Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013799.1 Kokia drynarioides strain JFW-HI SEQ_128827, 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: 52389
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.33
Warning! 5 characters in sequence are not A, C, G, or T
Found at i:614 original size:213 final size:209
Alignment explanation
Indices: 1--1534 Score: 1273
Period size: 216 Copynumber: 7.3 Consensus size: 209
* * *
1 GTCTTTAAATTTAAAACTTATTTACGTGAGAATTGTTTCTCTCTCTTTGCTTTTGGATGAACTTC
1 GTCTTTAAA-TTAAAACTTATTTACGTGAGAATTG--T-T-TCTC-TTGGTTGTGGACGAACTT-
* * *
66 CAAACTTTTCAAACTTTTACGAGTTCTTTTATAATTTCGGTTCCTTAAAGTATTCAAGACGATCC
59 CGAACTTTTCAAACTTTTACGAGTTCTTTTATAACTT-GGTTCCTTACAGTATTCAAGACGATCC
* * * *
131 ATTCCTTTGAAG-AATTTTTGAACATTCCATTCTCGGGAAATCACATCATTTAGTCTAAATAGTT
123 ATTCCTTCG-AGCAATTTCTGAACATTCCATGCTCGGGAAATCGCATCATTTAGTCTAAATAGTT
* * **
195 TTTAATTTTGTAAATGAGTTTTG
187 TGTCATTTTGTAAACAAGTTTTG
* * ** * * * *
218 ATCATTAAAACAAGAACATATTTTCCTGAGAATT-TTT-TCTTGGCTTTTGGACGAACTTCTGAA
1 GTCTTTAAATTAA-AACTTATTTACGTGAGAATTGTTTCTCTTGG-TTGTGGACGAACTTC-GAA
* *
281 CTTTTCAAACTTTTACGAGTTCTTATATAACTTGGTTCCTT-CTAGTATTCAAGACTATCCATTC
63 CTTTTCAAACTTTTACGAGTTCTTTTATAACTTGGTTCCTTAC-AGTATTCAAGACGATCCATTC
* * * *
345 CATCAAGCAATTTTCTGAACATTCCATGCTCGGGAAGTCGCATCATTTGGTCTAAATAGTTTGTC
127 CTTCGAGCAA-TTTCTGAACATTCCATGCTCGGGAAATCGCATCATTTAGTCTAAATAGTTTGTC
* * *
410 ATTTTCTAAAAAACTTTTG
191 ATTTTGTAAACAAGTTTTG
* * *
429 GTCTTTGAATTAAATACTCATTTACGTGAGAATTGTTTCTCTTGGTTCGTGGACAAACTTTCGAA
1 GTCTTTAAATTAAA-ACTTATTTACGTGAGAATTGTTTCTCTTGGTT-GTGGACGAAC-TTCGAA
* * * *
494 CTTGTCAAACTTTTACAAGTTCTTTTATAAC-TGCAGTTCCTTACAGCATTCAAGACGATACATT
63 CTTTTCAAACTTTTACGAGTTCTTTTATAACTTG--GTTCCTTACAGTATTCAAGACGATCCATT
* * ** * * *
558 CCTTCGAGCAACTTTCTTAACATTCTATGCTC-TAAAAGTCGGATCATTT-TTCTAAATTGTTTG
126 CCTTCGAGCAA-TTTCTGAACATTCCATGCTCGGGAAA-TCGCATCATTTAGTCTAAATAGTTTG
*
621 TCATTTTGTAGACAAGTTTT-
189 TCATTTTGTAAACAAGTTTTG
* * * ** **** *
641 GTCTTTAAATTAAAATTTTATTTATGTGAGAATTGTTTCTCACTCTTTGTTCTTGGA---CGAAC
1 GTCTTTAAATTAAAA-CTTATTTACGTGAGAATTGTTTCTC-TTGGTTGTGGACGAACTTCGAAC
* * * *
703 -TTCCAAACTTTTACGAGTTCTTTTATAA-TTCCAGTTCCTTAAAGTGTTCAAGAAC-ATCCATT
64 TTTTCAAACTTTTACGAGTTCTTTTATAACTT--GGTTCCTTACAGTATTCAAG-ACGATCCATT
* * *
765 CCTTTC-AGCAATTT-TGAACATTCCATTCTCGGGTAATCGCATCATTTAGTCTAAATAGTTTTT
126 CC-TTCGAGCAATTTCTGAACATTCCATGCTCGGGAAATCGCATCATTTAGTCTAAATAGTTTGT
*
828 CGTTTTGTAAACAAGTTTTG
190 CATTTTGTAAACAAGTTTTG
** * * *
848 GTCTTTAAAGCGAAAACTTATTTACGTGAGAATTGTTTCTCTTGGCTGTTGGATGAACTTCCAAA
1 GTCTTTAAA-TTAAAACTTATTTACGTGAGAATTGTTTCTCTTGGTTG-TGGACGAACTT-CGAA
* * * * * *
913 CTTTTTAAACTTTTATGAGTTCTGTTATAACTTGGTTCCTTACAATAATCAAGATGATCCATTCC
63 CTTTTCAAACTTTTACGAGTTCTTTTATAACTTGGTTCCTTACAGTATTCAAGACGATCCATTCC
* * * * * *
978 TTCGAGCTATTTTTTGTACATTCCATGCTCGGGAAATCGTATAATTTTGTCTAAATAGTTTGTCA
128 TTCGAGC-AATTTCTGAACATTCCATGCTCGGGAAATCGCATCATTTAGTCTAAATAGTTTGTCA
*
1043 TTTTGT------G----A
192 TTTTGTAAACAAGTTTTG
* * * *
1051 G-C--T--A--AAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTTGACGAACTTTCGA
1 GTCTTTAAATTAAAACTTATTTACGTGAGAA-T-TGTTTCTCTTGGTT-GTGGACGAAC-TTCGA
** * ** *
1109 ACTAGTCAAACTTTTACGAGTTCTTTCATTCCTTCGGTTCCTTAAAGTATTCAAGACGATCCATT
62 ACTTTTCAAACTTTTACGAGTTCTTTTATAACTT-GGTTCCTTACAGTATTCAAGACGATCCATT
* * *
1174 CCTTCGAGCAATTTTTCGAACATTCCATGCTCGGAAAATCGCATCATTTGGTCTAAATAGTTTGT
126 CCTTCGAGCAATTTCT-GAACATTCCATGCTCGGGAAATCGCATCATTTAGTCTAAATAGTTTGT
*
1239 CATTTTGTAAA-AGGGTTTTG
190 CATTTTGTAAACA-AGTTTTG
* * * * * *
1259 TTGTTTGAATTAAAAACTTATTCACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAGCTTTCG
1 GTCTTTAAATT-AAAACTTATTTACGTGAGAATTG-TT-TCTCTTGGTT-GTGGACGAAC-TTCG
** * ** * * *
1324 AACTAGTCAAACTTTTACGAGTTCTTTCATTCCTTCGGTTACTTAAAGTATTCAAGACGATCTAT
61 AACTTTTCAAACTTTTACGAGTTCTTTTATAACTT-GGTTCCTTACAGTATTCAAGACGATCCAT
* * * * * ** * * * *
1389 TCCTTCGAGCAATTTTTTGAACACTCGATTCTTGAAAAATAGCAGCATTTGGTCTAAAGAGTTTG
125 TCCTTCGAGCAA-TTTCTGAACATTCCATGCTCGGGAAATCGCATCATTTAGTCTAAATAGTTTG
*
1454 TCATTTTGAAAACAAGTTTTG
189 TCATTTTGTAAACAAGTTTTG
* * * *
1475 GTCTTTGAATCAGAAACTTATTTAGGTGAGAATTGTTTCTCTTGGTTGTTGGACTAACTT
1 GTCTTTAAATTA-AAACTTATTTACGTGAGAATTGTTTCTCTTGGTTG-TGGACGAACTT
1535 TTGAACTTGT
Statistics
Matches: 1071, Mismatches: 179, Indels: 138
0.77 0.13 0.10
Matches are distributed among these distances:
195 20 0.02
196 1 0.00
197 52 0.05
198 89 0.08
200 1 0.00
202 1 0.00
203 1 0.00
204 1 0.00
205 23 0.02
206 37 0.03
207 92 0.09
208 14 0.01
209 2 0.00
210 41 0.04
211 166 0.15
212 74 0.07
213 133 0.12
214 83 0.08
215 6 0.01
216 204 0.19
217 30 0.03
ACGTcount: A:0.27, C:0.17, G:0.15, T:0.41
Consensus pattern (209 bp):
GTCTTTAAATTAAAACTTATTTACGTGAGAATTGTTTCTCTTGGTTGTGGACGAACTTCGAACTT
TTCAAACTTTTACGAGTTCTTTTATAACTTGGTTCCTTACAGTATTCAAGACGATCCATTCCTTC
GAGCAATTTCTGAACATTCCATGCTCGGGAAATCGCATCATTTAGTCTAAATAGTTTGTCATTTT
GTAAACAAGTTTTG
Found at i:925 original size:419 final size:412
Alignment explanation
Indices: 13--1535 Score: 1284
Period size: 419 Copynumber: 3.6 Consensus size: 412
3 CTTTAAATTT
** * * * *
13 AAAACTTATTTACGTGAGAATTGTTTCTCTCTCTTTGCTTTTGGATGAACTTCCAAACTTTTCAA
1 AAAACTTATTTACGTGAGAATTGTTTCTCT-TGGTTG---TTGGACGAACTTTCGAACTTGTCAA
* * * *
78 ACTTTTACGAGTTCTTTTATAATTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTTGAAG
62 ACTTTTACGAGTTCTTTTATAACTGC-GTTCCTTACAGTATTCAAGACGAT-CATTCCTTCG-AG
* ** * * * *
143 -AA-TTTTTGAACATTCCATTCTCGGGAAATCACATCATTTAGTCTAAATAGTTTTTAATTTTGT
124 CAATTTTTTGAACATTCCATGCTC-TAAAATCGCATCATTT-TTCTAAATAGTTTGTCATTTTGT
* ** * * * * *
206 AAATGAGTTTTGATCATTAAAACAAGAACATATTTTCCTGAGAA-T-TTT-T--TCTTGGCTT-T
187 AGACAAGTTTTG-TC-TT-TAATAA-AACTTATTTACGTGAGAATTGTTTCTCCTCTTGG-TTCT
* **
265 TGGACGAACTTCTGAACTTTTCAAACTTTTACGAGTTCTTATATAACTT-GGTTCCTTCTAGTAT
247 TGGACGAACTT-T--AC---TCAAACTTTTACGAGTTCTTTTATAA-TTCGGTTCCTTAAAGTAT
* *
329 TCAAGACTATCCATTCCATCAAGCAATTTTCTGAACATTCCATGCTCGGGAAGTCGCATCATTTG
305 TCAAGACGATCCATTCCTTCAAGCAATTTT-TGAACATTCCATGCTCGGGAA-TCGCATCATTTG
* *
394 GTCTAAATAGTTTGTCATTTTCTAAAAAACTTTTGGTCTTTGAATTA
368 GTCTAAATAGTTTGTCATTTTGT-AAAAAGTTTTGGTCTTTGAA-TA
* * *
441 AATACTCATTTACGTGAGAATTGTTTCTCTTGGTTCG-TGGACAAACTTTCGAACTTGTCAAACT
1 AAAACTTATTTACGTGAGAATTGTTTCTCTTGGTT-GTTGGACGAACTTTCGAACTTGTCAAACT
* *
505 TTTACAAGTTCTTTTATAACTGCAGTTCCTTACAGCATTCAAGACGATACATTCCTTCGAGCAAC
65 TTTACGAGTTCTTTTATAACTGC-GTTCCTTACAGTATTCAAGACGAT-CATTCCTTCGAGCAA-
* * * *
570 TTTCTT-AACATTCTATGCTCTAAAAGTCGGATCATTTTTCTAAATTGTTTGTCATTTTGTAGAC
127 TTTTTTGAACATTCCATGCTCTAAAA-TCGCATCATTTTTCTAAATAGTTTGTCATTTTGTAGAC
* * *
634 AAGTTTTGTCTTTAAATTAAAATTTTATTTATGTGAGAATTGTTTCTCACTCTTTGTTCTTGGAC
191 AAGTTTTGTCTTT-AA-TAAAA-CTTATTTACGTGAGAATTGTTTCTC-CTCTTGGTTCTTGGAC
* *
699 GAAC-TT-C-CAAACTTTTACGAGTTCTTTTATAATTCCAGTTCCTTAAAGTGTTCAAGAAC-AT
252 GAACTTTACTCAAACTTTTACGAGTTCTTTTATAATT-CGGTTCCTTAAAGTATTCAAG-ACGAT
* *
760 CCATTCCTTTC-AGCAA-TTTTGAACATTCCATTCTCGGGTAATCGCATCATTTAGTCTAAATAG
315 CCATTCC-TTCAAGCAATTTTTGAACATTCCATGCTCGGG-AATCGCATCATTTGGTCTAAATAG
* * * **
823 TTTTTCGTTTTGTAAACAAGTTTTGGTCTTTAAAGCG
378 TTTGTCATTTTGTAAA-AAGTTTTGGTCTTTGAA-TA
* * * * * *
860 AAAACTTATTTACGTGAGAATTGTTTCTCTTGGCTGTTGGATGAACTTCCAAACTTTTTAAACTT
1 AAAACTTATTTACGTGAGAATTGTTTCTCTTGGTTGTTGGACGAACTTTCGAACTTGTCAAACTT
* * * * * *
925 TTATGAGTTCTGTTATAACTTG-GTTCCTTACAATAATCAAGATGATCCATTCCTTCGAGCTATT
66 TTACGAGTTCTTTTATAAC-TGCGTTCCTTACAGTATTCAAGACGAT-CATTCCTTCGAGCAATT
* ** * *
989 TTTTGTACATTCCATGCTCGGGAAATCGTATAATTTTGTCTAAATAGTTTGTCATTTTGT-G---
129 TTTTGAACATTCCATGCTC-TAAAATCGCATCATTTT-TCTAAATAGTTTGTCATTTTGTAGACA
*
1050 A-----G-C--T-A-AAAACTTATTTACGTGAGAATTGTTTCT-CTCTTGGTTCTTTGACGAACT
192 AGTTTTGTCTTTAATAAAACTTATTTACGTGAGAATTGTTTCTCCTCTTGGTTCTTGGACGAACT
* **
1104 TTCGAACTAGTCAAACTTTTACGAGTTCTTTCATTCCTTCGGTTCCTTAAAGTATTCAAGACGAT
257 TT---AC---TCAAACTTTTACGAGTTCTTTTA-TAATTCGGTTCCTTAAAGTATTCAAGACGAT
* *
1169 CCATTCCTTCGAGCAATTTTTCGAACATTCCATGCTCGGAAAATCGCATCATTTGGTCTAAATAG
315 CCATTCCTTCAAGCAATTTTT-GAACATTCCATGCTCGG-GAATCGCATCATTTGGTCTAAATAG
* * *
1234 TTTGTCATTTTGTAAAAGGGTTTTGTTGTTTGAATTA
378 TTTGTCATTTTGTAAAA-AGTTTTGGTCTTTGAA-TA
* * * *
1271 AAAACTTATTCACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAGCTTTCGAACTAGTCAAAC
1 AAAACTTATTTACGTGAGAATTG-TT-TCTCTTGGTTGTTGGACGAACTTTCGAACTTGTCAAAC
* ** * * *
1336 TTTTACGAGTTCTTTCATTCCTTCGGTTACTTAAAGTATTCAAGACGATCTATTCCTTCGAGCAA
64 TTTTACGAGTTCTTTTATAACTGC-GTTCCTTACAGTATTCAAGACGATC-ATTCCTTCGAGCAA
* * * * * * * * *
1401 TTTTTTGAACACTCGATTCT-TGAAAAATAGCAGCATTTGGTCTAAAGAGTTTGTCATTTTGAAA
127 TTTTTTGAACATTCCATGCTCT--AAAATCGCATCATTT-TTCTAAATAGTTTGTCATTTTGTAG
* *
1465 ACAAGTTTTGGTCTTTGAATCAGAAACTTATTTAGGTGAGAATTG-TT-T-CTCTTGGTTGTTGG
189 ACAAGTTTT-GTCTTT-AAT-A-AAACTTATTTACGTGAGAATTGTTTCTCCTCTTGGTTCTTGG
*
1527 ACTAACTTT
250 ACGAACTTT
1536 TGAACTTGTC
Statistics
Matches: 885, Mismatches: 142, Indels: 134
0.76 0.12 0.12
Matches are distributed among these distances:
400 18 0.02
401 2 0.00
402 22 0.02
403 4 0.00
405 2 0.00
407 1 0.00
408 5 0.01
409 55 0.06
410 9 0.01
411 87 0.10
412 3 0.00
413 46 0.05
414 78 0.09
415 1 0.00
417 5 0.01
418 62 0.07
419 160 0.18
420 31 0.04
421 30 0.03
422 10 0.01
423 17 0.02
424 109 0.12
425 25 0.03
426 5 0.01
427 5 0.01
428 32 0.04
429 16 0.02
430 21 0.02
431 3 0.00
432 21 0.02
ACGTcount: A:0.27, C:0.17, G:0.15, T:0.41
Consensus pattern (412 bp):
AAAACTTATTTACGTGAGAATTGTTTCTCTTGGTTGTTGGACGAACTTTCGAACTTGTCAAACTT
TTACGAGTTCTTTTATAACTGCGTTCCTTACAGTATTCAAGACGATCATTCCTTCGAGCAATTTT
TTGAACATTCCATGCTCTAAAATCGCATCATTTTTCTAAATAGTTTGTCATTTTGTAGACAAGTT
TTGTCTTTAATAAAACTTATTTACGTGAGAATTGTTTCTCCTCTTGGTTCTTGGACGAACTTTAC
TCAAACTTTTACGAGTTCTTTTATAATTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCA
AGCAATTTTTGAACATTCCATGCTCGGGAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGT
AAAAAGTTTTGGTCTTTGAATA
Found at i:1677 original size:55 final size:55
Alignment explanation
Indices: 1604--1766 Score: 188
Period size: 55 Copynumber: 3.0 Consensus size: 55
1594 AGCTGAAATG
* * * *
1604 GCTTTATGCTCTAACCGAGGA-GTAAGCAGACTAAAGCTTTACTTGAGCTATAATA
1 GCTTTATGCTCTAACCGA-GATGTAAGCAGACCAAAGCTCTACCTAAGCTATAATA
* *
1659 GCTTTACGCTCTAACCGAGATGTAAGCAGTCCAAAGCTCTACCTAAGCTATAATA
1 GCTTTATGCTCTAACCGAGATGTAAGCAGACCAAAGCTCTACCTAAGCTATAATA
* * * *
1714 TCTTTATGCTCTAACC-ATGATGTAAGCCA-ACCAAAGTTCTACCCAAGATATAA
1 GCTTTATGCTCTAACCGA-GATGTAAG-CAGACCAAAGCTCTACCTAAGCTATAA
1767 ACAGGTCAAA
Statistics
Matches: 93, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
54 3 0.03
55 88 0.95
56 2 0.02
ACGTcount: A:0.34, C:0.23, G:0.16, T:0.28
Consensus pattern (55 bp):
GCTTTATGCTCTAACCGAGATGTAAGCAGACCAAAGCTCTACCTAAGCTATAATA
Found at i:1860 original size:27 final size:28
Alignment explanation
Indices: 1745--1876 Score: 146
Period size: 28 Copynumber: 4.8 Consensus size: 28
1735 GTAAGCCAAC
* *
1745 CAAAGTTCTACCCAAGATATAAACAGGT
1 CAAAGTTCTACCCAAGCTATAAACAGAT
*
1773 CAAACCTT-TACCCAAGCTATAAACA-AGT
1 CAAA-GTTCTACCCAAGCTATAAACAGA-T
**
1801 CAAACCTCTACCTC-AGCTATAAACAGAT
1 CAAAGTTCTACC-CAAGCTATAAACAGAT
*
1829 CAAAGTTCTACCCGAGCTAT-AACAGAT
1 CAAAGTTCTACCCAAGCTATAAACAGAT
*
1856 CAAAGTTCTACCCGAGCTATA
1 CAAAGTTCTACCCAAGCTATA
1877 TTAAAGTATC
Statistics
Matches: 91, Mismatches: 6, Indels: 14
0.82 0.05 0.13
Matches are distributed among these distances:
27 30 0.33
28 57 0.63
29 4 0.04
ACGTcount: A:0.39, C:0.27, G:0.11, T:0.22
Consensus pattern (28 bp):
CAAAGTTCTACCCAAGCTATAAACAGAT
Found at i:4953 original size:6 final size:6
Alignment explanation
Indices: 4942--4971 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
4932 ACCCCGAGAG
*
4942 TGAAGA TGAAGA TGAAAA TGAAGA TGAAGA
1 TGAAGA TGAAGA TGAAGA TGAAGA TGAAGA
4972 GGATGCCATG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.53, C:0.00, G:0.30, T:0.17
Consensus pattern (6 bp):
TGAAGA
Found at i:9972 original size:34 final size:34
Alignment explanation
Indices: 9923--9987 Score: 112
Period size: 34 Copynumber: 1.9 Consensus size: 34
9913 GCTAAATAGA
* *
9923 AATTTTTTTTTTGGATCCAAAATTAAAACACAAT
1 AATTTTATTTATGGATCCAAAATTAAAACACAAT
9957 AATTTTATTTATGGATCCAAAATTAAAACAC
1 AATTTTATTTATGGATCCAAAATTAAAACAC
9988 TCAATTTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.43, C:0.12, G:0.06, T:0.38
Consensus pattern (34 bp):
AATTTTATTTATGGATCCAAAATTAAAACACAAT
Found at i:10433 original size:125 final size:124
Alignment explanation
Indices: 10205--10455 Score: 355
Period size: 125 Copynumber: 2.0 Consensus size: 124
10195 CTAAGACAGC
** * **
10205 GCTTAAATAAGAGTTGGCTTTGTTCAACACTATGCCGACACTTTTGGGGTGACACTTTCCTAAGT
1 GCTTAAATAAGAGTCAGCTTTGTCCAACACTATGCCGACACTTTTGGGCCGACACTTTCCTAAGT
* * *
10270 GTTGGCATAGACTTGCCGACATACGCTTTTGCCCACTCTTTTGTATAAGGGTTGGGATAT
66 GTTGGCATAGACTTGCAGACATACGCTTTGGCCAACTC-TTTGTATAAGGGTTGGGATAT
*
10330 GCTTAAATAAGAGTCAGCTTTGTCCATCACTATAG-CGACACTTTTGGGCCGACACTTTCCTAAG
1 GCTTAAATAAGAGTCAGCTTTGTCCAACACTAT-GCCGACACTTTTGGGCCGACACTTTCCTAAG
*
10394 TGTTAGG-ATAGATTTGTCAG-CATACGCTTTGGCCAACTCTTTGTATAAGGGTTGGGATAT
65 TGTT-GGCATAGACTTG-CAGACATACGCTTTGGCCAACTCTTTGTATAAGGGTTGGGATAT
10454 GC
1 GC
10456 GTGCCTAAGG
Statistics
Matches: 113, Mismatches: 10, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
124 23 0.20
125 85 0.75
126 5 0.04
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.33
Consensus pattern (124 bp):
GCTTAAATAAGAGTCAGCTTTGTCCAACACTATGCCGACACTTTTGGGCCGACACTTTCCTAAGT
GTTGGCATAGACTTGCAGACATACGCTTTGGCCAACTCTTTGTATAAGGGTTGGGATAT
Found at i:10563 original size:38 final size:37
Alignment explanation
Indices: 10504--10910 Score: 491
Period size: 36 Copynumber: 11.2 Consensus size: 37
10494 CAACACTACG
*
10504 CCAACCTTTTT-AAGGTTGCCTTAGAGAAGGTCTATC
1 CCAACCTTTTTAAAGGTTGCCTTAGACAAGGTCTATC
*
10540 CTAACCTTTTTAAAAGGTTGCCTTAGACAAGGTCTATC
1 CCAACCTTTTT-AAAGGTTGCCTTAGACAAGGTCTATC
*
10578 CCAACCTTTTTAAA-GTTTCCTTAGACAAGGTCTATC
1 CCAACCTTTTTAAAGGTTGCCTTAGACAAGGTCTATC
* **
10614 CTAACCTTTTTAAA-GTTTTCTTAGACAAGGTCTATC
1 CCAACCTTTTTAAAGGTTGCCTTAGACAAGGTCTATC
* * * * *
10650 CCAACCTTCTTTAAAGGTTGCCTCAAATAACGTCTATA
1 CCAACCTT-TTTAAAGGTTGCCTTAGACAAGGTCTATC
* * *
10688 CCAACCTTTTTTAAAGGTTGCCTCAAACAAGGCCTATC
1 CCAACC-TTTTTAAAGGTTGCCTTAGACAAGGTCTATC
10726 CCAACCTTTTT-AAGGTTGCCTTAGACAAGGTCTATC
1 CCAACCTTTTTAAAGGTTGCCTTAGACAAGGTCTATC
*
10762 ACAACC-TTTT-AAGGTTGCCTTAGAC-AGGTCTATC
1 CCAACCTTTTTAAAGGTTGCCTTAGACAAGGTCTATC
* * *
10796 CCAACATTTTTTGAAGGTTGCTTTAGAC-AGGTCTATC
1 CCAAC-CTTTTTAAAGGTTGCCTTAGACAAGGTCTATC
* *
10833 CCAACCTTTTTTAAAGGTTGCCTTAG---A-GCCTACC
1 CCAACC-TTTTTAAAGGTTGCCTTAGACAAGGTCTATC
10867 CCAACCTTTTTAAA-GTTGCCTTAGACAA-GTCTATC
1 CCAACCTTTTTAAAGGTTGCCTTAGACAAGGTCTATC
10902 CCAACCTTT
1 CCAACCTTT
10911 CAATAAAGTT
Statistics
Matches: 327, Mismatches: 32, Indels: 25
0.85 0.08 0.07
Matches are distributed among these distances:
32 10 0.03
33 8 0.02
34 24 0.07
35 35 0.11
36 103 0.31
37 59 0.18
38 86 0.26
39 2 0.01
ACGTcount: A:0.27, C:0.25, G:0.14, T:0.34
Consensus pattern (37 bp):
CCAACCTTTTTAAAGGTTGCCTTAGACAAGGTCTATC
Found at i:10582 original size:74 final size:72
Alignment explanation
Indices: 10504--10910 Score: 474
Period size: 74 Copynumber: 5.6 Consensus size: 72
10494 CAACACTACG
*
10504 CCAACCTTTTTAAGGTTGCCTTAGAGAAGGTCTATCCTAACCTTTTTAAAAGGTTGCCTTAGACA
1 CCAACCTTTTTAAGGTTGCCTTAGACAAGGTCTATCC-AACCTTTTT-AAAGGTTGCCTTAGACA
10569 AGGTCTATC
64 AGGTCTATC
* * **
10578 CCAACCTTTTTAAAGTTTCCTTAGACAAGGTCTATCCTAACCTTTTTAAA-GTTTTCTTAGACAA
1 CCAACCTTTTTAAGGTTGCCTTAGACAAGGTCTATCC-AACCTTTTTAAAGGTTGCCTTAGACAA
10642 GGTCTATC
65 GGTCTATC
* * * * * *
10650 CCAACCTTCTTTAAAGGTTGCCTCAAATAACGTCTATACCAACCTTTTTTAAAGGTTGCCTCAAA
1 CCAACCTT-TTT-AAGGTTGCCTTAGACAAGGTCTAT-CCAACC-TTTTTAAAGGTTGCCTTAGA
*
10715 CAAGGCCTATC
62 CAAGGTCTATC
10726 CCAACCTTTTTAAGGTTGCCTTAGACAAGGTCTATCACAACC-TTTT-AAGGTTGCCTTAGAC-A
1 CCAACCTTTTTAAGGTTGCCTTAGACAAGGTCTATC-CAACCTTTTTAAAGGTTGCCTTAGACAA
10788 GGTCTATC
65 GGTCTATC
* *
10796 CCAACATTTTTTGAAGGTTGCTTTAGAC-AGGTCTATCCCAACCTTTTTTAAAGGTTGCCTTAG-
1 CCAAC-CTTTTT-AAGGTTGCCTTAGACAAGGTCTAT-CCAACC-TTTTTAAAGGTTGCCTTAGA
* *
10859 --A-GCCTACC
62 CAAGGTCTATC
*
10867 CCAACCTTTTTAAAGTTGCCTTAGACAA-GTCTATCCCAACCTTT
1 CCAACCTTTTTAAGGTTGCCTTAGACAAGGTCTAT-CCAACCTTT
10911 CAATAAAGTT
Statistics
Matches: 290, Mismatches: 30, Indels: 32
0.82 0.09 0.09
Matches are distributed among these distances:
68 3 0.01
69 26 0.09
70 19 0.07
71 41 0.14
72 48 0.17
73 11 0.04
74 104 0.36
75 13 0.04
76 25 0.09
ACGTcount: A:0.27, C:0.25, G:0.14, T:0.34
Consensus pattern (72 bp):
CCAACCTTTTTAAGGTTGCCTTAGACAAGGTCTATCCAACCTTTTTAAAGGTTGCCTTAGACAAG
GTCTATC
Found at i:11656 original size:21 final size:20
Alignment explanation
Indices: 11625--11692 Score: 66
Period size: 22 Copynumber: 3.2 Consensus size: 20
11615 CATAACCTCG
11625 AACCCTAAAACCATAAATATTA
1 AACCCT-AAACCATAAATA-TA
11647 AACCCTAAACTCAT-AATCATA
1 AACCCTAAAC-CATAAAT-ATA
* *
11668 AATCCTTAAACCCTAAATATA
1 AA-CCCTAAACCATAAATATA
11689 AACC
1 AACC
11693 TTGAATCTTA
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
20 2 0.05
21 18 0.45
22 20 0.50
ACGTcount: A:0.50, C:0.26, G:0.00, T:0.24
Consensus pattern (20 bp):
AACCCTAAACCATAAATATA
Found at i:13235 original size:117 final size:119
Alignment explanation
Indices: 13083--13323 Score: 414
Period size: 117 Copynumber: 2.0 Consensus size: 119
13073 CTTTTGTGAT
13083 TTTTGGTATGGGTTGATGAATAGTGTGTTTTTAGCTGATTTGATTTTATGGGGTTTTGCTTAATT
1 TTTTGGTATGGGTTGATGAATAGTGTGTTTTTAGCTGATTTGATTTTATGGGGTTTTGCTTAATT
* *
13148 TCTCA-TTTT-GGGGGGATCTTCTATGCGAACTAAGCAAATGGATTTTTTGGCA
66 TCTCATTTTTGGGGGGGATCTTCTATGCGAACTAAGCAAAGGGATTTCTTGGCA
13200 TTTTGGTATGGGTTGATGAATAGTGTGTTTTTAGCTGATTTGATTTTATGGGGTTTTGCTTAATT
1 TTTTGGTATGGGTTGATGAATAGTGTGTTTTTAGCTGATTTGATTTTATGGGGTTTTGCTTAATT
* * *
13265 TCTCATTTTTGGGGGGGGATCTTCTTTGTGAACTAAGCGAAGGGATTTCTTGGCA
66 TCTCATTTTT-GGGGGGGATCTTCTATGCGAACTAAGCAAAGGGATTTCTTGGCA
13320 TTTT
1 TTTT
13324 TGTAGCCTTG
Statistics
Matches: 116, Mismatches: 5, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
117 70 0.60
118 4 0.03
120 42 0.36
ACGTcount: A:0.18, C:0.08, G:0.27, T:0.46
Consensus pattern (119 bp):
TTTTGGTATGGGTTGATGAATAGTGTGTTTTTAGCTGATTTGATTTTATGGGGTTTTGCTTAATT
TCTCATTTTTGGGGGGGATCTTCTATGCGAACTAAGCAAAGGGATTTCTTGGCA
Found at i:13493 original size:13 final size:14
Alignment explanation
Indices: 13475--13504 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
13465 TGACTTAGAA
13475 AAATAT-AATTACT
1 AAATATAAATTACT
13488 AAATATAAATTACT
1 AAATATAAATTACT
13502 AAA
1 AAA
13505 AATGCATGCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (14 bp):
AAATATAAATTACT
Found at i:14856 original size:32 final size:32
Alignment explanation
Indices: 14794--14856 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 32
14784 GCCATCCATA
* * **
14794 CATGTACCTAAAATATATTAATCAGTTAATTG
1 CATGTACCTAAAACACATTAATCAACTAATTG
*
14826 CATGTACCTGAAACACATTAATCAACTAATT
1 CATGTACCTAAAACACATTAATCAACTAATT
14857 AATTTCGACT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.41, C:0.17, G:0.08, T:0.33
Consensus pattern (32 bp):
CATGTACCTAAAACACATTAATCAACTAATTG
Found at i:17590 original size:39 final size:39
Alignment explanation
Indices: 17547--17645 Score: 171
Period size: 39 Copynumber: 2.5 Consensus size: 39
17537 TTAATTTGTC
* *
17547 TCAAACTTAGACACCTTAAAAACAACTATTAAATATGTA
1 TCAAACTAAGACACATTAAAAACAACTATTAAATATGTA
*
17586 TCAAAATAAGACACATTAAAAACAACTATTAAATATGTA
1 TCAAACTAAGACACATTAAAAACAACTATTAAATATGTA
17625 TCAAACTAAGACACATTAAAA
1 TCAAACTAAGACACATTAAAA
17646 CCCTATTCGA
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 56 1.00
ACGTcount: A:0.54, C:0.16, G:0.05, T:0.25
Consensus pattern (39 bp):
TCAAACTAAGACACATTAAAAACAACTATTAAATATGTA
Found at i:18467 original size:32 final size:32
Alignment explanation
Indices: 18431--18493 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 32
18421 GCCATCCATA
* *
18431 CATGTACCTGAAATATATTAATCAGCTAATTG
1 CATGTACCTGAAACACATTAATCAGCTAATTG
* *
18463 CATGTACCTGAAACACATTAGTCATCTAATT
1 CATGTACCTGAAACACATTAATCAGCTAATT
18494 AATTTCGGCT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (32 bp):
CATGTACCTGAAACACATTAATCAGCTAATTG
Found at i:18582 original size:39 final size:39
Alignment explanation
Indices: 18539--18637 Score: 171
Period size: 39 Copynumber: 2.5 Consensus size: 39
18529 TTAATTTGTC
* *
18539 TCAAACTTAGACACCTTAAAAACAACTATTAAATATGTA
1 TCAAACTAAGACACATTAAAAACAACTATTAAATATGTA
*
18578 TCAAAATAAGACACATTAAAAACAACTATTAAATATGTA
1 TCAAACTAAGACACATTAAAAACAACTATTAAATATGTA
18617 TCAAACTAAGACACATTAAAA
1 TCAAACTAAGACACATTAAAA
18638 CCCTATTCGA
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 56 1.00
ACGTcount: A:0.54, C:0.16, G:0.05, T:0.25
Consensus pattern (39 bp):
TCAAACTAAGACACATTAAAAACAACTATTAAATATGTA
Found at i:18918 original size:992 final size:990
Alignment explanation
Indices: 16994--18978 Score: 3422
Period size: 992 Copynumber: 2.0 Consensus size: 990
16984 AATAGACACT
* *
16994 TAGGGAACCGAATGGGCAGCATGTGTTCAGCTTAATGGAGCTGGAAACTTCCTTGAACCTTCTCT
1 TAGGGAACCGAATGGGCAGCATGTGTTCAGCTTAATAGAGCTGAAAACTTCCTTGAACCTTCTCT
17059 AGCATTGGTGATGCCATTAGACAAGTCCCTTGATGTTTCCAATCAACTTAAATTAAATGAAATTA
66 AGCATTGGTGATGCCATTAGACAAGTCCCTTGATGTTTCCAATCAACTT--ATTAAATGAAATTA
* *
17124 AGTAAGGAGCTGAATGGAGCTGAATGGACTAGGCTAGGCCAAGAGGTGTGAAAGGCTTTTAAGGG
129 AGTAAGGAGCTGAATGGAGCTAAATGGACTAGGCTAGGCCAAGAGGTGTGAAAGGATTTTAAGGG
17189 GCTGCCTTGAATATTTGGAGAGTCTTGGACTTTAAATGGCAGCATGGGACACTTCAACAGCCTTA
194 GCTGCCTTGAATATTTGGAGAGTCTTGGACTTTAAATGGCAGCATGGGACACTTCAACAGCCTTA
*
17254 GAGTGTGAACACACGAATTTGAACAGCCATGAGTGTGAAAGGAACCTCCAGCAAATGTGAAAGCA
259 GAGTGTGAACACACGAATTTGAACAGCCATGAGTGTGAAAGGAACCTCCAGCAAATGGGAAAGCA
* **
17319 CTTAAGCAGCTAATTGGACAGCTTTGGGGAGACAAATCAGCACCTCAATGGCTCTTGGCATACAC
324 CTTAAGCAGCTAAATGGACAGCTTTGGAAAGACAAATCAGCACCTCAATGGCTCTTGGCATACAC
17384 GAAGAGATGCTTGGAGCATTTCAATCAACAGCACACCATATTCAAGCCATCCATACATGTACCTG
389 GAAGAGATGCTTGGAGCATTTCAATCAACAGCACACCATATTCAAGCCATCCATACATGTACCTG
* * *
17449 AAATATATTAATCAGCTAATTGCATGTACCTGAAACACATTAATCARCTWATTAATTTCRGCTAG
454 AAATATATTAATCAGCTAATTGCATGTACCTGAAACACATTAATCATCTAATTAATTTCGGCTAG
**
17514 GACATATTAATTCAAACATGARRTTAATTTGTCTCAAACTTAGACACCTTAAAAACAACTATTAA
519 GACATATTAATTCAAACATGAAATTAATTTGTCTCAAACTTAGACACCTTAAAAACAACTATTAA
17579 ATATGTATCAAAATAAGACACATTAAAAACAACTATTAAATATGTATCAAACTAAGACACATTAA
584 ATATGTATCAAAATAAGACACATTAAAAACAACTATTAAATATGTATCAAACTAAGACACATTAA
17644 AACCCTATTCGATAAAAATGTCCAGATTATGACACATTTAATAACTTAAACTAAATAACTAAATT
649 AACCCTATTCGATAAAAATGTCCAGATTATGACACATTTAATAACTTAAACTAAATAACTAAATT
*
17709 AACTAAAACAAATTAAATATTTATTCCAACAAAATAATGCTAAGTTAAAAATGAGCTGAAGTTGA
714 AACTAAAACAAATTAAATATTTATTCCAACAAAATAATGCTAAGTTAAAAACGAGCTGAAGTTGA
* * * *
17774 GTTCAATGAGCTACGAATGAGCTAGATGAACTTGTAGGAGGTTGCAAGGCCGAATTAGTTTACTT
779 GTTCAATAAGCTACGAAAGAGCTAAATGAACTTGTAGGAGGTTGCAAGGCCGAATTAGTTGACTT
* * *
17839 GTCCAAGATTGATCGATAAGCCCCACAATAGTTTCTCCCCACGCTCGATCAATTAGAGCCGAAAC
844 GTCCAAGATTGATCAATAAGCCCCACAACAGTTTCTCCCCACACTCGATCAATTAGAGCCGAAAC
* * * * *
17904 AGGCCCCTTGAAACGTTTGGCTCGTGCTTGAGTTATAGGTCCTAGGGGTAGCTTCAAAGGTTCCT
909 AGACCCCTTGAAACGTTTGGCTCGTGCTCGAGTTATAGGTCCTAAGGGCAGCTCCAAAGGTTCCT
17969 TGTTAGCACTTGGTGAG
974 TGTTAGCACTTGGTGAG
17986 TAGGGAACCGAATGGGCAGCATGTGTTCAGCTTAATAGAGCTGAAAACTTCCTTGAACCTTCTCT
1 TAGGGAACCGAATGGGCAGCATGTGTTCAGCTTAATAGAGCTGAAAACTTCCTTGAACCTTCTCT
* *
18051 AGCATT-GTGATGCCATTAGATAAGTCCCTTGATGTTTCCAATCAGC-T-TTAAATGAAATTAAG
66 AGCATTGGTGATGCCATTAGACAAGTCCCTTGATGTTTCCAATCAACTTATTAAATGAAATTAAG
18113 TAAGGAGCTGAATGGAGCTAAATGGACTAGGCTAGATTCAGCCAAGAGGTGTGAAAGGATTTTAA
131 TAAGGAGCTGAATGGAGCTAAATGGACTAGGCTAG-----GCCAAGAGGTGTGAAAGGATTTTAA
**
18178 GGGGCTGCCTTGAATATTTGGAGAGTCTTGGACTTTAAATGGCAGTTTGGGACACTTCAACAGCC
191 GGGGCTGCCTTGAATATTTGGAGAGTCTTGGACTTTAAATGGCAGCATGGGACACTTCAACAGCC
* * * *
18243 TTGGAGTGTGAACACATGAATTTGAAC-GACCATGAGTGTGTAAGGAACCTCCAGTAAATGGGAA
256 TTAGAGTGTGAACACACGAATTTGAACAG-CCATGAGTGTGAAAGGAACCTCCAGCAAATGGGAA
*
18307 AGCACTTAAGCAGCTAAATGGACAGCTTTGGAAAGACAAATCAGCAGCTCAATGGCTCTTGGCAT
320 AGCACTTAAGCAGCTAAATGGACAGCTTTGGAAAGACAAATCAGCACCTCAATGGCTCTTGGCAT
18372 ACACGAAGAGATGCTTGGAGCATTTCAATCAACAGCACACCATATTCAAGCCATCCATACATGTA
385 ACACGAAGAGATGCTTGGAGCATTTCAATCAACAGCACACCATATTCAAGCCATCCATACATGTA
*
18437 CCTGAAATATATTAATCAGCTAATTGCATGTACCTGAAACACATTAGTCATCTAATTAATTTCGG
450 CCTGAAATATATTAATCAGCTAATTGCATGTACCTGAAACACATTAATCATCTAATTAATTTCGG
*
18502 CTAGGACATATTAATTCGAACATGAAATTAATTTGTCTCAAACTTAGACACCTTAAAAACAACTA
515 CTAGGACATATTAATTCAAACATGAAATTAATTTGTCTCAAACTTAGACACCTTAAAAACAACTA
18567 TTAAATATGTATCAAAATAAGACACATTAAAAACAACTATTAAATATGTATCAAACTAAGACACA
580 TTAAATATGTATCAAAATAAGACACATTAAAAACAACTATTAAATATGTATCAAACTAAGACACA
18632 TTAAAACCCTATTCGATAAAAATGTCCAGATTATGACACATTTAATAACTTAAACTAAATAACTA
645 TTAAAACCCTATTCGATAAAAATGTCCAGATTATGACACATTTAATAACTTAAACTAAATAACTA
* *
18697 AATTAACTAAAACAAATTAAATATTTATTCCAGCGAAATAATGCTAAGTTAAAAACGAGCTGAAG
710 AATTAACTAAAACAAATTAAATATTTATTCCAACAAAATAATGCTAAGTTAAAAACGAGCTGAAG
* * *
18762 TTGAGTTCAATAAGCTACGAAAGATCTAAATGAACTTGTAGGAGGTTGCAAGGTCGACTTAGTTG
775 TTGAGTTCAATAAGCTACGAAAGAGCTAAATGAACTTGTAGGAGGTTGCAAGGCCGAATTAGTTG
* *
18827 ACTTGTCCAAGATTGATCAATAAGCCCCGCAACGGTTTCTCCCCACACTCGATCAATTAGAGCCG
840 ACTTGTCCAAGATTGATCAATAAGCCCCACAACAGTTTCTCCCCACACTCGATCAATTAGAGCCG
* * *
18892 AAACA-ACCTTCTTGAAACGTTTGGCTCGTGCTCGATTTATAGGTCTTAAGGGCAGCTCCAAAGG
905 AAACAGACC-CCTTGAAACGTTTGGCTCGTGCTCGAGTTATAGGTCCTAAGGGCAGCTCCAAAGG
*
18956 TTCCTTGTTAGGACTTGGTGAG
969 TTCCTTGTTAGCACTTGGTGAG
18978 T
1 T
18979 CTCAGACTGT
Statistics
Matches: 938, Mismatches: 48, Indels: 14
0.94 0.05 0.01
Matches are distributed among these distances:
987 49 0.05
990 1 0.00
991 41 0.04
992 847 0.90
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.27
Consensus pattern (990 bp):
TAGGGAACCGAATGGGCAGCATGTGTTCAGCTTAATAGAGCTGAAAACTTCCTTGAACCTTCTCT
AGCATTGGTGATGCCATTAGACAAGTCCCTTGATGTTTCCAATCAACTTATTAAATGAAATTAAG
TAAGGAGCTGAATGGAGCTAAATGGACTAGGCTAGGCCAAGAGGTGTGAAAGGATTTTAAGGGGC
TGCCTTGAATATTTGGAGAGTCTTGGACTTTAAATGGCAGCATGGGACACTTCAACAGCCTTAGA
GTGTGAACACACGAATTTGAACAGCCATGAGTGTGAAAGGAACCTCCAGCAAATGGGAAAGCACT
TAAGCAGCTAAATGGACAGCTTTGGAAAGACAAATCAGCACCTCAATGGCTCTTGGCATACACGA
AGAGATGCTTGGAGCATTTCAATCAACAGCACACCATATTCAAGCCATCCATACATGTACCTGAA
ATATATTAATCAGCTAATTGCATGTACCTGAAACACATTAATCATCTAATTAATTTCGGCTAGGA
CATATTAATTCAAACATGAAATTAATTTGTCTCAAACTTAGACACCTTAAAAACAACTATTAAAT
ATGTATCAAAATAAGACACATTAAAAACAACTATTAAATATGTATCAAACTAAGACACATTAAAA
CCCTATTCGATAAAAATGTCCAGATTATGACACATTTAATAACTTAAACTAAATAACTAAATTAA
CTAAAACAAATTAAATATTTATTCCAACAAAATAATGCTAAGTTAAAAACGAGCTGAAGTTGAGT
TCAATAAGCTACGAAAGAGCTAAATGAACTTGTAGGAGGTTGCAAGGCCGAATTAGTTGACTTGT
CCAAGATTGATCAATAAGCCCCACAACAGTTTCTCCCCACACTCGATCAATTAGAGCCGAAACAG
ACCCCTTGAAACGTTTGGCTCGTGCTCGAGTTATAGGTCCTAAGGGCAGCTCCAAAGGTTCCTTG
TTAGCACTTGGTGAG
Found at i:21227 original size:12 final size:12
Alignment explanation
Indices: 21210--21235 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
21200 AGTTTCTCAC
21210 TAAAGTATGCAA
1 TAAAGTATGCAA
21222 TAAAGTATGCAA
1 TAAAGTATGCAA
21234 TA
1 TA
21236 GGCCTCCCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.08, G:0.15, T:0.27
Consensus pattern (12 bp):
TAAAGTATGCAA
Found at i:25821 original size:38 final size:39
Alignment explanation
Indices: 25779--25876 Score: 135
Period size: 39 Copynumber: 2.5 Consensus size: 39
25769 TTAATTTCTC
* *
25779 TCAAACTTAGACACCTTAAAAA-AACTATTAAATATGTA
1 TCAAACTAAGACACATTAAAAACAACTATTAAATATGTA
* **
25817 TCAAAATAAGGGACATTAAAAACAACTATTAAATATGTA
1 TCAAACTAAGACACATTAAAAACAACTATTAAATATGTA
*
25856 TCAAACTAAGACACGTTAAAA
1 TCAAACTAAGACACATTAAAA
25877 CCCTATTTAA
Statistics
Matches: 50, Mismatches: 9, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
38 17 0.34
39 33 0.66
ACGTcount: A:0.52, C:0.14, G:0.08, T:0.26
Consensus pattern (39 bp):
TCAAACTAAGACACATTAAAAACAACTATTAAATATGTA
Found at i:28528 original size:48 final size:48
Alignment explanation
Indices: 28474--28586 Score: 145
Period size: 48 Copynumber: 2.4 Consensus size: 48
28464 ATTTAACAAA
* * * *
28474 GCATTTAACAAACAAAACAGTTAATAATGCAGATTACTAAACCAAGAT
1 GCATTTAACAAAAAAAACACTTAATAATGCAAATTACTAAACAAAGAT
* * *
28522 GCATTTAACAAAGAAAACACTTAATGATGCAAATTATTAAACAAAGAT
1 GCATTTAACAAAAAAAACACTTAATAATGCAAATTACTAAACAAAGAT
* *
28570 GTATTTAGCAAAAAAAA
1 GCATTTAACAAAAAAAA
28587 AAAAAAACAC
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
48 56 1.00
ACGTcount: A:0.52, C:0.13, G:0.11, T:0.24
Consensus pattern (48 bp):
GCATTTAACAAAAAAAACACTTAATAATGCAAATTACTAAACAAAGAT
Found at i:31649 original size:26 final size:25
Alignment explanation
Indices: 31594--31650 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 25
31584 CTCATGTTTT
31594 TCTCTTTTTATTTTGTTTTTACCTCAC
1 TCTCTTTTTATTTTGTTTTTA-C-CAC
31621 TCTC-TTTTATTTTTGTTTTT-CCAC
1 TCTCTTTTTA-TTTTGTTTTTACCAC
31645 TCTCTT
1 TCTCTT
31651 CCTTTAAACG
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
24 7 0.25
25 2 0.07
26 5 0.18
27 14 0.50
ACGTcount: A:0.09, C:0.23, G:0.04, T:0.65
Consensus pattern (25 bp):
TCTCTTTTTATTTTGTTTTTACCAC
Found at i:34924 original size:48 final size:48
Alignment explanation
Indices: 34864--34982 Score: 175
Period size: 48 Copynumber: 2.5 Consensus size: 48
34854 TTAACAAAGA
* *
34864 ATTTAACAAACAAAACAGTTAATAATGTAGATTACTAAACAAAGATGC
1 ATTTAACAAACAAAACACTTAATAATGCAGATTACTAAACAAAGATGC
* * * *
34912 ATTTAACAAACAAAACACTTAGTGATGCAGATTATTAAACAAAGATTC
1 ATTTAACAAACAAAACACTTAATAATGCAGATTACTAAACAAAGATGC
*
34960 ATTTAACAAAAAAAACACTTAAT
1 ATTTAACAAACAAAACACTTAAT
34983 GAAGCATAAA
Statistics
Matches: 63, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 63 1.00
ACGTcount: A:0.52, C:0.13, G:0.08, T:0.26
Consensus pattern (48 bp):
ATTTAACAAACAAAACACTTAATAATGCAGATTACTAAACAAAGATGC
Found at i:35769 original size:26 final size:26
Alignment explanation
Indices: 35740--35841 Score: 141
Period size: 26 Copynumber: 3.9 Consensus size: 26
35730 GATAAGAGTG
* * *
35740 TATTCTGTCTAAGCTTGTATGAGCGT
1 TATTCTGTCTGAGCTTGTAAGAGCAT
35766 TATTCTGTCTGAGCTTGTAAGAGCAT
1 TATTCTGTCTGAGCTTGTAAGAGCAT
* *
35792 TATTCTATATGAGCTTGTAAGAGCAT
1 TATTCTGTCTGAGCTTGTAAGAGCAT
* *
35818 TATTCTGTCTGGGCTCGTAAGAGC
1 TATTCTGTCTGAGCTTGTAAGAGC
35842 TAAACTTTGT
Statistics
Matches: 67, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 67 1.00
ACGTcount: A:0.23, C:0.16, G:0.24, T:0.38
Consensus pattern (26 bp):
TATTCTGTCTGAGCTTGTAAGAGCAT
Found at i:38903 original size:25 final size:25
Alignment explanation
Indices: 38678--38902 Score: 272
Period size: 25 Copynumber: 9.0 Consensus size: 25
38668 ACAAAGTTTA
38678 GCTCTTACGAGCCTAGATAGAATATC
1 GCTCTTACGAGCC-AGATAGAATATC
*
38704 GCTCTTACGAGCCAGTTAGAATATC
1 GCTCTTACGAGCCAGATAGAATATC
* * *
38729 GCTTTTACGAGCTAGATGGAATATC
1 GCTCTTACGAGCCAGATAGAATATC
*
38754 GCTCTTACGAGCCA-ATCAGAATACC
1 GCTCTTACGAGCCAGAT-AGAATATC
*
38779 GCTCTTACGAGCCAGTTAGAATATC
1 GCTCTTACGAGCCAGATAGAATATC
* * * *
38804 GCTCTTATGAGCTAGACAAAATATC
1 GCTCTTACGAGCCAGATAGAATATC
* * *
38829 ACTCTTACGAGCCAGACAGAATATT
1 GCTCTTACGAGCCAGATAGAATATC
* * * *
38854 GCTCTTACGAGCTAGACAAAATATT
1 GCTCTTACGAGCCAGATAGAATATC
38879 GCTCTTACGAGCCAGATAGAATAT
1 GCTCTTACGAGCCAGATAGAATAT
38903 TTGCTCCACC
Statistics
Matches: 170, Mismatches: 27, Indels: 5
0.84 0.13 0.02
Matches are distributed among these distances:
24 2 0.01
25 154 0.91
26 14 0.08
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.27
Consensus pattern (25 bp):
GCTCTTACGAGCCAGATAGAATATC
Found at i:43195 original size:12 final size:12
Alignment explanation
Indices: 43178--43224 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
43168 CAGGTTCAGT
43178 TTCTTCCTTCTC
1 TTCTTCCTTCTC
43190 TTCTTCCTT-TCC
1 TTCTTCCTTCT-C
* *
43202 TTCTTCTTTTTC
1 TTCTTCCTTCTC
*
43214 TTCATCCTTCT
1 TTCTTCCTTCT
43225 TTTGATCACC
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
11 1 0.03
12 27 0.93
13 1 0.03
ACGTcount: A:0.02, C:0.36, G:0.00, T:0.62
Consensus pattern (12 bp):
TTCTTCCTTCTC
Found at i:51868 original size:29 final size:29
Alignment explanation
Indices: 51822--51886 Score: 103
Period size: 29 Copynumber: 2.2 Consensus size: 29
51812 TTTTAATTCG
*
51822 AGTTTAAATCATATTGGGTTCGGGTTTCA
1 AGTTTAAATCATACTGGGTTCGGGTTTCA
*
51851 AGTTTAAATCATACTGGGTTCGGGTTTTA
1 AGTTTAAATCATACTGGGTTCGGGTTTCA
*
51880 GGTTTAA
1 AGTTTAA
51887 TTATTATTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.25, C:0.09, G:0.25, T:0.42
Consensus pattern (29 bp):
AGTTTAAATCATACTGGGTTCGGGTTTCA
Done.