Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014625.1 Kokia drynarioides strain JFW-HI SEQ_129664, 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: 378628
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 251 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:682 original size:22 final size:22
Alignment explanation
Indices: 656--699 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
646 TAAGAAAAAT
*
656 CCTCTGATATTTTTTAAAATTG
1 CCTCTGATATTTTTGAAAATTG
678 CCTCTGATATTTTTGAAAATTG
1 CCTCTGATATTTTTGAAAATTG
700 AAACTGTATA
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:0.27, C:0.14, G:0.11, T:0.48
Consensus pattern (22 bp):
CCTCTGATATTTTTGAAAATTG
Found at i:1357 original size:10 final size:10
Alignment explanation
Indices: 1317--1370 Score: 54
Period size: 10 Copynumber: 5.3 Consensus size: 10
1307 AACATAAAAG
1317 AAATGTTATAA
1 AAAT-TTATAA
* *
1328 AAATTAATTA
1 AAATTTATAA
*
1338 AAATTCATAA
1 AAATTTATAA
*
1348 AATTTTATAA
1 AAATTTATAA
*
1358 AAAATTATAA
1 AAATTTATAA
1368 AAA
1 AAA
1371 ACCATAAATT
Statistics
Matches: 35, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
10 31 0.89
11 4 0.11
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (10 bp):
AAATTTATAA
Found at i:1377 original size:30 final size:30
Alignment explanation
Indices: 1317--1378 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 30
1307 AACATAAAAG
* **
1317 AAATGTTATAAAAATTAATTAAAATTCATA
1 AAATGTTATAAAAATTAATAAAAAACCATA
*
1347 AAATTTTATAAAAAATT-ATAAAAAACCATA
1 AAATGTTAT-AAAAATTAATAAAAAACCATA
1377 AA
1 AA
1379 TTGATGATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 20 0.74
31 7 0.26
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.32
Consensus pattern (30 bp):
AAATGTTATAAAAATTAATAAAAAACCATA
Found at i:2280 original size:10 final size:10
Alignment explanation
Indices: 2249--2306 Score: 50
Period size: 10 Copynumber: 5.8 Consensus size: 10
2239 ACTAACTTTT
*
2249 TTAATTAAGC
1 TTAATTAAGA
2259 TTAACATT-AGA
1 TT-A-ATTAAGA
2270 TTAATTAAGA
1 TTAATTAAGA
2280 TTTAATT-A-A
1 -TTAATTAAGA
*
2289 TTAATTATGA
1 TTAATTAAGA
2299 TTAATTAA
1 TTAATTAA
2307 TTATTAAAAG
Statistics
Matches: 39, Mismatches: 3, Indels: 12
0.72 0.06 0.22
Matches are distributed among these distances:
8 6 0.15
9 4 0.10
10 15 0.38
11 11 0.28
12 3 0.08
ACGTcount: A:0.45, C:0.03, G:0.07, T:0.45
Consensus pattern (10 bp):
TTAATTAAGA
Found at i:2303 original size:14 final size:14
Alignment explanation
Indices: 2284--2310 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2274 TTAAGATTTA
2284 ATTAATTAATTATG
1 ATTAATTAATTATG
2298 ATTAATTAATTAT
1 ATTAATTAATTAT
2311 TAAAAGAAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (14 bp):
ATTAATTAATTATG
Found at i:4063 original size:161 final size:159
Alignment explanation
Indices: 3798--4256 Score: 607
Period size: 161 Copynumber: 2.8 Consensus size: 159
3788 TCAAATGGTT
* * * *
3798 TAAAATGTATCCAAAACAGAGTCCATGTCGCAATGT-TGGGTGATGGTCGTCACGATGATCTCTG
1 TAAAATGTA-CCAAAACAAAGTCCATGTCGCAATGTCT-GGTGAT-GTCGTCACGACGAGCTCTA
* *
3862 GACTTCAGGAAATGGCGTGATGAGGAATCCTGTCATCACAACGAGACCAAATCAATATGTCACAT
63 GACTTCAAGAAATGGCGTGATGAGGAATCCTGTCATCACAACGAGACCAAGTCAATATGTCACAT
*
3927 CACGATGAGGAGCTTCATCACGTAGTGATTTC
128 CATGATGAGGAGCTTCATCACGTAGTGATTTC
* * *
3959 TAAAATGTACCTAAAACAAAGTCCATGTCACAATGTCTAGTGATGATCGTCACAACGAGCTCTAG
1 TAAAATGTACC-AAAACAAAGTCCATGTCGCAATGTCTGGTGATG-TCGTCACGACGAGCTCTAG
*
4024 ACTTCAAGAAATGGCGTGATGAGGAATCCTGTCATCACAACAAGACCAAGTCAATATGTCACATC
64 ACTTCAAGAAATGGCGTGATGAGGAATCCTGTCATCACAACGAGACCAAGTCAATATGTCACATC
* *
4089 GTGATGAGGAGCTTTATCACGTAGTGATTTC
129 ATGATGAGGAGCTTCATCACGTAGTGATTTC
* * ** * * *
4120 TAAAATGTACCCAAAACAAAGTCCATGTCGCGATGTCGGGCAATTGTTGTCATGACGAGCTCTAA
1 TAAAATGTA-CCAAAACAAAGTCCATGTCGCAATGTCTGGTGA-TGTCGTCACGACGAGCTCTAG
* * ** *
4185 ACTTCAAGCAATAGCGTGGCGAGGAATCCTGTCATCACAACGAGACCAAGTC-GTGATGTCACAT
64 ACTTCAAGAAATGGCGTGATGAGGAATCCTGTCATCACAACGAGACCAAGTCAAT-ATGTCACAT
4249 CATGATGA
128 CATGATGA
4257 CGAACTCCCT
Statistics
Matches: 262, Mismatches: 30, Indels: 12
0.86 0.10 0.04
Matches are distributed among these distances:
160 4 0.02
161 253 0.97
162 5 0.02
ACGTcount: A:0.32, C:0.21, G:0.22, T:0.25
Consensus pattern (159 bp):
TAAAATGTACCAAAACAAAGTCCATGTCGCAATGTCTGGTGATGTCGTCACGACGAGCTCTAGAC
TTCAAGAAATGGCGTGATGAGGAATCCTGTCATCACAACGAGACCAAGTCAATATGTCACATCAT
GATGAGGAGCTTCATCACGTAGTGATTTC
Found at i:6177 original size:14 final size:16
Alignment explanation
Indices: 6148--6180 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
6138 GCTTGAATTC
6148 TTTATTATTTTAAATA
1 TTTATTATTTTAAATA
6164 TTTATT-TTTT-AATA
1 TTTATTATTTTAAATA
6178 TTT
1 TTT
6181 TAGTCTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.41
15 4 0.24
16 6 0.35
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
TTTATTATTTTAAATA
Found at i:8298 original size:47 final size:47
Alignment explanation
Indices: 8229--8324 Score: 165
Period size: 47 Copynumber: 2.0 Consensus size: 47
8219 CATGTCAAAC
*
8229 TATGATAAATATGGTGTTCATTATCTCATATAAAATTTGAATTTGGA
1 TATGATAAATATGGTGTTCATTATCTCATATAAAATTTGAATTCGGA
* *
8276 TATGATAATTATGGTGTTCATTATTTCATATAAAATTTGAATTCGGA
1 TATGATAAATATGGTGTTCATTATCTCATATAAAATTTGAATTCGGA
8323 TA
1 TA
8325 ATTTTAAATT
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.35, C:0.06, G:0.15, T:0.44
Consensus pattern (47 bp):
TATGATAAATATGGTGTTCATTATCTCATATAAAATTTGAATTCGGA
Found at i:8650 original size:41 final size:41
Alignment explanation
Indices: 8602--8682 Score: 110
Period size: 41 Copynumber: 2.0 Consensus size: 41
8592 ACAGTTAAAA
8602 ATATTAAAACAA-ACATCAAAACAACAAACAAATTAAAAATG
1 ATATTAAAACAATACAT-AAAACAACAAACAAATTAAAAATG
* * * *
8643 ATATTAAAACAATTCGTAAAATAACAAACAAATTGAAAAT
1 ATATTAAAACAATACATAAAACAACAAACAAATTAAAAAT
8683 ACAATAAGAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
41 33 0.94
42 2 0.06
ACGTcount: A:0.63, C:0.12, G:0.04, T:0.21
Consensus pattern (41 bp):
ATATTAAAACAATACATAAAACAACAAACAAATTAAAAATG
Found at i:9748 original size:9 final size:9
Alignment explanation
Indices: 9734--9767 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
9724 ATAAAAAACA
9734 TTTTTATAT
1 TTTTTATAT
9743 TTTTTATAT
1 TTTTTATAT
*
9752 TTTTATATAA
1 TTTT-TATAT
9762 TTTTTA
1 TTTTTA
9768 AATAAAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 15 0.65
10 8 0.35
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (9 bp):
TTTTTATAT
Found at i:11375 original size:32 final size:29
Alignment explanation
Indices: 11339--11410 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 29
11329 ATTTTAAATT
11339 AATAATAACAAAATTACATTTTAATTCTCAAA
1 AATAATAA-AAAATTA-A-TTTAATTCTCAAA
* * **
11371 AATAATAAAAATTTAATTTAATTTTTTAA
1 AATAATAAAAAATTAATTTAATTCTCAAA
11400 AATAATAAAAA
1 AATAATAAAAA
11411 TATAAACTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
29 21 0.58
30 1 0.03
31 6 0.17
32 8 0.22
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.38
Consensus pattern (29 bp):
AATAATAAAAAATTAATTTAATTCTCAAA
Found at i:11920 original size:18 final size:18
Alignment explanation
Indices: 11893--11928 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
11883 TTCAGCCTCT
*
11893 TCATCGGAATCGTCATCG
1 TCATCAGAATCGTCATCG
*
11911 TCATCAGAATCTTCATCG
1 TCATCAGAATCGTCATCG
11929 GGAGAGTCAG
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:0.25, C:0.28, G:0.17, T:0.31
Consensus pattern (18 bp):
TCATCAGAATCGTCATCG
Found at i:13499 original size:9 final size:10
Alignment explanation
Indices: 13478--13504 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
13468 TTTAATTTTT
13478 AAAAATTCAA
1 AAAAATTCAA
13488 AAAAATTCAA
1 AAAAATTCAA
13498 AAAAATT
1 AAAAATT
13505 AAATTATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.70, C:0.07, G:0.00, T:0.22
Consensus pattern (10 bp):
AAAAATTCAA
Found at i:13964 original size:57 final size:58
Alignment explanation
Indices: 13849--13964 Score: 157
Period size: 58 Copynumber: 2.0 Consensus size: 58
13839 GTGAGTAGGG
* * *
13849 TTATATTATTATTTTCGATAAGCCTCCCCACATGTGTTTGGGAGCAGAGTTATATTAT
1 TTATATTATTACTTTCCATAAGCCTCCCCACATGTGTATGGGAGCAGAGTTATATTAT
*
13907 TTATATTATTACTTTCCATAAGCCTTCCC-CAT-TCGTATGGGAAG-AGAGTTATATTAT
1 TTATATTATTACTTTCCATAAGCCTCCCCACATGT-GTATGGG-AGCAGAGTTATATTAT
13964 T
1 T
13965 ACTTTTTGTA
Statistics
Matches: 52, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
56 1 0.02
57 23 0.44
58 28 0.54
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.41
Consensus pattern (58 bp):
TTATATTATTACTTTCCATAAGCCTCCCCACATGTGTATGGGAGCAGAGTTATATTAT
Found at i:17645 original size:15 final size:15
Alignment explanation
Indices: 17626--17706 Score: 126
Period size: 15 Copynumber: 5.4 Consensus size: 15
17616 ACCACCGTAA
*
17626 TCAGCATCGGGTCCA
1 TCAGCATCGGGTCCT
17641 TCAGCATCGGGTCCT
1 TCAGCATCGGGTCCT
17656 TCAGCATCGGGTCCT
1 TCAGCATCGGGTCCT
*
17671 TCAGCATCGGGTTCT
1 TCAGCATCGGGTCCT
* *
17686 TCAGCCTCGGATCCT
1 TCAGCATCGGGTCCT
17701 TCAGCA
1 TCAGCA
17707 GAGGGTCCCC
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 60 1.00
ACGTcount: A:0.16, C:0.33, G:0.25, T:0.26
Consensus pattern (15 bp):
TCAGCATCGGGTCCT
Found at i:17729 original size:6 final size:6
Alignment explanation
Indices: 17718--17764 Score: 94
Period size: 6 Copynumber: 7.8 Consensus size: 6
17708 AGGGTCCCCC
17718 GCTAGG GCTAGG GCTAGG GCTAGG GCTAGG GCTAGG GCTAGG GCTAG
1 GCTAGG GCTAGG GCTAGG GCTAGG GCTAGG GCTAGG GCTAGG GCTAG
17765 CGCTGATGGG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 41 1.00
ACGTcount: A:0.17, C:0.17, G:0.49, T:0.17
Consensus pattern (6 bp):
GCTAGG
Found at i:27815 original size:31 final size:30
Alignment explanation
Indices: 27758--27850 Score: 98
Period size: 31 Copynumber: 3.0 Consensus size: 30
27748 CTCAGCAGTC
* *
27758 TAATGACGTAAAT-AAAAACTTATGAATAGT
1 TAATGACTTAAATGAAAAA-TTTTGAATAGT
**
27788 TAAGTGACTTAAATGAAACTTTTTGAATAGT
1 TAA-TGACTTAAATGAAAAATTTTGAATAGT
* *
27819 CCAATGATTTAAATGAAAAATTTTGAATAGT
1 -TAATGACTTAAATGAAAAATTTTGAATAGT
27850 T
1 T
27851 TAGAGATAAT
Statistics
Matches: 51, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
30 3 0.06
31 43 0.84
32 5 0.10
ACGTcount: A:0.44, C:0.06, G:0.14, T:0.35
Consensus pattern (30 bp):
TAATGACTTAAATGAAAAATTTTGAATAGT
Found at i:30810 original size:17 final size:18
Alignment explanation
Indices: 30783--30816 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
30773 GCTTCAGGGA
30783 ATATGCCAAAATCTTCAC
1 ATATGCCAAAATCTTCAC
30801 ATAT-CCAAAATCTTCA
1 ATATGCCAAAATCTTCA
30817 TAATTGTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.41, C:0.26, G:0.03, T:0.29
Consensus pattern (18 bp):
ATATGCCAAAATCTTCAC
Found at i:31303 original size:21 final size:21
Alignment explanation
Indices: 31256--31308 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
31246 GTTAGGAATG
* *
31256 TTCTACCGAAACAACATTTCC
1 TTCTACCGATACAACATATCC
** *
31277 AACTACCGATACAATATATCC
1 TTCTACCGATACAACATATCC
31298 TTCTACCGATA
1 TTCTACCGATA
31309 TTAGAAACTC
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.36, C:0.30, G:0.06, T:0.28
Consensus pattern (21 bp):
TTCTACCGATACAACATATCC
Found at i:41267 original size:30 final size:30
Alignment explanation
Indices: 41233--41397 Score: 206
Period size: 30 Copynumber: 5.5 Consensus size: 30
41223 CACCCATGAC
* *
41233 CTGACCAACACCAGGCTTGCTGATGTGTTG
1 CTGACCAACTCCAGGATTGCTGATGTGTTG
*
41263 CTGACCAACTCCGGGATTGCTGATGTGTTG
1 CTGACCAACTCCAGGATTGCTGATGTGTTG
* * *
41293 CTGACCAACTCCGGGATAGCTAAT-TAGTTG
1 CTGACCAACTCCAGGATTGCTGATGT-GTTG
* *
41323 CTGACCAACACCAGGATTGTTGATGTGTTG
1 CTGACCAACTCCAGGATTGCTGATGTGTTG
* * *
41353 CTGACCAACTCCGGGATAGCTGATGAGTTG
1 CTGACCAACTCCAGGATTGCTGATGTGTTG
*
41383 CTGACCAACCCCAGG
1 CTGACCAACTCCAGG
41398 GTCATTGAGG
Statistics
Matches: 116, Mismatches: 17, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
29 1 0.01
30 114 0.98
31 1 0.01
ACGTcount: A:0.22, C:0.25, G:0.27, T:0.25
Consensus pattern (30 bp):
CTGACCAACTCCAGGATTGCTGATGTGTTG
Found at i:45758 original size:41 final size:41
Alignment explanation
Indices: 45711--45794 Score: 107
Period size: 41 Copynumber: 2.0 Consensus size: 41
45701 AACCTGATTG
* * * *
45711 AAAATATAACAATTAATTTTAAAGTCTAAAATCTAAAAT-TA
1 AAAATATAAAAAATAAGTTTAAAATC-AAAATCTAAAATCTA
*
45752 AAAATATAAAAAATAAGTTTAAAATCCAAATCTAAAATCTA
1 AAAATATAAAAAATAAGTTTAAAATCAAAATCTAAAATCTA
45793 AA
1 AA
45795 TGAAGCTTGA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
40 11 0.30
41 26 0.70
ACGTcount: A:0.60, C:0.08, G:0.02, T:0.30
Consensus pattern (41 bp):
AAAATATAAAAAATAAGTTTAAAATCAAAATCTAAAATCTA
Found at i:45872 original size:40 final size:39
Alignment explanation
Indices: 45804--45937 Score: 110
Period size: 39 Copynumber: 3.4 Consensus size: 39
45794 ATGAAGCTTG
* * * **
45804 AAATCAAAACCTAAAATCTAGTGGAAAACCTAAGAATTTA
1 AAATTAAAATCTAAAATCTAATTTAAAACCTAA-AATTTA
*
45844 AAATTAAAATCTAAAATCTAATTTAAAA-CT-TAATGTTA
1 AAATTAAAATCTAAAATCTAATTTAAAACCTAAAAT-TTA
* * * *
45882 AAACTTTAAATCTAAGATCTAATTTAAAACTTAATATTTA
1 AAA-TTAAAATCTAAAATCTAATTTAAAACCTAAAATTTA
* * *
45922 TAACTATAATCTAAAA
1 AAATTAAAATCTAAAA
45938 ATTTAACTTA
Statistics
Matches: 74, Mismatches: 16, Indels: 9
0.75 0.16 0.09
Matches are distributed among these distances:
37 3 0.04
38 6 0.08
39 34 0.46
40 29 0.39
41 2 0.03
ACGTcount: A:0.51, C:0.11, G:0.04, T:0.33
Consensus pattern (39 bp):
AAATTAAAATCTAAAATCTAATTTAAAACCTAAAATTTA
Found at i:45933 original size:39 final size:39
Alignment explanation
Indices: 45841--45937 Score: 126
Period size: 39 Copynumber: 2.5 Consensus size: 39
45831 ACCTAAGAAT
*
45841 TTAAAATTA-AAATCTAAAATCTAATTTAAAACTTAATG
1 TTAAAACTATAAATCTAAAATCTAATTTAAAACTTAATG
* * *
45879 TTAAAACTTTAAATCTAAGATCTAATTTAAAACTTAATAT
1 TTAAAACTATAAATCTAAAATCTAATTTAAAACTTAAT-G
*
45919 TTATAACTAT-AATCTAAAA
1 TTAAAACTATAAATCTAAAA
45938 ATTTAACTTA
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
38 7 0.14
39 35 0.70
40 8 0.16
ACGTcount: A:0.51, C:0.09, G:0.02, T:0.38
Consensus pattern (39 bp):
TTAAAACTATAAATCTAAAATCTAATTTAAAACTTAATG
Found at i:46328 original size:26 final size:25
Alignment explanation
Indices: 46298--46350 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 25
46288 CACCATCTTT
*
46298 TTATT-CAAAGATTATTCTATAAATAA
1 TTATTACAAAAATTATT-TATAAA-AA
*
46324 TTATTACAAAAATTCTTTATAAAAA
1 TTATTACAAAAATTATTTATAAAAA
46349 TT
1 TT
46351 GATACTTTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 4 0.17
26 11 0.46
27 9 0.38
ACGTcount: A:0.47, C:0.08, G:0.02, T:0.43
Consensus pattern (25 bp):
TTATTACAAAAATTATTTATAAAAA
Found at i:53008 original size:51 final size:51
Alignment explanation
Indices: 52945--53125 Score: 310
Period size: 51 Copynumber: 3.5 Consensus size: 51
52935 GAATCTATAA
52945 ACTCACGATGACACTTAGTCATCGGACCTTTAATCCATAAAGGATTCATTT
1 ACTCACGATGACACTTAGTCATCGGACCTTTAATCCATAAAGGATTCATTT
* *
52996 ACTCACAATGACACTTAGTCATCGGA-CTATTAATCCATAAAGGATTAATTT
1 ACTCACGATGACACTTAGTCATCGGACCT-TTAATCCATAAAGGATTCATTT
*
53047 ACTCACGATGACACTTAGTCATTGGACCTTTAATCCATAAAGGATTCATTT
1 ACTCACGATGACACTTAGTCATCGGACCTTTAATCCATAAAGGATTCATTT
*
53098 ACTCACGATGGCACTTAGTCATCGGACC
1 ACTCACGATGACACTTAGTCATCGGACC
53126 CTTTCGTTTA
Statistics
Matches: 121, Mismatches: 7, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
50 2 0.02
51 117 0.97
52 2 0.02
ACGTcount: A:0.32, C:0.23, G:0.14, T:0.30
Consensus pattern (51 bp):
ACTCACGATGACACTTAGTCATCGGACCTTTAATCCATAAAGGATTCATTT
Found at i:55251 original size:15 final size:15
Alignment explanation
Indices: 55231--55264 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
55221 AAGATATTTT
55231 CTCTCAAGTTTCTTC
1 CTCTCAAGTTTCTTC
55246 CTCTCAAGTTTCTTC
1 CTCTCAAGTTTCTTC
55261 CTCT
1 CTCT
55265 TTCCTTATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.12, C:0.35, G:0.06, T:0.47
Consensus pattern (15 bp):
CTCTCAAGTTTCTTC
Found at i:56168 original size:21 final size:21
Alignment explanation
Indices: 56144--56191 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
56134 ACACCTTTTT
* *
56144 AATAATTTTCTAATTTTAAAA
1 AATAATTTTATAATTTAAAAA
*
56165 AATACTTTTTATAATTTAAAAA
1 AATA-ATTTTATAATTTAAAAA
56187 AATAA
1 AATAA
56192 AAATTAAATA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 4 0.18
22 18 0.82
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (21 bp):
AATAATTTTATAATTTAAAAA
Found at i:56179 original size:22 final size:22
Alignment explanation
Indices: 56149--56190 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
56139 TTTTTAATAA
* *
56149 TTTTCTAATTTTAAAAAATACT
1 TTTTATAATTTAAAAAAATACT
56171 TTTTATAATTTAAAAAAATA
1 TTTTATAATTTAAAAAAATA
56191 AAAATTAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (22 bp):
TTTTATAATTTAAAAAAATACT
Found at i:58070 original size:37 final size:35
Alignment explanation
Indices: 58017--58085 Score: 95
Period size: 37 Copynumber: 1.9 Consensus size: 35
58007 ATTCCAAAAA
58017 TAATAATATCTTAATAGT-TTATTATTAAATTTAATT
1 TAATAATATCTTAATAGTATT-TTATT-AATTTAATT
*
58053 TAATAATTATTTTAATAGTATTTTATTAATTTA
1 TAATAA-TATCTTAATAGTATTTTATTAATTTA
58086 CTATTAAAGT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
36 12 0.40
37 16 0.53
38 2 0.07
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (35 bp):
TAATAATATCTTAATAGTATTTTATTAATTTAATT
Found at i:68741 original size:293 final size:294
Alignment explanation
Indices: 68176--69443 Score: 1515
Period size: 293 Copynumber: 4.4 Consensus size: 294
68166 AAATCCAGAG
* * **
68176 TACAACCACTAC--AAGACTTAAGACCTACAAGTAATGTTACATCAACTCTATGAAGTCAATTAA
1 TACATCCACTACAGAAGACTTAAGACCTACAAGTAATG-TACACCAACTCTATGAAGTCGGTTAA
* * * * *
68239 CATTTTATTTCCTAACTTTAGTACACTATAATACTCAAGCAGCAAGACCGACCATATATCTGATC
65 CCTTTTATTTCCTAACTTTAGTGCACTATAATACTCAGGCGGCAAGACCGACCATATATCTGACC
** * * * * * ** *
68304 AATAAATTTTGTAGTCACTAATTGTTTACCGACAGAGTCTCCCCTTAATGCCTTTATGCCACACC
130 AATAAGCTTCGCAGTCCCTGACTGTTTACCGGTAAAGTCTCCCCTTAATGCCTTTATGCCACACC
* * * *
68369 AACCAATGTAAATGCCCAATACCTACCGAAACTTCCTCCACCAGTGACAATCTCGAAACGCTTGC
195 AACCAATGTAAACGCCCAATGCTTACCGAAACTTCCTCCACTAGTGACAATCTCGAAACGCTTGC
* **
68434 TTTGATACCACTTATTGGGAACTCGACGGGCCCAA
260 TTTGATACCACTTATTAGGAACTCGACGAACCCAA
* * * * *
68469 TACATCCACTGCAGAGGACTTAAGACCTGCAACTAATG-ACATCAACTCTATGAAGTCGGTTAAC
1 TACATCCACTACAGAAGACTTAAGACCTACAAGTAATGTACACCAACTCTATGAAGTCGGTTAAC
* * *
68533 ATTTTATTTCCTAACTTTAGTGCACTATAATACTCAGGGGGCAAGACCGACCATATATCTAACCA
66 CTTTTATTTCCTAACTTTAGTGCACTATAATACTCAGGCGGCAAGACCGACCATATATCTGACCA
* * *
68598 ATAAGCTTCGCAGTCCCTGACTTTTTACCGGTAAAGTCTCTCATTAATGCCTTTATGCCACACCA
131 ATAAGCTTCGCAGTCCCTGACTGTTTACCGGTAAAGTCTCCCCTTAATGCCTTTATGCCACACCA
* * * * *
68663 ATCAATGTAAACGCCCAGTGCTTACCGAAACTTCCTCCACTAGTGGCAATCTCGGAACACTTGCT
196 ACCAATGTAAACGCCCAATGCTTACCGAAACTTCCTCCACTAGTGACAATCTCGAAACGCTTGCT
*
68728 TTGATACCACTTATTAGGAACTCGATGAACCCAA
261 TTGATACCACTTATTAGGAACTCGACGAACCCAA
* * * *
68762 TACATCCAGTACAAAAGACTT---ACTTACAAGTAATACTACACCAACTCTATGAAGTCGGTTAA
1 TACATCCACTACAGAAGACTTAAGACCTACAAGTAAT-GTACACCAACTCTATGAAGTCGGTTAA
* *
68824 CCTTTTATTTCCTAACTTTAGTGCACTATAATACTCAGGCGACAAGATCGACCATATATCTGACC
65 CCTTTTATTTCCTAACTTTAGTGCACTATAATACTCAGGCGGCAAGACCGACCATATATCTGACC
* * * *
68889 AATAAGCTTCGTAGTCCTTGACTGTTTACCTGTAGAA-TCTCCCTTTAATG------T--CACAC
130 AATAAGCTTCGCAGTCCCTGACTGTTTACCGGTA-AAGTCTCCCCTTAATGCCTTTATGCCACAC
* * * * * *
68945 CAACCAATGTAAACGCCCAATGCTTATCGAAACTTCCTCCACTAATGGCGATCTCGGAATGCTTG
194 CAACCAATGTAAACGCCCAATGCTTACCGAAACTTCCTCCACTAGTGACAATCTCGAAACGCTTG
* *
69010 CTTTGATACCACTTATTAAGAACTTGACGAACCCAA
259 CTTTGATACCACTTATTAGGAACTCGACGAACCCAA
* * * * * * * *
69046 TATATTCACTACAGAAGATTTAAGACCTATAAGGAATGTTACACCAACTCTATAAATTCGATTAA
1 TACATCCACTACAGAAGACTTAAGACCTACAAGTAATG-TACACCAACTCTATGAAGTCGGTTAA
*
69111 CCTTTTATTTCCTAACTTTAGTGCACTATAATACTCAGGCGGCAGGACCGACCATATATCTGACC
65 CCTTTTATTTCCTAACTTTAGTGCACTATAATACTCAGGCGGCAAGACCGACCATATATCTGACC
* *
69176 AATAAGCTTCGCAATCCCTGACTGTTTACCGGTAGAGTCTCCCCTTAATGCCTTTATGCCACACC
130 AATAAGCTTCGCAGTCCCTGACTGTTTACCGGTAAAGTCTCCCCTTAATGCCTTTATGCCACACC
* * * **
69241 AACCAATGCAAACTCCCAATGCTTACCAAAACTTCCTCCACTAGTGATGATAC-CGAAACGCTTG
195 AACCAATGTAAACGCCCAATGCTTACCGAAACTTCCTCCACTAGTGACAAT-CTCGAAACGCTTG
* * * * *
69305 CTTTGATTCCACTTATTGGGAACTTGACGAGCCTAA
259 CTTTGATACCACTTATTAGGAACTCGACGAACCCAA
* * *
69341 TA-A---A--A-AG--GACTTAAGACTTATAAGTAATGTTTCACCAACTCTATGAAGTCGGTTAA
1 TACATCCACTACAGAAGACTTAAGACCTACAAGTAATG-TACACCAACTCTATGAAGTCGGTTAA
* **
69397 CCTTTTATTTCCTAATTTTAGTGCACTATAATACTCAAACGGCAAGA
65 CCTTTTATTTCCTAACTTTAGTGCACTATAATACTCAGGCGGCAAGA
69444 TAGACTATAT
Statistics
Matches: 841, Mismatches: 115, Indels: 45
0.84 0.11 0.04
Matches are distributed among these distances:
284 112 0.13
286 87 0.10
287 137 0.16
288 2 0.00
289 1 0.00
290 10 0.01
291 1 0.00
292 125 0.15
293 251 0.30
294 1 0.00
295 113 0.13
296 1 0.00
ACGTcount: A:0.32, C:0.26, G:0.14, T:0.29
Consensus pattern (294 bp):
TACATCCACTACAGAAGACTTAAGACCTACAAGTAATGTACACCAACTCTATGAAGTCGGTTAAC
CTTTTATTTCCTAACTTTAGTGCACTATAATACTCAGGCGGCAAGACCGACCATATATCTGACCA
ATAAGCTTCGCAGTCCCTGACTGTTTACCGGTAAAGTCTCCCCTTAATGCCTTTATGCCACACCA
ACCAATGTAAACGCCCAATGCTTACCGAAACTTCCTCCACTAGTGACAATCTCGAAACGCTTGCT
TTGATACCACTTATTAGGAACTCGACGAACCCAA
Found at i:69307 original size:579 final size:575
Alignment explanation
Indices: 68201--69443 Score: 1566
Period size: 579 Copynumber: 2.1 Consensus size: 575
68191 ACTTAAGACC
* ** * *
68201 TACAAGTAATGTTACATCAACTCTATGAAGTCAATTAACATTTTATTTCCTAACTTTAGTACACT
1 TACAAGTAATGTTACACCAACTCTATGAAGTCGGTTAACCTTTTATTTCCTAACTTTAGTGCACT
* * * *
68266 ATAATACTCAAGCAGCAAGACCGACCATATATCTGATCAATAAATTTTGTAGTCACTAATTGTTT
66 ATAATACTCAAGCAGCAAGACCGACCATATATCTGACCAATAAACTTCGTAGTCACTAACTGTTT
* *
68331 ACCGACAGAGTCTCCCCTTAATGCCTTTATGCCACACCAACCAATGTAAATGCCCAATACCTACC
131 ACCGACAGAATCTCCCCTTAATG----T-T-CCACACCAACCAATGTAAACGCCCAATACCTACC
* **
68396 GAAACTTCCTCCACCAGTGACAATCTCGAAACGCTTGCTTTGATACCACTTATTGGGAACTCGAC
190 GAAACTTCCTCCACCAATGACAATCTCGAAACGCTTGCTTTGATACCACTTATTAAGAACTCGAC
** * * * * * *
68461 GGGCCCAATACATCCACTGCAGAGGACTTAAGACCTGCAACTAATGACATCAACTCTATGAAGTC
255 GAACCCAATACATCCACTACAGAAGACTTAAGACCTACAACGAATGACACCAACTCTATAAAGTC
* *
68526 GGTTAACATTTTATTTCCTAACTTTAGTGCACTATAATACTCAGGGGGCAAGACCGACCATATAT
320 GATTAACATTTTATTTCCTAACTTTAGTGCACTATAATACTCAGGCGGCAAGACCGACCATATAT
* * *
68591 CTAACCAATAAGCTTCGCAGTCCCTGACTTTTTACCGGTAAAGTCTCTCATTAATGCCTTTATGC
385 CTAACCAATAAGCTTCGCAATCCCTGACTGTTTACCGGTAAAGTCTCCCATTAATGCCTTTATGC
* * * * * *
68656 CACACCAATCAATGTAAACGCCCAGTGCTTACCGAAACTTCCTCCACTAGTGGCAATCTCGGAAC
450 CACACCAACCAATGCAAACGCCCAATGCTTACCAAAACTTCCTCCACTAGTGACAATCTCGAAAC
* ** *
68721 ACTTGCTTTGATACCACTTATTAGGAACTCGATGAACCCAATACATCCAGTACAAAAGACTTA
515 ACTTGCTTTGATACCACTTATTAGGAACTCGACGAACCCAATA-A-AAAGGACAAAAGACTTA
**
68784 CTTACAAGTAATACTACACCAACTCTATGAAGTCGGTTAACCTTTTATTTCCTAACTTTAGTGCA
1 --TACAAGTAATGTTACACCAACTCTATGAAGTCGGTTAACCTTTTATTTCCTAACTTTAGTGCA
* * * *
68849 CTATAATACTCAGGC-GACAAGATCGACCATATATCTGACCAATAAGCTTCGTAGTC-CTTGACT
64 CTATAATACTCAAGCAG-CAAGACCGACCATATATCTGACCAATAAACTTCGTAGTCAC-TAACT
* * * * *
68912 GTTTACCTG-TAGAATCTCCCTTTAATG-T-CACACCAACCAATGTAAACGCCCAATGCTTATCG
127 GTTTACC-GACAGAATCTCCCCTTAATGTTCCACACCAACCAATGTAAACGCCCAATACCTACCG
* * * * * *
68974 AAACTTCCTCCACTAATGGCGATCTCGGAATGCTTGCTTTGATACCACTTATTAAGAACTTGACG
191 AAACTTCCTCCACCAATGACAATCTCGAAACGCTTGCTTTGATACCACTTATTAAGAACTCGACG
* * * * * *
69039 AACCCAATATATTCACTACAGAAGATTTAAGACCTATAAGGAATGTTACACCAACTCTATAAATT
256 AACCCAATACATCCACTACAGAAGACTTAAGACCTACAACGAATG--ACACCAACTCTATAAAGT
* *
69104 CGATTAACCTTTTATTTCCTAACTTTAGTGCACTATAATACTCAGGCGGCAGGACCGACCATATA
319 CGATTAACATTTTATTTCCTAACTTTAGTGCACTATAATACTCAGGCGGCAAGACCGACCATATA
* * *
69169 TCTGACCAATAAGCTTCGCAATCCCTGACTGTTTACCGGTAGAGTCTCCCCTTAATGCCTTTATG
384 TCTAACCAATAAGCTTCGCAATCCCTGACTGTTTACCGGTAAAGTCTCCCATTAATGCCTTTATG
* **
69234 CCACACCAACCAATGCAAACTCCCAATGCTTACCAAAACTTCCTCCACTAGTGATGATAC-CGAA
449 CCACACCAACCAATGCAAACGCCCAATGCTTACCAAAACTTCCTCCACTAGTGACAAT-CTCGAA
* * * * * * **
69298 ACGCTTGCTTTGATTCCACTTATTGGGAACTTGACGAGCCTAATAAAAAGGACTTAAGACTTA
513 ACACTTGCTTTGATACCACTTATTAGGAACTCGACGAACCCAATAAAAAGGACAAAAGACTTA
* *
69361 T--AAGTAATGTTTCACCAACTCTATGAAGTCGGTTAACCTTTTATTTCCTAATTTTAGTGCACT
1 TACAAGTAATGTTACACCAACTCTATGAAGTCGGTTAACCTTTTATTTCCTAACTTTAGTGCACT
* *
69424 ATAATACTCAAACGGCAAGA
66 ATAATACTCAAGCAGCAAGA
69444 TAGACTATAT
Statistics
Matches: 569, Mismatches: 82, Indels: 26
0.84 0.12 0.04
Matches are distributed among these distances:
573 74 0.13
574 1 0.00
575 1 0.00
577 132 0.23
578 1 0.00
579 227 0.40
580 1 0.00
584 2 0.00
585 129 0.23
586 1 0.00
ACGTcount: A:0.32, C:0.26, G:0.14, T:0.29
Consensus pattern (575 bp):
TACAAGTAATGTTACACCAACTCTATGAAGTCGGTTAACCTTTTATTTCCTAACTTTAGTGCACT
ATAATACTCAAGCAGCAAGACCGACCATATATCTGACCAATAAACTTCGTAGTCACTAACTGTTT
ACCGACAGAATCTCCCCTTAATGTTCCACACCAACCAATGTAAACGCCCAATACCTACCGAAACT
TCCTCCACCAATGACAATCTCGAAACGCTTGCTTTGATACCACTTATTAAGAACTCGACGAACCC
AATACATCCACTACAGAAGACTTAAGACCTACAACGAATGACACCAACTCTATAAAGTCGATTAA
CATTTTATTTCCTAACTTTAGTGCACTATAATACTCAGGCGGCAAGACCGACCATATATCTAACC
AATAAGCTTCGCAATCCCTGACTGTTTACCGGTAAAGTCTCCCATTAATGCCTTTATGCCACACC
AACCAATGCAAACGCCCAATGCTTACCAAAACTTCCTCCACTAGTGACAATCTCGAAACACTTGC
TTTGATACCACTTATTAGGAACTCGACGAACCCAATAAAAAGGACAAAAGACTTA
Found at i:71418 original size:275 final size:275
Alignment explanation
Indices: 70927--71744 Score: 1521
Period size: 275 Copynumber: 3.0 Consensus size: 275
70917 CCCTGCATGC
*
70927 ATATGTTTAACAAATCAAGCAGTGAGTGTATGAACTCAGGCTGTTCTGATGGGGTAATCAAGTAG
1 ATATGTTTAACAAATCAAGCAGTGAGTGTATGAACTCAGGCTGTTCTGATGGGGTATTCAAGTAG
*
70992 TAGTCAAGTTAGTCTATA-CTTGTCTTTGGTATTAGAAGGATCATCTTTGGTAGATTTTTTTACT
66 TAGTCAAGTTAGTCTATATC-TGTCTTTGGTATTAGAAGGATCATCTTTGGTAGATTTTTTTATT
*
71056 TTGCAAGAGTTGTTGTAATCAAGCTTCTTCATAAAGCGTATGCAACTAGGTGCTTTGCCTACTAA
130 TTGCAAGAGTTGTTGTAATCAAGCTTCTTCATAGAGCGTATGCAACTAGGTGCTTTGCCTACTAA
71121 TCGAGAAGCGAATGGTCCCATCCTTTGTGCACTCTTTGTCTTGCCTTTCGATTCAAGCCAAGCTT
195 TCGAGAAGCGAATGGTCCCATCCTTTGTGCACTCTTTGTCTTGCCTTTCGATTCAAGCCAAGCTT
71186 GCAGTTTTGATGGGGT
260 GCAGTTTTGATGGGGT
71202 ATATGTTTAACAAATCAAGCAGTGAGTGTATGAACTCAGGCTGTTCTGATGGGGTATTCAAGTAG
1 ATATGTTTAACAAATCAAGCAGTGAGTGTATGAACTCAGGCTGTTCTGATGGGGTATTCAAGTAG
71267 TAGTCAAGTTAGTCTATATCTGTCTTTGGTATTAGAAGGATCATCTTTGGTAGATTTTTTTATTT
66 TAGTCAAGTTAGTCTATATCTGTCTTTGGTATTAGAAGGATCATCTTTGGTAGATTTTTTTATTT
71332 TGCAAGAGTTGTTGTAATCAAGCTTCTTCATAGAGCGTATGCAACTAGGTGCTTTGCCTACTAAT
131 TGCAAGAGTTGTTGTAATCAAGCTTCTTCATAGAGCGTATGCAACTAGGTGCTTTGCCTACTAAT
71397 CGAGAAGCGAATGGTCCCATCCTTTGTGCACTCTTTGTCTTGCCTTTCGATTCAAGCCAAGCTTG
196 CGAGAAGCGAATGGTCCCATCCTTTGTGCACTCTTTGTCTTGCCTTTCGATTCAAGCCAAGCTTG
71462 CAGTTTTGATGGGGT
261 CAGTTTTGATGGGGT
71477 ATATGTTTAACAAATCAAGCAGTGAGTGTATGAACTCAGGCTGTTCTGATGGGGTATTCAAGTAG
1 ATATGTTTAACAAATCAAGCAGTGAGTGTATGAACTCAGGCTGTTCTGATGGGGTATTCAAGTAG
71542 TAGTCAAGTTAGTCTATATCTGTCTTTGGTATTAGAAGGATCATCTTTGGTAGATTTTTTTATTT
66 TAGTCAAGTTAGTCTATATCTGTCTTTGGTATTAGAAGGATCATCTTTGGTAGATTTTTTTATTT
* * * *
71607 TGCAAGAGTTGTTGTAATCAAGCTTCTTCATAGAGCGTATGGAACTGGGTGTTTTGCCTACTAAC
131 TGCAAGAGTTGTTGTAATCAAGCTTCTTCATAGAGCGTATGCAACTAGGTGCTTTGCCTACTAAT
* * * *
71672 CGAGAAGCGAATGGTCTCATCCTTTGAGCACTCTTTATCTTGCCTTTTGATTCAAGCCAAGCTTG
196 CGAGAAGCGAATGGTCCCATCCTTTGTGCACTCTTTGTCTTGCCTTTCGATTCAAGCCAAGCTTG
71737 CAGTTTTG
261 CAGTTTTG
71745 CTTCCATATC
Statistics
Matches: 531, Mismatches: 11, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
275 530 1.00
276 1 0.00
ACGTcount: A:0.24, C:0.16, G:0.23, T:0.37
Consensus pattern (275 bp):
ATATGTTTAACAAATCAAGCAGTGAGTGTATGAACTCAGGCTGTTCTGATGGGGTATTCAAGTAG
TAGTCAAGTTAGTCTATATCTGTCTTTGGTATTAGAAGGATCATCTTTGGTAGATTTTTTTATTT
TGCAAGAGTTGTTGTAATCAAGCTTCTTCATAGAGCGTATGCAACTAGGTGCTTTGCCTACTAAT
CGAGAAGCGAATGGTCCCATCCTTTGTGCACTCTTTGTCTTGCCTTTCGATTCAAGCCAAGCTTG
CAGTTTTGATGGGGT
Found at i:72678 original size:336 final size:336
Alignment explanation
Indices: 72065--72728 Score: 1301
Period size: 336 Copynumber: 2.0 Consensus size: 336
72055 TTGTTGAACA
72065 TGCATAAATCACATTTGACAAAGCAAATAACTAATGGTTGATCTTAGCACTCTCTTAGAGGCGAA
1 TGCATAAATCACATTTGACAAAGCAAATAACTAATGGTTGATCTTAGCACTCTCTTAGAGGCGAA
72130 TGCCTTCATTGCAGGTACTCCTAGTATCCTCATCGCCTGCTAAGTCTATGAGGTTCAGCTTCCCC
66 TGCCTTCATTGCAGGTACTCCTAGTATCCTCATCGCCTGCTAAGTCTATGAGGTTCAGCTTCCCC
72195 ATCAAAACAGGCGTAGAATCATCATCACAAGGAGTGGAAACAACAATCACTAGGACACCATGGCT
131 ATCAAAACAGGCGTAGAATCATCATCACAAGGAGTGGAAACAACAATCACTAGGACACCATGGCT
72260 TCTACTGGAAACATCACTGAGACCAGTATGTGCAACTTTCCTTCTCTGAATTCCACAAGAGAAGA
196 TCTACTGGAAACATCACTGAGACCAGTATGTGCAACTTTCCTTCTCTGAATTCCACAAGAGAAGA
72325 CTTTATGGAATTCAGACATGATATTAATAGGCACCCAAGACAGGCCCCTTAGATGAATCTGCCCA
261 CTTTATGGAATTCAGACATGATATTAATAGGCACCCAAGACAGGCCCCTTAGATGAATCTGCCCA
72390 TCTAGTCAATT
326 TCTAGTCAATT
* *
72401 TGCATAAATCACATTTGACAAAGCAAATAACTACTGGTTGATCTTAGCACTCTCTTGGAGGCGAA
1 TGCATAAATCACATTTGACAAAGCAAATAACTAATGGTTGATCTTAGCACTCTCTTAGAGGCGAA
72466 TGCCTTCATTGCAGGTACTCCTAGTATCCTCATCGCCTGCTAAGTCTATGAGGTTCAGCTTCCCC
66 TGCCTTCATTGCAGGTACTCCTAGTATCCTCATCGCCTGCTAAGTCTATGAGGTTCAGCTTCCCC
72531 ATCAAAACAGGCGTAGAATCATCATCACAAGGAGTGGAAACAACAATCACTAGGACACCATGGCT
131 ATCAAAACAGGCGTAGAATCATCATCACAAGGAGTGGAAACAACAATCACTAGGACACCATGGCT
72596 TCTACTGGAAACATCACTGAGACCAGTATGTGCAACTTTCCTTCTCTGAATTCCACAAGAGAAGA
196 TCTACTGGAAACATCACTGAGACCAGTATGTGCAACTTTCCTTCTCTGAATTCCACAAGAGAAGA
*
72661 CTTTATGGAATTCAGACATGATATTAATAGGCACCCGAGACAGGCCCCTTAGATGAATCTGCCCA
261 CTTTATGGAATTCAGACATGATATTAATAGGCACCCAAGACAGGCCCCTTAGATGAATCTGCCCA
72726 TCT
326 TCT
72729 TTGTCATCCA
Statistics
Matches: 325, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
336 325 1.00
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.26
Consensus pattern (336 bp):
TGCATAAATCACATTTGACAAAGCAAATAACTAATGGTTGATCTTAGCACTCTCTTAGAGGCGAA
TGCCTTCATTGCAGGTACTCCTAGTATCCTCATCGCCTGCTAAGTCTATGAGGTTCAGCTTCCCC
ATCAAAACAGGCGTAGAATCATCATCACAAGGAGTGGAAACAACAATCACTAGGACACCATGGCT
TCTACTGGAAACATCACTGAGACCAGTATGTGCAACTTTCCTTCTCTGAATTCCACAAGAGAAGA
CTTTATGGAATTCAGACATGATATTAATAGGCACCCAAGACAGGCCCCTTAGATGAATCTGCCCA
TCTAGTCAATT
Found at i:72915 original size:100 final size:100
Alignment explanation
Indices: 72742--72936 Score: 372
Period size: 100 Copynumber: 1.9 Consensus size: 100
72732 TCATCCAAAA
*
72742 TTGAAATTTCTTTGGTTTTGACTTCTAAAAGATCATAGCACCTATCCATGTAGATCTCATAGTAT
1 TTGAAATTTCTTTGGTTTTGACTTCTAAAAGATCATAGCACCTATCCATGTAGACCTCATAGTAT
*
72807 GAAATCTCTGCTATGCACCCTGTGCTTTGGGATTT
66 GAAATCTCTACTATGCACCCTGTGCTTTGGGATTT
72842 TTGAAATTTCTTTGGTTTTGACTTCTAAAAGATCATAGCACCTATCCATGTAGACCTCATAGTAT
1 TTGAAATTTCTTTGGTTTTGACTTCTAAAAGATCATAGCACCTATCCATGTAGACCTCATAGTAT
72907 GAAATCTCTACTATGCACCCTGTGCTTTGG
66 GAAATCTCTACTATGCACCCTGTGCTTTGG
72937 CATATGGACA
Statistics
Matches: 93, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
100 93 1.00
ACGTcount: A:0.26, C:0.20, G:0.16, T:0.38
Consensus pattern (100 bp):
TTGAAATTTCTTTGGTTTTGACTTCTAAAAGATCATAGCACCTATCCATGTAGACCTCATAGTAT
GAAATCTCTACTATGCACCCTGTGCTTTGGGATTT
Found at i:73413 original size:32 final size:32
Alignment explanation
Indices: 73371--73452 Score: 119
Period size: 32 Copynumber: 2.6 Consensus size: 32
73361 TACTCCTTAC
* * *
73371 TTTTTAGAAAATTTTAATTATGCCCTCTTAAT
1 TTTTTTGAAAATTTTAATTAAGCCCTCTTAAA
*
73403 TTTTTTGAAAATTTTAATTAAGCTCTCTTAAA
1 TTTTTTGAAAATTTTAATTAAGCCCTCTTAAA
*
73435 TTTTTTGAAAATCTTAAT
1 TTTTTTGAAAATTTTAAT
73453 AATATCACAA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 45 1.00
ACGTcount: A:0.33, C:0.10, G:0.06, T:0.51
Consensus pattern (32 bp):
TTTTTTGAAAATTTTAATTAAGCCCTCTTAAA
Found at i:74270 original size:42 final size:42
Alignment explanation
Indices: 74211--74293 Score: 157
Period size: 42 Copynumber: 2.0 Consensus size: 42
74201 CTGGATTTTA
74211 AATTTTGTGACCGTTGCAACAGTTGATAGAGGAAAAGAAAAT
1 AATTTTGTGACCGTTGCAACAGTTGATAGAGGAAAAGAAAAT
*
74253 AATTTTGTGATCGTTGCAACAGTTGATAGAGGAAAAGAAAA
1 AATTTTGTGACCGTTGCAACAGTTGATAGAGGAAAAGAAAA
74294 CAACGTTGTT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.41, C:0.08, G:0.24, T:0.27
Consensus pattern (42 bp):
AATTTTGTGACCGTTGCAACAGTTGATAGAGGAAAAGAAAAT
Found at i:74737 original size:11 final size:10
Alignment explanation
Indices: 74698--74744 Score: 51
Period size: 11 Copynumber: 4.6 Consensus size: 10
74688 TTGAAGTAGA
74698 AATTTTTTA-
1 AATTTTTTAT
74707 AATTTTTTAT
1 AATTTTTTAT
*
74717 ATATTCTTTAT
1 A-ATTTTTTAT
*
74728 AACTTTTTTAG
1 AA-TTTTTTAT
74739 AATTTT
1 AATTTT
74745 ATTTTTTTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
9 9 0.28
10 6 0.19
11 17 0.53
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.64
Consensus pattern (10 bp):
AATTTTTTAT
Found at i:75531 original size:29 final size:30
Alignment explanation
Indices: 75478--75535 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 30
75468 TCTTAAAATT
* *
75478 ATATATGAATTTTGATTTAATATGTAATTTG
1 ATATATGAATTTTAATTT-AGATGTAATTTG
75509 ATATATGAATTTTAATTT-GATGTAATT
1 ATATATGAATTTTAATTTAGATGTAATT
75536 ATACACATGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 8 0.32
31 17 0.68
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.52
Consensus pattern (30 bp):
ATATATGAATTTTAATTTAGATGTAATTTG
Found at i:75752 original size:30 final size:29
Alignment explanation
Indices: 75718--75809 Score: 87
Period size: 29 Copynumber: 3.1 Consensus size: 29
75708 ATAATTTACG
* *
75718 AAAATTAGATC-AAATCAAATTTTCATGTAT
1 AAAATTAGA-CAAAATCAAA-ATACATGTAT
*
75748 AAAATTAGACAAAATTAAAATACATGTAT
1 AAAATTAGACAAAATCAAAATACATGTAT
* * *
75777 AAAATTACACATTAAATTAAAATTCATGTAT
1 AAAATTAGACA--AAATCAAAATACATGTAT
75808 AA
1 AA
75810 TTGTAAGATC
Statistics
Matches: 54, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
29 19 0.35
30 16 0.30
31 19 0.35
ACGTcount: A:0.53, C:0.09, G:0.05, T:0.33
Consensus pattern (29 bp):
AAAATTAGACAAAATCAAAATACATGTAT
Found at i:75774 original size:29 final size:30
Alignment explanation
Indices: 75741--75809 Score: 104
Period size: 31 Copynumber: 2.3 Consensus size: 30
75731 ATCAAATTTT
*
75741 CATGTATAAAATTAGACA-AAATTAAAATA
1 CATGTATAAAATTACACATAAATTAAAATA
*
75770 CATGTATAAAATTACACATTAAATTAAAATT
1 CATGTATAAAATTACACA-TAAATTAAAATA
75801 CATGTATAA
1 CATGTATAA
75810 TTGTAAGATC
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
29 17 0.47
31 19 0.53
ACGTcount: A:0.54, C:0.09, G:0.06, T:0.32
Consensus pattern (30 bp):
CATGTATAAAATTACACATAAATTAAAATA
Found at i:80063 original size:21 final size:21
Alignment explanation
Indices: 80025--80067 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
80015 TAATAATTAT
* *
80025 TTATAAAATTTAATTTTTTTA
1 TTATAAAATATAAATTTTTTA
*
80046 TTATATAATATAAATTTTTTA
1 TTATAAAATATAAATTTTTTA
80067 T
1 T
80068 GTTAAGCTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TTATAAAATATAAATTTTTTA
Found at i:82566 original size:31 final size:31
Alignment explanation
Indices: 82528--82597 Score: 122
Period size: 31 Copynumber: 2.3 Consensus size: 31
82518 TTCATGTTTC
*
82528 TAAATATAGTTTTAGAGAGAACTTTGTATAG
1 TAAATATAGCTTTAGAGAGAACTTTGTATAG
82559 TAAATATAGCTTTAGAGAGAACTTTGTATAG
1 TAAATATAGCTTTAGAGAGAACTTTGTATAG
*
82590 TATATATA
1 TAAATATA
82598 ATGGTGCTTC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.40, C:0.04, G:0.17, T:0.39
Consensus pattern (31 bp):
TAAATATAGCTTTAGAGAGAACTTTGTATAG
Found at i:89264 original size:14 final size:13
Alignment explanation
Indices: 89241--89280 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 13
89231 CAATTGAAAT
89241 ATAATTTTTTAAA
1 ATAATTTTTTAAA
*
89254 AGTAGTTTTTTATAA
1 A-TAATTTTTTA-AA
89269 ATAATTTTTTAA
1 ATAATTTTTTAA
89281 GAAATGTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
13 2 0.09
14 18 0.78
15 3 0.13
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (13 bp):
ATAATTTTTTAAA
Found at i:90716 original size:23 final size:22
Alignment explanation
Indices: 90684--90731 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 22
90674 AAATTTGAAC
*
90684 AAATACTCATTTTTATATTATGA
1 AAATACTCATTTTTATACTAT-A
*
90707 AAATATTCATTTTTATACTATA
1 AAATACTCATTTTTATACTATA
90729 AAA
1 AAA
90732 CATTTATTAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 4 0.17
23 19 0.83
ACGTcount: A:0.44, C:0.08, G:0.02, T:0.46
Consensus pattern (22 bp):
AAATACTCATTTTTATACTATA
Found at i:93370 original size:17 final size:16
Alignment explanation
Indices: 93348--93379 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
93338 AATTTGGAAT
93348 AAAAAATAGAAAAATAG
1 AAAAAATA-AAAAATAG
93365 AAAAAATAAAAAATA
1 AAAAAATAAAAAATA
93380 AAATATTGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.81, C:0.00, G:0.06, T:0.12
Consensus pattern (16 bp):
AAAAAATAAAAAATAG
Found at i:94029 original size:21 final size:23
Alignment explanation
Indices: 94004--94048 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
93994 TGTTTTATTT
94004 ATAAAATT-AT-TATTTTAATAA
1 ATAAAATTCATATATTTTAATAA
* *
94025 ATAAATTTCATATATTTTTATAA
1 ATAAAATTCATATATTTTAATAA
94048 A
1 A
94049 GTCTTATGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 7 0.35
22 2 0.10
23 11 0.55
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (23 bp):
ATAAAATTCATATATTTTAATAA
Found at i:95991 original size:3 final size:3
Alignment explanation
Indices: 95983--96012 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
95973 AAAGACTACA
*
95983 AAT AAT AAT AAT ACT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
96013 GGGAAGGCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:105662 original size:206 final size:203
Alignment explanation
Indices: 105234--105921 Score: 955
Period size: 206 Copynumber: 3.4 Consensus size: 203
105224 AACGGTTAGA
**
105234 TTCCTGATGAGATACAGAGAAGCGAATTGAAACAAACGACGTAGTCATCTTCCTGATGAGATACC
1 TTCCTGATGAGATACAGAGAAGCGAATTGAAACAAACGACGCGGTCATCTTCCTGATGAGATACC
* * * *
105299 AAGAAGAAGACTAAATCAAACTCACGCTCGATGTGAGTAAATCTTTAAATCCCAGCTTCCTGATG
66 GAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAGTAAATCTTCAAA-CCCAGCTTCCTGATG
* * * *
105364 AGACACCGAGAAGCAGATTGAAGTAATAAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGAAC
130 AGACA-CGAGAAGCAGATAGAAGCAATAAACGGTTAGCTTCCTGATGAGATACTGAGAAGTGGAC
*
105429 CAAATTTGTC
194 CAAATTCGTC
* * * *
105439 TTCCTGATGAGATACAGAGAAGCGAATTGAAACAATCAACGTGGTCATCTTCTTGATGAGATACC
1 TTCCTGATGAGATACAGAGAAGCGAATTGAAACAAACGACGCGGTCATCTTCCTGATGAGATACC
* * * *
105504 GAGAAGAAGACCAAATCAAACCCACGCTCAAAGCGAGCAAAATCTTCAAACCTCAGCTTCCTGAT
66 GAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAG-TAAATCTTCAAACC-CAGCTTCCTGAT
* * * * * * *
105569 GAGATACTGAGAAGCAGGTCGAAGCAATGAACGATTAGCTTCTTGATGAAATACTGAGAAGTGGA
129 GAGACAC-GAGAAGCAGATAGAAGCAATAAACGGTTAGCTTCCTGATGAGATACTGAGAAGTGGA
105634 CCAAATTCGTC
193 CCAAATTCGTC
* ** *
105645 TTCCTGATGAGATACAGAGAAGCGGATTGAAACAAACGACGCGACCATCTTCTTGATGAGATACC
1 TTCCTGATGAGATACAGAGAAGCGAATTGAAACAAACGACGCGGTCATCTTCCTGATGAGATACC
* * * * *
105710 GAGAAGAACACCAAATTAAACCCACGCTCGATGTGAGTAAATTTTCGAATCCCAGCTTCCTGTTG
66 GAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAGTAAATCTTC-AAACCCAGCTTCCTGATG
*
105775 AGACAC-AGAAGCAAATAGAAGCAATAAACGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACC
130 AGACACGAGAAGCAGATAGAAGCAATAAACGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACC
105839 AAATTCGTC
195 AAATTCGTC
* * * *
105848 TTCCTGATGAGATAAAGAGAAGCGGATTGAAACAAACGACGCGGTCATCTTCCTAATGAGATACT
1 TTCCTGATGAGATACAGAGAAGCGAATTGAAACAAACGACGCGGTCATCTTCCTGATGAGATACC
105913 GAGAAGAAG
66 GAGAAGAAG
105922 GTCAAGTCAA
Statistics
Matches: 426, Mismatches: 53, Indels: 10
0.87 0.11 0.02
Matches are distributed among these distances:
203 127 0.30
205 119 0.28
206 180 0.42
ACGTcount: A:0.36, C:0.20, G:0.22, T:0.22
Consensus pattern (203 bp):
TTCCTGATGAGATACAGAGAAGCGAATTGAAACAAACGACGCGGTCATCTTCCTGATGAGATACC
GAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAGTAAATCTTCAAACCCAGCTTCCTGATGA
GACACGAGAAGCAGATAGAAGCAATAAACGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCA
AATTCGTC
Found at i:106300 original size:6 final size:6
Alignment explanation
Indices: 106291--106367 Score: 61
Period size: 6 Copynumber: 13.2 Consensus size: 6
106281 CATATTTATT
* * **
106291 TTTAAA TTTAAA TTT-AT TTTAAA TGTAAA TTTATCT TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTA-AA TTTAAA TTTAAA
* **
106339 TCT-GC TTTAAA TTTAAA TTT-AA TTTAAA T
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T
106368 GTTTTTAAAA
Statistics
Matches: 53, Mismatches: 14, Indels: 8
0.71 0.19 0.11
Matches are distributed among these distances:
5 11 0.21
6 38 0.72
7 4 0.08
ACGTcount: A:0.40, C:0.04, G:0.03, T:0.53
Consensus pattern (6 bp):
TTTAAA
Found at i:106312 original size:17 final size:17
Alignment explanation
Indices: 106284--106367 Score: 96
Period size: 17 Copynumber: 4.8 Consensus size: 17
106274 ATTGATTCAT
106284 ATTTATTTTTAAATTTAA
1 ATTTA-TTTTAAATTTAA
*
106302 ATTTATTTTAAATGTAA
1 ATTTATTTTAAATTTAA
106319 ATTTATCTTTTAAATTTAA
1 ATTTA--TTTTAAATTTAA
* **
106338 ATCTGCTTTAAATTTAA
1 ATTTATTTTAAATTTAA
*
106355 ATTTAATTTAAAT
1 ATTTATTTTAAAT
106368 GTTTTTAAAA
Statistics
Matches: 56, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
17 37 0.66
18 5 0.09
19 14 0.25
ACGTcount: A:0.39, C:0.04, G:0.02, T:0.55
Consensus pattern (17 bp):
ATTTATTTTAAATTTAA
Found at i:106332 original size:36 final size:35
Alignment explanation
Indices: 106284--106367 Score: 107
Period size: 36 Copynumber: 2.4 Consensus size: 35
106274 ATTGATTCAT
* *
106284 ATTTATTTTTAAATTTAAATTTATTTTAAATGTAA
1 ATTTATTTTTAAATTTAAATCTACTTTAAATGTAA
* *
106319 ATTTATCTTTTAAATTTAAATCTGCTTTAAATTTAA
1 ATTTAT-TTTTAAATTTAAATCTACTTTAAATGTAA
*
106355 ATTTA-ATTTAAAT
1 ATTTATTTTTAAAT
106368 GTTTTTAAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
34 7 0.16
35 6 0.14
36 30 0.70
ACGTcount: A:0.39, C:0.04, G:0.02, T:0.55
Consensus pattern (35 bp):
ATTTATTTTTAAATTTAAATCTACTTTAAATGTAA
Found at i:108203 original size:29 final size:29
Alignment explanation
Indices: 108153--108435 Score: 214
Period size: 29 Copynumber: 10.0 Consensus size: 29
108143 GGAGGTCTTT
* * *
108153 AAACTGTCCAAAAACTCTATTTTTACCCCC
1 AAACT-TCCAAAAATTCCATTTTTACCCCA
* **
108183 GAACTTTAAAAAATTCCATTTTTGACCCCA
1 AAACTTCCAAAAATTCCATTTTT-ACCCCA
* *
108213 AAACTT-CAAAAATTCCATTTTAACCCCT
1 AAACTTCCAAAAATTCCATTTTTACCCCA
*
108241 AAACTTCCAAAAATCCCATTTTTGACCCCA
1 AAACTTCCAAAAATTCCATTTTT-ACCCCA
* *
108271 AAACTTCC----A-T---TTTTAACCCTA
1 AAACTTCCAAAAATTCCATTTTTACCCCA
*
108292 AAACTCCCAAAAATTCCATTTTTACCCTC-
1 AAACTTCCAAAAATTCCATTTTTACCC-CA
* * * * *
108321 GAACTTCTAAAAATCCCA-TTCTAACCCA
1 AAACTTCCAAAAATTCCATTTTTACCCCA
* *
108349 AAACTCCCAAAAATTCCATTTTTACCCCT
1 AAACTTCCAAAAATTCCATTTTTACCCCA
*
108378 AAACTT-CAAAAAATCTCATTTTTACCCCA
1 AAACTTCCAAAAATTC-CATTTTTACCCCA
* *
108407 GAA-TGTCTAAAAATTCCATTTTTAACCCC
1 AAACT-TCCAAAAATTCCATTTTT-ACCCC
108436 GAATTTTTCC
Statistics
Matches: 197, Mismatches: 38, Indels: 36
0.73 0.14 0.13
Matches are distributed among these distances:
21 12 0.06
22 4 0.02
25 1 0.01
26 2 0.01
27 1 0.01
28 40 0.20
29 98 0.50
30 39 0.20
ACGTcount: A:0.36, C:0.30, G:0.02, T:0.31
Consensus pattern (29 bp):
AAACTTCCAAAAATTCCATTTTTACCCCA
Found at i:108273 original size:21 final size:21
Alignment explanation
Indices: 108247--108300 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
108237 CCCTAAACTT
* *
108247 CCAAAAATCCCATTTTTGACC
1 CCAAAACTCCCATTTTTAACC
*
108268 CCAAAACTTCCATTTTTAACC
1 CCAAAACTCCCATTTTTAACC
*
108289 CTAAAACTCCCA
1 CCAAAACTCCCA
108301 AAAATTCCAT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.35, C:0.35, G:0.02, T:0.28
Consensus pattern (21 bp):
CCAAAACTCCCATTTTTAACC
Found at i:108327 original size:50 final size:50
Alignment explanation
Indices: 108219--108318 Score: 141
Period size: 51 Copynumber: 2.0 Consensus size: 50
108209 CCCAAAACTT
* *
108219 CAAAAATTCCATTTTAACCCCTAAACTTCCAAAAATCCCATTTTTGACCC
1 CAAAACTTCCATTTTAACCCCTAAACTCCCAAAAATCCCATTTTTGACCC
*
108269 CAAAACTTCCATTTTTAA-CCCTAAAACTCCCAAAAATTCCATTTTT-ACCC
1 CAAAACTTCCA-TTTTAACCCCT-AAACTCCCAAAAATCCCATTTTTGACCC
108319 TCGAACTTCT
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
50 18 0.40
51 27 0.60
ACGTcount: A:0.36, C:0.32, G:0.01, T:0.31
Consensus pattern (50 bp):
CAAAACTTCCATTTTAACCCCTAAACTCCCAAAAATCCCATTTTTGACCC
Found at i:108333 original size:80 final size:79
Alignment explanation
Indices: 108191--108340 Score: 212
Period size: 80 Copynumber: 1.9 Consensus size: 79
108181 CCGAACTTTA
* *
108191 AAAAATTCCATTTTTGACCCCAAAACTTCAAAAATTCCATTTTAACCCCTAAACTTCCAAAAATC
1 AAAAATTCCATTTTTAACCCCAAAACTCCAAAAATTCCATTTTAACCCCTAAACTTCCAAAAATC
108256 CCATTTTTGACCCC
66 CCATTTTTGACCCC
* * * * *
108270 AAAACTTCCATTTTTAACCCTAAAACTCCCAAAAATTCCATTTTTA-CCCTCGAACTTCTAAAAA
1 AAAAATTCCATTTTTAACCCCAAAACT-CCAAAAATTCCATTTTAACCCCT-AAACTTCCAAAAA
108334 TCCCATT
64 TCCCATT
108341 CTAACCCAAA
Statistics
Matches: 62, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
79 28 0.45
80 34 0.55
ACGTcount: A:0.37, C:0.30, G:0.02, T:0.31
Consensus pattern (79 bp):
AAAAATTCCATTTTTAACCCCAAAACTCCAAAAATTCCATTTTAACCCCTAAACTTCCAAAAATC
CCATTTTTGACCCC
Found at i:108355 original size:57 final size:58
Alignment explanation
Indices: 108284--108397 Score: 178
Period size: 57 Copynumber: 2.0 Consensus size: 58
108274 CTTCCATTTT
* *
108284 TAACCCTAAAACTCCCAAAAATTCCATTTTTA-CCCTCGAACTTCTAAAAATCCCATTC
1 TAACCCTAAAACTCCCAAAAATTCCATTTTTACCCCT-AAACTTCAAAAAATCCCATTC
*
108342 TAACCC-AAAACTCCCAAAAATTCCATTTTTACCCCTAAACTTCAAAAAATCTCATT
1 TAACCCTAAAACTCCCAAAAATTCCATTTTTACCCCTAAACTTCAAAAAATCCCATT
108398 TTTACCCCAG
Statistics
Matches: 52, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
57 42 0.81
58 10 0.19
ACGTcount: A:0.39, C:0.32, G:0.01, T:0.29
Consensus pattern (58 bp):
TAACCCTAAAACTCCCAAAAATTCCATTTTTACCCCTAAACTTCAAAAAATCCCATTC
Found at i:108416 original size:86 final size:87
Alignment explanation
Indices: 108267--108426 Score: 220
Period size: 86 Copynumber: 1.9 Consensus size: 87
108257 CATTTTTGAC
* *
108267 CCCAAAACTTCCATTTTTAACCCTAAAACTCCCAAAAATTCCATTTTTACCCTCGAACTTCTAAA
1 CCCAAAAATTCCATTTTTAACCCTAAAACTCCAAAAAATTCCATTTTTACCCTCGAACTTCTAAA
108332 AATCCCATTCTAACCCAAAACT
66 AATCCCATTCTAACCCAAAACT
* *
108354 CCCAAAAATTCCATTTTTACCCCT-AAACTTCAAAAAA-TCTCATTTTTACCC-CAGAA-TGTCT
1 CCCAAAAATTCCATTTTTAACCCTAAAACTCCAAAAAATTC-CATTTTTACCCTC-GAACT-TCT
*
108415 AAAAATTCCATT
63 AAAAATCCCATT
108427 TTTAACCCCG
Statistics
Matches: 65, Mismatches: 5, Indels: 7
0.84 0.06 0.09
Matches are distributed among these distances:
85 4 0.06
86 39 0.60
87 22 0.34
ACGTcount: A:0.37, C:0.31, G:0.02, T:0.31
Consensus pattern (87 bp):
CCCAAAAATTCCATTTTTAACCCTAAAACTCCAAAAAATTCCATTTTTACCCTCGAACTTCTAAA
AATCCCATTCTAACCCAAAACT
Found at i:113017 original size:51 final size:51
Alignment explanation
Indices: 112957--113059 Score: 206
Period size: 51 Copynumber: 2.0 Consensus size: 51
112947 GTGGGAAAAT
112957 GATAATGCTCTTCTGTGGCCATGAGAGGAACATAAACTAGTTCAATTTATG
1 GATAATGCTCTTCTGTGGCCATGAGAGGAACATAAACTAGTTCAATTTATG
113008 GATAATGCTCTTCTGTGGCCATGAGAGGAACATAAACTAGTTCAATTTATG
1 GATAATGCTCTTCTGTGGCCATGAGAGGAACATAAACTAGTTCAATTTATG
113059 G
1 G
113060 GAAAACTGAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.31
Consensus pattern (51 bp):
GATAATGCTCTTCTGTGGCCATGAGAGGAACATAAACTAGTTCAATTTATG
Found at i:114906 original size:2 final size:2
Alignment explanation
Indices: 114899--114935 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
114889 GTAACACTTT
114899 TC TC 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 TC TC T
114936 TTCTTCCATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:116474 original size:2 final size:2
Alignment explanation
Indices: 116467--116494 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
116457 AGGATTCTTC
116467 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
116495 TGGTAATGCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:117446 original size:9 final size:9
Alignment explanation
Indices: 117406--117451 Score: 58
Period size: 9 Copynumber: 5.1 Consensus size: 9
117396 TTGTTGTGCG
117406 TAATTTTTA
1 TAATTTTTA
*
117415 TAA-TATTA
1 TAATTTTTA
*
117423 TAATATTTAA
1 TAAT-TTTTA
117433 TAATTTTTA
1 TAATTTTTA
117442 TAATTTTTA
1 TAATTTTTA
117451 T
1 T
117452 TTTTCAGAAG
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
8 7 0.23
9 17 0.55
10 7 0.23
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (9 bp):
TAATTTTTA
Found at i:123037 original size:40 final size:40
Alignment explanation
Indices: 122982--123062 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
122972 GGAGCAGCTT
122982 CTCATTAATAGAAGATATATAAGGACTCATTAAACAACTA
1 CTCATTAATAGAAGATATATAAGGACTCATTAAACAACTA
123022 CTCATTAATAGAAGATATATAAGGACTCATTAAACAACTA
1 CTCATTAATAGAAGATATATAAGGACTCATTAAACAACTA
123062 C
1 C
123063 ATTCTCATAC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.47, C:0.16, G:0.10, T:0.27
Consensus pattern (40 bp):
CTCATTAATAGAAGATATATAAGGACTCATTAAACAACTA
Found at i:126393 original size:28 final size:29
Alignment explanation
Indices: 126361--126416 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
126351 TTACATCAGT
*
126361 AATATAAAAAATA-ATTAATTACGAAAAA
1 AATATAAAAAACAGATTAATTACGAAAAA
* *
126389 AATATAGAGAACAGATTAATTACGAAAA
1 AATATAAAAAACAGATTAATTACGAAAA
126417 TTGGTTTTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 10 0.42
29 14 0.58
ACGTcount: A:0.62, C:0.05, G:0.09, T:0.23
Consensus pattern (29 bp):
AATATAAAAAACAGATTAATTACGAAAAA
Found at i:126468 original size:21 final size:21
Alignment explanation
Indices: 126444--126484 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
126434 GTTTTGACTG
* *
126444 TACCACTTGATATATTGATGA
1 TACCACATGATATATGGATGA
*
126465 TACCCCATGATATATGGATG
1 TACCACATGATATATGGATG
126485 GTACAATATT
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:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (21 bp):
TACCACATGATATATGGATGA
Found at i:129728 original size:26 final size:26
Alignment explanation
Indices: 129678--129730 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 26
129668 GGCTGTGGAA
129678 TACAAGTGGTTACAAGCAGTGCAGTT
1 TACAAGTGGTTACAAGCAGTGCAGTT
129704 TACAAGTGGATTA-AA-CAGTGACAGTT
1 TACAAGTGG-TTACAAGCAGTG-CAGTT
129730 T
1 T
129731 TGTTATTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
25 5 0.20
26 17 0.68
27 3 0.12
ACGTcount: A:0.34, C:0.13, G:0.25, T:0.28
Consensus pattern (26 bp):
TACAAGTGGTTACAAGCAGTGCAGTT
Found at i:130130 original size:2 final size:2
Alignment explanation
Indices: 130123--130167 Score: 67
Period size: 2 Copynumber: 23.5 Consensus size: 2
130113 CCTAATTCTA
*
130123 AT AT AT AT AT AT AT AT AT AT AT AT AT -T CT A- 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
130163 AT AT A
1 AT AT A
130168 ATTACCCGAA
Statistics
Matches: 40, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
1 2 0.05
2 38 0.95
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:131455 original size:19 final size:19
Alignment explanation
Indices: 131431--131476 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
131421 AACTGCAATG
*
131431 TAAAATTTTTAAGCATTTT
1 TAAAATATTTAAGCATTTT
* *
131450 TAAAATATTTATGTATTTT
1 TAAAATATTTAAGCATTTT
131469 T-AAATATT
1 TAAAATATT
131477 ATTTTTAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
18 7 0.29
19 17 0.71
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.54
Consensus pattern (19 bp):
TAAAATATTTAAGCATTTT
Found at i:137571 original size:13 final size:14
Alignment explanation
Indices: 137529--137577 Score: 55
Period size: 15 Copynumber: 3.4 Consensus size: 14
137519 AAATTTTCAT
137529 ATTTTTTTCAAATAA
1 ATTTTTTTCAAAT-A
*
137544 ATTTTTTTGGTAAAT-
1 ATTTTTTT--CAAATA
137559 ATTTTTTTCAAATA
1 ATTTTTTTCAAATA
137573 ATTTT
1 ATTTT
137578 GATTTTGTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
13 4 0.14
14 5 0.17
15 16 0.55
17 4 0.14
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.59
Consensus pattern (14 bp):
ATTTTTTTCAAATA
Found at i:140814 original size:19 final size:19
Alignment explanation
Indices: 140792--140830 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
140782 TTTTCTTGCT
* *
140792 CATTTTTCTTCCTTCCTTC
1 CATTGTTCTTCATTCCTTC
*
140811 CATTGTTCTTGATTCCTTC
1 CATTGTTCTTCATTCCTTC
140830 C
1 C
140831 TCACAATAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.08, C:0.33, G:0.05, T:0.54
Consensus pattern (19 bp):
CATTGTTCTTCATTCCTTC
Found at i:153076 original size:2 final size:2
Alignment explanation
Indices: 153064--153092 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
153054 TAATTAATGG
153064 AT AT A- 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
153093 TTTTTTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:166393 original size:25 final size:25
Alignment explanation
Indices: 166348--166459 Score: 88
Period size: 25 Copynumber: 4.5 Consensus size: 25
166338 CTGGAAAGCC
* *
166348 TTGTGGCAAACTCTT-TGGAAAGCTT
1 TTGTGGCGAACT-TTCTAGAAAGCTT
* * *
166373 TTTTGGTGAACTTTCTAGAAAGCCT
1 TTGTGGCGAACTTTCTAGAAAGCTT
166398 TTGTGGCGAACTCTT-TAGAAAG-TCT
1 TTGTGGCGAACT-TTCTAGAAAGCT-T
*
166423 TTGTGACGAA-TTCTCTAGAAAGCTT
1 TTGTGGCGAACTT-TCTAGAAAGCTT
* *
166448 TTATGGTGAACT
1 TTGTGGCGAACT
166460 CCCTATAAAA
Statistics
Matches: 68, Mismatches: 12, Indels: 13
0.73 0.13 0.14
Matches are distributed among these distances:
23 1 0.01
24 4 0.06
25 59 0.87
26 4 0.06
ACGTcount: A:0.25, C:0.15, G:0.22, T:0.38
Consensus pattern (25 bp):
TTGTGGCGAACTTTCTAGAAAGCTT
Found at i:166440 original size:50 final size:50
Alignment explanation
Indices: 166341--166460 Score: 129
Period size: 50 Copynumber: 2.4 Consensus size: 50
166331 AAGTTACCTG
* * * **
166341 GAAAGCC-TTGTGGCAAACTCTTTGGAAAGCTTTTTTGGTGAACTTTCTA
1 GAAAGCCTTTGTGGCGAACTCTTTAGAAAGCTTTTGTGACGAACTTTCTA
166390 GAAAGCCTTTGTGGCGAACTCTTTAGAAAG-TCTTTGTGACGAA-TTCTCTA
1 GAAAGCCTTTGTGGCGAACTCTTTAGAAAGCT-TTTGTGACGAACTT-TCTA
* * *
166440 GAAAGCTTTTATGGTGAACTC
1 GAAAGCCTTTGTGGCGAACTC
166461 CCTATAAAAC
Statistics
Matches: 60, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
49 10 0.17
50 50 0.83
ACGTcount: A:0.26, C:0.17, G:0.23, T:0.35
Consensus pattern (50 bp):
GAAAGCCTTTGTGGCGAACTCTTTAGAAAGCTTTTGTGACGAACTTTCTA
Found at i:169481 original size:23 final size:22
Alignment explanation
Indices: 169454--169508 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 22
169444 AAAATGTACC
169454 TTAAAATAAATA-TAGAAAATATT
1 TTAAAATAAA-ACTA-AAAATATT
**
169477 TTAAACATAAAACTATTAATATT
1 TTAAA-ATAAAACTAAAAATATT
169500 TTAAAATAA
1 TTAAAATAA
169509 TGAAACGAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
22 4 0.14
23 17 0.61
24 7 0.25
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.36
Consensus pattern (22 bp):
TTAAAATAAAACTAAAAATATT
Found at i:172199 original size:3 final size:3
Alignment explanation
Indices: 172191--172235 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
172181 AAATTGAGAG
172191 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
172236 CAACGCTTTA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:177653 original size:7 final size:7
Alignment explanation
Indices: 177641--177674 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
177631 CTTGTTTTGC
177641 TGTGCAG
1 TGTGCAG
177648 TGTGCAG
1 TGTGCAG
177655 TGTGCAG
1 TGTGCAG
177662 TGTGCAG
1 TGTGCAG
177669 TGTGCA
1 TGTGCA
177675 CCGTCCCCCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.15, C:0.15, G:0.41, T:0.29
Consensus pattern (7 bp):
TGTGCAG
Found at i:187406 original size:16 final size:16
Alignment explanation
Indices: 187385--187428 Score: 88
Period size: 16 Copynumber: 2.8 Consensus size: 16
187375 TGTTTTTCTC
187385 TCTACTGTATTTACAG
1 TCTACTGTATTTACAG
187401 TCTACTGTATTTACAG
1 TCTACTGTATTTACAG
187417 TCTACTGTATTT
1 TCTACTGTATTT
187429 TACGGTATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.23, C:0.18, G:0.11, T:0.48
Consensus pattern (16 bp):
TCTACTGTATTTACAG
Found at i:190040 original size:27 final size:27
Alignment explanation
Indices: 190002--190055 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
189992 AAGTTTGGAA
190002 CCTAAGGATTCAATTTCAGAAGCAAAT
1 CCTAAGGATTCAATTTCAGAAGCAAAT
190029 CCTAAGGATTCAATTTCAGAAGCAAAT
1 CCTAAGGATTCAATTTCAGAAGCAAAT
190056 AGTTATCACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.41, C:0.19, G:0.15, T:0.26
Consensus pattern (27 bp):
CCTAAGGATTCAATTTCAGAAGCAAAT
Found at i:192005 original size:20 final size:21
Alignment explanation
Indices: 191973--192021 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 21
191963 TTAATAGTTC
** *
191973 AAAAAACTTCAAATAGAA-GT
1 AAAAAACAACAAATAAAACGT
191993 AAAAAACAACAAATAAAACGT
1 AAAAAACAACAAATAAAACGT
*
192014 TAAAAACA
1 AAAAAACA
192022 CTACATAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 15 0.62
21 9 0.38
ACGTcount: A:0.67, C:0.12, G:0.06, T:0.14
Consensus pattern (21 bp):
AAAAAACAACAAATAAAACGT
Found at i:195370 original size:2 final size:2
Alignment explanation
Indices: 195363--195394 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
195353 GAAAGATGTA
195363 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
195395 GATGTGTTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:202418 original size:31 final size:31
Alignment explanation
Indices: 202375--202452 Score: 104
Period size: 31 Copynumber: 2.5 Consensus size: 31
202365 AATATAACTT
* *
202375 TTGG-CCTCTAAACTTGGCAAGTAGGTCTATA
1 TTGGCCCT-TAAACTTGGCAAGTAGGTCCACA
202406 TTGGCCCTTAAACTTGGCAAGTAGGTCCACA
1 TTGGCCCTTAAACTTGGCAAGTAGGTCCACA
* *
202437 TTAGCCCTTGAACTTG
1 TTGGCCCTTAAACTTG
202453 ACCACTAAGT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
31 39 0.93
32 3 0.07
ACGTcount: A:0.24, C:0.23, G:0.22, T:0.31
Consensus pattern (31 bp):
TTGGCCCTTAAACTTGGCAAGTAGGTCCACA
Found at i:202751 original size:2 final size:2
Alignment explanation
Indices: 202744--202769 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
202734 AAAATTTTGA
202744 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
202770 TACTTTTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:221377 original size:3 final size:3
Alignment explanation
Indices: 221371--221402 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
221361 TCATCATGGA
*
221371 AAG AAG AAG AAG AAG AAG AAG AAG AAA AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
221403 AAAGCTGATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:225652 original size:41 final size:43
Alignment explanation
Indices: 225607--225694 Score: 126
Period size: 46 Copynumber: 2.0 Consensus size: 43
225597 TCACAAGAGC
*
225607 TGAATACGGATT-AAA-AAAAATTAAATTTTTAAATATTGCAG
1 TGAATACGGATTAAAATAAAAATTAAATTTTTAAATATTACAG
225648 TGAATACGGATTAAAAAATTAAAAATTAAATTTTTAAATATTACAG
1 TGAATACGGATT--AAAA-TAAAAATTAAATTTTTAAATATTACAG
225694 T
1 T
225695 CGAACATTAT
Statistics
Matches: 41, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
41 12 0.29
44 3 0.07
46 26 0.63
ACGTcount: A:0.50, C:0.05, G:0.10, T:0.35
Consensus pattern (43 bp):
TGAATACGGATTAAAATAAAAATTAAATTTTTAAATATTACAG
Found at i:230281 original size:24 final size:24
Alignment explanation
Indices: 230254--230310 Score: 114
Period size: 24 Copynumber: 2.4 Consensus size: 24
230244 AATAATAAAA
230254 TATACGAAAATCCCCAAAATAGAT
1 TATACGAAAATCCCCAAAATAGAT
230278 TATACGAAAATCCCCAAAATAGAT
1 TATACGAAAATCCCCAAAATAGAT
230302 TATACGAAA
1 TATACGAAA
230311 TAATAAAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.51, C:0.19, G:0.09, T:0.21
Consensus pattern (24 bp):
TATACGAAAATCCCCAAAATAGAT
Found at i:231441 original size:26 final size:26
Alignment explanation
Indices: 231384--231441 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
231374 AAAGTCAATT
* * * *
231384 GGTCAATGGAAAAGTCCACGGTCAAC
1 GGTCAACGAAAAAGTCAACAGTCAAC
* *
231410 GATCAACGAAAAAGTCAACAGTCAAG
1 GGTCAACGAAAAAGTCAACAGTCAAC
231436 GGTCAA
1 GGTCAA
231442 TGATTTGATT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.41, C:0.21, G:0.24, T:0.14
Consensus pattern (26 bp):
GGTCAACGAAAAAGTCAACAGTCAAC
Found at i:231610 original size:23 final size:23
Alignment explanation
Indices: 231560--231610 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
231550 TGTTGGGTTT
*
231560 GGTTTGGGTCAAAATGGGTTTCA
1 GGTTTGGGTCAAAATGGCTTTCA
* *
231583 AGTTTGGGTCAACATGGCTTAT-A
1 GGTTTGGGTCAAAATGGCTT-TCA
231606 GGTTT
1 GGTTT
231611 AGGTTTTTGG
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
23 22 0.96
24 1 0.04
ACGTcount: A:0.22, C:0.10, G:0.31, T:0.37
Consensus pattern (23 bp):
GGTTTGGGTCAAAATGGCTTTCA
Found at i:232150 original size:5 final size:5
Alignment explanation
Indices: 232140--232167 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
232130 CTATGTACCC
232140 AAAAT AAAAT AAAAT AAAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAA
232168 TATATAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:233234 original size:19 final size:19
Alignment explanation
Indices: 233200--233236 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
233190 GTTTCTCGAA
*
233200 AAAAGTCAATGATCAACGT
1 AAAAGTCAACGATCAACGT
*
233219 AAAAGTCAACGGTCAACG
1 AAAAGTCAACGATCAACG
233237 ATCAACTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.46, C:0.19, G:0.19, T:0.16
Consensus pattern (19 bp):
AAAAGTCAACGATCAACGT
Found at i:233271 original size:14 final size:14
Alignment explanation
Indices: 233254--233280 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
233244 ATTAACGGTA
233254 AACTGTCAATGGTT
1 AACTGTCAATGGTT
233268 AACTGTCAATGGT
1 AACTGTCAATGGT
233281 CAACGGGTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.33
Consensus pattern (14 bp):
AACTGTCAATGGTT
Found at i:233346 original size:20 final size:21
Alignment explanation
Indices: 233321--233367 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
233311 GGCTCACTTG
233321 GTTTGGGTCA-AAAGGTTTGA
1 GTTTGGGTCATAAAGGTTTGA
* * *
233341 GTTTGGTTCATATAGGTTTGG
1 GTTTGGGTCATAAAGGTTTGA
233362 GTTTGG
1 GTTTGG
233368 TGTTGATTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 9 0.39
21 14 0.61
ACGTcount: A:0.17, C:0.04, G:0.36, T:0.43
Consensus pattern (21 bp):
GTTTGGGTCATAAAGGTTTGA
Found at i:234673 original size:20 final size:19
Alignment explanation
Indices: 234636--234674 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
234626 TCTTTAGATT
* *
234636 TTTTTTAAAATTATTATAA
1 TTTTTAAAAAATATTATAA
234655 TTTTTAAAAAATATATATAA
1 TTTTTAAAAAATAT-TATAA
234675 ATATTGGAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TTTTTAAAAAATATTATAA
Found at i:234708 original size:19 final size:19
Alignment explanation
Indices: 234672--234729 Score: 53
Period size: 19 Copynumber: 3.0 Consensus size: 19
234662 AAAATATATA
** *
234672 TAAATATTGGAATATTTTT
1 TAAATATTTTAATTTTTTT
*
234691 TAAATATTTTAATTTTTTG
1 TAAATATTTTAATTTTTTT
* *
234710 AAAATTATTTTGATTTTTTT
1 TAAA-TATTTTAATTTTTTT
234730 GGTTTAATGA
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
19 18 0.58
20 13 0.42
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (19 bp):
TAAATATTTTAATTTTTTT
Found at i:235040 original size:19 final size:20
Alignment explanation
Indices: 235002--235041 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
234992 ATGCATGAAG
* *
235002 TTAAAAAAATAACTCTTAAT
1 TTAAAAAAATAAATCGTAAT
235022 TTAAAAAAATAAAT-GTAAT
1 TTAAAAAAATAAATCGTAAT
235041 T
1 T
235042 ATCTAAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.57, C:0.05, G:0.03, T:0.35
Consensus pattern (20 bp):
TTAAAAAAATAAATCGTAAT
Found at i:236012 original size:5 final size:5
Alignment explanation
Indices: 236002--236029 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
235992 AAAATTGAAT
236002 ATCTA ATCTA ATCTA ATCTA ATCTA ATC
1 ATCTA ATCTA ATCTA ATCTA ATCTA ATC
236030 ACTCTTTGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.39, C:0.21, G:0.00, T:0.39
Consensus pattern (5 bp):
ATCTA
Found at i:237274 original size:6 final size:6
Alignment explanation
Indices: 237263--237293 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
237253 ATTATCAGTC
237263 TAAAAT TAAAAT TAAAAT TAAAAT TAAAAT T
1 TAAAAT TAAAAT TAAAAT TAAAAT TAAAAT T
237294 TACCTACTCA
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:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (6 bp):
TAAAAT
Found at i:237646 original size:13 final size:14
Alignment explanation
Indices: 237623--237651 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
237613 AAATTTTTTT
237623 ATAATAAATAATTA
1 ATAATAAATAATTA
237637 ATAA-AAATAATTA
1 ATAATAAATAATTA
237650 AT
1 AT
237652 TTTTCATAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (14 bp):
ATAATAAATAATTA
Found at i:237955 original size:12 final size:12
Alignment explanation
Indices: 237930--237969 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
237920 AAATATTACA
237930 TTTTTA-AA-AT
1 TTTTTATAATAT
237940 TTTTTATAATAT
1 TTTTTATAATAT
*
237952 TTTTTATAATTT
1 TTTTTATAATAT
237964 TTTTTA
1 TTTTTA
237970 GTTTTGAACT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
10 6 0.22
11 2 0.07
12 19 0.70
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (12 bp):
TTTTTATAATAT
Found at i:239620 original size:45 final size:45
Alignment explanation
Indices: 239521--239608 Score: 162
Period size: 43 Copynumber: 2.0 Consensus size: 45
239511 ATCCCTCATT
239521 AATTTTTAAATTAGGGGTGTGTAGTTAGGGGTTGACAGTGGTCTC
1 AATTTTTAAATTAGGGGTGTGTAGTTAGGGGTTGACAGTGGTCTC
239566 AATTTTTAAATTA-GGG-GTGTAGTTAGGGGTTGACAGTGGTCTC
1 AATTTTTAAATTAGGGGTGTGTAGTTAGGGGTTGACAGTGGTCTC
239609 GGTTCTCTTA
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
43 27 0.63
44 3 0.07
45 13 0.30
ACGTcount: A:0.23, C:0.07, G:0.33, T:0.38
Consensus pattern (45 bp):
AATTTTTAAATTAGGGGTGTGTAGTTAGGGGTTGACAGTGGTCTC
Found at i:240107 original size:17 final size:18
Alignment explanation
Indices: 240085--240125 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
240075 TATTAATTTA
* *
240085 TAATTTTATTA-CTAAAT
1 TAATTTTAATATCAAAAT
240102 TAATTTTAATATCAAAAT
1 TAATTTTAATATCAAAAT
240120 TAATTT
1 TAATTT
240126 AGTCGAACGC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 10 0.48
18 11 0.52
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (18 bp):
TAATTTTAATATCAAAAT
Found at i:241383 original size:2 final size:2
Alignment explanation
Indices: 241376--241402 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
241366 TGTTAACTAT
241376 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
241403 CTGAAATTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:246944 original size:19 final size:19
Alignment explanation
Indices: 246920--246960 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
246910 ACACTAAACT
*
246920 CAAAAAATTTTCAAAACCC
1 CAAAAAATTTCCAAAACCC
*
246939 CAAAAAATTTCCAATACCC
1 CAAAAAATTTCCAAAACCC
246958 CAA
1 CAA
246961 CAAACATAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.51, C:0.29, G:0.00, T:0.20
Consensus pattern (19 bp):
CAAAAAATTTCCAAAACCC
Found at i:247726 original size:22 final size:22
Alignment explanation
Indices: 247684--247726 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
247674 CGACACCGAG
* *
247684 CCTCAAAGTCACAATTGCAAGT
1 CCTCAAAGTCACAACTCCAAGT
*
247706 CCTCAAGGTCACAACTCCAAG
1 CCTCAAAGTCACAACTCCAAG
247727 ACAATTGTTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.35, C:0.33, G:0.14, T:0.19
Consensus pattern (22 bp):
CCTCAAAGTCACAACTCCAAGT
Found at i:251704 original size:29 final size:29
Alignment explanation
Indices: 251646--251704 Score: 75
Period size: 28 Copynumber: 2.0 Consensus size: 29
251636 AATTGACAAG
**
251646 AAATTTCAAAAATTATTTATTAATTCATA
1 AAATTTCAAAAATTATTTATTAATAAATA
*
251675 AAATTT-AAAAATTCTTTATTATATAAATA
1 AAATTTCAAAAATTATTTATTA-ATAAATA
251704 A
1 A
251705 TTAAATTATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
28 14 0.54
29 12 0.46
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (29 bp):
AAATTTCAAAAATTATTTATTAATAAATA
Found at i:252326 original size:21 final size:21
Alignment explanation
Indices: 252302--252363 Score: 58
Period size: 21 Copynumber: 2.9 Consensus size: 21
252292 ATGAATTTTT
252302 TTTAATTAATATAATTATACA
1 TTTAATTAATATAATTATACA
252323 TTTAATCTTCAATAT--TTATACA
1 TTTAA--TT-AATATAATTATACA
*
252345 TTCT-ATTAATTTAATTATA
1 TT-TAATTAATATAATTATA
252364 AATCTAAATA
Statistics
Matches: 34, Mismatches: 1, Indels: 12
0.72 0.02 0.26
Matches are distributed among these distances:
19 4 0.12
20 2 0.06
21 10 0.29
22 10 0.29
23 3 0.09
24 5 0.15
ACGTcount: A:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (21 bp):
TTTAATTAATATAATTATACA
Found at i:253831 original size:2 final size:2
Alignment explanation
Indices: 253824--253853 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
253814 GAAATCTCTT
253824 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
253854 CATGTTTAAA
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:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:256036 original size:23 final size:23
Alignment explanation
Indices: 256009--256108 Score: 94
Period size: 23 Copynumber: 4.4 Consensus size: 23
255999 ATTTAAAACA
*
256009 AAACATTATGGCAACAGAGTTAC
1 AAACATAATGGCAACAGAGTTAC
**
256032 AAACATAATGGCAGGAGAGTTAC
1 AAACATAATGGCAACAGAGTTAC
** * * *
256055 AAACATAATGATAAGAGAATTAT
1 AAACATAATGGCAACAGAGTTAC
** *
256078 AAACATAATGGCAGGACAGTTAC
1 AAACATAATGGCAACAGAGTTAC
256101 AAA-ATAAT
1 AAACATAAT
256109 AAAAATTGGC
Statistics
Matches: 63, Mismatches: 14, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
22 5 0.08
23 58 0.92
ACGTcount: A:0.49, C:0.12, G:0.18, T:0.21
Consensus pattern (23 bp):
AAACATAATGGCAACAGAGTTAC
Found at i:261212 original size:23 final size:23
Alignment explanation
Indices: 261161--261287 Score: 116
Period size: 23 Copynumber: 5.3 Consensus size: 23
261151 CCAAAGTACT
*
261161 AACAGAGAGCACATA-AGTGCTA
1 AACAGAGAGCACACACAGTGCTA
261183 GGTAACAGAGAGCACACACAGTGCTA
1 ---AACAGAGAGCACACACAGTGCTA
* *
261209 AACAGAGA-CTACACAAAGTACTA
1 AACAGAGAGC-ACACACAGTGCTA
* *
261232 ATCAGATAGCACACACAGTGCTAA
1 AACAGAGAGCACACACAGTGCT-A
*
261256 TAACAGAGAGCACGAGAC-GTGCTA
1 -AACAGAGAGCAC-ACACAGTGCTA
261280 AACAGAGA
1 AACAGAGA
261288 CCGCGCTAGT
Statistics
Matches: 86, Mismatches: 10, Indels: 14
0.78 0.09 0.13
Matches are distributed among these distances:
22 1 0.01
23 43 0.50
24 3 0.03
25 29 0.34
26 10 0.12
ACGTcount: A:0.44, C:0.21, G:0.22, T:0.13
Consensus pattern (23 bp):
AACAGAGAGCACACACAGTGCTA
Found at i:261260 original size:71 final size:69
Alignment explanation
Indices: 261139--261288 Score: 205
Period size: 71 Copynumber: 2.1 Consensus size: 69
261129 TATACAGAAC
* * *
261139 AAACAGAGAATACCAAAGTACTAACAGAGAGCACATAAGTGCTAGGTAACAGAGAGCAC-ACACA
1 AAACAGAGACTACCAAAGTACTAACAGAGAGCACACAAGTGCTAGATAACAGAGAGCACGACAC-
261203 GTGCT
65 GTGCT
* *
261208 AAACAGAGACTACACAAAGTACTAATCAGATAGCACACACAGTGCTA-ATAACAGAGAGCACGAG
1 AAACAGAGACTAC-CAAAGTACTAA-CAGAGAGCACACA-AGTGCTAGATAACAGAGAGCACGAC
261272 ACGTGCT
63 ACGTGCT
261279 AAACAGAGAC
1 AAACAGAGAC
261289 CGCGCTAGTG
Statistics
Matches: 72, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
69 12 0.17
70 11 0.15
71 39 0.54
72 10 0.14
ACGTcount: A:0.45, C:0.21, G:0.21, T:0.13
Consensus pattern (69 bp):
AAACAGAGACTACCAAAGTACTAACAGAGAGCACACAAGTGCTAGATAACAGAGAGCACGACACG
TGCT
Found at i:262588 original size:18 final size:18
Alignment explanation
Indices: 262565--262625 Score: 54
Period size: 17 Copynumber: 3.3 Consensus size: 18
262555 AAGAGCTAAT
262565 ATTTTTGCCTTTTAATTG
1 ATTTTTGCCTTTTAATTG
* * *
262583 ATTTTTTTACCTTGCTGA-T-
1 A--TTTTTGCCTT-TTAATTG
262602 ATTTTTGCCTTTTAATTG
1 ATTTTTGCCTTTTAATTG
262620 ATTTTT
1 ATTTTT
262626 TTACCTTTCT
Statistics
Matches: 32, Mismatches: 6, Indels: 10
0.67 0.12 0.21
Matches are distributed among these distances:
16 2 0.06
17 10 0.31
18 7 0.22
19 1 0.03
20 10 0.31
21 2 0.06
ACGTcount: A:0.16, C:0.11, G:0.10, T:0.62
Consensus pattern (18 bp):
ATTTTTGCCTTTTAATTG
Found at i:262595 original size:20 final size:20
Alignment explanation
Indices: 262566--262633 Score: 70
Period size: 20 Copynumber: 3.5 Consensus size: 20
262556 AGAGCTAATA
*
262566 TTTTTGCCTTTTAATTGATT
1 TTTTTACCTTTTAATTGATT
** *
262586 TTTTTACC--TT-GCTGATA
1 TTTTTACCTTTTAATTGATT
*
262603 TTTTTGCCTTTTAATTGATT
1 TTTTTACCTTTTAATTGATT
262623 TTTTTACCTTT
1 TTTTTACCTTT
262634 CTCAAATTCT
Statistics
Matches: 36, Mismatches: 9, Indels: 6
0.71 0.18 0.12
Matches are distributed among these distances:
17 11 0.31
18 2 0.06
19 2 0.06
20 21 0.58
ACGTcount: A:0.15, C:0.13, G:0.09, T:0.63
Consensus pattern (20 bp):
TTTTTACCTTTTAATTGATT
Found at i:263767 original size:16 final size:16
Alignment explanation
Indices: 263746--263779 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
263736 ATAGTTAAAT
263746 ATTTTT-AATTATATTA
1 ATTTTTCAATT-TATTA
263762 ATTTTTCAATTTATTA
1 ATTTTTCAATTTATTA
263778 AT
1 AT
263780 AATATTTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (16 bp):
ATTTTTCAATTTATTA
Found at i:272035 original size:56 final size:56
Alignment explanation
Indices: 271949--272058 Score: 211
Period size: 56 Copynumber: 2.0 Consensus size: 56
271939 TAGATTTTAC
271949 ATAGTTGCAGTCCTTTTTGAGCTTGCTATAATCTAATATATATCTATAAACATTCT
1 ATAGTTGCAGTCCTTTTTGAGCTTGCTATAATCTAATATATATCTATAAACATTCT
*
272005 ATAGTTGCAGTCCTTTTTGAGCTTGCTATAATCTTATATATATCTATAAACATT
1 ATAGTTGCAGTCCTTTTTGAGCTTGCTATAATCTAATATATATCTATAAACATT
272059 TGCTTGTTAA
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 53 1.00
ACGTcount: A:0.30, C:0.15, G:0.11, T:0.44
Consensus pattern (56 bp):
ATAGTTGCAGTCCTTTTTGAGCTTGCTATAATCTAATATATATCTATAAACATTCT
Found at i:273451 original size:38 final size:38
Alignment explanation
Indices: 273406--273481 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
273396 CGTTTAGAGT
273406 CTAATATGTTAGCAAAACGGTGAGTTTAATGAAAGGGG
1 CTAATATGTTAGCAAAACGGTGAGTTTAATGAAAGGGG
*
273444 CTAATATGTTAGTAAAACGGTGAGTTTAATGAAAGGGG
1 CTAATATGTTAGCAAAACGGTGAGTTTAATGAAAGGGG
273482 TGGAACTATC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.37, C:0.07, G:0.29, T:0.28
Consensus pattern (38 bp):
CTAATATGTTAGCAAAACGGTGAGTTTAATGAAAGGGG
Found at i:276536 original size:19 final size:19
Alignment explanation
Indices: 276512--276573 Score: 58
Period size: 18 Copynumber: 3.3 Consensus size: 19
276502 ATACAGATTA
276512 TGTGCTAGGATGCACTTTG
1 TGTGCTAGGATGCACTTTG
*
276531 TGTGCTA-GATACATTCTTATG
1 TGTGCTAGGATGCA--CTT-TG
*
276552 TGT-C-AGGATGCACTTCG
1 TGTGCTAGGATGCACTTTG
276569 TGTGC
1 TGTGC
276574 CAAGTATGCA
Statistics
Matches: 35, Mismatches: 3, Indels: 11
0.71 0.06 0.22
Matches are distributed among these distances:
17 4 0.11
18 9 0.26
19 8 0.23
20 9 0.26
21 5 0.14
ACGTcount: A:0.18, C:0.18, G:0.27, T:0.37
Consensus pattern (19 bp):
TGTGCTAGGATGCACTTTG
Found at i:283697 original size:21 final size:21
Alignment explanation
Indices: 283649--283697 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
283639 ATTTGGAATT
*
283649 TTAGG-TTTTGGATTTAGGGC
1 TTAGGATTTTAGATTTAGGGC
*
283669 -TCGAGATTTTAGATTTAGGGC
1 TTAG-GATTTTAGATTTAGGGC
283690 TTAGGATT
1 TTAGGATT
283698 AAGGATTCGA
Statistics
Matches: 23, Mismatches: 3, Indels: 5
0.74 0.10 0.16
Matches are distributed among these distances:
19 2 0.09
20 1 0.04
21 18 0.78
22 2 0.09
ACGTcount: A:0.20, C:0.06, G:0.31, T:0.43
Consensus pattern (21 bp):
TTAGGATTTTAGATTTAGGGC
Found at i:283759 original size:14 final size:14
Alignment explanation
Indices: 283727--283753 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
283717 TTTAGGTTTT
283727 GGATTCGGGATTCA
1 GGATTCGGGATTCA
283741 GGATTCGGGATTC
1 GGATTCGGGATTC
283754 TAGATTAGAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.19, C:0.15, G:0.37, T:0.30
Consensus pattern (14 bp):
GGATTCGGGATTCA
Found at i:284223 original size:22 final size:22
Alignment explanation
Indices: 284198--284241 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
284188 TTTGTATAAA
* *
284198 TTTTGGCATCGAAATAAAATAC
1 TTTTGACATCAAAATAAAATAC
* *
284220 TTTTTACTTCAAAATAAAATAC
1 TTTTGACATCAAAATAAAATAC
284242 GTATCGACAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.43, C:0.14, G:0.07, T:0.36
Consensus pattern (22 bp):
TTTTGACATCAAAATAAAATAC
Found at i:286481 original size:2 final size:2
Alignment explanation
Indices: 286474--286519 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
286464 TCAAGATTTG
*
286474 AT AT AT AT AT AT AT GT A- 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
286515 AT AT A
1 AT AT A
286520 GGTTGGGATT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:287027 original size:2 final size:2
Alignment explanation
Indices: 287020--287053 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
287010 AGTTCGAACA
287020 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
287054 GGTTAAAATA
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:287126 original size:22 final size:19
Alignment explanation
Indices: 287090--287131 Score: 57
Period size: 22 Copynumber: 2.1 Consensus size: 19
287080 ATTCTTCATG
287090 AATTTTAAATTTTAAATTT
1 AATTTTAAATTTTAAATTT
287109 AATTGTTAATATTATTAAATTT
1 AATT-TTAA-ATT-TTAAATTT
287131 A
1 A
287132 TTGGTGTGAC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 4 0.20
20 4 0.20
21 3 0.15
22 9 0.45
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (19 bp):
AATTTTAAATTTTAAATTT
Done.