Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011399.1 Kokia drynarioides strain JFW-HI SEQ_126381, 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: 481736
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Warning! 81 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:216307 original size:43 final size:42
Alignment explanation
Indices: 216181--216328 Score: 156
Period size: 43 Copynumber: 3.5 Consensus size: 42
216171 ACCGTGCTTC
* * * **
216181 AAGTTTTCCATTTGTAAATAATCCTATGCTCTTGCTGAGACAT
1 AAGTCTTCCATTTAT-AATAATCTTATGCTCTACCTGAGACAT
** * * *
216224 TGGTCTTCAATTTATAATAATTTTATGCTCTACCCGAGACAT
1 AAGTCTTCCATTTATAATAATCTTATGCTCTACCTGAGACAT
* *
216266 AAGTCTTCCATTTATAGACAATCTTATGCTCTACCTAAGACAT
1 AAGTCTTCCATTTATA-ATAATCTTATGCTCTACCTGAGACAT
216309 AAGTCTTCCA-TTA-AATAATC
1 AAGTCTTCCATTTATAATAATC
216329 ACCAAGTCTT
Statistics
Matches: 86, Mismatches: 18, Indels: 5
0.79 0.17 0.05
Matches are distributed among these distances:
40 5 0.06
41 1 0.01
42 38 0.44
43 42 0.49
ACGTcount: A:0.31, C:0.20, G:0.11, T:0.38
Consensus pattern (42 bp):
AAGTCTTCCATTTATAATAATCTTATGCTCTACCTGAGACAT
Found at i:216367 original size:23 final size:23
Alignment explanation
Indices: 216309--216368 Score: 102
Period size: 23 Copynumber: 2.6 Consensus size: 23
216299 CCTAAGACAT
*
216309 AAGTCTTCCATTAAATAATCACC
1 AAGTCTTCCATTTAATAATCACC
*
216332 AAGTCTTCCATTTAATAATCATC
1 AAGTCTTCCATTTAATAATCACC
216355 AAGTCTTCCATTTA
1 AAGTCTTCCATTTA
216369 TTCAAATAGT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.35, C:0.23, G:0.05, T:0.37
Consensus pattern (23 bp):
AAGTCTTCCATTTAATAATCACC
Found at i:216575 original size:21 final size:21
Alignment explanation
Indices: 216534--216576 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
216524 CTCTATCAAA
* **
216534 TAAATGATGCAATTTTCTCAT
1 TAAATCATGCAATTTAATCAT
216555 TAAATCATGCAATTTAATCAT
1 TAAATCATGCAATTTAATCAT
216576 T
1 T
216577 TAGTACATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.37, C:0.14, G:0.07, T:0.42
Consensus pattern (21 bp):
TAAATCATGCAATTTAATCAT
Found at i:234134 original size:89 final size:89
Alignment explanation
Indices: 233954--234193 Score: 263
Period size: 88 Copynumber: 2.7 Consensus size: 89
233944 TTAAAGGTGT
* * ** * * * * *
233954 AAAAA-TCTCTCAAAC-TTTTCAAAAAAAGCATTTAAGCTTTTACTTTTTTTTACAGTTATTTGG
1 AAAAAGTCCCTCAAACTTTTTCAAAAAAAGCAATTAAGCTCCTGC-TTTTTTTGCAATCAATTGG
* * *
234017 GTACTTGAACTTTCAAAATACAT-C
65 ATACTTGAACTATCAAAATACATAA
* *
234041 AAAAAGTCCCTCAAACTTTTTCAAAAAAAGCAATTAAGCCCCTGCTTTTTTTGCACTCAATTGGA
1 AAAAAGTCCCTCAAACTTTTTCAAAAAAAGCAATTAAGCTCCTGCTTTTTTTGCAATCAATTGGA
234106 TACTTGAACTATCAAAATACATAAA
66 TACTTGAACTATCAAAATACAT-AA
* * *
234131 AAAAAGT-CCTCAAACTTTTTCAAAAAAATTACAATTAAACTCCTGATTTTTTTGCAATCAATT
1 AAAAAGTCCCTCAAACTTTTTCAAAAAAA--GCAATTAAGCTCCTGCTTTTTTTGCAATCAATT
234194 AAATACTTAA
Statistics
Matches: 129, Mismatches: 18, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
87 5 0.04
88 45 0.35
89 44 0.34
90 7 0.05
91 28 0.22
ACGTcount: A:0.39, C:0.18, G:0.07, T:0.35
Consensus pattern (89 bp):
AAAAAGTCCCTCAAACTTTTTCAAAAAAAGCAATTAAGCTCCTGCTTTTTTTGCAATCAATTGGA
TACTTGAACTATCAAAATACATAA
Found at i:234200 original size:91 final size:88
Alignment explanation
Indices: 234018--234201 Score: 244
Period size: 91 Copynumber: 2.1 Consensus size: 88
234008 GTTATTTGGG
* * * *
234018 TACTTGAACTTTCAAAATACATCAAAAAGTCCCTCAAACTTTTTCAAAAAAAGCAATTAAGCCCC
1 TACTTGAACTATCAAAATACATAAAAAAGTCCCTCAAACTTTTTCAAAAAAAACAATTAAACCCC
* * **
234083 TGCTTTTTTTGCACTCAATTGGA
66 TGATTTTTTTGCAATCAATTAAA
234106 TACTTGAACTATCAAAATACATAAAAAAAAGT-CCTCAAACTTTTTCAAAAAAATTACAATTAAA
1 TACTTGAACTATCAAAATACAT--AAAAAAGTCCCTCAAACTTTTTCAAAAAAA--ACAATTAAA
*
234170 CTCCTGATTTTTTTGCAATCAATTAAA
62 CCCCTGATTTTTTTGCAATCAATTAAA
234197 TACTT
1 TACTT
234202 AATTTATTGT
Statistics
Matches: 83, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
88 21 0.25
89 21 0.25
90 7 0.08
91 34 0.41
ACGTcount: A:0.41, C:0.20, G:0.07, T:0.33
Consensus pattern (88 bp):
TACTTGAACTATCAAAATACATAAAAAAGTCCCTCAAACTTTTTCAAAAAAAACAATTAAACCCC
TGATTTTTTTGCAATCAATTAAA
Found at i:234248 original size:40 final size:41
Alignment explanation
Indices: 234204--234281 Score: 131
Period size: 41 Copynumber: 1.9 Consensus size: 41
234194 AAATACTTAA
*
234204 TTTATTGTTTATTTA-TTTTATTAAAATATTATTTTTAAAC
1 TTTATTATTTATTTATTTTTATTAAAATATTATTTTTAAAC
*
234244 TTTATTATTTGTTTATTTTTATTAAAATATTATTTTTA
1 TTTATTATTTATTTATTTTTATTAAAATATTATTTTTA
234282 TAGGTGATGC
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
40 13 0.37
41 22 0.63
ACGTcount: A:0.31, C:0.01, G:0.03, T:0.65
Consensus pattern (41 bp):
TTTATTATTTATTTATTTTTATTAAAATATTATTTTTAAAC
Found at i:235445 original size:17 final size:18
Alignment explanation
Indices: 235412--235447 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
235402 ATGAAATTAA
235412 AATTACAAAAGATAAAAT
1 AATTACAAAAGATAAAAT
*
235430 AATTATAAAA-ATAAAAT
1 AATTACAAAAGATAAAAT
235447 A
1 A
235448 CACAAATGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.69, C:0.03, G:0.03, T:0.25
Consensus pattern (18 bp):
AATTACAAAAGATAAAAT
Found at i:239213 original size:23 final size:23
Alignment explanation
Indices: 239177--239226 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 23
239167 GAAAATAGAG
**
239177 AAATAAATTTACAACTAA-TACAT
1 AAATAAATACACAA-TAATTACAT
239200 AAATAAATACACAATAATTTACAT
1 AAATAAATACACAATAA-TTACAT
239224 AAA
1 AAA
239227 AAAAAACTCC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 3 0.13
23 12 0.52
24 8 0.35
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (23 bp):
AAATAAATACACAATAATTACAT
Found at i:239660 original size:18 final size:18
Alignment explanation
Indices: 239625--239667 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
239615 AATAAATATA
239625 AATACAATTTAAATTTAAT
1 AATA-AATTTAAATTTAAT
239644 AATAAATTGTAAA-TTAAT
1 AATAAATT-TAAATTTAAT
239662 AA-AAAT
1 AATAAAT
239668 AAATGAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 4 0.17
18 11 0.48
19 8 0.35
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.37
Consensus pattern (18 bp):
AATAAATTTAAATTTAAT
Found at i:242531 original size:29 final size:27
Alignment explanation
Indices: 242475--242532 Score: 64
Period size: 29 Copynumber: 2.1 Consensus size: 27
242465 CGAGAAATAG
* *
242475 AAATATCCTAAAATAACTTAAAATTAA
1 AAATATCCTAAAAGAACTTAAAACTAA
242502 AAATATCCTAAAAAAGAAC-TAAGAACTAA
1 AAATATCCT--AAAAGAACTTAA-AACTAA
242531 AA
1 AA
242533 GCTTACAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
27 9 0.35
28 3 0.12
29 14 0.54
ACGTcount: A:0.62, C:0.12, G:0.03, T:0.22
Consensus pattern (27 bp):
AAATATCCTAAAAGAACTTAAAACTAA
Found at i:244100 original size:13 final size:13
Alignment explanation
Indices: 244084--244108 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
244074 TTAAAACAAA
244084 AATTTAACTAAGT
1 AATTTAACTAAGT
244097 AATTTAACTAAG
1 AATTTAACTAAG
244109 AAAAATTAAA
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:0.48, C:0.08, G:0.08, T:0.36
Consensus pattern (13 bp):
AATTTAACTAAGT
Found at i:249249 original size:21 final size:21
Alignment explanation
Indices: 249225--249278 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
249215 CCTACGATAG
* *
249225 TTCTACCAATACAAGTGAAGC
1 TTCTACCAATACAAATCAAGC
*
249246 TTCTACCGAA-ACAAATCATGC
1 TTCTACC-AATACAAATCAAGC
249267 TTCTACCAATAC
1 TTCTACCAATAC
249279 TAAAAACTCC
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
20 2 0.07
21 24 0.86
22 2 0.07
ACGTcount: A:0.37, C:0.28, G:0.09, T:0.26
Consensus pattern (21 bp):
TTCTACCAATACAAATCAAGC
Found at i:257475 original size:14 final size:14
Alignment explanation
Indices: 257456--257483 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
257446 ATGAAAAAAA
257456 TGAAAAAAAATCTT
1 TGAAAAAAAATCTT
257470 TGAAAAAAAATCTT
1 TGAAAAAAAATCTT
257484 AAGTGAGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.07, G:0.07, T:0.29
Consensus pattern (14 bp):
TGAAAAAAAATCTT
Found at i:260174 original size:23 final size:24
Alignment explanation
Indices: 260129--260299 Score: 66
Period size: 23 Copynumber: 7.3 Consensus size: 24
260119 GTGGTTAAAT
* *
260129 CACTCAATAACATTGTGGCCAAG-
1 CACTCAATAACATTATGGACAAGC
* * *
260152 TACTCAATAGCGTTATGGACAAGC
1 CACTCAATAACATTATGGACAAGC
** * *
260176 CACTCAATAATGTTTTGGACAAAC
1 CACTCAATAACATTATGGACAAGC
* *** * *
260200 AACTC-ATAGTGTTATGGAAAATC
1 CACTCAATAACATTATGGACAAGC
* * * *
260223 CAATC-ATATCGTTGTGGACAAGC
1 CACTCAATAACATTATGGACAAGC
*** *
260246 CACTC-ATATTTTTGTGGACAAGC
1 CACTCAATAACATTATGGACAAGC
* *
260269 CAAC-C-ATATCGTTATGGACAAGC
1 C-ACTCAATAACATTATGGACAAGC
260292 CACTCAAT
1 CACTCAAT
260300 TTCGTAGTAA
Statistics
Matches: 116, Mismatches: 28, Indels: 7
0.77 0.19 0.05
Matches are distributed among these distances:
22 2 0.02
23 87 0.75
24 27 0.23
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.27
Consensus pattern (24 bp):
CACTCAATAACATTATGGACAAGC
Found at i:260251 original size:46 final size:46
Alignment explanation
Indices: 260191--260297 Score: 133
Period size: 46 Copynumber: 2.3 Consensus size: 46
260181 AATAATGTTT
* * * * *
260191 TGGACAAACAACTCATAGTGTTATGGAAAATCCAATCATATCGTTG
1 TGGACAAGCCACTCATAGTGTTATGGAAAAGCCAACCATATCGTTA
* * * *
260237 TGGACAAGCCACTCATATTTTTGTGGACAAGCCAACCATATCGTTA
1 TGGACAAGCCACTCATAGTGTTATGGAAAAGCCAACCATATCGTTA
260283 TGGACAAGCCACTCA
1 TGGACAAGCCACTCA
260298 ATTTCGTAGT
Statistics
Matches: 52, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
46 52 1.00
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.26
Consensus pattern (46 bp):
TGGACAAGCCACTCATAGTGTTATGGAAAAGCCAACCATATCGTTA
Found at i:267587 original size:19 final size:18
Alignment explanation
Indices: 267565--267601 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
267555 AATAATTTTG
267565 AAAATTCAAAATATTTATA
1 AAAATTCAAAA-ATTTATA
*
267584 AAAATTTAAAAATTTATA
1 AAAATTCAAAAATTTATA
267602 TTTCATAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (18 bp):
AAAATTCAAAAATTTATA
Found at i:274305 original size:65 final size:65
Alignment explanation
Indices: 274204--274334 Score: 244
Period size: 65 Copynumber: 2.0 Consensus size: 65
274194 ACATAAACAT
*
274204 AACACCTGTAAACTTAGGAGAACTTAGTGAGAGTTAAAACAAATACCTTGGCAAAGAATTTTATA
1 AACACCTGTAAACTCAGGAGAACTTAGTGAGAGTTAAAACAAATACCTTGGCAAAGAATTTTATA
*
274269 AACACCTGTAAACTCAGGAGAACTTAGTGAGAGTTAAAACAAATACCTTGGCAAAGACTTTTATA
1 AACACCTGTAAACTCAGGAGAACTTAGTGAGAGTTAAAACAAATACCTTGGCAAAGAATTTTATA
274334 A
1 A
274335 TCTTGAATGA
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
65 64 1.00
ACGTcount: A:0.43, C:0.15, G:0.17, T:0.25
Consensus pattern (65 bp):
AACACCTGTAAACTCAGGAGAACTTAGTGAGAGTTAAAACAAATACCTTGGCAAAGAATTTTATA
Found at i:275194 original size:26 final size:26
Alignment explanation
Indices: 275165--275226 Score: 88
Period size: 26 Copynumber: 2.4 Consensus size: 26
275155 AGTATGTCAC
275165 AAAGGCAACATACAGGAGTACACCAA
1 AAAGGCAACATACAGGAGTACACCAA
* * *
275191 AAAGGTAACATACAGGAGTACGCCAC
1 AAAGGCAACATACAGGAGTACACCAA
*
275217 GAAGGCAACA
1 AAAGGCAACA
275227 GAATGCGCCA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.47, C:0.23, G:0.23, T:0.08
Consensus pattern (26 bp):
AAAGGCAACATACAGGAGTACACCAA
Found at i:275275 original size:23 final size:22
Alignment explanation
Indices: 275211--275278 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 22
275201 TACAGGAGTA
*
275211 CGCCACGAAGGC-AACAGAATG
1 CGCCACAAAGGCTAACAGAATG
*
275232 CGCCACAAAGGCTAATTAGAATG
1 CGCCACAAAGGCTAA-CAGAATG
* *
275255 TGCCATAAAGGCCTAACAGAATG
1 CGCCACAAAGG-CTAACAGAATG
275278 C
1 C
275279 CACCTAGGCA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
21 11 0.29
22 2 0.05
23 21 0.55
24 4 0.11
ACGTcount: A:0.38, C:0.25, G:0.24, T:0.13
Consensus pattern (22 bp):
CGCCACAAAGGCTAACAGAATG
Found at i:279150 original size:29 final size:29
Alignment explanation
Indices: 279118--279188 Score: 108
Period size: 29 Copynumber: 2.4 Consensus size: 29
279108 TAAAATCAGT
279118 CACAAAGGCTTTCATATAACA-AAGTTAGC
1 CACAAAGGCTTTCATATAACAGAA-TTAGC
**
279147 CACAAAGGCTCACATATAACAGAATTAGC
1 CACAAAGGCTTTCATATAACAGAATTAGC
279176 CACAAAGGCTTTC
1 CACAAAGGCTTTC
279189 TTTTTTGAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
29 35 0.95
30 2 0.05
ACGTcount: A:0.41, C:0.24, G:0.14, T:0.21
Consensus pattern (29 bp):
CACAAAGGCTTTCATATAACAGAATTAGC
Found at i:290413 original size:17 final size:17
Alignment explanation
Indices: 290387--290431 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
290377 GTAGTATAAT
*
290387 TGTCCCTGCATTATTAG
1 TGTCACTGCATTATTAG
* * *
290404 TGTCATTGCATTTTTAT
1 TGTCACTGCATTATTAG
290421 TGTCACTGCAT
1 TGTCACTGCAT
290432 CTACATTTCC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.18, C:0.20, G:0.16, T:0.47
Consensus pattern (17 bp):
TGTCACTGCATTATTAG
Found at i:293612 original size:24 final size:24
Alignment explanation
Indices: 293585--293641 Score: 82
Period size: 24 Copynumber: 2.4 Consensus size: 24
293575 ACTGTCGATC
*
293585 GACTTAAA-TCGAACCGTTGACTTT
1 GACTTAAACT-GAACCATTGACTTT
293609 GACTTAAACTGAACCATTGACTTT
1 GACTTAAACTGAACCATTGACTTT
293633 GA-TTAAACT
1 GACTTAAACT
293642 ATTGACCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
23 7 0.23
24 23 0.74
25 1 0.03
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.33
Consensus pattern (24 bp):
GACTTAAACTGAACCATTGACTTT
Found at i:298309 original size:21 final size:21
Alignment explanation
Indices: 298285--298334 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
298275 AAGGTTCTAC
298285 CGATACAAGTA-TGACTACTAT
1 CGATACAAGTATTG-CTACTAT
* *
298306 CGATACAATTATTGCTTCTAT
1 CGATACAAGTATTGCTACTAT
298327 CGATACAA
1 CGATACAA
298335 CCAACTCCAG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 24 0.92
22 2 0.08
ACGTcount: A:0.36, C:0.20, G:0.12, T:0.32
Consensus pattern (21 bp):
CGATACAAGTATTGCTACTAT
Found at i:311110 original size:17 final size:17
Alignment explanation
Indices: 311075--311113 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
311065 ATTGTCATCA
*
311075 CATTTTAATTATCCCTG
1 CATTTTAATTATCCATG
* *
311092 CATTTTATTTATCGATG
1 CATTTTAATTATCCATG
311109 CATTT
1 CATTT
311114 GCATTGTAGT
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:0.23, C:0.18, G:0.08, T:0.51
Consensus pattern (17 bp):
CATTTTAATTATCCATG
Found at i:320188 original size:31 final size:30
Alignment explanation
Indices: 320153--320213 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
320143 AAAAAATTAT
*
320153 TTTAAATTATTTTAAAAATGAAAAACTTAAA
1 TTTAAATTA-ATTAAAAATGAAAAACTTAAA
* * *
320184 TTTAACTTAATTAAAAATGACAAATTTAAA
1 TTTAAATTAATTAAAAATGAAAAACTTAAA
320214 ATTTTATCTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
30 18 0.69
31 8 0.31
ACGTcount: A:0.54, C:0.05, G:0.03, T:0.38
Consensus pattern (30 bp):
TTTAAATTAATTAAAAATGAAAAACTTAAA
Found at i:320800 original size:21 final size:21
Alignment explanation
Indices: 320775--320815 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
320765 TTTAATAGTC
320775 GAAGAAGAAGAAGAACAAGAT
1 GAAGAAGAAGAAGAACAAGAT
*
320796 GAAGATGAAGAAGAACAAGA
1 GAAGAAGAAGAAGAACAAGA
320816 ACAAGATGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.61, C:0.05, G:0.29, T:0.05
Consensus pattern (21 bp):
GAAGAAGAAGAAGAACAAGAT
Found at i:320821 original size:21 final size:21
Alignment explanation
Indices: 320776--320824 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
320766 TTAATAGTCG
* **
320776 AAGAAGAAGAAGAACAAGATG
1 AAGATGAAGAAGAACAAGAAC
320797 AAGATGAAGAAGAACAAGAAC
1 AAGATGAAGAAGAACAAGAAC
320818 AAGATGA
1 AAGATGA
320825 GGAATTTGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.61, C:0.06, G:0.27, T:0.06
Consensus pattern (21 bp):
AAGATGAAGAAGAACAAGAAC
Found at i:321245 original size:46 final size:46
Alignment explanation
Indices: 321194--321284 Score: 130
Period size: 46 Copynumber: 2.0 Consensus size: 46
321184 GTGATTACTG
*
321194 TTGTTTAAGAGCGTATTATATATACTTCTCT-TGAATGTTGATTTTC
1 TTGTTTAAGAGCGTAGTATATATACTTCTCTAT-AATGTTGATTTTC
* * *
321240 TTGTTTAAGAGTGTAGTATATGTACTTTTCTATAATGTTGATTTT
1 TTGTTTAAGAGCGTAGTATATATACTTCTCTATAATGTTGATTTT
321285 TTTTTGTTAC
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
46 39 0.98
47 1 0.03
ACGTcount: A:0.24, C:0.08, G:0.16, T:0.52
Consensus pattern (46 bp):
TTGTTTAAGAGCGTAGTATATATACTTCTCTATAATGTTGATTTTC
Found at i:328066 original size:20 final size:20
Alignment explanation
Indices: 328031--328079 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
328021 TTTGAAAACC
* *
328031 ATTTTGA-TTTGTTAAAATG
1 ATTTTGACTTAGTTAAAATA
328050 ATTTTGACTTAGTTAAAATA
1 ATTTTGACTTAGTTAAAATA
*
328070 ATTTTAACTT
1 ATTTTGACTT
328080 TATTTTAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 7 0.27
20 19 0.73
ACGTcount: A:0.35, C:0.04, G:0.10, T:0.51
Consensus pattern (20 bp):
ATTTTGACTTAGTTAAAATA
Found at i:328197 original size:22 final size:24
Alignment explanation
Indices: 328172--328215 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
328162 AATTTTGTCA
*
328172 ATTTTAATTT-TTAT-TCAAAAAT
1 ATTTCAATTTATTATATCAAAAAT
328194 ATTTCAATTTATTATATCAAAA
1 ATTTCAATTTATTATATCAAAA
328216 TCTTTTATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 9 0.47
23 4 0.21
24 6 0.32
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (24 bp):
ATTTCAATTTATTATATCAAAAAT
Found at i:329053 original size:26 final size:26
Alignment explanation
Indices: 329010--329059 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
329000 TTTATTAGGG
* *
329010 TTTAGGTTTTTAATATTAGGGTTTAT
1 TTTAGGATTTTAAGATTAGGGTTTAT
* *
329036 TTTAGGATTTTAGGATTATGGTTT
1 TTTAGGATTTTAAGATTAGGGTTT
329060 TCGATTTGAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.22, C:0.00, G:0.22, T:0.56
Consensus pattern (26 bp):
TTTAGGATTTTAAGATTAGGGTTTAT
Found at i:351119 original size:20 final size:21
Alignment explanation
Indices: 351082--351120 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
351072 AATCAAACAA
* *
351082 TAATTAAAAATTTGTAAAAAT
1 TAATTAAAAATGTATAAAAAT
351103 TAATT-AAAATGTATAAAA
1 TAATTAAAAATGTATAAAA
351121 TAACACTACA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (21 bp):
TAATTAAAAATGTATAAAAAT
Found at i:354211 original size:87 final size:87
Alignment explanation
Indices: 354065--354246 Score: 276
Period size: 87 Copynumber: 2.1 Consensus size: 87
354055 TGTATCTTAT
* * *
354065 TGTCAACCATTGTCACAATAGCGAGAAGTTCTTATACCATAAACCATATTGTCAACCAATATAAT
1 TGTCAATCATTGTCACAATAGCGAGAAGTTCTTATACCATAAACCATATTATCAACCAATACAAT
*
354130 GCAAACAAAAACAAAAATATAA
66 GCAAACAAAAACAAAAACATAA
* * **
354152 TGTCAATCATTGTCACAATAGCGAGAAGTT-TCTATACCATAAATCATATTATCAACCAATGCGG
1 TGTCAATCATTGTCACAATAGCGAGAAGTTCT-TATACCATAAACCATATTATCAACCAATACAA
354216 TGCAAACAAAAACAAAAACATAA
65 TGCAAACAAAAACAAAAACATAA
354239 TGTCAATC
1 TGTCAATC
354247 GTAGACATTA
Statistics
Matches: 86, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
86 1 0.01
87 85 0.99
ACGTcount: A:0.45, C:0.20, G:0.10, T:0.25
Consensus pattern (87 bp):
TGTCAATCATTGTCACAATAGCGAGAAGTTCTTATACCATAAACCATATTATCAACCAATACAAT
GCAAACAAAAACAAAAACATAA
Found at i:354270 original size:87 final size:87
Alignment explanation
Indices: 354078--354270 Score: 228
Period size: 87 Copynumber: 2.2 Consensus size: 87
354068 CAACCATTGT
* * *
354078 CACAATAGCGAGAAG-TTCTTATACCATAAACCATATTGTCAACCAATATAATGCAAACAAAAAC
1 CACAATAGCGAAAAGTTTC-TATACCATAAACCATATTATCAACCAATACAATGCAAACAAAAAC
* * *
354142 AAAAATATAATGTCAATCATTGT
65 AAAAACATAATGTCAATCATAGA
* * * **
354165 CACAATAGCGAGAAGTTTCTATACCATAAATCATATTATCAACCAATGCGGTGCAAACAAAAACA
1 CACAATAGCGAAAAGTTTCTATACCATAAACCATATTATCAACCAATACAATGCAAACAAAAACA
*
354230 AAAACATAATGTCAATCGTAGA
66 AAAACATAATGTCAATCATAGA
**
354252 CATTATAGC-AAAAGGTTTC
1 CACAATAGCGAAAA-GTTTC
354271 CATGAAAAAT
Statistics
Matches: 91, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
86 3 0.03
87 85 0.93
88 3 0.03
ACGTcount: A:0.46, C:0.19, G:0.11, T:0.24
Consensus pattern (87 bp):
CACAATAGCGAAAAGTTTCTATACCATAAACCATATTATCAACCAATACAATGCAAACAAAAACA
AAAACATAATGTCAATCATAGA
Found at i:361082 original size:17 final size:17
Alignment explanation
Indices: 361060--361098 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
361050 AGGTGGAGAA
* *
361060 CTTGTTCGTCGAGATTT
1 CTTGTTCGTAGAGAATT
361077 CTTGTTCGTAGAGAATT
1 CTTGTTCGTAGAGAATT
361094 CTTGT
1 CTTGT
361099 CAAGGTGGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.15, C:0.15, G:0.23, T:0.46
Consensus pattern (17 bp):
CTTGTTCGTAGAGAATT
Found at i:363455 original size:78 final size:78
Alignment explanation
Indices: 363367--363520 Score: 220
Period size: 78 Copynumber: 2.0 Consensus size: 78
363357 CGAATTAACA
** * *
363367 CTTAATATTAAAATTTTAAAAATCTAAACTTGAA-AGATCTAATTTAAAACCTAATATCAAAACC
1 CTTAATATTAAAATACTAAAAATCTAAAATCGAACA-ATCTAATTTAAAACCTAATATCAAAACC
*
363431 TAAAATCTAAAAAG
65 CAAAATCTAAAAAG
* *
363445 CTTAATATTAAAATACTAAAAATCTAAAATCGAACAATTTAATTTAGAACCTAATATCAAAACCC
1 CTTAATATTAAAATACTAAAAATCTAAAATCGAACAATCTAATTTAAAACCTAATATCAAAACCC
*
363510 AAAATTTAAAA
66 AAAATCTAAAA
363521 TTTAAAAAGT
Statistics
Matches: 67, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
78 66 0.99
79 1 0.01
ACGTcount: A:0.53, C:0.14, G:0.03, T:0.30
Consensus pattern (78 bp):
CTTAATATTAAAATACTAAAAATCTAAAATCGAACAATCTAATTTAAAACCTAATATCAAAACCC
AAAATCTAAAAAG
Found at i:363656 original size:20 final size:19
Alignment explanation
Indices: 363633--363691 Score: 61
Period size: 20 Copynumber: 3.2 Consensus size: 19
363623 AAGACTAATT
363633 TAAAATATAATATTAAAATC
1 TAAAATATAAT-TTAAAATC
363653 T-AAA-A-AATTTAAAATC
1 TAAAATATAATTTAAAATC
* *
363669 GAAAGATCTAATTTAAAATC
1 TAAA-ATATAATTTAAAATC
363689 TAA
1 TAA
363692 TATCAAAACC
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
16 8 0.25
17 5 0.16
18 2 0.06
19 3 0.09
20 14 0.44
ACGTcount: A:0.58, C:0.07, G:0.03, T:0.32
Consensus pattern (19 bp):
TAAAATATAATTTAAAATC
Found at i:363659 original size:96 final size:95
Alignment explanation
Indices: 363446--363706 Score: 355
Period size: 96 Copynumber: 2.7 Consensus size: 95
363436 TCTAAAAAGC
*
363446 TTAATATTAAAATACTAAAAATCTAAAATCGAACAATTTAATTTAGAACCTAATATCAAAACCCA
1 TTAATATTAAAAT-CTAAAAATCTAAAATCGAA-AATTTAATTTAAAACCTAATATCAAAACCCA
* * * *
363511 AAATTTAAAATTTAAAAAGTCTAATTTGAAAC
64 AAATCTAAAATATAAAAAGACTAATTTGAAAA
*
363543 TTAATATTAAAATCTTAAAAATCTAAAATTGAAAATTTAAATTTAAAACCTAATATCAAAACCCA
1 TTAATATTAAAATC-TAAAAATCTAAAATCGAAAATTT-AATTTAAAACCTAATATCAAAACCCA
363608 AAATCTAAAATAT-AAAAGACTAATTT-AAAA
64 AAATCTAAAATATAAAAAGACTAATTTGAAAA
* * * *
363638 TATAATATTAAAATCTAAAAAATTTAAAATCGAAAGATCTAATTTAAAATCTAATATCAAAACCT
1 T-TAATATTAAAATCT-AAAAATCTAAAATCGAAA-ATTTAATTTAAAACCTAATATCAAAACCC
363703 AAAA
63 AAAA
363707 AAACTTAATA
Statistics
Matches: 148, Mismatches: 11, Indels: 11
0.87 0.06 0.06
Matches are distributed among these distances:
95 5 0.03
96 74 0.50
97 69 0.47
ACGTcount: A:0.55, C:0.11, G:0.03, T:0.31
Consensus pattern (95 bp):
TTAATATTAAAATCTAAAAATCTAAAATCGAAAATTTAATTTAAAACCTAATATCAAAACCCAAA
ATCTAAAATATAAAAAGACTAATTTGAAAA
Found at i:363666 original size:49 final size:49
Alignment explanation
Indices: 363484--363708 Score: 160
Period size: 49 Copynumber: 4.7 Consensus size: 49
363474 TCGAACAATT
* * ** * *
363484 TAATTTAGAACCTAATATCAAAA-C-CCAAAATTTAAAATTTAAAAAGTC
1 TAATTTAAAATCTAATATCAAAATCTAAAAAATCTAAAA-TTAAAAAGAC
* * * * **
363532 TAATTTGAAA-CTTAATATTAAAATCTTAAAAATCTAAAATTGAAAA-TT
1 TAATTTAAAATC-TAATATCAAAATCTAAAAAATCTAAAATTAAAAAGAC
* **
363580 TAAATTTAAAACCTAATATCAAAA-C-CCAAAATCTAAAA-TATAAAAGAC
1 T-AATTTAAAATCTAATATCAAAATCTAAAAAATCTAAAATTA-AAAAGAC
* * * **
363628 TAATTTAAAATATAATATTAAAATCTAAAAAATTTAAAA-TCGAAAGATC
1 TAATTTAAAATCTAATATCAAAATCTAAAAAATCTAAAATTAAAAAGA-C
*
363677 TAATTTAAAATCTAATATCAAAACCTAAAAAA
1 TAATTTAAAATCTAATATCAAAATCTAAAAAA
363709 ACTTAATATT
Statistics
Matches: 141, Mismatches: 26, Indels: 19
0.76 0.14 0.10
Matches are distributed among these distances:
46 1 0.01
47 35 0.25
48 28 0.20
49 66 0.47
50 11 0.08
ACGTcount: A:0.56, C:0.11, G:0.03, T:0.30
Consensus pattern (49 bp):
TAATTTAAAATCTAATATCAAAATCTAAAAAATCTAAAATTAAAAAGAC
Found at i:363772 original size:71 final size:72
Alignment explanation
Indices: 363640--363777 Score: 201
Period size: 72 Copynumber: 1.9 Consensus size: 72
363630 ATTTAAAATA
* *
363640 TAATATTAAAATCTAAAAAATTTAAAATCGAAAGATCTAATTTAAAATCTAATATCAAAACCTAA
1 TAATATTAAAATCTAAAAAATCTAAAATCCAAAGATCTAATTTAAAATCTAATATCAAAACCTAA
363705 AAAAACT
66 AAAAACT
* *
363712 TAATATTAAAGTCTTAAAAATCTAAAATCCACAA-AT-TAATTTAAAA-CATAATATCAAAACCT
1 TAATATTAAAATCTAAAAAATCTAAAATCCA-AAGATCTAATTTAAAATC-TAATATCAAAACCT
363774 AAAA
64 AAAA
363778 TAAAAAATCT
Statistics
Matches: 60, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
70 1 0.02
71 28 0.47
72 29 0.48
73 2 0.03
ACGTcount: A:0.57, C:0.12, G:0.02, T:0.29
Consensus pattern (72 bp):
TAATATTAAAATCTAAAAAATCTAAAATCCAAAGATCTAATTTAAAATCTAATATCAAAACCTAA
AAAAACT
Found at i:364324 original size:21 final size:20
Alignment explanation
Indices: 364298--364339 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
364288 CCAATTTTAT
364298 ATTTAAAAAAGAAAATAAAAA
1 ATTT-AAAAAGAAAATAAAAA
**
364319 ATTTAATTAGAAAATAAAAA
1 ATTTAAAAAGAAAATAAAAA
364339 A
1 A
364340 AAAACATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (20 bp):
ATTTAAAAAGAAAATAAAAA
Found at i:364577 original size:26 final size:23
Alignment explanation
Indices: 364519--364579 Score: 61
Period size: 26 Copynumber: 2.5 Consensus size: 23
364509 GCATAAAAAT
*
364519 AAAATAAAAATATTAACTTATAA
1 AAAATAAAAATATTAAATTATAA
*
364542 AAGAA-CAAAATGATTAAAAATTATAA
1 AA-AATAAAAAT-ATT--AAATTATAA
364568 AAAATAAAAATA
1 AAAATAAAAATA
364580 GTTATTTATG
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
23 7 0.23
24 5 0.17
25 3 0.10
26 15 0.50
ACGTcount: A:0.69, C:0.03, G:0.03, T:0.25
Consensus pattern (23 bp):
AAAATAAAAATATTAAATTATAA
Found at i:365207 original size:60 final size:62
Alignment explanation
Indices: 365115--365242 Score: 192
Period size: 60 Copynumber: 2.1 Consensus size: 62
365105 CAAAAAATAT
* *
365115 TTTAAT-ATAATTATATTAAGAATATCATTAAATTATATATTATTA-TTTTATTAAATTATA
1 TTTAATAATAATTATATTAAGAATATCATTAAATCATATATTATCATTTTTATTAAATTATA
* *
365175 TTTAATAATAATTATATTAA-AATATGATTAAATCATTTATTATCATTTTTATTAAATTATA
1 TTTAATAATAATTATATTAAGAATATCATTAAATCATATATTATCATTTTTATTAAATTATA
365236 -TTAATAA
1 TTTAATAA
365243 CAATAACAAT
Statistics
Matches: 62, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
60 34 0.55
61 28 0.45
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (62 bp):
TTTAATAATAATTATATTAAGAATATCATTAAATCATATATTATCATTTTTATTAAATTATA
Found at i:369469 original size:13 final size:14
Alignment explanation
Indices: 369441--369469 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
369431 AAAAACTTAG
369441 TAAACAAAAGAATA
1 TAAACAAAAGAATA
369455 TAAACAAAA-AATA
1 TAAACAAAAGAATA
369468 TA
1 TA
369470 TAAAACTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.72, C:0.07, G:0.03, T:0.17
Consensus pattern (14 bp):
TAAACAAAAGAATA
Found at i:370068 original size:13 final size:13
Alignment explanation
Indices: 370023--370068 Score: 53
Period size: 12 Copynumber: 3.7 Consensus size: 13
370013 AATATCGAAA
*
370023 AAAATAT-TATTT
1 AAAATATATAATT
370035 AAAATA-ATAATT
1 AAAATATATAATT
370047 AATAA-ATATAATT
1 AA-AATATATAATT
370060 AAAATATAT
1 AAAATATAT
370069 CAATCATTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
12 15 0.52
13 14 0.48
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (13 bp):
AAAATATATAATT
Found at i:371406 original size:22 final size:23
Alignment explanation
Indices: 371381--371424 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
371371 CATTTGTGTG
* *
371381 AAAATTTCAATATATAA-ATAGT
1 AAAATTACAATAAATAATATAGT
371403 AAAATTACAATAAATAATATAG
1 AAAATTACAATAAATAATATAG
371425 CATATAGTCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.59, C:0.05, G:0.05, T:0.32
Consensus pattern (23 bp):
AAAATTACAATAAATAATATAGT
Found at i:371815 original size:35 final size:35
Alignment explanation
Indices: 371776--371842 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
371766 TTTTTTTAAT
*
371776 GTTGCTTTAGACGTG-TCTGTCCCAACCTTTTTCGG
1 GTTGCTTTAGACG-GATCTATCCCAACCTTTTTCGG
*
371811 GTTGCTTTAGACGGATCTATCCTAACCTTTTT
1 GTTGCTTTAGACGGATCTATCCCAACCTTTTT
371843 AAAGTAGTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 1 0.03
35 28 0.97
ACGTcount: A:0.15, C:0.24, G:0.19, T:0.42
Consensus pattern (35 bp):
GTTGCTTTAGACGGATCTATCCCAACCTTTTTCGG
Found at i:375189 original size:17 final size:17
Alignment explanation
Indices: 375158--375195 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
375148 TTGAGCAAAC
375158 TTTTCTCTGCTC-TTTG
1 TTTTCTCTGCTCTTTTG
*
375174 TTTTCTTCTTCTCTTTTG
1 TTTTC-TCTGCTCTTTTG
375192 TTTT
1 TTTT
375196 TATTCGAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 5 0.26
17 6 0.32
18 8 0.42
ACGTcount: A:0.00, C:0.21, G:0.08, T:0.71
Consensus pattern (17 bp):
TTTTCTCTGCTCTTTTG
Found at i:376390 original size:50 final size:50
Alignment explanation
Indices: 376279--376377 Score: 180
Period size: 50 Copynumber: 2.0 Consensus size: 50
376269 ATCACAATTT
376279 ATACAATTACAAACTTGCAACTCAGAATACTAACTCCATTTAATCTTCAA
1 ATACAATTACAAACTTGCAACTCAGAATACTAACTCCATTTAATCTTCAA
* *
376329 ATACAATTACAAACTTGCAACTCAGAATACTAATTCCATTTAATGTTCA
1 ATACAATTACAAACTTGCAACTCAGAATACTAACTCCATTTAATCTTCA
376378 CATTCATTTA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 47 1.00
ACGTcount: A:0.41, C:0.22, G:0.05, T:0.31
Consensus pattern (50 bp):
ATACAATTACAAACTTGCAACTCAGAATACTAACTCCATTTAATCTTCAA
Found at i:377945 original size:92 final size:92
Alignment explanation
Indices: 377745--377987 Score: 240
Period size: 92 Copynumber: 2.6 Consensus size: 92
377735 AAATTATCTT
* * * * ** * * * **
377745 TGTTACTAGTATACGATGCTGCTCACACTAAGTTGATAAGAACATGCAACATATGCG-GCACCTT
1 TGTTACTAGCATACGATGCTACTCACACTAAGCTAACGAGGACACGCAACATATGCGTTCACAGT
* * *
377809 AACCATCGATATGGTATCTGTACATATAAT
66 -A--ATCGATACGGTATCTATACATATAAC
* * * * *
377839 TGTTACTAGTATACGATGCTACTTATACTAAGCTGACGAGGACTA-GCAATATATGCGTTCACAG
1 TGTTACTAGCATACGATGCTACTCACACTAAGCTAACGAGGAC-ACGCAACATATGCGTTCACAG
377903 TAATCGATACGGTATCTATACATATAAC
65 TAATCGATACGGTATCTATACATATAAC
*
377931 TGTTACCT-GCATACGATGCTGCTCACACTAAGCTAACGAGGACACGCAACATATGCG
1 TGTTA-CTAGCATACGATGCTACTCACACTAAGCTAACGAGGACACGCAACATATGCG
377988 GTACCTTAGC
Statistics
Matches: 125, Mismatches: 20, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
91 1 0.01
92 69 0.55
93 2 0.02
94 48 0.38
95 5 0.04
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.28
Consensus pattern (92 bp):
TGTTACTAGCATACGATGCTACTCACACTAAGCTAACGAGGACACGCAACATATGCGTTCACAGT
AATCGATACGGTATCTATACATATAAC
Found at i:380844 original size:2 final size:2
Alignment explanation
Indices: 380837--380863 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
380827 AGTAGTCAAT
380837 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
380864 CGCTTTCAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:382277 original size:31 final size:31
Alignment explanation
Indices: 382239--382300 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
382229 TCTACCAATA
382239 CTTGTTGGAAAAGTATCAGTAGAAGTCAAGT
1 CTTGTTGGAAAAGTATCAGTAGAAGTCAAGT
*
382270 CTTGTTGGAAAAGTATCGGTAGAAGTCAAGT
1 CTTGTTGGAAAAGTATCAGTAGAAGTCAAGT
382301 AAGTAAACAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.34, C:0.10, G:0.27, T:0.29
Consensus pattern (31 bp):
CTTGTTGGAAAAGTATCAGTAGAAGTCAAGT
Found at i:383412 original size:94 final size:94
Alignment explanation
Indices: 383149--383396 Score: 354
Period size: 94 Copynumber: 2.6 Consensus size: 94
383139 AAATTATATT
* * *
383149 TATTACCAGTATACGATGCTGCTCACACTAAGTTGATGAGGACTCACAACATATGCCGTACCTCA
1 TATTACCAGTATACGATGCTGCTCATACTAAGTTGACGAGGACTCACAACATATGTCGTACCTCA
* *
383214 GCAATCGATACAGTATTTGTACATATAAC
66 GCCATCGATACAGTATTTGCACATATAAC
* * * *
383243 TATGACCAATATACGATGCTGCTCATACTAAGTTGACGAGGACTCGCAACATATGTGGTACCTCA
1 TATTACCAGTATACGATGCTGCTCATACTAAGTTGACGAGGACTCACAACATATGTCGTACCTCA
383308 GCCATCGATACAGTATTTGCACATATAAC
66 GCCATCGATACAGTATTTGCACATATAAC
* * * * *
383337 TGTTACCAGTATACAATGTTG-TGCATACTAAGCTGACGTGGACTCACAACATATGTCGTA
1 TATTACCAGTATACGATGCTGCT-CATACTAAGTTGACGAGGACTCACAACATATGTCGTA
383397 TACCTACCTT
Statistics
Matches: 135, Mismatches: 18, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
93 1 0.01
94 134 0.99
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.28
Consensus pattern (94 bp):
TATTACCAGTATACGATGCTGCTCATACTAAGTTGACGAGGACTCACAACATATGTCGTACCTCA
GCCATCGATACAGTATTTGCACATATAAC
Found at i:390262 original size:16 final size:16
Alignment explanation
Indices: 390241--390272 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
390231 AGCATGCAAT
390241 CATGCTAAAATCAAGC
1 CATGCTAAAATCAAGC
*
390257 CATGCTTAAATCAAGC
1 CATGCTAAAATCAAGC
390273 AACGACTTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.25, G:0.12, T:0.22
Consensus pattern (16 bp):
CATGCTAAAATCAAGC
Found at i:390556 original size:18 final size:18
Alignment explanation
Indices: 390530--390564 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
390520 TTATCGTCCA
*
390530 ATGTGCATGAAATAATTC
1 ATGTCCATGAAATAATTC
390548 ATGTCCATGAAATAATT
1 ATGTCCATGAAATAATT
390565 TATATCATGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.40, C:0.11, G:0.14, T:0.34
Consensus pattern (18 bp):
ATGTCCATGAAATAATTC
Found at i:391841 original size:23 final size:23
Alignment explanation
Indices: 391822--392280 Score: 603
Period size: 23 Copynumber: 20.0 Consensus size: 23
391812 TCCATTTACA
391822 CATAAATCACATTAATATTTAAG
1 CATAAATCACATTAATATTTAAG
*
391845 CATAAATCACATTAACATTTAAG
1 CATAAATCACATTAATATTTAAG
391868 CATAAATCACATTAATATTTAAG
1 CATAAATCACATTAATATTTAAG
* * *
391891 TACAAATTACATTAATATTTAAG
1 CATAAATCACATTAATATTTAAG
*
391914 TATAAATCACATTAATATTTAAG
1 CATAAATCACATTAATATTTAAG
* * *
391937 CACAAATCACATGAATATTTAAA
1 CATAAATCACATTAATATTTAAG
* *
391960 CACAAATCATATTAATATTTAAG
1 CATAAATCACATTAATATTTAAG
* *
391983 CACAAATCACATGAATATTTAAG
1 CATAAATCACATTAATATTTAAG
* *
392006 CATAAATCTCATTAATATTTAAT
1 CATAAATCACATTAATATTTAAG
* *
392029 CACAAATCACATTAATATTGAAG
1 CATAAATCACATTAATATTTAAG
* *
392052 CATAAATAACATTAATTTTTAAG
1 CATAAATCACATTAATATTTAAG
* *
392075 CATAAATCATATTAACATTTAAG
1 CATAAATCACATTAATATTTAAG
392098 CATAAATCACATTAATATTTAAG
1 CATAAATCACATTAATATTTAAG
* * * *
392121 TACAAATTACATTGATATTTAAG
1 CATAAATCACATTAATATTTAAG
*
392144 CATAAATCACGTTAATATTTAAG
1 CATAAATCACATTAATATTTAAG
* ** *
392167 CACAAAAAACTTTAATATTTAAG
1 CATAAATCACATTAATATTTAAG
* *
392190 CACAAATCACATTAATATTTAAA
1 CATAAATCACATTAATATTTAAG
*
392213 CACAAATCACATTAATATTTAAG
1 CATAAATCACATTAATATTTAAG
* *
392236 CATAAATCATATTAACATTTAAG
1 CATAAATCACATTAATATTTAAG
*
392259 CATAAATCACAGTAATATTTAA
1 CATAAATCACATTAATATTTAA
392281 CACAATTAAT
Statistics
Matches: 378, Mismatches: 58, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 378 1.00
ACGTcount: A:0.48, C:0.14, G:0.05, T:0.34
Consensus pattern (23 bp):
CATAAATCACATTAATATTTAAG
Found at i:392735 original size:36 final size:36
Alignment explanation
Indices: 392683--392933 Score: 290
Period size: 36 Copynumber: 7.0 Consensus size: 36
392673 ATATTCATTA
* ** *
392683 TCACATGGAATGAATAACATATTCACATATTTATTG
1 TCACATGGCATGAATAACATACCCACATATTTACTG
** * *
392719 TCTTATGGCATAAATAACATACCCACATATTTACTA
1 TCACATGGCATGAATAACATACCCACATATTTACTG
* * *
392755 TCACATGGCATGAATAATATACCGACATATTAACTG
1 TCACATGGCATGAATAACATACCCACATATTTACTG
* * *
392791 TCATATGACATGAATAACATACCCACATAATTACTG
1 TCACATGGCATGAATAACATACCCACATATTTACTG
* *
392827 TCTCATGGCATGAATAATATACCCACATA-TTAGCTG
1 TCACATGGCATGAATAACATACCCACATATTTA-CTG
*
392863 TCACATGACATGAATAACATACCCACATATTTACTG
1 TCACATGGCATGAATAACATACCCACATATTTACTG
* * *
392899 TCTCATGGCATGAATAACGTACTCACA-AGTTTACT
1 TCACATGGCATGAATAACATACCCACATA-TTTACT
392934 TTCGCAACAA
Statistics
Matches: 180, Mismatches: 32, Indels: 6
0.83 0.15 0.03
Matches are distributed among these distances:
35 4 0.02
36 173 0.96
37 3 0.02
ACGTcount: A:0.37, C:0.21, G:0.11, T:0.31
Consensus pattern (36 bp):
TCACATGGCATGAATAACATACCCACATATTTACTG
Found at i:398568 original size:13 final size:14
Alignment explanation
Indices: 398530--398568 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
398520 TCTTGGGATA
*
398530 ATTTTTAATAATATT
1 ATTTTTAGT-ATATT
398545 ATTTTTAGTATATT
1 ATTTTTAGTATATT
398559 ATTTTT-GTAT
1 ATTTTTAGTAT
398569 TTTAAAATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 4 0.17
14 11 0.48
15 8 0.35
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (14 bp):
ATTTTTAGTATATT
Found at i:399032 original size:21 final size:23
Alignment explanation
Indices: 398989--399037 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
398979 AATAACAATT
*
398989 TTTTATAAATATATTTATTTATA
1 TTTTATAAAAATATTTATTTATA
399012 TTTTATAAAAATA-TT-TTTATA
1 TTTTATAAAAATATTTATTTATA
399033 TTTTA
1 TTTTA
399038 ATTTTTTTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 11 0.44
22 2 0.08
23 12 0.48
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (23 bp):
TTTTATAAAAATATTTATTTATA
Found at i:404920 original size:14 final size:14
Alignment explanation
Indices: 404901--404929 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
404891 ATTGATTGAT
404901 TAGGAGACTAACAA
1 TAGGAGACTAACAA
404915 TAGGAGACTAACAA
1 TAGGAGACTAACAA
404929 T
1 T
404930 TGGAAGGAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.48, C:0.14, G:0.21, T:0.17
Consensus pattern (14 bp):
TAGGAGACTAACAA
Found at i:410308 original size:41 final size:41
Alignment explanation
Indices: 410263--410344 Score: 146
Period size: 41 Copynumber: 2.0 Consensus size: 41
410253 GATTAATTTA
*
410263 AAATCCACATTTAGGTAGCATGAAAAAAATTAAAGTAAATT
1 AAATCCACATTTAGGTAGCATAAAAAAAATTAAAGTAAATT
*
410304 AAATCCATATTTAGGTAGCATAAAAAAAATTAAAGTAAATT
1 AAATCCACATTTAGGTAGCATAAAAAAAATTAAAGTAAATT
410345 TATTTTATTA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.52, C:0.09, G:0.11, T:0.28
Consensus pattern (41 bp):
AAATCCACATTTAGGTAGCATAAAAAAAATTAAAGTAAATT
Found at i:410356 original size:19 final size:20
Alignment explanation
Indices: 410332--410371 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
410322 CATAAAAAAA
410332 ATTAAAGTAAATTTAT-TTT
1 ATTAAAGTAAATTTATATTT
* *
410351 ATTAAATTTAATTTATATTT
1 ATTAAAGTAAATTTATATTT
410371 A
1 A
410372 AATGATTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (20 bp):
ATTAAAGTAAATTTATATTT
Found at i:411238 original size:29 final size:29
Alignment explanation
Indices: 411196--411258 Score: 126
Period size: 29 Copynumber: 2.2 Consensus size: 29
411186 TAATGCGGAG
411196 AAGTGATGAATACTCGGTTGATAAAGGTT
1 AAGTGATGAATACTCGGTTGATAAAGGTT
411225 AAGTGATGAATACTCGGTTGATAAAGGTT
1 AAGTGATGAATACTCGGTTGATAAAGGTT
411254 AAGTG
1 AAGTG
411259 TGGATTCTGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.35, C:0.06, G:0.29, T:0.30
Consensus pattern (29 bp):
AAGTGATGAATACTCGGTTGATAAAGGTT
Found at i:429861 original size:6 final size:6
Alignment explanation
Indices: 429850--429874 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
429840 TTGAACTTTG
429850 CATGCT CATGCT CATGCT CATGCT C
1 CATGCT CATGCT CATGCT CATGCT C
429875 TTTTTCTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.36, G:0.16, T:0.32
Consensus pattern (6 bp):
CATGCT
Found at i:431264 original size:18 final size:18
Alignment explanation
Indices: 431243--431301 Score: 82
Period size: 18 Copynumber: 3.3 Consensus size: 18
431233 CTCCACAGGA
* *
431243 TCTTCCTCAGGATCTTCT
1 TCTTCCTTAGGATCATCT
*
431261 TCTTCCTTAGGATCCTCT
1 TCTTCCTTAGGATCATCT
*
431279 TCTTCTTTAGGATCATCT
1 TCTTCCTTAGGATCATCT
431297 TCTTC
1 TCTTC
431302 TTCTTTAGCT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 37 1.00
ACGTcount: A:0.12, C:0.31, G:0.10, T:0.47
Consensus pattern (18 bp):
TCTTCCTTAGGATCATCT
Found at i:431307 original size:21 final size:21
Alignment explanation
Indices: 431254--431309 Score: 82
Period size: 18 Copynumber: 2.8 Consensus size: 21
431244 CTTCCTCAGG
*
431254 ATCTTCTTCTTCCTTAGGATC
1 ATCTTCTTCTTCTTTAGGATC
431275 --C-TCTTCTTCTTTAGGATC
1 ATCTTCTTCTTCTTTAGGATC
431293 ATCTTCTTCTTCTTTAG
1 ATCTTCTTCTTCTTTAG
431310 CTTGCTGTTG
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
18 16 0.52
19 1 0.03
20 1 0.03
21 13 0.42
ACGTcount: A:0.12, C:0.27, G:0.09, T:0.52
Consensus pattern (21 bp):
ATCTTCTTCTTCTTTAGGATC
Found at i:437354 original size:154 final size:154
Alignment explanation
Indices: 437001--437472 Score: 678
Period size: 154 Copynumber: 3.0 Consensus size: 154
436991 TGGTGGAGGA
* *
437001 TTTCTAACTTGAACTGACTGCTTCATTTTTTGTGCCACTTCTACATCTAAAGAAGTTGTTAGATC
1 TTTCTAACTTGAACTGGCTGCTTCATTTTTTGTGGCACTTCTACATCTAAAGAAGTTGTTAGATC
* * *
437066 ATCAGACTTGA-TTGGTTTTGAAGTCTCTTTCTCAACATTCATCGGTTTTGTTTCTGGTAAAACT
66 ATCAAACTTGACTT-GTTTTGAAGTCTCTTTCTCAACATTCATCGGTTCTGTTTCTGGTGAAAC-
437130 AGTTCTGGTTCTGGTTTTGGCAAAGTTGGAG
129 ---TC--GTTCTGGTTTTGGCAAAGTTGGAG
* *
437161 TTTCTAACTTGAACTAGCTGCTTCATTTTTTGTGGCACTTCTACATCTAAAGAAGTTGTTAGATA
1 TTTCTAACTTGAACTGGCTGCTTCATTTTTTGTGGCACTTCTACATCTAAAGAAGTTGTTAGATC
** * * * * *
437226 ATCTTACTTGACATGTTTTAAAGTCTCTTTCTCAATATTCA-CTGGTTCTATTTCTAGTGAAACT
66 ATCAAACTTGACTTGTTTTGAAGTCTCTTTCTCAACATTCATC-GGTTCTGTTTCTGGTGAAACT
437290 CGTTCTGGTTTTGGCAAAGTTGGAG
130 CGTTCTGGTTTTGGCAAAGTTGGAG
* * *
437315 TTTCTAACTTGAACTGGCTGCTTCATTTTTGGTGGCACTTTTATATCTAAAGAAGTTGTTAGATC
1 TTTCTAACTTGAACTGGCTGCTTCATTTTTTGTGGCACTTCTACATCTAAAGAAGTTGTTAGATC
*
437380 ATCAAACTTGACTTGTTTTGAAGTCTCTTTCTCAACATTCATCGGTTCTGTTTCTGGTGAAACTA
66 ATCAAACTTGACTTGTTTTGAAGTCTCTTTCTCAACATTCATCGGTTCTGTTTCTGGTGAAACTC
* *
437445 GTTCTAGTTCTGGCAAAGTTGGAG
131 GTTCTGGTTTTGGCAAAGTTGGAG
437469 TTTC
1 TTTC
437473 AACACTTGGT
Statistics
Matches: 281, Mismatches: 28, Indels: 12
0.88 0.09 0.04
Matches are distributed among these distances:
154 165 0.59
155 1 0.00
156 2 0.01
159 1 0.00
160 111 0.40
161 1 0.00
ACGTcount: A:0.23, C:0.17, G:0.18, T:0.42
Consensus pattern (154 bp):
TTTCTAACTTGAACTGGCTGCTTCATTTTTTGTGGCACTTCTACATCTAAAGAAGTTGTTAGATC
ATCAAACTTGACTTGTTTTGAAGTCTCTTTCTCAACATTCATCGGTTCTGTTTCTGGTGAAACTC
GTTCTGGTTTTGGCAAAGTTGGAG
Found at i:448567 original size:99 final size:99
Alignment explanation
Indices: 448396--448582 Score: 320
Period size: 99 Copynumber: 1.9 Consensus size: 99
448386 AAATGACTTG
* * *
448396 TTTATAAAGAAAACACAAAGAAAATGGAGGAGAGGAATGTTTTCAGAGAGAGTTGTTTTCTTTCT
1 TTTATAAAGAAAACACAAAGAAAATAGAGGAAAGAAATGTTTTCAGAGAGAGTTGTTTTCTTTCT
*
448461 GTTCAGTGTATAAAATGAGAAAACTAGTCCTCTA
66 GTTCAGTGTATAAAATGAAAAAACTAGTCCTCTA
* *
448495 TTTATAAAGAAAACACATAGAAAATAGAGGAAAGAAATGTTTTCAGAGAGAGTTGTTTTCTTTTT
1 TTTATAAAGAAAACACAAAGAAAATAGAGGAAAGAAATGTTTTCAGAGAGAGTTGTTTTCTTTCT
448560 GTTCAGTGTATAAAATGAAAAAA
66 GTTCAGTGTATAAAATGAAAAAA
448583 AAAACTATTC
Statistics
Matches: 82, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
99 82 1.00
ACGTcount: A:0.41, C:0.08, G:0.20, T:0.31
Consensus pattern (99 bp):
TTTATAAAGAAAACACAAAGAAAATAGAGGAAAGAAATGTTTTCAGAGAGAGTTGTTTTCTTTCT
GTTCAGTGTATAAAATGAAAAAACTAGTCCTCTA
Found at i:449291 original size:87 final size:85
Alignment explanation
Indices: 449139--449305 Score: 262
Period size: 87 Copynumber: 1.9 Consensus size: 85
449129 CTTCTCAAAT
449139 TTAAGTGGTGAATTCATCAAGTACGTCTCAATAGGACCATCCAAAATCTGGGATATGAACTCATT
1 TTAAGTGGTGAATTCATCAAGTACGTCTCAATAGGACCATCCAAAATCTGGGATATGAACTCATT
449204 AAGAGTAATAAACTCAACTTC
66 AAGAGTAA-AAACTCAACTTC
* * * * * *
449225 TTAAGTCGGTGAATTCATCAATTCCGTCTCAATAGTACCATCCAAAATTTGGGCTATGAATTCAT
1 TTAAGT-GGTGAATTCATCAAGTACGTCTCAATAGGACCATCCAAAATCTGGGATATGAACTCAT
449290 TAAGAGTAAAAACTCA
65 TAAGAGTAAAAACTCA
449306 TCCTGATGCA
Statistics
Matches: 74, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
86 13 0.18
87 61 0.82
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.29
Consensus pattern (85 bp):
TTAAGTGGTGAATTCATCAAGTACGTCTCAATAGGACCATCCAAAATCTGGGATATGAACTCATT
AAGAGTAAAAACTCAACTTC
Found at i:461801 original size:16 final size:16
Alignment explanation
Indices: 461755--461802 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 16
461745 CTGAGTCACT
**
461755 TGAAAAAGAAAAATGA
1 TGAAAAAGAAAAAAAA
* *
461771 -GAAAAAGGAAGAAAA
1 TGAAAAAGAAAAAAAA
461786 TGAAAAAGAAAAAAAA
1 TGAAAAAGAAAAAAAA
461802 T
1 T
461803 TTAAATGCTA
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
15 11 0.44
16 14 0.56
ACGTcount: A:0.73, C:0.00, G:0.19, T:0.08
Consensus pattern (16 bp):
TGAAAAAGAAAAAAAA
Found at i:466694 original size:16 final size:16
Alignment explanation
Indices: 466648--466695 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 16
466638 CTGAGTCACT
**
466648 TGAAAAAGAAAAATGA
1 TGAAAAAGAAAAAAAA
* *
466664 -GAAAAAGGAAGAAAA
1 TGAAAAAGAAAAAAAA
466679 TGAAAAAGAAAAAAAA
1 TGAAAAAGAAAAAAAA
466695 T
1 T
466696 TTAAATGCTA
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
15 11 0.44
16 14 0.56
ACGTcount: A:0.73, C:0.00, G:0.19, T:0.08
Consensus pattern (16 bp):
TGAAAAAGAAAAAAAA
Found at i:467790 original size:437 final size:437
Alignment explanation
Indices: 466976--467855 Score: 1566
Period size: 437 Copynumber: 2.0 Consensus size: 437
466966 CTTTCTCCCT
466976 AAATTTGGGTATTAATTGTCTCTTTTGTATCTTATTTTGCATGCATCATAAGTATTTCATACTTA
1 AAATTTGGGTATTAATTGTCTCTTTTGTATCTTATTTTGCATGCATCATAAGTATTTCATACTTA
467041 GTTTTCATATTTTCTAACTCATTACTAGTTGGTTTAAATTCTTGTTATTTTTACCTCTTTTTGTA
66 GTTTTCATATTTTCTAACTCATTACTAGTTGGTTTAAATTCTTGTTATTTTTACCTCTTTTTGTA
* * *
467106 CTAATGTCGTTGCAATCAGCCTACATGTTATGCCTTAGAATTGTCAACGCAGGAACTCATCTCAG
131 CTAATGTCGCTGAAATCAGCCTACATGTTACGCCTTAGAATTGTCAACGCAGGAACTCATCTCAG
467171 AAGATCAATGCTGGAAGAAGAATGCAGCCACAAGTATAGCTTGGAATTACAACTAGAGATGTTGA
196 AAGATCAATGCTGGAAGAAGAATGCAGCCACAAGTATAGCTTGGAATTACAACTAGAGATGTTGA
467236 CGCATTGAAAGCTTTACTTTGTTTGAGTGAATTCAAGCCACAAGCACATATGGAAGCACCAACGC
261 CGCATTGAAAGCTTTACTTTGTTTGAGTGAATTCAAGCCACAAGCACATATGGAAGCACCAACGC
* *
467301 AGGAATTTCACATGTTGTTACCGCAATTAAAGATTTCAGATCTCGACCAGAGATGCGGCGACAAT
326 AGGAATTTCACATGTTGTCACCGCAATTAAAGATTTCAGATCTCGACCAGAGATGCGGCAACAAT
467366 CTGCAGAATTATAAAGATCACACTAGATATGCGTGAGTGCATAGCTA
391 CTGCAGAATTATAAAGATCACACTAGATATGCGTGAGTGCATAGCTA
467413 AAATTTGGGTATTAATTGTCTCTTTTGTATCTTATTTTGCATGCATCATAAGTATTTCATACTTA
1 AAATTTGGGTATTAATTGTCTCTTTTGTATCTTATTTTGCATGCATCATAAGTATTTCATACTTA
* *
467478 GTTTTCATATTTTCTAGCTCATTACTAGTTGGTTTAAAATT-TTTTTATTTTTACCTCTTTTTGT
66 GTTTTCATATTTTCTAACTCATTACTAGTTGGTTT-AAATTCTTGTTATTTTTACCTCTTTTTGT
*
467542 ACTAATGTCGCTGAAATCAGCCTACATGTTGCGCCTTAGAATTGTCAACGCAGGAACTCATCTCA
130 ACTAATGTCGCTGAAATCAGCCTACATGTTACGCCTTAGAATTGTCAACGCAGGAACTCATCTCA
*
467607 GAATATCAATGCTGGAAGAAGAATGCAGCCACAAGTATAGCTTGGAATTACAACTAGAGATGTTG
195 GAAGATCAATGCTGGAAGAAGAATGCAGCCACAAGTATAGCTTGGAATTACAACTAGAGATGTTG
* *
467672 ACGCATTGAAAGCTTTACTTTGTTTGAGTGAATTCAAGCTACAAGCACATTTGGAAGCACCAACG
260 ACGCATTGAAAGCTTTACTTTGTTTGAGTGAATTCAAGCCACAAGCACATATGGAAGCACCAACG
* *
467737 CAGGAATTTCACATGTTGTCACTGTAATTAAAGATTTCAGATCGT-GACCAGAGATGCGGCAACA
325 CAGGAATTTCACATGTTGTCACCGCAATTAAAGATTTCAGATC-TCGACCAGAGATGCGGCAACA
* * * * *
467801 ATCTGTAGTATTATACAGATCACACTAGATATGCGTGAGTGCATAGTTG
389 ATCTGCAGAATTATAAAGATCACACTAGATATGCGTGAGTGCATAGCTA
467850 AAATTT
1 AAATTT
467856 AACTAACTGT
Statistics
Matches: 423, Mismatches: 18, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
437 417 0.99
438 6 0.01
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.34
Consensus pattern (437 bp):
AAATTTGGGTATTAATTGTCTCTTTTGTATCTTATTTTGCATGCATCATAAGTATTTCATACTTA
GTTTTCATATTTTCTAACTCATTACTAGTTGGTTTAAATTCTTGTTATTTTTACCTCTTTTTGTA
CTAATGTCGCTGAAATCAGCCTACATGTTACGCCTTAGAATTGTCAACGCAGGAACTCATCTCAG
AAGATCAATGCTGGAAGAAGAATGCAGCCACAAGTATAGCTTGGAATTACAACTAGAGATGTTGA
CGCATTGAAAGCTTTACTTTGTTTGAGTGAATTCAAGCCACAAGCACATATGGAAGCACCAACGC
AGGAATTTCACATGTTGTCACCGCAATTAAAGATTTCAGATCTCGACCAGAGATGCGGCAACAAT
CTGCAGAATTATAAAGATCACACTAGATATGCGTGAGTGCATAGCTA
Found at i:469295 original size:78 final size:78
Alignment explanation
Indices: 469141--469306 Score: 183
Period size: 78 Copynumber: 2.1 Consensus size: 78
469131 AAGACGATGA
* ** *
469141 AGATACTCTGGATTTCAGCTCGAAAGAGCAATATTTTGTCTCGCTCATAAGTGCGCTATTATGTT
1 AGATACTCTGGATTTCAGCTCGAAAGAGCAATATTTTGTCTCGCTCAAAAAAGCACTATTATGTT
469206 TGTCTCATAAGAG
66 TGTCTCATAAGAG
* * * * * * *
469219 TGATACTCTTGATTCTCA-CTCGAAAGAGCGATATTTTGTTTGGCTCAAAAAAGCATTATTCTGT
1 AGATACTCTGGATT-TCAGCTCGAAAGAGCAATATTTTGTCTCGCTCAAAAAAGCACTATTATGT
*
469283 CTTG-CTCGTAAGAG
65 -TTGTCTCATAAGAG
*
469297 AGATAATCTG
1 AGATACTCTG
469307 TTTGGGCTCG
Statistics
Matches: 71, Mismatches: 15, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
78 65 0.92
79 6 0.08
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (78 bp):
AGATACTCTGGATTTCAGCTCGAAAGAGCAATATTTTGTCTCGCTCAAAAAAGCACTATTATGTT
TGTCTCATAAGAG
Found at i:477004 original size:19 final size:19
Alignment explanation
Indices: 476980--477022 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
476970 AAACATAAAT
476980 TAAATACAAAT-TTAAATAA
1 TAAATA-AAATCTTAAATAA
* *
476999 TAAATAATATCTTAAATAT
1 TAAATAAAATCTTAAATAA
477018 TAAAT
1 TAAAT
477023 CCTAATATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAATAAAATCTTAAATAA
Found at i:478505 original size:13 final size:11
Alignment explanation
Indices: 478486--478543 Score: 53
Period size: 12 Copynumber: 4.7 Consensus size: 11
478476 TTTCCTAGAC
478486 AAAAATAAATAA
1 AAAAATAAA-AA
*
478498 ATAAAATAAGATAG
1 A-AAAATAA-A-AA
478512 AAAAATAAAATA
1 AAAAATAAAA-A
478524 AAAAATAAAAA
1 AAAAATAAAAA
478535 ATAAAATAA
1 A-AAAATAA
478544 TTGGGTTGCC
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
11 3 0.08
12 19 0.47
13 14 0.35
14 4 0.10
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.17
Consensus pattern (11 bp):
AAAAATAAAAA
Found at i:478519 original size:18 final size:17
Alignment explanation
Indices: 478487--478543 Score: 69
Period size: 18 Copynumber: 3.1 Consensus size: 17
478477 TTCCTAGACA
478487 AAAATAAATAAATAAAAT
1 AAAATAAA-AAATAAAAT
*
478505 AAGATAGAAAAATAAAAT
1 AAAATA-AAAAATAAAAT
478523 AAAAAATAAAAAATAAAAT
1 --AAAATAAAAAATAAAAT
478542 AA
1 AA
478544 TTGGGTTGCC
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
17 2 0.06
18 14 0.41
19 13 0.38
20 5 0.15
ACGTcount: A:0.79, C:0.00, G:0.04, T:0.18
Consensus pattern (17 bp):
AAAATAAAAAATAAAAT
Found at i:481314 original size:15 final size:16
Alignment explanation
Indices: 481287--481316 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
481277 TAAAGAAAAA
481287 TAAAAGAAAATAGAAT
1 TAAAAGAAAATAGAAT
481303 TAAAAG-AAATAGAA
1 TAAAAGAAAATAGAA
481317 AATAGGGAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.70, C:0.00, G:0.13, T:0.17
Consensus pattern (16 bp):
TAAAAGAAAATAGAAT
Done.