Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006614.1 Hibiscus syriacus cultivar Beakdansim tig00016230_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: 73103
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.32
Found at i:7815 original size:23 final size:24
Alignment explanation
Indices: 7787--7831 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
7777 GATAACTTTT
*
7787 TTTATTATTAT-ATACTTCATTTC
1 TTTATTATTATAATAATTCATTTC
7810 TTTATTATTATAATAATTCATT
1 TTTATTATTATAATAATTCATT
7832 GTTTTGTGAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.31, C:0.09, G:0.00, T:0.60
Consensus pattern (24 bp):
TTTATTATTATAATAATTCATTTC
Found at i:17770 original size:21 final size:19
Alignment explanation
Indices: 17723--17760 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
17713 GCCCCTAAAA
*
17723 ATTTCAAATTTTTTTATAT
1 ATTTTAAATTTTTTTATAT
17742 ATTTTAAATTTTTTTATAT
1 ATTTTAAATTTTTTTATAT
17761 TCTTATTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.66
Consensus pattern (19 bp):
ATTTTAAATTTTTTTATAT
Found at i:18267 original size:16 final size:18
Alignment explanation
Indices: 18245--18285 Score: 68
Period size: 16 Copynumber: 2.4 Consensus size: 18
18235 ACTCTTAATC
18245 TATTTTAAAA-ATTTTAA
1 TATTTTAAAATATTTTAA
18262 -ATTTTAAAATATTTTAA
1 TATTTTAAAATATTTTAA
18279 TATTTTA
1 TATTTTA
18286 TATTTTTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 9 0.41
17 7 0.32
18 6 0.27
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TATTTTAAAATATTTTAA
Found at i:20688 original size:94 final size:93
Alignment explanation
Indices: 20495--20696 Score: 205
Period size: 94 Copynumber: 2.1 Consensus size: 93
20485 AAGAAATGTG
* * *
20495 GTATTGATACCATGGTAAGGGTATCGATACCAGTAAACATCAAATCTAATTTGAGTATAGATACC
1 GTATCGATACCATGGTAAGGGTATCGATACCAGT-AACATCAAAGCTAATTTGAGTATAGATACA
* *
20560 TAGAGGGGGTATCGGTACCATAGCATAGGG
65 TAGAGGGGGTATCGATACCATA-CATAGGA
* * * * *
20590 GTATCGATACCATGGTGAGTGTATCGATACCAGCT-ATATCGAAGCTAATTTCG-GTATTGATAC
1 GTATCGATACCATGGTAAGGGTATCGATACCAG-TAACATCAAAGCTAATTT-GAGTATAGATAC
*
20653 AT-GAAGGGGGTATCGATACCCTA-ATAAGGTA
64 ATAG-AGGGGGTATCGATACCATACAT-AGG-A
*
20684 GTATCAATACCAT
1 GTATCGATACCAT
20697 AAGCAGGGAT
Statistics
Matches: 90, Mismatches: 12, Indels: 11
0.80 0.11 0.10
Matches are distributed among these distances:
92 2 0.02
93 4 0.04
94 52 0.58
95 31 0.34
96 1 0.01
ACGTcount: A:0.33, C:0.16, G:0.24, T:0.28
Consensus pattern (93 bp):
GTATCGATACCATGGTAAGGGTATCGATACCAGTAACATCAAAGCTAATTTGAGTATAGATACAT
AGAGGGGGTATCGATACCATACATAGGA
Found at i:21399 original size:90 final size:90
Alignment explanation
Indices: 21183--21399 Score: 335
Period size: 90 Copynumber: 2.4 Consensus size: 90
21173 AGGATGCCAT
* * * *
21183 AGTTGAAATGTATATGGGTACATTATCAATAGAAAAACATACTTTAGTTGAAATGTATATGGGTA
1 AGTTGAAATGCATATGGGTGCATTATCAATAGAAAAGCATACTATAGTTGAAATGTATATGGGTA
* *
21248 CATTATCAACATAAAAGTATGCTAG
66 CATTATCAACAGAAAAGTATACTAG
* * *
21273 AGTTGAAATGCATATGGGTGTATTATCAATAGAAAAGTATACTATGGTTGAAATGTATATGGGTA
1 AGTTGAAATGCATATGGGTGCATTATCAATAGAAAAGCATACTATAGTTGAAATGTATATGGGTA
21338 CATTATCAACAGAAAAGTATACTAG
66 CATTATCAACAGAAAAGTATACTAG
* *
21363 AGTTGAAATGCATATTGGTGCATTATCAACAGAAAAG
1 AGTTGAAATGCATATGGGTGCATTATCAATAGAAAAG
21400 ATGTTATAGT
Statistics
Matches: 115, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
90 115 1.00
ACGTcount: A:0.41, C:0.09, G:0.20, T:0.31
Consensus pattern (90 bp):
AGTTGAAATGCATATGGGTGCATTATCAATAGAAAAGCATACTATAGTTGAAATGTATATGGGTA
CATTATCAACAGAAAAGTATACTAG
Found at i:21430 original size:45 final size:45
Alignment explanation
Indices: 21183--21399 Score: 274
Period size: 45 Copynumber: 4.8 Consensus size: 45
21173 AGGATGCCAT
* * * ** **
21183 AGTTGAAATGTATATGGGTACATTATCAATAGAAAAACATACTTT
1 AGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTATACTAG
* * * *
21228 AGTTGAAATGTATATGGGTACATTATCAACATAAAAGTATGCTAG
1 AGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTATACTAG
* *
21273 AGTTGAAATGCATATGGGTGTATTATCAATAGAAAAGTATACTATG
1 AGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTATACTA-G
* *
21319 -GTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACTAG
1 AGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTATACTAG
*
21363 AGTTGAAATGCATATTGGTGCATTATCAACAGAAAAG
1 AGTTGAAATGCATATGGGTGCATTATCAACAGAAAAG
21400 ATGTTATAGT
Statistics
Matches: 150, Mismatches: 20, Indels: 4
0.86 0.11 0.02
Matches are distributed among these distances:
44 1 0.01
45 148 0.99
46 1 0.01
ACGTcount: A:0.41, C:0.09, G:0.20, T:0.31
Consensus pattern (45 bp):
AGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTATACTAG
Found at i:21460 original size:135 final size:135
Alignment explanation
Indices: 21186--21461 Score: 306
Period size: 135 Copynumber: 2.0 Consensus size: 135
21176 ATGCCATAGT
* ** *
21186 TGAAATGTATATGGGTACATTATCAATAGAAAAACATACTTTAGTTGAAATGTATATGGGTACAT
1 TGAAATGTATATGGGTACATTATCAACAGAAAAACATACTAGAGTTGAAATGCATATGGGTACAT
* * * * * * *
21251 TATCAACATAAAAGTATGCTAGAGTTGAAATGCATATGGGTGTATTATCAATAGAAAAGTATACT
66 TATCAACAGAAAAGTATGCTAGAGTTAAAATGCATATGGGTGCATGATAAACAGAAAAGGATACT
**
21316 ATGGT
131 ATGAA
** * *
21321 TGAAATGTATATGGGTACATTATCAACAGAAAAGTATACTAGAGTTGAAATGCATATTGGTGCAT
1 TGAAATGTATATGGGTACATTATCAACAGAAAAACATACTAGAGTTGAAATGCATATGGGTACAT
* * *
21386 TATCAACAGAAAAG-ATGTTATAGTTTAAAATGCATAAT-GGTGCATGATAAACATG-AATGGAT
66 TATCAACAGAAAAGTATGCTAGAG-TTAAAATGCAT-ATGGGTGCATGATAAACA-GAAAAGGAT
* *
21448 GCTATTAA
128 ACTATGAA
21456 TGAAAT
1 TGAAAT
21462 ACTTATGTAT
Statistics
Matches: 116, Mismatches: 22, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
134 7 0.06
135 106 0.91
136 3 0.03
ACGTcount: A:0.41, C:0.08, G:0.20, T:0.32
Consensus pattern (135 bp):
TGAAATGTATATGGGTACATTATCAACAGAAAAACATACTAGAGTTGAAATGCATATGGGTACAT
TATCAACAGAAAAGTATGCTAGAGTTAAAATGCATATGGGTGCATGATAAACAGAAAAGGATACT
ATGAA
Found at i:22955 original size:17 final size:17
Alignment explanation
Indices: 22902--22967 Score: 59
Period size: 16 Copynumber: 4.1 Consensus size: 17
22892 GAAATATAAT
*
22902 TTCAAAC-ATCCATAAA
1 TTCAAACAATCCACAAA
*
22918 TTCAAACAAAT--TCAAA
1 TTCAAAC-AATCCACAAA
*
22934 GTCAAACAATCCACAAA
1 TTCAAACAATCCACAAA
*
22951 TTCAAACATTCCA-AAA
1 TTCAAACAATCCACAAA
22967 T
1 T
22968 ATCCAAAATG
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
15 3 0.08
16 20 0.50
17 15 0.38
18 2 0.05
ACGTcount: A:0.52, C:0.24, G:0.02, T:0.23
Consensus pattern (17 bp):
TTCAAACAATCCACAAA
Found at i:23253 original size:18 final size:18
Alignment explanation
Indices: 23232--23270 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
23222 GCATATTATA
*
23232 CTCTGGACGAGGTTGTTC
1 CTCTGGACGAGCTTGTTC
* *
23250 CTCTGGAGGTGCTTGTTC
1 CTCTGGACGAGCTTGTTC
23268 CTC
1 CTC
23271 GTGCTGCTCC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.08, C:0.26, G:0.31, T:0.36
Consensus pattern (18 bp):
CTCTGGACGAGCTTGTTC
Found at i:24868 original size:22 final size:22
Alignment explanation
Indices: 24846--24928 Score: 94
Period size: 22 Copynumber: 3.7 Consensus size: 22
24836 AGAACCCCAG
* * *
24846 GGGGGTATCGATTCCCCTACAG
1 GGGGGAATCGATTCCCCTTCAA
*
24868 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGATTCCCCTTC-AA
*
24891 GGGGGAATCGGTTCCCCTTCAA
1 GGGGGAATCGATTCCCCTTCAA
**
24913 GGGGTTATCGATTCCC
1 GGGGGAATCGATTCCC
24929 TCTGCACTAA
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
22 32 0.60
23 21 0.40
ACGTcount: A:0.18, C:0.27, G:0.31, T:0.24
Consensus pattern (22 bp):
GGGGGAATCGATTCCCCTTCAA
Found at i:24894 original size:23 final size:22
Alignment explanation
Indices: 24846--24916 Score: 97
Period size: 22 Copynumber: 3.2 Consensus size: 22
24836 AGAACCCCAG
* * * *
24846 GGGGGTATCGATTCCCCTACAG
1 GGGGGAATCGGTTCCCCTTCAA
24868 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTTCCCCTTC-AA
24891 GGGGGAATCGGTTCCCCTTCAA
1 GGGGGAATCGGTTCCCCTTCAA
24913 GGGG
1 GGGG
24917 TTATCGATTC
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
22 23 0.52
23 21 0.48
ACGTcount: A:0.18, C:0.25, G:0.35, T:0.21
Consensus pattern (22 bp):
GGGGGAATCGGTTCCCCTTCAA
Found at i:32270 original size:21 final size:21
Alignment explanation
Indices: 32244--32290 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
32234 CAAAAGTAAT
32244 AAGGTTGATAATATTGAAAAG
1 AAGGTTGATAATATTGAAAAG
32265 AAGGTTGATAATATTGAAAAG
1 AAGGTTGATAATATTGAAAAG
32286 AAGGT
1 AAGGT
32291 CGAGATTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.26, T:0.28
Consensus pattern (21 bp):
AAGGTTGATAATATTGAAAAG
Found at i:33165 original size:2 final size:2
Alignment explanation
Indices: 33158--33235 Score: 147
Period size: 2 Copynumber: 39.0 Consensus size: 2
33148 TGTCAGGAAG
*
33158 AT AT AT AT AT AT AT AT AC 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
33200 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
33236 GACTTTTATG
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 74 1.00
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:33535 original size:2 final size:2
Alignment explanation
Indices: 33528--33559 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
33518 GTTTTTAGCA
33528 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
33560 TGTGTGTGTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:36085 original size:7 final size:7
Alignment explanation
Indices: 36073--36126 Score: 64
Period size: 7 Copynumber: 8.4 Consensus size: 7
36063 ATCAAAGAAA
36073 GTCAACG
1 GTCAACG
36080 GTCAACG
1 GTCAACG
*
36087 GTC-ACT
1 GTCAACG
36093 GTCAACG
1 GTCAACG
36100 GTCAACG
1 GTCAACG
36107 GTC-A-G
1 GTCAACG
36112 GTC-A-G
1 GTCAACG
36117 GTCAACG
1 GTCAACG
36124 GTC
1 GTC
36127 GGGTCGGGTC
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
5 9 0.21
6 7 0.17
7 26 0.62
ACGTcount: A:0.24, C:0.28, G:0.30, T:0.19
Consensus pattern (7 bp):
GTCAACG
Found at i:36098 original size:20 final size:19
Alignment explanation
Indices: 36073--36131 Score: 77
Period size: 20 Copynumber: 3.2 Consensus size: 19
36063 ATCAAAGAAA
*
36073 GTCAACGGTCAACGGTCACT
1 GTCAACGGTCAACGGTCA-G
36093 GTCAACGGTCAACGGTCAG
1 GTCAACGGTCAACGGTCAG
*
36112 GTC-A-GGTCAACGGTCGG
1 GTCAACGGTCAACGGTCAG
36129 GTC
1 GTC
36132 GGGTCAACAG
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
17 15 0.41
18 1 0.03
19 3 0.08
20 18 0.49
ACGTcount: A:0.22, C:0.27, G:0.32, T:0.19
Consensus pattern (19 bp):
GTCAACGGTCAACGGTCAG
Found at i:36121 original size:17 final size:17
Alignment explanation
Indices: 36099--36166 Score: 91
Period size: 17 Copynumber: 4.0 Consensus size: 17
36089 CACTGTCAAC
*
36099 GGTCAACGGTCAGGTCA
1 GGTCAACGGTCGGGTCA
*
36116 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCA
* *
36133 GGTCAACAGTCGGGTCG
1 GGTCAACGGTCGGGTCA
*
36150 GGTCAACAGTCGGGTCA
1 GGTCAACGGTCGGGTCA
36167 ACCCGGTTCA
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 47 1.00
ACGTcount: A:0.19, C:0.24, G:0.40, T:0.18
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCA
Found at i:36186 original size:19 final size:19
Alignment explanation
Indices: 36162--36251 Score: 119
Period size: 19 Copynumber: 4.7 Consensus size: 19
36152 TCAACAGTCG
*
36162 GGTCAACCCGGTTCAGACC
1 GGTCAAACCGGTTCAGACC
36181 GGTCAAACCGGTTCAGACC
1 GGTCAAACCGGTTCAGACC
36200 GGTCAAACCGGTTC-GAACC
1 GGTCAAACCGGTTCAG-ACC
* * *
36219 GGTCAAACCGATTCAAAACT
1 GGTCAAACCGGTTC-AGACC
36239 GGTCAAACCGGTT
1 GGTCAAACCGGTT
36252 TTCCAGCAGC
Statistics
Matches: 63, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
18 1 0.02
19 48 0.76
20 14 0.22
ACGTcount: A:0.28, C:0.30, G:0.24, T:0.18
Consensus pattern (19 bp):
GGTCAAACCGGTTCAGACC
Found at i:36200 original size:10 final size:10
Alignment explanation
Indices: 36164--36251 Score: 85
Period size: 9 Copynumber: 9.1 Consensus size: 10
36154 AACAGTCGGG
*
36164 TCAACCCGGT
1 TCAAACCGGT
*
36174 TCAGACCGG-
1 TCAAACCGGT
36183 TCAAACCGGT
1 TCAAACCGGT
*
36193 TCAGACCGG-
1 TCAAACCGGT
36202 TCAAACCGGT
1 TCAAACCGGT
*
36212 TCGAACCGG-
1 TCAAACCGGT
*
36221 TCAAACCGAT
1 TCAAACCGGT
*
36231 TCAAAACTGG-
1 TC-AAACCGGT
36241 TCAAACCGGT
1 TCAAACCGGT
36251 T
1 T
36252 TTCCAGCAGC
Statistics
Matches: 62, Mismatches: 11, Indels: 10
0.75 0.13 0.12
Matches are distributed among these distances:
9 29 0.47
10 28 0.45
11 5 0.08
ACGTcount: A:0.28, C:0.31, G:0.23, T:0.18
Consensus pattern (10 bp):
TCAAACCGGT
Found at i:37836 original size:22 final size:21
Alignment explanation
Indices: 37811--37860 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
37801 AGGGGGCATT
37811 GATACCCTAA-TAGGGTAGTATC
1 GATACCCTAAGTAGGG--GTATC
*
37833 GATACCATAAGTAGGGGTATC
1 GATACCCTAAGTAGGGGTATC
*
37854 GAAACCC
1 GATACCC
37861 AAGGGCCAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
21 10 0.42
22 9 0.38
23 5 0.21
ACGTcount: A:0.34, C:0.20, G:0.24, T:0.22
Consensus pattern (21 bp):
GATACCCTAAGTAGGGGTATC
Found at i:37854 original size:21 final size:21
Alignment explanation
Indices: 37811--37855 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
37801 AGGGGGCATT
*
37811 GATACCCTAATAGGGTAGTATC
1 GATACCATAATAGGG-AGTATC
37833 GATACCATAAGTAGGG-GTATC
1 GATACCATAA-TAGGGAGTATC
37854 GA
1 GA
37856 AACCCAAGGG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 7 0.33
22 9 0.43
23 5 0.24
ACGTcount: A:0.33, C:0.16, G:0.27, T:0.24
Consensus pattern (21 bp):
GATACCATAATAGGGAGTATC
Found at i:38377 original size:45 final size:45
Alignment explanation
Indices: 38325--38767 Score: 564
Period size: 45 Copynumber: 9.8 Consensus size: 45
38315 AAAGGATGCC
** * **
38325 ATAGTTGAAATGTATATGTATACATTGTCAACAGAAAAACATACT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
* * *
38370 TTAGTTGAAATGTATATGGGTACATTATCAACATAAAAGTATGCT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
* * ** **
38415 AGAGTTGAAATGCATATGGGTGTATTATCAACTTAAAAGTATACT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
* *
38460 ATAGTTGAAATGTATATGGGTACATTATTAATAGAAAAGTATACT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
* **
38505 ATGGTTGAAATGTATATGGGTACATTATCAACAGAAAAACATACT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
* * *
38550 TTAGTTGAAATGTATATGGGTACATTATCAACATAAAAGTATGCT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
* * * *
38595 AGAGTTGAAATGCATGTGGG-AGTATTATCAACAGAAAAGTATACT
1 ATAGTTGAAATGTATATGGGTA-CATTATCAACAGAAAAGTATACT
* * *
38640 ATGGTTGAAATGTATATGAGTACATTATCAACAAAAAAGTATACT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
* *
38685 ATGGTTGAAATGAATATGGGTACATTATCAACAGAAAAGTATACT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
* * *
38730 AGAGTTGAAATGCATATGGGTGCATTATCAACAGAAAA
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAA
38768 AATGTTATTG
Statistics
Matches: 341, Mismatches: 55, Indels: 4
0.85 0.14 0.01
Matches are distributed among these distances:
44 1 0.00
45 339 0.99
46 1 0.00
ACGTcount: A:0.41, C:0.09, G:0.19, T:0.31
Consensus pattern (45 bp):
ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
Found at i:40164 original size:21 final size:21
Alignment explanation
Indices: 40138--40184 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
40128 CAAAAGTAAT
40138 AAGGTTGATAATATTGAAAAG
1 AAGGTTGATAATATTGAAAAG
40159 AAGGTTGATAATATTGAAAAG
1 AAGGTTGATAATATTGAAAAG
40180 AAGGT
1 AAGGT
40185 CGAGATTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.26, T:0.28
Consensus pattern (21 bp):
AAGGTTGATAATATTGAAAAG
Found at i:42822 original size:20 final size:20
Alignment explanation
Indices: 42797--42850 Score: 108
Period size: 20 Copynumber: 2.7 Consensus size: 20
42787 CATAACATAG
42797 GGGTATCGATACCATGGTGA
1 GGGTATCGATACCATGGTGA
42817 GGGTATCGATACCATGGTGA
1 GGGTATCGATACCATGGTGA
42837 GGGTATCGATACCA
1 GGGTATCGATACCA
42851 GGCTATATCG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.26, C:0.17, G:0.33, T:0.24
Consensus pattern (20 bp):
GGGTATCGATACCATGGTGA
Found at i:42918 original size:115 final size:115
Alignment explanation
Indices: 42704--42926 Score: 263
Period size: 115 Copynumber: 1.9 Consensus size: 115
42694 CAAGGAATGC
* * *
42704 GTATCGATACCATGGTAAGGGTATCGACACCAGTAAACATCGAATCTAATTTGGGTATCGATACA
1 GTATCGATACCATGGTAAGGGTATCGACACCAGGAAACATCGAAGCTAATTTCGGTATCGATACA
* * *
42769 TAGAGGGGGTATCGGTATCATAACATAGGGGTATCGATACCATGGTGAGG
66 TAGAGGGGGCATCGATACCATAACATAGGGGTATCGATACCATGGTGAGG
* * ** * * *
42819 GTATCGATACCATGGTGAGGGTATCGATACCAGGCTATATCGAAGCTAATTTCGGTATTGATTCA
1 GTATCGATACCATGGTAAGGGTATCGACACCAGGAAACATCGAAGCTAATTTCGGTATCGATACA
* *
42884 T-GAAGGGGGCATTGATACCCT-A-ATAGGGTAGTATCGATACCAT
66 TAG-AGGGGGCATCGATACCATAACATAGGG--GTATCGATACCAT
42927 AAGTAGGGGT
Statistics
Matches: 90, Mismatches: 15, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
113 6 0.07
114 2 0.02
115 82 0.91
ACGTcount: A:0.30, C:0.16, G:0.27, T:0.27
Consensus pattern (115 bp):
GTATCGATACCATGGTAAGGGTATCGACACCAGGAAACATCGAAGCTAATTTCGGTATCGATACA
TAGAGGGGGCATCGATACCATAACATAGGGGTATCGATACCATGGTGAGG
Found at i:42940 original size:21 final size:21
Alignment explanation
Indices: 42897--42949 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 21
42887 AGGGGGCATT
42897 GATACCCTAA-TAGGGTAGTATC
1 GATA-CCTAAGTAGGG-AGTATC
42919 GATACCATAAGTAGGG-GTATC
1 GATACC-TAAGTAGGGAGTATC
*
42940 GAAACCTAAG
1 GATACCTAAG
42950 GGCTAGAAGT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
20 4 0.14
21 12 0.43
22 7 0.25
23 5 0.18
ACGTcount: A:0.36, C:0.17, G:0.25, T:0.23
Consensus pattern (21 bp):
GATACCTAAGTAGGGAGTATC
Found at i:43463 original size:45 final size:45
Alignment explanation
Indices: 43411--43815 Score: 497
Period size: 45 Copynumber: 9.0 Consensus size: 45
43401 AAAGGATGCC
** * **
43411 ATAGTTGAAATGTATATGTATACATTGTCAACAGAAAAACATACT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
* * *
43456 TTAGTTGAAATGTATATGGGTACATTATCAACATAAAAGTATGCT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
* * ** *
43501 AGAGTTGAAATGCATATGGGTGTATTATCAACATAAAAGTATACT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
* * *
43546 ATGGTTGAAATGTATATGGGTACATTATTAACAGAAATGTATACT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
* * **
43591 ATGGTTGAAATGTATATGGGTACATTATCAACATAAAAACATACT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
* * *
43636 TTAGTTGAAATGTATATGGGTACATTATCAACATAAAAGTATGCT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
* ** * * *
43681 AGAGTTGAAATACATGTGGG-AGTATTATCAATAGAAAAGTATACT
1 ATAGTTGAAATGTATATGGGTA-CATTATCAACAGAAAAGTATACT
* * *
43726 ATGGTTGAAATGTATATGAGTACATTATCAACAAAAAAGTATACT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
*
43771 ATGGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
43816 CACTACAGCA
Statistics
Matches: 306, Mismatches: 52, Indels: 4
0.85 0.14 0.01
Matches are distributed among these distances:
44 1 0.00
45 304 0.99
46 1 0.00
ACGTcount: A:0.41, C:0.09, G:0.18, T:0.32
Consensus pattern (45 bp):
ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
Found at i:44025 original size:43 final size:43
Alignment explanation
Indices: 43945--44043 Score: 119
Period size: 43 Copynumber: 2.3 Consensus size: 43
43935 TGAGAACAAA
* *
43945 AAACGCCGCAATAGGTCAATATCTATTACGGCATTTTTTGAAC
1 AAACGCCGCAAAAGGTCAATATCTATTACGGCATTTTTGGAAC
* * ** *
43988 AAACACCGCAAAAGGTCGATATCTA-TAGCGGTGTTTTTGGAAT
1 AAACGCCGCAAAAGGTCAATATCTATTA-CGGCATTTTTGGAAC
44031 AAACGCCGCAAAA
1 AAACGCCGCAAAA
44044 AGTTATGATA
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
42 2 0.04
43 45 0.96
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.25
Consensus pattern (43 bp):
AAACGCCGCAAAAGGTCAATATCTATTACGGCATTTTTGGAAC
Found at i:44058 original size:43 final size:42
Alignment explanation
Indices: 43973--44128 Score: 127
Period size: 43 Copynumber: 3.7 Consensus size: 42
43963 ATATCTATTA
* * * * * * *
43973 CGGCATTTTTTGAACAAACACCGCAAAAGGTCGATATCTATAG
1 CGGCGTTTTTGGAAAAAACGCCGCAAAAAGT-GAGATATATAG
* * *
44016 CGGTGTTTTTGGAATAAACGCCGCAAAAAGTTATGATATATAG
1 CGGCGTTTTTGGAAAAAACGCCGCAAAAAGTGA-GATATATAG
* * * *
44059 CGGCGTTTCT--AAAAGAATGCCGTAAAAAGTGAGATCTATAG
1 CGGCGTTTTTGGAAAA-AACGCCGCAAAAAGTGAGATATATAG
*
44100 CGGCGTTTTTGGATACAAACGCCGCAAAA
1 CGGCGTTTTTGGA-AAAAACGCCGCAAAA
44129 GATAAGACCT
Statistics
Matches: 88, Mismatches: 20, Indels: 10
0.75 0.17 0.08
Matches are distributed among these distances:
41 20 0.23
42 15 0.17
43 51 0.58
44 2 0.02
ACGTcount: A:0.35, C:0.17, G:0.22, T:0.26
Consensus pattern (42 bp):
CGGCGTTTTTGGAAAAAACGCCGCAAAAAGTGAGATATATAG
Found at i:44152 original size:43 final size:43
Alignment explanation
Indices: 44094--44294 Score: 167
Period size: 43 Copynumber: 4.7 Consensus size: 43
44084 AAAGTGAGAT
* * *
44094 CTATAGCGGCGTTTTTGGATACAAACGCCGCAAAAGATAAGAC
1 CTATATCGGCGTTTTTGGACACAAACGCCGCAAAAGATTAGAC
* * * * ** * *
44137 CTATATTGGCATTTTTAGA-ACAAACGTCGTTATAGGTCTA-AC
1 CTATATCGGCGTTTTTGGACACAAACGCCGCAAAAGAT-TAGAC
* * *
44179 CT-TTTGCGGCGTTTTTAGACACAAACGCCGCAAAAGGTTAGAC
1 CTATAT-CGGCGTTTTTGGACACAAACGCCGCAAAAGATTAGAC
* * *
44222 CTATAACGGCGTTTTTGAACACAAACGCCGCAAAA-AGTCAGAC
1 CTATATCGGCGTTTTTGGACACAAACGCCGCAAAAGA-TTAGAC
* * *
44265 TTATAGCGGCGTTTTTGGATACAAACGCCG
1 CTATATCGGCGTTTTTGGACACAAACGCCG
44295 TTAATTACCT
Statistics
Matches: 125, Mismatches: 27, Indels: 12
0.76 0.16 0.07
Matches are distributed among these distances:
41 2 0.02
42 30 0.24
43 92 0.74
44 1 0.01
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.26
Consensus pattern (43 bp):
CTATATCGGCGTTTTTGGACACAAACGCCGCAAAAGATTAGAC
Found at i:46777 original size:80 final size:79
Alignment explanation
Indices: 46668--46821 Score: 236
Period size: 80 Copynumber: 1.9 Consensus size: 79
46658 GGAATCCCTG
* * * *
46668 CAAGTAATATGAAGGACTAAACTTCTCAATTTACATTCAGGTCAAATTGATAACAGATATTTACA
1 CAAGTAAAATGAAGGACTAAACTTCTCAATTTACATTCAGATCAAATTGAAAACAAATATTTA-A
*
46733 GACCACTGCTAATTA
65 GACAACTGCTAATTA
* *
46748 CAAGTAAAATGAAGGACTAAACTTCTCAATTTTCATTCAGATCAAATTTAAAACAAATATTTAAG
1 CAAGTAAAATGAAGGACTAAACTTCTCAATTTACATTCAGATCAAATTGAAAACAAATATTTAAG
46813 ACAACTGCT
66 ACAACTGCT
46822 CATTGCAACA
Statistics
Matches: 67, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
79 10 0.15
80 57 0.85
ACGTcount: A:0.42, C:0.17, G:0.11, T:0.30
Consensus pattern (79 bp):
CAAGTAAAATGAAGGACTAAACTTCTCAATTTACATTCAGATCAAATTGAAAACAAATATTTAAG
ACAACTGCTAATTA
Found at i:49028 original size:41 final size:42
Alignment explanation
Indices: 48971--49150 Score: 210
Period size: 41 Copynumber: 4.4 Consensus size: 42
48961 GAGGATTGGC
*
48971 AACGCCACTATAGTAC-ATGTTTATAACGGCGTTTGTATAAA
1 AACGCCACTAAAGTACAATGTTTATAACGGCGTTTGTATAAA
* * *
49012 AACGCCACTATAGTAC-ATGTGTATAACGGCATTTGTATAAA
1 AACGCCACTAAAGTACAATGTTTATAACGGCGTTTGTATAAA
* * *
49053 AACGCCACTAAAGTACAAT-TCTATAGCGACGTTTGTAT-AA
1 AACGCCACTAAAGTACAATGTTTATAACGGCGTTTGTATAAA
* * *
49093 AACTGCCACTAAATTACGA-GTCTT-TAGCGGCGTTTGTATAAA
1 AAC-GCCACTAAAGTACAATGT-TTATAACGGCGTTTGTATAAA
49135 AACGCCACTAAAGTAC
1 AACGCCACTAAAGTAC
49151 TACTCTTTTG
Statistics
Matches: 122, Mismatches: 12, Indels: 10
0.85 0.08 0.07
Matches are distributed among these distances:
40 5 0.04
41 109 0.89
42 8 0.07
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.28
Consensus pattern (42 bp):
AACGCCACTAAAGTACAATGTTTATAACGGCGTTTGTATAAA
Found at i:49158 original size:41 final size:39
Alignment explanation
Indices: 48971--49186 Score: 202
Period size: 41 Copynumber: 5.3 Consensus size: 39
48961 GAGGATTGGC
* * *
48971 AACGCCACTATAGTACATGTTTATAACGGCGTTTGTATAAA
1 AACGCCACTAAAGTACAT-CTT-TAGCGGCGTTTGTATAAA
* * * *
49012 AACGCCACTATAGTACATGTGTATAACGGCATTTGTATAAA
1 AACGCCACTAAAGTACATCT-T-TAGCGGCGTTTGTATAAA
* *
49053 AACGCCACTAAAGTACAATTCTATAGCGACGTTTGTAT-AA
1 AACGCCACTAAAGTAC-A-TCTTTAGCGGCGTTTGTATAAA
*
49093 AACTGCCACTAAATTACGAGTCTTTAGCGGCGTTTGTATAAA
1 AAC-GCCACTAAAGTAC-A-TCTTTAGCGGCGTTTGTATAAA
*
49135 AACGCCACTAAAGTACTACTCTTTTGCGGCGTTTGT-TGAAAA
1 AACGCCACTAAAGTAC-A-TCTTTAGCGGCGTTTGTAT--AAA
49177 AACGCCACTA
1 AACGCCACTA
49187 TCGATGAACC
Statistics
Matches: 151, Mismatches: 17, Indels: 13
0.83 0.09 0.07
Matches are distributed among these distances:
40 7 0.05
41 123 0.81
42 19 0.13
43 2 0.01
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Consensus pattern (39 bp):
AACGCCACTAAAGTACATCTTTAGCGGCGTTTGTATAAA
Found at i:49168 original size:82 final size:82
Alignment explanation
Indices: 48971--49186 Score: 231
Period size: 82 Copynumber: 2.6 Consensus size: 82
48961 GAGGATTGGC
* ** * * * *
48971 AACGCCACTATAGTACATGTTTATAACGGCGTTTGTATAAAAACGCCACTATAGTACATGTGTAT
1 AACGCCACTAAAGTACAACTCTATAGCGGCGTTTGTATAAAAACGCCACTAAAGTACATGTCTAT
49036 AACGGCATTTGTATAAA
66 AACGGCATTTGTATAAA
* * *
49053 AACGCCACTAAAGTACAATTCTATAGCGACGTTTGTAT-AAAACTGCCACTAAATTACGA-GTCT
1 AACGCCACTAAAGTACAACTCTATAGCGGCGTTTGTATAAAAAC-GCCACTAAAGTAC-ATGTCT
* * *
49116 TTAGCGGCGTTTGTATAAA
64 ATAACGGCATTTGTATAAA
* * *
49135 AACGCCACTAAAGTACTACTCTTTTGCGGCGTTTGT-TGAAAAAACGCCACTA
1 AACGCCACTAAAGTACAACTCTATAGCGGCGTTTGTAT--AAAAACGCCACTA
49187 TCGATGAACC
Statistics
Matches: 112, Mismatches: 17, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
81 6 0.05
82 93 0.83
83 8 0.07
84 5 0.04
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Consensus pattern (82 bp):
AACGCCACTAAAGTACAACTCTATAGCGGCGTTTGTATAAAAACGCCACTAAAGTACATGTCTAT
AACGGCATTTGTATAAA
Found at i:50750 original size:21 final size:21
Alignment explanation
Indices: 50724--50770 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
50714 CAAAAGTAAT
50724 AAGGTTGATAATATTGAAAAG
1 AAGGTTGATAATATTGAAAAG
50745 AAGGTTGATAATATTGAAAAG
1 AAGGTTGATAATATTGAAAAG
50766 AAGGT
1 AAGGT
50771 CGAGATTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.26, T:0.28
Consensus pattern (21 bp):
AAGGTTGATAATATTGAAAAG
Found at i:51646 original size:2 final size:2
Alignment explanation
Indices: 51639--51682 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
51629 TGTCAGGAAG
51639 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
51681 AT
1 AT
51683 GACTTTTATG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:54138 original size:22 final size:21
Alignment explanation
Indices: 54113--54162 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
54103 AGGGGGCATT
54113 GATACCCTAA-TAGGGTAGTATC
1 GATACCCTAAGTAGGG--GTATC
*
54135 GATACCATAAGTAGGGGTATC
1 GATACCCTAAGTAGGGGTATC
*
54156 GAAACCC
1 GATACCC
54163 AAGGGCCAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
21 10 0.42
22 9 0.38
23 5 0.21
ACGTcount: A:0.34, C:0.20, G:0.24, T:0.22
Consensus pattern (21 bp):
GATACCCTAAGTAGGGGTATC
Found at i:54156 original size:21 final size:21
Alignment explanation
Indices: 54113--54157 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
54103 AGGGGGCATT
*
54113 GATACCCTAATAGGGTAGTATC
1 GATACCATAATAGGG-AGTATC
54135 GATACCATAAGTAGGG-GTATC
1 GATACCATAA-TAGGGAGTATC
54156 GA
1 GA
54158 AACCCAAGGG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 7 0.33
22 9 0.43
23 5 0.24
ACGTcount: A:0.33, C:0.16, G:0.27, T:0.24
Consensus pattern (21 bp):
GATACCATAATAGGGAGTATC
Found at i:54681 original size:45 final size:45
Alignment explanation
Indices: 54629--55033 Score: 524
Period size: 45 Copynumber: 9.0 Consensus size: 45
54619 AAAGGATGCC
** * **
54629 ATAGTTGAAATGTATATGTATACATTGTCAACAGAAAAACATACT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
* * *
54674 TTAGTTGAAATGTATATGGGTACATTATCAACATAAAAGTATGCT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
* * ** *
54719 AGAGTTGAAATGCATATGGGTGTATTATCAACATAAAAGTATACT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
* *
54764 ATGGTTGAAATGTATATGGGTACATTATTAACAGAAAAGTATACT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
* * **
54809 ATGGTTAAAATGTATATGGGTACATTATCAACAGAAAAACATACT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
* * *
54854 TTAGTTGAAATGTATATGGGTACATTATCAACATAAAAGTATGCT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
* * * *
54899 AGAGTTGAAATGCATGTGGG-AGTATTATCAACAGAAAAGTATACT
1 ATAGTTGAAATGTATATGGGTA-CATTATCAACAGAAAAGTATACT
* * *
54944 ATGGTTGAAATGTATATGAGTACATTATCAACAAAAAAGTATACT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
*
54989 ATGGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
55034 CACTACAGCA
Statistics
Matches: 310, Mismatches: 48, Indels: 4
0.86 0.13 0.01
Matches are distributed among these distances:
44 1 0.00
45 308 0.99
46 1 0.00
ACGTcount: A:0.41, C:0.09, G:0.18, T:0.32
Consensus pattern (45 bp):
ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
Found at i:54855 original size:180 final size:180
Alignment explanation
Indices: 54636--55026 Score: 692
Period size: 180 Copynumber: 2.2 Consensus size: 180
54626 GCCATAGTTG
** *
54636 AAATGTATATGTATACATTGTCAACAGAAAAACATACTTTAGTTGAAATGTATATGGGTACATTA
1 AAATGTATATGGGTACATTATCAACAGAAAAACATACTTTAGTTGAAATGTATATGGGTACATTA
* *
54701 TCAACATAAAAGTATGCTAGAGTTGAAATGCATATGGGTGTATTATCAACATAAAAGTATACTAT
66 TCAACATAAAAGTATGCTAGAGTTGAAATGCATATGGGAGTATTATCAACAGAAAAGTATACTAT
* * *
54766 GGTTGAAATGTATATGGGTACATTATTAACAGAAAAGTATACTATGGTTA
131 GGTTGAAATGTATATGAGTACATTATCAACAAAAAAGTATACTATGGTTA
54816 AAATGTATATGGGTACATTATCAACAGAAAAACATACTTTAGTTGAAATGTATATGGGTACATTA
1 AAATGTATATGGGTACATTATCAACAGAAAAACATACTTTAGTTGAAATGTATATGGGTACATTA
*
54881 TCAACATAAAAGTATGCTAGAGTTGAAATGCATGTGGGAGTATTATCAACAGAAAAGTATACTAT
66 TCAACATAAAAGTATGCTAGAGTTGAAATGCATATGGGAGTATTATCAACAGAAAAGTATACTAT
*
54946 GGTTGAAATGTATATGAGTACATTATCAACAAAAAAGTATACTATGGTTG
131 GGTTGAAATGTATATGAGTACATTATCAACAAAAAAGTATACTATGGTTA
54996 AAATGTATATGGGTACATTATCAACAGAAAA
1 AAATGTATATGGGTACATTATCAACAGAAAA
55027 GTATACTCAC
Statistics
Matches: 201, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
180 201 1.00
ACGTcount: A:0.41, C:0.09, G:0.18, T:0.31
Consensus pattern (180 bp):
AAATGTATATGGGTACATTATCAACAGAAAAACATACTTTAGTTGAAATGTATATGGGTACATTA
TCAACATAAAAGTATGCTAGAGTTGAAATGCATATGGGAGTATTATCAACAGAAAAGTATACTAT
GGTTGAAATGTATATGAGTACATTATCAACAAAAAAGTATACTATGGTTA
Found at i:55250 original size:43 final size:43
Alignment explanation
Indices: 55185--55407 Score: 136
Period size: 43 Copynumber: 5.2 Consensus size: 43
55175 TGAGAACGAA
* * *
55185 AAACGCCGCAATAGGTCAATATCTATTA-CGGCATTTTTTGAAC
1 AAACGCCGCAAAAGGTCAATATCCA-TAGCGGCATTTTTGGAAC
* * *
55228 AAACGCCGCAAAAGGTCGATATCCATAGCGGCGTTTTTGGAAT
1 AAACGCCGCAAAAGGTCAATATCCATAGCGGCATTTTTGGAAC
* * * ** * * *
55271 AAACGCTGCAAAAAGTTATGATAT--ATAGCGGTGTTTCTAGAAA
1 AAACGCCGCAAAAGGTCA--ATATCCATAGCGGCATTTTTGGAAC
* * * * *
55314 AAACGCCACAAAAAGTC-ATATCTATAGTGGCGTTTTTGGATAC
1 AAACGCCGCAAAAGGTCAATATCCATAGCGGCATTTTTGGA-AC
* * * *
55357 AAACACCGCAAAAGAT-AAGA-CCTATA-CTGGCATTTTTAGAAC
1 AAACGCCGCAAAAGGTCAATATCC-ATAGC-GGCATTTTTGGAAC
55399 AAACGCCGC
1 AAACGCCGC
55408 TAATTACCTT
Statistics
Matches: 139, Mismatches: 32, Indels: 19
0.73 0.17 0.10
Matches are distributed among these distances:
40 4 0.03
42 26 0.19
43 105 0.76
45 4 0.03
ACGTcount: A:0.36, C:0.20, G:0.19, T:0.25
Consensus pattern (43 bp):
AAACGCCGCAAAAGGTCAATATCCATAGCGGCATTTTTGGAAC
Found at i:55397 original size:85 final size:86
Alignment explanation
Indices: 55213--55405 Score: 203
Period size: 85 Copynumber: 2.3 Consensus size: 86
55203 ATATCTATTA
* * * * * *
55213 CGGCATTTTTTGAACAAACGCCGCAAAAGGTCGATATCCATAGCGGCGTTTTTGGAATAAACGCT
1 CGGCATTTTTAGAACAAACGCCACAAAAAGTCGATATCCATAGCGGCGTTTTTGGAACAAACACC
* * *
55278 GCAAAAAGTTATGATATATAG
66 GCAAAAAGATAAGACATATAG
** * * * *
55299 CGGTGTTTCTAGAAAAAACGCCACAAAAAGTC-ATATCTATAGTGGCGTTTTTGGATACAAACAC
1 CGGCATTTTTAGAACAAACGCCACAAAAAGTCGATATCCATAGCGGCGTTTTTGGA-ACAAACAC
*
55363 CGC-AAAAGATAAGACCTATA-
65 CGCAAAAAGATAAGACATATAG
55383 CTGGCATTTTTAGAACAAACGCC
1 C-GGCATTTTTAGAACAAACGCC
55406 GCTAATTACC
Statistics
Matches: 85, Mismatches: 20, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
84 1 0.01
85 51 0.60
86 33 0.39
ACGTcount: A:0.36, C:0.19, G:0.20, T:0.25
Consensus pattern (86 bp):
CGGCATTTTTAGAACAAACGCCACAAAAAGTCGATATCCATAGCGGCGTTTTTGGAACAAACACC
GCAAAAAGATAAGACATATAG
Found at i:60141 original size:41 final size:42
Alignment explanation
Indices: 60084--60263 Score: 226
Period size: 41 Copynumber: 4.4 Consensus size: 42
60074 GAGGATTGGC
*
60084 AACGCCACTATAGTAC-ATGTTTATAACGGCGTTTGTATAAA
1 AACGCCACTAAAGTACAATGTTTATAACGGCGTTTGTATAAA
* * *
60125 AACGCCACTATAGTAC-ATGTGTATAACGGTGTTTGTATAAA
1 AACGCCACTAAAGTACAATGTTTATAACGGCGTTTGTATAAA
* *
60166 AACGCCACTAAAGTACAAT-TCTATAGCGGCGTTTGTATAAA
1 AACGCCACTAAAGTACAATGTTTATAACGGCGTTTGTATAAA
* * * *
60207 AATGCCACTAAATTACGA-GTCTT-TAGCGGCGTTTGTATAAA
1 AACGCCACTAAAGTACAATGT-TTATAACGGCGTTTGTATAAA
60248 AACGCCACTAAAGTAC
1 AACGCCACTAAAGTAC
60264 TACTCTTTTG
Statistics
Matches: 124, Mismatches: 12, Indels: 6
0.87 0.08 0.04
Matches are distributed among these distances:
41 121 0.98
42 3 0.02
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (42 bp):
AACGCCACTAAAGTACAATGTTTATAACGGCGTTTGTATAAA
Found at i:60241 original size:82 final size:81
Alignment explanation
Indices: 60084--60299 Score: 247
Period size: 82 Copynumber: 2.6 Consensus size: 81
60074 GAGGATTGGC
* * * * *
60084 AACGCCACTATAGTACATGTTTATAACGGCGTTTGTATAAAAACGCCACTATAGTACATGTGTAT
1 AACGCCACTAAAGTACAT-TCTATAGCGGCGTTTGTATAAAAACGCCACTAAAGTACATGTCTAT
*
60149 AACGGTGTTTGTATAAA
65 AACGGCGTTTGTATAAA
* * *
60166 AACGCCACTAAAGTACAATTCTATAGCGGCGTTTGTATAAAAATGCCACTAAATTACGA-GTCTT
1 AACGCCACTAAAGTAC-ATTCTATAGCGGCGTTTGTATAAAAACGCCACTAAAGTAC-ATGTCTA
*
60230 TAGCGGCGTTTGTATAAA
64 TAACGGCGTTTGTATAAA
* * *
60248 AACGCCACTAAAGTACTACTCTTTTGCGGCGTTTGT-TGAAAAAACGCCACTA
1 AACGCCACTAAAGTAC-ATTCTATAGCGGCGTTTGTAT--AAAAACGCCACTA
60300 TCGATGAACC
Statistics
Matches: 115, Mismatches: 15, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
81 1 0.01
82 99 0.86
83 15 0.13
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (81 bp):
AACGCCACTAAAGTACATTCTATAGCGGCGTTTGTATAAAAACGCCACTAAAGTACATGTCTATA
ACGGCGTTTGTATAAA
Found at i:60271 original size:41 final size:39
Alignment explanation
Indices: 60084--60299 Score: 218
Period size: 41 Copynumber: 5.3 Consensus size: 39
60074 GAGGATTGGC
* * *
60084 AACGCCACTATAGTACATGTTTATAACGGCGTTTGTATAAA
1 AACGCCACTAAAGTACAT-CTT-TAGCGGCGTTTGTATAAA
* * * *
60125 AACGCCACTATAGTACATGTGTATAACGGTGTTTGTATAAA
1 AACGCCACTAAAGTACATCT-T-TAGCGGCGTTTGTATAAA
*
60166 AACGCCACTAAAGTACAATTCTATAGCGGCGTTTGTATAAA
1 AACGCCACTAAAGTAC-A-TCTTTAGCGGCGTTTGTATAAA
* *
60207 AATGCCACTAAATTACGAGTCTTTAGCGGCGTTTGTATAAA
1 AACGCCACTAAAGTAC-A-TCTTTAGCGGCGTTTGTATAAA
*
60248 AACGCCACTAAAGTACTACTCTTTTGCGGCGTTTGT-TGAAAA
1 AACGCCACTAAAGTAC-A-TCTTTAGCGGCGTTTGTAT--AAA
60290 AACGCCACTA
1 AACGCCACTA
60300 TCGATGAACC
Statistics
Matches: 153, Mismatches: 17, Indels: 9
0.85 0.09 0.05
Matches are distributed among these distances:
40 2 0.01
41 135 0.88
42 14 0.09
43 2 0.01
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (39 bp):
AACGCCACTAAAGTACATCTTTAGCGGCGTTTGTATAAA
Found at i:60320 original size:82 final size:81
Alignment explanation
Indices: 60084--60343 Score: 199
Period size: 82 Copynumber: 3.2 Consensus size: 81
60074 GAGGATTGGC
* ** * * **
60084 AACGCCACTATAGTACATGTTTATAACGGCGTTTGTATAAAAACGCCACT-AT-A-GTACATGTG
1 AACGCCACTAAAGTACAACTCTATAGCGGCGTTTGTATAAAAACGCCACTAATGACG-A-ACCT-
* *
60146 TATAACGGTGTTTGTATAAA
63 T-TAGCGGCGTTTGTATAAA
* * * **
60166 AACGCCACTAAAGTACAATTCTATAGCGGCGTTTGTATAAAAATGCCACTAAATTACGAGTCTTT
1 AACGCCACTAAAGTACAACTCTATAGCGGCGTTTGTATAAAAACGCCACT-AATGACGAACCTTT
60231 AGCGGCGTTTGTATAAA
65 AGCGGCGTTTGTATAAA
* * * *
60248 AACGCCACTAAAGTACTACTCTTTTGCGGCGTTTGT-TGAAAAAACGCCACT-ATCGATGAACCT
1 AACGCCACTAAAGTACAACTCTATAGCGGCGTTTGTAT--AAAAACGCCACTAAT-GACGAACCT
* *
60311 ATT-GTGGCGTTTTTATAAA
63 -TTAGCGGCGTTTGTATAAA
**
60330 AACGCTGCTAAAGT
1 AACGCCACTAAAGT
60344 TACCATTTTG
Statistics
Matches: 147, Mismatches: 23, Indels: 16
0.79 0.12 0.09
Matches are distributed among these distances:
81 3 0.02
82 123 0.84
83 14 0.10
84 4 0.03
85 2 0.01
86 1 0.01
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.30
Consensus pattern (81 bp):
AACGCCACTAAAGTACAACTCTATAGCGGCGTTTGTATAAAAACGCCACTAATGACGAACCTTTA
GCGGCGTTTGTATAAA
Found at i:61896 original size:21 final size:21
Alignment explanation
Indices: 61870--61916 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
61860 CAAAAGTAAT
*
61870 AAGGTTGATAATATTGAAAAG
1 AAGGTTGATAATAATGAAAAG
61891 AAGGTTGATAATAATGAAAAG
1 AAGGTTGATAATAATGAAAAG
61912 AAGGT
1 AAGGT
61917 CGAGATTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.49, C:0.00, G:0.26, T:0.26
Consensus pattern (21 bp):
AAGGTTGATAATAATGAAAAG
Found at i:62788 original size:2 final size:2
Alignment explanation
Indices: 62781--62842 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
62771 GATCAGGAAG
62781 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
62823 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
62843 GACTTTTATG
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:63143 original size:2 final size:2
Alignment explanation
Indices: 63136--63171 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
63126 TTTTAGCGAA
63136 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
63172 GTGTGTGTGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:65291 original size:22 final size:21
Alignment explanation
Indices: 65266--65315 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
65256 GAAGGGCATT
65266 GATACCCTAA-TAGGGTAGTATC
1 GATACCCTAAGTAGGG--GTATC
*
65288 GATACCATAAGTAGGGGTATC
1 GATACCCTAAGTAGGGGTATC
*
65309 GAAACCC
1 GATACCC
65316 AAGGGCCAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
21 10 0.42
22 9 0.38
23 5 0.21
ACGTcount: A:0.34, C:0.20, G:0.24, T:0.22
Consensus pattern (21 bp):
GATACCCTAAGTAGGGGTATC
Found at i:65309 original size:21 final size:21
Alignment explanation
Indices: 65266--65310 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
65256 GAAGGGCATT
*
65266 GATACCCTAATAGGGTAGTATC
1 GATACCATAATAGGG-AGTATC
65288 GATACCATAAGTAGGG-GTATC
1 GATACCATAA-TAGGGAGTATC
65309 GA
1 GA
65311 AACCCAAGGG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 7 0.33
22 9 0.43
23 5 0.24
ACGTcount: A:0.33, C:0.16, G:0.27, T:0.24
Consensus pattern (21 bp):
GATACCATAATAGGGAGTATC
Found at i:65881 original size:45 final size:45
Alignment explanation
Indices: 65776--66214 Score: 560
Period size: 45 Copynumber: 9.8 Consensus size: 45
65766 GGATGCCATA
** * ** * *
65776 GTTGAAATGTATATGTATACATTGTCAACAGAAAAACATACTTTA
1 GTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACTATG
* * * *
65821 GTTAAAAGGTATATGGGTACATTATCAACATAAAAGTATGCTA-G
1 GTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACTATG
** ** *
65865 AGTTGAAATGCGTATGGGTGTATTATCAACATAAAAGTATACTATG
1 -GTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACTATG
*
65911 GTTGAAATGTATATGGGTACATTATTAACAGAAAAGTATACTATG
1 GTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACTATG
* * *
65956 GTTGAAATGTATATGGGTACATTATCAACAGAAAA-CATACTTTA
1 GTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACTATG
* * *
66000 GTTGAAATGTATATGGGTACATTATCAACATAAAAGTATGCTATA
1 GTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACTATG
* * **
66045 GTTGAAATGCATGTGGGTGTATTATCAACAGAAAAGTATACTATG
1 GTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACTATG
* *
66090 GTTGAAATGTATATGAGTACATTATCAACAAAAAAGTATACTATG
1 GTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACTATG
66135 GTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACTA-G
1 GTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACTATG
* *
66179 AGTTGAAATGCATATGGGTGCATTATCAACAGAAAA
1 -GTTGAAATGTATATGGGTACATTATCAACAGAAAA
66215 AATGTTATTG
Statistics
Matches: 341, Mismatches: 49, Indels: 8
0.86 0.12 0.02
Matches are distributed among these distances:
44 41 0.12
45 299 0.88
46 1 0.00
ACGTcount: A:0.40, C:0.09, G:0.19, T:0.31
Consensus pattern (45 bp):
GTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACTATG
Found at i:66042 original size:179 final size:179
Alignment explanation
Indices: 65776--66214 Score: 698
Period size: 179 Copynumber: 2.4 Consensus size: 179
65766 GGATGCCATA
** * * *
65776 GTTGAAATGTATATGTATACATTGTCAACAGAAAAACATACTTTAGTTAAAAGGTATATGGGTAC
1 GTTGAAATGTATATGGGTACATTATCAACAG-AAAACATACTTTAGTTGAAATGTATATGGGTAC
* *
65841 ATTATCAACATAAAAGTATGCTAGAGTTGAAATGCGTATGGGTGTATTATCAACATAAAAGTATA
65 ATTATCAACATAAAAGTATGCTAGAGTTGAAATGCATATGGGTGTATTATCAACAGAAAAGTATA
* * *
65906 CTATGGTTGAAATGTATATGGGTACATTATTAACAGAAAAGTATACTATG
130 CTATGGTTGAAATGTATATGAGTACATTATCAACAAAAAAGTATACTATG
65956 GTTGAAATGTATATGGGTACATTATCAACAGAAAACATACTTTAGTTGAAATGTATATGGGTACA
1 GTTGAAATGTATATGGGTACATTATCAACAGAAAACATACTTTAGTTGAAATGTATATGGGTACA
* *
66021 TTATCAACATAAAAGTATGCTATAGTTGAAATGCATGTGGGTGTATTATCAACAGAAAAGTATAC
66 TTATCAACATAAAAGTATGCTAGAGTTGAAATGCATATGGGTGTATTATCAACAGAAAAGTATAC
66086 TATGGTTGAAATGTATATGAGTACATTATCAACAAAAAAGTATACTATG
131 TATGGTTGAAATGTATATGAGTACATTATCAACAAAAAAGTATACTATG
* ** * *
66135 GTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACTAGAGTTGAAATGCATATGGGTGC
1 GTTGAAATGTATATGGGTACATTATCAACAGAAAA-CATACTTTAGTTGAAATGTATATGGGTAC
*
66200 ATTATCAACAGAAAA
65 ATTATCAACATAAAA
66215 AATGTTATTG
Statistics
Matches: 240, Mismatches: 18, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
179 174 0.73
180 66 0.28
ACGTcount: A:0.40, C:0.09, G:0.19, T:0.31
Consensus pattern (179 bp):
GTTGAAATGTATATGGGTACATTATCAACAGAAAACATACTTTAGTTGAAATGTATATGGGTACA
TTATCAACATAAAAGTATGCTAGAGTTGAAATGCATATGGGTGTATTATCAACAGAAAAGTATAC
TATGGTTGAAATGTATATGAGTACATTATCAACAAAAAAGTATACTATG
Found at i:66096 original size:224 final size:224
Alignment explanation
Indices: 65774--66214 Score: 625
Period size: 224 Copynumber: 2.0 Consensus size: 224
65764 AAGGATGCCA
* * * *
65774 TAGTTGAAATGTATATGTATACATTGTCAACAGAAAAACATACTTTAGTTAAAAGGTATATGGGT
1 TAGTTGAAATGTATATGGATACATTATCAACAGAAAAACATACTATAGTTAAAAGGCATATGGGT
* * * * ** *
65839 ACATTATCAACATAAAAGTATGCTAGAGTTGAAATGCGTATGGGTGTATTATCAACATAAAAGTA
66 ACATTATCAACAGAAAAGTATACTAGAGTTGAAATGCATATGAGTACATTATCAACAAAAAAGTA
* *
65904 TACTATGGTTGAAATGTATATGGGTACATTATTAACAGAAAAGTATACTATG-GTTGAAATGTAT
131 TACTATGGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACTA-GAGTTGAAATGCAT
65968 ATGGGTACATTATCAACAGAAAACATACTT
195 ATGGGTACATTATCAACAGAAAACATACTT
* * ** * * * *
65998 TAGTTGAAATGTATATGGGTACATTATCAACATAAAAGTATGCTATAGTTGAAATGCATGTGGGT
1 TAGTTGAAATGTATATGGATACATTATCAACAGAAAAACATACTATAGTTAAAAGGCATATGGGT
** *
66063 GTATTATCAACAGAAAAGTATACTATG-GTTGAAATGTATATGAGTACATTATCAACAAAAAAGT
66 ACATTATCAACAGAAAAGTATACTA-GAGTTGAAATGCATATGAGTACATTATCAACAAAAAAGT
66127 ATACTATGGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACTAGAGTTGAAATGCAT
130 ATACTATGGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACTAGAGTTGAAATGCAT
*
66192 ATGGGTGCATTATCAACAGAAAA
195 ATGGGTACATTATCAACAGAAAA
66215 AATGTTATTG
Statistics
Matches: 190, Mismatches: 25, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
223 1 0.01
224 188 0.99
225 1 0.01
ACGTcount: A:0.40, C:0.09, G:0.19, T:0.31
Consensus pattern (224 bp):
TAGTTGAAATGTATATGGATACATTATCAACAGAAAAACATACTATAGTTAAAAGGCATATGGGT
ACATTATCAACAGAAAAGTATACTAGAGTTGAAATGCATATGAGTACATTATCAACAAAAAAGTA
TACTATGGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACTAGAGTTGAAATGCATA
TGGGTACATTATCAACAGAAAACATACTT
Found at i:69331 original size:15 final size:15
Alignment explanation
Indices: 69311--69341 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
69301 TGGTGCTATT
69311 ACATTCAAGATTCAC
1 ACATTCAAGATTCAC
69326 ACATTCAAGATTCAC
1 ACATTCAAGATTCAC
69341 A
1 A
69342 ACCGGTCAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.42, C:0.26, G:0.06, T:0.26
Consensus pattern (15 bp):
ACATTCAAGATTCAC
Done.