Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004991.1 Hibiscus syriacus cultivar Beakdansim tig00011203_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: 80707
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:4486 original size:21 final size:21
Alignment explanation
Indices: 4462--4502 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
4452 TCAAACAACT
* *
4462 AAAAATGTGTCATAAAAATAA
1 AAAAATATATCATAAAAATAA
4483 AAAAATATATCATAAAAATA
1 AAAAATATATCATAAAAATA
4503 GAATTATTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.66, C:0.05, G:0.05, T:0.24
Consensus pattern (21 bp):
AAAAATATATCATAAAAATAA
Found at i:5143 original size:19 final size:19
Alignment explanation
Indices: 5119--5157 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
5109 TCTCAACAAA
5119 ACAGTATCCTATAATCAAG
1 ACAGTATCCTATAATCAAG
5138 ACAGTATCCTATAATCAAG
1 ACAGTATCCTATAATCAAG
5157 A
1 A
5158 GATAATCAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.44, C:0.21, G:0.10, T:0.26
Consensus pattern (19 bp):
ACAGTATCCTATAATCAAG
Found at i:8501 original size:21 final size:20
Alignment explanation
Indices: 8464--8562 Score: 72
Period size: 21 Copynumber: 4.7 Consensus size: 20
8454 TTTTCATGTA
*
8464 AGTGTTATGATTTTGGGGTTT
1 AGTGTTGTGA-TTTGGGGTTT
*
8485 GAGTGTTGTGATTTGGGATTT
1 -AGTGTTGTGATTTGGGGTTT
* * * *
8506 AGATGTAGCGATATGGAGTTT
1 AG-TGTTGTGATTTGGGGTTT
* * *
8527 AGGGGTTGTAATTTGAGGTTT
1 A-GTGTTGTGATTTGGGGTTT
8548 AAGTGTTGTGATTTG
1 -AGTGTTGTGATTTG
8563 CAGTTTAGGT
Statistics
Matches: 58, Mismatches: 16, Indels: 7
0.72 0.20 0.09
Matches are distributed among these distances:
20 2 0.03
21 45 0.78
22 11 0.19
ACGTcount: A:0.19, C:0.01, G:0.35, T:0.44
Consensus pattern (20 bp):
AGTGTTGTGATTTGGGGTTT
Found at i:8568 original size:21 final size:20
Alignment explanation
Indices: 8521--8569 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
8511 TAGCGATATG
*
8521 GAGTTTAGGGGTTGTAATTT
1 GAGTTTAAGGGTTGTAATTT
* *
8541 GAGGTTTAAGTGTTGTGATTT
1 GA-GTTTAAGGGTTGTAATTT
8562 GCAGTTTA
1 G-AGTTTA
8570 GGTGATGCAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 2 0.08
21 21 0.88
22 1 0.04
ACGTcount: A:0.20, C:0.02, G:0.33, T:0.45
Consensus pattern (20 bp):
GAGTTTAAGGGTTGTAATTT
Found at i:9494 original size:2 final size:2
Alignment explanation
Indices: 9487--9513 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
9477 TAATTCCTTT
9487 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
9514 CCGTTAATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:18898 original size:28 final size:30
Alignment explanation
Indices: 18833--18899 Score: 81
Period size: 28 Copynumber: 2.4 Consensus size: 30
18823 AATTAAATTT
*
18833 TATT-TAAA-AATTTAAATATTAATGATTA
1 TATTCTAAATAATTTAAATAGTAATGATTA
*
18861 TTTTC-AAATAATTTAAA-AGTAAT-ATTA
1 TATTCTAAATAATTTAAATAGTAATGATTA
18888 TATTCTAAATAA
1 TATTCTAAATAA
18900 ATATTACAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
27 8 0.24
28 17 0.52
29 8 0.24
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.45
Consensus pattern (30 bp):
TATTCTAAATAATTTAAATAGTAATGATTA
Found at i:20641 original size:18 final size:18
Alignment explanation
Indices: 20612--20663 Score: 68
Period size: 18 Copynumber: 2.9 Consensus size: 18
20602 TGAAAATTTG
20612 TCCCGAAGGACCACTTTA
1 TCCCGAAGGACCACTTTA
* * * *
20630 TCTCGAATGACCACTATG
1 TCCCGAAGGACCACTTTA
20648 TCCCGAAGGACCACTT
1 TCCCGAAGGACCACTT
20664 ATAATCCCTC
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.27, C:0.33, G:0.17, T:0.23
Consensus pattern (18 bp):
TCCCGAAGGACCACTTTA
Found at i:24166 original size:17 final size:18
Alignment explanation
Indices: 24133--24172 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
24123 TTTTTAAAAA
24133 TTTAAAATTTATATATAT
1 TTTAAAATTTATATATAT
*
24151 TTTAAAATTGTTTATAT-T
1 TTTAAAATT-TATATATAT
24169 TTTA
1 TTTA
24173 TTAATAACTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.60
Consensus pattern (18 bp):
TTTAAAATTTATATATAT
Found at i:25162 original size:18 final size:19
Alignment explanation
Indices: 25126--25162 Score: 51
Period size: 18 Copynumber: 2.0 Consensus size: 19
25116 TATAAAAATA
25126 TTTAAATATTCATTTAATT
1 TTTAAATATTCATTTAATT
25145 TTTAAA-ATT-ATATTAATT
1 TTTAAATATTCAT-TTAATT
25163 AATTATTCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
17 2 0.12
18 9 0.53
19 6 0.35
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.57
Consensus pattern (19 bp):
TTTAAATATTCATTTAATT
Found at i:29352 original size:36 final size:36
Alignment explanation
Indices: 29302--29634 Score: 479
Period size: 36 Copynumber: 9.2 Consensus size: 36
29292 TGTTCATTCA
* *
29302 CCGATTCAAGTCGAACGGAGGGAAGCATCGACACTT
1 CCGATTCAAATCGAACGGAAGGAAGCATCGACACTT
* *
29338 CTGATTCAAATCGAACGGAAGGAAGCATCGGCACTT
1 CCGATTCAAATCGAACGGAAGGAAGCATCGACACTT
* * *
29374 CTGATTCAAATCAAACGGAAGGAAGCATCGGCACTT
1 CCGATTCAAATCGAACGGAAGGAAGCATCGACACTT
* * *
29410 CCGATTTAAAGT-GAACGAAAGGAAGCACCGACACTT
1 CCGATTCAAA-TCGAACGGAAGGAAGCATCGACACTT
* *
29446 CCGATTCAAGTCGAACGGAGGGAAGCATCGACACTT
1 CCGATTCAAATCGAACGGAAGGAAGCATCGACACTT
* *
29482 CCGATTCAAATCGAACAGAAGGAAGCATCGGCACTT
1 CCGATTCAAATCGAACGGAAGGAAGCATCGACACTT
* *
29518 CCGATTCAAGTTGAACGGAAGGAAGCATCGACACTT
1 CCGATTCAAATCGAACGGAAGGAAGCATCGACACTT
*
29554 CCGATTCAAATCGAACGGAAGGAAGCATCGGCACTT
1 CCGATTCAAATCGAACGGAAGGAAGCATCGACACTT
**
29590 CCGATTCAAATCGAACGGAAGGAAGCATTTACACTT
1 CCGATTCAAATCGAACGGAAGGAAGCATCGACACTT
29626 CCGATTCAA
1 CCGATTCAA
29635 GTGTTCATTT
Statistics
Matches: 265, Mismatches: 30, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
35 1 0.00
36 263 0.99
37 1 0.00
ACGTcount: A:0.34, C:0.24, G:0.24, T:0.18
Consensus pattern (36 bp):
CCGATTCAAATCGAACGGAAGGAAGCATCGACACTT
Found at i:30282 original size:45 final size:45
Alignment explanation
Indices: 30218--30308 Score: 164
Period size: 45 Copynumber: 2.0 Consensus size: 45
30208 ACATCATCAG
* *
30218 GATTCTAGCATCTGTTTCTAAGGTACAATATCTTAGTACTTTAGT
1 GATTCTAGCATCTGCTTCTAAGGTACAATATCTGAGTACTTTAGT
30263 GATTCTAGCATCTGCTTCTAAGGTACAATATCTGAGTACTTTAGT
1 GATTCTAGCATCTGCTTCTAAGGTACAATATCTGAGTACTTTAGT
30308 G
1 G
30309 GGCATATGTC
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.26, C:0.16, G:0.18, T:0.40
Consensus pattern (45 bp):
GATTCTAGCATCTGCTTCTAAGGTACAATATCTGAGTACTTTAGT
Found at i:32290 original size:17 final size:19
Alignment explanation
Indices: 32262--32310 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
32252 TATTTTGAAA
32262 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
32280 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
32299 CACCGATGCACT
1 CATCGATGCACT
32311 AAGGGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:37031 original size:25 final size:25
Alignment explanation
Indices: 36997--37044 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
36987 TTTTGGGACT
36997 CCAAATCAAGCAAAGAAAAGATGTC
1 CCAAATCAAGCAAAGAAAAGATGTC
37022 CCAAATCAAGCAAAGAAAAGATG
1 CCAAATCAAGCAAAGAAAAGATG
37045 GCATCTTCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.54, C:0.19, G:0.17, T:0.10
Consensus pattern (25 bp):
CCAAATCAAGCAAAGAAAAGATGTC
Found at i:38136 original size:20 final size:21
Alignment explanation
Indices: 38111--38164 Score: 58
Period size: 22 Copynumber: 2.6 Consensus size: 21
38101 GTGCTTCATG
38111 CATCGATACACC-TAACA-GTA
1 CATCGATACACCTTAA-ATGTA
* *
38131 CATCGATGCATCCTTAAATGTG
1 CATCGATACA-CCTTAAATGTA
38153 CATCGATACACC
1 CATCGATACACC
38165 ATGAAGGTGC
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
20 9 0.32
21 5 0.18
22 14 0.50
ACGTcount: A:0.33, C:0.30, G:0.13, T:0.24
Consensus pattern (21 bp):
CATCGATACACCTTAAATGTA
Found at i:39777 original size:21 final size:21
Alignment explanation
Indices: 39735--39778 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
39725 ACACCGAGAG
*
39735 CTAGCTCTTCATGAGCTTCTC
1 CTAGCTCTTCATGAGCTCCTC
*
39756 CTAGCTCTTC-TCGTGCTCCTC
1 CTAGCTCTTCAT-GAGCTCCTC
39777 CT
1 CT
39779 CCTCCGGCAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 19 0.95
ACGTcount: A:0.09, C:0.39, G:0.14, T:0.39
Consensus pattern (21 bp):
CTAGCTCTTCATGAGCTCCTC
Found at i:41004 original size:65 final size:64
Alignment explanation
Indices: 40874--41029 Score: 167
Period size: 65 Copynumber: 2.4 Consensus size: 64
40864 AATTAAATTG
* *
40874 AACATCGAATGCATTTCAT-TCATCGATGCACATACCATGAATCGATGCACTGAGGATTTTATGA
1 AACATCGAATGCATTTGATGT-ATCGATACACATACCATGAATCGATGCACTGAGGATTTTATG-
40938 A
64 A
* * *
40939 AACATCGAATGCATTTGATGTATCGATACACCA-ACCATGCATCGATGCACTTTA-GCTATTT-T
1 AACATCGAATGCATTTGATGTATCGATACA-CATACCATGAATCGATGCAC-TGAGGAT-TTTAT
41001 GA
63 GA
* * *
41003 AACATCAAATGCACTTGATGCATCGAT
1 AACATCGAATGCATTTGATGTATCGAT
41030 GCACTCTTAG
Statistics
Matches: 79, Mismatches: 8, Indels: 9
0.82 0.08 0.09
Matches are distributed among these distances:
64 25 0.32
65 46 0.58
66 8 0.10
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.29
Consensus pattern (64 bp):
AACATCGAATGCATTTGATGTATCGATACACATACCATGAATCGATGCACTGAGGATTTTATGA
Found at i:43756 original size:103 final size:103
Alignment explanation
Indices: 43577--43897 Score: 588
Period size: 103 Copynumber: 3.1 Consensus size: 103
43567 GTCGAGGGTC
43577 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
43642 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
*
43680 TATGTGGTCTTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
43745 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
* *
43783 TATGTGGTCCTTCGGGACATATATATATTCTTTGGAACATGTGTGATGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* * *
43848 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
43886 TATGTGGTCCTT
1 TATGTGGTCCTT
43898 ATGGACATTA
Statistics
Matches: 211, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 211 1.00
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:43963 original size:23 final size:23
Alignment explanation
Indices: 43904--43981 Score: 66
Period size: 23 Copynumber: 3.3 Consensus size: 23
43894 CCTTATGGAC
* * *
43904 ATTATTATATGGCACTACGGTACA
1 ATTA-TATGTGGCACTCCGGTGCA
* * * *
43928 ATTCTACGCGGCACTCCGGTGTA
1 ATTATATGTGGCACTCCGGTGCA
**
43951 ATTATATGTGGCACTTTGGTGCA
1 ATTATATGTGGCACTCCGGTGCA
43974 ATTATATG
1 ATTATATG
43982 AGCTGTGGTG
Statistics
Matches: 41, Mismatches: 13, Indels: 1
0.75 0.24 0.02
Matches are distributed among these distances:
23 38 0.93
24 3 0.07
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.35
Consensus pattern (23 bp):
ATTATATGTGGCACTCCGGTGCA
Found at i:49214 original size:103 final size:103
Alignment explanation
Indices: 49085--49405 Score: 597
Period size: 103 Copynumber: 3.1 Consensus size: 103
49075 GTCGAGGGTC
49085 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
49150 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
49188 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
49253 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
* *
49291 TATGTGGTCCTTCGGGACATATATATATTCTTTGGAACATGTGTGATGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* * *
49356 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
49394 TATGTGGTCCTT
1 TATGTGGTCCTT
49406 ATGGACATTA
Statistics
Matches: 213, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
103 213 1.00
ACGTcount: A:0.26, C:0.14, G:0.24, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:49471 original size:23 final size:23
Alignment explanation
Indices: 49412--49489 Score: 66
Period size: 23 Copynumber: 3.3 Consensus size: 23
49402 CCTTATGGAC
* * *
49412 ATTATTATATGGCACTACGGTACA
1 ATTA-TATGTGGCACTCCGGTGCA
* * * *
49436 ATTCTACGCGGCACTCCGGTGTA
1 ATTATATGTGGCACTCCGGTGCA
**
49459 ATTATATGTGGCACTTTGGTGCA
1 ATTATATGTGGCACTCCGGTGCA
49482 ATTATATG
1 ATTATATG
49490 AGCTGTGGTG
Statistics
Matches: 41, Mismatches: 13, Indels: 1
0.75 0.24 0.02
Matches are distributed among these distances:
23 38 0.93
24 3 0.07
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.35
Consensus pattern (23 bp):
ATTATATGTGGCACTCCGGTGCA
Found at i:53448 original size:20 final size:20
Alignment explanation
Indices: 53423--53467 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
53413 TTTTTAGGAT
53423 AATTAT-GTATTTAATAACTA
1 AATTATAGT-TTTAATAACTA
*
53443 AATTATCAGTTTTAATACCTA
1 AATTAT-AGTTTTAATAACTA
53464 AATT
1 AATT
53468 TTCAATTGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 6 0.27
21 14 0.64
22 2 0.09
ACGTcount: A:0.42, C:0.09, G:0.04, T:0.44
Consensus pattern (20 bp):
AATTATAGTTTTAATAACTA
Found at i:68097 original size:19 final size:19
Alignment explanation
Indices: 68075--68115 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
68065 TTAATGGTAG
68075 ATTAAAATTTACCTTTTGC
1 ATTAAAATTTACCTTTTGC
*
68094 ATTAAAATTTATCTTTTGC
1 ATTAAAATTTACCTTTTGC
68113 ATT
1 ATT
68116 TACTTGTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.32, C:0.12, G:0.05, T:0.51
Consensus pattern (19 bp):
ATTAAAATTTACCTTTTGC
Found at i:71322 original size:208 final size:208
Alignment explanation
Indices: 70958--71334 Score: 567
Period size: 208 Copynumber: 1.8 Consensus size: 208
70948 TGGTGGTTTA
* * * *
70958 TGTCGATACTTTATAAAAATGTATCGATCCACATCAATATAATAGGTAAAAATATGACAAAACCG
1 TGTCGATAATTTATAAAAATGTATCGATCCACAACAATATAACAGATAAAAATATGACAAAACCG
* * * ** * * *
71023 GTCTCGAAAAGATAAAACTTGTAAAGCGGTACCGGATATATTGCATGTGTCGATACTTTAATATA
66 GTCTCGAAAAGACAAAACTGGTAAAGAGCAACCAGATATATTGAAAGTGTCGATACTTTAATATA
*
71088 AGTATCGACACTTTGTGAAATTAAAAGAGAAGCATTTTTTTTGGATAATTAAGAGAGGCAGTTTT
131 AGTATCGACACTTTGTGAAATTAAAAGAGAAGCAGTTTTTTTGGATAATTAAGAGAGGCAGTTTT
71153 AGCGCATATAAAG
196 AGCGCATATAAAG
* *
71166 TGTCGATAATTTATAATAATGTATCGATCTACAACAATATAACAGATAAAAATATGACAAAACCG
1 TGTCGATAATTTATAAAAATGTATCGATCCACAACAATATAACAGATAAAAATATGACAAAACCG
* * *
71231 GTCTCTAAAGGACAAAA-TCGGTATAGAGCAACCAGATATATTGAAAGTGTCGATACTTTAATAT
66 GTCTCGAAAAGACAAAACT-GGTAAAGAGCAACCAGATATATTGAAAGTGTCGATACTTTAATAT
*
71295 AAGTATCGACACTTTGTGAATTTAAAAGAGAAGCAGTTTT
130 AAGTATCGACACTTTGTGAAATTAAAAGAGAAGCAGTTTT
71335 AGCACCCATA
Statistics
Matches: 149, Mismatches: 19, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
207 1 0.01
208 148 0.99
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.30
Consensus pattern (208 bp):
TGTCGATAATTTATAAAAATGTATCGATCCACAACAATATAACAGATAAAAATATGACAAAACCG
GTCTCGAAAAGACAAAACTGGTAAAGAGCAACCAGATATATTGAAAGTGTCGATACTTTAATATA
AGTATCGACACTTTGTGAAATTAAAAGAGAAGCAGTTTTTTTGGATAATTAAGAGAGGCAGTTTT
AGCGCATATAAAG
Found at i:71454 original size:182 final size:182
Alignment explanation
Indices: 71138--71657 Score: 765
Period size: 182 Copynumber: 2.9 Consensus size: 182
71128 TTGGATAATT
* * * * * *
71138 AAGAGAGGCAGTTTTAGCGCATATAAAGTGTCGATAATTTATAATAATGTATCGATCTACAACAA
1 AAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTTATAACAATGTATCGATCCACAACGA
* *
71203 TATAACAGATAAAAATATGACAAAACCGGTCTCTAAAGGACAAAATCGGTATAGAGCAACCAGAT
66 TATAACAGGTAAAAATATGACAAAACCGGTCTCTAAAGGACAAAACCGGTATAGAGCAACCAGAT
*
71268 ATATTGAAAGTGTCGATACTTTAATATAAGTATCGACACTTTGTGAATTTAA
131 ATATTTAAAGTGTCGATACTTTAATATAAGTATCGACACTTTGTGAATTTAA
* * *
71320 AAGAGAAGCAGTTTTAGCACCCATAAAGTGTCGATACTTTATAACAATGTAT-GATCCAAAACGA
1 AAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTTATAACAATGTATCGATCCACAACGA
* *
71384 TATAATAGGTAAAAATATGACAAAACCCGGTCTCTAAAGGACAAAACCGGTATAGAGCGACC-GA
66 TATAACAGGTAAAAATATGACAAAA-CCGGTCTCTAAAGGACAAAACCGGTATAGAGCAACCAG-
* *
71448 ATATATTTAAAGTGTCGATACTTTAATATAAGTATCGACATTTTTTGAATTTAA
129 ATATATTTAAAGTGTCGATACTTTAATATAAGTATCGACACTTTGTGAATTTAA
* *
71502 AAGAGAAGTAGTTTTAGCGCCTATAAAGTTTCGATACTTTATAACAATGTATCGATCCACAACGA
1 AAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTTATAACAATGTATCGATCCACAACGA
* * * * * * ** *
71567 TATAACATGTAAAAATATGACAAAATCGGTCTCGAAATGAAAAAACCGGTAAAGCTCTACCAGAT
66 TATAACAGGTAAAAATATGACAAAACCGGTCTCTAAAGGACAAAACCGGTATAGAGCAACCAGAT
71632 ATATTTAAAGTGTCGATACTTTAATA
131 ATATTTAAAGTGTCGATACTTTAATA
71658 AGTACACGTA
Statistics
Matches: 303, Mismatches: 31, Indels: 8
0.89 0.09 0.02
Matches are distributed among these distances:
181 33 0.11
182 235 0.78
183 35 0.12
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.28
Consensus pattern (182 bp):
AAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTTATAACAATGTATCGATCCACAACGA
TATAACAGGTAAAAATATGACAAAACCGGTCTCTAAAGGACAAAACCGGTATAGAGCAACCAGAT
ATATTTAAAGTGTCGATACTTTAATATAAGTATCGACACTTTGTGAATTTAA
Found at i:73963 original size:14 final size:15
Alignment explanation
Indices: 73939--73969 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
73929 ATGGTTTATT
73939 GGGGAATGACGGTGA
1 GGGGAATGACGGTGA
73954 GGGG-ATGACGGTGA
1 GGGGAATGACGGTGA
73968 GG
1 GG
73970 AAAATAGAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.75
15 4 0.25
ACGTcount: A:0.23, C:0.06, G:0.58, T:0.13
Consensus pattern (15 bp):
GGGGAATGACGGTGA
Found at i:74066 original size:21 final size:21
Alignment explanation
Indices: 74042--74084 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
74032 TATCATGCAA
74042 AGACAATCA-AGAGTCGAAGAG
1 AGAC-ATCAGAGAGTCGAAGAG
* *
74063 AGACTTGAGAGAGTCGAAGAG
1 AGACATCAGAGAGTCGAAGAG
74084 A
1 A
74085 CACTTGAGAG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.44, C:0.12, G:0.33, T:0.12
Consensus pattern (21 bp):
AGACATCAGAGAGTCGAAGAG
Found at i:74089 original size:21 final size:21
Alignment explanation
Indices: 74051--74094 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
74041 AAGACAATCA
*
74051 AGAGTCGAAGAGAGACTTGAG
1 AGAGTCGAAGAGACACTTGAG
74072 AGAGTCGAAGAGACACTTGAG
1 AGAGTCGAAGAGACACTTGAG
74093 AG
1 AG
74095 GCATAAGGGG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.39, C:0.11, G:0.36, T:0.14
Consensus pattern (21 bp):
AGAGTCGAAGAGACACTTGAG
Found at i:74394 original size:18 final size:18
Alignment explanation
Indices: 74371--74427 Score: 96
Period size: 18 Copynumber: 3.2 Consensus size: 18
74361 GAAAAAATAT
*
74371 GAAGAAGAAAATAAGGAG
1 GAAGAAGAAAAGAAGGAG
74389 GAAGAAGAAAAGAAGGAG
1 GAAGAAGAAAAGAAGGAG
*
74407 GAAGAAGAAAAGATGGAG
1 GAAGAAGAAAAGAAGGAG
74425 GAA
1 GAA
74428 ATGAGGAAGG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 37 1.00
ACGTcount: A:0.60, C:0.00, G:0.37, T:0.04
Consensus pattern (18 bp):
GAAGAAGAAAAGAAGGAG
Found at i:80595 original size:20 final size:20
Alignment explanation
Indices: 80570--80622 Score: 92
Period size: 18 Copynumber: 2.8 Consensus size: 20
80560 CGAAATATCC
80570 ATGCATCGATGCACCCCTTA
1 ATGCATCGATGCACCCCTTA
80590 ATGCATCGAT--ACCCCTTA
1 ATGCATCGATGCACCCCTTA
80608 ATGCATCGATGCACC
1 ATGCATCGATGCACC
80623 TTCAAAATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
18 18 0.58
20 13 0.42
ACGTcount: A:0.26, C:0.34, G:0.15, T:0.25
Consensus pattern (20 bp):
ATGCATCGATGCACCCCTTA
Done.