Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012509.1 Kokia drynarioides strain JFW-HI SEQ_127514, 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: 22005
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.28
Warning! 400 characters in sequence are not A, C, G, or T
Found at i:772 original size:30 final size:30
Alignment explanation
Indices: 730--1104 Score: 364
Period size: 30 Copynumber: 12.7 Consensus size: 30
720 CTAAATTATC
* *
730 CAAAAATCACATTTTGATCCTCAAACTTCT
1 CAAAAATTACATTTTGACCCTCAAACTTCT
* *
760 TAAAAATTACATTTTGACCCTCAAACTTTT
1 CAAAAATTACATTTTGACCCTCAAACTTCT
* *
790 CAAAAATTATATTTTTACCCTCAAACTTCT
1 CAAAAATTACATTTTGACCCTCAAACTTCT
* * * *
820 CAAAAATCACATTTTAACCCCCGAACTT-T
1 CAAAAATTACATTTTGACCCTCAAACTTCT
*
849 CCAAAAAATACATTTTGACCCTCAAACTTCT
1 -CAAAAATTACATTTTGACCCTCAAACTTCT
* * *
880 TAAAAATTACATTTTAACCCTCAAACTTTT
1 CAAAAATTACATTTTGACCCTCAAACTTCT
* *
910 CAAAAATTACATTTT-AACCTTAAACTTCT
1 CAAAAATTACATTTTGACCCTCAAACTTCT
*
939 CAAAAATTACATTTTTACCCTCAAACATT-T
1 CAAAAATTACATTTTGACCCTCAAAC-TTCT
969 -AAAAATTACATTTTTTG-CCCT-AAACTTC-
1 CAAAAATTACA--TTTTGACCCTCAAACTTCT
* *
997 CAAAAATCACATTTTTACCC-CAAACTTCT
1 CAAAAATTACATTTTGACCCTCAAACTTCT
1026 CAAAAATTACATTTTTG-CCCTCGAAA-TT-T
1 CAAAAATTACA-TTTTGACCCTC-AAACTTCT
* * * * *
1055 CGAAAATCACCATTTT-ACCCTCGAGCATC-
1 CAAAAATTA-CATTTTGACCCTCAAACTTCT
1084 CAAAAATTACCATTTT-ACCCT
1 CAAAAATTA-CATTTTGACCCT
1105 TAATTTTTTG
Statistics
Matches: 287, Mismatches: 40, Indels: 37
0.79 0.11 0.10
Matches are distributed among these distances:
27 4 0.01
28 13 0.05
29 100 0.35
30 160 0.56
31 10 0.03
ACGTcount: A:0.37, C:0.25, G:0.03, T:0.35
Consensus pattern (30 bp):
CAAAAATTACATTTTGACCCTCAAACTTCT
Found at i:13528 original size:33 final size:33
Alignment explanation
Indices: 13486--13552 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
13476 AGAGAAGTAT
13486 ACCAAATCAATGAAACAAAGCTCAATATGAGCG
1 ACCAAATCAATGAAACAAAGCTCAATATGAGCG
13519 ACCAAATCAATGAAACAAAGCTCAATATGAGCG
1 ACCAAATCAATGAAACAAAGCTCAATATGAGCG
13552 A
1 A
13553 AACTTCGAGC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.49, C:0.21, G:0.15, T:0.15
Consensus pattern (33 bp):
ACCAAATCAATGAAACAAAGCTCAATATGAGCG
Found at i:14142 original size:207 final size:208
Alignment explanation
Indices: 13776--14369 Score: 779
Period size: 208 Copynumber: 2.9 Consensus size: 208
13766 NNNNNNNNNN
* *
13776 GATTAAAACAAGTGAGGCAGTCATCTTCTTGATGAGGTACAGAGAAGTATACCAAATCAATGAAA
1 GATTAAAACAAGTGAGGC-GTCATCTTCCTGATGAGATACAGAGAAGTATACCAAATCAATGAAA
* * *
13841 CAAAGCTCAATATGAGCGAAACTTCG-AGCCTCAACTTCTTAATGAGATATTGAGAAGCAGGTCG
65 CAAAGCTCAATGTGAGCGAAACTTCGAACCCT-AACTTCTTAATGAGATACTGAGAAGCAGGTCG
* * *
13905 AAGCAATAAAAAG-TCAACTTCCTAATGAGATACAGAGAAGTGAACCAAATTCGTCTTCTTAATG
129 AAGCAATAAAATGATCAACTTCCTGATGAGATACAGAGAAGTGAACCAAATTCGTCTTCCTAATG
13969 A-ATACAGAGAAGCG
194 AGATACAGAGAAGCG
* * * *
13983 GATTGAAACAAGTGAGGCTGTCATCTTCCTGATGAGATGCAGAGAAGTATATCAAATCAATAAAA
1 GATTAAAACAAGTGAGGC-GTCATCTTCCTGATGAGATACAGAGAAGTATACCAAATCAATGAAA
* * * * *
14048 TAAAGC-AAATGTGAGCGAAACTTTGAACCCTAACTTCCTGATGAGATACTGAGAAGCAGGTCGA
65 CAAAGCTCAATGTGAGCGAAACTTCGAACCCTAACTTCTTAATGAGATACTGAGAAGCAGGTCGA
* * * *
14112 AGCAATAAAATGATCAGCTTCCTGATGAGATACTGAGAAGTGAACCTAATTCGTCTTCCTGATGA
130 AGCAATAAAATGATCAACTTCCTGATGAGATACAGAGAAGTGAACCAAATTCGTCTTCCTAATGA
* *
14177 GATATAGAGAAGTG
195 GATACAGAGAAGCG
* * * * *
14191 GATTAAAACGAGTGAGACGATCATCTTTCTGATAAGATATAGAGAAGTATACCAAATCAATGAAA
1 GATTAAAACAAGTGAGGCG-TCATCTTCCTGATGAGATACAGAGAAGTATACCAAATCAATGAAA
* * * * *
14256 CAAA-CTCAATAG-GAGTGAAACTTCGAGCCCCAGCTTCTTAATGAGATACTGAGAAGTAGGTCG
65 CAAAGCTCAAT-GTGAGCGAAACTTCGAACCCTAACTTCTTAATGAGATACTGAGAAGCAGGTCG
*
14319 AAGCAATAAAATGATCATCTTCCTGATGAGATACAGAGAAGT-ATACCAAAT
129 AAGCAATAAAATGATCAACTTCCTGATGAGATACAGAGAAGTGA-ACCAAAT
14370 CAATGAAACA
Statistics
Matches: 334, Mismatches: 46, Indels: 13
0.85 0.12 0.03
Matches are distributed among these distances:
206 57 0.17
207 116 0.35
208 160 0.48
209 1 0.00
ACGTcount: A:0.39, C:0.16, G:0.21, T:0.24
Consensus pattern (208 bp):
GATTAAAACAAGTGAGGCGTCATCTTCCTGATGAGATACAGAGAAGTATACCAAATCAATGAAAC
AAAGCTCAATGTGAGCGAAACTTCGAACCCTAACTTCTTAATGAGATACTGAGAAGCAGGTCGAA
GCAATAAAATGATCAACTTCCTGATGAGATACAGAGAAGTGAACCAAATTCGTCTTCCTAATGAG
ATACAGAGAAGCG
Found at i:14469 original size:123 final size:122
Alignment explanation
Indices: 14209--14492 Score: 370
Period size: 123 Copynumber: 2.3 Consensus size: 122
14199 CGAGTGAGAC
* * * * *
14209 GATCATCTTTCTGATAAGATATAGAGAAGTATACCAAATCAATGAAACAAACTCAATAGGAGTGA
1 GATCAGCTTCCTGATGAGATATAGAGAAGTATACCAAATCAATGAAACAAACTCAAAAGGAGCGA
* * *
14274 AACTTCGAGCCCCAGCTTCTTAATGAGATACTGAGAAGTAGGTCGAAGCAATAAAAT
66 AACTTCGAGCCCCAACTTCCTAATGAGATACTGAGAAGCAGGTCGAAGCAATAAAAT
* * * *
14331 GATCATCTTCCTGATGAGATACAGAGAAGTATACCAAATCAATGAAACAAAGTTCAAAATGAGCG
1 GATCAGCTTCCTGATGAGATATAGAGAAGTATACCAAATCAATGAAACAAA-CTCAAAAGGAGCG
* * * *
14396 AAACTTCTAGCCCCAACTTCCTGATGAGATACTGAGAAGCAGTTTGAAGCAATAAAAT
65 AAACTTCGAGCCCCAACTTCCTAATGAGATACTGAGAAGCAGGTCGAAGCAATAAAAT
* * * **
14454 GGTTAGCTTCTTGATGAGATATAGAGAAGTGGACCAAAT
1 GATCAGCTTCCTGATGAGATATAGAGAAGTATACCAAAT
14493 TCATCTTCCT
Statistics
Matches: 140, Mismatches: 21, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
122 48 0.34
123 92 0.66
ACGTcount: A:0.40, C:0.17, G:0.20, T:0.24
Consensus pattern (122 bp):
GATCAGCTTCCTGATGAGATATAGAGAAGTATACCAAATCAATGAAACAAACTCAAAAGGAGCGA
AACTTCGAGCCCCAACTTCCTAATGAGATACTGAGAAGCAGGTCGAAGCAATAAAAT
Found at i:14575 original size:331 final size:331
Alignment explanation
Indices: 14002--14701 Score: 924
Period size: 331 Copynumber: 2.1 Consensus size: 331
13992 AAGTGAGGCT
* * * *
14002 GTCATCTTCCTGATGAGATGCAGAGAAGTATATCAAATCAATAAAATAAAGCAAATGTGAGCGAA
1 GTCATCTTCCTGATGAGATACAGAGAAGTATACCAAATCAATAAAACAAAGCAAATATGAGCGAA
*
14067 ACTTTGAACCCTAACTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGATCAGCTT
66 ACTTTGAACCCCAACTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGATCAGCTT
* * * **
14132 CCTGATGAGATACTGAGAAGTGAACCTAATTCGTCTTCCTGATGAGATATAGAGAAGTGGATTAA
131 CCTGATGAGATACTGAGAAGTGAACCAAATTCATCTTCCTGATGAGATACAGAGAAGCAGATTAA
* * * * *
14197 AACGAGTGAGACGATCATCTTTCTGATAAGATATAGAGAAGTATACCAAATCAATGAAACAAA-C
196 AACAAGTGAGACGATCATCTTCCTGATAAGACACAGAGAAGTATACCAAATCAACGAAACAAAGC
** * * * * *
14261 TCAATAGGAGTGAAACTTCGAGCCCCAGCTTCTTAATGAGATACTGAGAAGTAGGTCGAAGCAAT
261 TCAATAGGAACGAAACTTCGAGCCCCAACTTCCTAATGAGATACTAAGAAGCAAGTCGAAGCAAT
14326 AAAAT-
326 AAAATA
*
14331 GATCATCTTCCTGATGAGATACAGAGAAGTATACCAAATCAATGAAACAAAGTTCAAA-ATGAGC
1 G-TCATCTTCCTGATGAGATACAGAGAAGTATACCAAATCAATAAAACAAAG--CAAATATGAGC
* * * * *
14395 GAAACTTCT-AGCCCCAACTTCCTGATGAGATACTGAGAAGCAGTTTGAAGCAATAAAATGGTTA
63 GAAACTT-TGAACCCCAACTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGATCA
* *
14459 GCTTCTTGATGAGATA-TAGAGAAGTGGACCAAATTCATCTTCCTGATGAGATACAGAGAAGCAG
127 GCTTCCTGATGAGATACT-GAGAAGTGAACCAAATTCATCTTCCTGATGAGATACAGAGAAGCAG
* *
14523 ATTAAAACAAGTGAGACGATCATCTTCCTGATGAGACACAGAGAATTATACCAAATCAACGAAAC
191 ATTAAAACAAGTGAGACGATCATCTTCCTGATAAGACACAGAGAAGTATACCAAATCAACGAAAC
* * * * * *
14588 AAAGCTCAATATGAACGAAACTTTGAGTCTCAACTTCCTGATGAGATACTAAGAGGCAAGTCGAA
256 AAAGCTCAATAGGAACGAAACTTCGAGCCCCAACTTCCTAATGAGATACTAAGAAGCAAGTCGAA
14653 GCAATAAAATA
321 GCAATAAAATA
* * * * **
14664 GTTAGCTTTCTGATGAGATATAGAGAAGTGGACCAAAT
1 GTCATCTTCCTGATGAGATACAGAGAAGTATACCAAAT
14702 TCGTCTTCCT
Statistics
Matches: 320, Mismatches: 44, Indels: 11
0.85 0.12 0.03
Matches are distributed among these distances:
329 1 0.00
330 47 0.15
331 177 0.55
332 94 0.29
333 1 0.00
ACGTcount: A:0.39, C:0.17, G:0.20, T:0.24
Consensus pattern (331 bp):
GTCATCTTCCTGATGAGATACAGAGAAGTATACCAAATCAATAAAACAAAGCAAATATGAGCGAA
ACTTTGAACCCCAACTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGATCAGCTT
CCTGATGAGATACTGAGAAGTGAACCAAATTCATCTTCCTGATGAGATACAGAGAAGCAGATTAA
AACAAGTGAGACGATCATCTTCCTGATAAGACACAGAGAAGTATACCAAATCAACGAAACAAAGC
TCAATAGGAACGAAACTTCGAGCCCCAACTTCCTAATGAGATACTAAGAAGCAAGTCGAAGCAAT
AAAATA
Found at i:14691 original size:209 final size:209
Alignment explanation
Indices: 14333--15192 Score: 1167
Period size: 209 Copynumber: 4.1 Consensus size: 209
14323 AATAAAATGA
* *
14333 TCATCTTCCTGATGAGATACAGAGAAGTATACCAAATCAATGAAACAAAGTTCAAAATGAGCGAA
1 TCATCTTCCTGATGAGATACAGAGAAGTATACCAAATCAATGAAACAAAGCTCAATATGAGCGAA
* * * *
14398 ACTTCTAGCCCCAACTTCCTGATGAGATACTGAGAAGC-AGTTTGAAGCAATAAAATGGTTAGCT
66 ACTTCGAGTCCCAACTTCCTGATGAGATACTGAGAAGCAAG-TCGAAGCAATAAAATGGTCAGCT
* * * *
14462 TCTTGATGAGATATAGAGAAGTGGACCAAATTCATCTTCCTGATGAGATACAGAGAAGCAGATTA
130 TCTTGATGAGATACAGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCAGATTG
* *
14527 AAACAAGTGAGACGA
195 AAACAAGTGAGGCGG
* * * *
14542 TCATCTTCCTGATGAGACACAGAGAATTATACCAAATCAACGAAACAAAGCTCAATATGAACGAA
1 TCATCTTCCTGATGAGATACAGAGAAGTATACCAAATCAATGAAACAAAGCTCAATATGAGCGAA
* * * * * *
14607 ACTTTGAGTCTCAACTTCCTGATGAGATACTAAGAGGCAAGTCGAAGCAATAAAATAGTTAGCTT
66 ACTTCGAGTCCCAACTTCCTGATGAGATACTGAGAAGCAAGTCGAAGCAATAAAATGGTCAGCTT
* * *
14672 -TCTGATGAGATATAGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAA-CCGAATT
131 CT-TGATGAGATACAGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCAG-ATT
*
14735 GAAACAAGTGATGCGG
194 GAAACAAGTGAGGCGG
* * *
14751 TCATCTACTTGATGAGATATAGAGAAGTATACCAAATCAATGAAACAAAGCTCAATATGAGCGAA
1 TCATCTTCCTGATGAGATACAGAGAAGTATACCAAATCAATGAAACAAAGCTCAATATGAGCGAA
* * * *
14816 ACATCGAGTCTCAACTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAAT-AAAGGGTCAGCTT
66 ACTTCGAGTCCCAACTTCCTGATGAGATACTGAGAAGCAAGTCGAAGCAATAAAATGGTCAGCTT
* * * * * *
14880 CCTAATGAGATACAGAGAAGTGAACCAAATTCGTCTTCTTGATAAGATACAGAGAAGCGGGTTGA
131 CTTGATGAGATACAGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCAGATTGA
*
14945 AACAAGTAAGGCGG
196 AACAAGTGAGGCGG
** * * *
14959 TCATCTTATTGATGAGATAC--A-AAGTATACCAAATCAATAAAACAAAGCTCAATGTGAGTGAA
1 TCATCTTCCTGATGAGATACAGAGAAGTATACCAAATCAATGAAACAAAGCTCAATATGAGCGAA
* * * *
15021 ACTTCGAGTCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTTGAAGTAATAAAATGGTCAGCTT
66 ACTTCGAGTCCCAACTTCCTGATGAGATACTGAGAAGCAAGTCGAAGCAATAAAATGGTCAGCTT
* *
15086 CTTGATGAGATACAAAGAAGTGAACCCAATTCGTCTTCCTGATGAGATACAGAGAAGCAGATTGA
131 CTTGATGAGATACAGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCAGATTGA
*
15151 AACAAGTGAGGTGG
196 AACAAGTGAGGCGG
*
15165 TCATCTTCCTGATGAGATACAAAGAAGT
1 TCATCTTCCTGATGAGATACAGAGAAGT
15193 GAACCTAATT
Statistics
Matches: 573, Mismatches: 69, Indels: 18
0.87 0.10 0.03
Matches are distributed among these distances:
205 84 0.15
206 100 0.17
208 96 0.17
209 291 0.51
210 2 0.00
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (209 bp):
TCATCTTCCTGATGAGATACAGAGAAGTATACCAAATCAATGAAACAAAGCTCAATATGAGCGAA
ACTTCGAGTCCCAACTTCCTGATGAGATACTGAGAAGCAAGTCGAAGCAATAAAATGGTCAGCTT
CTTGATGAGATACAGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCAGATTGA
AACAAGTGAGGCGG
Found at i:14890 original size:540 final size:537
Alignment explanation
Indices: 13807--14909 Score: 1475
Period size: 540 Copynumber: 2.0 Consensus size: 537
13797 CATCTTCTTG
* * *
13807 ATGAGGTACAGAGAAGTATACCAAATCAATGAAACAAAGCTCAATATGAGCGAAACTTCGAGCCT
1 ATGAGATACAGAGAAGTATACCAAATCAATGAAACAAAGCTCAAAATGAGCGAAACTTCGAGCCC
* *
13872 CAACTTCTTAATGAGATATTGAGAAGCAGGTCGAAGCAATAAAAAGTCAACTTCCTAATGAGATA
66 CAACTTCCTAATGAGATACTGAGAAGCAGGTCGAAGCAATAAAAAGTCAACTTCCTAATGAGATA
* * * * *
13937 CAGAGAAGTGAACCAAATTCGTCTTCTTAATGAATACAGAGAAGCGGATTGAAACAAGTGAGGCT
131 CAGAGAAGTGAACCAAATTCATCTTCCTAATGAATACAGAGAAGCAGATTAAAACAAGTGAGACT
** * * * * *
14002 GTCATCTTCCTGATGAGATGCAGAGAAGTATATCAAATCAATAAAATAAAGCAAATGTGAGCGAA
196 GTCATCTTCCTGATGAGACACAGAGAAGTATACCAAATCAACAAAACAAAGCAAATATGAACGAA
* *
14067 ACTTTGAACCCTAACTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGATCAGCTT
261 ACTTTGAACCCTAACTTCCTGATGAGATACTAAGAAGCAAGTCGAAGCAATAAAATGATCAGCTT
* * ** *
14132 CCTGATGAGATACTGAGAAGTGAACCTAATTCGTCTTCCTGATGAGATATAGAGAAGTGGATTAA
326 CCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAACCGAATTAA
* *
14197 AACGAGTGAGACGATCATCTTTCTGATAAGATATAGAGAAGTATACCAAATCAATGAAACAAACT
391 AACAAGTGAGACGATCATCTCTCTGATAAGATATAGAGAAGTATACCAAATCAATGAAACAAACT
* * * * *
14262 CAATAGGAGTGAAACTTCGAGCCCCAGCTTCTTAATGAGATACTGAGAAGTAGGTCGAAGCAATA
456 CAATAGGAGCGAAACATCGAGCCCCAACTTCCTAATGAGATACTGAGAAGCAGGTCGAAGCAATA
* * *
14327 AAATGATCATCTTCCTG
521 AAAGGATCAGCTTCCTA
* *
14344 ATGAGATACAGAGAAGTATACCAAATCAATGAAACAAAGTTCAAAATGAGCGAAACTTCTAGCCC
1 ATGAGATACAGAGAAGTATACCAAATCAATGAAACAAAGCTCAAAATGAGCGAAACTTCGAGCCC
* * * * * * * *
14409 CAACTTCCTGATGAGATACTGAGAAGCAGTTTGAAGCAATAAAATGGTTAGCTTCTTGATGAGAT
66 CAACTTCCTAATGAGATACTGAGAAGCAGGTCGAAGCAATAAAA-AGTCAACTTCCTAATGAGAT
* * *
14474 ATAGAGAAGTGGACCAAATTCATCTTCCTGATGAGATACAGAGAAGCAGATTAAAACAAGTGAGA
130 ACAGAGAAGTGAACCAAATTCATCTTCCTAATGA-ATACAGAGAAGCAGATTAAAACAAGTGAGA
* * *
14539 C-GATCATCTTCCTGATGAGACACAGAGAATTATACCAAATCAACGAAACAAAGCTCAATATGAA
194 CTG-TCATCTTCCTGATGAGACACAGAGAAGTATACCAAATCAACAAAACAAAGC-AAATATGAA
** *
14603 CGAAACTTTG-AGTCTCAACTTCCTGATGAGATACTAAGAGGCAAGTCGAAGCAATAAAAT-AGT
257 CGAAACTTTGAACCCT-AACTTCCTGATGAGATACTAAGAAGCAAGTCGAAGCAATAAAATGA-T
* * *
14666 TAGCTTTCTGATGAGATA-TAGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAACC
320 CAGCTTCCTGATGAGATACT-GAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAACC
* * *
14730 GAATTGAAACAAGTGATG-CGGTCATCTACT-TGATGAGATATAGAGAAGTATACCAAATCAATG
384 GAATTAAAACAAGTGA-GACGATCATCT-CTCTGATAAGATATAGAGAAGTATACCAAATCAATG
* * * *
14793 AAACAAAGCTCAATATGAGCGAAACATCGAGTCTCAACTTCCTGATGAGATACTGAGAAGCAGGT
447 AAACAAA-CTCAATAGGAGCGAAACATCGAGCCCCAACTTCCTAATGAGATACTGAGAAGCAGGT
*
14858 CGAAGCAAT-AAAGGGTCAGCTTCCTA
511 CGAAGCAATAAAAGGATCAGCTTCCTA
14884 ATGAGATACAGAGAAGTGA-ACCAAAT
1 ATGAGATACAGAGAAGT-ATACCAAAT
14910 TCGTCTTCTT
Statistics
Matches: 491, Mismatches: 64, Indels: 19
0.86 0.11 0.03
Matches are distributed among these distances:
537 99 0.20
538 45 0.09
539 77 0.16
540 210 0.43
541 60 0.12
ACGTcount: A:0.39, C:0.17, G:0.21, T:0.23
Consensus pattern (537 bp):
ATGAGATACAGAGAAGTATACCAAATCAATGAAACAAAGCTCAAAATGAGCGAAACTTCGAGCCC
CAACTTCCTAATGAGATACTGAGAAGCAGGTCGAAGCAATAAAAAGTCAACTTCCTAATGAGATA
CAGAGAAGTGAACCAAATTCATCTTCCTAATGAATACAGAGAAGCAGATTAAAACAAGTGAGACT
GTCATCTTCCTGATGAGACACAGAGAAGTATACCAAATCAACAAAACAAAGCAAATATGAACGAA
ACTTTGAACCCTAACTTCCTGATGAGATACTAAGAAGCAAGTCGAAGCAATAAAATGATCAGCTT
CCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAACCGAATTAA
AACAAGTGAGACGATCATCTCTCTGATAAGATATAGAGAAGTATACCAAATCAATGAAACAAACT
CAATAGGAGCGAAACATCGAGCCCCAACTTCCTAATGAGATACTGAGAAGCAGGTCGAAGCAATA
AAAGGATCAGCTTCCTA
Found at i:15127 original size:414 final size:417
Alignment explanation
Indices: 14333--15192 Score: 1181
Period size: 414 Copynumber: 2.1 Consensus size: 417
14323 AATAAAATGA
*
14333 TCATCTTCCTGATGAGATACAGAGAAGTATACCAAATCAATGAAACAAAGTTCAAAATGAGCGAA
1 TCATCTTCCTGATGAGATACAGAGAAGTATACCAAATCAATGAAACAAAGCTCAAAATGAGCGAA
* * * * * *
14398 ACTTCTAGCCCCAACTTCCTGATGAGATACTGAGAAGCAGTTTGAAGCAATAAAATGGTTAGCTT
66 ACATCGAGCCCCAACTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAAGGGTCAGCTT
* * * * *
14463 CTTGATGAGATATAGAGAAGTGGACCAAATTCATCTTCCTGATGAGATACAGAGAAGCAGATTAA
131 CCTAATGAGATACAGAGAAGTGAACCAAATTCATCTTCCTGATAAGATACAGAGAAGCAGATTAA
* * * *
14528 AACAAGTGAGACGATCATCTTCCTGATGAGACACAGAGAATTATACCAAATCAACGAAACAAAGC
196 AACAAGTAAGACGATCATCTTACTGATGAGACACA-AGAAGTATACCAAATCAACAAAACAAAGC
* * *
14593 TCAATATGAACGAAACTTTGAGTCTCAACTTCCTGATGAGATACTAAGAGGCAAGTCGAAGCAAT
260 TCAATATGAACGAAACTTCGAGTCCCAACTTCCTGATGAGATACTAAGAAGCAAGTCGAAGCAAT
* * * *
14658 AAAATAGTTAGCTTTCTGATGAGATATAGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACA
325 AAAATAGTCAGCTTTCTGATGAGATACAAAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACA
*
14723 GAGAACC-GAATTGAAACAAGTGATGCGG
390 GAGAACCAG-ATTGAAACAAGTGAGGCGG
* * * *
14751 TCATCTACTTGATGAGATATAGAGAAGTATACCAAATCAATGAAACAAAGCTCAATATGAGCGAA
1 TCATCTTCCTGATGAGATACAGAGAAGTATACCAAATCAATGAAACAAAGCTCAAAATGAGCGAA
* *
14816 ACATCGAGTCTCAACTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAAT-AAAGGGTCAGCTT
66 ACATCGAGCCCCAACTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAAGGGTCAGCTT
* * * * *
14880 CCTAATGAGATACAGAGAAGTGAACCAAATTCGTCTTCTTGATAAGATACAGAGAAGCGGGTTGA
131 CCTAATGAGATACAGAGAAGTGAACCAAATTCATCTTCCTGATAAGATACAGAGAAGCAGATTAA
* * * * *
14945 AACAAGTAAGGCGGTCATCTTATTGATGAGATAC-A-AAGTATACCAAATCAATAAAACAAAGCT
196 AACAAGTAAGACGATCATCTTACTGATGAGACACAAGAAGTATACCAAATCAACAAAACAAAGCT
* ** * * * * *
15008 CAATGTGAGTGAAACTTCGAGTCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTTGAAGTAATA
261 CAATATGAACGAAACTTCGAGTCCCAACTTCCTGATGAGATACTAAGAAGCAAGTCGAAGCAATA
* *
15073 AAATGGTCAGC-TTCTTGATGAGATACAAAGAAGTGAACCCAATTCGTCTTCCTGATGAGATACA
326 AAATAGTCAGCTTTC-TGATGAGATACAAAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACA
* *
15137 GAGAAGCAGATTGAAACAAGTGAGGTGG
390 GAGAACCAGATTGAAACAAGTGAGGCGG
*
15165 TCATCTTCCTGATGAGATACAAAGAAGT
1 TCATCTTCCTGATGAGATACAGAGAAGT
15193 GAACCTAATT
Statistics
Matches: 384, Mismatches: 56, Indels: 8
0.86 0.12 0.02
Matches are distributed among these distances:
413 3 0.01
414 180 0.47
415 2 0.01
417 94 0.24
418 105 0.27
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (417 bp):
TCATCTTCCTGATGAGATACAGAGAAGTATACCAAATCAATGAAACAAAGCTCAAAATGAGCGAA
ACATCGAGCCCCAACTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAAGGGTCAGCTT
CCTAATGAGATACAGAGAAGTGAACCAAATTCATCTTCCTGATAAGATACAGAGAAGCAGATTAA
AACAAGTAAGACGATCATCTTACTGATGAGACACAAGAAGTATACCAAATCAACAAAACAAAGCT
CAATATGAACGAAACTTCGAGTCCCAACTTCCTGATGAGATACTAAGAAGCAAGTCGAAGCAATA
AAATAGTCAGCTTTCTGATGAGATACAAAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAG
AGAACCAGATTGAAACAAGTGAGGCGG
Found at i:15129 original size:37 final size:37
Alignment explanation
Indices: 15083--15228 Score: 121
Period size: 37 Copynumber: 3.6 Consensus size: 37
15073 AAATGGTCAG
* *
15083 CTTCTTGATGAGATACAAAGAAGTGAACCCAATTCGT
1 CTTCCTGATGAGATACAAAGAAGTGAACCAAATTCGT
* * *
15120 CTTCCTGATGAGATACAGAGAAGCAGATTGAAACAAGTGAGGTGGTCAT
1 CTTCCTGATGAGATAC--A-AAG-A-AGTGAACCAA---A--T--TCGT
*
15169 CTTCCTGATGAGATACAAAGAAGTGAACCTAATTCGT
1 CTTCCTGATGAGATACAAAGAAGTGAACCAAATTCGT
*
15206 CTTCCTGATGAGATACAGAGAAG
1 CTTCCTGATGAGATACAAAGAAG
15229 CGGATTGAAA
Statistics
Matches: 87, Mismatches: 10, Indels: 24
0.72 0.08 0.20
Matches are distributed among these distances:
37 40 0.46
39 2 0.02
40 3 0.03
41 2 0.02
42 7 0.08
44 7 0.08
45 2 0.02
46 3 0.03
47 2 0.02
49 19 0.22
ACGTcount: A:0.35, C:0.17, G:0.23, T:0.25
Consensus pattern (37 bp):
CTTCCTGATGAGATACAAAGAAGTGAACCAAATTCGT
Found at i:15197 original size:86 final size:85
Alignment explanation
Indices: 15035--15238 Score: 300
Period size: 86 Copynumber: 2.4 Consensus size: 85
15025 CGAGTCCCAG
* * ** *
15035 CTTCCTGATGAGATACTGAGAAGCAGGTTGAAGTAATAAAATGGTCAGCTTCTTGATGAGATACA
1 CTTCCTGATGAGATACAGAGAAGCAGATTGAAACAATAAAATGGTCAGCTTCCTGATGAGATACA
15100 AAGAAGTGAACCCAATTCGT
66 AAGAAGTGAACCCAATTCGT
* ** *
15120 CTTCCTGATGAGATACAGAGAAGCAGATTGAAACAAGTGAGGTGGTCATCTTCCTGATGAGATAC
1 CTTCCTGATGAGATACAGAGAAGCAGATTGAAACAA-TAAAATGGTCAGCTTCCTGATGAGATAC
*
15185 AAAGAAGTGAACCTAATTCGT
65 AAAGAAGTGAACCCAATTCGT
*
15206 CTTCCTGATGAGATACAGAGAAGCGGATTGAAA
1 CTTCCTGATGAGATACAGAGAAGCAGATTGAAA
15239 NGATGAGATA
Statistics
Matches: 107, Mismatches: 11, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
85 32 0.30
86 75 0.70
ACGTcount: A:0.35, C:0.16, G:0.25, T:0.25
Consensus pattern (85 bp):
CTTCCTGATGAGATACAGAGAAGCAGATTGAAACAATAAAATGGTCAGCTTCCTGATGAGATACA
AAGAAGTGAACCCAATTCGT
Found at i:15252 original size:28 final size:27
Alignment explanation
Indices: 15212--15266 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 27
15202 TCGTCTTCCT
*
15212 GATGAGATACAGAGAAGCGGATTGAAA
1 GATGAGATACAGAGAAGCAGATTGAAA
15239 NGATGAGATACAGAGAAGCAGATTGAAA
1 -GATGAGATACAGAGAAGCAGATTGAAA
15267 CAAGTGAGGC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.45, C:0.07, G:0.31, T:0.15
Consensus pattern (27 bp):
GATGAGATACAGAGAAGCAGATTGAAA
Found at i:15835 original size:7 final size:7
Alignment explanation
Indices: 15823--15869 Score: 50
Period size: 7 Copynumber: 7.4 Consensus size: 7
15813 TTTTAAACTT
15823 ATTTTAA
1 ATTTTAA
15830 ATTTTAA
1 ATTTTAA
15837 A-TTT--
1 ATTTTAA
15841 ATTTT-A
1 ATTTTAA
*
15847 AGTTTAA
1 ATTTTAA
15854 A-TTTAA
1 ATTTTAA
15860 ATTTTAA
1 ATTTTAA
15867 ATT
1 ATT
15870 AAGTTTAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
4 1 0.03
5 3 0.09
6 13 0.37
7 18 0.51
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (7 bp):
ATTTTAA
Found at i:15836 original size:18 final size:18
Alignment explanation
Indices: 15813--15869 Score: 71
Period size: 18 Copynumber: 3.1 Consensus size: 18
15803 CAAGCCCAAT
*
15813 TTTTAAACTTATTTTAAA
1 TTTTAAATTTATTTTAAA
15831 TTTTAAATTTATTTT-AA
1 TTTTAAATTTATTTTAAA
*
15848 GTTTAAATTTAAATTTTAAA
1 TTTTAAATTT--ATTTTAAA
15868 TT
1 TT
15870 AAGTTTAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
17 11 0.33
18 14 0.42
19 5 0.15
20 3 0.09
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58
Consensus pattern (18 bp):
TTTTAAATTTATTTTAAA
Found at i:15845 original size:30 final size:30
Alignment explanation
Indices: 15813--15878 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
15803 CAAGCCCAAT
*
15813 TTTTAAACTT-ATTTTAAATTTTAAATTTA
1 TTTTAAACTTAAATTTAAATTTTAAATTTA
** *
15842 TTTTAAGTTTAAATTTAAATTTTAAATTAA
1 TTTTAAACTTAAATTTAAATTTTAAATTTA
*
15872 GTTTAAA
1 TTTTAAA
15879 AGTCCAAATA
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
29 8 0.27
30 22 0.73
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.55
Consensus pattern (30 bp):
TTTTAAACTTAAATTTAAATTTTAAATTTA
Found at i:15852 original size:24 final size:24
Alignment explanation
Indices: 15825--15878 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
15815 TTAAACTTAT
**
15825 TTTAAATTTTAAA-TTTATTTTAAG
1 TTTAAA-TTTAAATTTTAAATTAAG
15849 TTTAAATTTAAATTTTAAATTAAG
1 TTTAAATTTAAATTTTAAATTAAG
15873 TTTAAA
1 TTTAAA
15879 AGTCCAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
23 6 0.22
24 21 0.78
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.54
Consensus pattern (24 bp):
TTTAAATTTAAATTTTAAATTAAG
Found at i:16466 original size:21 final size:22
Alignment explanation
Indices: 16442--16487 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
16432 ATACGTATAT
16442 TTATTAATA-TA-TATCTATTTA
1 TTATTAATACTATTAT-TATTTA
*
16463 TTA-TATTACTATTATTATTTA
1 TTATTAATACTATTATTATTTA
16484 TTAT
1 TTAT
16488 GTTCAATCAC
Statistics
Matches: 21, Mismatches: 1, Indels: 5
0.78 0.04 0.19
Matches are distributed among these distances:
20 4 0.19
21 14 0.67
22 3 0.14
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (22 bp):
TTATTAATACTATTATTATTTA
Found at i:16478 original size:18 final size:18
Alignment explanation
Indices: 16439--16487 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 18
16429 ACTATACGTA
16439 TATTTATTA-ATATATATC
1 TATTTATTATAT-TATATC
16457 TATTTATTATATTACTAT-
1 TATTTATTATATTA-TATC
16475 TA-TTATT-TATTAT
1 TATTTATTATATTAT
16488 GTTCAATCAC
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
15 1 0.03
16 5 0.17
17 5 0.17
18 13 0.45
19 5 0.17
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (18 bp):
TATTTATTATATTATATC
Found at i:16532 original size:30 final size:30
Alignment explanation
Indices: 16496--16677 Score: 107
Period size: 30 Copynumber: 6.3 Consensus size: 30
16486 ATGTTCAATC
*
16496 ACATTTTAACCCTTAAACTTTCCAAATAA-T
1 ACATTTTAACCCCTAAACTTTCCAAA-AATT
* * *
16526 ACATTTTAACCCCCAAAATTTCTAAAAATT
1 ACATTTTAACCCCTAAACTTTCCAAAAATT
* *
16556 ACATTTTTACCCCTATAC-TTCCAAAAATT
1 ACATTTTAACCCCTAAACTTTCCAAAAATT
* *** * *
16585 GCATTTT--TTTC-ATACTTT-CAAAAATC
1 ACATTTTAACCCCTAAACTTTCCAAAAATT
*
16611 ACATTTTTA-CCCTAAAC-TTCTCAAAAATT
1 ACATTTTAACCCCTAAACTTTC-CAAAAATT
* *
16640 ACATTGTT--GCCCTCAAACTTT-CAAAAATC
1 ACATT-TTAACCCCT-AAACTTTCCAAAAATT
16669 ACCATTTTA
1 A-CATTTTA
16678 CCTCAAGCAT
Statistics
Matches: 119, Mismatches: 20, Indels: 26
0.72 0.12 0.16
Matches are distributed among these distances:
26 17 0.14
27 6 0.05
28 3 0.03
29 44 0.37
30 47 0.39
31 2 0.02
ACGTcount: A:0.37, C:0.24, G:0.02, T:0.37
Consensus pattern (30 bp):
ACATTTTAACCCCTAAACTTTCCAAAAATT
Found at i:16582 original size:29 final size:29
Alignment explanation
Indices: 16496--16676 Score: 113
Period size: 29 Copynumber: 6.2 Consensus size: 29
16486 ATGTTCAATC
* *
16496 ACATTTTAACCCTTAAACTTTCCAAATAA-T
1 ACATTTTTACCCCTAAAC-TTCCAAA-AATT
* * * *
16526 ACATTTTAACCCCCAAAATTTCTAAAAATT
1 ACATTTTTA-CCCCTAAACTTCCAAAAATT
*
16556 ACATTTTTACCCCTATACTTCCAAAAATT
1 ACATTTTTACCCCTAAACTTCCAAAAATT
* ** * * *
16585 GCATTTTT--TTC-ATACTTTCAAAAATC
1 ACATTTTTACCCCTAAACTTCCAAAAATT
16611 ACATTTTTA-CCCTAAACTTCTCAAAAATT
1 ACATTTTTACCCCTAAACTTC-CAAAAATT
* * * *
16640 ACATTGTT-GCCCTCAAACTTTCAAAAATC
1 ACATTTTTACCCCT-AAACTTCCAAAAATT
16669 ACCATTTT
1 A-CATTTT
16677 ACCTCAAGCA
Statistics
Matches: 119, Mismatches: 24, Indels: 16
0.75 0.15 0.10
Matches are distributed among these distances:
26 20 0.17
27 2 0.02
28 5 0.04
29 51 0.43
30 35 0.29
31 6 0.05
ACGTcount: A:0.36, C:0.24, G:0.02, T:0.38
Consensus pattern (29 bp):
ACATTTTTACCCCTAAACTTCCAAAAATT
Found at i:16718 original size:28 final size:29
Alignment explanation
Indices: 16615--16721 Score: 78
Period size: 28 Copynumber: 3.8 Consensus size: 29
16605 AAAATCACAT
* *
16615 TTTTACCCT-AAACTTCTCAAAAA-TTACA
1 TTTTACCCTCAACCTTC-CAAAAATTTCCA
* * * **
16643 TTGTTGCCCTCAAACTTTCAAAAATCACCA
1 TT-TTACCCTCAACCTTCCAAAAATTTCCA
* *
16673 TTTTA-CCTCAAGCATCCAAAAATTTCCA
1 TTTTACCCTCAACCTTCCAAAAATTTCCA
*
16701 TTTTACCCTCAA-TTTCCAAAA
1 TTTTACCCTCAACCTTCCAAAA
16722 GTTCGATTTT
Statistics
Matches: 62, Mismatches: 13, Indels: 8
0.75 0.16 0.10
Matches are distributed among these distances:
28 32 0.52
29 20 0.32
30 10 0.16
ACGTcount: A:0.36, C:0.28, G:0.03, T:0.34
Consensus pattern (29 bp):
TTTTACCCTCAACCTTCCAAAAATTTCCA
Done.