Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008014.1 Hibiscus syriacus cultivar Beakdansim tig00110480_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: 624021
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 4
Found at i:206882 original size:34 final size:34
Alignment explanation
Indices: 206839--206908 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
206829 GAGATATTAG
206839 AGCGGTCAAATTCTATTTTTCGCCCCGCTCCCTC
1 AGCGGTCAAATTCTATTTTTCGCCCCGCTCCCTC
206873 AGCGGTCAAATTCTATTTTTCGCCCCGCTCCCTC
1 AGCGGTCAAATTCTATTTTTCGCCCCGCTCCCTC
206907 AG
1 AG
206909 ATTTTCCTTC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.16, C:0.37, G:0.16, T:0.31
Consensus pattern (34 bp):
AGCGGTCAAATTCTATTTTTCGCCCCGCTCCCTC
Found at i:211651 original size:212 final size:213
Alignment explanation
Indices: 211258--211681 Score: 625
Period size: 212 Copynumber: 2.0 Consensus size: 213
211248 GTACAAAAGC
* ** *
211258 AAATTAACAAATAAGCAAATCCCAATCTTATTGACTTTTGAACTTTCTCATGCACCAACTAGCAA
1 AAATTAACAAATAAGCAAATCCCAATCTTATGGACTTTCAAACTTTCTCAAGCACCAACTAGCAA
* * * *
211323 TTAGAAAATGGAATTAATTTTCATCAAGGAAGCAACAAAGAGTGCTGACTAATGAGAACAATTTC
66 TTAGAAAATGGAAATAATTTTCATCAAGAAAGCAACAAAGACTGATGACTAATGAGAACAATTTC
* * * * * *
211388 ATTCTTTCAGAACCAAAGAACTAACATATGAATCAACCTATTTGGACAATCTCGGTTCACATTCT
131 ATTCTTTCAGAACCAAAGAACAAACACAGGAATCAACCTATTTGAACAATCTCGATTCACATTCC
*
211453 GGGATCTTTTCACTGGTG
196 GGGATCCTTTCACTGGTG
* *
211471 AAATTAACAAATAAGCAAATCCCACTCTTATGGCCTTTCAAACTTTCTCAAGCACCAACTAGCAA
1 AAATTAACAAATAAGCAAATCCCAATCTTATGGACTTTCAAACTTTCTCAAGCACCAACTAGCAA
*
211536 TTAGAAAATGGAAATAA-TTTCATCAAGAAAGTAACAAAGACTGATGACTAATGAGAACAATTTC
66 TTAGAAAATGGAAATAATTTTCATCAAGAAAGCAACAAAGACTGATGACTAATGAGAACAATTTC
* * * * * *
211600 ATTGTTTCGGAACCGACGAACAAACACCGGAATCAACCTATTTGAACAATCTCGATTCTCATTCC
131 ATTCTTTCAGAACCAAAGAACAAACACAGGAATCAACCTATTTGAACAATCTCGATTCACATTCC
211665 GGGATCCTTTCACTGGT
196 GGGATCCTTTCACTGGT
211682 ATGTTAAAAG
Statistics
Matches: 187, Mismatches: 24, Indels: 1
0.88 0.11 0.00
Matches are distributed among these distances:
212 112 0.60
213 75 0.40
ACGTcount: A:0.38, C:0.21, G:0.14, T:0.28
Consensus pattern (213 bp):
AAATTAACAAATAAGCAAATCCCAATCTTATGGACTTTCAAACTTTCTCAAGCACCAACTAGCAA
TTAGAAAATGGAAATAATTTTCATCAAGAAAGCAACAAAGACTGATGACTAATGAGAACAATTTC
ATTCTTTCAGAACCAAAGAACAAACACAGGAATCAACCTATTTGAACAATCTCGATTCACATTCC
GGGATCCTTTCACTGGTG
Found at i:238644 original size:10 final size:10
Alignment explanation
Indices: 238608--238636 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
238598 TTAATTGGTG
238608 CAATTGTTTC
1 CAATTGTTTC
238618 CAATTGTTTC
1 CAATTGTTTC
238628 CAATTGTTT
1 CAATTGTTT
238637 TCCATTGTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.21, C:0.17, G:0.10, T:0.52
Consensus pattern (10 bp):
CAATTGTTTC
Found at i:240810 original size:36 final size:36
Alignment explanation
Indices: 240763--240834 Score: 108
Period size: 36 Copynumber: 2.0 Consensus size: 36
240753 CATAAGCTCA
*
240763 CTTGAGAGGAACCTGATGAGAAAATCGGAGTCCTTG
1 CTTGAGAGGAACCTGATAAGAAAATCGGAGTCCTTG
* * *
240799 CTTGAGAGGAACTTGATAAGACAATCTGAGTCCTTG
1 CTTGAGAGGAACCTGATAAGAAAATCGGAGTCCTTG
240835 ATACGTAATG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.31, C:0.17, G:0.28, T:0.25
Consensus pattern (36 bp):
CTTGAGAGGAACCTGATAAGAAAATCGGAGTCCTTG
Found at i:241178 original size:37 final size:38
Alignment explanation
Indices: 241149--241223 Score: 100
Period size: 38 Copynumber: 2.0 Consensus size: 38
241139 ATTGTAAAAT
241149 ATTTATAT-A-TTTTCTTTAAAAAATTAAATTTATAAA
1 ATTTATATAATTTTTCTTTAAAAAATTAAATTTATAAA
* * **
241185 ATTTATATAATTTTTTTTTATAAAATTAAAAATATAAA
1 ATTTATATAATTTTTCTTTAAAAAATTAAATTTATAAA
241223 A
1 A
241224 AGATTTAATG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
36 8 0.24
37 1 0.03
38 24 0.73
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (38 bp):
ATTTATATAATTTTTCTTTAAAAAATTAAATTTATAAA
Found at i:249302 original size:19 final size:19
Alignment explanation
Indices: 249278--249314 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
249268 TTTAATAAGG
249278 CTTAAAGTAAAAATAAATC
1 CTTAAAGTAAAAATAAATC
249297 CTTAAAGTAAAAATAAAT
1 CTTAAAGTAAAAATAAAT
249315 ATTTAAACTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.59, C:0.08, G:0.05, T:0.27
Consensus pattern (19 bp):
CTTAAAGTAAAAATAAATC
Found at i:249320 original size:19 final size:19
Alignment explanation
Indices: 249278--249321 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
249268 TTTAATAAGG
*
249278 CTTAAAGTAAAAATAAATC
1 CTTAAAGTAAAAATAAATA
249297 CTTAAAGTAAAAATAAATA
1 CTTAAAGTAAAAATAAATA
*
249316 TTTAAA
1 CTTAAA
249322 CTATGTCTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.59, C:0.07, G:0.05, T:0.30
Consensus pattern (19 bp):
CTTAAAGTAAAAATAAATA
Found at i:249553 original size:20 final size:21
Alignment explanation
Indices: 249530--249570 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
249520 TTAATTTTGA
249530 TAAA-AAATAATTTAACGACT
1 TAAAGAAATAATTTAACGACT
* *
249550 TAAAGAATTAATTTAATGACT
1 TAAAGAAATAATTTAACGACT
249571 AATTTGTCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.51, C:0.07, G:0.07, T:0.34
Consensus pattern (21 bp):
TAAAGAAATAATTTAACGACT
Found at i:258845 original size:31 final size:34
Alignment explanation
Indices: 258786--258853 Score: 106
Period size: 31 Copynumber: 2.1 Consensus size: 34
258776 TATGGATATC
258786 AATTTTTAAAATATGAAAGATAGTGTAATAAATTT
1 AATTTTTAAAATATG-AAGATAGTGTAATAAATTT
258821 AATTTTTAAAATATG-A-A-AGTGTAATAAATTT
1 AATTTTTAAAATATGAAGATAGTGTAATAAATTT
258852 AA
1 AA
258854 ATTTAAGATT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
31 16 0.48
32 1 0.03
33 1 0.03
35 15 0.45
ACGTcount: A:0.50, C:0.00, G:0.10, T:0.40
Consensus pattern (34 bp):
AATTTTTAAAATATGAAGATAGTGTAATAAATTT
Found at i:260904 original size:21 final size:22
Alignment explanation
Indices: 260867--260912 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
260857 ATCCTTAAAA
260867 ATAATTTTTTACTTATATATTTT
1 ATAATTTTTTAC-TATATATTTT
*
260890 ATAATTTTTTA-TATATTTTTT
1 ATAATTTTTTACTATATATTTT
260911 AT
1 AT
260913 TAAAAAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 11 0.50
23 11 0.50
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (22 bp):
ATAATTTTTTACTATATATTTT
Found at i:262430 original size:28 final size:28
Alignment explanation
Indices: 262394--262457 Score: 83
Period size: 28 Copynumber: 2.3 Consensus size: 28
262384 CCGGTTCAAT
* * *
262394 CGGTTCAACCGGGAATTGTTGTTTAATC
1 CGGTTCAACCGGAAATCGTTGCTTAATC
* *
262422 CGGTTCAACCGGAAATCGTTGCTTAGTT
1 CGGTTCAACCGGAAATCGTTGCTTAATC
262450 CGGTTCAA
1 CGGTTCAA
262458 TCTAAATCGG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.22, C:0.20, G:0.25, T:0.33
Consensus pattern (28 bp):
CGGTTCAACCGGAAATCGTTGCTTAATC
Found at i:264777 original size:37 final size:37
Alignment explanation
Indices: 264705--264777 Score: 94
Period size: 37 Copynumber: 2.0 Consensus size: 37
264695 TATATTTTTT
*
264705 ATTTTGTAAAAAAAATTATATAAATATTATGAATTTA
1 ATTTTGTAAAAAAAATTATATAAATATTATCAATTTA
* * *
264742 ATTTTTTAAAGAAAA-TATATAAATATTTTACAATTT
1 ATTTTGTAAAAAAAATTATATAAATATTAT-CAATTT
264778 GTAATATTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
36 13 0.42
37 18 0.58
ACGTcount: A:0.49, C:0.01, G:0.04, T:0.45
Consensus pattern (37 bp):
ATTTTGTAAAAAAAATTATATAAATATTATCAATTTA
Found at i:266982 original size:7 final size:7
Alignment explanation
Indices: 266970--266999 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
266960 TCTCATTAAA
266970 AGTTTTG
1 AGTTTTG
266977 AGTTTTG
1 AGTTTTG
266984 AGTTTTG
1 AGTTTTG
266991 AGTTTTG
1 AGTTTTG
266998 AG
1 AG
267000 AAACTAGTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.17, C:0.00, G:0.30, T:0.53
Consensus pattern (7 bp):
AGTTTTG
Found at i:269265 original size:2 final size:2
Alignment explanation
Indices: 269258--269282 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
269248 AATCCCTTTA
269258 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
269283 ATCAACACTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:270682 original size:46 final size:46
Alignment explanation
Indices: 270615--270774 Score: 160
Period size: 46 Copynumber: 3.7 Consensus size: 46
270605 CTGGGCAGAG
*
270615 GGCC-CCAATCAAAG-TAAAATTAATTTTTATATTTTTTCTGTAGA
1 GGCCTCCAATCAAGGTTAAAATTAATTTTTATATTTTTTCTGTAGA
*
270659 GGCCTCCAATCAAGGTTAAAATT-A----T-TATTTTTTCTTGCCA-A
1 GGCCTCCAATCAAGGTTAAAATTAATTTTTATATTTTTTC-TG-TAGA
* * * * *
270700 GG-GTCCAATCAAGATTAAAATTAATTTTCATATTTTCTCTGTGGA
1 GGCCTCCAATCAAGGTTAAAATTAATTTTTATATTTTTTCTGTAGA
*
270745 GGCCTCCAACCAAGGTTAAAATTAATTTTT
1 GGCCTCCAATCAAGGTTAAAATTAATTTTT
270775 CTTTTTCCTA
Statistics
Matches: 92, Mismatches: 12, Indels: 22
0.73 0.10 0.17
Matches are distributed among these distances:
40 27 0.29
41 7 0.08
42 1 0.01
44 4 0.04
45 15 0.16
46 38 0.41
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.39
Consensus pattern (46 bp):
GGCCTCCAATCAAGGTTAAAATTAATTTTTATATTTTTTCTGTAGA
Found at i:270839 original size:42 final size:43
Alignment explanation
Indices: 270615--270844 Score: 132
Period size: 44 Copynumber: 5.3 Consensus size: 43
270605 CTGGGCAGAG
* * ** *
270615 GGCCCCAATCAAAG-TAAAATTAATTTTTATATTTTTTCTGTAGA
1 GGCCCCAACCAAAGTTAAAATTAA-TTTTCT-TTTTCCCTGTCGA
* * * * * *
270659 GGCCTCCAATCAAGGTTAAAATT-ATTAT-TTTTT-CTTGCCAA
1 GGCC-CCAACCAAAGTTAAAATTAATTTTCTTTTTCCCTGTCGA
** * * *
270700 GGGTCCAATC-AAGATTAAAATTAATTTTCATATTTTCTCTGTGGA
1 GGCCCCAACCAAAG-TTAAAATTAATTTTC-T-TTTTCCCTGTCGA
* * *
270745 GGCCTCCAACCAAGGTTAAAATTAATTTTTCTTTTT-CCTATCGG
1 GGCC-CCAACCAAAGTTAAAATTAA-TTTTCTTTTTCCCTGTCGA
* *
270789 GAGTCCCAACCAAAGTTGAAATTAA-TTTCTTTTTCCCTGTCGA
1 G-GCCCCAACCAAAGTTAAAATTAATTTTCTTTTTCCCTGTCGA
*
270832 GGCCCCAATCAAA
1 GGCCCCAACCAAA
270845 AAAAGTAAAA
Statistics
Matches: 142, Mismatches: 31, Indels: 28
0.71 0.15 0.14
Matches are distributed among these distances:
39 2 0.01
40 14 0.10
41 9 0.06
42 23 0.16
43 9 0.06
44 34 0.24
45 21 0.15
46 23 0.16
47 7 0.05
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.37
Consensus pattern (43 bp):
GGCCCCAACCAAAGTTAAAATTAATTTTCTTTTTCCCTGTCGA
Found at i:271822 original size:20 final size:21
Alignment explanation
Indices: 271797--271845 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
271787 ACTTGAATTT
*
271797 AATTTAAAATTATTTA-TTAA
1 AATTTAAAATTATTCATTTAA
* *
271817 AATTT-AATTTATTCATTTTA
1 AATTTAAAATTATTCATTTAA
271837 AATTTAAAA
1 AATTTAAAA
271846 AACAATTTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
19 8 0.35
20 13 0.57
21 2 0.09
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (21 bp):
AATTTAAAATTATTCATTTAA
Found at i:273384 original size:22 final size:23
Alignment explanation
Indices: 273359--273407 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 23
273349 AAGGTATATT
* *
273359 TATAAATTAGTTAAAATCTAA-A
1 TATAAATTAATTAAAATATAATA
*
273381 TATAATTTAATTAAAATATAATA
1 TATAAATTAATTAAAATATAATA
273404 TATA
1 TATA
273408 TATATATAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (23 bp):
TATAAATTAATTAAAATATAATA
Found at i:278160 original size:63 final size:63
Alignment explanation
Indices: 278088--278215 Score: 231
Period size: 63 Copynumber: 2.0 Consensus size: 63
278078 GTTTATTTAA
278088 TCTATTTATTTACCTATGTGAAGGAAAATAATTGAAGGGAAA-AATATTTGTTGCTGAGTGGAT
1 TCTATTTATTTACCTATGTGAAGGAAAATAATTGAA-GGAAATAATATTTGTTGCTGAGTGGAT
*
278151 TCTATTTATTTACCTATTTGAAGGAAAATAATTGAAGGAAATAATATTTGTTGCTGAGTGGAT
1 TCTATTTATTTACCTATGTGAAGGAAAATAATTGAAGGAAATAATATTTGTTGCTGAGTGGAT
278214 TC
1 TC
278216 GATCCACGGC
Statistics
Matches: 63, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
62 5 0.08
63 58 0.92
ACGTcount: A:0.34, C:0.07, G:0.20, T:0.38
Consensus pattern (63 bp):
TCTATTTATTTACCTATGTGAAGGAAAATAATTGAAGGAAATAATATTTGTTGCTGAGTGGAT
Found at i:278724 original size:15 final size:16
Alignment explanation
Indices: 278695--278726 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
278685 AAAAAGTGTA
278695 TATATTTTTTAAATAT
1 TATATTTTTTAAATAT
278711 TATATTTTTT-AATAT
1 TATATTTTTTAAATAT
278726 T
1 T
278727 TTTTTATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
TATATTTTTTAAATAT
Found at i:280785 original size:61 final size:61
Alignment explanation
Indices: 280717--280833 Score: 225
Period size: 61 Copynumber: 1.9 Consensus size: 61
280707 TTTATCATTA
280717 TATTTTCATTTGGTCATCGTTTTAGTTATTTATTGTCATTATTAAAACAAAATTAACGTTC
1 TATTTTCATTTGGTCATCGTTTTAGTTATTTATTGTCATTATTAAAACAAAATTAACGTTC
*
280778 TATTTTCATTTGGTCATCGTTTTAGTTATTTATTGTCGTTATTAAAACAAAATTAA
1 TATTTTCATTTGGTCATCGTTTTAGTTATTTATTGTCATTATTAAAACAAAATTAA
280834 AGTGGCTCAA
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 55 1.00
ACGTcount: A:0.30, C:0.10, G:0.10, T:0.50
Consensus pattern (61 bp):
TATTTTCATTTGGTCATCGTTTTAGTTATTTATTGTCATTATTAAAACAAAATTAACGTTC
Found at i:292162 original size:240 final size:240
Alignment explanation
Indices: 291739--292486 Score: 1489
Period size: 240 Copynumber: 3.1 Consensus size: 240
291729 TTGTTTTGAT
291739 GGAATTGTTTCAAACGCGATGAGATCGGCTATGGAATTGCCACTAACCGCATTGATTCCATCTTT
1 GGAATTGTTTCAAACGCGATGAGATCGGCTATGGAATTGCCACTAACCGCATTGATTCCATCTTT
291804 GGAAGTGAATGAAAACCAAGCTGGGATGTTTATATTTTCCTCCTTGAGAAGCTCTGCATATGCCT
66 GGAAGTGAATGAAAACCAAGCTGGGATGTTTATATTTTCCTCCTTGAGAAGCTCTGCATATGCCT
291869 GCATTCAATTTGATCGGAATGTAAGGTTACGGTCGTTATTTTATGATTTTGGTTTTTTTTTAGTA
131 GCATTCAATTTGATCGGAATGTAAGGTTACGGTCGTTATTTTATGATTTTGGTTTTTTTTTAGTA
291934 TGAACATCGATTTCATTGGCAGATACCTGTGCTTCTAGCTTGTTC
196 TGAACATCGATTTCATTGGCAGATACCTGTGCTTCTAGCTTGTTC
291979 GGAATTGTTTCAAACGCGATGAGATCGGCTATGGAATTGCCACTAACCGCATTGATTCCATCTTT
1 GGAATTGTTTCAAACGCGATGAGATCGGCTATGGAATTGCCACTAACCGCATTGATTCCATCTTT
292044 GGAAGTGAATGAAAACCAAGCTGGGATGTTTATATTTTCCTCCTTGAGAAGCTCTGCATATGCCT
66 GGAAGTGAATGAAAACCAAGCTGGGATGTTTATATTTTCCTCCTTGAGAAGCTCTGCATATGCCT
292109 GCATTCAATTTGATCGGAATGTAAGGTTACGGTCGTTATTTTATGATTTTGGTTTTTTTTTAGTA
131 GCATTCAATTTGATCGGAATGTAAGGTTACGGTCGTTATTTTATGATTTTGGTTTTTTTTTAGTA
292174 TGAACATCGATTTCATTGGCAGATACCTGTGCTTCTAGCTTGTTC
196 TGAACATCGATTTCATTGGCAGATACCTGTGCTTCTAGCTTGTTC
292219 GGAATTGTTTCAAACGCGATGAGATCGGCTATGGAATTGCCACTAACCGCATTGATTCCATCTTT
1 GGAATTGTTTCAAACGCGATGAGATCGGCTATGGAATTGCCACTAACCGCATTGATTCCATCTTT
292284 GGAAGTGAATGAAAACCAAGCTGGGATGTTTATATTTTCCTCCTTGAGAAGCTCTGCATATGCCT
66 GGAAGTGAATGAAAACCAAGCTGGGATGTTTATATTTTCCTCCTTGAGAAGCTCTGCATATGCCT
292349 GCATTCAATTTGATCGGAATGTAAGGTTACGGTCGTTATTTTATGATTTTGG-TTTTTTTTAGTA
131 GCATTCAATTTGATCGGAATGTAAGGTTACGGTCGTTATTTTATGATTTTGGTTTTTTTTTAGTA
292413 TGAACATCGATTTCATTGGCAGATACCTGTGCTTCTAGCTTGTTC
196 TGAACATCGATTTCATTGGCAGATACCTGTGCTTCTAGCTTGTTC
292458 GGAATTGTTTCAAACGCGATGAGATCGGC
1 GGAATTGTTTCAAACGCGATGAGATCGGC
292487 GCCGGAGTTG
Statistics
Matches: 508, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
239 86 0.17
240 422 0.83
ACGTcount: A:0.24, C:0.17, G:0.22, T:0.36
Consensus pattern (240 bp):
GGAATTGTTTCAAACGCGATGAGATCGGCTATGGAATTGCCACTAACCGCATTGATTCCATCTTT
GGAAGTGAATGAAAACCAAGCTGGGATGTTTATATTTTCCTCCTTGAGAAGCTCTGCATATGCCT
GCATTCAATTTGATCGGAATGTAAGGTTACGGTCGTTATTTTATGATTTTGGTTTTTTTTTAGTA
TGAACATCGATTTCATTGGCAGATACCTGTGCTTCTAGCTTGTTC
Found at i:294068 original size:26 final size:25
Alignment explanation
Indices: 294032--294080 Score: 80
Period size: 26 Copynumber: 1.9 Consensus size: 25
294022 TTTTCTTCAC
*
294032 ATTATGTTTATTTTATATACTATAAG
1 ATTATGTTTATCTTATA-ACTATAAG
294058 ATTATGTTTATCTTATAACTATA
1 ATTATGTTTATCTTATAACTATA
294081 GTTTAGTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 6 0.27
26 16 0.73
ACGTcount: A:0.35, C:0.06, G:0.06, T:0.53
Consensus pattern (25 bp):
ATTATGTTTATCTTATAACTATAAG
Found at i:296925 original size:20 final size:20
Alignment explanation
Indices: 296886--296930 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
296876 TCATAGAAAA
*
296886 ATAAATTACATTTATATTAT
1 ATAAATTACATTAATATTAT
* *
296906 ATAAATTTCATTAATTTTAT
1 ATAAATTACATTAATATTAT
*
296926 GTAAA
1 ATAAA
296931 AATATAATTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.49
Consensus pattern (20 bp):
ATAAATTACATTAATATTAT
Found at i:298289 original size:31 final size:31
Alignment explanation
Indices: 298251--298332 Score: 94
Period size: 32 Copynumber: 2.6 Consensus size: 31
298241 TTTTTATTAT
*
298251 TTCGGGTCGGGTCGGGTTTCTAATTCAT-ATA
1 TTCGGGTCGGGTCGGGTTTCTAAGT-ATGATA
* *
298282 TTCGGGTCGGGTCGGTTTTTTTAAGTATGATA
1 TTCGGGTCGGGTCGG-GTTTCTAAGTATGATA
*
298314 TTCTGGTCGGGTTCGGGTT
1 TTCGGGTCGGG-TCGGGTT
298333 CGGGTTTAGG
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
31 17 0.40
32 22 0.51
33 4 0.09
ACGTcount: A:0.12, C:0.13, G:0.33, T:0.41
Consensus pattern (31 bp):
TTCGGGTCGGGTCGGGTTTCTAAGTATGATA
Found at i:302588 original size:23 final size:23
Alignment explanation
Indices: 302562--302608 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
302552 GTCTCTAATG
302562 TTATCAAATGATTACTCCTCCAT
1 TTATCAAATGATTACTCCTCCAT
302585 TTATCAAATGATTACTCCTCCAT
1 TTATCAAATGATTACTCCTCCAT
302608 T
1 T
302609 ATCCCCGTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.30, C:0.26, G:0.04, T:0.40
Consensus pattern (23 bp):
TTATCAAATGATTACTCCTCCAT
Found at i:309711 original size:2 final size:2
Alignment explanation
Indices: 309704--309775 Score: 137
Period size: 2 Copynumber: 36.5 Consensus size: 2
309694 TATAAGTTGA
309704 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
309746 AT AT AT AT A- AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
309776 AATAAAGCTT
Statistics
Matches: 69, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 68 0.99
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:310870 original size:20 final size:20
Alignment explanation
Indices: 310845--310882 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
310835 TTTTCAATAG
310845 AAAATATATAGA-AATTTTTT
1 AAAATATAT-GATAATTTTTT
310865 AAAATATATGATAATTTT
1 AAAATATATGATAATTTT
310883 AAATTTTCAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (20 bp):
AAAATATATGATAATTTTTT
Found at i:311727 original size:18 final size:20
Alignment explanation
Indices: 311704--311744 Score: 59
Period size: 18 Copynumber: 2.1 Consensus size: 20
311694 AATTCAAATT
311704 TTTTCGAGTATA-G-TTAAA
1 TTTTCGAGTATATGTTTAAA
*
311722 TTTTCGTGTATATGTTTAAA
1 TTTTCGAGTATATGTTTAAA
311742 TTT
1 TTT
311745 AATTATAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 11 0.55
19 1 0.05
20 8 0.40
ACGTcount: A:0.27, C:0.05, G:0.15, T:0.54
Consensus pattern (20 bp):
TTTTCGAGTATATGTTTAAA
Found at i:314714 original size:16 final size:18
Alignment explanation
Indices: 314693--314726 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
314683 TGCTCCTATA
314693 TTTTCTTA-AAA-AATAT
1 TTTTCTTATAAATAATAT
314709 TTTTCTTATAAATAATAT
1 TTTTCTTATAAATAATAT
314727 AATTATTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
17 3 0.19
18 5 0.31
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.53
Consensus pattern (18 bp):
TTTTCTTATAAATAATAT
Found at i:315746 original size:24 final size:25
Alignment explanation
Indices: 315714--315774 Score: 61
Period size: 29 Copynumber: 2.3 Consensus size: 25
315704 TGTTAGTGAA
*
315714 ATCGATAA-GAAATCCATTAATCTC
1 ATCGGTAAGGAAATCCATTAATCTC
*
315738 ATCGGTAAGTAGTGAAATCTATTAATCTC
1 ATCGGT-A--AG-GAAATCCATTAATCTC
315767 ATCGGTAA
1 ATCGGTAA
315775 TTATCCTATT
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
24 5 0.17
25 1 0.03
26 1 0.03
27 1 0.03
28 1 0.03
29 21 0.70
ACGTcount: A:0.38, C:0.16, G:0.15, T:0.31
Consensus pattern (25 bp):
ATCGGTAAGGAAATCCATTAATCTC
Found at i:321665 original size:18 final size:18
Alignment explanation
Indices: 321642--321677 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
321632 AAAATATTAG
* *
321642 AATTTATTTAAGATTAAT
1 AATTTATTAAAAATTAAT
321660 AATTTATTAAAAATTAAT
1 AATTTATTAAAAATTAAT
321678 TATAATTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (18 bp):
AATTTATTAAAAATTAAT
Found at i:323551 original size:57 final size:58
Alignment explanation
Indices: 323490--323606 Score: 164
Period size: 57 Copynumber: 2.0 Consensus size: 58
323480 TCACTCTTTA
* * *
323490 AACTCAACACATGTCTTTGATTCAGCAGC-TTTTCTACCTCTATATCGTTGCTCATTC
1 AACTCAACACATATATTTGATTCAGCAGCTTTTTCTACCTCTATACCGTTGCTCATTC
* * * *
323547 AACTCAACATATATATTTGATTCAGCAGCTTTTTCTACCTCTCTCCCGTTGCTCTTTC
1 AACTCAACACATATATTTGATTCAGCAGCTTTTTCTACCTCTATACCGTTGCTCATTC
323605 AA
1 AA
323607 TTGAGAAAGG
Statistics
Matches: 52, Mismatches: 7, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
57 26 0.50
58 26 0.50
ACGTcount: A:0.23, C:0.28, G:0.09, T:0.39
Consensus pattern (58 bp):
AACTCAACACATATATTTGATTCAGCAGCTTTTTCTACCTCTATACCGTTGCTCATTC
Found at i:326348 original size:21 final size:21
Alignment explanation
Indices: 326324--326363 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
326314 CAACACAGTT
*
326324 TCCAAATTCGCAATGCGATAC
1 TCCAAATTCGCAAGGCGATAC
326345 TCCAAATTCGCAAGGCGAT
1 TCCAAATTCGCAAGGCGAT
326364 TTTCGTTTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.28, G:0.17, T:0.23
Consensus pattern (21 bp):
TCCAAATTCGCAAGGCGATAC
Found at i:326522 original size:58 final size:58
Alignment explanation
Indices: 326446--326581 Score: 209
Period size: 58 Copynumber: 2.3 Consensus size: 58
326436 CGCGATTCTC
* * * *
326446 CAAATTTGCAATGCTAATTACCGATATAGGTAAACACAATTATTCGGAACTCAGTTTT
1 CAAATTCGCAACGCTAATTACCGATATAGGTAAACACAACTATTCGCAACTCAGTTTT
*
326504 CAAATTCGCAACGCTAATTATCGATATAGGTAAACACAACTATTCGCAACTCAGTTTT
1 CAAATTCGCAACGCTAATTACCGATATAGGTAAACACAACTATTCGCAACTCAGTTTT
* *
326562 CAAATTCACAACGCGAATTA
1 CAAATTCGCAACGCTAATTA
326582 GCCAATTTTG
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
58 71 1.00
ACGTcount: A:0.38, C:0.21, G:0.12, T:0.29
Consensus pattern (58 bp):
CAAATTCGCAACGCTAATTACCGATATAGGTAAACACAACTATTCGCAACTCAGTTTT
Found at i:326534 original size:137 final size:137
Alignment explanation
Indices: 326371--326617 Score: 401
Period size: 137 Copynumber: 1.8 Consensus size: 137
326361 GATTTTCGTT
*
326371 TTCGCAACGCTAATTATCGGTATAGGTAAACACAACTATTCACAACTCAGTTTTCAAATT-AGCA
1 TTCGCAACGCTAATTATCGATATAGGTAAACACAACTATTCACAACTCAGTTTTCAAATTCA-CA
**
326435 ACGCG-ATTCTCCAAATTTGCAATGCT-AATTACCGATATAGGTAAACACAATTATTCGGAACTC
65 ACGCGAATTAGCCAAATTTGCAA--CTAAATTACCGATATAGGTAAACACAATTATTCGGAACTC
326498 AGTTTTCAAA
128 AGTTTTCAAA
*
326508 TTCGCAACGCTAATTATCGATATAGGTAAACACAACTATTCGCAACTCAGTTTTCAAATTCACAA
1 TTCGCAACGCTAATTATCGATATAGGTAAACACAACTATTCACAACTCAGTTTTCAAATTCACAA
*
326573 CGCGAATTAGCCAATTTTGCAACTAAATTACCGATATAGGTAAAC
66 CGCGAATTAGCCAAATTTGCAACTAAATTACCGATATAGGTAAAC
326618 TCGGTGGAAA
Statistics
Matches: 102, Mismatches: 5, Indels: 6
0.90 0.04 0.05
Matches are distributed among these distances:
136 2 0.02
137 85 0.83
138 15 0.15
ACGTcount: A:0.36, C:0.21, G:0.13, T:0.29
Consensus pattern (137 bp):
TTCGCAACGCTAATTATCGATATAGGTAAACACAACTATTCACAACTCAGTTTTCAAATTCACAA
CGCGAATTAGCCAAATTTGCAACTAAATTACCGATATAGGTAAACACAATTATTCGGAACTCAGT
TTTCAAA
Found at i:326949 original size:21 final size:21
Alignment explanation
Indices: 326923--326970 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
326913 TAGCATTACG
326923 AATTTGGAGAATCGCGTTGCT
1 AATTTGGAGAATCGCGTTGCT
326944 AATTTGGAGAATCGCGTTGCT
1 AATTTGGAGAATCGCGTTGCT
326965 AATTTG
1 AATTTG
326971 AAAACTGTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.25, C:0.12, G:0.27, T:0.35
Consensus pattern (21 bp):
AATTTGGAGAATCGCGTTGCT
Found at i:327551 original size:13 final size:13
Alignment explanation
Indices: 327535--327575 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
327525 AATTGATGAT
327535 AATAAACTATAAA
1 AATAAACTATAAA
327548 AAT-AAC-AT--A
1 AATAAACTATAAA
327557 AATAAACTATAAA
1 AATAAACTATAAA
327570 AATAAA
1 AATAAA
327576 GTAGTGTCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
9 4 0.17
10 3 0.12
11 4 0.17
12 3 0.12
13 10 0.42
ACGTcount: A:0.71, C:0.07, G:0.00, T:0.22
Consensus pattern (13 bp):
AATAAACTATAAA
Found at i:332984 original size:23 final size:23
Alignment explanation
Indices: 332949--333000 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
332939 TTCATGCTCG
* *
332949 TTCGTTTAGTGTTCGCGAACATA
1 TTCGTTCAATGTTCGCGAACATA
* *
332972 TTCGTTCAATGTTTGCGAACATG
1 TTCGTTCAATGTTCGCGAACATA
332995 TTCGTT
1 TTCGTT
333001 TATATATTCA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.19, C:0.17, G:0.21, T:0.42
Consensus pattern (23 bp):
TTCGTTCAATGTTCGCGAACATA
Found at i:338070 original size:23 final size:23
Alignment explanation
Indices: 338052--338118 Score: 80
Period size: 23 Copynumber: 2.9 Consensus size: 23
338042 ACGTTAAATG
338052 AACATGTTCACAAATGTTAAACA
1 AACATGTTCACAAATGTTAAACA
** *
338075 AACATGTTCATGAACGTTAAACA
1 AACATGTTCACAAATGTTAAACA
* * *
338098 AATATATTCACAAATGCTAAA
1 AACATGTTCACAAATGTTAAA
338119 TGAATGGACA
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.48, C:0.16, G:0.09, T:0.27
Consensus pattern (23 bp):
AACATGTTCACAAATGTTAAACA
Found at i:338238 original size:3 final size:3
Alignment explanation
Indices: 338230--338273 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
338220 ATTGTATTCT
338230 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
338274 TATTATTATT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:338382 original size:29 final size:29
Alignment explanation
Indices: 338350--338427 Score: 120
Period size: 29 Copynumber: 2.7 Consensus size: 29
338340 ACATAAATTA
*
338350 TAAATTTAATTTATATACTTTAATTTAAT
1 TAAATTTAATATATATACTTTAATTTAAT
* *
338379 TAAATTTGATATATATACTTTAATTTAGT
1 TAAATTTAATATATATACTTTAATTTAAT
*
338408 TAAATTTAATGTATATACTT
1 TAAATTTAATATATATACTT
338428 GAATACACAA
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 44 1.00
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.53
Consensus pattern (29 bp):
TAAATTTAATATATATACTTTAATTTAAT
Found at i:345636 original size:2 final size:2
Alignment explanation
Indices: 345629--345670 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
345619 TCCTGTTATT
345629 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
345671 AGACCTGATC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:347718 original size:15 final size:16
Alignment explanation
Indices: 347698--347727 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
347688 CCAATAACAG
347698 AATA-TTTAAGTTGAA
1 AATATTTTAAGTTGAA
347713 AATATTTTAAGTTGA
1 AATATTTTAAGTTGA
347728 TGAAAGAGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.43, C:0.00, G:0.13, T:0.43
Consensus pattern (16 bp):
AATATTTTAAGTTGAA
Found at i:350609 original size:60 final size:60
Alignment explanation
Indices: 350530--350671 Score: 153
Period size: 60 Copynumber: 2.4 Consensus size: 60
350520 TTTTAAATGC
* * * * *
350530 TCCAATTTTATTCCTAAACTATG-AGTACCATTCTAAATTAGTCCTCAAAC-TTTTGAACAT
1 TCCAA-TTTAATCCCAAACTATGAAAT-CCATTCTAAATTACTCCCCAAACTTTTTGAACAT
* * * *
350590 TTCATTTTAATCCCCAAACTATGAAATGCATTCTAAATTTCTCCCCAAACTTTTTGAACAT
1 TCCAATTTAAT-CCCAAACTATGAAATCCATTCTAAATTACTCCCCAAACTTTTTGAACAT
*
350651 TCCAATTTCATCCCAAACTAT
1 TCCAATTTAATCCCAAACTAT
350672 ATGTATGTAC
Statistics
Matches: 67, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
59 5 0.07
60 42 0.63
61 20 0.30
ACGTcount: A:0.33, C:0.25, G:0.05, T:0.37
Consensus pattern (60 bp):
TCCAATTTAATCCCAAACTATGAAATCCATTCTAAATTACTCCCCAAACTTTTTGAACAT
Found at i:350979 original size:27 final size:27
Alignment explanation
Indices: 350948--351006 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 27
350938 TATTACATGA
*
350948 TAATTAAATGTAAAATAAATAATTCAG
1 TAATTAAATGCAAAATAAATAATTCAG
* * * *
350975 TAATTCATTGCACAGTAAATAATTCAG
1 TAATTAAATGCAAAATAAATAATTCAG
351002 TAATT
1 TAATT
351007 TATTACATGA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.47, C:0.08, G:0.08, T:0.36
Consensus pattern (27 bp):
TAATTAAATGCAAAATAAATAATTCAG
Found at i:358279 original size:896 final size:896
Alignment explanation
Indices: 355780--358807 Score: 5324
Period size: 896 Copynumber: 3.4 Consensus size: 896
355770 AGAGGCAAAT
* * * *
355780 GGACAAGATCATTTAGTTCCTGCAGCTGAGGATAA-AAGTACTTGGGGAAATGAGACGGAATCGG
1 GGACAAGATCATTTATTTCCTGCAGCTGAGGATAACAA-TGCTCGGGGAAATGAGGCGGAATCGG
* * *
355844 CTTCTCTTAAACATGATGGCCTAGCATCTC-CTCGTATCGA-GTACCCAACACACAATAAGAAAG
65 ATTCTCTTGAACATGATGGCCTAGCATCTCAC-CGTATCGATG-ACCCGACACACAATAAGAAAG
*
355907 GTTAGGATATATCTTGATTACTGATATTTGGTTGGCTATTCCCACTTGCTAAAAGGTATATTTTT
128 GTTAGGATATATCTTGATTACTGATATATGGTTGGCTATTCCCACTTGCTAAAAGGTATATTTTT
355972 TTCGACTTACAATGATGATGGATCGATGTAGAACAAGATACTAGCACATTTCTTGAAGTAGAGGA
193 TTCGACTTACAATGATGATGGATCGATGTAGAACAAGATACTAGCACATTTCTTGAAGTAGAGGA
356037 AATACCTTTGAAAGAAGATGCTAGTACAGATGAAATAAATGCAGAAGCTCGCCCAGTTCCCGCAG
258 AATACCTTTGAAAGAAGATGCTAGTACAGATGAAATAAATGCAGAAGCTCGCCCAGTTCCCGCAG
* *
356102 GT------GG-AG-A--C--GGAAGCAAGACAGGGCTGGTTTTAGTTGATTGTGATGGAATGGTT
323 GTGGAGACGGAAGTACTCATGGAAGCAAGACAGGGCTGGTTTTAGGTGATTGTGAAGGAATGGTT
*
356155 CATCCGTGTATTGACAAGCCGAAACCTGACAAAAAAGGTTAATGGATATGATGTTTTGTTGTCTA
388 CATCCATGTATTGACAAGCCGAAACCTGACAAAAAAGGTTAATGGATATGATGTTTTGTTGTCTA
* * *
356220 TATGTTCCAATTCCAATGAACTAATGTAAAAAAACAATGTTTCAGCG-TCAGTATTACTAAGTTA
453 TATGTTCCAATTCCAATGAACTAATGCAAAAAAACAATGTTTCAGCGAT-AGTATTTCTAAATTA
*
356284 TATTTACATATTCGTACCGTGTTGAACCGGCGCAGGAGAGGATATGAACATAAATGATGAAATCG
517 TATTTACATATTCGTACCGTGTTGAACCGGCGCAGGAGGGGATATGAACATAAATGATGAAATCG
356349 TGGAGCGATCCTCACAAGAAGCTGGTAGCACAGATGTAATGGATAGACAAGGTCAATTACTTGCT
582 TGGAGCGATCCTCACAAGAAGCTGGTAGCACAGATGTAATGGATAGACAAGGTCAATTACTTGCT
356414 GTAGTTGAAGATAAAGCTACTTATGCAAATGAAACATGCTTAGTTTCCAGTGATCCCGAGGGAAC
647 GTAGTTGAAGATAAAGCTACTTATGCAAATGAAACATGCTTAGTTTCCAGTGATCCCGAGGGAAC
* *
356479 TGCAGATCTTCACGGTGACAATCCTAAAGACCATGAGAAAGGTTAGAAATACAGTGTTTTATTTG
712 TGCAGATCTTCACGGTGTCAATCCTAAAGACCATGAGAAAGGTTAGAAATACAGTGATTTATTTG
* * *
356544 CCAATAAATGGTTCTCTGTATATGATGACGATGATGATTGATGTAGAAGAAGATAATAACATGGT
777 CCAATATATGGTTCTCTGTATATGATGATGATGATGATTGATGTAGAAGAAGATAATAACATGAT
*
356609 TCCAGTAGATAAGGAAGATTCAATGAAAGAAACTGGTTATGCAGAAAAGGAAAAA
842 TCCAGTAGATAAGGAAGATTCCATGAAAGAAACTGGTTATGCAGAAAAGGAAAAA
*
356664 GGACAAGATCATTTATTTCCTGCAGCTGAGGATAACAATGCTCGGGGAAATGAGGCGGAATCGTA
1 GGACAAGATCATTTATTTCCTGCAGCTGAGGATAACAATGCTCGGGGAAATGAGGCGGAATCGGA
356729 TTCTCTTGAACATGATGGCCTAGCATCTCACCGTATCGATGACCCGACACACAATAAGAAAGGTT
66 TTCTCTTGAACATGATGGCCTAGCATCTCACCGTATCGATGACCCGACACACAATAAGAAAGGTT
*
356794 AGGATATCTCTTGATTACTGATATATGGTTGGCTATTCCCACTTGCTAAAAGG--TATTTTTTTC
131 AGGATATATCTTGATTACTGATATATGGTTGGCTATTCCCACTTGCTAAAAGGTATATTTTTTTC
*
356857 GACTTAC-ATGATGATGGATTGAT-TAGAACAAGATACTAGCACATTTCTTGAAGTAGAGGAAAT
196 GACTTACAATGATGATGGATCGATGTAGAACAAGATACTAGCACATTTCTTGAAGTAGAGGAAAT
356920 ACCTTTGAAAGAAGATGCTAGTACAGATGAAATAAATGCAGAAGCTCGCCCAGTTCCCGCAGGTG
261 ACCTTTGAAAGAAGATGCTAGTACAGATGAAATAAATGCAGAAGCTCGCCCAGTTCCCGCAGGTG
356985 GAGACGGAAGTACTCATGGAAGCAAGACAGGGCTGGTTTTAGGTGATTGTGAAGGAATGGTTCAT
326 GAGACGGAAGTACTCATGGAAGCAAGACAGGGCTGGTTTTAGGTGATTGTGAAGGAATGGTTCAT
357050 CCATGTATTGACAAGCCGAAACCTGACAAAAAAGGTTAATGGATATGATGTTTTGTTGTCTATAT
391 CCATGTATTGACAAGCCGAAACCTGACAAAAAAGGTTAATGGATATGATGTTTTGTTGTCTATAT
*
357115 GTTCCAATTCCAATGAACTAATGCAAAAAAACAATGTTTCAGCAATAGTATTTCTAAATTATATT
456 GTTCCAATTCCAATGAACTAATGCAAAAAAACAATGTTTCAGCGATAGTATTTCTAAATTATATT
357180 TACATATTCGTACCGTGTTGAACCGGCGCAGGAGGGGATATGAACATAAATGATGAAATCGTGGA
521 TACATATTCGTACCGTGTTGAACCGGCGCAGGAGGGGATATGAACATAAATGATGAAATCGTGGA
357245 GCGATCCTCACAAGAAGCTGGTAGCACAGATGTAATGGATAGACAAGGTCAATTACTTGCTGTAG
586 GCGATCCTCACAAGAAGCTGGTAGCACAGATGTAATGGATAGACAAGGTCAATTACTTGCTGTAG
357310 TTGAAGATAAAGCTACTTATGCAAATGAAACATGCTTAGTTTCCAGTGATCCCGAGGGAACTGCA
651 TTGAAGATAAAGCTACTTATGCAAATGAAACATGCTTAGTTTCCAGTGATCCCGAGGGAACTGCA
357375 GATCTTCACGGTGTCAATCCTAAAGACCATGAGAAAGGTTAGAAATACAGTGATTTATTTGCCAA
716 GATCTTCACGGTGTCAATCCTAAAGACCATGAGAAAGGTTAGAAATACAGTGATTTATTTGCCAA
357440 TATATGGTTCTCTGTATATGATGATGATGATGATTGATGTAGAAGAAGATAATAACATGATTCCA
781 TATATGGTTCTCTGTATATGATGATGATGATGATTGATGTAGAAGAAGATAATAACATGATTCCA
357505 GTAGATAAGGAAGATTCCATGAAAGAAACTGGTTATGCAGAAAAGGAAAAA
846 GTAGATAAGGAAGATTCCATGAAAGAAACTGGTTATGCAGAAAAGGAAAAA
357556 GGACAAGATCATTTATTTCCTGCAGCTGAGGATAACAATGCTCGGGGAAATGAGGCGGAATCGGA
1 GGACAAGATCATTTATTTCCTGCAGCTGAGGATAACAATGCTCGGGGAAATGAGGCGGAATCGGA
357621 TTCTCTTGAACATGATGGCCTAGCATCTCACCGTATCGATGACCCGACACACAATAAGAAAGGTT
66 TTCTCTTGAACATGATGGCCTAGCATCTCACCGTATCGATGACCCGACACACAATAAGAAAGGTT
*
357686 AGGATATCTCTTGATTACTGATATATGGTTGGCTATTCCCACTTGCTAAAAGGTATATTTTTTTC
131 AGGATATATCTTGATTACTGATATATGGTTGGCTATTCCCACTTGCTAAAAGGTATATTTTTTTC
*
357751 GACTTACAATGATGATGGATTGATGTAGAACAAGATACTAGCACATTTCTTGAAGTAGAGGAAAT
196 GACTTACAATGATGATGGATCGATGTAGAACAAGATACTAGCACATTTCTTGAAGTAGAGGAAAT
357816 ACCTTTGAAAGAAGATGCTAGTACAGATGAAATAAATGCAGAAGCTCGCCCAGTTCCCGCAGGTG
261 ACCTTTGAAAGAAGATGCTAGTACAGATGAAATAAATGCAGAAGCTCGCCCAGTTCCCGCAGGTG
357881 GAGACGGAAGTACTCATGGAAGCAAGACAGGGCTGGTTTTAGGTGATTGTGAAGGAATGGTTCAT
326 GAGACGGAAGTACTCATGGAAGCAAGACAGGGCTGGTTTTAGGTGATTGTGAAGGAATGGTTCAT
* *
357946 CCATGTATTGACAAGCCGAAACCTGACCAGAAAGGTTAATGGATATGATGTTTTGTTGTCTATAT
391 CCATGTATTGACAAGCCGAAACCTGACAAAAAAGGTTAATGGATATGATGTTTTGTTGTCTATAT
358011 GTTCCAATTCCAATGAACTAATGCAAAAAAACAATGTTTCAGCGATAGTATTTCTAAATTATATT
456 GTTCCAATTCCAATGAACTAATGCAAAAAAACAATGTTTCAGCGATAGTATTTCTAAATTATATT
358076 TACATATTCGTACCGTGTTGAACCGGCGCAGGAGGGGATATGAACATAAATGATGAAATCGTGGA
521 TACATATTCGTACCGTGTTGAACCGGCGCAGGAGGGGATATGAACATAAATGATGAAATCGTGGA
358141 GCGATCCTCACAAGAAGCTGGTAGCACAGATGTAATGGATAGACAAGGTCAATTACTTGCTGTAG
586 GCGATCCTCACAAGAAGCTGGTAGCACAGATGTAATGGATAGACAAGGTCAATTACTTGCTGTAG
358206 TTGAAGATAAAGCTACTTATGCAAATGAAACATGCTTAGTTTCCAGTGATCCCGAGGGAACTGCA
651 TTGAAGATAAAGCTACTTATGCAAATGAAACATGCTTAGTTTCCAGTGATCCCGAGGGAACTGCA
*
358271 GATCTTCACAGTGTCAATCCTAAAGACCATGAGAAAGGTTAGAAATACAGTGATTTATTTGCCAA
716 GATCTTCACGGTGTCAATCCTAAAGACCATGAGAAAGGTTAGAAATACAGTGATTTATTTGCCAA
358336 TATATGGTTCTCTGTATATGATGATGATGATGATTGATGTAGAAGAAGATAATAACATGATTCCA
781 TATATGGTTCTCTGTATATGATGATGATGATGATTGATGTAGAAGAAGATAATAACATGATTCCA
358401 GTAGATAAGGAAGATTCCATGAAAGAAACTGGTTATGCAGAAAAGGAAAAA
846 GTAGATAAGGAAGATTCCATGAAAGAAACTGGTTATGCAGAAAAGGAAAAA
*
358452 GGACAAGATCATTTATTTCCTGCAGCTGAGGATAACAATGCTCGGGGAAATGAGGCGGAATCGGC
1 GGACAAGATCATTTATTTCCTGCAGCTGAGGATAACAATGCTCGGGGAAATGAGGCGGAATCGGA
* * * * *
358517 TTCTCTTGAACATAATGGCCTAGCATCTCCCCGTATCAAGGACCCGACACACAATGAGAAAGGTT
66 TTCTCTTGAACATGATGGCCTAGCATCTCACCGTATCGATGACCCGACACACAATAAGAAAGGTT
* * *
358582 AGGATATATCTTGATTACTGATGTATGGTTGGTTATTCCCACTTGCTAAAAGATATA-TTTTTTC
131 AGGATATATCTTGATTACTGATATATGGTTGGCTATTCCCACTTGCTAAAAGGTATATTTTTTTC
* * * * *
358646 GACTTACTATGATGATGGATCCATGTAGAACAACATACTAGCACAATTCTTGAAGTAGAGGAATT
196 GACTTACAATGATGATGGATCGATGTAGAACAAGATACTAGCACATTTCTTGAAGTAGAGGAAAT
* * * * * *** * * * *
358711 GCCCTTGAAAGAAGGTGCTAGTACGGATGAAACAAATATGGAAGGTCTCCTAGTTCCTGCAGGTG
261 ACCTTTGAAAGAAGATGCTAGTACAGATGAAATAAATGCAGAAGCTCGCCCAGTTCCCGCAGGTG
* * * * *
358776 GAGATGAAAGTAGTCATGGAACCGAGACAGGG
326 GAGACGGAAGTACTCATGGAAGCAAGACAGGG
358808 ATATTTTCGA
Statistics
Matches: 2061, Mismatches: 63, Indels: 29
0.96 0.03 0.01
Matches are distributed among these distances:
880 104 0.05
881 15 0.01
882 17 0.01
884 166 0.08
885 4 0.00
886 2 0.00
887 2 0.00
888 1 0.00
890 1 0.00
892 720 0.35
893 1 0.00
894 17 0.01
895 162 0.08
896 849 0.41
ACGTcount: A:0.34, C:0.16, G:0.23, T:0.27
Consensus pattern (896 bp):
GGACAAGATCATTTATTTCCTGCAGCTGAGGATAACAATGCTCGGGGAAATGAGGCGGAATCGGA
TTCTCTTGAACATGATGGCCTAGCATCTCACCGTATCGATGACCCGACACACAATAAGAAAGGTT
AGGATATATCTTGATTACTGATATATGGTTGGCTATTCCCACTTGCTAAAAGGTATATTTTTTTC
GACTTACAATGATGATGGATCGATGTAGAACAAGATACTAGCACATTTCTTGAAGTAGAGGAAAT
ACCTTTGAAAGAAGATGCTAGTACAGATGAAATAAATGCAGAAGCTCGCCCAGTTCCCGCAGGTG
GAGACGGAAGTACTCATGGAAGCAAGACAGGGCTGGTTTTAGGTGATTGTGAAGGAATGGTTCAT
CCATGTATTGACAAGCCGAAACCTGACAAAAAAGGTTAATGGATATGATGTTTTGTTGTCTATAT
GTTCCAATTCCAATGAACTAATGCAAAAAAACAATGTTTCAGCGATAGTATTTCTAAATTATATT
TACATATTCGTACCGTGTTGAACCGGCGCAGGAGGGGATATGAACATAAATGATGAAATCGTGGA
GCGATCCTCACAAGAAGCTGGTAGCACAGATGTAATGGATAGACAAGGTCAATTACTTGCTGTAG
TTGAAGATAAAGCTACTTATGCAAATGAAACATGCTTAGTTTCCAGTGATCCCGAGGGAACTGCA
GATCTTCACGGTGTCAATCCTAAAGACCATGAGAAAGGTTAGAAATACAGTGATTTATTTGCCAA
TATATGGTTCTCTGTATATGATGATGATGATGATTGATGTAGAAGAAGATAATAACATGATTCCA
GTAGATAAGGAAGATTCCATGAAAGAAACTGGTTATGCAGAAAAGGAAAAA
Found at i:371056 original size:16 final size:16
Alignment explanation
Indices: 371030--371070 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
371020 TATTTATATA
371030 ATTTAATAATATAAATT
1 ATTTAA-AATATAAATT
*
371047 ATTTAAAATATATATT
1 ATTTAAAATATAAATT
*
371063 ATTGAAAA
1 ATTTAAAA
371071 GTTCGAGTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 16 0.73
17 6 0.27
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (16 bp):
ATTTAAAATATAAATT
Found at i:372526 original size:18 final size:17
Alignment explanation
Indices: 372503--372538 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
372493 GACCCGATTC
*
372503 AAAATTAATTATTTTAGA
1 AAAATTAA-TATTATAGA
372521 AAAATTAATATTATAGA
1 AAAATTAATATTATAGA
372538 A
1 A
372539 TTAAATGATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.39
Consensus pattern (17 bp):
AAAATTAATATTATAGA
Found at i:378434 original size:14 final size:14
Alignment explanation
Indices: 378415--378451 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
378405 GCACGATAAA
*
378415 AATAATAATATATT
1 AATAATAATAAATT
378429 AATAATAATAAATT
1 AATAATAATAAATT
378443 AA-AATAATA
1 AATAATAATA
378452 GAAAAAGTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 7 0.32
14 15 0.68
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
AATAATAATAAATT
Found at i:384177 original size:22 final size:22
Alignment explanation
Indices: 384152--384194 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
384142 AAAAGACAGC
384152 CTTAGGTACAATAATTAGAAGT
1 CTTAGGTACAATAATTAGAAGT
384174 CTTAGGTACAATAATTAGAAG
1 CTTAGGTACAATAATTAGAAG
384195 GCTAGATGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.42, C:0.09, G:0.19, T:0.30
Consensus pattern (22 bp):
CTTAGGTACAATAATTAGAAGT
Found at i:385031 original size:20 final size:21
Alignment explanation
Indices: 385006--385057 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
384996 TTTTCCCAAT
*
385006 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
385026 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
385047 TCGCAATGCGA
1 TCGCAATGCGA
385058 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:385071 original size:20 final size:20
Alignment explanation
Indices: 385046--385159 Score: 104
Period size: 20 Copynumber: 5.7 Consensus size: 20
385036 AATTGGGAAA
*
385046 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
385066 ATCGCAATGCGATACTTACT
1 ATCGCAACGCGATACTGACT
* * *
385086 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
*
385107 ATCGCAACGAGATACTGACT
1 ATCGCAACGCGATACTGACT
* * *
385127 TTTGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
385147 TTCGCAACGCGAT
1 ATCGCAACGCGAT
385160 TTACATAGCG
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
19 2 0.03
20 62 0.78
21 13 0.16
22 2 0.03
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:385090 original size:61 final size:61
Alignment explanation
Indices: 385043--385159 Score: 153
Period size: 61 Copynumber: 1.9 Consensus size: 61
385033 GCGAATTGGG
* * * * *
385043 AAAATCGCAATGCGATACTGACTATCGCAATGCGATACTTACTATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* * * *
385104 AAAATCGCAACGAGATACTGACTTTTGCAACGCGATTCTGACTTTCGCAACGCGAT
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGAT
385160 TTACATAGCG
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
61 47 1.00
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25
Consensus pattern (61 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:385762 original size:19 final size:19
Alignment explanation
Indices: 385740--385832 Score: 88
Period size: 19 Copynumber: 5.1 Consensus size: 19
385730 GAAACCAAAA
*
385740 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
385759 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
385773 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
385792 TCGCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATT
*
385811 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
385831 TC
1 TC
385833 AACCAAAAGA
Statistics
Matches: 60, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
14 10 0.17
16 2 0.03
17 3 0.05
19 28 0.47
20 17 0.28
ACGTcount: A:0.13, C:0.24, G:0.19, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:385832 original size:39 final size:33
Alignment explanation
Indices: 385745--385807 Score: 108
Period size: 33 Copynumber: 1.9 Consensus size: 33
385735 CAAAATCGCA
385745 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
**
385778 TTGCGATAGTCATTTCGCGTTGCGATTCTC
1 TTGCGATTTTCATTTCGCGTTGCGATTCTC
385808 ATTATCTCGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.11, C:0.24, G:0.22, T:0.43
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:387361 original size:63 final size:63
Alignment explanation
Indices: 387285--387415 Score: 253
Period size: 63 Copynumber: 2.1 Consensus size: 63
387275 GTTACGTGAT
*
387285 GAGGTCAATGCCTTGCGTGAGGAGATCGGTACTCTACGCGATAACGATGGTGCATGGCGTGTG
1 GAGGTCAATGCCTTGCGTGAGGAGATCGGTACTCAACGCGATAACGATGGTGCATGGCGTGTG
387348 GAGGTCAATGCCTTGCGTGAGGAGATCGGTACTCAACGCGATAACGATGGTGCATGGCGTGTG
1 GAGGTCAATGCCTTGCGTGAGGAGATCGGTACTCAACGCGATAACGATGGTGCATGGCGTGTG
387411 GAGGT
1 GAGGT
387416 GTCTACTTTA
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
63 67 1.00
ACGTcount: A:0.21, C:0.18, G:0.37, T:0.23
Consensus pattern (63 bp):
GAGGTCAATGCCTTGCGTGAGGAGATCGGTACTCAACGCGATAACGATGGTGCATGGCGTGTG
Found at i:388064 original size:42 final size:42
Alignment explanation
Indices: 387988--388160 Score: 202
Period size: 42 Copynumber: 4.1 Consensus size: 42
387978 GACTCGCCTG
* * * *
387988 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCACTA
* * * *
388030 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCACTA
* * * * *
388072 TCATCCCTCAAGAGTCCACTCCTATCATTGAAGAGGCCCCTA
1 TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCACTA
* * *
388114 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
1 TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCACTA
388156 TCATC
1 TCATC
388161 GTTGAAGAGG
Statistics
Matches: 105, Mismatches: 26, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
42 105 1.00
ACGTcount: A:0.23, C:0.38, G:0.16, T:0.23
Consensus pattern (42 bp):
TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCACTA
Found at i:388126 original size:84 final size:84
Alignment explanation
Indices: 387985--388160 Score: 334
Period size: 84 Copynumber: 2.1 Consensus size: 84
387975 CCCGACTCGC
*
387985 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCCACTCCTATCATTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
388050 CCCACCGTTCAAGAGGCCA
66 CCCACCGTTCAAGAGGCCA
388069 CTGTCATCCCTCAAGAGTCCACTCCTATCATTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCCACTCCTATCATTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
388134 CCCACCGTTCAAGAGGCCA
66 CCCACCGTTCAAGAGGCCA
*
388153 CTATCATC
1 CTGTCATC
388161 GTTGAAGAGG
Statistics
Matches: 90, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
84 90 1.00
ACGTcount: A:0.22, C:0.38, G:0.16, T:0.23
Consensus pattern (84 bp):
CTGTCATCCCTCAAGAGTCCACTCCTATCATTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
CCCACCGTTCAAGAGGCCA
Found at i:388163 original size:21 final size:21
Alignment explanation
Indices: 388055--388170 Score: 56
Period size: 21 Copynumber: 5.5 Consensus size: 21
388045 CCCCTCCCAC
*
388055 CGTTCAAGAGGCCACTGTCAT
1 CGTTCAAGAGGCCACTATCAT
** * *
388076 CCCTCAAGAGTCCACT-CCTAT
1 CGTTCAAGAGGCCACTATC-AT
* * *
388097 CATTGAAGAGGCCCCTATCATT
1 CGTTCAAGAGGCCACTATCA-T
* * * * ** *
388119 C-CTCGAGAGTCCCCTCCCAC
1 CGTTCAAGAGGCCACTATCAT
388139 CGTTCAAGAGGCCACTATCAT
1 CGTTCAAGAGGCCACTATCAT
*
388160 CGTTGAAGAGG
1 CGTTCAAGAGG
388171 TCCCTCCCAT
Statistics
Matches: 66, Mismatches: 25, Indels: 8
0.67 0.25 0.08
Matches are distributed among these distances:
20 2 0.03
21 61 0.92
22 3 0.05
ACGTcount: A:0.24, C:0.34, G:0.20, T:0.22
Consensus pattern (21 bp):
CGTTCAAGAGGCCACTATCAT
Found at i:388176 original size:42 final size:41
Alignment explanation
Indices: 388018--388190 Score: 152
Period size: 42 Copynumber: 4.1 Consensus size: 41
388008 CCTATCGTTG
* * *
388018 AAGAGGCCCCTATCATTCCTCG-AGAGTCCCCTCCCACCGTTC
1 AAGAGGCCACTATCA-TCCTTGAAGAGT-CCCTCCCACCATTC
* * * * * *
388060 AAGAGGCCACTGTCATCCCTCAAGAGTCCACTCCTATCATTG
1 AAGAGGCCACTATCATCCTTGAAGAGTCC-CTCCCACCATTC
* * *
388102 AAGAGGCCCCTATCATTCCTCG-AGAGTCCCCTCCCACCGTTC
1 AAGAGGCCACTATCA-TCCTTGAAGAGT-CCCTCCCACCATTC
* *
388144 AAGAGGCCACTATCATCGTTGAAGAGGTCCCTCCCATCATTC
1 AAGAGGCCACTATCATCCTTGAAGA-GTCCCTCCCACCATTC
388186 AAGAG
1 AAGAG
388191 CCCGATTCAC
Statistics
Matches: 102, Mismatches: 23, Indels: 12
0.74 0.17 0.09
Matches are distributed among these distances:
41 9 0.09
42 86 0.84
43 7 0.07
ACGTcount: A:0.24, C:0.36, G:0.18, T:0.22
Consensus pattern (41 bp):
AAGAGGCCACTATCATCCTTGAAGAGTCCCTCCCACCATTC
Found at i:388181 original size:21 final size:20
Alignment explanation
Indices: 388130--388190 Score: 59
Period size: 21 Copynumber: 3.0 Consensus size: 20
388120 CTCGAGAGTC
*
388130 CCCTCCCACCGTTCAAGAGG
1 CCCTCCCATCGTTCAAGAGG
** *
388150 CCACTATCATCGTTGAAGAGG
1 CC-CTCCCATCGTTCAAGAGG
*
388171 TCCCTCCCATCATTCAAGAG
1 -CCCTCCCATCGTTCAAGAG
388191 CCCGATTCAC
Statistics
Matches: 31, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
20 2 0.06
21 27 0.87
22 2 0.06
ACGTcount: A:0.25, C:0.36, G:0.18, T:0.21
Consensus pattern (20 bp):
CCCTCCCATCGTTCAAGAGG
Found at i:388190 original size:84 final size:84
Alignment explanation
Indices: 387988--388190 Score: 309
Period size: 84 Copynumber: 2.4 Consensus size: 84
387978 GACTCGCCTG
* * *
387988 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCTCCC
1 TCATCCCTCAAGAGTCCACTCCCATCATTCAAGAGGCCCCTATCATTCCTCGAGAGTCCCCTCCC
*
388053 ACCGTTCAAGAGGCCACTG
66 ACCGTTCAAGAGGCCACTA
* *
388072 TCATCCCTCAAGAGTCCACTCCTATCATTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCTCCC
1 TCATCCCTCAAGAGTCCACTCCCATCATTCAAGAGGCCCCTATCATTCCTCGAGAGTCCCCTCCC
388137 ACCGTTCAAGAGGCCACTA
66 ACCGTTCAAGAGGCCACTA
** *
388156 TCATCGTTGAAGAGGTCC-CTCCCATCATTCAAGAG
1 TCATCCCTCAAGA-GTCCACTCCCATCATTCAAGAG
388191 CCCGATTCAC
Statistics
Matches: 111, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
84 107 0.96
85 4 0.04
ACGTcount: A:0.23, C:0.36, G:0.17, T:0.23
Consensus pattern (84 bp):
TCATCCCTCAAGAGTCCACTCCCATCATTCAAGAGGCCCCTATCATTCCTCGAGAGTCCCCTCCC
ACCGTTCAAGAGGCCACTA
Found at i:389568 original size:14 final size:14
Alignment explanation
Indices: 389549--389584 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
389539 ATTGTTTAAT
389549 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
389563 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
389577 TGATTTGT
1 TGATTTGT
389585 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:389715 original size:19 final size:19
Alignment explanation
Indices: 389691--389737 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
389681 AAAAAGTACT
*
389691 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
389710 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
389729 ATCGCAACG
1 ATCGCAACG
389738 AGAGAATCAC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.45, C:0.21, G:0.21, T:0.13
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:389784 original size:19 final size:19
Alignment explanation
Indices: 389762--389912 Score: 62
Period size: 19 Copynumber: 8.7 Consensus size: 19
389752 CGAAATTAAA
389762 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
389781 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
389796 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* *
389814 TTCGCATTGCGA-----AA
1 TTCGCGTTGCGATTTTCAT
*
389828 TTAGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* *
389847 TTCGCATTACGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
389862 -TCTCGTTGCGATTTTTAT
1 TTCGCGTTGCGATTTTCAT
* ** *
389880 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
389899 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
389913 AGACATTAAG
Statistics
Matches: 92, Mismatches: 24, Indels: 31
0.63 0.16 0.21
Matches are distributed among these distances:
14 27 0.29
16 5 0.05
17 6 0.07
19 44 0.48
20 10 0.11
ACGTcount: A:0.16, C:0.22, G:0.20, T:0.42
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:389808 original size:33 final size:32
Alignment explanation
Indices: 389766--389892 Score: 175
Period size: 33 Copynumber: 3.9 Consensus size: 32
389756 ATTAAATTCG
389766 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
**
389799 CGTTGCGATTTTCATTTCGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
*
389832 CGTTGCGATTTTCATTTCGCATTACGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
*
389865 CGTTGCGATTTTTATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
389893 AGTAATTTCC
Statistics
Matches: 83, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
31 3 0.04
33 77 0.93
35 3 0.04
ACGTcount: A:0.16, C:0.22, G:0.19, T:0.43
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:389844 original size:66 final size:66
Alignment explanation
Indices: 389759--389891 Score: 230
Period size: 66 Copynumber: 2.0 Consensus size: 66
389749 ACGCGAAATT
* *
389759 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTACGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
389824 G
66 G
* *
389825 AAATTAGCGTTGCGATTTTCATTTCGCATTACGATTCTCTCGTTGCGATTTTTATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTACGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
389890 G
66 G
389891 A
1 A
389892 TAGTAATTTC
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 63 1.00
ACGTcount: A:0.17, C:0.22, G:0.19, T:0.42
Consensus pattern (66 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATTACGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
G
Found at i:392201 original size:12 final size:12
Alignment explanation
Indices: 392184--392208 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
392174 TCTTCGGGGA
392184 CTTTTTCTTCTT
1 CTTTTTCTTCTT
392196 CTTTTTCTTCTT
1 CTTTTTCTTCTT
392208 C
1 C
392209 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:393469 original size:19 final size:20
Alignment explanation
Indices: 393411--393480 Score: 124
Period size: 20 Copynumber: 3.5 Consensus size: 20
393401 ATTCATTTGA
393411 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
*
393431 CTATCGCAATGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
393451 CTATCGCAACGCG-AAATGG
1 CTATCGCAACGCGAAAATGG
393470 CTATCGCAACG
1 CTATCGCAACG
393481 AAAAAATCGC
Statistics
Matches: 48, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
19 17 0.35
20 31 0.65
ACGTcount: A:0.33, C:0.26, G:0.24, T:0.17
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:393487 original size:39 final size:40
Alignment explanation
Indices: 393411--393487 Score: 120
Period size: 39 Copynumber: 1.9 Consensus size: 40
393401 ATTCATTTGA
* **
393411 CTATCGCAACGCGAAAATGGCTATCGCAATGCGAAAATGG
1 CTATCGCAACGCGAAAATGGCTATCGCAACGAAAAAATGG
393451 CTATCGCAACGCG-AAATGGCTATCGCAACGAAAAAAT
1 CTATCGCAACGCGAAAATGGCTATCGCAACGAAAAAAT
393488 CGCAATGCGA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
39 21 0.62
40 13 0.38
ACGTcount: A:0.38, C:0.23, G:0.22, T:0.17
Consensus pattern (40 bp):
CTATCGCAACGCGAAAATGGCTATCGCAACGAAAAAATGG
Found at i:393547 original size:19 final size:19
Alignment explanation
Indices: 393506--393589 Score: 133
Period size: 19 Copynumber: 4.7 Consensus size: 19
393496 GAAATGAAAA
393506 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
393522 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
393539 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
393558 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
393577 TCGCATTGCGATT
1 TCGCATTGCGATT
393590 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 0, Indels: 7
0.90 0.00 0.10
Matches are distributed among these distances:
14 11 0.17
16 3 0.05
17 3 0.05
19 46 0.73
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:393576 original size:38 final size:33
Alignment explanation
Indices: 393506--393602 Score: 140
Period size: 38 Copynumber: 2.8 Consensus size: 33
393496 GAAATGAAAA
393506 TCGCATTGCGATTTTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCTCGTTGCGATTTTCATT
393539 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTC---TCG--TTGCGATTTTCATT
*
393577 TCGCATTGCGATTCTCTCGTTGCGAT
1 TCGCATTGCGATTTTCTCGTTGCGAT
393603 AGTCAGTTTT
Statistics
Matches: 58, Mismatches: 1, Indels: 10
0.84 0.01 0.14
Matches are distributed among these distances:
33 23 0.40
35 3 0.05
36 3 0.05
38 29 0.50
ACGTcount: A:0.13, C:0.23, G:0.19, T:0.45
Consensus pattern (33 bp):
TCGCATTGCGATTTTCTCGTTGCGATTTTCATT
Found at i:393623 original size:20 final size:20
Alignment explanation
Indices: 393595--393633 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
393585 CGATTCTCTC
393595 GTTGCGATAGTCAGTTTTGT
1 GTTGCGATAGTCAGTTTTGT
* *
393615 GTTGTGATAGTCTGTTTTG
1 GTTGCGATAGTCAGTTTTG
393634 CCTTCAACAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.13, C:0.08, G:0.31, T:0.49
Consensus pattern (20 bp):
GTTGCGATAGTCAGTTTTGT
Found at i:393735 original size:14 final size:14
Alignment explanation
Indices: 393716--393752 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
393706 CATCAATTAA
393716 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
393730 ACAAATCATCTTTT
1 ACAAATCAACATTT
393744 ACAAATCAA
1 ACAAATCAA
393753 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:395645 original size:20 final size:20
Alignment explanation
Indices: 395600--395665 Score: 60
Period size: 20 Copynumber: 3.3 Consensus size: 20
395590 TAGTTTACTT
* * **
395600 TCGCAACACGAAACTTAAAA
1 TCGCAACACGAAAATGACTA
395620 TCGCAACACGAAAATGACTA
1 TCGCAACACGAAAATGACTA
* * * *
395640 TTGCAACGCGGAAATGGCTA
1 TCGCAACACGAAAATGACTA
395660 TCGCAA
1 TCGCAA
395666 TGCGAAATGA
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.41, C:0.24, G:0.18, T:0.17
Consensus pattern (20 bp):
TCGCAACACGAAAATGACTA
Found at i:395674 original size:19 final size:20
Alignment explanation
Indices: 395619--395686 Score: 66
Period size: 20 Copynumber: 3.5 Consensus size: 20
395609 GAAACTTAAA
* *
395619 ATCGCAACACGAAAATGACT
1 ATCGCAACGCGGAAATGACT
* *
395639 ATTGCAACGCGGAAATGGCT
1 ATCGCAACGCGGAAATGACT
* **
395659 ATCGCAATGC-GAAATGAAA
1 ATCGCAACGCGGAAATGACT
395678 ATCGCAACG
1 ATCGCAACG
395687 ACAAAATCGC
Statistics
Matches: 38, Mismatches: 10, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
19 14 0.37
20 24 0.63
ACGTcount: A:0.40, C:0.22, G:0.22, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGGAAATGACT
Found at i:395694 original size:14 final size:14
Alignment explanation
Indices: 395675--395732 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
395665 ATGCGAAATG
395675 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
395689 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
395705 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
395721 AAAATCGCAACG
1 AAAATCGCAACG
395733 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:395717 original size:32 final size:33
Alignment explanation
Indices: 395659--395737 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
395649 GGAAATGGCT
395659 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
395692 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
395724 ATCGCAACGCGAAA
1 ATCGCAATGCGAAA
395738 CACAAATCGC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 29 0.64
33 16 0.36
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:395783 original size:14 final size:14
Alignment explanation
Indices: 395760--395823 Score: 67
Period size: 14 Copynumber: 4.4 Consensus size: 14
395750 TGCGATTTTC
395760 ATTTTG-CGTTGCG
1 ATTTTGTCGTTGCG
395773 ATTTTGTCGTTGCG
1 ATTTTGTCGTTGCG
*
395787 ATTTCATTTCGCATTGCG
1 ATTT--TGTCG--TTGCG
*
395805 ATTTTGTCATTGCG
1 ATTTTGTCGTTGCG
395819 ATTTT
1 ATTTT
395824 CATTTCGCAT
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
13 6 0.14
14 21 0.49
16 7 0.16
18 9 0.21
ACGTcount: A:0.12, C:0.16, G:0.22, T:0.50
Consensus pattern (14 bp):
ATTTTGTCGTTGCG
Found at i:395830 original size:33 final size:33
Alignment explanation
Indices: 395747--395839 Score: 152
Period size: 32 Copynumber: 2.8 Consensus size: 33
395737 ACACAAATCG
* *
395747 CATTGCGATTTTCATTTTGCGTTGCGATTTTGT
1 CATTGCGATTTTCATTTCGCATTGCGATTTTGT
*
395780 CGTTGCGA-TTTCATTTCGCATTGCGATTTTGT
1 CATTGCGATTTTCATTTCGCATTGCGATTTTGT
395812 CATTGCGATTTTCATTTCGCATTGCGAT
1 CATTGCGATTTTCATTTCGCATTGCGAT
395840 AGCCATTTCC
Statistics
Matches: 55, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
32 29 0.53
33 26 0.47
ACGTcount: A:0.14, C:0.18, G:0.20, T:0.47
Consensus pattern (33 bp):
CATTGCGATTTTCATTTCGCATTGCGATTTTGT
Found at i:395866 original size:20 final size:19
Alignment explanation
Indices: 395812--395867 Score: 58
Period size: 20 Copynumber: 2.9 Consensus size: 19
395802 GCGATTTTGT
**
395812 CATTGCGATTTTCATTTCG
1 CATTGCGATAGTCATTTCG
*
395831 CATTGCGATAGCCATTTCCG
1 CATTGCGATAGTCATTT-CG
* *
395851 CGTTGTGATAGTCATTT
1 CATTGCGATAGTCATTT
395868 TCGTGTTGCG
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.18, C:0.21, G:0.20, T:0.41
Consensus pattern (19 bp):
CATTGCGATAGTCATTTCG
Found at i:396386 original size:18 final size:18
Alignment explanation
Indices: 396360--396404 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
396350 GTCGATCAGA
*
396360 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
396378 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
396396 TGATGGCTC
1 TGATGGCTC
396405 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:397773 original size:20 final size:20
Alignment explanation
Indices: 397725--397783 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
397715 AATAGTTTCT
** *
397725 GAAAATGAAAATCGCAACAC
1 GAAAATGACTATCGCAACGC
397745 GAAAATGACTATCGCAACGC
1 GAAAATGACTATCGCAACGC
**
397765 GAATTTGACTATCGCAACG
1 GAAAATGACTATCGCAACG
397784 AGAGAATCGC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.42, C:0.22, G:0.19, T:0.17
Consensus pattern (20 bp):
GAAAATGACTATCGCAACGC
Found at i:398071 original size:22 final size:22
Alignment explanation
Indices: 398044--398087 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
398034 GATGGAGATA
398044 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
398066 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
398088 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:398285 original size:21 final size:22
Alignment explanation
Indices: 398255--398350 Score: 78
Period size: 20 Copynumber: 4.6 Consensus size: 22
398245 CGCTTTGAAA
*
398255 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGATTATGTAAGT
* * *
398276 ATCGCGTTGCGA--AAGTCAGT
1 ATCGCATTGCGATTATGTAAGT
* * * *
398296 ATCTCGTTGCGATTTTGT-ATT
1 ATCGCATTGCGATTATGTAAGT
398317 ATCGCATTGCGA-TA-GTAAGT
1 ATCGCATTGCGATTATGTAAGT
398337 ATCGCATTGCGATT
1 ATCGCATTGCGATT
398351 TTCCCAATTC
Statistics
Matches: 59, Mismatches: 11, Indels: 10
0.74 0.14 0.12
Matches are distributed among these distances:
19 5 0.08
20 28 0.47
21 24 0.41
22 2 0.03
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.38
Consensus pattern (22 bp):
ATCGCATTGCGATTATGTAAGT
Found at i:398318 original size:41 final size:41
Alignment explanation
Indices: 398255--398352 Score: 142
Period size: 41 Copynumber: 2.4 Consensus size: 41
398245 CGCTTTGAAA
* * *
398255 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGT
* * *
398296 ATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTAAGT
1 ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGT
398337 ATCGCATTGCGATTTT
1 ATCGCATTGCGATTTT
398353 CCCAATTCGC
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 49 1.00
ACGTcount: A:0.22, C:0.16, G:0.22, T:0.39
Consensus pattern (41 bp):
ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGT
Found at i:398368 original size:41 final size:41
Alignment explanation
Indices: 398255--398370 Score: 108
Period size: 41 Copynumber: 2.8 Consensus size: 41
398245 CGCTTTGAAA
* ** * * *
398255 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTAAGT
* * ** * *
398296 ATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTAAGT
1 ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTAAGT
398337 ATCGCATTGCGATTTTCCCAAT-TCGCGTTGCGAT
1 ATCGCATTGCGATTTT-CCAATATCGCGTTGCGAT
398371 TTACTTATTC
Statistics
Matches: 62, Mismatches: 12, Indels: 2
0.82 0.16 0.03
Matches are distributed among these distances:
41 60 0.97
42 2 0.03
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.37
Consensus pattern (41 bp):
ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTAAGT
Found at i:398460 original size:21 final size:21
Alignment explanation
Indices: 398420--398460 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
398410 ACTGTAGACC
**
398420 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
398441 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
398461 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATCCAACT
Found at i:407694 original size:37 final size:36
Alignment explanation
Indices: 407635--407753 Score: 170
Period size: 35 Copynumber: 3.3 Consensus size: 36
407625 ATCCCATTAT
*
407635 CATTTTTC-AACAAACATCTACCAAACTTTGAAAAAC
1 CATTTTTCAAACAAACATTTACCAAACTTTG-AAAAC
* *
407671 TATTTTTCAAATAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAACAAACATTTACCAAACTTTGAAAAC
*
407707 CA-TTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAACAAACATTTACCAAACTTTGAAAAC
407742 CATTTTTTCAAA
1 CA-TTTTTCAAA
407754 GTTGGTTACC
Statistics
Matches: 75, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
35 34 0.45
36 13 0.17
37 28 0.37
ACGTcount: A:0.44, C:0.20, G:0.03, T:0.33
Consensus pattern (36 bp):
CATTTTTCAAACAAACATTTACCAAACTTTGAAAAC
Found at i:407710 original size:21 final size:21
Alignment explanation
Indices: 407686--407746 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
407676 TTCAAATAAA
407686 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
*
407707 CATTT-TCAAA----G-AAA-
1 CATTTACCAAACTTTGAAAAC
407721 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
407742 CATTT
1 CATTT
407747 TTTCAAAGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 7 0.23
16 1 0.03
19 1 0.03
20 7 0.23
21 10 0.32
ACGTcount: A:0.43, C:0.21, G:0.05, T:0.31
Consensus pattern (21 bp):
CATTTACCAAACTTTGAAAAC
Found at i:407763 original size:35 final size:36
Alignment explanation
Indices: 407637--407781 Score: 133
Period size: 35 Copynumber: 4.1 Consensus size: 36
407627 CCCATTATCA
*
407637 TTTTTCAACA-AACA-TCTACCAAACTTTGAAAAAC-T
1 TTTTTCAA-AGAACAGT-TACCAAACTTTGAAAACCAT
* *
407672 ATTTTTCAAATAAACATTTACCAAACTTTGAAAACCA-
1 -TTTTTCAAA-GAACAGTTACCAAACTTTGAAAACCAT
*
407709 -TTTTCAAAGAAACATTTACCAAACTTTGAAAACCAT
1 TTTTTCAAAG-AACAGTTACCAAACTTTGAAAACCAT
***
407745 TTTTTCAAAG-TTGGTTACCAAAC-TTGAAAACCAT
1 TTTTTCAAAGAACAGTTACCAAACTTTGAAAACCAT
407779 TTT
1 TTT
407782 AATAATTTCA
Statistics
Matches: 96, Mismatches: 6, Indels: 16
0.81 0.05 0.14
Matches are distributed among these distances:
34 14 0.15
35 43 0.45
36 8 0.08
37 30 0.31
38 1 0.01
ACGTcount: A:0.41, C:0.19, G:0.06, T:0.34
Consensus pattern (36 bp):
TTTTTCAAAGAACAGTTACCAAACTTTGAAAACCAT
Found at i:416637 original size:60 final size:59
Alignment explanation
Indices: 416510--416649 Score: 142
Period size: 59 Copynumber: 2.4 Consensus size: 59
416500 TATTTGGATG
* * * *
416510 AATTTAGCGATGAAATTGGAATATTCAAAAGTTTGAAGACTAATTTAGAAAGAGGTCAT
1 AATTTAGGGATGAAATTAGAATACTCAAAAGTATGAAGACTAATTTAGAAAGAGGTCAT
* * *
416569 AGTTTAGGGATGAAATTAGAATGCTCAAAAGTAT-AATGACATAA-TTA-AAATGAGATTCAT
1 AATTTAGGGATGAAATTAGAATACTCAAAAGTATGAA-GAC-TAATTTAGAAA-GAG-GTCAT
* *
416629 AATTTAGGGATTAATTTAGAA
1 AATTTAGGGATGAAATTAGAA
416650 AGGCGGTCAT
Statistics
Matches: 67, Mismatches: 10, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
58 5 0.07
59 37 0.55
60 25 0.37
ACGTcount: A:0.44, C:0.06, G:0.19, T:0.31
Consensus pattern (59 bp):
AATTTAGGGATGAAATTAGAATACTCAAAAGTATGAAGACTAATTTAGAAAGAGGTCAT
Found at i:417153 original size:32 final size:32
Alignment explanation
Indices: 417098--417183 Score: 113
Period size: 32 Copynumber: 2.7 Consensus size: 32
417088 CTTTTAATAG
* * *
417098 AATAGTCATT-AATTTTATTAAAATGCTATAA
1 AATAGACATTAAATTTTATCAAAATGCTAAAA
*
417129 AATAGACATTAAATTTTATCAAAATGTTAAAA
1 AATAGACATTAAATTTTATCAAAATGCTAAAA
417161 AATA-ACCATTAAATTTTATCAAA
1 AATAGA-CATTAAATTTTATCAAA
417184 TTATTACAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
31 10 0.20
32 39 0.80
ACGTcount: A:0.50, C:0.08, G:0.05, T:0.37
Consensus pattern (32 bp):
AATAGACATTAAATTTTATCAAAATGCTAAAA
Found at i:417195 original size:32 final size:31
Alignment explanation
Indices: 417104--417205 Score: 98
Period size: 32 Copynumber: 3.2 Consensus size: 31
417094 ATAGAATAGT
* ** *
417104 CATT-AATTTTATTAAAATGCTATAAAATAGA
1 CATTAAATTTTATCAAAATATTAAAAAATA-A
*
417135 CATTAAATTTTATCAAAATGTTAAAAAATAA
1 CATTAAATTTTATCAAAATATTAAAAAATAA
* * *
417166 CCATTAAATTTTATCAAATTATTACAAAATGAT
1 -CATTAAATTTTATCAAAATATTAAAAAAT-AA
417199 CATTAAA
1 CATTAAA
417206 ACTCTTTGAA
Statistics
Matches: 61, Mismatches: 7, Indels: 5
0.84 0.10 0.07
Matches are distributed among these distances:
31 5 0.08
32 55 0.90
33 1 0.02
ACGTcount: A:0.50, C:0.09, G:0.04, T:0.37
Consensus pattern (31 bp):
CATTAAATTTTATCAAAATATTAAAAAATAA
Found at i:417459 original size:32 final size:31
Alignment explanation
Indices: 417392--417478 Score: 95
Period size: 32 Copynumber: 2.8 Consensus size: 31
417382 CTATAATGAA
* * *
417392 TTATAAAAGTTCGATAAATTTAATGACTATT
1 TTATAACAGTTTGATAAATTTAATGACTATC
* *
417423 TTATAATATTTTGATAAAATTTAATGA-TCATC
1 TTATAACAGTTTGAT-AAATTTAATGACT-ATC
*
417455 TTATAGCAGTTTGATAAATTTAAT
1 TTATAACAGTTTGATAAATTTAAT
417479 AATTTTTATA
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
31 22 0.47
32 25 0.53
ACGTcount: A:0.40, C:0.06, G:0.09, T:0.45
Consensus pattern (31 bp):
TTATAACAGTTTGATAAATTTAATGACTATC
Found at i:420523 original size:37 final size:40
Alignment explanation
Indices: 420468--420553 Score: 110
Period size: 37 Copynumber: 2.3 Consensus size: 40
420458 TGGTAACCAA
420468 CTTTGAAAAA-ATGGTTTTCAAAG-TT-TGGTAAATGTTT
1 CTTTGAAAAATATGGTTTTCAAAGTTTATGGTAAATGTTT
* *
420505 CTTTGAAAAATA-GTTTTTCAAAGTTTATGGTAGATGTTT
1 CTTTGAAAAATATGGTTTTCAAAGTTTATGGTAAATGTTT
*
420544 -GTTGAAAAAT
1 CTTTGAAAAAT
420554 GATAATGGGA
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
37 20 0.47
38 12 0.28
39 11 0.26
ACGTcount: A:0.34, C:0.05, G:0.19, T:0.43
Consensus pattern (40 bp):
CTTTGAAAAATATGGTTTTCAAAGTTTATGGTAAATGTTT
Found at i:425084 original size:21 final size:21
Alignment explanation
Indices: 425060--425120 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
425050 AACTTTGAAA
425060 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
*
425081 AAAT-G-TTT---A-TTT-GA
1 AAATGGTTTTCAAAGTTTGGT
425095 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
425116 AAATG
1 AAATG
425121 TTTCTTTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 4 0.13
16 4 0.13
19 4 0.13
20 4 0.13
21 10 0.32
ACGTcount: A:0.33, C:0.03, G:0.21, T:0.43
Consensus pattern (21 bp):
AAATGGTTTTCAAAGTTTGGT
Found at i:425098 original size:35 final size:34
Alignment explanation
Indices: 425059--425169 Score: 150
Period size: 35 Copynumber: 3.1 Consensus size: 34
425049 CAACTTTGAA
425059 AAAATGGTTTTCAAAGTTTGGTAAATGTTTATTTG
1 AAAATGGTTTTCAAAGTTTGGTAAATGTTT-TTTG
425094 AAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTG
1 AAAATGGTTTTCAAAGTTTGGTAAATGTTT-TTTG
* * *
425129 AAAAATAGTTTTTCAAAGTTATGGTAGATGTTTGTTG
1 -AAAAT-GGTTTTCAAAGTT-TGGTAAATGTTTTTTG
425166 AAAA
1 AAAA
425170 ATGATAATGG
Statistics
Matches: 69, Mismatches: 4, Indels: 5
0.88 0.05 0.06
Matches are distributed among these distances:
35 34 0.49
36 9 0.13
37 15 0.22
38 11 0.16
ACGTcount: A:0.33, C:0.04, G:0.20, T:0.43
Consensus pattern (34 bp):
AAAATGGTTTTCAAAGTTTGGTAAATGTTTTTTG
Found at i:431882 original size:2 final size:2
Alignment explanation
Indices: 431875--431909 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
431865 AAAGAAAATG
*
431875 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
431910 AAAGTATATG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:436067 original size:25 final size:25
Alignment explanation
Indices: 436039--436089 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
436029 ATAGAGAATA
* *
436039 CAAATCGACATGGATGACCATACTG
1 CAAATCGACATAGATAACCATACTG
*
436064 CAAATCGGCATAGATAACCATACTG
1 CAAATCGACATAGATAACCATACTG
436089 C
1 C
436090 TGAGATGAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (25 bp):
CAAATCGACATAGATAACCATACTG
Found at i:441541 original size:21 final size:21
Alignment explanation
Indices: 441515--441557 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
441505 TCATGGATGA
441515 TCTGTCTCTGTATTTTTCCTT
1 TCTGTCTCTGTATTTTTCCTT
*
441536 TCTGTCTCTTTATTTTTCCTT
1 TCTGTCTCTGTATTTTTCCTT
441557 T
1 T
441558 AATCATGTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.05, C:0.23, G:0.07, T:0.65
Consensus pattern (21 bp):
TCTGTCTCTGTATTTTTCCTT
Found at i:446380 original size:74 final size:73
Alignment explanation
Indices: 446166--446443 Score: 266
Period size: 73 Copynumber: 3.8 Consensus size: 73
446156 AATATAATTT
* * *
446166 TTTATTAACTATAATTTATAATAGTTTATATATTTTT-ATTTTTGTTAATGGAAGAAGTAATT-T
1 TTTATTAACTATAATTTAAAATAATTTATATATTTTTAATTTTTGTTAATGGAA-AAATAATTCT
446229 T-ATTTTTA
65 TAATTTTTA
* ** ** * *
446237 TTTATTAACTATAATTTACAAAAAAAATACGTATTTTAAATTTTTGTTAAT-GAAAGAATTAGTT
1 TTTATTAACTATAATTTA-AAATAATTTATATATTTTTAATTTTTGTTAATGGAAA-AA-TAATT
446301 CTTAATTTTTA
63 CTTAATTTTTA
* * * *
446312 TTTCTTAATTATAATTTAAAATATTTTATATATTTTTAATTTTTGTTATTGGACAAAATAATTCT
1 TTTATTAACTATAATTTAAAATAATTTATATATTTTTAATTTTTGTTAATGGA-AAAATAATTCT
446377 TAA-TTTTA
65 TAATTTTTA
* * *
446385 TTTATTAATTATAATTT--AATAA-TTATATATTATATTAAATTGTAGTTAATGGAATAAAT
1 TTTATTAACTATAATTTAAAATAATTTATATATT-T-TT-AATTTTTGTTAATGGAA-AAAT
446444 TATTTCTTTC
Statistics
Matches: 169, Mismatches: 26, Indels: 22
0.78 0.12 0.10
Matches are distributed among these distances:
70 9 0.05
71 24 0.14
72 18 0.11
73 54 0.32
74 35 0.21
75 27 0.16
76 2 0.01
ACGTcount: A:0.38, C:0.03, G:0.06, T:0.52
Consensus pattern (73 bp):
TTTATTAACTATAATTTAAAATAATTTATATATTTTTAATTTTTGTTAATGGAAAAATAATTCTT
AATTTTTA
Found at i:446451 original size:148 final size:146
Alignment explanation
Indices: 446170--446435 Score: 349
Period size: 147 Copynumber: 1.8 Consensus size: 146
446160 TAATTTTTTA
* * *
446170 TTAACTATAATTTATAATAGTTTATATATTTTTATTTTTGTTAATGGAAGAAGTAATTTTATTTT
1 TTAACTATAATTTAAAATAGTTTATATATTTTTATTTTTGTTAATGGAAGAAATAATTTTAATTT
* * *
446235 TATTTATTAACTATAATTTACAAAAAAAATACGTATTTTAAATTTTTGTTAATGAAAGAATTAGT
66 TATTTATTAACTATAATTTACAAAAAAAATACGTATATTAAATTGTAGTTAATGAAAGAATTAGT
446300 TCTTAATTTTTATTTC
131 TCTTAATTTTTATTTC
* * *
446316 TTAATTATAATTTAAAATATTTTATATATTTTTAATTTTTGTTATTGGACA-AAATAATTCTTAA
1 TTAACTATAATTTAAAATAGTTTATATATTTTT-ATTTTTGTTAATGGA-AGAAATAATT-TTAA
* ** * *
446380 TTTTATTTATTAATTATAATTTA-ATAATTATATA-TTATATTAAATTGTAGTTAATG
63 TTTTATTTATTAACTATAATTTACA-AAAAAAATACGTATATTAAATTGTAGTTAATG
446436 GAATAAATTA
Statistics
Matches: 102, Mismatches: 14, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
146 30 0.29
147 40 0.39
148 32 0.31
ACGTcount: A:0.38, C:0.03, G:0.06, T:0.53
Consensus pattern (146 bp):
TTAACTATAATTTAAAATAGTTTATATATTTTTATTTTTGTTAATGGAAGAAATAATTTTAATTT
TATTTATTAACTATAATTTACAAAAAAAATACGTATATTAAATTGTAGTTAATGAAAGAATTAGT
TCTTAATTTTTATTTC
Found at i:447994 original size:120 final size:120
Alignment explanation
Indices: 447727--447994 Score: 288
Period size: 120 Copynumber: 2.2 Consensus size: 120
447717 ATTAGTCTTT
* * * * * * * *
447727 AAATCTTTAAATGTTCCATTTTCATCCGTAAACTATAATTATCATTCTAAATTAATCCTCAAACT
1 AAATTTTTAAATATTTCAATTTCATCCATAAACTATAACTATAATTCTAAATCAATCCTCAAACT
* * * * * *
447792 TTTGAATATTTTAGTTCCATCCCCAAATATGATCTTCATTTTAAATTAGTCCATA
66 TTTGAACATTTCAATTCCATCCCCAAATAGGATCTTCATTCTAAATTAGTCCACA
* * * * *
447847 AAATTGTTAAACATTTCAA-TTCTATCCATAAACTATAACTATAATTCTAAATCAGTCCTTAATC
1 AAATTTTTAAATATTTCAATTTC-ATCCATAAACTATAACTATAATTCTAAATCAATCCTCAAAC
* * * *
447911 TTTTGAACATTTCAATAT-TATCCCGAAATAGGATCTTCATTCTAAATTGGTCCCCA
65 TTTTGAACATTTCAAT-TCCATCCCCAAATAGGATCTTCATTCTAAATTAGTCCACA
*
447967 AACTTTTTAAATATTTCAATTTCATCCA
1 AAATTTTTAAATATTTCAATTTCATCCA
447995 AAATTAATCG
Statistics
Matches: 119, Mismatches: 26, Indels: 6
0.79 0.17 0.04
Matches are distributed among these distances:
119 3 0.03
120 112 0.94
121 4 0.03
ACGTcount: A:0.35, C:0.19, G:0.05, T:0.40
Consensus pattern (120 bp):
AAATTTTTAAATATTTCAATTTCATCCATAAACTATAACTATAATTCTAAATCAATCCTCAAACT
TTTGAACATTTCAATTCCATCCCCAAATAGGATCTTCATTCTAAATTAGTCCACA
Found at i:448834 original size:25 final size:26
Alignment explanation
Indices: 448806--448856 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 26
448796 TTTTATTAAA
*
448806 AATAAATTAAAATA-TTAAAATATAT
1 AATAAATTAAAATATTTAAAAAATAT
*
448831 AATAATTTAAAATATTTAAAAAATAT
1 AATAAATTAAAATATTTAAAAAATAT
448857 TATTCTCATC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 13 0.57
26 10 0.43
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (26 bp):
AATAAATTAAAATATTTAAAAAATAT
Found at i:448843 original size:35 final size:35
Alignment explanation
Indices: 448777--448844 Score: 82
Period size: 35 Copynumber: 1.9 Consensus size: 35
448767 TTTAAAAATT
** *
448777 TTAAAAGATAAAAATATATTTTTATTAAAAATAAA
1 TTAAAAGATAAAAATATATAATAATTAAAAATAAA
* * *
448812 TTAAAATATTAAAATATATAATAATTTAAAATA
1 TTAAAAGATAAAAATATATAATAATTAAAAATA
448845 TTTAAAAAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
35 27 1.00
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.38
Consensus pattern (35 bp):
TTAAAAGATAAAAATATATAATAATTAAAAATAAA
Found at i:452812 original size:8 final size:8
Alignment explanation
Indices: 452799--452839 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
452789 CTCATTTTCA
452799 GAGAATTT
1 GAGAATTT
452807 GAGAATTT
1 GAGAATTT
*
452815 -AGAGTTT
1 GAGAATTT
*
452822 GGGAATTT
1 GAGAATTT
452830 GAGAATTT
1 GAGAATTT
452838 GA
1 GA
452840 AAGATTGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (8 bp):
GAGAATTT
Found at i:453235 original size:128 final size:128
Alignment explanation
Indices: 452907--453535 Score: 1183
Period size: 128 Copynumber: 4.9 Consensus size: 128
452897 CTATAATCGG
452907 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGT
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGT
452972 TATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAG--ATATCAGTACCTATTA-
66 TATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
*
453032 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCACCTTCCATTATTTCGTCAGAGAATATGT
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGT
*
453097 TATCATTGCCCTATTATGTCACTCATGTTCCTCGGGGACACTAGATATATCAGTACCTATTAT
66 TATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
453160 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGT
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGT
453225 TATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
66 TATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
453288 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGT
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGT
453353 TATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
66 TATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
** *
453416 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTTTATTATTTCATCAGAGAATATGT
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGT
*
453481 TATCATTGCCCTATTATGTCACTCATGTCCCTCAGGGACACTAGATATATCAGTA
66 TATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
453536 AATCAGGTAA
Statistics
Matches: 493, Mismatches: 8, Indels: 3
0.98 0.02 0.01
Matches are distributed among these distances:
125 107 0.22
127 16 0.03
128 370 0.75
ACGTcount: A:0.23, C:0.25, G:0.19, T:0.32
Consensus pattern (128 bp):
TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGT
TATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
Found at i:453810 original size:14 final size:14
Alignment explanation
Indices: 453791--453820 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
453781 CATAAGTTGA
*
453791 TTTTAATGTATACG
1 TTTTAATATATACG
453805 TTTTAATATATACG
1 TTTTAATATATACG
453819 TT
1 TT
453821 AATGATAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.30, C:0.07, G:0.10, T:0.53
Consensus pattern (14 bp):
TTTTAATATATACG
Found at i:453997 original size:33 final size:33
Alignment explanation
Indices: 453936--454035 Score: 128
Period size: 34 Copynumber: 3.0 Consensus size: 33
453926 AAATTTAATG
*
453936 TTAAATTTCGAATACTATAATTTATATTTTAAAT
1 TTAAATTT-GAATAATATAATTTATATTTTAAAT
* * * *
453970 TTAAATTTGAATAATATTATTTTTATTTTTATT
1 TTAAATTTGAATAATATAATTTATATTTTAAAT
*
454003 TTAAATTTTGAATAATATAATTTGTATTTTAAA
1 TTAAA-TTTGAATAATATAATTTATATTTTAAA
454036 AACATTTATC
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
33 25 0.45
34 31 0.55
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (33 bp):
TTAAATTTGAATAATATAATTTATATTTTAAAT
Found at i:454643 original size:21 final size:21
Alignment explanation
Indices: 454555--454648 Score: 129
Period size: 21 Copynumber: 4.5 Consensus size: 21
454545 TATGGTATAA
*
454555 AACCCTGCGGGCTAGGCATGT
1 AACCCTGCGGGCTAGGAATGT
*
454576 AA-CCTGGCGGGCTAGGCATGT
1 AACCCT-GCGGGCTAGGAATGT
454597 AA-CCTGGCGGGCTAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
*
454618 AACCCTGCGGGCTTGGAATGT
1 AACCCTGCGGGCTAGGAATGT
454639 AACCCTGCGG
1 AACCCTGCGG
454649 AGATGGCATA
Statistics
Matches: 69, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
20 3 0.04
21 63 0.91
22 3 0.04
ACGTcount: A:0.20, C:0.26, G:0.35, T:0.19
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:456459 original size:31 final size:32
Alignment explanation
Indices: 456424--456493 Score: 81
Period size: 31 Copynumber: 2.2 Consensus size: 32
456414 TCTAAATAAT
* *
456424 AATAATCATATAAAT-ATTATTTTAATA-AAAA
1 AATAAT-ATATAAATAAATATATTAATATAAAA
* *
456455 AATAATATTTACATAAATATATTAATATAAAA
1 AATAATATATAAATAAATATATTAATATAAAA
456487 AATAATA
1 AATAATA
456494 ACTATTTAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
30 6 0.18
31 16 0.48
32 11 0.33
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (32 bp):
AATAATATATAAATAAATATATTAATATAAAA
Found at i:456459 original size:34 final size:32
Alignment explanation
Indices: 456416--456494 Score: 88
Period size: 34 Copynumber: 2.4 Consensus size: 32
456406 AAAATAATTC
* *
456416 TAAATAATAATAATCATATAAATATTATTTTAATA
1 TAAAAAATAATAATCACATAAATA-TA--TTAATA
* *
456451 -AAAAAATAATATTTACATAAATATATTAATA
1 TAAAAAATAATAATCACATAAATATATTAATA
456482 TAAAAAATAATAA
1 TAAAAAATAATAA
456495 CTATTTAAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
31 6 0.16
32 11 0.29
33 2 0.05
34 19 0.50
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.37
Consensus pattern (32 bp):
TAAAAAATAATAATCACATAAATATATTAATA
Found at i:457689 original size:12 final size:14
Alignment explanation
Indices: 457649--457689 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
457639 AACATATTAA
457649 ATAATAAATATAATT
1 ATAA-AAATATAATT
*
457664 ATAAAACTATAATT
1 ATAAAAATATAATT
457678 A-AAAAATA-AATT
1 ATAAAAATATAATT
457690 TGAGGCTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 4 0.17
13 6 0.25
14 10 0.42
15 4 0.17
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.34
Consensus pattern (14 bp):
ATAAAAATATAATT
Found at i:460094 original size:29 final size:28
Alignment explanation
Indices: 460034--460306 Score: 214
Period size: 29 Copynumber: 9.4 Consensus size: 28
460024 AAAAATTACA
* * *
460034 AAAATTTCACATTTATTAAAAATAATTACC
1 AAAATGTCAC-TTT-TTACAAATAATTCCC
* *
460064 AAAATATCACTGTTTTACAAACAATTCCC
1 AAAATGTCACT-TTTTACAAATAATTCCC
* * *
460093 AAAATGTCATCATTTTAAAAATAATTACC
1 AAAATGTCA-CTTTTTACAAATAATTCCC
* ** *
460122 AGAATGTCACTATTTTA-AAA-AAAACAC
1 AAAATGTCACT-TTTTACAAATAATTCCC
*
460149 AAAATGTCACTTTTTTAAAAAAATAATTCCC
1 AAAATGTCAC-TTTTT--ACAAATAATTCCC
* *
460180 AAAATGTCACATTTTTCAAAAATAATTCTC
1 AAAATGTCAC-TTTTT-ACAAATAATTCCC
460210 AAAATGTCACCTTTTT-CAAAATAATTCCC
1 AAAATGTCA-CTTTTTAC-AAATAATTCCC
*
460239 AAAATATCACATTTTT-CAAAATAATTCCC
1 AAAATGTCAC-TTTTTAC-AAATAATTCCC
* *
460268 -AAATATCACTTTTTTCAAAATAATTCCC
1 AAAATGTCACTTTTTAC-AAATAATTCCC
460296 AAAATGTCACT
1 AAAATGTCACT
460307 AGGTCGGGTC
Statistics
Matches: 204, Mismatches: 26, Indels: 27
0.79 0.10 0.11
Matches are distributed among these distances:
27 21 0.10
28 28 0.14
29 94 0.46
30 41 0.20
31 20 0.10
ACGTcount: A:0.45, C:0.18, G:0.03, T:0.34
Consensus pattern (28 bp):
AAAATGTCACTTTTTACAAATAATTCCC
Found at i:460132 original size:58 final size:57
Alignment explanation
Indices: 460034--460306 Score: 259
Period size: 58 Copynumber: 4.7 Consensus size: 57
460024 AAAAATTACA
* * * * *
460034 AAAATTTCACATTTATTAAAAATAATTACCAAAATATCACTGTTTTACAAACAATTCCC
1 AAAATGTCAC-TTTTTTAAAAATAATTCCCAAAATGTCACT-TTTTACAAATAATTCCC
* * * ** *
460093 AAAATGTCA-TCATTTTAAAAATAATTACCAGAATGTCACTATTTTA-AAA-AAAACAC
1 AAAATGTCACT-TTTTTAAAAATAATTCCCAAAATGTCACT-TTTTACAAATAATTCCC
* *
460149 AAAATGTCACTTTTTTAAAAAAATAATTCCCAAAATGTCACATTTTTCAAAAATAATTCTC
1 AAAATGTCACTTTTTT--AAAAATAATTCCCAAAATGTCAC-TTTTT-ACAAATAATTCCC
* * *
460210 AAAATGTCACCTTTTTCAAAATAATTCCCAAAATATCACATTTTT-CAAAATAATTCCC
1 AAAATGTCACTTTTTTAAAAATAATTCCCAAAATGTCAC-TTTTTAC-AAATAATTCCC
* *
460268 -AAATATCACTTTTTTCAAAATAATTCCCAAAATGTCACT
1 AAAATGTCACTTTTTTAAAAATAATTCCCAAAATGTCACT
460307 AGGTCGGGTC
Statistics
Matches: 182, Mismatches: 23, Indels: 21
0.81 0.10 0.09
Matches are distributed among these distances:
56 18 0.10
57 40 0.22
58 65 0.36
59 37 0.20
60 3 0.02
61 19 0.10
ACGTcount: A:0.45, C:0.18, G:0.03, T:0.34
Consensus pattern (57 bp):
AAAATGTCACTTTTTTAAAAATAATTCCCAAAATGTCACTTTTTACAAATAATTCCC
Found at i:460203 original size:146 final size:147
Alignment explanation
Indices: 460034--460306 Score: 344
Period size: 146 Copynumber: 1.9 Consensus size: 147
460024 AAAAATTACA
*
460034 AAAATTTCACATTTATTAAAAATAATTAC-CAAAATATCA-CTGTTTT-ACAAACAATTCCCAAA
1 AAAATGTCACATTTATTAAAAATAATT-CTCAAAATATCACCT-TTTTCA-AAACAATTCCCAAA
* *
460096 ATGTCATCA-TTTTAAAAATAATTACCAGAATGTCACTATTTT-AAAA-AAAACACAAAATGTCA
63 ATATCA-CATTTTTAAAAATAATTACCA-AATATCACTATTTTCAAAATAAAACACAAAATGTCA
460158 CTTTTTTAAAAAAATAATTCCC
126 CTTTTTTAAAAAAATAATTCCC
* *
460180 AAAATGTCACATTT-TTCAAAAATAATTCTCAAAATGTCACCTTTTTCAAAATAATTCCCAAAAT
1 AAAATGTCACATTTATT-AAAAATAATTCTCAAAATATCACCTTTTTCAAAACAATTCCCAAAAT
* * * ** *
460244 ATCACATTTTTCAAAATAATTCCCAAATATCACTTTTTTCAAAATAATTCCCAAAATGTCACT
65 ATCACATTTTTAAAAATAATTACCAAATATCACTATTTTCAAAATAAAACACAAAATGTCACT
460307 AGGTCGGGTC
Statistics
Matches: 109, Mismatches: 11, Indels: 13
0.82 0.08 0.10
Matches are distributed among these distances:
145 17 0.16
146 74 0.68
147 18 0.17
ACGTcount: A:0.45, C:0.18, G:0.03, T:0.34
Consensus pattern (147 bp):
AAAATGTCACATTTATTAAAAATAATTCTCAAAATATCACCTTTTTCAAAACAATTCCCAAAATA
TCACATTTTTAAAAATAATTACCAAATATCACTATTTTCAAAATAAAACACAAAATGTCACTTTT
TTAAAAAAATAATTCCC
Found at i:460290 original size:116 final size:115
Alignment explanation
Indices: 460034--460306 Score: 286
Period size: 116 Copynumber: 2.4 Consensus size: 115
460024 AAAAATTACA
* * * * *
460034 AAAATTTCACATTTATT-AAAAATAATTACCAAAATATCACTGTTTTACAAACAATTCCCAAAAT
1 AAAATATCAC-TTTTTTAAAAAATAATTCCCAAAATGTCACTGTTTTAAAAACAATTCCCAAAAT
* * *
460098 GTCATCATTTTAAAAATAATTACCAGAATGTCACTATTTTAAAAAAAACAC
65 GTCACCATTTTAAAAATAATTACCAAAATATCACTATTTTAAAAAAAACAC
* * *
460149 AAAATGTCACTTTTTTAAAAAAATAATTCCCAAAATGTCACAT-TTTTCAAAAATAATTCTCAAA
1 AAAATATCACTTTTTT-AAAAAATAATTCCCAAAATGTCAC-TGTTTT-AAAAACAATTCCCAAA
* * * **
460213 ATGTCACCTTTTTCAAAATAATTCCCAAAATATCAC-ATTTTTCAAAATAATTC-C
63 ATGTCACCATTTTAAAAATAATTACCAAAATATCACTA-TTTT-AAAA-AAAACAC
* *
460267 CAAATATCACTTTTTT-CAAAATAATTCCCAAAATGTCACT
1 AAAATATCACTTTTTTAAAAAATAATTCCCAAAATGTCACT
460307 AGGTCGGGTC
Statistics
Matches: 133, Mismatches: 18, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
114 5 0.04
115 10 0.08
116 48 0.36
117 48 0.36
118 19 0.14
119 3 0.02
ACGTcount: A:0.45, C:0.18, G:0.03, T:0.34
Consensus pattern (115 bp):
AAAATATCACTTTTTTAAAAAATAATTCCCAAAATGTCACTGTTTTAAAAACAATTCCCAAAATG
TCACCATTTTAAAAATAATTACCAAAATATCACTATTTTAAAAAAAACAC
Found at i:467772 original size:28 final size:29
Alignment explanation
Indices: 467683--467773 Score: 96
Period size: 28 Copynumber: 3.1 Consensus size: 29
467673 AATATCACCG
* *
467683 TTTTATAAATAATTAACAGAATGTCATCTT
1 TTTTA-AAATAATTCACAAAATGTCATCTT
* * *
467713 TTATAAAA-AATTCCCAAAATGTCATTTTT
1 TTTTAAAATAATTCACAAAATGTCA-TCTT
*
467742 TTTTAAAATAATTCTCAAAATGTCA-CTT
1 TTTTAAAATAATTCACAAAATGTCATCTT
467770 TTTT
1 TTTT
467774 TTTCAAAATA
Statistics
Matches: 51, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
28 19 0.37
29 13 0.25
30 19 0.37
ACGTcount: A:0.38, C:0.12, G:0.04, T:0.45
Consensus pattern (29 bp):
TTTTAAAATAATTCACAAAATGTCATCTT
Done.