Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002897.1 Hibiscus syriacus cultivar Beakdansim tig00005986_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: 131174
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
File 2 of 2
Found at i:88876 original size:19 final size:19
Alignment explanation
Indices: 88855--88890 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
88845 AATATATTTA
88855 AAAACA-ATAAAATAAATT
1 AAAACATATAAAATAAATT
88873 AAAACATATAAAATAAAT
1 AAAACATATAAAATAAAT
88891 GACTAAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.72, C:0.06, G:0.00, T:0.22
Consensus pattern (19 bp):
AAAACATATAAAATAAATT
Found at i:90248 original size:20 final size:19
Alignment explanation
Indices: 90211--90269 Score: 57
Period size: 20 Copynumber: 3.1 Consensus size: 19
90201 CCTGTAATTA
* *
90211 TATATATATTT-TTTTATT
1 TATATATATTTAATATATT
* *
90229 TATTTATTTTTAATAATATT
1 TATATATATTTAAT-ATATT
*
90249 TATATGTATTTAATATATT
1 TATATATATTTAATATATT
90268 TA
1 TA
90270 ATAATAATAG
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
18 9 0.28
19 8 0.25
20 15 0.47
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (19 bp):
TATATATATTTAATATATT
Found at i:90276 original size:3 final size:3
Alignment explanation
Indices: 90268--90378 Score: 168
Period size: 3 Copynumber: 36.7 Consensus size: 3
90258 TTAATATATT
*
90268 TAA TAA TAA TAG TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
90316 TAA TAA TAA TAA TGA TAA TAG GAA TAA TAA TAAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA
*
90362 TAT TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TA
90379 TGGATAAAAA
Statistics
Matches: 97, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
3 94 0.97
4 3 0.03
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:91129 original size:113 final size:113
Alignment explanation
Indices: 90698--92274 Score: 2443
Period size: 113 Copynumber: 14.0 Consensus size: 113
90688 GAATTATGCC
* * *
90698 AAAA-GTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
*
90762 TATGAACTTTAACTGGAAAAGCTGATCCATTAAATGATGGATTCATAT
66 TATGAACTTTAACTGGAAAAGCTGATCCATCAAATGATGGATTCATAT
90810 AAAAGGTTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 AAAAGG-TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* ** *
90875 TTATGGACTTTCTCTGGAAAAGCTGATCCATTAAATGATGGATTCATAT
65 TTATGAACTTTAACTGGAAAAGCTGATCCATCAAATGATGGATTCATAT
90924 AAAAGGTTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 AAAAGG-TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* ** *
90989 TTATGGACTTTCTCTGGAAAAGCTGATCCATTAAATGATGGATTCATAT
65 TTATGAACTTTAACTGGAAAAGCTGATCCATCAAATGATGGATTCATAT
91038 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
**
91103 TATGAACTTTAACTGGAAAAGCTGATCCATCAAATGATGGATTCAGGT
66 TATGAACTTTAACTGGAAAAGCTGATCCATCAAATGATGGATTCATAT
* *
91151 AAAAGGTTGAACAAATTCTTCTAATTATGAACTTCTCCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
*** * *
91216 TATGAACTCGGACTGGAAAAGATGATCCACCAAATGATGGATTCATAT
66 TATGAACTTTAACTGGAAAAGCTGATCCATCAAATGATGGATTCATAT
91264 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
** * * * **
91329 TATGAACTCGAACTGGAAAAGATGGTCCACCAAATGATGGATTCAGGT
66 TATGAACTTTAACTGGAAAAGCTGATCCATCAAATGATGGATTCATAT
91377 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
*
91442 TATGAACTTTAACTGGAAAAGCTGATCCATTAAATGATGGATTCATAT
66 TATGAACTTTAACTGGAAAAGCTGATCCATCAAATGATGGATTCATAT
91490 AAAAGGTTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 AAAAGG-TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* ** *
91555 TTATGGACTTTCTCTGGAAAAGCTGATCCATTAAATGATGGATTCATAT
65 TTATGAACTTTAACTGGAAAAGCTGATCCATCAAATGATGGATTCATAT
91604 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* **
91669 TATGAACTTTAACTGGAAAAGTTGATCCATCAAATGATGGATTCAGGT
66 TATGAACTTTAACTGGAAAAGCTGATCCATCAAATGATGGATTCATAT
* *
91717 AAAAGGTTGAACAAATTCTTCTAATTATGAACTTCTCCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
*** * *
91782 TATGAACTCGGACTGGAAAAGATGATCCACCAAATGATGGATTCATAT
66 TATGAACTTTAACTGGAAAAGCTGATCCATCAAATGATGGATTCATAT
91830 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
**
91895 TATGAACTTTAACTGGAAAAGCTGATCCATCAAATGATGGATTCAGGT
66 TATGAACTTTAACTGGAAAAGCTGATCCATCAAATGATGGATTCATAT
*
91943 AAAAGGTTGAACAAATTCTTCTAATTATGAACTTC-TCATTCCTTCTTCAGATGAGTTCTTCTCA
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTC-TTCCTTCTTCAGATGAGTTCTTCTCA
*** * *
92007 TTATGAACTCGGACTGGAAAAGATGATCCACCAAATGATGGATTCATAT
65 TTATGAACTTTAACTGGAAAAGCTGATCCATCAAATGATGGATTCATAT
92056 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
** * * * * *
92121 TATGAACTCGACCT--AACAATGTTGATCCATCGAATGATGAATTCA-AGCG
66 TATGAACTTTAACTGGAA-AA-GCTGATCCATCAAATGATGGATTCATA--T
92170 AAAA-GTTGAACAAATTCTTCTCATTATGAACTTCTTCTT-CTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * * **
92233 TATGAACTCTT--CCGGAAATGTTGATCCATTGAATGATGGATT
66 TATGAACT-TTAACTGGAAAAGCTGATCCATCAAATGATGGATT
92275 TGAATCTTTG
Statistics
Matches: 1368, Mismatches: 85, Indels: 25
0.93 0.06 0.02
Matches are distributed among these distances:
111 24 0.02
112 42 0.03
113 965 0.71
114 337 0.25
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.37
Consensus pattern (113 bp):
AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
TATGAACTTTAACTGGAAAAGCTGATCCATCAAATGATGGATTCATAT
Found at i:91641 original size:566 final size:566
Alignment explanation
Indices: 90698--92274 Score: 2699
Period size: 566 Copynumber: 2.8 Consensus size: 566
90688 GAATTATGCC
* * *
90698 AAAA-GTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* **
90762 TATGAACTTTAACTGGAAAAGCTGATCCATTAAATGATGGATTCATATAAAAGGTTTGAACAAAT
66 TATGAACTTTAACTGGAAAAGCTGATCCATCAAATGATGGATTCAGGTAAAAGG-TTGAACAAAT
* **
90827 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGGACTTTCTCTGG
130 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTAACTGG
90892 AAAAGCTGATCCATTAAATGATGGATTCATATAAAAGGTTTGAACAAATTCTTCTCATTATGAAC
195 AAAAGCTGATCCATTAAATGATGGATTCATATAAAAGGTTTGAACAAATTCTTCTCATTATGAAC
90957 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGGACTTTCTCTGGAAAAGCTGATCCATTA
260 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGGACTTTCTCTGGAAAAGCTGATCCATTA
91022 AATGATGGATTCATATAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA
325 AATGATGGATTCATATAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA
*
91087 GATGAGTTCTTCTCATTATGAACTTTAACTGGAAAAGCTGATCCATCAAATGATGGATTCAGGTA
390 GATGAGTTCTTCTCATTATGAACTTTAACTGGAAAAGTTGATCCATCAAATGATGGATTCAGGTA
91152 AAAGGTTGAACAAATTCTTCTAATTATGAACTTCTCCTTCCTTCTTCAGATGAGTTCTTCTCATT
455 AAAGGTTGAACAAATTCTTCTAATTATGAACTTCTCCTTCCTTCTTCAGATGAGTTCTTCTCATT
91217 ATGAACTCGGACTGGAAAAGATGATCCACCAAATGATGGATTCATAT
520 ATGAACTCGGACTGGAAAAGATGATCCACCAAATGATGGATTCATAT
91264 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
** * * *
91329 TATGAACTCGAACTGGAAAAGATGGTCCACCAAATGATGGATTCAGGTAAAAGGTTGAACAAATT
66 TATGAACTTTAACTGGAAAAGCTGATCCATCAAATGATGGATTCAGGTAAAAGGTTGAACAAATT
91394 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTAACTGGA
131 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTAACTGGA
91459 AAAGCTGATCCATTAAATGATGGATTCATATAAAAGGTTTGAACAAATTCTTCTCATTATGAACT
196 AAAGCTGATCCATTAAATGATGGATTCATATAAAAGGTTTGAACAAATTCTTCTCATTATGAACT
91524 TCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGGACTTTCTCTGGAAAAGCTGATCCATTAA
261 TCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGGACTTTCTCTGGAAAAGCTGATCCATTAA
91589 ATGATGGATTCATATAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAG
326 ATGATGGATTCATATAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAG
91654 ATGAGTTCTTCTCATTATGAACTTTAACTGGAAAAGTTGATCCATCAAATGATGGATTCAGGTAA
391 ATGAGTTCTTCTCATTATGAACTTTAACTGGAAAAGTTGATCCATCAAATGATGGATTCAGGTAA
91719 AAGGTTGAACAAATTCTTCTAATTATGAACTTCTCCTTCCTTCTTCAGATGAGTTCTTCTCATTA
456 AAGGTTGAACAAATTCTTCTAATTATGAACTTCTCCTTCCTTCTTCAGATGAGTTCTTCTCATTA
91784 TGAACTCGGACTGGAAAAGATGATCCACCAAATGATGGATTCATAT
521 TGAACTCGGACTGGAAAAGATGATCCACCAAATGATGGATTCATAT
91830 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
91895 TATGAACTTTAACTGGAAAAGCTGATCCATCAAATGATGGATTCAGGTAAAAGGTTGAACAAATT
66 TATGAACTTTAACTGGAAAAGCTGATCCATCAAATGATGGATTCAGGTAAAAGGTTGAACAAATT
* ***
91960 CTTCTAATTATGAACTTC-TCATTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGGACTGG
131 CTTCTCATTATGAACTTCTTC-TTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTAACTGG
* **
92024 AAAAGATGATCCACCAAATGATGGATTCATATAAAAGG-TTGAACAAATTCTTCTCATTATGAAC
195 AAAAGCTGATCCATTAAATGATGGATTCATATAAAAGGTTTGAACAAATTCTTCTCATTATGAAC
* ** *
92088 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAC-CT--AACAATGTTGATCCA
260 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGGACT-TTCTCTGGAA-AA-GCTGATCCA
** * *
92150 TCGAATGATGAATTCA-AGCGAAAA-GTTGAACAAATTCTTCTCATTATGAACTTCTTCTT-CTT
322 TTAAATGATGGATTCATA--TAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTT
* * **
92212 CTTCAGATGAGTTCTTCTCATTATGAACTCTT--CCGGAAATGTTGATCCATTGAATGATGGATT
385 CTTCAGATGAGTTCTTCTCATTATGAACT-TTAACTGGAAAAGTTGATCCATCAAATGATGGATT
92275 TGAATCTTTG
Statistics
Matches: 964, Mismatches: 39, Indels: 19
0.94 0.04 0.02
Matches are distributed among these distances:
563 29 0.03
564 35 0.04
565 128 0.13
566 669 0.69
567 103 0.11
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.37
Consensus pattern (566 bp):
AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
TATGAACTTTAACTGGAAAAGCTGATCCATCAAATGATGGATTCAGGTAAAAGGTTGAACAAATT
CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTAACTGGA
AAAGCTGATCCATTAAATGATGGATTCATATAAAAGGTTTGAACAAATTCTTCTCATTATGAACT
TCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGGACTTTCTCTGGAAAAGCTGATCCATTAA
ATGATGGATTCATATAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAG
ATGAGTTCTTCTCATTATGAACTTTAACTGGAAAAGTTGATCCATCAAATGATGGATTCAGGTAA
AAGGTTGAACAAATTCTTCTAATTATGAACTTCTCCTTCCTTCTTCAGATGAGTTCTTCTCATTA
TGAACTCGGACTGGAAAAGATGATCCACCAAATGATGGATTCATAT
Found at i:92704 original size:22 final size:22
Alignment explanation
Indices: 92679--92752 Score: 103
Period size: 22 Copynumber: 3.4 Consensus size: 22
92669 AATAAAACTT
* *
92679 TCATATTTGAAAAGAGAATTTA
1 TCATCTTTGAAAAGAGAATCTA
*
92701 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
* *
92723 TCATCTTTGAAGAGAGAACCTA
1 TCATCTTTGAAAAGAGAATCTA
92745 TCATCTTT
1 TCATCTTT
92753 AAAGAGTGTA
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 46 1.00
ACGTcount: A:0.39, C:0.14, G:0.12, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:95358 original size:83 final size:83
Alignment explanation
Indices: 95213--95641 Score: 691
Period size: 83 Copynumber: 5.2 Consensus size: 83
95203 CTTATTTCTA
* *
95213 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGTCAAACCAGATCAGATAACTCAAA
1 CTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
95278 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
* * * **
95296 CTATTG-GCAAATTTATCTTCTAAATTCAATGATTGGTTCTGCCAAACTGGATCAGATAACTCAA
1 CTA-TGAGCACATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAA
*
95360 AGAACATTTCCAGAAGATG
65 AGAACACTTCCAGAAGATG
* *
95379 CTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTCTACCAAACCGGATCAGATAACTCAAA
1 CTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
*
95444 GAACATTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
* *
95462 CTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTCTGTCTAACCAGATCAGATAACTCAAA
1 CTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
95527 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
*
95545 CTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTTTGTCC-AACCAGATCAGATAACTCAA
1 CTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTCTG-CCAAACCAGATCAGATAACTCAA
95609 AGAACACTTCCAGAAGATG
65 AGAACACTTCCAGAAGATG
95628 CTATGGAGCACATT
1 CTAT-GAGCACATT
95642 ACATTTGTTC
Statistics
Matches: 324, Mismatches: 18, Indels: 7
0.93 0.05 0.02
Matches are distributed among these distances:
82 2 0.01
83 310 0.96
84 12 0.04
ACGTcount: A:0.35, C:0.22, G:0.15, T:0.28
Consensus pattern (83 bp):
CTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
GAACACTTCCAGAAGATG
Found at i:97878 original size:11 final size:11
Alignment explanation
Indices: 97862--97886 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
97852 TGATTCAATT
97862 TTTTTTTCTTC
1 TTTTTTTCTTC
97873 TTTTTTTCTTC
1 TTTTTTTCTTC
97884 TTT
1 TTT
97887 CTTTGCTGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTTTTCTTC
Found at i:103438 original size:18 final size:19
Alignment explanation
Indices: 103415--103450 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
103405 AATATATTTA
103415 AAAACA-ATAAAATAAATC
1 AAAACATATAAAATAAATC
103433 AAAACATATAAAATAAAT
1 AAAACATATAAAATAAAT
103451 GACTAAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.72, C:0.08, G:0.00, T:0.19
Consensus pattern (19 bp):
AAAACATATAAAATAAATC
Found at i:104788 original size:20 final size:19
Alignment explanation
Indices: 104748--104809 Score: 61
Period size: 20 Copynumber: 3.2 Consensus size: 19
104738 GGGCCTGTAA
**
104748 TTATATATATTTTTTATTAT
1 TTATATATATTTAATA-TAT
* *
104768 TTATTTATTTTTAATAATAT
1 TTATATATATTTAAT-ATAT
*
104788 TTATATGTATTTAATATAT
1 TTATATATATTTAATATAT
104807 TTA
1 TTA
104810 ATAATAATAG
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
19 7 0.21
20 26 0.76
21 1 0.03
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.65
Consensus pattern (19 bp):
TTATATATATTTAATATAT
Found at i:104799 original size:26 final size:30
Alignment explanation
Indices: 104760--104815 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
104750 ATATATATTT
*
104760 TTTATTATTTATTT-AT-T-TTTAATAATA
1 TTTATTATGTATTTAATATATTTAATAATA
104787 TTTA-TATGTATTTAATATATTTAATAATA
1 TTTATTATGTATTTAATATATTTAATAATA
104816 ATAGTAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
26 8 0.32
27 6 0.24
28 1 0.04
29 10 0.40
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (30 bp):
TTTATTATGTATTTAATATATTTAATAATA
Found at i:104816 original size:3 final size:3
Alignment explanation
Indices: 104808--104900 Score: 132
Period size: 3 Copynumber: 30.7 Consensus size: 3
104798 TTAATATATT
* *
104808 TAA TAA TAA TAG TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TGA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
104856 TAG GAA TAA TAA TAAA TAA TAA TAA TAA TAT TAA TAA TAA TAA TA
1 TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
104901 TGGATAAAAA
Statistics
Matches: 79, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
3 76 0.96
4 3 0.04
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:106333 original size:17 final size:18
Alignment explanation
Indices: 106299--106339 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
106289 TTTTTCATAA
106299 AAAATATATTAAAAAATTT
1 AAAATATATT-AAAAATTT
*
106318 AAAATATATT-ATAATTT
1 AAAATATATTAAAAATTT
106335 AAAAT
1 AAAAT
106340 TTTAAGAAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 11 0.52
19 10 0.48
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
AAAATATATTAAAAATTT
Found at i:107776 original size:17 final size:17
Alignment explanation
Indices: 107754--107790 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
107744 TTTATTGGTT
*
107754 TGGATTAGGGATGGGCA
1 TGGATTAGGGATGAGCA
107771 TGGATTAGGGATGAGCA
1 TGGATTAGGGATGAGCA
107788 TGG
1 TGG
107791 GCTAGGTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.24, C:0.05, G:0.46, T:0.24
Consensus pattern (17 bp):
TGGATTAGGGATGAGCA
Found at i:107796 original size:17 final size:17
Alignment explanation
Indices: 107754--107796 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
107744 TTTATTGGTT
* *
107754 TGGATTAGGGATGGGCA
1 TGGACTAGGGATGAGCA
*
107771 TGGATTAGGGATGAGCA
1 TGGACTAGGGATGAGCA
*
107788 TGGGCTAGG
1 TGGACTAGG
107797 TTTCGGCCAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.23, C:0.07, G:0.47, T:0.23
Consensus pattern (17 bp):
TGGACTAGGGATGAGCA
Found at i:109057 original size:30 final size:30
Alignment explanation
Indices: 109021--109081 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
109011 GCACATTTTC
*
109021 TCTACCTGAACCCGATCCGACCTGAAATTT
1 TCTACCTAAACCCGATCCGACCTGAAATTT
*
109051 TCTACCTAAATCCGATCCGACCTGAAATTT
1 TCTACCTAAACCCGATCCGACCTGAAATTT
109081 T
1 T
109082 GGCGTATAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.28, C:0.31, G:0.11, T:0.30
Consensus pattern (30 bp):
TCTACCTAAACCCGATCCGACCTGAAATTT
Found at i:115228 original size:26 final size:26
Alignment explanation
Indices: 115176--115228 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
115166 TGACTCAAGA
* *
115176 ATATCACCAAGCTCAGAAATGACTGG
1 ATATCACCAAGCTCAGAAAAGAATGG
* * *
115202 ATATCATCGAGCTCTGAAAAGAATGG
1 ATATCACCAAGCTCAGAAAAGAATGG
115228 A
1 A
115229 ATGAATCTGA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.40, C:0.19, G:0.21, T:0.21
Consensus pattern (26 bp):
ATATCACCAAGCTCAGAAAAGAATGG
Found at i:116409 original size:2 final size:2
Alignment explanation
Indices: 116402--116426 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
116392 CGGATGGGGG
116402 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
116427 GCTTTAAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:121782 original size:45 final size:45
Alignment explanation
Indices: 121718--121809 Score: 166
Period size: 45 Copynumber: 2.0 Consensus size: 45
121708 AGGGCTCTCC
* *
121718 TTACTCTCTTGCTAATCAAACAATATCAAAATATAAATCCAATCA
1 TTACTCTCTTACTAATCAAACAATATCAAAACATAAATCCAATCA
121763 TTACTCTCTTACTAATCAAACAATATCAAAACATAAATCCAATCA
1 TTACTCTCTTACTAATCAAACAATATCAAAACATAAATCCAATCA
121808 TT
1 TT
121810 CCAAATGATG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.45, C:0.23, G:0.01, T:0.32
Consensus pattern (45 bp):
TTACTCTCTTACTAATCAAACAATATCAAAACATAAATCCAATCA
Found at i:122939 original size:21 final size:22
Alignment explanation
Indices: 122899--122939 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
122889 TCGCCGATTT
122899 GGTTGAGTTTCAAATATTTTTC
1 GGTTGAGTTTCAAATATTTTTC
122921 GGTTGA-TTT-AAATTATTTT
1 GGTTGAGTTTCAAA-TATTTT
122940 GGGTTGAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 3 0.17
21 9 0.50
22 6 0.33
ACGTcount: A:0.24, C:0.05, G:0.17, T:0.54
Consensus pattern (22 bp):
GGTTGAGTTTCAAATATTTTTC
Found at i:125542 original size:36 final size:36
Alignment explanation
Indices: 125502--125615 Score: 95
Period size: 36 Copynumber: 3.2 Consensus size: 36
125492 GTTCAGTTCT
125502 AATCAAGCTGATAATTCCTTATATTGGTTCAACACC
1 AATCAAGCTGATAATTCCTTATATTGGTTCAACACC
* * * * * *** *
125538 AATCAA-CTGTTAATTTCTTATTACTAGTTTATTTCT
1 AATCAAGCTGATAATTCCTTA-TATTGGTTCAACACC
* * *
125574 GATCAAGCTGGTAATTCCTTATATAGGTTCAACACC
1 AATCAAGCTGATAATTCCTTATATTGGTTCAACACC
*
125610 GATCAA
1 AATCAA
125616 TTGGTAATTT
Statistics
Matches: 56, Mismatches: 20, Indels: 4
0.70 0.25 0.05
Matches are distributed among these distances:
35 12 0.21
36 32 0.57
37 12 0.21
ACGTcount: A:0.32, C:0.19, G:0.11, T:0.38
Consensus pattern (36 bp):
AATCAAGCTGATAATTCCTTATATTGGTTCAACACC
Found at i:128196 original size:20 final size:20
Alignment explanation
Indices: 128173--128222 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
128163 AACTGATCTC
128173 AGTCAACTCGGACCGAACCG
1 AGTCAACTCGGACCGAACCG
* *
128193 AGTCAACTCGGATCGAACTG
1 AGTCAACTCGGACCGAACCG
128213 AGTCAACTCG
1 AGTCAACTCG
128223 AACCAGCCTG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.30, C:0.30, G:0.24, T:0.16
Consensus pattern (20 bp):
AGTCAACTCGGACCGAACCG
Found at i:128246 original size:20 final size:20
Alignment explanation
Indices: 128210--128253 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
128200 TCGGATCGAA
*
128210 CTGAGTCAACTCGAACCAGC
1 CTGAGTCAACTCAAACCAGC
*
128230 CTGAGTCAAC-CTAAACCAGT
1 CTGAGTCAACTC-AAACCAGC
128250 CTGA
1 CTGA
128254 CTCGTTGACC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 1 0.05
20 20 0.95
ACGTcount: A:0.32, C:0.32, G:0.18, T:0.18
Consensus pattern (20 bp):
CTGAGTCAACTCAAACCAGC
Found at i:130032 original size:35 final size:35
Alignment explanation
Indices: 129986--130106 Score: 136
Period size: 35 Copynumber: 3.4 Consensus size: 35
129976 CTGATCAAGC
*
129986 TGGTAATTCCTTATATAGGTTTAACACCGATCAAT
1 TGGTAATTCCTTATATAGGTTCAACACCGATCAAT
** * *
130021 TGGTAATTCCTTAT-TGCAGGTTCAATTCTGATCAAGC
1 TGGTAATTCCTTATAT--AGGTTCAACACCGATCAA-T
* * *
130058 TGGTAATTCCTTATATAGGTTCATCACCGATTAGT
1 TGGTAATTCCTTATATAGGTTCAACACCGATCAAT
130093 TGGTAATTCCTTAT
1 TGGTAATTCCTTAT
130107 GGACCTAAAG
Statistics
Matches: 70, Mismatches: 12, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
34 1 0.01
35 28 0.40
36 26 0.37
37 14 0.20
38 1 0.01
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.40
Consensus pattern (35 bp):
TGGTAATTCCTTATATAGGTTCAACACCGATCAAT
Found at i:130052 original size:72 final size:72
Alignment explanation
Indices: 129966--130106 Score: 237
Period size: 72 Copynumber: 2.0 Consensus size: 72
129956 AGGTCTCTAT
* *
129966 AGGTTCAGTTCTGATCAAGCTGGTAATTCCTTATATAGGTTTAACACCGATCAATTGGTAATTCC
1 AGGTTCAATTCTGATCAAGCTGGTAATTCCTTATATAGGTTCAACACCGATCAATTGGTAATTCC
130031 TTATTGC
66 TTATTGC
* * *
130038 AGGTTCAATTCTGATCAAGCTGGTAATTCCTTATATAGGTTCATCACCGATTAGTTGGTAATTCC
1 AGGTTCAATTCTGATCAAGCTGGTAATTCCTTATATAGGTTCAACACCGATCAATTGGTAATTCC
130103 TTAT
66 TTAT
130107 GGACCTAAAG
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
72 64 1.00
ACGTcount: A:0.26, C:0.18, G:0.18, T:0.38
Consensus pattern (72 bp):
AGGTTCAATTCTGATCAAGCTGGTAATTCCTTATATAGGTTCAACACCGATCAATTGGTAATTCC
TTATTGC
Found at i:130069 original size:37 final size:36
Alignment explanation
Indices: 129963--130080 Score: 150
Period size: 36 Copynumber: 3.3 Consensus size: 36
129953 ATGAGGTCTC
*
129963 TATAGGTTCAGTTCTGATCAAGCTGGTAATTCCTTA
1 TATAGGTTCAATTCTGATCAAGCTGGTAATTCCTTA
* ** * *
129999 TATAGGTTTAACACCGATCAA-TTGGTAATTCCTTA
1 TATAGGTTCAATTCTGATCAAGCTGGTAATTCCTTA
130034 T-TGCAGGTTCAATTCTGATCAAGCTGGTAATTCCTTA
1 TAT--AGGTTCAATTCTGATCAAGCTGGTAATTCCTTA
130071 TATAGGTTCA
1 TATAGGTTCA
130081 TCACCGATTA
Statistics
Matches: 67, Mismatches: 11, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
34 1 0.01
35 14 0.21
36 37 0.55
37 14 0.21
38 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.18, T:0.38
Consensus pattern (36 bp):
TATAGGTTCAATTCTGATCAAGCTGGTAATTCCTTA
Done.