Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000631.1 Hibiscus syriacus cultivar Beakdansim tig00001227_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: 81378
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.33
Found at i:86 original size:45 final size:45
Alignment explanation
Indices: 1--87 Score: 104
Period size: 45 Copynumber: 1.9 Consensus size: 45
* *
1 CAATAACACATAGCTTATATCATATTCTCATGTAATCACATATGT
1 CAATAACACATAGCTTATATCATATTCACATATAATCACATATGT
* * * *
46 CAATATCACATATCTTATATCTTGTTCACATAT-ATCCACATA
1 CAATAACACATAGCTTATATCATATTCACATATAAT-CACATA
88 GATCATGTAA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
44 2 0.06
45 33 0.94
ACGTcount: A:0.37, C:0.22, G:0.05, T:0.37
Consensus pattern (45 bp):
CAATAACACATAGCTTATATCATATTCACATATAATCACATATGT
Found at i:1138 original size:36 final size:36
Alignment explanation
Indices: 1091--1165 Score: 150
Period size: 36 Copynumber: 2.1 Consensus size: 36
1081 TTTTATTCAA
1091 TCTCAGGTAACTTGCAAATCTTTTAGTTTCTACTTC
1 TCTCAGGTAACTTGCAAATCTTTTAGTTTCTACTTC
1127 TCTCAGGTAACTTGCAAATCTTTTAGTTTCTACTTC
1 TCTCAGGTAACTTGCAAATCTTTTAGTTTCTACTTC
1163 TCT
1 TCT
1166 TTAAGCTTCC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.21, C:0.23, G:0.11, T:0.45
Consensus pattern (36 bp):
TCTCAGGTAACTTGCAAATCTTTTAGTTTCTACTTC
Found at i:5256 original size:5 final size:5
Alignment explanation
Indices: 5248--5331 Score: 54
Period size: 5 Copynumber: 17.6 Consensus size: 5
5238 AAATGAATAG
* * * *
5248 AAAAT AAAAAT TAAAT AGAAT AAGAT AAAA- AAGAT -AAAT -AAAT AAAAT
1 AAAAT -AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
* *
5296 AAGA- AAAAT -AAAG AAAAT AAAAAT AAAAT -AAAT AAA
1 AAAAT AAAAT AAAAT AAAAT -AAAAT AAAAT AAAAT AAA
5332 CAAAACGAGG
Statistics
Matches: 60, Mismatches: 12, Indels: 13
0.71 0.14 0.15
Matches are distributed among these distances:
4 20 0.33
5 30 0.50
6 10 0.17
ACGTcount: A:0.76, C:0.00, G:0.06, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:5278 original size:27 final size:24
Alignment explanation
Indices: 5248--5331 Score: 73
Period size: 24 Copynumber: 3.3 Consensus size: 24
5238 AAATGAATAG
*
5248 AAAATAAAAATTAAATAGAATAAGA
1 AAAATAAAAA-TAAATAAAATAAGA
*
5273 TAAAAAAGATAAATAAATAAAATAAGA
1 -AAAATA-A-AAATAAATAAAATAAGA
*
5300 AAAATAAAGA-AAATAAAAATAA-A
1 AAAATAAAAATAAAT-AAAATAAGA
5323 ATAAATAAA
1 A-AAATAAA
5332 CAAAACGAGG
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
23 6 0.12
24 16 0.32
25 1 0.02
26 10 0.20
27 14 0.28
28 3 0.06
ACGTcount: A:0.76, C:0.00, G:0.06, T:0.18
Consensus pattern (24 bp):
AAAATAAAAATAAATAAAATAAGA
Found at i:5299 original size:18 final size:18
Alignment explanation
Indices: 5266--5331 Score: 71
Period size: 18 Copynumber: 3.6 Consensus size: 18
5256 AATTAAATAG
5266 AATAAGATAAAA-AAGATA
1 AATAA-ATAAAATAAGATA
*
5284 AATAAATAAAATAAGAAA
1 AATAAATAAAATAAGATA
* *
5302 AATAAAGAAAATAAAAATAA
1 AATAAATAAAAT-AAGAT-A
5322 AATAAATAAA
1 AATAAATAAA
5332 CAAAACGAGG
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
17 6 0.15
18 21 0.52
19 3 0.08
20 10 0.25
ACGTcount: A:0.77, C:0.00, G:0.06, T:0.17
Consensus pattern (18 bp):
AATAAATAAAATAAGATA
Found at i:5328 original size:9 final size:9
Alignment explanation
Indices: 5249--5331 Score: 64
Period size: 9 Copynumber: 8.8 Consensus size: 9
5239 AATGAATAGA
5249 AAATAAAAATT
1 AAAT-AAAA-T
*
5260 AAATAGAAT
1 AAATAAAAT
5269 AAGATAAAA-
1 AA-ATAAAAT
5278 AAGAT-AAAT
1 AA-ATAAAAT
5287 AAATAAAAT
1 AAATAAAAT
5296 AAGA-AAAAT
1 AA-ATAAAAT
*
5305 AAAGAAAAT
1 AAATAAAAT
5314 AAAAATAAAAT
1 --AAATAAAAT
5325 AAATAAA
1 AAATAAA
5332 CAAAACGAGG
Statistics
Matches: 62, Mismatches: 3, Indels: 16
0.77 0.04 0.20
Matches are distributed among these distances:
8 6 0.10
9 35 0.56
10 9 0.15
11 12 0.19
ACGTcount: A:0.76, C:0.00, G:0.06, T:0.18
Consensus pattern (9 bp):
AAATAAAAT
Found at i:5365 original size:61 final size:65
Alignment explanation
Indices: 5227--5366 Score: 145
Period size: 61 Copynumber: 2.2 Consensus size: 65
5217 TAATATGGAG
* * *
5227 ATAAGGAAATGAAATGAATAGAAAATAAAAATTAAATAGAATAAGATAAAAAAGATAAATAAATA
1 ATAA-GAAATAAAAT-AATAGAAAATAAAAATAAAATAGAATAAGACAAAAAAGATAAATAAATA
5292 AA
64 AA
*
5294 ATAAG--A-AAAATAA-AGAAAATAAAAATAAAATA-AATAA-ACAAAACGAGGA-AAA-AAATA
1 ATAAGAAATAAAATAATAGAAAATAAAAATAAAATAGAATAAGACAAAA--AAGATAAATAAATA
5351 AA
64 AA
5353 A-AAGAAATAAAATA
1 ATAAGAAATAAAATA
5367 TACATATATA
Statistics
Matches: 64, Mismatches: 4, Indels: 16
0.76 0.05 0.19
Matches are distributed among these distances:
58 3 0.05
59 13 0.20
60 9 0.14
61 27 0.42
62 2 0.03
63 4 0.06
64 1 0.02
66 1 0.02
67 4 0.06
ACGTcount: A:0.73, C:0.01, G:0.10, T:0.16
Consensus pattern (65 bp):
ATAAGAAATAAAATAATAGAAAATAAAAATAAAATAGAATAAGACAAAAAAGATAAATAAATAAA
Found at i:5447 original size:16 final size:15
Alignment explanation
Indices: 5411--5471 Score: 52
Period size: 16 Copynumber: 3.9 Consensus size: 15
5401 AGAAATAAAG
*
5411 TAAAT-ATATATATA
1 TAAATAATATAAATA
*
5425 TATATAATATAACATA
1 TAAATAATATAA-ATA
*
5441 TAAATAAAATAAATA
1 TAAATAATATAAATA
*
5456 AATAATAATAATAAAT
1 TA-AATAAT-ATAAAT
5472 GTATATACAT
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
14 4 0.11
15 9 0.24
16 18 0.49
17 6 0.16
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (15 bp):
TAAATAATATAAATA
Found at i:5459 original size:52 final size:50
Alignment explanation
Indices: 5345--5484 Score: 121
Period size: 50 Copynumber: 2.8 Consensus size: 50
5335 AACGAGGAAA
* * * *
5345 AAAATAAAAAAGAAATAAAATATACATATATATATATTAGCTTGTAAACT
1 AAAATAAAAAATAAATAAAATATACATATATATATATTAACATATAAACT
*
5395 AAAA-AAAGAAATAAAGT-AAATATATATATATATATAATATAACATATAAA-T
1 AAAATAAA-AAATAAA-TAAAATATACATATATATAT-AT-TAACATATAAACT
* *
5446 AAAATAAATAAAT-AATAATAATA-A-ATGTATATACATTAA
1 AAAATAAA-AAATAAATAA-AATATACATATATATATATTAA
5485 AATAAAATGA
Statistics
Matches: 75, Mismatches: 8, Indels: 16
0.76 0.08 0.16
Matches are distributed among these distances:
48 3 0.04
49 5 0.07
50 36 0.48
51 12 0.16
52 19 0.25
ACGTcount: A:0.62, C:0.04, G:0.04, T:0.30
Consensus pattern (50 bp):
AAAATAAAAAATAAATAAAATATACATATATATATATTAACATATAAACT
Found at i:6687 original size:2 final size:2
Alignment explanation
Indices: 6682--6738 Score: 52
Period size: 2 Copynumber: 30.0 Consensus size: 2
6672 AAAAGAATAA
*
6682 AT AT AT AA AT AT AT -T AT AT AT AT AT AT GA- AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT
6722 AGT AT AT -T AT AT A- AT AT
1 A-T AT AT AT AT AT AT AT AT
6739 GATAACGTAT
Statistics
Matches: 46, Mismatches: 2, Indels: 14
0.74 0.03 0.23
Matches are distributed among these distances:
1 5 0.11
2 38 0.83
3 3 0.07
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (2 bp):
AT
Found at i:6708 original size:21 final size:22
Alignment explanation
Indices: 6682--6738 Score: 80
Period size: 21 Copynumber: 2.5 Consensus size: 22
6672 AAAAGAATAA
6682 ATATATAAATATATTATATA-T
1 ATATATAAATATATTATATAGT
*
6703 ATATATGAATATATTATATAGT
1 ATATATAAATATATTATATAGT
6725 ATATTATATAATAT
1 ATA-TATA-AATAT
6739 GATAACGTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
21 19 0.61
22 4 0.13
23 3 0.10
24 5 0.16
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (22 bp):
ATATATAAATATATTATATAGT
Found at i:7682 original size:111 final size:110
Alignment explanation
Indices: 7537--7736 Score: 319
Period size: 111 Copynumber: 1.8 Consensus size: 110
7527 AACTGGGAAA
* *
7537 TTATTTGTTAACAGTCAGCCACCCCTTCGCTGTGAAGTTGAGCTTATGCTGTCTCGAGTCTAATA
1 TTATTTGTTAACAATCAGCCACCCCTTCGCTGTGAAGTTGAGCTTATGCTGTCTCGAGTCCAATA
*
7602 TCCTTCGTTGTGAAGTTAAAATTGACTCCGAATGAAACTGAAAAG
66 TCCTTCGCTGTGAAGTTAAAATTGACTCCGAATGAAACTGAAAAG
* * * * *
7647 TTATTTGTTGACAAATCAGCCACCCCTTCGTTGTGAAGTTGAGCTTGTGTTGTCTTGAGTCCAAT
1 TTATTTGTTAAC-AATCAGCCACCCCTTCGCTGTGAAGTTGAGCTTATGCTGTCTCGAGTCCAAT
7712 ATCCTTCGCTGTGAAGTTAAAATTG
65 ATCCTTCGCTGTGAAGTTAAAATTG
7737 GCTCTGAAAT
Statistics
Matches: 81, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
110 11 0.14
111 70 0.86
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.35
Consensus pattern (110 bp):
TTATTTGTTAACAATCAGCCACCCCTTCGCTGTGAAGTTGAGCTTATGCTGTCTCGAGTCCAATA
TCCTTCGCTGTGAAGTTAAAATTGACTCCGAATGAAACTGAAAAG
Found at i:8879 original size:17 final size:16
Alignment explanation
Indices: 8854--8901 Score: 51
Period size: 17 Copynumber: 2.9 Consensus size: 16
8844 CCCACCTTAT
*
8854 TTTTCTTCTCTTTTTTC
1 TTTTCTTCT-TTTTCTC
*
8871 TTTTGTTCTTTTTCTC
1 TTTTCTTCTTTTTCTC
*
8887 TTTTTCTTTTTTTTC
1 -TTTTCTTCTTTTTC
8902 AATTTAGGGC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
16 6 0.23
17 20 0.77
ACGTcount: A:0.00, C:0.19, G:0.02, T:0.79
Consensus pattern (16 bp):
TTTTCTTCTTTTTCTC
Found at i:8882 original size:15 final size:15
Alignment explanation
Indices: 8862--8898 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
8852 ATTTTTCTTC
8862 TCTTTTTTCT-TTTGT
1 TCTTTTTTCTCTTT-T
8877 TC-TTTTTCTCTTTT
1 TCTTTTTTCTCTTTT
8891 TCTTTTTT
1 TCTTTTTT
8899 TTCAATTTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 10 0.50
15 10 0.50
ACGTcount: A:0.00, C:0.16, G:0.03, T:0.81
Consensus pattern (15 bp):
TCTTTTTTCTCTTTT
Found at i:19184 original size:70 final size:70
Alignment explanation
Indices: 19071--19212 Score: 257
Period size: 70 Copynumber: 2.0 Consensus size: 70
19061 TTAGCACCCT
* * *
19071 TGAACTGCCCTTTCGGTACTATGTAATTTTCAATTGTCTTTAATTAAGAAAGTGGTAAATTTAAA
1 TGAACTGCCCTTTCGATACTATATAATTTCCAATTGTCTTTAATTAAGAAAGTGGTAAATTTAAA
19136 TTAAA
66 TTAAA
19141 TGAACTGCCCTTTCGATACTATATAATTTCCAATTGTCTTTAATTAAGAAAGTGGTAAATTTAAA
1 TGAACTGCCCTTTCGATACTATATAATTTCCAATTGTCTTTAATTAAGAAAGTGGTAAATTTAAA
19206 TTAAA
66 TTAAA
19211 TG
1 TG
19213 GTAAAATGAC
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
70 69 1.00
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.39
Consensus pattern (70 bp):
TGAACTGCCCTTTCGATACTATATAATTTCCAATTGTCTTTAATTAAGAAAGTGGTAAATTTAAA
TTAAA
Found at i:19458 original size:4 final size:4
Alignment explanation
Indices: 19449--19521 Score: 83
Period size: 4 Copynumber: 17.2 Consensus size: 4
19439 GCTAAAAAAG
* *
19449 ATAA ATAA ATAAA ATAA GAAAA ATAA ATAA ATCA ATAA ATAA ATAA ATAA
1 ATAA ATAA AT-AA ATAA -ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA
*
19499 AGAA ATAAA ATAAA ATAA ATAA A
1 ATAA AT-AA AT-AA ATAA ATAA A
19522 CAAAACGAGG
Statistics
Matches: 60, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
4 44 0.73
5 16 0.27
ACGTcount: A:0.75, C:0.01, G:0.03, T:0.21
Consensus pattern (4 bp):
ATAA
Found at i:19460 original size:22 final size:20
Alignment explanation
Indices: 19441--19521 Score: 90
Period size: 22 Copynumber: 3.8 Consensus size: 20
19431 TAGAATAAGC
19441 TAAAAAAGATAAATAAATAAAA
1 TAAAAAA-ATAAATAAAT-AAA
*
19463 TAAGAAAAATAAATAAATCAA
1 TAA-AAAAATAAATAAATAAA
* *
19484 TAAATAAATAAATAAAGAAA
1 TAAAAAAATAAATAAATAAA
19504 TAAAATAAAATAAATAAA
1 T-AAA-AAAATAAATAAA
19522 CAAAACGAGG
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
20 15 0.29
21 8 0.16
22 24 0.47
23 4 0.08
ACGTcount: A:0.75, C:0.01, G:0.04, T:0.20
Consensus pattern (20 bp):
TAAAAAAATAAATAAATAAA
Found at i:19487 original size:34 final size:34
Alignment explanation
Indices: 19441--19521 Score: 96
Period size: 34 Copynumber: 2.4 Consensus size: 34
19431 TAGAATAAGC
19441 TAAAA-AAGATAAATAAATAAAATAAGAAAAAT-AAA
1 TAAAATAA-ATAAATAAAT-AAATAA-AAAAATAAAA
* *
19476 T-AAATCAATAAATAAATAAATAAAGAAATAAAA
1 TAAAATAAATAAATAAATAAATAAAAAAATAAAA
19509 TAAAATAAATAAA
1 TAAAATAAATAAA
19522 CAAAACGAGG
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
32 5 0.12
33 10 0.25
34 23 0.57
35 2 0.05
ACGTcount: A:0.75, C:0.01, G:0.04, T:0.20
Consensus pattern (34 bp):
TAAAATAAATAAATAAATAAATAAAAAAATAAAA
Found at i:19545 original size:8 final size:8
Alignment explanation
Indices: 19451--19548 Score: 61
Period size: 8 Copynumber: 11.8 Consensus size: 8
19441 TAAAAAAGAT
19451 AAATAAATA
1 AAATAAA-A
19460 AAATAAGAA
1 AAATAA-AA
*
19469 AAATAAAT
1 AAATAAAA
* *
19477 AAATCAAT
1 AAATAAAA
*
19485 AAATAAAT
1 AAATAAAA
*
19493 AAATAAAG
1 AAATAAAA
19501 AAATAAAATA
1 AAAT-AAA-A
*
19511 AAATAAAT
1 AAATAAAA
*
19519 AAACAAAA
1 AAATAAAA
** **
19527 CGAGGAAA
1 AAATAAAA
19535 AAATAAAA
1 AAATAAAA
19543 AAATAA
1 AAATAA
19549 TATATATATA
Statistics
Matches: 70, Mismatches: 16, Indels: 7
0.75 0.17 0.08
Matches are distributed among these distances:
8 46 0.66
9 19 0.27
10 5 0.07
ACGTcount: A:0.76, C:0.03, G:0.05, T:0.16
Consensus pattern (8 bp):
AAATAAAA
Found at i:19553 original size:2 final size:2
Alignment explanation
Indices: 19548--19575 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
19538 TAAAAAAATA
19548 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
19576 TAGCTTGTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19661 original size:25 final size:25
Alignment explanation
Indices: 19633--19711 Score: 58
Period size: 25 Copynumber: 3.1 Consensus size: 25
19623 ATATATATAT
19633 ATAATATTACATATAAATAAAATAA
1 ATAATATTACATATAAATAAAATAA
* *
19658 ATAAATAATA-AAAT-AATAAAAATAA
1 AT-AATATTACATATAAAT-AAAATAA
*
19683 AT-GTATATACAT-TAAAATAAAATGAA
1 ATAATAT-TACATAT-AAATAAAAT-AA
19709 ATA
1 ATA
19712 GTAATAATAG
Statistics
Matches: 41, Mismatches: 5, Indels: 14
0.68 0.08 0.23
Matches are distributed among these distances:
23 2 0.05
24 6 0.15
25 20 0.49
26 13 0.32
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.29
Consensus pattern (25 bp):
ATAATATTACATATAAATAAAATAA
Found at i:19668 original size:61 final size:66
Alignment explanation
Indices: 19532--19677 Score: 171
Period size: 65 Copynumber: 2.3 Consensus size: 66
19522 CAAAACGAGG
* * *
19532 AAAAAATAAAAAAATAATA-TATATATATATATATATATATATATTAGCTTGTAAACTAAAAATA
1 AAAAAATAAAATAATAA-AGTA-ATATATATATATATATATATATTAGCATATAAACTAAAAATA
19596 ATA
64 ATA
*
19599 AAAAAATAAGA-AATAAAGTAATATATATATATATATA-ATATTA-CATATAAA-T-AAAATAA-
1 AAAAAATAAAATAATAAAGTAATATATATATATATATATATATTAGCATATAAACTAAAAATAAT
19658 A
66 A
*
19659 TAAATAATAAAATAATAAA
1 -AAAAAATAAAATAATAAA
19678 AATAAATGTA
Statistics
Matches: 71, Mismatches: 5, Indels: 11
0.82 0.06 0.13
Matches are distributed among these distances:
60 1 0.01
61 16 0.23
62 7 0.10
63 6 0.08
64 6 0.08
65 18 0.25
66 7 0.10
67 10 0.14
ACGTcount: A:0.64, C:0.02, G:0.03, T:0.32
Consensus pattern (66 bp):
AAAAAATAAAATAATAAAGTAATATATATATATATATATATATTAGCATATAAACTAAAAATAAT
A
Found at i:20973 original size:19 final size:20
Alignment explanation
Indices: 20951--20988 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
20941 TAAATATGTA
*
20951 AATATATTATATA-TATATC
1 AATATACTATATAGTATATC
20970 AATATACTATATAGTATAT
1 AATATACTATATAGTATAT
20989 TATATAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (20 bp):
AATATACTATATAGTATATC
Found at i:20987 original size:12 final size:12
Alignment explanation
Indices: 20953--20999 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
20943 AATATGTAAA
*
20953 TATATTATATA-
1 TATATAATATAC
20964 TATATCAATATAC
1 TATAT-AATATAC
* *
20977 TATATAGTATAT
1 TATATAATATAC
20989 TATATAATATA
1 TATATAATATA
21000 ATAACGTATA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
11 5 0.17
12 20 0.67
13 5 0.17
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (12 bp):
TATATAATATAC
Found at i:20993 original size:19 final size:19
Alignment explanation
Indices: 20951--20999 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
20941 TAAATATGTA
*
20951 AATATATTATATATATATC
1 AATATAATATATATATATC
*
20970 AATATACTATATAGTATAT-
1 AATATAATATATA-TATATC
*
20989 TATATAATATA
1 AATATAATATA
21000 ATAACGTATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
19 21 0.81
20 5 0.19
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (19 bp):
AATATAATATATATATATC
Found at i:27526 original size:21 final size:20
Alignment explanation
Indices: 27496--27542 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 20
27486 TCATGTATTT
* *
27496 TAAAACATATCATATATTGGA
1 TAAAAGATATAATATATT-GA
*
27517 TAAAAGATATAATATATTTA
1 TAAAAGATATAATATATTGA
27537 TAAAAG
1 TAAAAG
27543 TGTAATTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 7 0.30
21 16 0.70
ACGTcount: A:0.53, C:0.04, G:0.09, T:0.34
Consensus pattern (20 bp):
TAAAAGATATAATATATTGA
Found at i:28640 original size:22 final size:21
Alignment explanation
Indices: 28605--28647 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
28595 ATATTTAATT
*
28605 TTTTTAGTAATTTTATTTTTA
1 TTTTTAGTAATTTTATATTTA
*
28626 TTTTTAGTATTTTTTATATTTA
1 TTTTTAGTA-ATTTTATATTTA
28648 ATATTTTTCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.72
Consensus pattern (21 bp):
TTTTTAGTAATTTTATATTTA
Found at i:28660 original size:17 final size:16
Alignment explanation
Indices: 28594--28663 Score: 67
Period size: 16 Copynumber: 4.4 Consensus size: 16
28584 AAATTAAAAA
28594 TATATTTAAT-TTTTT
1 TATATTTAATATTTTT
28609 TAGTAATTT--TA-TTTT
1 TA-T-ATTTAATATTTTT
* *
28624 TATTTTTAGTATTTTT
1 TATATTTAATATTTTT
28640 TATATTTAATATTTTT
1 TATATTTAATATTTTT
28656 CTATATTT
1 -TATATTT
28664 GTATAGTTTA
Statistics
Matches: 45, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
13 3 0.07
14 1 0.02
15 11 0.24
16 19 0.42
17 11 0.24
ACGTcount: A:0.26, C:0.01, G:0.03, T:0.70
Consensus pattern (16 bp):
TATATTTAATATTTTT
Found at i:28896 original size:31 final size:31
Alignment explanation
Indices: 28858--28931 Score: 121
Period size: 31 Copynumber: 2.4 Consensus size: 31
28848 TTGTTGGTCA
28858 AAGGGTCACATTCAGTTTGTTTTCTAAATTT
1 AAGGGTCACATTCAGTTTGTTTTCTAAATTT
*
28889 AAGGGTCACATTCAGTTTGTTTTCTAAGTTT
1 AAGGGTCACATTCAGTTTGTTTTCTAAATTT
* *
28920 GAGGGCCACATT
1 AAGGGTCACATT
28932 AAGTGCAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.24, C:0.15, G:0.20, T:0.41
Consensus pattern (31 bp):
AAGGGTCACATTCAGTTTGTTTTCTAAATTT
Found at i:52434 original size:91 final size:90
Alignment explanation
Indices: 52254--52510 Score: 221
Period size: 91 Copynumber: 2.8 Consensus size: 90
52244 ACTCTAGCAT
* ** ** * * * * * *
52254 CTTTTCTGTTGATAATGCACTTATATGTATTTCATCTATGGTATACTTTTATGTTGATAATGTAC
1 CTTTTATGTTGATAATGCACACATATAAATTTCAACTCTAGCATACTTTTCTGTTGATAATGCAC
* * *
52319 CCATATACATCTCAACCATTGTATA
66 CCATATGCATTTCAACCATAGTATA
* * * *
52344 TTTTTTATGTTGATAATGTACACATATAAATTTTAATTCTAGCATACTTTTCTGTTGATAATGCA
1 -CTTTTATGTTGATAATGCACACATATAAATTTCAACTCTAGCATACTTTTCTGTTGATAATGCA
*
52409 CCCATATGCATTTTAACTC-TAGTATA
65 CCCATATGCATTTCAAC-CATAGTATA
* * ** * * ***
52435 CTTTTCTGTTGATAATGCACCCATATGCATTTCAACTCTGGCAT-CCTTTCATGCCCATAATGCA
1 CTTTTATGTTGATAATGCACACATATAAATTTCAACTCTAGCATACTTTTC-TGTTGATAATGCA
52499 CCCATATGCATT
65 CCCATATGCATT
52511 ATTCTTTTAC
Statistics
Matches: 132, Mismatches: 32, Indels: 5
0.78 0.19 0.03
Matches are distributed among these distances:
89 5 0.04
90 57 0.43
91 69 0.52
92 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.11, T:0.42
Consensus pattern (90 bp):
CTTTTATGTTGATAATGCACACATATAAATTTCAACTCTAGCATACTTTTCTGTTGATAATGCAC
CCATATGCATTTCAACCATAGTATA
Found at i:52472 original size:45 final size:45
Alignment explanation
Indices: 52232--52510 Score: 240
Period size: 45 Copynumber: 6.2 Consensus size: 45
52222 AATACATCAT
* **
52232 TATGCATTTTAAACTCTAGCAT-CTTTTCTGTTGATAATGCACTTA
1 TATGCA-TTTCAACTCTAGCATACTTTTCTGTTGATAATGCACCCA
* * * * * * *
52277 TATGTATTTCATCTATGGTATACTTTTATGTTGATAATGTACCCA
1 TATGCATTTCAACTCTAGCATACTTTTCTGTTGATAATGCACCCA
* * * * * * * *
52322 TATACATCTCAAC-CATTGTATATTTTTTATGTTGATAATGTACACA
1 TATGCATTTCAACTC-TAGCATA-CTTTTCTGTTGATAATGCACCCA
** * *
52368 TATAAATTTTAATTCTAGCATACTTTTCTGTTGATAATGCACCCA
1 TATGCATTTCAACTCTAGCATACTTTTCTGTTGATAATGCACCCA
* *
52413 TATGCATTTTAACTCTAGTATACTTTTCTGTTGATAATGCACCCA
1 TATGCATTTCAACTCTAGCATACTTTTCTGTTGATAATGCACCCA
* * ***
52458 TATGCATTTCAACTCTGGCAT-CCTTTCATGCCCATAATGCACCCA
1 TATGCATTTCAACTCTAGCATACTTTTC-TGTTGATAATGCACCCA
52503 TATGCATT
1 TATGCATT
52511 ATTCTTTTAC
Statistics
Matches: 190, Mismatches: 39, Indels: 10
0.79 0.16 0.04
Matches are distributed among these distances:
44 15 0.08
45 139 0.73
46 35 0.18
47 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.11, T:0.42
Consensus pattern (45 bp):
TATGCATTTCAACTCTAGCATACTTTTCTGTTGATAATGCACCCA
Found at i:52966 original size:22 final size:20
Alignment explanation
Indices: 52924--52984 Score: 86
Period size: 22 Copynumber: 2.9 Consensus size: 20
52914 TGGCCCTTCA
*
52924 GTATCGATACCCCCACTATG
1 GTATCGATACCCCTACTATG
52944 GTATCGATACTACCCTACTATG
1 GTATCGATAC--CCCTACTATG
52966 GTATCGATACCCCCTACTA
1 GTATCGATA-CCCCTACTA
52985 GTATCAATAC
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
20 10 0.27
21 8 0.22
22 18 0.49
23 1 0.03
ACGTcount: A:0.26, C:0.33, G:0.13, T:0.28
Consensus pattern (20 bp):
GTATCGATACCCCTACTATG
Found at i:52988 original size:19 final size:20
Alignment explanation
Indices: 52924--52995 Score: 85
Period size: 22 Copynumber: 3.5 Consensus size: 20
52914 TGGCCCTTCA
52924 GTATCGATACCCCC-ACTATG
1 GTATCGATACCCCCTACTA-G
*
52944 GTATCGATACTACCCTACTATG
1 GTATCGATAC-CCCCTACTA-G
52966 GTATCGATACCCCCTACTA-
1 GTATCGATACCCCCTACTAG
*
52985 GTATCAATACC
1 GTATCGATACC
52996 AAAATTAGAT
Statistics
Matches: 47, Mismatches: 3, Indels: 5
0.85 0.05 0.09
Matches are distributed among these distances:
19 10 0.21
20 10 0.21
21 11 0.23
22 16 0.34
ACGTcount: A:0.28, C:0.32, G:0.12, T:0.28
Consensus pattern (20 bp):
GTATCGATACCCCCTACTAG
Found at i:53046 original size:21 final size:21
Alignment explanation
Indices: 53020--53074 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
53010 TGTGACCCAA
53020 TATCGATACCC-ACACCATAAG
1 TATCGATACCCTACACCAT-AG
* *
53041 TATCGATACCACTACACTATGG
1 TATCGATACC-CTACACCATAG
53063 TATCGATACCCT
1 TATCGATACCCT
53075 CTATGGTATC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 12 0.40
22 12 0.40
23 6 0.20
ACGTcount: A:0.33, C:0.31, G:0.11, T:0.25
Consensus pattern (21 bp):
TATCGATACCCTACACCATAG
Found at i:53068 original size:22 final size:19
Alignment explanation
Indices: 53040--53091 Score: 70
Period size: 18 Copynumber: 2.6 Consensus size: 19
53030 CACACCATAA
53040 GTATCGATACCACTACACTATG
1 GTATCGATACCACT---CTATG
53062 GTATCGATACC-CTCTATG
1 GTATCGATACCACTCTATG
53080 GTATCGATACCA
1 GTATCGATACCA
53092 AAATTAGGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
18 16 0.55
21 2 0.07
22 11 0.38
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (19 bp):
GTATCGATACCACTCTATG
Found at i:53098 original size:95 final size:95
Alignment explanation
Indices: 52925--53146 Score: 288
Period size: 95 Copynumber: 2.3 Consensus size: 95
52915 GGCCCTTCAG
* * * *
52925 TATCGATACCCCCACTATGGTATCGATACTAC-CCTACTATGGTATCGATACCCCCTACTAGTAT
1 TATCGATACCCACACCATGGTATCGATACCACTACTACTATGGTATCGATACCCCCTACTAGTAT
52989 CAATACCAAAATTAGATTCGATGTGACCCAA
66 CAATACCAAAATTAGATTCGAT-TGACCCAA
* * *
53020 TATCGATACCCACACCATAAGTATCGATACCACTAC-ACTATGGTATCGATACCCTCTA-TGGTA
1 TATCGATACCCACACCAT-GGTATCGATACCACTACTACTATGGTATCGATACCCCCTACTAGTA
* * * *
53083 TCGATACCAAAATTAGGTTCGATTTACCCGA
65 TCAATACCAAAATTAGATTCGATTGACCCAA
* *
53114 TATCGATACCCTCACCATGGTATTGATACCACT
1 TATCGATACCCACACCATGGTATCGATACCACT
53147 TCATTAGGTT
Statistics
Matches: 111, Mismatches: 14, Indels: 6
0.85 0.11 0.05
Matches are distributed among these distances:
93 13 0.12
94 23 0.21
95 41 0.37
96 33 0.30
97 1 0.01
ACGTcount: A:0.31, C:0.28, G:0.13, T:0.28
Consensus pattern (95 bp):
TATCGATACCCACACCATGGTATCGATACCACTACTACTATGGTATCGATACCCCCTACTAGTAT
CAATACCAAAATTAGATTCGATTGACCCAA
Found at i:59358 original size:45 final size:45
Alignment explanation
Indices: 59309--59484 Score: 255
Period size: 45 Copynumber: 3.9 Consensus size: 45
59299 AATGCACCCA
* * *
59309 TATACATTTATGTTGATAATGTACCCATATACATCTCAAC-CATAG
1 TATACTTTTATGTTGATAATGCACCCATATACATTTCAACTC-TAG
*
59354 TATACTTTTATGTTGATAATGTACCCATATACATTTCAACTCTAG
1 TATACTTTTATGTTGATAATGCACCCATATACATTTCAACTCTAG
* * *
59399 CATACTTTTCTGTTGATAATGCACCCATATGCATTTCAACTCTAG
1 TATACTTTTATGTTGATAATGCACCCATATACATTTCAACTCTAG
* *
59444 TATACTTTTCTGTTGATAATGCACCCATATGCATTTCAACT
1 TATACTTTTATGTTGATAATGCACCCATATACATTTCAACT
59485 ATGGCATCCT
Statistics
Matches: 123, Mismatches: 7, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
45 122 0.99
46 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.10, T:0.39
Consensus pattern (45 bp):
TATACTTTTATGTTGATAATGCACCCATATACATTTCAACTCTAG
Found at i:59508 original size:90 final size:90
Alignment explanation
Indices: 59324--59523 Score: 251
Period size: 90 Copynumber: 2.2 Consensus size: 90
59314 ATTTATGTTG
* * * *
59324 ATAATGTACCCATATACATCTCAACCATAGTATACTTTTATGTTGATAATGTACCCATATACATT
1 ATAATGCACCCATATGCATTTCAACCATAGTATACTTTTATGTTGATAATGCACCCATATACATT
* * ***
59389 TCAACTCTAGCATACTTTTCTGTTG
66 TCAACTATAGCATACCTTTCTGCAC
* *
59414 ATAATGCACCCATATGCATTTCAACTC-TAGTATACTTTTCTGTTGATAATGCACCCATATGCAT
1 ATAATGCACCCATATGCATTTCAAC-CATAGTATACTTTTATGTTGATAATGCACCCATATACAT
*
59478 TTCAACTATGGCAT-CCTTTCATGCAC
65 TTCAACTATAGCATACCTTTC-TGCAC
*
59504 ATAATGCACTCATATGCATT
1 ATAATGCACCCATATGCATT
59524 ATTCTTTTAT
Statistics
Matches: 95, Mismatches: 13, Indels: 4
0.85 0.12 0.04
Matches are distributed among these distances:
89 5 0.05
90 89 0.94
91 1 0.01
ACGTcount: A:0.30, C:0.23, G:0.10, T:0.37
Consensus pattern (90 bp):
ATAATGCACCCATATGCATTTCAACCATAGTATACTTTTATGTTGATAATGCACCCATATACATT
TCAACTATAGCATACCTTTCTGCAC
Found at i:59518 original size:45 final size:45
Alignment explanation
Indices: 59324--59523 Score: 159
Period size: 45 Copynumber: 4.4 Consensus size: 45
59314 ATTTATGTTG
* * * * * * * ***
59324 ATAATGTACCCATATACATCTCAACCATAGTATACTTTTATGTTG
1 ATAATGCACCCATATGCATTTCAACTATAGCATACCTTTCTGCAC
* * * * ***
59369 ATAATGTACCCATATACATTTCAACTCTAGCATACTTTTCTGTTG
1 ATAATGCACCCATATGCATTTCAACTATAGCATACCTTTCTGCAC
* * * ***
59414 ATAATGCACCCATATGCATTTCAACTCTAGTATACTTTTCTGTTG
1 ATAATGCACCCATATGCATTTCAACTATAGCATACCTTTCTGCAC
*
59459 ATAATGCACCCATATGCATTTCAACTATGGCAT-CCTTTCATGCAC
1 ATAATGCACCCATATGCATTTCAACTATAGCATACCTTTC-TGCAC
*
59504 ATAATGCACTCATATGCATT
1 ATAATGCACCCATATGCATT
59524 ATTCTTTTAT
Statistics
Matches: 138, Mismatches: 16, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
44 5 0.04
45 133 0.96
ACGTcount: A:0.30, C:0.23, G:0.10, T:0.37
Consensus pattern (45 bp):
ATAATGCACCCATATGCATTTCAACTATAGCATACCTTTCTGCAC
Found at i:59558 original size:79 final size:79
Alignment explanation
Indices: 59461--59611 Score: 232
Period size: 79 Copynumber: 1.9 Consensus size: 79
59451 TTCTGTTGAT
* *
59461 AATGCACCCATATGCATTTCAACTATGGCATCCTTTCATG-CACATAATGCACTCATATGCATTA
1 AATGCACCCATATACATTTCAACTATGGCATCCTTTCATGCCA-ATAATGCACCCATATGCATTA
59525 TTCTTTTATGCTGAC
65 TTCTTTTATGCTGAC
* * * *
59540 AATGTACCCATATACATTTTAGCTATGGCATCCTTTCATGCCAATAGTGCACCCATATGCATTAT
1 AATGCACCCATATACATTTCAACTATGGCATCCTTTCATGCCAATAATGCACCCATATGCATTAT
59605 TCTTTTA
66 TCTTTTA
59612 CATTCGTTTT
Statistics
Matches: 65, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
79 63 0.97
80 2 0.03
ACGTcount: A:0.28, C:0.25, G:0.11, T:0.36
Consensus pattern (79 bp):
AATGCACCCATATACATTTCAACTATGGCATCCTTTCATGCCAATAATGCACCCATATGCATTAT
TCTTTTATGCTGAC
Found at i:60079 original size:19 final size:20
Alignment explanation
Indices: 60016--60086 Score: 74
Period size: 22 Copynumber: 3.5 Consensus size: 20
60006 AGCCCTTCAA
60016 TATCGATACCCCC-ACTATTG
1 TATCGATACCCCCTACTA-TG
*
60036 TATCGATACTACCCTACTATGG
1 TATCGATAC-CCCCTACTAT-G
*
60058 TATCGATACCCCCTACCA-G
1 TATCGATACCCCCTACTATG
*
60077 TATCAATACC
1 TATCGATACC
60087 AAAATTAGAT
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
19 10 0.23
20 9 0.20
21 11 0.25
22 14 0.32
ACGTcount: A:0.28, C:0.34, G:0.10, T:0.28
Consensus pattern (20 bp):
TATCGATACCCCCTACTATG
Found at i:68762 original size:22 final size:22
Alignment explanation
Indices: 68734--68793 Score: 111
Period size: 22 Copynumber: 2.7 Consensus size: 22
68724 ATAGAGGATT
68734 TGATTTCGAAATGGATAAATTA
1 TGATTTCGAAATGGATAAATTA
*
68756 TGATTTCGAAATGAATAAATTA
1 TGATTTCGAAATGGATAAATTA
68778 TGATTTCGAAATGGAT
1 TGATTTCGAAATGGAT
68794 TGAGGGCCCT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.40, C:0.05, G:0.18, T:0.37
Consensus pattern (22 bp):
TGATTTCGAAATGGATAAATTA
Found at i:71111 original size:14 final size:16
Alignment explanation
Indices: 71081--71113 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
71071 GCATAAGTAA
71081 AATGCATTCACCTAGT
1 AATGCATTCACCTAGT
71097 AATGC-TTCA-CTAGT
1 AATGCATTCACCTAGT
71111 AAT
1 AAT
71114 CTTACTTAGC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.47
15 4 0.24
16 5 0.29
ACGTcount: A:0.33, C:0.21, G:0.12, T:0.33
Consensus pattern (16 bp):
AATGCATTCACCTAGT
Found at i:74123 original size:14 final size:14
Alignment explanation
Indices: 74104--74158 Score: 69
Period size: 14 Copynumber: 4.0 Consensus size: 14
74094 AACCTTGTAA
74104 TAAACCTTAAACCC
1 TAAACCTTAAACCC
* *
74118 TAAACC-TAAATCA
1 TAAACCTTAAACCC
74131 TAAA-CTCTAAACCC
1 TAAACCT-TAAACCC
74145 TAAACCTTAAACCC
1 TAAACCTTAAACCC
74159 ATTTAGCGCA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
12 1 0.03
13 9 0.26
14 22 0.65
15 2 0.06
ACGTcount: A:0.45, C:0.33, G:0.00, T:0.22
Consensus pattern (14 bp):
TAAACCTTAAACCC
Found at i:80806 original size:30 final size:31
Alignment explanation
Indices: 80728--80806 Score: 81
Period size: 30 Copynumber: 2.5 Consensus size: 31
80718 TTTAGACTAT
* *
80728 TTCATTTATTCATATCATATCAGCATGTTTCA
1 TTCATTTATTCATTTCATAGCAGCATG-TTCA
* *
80760 TTCACTTCATTTATTTCATAGCA-CATG-TCA
1 TTCA-TTTATTCATTTCATAGCAGCATGTTCA
80790 TTCATTTAATTCATTTC
1 TTCATTT-ATTCATTTC
80807 GTAACTGTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
29 2 0.05
30 15 0.38
32 8 0.21
33 14 0.36
ACGTcount: A:0.27, C:0.20, G:0.05, T:0.48
Consensus pattern (31 bp):
TTCATTTATTCATTTCATAGCAGCATGTTCA
Done.