Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007448.1 Hibiscus syriacus cultivar Beakdansim tig00020368_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: 64691
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:3446 original size:21 final size:21
Alignment explanation
Indices: 3400--3447 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
3390 TATCAATTTA
*
3400 TCATGTCACATATTCACATGT
1 TCATATCACATATTCACATGT
* *
3421 ACATATCAC-TATTCATATGAT
1 TCATATCACATATTCACATG-T
3442 TCATAT
1 TCATAT
3448 TCATATATCA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 9 0.41
21 13 0.59
ACGTcount: A:0.33, C:0.21, G:0.06, T:0.40
Consensus pattern (21 bp):
TCATATCACATATTCACATGT
Found at i:3655 original size:30 final size:29
Alignment explanation
Indices: 3587--3655 Score: 70
Period size: 30 Copynumber: 2.3 Consensus size: 29
3577 CATAGATCTT
3587 ATCACTTAACTTATCCTTTATACTCATTTA
1 ATCACTTAACTTAT-CTTTATACTCATTTA
**
3617 ATTTCTTAACTTAT-TTTATATTCTC-TTATA
1 ATCACTTAACTTATCTTTATA--CTCATT-TA
3647 ATCACTTAA
1 ATCACTTAA
3656 TAGTGTCTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
28 6 0.19
29 2 0.06
30 24 0.75
ACGTcount: A:0.30, C:0.19, G:0.00, T:0.51
Consensus pattern (29 bp):
ATCACTTAACTTATCTTTATACTCATTTA
Found at i:6445 original size:30 final size:29
Alignment explanation
Indices: 6370--6447 Score: 77
Period size: 29 Copynumber: 2.7 Consensus size: 29
6360 ACTAGTGATT
* *
6370 AAAATGTAATTTTTGAAAGTTTAGTGGCT
1 AAAATGTAATTTTTAAAAGTTTAGTGGCA
* * * *
6399 AAAGTATAAATTTTAAAAGTTTAG-GAATCA
1 AAAATGTAATTTTTAAAAGTTTAGTG--GCA
6429 AAAATGTAATTTTTAAAAG
1 AAAATGTAATTTTTAAAAG
6448 GTTATATATT
Statistics
Matches: 38, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
28 1 0.03
29 20 0.53
30 17 0.45
ACGTcount: A:0.45, C:0.03, G:0.15, T:0.37
Consensus pattern (29 bp):
AAAATGTAATTTTTAAAAGTTTAGTGGCA
Found at i:9213 original size:16 final size:17
Alignment explanation
Indices: 9192--9287 Score: 104
Period size: 17 Copynumber: 5.5 Consensus size: 17
9182 TGAATTCTAA
*
9192 ATATTTACAG-TATCAT
1 ATATTTACAGTTATCAG
* *
9208 ATATTTTCAGTTATAAG
1 ATATTTACAGTTATCAG
9225 ATATTTACAGTTATCAG
1 ATATTTACAGTTATCAG
*
9242 ATGATTTTTCAGTTATCAG
1 AT-A-TTTACAGTTATCAG
*
9261 ATGATTTATAGTTATCAG
1 AT-ATTTACAGTTATCAG
*
9279 ATAATTACA
1 ATATTTACA
9288 AATATAAATT
Statistics
Matches: 67, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
16 9 0.13
17 26 0.39
18 15 0.22
19 17 0.25
ACGTcount: A:0.35, C:0.09, G:0.11, T:0.44
Consensus pattern (17 bp):
ATATTTACAGTTATCAG
Found at i:9256 original size:19 final size:19
Alignment explanation
Indices: 9211--9280 Score: 92
Period size: 19 Copynumber: 3.8 Consensus size: 19
9201 GTATCATATA
*
9211 TTTTCAGTTATAAGAT-A-
1 TTTTCAGTTATCAGATGAT
*
9228 TTTACAGTTATCAGATGAT
1 TTTTCAGTTATCAGATGAT
9247 TTTTCAGTTATCAGATGAT
1 TTTTCAGTTATCAGATGAT
*
9266 TTAT-AGTTATCAGAT
1 TTTTCAGTTATCAGAT
9281 AATTACAAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
17 14 0.30
18 12 0.26
19 21 0.45
ACGTcount: A:0.31, C:0.09, G:0.14, T:0.46
Consensus pattern (19 bp):
TTTTCAGTTATCAGATGAT
Found at i:9275 original size:37 final size:36
Alignment explanation
Indices: 9192--9280 Score: 121
Period size: 37 Copynumber: 2.5 Consensus size: 36
9182 TGAATTCTAA
*
9192 ATATTTACAG-TATCATAT-A-TTTTCAGTTATAAG
1 ATATTTACAGTTATCAGATGATTTTTCAGTTATAAG
*
9225 ATATTTACAGTTATCAGATGATTTTTCAGTTATCAG
1 ATATTTACAGTTATCAGATGATTTTTCAGTTATAAG
*
9261 ATGATTTATAGTTATCAGAT
1 AT-ATTTACAGTTATCAGAT
9281 AATTACAAAT
Statistics
Matches: 49, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
33 10 0.20
34 7 0.14
35 1 0.02
36 15 0.31
37 16 0.33
ACGTcount: A:0.34, C:0.09, G:0.12, T:0.45
Consensus pattern (36 bp):
ATATTTACAGTTATCAGATGATTTTTCAGTTATAAG
Found at i:11703 original size:29 final size:31
Alignment explanation
Indices: 11661--11721 Score: 74
Period size: 30 Copynumber: 2.0 Consensus size: 31
11651 ATCATCCTAA
*
11661 TAAAAATTAATTAT-ATATTAGACAC-CATTT
1 TAAAAATTAATTATAAAATTA-ACACTCATTT
*
11691 TAAAAA-TATTTATAAAATTAACACTCATTT
1 TAAAAATTAATTATAAAATTAACACTCATTT
11721 T
1 T
11722 TTACACGTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
29 10 0.37
30 17 0.63
ACGTcount: A:0.48, C:0.10, G:0.02, T:0.41
Consensus pattern (31 bp):
TAAAAATTAATTATAAAATTAACACTCATTT
Found at i:18372 original size:4 final size:4
Alignment explanation
Indices: 18363--18420 Score: 71
Period size: 4 Copynumber: 14.5 Consensus size: 4
18353 ATGTGAAAAG
* * * * *
18363 ATAT ATAT ATAT ATAT ACAT ACAT ACAT ACAT ACAT ATAT ATAT ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
18411 ATAT ATAT AT
1 ATAT ATAT AT
18421 GTTTATGTGA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 52 1.00
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (4 bp):
ATAT
Found at i:19439 original size:20 final size:20
Alignment explanation
Indices: 19414--19471 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
19404 ATCCTATTCC
**
19414 CTGGTAATCATACATTCCCA
1 CTGGTAATTTTACATTCCCA
19434 CTGGTAATTTTACATTCCCA
1 CTGGTAATTTTACATTCCCA
19454 CTGGTAATTTTACATTCC
1 CTGGTAATTTTACATTCC
19472 GTGAGCCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.26, C:0.26, G:0.10, T:0.38
Consensus pattern (20 bp):
CTGGTAATTTTACATTCCCA
Found at i:20241 original size:22 final size:23
Alignment explanation
Indices: 20216--20267 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
20206 CATTCGGTAC
20216 TGTTCAC-GATACTATTCA-ATAT
1 TGTTCACAG-TACTATTCAGATAT
*
20238 TGTTCACAGTACTGTTCATGATAT
1 TGTTCACAGTACTATTCA-GATAT
20262 TGTTCA
1 TGTTCA
20268 TACCGTATAG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
22 15 0.58
23 1 0.04
24 10 0.38
ACGTcount: A:0.27, C:0.17, G:0.13, T:0.42
Consensus pattern (23 bp):
TGTTCACAGTACTATTCAGATAT
Found at i:20496 original size:18 final size:18
Alignment explanation
Indices: 20473--20510 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
20463 ATGTAGGAGC
20473 CAACCTCCACATCATGCT
1 CAACCTCCACATCATGCT
20491 CAACCTCCACATCATGCT
1 CAACCTCCACATCATGCT
20509 CA
1 CA
20511 GGAATGCTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.29, C:0.45, G:0.05, T:0.21
Consensus pattern (18 bp):
CAACCTCCACATCATGCT
Found at i:20933 original size:87 final size:87
Alignment explanation
Indices: 20787--20949 Score: 290
Period size: 87 Copynumber: 1.9 Consensus size: 87
20777 TATGTTATAT
20787 TATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGAT
1 TATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGAT
20852 AGCGATTATATAATAAAATAGG
66 AGCGATTATATAATAAAATAGG
* * *
20874 TATTTAACGGGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGT
1 TATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGAT
*
20939 AGCGCTTATAT
66 AGCGATTATAT
20950 TGACCTATTT
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
87 72 1.00
ACGTcount: A:0.42, C:0.10, G:0.15, T:0.33
Consensus pattern (87 bp):
TATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGAT
AGCGATTATATAATAAAATAGG
Found at i:24668 original size:120 final size:120
Alignment explanation
Indices: 24455--24701 Score: 422
Period size: 120 Copynumber: 2.1 Consensus size: 120
24445 TTTTTCTTCC
* *
24455 ATTCTGGACATAAAGTACTGACACAATATTAAAAAGTGTCGACATAGGTTGTAGACCTATTCGCT
1 ATTCTGGACATAAAGTACCGACACAAAATTAAAAAGTGTCGACATAGGTTGTAGACCTATTCGCT
24520 AATAAAACCGGTATACTTATACCGGTTATATTACAAAATTATCTAGTACATTATA
66 AATAAAACCGGTATACTTATACCGGTTATATTACAAAATTATCTAGTACATTATA
*
24575 ATTCTGGACATAAAGTACCGACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
1 ATTCTGGACATAAAGTACCGACACAAAATTAAAAAGTGTCGACATAGGTTGTAGACCTATTCGCT
* * * * *
24640 CATAAAACTGGTATATTTATACCGGTTATATTACAAAATTATCTATTATATTATA
66 AATAAAACCGGTATACTTATACCGGTTATATTACAAAATTATCTAGTACATTATA
24695 ATTCTGG
1 ATTCTGG
24702 GTTCCGATGT
Statistics
Matches: 119, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
120 119 1.00
ACGTcount: A:0.38, C:0.15, G:0.14, T:0.33
Consensus pattern (120 bp):
ATTCTGGACATAAAGTACCGACACAAAATTAAAAAGTGTCGACATAGGTTGTAGACCTATTCGCT
AATAAAACCGGTATACTTATACCGGTTATATTACAAAATTATCTAGTACATTATA
Found at i:24918 original size:182 final size:183
Alignment explanation
Indices: 24575--25344 Score: 1386
Period size: 182 Copynumber: 4.2 Consensus size: 183
24565 GTACATTATA
*
24575 ATTCTGGACATAAAGTACCGACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
1 ATTCTGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
* *
24640 CATAAAACTGGTATATTTATACCGGTTATATTACAAAATTATCTATTATATTATAATTCTGGGTT
66 CATAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTT
24705 CCGATGTGTAAATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCC
131 CCGATGTGTAAATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCC
24758 ATTCTGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
1 ATTCTGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
24823 CATAAAACCGGTATA-TTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTT
66 CATAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTT
24887 CCGATGTGTAAATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCC
131 CCGATGTGTAAATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCC
24940 ATTCTGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
1 ATTCTGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
25005 CATAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTT
66 CATAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTT
*
25070 CCGATGTGTAAATGTCGACACTTTTTGACAAGGTATTGACACATTTTTCTTCC
131 CCGATGTGTAAATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCC
*
25123 ATTCTGGACATAAAGTA-CGACACAATATTAAAAAGTGTTGATATAGGTTGTAGACCTATTCGCT
1 ATTCTGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
* *
25187 CATAAAACCGGTATATTTATACCGATTATATTACAAAATTATCTATTACATTATAATTATGGGTT
66 CATAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTT
* * * *
25252 CCGATTTTTTTTCAA--TCGACACTTTTTGAAAAGGTATCGACACATTTTTCTTCC
131 CCGA---TGTGTAAATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCC
25306 ATTCTGGACATAAAGTACCGACACAATATTAAAAAGTGT
1 ATTCTGGACATAAAGTACCGACACAATATTAAAAAGTGT
25345 GAAAACTTTG
Statistics
Matches: 570, Mismatches: 12, Indels: 9
0.96 0.02 0.02
Matches are distributed among these distances:
182 294 0.52
183 250 0.44
184 21 0.04
185 5 0.01
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (183 bp):
ATTCTGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
CATAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTT
CCGATGTGTAAATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCC
Found at i:25252 original size:365 final size:364
Alignment explanation
Indices: 24575--25344 Score: 1382
Period size: 365 Copynumber: 2.1 Consensus size: 364
24565 GTACATTATA
*
24575 ATTCTGGACATAAAGTACCGACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
1 ATTCTGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
* *
24640 CATAAAACTGGTATATTTATACCGGTTATATTACAAAATTATCTATTATATTATAATTCTGGGTT
66 CATAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTT
24705 CCGATGTGTAAATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATA
131 CCGATGTGTAAATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATA
24770 AAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGT
196 AAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGT
* *
24835 ATATTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGA-TGTGTAAA
261 ATATTATACCGATTATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATTGTGTAAA
*
24899 TGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCC
326 --TCGACACTTTTTGAAAAGGTATCGACACATTTTTCTTCC
24940 ATTCTGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
1 ATTCTGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
25005 CATAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTT
66 CATAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTT
*
25070 CCGATGTGTAAATGTCGACACTTTTTGACAAGGTATTGACACATTTTTCTTCCATTCTGGACATA
131 CCGATGTGTAAATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATA
*
25135 AAGTA-CGACACAATATTAAAAAGTGTTGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGT
196 AAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGT
* *
25199 ATATTTATACCGATTATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATTTTTTTT
261 ATA-TTATACCGATTATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGA--TTGTGT
*
25264 CAATCGACACTTTTTGAAAAGGTATCGACACATTTTTCTTCC
323 AAATCGACACTTTTTGAAAAGGTATCGACACATTTTTCTTCC
25306 ATTCTGGACATAAAGTACCGACACAATATTAAAAAGTGT
1 ATTCTGGACATAAAGTACCGACACAATATTAAAAAGTGT
25345 GAAAACTTTG
Statistics
Matches: 390, Mismatches: 11, Indels: 7
0.96 0.03 0.02
Matches are distributed among these distances:
364 61 0.16
365 247 0.63
366 77 0.20
368 5 0.01
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (364 bp):
ATTCTGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
CATAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTT
CCGATGTGTAAATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATA
AAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGT
ATATTATACCGATTATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATTGTGTAAA
TCGACACTTTTTGAAAAGGTATCGACACATTTTTCTTCC
Found at i:26590 original size:12 final size:12
Alignment explanation
Indices: 26554--26617 Score: 65
Period size: 12 Copynumber: 5.3 Consensus size: 12
26544 GTTTGGATCA
* *
26554 TCATCATCATCA
1 TCATCTTCATCG
* *
26566 TCATCATCGTCG
1 TCATCTTCATCG
*
26578 TGATCTTCATCG
1 TCATCTTCATCG
26590 TCATCTTCATCG
1 TCATCTTCATCG
* *
26602 TCAGCTTCATCT
1 TCATCTTCATCG
26614 TCAT
1 TCAT
26618 TGACCGCTTG
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 43 1.00
ACGTcount: A:0.20, C:0.31, G:0.09, T:0.39
Consensus pattern (12 bp):
TCATCTTCATCG
Found at i:28458 original size:200 final size:200
Alignment explanation
Indices: 28108--28847 Score: 1309
Period size: 200 Copynumber: 3.7 Consensus size: 200
28098 ATATATACCA
* ** * *
28108 ATTCTCCCATAAAACAAGTATACTTATACCGGTTAGATTGAAAAATTACCTAATACATTATACTT
1 ATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACCTATTACATTATACTT
*
28173 TTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCC
66 ATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCC
*
28238 TGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTACAAAAGTGTCGACACATTATTTA
131 TGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTACAAAAGTGTCGATACATTATTTA
*
28303 GACAT
196 GACCT
28308 ATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACCTATTACATTATACTT
1 ATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACCTATTACATTATACTT
*
28373 ATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGATCGACACTTTATTGTTGCACCC
66 ATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCC
28438 TGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTACAAAAGTGTCGATACATTATTTA
131 TGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTACAAAAGTGTCGATACATTATTTA
28503 GACCT
196 GACCT
*
28508 ATTATCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACCTATTACATTATACTT
1 ATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACCTATTACATTATACTT
* * * *
28573 ATGAGTTTCGATGTTTATCGGATCGAAACTTTTTATATATGGATCGACACTTTATTGTTGCACCC
66 ATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCC
28638 TGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTACAAAAGTGTCGATACATTATTTA
131 TGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTACAAAAGTGTCGATACATTATTTA
28703 GACCT
196 GACCT
* *
28708 ATTCTCTCATAAAATCGGTATACTTGTACCGATTAGATTGAAAAATTACCTATTACATTATACTT
1 ATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACCTATTACATTATACTT
* * *
28773 TTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGATCGATACTTTATGGTTGCACCA
66 ATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCC
28838 TGTTTGCCAT
131 TGTTTGCCAT
28848 ATTGTAAATT
Statistics
Matches: 517, Mismatches: 23, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
200 517 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (200 bp):
ATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACCTATTACATTATACTT
ATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCC
TGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTACAAAAGTGTCGATACATTATTTA
GACCT
Found at i:29092 original size:18 final size:18
Alignment explanation
Indices: 29069--29129 Score: 59
Period size: 19 Copynumber: 3.3 Consensus size: 18
29059 TCTCATTCAT
*
29069 AATTATATTCACATACAA
1 AATTATAATCACATACAA
**
29087 AATTATAAATCGTATACAA
1 AATTAT-AATCACATACAA
**
29106 AATTATAAATCTTATACAA
1 AATTAT-AATCACATACAA
29125 AATTA
1 AATTA
29130 ACCCTACATT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
18 6 0.16
19 32 0.84
ACGTcount: A:0.52, C:0.11, G:0.02, T:0.34
Consensus pattern (18 bp):
AATTATAATCACATACAA
Found at i:29105 original size:19 final size:19
Alignment explanation
Indices: 29081--29129 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
29071 TTATATTCAC
29081 ATACAAAATTATAAATCGT
1 ATACAAAATTATAAATCGT
*
29100 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
29119 ATACAAAATTA
1 ATACAAAATTA
29130 ACCCTACATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.55, C:0.10, G:0.02, T:0.33
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:31806 original size:20 final size:19
Alignment explanation
Indices: 31760--31806 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
31750 TCCGGTATCG
*
31760 TTTTACTGGTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
31779 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
31800 TTTTACC
1 TTTTACC
31807 TGTTATATCG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.19, C:0.15, G:0.11, T:0.55
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:32031 original size:181 final size:182
Alignment explanation
Indices: 31727--32199 Score: 716
Period size: 181 Copynumber: 2.6 Consensus size: 182
31717 CGTACTTACG
* *
31727 AAAGTATCGACACTTTCAATATATCCGGTATCGTTTTACTGGTTTTATCATTTTGATACCGGTTT
1 AAAGTATCGACACTTTCAATATATTCGGTAACGTTTTACTGGTTTTATCATTTTGATACCGGTTT
* * *
31792 TATCATATTTTTACCTGTTATATCGTTGTGGATCGATATATTTTTTTAAAGTATCGACACATTAT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
*
31857 AGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATA-T
131 AGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
* * *
31908 AAAGTATCGACACTTTCAATATATTCGGTAACTTTTTACCGGTTTTATCATTTTGATACTGGTTT
1 AAAGTATCGACACTTTCAATATATTCGGTAACGTTTTACTGGTTTTATCATTTTGATACCGGTTT
* *
31973 TATCATATTTTTACCTGGTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACTTTAT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
** *
32038 AGGATTTAAAACTGCTTCTCTTTTAAATTCACGAAGTGTCGATCCTTATATT
131 AGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
* * * * **
32090 AAAGTACCGACACTTT-AGATGTATTCGGTAGCGCTTTACTGGTTTTATCATTTCAATACCGGTT
1 AAAGTATCGACACTTTCA-ATATATTCGGTAACGTTTTACTGGTTTTATCATTTTGATACCGGTT
* * *
32154 TTGTCATAGTTTTACCTGTTATATCGTTTTGGATCGACACATTTTT
65 TTATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTT
32200 AATTTGGATC
Statistics
Matches: 263, Mismatches: 27, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
181 167 0.63
182 96 0.37
ACGTcount: A:0.26, C:0.16, G:0.14, T:0.43
Consensus pattern (182 bp):
AAAGTATCGACACTTTCAATATATTCGGTAACGTTTTACTGGTTTTATCATTTTGATACCGGTTT
TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
AGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
Found at i:33176 original size:5 final size:5
Alignment explanation
Indices: 33166--33195 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
33156 TTAATGCTCC
33166 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG
33196 GGGGCAAGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:34045 original size:83 final size:82
Alignment explanation
Indices: 33875--34095 Score: 232
Period size: 83 Copynumber: 2.7 Consensus size: 82
33865 TTTAGCGACG
* * * * **
33875 TTTTTATACAAACGCTGCTATAGACTTGTACTTTAGTGGCATTTGTGTTTACAAATGCCGCTATA
1 TTTTT-TACAAACGCCGCTATAGACTAGTACTTTAGTGACATTTGTGTATACAAACACCGCTATA
* *
33940 GGCTTGTACTTAGTAGAA
65 GACTCGTACTTAGTAGAA
*
33958 TTTTTGTACAAACGCCGCTATAGACTAGTACATTAGTGACATTT-T-TATACAAACACCGCTATA
1 TTTTT-TACAAACGCCGCTATAGACTAGTACTTTAGTGACATTTGTGTATACAAACACCGCTATA
**
34021 GACTCGTACATTAG-AGCCGT
65 GACTCGTAC-TTAGTAG--AA
* * * * *
34041 TTTTTTACAAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTGTGTTTACAAAC
1 TTTTTTACAAACGCCGCTATAGACTAGTACTTTAGTGACATTTGTGTATACAAAC
34096 GCCGTAAGTT
Statistics
Matches: 115, Mismatches: 18, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
81 24 0.21
82 38 0.33
83 45 0.39
84 8 0.07
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (82 bp):
TTTTTTACAAACGCCGCTATAGACTAGTACTTTAGTGACATTTGTGTATACAAACACCGCTATAG
ACTCGTACTTAGTAGAA
Found at i:34083 original size:41 final size:41
Alignment explanation
Indices: 33875--34099 Score: 227
Period size: 41 Copynumber: 5.4 Consensus size: 41
33865 TTTAGCGACG
* * *
33875 TTTTTATACAAACGCTGCTATAGACTTGTACTTTAGTGGCA
1 TTTTTTTACAAACGCCGCTATAGACTCGTACTTTAGTGGCA
* * * * *
33916 TTTGTGTTTACAAATGCCGCTATAGGCTTGTAC-TTAGTAGAA
1 TTT-T-TTTACAAACGCCGCTATAGACTCGTACTTTAGTGGCA
* * * *
33958 TTTTTGTACAAACGCCGCTATAGACTAGTACATTAGTGACA
1 TTTTTTTACAAACGCCGCTATAGACTCGTACTTTAGTGGCA
* * * * * *
33999 TTTTTATACAAACACCGCTATAGACTCGTACATTAGAGCCG
1 TTTTTTTACAAACGCCGCTATAGACTCGTACTTTAGTGGCA
* *
34040 TTTTTTTACAAACGCCGCTAAAGACTCGTACTTTAGTGGCG
1 TTTTTTTACAAACGCCGCTATAGACTCGTACTTTAGTGGCA
34081 TTTGTGTTTACAAACGCCG
1 TTT-T-TTTACAAACGCCG
34100 TAAGTTTAAA
Statistics
Matches: 154, Mismatches: 25, Indels: 8
0.82 0.13 0.04
Matches are distributed among these distances:
40 23 0.15
41 83 0.54
42 12 0.08
43 36 0.23
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.35
Consensus pattern (41 bp):
TTTTTTTACAAACGCCGCTATAGACTCGTACTTTAGTGGCA
Found at i:36573 original size:43 final size:43
Alignment explanation
Indices: 36461--36654 Score: 202
Period size: 42 Copynumber: 4.6 Consensus size: 43
36451 GCGGTAATTA
* * *
36461 GCGGCTTTTGTTCTAAATACGCCGCTATAGAT-TCGACC-TTT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTCGACCTTTT
** *
36502 GTTGCGTTTGTTCC-AAAACGCCGCTATAGATCTTGACCTTTT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTCGACCTTTT
* * *
36544 GCGGCGTTTGTACCAAAAACGCCACTATAGA-CCCGACCTTTT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTCGACCTTTT
* *
36586 GCGGCGTTT-TCTCCAAAAATGCCGCTATAGATCTCGACCTATT
1 GCGGCGTTTGT-TCCAAAAACGCCGCTATAGATCTCGACCTTTT
** * *
36629 GCGATGTTT-TTTCACAAACGCCGCTA
1 GCGGCGTTTGTTCCAAAAACGCCGCTA
36655 ACTTTAGCGG
Statistics
Matches: 126, Mismatches: 22, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
40 16 0.13
41 16 0.13
42 62 0.49
43 32 0.25
ACGTcount: A:0.22, C:0.27, G:0.19, T:0.32
Consensus pattern (43 bp):
GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTCGACCTTTT
Found at i:36756 original size:21 final size:22
Alignment explanation
Indices: 36730--36785 Score: 87
Period size: 21 Copynumber: 2.6 Consensus size: 22
36720 AGCGACGCTT
36730 AAAAACGTCGCTATAGGACT-A
1 AAAAACGTCGCTATAGGACTAA
* *
36751 AAAAACGACGTTATAGGACTAA
1 AAAAACGTCGCTATAGGACTAA
36773 AAAAACGTCGCTA
1 AAAAACGTCGCTA
36786 AAGAATAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
21 18 0.60
22 12 0.40
ACGTcount: A:0.46, C:0.18, G:0.18, T:0.18
Consensus pattern (22 bp):
AAAAACGTCGCTATAGGACTAA
Found at i:40510 original size:20 final size:21
Alignment explanation
Indices: 40487--40533 Score: 71
Period size: 20 Copynumber: 2.3 Consensus size: 21
40477 GATGGTACTA
*
40487 ATATTGAACCT-TTGGTATCG
1 ATATTCAACCTGTTGGTATCG
40507 ATA-TCAACCTGTTGGTATCG
1 ATATTCAACCTGTTGGTATCG
40527 ATATTCA
1 ATATTCA
40534 CTGACTGATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 6 0.25
20 15 0.62
21 3 0.12
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (21 bp):
ATATTCAACCTGTTGGTATCG
Found at i:42716 original size:17 final size:18
Alignment explanation
Indices: 42678--42722 Score: 65
Period size: 17 Copynumber: 2.5 Consensus size: 18
42668 AATAAATCGT
*
42678 AAAATCATTATACAATATA
1 AAAAT-ATTATACAAAATA
42697 AAAATATTATA-AAAATA
1 AAAATATTATACAAAATA
42714 AAAATATTA
1 AAAATATTA
42723 ATATAATAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 14 0.56
18 6 0.24
19 5 0.20
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.31
Consensus pattern (18 bp):
AAAATATTATACAAAATA
Found at i:44034 original size:18 final size:19
Alignment explanation
Indices: 44011--44058 Score: 73
Period size: 18 Copynumber: 2.6 Consensus size: 19
44001 AGGATCTAAG
*
44011 AGTAAAATTAATATATA-T
1 AGTAAAATTAATATACAGT
44029 AGTAAAATTAATATACAGT
1 AGTAAAATTAATATACAGT
44048 -GTAAAATTAAT
1 AGTAAAATTAAT
44059 TTTACACAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
18 27 0.96
19 1 0.04
ACGTcount: A:0.54, C:0.02, G:0.08, T:0.35
Consensus pattern (19 bp):
AGTAAAATTAATATACAGT
Found at i:44368 original size:13 final size:13
Alignment explanation
Indices: 44352--44398 Score: 67
Period size: 13 Copynumber: 3.6 Consensus size: 13
44342 AACAATTAAA
44352 CAAATCAATTTCT
1 CAAATCAATTTCT
* **
44365 CAAATCAACTAAT
1 CAAATCAATTTCT
44378 CAAATCAATTTCT
1 CAAATCAATTTCT
44391 CAAATCAA
1 CAAATCAA
44399 CTAATCAAAT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
13 28 1.00
ACGTcount: A:0.47, C:0.23, G:0.00, T:0.30
Consensus pattern (13 bp):
CAAATCAATTTCT
Found at i:44381 original size:26 final size:26
Alignment explanation
Indices: 44352--44410 Score: 118
Period size: 26 Copynumber: 2.3 Consensus size: 26
44342 AACAATTAAA
44352 CAAATCAATTTCTCAAATCAACTAAT
1 CAAATCAATTTCTCAAATCAACTAAT
44378 CAAATCAATTTCTCAAATCAACTAAT
1 CAAATCAATTTCTCAAATCAACTAAT
44404 CAAATCA
1 CAAATCA
44411 GTTGGTCAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.47, C:0.24, G:0.00, T:0.29
Consensus pattern (26 bp):
CAAATCAATTTCTCAAATCAACTAAT
Found at i:44406 original size:13 final size:13
Alignment explanation
Indices: 44364--44410 Score: 67
Period size: 13 Copynumber: 3.6 Consensus size: 13
44354 AATCAATTTC
44364 TCAAATCAACTAA
1 TCAAATCAACTAA
* **
44377 TCAAATCAATTTC
1 TCAAATCAACTAA
44390 TCAAATCAACTAA
1 TCAAATCAACTAA
44403 TCAAATCA
1 TCAAATCA
44411 GTTGGTCAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
13 28 1.00
ACGTcount: A:0.49, C:0.23, G:0.00, T:0.28
Consensus pattern (13 bp):
TCAAATCAACTAA
Found at i:44419 original size:26 final size:26
Alignment explanation
Indices: 44352--44420 Score: 102
Period size: 26 Copynumber: 2.7 Consensus size: 26
44342 AACAATTAAA
*
44352 CAAATCAATTTCTCAAATCAACTAAT
1 CAAATCAATTGCTCAAATCAACTAAT
*
44378 CAAATCAATTTCTCAAATCAACTAAT
1 CAAATCAATTGCTCAAATCAACTAAT
* *
44404 CAAATCAGTTGGTCAAA
1 CAAATCAATTGCTCAAA
44421 CCATCAACTG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 40 1.00
ACGTcount: A:0.45, C:0.22, G:0.04, T:0.29
Consensus pattern (26 bp):
CAAATCAATTGCTCAAATCAACTAAT
Found at i:45931 original size:2 final size:2
Alignment explanation
Indices: 45924--45961 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
45914 AGACAAACAA
45924 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
45962 TAACAGTAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:46856 original size:24 final size:24
Alignment explanation
Indices: 46829--46935 Score: 88
Period size: 24 Copynumber: 4.5 Consensus size: 24
46819 AAACGGAGAT
* *
46829 ATCAAAAATCAAAACATAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * *
46853 ATCAGATATCATAACAGAATCCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * * * * *
46877 GTTAGGAATCAGAACATATTTCAG
1 ATCAGAAATCAAAACAGAATTCAG
** *
46901 ATCAGATGTCAAAACAGAATTCAA
1 ATCAGAAATCAAAACAGAATTCAG
46925 ATCAGAAATCA
1 ATCAGAAATCA
46936 GATAAAATAT
Statistics
Matches: 59, Mismatches: 24, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
24 59 1.00
ACGTcount: A:0.49, C:0.17, G:0.12, T:0.22
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATTCAG
Found at i:46935 original size:48 final size:48
Alignment explanation
Indices: 46829--46937 Score: 128
Period size: 48 Copynumber: 2.3 Consensus size: 48
46819 AAACGGAGAT
* * * *
46829 ATCAAAAATCAAAACATAATTCAGATCAGATATCATAACAGAATCCAG
1 ATCAGAAATCAGAACATAATTCAGATCAGATATCAAAACAGAATCCAA
* * * * * *
46877 GTTAGGAATCAGAACATATTTCAGATCAGATGTCAAAACAGAATTCAA
1 ATCAGAAATCAGAACATAATTCAGATCAGATATCAAAACAGAATCCAA
46925 ATCAGAAATCAGA
1 ATCAGAAATCAGA
46938 TAAAATATTC
Statistics
Matches: 48, Mismatches: 13, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.49, C:0.17, G:0.13, T:0.22
Consensus pattern (48 bp):
ATCAGAAATCAGAACATAATTCAGATCAGATATCAAAACAGAATCCAA
Found at i:49433 original size:7 final size:7
Alignment explanation
Indices: 49421--49453 Score: 57
Period size: 7 Copynumber: 4.6 Consensus size: 7
49411 TGGTCAACGC
49421 CGGTCAA
1 CGGTCAA
49428 CGGTCAA
1 CGGTCAA
49435 CGGGTCAA
1 C-GGTCAA
49443 CGGTCAA
1 CGGTCAA
49450 CGGT
1 CGGT
49454 TCGGGTTGGG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
7 18 0.72
8 7 0.28
ACGTcount: A:0.24, C:0.27, G:0.33, T:0.15
Consensus pattern (7 bp):
CGGTCAA
Found at i:49442 original size:15 final size:15
Alignment explanation
Indices: 49412--49452 Score: 64
Period size: 15 Copynumber: 2.6 Consensus size: 15
49402 AGTCAACAGT
49412 GGTCAACGCCGGTCAAC
1 GGTCAACG--GGTCAAC
49429 GGTCAACGGGTCAAC
1 GGTCAACGGGTCAAC
49444 GGTCAACGG
1 GGTCAACGG
49453 TTCGGGTTGG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 16 0.67
17 8 0.33
ACGTcount: A:0.24, C:0.29, G:0.34, T:0.12
Consensus pattern (15 bp):
GGTCAACGGGTCAAC
Found at i:50412 original size:13 final size:13
Alignment explanation
Indices: 50391--50420 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
50381 CGTGTTTTAT
50391 ATGCCTACACATA
1 ATGCCTACACATA
*
50404 ATGCTTACACATA
1 ATGCCTACACATA
50417 ATGC
1 ATGC
50421 AGCAAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.37, C:0.27, G:0.10, T:0.27
Consensus pattern (13 bp):
ATGCCTACACATA
Found at i:51779 original size:17 final size:20
Alignment explanation
Indices: 51739--51781 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 20
51729 AACAAAAATG
*
51739 TAATAATAATATTAATGATA
1 TAATAATAATATTAATAATA
51759 TAATAATAATATATAATTAATA
1 TAATAATAATAT-TAA-TAATA
51781 T
1 T
51782 TTATAACATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 12 0.60
21 3 0.15
22 5 0.25
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (20 bp):
TAATAATAATATTAATAATA
Found at i:51787 original size:13 final size:13
Alignment explanation
Indices: 51739--51780 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 13
51729 AACAAAAATG
*
51739 TAATA-ATAATAT
1 TAATATATAATAA
51751 TAATGATATAATAA
1 TAAT-ATATAATAA
51765 TAATATATAATTAA
1 TAATATATAA-TAA
51779 TA
1 TA
51781 TTTATAACAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
12 4 0.15
13 7 0.27
14 15 0.58
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (13 bp):
TAATATATAATAA
Found at i:51940 original size:33 final size:33
Alignment explanation
Indices: 51898--51962 Score: 121
Period size: 33 Copynumber: 2.0 Consensus size: 33
51888 AACTTAATTC
51898 TCACTCAAAAATCAAATGCATGAGAATATGATG
1 TCACTCAAAAATCAAATGCATGAGAATATGATG
*
51931 TCACTCAAAAATCAAATGCATTAGAATATGAT
1 TCACTCAAAAATCAAATGCATGAGAATATGAT
51963 AGTAACCTGA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.46, C:0.15, G:0.12, T:0.26
Consensus pattern (33 bp):
TCACTCAAAAATCAAATGCATGAGAATATGATG
Found at i:55045 original size:51 final size:49
Alignment explanation
Indices: 54970--55082 Score: 149
Period size: 51 Copynumber: 2.3 Consensus size: 49
54960 AAATATATCA
* * * *
54970 ATTTTTTTATTAAACCTACCAAAAGATTAGTGTAATGATTATATTTGTTTTC
1 ATTTTTTTATTAAAACTACCAAAAGATTAATATAATGA-T-TATGT-TTTTC
55022 ATTTTTTTATTAAAAC-ACCAAAAGATTAATATAATGATTATGTTTTTC
1 ATTTTTTTATTAAAACTACCAAAAGATTAATATAATGATTATGTTTTTC
55070 A-TTTTTTATTAAA
1 ATTTTTTTATTAAA
55083 GCTTTTTATC
Statistics
Matches: 57, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
47 12 0.21
48 6 0.11
49 4 0.07
50 1 0.02
51 19 0.33
52 15 0.26
ACGTcount: A:0.36, C:0.08, G:0.07, T:0.49
Consensus pattern (49 bp):
ATTTTTTTATTAAAACTACCAAAAGATTAATATAATGATTATGTTTTTC
Found at i:59288 original size:55 final size:55
Alignment explanation
Indices: 59219--59350 Score: 221
Period size: 55 Copynumber: 2.4 Consensus size: 55
59209 ATCAAATAAT
59219 AAAGCAGCAGCGTTTAGCAAAATTTAAAA-AGAAAAAACTAACAATTATTTTGTAA
1 AAAGCAGCAGCGTTTAGCAAAATTTAAAAGA-AAAAAACTAACAATTATTTTGTAA
59274 AAAGCAGCAGCGTTTAGCAAAATTTAAAAGAAAAAAACTAACAATTATTTTGTAA
1 AAAGCAGCAGCGTTTAGCAAAATTTAAAAGAAAAAAACTAACAATTATTTTGTAA
* **
59329 AAAGCAGAAGCGACTAGCAAAA
1 AAAGCAGCAGCGTTTAGCAAAA
59351 AATCAGAAAT
Statistics
Matches: 73, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
55 72 0.99
56 1 0.01
ACGTcount: A:0.52, C:0.12, G:0.14, T:0.22
Consensus pattern (55 bp):
AAAGCAGCAGCGTTTAGCAAAATTTAAAAGAAAAAAACTAACAATTATTTTGTAA
Found at i:60314 original size:17 final size:17
Alignment explanation
Indices: 60275--60315 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
60265 ACATAATTAT
60275 TAAAAA-TTAGAAAATA
1 TAAAAATTTAGAAAATA
60291 TAGAAAATTTAGATAAATA
1 TA-AAAATTTAGA-AAATA
60310 -AAAAAT
1 TAAAAAT
60316 AATTTAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 2 0.09
17 9 0.41
18 6 0.27
19 5 0.23
ACGTcount: A:0.66, C:0.00, G:0.07, T:0.27
Consensus pattern (17 bp):
TAAAAATTTAGAAAATA
Found at i:60496 original size:24 final size:22
Alignment explanation
Indices: 60435--60507 Score: 85
Period size: 22 Copynumber: 3.2 Consensus size: 22
60425 AGAAAATGTC
*
60435 TTTTAACATATATTAAAGAATT
1 TTTTAATATATATTAAAGAATT
*
60457 TTTTAATATATTTTAAAGAATT
1 TTTTAATATATATTAAAGAATT
*
60479 TTTTGGAT-TGAATATTAAAGAATT
1 TTTT-AATAT--ATATTAAAGAATT
60503 TTTTA
1 TTTTA
60508 TTATTATAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
22 25 0.58
23 2 0.05
24 16 0.37
ACGTcount: A:0.40, C:0.01, G:0.08, T:0.51
Consensus pattern (22 bp):
TTTTAATATATATTAAAGAATT
Found at i:62473 original size:16 final size:16
Alignment explanation
Indices: 62452--62482 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
62442 TTTAACATCT
*
62452 TGACAGTAAAAAAATC
1 TGACAGCAAAAAAATC
62468 TGACAGCAAAAAAAT
1 TGACAGCAAAAAAAT
62483 TGTTGTTTCC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.58, C:0.13, G:0.13, T:0.16
Consensus pattern (16 bp):
TGACAGCAAAAAAATC
Found at i:62861 original size:28 final size:26
Alignment explanation
Indices: 62820--62886 Score: 68
Period size: 25 Copynumber: 2.6 Consensus size: 26
62810 AATAATTCTA
62820 CACTTGAAA-TATTTTTTCATTAAATAAT
1 CACTT-AAATTATTTTTT-A-TAAATAAT
* *
62848 TACTTAAATTA-TTTTTATATATAAT
1 CACTTAAATTATTTTTTATAAATAAT
62873 CA-TTAAATTATTTT
1 CACTTAAATTATTTT
62887 AAAAAATCAA
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
24 8 0.24
25 11 0.32
26 1 0.03
27 8 0.24
28 6 0.18
ACGTcount: A:0.39, C:0.07, G:0.01, T:0.52
Consensus pattern (26 bp):
CACTTAAATTATTTTTTATAAATAAT
Found at i:62943 original size:24 final size:24
Alignment explanation
Indices: 62897--62943 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
62887 AAAAAATCAA
*
62897 ATTATATATAAAAATAATTTAATG
1 ATTATATATAAAAATAATATAATG
62921 ATTATATAT-AAAATAAATATAAT
1 ATTATATATAAAAAT-AATATAAT
62944 TTAAAAATCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 5 0.24
24 16 0.76
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (24 bp):
ATTATATATAAAAATAATATAATG
Done.