Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_272
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: 107515
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Found at i:73 original size:40 final size:40
Alignment explanation
Indices: 4--212 Score: 241
Period size: 40 Copynumber: 5.3 Consensus size: 40
1 ATG
* *
4 ATATCCGGGCTAAG-TCCGAAGGCAATTGTGCTAGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
* * *
43 TTATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGATT
* * *
83 ATACCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
* *
123 TTATCCGGGCT-AGA-CCGAAGGCATTTGTGCGAGTTGA-T
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGATT
* * *
161 AAATCCGGGCTAAGACCCGAAGGCATTTGTGCTTGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
201 ATATCC-GGCTAA
1 ATATCCGGGCTAA
213 ATTCCGAAGA
Statistics
Matches: 141, Mismatches: 22, Indels: 14
0.80 0.12 0.08
Matches are distributed among these distances:
38 27 0.19
39 32 0.23
40 80 0.57
41 2 0.01
ACGTcount: A:0.24, C:0.20, G:0.29, T:0.27
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
Found at i:179 original size:78 final size:80
Alignment explanation
Indices: 6--212 Score: 305
Period size: 78 Copynumber: 2.6 Consensus size: 80
1 ATGAT
*
6 ATCCGGGCTAAG-TCCGAAGGCAATTGTGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCATT
1 ATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCATT
* *
70 TGTGCGAGTTGCTAT
66 TGTGCGAGTTGATAA
* *
85 ACCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGATTTTATCCGGGCT-AGA-CCGAAGGCATT
1 ATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCATT
148 TGTGCGAGTTGATAA
66 TGTGCGAGTTGATAA
* * * *
163 ATCCGGGCTAAGACCCGAAGGCATTTGTGCTTGTGGTTATATCC-GGCTAA
1 ATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTTTATCCGGGCTAA
213 ATTCCGAAGA
Statistics
Matches: 115, Mismatches: 11, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
77 4 0.03
78 63 0.55
79 13 0.11
80 35 0.30
ACGTcount: A:0.24, C:0.20, G:0.29, T:0.27
Consensus pattern (80 bp):
ATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCATT
TGTGCGAGTTGATAA
Found at i:2067 original size:16 final size:16
Alignment explanation
Indices: 2046--2076 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
2036 ATGACCTCGA
2046 TAAACCTCATTTCATG
1 TAAACCTCATTTCATG
2062 TAAACCTCATTTCAT
1 TAAACCTCATTTCAT
2077 CGGTCTTACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.32, C:0.26, G:0.03, T:0.39
Consensus pattern (16 bp):
TAAACCTCATTTCATG
Found at i:17470 original size:40 final size:41
Alignment explanation
Indices: 17392--17473 Score: 114
Period size: 40 Copynumber: 2.0 Consensus size: 41
17382 TTAGTGCCAT
17392 CTCAAATAGCCAAAGCTACCTCAGTATCGCACACTTAGTGC
1 CTCAAATAGCCAAAGCTACCTCAGTATCGCACACTTAGTGC
* * *
17433 CTCATATAGCCAAAGCTA-TTCTA-TTTCGCACACTTAGTGC
1 CTCAAATAGCCAAAGCTACCTC-AGTATCGCACACTTAGTGC
17473 C
1 C
17474 GAATTCCTTC
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
40 19 0.51
41 18 0.49
ACGTcount: A:0.29, C:0.30, G:0.13, T:0.27
Consensus pattern (41 bp):
CTCAAATAGCCAAAGCTACCTCAGTATCGCACACTTAGTGC
Found at i:21523 original size:18 final size:19
Alignment explanation
Indices: 21457--21524 Score: 59
Period size: 20 Copynumber: 3.4 Consensus size: 19
21447 TAATAAAGGA
21457 AAATAAAATAAAAATTACAT
1 AAATAAAATAAAAA-TACAT
* *
21477 AAATAAGATAAATAA-AGAT
1 AAATAAAATAAA-AATACAT
21496 AAAAGTTAAAATAAAAATA-AT
1 -AAA--TAAAATAAAAATACAT
21517 AAATAAAA
1 AAATAAAA
21525 AGTTTTTAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 12
0.73 0.05 0.22
Matches are distributed among these distances:
18 5 0.12
19 3 0.08
20 17 0.43
21 6 0.15
22 9 0.22
ACGTcount: A:0.72, C:0.01, G:0.04, T:0.22
Consensus pattern (19 bp):
AAATAAAATAAAAATACAT
Found at i:25197 original size:22 final size:22
Alignment explanation
Indices: 25172--25215 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
25162 GTTATATTGA
*
25172 GTCTAATTGGAATGTTAATTTC
1 GTCTAAATGGAATGTTAATTTC
25194 GTCTAAATGGAATGTTAATTTC
1 GTCTAAATGGAATGTTAATTTC
25216 TTTCTCTATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.30, C:0.09, G:0.18, T:0.43
Consensus pattern (22 bp):
GTCTAAATGGAATGTTAATTTC
Found at i:32264 original size:13 final size:13
Alignment explanation
Indices: 32246--32272 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
32236 GGACGATGCT
32246 TTGTCCCAAGCAA
1 TTGTCCCAAGCAA
32259 TTGTCCCAAGCAA
1 TTGTCCCAAGCAA
32272 T
1 T
32273 GTTAAGGGTT
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:0.30, C:0.30, G:0.15, T:0.26
Consensus pattern (13 bp):
TTGTCCCAAGCAA
Found at i:38408 original size:25 final size:25
Alignment explanation
Indices: 38380--38428 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
38370 CCCTTATAAT
* *
38380 GTGAAAATGACCTTTTTACCCCTAA
1 GTGAAAATGACCATTATACCCCTAA
38405 GTGAAAATGACCATTATACCCCTA
1 GTGAAAATGACCATTATACCCCTA
38429 GGGTTATGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.35, C:0.24, G:0.12, T:0.29
Consensus pattern (25 bp):
GTGAAAATGACCATTATACCCCTAA
Found at i:38486 original size:10 final size:10
Alignment explanation
Indices: 38471--38509 Score: 69
Period size: 10 Copynumber: 3.8 Consensus size: 10
38461 TGCTTTTGTG
38471 CATGATATGC
1 CATGATATGC
38481 CATGATATGC
1 CATGATATGC
38491 ACATGATATGC
1 -CATGATATGC
38502 CATGATAT
1 CATGATAT
38510 ATTCACATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 18 0.64
11 10 0.36
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (10 bp):
CATGATATGC
Found at i:42200 original size:13 final size:13
Alignment explanation
Indices: 42182--42208 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
42172 TCCTGCCAAA
42182 GGGACACGACCGT
1 GGGACACGACCGT
42195 GGGACACGACCGT
1 GGGACACGACCGT
42208 G
1 G
42209 TGAGGGAGCC
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:0.22, C:0.30, G:0.41, T:0.07
Consensus pattern (13 bp):
GGGACACGACCGT
Found at i:45061 original size:26 final size:26
Alignment explanation
Indices: 44983--45064 Score: 66
Period size: 26 Copynumber: 3.3 Consensus size: 26
44973 GTGAGGTCAC
44983 ATGTGTAGTACTAAGTGCAGGCTACT
1 ATGTGTAGTACTAAGTGCAGGCTACT
* * * * *
45009 ACGTGTACCGGA-TAATTG--GTCGA--
1 ATGTGTA--GTACTAAGTGCAGGCTACT
45032 ATGTGTAGTACTAAGTGCAGGCTACT
1 ATGTGTAGTACTAAGTGCAGGCTACT
45058 ATGTGTA
1 ATGTGTA
45065 CCTGATAACT
Statistics
Matches: 39, Mismatches: 10, Indels: 14
0.62 0.16 0.22
Matches are distributed among these distances:
21 2 0.05
22 5 0.13
23 6 0.15
24 3 0.08
25 3 0.08
26 13 0.33
27 5 0.13
28 2 0.05
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (26 bp):
ATGTGTAGTACTAAGTGCAGGCTACT
Found at i:45158 original size:50 final size:49
Alignment explanation
Indices: 44977--45258 Score: 350
Period size: 50 Copynumber: 5.7 Consensus size: 49
44967 TCTATTGTGA
* *
44977 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATT
1 GGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
* * *
45026 GGTCGA-ATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCTGATAACTT
1 GGTC-ACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAA-TT
* * **
45076 CGATCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATGGTT
1 -GGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
* * **
45126 AGGTCATGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATGGTT
1 -GGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
* * *
45176 AGGTCATGTGTGCAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATT
1 -GGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
* *
45226 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTA
1 GGTCACGTGTGTAGTACTAAGTGCAGGCTACTA
45259 TGCGTACTAG
Statistics
Matches: 208, Mismatches: 21, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
49 72 0.35
50 98 0.47
51 38 0.18
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.30
Consensus pattern (49 bp):
GGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
Found at i:45304 original size:100 final size:101
Alignment explanation
Indices: 44984--45289 Score: 351
Period size: 100 Copynumber: 3.0 Consensus size: 101
44974 TGAGGTCACA
*
44984 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCGAATGTGTAGTACTAAGTG
1 TGTGCAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCGAATGTGTAGTACTAAGTG
* *
45049 CAGGCTACTATGTGTACCT-GATAACTTCGATC-AC-G
66 CAGGCTACTATGTGTA-CTAGATAGCTTAG-TCTACAG
* * * ** *
45084 TGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATGGTTAGGTC-ATGTGTGTAGTACTAAG
1 TGTGCAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATT-GGTCGA-ATGTGTAGTACTAAG
* * *
45148 TGCAGGCTACTACGTGTA-TCAGAT-GGTTAGGTC-A-TG
64 TGCAGGCTACTATGTGTACT-AGATAGCTTA-GTCTACAG
*
45184 TGTGCAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCGCATGTGTAGTACTAAGTG
1 TGTGCAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCGAATGTGTAGTACTAAGTG
*
45249 CAGGCTACTATGCGTACTAGATAGCCTT-GTCTACAAG
66 CAGGCTACTATGTGTACTAGATAG-CTTAGTCTAC-AG
45286 TGTG
1 TGTG
45290 AAAATATGTG
Statistics
Matches: 173, Mismatches: 20, Indels: 24
0.80 0.09 0.11
Matches are distributed among these distances:
99 42 0.24
100 85 0.49
101 41 0.24
102 5 0.03
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.30
Consensus pattern (101 bp):
TGTGCAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCGAATGTGTAGTACTAAGTG
CAGGCTACTATGTGTACTAGATAGCTTAGTCTACAG
Found at i:50806 original size:40 final size:40
Alignment explanation
Indices: 50762--50892 Score: 181
Period size: 40 Copynumber: 3.3 Consensus size: 40
50752 GGACTAAGAT
* * * *
50762 CCGAAGGCCTTTGTGCGAGATACTAAATTCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTATTAAATTCGGGTTAAGTC
*
50802 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTATTAAATTCGGGTTAAGTC
* * * *
50842 CCGAAGGCATTCGTGCGAGTTGTTAAAATCGGGCTATGTC
1 CCGAAGGCATTCGTGCGAGTTATTAAATTCGGGTTAAGTC
50882 CCGAAGGCATT
1 CCGAAGGCATT
50893 TGAACGAGGA
Statistics
Matches: 81, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 81 1.00
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
CCGAAGGCATTCGTGCGAGTTATTAAATTCGGGTTAAGTC
Found at i:58608 original size:40 final size:40
Alignment explanation
Indices: 58578--58708 Score: 163
Period size: 40 Copynumber: 3.3 Consensus size: 40
58568 GGACTAAGAT
* *
58578 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATACTAAATCCGGGTTAAGTC
* * *
58618 CCGAAGGCATTCGTGCGAGTTATTAAATTCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATACTAAATCCGGGTTAAGTC
* ** * * *
58658 CCGAAGGCATTCGTGCGAGTTGTTAAAACCGGGCTATGTC
1 CCGAAGGCATTCGTGCGAGATACTAAATCCGGGTTAAGTC
58698 CCGAAGGCATT
1 CCGAAGGCATT
58709 TGAACGAGGA
Statistics
Matches: 81, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 81 1.00
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.26
Consensus pattern (40 bp):
CCGAAGGCATTCGTGCGAGATACTAAATCCGGGTTAAGTC
Found at i:66462 original size:29 final size:29
Alignment explanation
Indices: 66430--66557 Score: 170
Period size: 29 Copynumber: 4.4 Consensus size: 29
66420 GGGAGTAACG
* *
66430 GGCCATAT-AATGGTGATTTAGGCCTAATA
1 GGCCATATGAAT-GTGAATTGGGCCTAATA
* *
66459 GGCCATATGAATATGAATTGGGCCTAATG
1 GGCCATATGAATGTGAATTGGGCCTAATA
*
66488 GGCCATATGAATGTGAATTGGGCCTGATA
1 GGCCATATGAATGTGAATTGGGCCTAATA
*
66517 GGCCATATGAATGTGAATTGGGCTTAAT-
1 GGCCATATGAATGTGAATTGGGCCTAATA
*
66545 GGGCATATGAATG
1 GGCCATATGAATG
66558 AGATGGGCCA
Statistics
Matches: 88, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
28 12 0.14
29 73 0.83
30 3 0.03
ACGTcount: A:0.30, C:0.12, G:0.29, T:0.29
Consensus pattern (29 bp):
GGCCATATGAATGTGAATTGGGCCTAATA
Found at i:66512 original size:58 final size:58
Alignment explanation
Indices: 66429--66557 Score: 190
Period size: 58 Copynumber: 2.2 Consensus size: 58
66419 TGGGAGTAAC
*
66429 GGGCCATAT-AATGGTGATTTAGGCCTAATAGGCCATATGAATATGAATTGGGCCTAAT
1 GGGCCATATGAAT-GTGAATTAGGCCTAATAGGCCATATGAATATGAATTGGGCCTAAT
* * * *
66487 GGGCCATATGAATGTGAATTGGGCCTGATAGGCCATATGAATGTGAATTGGGCTTAAT
1 GGGCCATATGAATGTGAATTAGGCCTAATAGGCCATATGAATATGAATTGGGCCTAAT
66545 GGG-CATATGAATG
1 GGGCCATATGAATG
66558 AGATGGGCCA
Statistics
Matches: 65, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
57 10 0.15
58 52 0.80
59 3 0.05
ACGTcount: A:0.29, C:0.12, G:0.29, T:0.29
Consensus pattern (58 bp):
GGGCCATATGAATGTGAATTAGGCCTAATAGGCCATATGAATATGAATTGGGCCTAAT
Found at i:70895 original size:28 final size:29
Alignment explanation
Indices: 70864--70924 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 29
70854 GTGAGCATGA
*
70864 ATAT-AAGGTGATTT-GAGCCTAACGGGCC
1 ATATAAAGGTGATTTAG-GCCTAACAGGCC
*
70892 ATATAAAGGTGATTTAGGCCTAATAGGCC
1 ATATAAAGGTGATTTAGGCCTAACAGGCC
70921 ATAT
1 ATAT
70925 CAATGGAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 4 0.14
29 24 0.83
30 1 0.03
ACGTcount: A:0.33, C:0.15, G:0.25, T:0.28
Consensus pattern (29 bp):
ATATAAAGGTGATTTAGGCCTAACAGGCC
Found at i:74574 original size:13 final size:13
Alignment explanation
Indices: 74556--74585 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
74546 ACAAATATTC
*
74556 ATATAAACATTTT
1 ATATAAACACTTT
74569 ATATAAACACTTT
1 ATATAAACACTTT
74582 ATAT
1 ATAT
74586 TATTATTTCC
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:0.47, C:0.10, G:0.00, T:0.43
Consensus pattern (13 bp):
ATATAAACACTTT
Found at i:75131 original size:135 final size:135
Alignment explanation
Indices: 74936--75244 Score: 356
Period size: 135 Copynumber: 2.3 Consensus size: 135
74926 TTCCAATATG
* * * ** * * *
74936 ATGCCATAGTATCTTTCAACTATGGTTTTATT-TTTTTGCGACAT-GATGCCATAGTTTCTTTTA
1 ATGCCATAGTGTCTTTCAACTATGGTCTTATTCATTTT-CGGTATAG-TACCATAGTGTCTTTCA
* ** * *
74999 ACTATGGTCTTATTTATTTTGGACA-AGATGCCATAGTGTCTTTCAACTATGGTCTTATTCATTT
64 ACTATGGTCTTATTCATTTCCGACATAG-TACCATAGTGTCTTTCAACTATGGTCTTATTCACTT
*
75063 TCGTCATG
128 TCGTCATA
*
75071 TTGCCATAGTGTCCTTT-AACTATGGTCTTATTCATTTTCGGTATAGTACCATAGTGTCTTTCAA
1 ATGCCATAGTGT-CTTTCAACTATGGTCTTATTCATTTTCGGTATAGTACCATAGTGTCTTTCAA
** *
75135 CTATTTTCTTATTCATTTCCGATATAGTACCATAGTGTCTTTCAACTATGGTCTTATTCACTTTC
65 CTATGGTCTTATTCATTTCCGACATAGTACCATAGTGTCTTTCAACTATGGTCTTATTCACTTTC
*
75200 GTTATA
130 GTCATA
* * *
75206 ATGCCATATTGTTTTTCAACTATGTTCTTATTCATTTTC
1 ATGCCATAGTGTCTTTCAACTATGGTCTTATTCATTTTC
75245 CAAGCCAATG
Statistics
Matches: 146, Mismatches: 23, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
134 3 0.02
135 132 0.90
136 11 0.08
ACGTcount: A:0.22, C:0.18, G:0.13, T:0.47
Consensus pattern (135 bp):
ATGCCATAGTGTCTTTCAACTATGGTCTTATTCATTTTCGGTATAGTACCATAGTGTCTTTCAAC
TATGGTCTTATTCATTTCCGACATAGTACCATAGTGTCTTTCAACTATGGTCTTATTCACTTTCG
TCATA
Found at i:75238 original size:45 final size:45
Alignment explanation
Indices: 74936--75244 Score: 318
Period size: 45 Copynumber: 6.9 Consensus size: 45
74926 TTCCAATATG
* * * ** *
74936 ATGCCATAGTATCTTTCAACTATGGTTTTATT-TTTTTGCGACATG
1 ATGCCATAGTGTCTTTCAACTATGGTCTTATTCATTTT-CGTTATA
* * * * **
74981 ATGCCATAGTTTCTTTTAACTATGGTCTTATTTATTTTGGACA-A
1 ATGCCATAGTGTCTTTCAACTATGGTCTTATTCATTTTCGTTATA
* *
75025 GATGCCATAGTGTCTTTCAACTATGGTCTTATTCATTTTCGTCATG
1 -ATGCCATAGTGTCTTTCAACTATGGTCTTATTCATTTTCGTTATA
* *
75071 TTGCCATAGTGTCCTTT-AACTATGGTCTTATTCATTTTCGGTATA
1 ATGCCATAGTGT-CTTTCAACTATGGTCTTATTCATTTTCGTTATA
* * ** * *
75116 GTACCATAGTGTCTTTCAACTATTTTCTTATTCATTTCCGATATA
1 ATGCCATAGTGTCTTTCAACTATGGTCTTATTCATTTTCGTTATA
* * *
75161 GTACCATAGTGTCTTTCAACTATGGTCTTATTCACTTTCGTTATA
1 ATGCCATAGTGTCTTTCAACTATGGTCTTATTCATTTTCGTTATA
* * *
75206 ATGCCATATTGTTTTTCAACTATGTTCTTATTCATTTTC
1 ATGCCATAGTGTCTTTCAACTATGGTCTTATTCATTTTC
75245 CAAGCCAATG
Statistics
Matches: 226, Mismatches: 33, Indels: 10
0.84 0.12 0.04
Matches are distributed among these distances:
44 4 0.02
45 214 0.95
46 8 0.04
ACGTcount: A:0.22, C:0.18, G:0.13, T:0.47
Consensus pattern (45 bp):
ATGCCATAGTGTCTTTCAACTATGGTCTTATTCATTTTCGTTATA
Found at i:76871 original size:49 final size:49
Alignment explanation
Indices: 76794--76975 Score: 213
Period size: 49 Copynumber: 3.7 Consensus size: 49
76784 ACTATTGTGA
* * *
76794 GGTCACATGTGTAGTACTACGTGCAGGCTACTACGTGTACTGGATAATT
1 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTACGTGTACTAGATAATT
* * * ** *
76843 GGTCGCATGTGTAGTACTAAGTGTAGGCTACTATGCGTACCCGAAAACTGT
1 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTACGTGTACTAGATAA-T-T
* * *
76894 GATCAG-GTGTGTAGTACTAAGTGCAGGCTACTACGTGTACTAGATTATT
1 GGTC-GCATGTGTAGTACTAAGTGCAGGCTACTACGTGTACTAGATAATT
*
76943 GGTCGCATGTGCAGTACTAAGTGCAGGCTACTA
1 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTA
76976 TGCGTACCAG
Statistics
Matches: 109, Mismatches: 20, Indels: 8
0.80 0.15 0.06
Matches are distributed among these distances:
48 1 0.01
49 68 0.62
50 2 0.02
51 37 0.34
52 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.29
Consensus pattern (49 bp):
GGTCGCATGTGTAGTACTAAGTGCAGGCTACTACGTGTACTAGATAATT
Found at i:76974 original size:100 final size:100
Alignment explanation
Indices: 76801--76983 Score: 321
Period size: 100 Copynumber: 1.8 Consensus size: 100
76791 TGAGGTCACA
* * *
76801 TGTGTAGTACTACGTGCAGGCTACTACGTGTACTGGATAATTGGTCGCATGTGTAGTACTAAGTG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACTAGATAATTGGTCGCATGTGCAGTACTAAGTG
*
76866 TAGGCTACTATGCGTACCCGAAAACTGTGATCAGG
66 CAGGCTACTATGCGTACCCGAAAACTGTGATCAGG
*
76901 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACTAGATTATTGGTCGCATGTGCAGTACTAAGTG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACTAGATAATTGGTCGCATGTGCAGTACTAAGTG
76966 CAGGCTACTATGCGTACC
66 CAGGCTACTATGCGTACC
76984 AGACAACTTC
Statistics
Matches: 78, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
100 78 1.00
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.30
Consensus pattern (100 bp):
TGTGTAGTACTAAGTGCAGGCTACTACGTGTACTAGATAATTGGTCGCATGTGCAGTACTAAGTG
CAGGCTACTATGCGTACCCGAAAACTGTGATCAGG
Found at i:82206 original size:46 final size:46
Alignment explanation
Indices: 82139--82313 Score: 187
Period size: 46 Copynumber: 3.8 Consensus size: 46
82129 TGTAACCCAC
82139 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCACAT
*
82185 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGG--G-C--GTTCACAT
* * * * * * *
82235 --TTCA-CGAACTCGGACTCAACTCAACGAGTTTGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCACAT
* *
82278 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGG
82314 ATGCTCAACC
Statistics
Matches: 107, Mismatches: 13, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 2 0.02
43 3 0.03
44 1 0.01
45 2 0.02
46 62 0.58
47 26 0.24
48 3 0.03
49 1 0.01
50 4 0.04
51 3 0.03
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCACAT
Found at i:82258 original size:93 final size:93
Alignment explanation
Indices: 82146--82317 Score: 290
Period size: 93 Copynumber: 1.8 Consensus size: 93
82136 CACCCATAAG
* *
82146 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCACATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCACATCCATAAGTGAACTCGGACTCAACTCA
82211 ACGAGCTCGGATGCCTAGTTACATTTCA
66 ACGAGCTCGGATGCCTAGTTACATTTCA
* * *
82239 CGAACTCGGACTCAACTCAACGAGTTTGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCACATCCATAAGTGAACTCGGACTCAACTCA
*
82304 ACGAGTTCGGATGC
66 ACGAGCTCGGATGC
82318 TCAACCATCC
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCACATCCATAAGTGAACTCGGACTCAACTCA
ACGAGCTCGGATGCCTAGTTACATTTCA
Found at i:88363 original size:93 final size:93
Alignment explanation
Indices: 88255--88426 Score: 292
Period size: 93 Copynumber: 1.8 Consensus size: 93
88245 CGCCCATAAG
* *
88255 CGAACTCGGACTCAACTCAACGAGCTCAGG-CGTTTGCATCCATAAGTGAACTCGGACTCAACTC
1 CGAACTCGGACTCAACTCAACGAGCTC-GGACATTCGCATCCATAAGTGAACTCGGACTCAACTC
88319 AACGAGCTCGGATGCCTAGTTACATTTCA
65 AACGAGCTCGGATGCCTAGTTACATTTCA
*
88348 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
*
88413 ACGAGTTCGGATGC
66 ACGAGCTCGGATGC
88427 TCAACCATCC
Statistics
Matches: 74, Mismatches: 4, Indels: 2
0.93 0.05 0.03
Matches are distributed among these distances:
92 2 0.03
93 72 0.97
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGCTCGGATGCCTAGTTACATTTCA
Found at i:88418 original size:46 final size:45
Alignment explanation
Indices: 88248--88423 Score: 180
Period size: 46 Copynumber: 3.8 Consensus size: 45
88238 TGTAACCCGC
*
88248 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCAGG-CGTTTGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTC-GGAC-ATTGCAT
* *
88294 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGA---C-A-TTGCAT
* * *
88344 --TTCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGACATT-GCAT
* *
88387 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGA
88424 TGCTCAACCA
Statistics
Matches: 109, Mismatches: 12, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 1 0.01
45 4 0.04
46 62 0.57
47 28 0.26
48 2 0.02
49 1 0.01
50 5 0.05
ACGTcount: A:0.30, C:0.29, G:0.20, T:0.21
Consensus pattern (45 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGACATTGCAT
Found at i:88880 original size:31 final size:30
Alignment explanation
Indices: 88845--88903 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
88835 TTAACTCAAG
88845 TTTTGGCAAACTTACAATTTTGCCCCTAAAC
1 TTTT-GCAAACTTACAATTTTGCCCCTAAAC
* * * *
88876 TTTTGCATATTTACATTTTTTCCCCTAA
1 TTTTGCAAACTTACAATTTTGCCCCTAA
88904 GCTCGAGATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 20 0.83
31 4 0.17
ACGTcount: A:0.25, C:0.24, G:0.07, T:0.44
Consensus pattern (30 bp):
TTTTGCAAACTTACAATTTTGCCCCTAAAC
Found at i:95847 original size:27 final size:27
Alignment explanation
Indices: 95816--95994 Score: 189
Period size: 27 Copynumber: 6.6 Consensus size: 27
95806 TAAATTTTAC
*
95816 AGCACTAAGTGTGTGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
95843 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
95869 ATGCACTAAGTGTGCGAATTGACCAATGC
1 A-GCACTAAGTGTGCGATTTGA-CTATGT
*
95898 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
95926 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
95953 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
95980 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
95995 GACTCAATAT
Statistics
Matches: 128, Mismatches: 20, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
27 87 0.68
28 37 0.29
29 4 0.03
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:95931 original size:83 final size:82
Alignment explanation
Indices: 95817--95973 Score: 226
Period size: 83 Copynumber: 1.9 Consensus size: 82
95807 AAATTTTACA
* * *
95817 GCACTAAGTGTGTGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
95881 TGCGAATTGACCAATGCG
65 TGCGAATTGACCAATGCG
** *
95899 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
95964 TGCGAGTTGA
65 TGCGAATTGA
95974 TTATATAGCA
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
82 14 0.21
83 51 0.77
84 1 0.02
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (82 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCAATGCG
Found at i:104033 original size:27 final size:27
Alignment explanation
Indices: 104002--104179 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
103992 TAAATTGTAC
104002 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
104029 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
104055 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
104083 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
104111 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
104138 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
104165 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
104180 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
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:104116 original size:82 final size:81
Alignment explanation
Indices: 104003--104158 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
103993 AAATTGTACA
* *
104003 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
104067 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
104084 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
104149 TGCGAGTTGA
65 TGCGAATTGA
104159 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:104170 original size:82 final size:81
Alignment explanation
Indices: 103999--104179 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
103989 GATTAAATTG
* *
103999 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
104064 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
104080 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
104144 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
104162 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
104180 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Done.