Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3375
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: 52334
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31
Found at i:2592 original size:40 final size:40
Alignment explanation
Indices: 2546--2770 Score: 253
Period size: 40 Copynumber: 5.7 Consensus size: 40
2536 AGCTCCTCTT
*
2546 CAAATGCCTTCGGGACATAGCCCGG-TCATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAT-ATAGTAACTCGCA
* * *
2586 CAAATGCCTTTGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* * *
2626 CAAATGCCTTCGGGACTTAACACGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* * *
2666 CCAATGCCTTCGGG-CTCTAGCCCGGA-ATAGTATCTCGTA
1 CAAATGCCTTCGGGACT-TAGCCCGGATATAGTAACTCGCA
* * * *
2705 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TCGCA
2746 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
2771 CATCATTCAA
Statistics
Matches: 158, Mismatches: 20, Indels: 14
0.82 0.10 0.07
Matches are distributed among these distances:
38 2 0.01
39 30 0.19
40 115 0.73
41 11 0.07
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
Found at i:2730 original size:119 final size:120
Alignment explanation
Indices: 2548--2763 Score: 278
Period size: 119 Copynumber: 1.8 Consensus size: 120
2538 CTCCTCTTCA
* *
2548 AATGCCTTCGGGACATAGCCCGGTCATAGTAACTCGCACAAATGCCTTTGGGACTTAACCCGGAT
1 AATGCCTTCGGGACATAGCCCGGTAATAGTAACTCGCACAAATGCCTTTCGGACTTAACCCGGAT
* *
2613 TTAGTAAC-TCGCACAAATGCCTTCGGGACTTAACACGGATTTAGTAACTCGCACC
66 ATAGTAACTTAGCACAAA-GCCTTCGGGACTTAACACGGATTTAGTAACTCGCACC
* * * **
2668 AATGCCTTCGGG-CTCTAGCCCGG-AATAGTATCTCGTACAAATGCC-TTCGGATCTTAGTCCGG
1 AATGCCTTCGGGAC-ATAGCCCGGTAATAGTAACTCGCACAAATGCCTTTCGGA-CTTAACCCGG
* *
2730 ATATGGTCACTTAGCACAAAGCCTTCGGGACTTA
64 ATATAGTAACTTAGCACAAAGCCTTCGGGACTTA
2764 GCCCGGACAT
Statistics
Matches: 82, Mismatches: 11, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
118 5 0.06
119 49 0.60
120 28 0.34
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (120 bp):
AATGCCTTCGGGACATAGCCCGGTAATAGTAACTCGCACAAATGCCTTTCGGACTTAACCCGGAT
ATAGTAACTTAGCACAAAGCCTTCGGGACTTAACACGGATTTAGTAACTCGCACC
Found at i:8036 original size:9 final size:9
Alignment explanation
Indices: 8024--8080 Score: 51
Period size: 9 Copynumber: 5.9 Consensus size: 9
8014 TTTGATAAAC
8024 ATGATATGT
1 ATGATATGT
*
8033 ATGATATGCAC
1 ATGATATG--T
*
8044 ATGACATGT
1 ATGATATGT
*
8053 ATGATATGCAC
1 ATGATATG--T
8064 ATGATATGT
1 ATGATATGT
8073 ATGATATG
1 ATGATATG
8081 CACACGAGAT
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
9 23 0.61
11 15 0.39
ACGTcount: A:0.35, C:0.09, G:0.21, T:0.35
Consensus pattern (9 bp):
ATGATATGT
Found at i:8047 original size:20 final size:20
Alignment explanation
Indices: 8022--8084 Score: 117
Period size: 20 Copynumber: 3.1 Consensus size: 20
8012 ATTTTGATAA
8022 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
*
8042 ACATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
8062 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
8082 ACA
1 ACA
8085 CGAGATGTTC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.32
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:8208 original size:26 final size:27
Alignment explanation
Indices: 8138--8214 Score: 119
Period size: 23 Copynumber: 3.0 Consensus size: 27
8128 GAGGAAGTGC
8138 AAAAGGGCTTATGCCCCAGTTATT---
1 AAAAGGGCTTATGCCCCAGTTATTAAA
8162 -AAAGGGCTTATGCCCCAGTTATTAAA
1 AAAAGGGCTTATGCCCCAGTTATTAAA
8188 AAAAGGGCTT-TGCCCCAGTTATTAAA
1 AAAAGGGCTTATGCCCCAGTTATTAAA
8214 A
1 A
8215 GAGGCTAGGC
Statistics
Matches: 49, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
23 23 0.47
26 17 0.35
27 9 0.18
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.27
Consensus pattern (27 bp):
AAAAGGGCTTATGCCCCAGTTATTAAA
Found at i:8230 original size:25 final size:24
Alignment explanation
Indices: 8138--8234 Score: 101
Period size: 23 Copynumber: 4.0 Consensus size: 24
8128 GAGGAAGTGC
8138 AAAAG-GGCTTATGCCCCAGTTATT
1 AAAAGAGGC-TATGCCCCAGTTATT
8162 -AAAG-GGCTTATGCCCCAGTTATT
1 AAAAGAGGC-TATGCCCCAGTTATT
* *
8185 AAAAAAAGGGCTTTGCCCCAGTTATT
1 -AAAAGA-GGCTATGCCCCAGTTATT
*
8211 AAAAGAGGCTAGGCCTCCAGTTAT
1 AAAAGAGGCTATGCC-CCAGTTAT
8235 ATGATAAAGC
Statistics
Matches: 63, Mismatches: 5, Indels: 9
0.82 0.06 0.12
Matches are distributed among these distances:
23 23 0.37
24 7 0.11
25 16 0.25
26 14 0.22
27 3 0.05
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.27
Consensus pattern (24 bp):
AAAAGAGGCTATGCCCCAGTTATT
Found at i:8462 original size:31 final size:31
Alignment explanation
Indices: 8427--8490 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
8417 CGGTTATAGT
8427 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
* ** *
8458 AAAGGCTTTGGCCCAGTGTTATGAATTATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
8489 AA
1 AA
8491 TATGAAAAGG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.27
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:9610 original size:13 final size:13
Alignment explanation
Indices: 9592--9617 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
9582 AATACTGACT
9592 TTAAAACATGGCC
1 TTAAAACATGGCC
9605 TTAAAACATGGCC
1 TTAAAACATGGCC
9618 ATGGCACACA
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:0.23, G:0.15, T:0.23
Consensus pattern (13 bp):
TTAAAACATGGCC
Found at i:10679 original size:47 final size:46
Alignment explanation
Indices: 10480--10790 Score: 196
Period size: 44 Copynumber: 6.7 Consensus size: 46
10470 GGGATAAGTT
* *
10480 GCCGATGCCATGTCCCAGACATGATCTTACACTAGCTA-TCCTCATCGAG
1 GCCGATG-CATGTCCCAGACATG-TCTTACACTGGC-ACTCATC-TCGAG
* * ** * *
10529 GCC-AAGCCATGTCCCAGACATGGTCTTATACT-ATATCTCTTATATACG-T
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTGGCA-CTC--ATCT-CGAG
* * * * * *
10578 GCTGATGCATGTCCTAGATATGTCTTACACTAGCA--CAACTCTTA-
1 GCCGATGCATGTCCCAGACATGTCTTACACTGGCACTCATCTC-GAG
*
10622 GCCGATGCATGTCCCAGACAGGTCTTACACTGGCTA-TCATCGTCGAG
1 GCCGATGCATGTCCCAGACATGTCTTACACTGGC-ACTCATC-TCGAG
* * *
10669 GCCGATGCATGTCCCAAACATGTC---CACTGGCACTCATCTCTAC
1 GCCGATGCATGTCCCAGACATGTCTTACACTGGCACTCATCTCGAG
* * *
10712 ACCGATGCCATGTCCCAGACATTGTCTTACACTGGCACTCATAAT-GTG
1 GCCGATG-CATGTCCCAGACA-TGTCTTACACTGGCACTCAT-CTCGAG
*
10760 CCCGATGCATGTCCCAGACATGTCTTACACT
1 GCCGATGCATGTCCCAGACATGTCTTACACT
10791 AGCCCACAAG
Statistics
Matches: 206, Mismatches: 35, Indels: 45
0.72 0.12 0.16
Matches are distributed among these distances:
43 11 0.05
44 55 0.27
45 5 0.02
46 17 0.08
47 37 0.18
48 55 0.27
49 21 0.10
50 5 0.02
ACGTcount: A:0.24, C:0.31, G:0.18, T:0.27
Consensus pattern (46 bp):
GCCGATGCATGTCCCAGACATGTCTTACACTGGCACTCATCTCGAG
Found at i:10692 original size:91 final size:94
Alignment explanation
Indices: 10581--10798 Score: 238
Period size: 91 Copynumber: 2.4 Consensus size: 94
10571 TATACGTGCT
* * *
10581 GATGCATGTCCTAGATATGTCTTACACTAGCACA-A-CTCTTA-GCCGATG-CATGTCCCAGACA
1 GATGCATGTCCCAGACATGTCTTACACTAGCACACATCTC-TACACCGATGCCATGTCCCAGACA
** *
10642 -GGTCTTACACTGGCTA-TCATCGTCGAGGCC
65 TGGTCTTACACTGGC-ACTCATAAT-GAGCCC
* * *
10672 GATGCATGTCCCAAACATGTC---CACTGGCACTCATCTCTACACCGATGCCATGTCCCAGACAT
1 GATGCATGTCCCAGACATGTCTTACACTAGCACACATCTCTACACCGATGCCATGTCCCAGACAT
* *
10734 TGTCTTACACTGGCACTCATAATGTGCCC
66 GGTCTTACACTGGCACTCATAATGAGCCC
*
10763 GATGCATGTCCCAGACATGTCTTACACTAGCCCACA
1 GATGCATGTCCCAGACATGTCTTACACTAGCACACA
10799 AGAAATCTGA
Statistics
Matches: 103, Mismatches: 15, Indels: 15
0.77 0.11 0.11
Matches are distributed among these distances:
88 8 0.08
89 3 0.03
90 9 0.09
91 56 0.54
92 18 0.17
94 9 0.09
ACGTcount: A:0.25, C:0.32, G:0.18, T:0.25
Consensus pattern (94 bp):
GATGCATGTCCCAGACATGTCTTACACTAGCACACATCTCTACACCGATGCCATGTCCCAGACAT
GGTCTTACACTGGCACTCATAATGAGCCC
Found at i:17123 original size:55 final size:55
Alignment explanation
Indices: 17062--17174 Score: 181
Period size: 55 Copynumber: 2.1 Consensus size: 55
17052 ATATAATGTG
* * *
17062 CAATACTAACTTTAAAACACGGCCATGGCACACGCCCGTGTGGCTTGCCCGTGTA
1 CAATACTAACTTTAAAACACGGCCATGGCACACGCCCATGTGGCCTACCCGTGTA
* *
17117 CAATACTGACTTTAAAACACGGCCATGGCACACGCCCATGTGGCCTACTCGTGTA
1 CAATACTAACTTTAAAACACGGCCATGGCACACGCCCATGTGGCCTACCCGTGTA
17172 CAA
1 CAA
17175 CAATGACTTA
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
55 53 1.00
ACGTcount: A:0.27, C:0.31, G:0.20, T:0.21
Consensus pattern (55 bp):
CAATACTAACTTTAAAACACGGCCATGGCACACGCCCATGTGGCCTACCCGTGTA
Found at i:17182 original size:55 final size:55
Alignment explanation
Indices: 17070--17187 Score: 175
Period size: 55 Copynumber: 2.2 Consensus size: 55
17060 TGCAATACTA
* * * * *
17070 ACTTTAAAACACGGCCATGGCACACGCCCGTGTGGCTTGCCCGTGTACAATACTG
1 ACTTTAAAACACGGCCATGGCACACGCCCATGTGGCCTACCCGTGTACAACAATG
*
17125 ACTTTAAAACACGGCCATGGCACACGCCCATGTGGCCTACTCGTGTACAACAATG
1 ACTTTAAAACACGGCCATGGCACACGCCCATGTGGCCTACCCGTGTACAACAATG
17180 AC-TTAAAA
1 ACTTTAAAA
17188 TTTTAAGTGC
Statistics
Matches: 57, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
54 6 0.11
55 51 0.89
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.21
Consensus pattern (55 bp):
ACTTTAAAACACGGCCATGGCACACGCCCATGTGGCCTACCCGTGTACAACAATG
Found at i:18172 original size:47 final size:46
Alignment explanation
Indices: 17973--18289 Score: 221
Period size: 47 Copynumber: 6.7 Consensus size: 46
17963 GGATAAGTTA
* *
17973 CTGATGCCATGTCCCAGACATGGTCTTACATTGGCTA-TCCTCATCGAGG
1 CTGATG-CATGTCCCAGACAT-GTCTTACACTGGC-ACTCATC-TCGAGG
** * * * * * * * **
18022 CCAATGCCATATCCCAAACATGGTCTTATACTAGCTCTCGTATATATGTG
1 CTGATG-CATGTCCCAGACAT-GTCTTACACTGGCACTCATCTCGA-G-G
* * ** *
18072 CTGATGCATGTCCCTGACATGTCTTACACTAGCACAAATCT-TA-G
1 CTGATGCATGTCCCAGACATGTCTTACACTGGCACTCATCTCGAGG
* * * *
18116 CCGATGCATGTTCCAGACAGGCCTTACACTGGCTA-TCATCGTCGAGG
1 CTGATGCATGTCCCAGACATGTCTTACACTGGC-ACTCATC-TCGAGG
* * *
18163 CTGATGCATGTCCCAGACATGTCTTACACTAGCACTCATCTCTACG
1 CTGATGCATGTCCCAGACATGTCTTACACTGGCACTCATCTCGAGG
* * *
18209 CTGATGCCATGTCCTAGACACTGTCTTACACTGGCACTCATAAT-GTGG
1 CTGATG-CATGTCCCAGACA-TGTCTTACACTGGCACTCAT-CTCGAGG
*
18257 CCGATGCATGTCCCAGACATGTCTTACACTGGC
1 CTGATGCATGTCCCAGACATGTCTTACACTGGC
18290 CCACAAGAAA
Statistics
Matches: 210, Mismatches: 47, Indels: 25
0.74 0.17 0.09
Matches are distributed among these distances:
44 31 0.15
45 2 0.01
46 26 0.12
47 60 0.29
48 42 0.20
49 44 0.21
50 5 0.02
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.28
Consensus pattern (46 bp):
CTGATGCATGTCCCAGACATGTCTTACACTGGCACTCATCTCGAGG
Found at i:18260 original size:141 final size:140
Alignment explanation
Indices: 17975--18289 Score: 343
Period size: 141 Copynumber: 2.2 Consensus size: 140
17965 ATAAGTTACT
* *
17975 GATGCCATGTCCCAGACATGGTCTTACATTGGCTATCCTCATCGAGGCCAATGCCATATCCCAAA
1 GATG-CATGTCCCAGACA-GGTCTTACACTGGCTATCATCATCGAGGCCAATGCCATATCCCAAA
* * **
18040 CATGGTCTTATACTAGCTCTCGTATATATGTGCTGATGCATGTCCCTGACATGTCTTACACTAGC
64 CATGGTCTTACACTAGCACTCG-ATATATACGCTGATGCATGTCCCTGACATGTCTTACACTAGC
*
18105 ACAAATCTTAGCC
128 ACAAATCGTAGCC
* * * ** * *
18118 GATGCATGTTCCAGACAGGCCTTACACTGGCTATCATCGTCGAGGCTGATG-CATGTCCCAGACA
1 GATGCATGTCCCAGACAGGTCTTACACTGGCTATCATCATCGAGGCCAATGCCATATCCCAAACA
* * *
18182 T-GTCTTACACTAGCACTC-ATCTCTACGCTGATGCCATGT-CCTAGACACTGTCTTACACTGGC
66 TGGTCTTACACTAGCACTCGATATATACGCTGATG-CATGTCCCT-GACA-TGTCTTACACTAGC
*
18244 ACTCATAAT-GTGGCC
128 A--CA-AATCGTAGCC
*
18259 GATGCATGTCCCAGACATGTCTTACACTGGC
1 GATGCATGTCCCAGACAGGTCTTACACTGGC
18290 CCACAAGAAA
Statistics
Matches: 145, Mismatches: 21, Indels: 14
0.81 0.12 0.08
Matches are distributed among these distances:
137 14 0.10
138 9 0.06
139 29 0.20
140 12 0.08
141 62 0.43
142 15 0.10
143 4 0.03
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.28
Consensus pattern (140 bp):
GATGCATGTCCCAGACAGGTCTTACACTGGCTATCATCATCGAGGCCAATGCCATATCCCAAACA
TGGTCTTACACTAGCACTCGATATATACGCTGATGCATGTCCCTGACATGTCTTACACTAGCACA
AATCGTAGCC
Found at i:18268 original size:94 final size:91
Alignment explanation
Indices: 18074--18286 Score: 261
Period size: 94 Copynumber: 2.3 Consensus size: 91
18064 TATATGTGCT
*
18074 GATGCATGTCCCTGACATGTCTTACACTAGCACAAATCTTAGCCGATGCATGTTCCAGACAGGCC
1 GATGCATGTCCCAGACATGTCTTACACTAGCACAAATCTTAGCCGATGCATGTTCCAGACAGGCC
** *
18139 TTACACTGGCTATCATCGTCGAGGCT
66 TTACACTGGCTATCATAATCGAGGCC
** *
18165 GATGCATGTCCCAGACATGTCTTACACTAGCACTCATCTCTACGCTGATGCCATG-TCCTAGACA
1 GATGCATGTCCCAGACATGTCTTACACTAGCACAAATCT-TA-GCCGATG-CATGTTCC-AGACA
* * *
18229 CTGTCTTACACTGGC-ACTCATAAT-GTGGCC
62 -GGCCTTACACTGGCTA-TCATAATCGAGGCC
18259 GATGCATGTCCCAGACATGTCTTACACT
1 GATGCATGTCCCAGACATGTCTTACACT
18287 GGCCCACAAG
Statistics
Matches: 106, Mismatches: 10, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
91 36 0.34
92 2 0.02
93 9 0.08
94 42 0.40
95 17 0.16
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.27
Consensus pattern (91 bp):
GATGCATGTCCCAGACATGTCTTACACTAGCACAAATCTTAGCCGATGCATGTTCCAGACAGGCC
TTACACTGGCTATCATAATCGAGGCC
Found at i:23578 original size:27 final size:27
Alignment explanation
Indices: 23476--23579 Score: 75
Period size: 27 Copynumber: 3.9 Consensus size: 27
23466 AATACTTTAG
* *
23476 TTTACCAAATTATTGAAATACCCTCGA
1 TTTACAAAATTATCGAAATACCCTCGA
* ** * *
23503 CTTGTAAAATTA-CCAAAGTACCCTCAA
1 TTTACAAAATTATCGAAA-TACCCTCGA
* * ***
23530 TTTACAGAATTACCGTTTTACCCTCGA
1 TTTACAAAATTATCGAAATACCCTCGA
*
23557 TTTACAAAATTATTGAAATACCC
1 TTTACAAAATTATCGAAATACCC
23580 CTGTAGGGTA
Statistics
Matches: 53, Mismatches: 22, Indels: 4
0.67 0.28 0.05
Matches are distributed among these distances:
26 3 0.06
27 49 0.92
28 1 0.02
ACGTcount: A:0.37, C:0.23, G:0.08, T:0.33
Consensus pattern (27 bp):
TTTACAAAATTATCGAAATACCCTCGA
Found at i:23594 original size:27 final size:27
Alignment explanation
Indices: 23564--23703 Score: 154
Period size: 27 Copynumber: 5.2 Consensus size: 27
23554 CGATTTACAA
23564 AATTATTGAAATACCCCTGTAGGGTAG
1 AATTATTGAAATACCCCTGTAGGGTAG
* *
23591 AATTACTGAAATACCCCTATAGGGTAG
1 AATTATTGAAATACCCCTGTAGGGTAG
* ** *
23618 AATCATCAAAATACCCTTGTAGGGTAG
1 AATTATTGAAATACCCCTGTAGGGTAG
* * *
23645 AAATAATGAAATACCCCTATAGGGTAG
1 AATTATTGAAATACCCCTGTAGGGTAG
* * * * *
23672 AATTATCGAGATACCCTTGTGGGGTAA
1 AATTATTGAAATACCCCTGTAGGGTAG
23699 AATTA
1 AATTA
23704 CCATTTTGCC
Statistics
Matches: 90, Mismatches: 23, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
27 90 1.00
ACGTcount: A:0.37, C:0.16, G:0.20, T:0.27
Consensus pattern (27 bp):
AATTATTGAAATACCCCTGTAGGGTAG
Found at i:23630 original size:54 final size:54
Alignment explanation
Indices: 23572--23704 Score: 194
Period size: 54 Copynumber: 2.5 Consensus size: 54
23562 AAAATTATTG
*
23572 AAATACCCCTGTAGGGTAGAATTACTGAAATACCCCTATAGGGTAGAATCATCA
1 AAATACCCTTGTAGGGTAGAATTACTGAAATACCCCTATAGGGTAGAATCATCA
* * * *
23626 AAATACCCTTGTAGGGTAGAAATAATGAAATACCCCTATAGGGTAGAATTATCG
1 AAATACCCTTGTAGGGTAGAATTACTGAAATACCCCTATAGGGTAGAATCATCA
* * *
23680 AGATACCCTTGTGGGGTAAAATTAC
1 AAATACCCTTGTAGGGTAGAATTAC
23705 CATTTTGCCC
Statistics
Matches: 69, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
54 69 1.00
ACGTcount: A:0.37, C:0.17, G:0.20, T:0.26
Consensus pattern (54 bp):
AAATACCCTTGTAGGGTAGAATTACTGAAATACCCCTATAGGGTAGAATCATCA
Found at i:24346 original size:27 final size:27
Alignment explanation
Indices: 24316--24423 Score: 87
Period size: 27 Copynumber: 4.0 Consensus size: 27
24306 ATTCTGCTAA
* *
24316 GTGGCTTTGCCAC-ATTATCTGTTTCTG
1 GTGGCTATGCCACAAATATCTG-TTCTG
24343 GTGGCTATGCCACAAATATCTGTTCTG
1 GTGGCTATGCCACAAATATCTGTTCTG
* * * *
24370 GTGGCTCTACCAC-AATATCAGTATTTG
1 GTGGCTATGCCACAAATATCTGT-TCTG
* * **
24397 GTGACTCTGTTAC-AATATCTGTTCTG
1 GTGGCTATGCCACAAATATCTGTTCTG
24423 G
1 G
24424 CAGTCATGCT
Statistics
Matches: 67, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
26 12 0.18
27 48 0.72
28 7 0.10
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.38
Consensus pattern (27 bp):
GTGGCTATGCCACAAATATCTGTTCTG
Found at i:24550 original size:6 final size:6
Alignment explanation
Indices: 24541--24640 Score: 64
Period size: 6 Copynumber: 16.3 Consensus size: 6
24531 TTGCATTCAC
* * *
24541 ATTCTG ATTCTG AGTCTG -TTACCT- ATTACTG ATTCTG ATTCTG -TCACATA
1 ATTCTG ATTCTG ATTCTG ATT--CTG ATT-CTG ATTCTG ATTCTG AT-TC-TG
* * *
24591 ATTCTA ATTCTG ATTCTG ATTCTG ATTCTC ATTTTG ATTCT- AGTTCTG
1 ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG A-TTCTG
24639 AT
1 AT
24641 AATGTTTCTT
Statistics
Matches: 74, Mismatches: 11, Indels: 18
0.72 0.11 0.17
Matches are distributed among these distances:
5 3 0.04
6 60 0.81
7 10 0.14
8 1 0.01
ACGTcount: A:0.21, C:0.18, G:0.13, T:0.48
Consensus pattern (6 bp):
ATTCTG
Found at i:24600 original size:25 final size:24
Alignment explanation
Indices: 24541--24608 Score: 82
Period size: 25 Copynumber: 2.8 Consensus size: 24
24531 TTGCATTCAC
* * *
24541 ATTCTGATTCTGAGTCTGTTACCT
1 ATTCTGATTCTGATTCTGTCACAT
24565 ATTACTGATTCTGATTCTGTCACAT
1 ATT-CTGATTCTGATTCTGTCACAT
*
24590 AATTCTAATTCTGATTCTG
1 -ATTCTGATTCTGATTCTG
24609 ATTCTGATTC
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
24 3 0.08
25 32 0.84
26 3 0.08
ACGTcount: A:0.22, C:0.19, G:0.13, T:0.46
Consensus pattern (24 bp):
ATTCTGATTCTGATTCTGTCACAT
Found at i:26831 original size:26 final size:27
Alignment explanation
Indices: 26707--26840 Score: 153
Period size: 27 Copynumber: 5.0 Consensus size: 27
26697 CAAAATTATT
* **
26707 GAAATACCCTTGTAAGGTAGAATTATT
1 GAAATACCCTTGTAGGGTAGAATTACC
* * * *
26734 GAAATACCCCTATAGGATAGAATTATC
1 GAAATACCCTTGTAGGGTAGAATTACC
* *
26761 GAAATACCCTAGTAGGGTAGAAATACC
1 GAAATACCCTTGTAGGGTAGAATTACC
*
26788 GAAATACCCCTGTAGGGTAGAATTACC
1 GAAATACCCTTGTAGGGTAGAATTACC
* *
26815 G-AATACCCTTGTGGGGTAAAATTACC
1 GAAATACCCTTGTAGGGTAGAATTACC
26841 ATTTTGCCCC
Statistics
Matches: 90, Mismatches: 17, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
26 22 0.24
27 68 0.76
ACGTcount: A:0.37, C:0.18, G:0.20, T:0.25
Consensus pattern (27 bp):
GAAATACCCTTGTAGGGTAGAATTACC
Found at i:38094 original size:50 final size:49
Alignment explanation
Indices: 37927--38165 Score: 254
Period size: 50 Copynumber: 4.9 Consensus size: 49
37917 AGGGTAGGGT
* * * * * * * * *
37927 GCCGATGCCATGTTCCGGATATGGTCTTACATTGGCTCACACATC-AAA
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATCTGAG
* * * *
37975 ACCGATGCCATGTCCCAGACATGGTCTTACACTA--ACACATATC--AA
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATCTGAG
* * *
38020 GTCGATGCCATGTCTCAAACATGGTCTTACACTAGCTCTCATATCTTGAG
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATC-TGAG
* *
38070 GCCGATGCCATATCCCAGACATGGTCTTACACTAGCTCTCAGATCTCGAG
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATCT-GAG
*
38120 ACCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATCT
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATCT
38166 CCCTAGTATC
Statistics
Matches: 162, Mismatches: 23, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
45 32 0.20
46 7 0.04
47 7 0.04
48 28 0.17
49 1 0.01
50 87 0.54
ACGTcount: A:0.26, C:0.30, G:0.18, T:0.27
Consensus pattern (49 bp):
GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATCTGAG
Found at i:38166 original size:50 final size:50
Alignment explanation
Indices: 37975--38166 Score: 259
Period size: 50 Copynumber: 3.9 Consensus size: 50
37965 ACACATCAAA
* * *
37975 ACCGATGCCATGTCCCAGACATGGTCTTACACTA--ACACATA--TCAAG
1 ACCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATCTCGAG
* * * *
38021 -TCGATGCCATGTCTCAAACATGGTCTTACACTAGCTCTCATATCTTGAG
1 ACCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATCTCGAG
* * *
38070 GCCGATGCCATATCCCAGACATGGTCTTACACTAGCTCTCAGATCTCGAG
1 ACCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATCTCGAG
38120 ACCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATCTC
1 ACCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATCTC
38167 CCTAGTATCA
Statistics
Matches: 125, Mismatches: 16, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
45 30 0.24
47 5 0.04
49 3 0.02
50 87 0.70
ACGTcount: A:0.26, C:0.31, G:0.17, T:0.27
Consensus pattern (50 bp):
ACCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATCTCGAG
Found at i:42983 original size:25 final size:25
Alignment explanation
Indices: 42954--43001 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
42944 TTATAACATG
* * *
42954 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
42979 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
43002 GTTTATGTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:43067 original size:20 final size:20
Alignment explanation
Indices: 43038--43084 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
43028 ATTTTGATAA
*
43038 ACATGGTATGTATGATATGC
1 ACATGATATGTATGATATGC
43058 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
43078 ACATGAT
1 ACATGAT
43085 GTATTCATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.34, C:0.11, G:0.21, T:0.34
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:43167 original size:23 final size:24
Alignment explanation
Indices: 43134--43207 Score: 105
Period size: 24 Copynumber: 3.1 Consensus size: 24
43124 GAGGAAGTGA
*
43134 AAAAGGGCTTACGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
* *
43158 AAAA-GGCTTATGCCCCAATTATA
1 AAAAGGGCTTATGCCCCAGTTATT
*
43181 AAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
43205 AAA
1 AAA
43208 CGAGGCAAGG
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
23 20 0.47
24 23 0.53
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.27
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATT
Found at i:43195 original size:24 final size:24
Alignment explanation
Indices: 43133--43203 Score: 99
Period size: 23 Copynumber: 3.0 Consensus size: 24
43123 GGAGGAAGTG
*
43133 AAAAAGGGCTTACGCCCCAGTTAT
1 AAAAAGGGCTTATGCCCCAGTTAT
* *
43157 TAAAA-GGCTTATGCCCCAATTAT
1 AAAAAGGGCTTATGCCCCAGTTAT
*
43180 AAAAAGGGCTTTTGCCCCAGTTAT
1 AAAAAGGGCTTATGCCCCAGTTAT
43204 TAAACGAGGC
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
23 20 0.50
24 20 0.50
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.27
Consensus pattern (24 bp):
AAAAAGGGCTTATGCCCCAGTTAT
Found at i:43457 original size:31 final size:31
Alignment explanation
Indices: 43422--43485 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
43412 CGTTTACAGT
* *
43422 AAAGGCTTCGGCCCAGTAATATGAAATTTGA
1 AAAGGCTTCGACCCAGTAATATGAAATATGA
**
43453 AAAGGCTTCGACCCAGTGTTATGAAATATGA
1 AAAGGCTTCGACCCAGTAATATGAAATATGA
43484 AA
1 AA
43486 TATGAAAAGG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.38, C:0.16, G:0.22, T:0.25
Consensus pattern (31 bp):
AAAGGCTTCGACCCAGTAATATGAAATATGA
Found at i:50966 original size:25 final size:25
Alignment explanation
Indices: 50937--50984 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
50927 TTATAACATG
* * *
50937 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
50962 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
50985 GTTTATGTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:51067 original size:11 final size:11
Alignment explanation
Indices: 51031--51086 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
51021 CATGGTATGT
51031 ATGATATGCAC
1 ATGATATGCAC
* *
51042 ATGACATG--T
1 ATGATATGCAC
51051 ATGATATGCAC
1 ATGATATGCAC
*
51062 ATGATATG--T
1 ATGATATGCAC
51071 ATGATATGCAC
1 ATGATATGCAC
51082 ATGAT
1 ATGAT
51087 GTATTCATAA
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
9 15 0.43
11 20 0.57
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:51086 original size:20 final size:20
Alignment explanation
Indices: 51020--51086 Score: 116
Period size: 20 Copynumber: 3.4 Consensus size: 20
51010 ATTTTGATAA
*
51020 ACATGGTATGTATGATATGC
1 ACATGATATGTATGATATGC
*
51040 ACATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
51060 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
51080 ACATGAT
1 ACATGAT
51087 GTATTCATAA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.34, C:0.12, G:0.21, T:0.33
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:51246 original size:68 final size:66
Alignment explanation
Indices: 51137--51270 Score: 232
Period size: 68 Copynumber: 2.0 Consensus size: 66
51127 AGGAAGTGAA
*
51137 AAAGGGCTTATGCCCAGTTATTAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGT
1 AAAGGGCTTACGCCCAGTTATTAAAGGGCTTATGCCCCAGTTAT-AAAAGGG-TTATGCCCCAGT
51202 TAT
64 TAT
*
51205 AAAGGGCTTACGCCCAGTTATTAAAGGGCTTATGCCCCAGTTATAAAAGGGTTTTGCCCCAGTTA
1 AAAGGGCTTACGCCCAGTTATTAAAGGGCTTATGCCCCAGTTATAAAAGGGTTATGCCCCAGTTA
51270 T
66 T
51271 TAAAAGAGGC
Statistics
Matches: 64, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
66 14 0.22
67 7 0.11
68 43 0.67
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Consensus pattern (66 bp):
AAAGGGCTTACGCCCAGTTATTAAAGGGCTTATGCCCCAGTTATAAAAGGGTTATGCCCCAGTTA
T
Found at i:51275 original size:23 final size:24
Alignment explanation
Indices: 51136--51295 Score: 203
Period size: 22 Copynumber: 7.0 Consensus size: 24
51126 GAGGAAGTGA
51136 AAAAGGGCTTATG-CCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
51159 -AAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATT
51182 AAAAGGGCTTATGCCCCAGTTA-T
1 AAAAGGGCTTATGCCCCAGTTATT
*
51205 -AAAGGGCTTACG-CCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
51227 -AAAGGGCTTATGCCCCAGTTA-T
1 AAAAGGGCTTATGCCCCAGTTATT
*
51249 AAAAGGG-TTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
51272 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
51296 ATGATAAAGC
Statistics
Matches: 121, Mismatches: 7, Indels: 16
0.84 0.05 0.11
Matches are distributed among these distances:
21 8 0.07
22 49 0.40
23 29 0.24
24 27 0.22
25 8 0.07
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.28
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATT
Found at i:51523 original size:31 final size:31
Alignment explanation
Indices: 51488--51551 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
51478 CGTTTACAGT
*
51488 AAAGGCTTCGGCCCAGTAATATGAAATTTGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
**
51519 AAAGGCTTCGGCCCAGTGTTATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
51550 AA
1 AA
51552 TATGAAAAGG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.25
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Done.