Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011265.1 Kokia drynarioides strain JFW-HI SEQ_126244, 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: 71647
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Warning! 20 characters in sequence are not A, C, G, or T
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--46 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
1 TA TA TA TA 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
43 TA TA
1 TA TA
47 GGAATTTAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:111 original size:30 final size:28
Alignment explanation
Indices: 70--222 Score: 155
Period size: 30 Copynumber: 5.2 Consensus size: 28
60 AACATTAAAA
**
70 TGGGGTC-AATTTTTATTTTTGAAAACTT
1 TGGGGTCAAATTTGAATTTTTGAAAA-TT
* *
98 TAGGGGTTAAATTTGAATTTTTGGAAATTT
1 T-GGGGTCAAATTTGAATTTTT-GAAAATT
128 TAGGGGTCAAATTTGAATTTTTAGAAAATT
1 T-GGGGTCAAATTTGAATTTTT-GAAAATT
*
158 TGAGGGTGAAATTTGAATTTTTGGAAAATT
1 TG-GGGTCAAATTTGAATTTTT-GAAAATT
* *
188 TGAGGGTCAAATTTGTATTCTTGAAAACTT
1 TG-GGGTCAAATTTGAATTTTTGAAAA-TT
218 TGGGG
1 TGGGG
223 GGTCAAAAAT
Statistics
Matches: 108, Mismatches: 12, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
28 1 0.01
29 14 0.13
30 89 0.82
31 4 0.04
ACGTcount: A:0.30, C:0.04, G:0.24, T:0.42
Consensus pattern (28 bp):
TGGGGTCAAATTTGAATTTTTGAAAATT
Found at i:148 original size:60 final size:58
Alignment explanation
Indices: 70--222 Score: 202
Period size: 60 Copynumber: 2.6 Consensus size: 58
60 AACATTAAAA
* * *
70 TGGGGTC-AATTTTTATTTTTGAAAACTTTAGGGGTTAAATTTGAATTTTTGGAAATTT
1 TGGGGTCAAATTTGTATTTTTGAAAACTTT-GGGGTGAAATTTGAATTTTTGGAAAATT
*
128 TAGGGGTCAAATTTGAATTTTTAGAAAA-TTTGAGGGTGAAATTTGAATTTTTGGAAAATT
1 T-GGGGTCAAATTTGTATTTTT-GAAAACTTTG-GGGTGAAATTTGAATTTTTGGAAAATT
*
188 TGAGGGTCAAATTTGTATTCTTGAAAACTTTGGGG
1 TG-GGGTCAAATTTGTATTTTTGAAAACTTTGGGG
223 GGTCAAAAAT
Statistics
Matches: 83, Mismatches: 6, Indels: 11
0.83 0.06 0.11
Matches are distributed among these distances:
58 1 0.01
59 16 0.19
60 61 0.73
61 5 0.06
ACGTcount: A:0.30, C:0.04, G:0.24, T:0.42
Consensus pattern (58 bp):
TGGGGTCAAATTTGTATTTTTGAAAACTTTGGGGTGAAATTTGAATTTTTGGAAAATT
Found at i:1846 original size:26 final size:27
Alignment explanation
Indices: 1815--1870 Score: 78
Period size: 26 Copynumber: 2.1 Consensus size: 27
1805 TTTTAAAATT
*
1815 AAAGAATGGATTTTG-TCTTTTAATGG
1 AAAGAATGGATTGTGTTCTTTTAATGG
* *
1841 AAAGAATGGGTTGTGTTTTTTTAATGG
1 AAAGAATGGATTGTGTTCTTTTAATGG
1868 AAA
1 AAA
1871 TAATCAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 13 0.50
27 13 0.50
ACGTcount: A:0.32, C:0.02, G:0.25, T:0.41
Consensus pattern (27 bp):
AAAGAATGGATTGTGTTCTTTTAATGG
Found at i:2199 original size:29 final size:30
Alignment explanation
Indices: 2145--2302 Score: 178
Period size: 30 Copynumber: 5.3 Consensus size: 30
2135 AAAATCATTT
* * *
2145 TTTGACCCTCAAAGTTTTCAAGAATTCAAA
1 TTTGACCCTCAAAATTTCCAAAAATTCAAA
*
2175 TTTGACCC-CAAAATTTCCAAAAATTTAAA
1 TTTGACCCTCAAAATTTCCAAAAATTCAAA
*
2204 TTTCACCCTC-AAATTTCCCAAAAATTCAAA
1 TTTGACCCTCAAAATTT-CCAAAAATTCAAA
*
2234 TATGA-CCTCTAAAATTTCCAAAAATTCAAA
1 TTTGACCCTC-AAAATTTCCAAAAATTCAAA
* * * * *
2264 TTTAACCCTTAAAGTTTTCAAAAATTAAAA
1 TTTGACCCTCAAAATTTCCAAAAATTCAAA
2294 TTTGACCCT
1 TTTGACCCT
2303 ATTTTAATGT
Statistics
Matches: 108, Mismatches: 15, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
29 34 0.31
30 65 0.60
31 9 0.08
ACGTcount: A:0.41, C:0.22, G:0.04, T:0.33
Consensus pattern (30 bp):
TTTGACCCTCAAAATTTCCAAAAATTCAAA
Found at i:2272 original size:60 final size:59
Alignment explanation
Indices: 2149--2301 Score: 209
Period size: 60 Copynumber: 2.6 Consensus size: 59
2139 TCATTTTTTG
* * *
2149 ACCCTCAAAGTTTTCAAGAATTCAAATTTGACCCCAAAATTTCCAAAAATTTAAATTTC
1 ACCCTCAAAGTTTTCAAAAATTCAAATTTGACCCCAAAATTTCCAAAAATTCAAATTTA
* * *
2208 ACCCTCAAA-TTTCCCAAAAATTCAAATATGACCTCTAAAATTTCCAAAAATTCAAATTTA
1 ACCCTCAAAGTTT-TCAAAAATTCAAATTTGACC-CCAAAATTTCCAAAAATTCAAATTTA
* *
2268 ACCCTTAAAGTTTTCAAAAATTAAAATTTGACCC
1 ACCCTCAAAGTTTTCAAAAATTCAAATTTGACCC
2302 TATTTTAATG
Statistics
Matches: 81, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
58 3 0.04
59 27 0.33
60 48 0.59
61 3 0.04
ACGTcount: A:0.42, C:0.22, G:0.04, T:0.31
Consensus pattern (59 bp):
ACCCTCAAAGTTTTCAAAAATTCAAATTTGACCCCAAAATTTCCAAAAATTCAAATTTA
Found at i:7104 original size:22 final size:21
Alignment explanation
Indices: 7056--7113 Score: 73
Period size: 20 Copynumber: 2.7 Consensus size: 21
7046 ATATGCATTC
*
7056 TAAAATTATTAAAA-AAACAT
1 TAAAATTATAAAAATAAACAT
*
7076 AAAAATTATAAAAATAAATCAT
1 TAAAATTATAAAAATAAA-CAT
7098 TAAAATTATTAAAAAT
1 TAAAATTA-TAAAAAT
7114 GTTAGAAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
20 12 0.38
21 3 0.09
22 10 0.31
23 7 0.22
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (21 bp):
TAAAATTATAAAAATAAACAT
Found at i:15243 original size:30 final size:30
Alignment explanation
Indices: 15209--15270 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
15199 TATTTTATTA
*
15209 TTAATTTTGTTATTATTTTAGAGACATTTG
1 TTAATTTTGTTACTATTTTAGAGACATTTG
15239 TTAATTTTGTTACTATTTTAGAGACATTTG
1 TTAATTTTGTTACTATTTTAGAGACATTTG
15269 TT
1 TT
15271 TGTTAAGTTG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.26, C:0.05, G:0.13, T:0.56
Consensus pattern (30 bp):
TTAATTTTGTTACTATTTTAGAGACATTTG
Found at i:17480 original size:25 final size:25
Alignment explanation
Indices: 17452--17502 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
17442 AGTCAAACAT
*
17452 TATTTTTAATTTCCCACTTAAACTC
1 TATTTTTAATTTCACACTTAAACTC
*
17477 TATTTTTAGTTTCACACTTAAACTC
1 TATTTTTAATTTCACACTTAAACTC
17502 T
1 T
17503 GATTAATATA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.27, C:0.22, G:0.02, T:0.49
Consensus pattern (25 bp):
TATTTTTAATTTCACACTTAAACTC
Found at i:21931 original size:48 final size:48
Alignment explanation
Indices: 21877--21995 Score: 184
Period size: 48 Copynumber: 2.5 Consensus size: 48
21867 AAAGTTTAAA
* * *
21877 AATATTATCGTTAATTCGTTAGTGAAGTGTGAGCTATCGTCACAGTTG
1 AATATTATCGTTAATTCGTTAATGAAGTGTGAGCCATCATCACAGTTG
* *
21925 AATATTATCGTTAATTCGTTAATGATGTGTGAGCCATCATCATAGTTG
1 AATATTATCGTTAATTCGTTAATGAAGTGTGAGCCATCATCACAGTTG
*
21973 AATATTATCGTTAATTCATTAAT
1 AATATTATCGTTAATTCGTTAAT
21996 ATTATCGTTG
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 65 1.00
ACGTcount: A:0.30, C:0.12, G:0.18, T:0.40
Consensus pattern (48 bp):
AATATTATCGTTAATTCGTTAATGAAGTGTGAGCCATCATCACAGTTG
Found at i:25651 original size:45 final size:45
Alignment explanation
Indices: 25580--25713 Score: 178
Period size: 45 Copynumber: 3.0 Consensus size: 45
25570 GAAGGAAAGT
* * * *
25580 TGATGATGTTAACACCAAGGGGGTTAAACAAGTTCCTGAAGAACA
1 TGATGATGATAACACCGAGGGCGTTAAACAAGATCCTGAAGAACA
*
25625 TGATGATGATAACACCGAGGGCGTTAAACAAGATCCCGAAGAACA
1 TGATGATGATAACACCGAGGGCGTTAAACAAGATCCTGAAGAACA
* * * * *
25670 CGAGGATGATAACACCGAGGGTGTTGAACAAGATCCTAAAGAAC
1 TGATGATGATAACACCGAGGGCGTTAAACAAGATCCTGAAGAAC
25714 TTGAAACCAA
Statistics
Matches: 78, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 78 1.00
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (45 bp):
TGATGATGATAACACCGAGGGCGTTAAACAAGATCCTGAAGAACA
Found at i:27295 original size:19 final size:19
Alignment explanation
Indices: 27258--27298 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
27248 ACTATTTTAT
* **
27258 TTTACATTAAATATTTAAA
1 TTTACATCAAATACATAAA
27277 TTTACATCAAATACATAAA
1 TTTACATCAAATACATAAA
27296 TTT
1 TTT
27299 CCCGCTTAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.46, C:0.10, G:0.00, T:0.44
Consensus pattern (19 bp):
TTTACATCAAATACATAAA
Found at i:29031 original size:338 final size:339
Alignment explanation
Indices: 28340--29036 Score: 1035
Period size: 338 Copynumber: 2.1 Consensus size: 339
28330 CTCCTTTCTC
* * * * *
28340 TTTAGGTAATTTTTTGAACTGTATGATCTACTTTACGTAATATAATATTAATAAATTAGTAAAAG
1 TTTACGTAA-TTTTTGAACCGTATGATCTACCTGACGTAATATAATATTAACAAATTAGTAAAAG
* *
28405 ATAAAAAAATGTAATTTTTAAAAGTTTAAAAATATTATCGTTAATTCGTTAGTAATGTGTAAGCC
65 ACAAAAAAA-GTAATTTTTAAAAGTTTAAAAATATTATCCTTAATTCGTTAGTAATGTGTAAGCC
* * *
28470 ATCGTCACAGTTGAATATTATCGTTAATTCGTTAATATTATCGTTGGGTTCAATTGTTGGATACT
129 ATCGTCACAATTGAATATTATCGTTAATTCATTAATATTACCGTTGGGTTCAATTGTTGGATACT
*
28535 CTTTAATATTACTTAAACTTGTAAAGCACATGCTACTATTTTATTTTACATTAAAAATTTAAATT
194 CTTTAATATTACTTAAACTTATAAAGCACATGCTACTATTTTATTTTACATTAAAAATTTAAATT
*
28600 TACATCAAATACATGAATTTCCCACTTAAAATATAAATATGAATTCCTCTTCTCAAAATAATTAA
259 TACATCAAATACATGAATTTCCCACTTAAAATATAAATATGAATTCCTCTTCTCAAAATAATAAA
**
28665 AAACCTTTTAAGGTAA
324 AAACCTTTTAAAATAA
*
28681 TTTACGTAATTTTTGAACCGTATGATCTACCTGGCGTAATATAATATTAACAAATTAGTAAAAGA
1 TTTACGTAATTTTTGAACCGTATGATCTACCTGACGTAATATAATATTAACAAATTAGTAAAAGA
* * *
28746 C-AAAAAAGATAATTTTTAAAAGTTTAAAAATATTGTCCTTAATTTGTTAGTGATGTGTGAA-CC
66 CAAAAAAAG-TAATTTTTAAAAGTTTAAAAATATTATCCTTAATTCGTTAGTAATGTGT-AAGCC
* *
28809 ATCGTCACAATTGAATATTATCGTTAATTCATTAATATTGCCGTTGGGTTCAATTGTTTGATACT
129 ATCGTCACAATTGAATATTATCGTTAATTCATTAATATTACCGTTGGGTTCAATTGTTGGATACT
* * * *
28874 C-TTAGATATTAC-TCAACTTATAAAGTATATGCTACTATTTTATTTTACATTAAATATTTAAAT
194 CTTTA-ATATTACTTAAACTTATAAAGCACATGCTACTATTTTATTTTACATTAAAAATTTAAAT
* * * * *
28937 TTACATCAAATACATTAATTTTCCGCTTAAAATATCAAT-TAGAATTTCTCTTCTCAAAATAATA
258 TTACATCAAATACATGAATTTCCCACTTAAAATATAAATAT-GAATTCCTCTTCTCAAAATAATA
29001 AAAAACCTTTTAAAATAA
322 AAAAACCTTTTAAAATAA
*
29019 TTTACTTAATTTTTGAAC
1 TTTACGTAATTTTTGAAC
29037 TGGTAATATT
Statistics
Matches: 322, Mismatches: 30, Indels: 11
0.89 0.08 0.03
Matches are distributed among these distances:
337 1 0.00
338 139 0.43
339 121 0.38
340 53 0.16
341 8 0.02
ACGTcount: A:0.38, C:0.12, G:0.10, T:0.40
Consensus pattern (339 bp):
TTTACGTAATTTTTGAACCGTATGATCTACCTGACGTAATATAATATTAACAAATTAGTAAAAGA
CAAAAAAAGTAATTTTTAAAAGTTTAAAAATATTATCCTTAATTCGTTAGTAATGTGTAAGCCAT
CGTCACAATTGAATATTATCGTTAATTCATTAATATTACCGTTGGGTTCAATTGTTGGATACTCT
TTAATATTACTTAAACTTATAAAGCACATGCTACTATTTTATTTTACATTAAAAATTTAAATTTA
CATCAAATACATGAATTTCCCACTTAAAATATAAATATGAATTCCTCTTCTCAAAATAATAAAAA
ACCTTTTAAAATAA
Found at i:29265 original size:48 final size:48
Alignment explanation
Indices: 29194--29297 Score: 181
Period size: 48 Copynumber: 2.2 Consensus size: 48
29184 GATTATTCTT
* *
29194 GTTAATTCGTTAGTGATGTGTGAGCCATCGTTACAGTTGAATATTGTC
1 GTTAATTCGTTAGTGATATGTGAGCCATCATTACAGTTGAATATTGTC
*
29242 GTTAATTCGTTAGTGATATGTGAGTCATCATTACAGTTGAATATTGTC
1 GTTAATTCGTTAGTGATATGTGAGCCATCATTACAGTTGAATATTGTC
29290 GTTAATTC
1 GTTAATTC
29298 ATTAATATTG
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
48 53 1.00
ACGTcount: A:0.25, C:0.12, G:0.22, T:0.41
Consensus pattern (48 bp):
GTTAATTCGTTAGTGATATGTGAGCCATCATTACAGTTGAATATTGTC
Found at i:29299 original size:27 final size:27
Alignment explanation
Indices: 29224--29301 Score: 71
Period size: 27 Copynumber: 3.1 Consensus size: 27
29214 TGAGCCATCG
*
29224 TTACAGTTGAATATTGTCGTTAATTCG
1 TTACAGTTGAATATTGTCGTTAATTCA
* *
29251 TT--AG-TG-ATA-TGT-GAGTCA-TCA
1 TTACAGTTGAATATTGTCG-TTAATTCA
29272 TTACAGTTGAATATTGTCGTTAATTCA
1 TTACAGTTGAATATTGTCGTTAATTCA
29299 TTA
1 TTA
29302 ATATTGCCAT
Statistics
Matches: 38, Mismatches: 5, Indels: 16
0.64 0.08 0.27
Matches are distributed among these distances:
21 5 0.13
22 5 0.13
23 5 0.13
24 4 0.11
25 5 0.13
26 5 0.13
27 9 0.24
ACGTcount: A:0.28, C:0.10, G:0.18, T:0.44
Consensus pattern (27 bp):
TTACAGTTGAATATTGTCGTTAATTCA
Found at i:29398 original size:19 final size:19
Alignment explanation
Indices: 29376--29418 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
29366 ACTATTTTAT
* *
29376 TTTACATTAAATATTTAAA
1 TTTACATCAAATATATAAA
*
29395 TTTACATCAAATATATGAA
1 TTTACATCAAATATATAAA
29414 TTTAC
1 TTTAC
29419 CGCTTATAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.44, C:0.09, G:0.02, T:0.44
Consensus pattern (19 bp):
TTTACATCAAATATATAAA
Found at i:33347 original size:45 final size:45
Alignment explanation
Indices: 33284--33376 Score: 152
Period size: 45 Copynumber: 2.1 Consensus size: 45
33274 GAAGGAAAGT
33284 TGATGATGATAACACCGAGGGGGTTAAACAA-ATTCATGAAGAACA
1 TGATGATGATAACACCGAGGGGGTTAAACAATATTC-TGAAGAACA
* *
33329 TGATGGTGATAACACCGAGGGTGTTAAACAATATTCTGAAGAACA
1 TGATGATGATAACACCGAGGGGGTTAAACAATATTCTGAAGAACA
33374 TGA
1 TGA
33377 AACCAATTGA
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
45 41 0.91
46 4 0.09
ACGTcount: A:0.40, C:0.13, G:0.25, T:0.23
Consensus pattern (45 bp):
TGATGATGATAACACCGAGGGGGTTAAACAATATTCTGAAGAACA
Found at i:34449 original size:96 final size:96
Alignment explanation
Indices: 34272--34456 Score: 234
Period size: 96 Copynumber: 1.9 Consensus size: 96
34262 GAAAAGGATA
***
34272 TTCGATTATCTCGATTCGAAGAAAGGTTGCACCTAGTAAGTTAAGGCACAATATTTCAGAATCGA
1 TTCGATTATCTCGATTCGAAGAAAAAATGCACCTAGTAAGTTAAGGCACAATATTTCAGAATCGA
*
34337 AGGTAAGGAAACATTGCCTCGATTAAGGGTG
66 AGATAAGGAAACATTGCCTCGATTAAGGGTG
* * *
34368 TTCGATTATTTCGATTTGAAGAAAAAATGCACCTAGTGAGTTAAGGCACAA-ATTTTC-GAAACT
1 TTCGATTATCTCGATTCGAAGAAAAAATGCACCTAGTAAGTTAAGGCACAATA-TTTCAG-AA-T
*
34431 CGAA-ATAAAGG-AATATTGCCTCGATT
63 CGAAGAT-AAGGAAACATTGCCTCGATT
34457 TTTTTTTTTA
Statistics
Matches: 77, Mismatches: 8, Indels: 8
0.83 0.09 0.09
Matches are distributed among these distances:
95 2 0.03
96 66 0.86
97 9 0.12
ACGTcount: A:0.35, C:0.15, G:0.21, T:0.29
Consensus pattern (96 bp):
TTCGATTATCTCGATTCGAAGAAAAAATGCACCTAGTAAGTTAAGGCACAATATTTCAGAATCGA
AGATAAGGAAACATTGCCTCGATTAAGGGTG
Found at i:34694 original size:29 final size:30
Alignment explanation
Indices: 34663--34895 Score: 216
Period size: 30 Copynumber: 7.9 Consensus size: 30
34653 GCACGGGGGC
* *
34663 AAAATGGTAGTTTTGGAAGGTTCGGAGTCA
1 AAAATGGTATTTTTGGAAGGTTCGGGGTCA
*
34693 AAAATGATATTTTTGGAA-GTTCGAGGGT--
1 AAAATGGTATTTTTGGAAGGTTCG-GGGTCA
*
34721 AAAATGGTAATTTTTGAAAGGTTCGGGGTCA
1 AAAATGGT-ATTTTTGGAAGGTTCGGGGTCA
* * *
34752 AAAATGGGATTTTTTGGAAGTTTGGGGGT--
1 AAAATGGTA-TTTTTGGAAGGTTCGGGGTCA
*
34781 AAAATGGTATTTTTTTAGAAGGTTCGGGGTCA
1 AAAATGGTA--TTTTTGGAAGGTTCGGGGTCA
* *
34813 AAAATGGGATTTTTGGAAGTTTCGGGGT--
1 AAAATGGTATTTTTGGAAGGTTCGGGGTCA
* * *
34841 -AAATGGTAATTTTCGAAAGGTTCGAGGTCA
1 AAAATGGT-ATTTTTGGAAGGTTCGGGGTCA
34871 AAAATGAG-ATTTTTGGAA-GTTCGGG
1 AAAATG-GTATTTTTGGAAGGTTCGGG
34896 ACCTTCGGGG
Statistics
Matches: 165, Mismatches: 24, Indels: 29
0.76 0.11 0.13
Matches are distributed among these distances:
27 6 0.04
28 23 0.14
29 32 0.19
30 67 0.41
31 28 0.17
32 9 0.05
ACGTcount: A:0.30, C:0.05, G:0.31, T:0.34
Consensus pattern (30 bp):
AAAATGGTATTTTTGGAAGGTTCGGGGTCA
Found at i:34795 original size:60 final size:59
Alignment explanation
Indices: 34657--34891 Score: 312
Period size: 60 Copynumber: 4.0 Consensus size: 59
34647 TCGGATGCAC
* * * * ** *
34657 GGGGGCAAAATGGT-AGTTTTGGAAGGTTCGGAGTCAAAAATGATATTTTTGGAAGTTC
1 GGGGGTAAAATGGTAATTTTTGAAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTT
*
34715 GAGGGTAAAATGGTAATTTTTGAAAGGTTCGGGGTCAAAAATGGGATTTTTTGGAAGTTT
1 GGGGGTAAAATGGTAATTTTTGAAAGGTTCGGGGTCAAAAATGGGA-TTTTTGGAAGTTT
* *
34775 GGGGGTAAAATGGTATTTTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTT
1 GGGGGTAAAATGGTAATTTTTGA-AAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTT
* * * *
34835 CGGGGT-AAATGGTAATTTTCGAAAGGTTCGAGGTCAAAAATGAGATTTTTGGAAGTT
1 GGGGGTAAAATGGTAATTTTTGAAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTT
34892 CGGGACCTTC
Statistics
Matches: 157, Mismatches: 17, Indels: 6
0.87 0.09 0.03
Matches are distributed among these distances:
58 45 0.29
59 39 0.25
60 50 0.32
61 23 0.15
ACGTcount: A:0.29, C:0.05, G:0.32, T:0.34
Consensus pattern (59 bp):
GGGGGTAAAATGGTAATTTTTGAAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTT
Found at i:36773 original size:6 final size:6
Alignment explanation
Indices: 36764--36841 Score: 67
Period size: 6 Copynumber: 13.5 Consensus size: 6
36754 TGAACTTTAT
* * *
36764 TTTAAA TTTATAA --TAAT TTTAAA TTTGAAA -ATAAA TTTAAA CTTAAA
1 TTTAAA TTTA-AA TTTAAA TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA
*
36811 TTTAAA -ATAAA TTTAAA TTT-AA TTTAAA TTT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT
36842 TTAACAAATT
Statistics
Matches: 57, Mismatches: 8, Indels: 14
0.72 0.10 0.18
Matches are distributed among these distances:
4 1 0.02
5 14 0.25
6 37 0.65
7 5 0.09
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.47
Consensus pattern (6 bp):
TTTAAA
Found at i:36826 original size:17 final size:17
Alignment explanation
Indices: 36764--36872 Score: 87
Period size: 17 Copynumber: 6.4 Consensus size: 17
36754 TGAACTTTAT
* *
36764 TTTAAATTTATAATAAT
1 TTTAAATTTAAAATAAA
36781 TTTAAATTTGAAAATAAA
1 TTTAAATTT-AAAATAAA
* *
36799 TTTAAACTTAAATTTAAA
1 TTTAAATTTAAA-ATAAA
* * *
36817 -ATAAATTTAAATTTAA
1 TTTAAATTTAAAATAAA
** *
36833 TTTAAATTTTTAACAAA
1 TTTAAATTTAAAATAAA
36850 TTT-AATCTTAAAATAAA
1 TTTAAAT-TTAAAATAAA
36867 TTTAAA
1 TTTAAA
36873 GGGAAGTTTG
Statistics
Matches: 71, Mismatches: 16, Indels: 9
0.74 0.17 0.09
Matches are distributed among these distances:
16 7 0.10
17 44 0.62
18 20 0.28
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:36841 original size:11 final size:11
Alignment explanation
Indices: 36782--36840 Score: 73
Period size: 11 Copynumber: 5.2 Consensus size: 11
36772 TATAATAATT
36782 TTAAATTTGAAA
1 TTAAATTT-AAA
*
36794 ATAAATTTAAA
1 TTAAATTTAAA
36805 CTTAAATTTAAA
1 -TTAAATTTAAA
*
36817 ATAAATTTAAA
1 TTAAATTTAAA
*
36828 TTTAATTTAAA
1 TTAAATTTAAA
36839 TT
1 TT
36841 TTTAACAAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
11 24 0.59
12 17 0.41
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (11 bp):
TTAAATTTAAA
Found at i:37437 original size:29 final size:30
Alignment explanation
Indices: 37406--37638 Score: 216
Period size: 30 Copynumber: 7.9 Consensus size: 30
37396 GCACGGGGGC
* *
37406 AAAATGGTAGTTTTGGAAGGTTCGGAGTCA
1 AAAATGGTATTTTTGGAAGGTTCGGGGTCA
*
37436 AAAATGATATTTTTGGAA-GTTCGAGGGT--
1 AAAATGGTATTTTTGGAAGGTTCG-GGGTCA
*
37464 AAAATGGTAATTTTTGAAAGGTTCGGGGTCA
1 AAAATGGT-ATTTTTGGAAGGTTCGGGGTCA
* * *
37495 AAAATGGGATTTTTTGGAAGTTTGGGGGT--
1 AAAATGGTA-TTTTTGGAAGGTTCGGGGTCA
*
37524 AAAATGGTATTTTTTTAGAAGGTTCGGGGTCA
1 AAAATGGTA--TTTTTGGAAGGTTCGGGGTCA
* *
37556 AAAATGGGATTTTTGGAAGTTTCGGGGT--
1 AAAATGGTATTTTTGGAAGGTTCGGGGTCA
* * *
37584 -AAATGGTAATTTTCGAAAGGTTCGAGGTCA
1 AAAATGGT-ATTTTTGGAAGGTTCGGGGTCA
37614 AAAATGAG-ATTTTTGGAA-GTTCGGG
1 AAAATG-GTATTTTTGGAAGGTTCGGG
37639 ACCTTCGGGG
Statistics
Matches: 165, Mismatches: 24, Indels: 29
0.76 0.11 0.13
Matches are distributed among these distances:
27 6 0.04
28 23 0.14
29 32 0.19
30 67 0.41
31 28 0.17
32 9 0.05
ACGTcount: A:0.30, C:0.05, G:0.31, T:0.34
Consensus pattern (30 bp):
AAAATGGTATTTTTGGAAGGTTCGGGGTCA
Found at i:37538 original size:60 final size:59
Alignment explanation
Indices: 37400--37634 Score: 312
Period size: 60 Copynumber: 4.0 Consensus size: 59
37390 TCGGATGCAC
* * * * ** *
37400 GGGGGCAAAATGGT-AGTTTTGGAAGGTTCGGAGTCAAAAATGATATTTTTGGAAGTTC
1 GGGGGTAAAATGGTAATTTTTGAAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTT
*
37458 GAGGGTAAAATGGTAATTTTTGAAAGGTTCGGGGTCAAAAATGGGATTTTTTGGAAGTTT
1 GGGGGTAAAATGGTAATTTTTGAAAGGTTCGGGGTCAAAAATGGGA-TTTTTGGAAGTTT
* *
37518 GGGGGTAAAATGGTATTTTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTT
1 GGGGGTAAAATGGTAATTTTTGA-AAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTT
* * * *
37578 CGGGGT-AAATGGTAATTTTCGAAAGGTTCGAGGTCAAAAATGAGATTTTTGGAAGTT
1 GGGGGTAAAATGGTAATTTTTGAAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTT
37635 CGGGACCTTC
Statistics
Matches: 157, Mismatches: 17, Indels: 6
0.87 0.09 0.03
Matches are distributed among these distances:
58 45 0.29
59 39 0.25
60 50 0.32
61 23 0.15
ACGTcount: A:0.29, C:0.05, G:0.32, T:0.34
Consensus pattern (59 bp):
GGGGGTAAAATGGTAATTTTTGAAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTT
Found at i:39516 original size:6 final size:6
Alignment explanation
Indices: 39507--39584 Score: 67
Period size: 6 Copynumber: 13.5 Consensus size: 6
39497 TGAACTTTAT
* * *
39507 TTTAAA TTTATAA --TAAT TTTAAA TTTGAAA -ATAAA TTTAAA CTTAAA
1 TTTAAA TTTA-AA TTTAAA TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA
*
39554 TTTAAA -ATAAA TTTAAA TTT-AA TTTAAA TTT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT
39585 TTAACAAATT
Statistics
Matches: 57, Mismatches: 8, Indels: 14
0.72 0.10 0.18
Matches are distributed among these distances:
4 1 0.02
5 14 0.25
6 37 0.65
7 5 0.09
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.47
Consensus pattern (6 bp):
TTTAAA
Found at i:39569 original size:17 final size:17
Alignment explanation
Indices: 39507--39615 Score: 87
Period size: 17 Copynumber: 6.4 Consensus size: 17
39497 TGAACTTTAT
* *
39507 TTTAAATTTATAATAAT
1 TTTAAATTTAAAATAAA
39524 TTTAAATTTGAAAATAAA
1 TTTAAATTT-AAAATAAA
* *
39542 TTTAAACTTAAATTTAAA
1 TTTAAATTTAAA-ATAAA
* * *
39560 -ATAAATTTAAATTTAA
1 TTTAAATTTAAAATAAA
** *
39576 TTTAAATTTTTAACAAA
1 TTTAAATTTAAAATAAA
39593 TTT-AATCTTAAAATAAA
1 TTTAAAT-TTAAAATAAA
39610 TTTAAA
1 TTTAAA
39616 GGGAAGTTTG
Statistics
Matches: 71, Mismatches: 16, Indels: 9
0.74 0.17 0.09
Matches are distributed among these distances:
16 7 0.10
17 44 0.62
18 20 0.28
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:39584 original size:11 final size:11
Alignment explanation
Indices: 39525--39583 Score: 73
Period size: 11 Copynumber: 5.2 Consensus size: 11
39515 TATAATAATT
39525 TTAAATTTGAAA
1 TTAAATTT-AAA
*
39537 ATAAATTTAAA
1 TTAAATTTAAA
39548 CTTAAATTTAAA
1 -TTAAATTTAAA
*
39560 ATAAATTTAAA
1 TTAAATTTAAA
*
39571 TTTAATTTAAA
1 TTAAATTTAAA
39582 TT
1 TT
39584 TTTAACAAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
11 24 0.59
12 17 0.41
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (11 bp):
TTAAATTTAAA
Found at i:40180 original size:29 final size:30
Alignment explanation
Indices: 40149--40381 Score: 216
Period size: 30 Copynumber: 7.9 Consensus size: 30
40139 GCACGGGGGC
* *
40149 AAAATGGTAGTTTTGGAAGGTTCGGAGTCA
1 AAAATGGTATTTTTGGAAGGTTCGGGGTCA
*
40179 AAAATGATATTTTTGGAA-GTTCGAGGGT--
1 AAAATGGTATTTTTGGAAGGTTCG-GGGTCA
*
40207 AAAATGGTAATTTTTGAAAGGTTCGGGGTCA
1 AAAATGGT-ATTTTTGGAAGGTTCGGGGTCA
* * *
40238 AAAATGGGATTTTTTGGAAGTTTGGGGGT--
1 AAAATGGTA-TTTTTGGAAGGTTCGGGGTCA
*
40267 AAAATGGTATTTTTTTAGAAGGTTCGGGGTCA
1 AAAATGGTA--TTTTTGGAAGGTTCGGGGTCA
* *
40299 AAAATGGGATTTTTGGAAGTTTCGGGGT--
1 AAAATGGTATTTTTGGAAGGTTCGGGGTCA
* * *
40327 -AAATGGTAATTTTCGAAAGGTTCGAGGTCA
1 AAAATGGT-ATTTTTGGAAGGTTCGGGGTCA
40357 AAAATGAG-ATTTTTGGAA-GTTCGGG
1 AAAATG-GTATTTTTGGAAGGTTCGGG
40382 ACCTTCGGGG
Statistics
Matches: 165, Mismatches: 24, Indels: 29
0.76 0.11 0.13
Matches are distributed among these distances:
27 6 0.04
28 23 0.14
29 32 0.19
30 67 0.41
31 28 0.17
32 9 0.05
ACGTcount: A:0.30, C:0.05, G:0.31, T:0.34
Consensus pattern (30 bp):
AAAATGGTATTTTTGGAAGGTTCGGGGTCA
Found at i:40281 original size:60 final size:59
Alignment explanation
Indices: 40143--40377 Score: 312
Period size: 60 Copynumber: 4.0 Consensus size: 59
40133 TCGGATGCAC
* * * * ** *
40143 GGGGGCAAAATGGT-AGTTTTGGAAGGTTCGGAGTCAAAAATGATATTTTTGGAAGTTC
1 GGGGGTAAAATGGTAATTTTTGAAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTT
*
40201 GAGGGTAAAATGGTAATTTTTGAAAGGTTCGGGGTCAAAAATGGGATTTTTTGGAAGTTT
1 GGGGGTAAAATGGTAATTTTTGAAAGGTTCGGGGTCAAAAATGGGA-TTTTTGGAAGTTT
* *
40261 GGGGGTAAAATGGTATTTTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTT
1 GGGGGTAAAATGGTAATTTTTGA-AAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTT
* * * *
40321 CGGGGT-AAATGGTAATTTTCGAAAGGTTCGAGGTCAAAAATGAGATTTTTGGAAGTT
1 GGGGGTAAAATGGTAATTTTTGAAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTT
40378 CGGGACCTTC
Statistics
Matches: 157, Mismatches: 17, Indels: 6
0.87 0.09 0.03
Matches are distributed among these distances:
58 45 0.29
59 39 0.25
60 50 0.32
61 23 0.15
ACGTcount: A:0.29, C:0.05, G:0.32, T:0.34
Consensus pattern (59 bp):
GGGGGTAAAATGGTAATTTTTGAAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTT
Found at i:42259 original size:6 final size:6
Alignment explanation
Indices: 42250--42327 Score: 67
Period size: 6 Copynumber: 13.5 Consensus size: 6
42240 TGAACTTTAT
* * *
42250 TTTAAA TTTATAA --TAAT TTTAAA TTTGAAA -ATAAA TTTAAA CTTAAA
1 TTTAAA TTTA-AA TTTAAA TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA
*
42297 TTTAAA -ATAAA TTTAAA TTT-AA TTTAAA TTT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT
42328 TTAACAAATT
Statistics
Matches: 57, Mismatches: 8, Indels: 14
0.72 0.10 0.18
Matches are distributed among these distances:
4 1 0.02
5 14 0.25
6 37 0.65
7 5 0.09
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.47
Consensus pattern (6 bp):
TTTAAA
Found at i:42312 original size:17 final size:17
Alignment explanation
Indices: 42250--42358 Score: 87
Period size: 17 Copynumber: 6.4 Consensus size: 17
42240 TGAACTTTAT
* *
42250 TTTAAATTTATAATAAT
1 TTTAAATTTAAAATAAA
42267 TTTAAATTTGAAAATAAA
1 TTTAAATTT-AAAATAAA
* *
42285 TTTAAACTTAAATTTAAA
1 TTTAAATTTAAA-ATAAA
* * *
42303 -ATAAATTTAAATTTAA
1 TTTAAATTTAAAATAAA
** *
42319 TTTAAATTTTTAACAAA
1 TTTAAATTTAAAATAAA
42336 TTT-AATCTTAAAATAAA
1 TTTAAAT-TTAAAATAAA
42353 TTTAAA
1 TTTAAA
42359 GGGAAGTTTG
Statistics
Matches: 71, Mismatches: 16, Indels: 9
0.74 0.17 0.09
Matches are distributed among these distances:
16 7 0.10
17 44 0.62
18 20 0.28
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:42327 original size:11 final size:11
Alignment explanation
Indices: 42268--42326 Score: 73
Period size: 11 Copynumber: 5.2 Consensus size: 11
42258 TATAATAATT
42268 TTAAATTTGAAA
1 TTAAATTT-AAA
*
42280 ATAAATTTAAA
1 TTAAATTTAAA
42291 CTTAAATTTAAA
1 -TTAAATTTAAA
*
42303 ATAAATTTAAA
1 TTAAATTTAAA
*
42314 TTTAATTTAAA
1 TTAAATTTAAA
42325 TT
1 TT
42327 TTTAACAAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
11 24 0.59
12 17 0.41
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (11 bp):
TTAAATTTAAA
Found at i:43262 original size:18 final size:19
Alignment explanation
Indices: 43224--43265 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
43214 AGCACATGCT
* *
43224 AATATTTTATTTTACATTA
1 AATATTTAAATTTACATTA
*
43243 AATATTTAAATTTACATAA
1 AATATTTAAATTTACATTA
43262 AATA
1 AATA
43266 CATGAATTTC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (19 bp):
AATATTTAAATTTACATTA
Found at i:43712 original size:347 final size:344
Alignment explanation
Indices: 43030--44043 Score: 1463
Period size: 347 Copynumber: 3.0 Consensus size: 344
43020 ATGGTTTACT
* *
43030 TGACGTAATATAATATTAATAAATTAATAAAAGA-TAAAAAAGGTAA-TTTTAAAAGTTTAAAAA
1 TGACGTAATATAATATTAATAAATTAGTAAAAGACAAAAAAAGGTAATTTTTAAAAGTTTAAAAA
* *
43093 TA-TT-G---TCGTTAATTCGTTAGTGATGTATGAGCCATTGTCACAGTTGAATATTATCGTTAA
66 TATTTCGTTATCGTTAATTCGTTAGTGATGTGTGAGCCATCGTCACAGTTGAATATTATCGTTAA
* * *
43153 TT-GATTAATATTGTCATTGGATTCAATTGTTGGATATTCTTTGATATTACTTAACTAATAAAGC
131 TTCG-TTAATATTGTCGTTGGATTCAATTGTTGGATACTCTTTGATATTACTTAACTTATAAAGC
* * *
43217 ACATGCTAATATTTTATTTTACATTAAATATTTAAATTTACATAAAATACATGAATTTCCCTCTT
195 ACATGCTAATATTTTATTTTACATTAAATATTTAAATTTACATCAAATACATGAATTTTCCGCTT
* * * *
43282 ACAATATCAATTTGAATTCCTCTTCTTAAAATAATTAAAAACCTTTTAAGGTAATTTATTTAATT
260 AAAATATCAATTTGAATTTCTCTTCTCAAAATAATTAAAAACCTTTTAAGGTAATTTACTTAATT
43347 TTTGAACTGTATGATCTACC
325 TTTGAACTGTATGATCTACC
* *
43367 TGACGTAATATAATATTAACAAATTAGTAAAAAACAAAAAAAGGTAATTTTTAAAAGTTTAAAAA
1 TGACGTAATATAATATTAATAAATTAGTAAAAGACAAAAAAAGGTAATTTTTAAAAGTTTAAAAA
* *
43432 TATTGTCGTTTATCCGTTAATTCGTTAGTGATGTGTGAACCATCGTCACAGTTGAATATAATCGT
66 TATT-TCG-TTAT-CGTTAATTCGTTAGTGATGTGTGAGCCATCGTCACAGTTGAATATTATCGT
* * * * *
43497 TATTTCGTTAATATTGCCGTTGGGTTCAATTATTGGATACTCTTTGATATTACTTAATTTATAAA
128 TAATTCGTTAATATTGTCGTTGGATTCAATTGTTGGATACTCTTTGATATTACTTAACTTATAAA
*
43562 GCACATGCTACTATTTTATTTTACATTAAATATTTAAATTTACATCAAATACATGAATTTTCCGC
193 GCACATGCTAATATTTTATTTTACATTAAATATTTAAATTTACATCAAATACATGAATTTTCCGC
*
43627 TTAAAATATCAATTTGAATTTCTCTTCTCAAAATAATTAAAAACCTTTTAAGGTAATTTACGTAA
258 TTAAAATATCAATTTGAATTTCTCTTCTCAAAATAATTAAAAACCTTTTAAGGTAATTTACTTAA
*
43692 TTTTTGAACTGTATGATCTACT
323 TTTTTGAACTGTATGATCTACC
* *
43714 TGGCCTAATATAATATTAATAAATTAGTAAAAGACAAAAAAA-GTAATTTTTAAAAGTTTAAAAA
1 TGACGTAATATAATATTAATAAATTAGTAAAAGACAAAAAAAGGTAATTTTTAAAAGTTTAAAAA
* * *
43778 TATTATCGTTAATTCGTTAATTCGTTAATGATGTGTGAGCCATCGTCATAGTTAAATATTATCGT
66 TATT-TCGTT-A-TCGTTAATTCGTTAGTGATGTGTGAGCCATCGTCACAGTTGAATATTATCGT
* * *
43843 TAATTCGTTAATATTGTCGTTGGATTTAATTGTTGGATACTCTTAGATATTATTTAACTTATAAA
128 TAATTCGTTAATATTGTCGTTGGATTCAATTGTTGGATACTCTTTGATATTACTTAACTTATAAA
* * * * * *
43908 ACATATGCTATTATTTTATTTCACATTAAATATTTAAATTTATATCAAATACAT-AAATTTCTCG
193 GCACATGCTAATATTTTATTTTACATTAAATATTTAAATTTACATCAAATACATGAATTTTC-CG
* * * * * * *
43972 CTTAAAATATCAATTTAAATTTCCCTTATCAAAATAATAAAAAATCTTTTATGATAATTTACTTA
257 CTTAAAATATCAATTTGAATTTCTCTTCTCAAAATAATTAAAAACCTTTTAAGGTAATTTACTTA
44037 ATTTTTG
322 ATTTTTG
44044 TGTGTGGTAA
Statistics
Matches: 605, Mismatches: 58, Indels: 19
0.89 0.09 0.03
Matches are distributed among these distances:
337 31 0.05
338 11 0.02
339 19 0.03
340 1 0.00
341 1 0.00
342 1 0.00
345 8 0.01
346 249 0.41
347 283 0.47
348 1 0.00
ACGTcount: A:0.38, C:0.11, G:0.10, T:0.41
Consensus pattern (344 bp):
TGACGTAATATAATATTAATAAATTAGTAAAAGACAAAAAAAGGTAATTTTTAAAAGTTTAAAAA
TATTTCGTTATCGTTAATTCGTTAGTGATGTGTGAGCCATCGTCACAGTTGAATATTATCGTTAA
TTCGTTAATATTGTCGTTGGATTCAATTGTTGGATACTCTTTGATATTACTTAACTTATAAAGCA
CATGCTAATATTTTATTTTACATTAAATATTTAAATTTACATCAAATACATGAATTTTCCGCTTA
AAATATCAATTTGAATTTCTCTTCTCAAAATAATTAAAAACCTTTTAAGGTAATTTACTTAATTT
TTGAACTGTATGATCTACC
Found at i:47500 original size:45 final size:45
Alignment explanation
Indices: 47429--47521 Score: 150
Period size: 45 Copynumber: 2.1 Consensus size: 45
47419 GAAGGAAAGT
* * *
47429 TGATGATGATAACACTAGGGGGGTTAAACAAGTTCCTGAAGAACA
1 TGATGATGATAACACCAAGGGGGTTAAACAAGATCCTGAAGAACA
*
47474 TGATGATGATAACACCAAGGGTGTTAAACAAGATCCTGAAGAACA
1 TGATGATGATAACACCAAGGGGGTTAAACAAGATCCTGAAGAACA
47519 TGA
1 TGA
47522 AACCAATTGA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.40, C:0.14, G:0.25, T:0.22
Consensus pattern (45 bp):
TGATGATGATAACACCAAGGGGGTTAAACAAGATCCTGAAGAACA
Found at i:51033 original size:253 final size:253
Alignment explanation
Indices: 50603--51333 Score: 1044
Period size: 231 Copynumber: 3.0 Consensus size: 253
50593 GAAGATATGT
* *
50603 ATCAAGAATGGTATCTAAACTCCGAACCTGGATTCGTCCTTCAATATTCAATATTTTAACATAGG
1 ATCAAGAACGGTATCTAAACTCCGAACCCGGATTCGTCCTTCAATATTCAATATTTTAACATAGG
* *
50668 AGAAACAAGGAACAAACATATGCATCGAGAATGACAATACAAGACATTTCATGATAAGCAAAGCA
66 AGAAACAAGGAAC-AAC--ATGCATCGAGAACGACAATACAAGACATTTCAAGATAAGCAAAGCA
* *
50733 TCAAATGAACATATGTATAGAGAATGGAATCTGAATTCGCAACCTGGATTTGTCCTTTCAAACTG
128 TCAAATGAACATATGTATAGAGAACGGAATCTGAACTCGCAACCTGGATTTGTCCTTTCAAACTG
* *
50798 CATCATGTCAATAAAAAGATTC-ATATTTTAACAAAGGAGAAACAAGGAACAAACATAAG-C
193 CATCATGTCAATAAAAAGACTCAATATTTTAACATAGGAGAAACAAGGAACAAACAT-AGTC
* *
50858 ATCAAGAACAGTATCTAAACTCCGAACCCGGATTCATCCTTCAATATTCAATATTTTAACATAGG
1 ATCAAGAACGGTATCTAAACTCCGAACCCGGATTCGTCCTTCAATATTCAATATTTTAACATAGG
* *
50923 AGAAACAAGGAACGAACATGCATCGAGAACGACAATACAAGAAATTTTAAGATAAGCAAAGCATC
66 AGAAACAAGGAAC-AACATGCATCGAGAACGACAATACAAGACATTTCAAGATAAGCAAAGCATC
* * *
50988 AAATGAACATATGTATGGAGAACAGAATCTGAACTCGCAACCTGGATTTGTCCTTTGAAACTGCA
130 AAATGAACATATGTATAGAGAACGGAATCTGAACTCGCAACCTGGATTTGTCCTTTCAAACTGCA
*
51053 TCATGTCAATAAAAAGACTCGATATTTTAACATAGGAGAAACAAGGAACAAACATAGTC
195 TCATGTCAATAAAAAGACTCAATATTTTAACATAGGAGAAACAAGGAACAAACATAGTC
*
51112 ATCGAGAACGGTATCTAAACTCCGAACCCGGA---GTCCTTCAATATTCAATATTTTAACATA--
1 ATCAAGAACGGTATCTAAACTCCGAACCCGGATTCGTCCTTCAATATTCAATATTTTAACATAGG
* *
51172 AG--AC-----A-AACA---A--G-GAACG---ATATAAGACATTTCAAGATAAGCAAAACATCA
66 AGAAACAAGGAACAACATGCATCGAGAACGACAATACAAGACATTTCAAGATAAGCAAAGCATCA
*
51220 AATGAACATATGTATCGAGAACGGAATCTGAACTCGCAACCTGGATTTGTCC-TTCAAAACTGCA
131 AATGAACATATGTATAGAGAACGGAATCTGAACTCGCAACCTGGATTTGTCCTTTC-AAACTGCA
*
51284 TCATGTCAATAAAAAGACTCAATATTTTAACATAGAAGAAACAAGGAACA
195 TCATGTCAATAAAAAGACTCAATATTTTAACATAGGAGAAACAAGGAACA
51334 TAGGCATCGA
Statistics
Matches: 445, Mismatches: 28, Indels: 30
0.88 0.06 0.06
Matches are distributed among these distances:
230 2 0.00
231 134 0.30
234 5 0.01
235 1 0.00
237 1 0.00
240 4 0.01
242 1 0.00
247 2 0.00
249 2 0.00
251 27 0.06
253 125 0.28
254 64 0.14
255 77 0.17
ACGTcount: A:0.43, C:0.18, G:0.16, T:0.24
Consensus pattern (253 bp):
ATCAAGAACGGTATCTAAACTCCGAACCCGGATTCGTCCTTCAATATTCAATATTTTAACATAGG
AGAAACAAGGAACAACATGCATCGAGAACGACAATACAAGACATTTCAAGATAAGCAAAGCATCA
AATGAACATATGTATAGAGAACGGAATCTGAACTCGCAACCTGGATTTGTCCTTTCAAACTGCAT
CATGTCAATAAAAAGACTCAATATTTTAACATAGGAGAAACAAGGAACAAACATAGTC
Found at i:54713 original size:25 final size:25
Alignment explanation
Indices: 54671--54747 Score: 68
Period size: 25 Copynumber: 3.1 Consensus size: 25
54661 ATAAAATTAT
* *
54671 ATTTTAACTTCTTT-AAAATTATGAA
1 ATTTTAA-TTTTTTAAAAATTATAAA
*
54696 ATTTTAATTTTTTAAAAAATATAAA
1 ATTTTAATTTTTTAAAAATTATAAA
* * * *
54721 AATATAAATTATTAAAAATTA-AAA
1 ATTTTAATTTTTTAAAAATTATAAA
54745 ATT
1 ATT
54748 AATTTCAATC
Statistics
Matches: 42, Mismatches: 9, Indels: 3
0.78 0.17 0.06
Matches are distributed among these distances:
24 10 0.24
25 32 0.76
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.44
Consensus pattern (25 bp):
ATTTTAATTTTTTAAAAATTATAAA
Found at i:57404 original size:30 final size:30
Alignment explanation
Indices: 57368--57496 Score: 127
Period size: 30 Copynumber: 4.3 Consensus size: 30
57358 ATTTAAAACC
*
57368 GGGTCAAATTTAAATTTTT-GAAAATTTTAG
1 GGGTCAAATTGAAATTTTTGGAAAA-TTTAG
* * * * *
57398 GGGTCAAATTGGAAGTTCTAGAAAGTTT-G
1 GGGTCAAATTGAAATTTTTGGAAAATTTAG
*
57427 GAGGTCAAATTGGAATTTTTTGGAAAATTTAG
1 G-GGTCAAATT-GAAATTTTTGGAAAATTTAG
* * *
57459 GGGTCGAATTAAAATTTTTGGAAAATTTAA
1 GGGTCAAATTGAAATTTTTGGAAAATTTAG
57489 GGGTCAAA
1 GGGTCAAA
57497 AAAACAATTT
Statistics
Matches: 79, Mismatches: 16, Indels: 8
0.77 0.16 0.08
Matches are distributed among these distances:
29 2 0.03
30 51 0.65
31 24 0.30
32 2 0.03
ACGTcount: A:0.36, C:0.05, G:0.24, T:0.36
Consensus pattern (30 bp):
GGGTCAAATTGAAATTTTTGGAAAATTTAG
Found at i:57506 original size:31 final size:30
Alignment explanation
Indices: 57443--57507 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 30
57433 AAATTGGAAT
* * **
57443 TTTTTGGAAAATTTAGGGGTCGAATTAAAA
1 TTTTTGGAAAATTTAAGGGTCAAAAAAAAA
57473 TTTTTGGAAAATTTAAGGGTCAAAAAAACAA
1 TTTTTGGAAAATTTAAGGGTCAAAAAAA-AA
57504 TTTT
1 TTTT
57508 AAAATAAAGT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 24 0.80
31 6 0.20
ACGTcount: A:0.40, C:0.05, G:0.18, T:0.37
Consensus pattern (30 bp):
TTTTTGGAAAATTTAAGGGTCAAAAAAAAA
Found at i:58525 original size:7 final size:7
Alignment explanation
Indices: 58513--58545 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
58503 TTTATTTATT
58513 TAATAAA
1 TAATAAA
58520 TAATAAA
1 TAATAAA
58527 TAATAAA
1 TAATAAA
58534 T-A-AAA
1 TAATAAA
58539 TAATAAA
1 TAATAAA
58546 ATTTGGGTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
5 4 0.17
6 2 0.08
7 18 0.75
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (7 bp):
TAATAAA
Found at i:59037 original size:50 final size:50
Alignment explanation
Indices: 58982--59166 Score: 280
Period size: 50 Copynumber: 3.7 Consensus size: 50
58972 TGTGAGTTTT
* * *
58982 AATCTGCCCCTCTATTACTTTAAGGGTATAAGATTCGCTTTTGTAGCTTT
1 AATCTGCCCCTCTATAACTTTAAGGGTATAAGATTTGCTTTTGTAGCTTC
*
59032 AATCTGCCCCTCTATAACTTTAAGGATATAAGATTTGCTTTTGTAGCTTC
1 AATCTGCCCCTCTATAACTTTAAGGGTATAAGATTTGCTTTTGTAGCTTC
* *
59082 AATCTGCCCTTCTGTAACTTTAAGGGTATAAGATTTGCTTTTGTAGCTTC
1 AATCTGCCCCTCTATAACTTTAAGGGTATAAGATTTGCTTTTGTAGCTTC
* * * *
59132 AATCTGCCCCTCTGTGACTTTAGGGGTAAAAGATT
1 AATCTGCCCCTCTATAACTTTAAGGGTATAAGATT
59167 GGATTGTTTC
Statistics
Matches: 124, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
50 124 1.00
ACGTcount: A:0.24, C:0.19, G:0.17, T:0.39
Consensus pattern (50 bp):
AATCTGCCCCTCTATAACTTTAAGGGTATAAGATTTGCTTTTGTAGCTTC
Found at i:59211 original size:39 final size:40
Alignment explanation
Indices: 59154--59306 Score: 184
Period size: 40 Copynumber: 3.9 Consensus size: 40
59144 TGTGACTTTA
* * *
59154 GGGGTAAAAGATTGGATTGT-TTCAACCTGCCCTATGGTT
1 GGGGTAAAAGATTAGATTGTCTTCAATCTGCCCTATGATT
* * *
59193 GGGGTAAAAGATTAGATTGTCTTTAATTTGCCCCATGATT
1 GGGGTAAAAGATTAGATTGTCTTCAATCTGCCCTATGATT
* *
59233 GGGGTAAGAGATTAGATTGTCTTCAATCTGCCCTCTGATT
1 GGGGTAAAAGATTAGATTGTCTTCAATCTGCCCTATGATT
* * *
59273 AGGGTAAAAGATTGGA-TGATCTTTAATCTGCCCT
1 GGGGTAAAAGATTAGATTG-TCTTCAATCTGCCCT
59307 CTGGTTAGGA
Statistics
Matches: 97, Mismatches: 15, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
39 21 0.22
40 76 0.78
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.35
Consensus pattern (40 bp):
GGGGTAAAAGATTAGATTGTCTTCAATCTGCCCTATGATT
Found at i:59279 original size:80 final size:79
Alignment explanation
Indices: 59154--59305 Score: 207
Period size: 80 Copynumber: 1.9 Consensus size: 79
59144 TGTGACTTTA
* * *
59154 GGGGTAAAAGATTGGATTGTTTCAACCTGCCCTATGGTTGGGGTAAAAGATTAGATTG-TCTTTA
1 GGGGTAAAAGATTAGATTGTTTCAACCTGCCCTATGATTAGGGTAAAAGATTAGA-TGATCTTTA
*
59218 ATTTGCCCCATGATT
65 ATCTGCCCCATGATT
* * * *
59233 GGGGTAAGAGATTAGATTGTCTTCAATCTGCCCTCTGATTAGGGTAAAAGATTGGATGATCTTTA
1 GGGGTAAAAGATTAGATTGT-TTCAACCTGCCCTATGATTAGGGTAAAAGATTAGATGATCTTTA
59298 ATCTGCCC
65 ATCTGCCC
59306 TCTGGTTAGG
Statistics
Matches: 63, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
79 20 0.32
80 43 0.68
ACGTcount: A:0.26, C:0.15, G:0.25, T:0.34
Consensus pattern (79 bp):
GGGGTAAAAGATTAGATTGTTTCAACCTGCCCTATGATTAGGGTAAAAGATTAGATGATCTTTAA
TCTGCCCCATGATT
Found at i:59306 original size:40 final size:40
Alignment explanation
Indices: 59128--59326 Score: 179
Period size: 40 Copynumber: 4.8 Consensus size: 40
59118 GCTTTTGTAG
59128 CTTCAATCTGCCCCTCTGTGACTTTAGGGGTAAAAGATTGGATTGT
1 CTTCAATCTG-CCCTC--TGA--TTA-GGGTAAAAGATTGGATTGT
* * * * *
59174 -TTCAACCTGCCCTATGGTTGGGGTAAAAGATTAGATTGT
1 CTTCAATCTGCCCTCTGATTAGGGTAAAAGATTGGATTGT
* * * * *
59213 CTTTAATTTGCCC-CATGATTGGGGTAAGAGATTAGATTGT
1 CTTCAATCTGCCCTC-TGATTAGGGTAAAAGATTGGATTGT
59253 CTTCAATCTGCCCTCTGATTAGGGTAAAAGATTGGA-TGAT
1 CTTCAATCTGCCCTCTGATTAGGGTAAAAGATTGGATTG-T
* * * *
59293 CTTTAATCTGCCCTCTGGTTAGGATAAGAGATTG
1 CTTCAATCTGCCCTCTGATTAGGGTAAAAGATTG
59327 AAGGTTCTAA
Statistics
Matches: 129, Mismatches: 20, Indels: 14
0.79 0.12 0.09
Matches are distributed among these distances:
39 20 0.16
40 94 0.73
41 1 0.01
42 2 0.02
44 4 0.03
45 8 0.06
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.35
Consensus pattern (40 bp):
CTTCAATCTGCCCTCTGATTAGGGTAAAAGATTGGATTGT
Found at i:59321 original size:80 final size:79
Alignment explanation
Indices: 59162--59325 Score: 197
Period size: 80 Copynumber: 2.1 Consensus size: 79
59152 TAGGGGTAAA
* * * *
59162 AGATTGGATTGTTTCAACCTGCCCTATGGTTGGGGTAAAAGATTAGATTGTCTTTAATTTGCCCC
1 AGATTAGATTGTTTCAACCTGCCCTATGATTAGGGTAAAAGATTAGATTGTCTTTAATCTGCCCC
* *
59227 ATGATTGGGGTAAG
66 ATGATTAGGATAAG
* * *
59241 AGATTAGATTGTCTTCAATCTGCCCTCTGATTAGGGTAAAAGATTGGA-TGATCTTTAATCTGCC
1 AGATTAGATTGT-TTCAACCTGCCCTATGATTAGGGTAAAAGATTAGATTG-TCTTTAATCTGCC
*
59305 CTC-TGGTTAGGATAAG
64 C-CATGATTAGGATAAG
59321 AGATT
1 AGATT
59326 GAAGGTTCTA
Statistics
Matches: 72, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
79 13 0.18
80 58 0.81
81 1 0.01
ACGTcount: A:0.26, C:0.15, G:0.24, T:0.35
Consensus pattern (79 bp):
AGATTAGATTGTTTCAACCTGCCCTATGATTAGGGTAAAAGATTAGATTGTCTTTAATCTGCCCC
ATGATTAGGATAAG
Found at i:59460 original size:49 final size:50
Alignment explanation
Indices: 59383--59508 Score: 182
Period size: 49 Copynumber: 2.5 Consensus size: 50
59373 TCCTTGTGAC
*
59383 TTCAATCTGCCCCTCTACAGTTTTAGGTGAATGAGAGTTGCCATTGCGG-
1 TTCAATCTGCCCCTCTACAGCTTTAGGTGAATGAGAGTTGCCATTGCGGT
* * * *
59432 TTCATTCTGCCCCTCTACAGCTTTAGGTGTATGAGATTTGCCTTTGCGGT
1 TTCAATCTGCCCCTCTACAGCTTTAGGTGAATGAGAGTTGCCATTGCGGT
* *
59482 TTCAATCTGCACCTCTATAGCTTTAGG
1 TTCAATCTGCCCCTCTACAGCTTTAGG
59509 GGTAAAAGAT
Statistics
Matches: 68, Mismatches: 8, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
49 44 0.65
50 24 0.35
ACGTcount: A:0.18, C:0.24, G:0.21, T:0.37
Consensus pattern (50 bp):
TTCAATCTGCCCCTCTACAGCTTTAGGTGAATGAGAGTTGCCATTGCGGT
Found at i:59519 original size:50 final size:49
Alignment explanation
Indices: 59383--59526 Score: 173
Period size: 49 Copynumber: 2.9 Consensus size: 49
59373 TCCTTGTGAC
* *
59383 TTCAATCTGCCCCTCTACAGTTTTAGGTG-AATGAGAGTTGCCATTGCGG
1 TTCAATCTGCCCCTCTACAGCTTTAGGTGTAA-GAGATTTGCCATTGCGG
* * *
59432 TTCATTCTGCCCCTCTACAGCTTTAGGTGTATGAGATTTGCCTTTGCGG
1 TTCAATCTGCCCCTCTACAGCTTTAGGTGTAAGAGATTTGCCATTGCGG
* * * * *
59481 TTTCAATCTGCACCTCTATAGCTTTAGGGGTAAAAGATTTGTCATT
1 -TTCAATCTGCCCCTCTACAGCTTTAGGTGTAAGAGATTTGCCATT
59527 TTATCGCCAT
Statistics
Matches: 80, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
49 42 0.52
50 38 0.47
ACGTcount: A:0.20, C:0.22, G:0.22, T:0.37
Consensus pattern (49 bp):
TTCAATCTGCCCCTCTACAGCTTTAGGTGTAAGAGATTTGCCATTGCGG
Done.