Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005723.1 Kokia drynarioides strain JFW-HI SEQ_119955, 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: 48930
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.32
Warning! 5 characters in sequence are not A, C, G, or T
Found at i:14771 original size:20 final size:19
Alignment explanation
Indices: 14746--14783 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
14736 TTTCTACCCT
14746 CTTTCTTTGCTCTTTTTCTG
1 CTTTCTTT-CTCTTTTTCTG
*
14766 CTTTCTTTTTCTTTTTCT
1 CTTTCTTTCTCTTTTTCT
14784 CAATAGAGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.00, C:0.24, G:0.05, T:0.71
Consensus pattern (19 bp):
CTTTCTTTCTCTTTTTCTG
Found at i:19293 original size:59 final size:58
Alignment explanation
Indices: 19163--19295 Score: 162
Period size: 59 Copynumber: 2.3 Consensus size: 58
19153 ATTCATATTT
* * *
19163 TAATAATATTAAAAATGTTATTAAATTTGTATATTATTTTATTAAATTGCATTTAATAA
1 TAATTATATT-AAAATGTTATTAAATTTGTATATTATTTTATTAAATTACAATTAATAA
* * *
19222 TAATTATGTTAAAATGTTATTAAATTATTTATTATT-TTTTATTAAATTATAATTAATAA
1 TAATTATATTAAAATGTTATTAAATT-TGTA-TATTATTTTATTAAATTACAATTAATAA
19281 TAATCT-TATTAAAAT
1 TAAT-TATATTAAAAT
19296 TTAATAATAA
Statistics
Matches: 64, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
58 16 0.25
59 43 0.67
60 5 0.08
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.51
Consensus pattern (58 bp):
TAATTATATTAAAATGTTATTAAATTTGTATATTATTTTATTAAATTACAATTAATAA
Found at i:19309 original size:25 final size:26
Alignment explanation
Indices: 19260--19310 Score: 79
Period size: 25 Copynumber: 2.0 Consensus size: 26
19250 TTATTATTTT
19260 TTATTAAATTATAATTAATAATAATC
1 TTATTAAATTATAATTAATAATAATC
19286 TTATTAAAATT-TAA-TAATAATAATC
1 TTATT-AAATTATAATTAATAATAATC
19311 ATTTACCAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
25 11 0.46
26 8 0.33
27 5 0.21
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (26 bp):
TTATTAAATTATAATTAATAATAATC
Found at i:19475 original size:16 final size:16
Alignment explanation
Indices: 19454--19499 Score: 67
Period size: 16 Copynumber: 2.9 Consensus size: 16
19444 TGAATTACTG
19454 ATTACAG-TCATATTCT
1 ATTACAGCTC-TATTCT
19470 ATTACAGCTCTATTCT
1 ATTACAGCTCTATTCT
*
19486 ATTACAACTCTATT
1 ATTACAGCTCTATT
19500 TCATTACAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
16 26 0.93
17 2 0.07
ACGTcount: A:0.30, C:0.22, G:0.04, T:0.43
Consensus pattern (16 bp):
ATTACAGCTCTATTCT
Found at i:19505 original size:16 final size:16
Alignment explanation
Indices: 19464--19509 Score: 67
Period size: 16 Copynumber: 2.9 Consensus size: 16
19454 ATTACAGTCA
*
19464 TATTCTATTACAGCTC
1 TATTCTATTACAACTC
19480 TATTCTATTACAACTC
1 TATTCTATTACAACTC
19496 TATT-TCATTACAAC
1 TATTCT-ATTACAAC
19510 GAATCAAACA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
15 1 0.04
16 27 0.96
ACGTcount: A:0.30, C:0.24, G:0.02, T:0.43
Consensus pattern (16 bp):
TATTCTATTACAACTC
Found at i:20002 original size:13 final size:14
Alignment explanation
Indices: 19979--20009 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
19969 CATTAAACTC
19979 AAATAAAAATAAAT
1 AAATAAAAATAAAT
19993 AAAT-AAAATAAAT
1 AAATAAAAATAAAT
20006 AAAT
1 AAAT
20010 TTTATTTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 13 0.76
14 4 0.24
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (14 bp):
AAATAAAAATAAAT
Found at i:20486 original size:2 final size:2
Alignment explanation
Indices: 20479--20541 Score: 101
Period size: 2 Copynumber: 32.0 Consensus size: 2
20469 TCGTTCATAC
20479 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
20521 AT TT AT AT AT TT AT -T AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
20542 TGCTCATTTA
Statistics
Matches: 56, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
1 1 0.02
2 55 0.98
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
AT
Found at i:21605 original size:30 final size:30
Alignment explanation
Indices: 21569--21998 Score: 290
Period size: 30 Copynumber: 14.4 Consensus size: 30
21559 TTTTGACTGT
*
21569 AAAATTACATTTTGACCCTTGAACTTCTCC
1 AAAATTACATTTTGACCCTTAAACTTCTCC
* *
21599 AAAATTACATTTTAACCCTAAAACTTCTCC
1 AAAATTACATTTTGACCCTTAAACTTCTCC
*
21629 AAAATTACATTTTAACCCTTAAACTTCTCC
1 AAAATTACATTTTGACCCTTAAACTTCTCC
* * * *
21659 AAAATCACATTTTAACCC-TAAAATTTTCC
1 AAAATTACATTTTGACCCTTAAACTTCTCC
21688 AAAATTACAATTTTTGACTCC--AAACTT-TCCC
1 AAAATTAC-A-TTTTGAC-CCTTAAACTTCT-CC
*
21719 AAAATTACATTTTGA-CCTTAAACTTTTCC
1 AAAATTACATTTTGACCCTTAAACTTCTCC
* ** * *
21748 AAAATCACATTTTGACCCTCGAATTTTTCC
1 AAAATTACATTTTGACCCTTAAACTTCTCC
**
21778 AAAATTGTATTTTGACCCTTAAACTTCTCC
1 AAAATTACATTTTGACCCTTAAACTTCTCC
* * *** *
21808 AAAATCACATTTTAACCCCCGAACTTTTCC
1 AAAATTACATTTTGACCCTTAAACTTCTCC
*** * * ** * *
21838 -AAATCGTATTTTCACTCTCGAACTTATCT
1 AAAATTACATTTTGACCCTTAAACTTCTCC
* * *
21867 AAAATCACATTTTGGTCACC--AAACCTTCT-T
1 AAAATTACATTTT-GAC-CCTTAAA-CTTCTCC
* * * *
21897 GAAATCACATTTTGACCC-CAAACTTCTCT
1 AAAATTACATTTTGACCCTTAAACTTCTCC
* * *
21926 AAAATCATATTTTAACCC-TAAACTT-TCCC
1 AAAATTACATTTTGACCCTTAAACTTCT-CC
* * *
21955 AAAATTACATTTTTTACCCCTAAACTTTTCC
1 AAAATTACA-TTTTGACCCTTAAACTTCTCC
*
21986 AAAATTATATTTT
1 AAAATTACATTTT
21999 AACCTCGAAT
Statistics
Matches: 328, Mismatches: 54, Indels: 36
0.78 0.13 0.09
Matches are distributed among these distances:
27 2 0.01
28 8 0.02
29 101 0.31
30 170 0.52
31 43 0.13
32 4 0.01
ACGTcount: A:0.34, C:0.26, G:0.03, T:0.37
Consensus pattern (30 bp):
AAAATTACATTTTGACCCTTAAACTTCTCC
Found at i:21755 original size:89 final size:88
Alignment explanation
Indices: 21569--22004 Score: 328
Period size: 89 Copynumber: 4.9 Consensus size: 88
21559 TTTTGACTGT
* * ** * *
21569 AAAATTACATTTTGACCCTTGAACTTCTCCAAAATTACA-TTTTAACCCTAAAACTTCTCCAAAA
1 AAAATCACATTTTAACCCTCAAACTTTTCCAAAATTACATTTTTGACCCT-AAACTTC-CCAAAA
*
21633 TTACATTTTAACCCTTAAACTTCTCC
64 TTACATTTTAA-CCTCAAACTTCTCC
*
21659 AAAATCACATTTTAACCCT-AAAATTTTCCAAAATTACAATTTTTGACTCC-AAACTTTCCCAAA
1 AAAATCACATTTTAACCCTCAAACTTTTCCAAAATTAC-ATTTTTGAC-CCTAAAC-TTCCCAAA
* * *
21722 ATTACATTTTGACCTTAAACTTTTCC
63 ATTACATTTTAACCTCAAACTTCTCC
* * * **
21748 AAAATCACATTTTGACCCTCGAATTTTTCCAAAATTGTA-TTTTGACCCTTAAACTTCTCCAAAA
1 AAAATCACATTTTAACCCTCAAACTTTTCCAAAATTACATTTTTGACCC-TAAACTTC-CCAAAA
* * * *
21812 TCACATTTTAACCCCCGAACTTTTCC
64 TTACATTTTAA-CCTCAAACTTCTCC
** * * * * * * * * ***
21838 -AAATCGTATTTTCACTCTCGAACTTATCTAAAATCACATTTTGGTCACC-AAACCTTCTTGAAA
1 AAAATCACATTTTAACCCTCAAACTTTTCCAAAATTACATTTTTGAC-CCTAAA-CTTCCCAAAA
* * * *
21901 TCACATTTTGACCCCAAACTTCTCT
64 TTACATTTTAACCTCAAACTTCTCC
* * * *
21926 AAAATCATATTTTAACCCT-AAACTTTCCCAAAATTACATTTTTTACCCCTAAACTTTTCCAAAA
1 AAAATCACATTTTAACCCTCAAACTTTTCCAAAATTACATTTTTGA-CCCTAAAC-TTCCCAAAA
*
21990 TTATATTTTAACCTC
64 TTACATTTTAACCTC
22005 GAATTCCCTG
Statistics
Matches: 274, Mismatches: 56, Indels: 33
0.75 0.15 0.09
Matches are distributed among these distances:
87 2 0.01
88 42 0.15
89 145 0.53
90 72 0.26
91 11 0.04
92 2 0.01
ACGTcount: A:0.34, C:0.26, G:0.03, T:0.36
Consensus pattern (88 bp):
AAAATCACATTTTAACCCTCAAACTTTTCCAAAATTACATTTTTGACCCTAAACTTCCCAAAATT
ACATTTTAACCTCAAACTTCTCC
Found at i:21976 original size:31 final size:31
Alignment explanation
Indices: 21935--21998 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
21925 TAAAATCATA
21935 TTTTAACCCTAAACTTTCCCAAAATTACATT
1 TTTTAACCCTAAACTTTCCCAAAATTACATT
* * *
21966 TTTTACCCCTAAACTTTTCCAAAATTATATT
1 TTTTAACCCTAAACTTTCCCAAAATTACATT
21997 TT
1 TT
21999 AACCTCGAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.33, C:0.23, G:0.00, T:0.44
Consensus pattern (31 bp):
TTTTAACCCTAAACTTTCCCAAAATTACATT
Found at i:25791 original size:22 final size:20
Alignment explanation
Indices: 25754--25794 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
25744 TCAACATGTT
25754 AAAAAAAAAAAGAAAAAAGA
1 AAAAAAAAAAAGAAAAAAGA
*
25774 AAAATAAAACAAATAAAAAAG
1 AAAA-AAAA-AAAGAAAAAAG
25795 CGTCAAGATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 4 0.22
22 10 0.56
ACGTcount: A:0.85, C:0.02, G:0.07, T:0.05
Consensus pattern (20 bp):
AAAAAAAAAAAGAAAAAAGA
Found at i:25859 original size:16 final size:17
Alignment explanation
Indices: 25833--25864 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
25823 CTTGAAACCC
25833 AAGGCAAAAAAAGAAAA
1 AAGGCAAAAAAAGAAAA
25850 AAGG-AAAAAAAGAAA
1 AAGGCAAAAAAAGAAA
25865 GGAAAGTCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.78, C:0.03, G:0.19, T:0.00
Consensus pattern (17 bp):
AAGGCAAAAAAAGAAAA
Found at i:27876 original size:49 final size:49
Alignment explanation
Indices: 27646--28138 Score: 336
Period size: 50 Copynumber: 10.0 Consensus size: 49
27636 CTGAGAAAAA
* * *
27646 CATGAAGATTTGGAGGGAAAGGTTGAGG-CTGCAACGGTGAACCCGATAC
1 CATGAAGATGTGAAGGGAAAGGTTGAGGTC-GCAACGGTGAACCCGGTAC
* * * * * * * * *
27695 CTTAGAAGATGTGATGGGAATGATTGAGGCCGCGATGGTGAATCTGGTAC
1 CAT-GAAGATGTGAAGGGAAAGGTTGAGGTCGCAACGGTGAACCCGGTAC
* * * ** * **
27745 C-TCAGAAGATGTGATGGGAAAGATTGAGGCCATAACGGTGAATCTAGTAC
1 CAT--GAAGATGTGAAGGGAAAGGTTGAGGTCGCAACGGTGAACCCGGTAC
* * * * * *
27795 CATGAA-ATGTGATGGGAAAGATTGAGGCCGCAACAGCGAACCCAGTAC
1 CATGAAGATGTGAAGGGAAAGGTTGAGGTCGCAACGGTGAACCCGGTAC
* *
27843 CATGAAGATTTGAAGGGAAAGGTTGAGGTCGCAATGGTGAACCCGGTAC
1 CATGAAGATGTGAAGGGAAAGGTTGAGGTCGCAACGGTGAACCCGGTAC
* * * * * *
27892 CTTAAAAGATGTG-ACGGAAAGGTTGAGGTCGCAACAGTGAACTCGATAC
1 CAT-GAAGATGTGAAGGGAAAGGTTGAGGTCGCAACGGTGAACCCGGTAC
* * * *** ** *
27941 C-TCAGAAGATGTGACGGGAAAGATTGAGGTCACAATAATGAATTCGATAC
1 CAT--GAAGATGTGAAGGGAAAGGTTGAGGTCGCAACGGTGAACCCGGTAC
* * * *
27991 CATGAA-ATGTGATGGGAAAGGTTGAGG-CTGCAATGGCGAACTCGGTAC
1 CATGAAGATGTGAAGGGAAAGGTTGAGGTC-GCAACGGTGAACCCGGTAC
* * * *
28039 CATGAAGATTTTAAGGGAAAGGTTGAGGCTAG-AACGGTGAACCTGGTAC
1 CATGAAGATGTGAAGGGAAAGGTTGAGG-TCGCAACGGTGAACCCGGTAC
** * * *
28088 GTTAAAAGATATGAAGGGAAAGGTTGAGGCCGCAACGGTGAACCCGGTAC
1 CAT-GAAGATGTGAAGGGAAAGGTTGAGGTCGCAACGGTGAACCCGGTAC
28138 C
1 C
28139 TTAGAAAACA
Statistics
Matches: 357, Mismatches: 72, Indels: 29
0.78 0.16 0.06
Matches are distributed among these distances:
47 1 0.00
48 81 0.23
49 119 0.33
50 153 0.43
51 3 0.01
ACGTcount: A:0.32, C:0.15, G:0.32, T:0.20
Consensus pattern (49 bp):
CATGAAGATGTGAAGGGAAAGGTTGAGGTCGCAACGGTGAACCCGGTAC
Found at i:28009 original size:196 final size:196
Alignment explanation
Indices: 27646--28144 Score: 628
Period size: 196 Copynumber: 2.5 Consensus size: 196
27636 CTGAGAAAAA
* * *
27646 CATGAAGATTTGGAGGGAAAGGTTGAGG-CTGCAACGGTGAACCCGATACCTTAGAAGATGTGAT
1 CATGAAGATTTGAAGGGAAAGGTTGAGGTC-GCAACGGTGAACCCGGTACCTTAAAAGATGTGA-
* * * * *
27710 GGGAATGATTGAGGCCGCGATGGTGAA-TCTGGTACCTCAGAAGATGTGATGGGAAAGATTGAGG
64 GGGAAAGGTTGAGGCCGCAACGGTGAACTC-GGTACCTCAGAAGATGTGACGGGAAAGATTGAGG
* ** *
27774 CCATAACGGTGAATCTAGTACCATGAAATGTGATGGGAAAGATTGAGGCCGCAACAGCGAACCCA
128 CCACAACAATGAATCGAGTACCATGAAATGTGATGGGAAAGATTGAGGCCGCAACAGCGAACCCA
27839 GTAC
193 GTAC
* *
27843 CATGAAGATTTGAAGGGAAAGGTTGAGGTCGCAATGGTGAACCCGGTACCTTAAAAGATGTGACG
1 CATGAAGATTTGAAGGGAAAGGTTGAGGTCGCAACGGTGAACCCGGTACCTTAAAAGATGTGAGG
* * * *
27908 GAAAGGTTGAGGTCGCAACAGTGAACTCGATACCTCAGAAGATGTGACGGGAAAGATTGAGGTCA
66 GAAAGGTTGAGGCCGCAACGGTGAACTCGGTACCTCAGAAGATGTGACGGGAAAGATTGAGGCCA
* * * ** * *
27973 CAATAATGAATTCGA-TACCATGAAATGTGATGGGAAAGGTTGAGGCTGCAATGGCGAACTCGGT
131 CAACAATGAA-TCGAGTACCATGAAATGTGATGGGAAAGATTGAGGCCGCAACAGCGAACCCAGT
28037 AC
195 AC
* * * * *
28039 CATGAAGATTTTAAGGGAAAGGTTGAGGCTAG-AACGGTGAACCTGGTACGTTAAAAGATATGAA
1 CATGAAGATTTGAAGGGAAAGGTTGAGG-TCGCAACGGTGAACCCGGTACCTTAAAAGATGTG-A
* *
28103 GGGAAAGGTTGAGGCCGCAACGGTGAACCCGGTACCTTAGAA
64 GGGAAAGGTTGAGGCCGCAACGGTGAACTCGGTACCTCAGAA
28145 AACAAGATGG
Statistics
Matches: 260, Mismatches: 37, Indels: 10
0.85 0.12 0.03
Matches are distributed among these distances:
196 158 0.61
197 101 0.39
198 1 0.00
ACGTcount: A:0.33, C:0.15, G:0.32, T:0.20
Consensus pattern (196 bp):
CATGAAGATTTGAAGGGAAAGGTTGAGGTCGCAACGGTGAACCCGGTACCTTAAAAGATGTGAGG
GAAAGGTTGAGGCCGCAACGGTGAACTCGGTACCTCAGAAGATGTGACGGGAAAGATTGAGGCCA
CAACAATGAATCGAGTACCATGAAATGTGATGGGAAAGATTGAGGCCGCAACAGCGAACCCAGTA
C
Found at i:28097 original size:147 final size:148
Alignment explanation
Indices: 27840--28116 Score: 321
Period size: 147 Copynumber: 1.9 Consensus size: 148
27830 GCGAACCCAG
* * * *
27840 TACCATGAAGATTTGAAGGGAAAGGTTGAGGTCGCAATGGTGAACCCGGTACCTTAAAAGATGTG
1 TACCATGAAGATGTGAAGGGAAAGGTTGAGGTCGCAATGGCGAACCCGGTACCATAAAAGATGTA
* * * *
27905 ACGGAAAGGTTGAGGTCGCAACAGTGAACTCGATACCTCAGAAGATGTGACGGGAAAGATTGAGG
66 ACGGAAAGGTTGAGGTAGCAACAGTGAACTCGATACCTCAAAAGATATGAAGGGAAAGATTGAGG
27970 TCACAATAATGAATTCGA
131 TCACAATAATGAATTCGA
* * * *
27988 TACCATGAA-ATGTGATGGGAAAGGTTGAGG-CTGCAATGGCGAACTCGGTACCAT-GAAGATTT
1 TACCATGAAGATGTGAAGGGAAAGGTTGAGGTC-GCAATGGCGAACCCGGTACCATAAAAGA-TG
* * * * * *
28050 TAAGGGAAAGGTTGAGGCTAG-AACGGTGAAC-CTGGTACGTTAAAAGATATGAAGGGAAAGGTT
64 TAACGGAAAGGTTGAGG-TAGCAACAGTGAACTC-GATACCTCAAAAGATATGAAGGGAAAGATT
28113 GAGG
127 GAGG
28117 CCGCAACGGT
Statistics
Matches: 107, Mismatches: 18, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
146 6 0.06
147 90 0.84
148 11 0.10
ACGTcount: A:0.34, C:0.13, G:0.32, T:0.21
Consensus pattern (148 bp):
TACCATGAAGATGTGAAGGGAAAGGTTGAGGTCGCAATGGCGAACCCGGTACCATAAAAGATGTA
ACGGAAAGGTTGAGGTAGCAACAGTGAACTCGATACCTCAAAAGATATGAAGGGAAAGATTGAGG
TCACAATAATGAATTCGA
Found at i:28439 original size:41 final size:41
Alignment explanation
Indices: 28382--28474 Score: 150
Period size: 41 Copynumber: 2.3 Consensus size: 41
28372 TCATCATTCA
* *
28382 GTCTTTTACCCTTAATCAAGAAGGGCAGATTGAAGATTTCT
1 GTCTTTTACCCTTAATCAAGAAGAGCAGAATGAAGATTTCT
*
28423 GTCTTTTACCCTTAATCAAGAAGAGCATAATGAAGATTTCT
1 GTCTTTTACCCTTAATCAAGAAGAGCAGAATGAAGATTTCT
*
28464 ATCTTTTACCC
1 GTCTTTTACCC
28475 CGAGCCTAGG
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 48 1.00
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.35
Consensus pattern (41 bp):
GTCTTTTACCCTTAATCAAGAAGAGCAGAATGAAGATTTCT
Found at i:28526 original size:39 final size:38
Alignment explanation
Indices: 28464--29334 Score: 382
Period size: 39 Copynumber: 22.5 Consensus size: 38
28454 GAAGATTTCT
* * *
28464 ATCTTTTACCCCGAGCCTAGGGCAGATCACCATTAGTCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCATTA-CCA
* *
28503 ATCTCTTACCCCGAACCTGGGGCAGATTGCAGCCA-T-CCG
1 ATCTCTTACCCCGAGCCTGGGGCAGA-T-CA-CCATTACCA
* * * *
28542 ATCTTTTACCCTGAGCCTGGGGCAGATCACCATCAGTCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCATTA-CCA
** * * * * *
28581 ATCTCTTACCCCGAGCCTAAGGTAGATTACAACTATCCG
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCATTA-CCA
* * * * * * *
28620 ATCTTTTATCCCGAGCTTGGGGCAAATCACTATCAGTCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCATTA-CCA
* *
28659 ATCTCTTACCCCGAGCCTGGGGTAGATCACCATCAGCCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCATTA-CCA
* * * * *
28698 ATCTCTTACCCCAAGCCTGAGGTAGATTGTAGCCA-T-CCG
1 ATCTCTTACCCCGAGCCTGGGGCAGA-T-CA-CCATTACCA
* * * *
28737 ATCTCTTACCCTGAGCTTGGGACAGATCACCATCAACCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCAT-TACCA
* *
28776 ATCTCTTACCCCGAGCCTGAGGCAGATTACAGCCA-T-CCG
1 ATCTCTTACCCCGAGCCTGGGGCAGA-T-CA-CCATTACCA
* **** * * *
28815 ATCTTTTACCCCGAGCCTACAACATATCACCATCAGTCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCATTA-CCA
* * * *
28854 ATCTCTTACCCCGAGCCTAGGGTAGATTGAGCCA-T-CCG
1 ATCTCTTACCCCGAGCCTGGGGCAGA-TCA-CCATTACCA
* * * * * *
28892 ATCTTTTATCCTGAGCCTGGAGCAGATCACCATCAGTCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCATTA-CCA
* * *
28931 ATCTCTTACCCCGAGCCTGGGGTAGATTATAGCCA-T-CCG
1 ATCTCTTACCCCGAGCCTGGGGCAGA-T-CA-CCATTACCA
* *
28970 ATCTTTTACCCCGAGCATGGGGCAGATCACCA-T--CA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCATTACCA
* * *
29005 ATCTCTTACCCCAAGCTTGGGGCAGATTACAGCCA-T-CCG
1 ATCTCTTACCCCGAGCCTGGGGCAGA-T-CA-CCATTACCA
* * * * *
29044 ATCTTTTACCCCGAGCCTGCGACAGATCACCATCAGTCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCATTA-CCA
* * * *
29083 ATCTCTTATCTCGAGCCTGGGGCAAATTGCAGCCA-T-CCG
1 ATCTCTTACCCCGAGCCTGGGGCAGA-T-CA-CCATTACCA
* * * * *
29122 ATCTTTTACCCCAAGCTTGGGGCAGATCACCGTCAGCCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCATTA-CCA
* * * *
29161 ATCTCTTACCCCGAACTTGGGGCAGATTATAGCCATT--CG
1 ATCTCTTACCCCGAGCCTGGGGCAGA-T-CA-CCATTACCA
* * * **
29200 ATCTTTTACCCCGAGCTTGGGGTAGATCACCAACATCCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCATTA-CCA
* * *
29239 ATCTCTTACCCTGAGCCTGGGGTAGATTGCAGCCA-T-CCG
1 ATCTCTTACCCCGAGCCTGGGGCAGA-T-CA-CCATTACCA
* * * * *
29278 ATCTTTTACCTCGA-CCTTGGGGCTGATCACTATCAGCCA
1 ATCTCTTACCCCGAGCC-TGGGGCAGATCACCATTA-CCA
* *
29317 ATCTCTAACCCCAAGCCT
1 ATCTCTTACCCCGAGCCT
29335 AGGGAAAATT
Statistics
Matches: 611, Mismatches: 168, Indels: 106
0.69 0.19 0.12
Matches are distributed among these distances:
35 24 0.04
36 27 0.04
37 17 0.03
38 35 0.06
39 461 0.75
40 11 0.02
41 15 0.02
42 21 0.03
ACGTcount: A:0.24, C:0.32, G:0.19, T:0.25
Consensus pattern (38 bp):
ATCTCTTACCCCGAGCCTGGGGCAGATCACCATTACCA
Found at i:28643 original size:117 final size:113
Alignment explanation
Indices: 28503--29265 Score: 534
Period size: 117 Copynumber: 6.6 Consensus size: 113
28493 CCATTAGTCA
* * * * *
28503 ATCTCTTACCCCGAACCTGGGGCAGATTGCAGCCATCCGATCTTTTACCCTGAGCCTGGGGCAGA
1 ATCTCTTACCCCGAGCTTGGGGCAGA-T-CA-CCATCCAATCTCTTACCCCGAGCCTGGGGCAGA
* * *
28568 TCACCATCAGTCAATCTCTTACCCCGAGCCTAAGGTAGATTACAACTATCCG
63 TCACCATCAG-CAATCTCTTACCCCGAGCCTGAGGCAGATTACAACCATCCG
* * * * *
28620 ATCTTTTATCCCGAGCTTGGGGCAAATCACTATCAGTCAATCTCTTACCCCGAGCCTGGGGTAGA
1 ATCTCTTACCCCGAGCTTGGGGCAGATCACCATC---CAATCTCTTACCCCGAGCCTGGGGCAGA
* * ** *
28685 TCACCATCAGCCAATCTCTTACCCCAAGCCTGAGGTAGATTGTAGCCATCCG
63 TCACCATCAG-CAATCTCTTACCCCGAGCCTGAGGCAGATTACAACCATCCG
* * *
28737 ATCTCTTACCCTGAGCTTGGGACAGATCACCATCAACCAATCTCTTACCCCGAGCCTGAGGCAGA
1 ATCTCTTACCCCGAGCTTGGGGCAGATCACCAT---CCAATCTCTTACCCCGAGCCTGGGGCAGA
* * ** * * * * *
28802 TTACAGCCATC--CGATCTTTTACCCCGAGCCT-ACAACATATCACCATCAGT-CA
63 -T-CA-CCATCAGCAATCTCTTACCCCGAGCCTGA-GGCAGATTACAACCA-TCCG
* * * * * * * * *
28854 ATCTCTTACCCCGAGCCTAGGGTAGATTGAGCCATCCGATCTTTTATCCTGAGCCTGGAGCAGAT
1 ATCTCTTACCCCGAGCTTGGGGCAGA-TCA-CCATCCAATCTCTTACCCCGAGCCTGGGGCAGAT
* * * *
28919 CACCATCAGTCAATCTCTTACCCCGAGCCTGGGGTAGATTATAGCCATCCG
64 CACCATCAG-CAATCTCTTACCCCGAGCCTGAGGCAGATTACAACCATCCG
* * * *
28970 ATCTTTTACCCCGAGCATGGGGCAGATCACCAT-CAATCTCTTACCCCAAGCTTGGGGCAGATTA
1 ATCTCTTACCCCGAGCTTGGGGCAGATCACCATCCAATCTCTTACCCCGAGCCTGGGGCAGA-T-
* * * * * * * *
29034 CAGCCATC--CGATCTTTTACCCCGAGCCTGCGACAGATCACCATCAGT-CA
64 CA-CCATCAGCAATCTCTTACCCCGAGCCTGAGGCAGATTACAACCA-TCCG
* * * * * * * *
29083 ATCTCTTATCTCGAGCCTGGGGCAAATTGCAGCCATCCGATCTTTTACCCCAAGCTTGGGGCAGA
1 ATCTCTTACCCCGAGCTTGGGGCAGA-T-CA-CCATCCAATCTCTTACCCCGAGCCTGGGGCAGA
* * * * * * *
29148 TCACCGTCAGCCAATCTCTTACCCCGAACTTGGGGCAGATTATAGCCATTCG
63 TCACCATCAG-CAATCTCTTACCCCGAGCCTGAGGCAGATTACAACCATCCG
* * * *
29200 ATCTTTTACCCCGAGCTTGGGGTAGATCACCAACATCCAATCTCTTACCCTGAGCCTGGGGTAGA
1 ATCTCTTACCCCGAGCTTGGGGCAGATCA-C--CATCCAATCTCTTACCCCGAGCCTGGGGCAGA
29265 T
63 T
29266 TGCAGCCATC
Statistics
Matches: 494, Mismatches: 120, Indels: 64
0.73 0.18 0.09
Matches are distributed among these distances:
113 75 0.15
114 17 0.03
115 15 0.03
116 84 0.17
117 287 0.58
118 4 0.01
119 6 0.01
120 6 0.01
ACGTcount: A:0.24, C:0.32, G:0.19, T:0.25
Consensus pattern (113 bp):
ATCTCTTACCCCGAGCTTGGGGCAGATCACCATCCAATCTCTTACCCCGAGCCTGGGGCAGATCA
CCATCAGCAATCTCTTACCCCGAGCCTGAGGCAGATTACAACCATCCG
Found at i:28741 original size:78 final size:78
Alignment explanation
Indices: 28659--29365 Score: 798
Period size: 78 Copynumber: 9.1 Consensus size: 78
28649 CTATCAGTCA
* * * * *
28659 ATCTCTTACCCCGAGCCTGGGGTAGATCACCATCAGCCAATCTCTTACCCCAAGCCTGAGGTAGA
1 ATCTTTTACCCCGAGCCTGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCTGGGGCAGA
**
28724 TTGTAGCCATCCG
66 TTACAGCCATCCG
* * * * * *
28737 ATCTCTTACCCTGAGCTTGGGACAGATCACCATCAACCAATCTCTTACCCCGAGCCTGAGGCAGA
1 ATCTTTTACCCCGAGCCTGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCTGGGGCAGA
28802 TTACAGCCATCCG
66 TTACAGCCATCCG
**** * * * *
28815 ATCTTTTACCCCGAGCCTACAACATATCACCATCAGTCAATCTCTTACCCCGAGCCTAGGGTAGA
1 ATCTTTTACCCCGAGCCTGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCTGGGGCAGA
*
28880 TT-GAGCCATCCG
66 TTACAGCCATCCG
* * * * *
28892 ATCTTTTATCCTGAGCCTGGAGCAGATCACCATCAGTCAATCTCTTACCCCGAGCCTGGGGTAGA
1 ATCTTTTACCCCGAGCCTGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCTGGGGCAGA
*
28957 TTATAGCCATCCG
66 TTACAGCCATCCG
* * *
28970 ATCTTTTACCCCGAGCATGGGGCAGATCACCAT----CAATCTCTTACCCCAAGCTTGGGGCAGA
1 ATCTTTTACCCCGAGCCTGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCTGGGGCAGA
29031 TTACAGCCATCCG
66 TTACAGCCATCCG
* * * * * *
29044 ATCTTTTACCCCGAGCCTGCGACAGATCACCATCAGTCAATCTCTTATCTCGAGCCTGGGGCAAA
1 ATCTTTTACCCCGAGCCTGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCTGGGGCAGA
*
29109 TTGCAGCCATCCG
66 TTACAGCCATCCG
* * * * *
29122 ATCTTTTACCCCAAGCTTGGGGCAGATCACCGTCAGCCAATCTCTTACCCCGAACTTGGGGCAGA
1 ATCTTTTACCCCGAGCCTGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCTGGGGCAGA
* *
29187 TTATAGCCATTCG
66 TTACAGCCATCCG
* * * * * *
29200 ATCTTTTACCCCGAGCTTGGGGTAGATCACCAACATCCAATCTCTTACCCTGAGCCTGGGGTAGA
1 ATCTTTTACCCCGAGCCTGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCTGGGGCAGA
*
29265 TTGCAGCCATCCG
66 TTACAGCCATCCG
* * * * * * * *
29278 ATCTTTTACCTCGA-CCTTGGGGCTGATCACTATCAGCCAATCTCTAACCCCAAGCCTAGGGAAA
1 ATCTTTTACCCCGAGCC-TGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCTGGGGCAG
*
29342 ATTACAACCAGT-CG
65 ATTACAGCCA-TCCG
29356 ATCTTTTACC
1 ATCTTTTACC
29366 TCAATTATAG
Statistics
Matches: 534, Mismatches: 88, Indels: 14
0.84 0.14 0.02
Matches are distributed among these distances:
74 67 0.13
77 70 0.13
78 396 0.74
79 1 0.00
ACGTcount: A:0.24, C:0.32, G:0.19, T:0.25
Consensus pattern (78 bp):
ATCTTTTACCCCGAGCCTGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCTGGGGCAGA
TTACAGCCATCCG
Found at i:29495 original size:18 final size:18
Alignment explanation
Indices: 29472--29549 Score: 53
Period size: 17 Copynumber: 4.7 Consensus size: 18
29462 AGATAACAGA
29472 GAAGTGGATCAAAATGAT
1 GAAGTGGATCAAAATGAT
** **
29490 GAAGTGG-TCAACTTCCT
1 GAAGTGGATCAAAATGAT
*
29507 G-A-TGAGAT-AACA-GA-
1 GAAGTG-GATCAAAATGAT
29521 GAAGTGGATCAAAATGAT
1 GAAGTGGATCAAAATGAT
29539 GAAGTGG-TCAA
1 GAAGTGGATCAA
29550 CTTCCTGATG
Statistics
Matches: 45, Mismatches: 8, Indels: 15
0.66 0.12 0.22
Matches are distributed among these distances:
14 1 0.02
15 6 0.13
16 10 0.22
17 14 0.31
18 14 0.31
ACGTcount: A:0.40, C:0.10, G:0.28, T:0.22
Consensus pattern (18 bp):
GAAGTGGATCAAAATGAT
Found at i:29507 original size:49 final size:49
Alignment explanation
Indices: 29439--29573 Score: 245
Period size: 49 Copynumber: 2.8 Consensus size: 49
29429 ATCCAGAACA
* *
29439 ATGAAGTGATCATCTTCCTGATGAGATAACAGAGAAGTGGATCAAAATG
1 ATGAAGTGGTCAACTTCCTGATGAGATAACAGAGAAGTGGATCAAAATG
29488 ATGAAGTGGTCAACTTCCTGATGAGATAACAGAGAAGTGGATCAAAATG
1 ATGAAGTGGTCAACTTCCTGATGAGATAACAGAGAAGTGGATCAAAATG
29537 ATGAAGTGGTCAACTTCCTGATGAGAT-ACAGAGAAGT
1 ATGAAGTGGTCAACTTCCTGATGAGATAACAGAGAAGT
29574 AGACCAAGAG
Statistics
Matches: 84, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
48 10 0.12
49 74 0.88
ACGTcount: A:0.38, C:0.13, G:0.26, T:0.24
Consensus pattern (49 bp):
ATGAAGTGGTCAACTTCCTGATGAGATAACAGAGAAGTGGATCAAAATG
Found at i:31569 original size:61 final size:59
Alignment explanation
Indices: 31428--31599 Score: 177
Period size: 61 Copynumber: 2.9 Consensus size: 59
31418 CTGACCCCAA
* * * * * * * *
31428 AACTTCTCTAAAATTATATTTTAACCCCTAAACTTCTCC-AAAATAACATTTTTACTCTCG
1 AACTTTTCTAAAATCACATTTTAA-CCTTAAAC-TCTCCTAAATTTACATTTTGACCCTCG
*
31488 AACTTTTCTAAAATTACATTTTAACCTTAAAACTC-CTCTAAAATTTACATTTTGACCCTCG
1 AACTTTTCTAAAATCACATTTTAACCTT-AAACTCTC-CT-AAATTTACATTTTGACCCTCG
* * *
31549 AACTTTTCTAAAATCGCATTTTGACCTTAAACTTTCCTAAATTTACATTTT
1 AACTTTTCTAAAATCACATTTTAACCTTAAACTCTCCTAAATTTACATTTT
31600 AACATTAAAT
Statistics
Matches: 96, Mismatches: 11, Indels: 11
0.81 0.09 0.09
Matches are distributed among these distances:
58 1 0.01
59 19 0.20
60 33 0.34
61 43 0.45
ACGTcount: A:0.34, C:0.23, G:0.03, T:0.41
Consensus pattern (59 bp):
AACTTTTCTAAAATCACATTTTAACCTTAAACTCTCCTAAATTTACATTTTGACCCTCG
Found at i:31588 original size:29 final size:28
Alignment explanation
Indices: 31369--31857 Score: 221
Period size: 30 Copynumber: 16.5 Consensus size: 28
31359 TAGGTCCTTG
*
31369 AACTTTCCATAAATCATATTTTGACCTCAA
1 AACTTTCCA-AAATCACATTTTGACCTC-A
* * * *
31399 AAC-TTCTCAAAA-AACTAATCTGACCCCAA
1 AACTTTC-CAAAATCAC-ATTTTGACCTC-A
* * * * *
31428 AACTTCTCTAAAATTATATTTTAACCCCTA
1 AACTT-TCCAAAATCACATTTTGACCTC-A
* * *
31458 AACTTCTCCAAAATAACATTTTTACTCTCG
1 AACTT-TCCAAAATCACATTTTGAC-CTCA
* * * *
31488 AACTTTTCTAAAATTACATTTTAACCTTAA
1 AAC-TTTCCAAAATCACATTTTGACC-TCA
* * * *
31518 AACTCCTCTAAAATTTACATTTTGACCCTCG
1 AACT-TTCCAAAA-TCACATTTTGA-CCTCA
* * *
31549 AACTTTTCTAAAATCGCATTTTGACCTTA
1 AAC-TTTCCAAAATCACATTTTGACCTCA
* * * * *
31578 AACTTTCCTAAATTTACATTTTAACATTA
1 AACTTTCC-AAAATCACATTTTGACCTCA
* *
31607 AATTTTTCCAAAATCACATTTTGACTCTCG
1 AA-CTTTCCAAAATCACATTTTGAC-CTCA
*** *
31637 AACTTTTCCAAAATTGTATTTTGACCCTTA
1 AAC-TTTCCAAAATCACATTTTGA-CCTCA
*
31667 AACTTCTCCAAAATCACGTTTTGATCCTCGA
1 AACTT-TCCAAAATCACATTTTGA-CCTC-A
** * **
31698 ATA-TTTCCAAAATCGTATTTTCACTCTTG
1 A-ACTTTCCAAAATCACATTTTGAC-CTCA
*
31727 AACTTATCCAAAATCACATTTTGGTCAC-CA
1 AACTT-TCCAAAATCACATTTT-GAC-CTCA
* *
31757 AACCTTCTCAAAATCACATTTTGACCCCA
1 AACTTTC-CAAAATCACATTTTGACCTCA
* *
31786 AACTTCTCCAAAATCACATTTTAACCTCG
1 AACTT-TCCAAAATCACATTTTGACCTCA
* * *
31815 AACTTTCCAAAATTACATTTTTACCCCTA
1 AACTTTCCAAAATCACATTTTGACCTC-A
31844 AACTTTTCCAAAAT
1 AAC-TTTCCAAAAT
31858 TATGTTTTGA
Statistics
Matches: 350, Mismatches: 80, Indels: 58
0.72 0.16 0.12
Matches are distributed among these distances:
28 26 0.07
29 99 0.28
30 186 0.53
31 35 0.10
32 4 0.01
ACGTcount: A:0.34, C:0.25, G:0.04, T:0.37
Consensus pattern (28 bp):
AACTTTCCAAAATCACATTTTGACCTCA
Found at i:31658 original size:88 final size:91
Alignment explanation
Indices: 31488--31680 Score: 239
Period size: 88 Copynumber: 2.1 Consensus size: 91
31478 TTTACTCTCG
* * * * *
31488 AACTTTTCTAAAATTACATTTTAACCTTAAAACTCCTCTAAAATTTACATTTTGACCCTCGAACT
1 AACTTTCCTAAATTTACATTTTAACATTAAAACTCCTCCAAAATTCACATTTTGACCCTCGAACT
*
31553 TTTCTAAAATCGCATTTTGA-CCTTA
66 TTTCCAAAATCGCATTTTGACCCTTA
* ** *
31578 AACTTTCCTAAATTTACATTTTAACATT-AAATTTTTCCAAAA-TCACATTTTGACTCTCGAACT
1 AACTTTCCTAAATTTACATTTTAACATTAAAACTCCTCCAAAATTCACATTTTGACCCTCGAACT
* *
31641 TTTCCAAAATTGTATTTTGACCCTTA
66 TTTCCAAAATCGCATTTTGACCCTTA
*
31667 AACTTCTCCAAAAT
1 AACTT-TCCTAAAT
31681 CACGTTTTGA
Statistics
Matches: 88, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
88 36 0.41
89 20 0.23
90 32 0.36
ACGTcount: A:0.34, C:0.22, G:0.04, T:0.40
Consensus pattern (91 bp):
AACTTTCCTAAATTTACATTTTAACATTAAAACTCCTCCAAAATTCACATTTTGACCCTCGAACT
TTTCCAAAATCGCATTTTGACCCTTA
Found at i:31677 original size:60 final size:59
Alignment explanation
Indices: 31527--31857 Score: 251
Period size: 60 Copynumber: 5.6 Consensus size: 59
31517 AAACTCCTCT
* ** * * **
31527 AAAATTTACATTTTGACCCTCGAACTTTTCTAAAATCGCATTTTGAC-CTTAAACTTTCC
1 AAAA-TTATATTTTGACCCTTAAACTTTTCCAAAATCACATTTTGACTCTCGAACTTTCC
* * * * *
31586 TAAATTTACATTTT-AACATTAAATTTTTCCAAAATCACATTTTGACTCTCGAACTTTTCC
1 -AAAATTATATTTTGACCCTTAAACTTTTCCAAAATCACATTTTGACTCTCGAAC-TTTCC
* * * *
31646 AAAATTGTATTTTGACCCTTAAACTTCTCCAAAATCACGTTTTGA-TCCTCGAATATTTCC
1 AAAATTATATTTTGACCCTTAAACTTTTCCAAAATCACATTTTGACT-CTCGAA-CTTTCC
** * * * * * * * *
31706 AAAATCGTATTTTCACTCTTGAACTTATCCAAAATCACATTTTG-GTCACCAAACCTTCTC
1 AAAATTATATTTTGACCCTTAAACTTTTCCAAAATCACATTTTGACTC-TCGAACTTTC-C
* * * * *
31766 AAAATCACATTTTGACCC-CAAACTTCTCCAAAATCACATTTTAAC-CTCGAACTTTCC
1 AAAATTATATTTTGACCCTTAAACTTTTCCAAAATCACATTTTGACTCTCGAACTTTCC
* * *
31823 AAAATTACATTTTTACCCCTAAACTTTTCCAAAAT
1 AAAATTATATTTTGACCCTTAAACTTTTCCAAAAT
31858 TATGTTTTGA
Statistics
Matches: 216, Mismatches: 45, Indels: 22
0.76 0.16 0.08
Matches are distributed among these distances:
57 17 0.08
58 46 0.21
59 51 0.24
60 102 0.47
ACGTcount: A:0.33, C:0.25, G:0.05, T:0.37
Consensus pattern (59 bp):
AAAATTATATTTTGACCCTTAAACTTTTCCAAAATCACATTTTGACTCTCGAACTTTCC
Found at i:31981 original size:21 final size:22
Alignment explanation
Indices: 31937--31981 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
31927 GTATATAAAA
* *
31937 TTTAATTATTGTTCTTTGTATT
1 TTTAATTAATCTTCTTTGTATT
*
31959 TTTAATTAATCTT-TTTTTATT
1 TTTAATTAATCTTCTTTGTATT
31980 TT
1 TT
31982 GATTCGTGAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.20, C:0.04, G:0.04, T:0.71
Consensus pattern (22 bp):
TTTAATTAATCTTCTTTGTATT
Found at i:33580 original size:23 final size:23
Alignment explanation
Indices: 33554--33598 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
33544 ATTAATCGTA
*
33554 ACTAAAACTCCATTTTCTTCTTC
1 ACTAAAACTCCATCTTCTTCTTC
* *
33577 ACTAAAGCTTCATCTTCTTCTT
1 ACTAAAACTCCATCTTCTTCTT
33599 TTACAATATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.24, C:0.29, G:0.02, T:0.44
Consensus pattern (23 bp):
ACTAAAACTCCATCTTCTTCTTC
Found at i:35011 original size:3 final size:3
Alignment explanation
Indices: 34998--35055 Score: 100
Period size: 3 Copynumber: 19.7 Consensus size: 3
34988 ACAATCCCAA
*
34998 AAT AA- AAT AAT AAT AGT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
35045 AAT AAT AAT AA
1 AAT AAT AAT AA
35056 CATAATTTGA
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
2 2 0.04
3 50 0.96
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:35499 original size:12 final size:12
Alignment explanation
Indices: 35484--35513 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
35474 TAACATGTAT
*
35484 ATCTCAGTCTTA
1 ATCTCAATCTTA
35496 ATCTCAATCTTA
1 ATCTCAATCTTA
35508 ATCTCA
1 ATCTCA
35514 TGATAATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.30, C:0.27, G:0.03, T:0.40
Consensus pattern (12 bp):
ATCTCAATCTTA
Found at i:42210 original size:4 final size:4
Alignment explanation
Indices: 42201--42257 Score: 60
Period size: 4 Copynumber: 14.2 Consensus size: 4
42191 TACTGAAATA
* * * * * *
42201 ATAT ATAT ATAT ATAT GTAT GTAT GTAT ATAT ATGT ATGT ATGT ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
42249 ATAT ATAT A
1 ATAT ATAT A
42258 GAAAACAAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 49 1.00
ACGTcount: A:0.40, C:0.00, G:0.11, T:0.49
Consensus pattern (4 bp):
ATAT
Found at i:42231 original size:18 final size:18
Alignment explanation
Indices: 42208--42252 Score: 90
Period size: 18 Copynumber: 2.5 Consensus size: 18
42198 ATAATATATA
42208 TATATATATGTATGTATG
1 TATATATATGTATGTATG
42226 TATATATATGTATGTATG
1 TATATATATGTATGTATG
42244 TATATATAT
1 TATATATAT
42253 ATATAGAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.36, C:0.00, G:0.13, T:0.51
Consensus pattern (18 bp):
TATATATATGTATGTATG
Found at i:42232 original size:22 final size:22
Alignment explanation
Indices: 42201--42257 Score: 96
Period size: 22 Copynumber: 2.6 Consensus size: 22
42191 TACTGAAATA
42201 ATATATATATATATATGTATGT
1 ATATATATATATATATGTATGT
* *
42223 ATGTATATATATGTATGTATGT
1 ATATATATATATATATGTATGT
42245 ATATATATATATA
1 ATATATATATATA
42258 GAAAACAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.40, C:0.00, G:0.11, T:0.49
Consensus pattern (22 bp):
ATATATATATATATATGTATGT
Found at i:43311 original size:20 final size:20
Alignment explanation
Indices: 43286--43324 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
43276 AGAGTTTTTC
43286 GAAAAAAGTCAACGATCAAT
1 GAAAAAAGTCAACGATCAAT
*
43306 GAAAAAAGTCAACGGTCAA
1 GAAAAAAGTCAACGATCAA
43325 CGATCAACGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.54, C:0.15, G:0.18, T:0.13
Consensus pattern (20 bp):
GAAAAAAGTCAACGATCAAT
Found at i:43390 original size:22 final size:23
Alignment explanation
Indices: 43340--43393 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
43330 AACGGTTGGG
* *
43340 CAAAGTAAACGATTTGATTTGAT
1 CAAAGTCAACGATTTCATTTGAT
43363 CAAAGTCAACGA-TTCATTTCGAT
1 CAAAGTCAACGATTTCATTT-GAT
43386 C-AAGTCAA
1 CAAAGTCAA
43394 TGGTTCGGGT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 13 0.46
23 15 0.54
ACGTcount: A:0.39, C:0.17, G:0.15, T:0.30
Consensus pattern (23 bp):
CAAAGTCAACGATTTCATTTGAT
Found at i:44222 original size:30 final size:30
Alignment explanation
Indices: 44166--44223 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
44156 ACTAGAGTTC
* *
44166 AATTAAGTCCTTAATTTTACAAAATTTATG
1 AATTAAGTCCTAAATTCTACAAAATTTATG
*
44196 AATTAAGTCCTCAAATTCT-CATAATTTA
1 AATTAAGTCCT-AAATTCTACAAAATTTA
44224 CCAATTTAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 19 0.79
31 5 0.21
ACGTcount: A:0.40, C:0.14, G:0.05, T:0.41
Consensus pattern (30 bp):
AATTAAGTCCTAAATTCTACAAAATTTATG
Found at i:48858 original size:6 final size:6
Alignment explanation
Indices: 48847--48889 Score: 59
Period size: 6 Copynumber: 7.2 Consensus size: 6
48837 TTTGTGATCA
* * *
48847 AAAGTG AAAGTG AAAGTG AAAGTG AAATTG GAATTG AAAGTG A
1 AAAGTG AAAGTG AAAGTG AAAGTG AAAGTG AAAGTG AAAGTG A
48890 TATGAATTGT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.30, T:0.21
Consensus pattern (6 bp):
AAAGTG
Done.