Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold649
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: 46039
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.32
Found at i:11731 original size:52 final size:52
Alignment explanation
Indices: 11583--11711 Score: 240
Period size: 52 Copynumber: 2.5 Consensus size: 52
11573 CGAAATATGA
11583 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
* *
11635 CAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
11687 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
11712 AAGATCAGTG
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 74 1.00
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
Found at i:11738 original size:13 final size:13
Alignment explanation
Indices: 11720--11744 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11710 CAAAGATCAG
11720 TGTATCGATACAA
1 TGTATCGATACAA
11733 TGTATCGATACA
1 TGTATCGATACA
11745 TTTTTTGGCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:11802 original size:32 final size:32
Alignment explanation
Indices: 11761--11842 Score: 146
Period size: 32 Copynumber: 2.6 Consensus size: 32
11751 GGCAGTAGCT
11761 TACATTGTATCGATACAAAACTTATATATCGA
1 TACATTGTATCGATACAAAACTTATATATCGA
* *
11793 TACATTGTATCGATACAACACTTATGTATCGA
1 TACATTGTATCGATACAAAACTTATATATCGA
11825 TACATTGTATCGATACAA
1 TACATTGTATCGATACAA
11843 TATTTTATGA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 48 1.00
ACGTcount: A:0.38, C:0.17, G:0.11, T:0.34
Consensus pattern (32 bp):
TACATTGTATCGATACAAAACTTATATATCGA
Found at i:11805 original size:13 final size:13
Alignment explanation
Indices: 11787--11841 Score: 56
Period size: 13 Copynumber: 3.8 Consensus size: 13
11777 AAAACTTATA
11787 TATCGATACATTG
1 TATCGATACATTG
11800 TATCGATACAACACTTATG
1 TATCGAT---ACA--T-TG
11819 TATCGATACATTG
1 TATCGATACATTG
11832 TATCGATACA
1 TATCGATACA
11842 ATATTTTATG
Statistics
Matches: 36, Mismatches: 0, Indels: 12
0.75 0.00 0.25
Matches are distributed among these distances:
13 19 0.53
14 1 0.03
16 6 0.17
18 1 0.03
19 9 0.25
ACGTcount: A:0.35, C:0.18, G:0.13, T:0.35
Consensus pattern (13 bp):
TATCGATACATTG
Found at i:11822 original size:19 final size:19
Alignment explanation
Indices: 11766--11828 Score: 66
Period size: 19 Copynumber: 3.6 Consensus size: 19
11756 TAGCTTACAT
*
11766 TGTATCGATACAAAACTTA
1 TGTATCGATACAACACTTA
*
11785 TATATCGAT---ACA--T-
1 TGTATCGATACAACACTTA
11798 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
11817 TGTATCGATACA
1 TGTATCGATACA
11829 TTGTATCGAT
Statistics
Matches: 35, Mismatches: 3, Indels: 12
0.70 0.06 0.24
Matches are distributed among these distances:
13 8 0.23
14 1 0.03
16 5 0.14
18 1 0.03
19 20 0.57
ACGTcount: A:0.38, C:0.17, G:0.11, T:0.33
Consensus pattern (19 bp):
TGTATCGATACAACACTTA
Found at i:12705 original size:13 final size:13
Alignment explanation
Indices: 12689--12731 Score: 86
Period size: 13 Copynumber: 3.3 Consensus size: 13
12679 ATACATTGTT
12689 CATTGTATCGATA
1 CATTGTATCGATA
12702 CATTGTATCGATA
1 CATTGTATCGATA
12715 CATTGTATCGATA
1 CATTGTATCGATA
12728 CATT
1 CATT
12732 CTGGGTTTAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 30 1.00
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.40
Consensus pattern (13 bp):
CATTGTATCGATA
Found at i:14896 original size:28 final size:28
Alignment explanation
Indices: 14837--14905 Score: 95
Period size: 28 Copynumber: 2.4 Consensus size: 28
14827 TTCTACAATT
*
14837 GGGAGTACTCCAATCCCGTTATTTCATCG
1 GGGA-TACTCCAATCCCGTTATTTCATAG
14866 GGGATACTCCAATCCCGTTATTTC-TGAG
1 GGGATACTCCAATCCCGTTATTTCAT-AG
*
14894 GGGAAACTCCAA
1 GGGATACTCCAA
14906 CCTCGATTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
27 1 0.03
28 32 0.86
29 4 0.11
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.28
Consensus pattern (28 bp):
GGGATACTCCAATCCCGTTATTTCATAG
Found at i:14954 original size:51 final size:52
Alignment explanation
Indices: 14893--15012 Score: 158
Period size: 51 Copynumber: 2.4 Consensus size: 52
14883 TTATTTCTGA
* * *
14893 GGGGAAACTCCAACCT-CGATTTTA-TTTCTAAAATACCAATTTTTCACAAGC
1 GGGGATACTCCAACCTCCGATTTTATTTTC-AAAACACCAATTTCTCACAAGC
* *
14944 GGGGATACTCCAA-CTCCGATTTTATTTTCAAAACACTAATTTCTCACAATC
1 GGGGATACTCCAACCTCCGATTTTATTTTCAAAACACCAATTTCTCACAAGC
14995 GGGGATACTCCAA-CTCCG
1 GGGGATACTCCAACCTCCG
15013 TTATTTTTGC
Statistics
Matches: 62, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
50 2 0.03
51 56 0.90
52 4 0.06
ACGTcount: A:0.31, C:0.26, G:0.13, T:0.30
Consensus pattern (52 bp):
GGGGATACTCCAACCTCCGATTTTATTTTCAAAACACCAATTTCTCACAAGC
Found at i:15142 original size:157 final size:158
Alignment explanation
Indices: 14945--15251 Score: 415
Period size: 157 Copynumber: 1.9 Consensus size: 158
14935 TTCACAAGCG
* * * *
14945 GGGATACTCCAACTCCGATTTTATTTTCAAAACACTAA-TTTCTCACAATCGGGGATACTCCAAC
1 GGGATACTCCAACCCCAATTTTATTTTCAAAACACCAATTTTCT-ACAATCAGGGATACTCCAAC
* * * *
15009 TCC-GTTATTTTTGCGGGGATACTCCAACCCCGGCCTTA-TTTCTAAAGCATCGATTTTCCACAA
65 -CCTGTTATTTCTGAGGGGATACTCCAACCCCGACCTTATTTTC-AAAACATCGATTTTCCACAA
15072 TCA-GGGATACTCCAACCCCGTTATTTTCGA
128 TCAGGGGATACTCCAACCCCGTTATTTTCGA
*
15102 GGGATACTCCAACCCCAATTTTATTTTCAAAACACCAATTTTCTATAATCAGGGATACTCCAACC
1 GGGATACTCCAACCCCAATTTTATTTTCAAAACACCAATTTTCTACAATCAGGGATACTCCAACC
** * * *
15167 CTGTTATTTCTGAGGGGATACTCCAACCCCGATTTTATTTTCAAAATATTGATTTTCCATAATCA
66 CTGTTATTTCTGAGGGGATACTCCAACCCCGACCTTATTTTCAAAACATCGATTTTCCACAATCA
* *
15232 GGGGATACTTCAGCCCCGTT
131 GGGGATACTCCAACCCCGTT
15252 GTCATCCCCA
Statistics
Matches: 130, Mismatches: 16, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
156 2 0.02
157 102 0.78
158 26 0.20
ACGTcount: A:0.27, C:0.26, G:0.14, T:0.32
Consensus pattern (158 bp):
GGGATACTCCAACCCCAATTTTATTTTCAAAACACCAATTTTCTACAATCAGGGATACTCCAACC
CTGTTATTTCTGAGGGGATACTCCAACCCCGACCTTATTTTCAAAACATCGATTTTCCACAATCA
GGGGATACTCCAACCCCGTTATTTTCGA
Found at i:15152 original size:78 final size:78
Alignment explanation
Indices: 14945--15251 Score: 334
Period size: 79 Copynumber: 3.9 Consensus size: 78
14935 TTCACAAGCG
* * *
14945 GGGATACTCCAACTCCGATTTTATTTTCAAAACACTAA-TTTCTCACAATCGGGGATACTCCAAC
1 GGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTC-CACAATCAGGGATACTCCAAC
*
15009 TCCGTTATTTTTGCG-
65 CCCGTTA-TTTT-CGA
*** * * *
15024 GGGATACTCCAACCCCGGCCTTA-TTTCTAAAGCATCGATTTTCCACAATCAGGGATACTCCAAC
1 GGGATACTCCAACCCCGATTTTATTTTC-AAAACACCAATTTTCCACAATCAGGGATACTCCAAC
15088 CCCGTTATTTTCGA
65 CCCGTTATTTTCGA
* * *
15102 GGGATACTCCAACCCCAATTTTATTTTCAAAACACCAATTTTCTATAATCAGGGATACTCCAACC
1 GGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCCACAATCAGGGATACTCCAACC
*
15167 CTGTTA-TTTCTGA
66 CCGTTATTTTC-GA
* *** * * *
15180 GGGGATACTCCAACCCCGATTTTATTTTCAAAATATTGATTTTCCATAATCAGGGGATACTTCAG
1 -GGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCCACAATCA-GGGATACTCCAA
15245 CCCCGTT
64 CCCCGTT
15252 GTCATCCCCA
Statistics
Matches: 192, Mismatches: 29, Indels: 13
0.82 0.12 0.06
Matches are distributed among these distances:
77 6 0.03
78 66 0.34
79 100 0.52
80 20 0.10
ACGTcount: A:0.27, C:0.26, G:0.14, T:0.32
Consensus pattern (78 bp):
GGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCCACAATCAGGGATACTCCAACC
CCGTTATTTTCGA
Found at i:15527 original size:31 final size:31
Alignment explanation
Indices: 15487--15555 Score: 129
Period size: 31 Copynumber: 2.2 Consensus size: 31
15477 TTATCCACAC
*
15487 TCATTAAAAATTGGTACCATTCATTAAACTT
1 TCATCAAAAATTGGTACCATTCATTAAACTT
15518 TCATCAAAAATTGGTACCATTCATTAAACTT
1 TCATCAAAAATTGGTACCATTCATTAAACTT
15549 TCATCAA
1 TCATCAA
15556 TTGGTATCAA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.39, C:0.19, G:0.06, T:0.36
Consensus pattern (31 bp):
TCATCAAAAATTGGTACCATTCATTAAACTT
Found at i:16310 original size:87 final size:87
Alignment explanation
Indices: 16164--16343 Score: 290
Period size: 87 Copynumber: 2.1 Consensus size: 87
16154 ATTCGGTTTA
* *
16164 AATTTGGTTTTATCAACTTAGCTTATAACACAAAGGGGGAGAAATTATTGTTTATTGGTTTAAGG
1 AATTTGGTTTTATCAACTTAGCTTATAACACAAAGGGAGAGAAATTATTATTTATTGGTTTAAGG
16229 GTGAGAACATATT-AAGGGGGAG
66 GTGAGAACATATTGAA-GGGGAG
* *
16251 AATTTGGTTTTATCAACTTAGTTTATAACACAAAGGGAGAGAGATTATTATTTATTGGTTTAAGG
1 AATTTGGTTTTATCAACTTAGCTTATAACACAAAGGGAGAGAAATTATTATTTATTGGTTTAAGG
*
16316 GTGAGAACGTATTGAAGGGGAG
66 GTGAGAACATATTGAAGGGGAG
*
16338 AGTTTG
1 AATTTG
16344 CATAAAATTC
Statistics
Matches: 86, Mismatches: 6, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
87 84 0.98
88 2 0.02
ACGTcount: A:0.33, C:0.06, G:0.27, T:0.34
Consensus pattern (87 bp):
AATTTGGTTTTATCAACTTAGCTTATAACACAAAGGGAGAGAAATTATTATTTATTGGTTTAAGG
GTGAGAACATATTGAAGGGGAG
Found at i:17099 original size:21 final size:21
Alignment explanation
Indices: 17056--17099 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
17046 GTTAAGTATA
*
17056 AATGTTTTTCAAGCATAAGAAT
1 AATGTTTTTCAAG-ATAAAAAT
17078 AATGTTTTTCAA-AGTAAAAAT
1 AATGTTTTTCAAGA-TAAAAAT
17099 A
1 A
17100 TTTCAAAGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 1 0.05
21 7 0.35
22 12 0.60
ACGTcount: A:0.45, C:0.07, G:0.11, T:0.36
Consensus pattern (21 bp):
AATGTTTTTCAAGATAAAAAT
Found at i:17236 original size:13 final size:13
Alignment explanation
Indices: 17218--17242 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17208 ATATTGCTTA
17218 GTATCGATACATT
1 GTATCGATACATT
17231 GTATCGATACAT
1 GTATCGATACAT
17243 GTTCTTGGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:17259 original size:32 final size:33
Alignment explanation
Indices: 17197--17261 Score: 105
Period size: 32 Copynumber: 2.0 Consensus size: 33
17187 CACACCCAGA
17197 TGTATCGATACATATTGCTTAGTATCGATACAT
1 TGTATCGATACATATTGCTTAGTATCGATACAT
* *
17230 TGTATCGATACATGTT-CTTGGTATCGATACAT
1 TGTATCGATACATATTGCTTAGTATCGATACAT
17262 ATGGAATTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 15 0.50
33 15 0.50
ACGTcount: A:0.28, C:0.15, G:0.17, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATATTGCTTAGTATCGATACAT
Found at i:17830 original size:32 final size:30
Alignment explanation
Indices: 17789--17942 Score: 127
Period size: 32 Copynumber: 4.8 Consensus size: 30
17779 TGATTGAGAA
17789 GTTCTATCTTAGACTTG-AAAGATAGTATAGAG
1 GTTCTATCTTAG-CTTGAAAAGATAG-A-AGAG
*
17821 GTTCTATCTTAGCCTTTGTAAAAGATAG-GGAG
1 GTTCTATCTTAG-C-TTG-AAAAGATAGAAGAG
*
17853 GTTCTATCTTAGCCTGCAAAAGATAGGGAAGAG
1 GTTCTATCTTAGCTTG-AAAAGATA--GAAGAG
* *
17886 GTTCTACCTTAGCTCGCGAAAAGATAG-AGAG
1 GTTCTATCTTAGCT--TGAAAAGATAGAAGAG
17917 GTTTCTATCTTAGCCTTG-AAAGATAG
1 G-TTCTATCTTAG-CTTGAAAAGATAG
17943 TATTGTAAGG
Statistics
Matches: 102, Mismatches: 10, Indels: 22
0.76 0.07 0.16
Matches are distributed among these distances:
30 18 0.18
31 7 0.07
32 40 0.39
33 20 0.20
34 8 0.08
35 9 0.09
ACGTcount: A:0.31, C:0.14, G:0.24, T:0.31
Consensus pattern (30 bp):
GTTCTATCTTAGCTTGAAAAGATAGAAGAG
Found at i:17897 original size:33 final size:31
Alignment explanation
Indices: 17817--17932 Score: 130
Period size: 32 Copynumber: 3.6 Consensus size: 31
17807 AAGATAGTAT
*
17817 AGAGGTTCTATCTTAGCCTTTGTAAAAGATAGG
1 AGAGGTTCTATCTTAGCC--TGCAAAAGATAGG
17850 -GAGGTTCTATCTTAGCCTGCAAAAGATAGGG
1 AGAGGTTCTATCTTAGCCTGCAAAAGATA-GG
*
17881 AAGAGGTTCTACCTTAG-CTCGCGAAAAGATA-G
1 -AGAGGTTCTATCTTAGCCT-GC-AAAAGATAGG
17913 AGAGGTTTCTATCTTAGCCT
1 AGAGG-TTCTATCTTAGCCT
17933 TGAAAGATAG
Statistics
Matches: 73, Mismatches: 3, Indels: 14
0.81 0.03 0.16
Matches are distributed among these distances:
30 10 0.14
31 7 0.10
32 30 0.41
33 18 0.25
34 8 0.11
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.29
Consensus pattern (31 bp):
AGAGGTTCTATCTTAGCCTGCAAAAGATAGG
Found at i:17941 original size:64 final size:65
Alignment explanation
Indices: 17784--17942 Score: 184
Period size: 64 Copynumber: 2.5 Consensus size: 65
17774 TCAAGTGATT
* * * * * *
17784 GAGAAGTTCTATCTTAGACTTGAAAGATA-GTATAGAGGTTCTATCTTAGCCTTTGTAAAAGATA
1 GAGAGGTTCTATCTTAGCCTTGAAAGATAGGGATAGAGGTTCTACCTTAGCCTTCGGAAAAGATA
*
17848 GGGAGGTTCTATCTTAGCC-TGCAAAAGATAGGGA-AGAGGTTCTACCTTAG-C-TCGCGAAAAG
1 GAGAGGTTCTATCTTAGCCTTG--AAAGATAGGGATAGAGGTTCTACCTTAGCCTTCG-GAAAAG
17909 ATA
63 ATA
17912 GAGAGGTTTCTATCTTAGCCTTGAAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTGAAAGATAG
17943 TATTGTAAGG
Statistics
Matches: 81, Mismatches: 8, Indels: 12
0.80 0.08 0.12
Matches are distributed among these distances:
63 4 0.05
64 38 0.47
65 35 0.43
66 4 0.05
ACGTcount: A:0.32, C:0.14, G:0.25, T:0.30
Consensus pattern (65 bp):
GAGAGGTTCTATCTTAGCCTTGAAAGATAGGGATAGAGGTTCTACCTTAGCCTTCGGAAAAGATA
Found at i:18979 original size:20 final size:20
Alignment explanation
Indices: 18954--19008 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
18944 TTTTCATAAT
18954 TTGTATCGATACATTATTCA
1 TTGTATCGATACATTATTCA
* *
18974 TTGTATCGATACACTGTTCA
1 TTGTATCGATACATTATTCA
18994 TTGTATCGATACATT
1 TTGTATCGATACATT
19009 GTATCGATAC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.27, C:0.16, G:0.13, T:0.44
Consensus pattern (20 bp):
TTGTATCGATACATTATTCA
Found at i:19010 original size:13 final size:13
Alignment explanation
Indices: 18992--19021 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
18982 ATACACTGTT
18992 CATTGTATCGATA
1 CATTGTATCGATA
19005 CATTGTATCGATA
1 CATTGTATCGATA
19018 CATT
1 CATT
19022 CTGGGTTTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (13 bp):
CATTGTATCGATA
Found at i:19066 original size:20 final size:20
Alignment explanation
Indices: 19037--19090 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
19027 TTTACCCAGA
*
19037 TGTATCGATACATT-TTGCAT
1 TGTATCGATACATTGCT-CAT
*
19057 TGTATTGATACATTGCTCAT
1 TGTATCGATACATTGCTCAT
19077 TGTATCGATACATT
1 TGTATCGATACATT
19091 ATATCGATAC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
20 29 0.97
21 1 0.03
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.44
Consensus pattern (20 bp):
TGTATCGATACATTGCTCAT
Found at i:19090 original size:13 final size:13
Alignment explanation
Indices: 19074--19103 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
19064 ATACATTGCT
*
19074 CATTGTATCGATA
1 CATTATATCGATA
19087 CATTATATCGATA
1 CATTATATCGATA
19100 CATT
1 CATT
19104 TTGGATTTAC
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:0.33, C:0.17, G:0.10, T:0.40
Consensus pattern (13 bp):
CATTATATCGATA
Found at i:19096 original size:82 final size:81
Alignment explanation
Indices: 18955--19152 Score: 306
Period size: 82 Copynumber: 2.4 Consensus size: 81
18945 TTTCATAATT
* * *
18955 TGTATCGATACATTATTCATTGTATCGATACACTGTTCATTGTATCGATACATTGTATCGATACA
1 TGTATCGATACATT-TTCATTGTATCGATACATTGCTCATTGTATCGATACATTATATCGATACA
*
19020 TTCTGGGTTTACCCAGA
65 TTCTGGATTTACCCAGA
*
19037 TGTATCGATACATTTTGCATTGTATTGATACATTGCTCATTGTATCGATACATTATATCGATACA
1 TGTATCGATACATTTT-CATTGTATCGATACATTGCTCATTGTATCGATACATTATATCGATACA
*
19102 TTTTGGATTTACCCAGA
65 TTCTGGATTTACCCAGA
*
19119 TGTATCGATACATTTTACAATGTATCGATACATT
1 TGTATCGATACATTTT-CATTGTATCGATACATT
19153 CAAGCTTTTT
Statistics
Matches: 106, Mismatches: 9, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
81 2 0.02
82 104 0.98
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (81 bp):
TGTATCGATACATTTTCATTGTATCGATACATTGCTCATTGTATCGATACATTATATCGATACAT
TCTGGATTTACCCAGA
Found at i:20850 original size:28 final size:28
Alignment explanation
Indices: 20821--20894 Score: 94
Period size: 28 Copynumber: 2.6 Consensus size: 28
20811 TTCCACAATC
*
20821 GGGAGTACTCCAATCTTGTTATTTCATCG
1 GGGA-TACTCCAATCTCGTTATTTCATCG
***
20850 GGGATACTCCAATCTCGTTATTTCCGAG
1 GGGATACTCCAATCTCGTTATTTCATCG
*
20878 GGGATACTCCAACCTCG
1 GGGATACTCCAATCTCG
20895 ATTTTATTTC
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
28 36 0.90
29 4 0.10
ACGTcount: A:0.22, C:0.26, G:0.22, T:0.31
Consensus pattern (28 bp):
GGGATACTCCAATCTCGTTATTTCATCG
Found at i:20935 original size:51 final size:52
Alignment explanation
Indices: 20877--20995 Score: 158
Period size: 51 Copynumber: 2.4 Consensus size: 52
20867 TTATTTCCGA
* *
20877 GGGGATACTCCAACCT-CGATTTTATTTCTAAAATACCAAGTTT-TCACAAGC
1 GGGGATACTCCAACCTCCGATTTTATTTCCAAAACACCAA-TTTCTCACAAGC
*
20928 GGGGATACTCCAA-CTCCGATTTTATTTCCAAAACACCAATTTCTCACAATC
1 GGGGATACTCCAACCTCCGATTTTATTTCCAAAACACCAATTTCTCACAAGC
*
20979 -GGAATACTCCAA-CTCCG
1 GGGGATACTCCAACCTCCG
20996 TTATTTTTGT
Statistics
Matches: 62, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
50 21 0.34
51 41 0.66
ACGTcount: A:0.31, C:0.28, G:0.13, T:0.29
Consensus pattern (52 bp):
GGGGATACTCCAACCTCCGATTTTATTTCCAAAACACCAATTTCTCACAAGC
Found at i:21091 original size:79 final size:78
Alignment explanation
Indices: 20928--21235 Score: 307
Period size: 79 Copynumber: 3.9 Consensus size: 78
20918 TTTCACAAGC
* * * ** *
20928 GGGGATACTCCAACTCCGATTTTATTTCCAAAACACCAATTTCTC-ACAATC-GGAATACTCCAA
1 GGGGATACTCCAACCCCAATTTTATTT-TAAAACACTGATTT-TCAACAATCAGGGATACTCCAA
* **
20991 CTCCGTTATTTTTGTA
64 CCCCGTTA-TTTTCAA
**** * *
21007 -GGGATACTCCAACCCCGGCCTTATTTCTAAAGCATTGATTTTCAACAATCAGGGATACTCCAAC
1 GGGGATACTCCAACCCCAATTTTATTT-TAAAACACTGATTTTCAACAATCAGGGATACTCCAAC
21071 CCCGTTATTTTCAA
65 CCCGTTATTTTCAA
* * *
21085 GGGGATACTCCAACCCCAATTTTATTTTCAAAACACTAATTTTCTATAATCAGGGATACTCCAAC
1 GGGGATACTCCAACCCCAATTTTATTTT-AAAACACTGATTTTCAACAATCAGGGATACTCCAAC
** *
21150 CCTATTATTTTCGA
65 CCCGTTATTTTCAA
* * * *
21164 GGGGATACTCCAACCCCAATTTTATTTTTAAAATACTGATTTTCCATAATCAGGGGATACTCCAG
1 GGGGATACTCCAACCCCAATTTTA-TTTTAAAACACTGATTTTCAACAATCA-GGGATACTCCAA
21229 CCCCGTT
64 CCCCGTT
21236 GTCATCTCCA
Statistics
Matches: 192, Mismatches: 31, Indels: 11
0.82 0.13 0.05
Matches are distributed among these distances:
77 2 0.01
78 44 0.23
79 126 0.66
80 20 0.10
ACGTcount: A:0.29, C:0.26, G:0.13, T:0.32
Consensus pattern (78 bp):
GGGGATACTCCAACCCCAATTTTATTTTAAAACACTGATTTTCAACAATCAGGGATACTCCAACC
CCGTTATTTTCAA
Found at i:21215 original size:158 final size:158
Alignment explanation
Indices: 20928--21235 Score: 381
Period size: 158 Copynumber: 1.9 Consensus size: 158
20918 TTTCACAAGC
* *
20928 GGGGATACTCCAACTCCGATTTTATTTCCAAAACACCAATTTCTCACAATCGGAATACTCCAACT
1 GGGGATACTCCAACCCCAATTTTATTTCCAAAACACCAATTTCTCACAATCGGAATACTCCAACT
* * ** * *
20993 CCGTTATTTTTGTAGGGATACTCCAACCCCGGCCTTATTTCTAAAGCATTGATTTTCAACAATCA
66 CCATTATTTTCGTAGGGATACTCCAACCCCAACCTTATTTCTAAAACACTGATTTTCAACAATCA
21058 -GGGATACTCCAACCCCGTTATTTTCAA
131 GGGGATACTCCAACCCCGTTATTTTCAA
* * * *
21085 GGGGATACTCCAACCCCAATTTTATTTTCAAAACACTAATTT-TCTATAATCAGGGATACTCCAA
1 GGGGATACTCCAACCCCAATTTTATTTCCAAAACACCAATTTCTC-ACAATC-GGAATACTCCAA
** * * * *
21149 C-CCTATTATTTTCG-AGGGGATACTCCAACCCCAATTTTATTTTTAAAATACTGATTTTCCATA
64 CTCC-ATTATTTTCGTA-GGGATACTCCAACCCCAACCTTATTTCTAAAACACTGATTTTCAACA
*
21212 ATCAGGGGATACTCCAGCCCCGTT
127 ATCAGGGGATACTCCAACCCCGTT
21236 GTCATCTCCA
Statistics
Matches: 127, Mismatches: 19, Indels: 8
0.82 0.12 0.05
Matches are distributed among these distances:
156 2 0.02
157 46 0.36
158 61 0.48
159 18 0.14
ACGTcount: A:0.29, C:0.26, G:0.13, T:0.32
Consensus pattern (158 bp):
GGGGATACTCCAACCCCAATTTTATTTCCAAAACACCAATTTCTCACAATCGGAATACTCCAACT
CCATTATTTTCGTAGGGATACTCCAACCCCAACCTTATTTCTAAAACACTGATTTTCAACAATCA
GGGGATACTCCAACCCCGTTATTTTCAA
Found at i:29875 original size:52 final size:52
Alignment explanation
Indices: 29797--29925 Score: 231
Period size: 52 Copynumber: 2.5 Consensus size: 52
29787 CGAAATATGA
* *
29797 AAATTTACCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGC
*
29849 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGC
29901 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
29926 AAGATCAGTG
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 74 1.00
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGC
Found at i:29938 original size:52 final size:51
Alignment explanation
Indices: 29797--29945 Score: 219
Period size: 52 Copynumber: 2.9 Consensus size: 51
29787 CGAAATATGA
*
29797 AAATTTACCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGC
* *
29849 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGC
*
29901 AAATTTGCCTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
29946 ATGTATCGAC
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
51 2 0.02
52 87 0.98
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (51 bp):
AAATTTGCCTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGC
Found at i:30036 original size:33 final size:33
Alignment explanation
Indices: 29999--30065 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
29989 AGTAGCTTAA
*
29999 ATTGTATTGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
30032 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
30065 A
1 A
30066 AATCGTTGAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:30039 original size:13 final size:13
Alignment explanation
Indices: 30021--30045 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
30011 CAAAAAAATA
30021 TGTATCGATACAT
1 TGTATCGATACAT
30034 TGTATCGATACA
1 TGTATCGATACA
30046 ACACTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:36816 original size:20 final size:22
Alignment explanation
Indices: 36781--36821 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
36771 TGGACATGTT
36781 AAAATGCATGGAACAT-GGCTC
1 AAAATGCATGGAACATAGGCTC
36802 AAAATGCAT-GAACATAGGCT
1 AAAATGCATGGAACATAGGCT
36822 GTTTAGCTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.41, C:0.17, G:0.22, T:0.20
Consensus pattern (22 bp):
AAAATGCATGGAACATAGGCTC
Found at i:37722 original size:20 final size:20
Alignment explanation
Indices: 37697--37749 Score: 106
Period size: 20 Copynumber: 2.6 Consensus size: 20
37687 TTAGCTAGAC
37697 GTATCGATACATTGAAGAAT
1 GTATCGATACATTGAAGAAT
37717 GTATCGATACATTGAAGAAT
1 GTATCGATACATTGAAGAAT
37737 GTATCGATACATT
1 GTATCGATACATT
37750 TGGTTCAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.38, C:0.11, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATTGAAGAAT
Found at i:37776 original size:52 final size:50
Alignment explanation
Indices: 37714--37881 Score: 185
Period size: 52 Copynumber: 3.3 Consensus size: 50
37704 TACATTGAAG
* * *
37714 AATGTATCGATACATTGAAGAATGTATCGATACATTTGGTTCAAAAACCTAA
1 AATGTATCGATACAATGAAGAATGTATCGATACATTCGG-ACAAAAACC-AA
* *
37766 AATGTATCGATACAATGAAGAATGTATC-ATTACATTCGGGCAAAAAACCGAG
1 AATGTATCGATACAATGAAGAATGTATCGA-TACATTCGGAC-AAAAACC-AA
* * * * * *
37818 AATGTGTCGATACAAAGAAAAATGTATCGATACATTCAGACTAAATCCAA
1 AATGTATCGATACAATGAAGAATGTATCGATACATTCGGACAAAAACCAA
37868 AATGTATCGATACA
1 AATGTATCGATACA
37882 TTTTTTCCAA
Statistics
Matches: 99, Mismatches: 14, Indels: 8
0.82 0.12 0.07
Matches are distributed among these distances:
50 14 0.14
51 7 0.07
52 77 0.78
53 1 0.01
ACGTcount: A:0.43, C:0.15, G:0.16, T:0.26
Consensus pattern (50 bp):
AATGTATCGATACAATGAAGAATGTATCGATACATTCGGACAAAAACCAA
Found at i:37962 original size:20 final size:21
Alignment explanation
Indices: 37939--37992 Score: 83
Period size: 20 Copynumber: 2.6 Consensus size: 21
37929 CATTTCAATC
37939 ATGTATCGATACATTCACTT-
1 ATGTATCGATACATTCACTTG
37959 ATGTATCGATACATTCACTTG
1 ATGTATCGATACATTCACTTG
* *
37980 TTGTATCAATACA
1 ATGTATCGATACA
37993 AATTGTAGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 20 0.65
21 11 0.35
ACGTcount: A:0.31, C:0.19, G:0.11, T:0.39
Consensus pattern (21 bp):
ATGTATCGATACATTCACTTG
Found at i:39639 original size:48 final size:48
Alignment explanation
Indices: 39583--39681 Score: 189
Period size: 48 Copynumber: 2.1 Consensus size: 48
39573 AGCCAACACA
39583 TGTTTATGTTAAATATATGTTGAATACGTGGTGAAACTAGTATTTAAG
1 TGTTTATGTTAAATATATGTTGAATACGTGGTGAAACTAGTATTTAAG
*
39631 TGTTTATGTTAAATATATGTTGAATATGTGGTGAAACTAGTATTTAAG
1 TGTTTATGTTAAATATATGTTGAATACGTGGTGAAACTAGTATTTAAG
39679 TGT
1 TGT
39682 CCTACGCTTA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 50 1.00
ACGTcount: A:0.32, C:0.03, G:0.21, T:0.43
Consensus pattern (48 bp):
TGTTTATGTTAAATATATGTTGAATACGTGGTGAAACTAGTATTTAAG
Done.