Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1857
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: 16197
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.33
Found at i:1631 original size:15 final size:15
Alignment explanation
Indices: 1611--1661 Score: 66
Period size: 16 Copynumber: 3.3 Consensus size: 15
1601 TTGCTGTTCG
1611 TCTTGCTATTTTGTT
1 TCTTGCTATTTTGTT
* *
1626 TCTTGCTGTTTTTTTT
1 TCTTGCT-ATTTTGTT
1642 GTCTTGCTATTTTGTT
1 -TCTTGCTATTTTGTT
1658 TCTT
1 TCTT
1662 ATTTTGATTC
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
15 11 0.37
16 12 0.40
17 7 0.23
ACGTcount: A:0.04, C:0.14, G:0.14, T:0.69
Consensus pattern (15 bp):
TCTTGCTATTTTGTT
Found at i:1639 original size:17 final size:17
Alignment explanation
Indices: 1610--1654 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 17
1600 GTTGCTGTTC
*
1610 GTCTTGCTA-TTTTGTT
1 GTCTTGCTATTTTTTTT
*
1626 -TCTTGCTGTTTTTTTT
1 GTCTTGCTATTTTTTTT
1642 GTCTTGCTATTTT
1 GTCTTGCTATTTT
1655 GTTTCTTATT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
15 7 0.29
16 6 0.25
17 11 0.46
ACGTcount: A:0.04, C:0.13, G:0.16, T:0.67
Consensus pattern (17 bp):
GTCTTGCTATTTTTTTT
Found at i:1875 original size:4 final size:4
Alignment explanation
Indices: 1866--1892 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
1856 TTTTTGTTTT
1866 TTAA TTAA TTAA TTAA TTAA TTAA TTA
1 TTAA TTAA TTAA TTAA TTAA TTAA TTA
1893 TCATTATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
TTAA
Found at i:1924 original size:8 final size:8
Alignment explanation
Indices: 1911--1974 Score: 80
Period size: 8 Copynumber: 8.0 Consensus size: 8
1901 ATTATGCATA
1911 TATATTTT
1 TATATTTT
1919 TATATTTT
1 TATATTTT
1927 CT-TA-TTT
1 -TATATTTT
1934 TATATTTTT
1 TATA-TTTT
1943 ATATATTTT
1 -TATATTTT
1952 TATATTTT
1 TATATTTT
1960 TATA-TTT
1 TATATTTT
1967 TATATTTT
1 TATATTTT
1975 GAGACAAGGT
Statistics
Matches: 50, Mismatches: 0, Indels: 12
0.81 0.00 0.19
Matches are distributed among these distances:
6 1 0.02
7 12 0.24
8 25 0.50
9 8 0.16
10 4 0.08
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (8 bp):
TATATTTT
Found at i:1931 original size:10 final size:10
Alignment explanation
Indices: 1909--1964 Score: 55
Period size: 10 Copynumber: 5.5 Consensus size: 10
1899 TTATTATGCA
1909 TATATATTTT
1 TATATATTTT
1919 TATAT-TTTCT
1 TATATATTT-T
1929 TATTTTATATTTT
1 TA---TATATTTT
1942 TATATA-TTT
1 TATATATTTT
1951 T-TATATTTT
1 TATATATTTT
1960 TATAT
1 TATAT
1965 TTTATATTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
8 4 0.10
9 11 0.28
10 15 0.38
13 6 0.15
14 3 0.08
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (10 bp):
TATATATTTT
Found at i:1937 original size:23 final size:23
Alignment explanation
Indices: 1911--1974 Score: 85
Period size: 23 Copynumber: 2.7 Consensus size: 23
1901 ATTATGCATA
1911 TATATTTTTATATTTTCTTAT-TT
1 TATATTTTTATATTTT-TTATATT
1934 TATATTTTTATATATTTTTATATT
1 TATATTTTTATAT-TTTTTATATT
*
1958 TTTATATTTTATATTTT
1 TATAT-TTTTATATTTT
1975 GAGACAAGGT
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
23 17 0.46
24 12 0.32
25 8 0.22
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (23 bp):
TATATTTTTATATTTTTTATATT
Found at i:1937 original size:25 final size:25
Alignment explanation
Indices: 1909--1974 Score: 86
Period size: 25 Copynumber: 2.7 Consensus size: 25
1899 TTATTATGCA
1909 TATATATTTTTATATTTTCT-TATTT
1 TATATATTTTTATATTTT-TATATTT
1934 TATAT-TTTTATATATTTTTATATTT
1 TATATATTTT-TATATTTTTATATTT
1959 T-TATA-TTTTATATTTT
1 TATATATTTTTATATTTT
1975 GAGACAAGGT
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
23 8 0.21
24 11 0.29
25 19 0.50
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.73
Consensus pattern (25 bp):
TATATATTTTTATATTTTTATATTT
Found at i:1946 original size:33 final size:33
Alignment explanation
Indices: 1909--1974 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
1899 TTATTATGCA
1909 TATATATTTTTATATTTTCT-TATTTTATATTTT
1 TATATATTTTTATATTTT-TATATTTTATATTTT
1942 TATATATTTTTATATTTTTATATTTTATATTTT
1 TATATATTTTTATATTTTTATATTTTATATTTT
1975 GAGACAAGGT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 1 0.03
33 31 0.97
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.73
Consensus pattern (33 bp):
TATATATTTTTATATTTTTATATTTTATATTTT
Found at i:2251 original size:103 final size:104
Alignment explanation
Indices: 2066--2278 Score: 306
Period size: 103 Copynumber: 2.0 Consensus size: 104
2056 TACTATTTTG
* * * *
2066 ATTATGAATGTGTGAAGTCCATTTGTTGGAAGTGGATTTCTATTATAATGGCTACTATATCGAAT
1 ATTA-GAATGTGTGAAGTCCATTTGATGGAAGTGAATTTCTATTATAATGACTACTATATCAAAT
* *
2131 CTCAGATAATCCGAAA-TTCTAAGAAAAAGACTC-GACGAA
65 CTCAGATAATCCAAAATTTC-AAGAAAAAGACCCAGACGAA
*
2170 ATTAGAATGTGTGAAGTCCATTTGATGGAATTGAATTT-TCATTATAATGACTACTATATCAAAT
1 ATTAGAATGTGTGAAGTCCATTTGATGGAAGTGAATTTCT-ATTATAATGACTACTATATCAAAT
*
2234 CTCGGATAATCCAAAATTTCAAGAAAAAGACCCAGACGAA
65 CTCAGATAATCCAAAATTTCAAGAAAAAGACCCAGACGAA
2274 ATTAG
1 ATTAG
2279 GTGTCTACAC
Statistics
Matches: 98, Mismatches: 8, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
102 1 0.01
103 79 0.81
104 18 0.18
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.31
Consensus pattern (104 bp):
ATTAGAATGTGTGAAGTCCATTTGATGGAAGTGAATTTCTATTATAATGACTACTATATCAAATC
TCAGATAATCCAAAATTTCAAGAAAAAGACCCAGACGAA
Found at i:5354 original size:164 final size:159
Alignment explanation
Indices: 5062--5354 Score: 390
Period size: 164 Copynumber: 1.8 Consensus size: 159
5052 AAATCCACCC
* * *
5062 AAAAAATTATGAAGTAGAAAAAAACGAATTTCGAAAAAAAATTTGAGGAAAAAATTAAAAAACTC
1 AAAAAATTATAAAGTAGAAAAAAACGAATTTCAAAAAAAAATTTAAGGAAAAAATTAAAAAACTC
*
5127 ATAAAAATGATAATTTTTAAAAAATAATTTAATATGAAATAAATAATAATATTTCATGAATTTTA
66 ATAAAAATGATAATTTTTAAAAAATAATTTAATATGAAATAAATAATAATATTTCAAGAATTTTA
5192 AAAATTAAAAACTAAGAAAAATATCCCCA
131 AAAATTAAAAACTAAGAAAAATATCCCCA
* * *
5221 AAAAAATTATAAAGTAGAAAATAACGTATTTCAAAAAAGGAAAATTTCAAGG-AAAAATTTAAAA
1 AAAAAATTATAAAGTAGAAAAAAACGAATTTC-AAAAA--AAAATTT-AAGGAAAAAATTAAAAA
* * ** * * * *
5285 ATTCATGAAAATGAATAAATTTTTGGAAACTGATTTAATATGAAATAAATAATGATATTTGAAGA
62 ACTCATAAAAATG-AT-AATTTTTAAAAAATAATTTAATATGAAATAAATAATAATATTTCAAGA
5350 ATTTT
125 ATTTT
5355 GATGTTTGAA
Statistics
Matches: 113, Mismatches: 15, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
159 29 0.26
160 4 0.04
162 29 0.26
163 5 0.04
164 46 0.41
ACGTcount: A:0.56, C:0.05, G:0.10, T:0.29
Consensus pattern (159 bp):
AAAAAATTATAAAGTAGAAAAAAACGAATTTCAAAAAAAAATTTAAGGAAAAAATTAAAAAACTC
ATAAAAATGATAATTTTTAAAAAATAATTTAATATGAAATAAATAATAATATTTCAAGAATTTTA
AAAATTAAAAACTAAGAAAAATATCCCCA
Found at i:6410 original size:60 final size:59
Alignment explanation
Indices: 6332--7429 Score: 599
Period size: 60 Copynumber: 18.3 Consensus size: 59
6322 TGAAGAAAAA
* * * * * ** *
6332 CTTGACCGAATACTGTCAAGTAGGGTAAGATTTAACTGAGTACAGTCAAATAAGGATTGT
1 CTTGAACGAATACAGTCAAG-AGGGTAAAATTTGACTGAGTACAGTCAAATGAGGAAAGG
* * * * * * * * *
6392 CTTGAATGAATACAGTCAATAGAGATAAGATTT-AATCGAGTACTGTCAAATAAGGGAAGAC
1 CTTGAACGAATACAGTCAAGAG-GGTAAAATTTGACT-GAGTACAGTCAAATGAGGAAAG-G
* ** * * ** *
6453 CTGAGAAAAAATA-A-TCAAGGAGGGTAAGATTTGACTGAGTATAGTCAAATGAGGATTGA
1 CT-TGAACGAATACAGTCAA-GAGGGTAAAATTTGACTGAGTACAGTCAAATGAGGAAAGG
* * * * * * * * * ** ** *
6512 TTTGACCAAAAATAATCAATG-GGGGAAGATTTGACCGAGTATTGTCAAATGAGGATTGC
1 CTTGAACGAATACAGTCAA-GAGGGTAAAATTTGACTGAGTACAGTCAAATGAGGAAAGG
* * * * * * * ** *
6571 CTTGACCAAATATAGTCAAAAAGGGTAAAATTTGACTAAGCACAGTCAAATAAGGATTGT
1 CTTGAACGAATACAGTC-AAGAGGGTAAAATTTGACTGAGTACAGTCAAATGAGGAAAGG
* * * * * ** *
6631 CTTGATCGAATACAGTCAATAGGGGTAAAATTTGA-TCAAGCACAGTCAAATAAGGATTGT
1 CTTGAACGAATACAGTCAAGA-GGGTAAAATTTGACT-GAGTACAGTCAAATGAGGAAAGG
* * * * * *
6691 CTTGACCGAATATAGTCAAGAGGGGTAAAATTTGACCGAGCACAATCAAATGAGAAAAGG
1 CTTGAACGAATACAGTCAAGA-GGGTAAAATTTGACTGAGTACAGTCAAATGAGGAAAGG
* * * * *
6751 CTTGACCGAATACAGTCAAAAGGGGTAAAATTTGACCGAGTACAATCAAATGAGGAAAGA
1 CTTGAACGAATACAGTCAAGA-GGGTAAAATTTGACTGAGTACAGTCAAATGAGGAAAGG
** * * * *
6811 CTT-AACGAATACAGTTTAGAGGGCTAAAATTTGATTGAGTACAATTAAATGAGGAAATG
1 CTTGAACGAATACAGTCAAGAGGG-TAAAATTTGACTGAGTACAGTCAAATGAGGAAAGG
* * * * * *
6870 CTTGACCGAATATATTCAAAAGTGATAAAATTTGACCGAGTACAGTCAAATGAGGAAAGG
1 CTTGAACGAATACAGTCAAGAG-GGTAAAATTTGACTGAGTACAGTCAAATGAGGAAAGG
* * *
6930 CTTGACCGAATACAATCAAGAAGGGTAAAATTTGA-TCGAGTACAGTCAAATAAGGAAAGG
1 CTTGAACGAATACAGTCAAG-AGGGTAAAATTTGACT-GAGTACAGTCAAATGAGGAAAGG
* *
6990 CTTGATCGAATATAGTCAAGAGGGGTAAAATTTGA-TCGAGTACAGTCAAATGAGGAAAGG
1 CTTGAACGAATACAGTCAAGA-GGGTAAAATTTGACT-GAGTACAGTCAAATGAGGAAAGG
*
7050 CTTGACCGAATACAGTCAAGAGGGGTAAAATTTGA-TCGAGTACAGTCAAATGAGGAAAGG
1 CTTGAACGAATACAGTCAAGA-GGGTAAAATTTGACT-GAGTACAGTCAAATGAGGAAAGG
* * ** * * * * * *
7110 CCT-AATCGAATACAATCAAGAAGGG-ATGGATTCGACCGAATATAGTCAAATAAGGAAAGT
1 CTTGAA-CGAATACAGTCAAG-AGGGTA-AAATTTGACTGAGTACAGTCAAATGAGGAAAGG
* * * * * * *
7170 CTTGACCGAATACAATTAAGAGAGTTGAGATTTGAAC-GAGTATAGTCAAATGAGGAAAGG
1 CTTGAACGAATACAGTCAAGAG-GGTAAAATTTG-ACTGAGTACAGTCAAATGAGGAAAGG
* * * * *** * * *
7230 ATT-AACCGAATACAGTTAAGCGACGTTGGATTCGACTGAATACAGTCAAATAAGG-AAGG
1 CTTGAA-CGAATACAGTCAAGAG-GGTAAAATTTGACTGAGTACAGTCAAATGAGGAAAGG
* * * ** *
7289 TCTT-AACCGAATACAGTCAAGCAAGGTGAGATTTGACTGAGTGTAATCAAATGAGGAAAGG
1 -CTTGAA-CGAATACAGTCAAG-AGGGTAAAATTTGACTGAGTACAGTCAAATGAGGAAAGG
* * * *** * * * * * * *
7350 CTT-AACCGAATAAAGTTAAGTGAGGTTGGATTCGACGGAATATAGTCAAATAATGAAAGT
1 CTTGAA-CGAATACAGTCAAGAG-GGTAAAATTTGACTGAGTACAGTCAAATGAGGAAAGG
*
7410 CTTGACCGAATACAGTCAAG
1 CTTGAACGAATACAGTCAAG
7430 CAAGGAGGGT
Statistics
Matches: 841, Mismatches: 163, Indels: 68
0.78 0.15 0.06
Matches are distributed among these distances:
58 9 0.01
59 116 0.14
60 690 0.82
61 19 0.02
62 7 0.01
ACGTcount: A:0.40, C:0.13, G:0.24, T:0.23
Consensus pattern (59 bp):
CTTGAACGAATACAGTCAAGAGGGTAAAATTTGACTGAGTACAGTCAAATGAGGAAAGG
Found at i:6516 original size:30 final size:30
Alignment explanation
Indices: 6480--6590 Score: 91
Period size: 30 Copynumber: 3.7 Consensus size: 30
6470 AGGAGGGTAA
*
6480 GATTTGACTGAGTATAGTCAAATGAGGATT
1 GATTTGACCGAGTATAGTCAAATGAGGATT
* ** * * *
6510 GATTTGACCAAAAATAATC-AATGGGGGA-A
1 GATTTGACCGAGTATAGTCAAAT-GAGGATT
*
6539 GATTTGACCGAGTATTGTCAAATGAGGATT
1 GATTTGACCGAGTATAGTCAAATGAGGATT
** * *
6569 GCCTTGACCAAATATAGTCAAA
1 GATTTGACCGAGTATAGTCAAA
6591 AAGGGTAAAA
Statistics
Matches: 59, Mismatches: 19, Indels: 6
0.70 0.23 0.07
Matches are distributed among these distances:
29 21 0.36
30 38 0.64
ACGTcount: A:0.37, C:0.12, G:0.23, T:0.28
Consensus pattern (30 bp):
GATTTGACCGAGTATAGTCAAATGAGGATT
Found at i:6646 original size:30 final size:30
Alignment explanation
Indices: 6612--6709 Score: 85
Period size: 30 Copynumber: 3.3 Consensus size: 30
6602 TTGACTAAGC
6612 ACAGTCAAATAAGGATTGTCTTGATCGAAT
1 ACAGTCAAATAAGGATTGTCTTGATCGAAT
* *** *
6642 ACAGTC-AATAGGGGTAAAAT-TTGATC-AAGC
1 ACAGTCAAATA-AGG-ATTGTCTTGATCGAA-T
*
6672 ACAGTCAAATAAGGATTGTCTTGACCGAAT
1 ACAGTCAAATAAGGATTGTCTTGATCGAAT
*
6702 ATAGTCAA
1 ACAGTCAA
6710 GAGGGGTAAA
Statistics
Matches: 50, Mismatches: 12, Indels: 12
0.68 0.16 0.16
Matches are distributed among these distances:
29 8 0.16
30 34 0.68
31 8 0.16
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.27
Consensus pattern (30 bp):
ACAGTCAAATAAGGATTGTCTTGATCGAAT
Found at i:6726 original size:30 final size:29
Alignment explanation
Indices: 6692--7099 Score: 166
Period size: 30 Copynumber: 13.7 Consensus size: 29
6682 AAGGATTGTC
*
6692 TTGACCGAATATAGTCAAGAGGGGTAAAAT
1 TTGACCGAATACAGTCAA-AGGGGTAAAAT
** * * * *
6722 TTGACCGAGCACAATCAAATGAG-AAAAGGC
1 TTGACCGAATACAGTCAAAGGGGTAAAA--T
6752 TTGACCGAATACAGTCAAAAGGGGTAAAAT
1 TTGACCGAATACAGTC-AAAGGGGTAAAAT
* * * *
6782 TTGACCGAGTACAATCAAATGAGG-AAAGAC
1 TTGACCGAATACAGTCAAA-GGGGTAAA-AT
* * * *
6812 TT-AACGAATACAGTTTAGAGGGCTAAAAT
1 TTGACCGAATACAG-TCAAAGGGGTAAAAT
** * * * *
6841 TTGATTGAGTACAATTAAATGAGG--AAAT
1 TTGACCGAATACAGTCAAA-GGGGTAAAAT
* * * *
6869 GCTTGACCGAATATATTCAAAAGTGATAAAAT
1 --TTGACCGAATACAGTC-AAAGGGGTAAAAT
* * **
6901 TTGACCGAGTACAGTCAAATGAGG-AAAGGC
1 TTGACCGAATACAGTCAAA-GGGGTAAA-AT
* *
6931 TTGACCGAATACAATCAAGAAGGGTAAAAT
1 TTGACCGAATACAGTCAA-AGGGGTAAAAT
* * ** **
6961 TTGATCGAGTACAGTCAAATAAGG-AAAGGC
1 TTGACCGAATACAGTCAAA-GGGGTAAA-AT
* *
6991 TTGATCGAATATAGTCAAGAGGGGTAAAAT
1 TTGACCGAATACAGTCAA-AGGGGTAAAAT
* * * **
7021 TTGATCGAGTACAGTCAAATGAGG-AAAGGC
1 TTGACCGAATACAGTCAAA-GGGGTAAA-AT
7051 TTGACCGAATACAGTCAAGAGGGGTAAAAT
1 TTGACCGAATACAGTCAA-AGGGGTAAAAT
* *
7081 TTGATCGAGTACAGTCAAA
1 TTGACCGAATACAGTCAAA
7100 TGAGGAAAGG
Statistics
Matches: 274, Mismatches: 77, Indels: 55
0.67 0.19 0.14
Matches are distributed among these distances:
28 8 0.03
29 41 0.15
30 197 0.72
31 20 0.07
32 8 0.03
ACGTcount: A:0.41, C:0.13, G:0.24, T:0.22
Consensus pattern (29 bp):
TTGACCGAATACAGTCAAAGGGGTAAAAT
Found at i:6958 original size:299 final size:300
Alignment explanation
Indices: 6558--7123 Score: 823
Period size: 299 Copynumber: 1.9 Consensus size: 300
6548 GAGTATTGTC
* * *
6558 AAATGAGGATTGCCTTGACCAAATATAGTCAAAAAGGGTAAAATTTGACTAAGCACAGTCAAATA
1 AAATGAGGAATGCCTTGACCAAATATAGTCAAAAAGGATAAAATTTGACCAAGCACAGTCAAATA
** * * * * * *
6623 AGGATTGTCTTGATCGAATACAGTCAATAGGGGTAAAATTTGATCAAGCACAGTCAAATAAGGAT
66 AGGAAAGGCTTGACCGAATACAATCAAGAAGGGTAAAATTTGATCAAGCACAGTCAAATAAGGAA
* *
6688 TGTCTTGACCGAATATAGTCAAGAGGGGTAAAATTTGACCGAGCACAATCAAATGAGAAAAGGCT
131 AGGCTTGACCGAATATAGTCAAGAGGGGTAAAATTTGACCGAGCACAATCAAATGAGAAAAGGCT
*
6753 TGACCGAATACAGTCAAAAGGGGTAAAATTTGACCGAGTACAATCAAATGAGGAAAGACTTAA-C
196 TGACCGAATACAGTCAAAAGGGGTAAAATTTGACCGAGTACAATCAAATGAGGAAAGACCTAATC
6817 GAATACAGTTTAGAGGGCTAAAATTTGATTGAGTACAATT
261 GAATACAGTTTAGAGGGCTAAAATTTGATTGAGTACAATT
* * * *
6857 AAATGAGGAAATG-CTTGACCGAATATATTC-AAAAGTGATAAAATTTGACCGAGTACAGTCAAA
1 AAATGAGG-AATGCCTTGACCAAATATAGTCAAAAAG-GATAAAATTTGACCAAGCACAGTCAAA
* * *
6920 TGAGGAAAGGCTTGACCGAATACAATCAAGAAGGGTAAAATTTGATCGAGTACAGTCAAATAAGG
64 TAAGGAAAGGCTTGACCGAATACAATCAAGAAGGGTAAAATTTGATCAAGCACAGTCAAATAAGG
* * * * *
6985 AAAGGCTTGATCGAATATAGTCAAGAGGGGTAAAATTTGATCGAGTACAGTCAAATGAGGAAAGG
129 AAAGGCTTGACCGAATATAGTCAAGAGGGGTAAAATTTGACCGAGCACAATCAAATGAGAAAAGG
* * * *
7050 CTTGACCGAATACAGTCAAGAGGGGTAAAATTTGATCGAGTACAGTCAAATGAGGAAAGGCCTAA
194 CTTGACCGAATACAGTCAAAAGGGGTAAAATTTGACCGAGTACAATCAAATGAGGAAAGACCTAA
7115 TCGAATACA
259 TCGAATACA
7124 ATCAAGAAGG
Statistics
Matches: 234, Mismatches: 30, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
298 5 0.02
299 218 0.93
300 11 0.05
ACGTcount: A:0.41, C:0.13, G:0.23, T:0.23
Consensus pattern (300 bp):
AAATGAGGAATGCCTTGACCAAATATAGTCAAAAAGGATAAAATTTGACCAAGCACAGTCAAATA
AGGAAAGGCTTGACCGAATACAATCAAGAAGGGTAAAATTTGATCAAGCACAGTCAAATAAGGAA
AGGCTTGACCGAATATAGTCAAGAGGGGTAAAATTTGACCGAGCACAATCAAATGAGAAAAGGCT
TGACCGAATACAGTCAAAAGGGGTAAAATTTGACCGAGTACAATCAAATGAGGAAAGACCTAATC
GAATACAGTTTAGAGGGCTAAAATTTGATTGAGTACAATT
Found at i:7085 original size:120 final size:120
Alignment explanation
Indices: 6540--7245 Score: 725
Period size: 120 Copynumber: 5.9 Consensus size: 120
6530 ATGGGGGAAG
** ** * * * * *
6540 ATTTGACCGAGTATTGTCAAATGAGGATTGCCTTGACCAAATATAGTCAAAAAGGGTAAAATTTG
1 ATTTGACCGAGTACAGTCAAATGAGGAAAGGCTTGACCGAATACAGTCAAGAGGGGTAAAATTTG
* * * ** * *
6605 A-CTAAGCACAGTCAAATAAGGATTGTCTTGATCGAATACAGTCAATAGGGGTAAA
66 ATC-GAGTACAGTCAAATGAGGAAAGGCTTGATCGAATACAGTCAAAAGGGGTAAA
* * * * ** * *
6660 ATTTGATCAAGCACAGTCAAATAAGGATTGTCTTGACCGAATATAGTCAAGAGGGGTAAAATTTG
1 ATTTGACCGAGTACAGTCAAATGAGGAAAGGCTTGACCGAATACAGTCAAGAGGGGTAAAATTTG
* * * * *
6725 ACCGAGCACAATCAAATGAGAAAAGGCTTGACCGAATACAGTCAAAAGGGGTAAA
66 ATCGAGTACAGTCAAATGAGGAAAGGCTTGATCGAATACAGTCAAAAGGGGTAAA
* * * ** *
6780 ATTTGACCGAGTACAATCAAATGAGGAAAGACTT-AACGAATACAGTTTAGAGGGCTAAAATTTG
1 ATTTGACCGAGTACAGTCAAATGAGGAAAGGCTTGACCGAATACAGTCAAGAGGGGTAAAATTTG
* * * * * * * * *
6844 ATTGAGTACAATTAAATGAGGAAATGCTTGACCGAATATATTCAAAAGTGATAAA
66 ATCGAGTACAGTCAAATGAGGAAAGGCTTGATCGAATACAGTCAAAAGGGGTAAA
* *
6899 ATTTGACCGAGTACAGTCAAATGAGGAAAGGCTTGACCGAATACAATCAAGAAGGGTAAAATTTG
1 ATTTGACCGAGTACAGTCAAATGAGGAAAGGCTTGACCGAATACAGTCAAGAGGGGTAAAATTTG
* * *
6964 ATCGAGTACAGTCAAATAAGGAAAGGCTTGATCGAATATAGTCAAGAGGGGTAAA
66 ATCGAGTACAGTCAAATGAGGAAAGGCTTGATCGAATACAGTCAAAAGGGGTAAA
*
7019 ATTTGATCGAGTACAGTCAAATGAGGAAAGGCTTGACCGAATACAGTCAAGAGGGGTAAAATTTG
1 ATTTGACCGAGTACAGTCAAATGAGGAAAGGCTTGACCGAATACAGTCAAGAGGGGTAAAATTTG
* * * * **
7084 ATCGAGTACAGTCAAATGAGGAAAGGCCTAATCGAATACAATCAAGAAGGGAT-GG
66 ATCGAGTACAGTCAAATGAGGAAAGGCTTGATCGAATACAGTCAA-AAGGGGTAAA
* * * * * * * * * * *
7139 ATTCGACCGAATATAGTCAAATAAGGAAAGTCTTGACCGAATACAATTAAGAGAGTTGAGATTTG
1 ATTTGACCGAGTACAGTCAAATGAGGAAAGGCTTGACCGAATACAGTCAAGAGGGGTAAAATTTG
* * * * *
7204 AACGAGTATAGTCAAATGAGGAAAGGATTAACCGAATACAGT
66 ATCGAGTACAGTCAAATGAGGAAAGGCTTGATCGAATACAGT
7246 TAAGCGACGT
Statistics
Matches: 493, Mismatches: 90, Indels: 6
0.84 0.15 0.01
Matches are distributed among these distances:
119 102 0.21
120 385 0.78
121 6 0.01
ACGTcount: A:0.41, C:0.13, G:0.24, T:0.23
Consensus pattern (120 bp):
ATTTGACCGAGTACAGTCAAATGAGGAAAGGCTTGACCGAATACAGTCAAGAGGGGTAAAATTTG
ATCGAGTACAGTCAAATGAGGAAAGGCTTGATCGAATACAGTCAAAAGGGGTAAA
Found at i:7118 original size:30 final size:30
Alignment explanation
Indices: 6901--7183 Score: 168
Period size: 30 Copynumber: 9.4 Consensus size: 30
6891 GTGATAAAAT
* *
6901 TTGACCGAGTACAGTCAAATGAGGAAAGGC
1 TTGATCGAATACAGTCAAATGAGGAAAGGC
* * * **
6931 TTGACCGAATACAATCAAGAAG-GGTAAA-AT
1 TTGATCGAATACAGTCAA-ATGAGG-AAAGGC
* *
6961 TTGATCGAGTACAGTCAAATAAGGAAAGGC
1 TTGATCGAATACAGTCAAATGAGGAAAGGC
* * **
6991 TTGATCGAATATAGTCAAGA-GGGGTAAA-AT
1 TTGATCGAATACAGTCAA-ATGAGG-AAAGGC
*
7021 TTGATCGAGTACAGTCAAATGAGGAAAGGC
1 TTGATCGAATACAGTCAAATGAGGAAAGGC
* * **
7051 TTGACCGAATACAGTCAAGA-GGGGTAAA-AT
1 TTGATCGAATACAGTCAA-ATGAGG-AAAGGC
*
7081 TTGATCGAGTACAGTCAAATGAGGAAAGGC
1 TTGATCGAATACAGTCAAATGAGGAAAGGC
* * * * * *
7111 CTAATCGAATACAATC-AA-GAAGGGATGGA
1 TTGATCGAATACAGTCAAATG-AGGAAAGGC
* * * *
7140 TTCGACCGAATATAGTCAAATAAGGAAAGTC
1 TT-GATCGAATACAGTCAAATGAGGAAAGGC
*
7171 TTGACCGAATACA
1 TTGATCGAATACA
7184 ATTAAGAGAG
Statistics
Matches: 186, Mismatches: 51, Indels: 32
0.69 0.19 0.12
Matches are distributed among these distances:
28 1 0.01
29 21 0.11
30 142 0.76
31 22 0.12
ACGTcount: A:0.40, C:0.14, G:0.25, T:0.20
Consensus pattern (30 bp):
TTGATCGAATACAGTCAAATGAGGAAAGGC
Found at i:8438 original size:21 final size:20
Alignment explanation
Indices: 8400--8442 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
8390 TCTTTTCCCC
* *
8400 TTTTATTGATTTTTTTTTCTT
1 TTTTATTGATTATCTTTT-TT
*
8421 TTTTATTGCTTATCTTTTTT
1 TTTTATTGATTATCTTTTTT
8441 TT
1 TT
8443 ATTGCCCCAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.09, C:0.07, G:0.05, T:0.79
Consensus pattern (20 bp):
TTTTATTGATTATCTTTTTT
Found at i:8733 original size:9 final size:9
Alignment explanation
Indices: 8721--8786 Score: 50
Period size: 9 Copynumber: 7.6 Consensus size: 9
8711 CTTTTCATGA
8721 TTTTTCATT
1 TTTTTCATT
8730 TTTTTC--T
1 TTTTTCATT
*
8737 TGTTTC--T
1 TTTTTCATT
*
8744 ATTTTCATT
1 TTTTTCATT
*
8753 TCTTTCATT
1 TTTTTCATT
*
8762 CTTTTCATT
1 TTTTTCATT
8771 TCTTTTCATT
1 T-TTTTCATT
8781 CTTTTT
1 -TTTTT
8787 TCTTATTTTT
Statistics
Matches: 45, Mismatches: 8, Indels: 7
0.75 0.13 0.12
Matches are distributed among these distances:
7 11 0.24
9 21 0.47
10 12 0.27
11 1 0.02
ACGTcount: A:0.09, C:0.17, G:0.02, T:0.73
Consensus pattern (9 bp):
TTTTTCATT
Found at i:8768 original size:18 final size:19
Alignment explanation
Indices: 8745--8785 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
8735 CTTGTTTCTA
8745 TTTTCATTTC-TTTCATTC
1 TTTTCATTTCTTTTCATTC
8763 TTTTCATTTCTTTTCATTC
1 TTTTCATTTCTTTTCATTC
8782 TTTT
1 TTTT
8786 TTCTTATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 10 0.45
19 12 0.55
ACGTcount: A:0.10, C:0.20, G:0.00, T:0.71
Consensus pattern (19 bp):
TTTTCATTTCTTTTCATTC
Found at i:11295 original size:79 final size:79
Alignment explanation
Indices: 11199--11576 Score: 379
Period size: 79 Copynumber: 4.8 Consensus size: 79
11189 ATAAAAGCGA
* * **
11199 GGTTGGAGTAACCCCAAGATGAAAATTTTAATATTTTTGAAATAAAAACAGGGTTGGAGTAT-CC
1 GGTTGGAGTATCCCCAAGATGAAAATTTTAATATTTTGGAAATAAAAATGGGGTTGGAGTATCCC
*
11263 TCTC-GAAAATAATAG
66 T-TCAG-AAATAATGG
* *
11278 GGTTGGAGTATCCCCAAGAAGAAAA--TTAATATTTTGGAAATAAAAGTGGGGTTGGAGTATCCC
1 GGTTGGAGTATCCCCAAGATGAAAATTTTAATATTTTGGAAATAAAAATGGGGTTGGAGTATCCC
* *
11341 TTCAGAATTGATGG
66 TTCAGAAATAATGG
* * * * *
11355 GGTTGAAGTATCCCTAAGAAGAAAATTTTAATATTTTGGAAATGAAAATGGGGTTAGAGTATCCC
1 GGTTGGAGTATCCCCAAGATGAAAATTTTAATATTTTGGAAATAAAAATGGGGTTGGAGTATCCC
* * *
11420 TTCGGAATTGATGG
66 TTCAGAAATAATGG
* * * * ** * **
11434 AGTTGGAGTATCCCCAAAATAAAAAATTTAATATTTTAAAAATAAAAATAGGGTTTAAGTATCCC
1 GGTTGGAGTATCCCCAAGATGAAAATTTTAATATTTTGGAAATAAAAATGGGGTTGGAGTATCCC
* *
11499 CTCAGAAATAACGG
66 TTCAGAAATAATGG
*** * * * *
11513 GGCTT-GAGTATCCCCGTCATGAAAACTTCAATATTTTGGAAATAAAAACGGGGTTGGAATATCC
1 GG-TTGGAGTATCCCCAAGATGAAAATTTTAATATTTTGGAAATAAAAATGGGGTTGGAGTATCC
11577 TCGAGATAAA
Statistics
Matches: 247, Mismatches: 47, Indels: 10
0.81 0.15 0.03
Matches are distributed among these distances:
77 62 0.25
78 4 0.02
79 179 0.72
80 2 0.01
ACGTcount: A:0.37, C:0.12, G:0.22, T:0.29
Consensus pattern (79 bp):
GGTTGGAGTATCCCCAAGATGAAAATTTTAATATTTTGGAAATAAAAATGGGGTTGGAGTATCCC
TTCAGAAATAATGG
Found at i:14016 original size:20 final size:20
Alignment explanation
Indices: 13991--14046 Score: 103
Period size: 20 Copynumber: 2.8 Consensus size: 20
13981 TAAACAGTAA
13991 ATGTATCGATACATTTACTT
1 ATGTATCGATACATTTACTT
14011 ATGTATCGATACATTTACTT
1 ATGTATCGATACATTTACTT
*
14031 ATGTATCGATATATTT
1 ATGTATCGATACATTT
14047 TCTTGGCAGT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.30, C:0.12, G:0.11, T:0.46
Consensus pattern (20 bp):
ATGTATCGATACATTTACTT
Found at i:15074 original size:62 final size:62
Alignment explanation
Indices: 14864--15696 Score: 862
Period size: 62 Copynumber: 13.4 Consensus size: 62
14854 TGGCACACTT
* * * * * *
14864 TCTTTGAGGACTAAAAGGTGCCACCAACTTGTAT-GGTTTTTAAGAGGAAAAAAGAAAGTGTCCT
1 TCTTTGAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTTGAA-AAG-AAAAAG--A-CGTCCT
14928 GC
61 GC
* * *
14930 TCTTTGAGGACTAAAAGGTGTCACCAACTCGTGTGGGGTTT-AAAAGAAAAAAACGTCCTGC
1 TCTTTGAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGACGTCCTGC
* * **
14991 TCTTTGAGGACAAAAAGGGTGCCACCAACTCGTGTAGGCTTTGAAAAGAAAAAGGTGTCCTGC
1 TCTTTGAGGACTAAAA-GGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGACGTCCTGC
* * *
15054 TCTTTGAGGACTAAAAGGTGCAACCAACTCGTGTGGGCTTTGAAAAGAAAAAGACATCCTTC
1 TCTTTGAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGACGTCCTGC
* * *
15116 TCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTTAAAAAGAAAAAGACATCCTGC
1 TCTTTGAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGACGTCCTGC
* * * * ** * * * *
15178 TTTTTGAGAACTAAAGGGTACCACCAACTTATGTAGGCTTTG-AAA-AAAAAGATGACTTGC
1 TCTTTGAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGACGTCCTGC
* * ** ** *
15238 TTTTTGAGGACTAAAGGGTGCCATGAACTCGTGTGGGCTTTGAAAAGGAAAAAGGTGTCTTGC
1 TCTTTGAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTTGAAAA-GAAAAAGACGTCCTGC
* * * * *
15301 TCTTTGAGGACTAAAGGGTGCCACCAATTCATATGGGCTTTGAAAAGAAAAATG-CTTCCTGC
1 TCTTTGAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAA-GACGTCCTGC
* * * * *
15363 TCTTTGAGGAATAAAAAGGTGCCACCAACTCGTGTGAGCTTTGTAAAGAAAAAGGCGTCATGC
1 TCTTTGAGGACT-AAAAGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGACGTCCTGC
* * * *
15426 TCTTTGAGGACTAAAAGGTG-CACCAACTTGTGTGGGCTTTTAAAAAGGAAAAGCAC--CTTGC
1 TCTTTGAGGACTAAAAGGTGCCACCAACTCGTGTGGGC-TTTGAAAAGAAAAAG-ACGTCCTGC
* * * ** * * * *
15487 CCTTTGAGAACTAAAAGGTGCCACCACCTTATGTGGGCTTTG-AAGGGAAAAGACATCTTGC
1 TCTTTGAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGACGTCCTGC
* *
15548 TCTTTGAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTTTAAAAGAAAAAGACGT-C-AC
1 TCTTTGAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGACGTCCTGC
*
15608 TCTTTGAGGACTAGAAAGGTGCCACCAACTCGTAGTGGGCTTTGAAAAGAGAAAATG-CGTCTTG
1 TCTTTGAGGACTA-AAAGGTGCCACCAACTCGT-GTGGGCTTTGAAAAGA-AAAA-GACGTCCTG
15672 C
62 C
* *
15673 TTTTTTGAGGACTAAAGGGTGCCA
1 -TCTTTGAGGACTAAAAGGTGCCA
15697 AGGGTGCCAA
Statistics
Matches: 652, Mismatches: 93, Indels: 45
0.83 0.12 0.06
Matches are distributed among these distances:
59 2 0.00
60 69 0.11
61 128 0.20
62 240 0.37
63 145 0.22
64 6 0.01
65 12 0.02
66 45 0.07
67 5 0.01
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.25
Consensus pattern (62 bp):
TCTTTGAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGACGTCCTGC
Found at i:15597 original size:184 final size:184
Alignment explanation
Indices: 14927--16197 Score: 1140
Period size: 184 Copynumber: 6.8 Consensus size: 184
14917 GAAAGTGTCC
* * * * * *
14927 TGCTCTTTGAGGACTAAAAGGTGTCACCAACTCGTGTGGGGTTTAAAAGAAAAAAACGTCCTGCT
1 TGCTCTTTGAGGACTAAAAGGTGCCACCAACTCATGTGGGCTTTGAAAGAAAAAGACATCCTGCT
* * * * *
14992 CTTTGAGGACAAAAAGGGTGCCACCAACTCGTGTAGGCTTTGAAAAGAAAAAGGTGTCCTGCTCT
66 CTTTGAGGAC-TAAAGGGTGCCACCAACTCGTGTGGGCTTTTAAAAGAAAAAGGCGTCTTGCTCT
* *
15057 TTGAGGACTAAAAGGTGCAACCAACTCGTGTGGGCTTTGAAAAGAAAAAGACATCCT
130 TTGAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTTGAAAAGGAAAAG-CA-CCT
* * *
15114 T-CTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTTAAAAAGAAAAAGACATCCTGC
1 TGCTCTTTGAGGACTAAAAGGTGCCACCAACTCATGTGGGCTTT-GAAAGAAAAAGACATCCTGC
* * * ** * * ** * *
15178 TTTTTGAGAACTAAAGGGTACCACCAACTTATGTAGGC-TTTGAAA-AAAAAGATGACTTGCTTT
65 TCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTTTAAAAGAAAAAGGCGTCTTGCTCT
* ** ***
15241 TTGAGGACTAAAGGGTGCCATGAACTCGTGTGGGCTTTGAAAAGGAAAAAGGTGTCT
130 TTGAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTTGAAAAGG-AAAA-GCACCT
* * * *
15298 TGCTCTTTGAGGACTAAAGGGTGCCACCAATTCATATGGGCTTTGAAAAGAAAAATG-CTTCCTG
1 TGCTCTTTGAGGACTAAAAGGTGCCACCAACTCATGTGGGCTTTG-AAAGAAAAA-GACATCCTG
* * * *
15362 CTCTTTGAGGAATAAAAAGGTGCCACCAACTCGTGTGAGCTTTGT-AAAGAAAAAGGCGTCATGC
64 CTCTTTGAGGACT-AAAGGGTGCCACCAACTCGTGTGGGCTTT-TAAAAGAAAAAGGCGTCTTGC
* *
15426 TCTTTGAGGACTAAAAGGTG-CACCAACTTGTGTGGGCTTTTAAAAAGGAAAAGCACCT
127 TCTTTGAGGACTAAAAGGTGCCACCAACTCGTGTGGGC-TTTGAAAAGGAAAAGCACCT
* * * * * * *
15484 TGCCCTTTGAGAACTAAAAGGTGCCACCACCTTATGTGGGCTTTGAAGGGAAAAGACATCTTGCT
1 TGCTCTTTGAGGACTAAAAGGTGCCACCAACTCATGTGGGCTTTGAAAGAAAAAGACATCCTGCT
* * *
15549 CTTTGAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTTTAAAAGAAAAAGACGTC--ACTCTT
66 CTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTTTAAAAGAAAAAGGCGTCTTGCTCTT
**
15612 TGAGGACTAGAAAGGTGCCACCAACTCGTAGTGGGCTTTGAAAAGAGAAAATGCGTCT
131 TGAGGACTA-AAAGGTGCCACCAACTCGT-GTGGGCTTTGAAAAG-GAAAA-GCACCT
* *
15670 TGCTTTTTTGAGGACTAAAGGGTGCCAAGGGTGCCAAGGGTGCCACCAACTCACGTGGGCTTTGA
1 TGC-TCTTTGAGGAC-------T---AA-------AA-GGTGCCACCAACTCATGTGGGCTTTG-
* * * *
15735 AAAGAAAAAAGGCATCCTACTCTTTGAGGACTAAAGGGTGCCACCAATTCGTGTGGG-TTTTGAA
46 AAAG-AAAAAGACATCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTTTAAA
* * *
15799 A-AAAAAGGCATCTTGC-CTTTTGAGGACT-AAAGAGTGCCACCAACTCATGTGGACTTTGAAAA
110 AGAAAAAGGCGTCTTGCTC-TTTGAGGACTAAAAG-GTGCCACCAACTCGTGTGGGCTTTGAAAA
*
15861 GAAAAAAGCATCC-
173 G-GAAAAGCA-CCT
* * * * ** * *
15874 TGCTCTTTGAAGACTAAAGGGTGCTATCAACTTGTGTGGGCTTTGAAAAGAAAAAGGCATCCTAC
1 TGCTCTTTGAGGACTAAAAGGTGCCACCAACTCATGTGGGCTTTG-AAAGAAAAAGACATCCTGC
* * * * * * *
15939 TCTTTGAGGACTAGAAGGGTGCCATCAACTCATTTGGGC-TTGAAAAGAGAAAGGCATCTTACTC
65 TCTTTGAGGACTA-AAGGGTGCCACCAACTCGTGTGGGCTTTTAAAAGAAAAAGGCGTCTTGCTC
* * * *
16003 TTTGAGGACT-AAGGGTGCCACCAACTCGTGTGGGTTTTGAAAA-AAAAAG-ACGTCC
129 TTTGAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTTGAAAAGGAAAAGCAC--CT
* ** *
16058 TGCTTTTTGAGGACT-AAAGAGTGCCACCAACTCATGTGGATTTTGAAAAGAAAAAGGCATCCTG
1 TGCTCTTTGAGGACTAAAAG-GTGCCACCAACTCATGTGGGCTTTG-AAAGAAAAAGACATCCTG
* * * * * * *
16122 CTCTTTGAGGACTAAAGGGTGCCATCAACTTGTGTGGGCTTTGAAAAGAAACAGGCATCCTACTC
64 CTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTTTAAAAGAAAAAGGCGTCTTGCTC
16187 -TTGAGGACTAA
129 TTTGAGGACTAA
Statistics
Matches: 901, Mismatches: 129, Indels: 111
0.79 0.11 0.10
Matches are distributed among these distances:
181 1 0.00
182 15 0.02
183 49 0.05
184 233 0.26
185 185 0.21
186 159 0.18
187 60 0.07
188 39 0.04
193 2 0.00
194 1 0.00
196 1 0.00
197 2 0.00
203 9 0.01
204 7 0.01
205 56 0.06
206 25 0.03
207 57 0.06
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.25
Consensus pattern (184 bp):
TGCTCTTTGAGGACTAAAAGGTGCCACCAACTCATGTGGGCTTTGAAAGAAAAAGACATCCTGCT
CTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTTTAAAAGAAAAAGGCGTCTTGCTCTT
TGAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTTGAAAAGGAAAAGCACCT
Found at i:15701 original size:9 final size:9
Alignment explanation
Indices: 15687--15714 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
15677 TTGAGGACTA
15687 AAGGGTGCC
1 AAGGGTGCC
15696 AAGGGTGCC
1 AAGGGTGCC
15705 AAGGGTGCC
1 AAGGGTGCC
15714 A
1 A
15715 CCAACTCACG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.25, C:0.21, G:0.43, T:0.11
Consensus pattern (9 bp):
AAGGGTGCC
Found at i:15772 original size:81 final size:82
Alignment explanation
Indices: 15625--15777 Score: 220
Period size: 82 Copynumber: 1.9 Consensus size: 82
15615 GGACTAGAAA
* * * * * *
15625 GGTGCCACCAACTCGTAGTGGGCTTTGAAAAGAGAAAATGCGTCTTGCTTTTTTGAGGACTAAAG
1 GGTGCCACCAACTCG-AGTGGGCTTTGAAAAGAAAAAAGGCATCCTACTTCTTTGAGGACTAAAG
15690 GGTGCCAAGGGTGCCAAG
65 GGTGCCAAGGGTGCCAAG
15708 GGTGCCACCAACTC-ACGTGGGCTTTGAAAAGAAAAAAGGCATCCTAC-TCTTTGAGGACTAAAG
1 GGTGCCACCAACTCGA-GTGGGCTTTGAAAAGAAAAAAGGCATCCTACTTCTTTGAGGACTAAAG
15771 GGTGCCA
65 GGTGCCA
15778 CCAATTCGTG
Statistics
Matches: 63, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
81 23 0.37
82 26 0.41
83 14 0.22
ACGTcount: A:0.29, C:0.20, G:0.29, T:0.22
Consensus pattern (82 bp):
GGTGCCACCAACTCGAGTGGGCTTTGAAAAGAAAAAAGGCATCCTACTTCTTTGAGGACTAAAGG
GTGCCAAGGGTGCCAAG
Found at i:15905 original size:62 final size:62
Alignment explanation
Indices: 15705--16197 Score: 613
Period size: 62 Copynumber: 8.0 Consensus size: 62
15695 CAAGGGTGCC
*
15705 AAGGGTGCCACCAACTCACGTGGGCTTTGAAAAGAAAAAAGGCATCCTACTCTTTGAGGACTA
1 AAGGGTGCCACCAACTCATGTGGGCTTTGAAAAG-AAAAAGGCATCCTACTCTTTGAGGACTA
* * * * *
15768 AAGGGTGCCACCAATTCGTGTGGGTTTTG-AAA-AAAAAGGCATCTTGC-CTTTTGAGGACTA
1 AAGGGTGCCACCAACTCATGTGGGCTTTGAAAAGAAAAAGGCATCCTACTC-TTTGAGGACTA
* * * * *
15828 AAGAGTGCCACCAACTCATGTGGACTTTGAAAAGAAAAAAGCATCCTGCTCTTTGAAGACTA
1 AAGGGTGCCACCAACTCATGTGGGCTTTGAAAAGAAAAAGGCATCCTACTCTTTGAGGACTA
* * **
15890 AAGGGTGCTATCAACTTGTGTGGGCTTTGAAAAGAAAAAGGCATCCTACTCTTTGAGGACTA
1 AAGGGTGCCACCAACTCATGTGGGCTTTGAAAAGAAAAAGGCATCCTACTCTTTGAGGACTA
* * * *
15952 GAAGGGTGCCATCAACTCATTTGGGC-TTGAAAAGAGAAAGGCATCTTACTCTTTGAGGACT-
1 -AAGGGTGCCACCAACTCATGTGGGCTTTGAAAAGAAAAAGGCATCCTACTCTTTGAGGACTA
* * * * * *
16013 AAGGGTGCCACCAACTCGTGTGGGTTTTGAAAA-AAAAAGACGTCCTGCTTTTTGAGGACTA
1 AAGGGTGCCACCAACTCATGTGGGCTTTGAAAAGAAAAAGGCATCCTACTCTTTGAGGACTA
* ** *
16074 AAGAGTGCCACCAACTCATGTGGATTTTGAAAAGAAAAAGGCATCCTGCTCTTTGAGGACTA
1 AAGGGTGCCACCAACTCATGTGGGCTTTGAAAAGAAAAAGGCATCCTACTCTTTGAGGACTA
* ** *
16136 AAGGGTGCCATCAACTTGTGTGGGCTTTGAAAAGAAACAGGCATCCTACTC-TTGAGGACTA
1 AAGGGTGCCACCAACTCATGTGGGCTTTGAAAAGAAAAAGGCATCCTACTCTTTGAGGACTA
16197 A
1 A
Statistics
Matches: 369, Mismatches: 53, Indels: 18
0.84 0.12 0.04
Matches are distributed among these distances:
59 1 0.00
60 90 0.24
61 51 0.14
62 180 0.49
63 47 0.13
ACGTcount: A:0.32, C:0.19, G:0.25, T:0.25
Consensus pattern (62 bp):
AAGGGTGCCACCAACTCATGTGGGCTTTGAAAAGAAAAAGGCATCCTACTCTTTGAGGACTA
Found at i:16180 original size:246 final size:247
Alignment explanation
Indices: 15705--16196 Score: 810
Period size: 246 Copynumber: 2.0 Consensus size: 247
15695 CAAGGGTGCC
15705 AAGGGTGCCACCAACTCACGTGGGCTTTGAAAAGAAAAAAGGCATCCTACTCTTTGAGGACTAAA
1 AAGGGTGCCACCAACTCACGTGGGCTTTGAAAAGAAAAAAGGCATCCTACTCTTTGAGGACTAAA
* * *
15770 GGGTGCCACCAATTCGTGTGGGTTTTGAAAAAAAAGGCATCTTGCCTTTTGAGGACTAAAGAGTG
66 GGGTGCCACCAACTCGTGTGGGTTTTGAAAAAAAAGACATCCTGCCTTTTGAGGACTAAAGAGTG
*
15835 CCACCAACTCATGTGGACTTTGAAAAGAAAAAAGCATCCTGCTCTTTGAAGACTAAAGGGTGCTA
131 CCACCAACTCATGTGGACTTTGAAAAGAAAAAAGCATCCTGCTCTTTGAAGACTAAAGGGTGCCA
15900 TCAACTTGTGTGGGCTTTGAAAAGAAAAAGGCATCCTACTCTTTGAGGACTAG
196 TCAACTTGTGTGGGCTTTGAAAAGAAAAAGGCATCCTACTC-TTGAGGACTAG
* ** * *
15953 AAGGGTGCCATCAACTCATTTGGGC-TTGAAAAG-AGAAAGGCATCTTACTCTTTGAGGACT-AA
1 AAGGGTGCCACCAACTCACGTGGGCTTTGAAAAGAAAAAAGGCATCCTACTCTTTGAGGACTAAA
* *
16015 GGGTGCCACCAACTCGTGTGGGTTTTGAAAAAAAAAGACGTCCTGCTTTTTGAGGACTAAAGAGT
66 GGGTGCCACCAACTCGTGTGGGTTTTG-AAAAAAAAGACATCCTGCCTTTTGAGGACTAAAGAGT
* * *
16080 GCCACCAACTCATGTGGATTTTGAAAAGAAAAAGGCATCCTGCTCTTTGAGGACTAAAGGGTGCC
130 GCCACCAACTCATGTGGACTTTGAAAAGAAAAAAGCATCCTGCTCTTTGAAGACTAAAGGGTGCC
*
16145 ATCAACTTGTGTGGGCTTTGAAAAGAAACAGGCATCCTACTCTTGAGGACTA
195 ATCAACTTGTGTGGGCTTTGAAAAGAAAAAGGCATCCTACTCTTGAGGACTA
16197 A
Statistics
Matches: 228, Mismatches: 15, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
245 38 0.17
246 160 0.70
247 8 0.04
248 22 0.10
ACGTcount: A:0.32, C:0.19, G:0.25, T:0.25
Consensus pattern (247 bp):
AAGGGTGCCACCAACTCACGTGGGCTTTGAAAAGAAAAAAGGCATCCTACTCTTTGAGGACTAAA
GGGTGCCACCAACTCGTGTGGGTTTTGAAAAAAAAGACATCCTGCCTTTTGAGGACTAAAGAGTG
CCACCAACTCATGTGGACTTTGAAAAGAAAAAAGCATCCTGCTCTTTGAAGACTAAAGGGTGCCA
TCAACTTGTGTGGGCTTTGAAAAGAAAAAGGCATCCTACTCTTGAGGACTAG
Done.