Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013174.1 Kokia drynarioides strain JFW-HI SEQ_128193, 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: 308382
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Warning! 268 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:243002 original size:19 final size:20
Alignment explanation
Indices: 242947--243004 Score: 59
Period size: 19 Copynumber: 2.9 Consensus size: 20
242937 TCAAAGTGTT
242947 TTTAATATA-TATTAATATA
1 TTTAATATATTATTAATATA
242966 TTTAATATTTATTTATTAA-ATA
1 TTTAATA--TA-TTATTAATATA
242988 -TTAATATACTTATTAAT
1 TTTAATATA-TTATTAAT
243005 TGTTATTTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
19 16 0.48
21 8 0.24
22 3 0.09
23 6 0.18
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (20 bp):
TTTAATATATTATTAATATA
Found at i:244016 original size:30 final size:30
Alignment explanation
Indices: 243982--244055 Score: 96
Period size: 30 Copynumber: 2.5 Consensus size: 30
243972 CTATTTTGTC
* *
243982 TAAAAATTACATTTTGACTATTAAACTTT-T
1 TAAAAATTACATTTTGACCATTAAA-TTTCA
* *
244012 TAAAAATCACATTTTGACCCTTAAATTTCA
1 TAAAAATTACATTTTGACCATTAAATTTCA
244042 TAAAAATTACATTT
1 TAAAAATTACATTT
244056 CAACCCCATA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
29 3 0.08
30 35 0.92
ACGTcount: A:0.42, C:0.14, G:0.03, T:0.42
Consensus pattern (30 bp):
TAAAAATTACATTTTGACCATTAAATTTCA
Found at i:244083 original size:29 final size:30
Alignment explanation
Indices: 244044--244208 Score: 138
Period size: 31 Copynumber: 5.4 Consensus size: 30
244034 AAATTTCATA
* * * *
244044 AAAATTACATTTCAACCCC-ATACTTCTCT
1 AAAATTACATTTTAACCCCAAAAATTCTCC
* *
244073 AAAATTACATTTTGA-CCC-TAAATTCTTCC
1 AAAATTACATTTTAACCCCAAAAATTC-TCC
*
244102 AAAATTACATTTTAACCCTCAAAAATTTTCC
1 AAAATTACATTTTAACCC-CAAAAATTCTCC
* * *
244133 AAAATTACATTTTAACCCCTAAAACTTTTCT
1 AAAATTACATTTTAACCCC-AAAAATTCTCC
* * * *
244164 AAAATTACATTTTTGACCCCTAAATTTTTCC
1 AAAATTACA-TTTTAACCCCAAAAATTCTCC
244195 AAAATTATCATTTT
1 AAAATTA-CATTTT
244209 GCCCCTCAAA
Statistics
Matches: 114, Mismatches: 15, Indels: 12
0.81 0.11 0.09
Matches are distributed among these distances:
28 7 0.06
29 29 0.25
30 3 0.03
31 59 0.52
32 16 0.14
ACGTcount: A:0.37, C:0.23, G:0.01, T:0.39
Consensus pattern (30 bp):
AAAATTACATTTTAACCCCAAAAATTCTCC
Found at i:244136 original size:31 final size:29
Alignment explanation
Indices: 244044--244308 Score: 202
Period size: 29 Copynumber: 8.9 Consensus size: 29
244034 AAATTTCATA
* * * *
244044 AAAATTACATTTCAACCC-CATACTTCTCT
1 AAAATTACATTTTAACCCTCA-AATTTTCC
*
244073 AAAATTACATTTTGACCCT-AAATTCTTCC
1 AAAATTACATTTTAACCCTCAAATT-TTCC
244102 AAAATTACATTTTAACCCTCAAAAATTTTCC
1 AAAATTACATTTTAACCCTC--AAATTTTCC
* *
244133 AAAATTACATTTTAACCCCTAAAACTTTTCT
1 AAAATTACATTTTAA-CCCTCAAA-TTTTCC
*
244164 AAAATTACATTTTTGACCC-CTAAATTTTTCC
1 AAAATTACA-TTTTAACCCTC-AAA-TTTTCC
**
244195 AAAATTATCATTTTGCCCCTCAAA-TTTCC
1 AAAATTA-CATTTTAACCCTCAAATTTTCC
* * *
244224 AAAAGTCATATTTTCGA-CCTCAAATTTTCC
1 AAAA-TTACATTTT-AACCCTCAAATTTTCC
*
244254 AAAAGTT-CAATTTTAATCC-CAAATTTTCC
1 AAAA-TTAC-ATTTTAACCCTCAAATTTTCC
* *
244283 AAAATTTCAATTTTAACCCTTAAATT
1 AAAATTAC-ATTTTAACCCTCAAATT
244309 CCTCAAAAAT
Statistics
Matches: 197, Mismatches: 21, Indels: 35
0.78 0.08 0.14
Matches are distributed among these distances:
28 5 0.03
29 84 0.43
30 29 0.15
31 62 0.31
32 17 0.09
ACGTcount: A:0.36, C:0.23, G:0.02, T:0.38
Consensus pattern (29 bp):
AAAATTACATTTTAACCCTCAAATTTTCC
Found at i:244176 original size:62 final size:60
Alignment explanation
Indices: 244073--244301 Score: 181
Period size: 62 Copynumber: 3.8 Consensus size: 60
244063 ATACTTCTCT
*
244073 AAAATTACATTTTGACCCTAAATTCTTCCAAAATTACA-TTTTAACCCTCAAAAATTTTCC
1 AAAATTACATTTTAACCCTAAATTCTTCCAAAATTACATTTTTAACCC-CAAAAATTTTCC
* * * *
244133 AAAATTACATTTTAACCCCTAAAACTT-TTCTAAAATTACATTTTTGACCCCTAAATTTTTCC
1 AAAATTACATTTTAA-CCCT-AAA-TTCTTCCAAAATTACATTTTTAACCCCAAAAATTTTCC
** * * *
244195 AAAATTATCATTTTGCCCCTCAAA-T-TTCCAAAAGT-CATATTTTCGACCTC--AAATTTTCC
1 AAAATTA-CATTTTAACCCT-AAATTCTTCCAAAATTACAT-TTTT-AACCCCAAAAATTTTCC
* *
244254 AAAAGTT-CAATTTTAATCCC-AAATT-TTCCAAAATTTCAATTTTAACCC
1 AAAA-TTAC-ATTTTAA-CCCTAAATTCTTCCAAAATTACATTTTTAACCC
244302 TTAAATTCCT
Statistics
Matches: 139, Mismatches: 18, Indels: 26
0.76 0.10 0.14
Matches are distributed among these distances:
58 7 0.05
59 34 0.24
60 34 0.24
61 9 0.06
62 39 0.28
63 16 0.12
ACGTcount: A:0.36, C:0.23, G:0.03, T:0.38
Consensus pattern (60 bp):
AAAATTACATTTTAACCCTAAATTCTTCCAAAATTACATTTTTAACCCCAAAAATTTTCC
Found at i:244291 original size:29 final size:31
Alignment explanation
Indices: 244092--244302 Score: 149
Period size: 31 Copynumber: 6.9 Consensus size: 31
244082 TTTTGACCCT
*
244092 AAATTCTTCCAAAATTAC-ATTTTAACCCTCAA
1 AAATT-TTCCAAAATTTCAATTTTAACCCTC-A
*
244124 AAATTTTCCAAAATTAC-ATTTTAACCC-CTA
1 AAATTTTCCAAAATTTCAATTTTAACCCTC-A
* * * *
244154 AAACTTTTCTAAAATTACATTTTTGACCC-CTA
1 AAA-TTTTCCAAAATTTCAATTTTAACCCTC-A
* **
244186 AATTTTTCCAAAATTATC-ATTTTGCCCCTC-
1 AAATTTTCCAAAATT-TCAATTTTAACCCTCA
* *
244216 AAA-TTTCCAAAA-GTCATATTTTCGA-CCTC-
1 AAATTTTCCAAAATTTCA-ATTTT-AACCCTCA
* *
244245 AAATTTTCCAAAAGTTCAATTTTAATCC-C-
1 AAATTTTCCAAAATTTCAATTTTAACCCTCA
244274 AAATTTTCCAAAATTTCAATTTTAACCCT
1 AAATTTTCCAAAATTTCAATTTTAACCCT
244303 TAAATTCCTC
Statistics
Matches: 152, Mismatches: 16, Indels: 24
0.79 0.08 0.12
Matches are distributed among these distances:
27 2 0.01
29 49 0.32
30 24 0.16
31 57 0.38
32 20 0.13
ACGTcount: A:0.36, C:0.23, G:0.02, T:0.38
Consensus pattern (31 bp):
AAATTTTCCAAAATTTCAATTTTAACCCTCA
Found at i:244316 original size:30 final size:29
Alignment explanation
Indices: 244215--244341 Score: 88
Period size: 29 Copynumber: 4.3 Consensus size: 29
244205 TTTTGCCCCT
*
244215 CAAATT-TCCAAAAG-TCATATTTTCGA-CC
1 CAAATTCTCCAAAAGTTCA-ATTTT-AATCC
*
244243 TCAAATTTTCCAAAAGTTCAATTTTAATCC
1 -CAAATTCTCCAAAAGTTCAATTTTAATCC
* *
244273 CAAATTTTCCAAAATTTCAATTTTAA-CC
1 CAAATTCTCCAAAAGTTCAATTTTAATCC
*
244301 CTTAAATTC-CTCAAAAATT--ATGTTTACATCC
1 C--AAATTCTC-CAAAAGTTCAAT-TTTA-ATCC
244332 CAAATTCTCC
1 CAAATTCTCC
244342 GAAGCTCCAT
Statistics
Matches: 84, Mismatches: 4, Indels: 20
0.78 0.04 0.19
Matches are distributed among these distances:
28 5 0.06
29 44 0.52
30 29 0.35
31 6 0.07
ACGTcount: A:0.36, C:0.24, G:0.03, T:0.37
Consensus pattern (29 bp):
CAAATTCTCCAAAAGTTCAATTTTAATCC
Found at i:251640 original size:31 final size:31
Alignment explanation
Indices: 251605--251673 Score: 111
Period size: 31 Copynumber: 2.2 Consensus size: 31
251595 TTTCTTGCAT
*
251605 ATGCATTCATAAAATTTCGCATCGCATTTTC
1 ATGCATTCATAAAATTTCGCATCACATTTTC
* *
251636 ATGCATTCATAAAGTTTTGCATCACATTTTC
1 ATGCATTCATAAAATTTCGCATCACATTTTC
251667 ATGCATT
1 ATGCATT
251674 AAAAGTTTGA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.29, C:0.20, G:0.10, T:0.41
Consensus pattern (31 bp):
ATGCATTCATAAAATTTCGCATCACATTTTC
Found at i:256696 original size:40 final size:40
Alignment explanation
Indices: 256586--257189 Score: 307
Period size: 40 Copynumber: 15.2 Consensus size: 40
256576 ACCATAGGGT
* * *
256586 AAATTGAAG-CAATCCAATCTTTTACCCTAATCAGAAAGC
1 AAATTGAAGACTATCTAATCTTTTACCCTAATCAGAGAGC
* * * *
256625 AGATTGAAG-CAATATGATCTTTTACCCTAATCAGAGAGC
1 AAATTGAAGACTATCTAATCTTTTACCCTAATCAGAGAGC
* * *
256664 AAATTAAAGACTATCTAATCTTTTACCCTAATCAAAGGGC
1 AAATTGAAGACTATCTAATCTTTTACCCTAATCAGAGAGC
* * * *
256704 AGATTGAAGATTATCAAATCTTTTACTCTAATCAGAGAGC
1 AAATTGAAGACTATCTAATCTTTTACCCTAATCAGAGAGC
*
256744 AAATTGAAGACTATCAAATCTTTTACCCTAATCAGATG-GC
1 AAATTGAAGACTATCTAATCTTTTACCCTAATCAGA-GAGC
* * * * * *
256784 ATATT-AATGACCATCCAATCTCTTA-CCTCGATCATG-GGGC
1 AAATTGAA-GACTATCTAATCTTTTACCCT-AATCA-GAGAGC
* * * **
256824 AAATTAAAGA-TCATCCAATCTCTTACCCCGATCATGAG-GC
1 AAATTGAAGACT-ATCTAATCTTTTACCCTAATCA-GAGAGC
* * * ** * *
256864 AAATTGAAGACCATCCAATTTTTTACCCCGATCATAGGGC
1 AAATTGAAGACTATCTAATCTTTTACCCTAATCAGAGAGC
* * * *
256904 AGATTGAAG-CAATCTAATCTTTTACCCTAA-CTAGAGGGA
1 AAATTGAAGACTATCTAATCTTTTACCCTAATC-AGAGAGC
* ** *
256943 AAATTGAAGA-TCATCTGATCTTTTACCCCGACCATGAGA-C
1 AAATTGAAGACT-ATCTAATCTTTTACCCTAATCA-GAGAGC
* * * * *
256983 AGATTGAAG-CAATCCAATCTTTTACCCTAA-CTAAAGGGC
1 AAATTGAAGACTATCTAATCTTTTACCCTAATC-AGAGAGC
* * * * *
257022 AGATTGAAGACCAT-TCAATCTCTTATCCC-GACCATGAGA-C
1 AAATTGAAGACTATCT-AATCTTTTA-CCCTAATCA-GAGAGC
* * *
257062 AAATT-AAAACAATCTAATCTTTTACCCTAACCAGAG-GAC
1 AAATTGAAGACTATCTAATCTTTTACCCTAATCAGAGAG-C
* ** * ** * *
257101 AAATTGAAGACCATCCGATCTCTTACCCCGACCATG-GGGC
1 AAATTGAAGACTATCTAATCTTTTACCCTAATCA-GAGAGC
* * * * *
257141 AAATTGAAG-CAATCCAA-CTTTTTACCCTAACCAAAGGGC
1 AAATTGAAGACTATCTAATC-TTTTACCCTAATCAGAGAGC
257180 AAATTGAAGA
1 AAATTGAAGA
257190 TCATTTGATC
Statistics
Matches: 448, Mismatches: 82, Indels: 69
0.75 0.14 0.12
Matches are distributed among these distances:
38 11 0.02
39 158 0.35
40 260 0.58
41 19 0.04
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.27
Consensus pattern (40 bp):
AAATTGAAGACTATCTAATCTTTTACCCTAATCAGAGAGC
Found at i:256804 original size:120 final size:118
Alignment explanation
Indices: 256601--257012 Score: 345
Period size: 120 Copynumber: 3.5 Consensus size: 118
256591 GAAGCAATCC
* * * *
256601 AATCTTTTACCCTAATCA-GAAAGCAGATTGAAGCAAT-ATGATCTTTTACCCTAATCAGAGAGC
1 AATCTTTTACCCCAATCATGAGAGCAAATTGAAGCAATCA-AATCTTTTACCCTAATCAGAG-GC
* * *
256664 AAATTAAAGACTATCTAATCTTTTACCCTAATCAAAGGGCAGATTGAAGATTATCA
64 AAATT-AAGACAATCTAATCTTTTACCCTAATCAAAGGGCAAATTGAAGATCATCA
* * *
256720 AATCTTTTACTCTAATCA-GAGAGCAAATTGAAGACTATCAAATCTTTTACCCTAATCAGATGGC
1 AATCTTTTACCCCAATCATGAGAGCAAATTGAAG-CAATCAAATCTTTTACCCTAATCAGA-GGC
* * * * * ** * *
256784 ATATTAATGACCATCCAATCTCTTA-CCTCGATCATGGGGCAAATTAAAGATCATCC
64 AAATTAA-GACAATCTAATCTTTTACCCT-AATCAAAGGGCAAATTGAAGATCATCA
* * * * * ** *
256840 AATCTCTTACCCCGATCATGAG-GCAAATTGAAGACCATCCAATTTTTTACCCCGATCATAGGGC
1 AATCTTTTACCCCAATCATGAGAGCAAATTGAAG-CAATCAAATCTTTTACCCTAATCAGA-GGC
* * * *
256904 AGATTGAAG-CAATCTAATCTTTTACCCTAA-CTAGAGGGAAAATTGAAGATCATCT
64 AAATT-AAGACAATCTAATCTTTTACCCTAATC-AAAGGGCAAATTGAAGATCATCA
* * * * *
256959 GATCTTTTACCCCGACCATGAGA-CAGATTGAAGCAATCCAATCTTTTACCCTAA
1 AATCTTTTACCCCAATCATGAGAGCAAATTGAAGCAATCAAATCTTTTACCCTAA
257013 CTAAAGGGCA
Statistics
Matches: 238, Mismatches: 45, Indels: 21
0.78 0.15 0.07
Matches are distributed among these distances:
118 18 0.08
119 94 0.39
120 119 0.50
121 7 0.03
ACGTcount: A:0.35, C:0.22, G:0.14, T:0.29
Consensus pattern (118 bp):
AATCTTTTACCCCAATCATGAGAGCAAATTGAAGCAATCAAATCTTTTACCCTAATCAGAGGCAA
ATTAAGACAATCTAATCTTTTACCCTAATCAAAGGGCAAATTGAAGATCATCA
Found at i:256967 original size:79 final size:79
Alignment explanation
Indices: 256555--257420 Score: 552
Period size: 79 Copynumber: 10.8 Consensus size: 79
256545 TGAAGTAACA
* * * *
256555 ACCATCAGATCTCTTACCCTGACCATAGGGTAAATTGAAGCAATCCAATCTTTTACCCTAA-TCA
1 ACCATCTGATCTCTTACCCCGATCATAGGGCAAATTGAAGCAATCCAATCTTTTACCCTAACT-A
**
256619 GAAAGCAGATTGAAG
65 GAGGGCAGATTGAAG
* * * ** * * * * *
256634 -CAATATGATCTTTTACCCTAATCAGAGAGCAAATTAAAGACTATCTAATCTTTTACCCTAA-TC
1 ACCATCTGATCTCTTACCCCGATCATAGGGCAAATTGAAG-CAATCCAATCTTTTACCCTAACT-
*
256697 AAAGGGCAGATTGAAG
64 AGAGGGCAGATTGAAG
** ** * * ** * * * *
256713 ATTATCAAATCTTTTACTCTAATCAGAGAGCAAATTGAAGACTATCAAATCTTTTACCCTAA-TC
1 ACCATCTGATCTCTTACCCCGATCATAGGGCAAATTGAAG-CAATCCAATCTTTTACCCTAACT-
* *
256777 AGATGGCATATT-AATG
64 AGAGGGCAGATTGAA-G
** * * * * **
256793 ACCATCCAATCTCTTACCTCGATCATGGGGCAAATTAAAG-ATCATCCAATCTCTTACCCCGA-T
1 ACCATCTGATCTCTTACCCCGATCATAGGGCAAATTGAAGCA--ATCCAATCTTTTACCCTAACT
*
256856 CATGA-GGCAAATTGAAG
64 -A-GAGGGCAGATTGAAG
** * * * *
256873 ACCATCCAATTTTTTACCCCGATCATAGGGCAGATTGAAGCAATCTAATCTTTTACCCTAACTAG
1 ACCATCTGATCTCTTACCCCGATCATAGGGCAAATTGAAGCAATCCAATCTTTTACCCTAACTAG
* *
256938 AGGGAAAATTGAAG
66 AGGGCAGATTGAAG
* * * * *
256952 ATCATCTGATCTTTTACCCCGACCAT-GAGACAGATTGAAGCAATCCAATCTTTTACCCTAACTA
1 ACCATCTGATCTCTTACCCCGATCATAG-GGCAAATTGAAGCAATCCAATCTTTTACCCTAACTA
*
257016 AAGGGCAGATTGAAG
65 GAGGGCAGATTGAAG
* * * * * * * *
257031 ACCAT-TCAATCTCTTATCCCGACCAT-GAGACAAATTAAAACAATCTAATCTTTTACCCTAACC
1 ACCATCT-GATCTCTTACCCCGATCATAG-GGCAAATTGAAGCAATCCAATCTTTTACCCTAACT
* *
257094 AGAGGACAAATTGAAG
64 AGAGGGCAGATTGAAG
* * * *
257110 ACCATCCGATCTCTTACCCCGACCATGGGGCAAATTGAAGCAATCCAA-CTTTTTACCCTAACCA
1 ACCATCTGATCTCTTACCCCGATCATAGGGCAAATTGAAGCAATCCAATC-TTTTACCCTAACTA
* *
257174 AAGGGCAAATTGAAG
65 GAGGGCAGATTGAAG
* * * *
257189 ATCATTTGATCTCTTACCCCGACCATGAGGCAGATTGGAAGCAGATTGAAGCAATCCAATCTTTT
1 ACCATCTGATCTCTTACCCCG---AT----C--ATAGG--GCAAATTGAAGCAATCCAATC-TTT
* *
257254 TACCCTAACTAAAAGGCAGATTGAAG
54 TACCCTAACTAGAGGGCAGATTGAAG
* * * * * * *
257280 ACCATTTGATCTCTTACCCCGACCATGGGGTATATTGAAGTAATCCAATCTTTTACCCTAACCAG
1 ACCATCTGATCTCTTACCCCGATCATAGGGCAAATTGAAGCAATCCAATCTTTTACCCTAACTAG
* *
257345 GGGGCAGATTAAAG
66 AGGGCAGATTGAAG
* * * * * ** *
257359 ACCATCCT-ATCTTTTGCACCAATCATGGGGCAGGTTGAAACAATCCAATCTTTTACCTCTAA
1 ACCAT-CTGATCTCTTACCCCGATCATAGGGCAAATTGAAGCAATCCAATCTTTTACC-CTAA
257421 AACTATAAAG
Statistics
Matches: 641, Mismatches: 117, Indels: 57
0.79 0.14 0.07
Matches are distributed among these distances:
78 34 0.05
79 346 0.54
80 178 0.28
81 5 0.01
82 5 0.01
84 1 0.00
86 1 0.00
88 5 0.01
90 18 0.03
91 48 0.07
ACGTcount: A:0.34, C:0.24, G:0.15, T:0.27
Consensus pattern (79 bp):
ACCATCTGATCTCTTACCCCGATCATAGGGCAAATTGAAGCAATCCAATCTTTTACCCTAACTAG
AGGGCAGATTGAAG
Found at i:257031 original size:158 final size:158
Alignment explanation
Indices: 256555--257420 Score: 631
Period size: 158 Copynumber: 5.4 Consensus size: 158
256545 TGAAGTAACA
* * * *
256555 ACCAT-CAGATCTCTTACCCTGACCATAGGGTAAATTGAAGCAATCCAATCTTTTACCCTAA-TC
1 ACCATCCA-ATCTTTTACCCCGATCATAGGGCAAATTGAAGCAATCCAATCTTTTACCCTAACT-
* * * * * ** * * * * *
256618 AGAAAGCAGATTGAAG-CAATATGATCTTTTACCCTAATCA-GAGAGCAAATTAAAGACTATCTA
64 AGAAGGCAAATTGAAGACCATCTGATCTCTTACCCCGACCATG-GGGCAAATTGAAG-CAATCCA
256681 ATCTTTTACCCTAA-TCAAAGGGCAGATTGAAG
127 ATCTTTTACCCTAACT-AAAGGGCAGATTGAAG
** * * ** * * * *
256713 ATTATCAAATCTTTTACTCTAATCAGAGAGCAAATTGAAGACTATCAAATCTTTTACCCTAA-TC
1 ACCATCCAATCTTTTACCCCGATCATAGGGCAAATTGAAG-CAATCCAATCTTTTACCCTAACT-
* * ** * * *
256777 AGATGGCATATT-AATGACCATCCAATCTCTTACCTCGATCATGGGGCAAATTAAAG-ATCATCC
64 AGAAGGCAAATTGAA-GACCATCTGATCTCTTACCCCGACCATGGGGCAAATTGAAGCA--ATCC
* ** * * *
256840 AATCTCTTACCCCGA-TCATGAGGCAAATTGAAG
126 AATCTTTTACCCTAACTAAAG-GGCAGATTGAAG
* * *
256873 ACCATCCAATTTTTTACCCCGATCATAGGGCAGATTGAAGCAATCTAATCTTTTACCCTAACTAG
1 ACCATCCAATCTTTTACCCCGATCATAGGGCAAATTGAAGCAATCCAATCTTTTACCCTAACTAG
* * * * * * *
256938 AGGGAAAATTGAAGATCATCTGATCTTTTACCCCGACCATGAGACAGATTGAAGCAATCCAATCT
66 AAGGCAAATTGAAGACCATCTGATCTCTTACCCCGACCATGGGGCAAATTGAAGCAATCCAATCT
257003 TTTACCCTAACTAAAGGGCAGATTGAAG
131 TTTACCCTAACTAAAGGGCAGATTGAAG
* * * * * * * * *
257031 ACCATTCAATCTCTTATCCCGACCAT-GAGACAAATTAAAACAATCTAATCTTTTACCCTAACCA
1 ACCATCCAATCTTTTACCCCGATCATAG-GGCAAATTGAAGCAATCCAATCTTTTACCCTAACTA
*
257095 G-AGGACAAATTGAAGACCATCCGATCTCTTACCCCGACCATGGGGCAAATTGAAGCAATCCAA-
65 GAAGG-CAAATTGAAGACCATCTGATCTCTTACCCCGACCATGGGGCAAATTGAAGCAATCCAAT
* *
257158 CTTTTTACCCTAACCAAAGGGCAAATTGAAG
129 C-TTTTACCCTAACTAAAGGGCAGATTGAAG
* *** * * *
257189 ATCATTTGATCTCTTACCCCGACCATGAGGCAGATTGGAAGCAGATTGAAGCAATCCAATCTTTT
1 ACCATCCAATCTTTTACCCCG---AT----C--ATAGG--GCAAATTGAAGCAATCCAATC-TTT
* * * * *
257254 TACCCTAACTAAAAGGCAGATTGAAGACCATTTGATCTCTTACCCCGACCATGGGGTATATTGAA
54 TACCCTAACTAGAAGGCAAATTGAAGACCATCTGATCTCTTACCCCGACCATGGGGCAAATTGAA
* * ** *
257319 GTAATCCAATCTTTTACCCTAACCAGGGGGCAGATTAAAG
119 GCAATCCAATCTTTTACCCTAACTAAAGGGCAGATTGAAG
* * * * * ** *
257359 ACCATCCTATCTTTTGCACCAATCATGGGGCAGGTTGAAACAATCCAATCTTTTACCTCTAA
1 ACCATCCAATCTTTTACCCCGATCATAGGGCAAATTGAAGCAATCCAATCTTTTACC-CTAA
257421 AACTATAAAG
Statistics
Matches: 561, Mismatches: 116, Indels: 61
0.76 0.16 0.08
Matches are distributed among these distances:
157 4 0.01
158 212 0.38
159 119 0.21
160 89 0.16
161 6 0.01
163 1 0.00
165 1 0.00
167 5 0.01
168 1 0.00
169 16 0.03
170 103 0.18
171 4 0.01
ACGTcount: A:0.34, C:0.24, G:0.15, T:0.27
Consensus pattern (158 bp):
ACCATCCAATCTTTTACCCCGATCATAGGGCAAATTGAAGCAATCCAATCTTTTACCCTAACTAG
AAGGCAAATTGAAGACCATCTGATCTCTTACCCCGACCATGGGGCAAATTGAAGCAATCCAATCT
TTTACCCTAACTAAAGGGCAGATTGAAG
Found at i:258076 original size:63 final size:65
Alignment explanation
Indices: 257930--258108 Score: 247
Period size: 67 Copynumber: 2.7 Consensus size: 65
257920 TTTCTTATTA
*
257930 TTTTTATTTATTTATTTATTATTTTTATGAATATAAATAAAGAAATAAAAAATAATATTAATTCT
1 TTTTTATTTATTTATTTATTA-TTTTATGAATATAAATAAATAAATAAAAAATAATATTAATTCT
257995 G
65 G
* **
257996 TTTTATTATTTATTTATTTATTATTATATGAATATAAATAAATAAATGTAAAATAATATTAATGT
1 -TTT-TTATTTATTTATTTATTATTTTATGAATATAAATAAATAAATAAAAAATAATATTAAT-T
258061 -TG
63 CTG
* *
258063 -TTTTA-TTATTTATTTGTTATTTTATGAATATAGATAAATAAATAAA
1 TTTTTATTTATTTATTTATTATTTTATGAATATAAATAAATAAATAAA
258109 TAACAAACCC
Statistics
Matches: 101, Mismatches: 9, Indels: 8
0.86 0.08 0.07
Matches are distributed among these distances:
63 36 0.36
64 3 0.03
65 2 0.02
67 41 0.41
68 19 0.19
ACGTcount: A:0.43, C:0.01, G:0.06, T:0.51
Consensus pattern (65 bp):
TTTTTATTTATTTATTTATTATTTTATGAATATAAATAAATAAATAAAAAATAATATTAATTCTG
Found at i:262968 original size:138 final size:139
Alignment explanation
Indices: 262584--262994 Score: 621
Period size: 139 Copynumber: 3.0 Consensus size: 139
262574 TATGAAATAG
262584 CAGCAGGTCGACCATACCATCATCCTATTAGAGTTATGTAGAATGCAATGCTTTTAAGTATTAAC
1 CAGCAGGTCGACCATACCATCATCCTATTAGAGTTATGTAGAATGCAATGCTTTTAAGTATTAAC
*
262649 CACACTACGATTGCAAGTTTCTGTAAACTAGTCAAGTTTTAGTTTTGATTTATT-TTTTTTGTAG
66 CACACTACGATTGCAAGTTTCTGTAAACTAGTCAAGTTTTAGTTTTGATTT-TTGCTTTTTGTAG
262713 TTCATAGCAA
130 TTCATAGCAA
262723 CAGCAGGTCGACCATACCATCATCCTATTAGAGTTATGTAGAATGCAATGCTTTTAAGTATTAAC
1 CAGCAGGTCGACCATACCATCATCCTATTAGAGTTATGTAGAATGCAATGCTTTTAAGTATTAAC
* * *
262788 CACACTGCGATTGCAAGTTTCCGTAAACTAGTAAAGTTTTAGTTTTGATTTTTGCTTTTTGTAGT
66 CACACTACGATTGCAAGTTTCTGTAAACTAGTCAAGTTTTAGTTTTGATTTTTGCTTTTTGTAGT
262853 TCATAGCAA
131 TCATAGCAA
* * * * * * *
262862 CAGCAGGTC-AGCCATACCATCAGCGTA-TAGGGTTGTGTAGAATGCAATGCTTATAACTATTAC
1 CAGCAGGTCGA-CCATACCATCATCCTATTAGAGTTATGTAGAATGCAATGCTTTTAAGTATTAA
** * ** *
262925 CCACACTACGATTGCAAGTTTCTGTAAACTAGTCGTGTCTTAGTTCCGATTTATGCTTTTTGTAG
65 CCACACTACGATTGCAAGTTTCTGTAAACTAGTCAAGTTTTAGTTTTGATTTTTGCTTTTTGTAG
*
262990 GTCAT
130 TTCAT
262995 TCGATGAAGA
Statistics
Matches: 249, Mismatches: 21, Indels: 5
0.91 0.08 0.02
Matches are distributed among these distances:
138 94 0.38
139 155 0.62
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (139 bp):
CAGCAGGTCGACCATACCATCATCCTATTAGAGTTATGTAGAATGCAATGCTTTTAAGTATTAAC
CACACTACGATTGCAAGTTTCTGTAAACTAGTCAAGTTTTAGTTTTGATTTTTGCTTTTTGTAGT
TCATAGCAA
Found at i:268311 original size:14 final size:14
Alignment explanation
Indices: 268292--268330 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
268282 TTGTTTGACT
*
268292 GAAAATGGTTTCTG
1 GAAAATGGTTTCAG
*
268306 GAAAATGATTTCAG
1 GAAAATGGTTTCAG
268320 GAAAATGGTTT
1 GAAAATGGTTT
268331 ACTTTTCTGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.36, C:0.05, G:0.26, T:0.33
Consensus pattern (14 bp):
GAAAATGGTTTCAG
Found at i:272173 original size:31 final size:31
Alignment explanation
Indices: 272110--272174 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
272100 TCTTTAGTTA
* ** *
272110 AATTTGATTCTTAAATTTTTAAAACTAGTCG
1 AATTTGATTCTTAAACTTTTAAAAAAAATCG
272141 AATTTGA-TCATTAAACTTTTAAAAAAAATCG
1 AATTTGATTC-TTAAACTTTTAAAAAAAATCG
272172 AAT
1 AAT
272175 AATTGTTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 2 0.07
31 27 0.93
ACGTcount: A:0.43, C:0.09, G:0.08, T:0.40
Consensus pattern (31 bp):
AATTTGATTCTTAAACTTTTAAAAAAAATCG
Found at i:272906 original size:5 final size:5
Alignment explanation
Indices: 272886--272921 Score: 54
Period size: 5 Copynumber: 7.2 Consensus size: 5
272876 ATAAAAGTTA
* *
272886 AATAT AAAAA AATAT AATAT AATAT AATAT AATAT A
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT A
272922 GAGGGTAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (5 bp):
AATAT
Found at i:279308 original size:23 final size:23
Alignment explanation
Indices: 279275--279334 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
279265 CAAAAGGCAG
*
279275 AAGCGTTCCACAAGACAGAAAAA
1 AAGCGTGCCACAAGACAGAAAAA
**
279298 AAGCGTGCCACAAGACAGAGGAA
1 AAGCGTGCCACAAGACAGAAAAA
*
279321 AAGCATGCCACAAG
1 AAGCGTGCCACAAG
279335 TAGAGGAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.47, C:0.23, G:0.23, T:0.07
Consensus pattern (23 bp):
AAGCGTGCCACAAGACAGAAAAA
Found at i:279342 original size:22 final size:23
Alignment explanation
Indices: 279282--279355 Score: 105
Period size: 23 Copynumber: 3.3 Consensus size: 23
279272 CAGAAGCGTT
** *
279282 CCACAAGACAGAAAAAAAGCGTG
1 CCACAAGACAGAGGAAAAGCATG
279305 CCACAAGACAGAGGAAAAGCATG
1 CCACAAGACAGAGGAAAAGCATG
*
279328 CCACAAG-TAGAGGAAAAGCATG
1 CCACAAGACAGAGGAAAAGCATG
279350 CCACAA
1 CCACAA
279356 AAACATATAA
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
22 20 0.43
23 27 0.57
ACGTcount: A:0.49, C:0.23, G:0.23, T:0.05
Consensus pattern (23 bp):
CCACAAGACAGAGGAAAAGCATG
Found at i:279784 original size:3 final size:3
Alignment explanation
Indices: 279776--279800 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
279766 TTTTAGTTTC
279776 GTT GTT GTT GTT GTT GTT GTT GTT G
1 GTT GTT GTT GTT GTT GTT GTT GTT G
279801 CAATAAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.36, T:0.64
Consensus pattern (3 bp):
GTT
Found at i:282040 original size:15 final size:14
Alignment explanation
Indices: 282022--282052 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
282012 CATTTTGGGG
282022 TTTTTGAATTTTCTT
1 TTTTTGAATTTT-TT
282037 TTTTTGAATTTTTT
1 TTTTTGAATTTTTT
282051 TT
1 TT
282053 ATAAGTTTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.25
15 12 0.75
ACGTcount: A:0.13, C:0.03, G:0.06, T:0.77
Consensus pattern (14 bp):
TTTTTGAATTTTTT
Found at i:288022 original size:63 final size:62
Alignment explanation
Indices: 287943--288098 Score: 197
Period size: 62 Copynumber: 2.5 Consensus size: 62
287933 AATTTGAGGA
287943 TTTAGGTTTTAAAAATTTAGGGATTTTCGAGATTTTTAACGTTGTTGGGTTTGGGAAATTTGG
1 TTTAGG-TTTAAAAATTTAGGGATTTTCGAGATTTTTAACGTTGTTGGGTTTGGGAAATTTGG
* * * ** * *
288006 TTTAGGTTTAAGAAATTTCGGGA-TTTGGGGATTTTTAGGGTTTTTGGGTTTGGGAATTTTGG
1 TTTAGGTTTAA-AAATTTAGGGATTTTCGAGATTTTTAACGTTGTTGGGTTTGGGAAATTTGG
* * *
288068 TTTAAGTTTAAAATTTTGGGGATTTTCGAGA
1 TTTAGGTTTAAAAATTTAGGGATTTTCGAGA
288099 CTTAGGTTCC
Statistics
Matches: 79, Mismatches: 12, Indels: 5
0.82 0.12 0.05
Matches are distributed among these distances:
61 9 0.11
62 54 0.68
63 16 0.20
ACGTcount: A:0.22, C:0.03, G:0.29, T:0.46
Consensus pattern (62 bp):
TTTAGGTTTAAAAATTTAGGGATTTTCGAGATTTTTAACGTTGTTGGGTTTGGGAAATTTGG
Found at i:290408 original size:25 final size:25
Alignment explanation
Indices: 290374--290422 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
290364 TTGTAACCAA
* *
290374 ATTTTTAAT-GTTATGTTAGTGCCT
1 ATTTTTAATGGTCATATTAGTGCCT
290398 ATTTTTGAATGGTCATATTAGTGCC
1 ATTTTT-AATGGTCATATTAGTGCC
290423 GATATATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 6 0.29
25 3 0.14
26 12 0.57
ACGTcount: A:0.22, C:0.10, G:0.18, T:0.49
Consensus pattern (25 bp):
ATTTTTAATGGTCATATTAGTGCCT
Found at i:291492 original size:28 final size:28
Alignment explanation
Indices: 291460--291513 Score: 108
Period size: 28 Copynumber: 1.9 Consensus size: 28
291450 TGATAAGATG
291460 TCAAAAGAATATTCATGTAAATTCTATA
1 TCAAAAGAATATTCATGTAAATTCTATA
291488 TCAAAAGAATATTCATGTAAATTCTA
1 TCAAAAGAATATTCATGTAAATTCTA
291514 CCTTTTTTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.35
Consensus pattern (28 bp):
TCAAAAGAATATTCATGTAAATTCTATA
Found at i:293277 original size:64 final size:64
Alignment explanation
Indices: 293204--293330 Score: 236
Period size: 64 Copynumber: 2.0 Consensus size: 64
293194 TTCCTGGGCA
293204 AAGTTTCGACAACTTATTAAAGGAGGAACTGGGTTGAAAGGAAAATTGAAAAATCAAAACAGAT
1 AAGTTTCGACAACTTATTAAAGGAGGAACTGGGTTGAAAGGAAAATTGAAAAATCAAAACAGAT
**
293268 AAGTTTCGACAACTTATTTGAGGAGGAACTGGGTTGAAAGGAAAATTGAAAAATCAAAACAGA
1 AAGTTTCGACAACTTATTAAAGGAGGAACTGGGTTGAAAGGAAAATTGAAAAATCAAAACAGA
293331 AATCCAAATT
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
64 61 1.00
ACGTcount: A:0.46, C:0.09, G:0.23, T:0.22
Consensus pattern (64 bp):
AAGTTTCGACAACTTATTAAAGGAGGAACTGGGTTGAAAGGAAAATTGAAAAATCAAAACAGAT
Found at i:295823 original size:3 final size:3
Alignment explanation
Indices: 295815--295840 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
295805 ACTTGCTGAT
295815 GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GA
295841 TAGTTTCCAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:298250 original size:68 final size:69
Alignment explanation
Indices: 298167--298333 Score: 166
Period size: 67 Copynumber: 2.4 Consensus size: 69
298157 TTTAAGAAAA
*
298167 AAAATTCATTTAAAAAATATTAAAAATTATAAA-AATGTGTGAAATTTTATAAAAAAAAACGTAA
1 AAAATTCA--TAAAAAATATTAAAAATTATAAACAATGTAT-AAATTTT-TAAAAAAAAACGTAA
298231 AAAAA-AT
62 AAAAATAT
* * * * * *
298238 -ATATAT-ATAAAAAAT-TTAGAAATATAGAAACAATTTATAAATTTTTATAAAAAAATGTAAAA
1 AAAAT-TCATAAAAAATATTAAAAAT-TATAAACAATGTATAAATTTTTAAAAAAAAACGTAAAA
298300 AAATAT
64 AAATAT
298306 AAAATTCATAAAAAA-ATATAAAAATTAT
1 AAAATTCATAAAAAATAT-TAAAAATTAT
298334 CATACCAAAA
Statistics
Matches: 78, Mismatches: 10, Indels: 18
0.74 0.09 0.17
Matches are distributed among these distances:
67 25 0.32
68 23 0.29
69 19 0.24
70 10 0.13
71 1 0.01
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.31
Consensus pattern (69 bp):
AAAATTCATAAAAAATATTAAAAATTATAAACAATGTATAAATTTTTAAAAAAAAACGTAAAAAA
ATAT
Found at i:298262 original size:19 final size:19
Alignment explanation
Indices: 298240--298279 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
298230 AAAAAAATAT
*
298240 ATATATAAAAAATTTAGAA
1 ATATAGAAAAAATTTAGAA
* *
298259 ATATAGAAACAATTTATAA
1 ATATAGAAAAAATTTAGAA
298278 AT
1 AT
298280 TTTTATAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.60, C:0.03, G:0.05, T:0.33
Consensus pattern (19 bp):
ATATAGAAAAAATTTAGAA
Found at i:298298 original size:10 final size:10
Alignment explanation
Indices: 298283--298329 Score: 53
Period size: 10 Copynumber: 4.8 Consensus size: 10
298273 TATAAATTTT
298283 TATAAAAAAA
1 TATAAAAAAA
*
298293 TGTAAAAAAA
1 TATAAAAAAA
*
298303 TAT--AAAAT
1 TATAAAAAAA
298311 TCATAAAAAAA
1 T-ATAAAAAAA
298322 TATAAAAA
1 TATAAAAA
298330 TTATCATACC
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
8 5 0.17
9 2 0.07
10 18 0.60
11 5 0.17
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.23
Consensus pattern (10 bp):
TATAAAAAAA
Found at i:298527 original size:9 final size:9
Alignment explanation
Indices: 298513--298645 Score: 50
Period size: 9 Copynumber: 13.7 Consensus size: 9
298503 TTTTGATGTA
298513 TTTTATAAT
1 TTTTATAAT
*
298522 TTTTATGAT
1 TTTTATAAT
298531 TTTTATAAGT
1 TTTTATAA-T
*
298541 TTTTTTACACTT
1 TTTTATA-A--T
*
298553 TTTTACAAT
1 TTTTATAAT
**
298562 TTTTAATTTT
1 TTTT-ATAAT
*
298572 TTTTCTAAT
1 TTTTATAAT
*
298581 TTTTAATAAA
1 TTTT-ATAAT
* *
298591 ATTTAAATAT
1 TTTTATA-AT
*
298601 TTTTATTAAAA
1 TTTTA-T-AAT
* * *
298612 TTTAACAAA
1 TTTTATAAT
298621 TTTTATAACT
1 TTTTATAA-T
*
298631 TTTAATAAT
1 TTTTATAAT
298640 TTTTAT
1 TTTTAT
298646 TTTATATATT
Statistics
Matches: 88, Mismatches: 27, Indels: 18
0.66 0.20 0.14
Matches are distributed among these distances:
9 43 0.49
10 31 0.35
11 7 0.08
12 7 0.08
ACGTcount: A:0.34, C:0.05, G:0.02, T:0.60
Consensus pattern (9 bp):
TTTTATAAT
Found at i:298566 original size:19 final size:19
Alignment explanation
Indices: 298542--298586 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
298532 TTTATAAGTT
298542 TTTTTACACTTTTTTAC-AA
1 TTTTTA-ACTTTTTTACTAA
* *
298561 TTTTTAATTTTTTTTCTAA
1 TTTTTAACTTTTTTACTAA
298580 TTTTTAA
1 TTTTTAA
298587 TAAAATTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 8 0.35
19 15 0.65
ACGTcount: A:0.24, C:0.09, G:0.00, T:0.67
Consensus pattern (19 bp):
TTTTTAACTTTTTTACTAA
Found at i:298602 original size:20 final size:20
Alignment explanation
Indices: 298579--298616 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
298569 TTTTTTTCTA
298579 ATTTTTAATAAAATTTAAAT
1 ATTTTTAATAAAATTTAAAT
*
298599 ATTTTTATTAAAATTTAA
1 ATTTTTAATAAAATTTAA
298617 CAAATTTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
ATTTTTAATAAAATTTAAAT
Found at i:298624 original size:20 final size:20
Alignment explanation
Indices: 298581--298626 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
298571 TTTTTCTAAT
* *
298581 TTTTAATAAAATTTAAATAT
1 TTTTATTAAAATTTAAATAA
298601 TTTTATTAAAATTTAACA-AA
1 TTTTATTAAAATTTAA-ATAA
298621 TTTTAT
1 TTTTAT
298627 AACTTTTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 22 0.96
21 1 0.04
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (20 bp):
TTTTATTAAAATTTAAATAA
Found at i:299438 original size:85 final size:85
Alignment explanation
Indices: 299294--299457 Score: 219
Period size: 85 Copynumber: 1.9 Consensus size: 85
299284 TCAAAGGGCC
* * *
299294 TTTTTGATGTATTTTAACAGTTCAAGTATCCAATTGAGTGTAAAAAAATAAGAGTTTAATT-TTT
1 TTTTTGATGCATTTTAACAGTTCAAGTATCCAATTGAGTGTAAAAAAATAAGAGCTTAATTATTA
299358 TTTAGAAAAAGTTTAAGAGCT
66 TTTA-AAAAAGTTTAAGAGCT
*
299379 TTTTTGATGCATTTTGAA-AGTTTAAGTATCCAATTGAGTG-AAAAAAAGT-AGAGACTTAATTA
1 TTTTTGATGCATTTT-AACAGTTCAAGTATCCAATTGAGTGTAAAAAAA-TAAGAG-CTTAATTA
299441 CTTATTTAAAAAAGTTT
63 -TTATTTAAAAAAGTTT
299458 GAGGGATTTT
Statistics
Matches: 70, Mismatches: 4, Indels: 9
0.84 0.05 0.11
Matches are distributed among these distances:
84 11 0.16
85 42 0.60
86 11 0.16
87 6 0.09
ACGTcount: A:0.38, C:0.06, G:0.15, T:0.40
Consensus pattern (85 bp):
TTTTTGATGCATTTTAACAGTTCAAGTATCCAATTGAGTGTAAAAAAATAAGAGCTTAATTATTA
TTTAAAAAAGTTTAAGAGCT
Found at i:308029 original size:25 final size:23
Alignment explanation
Indices: 307955--308035 Score: 99
Period size: 23 Copynumber: 3.4 Consensus size: 23
307945 TGCTGGGCAA
** *
307955 CAGAGAGCACACAAAGTATTAGT
1 CAGAGAGCACACAAAGTGCTAAT
307978 CAGAGAGCACACAAAGTGCTAAT
1 CAGAGAGCACACAAAGTGCTAAT
* *
308001 CAGAAAGCACACACAGTGCTAAT
1 CAGAGAGCACACAAAGTGCTAAT
308024 AACAGAGAGCAC
1 --CAGAGAGCAC
308036 GAGACGTGCT
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
23 41 0.82
25 9 0.18
ACGTcount: A:0.44, C:0.22, G:0.21, T:0.12
Consensus pattern (23 bp):
CAGAGAGCACACAAAGTGCTAAT
Found at i:308054 original size:23 final size:23
Alignment explanation
Indices: 307953--308056 Score: 93
Period size: 23 Copynumber: 4.4 Consensus size: 23
307943 AGTGCTGGGC
* **
307953 AACAGAGAGCACACAAAGTATTA
1 AACAGAGAGCACACACAGTGCTA
** *
307976 GTCAGAGAGCACACAAAGTGCTA
1 AACAGAGAGCACACACAGTGCTA
* *
307999 ATCAGAAAGCACACACAGTGCTAA
1 AACAGAGAGCACACACAGTGCT-A
*
308023 TAACAGAGAGCACGAGAC-GTGCTA
1 -AACAGAGAGCAC-ACACAGTGCTA
308047 AACAGAGAGC
1 AACAGAGAGC
308057 GCGCTAGTGT
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
23 48 0.71
24 2 0.03
25 15 0.22
26 3 0.04
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.12
Consensus pattern (23 bp):
AACAGAGAGCACACACAGTGCTA
Done.