Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004945.1 Kokia drynarioides strain JFW-HI SEQ_118656, 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: 73814
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Warning! 112 characters in sequence are not A, C, G, or T
Found at i:12233 original size:3 final size:3
Alignment explanation
Indices: 12225--12253 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
12215 TTATGAAATA
12225 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
12254 AGAAGTAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:23950 original size:31 final size:31
Alignment explanation
Indices: 23915--24013 Score: 112
Period size: 31 Copynumber: 3.2 Consensus size: 31
23905 TTTTTATTTC
23915 ATGTTGTTTTAAGCTTTTTCTTTTTTAATGA
1 ATGTTGTTTTAAGCTTTTTCTTTTTTAATGA
* * * **
23946 ATG-T-TTTTAACACATTTTACATTTTTTATTTC
1 ATGTTGTTTTAA-GC-TTTTTC-TTTTTTAATGA
23978 ATGTTGTTTTAAGCTTTTTCTTTTTTAATGA
1 ATGTTGTTTTAAGCTTTTTCTTTTTTAATGA
24009 ATGTT
1 ATGTT
24014 TTTAACACAT
Statistics
Matches: 53, Mismatches: 10, Indels: 10
0.73 0.14 0.14
Matches are distributed among these distances:
29 6 0.11
30 2 0.04
31 21 0.40
32 16 0.30
33 2 0.04
34 6 0.11
ACGTcount: A:0.21, C:0.08, G:0.10, T:0.61
Consensus pattern (31 bp):
ATGTTGTTTTAAGCTTTTTCTTTTTTAATGA
Found at i:23967 original size:63 final size:64
Alignment explanation
Indices: 23894--24025 Score: 257
Period size: 63 Copynumber: 2.1 Consensus size: 64
23884 TTCTTTCACT
23894 CATTATTACATTTTTTATTTCATGTTGTTTTAAGCTTTTTCTTTTTTAATGAATGTTTTTAACA
1 CATTATTACATTTTTTATTTCATGTTGTTTTAAGCTTTTTCTTTTTTAATGAATGTTTTTAACA
23958 CATT-TTACATTTTTTATTTCATGTTGTTTTAAGCTTTTTCTTTTTTAATGAATGTTTTTAACA
1 CATTATTACATTTTTTATTTCATGTTGTTTTAAGCTTTTTCTTTTTTAATGAATGTTTTTAACA
24021 CATTA
1 CATTA
24026 GCTTCTTTAG
Statistics
Matches: 67, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
63 63 0.94
64 4 0.06
ACGTcount: A:0.23, C:0.10, G:0.08, T:0.59
Consensus pattern (64 bp):
CATTATTACATTTTTTATTTCATGTTGTTTTAAGCTTTTTCTTTTTTAATGAATGTTTTTAACA
Found at i:23971 original size:32 final size:31
Alignment explanation
Indices: 23929--24024 Score: 97
Period size: 31 Copynumber: 3.1 Consensus size: 31
23919 TGTTTTAAGC
*
23929 TTTTTCTTTTTTAATGAATGTTTTTAACACA
1 TTTTACTTTTTTAATGAATGTTTTTAACACA
* ** *
23960 TTTTACATTTTTTATTTCATGTTGTTTTAA-GC-
1 TTTTAC-TTTTTTAATGAATG-T-TTTTAACACA
*
23992 TTTTTCTTTTTTAATGAATGTTTTTAACACA
1 TTTTACTTTTTTAATGAATGTTTTTAACACA
24023 TT
1 TT
24025 AGCTTCTTTA
Statistics
Matches: 50, Mismatches: 10, Indels: 10
0.71 0.14 0.14
Matches are distributed among these distances:
29 6 0.12
30 2 0.04
31 18 0.36
32 16 0.32
33 2 0.04
34 6 0.12
ACGTcount: A:0.23, C:0.09, G:0.07, T:0.60
Consensus pattern (31 bp):
TTTTACTTTTTTAATGAATGTTTTTAACACA
Found at i:26102 original size:32 final size:31
Alignment explanation
Indices: 26060--26154 Score: 85
Period size: 32 Copynumber: 3.1 Consensus size: 31
26050 ATATTAGGAT
*
26060 TTAGGGCAAGTATCATTAATTTAAAATTAACA
1 TTAGGACAAGTAT-ATTAATTTAAAATTAACA
26092 TTAGGACAAGTATA--AA---AAAA-TAATCA
1 TTAGGACAAGTATATTAATTTAAAATTAA-CA
**
26118 TTAATTACAAGTATTATTAATTTAAAATTAACA
1 TT-AGGACAAGTA-TATTAATTTAAAATTAACA
26151 TTAG
1 TTAG
26155 CATTTAGGGC
Statistics
Matches: 50, Mismatches: 4, Indels: 18
0.69 0.06 0.25
Matches are distributed among these distances:
25 3 0.06
26 8 0.16
27 8 0.16
28 2 0.04
29 2 0.04
30 2 0.04
31 1 0.02
32 13 0.26
33 8 0.16
34 3 0.06
ACGTcount: A:0.48, C:0.07, G:0.09, T:0.35
Consensus pattern (31 bp):
TTAGGACAAGTATATTAATTTAAAATTAACA
Found at i:29188 original size:18 final size:19
Alignment explanation
Indices: 29165--29227 Score: 53
Period size: 18 Copynumber: 3.5 Consensus size: 19
29155 TAAACCCATT
*
29165 TTTAAAATTCA-TTTTGAG
1 TTTAAAATTCAGTTTTAAG
*
29183 TTT-AAATTTAGTTTTAAG
1 TTTAAAATTCAGTTTTAAG
* *
29201 TTTAAACTTTC-CTTTTAAG
1 TTTAAA-ATTCAGTTTTAAG
29220 -TTAAAATT
1 TTTAAAATT
29228 TAAATTAAGT
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
17 8 0.22
18 17 0.47
19 9 0.25
20 2 0.06
ACGTcount: A:0.33, C:0.06, G:0.08, T:0.52
Consensus pattern (19 bp):
TTTAAAATTCAGTTTTAAG
Found at i:29218 original size:19 final size:18
Alignment explanation
Indices: 29176--29264 Score: 74
Period size: 18 Copynumber: 4.9 Consensus size: 18
29166 TTAAAATTCA
* *
29176 TTTTGAGTTTAAATTTAG
1 TTTTAAGTTTAAATTTAC
*
29194 TTTTAAGTTTAAACTTTCC
1 TTTTAAGTTTAAA-TTTAC
*
29213 TTTTAAGTTAAAATTTA-
1 TTTTAAGTTTAAATTTAC
** *
29230 AATTAAGTTTAAATTTAA
1 TTTTAAGTTTAAATTTAC
*
29248 TTTGAA-TTTAAAATTTA
1 TTTTAAGTTT-AAATTTA
29265 AAAGTCTAGT
Statistics
Matches: 57, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
17 17 0.30
18 25 0.44
19 15 0.26
ACGTcount: A:0.37, C:0.03, G:0.08, T:0.52
Consensus pattern (18 bp):
TTTTAAGTTTAAATTTAC
Found at i:29237 original size:17 final size:17
Alignment explanation
Indices: 29215--29266 Score: 68
Period size: 17 Copynumber: 3.0 Consensus size: 17
29205 AACTTTCCTT
29215 TTAAGTTAAAATTTAAA
1 TTAAGTTAAAATTTAAA
* *
29232 TTAAGTTTAAATTTAAT
1 TTAAGTTAAAATTTAAA
*
29249 TTGAATTTAAAATTTAAA
1 TT-AAGTTAAAATTTAAA
29267 AGTCTAGTCA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
17 17 0.59
18 12 0.41
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.46
Consensus pattern (17 bp):
TTAAGTTAAAATTTAAA
Found at i:40746 original size:115 final size:115
Alignment explanation
Indices: 40539--40746 Score: 290
Period size: 115 Copynumber: 1.8 Consensus size: 115
40529 GACTCAAAGC
*
40539 GAGCAAATCTTCGAACCCCAACTTCCTGATGAGATACTGAGAAGCAGGGCAAAGCAATAAAAAGG
1 GAGCAAATCTTCGAACCCCAACTTCCTGATGAGATACTAAGAAGCAGGGCAAAGCAATAAAAAGG
* *
40604 TTAGCTTCCTGATGAGATACAGTGAAGTATACCAACTCAGGGCTCGATGT
66 TTAGCTTCCTGATGAGACACAGAGAAGTATACCAACTCAGGGCTCGATGT
* * * * * * ***
40654 GAGCAAATTTTCGAATCCCAGCTTCTTGATGAGATACTAAGAAGCAGGGCGAAGCAGTAAGGCGG
1 GAGCAAATCTTCGAACCCCAACTTCCTGATGAGATACTAAGAAGCAGGGCAAAGCAATAAAAAGG
* *
40719 TTAGCTTCCTGATGAGGCACTGAGAAGT
66 TTAGCTTCCTGATGAGACACAGAGAAGT
40747 GGACCAAATT
Statistics
Matches: 79, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
115 79 1.00
ACGTcount: A:0.33, C:0.20, G:0.26, T:0.22
Consensus pattern (115 bp):
GAGCAAATCTTCGAACCCCAACTTCCTGATGAGATACTAAGAAGCAGGGCAAAGCAATAAAAAGG
TTAGCTTCCTGATGAGACACAGAGAAGTATACCAACTCAGGGCTCGATGT
Found at i:40839 original size:86 final size:85
Alignment explanation
Indices: 40675--40839 Score: 188
Period size: 86 Copynumber: 1.9 Consensus size: 85
40665 CGAATCCCAG
* * * * * *
40675 CTTCTTGATGAGATACTAAGAAGCAGGGCGAAGCAGTAAGGCGGTTAGCTTCCTGATGAGGCACT
1 CTTCCTGATGAGATACAAAGAAGCAGAGCGAAACAGTAAGGCGGTCAGCTTCCTGATGAGACACT
*
40740 GAGAAGTGGACCAAATTCGT
66 GAGAAGTAGACCAAATTCGT
** * * *
40760 CTTCCTGATGAGATACAAAGAAGCAGATTGAAACAAGTGAGGCGGTCATCTTCCTGATGAGATA-
1 CTTCCTGATGAGATACAAAGAAGCAGAGCGAAAC-AGTAAGGCGGTCAGCTTCCTGATGAGACAC
*
40824 TAGAGAAGTATACCAA
65 T-GAGAAGTAGACCAA
40840 CTCAATACGA
Statistics
Matches: 65, Mismatches: 13, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
85 29 0.45
86 36 0.55
ACGTcount: A:0.33, C:0.17, G:0.27, T:0.22
Consensus pattern (85 bp):
CTTCCTGATGAGATACAAAGAAGCAGAGCGAAACAGTAAGGCGGTCAGCTTCCTGATGAGACACT
GAGAAGTAGACCAAATTCGT
Found at i:41511 original size:197 final size:194
Alignment explanation
Indices: 40608--41625 Score: 1180
Period size: 203 Copynumber: 5.1 Consensus size: 194
40598 AAAAGGTTAG
* * * * *
40608 CTTCCTGATGAGATACAGTGAAGTATACCAACTCAGGGCTCGATGTGAGCAAATTTTCGAATCCC
1 CTTCCTGATGAGATACAGAGAAGTATACCAACTCA-------ATGCGAACAAATCTTCGAACCCC
* * * *** **
40673 AGCTTCTTGATGAGATACTAAGAAGCAGGGCGAAGCAGTAAGGCGGTTAGCTTCCTGATGAGGCA
59 AGCTTCCTGATGAGATACTGAGAAGCAGGGCGAAGCAATAAAAAGGTTAGCTTCCTGATGAGATA
* * *
40738 CTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAAAGAAGCAGATTGAAACAAGTGAGGC
124 CTGAGAAGTTGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAGTGAGGC
40803 GGTCAT
189 GGTCAT
* * *
40809 CTTCCTGATGAGATATAGAGAAGTATACCAACTCAATACGAACAAATCTTCGAACCCCAGCTTCT
1 CTTCCTGATGAGATACAGAGAAGTATACCAACTCAATGCGAACAAATCTTCGAACCCCAGCTTCC
* * * *
40874 TGATGAGATACTAAGAAGCAGGGCGAAGCAAT-AAAAGGTTAGCTTTCTGATGAGATATTGAAAA
66 TGATGAGATACTGAGAAGCAGGGCGAAGCAATAAAAAGGTTAGCTTCCTGATGAGATACTGAGAA
* * * *
40938 GTGGACCAAATTCGTCTTCCTGATGAGGTACAGAGAAGCGGATTGAAACAAGTAAGGCGATCAT
131 GTTGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAGTGAGGCGGTCAT
* * * *
41002 CTTCCTGATAAGATACAAAGAAGAATACCAACTCAGGGCTCGATGCGAGCAAATCTTCGAACCCC
1 CTTCCTGATGAGATACAGAGAAGTATACCAACTCA-------ATGCGAACAAATCTTCGAACCCC
** * * *
41067 AGCTTCCTGATGAGATACTGAGAAGCAGGTTGAAGCAATAAAATGGTTAACGTCCTGATGAGATA
59 AGCTTCCTGATGAGATACTGAGAAGCAGGGCGAAGCAATAAAAAGGTTAGCTTCCTGATGAGATA
* * * * *
41132 CTGAGAAG-TGAACCAAATTTGTCTTCTTGATGAGATACAAAGAAGCGGATTGAAACAAGCGATG
124 CTGAGAAGTTG-ACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAGTGAGG
*
41196 CGGTCAC
188 CGGTCAT
* * *
41203 CTTCCTGATGAGATACTGAGAAGACCAAATCAAACTCATGCTCAATGCGAACAAATCTTCGAACC
1 CTTCCTGATGAGATAC--AG-AG---AAGT-ATAC-CA-ACTCAATGCGAACAAATCTTCGAACC
*
41268 CTAGCTTCCTGATGAGATACTGAGAAGCAGGGCGAAGCAATAAAAAGGTTAGCTTCCTGATGAGA
57 CCAGCTTCCTGATGAGATACTGAGAAGCAGGGCGAAGCAATAAAAAGGTTAGCTTCCTGATGAGA
*
41333 TACTGAGAAGTTGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCAGATTGAAAAAACAAGT
122 TACTGAGAAGTTGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTG---AAACAAGT
41398 GAGGCGGTCAT
184 GAGGCGGTCAT
* * *
41409 CTTCTTGATGAGATACAGAGAAGTATATCAACTCAATGCGAACAAATCCTCG-ACCCTCAGCTTC
1 CTTCCTGATGAGATACAGAGAAGTATACCAACTCAATGCGAACAAATCTTCGAACCC-CAGCTTC
* *
41473 CTGATGAGATACTGAGAAGCAGGGCGAAGCAATAAAAAGGTTAACTTCCTGATGAGATACGGAGA
65 CTGATGAGATACTGAGAAGCAGGGCGAAGCAATAAAAAGGTTAGCTTCCTGATGAGATACTGAGA
* * * * * ** * *
41538 AG-TGAACCAAATCCGTCTTTCTGATGAAACACAGAGAAGTGGATCAAAACAAGTGATGCGGACA
130 AGTTG-ACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAGTGAGGCGGTCA
41602 T
194 T
* *
41603 ATTCCTGATGAGATACTGAGAAG
1 CTTCCTGATGAGATACAGAGAAG
41626 AAGGCCAAGT
Statistics
Matches: 704, Mismatches: 89, Indels: 55
0.83 0.10 0.06
Matches are distributed among these distances:
193 114 0.16
194 93 0.13
196 6 0.01
197 124 0.18
198 2 0.00
199 2 0.00
200 60 0.09
201 126 0.18
203 129 0.18
204 6 0.01
206 31 0.04
207 2 0.00
208 3 0.00
209 2 0.00
210 4 0.01
ACGTcount: A:0.35, C:0.19, G:0.24, T:0.22
Consensus pattern (194 bp):
CTTCCTGATGAGATACAGAGAAGTATACCAACTCAATGCGAACAAATCTTCGAACCCCAGCTTCC
TGATGAGATACTGAGAAGCAGGGCGAAGCAATAAAAAGGTTAGCTTCCTGATGAGATACTGAGAA
GTTGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAGTGAGGCGGTCAT
Found at i:41540 original size:400 final size:392
Alignment explanation
Indices: 40664--41627 Score: 1249
Period size: 400 Copynumber: 2.4 Consensus size: 392
40654 GAGCAAATTT
* * * * *** *
40664 TCGAATCCCAGCTTCTTGATGAGATACTAAGAAGCAGGGCGAAGCAGTAAGGCGGTTAGCTTCCT
1 TCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGGCGAAGCAATAAAAAGGTTAACTTCCT
** * * *
40729 GATGAGGCACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAAAGAAGCAGATTGAAAC
66 GATGAGATACTGAGAAGTGAACCAAATTCGTCTTCTTGATGAGATACAAAGAAGCGGATTGAAAC
* * *
40794 AAGTGAGGCGGTCATCTTCCTGATGAGATA-T-AG-AG-AAGTATACCAACTCAATACGAACAAA
131 AAGTGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAAATAAACCAACTCAATACGAACAAA
* *
40855 TCTTCGAACCCCAGCTTCTTGATGAGATACTAAGAAGCAGGGCGAAGCAATAAAAGGTTAGCTTT
196 TCTTCGAACCCCAGCTTCCTGATGAGATACTAAGAAGCAGGGCGAAGCAATAAAAGGTTAGCTTC
* * *
40920 CTGATGAGATATTGAAAAGTGGACCAAATTCGTCTTCCTGATGAGGTACAGAGAAGCGGATTGAA
261 CTGATGAGATACTGAAAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCAGATTGAA
40985 ACAAGTAAGGCGATCATCTTCCTGATAAGATACAAAGAAGAATACCAACTCAGGGCTCGATGCGA
326 ACAAGTAAGGCGATCATCTTCCTGATAAGATACAAAGAAGAATACCAACTCA------GATGCGA
* *
41050 GCAAATCT
385 ACAAATCC
** * *
41058 TCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTTGAAGCAATAAAATGGTTAACGTCCT
1 TCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGGCGAAGCAATAAAAAGGTTAACTTCCT
*
41123 GATGAGATACTGAGAAGTGAACCAAATTTGTCTTCTTGATGAGATACAAAGAAGCGGATTGAAAC
66 GATGAGATACTGAGAAGTGAACCAAATTCGTCTTCTTGATGAGATACAAAGAAGCGGATTGAAAC
* * * *
41188 AAGCGATGCGGTCACCTTCCTGATGAGATACTGAGAAGACCAAATCAAACTCATGCTCAATGCGA
131 AAGTGATGCGGTCATCTTCCTGATGAGATACTGAGAAGA--AAAT-AAAC-CA-ACTCAATACGA
* *
41253 ACAAATCTTCGAACCCTAGCTTCCTGATGAGATACTGAGAAGCAGGGCGAAGCAATAAAAAGGTT
191 ACAAATCTTCGAACCCCAGCTTCCTGATGAGATACTAAGAAGCAGGGCGAAGCAAT-AAAAGGTT
* *
41318 AGCTTCCTGATGAGATACTGAGAAGTTGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCAG
255 AGCTTCCTGATGAGATACTGAAAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCAG
* * * * * * *
41383 ATTGAAAAAACAAGTGAGGCGGTCATCTTCTTGATGAGATACAGAGAAGTATATCAACTCA-ATG
320 ATTG---AAACAAGTAAGGCGATCATCTTCCTGATAAGATACAAAGAAGAATACCAACTCAGATG
41447 CGAACAAATCC
382 CGAACAAATCC
41458 TCG-ACCCTCAGCTTCCTGATGAGATACTGAGAAGCAGGGCGAAGCAATAAAAAGGTTAACTTCC
1 TCGAACCC-CAGCTTCCTGATGAGATACTGAGAAGCAGGGCGAAGCAATAAAAAGGTTAACTTCC
* * * * * * **
41522 TGATGAGATACGGAGAAGTGAACCAAATCCGTCTT-TCTGATGAAACACAGAGAAGTGGATCAAA
65 TGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCT-TGATGAGATACAAAGAAGCGGATTGAA
* *
41586 ACAAGTGATGCGGACATATTCCTGATGAGATACTGAGAAGAA
129 ACAAGTGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAA
41628 GGCCAAGTTA
Statistics
Matches: 496, Mismatches: 59, Indels: 26
0.85 0.10 0.04
Matches are distributed among these distances:
394 140 0.28
395 1 0.00
396 2 0.00
397 2 0.00
398 1 0.00
399 5 0.01
400 160 0.32
401 3 0.01
402 2 0.00
403 62 0.12
404 71 0.14
407 47 0.09
ACGTcount: A:0.35, C:0.19, G:0.24, T:0.22
Consensus pattern (392 bp):
TCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGGCGAAGCAATAAAAAGGTTAACTTCCT
GATGAGATACTGAGAAGTGAACCAAATTCGTCTTCTTGATGAGATACAAAGAAGCGGATTGAAAC
AAGTGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAAATAAACCAACTCAATACGAACAAA
TCTTCGAACCCCAGCTTCCTGATGAGATACTAAGAAGCAGGGCGAAGCAATAAAAGGTTAGCTTC
CTGATGAGATACTGAAAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCAGATTGAA
ACAAGTAAGGCGATCATCTTCCTGATAAGATACAAAGAAGAATACCAACTCAGATGCGAACAAAT
CC
Found at i:42023 original size:36 final size:37
Alignment explanation
Indices: 41983--42063 Score: 87
Period size: 36 Copynumber: 2.2 Consensus size: 37
41973 AAACCCATTT
* *
41983 TTTAATTTTTTAAA-TTCATTTTGAGTTTAAATTTAG
1 TTTAATTTTTTAAACTTCATTTTAAGTTTAAATTTAA
* *
42019 TTTAA--GTTTAAACTTTCCTTTTAAGTTTAAATTTAA
1 TTTAATTTTTTAAAC-TTCATTTTAAGTTTAAATTTAA
42055 TTTGAATTT
1 TTT-AATTT
42064 AAAATTTAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
34 6 0.17
36 27 0.77
37 2 0.06
ACGTcount: A:0.31, C:0.05, G:0.07, T:0.57
Consensus pattern (37 bp):
TTTAATTTTTTAAACTTCATTTTAAGTTTAAATTTAA
Found at i:42066 original size:17 final size:18
Alignment explanation
Indices: 41991--42072 Score: 71
Period size: 17 Copynumber: 4.6 Consensus size: 18
41981 TTTTTAATTT
* *
41991 TTTAAATTCATTTTG-AG
1 TTTAAATTTAATTTGAAG
*
42008 TTTAAATTTAGTTT-AAG
1 TTTAAATTTAATTTGAAG
** *
42025 TTTAAACTTTCCTTTTAAG
1 TTTAAA-TTTAATTTGAAG
42044 TTTAAATTTAATTTGAA-
1 TTTAAATTTAATTTGAAG
42061 TTTAAAATTTAA
1 TTT-AAATTTAA
42073 AAGTCTAGTC
Statistics
Matches: 54, Mismatches: 7, Indels: 7
0.79 0.10 0.10
Matches are distributed among these distances:
17 23 0.43
18 22 0.41
19 9 0.17
ACGTcount: A:0.35, C:0.05, G:0.07, T:0.52
Consensus pattern (18 bp):
TTTAAATTTAATTTGAAG
Found at i:42734 original size:15 final size:15
Alignment explanation
Indices: 42716--42750 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
42706 TATTACAATA
42716 AATAACATTAATAAT
1 AATAACATTAATAAT
**
42731 AATAGTATTAATAAT
1 AATAACATTAATAAT
42746 AATAA
1 AATAA
42751 ACATGACCTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.34
Consensus pattern (15 bp):
AATAACATTAATAAT
Found at i:43823 original size:29 final size:29
Alignment explanation
Indices: 43790--43943 Score: 175
Period size: 29 Copynumber: 5.2 Consensus size: 29
43780 CTAAACTGTT
**
43790 CAAAAATTACATTTTTACCCTTGAACTTC
1 CAAAAATTACATTTTTACCCCCGAACTTC
* ** **
43819 CAAAAATTCCATTTTTGATACCAAAACTTC
1 CAAAAATTACATTTTT-ACCCCCGAACTTC
43849 CAAAAATTACATTTTTACCCCCGAACTTC
1 CAAAAATTACATTTTTACCCCCGAACTTC
* *
43878 CAAAAATTCCATTTTTGA-CCTCGAAACTTC
1 CAAAAATTACATTTTT-ACCCCCG-AACTTC
* *
43908 TAAAAATTACATTTTTACCCCCGAACCTC
1 CAAAAATTACATTTTTACCCCCGAACTTC
43937 CAAAAAT
1 CAAAAAT
43944 CCTACCTCAA
Statistics
Matches: 103, Mismatches: 18, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
29 55 0.53
30 48 0.47
ACGTcount: A:0.37, C:0.27, G:0.04, T:0.32
Consensus pattern (29 bp):
CAAAAATTACATTTTTACCCCCGAACTTC
Found at i:43882 original size:59 final size:59
Alignment explanation
Indices: 43790--44062 Score: 241
Period size: 59 Copynumber: 4.8 Consensus size: 59
43780 CTAAACTGTT
**
43790 CAAAAATTACATTTTTACCCTTGAACTTCCAAAAATTCCATTTTTGATAC-CAAAACTTC
1 CAAAAATTACATTTTTACCCCCGAACTTCCAAAAATTCCATTTTTGA-ACTCAAAACTTC
* *
43849 CAAAAATTACATTTTTACCCCCGAACTTCCAAAAATTCCATTTTTGACCTCGAAACTTC
1 CAAAAATTACATTTTTACCCCCGAACTTCCAAAAATTCCATTTTTGAACTCAAAACTTC
* * * *
43908 TAAAAATTACATTTTTACCCCCGAACCTCCAAAAA-TCC-----T-ACCTCAAAACTTT
1 CAAAAATTACATTTTTACCCCCGAACTTCCAAAAATTCCATTTTTGAACTCAAAACTTC
* * * * **
43960 CAAAAATTAC-TATTTTACCCTCTAA-TGTCCAAAAACTCCA-TTTTGACCTTTAAAC-TC
1 CAAAAATTACAT-TTTTACCCCCGAACT-TCCAAAAATTCCATTTTTGAACTCAAAACTTC
* * *
44017 TAAAAAATTACCA-TTTTACCCTCGAA-TGTCCAAAAATTCTATTTTT
1 -CAAAAATTA-CATTTTTACCCCCGAACT-TCCAAAAATTCCATTTTT
44063 TATCTCAATT
Statistics
Matches: 182, Mismatches: 19, Indels: 26
0.80 0.08 0.11
Matches are distributed among these distances:
51 1 0.01
52 39 0.21
53 4 0.02
57 2 0.01
58 45 0.25
59 91 0.50
ACGTcount: A:0.36, C:0.26, G:0.04, T:0.34
Consensus pattern (59 bp):
CAAAAATTACATTTTTACCCCCGAACTTCCAAAAATTCCATTTTTGAACTCAAAACTTC
Found at i:43992 original size:111 final size:110
Alignment explanation
Indices: 43840--44053 Score: 274
Period size: 110 Copynumber: 1.9 Consensus size: 110
43830 TTTTTGATAC
*
43840 CAAAACTTCCAAAAATTACATTTTTACCCCCGAACTTCCAAAAATTCCATTTTTGACCTCGAAAC
1 CAAAACTTCCAAAAATTACATTTTTACCCCCGAACTTCCAAAAACTCCA-TTTTGACCTCGAAAC
43905 TTCT-AAAAATTA-CATTTTTACCCCCGAACCTCCAAAAATCCTACCT
65 -TCTAAAAAATTACCA-TTTTACCCCCGAACCTCCAAAAATCCTACCT
* * * **
43951 CAAAACTTTCAAAAATTAC-TATTTTACCCTCTAA-TGTCCAAAAACTCCATTTTGACCTTTAAA
1 CAAAACTTCCAAAAATTACAT-TTTTACCCCCGAACT-TCCAAAAACTCCATTTTGACCTCGAAA
* **
44014 CTCTAAAAAATTACCATTTTACCCTCGAATGTCCAAAAAT
64 CTCTAAAAAATTACCATTTTACCCCCGAACCTCCAAAAAT
44054 TCTATTTTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 9
0.83 0.08 0.08
Matches are distributed among these distances:
109 3 0.03
110 44 0.49
111 43 0.48
ACGTcount: A:0.37, C:0.28, G:0.04, T:0.31
Consensus pattern (110 bp):
CAAAACTTCCAAAAATTACATTTTTACCCCCGAACTTCCAAAAACTCCATTTTGACCTCGAAACT
CTAAAAAATTACCATTTTACCCCCGAACCTCCAAAAATCCTACCT
Found at i:44052 original size:30 final size:30
Alignment explanation
Indices: 43961--44052 Score: 91
Period size: 30 Copynumber: 3.1 Consensus size: 30
43951 CAAAACTTTC
*
43961 AAAAATTACTATTTTACCCTCTAATGTCC-
1 AAAAATTACCATTTTACCCTCTAATGTCCA
* * ** *
43990 AAAAACT-CCATTTTGA-CCTTTAAACTCTA
1 AAAAATTACCATTTT-ACCCTCTAATGTCCA
*
44019 AAAAATTACCATTTTACCCTCGAATGTCCA
1 AAAAATTACCATTTTACCCTCTAATGTCCA
44049 AAAA
1 AAAA
44053 TTCTATTTTT
Statistics
Matches: 47, Mismatches: 12, Indels: 7
0.71 0.18 0.11
Matches are distributed among these distances:
28 14 0.30
29 14 0.30
30 19 0.40
ACGTcount: A:0.39, C:0.24, G:0.04, T:0.33
Consensus pattern (30 bp):
AAAAATTACCATTTTACCCTCTAATGTCCA
Found at i:44062 original size:29 final size:29
Alignment explanation
Indices: 43960--44181 Score: 104
Period size: 29 Copynumber: 7.7 Consensus size: 29
43950 TCAAAACTTT
*
43960 CAAAAATTACTATTTTACCCTCTAATGTC
1 CAAAAATTACCATTTTACCCTCTAATGTC
* * **
43989 CAAAAACT-CCATTTTGA-CCTTTAAACTC
1 CAAAAATTACCATTTT-ACCCTCTAATGTC
* *
44017 TAAAAAATTACCATTTTACCCTCGAATGTC
1 -CAAAAATTACCATTTTACCCTCTAATGTC
* * *
44047 CAAAAATT-CTATTTTTTA-TCTC-AATTTTTC
1 CAAAAATTACCA--TTTTACCCTCTAA--TGTC
* * *
44077 TAAAAATTATCATTTTACCCTCGAATGT-
1 CAAAAATTACCATTTTACCCTCTAATGTC
* * * *
44105 CTAAAATT-TCATTTTATTCCC-CAAAATTTC
1 CAAAAATTACCATTTTA--CCCTC-TAATGTC
* * * *
44135 CTAAAATTACCATTTT-GCCTCCAAAGTC
1 CAAAAATTACCATTTTACCCTCTAATGTC
44163 C-AAAATTACCATTTTACCC
1 CAAAAATTACCATTTTACCC
44182 CCCGGGTATC
Statistics
Matches: 145, Mismatches: 30, Indels: 37
0.68 0.14 0.17
Matches are distributed among these distances:
27 22 0.15
28 34 0.23
29 40 0.28
30 40 0.28
31 9 0.06
ACGTcount: A:0.34, C:0.24, G:0.04, T:0.38
Consensus pattern (29 bp):
CAAAAATTACCATTTTACCCTCTAATGTC
Found at i:44143 original size:58 final size:59
Alignment explanation
Indices: 43961--44167 Score: 167
Period size: 58 Copynumber: 3.6 Consensus size: 59
43951 CAAAACTTTC
* * * * * ** *
43961 AAAAATTACTATTTTACCCTCTAATGTCCAAAAACTCCA-TTTTGACCTTTAAA-CT-CT
1 AAAAATTACCATTTTACCCTCGAATGTCCAAAAATTCTATTTTTTACC-CCAAATTTCCT
* * * *
44018 AAAAAATTACCATTTTACCCTCGAATGTCCAAAAATTCTATTTTTTATCTCAATTTTTCT
1 -AAAAATTACCATTTTACCCTCGAATGTCCAAAAATTCTATTTTTTACCCCAAATTTCCT
* * *
44078 AAAAATTATCATTTTACCCTCGAATGTCTAAAATTTC-ATTTTATT-CCCCAAAATTTCCT
1 AAAAATTACCATTTTACCCTCGAATGTCCAAAAATTCTATTTT-TTACCCC-AAATTTCCT
* * *
44137 -AAAATTACCATTTT-GCCTCCAAAGTCCAAAA
1 AAAAATTACCATTTTACCCTCGAATGTCCAAAA
44168 TTACCATTTT
Statistics
Matches: 123, Mismatches: 21, Indels: 11
0.79 0.14 0.07
Matches are distributed among these distances:
57 13 0.11
58 58 0.47
59 50 0.41
60 2 0.02
ACGTcount: A:0.35, C:0.23, G:0.04, T:0.38
Consensus pattern (59 bp):
AAAAATTACCATTTTACCCTCGAATGTCCAAAAATTCTATTTTTTACCCCAAATTTCCT
Found at i:44515 original size:96 final size:96
Alignment explanation
Indices: 44410--44594 Score: 266
Period size: 96 Copynumber: 1.9 Consensus size: 96
44400 AAAAATTTAA
* * *
44410 AATCGAGGCAATA-TTCTTTTAT-TTCTAGTTTTGAAAATTTGCGCATTAACTTACTAGGTGCAA
1 AATCGAGGCAATATTTC-CTTATCTTCGA-TTCTGAAAATTTGCGCATTAACTTACTAGGTGCAA
**
44473 TTTTTCTTCAAATCGAAATAATCGAATACCTTT
64 CCTTTCTTCAAATCGAAATAATCGAATACCTTT
* *
44506 AATCGAGGCAATGTTTCCTTATCTTCGATTCTGAAAATTTGCGCCTTAACTTACTAGGTGCAACC
1 AATCGAGGCAATATTTCCTTATCTTCGATTCTGAAAATTTGCGCATTAACTTACTAGGTGCAACC
*
44571 TTTCTTCAAATCGAGATAATCGAA
66 TTTCTTCAAATCGAAATAATCGAA
44595 CATCCTTTTT
Statistics
Matches: 79, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
96 72 0.91
97 7 0.09
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.37
Consensus pattern (96 bp):
AATCGAGGCAATATTTCCTTATCTTCGATTCTGAAAATTTGCGCATTAACTTACTAGGTGCAACC
TTTCTTCAAATCGAAATAATCGAATACCTTT
Found at i:45452 original size:13 final size:14
Alignment explanation
Indices: 45428--45458 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
45418 TACTGGTTGA
45428 TAAAATAATAAATT
1 TAAAATAATAAATT
45442 TAAAA-AATAAATT
1 TAAAATAATAAATT
45455 TAAA
1 TAAA
45459 TTTAAAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (14 bp):
TAAAATAATAAATT
Found at i:55166 original size:59 final size:57
Alignment explanation
Indices: 55054--55171 Score: 146
Period size: 59 Copynumber: 2.0 Consensus size: 57
55044 TAAGAATGTT
* * * * *
55054 ATTAAATTATATATTATTTTATTAAATTGTATTTAATAGTAATTATGTTAAAATATA
1 ATTAAATTATATATTATTTTATTAAATTATATCTAATAATAATTATATAAAAATATA
* * *
55111 ATTAAATTATTTATTATTTTTTATTAAATTATATCTAATAATAATTTTATAAAAATTTA
1 ATTAAATTATATATTA--TTTTATTAAATTATATCTAATAATAATTATATAAAAATATA
55170 AT
1 AT
55172 AACAATAAAA
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
57 15 0.29
59 36 0.71
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.53
Consensus pattern (57 bp):
ATTAAATTATATATTATTTTATTAAATTATATCTAATAATAATTATATAAAAATATA
Found at i:66223 original size:10 final size:11
Alignment explanation
Indices: 66207--66236 Score: 53
Period size: 10 Copynumber: 2.8 Consensus size: 11
66197 TTTTTTTGCA
66207 AAAAAGAAAAG
1 AAAAAGAAAAG
66218 -AAAAGAAAAG
1 AAAAAGAAAAG
66228 AAAAAGAAA
1 AAAAAGAAA
66237 TTATTTATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAAG
Found at i:67751 original size:3 final size:3
Alignment explanation
Indices: 67743--67767 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
67733 CCCCTAATAT
67743 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
67768 CATGGTGTAT
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:71768 original size:19 final size:21
Alignment explanation
Indices: 71739--71782 Score: 58
Period size: 19 Copynumber: 2.2 Consensus size: 21
71729 TAATTTTTAA
71739 ATTTAAAAAAT-TCAAAAAT-T
1 ATTTAAAAAATAT-AAAAATAT
71759 ATTT-AAAAATATAAAAATAT
1 ATTTAAAAAATATAAAAATAT
71779 ATTT
1 ATTT
71783 TTAATATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 12 0.55
20 10 0.45
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (21 bp):
ATTTAAAAAATATAAAAATAT
Found at i:72497 original size:29 final size:29
Alignment explanation
Indices: 72473--72530 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
72463 CAAATAGTAG
72473 TTCCT-AAAATTACAGATCCTAAATAAAA
1 TTCCTAAAAATTACAGATCCTAAATAAAA
* * *
72501 TTTCTAAAAATTACAGTTCCTAATTAAAA
1 TTCCTAAAAATTACAGATCCTAAATAAAA
72530 T
1 T
72531 ACAAATCATA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 4 0.15
29 22 0.85
ACGTcount: A:0.47, C:0.16, G:0.03, T:0.34
Consensus pattern (29 bp):
TTCCTAAAAATTACAGATCCTAAATAAAA
Found at i:72810 original size:27 final size:27
Alignment explanation
Indices: 72780--72854 Score: 132
Period size: 27 Copynumber: 2.8 Consensus size: 27
72770 ATTTCTCTTT
*
72780 TTCTCCTTTTCCCTTTCCCTTCCTCCA
1 TTCTCCTTTCCCCTTTCCCTTCCTCCA
72807 TTCTCCTTTCCCCTTTCCCTTCCTCCA
1 TTCTCCTTTCCCCTTTCCCTTCCTCCA
*
72834 TTCTCCTTTCCCCTTCCCCTT
1 TTCTCCTTTCCCCTTTCCCTT
72855 TGAGAGACTT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 46 1.00
ACGTcount: A:0.03, C:0.51, G:0.00, T:0.47
Consensus pattern (27 bp):
TTCTCCTTTCCCCTTTCCCTTCCTCCA
Found at i:72832 original size:20 final size:21
Alignment explanation
Indices: 72809--72855 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
72799 TTCCTCCATT
72809 CTCCTTTCCCCTTT-CCCTTC
1 CTCCTTTCCCCTTTCCCCTTC
* *
72829 CTCCATTCTCCTTTCCCCTTC
1 CTCCTTTCCCCTTTCCCCTTC
72850 C-CCTTT
1 CTCCTTT
72856 GAGAGACTTC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 16 0.70
21 7 0.30
ACGTcount: A:0.02, C:0.53, G:0.00, T:0.45
Consensus pattern (21 bp):
CTCCTTTCCCCTTTCCCCTTC
Done.