Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015266.1 Kokia drynarioides strain JFW-HI SEQ_130311, 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: 514914
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 275 characters in sequence are not A, C, G, or T
File 1 of 3
Found at i:2259 original size:26 final size:27
Alignment explanation
Indices: 2212--2264 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
2202 AATATATGCA
* *
2212 TAAAAAATATGTATAAAGTATACAATT
1 TAAAAAATATATATAAAGTATAAAATT
*
2239 TAAAAAATATATATGAA-TATAAAATT
1 TAAAAAATATATATAAAGTATAAAATT
2265 ACTAATCTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 8 0.35
27 15 0.65
ACGTcount: A:0.58, C:0.02, G:0.06, T:0.34
Consensus pattern (27 bp):
TAAAAAATATATATAAAGTATAAAATT
Found at i:2842 original size:2 final size:2
Alignment explanation
Indices: 2835--2867 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2825 AAATCAAGTA
2835 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2868 CACACACACA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:11150 original size:15 final size:13
Alignment explanation
Indices: 11120--11158 Score: 60
Period size: 15 Copynumber: 2.8 Consensus size: 13
11110 CTAAACGTTT
11120 TAATAAATAAATA
1 TAATAAATAAATA
11133 TAATAAATATAATAA
1 TAATAAATA-AAT-A
11148 TAATAAATAAA
1 TAATAAATAAA
11159 AGAAGTTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
13 9 0.38
14 5 0.21
15 10 0.42
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
TAATAAATAAATA
Found at i:12316 original size:29 final size:29
Alignment explanation
Indices: 12128--12316 Score: 168
Period size: 29 Copynumber: 6.5 Consensus size: 29
12118 AAGGTCCCCG
* * * *
12128 AACTTTGCAAAAATTACATTTTGACTCTTA
1 AACTTTTCCAAAATTACATTTTAAC-CCTA
* * *
12158 AACTTCTCAAAAATTACATTTTAACCC-C
1 AACTTTTCCAAAATTACATTTTAACCCTA
* *
12186 AACTTTTTACAAAATTACATTTT-AGCCTCA
1 AAC-TTTTCCAAAATTACATTTTAACCCT-A
* * * * *
12216 ACCTTTTACTAAATTACATTTGACCCCTA
1 AACTTTTCCAAAATTACATTTTAACCCTA
12245 AACTTTTCCAAAATTACATTTTAACTCC-A
1 AACTTTTCCAAAATTACATTTTAAC-CCTA
* *
12274 AAATTTTCCTAAATTACATTTTAACCCTA
1 AACTTTTCCAAAATTACATTTTAACCCTA
*
12303 AACTTCTCCAAAAT
1 AACTTTTCCAAAAT
12317 CCCATTTCGA
Statistics
Matches: 128, Mismatches: 25, Indels: 13
0.77 0.15 0.08
Matches are distributed among these distances:
28 8 0.06
29 91 0.71
30 29 0.23
ACGTcount: A:0.37, C:0.23, G:0.02, T:0.38
Consensus pattern (29 bp):
AACTTTTCCAAAATTACATTTTAACCCTA
Found at i:12322 original size:29 final size:28
Alignment explanation
Indices: 12137--12347 Score: 125
Period size: 29 Copynumber: 7.2 Consensus size: 28
12127 GAACTTTGCA
* * * *
12137 AAAATTACATTTTGACTCTTAAACTTCTCA
1 AAAATTACATTTTAAC-C-CAAAATTCTCC
** * *
12167 AAAATTACATTTTAACCCCAACTTTTTAC
1 AAAATTACATTTTAA-CCCAAAATTCTCC
* ** * *
12196 AAAATTACATTTTAGCCTCAACCTTTTAC
1 AAAATTACATTTTAACC-CAAAATTCTCC
* * * * *
12225 TAAATTACATTTGACCCCTAAACTTTTCC
1 AAAATTACATTTTAACCC-AAAATTCTCC
*
12254 AAAATTACATTTTAACTCCAAAATTTTCC
1 AAAATTACATTTTAAC-CCAAAATTCTCC
* *
12283 TAAATTACATTTTAACCCTAAACTTCTCC
1 AAAATTACATTTTAACCC-AAAATTCTCC
** * *
12312 AAAATCCCATTTCGATCCCAAAATTCTCC
1 AAAATTACATTT-TAACCCAAAATTCTCC
12341 AAAATTA
1 AAAATTA
12348 TGATTTTGCC
Statistics
Matches: 146, Mismatches: 29, Indels: 13
0.78 0.15 0.07
Matches are distributed among these distances:
28 5 0.03
29 119 0.82
30 21 0.14
31 1 0.01
ACGTcount: A:0.37, C:0.25, G:0.02, T:0.36
Consensus pattern (28 bp):
AAAATTACATTTTAACCCAAAATTCTCC
Found at i:12323 original size:87 final size:87
Alignment explanation
Indices: 12137--12347 Score: 210
Period size: 87 Copynumber: 2.4 Consensus size: 87
12127 GAACTTTGCA
* * * * **
12137 AAAATTACATTTTGACTCTTAAACTTCTCAAAAATTACATTTTAACCCCAACTTTTTACAAAATT
1 AAAATCACA-TTTGACCCCTAAACTTCTCCAAAATTACATTTTAACCCCAAAATTTTACAAAATT
* * *
12202 ACATTTTAGCCTCAACCTTTTAC
65 ACATTTTACCCTCAAACTTCTAC
* * * * * *
12225 TAAATTACATTTGACCCCTAAACTTTTCCAAAATTACATTTTAACTCCAAAATTTTCCTAAATTA
1 AAAATCACATTTGACCCCTAAACTTCTCCAAAATTACATTTTAACCCCAAAATTTTACAAAATTA
*
12290 CATTTTAACCCT-AAACTTCTCC
66 CATTTT-ACCCTCAAACTTCTAC
* * *
12312 AAAATCCCATTTCGATCCC-AAAATTCTCCAAAATTA
1 AAAATCACATTT-GACCCCTAAACTTCTCCAAAATTA
12348 TGATTTTGCC
Statistics
Matches: 101, Mismatches: 20, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
87 84 0.83
88 17 0.17
ACGTcount: A:0.37, C:0.25, G:0.02, T:0.36
Consensus pattern (87 bp):
AAAATCACATTTGACCCCTAAACTTCTCCAAAATTACATTTTAACCCCAAAATTTTACAAAATTA
CATTTTACCCTCAAACTTCTAC
Found at i:12333 original size:58 final size:58
Alignment explanation
Indices: 12219--12347 Score: 152
Period size: 58 Copynumber: 2.2 Consensus size: 58
12209 AGCCTCAACC
* * * * *
12219 TTTTACTAAATTACATTTGACCCCTAAACTTTTCCAAAATTACATTTTAACTCCAAAA
1 TTTTCCTAAATTACATTTGAACCCTAAACTTCTCCAAAATCACATTTGAACTCCAAAA
* * *
12277 TTTTCCTAAATTACATTTTAACCCTAAACTTCTCCAAAATCCCATTTCGATC-CCAAAA
1 TTTTCCTAAATTACATTTGAACCCTAAACTTCTCCAAAATCACATTT-GAACTCCAAAA
* *
12335 TTCTCCAAAATTA
1 TTTTCCTAAATTA
12348 TGATTTTGCC
Statistics
Matches: 60, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
58 58 0.97
59 2 0.03
ACGTcount: A:0.36, C:0.26, G:0.02, T:0.36
Consensus pattern (58 bp):
TTTTCCTAAATTACATTTGAACCCTAAACTTCTCCAAAATCACATTTGAACTCCAAAA
Found at i:12364 original size:29 final size:29
Alignment explanation
Indices: 12332--12439 Score: 84
Period size: 29 Copynumber: 3.8 Consensus size: 29
12322 TTCGATCCCA
* *
12332 AAATTCTCCAAAATTATGATTTTGCCCCT
1 AAATTCTCAAAAATTATCATTTTGCCCCT
* *
12361 AAATATC-CAAAAATTACCATTTTGCCTCCG
1 AAAT-TCTCAAAAATTATCATTTTGCC-CCT
*
12391 AACA-TCT-AAAAATTATCATTTT-ACCCT
1 AA-ATTCTCAAAAATTATCATTTTGCCCCT
*
12418 AAATT-TCCAAAAATCA-CATTTT
1 AAATTCT-CAAAAATTATCATTTT
12440 CAACCTCAAA
Statistics
Matches: 64, Mismatches: 8, Indels: 16
0.73 0.09 0.18
Matches are distributed among these distances:
26 2 0.03
27 11 0.17
28 8 0.12
29 36 0.56
30 6 0.09
31 1 0.02
ACGTcount: A:0.38, C:0.23, G:0.04, T:0.35
Consensus pattern (29 bp):
AAATTCTCAAAAATTATCATTTTGCCCCT
Found at i:21070 original size:49 final size:49
Alignment explanation
Indices: 21003--21387 Score: 260
Period size: 49 Copynumber: 7.8 Consensus size: 49
20993 TGATACCTTA
* * * *
21003 AAAGATGTGAATGGAAAGGTTGAGGCCGCAACAACGAACCTGGTACCAT
1 AAAGATATGAAGGGAAAGGTTGAGGCCGCAACAGCGAACCCGGTACCAT
* * * * **
21052 AAAGATATGAAGGAAAAGGTTGAGGTCGTAACGGTAAACCCGGTACC-T
1 AAAGATATGAAGGGAAAGGTTGAGGCCGCAACAGCGAACCCGGTACCAT
* * *
21100 AAGAAGATGTGATA-GGAAAGGTTGAGGCCGCAATAGTGAACCCGGTACCAT
1 -A-AAGATATGA-AGGGAAAGGTTGAGGCCGCAACAGCGAACCCGGTACCAT
* * * * * *
21151 GAAGATACGAAGGGAAAGGTCGAGGCCACAATAGCGAACCCAGTACC-T
1 AAAGATATGAAGGGAAAGGTTGAGGCCGCAACAGCGAACCCGGTACCAT
* ** * * * *
21199 AAGAAGAT-CGAAGGGAAAGGTTGAGGTTGCAACAGCGAACTCGTTACAAC
1 -A-AAGATATGAAGGGAAAGGTTGAGGCCGCAACAGCGAACCCGGTACCAT
* * * ** * * *
21249 AGAGATATAAAGGGAAAGGTTGAGGTCATAACGGCGAACCCGATACCTT
1 AAAGATATGAAGGGAAAGGTTGAGGCCGCAACAGCGAACCCGGTACCAT
* * * * * *
21298 AGA-ATATGCGATGGG-AAGGATTCAAGTCGCAACAGCGAACCCGATACCAT
1 AAAGATAT--GAAGGGAAAGG-TTGAGGCCGCAACAGCGAACCCGGTACCAT
* ** *
21348 GAAGATATGAAGGGAAAGGTTGAGGCTACAACAACGAACC
1 AAAGATATGAAGGGAAAGGTTGAGGCCGCAACAGCGAACC
21388 TAGCACCTTA
Statistics
Matches: 258, Mismatches: 64, Indels: 28
0.74 0.18 0.08
Matches are distributed among these distances:
48 11 0.04
49 166 0.64
50 75 0.29
51 6 0.02
ACGTcount: A:0.37, C:0.18, G:0.29, T:0.16
Consensus pattern (49 bp):
AAAGATATGAAGGGAAAGGTTGAGGCCGCAACAGCGAACCCGGTACCAT
Found at i:21147 original size:99 final size:99
Alignment explanation
Indices: 20996--21372 Score: 375
Period size: 99 Copynumber: 3.8 Consensus size: 99
20986 ACAAATCTGA
* * * *
20996 TACCTTAA-AAGATGTGAATGGAAAGGTTGAGGCCGCAACAACGAACCTGGTACCATAAAGATAT
1 TACC-TAAGAAGATGCGAAGGGAAAGGTTGAGGCCGCAACAGCGAACCCGGTACCATAAAGATAT
* * **
21060 GAAGGAAAAGGTTGAGGTCGTAACGGTAAACCCGG
65 GAAGGGAAAGGTTGAGGTCATAACGGCGAACCCGG
* * * * *
21095 TACCTAAGAAGATGTGATA-GGAAAGGTTGAGGCCGCAATAGTGAACCCGGTACCATGAAGATAC
1 TACCTAAGAAGATGCGA-AGGGAAAGGTTGAGGCCGCAACAGCGAACCCGGTACCATAAAGATAT
* * * ** *
21159 GAAGGGAAAGGTCGAGGCCACAATAGCGAACCCAG
65 GAAGGGAAAGGTTGAGGTCATAACGGCGAACCCGG
** * * * * * *
21194 TACCTAAGAAGAT-CGAAGGGAAAGGTTGAGGTTGCAACAGCGAACTCGTTACAACAGAGATATA
1 TACCTAAGAAGATGCGAAGGGAAAGGTTGAGGCCGCAACAGCGAACCCGGTACCATAAAGATATG
*
21258 AAGGGAAAGGTTGAGGTCATAACGGCGAACCCGA
66 AAGGGAAAGGTTGAGGTCATAACGGCGAACCCGG
* * * * * * * *
21292 TACCTTAGAATATGCGATGGG-AAGGATTCAAGTCGCAACAGCGAACCCGATACCATGAAGATAT
1 TACCTAAGAAGATGCGAAGGGAAAGG-TTGAGGCCGCAACAGCGAACCCGGTACCATAAAGATAT
21356 GAAGGGAAAGGTTGAGG
65 GAAGGGAAAGGTTGAGG
21373 CTACAACAAC
Statistics
Matches: 224, Mismatches: 49, Indels: 10
0.79 0.17 0.04
Matches are distributed among these distances:
97 1 0.00
98 81 0.36
99 141 0.63
100 1 0.00
ACGTcount: A:0.37, C:0.17, G:0.29, T:0.17
Consensus pattern (99 bp):
TACCTAAGAAGATGCGAAGGGAAAGGTTGAGGCCGCAACAGCGAACCCGGTACCATAAAGATATG
AAGGGAAAGGTTGAGGTCATAACGGCGAACCCGG
Found at i:28312 original size:12 final size:12
Alignment explanation
Indices: 28295--28319 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28285 CAAAAAAAAG
28295 AGAAAAGAATAA
1 AGAAAAGAATAA
28307 AGAAAAGAATAA
1 AGAAAAGAATAA
28319 A
1 A
28320 TTACCGAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (12 bp):
AGAAAAGAATAA
Found at i:32450 original size:37 final size:39
Alignment explanation
Indices: 32408--32486 Score: 126
Period size: 37 Copynumber: 2.1 Consensus size: 39
32398 TAAAATAACG
*
32408 TAATAATTTTATATTTCCAAAAAAT-A-TATAATAATTT
1 TAATAATTTTATATTTCAAAAAAATAATTATAATAATTT
*
32445 TAATAATTTTATATTTCAAAAAAATAATTTTAATAATTT
1 TAATAATTTTATATTTCAAAAAAATAATTATAATAATTT
32484 TAA
1 TAA
32487 AATCATTTAC
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
37 24 0.63
38 1 0.03
39 13 0.34
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (39 bp):
TAATAATTTTATATTTCAAAAAAATAATTATAATAATTT
Found at i:35555 original size:22 final size:22
Alignment explanation
Indices: 35530--35572 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
35520 CCTATTTCCC
35530 CTTTTCCCTT-TCTTTCTTTCTT
1 CTTTT-CCTTGTCTTTCTTTCTT
*
35552 CTTTTTCTTGTCTTTCTTTCT
1 CTTTTCCTTGTCTTTCTTTCT
35573 CTCCTTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 3 0.16
22 16 0.84
ACGTcount: A:0.00, C:0.28, G:0.02, T:0.70
Consensus pattern (22 bp):
CTTTTCCTTGTCTTTCTTTCTT
Found at i:36889 original size:16 final size:15
Alignment explanation
Indices: 36865--36907 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
36855 TCACTATTGT
*
36865 TTCAGATACAAGACAA
1 TTCAAATACAAG-CAA
36881 TTCAAATACACAGCAA
1 TTCAAATACA-AGCAA
*
36897 ATCAAATACAA
1 TTCAAATACAA
36908 AAACGGATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 1 0.04
16 21 0.88
17 2 0.08
ACGTcount: A:0.53, C:0.21, G:0.07, T:0.19
Consensus pattern (15 bp):
TTCAAATACAAGCAA
Found at i:46499 original size:19 final size:20
Alignment explanation
Indices: 46464--46501 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
46454 GGGACTAGTT
46464 TGGAACAAATTAGAAAATTA
1 TGGAACAAATTAGAAAATTA
46484 TGGAA-AAATCTA-AAAATT
1 TGGAACAAAT-TAGAAAATT
46502 TTAGAAACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.55, C:0.05, G:0.13, T:0.26
Consensus pattern (20 bp):
TGGAACAAATTAGAAAATTA
Found at i:50339 original size:21 final size:23
Alignment explanation
Indices: 50286--50349 Score: 80
Period size: 23 Copynumber: 2.8 Consensus size: 23
50276 AACATAAGCG
50286 AAACAACAGA-AAAAATAACAGTA
1 AAACAACA-ACAAAAATAACAGTA
*
50309 AAACAACAACAAAAATAGCA-TA
1 AAACAACAACAAAAATAACAGTA
50331 AAA-AACAACAAAAACTAAC
1 AAACAACAACAAAAA-TAAC
50350 GGCAAAAGTA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
21 11 0.30
22 9 0.24
23 17 0.46
ACGTcount: A:0.70, C:0.17, G:0.05, T:0.08
Consensus pattern (23 bp):
AAACAACAACAAAAATAACAGTA
Found at i:52597 original size:17 final size:17
Alignment explanation
Indices: 52563--52611 Score: 53
Period size: 18 Copynumber: 2.8 Consensus size: 17
52553 AATATAAATC
*
52563 ATTTTTTAATTTTTATAT
1 ATTTTTTAA-TTTAATAT
52581 ATTTTTTAATTTAATAT
1 ATTTTTTAATTTAATAT
* *
52598 TTTATTTTATTTTA
1 ATT-TTTTAATTTA
52612 TTTTATTTTG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
17 9 0.33
18 18 0.67
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
ATTTTTTAATTTAATAT
Found at i:52603 original size:5 final size:5
Alignment explanation
Indices: 52595--52627 Score: 57
Period size: 5 Copynumber: 6.4 Consensus size: 5
52585 TTTAATTTAA
52595 TATTT TATTT TATTT TATTT TATTT TGATTT TA
1 TATTT TATTT TATTT TATTT TATTT T-ATTT TA
52628 GGGACTAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 22 0.81
6 5 0.19
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (5 bp):
TATTT
Found at i:53765 original size:31 final size:29
Alignment explanation
Indices: 53700--53765 Score: 71
Period size: 31 Copynumber: 2.2 Consensus size: 29
53690 GTCCAATATT
* *
53700 GTATTTATTAATTTTTATTATTTTATTAT
1 GTATTTATTAATTTTTAATATTTTATTAA
*
53729 TTATTTATTCTAATTTTTGAATATTTT-TTAA
1 GTATTTA-T-TAATTTTT-AATATTTTATTAA
53760 GTATTT
1 GTATTT
53766 TAAGTTGTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
29 6 0.20
30 1 0.03
31 16 0.53
32 7 0.23
ACGTcount: A:0.27, C:0.02, G:0.05, T:0.67
Consensus pattern (29 bp):
GTATTTATTAATTTTTAATATTTTATTAA
Found at i:56000 original size:24 final size:23
Alignment explanation
Indices: 55946--56015 Score: 70
Period size: 24 Copynumber: 3.0 Consensus size: 23
55936 TTGCACATAT
55946 TTGGTGATAGGGGTTCGTAGGTATC
1 TTGGTGATAGGGGTTCGTA-G-ATC
* *
55971 -TAGTGATAGAGGTTCGTAGATCC
1 TTGGTGATAGGGGTTCGTAGAT-C
* *
55994 TTGGTGATTGGGGTTCGCAGAT
1 TTGGTGATAGGGGTTCGTAGAT
56016 ATCACATATA
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
22 2 0.05
23 2 0.05
24 33 0.89
ACGTcount: A:0.19, C:0.10, G:0.37, T:0.34
Consensus pattern (23 bp):
TTGGTGATAGGGGTTCGTAGATC
Found at i:62812 original size:157 final size:157
Alignment explanation
Indices: 62526--62843 Score: 575
Period size: 157 Copynumber: 2.0 Consensus size: 157
62516 TGAAGGTGGA
* *
62526 GTTGTGCGTATGGAAAATGATTCATCTAGTAAGGTAATCGATATCGGTACTATTAAAATTAGGAT
1 GTTGTGCGTATGGAAAACGATTCATCTAGTAAGGTAATCAATATCGGTACTATTAAAATTAGGAT
*
62591 GCACAATGGTACGATTAGGACACTCTCAGATGTCAAATATGTACTTGATTTACGAAAGAATCTCA
66 GCACAATGGTACGATTAGGACACTCTCAGATGTCAAATATGTACCTGATTTACGAAAGAATCTCA
62656 CCTCCTTGAGTATTTTAGACTCGAAAG
131 CCTCCTTGAGTATTTTAGACTCGAAAG
* *
62683 GTTGTGTGTATGG-AAACGATTTATCTAGTAAAGGTAATCAATATCGGTACTATTAAAATTAGGA
1 GTTGTGCGTATGGAAAACGATTCATCTAGT-AAGGTAATCAATATCGGTACTATTAAAATTAGGA
62747 TGCACAATGGTACGATTAGGACACTCTCAGATGTCAAATATGTACCTGATTTACGAAAGAATCTC
65 TGCACAATGGTACGATTAGGACACTCTCAGATGTCAAATATGTACCTGATTTACGAAAGAATCTC
62812 ACCTCCTTGAGTATTTTAGACTCGAAAG
130 ACCTCCTTGAGTATTTTAGACTCGAAAG
62840 GTTG
1 GTTG
62844 CAGGATCAAC
Statistics
Matches: 155, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
156 14 0.09
157 141 0.91
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.31
Consensus pattern (157 bp):
GTTGTGCGTATGGAAAACGATTCATCTAGTAAGGTAATCAATATCGGTACTATTAAAATTAGGAT
GCACAATGGTACGATTAGGACACTCTCAGATGTCAAATATGTACCTGATTTACGAAAGAATCTCA
CCTCCTTGAGTATTTTAGACTCGAAAG
Found at i:69434 original size:18 final size:18
Alignment explanation
Indices: 69383--69434 Score: 52
Period size: 18 Copynumber: 2.7 Consensus size: 18
69373 TTTTTTTATA
*
69383 ATATTTTACTAT-ACTTTT
1 ATATTTTA-TATGTCTTTT
69401 ATATTTTCTCATATGTCTTTT
1 ATA-TTT-T-ATATGTCTTTT
69422 ATATTTTATATGT
1 ATATTTTATATGT
69435 TCAGGGTTCA
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
18 9 0.31
19 4 0.14
20 7 0.24
21 9 0.31
ACGTcount: A:0.25, C:0.10, G:0.04, T:0.62
Consensus pattern (18 bp):
ATATTTTATATGTCTTTT
Found at i:75320 original size:31 final size:31
Alignment explanation
Indices: 75277--75335 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
75267 TTGGTCCAAA
* *
75277 TTGGTACTTAAACTTGACATTTTTTTTTGAT
1 TTGGTACCTAAACTTGACACTTTTTTTTGAT
*
75308 TTGGTACCTAAACTTGATACTTTTTTTT
1 TTGGTACCTAAACTTGACACTTTTTTTT
75336 ATATTGATAC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.22, C:0.12, G:0.12, T:0.54
Consensus pattern (31 bp):
TTGGTACCTAAACTTGACACTTTTTTTTGAT
Found at i:75637 original size:31 final size:31
Alignment explanation
Indices: 75591--75717 Score: 129
Period size: 31 Copynumber: 4.2 Consensus size: 31
75581 GGTTAGGTAT
75591 CAAATTAGAAAAAAAATGTCAAGTTCAAGTAC
1 CAAATTA-AAAAAAAATGTCAAGTTCAAGTAC
* *
75623 CAAATTAAAAAAAAATATCAAGTTC-TGATAC
1 CAAATTAAAAAAAAATGTCAAGTTCAAG-TAC
* * *
75654 CAAATTAAGTAAAAAA----AAGTTTAAGTAT
1 CAAATTAA-AAAAAAATGTCAAGTTCAAGTAC
* *
75682 CAAATTAAGAAAAAATGTCAAGTTTAAGTAC
1 CAAATTAAAAAAAAATGTCAAGTTCAAGTAC
75713 CAAAT
1 CAAAT
75718 ATTATATTAA
Statistics
Matches: 80, Mismatches: 8, Indels: 15
0.78 0.08 0.15
Matches are distributed among these distances:
27 6 0.08
28 15 0.19
29 1 0.01
30 1 0.01
31 44 0.55
32 13 0.16
ACGTcount: A:0.54, C:0.10, G:0.10, T:0.25
Consensus pattern (31 bp):
CAAATTAAAAAAAAATGTCAAGTTCAAGTAC
Found at i:87689 original size:49 final size:49
Alignment explanation
Indices: 87636--87806 Score: 159
Period size: 49 Copynumber: 3.5 Consensus size: 49
87626 AAAAACAATT
* *
87636 ATTATTGGGCTATTC-AGGATGGTATAATGTATAGGTATTGAATGCCATC
1 ATTATTGAGCTATCCGA-GATGGTATAATGTATAGGTATTGAATGCCATC
** * * * ** *
87685 ATTATCAAGCTATCCGAGATGGTAAGATATGTCTA--TAGTGAAAACCATT
1 ATTATTGAGCTATCCGAGATGGT-ATA-ATGTATAGGTATTGAATGCCATC
* * *
87734 ATTATAGGGTTATCCGAGATGGTATAATGTATAGGTATTGAATGCCATC
1 ATTATTGAGCTATCCGAGATGGTATAATGTATAGGTATTGAATGCCATC
* *
87783 ATTGTTGAGCTATCCGGGATGGTA
1 ATTATTGAGCTATCCGAGATGGTA
87807 GAATAAGTAA
Statistics
Matches: 92, Mismatches: 25, Indels: 10
0.72 0.20 0.08
Matches are distributed among these distances:
47 6 0.07
48 2 0.02
49 75 0.82
50 3 0.03
51 6 0.07
ACGTcount: A:0.30, C:0.12, G:0.24, T:0.34
Consensus pattern (49 bp):
ATTATTGAGCTATCCGAGATGGTATAATGTATAGGTATTGAATGCCATC
Found at i:87755 original size:98 final size:97
Alignment explanation
Indices: 87595--87834 Score: 286
Period size: 98 Copynumber: 2.4 Consensus size: 97
87585 TCATTATTGG
* * ** * * *
87595 GCTATCC-AGGATGGTTGGATATGTTTATAGCAAAAACAATTATTATTGGGCTATTCAGGATGGT
1 GCTATCCGA-GATGG-TAGATATGTATATAGTGAAAACCATTATTATAGGGCTATCCAGGATGGT
87659 ATAATGTATAGGTATTGAATGCCATCATTATCAA
64 ATAATGTATAGGTATTGAATGCCATCATTATCAA
* *
87693 GCTATCCGAGATGGTAAGATATGTCTATAGTGAAAACCATTATTATAGGGTTATCC-GAGATGGT
1 GCTATCCGAGATGGT-AGATATGTATATAGTGAAAACCATTATTATAGGGCTATCCAG-GATGGT
* **
87757 ATAATGTATAGGTATTGAATGCCATCATTGTTGA
64 ATAATGTATAGGTATTGAATGCCATCATTATCAA
* * *
87791 GCTATCCGGGATGGTAGAATAAGTAAATAGTGAAAACCATTATT
1 GCTATCCGAGATGGTAG-ATATGTATATAGTGAAAACCATTATT
87835 GTTGAGACAT
Statistics
Matches: 123, Mismatches: 15, Indels: 8
0.84 0.10 0.05
Matches are distributed among these distances:
97 4 0.03
98 118 0.96
99 1 0.01
ACGTcount: A:0.33, C:0.11, G:0.23, T:0.33
Consensus pattern (97 bp):
GCTATCCGAGATGGTAGATATGTATATAGTGAAAACCATTATTATAGGGCTATCCAGGATGGTAT
AATGTATAGGTATTGAATGCCATCATTATCAA
Found at i:100254 original size:55 final size:55
Alignment explanation
Indices: 100188--100298 Score: 204
Period size: 55 Copynumber: 2.0 Consensus size: 55
100178 CAAAAAGCCA
*
100188 AGTGATGTTATAAAAATCCCCTCTTGTGATGAGATTTAGGTCATATCAACCAAAG
1 AGTGATGTTATAAAAATCCCCTCTTGTGATGAGATTTAGGTCAAATCAACCAAAG
*
100243 AGTGATGTTATAAAAATCCCCTTTTGTGATGAGATTTAGGTCAAATCAACCAAAG
1 AGTGATGTTATAAAAATCCCCTCTTGTGATGAGATTTAGGTCAAATCAACCAAAG
100298 A
1 A
100299 ACTGTCGTTA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 54 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (55 bp):
AGTGATGTTATAAAAATCCCCTCTTGTGATGAGATTTAGGTCAAATCAACCAAAG
Found at i:100807 original size:21 final size:21
Alignment explanation
Indices: 100753--100809 Score: 89
Period size: 21 Copynumber: 2.7 Consensus size: 21
100743 TTGTGCTAGC
100753 TCTACCGATACAAGTATGGTT
1 TCTACCGATACAAGTATGGTT
*
100774 TCTACAGATACAAGTATGGTT
1 TCTACCGATACAAGTATGGTT
100795 TCTACCGGA-ACAAGT
1 TCTACC-GATACAAGT
100810 CATGCATCTA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
21 31 0.94
22 2 0.06
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (21 bp):
TCTACCGATACAAGTATGGTT
Found at i:101616 original size:52 final size:52
Alignment explanation
Indices: 101523--101768 Score: 334
Period size: 52 Copynumber: 4.7 Consensus size: 52
101513 TTCACTTCAC
* * * * * *
101523 TCATATACTCACGATGACACATAGCCA-CAGA-ATCTTATAATCCGCAAGGGAT
1 TCATATACTCACGATGACACTTAGTCATCGGACCTC-T-TAATCCGTAAAGGAT
**
101575 TCATATACTCACGATGACACAGAGTCATCGGACCTCTTAATCCGTAAAGGAT
1 TCATATACTCACGATGACACTTAGTCATCGGACCTCTTAATCCGTAAAGGAT
* *
101627 TCATATACTCATGATGACACTTAGTCATCGAACCTCTTAATCCGTAAAGGAT
1 TCATATACTCACGATGACACTTAGTCATCGGACCTCTTAATCCGTAAAGGAT
* * *
101679 TGATATACTCACGATAACACTTAGTCATCGGACCTCCTAATCCGTAAAGGAT
1 TCATATACTCACGATGACACTTAGTCATCGGACCTCTTAATCCGTAAAGGAT
*
101731 TCATATACTCACGATGAAACTTAGTCATCGGACCTCTT
1 TCATATACTCACGATGACACTTAGTCATCGGACCTCTT
101769 CGTTTATGGC
Statistics
Matches: 173, Mismatches: 19, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
52 167 0.97
53 4 0.02
54 2 0.01
ACGTcount: A:0.33, C:0.25, G:0.15, T:0.27
Consensus pattern (52 bp):
TCATATACTCACGATGACACTTAGTCATCGGACCTCTTAATCCGTAAAGGAT
Found at i:105347 original size:24 final size:25
Alignment explanation
Indices: 105298--105359 Score: 69
Period size: 24 Copynumber: 2.6 Consensus size: 25
105288 TATGATGATT
*
105298 ATGT-ATATGTGAATAGTAATGTAA
1 ATGTGATATGTGAATAGTAATGGAA
105322 ATGTGATATGTGAA-A-TAATGAGAA
1 ATGTGATATGTGAATAGTAATG-GAA
105346 ATGATGA-ATGTGAA
1 ATG-TGATATGTGAA
105360 GTGTTATGCC
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
23 5 0.15
24 17 0.50
25 12 0.35
ACGTcount: A:0.44, C:0.00, G:0.24, T:0.32
Consensus pattern (25 bp):
ATGTGATATGTGAATAGTAATGGAA
Found at i:105457 original size:23 final size:23
Alignment explanation
Indices: 105427--105477 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
105417 GGAGCGCTAG
*
105427 TGTGCTTACTGTTTCGCACTTCA
1 TGTGCTTACTGTTTCGCACCTCA
*
105450 TGTGCTTACTGTTTCGCACCTCG
1 TGTGCTTACTGTTTCGCACCTCA
105473 TGTGC
1 TGTGC
105478 CTATTGATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.10, C:0.27, G:0.22, T:0.41
Consensus pattern (23 bp):
TGTGCTTACTGTTTCGCACCTCA
Found at i:105516 original size:22 final size:22
Alignment explanation
Indices: 105476--105535 Score: 66
Period size: 22 Copynumber: 2.6 Consensus size: 22
105466 CACCTCGTGT
* *
105476 GCCTATTGATTTGCGCTATGTGC
1 GCCTACTGA-TTGCACTATGTGC
*
105499 GCCTACTGATTGCACTATGTGT
1 GCCTACTGATTGCACTATGTGC
*
105521 GCTTACTGGATTGCA
1 GCCTACT-GATTGCA
105536 TTGCATGTGC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
22 17 0.53
23 15 0.47
ACGTcount: A:0.17, C:0.22, G:0.25, T:0.37
Consensus pattern (22 bp):
GCCTACTGATTGCACTATGTGC
Found at i:108095 original size:52 final size:52
Alignment explanation
Indices: 108028--108182 Score: 247
Period size: 52 Copynumber: 3.0 Consensus size: 52
108018 TTTCTTATCG
* * * * *
108028 ATCCATAAAGGATTCATATACTTACGATGACTCTTAGTCATCGAACCTTTTA
1 ATCCGTAAAGGATTCATATACTCACGATGACACTTAGTCATCGGACCTCTTA
* *
108080 ATTCGTAAAGGATTCATGTACTCACGATGACACTTAGTCATCGGACCTCTTA
1 ATCCGTAAAGGATTCATATACTCACGATGACACTTAGTCATCGGACCTCTTA
108132 ATCCGTAAAGGATTCATATACTCACGATGACACTTAGTCATCGGACCTCTT
1 ATCCGTAAAGGATTCATATACTCACGATGACACTTAGTCATCGGACCTCTT
108183 CGTTTATGGC
Statistics
Matches: 94, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 94 1.00
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.32
Consensus pattern (52 bp):
ATCCGTAAAGGATTCATATACTCACGATGACACTTAGTCATCGGACCTCTTA
Found at i:113964 original size:14 final size:14
Alignment explanation
Indices: 113941--113979 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
113931 TTCTCATCTC
*
113941 TATTTCCTTTATTT
1 TATTTTCTTTATTT
113955 TATTTTCTTTATTT
1 TATTTTCTTTATTT
*
113969 TATGTTCTTTA
1 TATTTTCTTTA
113980 ATTCAAATCT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.15, C:0.10, G:0.03, T:0.72
Consensus pattern (14 bp):
TATTTTCTTTATTT
Found at i:118408 original size:30 final size:31
Alignment explanation
Indices: 118344--118415 Score: 94
Period size: 30 Copynumber: 2.4 Consensus size: 31
118334 ACAACAAGAG
* *
118344 GACTATTTTGTCACTTTTCGATAACTTTAGT
1 GACTATTTTGTCACTTTTCGATAAATTGAGT
118375 GACTATTTTGTCACATTTTC-A-AAATTGAGT
1 GACTATTTTGTCAC-TTTTCGATAAATTGAGT
*
118405 GACTGTTTTGT
1 GACTATTTTGT
118416 TAAATGTGAC
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
30 17 0.46
31 15 0.41
32 5 0.14
ACGTcount: A:0.24, C:0.14, G:0.15, T:0.47
Consensus pattern (31 bp):
GACTATTTTGTCACTTTTCGATAAATTGAGT
Found at i:119443 original size:20 final size:19
Alignment explanation
Indices: 119420--119483 Score: 69
Period size: 20 Copynumber: 3.2 Consensus size: 19
119410 TAAAAAAACC
119420 CAAAATAATTTTCAAAAATT
1 CAAAATAATTTT-AAAAATT
119440 CAAAATAAACTTTT-AAAATT
1 CAAAAT-AA-TTTTAAAAATT
119460 CAAAAT-ATTTATAAAAATTT
1 CAAAATAATTT-TAAAAA-TT
119480 CAAA
1 CAAA
119484 TTATATATAT
Statistics
Matches: 39, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
17 3 0.08
18 2 0.05
19 4 0.10
20 24 0.62
21 2 0.05
22 4 0.10
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.34
Consensus pattern (19 bp):
CAAAATAATTTTAAAAATT
Found at i:119492 original size:20 final size:19
Alignment explanation
Indices: 119433--119492 Score: 57
Period size: 20 Copynumber: 3.1 Consensus size: 19
119423 AATAATTTTC
* *
119433 AAAAATTCAAAATAAACTTT
1 AAAAATTCAAAATATA-TAT
* *
119453 TAAAATTCAAAATATTTAT
1 AAAAATTCAAAATATATAT
*
119472 AAAAATTTCAAATTATATAT
1 AAAAA-TTCAAAATATATAT
119492 A
1 A
119493 TATATATATT
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
19 6 0.19
20 26 0.81
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.37
Consensus pattern (19 bp):
AAAAATTCAAAATATATAT
Found at i:125809 original size:41 final size:41
Alignment explanation
Indices: 125739--125951 Score: 183
Period size: 41 Copynumber: 5.2 Consensus size: 41
125729 CGTAAATCAA
* * * * * *
125739 TAAAAGTCAAAGCATTAGCGGCGCTTGTGTGAAACCGCCGC
1 TAAAGGTCAGAGCATTAGCGACGCTTATGGGAAAACGCCGC
* * *
125780 TAAAGGTCAGAGTATTAGCGACGCTTGTGTGAAAACGCCGC
1 TAAAGGTCAGAGCATTAGCGACGCTTATGGGAAAACGCCGC
* * * * * *
125821 TAAAGGTCAGAACATTAGTGGCGCTTATGGGAAAGCGTCGT
1 TAAAGGTCAGAGCATTAGCGACGCTTATGGGAAAACGCCGC
* * * ** * *
125862 TAAAGGTAATAGAATTAGCGACATTTATGGGAAAGCGCCGT
1 TAAAGGTCAGAGCATTAGCGACGCTTATGGGAAAACGCCGC
* * **
125903 TAAAGGTCAAAGCATTAGCGGCATTTATGGGAAAAACGCCGC
1 TAAAGGTCAGAGCATTAGCGACGCTTATGGG-AAAACGCCGC
125945 TAAAGGT
1 TAAAGGT
125952 TAAGTAGTAG
Statistics
Matches: 142, Mismatches: 29, Indels: 1
0.83 0.17 0.01
Matches are distributed among these distances:
41 127 0.89
42 15 0.11
ACGTcount: A:0.32, C:0.17, G:0.28, T:0.22
Consensus pattern (41 bp):
TAAAGGTCAGAGCATTAGCGACGCTTATGGGAAAACGCCGC
Found at i:125963 original size:82 final size:82
Alignment explanation
Indices: 125739--125965 Score: 233
Period size: 82 Copynumber: 2.8 Consensus size: 82
125729 CGTAAATCAA
* * * * * *
125739 TAAAAGTCAAAGCATTAGCGGCGCTTGTGTGAAACCGCCGCTAAAGGTCAGAGTATTAGCGACGC
1 TAAAGGTCAAAGCATTAGCGGCGCTTATGGGAAAACGCCGCTAAAGGTAAGAGTATTAGCGACAC
* *
125804 TTGTGTGAAAACGCCGC
66 TTATGGGAAAACGCCGC
* * * * * *
125821 TAAAGGTCAGAA-CATTAGTGGCGCTTATGGGAAAGCGTCGTTAAAGGTAATAGAATTAGCGACA
1 TAAAGGTCA-AAGCATTAGCGGCGCTTATGGGAAAACGCCGCTAAAGGTAAGAGTATTAGCGACA
* * *
125885 TTTATGGGAAAGCGCCGT
65 CTTATGGGAAAACGCCGC
** * *
125903 TAAAGGTCAAAGCATTAGCGGCATTTATGGGAAAAACGCCGCTAAAGGTTA-AGTAGTAGCGAC
1 TAAAGGTCAAAGCATTAGCGGCGCTTATGGG-AAAACGCCGCTAAAGGTAAGAGTATTAGCGAC
125966 GTTTTCCCAT
Statistics
Matches: 117, Mismatches: 25, Indels: 6
0.79 0.17 0.04
Matches are distributed among these distances:
81 2 0.02
82 98 0.84
83 17 0.15
ACGTcount: A:0.33, C:0.17, G:0.28, T:0.22
Consensus pattern (82 bp):
TAAAGGTCAAAGCATTAGCGGCGCTTATGGGAAAACGCCGCTAAAGGTAAGAGTATTAGCGACAC
TTATGGGAAAACGCCGC
Found at i:126831 original size:57 final size:57
Alignment explanation
Indices: 126707--126815 Score: 141
Period size: 57 Copynumber: 1.9 Consensus size: 57
126697 TTTGCTACTC
* * *
126707 ATATGGAATTAGTTATTTGACTCAAATCTCCTTATATAGTAATAATATATATTAATCA
1 ATATGTAA-TAGTTAATTGACTCAAATCTCCTTATATACTAATAATATATATTAATCA
*
126765 ATATTTAATAGTTAATTGACTC-AATCTCC-TATTATACTAATATATATATAT
1 ATATGTAATAGTTAATTGACTCAAATCTCCTTA-TATACTAATA-ATATATAT
126816 ATATAGTAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
55 2 0.04
56 16 0.36
57 21 0.47
58 6 0.13
ACGTcount: A:0.39, C:0.11, G:0.06, T:0.43
Consensus pattern (57 bp):
ATATGTAATAGTTAATTGACTCAAATCTCCTTATATACTAATAATATATATTAATCA
Found at i:127691 original size:20 final size:20
Alignment explanation
Indices: 127662--127703 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
127652 TCCGTAAACG
127662 TGTTAAATTTGA-AAAAAATT
1 TGTTAAATTT-ATAAAAAATT
*
127682 TGTTATATTTATAAAAAATT
1 TGTTAAATTTATAAAAAATT
127702 TG
1 TG
127704 AAAATAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 1 0.05
20 19 0.95
ACGTcount: A:0.45, C:0.00, G:0.10, T:0.45
Consensus pattern (20 bp):
TGTTAAATTTATAAAAAATT
Found at i:127843 original size:42 final size:42
Alignment explanation
Indices: 127763--127854 Score: 109
Period size: 42 Copynumber: 2.2 Consensus size: 42
127753 GGGACAAATA
* *
127763 CCGCTAAAA-GTCAGAGCATTAGCGACGCTTGTAGGAAAAACG
1 CCGCTAAAATATCAGAGCATTAGCGACGCTTATAGG-AAAACG
* *
127805 CCGC-AAAATATCAGAGCATTAGTGTCGCTTAT-GAGAAAACG
1 CCGCTAAAATATCAGAGCATTAGCGACGCTTATAG-GAAAACG
127846 CCGCTAAAA
1 CCGCTAAAA
127855 GTTAAATAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
41 15 0.35
42 28 0.65
ACGTcount: A:0.37, C:0.22, G:0.23, T:0.18
Consensus pattern (42 bp):
CCGCTAAAATATCAGAGCATTAGCGACGCTTATAGGAAAACG
Found at i:130331 original size:8 final size:8
Alignment explanation
Indices: 130320--130443 Score: 60
Period size: 8 Copynumber: 15.4 Consensus size: 8
130310 AAATTAACAA
130320 ATTTAATT
1 ATTTAATT
130328 ATTTAATT
1 ATTTAATT
*
130336 ATTTAAAT
1 ATTTAATT
*
130344 GTTTAATT
1 ATTTAATT
* *
130352 A-CTAATAAC
1 ATTTAAT--T
130361 ATTTAATT
1 ATTTAATT
130369 A---AA-T
1 ATTTAATT
*
130373 ATTTAAAT
1 ATTTAATT
*
130381 ATTTAATA
1 ATTTAATT
130389 ATTTAATT
1 ATTTAATT
* **
130397 ATTAAAAAC
1 ATT-TAATT
* *
130406 ATCTCAAAT
1 AT-TTAATT
130415 ATTTAATT
1 ATTTAATT
130423 ATTTAATTAT
1 ATTTAA-T-T
130433 ATTTAATT
1 ATTTAATT
130441 ATT
1 ATT
130444 AAAAATAACC
Statistics
Matches: 87, Mismatches: 18, Indels: 22
0.69 0.14 0.17
Matches are distributed among these distances:
4 2 0.02
5 2 0.02
7 6 0.07
8 53 0.61
9 12 0.14
10 12 0.14
ACGTcount: A:0.44, C:0.04, G:0.01, T:0.51
Consensus pattern (8 bp):
ATTTAATT
Found at i:130384 original size:45 final size:42
Alignment explanation
Indices: 130327--130483 Score: 158
Period size: 44 Copynumber: 3.6 Consensus size: 42
130317 CAAATTTAAT
* * * *
130327 TATTTAATTATTTAAATGTTTAATTACTAATAACATTTAATTAAA
1 TATTTAAATATTTAAATATTTAATTATTAA-AACA--TAATCAAA
*
130372 TATTTAAATATTT-AATAATTTAATTATTAAAAACAT-CTCAAA
1 TATTTAAATATTTAAAT-ATTTAATTATT-AAAACATAATCAAA
* *
130414 TATTTAATTATTTAATTATATTTAATTATTAAAA-ATAACCCAAA
1 TATTTAAATATTTAA--ATATTTAATTATTAAAACATAA-TCAAA
130458 TATTTAAATATTTAAATATTTAATTA
1 TATTTAAATATTTAAATATTTAATTA
130484 GTTATTTATT
Statistics
Matches: 96, Mismatches: 9, Indels: 17
0.79 0.07 0.14
Matches are distributed among these distances:
42 29 0.30
43 6 0.06
44 32 0.33
45 27 0.28
46 2 0.02
ACGTcount: A:0.47, C:0.05, G:0.01, T:0.47
Consensus pattern (42 bp):
TATTTAAATATTTAAATATTTAATTATTAAAACATAATCAAA
Found at i:130388 original size:15 final size:16
Alignment explanation
Indices: 130373--130439 Score: 53
Period size: 18 Copynumber: 3.9 Consensus size: 16
130363 TTAATTAAAT
130373 ATTTAAATATTTAATA
1 ATTTAAATATTTAATA
* * *
130389 ATTTAATTATTAAAAA
1 ATTTAAATATTTAATA
* *
130405 CATCTCAAATATTTAATT
1 -AT-TTAAATATTTAATA
130423 ATTTAATTATATTTAAT
1 ATTTAA--ATATTTAAT
130440 TATTAAAAAT
Statistics
Matches: 38, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
16 16 0.42
17 4 0.11
18 18 0.47
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.49
Consensus pattern (16 bp):
ATTTAAATATTTAATA
Found at i:130458 original size:44 final size:43
Alignment explanation
Indices: 130369--130483 Score: 171
Period size: 44 Copynumber: 2.7 Consensus size: 43
130359 ACATTTAATT
* *
130369 AAATATTTAAATATTTAATA-ATTTAATTATTAAAAACATCTC
1 AAATATTTAAATATTTAATATATTTAATTATTAAAAACAACCC
* *
130411 AAATATTTAATTATTTAATTATATTTAATTATTAAAAATAACCC
1 AAATATTTAAATATTTAA-TATATTTAATTATTAAAAACAACCC
130455 AAATATTTAAATATTTAA-ATATTTAATTA
1 AAATATTTAAATATTTAATATATTTAATTA
130484 GTTATTTATT
Statistics
Matches: 66, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
42 28 0.42
43 2 0.03
44 36 0.55
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (43 bp):
AAATATTTAAATATTTAATATATTTAATTATTAAAAACAACCC
Found at i:130468 original size:8 final size:8
Alignment explanation
Indices: 130455--130480 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
130445 AAAATAACCC
130455 AAATATTT
1 AAATATTT
130463 AAATATTT
1 AAATATTT
130471 AAATATTT
1 AAATATTT
130479 AA
1 AA
130481 TTAGTTATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (8 bp):
AAATATTT
Found at i:130512 original size:50 final size:52
Alignment explanation
Indices: 130411--130519 Score: 150
Period size: 50 Copynumber: 2.1 Consensus size: 52
130401 AAAACATCTC
* * *
130411 AAATATTTAATTATTTAATTATATTTAATTATTAAAAATAACCCAAATATTT
1 AAATATTTAAATATTTAATTATAGTTAATTATTAAAAACAACCCAAATATTT
* *
130463 AAATATTTAAATATTTAA-T-TAGTTATTTATTAACAACAACCCAAATATTT
1 AAATATTTAAATATTTAATTATAGTTAATTATTAAAAACAACCCAAATATTT
*
130513 AATTATT
1 AAATATT
130520 AAAAACAACC
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
50 33 0.65
51 1 0.02
52 17 0.33
ACGTcount: A:0.47, C:0.07, G:0.01, T:0.45
Consensus pattern (52 bp):
AAATATTTAAATATTTAATTATAGTTAATTATTAAAAACAACCCAAATATTT
Found at i:130543 original size:27 final size:26
Alignment explanation
Indices: 130431--130546 Score: 110
Period size: 26 Copynumber: 4.5 Consensus size: 26
130421 TTATTTAATT
*
130431 ATATTTAATTATTAAAAATAACCCAA
1 ATATTTAATTATTAAAAACAACCCAA
* * * ***
130457 ATATTTAAATATT-TAAA-TATTTAA
1 ATATTTAATTATTAAAAACAACCCAA
* * * *
130481 TTAGTTATTTATTAACAACAACCCAA
1 ATATTTAATTATTAAAAACAACCCAA
130507 ATATTTAATTATTAAAAACAACCCGAA
1 ATATTTAATTATTAAAAACAACCC-AA
130534 ATATTTAATTATT
1 ATATTTAATTATT
130547 GAATTAGTTA
Statistics
Matches: 67, Mismatches: 20, Indels: 5
0.73 0.22 0.05
Matches are distributed among these distances:
24 12 0.18
25 5 0.07
26 35 0.52
27 15 0.22
ACGTcount: A:0.48, C:0.10, G:0.02, T:0.40
Consensus pattern (26 bp):
ATATTTAATTATTAAAAACAACCCAA
Found at i:135970 original size:43 final size:43
Alignment explanation
Indices: 135909--135990 Score: 164
Period size: 43 Copynumber: 1.9 Consensus size: 43
135899 GACTTATTAG
135909 GATAAATTAAAGGATAAGAAGGTGAAGTATGAAGCGATGGCTT
1 GATAAATTAAAGGATAAGAAGGTGAAGTATGAAGCGATGGCTT
135952 GATAAATTAAAGGATAAGAAGGTGAAGTATGAAGCGATG
1 GATAAATTAAAGGATAAGAAGGTGAAGTATGAAGCGATG
135991 ACTTCAAGTG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.44, C:0.04, G:0.30, T:0.22
Consensus pattern (43 bp):
GATAAATTAAAGGATAAGAAGGTGAAGTATGAAGCGATGGCTT
Found at i:136341 original size:21 final size:21
Alignment explanation
Indices: 136300--136365 Score: 78
Period size: 21 Copynumber: 3.1 Consensus size: 21
136290 CTACAACTTA
* * *
136300 AAGCGGAGGCAACAACAAGGG
1 AAGCGAAGGCAACAGCGAGGG
*
136321 AAGCGAAGGCAACAGTGAGGG
1 AAGCGAAGGCAACAGCGAGGG
* *
136342 AAGCGAAGGTAGCAGCGAGGG
1 AAGCGAAGGCAACAGCGAGGG
136363 AAG
1 AAG
136366 TAGAGACAAC
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.39, C:0.15, G:0.42, T:0.03
Consensus pattern (21 bp):
AAGCGAAGGCAACAGCGAGGG
Found at i:136731 original size:43 final size:42
Alignment explanation
Indices: 136676--136793 Score: 155
Period size: 43 Copynumber: 2.8 Consensus size: 42
136666 GCTTATGGGA
* *
136676 GAAAAGCGCTGCTAAAGACCATGTTCTTTAGTGATGTTTGTGG
1 GAAAAGCGCTGCTAAAGACCATGTTCTTTAGCGAGGTTTGT-G
* * * *
136719 GGAAAGTGCTGCTAAAGATCATGTTCTTTAGCGGGGTTTGTG
1 GAAAAGCGCTGCTAAAGACCATGTTCTTTAGCGAGGTTTGTG
* *
136761 GAAAAGCGCCGCTAAAGACCATGTTCTATAGCG
1 GAAAAGCGCTGCTAAAGACCATGTTCTTTAGCG
136794 GAGTTTTTCT
Statistics
Matches: 64, Mismatches: 11, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
42 29 0.45
43 35 0.55
ACGTcount: A:0.26, C:0.16, G:0.29, T:0.29
Consensus pattern (42 bp):
GAAAAGCGCTGCTAAAGACCATGTTCTTTAGCGAGGTTTGTG
Found at i:136793 original size:42 final size:43
Alignment explanation
Indices: 136676--136799 Score: 162
Period size: 42 Copynumber: 2.9 Consensus size: 43
136666 GCTTATGGGA
*
136676 GAAAAGCGCTGCTAAAGACCATGTTCTTTAG-TGATGTTTGTGG
1 GAAAAGCGCTGCTAAAGACCATGTTCTTTAGCGGA-GTTTGTGG
* * * *
136719 GGAAAGTGCTGCTAAAGATCATGTTCTTTAGCGGGGTTTGT-G
1 GAAAAGCGCTGCTAAAGACCATGTTCTTTAGCGGAGTTTGTGG
* *
136761 GAAAAGCGCCGCTAAAGACCATGTTCTATAGCGGAGTTT
1 GAAAAGCGCTGCTAAAGACCATGTTCTTTAGCGGAGTTT
136800 TTCTTAATAA
Statistics
Matches: 69, Mismatches: 11, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
42 34 0.49
43 34 0.49
44 1 0.01
ACGTcount: A:0.26, C:0.15, G:0.29, T:0.30
Consensus pattern (43 bp):
GAAAAGCGCTGCTAAAGACCATGTTCTTTAGCGGAGTTTGTGG
Found at i:137280 original size:9 final size:9
Alignment explanation
Indices: 137266--137302 Score: 56
Period size: 9 Copynumber: 4.0 Consensus size: 9
137256 TCACTTAAAT
137266 CTCTCTCAA
1 CTCTCTCAA
137275 CTCTCTCAA
1 CTCTCTCAA
*
137284 CTTTCTCAAA
1 CTCTCTC-AA
137294 CTCTCTCAA
1 CTCTCTCAA
137303 ATCCATTACC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
9 17 0.68
10 8 0.32
ACGTcount: A:0.24, C:0.41, G:0.00, T:0.35
Consensus pattern (9 bp):
CTCTCTCAA
Found at i:138635 original size:25 final size:25
Alignment explanation
Indices: 138607--138668 Score: 65
Period size: 25 Copynumber: 2.5 Consensus size: 25
138597 TATTAAATTA
*
138607 AATATAATATTAAGATAATCACT-TT
1 AATATAATATTAAGAAAAT-ACTATT
*
138632 AATATTAA-ATTAATAAAATACTATT
1 AATA-TAATATTAAGAAAATACTATT
*
138657 AAAATAATATTA
1 AATATAATATTA
138669 TCTTTGGAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
24 6 0.19
25 22 0.71
26 3 0.10
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.39
Consensus pattern (25 bp):
AATATAATATTAAGAAAATACTATT
Found at i:138645 original size:20 final size:18
Alignment explanation
Indices: 138595--138666 Score: 58
Period size: 19 Copynumber: 3.9 Consensus size: 18
138585 ATACAAGATA
138595 AATATTAAATTAA-ATAT
1 AATATTAAATTAATATAT
*
138612 AATATTAAGA-TAATCACTTT
1 AATATTAA-ATTAAT-A-TAT
*
138632 AATATTAAATTAATAAAAT
1 AATATTAAATTAAT-ATAT
* *
138651 ACTATTAAAATAATAT
1 AATATTAAATTAATAT
138667 TATCTTTGGA
Statistics
Matches: 43, Mismatches: 7, Indels: 9
0.73 0.12 0.15
Matches are distributed among these distances:
17 11 0.26
18 2 0.05
19 15 0.35
20 15 0.35
ACGTcount: A:0.56, C:0.04, G:0.01, T:0.39
Consensus pattern (18 bp):
AATATTAAATTAATATAT
Found at i:144420 original size:15 final size:15
Alignment explanation
Indices: 144402--144478 Score: 70
Period size: 15 Copynumber: 5.1 Consensus size: 15
144392 AATATGCAAG
144402 CACTAGTGTTGCGAA
1 CACTAGTGTTGCGAA
144417 CACTCA-TGTTGCGAA
1 CACT-AGTGTTGCGAA
* *
144432 CACT-GAAGTTGTGAA
1 CACTAG-TGTTGCGAA
* *
144447 CACTAGTGTTGTGAG
1 CACTAGTGTTGCGAA
144462 CACTCA-TGTTGCGAA
1 CACT-AGTGTTGCGAA
144477 CA
1 CA
144479 ATGGAGCTGC
Statistics
Matches: 51, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
15 48 0.94
16 3 0.06
ACGTcount: A:0.27, C:0.21, G:0.25, T:0.27
Consensus pattern (15 bp):
CACTAGTGTTGCGAA
Found at i:144457 original size:30 final size:30
Alignment explanation
Indices: 144408--144520 Score: 86
Period size: 30 Copynumber: 3.8 Consensus size: 30
144398 CAAGCACTAG
*
144408 TGTTGCGAACACTCA-TGTTGCGAACACTGA
1 TGTTGCGAACACT-AGTGTTGCGAACACTCA
* * * *
144438 AGTTGTGAACACTAGTGTTGTGAGCACTCA
1 TGTTGCGAACACTAGTGTTGCGAACACTCA
* * * * *
144468 TGTTGCGAACAATGGAGCTGC-AAGCACTTA
1 TGTTGCGAACACTAGTGTTGCGAA-CACTCA
* *
144498 TGTTGTGAACACTCGTGTTGCGA
1 TGTTGCGAACACTAGTGTTGCGA
144521 CCATGGATGA
Statistics
Matches: 61, Mismatches: 19, Indels: 5
0.72 0.22 0.06
Matches are distributed among these distances:
29 2 0.03
30 58 0.95
31 1 0.02
ACGTcount: A:0.26, C:0.19, G:0.27, T:0.28
Consensus pattern (30 bp):
TGTTGCGAACACTAGTGTTGCGAACACTCA
Found at i:144502 original size:45 final size:45
Alignment explanation
Indices: 144396--144520 Score: 155
Period size: 45 Copynumber: 2.8 Consensus size: 45
144386 GCTTGGAATA
* * *
144396 TGCAAGCACTAGTGTTGCGAACACTCATGTTGCGAACACTGAAGT
1 TGCAAGCACTAGTGTTGTGAACACTCATGTTGCGAACAATGAAGC
* * *
144441 TGTGAA-CACTAGTGTTGTGAGCACTCATGTTGCGAACAATGGAGC
1 TG-CAAGCACTAGTGTTGTGAACACTCATGTTGCGAACAATGAAGC
*
144486 TGCAAGCACTTA-TGTTGTGAACACTCGTGTTGCGA
1 TGCAAGCAC-TAGTGTTGTGAACACTCATGTTGCGA
144521 CCATGGATGA
Statistics
Matches: 68, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
44 2 0.03
45 62 0.91
46 4 0.06
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.27
Consensus pattern (45 bp):
TGCAAGCACTAGTGTTGTGAACACTCATGTTGCGAACAATGAAGC
Found at i:145907 original size:10 final size:10
Alignment explanation
Indices: 145892--145921 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
145882 AATTTGTATC
145892 AAAAAAAGAA
1 AAAAAAAGAA
145902 AAAAAAAGAA
1 AAAAAAAGAA
*
145912 AAAAGAAGAA
1 AAAAAAAGAA
145922 GAAGAAGAGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (10 bp):
AAAAAAAGAA
Found at i:162956 original size:15 final size:15
Alignment explanation
Indices: 162938--163058 Score: 97
Period size: 15 Copynumber: 8.1 Consensus size: 15
162928 TAGTATTGTA
*
162938 AACACTCATGTTGCG
1 AACACTGATGTTGCG
* *
162953 AACATTGGA-GCTGCG
1 AACACT-GATGTTGCG
*
162968 AACACTGATGTTGTG
1 AACACTGATGTTGCG
162983 AACACT-AGTGTTGCG
1 AACACTGA-TGTTGCG
* *
162998 AGCACTCATGTTGCG
1 AACACTGATGTTGCG
* *
163013 AACAATGGA-GCTGCG
1 AACACT-GATGTTGCG
*
163028 AACACTGATGTTGTG
1 AACACTGATGTTGCG
163043 AACACTCG-TGTTGCG
1 AACACT-GATGTTGCG
163058 A
1 A
163059 GCATGGATGA
Statistics
Matches: 83, Mismatches: 16, Indels: 14
0.73 0.14 0.12
Matches are distributed among these distances:
14 5 0.06
15 74 0.89
16 4 0.05
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (15 bp):
AACACTGATGTTGCG
Found at i:162972 original size:30 final size:30
Alignment explanation
Indices: 162938--163046 Score: 128
Period size: 30 Copynumber: 3.6 Consensus size: 30
162928 TAGTATTGTA
*
162938 AACACTCATGTTGCGAACATTGGAGCTGCG
1 AACACTCATGTTGCGAACAATGGAGCTGCG
* * * * * *
162968 AACACTGATGTTGTGAACACTAGTGTTGCG
1 AACACTCATGTTGCGAACAATGGAGCTGCG
*
162998 AGCACTCATGTTGCGAACAATGGAGCTGCG
1 AACACTCATGTTGCGAACAATGGAGCTGCG
* *
163028 AACACTGATGTTGTGAACA
1 AACACTCATGTTGCGAACA
163047 CTCGTGTTGC
Statistics
Matches: 63, Mismatches: 16, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
30 63 1.00
ACGTcount: A:0.28, C:0.20, G:0.27, T:0.25
Consensus pattern (30 bp):
AACACTCATGTTGCGAACAATGGAGCTGCG
Found at i:163022 original size:60 final size:60
Alignment explanation
Indices: 162940--163061 Score: 226
Period size: 60 Copynumber: 2.0 Consensus size: 60
162930 GTATTGTAAA
*
162940 CACTCATGTTGCGAACATTGGAGCTGCGAACACTGATGTTGTGAACACTAGTGTTGCGAG
1 CACTCATGTTGCGAACAATGGAGCTGCGAACACTGATGTTGTGAACACTAGTGTTGCGAG
*
163000 CACTCATGTTGCGAACAATGGAGCTGCGAACACTGATGTTGTGAACACTCGTGTTGCGAG
1 CACTCATGTTGCGAACAATGGAGCTGCGAACACTGATGTTGTGAACACTAGTGTTGCGAG
163060 CA
1 CA
163062 TGGATGAAGG
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
60 60 1.00
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.25
Consensus pattern (60 bp):
CACTCATGTTGCGAACAATGGAGCTGCGAACACTGATGTTGTGAACACTAGTGTTGCGAG
Found at i:163058 original size:30 final size:30
Alignment explanation
Indices: 162964--163058 Score: 118
Period size: 30 Copynumber: 3.2 Consensus size: 30
162954 ACATTGGAGC
162964 TGCGAACACTGATGTTGTGAACACTAGTGT
1 TGCGAACACTGATGTTGTGAACACTAGTGT
* * * * * * *
162994 TGCGAGCACTCATGTTGCGAACAATGGAGC
1 TGCGAACACTGATGTTGTGAACACTAGTGT
*
163024 TGCGAACACTGATGTTGTGAACACTCGTGT
1 TGCGAACACTGATGTTGTGAACACTAGTGT
163054 TGCGA
1 TGCGA
163059 GCATGGATGA
Statistics
Matches: 51, Mismatches: 14, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
30 51 1.00
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.26
Consensus pattern (30 bp):
TGCGAACACTGATGTTGTGAACACTAGTGT
Found at i:165366 original size:32 final size:32
Alignment explanation
Indices: 165329--165389 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
165319 AAACCTTGAG
165329 ATTCTTAAGATATTTGAAAAATAAGGATCACA
1 ATTCTTAAGATATTTGAAAAATAAGGATCACA
** *
165361 ATTCTTGGGATATTTGAAAAATGAGGATC
1 ATTCTTAAGATATTTGAAAAATAAGGATC
165390 GGGATTATTG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.41, C:0.08, G:0.18, T:0.33
Consensus pattern (32 bp):
ATTCTTAAGATATTTGAAAAATAAGGATCACA
Found at i:166160 original size:22 final size:23
Alignment explanation
Indices: 166122--166167 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
166112 AGCATTATTT
*
166122 ATTAAACAAAGAAAAGGAACGCC
1 ATTAAACAAAGAAAAGGAAAGCC
*
166145 ATTAAAC-ATGAAAAGGAAAGCC
1 ATTAAACAAAGAAAAGGAAAGCC
166167 A
1 A
166168 AATCCATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.57, C:0.15, G:0.17, T:0.11
Consensus pattern (23 bp):
ATTAAACAAAGAAAAGGAAAGCC
Found at i:168793 original size:20 final size:20
Alignment explanation
Indices: 168765--168803 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
168755 TACTGGAAAG
*
168765 TAAATTTAATTCTAAAAAAA
1 TAAAATTAATTCTAAAAAAA
*
168785 TAAAATTAATTTTAAAAAA
1 TAAAATTAATTCTAAAAAA
168804 TAGATGAGTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (20 bp):
TAAAATTAATTCTAAAAAAA
Found at i:175434 original size:18 final size:19
Alignment explanation
Indices: 175402--175440 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
175392 AAAATTAAAT
* *
175402 AATTTAAAATAATTTTTAA
1 AATTAAAAATAATTTATAA
175421 AATTAAAAAT-ATTTATAA
1 AATTAAAAATAATTTATAA
175439 AA
1 AA
175441 ATACCAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
AATTAAAAATAATTTATAA
Found at i:175441 original size:19 final size:19
Alignment explanation
Indices: 175396--175442 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 19
175386 TCAATAAAAA
*
175396 TTAAATAATTTAAAATAATT
1 TTAAA-AATTAAAAATAATT
*
175416 TTTAAAATTAAAAAT-ATT
1 TTAAAAATTAAAAATAATT
175434 TATAAAAAT
1 T-TAAAAAT
175443 ACCAAAATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
18 4 0.17
19 15 0.65
20 4 0.17
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
TTAAAAATTAAAAATAATT
Found at i:180322 original size:20 final size:18
Alignment explanation
Indices: 180280--180337 Score: 75
Period size: 17 Copynumber: 3.3 Consensus size: 18
180270 TCAAAAATCA
180280 TATGATGAAAATATTATT
1 TATGATGAAAATATTATT
180298 T-TGATGAAAATATTATT
1 TATGATGAAAATATTATT
* *
180315 T-TGATGATATATTTTATT
1 TATGATGA-AAATATTATT
180333 TATGA
1 TATGA
180338 AATTAATTTG
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
17 23 0.64
18 10 0.28
19 3 0.08
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (18 bp):
TATGATGAAAATATTATT
Found at i:180333 original size:18 final size:17
Alignment explanation
Indices: 180282--180321 Score: 80
Period size: 17 Copynumber: 2.4 Consensus size: 17
180272 AAAAATCATA
180282 TGATGAAAATATTATTT
1 TGATGAAAATATTATTT
180299 TGATGAAAATATTATTT
1 TGATGAAAATATTATTT
180316 TGATGA
1 TGATGA
180322 TATATTTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.40, C:0.00, G:0.15, T:0.45
Consensus pattern (17 bp):
TGATGAAAATATTATTT
Found at i:182313 original size:33 final size:34
Alignment explanation
Indices: 182257--182334 Score: 115
Period size: 33 Copynumber: 2.4 Consensus size: 34
182247 TAGATTTTGA
*
182257 AACC-ATTAACTCTTTTTTCTTTTTGGTTACATG
1 AACCAATTAACTCTCTTTTCTTTTTGGTTACATG
* *
182290 AACCAATTAATTCTCTTTT-TTTTTTGTTACATG
1 AACCAATTAACTCTCTTTTCTTTTTGGTTACATG
182323 AACCAATTAACT
1 AACCAATTAACT
182335 TGGATACATA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
33 28 0.70
34 12 0.30
ACGTcount: A:0.27, C:0.18, G:0.06, T:0.49
Consensus pattern (34 bp):
AACCAATTAACTCTCTTTTCTTTTTGGTTACATG
Found at i:182495 original size:27 final size:26
Alignment explanation
Indices: 182445--182508 Score: 101
Period size: 27 Copynumber: 2.4 Consensus size: 26
182435 AAATATTCTC
182445 TAAATTAATAAATATTAATTTATCGA
1 TAAATTAATAAATATTAATTTATCGA
*
182471 TAAATTAATAAATTATTTATTTATCGA
1 TAAATTAATAAA-TATTAATTTATCGA
*
182498 TAAACTAATAA
1 TAAATTAATAA
182509 CATCGAAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
26 12 0.34
27 23 0.66
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (26 bp):
TAAATTAATAAATATTAATTTATCGA
Found at i:187942 original size:21 final size:22
Alignment explanation
Indices: 187909--187949 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
187899 TGAATCCAAA
*
187909 TTTAGGTCCTTTTT-TTTCTAC
1 TTTAGATCCTTTTTATTTCTAC
*
187930 TTTAGATCTTTTTTATTTCT
1 TTTAGATCCTTTTTATTTCT
187950 TTTCATTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.12, C:0.15, G:0.07, T:0.66
Consensus pattern (22 bp):
TTTAGATCCTTTTTATTTCTAC
Found at i:188225 original size:21 final size:21
Alignment explanation
Indices: 188201--188241 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
188191 CTAATTCTTT
188201 TAATTTCTATATCTTTTAAAA
1 TAATTTCTATATCTTTTAAAA
* *
188222 TAATTTCTTTATTTTTTAAA
1 TAATTTCTATATCTTTTAAA
188242 GATTTAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.34, C:0.07, G:0.00, T:0.59
Consensus pattern (21 bp):
TAATTTCTATATCTTTTAAAA
Found at i:188256 original size:96 final size:94
Alignment explanation
Indices: 188146--188391 Score: 275
Period size: 96 Copynumber: 2.6 Consensus size: 94
188136 AACAAAAAAG
188146 AGATTTTAAATCTTTTTTATTAATCATTTCTATCCGTTTTTAAATCTAATTCTTTTAATTTCTAT
1 AGATTTTAAATCTTTTTTATTAATCATTTCTATCCGTTTTTAAATCTAATTCTTTTAATTTCTAT
**
188211 ATCTTTTAAAATAATTTCTTTATTTTTTAA
66 ATCTTTTAAAATAATCCCTTTATTTTTT-A
* * * * * *
188241 AGATTTAAAAT-TCTTTTATTAACCATCTCT-GCCTGTATCTTTTAAATCTAATTCTTTT-TTTT
1 AGATTTTAAATCTTTTTTATTAATCATTTCTATCC-G--T-TTTTAAATCTAATTCTTTTAATTT
* * *
188303 TTATTTCTTTTAAAATAATCCCTTTATTTTTTT
62 CTATATCTTTTAAAATAATCCCTTTATTTTTTA
* * * * *
188336 AGATTTTAAATCTTTTTTATTTATCATTTTTAT-CTTTTTTTAATTTAATTCTTTTA
1 AGATTTTAAATCTTTTTTATTAATCATTTCTATCCGTTTTTAAATCTAATTCTTTTA
188392 CTTTTTTATC
Statistics
Matches: 123, Mismatches: 21, Indels: 16
0.77 0.13 0.10
Matches are distributed among these distances:
92 17 0.14
93 3 0.02
94 17 0.14
95 20 0.16
96 47 0.38
97 19 0.15
ACGTcount: A:0.27, C:0.11, G:0.02, T:0.59
Consensus pattern (94 bp):
AGATTTTAAATCTTTTTTATTAATCATTTCTATCCGTTTTTAAATCTAATTCTTTTAATTTCTAT
ATCTTTTAAAATAATCCCTTTATTTTTTA
Found at i:194806 original size:49 final size:49
Alignment explanation
Indices: 194753--195291 Score: 239
Period size: 49 Copynumber: 11.0 Consensus size: 49
194743 GATGAACTTT
* *
194753 GTACCTCAGAAACATGAAGGGGAAGATTTAAGCCGCGATGGCGAATCTA
1 GTACCTCAGAAACATGAAGGGAAAGATTTAAGCCGCAATGGCGAATCTA
* * * * ** * ** * *
194802 GTA-C-CATGAAGATATGGAGGGAAAGGTTTATGTTGCAACGATGAACCTT
1 GTACCTCA-GAA-ACATGAAGGGAAAGATTTAAGCCGCAATGGCGAATCTA
* * *
194851 GTACCTCAGAAACATGAAGGGAAAGATTTCAGCCGCAACGACGAATCTA
1 GTACCTCAGAAACATGAAGGGAAAGATTTAAGCCGCAATGGCGAATCTA
* * * * * **** * ** * *
194900 ATTCCAC-GAAGATATGAAGGGAAAGGTTTAAGTTATAACGATGAACCTG
1 GTACCTCAGAA-ACATGAAGGGAAAGATTTAAGCCGCAATGGCGAATCTA
* * *
194949 GTACATCAAAAACATGAAGGGAAAGATTTAAGCCGCAATAGCGAATCTA
1 GTACCTCAGAAACATGAAGGGAAAGATTTAAGCCGCAATGGCGAATCTA
* * * * * * ** * *
194998 ATACCAC-GAAGATATGGAGGGAAAGGTTCAATTCACAATGGCGAACCTTA
1 GTACCTCAGAA-ACATGAAGGGAAAGATTTAAGCCGCAATGGCGAATC-TA
* * *
195048 -TACCTCAGAAACATGAAGGAAAATATTTAAGCCGCAATGGCGAATCTG
1 GTACCTCAGAAACATGAAGGGAAAGATTTAAGCCGCAATGGCGAATCTA
* * * * * * * * * *
195096 GTACCAC-GAAGATATGGAGGGAAAGGTTTAAGTCGTAACGGTGAACCTG
1 GTACCTCAGAA-ACATGAAGGGAAAGATTTAAGCCGCAATGGCGAATCTA
** ** * * *
195145 GTACCTCAGAAACATGTTGGGAAAGATGGAAGCCGCAACGACGAATCTG
1 GTACCTCAGAAACATGAAGGGAAAGATTTAAGCCGCAATGGCGAATCTA
* * * * * * * *
195194 GTA-C-CATGAATATATGAAGGGAAAGGTTTAAGTCGTAACGACGAACCTT
1 GTACCTCA-GAA-ACATGAAGGGAAAGATTTAAGCCGCAATGGCGAATCTA
* ** * * * *
195243 GTACCTCAAAAATTTGACAGGGAAAGATTGAAGCCACAACGGTGAATCT
1 GTACCTCAGAAACATGA-AGGGAAAGATTTAAGCCGCAATGGCGAATCT
195292 TATACCCTGA
Statistics
Matches: 352, Mismatches: 121, Indels: 33
0.70 0.24 0.07
Matches are distributed among these distances:
47 4 0.01
48 17 0.05
49 287 0.82
50 40 0.11
51 4 0.01
ACGTcount: A:0.37, C:0.17, G:0.25, T:0.21
Consensus pattern (49 bp):
GTACCTCAGAAACATGAAGGGAAAGATTTAAGCCGCAATGGCGAATCTA
Found at i:194877 original size:98 final size:98
Alignment explanation
Indices: 194705--195291 Score: 688
Period size: 98 Copynumber: 6.0 Consensus size: 98
194695 CATGTTTCAT
* *
194705 TACCACGAAGATATGGAGGGAAAGGTTTAAGTTGCAACGATGAACTTTGTACCTCAGAAACATGA
1 TACCACGAAGATATGGAGGGAAAGGTTTAAGTCGCAACGATGAACCTTGTACCTCAGAAACATGA
* *
194770 AGGGGAAGATTTAAGCCGCGATGGCGAATCTAG
66 AGGGAAAGATTTAAGCCGCAATGGCGAATCTAG
* * *
194803 TACCATGAAGATATGGAGGGAAAGGTTTATGTTGCAACGATGAACCTTGTACCTCAGAAACATGA
1 TACCACGAAGATATGGAGGGAAAGGTTTAAGTCGCAACGATGAACCTTGTACCTCAGAAACATGA
* * * *
194868 AGGGAAAGATTTCAGCCGCAACGACGAATCTAA
66 AGGGAAAGATTTAAGCCGCAATGGCGAATCTAG
* * *** * * *
194901 TTCCACGAAGATATGAAGGGAAAGGTTTAAGTTATAACGATGAACCTGGTACATCAAAAACATGA
1 TACCACGAAGATATGGAGGGAAAGGTTTAAGTCGCAACGATGAACCTTGTACCTCAGAAACATGA
* *
194966 AGGGAAAGATTTAAGCCGCAATAGCGAATCTAA
66 AGGGAAAGATTTAAGCCGCAATGGCGAATCTAG
* * * * ** *
194999 TACCACGAAGATATGGAGGGAAAGGTTCAATTCACAATGGCGAACCTTATACCTCAGAAACATGA
1 TACCACGAAGATATGGAGGGAAAGGTTTAAGTCGCAACGATGAACCTTGTACCTCAGAAACATGA
* * *
195064 AGGAAAATATTTAAGCCGCAATGGCGAATCTGG
66 AGGGAAAGATTTAAGCCGCAATGGCGAATCTAG
* * * *
195097 TACCACGAAGATATGGAGGGAAAGGTTTAAGTCGTAACGGTGAACCTGGTACCTCAGAAACATGT
1 TACCACGAAGATATGGAGGGAAAGGTTTAAGTCGCAACGATGAACCTTGTACCTCAGAAACATGA
* ** * * *
195162 TGGGAAAGATGGAAGCCGCAACGACGAATCTGG
66 AGGGAAAGATTTAAGCCGCAATGGCGAATCTAG
* * * * * * **
195195 TACCATGAATATATGAAGGGAAAGGTTTAAGTCGTAACGACGAACCTTGTACCTCAAAAATTTGA
1 TACCACGAAGATATGGAGGGAAAGGTTTAAGTCGCAACGATGAACCTTGTACCTCAGAAACATGA
* * * *
195260 CAGGGAAAGATTGAAGCCACAACGGTGAATCT
66 -AGGGAAAGATTTAAGCCGCAATGGCGAATCT
195292 TATACCCTGA
Statistics
Matches: 417, Mismatches: 71, Indels: 1
0.85 0.15 0.00
Matches are distributed among these distances:
98 391 0.94
99 26 0.06
ACGTcount: A:0.37, C:0.17, G:0.25, T:0.21
Consensus pattern (98 bp):
TACCACGAAGATATGGAGGGAAAGGTTTAAGTCGCAACGATGAACCTTGTACCTCAGAAACATGA
AGGGAAAGATTTAAGCCGCAATGGCGAATCTAG
Found at i:199195 original size:17 final size:16
Alignment explanation
Indices: 199162--199199 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
199152 CAACTCAAAC
*
199162 TTTTCCTTTATTTTTA
1 TTTTACTTTATTTTTA
199178 TTTTACTTTATCTTTTA
1 TTTTACTTTAT-TTTTA
199195 TTTTA
1 TTTTA
199200 TGCTTTGTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 10 0.50
17 10 0.50
ACGTcount: A:0.16, C:0.11, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTTACTTTATTTTTA
Found at i:202285 original size:19 final size:20
Alignment explanation
Indices: 202247--202285 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
202237 ATGACTGAAT
*
202247 TCTTTTGTGGTTTCTCAAGA
1 TCTTTTGTGGCTTCTCAAGA
*
202267 TCTTTTGTTGCTT-TCAAGA
1 TCTTTTGTGGCTTCTCAAGA
202286 GAAGGGTAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.15, C:0.15, G:0.18, T:0.51
Consensus pattern (20 bp):
TCTTTTGTGGCTTCTCAAGA
Found at i:211382 original size:2 final size:2
Alignment explanation
Indices: 211377--211424 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
211367 TATTTTATTT
211377 TA TA TA -A TA TA 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 TA TA
211418 TA TA TA T
1 TA TA TA T
211425 TTGCATTTGA
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 44 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:218109 original size:23 final size:23
Alignment explanation
Indices: 218045--218111 Score: 68
Period size: 25 Copynumber: 2.9 Consensus size: 23
218035 AATACTCGAA
218045 TTTTTTTCTTC-TTTTC-AATCT
1 TTTTTTTCTTCTTTTTCAAATCT
*
218066 TTTTTTTCTTTTTTTAATTCAAAT-T
1 TTTTTTTC-TTCTTT--TTCAAATCT
218091 TTTTTCTTCTTCTTTTTCAAA
1 TTTTT-TTCTTCTTTTTCAAA
218112 CTTCAAATTT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
21 8 0.21
22 2 0.05
23 8 0.21
25 14 0.37
26 6 0.16
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.70
Consensus pattern (23 bp):
TTTTTTTCTTCTTTTTCAAATCT
Found at i:219457 original size:50 final size:50
Alignment explanation
Indices: 219380--219517 Score: 154
Period size: 50 Copynumber: 2.7 Consensus size: 50
219370 TGCATGACTT
* *
219380 GATTTAATGATGCAAACTTTAACTAACATGGGAGTTACATAATGTATG-ATAG
1 GATTT-ATGATGCAAA-TTTAACTAACATGAGAGTTACATAATGCATGTA-AG
* * *
219432 GATTTATGATGCATATTTAACTAACATGTA-AGTTACTTAATGCATGTAAT
1 GATTTATGATGCAAATTTAACTAACATG-AGAGTTACATAATGCATGTAAG
* *
219482 TATTTATGATGCAAACTTAACTAATCATGAGAGTTA
1 GATTTATGATGCAAATTTAACTAA-CATGAGAGTTA
219518 ATGGATGTCA
Statistics
Matches: 74, Mismatches: 8, Indels: 9
0.81 0.09 0.10
Matches are distributed among these distances:
50 50 0.68
51 19 0.26
52 5 0.07
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (50 bp):
GATTTATGATGCAAATTTAACTAACATGAGAGTTACATAATGCATGTAAG
Found at i:221770 original size:50 final size:50
Alignment explanation
Indices: 221687--221807 Score: 145
Period size: 50 Copynumber: 2.4 Consensus size: 50
221677 AGGAAAATGG
*
221687 TGCAAACTTTAACTAACATGGGAGTTACATAATGCATG-ATAGGATTTATGA
1 TGCAAA-TTTAACTAACATGGAAGTTACATAATGCATGTA-AGGATTTATGA
* * * **
221738 TGCATATTTAACTAACATGTAAGTTACTTAATGCATGTAATTATTTATGA
1 TGCAAATTTAACTAACATGGAAGTTACATAATGCATGTAAGGATTTATGA
*
221788 TGCAAACTTAACTAATCATG
1 TGCAAATTTAACTAA-CATG
221808 AGAGTTAATG
Statistics
Matches: 60, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
50 50 0.83
51 10 0.17
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.36
Consensus pattern (50 bp):
TGCAAATTTAACTAACATGGAAGTTACATAATGCATGTAAGGATTTATGA
Found at i:222040 original size:17 final size:17
Alignment explanation
Indices: 222009--222041 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
221999 CAAACACTTA
222009 TTAAACTAAAATAAAAC
1 TTAAACTAAAATAAAAC
222026 TTAAA-TAAAATTAAAA
1 TTAAACTAAAA-TAAAA
222042 AGTCCTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (17 bp):
TTAAACTAAAATAAAAC
Found at i:222940 original size:28 final size:27
Alignment explanation
Indices: 222874--222952 Score: 86
Period size: 28 Copynumber: 2.8 Consensus size: 27
222864 TGACCATCGC
*
222874 AAAAAATTTAAAATATTAAAAATGGTAA
1 AAAAAATTTAAAATA-TAAAAATGGCAA
* *
222902 AAAAAAATTAAAATATAAAAATTGCAA
1 AAAAAATTTAAAATATAAAAATGGCAA
*
222929 AATAATATTTAAAATTAATAAAAA
1 AA-AAAATTTAAAA-T-ATAAAAA
222953 ATTATATATT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
27 12 0.28
28 23 0.53
29 1 0.02
30 7 0.16
ACGTcount: A:0.67, C:0.01, G:0.04, T:0.28
Consensus pattern (27 bp):
AAAAAATTTAAAATATAAAAATGGCAA
Found at i:223960 original size:20 final size:19
Alignment explanation
Indices: 223937--224030 Score: 75
Period size: 20 Copynumber: 4.8 Consensus size: 19
223927 ATATTTTTTT
223937 TAATTATTTACAATTTTAAA
1 TAATT-TTTACAATTTTAAA
* *
223957 TAATGTTTTATAATTTTTAA
1 TAAT-TTTTACAATTTTAAA
* *
223977 TATTTTTTTACAATTTT-TA
1 TA-ATTTTTACAATTTTAAA
* *
223996 TAA-TTTTAGTAACTTTAAA
1 TAATTTTTA-CAATTTTAAA
*
224015 TATTTTTTACAATTTT
1 TAATTTTTACAATTTT
224031 TATACGTTTT
Statistics
Matches: 57, Mismatches: 12, Indels: 11
0.71 0.15 0.14
Matches are distributed among these distances:
17 5 0.09
18 5 0.09
19 11 0.19
20 34 0.60
21 2 0.04
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.59
Consensus pattern (19 bp):
TAATTTTTACAATTTTAAA
Found at i:223969 original size:10 final size:9
Alignment explanation
Indices: 223931--224034 Score: 57
Period size: 9 Copynumber: 10.9 Consensus size: 9
223921 CAATCCATAT
*
223931 TTTTTTTAA
1 TTTTTATAA
*
223940 TTATTTACAA
1 TT-TTTATAA
*
223950 TTTTAAATAA
1 TTTT-TATAA
223960 TGTTTTATAA
1 T-TTTTATAA
*
223970 TTTTTAATATT
1 TTTTT-ATA-A
*
223981 TTTTTACAA
1 TTTTTATAA
223990 TTTTTATAA
1 TTTTTATAA
223999 -TTTTAGTAA
1 TTTTTA-TAA
** *
224008 CTTTAAATAT
1 -TTTTTATAA
*
224018 TTTTTACAA
1 TTTTTATAA
224027 TTTTTATA
1 TTTTTATA
224035 CGTTTTAAAT
Statistics
Matches: 70, Mismatches: 17, Indels: 16
0.68 0.17 0.16
Matches are distributed among these distances:
8 5 0.07
9 31 0.44
10 23 0.33
11 11 0.16
ACGTcount: A:0.34, C:0.04, G:0.02, T:0.61
Consensus pattern (9 bp):
TTTTTATAA
Found at i:224003 original size:37 final size:37
Alignment explanation
Indices: 223943--224060 Score: 114
Period size: 37 Copynumber: 3.1 Consensus size: 37
223933 TTTTTAATTA
*
223943 TTTACAATTTTAAATAATGTTTTATAATTTTTAATATTTT
1 TTTACAATTTT-TATAA--TTTTATAATTTTTAATATTTT
* *
223983 TTTACAATTTTTATAATTTTAGTAACTTTAAATA-TTT
1 TTTACAATTTTTATAATTTTA-TAATTTTTAATATTTT
* * * *
224020 TTTACAATTTTTATACGTTTTA-AATATTTAAAATATT
1 TTTACAATTTTTATA-ATTTTATAATTTTTAATATTTT
224057 TTTA
1 TTTA
224061 TGCATTTTAA
Statistics
Matches: 66, Mismatches: 9, Indels: 9
0.79 0.11 0.11
Matches are distributed among these distances:
36 7 0.11
37 29 0.44
38 15 0.23
39 4 0.06
40 11 0.17
ACGTcount: A:0.36, C:0.04, G:0.03, T:0.58
Consensus pattern (37 bp):
TTTACAATTTTTATAATTTTATAATTTTTAATATTTT
Found at i:224032 original size:29 final size:27
Alignment explanation
Indices: 223990--224048 Score: 66
Period size: 29 Copynumber: 2.1 Consensus size: 27
223980 TTTTTTACAA
*
223990 TTTTTATAATTTTAGTAAC-TTTAAATAT
1 TTTTTACAATTTTA-T-ACGTTTAAATAT
224018 TTTTTACAATTTTTATACGTTTTAAATAT
1 TTTTTACAA-TTTTATACG-TTTAAATAT
224047 TT
1 TT
224049 AAAATATTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
27 2 0.07
28 9 0.33
29 16 0.59
ACGTcount: A:0.32, C:0.05, G:0.03, T:0.59
Consensus pattern (27 bp):
TTTTTACAATTTTATACGTTTAAATAT
Found at i:224205 original size:9 final size:9
Alignment explanation
Indices: 224193--224297 Score: 85
Period size: 9 Copynumber: 11.7 Consensus size: 9
224183 TTTTTTTACA
224193 ATTTTTAAT
1 ATTTTTAAT
*
224202 ATTTTTTAT
1 ATTTTTAAT
224211 A-TTTTAATTT
1 ATTTTTAA--T
*
224221 TTTTTTAAT
1 ATTTTTAAT
*
224230 ATTTTTTAT
1 ATTTTTAAT
224239 A-TTTTAAT
1 ATTTTTAAT
224247 -TTTTTACAT
1 ATTTTTA-AT
*
224256 -TTTTAAAT
1 ATTTTTAAT
*
224264 ATTTTTTAT
1 ATTTTTAAT
224273 GATTTTTAAT
1 -ATTTTTAAT
224283 ATTTTTTAAT
1 A-TTTTTAAT
224293 -TTTTT
1 ATTTTT
224298 GGTCCGGTTA
Statistics
Matches: 78, Mismatches: 10, Indels: 17
0.74 0.10 0.16
Matches are distributed among these distances:
8 23 0.29
9 32 0.41
10 17 0.22
11 6 0.08
ACGTcount: A:0.27, C:0.01, G:0.01, T:0.71
Consensus pattern (9 bp):
ATTTTTAAT
Found at i:224208 original size:11 final size:10
Alignment explanation
Indices: 224194--224297 Score: 79
Period size: 10 Copynumber: 11.4 Consensus size: 10
224184 TTTTTTACAA
224194 TTTTTAATAT
1 TTTTTAATAT
224204 TTTTT-ATA-
1 TTTTTAATAT
*
224212 -TTTTAATTTT
1 TTTTTAA-TAT
224222 TTTTTAATAT
1 TTTTTAATAT
224232 TTTTT-ATA-
1 TTTTTAATAT
224240 -TTTT-A-AT
1 TTTTTAATAT
*
224247 TTTTT-ACAT
1 TTTTTAATAT
*
224256 TTTTAAATAT
1 TTTTTAATAT
224266 TTTTT-ATGA-
1 TTTTTAAT-AT
224275 TTTTTAATAT
1 TTTTTAATAT
224285 TTTTTAAT-T
1 TTTTTAATAT
224294 TTTT
1 TTTT
224298 GGTCCGGTTA
Statistics
Matches: 78, Mismatches: 5, Indels: 23
0.74 0.05 0.22
Matches are distributed among these distances:
6 1 0.01
7 9 0.12
8 6 0.08
9 26 0.33
10 30 0.38
11 6 0.08
ACGTcount: A:0.26, C:0.01, G:0.01, T:0.72
Consensus pattern (10 bp):
TTTTTAATAT
Found at i:224222 original size:15 final size:15
Alignment explanation
Indices: 224202--224258 Score: 66
Period size: 15 Copynumber: 3.9 Consensus size: 15
224192 AATTTTTAAT
224202 ATTTTTTATATTTTA
1 ATTTTTTATATTTTA
*
224217 A-TTTTT-T-TTTAA
1 ATTTTTTATATTTTA
224229 TATTTTTTATATTTTA
1 -ATTTTTTATATTTTA
*
224245 ATTTTTTACATTTT
1 ATTTTTTATATTTT
224259 TAAATATTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
12 4 0.11
13 2 0.06
14 10 0.29
15 15 0.43
16 4 0.11
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.74
Consensus pattern (15 bp):
ATTTTTTATATTTTA
Found at i:224226 original size:28 final size:28
Alignment explanation
Indices: 224194--224251 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
224184 TTTTTTACAA
224194 TTTTTAATATTTTTTATATTTTAATTTT
1 TTTTTAATATTTTTTATATTTTAATTTT
224222 TTTTTAATATTTTTTATATTTTAATTTT
1 TTTTTAATATTTTTTATATTTTAATTTT
224250 TT
1 TT
224252 ACATTTTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (28 bp):
TTTTTAATATTTTTTATATTTTAATTTT
Found at i:224231 original size:19 final size:19
Alignment explanation
Indices: 224179--224234 Score: 64
Period size: 18 Copynumber: 3.1 Consensus size: 19
224169 AATTTTGAAA
*
224179 TAATTTTTTTTACAAT-TTT
1 TAATTTTTTTT-TAATATTT
*
224198 TAA-TATTTTTT-ATATTT
1 TAATTTTTTTTTAATATTT
224215 TAATTTTTTTTTAATATTT
1 TAATTTTTTTTTAATATTT
224234 T
1 T
224235 TTATATTTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
16 2 0.06
17 6 0.19
18 13 0.42
19 10 0.32
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (19 bp):
TAATTTTTTTTTAATATTT
Found at i:224234 original size:37 final size:36
Alignment explanation
Indices: 224180--224295 Score: 101
Period size: 43 Copynumber: 3.0 Consensus size: 36
224170 ATTTTGAAAT
224180 AATTTTTTTTACA-ATTTTTAATATTTTTTATATTTTA
1 AATTTTTTTTA-ATATTTTTAATATTTTTTA-ATTTTA
*
224217 ATTTTTTTTTAATATTTTTTATATTTTAATTTTTTACATTTTTA
1 AATTTTTTTTAATA-TTTTTA-A---T-ATTTTTTA-A-TTTTA
*
224261 AATATTTTTT-ATGATTTTTAATATTTTTTAATTTT
1 AATTTTTTTTAAT-ATTTTTAATATTTTTTAATTTT
224296 TTGGTCCGGT
Statistics
Matches: 66, Mismatches: 4, Indels: 19
0.74 0.04 0.21
Matches are distributed among these distances:
36 5 0.08
37 12 0.18
38 14 0.21
39 2 0.03
42 2 0.03
43 17 0.26
44 14 0.21
ACGTcount: A:0.28, C:0.02, G:0.01, T:0.70
Consensus pattern (36 bp):
AATTTTTTTTAATATTTTTAATATTTTTTAATTTTA
Found at i:224268 original size:53 final size:51
Alignment explanation
Indices: 224192--224295 Score: 122
Period size: 53 Copynumber: 2.0 Consensus size: 51
224182 TTTTTTTTAC
* * *
224192 AATTTTTAATATTTTTTATATTTTAATT-T-TTTTTTAATATTTTTTATATTTT
1 AATTTTTAACATTTTTAATATTTT--TTATGATTTTTAATATTTTTTA-ATTTT
*
224244 AATTTTTTACATTTTTAAATATTTTTTATGATTTTTAATATTTTTTAATTTT
1 AATTTTTAACATTTTT-AATATTTTTTATGATTTTTAATATTTTTTAATTTT
224296 TTGGTCCGGT
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
51 2 0.04
52 20 0.44
53 23 0.51
ACGTcount: A:0.28, C:0.01, G:0.01, T:0.70
Consensus pattern (51 bp):
AATTTTTAACATTTTTAATATTTTTTATGATTTTTAATATTTTTTAATTTT
Found at i:228819 original size:19 final size:20
Alignment explanation
Indices: 228795--228836 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
228785 TTTTTGTTCC
*
228795 TTATTTTTTATAATTTC-TT
1 TTATTTTTGATAATTTCATT
*
228814 TTATTTTTGATATTTTCATT
1 TTATTTTTGATAATTTCATT
228834 TTA
1 TTA
228837 AAATTTTCTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.21, C:0.05, G:0.02, T:0.71
Consensus pattern (20 bp):
TTATTTTTGATAATTTCATT
Found at i:229282 original size:23 final size:23
Alignment explanation
Indices: 229256--229345 Score: 83
Period size: 23 Copynumber: 3.9 Consensus size: 23
229246 GAATTAAATT
*
229256 TTAAATTTAGATTTCAAATTTTA
1 TTAAATTTAGATTTTAAATTTTA
* * ** * *
229279 TTAAAATAAGAGCTTAAGTATTA
1 TTAAATTTAGATTTTAAATTTTA
*
229302 TTAGATTTAGATTTTAAATTTCT-
1 TTAAATTTAGATTTTAAATTT-TA
*
229325 TTAAATTTAGTTTTTAAATTT
1 TTAAATTTAGATTTTAAATTT
229346 AGATTTGTTC
Statistics
Matches: 50, Mismatches: 16, Indels: 2
0.74 0.24 0.03
Matches are distributed among these distances:
23 49 0.98
24 1 0.02
ACGTcount: A:0.38, C:0.03, G:0.08, T:0.51
Consensus pattern (23 bp):
TTAAATTTAGATTTTAAATTTTA
Found at i:232001 original size:207 final size:202
Alignment explanation
Indices: 231646--232054 Score: 593
Period size: 207 Copynumber: 2.0 Consensus size: 202
231636 TCCTAGGAAT
* * *
231646 TCTTCTTGACAAACCTGCGAAGGTATGTGATTCATAATCATTTGCACCATCTCCGATAGAGGAAA
1 TCTTCTTAACAAACCTGCGAAGGTATGTGATTCATAATCATCTACACCATCTCCGATAGAGGAAA
* * **
231711 GGGTATTATTGCGGCCATTAGGCGTACTGGTATACCATGGAAATCGGTTTACTGCAACCAACACA
66 GGGTATTATTGCGGCCATTAGGCATACTGGTATACCATGAAAATCAATTTACTGCAACCAACACA
* *
231776 TTGCGACTAACATCCAATGAGAATATAAGAATACATAATAGCGGAGACGAATTGTGAAAATGGGT
131 TTGCGACTAACATCCAATGAGAATATAAGAATACAGAATAGCAGAGACGAATTGTGAAAATGGGT
231841 AAAAAAA
196 AAAAAAA
* * *
231848 TCTTCTTAACAAATCTGCGGAGGTATGTGATTCATAACGATAACATCTACATCATCTCCGATAGA
1 TCTTCTTAACAAACCTGCGAAGGTATGTGATTCAT-A--AT--CATCTACACCATCTCCGATAGA
* *
231913 GGAAAGGGTATTATTGCGGCCATTAGGCATACTGGTGTACCATGAAAATCAATTTACTGCAGCCA
61 GGAAAGGGTATTATTGCGGCCATTAGGCATACTGGTATACCATGAAAATCAATTTACTGCAACCA
* * * * * *
231978 ACACATTGCGGCTAACTTCCAATGAGAATATAAGAATGCAGACTAGTAGAGACGACTTGTGAAAA
126 ACACATTGCGACTAACATCCAATGAGAATATAAGAATACAGAATAGCAGAGACGAATTGTGAAAA
232043 TGGGTAAAAAAA
191 TGGGTAAAAAAA
232055 ATTAAGTTTC
Statistics
Matches: 182, Mismatches: 20, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
202 32 0.18
203 1 0.01
205 2 0.01
207 147 0.81
ACGTcount: A:0.36, C:0.18, G:0.21, T:0.25
Consensus pattern (202 bp):
TCTTCTTAACAAACCTGCGAAGGTATGTGATTCATAATCATCTACACCATCTCCGATAGAGGAAA
GGGTATTATTGCGGCCATTAGGCATACTGGTATACCATGAAAATCAATTTACTGCAACCAACACA
TTGCGACTAACATCCAATGAGAATATAAGAATACAGAATAGCAGAGACGAATTGTGAAAATGGGT
AAAAAAA
Found at i:233013 original size:14 final size:14
Alignment explanation
Indices: 232974--233013 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 14
232964 GGTTTAATGG
232974 TTTAGTGTTTTAAAT
1 TTTAG-GTTTTAAAT
232989 TTTAGGGTTTTAAAT
1 TTTA-GGTTTTAAAT
233004 TTTAGGTTTT
1 TTTAGGTTTT
233014 GAAGAAATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.25
15 17 0.71
16 1 0.04
ACGTcount: A:0.23, C:0.00, G:0.17, T:0.60
Consensus pattern (14 bp):
TTTAGGTTTTAAAT
Found at i:233048 original size:21 final size:21
Alignment explanation
Indices: 233024--233075 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
233014 GAAGAAATGA
* *
233024 TTTAGGGTTTTAAATTTATGG
1 TTTAGGATTTTAAATTTAAGG
* *
233045 TTTAAGATTTTAAGTTTAAGG
1 TTTAGGATTTTAAATTTAAGG
233066 TTTAGGATTT
1 TTTAGGATTT
233076 AGGGTTTTAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.27, C:0.00, G:0.21, T:0.52
Consensus pattern (21 bp):
TTTAGGATTTTAAATTTAAGG
Found at i:233054 original size:14 final size:14
Alignment explanation
Indices: 233053--233124 Score: 76
Period size: 14 Copynumber: 5.1 Consensus size: 14
233043 GGTTTAAGAT
*
233053 TTTAAG-TTTAAGG
1 TTTAAGATTTAGGG
*
233066 TTTAGGATTTAGGG
1 TTTAAGATTTAGGG
233080 TTTTAA-ATTTAGGG
1 -TTTAAGATTTAGGG
*
233094 TTTAAGGTTTAAGGG
1 TTTAAGATTT-AGGG
*
233109 TTTAAGATGTAGGG
1 TTTAAGATTTAGGG
233123 TT
1 TT
233125 AAGGGTTTAT
Statistics
Matches: 49, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
13 10 0.20
14 23 0.47
15 16 0.33
ACGTcount: A:0.26, C:0.00, G:0.29, T:0.44
Consensus pattern (14 bp):
TTTAAGATTTAGGG
Found at i:233064 original size:6 final size:7
Alignment explanation
Indices: 233038--233114 Score: 52
Period size: 7 Copynumber: 10.9 Consensus size: 7
233028 GGGTTTTAAA
*
233038 TTTATGG
1 TTTAAGG
*
233045 TTTAAGAT
1 TTTAAG-G
233053 TTTAA-G
1 TTTAAGG
233059 TTTAAGG
1 TTTAAGG
233066 TTT-AGG
1 TTTAAGG
*
233072 ATTTAGGG
1 -TTTAAGG
*
233080 TTTTAA-A
1 -TTTAAGG
*
233087 TTTAGGG
1 TTTAAGG
233094 TTTAAGG
1 TTTAAGG
233101 TTTAAGGG
1 TTTAA-GG
233109 TTTAAG
1 TTTAAG
233115 ATGTAGGGTT
Statistics
Matches: 54, Mismatches: 10, Indels: 12
0.71 0.13 0.16
Matches are distributed among these distances:
6 12 0.22
7 24 0.44
8 18 0.33
ACGTcount: A:0.27, C:0.00, G:0.26, T:0.47
Consensus pattern (7 bp):
TTTAAGG
Found at i:233082 original size:21 final size:21
Alignment explanation
Indices: 233058--233154 Score: 81
Period size: 21 Copynumber: 4.6 Consensus size: 21
233048 AAGATTTTAA
233058 GTTTAAGGTTTAGGATTTAGG
1 GTTTAAGGTTTAGGATTTAGG
* * *
233079 GTTTTAA-ATTTAGGGTTTAAG
1 G-TTTAAGGTTTAGGATTTAGG
* *
233100 GTTTAAGGGTTTAAGATGTAGG
1 GTTTAA-GGTTTAGGATTTAGG
* *
233122 G-TTAAGGGTTTATGATTTAGT
1 GTTTAA-GGTTTAGGATTTAGG
*
233143 GTTTAGGGTTTA
1 GTTTAAGGTTTA
233155 TAAGTATGAA
Statistics
Matches: 60, Mismatches: 12, Indels: 8
0.75 0.15 0.10
Matches are distributed among these distances:
20 5 0.08
21 37 0.62
22 18 0.30
ACGTcount: A:0.25, C:0.00, G:0.31, T:0.44
Consensus pattern (21 bp):
GTTTAAGGTTTAGGATTTAGG
Found at i:233097 original size:7 final size:7
Alignment explanation
Indices: 233058--233154 Score: 61
Period size: 7 Copynumber: 13.7 Consensus size: 7
233048 AAGATTTTAA
*
233058 GTTTAAG
1 GTTTAGG
233065 GTTTAGG
1 GTTTAGG
*
233072 ATTTAGG
1 GTTTAGG
*
233079 GTTTTA-A
1 G-TTTAGG
*
233086 ATTTAGG
1 GTTTAGG
*
233093 GTTTAAG
1 GTTTAGG
233100 GTTTAAGG
1 GTTT-AGG
*
233108 GTTTAAG
1 GTTTAGG
* *
233115 ATGTAGG
1 GTTTAGG
*
233122 GTTAAGG
1 GTTTAGG
*
233129 GTTTATG
1 GTTTAGG
* *
233136 ATTTAGT
1 GTTTAGG
233143 GTTTAGG
1 GTTTAGG
233150 GTTTA
1 GTTTA
233155 TAAGTATGAA
Statistics
Matches: 64, Mismatches: 23, Indels: 6
0.69 0.25 0.06
Matches are distributed among these distances:
6 4 0.06
7 50 0.78
8 10 0.16
ACGTcount: A:0.25, C:0.00, G:0.31, T:0.44
Consensus pattern (7 bp):
GTTTAGG
Found at i:235571 original size:21 final size:21
Alignment explanation
Indices: 235547--235587 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
235537 TTATTTACTA
235547 CTACTAACAAAATAAAATTAC
1 CTACTAACAAAATAAAATTAC
*
235568 CTACTAACAAAATTAAATTA
1 CTACTAACAAAATAAAATTA
235588 AAATAAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.56, C:0.17, G:0.00, T:0.27
Consensus pattern (21 bp):
CTACTAACAAAATAAAATTAC
Found at i:235931 original size:17 final size:17
Alignment explanation
Indices: 235911--235947 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
235901 TCCTTCTCCT
235911 TTTTCCTTCTTTCTTTC
1 TTTTCCTTCTTTCTTTC
* *
235928 TTTTCTTTCTTTTTTTC
1 TTTTCCTTCTTTCTTTC
235945 TTT
1 TTT
235948 GTTCTGCCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTTCCTTCTTTCTTTC
Found at i:248845 original size:123 final size:125
Alignment explanation
Indices: 248624--248863 Score: 333
Period size: 123 Copynumber: 1.9 Consensus size: 125
248614 GGTGTATAAA
* * * * *
248624 AAGGAAGACTCATGTCTCGGGTTAAGCATGAGAAATTGTATAAATGGAAGACTCATGTCTCGAGA
1 AAGGAAGACTCATGTCTCGAGATAAGAATGAGAAATTGAATAAATGGAAGACTCATGTCTCGAAA
* * *
248689 TGAGAATGAGATTACGAATAAGGAAGACTCATGTCTCAAGATGAGAATGAGATTACGAAT
66 TGAGAACGAGATTACGAATAAAGAAGACTCATGTCTCAAGATGAGAACGAGATTACGAAT
* * *
248749 AAGGAAGACTCATGTCTCGAGATGAGAATGAG-ATTATGAAT-AA-GGAAGACTCATTTCTCGAA
1 AAGGAAGACTCATGTCTCGAGATAAGAATGAGAAAT-TGAATAAATGGAAGACTCATGTCTCGAA
**
248811 ATGAGAACGAGATTTTGAATAAAGAAGACTCATGTCTCAAGATGAGAACGAGA
65 ATGAGAACGAGATTACGAATAAAGAAGACTCATGTCTCAAGATGAGAACGAGA
248864 ATATGGTTAA
Statistics
Matches: 101, Mismatches: 13, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
123 65 0.64
124 4 0.04
125 32 0.32
ACGTcount: A:0.40, C:0.12, G:0.25, T:0.23
Consensus pattern (125 bp):
AAGGAAGACTCATGTCTCGAGATAAGAATGAGAAATTGAATAAATGGAAGACTCATGTCTCGAAA
TGAGAACGAGATTACGAATAAAGAAGACTCATGTCTCAAGATGAGAACGAGATTACGAAT
Found at i:248877 original size:41 final size:41
Alignment explanation
Indices: 248669--248868 Score: 294
Period size: 41 Copynumber: 4.9 Consensus size: 41
248659 TTGTATAAAT
* *
248669 GGAAGACTCATGTCTCGAGATGAGAATGAGATTACGAATAA
1 GGAAGACTCATGTCTCAAGATGAGAATGAGATTATGAATAA
*
248710 GGAAGACTCATGTCTCAAGATGAGAATGAGATTACGAATAA
1 GGAAGACTCATGTCTCAAGATGAGAATGAGATTATGAATAA
*
248751 GGAAGACTCATGTCTCGAGATGAGAATGAGATTATGAATAA
1 GGAAGACTCATGTCTCAAGATGAGAATGAGATTATGAATAA
* * *
248792 GGAAGACTCATTTCTCGAA-ATGAGAACGAGATTTTGAATAA
1 GGAAGACTCATGTCTC-AAGATGAGAATGAGATTATGAATAA
* * *
248833 AGAAGACTCATGTCTCAAGATGAGAACGAGAATATG
1 GGAAGACTCATGTCTCAAGATGAGAATGAGATTATG
248869 GTTAAAGAAA
Statistics
Matches: 146, Mismatches: 11, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
40 2 0.01
41 143 0.98
42 1 0.01
ACGTcount: A:0.40, C:0.12, G:0.25, T:0.23
Consensus pattern (41 bp):
GGAAGACTCATGTCTCAAGATGAGAATGAGATTATGAATAA
Found at i:254501 original size:3 final size:3
Alignment explanation
Indices: 254493--254521 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
254483 GTGCCCTATG
254493 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
254522 AATTTCGGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:255882 original size:21 final size:20
Alignment explanation
Indices: 255866--255919 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 20
255856 GTTGTAATGG
*
255866 TTCTACCGATACATGTATAAC
1 TTCTACCGATACATGTAT-GC
255887 TTCTACCGATACATGTTATGC
1 TTCTACCGATACATG-TATGC
255908 TTCTACCGATAC
1 TTCTACCGATAC
255920 TAAAAACTCT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
21 28 0.90
22 3 0.10
ACGTcount: A:0.28, C:0.26, G:0.11, T:0.35
Consensus pattern (20 bp):
TTCTACCGATACATGTATGC
Found at i:256708 original size:18 final size:18
Alignment explanation
Indices: 256685--256726 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
256675 TATGAGCAAA
* *
256685 TATGCTTAAACGAGTCAG
1 TATGCTCAAACGAGCCAG
256703 TATGCTCAAACGAGCCAG
1 TATGCTCAAACGAGCCAG
256721 TATGCT
1 TATGCT
256727 ATTCCTTCCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.26
Consensus pattern (18 bp):
TATGCTCAAACGAGCCAG
Found at i:261418 original size:43 final size:42
Alignment explanation
Indices: 261336--261423 Score: 106
Period size: 43 Copynumber: 2.1 Consensus size: 42
261326 ATAGTTTTAA
* * * *
261336 ATTAAATTATAATTTTTTAAATGTTTAATTATTAAAACTTTT
1 ATTAAATTATAATTTTTTAAATATATAATTATCAAAACTTCT
*
261378 ATTAAATTAT-ATTTAATTTAAATATATAATTATCATAACTTCT
1 ATTAAATTATAATTT--TTTAAATATATAATTATCAAAACTTCT
261421 ATT
1 ATT
261424 TTACTTAAAC
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
41 4 0.10
42 10 0.26
43 25 0.64
ACGTcount: A:0.42, C:0.05, G:0.01, T:0.52
Consensus pattern (42 bp):
ATTAAATTATAATTTTTTAAATATATAATTATCAAAACTTCT
Found at i:262175 original size:23 final size:23
Alignment explanation
Indices: 262149--262197 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
262139 TGAATTACAC
262149 AATTCTAGTTTTTCTAAAATCCA
1 AATTCTAGTTTTTCTAAAATCCA
262172 AATTCTAGTTTTTCTAAAATCCA
1 AATTCTAGTTTTTCTAAAATCCA
262195 AAT
1 AAT
262198 AAGAAAAGAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.37, C:0.16, G:0.04, T:0.43
Consensus pattern (23 bp):
AATTCTAGTTTTTCTAAAATCCA
Found at i:262927 original size:9 final size:9
Alignment explanation
Indices: 262915--262957 Score: 54
Period size: 9 Copynumber: 4.8 Consensus size: 9
262905 ATAAAATTGA
262915 ATTAATTCG
1 ATTAATTCG
262924 ATTAATTC-
1 ATTAATTCG
262932 ATTAAATTCG
1 ATT-AATTCG
262942 ATTAA-TCG
1 ATTAATTCG
262950 AATTAATT
1 -ATTAATT
262958 TTGTGGGAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
8 6 0.20
9 20 0.67
10 4 0.13
ACGTcount: A:0.40, C:0.09, G:0.07, T:0.44
Consensus pattern (9 bp):
ATTAATTCG
Found at i:262957 original size:18 final size:19
Alignment explanation
Indices: 262909--262957 Score: 61
Period size: 18 Copynumber: 2.7 Consensus size: 19
262899 TTTCGAATAA
262909 AATT-GAATTAATTCGATT
1 AATTCGAATTAATTCGATT
262927 AATTC--ATTAAATTCGATT
1 AATTCGAATT-AATTCGATT
262945 AA-TCGAATTAATT
1 AATTCGAATTAATT
262958 TTGTGGGAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
17 5 0.19
18 19 0.70
19 3 0.11
ACGTcount: A:0.41, C:0.08, G:0.08, T:0.43
Consensus pattern (19 bp):
AATTCGAATTAATTCGATT
Found at i:263008 original size:16 final size:16
Alignment explanation
Indices: 262987--263039 Score: 65
Period size: 16 Copynumber: 3.2 Consensus size: 16
262977 ATTTTTTAAA
262987 AATTCGATTAACAATT
1 AATTCGATTAACAATT
263003 AATTCGATTCAA-AATT
1 AATTCGATT-AACAATT
263019 AATT-GATTAATCAAATT
1 AATTCGATTAA-C-AATT
263036 AATT
1 AATT
263040 GAATTAATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
14 2 0.06
15 4 0.12
16 17 0.52
17 10 0.30
ACGTcount: A:0.45, C:0.09, G:0.06, T:0.40
Consensus pattern (16 bp):
AATTCGATTAACAATT
Found at i:263036 original size:17 final size:17
Alignment explanation
Indices: 263014--263051 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 17
263004 ATTCGATTCA
263014 AAATTAATTG-ATTAAT
1 AAATTAATTGAATTAAT
263030 CAAATTAATTGAATTAAT
1 -AAATTAATTGAATTAAT
263048 AAAT
1 AAAT
263052 AATATTATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 14 0.70
18 6 0.30
ACGTcount: A:0.53, C:0.03, G:0.05, T:0.39
Consensus pattern (17 bp):
AAATTAATTGAATTAAT
Found at i:268863 original size:19 final size:19
Alignment explanation
Indices: 268839--268876 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
268829 GAAAGTTAAT
268839 AACAAATTTGATTACGGTG
1 AACAAATTTGATTACGGTG
*
268858 AACAAATTTGATTATGGTG
1 AACAAATTTGATTACGGTG
268877 GGTAATAGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.37, C:0.08, G:0.21, T:0.34
Consensus pattern (19 bp):
AACAAATTTGATTACGGTG
Done.