Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011852.1 Kokia drynarioides strain JFW-HI SEQ_126848, 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: 19424
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Warning! 69 characters in sequence are not A, C, G, or T
Found at i:452 original size:3 final size:3
Alignment explanation
Indices: 440--503 Score: 83
Period size: 3 Copynumber: 21.3 Consensus size: 3
430 ATTATTAATT
* * * *
440 TAA TAT TAA TAA TGA CAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAG
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
488 TAA TAA TAA TAT TAA T
1 TAA TAA TAA TAA TAA T
504 TAGCATAGAT
Statistics
Matches: 51, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.59, C:0.02, G:0.03, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:1096 original size:12 final size:12
Alignment explanation
Indices: 1074--1102 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
1064 CCGGACTATT
1074 ACCCG-AATTCG
1 ACCCGAAATTCG
1085 ACCCGAAATTCG
1 ACCCGAAATTCG
1097 ACCCGA
1 ACCCGA
1103 CTTGACTTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 5 0.29
12 12 0.71
ACGTcount: A:0.31, C:0.38, G:0.17, T:0.14
Consensus pattern (12 bp):
ACCCGAAATTCG
Found at i:1462 original size:172 final size:172
Alignment explanation
Indices: 1267--1612 Score: 647
Period size: 172 Copynumber: 2.0 Consensus size: 172
1257 CCTTTTAAAA
*
1267 GCACCAGGAGTTGCCACGTGTCATAATTTTGGCTTATTTGTGCAAATGGACCCTTTTACTTTTTA
1 GCACCAGGAGTTGCCACGTGTCATAATTTTGGCTTATTTATGCAAATGGACCCTTTTACTTTTTA
*
1332 ATTTGTTTTAATTTAATCCTTAAATCAAGTTCGTTTTAATTACAAAATTGACCCAGAAATTTTCC
66 ATTTGTTTTAATTTAATCCTTAAATCAAGTTCGTTTTAATTACAAAATTGACCCAAAAATTTTCC
*
1397 ATGGTTTTCAAACTGGTCCTTTGACTTCAGGATGCCTGAAGG
131 ATGGTTTTCAAACTGGTCCTTTGACTTCAGGATGCCTAAAGG
*
1439 GCACCAGGAGTTGCCACGTGTCATAATTTTGGCTTATTTATGCAAATGGTCCCTTTTACTTTTTA
1 GCACCAGGAGTTGCCACGTGTCATAATTTTGGCTTATTTATGCAAATGGACCCTTTTACTTTTTA
*
1504 ATTTGTTTTAATTTAATCCTTATATCAAGTTCGTTTTAATTACAAAATTGACCCAAAAATTTTCC
66 ATTTGTTTTAATTTAATCCTTAAATCAAGTTCGTTTTAATTACAAAATTGACCCAAAAATTTTCC
1569 ATGGTTTTCAAACTGGTCCTTTGACTTCAGGATGCCTAAAGG
131 ATGGTTTTCAAACTGGTCCTTTGACTTCAGGATGCCTAAAGG
1611 GC
1 GC
1613 TGCCACGTGT
Statistics
Matches: 169, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
172 169 1.00
ACGTcount: A:0.26, C:0.18, G:0.16, T:0.39
Consensus pattern (172 bp):
GCACCAGGAGTTGCCACGTGTCATAATTTTGGCTTATTTATGCAAATGGACCCTTTTACTTTTTA
ATTTGTTTTAATTTAATCCTTAAATCAAGTTCGTTTTAATTACAAAATTGACCCAAAAATTTTCC
ATGGTTTTCAAACTGGTCCTTTGACTTCAGGATGCCTAAAGG
Found at i:1824 original size:59 final size:58
Alignment explanation
Indices: 1746--2030 Score: 412
Period size: 59 Copynumber: 4.8 Consensus size: 58
1736 TTTTACCCCG
* *
1746 AACTTCCAAAAATCTCATTTTTACCCTCGAACTTACAAAAATCCCATTTTTGACCCTAA
1 AACTTCC-AAAATTTCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCTAA
*
1805 AACTTCCAAAGATTTCATTTTTACCC-CAAAACTTCCAAAAATCCCATTTTTGA-CCTCAA
1 AACTTCCAAA-ATTTCATTTTTACCCTC-GAACTTCCAAAAATCCCATTTTTGACCCT-AA
1864 AACTTCCAAAATTTTCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCTAA
1 AACTTCCAAAA-TTTCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCTAA
* * **
1923 AACTTCCAAAATTCCATTTTTACCCTCGAACTTCCCAAAATCCCATTTTTGACCCCGA
1 AACTTCCAAAATTTCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCTAA
* * *
1981 AACTTCCAAAAATTCTATTTTTACCCCCGAATTTCCAAAAATCCCATTTT
1 AACTTCCAAAATTTC-ATTTTTACCCTCGAACTTCCAAAAATCCCATTTT
2031 CAACCTCAAA
Statistics
Matches: 206, Mismatches: 13, Indels: 14
0.88 0.06 0.06
Matches are distributed among these distances:
58 64 0.31
59 138 0.67
60 4 0.02
ACGTcount: A:0.33, C:0.30, G:0.04, T:0.33
Consensus pattern (58 bp):
AACTTCCAAAATTTCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCTAA
Found at i:1890 original size:88 final size:87
Alignment explanation
Indices: 1659--2040 Score: 382
Period size: 88 Copynumber: 4.4 Consensus size: 87
1649 GAGGTCCCGG
**** * ** *
1659 AAACTTCCAAAAATTTTTTTTTTACCCTCGAACTTTAGAAAATCCCATTTTTGAACCTGAAACTT
1 AAACTTCCAAAAATCCCATTTTTACCCTCAAAC-TTCCAAAATCCCATTTTTGACCCTGAAACTT
1724 CCAAAA-TTCTATTTTTACCCC-
65 CCAAAATTTCTATTTTTACCCCA
* * * * *
1745 GAACTTCCAAAAATCTCATTTTTACCCTCGAACTTACAAAAATCCCATTTTTGACCCTAAAACTT
1 AAACTTCCAAAAATCCCATTTTTACCCTCAAACTT-CCAAAATCCCATTTTTGACCCTGAAACTT
1810 CCAAAGATTTC-ATTTTTACCCCA
65 CCAAA-ATTTCTATTTTTACCCCA
**
1833 AAACTTCCAAAAATCCCATTTTTGA-CCTCAAAACTTCCAAAATTTTCATTTTT-ACCCTCG-AA
1 AAACTTCCAAAAATCCCATTTTT-ACCCTC-AAACTTCCAAAA-TCCCATTTTTGACCCT-GAAA
* * * *
1895 CTTCCAAAAATCCCATTTTTGACCCTA
62 CTTCCAAAATTTCTATTTTT-ACCCCA
* * *
1922 AAACTTCC-AAAATTCCATTTTTACCCTCGAACTTCCCAAAATCCCATTTTTGACCCCGAAACTT
1 AAACTTCCAAAAATCCCATTTTTACCCTCAAACTT-CCAAAATCCCATTTTTGACCCTGAAACTT
* *
1986 CCAAAAATTCTATTTTTACCCCC
65 CCAAAATTTCTATTTTTACCCCA
* * * *
2009 GAATTTCCAAAAATCCCATTTTCAACCTCAAA
1 AAACTTCCAAAAATCCCATTTTTACCCTCAAA
2041 ACTCTTAAAA
Statistics
Matches: 248, Mismatches: 33, Indels: 28
0.80 0.11 0.09
Matches are distributed among these distances:
85 2 0.01
86 59 0.24
87 40 0.16
88 120 0.48
89 27 0.11
ACGTcount: A:0.34, C:0.29, G:0.04, T:0.34
Consensus pattern (87 bp):
AAACTTCCAAAAATCCCATTTTTACCCTCAAACTTCCAAAATCCCATTTTTGACCCTGAAACTTC
CAAAATTTCTATTTTTACCCCA
Found at i:2062 original size:58 final size:57
Alignment explanation
Indices: 1746--2098 Score: 392
Period size: 59 Copynumber: 6.0 Consensus size: 57
1736 TTTTACCCCG
*
1746 AACTTCCAAAAATCTCATTTTTACCCTCGAACTTACAAAAATCCCATTTTTGACC-CTAA
1 AACTTCC-AAAAT-TCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCTC-AA
*
1805 AACTTCCAAAGATTTCATTTTTACCC-CAAAACTTCCAAAAATCCCATTTTTGACCTCAA
1 AACTTCCAAA-A-TTCATTTTTACCCTC-GAACTTCCAAAAATCCCATTTTTGACCTCAA
1864 AACTTCCAAAATTTTCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACC-CTAA
1 AACTTCCAAAA--TTCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCTC-AA
* * *
1923 AACTTCCAAAATTCCATTTTTACCCTCGAACTTCCCAAAATCCCATTTTTGACCCCGA
1 AACTTCCAAAATT-CATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCTCAA
* * **
1981 AACTTCCAAAAATTCTATTTTTACCCCCGAATTTCCAAAAATCCCATTTTCAACCTCAA
1 AACTTCC-AAAATTC-ATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCTCAA
* ** * * * *
2040 AAC-TCTTAAAATTACCCTTTTACCCTCGAA-TATCTAAAAATTCCATTTTTAACATCAA
1 AACTTC-CAAAATT-CATTTTTACCCTCGAACT-TCCAAAAATCCCATTTTTGACCTCAA
2098 A
1 A
2099 TTTTCCCAAA
Statistics
Matches: 260, Mismatches: 20, Indels: 29
0.84 0.06 0.09
Matches are distributed among these distances:
57 3 0.01
58 97 0.37
59 157 0.60
60 3 0.01
ACGTcount: A:0.35, C:0.29, G:0.03, T:0.33
Consensus pattern (57 bp):
AACTTCCAAAATTCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCTCAA
Found at i:2080 original size:117 final size:117
Alignment explanation
Indices: 1734--2089 Score: 426
Period size: 117 Copynumber: 3.1 Consensus size: 117
1724 CCAAAATTCT
*
1734 ATTTTT-ACCCCG-AACTTCCAAAAA-TCTCATTTTTACCCTCGAACTTACAAAAATCCCATTTT
1 ATTTTTGACCCCGAAACTTCCAAAAATTCTCATTTTTACCCTCGAACTTCCAAAAATCCCATTTT
* *
1796 TGACCCTAAAACTTCCAAAGATTTCATTTTTACCC-C-AAAACTTCCAAAAATCCC
66 TGACCCTAAAACTTCCAAA-A-TTCCTTTTTACCCTCGAATA--TCCAAAAATCCC
* * *
1850 ATTTTTGACCTCAAAACTTCC-AAAATTTTCATTTTTACCCTCGAACTTCCAAAAATCCCATTTT
1 ATTTTTGACCCCGAAACTTCCAAAAATTCTCATTTTTACCCTCGAACTTCCAAAAATCCCATTTT
*
1914 TGACCCTAAAACTTCCAAAATTCCATTTTTACCCTCGAACT-TCCCAAAATCCC
66 TGACCCTAAAACTTCCAAAATTCC-TTTTTACCCTCGAA-TATCCAAAAATCCC
* *
1967 ATTTTTGACCCCGAAACTTCCAAAAATTCT-ATTTTTACCCCCGAATTTCCAAAAATCCCA-TTT
1 ATTTTTGACCCCGAAACTTCCAAAAATTCTCATTTTTACCCTCGAACTTCCAAAAATCCCATTTT
* * * * * *
2030 TCAACCTCAAAAC-TCTTAAAATTACCCTTTTACCCTCGAATATCTAAAAATTCC
66 TGACCCT-AAAACTTC-CAAAATT-CCTTTTTACCCTCGAATATCCAAAAATCCC
2084 ATTTTT
1 ATTTTT
2090 AACATCAAAT
Statistics
Matches: 209, Mismatches: 19, Indels: 23
0.83 0.08 0.09
Matches are distributed among these distances:
116 20 0.10
117 115 0.55
118 72 0.34
119 2 0.01
ACGTcount: A:0.33, C:0.29, G:0.03, T:0.34
Consensus pattern (117 bp):
ATTTTTGACCCCGAAACTTCCAAAAATTCTCATTTTTACCCTCGAACTTCCAAAAATCCCATTTT
TGACCCTAAAACTTCCAAAATTCCTTTTTACCCTCGAATATCCAAAAATCCC
Found at i:2089 original size:29 final size:29
Alignment explanation
Indices: 1660--2090 Score: 346
Period size: 29 Copynumber: 14.8 Consensus size: 29
1650 AGGTCCCGGA
***
1660 AACTTCCAAAAATTTTTTTTTTACCCTCG
1 AACTTCCAAAAATTCCATTTTTACCCTCG
* * *
1689 AACTT-TAGAAAATCCCATTTTTGAACCT-G
1 AACTTCCA-AAAATTCCATTTTT-ACCCTCG
*
1718 AAACTTCC-AAAATTCTATTTTTACCC-CG
1 -AACTTCCAAAAATTCCATTTTTACCCTCG
1746 AACTTCCAAAAA-TCTCATTTTTACCCTCG
1 AACTTCCAAAAATTC-CATTTTTACCCTCG
* * **
1775 AACTTACAAAAATCCCATTTTTGACCCTAA
1 AACTTCCAAAAATTCCATTTTT-ACCCTCG
* * *
1805 AACTTCCAAAGATTTCATTTTTACCC-CAA
1 AACTTCCAAAAATTCCATTTTTACCCTC-G
* *
1834 AACTTCCAAAAATCCCATTTTTGA-CCTCAA
1 AACTTCCAAAAATTCCATTTTT-ACCCTC-G
* *
1864 AACTTCCAAAATTTTCATTTTTACCCTCG
1 AACTTCCAAAAATTCCATTTTTACCCTCG
* **
1893 AACTTCCAAAAATCCCATTTTTGACCCTAA
1 AACTTCCAAAAATTCCATTTTT-ACCCTCG
1923 AACTTCC-AAAATTCCATTTTTACCCTCG
1 AACTTCCAAAAATTCCATTTTTACCCTCG
* *
1951 AACTTCCCAAAATCCCATTTTTGACCC-CG
1 AACTTCCAAAAATTCCATTTTT-ACCCTCG
* *
1980 AAACTTCCAAAAATTCTATTTTTACCCCCG
1 -AACTTCCAAAAATTCCATTTTTACCCTCG
* * * * *
2010 AATTTCCAAAAATCCCATTTTCAACCTCAA
1 AACTTCCAAAAATTCCATTTTTACCCTC-G
** *
2040 AAC-TCTTAAAATTACC-CTTTTACCCTCG
1 AACTTCCAAAAATT-CCATTTTTACCCTCG
*
2068 AA-TATCTAAAAATTCCATTTTTA
1 AACT-TCCAAAAATTCCATTTTTA
2091 ACATCAAATT
Statistics
Matches: 322, Mismatches: 56, Indels: 48
0.76 0.13 0.11
Matches are distributed among these distances:
27 9 0.03
28 35 0.11
29 177 0.55
30 101 0.31
ACGTcount: A:0.33, C:0.28, G:0.04, T:0.35
Consensus pattern (29 bp):
AACTTCCAAAAATTCCATTTTTACCCTCG
Found at i:2110 original size:117 final size:116
Alignment explanation
Indices: 1719--2118 Score: 386
Period size: 117 Copynumber: 3.4 Consensus size: 116
1709 TTGAACCTGA
* * * * * * *
1719 AACTTCC-AAAATTCTATTTTT-ACCCCGAACTT-CCAAAAATCTCATTTTTACCCTCGAACTTA
1 AACTTCCAAAAATCCCATTTTTGACCTCAAACTTCCCAAAATTCT-ATTTTTACCCCCGAACTTC
** * * *
1781 CAAAAATCCCATTTTTGACCCTAAAACTTCCAAAGATTTCATTTTTACCC-CAA
65 CAAAAATCCCATTTTCAACCCTAAAACTTCCAAA-ATTCCACTTTTACCCTC-G
* *
1834 AACTTCCAAAAATCCCATTTTTGACCTCAAAACTT-CCAAAATTTTCATTTTTACCCTCGAACTT
1 AACTTCCAAAAATCCCATTTTTGACCTC-AAACTTCCCAAAATTCT-ATTTTTACCCCCGAACTT
** *
1898 CCAAAAATCCCATTTTTGACCCTAAAACTTCCAAAATTCCATTTTTACCCTCG
64 CCAAAAATCCCATTTTCAACCCTAAAACTTCCAAAATTCCACTTTTACCCTCG
* * * *
1951 AACTTCCCAAAATCCCATTTTTGACCCCGAAACTTCCAAAAATTCTATTTTTACCCCCGAATTTC
1 AACTTCCAAAAATCCCATTTTTGACCTC-AAACTTCCCAAAATTCTATTTTTACCCCCGAACTTC
*
2016 CAAAAATCCCATTTTCAA-CCTCAAAAC-TCTTAAAATTACC-CTTTTACCCTCG
65 CAAAAATCCCATTTTCAACCCT-AAAACTTC-CAAAATT-CCACTTTTACCCTCG
* * * * *
2068 AA-TATCTAAAAATTCCATTTTTAACATCAAATTTTCCCAAAATTACTATTT
1 AACT-TCCAAAAATCCCATTTTTGACCTCAAA-CTTCCCAAAATT-CTATTT
2119 CACCCTCGAG
Statistics
Matches: 246, Mismatches: 28, Indels: 19
0.84 0.10 0.06
Matches are distributed among these distances:
115 7 0.03
116 21 0.09
117 135 0.55
118 83 0.34
ACGTcount: A:0.34, C:0.29, G:0.03, T:0.34
Consensus pattern (116 bp):
AACTTCCAAAAATCCCATTTTTGACCTCAAACTTCCCAAAATTCTATTTTTACCCCCGAACTTCC
AAAAATCCCATTTTCAACCCTAAAACTTCCAAAATTCCACTTTTACCCTCG
Found at i:13192 original size:27 final size:27
Alignment explanation
Indices: 13153--13212 Score: 102
Period size: 27 Copynumber: 2.2 Consensus size: 27
13143 AATTTTCAAC
*
13153 TAATGATTGTTTCCTTTGATCCTCTTTT
1 TAAT-ATTGTTTCCTTTGATCCTCTTCT
13181 TAATATTGTTTCCTTTGATCCTCTTCT
1 TAATATTGTTTCCTTTGATCCTCTTCT
13208 TAATA
1 TAATA
13213 GAATTTTTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 27 0.87
28 4 0.13
ACGTcount: A:0.18, C:0.18, G:0.08, T:0.55
Consensus pattern (27 bp):
TAATATTGTTTCCTTTGATCCTCTTCT
Found at i:14059 original size:206 final size:206
Alignment explanation
Indices: 13705--14471 Score: 1118
Period size: 206 Copynumber: 3.7 Consensus size: 206
13695 CACAAAAAAT
* * * *
13705 GACGCGGTCATCTGCCAGATGAAATACTGAGAAGAAGACCAAATCAAA-CCAATGCTCGATGTGA
1 GACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAATCC-ACGCTCGATGT-A
* * *
13769 A-TAAATTTTCGAA-CCACAGCTTCCTGATGAGA-ACCCGAGAAGCAGGTCGAAGGAATAAAATG
64 AGCAAATCTTCGAATCC-CAGCTTCCTGATGAGACA-CCGAGAAGCAGGTCGAAGCAATAAAATG
* *
13831 GTTAGCTCCCTGATGAGATACTGAAAAGTGAACCAAATAT-TTCTT-TCTAATGAGATACAGAGA
127 GTTAGCTCCCTGATGAGATACTGAAAAGTGAACCAAAT-TCGTCTTCT-TGATGAGATACAGAGA
13894 AGCGAATTGAAACAAAC
190 AGCGAATTGAAACAAAC
* *
13911 GACGCGGTCATCTTCCTGATGAGATATTGAGAAGAAGACCAAATCAAATCCACGCTTGATGTAAG
1 GACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAATCCACGCTCGATGTAAG
*
13976 CAAATCTTCGAATCCTAGCTTCCTGATGAGACACCGAGAAGCAGGTCGAAGCAATAAAATGGTTA
66 CAAATCTTCGAATCCCAGCTTCCTGATGAGACACCGAGAAGCAGGTCGAAGCAATAAAATGGTTA
* *
14041 GCTCCCTGATGAGATACTGAAAAGTAAACCAAATTCGTCTTCTTGATGAGATACAGAGAAGCAAA
131 GCTCCCTGATGAGATACTGAAAAGTGAACCAAATTCGTCTTCTTGATGAGATACAGAGAAGCGAA
14106 TTGAAACAAAC
196 TTGAAACAAAC
*
14117 GACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAATCCACGCTTGATGTAAG
1 GACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAATCCACGCTCGATGTAAG
* * *
14182 AAAATCTTCGAATCCCAGCTTCTTGATGAGACACCGAGAAGCAGGTCGAAGCAATAAAAAGGTTA
66 CAAATCTTCGAATCCCAGCTTCCTGATGAGACACCGAGAAGCAGGTCGAAGCAATAAAATGGTTA
* * * *
14247 GCTTCCTGATGAGATACTGAGAAGTGTACCAAATTCGTCTTCTTGATGAGATACAGAGAAGCGGA
131 GCTCCCTGATGAGATACTGAAAAGTGAACCAAATTCGTCTTCTTGATGAGATACAGAGAAGCGAA
*
14312 TTGAAACAAAT
196 TTGAAACAAAC
* * *
14323 GATGCGGTCATCTTCCTGATAAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGATGTAAG
1 GACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAATCCACGCTCGATGTAAG
* * * *
14388 CAAATCTTTGAATCCCAGCTTCCTGATGGGACACCGA-ATAGCAGGTCGAAGCAAT-AAACGGCT
66 CAAATCTTCGAATCCCAGCTTCCTGATGAGACACCGAGA-AGCAGGTCGAAGCAATAAAATGGTT
* * *
14451 AGTTTCCTAATGAGATACTGA
130 AGCTCCCTGATGAGATACTGA
14472 GAAGAAGGCC
Statistics
Matches: 516, Mismatches: 38, Indels: 15
0.91 0.07 0.03
Matches are distributed among these distances:
205 29 0.06
206 481 0.93
207 6 0.01
ACGTcount: A:0.36, C:0.20, G:0.22, T:0.22
Consensus pattern (206 bp):
GACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAATCCACGCTCGATGTAAG
CAAATCTTCGAATCCCAGCTTCCTGATGAGACACCGAGAAGCAGGTCGAAGCAATAAAATGGTTA
GCTCCCTGATGAGATACTGAAAAGTGAACCAAATTCGTCTTCTTGATGAGATACAGAGAAGCGAA
TTGAAACAAAC
Found at i:14831 original size:17 final size:18
Alignment explanation
Indices: 14800--14842 Score: 63
Period size: 17 Copynumber: 2.5 Consensus size: 18
14790 ACCGGGCCCA
14800 TAAAATTTAAATTTATTT
1 TAAAATTTAAATTTATTT
*
14818 TAAAA-TTAAGTTTATTT
1 TAAAATTTAAATTTATTT
14835 T-AAATTTA
1 TAAAATTTA
14843 TTATAAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 3 0.13
17 15 0.65
18 5 0.22
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (18 bp):
TAAAATTTAAATTTATTT
Found at i:14894 original size:14 final size:14
Alignment explanation
Indices: 14875--14905 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
14865 TCATTTAAAT
14875 AATGTCCAATACAA
1 AATGTCCAATACAA
14889 AATGTCCAATACAA
1 AATGTCCAATACAA
14903 AAT
1 AAT
14906 TACAAAGCCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.52, C:0.19, G:0.06, T:0.23
Consensus pattern (14 bp):
AATGTCCAATACAA
Found at i:15638 original size:3 final size:3
Alignment explanation
Indices: 15632--15672 Score: 64
Period size: 3 Copynumber: 13.7 Consensus size: 3
15622 AATAATGACC
* *
15632 ATA ATA ATA ATA ATA ATA ATA ATA GTA ATA ATA ATA TTA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
15673 TAGCATAGAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (3 bp):
ATA
Found at i:16751 original size:29 final size:29
Alignment explanation
Indices: 16701--16987 Score: 246
Period size: 29 Copynumber: 9.8 Consensus size: 29
16691 GAGGTCCCCG
* **
16701 AAACTTCCAAAAATTCTGTTTTTACCCAC
1 AAACTTCCAAAAATCCCATTTTTACCCAC
* *
16730 GAACTTCCAAAAAACCCATTTTTGACCTCA-
1 AAACTTCCAAAAATCCCATTTTT-ACC-CAC
*
16760 AAACTTCCAAAATTCCGC--TTTTACACC-C
1 AAACTTCCAAAAATCC-CATTTTTAC-CCAC
*
16788 GAACTTCCAAAAATCCCATTTTTGACCTCA-
1 AAACTTCCAAAAATCCCATTTTT-ACC-CAC
16818 AAACTTCCAAAAATCCCATTTTTACCC-C
1 AAACTTCCAAAAATCCCATTTTTACCCAC
* *
16846 TAAACTTCCAAAAATCCTATTTTAACCCTA-
1 -AAACTTCCAAAAATCCCATTTTTACCC-AC
* **
16876 AAACTTCCAAAAATTCCATTTTTACCCTT
1 AAACTTCCAAAAATCCCATTTTTACCCAC
* ** *
16905 GAACTTTTAAAAAATCCCATTTTTGACCCCC
1 AAAC-TTCCAAAAATCCCATTTTT-ACCCAC
* *
16936 AAAACTTCCAAAAATTCCATTTTTACCCCC
1 -AAACTTCCAAAAATCCCATTTTTACCCAC
* *
16966 GAATTTCCAAAAATCCCATTTT
1 AAACTTCCAAAAATCCCATTTT
16988 CAACCTCGAA
Statistics
Matches: 210, Mismatches: 30, Indels: 36
0.76 0.11 0.13
Matches are distributed among these distances:
27 1 0.00
28 18 0.09
29 102 0.49
30 63 0.30
31 23 0.11
32 3 0.01
ACGTcount: A:0.35, C:0.30, G:0.03, T:0.32
Consensus pattern (29 bp):
AAACTTCCAAAAATCCCATTTTTACCCAC
Found at i:16792 original size:58 final size:57
Alignment explanation
Indices: 16701--17052 Score: 320
Period size: 58 Copynumber: 6.0 Consensus size: 57
16691 GAGGTCCCCG
** *
16701 AAACTTCCAAAAATTCTGTTTTTACCCACGAACTTCCAAAAAACCCATTTTTGACCTCA
1 AAACTTCCAAAAATTC-CCTTTTACCC-CGAACTTCCAAAAATCCCATTTTTGACCTCA
16760 AAACTTCC-AAAATTCCGCTTTTACACCCGAACTTCCAAAAATCCCATTTTTGACCTCA
1 AAACTTCCAAAAATTCC-CTTTTAC-CCCGAACTTCCAAAAATCCCATTTTTGACCTCA
* * *
16818 AAACTTCCAAAAA-TCCCATTTTTACCCCTAAACTTCCAAAAATCCTA-TTTTAACC-CTA
1 AAACTTCCAAAAATTCCC--TTTTACCCC-GAACTTCCAAAAATCCCATTTTTGACCTC-A
* * ** *
16876 AAACTTCCAAAAATTCCATTTTTACCCTTGAACTTTTAAAAAATCCCATTTTTGACCCCCA
1 AAACTTCCAAAAATTCC-CTTTTACCC-CGAAC-TTCCAAAAATCCCATTTTTGA-CCTCA
* * ** *
16937 AAACTTCCAAAAATTCCATTTTTACCCCCGAATTTCCAAAAATCCCATTTTCAACCTCG
1 AAACTTCCAAAAATTCC-CTTTTA-CCCCGAACTTCCAAAAATCCCATTTTTGACCTCA
* * * * *
16996 AAAC-TCTC-AAAATTACCCTTTTACCCCCAAATATCTAAAAATTCCATTTTTAACCTC
1 AAACTTC-CAAAAATT-CCCTTTTACCCCGAACT-TCCAAAAATCCCATTTTTGACCTC
17053 GAATTTTTCC
Statistics
Matches: 248, Mismatches: 27, Indels: 37
0.79 0.09 0.12
Matches are distributed among these distances:
57 9 0.04
58 123 0.50
59 60 0.24
60 22 0.09
61 30 0.12
62 4 0.02
ACGTcount: A:0.35, C:0.30, G:0.03, T:0.32
Consensus pattern (57 bp):
AAACTTCCAAAAATTCCCTTTTACCCCGAACTTCCAAAAATCCCATTTTTGACCTCA
Found at i:16997 original size:29 final size:29
Alignment explanation
Indices: 16701--17052 Score: 227
Period size: 29 Copynumber: 12.0 Consensus size: 29
16691 GAGGTCCCCG
* ** * *
16701 AAACTTCCAAAAATTCTGTTTTTACCCAC
1 AAACTTCCAAAAATCCCATTTTTAACCTC
* * *
16730 GAACTTCCAAAAAACCCATTTTTGACCTC
1 AAACTTCCAAAAATCCCATTTTTAACCTC
*
16759 AAAACTTCCAAAATTCCGC--TTTTACACC-C
1 -AAACTTCCAAAAATCC-CATTTTTA-ACCTC
* *
16788 GAACTTCCAAAAATCCCATTTTTGACCTC
1 AAACTTCCAAAAATCCCATTTTTAACCTC
*
16817 AAAACTTCCAAAAATCCCATTTTT-ACCCC
1 -AAACTTCCAAAAATCCCATTTTTAACCTC
* *
16846 TAAACTTCCAAAAATCCTA-TTTTAACCCTA
1 -AAACTTCCAAAAATCCCATTTTTAA-CCTC
* * *
16876 AAACTTCCAAAAATTCCATTTTTACCCTT
1 AAACTTCCAAAAATCCCATTTTTAACCTC
* ** * *
16905 GAACTTTTAAAAAATCCCATTTTTGACCCCC
1 AAAC-TTCCAAAAATCCCATTTTT-AACCTC
* * *
16936 AAAACTTCCAAAAATTCCATTTTTACCCCC
1 -AAACTTCCAAAAATCCCATTTTTAACCTC
* * *
16966 GAATTTCCAAAAATCCCATTTTCAACCTC
1 AAACTTCCAAAAATCCCATTTTTAACCTC
* * *
16995 GAAAC-TCTCAAAATTACCC--TTTTACCCCC
1 -AAACTTC-CAAAAAT-CCCATTTTTAACCTC
* *
17024 AAA-TATCTAAAAATTCCATTTTTAACCTC
1 AAACT-TCCAAAAATCCCATTTTTAACCTC
17053 GAATTTTTCC
Statistics
Matches: 251, Mismatches: 52, Indels: 40
0.73 0.15 0.12
Matches are distributed among these distances:
27 3 0.01
28 29 0.12
29 117 0.47
30 75 0.30
31 24 0.10
32 3 0.01
ACGTcount: A:0.35, C:0.30, G:0.03, T:0.32
Consensus pattern (29 bp):
AAACTTCCAAAAATCCCATTTTTAACCTC
Found at i:17056 original size:87 final size:86
Alignment explanation
Indices: 16945--17108 Score: 215
Period size: 87 Copynumber: 1.9 Consensus size: 86
16935 CAAAACTTCC
* *
16945 AAAAATTCCATTTTTACCCCCGAA-TTTCCAAAAATCCCATTTTCAACCTCGA-AACTCTCAAAA
1 AAAAATTCCATTTTTAACCCCGAATTTTCCAAAAATACCA-TTTCAACCTCGAGAA-TC-CAAAA
*
17008 TTACCCTTTTACCCCCAAATATCT
63 TTACCATTTTACCCCCAAATATCT
* * * *
17032 AAAAATTCCATTTTTAACCTCGAATTTTTCCAAAATTACTATTTCACCCTCGAGAATCCAAAATT
1 AAAAATTCCATTTTTAACCCCGAA-TTTTCCAAAAATACCATTTCAACCTCGAGAATCCAAAATT
17097 ACCATTTTACCC
65 ACCATTTTACCC
17109 TCGGTATCCG
Statistics
Matches: 67, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
87 40 0.60
88 13 0.19
89 14 0.21
ACGTcount: A:0.35, C:0.29, G:0.03, T:0.33
Consensus pattern (86 bp):
AAAAATTCCATTTTTAACCCCGAATTTTCCAAAAATACCATTTCAACCTCGAGAATCCAAAATTA
CCATTTTACCCCCAAATATCT
Done.