Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2204
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: 19864
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Found at i:1914 original size:155 final size:155
Alignment explanation
Indices: 1626--2006 Score: 446
Period size: 155 Copynumber: 2.5 Consensus size: 155
1616 CAATCTTTTG
* * * * * * * * *
1626 AGTCTTTTAGGGGTATCAGGTATTTTTAAGTCGAAAGTATCTCCTAGGGGTATTTTCATAATTTT
1 AGTCTTATAGAGGTATCAGGTACTTATACGTCGAAGGTATCCCCTAAGGGCATTTTCATAATTTT
* * * * * **
1691 TTAAAATCGAGTCTTAGATTGTCACCGGGTCCGCTTTTATGCTAAATGTAAATATTTTGGATAAG
66 TTAAAACCGAGTCTAAGATTGTCACCGAGTCCGCTTTTATCCGAAATGTAAATATTTAAGATAAG
1756 TTCATCTCATCTATTATCCTCTTTA
131 TTCATCTCATCTATTATCCTCTTTA
* * * *
1781 AGTCCTT-TAGGGGTA-CTGGGTACTTATACGTTGAATGTATCCCCTAAGGGCATTTTCATAATT
1 AGT-CTTATAGAGGTATC-AGGTACTTATACGTCGAAGGTATCCCCTAAGGGCATTTTCATAATT
* * *
1844 TTTTAGAACCGAGTCCTAAG-TTGTCATCGAGTCCGCTTTTATACCGAAA-GTAGATATTTAAGA
64 TTTTAAAACCGAGT-CTAAGATTGTCACCGAGTCCGCTTTTAT-CCGAAATGTAAATATTTAAGA
* *
1907 TAGGTTCATCTCATCTATTATCCTTTTTA
127 TAAGTTCATCTCATCTATTATCCTCTTTA
* * *
1936 AGTCTTATAGAGGTATCAGGTACTTTTACGTCGAAGGTATCCCCTAAGGGCATTTTCGTAAATTT
1 AGTCTTATAGAGGTATCAGGTACTTATACGTCGAAGGTATCCCCTAAGGGCATTTTCATAATTTT
2001 TTAAAA
66 TTAAAA
2007 TAACTCTTAG
Statistics
Matches: 191, Mismatches: 29, Indels: 12
0.82 0.12 0.05
Matches are distributed among these distances:
154 4 0.02
155 175 0.92
156 12 0.06
ACGTcount: A:0.27, C:0.16, G:0.18, T:0.39
Consensus pattern (155 bp):
AGTCTTATAGAGGTATCAGGTACTTATACGTCGAAGGTATCCCCTAAGGGCATTTTCATAATTTT
TTAAAACCGAGTCTAAGATTGTCACCGAGTCCGCTTTTATCCGAAATGTAAATATTTAAGATAAG
TTCATCTCATCTATTATCCTCTTTA
Found at i:7082 original size:72 final size:73
Alignment explanation
Indices: 6964--7366 Score: 206
Period size: 73 Copynumber: 5.4 Consensus size: 73
6954 ACACAAGTTA
*
6964 GTGGCACCCCTTTTTTTTAAAGCCCGCACAAGCTGACAACACCC-TTTTCCTTCCTTAAGCCCAC
1 GTGGCACCCCTTTTTTTTAAAGCCCACACAAGCTGACAACACCCTTTTTCCTTCCTTAAGCCCAC
7028 ATAGGTTG
66 ATAGGTTG
* * * * *
7036 GTGGCACCCCTTTCTTTTTAAAGCCTACATAAGCT-AGCAGCA-CCTTTTTCTTTCTTTAAGCCC
1 GTGGCACCCCTTT-TTTTTAAAGCCCACACAAGCTGA-CAACACCCTTTTTCCTTCCTTAAGCCC
* *** *
7099 ACAAAAAATA
64 ACATAGGTTG
* ** * * ** * * *
7109 GTGGTACCTTTTTCTTTTTTAAAGCCCACACAAGCTAATAGTA-TCTTTTTCCTTCTTTAAGCCT
1 GTGGCACC-CCTT-TTTTTTAAAGCCCACACAAGCTGACAACACCCTTTTTCCTTCCTTAAGCCC
* * *
7173 ACACAAGTTA
64 ACATAGGTTG
** * * *** * * * *
7183 GTGGCACCTTTTTTTTTTAAAGCACACACAAGTTGACGGTACCTTTTTTTCTT-TTTAGGCCCAC
1 GTGGCACCCCTTTTTTTTAAAGCCCACACAAGCTGACAACACCCTTTTTCCTTCCTTAAGCCCAC
*
7247 ATAAGTTG
66 ATAGGTTG
* * ** **** * * *
7255 GTGACACCCTTTTTTTTTCCTTCTTAAAGCCCGTACAAGCTGGTGGCACTCGTTTT-CTTCTTTA
1 GTGGCACCC----CTTTT--TT-TTAAAGCCCACACAAGCTGACAACACCCTTTTTCCTTCCTTA
* *
7319 AGCCCACACAAGTTG
59 AGCCCACATAGGTTG
*
7334 GTGGCACCCCTTTCTTTTCAAAGCCCACACAAG
1 GTGGCACCCCTTT-TTTTTAAAGCCCACACAAG
7367 TCAGTAGTAA
Statistics
Matches: 259, Mismatches: 56, Indels: 31
0.75 0.16 0.09
Matches are distributed among these distances:
72 62 0.24
73 75 0.29
74 58 0.22
75 5 0.02
76 6 0.02
78 5 0.02
79 48 0.19
ACGTcount: A:0.24, C:0.27, G:0.14, T:0.35
Consensus pattern (73 bp):
GTGGCACCCCTTTTTTTTAAAGCCCACACAAGCTGACAACACCCTTTTTCCTTCCTTAAGCCCAC
ATAGGTTG
Found at i:7095 original size:73 final size:73
Alignment explanation
Indices: 6952--7575 Score: 324
Period size: 72 Copynumber: 8.6 Consensus size: 73
6942 TTTTCAAAGT
* * * *
6952 CCACACAAGTTAGTGGCACCCCTTT-TTTTTAAAGCCCGCACAAGCT-GACAACACCCTTTTCCT
1 CCACACAAGTTGGTGGCACCCCTTTCTTTTTAAAGCCCACACAAGCTAG-CAGCACCTTTTTCCT
*
7015 TCCTTAAGC
65 TCTTTAAGC
* * * * *
7024 CCACATAGGTTGGTGGCACCCCTTTCTTTTTAAAGCCTACATAAGCTAGCAGCACCTTTTTCTTT
1 CCACACAAGTTGGTGGCACCCCTTTCTTTTTAAAGCCCACACAAGCTAGCAGCACCTTTTTCCTT
7089 CTTTAAGC
66 CTTTAAGC
* ** * * ** ** * *
7097 CCACAAAAAATAGTGGTACCTTTTTCTTTTTTAAAGCCCACACAAGCTAATAGTATCTTTTTCCT
1 CCACACAAGTTGGTGGCACCCCTTTC-TTTTTAAAGCCCACACAAGCTAGCAGCACCTTTTTCCT
7162 TCTTTAAGC
65 TCTTTAAGC
* * * * * * * * *
7171 CTACACAAGTTAGTGGCA-CCTTTTTTTTTTAAAGCACACACAAG-TTGACGGTACCTTTTTTTC
1 CCACACAAGTTGGTGGCACCCCTTTCTTTTTAAAGCCCACACAAGCTAG-CAGCACC-TTTTTCC
*
7234 TT-TTTAGGC
64 TTCTTTAAGC
* * * * ** * ** *
7243 CCACATAAGTTGGTGACACCCTTTTTTTTTCCTTCTTAAAGCCCGTACAAGCTGGTGGCACTCGT
1 CCACACAAGTTGGTGGCACCC-----CTTT-CTTTTTAAAGCCCACACAAGCTAGCAGCAC-CTT
7308 TTT-CTTCTTTAAGC
59 TTTCCTTCTTTAAGC
* * * *
7322 CCACACAAGTTGGTGGCACCCCTTTCTTTTCAAAGCCCACACAAG-TCAGTAGTAACC--GTT--
1 CCACACAAGTTGGTGGCACCCCTTTCTTTTTAAAGCCCACACAAGCT-AGCAG-CACCTTTTTCC
**
7382 TTC-AAAAGC
64 TTCTTTAAGC
* * ** * * * * * ** * *
7391 CCACACAAATTGGTAGCACCTATTTATTTTTAAAGTCCATACAAACTGGTGGTACCTTTTTCTTT
1 CCACACAAGTTGGTGGCACCCCTTTCTTTTTAAAGCCCACACAAGCTAGCAGCACCTTTTTCCTT
*
7456 CTTAAAGC
66 CTTTAAGC
* *** * * * ** *
7464 CCTACA-AA-TTGGTGGCACCCCTTTCTTTTCAAAGCTTGCACAAGTTGGCGGCATATTTTTTCT
1 CC-ACACAAGTTGGTGGCACCCCTTTCTTTTTAAAGCCCACACAAGCTAGCAGCACCTTTTTCCT
**
7527 TCTCAAAGC
65 TCTTTAAGC
* * * *
7536 CCACATAATTTGGTGGCATCCATTTCTTTTT-AAGCCCACA
1 CCACACAAGTTGGTGGCACCCCTTTCTTTTTAAAGCCCACA
7576 TAAGTTGTTG
Statistics
Matches: 420, Mismatches: 106, Indels: 52
0.73 0.18 0.09
Matches are distributed among these distances:
68 3 0.01
69 43 0.10
70 6 0.01
71 6 0.01
72 123 0.29
73 119 0.28
74 62 0.15
78 7 0.02
79 48 0.11
80 3 0.01
ACGTcount: A:0.25, C:0.26, G:0.14, T:0.35
Consensus pattern (73 bp):
CCACACAAGTTGGTGGCACCCCTTTCTTTTTAAAGCCCACACAAGCTAGCAGCACCTTTTTCCTT
CTTTAAGC
Found at i:7118 original size:37 final size:37
Alignment explanation
Indices: 7077--7214 Score: 138
Period size: 37 Copynumber: 3.8 Consensus size: 37
7067 AGCTAGCAGC
* *
7077 ACCTTTTTCTTTCTTTAAGCCCACAAAAAATAGTGGT
1 ACCTTTTTCTTTCTTTAAGCCCACACAAGATAGTGGT
* * *
7114 ACCTTTTTCTTT-TTTAAAGCCCACACAAGCTAATAGT
1 ACCTTTTTCTTTCTTT-AAGCCCACACAAGATAGTGGT
* * * * *
7151 ATCTTTTTCCTTCTTTAAGCCTACACAAGTTAGTGGC
1 ACCTTTTTCTTTCTTTAAGCCCACACAAGATAGTGGT
* *
7188 ACCTTTTT-TTT-TTAAAGCACACACAAG
1 ACCTTTTTCTTTCTTTAAGCCCACACAAG
7215 TTGACGGTAC
Statistics
Matches: 82, Mismatches: 17, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
35 13 0.16
36 5 0.06
37 61 0.74
38 3 0.04
ACGTcount: A:0.28, C:0.23, G:0.10, T:0.38
Consensus pattern (37 bp):
ACCTTTTTCTTTCTTTAAGCCCACACAAGATAGTGGT
Found at i:7158 original size:74 final size:73
Alignment explanation
Indices: 6962--7214 Score: 233
Period size: 73 Copynumber: 3.5 Consensus size: 73
6952 CCACACAAGT
** * * * * *
6962 TAGTGGCACCCCTT-TTTTTTAAAGCCCGCACAAGCTGACAACACCCTTTTCCTTCCTTAAGCCC
1 TAGTGGCACCTTTTCTTTTTTAAAGCCCACACAAGCTAACAGCACCTTTTTCCTTCTTTAAGCCC
* ***
7026 ACATAGGT
66 ACAAAAAA
* * * * * *
7034 TGGTGGCACCCCTTTC-TTTTTAAAGCCTACATAAGCTAGCAGCACCTTTTTCTTTCTTTAAGCC
1 TAGTGGCA-CCTTTTCTTTTTTAAAGCCCACACAAGCTAACAGCACCTTTTTCCTTCTTTAAGCC
7098 CACAAAAAA
65 CACAAAAAA
* * * *
7107 TAGTGGTACCTTTTTCTTTTTTAAAGCCCACACAAGCTAATAGTATCTTTTTCCTTCTTTAAGCC
1 TAGTGGCACC-TTTTCTTTTTTAAAGCCCACACAAGCTAACAGCACCTTTTTCCTTCTTTAAGCC
* * **
7172 TACACAAGT
65 CACAAAAAA
*
7181 TAGTGGCACCTTTT-TTTTTTAAAGCACACACAAG
1 TAGTGGCACCTTTTCTTTTTTAAAGCCCACACAAG
7215 TTGACGGTAC
Statistics
Matches: 146, Mismatches: 31, Indels: 8
0.79 0.17 0.04
Matches are distributed among these distances:
72 28 0.19
73 63 0.43
74 55 0.38
ACGTcount: A:0.26, C:0.27, G:0.13, T:0.34
Consensus pattern (73 bp):
TAGTGGCACCTTTTCTTTTTTAAAGCCCACACAAGCTAACAGCACCTTTTTCCTTCTTTAAGCCC
ACAAAAAA
Found at i:7322 original size:37 final size:38
Alignment explanation
Indices: 7269--7366 Score: 105
Period size: 37 Copynumber: 2.7 Consensus size: 38
7259 CACCCTTTTT
**
7269 TTTTCCTTCTTAAAGCCCGTACAAGCTGGTGGCACTCG
1 TTTTCCTTCTTAAAGCCCACACAAGCTGGTGGCACTCG
* * *
7307 TTTT-CTTCTTTAAGCCCACACAAGTTGGTGGCAC-CC
1 TTTTCCTTCTTAAAGCCCACACAAGCTGGTGGCACTCG
*
7343 CTTT-CTT-TTCAAAGCCCACACAAG
1 TTTTCCTTCTT-AAAGCCCACACAAG
7367 TCAGTAGTAA
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
35 2 0.04
36 20 0.38
37 26 0.50
38 4 0.08
ACGTcount: A:0.21, C:0.31, G:0.16, T:0.32
Consensus pattern (38 bp):
TTTTCCTTCTTAAAGCCCACACAAGCTGGTGGCACTCG
Found at i:7358 original size:36 final size:36
Alignment explanation
Indices: 7318--7600 Score: 148
Period size: 36 Copynumber: 7.9 Consensus size: 36
7308 TTTCTTCTTT
7318 AAGCCCACACAAGTTGGTGGCACCCCTTTCTTTTCA
1 AAGCCCACACAAGTTGGTGGCACCCCTTTCTTTTCA
** * * * *
7354 AAGCCCACACAAGTCAGTAGTA-ACC---GTTTTCAA
1 AAGCCCACACAAGTTGGTGGCACCCCTTTCTTTTC-A
* * ** * *
7387 AAGCCCACACAAATTGGTAGCACCTATTTATTTTTA
1 AAGCCCACACAAGTTGGTGGCACCCCTTTCTTTTCA
* * ** * ** *
7423 AAGTCCATACAAACTGGTGGTACCTTTTTCTTTCTTA
1 AAGCCCACACAAGTTGGTGGCACCCCTTTCTTT-TCA
7460 AAGCCCTACA-AA-TTGGTGGCACCCCTTTCTTTTCA
1 AAGCCC-ACACAAGTTGGTGGCACCCCTTTCTTTTCA
*** * **** *
7495 AAGCTTGCACAAGTTGGCGGCATATTTTTTCTTCTCA
1 AAGCCCACACAAGTTGGTGGCA-CCCCTTTCTTTTCA
* * * * *
7532 AAGCCCACATAATTTGGTGGCATCCATTTCTTTT-T
1 AAGCCCACACAAGTTGGTGGCACCCCTTTCTTTTCA
* * *
7567 AAGCCCACATAAGTTGTTGGCACCCTTTTCTTTT
1 AAGCCCACACAAGTTGGTGGCACCCCTTTCTTTT
7601 TTACTTTTTA
Statistics
Matches: 183, Mismatches: 54, Indels: 21
0.71 0.21 0.08
Matches are distributed among these distances:
32 5 0.03
33 19 0.10
34 2 0.01
35 40 0.22
36 76 0.42
37 39 0.21
38 2 0.01
ACGTcount: A:0.25, C:0.26, G:0.15, T:0.34
Consensus pattern (36 bp):
AAGCCCACACAAGTTGGTGGCACCCCTTTCTTTTCA
Found at i:7572 original size:35 final size:35
Alignment explanation
Indices: 7532--7601 Score: 104
Period size: 35 Copynumber: 2.0 Consensus size: 35
7522 TTTCTTCTCA
* *
7532 AAGCCCACATAATTTGGTGGCATCCATTTCTTTTT
1 AAGCCCACATAAGTTGGTGGCACCCATTTCTTTTT
* *
7567 AAGCCCACATAAGTTGTTGGCACCCTTTTCTTTTT
1 AAGCCCACATAAGTTGGTGGCACCCATTTCTTTTT
7602 TACTTTTTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.21, C:0.24, G:0.14, T:0.40
Consensus pattern (35 bp):
AAGCCCACATAAGTTGGTGGCACCCATTTCTTTTT
Found at i:7743 original size:37 final size:35
Alignment explanation
Indices: 7648--7744 Score: 104
Period size: 37 Copynumber: 2.7 Consensus size: 35
7638 TTTTTTCTTT
* *
7648 AAGCCCACACAAGTTGGTGGCACCCCTTTCTTTTTA
1 AAGCCCACA-TAGCTGGTGGCACCCCTTTCTTTTTA
* * * *
7684 AAGCCCGCATGAGCTAGCGGCACCCTTTCTCTTTTTA
1 AAGCCCACAT-AGCTGGTGGCACCCCTT-TCTTTTTA
7721 AAGCCCACATATGCTGGTGGCACC
1 AAGCCCACATA-GCTGGTGGCACC
7745 TTTTGCCTTT
Statistics
Matches: 49, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
36 22 0.45
37 27 0.55
ACGTcount: A:0.22, C:0.32, G:0.20, T:0.27
Consensus pattern (35 bp):
AAGCCCACATAGCTGGTGGCACCCCTTTCTTTTTA
Found at i:7892 original size:52 final size:52
Alignment explanation
Indices: 7817--7964 Score: 199
Period size: 52 Copynumber: 2.8 Consensus size: 52
7807 TGATGGCATT
* *
7817 ATCTTTAAGTCTAATGTCACTGGCCTTGAATTAGCACATTGGCACTCTTATC
1 ATCTTTAAGTCTAATGTCGCTGGCCTTGAATTAGCACATTGGCACCCTTATC
*
7869 A-CTTTTAAGTCCAATGTCGCTGGCCTTGAATTAGCACATTGGCACCCTTATC
1 ATC-TTTAAGTCTAATGTCGCTGGCCTTGAATTAGCACATTGGCACCCTTATC
* * * ** *
7921 ATCTTTAAATCTAACGTTGCTACCCTTGAAGTAGCACATTGGCA
1 ATCTTTAAGTCTAATGTCGCTGGCCTTGAATTAGCACATTGGCA
7965 TCATACCTTC
Statistics
Matches: 84, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
51 1 0.01
52 82 0.98
53 1 0.01
ACGTcount: A:0.26, C:0.24, G:0.16, T:0.34
Consensus pattern (52 bp):
ATCTTTAAGTCTAATGTCGCTGGCCTTGAATTAGCACATTGGCACCCTTATC
Found at i:8775 original size:29 final size:29
Alignment explanation
Indices: 8739--8823 Score: 152
Period size: 29 Copynumber: 2.9 Consensus size: 29
8729 GATACATTTT
8739 TCATTGTATCGATACATTATGGGTTTTGC
1 TCATTGTATCGATACATTATGGGTTTTGC
8768 TCATTGTATCGATACATTATGGGTTTTGC
1 TCATTGTATCGATACATTATGGGTTTTGC
* *
8797 TCATTGTATCGATACATTCTAGGTTTT
1 TCATTGTATCGATACATTATGGGTTTT
8824 TAACCTAAAT
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 54 1.00
ACGTcount: A:0.21, C:0.14, G:0.19, T:0.46
Consensus pattern (29 bp):
TCATTGTATCGATACATTATGGGTTTTGC
Found at i:11331 original size:79 final size:79
Alignment explanation
Indices: 11192--11452 Score: 213
Period size: 79 Copynumber: 3.3 Consensus size: 79
11182 GTCAAAAAGT
* * * ** * *
11192 GGATAATCCAACCCCACCATCTCCAAGGAGATACTCCAACCTCATTTTTGCTTTCGAAATA-TGA
1 GGATACTCCAACCCCACCATTTCCAAGGAGAAACTCCAACCTCATTTTAACTTCCAAAATATTG-
*
11256 AAATTTTCATC-CTTG
65 AAATTTTCATCTC-TA
** * * * *
11271 GGATACTTGAACCCCACCATTTCCGAGGAGAAATTCTAACCTCGTTTTAACTTCCAAAATATTGA
1 GGATACTCCAACCCCACCATTTCCAAGGAGAAACTCCAACCTCATTTTAACTTCCAAAATATTGA
11336 AATTTTCATCTCTA
66 AATTTTCATCTCTA
* * * * ** ** *
11350 GGATACTCCAACCCCATCATTTTCAAGGAGATACTCCAACGC-CTTTTTATTTTGTAAAACATTG
1 GGATACTCCAACCCCACCATTTCCAAGGAGAAACTCCAAC-CTCATTTTAACTTCCAAAATATTG
* * *
11414 AATTTCTTCATCTTTG
65 AAATT-TTCATCTCTA
*
11430 GGAATACTCTAACCCCACCATTT
1 GG-ATACTCCAACCCCACCATTT
11453 TTGAGGGGAT
Statistics
Matches: 144, Mismatches: 33, Indels: 8
0.78 0.18 0.04
Matches are distributed among these distances:
79 112 0.78
80 14 0.10
81 18 0.12
ACGTcount: A:0.30, C:0.26, G:0.11, T:0.33
Consensus pattern (79 bp):
GGATACTCCAACCCCACCATTTCCAAGGAGAAACTCCAACCTCATTTTAACTTCCAAAATATTGA
AATTTTCATCTCTA
Found at i:11464 original size:28 final size:28
Alignment explanation
Indices: 11433--11499 Score: 98
Period size: 28 Copynumber: 2.4 Consensus size: 28
11423 ATCTTTGGGA
* *
11433 ATACTCTAACCCCACCATTTTTGAGGGG
1 ATACTCCAACCCCACCATTTCTGAGGGG
*
11461 ATACTCCAACCCCATCATTTCTGAGGGG
1 ATACTCCAACCCCACCATTTCTGAGGGG
*
11489 ACACTCCAACC
1 ATACTCCAACC
11500 TTGTTTTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.27, C:0.34, G:0.15, T:0.24
Consensus pattern (28 bp):
ATACTCCAACCCCACCATTTCTGAGGGG
Found at i:11541 original size:111 final size:109
Alignment explanation
Indices: 11349--11574 Score: 267
Period size: 111 Copynumber: 2.1 Consensus size: 109
11339 TTTCATCTCT
* *
11349 AGGATACTCCAACCCCATCATTTTCAAGGAGATACTCCAACGCCTTTTTATTTTGTAAAACATTG
1 AGGATACTCCAACCCCATCATTTTCAAGGAGACACTCCAACGCCTTTTTATTTTCTAAAACATTG
* *
11414 AATTTCTTCATCTTTGGGAATACTCTAACCCCACCATTTTTGAG
66 AATTTCTTCATCTTTGGGAATACTCCAACCCCACCATTTTCGAG
* * * * *
11458 GGGATACTCCAACCCCATCA-TTTCTGAGGGGACACTCCAAC-CTTGTTTTTTTTTTTCTAAAAC
1 AGGATACTCCAACCCCATCATTTTC-AAGGAGACACTCCAACGC---CTTTTTATTTTCTAAAAC
* * * * * *
11521 ATTGAATTTTTTCATTTTTGGGGATGCTCCAACCTCATCATTTTCGAG
62 ATTGAATTTCTTCATCTTTGGGAATACTCCAACCCCACCATTTTCGAG
11569 AGGATA
1 AGGATA
11575 TTGGGGATAC
Statistics
Matches: 97, Mismatches: 16, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
108 5 0.05
109 32 0.33
111 60 0.62
ACGTcount: A:0.26, C:0.23, G:0.14, T:0.36
Consensus pattern (109 bp):
AGGATACTCCAACCCCATCATTTTCAAGGAGACACTCCAACGCCTTTTTATTTTCTAAAACATTG
AATTTCTTCATCTTTGGGAATACTCCAACCCCACCATTTTCGAG
Found at i:11579 original size:37 final size:37
Alignment explanation
Indices: 11538--11611 Score: 139
Period size: 37 Copynumber: 2.0 Consensus size: 37
11528 TTTTTCATTT
*
11538 TTGGGGATGCTCCAACCTCATCATTTTCGAGAGGATA
1 TTGGGGATACTCCAACCTCATCATTTTCGAGAGGATA
11575 TTGGGGATACTCCAACCTCATCATTTTCGAGAGGATA
1 TTGGGGATACTCCAACCTCATCATTTTCGAGAGGATA
11612 CTTTAACCCC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.26, C:0.22, G:0.23, T:0.30
Consensus pattern (37 bp):
TTGGGGATACTCCAACCTCATCATTTTCGAGAGGATA
Found at i:11779 original size:79 final size:79
Alignment explanation
Indices: 11577--11785 Score: 183
Period size: 80 Copynumber: 2.6 Consensus size: 79
11567 AGAGGATATT
* * * * * ** *
11577 GGGGATACTCCAACCTCATCAT-TTTCG-AGAGGATACTTTAACCCCATTTTTACTTTTAAAACG
1 GGGGATACTCCAACCCCACCATATCT-GAAG-GGATACTCTAACCCAATTTTTACTTCCAAAACA
*
11640 CCAAAATTTTTATCTTA
64 CC-AAATTTTCATCTTA
* * * * * *
11657 GGGGATACTCCAACTCCACTATATTTTAAGGGATACTCCAACCCTATTTTTACTTCCAAAACACC
1 GGGGATACTCCAACCCCACCATATCTGAAGGGATACTCTAACCCAATTTTTACTTCCAAAACACC
11722 -AATTTTACATCTTTA
66 AAATTTT-CATC-TTA
* * *
11737 -GGGATACTCTAACCCCACCATCTCTGAGGGGATACTCTAACCCAATTTT
1 GGGGATACTCCAACCCCACCATATCTGAAGGGATACTCTAACCCAATTTT
11786 CACCAAAAAA
Statistics
Matches: 104, Mismatches: 21, Indels: 9
0.78 0.16 0.07
Matches are distributed among these distances:
78 6 0.06
79 43 0.41
80 50 0.48
81 5 0.05
ACGTcount: A:0.30, C:0.26, G:0.11, T:0.33
Consensus pattern (79 bp):
GGGGATACTCCAACCCCACCATATCTGAAGGGATACTCTAACCCAATTTTTACTTCCAAAACACC
AAATTTTCATCTTA
Found at i:16574 original size:19 final size:21
Alignment explanation
Indices: 16530--16580 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
16520 CAAGTGGAGC
* *
16530 ATGTATCAATACATTCTAATT
1 ATGTATCGATACATTCTAACT
16551 ATGTATCGATACATT-T-ACT
1 ATGTATCGATACATTCTAACT
16570 ATGTATCGATA
1 ATGTATCGATA
16581 TATTATGTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 13 0.46
20 1 0.04
21 14 0.50
ACGTcount: A:0.35, C:0.14, G:0.10, T:0.41
Consensus pattern (21 bp):
ATGTATCGATACATTCTAACT
Done.