Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold4509.1
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: 56062
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.29
Warning! 3582 characters in sequence are not A, C, G, or T
Found at i:1872 original size:12 final size:12
Alignment explanation
Indices: 1857--1887 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
1847 TTCCTTTTGC
1857 TTTTCAAAGGCT
1 TTTTCAAAGGCT
1869 TTTTCAAAGGCT
1 TTTTCAAAGGCT
1881 TTTTCAA
1 TTTTCAA
1888 GTTCTCTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (12 bp):
TTTTCAAAGGCT
Found at i:1964 original size:6 final size:6
Alignment explanation
Indices: 1948--1997 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
1938 TTTCTTTTTA
*
1948 TTTCAT TTTCTT TTTCTT CTCTTGCTT TTTCTT TTTC-T TTTC-T TTTCTT
1 TTTCTT TTTCTT TTTCTT -T-TT-CTT TTTCTT TTTCTT TTTCTT TTTCTT
1997 T
1 T
1998 GTTTTCTCTT
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
5 10 0.26
6 20 0.51
7 3 0.08
8 3 0.08
9 3 0.08
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.76
Consensus pattern (6 bp):
TTTCTT
Found at i:1980 original size:37 final size:37
Alignment explanation
Indices: 1937--2007 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
1927 CTTGCCTCTC
1937 TTTTCTTTTT-ATTTCATTTTCTTT-TTCTTCTCTTGCT
1 TTTTCTTTTTCATTTC-TTTTCTTTGTT-TTCTCTTGCT
*
1974 TTTTCTTTTTCTTTTCTTTTCTTTGTTTTCTCTT
1 TTTTCTTTTTCATTTCTTTTCTTTGTTTTCTCTT
2008 TTACAAGAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 25 0.81
38 6 0.19
ACGTcount: A:0.03, C:0.18, G:0.03, T:0.76
Consensus pattern (37 bp):
TTTTCTTTTTCATTTCTTTTCTTTGTTTTCTCTTGCT
Found at i:2009 original size:16 final size:16
Alignment explanation
Indices: 1933--1993 Score: 63
Period size: 16 Copynumber: 3.8 Consensus size: 16
1923 GCCTCTTGCC
*
1933 TCTCTTTTCTTTTTAT
1 TCTCTTTTCTTTTTCT
1949 T-TCATTTTCTTTTTCT
1 TCTC-TTTTCTTTTTCT
*
1965 TCTC-TTGCTTTTTCTT
1 TCTCTTTTCTTTTTC-T
*
1981 TTTCTTTTCTTTT
1 TCTCTTTTCTTTT
1994 CTTTGTTTTC
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
15 11 0.30
16 17 0.46
17 9 0.24
ACGTcount: A:0.03, C:0.20, G:0.02, T:0.75
Consensus pattern (16 bp):
TCTCTTTTCTTTTTCT
Found at i:2965 original size:12 final size:13
Alignment explanation
Indices: 2950--2989 Score: 57
Period size: 12 Copynumber: 3.2 Consensus size: 13
2940 CTTTTTTTCC
2950 TTTTTTTTCG-AT
1 TTTTTTTTCGAAT
2962 TTTTTTTT-GAAT
1 TTTTTTTTCGAAT
2974 TTTTTTTTCTGAAT
1 TTTTTTTTC-GAAT
2988 TT
1 TT
2990 CTTCTCCTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 1 0.04
12 18 0.72
14 6 0.24
ACGTcount: A:0.12, C:0.05, G:0.07, T:0.75
Consensus pattern (13 bp):
TTTTTTTTCGAAT
Found at i:2978 original size:14 final size:14
Alignment explanation
Indices: 2950--2989 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 14
2940 CTTTTTTTCC
2950 TTTTTTTTC-G-A-
1 TTTTTTTTCTGAAT
2961 TTTTTTTT-TGAAT
1 TTTTTTTTCTGAAT
2974 TTTTTTTTCTGAAT
1 TTTTTTTTCTGAAT
2988 TT
1 TT
2990 CTTCTCCTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
11 9 0.36
12 1 0.04
13 8 0.32
14 7 0.28
ACGTcount: A:0.12, C:0.05, G:0.07, T:0.75
Consensus pattern (14 bp):
TTTTTTTTCTGAAT
Found at i:4083 original size:9 final size:10
Alignment explanation
Indices: 4076--4138 Score: 56
Period size: 11 Copynumber: 6.0 Consensus size: 10
4066 AAGAGAAAAC
4076 AAAGAAAAGA
1 AAAGAAAAGA
4086 AAAGAAAAAGA
1 AAAG-AAAAGA
**
4097 AAAGGCAAGA
1 AAAGAAAAGA
*
4107 GAAGAAAAAGA
1 AAAG-AAAAGA
4118 AAATGAAATA-A
1 AAA-GAAA-AGA
4129 AAAGAAAAGA
1 AAAGAAAAGA
4139 GAGGCAAGAG
Statistics
Matches: 42, Mismatches: 6, Indels: 10
0.72 0.10 0.17
Matches are distributed among these distances:
9 1 0.02
10 16 0.38
11 23 0.55
12 2 0.05
ACGTcount: A:0.75, C:0.02, G:0.21, T:0.03
Consensus pattern (10 bp):
AAAGAAAAGA
Found at i:4086 original size:5 final size:5
Alignment explanation
Indices: 4076--4138 Score: 56
Period size: 5 Copynumber: 12.0 Consensus size: 5
4066 AAGAGAAAAC
* * *
4076 AAAGA AAAGA AAAGAA AAAGA AAAGG CAAGA GAAGAA AAAGA AAATGA
1 AAAGA AAAGA AAAG-A AAAGA AAAGA AAAGA AAAG-A AAAGA AAA-GA
4124 AATA-A AAAGA AAAGA
1 AA-AGA AAAGA AAAGA
4139 GAGGCAAGAG
Statistics
Matches: 48, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
4 1 0.02
5 33 0.69
6 13 0.27
7 1 0.02
ACGTcount: A:0.75, C:0.02, G:0.21, T:0.03
Consensus pattern (5 bp):
AAAGA
Found at i:4095 original size:16 final size:16
Alignment explanation
Indices: 4076--4138 Score: 58
Period size: 16 Copynumber: 3.9 Consensus size: 16
4066 AAGAGAAAAC
4076 AAAGAAAAGAAAAGAA
1 AAAGAAAAGAAAAGAA
**
4092 AAAGAAAAGGCAAG-A
1 AAAGAAAAGAAAAGAA
*
4107 GAAGAAAAAGAAAATGAA
1 AAAG-AAAAGAAAA-GAA
*
4125 ATA-AAAAGAAAAGA
1 AAAGAAAAGAAAAGA
4139 GAGGCAAGAG
Statistics
Matches: 37, Mismatches: 7, Indels: 7
0.73 0.14 0.14
Matches are distributed among these distances:
15 6 0.16
16 28 0.76
17 1 0.03
18 2 0.05
ACGTcount: A:0.75, C:0.02, G:0.21, T:0.03
Consensus pattern (16 bp):
AAAGAAAAGAAAAGAA
Found at i:4100 original size:21 final size:21
Alignment explanation
Indices: 4076--4136 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
4066 AAGAGAAAAC
4076 AAAGAAAAGAAAAGAAAAAGA
1 AAAGAAAAGAAAAGAAAAAGA
** *
4097 AAAGGCAAGAGAAGAAAAAGA
1 AAAGAAAAGAAAAGAAAAAGA
4118 AAATGAAATA-AAAAGAAAA
1 AAA-GAAA-AGAAAAGAAAA
4137 GAGAGGCAAG
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
21 21 0.66
22 10 0.31
23 1 0.03
ACGTcount: A:0.75, C:0.02, G:0.20, T:0.03
Consensus pattern (21 bp):
AAAGAAAAGAAAAGAAAAAGA
Found at i:4117 original size:37 final size:37
Alignment explanation
Indices: 4066--4137 Score: 103
Period size: 37 Copynumber: 1.9 Consensus size: 37
4056 CATTCTTGTA
4066 AAGAGAAAACAAAGAAAA-GAAAAGAAAAAGAAAAGGC
1 AAGAGAAAACAAAGAAAATG-AAAGAAAAAGAAAAGGC
*
4103 AAGAGAAGAA-AAAGAAAATGAAATAAAAAGAAAAG
1 AAGAGAA-AACAAAGAAAATGAAAGAAAAAGAAAAG
4138 AGAGGCAAGA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 29 0.91
38 3 0.09
ACGTcount: A:0.74, C:0.03, G:0.21, T:0.03
Consensus pattern (37 bp):
AAGAGAAAACAAAGAAAATGAAAGAAAAAGAAAAGGC
Found at i:4218 original size:11 final size:12
Alignment explanation
Indices: 4186--4216 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
4176 TTGAGAGAAC
4186 TTGAAAAAGCCT
1 TTGAAAAAGCCT
4198 TTGAAAAAGCCT
1 TTGAAAAAGCCT
4210 TTGAAAA
1 TTGAAAA
4217 GCAAAAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:6164 original size:10 final size:9
Alignment explanation
Indices: 6124--6166 Score: 59
Period size: 9 Copynumber: 4.6 Consensus size: 9
6114 TATACAAGTT
6124 AAAAAAATA
1 AAAAAAATA
*
6133 AAAAAAATTG
1 AAAAAAA-TA
6143 AAAAAAATA
1 AAAAAAATA
6152 AAAAAAATCA
1 AAAAAAAT-A
6162 AAAAA
1 AAAAA
6167 GAAAAGTGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
9 16 0.53
10 14 0.47
ACGTcount: A:0.84, C:0.02, G:0.02, T:0.12
Consensus pattern (9 bp):
AAAAAAATA
Found at i:6165 original size:19 final size:19
Alignment explanation
Indices: 6124--6166 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
6114 TATACAAGTT
**
6124 AAAAAAATAAAAAAAATTG
1 AAAAAAATAAAAAAAATCA
6143 AAAAAAATAAAAAAAATCA
1 AAAAAAATAAAAAAAATCA
6162 AAAAA
1 AAAAA
6167 GAAAAGTGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.84, C:0.02, G:0.02, T:0.12
Consensus pattern (19 bp):
AAAAAAATAAAAAAAATCA
Found at i:11080 original size:30 final size:30
Alignment explanation
Indices: 11046--11142 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
11036 TAAACTAAAA
11046 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
11076 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
* *
11106 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
11136 TGAGCTA
1 TGAGCTA
11143 GGAGTGAGCT
Statistics
Matches: 50, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
29 2 0.04
30 42 0.84
31 6 0.12
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:13327 original size:30 final size:30
Alignment explanation
Indices: 13256--13338 Score: 89
Period size: 30 Copynumber: 2.7 Consensus size: 30
13246 CTTTTGTTTC
* *
13256 AATTTCTTTTTCATCTTCTTTTTCATTCTCA
1 AATTTCTTTTTCTTC-TCTTTTTCAATCTCA
13287 AATTTC-TTTTCGTTCTCTTTTTCAATCTC-
1 AATTTCTTTTTC-TTCTCTTTTTCAATCTCA
* *
13316 ATTTTCTTTTTCATTTTCTTTTT
1 AATTTCTTTTTC-TTCTCTTTTT
13339 GCTTTTCAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
29 5 0.11
30 32 0.71
31 8 0.18
ACGTcount: A:0.13, C:0.20, G:0.01, T:0.65
Consensus pattern (30 bp):
AATTTCTTTTTCTTCTCTTTTTCAATCTCA
Found at i:13338 original size:18 final size:18
Alignment explanation
Indices: 13289--13344 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
13279 CATTCTCAAA
* *
13289 TTTC-TTTTCGTTCTCTT
1 TTTCATTTTCATTTTCTT
* *
13306 TTTCAATCTCATTTTCTT
1 TTTCATTTTCATTTTCTT
*
13324 TTTCATTTTCTTTTTGCTT
1 TTTCATTTTCATTTT-CTT
13343 TT
1 TT
13345 CAAAGGCTTT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 4 0.13
18 21 0.70
19 5 0.17
ACGTcount: A:0.07, C:0.20, G:0.04, T:0.70
Consensus pattern (18 bp):
TTTCATTTTCATTTTCTT
Found at i:13345 original size:12 final size:12
Alignment explanation
Indices: 13252--13338 Score: 59
Period size: 12 Copynumber: 7.2 Consensus size: 12
13242 GTTTCTTTTG
*
13252 TTTCAATTTCTT
1 TTTCATTTTCTT
*
13264 TTTCATCTTCTT
1 TTTCATTTTCTT
* **
13276 TTTCATTCTCAAA
1 TTTCATTTTC-TT
*
13289 TTTC-TTTTCGT
1 TTTCATTTTCTT
* * **
13300 TCTCTTTTTCAA
1 TTTCATTTTCTT
*
13312 TCTCATTTTCTT
1 TTTCATTTTCTT
13324 TTTCATTTTCTT
1 TTTCATTTTCTT
13336 TTT
1 TTT
13339 GCTTTTCAAA
Statistics
Matches: 57, Mismatches: 16, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
11 3 0.05
12 50 0.88
13 4 0.07
ACGTcount: A:0.13, C:0.21, G:0.01, T:0.66
Consensus pattern (12 bp):
TTTCATTTTCTT
Found at i:13473 original size:16 final size:16
Alignment explanation
Indices: 13405--13474 Score: 83
Period size: 16 Copynumber: 4.4 Consensus size: 16
13395 GCCTCTTGCC
13405 TCTCTTTTCTTTTTAT
1 TCTCTTTTCTTTTTAT
*
13421 T-TCGTTTTCTTTTTCT
1 TCTC-TTTTCTTTTTAT
13437 TCT-TTTTCTTTTTAT
1 TCTCTTTTCTTTTTAT
*
13452 TTTCTTTTCTTTGTT-T
1 TCTCTTTTCTTT-TTAT
13468 TCTCTTT
1 TCTCTTT
13475 ACAAGAATGT
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
15 15 0.33
16 28 0.61
17 3 0.07
ACGTcount: A:0.03, C:0.17, G:0.03, T:0.77
Consensus pattern (16 bp):
TCTCTTTTCTTTTTAT
Found at i:16131 original size:30 final size:30
Alignment explanation
Indices: 16097--16193 Score: 81
Period size: 30 Copynumber: 3.2 Consensus size: 30
16087 TAAACTAAAA
* *
16097 TGAGCTAAGCTTTATCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAACTCGTGAGTTAAAGT
* * * * *
16127 TGAGCTGAGGC-TAAACTCCTAAGTTGAAGT
1 TGAGCT-AAGCTTTAACTCGTGAGTTAAAGT
* *
16157 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAACTCGTGAGTT-AAAGT
16187 TGAGCTA
1 TGAGCTA
16194 GGAGTCAGCT
Statistics
Matches: 50, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
29 2 0.04
30 42 0.84
31 6 0.12
ACGTcount: A:0.28, C:0.14, G:0.28, T:0.30
Consensus pattern (30 bp):
TGAGCTAAGCTTTAACTCGTGAGTTAAAGT
Found at i:16204 original size:41 final size:41
Alignment explanation
Indices: 16159--16255 Score: 169
Period size: 41 Copynumber: 2.4 Consensus size: 41
16149 GTTGAAGTTG
16159 AGCTAAGGTTTAGCTCGTGAGTTGAAAGTGAGCTAGGAGTC
1 AGCTAAGGTTTAGCTCGTGAGTTGAAAGTGAGCTAGGAGTC
*
16200 AGCTAAGGTTTAGCTCGTGAGTTGAAAGTGAGCTAGGAGTG
1 AGCTAAGGTTTAGCTCGTGAGTTGAAAGTGAGCTAGGAGTC
*
16241 AGCT-CGGTTTAGCTC
1 AGCTAAGGTTTAGCTC
16256 AGGCAAGATG
Statistics
Matches: 54, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
40 10 0.19
41 44 0.81
ACGTcount: A:0.25, C:0.13, G:0.34, T:0.28
Consensus pattern (41 bp):
AGCTAAGGTTTAGCTCGTGAGTTGAAAGTGAGCTAGGAGTC
Found at i:18993 original size:30 final size:30
Alignment explanation
Indices: 18898--18994 Score: 81
Period size: 30 Copynumber: 3.2 Consensus size: 30
18888 AGCTCACTCC
* *
18898 TAGCTC-ACTTTCAACTCACAAGCTAAACCT
1 TAGCTCAACTTT-AGCTCACAAGCTAAAGCT
* * ** **
18928 TAGCTCAACTTCAGCTTAGGAG-TTTAGCCT
1 TAGCTCAACTTTAGCTCACAAGCTAAAG-CT
*
18958 CAGCTCAACTTTAGCTCACAAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACAAGCTAAAGCT
18988 TAGCTCA
1 TAGCTCA
18995 TTTTAGTTTA
Statistics
Matches: 48, Mismatches: 16, Indels: 6
0.69 0.23 0.09
Matches are distributed among these distances:
29 2 0.04
30 39 0.81
31 7 0.15
ACGTcount: A:0.30, C:0.29, G:0.13, T:0.28
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACAAGCTAAAGCT
Found at i:19425 original size:59 final size:59
Alignment explanation
Indices: 19353--19471 Score: 229
Period size: 59 Copynumber: 2.0 Consensus size: 59
19343 CTTGATTCCC
19353 TCGAGCTTCCATAGGGACCAATGACCCGAGCTAGGTCCAAGCGATTTCATGAAGTTGTT
1 TCGAGCTTCCATAGGGACCAATGACCCGAGCTAGGTCCAAGCGATTTCATGAAGTTGTT
*
19412 TCGAGCTTCCATAGGGACCAATGACCCGAGCTAGGTCCAAGTGATTTCATGAAGTTGTT
1 TCGAGCTTCCATAGGGACCAATGACCCGAGCTAGGTCCAAGCGATTTCATGAAGTTGTT
19471 T
1 T
19472 TAGCTTTGTT
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 59 1.00
ACGTcount: A:0.25, C:0.23, G:0.25, T:0.27
Consensus pattern (59 bp):
TCGAGCTTCCATAGGGACCAATGACCCGAGCTAGGTCCAAGCGATTTCATGAAGTTGTT
Found at i:19631 original size:10 final size:10
Alignment explanation
Indices: 19615--19672 Score: 64
Period size: 10 Copynumber: 5.7 Consensus size: 10
19605 CAACTCCGAC
19615 CAGCTCAATT
1 CAGCTCAATT
* *
19625 GAGCTCATTT
1 CAGCTCAATT
19635 CAGCTCAA-T
1 CAGCTCAATT
19644 CGAGCTCAATT
1 C-AGCTCAATT
*
19655 TAGCTACAATT
1 CAGCT-CAATT
19666 CAGCTCA
1 CAGCTCA
19673 TTTATTTTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 2 0.05
10 27 0.69
11 10 0.26
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:19638 original size:20 final size:20
Alignment explanation
Indices: 19615--19675 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
19605 CAACTCCGAC
19615 CAGCTCAATTGAGCTCATTT
1 CAGCTCAATTGAGCTCATTT
*
19635 CAGCTCAATCGAGCTCAATTT
1 CAGCTCAATTGAGCTC-ATTT
*
19656 -AGCTACAATTCAGCTCATTT
1 CAGCT-CAATTGAGCTCATTT
19676 ATTTTATTGG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (20 bp):
CAGCTCAATTGAGCTCATTT
Found at i:27529 original size:11 final size:12
Alignment explanation
Indices: 27526--27558 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
27516 AAAAATCAAA
27526 AAAAAAAGAAGTC
1 AAAAAAA-AAGTC
27539 AAAAAAAAA-TC
1 AAAAAAAAAGTC
27550 AAAAAAAAA
1 AAAAAAAAA
27559 AAATTTTAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 11 0.55
12 2 0.10
13 7 0.35
ACGTcount: A:0.82, C:0.06, G:0.06, T:0.06
Consensus pattern (12 bp):
AAAAAAAAAGTC
Found at i:27540 original size:16 final size:14
Alignment explanation
Indices: 27513--27562 Score: 61
Period size: 14 Copynumber: 3.6 Consensus size: 14
27503 GTTCATAACG
27513 AAAAAAAATCAAAA
1 AAAAAAAATCAAAA
27527 AAAAAAGAAGTC---A
1 AAAAAA-AA-TCAAAA
27540 AAAAAAAATCAAAA
1 AAAAAAAATCAAAA
27554 AAAAAAAAT
1 AAAAAAAAT
27563 TTTAAGTTGG
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
11 2 0.06
12 2 0.06
13 7 0.23
14 16 0.52
15 2 0.06
16 2 0.06
ACGTcount: A:0.82, C:0.06, G:0.04, T:0.08
Consensus pattern (14 bp):
AAAAAAAATCAAAA
Found at i:27561 original size:15 final size:16
Alignment explanation
Indices: 27513--27547 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
27503 GTTCATAACG
27513 AAAAA-AAATCAAAAA
1 AAAAAGAAATCAAAAA
*
27528 AAAAAGAAGTCAAAAA
1 AAAAAGAAATCAAAAA
27544 AAAA
1 AAAA
27548 TCAAAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.83, C:0.06, G:0.06, T:0.06
Consensus pattern (16 bp):
AAAAAGAAATCAAAAA
Found at i:27661 original size:12 final size:13
Alignment explanation
Indices: 27637--27676 Score: 64
Period size: 13 Copynumber: 3.1 Consensus size: 13
27627 AAAGGAGAAG
27637 AAATTCAAAAAAA
1 AAATTCAAAAAAA
27650 AAATTCAAAAAAA
1 AAATTCAAAAAAA
27663 AAA-TCGAAAAAAA
1 AAATTC-AAAAAAA
27676 A
1 A
27677 GGAAAAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
12 2 0.08
13 24 0.92
ACGTcount: A:0.78, C:0.07, G:0.03, T:0.12
Consensus pattern (13 bp):
AAATTCAAAAAAA
Found at i:27684 original size:12 final size:13
Alignment explanation
Indices: 27642--27700 Score: 52
Period size: 13 Copynumber: 4.7 Consensus size: 13
27632 AGAAGAAATT
* *
27642 CAAAAAAAAAATT
1 CAAAAAAAAAGTG
*
27655 CAAAAAAAAAAT-
1 CAAAAAAAAAGTG
*
27667 CGAAAAAAAAG-G
1 CAAAAAAAAAGTG
27679 -AAAAAAAAAGTG
1 CAAAAAAAAAGTG
27691 ACAAAAAAAA
1 -CAAAAAAAA
27701 TCGAGTTAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
11 9 0.23
12 10 0.26
13 12 0.31
14 8 0.21
ACGTcount: A:0.78, C:0.07, G:0.08, T:0.07
Consensus pattern (13 bp):
CAAAAAAAAAGTG
Found at i:27687 original size:11 final size:13
Alignment explanation
Indices: 27669--27700 Score: 50
Period size: 11 Copynumber: 2.6 Consensus size: 13
27659 AAAAAAATCG
27669 AAAAAAAAG-GA-
1 AAAAAAAAGTGAC
27680 AAAAAAAAGTGAC
1 AAAAAAAAGTGAC
27693 AAAAAAAA
1 AAAAAAAA
27701 TCGAGTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 9 0.47
12 2 0.11
13 8 0.42
ACGTcount: A:0.81, C:0.03, G:0.12, T:0.03
Consensus pattern (13 bp):
AAAAAAAAGTGAC
Found at i:28668 original size:37 final size:37
Alignment explanation
Indices: 28617--28687 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
28607 CATTCTTGTA
28617 AAGAGAAAACAAAGAAAA-GAAAAGAAAAAGAAAAAGC
1 AAGAGAAAACAAAGAAAATG-AAAGAAAAAGAAAAAGC
*
28654 AAGAGAAGAA-AAAGAAAATGAAATAAAAAGAAAA
1 AAGAGAA-AACAAAGAAAATGAAAGAAAAAGAAAA
28688 GAGAGGCAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 28 0.90
38 3 0.10
ACGTcount: A:0.76, C:0.03, G:0.18, T:0.03
Consensus pattern (37 bp):
AAGAGAAAACAAAGAAAATGAAAGAAAAAGAAAAAGC
Found at i:28687 original size:6 final size:6
Alignment explanation
Indices: 28627--28676 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
28617 AAGAGAAAAC
*
28627 AAAG-A AAAG-A AAAGAA AAAGAA AAAGCAA GAGAAGAA AAAGAA AATGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAG-AA -A-AAGAA AAAGAA AAAGAA
28676 A
1 A
28677 TAAAAAGAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
5 9 0.22
6 22 0.55
7 3 0.08
8 3 0.08
9 3 0.08
ACGTcount: A:0.76, C:0.02, G:0.20, T:0.02
Consensus pattern (6 bp):
AAAGAA
Found at i:28769 original size:11 final size:12
Alignment explanation
Indices: 28737--28767 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
28727 TTGAGAGAAC
28737 TTGAAAAAGCCT
1 TTGAAAAAGCCT
28749 TTGAAAAAGCCT
1 TTGAAAAAGCCT
28761 TTGAAAA
1 TTGAAAA
28768 GCAAAAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:31042 original size:30 final size:30
Alignment explanation
Indices: 30947--31043 Score: 88
Period size: 30 Copynumber: 3.2 Consensus size: 30
30937 AGCTCACTCC
*
30947 TAGCTCATA-TTTAGCTCTCGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * * *
30977 TGGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
31007 CAGCTCAACTTTAGCTCACGAGCTAAAACT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
31037 TAGCTCA
1 TAGCTCA
31044 TTTTAGTTTA
Statistics
Matches: 48, Mismatches: 18, Indels: 2
0.71 0.26 0.03
Matches are distributed among these distances:
29 1 0.02
30 47 0.98
ACGTcount: A:0.27, C:0.27, G:0.16, T:0.30
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:36774 original size:20 final size:20
Alignment explanation
Indices: 36751--36798 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
36741 AGCTCCGTCC
36751 AGCTCAACTCAGCTCATTTG
1 AGCTCAACTCAGCTCATTTG
*** * *
36771 AGCTCGTTTTAGCTCGTTTG
1 AGCTCAACTCAGCTCATTTG
36791 AGCTCAAC
1 AGCTCAAC
36799 CGAGCTTACT
Statistics
Matches: 20, Mismatches: 8, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.21, C:0.27, G:0.19, T:0.33
Consensus pattern (20 bp):
AGCTCAACTCAGCTCATTTG
Found at i:40937 original size:42 final size:42
Alignment explanation
Indices: 40875--40971 Score: 142
Period size: 42 Copynumber: 2.3 Consensus size: 42
40865 AGATTATGAG
* * *
40875 AGAAAATGAGAGGATTTTGAATGAAATCGAGAGAAGAAACAA
1 AGAAAATGAGAGAATCTTGAATGAAATCGAGAAAAGAAACAA
*
40917 AGAAAATGAGAGAATCTTGAATGAAATCGAGAAAAGAAATAA
1 AGAAAATGAGAGAATCTTGAATGAAATCGAGAAAAGAAACAA
*
40959 AG-AAATGAAAGAA
1 AGAAAATGAGAGAA
40972 AAAAATGAGA
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
41 10 0.20
42 40 0.80
ACGTcount: A:0.57, C:0.04, G:0.24, T:0.15
Consensus pattern (42 bp):
AGAAAATGAGAGAATCTTGAATGAAATCGAGAAAAGAAACAA
Found at i:41004 original size:18 final size:18
Alignment explanation
Indices: 40983--41021 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
40973 AAAATGAGAT
40983 TGAGAGTGAAAAAGAAAA
1 TGAGAGTGAAAAAGAAAA
* *
41001 TGAGATTGAAAAAGAGAA
1 TGAGAGTGAAAAAGAAAA
41019 TGA
1 TGA
41022 AAAAGAGTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.56, C:0.00, G:0.28, T:0.15
Consensus pattern (18 bp):
TGAGAGTGAAAAAGAAAA
Found at i:41023 original size:24 final size:24
Alignment explanation
Indices: 40973--41033 Score: 59
Period size: 24 Copynumber: 2.5 Consensus size: 24
40963 ATGAAAGAAA
* **
40973 AAAATGAGATTGAGAGTGAAAAAG
1 AAAATGAGATTGAAAAAGAAAAAG
* *
40997 AAAATGAGATTGAAAAAGAGAATG
1 AAAATGAGATTGAAAAAGAAAAAG
* *
41021 AAAAAGAGTTTGA
1 AAAATGAGATTGA
41034 GAGGGTACAT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.56, C:0.00, G:0.26, T:0.18
Consensus pattern (24 bp):
AAAATGAGATTGAAAAAGAAAAAG
Found at i:44579 original size:29 final size:30
Alignment explanation
Indices: 44547--44603 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 30
44537 TTCTTCCACG
* *
44547 CTTT-CTTT-TTGCTCACTCTCTCTTTTCAA
1 CTTTACTTTCTTGCACACACTCT-TTTTCAA
44576 CTTTACTTTCTTGCACACACTCTTTTTC
1 CTTTACTTTCTTGCACACACTCTTTTTC
44604 TTTTTCGCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 4 0.17
30 9 0.38
31 11 0.46
ACGTcount: A:0.12, C:0.32, G:0.04, T:0.53
Consensus pattern (30 bp):
CTTTACTTTCTTGCACACACTCTTTTTCAA
Found at i:50598 original size:17 final size:17
Alignment explanation
Indices: 50568--50622 Score: 65
Period size: 19 Copynumber: 3.1 Consensus size: 17
50558 AGCAACTCAT
50568 TTATTAATCTAAGATGAG
1 TTATTAA-CTAAGATGAG
*
50586 TTATTAACTAAGATGAAC
1 TTATTAACTAAGATG-AG
*
50604 TCAATTAACTAAGATGAG
1 T-TATTAACTAAGATGAG
50622 T
1 T
50623 AATTTATTCA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
17 8 0.25
18 11 0.34
19 13 0.41
ACGTcount: A:0.42, C:0.09, G:0.15, T:0.35
Consensus pattern (17 bp):
TTATTAACTAAGATGAG
Done.