Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006537.1 Hibiscus syriacus cultivar Beakdansim tig00015959_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: 372459
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
File 2 of 2
Found at i:301418 original size:14 final size:13
Alignment explanation
Indices: 301379--301421 Score: 59
Period size: 13 Copynumber: 3.2 Consensus size: 13
301369 CATATGTAAT
* *
301379 TTAAGTAATTTAT
1 TTAAGTGATTTAA
301392 TTAAGTGATTTAA
1 TTAAGTGATTTAA
301405 TTAAGTGCATTTAA
1 TTAAGTG-ATTTAA
301419 TTA
1 TTA
301422 GATTTAAGGG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
13 18 0.67
14 9 0.33
ACGTcount: A:0.37, C:0.02, G:0.12, T:0.49
Consensus pattern (13 bp):
TTAAGTGATTTAA
Found at i:313256 original size:17 final size:17
Alignment explanation
Indices: 313216--313259 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 17
313206 CAACCTATTC
*
313216 TAATCAATCCCATCTAT
1 TAATCATTCCCATCTAT
313233 TAATCATTCCCATCTAT
1 TAATCATTCCCATCTAT
*
313250 TGATCATTCC
1 TAATCATTCC
313260 TAATGTAACA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.30, C:0.30, G:0.02, T:0.39
Consensus pattern (17 bp):
TAATCATTCCCATCTAT
Found at i:314730 original size:20 final size:21
Alignment explanation
Indices: 314697--314736 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
314687 ATTTAATTTA
314697 ATAAATTTAATCCT-TTAATC
1 ATAAATTTAATCCTATTAATC
**
314717 ATAAATTTGGTCCTATTAAT
1 ATAAATTTAATCCTATTAAT
314737 GGTTTATAGC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.38, C:0.12, G:0.05, T:0.45
Consensus pattern (21 bp):
ATAAATTTAATCCTATTAATC
Found at i:315349 original size:33 final size:33
Alignment explanation
Indices: 315281--315349 Score: 88
Period size: 33 Copynumber: 2.1 Consensus size: 33
315271 AAGTTATTTC
* *
315281 AATAATTTAATTTTTTTCAAATTAATTTGAATA
1 AATAATTTAATTTTTTTCAAATTAAGTCGAATA
315314 AATAATTTAA-TTTTTT-AAATTTAAGTCGAATTA
1 AATAATTTAATTTTTTTCAAA-TTAAGTCGAA-TA
315347 AAT
1 AAT
315350 TTTAATAACT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
31 3 0.09
32 14 0.44
33 15 0.47
ACGTcount: A:0.43, C:0.03, G:0.04, T:0.49
Consensus pattern (33 bp):
AATAATTTAATTTTTTTCAAATTAAGTCGAATA
Found at i:315785 original size:16 final size:16
Alignment explanation
Indices: 315761--315791 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
315751 TCTGTAATGG
*
315761 TCGATGACGATGATGA
1 TCGACGACGATGATGA
315777 TCGACGACGATGATG
1 TCGACGACGATGATG
315792 GGTTAGAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.16, G:0.32, T:0.23
Consensus pattern (16 bp):
TCGACGACGATGATGA
Found at i:322106 original size:16 final size:16
Alignment explanation
Indices: 322067--322115 Score: 55
Period size: 15 Copynumber: 3.1 Consensus size: 16
322057 ATATTTTCAT
* **
322067 ATATAAAATATATCAA
1 ATATAAATTATAAAAA
322083 AT-TAAATTATAAAAA
1 ATATAAATTATAAAAA
322098 ATATAAATTATAATAAA
1 ATATAAATTATAA-AAA
322115 A
1 A
322116 ATACAAAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
15 12 0.43
16 12 0.43
17 4 0.14
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (16 bp):
ATATAAATTATAAAAA
Found at i:325778 original size:187 final size:188
Alignment explanation
Indices: 325209--325777 Score: 845
Period size: 190 Copynumber: 3.0 Consensus size: 188
325199 TTGAATTATT
*
325209 TTATCATGTACCAATGTCATCCTTCATCGATCATCTTTTTTTTCTTTAAATCACCGTCTCGTCTC
1 TTATCATGTACCAATGTCATCCTTCATCGATCATCTTTTTTCTCTTTAAATCACCGTCTCGTCTC
* * * * * *
325274 TCCCATCGTATTACATCTTTAAGTATAGCAAATCAAGCCACTACTATCAAGCTTCTAATAGATTC
66 TCCCATCGTATGACACCTTTAAGTATAGCAAATCAAGCCAATACTATCAAGCTTATGATAGATCC
* * *
325339 AAGAGCTTTTCTAAAGGTATCATCGTCGTTTCAACCATCTCAGATTCAATAAGAGTCC
131 AAGAGCTTTTCCAAAGGTATCATCGTCGTTTCAACCATCTCAGATTCAGTAAGAGCCC
* * *
325397 TTATCATGTACCAATATCATCCTTAATCGATCATCTTTTTTCTTTCTTTAAATCACTGTCTCGTC
1 TTATCATGTACCAATGTCATCCTTCATCGATCATCTTTTTTC--TCTTTAAATCACCGTCTCGTC
*
325462 TCTCCCATTGTATGACACCTTTAAGTATAGCAAATCAAG-CAACTACTATCAAGCTTATGATAGA
64 TCTCCCATCGTATGACACCTTTAAGTATAGCAAATCAAGCCAA-TACTATCAAGCTTATGATAGA
* * * * *
325526 TCCAAAAGCTTTTCCAAAGGTATCATTGTCATTTCTACCTTCTCAGATTCAGTAAGAGCCC
128 TCCAAGAGCTTTTCCAAAGGTATCATCGTCGTTTCAACCATCTCAGATTCAGTAAGAGCCC
* * *
325587 TTATTATGTACCAACGTCAACCTTCATCGATCAT-TTTTTTCTCTTTAAATCACCGTCTCGTCTC
1 TTATCATGTACCAATGTCATCCTTCATCGATCATCTTTTTTCTCTTTAAATCACCGTCTCGTCTC
* *
325651 TCCCATCGTATGACACCTTTAAGTATAGCAAGTCAAGCCAATACTATCAAGCTTTTGATAGATCC
66 TCCCATCGTATGACACCTTTAAGTATAGCAAATCAAGCCAATACTATCAAGCTTATGATAGATCC
* * * *
325716 AAGAGCTTTTCCAAAGGTATCATCATTGTTTCCACCATCTCAGATTTAGTAAGAGCCC
131 AAGAGCTTTTCCAAAGGTATCATCGTCGTTTCAACCATCTCAGATTCAGTAAGAGCCC
325774 TTAT
1 TTAT
325778 TTCCTTTCCT
Statistics
Matches: 341, Mismatches: 36, Indels: 9
0.88 0.09 0.02
Matches are distributed among these distances:
187 134 0.39
188 42 0.12
189 9 0.03
190 156 0.46
ACGTcount: A:0.28, C:0.25, G:0.11, T:0.36
Consensus pattern (188 bp):
TTATCATGTACCAATGTCATCCTTCATCGATCATCTTTTTTCTCTTTAAATCACCGTCTCGTCTC
TCCCATCGTATGACACCTTTAAGTATAGCAAATCAAGCCAATACTATCAAGCTTATGATAGATCC
AAGAGCTTTTCCAAAGGTATCATCGTCGTTTCAACCATCTCAGATTCAGTAAGAGCCC
Found at i:328850 original size:22 final size:23
Alignment explanation
Indices: 328809--328851 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
328799 ATATTGATAC
*
328809 TCCTCATAGCAGTATTGATACTA
1 TCCTCATAGCAGTATCGATACTA
*
328832 TCCTCATAG-GGTATCGATAC
1 TCCTCATAGCAGTATCGATAC
328852 CCTCCTTGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 9 0.50
23 9 0.50
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.33
Consensus pattern (23 bp):
TCCTCATAGCAGTATCGATACTA
Found at i:328857 original size:22 final size:23
Alignment explanation
Indices: 328808--328857 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
328798 AATATTGATA
* *
328808 CTCCTCATAGCAGTATTGATACT
1 CTCCTCATAGCAGTATCGATACC
* *
328831 ATCCTCATAG-GGTATCGATACC
1 CTCCTCATAGCAGTATCGATACC
328853 CTCCT
1 CTCCT
328858 TGATATTGAT
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
22 13 0.59
23 9 0.41
ACGTcount: A:0.24, C:0.30, G:0.14, T:0.32
Consensus pattern (23 bp):
CTCCTCATAGCAGTATCGATACC
Found at i:336693 original size:16 final size:16
Alignment explanation
Indices: 336672--336703 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
336662 GTGCGTAAAT
336672 GACCGAATTTCACAAC
1 GACCGAATTTCACAAC
336688 GACCGAATTTCACAAC
1 GACCGAATTTCACAAC
336704 AACAAGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.31, G:0.12, T:0.19
Consensus pattern (16 bp):
GACCGAATTTCACAAC
Found at i:346577 original size:23 final size:23
Alignment explanation
Indices: 346541--346589 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
346531 CGGTAAAATA
* *
346541 AAATAGGCGTTACCTATTACGTT
1 AAATAAGCGCTACCTATTACGTT
*
346564 AAATAAGCGCTACCTATTATGTT
1 AAATAAGCGCTACCTATTACGTT
346587 AAA
1 AAA
346590 CTACCTACCG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (23 bp):
AAATAAGCGCTACCTATTACGTT
Found at i:346738 original size:74 final size:75
Alignment explanation
Indices: 346564--346731 Score: 257
Period size: 74 Copynumber: 2.3 Consensus size: 75
346554 CTATTACGTT
* * * *
346564 AAATAAGCGCTACCTATTATGTTAAACTACCTACCGGTTTGTTTGAAGGTTACTAATAATGTAAA
1 AAATAGGCGCTACCTATTATGTTAAAATACCTACAGGTTTGTTTGAAGGCTACTAATAATGTAAA
*
346629 CGGTACAATA
66 CGGTAAAATA
* * *
346639 AAATAGGCGCTACATATTATGTTAAAATATCTACAGGTTT-TTTTAAGGCTACTAATAATGTAAA
1 AAATAGGCGCTACCTATTATGTTAAAATACCTACAGGTTTGTTTGAAGGCTACTAATAATGTAAA
346703 CGGTAAAATA
66 CGGTAAAATA
346713 AAATAGGCGCTACCTATTA
1 AAATAGGCGCTACCTATTA
346732 CATTAAATAA
Statistics
Matches: 84, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
74 49 0.58
75 35 0.42
ACGTcount: A:0.38, C:0.14, G:0.15, T:0.32
Consensus pattern (75 bp):
AAATAGGCGCTACCTATTATGTTAAAATACCTACAGGTTTGTTTGAAGGCTACTAATAATGTAAA
CGGTAAAATA
Found at i:346761 original size:97 final size:98
Alignment explanation
Indices: 346653--346836 Score: 253
Period size: 98 Copynumber: 1.9 Consensus size: 98
346643 AGGCGCTACA
* * * *
346653 TATTATGTTAAAATATCTACAGGTTT-TTTTAAGGCTACTAATAATGTAAACGGTAAAATAAAAT
1 TATTATATTAAAATACCTACAGATTTGTTTGAAGGCTACTAATAATGTAAACGGTAAAATAAAAT
*
346717 AGGCGCTACCTATTACATTAAATAAGTGCCACC
66 AGACGCTACCTATTACATTAAATAAGTGCCACC
* ** * * *
346750 TATTATATTAAACTACCTACCTATTTGTTTGAAGGTTGCTAATAATGTCAACGGTAAAATAAAAT
1 TATTATATTAAAATACCTACAGATTTGTTTGAAGGCTACTAATAATGTAAACGGTAAAATAAAAT
*
346815 AGACGTTACCTATTACATTAAA
66 AGACGCTACCTATTACATTAAA
346837 ATACCTACCG
Statistics
Matches: 74, Mismatches: 12, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
97 20 0.27
98 54 0.73
ACGTcount: A:0.39, C:0.14, G:0.12, T:0.34
Consensus pattern (98 bp):
TATTATATTAAAATACCTACAGATTTGTTTGAAGGCTACTAATAATGTAAACGGTAAAATAAAAT
AGACGCTACCTATTACATTAAATAAGTGCCACC
Found at i:346805 original size:172 final size:173
Alignment explanation
Indices: 346503--346904 Score: 590
Period size: 172 Copynumber: 2.3 Consensus size: 173
346493 TACCTATCGA
* * *
346503 TTTGTTTAAATGCTACTAATAATGTAAACGGTAAAATAAAATAGGCGTTACCTATTACGTTAAAT
1 TTTGTTTAAAGGCTACTAATAATGTAAACGGTAAAATAAAATAGGCGCTACCTATTACATTAAAT
* * *
346568 AAGCGCTACCTATTATGTTAAACTACCTACCGGTTTGTTTGAAGGTTACTAATAATGTAAACGGT
66 AAGCGCCACCTATTATATTAAACTACCTACCGATTTGTTTGAAGGTTACTAATAATGTAAACGGT
* * ** *
346633 ACAATAAAATAGGCGCTACATATTATGTTAAAATATCTACAGG
131 AAAATAAAATAGACGCTACATATTACATTAAAATACCTACAGG
*
346676 TTT-TTTTAAGGCTACTAATAATGTAAACGGTAAAATAAAATAGGCGCTACCTATTACATTAAAT
1 TTTGTTTAAAGGCTACTAATAATGTAAACGGTAAAATAAAATAGGCGCTACCTATTACATTAAAT
* * * *
346740 AAGTGCCACCTATTATATTAAACTACCTACCTATTTGTTTGAAGGTTGCTAATAATGTCAACGGT
66 AAGCGCCACCTATTATATTAAACTACCTACCGATTTGTTTGAAGGTTACTAATAATGTAAACGGT
* * *
346805 AAAATAAAATAGACGTTACCTATTACATTAAAATACCTACCGG
131 AAAATAAAATAGACGCTACATATTACATTAAAATACCTACAGG
** * *
346848 TTTGTTTAAAGATTACTAATAATGTAAACAGTAAAATAAAATAGGAGCTACCTATTA
1 TTTGTTTAAAGGCTACTAATAATGTAAACGGTAAAATAAAATAGGCGCTACCTATTA
346905 TGTTATTATG
Statistics
Matches: 204, Mismatches: 24, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
172 153 0.75
173 51 0.25
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.33
Consensus pattern (173 bp):
TTTGTTTAAAGGCTACTAATAATGTAAACGGTAAAATAAAATAGGCGCTACCTATTACATTAAAT
AAGCGCCACCTATTATATTAAACTACCTACCGATTTGTTTGAAGGTTACTAATAATGTAAACGGT
AAAATAAAATAGACGCTACATATTACATTAAAATACCTACAGG
Found at i:346854 original size:75 final size:75
Alignment explanation
Indices: 346747--346904 Score: 210
Period size: 75 Copynumber: 2.1 Consensus size: 75
346737 AATAAGTGCC
* * * * * * * *
346747 ACCTATTATATTAAACTACCTACCTATTTGTTTGAAGGTTGCTAATAATGTCAACGGTAAAATAA
1 ACCTATTACATTAAAATACCTACCGATTTGTTTAAAGATTACTAATAATGTAAACAGTAAAATAA
*
346812 AATA-GACGTT
66 AATAGGA-GCT
*
346822 ACCTATTACATTAAAATACCTACCGGTTTGTTTAAAGATTACTAATAATGTAAACAGTAAAATAA
1 ACCTATTACATTAAAATACCTACCGATTTGTTTAAAGATTACTAATAATGTAAACAGTAAAATAA
346887 AATAGGAGCT
66 AATAGGAGCT
346897 ACCTATTA
1 ACCTATTA
346905 TGTTATTATG
Statistics
Matches: 72, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
75 70 0.97
76 2 0.03
ACGTcount: A:0.41, C:0.15, G:0.12, T:0.33
Consensus pattern (75 bp):
ACCTATTACATTAAAATACCTACCGATTTGTTTAAAGATTACTAATAATGTAAACAGTAAAATAA
AATAGGAGCT
Found at i:353968 original size:10 final size:10
Alignment explanation
Indices: 353953--353978 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
353943 CAAAAGAAAC
353953 GAAGAAGATT
1 GAAGAAGATT
353963 GAAGAAGATT
1 GAAGAAGATT
353973 GAAGAA
1 GAAGAA
353979 AACTGAAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.54, C:0.00, G:0.31, T:0.15
Consensus pattern (10 bp):
GAAGAAGATT
Found at i:354644 original size:60 final size:60
Alignment explanation
Indices: 354543--354657 Score: 151
Period size: 60 Copynumber: 1.9 Consensus size: 60
354533 GAGGTGGCAC
* * * *
354543 AAAGGCGCATCCCCGGGGACGCGCTTTACCCGAATTATGCTGACTCGGCTGCCACATGTG
1 AAAGGCGCATCCCCGAGGACGCGCATTACACGAATTATGCTGACTCGGCTACCACATGTG
* * *
354603 AAAGGCGCATCCCCGAGGACGCGCATT-CACGAGGTTCTGCTGAGTCGGCTACCAC
1 AAAGGCGCATCCCCGAGGACGCGCATTACACGA-ATTATGCTGACTCGGCTACCAC
354658 GCTGGTATTT
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
59 4 0.09
60 43 0.91
ACGTcount: A:0.21, C:0.32, G:0.29, T:0.18
Consensus pattern (60 bp):
AAAGGCGCATCCCCGAGGACGCGCATTACACGAATTATGCTGACTCGGCTACCACATGTG
Found at i:358242 original size:116 final size:115
Alignment explanation
Indices: 358061--358630 Score: 489
Period size: 116 Copynumber: 4.7 Consensus size: 115
358051 TGGGGGCGTG
*
358061 CCTTCCATTATTTTGTCAGATAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCTCGGGG
1 CCTTCCATTATTTTGTCAAATAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCTCGGGG
* *
358126 GCACTATTCATGTCAGTACCCAAAATGGTGAAAACGCATTCCTGGGGGACA
66 GCACTATTCATATCAGTACCCAAAATGGTGAAAACGCATTCCCGGGGG-CA
*
358177 CCTTCCATTATTTTGTCAAATAATATGTTATCATTGCCATATTATGTCACTCATGTCCCTCGGGG
1 CCTTCCATTATTTTGTCAAATAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCTCGGGG
* ** * *
358242 GCATTATTCATATCAGTACCCAAAATGGTGAAGGCGCGTTCCCGGGGGCG
66 GCACTATTCATATCAGTACCCAAAATGGTGAAAACGCATTCCCGGGGGCA
** * *
358292 CGTCTTCCATTATTTTGTGTAAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCC-CTG
1 C--CTTCCATTATTTTGTCAAATAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCTCGG
* * * * ** * *
358356 GGGAACTATTCATATCAATACCTATTATTTCTAAGGGGACTTGAAGGCGCGTTCCCAGGGGCA
64 GGGCACTATTCATATCAGTACCCA--A-----AA-TGG---TGAAAACGCATTCCCGGGGGCA
* ** * * * *
358419 CGCCTTTCATTATTTTGTGTAAGAATATGTTATTATTACCCTATTATGTCACTCATGTCCC-CTG
1 --CCTTCCATTATTTTGTCAAATAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCTCGG
* ** ** ** *
358483 GGGAACTATTCATATCAGTACCTATTTTTCTGAGGGGACTTGAAGGCGCATTCCCGGGGGCGCG
64 GGGCACTATTCATATCAGTACC-------CAAAATGG---TGAAAACGCATTCCC-GGGG-GCA
* * * *
358547 CCTTCCATTATTGTGTCAGAGAATATGTTATCATTGCCCTATTATGTCAATCATGTCCCTC-GGG
1 CCTTCCATTATTTTGTCAAATAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCTCGGGG
* *
358611 GAACTAATCATATCAGTACC
66 GCACTATTCATATCAGTACC
358631 TATTATTTCT
Statistics
Matches: 388, Mismatches: 41, Indels: 40
0.83 0.09 0.09
Matches are distributed among these distances:
115 2 0.01
116 127 0.33
117 54 0.14
118 1 0.00
123 2 0.01
124 2 0.01
126 93 0.24
127 104 0.27
128 2 0.01
129 1 0.00
ACGTcount: A:0.24, C:0.23, G:0.20, T:0.34
Consensus pattern (115 bp):
CCTTCCATTATTTTGTCAAATAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCTCGGGG
GCACTATTCATATCAGTACCCAAAATGGTGAAAACGCATTCCCGGGGGCA
Found at i:358496 original size:127 final size:128
Alignment explanation
Indices: 358270--358744 Score: 694
Period size: 127 Copynumber: 3.8 Consensus size: 128
358260 CCCAAAATGG
*
358270 TGAAGGCGCGTTCCCGGGGGCGCGTCTTCCATTATTTTGTGTA-AGAATATGTTATCATTGCCCT
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTGTAGAGAATATGTTATCATTGCCCT
* *
358334 ATTATGTCACTCATGTCCCCTGGGGAACTATTCATATCAATACCTATTATTTCTAAGGGGACT
66 ATTATGTCACTCATGTCCCCTGGGGAACTATTCATATCAGTACCTATTATTTCTGAGGGGACT
* * * * *
358397 TGAAGGCGCGTTCCCAGGGGCACGCCTTTCATTATTTTGTGTA-AGAATATGTTATTATTACCCT
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTGTAGAGAATATGTTATCATTGCCCT
358461 ATTATGTCACTCATGTCCCCTGGGGAACTATTCATATCAGTACCTATT-TTTCTGAGGGGACT
66 ATTATGTCACTCATGTCCCCTGGGGAACTATTCATATCAGTACCTATTATTTCTGAGGGGACT
*
358523 TGAAGGCGCATTCCCGGGGGCGCGCCTTCCATTA--TTGTGTCAGAGAATATGTTATCATTGCCC
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTGT-AGAGAATATGTTATCATTGCCC
* *
358586 TATTATGTCAATCATGT-CCCTCGGGGAACTAATCATATCAGTACCTATTATTTCTGAGGGGACT
65 TATTATGTCACTCATGTCCCCT-GGGGAACTATTCATATCAGTACCTATTATTTCTGAGGGGACT
* ** * * * *
358650 TGAAGGTGCGTTCATGGGGGTGCGCCTTTCATTATTTTGT-CAGAGAATATGTTATCATTGTCCT
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTGTAGAGAATATGTTATCATTGCCCT
* * *
358714 ATTATGTTAGTCATGTCCCCCGGGGAACTAT
66 ATTATGTCACTCATGTCCCCTGGGGAACTAT
358745 ATATGGATGG
Statistics
Matches: 313, Mismatches: 28, Indels: 14
0.88 0.08 0.04
Matches are distributed among these distances:
124 6 0.02
125 5 0.02
126 103 0.33
127 192 0.61
128 3 0.01
129 4 0.01
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.35
Consensus pattern (128 bp):
TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTGTAGAGAATATGTTATCATTGCCCT
ATTATGTCACTCATGTCCCCTGGGGAACTATTCATATCAGTACCTATTATTTCTGAGGGGACT
Found at i:358624 original size:253 final size:252
Alignment explanation
Indices: 358270--358744 Score: 713
Period size: 253 Copynumber: 1.9 Consensus size: 252
358260 CCCAAAATGG
* *
358270 TGAAGGCGCGTTCCCGGGGGCGCGTCTTCCATTATTTTGTGTAAGAATATGTTATCATTGCCCTA
1 TGAAGGCGCATTCCCGGGGGCGCGCCTTCCATTA-TTTGTGTAAGAATATGTTATCATTGCCCTA
* *
358335 TTATGTCACTCATGTCCCCTGGGGAACTATTCATATCAATACCTATTATTTCTAAGGGGACTTGA
65 TTATGTCAATCATGTCCCCTGGGGAACTAATCATATCAATACCTATTATTTCTAAGGGGACTTGA
* * *
358400 AGGCGCGTTCCCAGGGGCACGCCTTTCATTATTTTGTGTA-AGAATATGTTATTATTACCCTATT
130 AGGCGCGTTCACAGGGGCACGCCTTTCATTATTTTGT-CAGAGAATATGTTATCATTACCCTATT
*
358464 ATGTCACTCATGTCCCCTGGGGAACTATTCATATCAGTACCTATTTTTCTGAGGGGACT
194 ATGTCACTCATGTCCCCCGGGGAACTATTCATATCAGTACCTATTTTTCTGAGGGGACT
358523 TGAAGGCGCATTCCCGGGGGCGCGCCTTCCATTA-TTGTGTCAGAGAATATGTTATCATTGCCCT
1 TGAAGGCGCATTCCCGGGGGCGCGCCTTCCATTATTTGTGT-A-AGAATATGTTATCATTGCCCT
* *
358587 ATTATGTCAATCATGT-CCCTCGGGGAACTAATCATATCAGTACCTATTATTTCTGAGGGGACTT
64 ATTATGTCAATCATGTCCCCT-GGGGAACTAATCATATCAATACCTATTATTTCTAAGGGGACTT
* ** ** **
358651 GAAGGTGCGTTCATGGGGGTGCGCCTTTCATTATTTTGTCAGAGAATATGTTATCATTGTCCTAT
128 GAAGGCGCGTTCACAGGGGCACGCCTTTCATTATTTTGTCAGAGAATATGTTATCATTACCCTAT
* *
358716 TATGTTAGTCATGTCCCCCGGGGAACTAT
193 TATGTCACTCATGTCCCCCGGGGAACTAT
358745 ATATGGATGG
Statistics
Matches: 199, Mismatches: 19, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
251 6 0.03
252 6 0.03
253 187 0.94
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.35
Consensus pattern (252 bp):
TGAAGGCGCATTCCCGGGGGCGCGCCTTCCATTATTTGTGTAAGAATATGTTATCATTGCCCTAT
TATGTCAATCATGTCCCCTGGGGAACTAATCATATCAATACCTATTATTTCTAAGGGGACTTGAA
GGCGCGTTCACAGGGGCACGCCTTTCATTATTTTGTCAGAGAATATGTTATCATTACCCTATTAT
GTCACTCATGTCCCCCGGGGAACTATTCATATCAGTACCTATTTTTCTGAGGGGACT
Found at i:358945 original size:63 final size:63
Alignment explanation
Indices: 358873--359000 Score: 231
Period size: 63 Copynumber: 2.0 Consensus size: 63
358863 ATTATGTGAA
358873 GTTTGAATAAATTGGATAAAATGTTATAGATAAATTGAATAAATGTGAAGTGATC-AGTTGGTT
1 GTTTGAATAAATTGGATAAAATGTTATAGATAAATTGAATAAATGTGAAGTGA-CAAGTTGGTT
*
358936 GTTTGAATAAATTGGATAAAATGTTATAGATAAATTGAATATATGTGAAGTGACAAGTTGGTT
1 GTTTGAATAAATTGGATAAAATGTTATAGATAAATTGAATAAATGTGAAGTGACAAGTTGGTT
358999 GT
1 GT
359001 GACATTGAAA
Statistics
Matches: 63, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
62 1 0.02
63 62 0.98
ACGTcount: A:0.39, C:0.02, G:0.23, T:0.37
Consensus pattern (63 bp):
GTTTGAATAAATTGGATAAAATGTTATAGATAAATTGAATAAATGTGAAGTGACAAGTTGGTT
Found at i:359137 original size:57 final size:55
Alignment explanation
Indices: 359018--359156 Score: 192
Period size: 57 Copynumber: 2.5 Consensus size: 55
359008 AAATTGTATG
*
359018 GAATGAGCATCGACATGTTTTTACGAATAAATGTGAAGTGATAAGTACTCGGGACT
1 GAATGAGCATCGACATGTTTTTACGAATAAATGTGAAGTGATAAGTA-TCGGGAAT
*
359074 GAAATGAGCATCGACATGTTTTTACGAATAAATGTGAAGTGATAAGT-T-GGTTTTAAT
1 G-AATGAGCATCGACATGTTTTTACGAATAAATGTGAAGTGATAAGTATCGG---GAAT
359131 AGAATGAGCATCGACATGTTTTTACG
1 -GAATGAGCATCGACATGTTTTTACG
359157 TATGGATAAA
Statistics
Matches: 76, Mismatches: 2, Indels: 9
0.87 0.02 0.10
Matches are distributed among these distances:
54 2 0.03
55 1 0.01
56 1 0.01
57 71 0.93
58 1 0.01
ACGTcount: A:0.34, C:0.11, G:0.24, T:0.32
Consensus pattern (55 bp):
GAATGAGCATCGACATGTTTTTACGAATAAATGTGAAGTGATAAGTATCGGGAAT
Found at i:359319 original size:28 final size:28
Alignment explanation
Indices: 359245--359320 Score: 82
Period size: 34 Copynumber: 2.5 Consensus size: 28
359235 TATTAAGTTG
*
359245 AATTTA-ATGTTAAATTTCGAATACTAT
1 AATTTATATTTTAAATTTCGAATACTAT
359272 AATTTTTATTTTTATTTTAAATTTCGAATACTAT
1 AA--TTTA----TATTTTAAATTTCGAATACTAT
359306 AATTTATATTTTAAA
1 AATTTATATTTTAAA
359321 AACATTTAAC
Statistics
Matches: 41, Mismatches: 1, Indels: 13
0.75 0.02 0.24
Matches are distributed among these distances:
27 2 0.05
28 9 0.22
29 4 0.10
32 4 0.10
34 22 0.54
ACGTcount: A:0.38, C:0.05, G:0.04, T:0.53
Consensus pattern (28 bp):
AATTTATATTTTAAATTTCGAATACTAT
Found at i:359874 original size:21 final size:21
Alignment explanation
Indices: 359848--359887 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
359838 ATAAAACTCT
*
359848 GCGGGCTAGGCATGTAACCTG
1 GCGGGCTAGGAATGTAACCTG
359869 GCGGGCTAGGAATGTAACC
1 GCGGGCTAGGAATGTAACC
359888 CTGCGGAGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.23, C:0.23, G:0.38, T:0.17
Consensus pattern (21 bp):
GCGGGCTAGGAATGTAACCTG
Found at i:359893 original size:21 final size:20
Alignment explanation
Indices: 359846--359893 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 20
359836 TCATAAAACT
*
359846 CTGCGGGCTAGGCATGTAAC
1 CTGCGGGCTAGGAATGTAAC
359866 CTGGCGGGCTAGGAATGTAACC
1 CT-GCGGGCTAGGAATGTAA-C
359888 CTGCGG
1 CTGCGG
359894 AGATGGCATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 2 0.08
21 20 0.80
22 3 0.12
ACGTcount: A:0.19, C:0.25, G:0.38, T:0.19
Consensus pattern (20 bp):
CTGCGGGCTAGGAATGTAAC
Found at i:361523 original size:23 final size:26
Alignment explanation
Indices: 361487--361535 Score: 77
Period size: 23 Copynumber: 2.0 Consensus size: 26
361477 TAATTAATAT
361487 AAATACATAATAAAT-TTAA-ATTAA
1 AAATACATAATAAATATTAACATTAA
361511 AAATA-ATAATAAATATTAACATTAA
1 AAATACATAATAAATATTAACATTAA
361536 TTATAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 9 0.39
24 9 0.39
25 5 0.22
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (26 bp):
AAATACATAATAAATATTAACATTAA
Found at i:361529 original size:24 final size:25
Alignment explanation
Indices: 361487--361552 Score: 75
Period size: 24 Copynumber: 2.7 Consensus size: 25
361477 TAATTAATAT
361487 AAATACATAATAAAT-TTAA-ATTAA
1 AAATA-ATAATAAATATTAACATTAA
361511 AAATAATAATAAATATTAACATTAA
1 AAATAATAATAAATATTAACATTAA
** *
361536 TTATAA-AAAAAATATTA
1 AAATAATAATAAATATTA
361553 CAACAACAGC
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
23 9 0.24
24 19 0.51
25 9 0.24
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (25 bp):
AAATAATAATAAATATTAACATTAA
Found at i:361744 original size:13 final size:13
Alignment explanation
Indices: 361726--361752 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
361716 CATAGTTGAA
361726 CAGTCTTCATATG
1 CAGTCTTCATATG
361739 CAGTCTTCATATG
1 CAGTCTTCATATG
361752 C
1 C
361753 GCGTCTGTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.26, G:0.15, T:0.37
Consensus pattern (13 bp):
CAGTCTTCATATG
Found at i:362204 original size:14 final size:14
Alignment explanation
Indices: 362162--362204 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
362152 AAATATTATT
362162 TTAATAAAAAAATA
1 TTAATAAAAAAATA
* * **
362176 TTTATATAATTATA
1 TTAATAAAAAAATA
362190 TTAATAAAAAAATA
1 TTAATAAAAAAATA
362204 T
1 T
362205 AAAAACTATT
Statistics
Matches: 21, Mismatches: 8, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
TTAATAAAAAAATA
Found at i:364634 original size:23 final size:23
Alignment explanation
Indices: 364577--364635 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 23
364567 AAACTAATGT
* *
364577 TTTATAAATATTATTTTTAATTAA
1 TTTATAATTA-TATTTTTAACTAA
* * *
364601 ATTACATTTATATTTTTAACTAA
1 TTTATAATTATATTTTTAACTAA
364624 TTTATAATTATA
1 TTTATAATTATA
364636 CATTTAGTAC
Statistics
Matches: 27, Mismatches: 8, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
23 21 0.78
24 6 0.22
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (23 bp):
TTTATAATTATATTTTTAACTAA
Found at i:370941 original size:13 final size:13
Alignment explanation
Indices: 370923--370948 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
370913 TCAATTTTTC
370923 CCATAAAATTCAT
1 CCATAAAATTCAT
370936 CCATAAAATTCAT
1 CCATAAAATTCAT
370949 GACATCTACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.23, G:0.00, T:0.31
Consensus pattern (13 bp):
CCATAAAATTCAT
Done.