Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_534
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: 61817
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Found at i:687 original size:37 final size:37
Alignment explanation
Indices: 637--715 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 37
627 TTATTACGAA
* *
637 GTCTTACCCGGACATAA-TCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATTC-CCACACGAAGTCATCGG
*
674 GTCTTACCCGGACAAAATTCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
711 GTCTT
1 GTCTT
716 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 36 0.95
38 2 0.05
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.25
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
Found at i:917 original size:43 final size:42
Alignment explanation
Indices: 837--1001 Score: 152
Period size: 43 Copynumber: 3.8 Consensus size: 42
827 TTCGGGACTT
* * * * *
837 ATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGC
1 ATCACATATATACA-TTTCACATTCATCACATCGGCCA-TCGGC
* * ***
881 GTCACATATATACGTTTCACATTCATCACATCGGCCATACCTT
1 ATCACATATATACATTTCACATTCATCACATCGGCCAT-CGGC
*
924 ATCACATATATACATTTCACATTCATCACATCGGCCATTAGGCC
1 ATCACATATATACATTTCACATTCATCACATCGGCCA-TCGG-C
968 TTAT-ACATATATACACTTTCACATTCATCACATC
1 --ATCACATATATACA-TTTCACATTCATCACATC
1002 ACATCACTAT
Statistics
Matches: 99, Mismatches: 16, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
42 1 0.01
43 56 0.57
44 11 0.11
45 11 0.11
46 20 0.20
ACGTcount: A:0.29, C:0.30, G:0.08, T:0.32
Consensus pattern (42 bp):
ATCACATATATACATTTCACATTCATCACATCGGCCATCGGC
Found at i:990 original size:46 final size:46
Alignment explanation
Indices: 884--1238 Score: 285
Period size: 46 Copynumber: 8.0 Consensus size: 46
874 ACTCGGCGTC
*
884 ACATATATAC-GTTTCACATTCATCACATCGGCCA-TA--CCTTAT
1 ACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTAT
926 CACATATATACA-TTTCACATTCATCACATCGGCCATTAGGCCTTAT
1 -ACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTAT
** *
972 ACATATATACACTTTCACATTCATCACATCACATCACTATTAACGCCTTA-
1 ACATATATACACTTTCACATTCATCACAT--CGGC-C-ATT-AGGCCTTAT
* * *
1022 CCACTA-ATAC-CATTCA-ATTCATCACATCGG-CATTAGGCCCTAT
1 ACA-TATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTAT
*
1065 -CGTATATACACTTT-A-ATTC-T-AC-TCCGG-CATTAGGCCTTAT
1 ACATATATACACTTTCACATTCATCACAT-CGGCCATTAGGCCTTAT
*
1105 AC-CATATACA-TTTCACATTCATCACATC-GCC-TTAGGGCCGTTAT
1 ACATATATACACTTTCACATTCATCACATCGGCCATTA-GGCC-TTAT
* * **
1149 CCACATATACACTTTC-CAATTC-TCACATC-GTTATGT-GGTCCTTAT
1 ACATATATACACTTTCAC-ATTCATCACATCGGCCAT-TAGG-CCTTAT
1194 CACATATATACACTTTC-CATTCATCACATCGGCCATTAGGCCTTA
1 -ACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
1239 CTATCATTTC
Statistics
Matches: 258, Mismatches: 20, Indels: 65
0.75 0.06 0.19
Matches are distributed among these distances:
39 4 0.02
40 25 0.10
41 8 0.03
42 21 0.08
43 47 0.18
44 9 0.03
45 38 0.15
46 63 0.24
47 6 0.02
48 13 0.05
49 6 0.02
50 9 0.03
51 9 0.03
ACGTcount: A:0.29, C:0.29, G:0.08, T:0.33
Consensus pattern (46 bp):
ACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTAT
Found at i:4885 original size:40 final size:39
Alignment explanation
Indices: 4820--4981 Score: 157
Period size: 36 Copynumber: 4.4 Consensus size: 39
4810 AGCAGAATCT
4820 GGGACTTAG-CC-GATAATCACTAGCATGAATGCTCTTC
1 GGGACTTAGCCCGGATAATCACTAGCATGAATGCTCTTC
4857 GGGACTTAGCCCGGATACATCACTAGCATGAATGCTCTTC
1 GGGACTTAGCCCGGATA-ATCACTAGCATGAATGCTCTTC
* * * **
4897 GAGAC-TAGCCCGGAT-GT-ACTCGCACCAATGC-CTTC
1 GGGACTTAGCCCGGATAATCACTAGCATGAATGCTCTTC
* * *
4932 -GGATCTTAGTCCGGAT-ATCACTAGCA-CAAAG--CTTC
1 GGGA-CTTAGCCCGGATAATCACTAGCATGAATGCTCTTC
4967 GGGACTTAGCCCGGA
1 GGGACTTAGCCCGGA
4982 CATCATTCGA
Statistics
Matches: 107, Mismatches: 11, Indels: 16
0.80 0.08 0.12
Matches are distributed among these distances:
34 2 0.02
35 19 0.18
36 28 0.26
37 16 0.15
38 2 0.02
39 14 0.13
40 26 0.24
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.23
Consensus pattern (39 bp):
GGGACTTAGCCCGGATAATCACTAGCATGAATGCTCTTC
Found at i:5399 original size:42 final size:42
Alignment explanation
Indices: 5327--5426 Score: 168
Period size: 42 Copynumber: 2.4 Consensus size: 42
5317 TGCATTTCAA
*
5327 GCCC-CACACTTAGTGCCATCTCACAACCGTGAATACTTATT
1 GCCCGCACACTTAGTGCCATCTCACAACCGTGAACACTTATT
5368 G-CCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
1 GCCCGCACACTTAGTGCC-ATCTCACAACCGTGAACACTTATT
5410 GCCCGCACACTTAGTGC
1 GCCCGCACACTTAGTGC
5427 TGAAAGCCAA
Statistics
Matches: 55, Mismatches: 1, Indels: 4
0.92 0.02 0.07
Matches are distributed among these distances:
40 2 0.04
41 14 0.25
42 24 0.44
43 15 0.27
ACGTcount: A:0.26, C:0.35, G:0.15, T:0.24
Consensus pattern (42 bp):
GCCCGCACACTTAGTGCCATCTCACAACCGTGAACACTTATT
Found at i:7317 original size:37 final size:37
Alignment explanation
Indices: 7267--7345 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 37
7257 TTATTACGAA
* *
7267 GTCTTACCCGGACATAA-TCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATTC-CCACACGAAGTCATCGG
*
7304 GTCTTACCCGGACAAAATTCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
7341 GTCTT
1 GTCTT
7346 TAGAGCTCAG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 36 0.95
38 2 0.05
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.25
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
Found at i:7644 original size:47 final size:47
Alignment explanation
Indices: 7464--8030 Score: 915
Period size: 47 Copynumber: 12.1 Consensus size: 47
7454 CCCTTCGGGA
* * * * * * *
7464 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
**
7511 C-CGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
7557 CTTATCACATATATACA-TTTCACATTCATCACATCAGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
7603 CTTATTACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
7650 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
7697 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
7744 CTTATCACACATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
7791 CTTATCACACATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
7838 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
7885 CTTATCACATATATATACACTTTCACATTCATTACATCGGCTATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
7934 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGG-
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
7980 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
8027 CTTA
1 CTTA
8031 CTATCATTTC
Statistics
Matches: 492, Mismatches: 23, Indels: 10
0.94 0.04 0.02
Matches are distributed among these distances:
46 127 0.26
47 321 0.65
49 44 0.09
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:12051 original size:47 final size:45
Alignment explanation
Indices: 11938--12198 Score: 192
Period size: 47 Copynumber: 5.6 Consensus size: 45
11928 TACAAGTGCT
* ** *
11938 GATGCATGTCCCAGACATGTCTTACACTAGCACAAAGCTTA-GCC
1 GATGCATGTCCCAGACATGTCTTACACTGGCACTCATCTTAGGCC
* * * *
11982 AATGAATGTCCCAAACACGTCTTACACTGGCTAC-CATCATTGAGGCC
1 GATGCATGTCCCAGACATGTCTTACACTGGC-ACTCATC-TT-AGGCC
**
12029 GATGCATGTCCCAGACATGTCTTACACTGGCACTCATCTCTACACC
1 GATGCATGTCCCAGACATGTCTTACACTGGCACTCATCT-TAGGCC
* * * * *
12075 AATGCCATGTCCCAGACATGGTCATACGCT-G-ACT-ATCGTAATGTGGCT
1 GATG-CATGTCCCAGACAT-GTCTTACACTGGCACTCATC-T--T-AGGCC
* * * *
12123 GATGCATGTCCCAGACATGTCTTACACTAGC-CTCGTCTCAATGCC
1 GATGCATGTCCCAGACATGTCTTACACTGGCACTCATCT-TAGGCC
12168 GATGCCATGTCCCAGACATGGTCTTACACTG
1 GATG-CATGTCCCAGACAT-GTCTTACACTG
12199 ACTCTCACAT
Statistics
Matches: 170, Mismatches: 31, Indels: 29
0.74 0.13 0.13
Matches are distributed among these distances:
44 28 0.16
45 13 0.08
46 36 0.21
47 79 0.46
48 14 0.08
ACGTcount: A:0.26, C:0.30, G:0.19, T:0.25
Consensus pattern (45 bp):
GATGCATGTCCCAGACATGTCTTACACTGGCACTCATCTTAGGCC
Found at i:12142 original size:94 final size:94
Alignment explanation
Indices: 11935--12201 Score: 310
Period size: 93 Copynumber: 2.9 Consensus size: 94
11925 GTGTACAAGT
** * * *
11935 GCTGATGCATGTCCCAGACATGTCTTACACTAGCACAAAGCT-TAGCCAATG-AATGTCCCAAAC
1 GCTGATGCATGTCCCAGACATGTCTTACACTAGCACTCATCTCTAGCCAATGCCATGTCCCAGAC
* * *
11998 A-CGTCTTACACTGGCTACCATCATTGAG
66 ATGGTCTTACACTGACTACCATCAATGAG
* * *
12026 GCCGATGCATGTCCCAGACATGTCTTACACTGGCACTCATCTCTACACCAATGCCATGTCCCAGA
1 GCTGATGCATGTCCCAGACATGTCTTACACTAGCACTCATCTCTA-GCCAATGCCATGTCCCAGA
* * * * *
12091 CATGGTCATACGCTGACTATCGT-AATGTG
65 CATGGTCTTACACTGACTACCATCAATGAG
* * *
12120 GCTGATGCATGTCCCAGACATGTCTTACACTAGC-CTCGTCTCAATGCCGATGCCATGTCCCAGA
1 GCTGATGCATGTCCCAGACATGTCTTACACTAGCACTCATCTCTA-GCCAATGCCATGTCCCAGA
12184 CATGGTCTTACACTGACT
65 CATGGTCTTACACTGACT
12202 CTCACATAAT
Statistics
Matches: 147, Mismatches: 25, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
91 37 0.25
92 2 0.01
93 47 0.32
94 47 0.32
95 14 0.10
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.25
Consensus pattern (94 bp):
GCTGATGCATGTCCCAGACATGTCTTACACTAGCACTCATCTCTAGCCAATGCCATGTCCCAGAC
ATGGTCTTACACTGACTACCATCAATGAG
Found at i:17806 original size:47 final size:46
Alignment explanation
Indices: 17694--18004 Score: 238
Period size: 47 Copynumber: 6.7 Consensus size: 46
17684 ATTTGTTTGT
* ** * *
17694 GAGCTAGTGTAAGACATGTCTAGGACAT-GCATCGGAC-ACATTATGA
1 GAGCTAGTGTAAGACATGTCTGGGACATGGCATCGG-CTTGA-GATAA
* *
17740 GAGCTAGTGTAAGACCATGTCTGGGACATGGAATCGGCATTGAGACAA
1 GAGCTAGTGTAAGA-CATGTCTGGGACATGGCATCGGC-TTGAGATAA
*
17788 GAGCTAGTGTAAGACATGTCAGGGACAT-GCATCGGCCTTGAGACGT-A
1 GAGCTAGTGTAAGACATGTCTGGGACATGGCATCGG-CTTGAGA--TAA
* * * *
17835 -AGCCAGTGTAAGACATGTCTAGGACAT-GCATCGGCTACGAGATGA
1 GAGCTAGTGTAAGACATGTCTGGGACATGGCATCGGCT-TGAGATAA
* * * * * *
17880 TAGTTAGTGTAAGACAGTGTTTGGGACATGGCATTGACTTGAGATAT
1 GAGCTAGTGTAAGACA-TGTCTGGGACATGGCATCGGCTTGAGATAA
* * * * * *
17927 GAGCCAGTGTAAGACTGTGTCTGAGATATGGCATCGACTTGAGATAT
1 GAGCTAGTGTAAGAC-ATGTCTGGGACATGGCATCGGCTTGAGATAA
* * *
17974 GAGCCAGTGTAAGACTGTGTCTAGGACATGG
1 GAGCTAGTGTAAGAC-ATGTCTGGGACATGG
18005 AATTGGCACC
Statistics
Matches: 218, Mismatches: 34, Indels: 25
0.79 0.12 0.09
Matches are distributed among these distances:
44 1 0.00
45 3 0.01
46 74 0.34
47 110 0.50
48 29 0.13
49 1 0.00
ACGTcount: A:0.29, C:0.16, G:0.30, T:0.24
Consensus pattern (46 bp):
GAGCTAGTGTAAGACATGTCTGGGACATGGCATCGGCTTGAGATAA
Found at i:17843 original size:46 final size:45
Alignment explanation
Indices: 17695--17909 Score: 197
Period size: 46 Copynumber: 4.6 Consensus size: 45
17685 TTTGTTTGTG
17695 AGCTAGTGTAAGACATGTCTAGGACATGCATCGGACACATT-ATGA-G-
1 AGCTAGTGTAAGACATGTCTAGGACATGCATCGG-C-C-TTGA-GACGA
* * * *
17741 AGCTAGTGTAAGACCATGTCTGGGACATGGAATCGGCATTGAGACAA
1 AGCTAGTGTAAGA-CATGTCTAGGACAT-GCATCGGCCTTGAGACGA
17788 GAGCTAGTGTAAGACATGTC-AGGGACATGCATCGGCCTTGAGACGTA
1 -AGCTAGTGTAAGACATGTCTA-GGACATGCATCGGCCTTGAGACG-A
* * *
17835 AGCCAGTGTAAGACATGTCTAGGACATGCATCGG-CTACGAGATGA
1 AGCTAGTGTAAGACATGTCTAGGACATGCATCGGCCT-TGAGACGA
* * *
17880 TAGTTAGTGTAAGACAGTGTTTGGGACATG
1 -AGCTAGTGTAAGACA-TGTCTAGGACATG
17910 GCATTGACTT
Statistics
Matches: 142, Mismatches: 15, Indels: 23
0.79 0.08 0.13
Matches are distributed among these distances:
45 7 0.05
46 77 0.54
47 39 0.27
48 19 0.13
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.23
Consensus pattern (45 bp):
AGCTAGTGTAAGACATGTCTAGGACATGCATCGGCCTTGAGACGA
Found at i:17968 original size:140 final size:140
Alignment explanation
Indices: 17699--18003 Score: 350
Period size: 140 Copynumber: 2.2 Consensus size: 140
17689 TTTGTGAGCT
*
17699 AGTGTAAGACATGTCTAGGACATGCATCGGACACATTATGAGAGCTAGTGTAAGACCATGTCTGG
1 AGTGTAAGACATGTCTAGGACATGCATCGGACACATGATGAGAGCTAGTGTAAGACCATGTCTGG
* * * *
17764 GACATGGAATCGGCATTGAGACAAGAGCTAGTGTAAGACATGTCAGGGACATGCATCGGCCTTGA
66 GACATGGAATCGACATTGAGACAAGAGCCAGTGTAAGACATGTCAGAGACATGCATCGGACTTGA
*
17829 GACGTAAGCC
131 GACATAAGCC
* * *
17839 AGTGTAAGACATGTCTAGGACATGCATCGG-CTACGA-GATGATAGTTAGTGTAAGA-CAGTGTT
1 AGTGTAAGACATGTCTAGGACATGCATCGGAC-AC-ATGATGAGAGCTAGTGTAAGACCA-TGTC
* * * * * * *
17901 TGGGACATGGCATTGAC-TTGAGATATGAGCCAGTGTAAGACTGTGTCTGAGATATGGCATC-GA
63 TGGGACATGGAATCGACATTGAGACAAGAGCCAGTGTAAGAC-ATGTCAGAGACAT-GCATCGGA
* *
17964 CTTGAGATATGAGCC
126 CTTGAGACATAAGCC
*
17979 AGTGTAAGACTGTGTCTAGGACATG
1 AGTGTAAGAC-ATGTCTAGGACATG
18004 GAATTGGCAC
Statistics
Matches: 140, Mismatches: 19, Indels: 11
0.82 0.11 0.06
Matches are distributed among these distances:
139 24 0.17
140 97 0.69
141 19 0.14
ACGTcount: A:0.30, C:0.16, G:0.30, T:0.25
Consensus pattern (140 bp):
AGTGTAAGACATGTCTAGGACATGCATCGGACACATGATGAGAGCTAGTGTAAGACCATGTCTGG
GACATGGAATCGACATTGAGACAAGAGCCAGTGTAAGACATGTCAGAGACATGCATCGGACTTGA
GACATAAGCC
Found at i:20809 original size:27 final size:27
Alignment explanation
Indices: 20770--20886 Score: 135
Period size: 27 Copynumber: 4.3 Consensus size: 27
20760 GCGTACCTGA
*
20770 ACCCTCATGTGATAAAATGATGATTTT
1 ACCCTCATGTGATAAAATGACGATTTT
* *
20797 ACCCTTATATGATAAAATGACGATTTT
1 ACCCTCATGTGATAAAATGACGATTTT
** * *
20824 GTCCTCACGTGATAAAATGATGATTTT
1 ACCCTCATGTGATAAAATGACGATTTT
* * *
20851 TCCCTTATGTGATAAAATGACGACTTAT
1 ACCCTCATGTGATAAAATGACGA-TTTT
20879 ACCCTCAT
1 ACCCTCAT
20887 AGGGTAAAAT
Statistics
Matches: 72, Mismatches: 17, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
27 63 0.88
28 9 0.12
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.36
Consensus pattern (27 bp):
ACCCTCATGTGATAAAATGACGATTTT
Found at i:20955 original size:27 final size:27
Alignment explanation
Indices: 20877--21009 Score: 124
Period size: 27 Copynumber: 4.9 Consensus size: 27
20867 ATGACGACTT
**
20877 ATACCCTCATAGGGTAAAATGAGTGAA
1 ATACCCTCATAGGGTAAAATGACCGAA
*
20904 ATACCCTATATAGGGGTAAAATGACCGAA
1 ATACCCT-CATA-GGGTAAAATGACCGAA
* *
20933 ATACCCTCATAGGGTAGAATGACCAAA
1 ATACCCTCATAGGGTAAAATGACCGAA
* * *
20960 ATACCC-CTATAAGGTAAAATGACTGCA
1 ATACCCTC-ATAGGGTAAAATGACCGAA
* ** *
20987 ATATCCTGGTAAGGTAAAATGAC
1 ATACCCTCATAGGGTAAAATGAC
21010 AGATTTGTTC
Statistics
Matches: 88, Mismatches: 14, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
26 1 0.01
27 60 0.68
28 6 0.07
29 21 0.24
ACGTcount: A:0.41, C:0.18, G:0.20, T:0.22
Consensus pattern (27 bp):
ATACCCTCATAGGGTAAAATGACCGAA
Found at i:20962 original size:56 final size:54
Alignment explanation
Indices: 20877--21009 Score: 142
Period size: 54 Copynumber: 2.4 Consensus size: 54
20867 ATGACGACTT
***
20877 ATACCCTCATAGGGTAAAATGAGTGAAATA-CCCTATATAGGGGTAAAATGACCGAA
1 ATACCCTCATAGGGTAAAATGACCAAAATACCCCTATA-A--GGTAAAATGACCGAA
* * *
20933 ATACCCTCATAGGGTAGAATGACCAAAATACCCCTATAAGGTAAAATGACTGCA
1 ATACCCTCATAGGGTAAAATGACCAAAATACCCCTATAAGGTAAAATGACCGAA
* ** *
20987 ATATCCTGGTAAGGTAAAATGAC
1 ATACCCTCATAGGGTAAAATGAC
21010 AGATTTGTTC
Statistics
Matches: 65, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
54 31 0.48
56 27 0.42
57 7 0.11
ACGTcount: A:0.41, C:0.18, G:0.20, T:0.22
Consensus pattern (54 bp):
ATACCCTCATAGGGTAAAATGACCAAAATACCCCTATAAGGTAAAATGACCGAA
Found at i:21372 original size:18 final size:18
Alignment explanation
Indices: 21349--21406 Score: 55
Period size: 18 Copynumber: 3.2 Consensus size: 18
21339 TCTACTTGCA
21349 TACTGCACTGATTACTAT
1 TACTGCACTGATTACTAT
* * *
21367 TACTGCATTGATCA-TGGT
1 TACTGCACTGATTACT-AT
**
21385 TACTATACTGATTACTAT
1 TACTGCACTGATTACTAT
21403 TACT
1 TACT
21407 AAAACGAGCT
Statistics
Matches: 30, Mismatches: 8, Indels: 4
0.71 0.19 0.10
Matches are distributed among these distances:
17 1 0.03
18 28 0.93
19 1 0.03
ACGTcount: A:0.28, C:0.19, G:0.12, T:0.41
Consensus pattern (18 bp):
TACTGCACTGATTACTAT
Found at i:21440 original size:34 final size:34
Alignment explanation
Indices: 21397--21466 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 34
21387 CTATACTGAT
21397 TACTATTACTAAAACGAGCTAAAGCCCAGACTGC
1 TACTATTACTAAAACGAGCTAAAGCCCAGACTGC
* * * *
21431 TACTATTACTAAAATGGGCTAAGGCCTAGACTGC
1 TACTATTACTAAAACGAGCTAAAGCCCAGACTGC
21465 TA
1 TA
21467 GTGTCACTGA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.36, C:0.23, G:0.17, T:0.24
Consensus pattern (34 bp):
TACTATTACTAAAACGAGCTAAAGCCCAGACTGC
Found at i:25634 original size:21 final size:19
Alignment explanation
Indices: 25605--25643 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
25595 CAATTGGGTA
*
25605 TGTGTTTTTTATCGGTTTTTT
1 TGTGATTTTTA-C-GTTTTTT
25626 TGTGATTTTTACGTTTTT
1 TGTGATTTTTACGTTTTT
25644 GAAATCGTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 1 0.06
21 10 0.59
ACGTcount: A:0.08, C:0.05, G:0.18, T:0.69
Consensus pattern (19 bp):
TGTGATTTTTACGTTTTTT
Found at i:26370 original size:40 final size:40
Alignment explanation
Indices: 26276--26370 Score: 118
Period size: 40 Copynumber: 2.4 Consensus size: 40
26266 GACTATGTTC
* *
26276 GGCACTAAGTGTGCGATTTGAAATAGCTTTGGCTATAAAT
1 GGCACTAAGTGTGCGAATTGAAATAGCTTCGGCTATAAAT
* * * **
26316 AGCACTAAGAGTGCGAATTGGAATAGCTTCGGCTATATGT
1 GGCACTAAGTGTGCGAATTGAAATAGCTTCGGCTATAAAT
*
26356 GGCAATAAGTGTGCG
1 GGCACTAAGTGTGCG
26371 GTATTGAGAT
Statistics
Matches: 45, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
40 45 1.00
ACGTcount: A:0.29, C:0.14, G:0.28, T:0.28
Consensus pattern (40 bp):
GGCACTAAGTGTGCGAATTGAAATAGCTTCGGCTATAAAT
Found at i:28672 original size:55 final size:54
Alignment explanation
Indices: 28585--28839 Score: 226
Period size: 55 Copynumber: 4.8 Consensus size: 54
28575 ATTAGGATTT
*
28585 AAGGATACCATGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTCTAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATTGGTAA-GTTTCTAAGGC
* * ** * *
28640 AAGGATACCATCTAAGACCATGTCAAGACATGGC-ATTTATAAGTTACTATAAGAC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATTGGTAAGTT--TCTAAGGC
* *
28695 AAAGG-T-CCTATGTAAGACCATGCCAAGGCATGGC-ATTGGTGAG-TTCATAAGGC
1 -AAGGATACC-ATGTAAGACCATGCCAAGACATGGCAATTGGTAAGTTTC-TAAGGC
*** * *
28748 AAGGATACCATGTAAGACCATGTTGAGACATGG-AAATGGTAAGCTTC-AA---
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATTGGTAAGTTTCTAAGGC
* * *
28797 AAGGATACCACGTAAGACCATGACAAGTCATGGCAA-TGGTAAG
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATTGGTAAG
28840 GTACCTATGT
Statistics
Matches: 164, Mismatches: 26, Indels: 26
0.76 0.12 0.12
Matches are distributed among these distances:
49 35 0.21
50 2 0.01
52 7 0.04
53 36 0.22
54 14 0.09
55 66 0.40
56 4 0.02
ACGTcount: A:0.36, C:0.18, G:0.24, T:0.22
Consensus pattern (54 bp):
AAGGATACCATGTAAGACCATGCCAAGACATGGCAATTGGTAAGTTTCTAAGGC
Found at i:32126 original size:40 final size:40
Alignment explanation
Indices: 32043--32305 Score: 325
Period size: 40 Copynumber: 6.6 Consensus size: 40
32033 TTGAATGCTG
* * * * * *
32043 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAA
* * * * *
32083 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTATTAAA
32123 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
32163 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
*
32203 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
32243 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
32282 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
32306 TGAACGAGGA
Statistics
Matches: 201, Mismatches: 19, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
39 35 0.17
40 158 0.79
41 8 0.04
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
Found at i:32325 original size:79 final size:80
Alignment explanation
Indices: 32082--32340 Score: 256
Period size: 80 Copynumber: 3.3 Consensus size: 80
32072 AAGTGAATAT
* * * * * *
32082 ATCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCAT
1 ATCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCAT
** * *
32146 TCGTGCGAGTTA-TTAA
65 TCGAACGAG-GAGCTAA
* * *
32162 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATT
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
** ** *
32227 CGTGCGAGTTGTTAA
66 CGAACGAGGAGCTAA
* * *
32242 ATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATT
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
* *
32306 TGAACGAGGAGCTAT
66 CGAACGAGGAGCTAA
*
32321 ATCC-GGTTAAATCCCGAAGG
1 ATCCGGGTTAAGTCCCGAAGG
32341 TACGTGATTT
Statistics
Matches: 156, Mismatches: 21, Indels: 6
0.85 0.11 0.03
Matches are distributed among these distances:
78 14 0.09
79 48 0.31
80 94 0.60
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (80 bp):
ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
CGAACGAGGAGCTAA
Found at i:40060 original size:40 final size:40
Alignment explanation
Indices: 39977--40238 Score: 325
Period size: 40 Copynumber: 6.6 Consensus size: 40
39967 TTGAATGCTG
* * * * * *
39977 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAA
* * * * *
40017 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTATTAAA
40057 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
40097 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
*
40137 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
40177 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* *
40216 -CCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
40239 TGAACGAGGA
Statistics
Matches: 201, Mismatches: 18, Indels: 8
0.89 0.08 0.04
Matches are distributed among these distances:
38 22 0.11
39 13 0.06
40 158 0.79
41 8 0.04
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
Found at i:47465 original size:27 final size:27
Alignment explanation
Indices: 47375--47549 Score: 187
Period size: 27 Copynumber: 6.6 Consensus size: 27
47365 TAAATTGTAC
47375 AGCACTAAGTGTGCGATTTGACTA-GT
1 AGCACTAAGTGTGCGATTTGACTATGT
* **
47401 -TCACTAAGTGTGCGAAATGA-TATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
47425 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
47453 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
47481 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
47508 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
47535 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
47550 GACTCAATAT
Statistics
Matches: 126, Mismatches: 17, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
24 2 0.02
25 18 0.14
26 18 0.14
27 65 0.52
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:47495 original size:55 final size:51
Alignment explanation
Indices: 47375--47549 Score: 181
Period size: 55 Copynumber: 3.3 Consensus size: 51
47365 TAAATTGTAC
** **
47375 AGCACTAAGTGTGCGATTTGACTAGTTCACTAAGTGTGCGAAATGATATG-
1 AGCACTAAGTGTGCGATTTGACTAGAGCACTAAGTGTGCGAGTTGATATGT
* * *
47425 ATGCACTAAGTGTGCGAATTGACCATGCGGCACTAAGTGTGCGAGTTTGACTATGT
1 A-GCACTAAGTGTGCGATTTGACTA-G-AGCACTAAGTGTGCGAG-TTGA-TATGT
* *
47481 AGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTA-G-AGCACTAAGTGTGCGAGTTGA-TATGT
*
47535 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
47550 GACTCAATAT
Statistics
Matches: 104, Mismatches: 15, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
50 1 0.01
51 21 0.20
52 1 0.01
53 14 0.13
54 25 0.24
55 41 0.39
56 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (51 bp):
AGCACTAAGTGTGCGATTTGACTAGAGCACTAAGTGTGCGAGTTGATATGT
Found at i:47540 original size:82 final size:78
Alignment explanation
Indices: 47372--47549 Score: 205
Period size: 82 Copynumber: 2.2 Consensus size: 78
47362 GATTAAATTG
* *
47372 TACAGCACTAAGTGTGCGATTTGACTAGTTCACTAAGTGTGCGAAATGATATGATGCACTAAGTG
1 TACAGCACTAAGTGTGCGATTTGACTAGTGCACTAAGTGTGCGAAATGATACGATGCACTAAGTG
47437 TGCGAATTGACCA
66 TGCGAATTGACCA
* * **
47450 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTA-GT-GCACTAAGTGTGCGAAATGA-TACGAT-GCACT
* **
47514 AAGTGTGCGAGTTGATTA
61 AAGTGTGCGAATTGACCA
* *
47532 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
47550 GACTCAATAT
Statistics
Matches: 82, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
78 17 0.21
79 8 0.10
80 2 0.02
81 18 0.22
82 37 0.45
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.30
Consensus pattern (78 bp):
TACAGCACTAAGTGTGCGATTTGACTAGTGCACTAAGTGTGCGAAATGATACGATGCACTAAGTG
TGCGAATTGACCA
Found at i:51687 original size:55 final size:54
Alignment explanation
Indices: 51600--51850 Score: 226
Period size: 55 Copynumber: 4.8 Consensus size: 54
51590 ATTAGGGTTT
* *
51600 AAGGATACCGTGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTCTAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATTGGTAA-GTTTCTAAGGC
* * * *
51655 AAGGATACCATGTAAGACCATGTCAAGACATGGC-ATTGATAAGTTAATATAAGGGA
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATTGGTAAGTT--TCTAA-GGC
* *
51711 AAGG-T-CCTATGTAAGACCATGCCAAGGCATGGC-ATTGGTGAG-TTCATAAGGC
1 AAGGATACC-ATGTAAGACCATGCCAAGACATGGCAATTGGTAAGTTTC-TAAGGC
* *
51763 AAGGATACCATGTAAGACCATGTCGAGACATGGCAA-TGGT-AGTTTC--A---
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATTGGTAAGTTTCTAAGGC
* * *
51810 AAGG-TACCACGTAAGACCATGACAAGTCATGG-AA-TGGTAAG
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATTGGTAAG
51851 GTACCTATGT
Statistics
Matches: 167, Mismatches: 19, Indels: 29
0.78 0.09 0.13
Matches are distributed among these distances:
45 6 0.04
46 26 0.16
47 4 0.02
50 1 0.01
52 9 0.05
53 36 0.22
54 13 0.08
55 66 0.40
56 6 0.04
ACGTcount: A:0.35, C:0.17, G:0.27, T:0.22
Consensus pattern (54 bp):
AAGGATACCATGTAAGACCATGCCAAGACATGGCAATTGGTAAGTTTCTAAGGC
Found at i:57241 original size:12 final size:13
Alignment explanation
Indices: 57224--57252 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
57214 AGGGTCTTAC
57224 TCGAAA-CACATA
1 TCGAAATCACATA
57236 TCGAAATCACATA
1 TCGAAATCACATA
57249 TCGA
1 TCGA
57253 TGCCAACATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.38
13 10 0.62
ACGTcount: A:0.45, C:0.24, G:0.10, T:0.21
Consensus pattern (13 bp):
TCGAAATCACATA
Found at i:57344 original size:43 final size:43
Alignment explanation
Indices: 57240--57460 Score: 261
Period size: 42 Copynumber: 5.2 Consensus size: 43
57230 CACATATCGA
* *** *
57240 AATCACATATCGATGCCAACATATTAAACGTGGTCTTACTC-T
1 AATCACATATCGATGCCAACGTCCCAAACGTGGTCTTACACAT
* * * *
57282 TATCACATATCGATGCCAACATCCCAAACGTGGTTTTACACGT
1 AATCACATATCGATGCCAACGTCCCAAACGTGGTCTTACACAT
* *
57325 AATCACATATCGATGCCAACGTCCCAGACGTGGTCTTACACGT
1 AATCACATATCGATGCCAACGTCCCAAACGTGGTCTTACACAT
* *
57368 -AT-ACATATTGATGCCAACGTCCCAAACGTTGTCTTACACAT
1 AATCACATATCGATGCCAACGTCCCAAACGTGGTCTTACACAT
* * * *
57409 AATCACATATTGATGCCAATGTCCC-AACGTAGTCGTACACAT
1 AATCACATATCGATGCCAACGTCCCAAACGTGGTCTTACACAT
57451 AATCACATAT
1 AATCACATAT
57461 TGAAATCCTA
Statistics
Matches: 159, Mismatches: 17, Indels: 6
0.87 0.09 0.03
Matches are distributed among these distances:
41 35 0.22
42 64 0.40
43 60 0.38
ACGTcount: A:0.32, C:0.27, G:0.14, T:0.28
Consensus pattern (43 bp):
AATCACATATCGATGCCAACGTCCCAAACGTGGTCTTACACAT
Found at i:57474 original size:43 final size:43
Alignment explanation
Indices: 57283--57463 Score: 197
Period size: 43 Copynumber: 4.3 Consensus size: 43
57273 TCTTACTCTT
* ** * ** *
57283 ATCACATATCGATGCCAACATCCCAAACGTGGTTTTACACGTA
1 ATCACATATTGATGCCAATGTCCCAAACGTAGTCGTACACATA
* * * * * *
57326 ATCACATATCGATGCCAACGTCCCAGACGTGGTCTTACACGT-
1 ATCACATATTGATGCCAATGTCCCAAACGTAGTCGTACACATA
* * *
57368 AT-ACATATTGATGCCAACGTCCCAAACGTTGTCTTACACATA
1 ATCACATATTGATGCCAATGTCCCAAACGTAGTCGTACACATA
57410 ATCACATATTGATGCCAATGTCCC-AACGTAGTCGTACACATA
1 ATCACATATTGATGCCAATGTCCCAAACGTAGTCGTACACATA
57452 ATCACATATTGA
1 ATCACATATTGA
57464 AATCCTATGT
Statistics
Matches: 126, Mismatches: 10, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
41 35 0.28
42 32 0.25
43 59 0.47
ACGTcount: A:0.32, C:0.27, G:0.14, T:0.27
Consensus pattern (43 bp):
ATCACATATTGATGCCAATGTCCCAAACGTAGTCGTACACATA
Done.