Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005864.1 Hibiscus syriacus cultivar Beakdansim tig00013783_pilon, whole genome shotgun sequence
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: 72299
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:5028 original size:32 final size:31
Alignment explanation
Indices: 4992--5096 Score: 77
Period size: 33 Copynumber: 3.2 Consensus size: 31
4982 GGTAAGAAAT
* * *
4992 TTATTTTATGT-TAGTATTTTTTTAAATAGTTA
1 TTATTTTATATATA-TATTTATGTAAATA-TTA
5024 TTATTTTTATATATATATTTATGTAAATATTA
1 TTA-TTTTATATATATATTTATGTAAATATTA
* * * *
5056 TTTTTTTATTAAAATAATATTTATATAATTATTA
1 TTATTTTA-T-ATAT-ATATTTATGTAAATATTA
5090 TTTATTT
1 -TTATTT
5097 AGAATTATTA
Statistics
Matches: 59, Mismatches: 8, Indels: 9
0.78 0.11 0.12
Matches are distributed among these distances:
31 5 0.08
32 9 0.15
33 22 0.37
34 18 0.31
35 5 0.08
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (31 bp):
TTATTTTATATATATATTTATGTAAATATTA
Found at i:5078 original size:34 final size:31
Alignment explanation
Indices: 5014--5097 Score: 87
Period size: 34 Copynumber: 2.5 Consensus size: 31
5004 AGTATTTTTT
* *
5014 TAAATAGTTATTATTTTTATATATATATTTATG
1 TAAATA-TTATT-TTTTTATAAATATATTTATA
5047 TAAATATTATTTTTTTATTAAAATAATATTTATA
1 TAAATATTATTTTTTTA-T-AAAT-ATATTTATA
* *
5081 TAATTATTATTTATTTA
1 TAAATATTATTTTTTTA
5098 GAATTATTAT
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
31 6 0.14
32 6 0.14
33 9 0.20
34 23 0.52
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.58
Consensus pattern (31 bp):
TAAATATTATTTTTTTATAAATATATTTATA
Found at i:5119 original size:17 final size:16
Alignment explanation
Indices: 5081--5131 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 16
5071 AATATTTATA
5081 TAATTATTATTTATTTAG
1 TAATTATTATTT-TTT-G
5099 -AATTATTATTTTTTG
1 TAATTATTATTTTTTG
5114 CTAATTA-TATTGTTTTG
1 -TAATTATTATT-TTTTG
5131 T
1 T
5132 CTACATTTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
15 1 0.03
16 8 0.27
17 21 0.70
ACGTcount: A:0.27, C:0.02, G:0.08, T:0.63
Consensus pattern (16 bp):
TAATTATTATTTTTTG
Found at i:6865 original size:21 final size:21
Alignment explanation
Indices: 6839--6920 Score: 103
Period size: 21 Copynumber: 3.9 Consensus size: 21
6829 CATCTCCGCA
* *
6839 TACATTTCGAGCCTGCAGGGT
1 TACATTCCGAGCCCGCAGGGT
6860 TACATTCCGAGCCCGCAGGGT
1 TACATTCCGAGCCCGCAGGGT
*
6881 TACATTCCTAGCCCGCCA-GGT
1 TACATTCCGAGCCCG-CAGGGT
* *
6902 TACATGCCTAGCCCGCAGG
1 TACATTCCGAGCCCGCAGG
6921 TTTTATACCA
Statistics
Matches: 55, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
20 2 0.04
21 51 0.93
22 2 0.04
ACGTcount: A:0.20, C:0.33, G:0.26, T:0.22
Consensus pattern (21 bp):
TACATTCCGAGCCCGCAGGGT
Found at i:9993 original size:13 final size:13
Alignment explanation
Indices: 9975--9999 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
9965 AATACATAAA
9975 TATTTAATATATT
1 TATTTAATATATT
9988 TATTTAATATAT
1 TATTTAATATAT
10000 AATTAATATT
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:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TATTTAATATATT
Found at i:11151 original size:21 final size:21
Alignment explanation
Indices: 11118--11188 Score: 117
Period size: 21 Copynumber: 3.4 Consensus size: 21
11108 CGCGAATATG
*
11118 TAAA-TCGCATTGCGATTTTC
1 TAAATTCGCGTTGCGATTTTC
11138 TAAATTCGCGTTGCGATTTTC
1 TAAATTCGCGTTGCGATTTTC
*
11159 TAAATTCGCGTTACGATTTTC
1 TAAATTCGCGTTGCGATTTTC
11180 TAAATTCGC
1 TAAATTCGC
11189 AACGCGATAG
Statistics
Matches: 48, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
20 4 0.08
21 44 0.92
ACGTcount: A:0.24, C:0.20, G:0.15, T:0.41
Consensus pattern (21 bp):
TAAATTCGCGTTGCGATTTTC
Found at i:11196 original size:21 final size:21
Alignment explanation
Indices: 11078--11196 Score: 80
Period size: 21 Copynumber: 5.8 Consensus size: 21
11068 AATGGCCAAC
* * *
11078 AAATTCACAACGCGA-ATTCC
1 AAATTCGCAACGCGATTTTCT
* * * *
11098 AATTTCGCAACGCGAATATGT
1 AAATTCGCAACGCGATTTTCT
**
11119 AAA-TCGCATTGCGATTTTCT
1 AAATTCGCAACGCGATTTTCT
***
11139 AAATTCGCGTTGCGATTTTCT
1 AAATTCGCAACGCGATTTTCT
****
11160 AAATTCGCGTTACGATTTTCT
1 AAATTCGCAACGCGATTTTCT
11181 AAATTCGCAACGCGAT
1 AAATTCGCAACGCGAT
11197 AGTCAAATTC
Statistics
Matches: 79, Mismatches: 18, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
20 28 0.35
21 51 0.65
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.33
Consensus pattern (21 bp):
AAATTCGCAACGCGATTTTCT
Found at i:11196 original size:42 final size:41
Alignment explanation
Indices: 11101--11196 Score: 111
Period size: 42 Copynumber: 2.3 Consensus size: 41
11091 GAATTCCAAT
* * *
11101 TTCGCAACGCGAATATGTAAATCGCATTGCGATTTTCTAAA
1 TTCGCAACGCGATTATCTAAATCGCATTACGATTTTCTAAA
*** * *
11142 TTCGCGTTGCGATTTTCTAAATTCGCGTTACGATTTTCTAAA
1 TTCGCAACGCGATTATCTAAA-TCGCATTACGATTTTCTAAA
11184 TTCGCAACGCGAT
1 TTCGCAACGCGAT
11197 AGTCAAATTC
Statistics
Matches: 43, Mismatches: 11, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
41 15 0.35
42 28 0.65
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.35
Consensus pattern (41 bp):
TTCGCAACGCGATTATCTAAATCGCATTACGATTTTCTAAA
Found at i:11206 original size:20 final size:20
Alignment explanation
Indices: 11181--11231 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
11171 ACGATTTTCT
*
11181 AAATTCGCAACGCGATAGTC
1 AAATTCGCAACGCGAAAGTC
* *
11201 AAATTCTCAATGCGAAAGTC
1 AAATTCGCAACGCGAAAGTC
11221 AAATTCGCAAC
1 AAATTCGCAAC
11232 TGAATTTCAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.39, C:0.24, G:0.16, T:0.22
Consensus pattern (20 bp):
AAATTCGCAACGCGAAAGTC
Found at i:11243 original size:19 final size:19
Alignment explanation
Indices: 11219--11269 Score: 93
Period size: 19 Copynumber: 2.7 Consensus size: 19
11209 AATGCGAAAG
11219 TCAAATTCGCAACTGAATT
1 TCAAATTCGCAACTGAATT
*
11238 TCAAATTCACAACTGAATT
1 TCAAATTCGCAACTGAATT
11257 TCAAATTCGCAAC
1 TCAAATTCGCAAC
11270 AGGTTTTAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.39, C:0.24, G:0.08, T:0.29
Consensus pattern (19 bp):
TCAAATTCGCAACTGAATT
Found at i:12032 original size:12 final size:12
Alignment explanation
Indices: 12011--12044 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
12001 ACCACATTTC
*
12011 CAATACCAAACA
1 CAATATCAAACA
12023 CAATATCAAACA
1 CAATATCAAACA
*
12035 CAATCTCAAA
1 CAATATCAAA
12045 ACCCACAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:14502 original size:24 final size:24
Alignment explanation
Indices: 14463--14509 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
14453 AAGCAAAAGG
** *
14463 AAATCAAAATTGCAATCGCAATCA
1 AAATCAAAATCCCAATCACAATCA
14487 AAATCAAAATCCCAATCACAATC
1 AAATCAAAATCCCAATCACAATC
14510 GGCTTCATCT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.51, C:0.26, G:0.04, T:0.19
Consensus pattern (24 bp):
AAATCAAAATCCCAATCACAATCA
Found at i:14852 original size:20 final size:20
Alignment explanation
Indices: 14824--14885 Score: 106
Period size: 20 Copynumber: 3.1 Consensus size: 20
14814 CGCGAAATAA
14824 GCGTTGCGAATTTGACTATC
1 GCGTTGCGAATTTGACTATC
* *
14844 GCGTAGCGAATTTGACTTTC
1 GCGTTGCGAATTTGACTATC
14864 GCGTTGCGAATTTGACTATC
1 GCGTTGCGAATTTGACTATC
14884 GC
1 GC
14886 AACGCTTATT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.19, C:0.21, G:0.26, T:0.34
Consensus pattern (20 bp):
GCGTTGCGAATTTGACTATC
Found at i:15014 original size:25 final size:25
Alignment explanation
Indices: 14976--15025 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
14966 AAATCAATTA
*
14976 AACATTGTTGTGGGTACATTATTTG
1 AACATTGTTATGGGTACATTATTTG
15001 AACATTGTTATGGGTACATTATTTG
1 AACATTGTTATGGGTACATTATTTG
15026 GAAAAATAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.26, C:0.08, G:0.22, T:0.44
Consensus pattern (25 bp):
AACATTGTTATGGGTACATTATTTG
Found at i:15455 original size:24 final size:24
Alignment explanation
Indices: 15404--15455 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
15394 TTTCATATGT
* *
15404 AATTGGAGTTTGAATTTAAATTTC
1 AATTGGAGTTTGAATTTAAATATA
*
15428 AATTGGAGTTTGAATTTCAATATA
1 AATTGGAGTTTGAATTTAAATATA
15452 AATT
1 AATT
15456 TCGACTCCAC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.37, C:0.04, G:0.15, T:0.44
Consensus pattern (24 bp):
AATTGGAGTTTGAATTTAAATATA
Found at i:17605 original size:21 final size:21
Alignment explanation
Indices: 17581--17676 Score: 88
Period size: 21 Copynumber: 4.6 Consensus size: 21
17571 GGCGGGACCA
*
17581 CTTGAACGATGACAGGGGCCT
1 CTTGAACGATGAGAGGGGCCT
* * *
17602 CTTGAACGGTGAGAGGAGCTT
1 CTTGAACGATGAGAGGGGCCT
* *
17623 CTTCG-ATGATGATAGGGGCCT
1 CTT-GAACGATGAGAGGGGCCT
*
17644 CTTGAACGAT-AGGAGGCGCCT
1 CTTGAACGATGA-GAGGGGCCT
*
17665 CTTGAATGATGA
1 CTTGAACGATGA
17677 TAGGTGCATC
Statistics
Matches: 58, Mismatches: 13, Indels: 7
0.74 0.17 0.09
Matches are distributed among these distances:
20 2 0.03
21 54 0.93
22 2 0.03
ACGTcount: A:0.24, C:0.19, G:0.33, T:0.24
Consensus pattern (21 bp):
CTTGAACGATGAGAGGGGCCT
Found at i:17674 original size:42 final size:42
Alignment explanation
Indices: 17581--17680 Score: 123
Period size: 42 Copynumber: 2.4 Consensus size: 42
17571 GGCGGGACCA
* * * *
17581 CTTGAACGATGACAGGGGCCTCTTGAACGGTGAGAGGAGCTT
1 CTTGAATGATGATAGGGGCCTCTTGAACGATGAGAGGAGCCT
*
17623 CTTCG-ATGATGATAGGGGCCTCTTGAACGAT-AGGAGGCGCCT
1 CTT-GAATGATGATAGGGGCCTCTTGAACGATGA-GAGGAGCCT
17665 CTTGAATGATGATAGG
1 CTTGAATGATGATAGG
17681 TGCATCGGGC
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
41 2 0.04
42 47 0.94
43 1 0.02
ACGTcount: A:0.24, C:0.18, G:0.34, T:0.24
Consensus pattern (42 bp):
CTTGAATGATGATAGGGGCCTCTTGAACGATGAGAGGAGCCT
Found at i:18108 original size:21 final size:21
Alignment explanation
Indices: 18080--18129 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
18070 ATCATTATCT
**
18080 TCACGTAAAGTGCCAACCTCA
1 TCACGTAAAGCACCAACCTCA
* *
18101 TGACGTAAAGCACCGACCTCA
1 TCACGTAAAGCACCAACCTCA
18122 TCACGTAA
1 TCACGTAA
18130 TTCCCCTAAC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.34, C:0.32, G:0.16, T:0.18
Consensus pattern (21 bp):
TCACGTAAAGCACCAACCTCA
Found at i:20152 original size:22 final size:22
Alignment explanation
Indices: 20122--20172 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
20112 GATGGAGATA
*
20122 GACGAATTTCATCGGAAATGGG
1 GACGGATTTCATCGGAAATGGG
** *
20144 GACGGATTTTGTCGGAGATGGG
1 GACGGATTTCATCGGAAATGGG
20166 GACGGAT
1 GACGGAT
20173 GTCGCCGTAG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.25, C:0.12, G:0.39, T:0.24
Consensus pattern (22 bp):
GACGGATTTCATCGGAAATGGG
Found at i:30729 original size:92 final size:90
Alignment explanation
Indices: 30560--30729 Score: 236
Period size: 92 Copynumber: 1.9 Consensus size: 90
30550 TCAAGAAAAT
* * *
30560 ATTATTTTTAAATAATTTGTAATATTAATTAAAAATTTTAAATAAAAAATTATGGAACTCGTCTC
1 ATTATTTTTAAATAATTTGTAAAATTAATTAAAAATATTAAATAAAAAATGATGGAACTCGTCTC
*
30625 TTCGAGATGACGACTCGCTTAAGAA
66 CTCGAGATGACGACTCGCTTAAGAA
* *
30650 ATTATTTTTTAAATAATTTGTAAAATTAATTTTAAAAA-ATTAAATAAAAAGTGATGGAATTCGT
1 ATTA-TTTTTAAATAATTTGTAAAATTAA--TTAAAAATATTAAATAAAAAATGATGGAACTCGT
30714 CTCCTCGA-AGTGACGA
63 CTCCTCGAGA-TGACGA
30730 GTCCTGCCTG
Statistics
Matches: 70, Mismatches: 6, Indels: 6
0.85 0.07 0.07
Matches are distributed among these distances:
90 4 0.06
91 24 0.34
92 35 0.50
93 7 0.10
ACGTcount: A:0.42, C:0.09, G:0.12, T:0.38
Consensus pattern (90 bp):
ATTATTTTTAAATAATTTGTAAAATTAATTAAAAATATTAAATAAAAAATGATGGAACTCGTCTC
CTCGAGATGACGACTCGCTTAAGAA
Found at i:32208 original size:159 final size:159
Alignment explanation
Indices: 31919--32236 Score: 636
Period size: 159 Copynumber: 2.0 Consensus size: 159
31909 TTGTACGACT
31919 GGATTTATGGACGACGTGCGATTTCGGATGAGACGACAAAATGATTGACCGGCCAATGACATAAG
1 GGATTTATGGACGACGTGCGATTTCGGATGAGACGACAAAATGATTGACCGGCCAATGACATAAG
31984 TATTATTTTATTCGAAAAATACAGTAACTAAATATGGGTTAATCCTTTGAATCTCTGTTTATAAA
66 TATTATTTTATTCGAAAAATACAGTAACTAAATATGGGTTAATCCTTTGAATCTCTGTTTATAAA
32049 ATTAATTAAATAATATGATTGAAGAGGGA
131 ATTAATTAAATAATATGATTGAAGAGGGA
32078 GGATTTATGGACGACGTGCGATTTCGGATGAGACGACAAAATGATTGACCGGCCAATGACATAAG
1 GGATTTATGGACGACGTGCGATTTCGGATGAGACGACAAAATGATTGACCGGCCAATGACATAAG
32143 TATTATTTTATTCGAAAAATACAGTAACTAAATATGGGTTAATCCTTTGAATCTCTGTTTATAAA
66 TATTATTTTATTCGAAAAATACAGTAACTAAATATGGGTTAATCCTTTGAATCTCTGTTTATAAA
32208 ATTAATTAAATAATATGATTGAAGAGGGA
131 ATTAATTAAATAATATGATTGAAGAGGGA
32237 AAAAGGTTTA
Statistics
Matches: 159, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
159 159 1.00
ACGTcount: A:0.37, C:0.11, G:0.20, T:0.31
Consensus pattern (159 bp):
GGATTTATGGACGACGTGCGATTTCGGATGAGACGACAAAATGATTGACCGGCCAATGACATAAG
TATTATTTTATTCGAAAAATACAGTAACTAAATATGGGTTAATCCTTTGAATCTCTGTTTATAAA
ATTAATTAAATAATATGATTGAAGAGGGA
Found at i:38610 original size:30 final size:31
Alignment explanation
Indices: 38567--38639 Score: 112
Period size: 31 Copynumber: 2.4 Consensus size: 31
38557 TTCACATAGT
* *
38567 TTTATCGCGTAGACATATCA-TTTCCATACC
1 TTTATCACATAGACATATCATTTTCCATACC
38597 TTTATCACATAGACATATCATTTTCCATACC
1 TTTATCACATAGACATATCATTTTCCATACC
*
38628 TTTATTACATAG
1 TTTATCACATAG
38640 CTCATATAAC
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
30 18 0.46
31 21 0.54
ACGTcount: A:0.30, C:0.23, G:0.07, T:0.40
Consensus pattern (31 bp):
TTTATCACATAGACATATCATTTTCCATACC
Found at i:39712 original size:8 final size:8
Alignment explanation
Indices: 39699--39724 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
39689 TTGCTCAATG
39699 ACCCTTTT
1 ACCCTTTT
39707 ACCCTTTT
1 ACCCTTTT
39715 ACCCTTTT
1 ACCCTTTT
39723 AC
1 AC
39725 TTCTCCTTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.15, C:0.38, G:0.00, T:0.46
Consensus pattern (8 bp):
ACCCTTTT
Found at i:42025 original size:30 final size:30
Alignment explanation
Indices: 41991--42053 Score: 126
Period size: 30 Copynumber: 2.1 Consensus size: 30
41981 TTATATCGAG
41991 TAGACATATCATTTCCATACCTTTATCACA
1 TAGACATATCATTTCCATACCTTTATCACA
42021 TAGACATATCATTTCCATACCTTTATCACA
1 TAGACATATCATTTCCATACCTTTATCACA
42051 TAG
1 TAG
42054 CTCATATAAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.33, C:0.25, G:0.05, T:0.37
Consensus pattern (30 bp):
TAGACATATCATTTCCATACCTTTATCACA
Found at i:50714 original size:586 final size:576
Alignment explanation
Indices: 49013--50738 Score: 3190
Period size: 569 Copynumber: 3.0 Consensus size: 576
49003 AAAGCCCCTC
*
49013 CTACCCTTATAATTTTATGTAGGGATGGGTATGGATTAGATAGAGTC---TTTTGGCCATTCTAA
1 CTACCCCTATAATTTTATGTAGGGATGGGTATGGATTAGATAGAGTCAAGTTTTGGCCATTCTAA
* *
49075 TATGAAAATTTTGTATGTCTACCTAATAATCGAAATGATTTTAGAAGAATCTTATACTCTCCTCG
66 TATGAAATTTTTGTATATCTACCTAATAATCGAAATGATTTTAGAAGAATCTTATACTCTCCTCG
*
49140 AATCCGATTCGAAACTTGAGAGTGAGAATTCGTTCAACCCTATCTAACTTGACATCAACCATCCA
131 AATCCGATTCGAAACTTGAGAGTGAGAATTCGTTCAACCCTACCTAACTTGACATCAACCATCCA
49205 AAGCTTAGATTCACTAAATCAAAAGAAAATTTCACAACAAAAT-AAAAAAATAAAAAGAACACAA
196 AAGCTTAGATTCACTAAATCAAAAGAAAATTTCACAACAAAATAAAAAAAATAAAAAGAACACAA
49269 AAATCC-AAAAGAAAATAGAAAACAATGGAGAG-AAAAGAGACTTGTCATTTTGGCATAGTTTTT
261 AAATCCAAAAAGAAAATAGAAAACAATGGAGAGAAAAAGAGACTTGTCATTTTGGCATAGTTTTT
49332 TTTTTGACAATTCTAATAATGAATAAGCTTCTATTGACGAGGAAAATAGTATAATTTTATTTTGA
326 TTTTTGACAATTCTAATAATGAATAAGCTTCTATTGACGAGGAAAATAGTATAATTTTATTTTGA
49397 CCCGATCTGACGGTGGAAGAAGGAGATCAAAACAAAAGAGATAAATGATTTTGGGCTAGATTTAT
391 CCCGATCTGACGGTGGAAGAAGGAGATCAAAACAAAAGAGATAAATGATTTTGGGCTAGATTTAT
49462 AAACATCAAAGTATTCTCCGATGGAACAAACACCAAATTTAAAATTAAGAAGTTTGGAAAGTAAT
456 AAACATCAAAGTATTCTCCGATGGAACAAACACCAAATTTAAAATTAAGAAGTTTGGAAAGTAAT
*
49527 GTTAAAAAATTTTGGAGTTTAATGGC-ACTAGCACGACGACCGGTGTCGGCCTATA
521 GTTAAAAAATTTTGGAGTTTAATGGCAACTAGCACGACGACCGATGTCGGCCTATA
49582 CTACCCCTATAATTTTATGTAGGGAT--G---GGA-TAGATAGAGTCAAGTTTTGGCCATTCTAA
1 CTACCCCTATAATTTTATGTAGGGATGGGTATGGATTAGATAGAGTCAAGTTTTGGCCATTCTAA
49641 TATGAAATTTTTGTATATCTACCTAATAATCGAAATGATTTTAGAAGAATCTTATACTCTCCTCG
66 TATGAAATTTTTGTATATCTACCTAATAATCGAAATGATTTTAGAAGAATCTTATACTCTCCTCG
49706 AATCCGATTCGAAACTTGAGAGTGAGAATTCGTTCAACCCTACCTAACTTGACATCAACCATCCA
131 AATCCGATTCGAAACTTGAGAGTGAGAATTCGTTCAACCCTACCTAACTTGACATCAACCATCCA
49771 AAGCTTAGATTCACTAAATCAAAAGAAAATTTCACAACAAAATAAAAAAAATAAAAAGAACACAA
196 AAGCTTAGATTCACTAAATCAAAAGAAAATTTCACAACAAAATAAAAAAAATAAAAAGAACACAA
49836 AAATCCAAAAAGAAAATAGAAAACAATGGAGAGAAAAAGAGACTTGTCATTTTGGCATAGTTTTT
261 AAATCCAAAAAGAAAATAGAAAACAATGGAGAGAAAAAGAGACTTGTCATTTTGGCATAGTTTTT
49901 TTTTTGACAATTCTAATAATGAATAAGCTTCTATTGACGAGGAAAATAGTATAATTTTATTTTGA
326 TTTTTGACAATTCTAATAATGAATAAGCTTCTATTGACGAGGAAAATAGTATAATTTTATTTTGA
49966 CCCGATCTGACGGTGGAAGAAGGAGATCAAAACAAAAGAGATAAATGATTTTGGGCTAGATTTAT
391 CCCGATCTGACGGTGGAAGAAGGAGATCAAAACAAAAGAGATAAATGATTTTGGGCTAGATTTAT
50031 AAACATCAAAGTATTCTCCGATGGAACAAACACCAAATTTAAAATTAAGAAGTTTGGAAAGTAAT
456 AAACATCAAAGTATTCTCCGATGGAACAAACACCAAATTTAAAATTAAGAAGTTTGGAAAGTAAT
50096 GTTAAAAAATTTTGGAGTTTAATGGCAACTAGCACGACGACCGATGTCGGCCTATA
521 GTTAAAAAATTTTGGAGTTTAATGGCAACTAGCACGACGACCGATGTCGGCCTATA
50152 CTACCCCTATAATTTTATGTAGGGATGGGTATGGATTAGATAGAGTCAAGTTTTGGCCATTCTAA
1 CTACCCCTATAATTTTATGTAGGGATGGGTATGGATTAGATAGAGTCAAGTTTTGGCCATTCTAA
50217 TATGAAATTTTTGTATATCTACCTAATAATCGAAATGATTTTAGAAGAATCTTATACTCTCCTCG
66 TATGAAATTTTTGTATATCTACCTAATAATCGAAATGATTTTAGAAGAATCTTATACTCTCCTCG
50282 AATCCGATTCGAAACTTGAGAGTGAGAATTCGTTCAACCCTACCTAACTTGACATCAACCATCCA
131 AATCCGATTCGAAACTTGAGAGTGAGAATTCGTTCAACCCTACCTAACTTGACATCAACCATCCA
50347 AAGCTTAGATTCACTAAATCAAAAGAAAATTTCACAACAAAATAAAAAAAATAAAAAAGAACACA
196 AAGCTTAGATTCACTAAATCAAAAGAAAATTTCACAACAAAATAAAAAAAAT-AAAAAGAACACA
50412 AAAATCCAAAAAGAAAATAGAAAACAATGGAGAGAAAAAGAAAAAGAGACTTGTCATTTTGGCAT
260 AAAATCCAAAAAGAAAATAGAAAACAAT-G-GAG----AGAAAAAGAGACTTGTCATTTTGGCAT
50477 AGTTTTTTTTTTTTTGACAATTCTAATAATGAATAAGCTTCTATTGACGAGGAAAATAGTATAAT
319 AG---TTTTTTTTTTGACAATTCTAATAATGAATAAGCTTCTATTGACGAGGAAAATAGTATAAT
50542 TTTATTTTGACCCGATCTGACGGTGGAAGAAGGAGATCAAAACAAAAGAGATAAATGATTTTGGG
381 TTTATTTTGACCCGATCTGACGGTGGAAGAAGGAGATCAAAACAAAAGAGATAAATGATTTTGGG
* *
50607 CTAGATTTATAAACATCAAAGTATTCTCCGATGAAACAAACACCAAATTTAAAATTAAAAAGTTT
446 CTAGATTTATAAACATCAAAGTATTCTCCGATGGAACAAACACCAAATTTAAAATTAAGAAGTTT
* *
50672 GGAAAATAATGTTAAAAAATTTTGGAATTTAATGGCAACTAGCACGACGACCGATGTCGGCCTAT
511 GGAAAGTAATGTTAAAAAATTTTGGAGTTTAATGGCAACTAGCACGACGACCGATGTCGGCCTAT
50737 A
576 A
50738 C
1 C
50739 GTTATTGATG
Statistics
Matches: 1125, Mismatches: 9, Indels: 29
0.97 0.01 0.02
Matches are distributed among these distances:
563 11 0.01
564 3 0.00
566 185 0.16
567 28 0.02
568 26 0.02
569 277 0.25
570 54 0.05
572 1 0.00
575 3 0.00
576 211 0.19
577 40 0.04
578 1 0.00
579 3 0.00
583 29 0.03
586 253 0.22
ACGTcount: A:0.40, C:0.15, G:0.16, T:0.29
Consensus pattern (576 bp):
CTACCCCTATAATTTTATGTAGGGATGGGTATGGATTAGATAGAGTCAAGTTTTGGCCATTCTAA
TATGAAATTTTTGTATATCTACCTAATAATCGAAATGATTTTAGAAGAATCTTATACTCTCCTCG
AATCCGATTCGAAACTTGAGAGTGAGAATTCGTTCAACCCTACCTAACTTGACATCAACCATCCA
AAGCTTAGATTCACTAAATCAAAAGAAAATTTCACAACAAAATAAAAAAAATAAAAAGAACACAA
AAATCCAAAAAGAAAATAGAAAACAATGGAGAGAAAAAGAGACTTGTCATTTTGGCATAGTTTTT
TTTTTGACAATTCTAATAATGAATAAGCTTCTATTGACGAGGAAAATAGTATAATTTTATTTTGA
CCCGATCTGACGGTGGAAGAAGGAGATCAAAACAAAAGAGATAAATGATTTTGGGCTAGATTTAT
AAACATCAAAGTATTCTCCGATGGAACAAACACCAAATTTAAAATTAAGAAGTTTGGAAAGTAAT
GTTAAAAAATTTTGGAGTTTAATGGCAACTAGCACGACGACCGATGTCGGCCTATA
Found at i:51151 original size:2 final size:2
Alignment explanation
Indices: 51144--51219 Score: 152
Period size: 2 Copynumber: 38.0 Consensus size: 2
51134 AATCTATTGA
51144 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
51186 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
51220 TCAATAGATT
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 74 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:51368 original size:11 final size:11
Alignment explanation
Indices: 51354--51384 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
51344 TAATGAGTTA
51354 AGTAGTTCGTG
1 AGTAGTTCGTG
51365 AGTAGTTCGTG
1 AGTAGTTCGTG
51376 AGTAGTTCG
1 AGTAGTTCG
51385 AACTCCACTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.19, C:0.10, G:0.35, T:0.35
Consensus pattern (11 bp):
AGTAGTTCGTG
Found at i:52639 original size:46 final size:46
Alignment explanation
Indices: 52572--52669 Score: 196
Period size: 46 Copynumber: 2.1 Consensus size: 46
52562 AATGATTAAT
52572 AAAGATTCTGAATGGATATTATCTTTTAATTATCTTAAATTATTTA
1 AAAGATTCTGAATGGATATTATCTTTTAATTATCTTAAATTATTTA
52618 AAAGATTCTGAATGGATATTATCTTTTAATTATCTTAAATTATTTA
1 AAAGATTCTGAATGGATATTATCTTTTAATTATCTTAAATTATTTA
52664 AAAGAT
1 AAAGAT
52670 ATTTAATTAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 52 1.00
ACGTcount: A:0.39, C:0.06, G:0.09, T:0.46
Consensus pattern (46 bp):
AAAGATTCTGAATGGATATTATCTTTTAATTATCTTAAATTATTTA
Found at i:64839 original size:22 final size:24
Alignment explanation
Indices: 64794--64853 Score: 72
Period size: 23 Copynumber: 2.6 Consensus size: 24
64784 TGAAAATGAA
*
64794 AATAAAAT-TTTTTCAATTAAGTT
1 AATAAAATATATTTCAATTAAGTT
64817 AATAAAATATATTT-AA-TAAGTT
1 AATAAAATATATTTCAATTAAGTT
*
64839 AATATAAAAATATTT
1 AATA-AAATATATTT
64854 TTTAAGTTCA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
22 10 0.30
23 19 0.58
24 4 0.12
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.43
Consensus pattern (24 bp):
AATAAAATATATTTCAATTAAGTT
Found at i:64859 original size:23 final size:23
Alignment explanation
Indices: 64809--64867 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
64799 AATTTTTTCA
*
64809 ATTAAGTTAATA-AAATATATTT
1 ATTAAGTTAATATAAAAATATTT
*
64831 AATAAGTTAATATAAAAATATTT
1 ATTAAGTTAATATAAAAATATTT
* *
64854 TTTAAGTTCATATA
1 ATTAAGTTAATATA
64868 TATAAAAAAG
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
22 11 0.35
23 20 0.65
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (23 bp):
ATTAAGTTAATATAAAAATATTT
Found at i:69341 original size:3 final size:3
Alignment explanation
Indices: 69333--69357 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
69323 AATAAGGGTC
69333 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
69358 GGATTCTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:70174 original size:23 final size:23
Alignment explanation
Indices: 70148--70215 Score: 68
Period size: 22 Copynumber: 3.0 Consensus size: 23
70138 CACCACAGCT
70148 CGTATAAAATGCACCG-AGTGCCC
1 CGTA-AAAATGCACCGAAGTGCCC
* *
70171 CGTAGAATTGCACCGAAGTG-CC
1 CGTAAAAATGCACCGAAGTGCCC
* * *
70193 CGTAGAATTACACCGAAGTGCCC
1 CGTAAAAATGCACCGAAGTGCCC
70216 GTAGAATTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
22 30 0.75
23 10 0.25
ACGTcount: A:0.29, C:0.29, G:0.24, T:0.18
Consensus pattern (23 bp):
CGTAAAAATGCACCGAAGTGCCC
Found at i:70182 original size:22 final size:22
Alignment explanation
Indices: 70157--70223 Score: 109
Period size: 22 Copynumber: 3.0 Consensus size: 22
70147 TCGTATAAAA
70157 TGCACCG-AGTGCCCCGTAGAAT
1 TGCACCGAAGTG-CCCGTAGAAT
70179 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
*
70201 TACACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
70223 T
1 T
70224 ATGTCCATAA
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
22 39 0.91
23 4 0.09
ACGTcount: A:0.27, C:0.28, G:0.25, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:70990 original size:2 final size:2
Alignment explanation
Indices: 70978--71009 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
70968 ATTTCATTTC
*
70978 AT AT CT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
71010 CCTCAAGATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:71862 original size:21 final size:20
Alignment explanation
Indices: 71832--71875 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
71822 TCTTGTTCGT
* *
71832 TTGAAGGGTATCGGTTCCCC
1 TTGAAGGGTACCGATTCCCC
71852 TTGAATGGGTACCGATTCCCC
1 TTGAA-GGGTACCGATTCCCC
71873 TTG
1 TTG
71876 CCCAAAATCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.16, C:0.25, G:0.27, T:0.32
Consensus pattern (20 bp):
TTGAAGGGTACCGATTCCCC
Done.