Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold28
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: 2815568
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.30
Warning! 166732 characters in sequence are not A, C, G, or T
File 2 of 16
Found at i:166936 original size:124 final size:122
Alignment explanation
Indices: 166695--166991 Score: 408
Period size: 124 Copynumber: 2.4 Consensus size: 122
166685 GACTAGGAAA
* *
166695 TGCCACCAACTTGTGTGGGCTTT-----AAAAGGCATCCTGCTCTTTGAGGCCTAAAAAAAATAC
1 TGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCATCCTACTCTTTGAGGACTAAAAAAAATAC
*
166755 CACCAACTTGTGTGGGCCTTAAAAGGAAAAGACGTCCTGCTCTTTGAGGACTAAAGG
66 CACCAACTTGTGTGGGCCTTAAAAGGAAAAGACATCCTGCTCTTTGAGGACTAAAGG
* * * *
166812 TGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCCTACTCTTTGAAGACT-AGAAAAGTG
1 TGCCACCAACTTGTGTGGGCTTTAAAA-GAAAAGGCATCCTACTCTTTGAGGACTAAAAAAAATA
* *
166876 CCACCAACTTGTGTGGGCTTTAAAAGGCAAAAAGGCATCCTGCTCTTTGAGGACTAAAGG
65 CCACCAACTTGTGTGGGCCTTAAAAGG--AAAAGACATCCTGCTCTTTGAGGACTAAAGG
* *
166936 TGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGGCGTCCTACTCTTTGAGGACT
1 TGCCACCAACTTGTGTGGGCTTT-AAAAG-AAAAGGCATCCTACTCTTTGAGGACT
166992 GGAAGGGCTA
Statistics
Matches: 158, Mismatches: 12, Indels: 12
0.87 0.07 0.07
Matches are distributed among these distances:
117 23 0.15
122 32 0.20
123 23 0.15
124 52 0.33
125 28 0.18
ACGTcount: A:0.30, C:0.22, G:0.24, T:0.25
Consensus pattern (122 bp):
TGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCATCCTACTCTTTGAGGACTAAAAAAAATAC
CACCAACTTGTGTGGGCCTTAAAAGGAAAAGACATCCTGCTCTTTGAGGACTAAAGG
Found at i:172723 original size:20 final size:20
Alignment explanation
Indices: 172700--172764 Score: 81
Period size: 20 Copynumber: 3.6 Consensus size: 20
172690 CACCCAGATG
172700 TATCGATACATTATGTTTTA
1 TATCGATACATTATGTTTTA
172720 TATCGATACA-T-TG-----
1 TATCGATACATTATGTTTTA
172733 TATCGATACATTATGTTTTA
1 TATCGATACATTATGTTTTA
172753 TATCGATACATT
1 TATCGATACATT
172765 GTATCGATAC
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
13 10 0.26
14 1 0.03
15 2 0.05
18 2 0.05
19 1 0.03
20 22 0.58
ACGTcount: A:0.31, C:0.12, G:0.11, T:0.46
Consensus pattern (20 bp):
TATCGATACATTATGTTTTA
Found at i:172738 original size:13 final size:13
Alignment explanation
Indices: 172720--172776 Score: 54
Period size: 13 Copynumber: 4.8 Consensus size: 13
172710 TTATGTTTTA
172720 TATCGATACATTG
1 TATCGATACATTG
172733 TATCGATACA-T-
1 TATCGATACATTG
* *
172744 TAT-G-T--TTTA
1 TATCGATACATTG
172753 TATCGATACATTG
1 TATCGATACATTG
172766 TATCGATACAT
1 TATCGATACAT
172777 GATCATTGTA
Statistics
Matches: 35, Mismatches: 3, Indels: 12
0.70 0.06 0.24
Matches are distributed among these distances:
8 1 0.03
9 4 0.11
10 2 0.06
11 4 0.11
12 1 0.03
13 23 0.66
ACGTcount: A:0.32, C:0.14, G:0.12, T:0.42
Consensus pattern (13 bp):
TATCGATACATTG
Found at i:172740 original size:33 final size:33
Alignment explanation
Indices: 172698--172776 Score: 158
Period size: 33 Copynumber: 2.4 Consensus size: 33
172688 CACACCCAGA
172698 TGTATCGATACATTATGTTTTATATCGATACAT
1 TGTATCGATACATTATGTTTTATATCGATACAT
172731 TGTATCGATACATTATGTTTTATATCGATACAT
1 TGTATCGATACATTATGTTTTATATCGATACAT
172764 TGTATCGATACAT
1 TGTATCGATACAT
172777 GATCATTGTA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.30, C:0.13, G:0.13, T:0.44
Consensus pattern (33 bp):
TGTATCGATACATTATGTTTTATATCGATACAT
Found at i:172785 original size:19 final size:19
Alignment explanation
Indices: 172761--172797 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
172751 TATATCGATA
172761 CATTGTATCGATACATGAT
1 CATTGTATCGATACATGAT
172780 CATTGTATCGATACATGA
1 CATTGTATCGATACATGA
172798 AACTGGTAGT
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:0.32, C:0.16, G:0.16, T:0.35
Consensus pattern (19 bp):
CATTGTATCGATACATGAT
Found at i:172850 original size:20 final size:20
Alignment explanation
Indices: 172825--172878 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
172815 CTACCACTAT
*
172825 TTGTATCGATACATGGT-ACA
1 TTGTATCGATACATGATGA-A
172845 TTGTATCGATACATGATGAA
1 TTGTATCGATACATGATGAA
*
172865 TTGTATCAATACAT
1 TTGTATCGATACAT
172879 TGCTTGTAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 30 0.97
21 1 0.03
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (20 bp):
TTGTATCGATACATGATGAA
Found at i:179056 original size:13 final size:13
Alignment explanation
Indices: 179038--179064 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
179028 ACAACATTCC
179038 TTGTATCGATACA
1 TTGTATCGATACA
179051 TTGTATCGATACA
1 TTGTATCGATACA
179064 T
1 T
179065 GGGTTACTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:179228 original size:20 final size:22
Alignment explanation
Indices: 179194--179234 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
179184 ACAAATTTTC
*
179194 TCATTTTTACTTC-AAATCACT
1 TCATTTTTACATCAAAATCACT
179215 TCATTTTT-CATCAAAATCAC
1 TCATTTTTACATCAAAATCAC
179235 CAACAAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.32, C:0.24, G:0.00, T:0.44
Consensus pattern (22 bp):
TCATTTTTACATCAAAATCACT
Found at i:181662 original size:20 final size:20
Alignment explanation
Indices: 181637--181690 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
181627 CTACCACTGT
* *
181637 TTGTATCGATATATGGT-ACA
1 TTGTATCGATACATGATGA-A
181657 TTGTATCGATACATGATGAA
1 TTGTATCGATACATGATGAA
181677 TTGTATCGATACAT
1 TTGTATCGATACAT
181691 TTCTTGTAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 30 0.97
21 1 0.03
ACGTcount: A:0.31, C:0.11, G:0.19, T:0.39
Consensus pattern (20 bp):
TTGTATCGATACATGATGAA
Found at i:183492 original size:132 final size:132
Alignment explanation
Indices: 183249--183485 Score: 297
Period size: 128 Copynumber: 1.8 Consensus size: 132
183239 TTTTAATAAA
* * *
183249 TTCTTTATCACTAAACTTTTGAGATAATTTTATTAAATTATTTCAAATAAGGAACATAATGCATT
1 TTCTTTATCAC-AAACTTTTGAAATAATTTTATTAAATTAGTTCAAATAA-GAACATAATACATT
* * *
183314 TATTTCAAAATTAATATGCTAGATACAAAATAAATTTAAATATTTAAATGTACTTACATCTAATT
64 TATTTCAAAATTAATATACTAGATACAAAACAAATTAAAATATTTAAATGTACTTACATCTAATT
183379 AATT
129 AATT
* *
183383 TTCTTTATCA-AAACCTTTT-AAATAATTTTATTAATTTAGTTCAAATAA-AA-A-AATATATTT
1 TTCTTTATCACAAA-CTTTTGAAATAATTTTATTAAATTAGTTCAAATAAGAACATAATACATTT
* *
183443 ATTTCAAAATTAATATATTGGATTA-AAAACAAAGTTAAAATAT
65 ATTTCAAAATTAATATACTAGA-TACAAAACAAA-TTAAAATAT
183486 AATTTAATTA
Statistics
Matches: 90, Mismatches: 10, Indels: 11
0.81 0.09 0.10
Matches are distributed among these distances:
128 33 0.37
129 11 0.12
130 2 0.02
132 29 0.32
133 5 0.06
134 10 0.11
ACGTcount: A:0.45, C:0.08, G:0.05, T:0.42
Consensus pattern (132 bp):
TTCTTTATCACAAACTTTTGAAATAATTTTATTAAATTAGTTCAAATAAGAACATAATACATTTA
TTTCAAAATTAATATACTAGATACAAAACAAATTAAAATATTTAAATGTACTTACATCTAATTAA
TT
Found at i:184325 original size:32 final size:33
Alignment explanation
Indices: 184247--184325 Score: 124
Period size: 33 Copynumber: 2.4 Consensus size: 33
184237 TTAAGAAATT
184247 TGATCAAAGTTAACCAAAAGTGTATAATATCTA
1 TGATCAAAGTTAACCAAAAGTGTATAATATCTA
* *
184280 AGATCAAAGTTAACCAAAAGTGTATAA-ATTTA
1 TGATCAAAGTTAACCAAAAGTGTATAATATCTA
*
184312 TGATCAAAATTAAC
1 TGATCAAAGTTAAC
184326 AGCTTTAGAA
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
32 16 0.38
33 26 0.62
ACGTcount: A:0.48, C:0.11, G:0.11, T:0.29
Consensus pattern (33 bp):
TGATCAAAGTTAACCAAAAGTGTATAATATCTA
Found at i:188005 original size:19 final size:19
Alignment explanation
Indices: 187981--188043 Score: 84
Period size: 19 Copynumber: 3.6 Consensus size: 19
187971 AAACAGTAAC
187981 TGTATCGATACATAAGTGT
1 TGTATCGATACATAAGTGT
188000 TGTATCGATAC--AA----
1 TGTATCGATACATAAGTGT
188013 TGTATCGATACATAAGTGT
1 TGTATCGATACATAAGTGT
188032 TGTATCGATACA
1 TGTATCGATACA
188044 ATGTATTGCT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 11 0.29
15 2 0.05
17 2 0.05
19 23 0.61
ACGTcount: A:0.33, C:0.13, G:0.19, T:0.35
Consensus pattern (19 bp):
TGTATCGATACATAAGTGT
Found at i:188018 original size:13 final size:13
Alignment explanation
Indices: 188000--188024 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
187990 ACATAAGTGT
188000 TGTATCGATACAA
1 TGTATCGATACAA
188013 TGTATCGATACA
1 TGTATCGATACA
188025 TAAGTGTTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:188022 original size:32 final size:32
Alignment explanation
Indices: 187981--188049 Score: 138
Period size: 32 Copynumber: 2.2 Consensus size: 32
187971 AAACAGTAAC
187981 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
188013 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
188045 TGTAT
1 TGTAT
188050 TGCTACAAAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.33, C:0.12, G:0.19, T:0.36
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:188835 original size:33 final size:33
Alignment explanation
Indices: 188798--188862 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 33
188788 TTCAATGATT
188798 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
188831 TGTATCGATACATATTTTTTTGTATCGATACA
1 TGTATCGATACATAAAATGTTGTATCGATACA
188863 TTTTAAGCTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.34, C:0.12, G:0.14, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:188836 original size:13 final size:13
Alignment explanation
Indices: 188818--188842 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
188808 CATAAAATGT
188818 TGTATCGATACAA
1 TGTATCGATACAA
188831 TGTATCGATACA
1 TGTATCGATACA
188843 TATTTTTTTG
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:188923 original size:13 final size:13
Alignment explanation
Indices: 188905--188932 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
188895 ATTACTCAAA
188905 TGTATCGATACAT
1 TGTATCGATACAT
188918 TGTATCGATACAT
1 TGTATCGATACAT
188931 TG
1 TG
188933 ATCTTTGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:201457 original size:16 final size:16
Alignment explanation
Indices: 201436--201477 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
201426 GATTTGAGTT
201436 ATTTTAGTTTCAAGTA
1 ATTTTAGTTTCAAGTA
* * *
201452 ATTTTAGATTCATGTT
1 ATTTTAGTTTCAAGTA
201468 ATTTTAGTTT
1 ATTTTAGTTT
201478 TAAGAAAATC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.26, C:0.05, G:0.12, T:0.57
Consensus pattern (16 bp):
ATTTTAGTTTCAAGTA
Found at i:201493 original size:32 final size:32
Alignment explanation
Indices: 201433--201493 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 32
201423 TCAGATTTGA
* * **
201433 GTTATTTTAGTTTCAAGTAATTTTAGATTCAT
1 GTTATTTTAGTTTCAAGAAAATCAAGATTCAT
*
201465 GTTATTTTAGTTTTAAGAAAATCAAGATT
1 GTTATTTTAGTTTCAAGAAAATCAAGATT
201494 AACGCTTAAG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 24 1.00
ACGTcount: A:0.33, C:0.05, G:0.13, T:0.49
Consensus pattern (32 bp):
GTTATTTTAGTTTCAAGAAAATCAAGATTCAT
Found at i:201741 original size:16 final size:16
Alignment explanation
Indices: 201722--201754 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
201712 TAATTTTTTA
201722 TTAAA-TTAAATTAAAT
1 TTAAATTTAAA-TAAAT
201738 TTAAATTTAAATAAAT
1 TTAAATTTAAATAAAT
201754 T
1 T
201755 AATTATATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAATTTAAATAAAT
Found at i:207406 original size:27 final size:27
Alignment explanation
Indices: 207365--207418 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
207355 CAGGATTGTG
207365 ATGCTCCTGAAATACAAAAGAAAGTTT
1 ATGCTCCTGAAATACAAAAGAAAGTTT
*
207392 ATGCTCCTGATATACAAAAGAAAGTTT
1 ATGCTCCTGAAATACAAAAGAAAGTTT
207419 TATTTGGCTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.43, C:0.15, G:0.15, T:0.28
Consensus pattern (27 bp):
ATGCTCCTGAAATACAAAAGAAAGTTT
Found at i:208365 original size:14 final size:14
Alignment explanation
Indices: 208346--208395 Score: 75
Period size: 14 Copynumber: 3.6 Consensus size: 14
208336 CCGTGGAATC
208346 TAATTTTTATTATT
1 TAATTTTTATTATT
*
208360 TAATTTTT-TTCATC
1 TAATTTTTATT-ATT
208374 TAATTTTTATTATT
1 TAATTTTTATTATT
208388 TAATTTTT
1 TAATTTTT
208396 TTCGTCCTAC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
13 2 0.06
14 28 0.88
15 2 0.06
ACGTcount: A:0.26, C:0.04, G:0.00, T:0.70
Consensus pattern (14 bp):
TAATTTTTATTATT
Found at i:208383 original size:28 final size:28
Alignment explanation
Indices: 208343--208398 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
208333 GAGCCGTGGA
208343 ATCTAATTTTTATTATTTAATTTTTTTC
1 ATCTAATTTTTATTATTTAATTTTTTTC
208371 ATCTAATTTTTATTATTTAATTTTTTTC
1 ATCTAATTTTTATTATTTAATTTTTTTC
208399 GTCCTACCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.25, C:0.07, G:0.00, T:0.68
Consensus pattern (28 bp):
ATCTAATTTTTATTATTTAATTTTTTTC
Found at i:208411 original size:29 final size:28
Alignment explanation
Indices: 208351--208412 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
208341 GAATCTAATT
**
208351 TTTATTATTTAATTTTTTTCATCTAATT
1 TTTATTATTTAATTTTTTTCATCTAACA
* *
208379 TTTATTATTTAATTTTTTTCGTCCTACCA
1 TTTATTATTTAATTTTTTTCAT-CTAACA
208408 TTTAT
1 TTTAT
208413 CTGTGGTATA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 21 0.72
29 8 0.28
ACGTcount: A:0.23, C:0.11, G:0.02, T:0.65
Consensus pattern (28 bp):
TTTATTATTTAATTTTTTTCATCTAACA
Found at i:212690 original size:21 final size:20
Alignment explanation
Indices: 212661--212705 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
212651 TATTGAACCC
212661 ATTTATAATAATTTACTATAT
1 ATTTATAATAATTTA-TATAT
* * *
212682 ATTTCTAATATTTTATATTT
1 ATTTATAATAATTTATATAT
212702 ATTT
1 ATTT
212706 GATGTTTAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (20 bp):
ATTTATAATAATTTATATAT
Found at i:218216 original size:18 final size:16
Alignment explanation
Indices: 218186--218238 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
218176 TGATCTATTT
*
218186 AATATATATTTTTTAA
1 AATAAATATTTTTTAA
218202 AATAAATATTATTTTTAA
1 AATAAATA-T-TTTTTAA
**
218220 TTTAAATATTTTTTAA
1 AATAAATATTTTTTAA
218236 AAT
1 AAT
218239 TTAAAATTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
16 15 0.50
17 2 0.07
18 13 0.43
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
AATAAATATTTTTTAA
Found at i:218230 original size:34 final size:33
Alignment explanation
Indices: 218191--218310 Score: 109
Period size: 34 Copynumber: 3.4 Consensus size: 33
218181 TATTTAATAT
218191 ATATTTTTTAAAATAAATATTATTTTTAATTTAA
1 ATATTTTTTAAAATAAAT-TTATTTTTAATTTAA
218225 ATATTTTTTAAAATTTAAAATTTTTATTTTTAATTTAA
1 ATATTTTTTAAAA--T-AAA--TTTATTTTTAATTTAA
* * *
218263 GTATTTTTTTAAA-AAATTTAAAATTTTT-ACTTAA
1 ATATTTTTTAAAATAAATTT---ATTTTTAATTTAA
*
218297 ATATTTTTAAAAAT
1 ATATTTTTTAAAAT
218311 CGTTTGAACA
Statistics
Matches: 71, Mismatches: 6, Indels: 17
0.76 0.06 0.18
Matches are distributed among these distances:
32 3 0.04
34 31 0.44
35 6 0.08
36 1 0.01
37 3 0.04
38 26 0.37
39 1 0.01
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.56
Consensus pattern (33 bp):
ATATTTTTTAAAATAAATTTATTTTTAATTTAA
Found at i:218239 original size:18 final size:18
Alignment explanation
Indices: 218191--218290 Score: 73
Period size: 19 Copynumber: 5.4 Consensus size: 18
218181 TATTTAATAT
218191 ATATTTTTTAAAA--TAA
1 ATATTTTTTAAAATTTAA
*
218207 ATATTATTTT-TAATTTAA
1 ATATT-TTTTAAAATTTAA
218225 ATATTTTTTAAAATTTAAA
1 ATATTTTTTAAAATTT-AA
* **
218244 ATTTTTATTTTTAATTTAA
1 ATATTT-TTTAAAATTTAA
*
218263 GTATTTTTTTAAAAAATTTAA
1 ATA-TTTTTT--AAAATTTAA
218284 A-ATTTTT
1 ATATTTTT
218291 ACTTAAATAT
Statistics
Matches: 65, Mismatches: 10, Indels: 15
0.72 0.11 0.17
Matches are distributed among these distances:
16 7 0.11
17 8 0.12
18 13 0.20
19 18 0.28
20 12 0.18
21 7 0.11
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (18 bp):
ATATTTTTTAAAATTTAA
Found at i:218252 original size:38 final size:40
Alignment explanation
Indices: 218210--218291 Score: 132
Period size: 38 Copynumber: 2.1 Consensus size: 40
218200 AAAATAAATA
218210 TTATTTTTAATTTAAATA-TTTTTT-AAAATTTAAAATTT
1 TTATTTTTAATTTAAATATTTTTTTAAAAATTTAAAATTT
*
218248 TTATTTTTAATTTAAGTATTTTTTTAAAAAATTTAAAATTT
1 TTATTTTTAATTTAAATATTTTTTT-AAAAATTTAAAATTT
218289 TTA
1 TTA
218292 CTTAAATATT
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
38 17 0.43
39 6 0.15
41 17 0.43
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (40 bp):
TTATTTTTAATTTAAATATTTTTTTAAAAATTTAAAATTT
Found at i:218302 original size:21 final size:19
Alignment explanation
Indices: 218218--218302 Score: 59
Period size: 20 Copynumber: 4.3 Consensus size: 19
218208 TATTATTTTT
218218 AATTT-AAATATTTT-TTAA
1 AATTTAAAAT-TTTTATTAA
**
218236 AATTTAAAATTTTTATTTTT
1 AATTTAAAATTTTTA-TTAA
*
218256 AATTTAAGTATTTTT-TTAAAA
1 AATTTAA-AATTTTTATT--AA
218277 AATTTAAAATTTTTACTTAA
1 AATTTAAAATTTTTA-TTAA
218297 ATATTT
1 A-ATTT
218303 TTAAAAATCG
Statistics
Matches: 52, Mismatches: 6, Indels: 15
0.71 0.08 0.21
Matches are distributed among these distances:
18 9 0.17
19 6 0.12
20 18 0.35
21 17 0.33
22 2 0.04
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.56
Consensus pattern (19 bp):
AATTTAAAATTTTTATTAA
Found at i:218762 original size:2 final size:2
Alignment explanation
Indices: 218755--218787 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
218745 CCTAAGGTAA
218755 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
218788 GGATCTCTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:222115 original size:16 final size:17
Alignment explanation
Indices: 222096--222136 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
222086 TATTTTAAAC
222096 ATGAATTATTAAAT-TT
1 ATGAATTATTAAATCTT
*
222112 ATGAA-TATTTAATCTT
1 ATGAATTATTAAATCTT
*
222128 ATAAATTAT
1 ATGAATTAT
222137 GATGGTGAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 7 0.33
16 11 0.52
17 3 0.14
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (17 bp):
ATGAATTATTAAATCTT
Found at i:222192 original size:14 final size:14
Alignment explanation
Indices: 222175--222203 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
222165 TGCGTAAATA
222175 TAAATAAAATTTAG
1 TAAATAAAATTTAG
222189 TAAATAAAATTTAG
1 TAAATAAAATTTAG
222203 T
1 T
222204 TTTCAACTTG
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:0.55, C:0.00, G:0.07, T:0.38
Consensus pattern (14 bp):
TAAATAAAATTTAG
Found at i:222306 original size:13 final size:13
Alignment explanation
Indices: 222290--222329 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
222280 AGTAATATAA
222290 AATATTTATATTT
1 AATATTTATATTT
222303 AATATTTATATTT
1 AATATTTATATTT
*
222316 AA-A-ATATATTT
1 AATATTTATATTT
222327 AAT
1 AAT
222330 TATGGACATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
11 9 0.36
12 1 0.04
13 15 0.60
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
AATATTTATATTT
Found at i:223173 original size:15 final size:15
Alignment explanation
Indices: 223155--223184 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
223145 GAATTTGATT
223155 TATTTTTAAAATTAA
1 TATTTTTAAAATTAA
223170 TATTTTTAAAATTAA
1 TATTTTTAAAATTAA
223185 AGTTAAATAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TATTTTTAAAATTAA
Found at i:223530 original size:25 final size:24
Alignment explanation
Indices: 223485--223548 Score: 60
Period size: 23 Copynumber: 2.7 Consensus size: 24
223475 CTTTTATATC
* *
223485 TTTATTATATAAGATTTTTATATTT
1 TTTATTATATAAAATTATTAT-TTT
223510 TTTACTTAT-TAAAATTATTA-TTT
1 TTTA-TTATATAAAATTATTATTTT
* *
223533 TTTATTGTTTAAAATT
1 TTTATTATATAAAATT
223549 GAATTTAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
22 3 0.09
23 14 0.41
25 13 0.38
26 4 0.12
ACGTcount: A:0.33, C:0.02, G:0.03, T:0.62
Consensus pattern (24 bp):
TTTATTATATAAAATTATTATTTT
Found at i:231338 original size:3 final size:3
Alignment explanation
Indices: 231330--231355 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
231320 TAAGCGAGAT
231330 AGA AGA AGA AGA AGA AGA AGA AGA AG
1 AGA AGA AGA AGA AGA AGA AGA AGA AG
231356 CAGGAGAAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:236175 original size:79 final size:79
Alignment explanation
Indices: 236080--236237 Score: 280
Period size: 79 Copynumber: 2.0 Consensus size: 79
236070 CAAGCAGCTA
236080 TGCAACTTAGGATTGAAAGCAAGCTCAACATCGATAATTGAAAAGGAAAAGAACAAGAAAAAGAA
1 TGCAACTTAGGATTGAAAGCAAGCTCAACATCGATAATTGAAAAGGAAAAGAACAAGAAAAAGAA
*
236145 TGCACACGATAGTG
66 TACACACGATAGTG
* *
236159 TGCAACTTAGGATTGAAAGCAAGCTCATCATCGATAATTGAACAGGAAAAGAACAAGAAAAAGAA
1 TGCAACTTAGGATTGAAAGCAAGCTCAACATCGATAATTGAAAAGGAAAAGAACAAGAAAAAGAA
*
236224 TACACAGGATAGTG
66 TACACACGATAGTG
236238 AAGAACATGA
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
79 75 1.00
ACGTcount: A:0.47, C:0.14, G:0.22, T:0.17
Consensus pattern (79 bp):
TGCAACTTAGGATTGAAAGCAAGCTCAACATCGATAATTGAAAAGGAAAAGAACAAGAAAAAGAA
TACACACGATAGTG
Found at i:238161 original size:2 final size:2
Alignment explanation
Indices: 238154--238183 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
238144 GATAAAAAGA
238154 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
238184 TACCAATGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:238842 original size:17 final size:17
Alignment explanation
Indices: 238820--238860 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
238810 AAGTAAAATT
238820 TTTAAATATTT-TATTAA
1 TTTAAA-ATTTATATTAA
238837 TTTAAAATTTATATT-A
1 TTTAAAATTTATATTAA
238853 -TTAAAATT
1 TTTAAAATT
238861 ATTAAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 8 0.35
16 5 0.22
17 10 0.43
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TTTAAAATTTATATTAA
Found at i:242351 original size:13 final size:13
Alignment explanation
Indices: 242333--242358 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
242323 AATTTTTTGG
242333 TGTATCGATACAT
1 TGTATCGATACAT
242346 TGTATCGATACAT
1 TGTATCGATACAT
242359 ACTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:243058 original size:38 final size:39
Alignment explanation
Indices: 242999--243084 Score: 104
Period size: 38 Copynumber: 2.3 Consensus size: 39
242989 TTTCTTTTCT
**
242999 TTCT-CCCTTAATCAAAATAATTTTAACAAATTCGTACA
1 TTCTCCCCTTAATCAAAATAATTTTAACAAATTCACACA
** * *
243037 TTCTCCCCTTAAT-AAGGTAATTTTAGCAAATTCACGCA
1 TTCTCCCCTTAATCAAAATAATTTTAACAAATTCACACA
243075 TTCTCCCCTT
1 TTCTCCCCTT
243085 TTAAAAAAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
38 33 0.80
39 8 0.20
ACGTcount: A:0.31, C:0.26, G:0.06, T:0.37
Consensus pattern (39 bp):
TTCTCCCCTTAATCAAAATAATTTTAACAAATTCACACA
Found at i:244945 original size:13 final size:13
Alignment explanation
Indices: 244927--244965 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
244917 ATAATCCCCC
*
244927 TGTATCGATACAG
1 TGTATCGATACAA
244940 TGTATCGATACAA
1 TGTATCGATACAA
244953 TGTATCGATACAA
1 TGTATCGATACAA
244966 AGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:251165 original size:13 final size:13
Alignment explanation
Indices: 251147--251172 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
251137 AATTTTTTGG
251147 TGTATCGATACAT
1 TGTATCGATACAT
251160 TGTATCGATACAT
1 TGTATCGATACAT
251173 ACTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:252210 original size:13 final size:13
Alignment explanation
Indices: 252192--252226 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
252182 ACAATTCATC
252192 ATGTATCCATACA
1 ATGTATCCATACA
*
252205 ATGTATCGATACA
1 ATGTATCCATACA
252218 ATGTA-CCAT
1 ATGTATCCAT
252227 GTATCGATAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
12 3 0.15
13 17 0.85
ACGTcount: A:0.37, C:0.20, G:0.11, T:0.31
Consensus pattern (13 bp):
ATGTATCCATACA
Found at i:252210 original size:33 final size:33
Alignment explanation
Indices: 252170--252238 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
252160 CCGTTACAAG
*
252170 CAATGTATCGATACAAT-TCATCATGTATCCATA
1 CAATGTATCGATACAATGT-ACCATGTATCCATA
*
252203 CAATGTATCGATACAATGTACCATGTATCGATA
1 CAATGTATCGATACAATGTACCATGTATCCATA
252236 CAA
1 CAA
252239 ACAATGGTAG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
33 32 0.97
34 1 0.03
ACGTcount: A:0.38, C:0.20, G:0.12, T:0.30
Consensus pattern (33 bp):
CAATGTATCGATACAATGTACCATGTATCCATA
Found at i:252332 original size:20 final size:19
Alignment explanation
Indices: 252288--252338 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
252278 ACAGTTGTCC
* *
252288 ATGTATCGATACAATGATC
1 ATGTATCGATACAAAGATA
252307 ATGTATCGATACAAAGCATA
1 ATGTATCGATACAAAG-ATA
*
252327 ATGTATTGATAC
1 ATGTATCGATAC
252339 TTTTAGGTGT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.31
Consensus pattern (19 bp):
ATGTATCGATACAAAGATA
Found at i:255521 original size:93 final size:97
Alignment explanation
Indices: 255327--255554 Score: 277
Period size: 97 Copynumber: 2.4 Consensus size: 97
255317 TGAAAAGTAG
* * * * * * *
255327 GGTTAGAGTATCCCTTAGGAAGAATGTGGTTGAGGTATCCCCGATAATGATAATTAAGGTGAAAA
1 GGTTGGAGTATCCCTTCGGAAAAATGAGGTTGAAGTATCCCCGATAATGACAATTAAGGTCAAAA
*
255392 TAAGATTTAAAGCTTAACAAGTTTAAAAACGA
66 TAAGATTTAAAGCTTAACAAGCTTAAAAACGA
* * *
255424 GGTTGGAGTATCCATTCGGAAAAATGAGGTTGAAGTATCCCCGATGATGACAATTTAGG-CAAAA
1 GGTTGGAGTATCCCTTCGGAAAAATGAGGTTGAAGTATCCCCGATAATGACAATTAAGGTCAAAA
* *
255488 -AA-A-TTAAATCTTGACAAGCTTAAAAACGA
66 TAAGATTTAAAGCTTAACAAGCTTAAAAACGA
* * *
255517 GGTTGGAGTATCCCCTC-GAAAAATGGGGTTGGAGTATC
1 GGTTGGAGTATCCCTTCGGAAAAATGAGGTTGAAGTATC
255555 TTGATAAATA
Statistics
Matches: 114, Mismatches: 17, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
92 19 0.17
93 38 0.33
94 1 0.01
95 2 0.02
96 4 0.04
97 50 0.44
ACGTcount: A:0.37, C:0.13, G:0.24, T:0.26
Consensus pattern (97 bp):
GGTTGGAGTATCCCTTCGGAAAAATGAGGTTGAAGTATCCCCGATAATGACAATTAAGGTCAAAA
TAAGATTTAAAGCTTAACAAGCTTAAAAACGA
Found at i:256767 original size:35 final size:35
Alignment explanation
Indices: 256723--256807 Score: 154
Period size: 35 Copynumber: 2.4 Consensus size: 35
256713 GAGCTCAAAA
256723 AAAGGATAGCTTCCAGCAGCCTCCCAT-TCACGATC
1 AAAGGATAGCTTCCAGCAGCCTCCCATCT-ACGATC
256758 AAAGGATAGCTTCCAGCAGCCTCCCATCTACGATC
1 AAAGGATAGCTTCCAGCAGCCTCCCATCTACGATC
256793 AAAGGATAGCTTCCA
1 AAAGGATAGCTTCCA
256808 AGTTAATTTT
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
35 48 0.98
36 1 0.02
ACGTcount: A:0.31, C:0.32, G:0.18, T:0.20
Consensus pattern (35 bp):
AAAGGATAGCTTCCAGCAGCCTCCCATCTACGATC
Found at i:260324 original size:22 final size:23
Alignment explanation
Indices: 260280--260324 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
260270 ATATTCATGG
*
260280 CATTCATTCAAAATTTTCATAAT
1 CATTCATTCAAAATTTGCATAAT
* *
260303 CATTCA-TCAATATTTGCTTAAT
1 CATTCATTCAAAATTTGCATAAT
260325 TACTAAGAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.36, C:0.18, G:0.02, T:0.44
Consensus pattern (23 bp):
CATTCATTCAAAATTTGCATAAT
Found at i:265613 original size:301 final size:301
Alignment explanation
Indices: 265071--265675 Score: 1192
Period size: 301 Copynumber: 2.0 Consensus size: 301
265061 ATCCCGACAA
265071 GATCAAAGCCATTTAAGGGTTACCGCCTCTTCGAACCCATAAAGAAGTAAGAAGTTTCCTTGGAA
1 GATCAAAGCCATTTAAGGGTTACCGCCTCTTCGAACCCATAAAGAAGTAAGAAGTTTCCTTGGAA
265136 GATTGAATTACATTGCCCACTTTATTTTTCATCTTATGGACAAATGTGATCCAATCTTTCCCCTC
66 GATTGAATTACATTGCCCACTTTATTTTTCATCTTATGGACAAATGTGATCCAATCTTTCCCCTC
*
265201 ATTCGAAAACATAATCCGGGGGAATGGGATGAAGAGTGCCAGAACGCCTTTGAAAAGGTTAAACA
131 ATTCGAAAACATAATCCGAGGGAATGGGATGAAGAGTGCCAGAACGCCTTTGAAAAGGTTAAACA
*
265266 ATATCTCTCCAACCCATCAGTATTGGTGCCGCTTACTCTAGGGTGACATTTGATCTTGTACTTGT
196 ATATCTCTCCAACCCATCAGTATTGGTGCCGCCTACTCTAGGGTGACATTTGATCTTGTACTTGT
265331 CAGTCTTTGAAAAATCTATGGGGTGTATACTAGGACAACAC
261 CAGTCTTTGAAAAATCTATGGGGTGTATACTAGGACAACAC
265372 GATCAAAGCCATTTAAGGGTTACCGCCTCTTCGAACCCATAAAGAAGTAAGAAGTTTCCTTGGAA
1 GATCAAAGCCATTTAAGGGTTACCGCCTCTTCGAACCCATAAAGAAGTAAGAAGTTTCCTTGGAA
265437 GATTGAATTACATTGCCCACTTTATTTTTCATCTTATGGACAAATGTGATCCAATCTTTCCCCTC
66 GATTGAATTACATTGCCCACTTTATTTTTCATCTTATGGACAAATGTGATCCAATCTTTCCCCTC
265502 ATTCGAAAACATAATCCGAGGGAATGGGATGAAGAGTGCCAGAACGCCTTTGAAAAGGTTAAACA
131 ATTCGAAAACATAATCCGAGGGAATGGGATGAAGAGTGCCAGAACGCCTTTGAAAAGGTTAAACA
265567 ATATCTCTCCAACCCATCAGTATTGGTGCCGCCTACTCTAGGGTGACATTTGATCTTGTACTTGT
196 ATATCTCTCCAACCCATCAGTATTGGTGCCGCCTACTCTAGGGTGACATTTGATCTTGTACTTGT
265632 CAGTCTTTGAAAAATCTATGGGGTGTATACTAGGACAACAC
261 CAGTCTTTGAAAAATCTATGGGGTGTATACTAGGACAACAC
265673 GAT
1 GAT
265676 GATATAGGAA
Statistics
Matches: 302, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
301 302 1.00
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.29
Consensus pattern (301 bp):
GATCAAAGCCATTTAAGGGTTACCGCCTCTTCGAACCCATAAAGAAGTAAGAAGTTTCCTTGGAA
GATTGAATTACATTGCCCACTTTATTTTTCATCTTATGGACAAATGTGATCCAATCTTTCCCCTC
ATTCGAAAACATAATCCGAGGGAATGGGATGAAGAGTGCCAGAACGCCTTTGAAAAGGTTAAACA
ATATCTCTCCAACCCATCAGTATTGGTGCCGCCTACTCTAGGGTGACATTTGATCTTGTACTTGT
CAGTCTTTGAAAAATCTATGGGGTGTATACTAGGACAACAC
Found at i:268892 original size:42 final size:42
Alignment explanation
Indices: 268845--269346 Score: 565
Period size: 42 Copynumber: 11.9 Consensus size: 42
268835 AAAATTCTGA
* * *
268845 AGACTTTCCTACCGTTAGTCTGCTTGTCGGCTTTGACCTTGG
1 AGACTTTCCTACCCTTAGTCTGCCTGTCGGCTTTGACCCTGG
* **
268887 AGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACCCTAT
1 AGACTTTCCTACCCTTAGTCTGCCTGTCGGCTTTGACCCTGG
* *
268929 AGACTTTCCTACCCTTAGTCTGCCTGTCGGCTTTAACCTTGG
1 AGACTTTCCTACCCTTAGTCTGCCTGTCGGCTTTGACCCTGG
* * * * *
268971 AGACTTTTCTTCCTTTAGTCTGCCTGTCGGTTTTGACGCTGG
1 AGACTTTCCTACCCTTAGTCTGCCTGTCGGCTTTGACCCTGG
* * * * * *
269013 AGACTTTTCTACCCTCAATCTGCCTGTCGACTTTAACCCTAG
1 AGACTTTCCTACCCTTAGTCTGCCTGTCGGCTTTGACCCTGG
* * *
269055 AGACTTTCTTACCCTTAGTCTGCCTGTCGGCTTTGACCTTAG
1 AGACTTTCCTACCCTTAGTCTGCCTGTCGGCTTTGACCCTGG
* * * * **
269097 AAACTTTCCTTCCTTTAGTCTGTCTGTCGGCTTTGACCCTAA
1 AGACTTTCCTACCCTTAGTCTGCCTGTCGGCTTTGACCCTGG
* * * * *
269139 AGACTTTCTTTCCCTTAGTCTGCCTGTCAGCTTTGACTCTAG
1 AGACTTTCCTACCCTTAGTCTGCCTGTCGGCTTTGACCCTGG
* * * *
269181 AGACTTTCCTTCCTTTAGTCTGCCTGTCAGCTTTGTCGCCTGG
1 AGACTTTCCTACCCTTAGTCTGCCTGTCGGCTTTGAC-CCTGG
* *
269224 AGACTTTCCTACCCTTAGTCTGCCTGTTGGCTTTGGCCCTGG
1 AGACTTTCCTACCCTTAGTCTGCCTGTCGGCTTTGACCCTGG
* * *
269266 AGACTTTCCTTCCCTTACTCTACCTGTCGGCTTTGACCCTGG
1 AGACTTTCCTACCCTTAGTCTGCCTGTCGGCTTTGACCCTGG
** * *
269308 AGACTTTTTTACCTTTAG-CTTGCCTGTCGGTTTTGACCC
1 AGACTTTCCTACCCTTAGTC-TGCCTGTCGGCTTTGACCC
269347 GAAAGAATTT
Statistics
Matches: 388, Mismatches: 70, Indels: 4
0.84 0.15 0.01
Matches are distributed among these distances:
41 1 0.00
42 352 0.91
43 35 0.09
ACGTcount: A:0.13, C:0.30, G:0.19, T:0.38
Consensus pattern (42 bp):
AGACTTTCCTACCCTTAGTCTGCCTGTCGGCTTTGACCCTGG
Found at i:270451 original size:35 final size:36
Alignment explanation
Indices: 270404--270495 Score: 125
Period size: 35 Copynumber: 2.6 Consensus size: 36
270394 AAACTCAAAA
* * *
270404 AAAGGATGGCTTCCAGCAGCTTTC-CATTCACGATC
1 AAAGGATAGCTTCCAGCAGCTCTCGCATCCACGATC
*
270439 AAAGGATAGCTTCTAGCAGC-CTCGCATCCACGATC
1 AAAGGATAGCTTCCAGCAGCTCTCGCATCCACGATC
*
270474 AAAGGATAGCTTCCAACAGCTC
1 AAAGGATAGCTTCCAGCAGCTC
270496 CCACCCCACG
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
34 2 0.04
35 46 0.94
36 1 0.02
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (36 bp):
AAAGGATAGCTTCCAGCAGCTCTCGCATCCACGATC
Found at i:270604 original size:47 final size:47
Alignment explanation
Indices: 270547--270651 Score: 138
Period size: 47 Copynumber: 2.2 Consensus size: 47
270537 CAGCAGCTTC
* *
270547 CAGCACCCACTCTAGCAAACAGCTCCCAACCCACGAACAGTTTCCAA
1 CAGCATCCACTCAAGCAAACAGCTCCCAACCCACGAACAGTTTCCAA
* * * * *
270594 CAGCATCCACTCAAGCAAACAGCTCTCAGCCCACGGACAGTTTCTAG
1 CAGCATCCACTCAAGCAAACAGCTCCCAACCCACGAACAGTTTCCAA
*
270641 TAGCATCCACT
1 CAGCATCCACT
270652 TCAACAAGCA
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
47 50 1.00
ACGTcount: A:0.31, C:0.39, G:0.13, T:0.16
Consensus pattern (47 bp):
CAGCATCCACTCAAGCAAACAGCTCCCAACCCACGAACAGTTTCCAA
Found at i:270858 original size:76 final size:76
Alignment explanation
Indices: 270761--270986 Score: 317
Period size: 76 Copynumber: 3.0 Consensus size: 76
270751 AACCAGCTTT
* * * *
270761 CAGCGTCCACTCCAGCAAGCAGCAGCTTCTAGCATCCCCTCTAGCAAACAGCTTCCAGCCCACGG
1 CAGCATCCACTCCAGCAAGCAGCAGCTTCCAGCATCCACTCTAGCAAACAGCTCCCAGCCCACGG
*
270826 ACAGTTTCCAG
66 ACAGTTTCCAC
* ** * * * *
270837 TAGCATCCACTTTAGCAAGCAGCAACTTCCAGCATCCATTCTAGCAAATAGCTCCCAGCCCACAG
1 CAGCATCCACTCCAGCAAGCAGCAGCTTCCAGCATCCACTCTAGCAAACAGCTCCCAGCCCACGG
270902 ACAGTTTCCAC
66 ACAGTTTCCAC
* *
270913 CAGCATCCACTCCAACAAGCAGCAGCTTCCAGCATCCACTCTAGCAAGCAGCTCCCAGCCCACGG
1 CAGCATCCACTCCAGCAAGCAGCAGCTTCCAGCATCCACTCTAGCAAACAGCTCCCAGCCCACGG
270978 ACAGCTTTC
66 ACAG-TTTC
270987 AGCATCCATT
Statistics
Matches: 128, Mismatches: 21, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
76 124 0.97
77 4 0.03
ACGTcount: A:0.27, C:0.39, G:0.16, T:0.18
Consensus pattern (76 bp):
CAGCATCCACTCCAGCAAGCAGCAGCTTCCAGCATCCACTCTAGCAAACAGCTCCCAGCCCACGG
ACAGTTTCCAC
Found at i:270993 original size:196 final size:194
Alignment explanation
Indices: 270491--270994 Score: 456
Period size: 196 Copynumber: 2.5 Consensus size: 194
270481 AGCTTCCAAC
* * * *
270491 AGCTCCCACCCCACGGACAGTTTTTAGCAGCATCCACTCCAGCAAGCAGCAGCTTCCAGCACCCA
1 AGCTCCCAGCCCACGGACAG-TTTCA-CAGCATCCACTCCAACAAGCAGCAGCTTCCAGCATCCA
270556 CTCTAGCAAACAGCTCCCAACCCACGAACAG-TTTCCAACAGCATCCACTCAAGCAAACAGCTCT
64 CTCTAGCAAACAGCTCCC-ACCCACGAACAGCTTT----CAGCATCCACTCAAGCAAACAGCTCT
* * * *
270620 CAGCCCACGGACAGTTTCTAGTAGCATCCACTTCAACAAGCAGTAGCTTCTAGCATCCACTCTAG
124 CAGCCCACGGACAGTTTCCAGTAGCATCCACTTCAACAAGCAGCAACTTCCAGCATCCACTCTAG
270685 CAAGCAT
189 CAA-CAT
* * * ** * *
270692 -G-TCCCAGCCCACGGATAGCTTTCA-A-CATCCAATCCAACAACCTCCA--ATCCATG-ATCAA
1 AGCTCCCAGCCCACGGACAG-TTTCACAGCATCCACTCCAACAAGCAGCAGCTTCCA-GCATC-C
** * *** * * *
270750 AAACCAGCTTTCAGCGT-CCACTCCA-GCAAGCAGCAGCTTCTAGCATCCCCTCTAGCAAACAGC
63 ACTCTAGCAAACAGC-TCCCAC-CCACG-AA-CAGC--TTTC-AGCATCCACTCAAGCAAACAGC
* * *
270813 T-TCCAGCCCACGGACAGTTTCCAGTAGCATCCACTTTAGCAAGCAGCAACTTCCAGCATCCATT
121 TCT-CAGCCCACGGACAGTTTCCAGTAGCATCCACTTCAACAAGCAGCAACTTCCAGCATCCACT
270877 CTAGCAA-AT
185 CTAGCAACAT
*
270886 AGCTCCCAGCCCACAGACAGTTTCCACCAGCATCCACTCCAACAAGCAGCAGCTTCCAGCATCCA
1 AGCTCCCAGCCCACGGACAGTTT-CA-CAGCATCCACTCCAACAAGCAGCAGCTTCCAGCATCCA
* *
270951 CTCTAGCAAGCAGCTCCCAGCCCACGGACAGCTTTCAGCATCCA
64 CTCTAGCAAACAGCTCCCA-CCCACGAACAGCTTTCAGCATCCA
270995 TTCCAATAGC
Statistics
Matches: 235, Mismatches: 45, Indels: 51
0.71 0.14 0.15
Matches are distributed among these distances:
194 11 0.05
195 23 0.10
196 126 0.54
197 4 0.02
198 1 0.00
199 43 0.18
200 18 0.08
201 9 0.04
ACGTcount: A:0.29, C:0.38, G:0.15, T:0.18
Consensus pattern (194 bp):
AGCTCCCAGCCCACGGACAGTTTCACAGCATCCACTCCAACAAGCAGCAGCTTCCAGCATCCACT
CTAGCAAACAGCTCCCACCCACGAACAGCTTTCAGCATCCACTCAAGCAAACAGCTCTCAGCCCA
CGGACAGTTTCCAGTAGCATCCACTTCAACAAGCAGCAACTTCCAGCATCCACTCTAGCAACAT
Found at i:272596 original size:58 final size:57
Alignment explanation
Indices: 272500--272657 Score: 183
Period size: 57 Copynumber: 2.8 Consensus size: 57
272490 CATAGGCAAG
* * * *
272500 GTGCCAATATGCTGATTCAAGGCCAGC-AACATTGGGCTTGAGATAGAAGATTTGACAA
1 GTGCCAATGTGTTGATTCAAGGCCAACGAA-ATTAGGCTT-AGATAGAAGATTTGACAA
* * * *
272558 GTGCCAATGTGTTGGTTCAAGGCCAACGAAATTAGGCTTAGAAATAAGGTTTGACAA
1 GTGCCAATGTGTTGATTCAAGGCCAACGAAATTAGGCTTAGATAGAAGATTTGACAA
* * * *
272615 ATGCCAATGTGTTGATTCAAAGCCAATGACATTAGGCTTAGAT
1 GTGCCAATGTGTTGATTCAAGGCCAACGAAATTAGGCTTAGAT
272658 GGAGATGCCA
Statistics
Matches: 85, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
57 52 0.61
58 31 0.36
59 2 0.02
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.27
Consensus pattern (57 bp):
GTGCCAATGTGTTGATTCAAGGCCAACGAAATTAGGCTTAGATAGAAGATTTGACAA
Found at i:272699 original size:32 final size:28
Alignment explanation
Indices: 272663--273038 Score: 211
Period size: 28 Copynumber: 12.8 Consensus size: 28
272653 TAGATGGAGA
* *
272663 TGCCACTAACTTGTATGGGCTTTGAGAGGGG
1 TGCCACTAACTTG--TGGGCTTTGA-AAGAG
272694 TTGCCA-TCAACTTGTGGGCTTTGAAAGAG
1 -TGCCACT-AACTTGTGGGCTTTGAAAGAG
* *
272723 TGCCACTACCTTGTGGGCTTTGAAA-ATA
1 TGCCACTAACTTGTGGGCTTTGAAAGA-G
*
272751 TGCCACTAACTTGTGGGCTTTGAAAAAGG
1 TGCCACTAACTTGTGGGCTTTGAAAGA-G
* * * *
272780 ATGCCATTGACTAGTGGGCTTTGAAAAGGG
1 -TGCCACTAACTTGTGGGCTTTG-AAAGAG
* * *
272810 TGCCACTAACTTATAGGCTTTGAAAAAGG
1 TGCCACTAACTTGTGGGCTTTGAAAGA-G
* * *
272839 ATGCCACTAACTCGTGGGCTTTAAAAAGGG
1 -TGCCACTAACTTGTGGGCTTT-GAAAGAG
* *
272869 TGCCACTAACTTGTGGGCTTTAATAAAAAAG
1 TGCCACTAACTTGTGGGC-TT--TGAAAGAG
* ** * *
272900 ATGCCATTGGCTTATGGGATTT-AAAGAAGG
1 -TGCCACTAACTTGTGGGCTTTGAAAG-A-G
** *
272930 ATGCCACTAACTCATGGGCTTTGAAAGGGG
1 -TGCCACTAACTTGTGGGCTTTGAAA-GAG
** * * *
272960 TTGCCACCGACTTATGGGCTATGAAAGAA
1 -TGCCACTAACTTGTGGGCTTTGAAAGAG
* *
272989 TGCTACTGACTTGTGGGCTTTGAAA-AGG
1 TGCCACTAACTTGTGGGCTTTGAAAGA-G
* * *
273017 TGCCATTGACTTATGGGCTTTG
1 TGCCACTAACTTGTGGGCTTTG
273039 TAGACACCTC
Statistics
Matches: 271, Mismatches: 55, Indels: 40
0.74 0.15 0.11
Matches are distributed among these distances:
27 2 0.01
28 92 0.34
29 43 0.16
30 91 0.34
31 17 0.06
32 26 0.10
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.29
Consensus pattern (28 bp):
TGCCACTAACTTGTGGGCTTTGAAAGAG
Found at i:272831 original size:59 final size:59
Alignment explanation
Indices: 272676--273038 Score: 312
Period size: 59 Copynumber: 6.2 Consensus size: 59
272666 CACTAACTTG
** * * *
272676 TATGGGCTTTGAGAGGGGTTGCCA-TCAACTTGTGGGCTTTGAAAGA-G-TGCCACT-ACCT
1 TATGGGCTTTGA-AAAGGATGCCACT-AACTTGTGGGCTTTGAAAAAGGATGCCATTGA-CT
* *
272734 TGTGGGCTTTGAAAA-TATGCCACTAACTTGTGGGCTTTGAAAAAGGATGCCATTGAC-
1 TATGGGCTTTGAAAAGGATGCCACTAACTTGTGGGCTTTGAAAAAGGATGCCATTGACT
* * * * *
272791 TAGTGGGCTTTGAAAAGGGTGCCACTAACTTATAGGCTTTGAAAAAGGATGCCACTAACT
1 TA-TGGGCTTTGAAAAGGATGCCACTAACTTGTGGGCTTTGAAAAAGGATGCCATTGACT
** * * * * *
272851 CGTGGGCTTTAAAAAGGGTGCCACTAACTTGTGGGCTTTAATAAAAAAGATGCCATTGGCT
1 TATGGGCTTTGAAAAGGATGCCACTAACTTGTGGGCTTT--GAAAAAGGATGCCATTGACT
* * ** ** * **
272912 TATGGGATTTAAAGAAGGATGCCACTAACTCATGGGCTTTGAAAGGGGTTGCCACCGACT
1 TATGGGCTTTGAA-AAGGATGCCACTAACTTGTGGGCTTTGAAAAAGGATGCCATTGACT
* * * *
272972 TATGGGCTATG-AAAGAATGCTACTGACTTGTGGGCTTTG-AAAAGG-TGCCATTGACT
1 TATGGGCTTTGAAAAGGATGCCACTAACTTGTGGGCTTTGAAAAAGGATGCCATTGACT
273028 TATGGGCTTTG
1 TATGGGCTTTG
273039 TAGACACCTC
Statistics
Matches: 244, Mismatches: 51, Indels: 22
0.77 0.16 0.07
Matches are distributed among these distances:
56 43 0.18
57 8 0.03
58 53 0.22
59 72 0.30
60 20 0.08
61 25 0.10
62 23 0.09
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.29
Consensus pattern (59 bp):
TATGGGCTTTGAAAAGGATGCCACTAACTTGTGGGCTTTGAAAAAGGATGCCATTGACT
Found at i:272965 original size:30 final size:30
Alignment explanation
Indices: 272661--273038 Score: 260
Period size: 30 Copynumber: 12.8 Consensus size: 30
272651 CTTAGATGGA
* *
272661 GATGCCACTAACTTGTATGGGCTTTGAGAGGG
1 GATGCCACTAAC-T-TATGGGCTTTGAAAAGG
* * *
272693 GTTGCCA-TCAACTTGTGGGCTTTG-AAAGA
1 GATGCCACT-AACTTATGGGCTTTGAAAAGG
* *
272722 G-TGCCACTACCTTGTGGGCTTTGAAAA--
1 GATGCCACTAACTTATGGGCTTTGAAAAGG
* * *
272749 TATGCCACTAACTTGTGGGCTTTGAAAAAG
1 GATGCCACTAACTTATGGGCTTTGAAAAGG
* *
272779 GATGCCATTGAC-TAGTGGGCTTTGAAAAGG
1 GATGCCACTAACTTA-TGGGCTTTGAAAAGG
* *
272809 G-TGCCACTAACTTATAGGCTTTGAAAAAG
1 GATGCCACTAACTTATGGGCTTTGAAAAGG
** *
272838 GATGCCACTAACTCGTGGGCTTTAAAAAGG
1 GATGCCACTAACTTATGGGCTTTGAAAAGG
* * **
272868 G-TGCCACTAACTTGTGGGCTTTAATAAAAAA
1 GATGCCACTAACTTATGGGCTTT--GAAAAGG
* ** * *
272899 GATGCCATTGGCTTATGGGATTT-AAAGAAG
1 GATGCCACTAACTTATGGGCTTTGAAA-AGG
* *
272929 GATGCCACTAACTCATGGGCTTTGAAAGGG
1 GATGCCACTAACTTATGGGCTTTGAAAAGG
* ** *
272959 GTTGCCACCGACTTATGGGCTATG-AAA-G
1 GATGCCACTAACTTATGGGCTTTGAAAAGG
* * * *
272987 AATGCTACTGACTTGTGGGCTTTGAAAA-G
1 GATGCCACTAACTTATGGGCTTTGAAAAGG
* *
273016 G-TGCCATTGACTTATGGGCTTTG
1 GATGCCACTAACTTATGGGCTTTG
273039 TAGACACCTC
Statistics
Matches: 276, Mismatches: 55, Indels: 34
0.76 0.15 0.09
Matches are distributed among these distances:
28 82 0.30
29 59 0.21
30 100 0.36
31 10 0.04
32 25 0.09
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.29
Consensus pattern (30 bp):
GATGCCACTAACTTATGGGCTTTGAAAAGG
Found at i:273327 original size:21 final size:21
Alignment explanation
Indices: 273301--273353 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
273291 TTTTACTATT
* *
273301 TGTATCGATACAATTAGTGAA
1 TGTATCGATACAATAAATGAA
273322 TGTATCGATAC-ATAAATGAA
1 TGTATCGATACAATAAATGAA
*
273342 TATATCGATACA
1 TGTATCGATACA
273354 TGCCTAAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.42, C:0.11, G:0.15, T:0.32
Consensus pattern (21 bp):
TGTATCGATACAATAAATGAA
Found at i:274052 original size:10 final size:10
Alignment explanation
Indices: 274037--274061 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
274027 TTACCCAAAG
274037 AAACACCTCC
1 AAACACCTCC
274047 AAACACCTCC
1 AAACACCTCC
274057 AAACA
1 AAACA
274062 TCTCTTTCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.48, C:0.44, G:0.00, T:0.08
Consensus pattern (10 bp):
AAACACCTCC
Found at i:278530 original size:16 final size:16
Alignment explanation
Indices: 278498--278582 Score: 73
Period size: 16 Copynumber: 5.2 Consensus size: 16
278488 GAAACCAACC
278498 GACCCGAAACTCAAAAT
1 GACCCG-AACTCAAAAT
278515 GACCCGAA-TCCAAAAT
1 GACCCGAACT-CAAAAT
*
278531 GACTCGAACTCAAAAT
1 GACCCGAACTCAAAAT
* * * *
278547 GGCTCAAACTCGAAAT
1 GACCCGAACTCAAAAT
* * *
278563 GATCCGAACCCGAAAT
1 GACCCGAACTCAAAAT
278579 GACC
1 GACC
278583 TAGACAATTA
Statistics
Matches: 56, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
15 1 0.02
16 48 0.86
17 7 0.12
ACGTcount: A:0.41, C:0.29, G:0.15, T:0.14
Consensus pattern (16 bp):
GACCCGAACTCAAAAT
Found at i:280181 original size:20 final size:19
Alignment explanation
Indices: 280155--280270 Score: 81
Period size: 20 Copynumber: 5.7 Consensus size: 19
280145 TTGCTAGTTT
*
280155 CATGTATCGATACAATTGAG
1 CATGTATCGATACAA-TGAA
*
280175 TATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
*
280194 CATGTATCGATACATTGTCGATA
1 CATGTATCGATACA--AT-GA-A
*
280217 CATTGTATCGATACAAAGCATA
1 CA-TGTATCGATACAATG-A-A
* *
280239 -ATGTATCGATACATCTGGA
1 CATGTATCGATACA-ATGAA
*
280258 TATGTATCGATAC
1 CATGTATCGATAC
280271 TCTCTAGGGT
Statistics
Matches: 79, Mismatches: 9, Indels: 16
0.76 0.09 0.15
Matches are distributed among these distances:
19 17 0.22
20 38 0.48
21 4 0.05
22 5 0.06
23 3 0.04
24 12 0.15
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:280229 original size:13 final size:13
Alignment explanation
Indices: 280196--280231 Score: 58
Period size: 11 Copynumber: 2.9 Consensus size: 13
280186 ACAATGAACA
280196 TGTATCGATACAT
1 TGTATCGATACAT
280209 TG--TCGATACAT
1 TGTATCGATACAT
280220 TGTATCGATACA
1 TGTATCGATACA
280232 AAGCATAATG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
11 11 0.52
13 10 0.48
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:288575 original size:13 final size:13
Alignment explanation
Indices: 288557--288581 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
288547 CAATTCTTCA
288557 TGTATCGATACAT
1 TGTATCGATACAT
288570 TGTATCGATACA
1 TGTATCGATACA
288582 ATATGCCATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:288581 original size:33 final size:33
Alignment explanation
Indices: 288537--288601 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
288527 TTTGGGACAA
288537 TGTATCAATACAAT-T-CTTCATGTATCGATACAT
1 TGTATCAATACAATATGC--CATGTATCGATACAT
*
288570 TGTATCGATACAATATGCCATGTATCGATACA
1 TGTATCAATACAATATGCCATGTATCGATACA
288602 AATCATGGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 27 0.93
34 1 0.03
35 1 0.03
ACGTcount: A:0.34, C:0.18, G:0.12, T:0.35
Consensus pattern (33 bp):
TGTATCAATACAATATGCCATGTATCGATACAT
Found at i:288676 original size:19 final size:20
Alignment explanation
Indices: 288633--288683 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
288623 GCCAGTTTCT
* **
288633 TGTATTGATACAATTGAGTA
1 TGTATCGATACAATTGAACA
288653 TGTATCGATACAA-TGAACA
1 TGTATCGATACAATTGAACA
288672 TGTATCGATACA
1 TGTATCGATACA
288684 TCTGGATAGG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 16 0.57
20 12 0.43
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.33
Consensus pattern (20 bp):
TGTATCGATACAATTGAACA
Found at i:289068 original size:16 final size:16
Alignment explanation
Indices: 289047--289081 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
289037 TAAACCTGAT
289047 TGACCCAAATCTGAAA
1 TGACCCAAATCTGAAA
*
289063 TGACCCGAATCTGAAA
1 TGACCCAAATCTGAAA
289079 TGA
1 TGA
289082 TCTGAACCCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.40, C:0.23, G:0.17, T:0.20
Consensus pattern (16 bp):
TGACCCAAATCTGAAA
Found at i:289110 original size:16 final size:16
Alignment explanation
Indices: 289054--289112 Score: 64
Period size: 16 Copynumber: 3.7 Consensus size: 16
289044 GATTGACCCA
* * *
289054 AATCTGAAATGACCCG
1 AATCTGAAATAATCTG
*
289070 AATCTGAAATGATCTG
1 AATCTGAAATAATCTG
* *
289086 AACCCGAAATAATCTG
1 AATCTGAAATAATCTG
289102 AATCTGAAATA
1 AATCTGAAATA
289113 CCCCGAATTC
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.42, C:0.19, G:0.15, T:0.24
Consensus pattern (16 bp):
AATCTGAAATAATCTG
Found at i:291624 original size:16 final size:16
Alignment explanation
Indices: 291605--291639 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
291595 AAATGATGAA
*
291605 AAAATAAAAAAAAAAG
1 AAAAGAAAAAAAAAAG
*
291621 AAAAGAAAAACAAAAG
1 AAAAGAAAAAAAAAAG
291637 AAA
1 AAA
291640 GTGCAAAAGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.86, C:0.03, G:0.09, T:0.03
Consensus pattern (16 bp):
AAAAGAAAAAAAAAAG
Found at i:292202 original size:33 final size:33
Alignment explanation
Indices: 292160--292284 Score: 153
Period size: 33 Copynumber: 3.8 Consensus size: 33
292150 AAACCATCAA
*
292160 ACCTTTTTCTTTTTAAGTCCATAACTCCGTGGC
1 ACCTTTTTCTTTTTAAGTCCATAACTCCATGGC
* * * **
292193 ACCTTTTTC-TATTAAGTCCATGACTCTATGAT
1 ACCTTTTTCTTTTTAAGTCCATAACTCCATGGC
*
292225 ACCTTTTTCTTTTTAAGTCCATGACTCCATGGC
1 ACCTTTTTCTTTTTAAGTCCATAACTCCATGGC
* * *
292258 ACCTTTTTCTTTTGAGGTCCACAACTC
1 ACCTTTTTCTTTTTAAGTCCATAACTC
292285 TGTTGCATCT
Statistics
Matches: 77, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
32 26 0.34
33 51 0.66
ACGTcount: A:0.20, C:0.26, G:0.11, T:0.42
Consensus pattern (33 bp):
ACCTTTTTCTTTTTAAGTCCATAACTCCATGGC
Found at i:292213 original size:32 final size:33
Alignment explanation
Indices: 292160--292270 Score: 161
Period size: 33 Copynumber: 3.4 Consensus size: 33
292150 AAACCATCAA
* *
292160 ACCTTTTTCTTTTTAAGTCCATAACTCCGTGGC
1 ACCTTTTTCTTTTTAAGTCCATGACTCCATGGC
* * **
292193 ACCTTTTTC-TATTAAGTCCATGACTCTATGAT
1 ACCTTTTTCTTTTTAAGTCCATGACTCCATGGC
292225 ACCTTTTTCTTTTTAAGTCCATGACTCCATGGC
1 ACCTTTTTCTTTTTAAGTCCATGACTCCATGGC
292258 ACCTTTTTCTTTT
1 ACCTTTTTCTTTT
292271 GAGGTCCACA
Statistics
Matches: 67, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
32 26 0.39
33 41 0.61
ACGTcount: A:0.19, C:0.25, G:0.10, T:0.46
Consensus pattern (33 bp):
ACCTTTTTCTTTTTAAGTCCATGACTCCATGGC
Found at i:292502 original size:131 final size:131
Alignment explanation
Indices: 292328--292657 Score: 430
Period size: 131 Copynumber: 2.5 Consensus size: 131
292318 AGTGGCACCT
* * * * * *
292328 TTCTCTAAAGCTCACACAAGTCAGTGGCAGCCC-TCTTCCAAAGCCCATACAAGTCGGTGGCAAC
1 TTCTCTAAAGCCCACACAAGTTAGTGGCAACCCTTC-TCTAAAGCCCACACAAGTCAGTGGCAAC
* * * *
292392 CCTTTCCCAAAGCCCACACAAGTTAGTGGTAACCTTTTTTAAAGCCCACACAAGTCGGTGGCAAA
65 CCTTTCCCAAAGCCCACACAAGTTAGTGGCAACCCTTCTTAAAGCCCACACAAGTCGGTCGCAAA
292457 CC
130 CC
* * *
292459 TTCTCTAAAGCCCACACAAGTTGGTGGCAACCCTTCTCTAAAGCCCACACAAGTTAGTGACAACC
1 TTCTCTAAAGCCCACACAAGTTAGTGGCAACCCTTCTCTAAAGCCCACACAAGTCAGTGGCAACC
* * * * * *
292524 TTTTTCCAAAGCCCATACAAGTTGGTGGCAACCCTTCTTAAAGCCCACACAAGTCGGTCGTAACC
66 CTTTCCCAAAGCCCACACAAGTTAGTGGCAACCCTTCTTAAAGCCCACACAAGTCGGTCGCAAAC
292589 C
131 C
* * *
292590 TTCTCTAAAGCCCACACAA-TTCAGTAGCAACCCTTCTCTAAAGCCCACACAATTCAGTAGCAAC
1 TTCTCTAAAGCCCACACAAGTT-AGTGGCAACCCTTCTCTAAAGCCCACACAAGTCAGTGGCAAC
292654 CCTT
65 CCTT
292658 CTAAGCCCAA
Statistics
Matches: 171, Mismatches: 26, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
130 2 0.01
131 167 0.98
132 2 0.01
ACGTcount: A:0.30, C:0.33, G:0.15, T:0.22
Consensus pattern (131 bp):
TTCTCTAAAGCCCACACAAGTTAGTGGCAACCCTTCTCTAAAGCCCACACAAGTCAGTGGCAACC
CTTTCCCAAAGCCCACACAAGTTAGTGGCAACCCTTCTTAAAGCCCACACAAGTCGGTCGCAAAC
C
Found at i:292657 original size:98 final size:97
Alignment explanation
Indices: 292328--292666 Score: 384
Period size: 98 Copynumber: 3.5 Consensus size: 97
292318 AGTGGCACCT
* * *
292328 TTCTCTAAAGCTCACACAAGTCAGTGGCAGCCC-TCTTCCAAAGCCCATACAAGTCGGTGGCAAC
1 TTCTCTAAAGCCCACACAAGTCAGTGGCAACCCTTCTT--AAAGCCCACACAAGTCGGTGGCAAC
* *
292392 CCTT-TCCCAAAGCCCACACAAGTTAGTGGTAA-CC
64 CCTTCT-CTAAAGCCCACACAAGTTAGT-GCAACCC
* * * * *
292426 TTTTTTAAAGCCCACACAAGTCGGTGGCAAACCTTCTCTAAAGCCCACACAAGTTGGTGGCAACC
1 TTCTCTAAAGCCCACACAAGTCAGTGGCAACCCTTCT-TAAAGCCCACACAAGTCGGTGGCAACC
*
292491 CTTCTCTAAAGCCCACACAAGTTAGTGACAACCT
65 CTTCTCTAAAGCCCACACAAGTTAGTG-CAACCC
* * * ** * *
292525 TTTTCCAAAGCCCATACAAGTTGGTGGCAACCCTTCTTAAAGCCCACACAAGTCGGTCGTAACCC
1 TTCTCTAAAGCCCACACAAGTCAGTGGCAACCCTTCTTAAAGCCCACACAAGTCGGTGGCAACCC
292590 TTCTCTAAAGCCCACACAA-TTCAGTAGCAACCC
66 TTCTCTAAAGCCCACACAAGTT-AGT-GCAACCC
* *
292623 TTCTCTAAAGCCCACACAATTCAGTAGCAACCCTTC-T-AAGCCCA
1 TTCTCTAAAGCCCACACAAGTCAGTGGCAACCCTTCTTAAAGCCCA
292667 ATAGCGTTGG
Statistics
Matches: 207, Mismatches: 27, Indels: 16
0.83 0.11 0.06
Matches are distributed among these distances:
96 7 0.03
97 4 0.02
98 157 0.76
99 38 0.18
100 1 0.00
ACGTcount: A:0.30, C:0.33, G:0.15, T:0.22
Consensus pattern (97 bp):
TTCTCTAAAGCCCACACAAGTCAGTGGCAACCCTTCTTAAAGCCCACACAAGTCGGTGGCAACCC
TTCTCTAAAGCCCACACAAGTTAGTGCAACCC
Found at i:292658 original size:33 final size:33
Alignment explanation
Indices: 292318--292659 Score: 315
Period size: 33 Copynumber: 10.5 Consensus size: 33
292308 TACATGACCT
* * *
292318 AGTGGC-ACCTTTCTCTAAAGCTCACACAAGTC
1 AGTGGCAACCCTTCTCTAAAGCCCACACAATTC
* * * *
292350 AGTGGCAGCCC-TCTTCCAAAGCCCATACAAGTC
1 AGTGGCAACCCTTC-TCTAAAGCCCACACAATTC
* *
292383 GGTGGCAACCCTT-TCCCAAAGCCCACACAAGTT-
1 AGTGGCAACCCTTCT-CTAAAGCCCACACAA-TTC
* * * *
292416 AGTGGTAA-CCTTTTTTAAAGCCCACACAAGTC
1 AGTGGCAACCCTTCTCTAAAGCCCACACAATTC
* *
292448 GGTGGCAAACCTTCTCTAAAGCCCACACAAGTT-
1 AGTGGCAACCCTTCTCTAAAGCCCACACAA-TTC
*
292481 GGTGGCAACCCTTCTCTAAAGCCCACACAAGTT-
1 AGTGGCAACCCTTCTCTAAAGCCCACACAA-TTC
* * * * *
292514 AGTGACAACCTTTTTCCAAAGCCCATACAAGTT-
1 AGTGGCAACCCTTCTCTAAAGCCCACACAA-TTC
* *
292547 GGTGGCAACCCTTCT-TAAAGCCCACACAAGTC
1 AGTGGCAACCCTTCTCTAAAGCCCACACAATTC
* * *
292579 GGTCGTAACCCTTCTCTAAAGCCCACACAATTC
1 AGTGGCAACCCTTCTCTAAAGCCCACACAATTC
*
292612 AGTAGCAACCCTTCTCTAAAGCCCACACAATTC
1 AGTGGCAACCCTTCTCTAAAGCCCACACAATTC
*
292645 AGTAGCAACCCTTCT
1 AGTGGCAACCCTTCT
292660 AAGCCCAATA
Statistics
Matches: 260, Mismatches: 39, Indels: 21
0.81 0.12 0.07
Matches are distributed among these distances:
31 2 0.01
32 57 0.22
33 198 0.76
34 3 0.01
ACGTcount: A:0.29, C:0.33, G:0.15, T:0.23
Consensus pattern (33 bp):
AGTGGCAACCCTTCTCTAAAGCCCACACAATTC
Found at i:292792 original size:52 final size:52
Alignment explanation
Indices: 292736--293977 Score: 912
Period size: 52 Copynumber: 23.7 Consensus size: 52
292726 ATATCATTGT
* * *
292736 CCTTGAATCAGCATATTGGCAGCTTTGTCATCTTTAAGTCCAATGTTGTTGG
1 CCTTGAATCAGCATATTGGCAGCTTTGTCATCTTTAAGTCCAATATCGCTGG
* * * * * ** *
292788 CCTTGAATTAGCACATTGGCA-CTTTTTTTC-TTTCTTAAGTCTAATATTACTAG
1 CCTTGAATCAGCATATTGGCAGC--TTTGTCATCT-TTAAGTCCAATATCGCTGG
* * *
292841 CCTTGAATCAGCATATTGGCACCTTTGTCATCTTTAAGTTCAATATCGTTGG
1 CCTTGAATCAGCATATTGGCAGCTTTGTCATCTTTAAGTCCAATATCGCTGG
* * *
292893 CCTTGAAT---CATATTGGCACCTTTGTCATCTTTAAGTCCAATGTCGTTGG
1 CCTTGAATCAGCATATTGGCAGCTTTGTCATCTTTAAGTCCAATATCGCTGG
* * ** * **
292942 CCTTGAATCAGGACATTGGCA-CATTT-TTTTGTCTTAAGTCCAATATCATTGG
1 CCTTGAATCAGCATATTGGCAGC-TTTGTCATCT-TTAAGTCCAATATCGCTGG
* *
292994 CCTTGAATCAGCATATTGG-TGCTTTTGTCATCTTTAAGTCTAATATCGCTGG
1 CCTTGAATCAGCATATTGGCAGC-TTTGTCATCTTTAAGTCCAATATCGCTGG
* * **
293046 CCTTGAATCAGCATATT--CACGCCTTTATCATCTTTAAGTCCAATGTCATTGG
1 CCTTGAATCAGCATATTGGCA-G-CTTTGTCATCTTTAAGTCCAATATCGCTGG
* * * * * * * * *
293098 CCTTGAATTAGCACATTAGCACCTTTTTC-TTTCTTAAGTCTAATATCGATAG
1 CCTTGAATCAGCATATTGGCAGCTTTGTCATCT-TTAAGTCCAATATCGCTGG
* * * *
293150 CCTTGAATCAGCAAATTGGC-GCTTTTGTCATCTTTAAGTCTAACATCGCTAG
1 CCTTGAATCAGCATATTGGCAGC-TTTGTCATCTTTAAGTCCAATATCGCTGG
* * * ** *
293202 CCTTTAATCAAGCATATTGGCACCATTGTCATCTTTTTAAAGTTTAATATCACTGG
1 CCTTGAATC-AGCATATTGGCAGCTTTGTCATC--TTT-AAGTCCAATATCGCTGG
** * * * * *
293258 CCTTGAATCAGCATATTGGCTCCTTTATGATCTTTATGTCCAATGTCACTGG
1 CCTTGAATCAGCATATTGGCAGCTTTGTCATCTTTAAGTCCAATATCGCTGG
* * * * *
293310 CCTTAAAGCAGCATATTGGC-GTCTTTTTC-TTTCTTAAGTCTAATATCGCTGG
1 CCTTGAATCAGCATATTGGCAG-CTTTGTCATCT-TTAAGTCCAATATCGCTGG
* * ** *
293362 CCTTGAATCAACATATT--AATGCCTTTGTCATCTTTAAGTGTAATA-CGGTTGG
1 CCTTGAATCAGCATATTGGCA-G-CTTTGTCATCTTTAAGTCCAATATC-GCTGG
* * * * * * **
293414 TCTTGAATCAGCAAATTGGTACCTTTGTCATCTTTCTTAAGTCTAATATCACAAG
1 CCTTGAATCAGCATATTGGCAGCTTTGTCATC--T-TTAAGTCCAATATCGCTGG
* * * * *
293469 CCTTGAATCAACATATTGGC-GCTTTTTTGATCTTTAAGTCCAATGTCACTGG
1 CCTTGAATCAGCATATTGGCAGC-TTTGTCATCTTTAAGTCCAATATCGCTGG
* * * * **
293521 CCTTGAATCAGCACATTGGCA-CATTTTTCTTTTTTAAGTCCAATATCTTTGG
1 CCTTGAATCAGCATATTGGCAGC-TTTGTCATCTTTAAGTCCAATATCGCTGG
* * *
293573 CCTTGAATCAGCATATTGGC-GCCTTTGTCAGCTTTTTTATGTCCAATATCGCTTG
1 CCTTGAATCAGCATATTGGCAG-CTTTGTCA---TCTTTAAGTCCAATATCGCTGG
* * ***
293628 CCTTGAATCAGTATATTGGC-GCCTTTGTCATCTTTAAGTCGAATATTATTGG
1 CCTTGAATCAGCATATTGGCAG-CTTTGTCATCTTTAAGTCCAATATCGCTGG
* * * * * *
293680 CCTTGAATCAACATATTGCCACCTTTGTCATCTTTCTTAAGTCTAATATCTCAGG
1 CCTTGAATCAGCATATTGGCAGCTTTGTCATC--T-TTAAGTCCAATATCGCTGG
* * * *
293735 CCTTGAATCAACATATTGG-TGCCTTTGTCATCTTTAAGTCCAATGTCGCTAG
1 CCTTGAATCAGCATATTGGCAG-CTTTGTCATCTTTAAGTCCAATATCGCTGG
* * * * *
293787 CCTTGAATCAGCACATTAGCACCTTTTTC-TTTCTTAAGTCCAATATCGCTGG
1 CCTTGAATCAGCATATTGGCAGCTTTGTCATCT-TTAAGTCCAATATCGCTGG
* * *
293839 CCTTGAATCAGCATATTGGC-GCCTTTGTCATCTTTAAGTCTAATGTCACTGG
1 CCTTGAATCAGCATATTGGCAG-CTTTGTCATCTTTAAGTCCAATATCGCTGG
* * * * *
293891 CCTTGAATCAGCACATTGGCACCCTTGTCATCTTTAAGCCCAATATCGCTAG
1 CCTTGAATCAGCATATTGGCAGCTTTGTCATCTTTAAGTCCAATATCGCTGG
* * * *
293943 CCTTGGATTAGCATATTGGCACCTTTATCAATCTT
1 CCTTGAATCAGCATATTGGCAGCTTTGTC-ATCTT
293978 CTATTCTTTA
Statistics
Matches: 945, Mismatches: 190, Indels: 109
0.76 0.15 0.09
Matches are distributed among these distances:
49 47 0.05
51 13 0.01
52 630 0.67
53 79 0.08
54 8 0.01
55 146 0.15
56 22 0.02
ACGTcount: A:0.24, C:0.22, G:0.16, T:0.38
Consensus pattern (52 bp):
CCTTGAATCAGCATATTGGCAGCTTTGTCATCTTTAAGTCCAATATCGCTGG
Found at i:293517 original size:211 final size:209
Alignment explanation
Indices: 292736--293964 Score: 984
Period size: 211 Copynumber: 5.9 Consensus size: 209
292726 ATATCATTGT
* ** * *
292736 CCTTGAATCAGCATATTGGCAG-CTTTGTCATCTTTAAGTCCAATGTTGTTGGCCTTGAATTAGC
1 CCTTGAATCAGCATATTGGC-GCCTTTGTCATCTTTAAGTCTAACATCGTTGGCCTTGAATCAGC
* * ** * * *
292800 ACATTGGCA-CTTT-TTTTCTTTCTTAAGTCTAATATTACTAGCCTTGAATCAGCATATTGGCAC
65 ATATTGGTACCTTTGTCATCTTT-TTAAGTCTAATATCACTGGCCTTGAATCAGCATATTGGCGC
* * * * ** * * *
292863 CTTTGTCATCTTTAAGTTCAATATCGTTGGCCTTGAAT---CATATTGGCACCTTTGTC-ATCTT
129 CTTTATGATCTTTAAGTCCAATGTCACTGGCCTTGAATCAGCACATTGGCA-CTTTTTCTTTC-T
* * *
292924 TAAGTCCAATGTCGTTGG
192 TAAGTCTAATATCGATGG
* * * * ** * * * *
292942 CCTTGAATCAGGACATTGGCACATTT-TTTTGTCTTAAGTCCAATATCATTGGCCTTGAATCAGC
1 CCTTGAATCAGCATATTGGCGCCTTTGTCATCT-TTAAGTCTAACATCGTTGGCCTTGAATCAGC
* * * **
293006 ATATTGGTGCTTTTGTCATC--TTTAAGTCTAATATCGCTGGCCTTGAATCAGCATATTCACGCC
65 ATATTGGTACCTTTGTCATCTTTTTAAGTCTAATATCACTGGCCTTGAATCAGCATATTGGCGCC
* * * *
293069 TTTATCATCTTTAAGTCCAATGTCATTGGCCTTGAATTAGCACATTAGCACCTTTTTCTTTCTTA
130 TTTATGATCTTTAAGTCCAATGTCACTGGCCTTGAATCAGCACATTGGCA-CTTTTTCTTTCTTA
*
293134 AGTCTAATATCGATAG
194 AGTCTAATATCGATGG
* * * * *
293150 CCTTGAATCAGCAAATTGGCGCTTTTGTCATCTTTAAGTCTAACATCGCTAGCCTTTAATCAAGC
1 CCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTAAGTCTAACATCGTTGGCCTTGAATC-AGC
* * * *
293215 ATATTGGCACCATTGTCATCTTTTTAAAGTTTAATATCACTGGCCTTGAATCAGCATATTGGCTC
65 ATATTGGTACCTTTGTCATCTTTTT-AAGTCTAATATCACTGGCCTTGAATCAGCATATTGGCGC
* * * * *
293280 CTTTATGATCTTTATGTCCAATGTCACTGGCCTTAAAGCAGCATATTGGCGTCTTTTTCTTTCTT
129 CTTTATGATCTTTAAGTCCAATGTCACTGGCCTTGAATCAGCACATTGGC-ACTTTTTCTTTCTT
*
293345 AAGTCTAATATCGCTGG
193 AAGTCTAATATCGATGG
* *** * * *
293362 CCTTGAATCAACATATTAATGCCTTTGTCATCTTTAAGTGTAATA-CGGTTGGTCTTGAATCAGC
1 CCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTAAGTCTAACATC-GTTGGCCTTGAATCAGC
* ** *
293426 AAATTGGTACCTTTGTCATCTTTCTTAAGTCTAATATCACAAGCCTTGAATCAACATATTGGCGC
65 ATATTGGTACCTTTGTCATCTTT-TTAAGTCTAATATCACTGGCCTTGAATCAGCATATTGGCGC
* * *
293491 TTTTTTGATCTTTAAGTCCAATGTCACTGGCCTTGAATCAGCACATTGGCACATTTTTCTTTTTT
129 CTTTATGATCTTTAAGTCCAATGTCACTGGCCTTGAATCAGCACATTGGCAC-TTTTTCTTTCTT
* **
293556 AAGTCCAATATCTTTGG
193 AAGTCTAATATCGATGG
* * * *
293573 CCTTGAATCAGCATATTGGCGCCTTTGTCAGCTTTTTTATGTCCAATATCGCTT-GCCTTGAATC
1 CCTTGAATCAGCATATTGGCGCCTTTGTCA---TCTTTAAGTCTAACATCG-TTGGCCTTGAATC
* ** * * * * *
293637 AGTATATTGGCGCCTTTGTCATC--TTTAAGTCGAATATTATTGGCCTTGAATCAACATATTGCC
62 AGCATATTGGTACCTTTGTCATCTTTTTAAGTCTAATATCACTGGCCTTGAATCAGCATATTGGC
* * * * * * * * * *
293700 ACCTTTGTCATCTTTCTTAAGTCTAATATCTCAGGCCTTGAATCAACATATTGGTGC-CTTTGTC
127 GCCTTTATGATC--T-TTAAGTCCAATGTCACTGGCCTTGAATCAGCACATT-G-GCACTTTTTC
* * * * *
293764 -ATCTTTAAGTCCAATGTCGCTAG
187 TTTC-TTAAGTCTAATATCGATGG
* * * * * * * *
293787 CCTTGAATCAGCACATTAGCACCTTTTTC-TTTCTTAAGTCCAATATCGCTGGCCTTGAATCAGC
1 CCTTGAATCAGCATATTGGCGCCTTTGTCATCT-TTAAGTCTAACATCGTTGGCCTTGAATCAGC
** * * *
293851 ATATTGGCGCCTTTGTCATC--TTTAAGTCTAATGTCACTGGCCTTGAATCAGCACATTGGCACC
65 ATATTGGTACCTTTGTCATCTTTTTAAGTCTAATATCACTGGCCTTGAATCAGCATATTGGCGCC
* * * * * * * * * *
293914 CTTGTCATCTTTAAGCCCAATATCGCTAGCCTTGGATTAGCATATTGGCAC
130 TTTATGATCTTTAAGTCCAATGTCACTGGCCTTGAATCAGCACATTGGCAC
293965 CTTTATCAAT
Statistics
Matches: 834, Mismatches: 158, Indels: 61
0.79 0.15 0.06
Matches are distributed among these distances:
205 72 0.09
206 57 0.07
207 5 0.01
208 105 0.13
209 25 0.03
210 5 0.01
211 287 0.34
212 154 0.18
213 2 0.00
214 115 0.14
215 5 0.01
216 2 0.00
ACGTcount: A:0.24, C:0.22, G:0.16, T:0.38
Consensus pattern (209 bp):
CCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTAAGTCTAACATCGTTGGCCTTGAATCAGCA
TATTGGTACCTTTGTCATCTTTTTAAGTCTAATATCACTGGCCTTGAATCAGCATATTGGCGCCT
TTATGATCTTTAAGTCCAATGTCACTGGCCTTGAATCAGCACATTGGCACTTTTTCTTTCTTAAG
TCTAATATCGATGG
Found at i:294047 original size:61 final size:62
Alignment explanation
Indices: 293919--294056 Score: 163
Period size: 61 Copynumber: 2.3 Consensus size: 62
293909 GCACCCTTGT
* * *
293919 CATCTTTAAGCCCAATATCGCTAGCCTTGGATTAGCATATTGGCACCTTTATCAATCTTCTA
1 CATCTTTAAGCCCAATATCGCTAGCCGTGAATCAGCATATTGGCACCTTTATCAATCTTCTA
* * ** ** *
293981 -TTCTTTAAGCTCGGTATCGCTAGCCGTGAATCAGCATATTGGCATTTTTATCATTCTTC-A
1 CATCTTTAAGCCCAATATCGCTAGCCGTGAATCAGCATATTGGCACCTTTATCAATCTTCTA
*
294041 CATCTTTAAGTCCAAT
1 CATCTTTAAGCCCAAT
294057 GTCGTTAACC
Statistics
Matches: 60, Mismatches: 15, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
60 1 0.02
61 59 0.98
ACGTcount: A:0.25, C:0.24, G:0.14, T:0.38
Consensus pattern (62 bp):
CATCTTTAAGCCCAATATCGCTAGCCGTGAATCAGCATATTGGCACCTTTATCAATCTTCTA
Found at i:294072 original size:61 final size:61
Alignment explanation
Indices: 293919--294087 Score: 162
Period size: 61 Copynumber: 2.8 Consensus size: 61
293909 GCACCCTTGT
* *
293919 CATCTTTAAGCCCAATATCGCTAGCCTTGGATTAGCATATTGGCACCTTTATCAATCTTCTA
1 CATCTTTAAG-CCAATATCGCTAGCCTTGAATCAGCATATTGGCACCTTTATCAATCTTCTA
* ** * ** *
293981 -TTCTTTAAGCTCGGTATCGCTAGCCGTGAATCAGCATATTGGCATTTTTATCATTCTTC-A
1 CATCTTTAAGC-CAATATCGCTAGCCTTGAATCAGCATATTGGCACCTTTATCAATCTTCTA
* * * * * *
294041 CATCTTTAAGTCCAATGTCGTTAACCTTGAATTATCACATTGGCACC
1 CATCTTTAAG-CCAATATCGCTAGCCTTGAATCAGCATATTGGCACC
294088 CTTCTCATCC
Statistics
Matches: 83, Mismatches: 21, Indels: 7
0.75 0.19 0.06
Matches are distributed among these distances:
60 2 0.02
61 80 0.96
62 1 0.01
ACGTcount: A:0.25, C:0.24, G:0.14, T:0.37
Consensus pattern (61 bp):
CATCTTTAAGCCAATATCGCTAGCCTTGAATCAGCATATTGGCACCTTTATCAATCTTCTA
Found at i:294858 original size:20 final size:20
Alignment explanation
Indices: 294830--294908 Score: 70
Period size: 20 Copynumber: 3.9 Consensus size: 20
294820 AATGCCAAGG
*
294830 AAATGTATCGATACATTACT
1 AAATATATCGATACATTACT
*
294850 AAATATATCAATACA-TACTT
1 AAATATATCGATACATTAC-T
*
294870 ATAATTATATCGATACATTTCT
1 A-AA-TATATCGATACATTACT
* * *
294892 CACTGTATCGATACATT
1 AAATATATCGATACATT
294909 CTGGGTTTTT
Statistics
Matches: 48, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
19 3 0.06
20 28 0.58
21 3 0.06
22 12 0.25
23 2 0.04
ACGTcount: A:0.39, C:0.16, G:0.06, T:0.38
Consensus pattern (20 bp):
AAATATATCGATACATTACT
Found at i:298374 original size:29 final size:28
Alignment explanation
Indices: 298339--298505 Score: 164
Period size: 26 Copynumber: 6.0 Consensus size: 28
298329 AAGGTACCAA
298339 TGACTTGTGGGCTTTGAAAAGGGTGCCAC
1 TGACTTGTGGGCTTT-AAAAGGGTGCCAC
* * **
298368 TAACTTGTGGGCTTTGAAATAGTGCCAC
1 TGACTTGTGGGCTTTAAAAGGGTGCCAC
298396 TGACTTG-GGAGCTTTGAAAAGGGTGCCAC
1 TGACTTGTGG-GCTTT-AAAAGGGTGCCAC
*
298425 TGACTTGTGGGCTTT--AGGGGTGCCAC
1 TGACTTGTGGGCTTTAAAAGGGTGCCAC
** * *
298451 TGACTCATAGGCTTT--AGGGGTGCCAC
1 TGACTTGTGGGCTTTAAAAGGGTGCCAC
** *
298477 TGACTCCTGAGCTTTAAAAGGGTGCCAC
1 TGACTTGTGGGCTTTAAAAGGGTGCCAC
298505 T
1 T
298506 AACTCGTCGC
Statistics
Matches: 117, Mismatches: 16, Indels: 11
0.81 0.11 0.08
Matches are distributed among these distances:
26 45 0.38
27 2 0.02
28 32 0.27
29 36 0.31
30 2 0.02
ACGTcount: A:0.21, C:0.20, G:0.31, T:0.28
Consensus pattern (28 bp):
TGACTTGTGGGCTTTAAAAGGGTGCCAC
Found at i:298401 original size:28 final size:28
Alignment explanation
Indices: 298327--298455 Score: 149
Period size: 29 Copynumber: 4.6 Consensus size: 28
298317 AGACTTTGAA
* *
298327 AAAAGGTACCAATGACTTGTGGGCTTTG
1 AAAAGGTGCCACTGACTTGTGGGCTTTG
*
298355 AAAAGGGTGCCACTAACTTGTGGGCTTTG
1 AAAA-GGTGCCACTGACTTGTGGGCTTTG
298384 AAATA-GTGCCACTGACTTG-GGAGCTTTG
1 AAA-AGGTGCCACTGACTTGTGG-GCTTTG
298412 AAAAGGGTGCCACTGACTTGTGGGCTTT-
1 AAAA-GGTGCCACTGACTTGTGGGCTTTG
**
298440 -AGGGGTGCCACTGACT
1 AAAAGGTGCCACTGACT
298456 CATAGGCTTT
Statistics
Matches: 89, Mismatches: 6, Indels: 14
0.82 0.06 0.13
Matches are distributed among these distances:
26 13 0.15
27 4 0.04
28 26 0.29
29 43 0.48
30 3 0.03
ACGTcount: A:0.24, C:0.18, G:0.31, T:0.27
Consensus pattern (28 bp):
AAAAGGTGCCACTGACTTGTGGGCTTTG
Found at i:298953 original size:58 final size:58
Alignment explanation
Indices: 298867--299022 Score: 154
Period size: 58 Copynumber: 2.7 Consensus size: 58
298857 AAATTGCATG
* * ** * * *
298867 AAAGTCCTTAAATCATGAAAAGCGACCTAAATGATATCAAAATTGATAAAAT-TATATC
1 AAAGTCCCTAAATCATAAAAAATGACCTAAATGACATCAAAATTCATAAAATGGA-ATC
* * * * *
298925 CAAGTCCCTAAATCATAAAAAATTACCTAAATAACACCAACATTCATAAAATGGAATC
1 AAAGTCCCTAAATCATAAAAAATGACCTAAATGACATCAAAATTCATAAAATGGAATC
* *
298983 AAAGT-CCTAGATCACTAGAAAATGACCTAAATGACATCAA
1 AAAGTCCCTAAATCA-TAAAAAATGACCTAAATGACATCAA
299023 GATAATCTTT
Statistics
Matches: 78, Mismatches: 18, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
57 8 0.10
58 69 0.88
59 1 0.01
ACGTcount: A:0.49, C:0.19, G:0.09, T:0.24
Consensus pattern (58 bp):
AAAGTCCCTAAATCATAAAAAATGACCTAAATGACATCAAAATTCATAAAATGGAATC
Found at i:306922 original size:164 final size:163
Alignment explanation
Indices: 306719--307199 Score: 454
Period size: 165 Copynumber: 2.9 Consensus size: 163
306709 TTTTAAATTG
* * * * * * *
306719 AGAAAAATTCCTCTGAAAATATTTATGGAGTTGAAAACTCCGTTTTTCGAAAATAGGAGAAGTTC
1 AGAAAAA-TCCTTTGAAAACATTTACGAAGTAGAAAACTCCGTATTTCAAAAATA-GAGAAGTTC
* * *
306784 GAAGAAAAAAAT-CAAAACTCATAAAAATAAATTAA-TTTTCAAACTAATTT-ACTATGAATTAA
64 GAAG-AAAAAATGAAAAACTCATAAAAATAAATGAATTTTTAAAACTAATTTAAC-ATGAATTAA
* * * *
306846 ATAATAATATTTGATGAATTTTTAAAGTTGAAAACCA
127 ATAATAATATTTAATGAATTTTAAAAATTAAAAACCA
* * * **
306883 AGAAAAATCCTTTCGAAAACATTTACGTAGTAGAAAACTCCGTATTTCAAAAATATAGGAGTTTT
1 AGAAAAATCCTTT-GAAAACATTTACGAAGTAGAAAACTCCGTATTTCAAAAATAGAGAAGTTCG
* * * * *
306948 AAGGAAAAATGAAAAACTCATGAAGATAAGTGAATTTTTTAAAACTGATTTAACATGAATTAAAT
65 AAGAAAAAATGAAAAACTCATAAAAATAAATGAA-TTTTTAAAACTAATTTAACATGAATTAAAT
307013 AATAATATTTAATGAATTTTAAAAATTAAAAACCA
129 AATAATATTTAATGAATTTTAAAAATTAAAAACCA
** ** * *
307048 AGAAAAATCCCTAGGAAAACATTTACGAAGTAGAAAACTTTGT-TTTCTGAAAACA-AGAATAAT
1 AGAAAAAT-CCTTTGAAAACATTTACGAAGTAGAAAACTCCGTATTTC--AAAA-ATAG-AGAAG
* * * * * **
307111 TTC-AGAGAAAAAATGAAAAACTCATGAAGATGAATGGATTTTTGAAAACTGATTTAATGGTG-A
61 TTCGA-AGAAAAAATGAAAAACTCATAAAAATAAATGAATTTTT-AAAACTAATTTAA-CATGAA
307174 TTAAATAATAATATTTAATGAATTTT
123 TTAAATAATAATATTTAATGAATTTT
307200 GACGTTTTAA
Statistics
Matches: 265, Mismatches: 39, Indels: 23
0.81 0.12 0.07
Matches are distributed among these distances:
162 6 0.02
163 32 0.12
164 46 0.17
165 89 0.34
166 16 0.06
167 74 0.28
168 2 0.01
ACGTcount: A:0.47, C:0.09, G:0.13, T:0.31
Consensus pattern (163 bp):
AGAAAAATCCTTTGAAAACATTTACGAAGTAGAAAACTCCGTATTTCAAAAATAGAGAAGTTCGA
AGAAAAAATGAAAAACTCATAAAAATAAATGAATTTTTAAAACTAATTTAACATGAATTAAATAA
TAATATTTAATGAATTTTAAAAATTAAAAACCA
Found at i:307013 original size:165 final size:166
Alignment explanation
Indices: 306819--307199 Score: 470
Period size: 165 Copynumber: 2.3 Consensus size: 166
306809 AATAAATTAA
* * * * * *
306819 TTTTCAAACTAATTT-ACTATGAATTAAATAATAATATTTGATGAATTTTTAAAGTTGAAAACCA
1 TTTTAAAACTGATTTAAC-ATGAATTAAATAATAATATTTAATGAATTTTAAAAATTAAAAACCA
* * * * *
306883 AGAAAAATCCTTTCGAAAACATTTACGTAGTAGAAAACTCCGTATTTC-AAAAATATAGGAGT-T
65 AGAAAAATCCCTACGAAAACATTTACGAAGTAGAAAACTCCGT-TTTCTAAAAACA-A-GAATAT
*
306946 TT-A-AGGAAAAATGAAAAACTCATGAAGAT-AAGTGAATT
127 TTCAGAGAAAAAATGAAAAACTCATGAAGATGAA-TGAATT
306984 TTTTAAAACTGATTTAACATGAATTAAATAATAATATTTAATGAATTTTAAAAATTAAAAACCAA
1 TTTTAAAACTGATTTAACATGAATTAAATAATAATATTTAATGAATTTTAAAAATTAAAAACCAA
* ** *
307049 GAAAAATCCCTAGGAAAACATTTACGAAGTAGAAAACTTTGTTTTCTGAAAACAAGAATAATTTC
66 GAAAAATCCCTACGAAAACATTTACGAAGTAGAAAACTCCGTTTTCTAAAAACAAGAAT-ATTTC
*
307114 AGAGAAAAAATGAAAAACTCATGAAGATGAATGGATT
130 AGAGAAAAAATGAAAAACTCATGAAGATGAATGAATT
* **
307151 TTTGAAAACTGATTTAATGGTG-ATTAAATAATAATATTTAATGAATTTT
1 TTTTAAAACTGATTTAA-CATGAATTAAATAATAATATTTAATGAATTTT
307200 GACGTTTTAA
Statistics
Matches: 188, Mismatches: 20, Indels: 14
0.85 0.09 0.06
Matches are distributed among these distances:
163 3 0.02
164 5 0.03
165 100 0.53
166 3 0.02
167 73 0.39
168 4 0.02
ACGTcount: A:0.47, C:0.08, G:0.12, T:0.33
Consensus pattern (166 bp):
TTTTAAAACTGATTTAACATGAATTAAATAATAATATTTAATGAATTTTAAAAATTAAAAACCAA
GAAAAATCCCTACGAAAACATTTACGAAGTAGAAAACTCCGTTTTCTAAAAACAAGAATATTTCA
GAGAAAAAATGAAAAACTCATGAAGATGAATGAATT
Found at i:308586 original size:21 final size:21
Alignment explanation
Indices: 308561--308602 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
308551 CATGGAGAAA
308561 ATAAAAAGCATGTAACATACT
1 ATAAAAAGCATGTAACATACT
* *
308582 ATAAAATGTATGTAACATACT
1 ATAAAAAGCATGTAACATACT
308603 CATCATGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.29
Consensus pattern (21 bp):
ATAAAAAGCATGTAACATACT
Found at i:310632 original size:16 final size:16
Alignment explanation
Indices: 310613--310643 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
310603 TTCGAGTTAT
*
310613 TTTAGATTCAGGTCAC
1 TTTAGATTCAAGTCAC
310629 TTTAGATTCAAGTCA
1 TTTAGATTCAAGTCA
310644 TTCCAAGTTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.39
Consensus pattern (16 bp):
TTTAGATTCAAGTCAC
Found at i:311536 original size:30 final size:29
Alignment explanation
Indices: 311476--311536 Score: 70
Period size: 30 Copynumber: 2.1 Consensus size: 29
311466 TATTGTTTTT
*
311476 TAAAATTTTTTAATAATTTATATTAGAAA
1 TAAAATTTTTTAATAAATTATATTAGAAA
* *
311505 TAAAGTTTTTTAAATATAATTAT-TTATAAA
1 TAAAATTTTTT-AATA-AATTATATTAGAAA
311535 TA
1 TA
311537 TTTATTTTCA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 10 0.37
30 12 0.44
31 5 0.19
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (29 bp):
TAAAATTTTTTAATAAATTATATTAGAAA
Found at i:313567 original size:20 final size:20
Alignment explanation
Indices: 313539--313592 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
313529 CAATTGGTGC
*
313539 ATGTCTCGATACATAAGTGA
1 ATGTATCGATACATAAGTGA
313559 ATGTATCGATACATAAGTGA
1 ATGTATCGATACATAAGTGA
*
313579 ATGTATTGATACAT
1 ATGTATCGATACAT
313593 GTCTCAAATG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.37, C:0.11, G:0.19, T:0.33
Consensus pattern (20 bp):
ATGTATCGATACATAAGTGA
Found at i:317217 original size:13 final size:13
Alignment explanation
Indices: 317199--317224 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
317189 CAAGGTGGTT
317199 TTGTATCGATACA
1 TTGTATCGATACA
317212 TTGTATCGATACA
1 TTGTATCGATACA
317225 AAACTTATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:322216 original size:112 final size:112
Alignment explanation
Indices: 322056--322299 Score: 305
Period size: 112 Copynumber: 2.2 Consensus size: 112
322046 GAATTTCCAT
* * * *
322056 GCAATGTATCGATACATGAAGGCTTGGTATTGATACCCAAGGTGTGGTATCGATACCTAATGTGA
1 GCAA-GTATCGATACATCAAGGCTTGATATCGATACCCAAGGTGTGGTATCGATACCTAATATGA
* * * * *
322121 TTGTTTCGATACA-AACCTTGGCAGTAGCTAAAATTC-ACTTTCTGGACA
65 TTCTATCAATACATAACCTTGGCAATAGCAAAAATTCGA-TTT-TGGACA
* * *
322169 GCAAGTATCGATTCATCAAGGCTTGATATCGATACCTAAGGTGTGGTATCGATACCTAGTATGAT
1 GCAAGTATCGATACATCAAGGCTTGATATCGATACCCAAGGTGTGGTATCGATACCTAATATGAT
* **
322234 TCTATCAATGCATGGCCTTGGCAATAGCAAAAATTCGATTTTGGACA
66 TCTATCAATACATAACCTTGGCAATAGCAAAAATTCGATTTTGGACA
322281 GCAAGTATCGATAC-TCAAG
1 GCAAGTATCGATACATCAAG
322300 TAATTATATT
Statistics
Matches: 113, Mismatches: 16, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
111 5 0.04
112 81 0.72
113 26 0.23
114 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.30
Consensus pattern (112 bp):
GCAAGTATCGATACATCAAGGCTTGATATCGATACCCAAGGTGTGGTATCGATACCTAATATGAT
TCTATCAATACATAACCTTGGCAATAGCAAAAATTCGATTTTGGACA
Found at i:322360 original size:20 final size:21
Alignment explanation
Indices: 322335--322377 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
322325 TTTTGCCCAA
*
322335 ATGTATCGATACA-ATAAGCT
1 ATGTATCAATACATATAAGCT
*
322355 ATGTATCAATACATATAGGCT
1 ATGTATCAATACATATAAGCT
322376 AT
1 AT
322378 TTTGACAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.33
Consensus pattern (21 bp):
ATGTATCAATACATATAAGCT
Found at i:324825 original size:80 final size:80
Alignment explanation
Indices: 324756--324966 Score: 316
Period size: 80 Copynumber: 2.6 Consensus size: 80
324746 TTCATTCTTG
* * * * *
324756 AGGATACTCCAACCCCACTATCTTCAAGGGGATACTCCAACCCTATTTTTACTTCCAAAACATTA
1 AGGATACTCCAACTCCACCATTTTGAAGGAGATACTCCAACCCTATTTTTACTTCCAAAACATTA
324821 AATTTATCATCTTTA
66 AATTTATCATCTTTA
* *
324836 AGGATACTCTAACTCCACCATTTTGGAA-GAGATACTCCAACCCTATTTTTACTTCCACAACATT
1 AGGATACTCCAACTCCACCATTTT-GAAGGAGATACTCCAACCCTATTTTTACTTCCAAAACATT
324900 AAATTTATCATCTTTA
65 AAATTTATCATCTTTA
* * *
324916 AGGATACTCCAACTCCACCATTTTGGAGGAGATACTCCAACCTTGTTTTTA
1 AGGATACTCCAACTCCACCATTTTGAAGGAGATACTCCAACCCTATTTTTA
324967 TACTAAAATT
Statistics
Matches: 118, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
79 2 0.02
80 114 0.97
81 2 0.02
ACGTcount: A:0.31, C:0.26, G:0.09, T:0.33
Consensus pattern (80 bp):
AGGATACTCCAACTCCACCATTTTGAAGGAGATACTCCAACCCTATTTTTACTTCCAAAACATTA
AATTTATCATCTTTA
Found at i:325073 original size:52 final size:52
Alignment explanation
Indices: 324968--325073 Score: 135
Period size: 52 Copynumber: 2.0 Consensus size: 52
324958 TTGTTTTTAT
* *
324968 ACTAAAATTTGATTGATGAAAACATCAAATTGTCATCTTTAGGGGCACTCCA
1 ACTAAAATTTGATTGATGAAAACATCAAATTGTCATCTTGAGGGGCACCCCA
* * *
325020 ACTAAAATTTGATTTAT-AAATATATCAAATTGTCATCTATGA-GGGTACCCCA
1 ACTAAAATTTGATTGATGAAA-ACATCAAATTGTCATCT-TGAGGGGCACCCCA
325072 AC
1 AC
325074 CTCAACTTTC
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
51 3 0.06
52 42 0.89
53 2 0.04
ACGTcount: A:0.38, C:0.17, G:0.13, T:0.32
Consensus pattern (52 bp):
ACTAAAATTTGATTGATGAAAACATCAAATTGTCATCTTGAGGGGCACCCCA
Found at i:327114 original size:16 final size:16
Alignment explanation
Indices: 327090--327142 Score: 70
Period size: 16 Copynumber: 3.3 Consensus size: 16
327080 GGTCAATTTG
* * *
327090 AGTTTGGGTTATTTCA
1 AGTTCGGGTCATTCCA
327106 AGTTCGGGTCATTCCA
1 AGTTCGGGTCATTCCA
*
327122 AGTTCAGGTCATTCCA
1 AGTTCGGGTCATTCCA
327138 AGTTC
1 AGTTC
327143 AAGTCATTTC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.38
Consensus pattern (16 bp):
AGTTCGGGTCATTCCA
Found at i:327143 original size:16 final size:16
Alignment explanation
Indices: 327104--327150 Score: 76
Period size: 16 Copynumber: 2.9 Consensus size: 16
327094 TGGGTTATTT
*
327104 CAAGTTCGGGTCATTC
1 CAAGTTCAGGTCATTC
327120 CAAGTTCAGGTCATTC
1 CAAGTTCAGGTCATTC
*
327136 CAAGTTCAAGTCATT
1 CAAGTTCAGGTCATT
327151 TCGGGTTAGG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (16 bp):
CAAGTTCAGGTCATTC
Found at i:328038 original size:13 final size:13
Alignment explanation
Indices: 328017--328048 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
328007 TCGATACATT
*
328017 ATACTTTGTATCG
1 ATACATTGTATCG
328030 ATACATTGTATCG
1 ATACATTGTATCG
328043 ATACAT
1 ATACAT
328049 GTTCATTGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.16, G:0.12, T:0.41
Consensus pattern (13 bp):
ATACATTGTATCG
Found at i:328045 original size:33 final size:32
Alignment explanation
Indices: 328003--328065 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 32
327993 CATATCCAGA
*
328003 TGTATCGATACAT-TATACTTTGTATCGATACAT
1 TGTATCGATACATGT-T-CATTGTATCGATACAT
328036 TGTATCGATACATGTTCATTGTATCGATAC
1 TGTATCGATACATGTTCATTGTATCGATAC
328066 GTACTCAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 13 0.46
33 14 0.50
34 1 0.04
ACGTcount: A:0.29, C:0.16, G:0.14, T:0.41
Consensus pattern (32 bp):
TGTATCGATACATGTTCATTGTATCGATACAT
Found at i:328057 original size:19 final size:19
Alignment explanation
Indices: 328033--328088 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
328023 TGTATCGATA
*
328033 CATTGTATCGATACATGTT
1 CATTGTATCGATACATGCT
* *
328052 CATTGTATCGATACGTACT
1 CATTGTATCGATACATGCT
328071 CAATTGTATCGATACATG
1 C-ATTGTATCGATACATG
328089 AAACTGGCAG
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
19 17 0.55
20 14 0.45
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.38
Consensus pattern (19 bp):
CATTGTATCGATACATGCT
Found at i:336792 original size:13 final size:13
Alignment explanation
Indices: 336774--336800 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
336764 ACATTATGCT
336774 TTGTATCGATATA
1 TTGTATCGATATA
336787 TTGTATCGATATA
1 TTGTATCGATATA
336800 T
1 T
336801 GTTCATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.07, G:0.15, T:0.48
Consensus pattern (13 bp):
TTGTATCGATATA
Found at i:338134 original size:36 final size:34
Alignment explanation
Indices: 338051--338143 Score: 111
Period size: 36 Copynumber: 2.8 Consensus size: 34
338041 CAATACTATC
*
338051 TTTC-AAGGCTAAGATAGAAAC-CTCCCTATCTT
1 TTTCAAAGGCTAAGATAGAACCTCTCCCTATCTT
**
338083 TTT-ACGGGCTAAGATAGAACCTCTCTCTCTATCTT
1 TTTCAAAGGCTAAGATAGAACCTCTC-C-CTATCTT
*
338118 TTTCAAAGGCTAAGATATAACCTCTC
1 TTTCAAAGGCTAAGATAGAACCTCTC
338144 AATTACTTAG
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
32 17 0.34
33 3 0.06
34 1 0.02
35 10 0.20
36 19 0.38
ACGTcount: A:0.29, C:0.25, G:0.13, T:0.33
Consensus pattern (34 bp):
TTTCAAAGGCTAAGATAGAACCTCTCCCTATCTT
Found at i:338622 original size:13 final size:13
Alignment explanation
Indices: 338604--338642 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
338594 TATTATTCAC
338604 ATGTATCGATACA
1 ATGTATCGATACA
338617 ATGTATCGATACA
1 ATGTATCGATACA
*
338630 ATATATCGATACA
1 ATGTATCGATACA
338643 TGAACAATGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.41, C:0.15, G:0.13, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:338773 original size:13 final size:13
Alignment explanation
Indices: 338755--338779 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
338745 TACCAAGAAC
338755 ATGTATCAATACA
1 ATGTATCAATACA
338768 ATGTATCAATAC
1 ATGTATCAATAC
338780 TAAGCAATAT
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:0.44, C:0.16, G:0.08, T:0.32
Consensus pattern (13 bp):
ATGTATCAATACA
Found at i:338794 original size:33 final size:32
Alignment explanation
Indices: 338736--338800 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
338726 ACAATTCATG
*
338736 ATGTATCGATACCAAGAACATGTATCAATACA
1 ATGTATCAATACCAAGAACATGTATCAATACA
* * *
338768 ATGTATCAATACTAAGCAATATGTATCGATACA
1 ATGTATCAATACCAAG-AACATGTATCAATACA
338801 TCTTTGTGTG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
32 14 0.50
33 14 0.50
ACGTcount: A:0.43, C:0.17, G:0.12, T:0.28
Consensus pattern (32 bp):
ATGTATCAATACCAAGAACATGTATCAATACA
Found at i:347277 original size:36 final size:32
Alignment explanation
Indices: 347203--347295 Score: 89
Period size: 32 Copynumber: 2.8 Consensus size: 32
347193 ATTATCTTTC
347203 AAGGCTAAGATAGAAACCTCCCAATCTTTTTA
1 AAGGCTAAGATAGAAACCTCCCAATCTTTTTA
** * *
347235 CGGGCTAAGATAGAACCTCTGTCCCTATCTTTTTTA
1 AAGGCTAAGATAGAAAC-C--TCCCAATC-TTTTTA
* *
347271 AAGGCTAAGATA-AAATCTCTCAATC
1 AAGGCTAAGATAGAAACCTCCCAATC
347296 ACTTAGAGAA
Statistics
Matches: 47, Mismatches: 10, Indels: 8
0.72 0.15 0.12
Matches are distributed among these distances:
32 20 0.43
33 1 0.02
34 1 0.02
35 9 0.19
36 16 0.34
ACGTcount: A:0.33, C:0.23, G:0.14, T:0.30
Consensus pattern (32 bp):
AAGGCTAAGATAGAAACCTCCCAATCTTTTTA
Found at i:347459 original size:19 final size:19
Alignment explanation
Indices: 347432--347472 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
347422 TACAAGGAAT
*
347432 GAATGAAAGAGCTTTGATA
1 GAATAAAAGAGCTTTGATA
347451 GAATAAAAGAGCTTTGATA
1 GAATAAAAGAGCTTTGATA
347470 GAA
1 GAA
347473 AAACAATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.46, C:0.05, G:0.24, T:0.24
Consensus pattern (19 bp):
GAATAAAAGAGCTTTGATA
Found at i:350517 original size:6 final size:6
Alignment explanation
Indices: 350506--350536 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
350496 TAAATTGAAT
350506 AATTGC AATTGC AATTGC AATTGC AATTGC A
1 AATTGC AATTGC AATTGC AATTGC AATTGC A
350537 GCTGTAATCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.32
Consensus pattern (6 bp):
AATTGC
Found at i:350942 original size:21 final size:20
Alignment explanation
Indices: 350918--350963 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 20
350908 GCGTGAGTTC
*
350918 TATTTAATTATATGTTAAATT
1 TATTTAATTATATATT-AATT
350939 TATTTAATTATATATTAATT
1 TATTTAATTATATATTAATT
350959 TATTT
1 TATTT
350964 GATATTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 9 0.38
21 15 0.62
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (20 bp):
TATTTAATTATATATTAATT
Found at i:350958 original size:11 final size:10
Alignment explanation
Indices: 350918--350963 Score: 51
Period size: 10 Copynumber: 4.5 Consensus size: 10
350908 GCGTGAGTTC
350918 TATTTAATTA
1 TATTTAATTA
350928 TATGTTAAATT-
1 TAT-TT-AATTA
350939 TATTTAATTA
1 TATTTAATTA
350949 TATATTAATT-
1 TAT-TTAATTA
350959 TATTT
1 TATTT
350964 GATATTTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
9 6 0.19
10 11 0.34
11 11 0.34
12 4 0.12
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (10 bp):
TATTTAATTA
Found at i:351658 original size:8 final size:8
Alignment explanation
Indices: 351647--351754 Score: 69
Period size: 8 Copynumber: 12.4 Consensus size: 8
351637 AGATTTGGTA
351647 ATTTATAT
1 ATTTATAT
351655 ATTTATATT
1 ATTTATA-T
351664 ATATT-TAT
1 AT-TTATAT
351672 ATTTATAT
1 ATTTATAT
351680 ATTTTATTAT
1 A-TTTA-TAT
351690 ATTATAATTAT
1 ATT-T-A-TAT
*
351701 ATTTAAAAT
1 ATTT-ATAT
351710 ATTT-TAT
1 ATTTATAT
351717 ATTTATAT
1 ATTTATAT
351725 AAATTTTAATAT
1 --A-TTT-ATAT
*
351737 ATTAATA-
1 ATTTATAT
351744 ATTTATAT
1 ATTTATAT
351752 ATT
1 ATT
351755 ATAAAATTTA
Statistics
Matches: 83, Mismatches: 4, Indels: 26
0.73 0.04 0.23
Matches are distributed among these distances:
7 14 0.17
8 23 0.28
9 19 0.23
10 12 0.14
11 11 0.13
12 4 0.05
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (8 bp):
ATTTATAT
Found at i:351663 original size:6 final size:6
Alignment explanation
Indices: 351652--351724 Score: 66
Period size: 6 Copynumber: 12.8 Consensus size: 6
351642 TGGTAATTTA
* *
351652 TATATT TATA-T TATATT TATATT TATATAT TTTA-T TATA-T TATAAT
1 TATATT TATATT TATATT TATATT TATAT-T TATATT TATATT TATATT
**
351698 TATATT TA-AAA TAT-TT TATATT TATAT
1 TATATT TATATT TATATT TATATT TATAT
351725 AAATTTTAAT
Statistics
Matches: 55, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
5 20 0.36
6 31 0.56
7 4 0.07
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (6 bp):
TATATT
Found at i:351675 original size:25 final size:24
Alignment explanation
Indices: 351647--351754 Score: 105
Period size: 25 Copynumber: 4.5 Consensus size: 24
351637 AGATTTGGTA
*
351647 ATTTATATATTTATATTATATTTAT
1 ATTTATATATTT-TAATATATTTAT
*
351672 ATTTATATATTTTATTATA-TTAT
1 ATTTATATATTTTAATATATTTAT
* **
351695 AATTATAT-TTAAAATAT-TTTAT
1 ATTTATATATTTTAATATATTTAT
*
351717 ATTTATATAAATTTTAATATATTAAT
1 ATTTATAT--ATTTTAATATATTTAT
351743 AATTTATATATT
1 -ATTTATATATT
351755 ATAAAATTTA
Statistics
Matches: 69, Mismatches: 8, Indels: 12
0.78 0.09 0.13
Matches are distributed among these distances:
22 17 0.25
23 11 0.16
24 7 0.10
25 22 0.32
26 4 0.06
27 8 0.12
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (24 bp):
ATTTATATATTTTAATATATTTAT
Found at i:351694 original size:29 final size:30
Alignment explanation
Indices: 351657--351724 Score: 97
Period size: 29 Copynumber: 2.4 Consensus size: 30
351647 ATTTATATAT
*
351657 TTATATTATATTTATATTT-ATATATTTTA
1 TTATATTATATTTATATTTAAAATATTTTA
*
351686 TTATATTATAATTATATTTAAAATATTTTA
1 TTATATTATATTTATATTTAAAATATTTTA
351716 -TAT-TTATAT
1 TTATATTATAT
351725 AAATTTTAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
28 5 0.14
29 21 0.60
30 9 0.26
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (30 bp):
TTATATTATATTTATATTTAAAATATTTTA
Found at i:351700 original size:35 final size:34
Alignment explanation
Indices: 351648--351754 Score: 96
Period size: 35 Copynumber: 3.0 Consensus size: 34
351638 GATTTGGTAA
351648 TTTA-TATATTTATATTATATTTATATTTATATAT
1 TTTATTATATTTA-ATTATATTTATATTTATATAT
351682 TTTATTATATTATAATTATATTTAAAATATTT-TATA-
1 TTTATTATATT-TAATTATATTT---ATATTTATATAT
* *
351718 TTTATATAAATTTTAA-TATATTAATAATTTATATAT
1 TTTAT-TATA-TTTAATTATATTTAT-ATTTATATAT
351754 T
1 T
351755 ATAAAATTTA
Statistics
Matches: 61, Mismatches: 2, Indels: 18
0.75 0.02 0.22
Matches are distributed among these distances:
33 2 0.03
34 8 0.13
35 19 0.31
36 14 0.23
37 10 0.16
38 8 0.13
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (34 bp):
TTTATTATATTTAATTATATTTATATTTATATAT
Found at i:351749 original size:33 final size:32
Alignment explanation
Indices: 351707--351771 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 32
351697 TTATATTTAA
* *
351707 AATATTTTATAT-TTATATAAATTTTAATATATT
1 AATAATTTATATATTATA-AAA-TTTAAAATATT
351740 AATAATTTATATATTATAAAATTTAAAATATT
1 AATAATTTATATATTATAAAATTTAAAATATT
351772 TAAATTATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
32 10 0.34
33 14 0.48
34 5 0.17
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (32 bp):
AATAATTTATATATTATAAAATTTAAAATATT
Found at i:351770 original size:17 final size:17
Alignment explanation
Indices: 351722--351775 Score: 60
Period size: 16 Copynumber: 3.4 Consensus size: 17
351712 TTTATATTTA
*
351722 TATAAATTTTAATATAT
1 TATAAAATTTAATATAT
*
351739 TA-ATAATTT-ATATAT
1 TATAAAATTTAATATAT
*
351754 TATAAAATTTAAAATAT
1 TATAAAATTTAATATAT
351771 T-TAAA
1 TATAAA
351776 TTATTTTTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
15 8 0.26
16 15 0.48
17 8 0.26
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
TATAAAATTTAATATAT
Found at i:353381 original size:7 final size:7
Alignment explanation
Indices: 353369--353398 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
353359 AAAACCCATA
353369 ATTAGTG
1 ATTAGTG
353376 ATTAGTG
1 ATTAGTG
353383 ATTAGTG
1 ATTAGTG
*
353390 ATTAATG
1 ATTAGTG
353397 AT
1 AT
353399 GTATCATAGG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.33, C:0.00, G:0.23, T:0.43
Consensus pattern (7 bp):
ATTAGTG
Found at i:356490 original size:2 final size:2
Alignment explanation
Indices: 356483--356516 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
356473 CACTAACCAG
356483 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
356517 ATATATGTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:356521 original size:2 final size:2
Alignment explanation
Indices: 356516--356553 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
356506 TGTGTGTGTG
*
356516 TA TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
356554 GGCCAGGACT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Done.