Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005123.1 Hibiscus syriacus cultivar Beakdansim tig00011522_pilon, 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: 68205
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:2545 original size:179 final size:181
Alignment explanation
Indices: 2199--3341 Score: 1575
Period size: 179 Copynumber: 6.4 Consensus size: 181
2189 TGTCGGTTTA
* * * * * *
2199 TGTCGATACTTTA-AAAAATGTATCAATCCACATCAATATAACAGGAAAAAATATGACAAAACCG
1 TGTCGATTCTTTATAAATATGTATCGATCCACAACGATATAACAGGTAAAAATATGACAAAACCG
* * ** * * *
2263 ATCACGAAAAGACAAGACCAATAAAGCGCTACCGAATATATTGC-AGTGTCGATACTTTAATATA
66 GTCAGGAAAAGACAA-ACCGGTAAAGAGATACCGGATATATTGCAAGTGTCGATACTTTAATATA
* *
2327 AGTATCGACACATAGTGAATTTAAAGGTGAAAT-AGTTTTAGCGCCTATAAAG
130 AGTATCGACACATTGTGAATTTAAAGGAG-AATCAGTTTTAGCGCCTATAAAG
* *
2379 TGTCGATTCTTTATAAATATGTATCGATCCTCAACGATATAACAGGTAAAAACATGACAAAACCG
1 TGTCGATTCTTTATAAATATGTATCGATCCACAACGATATAACAGGTAAAAATATGACAAAACCG
*
2444 GTCAGGAAAAGAC-AACC-GTAAAGAGATACCGGATATATTGCAAGTGTCGATAGTTTAATATAA
66 GTCAGGAAAAGACAAACCGGTAAAGAGATACCGGATATATTGCAAGTGTCGATACTTTAATATAA
* * *
2507 GTACCAACACATTGTGAATTTAAAGGAGAATCAGTTTTAACGCCTATAAAG
131 GTATCGACACATTGTGAATTTAAAGGAGAATCAGTTTTAGCGCCTATAAAG
2558 TGTCGATTCTTTATAAATATGTATCGAT-C-CAACGATATAACAGGTAAAAATATGACAAAACCG
1 TGTCGATTCTTTATAAATATGTATCGATCCACAACGATATAACAGGTAAAAATATGACAAAACCG
* **
2621 GTCAGGAAAAGATAAAACCGGTAAAGA-ATACCATATATATTGCAAGTGTCGATACTTTAATATA
66 GTCAGGAAAAGA-CAAACCGGTAAAGAGATACCGGATATATTGCAAGTGTCGATACTTTAATATA
* * * *
2685 AGTATCGACACTTTGTGAATTTAAAGGAGAAGCAGTTTTAGCTCCTAGAAAG
130 AGTATCGACACATTGTGAATTTAAAGGAGAATCAGTTTTAGCGCCTATAAAG
* * *
2737 TGTTGATTCTTTATAAATATGTATCGACCCACAACGATATAACAGGTAAAAATATGACAAAACCA
1 TGTCGATTCTTTATAAATATGTATCGATCCACAACGATATAACAGGTAAAAATATGACAAAACCG
* *
2802 GTCAGGAAAAGATAAAACC-GTAAAGAGATACTGGATATATTGCAAGTGTCGATACTTTAATATA
66 GTCAGGAAAAGA-CAAACCGGTAAAGAGATACCGGATATATTGCAAGTGTCGATACTTTAATATA
* *
2866 AGTATCGACACATTGTGAATTTAAAGGAGAAGCAGTTTTAGCGCCTAGAAAG
130 AGTATCGACACATTGTGAATTTAAAGGAGAATCAGTTTTAGCGCCTATAAAG
*
2918 TGTCGATTCTTTAT-AA-AT-TATCGATCCACAACGATATAACATGTAAAAATATGACAAAACCG
1 TGTCGATTCTTTATAAATATGTATCGATCCACAACGATATAACAGGTAAAAATATGACAAAACCG
* *
2980 GTTAGGAAAAGACAAAACCGGTAAAGAGATACTGGATATATTGCAAGTGTCGATACTTTAATATA
66 GTCAGGAAAAGAC-AAACCGGTAAAGAGATACCGGATATATTGCAAGTGTCGATACTTTAATATA
* *
3045 AGTATCGACACATTGTGAATTTAAAGGAGAAACAGTTTTAGTGCCTATAAAG
130 AGTATCGACACATTGTGAATTTAAAGGAGAATCAGTTTTAGCGCCTATAAAG
*
3097 TGTCGATTC-TTAT-AA-ATGTATCGATCCACAACGATATAACAGGTAAAAATATGATAAAACCG
1 TGTCGATTCTTTATAAATATGTATCGATCCACAACGATATAACAGGTAAAAATATGACAAAACCG
** * * * * * *
3159 GTCTTGAAAAGACAAAACTGGTAAAGAGCTACCGGATACATTGAAAGTGCCGATAATTTAATATA
66 GTCAGGAAAAGAC-AAACCGGTAAAGAGATACCGGATATATTGCAAGTGTCGATACTTTAATATA
* * * *
3224 AGTATCGACAC-TTGTGAATTTAAAAGAGAAGT--TTTTTAGCACCTTTAAAG
130 AGTATCGACACATTGTGAATTTAAAGGAGAA-TCAGTTTTAGCGCCTATAAAG
* * * * *
3274 TGTCGATACTTTATAAAAATGTATCGATCCATAACGATATAACGGGTAAAAATATGATAAAACCG
1 TGTCGATTCTTTATAAATATGTATCGATCCACAACGATATAACAGGTAAAAATATGACAAAACCG
3339 GTC
66 GTC
3342 TTTAAATAAC
Statistics
Matches: 877, Mismatches: 70, Indels: 32
0.90 0.07 0.03
Matches are distributed among these distances:
177 67 0.08
178 111 0.13
179 417 0.48
180 78 0.09
181 204 0.23
ACGTcount: A:0.41, C:0.15, G:0.17, T:0.27
Consensus pattern (181 bp):
TGTCGATTCTTTATAAATATGTATCGATCCACAACGATATAACAGGTAAAAATATGACAAAACCG
GTCAGGAAAAGACAAACCGGTAAAGAGATACCGGATATATTGCAAGTGTCGATACTTTAATATAA
GTATCGACACATTGTGAATTTAAAGGAGAATCAGTTTTAGCGCCTATAAAG
Found at i:3233 original size:539 final size:537
Alignment explanation
Indices: 2199--3338 Score: 1650
Period size: 539 Copynumber: 2.1 Consensus size: 537
2189 TGTCGGTTTA
* * * *
2199 TGTCGATACTTTA-AAAAATGTATCAATCCACATCAATATAACAGGAAAAAATATGACAAAACCG
1 TGTCGATACTTTATAAAAATGTATCGATCCACAACGATATAACAGGTAAAAATATGACAAAACCG
* * *
2263 ATCACGAAAAGACAAGACCAATAAAGCGCTACCGAATATATTGCAGTGTCGATACTTTAATATAA
66 ATCACGAAAAGACAAAACCAATAAAGAGATACCGAATATATTGCAGTGTCGATACTTTAATATAA
* * *
2328 GTATCGACACATAGTGAATTTAAAGGTGAAATAGTTTTAGCGCCTATAAAGTGTCGATTCTTTAT
131 GTATCGACACATAGTGAATTTAAAGGAGAAACAGTTTTAGCGCCTAGAAAGTGTCGATTCTTTAT
*
2393 AAATATGTATCGATCCTCAACGATATAACAGGTAAAAACATGACAAAACCGGTCAGGAAAAGACA
196 AAATATGTATCGATCCACAACGATATAACAGGTAAAAACATGACAAAACCGGTCAGGAAAAGACA
*
2458 ACCGTAAAGAGATACCGGATATATTGCAAGTGTCGATAGTTTAATATAAGTACCAACACATTGTG
261 ACCGTAAAGAGATACCGGATATATTGCAAGTGTCGATACTTTAATATAAGTACCAACACATTGTG
*
2523 AATTTAAAGGAGAATCAGTTTTAACGCCTATAAAGTGTCGATTCTTTATAAATATGTATCGATCC
326 AATTTAAAGGAGAAACAGTTTTAACGCCTATAAAGTGTCGATTCTTTATAAATATGTATCGATCC
*
2588 AACGATATAACAGGTAAAAATATGACAAAACCGGTCAGGAAAAGATAAAACCGGTAAAGAATACC
391 AACGATATAACAGGTAAAAATATGACAAAACCGGTCAGGAAAAGACAAAACCGGTAAAGAATACC
* * * * * *
2653 ATATATATTGCAAGTGTCGATACTTTAATATAAGTATCGACACTTTGTGAATTTAAAGGAGAAGC
456 AGATACATTGAAAGTGCCGATAATTTAATATAAGTATCGACAC-TTGTGAATTTAAAAGAGAAG-
*
2718 AGTTTTAGCTCCTAGAAAG
519 AGTTTTAGCACCTAGAAAG
* * * *
2737 TGTTGATTCTTTATAAATATGTATCGACCCACAACGATATAACAGGTAAAAATATGACAAAACC-
1 TGTCGATACTTTATAAAAATGTATCGATCCACAACGATATAACAGGTAAAAATATGACAAAACCG
* * * * *
2801 AGTCAGGAAAAGATAAAACC-GTAAAGAGATACTGGATATATTGCAAGTGTCGATACTTTAATAT
66 A-TCACGAAAAGACAAAACCAATAAAGAGATACCGAATATATTGC-AGTGTCGATACTTTAATAT
* *
2865 AAGTATCGACACATTGTGAATTTAAAGGAGAAGCAGTTTTAGCGCCTAGAAAGTGTCGATTCTTT
129 AAGTATCGACACATAGTGAATTTAAAGGAGAAACAGTTTTAGCGCCTAGAAAGTGTCGATTCTTT
* * *
2930 AT-AA-AT-TATCGATCCACAACGATATAACATGTAAAAATATGACAAAACCGGTTAGGAAAAGA
194 ATAAATATGTATCGATCCACAACGATATAACAGGTAAAAACATGACAAAACCGGTCAGGAAAAGA
* * *
2992 CAAAACCGGTAAAGAGATACTGGATATATTGCAAGTGTCGATACTTTAATATAAGTATCGACACA
259 C--AACC-GTAAAGAGATACCGGATATATTGCAAGTGTCGATACTTTAATATAAGTACCAACACA
**
3057 TTGTGAATTTAAAGGAGAAACAGTTTTAGTGCCTATAAAGTGTCGATTC-TTAT-AA-ATGTATC
321 TTGTGAATTTAAAGGAGAAACAGTTTTAACGCCTATAAAGTGTCGATTCTTTATAAATATGTATC
* ** *
3119 GATCCACAACGATATAACAGGTAAAAATATGATAAAACCGGTCTTGAAAAGACAAAACTGGTAAA
386 GAT-C-CAACGATATAACAGGTAAAAATATGACAAAACCGGTCAGGAAAAGACAAAACCGGTAAA
* *
3184 GAGCTACCGGATACATTGAAAGTGCCGATAATTTAATATAAGTATCGACACTTGTGAATTTAAAA
449 GA-ATACCAGATACATTGAAAGTGCCGATAATTTAATATAAGTATCGACACTTGTGAATTTAAAA
** **
3249 GAGAAGTTTTTTAGCACCTTTAAAG
513 GAGAAGAGTTTTAGCACCTAGAAAG
* * *
3274 TGTCGATACTTTATAAAAATGTATCGATCCATAACGATATAACGGGTAAAAATATGATAAAACCG
1 TGTCGATACTTTATAAAAATGTATCGATCCACAACGATATAACAGGTAAAAATATGACAAAACCG
3339 GTCTTTAAAT
Statistics
Matches: 535, Mismatches: 57, Indels: 20
0.87 0.09 0.03
Matches are distributed among these distances:
536 63 0.12
537 76 0.14
538 116 0.22
539 280 0.52
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.27
Consensus pattern (537 bp):
TGTCGATACTTTATAAAAATGTATCGATCCACAACGATATAACAGGTAAAAATATGACAAAACCG
ATCACGAAAAGACAAAACCAATAAAGAGATACCGAATATATTGCAGTGTCGATACTTTAATATAA
GTATCGACACATAGTGAATTTAAAGGAGAAACAGTTTTAGCGCCTAGAAAGTGTCGATTCTTTAT
AAATATGTATCGATCCACAACGATATAACAGGTAAAAACATGACAAAACCGGTCAGGAAAAGACA
ACCGTAAAGAGATACCGGATATATTGCAAGTGTCGATACTTTAATATAAGTACCAACACATTGTG
AATTTAAAGGAGAAACAGTTTTAACGCCTATAAAGTGTCGATTCTTTATAAATATGTATCGATCC
AACGATATAACAGGTAAAAATATGACAAAACCGGTCAGGAAAAGACAAAACCGGTAAAGAATACC
AGATACATTGAAAGTGCCGATAATTTAATATAAGTATCGACACTTGTGAATTTAAAAGAGAAGAG
TTTTAGCACCTAGAAAG
Found at i:15067 original size:30 final size:30
Alignment explanation
Indices: 15031--15108 Score: 79
Period size: 30 Copynumber: 2.6 Consensus size: 30
15021 ATGCATAAGT
* * *
15031 TAAAGTTTAAGGACTTGTTT-AGGTGCAAAC
1 TAAAGTTTAAGGACTTATTTGA-ATACAAAC
*
15061 TAAAGTTTATAGG-CTTATTTGAATACAAAT
1 TAAAGTTTA-AGGACTTATTTGAATACAAAC
*
15091 TAAAGTTTAAGGATTTAT
1 TAAAGTTTAAGGACTTAT
15109 CTAAAAACAA
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
29 3 0.08
30 33 0.82
31 4 0.10
ACGTcount: A:0.37, C:0.06, G:0.18, T:0.38
Consensus pattern (30 bp):
TAAAGTTTAAGGACTTATTTGAATACAAAC
Found at i:15404 original size:18 final size:18
Alignment explanation
Indices: 15378--15412 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
15368 TTTAAAAAGA
*
15378 AAACACAAATTTTGAAAT
1 AAACACAAACTTTGAAAT
*
15396 AAACCCAAACTTTGAAA
1 AAACACAAACTTTGAAA
15413 ACCTTCATTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.17, G:0.06, T:0.23
Consensus pattern (18 bp):
AAACACAAACTTTGAAAT
Found at i:17890 original size:28 final size:30
Alignment explanation
Indices: 17833--17894 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 30
17823 AAAAATATTT
17833 TATACTATTTAAATATTTTCATTATCTTTA
1 TATACTATTTAAATATTTTCATTATCTTTA
*
17863 TATA-TATTTGAAATATTTTTATT-T-TTTA
1 TATACTATTT-AAATATTTTCATTATCTTTA
17891 TATA
1 TATA
17895 ATTAGATAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
28 8 0.27
29 6 0.20
30 16 0.53
ACGTcount: A:0.34, C:0.05, G:0.02, T:0.60
Consensus pattern (30 bp):
TATACTATTTAAATATTTTCATTATCTTTA
Found at i:19618 original size:29 final size:28
Alignment explanation
Indices: 19575--19685 Score: 80
Period size: 29 Copynumber: 3.8 Consensus size: 28
19565 CTAATTAAAA
19575 GGACTAAGATGGTAAAAAACTAAAGTCTAG
1 GGACTAAG-T-GTAAAAAACTAAAGTCTAG
* *
19605 GGACTAAAGTGTAAAAGATCTAAATTCTAAG
1 GGACT-AAGTGTAAAA-AACTAAAGTCT-AG
* * * * *
19636 GGTCTATGTGTCAAAATA-TAAAGTATAA
1 GGACTAAGTGT-AAAAAACTAAAGTCTAG
*
19664 GGACCTAAGTGTAAAAATCTAA
1 GGA-CTAAGTGTAAAAAACTAA
19686 TCCTATAGGG
Statistics
Matches: 62, Mismatches: 13, Indels: 13
0.70 0.15 0.15
Matches are distributed among these distances:
28 7 0.11
29 22 0.35
30 20 0.32
31 13 0.21
ACGTcount: A:0.45, C:0.10, G:0.20, T:0.25
Consensus pattern (28 bp):
GGACTAAGTGTAAAAAACTAAAGTCTAG
Found at i:20181 original size:32 final size:31
Alignment explanation
Indices: 20141--20202 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 31
20131 AGCTAATTTT
20141 AAATAAGGA-TAAAATTGAAATAAAATAAATA
1 AAATAAGGACT-AAATTGAAATAAAATAAATA
* *
20172 AAATCAAGGACTAAATTGTAATTAAATAAAT
1 AAAT-AAGGACTAAATTGAAATAAAATAAAT
20203 CAATTTTGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
31 4 0.15
32 22 0.81
33 1 0.04
ACGTcount: A:0.61, C:0.03, G:0.10, T:0.26
Consensus pattern (31 bp):
AAATAAGGACTAAATTGAAATAAAATAAATA
Found at i:24655 original size:30 final size:30
Alignment explanation
Indices: 24621--24678 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 30
24611 CCCCTAATTA
24621 ATGGACT-AAGATGGTAAAA-ATCTAAAGTAT
1 ATGGACTAAAG-T-GTAAAAGATCTAAAGTAT
24651 ATGGACTAAAGTGTAAAAGATCTAAAGT
1 ATGGACTAAAGTGTAAAAGATCTAAAGT
24679 GTAAGGGCCT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
29 6 0.23
30 17 0.65
31 3 0.12
ACGTcount: A:0.47, C:0.07, G:0.21, T:0.26
Consensus pattern (30 bp):
ATGGACTAAAGTGTAAAAGATCTAAAGTAT
Found at i:24718 original size:29 final size:29
Alignment explanation
Indices: 24634--24729 Score: 106
Period size: 29 Copynumber: 3.3 Consensus size: 29
24624 GACTAAGATG
*
24634 GTAAAAATCTAAAGTATATGGA-CTAAAGT
1 GTAAAAATCTAAAGTATAGGGACCT-AAGT
* *
24663 GTAAAAGATCTAAAGTGTAAGGG-CCTAACT
1 GTAAAA-ATCTAAAGTAT-AGGGACCTAAGT
*
24693 GTAAAAATCTAAAGTCTAGGGACCTAAGT
1 GTAAAAATCTAAAGTATAGGGACCTAAGT
*
24722 ATAAAAAT
1 GTAAAAAT
24730 GTAATCCTAG
Statistics
Matches: 57, Mismatches: 6, Indels: 8
0.80 0.08 0.11
Matches are distributed among these distances:
28 4 0.07
29 29 0.51
30 19 0.33
31 5 0.09
ACGTcount: A:0.46, C:0.10, G:0.19, T:0.25
Consensus pattern (29 bp):
GTAAAAATCTAAAGTATAGGGACCTAAGT
Found at i:25207 original size:32 final size:31
Alignment explanation
Indices: 25161--25222 Score: 97
Period size: 32 Copynumber: 2.0 Consensus size: 31
25151 AGCTAATTTT
*
25161 AAATAAGGATAAAATTGGAATTAAATAAATA
1 AAATAAGGACAAAATTGGAATTAAATAAATA
*
25192 AAATCAAGGACAAAATTGTAATTAAATAAAT
1 AAAT-AAGGACAAAATTGGAATTAAATAAAT
25223 CAATTTTAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
31 4 0.14
32 24 0.86
ACGTcount: A:0.60, C:0.03, G:0.11, T:0.26
Consensus pattern (31 bp):
AAATAAGGACAAAATTGGAATTAAATAAATA
Found at i:25938 original size:44 final size:44
Alignment explanation
Indices: 25889--25979 Score: 173
Period size: 44 Copynumber: 2.1 Consensus size: 44
25879 CCTCGGCTTC
*
25889 TGAGGCTCCTACCGCCATCGTCCACCGTCAGATTGACTCTGTTT
1 TGAGGCTCCTACCGCCATCGTCCACCGTCAGATTGACTCTCTTT
25933 TGAGGCTCCTACCGCCATCGTCCACCGTCAGATTGACTCTCTTT
1 TGAGGCTCCTACCGCCATCGTCCACCGTCAGATTGACTCTCTTT
25977 TGA
1 TGA
25980 CAATTCAGGT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.16, C:0.34, G:0.20, T:0.30
Consensus pattern (44 bp):
TGAGGCTCCTACCGCCATCGTCCACCGTCAGATTGACTCTCTTT
Found at i:26521 original size:12 final size:11
Alignment explanation
Indices: 26498--26541 Score: 52
Period size: 12 Copynumber: 3.8 Consensus size: 11
26488 ATGTATTTTG
*
26498 TAATATAATAA
1 TAATAAAATAA
26509 TAATAACAATAA
1 TAATAA-AATAA
26521 TAATAAAATAAA
1 TAATAAAAT-AA
*
26533 TAAAAAAAT
1 TAATAAAAT
26542 GGTGATTTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
11 8 0.28
12 21 0.72
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.27
Consensus pattern (11 bp):
TAATAAAATAA
Found at i:28693 original size:2 final size:2
Alignment explanation
Indices: 28686--28765 Score: 160
Period size: 2 Copynumber: 40.0 Consensus size: 2
28676 TTGGTTTGTA
28686 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28728 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28766 TATTATTATT
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 78 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:30011 original size:2 final size:2
Alignment explanation
Indices: 30006--30049 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
29996 AAGATTCTTT
30006 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
30048 TA
1 TA
30050 CAGAATTAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:30686 original size:184 final size:186
Alignment explanation
Indices: 30465--30841 Score: 580
Period size: 184 Copynumber: 2.0 Consensus size: 186
30455 TATAAAAATT
* *
30465 AAATGTTTTTAACTCAAAAAAAAGTTTATAATTAATTTAAATAATATATAATTATAAAATAAAAA
1 AAAT-TTTTTAACTCAAAAAAAAGTTTACAATTAATTTAAATAACATATAATTATAAAATAAAAA
* * *
30530 TTTCAGATAATTTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTGGATCTT-AAATT
65 TTTCAGATAAATTTTTTAATTAACTAATATTGATTTAGGTTTAAAAGTTATTAGATCTTAAAATT
*
30594 ATTAATTGGGTTTTAAATAGTTTGGACTGAG-TCCATATGTTATATATAATATATTTA
130 ATTAATTGAGTTTTAAATAGTTTGGACTGAGCT-CATATGTTATATATAATATATTTA
* * *
30651 ATATTTTTTAA-TTAAAAAATAGTTTACAATTAATTTAAATAACATATAATTATAAAATAAAAAT
1 AAATTTTTTAACTCAAAAAAAAGTTTACAATTAATTTAAATAACATATAATTATAAAATAAAAAT
* *
30715 TTTATATAAATTTTTTAATTAACTAATATTGATTTAGGTTTAAAAGTTATTAGATCTTAAAATTA
66 TTCAGATAAATTTTTTAATTAACTAATATTGATTTAGGTTTAAAAGTTATTAGATCTTAAAATTA
* * **
30780 TTCATTGAGTTTTAAATGGTTTGGGTTGAGCTCATATGTTATATATAATATATTTA
131 TTAATTGAGTTTTAAATAGTTTGGACTGAGCTCATATGTTATATATAATATATTTA
30836 AAATTT
1 AAATTT
30842 AAAATTTAAT
Statistics
Matches: 173, Mismatches: 16, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
184 102 0.59
185 67 0.39
186 4 0.02
ACGTcount: A:0.42, C:0.04, G:0.09, T:0.45
Consensus pattern (186 bp):
AAATTTTTTAACTCAAAAAAAAGTTTACAATTAATTTAAATAACATATAATTATAAAATAAAAAT
TTCAGATAAATTTTTTAATTAACTAATATTGATTTAGGTTTAAAAGTTATTAGATCTTAAAATTA
TTAATTGAGTTTTAAATAGTTTGGACTGAGCTCATATGTTATATATAATATATTTA
Found at i:31102 original size:14 final size:14
Alignment explanation
Indices: 31083--31113 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
31073 TTAGATTTAT
31083 GGAGGACCCAGAAA
1 GGAGGACCCAGAAA
31097 GGAGGACCCAGAAA
1 GGAGGACCCAGAAA
31111 GGA
1 GGA
31114 CAACCCTGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.42, C:0.19, G:0.39, T:0.00
Consensus pattern (14 bp):
GGAGGACCCAGAAA
Found at i:31119 original size:14 final size:14
Alignment explanation
Indices: 31088--31126 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
31078 TTTATGGAGG
**
31088 ACCCAGAAAGGAGG
1 ACCCAGAAAGGACA
31102 ACCCAGAAAGGACA
1 ACCCAGAAAGGACA
*
31116 ACCCTGAAAGG
1 ACCCAGAAAGG
31127 TGATGATAAT
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:0.44, C:0.26, G:0.28, T:0.03
Consensus pattern (14 bp):
ACCCAGAAAGGACA
Found at i:37584 original size:2 final size:2
Alignment explanation
Indices: 37577--37614 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
37567 GATGCATAAC
37577 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
37615 CTTTTTTCTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39071 original size:21 final size:21
Alignment explanation
Indices: 39018--39076 Score: 61
Period size: 20 Copynumber: 2.9 Consensus size: 21
39008 AAAACTTATT
39018 AAAATATTATTT-AATA-TTCC
1 AAAATATT-TTTCAATATTTCC
* *
39038 AAAATCATATTTCAATATTTTC
1 AAAAT-ATTTTTCAATATTTCC
39060 AAAATATTTTTC-ATATT
1 AAAATATTTTTCAATATT
39077 AAATTTCAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
20 13 0.39
21 12 0.36
22 8 0.24
ACGTcount: A:0.42, C:0.10, G:0.00, T:0.47
Consensus pattern (21 bp):
AAAATATTTTTCAATATTTCC
Found at i:42335 original size:20 final size:20
Alignment explanation
Indices: 42310--42367 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 20
42300 GAAGGTTCTT
42310 GGTATCGATACTCCACATAG
1 GGTATCGATACTCCACATAG
*
42330 GGTATCGATACTCCACCTAG
1 GGTATCGATACTCCACATAG
* *
42350 GGTAACGATACTCAACAT
1 GGTATCGATACTCCACAT
42368 CAAATTTTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.31, C:0.26, G:0.19, T:0.24
Consensus pattern (20 bp):
GGTATCGATACTCCACATAG
Found at i:62364 original size:43 final size:43
Alignment explanation
Indices: 62315--62407 Score: 186
Period size: 43 Copynumber: 2.2 Consensus size: 43
62305 GTAAAACTCA
62315 AAAGGAAGTTTTGTCATTTTTAACTCGATCGTCGCTTATAAAT
1 AAAGGAAGTTTTGTCATTTTTAACTCGATCGTCGCTTATAAAT
62358 AAAGGAAGTTTTGTCATTTTTAACTCGATCGTCGCTTATAAAT
1 AAAGGAAGTTTTGTCATTTTTAACTCGATCGTCGCTTATAAAT
62401 AAAGGAA
1 AAAGGAA
62408 ATACATAATA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 50 1.00
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (43 bp):
AAAGGAAGTTTTGTCATTTTTAACTCGATCGTCGCTTATAAAT
Found at i:67037 original size:3 final size:3
Alignment explanation
Indices: 67031--67075 Score: 69
Period size: 3 Copynumber: 16.0 Consensus size: 3
67021 TAATTAGTTT
67031 TAA TAA TAA TAA TAA TAA T-A TAA TAA T-A TAA TAA TAA T-A TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
67076 AAAATAGAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
2 6 0.15
3 33 0.85
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:67055 original size:11 final size:11
Alignment explanation
Indices: 67031--67075 Score: 65
Period size: 11 Copynumber: 4.0 Consensus size: 11
67021 TAATTAGTTT
67031 TAATAATAATAA
1 TAAT-ATAATAA
67043 TAATA-ATATAA
1 TAATATA-ATAA
67054 TAATATAATAA
1 TAATATAATAA
67065 TAATATAATAA
1 TAATATAATAA
67076 AAAATAGAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
10 1 0.03
11 25 0.81
12 5 0.16
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (11 bp):
TAATATAATAA
Found at i:67075 original size:8 final size:8
Alignment explanation
Indices: 67033--67066 Score: 59
Period size: 8 Copynumber: 4.1 Consensus size: 8
67023 ATTAGTTTTA
67033 ATAATAAT
1 ATAATAAT
67041 AATAATAAT
1 -ATAATAAT
67050 ATAATAAT
1 ATAATAAT
67058 ATAATAAT
1 ATAATAAT
67066 A
1 A
67067 ATATAATAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 17 0.68
9 8 0.32
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (8 bp):
ATAATAAT
Found at i:68011 original size:217 final size:218
Alignment explanation
Indices: 67633--68081 Score: 749
Period size: 216 Copynumber: 2.1 Consensus size: 218
67623 AAACATCCTA
*
67633 CCCGGAGGTCTTATCATCTTGCTCAAAAGGCTTACAGATGACCCGGAGGATTTAAACATCAAGAA
1 CCCGGAGGTCTTATCATCTTGCTCAAAAGGCTTACAGATGACCCAGAGGATTTAAACATCAAGAA
* *
67698 ACCTTGAAAATCAAGCTTAGTTCTTGGTTATCAATGAACCCATTCAAAGGCTTAGCTTTCTTTAA
66 ACCTTGAAAATCAAGCTTAGTTCTTGGTTATCAAGGAACCCATTCAAAGGCTTAGCTTCCTTTAA
67763 CAACTCTTTGAGATAATTAAGAAACCCCTGAAAGGC-AGTTTCCAAAA-ATCATTTGAAAACATC
131 CAACTCTTTGAGATAATTAAGAAACCCCTGAAAGGCTAGTTTCCAAAATATCATTTGAAAACATC
* *
67826 CTTCCCGGAGGTCTTATGGATGG
196 CTGCCCAGAGGTCTTATGGATGG
* ** *
67849 CTCGGAGGTCTTATCATCTTGCTCGGAAGGCTTACAGTTGACCCAGAGGATTTAAACATCAAGAA
1 CCCGGAGGTCTTATCATCTTGCTCAAAAGGCTTACAGATGACCCAGAGGATTTAAACATCAAGAA
67914 ACCTTGAAAATCAAGCTTAGTTTCTTGGTTATCAAGGAACCCATTCAAAGGCTTAGCTTCCTTTA
66 ACCTTGAAAATCAAGCTTAG-TTCTTGGTTATCAAGGAACCCATTCAAAGGCTTAGCTTCCTTTA
*
67979 ACAACTCTTTGAGATAATTAAGAAACCCCTGAAAGGCTTAGTTTCCAAAATCTCATTTGAAAACA
130 ACAACTCTTTGAGATAATTAAGAAACCCCTGAAAGGC-TAGTTTCCAAAATATCATTTGAAAACA
* *
68044 TCCTGCCTAGAGGTCTTGTGGATGG
194 TCCTGCCCAGAGGTCTTATGGATGG
*
68069 CCCGGAGGACTTA
1 CCCGGAGGTCTTA
68082 AAATTAAGGA
Statistics
Matches: 215, Mismatches: 14, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
216 80 0.37
217 79 0.37
219 11 0.05
220 45 0.21
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29
Consensus pattern (218 bp):
CCCGGAGGTCTTATCATCTTGCTCAAAAGGCTTACAGATGACCCAGAGGATTTAAACATCAAGAA
ACCTTGAAAATCAAGCTTAGTTCTTGGTTATCAAGGAACCCATTCAAAGGCTTAGCTTCCTTTAA
CAACTCTTTGAGATAATTAAGAAACCCCTGAAAGGCTAGTTTCCAAAATATCATTTGAAAACATC
CTGCCCAGAGGTCTTATGGATGG
Done.