Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011598.1 Kokia drynarioides strain JFW-HI SEQ_126588, 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: 41021
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Warning! 53 characters in sequence are not A, C, G, or T
Found at i:1656 original size:858 final size:848
Alignment explanation
Indices: 1--1678 Score: 3266
Period size: 858 Copynumber: 2.0 Consensus size: 848
1 TAGATTCATCTTTGTGGTGATTGACTATTTCACTAAATGGGTAGAGGCAACCTCATATGCGAATG
1 TAGATTCATCTTTGTGGTGATTGACTATTTCACTAAATGGGTAGAGGCAACCTCATATGCGAATG
66 TTACCAAGTCTGCGGTTAGTAGGTTCTTGAAAAAGGAAATCATTTGCTGATATGGGATGCCTGAA
66 TTACCAAGTCTGCGGTTAGTAGGTTCTTGAAAAAGGAAATCATTTGCTGATATGGGATGCCTGAA
131 AGGATCATATCCGACAATGCACTCAATCTGAACAACAGTACGATAGCAGAAGTTTGTGAATAGTT
131 AGGATCATATCCGACAATGCACTCAATCTGAACAACAGTACGATAGCAGAAGTTTGTGAATAGTT
196 CAAGATTAAGCATCATAATTCTTCTCCCTATCGCCCAAAAATGAATGGGGCTGTGGAGGCAGCTA
196 CAAGATTAAGCATCATAATTCTTCTCCCTATCGCCCAAAAATGAATGGGGCTGTGGAGGCAGCTA
261 ATAAGAATATCAAGAAGATTGTGGCCAAAATGACTGAGACTTACAAGGACTGGCACGAAAAATTA
261 ATAAGAATATCAAGAAGATTGTGGCCAAAATGACTGAGACTTACAAGGACTGGCACGAAAAATTA
326 CCATTTTCCCTCTTTACTTACAGAACTTCAGTCAGAACTTCTATTGGGGCAACGACATTCTCGTT
326 CCATTTTCCCTCTTTACTTACAGAACTTCAGTCAGAACTTCTATTGGGGCAACGACATTCTCGTT
391 GGCATACGGTATGGAAGCAATCTTGCCTATTGAGGTTGAAATACCTTCCCTTCGAGTCTTAACGA
391 GGCATACGGTATGGAAGCAATCTTGCCTATTGAGGTTGAAATACCTTCCCTTCGAGTCTTAACGA
456 AGCTTCAACTTGACGAGGCAGAATAGGTCCAGGCTCGATATGACCAATTGAATTTAATCGAGGAA
456 AGCTTCAACTTGACGAGGCAGAATAGGTCCAGGCTCGATATGACCAATTGAATTTAATCGAGGAA
521 AAGAGATTAAAAGCCATTCGCCACGGCCAAATGTACCAGAAAAGAATGATGCGAGCTTACGACAA
521 AAGAGATTAAAAGCCATTCGCCACGGCCAAATGTACCAGAAAAGAATGATGCGAGCTTACGACAA
586 AAAAGTCCGTCCCAGGGAATTCTATGAGGGAGATCTAGTTTTGAAAAAGATACTTCACATACATA
586 AAAAGTCCGTCCCAGGGAATTCTATGAGGGAGATCTAGTTTTGAAAAAGATACTTCACATACATA
651 AAGATTTCCGTGGGAAATGGATGCCCAATTGGGAAGGGTCCTACGTGGTAAAAATGGCTTTCTCA
651 AAGATTTCCGTGGGAAATGGATGCCCAATTGGGAAGGGTCCTACGTGGTAAAAATGGCTTTCTCA
716 GGAGGAGCTCTCATCTTAACAGAGATGGACGGCAAAGAGCTGTACAACCCCGTCAATTCAGACTC
716 GGAGGAGCTCTCATCTTAACAGAGATGGACGGCAAAGAGCTGTACAACCCCGTCAATTCAGACTC
781 GGTAAAAAAATACTTTGCCTAGAAACCAAATAAGAATTGANNNNNNNNNNCAATTTCTCCAAAGG
781 GGTAAAAAAATACTTTGCCTAGAAACCAAATAAGAATTGA----------CAATTTCTCCAAAGG
846 CTTCCAATGGCCA
836 CTTCCAATGGCCA
859 TAGATTCATCTTTGTGGTGATTGACTATTTCACTAAATGGGTAGAGGCAACCTCATATGCGAATG
1 TAGATTCATCTTTGTGGTGATTGACTATTTCACTAAATGGGTAGAGGCAACCTCATATGCGAATG
924 TTACCAAGTCTGCGGTTAGTAGGTTCTTGAAAAAGGAAATCATTTGCTGATATGGGATGCCTGAA
66 TTACCAAGTCTGCGGTTAGTAGGTTCTTGAAAAAGGAAATCATTTGCTGATATGGGATGCCTGAA
989 AGGATCATATCCGACAATGCACTCAATCTGAACAACAGTACGATAGCAGAAGTTTGTGAATAGTT
131 AGGATCATATCCGACAATGCACTCAATCTGAACAACAGTACGATAGCAGAAGTTTGTGAATAGTT
1054 CAAGATTAAGCATCATAATTCTTCTCCCTATCGCCCAAAAATGAATGGGGCTGTGGAGGCAGCTA
196 CAAGATTAAGCATCATAATTCTTCTCCCTATCGCCCAAAAATGAATGGGGCTGTGGAGGCAGCTA
1119 ATAAGAATATCAAGAAGATTGTGGCCAAAATGACTGAGACTTACAAGGACTGGCACGAAAAATTA
261 ATAAGAATATCAAGAAGATTGTGGCCAAAATGACTGAGACTTACAAGGACTGGCACGAAAAATTA
1184 CCATTTTCCCTCTTTACTTACAGAACTTCAGTCAGAACTTCTATTGGGGCAACGACATTCTCGTT
326 CCATTTTCCCTCTTTACTTACAGAACTTCAGTCAGAACTTCTATTGGGGCAACGACATTCTCGTT
1249 GGCATACGGTATGGAAGCAATCTTGCCTATTGAGGTTGAAATACCTTCCCTTCGAGTCTTAACGA
391 GGCATACGGTATGGAAGCAATCTTGCCTATTGAGGTTGAAATACCTTCCCTTCGAGTCTTAACGA
1314 AGCTTCAACTTGACGAGGCAGAATAGGTCCAGGCTCGATATGACCAATTGAATTTAATCGAGGAA
456 AGCTTCAACTTGACGAGGCAGAATAGGTCCAGGCTCGATATGACCAATTGAATTTAATCGAGGAA
1379 AAGAGATTAAAAGCCATTCGCCACGGCCAAATGTACCAGAAAAGAATGATGCGAGCTTACGACAA
521 AAGAGATTAAAAGCCATTCGCCACGGCCAAATGTACCAGAAAAGAATGATGCGAGCTTACGACAA
1444 AAAAGTCCGTCCCAGGGAATTCTATGAGGGAGATCTAGTTTTGAAAAAGATACTTCACATACATA
586 AAAAGTCCGTCCCAGGGAATTCTATGAGGGAGATCTAGTTTTGAAAAAGATACTTCACATACATA
1509 AAGATTTCCGTGGGAAATGGATGCCCAATTGGGAAGGGTCCTACGTGGTAAAAATGGCTTTCTCA
651 AAGATTTCCGTGGGAAATGGATGCCCAATTGGGAAGGGTCCTACGTGGTAAAAATGGCTTTCTCA
1574 GGAGGAGCTCTCATCTTAACAGAGATGGACGGCAAAGAGCTGTACAACCCCGTCAATTCAGACTC
716 GGAGGAGCTCTCATCTTAACAGAGATGGACGGCAAAGAGCTGTACAACCCCGTCAATTCAGACTC
1639 GGTAAAAAAATACTTTGCCTAGAAACCAAATAAGAATTGA
781 GGTAAAAAAATACTTTGCCTAGAAACCAAATAAGAATTGA
1679 NNNNNNNNNN
Statistics
Matches: 820, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
858 820 1.00
ACGTcount: A:0.33, C:0.19, G:0.22, T:0.25
Consensus pattern (848 bp):
TAGATTCATCTTTGTGGTGATTGACTATTTCACTAAATGGGTAGAGGCAACCTCATATGCGAATG
TTACCAAGTCTGCGGTTAGTAGGTTCTTGAAAAAGGAAATCATTTGCTGATATGGGATGCCTGAA
AGGATCATATCCGACAATGCACTCAATCTGAACAACAGTACGATAGCAGAAGTTTGTGAATAGTT
CAAGATTAAGCATCATAATTCTTCTCCCTATCGCCCAAAAATGAATGGGGCTGTGGAGGCAGCTA
ATAAGAATATCAAGAAGATTGTGGCCAAAATGACTGAGACTTACAAGGACTGGCACGAAAAATTA
CCATTTTCCCTCTTTACTTACAGAACTTCAGTCAGAACTTCTATTGGGGCAACGACATTCTCGTT
GGCATACGGTATGGAAGCAATCTTGCCTATTGAGGTTGAAATACCTTCCCTTCGAGTCTTAACGA
AGCTTCAACTTGACGAGGCAGAATAGGTCCAGGCTCGATATGACCAATTGAATTTAATCGAGGAA
AAGAGATTAAAAGCCATTCGCCACGGCCAAATGTACCAGAAAAGAATGATGCGAGCTTACGACAA
AAAAGTCCGTCCCAGGGAATTCTATGAGGGAGATCTAGTTTTGAAAAAGATACTTCACATACATA
AAGATTTCCGTGGGAAATGGATGCCCAATTGGGAAGGGTCCTACGTGGTAAAAATGGCTTTCTCA
GGAGGAGCTCTCATCTTAACAGAGATGGACGGCAAAGAGCTGTACAACCCCGTCAATTCAGACTC
GGTAAAAAAATACTTTGCCTAGAAACCAAATAAGAATTGACAATTTCTCCAAAGGCTTCCAATGG
CCA
Found at i:2815 original size:139 final size:139
Alignment explanation
Indices: 2615--3640 Score: 1534
Period size: 139 Copynumber: 7.4 Consensus size: 139
2605 AAACGGTTAG
* *
2615 CTTCCTGATGAGATACTGAGAAGTGATCCAAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAA
1 CTTCCAGATGAGATACTGAGAAGTGAACC-AAATTCGTCTTCCTGATGAGATACAGAGAAGCGAA
* * * *
2680 TTGAAACGGTGATGGGGTCATCTTCCTGATGAGACACTGAGAAGAAGACCCAAATGAGGCTCGAA
65 TTGAAACAGTGATAGGATCATCTTCCTGATGAGACACTGAGAAGAAGACCCAAACGAGGCTCGAA
2745 ACGAGCAAAT
130 ACGAGCAAAT
* * * * * * *
2755 CTTCCAGATGAGGTACTAAGAAGTGCACCAAATTCGTCTTCCTGGTAAAATACAGAGAAGCAAAT
1 CTTCCAGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAAT
*
2820 TGAAACAGTGATAGGATCATCTTCCTGATGAGACACTGAGCAGAAGACCCAAACGAGGCTCGAAA
66 TGAAACAGTGATAGGATCATCTTCCTGATGAGACACTGAGAAGAAGACCCAAACGAGGCTCGAAA
2885 CGAGCAAAT
131 CGAGCAAAT
* * *
2894 CTTCCAAACGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGAT
1 CTTCCAGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAAT
* *
2959 GGAAACAGTGATAGGATCATCTTCCTGATAAGACACTGAGAAGAAGACCCAAACGAGGCTCGAAA
66 TGAAACAGTGATAGGATCATCTTCCTGATGAGACACTGAGAAGAAGACCCAAACGAGGCTCGAAA
3024 CGAGCAAAT
131 CGAGCAAAT
* * * * * *
3033 CTTCTAGATGAGGTACTAAGAAGTGCACCAAATTCGTCTTCCTAATGAAATACAGAGAAGC-AGA
1 CTTCCAGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGA-A
* * *
3097 TTGAAACAGTGATGGGATCATCTTCCTGATGAGACATTGAGAAGAAGACCCAAATGAGGCTCGAA
65 TTGAAACAGTGATAGGATCATCTTCCTGATGAGACACTGAGAAGAAGACCCAAACGAGGCTCGAA
3162 ACGAGCAAAT
130 ACGAGCAAAT
* * *
3172 CTTCCAGACGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAAAGAAGCGGAT
1 CTTCCAGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAAT
* * *
3237 GGAAACAGTGATAGGATCATCTTCCTGATAAGACACTTAGAAGAAGACCCAAACGAGGCTCGAAA
66 TGAAACAGTGATAGGATCATCTTCCTGATGAGACACTGAGAAGAAGACCCAAACGAGGCTCGAAA
* *
3302 CAAGCAGAT
131 CGAGCAAAT
* * * * *
3311 CTTCCAGATGAGGTACTAAGTAGTGAATCAAATTCGTCTTCCTGATGAAATACAGAGAAGC-AGA
1 CTTCCAGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGA-A
* *
3375 TTGAAACAGTGATGGGATCATCTTCCTGATGAGACACTGAGAAGAAGACCCAAACGAGGATCGAA
65 TTGAAACAGTGATAGGATCATCTTCCTGATGAGACACTGAGAAGAAGACCCAAACGAGGCTCGAA
3440 ACGAGCAAAT
130 ACGAGCAAAT
* * *
3450 CTTCCAGACGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATATAGAGAAGCGGAT
1 CTTCCAGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAAT
* * * * *
3515 GGAAACAGTGATAGGATCATCTTCCTGATAAGACATTGAGAAGAAAACCCAAACAAGGCTCGAAA
66 TGAAACAGTGATAGGATCATCTTCCTGATGAGACACTGAGAAGAAGACCCAAACGAGGCTCGAAA
*
3580 CGAGCAGAT
131 CGAGCAAAT
*
3589 CTTCCAGATGAGGTACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATA
1 CTTCCAGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATA
3641 AGCGAATTGA
Statistics
Matches: 791, Mismatches: 91, Indels: 9
0.89 0.10 0.01
Matches are distributed among these distances:
139 767 0.97
140 24 0.03
ACGTcount: A:0.37, C:0.19, G:0.24, T:0.20
Consensus pattern (139 bp):
CTTCCAGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAAT
TGAAACAGTGATAGGATCATCTTCCTGATGAGACACTGAGAAGAAGACCCAAACGAGGCTCGAAA
CGAGCAAAT
Found at i:3145 original size:278 final size:278
Alignment explanation
Indices: 2615--3636 Score: 1720
Period size: 278 Copynumber: 3.7 Consensus size: 278
2605 AAACGGTTAG
* * * *
2615 CTTCCTGATGAGATACTGAGAAGTGATCCAAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAA
1 CTTCCAGACGAGATACTGAGAAGTGAACC-AAATTCGTCTTCCTGATGAGATACAGAGAAGCGGA
* * * * * *
2680 TTGAAACGGTGATGGGGTCATCTTCCTGATGAGACACTGAGAAGAAGACCCAAATGAGGCTCGAA
65 TGGAAACAGTGATAGGATCATCTTCCTGATAAGACACTGAGAAGAAGACCCAAACGAGGCTCGAA
* * *
2745 ACGAGCAAATCTTCCAGATGAGGTACTAAGAAGTGCACCAAATTCGTCTTCCTGGTAAAATACAG
130 ACGAGCAAATCTTCCAGATGAGGTACTAAGAAGTGAACCAAATTCGTCTTCCTGATGAAATACAG
* * *
2810 AGAAGCAAATTGAAACAGTGATAGGATCATCTTCCTGATGAGACACTGAGCAGAAGACCCAAACG
195 AGAAGCAGATTGAAACAGTGATGGGATCATCTTCCTGATGAGACACTGAGAAGAAGACCCAAACG
2875 AGGCTCGAAACGAGCAAAT
260 AGGCTCGAAACGAGCAAAT
*
2894 CTTCCAAACGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGAT
1 CTTCCAGACGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGAT
2959 GGAAACAGTGATAGGATCATCTTCCTGATAAGACACTGAGAAGAAGACCCAAACGAGGCTCGAAA
66 GGAAACAGTGATAGGATCATCTTCCTGATAAGACACTGAGAAGAAGACCCAAACGAGGCTCGAAA
* * *
3024 CGAGCAAATCTTCTAGATGAGGTACTAAGAAGTGCACCAAATTCGTCTTCCTAATGAAATACAGA
131 CGAGCAAATCTTCCAGATGAGGTACTAAGAAGTGAACCAAATTCGTCTTCCTGATGAAATACAGA
* *
3089 GAAGCAGATTGAAACAGTGATGGGATCATCTTCCTGATGAGACATTGAGAAGAAGACCCAAATGA
196 GAAGCAGATTGAAACAGTGATGGGATCATCTTCCTGATGAGACACTGAGAAGAAGACCCAAACGA
3154 GGCTCGAAACGAGCAAAT
261 GGCTCGAAACGAGCAAAT
*
3172 CTTCCAGACGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAAAGAAGCGGAT
1 CTTCCAGACGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGAT
*
3237 GGAAACAGTGATAGGATCATCTTCCTGATAAGACACTTAGAAGAAGACCCAAACGAGGCTCGAAA
66 GGAAACAGTGATAGGATCATCTTCCTGATAAGACACTGAGAAGAAGACCCAAACGAGGCTCGAAA
* * * *
3302 CAAGCAGATCTTCCAGATGAGGTACTAAGTAGTGAATCAAATTCGTCTTCCTGATGAAATACAGA
131 CGAGCAAATCTTCCAGATGAGGTACTAAGAAGTGAACCAAATTCGTCTTCCTGATGAAATACAGA
3367 GAAGCAGATTGAAACAGTGATGGGATCATCTTCCTGATGAGACACTGAGAAGAAGACCCAAACGA
196 GAAGCAGATTGAAACAGTGATGGGATCATCTTCCTGATGAGACACTGAGAAGAAGACCCAAACGA
*
3432 GGATCGAAACGAGCAAAT
261 GGCTCGAAACGAGCAAAT
*
3450 CTTCCAGACGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATATAGAGAAGCGGAT
1 CTTCCAGACGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGAT
* * *
3515 GGAAACAGTGATAGGATCATCTTCCTGATAAGACATTGAGAAGAAAACCCAAACAAGGCTCGAAA
66 GGAAACAGTGATAGGATCATCTTCCTGATAAGACACTGAGAAGAAGACCCAAACGAGGCTCGAAA
* *
3580 CGAGCAGATCTTCCAGATGAGGTACTGAGAAGTGAACCAAATTCGTCTTCCTGATGA
131 CGAGCAAATCTTCCAGATGAGGTACTAAGAAGTGAACCAAATTCGTCTTCCTGATGA
3637 GATAAGCGAA
Statistics
Matches: 700, Mismatches: 43, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
278 675 0.96
279 25 0.04
ACGTcount: A:0.37, C:0.19, G:0.24, T:0.20
Consensus pattern (278 bp):
CTTCCAGACGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGAT
GGAAACAGTGATAGGATCATCTTCCTGATAAGACACTGAGAAGAAGACCCAAACGAGGCTCGAAA
CGAGCAAATCTTCCAGATGAGGTACTAAGAAGTGAACCAAATTCGTCTTCCTGATGAAATACAGA
GAAGCAGATTGAAACAGTGATGGGATCATCTTCCTGATGAGACACTGAGAAGAAGACCCAAACGA
GGCTCGAAACGAGCAAAT
Found at i:4791 original size:3 final size:3
Alignment explanation
Indices: 4785--4820 Score: 63
Period size: 3 Copynumber: 11.7 Consensus size: 3
4775 TAAAAAAAAC
4785 AAT AAT AAT AAT AAT AAT AAT AAT AATT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AA
4821 AAAAGGGCAT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:5894 original size:30 final size:29
Alignment explanation
Indices: 5859--6272 Score: 186
Period size: 30 Copynumber: 14.0 Consensus size: 29
5849 ACCTTCCAAG
5859 AATTACCATTTTACCCTCGAATCTTTCAAA
1 AATTACCATTTTACCCTCGAA-CTTTCAAA
* *
5889 AATTACCATTTTACCC-CTAAACTTCCAAA
1 AATTACCATTTTACCCTC-GAACTTTCAAA
** * *
5918 AA-T-CCTATTTTTGGTCC-CGATCCTTCTAAA
1 AATTACC-A-TTTT-ACCCTCGAACTTTC-AAA
* * *
5948 AATTATCATTTTACCCCCGAACTTCCAAA
1 AATTACCATTTTACCCTCGAACTTTCAAA
* *
5977 AA-T-CCTATTTTTGGCCCT-GAA-TCTTCCAA
1 AATTACC-A-TTTT-ACCCTCGAACT-TTCAAA
* *
6006 AATTACCATTTTACCC-CTAAAC-TTCCAA
1 AATTACCATTTTACCCTC-GAACTTTCAAA
* * *
6034 GATTCCCATTTTTAGCCCT-GAACCTTCTAAA
1 AATTACCA-TTTTA-CCCTCGAACTTTC-AAA
* *
6065 AATTACCATTTTACCCTCGCACTTCCAAA
1 AATTACCATTTTACCCTCGAACTTTCAAA
*
6094 AA-T-CCTATTTTTAACCC-CGAATCTTCCAAA
1 AATTACC-A-TTTT-ACCCTCGAA-CTTTCAAA
* * *
6124 AATTACTATTTTACCCTCTAACTTCCAAA
1 AATTACCATTTTACCCTCGAACTTTCAAA
*
6153 AA-TCCCATTATTGA-CCTCGAA-TCTTCTAAA
1 AATTACCATT-TT-ACCCTCGAACT-TTC-AAA
* * *
6183 AATTACAATTTTACCCCCCGAACTTCCAAA
1 AATTACCATTTTA-CCCTCGAACTTTCAAA
*
6213 AA-T-CTCATTTTTGA-CCTCGAA-TCTTCTTAA
1 AATTAC-CA-TTTT-ACCCTCGAACT-TTC-AAA
6243 AATTACCATTTTACCCTCGAACTTTCAAA
1 AATTACCATTTTACCCTCGAACTTTCAAA
6272 A
1 A
6273 TTCTATTTTT
Statistics
Matches: 291, Mismatches: 46, Indels: 95
0.67 0.11 0.22
Matches are distributed among these distances:
27 5 0.02
28 30 0.10
29 107 0.37
30 113 0.39
31 32 0.11
32 4 0.01
ACGTcount: A:0.32, C:0.29, G:0.05, T:0.35
Consensus pattern (29 bp):
AATTACCATTTTACCCTCGAACTTTCAAA
Found at i:5929 original size:29 final size:29
Alignment explanation
Indices: 5897--6157 Score: 144
Period size: 29 Copynumber: 8.9 Consensus size: 29
5887 AAAATTACCA
5897 TTTTACCCCTAAACTTCCAAAAATCCTAT
1 TTTTACCCCTAAACTTCCAAAAATCCTAT
** * ** *
5926 TTTTGGTCCCGATCCTTCTAAAAAT--TAT
1 TTTT-ACCCCTAAACTTCCAAAAATCCTAT
**
5954 CATTTTACCCCCGAACTTCCAAAAATCCTAT
1 --TTTTACCCCTAAACTTCCAAAAATCCTAT
** * *
5985 TTTTGGCCCTGAATCTTCCAAAATTACC-A-
1 TTTTACCCCT-AAACTTCCAAAAAT-CCTAT
* * *
6014 TTTTACCCCTAAACTTCCAAGATTCCCAT
1 TTTTACCCCTAAACTTCCAAAAATCCTAT
* * *
6043 TTTTAGCCCTGAACCTTCTAAAAATTACC-A-
1 TTTTACCCCT-AAACTTCCAAAAA-T-CCTAT
**
6073 TTTTA-CCCTCGCACTTCCAAAAATCCTAT
1 TTTTACCCCT-AAACTTCCAAAAATCCTAT
* * *
6102 TTTTAACCCCGAATCTTCCAAAAATTACTA-
1 TTTT-ACCCCTAAACTTCCAAAAA-TCCTAT
6132 TTTTACCCTCT-AACTTCCAAAAATCC
1 TTTTACCC-CTAAACTTCCAAAAATCC
6158 CATTATTGAC
Statistics
Matches: 173, Mismatches: 41, Indels: 37
0.69 0.16 0.15
Matches are distributed among these distances:
27 4 0.02
28 20 0.12
29 73 0.42
30 60 0.35
31 14 0.08
32 2 0.01
ACGTcount: A:0.31, C:0.30, G:0.05, T:0.34
Consensus pattern (29 bp):
TTTTACCCCTAAACTTCCAAAAATCCTAT
Found at i:5949 original size:59 final size:58
Alignment explanation
Indices: 5876--6283 Score: 427
Period size: 59 Copynumber: 6.9 Consensus size: 58
5866 ATTTTACCCT
*
5876 CGAATCTT-TCAAAAATTACCATTTTACCCCTAAACTTCCAAAAATCCTATTTTTGGTCC
1 CGAATCTTCT-AAAAATTACCATTTTACCCCTGAACTTCCAAAAATCCTATTTTTGG-CC
* *
5935 CG-ATCCTTCTAAAAATTATCATTTTACCCCCGAACTTCCAAAAATCCTATTTTTGGCC
1 CGAAT-CTTCTAAAAATTACCATTTTACCCCTGAACTTCCAAAAATCCTATTTTTGGCC
* * * * * *
5993 CTGAATCTTC-CAAAATTACCATTTTACCCCTAAACTTCCAAGATTCCCATTTTTAGCC
1 C-GAATCTTCTAAAAATTACCATTTTACCCCTGAACTTCCAAAAATCCTATTTTTGGCC
* * **
6051 CTGAACCTTCTAAAAATTACCATTTTA-CCCTCGCACTTCCAAAAATCCTATTTTTAACCC
1 C-GAATCTTCTAAAAATTACCATTTTACCCCT-GAACTTCCAAAAATCCTATTTTT-GGCC
* * * * *
6111 CGAATCTTCCAAAAATTACTATTTTACCCTCT-AACTTCCAAAAATCCCATTATTGACC
1 CGAATCTTCTAAAAATTACCATTTTACCC-CTGAACTTCCAAAAATCCTATTTTTGGCC
* * *
6169 TCGAATCTTCTAAAAATTACAATTTTACCCCCCGAACTTCCAAAAAT-CTCATTTTTGACC
1 -CGAATCTTCTAAAAATTACCATTTTA-CCCCTGAACTTCCAAAAATCCT-ATTTTTGGCC
* * *
6229 TCGAATCTTCTTAAAATTACCATTTTA-CCCTCGAACTTTC-AAAATTCTATTTTTG
1 -CGAATCTTCTAAAAATTACCATTTTACCCCT-GAACTTCCAAAAATCCTATTTTTG
6284 ATTCCGAACA
Statistics
Matches: 298, Mismatches: 36, Indels: 31
0.82 0.10 0.08
Matches are distributed among these distances:
58 75 0.25
59 162 0.54
60 59 0.20
61 2 0.01
ACGTcount: A:0.31, C:0.28, G:0.05, T:0.35
Consensus pattern (58 bp):
CGAATCTTCTAAAAATTACCATTTTACCCCTGAACTTCCAAAAATCCTATTTTTGGCC
Found at i:6017 original size:89 final size:89
Alignment explanation
Indices: 5850--6155 Score: 227
Period size: 89 Copynumber: 3.5 Consensus size: 89
5840 GGTCCCTAAA
* * *
5850 CCTTCCAAGAATTACCATTTTACCCTCGAATCTTTCAAAAATTACCATTTTACCCCTAAACTTCC
1 CCTTCCAAAAATTACCATTTTACCCCCGAATCTTCCAAAAATTACCATTTTACCCCTAAACTTCC
5915 AAAAATCCTATTTTTGGTCCCGAT
66 AAAAATCCTATTTTTGGTCCCGAT
* * ** *
5939 CCTTCTAAAAATTATCATTTTACCCCCGAA-CTTCCAAAAA-T-CCTATTTTTGGCCCTGAATCT
1 CCTTCCAAAAATTACCATTTTACCCCCGAATCTTCCAAAAATTACC-A-TTTTACCCCT-AAACT
* ** * *
6001 TCCAAAATTACC-A-TTTT-ACCCCTAA
63 TCCAAAAAT-CCTATTTTTGGTCCCGAT
* * * * * * * **
6026 ACTTCC-AAGATTCCCATTTTTAGCCCTGAACCTTCTAAAAATTACCATTTTA-CCCTCGCACTT
1 CCTTCCAAAAATTACCA-TTTTACCCCCGAATCTTCCAAAAATTACCATTTTACCCCT-AAACTT
***
6089 CCAAAAATCCTATTTTTAACCCCGAAT
64 CCAAAAATCCTATTTTTGGTCCCG-AT
* * *
6116 -CTTCCAAAAATTACTATTTTACCCTCTAA-CTTCCAAAAAT
1 CCTTCCAAAAATTACCATTTTACCCCCGAATCTTCCAAAAAT
6156 CCCATTATTG
Statistics
Matches: 167, Mismatches: 37, Indels: 27
0.72 0.16 0.12
Matches are distributed among these distances:
86 11 0.07
87 36 0.22
88 48 0.29
89 60 0.36
90 12 0.07
ACGTcount: A:0.31, C:0.30, G:0.05, T:0.34
Consensus pattern (89 bp):
CCTTCCAAAAATTACCATTTTACCCCCGAATCTTCCAAAAATTACCATTTTACCCCTAAACTTCC
AAAAATCCTATTTTTGGTCCCGAT
Found at i:6060 original size:117 final size:115
Alignment explanation
Indices: 5867--6258 Score: 479
Period size: 117 Copynumber: 3.3 Consensus size: 115
5857 AGAATTACCA
* * *
5867 TTTTACCCTCGAATCTTTCAAAAATTACCATTTTACCCCTAAACTTCCAAAAATCCTATTTTTGG
1 TTTTGCCCTCGAATC-TTCCAAAATTACCATTTTACCCCTAAACTTCCAAAAATCCCATTTTT-G
*
5932 TCCC-GATCCTTCTAAAAATTATCATTTTACCCCCGAACTTCCAAAAATCCTAT
64 -CCCTGAACCTTCTAAAAATTA-CATTTTACCCCCGAACTTCCAAAAATCCTAT
* *
5985 TTTTGGCCCT-GAATCTTCCAAAATTACCATTTTACCCCTAAACTTCCAAGATTCCCATTTTTAG
1 TTTT-GCCCTCGAATCTTCCAAAATTACCATTTTACCCCTAAACTTCCAAAAATCCCATTTTT-G
* *
6049 CCCTGAACCTTCTAAAAATTACCATTTTACCCTCGCACTTCCAAAAATCCTAT
64 CCCTGAACCTTCTAAAAATTA-CATTTTACCCCCGAACTTCCAAAAATCCTAT
* * *
6102 TTTTAACCC-CGAATCTTCCAAAAATTACTATTTTACCCTCT-AACTTCCAAAAATCCCATTATT
1 TTTT-GCCCTCGAATCTTCC-AAAATTACCATTTTACCC-CTAAACTTCCAAAAATCCCATTTTT
* *
6165 GACCTCGAATCTTCTAAAAATTACAATTTTACCCCCCGAACTTCCAAAAAT-CTCAT
63 GCCCT-GAACCTTCTAAAAATTAC-ATTTTA-CCCCCGAACTTCCAAAAATCCT-AT
* *
6221 TTTTGACCTCGAATCTTCTTAAAATTACCATTTTACCC
1 TTTTGCCCTCGAATCTTC-CAAAATTACCATTTTACCC
6259 TCGAACTTTC
Statistics
Matches: 239, Mismatches: 24, Indels: 21
0.84 0.08 0.07
Matches are distributed among these distances:
116 3 0.01
117 110 0.46
118 71 0.30
119 55 0.23
ACGTcount: A:0.31, C:0.29, G:0.05, T:0.35
Consensus pattern (115 bp):
TTTTGCCCTCGAATCTTCCAAAATTACCATTTTACCCCTAAACTTCCAAAAATCCCATTTTTGCC
CTGAACCTTCTAAAAATTACATTTTACCCCCGAACTTCCAAAAATCCTAT
Found at i:10446 original size:24 final size:24
Alignment explanation
Indices: 10409--10464 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
10399 TAGACTAACA
* * *
10409 AGAGTTTGACTGAAAGAAATAAAT
1 AGAGTTTAACTGAAACAAATAAAC
*
10433 AGAGTTTAATTGAAACAAATAAAC
1 AGAGTTTAACTGAAACAAATAAAC
10457 AGAGTTTA
1 AGAGTTTA
10465 TCTGGAAGAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.50, C:0.05, G:0.18, T:0.27
Consensus pattern (24 bp):
AGAGTTTAACTGAAACAAATAAAC
Found at i:12421 original size:24 final size:24
Alignment explanation
Indices: 12394--12444 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
12384 AGTTTGACTT
*
12394 AAACAAATAAATAGAGTTTAATTG
1 AAACAAATAAACAGAGTTTAATTG
*
12418 AAACAAATAAACAGAGTTTATTTG
1 AAACAAATAAACAGAGTTTAATTG
12442 AAA
1 AAA
12445 TATTATTTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.55, C:0.06, G:0.12, T:0.27
Consensus pattern (24 bp):
AAACAAATAAACAGAGTTTAATTG
Found at i:16261 original size:3 final size:3
Alignment explanation
Indices: 16255--16290 Score: 63
Period size: 3 Copynumber: 11.7 Consensus size: 3
16245 TAAAAAAAAC
16255 AAT AAT AAT AAT AAT AAT AAT AAT AATT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AA
16291 AAAAGGGCAT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:17364 original size:30 final size:29
Alignment explanation
Indices: 17329--17742 Score: 186
Period size: 30 Copynumber: 14.0 Consensus size: 29
17319 ACCTTCCAAG
17329 AATTACCATTTTACCCTCGAATCTTTCAAA
1 AATTACCATTTTACCCTCGAA-CTTTCAAA
* *
17359 AATTACCATTTTACCC-CTAAACTTCCAAA
1 AATTACCATTTTACCCTC-GAACTTTCAAA
** * *
17388 AA-T-CCTATTTTTGGTCC-CGATCCTTCTAAA
1 AATTACC-A-TTTT-ACCCTCGAACTTTC-AAA
* * *
17418 AATTATCATTTTACCCCCGAACTTCCAAA
1 AATTACCATTTTACCCTCGAACTTTCAAA
* *
17447 AA-T-CCTATTTTTGGCCCT-GAA-TCTTCCAA
1 AATTACC-A-TTTT-ACCCTCGAACT-TTCAAA
* *
17476 AATTACCATTTTACCC-CTAAAC-TTCCAA
1 AATTACCATTTTACCCTC-GAACTTTCAAA
* * *
17504 GATTCCCATTTTTAGCCCT-GAACCTTCTAAA
1 AATTACCA-TTTTA-CCCTCGAACTTTC-AAA
* *
17535 AATTACCATTTTACCCTCGCACTTCCAAA
1 AATTACCATTTTACCCTCGAACTTTCAAA
*
17564 AA-T-CCTATTTTTAACCC-CGAATCTTCCAAA
1 AATTACC-A-TTTT-ACCCTCGAA-CTTTCAAA
* * *
17594 AATTACTATTTTACCCTCTAACTTCCAAA
1 AATTACCATTTTACCCTCGAACTTTCAAA
*
17623 AA-TCCCATTATTGA-CCTCGAA-TCTTCTAAA
1 AATTACCATT-TT-ACCCTCGAACT-TTC-AAA
* * *
17653 AATTACAATTTTACCCCCCGAACTTCCAAA
1 AATTACCATTTTA-CCCTCGAACTTTCAAA
*
17683 AA-T-CTCATTTTTGA-CCTCGAA-TCTTCTTAA
1 AATTAC-CA-TTTT-ACCCTCGAACT-TTC-AAA
17713 AATTACCATTTTACCCTCGAACTTTCAAA
1 AATTACCATTTTACCCTCGAACTTTCAAA
17742 A
1 A
17743 TTCTATTTTT
Statistics
Matches: 291, Mismatches: 46, Indels: 95
0.67 0.11 0.22
Matches are distributed among these distances:
27 5 0.02
28 30 0.10
29 107 0.37
30 113 0.39
31 32 0.11
32 4 0.01
ACGTcount: A:0.32, C:0.29, G:0.05, T:0.35
Consensus pattern (29 bp):
AATTACCATTTTACCCTCGAACTTTCAAA
Found at i:17399 original size:29 final size:29
Alignment explanation
Indices: 17367--17627 Score: 144
Period size: 29 Copynumber: 8.9 Consensus size: 29
17357 AAAATTACCA
17367 TTTTACCCCTAAACTTCCAAAAATCCTAT
1 TTTTACCCCTAAACTTCCAAAAATCCTAT
** * ** *
17396 TTTTGGTCCCGATCCTTCTAAAAAT--TAT
1 TTTT-ACCCCTAAACTTCCAAAAATCCTAT
**
17424 CATTTTACCCCCGAACTTCCAAAAATCCTAT
1 --TTTTACCCCTAAACTTCCAAAAATCCTAT
** * *
17455 TTTTGGCCCTGAATCTTCCAAAATTACC-A-
1 TTTTACCCCT-AAACTTCCAAAAAT-CCTAT
* * *
17484 TTTTACCCCTAAACTTCCAAGATTCCCAT
1 TTTTACCCCTAAACTTCCAAAAATCCTAT
* * *
17513 TTTTAGCCCTGAACCTTCTAAAAATTACC-A-
1 TTTTACCCCT-AAACTTCCAAAAA-T-CCTAT
**
17543 TTTTA-CCCTCGCACTTCCAAAAATCCTAT
1 TTTTACCCCT-AAACTTCCAAAAATCCTAT
* * *
17572 TTTTAACCCCGAATCTTCCAAAAATTACTA-
1 TTTT-ACCCCTAAACTTCCAAAAA-TCCTAT
17602 TTTTACCCTCT-AACTTCCAAAAATCC
1 TTTTACCC-CTAAACTTCCAAAAATCC
17628 CATTATTGAC
Statistics
Matches: 173, Mismatches: 41, Indels: 37
0.69 0.16 0.15
Matches are distributed among these distances:
27 4 0.02
28 20 0.12
29 73 0.42
30 60 0.35
31 14 0.08
32 2 0.01
ACGTcount: A:0.31, C:0.30, G:0.05, T:0.34
Consensus pattern (29 bp):
TTTTACCCCTAAACTTCCAAAAATCCTAT
Found at i:17419 original size:59 final size:58
Alignment explanation
Indices: 17346--17753 Score: 427
Period size: 59 Copynumber: 6.9 Consensus size: 58
17336 ATTTTACCCT
*
17346 CGAATCTT-TCAAAAATTACCATTTTACCCCTAAACTTCCAAAAATCCTATTTTTGGTCC
1 CGAATCTTCT-AAAAATTACCATTTTACCCCTGAACTTCCAAAAATCCTATTTTTGG-CC
* *
17405 CG-ATCCTTCTAAAAATTATCATTTTACCCCCGAACTTCCAAAAATCCTATTTTTGGCC
1 CGAAT-CTTCTAAAAATTACCATTTTACCCCTGAACTTCCAAAAATCCTATTTTTGGCC
* * * * * *
17463 CTGAATCTTC-CAAAATTACCATTTTACCCCTAAACTTCCAAGATTCCCATTTTTAGCC
1 C-GAATCTTCTAAAAATTACCATTTTACCCCTGAACTTCCAAAAATCCTATTTTTGGCC
* * **
17521 CTGAACCTTCTAAAAATTACCATTTTA-CCCTCGCACTTCCAAAAATCCTATTTTTAACCC
1 C-GAATCTTCTAAAAATTACCATTTTACCCCT-GAACTTCCAAAAATCCTATTTTT-GGCC
* * * * *
17581 CGAATCTTCCAAAAATTACTATTTTACCCTCT-AACTTCCAAAAATCCCATTATTGACC
1 CGAATCTTCTAAAAATTACCATTTTACCC-CTGAACTTCCAAAAATCCTATTTTTGGCC
* * *
17639 TCGAATCTTCTAAAAATTACAATTTTACCCCCCGAACTTCCAAAAAT-CTCATTTTTGACC
1 -CGAATCTTCTAAAAATTACCATTTTA-CCCCTGAACTTCCAAAAATCCT-ATTTTTGGCC
* * *
17699 TCGAATCTTCTTAAAATTACCATTTTA-CCCTCGAACTTTC-AAAATTCTATTTTTG
1 -CGAATCTTCTAAAAATTACCATTTTACCCCT-GAACTTCCAAAAATCCTATTTTTG
17754 ATTCCGAACA
Statistics
Matches: 298, Mismatches: 36, Indels: 31
0.82 0.10 0.08
Matches are distributed among these distances:
58 75 0.25
59 162 0.54
60 59 0.20
61 2 0.01
ACGTcount: A:0.31, C:0.28, G:0.05, T:0.35
Consensus pattern (58 bp):
CGAATCTTCTAAAAATTACCATTTTACCCCTGAACTTCCAAAAATCCTATTTTTGGCC
Found at i:17487 original size:89 final size:89
Alignment explanation
Indices: 17320--17625 Score: 227
Period size: 89 Copynumber: 3.5 Consensus size: 89
17310 GGTCCCTAAA
* * *
17320 CCTTCCAAGAATTACCATTTTACCCTCGAATCTTTCAAAAATTACCATTTTACCCCTAAACTTCC
1 CCTTCCAAAAATTACCATTTTACCCCCGAATCTTCCAAAAATTACCATTTTACCCCTAAACTTCC
17385 AAAAATCCTATTTTTGGTCCCGAT
66 AAAAATCCTATTTTTGGTCCCGAT
* * ** *
17409 CCTTCTAAAAATTATCATTTTACCCCCGAA-CTTCCAAAAA-T-CCTATTTTTGGCCCTGAATCT
1 CCTTCCAAAAATTACCATTTTACCCCCGAATCTTCCAAAAATTACC-A-TTTTACCCCT-AAACT
* ** * *
17471 TCCAAAATTACC-A-TTTT-ACCCCTAA
63 TCCAAAAAT-CCTATTTTTGGTCCCGAT
* * * * * * * **
17496 ACTTCC-AAGATTCCCATTTTTAGCCCTGAACCTTCTAAAAATTACCATTTTA-CCCTCGCACTT
1 CCTTCCAAAAATTACCA-TTTTACCCCCGAATCTTCCAAAAATTACCATTTTACCCCT-AAACTT
***
17559 CCAAAAATCCTATTTTTAACCCCGAAT
64 CCAAAAATCCTATTTTTGGTCCCG-AT
* * *
17586 -CTTCCAAAAATTACTATTTTACCCTCTAA-CTTCCAAAAAT
1 CCTTCCAAAAATTACCATTTTACCCCCGAATCTTCCAAAAAT
17626 CCCATTATTG
Statistics
Matches: 167, Mismatches: 37, Indels: 27
0.72 0.16 0.12
Matches are distributed among these distances:
86 11 0.07
87 36 0.22
88 48 0.29
89 60 0.36
90 12 0.07
ACGTcount: A:0.31, C:0.30, G:0.05, T:0.34
Consensus pattern (89 bp):
CCTTCCAAAAATTACCATTTTACCCCCGAATCTTCCAAAAATTACCATTTTACCCCTAAACTTCC
AAAAATCCTATTTTTGGTCCCGAT
Found at i:17530 original size:117 final size:115
Alignment explanation
Indices: 17337--17728 Score: 479
Period size: 117 Copynumber: 3.3 Consensus size: 115
17327 AGAATTACCA
* * *
17337 TTTTACCCTCGAATCTTTCAAAAATTACCATTTTACCCCTAAACTTCCAAAAATCCTATTTTTGG
1 TTTTGCCCTCGAATC-TTCCAAAATTACCATTTTACCCCTAAACTTCCAAAAATCCCATTTTT-G
*
17402 TCCC-GATCCTTCTAAAAATTATCATTTTACCCCCGAACTTCCAAAAATCCTAT
64 -CCCTGAACCTTCTAAAAATTA-CATTTTACCCCCGAACTTCCAAAAATCCTAT
* *
17455 TTTTGGCCCT-GAATCTTCCAAAATTACCATTTTACCCCTAAACTTCCAAGATTCCCATTTTTAG
1 TTTT-GCCCTCGAATCTTCCAAAATTACCATTTTACCCCTAAACTTCCAAAAATCCCATTTTT-G
* *
17519 CCCTGAACCTTCTAAAAATTACCATTTTACCCTCGCACTTCCAAAAATCCTAT
64 CCCTGAACCTTCTAAAAATTA-CATTTTACCCCCGAACTTCCAAAAATCCTAT
* * *
17572 TTTTAACCC-CGAATCTTCCAAAAATTACTATTTTACCCTCT-AACTTCCAAAAATCCCATTATT
1 TTTT-GCCCTCGAATCTTCC-AAAATTACCATTTTACCC-CTAAACTTCCAAAAATCCCATTTTT
* *
17635 GACCTCGAATCTTCTAAAAATTACAATTTTACCCCCCGAACTTCCAAAAAT-CTCAT
63 GCCCT-GAACCTTCTAAAAATTAC-ATTTTA-CCCCCGAACTTCCAAAAATCCT-AT
* *
17691 TTTTGACCTCGAATCTTCTTAAAATTACCATTTTACCC
1 TTTTGCCCTCGAATCTTC-CAAAATTACCATTTTACCC
17729 TCGAACTTTC
Statistics
Matches: 239, Mismatches: 24, Indels: 21
0.84 0.08 0.07
Matches are distributed among these distances:
116 3 0.01
117 110 0.46
118 71 0.30
119 55 0.23
ACGTcount: A:0.31, C:0.29, G:0.05, T:0.35
Consensus pattern (115 bp):
TTTTGCCCTCGAATCTTCCAAAATTACCATTTTACCCCTAAACTTCCAAAAATCCCATTTTTGCC
CTGAACCTTCTAAAAATTACATTTTACCCCCGAACTTCCAAAAATCCTAT
Found at i:21916 original size:24 final size:24
Alignment explanation
Indices: 21879--21934 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
21869 TAGACTAACA
* * *
21879 AGAGTTTGACTGAAAGAAATAAAT
1 AGAGTTTAACTGAAACAAATAAAC
*
21903 AGAGTTTAATTGAAACAAATAAAC
1 AGAGTTTAACTGAAACAAATAAAC
21927 AGAGTTTA
1 AGAGTTTA
21935 TCTGGAAGAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.50, C:0.05, G:0.18, T:0.27
Consensus pattern (24 bp):
AGAGTTTAACTGAAACAAATAAAC
Found at i:23891 original size:24 final size:24
Alignment explanation
Indices: 23864--23914 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
23854 AGTTTGACTT
*
23864 AAACAAATAAATAGAGTTTAATTG
1 AAACAAATAAACAGAGTTTAATTG
*
23888 AAACAAATAAACAGAGTTTATTTG
1 AAACAAATAAACAGAGTTTAATTG
23912 AAA
1 AAA
23915 TATTATTTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.55, C:0.06, G:0.12, T:0.27
Consensus pattern (24 bp):
AAACAAATAAACAGAGTTTAATTG
Found at i:27559 original size:21 final size:19
Alignment explanation
Indices: 27518--27586 Score: 66
Period size: 20 Copynumber: 3.5 Consensus size: 19
27508 ACATTTTTCA
* **
27518 AAAACTTTTATAACATTTT
1 AAAATTTTTATAATTTTTT
27537 AAAATTTTCTATATATTTTTT
1 AAAATTTT-TATA-ATTTTTT
* *
27558 AATATTTTTATAATTATTT
1 AAAATTTTTATAATTTTTT
27577 ATAAATTTTT
1 A-AAATTTTT
27587 TTATTTATTT
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
19 14 0.34
20 15 0.37
21 12 0.29
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (19 bp):
AAAATTTTTATAATTTTTT
Found at i:27575 original size:22 final size:20
Alignment explanation
Indices: 27533--27586 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 20
27523 TTTTATAACA
*
27533 TTTTAAAATTTTCTATATATT
1 TTTTAATATTTT-TATATATT
27554 TTTTAATATTTTTATA-ATT
1 TTTTAATATTTTTATATATT
27573 ATTTATAA-ATTTTT
1 -TTT-TAATATTTTT
27587 TTATTTATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
19 3 0.10
20 13 0.43
21 14 0.47
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (20 bp):
TTTTAATATTTTTATATATT
Found at i:27586 original size:20 final size:20
Alignment explanation
Indices: 27534--27605 Score: 69
Period size: 20 Copynumber: 3.6 Consensus size: 20
27524 TTTATAACAT
27534 TTTA-AAATTTTCTATATATT-
1 TTTATAAATTTT-TATA-ATTA
27554 TTT-TAATATTTTTATAATTA
1 TTTATAA-ATTTTTATAATTA
* *
27574 TTTATAAATTTTTTTATTTA
1 TTTATAAATTTTTATAATTA
*
27594 TTTATGAATTTT
1 TTTATAAATTTT
27606 AAAATCTATG
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
19 3 0.07
20 34 0.76
21 8 0.18
ACGTcount: A:0.32, C:0.01, G:0.01, T:0.65
Consensus pattern (20 bp):
TTTATAAATTTTTATAATTA
Found at i:27598 original size:30 final size:31
Alignment explanation
Indices: 27546--27603 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 31
27536 TAAAATTTTC
*
27546 TATATATTTTTTAATATTTTTAT-AATTATT
1 TATAAATTTTTTAATATTTTTATGAATTATT
*
27576 TATAAATTTTTTTAT-TTATTTATGAATT
1 TATAAATTTTTTAATATT-TTTATGAATT
27604 TTAAAATCTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 2 0.08
30 18 0.75
31 4 0.17
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.66
Consensus pattern (31 bp):
TATAAATTTTTTAATATTTTTATGAATTATT
Found at i:27931 original size:7 final size:7
Alignment explanation
Indices: 27919--27944 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
27909 TAAATTTGCG
27919 CTCATAA
1 CTCATAA
27926 CTCATAA
1 CTCATAA
27933 CTCATAA
1 CTCATAA
27940 CTCAT
1 CTCAT
27945 TCGTTTATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.38, C:0.31, G:0.00, T:0.31
Consensus pattern (7 bp):
CTCATAA
Found at i:29947 original size:28 final size:27
Alignment explanation
Indices: 29856--29949 Score: 91
Period size: 28 Copynumber: 3.4 Consensus size: 27
29846 GTGTCCATTG
*
29856 TTTTAGATTTTGCAATTT-CCCCTATT
1 TTTTAGATTTTACAATTTCCCCCTATT
* * *
29882 TTTTAGATTTTATAGTTTCGCCCCTACT
1 TTTTAGATTTTACAATTTC-CCCCTATT
* * *
29910 ATTCATATTTTACAATTTTCCCCCTATT
1 TTTTAGATTTTACAA-TTTCCCCCTATT
*
29938 TTTTTGATTTTA
1 TTTTAGATTTTA
29950 TAGTTTTGTC
Statistics
Matches: 51, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
26 15 0.29
28 32 0.63
29 4 0.08
ACGTcount: A:0.20, C:0.19, G:0.06, T:0.54
Consensus pattern (27 bp):
TTTTAGATTTTACAATTTCCCCCTATT
Found at i:29962 original size:28 final size:28
Alignment explanation
Indices: 29874--29962 Score: 81
Period size: 28 Copynumber: 3.2 Consensus size: 28
29864 TTTGCAATTT
* *
29874 CCCCTATTTTTTAGATTTTATAGTTTCG
1 CCCCTATTTTTTTGATTTTATAGTTTTG
* ** * * *
29902 CCCCTACTATTCAT-ATTTTACAATTTTC
1 CCCCTA-TTTTTTTGATTTTATAGTTTTG
29930 CCCCTATTTTTTTGATTTTATAGTTTTG
1 CCCCTATTTTTTTGATTTTATAGTTTTG
*
29958 TCCCT
1 CCCCT
29963 TCTTTGAATT
Statistics
Matches: 44, Mismatches: 15, Indels: 4
0.70 0.24 0.06
Matches are distributed among these distances:
27 4 0.09
28 37 0.84
29 3 0.07
ACGTcount: A:0.18, C:0.22, G:0.07, T:0.53
Consensus pattern (28 bp):
CCCCTATTTTTTTGATTTTATAGTTTTG
Found at i:33046 original size:28 final size:26
Alignment explanation
Indices: 32953--33048 Score: 84
Period size: 28 Copynumber: 3.5 Consensus size: 26
32943 GTGTCCACTG
32953 TTTTTAGATTTTACAATTTTCCCCTAT
1 TTTTTAGATTTTACAA-TTTCCCCTAT
** * *
32980 TTTAAAGATTTTATAGTTTCGCCCCTAT
1 TTTTTAGATTTTACAATTT--CCCCTAT
* * *
33008 TGTTCATATTTTACAATCTTCCCTCTAT
1 TTTTTAGATTTTACAAT-TTCCC-CTAT
33036 TTTTTAGATTTTA
1 TTTTTAGATTTTA
33049 TATTTTTGTT
Statistics
Matches: 52, Mismatches: 13, Indels: 7
0.72 0.18 0.10
Matches are distributed among these distances:
26 3 0.06
27 15 0.29
28 32 0.62
29 2 0.04
ACGTcount: A:0.23, C:0.18, G:0.06, T:0.53
Consensus pattern (26 bp):
TTTTTAGATTTTACAATTTCCCCTAT
Found at i:33075 original size:56 final size:55
Alignment explanation
Indices: 32960--33076 Score: 128
Period size: 56 Copynumber: 2.1 Consensus size: 55
32950 CTGTTTTTAG
* * *
32960 ATTTTACAATTTTCCCCTATTTTAAAGATTTTATAGTTTCGCCCCTATTGTTCAT
1 ATTTTACAATCTTCCCCTATTTTAAAGATTTTATAGTTTCGCCCCTATTGTACAA
** * * * *
33015 ATTTTACAATCTTCCCTCTATTTTTTAGATTTTATATTTTTGTTCCCTCTT-TACAA
1 ATTTTACAATCTTCCC-CTATTTTAAAGATTTTATAGTTTCG-CCCCTATTGTACAA
33071 ATTTTA
1 ATTTTA
33077 AAATTTTACC
Statistics
Matches: 51, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
55 15 0.29
56 30 0.59
57 6 0.12
ACGTcount: A:0.23, C:0.19, G:0.05, T:0.53
Consensus pattern (55 bp):
ATTTTACAATCTTCCCCTATTTTAAAGATTTTATAGTTTCGCCCCTATTGTACAA
Found at i:37319 original size:36 final size:36
Alignment explanation
Indices: 37243--37321 Score: 95
Period size: 36 Copynumber: 2.2 Consensus size: 36
37233 TGTGAAAGTG
* * * *
37243 AATATGTGGGTATGTTATTCATGCCATATGACTGAA
1 AATATATGGGTATGTTATTAATGCCATATAACAGAA
* **
37279 AATATATGGGTATGTTATTAATGCCATGTAACAGTT
1 AATATATGGGTATGTTATTAATGCCATATAACAGAA
37315 AATATAT
1 AATATAT
37322 TGTGCTAATG
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.34, C:0.09, G:0.19, T:0.38
Consensus pattern (36 bp):
AATATATGGGTATGTTATTAATGCCATATAACAGAA
Found at i:37686 original size:11 final size:10
Alignment explanation
Indices: 37645--37801 Score: 67
Period size: 10 Copynumber: 15.0 Consensus size: 10
37635 CCAAATTATC
37645 ATTAAATGTG
1 ATTAAATGTG
*
37655 -TAAAATGTG
1 ATTAAATGTG
*
37664 ACTAAATGTG
1 ATTAAATGTG
37674 ATTAATATGTG
1 ATTAA-ATGTG
*
37685 ATGTGATAA-AT-
1 AT-T-A-AATGTG
*
37696 ATTAAA-AT-
1 ATTAAATGTG
*
37704 ATT-CATGTG
1 ATTAAATGTG
37713 ATTAAATGTG
1 ATTAAATGTG
*
37723 ACTAAATGTG
1 ATTAAATGTG
37733 ATTAATATGTG
1 ATTAA-ATGTG
37744 ATGTGATAAATGTTG
1 A--T--TAAATG-TG
*
37759 AAATATTAATGTG
1 --AT-TAAATGTG
*
37772 ACT-AATGTG
1 ATTAAATGTG
37781 ATTAAATGTG
1 ATTAAATGTG
37791 ATTAATATGTG
1 ATTAA-ATGTG
37802 TTATGTTAAA
Statistics
Matches: 116, Mismatches: 13, Indels: 35
0.71 0.08 0.21
Matches are distributed among these distances:
7 1 0.01
8 8 0.07
9 20 0.17
10 42 0.36
11 21 0.18
12 2 0.02
13 5 0.04
14 10 0.09
15 6 0.05
17 1 0.01
ACGTcount: A:0.39, C:0.03, G:0.19, T:0.39
Consensus pattern (10 bp):
ATTAAATGTG
Found at i:37729 original size:59 final size:59
Alignment explanation
Indices: 37657--37801 Score: 238
Period size: 59 Copynumber: 2.5 Consensus size: 59
37647 TAAATGTGTA
* *
37657 AAATGTGACTAAATGTGATTAATATGTGATGTGATAAATATTAAAATATTCATGTGATT
1 AAATGTGACTAAATGTGATTAATATGTGATGTGATAAATATTAAAATATTAATGTGACT
* *
37716 AAATGTGACTAAATGTGATTAATATGTGATGTGATAAATGTTGAAATATTAATGTGACT
1 AAATGTGACTAAATGTGATTAATATGTGATGTGATAAATATTAAAATATTAATGTGACT
*
37775 -AATGTGATTAAATGTGATTAATATGTG
1 AAATGTGACTAAATGTGATTAATATGTG
37802 TTATGTTAAA
Statistics
Matches: 81, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
58 26 0.32
59 55 0.68
ACGTcount: A:0.39, C:0.03, G:0.19, T:0.39
Consensus pattern (59 bp):
AAATGTGACTAAATGTGATTAATATGTGATGTGATAAATATTAAAATATTAATGTGACT
Found at i:37779 original size:9 final size:9
Alignment explanation
Indices: 37763--37796 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
37753 ATGTTGAAAT
37763 ATTAATGTG
1 ATTAATGTG
*
37772 ACTAATGTG
1 ATTAATGTG
37781 ATTAAATGTG
1 ATT-AATGTG
37791 ATTAAT
1 ATTAAT
37797 ATGTGTTATG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
9 13 0.59
10 9 0.41
ACGTcount: A:0.38, C:0.03, G:0.18, T:0.41
Consensus pattern (9 bp):
ATTAATGTG
Found at i:37779 original size:23 final size:26
Alignment explanation
Indices: 37717--37776 Score: 74
Period size: 26 Copynumber: 2.4 Consensus size: 26
37707 CATGTGATTA
37717 AATGTGACTAAATG-TGATTAATATGT
1 AATGTGACTAAATGTTGA-TAATATGT
*
37743 GATGTGA-TAAATGTTGA-AATAT-T
1 AATGTGACTAAATGTTGATAATATGT
37766 AATGTGACTAA
1 AATGTGACTAA
37777 TGTGATTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
23 7 0.23
24 8 0.27
25 6 0.20
26 9 0.30
ACGTcount: A:0.40, C:0.03, G:0.20, T:0.37
Consensus pattern (26 bp):
AATGTGACTAAATGTTGATAATATGT
Found at i:37829 original size:58 final size:58
Alignment explanation
Indices: 37650--37838 Score: 238
Period size: 58 Copynumber: 3.2 Consensus size: 58
37640 TTATCATTAA
*
37650 ATGTGTAA-AATGTGACTAAATGTGATTAATATGTGATGTGATAAATATTAAAATATTC
1 ATGTG-AATAATGTGACTAAATGTGATTAATATGTGATGTGATAAATGTTAAAATATTC
* * *
37708 ATGTGATTAAATGTGACTAAATGTGATTAATATGTGATGTGATAAATGTTGAAATATTA
1 ATGTGAAT-AATGTGACTAAATGTGATTAATATGTGATGTGATAAATGTTAAAATATTC
* * * * * * *
37767 ATGTGACTAATGTGATTAAATGTGATTAATATGTGTTATGTTAAATGGTT-AAGTACTC
1 ATGTGAATAATGTGACTAAATGTGATTAATATGTGATGTGATAAAT-GTTAAAATATTC
37825 ATGTGAATAATGTG
1 ATGTGAATAATGTG
37839 CTTACTGTGT
Statistics
Matches: 115, Mismatches: 13, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
57 1 0.01
58 57 0.50
59 57 0.50
ACGTcount: A:0.38, C:0.03, G:0.20, T:0.39
Consensus pattern (58 bp):
ATGTGAATAATGTGACTAAATGTGATTAATATGTGATGTGATAAATGTTAAAATATTC
Found at i:40139 original size:10 final size:10
Alignment explanation
Indices: 40118--40171 Score: 51
Period size: 10 Copynumber: 5.5 Consensus size: 10
40108 TTTTATAACA
*
40118 TTTTAAAATT
1 TTTTAATATT
*
40128 TTCT-ATATT
1 TTTTAATATT
40137 TTTTAATATT
1 TTTTAATATT
40147 TTTATAAT-TAT
1 TTT-TAATAT-T
40158 TTTTAAT-TT
1 TTTTAATATT
40167 TTTTA
1 TTTTA
40172 TGAATTTTAT
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
9 13 0.34
10 17 0.45
11 8 0.21
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.69
Consensus pattern (10 bp):
TTTTAATATT
Found at i:40162 original size:21 final size:22
Alignment explanation
Indices: 40136--40177 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
40126 TTTTCTATAT
40136 TTTTTAATATTTTTAT-AATTA
1 TTTTTAATATTTTTATGAATTA
*
40157 TTTTTAATTTTTTTATGAATT
1 TTTTTAATATTTTTATGAATT
40178 TTATAATCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (22 bp):
TTTTTAATATTTTTATGAATTA
Done.