Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007047.1 Hibiscus syriacus cultivar Beakdansim tig00018272_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: 93584
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:1336 original size:36 final size:36
Alignment explanation
Indices: 1278--1347 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
1268 AATGAATGGG
*
1278 TTGATTACCAACAAATGTTCATATCTACTTAATTGT
1 TTGATTACCAACAAATGGTCATATCTACTTAATTGT
* **
1314 TTGATTACTAACATGTGGTCATATCTACTTAATT
1 TTGATTACCAACAAATGGTCATATCTACTTAATT
1348 CATCAATAAC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.31, C:0.16, G:0.10, T:0.43
Consensus pattern (36 bp):
TTGATTACCAACAAATGGTCATATCTACTTAATTGT
Found at i:1550 original size:225 final size:222
Alignment explanation
Indices: 1153--1590 Score: 561
Period size: 224 Copynumber: 2.0 Consensus size: 222
1143 AATCACATAT
* *
1153 ATGTGCTCAGAACTCTCAAACTGTTGATTGCAAACACCTGCTCAGTAATCAATGGGTAATTTCTA
1 ATGTGCTCAGAACTCTCAAACTGTTGATTGCAAACACCTGCTCAGGAATCAATCGGTAATTTCTA
* * * * **
1218 AACGTGCTCAGAACCTCTCAATCCGTTAATTATAGCATGTACTTAGAGCTAATGAATGGGTTGAT
66 AACATGCTCAGAACCACTCAATACGTTAATTATAGCATGTACTCAGAGCTAATGAATCAGTTGAT
* * **
1283 TACCAACAAATGTTCATATCTACTTAATTGTTTGATTACTAACATGTGGTCATATCTACTTAATT
131 TACCAACAAATGTTCATATCGACTTAATTGTTTGATTACTAACACGTGGTCATATCTACTTAAAC
1348 CATCAATAACTAACAAAGCTCACAACC
196 CATCAATAACTAACAAAGCTCACAACC
* * * * * * * *
1375 ATGTGCTCGGAACTACTCAAACTGTTGATTGCTAACACGTGCTCGGGACTCAGTCGTTAGTTTCT
1 ATGTGCTCAGAACT-CTCAAACTGTTGATTGCAAACACCTGCTCAGGAATCAATCGGTAATTTCT
* * * * * *
1440 AGAACATGCTTAGAACCACTCGATACGTTCATTGTAGCATGTGCTCAGAGCTACTGAATCAGTTG
65 A-AACATGCTCAGAACCACTCAATACGTTAATTATAGCATGTACTCAGAGCTAATGAATCAGTTG
* * **
1505 ATTTCTAACACGTGTTCAGTATCGACTTAATTGTTTGATTACTAACACGTGGTCATATCTACTTA
129 ATTACCAACAAATGTTCA-TATCGACTTAATTGTTTGATTACTAACACGTGGTCATATCTACTTA
* *
1570 AACCGTCATTAACTAACAAAG
193 AACCATCAATAACTAACAAAG
1591 GTCATAACTA
Statistics
Matches: 181, Mismatches: 32, Indels: 3
0.84 0.15 0.01
Matches are distributed among these distances:
222 13 0.07
223 42 0.23
224 65 0.36
225 61 0.34
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.32
Consensus pattern (222 bp):
ATGTGCTCAGAACTCTCAAACTGTTGATTGCAAACACCTGCTCAGGAATCAATCGGTAATTTCTA
AACATGCTCAGAACCACTCAATACGTTAATTATAGCATGTACTCAGAGCTAATGAATCAGTTGAT
TACCAACAAATGTTCATATCGACTTAATTGTTTGATTACTAACACGTGGTCATATCTACTTAAAC
CATCAATAACTAACAAAGCTCACAACC
Found at i:2818 original size:35 final size:36
Alignment explanation
Indices: 2754--2838 Score: 120
Period size: 35 Copynumber: 2.4 Consensus size: 36
2744 AAAATGTGTT
*
2754 CATATCTACTTAATCGTTTGATTAATAACACGTGGC
1 CATATCTACTTAATCGATTGATTAATAACACGTGGC
* * *
2790 CGTATCTACTTAATC-ATTGATTACTAACACGTGGT
1 CATATCTACTTAATCGATTGATTAATAACACGTGGC
2825 CAT-TCTACTTAATC
1 CATATCTACTTAATC
2839 CATCAATAAC
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
34 11 0.25
35 19 0.43
36 14 0.32
ACGTcount: A:0.29, C:0.21, G:0.12, T:0.38
Consensus pattern (36 bp):
CATATCTACTTAATCGATTGATTAATAACACGTGGC
Found at i:2851 original size:35 final size:35
Alignment explanation
Indices: 2779--2853 Score: 89
Period size: 35 Copynumber: 2.1 Consensus size: 35
2769 GTTTGATTAA
* ** *
2779 TAACACGTGGCCGTATCTACTTAATCATTGATTAC
1 TAACACGTGGCCATATCTACTTAATCATCAATAAC
*
2814 TAACACGTGGTCAT-TCTACTTAATCCATCAATAAC
1 TAACACGTGGCCATATCTACTTAAT-CATCAATAAC
2849 TAACA
1 TAACA
2854 AAGCTCATAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
34 10 0.29
35 24 0.71
ACGTcount: A:0.33, C:0.24, G:0.11, T:0.32
Consensus pattern (35 bp):
TAACACGTGGCCATATCTACTTAATCATCAATAAC
Found at i:3109 original size:35 final size:36
Alignment explanation
Indices: 3044--3129 Score: 131
Period size: 35 Copynumber: 2.4 Consensus size: 36
3034 CTAAATGTGT
3044 TCATATCTACTTAATCGTTTGATTAATAACACGTGG
1 TCATATCTACTTAATCGTTTGATTAATAACACGTGG
* * *
3080 TCGTATCTACTTAATCG-TTGATTACTAACACTTGG
1 TCATATCTACTTAATCGTTTGATTAATAACACGTGG
3115 TCAT-TCTACTTAATC
1 TCATATCTACTTAATC
3130 CATCAATAAC
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
34 11 0.24
35 19 0.41
36 16 0.35
ACGTcount: A:0.28, C:0.20, G:0.12, T:0.41
Consensus pattern (36 bp):
TCATATCTACTTAATCGTTTGATTAATAACACGTGG
Found at i:3394 original size:288 final size:291
Alignment explanation
Indices: 2522--3395 Score: 1158
Period size: 293 Copynumber: 3.0 Consensus size: 291
2512 TATTTGACAC
* * * * * *
2522 AACATGTGATCATTCTACTTAATCCATCAATAACTAACAAAGCTCACAGCTACTATCCAATTACT
1 AACACGTGGTCATTCTACTTAATCCATC-A-AACTAACAAAGCTCATAACTACTATCCAATAATT
* * * * * * *
2587 ACTAACATGTTTCTCCAAG-CAATCAGTTGTTGGTAAACTAAAAATATTTCATCTGACTGATGCA
64 ACTAACATGTTTCTCCAAGCCATTGA-CTGTTGGCAAACTAAAAACATTTTATCTGACTTATGCA
* ** * * * *
2651 TGTTGGAAAGAAAAAAATGAGAAAGAAACACAAGAACACCAAAACTAGTATGCATCCCTAACTTT
128 TGTAGGAAAGAACCAAATGAGAAAGAAACATATGCACATCAAAACTAGTATGCATCCCTAACTTT
2716 -TAGGATTGGTAAACAGTCATTATGCTCTAAAATGTGTTCATATCTACTTAATCGTTTGATTAAT
193 CT-GGATTGGTAAACAGTCATTATGCTCTAAAATGTGTTCATATCTACTTAATCGTTTGATTAAT
**
2780 AACACGTGGC-CGTATCTACTTAAT-CATTGATTACT
257 AACAC-AAGCTCGTATCTACTTAATCCA-TGATTACT
2815 AACACGTGGTCATTCTACTTAATCCATCAATAACTAACAAAGCTCATAACTACTATCCAATAATT
1 AACACGTGGTCATTCTACTTAATCCATC-A-AACTAACAAAGCTCATAACTACTATCCAATAATT
* * * * * *
2880 ACTAACATGCTTCTCCAAGCAATTGACGGTTGGCAAACTAAGAACATTCTATCTGACTTGTGCAT
64 ACTAACATGTTTCTCCAAGCCATTGACTGTTGGCAAACTAAAAACATTTTATCTGACTTATGCAT
2945 GTAGGAAAGAACCAAATGAGAAAGAAACATATGCACATCAAAAC-AGTATGCATCCCTAACTTTC
129 GTAGGAAAGAACCAAATGAGAAAGAAACATATGCACATCAAAACTAGTATGCATCCCTAACTTTC
*
3009 CGGATTGGTAAACAGTCATTATGCTCT-AAATGTGTTCATATCTACTTAATCGTTTGATTAATAA
194 TGGATTGGTAAACAGTCATTATGCTCTAAAATGTGTTCATATCTACTTAATCGTTTGATTAATAA
** * **
3073 CACGTGGTCGTATCTACTTAATCGTTGATTACT
259 CACAAGCTCGTATCTACTTAATCCATGATTACT
* *
3106 AACACTTGGTCATTCTACTTAATCCATC-AA-TAACAAAGCTCATAATTACTATCCAATAATTTA
1 AACACGTGGTCATTCTACTTAATCCATCAAACTAACAAAGCTCATAACTACTATCCAATAA-TTA
**
3169 CTAACATGTTTCTCCAAGCCATTGACTGTTGGCAAACTATTAACATTTTATCTGACTTATGCATG
65 CTAACATGTTTCTCCAAGCCATTGACTGTTGGCAAACTAAAAACATTTTATCTGACTTATGCATG
* *
3234 TAGGAAAGAACCAAATGAGAAAGAAACGTATGCACATCAAAACTAGTATGGATCCCTAACTTTCT
130 TAGGAAAGAACCAAATGAGAAAGAAACATATGCACATCAAAACTAGTATGCATCCCTAACTTTCT
* * * *
3299 GGATAGGTGAACAGTCATTATGCTCTAAAACGTGTTCATATCTACTTAATCGTTTGATTACTAAC
195 GGATTGGTAAACAGTCATTATGCTCTAAAATGTGTTCATATCTACTTAATCGTTTGATTAATAAC
* * *
3364 A-AAGCTCATAACTAC-T-ATCCCATAATTACT
260 ACAAGCTCGTATCTACTTAAT-CCATGATTACT
3394 AA
1 AA
3396 TGTGTTTATC
Statistics
Matches: 517, Mismatches: 56, Indels: 21
0.87 0.09 0.04
Matches are distributed among these distances:
287 30 0.06
288 116 0.22
289 52 0.10
290 38 0.07
291 89 0.17
292 45 0.09
293 144 0.28
294 3 0.01
ACGTcount: A:0.36, C:0.20, G:0.13, T:0.31
Consensus pattern (291 bp):
AACACGTGGTCATTCTACTTAATCCATCAAACTAACAAAGCTCATAACTACTATCCAATAATTAC
TAACATGTTTCTCCAAGCCATTGACTGTTGGCAAACTAAAAACATTTTATCTGACTTATGCATGT
AGGAAAGAACCAAATGAGAAAGAAACATATGCACATCAAAACTAGTATGCATCCCTAACTTTCTG
GATTGGTAAACAGTCATTATGCTCTAAAATGTGTTCATATCTACTTAATCGTTTGATTAATAACA
CAAGCTCGTATCTACTTAATCCATGATTACT
Found at i:4586 original size:42 final size:42
Alignment explanation
Indices: 4517--5049 Score: 481
Period size: 42 Copynumber: 12.7 Consensus size: 42
4507 ACGGTGTAGA
* ** * * *
4517 CGAAACACCAGAACCGTCAATGACTTTCTTGTCTGAAGTAAC
1 CGAAACACCAGAACCATTGATGACTTTCTTCTCCGAAGGAAC
** *
4559 CGAAACACCAGAACTGTTGATGGCTTTCTTCTTCTCCGAAGGAAC
1 CGAAACACCAGAACCATTGATGAC--T-TTCTTCTCCGAAGGAAC
* **
4604 CGAAACGCCAGAACTGTTGATGACTTTCTTCTCCGAAGGAAC
1 CGAAACACCAGAACCATTGATGACTTTCTTCTCCGAAGGAAC
** *
4646 CGAACCACTAGTAGAACCAATGATGACTTTCTTCTCCGAAGGAAC
1 CGAA--AC-ACCAGAACCATTGATGACTTTCTTCTCCGAAGGAAC
* * *
4691 CGAACCGCCAGAACC-TTCGATGATTTTCTTCTCCGAAGGAAC
1 CGAAACACCAGAACCATT-GATGACTTTCTTCTCCGAAGGAAC
* * * *
4733 CGAAACCCCCGAACCAATGATGACTTTTTTCTCCGAAGGAAC
1 CGAAACACCAGAACCATTGATGACTTTCTTCTCCGAAGGAAC
**
4775 CGAAACACCAGAACCAACGATGACTTTCTTCTCCGAAGGAAC
1 CGAAACACCAGAACCATTGATGACTTTCTTCTCCGAAGGAAC
* * ** * * *
4817 CGAAGCACCAGCACCAAAGATGAATTTCTTTTCCGAAGGAAT
1 CGAAACACCAGAACCATTGATGACTTTCTTCTCCGAAGGAAC
**
4859 CGAAACACCAGAACTGTTGATGACTTTCTTCTCC------AC
1 CGAAACACCAGAACCATTGATGACTTTCTTCTCCGAAGGAAC
* ** * * *
4895 AGAAACACCAGAACCAAAGATGAATTTCTTCTCCGGAGGAGC
1 CGAAACACCAGAACCATTGATGACTTTCTTCTCCGAAGGAAC
* * ** *
4937 AGAAATACCAGAACTGTTGATGACTTTCTTCTCCGAAGGGAC
1 CGAAACACCAGAACCATTGATGACTTTCTTCTCCGAAGGAAC
* * * *
4979 TGAAACACCAGAACCAATAATGACTTTCTTCTCAGAAGGAA-
1 CGAAACACCAGAACCATTGATGACTTTCTTCTCCGAAGGAAC
* * *
5020 -GAAACACCAGAACCGTGGATGACCTTCTTC
1 CGAAACACCAGAACCATTGATGACTTTCTTC
5050 ATCGAAGTTA
Statistics
Matches: 402, Mismatches: 75, Indels: 30
0.79 0.15 0.06
Matches are distributed among these distances:
36 29 0.07
40 25 0.06
41 1 0.00
42 271 0.67
43 3 0.01
44 3 0.01
45 70 0.17
ACGTcount: A:0.32, C:0.27, G:0.18, T:0.23
Consensus pattern (42 bp):
CGAAACACCAGAACCATTGATGACTTTCTTCTCCGAAGGAAC
Found at i:4787 original size:84 final size:85
Alignment explanation
Indices: 4517--5049 Score: 538
Period size: 84 Copynumber: 6.4 Consensus size: 85
4507 ACGGTGTAGA
* * * * ***
4517 CGAAACACCAGAACC-GTCAATGACTTTCTTGTCTGAAGTAACCGAAACACCAGAACTGTTGATG
1 CGAAACACCAGAACCTGTCGATGACTTTCTTCTCCGAAGGAACCGAAACACCAGAACCAATGATG
*
4581 GCTTTCTTCTTCTCCGAAGGAAC
66 AC--T-TTCTTCTCCGAAGGAAC
* * **
4604 CGAAACGCCAGAA-CTGTTGATGACTTTCTTCTCCGAAGGAACCGAACCACTAGTAGAACCAATG
1 CGAAACACCAGAACCTGTCGATGACTTTCTTCTCCGAAGGAACCGAA--AC-ACCAGAACCAATG
4668 ATGACTTTCTTCTCCGAAGGAAC
63 ATGACTTTCTTCTCCGAAGGAAC
* * * * *
4691 CGAACCGCCAGAACCT-TCGATGATTTTCTTCTCCGAAGGAACCGAAACCCCCGAACCAATGATG
1 CGAAACACCAGAACCTGTCGATGACTTTCTTCTCCGAAGGAACCGAAACACCAGAACCAATGATG
*
4755 ACTTTTTTCTCCGAAGGAAC
66 ACTTTCTTCTCCGAAGGAAC
** * * *
4775 CGAAACACCAGAACC-AACGATGACTTTCTTCTCCGAAGGAACCGAAGCACCAGCACCAAAGATG
1 CGAAACACCAGAACCTGTCGATGACTTTCTTCTCCGAAGGAACCGAAACACCAGAACCAATGATG
* * *
4839 AATTTCTTTTCCGAAGGAAT
66 ACTTTCTTCTCCGAAGGAAC
* * *
4859 CGAAACACCAGAA-CTGTTGATGACTTTCTTCTCC------ACAGAAACACCAGAACCAAAGATG
1 CGAAACACCAGAACCTGTCGATGACTTTCTTCTCCGAAGGAACCGAAACACCAGAACCAATGATG
* * *
4917 AATTTCTTCTCCGGAGGAGC
66 ACTTTCTTCTCCGAAGGAAC
* * * * * *
4937 AGAAATACCAGAA-CTGTTGATGACTTTCTTCTCCGAAGGGACTGAAACACCAGAACCAATAATG
1 CGAAACACCAGAACCTGTCGATGACTTTCTTCTCCGAAGGAACCGAAACACCAGAACCAATGATG
*
5001 ACTTTCTTCTCAGAAGGAA-
66 ACTTTCTTCTCCGAAGGAAC
* *
5020 -GAAACACCAGAACC-GTGGATGACCTTCTTC
1 CGAAACACCAGAACCTGTCGATGACTTTCTTC
5050 ATCGAAGTTA
Statistics
Matches: 377, Mismatches: 55, Indels: 33
0.81 0.12 0.07
Matches are distributed among these distances:
78 69 0.18
82 25 0.07
83 2 0.01
84 166 0.44
85 2 0.01
86 1 0.00
87 95 0.25
88 3 0.01
89 2 0.01
90 12 0.03
ACGTcount: A:0.32, C:0.27, G:0.18, T:0.23
Consensus pattern (85 bp):
CGAAACACCAGAACCTGTCGATGACTTTCTTCTCCGAAGGAACCGAAACACCAGAACCAATGATG
ACTTTCTTCTCCGAAGGAAC
Found at i:4965 original size:120 final size:120
Alignment explanation
Indices: 4658--5011 Score: 332
Period size: 120 Copynumber: 2.9 Consensus size: 120
4648 AACCACTAGT
* * * * * *** *
4658 AGAACCAATGATGACTTTCTTCTCCGAAGGAACCGAACCGCCAGAACCTTCGATGATTTTCTTCT
1 AGAACCAAAGATGAATTTCTTCTCCGAAGGAACAGAAACACCAGAACCAAAGATGAATTTCTTCT
* * * * * *
4723 CCGAAGGAACCGAAACCCCCGAACCAATGATGACTTTTTTCTCCGAAGGAACCGAAACACC
66 CCGAAGGAACTGAAACACCAGAACCAATAATGACTTTCTTCTCC------ACAGAAACACC
* * * * * *
4784 AGAACCAACGATGACTTTCTTCTCCGAAGGAACCGAAGCACCAGCACCAAAGATGAATTTCTTTT
1 AGAACCAAAGATGAATTTCTTCTCCGAAGGAACAGAAACACCAGAACCAAAGATGAATTTCTTCT
*** *
4849 CCGAAGGAA-TCGAAACACCAGAACTGTTGATGACTTTCTTCTCCACAGAAACACC
66 CCGAAGGAACT-GAAACACCAGAACCAATAATGACTTTCTTCTCCACAGAAACACC
* * * **** *
4904 AGAACCAAAGATGAATTTCTTCTCCGGAGGAGCAGAAATACCAGAACTGTTGATGACTTTCTTCT
1 AGAACCAAAGATGAATTTCTTCTCCGAAGGAACAGAAACACCAGAACCAAAGATGAATTTCTTCT
*
4969 CCGAAGGGACTGAAACACCAGAACCAATAATGACTTTCTTCTC
66 CCGAAGGAACTGAAACACCAGAACCAATAATGACTTTCTTCTC
5012 AGAAGGAAGA
Statistics
Matches: 190, Mismatches: 36, Indels: 10
0.81 0.15 0.04
Matches are distributed among these distances:
120 97 0.51
121 1 0.01
126 92 0.48
ACGTcount: A:0.33, C:0.27, G:0.18, T:0.23
Consensus pattern (120 bp):
AGAACCAAAGATGAATTTCTTCTCCGAAGGAACAGAAACACCAGAACCAAAGATGAATTTCTTCT
CCGAAGGAACTGAAACACCAGAACCAATAATGACTTTCTTCTCCACAGAAACACC
Found at i:5221 original size:42 final size:43
Alignment explanation
Indices: 5094--5328 Score: 187
Period size: 42 Copynumber: 5.6 Consensus size: 43
5084 ACCAGAAGGT
* * * * *
5094 CCAGAACTGTTGGTGAATTTC-CTCTCCGGAGTGACCGAAACG
1 CCAGAACCGTTGATGACTTTCTCTCTCCGAAGTGACCGAAACA
* * ** *
5136 CCAGAACCGCTGATGAC-TT-TATCTCCGAAGAAACCCAAACA
1 CCAGAACCGTTGATGACTTTCTCTCTCCGAAGTGACCGAAACA
* * *
5177 CCAGAACTGTTGATGGCTTTCTCTC-CCGAAGTGACCGAAGCA
1 CCAGAACCGTTGATGACTTTCTCTCTCCGAAGTGACCGAAACA
* * * * * *
5219 CCAGGACCGTTGATGAATTTCT-TCTCCGGATTAATCGAAACA
1 CCAGAACCGTTGATGACTTTCTCTCTCCGAAGTGACCGAAACA
* * * *
5261 CCAGAACCGGTGGTGACTTTCT-TCTCCGAAGAGATCGAAACA
1 CCAGAACCGTTGATGACTTTCTCTCTCCGAAGTGACCGAAACA
** *
5303 CCAGAATTGTTGATGACTCTCT-TCTC
1 CCAGAACCGTTGATGACTTTCTCTCTC
5329 AGGAGTAACC
Statistics
Matches: 149, Mismatches: 40, Indels: 8
0.76 0.20 0.04
Matches are distributed among these distances:
41 33 0.22
42 113 0.76
43 3 0.02
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (43 bp):
CCAGAACCGTTGATGACTTTCTCTCTCCGAAGTGACCGAAACA
Found at i:5616 original size:3 final size:3
Alignment explanation
Indices: 5608--5644 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
5598 TCACAGCAGG
*
5608 AGA AGA AGA AGA AGA AGA AGA AGA CGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
5645 ACCATCCCCA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.65, C:0.03, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:12965 original size:15 final size:15
Alignment explanation
Indices: 12927--12969 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
12917 TTAGCTGGGC
* *
12927 GGGCGGATG-TGGGT
1 GGGCGGATGCGGGGG
*
12941 GGGTGGATGCGGGGG
1 GGGCGGATGCGGGGG
12956 GGGCGGATGCGGGG
1 GGGCGGATGCGGGG
12970 CGGGTAATGT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
14 8 0.33
15 16 0.67
ACGTcount: A:0.07, C:0.09, G:0.70, T:0.14
Consensus pattern (15 bp):
GGGCGGATGCGGGGG
Found at i:14280 original size:15 final size:15
Alignment explanation
Indices: 14250--14292 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
14240 GAATAATAAC
*
14250 ATTTATTTAATATATT
1 ATTTA-TTATTATATT
* *
14266 TTTTATTTTTATATT
1 ATTTATTATTATATT
14281 ATTTATTATTAT
1 ATTTATTATTAT
14293 TATATATGAT
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
15 18 0.82
16 4 0.18
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
ATTTATTATTATATT
Found at i:14283 original size:18 final size:18
Alignment explanation
Indices: 14262--14297 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
14252 TTATTTAATA
* *
14262 TATTTTTTATTTTTATAT
1 TATTTATTATTATTATAT
14280 TATTTATTATTATTATAT
1 TATTTATTATTATTATAT
14298 ATGATTTTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (18 bp):
TATTTATTATTATTATAT
Found at i:15451 original size:19 final size:18
Alignment explanation
Indices: 15427--15489 Score: 63
Period size: 19 Copynumber: 3.3 Consensus size: 18
15417 GAAACATTAT
15427 TATTTTAAGTTAGAAACCA
1 TATTTTAAGTT-GAAACCA
* *
15446 TATTTTAGGTTGCAACTCA
1 TATTTTAAGTTGAAAC-CA
*
15465 AATTTTAAGGTTGAAATCCA
1 TATTTTAA-GTTGAAA-CCA
15485 TATTT
1 TATTT
15490 AGGTTGCAAC
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
18 4 0.11
19 18 0.51
20 12 0.34
21 1 0.03
ACGTcount: A:0.35, C:0.11, G:0.13, T:0.41
Consensus pattern (18 bp):
TATTTTAAGTTGAAACCA
Found at i:15477 original size:20 final size:19
Alignment explanation
Indices: 15447--15553 Score: 69
Period size: 20 Copynumber: 5.5 Consensus size: 19
15437 TAGAAACCAT
*
15447 ATTTTAGGTTGCAACTCAA
1 ATTTTAGGTTGCAAATCAA
*
15466 ATTTTAAGGTTG-AAATC-C
1 ATTTT-AGGTTGCAAATCAA
* *
15484 ATATTTAGGTTGC-AACCTAG
1 AT-TTTAGGTTGCAAATC-AA
* *
15504 ATTTTCATGTTG-GAATCCAA
1 ATTTT-AGGTTGCAAAT-CAA
15524 ATTTTAGGTTGCAAATCAGA
1 ATTTTAGGTTGCAAATCA-A
*
15544 TTTTTAGGTT
1 ATTTTAGGTT
15554 ATAAGCAAGG
Statistics
Matches: 68, Mismatches: 10, Indels: 19
0.70 0.10 0.20
Matches are distributed among these distances:
18 11 0.16
19 22 0.32
20 34 0.50
21 1 0.01
ACGTcount: A:0.30, C:0.12, G:0.18, T:0.40
Consensus pattern (19 bp):
ATTTTAGGTTGCAAATCAA
Found at i:15490 original size:19 final size:18
Alignment explanation
Indices: 15430--15500 Score: 56
Period size: 18 Copynumber: 3.8 Consensus size: 18
15420 ACATTATTAT
15430 TTTAA-GTTAGAAACCATA
1 TTTAAGGTT-GAAACCATA
* * *
15448 TTTTAGGTTGCAACTCAAA
1 TTTAAGGTTGAAAC-CATA
15467 TTTTAAGGTTGAAATCCATA
1 -TTTAAGGTTGAAA-CCATA
*
15487 TTT-AGGTTGCAACC
1 TTTAAGGTTGAAACC
15501 TAGATTTTCA
Statistics
Matches: 42, Mismatches: 7, Indels: 9
0.72 0.12 0.16
Matches are distributed among these distances:
17 2 0.05
18 16 0.38
19 9 0.21
20 14 0.33
21 1 0.02
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.37
Consensus pattern (18 bp):
TTTAAGGTTGAAACCATA
Found at i:15491 original size:38 final size:39
Alignment explanation
Indices: 15428--15553 Score: 143
Period size: 38 Copynumber: 3.3 Consensus size: 39
15418 AAACATTATT
*
15428 ATTTTAA-GTTAGAAA-CCATATTTTAGGTTGCAACTCAA
1 ATTTTAAGGTT-GAAATCCATATTTTAGGTTGCAACTCAG
15466 ATTTTAAGGTTGAAATCCATA-TTTAGGTTGCAAC-CTAG
1 ATTTTAAGGTTGAAATCCATATTTTAGGTTGCAACTC-AG
* * * * *
15504 ATTTTCATGTTGGAATCCAAATTTTAGGTTGCAAATCAG
1 ATTTTAAGGTTGAAATCCATATTTTAGGTTGCAACTCAG
*
15543 ATTTTTAGGTT
1 ATTTTAAGGTT
15554 ATAAGCAAGG
Statistics
Matches: 75, Mismatches: 8, Indels: 9
0.82 0.09 0.10
Matches are distributed among these distances:
37 1 0.01
38 42 0.56
39 31 0.41
40 1 0.01
ACGTcount: A:0.32, C:0.12, G:0.17, T:0.40
Consensus pattern (39 bp):
ATTTTAAGGTTGAAATCCATATTTTAGGTTGCAACTCAG
Found at i:15691 original size:81 final size:81
Alignment explanation
Indices: 15556--15773 Score: 292
Period size: 81 Copynumber: 2.7 Consensus size: 81
15546 TTTAGGTTAT
* * * *
15556 AAGCAAGGTGATGTATCGTACGAGGTACACACATAAATATGTAAGTGGTGATGTATTGTACGAGA
1 AAGCAAGGTGATGTATCGTACGGGGTACACACCTAAATATGAAAGTGGTGATGTATTGAACGAGA
** *
15621 TACATTCCCAGTTACA
66 TACACACCCAATTACA
* * * * * *
15637 AAGCAAAGTGATGTATTGTACGGGGTACACGCCTAAATATGAAAGTGGTAATGTATTGAATGGGA
1 AAGCAAGGTGATGTATCGTACGGGGTACACACCTAAATATGAAAGTGGTGATGTATTGAACGAGA
15702 TACACACCCAATTACA
66 TACACACCCAATTACA
* * *
15718 AAGCAAGGTGATGTATCGCACGGGGTACATATCTAAATATGAAAGTGGTGATGTAT
1 AAGCAAGGTGATGTATCGTACGGGGTACACACCTAAATATGAAAGTGGTGATGTAT
15774 CGCACGGGTA
Statistics
Matches: 117, Mismatches: 20, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
81 117 1.00
ACGTcount: A:0.35, C:0.14, G:0.25, T:0.26
Consensus pattern (81 bp):
AAGCAAGGTGATGTATCGTACGGGGTACACACCTAAATATGAAAGTGGTGATGTATTGAACGAGA
TACACACCCAATTACA
Found at i:15794 original size:39 final size:40
Alignment explanation
Indices: 15724--15810 Score: 167
Period size: 39 Copynumber: 2.2 Consensus size: 40
15714 TACAAAGCAA
15724 GGTGATGTATCGCACGGGGTACATATCTAAATATGAAAGT
1 GGTGATGTATCGCACGGGGTACATATCTAAATATGAAAGT
15764 GGTGATGTATCGCAC-GGGTACATATCTAAATATGAAAGT
1 GGTGATGTATCGCACGGGGTACATATCTAAATATGAAAGT
15803 GGTGATGT
1 GGTGATGT
15811 TTTGTATGGA
Statistics
Matches: 47, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
39 32 0.68
40 15 0.32
ACGTcount: A:0.31, C:0.11, G:0.29, T:0.29
Consensus pattern (40 bp):
GGTGATGTATCGCACGGGGTACATATCTAAATATGAAAGT
Found at i:15876 original size:60 final size:60
Alignment explanation
Indices: 15789--15903 Score: 187
Period size: 60 Copynumber: 1.9 Consensus size: 60
15779 GGGTACATAT
* * *
15789 CTAAATATGAAAGTGGTGATGTTTTGTA-TGGATACACACCCAATTACAAGCAAGGTACAC
1 CTAAATATGAAAGTGGTGATGTATTGTACGGGATACACACACAATTACAAG-AAGGTACAC
15849 CTAAATATGAAAGTGGTGATGTATTGTACGGGATACACACACAATTACAAGAAGG
1 CTAAATATGAAAGTGGTGATGTATTGTACGGGATACACACACAATTACAAGAAGG
15904 GTGATGTATC
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
60 31 0.61
61 20 0.39
ACGTcount: A:0.38, C:0.15, G:0.22, T:0.25
Consensus pattern (60 bp):
CTAAATATGAAAGTGGTGATGTATTGTACGGGATACACACACAATTACAAGAAGGTACAC
Found at i:17617 original size:16 final size:15
Alignment explanation
Indices: 17576--17623 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 15
17566 TCAAAATTAA
*
17576 TAAATAATTAAATTAT
1 TAAATAATT-AATTTT
*
17592 TAAATTATTATATTTT
1 TAAATAATTA-ATTTT
*
17608 TATATAATTAATTTT
1 TAAATAATTAATTTT
17623 T
1 T
17624 TAACTATATT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
15 7 0.26
16 20 0.74
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TAAATAATTAATTTT
Found at i:29263 original size:6 final size:6
Alignment explanation
Indices: 29252--29281 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
29242 CTAAAAGCAT
29252 AGGGAC AGGGAC AGGGAC AGGGAC AGGGAC
1 AGGGAC AGGGAC AGGGAC AGGGAC AGGGAC
29282 GAAGCCAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.33, C:0.17, G:0.50, T:0.00
Consensus pattern (6 bp):
AGGGAC
Found at i:33163 original size:37 final size:37
Alignment explanation
Indices: 33104--33177 Score: 103
Period size: 37 Copynumber: 2.0 Consensus size: 37
33094 AGTCATAAAA
* *
33104 TTCAACAAAATAACACTCTATAGTCGGGAACTGTTTT
1 TTCAACAAAATAACACTCTATAGTCGGAAACTATTTT
* * *
33141 TTCAACAAAATAATATTTTATAGTCGGAAACTATTTT
1 TTCAACAAAATAACACTCTATAGTCGGAAACTATTTT
33178 ATAACTTTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.38, C:0.15, G:0.11, T:0.36
Consensus pattern (37 bp):
TTCAACAAAATAACACTCTATAGTCGGAAACTATTTT
Found at i:34294 original size:2 final size:2
Alignment explanation
Indices: 34287--34316 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
34277 ATGTCACTCA
34287 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
34317 TTTGATGATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:42816 original size:40 final size:40
Alignment explanation
Indices: 42761--42842 Score: 164
Period size: 40 Copynumber: 2.0 Consensus size: 40
42751 GAGTGCATTT
42761 TCTGCATATTTGGATCCGAATTGTATCATGAACAGATCGA
1 TCTGCATATTTGGATCCGAATTGTATCATGAACAGATCGA
42801 TCTGCATATTTGGATCCGAATTGTATCATGAACAGATCGA
1 TCTGCATATTTGGATCCGAATTGTATCATGAACAGATCGA
42841 TC
1 TC
42843 CGAATTGTAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (40 bp):
TCTGCATATTTGGATCCGAATTGTATCATGAACAGATCGA
Found at i:48199 original size:21 final size:21
Alignment explanation
Indices: 48175--48230 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
48165 GATTTTGTAT
*
48175 TATCGCAATGAATTTGGAGAC
1 TATCGCAACGAATTTGGAGAC
*
48196 TATCGCAACGAACTTGGAGAC
1 TATCGCAACGAATTTGGAGAC
*
48217 TATTGCAACGAATT
1 TATCGCAACGAATT
48231 ATGTAAATCG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (21 bp):
TATCGCAACGAATTTGGAGAC
Found at i:49257 original size:14 final size:15
Alignment explanation
Indices: 49238--49270 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
49228 CGAATGAATC
49238 ATTTAA-AAAATATT
1 ATTTAATAAAATATT
49252 ATTTAATTAAAATATT
1 ATTTAA-TAAAATATT
49268 ATT
1 ATT
49271 ATATTATTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.35
16 11 0.65
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTTAATAAAATATT
Found at i:52971 original size:15 final size:17
Alignment explanation
Indices: 52932--52977 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
52922 TGAAATTTTA
*
52932 TAATTAAAATATATTAT
1 TAATAAAAATATATTAT
*
52949 TAATAAAAATAT-TTTT
1 TAATAAAAATATATTAT
*
52965 TAA-AAAATTATAT
1 TAATAAAAATATAT
52978 GAGAATTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
15 7 0.28
16 7 0.28
17 11 0.44
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
TAATAAAAATATATTAT
Found at i:56031 original size:35 final size:35
Alignment explanation
Indices: 55990--56065 Score: 116
Period size: 35 Copynumber: 2.2 Consensus size: 35
55980 AAAATAGTCC
* * *
55990 TCAATTTCATTTTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
*
56025 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
56060 TCAATT
1 TCAATT
56066 AAATTCAATT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.39, C:0.22, G:0.01, T:0.37
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
Found at i:56608 original size:130 final size:130
Alignment explanation
Indices: 56461--56708 Score: 397
Period size: 130 Copynumber: 1.9 Consensus size: 130
56451 TATTTATATA
* * **
56461 ATCAATTTGGTCCTAAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTG
1 ATCAATTTGGTCATAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
* *
56526 TTAGCACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
66 TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
56591 ATCAATTTGGTCATAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
1 ATCAATTTGGTCATAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
* * * * *
56656 TTAATACATGATCATGATATATGTTATTGGTGACACATGTCGCCACCTAATTA
66 TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTA
56709 GAAGAAAATT
Statistics
Matches: 107, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
130 107 1.00
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (130 bp):
ATCAATTTGGTCATAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
Found at i:57227 original size:35 final size:35
Alignment explanation
Indices: 57181--57256 Score: 125
Period size: 35 Copynumber: 2.2 Consensus size: 35
57171 AAAATAGTTC
* *
57181 TCAATTTCATTCTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
*
57216 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
57251 TCAATT
1 TCAATT
57257 AAATTCAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.39, C:0.24, G:0.01, T:0.36
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
Found at i:57796 original size:130 final size:130
Alignment explanation
Indices: 57651--57898 Score: 415
Period size: 130 Copynumber: 1.9 Consensus size: 130
57641 TATTTATATA
* **
57651 ATCAATTTGGTCCTAAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
* *
57716 TTAGCACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
66 TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
57781 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
* * * *
57846 TTAACACATGATCATGATATATGTTATTGGTGACATATGTCACCACCTAATTA
66 TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTA
57899 GAAGAAAATT
Statistics
Matches: 109, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
130 109 1.00
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (130 bp):
ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
Found at i:57929 original size:130 final size:129
Alignment explanation
Indices: 57665--57929 Score: 300
Period size: 130 Copynumber: 2.0 Consensus size: 129
57655 ATTTGGTCCT
* ** *
57665 AAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTGTTAGCACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
* *** * * **** *
57730 TGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCTATCAATTTGGTCCT
66 TGACACATGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGT-CA
57795 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
* * * * *
57860 TGATATATGTTATTGGTGACATATGTCACCACCTAATTAGAAGAAAATTAAGTTA-CAAAGAAGT
66 TGACACATGTCATTGGTGACACATGTCACCACCTAATT--AAGAAAA-TAAGCTATCAAAGAAGT
57924 -A
128 CA
57925 AAATT
1 AAATT
57930 TGGGTCTTGG
Statistics
Matches: 112, Mismatches: 20, Indels: 6
0.81 0.14 0.04
Matches are distributed among these distances:
130 99 0.88
132 8 0.07
133 5 0.04
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.34
Consensus pattern (129 bp):
AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
TGACACATGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGTCA
Found at i:58256 original size:28 final size:27
Alignment explanation
Indices: 58225--58287 Score: 63
Period size: 28 Copynumber: 2.3 Consensus size: 27
58215 AGTTGATACA
*
58225 ATATTTTAAAAGAATAAATTTAAGATTT
1 ATATTTTAAAA-AATAAATTTAAGAATT
** * *
58253 ATATATTTTTAAACTAAATTTAATAATT
1 ATAT-TTTAAAAAATAAATTTAAGAATT
58281 ATATTTT
1 ATATTTT
58288 TCATATTTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
27 3 0.10
28 21 0.72
29 5 0.17
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (27 bp):
ATATTTTAAAAAATAAATTTAAGAATT
Found at i:58978 original size:28 final size:27
Alignment explanation
Indices: 58947--59009 Score: 63
Period size: 28 Copynumber: 2.3 Consensus size: 27
58937 AGTTGATACA
*
58947 ATATTTTAAAAGAATAAATTTAAGATTT
1 ATATTTTAAAA-AATAAATTTAAGAATT
** * *
58975 ATATATTTTTAAACTAAATTTAATAATT
1 ATAT-TTTAAAAAATAAATTTAAGAATT
59003 ATATTTT
1 ATATTTT
59010 TCATATTTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
27 3 0.10
28 21 0.72
29 5 0.17
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (27 bp):
ATATTTTAAAAAATAAATTTAAGAATT
Found at i:59110 original size:16 final size:18
Alignment explanation
Indices: 59089--59122 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
59079 ATTTCTTATT
59089 AAAAATA-AAAT-ATTCA
1 AAAAATATAAATGATTCA
59105 AAAAATATAAATGATTCA
1 AAAAATATAAATGATTCA
59123 TACATTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (18 bp):
AAAAATATAAATGATTCA
Found at i:59596 original size:720 final size:721
Alignment explanation
Indices: 58144--59593 Score: 2755
Period size: 720 Copynumber: 2.0 Consensus size: 721
58134 GGGAAAATAT
58144 TATATTTTTTTACAATAAAAATATTATATTTGATAAATTGTTTGATAGATTTAATATATTTTTTA
1 TATATTTTTTTACAATAAAAATATTATATTTGATAAATTGTTTGATAGATTTAATATATTTTTTA
58209 AATATTAGTTGATACAATATTTTAAAAGAATAAATTTAAGATTTATATATTTTTAAACTAAATTT
66 AATATTAGTTGATACAATATTTTAAAAGAATAAATTTAAGATTTATATATTTTTAAACTAAATTT
58274 AATAATTATATTTTTCATATTTATAATTCATGATTATATATATAATCTTAAGTTGAGTATTTCTA
131 AATAATTATATTTTTCATATTTATAATTCATGATTATATATATAATCTTAAGTTGAGTATTTCTA
*
58339 ATATAATTAATAATTTTAATTTCTTATTAATAATAAAATATTCAAAAAATATAAATGATTCATAC
196 ATATAATTAATAATTTTAATTTCTTATTAAAAATAAAATATTCAAAAAATATAAATGATTCATAC
58404 ATTAATATATGAATATATTTTTTTTATTTATACATCTAAATATAAATATACATTTATATAAATAT
261 ATTAATATATGAATATATTTTTTTTATTTATACATCTAAATATAAATATACATTTATATAAATAT
*
58469 ATTTTTATTTGTATATTGAAATATTTTGATTAAAATATAAACATATTTTAAATACTAGTTTATAC
326 ATTTTTATTCGTATATTGAAATATTTTGATTAAAATATAAACATATTTTAAATACTAGTTTATAC
*
58534 AAGAAAAATAAAATATATCAAAAATTTAAATGATTCATACATTTAAATATAAATTGAATCATTTA
391 AAGAAAAATAAAATATATCAAAAATATAAATGATTCATACATTTAAATATAAATTGAATCATTTA
58599 TATTTTCTATACATCTATATTTAATAAGAAAATAAAATTATCAGGGGACTGTTTTGCAAGTTTTA
456 TATTTTCTATACATCTATATTTAATAAGAAAATAAAATTATCAGGGGACTGTTTTGCAAGTTTTA
*
58664 AAAGTTGGGGACCTAAATTCAAGTGCCTGAAAAGTTTAATGACCGTTTATATAATTTACCCTAAT
521 AAAGTTGGGGACCTAAATTCAAGTGCCTGAAAAGTTCAATGACCGTTTATATAATTTACCCTAAT
*
58729 TTTCTAACAGTGATTTAAGTTGGGGGACCATATTGCAAACGGAATAAATGTTGGGGGATTGTATT
586 TTTCTAACAGTGATTTAAGTT-GGGGACCATATTGCAAACGGAATAAATGTTGGGGGACTGTATT
*
58794 ACAAGTTTTAAAATTTGGGGGACCTAAATGCAAGCTTCAGAAATGTTCAGTGACCATTACTATAC
650 ACAAGTTTTAAAAGTTGGGGGACCTAAATGCAAGCTTCAGAAATGTTCAGTGACCATTACTATAC
58859 TTTACCC
715 TTTACCC
58866 TATATTTTTTTACAATAAAAATATTATATTTGATAAATTGTTTGATAGATTTAATATATTTTTTA
1 TATATTTTTTTACAATAAAAATATTATATTTGATAAATTGTTTGATAGATTTAATATATTTTTTA
58931 AATATTAGTTGATACAATATTTTAAAAGAATAAATTTAAGATTTATATATTTTTAAACTAAATTT
66 AATATTAGTTGATACAATATTTTAAAAGAATAAATTTAAGATTTATATATTTTTAAACTAAATTT
58996 AATAATTATATTTTTCATATTTATAATTCATGATTATATATATAATCTTAAGTTGAGTATTTCTA
131 AATAATTATATTTTTCATATTTATAATTCATGATTATATATATAATCTTAAGTTGAGTATTTCTA
59061 ATATAATTAATAATTTTAATTTCTTATTAAAAATAAAATATTCAAAAAATATAAATGATTCATAC
196 ATATAATTAATAATTTTAATTTCTTATTAAAAATAAAATATTCAAAAAATATAAATGATTCATAC
59126 ATTAATATATG-A-ATATTTTTTTTATTTATACATCTAAATATAAATATACATTTATATAAATAT
261 ATTAATATATGAATATATTTTTTTTATTTATACATCTAAATATAAATATACATTTATATAAATAT
*
59189 ATTTTTATTCGTATATTGAAATATTTTGATTAAAATATAAACATATTTTAAATACTATTTTATAC
326 ATTTTTATTCGTATATTGAAATATTTTGATTAAAATATAAACATATTTTAAATACTAGTTTATAC
59254 AAGAAAAATAAAATATATCAAAAATATAAATGATTCATACATTTAAATATAAATTGAATCATTTA
391 AAGAAAAATAAAATATATCAAAAATATAAATGATTCATACATTTAAATATAAATTGAATCATTTA
**
59319 TATTTTCTATACATCTATATTTAATAAGAAAATAAAATTATTGGGGGACTGTTTTGCAAGTTTTA
456 TATTTTCTATACATCTATATTTAATAAGAAAATAAAATTATCAGGGGACTGTTTTGCAAGTTTTA
59384 AAAGTTGGGGACCTAAATTCAAGTGCCTGAAAAGTTCAATGACCGTTTATATAATTTACCCTAAT
521 AAAGTTGGGGACCTAAATTCAAGTGCCTGAAAAGTTCAATGACCGTTTATATAATTTACCCTAAT
* * *
59449 TTTCTAACAGTGATTTAAGTT-GGGACCATATTGCAAATGGAATAAATGTTTGGGGACTGTATTG
586 TTTCTAACAGTGATTTAAGTTGGGGACCATATTGCAAACGGAATAAATGTTGGGGGACTGTATTA
59513 CAAGTTTTAAAAGTTGGGGGACCTAAATGCAAGCTTCAGAAATGTTCAGTGACCATTACTATACT
651 CAAGTTTTAAAAGTTGGGGGACCTAAATGCAAGCTTCAGAAATGTTCAGTGACCATTACTATACT
59578 TTACCC
716 TTACCC
59584 TA-ATTTTTTT
1 TATATTTTTTT
59594 TTTCTTTTTA
Statistics
Matches: 716, Mismatches: 12, Indels: 5
0.98 0.02 0.01
Matches are distributed among these distances:
717 8 0.01
718 111 0.16
720 326 0.46
721 1 0.00
722 270 0.38
ACGTcount: A:0.40, C:0.08, G:0.10, T:0.42
Consensus pattern (721 bp):
TATATTTTTTTACAATAAAAATATTATATTTGATAAATTGTTTGATAGATTTAATATATTTTTTA
AATATTAGTTGATACAATATTTTAAAAGAATAAATTTAAGATTTATATATTTTTAAACTAAATTT
AATAATTATATTTTTCATATTTATAATTCATGATTATATATATAATCTTAAGTTGAGTATTTCTA
ATATAATTAATAATTTTAATTTCTTATTAAAAATAAAATATTCAAAAAATATAAATGATTCATAC
ATTAATATATGAATATATTTTTTTTATTTATACATCTAAATATAAATATACATTTATATAAATAT
ATTTTTATTCGTATATTGAAATATTTTGATTAAAATATAAACATATTTTAAATACTAGTTTATAC
AAGAAAAATAAAATATATCAAAAATATAAATGATTCATACATTTAAATATAAATTGAATCATTTA
TATTTTCTATACATCTATATTTAATAAGAAAATAAAATTATCAGGGGACTGTTTTGCAAGTTTTA
AAAGTTGGGGACCTAAATTCAAGTGCCTGAAAAGTTCAATGACCGTTTATATAATTTACCCTAAT
TTTCTAACAGTGATTTAAGTTGGGGACCATATTGCAAACGGAATAAATGTTGGGGGACTGTATTA
CAAGTTTTAAAAGTTGGGGGACCTAAATGCAAGCTTCAGAAATGTTCAGTGACCATTACTATACT
TTACCC
Found at i:60467 original size:20 final size:20
Alignment explanation
Indices: 60442--60487 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
60432 GAATTCAACT
60442 GTTAATGTCTTGGAATATGG
1 GTTAATGTCTTGGAATATGG
60462 GTTAATGTCTTGGAATATGG
1 GTTAATGTCTTGGAATATGG
60482 GTTAAT
1 GTTAAT
60488 CTTTGGGAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.26, C:0.04, G:0.28, T:0.41
Consensus pattern (20 bp):
GTTAATGTCTTGGAATATGG
Found at i:60496 original size:20 final size:20
Alignment explanation
Indices: 60442--60493 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
60432 GAATTCAACT
*
60442 GTTAATGTCTTGGAATATGG
1 GTTAATCTCTTGGAATATGG
*
60462 GTTAATGTCTTGGAATATGG
1 GTTAATCTCTTGGAATATGG
60482 GTTAATCT-TTGG
1 GTTAATCTCTTGG
60494 GAAGCAATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 4 0.13
20 27 0.87
ACGTcount: A:0.23, C:0.06, G:0.29, T:0.42
Consensus pattern (20 bp):
GTTAATCTCTTGGAATATGG
Found at i:65022 original size:41 final size:41
Alignment explanation
Indices: 64977--65060 Score: 132
Period size: 41 Copynumber: 2.0 Consensus size: 41
64967 TTCAAATAGT
* *
64977 TCAGTTAAACATCATTATCAACTATGGGTATCTTTTGTCAG
1 TCAGTCAAACATCATTATCAACTATGGGCATCTTTTGTCAG
* *
65018 TCAGTCATACATCATTATCAACTATGGGCATCTTTTGTTAG
1 TCAGTCAAACATCATTATCAACTATGGGCATCTTTTGTCAG
65059 TC
1 TC
65061 TAAACAACGT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.39
Consensus pattern (41 bp):
TCAGTCAAACATCATTATCAACTATGGGCATCTTTTGTCAG
Found at i:72371 original size:21 final size:21
Alignment explanation
Indices: 72345--72388 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
72335 ATAAAAAAAA
* *
72345 TTATCTAAAATATTATTATTT
1 TTATCTAAAATATCAATATTT
*
72366 TTATCTGAAATATCAATATTT
1 TTATCTAAAATATCAATATTT
72387 TT
1 TT
72389 TTAATATTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.36, C:0.07, G:0.02, T:0.55
Consensus pattern (21 bp):
TTATCTAAAATATCAATATTT
Found at i:74139 original size:26 final size:26
Alignment explanation
Indices: 74110--74165 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 26
74100 TATAATTTTC
74110 AATTATA-ATATAAATTTAGTTTTTGG
1 AATTATATAT-TAAATTTAGTTTTTGG
* * * *
74136 AATTCTTTATTTAATTTAGTTTTTTG
1 AATTATATATTAAATTTAGTTTTTGG
74162 AATT
1 AATT
74166 CTTTATTTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
26 23 0.92
27 2 0.08
ACGTcount: A:0.32, C:0.02, G:0.09, T:0.57
Consensus pattern (26 bp):
AATTATATATTAAATTTAGTTTTTGG
Found at i:74166 original size:26 final size:26
Alignment explanation
Indices: 74122--74173 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
74112 TTATAATATA
74122 AATTTAGTTTTTGGAATTCTTTATTT
1 AATTTAGTTTTTGGAATTCTTTATTT
*
74148 AATTTAGTTTTTTGAATTCTTTATTT
1 AATTTAGTTTTTGGAATTCTTTATTT
74174 TTAAAGAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.23, C:0.04, G:0.10, T:0.63
Consensus pattern (26 bp):
AATTTAGTTTTTGGAATTCTTTATTT
Found at i:74592 original size:31 final size:29
Alignment explanation
Indices: 74523--74594 Score: 74
Period size: 31 Copynumber: 2.4 Consensus size: 29
74513 AACAACTCAA
**
74523 TGATCAAAATGTAATAATTGATAATGTAAG
1 TGATCAAAAT-TAATAATTGATAAAATAAG
*
74553 T-AGCCAAAAGTTAATAAATTGATAAAATAAG
1 TGA-TCAAAA-TTAAT-AATTGATAAAATAAG
74584 TGATCAAAATT
1 TGATCAAAATT
74595 TAAATTTTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
29 1 0.03
30 12 0.35
31 20 0.59
32 1 0.03
ACGTcount: A:0.50, C:0.06, G:0.14, T:0.31
Consensus pattern (29 bp):
TGATCAAAATTAATAATTGATAAAATAAG
Found at i:77672 original size:26 final size:26
Alignment explanation
Indices: 77639--77725 Score: 165
Period size: 26 Copynumber: 3.3 Consensus size: 26
77629 CCAACCGTAC
77639 AAAAAATAAGTTATATATATCACATT
1 AAAAAATAAGTTATATATATCACATT
77665 AAAAAATAAGTTATATATATCACATT
1 AAAAAATAAGTTATATATATCACATT
*
77691 AAAAAATAAGTTATATATGTCACATT
1 AAAAAATAAGTTATATATATCACATT
77717 AAAAAATAA
1 AAAAAATAA
77726 TTAACGTCAA
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 60 1.00
ACGTcount: A:0.56, C:0.07, G:0.05, T:0.32
Consensus pattern (26 bp):
AAAAAATAAGTTATATATATCACATT
Found at i:79259 original size:22 final size:23
Alignment explanation
Indices: 79234--79290 Score: 62
Period size: 24 Copynumber: 2.5 Consensus size: 23
79224 TATTAGAACT
79234 ATATATATTAAAT-ATGATTTTG
1 ATATATATTAAATCATGATTTTG
* * *
79256 ATATATTTTATTATCATGATTTTT
1 ATATATATTA-AATCATGATTTTG
*
79280 ATATCTATTAA
1 ATATATATTAA
79291 GATAGAATTA
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
22 9 0.33
23 2 0.07
24 16 0.59
ACGTcount: A:0.37, C:0.04, G:0.05, T:0.54
Consensus pattern (23 bp):
ATATATATTAAATCATGATTTTG
Found at i:82610 original size:21 final size:21
Alignment explanation
Indices: 82568--82610 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
82558 TTTCTGGGCT
*
82568 AGGGGAATCGATACCCATTCA
1 AGGGGAATCGATACCCACTCA
*
82589 AGGGGAATCGATACCCCCTCA
1 AGGGGAATCGATACCCACTCA
82610 A
1 A
82611 ACGAATATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.28, G:0.23, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:83291 original size:21 final size:20
Alignment explanation
Indices: 83238--83292 Score: 51
Period size: 21 Copynumber: 2.8 Consensus size: 20
83228 CTTGGTATAT
83238 ATATATG-ATTC-TTAAGGA
1 ATATATGTATTCTTTAAGGA
** *
83256 ATGATATGTGGTCTTTCAGGA
1 AT-ATATGTATTCTTTAAGGA
83277 CATATATGTATTCTTT
1 -ATATATGTATTCTTT
83293 GGAACATATG
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
18 2 0.07
19 5 0.18
20 2 0.07
21 17 0.61
22 2 0.07
ACGTcount: A:0.29, C:0.09, G:0.18, T:0.44
Consensus pattern (20 bp):
ATATATGTATTCTTTAAGGA
Found at i:83336 original size:103 final size:103
Alignment explanation
Indices: 83157--83382 Score: 373
Period size: 103 Copynumber: 2.2 Consensus size: 103
83147 GTAGAGGGTC
* * * *
83157 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTATGAGGTCTGGTGAGACACCTAC
1 TATGTGGTCCTTCAGGACATATATGTATTCTTTGGAACATATATGAGGTATGGTGAGACACATAC
83222 TTGATCCTTGGTATATATATATGATTCTTAAGGAATGA
66 TTGATCCTTGGTATATATATATGATTCTTAAGGAATGA
* *
83260 TATGTGGTCTTTCAGGACATATATGTATTCTTTGGAACATATGTGAGGTATGGTGAGACACATAC
1 TATGTGGTCCTTCAGGACATATATGTATTCTTTGGAACATATATGAGGTATGGTGAGACACATAC
*
83325 TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGTATATATATATGATTCTTAAGGAATGA
83363 TATGTGGTCCTT-ATGGACAT
1 TATGTGGTCCTTCA-GGACAT
83383 TATTATATTA
Statistics
Matches: 114, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
102 1 0.01
103 113 0.99
ACGTcount: A:0.27, C:0.12, G:0.23, T:0.38
Consensus pattern (103 bp):
TATGTGGTCCTTCAGGACATATATGTATTCTTTGGAACATATATGAGGTATGGTGAGACACATAC
TTGATCCTTGGTATATATATATGATTCTTAAGGAATGA
Found at i:86190 original size:16 final size:16
Alignment explanation
Indices: 86169--86221 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
86159 ATAGCTTCTT
86169 TCACATATACATGTAG
1 TCACATATACATGTAG
* * * *
86185 TCACATA-GCTTCT-T
1 TCACATATACATGTAG
86199 TCACATATACATGTAG
1 TCACATATACATGTAG
86215 TCACATA
1 TCACATA
86222 GCTTCTTTTC
Statistics
Matches: 27, Mismatches: 8, Indels: 4
0.69 0.21 0.10
Matches are distributed among these distances:
14 7 0.26
15 6 0.22
16 14 0.52
ACGTcount: A:0.34, C:0.23, G:0.09, T:0.34
Consensus pattern (16 bp):
TCACATATACATGTAG
Found at i:86194 original size:30 final size:30
Alignment explanation
Indices: 86158--86229 Score: 144
Period size: 30 Copynumber: 2.4 Consensus size: 30
86148 TATATAAGCT
86158 CATAGCTTCTTTCACATATACATGTAGTCA
1 CATAGCTTCTTTCACATATACATGTAGTCA
86188 CATAGCTTCTTTCACATATACATGTAGTCA
1 CATAGCTTCTTTCACATATACATGTAGTCA
86218 CATAGCTTCTTT
1 CATAGCTTCTTT
86230 TCATATTCTC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 42 1.00
ACGTcount: A:0.28, C:0.24, G:0.10, T:0.39
Consensus pattern (30 bp):
CATAGCTTCTTTCACATATACATGTAGTCA
Done.