Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004563.1 Hibiscus syriacus cultivar Beakdansim tig00010141_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: 86838
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:521 original size:21 final size:22
Alignment explanation
Indices: 497--555 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 22
487 ACAAAAATTG
497 ATTTTCAAAAATCAAAAT-GAA
1 ATTTTCAAAAATCAAAATAGAA
* * **
518 ATTTTGAAAAAT-GATTTAGAA
1 ATTTTCAAAAATCAAAATAGAA
539 A-TTTCAAAAATCAAAAT
1 ATTTTCAAAAATCAAAAT
556 CAATGATTTA
Statistics
Matches: 28, Mismatches: 8, Indels: 4
0.70 0.20 0.10
Matches are distributed among these distances:
20 11 0.39
21 17 0.61
ACGTcount: A:0.54, C:0.07, G:0.07, T:0.32
Consensus pattern (22 bp):
ATTTTCAAAAATCAAAATAGAA
Found at i:1778 original size:21 final size:22
Alignment explanation
Indices: 1752--1792 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
1742 CCAGGACAGG
1752 GAGTATCGGTACT-CCTTTAAT
1 GAGTATCGGTACTACCTTTAAT
1773 GAGTATCGGTACTACCTTTA
1 GAGTATCGGTACTACCTTTA
1793 TAATATTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.37
Consensus pattern (22 bp):
GAGTATCGGTACTACCTTTAAT
Found at i:5558 original size:16 final size:16
Alignment explanation
Indices: 5537--5570 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
5527 AAACCTCTGT
5537 TCAAAAATCAAATC-AA
1 TCAAAAA-CAAATCTAA
5553 TCAAAAACAAATCTAA
1 TCAAAAACAAATCTAA
5569 TC
1 TC
5571 CATCAGACTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.59, C:0.21, G:0.00, T:0.21
Consensus pattern (16 bp):
TCAAAAACAAATCTAA
Found at i:8278 original size:17 final size:18
Alignment explanation
Indices: 8256--8290 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
8246 TATTAGTAAT
8256 ATTTA-TCATTTATTTTA
1 ATTTATTCATTTATTTTA
*
8273 ATTTATTTATTTATTTTA
1 ATTTATTCATTTATTTTA
8291 TGTTAGTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.69
Consensus pattern (18 bp):
ATTTATTCATTTATTTTA
Found at i:12790 original size:14 final size:14
Alignment explanation
Indices: 12771--12803 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
12761 TCCCATTGGG
12771 TTTTTCTGGAAATA
1 TTTTTCTGGAAATA
*
12785 TTTTTCTGGAAATG
1 TTTTTCTGGAAATA
12799 TTTTT
1 TTTTT
12804 AATGAGGTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.21, C:0.06, G:0.15, T:0.58
Consensus pattern (14 bp):
TTTTTCTGGAAATA
Found at i:15153 original size:21 final size:21
Alignment explanation
Indices: 15127--15181 Score: 110
Period size: 21 Copynumber: 2.6 Consensus size: 21
15117 TTATTATAAC
15127 AGTATCGATACTCCAAGCCCG
1 AGTATCGATACTCCAAGCCCG
15148 AGTATCGATACTCCAAGCCCG
1 AGTATCGATACTCCAAGCCCG
15169 AGTATCGATACTC
1 AGTATCGATACTC
15182 TTGTGTTTGG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.29, C:0.31, G:0.18, T:0.22
Consensus pattern (21 bp):
AGTATCGATACTCCAAGCCCG
Found at i:18985 original size:15 final size:15
Alignment explanation
Indices: 18965--18994 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
18955 TACCACCAAA
18965 ACAGAACAAACGTGC
1 ACAGAACAAACGTGC
18980 ACAGAACAAACGTGC
1 ACAGAACAAACGTGC
18995 TCTGTTTTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.27, G:0.20, T:0.07
Consensus pattern (15 bp):
ACAGAACAAACGTGC
Found at i:19582 original size:31 final size:31
Alignment explanation
Indices: 19538--19596 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
19528 TCGTTAAATT
*
19538 TATTAAATTATTATAAAA-TGATTATGAAAA
1 TATTAAATAATTATAAAAGTGATTATGAAAA
*
19568 TATTACAATAATTATAAAAGTTATTATGA
1 TATTA-AATAATTATAAAAGTGATTATGA
19597 TAAAATTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 5 0.20
31 12 0.48
32 8 0.32
ACGTcount: A:0.51, C:0.02, G:0.07, T:0.41
Consensus pattern (31 bp):
TATTAAATAATTATAAAAGTGATTATGAAAA
Found at i:20636 original size:2 final size:2
Alignment explanation
Indices: 20629--20673 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
20619 AAAGATCATA
20629 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20671 AT A
1 AT A
20674 AATGCAAGAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:20780 original size:3 final size:3
Alignment explanation
Indices: 20772--20803 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
20762 AAAAGTAAAA
20772 AAT AAT AAT AAT AA- AAT AAT AAT AAT AA- AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
20804 TAGTGACACA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
2 4 0.15
3 23 0.85
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:20787 original size:14 final size:14
Alignment explanation
Indices: 20770--20803 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
20760 TAAAAAGTAA
20770 AAAATAATAATAAT
1 AAAATAATAATAAT
20784 AAAATAATAATAAT
1 AAAATAATAATAAT
20798 AAAATA
1 AAAATA
20804 TAGTGACACA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (14 bp):
AAAATAATAATAAT
Found at i:20792 original size:17 final size:16
Alignment explanation
Indices: 20767--20799 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
20757 AAGTAAAAAG
20767 TAAAAAATAATAATAA
1 TAAAAAATAATAATAA
20783 TAAAATAATAATAATAA
1 TAAAA-AATAATAATAA
20800 AATATAGTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (16 bp):
TAAAAAATAATAATAA
Found at i:20861 original size:44 final size:43
Alignment explanation
Indices: 20781--20873 Score: 113
Period size: 43 Copynumber: 2.2 Consensus size: 43
20771 AAATAATAAT
20781 AATAAA-ATA-ATAATAATAAAATATAGTGACACAAAAAAGAACA
1 AATAAATATATATAATAATAAAATATAGTGACA-AAAAAAGAA-A
* *
20824 AA-AAATATATATAATAATTAAATATAGT-ATTAAAAAAAGAAA
1 AATAAATATATATAATAATAAAATATAGTGA-CAAAAAAAGAAA
20866 AATAAATA
1 AATAAATA
20874 AAGTTGAAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
42 6 0.14
43 20 0.45
44 18 0.41
ACGTcount: A:0.68, C:0.03, G:0.05, T:0.24
Consensus pattern (43 bp):
AATAAATATATATAATAATAAAATATAGTGACAAAAAAAGAAA
Found at i:21074 original size:34 final size:34
Alignment explanation
Indices: 21031--21115 Score: 161
Period size: 34 Copynumber: 2.5 Consensus size: 34
21021 GGATGGCCCT
21031 TTCGTCGTGAAGTTGAACATTGACTTGAATATCC
1 TTCGTCGTGAAGTTGAACATTGACTTGAATATCC
*
21065 TTCGTCGTGAAGTTGAACCTTGACTTGAATATCC
1 TTCGTCGTGAAGTTGAACATTGACTTGAATATCC
21099 TTCGTCGTGAAGTTGAA
1 TTCGTCGTGAAGTTGAA
21116 ATCCAAGTTT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 50 1.00
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.35
Consensus pattern (34 bp):
TTCGTCGTGAAGTTGAACATTGACTTGAATATCC
Found at i:21333 original size:43 final size:43
Alignment explanation
Indices: 21275--21385 Score: 159
Period size: 43 Copynumber: 2.6 Consensus size: 43
21265 CGATATCTTT
* * *
21275 CGTCGTGAAGATGAAATCGTGGATGTGTGGGCACAATATCCTC
1 CGTCGTGGAGTTGAAATCGTGGATGTATGGGCACAATATCCTC
* * * *
21318 CGTCGTGGAGTTGAAATCATGGATTTATGGGTACGATATCCTC
1 CGTCGTGGAGTTGAAATCGTGGATGTATGGGCACAATATCCTC
21361 CGTCGTGGAGTTGAAATCGTGGATG
1 CGTCGTGGAGTTGAAATCGTGGATG
21386 ACCCATTCGT
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 59 1.00
ACGTcount: A:0.23, C:0.16, G:0.32, T:0.29
Consensus pattern (43 bp):
CGTCGTGGAGTTGAAATCGTGGATGTATGGGCACAATATCCTC
Found at i:22408 original size:17 final size:17
Alignment explanation
Indices: 22388--22420 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
22378 ACCCTAAACG
22388 TTTTT-TTTGTTCTTTTC
1 TTTTTCTTT-TTCTTTTC
22405 TTTTTCTTTTTCTTTT
1 TTTTTCTTTTTCTTTT
22421 TCTTCTTCGA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.00, C:0.12, G:0.03, T:0.85
Consensus pattern (17 bp):
TTTTTCTTTTTCTTTTC
Found at i:22411 original size:6 final size:6
Alignment explanation
Indices: 22388--22424 Score: 51
Period size: 6 Copynumber: 6.3 Consensus size: 6
22378 ACCCTAAACG
22388 TTTTT- TTTGTTC -TTTTC TTTTTC TTTTTC TTTTTC TT
1 TTTTTC TTT-TTC TTTTTC TTTTTC TTTTTC TTTTTC TT
22425 CTTCGACTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
5 6 0.21
6 23 0.79
ACGTcount: A:0.00, C:0.14, G:0.03, T:0.84
Consensus pattern (6 bp):
TTTTTC
Found at i:24611 original size:16 final size:16
Alignment explanation
Indices: 24571--24603 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
24561 ATTATTATGA
*
24571 CAAATTTAA-TTTTGT
1 CAAAATTAATTTTTGT
24586 CAAAATTAATTTTTGT
1 CAAAATTAATTTTTGT
24602 CA
1 CA
24604 CTATTAATAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.36, C:0.09, G:0.06, T:0.48
Consensus pattern (16 bp):
CAAAATTAATTTTTGT
Found at i:25825 original size:416 final size:415
Alignment explanation
Indices: 25103--25896 Score: 1039
Period size: 416 Copynumber: 1.9 Consensus size: 415
25093 ATGTTTTAAT
*
25103 TATAGTGACAAAATATAATGTCACAAAGATTTCCCTCCATATTGTTTTGCGCCAAAAAAGTCATA
1 TATAGTAACAAAATATAATGTCACAAAGATTTCCCTCCATATTGTTTTGCGCCAAAAAAGTCATA
* * * *
25168 TAGTGACAAATTTTGAAACTAGAAGTGTTAATAATTATTATAAAAATATTGTCACAAAAAATAAT
66 TAGTAACAAATTTTGAAACTAGAAGTGTTAATAATTATTAAAAAAACATTGTCACAAAAAATAAA
* * * **
25233 GTTATTCATGATTTTGTGATAAATTATATTTGTAGTTATAAATTTTAACTAAAGTGATAGTATAT
131 GTTATTCATCATTTTGTGACAAATTATATTTGTAGATATAAATTTTAACTAAAGTGATAACATAT
* * * *
25298 ATCGTCATAACTATTTTTTCTCAACTTTTTTATTTCAAAAGTTATATTGACAATTTTTATAATTA
196 ATCGTCACAAATATTTTTTCTCAACTTTTTTATTTCAAAAGTTATATAGACAAGTTTTATAATTA
* * *
25363 TAATTTATAGTTATTTTTACAGAAAAAAGTATTACATCAAATAATAAAATTCAAGTTTTT-GTAA
261 TAATTTATAGTTATTGTTACAGAAAAAAGTATCACATCAAATAATAAAAATCAAGTTTTTCGTAA
25427 TAAATTATTTTTGTACTTATATATTTTAATCATTATGAAAAATAATACTATCAGAACAATTTCTC
326 TAAATTATTTTTGTACTTATATATTTTAATCATTATGAAAAATAATACTATCAGAACAATTTCTC
25492 CCTATTTTTAGTGTCAAAAATGTTA
391 CCTATTTTTAGTGTCAAAAATGTTA
* * * * * *
25517 TATAGTAACAAAATATATTGTTATAAAGATTTTCCTCCATATTTTTTTGTGCCAAAAAA-TCATA
1 TATAGTAACAAAATATAATGTCACAAAGATTTCCCTCCATATTGTTTTGCGCCAAAAAAGTCATA
* * *
25581 TAGTAAC-AATTTTCGTAACTATAAGTGTTTATAATTATTACAAAAAAAACATTGTCACAAAAAA
66 TAGTAACAAATTTT-GAAACTAGAAGTGTTAATAATTATT---AAAAAAACATTGTCACAAAAAA
* ** *
25645 TAACAG-TATTCA-CACTTTTGTGGCAAATTATACTTT-TAGATATACTTTTTAATTATAA-TGA
127 TAA-AGTTATTCATCA-TTTTGTGACAAATTATA-TTTGTAGATATAAATTTTAACTA-AAGTGA
* * * * *
25706 TAACATATATTGTGACAAATA-TTTTTCTCCACTTTTTTTGTTTCAAAAGTTTATATAGATAAGT
188 TAACATATATCGTCACAAATATTTTTTCTCAAC-TTTTTTATTTCAAAAG-TTATATAGACAAGT
* * * * * *
25770 TTTGTAATTATAATTTATAGTTATTGTTATAG-AAAAATTATCACTTTAGATAATAAAAATCAAG
251 TTTATAATTATAATTTATAGTTATTGTTACAGAAAAAAGTATCACATCAAATAATAAAAATCAAG
* * *
25834 TTTTTCGTAATCAATTATTTTTGTAGTTATATATTTTAATCATTATGAAAAATTATACTATCA
316 TTTTTCGTAATAAATTATTTTTGTACTTATATATTTTAATCATTATGAAAAATAATACTATCA
25897 ACAAAAATAA
Statistics
Matches: 325, Mismatches: 44, Indels: 19
0.84 0.11 0.05
Matches are distributed among these distances:
412 6 0.02
413 33 0.10
414 52 0.16
415 11 0.03
416 123 0.38
417 100 0.31
ACGTcount: A:0.39, C:0.10, G:0.09, T:0.42
Consensus pattern (415 bp):
TATAGTAACAAAATATAATGTCACAAAGATTTCCCTCCATATTGTTTTGCGCCAAAAAAGTCATA
TAGTAACAAATTTTGAAACTAGAAGTGTTAATAATTATTAAAAAAACATTGTCACAAAAAATAAA
GTTATTCATCATTTTGTGACAAATTATATTTGTAGATATAAATTTTAACTAAAGTGATAACATAT
ATCGTCACAAATATTTTTTCTCAACTTTTTTATTTCAAAAGTTATATAGACAAGTTTTATAATTA
TAATTTATAGTTATTGTTACAGAAAAAAGTATCACATCAAATAATAAAAATCAAGTTTTTCGTAA
TAAATTATTTTTGTACTTATATATTTTAATCATTATGAAAAATAATACTATCAGAACAATTTCTC
CCTATTTTTAGTGTCAAAAATGTTA
Found at i:36622 original size:12 final size:11
Alignment explanation
Indices: 36588--36630 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 11
36578 GCAAAAAGTT
36588 AGTAAAATAAA
1 AGTAAAATAAA
*
36599 AATATAAATAAA
1 AGTA-AAATAAA
36611 AGTAAAAGTAAA
1 AGTAAAA-TAAA
36623 AGGTAAAA
1 A-GTAAAA
36631 AGAAAGTAGC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 6 0.22
12 15 0.56
13 6 0.22
ACGTcount: A:0.70, C:0.00, G:0.12, T:0.19
Consensus pattern (11 bp):
AGTAAAATAAA
Found at i:37579 original size:20 final size:20
Alignment explanation
Indices: 37556--37600 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
37546 AATGTAGAAC
37556 ATAAAAAATAAAGCAA-AAAA
1 ATAAAAAATAAA-CAAGAAAA
*
37576 ATAAAAAATAAACAAGACAA
1 ATAAAAAATAAACAAGAAAA
37596 ATAAA
1 ATAAA
37601 GTGAAATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 3 0.13
20 20 0.87
ACGTcount: A:0.78, C:0.07, G:0.04, T:0.11
Consensus pattern (20 bp):
ATAAAAAATAAACAAGAAAA
Found at i:41053 original size:22 final size:21
Alignment explanation
Indices: 41028--41069 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
41018 ATATACAAAA
41028 GTATTTTTATTAAATATTTTTG
1 GTATTTTTATTAAAT-TTTTTG
*
41050 GTATTTTTATTTAATTTTTT
1 GTATTTTTATTAAATTTTTT
41070 AAATAATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.69
Consensus pattern (21 bp):
GTATTTTTATTAAATTTTTTG
Found at i:61564 original size:17 final size:17
Alignment explanation
Indices: 61544--61582 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
61534 ATTAAAGAGT
* *
61544 TAGTTAGATTAACGAAC
1 TAGTTAAATGAACGAAC
*
61561 TAGTTAAATGAATGAAC
1 TAGTTAAATGAACGAAC
61578 TAGTT
1 TAGTT
61583 TAATTAAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.41, C:0.08, G:0.18, T:0.33
Consensus pattern (17 bp):
TAGTTAAATGAACGAAC
Found at i:61661 original size:17 final size:18
Alignment explanation
Indices: 61589--61685 Score: 67
Period size: 17 Copynumber: 5.6 Consensus size: 18
61579 AGTTTAATTA
* * *
61589 AAATGAACTAACTTTATT
1 AAATGAACTAAATTCACT
* *
61607 GAATGAACTAAGATGCA-T
1 AAATGAACTAA-ATTCACT
* **
61625 AAATGAAGTAGCTT-ACT
1 AAATGAACTAAATTCACT
61642 AAATGAACTAAATTCA-T
1 AAATGAACTAAATTCACT
* *
61659 AAATGAACT-ACTTCCCT
1 AAATGAACTAAATTCACT
61676 AAATGAACTA
1 AAATGAACTA
61686 GAAACTTAAA
Statistics
Matches: 60, Mismatches: 14, Indels: 10
0.71 0.17 0.12
Matches are distributed among these distances:
16 5 0.08
17 33 0.55
18 20 0.33
19 2 0.03
ACGTcount: A:0.45, C:0.14, G:0.11, T:0.29
Consensus pattern (18 bp):
AAATGAACTAAATTCACT
Found at i:61665 original size:34 final size:35
Alignment explanation
Indices: 61589--61685 Score: 108
Period size: 34 Copynumber: 2.8 Consensus size: 35
61579 AGTTTAATTA
* * *
61589 AAATGAACTAACTTTATTGAATGAACTAAGATGCAT
1 AAATGAACT-ACTTCACTAAATGAACTAAGATGCAT
* *
61625 AAATGAAGTAGCTT-ACTAAATGAACTAA-ATTCAT
1 AAATGAACTA-CTTCACTAAATGAACTAAGATGCAT
*
61659 AAATGAACTACTTCCCTAAATGAACTA
1 AAATGAACTACTTCACTAAATGAACTA
61686 GAAACTTAAA
Statistics
Matches: 53, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
33 3 0.06
34 26 0.49
35 13 0.25
36 11 0.21
ACGTcount: A:0.45, C:0.14, G:0.11, T:0.29
Consensus pattern (35 bp):
AAATGAACTACTTCACTAAATGAACTAAGATGCAT
Found at i:65732 original size:30 final size:30
Alignment explanation
Indices: 65696--65756 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
65686 CGCCATCGAT
65696 CATTTTTGAATTAGGCGGATCAAACACCTA
1 CATTTTTGAATTAGGCGGATCAAACACCTA
* *
65726 CATTTTTTAATTAGGCGGATCAGACACCTA
1 CATTTTTGAATTAGGCGGATCAAACACCTA
65756 C
1 C
65757 TTACCAATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.31
Consensus pattern (30 bp):
CATTTTTGAATTAGGCGGATCAAACACCTA
Found at i:67386 original size:18 final size:18
Alignment explanation
Indices: 67363--67406 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
67353 AAAACAGAAC
*
67363 AAAATAAATAAGTAAAT-A
1 AAAATAAATAA-AAAATAA
*
67381 AAAATACATAAAAAATAA
1 AAAATAAATAAAAAATAA
67399 AAAATAAA
1 AAAATAAA
67407 ACAAAGATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 4 0.18
18 18 0.82
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.18
Consensus pattern (18 bp):
AAAATAAATAAAAAATAA
Found at i:67420 original size:29 final size:29
Alignment explanation
Indices: 67363--67420 Score: 66
Period size: 29 Copynumber: 2.0 Consensus size: 29
67353 AAAACAGAAC
* *
67363 AAAATAAATAAGTAAATAAAAATACATAA
1 AAAATAAATAAATAAATAAAAATAAATAA
67392 AAAATAAA-AAATAAA-ACAAAGATAAATAA
1 AAAATAAATAAATAAATA-AAA-ATAAATAA
67421 TAACAATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
27 1 0.04
28 9 0.36
29 15 0.60
ACGTcount: A:0.76, C:0.03, G:0.03, T:0.17
Consensus pattern (29 bp):
AAAATAAATAAATAAATAAAAATAAATAA
Found at i:68647 original size:37 final size:38
Alignment explanation
Indices: 68587--68660 Score: 105
Period size: 37 Copynumber: 1.9 Consensus size: 38
68577 TGTTCTTTTT
* *
68587 TGAGTGATGATTCAGTGAGTGATTGCTTTTTCTTATCTG
1 TGAGTGATGATTCAGT-AGTGATTCCGTTTTCTTATCTG
*
68626 TGAGTGATGATTCAGT-TTGATTCCGTTTTCTTATC
1 TGAGTGATGATTCAGTAGTGATTCCGTTTTCTTATC
68661 ATCACGATAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
37 16 0.50
39 16 0.50
ACGTcount: A:0.18, C:0.12, G:0.23, T:0.47
Consensus pattern (38 bp):
TGAGTGATGATTCAGTAGTGATTCCGTTTTCTTATCTG
Found at i:70410 original size:117 final size:122
Alignment explanation
Indices: 70277--70495 Score: 317
Period size: 123 Copynumber: 1.8 Consensus size: 122
70267 AACAAAAATA
*
70277 ATTTACATCTTTTTATTATTATGAATATC-TA-TGAAGAAT-TT-T-CACAA-TGTAA-ACATTT
1 ATTTACATCTTTTTATTATTATGAATATCTTAGT-AA-AATGTTATGCAAAATTGTAATACATTT
70335 TTACATAAATTATGTAAAATTTAATATTAATTAAAATATCTTAAATTATAAACATTTTT
64 TTACATAAATTATGTAAAATTTAATATTAATTAAAATATCTTAAATTATAAACATTTTT
* * * *
70394 ATTTACATCTTTTTATTATTATGAATATCTTAGTTAAATGTTGATGTAAAATTTTAATATATTTT
1 ATTTACATCTTTTTATTATTATGAATATCTTAGTAAAATGTT-ATGCAAAATTGTAATACATTTT
70459 TACATAAATTATGTAAAATTTAATATTAATTAAAATA
65 TACATAAATTATGTAAAATTTAATATTAATTAAAATA
70496 AAAATAATAC
Statistics
Matches: 89, Mismatches: 5, Indels: 10
0.86 0.05 0.10
Matches are distributed among these distances:
117 32 0.36
118 5 0.06
119 1 0.01
120 1 0.01
121 3 0.03
122 4 0.04
123 43 0.48
ACGTcount: A:0.42, C:0.06, G:0.05, T:0.47
Consensus pattern (122 bp):
ATTTACATCTTTTTATTATTATGAATATCTTAGTAAAATGTTATGCAAAATTGTAATACATTTTT
ACATAAATTATGTAAAATTTAATATTAATTAAAATATCTTAAATTATAAACATTTTT
Found at i:73981 original size:4 final size:4
Alignment explanation
Indices: 73972--74000 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
73962 TCATATGATC
73972 AAAT AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT A
74001 TATATATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:79091 original size:18 final size:17
Alignment explanation
Indices: 79070--79103 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
79060 CATTTATTTT
79070 TATCAAGTAATTTAATTA
1 TATCAA-TAATTTAATTA
*
79088 TATCAATTATTTAATT
1 TATCAATAATTTAATT
79104 TTAAATAGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.41, C:0.06, G:0.03, T:0.50
Consensus pattern (17 bp):
TATCAATAATTTAATTA
Done.