 AAAAATTAATTTTATATA
49857 AAAAATTAATTTTATATA
1 AAAAATTAATTTTATATA
49875 TAAATATAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
AAAAATTAATTTTATATA
Found at i:49927 original size:19 final size:19
Alignment explanation
Indices: 49896--49935 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
49886 TTCAATAAAT
*
49896 AAATAATAAAATATATTAA
1 AAATAATAAAATATAATAA
49915 AAAT-ATAATAATATAATAA
1 AAATAATAA-AATATAATAA
49934 AA
1 AA
49936 TTTTACTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (19 bp):
AAATAATAAAATATAATAA
Found at i:50113 original size:16 final size:16
Alignment explanation
Indices: 50070--50113 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
50060 ACTCGAACTT
*
50070 GAACTTGAAAAAGCCC
1 GAACTTGAAAAGGCCC
* *
50086 AAACTCGAAAAGGCCC
1 GAACTTGAAAAGGCCC
50102 GAACTTGAAAAG
1 GAACTTGAAAAG
50114 TCGGAACCTG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.45, C:0.23, G:0.20, T:0.11
Consensus pattern (16 bp):
GAACTTGAAAAGGCCC
Found at i:50179 original size:16 final size:16
Alignment explanation
Indices: 50160--50221 Score: 88
Period size: 16 Copynumber: 3.9 Consensus size: 16
50150 AACTCGAACA
* *
50160 AGCCTAAACCTGAATG
1 AGCCCAAACCCGAATG
*
50176 AGCCCAAACCCGAACG
1 AGCCCAAACCCGAATG
*
50192 AGCTCAAACCCGAATG
1 AGCCCAAACCCGAATG
50208 AGCCCAAACCCGAA
1 AGCCCAAACCCGAA
50222 CCTGCCTAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 40 1.00
ACGTcount: A:0.39, C:0.35, G:0.18, T:0.08
Consensus pattern (16 bp):
AGCCCAAACCCGAATG
Found at i:50233 original size:32 final size:32
Alignment explanation
Indices: 50144--50233 Score: 110
Period size: 32 Copynumber: 2.8 Consensus size: 32
50134 AACCCAAAAA
* * * *
50144 AGCCTAAACTCGAACAAGCCTAAACCTGAATG
1 AGCCCAAACCCGAACCAGCCTAAACCCGAATG
*
50176 AGCCCAAACCCGAACGAG-CTCAAACCCGAATG
1 AGCCCAAACCCGAACCAGCCT-AAACCCGAATG
*
50208 AGCCCAAACCCGAACCTGCCTAAACC
1 AGCCCAAACCCGAACCAGCCTAAACC
50234 TGCCCAATTG
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
31 2 0.04
32 46 0.92
33 2 0.04
ACGTcount: A:0.38, C:0.37, G:0.16, T:0.10
Consensus pattern (32 bp):
AGCCCAAACCCGAACCAGCCTAAACCCGAATG
Found at i:51682 original size:21 final size:21
Alignment explanation
Indices: 51656--51729 Score: 87
Period size: 21 Copynumber: 3.5 Consensus size: 21
51646 TTAATGATGC
*
51656 ATTGATACATTAGCCTAATGT
1 ATTGATATATTAGCCTAATGT
* * *
51677 TTTGATATATTA-CTTTGATGT
1 ATTGATATATTAGC-CTAATGT
*
51698 ATTAATATATTAGCCTAATGT
1 ATTGATATATTAGCCTAATGT
51719 ATTGATATATT
1 ATTGATATATT
51730 CTATGAAGTA
Statistics
Matches: 42, Mismatches: 9, Indels: 4
0.76 0.16 0.07
Matches are distributed among these distances:
20 1 0.02
21 40 0.95
22 1 0.02
ACGTcount: A:0.32, C:0.08, G:0.12, T:0.47
Consensus pattern (21 bp):
ATTGATATATTAGCCTAATGT
Found at i:51710 original size:42 final size:42
Alignment explanation
Indices: 51650--51729 Score: 124
Period size: 42 Copynumber: 1.9 Consensus size: 42
51640 ATATATTTAA
* *
51650 TGATGCATTGATACATTAGCCTAATGTTTTGATATATTACTT
1 TGATGCATTAATACATTAGCCTAATGTATTGATATATTACTT
* *
51692 TGATGTATTAATATATTAGCCTAATGTATTGATATATT
1 TGATGCATTAATACATTAGCCTAATGTATTGATATATT
51730 CTATGAAGTA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.31, C:0.09, G:0.14, T:0.46
Consensus pattern (42 bp):
TGATGCATTAATACATTAGCCTAATGTATTGATATATTACTT
Found at i:59820 original size:32 final size:28
Alignment explanation
Indices: 59783--59845 Score: 81
Period size: 28 Copynumber: 2.1 Consensus size: 28
59773 TATCCAAGAT
59783 TTTAACTTAAAAGTCCATTAAATATATTAACA
1 TTTAACTTAAAA-T-CA--AAATATATTAACA
*
59815 TTTAACTTGAAATCAAAATATATTAACA
1 TTTAACTTAAAATCAAAATATATTAACA
59843 TTT
1 TTT
59846 TTTATGTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
28 16 0.53
30 2 0.07
31 1 0.03
32 11 0.37
ACGTcount: A:0.46, C:0.11, G:0.03, T:0.40
Consensus pattern (28 bp):
TTTAACTTAAAATCAAAATATATTAACA
Found at i:62907 original size:3 final size:3
Alignment explanation
Indices: 62901--62939 Score: 60
Period size: 3 Copynumber: 12.3 Consensus size: 3
62891 GAGAAGAAAA
62901 AGG AGG AGG AGG AGG AGG AGG AGGG AGG AGGG AGG AGG A
1 AGG AGG AGG AGG AGG AGG AGG A-GG AGG A-GG AGG AGG A
62940 AAGGCTCTGA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
3 28 0.82
4 6 0.18
ACGTcount: A:0.33, C:0.00, G:0.67, T:0.00
Consensus pattern (3 bp):
AGG
Done.