Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000748.1 Hibiscus syriacus cultivar Beakdansim tig00001441_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: 134572
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:92 original size:40 final size:41
Alignment explanation
Indices: 48--129 Score: 123
Period size: 40 Copynumber: 2.0 Consensus size: 41
38 ACTAGCGTTG
* *
48 CAGCCTTCG-TGCATGGATGCACAGTAGGA-GCATCGATGCA
1 CAGCCTT-GATGCATCGATGCACAGAAGGATGCATCGATGCA
88 CAGCCTTGATGCATCGATGCACAGAAGGATGCATCGATGCA
1 CAGCCTTGATGCATCGATGCACAGAAGGATGCATCGATGCA
129 C
1 C
130 TAATTGCATT
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
39 1 0.03
40 25 0.66
41 12 0.32
ACGTcount: A:0.27, C:0.26, G:0.28, T:0.20
Consensus pattern (41 bp):
CAGCCTTGATGCATCGATGCACAGAAGGATGCATCGATGCA
Found at i:120 original size:20 final size:20
Alignment explanation
Indices: 57--129 Score: 85
Period size: 20 Copynumber: 3.6 Consensus size: 20
47 GCAGCCTTCG
* *
57 TGCATGGATGCACAGTAGGA
1 TGCATCGATGCACAGAAGGA
***
77 -GCATCGATGCACAGCCTTGA
1 TGCATCGATGCACAG-AAGGA
97 TGCATCGATGCACAGAAGGA
1 TGCATCGATGCACAGAAGGA
117 TGCATCGATGCAC
1 TGCATCGATGCAC
130 TAATTGCATT
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
19 13 0.30
20 17 0.39
21 14 0.32
ACGTcount: A:0.29, C:0.23, G:0.29, T:0.19
Consensus pattern (20 bp):
TGCATCGATGCACAGAAGGA
Found at i:302 original size:29 final size:31
Alignment explanation
Indices: 270--329 Score: 106
Period size: 29 Copynumber: 2.0 Consensus size: 31
260 AAACTTTGAA
270 TAAATTCAATT-AAGTCCAAAAA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
299 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
330 CCTTAAATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 11 0.38
31 7 0.24
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:6449 original size:23 final size:23
Alignment explanation
Indices: 6393--6449 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 23
6383 TTTATATGGA
*
6393 ACTTTGGTGCAATTCTACGCGGC
1 ACTTAGGTGCAATTCTACGCGGC
* * * *
6416 ACTTCGATGCAATTCTACGTGGT
1 ACTTAGGTGCAATTCTACGCGGC
6439 ACTTAGGTGCA
1 ACTTAGGTGCA
6450 TTTATACGAG
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.21, C:0.23, G:0.25, T:0.32
Consensus pattern (23 bp):
ACTTAGGTGCAATTCTACGCGGC
Found at i:16333 original size:15 final size:15
Alignment explanation
Indices: 16313--16341 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
16303 GAAGAGAACA
16313 CTAAAGTACAATGTG
1 CTAAAGTACAATGTG
16328 CTAAAGTACAATGT
1 CTAAAGTACAATGT
16342 TAGTGGATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.28
Consensus pattern (15 bp):
CTAAAGTACAATGTG
Found at i:17017 original size:200 final size:200
Alignment explanation
Indices: 16605--17102 Score: 658
Period size: 200 Copynumber: 2.5 Consensus size: 200
16595 TTTTCTAACT
* * * * *
16605 AAACCGGTATATTTATACCGGTAACATTATAAATTTACCTATTACATTATAATTATCGGTTTCGA
1 AAACTGGTATATTTATATCGGTAACATTGTAAATTTACATATTATATTATAATTATCGGTTTCGA
* ** * * *
16670 CGTTTTTTTGATCGATACTTTTAATAAATGTATCGACACTTAATGTGTGCACTTCGTTTGGCATT
66 TGTTTTTGGGATCGATACTTTTAATAAATGTATCGACACTTAAGGCGTGCACATCGTTTGGCATT
* * *
16735 CATTCTGGACAAAATATATCGACATAAATTTAAAAAGTGTCGATACATTATGTTGACATATTCTC
131 CATTATGGACAAAATATATCGACACAAATTCAAAAAGTGTCGATACATTATGTTGACATATTCTC
*
16800 TCATA
196 TAATA
* * *
16805 AAACTAGTATATTTATATCGGTTACATTGTAAATTTACTTATTATATTATAATTATCGGTTTCGA
1 AAACTGGTATATTTATATCGGTAACATTGTAAATTTACATATTATATTATAATTATCGGTTTCGA
* * *
16870 TATTTTTGGGATAGATACTTTTAATAAATGTATCGACACTTTAGGCGTGCACATCGTTTGGGCAT
66 TGTTTTTGGGATCGATACTTTTAATAAATGTATCGACACTTAAGGCGTGCACATCGTTT-GGCAT
* * * * * *
16935 TCATTATGGACAATAA-GTATCGACACAAATTCCACAAGTGTTGATACATTATGTTGACATGTTT
130 TCATTATGGACAA-AATATATCGACACAAATTCAAAAAGTGTCGATACATTATGTTGACATATTC
*
16999 TTTAAT-
194 TCTAATA
* * * *
17005 TAACTGGTATATTTATATCGGTGACATTGTTAATTTACATATTATATTATAATTATTGGTTTCGA
1 AAACTGGTATATTTATATCGGTAACATTGTAAATTTACATATTATATTATAATTATCGGTTTCGA
* *
17070 TGTTTTTGGGGTCGATACTTTTAAAAAATGTAT
66 TGTTTTTGGGATCGATACTTTTAATAAATGTAT
17103 TAACACATAT
Statistics
Matches: 259, Mismatches: 37, Indels: 4
0.86 0.12 0.01
Matches are distributed among these distances:
200 196 0.76
201 61 0.24
202 2 0.01
ACGTcount: A:0.32, C:0.13, G:0.15, T:0.41
Consensus pattern (200 bp):
AAACTGGTATATTTATATCGGTAACATTGTAAATTTACATATTATATTATAATTATCGGTTTCGA
TGTTTTTGGGATCGATACTTTTAATAAATGTATCGACACTTAAGGCGTGCACATCGTTTGGCATT
CATTATGGACAAAATATATCGACACAAATTCAAAAAGTGTCGATACATTATGTTGACATATTCTC
TAATA
Found at i:20074 original size:18 final size:18
Alignment explanation
Indices: 20051--20090 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
20041 CATCCACCTC
20051 CTTCCTCCATCTTTTCTT
1 CTTCCTCCATCTTTTCTT
20069 CTTCCTCCATCTTTTCTT
1 CTTCCTCCATCTTTTCTT
20087 CTTC
1 CTTC
20091 ATATTTTTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.05, C:0.40, G:0.00, T:0.55
Consensus pattern (18 bp):
CTTCCTCCATCTTTTCTT
Found at i:20338 original size:66 final size:65
Alignment explanation
Indices: 20199--20326 Score: 143
Period size: 66 Copynumber: 2.0 Consensus size: 65
20189 CTCTCTTCAC
* * *
20199 CCCCGTAAGTTCACCCCTCAAATCCACAACTTTCTTCACCACTCCATCAATTTTTCCACCCATCA
1 CCCCTTAACTTCACCCCTCAAATCCACAACTTTCTTCACCACTCCATCAATTTTTCCACCAATCA
* * * * *
20264 CCATCTTAACTTCACCCTTCAACTCCA-AA-TCTTCTTTCACCACTTCATCTATTTTTCCACCAA
1 CC-CCTTAACTTCACCCCTCAAATCCACAACT-TTC-TTCACCACTCCATCAATTTTTCCACCAA
20327 CTTTCCCCTT
Statistics
Matches: 52, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
64 1 0.02
65 7 0.13
66 44 0.85
ACGTcount: A:0.26, C:0.41, G:0.02, T:0.32
Consensus pattern (65 bp):
CCCCTTAACTTCACCCCTCAAATCCACAACTTTCTTCACCACTCCATCAATTTTTCCACCAATCA
Found at i:21227 original size:20 final size:21
Alignment explanation
Indices: 21202--21241 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
21192 TGTTTGGCTC
21202 TGAATG-GAACCATTCAGCGT
1 TGAATGTGAACCATTCAGCGT
*
21222 TGAATGTTGAACCGTTCAGC
1 TGAATG-TGAACCATTCAGC
21242 ATTCAGACTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
22 11 0.65
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.28
Consensus pattern (21 bp):
TGAATGTGAACCATTCAGCGT
Found at i:23866 original size:182 final size:182
Alignment explanation
Indices: 23082--23864 Score: 1074
Period size: 182 Copynumber: 4.3 Consensus size: 182
23072 GGTAGCGCTT
23082 AACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCG
1 AACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCG
* * * * *
23147 ACACTTTATAGGTGGTATTAATGCTTCTCTTTTTAATTCCAAAGGTGTCGATACTTATATTAAAG
66 ACACTTTATAGGCGCTATTACTGCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTATATTAAAG
** * *
23212 TATCGACACTTTCAACATAT-TCGGTAGCGTTTTACCCGCTTTGTCATTTCGA
131 TATCGACACTTTCAACATATCT-GGTAGCACTTTACCGGTTTTGTCATTTCGA
* * *
23264 GATCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAATATCG
1 AACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCG
* * * * *
23329 ACACTTTATATGCGCTATAATTGCTTCTCTTTTAAATTCCAAAACTGTCCATACTTATATTAAAG
66 ACACTTTATAGGCGCTATTACTGCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTATATTAAAG
*
23394 TATCGACA-TGTTCAACATATCTGGTAGCTCTTTACCGGTTTTGTCATTTC-A
131 TATCGACACT-TTCAACATATCTGGTAGCACTTTACCGGTTTTGTCATTTCGA
* * *
23445 AGACCGGTTTTGTCATATTTTTACCTATTATATTATTATGGATCGATACATTTTTATAAACTATC
1 A-ACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATC
** * *
23510 GACACTTTATAAACGCTATTACTGATTCTCTTTTAAATTCCAAACGTGTCGATACTTATATTAAA
65 GACACTTTATAGGCGCTATTACTGCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTATATTAAA
* * * * *
23575 ATATCGACACTTTCAATATATCCGATAGCACTTTACCAGTTTTGTCATTTCGA
130 GTATCGACACTTTCAACATATCTGGTAGCACTTTACCGGTTTTGTCATTTCGA
* * * *
23628 TACCGATTTTGTCATATTTTTGCCTGTTATATTGTTATGGATCGATACATTTTTTTAAAGTATCG
1 AACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCG
* *
23693 ACACTTTATAGGCGCTATTACTGCTTCTCTTTTAAATTCCAAAAGTGTTGATACTTAT-TTCAAT
66 ACACTTTATAGGCGCTATTACTGCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTATATT-AAA
* * * *
23757 CTAATCGATACTTTCAACATATCTGGTACCACTTTACCGGTTCTT-TCATAAT-GA
130 GT-ATCGACACTTTCAACATATCTGGTAGCACTTTACCGGTT-TTGTCAT-TTCGA
* * *
23811 AACCGGTTTTATCATATTTTAACCTGTTATATTGCTATGGATCGATACATTTTT
1 AACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
23865 TATTTGTATC
Statistics
Matches: 530, Mismatches: 62, Indels: 17
0.87 0.10 0.03
Matches are distributed among these distances:
181 4 0.01
182 433 0.82
183 90 0.17
184 3 0.01
ACGTcount: A:0.27, C:0.17, G:0.13, T:0.43
Consensus pattern (182 bp):
AACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCG
ACACTTTATAGGCGCTATTACTGCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTATATTAAAG
TATCGACACTTTCAACATATCTGGTAGCACTTTACCGGTTTTGTCATTTCGA
Found at i:24171 original size:3 final size:3
Alignment explanation
Indices: 24163--24226 Score: 128
Period size: 3 Copynumber: 21.3 Consensus size: 3
24153 ACCCCATCTG
24163 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
24211 TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA T
24227 ATTGTTGTCT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 61 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:28986 original size:20 final size:20
Alignment explanation
Indices: 28950--29099 Score: 85
Period size: 19 Copynumber: 7.6 Consensus size: 20
28940 AAACATTTGT
*
28950 GTTGCGAAATT-AAATTCGC
1 GTTGCGAATTTGAAATTCGC
*
28969 GTTGCGAATTTGAAATTC-A
1 GTTGCGAATTTGAAATTCGC
* **
28988 GTTGTGAATTTGACTTTCGC
1 GTTGCGAATTTGAAATTCGC
* *
29008 GTTGCGAATTTGGAAAATCGT
1 GTTGCGAATTT-GAAATTCGC
*** * * *
29029 AACGCGAAATTGGAAACT-GA
1 GTTGCG-AATTTGAAATTCGC
* * *
29049 GTTGCGAAATTGGAATTCGT
1 GTTGCGAATTTGAAATTCGC
*
29069 GTTGCGAATTTGAGATAT--C
1 GTTGCGAATTTGAAAT-TCGC
29088 GTTGCGAATTTG
1 GTTGCGAATTTG
29100 TTGGTCATTT
Statistics
Matches: 96, Mismatches: 29, Indels: 12
0.70 0.21 0.09
Matches are distributed among these distances:
19 44 0.46
20 34 0.35
21 14 0.15
22 4 0.04
ACGTcount: A:0.28, C:0.12, G:0.26, T:0.34
Consensus pattern (20 bp):
GTTGCGAATTTGAAATTCGC
Found at i:32154 original size:26 final size:24
Alignment explanation
Indices: 32125--32174 Score: 82
Period size: 26 Copynumber: 2.0 Consensus size: 24
32115 TGTATACATC
32125 ACCAACTCTTCATTGTGCTTGTTTTT
1 ACCAACTCTTCATTGT--TTGTTTTT
32151 ACCAACTCTTCATTGTTTGTTTTT
1 ACCAACTCTTCATTGTTTGTTTTT
32175 GTCACGTGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 8 0.33
26 16 0.67
ACGTcount: A:0.16, C:0.22, G:0.10, T:0.52
Consensus pattern (24 bp):
ACCAACTCTTCATTGTTTGTTTTT
Found at i:33140 original size:19 final size:19
Alignment explanation
Indices: 33106--33153 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
33096 TTAGCATTGT
33106 GAAAAG-AAAATAATGAAA
1 GAAAAGTAAAATAATGAAA
33124 GAAAAGTAAAA-AGATGAAA
1 GAAAAGTAAAATA-ATGAAA
*
33143 GAAAAATAAAA
1 GAAAAGTAAAA
33154 CTTCAATAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 7 0.26
19 20 0.74
ACGTcount: A:0.73, C:0.00, G:0.17, T:0.10
Consensus pattern (19 bp):
GAAAAGTAAAATAATGAAA
Found at i:41706 original size:21 final size:22
Alignment explanation
Indices: 41602--41705 Score: 131
Period size: 22 Copynumber: 4.8 Consensus size: 22
41592 CAGAACCCTC
* *
41602 AGGGGGTATCGATTCCCCTAC-
1 AGGGGGAATCGATTCCCCTTCA
* *
41623 AGGGGGAATCGGTTCCCCTACA
1 AGGGGGAATCGATTCCCCTTCA
*
41645 GGGGGGAATC-AGTTCCCCTTCA
1 AGGGGGAATCGA-TTCCCCTTCA
41667 AGGGGGAATCGATTCCCCTTCA
1 AGGGGGAATCGATTCCCCTTCA
*
41689 AGGGGGTATCGATTCCC
1 AGGGGGAATCGATTCCC
41706 TCTGCACTAA
Statistics
Matches: 73, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
21 19 0.26
22 53 0.73
23 1 0.01
ACGTcount: A:0.20, C:0.27, G:0.31, T:0.22
Consensus pattern (22 bp):
AGGGGGAATCGATTCCCCTTCA
Found at i:45782 original size:117 final size:117
Alignment explanation
Indices: 45562--45783 Score: 286
Period size: 117 Copynumber: 1.9 Consensus size: 117
45552 CTTTCAAATC
* * *
45562 GAAATTTTCTTTTTCAATACTTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTATTCAAGATTT
1 GAAAATTTCTTTTTCAATACTTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTACTCAACATTT
* *
45627 CATTTTGATTTTCAAAATCCATTTTCGTTTCTAGAAGAAGTTTGTTTAATTT
66 CATTTTGATTTTCAAAATCCATTTTAGTTTCTAAAAGAAGTTTGTTTAATTT
* * * * *
45679 GAAAATTTCTTTTTCAA-AGTTTTCAGATTTTATTTTTGAAAGCTCTAACTCCTTGCTCAACATT
1 GAAAATTTCTTTTTCAATA-CTTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTACTCAACATT
* * **
45743 TCATTTTGATTTTCCAATTCTGTTTTAGCTTTC-AAAAGAAG
65 TCATTTTGATTTTCAAAATCCATTTTAG-TTTCTAAAAGAAG
45784 ATCATTTTTA
Statistics
Matches: 89, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
116 1 0.01
117 84 0.94
118 4 0.04
ACGTcount: A:0.28, C:0.15, G:0.09, T:0.47
Consensus pattern (117 bp):
GAAAATTTCTTTTTCAATACTTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTACTCAACATTT
CATTTTGATTTTCAAAATCCATTTTAGTTTCTAAAAGAAGTTTGTTTAATTT
Found at i:46861 original size:10 final size:10
Alignment explanation
Indices: 46846--46880 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
46836 GTTTGATGCT
46846 TTCTCTTTGA
1 TTCTCTTTGA
46856 TTCTCTTTGA
1 TTCTCTTTGA
*
46866 TTATCTCTTGA
1 TTCTCT-TTGA
46877 TTCT
1 TTCT
46881 TGTTGATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 15 0.68
11 7 0.32
ACGTcount: A:0.11, C:0.20, G:0.09, T:0.60
Consensus pattern (10 bp):
TTCTCTTTGA
Found at i:46878 original size:21 final size:22
Alignment explanation
Indices: 46847--46888 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
46837 TTTGATGCTT
46847 TCTCTTTGATTCTCT-TTGATTA
1 TCTCTTTGATTCT-TGTTGATTA
46869 TCTC-TTGATTCTTGTTGATT
1 TCTCTTTGATTCTTGTTGATT
46889 TTTGTTTCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 1 0.05
21 14 0.74
22 4 0.21
ACGTcount: A:0.12, C:0.17, G:0.12, T:0.60
Consensus pattern (22 bp):
TCTCTTTGATTCTTGTTGATTA
Found at i:49013 original size:20 final size:21
Alignment explanation
Indices: 48988--49027 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
48978 ATCTAAATTT
48988 TTAAATATTA-AAAGAGAAAA
1 TTAAATATTATAAAGAGAAAA
*
49008 TTAAATATTATACAGAGAAA
1 TTAAATATTATAAAGAGAAA
49028 TAAATCTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.60, C:0.03, G:0.10, T:0.28
Consensus pattern (21 bp):
TTAAATATTATAAAGAGAAAA
Found at i:54254 original size:3 final size:3
Alignment explanation
Indices: 54241--54294 Score: 54
Period size: 3 Copynumber: 17.7 Consensus size: 3
54231 CATTTTAATG
* * * * *
54241 TTA TAA TTA TTA TTA TTA TAA TTA TAA TGA TTA TTA TTA TTA ATA TATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
54290 TTA TT
1 TTA TT
54295 TAATATTACA
Statistics
Matches: 41, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
3 38 0.93
4 3 0.07
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (3 bp):
TTA
Found at i:68171 original size:43 final size:41
Alignment explanation
Indices: 68044--68375 Score: 244
Period size: 42 Copynumber: 7.9 Consensus size: 41
68034 ATTTTTGCCA
* * ** * *
68044 TTTTACCTTTATAATTAAAGTTCATAATTTTTGTAA-CTCGCC
1 TTTTACCTTTATAATTGAGGCCCATAATTTTT-CAATCTC-AC
* **
68086 TTTTACCTTTATAATTGA-GCCCTTGTTTTTTTCAATCTCAC
1 TTTTACCTTTATAATTGAGGCCCAT-AATTTTTCAATCTCAC
* *
68127 TTTTCACCTTTATAATTAAGGCACATAATTTTGTCAATCTCAC
1 TTTT-ACCTTTATAATTGAGGCCCATAATTTT-TCAATCTCAC
* * *
68170 TTTTATCTTTATAATTGAGACCCATAATTTTTTTTCAACCTCAC
1 TTTTACCTTTATAATTGAGGCCCATAA---TTTTTCAATCTCAC
* * * * *
68214 TTCCTACTTTTAAAATTGAGGCCTCA-AGCTTTTTTAATCTCAC
1 TT-TTACCTTTATAATTGAGGCC-CATA-ATTTTTCAATCTCAC
* *
68257 TTTTTATCTTTATAATTGA-GCCCGGTAATTTTTCAATCTCAC
1 -TTTTACCTTTATAATTGAGGCCC-ATAATTTTTCAATCTCAC
* * * *
68299 TTTTTGCATTTATAATT-AGACCCCTAATTTTT-AATCTCAC
1 -TTTTACCTTTATAATTGAGGCCCATAATTTTTCAATCTCAC
* *
68339 TTTTTACCTTTATAATTGAGACCCCTAATTTTTCAAT
1 -TTTTACCTTTATAATTGAGGCCCATAATTTTTCAAT
68376 TTCATAAAAT
Statistics
Matches: 233, Mismatches: 40, Indels: 34
0.76 0.13 0.11
Matches are distributed among these distances:
40 23 0.10
41 35 0.15
42 97 0.42
43 43 0.18
44 13 0.06
45 20 0.09
46 2 0.01
ACGTcount: A:0.26, C:0.20, G:0.07, T:0.47
Consensus pattern (41 bp):
TTTTACCTTTATAATTGAGGCCCATAATTTTTCAATCTCAC
Found at i:74978 original size:20 final size:20
Alignment explanation
Indices: 74953--75007 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 20
74943 TTTTGGTGCA
*
74953 GAGGGAATCGATCCCCCCTT
1 GAGGGAACCGATCCCCCCTT
*
74973 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGA-TCCCCCCTT
74994 GAAGGGGAACCGAT
1 G-A-GGGAACCGAT
75008 TCAGGGAACC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 10 0.33
21 9 0.30
22 2 0.07
23 9 0.30
ACGTcount: A:0.24, C:0.29, G:0.29, T:0.18
Consensus pattern (20 bp):
GAGGGAACCGATCCCCCCTT
Found at i:75005 original size:23 final size:21
Alignment explanation
Indices: 74953--75009 Score: 71
Period size: 23 Copynumber: 2.7 Consensus size: 21
74943 TTTTGGTGCA
*
74953 GAGGGAATCGA-TCCCCCCTT
1 GAGGGAACCGATTCCCCCCTT
*
74973 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCCCTT
74994 GAAGGGGAACCGATTC
1 G-A-GGGAACCGATTC
75010 AGGGAACCGA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
20 10 0.31
21 9 0.28
22 1 0.03
23 12 0.38
ACGTcount: A:0.23, C:0.30, G:0.28, T:0.19
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCCTT
Found at i:75016 original size:13 final size:13
Alignment explanation
Indices: 74998--75022 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
74988 CCCTTTGAAG
74998 GGGAACCGATTCA
1 GGGAACCGATTCA
75011 GGGAACCGATTC
1 GGGAACCGATTC
75023 CCCCCATAGG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.28, C:0.24, G:0.32, T:0.16
Consensus pattern (13 bp):
GGGAACCGATTCA
Found at i:84063 original size:2 final size:2
Alignment explanation
Indices: 84050--84086 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
84040 ATATCAATTG
*
84050 TA TA TC TA TA TA TA TA -A TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
84087 GTCGTTTTCG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:84628 original size:2 final size:2
Alignment explanation
Indices: 84621--84680 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
84611 CTTTTTCTCG
84621 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
84663 TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA
84681 GATAAGGGGA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:87599 original size:2 final size:2
Alignment explanation
Indices: 87592--87623 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
87582 TGTTATTTTA
87592 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
87624 TACCTAGTCT
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:97525 original size:15 final size:16
Alignment explanation
Indices: 97507--97542 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
97497 TAAATTAATT
*
97507 TATAAAATGTTAAA-A
1 TATAAAATATTAAACA
97522 TATAAAATATTAAACA
1 TATAAAATATTAAACA
97538 TATAA
1 TATAA
97543 TTACAAGTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 13 0.68
16 6 0.32
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.33
Consensus pattern (16 bp):
TATAAAATATTAAACA
Found at i:98930 original size:18 final size:17
Alignment explanation
Indices: 98905--98955 Score: 84
Period size: 18 Copynumber: 2.9 Consensus size: 17
98895 ACCCGTTTAC
98905 CCGTTTACCCGACCCGA
1 CCGTTTACCCGACCCGA
98922 CCAGTTTACCCGACCCGA
1 CC-GTTTACCCGACCCGA
*
98940 CCGTTGACCCGACCCG
1 CCGTTTACCCGACCCG
98956 TTTGACTGTT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
17 15 0.47
18 17 0.53
ACGTcount: A:0.18, C:0.47, G:0.20, T:0.16
Consensus pattern (17 bp):
CCGTTTACCCGACCCGA
Found at i:99037 original size:29 final size:29
Alignment explanation
Indices: 98977--99044 Score: 91
Period size: 29 Copynumber: 2.3 Consensus size: 29
98967 ACCGTTGACC
* ****
98977 GGTGCTATTCTGGGAATTAATTCGGTTTT
1 GGTGCTATTTTGGGAATTAATTCGAAAAT
99006 GGTGCTATTTTGGGAATTAATTCGAAAAT
1 GGTGCTATTTTGGGAATTAATTCGAAAAT
99035 GGTGCTATTT
1 GGTGCTATTT
99045 GTGTAAAATG
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.22, C:0.09, G:0.26, T:0.43
Consensus pattern (29 bp):
GGTGCTATTTTGGGAATTAATTCGAAAAT
Found at i:106122 original size:19 final size:19
Alignment explanation
Indices: 106098--106153 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
106088 GAACGCTGGA
106098 AACCGGTTTTGACCGGTTT
1 AACCGGTTTTGACCGGTTT
106117 AACCGGTTTTGAACCGGTTTT
1 AACCGGTTTTG-ACCGG-TTT
*
106138 GACCGG-TTTGACCGGT
1 AACCGGTTTTGACCGGT
106154 CACGACCCGT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
18 1 0.03
19 16 0.47
20 9 0.26
21 8 0.24
ACGTcount: A:0.16, C:0.21, G:0.29, T:0.34
Consensus pattern (19 bp):
AACCGGTTTTGACCGGTTT
Found at i:106133 original size:11 final size:11
Alignment explanation
Indices: 106098--106146 Score: 70
Period size: 10 Copynumber: 4.8 Consensus size: 11
106088 GAACGCTGGA
106098 AACCGGTTTTG
1 AACCGGTTTTG
106109 -ACCGG-TTT-
1 AACCGGTTTTG
106117 AACCGGTTTTG
1 AACCGGTTTTG
106128 AACCGGTTTTG
1 AACCGGTTTTG
106139 -ACCGGTTT
1 AACCGGTTT
106147 GACCGGTCAC
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
9 8 0.23
10 16 0.46
11 11 0.31
ACGTcount: A:0.16, C:0.20, G:0.27, T:0.37
Consensus pattern (11 bp):
AACCGGTTTTG
Found at i:106149 original size:9 final size:10
Alignment explanation
Indices: 106099--106153 Score: 78
Period size: 9 Copynumber: 5.6 Consensus size: 10
106089 AACGCTGGAA
106099 ACCGGTTTTG
1 ACCGGTTTTG
*
106109 ACCGG-TTTA
1 ACCGGTTTTG
106118 ACCGGTTTTG
1 ACCGGTTTTG
106128 AACCGGTTTTG
1 -ACCGGTTTTG
106139 ACCGG-TTTG
1 ACCGGTTTTG
106148 ACCGGT
1 ACCGGT
106154 CACGACCCGT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
9 17 0.43
10 13 0.32
11 10 0.25
ACGTcount: A:0.15, C:0.22, G:0.29, T:0.35
Consensus pattern (10 bp):
ACCGGTTTTG
Found at i:106193 original size:18 final size:17
Alignment explanation
Indices: 106168--106218 Score: 84
Period size: 18 Copynumber: 2.9 Consensus size: 17
106158 ACCCGTTTAC
106168 CCGTTTACCCGACCCGA
1 CCGTTTACCCGACCCGA
106185 CCAGTTTACCCGACCCGA
1 CC-GTTTACCCGACCCGA
*
106203 CCGTTGACCCGACCCG
1 CCGTTTACCCGACCCG
106219 TTGACCGTTG
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
17 15 0.47
18 17 0.53
ACGTcount: A:0.18, C:0.47, G:0.20, T:0.16
Consensus pattern (17 bp):
CCGTTTACCCGACCCGA
Found at i:106221 original size:13 final size:12
Alignment explanation
Indices: 106196--106238 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 12
106186 CAGTTTACCC
106196 GACCCGACCGTT
1 GACCCGACCGTT
106208 GACCCGACCCGTT
1 GACCCGA-CCGTT
*
106221 GACCGTTGACCGTT
1 GACC--CGACCGTT
106235 GACC
1 GACC
106239 GTTGACCGGT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
12 7 0.26
13 9 0.33
14 9 0.33
15 2 0.07
ACGTcount: A:0.16, C:0.40, G:0.26, T:0.19
Consensus pattern (12 bp):
GACCCGACCGTT
Found at i:106226 original size:7 final size:7
Alignment explanation
Indices: 106216--106246 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
106206 TTGACCCGAC
106216 CCGTTGA
1 CCGTTGA
106223 CCGTTGA
1 CCGTTGA
106230 CCGTTGA
1 CCGTTGA
106237 CCGTTGA
1 CCGTTGA
106244 CCG
1 CCG
106247 GTGCTATTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.13, C:0.32, G:0.29, T:0.26
Consensus pattern (7 bp):
CCGTTGA
Found at i:106306 original size:29 final size:29
Alignment explanation
Indices: 106246--106313 Score: 91
Period size: 29 Copynumber: 2.3 Consensus size: 29
106236 ACCGTTGACC
* ****
106246 GGTGCTATTCTGGGAATTAATTCGGTTTT
1 GGTGCTATTTTGGGAATTAATTCGAAAAT
106275 GGTGCTATTTTGGGAATTAATTCGAAAAT
1 GGTGCTATTTTGGGAATTAATTCGAAAAT
106304 GGTGCTATTT
1 GGTGCTATTT
106314 GTGTAAAATG
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.22, C:0.09, G:0.26, T:0.43
Consensus pattern (29 bp):
GGTGCTATTTTGGGAATTAATTCGAAAAT
Found at i:109144 original size:25 final size:23
Alignment explanation
Indices: 109091--109144 Score: 54
Period size: 25 Copynumber: 2.3 Consensus size: 23
109081 TAGATTATAT
* *
109091 CATTTTTTTATTTAGGTGTTTAA
1 CATTTTTTTATTCAGGTGTCTAA
**
109114 TTTTTTTGTTAATTCAGGTGTCTAA
1 CATTTTT-TT-ATTCAGGTGTCTAA
109139 CATTTT
1 CATTTT
109145 AAACGTTACA
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
23 5 0.22
24 2 0.09
25 16 0.70
ACGTcount: A:0.20, C:0.07, G:0.13, T:0.59
Consensus pattern (23 bp):
CATTTTTTTATTCAGGTGTCTAA
Found at i:117218 original size:194 final size:193
Alignment explanation
Indices: 116961--117315 Score: 539
Period size: 194 Copynumber: 1.8 Consensus size: 193
116951 AACTAATTAT
** * ***
116961 GTCACTAAATTATGTAAAATTTCGTTATTGATGATTTATATCGTCACGGATAATACATTAAAATC
1 GTCACTAAATTAAATAAAATTTCGTTATTGATAATTTATATCGTCAAAAATAATACATTAAAATC
* *
117026 AACCTATATGTGACGAAAGAGATATTGTCAAATTTTTAGTGGCATAATATAAATGTTACCTAATA
66 AACCTATATGTGACGAAAGAGATATTGTCAAATTTTTAGTGACATAATAT-AACGTTACCTAATA
*
117091 ATATTATGAATGACGTTTATGCATAACGTCACTTTATAGTTTATATTCTATGACAGTTGGTTAC
130 ATATTATGAATGACGATTATGCATAACGTCACTTTATAGTTTATATTCTATGACAGTTGGTTAC
* * **
117155 GTCACTAAATTAAATAAGATTTCGTTATTGATAATTTATATTGTCAAAAATAATGTATTAAAATC
1 GTCACTAAATTAAATAAAATTTCGTTATTGATAATTTATATCGTCAAAAATAATACATTAAAATC
* ** *
117220 AACTTATATGTGACGAAAGAGATATTGTCACCTTTTTAGTGACATAATATACCGTTACCTAATAA
66 AACCTATATGTGACGAAAGAGATATTGTCAAATTTTTAGTGACATAATATAACGTTACCTAATAA
*
117285 TATTATGAATGATGATTATGCATAACGTCAC
131 TATTATGAATGACGATTATGCATAACGTCAC
117316 CATATATAAT
Statistics
Matches: 143, Mismatches: 18, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
193 42 0.29
194 101 0.71
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.37
Consensus pattern (193 bp):
GTCACTAAATTAAATAAAATTTCGTTATTGATAATTTATATCGTCAAAAATAATACATTAAAATC
AACCTATATGTGACGAAAGAGATATTGTCAAATTTTTAGTGACATAATATAACGTTACCTAATAA
TATTATGAATGACGATTATGCATAACGTCACTTTATAGTTTATATTCTATGACAGTTGGTTAC
Found at i:117329 original size:15 final size:15
Alignment explanation
Indices: 117306--117381 Score: 59
Period size: 15 Copynumber: 5.1 Consensus size: 15
117296 ATGATTATGC
*
117306 ATAACGTCACCATAT
1 ATAATGTCACCATAT
117321 ATAATGTCACCAT-T
1 ATAATGTCACCATAT
* * **
117335 ATAGTGGCAAAACTA-
1 ATAATGTCACCA-TAT
*
117350 AAAATTGTCACCATAT
1 ATAA-TGTCACCATAT
117366 ATAATGTCACCA-AT
1 ATAATGTCACCATAT
117380 AT
1 AT
117382 CGTTTTGTTT
Statistics
Matches: 46, Mismatches: 11, Indels: 9
0.70 0.17 0.14
Matches are distributed among these distances:
14 13 0.28
15 25 0.54
16 8 0.17
ACGTcount: A:0.42, C:0.20, G:0.09, T:0.29
Consensus pattern (15 bp):
ATAATGTCACCATAT
Found at i:119974 original size:31 final size:30
Alignment explanation
Indices: 119852--120006 Score: 249
Period size: 30 Copynumber: 5.1 Consensus size: 30
119842 GAAGGACCTA
** *
119852 TCCAGAGGTCACCAAGA-CCCCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
119881 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
119911 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
119941 TCCAGAGGTCATAAAGATCCTCGGTAAACTG
1 TCCAGAGGTCATAAAGATCCTCGGT-AACTG
*
119972 TCCAGAGGTCATAAAGATTCTCGGTAAACTG
1 TCCAGAGGTCATAAAGATCCTCGGT-AACTG
120003 TCCA
1 TCCA
120007 TATGTCTCGA
Statistics
Matches: 120, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
29 15 0.12
30 66 0.55
31 39 0.32
ACGTcount: A:0.30, C:0.25, G:0.23, T:0.22
Consensus pattern (30 bp):
TCCAGAGGTCATAAAGATCCTCGGTAACTG
Found at i:121323 original size:21 final size:21
Alignment explanation
Indices: 121299--121343 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
121289 TGTTGTTCGT
* *
121299 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
121320 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
121341 TTG
1 TTG
121344 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:123537 original size:3 final size:3
Alignment explanation
Indices: 123525--123586 Score: 117
Period size: 3 Copynumber: 21.0 Consensus size: 3
123515 AAAAATTCAT
123525 TAA T-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
123572 TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA
123587 ATTGATAAAG
Statistics
Matches: 58, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 56 0.97
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:125024 original size:23 final size:25
Alignment explanation
Indices: 124979--125029 Score: 70
Period size: 26 Copynumber: 2.1 Consensus size: 25
124969 CAGCTATTAC
*
124979 TTTTTTTTGTGTACTTGAGTTAGCAG
1 TTTTTTTTGTGTACTT-ACTTAGCAG
125005 TTTTTTTTGTGTAC-T-CTTAGCAG
1 TTTTTTTTGTGTACTTACTTAGCAG
125028 TT
1 TT
125030 AATTCTTTCT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 9 0.38
25 1 0.04
26 14 0.58
ACGTcount: A:0.14, C:0.10, G:0.20, T:0.57
Consensus pattern (25 bp):
TTTTTTTTGTGTACTTACTTAGCAG
Done.