Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2648
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: 154102
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Found at i:4011 original size:40 final size:40
Alignment explanation
Indices: 3915--4178 Score: 302
Period size: 40 Copynumber: 6.7 Consensus size: 40
3905 TTGAATGCTG
* * * * *
3915 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTATTAAA
* * * *
3955 TCC-GGATAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTATTAAA
*
3994 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAA
*
4034 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAA
* * *
4074 TCCGGGTTAAGTCCCGAAGGCAGTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAA
* * *
4114 TCCGGGTTATGTCCCGAAGGCA-TTGTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAA
* * *
4153 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCATTTG
4179 AACGAGGAGC
Statistics
Matches: 199, Mismatches: 20, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
39 57 0.29
40 142 0.71
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAA
Found at i:4196 original size:79 final size:80
Alignment explanation
Indices: 3967--4211 Score: 235
Period size: 80 Copynumber: 3.1 Consensus size: 80
3957 CGGATAAGAT
* * * * * * ** * *
3967 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTA-TT
1 CCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCAGTCGAACGAG-GAGCT
4031 AAATCCGGGTTAAGTC
65 AAATCCGGGTTAAGTC
* * * ** ** *
4047 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCAGTCGTGCGAGTTGTTA
1 CCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCAGTCGAACGAGGAGCTA
*
4112 AATCCGGGTTATGTC
66 AATCCGGGTTAAGTC
* * * *
4127 CCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTTGAACGAGGAGCTA
1 CCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCAGTCGAACGAGGAGCTA
* *
4191 TATCC-GGTTAAATC
66 AATCCGGGTTAAGTC
4205 CCGAAGG
1 CCGAAGG
4212 TACGTGATTT
Statistics
Matches: 142, Mismatches: 22, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
78 14 0.10
79 46 0.32
80 82 0.58
ACGTcount: A:0.25, C:0.21, G:0.29, T:0.25
Consensus pattern (80 bp):
CCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCAGTCGAACGAGGAGCTA
AATCCGGGTTAAGTC
Found at i:9704 original size:28 final size:27
Alignment explanation
Indices: 9647--9798 Score: 241
Period size: 27 Copynumber: 5.6 Consensus size: 27
9637 TAAATTGTGC
*
9647 AGCACTAAGTGTGCGAATTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
9674 AGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAG-TTGACTATGT
9702 AGCACTAAGTGTGCGAGTTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
*
9729 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAG-TTGACTATGT
* *
9757 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAGTTGACTATGT
*
9784 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
9799 GACTAAATAT
Statistics
Matches: 119, Mismatches: 4, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
27 66 0.55
28 53 0.45
ACGTcount: A:0.26, C:0.14, G:0.29, T:0.31
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGTTGACTATGT
Found at i:9711 original size:55 final size:55
Alignment explanation
Indices: 9647--9798 Score: 259
Period size: 55 Copynumber: 2.8 Consensus size: 55
9637 TAAATTGTGC
*
9647 AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
*
9702 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
* * *
9757 AGCACTAAGTGTGCGAGTTGATTATATAGCACTGAGTGTGCG
1 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCG
9799 GACTAAATAT
Statistics
Matches: 92, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 92 1.00
ACGTcount: A:0.26, C:0.14, G:0.29, T:0.31
Consensus pattern (55 bp):
AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
Found at i:15885 original size:48 final size:47
Alignment explanation
Indices: 15776--16174 Score: 278
Period size: 48 Copynumber: 8.4 Consensus size: 47
15766 TATGTGTGCT
* * * * *
15776 AGTGTAAGACATGTCTGGCACATGCATCAGCCAC-A-TTATGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATAT-AAAGCC
*
15822 AGTGTAAGACATGTCTGGGACATGCAACGGCCTCGAGATATACAAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATATA-AAGCC
*
15870 AGTGTAAGACATGTCTGGGACATGCAAT-GGCCTCAAGATATACAAGCC
1 AGTGTAAGACATGTCTGGGACATGC-ATCGGCCTCGAGATATA-AAGCC
** * * ** * *
15918 AGTGTAAGACATGTCTGGGACATGTGTCGGCATTGAGA-CGAGAGCT
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATATAAAGCC
* *
15964 AGTGTAAGACATGTCTGGGACATGCATCAGCCTCGAGATATATAAGCT
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATATA-AAGCC
* * * * * * *
16012 GGTGTAAGACCTGTCTGGGACATGACGTCAG-CTTGTTG-TGT---GCC
1 AGTGTAAGACATGTCTGGGACATG-CATCGGCCTCG-AGATATAAAGCC
* * * * *
16056 AGTGTAAGACCTGTCTGGGACATGGCATCGACAC-CGATAGATGAGAGCC
1 AGTGTAAGACATGTCTGGGACAT-GCATCGGC-CTCGAGATAT-AAAGCC
* * * * * * *
16105 ATTGTAAGACCTGTCTGGGACACGACATCAGCCTCGATATACGAAAGTC
1 AGTGTAAGACATGTCTGGGACATG-CATCGGCCTCGAGATA-TAAAGCC
* *
16154 AGTGTAAGACCTATCTGGGAC
1 AGTGTAAGACATGTCTGGGAC
16175 GTGGCATCAA
Statistics
Matches: 282, Mismatches: 51, Indels: 37
0.76 0.14 0.10
Matches are distributed among these distances:
44 27 0.10
45 3 0.01
46 67 0.24
47 5 0.02
48 115 0.41
49 65 0.23
ACGTcount: A:0.29, C:0.21, G:0.28, T:0.23
Consensus pattern (47 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATATAAAGCC
Found at i:15968 original size:94 final size:96
Alignment explanation
Indices: 15776--16035 Score: 289
Period size: 94 Copynumber: 2.8 Consensus size: 96
15766 TATGTGTGCT
* * * *
15776 AGTGTAAGACATGTCTGGCACATGCATCAGCCAC-A-TTATGA-GAGCCAGTGTAAGACATGTCT
1 AGTGTAAGACATGTCTGGGACATGCATCAGCCTCAAGATAT-ACAAGCCAGTGTAAGACATGTCT
* *
15838 GGGACATGCAACGGCCTCGAGATATACAAGCC
65 GGGACATGCAACGGCATCGAGATAGACAAGCC
*
15870 AGTGTAAGACATGTCTGGGACATGCAAT-GGCCTCAAGATATACAAGCCAGTGTAAGACATGTCT
1 AGTGTAAGACATGTCTGGGACATGC-ATCAGCCTCAAGATATACAAGCCAGTGTAAGACATGTCT
*** * * * *
15934 GGGACATGTGTCGGCATTGAGA-CGA-GAGCT
65 GGGACATGCAACGGCATCGAGATAGACAAGCC
* * ** *
15964 AGTGTAAGACATGTCTGGGACATGCATCAGCCTCGAGATATATAAGCTGGTGTAAGACCTGTCTG
1 AGTGTAAGACATGTCTGGGACATGCATCAGCCTCAAGATATACAAGCCAGTGTAAGACATGTCTG
16029 GGACATG
66 GGACATG
16036 ACGTCAGCTT
Statistics
Matches: 141, Mismatches: 20, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
93 2 0.01
94 94 0.67
95 5 0.04
96 40 0.28
ACGTcount: A:0.30, C:0.20, G:0.28, T:0.22
Consensus pattern (96 bp):
AGTGTAAGACATGTCTGGGACATGCATCAGCCTCAAGATATACAAGCCAGTGTAAGACATGTCTG
GGACATGCAACGGCATCGAGATAGACAAGCC
Found at i:16134 original size:142 final size:142
Alignment explanation
Indices: 15815--16228 Score: 346
Period size: 142 Copynumber: 2.9 Consensus size: 142
15805 GCCACATTAT
* * * * *
15815 GAGAGCCAGTGTAAGACATGTCTGGGACATGCAACGGCCTCGAGATA-TACAAGCCAGTGTAAGA
1 GAGAGCCAGTGTAAGACATGTCTGGGACACGCATCAGCCTCGAGATACGA-AAGTCAGTGTAAGA
* * * * * *** *
15879 CATGTCTGGGACATG-CA--ATGGCCTCAAGATATACAAGCCAGTGTAAGACATGTCTGGGACAT
65 CCTATCTGGGACATGACATCA-AG-CT--TGATGTGTTAGCCAGTGTAAGACCTGTCTGGGACAT
* **
15941 GTG--TCGGCATTGAGAC
126 G-GCATCGACACCGAGAC
* * * *
15957 GAGAGCTAGTGTAAGACATGTCTGGGACATGCATCAGCCTCGAGATA-TATAAG-CTGGTGTAAG
1 GAGAGCCAGTGTAAGACATGTCTGGGACACGCATCAGCCTCGAGATACGA-AAGTC-AGTGTAAG
* * *
16020 ACCTGTCTGGGACATGACGTC-AGCTTGTTGTG-T-GCCAGTGTAAGACCTGTCTGGGACATGGC
64 ACCTATCTGGGACATGACATCAAGCTTGATGTGTTAGCCAGTGTAAGACCTGTCTGGGACATGGC
*
16082 ATCGACACCGATAGAT
129 ATCGACACCG--AGAC
* * *
16098 GAGAGCCATTGTAAGACCTGTCTGGGACACGACATCAGCCTCGATATACGAAAGTCAGTGTAAGA
1 GAGAGCCAGTGTAAGACATGTCTGGGACACG-CATCAGCCTCGAGATACGAAAGTCAGTGTAAGA
* * ** *
16163 CCTATCTGGGACGTGGCATCAATTTTGATGTGTTAGCCAGTGTAAGACCACGTCTGGGACATGGC
65 CCTATCTGGGACATGACATCAAGCTTGATGTGTTAGCCAGTGTAAGACC-TGTCTGGGACATGGC
16228 A
129 A
16229 AGACCATGTC
Statistics
Matches: 224, Mismatches: 33, Indels: 26
0.79 0.12 0.09
Matches are distributed among these distances:
137 1 0.00
138 26 0.12
139 6 0.03
140 3 0.01
141 31 0.14
142 115 0.51
143 12 0.05
144 1 0.00
145 14 0.06
146 15 0.07
ACGTcount: A:0.28, C:0.21, G:0.29, T:0.23
Consensus pattern (142 bp):
GAGAGCCAGTGTAAGACATGTCTGGGACACGCATCAGCCTCGAGATACGAAAGTCAGTGTAAGAC
CTATCTGGGACATGACATCAAGCTTGATGTGTTAGCCAGTGTAAGACCTGTCTGGGACATGGCAT
CGACACCGAGAC
Found at i:16234 original size:22 final size:22
Alignment explanation
Indices: 16206--16249 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
16196 TAGCCAGTGT
16206 AAGACCACGTCTGGGACATGGC
1 AAGACCACGTCTGGGACATGGC
*
16228 AAGACCATGTCTGGGACATGGC
1 AAGACCACGTCTGGGACATGGC
16250 GTCGGCACCT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.27, C:0.25, G:0.32, T:0.16
Consensus pattern (22 bp):
AAGACCACGTCTGGGACATGGC
Found at i:24732 original size:55 final size:54
Alignment explanation
Indices: 24596--24791 Score: 182
Period size: 55 Copynumber: 3.6 Consensus size: 54
24586 TTCCTTTTTA
* * * * * * *
24596 AACTTACCATTTCCATGTCATGGCATGGTCTTACGTG-GTATCCTTGCCTTAT-G
1 AACTTACCAATGCCATGCCTTGACATGGTCTTACATGAG-ATCCTTGCCTTGTAG
* * * *
24649 AACTCACCATTGCCATGCCTTGGA-ATGGTCTTACATGGGATCTTTGCCTTGTAG
1 AACTTACCAATGCCATGCCTT-GACATGGTCTTACATGAGATCCTTGCCTTGTAG
** * **
24703 TAGTTTATCAATGCCATGCCTTGACATGGTCTTACATGATTTCCTTGCCTTGTAG
1 -AACTTACCAATGCCATGCCTTGACATGGTCTTACATGAGATCCTTGCCTTGTAG
* *
24758 AACTTACCGATGCCATGCCTTGGCATGGTCTTAC
1 AACTTACCAATGCCATGCCTTGACATGGTCTTAC
24792 TTGGTATCCT
Statistics
Matches: 116, Mismatches: 22, Indels: 9
0.79 0.15 0.06
Matches are distributed among these distances:
53 40 0.34
54 34 0.29
55 42 0.36
ACGTcount: A:0.20, C:0.24, G:0.20, T:0.36
Consensus pattern (54 bp):
AACTTACCAATGCCATGCCTTGACATGGTCTTACATGAGATCCTTGCCTTGTAG
Found at i:24802 original size:54 final size:53
Alignment explanation
Indices: 24596--24802 Score: 218
Period size: 53 Copynumber: 3.8 Consensus size: 53
24586 TTCCTTTTTA
* * * * *
24596 AACTTACCATTTCCATGTCATGGCATGGTCTTACGTGGTATCCTTGCCTTAT-G
1 AACTTACCA-TGCCATGCCTTGGCATGGTCTTACATGGTATCCTTGCCTTGTAG
* * * *
24649 AACTCACCATTGCCATGCCTTGGAATGGTCTTACATGGGATCTTTGCCTTGTAG
1 AACTTACCA-TGCCATGCCTTGGCATGGTCTTACATGGTATCCTTGCCTTGTAG
** * * * *
24703 TAGTTTATCAATGCCATGCCTTGACATGGTCTTACATGATTTCCTTGCCTTGTAG
1 -AACTTA-CCATGCCATGCCTTGGCATGGTCTTACATGGTATCCTTGCCTTGTAG
*
24758 AACTTACCGATGCCATGCCTTGGCATGGTCTTACTTGGTATCCTT
1 AACTTACC-ATGCCATGCCTTGGCATGGTCTTACATGGTATCCTT
24803 AAACCCTAAT
Statistics
Matches: 124, Mismatches: 26, Indels: 7
0.79 0.17 0.04
Matches are distributed among these distances:
53 44 0.35
54 37 0.30
55 41 0.33
56 2 0.02
ACGTcount: A:0.19, C:0.24, G:0.20, T:0.37
Consensus pattern (53 bp):
AACTTACCATGCCATGCCTTGGCATGGTCTTACATGGTATCCTTGCCTTGTAG
Found at i:26787 original size:10 final size:10
Alignment explanation
Indices: 26772--26805 Score: 68
Period size: 10 Copynumber: 3.4 Consensus size: 10
26762 TTTGACTGAA
26772 TATCCTCAAG
1 TATCCTCAAG
26782 TATCCTCAAG
1 TATCCTCAAG
26792 TATCCTCAAG
1 TATCCTCAAG
26802 TATC
1 TATC
26806 TGAATAACTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.32
Consensus pattern (10 bp):
TATCCTCAAG
Found at i:30465 original size:40 final size:40
Alignment explanation
Indices: 30410--30486 Score: 136
Period size: 40 Copynumber: 1.9 Consensus size: 40
30400 CGAAACTCTT
*
30410 TGGCCCCCTGTTTTCTAAATTTATCAACTGGTGGCTTCTA
1 TGGCCCCCTGTTTTCTAAATTTATCAACCGGTGGCTTCTA
*
30450 TGGCCCCCTGTTTTCTAATTTTATCAACCGGTGGCTT
1 TGGCCCCCTGTTTTCTAAATTTATCAACCGGTGGCTT
30487 TTATCTTCTG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.16, C:0.26, G:0.18, T:0.40
Consensus pattern (40 bp):
TGGCCCCCTGTTTTCTAAATTTATCAACCGGTGGCTTCTA
Found at i:37541 original size:23 final size:23
Alignment explanation
Indices: 37515--37569 Score: 92
Period size: 23 Copynumber: 2.4 Consensus size: 23
37505 CCAGGGACAC
*
37515 GGGCGTGTGCATTGCCTTTACAA
1 GGGCGTGTGCATTGCCTCTACAA
*
37538 GGGCGTGTGCATTGCCTCTACAC
1 GGGCGTGTGCATTGCCTCTACAA
37561 GGGCGTGTG
1 GGGCGTGTG
37570 AGGCTTAACT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.13, C:0.24, G:0.36, T:0.27
Consensus pattern (23 bp):
GGGCGTGTGCATTGCCTCTACAA
Found at i:50351 original size:31 final size:31
Alignment explanation
Indices: 50313--50376 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
50303 CCTTTTCATA
*
50313 TTTCATATTTCATAACACTGGGCCGAAGCCT
1 TTTCATATTTCATAACACTAGGCCGAAGCCT
**
50344 TTTCATATTTCATATTACTAGGCCGAAGCCT
1 TTTCATATTTCATAACACTAGGCCGAAGCCT
50375 TT
1 TT
50377 ACTGTAAATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.25, C:0.23, G:0.14, T:0.38
Consensus pattern (31 bp):
TTTCATATTTCATAACACTAGGCCGAAGCCT
Found at i:50724 original size:23 final size:23
Alignment explanation
Indices: 50591--50761 Score: 234
Period size: 25 Copynumber: 7.1 Consensus size: 23
50581 CCTAGCCTCT
* *
50591 TTTAGTAACTGGGGCAAAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
*
50614 TTTTTATAACTGGGGCATAAGCCC
1 -TTTAATAACTGGGGCATAAGCCC
*
50638 TTTATCGTAACTGGGGCATAAGCCC
1 TTTA--ATAACTGGGGCATAAGCCC
*
50663 TTCATCATAACTGGGGCATAAGCCC
1 TT--TAATAACTGGGGCATAAGCCC
50688 TTTATCATAACTGGGGCATAAGCCC
1 TTTA--ATAACTGGGGCATAAGCCC
50713 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
50736 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
50759 TTT
1 TTT
50762 TGCACTTCCT
Statistics
Matches: 133, Mismatches: 8, Indels: 13
0.86 0.05 0.08
Matches are distributed among these distances:
23 49 0.37
24 20 0.15
25 63 0.47
27 1 0.01
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.28
Consensus pattern (23 bp):
TTTAATAACTGGGGCATAAGCCC
Found at i:50836 original size:20 final size:20
Alignment explanation
Indices: 50808--50878 Score: 115
Period size: 20 Copynumber: 3.5 Consensus size: 20
50798 GCAATTATGA
* *
50808 ACATGTCATGTGTATATCAT
1 ACATATCATGTGCATATCAT
50828 ACATATCATGTGCATATCAT
1 ACATATCATGTGCATATCAT
*
50848 ACATGTCATGTGCATATCAT
1 ACATATCATGTGCATATCAT
50868 ACATATCATGT
1 ACATATCATGT
50879 TTATCAAAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.32, C:0.18, G:0.13, T:0.37
Consensus pattern (20 bp):
ACATATCATGTGCATATCAT
Found at i:52213 original size:26 final size:27
Alignment explanation
Indices: 52120--52203 Score: 116
Period size: 27 Copynumber: 3.1 Consensus size: 27
52110 GGGCATATTC
* *
52120 GTCATTTTACCATACAGGGG-TATTACG
1 GTCACTTTACCCTACAGGGGCT-TTACG
*
52147 GTCACTTTACCCTACAAGGGCTTTACG
1 GTCACTTTACCCTACAGGGGCTTTACG
*
52174 GTCACTTTACCCTATAGGGGCTTTACG
1 GTCACTTTACCCTACAGGGGCTTTACG
52201 GTC
1 GTC
52204 TTTTTACCTA
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
27 50 0.98
28 1 0.02
ACGTcount: A:0.21, C:0.25, G:0.21, T:0.32
Consensus pattern (27 bp):
GTCACTTTACCCTACAGGGGCTTTACG
Found at i:52217 original size:27 final size:27
Alignment explanation
Indices: 52120--52220 Score: 107
Period size: 27 Copynumber: 3.7 Consensus size: 27
52110 GGGCATATTC
* * *
52120 GTCATTTTACCATACAGGGG-TATTACG
1 GTCACTTTACCCTATAGGGGCT-TTACG
* *
52147 GTCACTTTACCCTACAAGGGCTTTACG
1 GTCACTTTACCCTATAGGGGCTTTACG
52174 GTCACTTTACCCTATAGGGGCTTTACG
1 GTCACTTTACCCTATAGGGGCTTTACG
**
52201 GTCTTTTTA-CCTAATAGGGG
1 GTCACTTTACCCT-ATAGGGG
52221 TATTTTAGTC
Statistics
Matches: 65, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
26 3 0.05
27 61 0.94
28 1 0.02
ACGTcount: A:0.22, C:0.23, G:0.22, T:0.34
Consensus pattern (27 bp):
GTCACTTTACCCTATAGGGGCTTTACG
Found at i:52295 original size:27 final size:27
Alignment explanation
Indices: 52265--52316 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
52255 GTAAATCTAC
52265 AAACCAAAGGTATTT-CAGTAATTTTGT
1 AAACCAAAGGTATTTCCA-TAATTTTGT
* *
52292 AAACCAATGGTGTTTCCATAATTTT
1 AAACCAAAGGTATTTCCATAATTTT
52317 TAGAAAGTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 20 0.91
28 2 0.09
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.38
Consensus pattern (27 bp):
AAACCAAAGGTATTTCCATAATTTTGT
Found at i:52448 original size:81 final size:81
Alignment explanation
Indices: 52353--52519 Score: 255
Period size: 81 Copynumber: 2.1 Consensus size: 81
52343 TTTGTAAATC
*
52353 AGGGGTATTTTGGTAATTATACAAATTGAGGGTATTTCGGTAATTTCACAAACC-AGTGGTATTT
1 AGGGTTATTTTGGTAATTATACAAATTGAGGGTATTTCGGTAATTTCACAAACCAAG-GGTATTT
* *
52417 TGGTAATTTTACAAACT
65 TAGCAATTTTACAAACT
* * *
52434 AGGGTTATTTTGGTAATTTTACAAATTGAGGGTATTTCTGTAATTTTACAAACCAAGGGTATTTT
1 AGGGTTATTTTGGTAATTATACAAATTGAGGGTATTTCGGTAATTTCACAAACCAAGGGTATTTT
*
52499 AGCAATTTTACAGACT
66 AGCAATTTTACAAACT
52515 AGGGT
1 AGGGT
52520 ATTCTAGTAA
Statistics
Matches: 78, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
81 76 0.97
82 2 0.03
ACGTcount: A:0.31, C:0.10, G:0.21, T:0.39
Consensus pattern (81 bp):
AGGGTTATTTTGGTAATTATACAAATTGAGGGTATTTCGGTAATTTCACAAACCAAGGGTATTTT
AGCAATTTTACAAACT
Found at i:52534 original size:27 final size:26
Alignment explanation
Indices: 52355--52533 Score: 171
Period size: 27 Copynumber: 6.7 Consensus size: 26
52345 TGTAAATCAG
* * *
52355 GGGTATTTTGGTAATTATACAAATTGA
1 GGGTATTTTAGTAATTTTACAAACT-A
** * *
52382 GGGTATTTCGGTAATTTCACAAACCA
1 GGGTATTTTAGTAATTTTACAAACTA
*
52408 GTGGTATTTTGGTAATTTTACAAACTA
1 G-GGTATTTTAGTAATTTTACAAACTA
* *
52435 GGGTTATTTTGGTAATTTTACAAATTGA
1 GGG-TATTTTAGTAATTTTACAAACT-A
*
52463 GGGTATTTCT-GTAATTTTACAAACCAA
1 GGGTATTT-TAGTAATTTTACAAA-CTA
* *
52490 GGGTATTTTAGCAATTTTACAGACTA
1 GGGTATTTTAGTAATTTTACAAACTA
*
52516 GGGTATTCTAGTAATTTT
1 GGGTATTTTAGTAATTTT
52534 TTAAATCGAA
Statistics
Matches: 130, Mismatches: 16, Indels: 13
0.82 0.10 0.08
Matches are distributed among these distances:
26 23 0.18
27 102 0.78
28 5 0.04
ACGTcount: A:0.30, C:0.09, G:0.20, T:0.41
Consensus pattern (26 bp):
GGGTATTTTAGTAATTTTACAAACTA
Found at i:52704 original size:27 final size:27
Alignment explanation
Indices: 52526--52709 Score: 208
Period size: 27 Copynumber: 6.8 Consensus size: 27
52516 GGGTATTCTA
* * * *
52526 GTAATTTTTTAAATCGAAGGTAAAACA
1 GTAATTCTGTAAATCGAGGGTAAAACG
* *
52553 GTAATTCTATAAATCAAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAACG
* * *
52580 ATACTTCTGTAAGTCGAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAACG
*
52607 GTAATTCTGTAAATCAAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAACG
* *
52634 GTAATTATGTAAATCG-GGGTTAAAATG
1 GTAATTCTGTAAATCGAGGG-TAAAACG
* * *
52661 GTAATTATGTAAATCGGGGGTAAAATG
1 GTAATTCTGTAAATCGAGGGTAAAACG
*
52688 GTAATTCTGTAAATCGGGGGTA
1 GTAATTCTGTAAATCGAGGGTA
52710 CTTTGGTAAT
Statistics
Matches: 137, Mismatches: 18, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
26 3 0.02
27 131 0.96
28 3 0.02
ACGTcount: A:0.38, C:0.09, G:0.24, T:0.29
Consensus pattern (27 bp):
GTAATTCTGTAAATCGAGGGTAAAACG
Found at i:52736 original size:27 final size:26
Alignment explanation
Indices: 52706--52781 Score: 89
Period size: 27 Copynumber: 2.8 Consensus size: 26
52696 GTAAATCGGG
* *
52706 GGTACTTTGGTAATTTTACAAGTCGAA
1 GGTA-TTTAGTAATTTTACAAATCGAA
*
52733 GGTATTTCAGTAATTTTACAAATCGAG
1 GGTATTT-AGTAATTTTACAAATCGAA
*
52760 GGTATTTTAGTATTTTTACAAA
1 GGTA-TTTAGTAATTTTACAAA
52782 CTAAGCGCAT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
26 3 0.07
27 37 0.86
28 3 0.07
ACGTcount: A:0.32, C:0.09, G:0.18, T:0.41
Consensus pattern (26 bp):
GGTATTTAGTAATTTTACAAATCGAA
Found at i:55355 original size:21 final size:21
Alignment explanation
Indices: 55331--55373 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
55321 TACTACTTAT
*
55331 TTTATAACTTTTACAAATAAG
1 TTTAAAACTTTTACAAATAAG
55352 TTTAAAACTTTTACAAATAAG
1 TTTAAAACTTTTACAAATAAG
55373 T
1 T
55374 CCTTTTTGAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.44, C:0.09, G:0.05, T:0.42
Consensus pattern (21 bp):
TTTAAAACTTTTACAAATAAG
Found at i:59880 original size:22 final size:22
Alignment explanation
Indices: 59852--59896 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
59842 GAACACAGAG
59852 AGAGAACATTCACAATAAGATA
1 AGAGAACATTCACAATAAGATA
59874 AGAGAACATTCACAATAAGATA
1 AGAGAACATTCACAATAAGATA
59896 A
1 A
59897 AAGTTCATCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.56, C:0.13, G:0.13, T:0.18
Consensus pattern (22 bp):
AGAGAACATTCACAATAAGATA
Found at i:60808 original size:22 final size:20
Alignment explanation
Indices: 60782--60822 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
60772 ACTGTTAAAG
60782 ATTTTAAGAGTTTCTATTGATT
1 ATTTTAAGAG-TTCT-TTGATT
*
60804 ATTTTATGAGTTCTTTGAT
1 ATTTTAAGAGTTCTTTGAT
60823 GTTTGAAGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 4 0.22
22 9 0.50
ACGTcount: A:0.24, C:0.05, G:0.15, T:0.56
Consensus pattern (20 bp):
ATTTTAAGAGTTCTTTGATT
Found at i:61494 original size:29 final size:29
Alignment explanation
Indices: 61452--61525 Score: 130
Period size: 29 Copynumber: 2.6 Consensus size: 29
61442 ATAAGTTGAG
*
61452 TTGGATTCGAGCCATGCATATCAGATGAT
1 TTGGCTTCGAGCCATGCATATCAGATGAT
61481 TTGGCTTCGAGCCATGCATATCAGATGAT
1 TTGGCTTCGAGCCATGCATATCAGATGAT
*
61510 TTGGCTTCGGGCCATG
1 TTGGCTTCGAGCCATG
61526 ATAATTATTC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.22, C:0.20, G:0.27, T:0.31
Consensus pattern (29 bp):
TTGGCTTCGAGCCATGCATATCAGATGAT
Found at i:69008 original size:27 final size:27
Alignment explanation
Indices: 68951--69156 Score: 156
Period size: 27 Copynumber: 7.7 Consensus size: 27
68941 AAAATTAATT
* *
68951 AAATTACTGAAATACCCT-AATTTGTA
1 AAATTACTAAAATACCCTCGATTTGTA
*
68977 AAATTA-TCAAAATACCCCCGATTTGTA
1 AAATTACT-AAAATACCCTCGATTTGTA
*
69004 AAATTACTGAAATACCCTCGATTTGTA
1 AAATTACTAAAATACCCTCGATTTGTA
** ** *
69031 AAATTACCGAAATACCCTTAATTTGGA
1 AAATTACTAAAATACCCTCGATTTGTA
* *
69058 AAATTACTAAAATACCCTTG-TAGTGTA
1 AAATTACTAAAATACCCTCGAT-TTGTA
** * *
69085 AAATTACCGAAATACCCTTG-TAGTGTA
1 AAATTACTAAAATACCCTCGAT-TTGTA
* *
69112 AAATTAGC-AAAATACCCT-TATAGTGTA
1 AAATTA-CTAAAATACCCTCGAT-TTGTA
69139 AAATTA-TAAAAATACCCT
1 AAATTACT-AAAATACCCT
69157 TGTAGTGTAA
Statistics
Matches: 154, Mismatches: 18, Indels: 15
0.82 0.10 0.08
Matches are distributed among these distances:
25 1 0.01
26 15 0.10
27 136 0.88
28 2 0.01
ACGTcount: A:0.42, C:0.17, G:0.10, T:0.31
Consensus pattern (27 bp):
AAATTACTAAAATACCCTCGATTTGTA
Found at i:69070 original size:81 final size:81
Alignment explanation
Indices: 68951--69182 Score: 240
Period size: 81 Copynumber: 2.9 Consensus size: 81
68941 AAAATTAATT
* * * *
68951 AAATTACTGAAATACCC-TAATTTGTAAAATTATCAAAATACCCCCG-ATTTGTAAAATTACTGA
1 AAATTACCGAAATACCCTTAATTTGGAAAATTATCAAAATACCCCCGTA-GTGTAAAATTACCGA
*
69014 AATACCCTCG-ATTTGTA
65 AATACCCTCGTA-GTGTA
**
69031 AAATTACCGAAATACCCTTAATTTGGAAAATTA-CTAAAATACCCTTGTAGTGTAAAATTACCGA
1 AAATTACCGAAATACCCTTAATTTGGAAAATTATC-AAAATACCCCCGTAGTGTAAAATTACCGA
*
69095 AATACCCTTGTAGTGTA
65 AATACCCTCGTAGTGTA
* * * * * ** * *
69112 AAATTAGCAAAATACCCTT-ATAGTGTAAAATTATAAAAATACCCTTGTAGTGTAAAACTACGGA
1 AAATTACCGAAATACCCTTAAT-TTGGAAAATTATCAAAATACCCCCGTAGTGTAAAATTACCGA
69176 AATACCC
65 AATACCC
69183 CTGTAGGGCA
Statistics
Matches: 131, Mismatches: 15, Indels: 11
0.83 0.10 0.07
Matches are distributed among these distances:
80 19 0.15
81 110 0.84
82 2 0.02
ACGTcount: A:0.41, C:0.18, G:0.11, T:0.30
Consensus pattern (81 bp):
AAATTACCGAAATACCCTTAATTTGGAAAATTATCAAAATACCCCCGTAGTGTAAAATTACCGAA
ATACCCTCGTAGTGTA
Found at i:69102 original size:54 final size:53
Alignment explanation
Indices: 68951--69144 Score: 196
Period size: 54 Copynumber: 3.6 Consensus size: 53
68941 AAAATTAATT
* * * * * **
68951 AAATTACTGAAATACCCTAAT-TTGTAAAATTATCAAAATACCCCCGATTTGTA
1 AAATTACTAAAATACCCTTATAGTGTAAAATTACCGAAATA-CCCTTATTTGTA
* * * *
69004 AAATTACTGAAATACCCTCGAT-TTGTAAAATTACCGAAATACCCTTAATTTGGA
1 AAATTACTAAAATACCCT-TATAGTGTAAAATTACCGAAATACCCTT-ATTTGTA
* * *
69058 AAATTACTAAAATACCCTTGTAGTGTAAAATTACCGAAATACCCTTGTAGTGTA
1 AAATTACTAAAATACCCTTATAGTGTAAAATTACCGAAATACCCTTAT-TTGTA
69112 AAATTAGC-AAAATACCCTTATAGTGTAAAATTA
1 AAATTA-CTAAAATACCCTTATAGTGTAAAATTA
69145 TAAAAATACC
Statistics
Matches: 122, Mismatches: 14, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
53 23 0.19
54 98 0.80
55 1 0.01
ACGTcount: A:0.41, C:0.17, G:0.10, T:0.31
Consensus pattern (53 bp):
AAATTACTAAAATACCCTTATAGTGTAAAATTACCGAAATACCCTTATTTGTA
Found at i:69152 original size:54 final size:54
Alignment explanation
Indices: 68951--69182 Score: 188
Period size: 54 Copynumber: 4.3 Consensus size: 54
68941 AAAATTAATT
* * * ** *
68951 AAATTACTGAAATACCCTAAT-TTGTAAAATTATC-AAAATACCCCCG-ATTTGTA
1 AAATTACTAAAATACCCTTATAGTGTAAAATTA-CAAAAATACCCTTGTA-GTGTA
* * * ** * * *
69004 AAATTACTGAAATACCCTCGAT-TTGTAAAATTACCGAAATACCCTT-AATTTGGA
1 AAATTACTAAAATACCCT-TATAGTGTAAAATTACAAAAATACCCTTGTA-GTGTA
* **
69058 AAATTACTAAAATACCCTTGTAGTGTAAAATTACCGAAATACCCTTGTAGTGTA
1 AAATTACTAAAATACCCTTATAGTGTAAAATTACAAAAATACCCTTGTAGTGTA
*
69112 AAATTAGC-AAAATACCCTTATAGTGTAAAATTATAAAAATACCCTTGTAGTGTA
1 AAATTA-CTAAAATACCCTTATAGTGTAAAATTACAAAAATACCCTTGTAGTGTA
* **
69166 AAACTACGGAAATACCC
1 AAATTACTAAAATACCC
69183 CTGTAGGGCA
Statistics
Matches: 154, Mismatches: 18, Indels: 13
0.83 0.10 0.07
Matches are distributed among these distances:
53 21 0.14
54 131 0.85
55 2 0.01
ACGTcount: A:0.41, C:0.18, G:0.11, T:0.30
Consensus pattern (54 bp):
AAATTACTAAAATACCCTTATAGTGTAAAATTACAAAAATACCCTTGTAGTGTA
Found at i:69157 original size:27 final size:27
Alignment explanation
Indices: 68973--69168 Score: 168
Period size: 27 Copynumber: 7.3 Consensus size: 27
68963 TACCCTAATT
** *
68973 TGTAAAATTATCAAAATACCCCCG-ATT
1 TGTAAAATTATCAAAATACCCTTGTA-G
* * *
69000 TGTAAAATTA-CTGAAATACCCTCG-ATT
1 TGTAAAATTATC-AAAATACCCTTGTA-G
* * * *
69027 TGTAAAATTACCGAAATACCCTT-AATT
1 TGTAAAATTATCAAAATACCCTTGTA-G
*
69054 TGGAAAATTA-CTAAAATACCCTTGTAG
1 TGTAAAATTATC-AAAATACCCTTGTAG
* *
69081 TGTAAAATTACCGAAATACCCTTGTAG
1 TGTAAAATTATCAAAATACCCTTGTAG
* *
69108 TGTAAAATTAGCAAAATACCCTTATAG
1 TGTAAAATTATCAAAATACCCTTGTAG
*
69135 TGTAAAATTATAAAAATACCCTTGTAG
1 TGTAAAATTATCAAAATACCCTTGTAG
69162 TGTAAAA
1 TGTAAAA
69169 CTACGGAAAT
Statistics
Matches: 148, Mismatches: 15, Indels: 12
0.85 0.09 0.07
Matches are distributed among these distances:
26 2 0.01
27 143 0.97
28 3 0.02
ACGTcount: A:0.41, C:0.16, G:0.11, T:0.31
Consensus pattern (27 bp):
TGTAAAATTATCAAAATACCCTTGTAG
Found at i:69178 original size:27 final size:27
Alignment explanation
Indices: 69000--69188 Score: 174
Period size: 27 Copynumber: 7.0 Consensus size: 27
68990 ACCCCCGATT
* *
69000 TGTAAAATTACTG-AAATACCCTCG-ATT
1 TGTAAAATTAC-GAAAATACCCTTGTA-G
* *
69027 TGTAAAATTACCG-AAATACCCTT-AATT
1 TGTAAAATTA-CGAAAATACCCTTGTA-G
* *
69054 TGGAAAATTACTAAAATACCCTTGTAG
1 TGTAAAATTACGAAAATACCCTTGTAG
69081 TGTAAAATTACCG-AAATACCCTTGTAG
1 TGTAAAATTA-CGAAAATACCCTTGTAG
*
69108 TGTAAAATTA-GCAAAATACCCTTATAG
1 TGTAAAATTACG-AAAATACCCTTGTAG
**
69135 TGTAAAATTATAAAAATACCCTTGTAG
1 TGTAAAATTACGAAAATACCCTTGTAG
* * *
69162 TGTAAAACTACGGAAATACCCCTGTAG
1 TGTAAAATTACGAAAATACCCTTGTAG
69189 GGCAAAATGA
Statistics
Matches: 139, Mismatches: 15, Indels: 16
0.82 0.09 0.09
Matches are distributed among these distances:
25 1 0.01
26 1 0.01
27 134 0.96
28 3 0.02
ACGTcount: A:0.40, C:0.17, G:0.13, T:0.30
Consensus pattern (27 bp):
TGTAAAATTACGAAAATACCCTTGTAG
Found at i:69213 original size:81 final size:81
Alignment explanation
Indices: 69040--69198 Score: 214
Period size: 81 Copynumber: 2.0 Consensus size: 81
69030 AAAATTACCG
* * * *
69040 AAATACCCTTA-ATTTGGAAAATTACTAAAATACCCTTGTAGTGTAAAATTACCGAAATACCCTT
1 AAATACCCTTATA-GTGTAAAATTACTAAAATACCCTTGTAGTGTAAAACTACCGAAATACCCCT
* * *
69104 GTAGTGTAAAATTAGCA
65 GTAGGGCAAAATGAGCA
*
69121 AAATACCCTTATAGTGTAAAATTA-TAAAAATACCCTTGTAGTGTAAAACTACGGAAATACCCCT
1 AAATACCCTTATAGTGTAAAATTACT-AAAATACCCTTGTAGTGTAAAACTACCGAAATACCCCT
69185 GTAGGGCAAAATGA
65 GTAGGGCAAAATGA
69199 TTGTTTTGCC
Statistics
Matches: 68, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
80 1 0.01
81 66 0.97
82 1 0.01
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (81 bp):
AAATACCCTTATAGTGTAAAATTACTAAAATACCCTTGTAGTGTAAAACTACCGAAATACCCCTG
TAGGGCAAAATGAGCA
Found at i:71137 original size:39 final size:40
Alignment explanation
Indices: 71092--71316 Score: 233
Period size: 40 Copynumber: 5.7 Consensus size: 40
71082 GCTCCTCGTT
* * * *
71092 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
*
71132 C-AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* *
71171 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * * *
71211 CAAAGGCCTTCGGGGCTTAACCCGGAACTT-GTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCA
** * * * *
71251 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
71292 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
71317 CAGCATTCAA
Statistics
Matches: 157, Mismatches: 22, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
39 38 0.24
40 105 0.67
41 14 0.09
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:71325 original size:41 final size:41
Alignment explanation
Indices: 71248--71325 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
71238 CTTGTATCTC
* * *
71248 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
71289 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
71326 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:79053 original size:39 final size:40
Alignment explanation
Indices: 79008--79232 Score: 233
Period size: 40 Copynumber: 5.7 Consensus size: 40
78998 GCTCCTCGTT
* * * *
79008 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
*
79048 C-AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* *
79087 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * * *
79127 CAAAGGCCTTCGGGGCTTAACCCGGAACTT-GTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCA
** * * * *
79167 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
79208 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
79233 CAGCATTCAA
Statistics
Matches: 157, Mismatches: 22, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
39 38 0.24
40 105 0.67
41 14 0.09
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:79241 original size:41 final size:41
Alignment explanation
Indices: 79164--79241 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
79154 CTTGTATCTC
* * *
79164 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
79205 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
79242 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:96647 original size:30 final size:30
Alignment explanation
Indices: 96611--96671 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
96601 TCCTTAACTC
*
96611 AAACTTTTTCAAAATTACAATTTTGCCCCT
1 AAACTTTTGCAAAATTACAATTTTGCCCCT
* * *
96641 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTTGCAAAATTACAATTTTGCCCCT
96671 A
1 A
96672 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.25, G:0.05, T:0.41
Consensus pattern (30 bp):
AAACTTTTGCAAAATTACAATTTTGCCCCT
Found at i:102624 original size:17 final size:18
Alignment explanation
Indices: 102597--102639 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
102587 GGCGTGTGAC
*
102597 CTTTTAAAAGTT-GAAAA
1 CTTTTATAAGTTCGAAAA
* *
102614 TTTTTATAAGTTCTAAAA
1 CTTTTATAAGTTCGAAAA
102632 CTTTTATA
1 CTTTTATA
102640 TGTTATTGAA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 10 0.48
18 11 0.52
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.47
Consensus pattern (18 bp):
CTTTTATAAGTTCGAAAA
Found at i:109905 original size:102 final size:104
Alignment explanation
Indices: 109684--109934 Score: 298
Period size: 102 Copynumber: 2.4 Consensus size: 104
109674 ATTAGGGTTT
* *
109684 AAGGATACCATGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTCTAAGGCAAGGAAATCA
1 AAGGATACCATGTAAGACCATGCCAAGGCATAGCAATTGGTAAGGTTTCTAAGGCAAGGAAACCA
**
109749 TGTAAGACCATGTCAAGACATGGCATTGATAAGTAAGGCA
66 TGTAAGACCATGTCAAGACATGGCAAAGATAAGT-AGGCA
* * *
109789 AAGG-TCCCATGTAAGACCATGCCAAGGCATAGC-ATTGGTGA-G-TTCATAAGGCAAGGATACC
1 AAGGATACCATGTAAGACCATGCCAAGGCATAGCAATTGGTAAGGTTTC-TAAGGCAAGGAAACC
* **
109850 ATGTAAGACCATGTCAAGACATGGCAAAGGTAAGT-TTCAA
65 ATGTAAGACCATGTCAAGACATGGCAAAGATAAGTAGGC-A
* * * * *
109890 AAGGATACCACGTAAGAACATGACAAGTCATGGCAA-TGGTAAGGT
1 AAGGATACCATGTAAGACCATGCCAAGGCATAGCAATTGGTAAGGT
109935 ACCCGTGTAT
Statistics
Matches: 123, Mismatches: 17, Indels: 13
0.80 0.11 0.08
Matches are distributed among these distances:
100 1 0.01
101 8 0.07
102 74 0.60
103 9 0.07
104 27 0.22
105 4 0.03
ACGTcount: A:0.37, C:0.17, G:0.25, T:0.20
Consensus pattern (104 bp):
AAGGATACCATGTAAGACCATGCCAAGGCATAGCAATTGGTAAGGTTTCTAAGGCAAGGAAACCA
TGTAAGACCATGTCAAGACATGGCAAAGATAAGTAGGCA
Found at i:110027 original size:23 final size:24
Alignment explanation
Indices: 110001--110045 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
109991 AAGGTAAGGT
*
110001 AAGGTAAGACGAGTT-ATGCTAAA
1 AAGGTAAGACAAGTTCATGCTAAA
110024 AAGGTAAGACAAGTTCATGCTA
1 AAGGTAAGACAAGTTCATGCTA
110046 GAAGAGCAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.42, C:0.11, G:0.24, T:0.22
Consensus pattern (24 bp):
AAGGTAAGACAAGTTCATGCTAAA
Found at i:110145 original size:16 final size:16
Alignment explanation
Indices: 110124--110154 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
110114 ATAAATTTGA
110124 TTAAGTAAGTAAGTAT
1 TTAAGTAAGTAAGTAT
*
110140 TTAAGTAAGTGAGTA
1 TTAAGTAAGTAAGTA
110155 AGTGAAGAAG
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:0.42, C:0.00, G:0.23, T:0.35
Consensus pattern (16 bp):
TTAAGTAAGTAAGTAT
Found at i:116662 original size:23 final size:24
Alignment explanation
Indices: 116636--116680 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
116626 AAGGTAAGGT
*
116636 AAGGTAAGACGAGTT-ATGCTAAA
1 AAGGTAAGACAAGTTCATGCTAAA
116659 AAGGTAAGACAAGTTCATGCTA
1 AAGGTAAGACAAGTTCATGCTA
116681 GAAGAGCAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.42, C:0.11, G:0.24, T:0.22
Consensus pattern (24 bp):
AAGGTAAGACAAGTTCATGCTAAA
Found at i:116780 original size:16 final size:16
Alignment explanation
Indices: 116759--116789 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
116749 ATAAATTTGA
116759 TTAAGTAAGTAAGTAT
1 TTAAGTAAGTAAGTAT
*
116775 TTAAGTAAGTGAGTA
1 TTAAGTAAGTAAGTA
116790 AGTGAAGAGG
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:0.42, C:0.00, G:0.23, T:0.35
Consensus pattern (16 bp):
TTAAGTAAGTAAGTAT
Found at i:123134 original size:20 final size:20
Alignment explanation
Indices: 123068--123128 Score: 95
Period size: 20 Copynumber: 3.0 Consensus size: 20
123058 ATTTCGATAA
*
123068 ACATGGTATGTATGATATGC
1 ACATGATATGTATGATATGC
* *
123088 ACATGACATGTACGATATGC
1 ACATGATATGTATGATATGC
123108 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
123128 A
1 A
123129 TGTGATGTAA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.34, C:0.13, G:0.21, T:0.31
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:123240 original size:24 final size:24
Alignment explanation
Indices: 123184--123264 Score: 103
Period size: 24 Copynumber: 3.4 Consensus size: 24
123174 GAGGAAGTGA
*
123184 AAAAGGGCTTATGCCCTAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
123208 -AAAGGGCTTAT-CCCACAGTTATT
1 AAAAGGGCTTATGCCC-CAGTTATT
*
123231 AAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
123255 CAAAGAGGCT
1 AAAAG-GGCT
123265 AGGCCTCCAG
Statistics
Matches: 50, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
22 3 0.06
23 18 0.36
24 22 0.44
25 7 0.14
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.30
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATT
Found at i:129471 original size:27 final size:27
Alignment explanation
Indices: 129441--129618 Score: 115
Period size: 27 Copynumber: 6.6 Consensus size: 27
129431 ATATTGAGCC
* * *
129441 CGCACACTCAGTGCTATACAATCAACT
1 CGCACACTTAGTGCTACACAATCAAAT
* **
129468 CGCACACTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACACAATCAAAT
* * * *
129495 CGCACACTTAGTGCTACATAGTTAGACT
1 CGCACACTTAGTGCTACACAATCA-AAT
** *** *
129523 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACACAATCAAAT
* * **
129550 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CACAATCAAAT
* * * *
129577 CGCACACTTAGTGCAACATAGTCGAAT
1 CGCACACTTAGTGCTACACAATCAAAT
129604 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
129619 GTACAATTTA
Statistics
Matches: 123, Mismatches: 25, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
27 100 0.81
28 23 0.19
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACACAATCAAAT
Found at i:129534 original size:55 final size:55
Alignment explanation
Indices: 129441--129618 Score: 204
Period size: 54 Copynumber: 3.3 Consensus size: 55
129431 ATATTGAGCC
* * *
129441 CGCACACTCAGTGCTATACA-A-TCAACTCGCACACTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTAT-CATATTCAACTCGCACACTTAGTGCCACATAGTCAAAT
* * *
129495 CGCACACTTAGTGCTA-CATAGTT-AGACTCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTATCATA-TTCA-ACTCGCACACTTAGTGCCACATAGTCAAAT
** * *
129550 CGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCGAAT
1 CGCACACTTAGTGCTATCATATTCAACTCGCACACTTAGTGCCACATAGTCAAAT
129604 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
129619 GTACAATTTA
Statistics
Matches: 104, Mismatches: 13, Indels: 13
0.80 0.10 0.10
Matches are distributed among these distances:
52 2 0.02
53 1 0.01
54 56 0.54
55 45 0.43
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.26
Consensus pattern (55 bp):
CGCACACTTAGTGCTATCATATTCAACTCGCACACTTAGTGCCACATAGTCAAAT
Found at i:129580 original size:82 final size:81
Alignment explanation
Indices: 129462--129617 Score: 215
Period size: 82 Copynumber: 1.9 Consensus size: 81
129452 TGCTATACAA
* * *
129462 TCAACTCGCACACTTAGTGCCACGTAATCAAATCGCACACTTAGTGCTACATAGTTAGACTCGCA
1 TCAACTCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCAACATAG-TAGAATCGCA
129527 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * ** *
129544 TCAATTCGCACACTTAGTG-CATCATATTCATTTCGCACACTTAGTGCAACATAGTCGAATCGCA
1 TCAACTCGCACACTTAGTGCCA-CATAATCAAATCGCACACTTAGTGCAACATAGTAGAATCGCA
129608 CACTTAGTGC
65 CACTTAGTGC
129618 TGTACAATTT
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
81 20 0.31
82 45 0.69
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCAACATAGTAGAATCGCAC
ACTTAGTGCCGCATGG
Found at i:137575 original size:27 final size:27
Alignment explanation
Indices: 137545--137722 Score: 115
Period size: 27 Copynumber: 6.6 Consensus size: 27
137535 ATATTGAGCC
* * *
137545 CGCACACTCAGTGCTATACAATCAACT
1 CGCACACTTAGTGCTACACAATCAAAT
* **
137572 CGCACACTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACACAATCAAAT
* * * *
137599 CGCACACTTAGTGCTACATAGTTAGACT
1 CGCACACTTAGTGCTACACAATCA-AAT
** *** *
137627 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACACAATCAAAT
* * **
137654 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CACAATCAAAT
* * * *
137681 CGCACACTTAGTGCAACATAGTCGAAT
1 CGCACACTTAGTGCTACACAATCAAAT
137708 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
137723 GTACAATTTA
Statistics
Matches: 123, Mismatches: 25, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
27 100 0.81
28 23 0.19
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACACAATCAAAT
Found at i:137638 original size:55 final size:55
Alignment explanation
Indices: 137545--137722 Score: 204
Period size: 54 Copynumber: 3.3 Consensus size: 55
137535 ATATTGAGCC
* * *
137545 CGCACACTCAGTGCTATACA-A-TCAACTCGCACACTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTAT-CATATTCAACTCGCACACTTAGTGCCACATAGTCAAAT
* * *
137599 CGCACACTTAGTGCTA-CATAGTT-AGACTCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTATCATA-TTCA-ACTCGCACACTTAGTGCCACATAGTCAAAT
** * *
137654 CGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCGAAT
1 CGCACACTTAGTGCTATCATATTCAACTCGCACACTTAGTGCCACATAGTCAAAT
137708 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
137723 GTACAATTTA
Statistics
Matches: 104, Mismatches: 13, Indels: 13
0.80 0.10 0.10
Matches are distributed among these distances:
52 2 0.02
53 1 0.01
54 56 0.54
55 45 0.43
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.26
Consensus pattern (55 bp):
CGCACACTTAGTGCTATCATATTCAACTCGCACACTTAGTGCCACATAGTCAAAT
Found at i:137684 original size:82 final size:81
Alignment explanation
Indices: 137566--137721 Score: 215
Period size: 82 Copynumber: 1.9 Consensus size: 81
137556 TGCTATACAA
* * *
137566 TCAACTCGCACACTTAGTGCCACGTAATCAAATCGCACACTTAGTGCTACATAGTTAGACTCGCA
1 TCAACTCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCAACATAG-TAGAATCGCA
137631 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * ** *
137648 TCAATTCGCACACTTAGTG-CATCATATTCATTTCGCACACTTAGTGCAACATAGTCGAATCGCA
1 TCAACTCGCACACTTAGTGCCA-CATAATCAAATCGCACACTTAGTGCAACATAGTAGAATCGCA
137712 CACTTAGTGC
65 CACTTAGTGC
137722 TGTACAATTT
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
81 20 0.31
82 45 0.69
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCAACATAGTAGAATCGCAC
ACTTAGTGCCGCATGG
Found at i:149646 original size:40 final size:39
Alignment explanation
Indices: 149522--149706 Score: 178
Period size: 40 Copynumber: 4.7 Consensus size: 39
149512 TTGAATGCTG
* * *
149522 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGT-TATAAA
* * * *
149562 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACAAGT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTATAA-A
* *
149602 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-TAAA
* *
149642 TCCGGGTTAAGTCCCGAAGGCA-TTGTGTGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-TAAA
* *
149681 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
149707 AACGAGGAGC
Statistics
Matches: 120, Mismatches: 19, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
39 36 0.30
40 74 0.62
41 10 0.08
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (39 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTATAAA
Done.