Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1599
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: 108545
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:187 original size:61 final size:61
Alignment explanation
Indices: 1--1708 Score: 2123
Period size: 61 Copynumber: 28.2 Consensus size: 61
* * * * *
1 TAGTCCTTAAAGAGTAGGACACC-ATTTCTTTTCAAAGCCCACACCAGTTAGTGGCACCTT
1 TAGTCCTCAAAGAGCAGGACACCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTT
*
61 TAGTACTC-AA-AG-A-G-CACC-TTTTCTTTT-AAAGCCCACACAAGTTGGTGGCACCTTT
1 TAGTCCTCAAAGAGCAGGACACCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACC-TT
* * * *
116 TAGTCTTCAAAGAGTAGGACACCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACATT
1 TAGTCCTCAAAGAGCAGGACACCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTT
* *
177 TAGTCCTCAAAGAGCAAGACACCTTTTCCTTTT-AAAGCCCACACAAGTTGGTGGCACCTTT
1 TAGTCCTCAAAGAGCAGGACACCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACC-TT
* * *
238 TAGTCTTCAAAGAGTAGGACA-CTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCTTT
1 TAGTCCTCAAAGAGCAGGACACCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACC-TT
* * * **
299 TAGTCCTCAAAAAGCAGGACAACTTTTTCTCTTCAAAGCCCACATGAGTTGGTGGCACCTT
1 TAGTCCTCAAAGAGCAGGACACCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTT
360 TAGTCCTCAAAGAGCAGGACACCTTTTT-TTTT-AAAGCCCACACAAGTTGGTGGCACCTTT
1 TAGTCCTCAAAGAGCAGGACACCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACC-TT
* *
420 TAGTCCTCAAAGAGCAGG--ACCTTTTTCTTTTCAAAGCTCACACGAGTTGGTGGCACCCTT
1 TAGTCCTCAAAGAGCAGGACACCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCA-CCTT
* ** *
480 TAGTCCTCAAAAAGCAGGATGCCTTTTT-TTTTCAAA-CTCACACAAGTTGGTGGCACCTT
1 TAGTCCTCAAAGAGCAGGACACCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTT
*
539 TAGTCCTCAAAGAGCAGGACACCTTTTTCTTTTCAAAGCCCACACTAGTTGGTGGCACTCTT
1 TAGTCCTCAAAGAGCAGGACACCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCAC-CTT
* *
601 TAGCCCTCAAAGAGCAGGACACCTTTTTCTTTTCAAAGCCCA-ACGAGTTGGTGGCACCTT
1 TAGTCCTCAAAGAGCAGGACACCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTT
* * * ** *
661 TACTCATCAAAGAGTAGGACGTCTTTTCCTTTT-AAAGCCCACACAAGTTGGTGGCACCTT
1 TAGTCCTCAAAGAGCAGGACACCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTT
* * *
721 CTAGTCCTCAAAGAGCAGAACACC-TTTTC-CTTCAAAGCCCACACAAGTTGGTGGCACTTTT
1 -TAGTCCTCAAAGAGCAGGACACCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCAC-CTT
* * *
782 TAGTCTTCAAAGAACAGGACACCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCTT
1 TAGTCCTCAAAGAGCAGGACACCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTT
* *
843 TAGTCCTCAAAGTGCAGGACACCTTTTCCTTTT-AAAGCCCACACAAGTTGGTGGCACCTTT
1 TAGTCCTCAAAGAGCAGGACACCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACC-TT
* * * *
904 TAGTCTTCAAAGAGTAGGACACTTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCTT
1 TAGTCCTCAAAGAGCAGGACACCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTT
* * * * * **
965 TAGGTCCTCAAAAAGCAAGACAAC-GTTTCTCTTCAAAGCCCACATGAGTTGGTGGCACCTT
1 TA-GTCCTCAAAGAGCAGGACACCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTT
*
1026 TAGTCCTCAAAGAGCAGGACACCTTTTCCTTTT-AAAGCCCACACAAGTTGGTGGCACCTTT
1 TAGTCCTCAAAGAGCAGGACACCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACC-TT
*
1087 TAGTCCTCAAAGAGCAGGACACCTTTTCCTTTT-AAAGCCCACACAAGTTGGTGGCACCTTT
1 TAGTCCTCAAAGAGCAGGACACCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACC-TT
*
1148 TAGTCCTCAAAGAGCAGGACACC-TTTTCTTTTCAAAGCCCACACGAGTTTGGTGGCACCCTT
1 TAGTCCTCAAAGAGCAGGACACCTTTTTCTTTTCAAAGCCCACACAAG-TTGGTGGCA-CCTT
* **
1210 TAGTCCTCAAAAAGCAGGATGCCTTTTTCTTTTCAAA-CCCACACAAGTTGGTGGCACCTT
1 TAGTCCTCAAAGAGCAGGACACCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTT
* *
1270 TAGTCCTCAAAGAGCAGGATACCTTTTCCTTTT-AAAGCCCACACAAGTTGGTGGCACCTTT
1 TAGTCCTCAAAGAGCAGGACACCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACC-TT
* * * *
1331 TAGTCCTCAAACAGCAGGACATCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACGTTT
1 TAGTCCTCAAAGAGCAGGACACCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCAC-CTT
* * ** *
1393 TAGCCCTCAAAGAGTAGGATGCCTTTTCCTTTT-AAAGCCCACACAAGTTGGTGGCACCTT
1 TAGTCCTCAAAGAGCAGGACACCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTT
* * * * * *
1453 CTAGTCCTCAAGGAGCAAGACGCC-TTCTC-CTTGAAAGCCCACACAAGTTGGTGGCACCTTT
1 -TAGTCCTCAAAGAGCAGGACACCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACC-TT
* * * * **
1514 TAGTCCTCAAAAAGCAGGACACATTTTTCTTTTCAAGGCCAACATGAGTTGGTGGCACCCTT
1 TAGTCCTCAAAGAGCAGGACACCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCA-CCTT
* * * * * *
1576 TAGTCCTTAGAGAGTAGGACGCCTTTTCCTTTT-AAAGCCCATACAAGTTGGTGGCACCTT
1 TAGTCCTCAAAGAGCAGGACACCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTT
* * * * * ** *
1636 CTAGTCCTCAAAGAGTAGGACGCC-TTCTC-TTTAAAAGCCCATATTAGTTGGTGGCACCTCC
1 -TAGTCCTCAAAGAGCAGGACACCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCT-T
1697 TAGTCCTCAAAG
1 TAGTCCTCAAAG
1709 GGGAGGACGC
Statistics
Matches: 1444, Mismatches: 156, Indels: 96
0.85 0.09 0.06
Matches are distributed among these distances:
54 23 0.02
55 20 0.01
56 3 0.00
57 3 0.00
58 11 0.01
59 77 0.05
60 445 0.31
61 531 0.37
62 314 0.22
63 17 0.01
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.29
Consensus pattern (61 bp):
TAGTCCTCAAAGAGCAGGACACCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTT
Found at i:1764 original size:45 final size:45
Alignment explanation
Indices: 1699--2035 Score: 305
Period size: 45 Copynumber: 7.6 Consensus size: 45
1689 GCACCTCCTA
* * * * **
1699 GTCCTCAAAGGGGAGGACGCACTGCATTTTTTTCTTTTCCCTTTT
1 GTCCTCAAAGAGCAGGACACACTTCATTTCCTTCTTTTCCCTTTT
* * * * **
1744 ATCCTCAAAGAGCAGGACGCACTTTATTT--TCCTTTTCCCCCTT
1 GTCCTCAAAGAGCAGGACACACTTCATTTCCTTCTTTTCCCTTTT
* * * * * *
1787 ATCCTTAAAAAGCACGACACA-TTCCATTCCCTTCTTTGCCCCTTTT
1 GTCCTCAAAGAGCAGGACACACTT-CATTTCCTTCTTT-TCCCTTTT
* * *
1833 GTCCTCAAAGAGCAAGACCCACTTCATTTCTTTCTTTTCCCTTTT
1 GTCCTCAAAGAGCAGGACACACTTCATTTCCTTCTTTTCCCTTTT
** * *
1878 -TCCCTCAAAGAGCAGGATGCACTTTATTTTCCTT-TTTT-CC-ATT
1 GT-CCTCAAAGAGCAGGACACACTTCA-TTTCCTTCTTTTCCCTTTT
* *
1921 GTCCTCAAAGAGCAGGACAC-GTTCCATTCCCTTCTTTTCTCCTTTT
1 GTCCTCAAAGAGCAGGACACACTT-CATTTCCTTCTTTTC-CCTTTT
1967 GTCCTCAAAGAGCAGGACACACTTCATTTCCTTCTTTTCCCTTTT
1 GTCCTCAAAGAGCAGGACACACTTCATTTCCTTCTTTTCCCTTTT
*
2012 GTCCTCAAAGAACAGGACAC-CTTC
1 GTCCTCAAAGAGCAGGACACACTTC
2036 TCCTTCGAAG
Statistics
Matches: 237, Mismatches: 41, Indels: 29
0.77 0.13 0.09
Matches are distributed among these distances:
42 10 0.04
43 54 0.23
44 8 0.03
45 87 0.37
46 74 0.31
47 4 0.02
ACGTcount: A:0.21, C:0.31, G:0.12, T:0.36
Consensus pattern (45 bp):
GTCCTCAAAGAGCAGGACACACTTCATTTCCTTCTTTTCCCTTTT
Found at i:1940 original size:134 final size:134
Alignment explanation
Indices: 1699--2029 Score: 457
Period size: 134 Copynumber: 2.5 Consensus size: 134
1689 GCACCTCCTA
* * * * *
1699 GTCCTCAAAGGGGAGGACGCACTGCATTTTTTTCTTTTCCCTTTTATCCTCAAAGAGCAGGACGC
1 GTCCTCAAAGAGCAGGACACACTTCATTTCTTTCTTTTCCCTTTTATCCTCAAAGAGCAGGACGC
* *
1764 ACTTTATTTTCCTTTTCCCCCTTATCCTTAAAAAGCACGACACATTCCATTCCCTTCTTTGCCCC
66 ACTTTATTTTCCTTTTCCCCATTATCCTCAAAAAGCACGACACATTCCATTCCCTTCTTTGCCCC
1829 TTTT
131 TTTT
* * *
1833 GTCCTCAAAGAGCAAGACCCACTTCATTTCTTTCTTTTCCCTTTT-TCCCTCAAAGAGCAGGATG
1 GTCCTCAAAGAGCAGGACACACTTCATTTCTTTCTTTTCCCTTTTAT-CCTCAAAGAGCAGGACG
** * * * * * *
1897 CACTTTATTTTCCTTTTTTCCATTGTCCTCAAAGAGCAGGACACGTTCCATTCCCTTCTTTTCTC
65 CACTTTATTTTCCTTTTCCCCATTATCCTCAAAAAGCACGACACATTCCATTCCCTTCTTTGCCC
1962 CTTTT
130 CTTTT
* * *
1967 GTCCTCAAAGAGCAGGACACACTTCATTTCCTTCTTTTCCCTTTTGTCCTCAAAGAACAGGAC
1 GTCCTCAAAGAGCAGGACACACTTCATTTCTTTCTTTTCCCTTTTATCCTCAAAGAGCAGGAC
2030 ACCTTCTCCT
Statistics
Matches: 173, Mismatches: 22, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
133 1 0.01
134 171 0.99
135 1 0.01
ACGTcount: A:0.21, C:0.30, G:0.12, T:0.37
Consensus pattern (134 bp):
GTCCTCAAAGAGCAGGACACACTTCATTTCTTTCTTTTCCCTTTTATCCTCAAAGAGCAGGACGC
ACTTTATTTTCCTTTTCCCCATTATCCTCAAAAAGCACGACACATTCCATTCCCTTCTTTGCCCC
TTTT
Found at i:2137 original size:45 final size:44
Alignment explanation
Indices: 2073--2379 Score: 234
Period size: 45 Copynumber: 6.9 Consensus size: 44
2063 CACCTCCTAA
*
2073 TCCTCAAAGGGCAGGATGCACTTCATTTCCTTCATTTCCTTTTTG
1 TCCTCAAAGAGCAGGATGCACTTCATTTCCTTC-TTTCCTTTTTG
* * **
2118 TCCTCAAAGAGCTGGATGCACTTTATTTTCC-T-TTTCC-CCTTG
1 TCCTCAAAGAGCAGGATGCACTTCA-TTTCCTTCTTTCCTTTTTG
* * * *
2160 TCCTTAAAGGGCAGGA--CACATTCCATTCCCTTCTTTTCCTCTTTTT
1 TCCTCAAAGAGCAGGATGCAC-TT-CATTTCCTTC-TTTCCT-TTTTG
* * * * * * *
2206 TCCTCAAAGGGTAGGACGTACTTTATTTCCTTCTTTTCTCTTTTA
1 TCCTCAAAGAGCAGGATGCACTTCATTTCCTTCTTTCCT-TTTTG
* * * *
2251 TCCTCAAAGAACAAGATGCACTTCATTTCCTTCTTTTCCCTTTTA
1 TCCTCAAAGAGCAGGATGCACTTCATTTCCTTC-TTTCCTTTTTG
*
2296 TCCTCAAAGAGCAGGATGCACTTTATTTTCCTT-TTT-C-TTTTG
1 TCCTCAAAGAGCAGGATGCACTTCA-TTTCCTTCTTTCCTTTTTG
* * * * *
2338 TCCTCAAAGAGCAAGACGCATTTCGTTTTCCTTTTTTCCTTT
1 TCCTCAAAGAGCAGGATGCACTTC-ATTTCCTTCTTTCCTTT
2380 GTCCTCGAAA
Statistics
Matches: 208, Mismatches: 38, Indels: 32
0.75 0.14 0.12
Matches are distributed among these distances:
40 3 0.01
41 6 0.03
42 49 0.24
43 9 0.04
44 9 0.04
45 88 0.42
46 40 0.19
47 2 0.01
48 2 0.01
ACGTcount: A:0.19, C:0.26, G:0.12, T:0.42
Consensus pattern (44 bp):
TCCTCAAAGAGCAGGATGCACTTCATTTCCTTCTTTCCTTTTTG
Found at i:2235 original size:87 final size:86
Alignment explanation
Indices: 2073--2346 Score: 246
Period size: 87 Copynumber: 3.1 Consensus size: 86
2063 CACCTCCTAA
* *
2073 TCCTCAAAGGGCAGGATGCACTTCATTTCCTTCATTTCCTTTTTGTCCTCAAAGAGCTGGATGCA
1 TCCTCAAAGGGCAGGA-GCACTTCATTCCCTTCATTTCCTTTTTGTCCTCAAAGAGCTGGACGCA
2138 CTTTATTTTCCTTTTCCCCTTG
65 CTTTATTTTCCTTTTCCCCTTG
* * * *
2160 TCCTTAAAGGGCAGGA-CACATTCCATTCCCTTCTTTTCCTCTTTTTTCCTCAAAG-GGTAGGAC
1 TCCTCAAAGGGCAGGAGCAC-TT-CATTCCCTTCATTTCCT-TTTTGTCCTCAAAGAGCT-GGAC
* * ** *
2223 GTACTTTATTTCCTTCTTTTCTCTTTTA
62 GCACTTTATTT--TCCTTTTC-CCCTTG
** * * * * * * *
2251 TCCTCAAAGAACAAGATGCACTTCATTTCCTTCTTTTCCCTTTTATCCTCAAAGAGCAGGATGCA
1 TCCTCAAAGGGCAGGA-GCACTTCATTCCCTTCATTTCCTTTTTGTCCTCAAAGAGCTGGACGCA
* **
2316 CTTTATTTTCCTTTTTCTTTTG
65 CTTTATTTTCCTTTTCCCCTTG
2338 TCCTCAAAG
1 TCCTCAAAG
2347 AGCAAGACGC
Statistics
Matches: 152, Mismatches: 25, Indels: 20
0.77 0.13 0.10
Matches are distributed among these distances:
85 3 0.02
86 2 0.01
87 46 0.30
88 32 0.21
90 33 0.22
91 31 0.20
92 2 0.01
93 3 0.02
ACGTcount: A:0.19, C:0.27, G:0.12, T:0.42
Consensus pattern (86 bp):
TCCTCAAAGGGCAGGAGCACTTCATTCCCTTCATTTCCTTTTTGTCCTCAAAGAGCTGGACGCAC
TTTATTTTCCTTTTCCCCTTG
Found at i:2257 original size:238 final size:239
Alignment explanation
Indices: 1834--2263 Score: 632
Period size: 238 Copynumber: 1.8 Consensus size: 239
1824 GCCCCTTTTG
* *
1834 TCCTCAAAGAGCAAGACCCACTTCATTTCTTTCTTTTCCCTTTTTCCCTCAAAGAGCAGGATGCA
1 TCCTCAAAGAGCAAGACCCACTTCATTTCCTTCATTTCCCTTTTTCCCTCAAAGAGCAGGATGCA
* *
1899 CTTTATTTTCCTTTTTTCCATTGTCCTCAAAGAGCAGGACACGTTCCATTCCCTTCTTTTCTCCT
66 CTTTATTTTCCTTTTTCCCATTGTCCTCAAAGAGCAGGACACATTCCATTCCCTTCTTTTCTCCT
*
1964 TTTGTCCTCAAAGAGCAGGACACACTTCATTTCCTTCTTTTCCCTTTTGTCCTCAAAGAACAGGA
131 TTTGTCCTCAAAGAGCAGGACACACTTCATTTCCTTCTTTTCCCTTTTATCCTCAAAGAACAGGA
2029 CACCTTCTCCTTCGAAGCCCACACAAGTTAGTGGCACCTCCTAA
196 CACCTTCTCCTTCGAAGCCCACACAAGTTAGTGGCACCTCCTAA
* * ** * *
2073 TCCTCAAAGGGCAGGATGCACTTCATTTCCTTCATTT-CCTTTTTGTCCTCAAAGAGCTGGATGC
1 TCCTCAAAGAGCAAGACCCACTTCATTTCCTTCATTTCCCTTTTT-CCCTCAAAGAGCAGGATGC
* * *
2137 ACTTTATTTTCC-TTTTCCCCTTGTCCTTAAAGGGCAGGACACATTCCATTCCCTTCTTTTC-CT
65 ACTTTATTTTCCTTTTTCCCATTGTCCTCAAAGAGCAGGACACATTCCATTCCCTTCTTTTCTC-
* * * ** * *
2200 CTTTTTTCCTCAAAGGGTAGGACGTACTTTATTTCCTTCTTTTCTCTTTTATCCTCAAAGAACA
129 CTTTTGTCCTCAAAGAGCAGGACACACTTCATTTCCTTCTTTTCCCTTTTATCCTCAAAGAACA
2264 AGATGCACTT
Statistics
Matches: 168, Mismatches: 21, Indels: 5
0.87 0.11 0.03
Matches are distributed among these distances:
237 1 0.01
238 107 0.64
239 60 0.36
ACGTcount: A:0.21, C:0.30, G:0.13, T:0.37
Consensus pattern (239 bp):
TCCTCAAAGAGCAAGACCCACTTCATTTCCTTCATTTCCCTTTTTCCCTCAAAGAGCAGGATGCA
CTTTATTTTCCTTTTTCCCATTGTCCTCAAAGAGCAGGACACATTCCATTCCCTTCTTTTCTCCT
TTTGTCCTCAAAGAGCAGGACACACTTCATTTCCTTCTTTTCCCTTTTATCCTCAAAGAACAGGA
CACCTTCTCCTTCGAAGCCCACACAAGTTAGTGGCACCTCCTAA
Found at i:5546 original size:51 final size:51
Alignment explanation
Indices: 5486--5598 Score: 156
Period size: 51 Copynumber: 2.2 Consensus size: 51
5476 TTTTCAAGGG
* * * *
5486 GATACTCCAA-TCCCGGTTTTATTTCTAAAACACTAATTTTTCATAATCGGA
1 GATACTCCAACT-CCGATTTTATTTCCAAAACACCAATTTTTCACAATCGGA
* *
5537 GATACTCCAACTCTGATTTTATTTCCAAAACACCAATTTTTCACAATCGGG
1 GATACTCCAACTCCGATTTTATTTCCAAAACACCAATTTTTCACAATCGGA
5588 GATACTCCAAC
1 GATACTCCAAC
5599 CCTATTATTT
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
51 54 0.98
52 1 0.02
ACGTcount: A:0.32, C:0.25, G:0.10, T:0.34
Consensus pattern (51 bp):
GATACTCCAACTCCGATTTTATTTCCAAAACACCAATTTTTCACAATCGGA
Found at i:5614 original size:28 final size:28
Alignment explanation
Indices: 5582--5654 Score: 112
Period size: 28 Copynumber: 2.6 Consensus size: 28
5572 ATTTTTCACA
5582 ATCGGGGATACTCCAACCCTATTATTTC
1 ATCGGGGATACTCCAACCCTATTATTTC
*
5610 ATCGGGGGTACTCCAACCCTATTATTTC
1 ATCGGGGATACTCCAACCCTATTATTTC
*
5638 -TGAGGGGATACTCCAAC
1 AT-CGGGGATACTCCAAC
5655 TCCGGTTTTA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
27 1 0.02
28 40 0.98
ACGTcount: A:0.25, C:0.27, G:0.19, T:0.29
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCTATTATTTC
Found at i:5695 original size:79 final size:79
Alignment explanation
Indices: 5610--5865 Score: 221
Period size: 79 Copynumber: 3.3 Consensus size: 79
5600 CTATTATTTC
* * *** *
5610 ATCGGGGGTACTCCAACCCTATTATTTCTGAGGGGATACTCCAACTCCGGTTTTATTCCTAAAAT
1 ATCGGGGATACTCCAACCCTATTATTTCTGAGGGGATACTCCAACCCCAACTTTATTCCTAAAAC
*
5675 ATTGA-TTTCTCACA
66 ACTGACTTTC-CACA
* * * * * ** * *
5689 ATCGGGGATATTCTAACCCCATTATTTC-GTGTGGATACTCTGACCCCAACTTTATTTCTAAAGC
1 ATCGGGGATACTCCAACCCTATTATTTCTGAGGGGATACTCCAACCCCAACTTTATTCCTAAAAC
5753 ACTGACTTTCCACA
66 ACTGACTTTCCACA
* * * * * * *
5767 ATCGGGGATACTCCAACCCTGTTATTTTTGAGGGGATATTCCAACCCTAATTTTATT-TTCAGAA
1 ATCGGGGATACTCCAACCCTATTATTTCTGAGGGGATACTCCAACCCCAACTTTATTCCT-AAAA
* * *
5831 CACCGATTTTCCATA
65 CACTGACTTTCCACA
* *
5846 ATCGAGGATACTCCAGCCCT
1 ATCGGGGATACTCCAACCCT
5866 GTTGTTATCC
Statistics
Matches: 138, Mismatches: 36, Indels: 6
0.77 0.20 0.03
Matches are distributed among these distances:
78 57 0.41
79 81 0.59
ACGTcount: A:0.26, C:0.25, G:0.16, T:0.33
Consensus pattern (79 bp):
ATCGGGGATACTCCAACCCTATTATTTCTGAGGGGATACTCCAACCCCAACTTTATTCCTAAAAC
ACTGACTTTCCACA
Found at i:7719 original size:16 final size:16
Alignment explanation
Indices: 7698--7728 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
7688 ATTACAAAAT
*
7698 ATCTTTCCCTCTTTTC
1 ATCTTTCCCCCTTTTC
7714 ATCTTTCCCCCTTTT
1 ATCTTTCCCCCTTTT
7729 ACAAATTTAT
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:0.06, C:0.39, G:0.00, T:0.55
Consensus pattern (16 bp):
ATCTTTCCCCCTTTTC
Found at i:9586 original size:13 final size:13
Alignment explanation
Indices: 9564--9624 Score: 95
Period size: 13 Copynumber: 4.7 Consensus size: 13
9554 AGTGCTCTTT
9564 TATCGATACAATG
1 TATCGATACAATG
* *
9577 CATTGATACAATG
1 TATCGATACAATG
*
9590 TATCGATACAGTG
1 TATCGATACAATG
9603 TATCGATACAATG
1 TATCGATACAATG
9616 TATCGATAC
1 TATCGATAC
9625 TAAGATCATT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 42 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.31
Consensus pattern (13 bp):
TATCGATACAATG
Found at i:14941 original size:3 final size:3
Alignment explanation
Indices: 14933--14967 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
14923 CGAGTCAACT
*
14933 TCA TCA TCA TCA TCA TCA TCA TCA TCC TCA TCA TC
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
14968 TTTGATGGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.29, C:0.37, G:0.00, T:0.34
Consensus pattern (3 bp):
TCA
Found at i:16588 original size:20 final size:20
Alignment explanation
Indices: 16546--16600 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 20
16536 GTTAGGCTCA
* *
16546 ATGTATCGATACATTTCACC
1 ATGTATCGATACAATCCACC
**
16566 ATGTATCGATACAATCCTTC
1 ATGTATCGATACAATCCACC
*
16586 ATGTATCGATCCAAT
1 ATGTATCGATACAAT
16601 GTATCGATAC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.31, C:0.24, G:0.11, T:0.35
Consensus pattern (20 bp):
ATGTATCGATACAATCCACC
Found at i:16604 original size:13 final size:13
Alignment explanation
Indices: 16586--16615 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
16576 ACAATCCTTC
*
16586 ATGTATCGATCCA
1 ATGTATCGATACA
16599 ATGTATCGATACA
1 ATGTATCGATACA
16612 ATGT
1 ATGT
16616 GAGTTTTACC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:16697 original size:13 final size:13
Alignment explanation
Indices: 16679--16705 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
16669 TACAATAAAC
16679 ATGTATCGATACA
1 ATGTATCGATACA
16692 ATGTATCGATACA
1 ATGTATCGATACA
16705 A
1 A
16706 AGCAATATGT
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:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:20635 original size:10 final size:10
Alignment explanation
Indices: 20605--20638 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
20595 TGAAGATCGA
*
20605 TTTAAAAATA
1 TTTAAAAATC
20615 TTTCAAAAATC
1 TTT-AAAAATC
20626 TTTAAAAATC
1 TTTAAAAATC
20636 TTT
1 TTT
20639 TTCCTAGTGG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 13 0.59
11 9 0.41
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.44
Consensus pattern (10 bp):
TTTAAAAATC
Found at i:22534 original size:20 final size:20
Alignment explanation
Indices: 22509--22579 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
22499 AAAAAAAGAC
22509 AGAATGTATCGATACATTGA
1 AGAATGTATCGATACATTGA
22529 AGAATGTATCGATACATT--
1 AGAATGTATCGATACATTGA
* *
22547 --CATGTATCGATGCATTGA
1 AGAATGTATCGATACATTGA
*
22565 AAAATGTATCGATAC
1 AGAATGTATCGATAC
22580 GTCTAGGTAA
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
16 14 0.33
20 29 0.67
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (20 bp):
AGAATGTATCGATACATTGA
Found at i:22553 original size:16 final size:16
Alignment explanation
Indices: 22532--22562 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
22522 ACATTGAAGA
22532 ATGTATCGATACATTC
1 ATGTATCGATACATTC
*
22548 ATGTATCGATGCATT
1 ATGTATCGATACATT
22563 GAAAAATGTA
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:0.29, C:0.16, G:0.16, T:0.39
Consensus pattern (16 bp):
ATGTATCGATACATTC
Found at i:22611 original size:87 final size:87
Alignment explanation
Indices: 22471--22683 Score: 293
Period size: 87 Copynumber: 2.4 Consensus size: 87
22461 ATGTATCGCC
* * *
22471 ACATTGAATAATGTATCGATACATCAGGAAAAAAAGACAGAATGTATCGATACATTGAAGAATGT
1 ACATTGAAAAATGTATCGATACATCAGG-TAAAAAGACAGAATGTATCAATACATTGAAGAATGT
* *
22536 ATCGATA-CATTCATGTATCGAT
65 ATCGATATCATACATGCATCGAT
* *
22558 GCATTGAAAAATGTATCGATACGTCTAGGTAAAAAGACAGAATGTATCAATACATTGAAGAATGT
1 ACATTGAAAAATGTATCGATACATC-AGGTAAAAAGACAGAATGTATCAATACATTGAAGAATGT
*
22623 ATTGATATGTTCATACATGCATCGAT
65 ATCGATA---TCATACATGCATCGAT
22649 ACATTGAAAAATGTATCGATACATCCAGGTAAAAA
1 ACATTGAAAAATGTATCGATACAT-CAGGTAAAAA
22684 TGTGACTTTT
Statistics
Matches: 110, Mismatches: 10, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
87 62 0.56
88 3 0.03
91 44 0.40
92 1 0.01
ACGTcount: A:0.42, C:0.13, G:0.17, T:0.28
Consensus pattern (87 bp):
ACATTGAAAAATGTATCGATACATCAGGTAAAAAGACAGAATGTATCAATACATTGAAGAATGTA
TCGATATCATACATGCATCGAT
Found at i:22666 original size:20 final size:20
Alignment explanation
Indices: 22598--22672 Score: 69
Period size: 20 Copynumber: 3.8 Consensus size: 20
22588 AAAAAGACAG
* *
22598 AATGTATCAATACATTGAAG
1 AATGTATCGATACATTGAAA
* ** * *
22618 AATGTATTGATATGTTCATA
1 AATGTATCGATACATTGAAA
* *
22638 CATGCATCGATACATTGAAA
1 AATGTATCGATACATTGAAA
22658 AATGTATCGATACAT
1 AATGTATCGATACAT
22673 CCAGGTAAAA
Statistics
Matches: 39, Mismatches: 16, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.33
Consensus pattern (20 bp):
AATGTATCGATACATTGAAA
Found at i:23466 original size:32 final size:31
Alignment explanation
Indices: 23417--23499 Score: 116
Period size: 32 Copynumber: 2.7 Consensus size: 31
23407 CCAACGACAT
* *
23417 TGGG-TTTAGAAGGGTTGCCACCAACTTGTG
1 TGGGCTTTAGAAAGGTTGCCACCAACTTGTA
23447 TGGGCTTTAGAGAAGGTTGCCACCAACTTGTA
1 TGGGCTTTAGA-AAGGTTGCCACCAACTTGTA
*
23479 TGGGCTTTA-AAAGGATGCCAC
1 TGGGCTTTAGAAAGGTTGCCAC
23500 TGACTCGTGG
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
30 14 0.29
31 7 0.15
32 27 0.56
ACGTcount: A:0.24, C:0.18, G:0.30, T:0.28
Consensus pattern (31 bp):
TGGGCTTTAGAAAGGTTGCCACCAACTTGTA
Found at i:23512 original size:28 final size:28
Alignment explanation
Indices: 23445--24881 Score: 858
Period size: 28 Copynumber: 51.6 Consensus size: 28
23435 CACCAACTTG
* **
23445 TGTGGGCTTTAGAGAAGGTTGCCACCAACT
1 TGTGGGCTTTA-A-AAGGATGCCACTGACT
23475 TGTATGGGCTTTAAAAGGATGCCACTGACT
1 TG--TGGGCTTTAAAAGGATGCCACTGACT
* * *
23505 CGTGGGCTTTGAAAAAG-TGCCTCTGACT
1 TGTGGGCTTT-AAAAGGATGCCACTGACT
* * *
23533 CGTTGGCTTTGAAAAGG-TGCCACTAACT
1 TGTGGGCTTT-AAAAGGATGCCACTGACT
* * * *
23561 TATGGTCTTTGAAAGGATGCCACCGACT
1 TGTGGGCTTTAAAAGGATGCCACTGACT
* ** *
23589 TATGGGCTTTGAAAATAATGCCACTAACTT
1 TGTGGGCTTT-AAAAGGATGCCACTGAC-T
** *
23619 GTGTGGGCTTCGAAAGGATGCCATTGACT
1 -TGTGGGCTTTAAAAGGATGCCACTGACT
** * * * *
23648 CATGGGCTTTAGACGGATGCCACTAATT
1 TGTGGGCTTTAAAAGGATGCCACTGACT
*
23676 TGTGGGCTTT-GAAGAGATGCCACTGACT
1 TGTGGGCTTTAAAAG-GATGCCACTGACT
*
23704 AGTGGGCTTTAAAAGGATGCCACTGACT
1 TGTGGGCTTTAAAAGGATGCCACTGACT
* *
23732 TGTGGGCTATGAAAAGG-TGCCACTGAAT
1 TGTGGGCT-TTAAAAGGATGCCACTGACT
* * *
23760 TGTGGGCTTGGAAAA-TATGCCATTGACT
1 TGTGGGCTT-TAAAAGGATGCCACTGACT
* * * *
23788 TATGGGCTTGGAAAA-AATGCCACTGAGT
1 TGTGGGCTT-TAAAAGGATGCCACTGACT
** * * *
23816 CATGGGCTTTGAAAGGGTGTCACTGA-T
1 TGTGGGCTTTAAAAGGATGCCACTGACT
* * *
23843 TCATGGTCTTTGAAAGGATGCCACTGACT
1 T-GTGGGCTTTAAAAGGATGCCACTGACT
* ** * *
23872 TGTGGGCTATGGAAGGGTGCCACTGACA
1 TGTGGGCTTTAAAAGGATGCCACTGACT
* * *
23900 TATGGGCTTGGAAAA-GATGCCATTGACT
1 TGTGGGCTT-TAAAAGGATGCCACTGACT
*
23928 TGTGGGCTTT-GAAGAGATGCCACTGACT
1 TGTGGGCTTTAAAAG-GATGCCACTGACT
* * * * *
23956 TGTAGGCTTTGAAAGTATACTACTGACT
1 TGTGGGCTTTAAAAGGATGCCACTGACT
*
23984 TGTGGGCTATCAAAAGG-TGCCACTGACT
1 TGTGGGCT-TTAAAAGGATGCCACTGACT
* * *
24012 TGTGTGCTATGAAAAAG-TGCCACTGACT
1 TGTGGGCT-TTAAAAGGATGCCACTGACT
24040 TGTGGG-TTTGGAAAA-GATGCCACTGACT
1 TGTGGGCTTT--AAAAGGATGCCACTGACT
** * *
24068 TGTGGGCTTGGAAA-TATTCCACTGACT
1 TGTGGGCTTTAAAAGGATGCCACTGACT
* *
24095 TGTGGGCTTTGAAAGGGTGCCACTGA-T
1 TGTGGGCTTTAAAAGGATGCCACTGACT
* *
24122 TCGTGGGCTTTGAAAAGGATGCCACTAAAT
1 T-GTGGGCTTT-AAAAGGATGCCACTGACT
* * *
24152 AGTGGGCTATGAAAGGATGCCACTG---
1 TGTGGGCTTTAAAAGGATGCCACTGACT
* *
24177 TGTGGGCTTTGAAAGGATGCCACTAACT
1 TGTGGGCTTTAAAAGGATGCCACTGACT
* *
24205 TGTAGGC-TTAGAAATGATGCCACTGACT
1 TGTGGGCTTTA-AAAGGATGCCACTGACT
*
24233 TGTGGGCTTGAAAAGGATGCCACTGACT
1 TGTGGGCTTTAAAAGGATGCCACTGACT
* *
24261 TGTGGGCTTTGAAAGGGTGCCACTGA-T
1 TGTGGGCTTTAAAAGGATGCCACTGACT
* *
24288 TCTTGGGCTTTGAAAAGGATGCCACTGGCT
1 T-GTGGGCTTT-AAAAGGATGCCACTGACT
* *
24318 TGTGGGCTTTGAAAGGATGCCAATGACT
1 TGTGGGCTTTAAAAGGATGCCACTGACT
24346 TGTGGGCTTCTGAAAAGG-TGCCACTGACT
1 TGTGGGCTT-T-AAAAGGATGCCACTGACT
* * * *
24375 TATGGAC-TTAAAAGGATGCCACGGAGT
1 TGTGGGCTTTAAAAGGATGCCACTGACT
* * * *
24402 TATGGACTTTAAAAGGATGCCACGGAGT
1 TGTGGGCTTTAAAAGGATGCCACTGACT
* *
24430 TGTGGACTTTAAAAGGATGCCA-TGGAGT
1 TGTGGGCTTTAAAAGGATGCCACT-GACT
* * * *
24458 TGTGGAC-TTAAAAGGGTGCCACAGAGT
1 TGTGGGCTTTAAAAGGATGCCACTGACT
* * * *
24485 TGTGGAC-TTAAAAGGTTGCCACGGAGT
1 TGTGGGCTTTAAAAGGATGCCACTGACT
* * * *
24512 TGTGGAC-TTAAAAGGTTGCCACGGAGT
1 TGTGGGCTTTAAAAGGATGCCACTGACT
* * *
24539 TGTGGAC-TTAAAAGGTTGCCACAGAGC-
1 TGTGGGCTTTAAAAGGATGCCACTGA-CT
* * *
24566 TGTGGACTTAAAAAGGATGCCA-TGGAGT
1 TGTGGGCTTTAAAAGGATGCCACT-GACT
* * *
24594 TGTGGACTTTAAAAAGATGCCAC-GAAGT
1 TGTGGGCTTTAAAAGGATGCCACTG-ACT
* ** * *
24622 TGTGGAC-TTAAAAGTTTGCTA-TGGAGT
1 TGTGGGCTTTAAAAGGATGCCACT-GACT
* * * *
24649 TGTGGAC-TTAAAAGGTTGTCACGGAGC-
1 TGTGGGCTTTAAAAGGATGCCACTGA-CT
* * *
24676 TGTGGAC-TTAAAAGGTTGCCA-TGGAGT
1 TGTGGGCTTTAAAAGGATGCCACT-GACT
* * * *
24703 TATGGACTTTAAAAGGATGCCACGGAGT
1 TGTGGGCTTTAAAAGGATGCCACTGACT
* ** *
24731 TGTGGAC-TTAAAAGTTTGCCAC-GAAGT
1 TGTGGGCTTTAAAAGGATGCCACTG-ACT
* * *
24758 TGT-GGTTTTAAAAGGTTGCCACAGAGC-
1 TGTGGGCTTTAAAAGGATGCCACTGA-CT
* * *
24785 TGTGGAC-TTATAAAGGATGCCACGGAGT
1 TGTGGGCTTTA-AAAGGATGCCACTGACT
** * *
24813 TGTGAAC-TTAAAAGGTTGCCA-TGGAGT
1 TGTGGGCTTTAAAAGGATGCCACT-GACT
* * * *
24840 TGTGGAC-TTAAAAGGTTGCCACAGAGT
1 TGTGGGCTTTAAAAGGATGCCACTGACT
*
24867 TGTGGAC-TTAAAAGG
1 TGTGGGCTTTAAAAGG
24882 TTGCACGGAG
Statistics
Matches: 1154, Mismatches: 188, Indels: 133
0.78 0.13 0.09
Matches are distributed among these distances:
25 22 0.02
26 11 0.01
27 320 0.28
28 644 0.56
29 102 0.09
30 37 0.03
31 9 0.01
32 9 0.01
ACGTcount: A:0.27, C:0.16, G:0.30, T:0.28
Consensus pattern (28 bp):
TGTGGGCTTTAAAAGGATGCCACTGACT
Found at i:24404 original size:27 final size:27
Alignment explanation
Indices: 24358--25040 Score: 845
Period size: 27 Copynumber: 25.2 Consensus size: 27
24348 TGGGCTTCTG
* * *
24358 AAAAGG-TGCCACTGACTTATGGACTT
1 AAAAGGTTGCCACGGAGTTGTGGACTT
* *
24384 AAAAGGATGCCACGGAGTTATGGACTTT
1 AAAAGGTTGCCACGGAGTTGTGGAC-TT
*
24412 AAAAGGATGCCACGGAGTTGTGGACTTT
1 AAAAGGTTGCCACGGAGTTGTGGAC-TT
* *
24440 AAAAGGATGCCATGGAGTTGTGGACTT
1 AAAAGGTTGCCACGGAGTTGTGGACTT
* *
24467 AAAAGGGTGCCACAGAGTTGTGGACTT
1 AAAAGGTTGCCACGGAGTTGTGGACTT
24494 AAAAGGTTGCCACGGAGTTGTGGACTT
1 AAAAGGTTGCCACGGAGTTGTGGACTT
24521 AAAAGGTTGCCACGGAGTTGTGGACTT
1 AAAAGGTTGCCACGGAGTTGTGGACTT
* *
24548 AAAAGGTTGCCACAGAGCTGTGGACTT
1 AAAAGGTTGCCACGGAGTTGTGGACTT
* *
24575 AAAAAGGATGCCATGGAGTTGTGGACTTT
1 -AAAAGGTTGCCACGGAGTTGTGGAC-TT
* * *
24604 AAAAAGATGCCACGAAGTTGTGGACTT
1 AAAAGGTTGCCACGGAGTTGTGGACTT
* * *
24631 AAAAGTTTGCTATGGAGTTGTGGACTT
1 AAAAGGTTGCCACGGAGTTGTGGACTT
* *
24658 AAAAGGTTGTCACGGAGCTGTGGACTT
1 AAAAGGTTGCCACGGAGTTGTGGACTT
* *
24685 AAAAGGTTGCCATGGAGTTATGGACTTT
1 AAAAGGTTGCCACGGAGTTGTGGAC-TT
*
24713 AAAAGGATGCCACGGAGTTGTGGACTT
1 AAAAGGTTGCCACGGAGTTGTGGACTT
* * **
24740 AAAAGTTTGCCACGAAGTTGTGGTTTT
1 AAAAGGTTGCCACGGAGTTGTGGACTT
* *
24767 AAAAGGTTGCCACAGAGCTGTGGACTT
1 AAAAGGTTGCCACGGAGTTGTGGACTT
* *
24794 ATAAAGGATGCCACGGAGTTGTGAACTT
1 A-AAAGGTTGCCACGGAGTTGTGGACTT
*
24822 AAAAGGTTGCCATGGAGTTGTGGACTT
1 AAAAGGTTGCCACGGAGTTGTGGACTT
*
24849 AAAAGGTTGCCACAGAGTTGTGGACTT
1 AAAAGGTTGCCACGGAGTTGTGGACTT
*
24876 AAAAGGTTG-CACGGAGCTGTGGACTT
1 AAAAGGTTGCCACGGAGTTGTGGACTT
* *
24902 -AAAGGTTGCCACAGAGTTGTAGACTT
1 AAAAGGTTGCCACGGAGTTGTGGACTT
* * *
24928 TAAAGGTTGCCATGGAGTTGTAGACTT
1 AAAAGGTTGCCACGGAGTTGTGGACTT
* * *
24955 AAAAGGTTGCCGCAGAGCTGTGGACTT
1 AAAAGGTTGCCACGGAGTTGTGGACTT
*
24982 AAAAGGGTGCCACGGAGTTGTAGG-CTT
1 AAAAGGTTGCCACGGAGTTGT-GGACTT
*
25009 AAAA-GTGTGCCATGGAGTTGTGGACTT
1 AAAAGGT-TGCCACGGAGTTGTGGACTT
25036 AAAAG
1 AAAAG
25041 AACAAGGTTG
Statistics
Matches: 570, Mismatches: 75, Indels: 22
0.85 0.11 0.03
Matches are distributed among these distances:
25 8 0.01
26 38 0.07
27 377 0.66
28 145 0.25
29 2 0.00
ACGTcount: A:0.29, C:0.14, G:0.31, T:0.26
Consensus pattern (27 bp):
AAAAGGTTGCCACGGAGTTGTGGACTT
Found at i:24582 original size:164 final size:163
Alignment explanation
Indices: 24358--25040 Score: 867
Period size: 164 Copynumber: 4.2 Consensus size: 163
24348 TGGGCTTCTG
* * * * *
24358 AAAAGG-TGCCACTGACTTATGGACTTAAAAGGATGCCACGGAGTTATGGACTTTAAAAGGATGC
1 AAAAGGTTGCCACGGAGTTGTGGACTTAAAAGGATGCCACGGAGCTGTGGAC-TTAAAAGGATGC
* *
24422 CACGGAGTTGTGGACTTTAAAAGGATGCCATGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTG
65 CACGGAGTTGTGGACTTTAAAAGGATGCCACGGAGTTGTGGACTTAAAAGGTTGCCACAGAGTTG
24487 TGGACTTAAAAGGTTGCCACGGAGTTGTGGACTT
130 TGGACTTAAAAGGTTGCCACGGAGTTGTGGACTT
* *
24521 AAAAGGTTGCCACGGAGTTGTGGACTTAAAAGGTTGCCACAGAGCTGTGGACTTAAAAAGGATGC
1 AAAAGGTTGCCACGGAGTTGTGGACTTAAAAGGATGCCACGGAGCTGTGGACTT-AAAAGGATGC
* * * * * **
24586 CATGGAGTTGTGGACTTTAAAAAGATGCCACGAAGTTGTGGACTTAAAAGTTTGCTATGGAGTTG
65 CACGGAGTTGTGGACTTTAAAAGGATGCCACGGAGTTGTGGACTTAAAAGGTTGCCACAGAGTTG
* *
24651 TGGACTTAAAAGGTTGTCACGGAGCTGTGGACTT
130 TGGACTTAAAAGGTTGCCACGGAGTTGTGGACTT
* * * **
24685 AAAAGGTTGCCATGGAGTTATGGACTTTAAAAGGATGCCACGGAGTTGTGGACTTAAAAGTTTGC
1 AAAAGGTTGCCACGGAGTTGTGGAC-TTAAAAGGATGCCACGGAGCTGTGGACTTAAAAGGATGC
* * * * * * *
24750 CACGAAGTTGTGG-TTTTAAAAGGTTGCCACAGAGCTGTGGACTTATAAAGGATGCCACGGAGTT
65 CACGGAGTTGTGGACTTTAAAAGGATGCCACGGAGTTGTGGACTTA-AAAGGTTGCCACAGAGTT
* *
24814 GTGAACTTAAAAGGTTGCCATGGAGTTGTGGACTT
129 GTGGACTTAAAAGGTTGCCACGGAGTTGTGGACTT
* * *
24849 AAAAGGTTGCCACAGAGTTGTGGACTTAAAAGGTTG-CACGGAGCTGTGGACTT-AAAGGTTGCC
1 AAAAGGTTGCCACGGAGTTGTGGACTTAAAAGGATGCCACGGAGCTGTGGACTTAAAAGGATGCC
* * * * * * *
24912 ACAGAGTTGTAGACTTT-AAAGGTTGCCATGGAGTTGTAGACTTAAAAGGTTGCCGCAGAGCTGT
66 ACGGAGTTGTGGACTTTAAAAGGATGCCACGGAGTTGTGGACTTAAAAGGTTGCCACAGAGTTGT
*
24976 GGACTTAAAAGGGTGCCACGGAGTTGTAGG-CTT
131 GGACTTAAAAGGTTGCCACGGAGTTGT-GGACTT
*
25009 AAAA-GTGTGCCATGGAGTTGTGGACTTAAAAG
1 AAAAGGT-TGCCACGGAGTTGTGGACTTAAAAG
25041 AACAAGGTTG
Statistics
Matches: 449, Mismatches: 64, Indels: 17
0.85 0.12 0.03
Matches are distributed among these distances:
159 2 0.00
160 70 0.16
161 43 0.10
162 19 0.04
163 44 0.10
164 245 0.55
165 26 0.06
ACGTcount: A:0.29, C:0.14, G:0.31, T:0.26
Consensus pattern (163 bp):
AAAAGGTTGCCACGGAGTTGTGGACTTAAAAGGATGCCACGGAGCTGTGGACTTAAAAGGATGCC
ACGGAGTTGTGGACTTTAAAAGGATGCCACGGAGTTGTGGACTTAAAAGGTTGCCACAGAGTTGT
GGACTTAAAAGGTTGCCACGGAGTTGTGGACTT
Found at i:33636 original size:71 final size:71
Alignment explanation
Indices: 33514--33688 Score: 228
Period size: 71 Copynumber: 2.5 Consensus size: 71
33504 TTTAACTAGA
* *
33514 TGTATCGATACATTGAATAATGTATCGATACATCTGGGAAAAAAAAAAGAATGTATCGATACATT
1 TGTATCGATACATTGAAAAATGTATCGATACATCTGGGAAAAAAAAAAGAATGTATCAATACATT
33579 CATACG
66 CATACG
* * * *
33585 TGTATTGATACATTGAAAAATGTATCGATACATCTGGGAAAAAAGACAGAATGTATCAATACTTT
1 TGTATCGATACATTGAAAAATGTATCGATACATCTGGGAAAAAAAAAAGAATGTATCAATACATT
*
33650 GA-A-G
66 CATACG
* * *
33654 AATGTATCGATACATTCATACATGTATCGATACAT
1 --TGTATCGATACATTGAAAAATGTATCGATACAT
33689 TGAAAAATGT
Statistics
Matches: 91, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
69 1 0.01
70 1 0.01
71 89 0.98
ACGTcount: A:0.41, C:0.13, G:0.17, T:0.30
Consensus pattern (71 bp):
TGTATCGATACATTGAAAAATGTATCGATACATCTGGGAAAAAAAAAAGAATGTATCAATACATT
CATACG
Found at i:33640 original size:51 final size:49
Alignment explanation
Indices: 33592--33759 Score: 183
Period size: 51 Copynumber: 3.5 Consensus size: 49
33582 ACGTGTATTG
33592 ATACATTGAAAAATGTATCGATACATCTGGGAAAAAAGACAGAATGTATCA
1 ATACATTGAAAAATGTATCGATACATCTGGG-AAAAAGACA-AATGTATCA
* * * * *
33643 ATACTTTGAAGAATGTATCGATACAT-T------CATAC--ATGTATCG
1 ATACATTGAAAAATGTATCGATACATCTGGGAAAAAGACAAATGTATCA
33683 ATACATTGAAAAATGTATCGATACATCTGGGTAAAAAGACTAAATGTATCA
1 ATACATTGAAAAATGTATCGATACATCTGGG-AAAAAGAC-AAATGTATCA
*
33734 ATACATTGAAGAATGTATCGATACAT
1 ATACATTGAAAAATGTATCGATACAT
33760 TCATAAACGT
Statistics
Matches: 95, Mismatches: 11, Indels: 22
0.74 0.09 0.17
Matches are distributed among these distances:
40 31 0.33
41 1 0.01
43 3 0.03
48 3 0.03
50 1 0.01
51 56 0.59
ACGTcount: A:0.43, C:0.12, G:0.16, T:0.29
Consensus pattern (49 bp):
ATACATTGAAAAATGTATCGATACATCTGGGAAAAAGACAAATGTATCA
Found at i:33657 original size:20 final size:20
Alignment explanation
Indices: 33632--33799 Score: 115
Period size: 20 Copynumber: 7.8 Consensus size: 20
33622 GAAAAAAGAC
* *
33632 AGAATGTATCAATACTTTGA
1 AGAATGTATCGATACATTGA
*
33652 AGAATGTATCGATACATTCA
1 AGAATGTATCGATACATTGA
*
33672 TA-CATGTATCGATACATTGA
1 -AGAATGTATCGATACATTGA
*
33692 AAAATGTATCGATACATCTGGGTAAAA
1 AGAATGTATCGATACAT-T--G----A
*
33719 AGACTAAATGTATCAATACATTGA
1 AG----AATGTATCGATACATTGA
*
33743 AGAATGTATCGATACATTCA
1 AGAATGTATCGATACATTGA
*
33763 TA-AACGTATCGATACATTGA
1 -AGAATGTATCGATACATTGA
* *
33783 AAAATGTATCAATACAT
1 AGAATGTATCGATACAT
33800 CCAGGTAAAA
Statistics
Matches: 119, Mismatches: 14, Indels: 30
0.73 0.09 0.18
Matches are distributed among these distances:
19 2 0.02
20 92 0.77
21 3 0.03
23 1 0.01
24 3 0.03
27 2 0.02
28 1 0.01
30 1 0.01
31 14 0.12
ACGTcount: A:0.42, C:0.13, G:0.14, T:0.30
Consensus pattern (20 bp):
AGAATGTATCGATACATTGA
Found at i:33692 original size:40 final size:40
Alignment explanation
Indices: 33634--33799 Score: 152
Period size: 40 Copynumber: 3.9 Consensus size: 40
33624 AAAAAGACAG
* *
33634 AATGTATCAATACTTTGAAGAATGTATCGATACATTCATA
1 AATGTATCAATACATTGAAAAATGTATCGATACATTCATA
* * *
33674 CATGTATCGATACATTGAAAAATGTATCGATACATCTGGGTAAAAAGACTA
1 AATGTATCAATACATTGAAAAATGTATCGATACA--T---T-----CA-TA
*
33725 AATGTATCAATACATTGAAGAATGTATCGATACATTCATA
1 AATGTATCAATACATTGAAAAATGTATCGATACATTCATA
* * *
33765 AACGTATCGATACATTGAAAAATGTATCAATACAT
1 AATGTATCAATACATTGAAAAATGTATCGATACAT
33800 CCAGGTAAAA
Statistics
Matches: 102, Mismatches: 13, Indels: 22
0.74 0.09 0.16
Matches are distributed among these distances:
40 63 0.62
41 1 0.01
42 1 0.01
45 1 0.01
46 1 0.01
49 1 0.01
50 1 0.01
51 33 0.32
ACGTcount: A:0.42, C:0.13, G:0.14, T:0.31
Consensus pattern (40 bp):
AATGTATCAATACATTGAAAAATGTATCGATACATTCATA
Found at i:33807 original size:91 final size:91
Alignment explanation
Indices: 33560--33810 Score: 405
Period size: 91 Copynumber: 2.8 Consensus size: 91
33550 GGAAAAAAAA
* * *
33560 AAGAATGTATCGATACATTCATACGTGTATTGATACATTGAAAAATGTATCGATACATCTGGGAA
1 AAGAATGTATCGATACATTCATACATGTATCGATACATTGAAAAATGTATCGATACATCTGGGTA
*
33625 AAAAGACAGAATGTATCAATACTTTG
66 AAAAGACAGAATGTATCAATACATTG
33651 AAGAATGTATCGATACATTCATACATGTATCGATACATTGAAAAATGTATCGATACATCTGGGTA
1 AAGAATGTATCGATACATTCATACATGTATCGATACATTGAAAAATGTATCGATACATCTGGGTA
33716 AAAAGACTA-AATGTATCAATACATTG
66 AAAAGAC-AGAATGTATCAATACATTG
* * * **
33742 AAGAATGTATCGATACATTCATAAACGTATCGATACATTGAAAAATGTATCAATACATCCAGGTA
1 AAGAATGTATCGATACATTCATACATGTATCGATACATTGAAAAATGTATCGATACATCTGGGTA
33807 AAAA
66 AAAA
33811 TGTGACTTTT
Statistics
Matches: 150, Mismatches: 9, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
91 149 0.99
92 1 0.01
ACGTcount: A:0.43, C:0.13, G:0.16, T:0.29
Consensus pattern (91 bp):
AAGAATGTATCGATACATTCATACATGTATCGATACATTGAAAAATGTATCGATACATCTGGGTA
AAAAGACAGAATGTATCAATACATTG
Found at i:34629 original size:34 final size:34
Alignment explanation
Indices: 34590--34744 Score: 208
Period size: 34 Copynumber: 4.9 Consensus size: 34
34580 ATATACATGT
34590 TAACACACCTAACATTCTCACCAAATACATCACC
1 TAACACACCTAACATTCTCACCAAATACATCACC
*
34624 TAACACACCTAACATTCTCACC-TA-ACA-CACC
1 TAACACACCTAACATTCTCACCAAATACATCACC
*
34655 T---A-A-C--A--TTCTCACCAAACACATCACC
1 TAACACACCTAACATTCTCACCAAATACATCACC
34680 TAACACACCTAACATTCTCACCAAATACATCACC
1 TAACACACCTAACATTCTCACCAAATACATCACC
34714 TAACACACCTAACATTCTCACCAAATACATC
1 TAACACACCTAACATTCTCACCAAATACATC
34745 TTAACGAAGA
Statistics
Matches: 106, Mismatches: 3, Indels: 24
0.80 0.02 0.18
Matches are distributed among these distances:
22 8 0.08
23 1 0.01
24 4 0.04
25 5 0.05
26 1 0.01
27 1 0.01
28 2 0.02
29 1 0.01
30 1 0.01
31 5 0.05
32 4 0.04
33 1 0.01
34 72 0.68
ACGTcount: A:0.41, C:0.39, G:0.00, T:0.21
Consensus pattern (34 bp):
TAACACACCTAACATTCTCACCAAATACATCACC
Found at i:34647 original size:22 final size:22
Alignment explanation
Indices: 34619--34674 Score: 103
Period size: 22 Copynumber: 2.5 Consensus size: 22
34609 ACCAAATACA
34619 TCACCTAACACACCTAACATTC
1 TCACCTAACACACCTAACATTC
34641 TCACCTAACACACCTAACATTC
1 TCACCTAACACACCTAACATTC
*
34663 TCACCAAACACA
1 TCACCTAACACA
34675 TCACCTAACA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.39, C:0.41, G:0.00, T:0.20
Consensus pattern (22 bp):
TCACCTAACACACCTAACATTC
Found at i:34676 original size:56 final size:56
Alignment explanation
Indices: 34590--34701 Score: 215
Period size: 56 Copynumber: 2.0 Consensus size: 56
34580 ATATACATGT
*
34590 TAACACACCTAACATTCTCACCAAATACATCACCTAACACACCTAACATTCTCACC
1 TAACACACCTAACATTCTCACCAAACACATCACCTAACACACCTAACATTCTCACC
34646 TAACACACCTAACATTCTCACCAAACACATCACCTAACACACCTAACATTCTCACC
1 TAACACACCTAACATTCTCACCAAACACATCACCTAACACACCTAACATTCTCACC
34702 AAATACATCA
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 55 1.00
ACGTcount: A:0.39, C:0.40, G:0.00, T:0.21
Consensus pattern (56 bp):
TAACACACCTAACATTCTCACCAAACACATCACCTAACACACCTAACATTCTCACC
Found at i:34735 original size:56 final size:55
Alignment explanation
Indices: 34591--34718 Score: 175
Period size: 56 Copynumber: 2.2 Consensus size: 55
34581 TATACATGTT
* * *
34591 AACACACCTAACATTCTCACCAAATACATCACCTAACACACCTAACATTCTCACCT
1 AACACACCTAACA-TCACACCAAACACATCACCTAACACACCTAACATTCTCACCA
*
34647 AACACACCTAACATTCTCACCAAACACATCACCTAACACACCTAACATTCTCACCAA
1 AACACACCTAACA-TCACACCAAACACATCACCTAACACACCTAACATTCTCACC-A
34704 ATACATCACCTAACA
1 A-ACA-CACCTAACA
34719 CACCTAACAT
Statistics
Matches: 67, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
56 54 0.81
57 1 0.01
58 3 0.04
59 9 0.13
ACGTcount: A:0.41, C:0.39, G:0.00, T:0.20
Consensus pattern (55 bp):
AACACACCTAACATCACACCAAACACATCACCTAACACACCTAACATTCTCACCA
Found at i:39456 original size:34 final size:34
Alignment explanation
Indices: 39417--39657 Score: 269
Period size: 34 Copynumber: 7.8 Consensus size: 34
39407 ATATACATGT
39417 TAACACACCTAACATTCTCACCAAATACATCACC
1 TAACACACCTAACATTCTCACCAAATACATCACC
*
39451 TAACACACCTAACATTCTCACC-TA-ACA-CACC
1 TAACACACCTAACATTCTCACCAAATACATCACC
*
39482 T---A-A-C--A--TTCTCACCAAACACATCACC
1 TAACACACCTAACATTCTCACCAAATACATCACC
*
39507 TAACACATCTAACATTCTCACCAAATACATCACC
1 TAACACACCTAACATTCTCACCAAATACATCACC
*
39541 TAACACACCTAACATTCTCACC-TA-ACA-CACC
1 TAACACACCTAACATTCTCACCAAATACATCACC
*
39572 T---A-A-C--A--TTCTCACCAAACACATCACC
1 TAACACACCTAACATTCTCACCAAATACATCACC
39597 TAACACACCTAACATTCTCACCAAATACATCACC
1 TAACACACCTAACATTCTCACCAAATACATCACC
39631 TAACACACCTAACATTCTCACCAAATA
1 TAACACACCTAACATTCTCACCAAATA
39658 TATCTTAACA
Statistics
Matches: 176, Mismatches: 7, Indels: 48
0.76 0.03 0.21
Matches are distributed among these distances:
22 16 0.09
23 2 0.01
24 8 0.05
25 10 0.06
26 2 0.01
27 2 0.01
28 4 0.02
29 2 0.01
30 2 0.01
31 10 0.06
32 8 0.05
33 2 0.01
34 108 0.61
ACGTcount: A:0.41, C:0.39, G:0.00, T:0.21
Consensus pattern (34 bp):
TAACACACCTAACATTCTCACCAAATACATCACC
Found at i:39474 original size:22 final size:22
Alignment explanation
Indices: 39446--39591 Score: 154
Period size: 22 Copynumber: 6.5 Consensus size: 22
39436 ACCAAATACA
39446 TCACCTAACACACCTAACATTC
1 TCACCTAACACACCTAACATTC
39468 TCACCTAACACACCTAACATTC
1 TCACCTAACACACCTAACATTC
* *
39490 TCACCAAACACATCACCTAACACATC
1 TCACC-TA-ACA-CACCTAACA-TTC
* * * * *
39516 TAACAT-TCTCACC-AA-ATAC
1 TCACCTAACACACCTAACATTC
39535 ATCACCTAACACACCTAACATTC
1 -TCACCTAACACACCTAACATTC
39558 TCACCTAACACACCTAACATTC
1 TCACCTAACACACCTAACATTC
*
39580 TCACCAAACACA
1 TCACCTAACACA
39592 TCACCTAACA
Statistics
Matches: 101, Mismatches: 15, Indels: 16
0.77 0.11 0.12
Matches are distributed among these distances:
19 1 0.01
20 5 0.05
21 7 0.07
22 66 0.65
23 5 0.05
24 3 0.03
25 9 0.09
26 5 0.05
ACGTcount: A:0.40, C:0.40, G:0.00, T:0.21
Consensus pattern (22 bp):
TCACCTAACACACCTAACATTC
Found at i:39503 original size:56 final size:56
Alignment explanation
Indices: 39417--39652 Score: 239
Period size: 56 Copynumber: 4.0 Consensus size: 56
39407 ATATACATGT
*
39417 TAACACACCTAACATTCTCACCAAATACATCACCTAACACACCTAACATTCTCACC
1 TAACACACCTAACATTCTCACCAAACACATCACCTAACACACCTAACATTCTCACC
*
39473 TAACACACCTAACATTCTCACCAAACACATCACCTAACACATCTAACATTCTCACC
1 TAACACACCTAACATTCTCACCAAACACATCACCTAACACACCTAACATTCTCACC
* *
39529 AAATACATCACCTAACA----CACCTAACATTC-TCACCTAACACACCTAACATTCTCACCAAAC
1 -TA-ACA-CACCTAACATTCTCACCAAACA--CATCACCTAACACACCTAACA-T-T--------
39589 ACATCACC
51 -C-TCACC
*
39597 TAACACACCTAACATTCTCACCAAATACATCACCTAACACACCTAACATTCTCACC
1 TAACACACCTAACATTCTCACCAAACACATCACCTAACACACCTAACATTCTCACC
39653 AAATATATCT
Statistics
Matches: 150, Mismatches: 8, Indels: 44
0.74 0.04 0.22
Matches are distributed among these distances:
55 8 0.05
56 77 0.51
57 4 0.03
58 4 0.03
59 9 0.06
65 9 0.06
66 4 0.03
67 4 0.03
68 24 0.16
69 7 0.05
ACGTcount: A:0.40, C:0.39, G:0.00, T:0.21
Consensus pattern (56 bp):
TAACACACCTAACATTCTCACCAAACACATCACCTAACACACCTAACATTCTCACC
Found at i:39570 original size:90 final size:90
Alignment explanation
Indices: 39417--39652 Score: 463
Period size: 90 Copynumber: 2.6 Consensus size: 90
39407 ATATACATGT
39417 TAACACACCTAACATTCTCACCAAATACATCACCTAACACACCTAACATTCTCACCTAACACACC
1 TAACACACCTAACATTCTCACCAAATACATCACCTAACACACCTAACATTCTCACCTAACACACC
39482 TAACATTCTCACCAAACACATCACC
66 TAACATTCTCACCAAACACATCACC
*
39507 TAACACATCTAACATTCTCACCAAATACATCACCTAACACACCTAACATTCTCACCTAACACACC
1 TAACACACCTAACATTCTCACCAAATACATCACCTAACACACCTAACATTCTCACCTAACACACC
39572 TAACATTCTCACCAAACACATCACC
66 TAACATTCTCACCAAACACATCACC
39597 TAACACACCTAACATTCTCACCAAATACATCACCTAACACACCTAACATTCTCACC
1 TAACACACCTAACATTCTCACCAAATACATCACCTAACACACCTAACATTCTCACC
39653 AAATATATCT
Statistics
Matches: 144, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
90 144 1.00
ACGTcount: A:0.40, C:0.39, G:0.00, T:0.21
Consensus pattern (90 bp):
TAACACACCTAACATTCTCACCAAATACATCACCTAACACACCTAACATTCTCACCTAACACACC
TAACATTCTCACCAAACACATCACC
Found at i:40010 original size:28 final size:28
Alignment explanation
Indices: 39911--40805 Score: 740
Period size: 28 Copynumber: 31.6 Consensus size: 28
39901 TTGGGTTTAG
*
39911 AAAGGTTGCCACTAACTTGTGTGGGCTTTAGA
1 AAAGG-TGCCACTGAC-T-TGTGGGCTTT-GA
* *
39943 GAAGGTTGCCACTAACTTGTGTGGGCTTTG-
1 AAAGG-TGCCACTGAC-T-TGTGGGCTTTGA
* * **
39973 GAAGGATGCCACTAACTCATGGGCTTTGA
1 AAAGG-TGCCACTGACTTGTGGGCTTTGA
* * *
40002 AAAGGTGCCACTAACTTATGGTCTTTG-
1 AAAGGTGCCACTGACTTGTGGGCTTTGA
40029 AAAGGATGCCACTGACTTGTGGGCTTTGA
1 AAAGG-TGCCACTGACTTGTGGGCTTTGA
** * *
40058 AAATAATGCCACCGACTTGTGTAGGCTTCG-
1 AAA-GGTGCCACTGACTTGTG--GGCTTTGA
* * *
40088 AAAGGATGCCATTGACTCGTGGGCTTTGG
1 AAAGG-TGCCACTGACTTGTGGGCTTTGA
* * *
40117 AGAGATGCCACTGACTTATGGGCTTTGA
1 AAAGGTGCCACTGACTTGTGGGCTTTGA
* * * *
40145 AGAGATGCCATTGACTTGTGGGCTTCG-
1 AAAGGTGCCACTGACTTGTGGGCTTTGA
* * * *
40172 AAAGGATGCTACTAATTTGTGGGCTATGA
1 AAAGG-TGCCACTGACTTGTGGGCTTTGA
*
40201 AAAGGTGCCACTGACTTGTGGGCTATGA
1 AAAGGTGCCACTGACTTGTGGGCTTTGA
* * * *
40229 AAAAGTGCTACTGAATTGCGGGC-TTGAA
1 AAAGGTGCCACTGACTTGTGGGCTTTG-A
* * *
40257 AAAGATGCCACTGACTTGTGGACTTGGA
1 AAAGGTGCCACTGACTTGTGGGCTTTGA
* * *
40285 AAAGATGCCATTGACTTGTGGGCTTCGA
1 AAAGGTGCCACTGACTTGTGGGCTTTGA
* *
40313 AAGGGTGTCACT-A-TTCGTGGGCTTTGA
1 AAAGGTGCCACTGACTT-GTGGGCTTTGA
* * *
40340 AAAGGATGCCACTAACTGGTGGGCTCT-A
1 AAAGG-TGCCACTGACTTGTGGGCTTTGA
*
40368 AAAGGATGTCACTGACTTGTGGGCTTTGA
1 AAAGG-TGCCACTGACTTGTGGGCTTTGA
* * *
40397 AAGGGTACCACTGACTTGTGGGCTTGGA
1 AAAGGTGCCACTGACTTGTGGGCTTTGA
* ** *
40425 AAAGATGCCACAAACTTGTGGGCTTGGA
1 AAAGGTGCCACTGACTTGTGGGCTTTGA
* *
40453 AAAGATGCCACTAACTTGTGGGCTTTGA
1 AAAGGTGCCACTGACTTGTGGGCTTTGA
* *
40481 AAAGATGCCACTAACTTGTGGGCTTTG-
1 AAAGGTGCCACTGACTTGTGGGCTTTGA
* *
40508 AAAGGATGCCACTAACTTGTGGGCTATGA
1 AAAGG-TGCCACTGACTTGTGGGCTTTGA
* *
40537 AAAGGTGCCACTAACTTGTGGGCTATGA
1 AAAGGTGCCACTGACTTGTGGGCTTTGA
* *
40565 AAAGGTGCCACTAACTTTTGGGC-TTGAA
1 AAAGGTGCCACTGACTTGTGGGCTTTG-A
* * *
40593 AAAGATGCCACTCACTTGTGGGCTTGGA
1 AAAGGTGCCACTGACTTGTGGGCTTTGA
*
40621 AAAGATGCCACTGACTTGTGGGCTTTG-
1 AAAGGTGCCACTGACTTGTGGGCTTTGA
* *
40648 AAAGCGTGCCACTGA-TTCATGAGCTTTGA
1 AAAG-GTGCCACTGACTT-GTGGGCTTTGA
* * *
40677 AAAGGATACCACTGACTGGTGGG-TCTG-
1 AAAGG-TGCCACTGACTTGTGGGCTTTGA
*
40704 AAAGGATGCCACTGACTTATGGGCTTTGA
1 AAAGG-TGCCACTGACTTGTGGGCTTTGA
* * * *
40733 AAAGGTGCCGCTCACTTGTGGACTTGGA
1 AAAGGTGCCACTGACTTGTGGGCTTTGA
* **
40761 AAAGATGCCACTGACTTGCAGGCTTTGA
1 AAAGGTGCCACTGACTTGTGGGCTTTGA
* *
40789 AAGGGCGCCACTG-CTTG
1 AAAGGTGCCACTGACTTG
40806 AAAAATGTAT
Statistics
Matches: 719, Mismatches: 116, Indels: 61
0.80 0.13 0.07
Matches are distributed among these distances:
26 2 0.00
27 61 0.08
28 516 0.72
29 73 0.10
30 32 0.04
31 7 0.01
32 28 0.04
ACGTcount: A:0.26, C:0.18, G:0.29, T:0.27
Consensus pattern (28 bp):
AAAGGTGCCACTGACTTGTGGGCTTTGA
Found at i:41113 original size:15 final size:15
Alignment explanation
Indices: 41095--41127 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
41085 AAAATTTTTC
41095 TTTTCTATAAAGGTA
1 TTTTCTATAAAGGTA
41110 TTTTCTATAAAGGTA
1 TTTTCTATAAAGGTA
41125 TTT
1 TTT
41128 GCCCCATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.30, C:0.06, G:0.12, T:0.52
Consensus pattern (15 bp):
TTTTCTATAAAGGTA
Found at i:43117 original size:18 final size:18
Alignment explanation
Indices: 43078--43137 Score: 59
Period size: 20 Copynumber: 3.2 Consensus size: 18
43068 GACATAATTG
43078 AAATG-TAAAAAAAAAAGTA
1 AAATGATAAAAAAAAAA--A
*
43097 AAATGATAAAAATAAAAA
1 AAATGATAAAAAAAAAAA
*
43115 AAATAATAAATAAGAAAAAA
1 AAATGATAAA-AA-AAAAAA
43135 AAA
1 AAA
43138 AGGATTGCCA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
18 10 0.29
19 7 0.20
20 18 0.51
ACGTcount: A:0.78, C:0.00, G:0.07, T:0.15
Consensus pattern (18 bp):
AAATGATAAAAAAAAAAA
Found at i:43125 original size:16 final size:16
Alignment explanation
Indices: 43102--43138 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
43092 AAGTAAAATG
43102 ATAAAAATAA-AAAAA
1 ATAAAAATAAGAAAAA
43117 ATAATAAATAAGAAAAA
1 ATAA-AAATAAGAAAAA
43134 A-AAAA
1 ATAAAA
43139 GGATTGCCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 6 0.30
16 8 0.40
17 6 0.30
ACGTcount: A:0.84, C:0.00, G:0.03, T:0.14
Consensus pattern (16 bp):
ATAAAAATAAGAAAAA
Found at i:43133 original size:26 final size:26
Alignment explanation
Indices: 43083--43138 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
43073 AATTGAAATG
*
43083 TAAAAAAAAAAGTAAAATGATAAAAA
1 TAAAAAAAAAAGTAAAAAGATAAAAA
43109 TAAAAAAAATAA-TAAATAAGA-AAAAA
1 TAAAAAAAA-AAGTAAA-AAGATAAAAA
43135 -AAAA
1 TAAAA
43139 GGATTGCCAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
25 4 0.15
26 18 0.67
27 5 0.19
ACGTcount: A:0.80, C:0.00, G:0.05, T:0.14
Consensus pattern (26 bp):
TAAAAAAAAAAGTAAAAAGATAAAAA
Found at i:44454 original size:20 final size:19
Alignment explanation
Indices: 44407--44457 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 19
44397 GTAAAAAAAA
44407 TATAATGTATCAATACATT
1 TATAATGTATCAATACATT
* *
44426 GAAAAATGTATCAATACATT
1 -TATAATGTATCAATACATT
44446 TATACATGTATC
1 TATA-ATGTATC
44458 GATATATCTG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
19 2 0.08
20 24 0.92
ACGTcount: A:0.43, C:0.12, G:0.08, T:0.37
Consensus pattern (19 bp):
TATAATGTATCAATACATT
Found at i:48371 original size:10 final size:10
Alignment explanation
Indices: 48358--48407 Score: 50
Period size: 10 Copynumber: 5.0 Consensus size: 10
48348 AAACTAAAAG
48358 AGAAAAAGAA
1 AGAAAAAGAA
48368 AGAAAAAGAA
1 AGAAAAAGAA
48378 A-AAAAA-AA
1 AGAAAAAGAA
*
48386 GAGAAAAATAAA
1 -AGAAAAA-GAA
*
48398 ACAAAAAGAA
1 AGAAAAAGAA
48408 GGTTTTTTCA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
8 2 0.06
9 6 0.18
10 18 0.53
11 6 0.18
12 2 0.06
ACGTcount: A:0.82, C:0.02, G:0.14, T:0.02
Consensus pattern (10 bp):
AGAAAAAGAA
Found at i:48382 original size:19 final size:19
Alignment explanation
Indices: 48353--48406 Score: 65
Period size: 19 Copynumber: 2.9 Consensus size: 19
48343 AAAGAAAACT
* *
48353 AAAAGAGAAAAAGAA-AGA
1 AAAAGAAAAAAAAAAGAGA
48371 AAAAGAAAAAAAAAAGAGA
1 AAAAGAAAAAAAAAAGAGA
* *
48390 AAAATAAAACAAAAAGA
1 AAAAGAAAAAAAAAAGA
48407 AGGTTTTTTC
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
18 13 0.42
19 18 0.58
ACGTcount: A:0.81, C:0.02, G:0.15, T:0.02
Consensus pattern (19 bp):
AAAAGAAAAAAAAAAGAGA
Found at i:48385 original size:29 final size:30
Alignment explanation
Indices: 48343--48407 Score: 87
Period size: 29 Copynumber: 2.2 Consensus size: 30
48333 GTTTTTAGCT
** * *
48343 AAAGAAAACTAAAAGAGAAAAA-GAAAGAA
1 AAAGAAAAAAAAAAGAGAAAAATAAAACAA
48372 AAAGAAAAAAAAAAGAGAAAAATAAAACAA
1 AAAGAAAAAAAAAAGAGAAAAATAAAACAA
48402 AAAGAA
1 AAAGAA
48408 GGTTTTTTCA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 20 0.65
30 11 0.35
ACGTcount: A:0.80, C:0.03, G:0.14, T:0.03
Consensus pattern (30 bp):
AAAGAAAAAAAAAAGAGAAAAATAAAACAA
Found at i:48398 original size:17 final size:18
Alignment explanation
Indices: 48353--48406 Score: 58
Period size: 18 Copynumber: 2.9 Consensus size: 18
48343 AAAGAAAACT
*
48353 AAAAGAGAAAAAGAAAGA-
1 AAAAGA-AAAAAAAAAGAG
48371 AAAAGAAAAAAAAAAGAG
1 AAAAGAAAAAAAAAAGAG
48389 AAAA-ATAAAACAAAAAGA
1 AAAAGA-AAAA-AAAAAGA
48407 AGGTTTTTTC
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
17 11 0.34
18 14 0.44
19 7 0.22
ACGTcount: A:0.81, C:0.02, G:0.15, T:0.02
Consensus pattern (18 bp):
AAAAGAAAAAAAAAAGAG
Found at i:49894 original size:58 final size:57
Alignment explanation
Indices: 49787--49904 Score: 155
Period size: 58 Copynumber: 2.1 Consensus size: 57
49777 CACCAAATTA
* * * *
49787 AAATAGTCCATGATGTTCTTCCAATATATAGAAGTTACCTCATCGATTATTTTAAAC
1 AAATAGTCCATGATGTGCTTCCAATATAGAGAAGTCACCTCATCAATTATTTTAAAC
* * * *
49844 AAATAGTCCATGGGTGTGCTTTCAGTATAGATAAGTCACCTCATCAATTATTTTAAAC
1 AAATAGTCCAT-GATGTGCTTCCAATATAGAGAAGTCACCTCATCAATTATTTTAAAC
49902 AAA
1 AAA
49905 GGAATACATT
Statistics
Matches: 52, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
57 11 0.21
58 41 0.79
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.35
Consensus pattern (57 bp):
AAATAGTCCATGATGTGCTTCCAATATAGAGAAGTCACCTCATCAATTATTTTAAAC
Found at i:51361 original size:155 final size:155
Alignment explanation
Indices: 51104--51385 Score: 336
Period size: 155 Copynumber: 1.8 Consensus size: 155
51094 ATACCCCTAA
* * * * *
51104 TGTGTACCTTCGACATGAAAGTATCTAGTAATAACATAGGACTTGGTTCTAATACAAAATTATCA
1 TGTGTACCTTCGACATGAAAGTATCCAGTAATAACACAAGACATGGTTCTAATACAAAATTACCA
* * * *
51169 AAATGCCCTTAGGATATATCTCTAATATAAAAATATCTCAGTAAC-CTTAAAAGACTGAAAAACA
66 AAATACCCTTAGGACATATCTCTAACATAAAAATATCTCAGTAACTC-TAAAAGACTCAAAAACA
51233 GTATAAAATAATGAACCTATCCTTGG
130 GTATAAAATAATGAACCTATCCTTGG
* *
51259 TGTGTACCTTCGACAT-AGAAGTATCCAGTAATCACACAAGACATGGTTCTAATGCAAAATTACC
1 TGTGTACCTTCGACATGA-AAGTATCCAGTAATAACACAAGACATGGTTCTAATACAAAATTACC
** * ** * * * *
51323 AAAATACTTTTAGGGCATATCT-TCGGCATGATAGTATCTCAGTAACTCTAAAATACTCAAAAA
65 AAAATACCCTTAGGACATATCTCT-AACATAAAAATATCTCAGTAACTCTAAAAGACTCAAAAA
51386 TAATCATAGA
Statistics
Matches: 104, Mismatches: 20, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
154 2 0.02
155 101 0.97
156 1 0.01
ACGTcount: A:0.40, C:0.18, G:0.13, T:0.29
Consensus pattern (155 bp):
TGTGTACCTTCGACATGAAAGTATCCAGTAATAACACAAGACATGGTTCTAATACAAAATTACCA
AAATACCCTTAGGACATATCTCTAACATAAAAATATCTCAGTAACTCTAAAAGACTCAAAAACAG
TATAAAATAATGAACCTATCCTTGG
Found at i:51603 original size:155 final size:154
Alignment explanation
Indices: 51373--51694 Score: 382
Period size: 155 Copynumber: 2.1 Consensus size: 154
51363 AGTAACTCTA
* *
51373 AAAT-ACTCAAAAATAATCATAGAAGGGTGAACCCATCCTCAATGCACAACTTTGGCATAAATGT
1 AAATGACTCAAAAATAATCATAGAAGGGTGAACCCATCCTAAATGCACAACTTTGGCATAAAAGT
* * ** * * * * *
51437 ATCCTGATGACTATATCGGACTTGATTTTAAGGGAAATTACCAAAATGCTTTTGGAGATTACCAT
66 ATCATGATGACTATATCGCACTCAATTTTAA-AGAAATTACCAAAATACTCTTAGAGACTACCAT
* *
51502 CATCTTGAAAGCATCTCAGTGGCCTT
130 CATCTTAAAAGCATCTCA-TGACCTT
* * *
51528 AAATGACTCAAAAATAATC-TAGAAGGGTGAACCTATCCTAAATGCACATCTTTGGTATAAAAG-
1 AAATGACTCAAAAATAATCATAGAAGGGTGAACCCATCCTAAATGCACAACTTTGGCATAAAAGT
* * *
51591 ATTCAT-AGTGACTATATTGCACTCAATTTTAAAGAAATTACCAAAATACTCTTATAGACTACCT
66 A-TCATGA-TGACTATATCGCACTCAATTTTAAAGAAATTACCAAAATACTCTTAGAGACTACCA
*
51655 TCATCTTAAAAGCATCTGATGACCTT
129 TCATCTTAAAAGCATCTCATGACCTT
* *
51681 AAAAGACTAAAAAA
1 AAATGACTCAAAAA
51695 ATTATTAAAA
Statistics
Matches: 142, Mismatches: 22, Indels: 8
0.83 0.13 0.05
Matches are distributed among these distances:
153 18 0.13
154 44 0.31
155 66 0.46
156 14 0.10
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (154 bp):
AAATGACTCAAAAATAATCATAGAAGGGTGAACCCATCCTAAATGCACAACTTTGGCATAAAAGT
ATCATGATGACTATATCGCACTCAATTTTAAAGAAATTACCAAAATACTCTTAGAGACTACCATC
ATCTTAAAAGCATCTCATGACCTT
Found at i:58512 original size:13 final size:13
Alignment explanation
Indices: 58494--58519 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
58484 TACACCAAGT
58494 ATGTATCGATACA
1 ATGTATCGATACA
58507 ATGTATCGATACA
1 ATGTATCGATACA
58520 CCAAAAATTG
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:58517 original size:32 final size:33
Alignment explanation
Indices: 58476--58539 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
58466 TAGCCAAACT
**
58476 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACCAAAAATTGTATCGATACAA
58508 TGTATCGATACACCAAAAATTGTATCGATACA
1 TGTATCGATACACCAAAAATTGTATCGATACA
58540 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACCAAAAATTGTATCGATACAA
Found at i:60252 original size:20 final size:20
Alignment explanation
Indices: 60227--60298 Score: 71
Period size: 20 Copynumber: 3.6 Consensus size: 20
60217 TGCCAGTTTC
60227 ATGTATCGATACAATTGAGT
1 ATGTATCGATACAATTGAGT
*
60247 ATGTATCGATACAA-AGCA-T
1 ATGTATCGATACAATTG-AGT
60266 AATGTATCGATAC-ATCT-AGAT
1 -ATGTATCGATACAAT-TGAG-T
60287 ATGTATCGATAC
1 ATGTATCGATAC
60299 TTTCTAGGGT
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
19 4 0.09
20 39 0.89
21 1 0.02
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.32
Consensus pattern (20 bp):
ATGTATCGATACAATTGAGT
Found at i:60904 original size:21 final size:20
Alignment explanation
Indices: 60880--60925 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
60870 TAAAATTTTC
60880 AATAAAACTCTCCCTTAATAA
1 AATAAAACTC-CCCTTAATAA
** *
60901 AATAATTCTCCCCTTGATAA
1 AATAAAACTCCCCTTAATAA
60921 AATAA
1 AATAA
60926 TTAAAGCTCT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 14 0.64
21 8 0.36
ACGTcount: A:0.46, C:0.22, G:0.02, T:0.30
Consensus pattern (20 bp):
AATAAAACTCCCCTTAATAA
Found at i:65992 original size:11 final size:11
Alignment explanation
Indices: 65972--66004 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
65962 ATACTAGTAT
*
65972 CAATTATGTGA
1 CAATTTTGTGA
65983 CAATTTTGTGA
1 CAATTTTGTGA
65994 CAATTTTGTGA
1 CAATTTTGTGA
66005 TTCAAACACT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.30, C:0.09, G:0.18, T:0.42
Consensus pattern (11 bp):
CAATTTTGTGA
Found at i:69921 original size:20 final size:21
Alignment explanation
Indices: 69892--69933 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
69882 ATTTTTATTA
*
69892 ATTAATTTTAAATTATATTTT
1 ATTAATTTTAAAGTATATTTT
*
69913 ATTAA-TTTAAAGTATTTTTT
1 ATTAATTTTAAAGTATATTTT
69933 A
1 A
69934 ATTTTTTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (21 bp):
ATTAATTTTAAAGTATATTTT
Found at i:70645 original size:30 final size:31
Alignment explanation
Indices: 70590--70652 Score: 78
Period size: 30 Copynumber: 2.1 Consensus size: 31
70580 TTTTGATTTT
*
70590 TTAAATATCTTTTTAATTTAATTTTAAT-AA
1 TTAAATATATTTTTAATTTAATTTTAATCAA
70620 TTAAATATATTTTT-A-TTAAGTTTTTAATCAA
1 TTAAATATATTTTTAATTTAA--TTTTAATCAA
70651 TT
1 TT
70653 TTCTTTTAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
28 4 0.14
29 1 0.03
30 20 0.69
31 4 0.14
ACGTcount: A:0.38, C:0.03, G:0.02, T:0.57
Consensus pattern (31 bp):
TTAAATATATTTTTAATTTAATTTTAATCAA
Found at i:70720 original size:20 final size:21
Alignment explanation
Indices: 70683--70739 Score: 59
Period size: 20 Copynumber: 2.8 Consensus size: 21
70673 AACTAAAAAA
*
70683 ATAAAAT-TATTATTATT-ATT
1 ATAAAATATA-TATAATTAATT
70703 ATAAAATATATATAATTACATT
1 ATAAAATATATATAATTA-ATT
70725 ATAAAA-ATATA-AATT
1 ATAAAATATATATAATT
70740 TTCTAGTAGA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
20 17 0.52
21 7 0.21
22 9 0.27
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (21 bp):
ATAAAATATATATAATTAATT
Found at i:70728 original size:22 final size:20
Alignment explanation
Indices: 70700--70739 Score: 62
Period size: 22 Copynumber: 1.9 Consensus size: 20
70690 TATTATTATT
70700 ATTATAAAATATATATAATTAC
1 ATTATAAAA-ATATA-AATTAC
70722 ATTATAAAAATATAAATT
1 ATTATAAAAATATAAATT
70740 TTCTAGTAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 4 0.22
21 5 0.28
22 9 0.50
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (20 bp):
ATTATAAAAATATAAATTAC
Found at i:71295 original size:19 final size:19
Alignment explanation
Indices: 71266--71363 Score: 76
Period size: 20 Copynumber: 4.8 Consensus size: 19
71256 CATAAATTTT
71266 TTTTTCATTTTTCTCCTTTC
1 TTTTTC-TTTTTCTCCTTTC
71286 TTTTTCTTTTT-TCCATTTTC
1 TTTTTCTTTTTCTCC--TTTC
*
71306 TTTTTCTTTTTC-CTTGTTC
1 TTTTTCTTTTTCTCCT-TTC
71325 TTTTTTCTTTTTTTCTCTCTTTCC
1 -TTTTTC--TTTTTCTC-CTTT-C
*
71349 TTTTT-TTTCTCTCCT
1 TTTTTCTTTTTCTCCT
71364 ATTAGGAAAA
Statistics
Matches: 65, Mismatches: 3, Indels: 21
0.73 0.03 0.24
Matches are distributed among these distances:
18 4 0.06
19 10 0.15
20 35 0.54
22 6 0.09
23 8 0.12
24 2 0.03
ACGTcount: A:0.02, C:0.23, G:0.01, T:0.73
Consensus pattern (19 bp):
TTTTTCTTTTTCTCCTTTC
Found at i:71311 original size:26 final size:26
Alignment explanation
Indices: 71264--71336 Score: 74
Period size: 26 Copynumber: 2.7 Consensus size: 26
71254 CACATAAATT
* *
71264 TTTTTTTCATTTTTCTCCTTTCTTTTTC
1 TTTTTTCCA-TTTTCT-TTTTCTTTTTC
71292 TTTTTTCCATTTTCTTTTTCTTTTTC
1 TTTTTTCCATTTTCTTTTTCTTTTTC
* * **
71318 CTTGTTCTTTTTTCTTTTT
1 TTTTTTCCATTTTCTTTTT
71337 TTCTCTCTTT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
26 25 0.64
27 6 0.15
28 8 0.21
ACGTcount: A:0.03, C:0.19, G:0.01, T:0.77
Consensus pattern (26 bp):
TTTTTTCCATTTTCTTTTTCTTTTTC
Found at i:71337 original size:7 final size:7
Alignment explanation
Indices: 71265--71337 Score: 62
Period size: 7 Copynumber: 10.9 Consensus size: 7
71255 ACATAAATTT
71265 TTTTTTC
1 TTTTTTC
*
71272 ATTTTTC
1 TTTTTTC
**
71279 TCCTTTC
1 TTTTTTC
71286 -TTTTTC
1 TTTTTTC
71292 TTTTTTC
1 TTTTTTC
**
71299 CATTTTC
1 TTTTTTC
71306 -TTTTTC
1 TTTTTTC
71312 -TTTTTC
1 TTTTTTC
* *
71318 CTTGTTC
1 TTTTTTC
71325 TTTTTTC
1 TTTTTTC
71332 TTTTTT
1 TTTTTT
71338 TCTCTCTTTC
Statistics
Matches: 52, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
6 15 0.29
7 37 0.71
ACGTcount: A:0.03, C:0.19, G:0.01, T:0.77
Consensus pattern (7 bp):
TTTTTTC
Found at i:71778 original size:13 final size:13
Alignment explanation
Indices: 71760--71784 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
71750 AGATTGCTTA
71760 GTATCGATACATT
1 GTATCGATACATT
71773 GTATCGATACAT
1 GTATCGATACAT
71785 GCTCATAATA
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):
GTATCGATACATT
Found at i:75879 original size:841 final size:841
Alignment explanation
Indices: 74258--75934 Score: 2725
Period size: 841 Copynumber: 2.0 Consensus size: 841
74248 TTAGCTAATT
*
74258 ATGTGACAAGGGTATGAAAGTTACATTTGAATCACAAAATTATCACGTAATTGATACTAACACTA
1 ATGTGACAAGGGTATGAAAGCTACATTTGAATCACAAAATTATCACGTAATTGATACTAACACTA
* **
74323 ATAAAACAATTTTTCTCGAACGTAGAGAAAGGAACATTTATGTTGTACATTTAAATGTTCTAAGT
66 ATAAAACAATTTTTATCGAACAAAGAGAAAGGAACATTTATGTTGTACATTTAAATGTTCTAAGT
*
74388 TCCCAAAATGTATGTTTTGTTGCGAACAACAATGACATACCTTGGCTATAGCATCGTAGGTTAAG
131 TCCCAAAATGTATGTTTTGTTGCGAACAACAATGACATACCTTAGCTATAGCATCGTAGGTTAAG
74453 ACATGCAAGTATGAGCATATTTTCAAAATGGTCTAGGAAAAACCTTGTTGTTGGATTGCCTAAGC
196 ACATGCAAGTATGAGCATATTTTCAAAATGGTCTAGGAAAAACCTTGTTGTTGGATTGCCTAAGC
* * *
74518 TTAAGTTTGAATGTGATAAGGTGTGTGATGCATGCATTAAAGGCAAACATAGAAGAACTTTTTTT
261 TTAAGTTTGAATGTGACAAGGTGTGTGATGCATGCATTAAAGGCAAACATAAAAGAACTTCTTTT
*
74583 AAGCCTTTAAATATTGTCACAACCACTAAAACTTTACAATTAGTTCATATTGATTTGTTTGGTCC
326 AAGCCTTTAAATATTGTCACAACCACTAAAACTTTACAATTAGTTCATATTGATTTATTTGGTCC
*
74648 GACTAGAATGCAAAGTCTAGGTGGTAAAAGATATGGATTTGTAATTGTGAATGATTATTCAAGAT
391 GACTAGAATGCAAAATCTAGGTGGTAAAAGATATGGATTTGTAATTGTGAATGATTATTCAAGAT
* * * *
74713 ATACTTAGGTTTTGTTCTTAAGCACCAAGTATGAAGCTTTAGAAAAATTCATCACATTTTGTAAA
456 ATACTTAGGTTCTATTCTTAAGCACCAAGGATAAAGCTTTAGAAAAATTCATCACATTTTGTAAA
* * * * *
74778 ATTGTTTTAAAAGAAAAAGGTTACTCTTTATCTAGTATAAGAAGTGACCATGGTAAAAAATTTGA
521 ATTGATTCAAAAGAAAAAGGTTAATCTTTATCTAGTATAAGAACTGACCATGGTAAAAAATTTAA
* *
74843 AAATCTTGGTTTTGATAATTTTGGTAATGAAAATGATATTAGCAATAACTTCATAGGTCCTAGAA
586 AAATCTTGGTTTTGATAATTTTGGTAATGAAAATGATACTAGCAATAACTTCACAGGTCCTAGAA
*
74908 CTTCTCAACAAAATGGAGTTATTGAAAGAAAAAATCGAACTTTGAAAGAAATGGCTAGGACTATG
651 CTCCTCAACAAAATGGAGTTATTGAAAGAAAAAATCGAACTTTGAAAGAAATGGCTAGGACTATG
*
74973 CTTTGTGAAAATAATTTACCAAGATATTTTTAAGCAGAAGCTATGAATACAGCTTGTTATATTGT
716 CTTTGTGAAAATAATTTACCAAGATATTTTTAAGCAAAAGCTATGAATACAGCTTGTTATATTGT
*
75038 AAACCAAGCTATGATTAGG-CTAATTTTAAAGAAAACTCAATATGAA-CTTTATAAAACAATC
781 AAACCAAGCTATGATTAGGTC-AATTTTAAAGAAAACTCAATA-CAAGCTTTATAAAACAATC
** *
75099 ATGTGACAAGGGTATGAAAGCTGTATTTGAATCACAAAATTATCACGTAATTGATACTAGCACTA
1 ATGTGACAAGGGTATGAAAGCTACATTTGAATCACAAAATTATCACGTAATTGATACTAACACTA
* ** *
75164 ATTAAACAATTTTTATCGGCCAAAGA-AAAGGGAACATTTATGTTGTACATTTAGATGTTCTAAG
66 ATAAAACAATTTTTATCGAACAAAGAGAAA-GGAACATTTATGTTGTACATTTAAATGTTCTAAG
* * *
75228 TTCCCAAAATGTATGTTTTGTTGCGAATAACAATGACATACCTTAGCTATGGCATCGTAGGTTAG
130 TTCCCAAAATGTATGTTTTGTTGCGAACAACAATGACATACCTTAGCTATAGCATCGTAGGTTAA
* ** *
75293 GACATGCAAGTATGAGCTTATTTTTGAAATTGTCTAGGAAAAACCTTGTTGTTGGATTGCCTAAG
195 GACATGCAAGTATGAGCATATTTTCAAAATGGTCTAGGAAAAACCTTGTTGTTGGATTGCCTAAG
* *
75358 GTTAAGTTTGAATGTGACAAGGTGTGTGATGCATTCATTAAAGGCAAACATAAAAGAACTTCTTT
260 CTTAAGTTTGAATGTGACAAGGTGTGTGATGCATGCATTAAAGGCAAACATAAAAGAACTTCTTT
* *
75423 TAAGCCTTTAAATATTGTCACAACCACTAGAACTTTGCAATTAGTTCATATTGATTTATTTGGTC
325 TAAGCCTTTAAATATTGTCACAACCACTAAAACTTTACAATTAGTTCATATTGATTTATTTGGTC
* *
75488 TGACTAGAATGCAAAATCTAGGTGGTAAACGATATGGATTTGTAATTGT-AGATGATTATTCAAG
390 CGACTAGAATGCAAAATCTAGGTGGTAAAAGATATGGATTTGTAATTGTGA-ATGATTATTCAAG
*
75552 ATATACTTGGGTTCTATTCTTAAGCACCAAGGATAAAGCTTTAGAAAAATTCATCACATTTTGTA
454 ATATACTTAGGTTCTATTCTTAAGCACCAAGGATAAAGCTTTAGAAAAATTCATCACATTTTGTA
*
75617 AAATT-ATTCAAAATGAAAAAGGTTAATCTTTATCTAGTATTAGAACTGACCATGGTAAAAAATT
519 AAATTGATTCAAAA-GAAAAAGGTTAATCTTTATCTAGTATAAGAACTGACCATGGTAAAAAATT
* *
75681 TAAAAATCTTGGTTTTGATAATTTTTGTAATGAAAATGATACTAGCAATAACTTCACAGGTCTTA
583 TAAAAATCTTGGTTTTGATAATTTTGGTAATGAAAATGATACTAGCAATAACTTCACAGGTCCTA
* * * * * *
75746 GAACTCCTCAATAAAATGGAGTTGTTGAAAGGAAAAATCGCACTTTGGAATAAATGGCTAGGACT
648 GAACTCCTCAACAAAATGGAGTTATTGAAAGAAAAAATCGAACTTTGAAAGAAATGGCTAGGACT
* * * *
75811 ATGCTTTGTGAAAATAATTTACCAATATATTTTTAGGCAAAAGCTATTAATACCGCTTGTTATAT
713 ATGCTTTGTGAAAATAATTTACCAAGATATTTTTAAGCAAAAGCTATGAATACAGCTTGTTATAT
* * *
75876 TGTAAACCGAGTTATGATTAGGTCAATTTTAAAGAAAACTCCATACAAGCTTTATAAAA
778 TGTAAACCAAGCTATGATTAGGTCAATTTTAAAGAAAACTCAATACAAGCTTTATAAAA
75935 AAAAGGCTAA
Statistics
Matches: 770, Mismatches: 61, Indels: 10
0.92 0.07 0.01
Matches are distributed among these distances:
840 12 0.02
841 757 0.98
842 1 0.00
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.34
Consensus pattern (841 bp):
ATGTGACAAGGGTATGAAAGCTACATTTGAATCACAAAATTATCACGTAATTGATACTAACACTA
ATAAAACAATTTTTATCGAACAAAGAGAAAGGAACATTTATGTTGTACATTTAAATGTTCTAAGT
TCCCAAAATGTATGTTTTGTTGCGAACAACAATGACATACCTTAGCTATAGCATCGTAGGTTAAG
ACATGCAAGTATGAGCATATTTTCAAAATGGTCTAGGAAAAACCTTGTTGTTGGATTGCCTAAGC
TTAAGTTTGAATGTGACAAGGTGTGTGATGCATGCATTAAAGGCAAACATAAAAGAACTTCTTTT
AAGCCTTTAAATATTGTCACAACCACTAAAACTTTACAATTAGTTCATATTGATTTATTTGGTCC
GACTAGAATGCAAAATCTAGGTGGTAAAAGATATGGATTTGTAATTGTGAATGATTATTCAAGAT
ATACTTAGGTTCTATTCTTAAGCACCAAGGATAAAGCTTTAGAAAAATTCATCACATTTTGTAAA
ATTGATTCAAAAGAAAAAGGTTAATCTTTATCTAGTATAAGAACTGACCATGGTAAAAAATTTAA
AAATCTTGGTTTTGATAATTTTGGTAATGAAAATGATACTAGCAATAACTTCACAGGTCCTAGAA
CTCCTCAACAAAATGGAGTTATTGAAAGAAAAAATCGAACTTTGAAAGAAATGGCTAGGACTATG
CTTTGTGAAAATAATTTACCAAGATATTTTTAAGCAAAAGCTATGAATACAGCTTGTTATATTGT
AAACCAAGCTATGATTAGGTCAATTTTAAAGAAAACTCAATACAAGCTTTATAAAACAATC
Found at i:81237 original size:20 final size:19
Alignment explanation
Indices: 81190--81240 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
81180 GTATCAATAC
**
81190 ATTGTATCGATACATGTTA
1 ATTGTATCGATACACCTTA
*
81209 ATAGTATCGATACACCTTAA
1 ATTGTATCGATACACCTT-A
81229 ATTGTATCGATA
1 ATTGTATCGATA
81241 TATGAAACTA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
19 15 0.56
20 12 0.44
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.37
Consensus pattern (19 bp):
ATTGTATCGATACACCTTA
Found at i:88612 original size:81 final size:81
Alignment explanation
Indices: 88460--88628 Score: 189
Period size: 81 Copynumber: 2.1 Consensus size: 81
88450 CATACAAGGA
** * * *
88460 TCAATATCCTTAGAAGTTTACTAGTCAAATTGTGATTTTGGACAACAACATGCAAGGATCGATAC
1 TCAA-ATCCTTAGAAGCCTACTAGTCAAATTATGATTCTGGACAACAACATGCAAGGATAGATAC
* * *
88525 CTTTAGATGCCTACTGG
65 CTTTAGATACCAACCGG
* * * *
88542 TCAAATCCTTAGATGCCTACTAGTCTAATTATGATTCTGGATAACAACATGCGAA-GATAGATGT
1 TCAAATCCTTAGAAGCCTACTAGTCAAATTATGATTCTGGACAACAACATGC-AAGGATAGAT-A
88606 CC-TTAGATACCAACCGG
64 CCTTTAGATACCAACCGG
88623 TCAAAT
1 TCAAAT
88629 GGTGATTTTG
Statistics
Matches: 73, Mismatches: 12, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
81 65 0.89
82 8 0.11
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (81 bp):
TCAAATCCTTAGAAGCCTACTAGTCAAATTATGATTCTGGACAACAACATGCAAGGATAGATACC
TTTAGATACCAACCGG
Found at i:89330 original size:27 final size:27
Alignment explanation
Indices: 89300--89384 Score: 134
Period size: 27 Copynumber: 3.1 Consensus size: 27
89290 TGATGACGAC
*
89300 CATGCTTGGCGACTAGACCTGGGCGGT
1 CATGCTTGGCGACCAGACCTGGGCGGT
* *
89327 CATGCTTGGTGACCAGACCTGGGTGGT
1 CATGCTTGGCGACCAGACCTGGGCGGT
*
89354 CATGCTTGGCAACCAGACCTGGGCGGT
1 CATGCTTGGCGACCAGACCTGGGCGGT
89381 CATG
1 CATG
89385 TGGCGATTAG
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 52 1.00
ACGTcount: A:0.16, C:0.26, G:0.35, T:0.22
Consensus pattern (27 bp):
CATGCTTGGCGACCAGACCTGGGCGGT
Found at i:93136 original size:20 final size:21
Alignment explanation
Indices: 93084--93135 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
93074 GCCTTTGACT
*
93084 ATGCTTTTTTTATTATGTTTC
1 ATGCATTTTTTATTATGTTTC
93105 ATGCATTTTTTATTATGTTTC
1 ATGCATTTTTTATTATGTTTC
93126 ATGCATTTTT
1 ATGCATTTTT
93136 AACATGTCCA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.17, C:0.10, G:0.10, T:0.63
Consensus pattern (21 bp):
ATGCATTTTTTATTATGTTTC
Found at i:93142 original size:20 final size:21
Alignment explanation
Indices: 93084--93142 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 21
93074 GCCTTTGACT
* **
93084 ATGCTTTTTTTATTATGTTTC
1 ATGCATTTTTTAACATGTTTC
**
93105 ATGCATTTTTTATTATGTTTC
1 ATGCATTTTTTAACATGTTTC
93126 ATGCA-TTTTTAACATGT
1 ATGCATTTTTTAACATGT
93143 CCAGCATCTC
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
20 10 0.29
21 25 0.71
ACGTcount: A:0.20, C:0.10, G:0.10, T:0.59
Consensus pattern (21 bp):
ATGCATTTTTTAACATGTTTC
Found at i:105870 original size:11 final size:11
Alignment explanation
Indices: 105854--105902 Score: 73
Period size: 11 Copynumber: 4.5 Consensus size: 11
105844 TTACACCTAA
105854 AAAAAAAAAAC
1 AAAAAAAAAAC
105865 -AAAAAAAAAC
1 AAAAAAAAAAC
*
105875 AAACAAAAAAC
1 AAAAAAAAAAC
*
105886 AAAAAAAAAAG
1 AAAAAAAAAAC
105897 AAAAAA
1 AAAAAA
105903 TAGCAAAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
10 10 0.29
11 24 0.71
ACGTcount: A:0.90, C:0.08, G:0.02, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAC
Found at i:105902 original size:10 final size:10
Alignment explanation
Indices: 105855--105894 Score: 71
Period size: 10 Copynumber: 3.9 Consensus size: 10
105845 TACACCTAAA
105855 AAAAAAAAAC
1 AAAAAAAAAC
105865 AAAAAAAAAC
1 AAAAAAAAAC
105875 AAACAAAAAAC
1 AAA-AAAAAAC
105886 AAAAAAAAA
1 AAAAAAAAA
105895 AGAAAAAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
10 19 0.66
11 10 0.34
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAC
Found at i:105911 original size:1 final size:1
Alignment explanation
Indices: 105852--105902 Score: 57
Period size: 1 Copynumber: 51.0 Consensus size: 1
105842 CCTTACACCT
* * * * *
105852 AAAAAAAAAAAACAAAAAAAAACAAACAAAAAACAAAAAAAAAAGAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
105903 TAGCAAAAAT
Statistics
Matches: 40, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
1 40 1.00
ACGTcount: A:0.90, C:0.08, G:0.02, T:0.00
Consensus pattern (1 bp):
A
Done.