Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004579.1 Hibiscus syriacus cultivar Beakdansim tig00010217_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: 79293
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:3366 original size:199 final size:199
Alignment explanation
Indices: 2581--3504 Score: 1238
Period size: 201 Copynumber: 4.6 Consensus size: 199
2571 TCGGTGTTTT
* * **** *
2581 CATACTGGACCAAAAGTATCGATATATATACAAAAAGTATTGGTACTTTATGTTTACGTATTTTG
1 CATACTGGAACAAAAGTATCGATACATATACAAAAAGTATCAAAACTTTATGTTTACATATTTTG
** * *
2646 TCATTAAACC-AGTATATTTTTACTGTTTACATTGTAAATTTACCTATTAATTTAAAGTAAT-AG
66 TCATTAAACCGA-TATATTTTTAC-CCTTACATTGTAAATTTACCTATTACTTTAAATTAATCAG
* * * *
2709 ATTTCAAAGTTTTTAGAATTGATACTTTTGATACGTGTATCGATACTT-TCTGCGTGCATTTAGT
129 -TTTCAAAGTTTTAAGAATCGATACTTTTCATACGTGTATCGATACTTCT-TGCGTGCATCTAGT
2773 TTGGGAAG
192 TTGGGAAG
* *
2781 CATACTAG-ACAAAAAGTATCGATACATATACAAAAAGTATCAAAACGTTATGTTTACATA--TT
1 CATACTGGAAC-AAAAGTATCGATACATATACAAAAAGTATCAAAACTTTATGTTTACATATTTT
* * *
2843 GTCATTAAACTGATATATTTTTACCGCTAACATTGTAAATTTATCTATTACTTTAAATTAATCAG
65 GTCATTAAACCGATATATTTTTACC-CTTACATTGTAAATTTACCTATTACTTTAAATTAATCAG
* * *
2908 TTTCAAAGTTTTAAGAATCGATGCTTTTCATACGTGTATCAATACTTCTTGTGTGCATCTAGTTT
129 TTTCAAAGTTTTAAGAATCGATACTTTTCATACGTGTATCGATACTTCTTGCGTGCATCTAGTTT
2973 GGGAAG
194 GGGAAG
* * * *
2979 CATATTGGACCAAAATTATCGATACATATACAAAAAGTATCAAAACTTTATGTTTACGTATTTTG
1 CATACTGGAACAAAAGTATCGATACATATACAAAAAGTATCAAAACTTTATGTTTACATATTTTG
* *
3044 TCATTAAACCGATATATTTTTTACAGCTTACATTGTAAATTTACCTATTACTTTAAATTAATCGG
66 TCATTAAACCGATATA-TTTTTAC-CCTTACATTGTAAATTTACCTATTACTTTAAATTAATCAG
*
3109 TTTCAAAGTTTTAAGAATCGATACTTTTCATACATGTATCGATACTTCTTGCGTGCATCTAGTTT
129 TTTCAAAGTTTTAAGAATCGATACTTTTCATACGTGTATCGATACTTCTTGCGTGCATCTAGTTT
* *
3174 GGTAAT
194 GGGAAG
* *
3180 CATACTGGAACAAACGTATCGATACATATACAAAAAGGATCAAAACTTTATGTTTACATATTTTG
1 CATACTGGAACAAAAGTATCGATACATATACAAAAAGTATCAAAACTTTATGTTTACATATTTTG
* * * *
3245 TCATTAAACTGGTATATTTTAACCCTTACATTGTAAATTTACCTATTACTTTAAATTAATTAGTT
66 TCATTAAACCGATATATTTTTACCCTTACATTGTAAATTTACCTATTACTTTAAATTAATCAGTT
* * *
3310 TCAAAGTTGTAAGAATCTATACTTTTCATACGTGTATCGATACTT-TCTGTGTGCATCTCA-TTT
131 TCAAAGTTTTAAGAATCGATACTTTTCATACGTGTATCGATACTTCT-TGCGTGCATCT-AGTTT
3373 GGGAAG
194 GGGAAG
* * * * *
3379 CATATTGG-ACAATAAGTATCGATACATATACAAAAAAG-ATCGAAACTTTATATTTAAACATTT
1 CATACTGGAACAA-AAGTATCGATACATATAC-AAAAAGTATCAAAACTTTATGTTTACATATTT
*
3442 TGTCATTAAACCGATATATTTTTACCTCTTACATTGTAAATTTACCTATTACTTTAAAGTAAT
64 TGTCATTAAACCGATATATTTTTACC-CTTACATTGTAAATTTACCTATTACTTTAAATTAAT
3505 AAATGTTGAA
Statistics
Matches: 641, Mismatches: 68, Indels: 30
0.87 0.09 0.04
Matches are distributed among these distances:
198 173 0.27
199 172 0.27
200 115 0.18
201 181 0.28
ACGTcount: A:0.34, C:0.14, G:0.12, T:0.39
Consensus pattern (199 bp):
CATACTGGAACAAAAGTATCGATACATATACAAAAAGTATCAAAACTTTATGTTTACATATTTTG
TCATTAAACCGATATATTTTTACCCTTACATTGTAAATTTACCTATTACTTTAAATTAATCAGTT
TCAAAGTTTTAAGAATCGATACTTTTCATACGTGTATCGATACTTCTTGCGTGCATCTAGTTTGG
GAAG
Found at i:3427 original size:400 final size:398
Alignment explanation
Indices: 2581--3505 Score: 1353
Period size: 399 Copynumber: 2.3 Consensus size: 398
2571 TCGGTGTTTT
* * * **
2581 CATACTGGACCAAAAGTATCGATATATATACAAAAAGTATTGGTACTTTATGTTTACGTATTTTG
1 CATATTGGACCAAAAGTATCGATACATATACAAAAAGTATCGAAACTTTATGTTTACGTATTTTG
* * *
2646 TCATTAAACC-AGTATATTTTTACTGTTTACATTGTAAATTTACCTATTAATTTAAAGTAATAGA
66 TCATTAAACCGA-TATATTTTTACAGCTTACATTGTAAATTTACCTATTACTTTAAAGTAATAGA
* * * * *
2710 TTTCAAAGTTTTTAGAATTGATACTTTTGATACGTGTATCGATACTTTCTGCGTGCATTTAGTTT
130 TTTCAAAGTTTTAAGAATCGATACTTTTCATACATGTATCGATACTTTCTGCGTGCATCTAGTTT
*
2775 GGGAAGCATACTAGACAAAAAGTATCGATACATATACAAAAAGTATCAAAACGTTATGTTTACAT
195 GGGAAGCATACTAGACAAAAAGTATCGATACATATACAAAAAGGATCAAAACGTTATGTTTACAT
* *
2840 ATTGTCATTAAACTGATATATTTTTACCGCTAACATTGTAAATTTATCTATTACTTTAAATTAAT
260 ATTGTCATTAAACTGATATATTTTAACCGCTAACATTGTAAATTTACCTATTACTTTAAATTAAT
* *
2905 CAGTTTCAAAGTTTTAAGAATCGATGCTTTTCATACGTGTATCAATACTTCTTGTGTGCATCTAG
325 CAGTTTCAAAGTTGTAAGAATCGATACTTTTCATACGTGTATCAATACTTCTTGTGTGCATCTAG
2970 TTTGGGAAG
390 TTTGGGAAG
* *
2979 CATATTGGACCAAAATTATCGATACATATACAAAAAGTATCAAAACTTTATGTTTACGTATTTTG
1 CATATTGGACCAAAAGTATCGATACATATACAAAAAGTATCGAAACTTTATGTTTACGTATTTTG
* * *
3044 TCATTAAACCGATATATTTTTTACAGCTTACATTGTAAATTTACCTATTACTTTAAATTAATCGG
66 TCATTAAACCGATATA-TTTTTACAGCTTACATTGTAAATTTACCTATTACTTTAAAGTAATAGA
3109 TTTCAAAGTTTTAAGAATCGATACTTTTCATACATGTATCGATAC-TTCTTGCGTGCATCTAGTT
130 TTTCAAAGTTTTAAGAATCGATACTTTTCATACATGTATCGATACTTTC-TGCGTGCATCTAGTT
* * * * *
3173 TGGTAATCATACTGGA-ACAAACGTATCGATACATATACAAAAAGGATCAAAACTTTATGTTTAC
194 TGGGAAGCATACTAGACA-AAAAGTATCGATACATATACAAAAAGGATCAAAACGTTATGTTTAC
* *
3237 ATATTTTGTCATTAAACTGGTATATTTTAACC-CTTACATTGTAAATTTACCTATTACTTTAAAT
258 ATA--TTGTCATTAAACTGATATATTTTAACCGCTAACATTGTAAATTTACCTATTACTTTAAAT
* * *
3301 TAATTAGTTTCAAAGTTGTAAGAATCTATACTTTTCATACGTGTATCGATACTT-TCTGTGTGCA
321 TAATCAGTTTCAAAGTTGTAAGAATCGATACTTTTCATACGTGTATCAATACTTCT-TGTGTGCA
3365 TCTCA-TTTGGGAAG
385 TCT-AGTTTGGGAAG
* ***
3379 CATATTGGA-CAATAAGTATCGATACATATACAAAAAAG-ATCGAAACTTTATATTTAAACATTT
1 CATATTGGACCAA-AAGTATCGATACATATAC-AAAAAGTATCGAAACTTTATGTTTACGTATTT
**
3442 TGTCATTAAACCGATATATTTTTACCTCTTACATTGTAAATTTACCTATTACTTTAAAGTAATA
64 TGTCATTAAACCGATATATTTTTACAGCTTACATTGTAAATTTACCTATTACTTTAAAGTAATA
3506 AATGTTGAAT
Statistics
Matches: 474, Mismatches: 43, Indels: 19
0.88 0.08 0.04
Matches are distributed among these distances:
398 76 0.16
399 203 0.43
400 163 0.34
401 32 0.07
ACGTcount: A:0.34, C:0.14, G:0.12, T:0.39
Consensus pattern (398 bp):
CATATTGGACCAAAAGTATCGATACATATACAAAAAGTATCGAAACTTTATGTTTACGTATTTTG
TCATTAAACCGATATATTTTTACAGCTTACATTGTAAATTTACCTATTACTTTAAAGTAATAGAT
TTCAAAGTTTTAAGAATCGATACTTTTCATACATGTATCGATACTTTCTGCGTGCATCTAGTTTG
GGAAGCATACTAGACAAAAAGTATCGATACATATACAAAAAGGATCAAAACGTTATGTTTACATA
TTGTCATTAAACTGATATATTTTAACCGCTAACATTGTAAATTTACCTATTACTTTAAATTAATC
AGTTTCAAAGTTGTAAGAATCGATACTTTTCATACGTGTATCAATACTTCTTGTGTGCATCTAGT
TTGGGAAG
Found at i:6957 original size:20 final size:20
Alignment explanation
Indices: 6926--6974 Score: 80
Period size: 20 Copynumber: 2.4 Consensus size: 20
6916 GACAAGTGGT
*
6926 GATACTTTTGATACGTGTATC
1 GATAC-TTTGATACGTCTATC
6947 GATACTTTGATACGTCTATC
1 GATACTTTGATACGTCTATC
6967 GATACTTT
1 GATACTTT
6975 CTGCATGCAT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
20 22 0.81
21 5 0.19
ACGTcount: A:0.24, C:0.16, G:0.16, T:0.43
Consensus pattern (20 bp):
GATACTTTGATACGTCTATC
Found at i:7460 original size:199 final size:200
Alignment explanation
Indices: 6944--7719 Score: 1093
Period size: 199 Copynumber: 3.9 Consensus size: 200
6934 TGATACGTGT
* * * * *
6944 ATCGATAC-TTTGATACGTCTATCGATACTTTCTGCATGCATTTAGTTTGGGAAGCATACTAG-A
1 ATCGATACTTTTCATACGTGTATCGATACTTTCTGCGTGCATCTAGTTTGGGAAGCATACTGGAA
*
7007 CAAAAAGTATCGATACATATACAAAAAGTATCGAAACTTTATGTTTACATA--TTGTCATTAAAC
66 C-AAAAGTATCGATACATATACAAAAAGGATCGAAACTTTATGTTTACATATTTTGTCATTAAAC
* * * *
7070 CGATATATTTTTACCGCTAACATTGTAAATTTACCTATTACTTTAAATTTATCAGTTTCAAAATT
130 CGATATATTTTTACCGCTTACATTGTAAATTTACCTATTACTTTAAATTAATCGGTTTCAAAGTT
*
7135 TTAATA
195 TTAAGA
* * * * *
7141 ATCGATGCTTTTCATACGTGTATCGATACTTTTTGTGTGCATCTAGTTTGGGAAGCATATTGGAC
1 ATCGATACTTTTCATACGTGTATCGATACTTTCTGCGTGCATCTAGTTTGGGAAGCATACTGGAA
* * *
7206 CAAAATTATCGATACATATACAAAAAGTATCGAAACTTTATGTTTACGTATTTTGTCATTAAACC
66 CAAAAGTATCGATACATATACAAAAAGGATCGAAACTTTATGTTTACATATTTTGTCATTAAACC
*
7271 GATATATTTTTACAGCTTACATTGTAAATTTACCTATTACTTTAAATTAATCGGTTTCAAAGTTT
131 GATATATTTTTACCGCTTACATTGTAAATTTACCTATTACTTTAAATTAATCGGTTTCAAAGTTT
7336 TAAGA
196 TAAGA
* * * *
7341 ATCGATAC-TTTCCTACATGTATCGATAC-TTCTTGCGTGCATCTAGTTTGGTAATCATACTGGA
1 ATCGATACTTTTCATACGTGTATCGATACTTTC-TGCGTGCATCTAGTTTGGGAAGCATACTGGA
** * *
7404 ACAAGCGTATCGATACATATACAAAAAGGATCAAAACTTTATGTTTATATATTTTGTCATTAAAC
65 ACAAAAGTATCGATACATATACAAAAAGGATCGAAACTTTATGTTTACATATTTTGTCATTAAAC
* *
7469 TGGTATATTTTTACC-CTTACATTGTAAATTTACCTATTACTTTAAATTAATCGGTTTCAAAGTT
130 CGATATATTTTTACCGCTTACATTGTAAATTTACCTATTACTTTAAATTAATCGGTTTCAAAGTT
*
7533 GTAAGA
195 TTAAGA
* * *
7539 ATCGATACTTTTCATACGTTTATCAATACTTTCTGTGTGCATCTCA-TTTGGGAAGCATACTGGA
1 ATCGATACTTTTCATACGTGTATCGATACTTTCTGCGTGCATCT-AGTTTGGGAAGCATACTGGA
* * *
7603 A-AATAAGTATCGATACATATACAAAAAAGATCGAAACTTTATATTTACACATTTTGTCATTAAA
65 ACAA-AAGTATCGATACATATACAAAAAGGATCGAAACTTTATGTTTACATATTTTGTCATTAAA
* * *
7667 CCGATATTTTTTTACCTCTTACATTGTAAATTTACCTATTACTTTAAAGTAAT
129 CCGATATATTTTTACCGCTTACATTGTAAATTTACCTATTACTTTAAATTAAT
7720 AAATGTTGAA
Statistics
Matches: 513, Mismatches: 56, Indels: 17
0.88 0.10 0.03
Matches are distributed among these distances:
197 7 0.01
198 159 0.31
199 224 0.44
200 123 0.24
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.39
Consensus pattern (200 bp):
ATCGATACTTTTCATACGTGTATCGATACTTTCTGCGTGCATCTAGTTTGGGAAGCATACTGGAA
CAAAAGTATCGATACATATACAAAAAGGATCGAAACTTTATGTTTACATATTTTGTCATTAAACC
GATATATTTTTACCGCTTACATTGTAAATTTACCTATTACTTTAAATTAATCGGTTTCAAAGTTT
TAAGA
Found at i:10064 original size:718 final size:718
Alignment explanation
Indices: 8689--10123 Score: 2609
Period size: 718 Copynumber: 2.0 Consensus size: 718
8679 GATATAATTG
*
8689 CGTTCGACACACCGTACAAAGATAATTTATGTTGTCGACCAATTATGCTTATTATCAATGTCAAT
1 CGTTCGACACACCGTACAAAGATAATTCATGTTGTCGACCAATTATGCTTATTATCAATGTCAAT
*
8754 GATCATCATAGCACAATAGTGTTTGCTACTGACATAATCACTGACGAAATGTCCCAATCTTTTGA
66 GATCATCATAGCACAATAGTGTTTGCTACTGACATAATCACTGACGAAACGTCCCAATCTTTTGA
8819 GTGGGTGCTGAAGAATTTTTTAGAAGCCATGATTAATAAATCACCTATTTCAGTTGTTACCGATG
131 GTGGGTGCTGAAGAATTTTTTAGAAGCCATGATTAATAAATCACCTATTTCAGTTGTTACCGATG
*
8884 GAGATAGAGCAATACAGAGGGCTATAAATTTATTATCTCTTTTGCTAAGCACAAATTATGTTCTT
196 GAGATAGAGCAATACAGAGGGCTATAAATTTATTATCTCTTTTGCTAAGCACAAATTATGCTCTT
** **
8949 GGCATCTTTCTCGCAATGCACAAGCTAATGTTGGTGACCCCAAATTTATAGCTGCATTCTCAAAA
261 GGCATCTTTCTCGCAATGCACAAGCTAACATTGGTGACCCCAAATTTATAGCAACATTCTCAAAA
* *
9014 TGCATGACTTCCTGGTGCACAACAGAGGAATTTGATACTCAATGGCGTTCAATTATTTCATAATT
326 TACATGACTTCCTGGTGCACAACAGAGGAATTTGATACTCAATGGCGTTCAATTATTTCAGAATT
9079 CAATGTCGAAAAGCATCCATGGGTGATTGAGAAGGGAAATACTCAGCACTTATGGGCATAAGCAT
391 CAATGTCGAAAAGCATCCATGGGTGATTGAGAAGGGAAATACTCAGCACTTATGGGCATAAGCAT
* * *
9144 CTCTAACCGGTTATTTCTTTGCCAATATTCACTCAACACAAAGGTGTAAGTCTATGAATGCTTTA
456 ATCTAACCGGTCATTTCTTTGCCAATATTCACTCAACACAAAGGTGCAAGTCTATGAATGCTTTA
*
9209 CTTGCGATTGCACTGAAAAACAGGAAGATATATTTAGATGTTGTTCGTGCAATTGAAGAAGGAAT
521 CTTGCGATTGCACTGAAAAACAAGAAGATATATTTAGATGTTGTTCGTGCAATTGAAGAAGGAAT
9274 TAGTAGAATGCGTATCAATGAGTTGAAAGTGGATTACTTAAGTTCCTAGACAAAGCCATTCTAGA
586 TAGTAGAATGCGTATCAATGAGTTGAAAGTGGATTACTTAAGTTCCTAGACAAAGCCATTCTAGA
*
9339 TCACAAAACTTATTGACCTTGAAAGCCATGATGCTGAAATTTATATGCATGAATCATTTCGTTTG
651 TCACAAAACTTATTGACCTTGAAAGCCATGATGCTGAAATTTATACGCATGAATCATTTCGTTTG
9404 TTA
716 TTA
* *
9407 CGTTCGACACACCGTACAAAGATAATTCGTGTTGTCGACCTATTATGCTTATTATCAATGTCAAT
1 CGTTCGACACACCGTACAAAGATAATTCATGTTGTCGACCAATTATGCTTATTATCAATGTCAAT
* * * *
9472 GATCATCATATCATAATAGTGTTTGCTACTGCCATAATCACTGACGAAACGTCCTAATCTTTTGA
66 GATCATCATAGCACAATAGTGTTTGCTACTGACATAATCACTGACGAAACGTCCCAATCTTTTGA
* *
9537 GTGGGTGCTGAAGAATTTTTTAGAAGCCATGATTAATAAATCACTTATTTCAGTTGTTACTGATG
131 GTGGGTGCTGAAGAATTTTTTAGAAGCCATGATTAATAAATCACCTATTTCAGTTGTTACCGATG
9602 GAGATAGAGCAATACAGAGGGCTATAAATTTATTATCTCTTTTGCTAAGCACAAATTATGCTCTT
196 GAGATAGAGCAATACAGAGGGCTATAAATTTATTATCTCTTTTGCTAAGCACAAATTATGCTCTT
9667 GGCATCTTTCTCGCAATGCACAAGCTAACATTGGTGACCCCAAATTTATAGCAACATTCTCAAAA
261 GGCATCTTTCTCGCAATGCACAAGCTAACATTGGTGACCCCAAATTTATAGCAACATTCTCAAAA
* *
9732 TACATGACTTTCTGGTGGACAACAGAGGAATTTGATACTCAATGGCGTTCAATTATTTCAGAATT
326 TACATGACTTCCTGGTGCACAACAGAGGAATTTGATACTCAATGGCGTTCAATTATTTCAGAATT
*
9797 CAATGTCGAAAAGCATCCATGGGTGATTGAGAAGGGAAATACTCAGCACTTATGGGCATCAGCAT
391 CAATGTCGAAAAGCATCCATGGGTGATTGAGAAGGGAAATACTCAGCACTTATGGGCATAAGCAT
*
9862 ATCTAACCGGTCATTTCTTTGCCAATATTCACTCAACATAAAGGTGCAAGTCTATGAATGCTTTA
456 ATCTAACCGGTCATTTCTTTGCCAATATTCACTCAACACAAAGGTGCAAGTCTATGAATGCTTTA
9927 CTTGCGATTGCACTGAAAAACAAGAAGATATATTTAGATGTTGTTCGTGCAATTGAAGAAGGAAT
521 CTTGCGATTGCACTGAAAAACAAGAAGATATATTTAGATGTTGTTCGTGCAATTGAAGAAGGAAT
*
9992 TATTAGAATGCGTATCAATGAGTTGAAAGTGGATTACTTAAGTTCCTAGACAAAGCCATTCTAGA
586 TAGTAGAATGCGTATCAATGAGTTGAAAGTGGATTACTTAAGTTCCTAGACAAAGCCATTCTAGA
* *
10057 TCACAAAACTTATTGACCTTGAAAGCCATGCTGCTGAAATTTATACGCGTGAATCATTTCGTTTG
651 TCACAAAACTTATTGACCTTGAAAGCCATGATGCTGAAATTTATACGCATGAATCATTTCGTTTG
10122 TT
716 TT
10124 CCAAGAAGAA
Statistics
Matches: 688, Mismatches: 29, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
718 688 1.00
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (718 bp):
CGTTCGACACACCGTACAAAGATAATTCATGTTGTCGACCAATTATGCTTATTATCAATGTCAAT
GATCATCATAGCACAATAGTGTTTGCTACTGACATAATCACTGACGAAACGTCCCAATCTTTTGA
GTGGGTGCTGAAGAATTTTTTAGAAGCCATGATTAATAAATCACCTATTTCAGTTGTTACCGATG
GAGATAGAGCAATACAGAGGGCTATAAATTTATTATCTCTTTTGCTAAGCACAAATTATGCTCTT
GGCATCTTTCTCGCAATGCACAAGCTAACATTGGTGACCCCAAATTTATAGCAACATTCTCAAAA
TACATGACTTCCTGGTGCACAACAGAGGAATTTGATACTCAATGGCGTTCAATTATTTCAGAATT
CAATGTCGAAAAGCATCCATGGGTGATTGAGAAGGGAAATACTCAGCACTTATGGGCATAAGCAT
ATCTAACCGGTCATTTCTTTGCCAATATTCACTCAACACAAAGGTGCAAGTCTATGAATGCTTTA
CTTGCGATTGCACTGAAAAACAAGAAGATATATTTAGATGTTGTTCGTGCAATTGAAGAAGGAAT
TAGTAGAATGCGTATCAATGAGTTGAAAGTGGATTACTTAAGTTCCTAGACAAAGCCATTCTAGA
TCACAAAACTTATTGACCTTGAAAGCCATGATGCTGAAATTTATACGCATGAATCATTTCGTTTG
TTA
Found at i:11079 original size:19 final size:18
Alignment explanation
Indices: 11042--11090 Score: 71
Period size: 19 Copynumber: 2.7 Consensus size: 18
11032 TTGCTCATCT
* *
11042 CATACATAATTTCATTCA
1 CATACAAAATTTAATTCA
11060 CATACAAAATTATAATTCA
1 CATACAAAATT-TAATTCA
11079 CATACAAAATTT
1 CATACAAAATTT
11091 GGCTTACATC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 11 0.39
19 17 0.61
ACGTcount: A:0.47, C:0.18, G:0.00, T:0.35
Consensus pattern (18 bp):
CATACAAAATTTAATTCA
Found at i:12638 original size:15 final size:15
Alignment explanation
Indices: 12608--12636 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
12598 CTTCCTCCTC
12608 ACTTCATTCATCTTT
1 ACTTCATTCATCTTT
12623 ACTTC-TTCATCTTT
1 ACTTCATTCATCTTT
12637 TATTAAATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.17, C:0.28, G:0.00, T:0.55
Consensus pattern (15 bp):
ACTTCATTCATCTTT
Found at i:14932 original size:223 final size:223
Alignment explanation
Indices: 14557--14987 Score: 702
Period size: 223 Copynumber: 1.9 Consensus size: 223
14547 AATGAGTGTT
* * *
14557 AATACTCTCTACTATAAGTATTGGTACATTTATACAACCTACAATATCATTTTCTACCTATAATA
1 AATACTCTCTACTACAAGTATCGATACATTTATACAACCTACAATATCATTTTCTACCTATAATA
* *
14622 TTATATAAAAGTATCGATATTTATTTTCTACCTAGAATATCACTTTCTAACTCTAATCGATCCCA
66 TTATATAAAAGCATCAATATTTATTTTCTACCTAGAATATCACTTTCTAACTCTAATCGATCCCA
* * * * *
14687 AATCCTACTTAACTTTAAAAACCCTAAACCCATAA-ACCCTATTTCTGAATACTGTAATACTAAA
131 AATACTACTTAACTTCAAAAACCCCAAACACATAATACCATATTTCTGAATACTGTAATACT-AA
14751 AAAACTAGGGTTTCCTTTAAAGGAATAAG
195 AAAACTAGGGTTTCCTTTAAAGGAATAAG
*
14780 AATACTCTCTACTACAAGTATCGATACATTTATACAACCTATAATATCATTTTCTACCTATAATA
1 AATACTCTCTACTACAAGTATCGATACATTTATACAACCTACAATATCATTTTCTACCTATAATA
* *
14845 TTATATAAAAGCATCAATATTTATTTTCTACCTAGAATATCACTTTCTACCTGTAATCGATCCCA
66 TTATATAAAAGCATCAATATTTATTTTCTACCTAGAATATCACTTTCTAACTCTAATCGATCCCA
* * *
14910 AATACTTCTTTACTTCAAAAACCCCAAACACATAATACCATATTTCTGATTACTGTAATACTAAA
131 AATACTACTTAACTTCAAAAACCCCAAACACATAATACCATATTTCTGAATACTGTAATACTAAA
14975 AAACTAGGGTTTC
196 AAACTAGGGTTTC
14988 AACAATGTAC
Statistics
Matches: 191, Mismatches: 16, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
223 167 0.87
224 24 0.13
ACGTcount: A:0.38, C:0.21, G:0.06, T:0.35
Consensus pattern (223 bp):
AATACTCTCTACTACAAGTATCGATACATTTATACAACCTACAATATCATTTTCTACCTATAATA
TTATATAAAAGCATCAATATTTATTTTCTACCTAGAATATCACTTTCTAACTCTAATCGATCCCA
AATACTACTTAACTTCAAAAACCCCAAACACATAATACCATATTTCTGAATACTGTAATACTAAA
AAACTAGGGTTTCCTTTAAAGGAATAAG
Found at i:15285 original size:32 final size:32
Alignment explanation
Indices: 15248--15325 Score: 147
Period size: 32 Copynumber: 2.4 Consensus size: 32
15238 TTTGTTCTTT
15248 TAAAAGTATCGATAATATGATACATATACTTA
1 TAAAAGTATCGATAATATGATACATATACTTA
*
15280 TAAAAGTATTGATAATATGATACATATACTTA
1 TAAAAGTATCGATAATATGATACATATACTTA
15312 TAAAAGTATCGATA
1 TAAAAGTATCGATA
15326 CCTTCAACAT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 44 1.00
ACGTcount: A:0.47, C:0.08, G:0.10, T:0.35
Consensus pattern (32 bp):
TAAAAGTATCGATAATATGATACATATACTTA
Found at i:19904 original size:27 final size:27
Alignment explanation
Indices: 19863--19922 Score: 95
Period size: 26 Copynumber: 2.2 Consensus size: 27
19853 AATCGATCTG
19863 AAAAGAAAATGTTTTTAATTCGT-ATTT
1 AAAA-AAAATGTTTTTAATTCGTAATTT
19890 AAAAAAAATGTTTTTAATTCGTAATTT
1 AAAAAAAATGTTTTTAATTCGTAATTT
*
19917 TAAAAA
1 AAAAAA
19923 TATAACATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
26 18 0.58
27 13 0.42
ACGTcount: A:0.47, C:0.03, G:0.08, T:0.42
Consensus pattern (27 bp):
AAAAAAAATGTTTTTAATTCGTAATTT
Found at i:21644 original size:2 final size:2
Alignment explanation
Indices: 21639--21704 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
21629 ATATTTTAAT
21639 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
21681 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
21705 CTAACATGTG
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:23553 original size:3 final size:3
Alignment explanation
Indices: 23545--23584 Score: 62
Period size: 3 Copynumber: 12.7 Consensus size: 3
23535 TAATTTGTAT
23545 TAA TAA TAA TAA TAA TAA TAA TAA TAA TATA TAA TTAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA -TAA TA
23585 TTTTTAATAT
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
3 29 0.83
4 6 0.17
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:24056 original size:42 final size:42
Alignment explanation
Indices: 23951--24183 Score: 208
Period size: 42 Copynumber: 5.6 Consensus size: 42
23941 AATTCTTATC
* * * * * *
23951 CGAAAGTCTTATGGATGACCCGAAAGACTT-ATCATCTTGCT
1 CGAAAGACTTATAGATGTCCCGAAGGATTTAATCATCATGCT
* * * *
23992 C-AAAAAGCTTATAGATGACCCGAAGGATTTAATCTTAATGCT
1 CGAAAGA-CTTATAGATGTCCCGAAGGATTTAATCATCATGCT
*
24034 CGAAAGACTTACT-GATGTCCCGAAGGATTTAATCACCATGCT
1 CGAAAGACTTA-TAGATGTCCCGAAGGATTTAATCATCATGCT
* * * *
24076 CGAAAGGCTTATAGATGAT-CAGAAAGATTTAATCATTATGCT
1 CGAAAGACTTATAGATG-TCCCGAAGGATTTAATCATCATGCT
* *
24118 CGAACGGCTTATAGATGAT-CCGAAGGATTTAATCATCATGCT
1 CGAAAGACTTATAGATG-TCCCGAAGGATTTAATCATCATGCT
* *
24160 CAAAAGACTTACT-GATGGCCCGAA
1 CGAAAGACTTA-TAGATGTCCCGAA
24184 TGACTTATTA
Statistics
Matches: 158, Mismatches: 26, Indels: 15
0.79 0.13 0.08
Matches are distributed among these distances:
40 3 0.02
41 22 0.14
42 126 0.80
43 7 0.04
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.27
Consensus pattern (42 bp):
CGAAAGACTTATAGATGTCCCGAAGGATTTAATCATCATGCT
Found at i:24090 original size:84 final size:84
Alignment explanation
Indices: 23951--24183 Score: 242
Period size: 84 Copynumber: 2.8 Consensus size: 84
23941 AATTCTTATC
* * * * * * * *
23951 CGAAAGTCTTATGGATGACCCGAAAGACTT-ATCATCTTGCTCAAAAAGCTTATAGATGACCCGA
1 CGAAAGACTTATAGATGATCCGAAGGATTTAATCACCATGCTCAAAAGGCTTATAGATGACCCGA
*
24015 AGGATTTAATC-TTAATGCT
66 AAGATTTAATCATT-ATGCT
* * *
24034 CGAAAGACTTACT-GATG-TCCCGAAGGATTTAATCACCATGCTCGAAAGGCTTATAGATGATCA
1 CGAAAGACTTA-TAGATGAT-CCGAAGGATTTAATCACCATGCTCAAAAGGCTTATAGATGACCC
24097 GAAAGATTTAATCATTATGCT
64 GAAAGATTTAATCATTATGCT
* * * * *
24118 CGAACGGCTTATAGATGATCCGAAGGATTTAATCATCATGCTCAAAAGACTTACT-GATGGCCCG
1 CGAAAGACTTATAGATGATCCGAAGGATTTAATCACCATGCTCAAAAGGCTTA-TAGATGACCCG
24182 AA
65 AA
24184 TGACTTATTA
Statistics
Matches: 124, Mismatches: 19, Indels: 13
0.79 0.12 0.08
Matches are distributed among these distances:
83 24 0.19
84 96 0.77
85 4 0.03
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.27
Consensus pattern (84 bp):
CGAAAGACTTATAGATGATCCGAAGGATTTAATCACCATGCTCAAAAGGCTTATAGATGACCCGA
AAGATTTAATCATTATGCT
Found at i:24520 original size:216 final size:216
Alignment explanation
Indices: 24107--24626 Score: 692
Period size: 216 Copynumber: 2.4 Consensus size: 216
24097 GAAAGATTTA
* * * * *
24107 ATCATTATGCTCGAACGGCTTATAGATGATCCGAAGGATTTAATCATCATGCTCAAAAGACTTAC
1 ATCATTTTGCTCTAAAGGCTTACAGATGACCCGAAGGATTTAATCATCATGCTCAAAAGACTTAC
* * *
24172 TGATGGCCCGAATGACTTATTAAGTGCAAAATTTTGGAAATCACTGTTTTAGTTTTCAAAGATTT
66 TGATGGCCCGAAAGACTTATAAAGTGCAAAATTTTGGAAATCACTGTCTTAGTTTTCAAAGATTT
* * * * ** *
24237 CATTTTCTTAAACATCACTTTCTCATTTTTGAACTTAATGGGAATACATTTTTGCCCGAAAGTCT
131 CATTTTCTTAAACATCACTTTCTCATTGTTCAAATTAATGGGAAAACATTCCTACCCGAAAGTCT
*
24302 TATGGATGG-CTCAAAGGACTT
196 TATGGATGGCCT-AAAGAACTT
24323 ATCATTTTGCTCTAAAGGCTTACAGATGACCCGAAGGATTTAATCATCATGCTCAAAAGACTT-C
1 ATCATTTTGCTCTAAAGGCTTACAGATGACCCGAAGGATTTAATCATCATGCTCAAAAGACTTAC
*
24387 TTGATGGCCCGAAAGACTTATAAAGTGCGAAATTTTGGAAATCACCT-TCTTAGTTTTCAAAGAT
66 -TGATGGCCCGAAAGACTTATAAAGTGCAAAATTTTGGAAATCA-CTGTCTTAGTTTTCAAAGAT
* ** *
24451 TTCATTTTCTTAAAACATCAAC-TTCTCATTGTTCAAATTCATTTGAAAACA-TCCTACCCGAAG
129 TTCATTTTCTT-AAACATC-ACTTTCTCATTGTTCAAATTAATGGGAAAACATTCCTACCCGAAA
*
24514 GTCTTATGGATGGCCTGAAGAACTT
192 GTCTTATGGATGGCCTAAAGAACTT
* * **
24539 ATCATCTTGCTCTAAAGGCTTACAGATGACCCGAAGTATTTAATCATCATGCTTGAAAGACTTAC
1 ATCATTTTGCTCTAAAGGCTTACAGATGACCCGAAGGATTTAATCATCATGCTCAAAAGACTTAC
* *
24604 GGATGACCCG-AAGAACTTATAAA
66 TGATGGCCCGAAAG-ACTTATAAA
24627 TTTTGGAAAT
Statistics
Matches: 269, Mismatches: 28, Indels: 14
0.86 0.09 0.05
Matches are distributed among these distances:
215 4 0.01
216 229 0.85
217 34 0.13
218 2 0.01
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Consensus pattern (216 bp):
ATCATTTTGCTCTAAAGGCTTACAGATGACCCGAAGGATTTAATCATCATGCTCAAAAGACTTAC
TGATGGCCCGAAAGACTTATAAAGTGCAAAATTTTGGAAATCACTGTCTTAGTTTTCAAAGATTT
CATTTTCTTAAACATCACTTTCTCATTGTTCAAATTAATGGGAAAACATTCCTACCCGAAAGTCT
TATGGATGGCCTAAAGAACTT
Found at i:26141 original size:5 final size:5
Alignment explanation
Indices: 26131--26160 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
26121 TCAACCTCAC
26131 AATCA AATCA AATCA AATCA AATCA AATCA
1 AATCA AATCA AATCA AATCA AATCA AATCA
26161 TAAACATGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.60, C:0.20, G:0.00, T:0.20
Consensus pattern (5 bp):
AATCA
Found at i:33011 original size:2 final size:2
Alignment explanation
Indices: 32999--33123 Score: 115
Period size: 2 Copynumber: 67.0 Consensus size: 2
32989 AGACAAAAAG
* * * *
32999 TA TA TA CA TA TA T- TT TA AA TA TA AA T- TA TA TA TA TA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
33038 TT TA -A T- TA TA AA T- TA TA TA TA TA TT TA -A T- TA TA AA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
33074 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
33116 TA TA TA TA
1 TA TA TA TA
33124 CTACATGTGA
Statistics
Matches: 100, Mismatches: 14, Indels: 18
0.76 0.11 0.14
Matches are distributed among these distances:
1 9 0.09
2 91 0.91
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:35314 original size:3 final size:3
Alignment explanation
Indices: 35306--35391 Score: 158
Period size: 3 Copynumber: 29.3 Consensus size: 3
35296 GTTGTGTAAT
35306 TAA TAA TAA TAA 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
35354 TAA TAA TAA TAA TAA TAA TAA TAA T-A TAA T-A TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
35392 CTGAAAAAAT
Statistics
Matches: 81, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
2 4 0.05
3 77 0.95
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:35842 original size:91 final size:91
Alignment explanation
Indices: 35682--36136 Score: 689
Period size: 91 Copynumber: 5.0 Consensus size: 91
35672 TGATGGAAAC
* * * * *
35682 GAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTATTCTCCCTCATCGGATGAGTTCTTCTT
1 GAGCCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTC
*
35747 ATTATGAACTCTCCATTGAAAATGTT
66 ATTATGAACTCTCCACTGAAAATGTT
*
35773 GAGCCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGACGAGTTCTTCTC
1 GAGCCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTC
*
35838 ATTATGAACTCTCCACT-AGAAATTTT
66 ATTATGAACTCTCCACTGA-AAATGTT
* *
35864 GAGCCAAGGTTGAACAAGTTCTTCTCATTATGAACTTATTCTCACTCGTTGGATGAGTTCTTCTC
1 GAGCCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTC
* *
35929 ATTATGAACTATCCACTGGAAATGTT
66 ATTATGAACTCTCCACTGAAAATGTT
* * *
35955 GATCCAATGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGCTCTTCTC
1 GAGCCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTC
* * * *
36020 AATATGAACACTCCATTG-GAATGTT
66 ATTATGAACTCTCCACTGAAAATGTT
* *
36045 GAGCCAAGGTTTAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTATTCTC
1 GAGCCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTC
*
36110 ATTATGAACTCTCCACTGGAAATGTT
66 ATTATGAACTCTCCACTGAAAATGTT
36136 G
1 G
36137 GTTGGTTTAT
Statistics
Matches: 328, Mismatches: 33, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
90 82 0.25
91 246 0.75
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.37
Consensus pattern (91 bp):
GAGCCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTC
ATTATGAACTCTCCACTGAAAATGTT
Found at i:38197 original size:17 final size:17
Alignment explanation
Indices: 38175--38286 Score: 60
Period size: 16 Copynumber: 6.8 Consensus size: 17
38165 TTAAAAAATT
38175 TCTTTTCTTTTTTTATC
1 TCTTTTCTTTTTTTATC
*
38192 TCTTTT-TTTCTTT-TC
1 TCTTTTCTTTTTTTATC
*
38207 TTCTTTT-TTTTTCTCAT-
1 -TCTTTTCTTTTT-TTATC
*
38224 TTTTCTTCTTTTTTTAT-
1 TCTT-TTCTTTTTTTATC
* *
38241 T-TTTCCTTTCTTTTTTC
1 TCTTTTCTTT-TTTTATC
*
38258 T-TTTTCTATTTTT-TC
1 TCTTTTCTTTTTTTATC
*
38273 TATTTTTCTTTTTT
1 T-CTTTTCTTTTTT
38287 CTCTCTCTCT
Statistics
Matches: 76, Mismatches: 10, Indels: 18
0.73 0.10 0.17
Matches are distributed among these distances:
15 10 0.13
16 30 0.39
17 30 0.39
18 6 0.08
ACGTcount: A:0.04, C:0.16, G:0.00, T:0.79
Consensus pattern (17 bp):
TCTTTTCTTTTTTTATC
Found at i:38199 original size:19 final size:19
Alignment explanation
Indices: 38177--38294 Score: 71
Period size: 19 Copynumber: 5.9 Consensus size: 19
38167 AAAAAATTTC
*
38177 TTTTCTTTTTTTATCTCTTT
1 TTTTCTTTTTTTCTCTC-TT
* *
38197 TTTTCTTTTCTTCT-TTTT
1 TTTTCTTTTTTTCTCTCTT
*
38215 TTTTCTCATTTTTCT-TCTT
1 TTTTCT-TTTTTTCTCTCTT
* *
38234 TTTT-TATTTTTCCTTTCTT
1 TTTTCT-TTTTTTCTCTCTT
* *
38253 TTTTCTTTTTCTATTTTTTCTAT
1 TTTTC-TTTT-T-TTCTCTCT-T
38276 TTTTCTTTTTTCTCTCTCT
1 TTTTCTTTTTT-TCTCTCT
38295 CTCTCTCTTT
Statistics
Matches: 77, Mismatches: 13, Indels: 15
0.73 0.12 0.14
Matches are distributed among these distances:
18 15 0.19
19 22 0.29
20 16 0.21
21 8 0.10
22 10 0.13
23 6 0.08
ACGTcount: A:0.04, C:0.18, G:0.00, T:0.78
Consensus pattern (19 bp):
TTTTCTTTTTTTCTCTCTT
Found at i:38205 original size:18 final size:17
Alignment explanation
Indices: 38175--38315 Score: 83
Period size: 17 Copynumber: 7.9 Consensus size: 17
38165 TTAAAAAATT
*
38175 TCTTTTCTTT-TTTTATC
1 TCTTTT-TTTCTTTTTTC
38192 TCTTTTTTTCTTTTCTTC
1 TCTTTTTTTCTTTT-TTC
*
38210 TTTTTTTTTCTCATTTTTC
1 TCTTTTTTTCT--TTTTTC
* *
38229 TTCTTTTTTTATTTTTCC
1 -TCTTTTTTTCTTTTTTC
*
38247 TTTCTTTTTTC-TTTTTC
1 TCT-TTTTTTCTTTTTTC
*
38264 T-ATTTTTTCTATTTTTC
1 TCTTTTTTTCT-TTTTTC
* *
38281 T-TTTTTCTCTCTCTCTCTC
1 TCTTTTT-T-TCT-TTTTTC
38300 TCTTTTATTTCTTTTT
1 TCTTTT-TTTCTTTTT
38316 GTTTTTTCTT
Statistics
Matches: 97, Mismatches: 15, Indels: 23
0.72 0.11 0.17
Matches are distributed among these distances:
15 7 0.07
16 3 0.03
17 29 0.30
18 26 0.27
19 14 0.14
20 17 0.18
21 1 0.01
ACGTcount: A:0.04, C:0.19, G:0.00, T:0.77
Consensus pattern (17 bp):
TCTTTTTTTCTTTTTTC
Found at i:38216 original size:30 final size:30
Alignment explanation
Indices: 38173--38244 Score: 87
Period size: 29 Copynumber: 2.4 Consensus size: 30
38163 TTTTAAAAAA
38173 TTTCTTTTCTTTTTTTATCTC-TTTTT-TTCT
1 TTTCTTTT-TTTTTTT-TCTCATTTTTCTTCT
*
38203 TTTCTTCTTTTTTTTTCTCATTTTTCTTCT
1 TTTCTTTTTTTTTTTTCTCATTTTTCTTCT
*
38233 TTT-TTTATTTTT
1 TTTCTTTTTTTTT
38245 CCTTTCTTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
28 4 0.11
29 19 0.51
30 14 0.38
ACGTcount: A:0.04, C:0.15, G:0.00, T:0.81
Consensus pattern (30 bp):
TTTCTTTTTTTTTTTTCTCATTTTTCTTCT
Found at i:38220 original size:38 final size:38
Alignment explanation
Indices: 38177--38262 Score: 104
Period size: 38 Copynumber: 2.3 Consensus size: 38
38167 AAAAAATTTC
* *
38177 TTTTCTTTTTTTATC-TCTTTTTTTCTTTTCTTCTTT-TT
1 TTTTCTTTTTTT-TCTTCTTTTTTTATTTT-TCCTTTCTT
**
38215 TTTTCTCATTTTTCTTCTTTTTTTATTTTTCCTTTCTT
1 TTTTCTTTTTTTTCTTCTTTTTTTATTTTTCCTTTCTT
38253 TTTTCTTTTT
1 TTTTCTTTTT
38263 CTATTTTTTC
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
37 7 0.17
38 33 0.82
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.80
Consensus pattern (38 bp):
TTTTCTTTTTTTTCTTCTTTTTTTATTTTTCCTTTCTT
Found at i:38250 original size:22 final size:20
Alignment explanation
Indices: 38194--38288 Score: 68
Period size: 22 Copynumber: 4.5 Consensus size: 20
38184 TTTTTATCTC
38194 TTTTTTTCTTTTCTTCTTTTT
1 TTTTTTTC-TTTCTTCTTTTT
38215 TTTTCTCATT-TTTCTTCTTTTT
1 TTTT-T--TTCTTTCTTCTTTTT
*
38237 TTATTTTTCCTTTCTT-TTTTC
1 TT-TTTTT-CTTTCTTCTTTTT
* * *
38258 TTTTTCTATTTTTTCTATTTT
1 TTTTTTTCTTTCTTCT-TTTT
38279 TCTTTTTTCT
1 T-TTTTTTCT
38289 CTCTCTCTCT
Statistics
Matches: 58, Mismatches: 7, Indels: 17
0.71 0.09 0.21
Matches are distributed among these distances:
19 5 0.09
20 7 0.12
21 14 0.24
22 28 0.48
23 2 0.03
24 2 0.03
ACGTcount: A:0.04, C:0.16, G:0.00, T:0.80
Consensus pattern (20 bp):
TTTTTTTCTTTCTTCTTTTT
Found at i:45053 original size:20 final size:21
Alignment explanation
Indices: 45024--45063 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
45014 CTATCTAGGC
45024 CTAAAGAA-CCAAAAAAGGTA
1 CTAAAGAACCCAAAAAAGGTA
*
45044 CTAAATAACCCAAAAAAGGT
1 CTAAAGAACCCAAAAAAGGT
45064 CCATTGACCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.57, C:0.17, G:0.12, T:0.12
Consensus pattern (21 bp):
CTAAAGAACCCAAAAAAGGTA
Found at i:45794 original size:5 final size:5
Alignment explanation
Indices: 45751--45792 Score: 75
Period size: 5 Copynumber: 8.4 Consensus size: 5
45741 AATAATAATA
*
45751 ATAGC ATAGC ATAGC ATAGC ATAGC ATAGC ATAGC ATTGC AT
1 ATAGC ATAGC ATAGC ATAGC ATAGC ATAGC ATAGC ATAGC AT
45793 TGTATGAGAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.24
Consensus pattern (5 bp):
ATAGC
Found at i:46707 original size:24 final size:23
Alignment explanation
Indices: 46645--46708 Score: 56
Period size: 24 Copynumber: 2.6 Consensus size: 23
46635 TTTTAAAAAT
*
46645 AAAGAAATGCATTTTAAGATTTTAA
1 AAAGAAATG--TTTTAACATTTTAA
* **
46670 AGAACAAAAATTTTAACATTTTCAA
1 A-AAGAAATGTTTTAACATTTT-AA
46695 AAAGAAATGTTTTA
1 AAAGAAATGTTTTA
46709 TACGATTGGT
Statistics
Matches: 30, Mismatches: 7, Indels: 5
0.71 0.17 0.12
Matches are distributed among these distances:
24 21 0.70
25 4 0.13
26 5 0.17
ACGTcount: A:0.50, C:0.06, G:0.09, T:0.34
Consensus pattern (23 bp):
AAAGAAATGTTTTAACATTTTAA
Found at i:52354 original size:21 final size:21
Alignment explanation
Indices: 52325--52462 Score: 147
Period size: 21 Copynumber: 6.7 Consensus size: 21
52315 ATTCTGACTA
* *
52325 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTTCCTAAT
*
52346 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTTCCTAAT
* *
52367 TCGCAATGCGATTTTTCTAAT
1 TCGCATTGCGATTTTCCTAAT
* *
52388 TCGCATTGCGATTTACGTAA-
1 TCGCATTGCGATTTTCCTAAT
*
52408 TCACATTGCGATTTTCCTAAT
1 TCGCATTGCGATTTTCCTAAT
* * *
52429 TCGCACTT-CAATTTACGTAA-
1 TCGCA-TTGCGATTTTCCTAAT
52449 TCGCATTGCGATTT
1 TCGCATTGCGATTT
52463 AGTAAATCGC
Statistics
Matches: 96, Mismatches: 18, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
19 2 0.02
20 27 0.28
21 65 0.68
22 2 0.02
ACGTcount: A:0.22, C:0.23, G:0.15, T:0.39
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCTAAT
Found at i:52378 original size:62 final size:62
Alignment explanation
Indices: 52303--52463 Score: 161
Period size: 62 Copynumber: 2.6 Consensus size: 62
52293 CAGTTTCTAG
* * *
52303 ATTCGCAACGCGATTCTGACT-A-TCGCATTGCGATTTCCCAAATTCGCGTTGCGATTTTCCTA
1 ATTCGCAACGCGATT-TGACTAATTCGCATTGCGATTTACCAAA-TCACATTGCGATTTTCCTA
* ** **
52365 ATTCGCAATGCGATTTTTCTAATTCGCATTGCGATTTACGTAATCACATTGCGATTTTCCTA
1 ATTCGCAACGCGATTTGACTAATTCGCATTGCGATTTACCAAATCACATTGCGATTTTCCTA
* *
52427 ATTCGC-ACTTCAATTT-ACGTAA-TCGCATTGCGATTTA
1 ATTCGCAAC-GCGATTTGAC-TAATTCGCATTGCGATTTA
52464 GTAAATCGCA
Statistics
Matches: 83, Mismatches: 12, Indels: 9
0.80 0.12 0.09
Matches are distributed among these distances:
61 20 0.24
62 46 0.55
63 17 0.20
ACGTcount: A:0.24, C:0.24, G:0.16, T:0.37
Consensus pattern (62 bp):
ATTCGCAACGCGATTTGACTAATTCGCATTGCGATTTACCAAATCACATTGCGATTTTCCTA
Found at i:52433 original size:41 final size:41
Alignment explanation
Indices: 52324--52462 Score: 172
Period size: 41 Copynumber: 3.4 Consensus size: 41
52314 GATTCTGACT
* * * * *
52324 ATCGCATTGCGATTTCCCAAATTCGCGTTGCGATTTTCCTA
1 ATCGCATTGCGATTTTCCTAATTCGCATTGCGATTTACGTA
* *
52365 ATTCGCAATGCGATTTTTCTAATTCGCATTGCGATTTACGTA
1 A-TCGCATTGCGATTTTCCTAATTCGCATTGCGATTTACGTA
* *
52407 ATCACATTGCGATTTTCCTAATTCGCACTT-CAATTTACGTA
1 ATCGCATTGCGATTTTCCTAATTCGCA-TTGCGATTTACGTA
52448 ATCGCATTGCGATTT
1 ATCGCATTGCGATTT
52463 AGTAAATCGC
Statistics
Matches: 84, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
41 48 0.57
42 36 0.43
ACGTcount: A:0.23, C:0.23, G:0.15, T:0.39
Consensus pattern (41 bp):
ATCGCATTGCGATTTTCCTAATTCGCATTGCGATTTACGTA
Found at i:53363 original size:24 final size:24
Alignment explanation
Indices: 53336--53389 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
53326 GTATTCGAAA
53336 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
53360 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
53384 TTTGAT
1 TTTGAT
53390 GATTTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:55928 original size:20 final size:19
Alignment explanation
Indices: 55900--55954 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
55890 CAATCATCTT
*
55900 AATGTCTATCGCAATGCAAA
1 AATGACTATCGCAATGC-AA
*
55920 AATGACTATCGCAATGCGA
1 AATGACTATCGCAATGCAA
**
55939 AATGAAAATCGCAATG
1 AATGACTATCGCAATG
55955 AGAGAATCGC
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 15 0.48
20 16 0.52
ACGTcount: A:0.42, C:0.18, G:0.18, T:0.22
Consensus pattern (19 bp):
AATGACTATCGCAATGCAA
Found at i:55943 original size:19 final size:17
Alignment explanation
Indices: 55907--56076 Score: 88
Period size: 19 Copynumber: 9.8 Consensus size: 17
55897 CTTAATGTCT
*
55907 ATCGCAATGCAAAAATGA
1 ATCGCAATGC-GAAATGA
55925 CTATCGCAATGCGAAATGAAA
1 --ATCGCAATGCGAAATG--A
*
55946 ATCGCAAT--GAGA-GA
1 ATCGCAATGCGAAATGA
55960 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATG--A
*
55979 ATCGCAA--CGAGA-GA
1 ATCGCAATGCGAAATGA
55993 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATG--A
**
56012 ATCGCAA--CG-AGGGA
1 ATCGCAATGCGAAATGA
*
56026 ATCGCAAAGCGAAATGAAA
1 ATCGCAATGCGAAATG--A
*
56045 ATCGCAAAGCGAAATGAAA
1 ATCGCAATGCGAAATG--A
*
56064 ATCGCAACGCGAA
1 ATCGCAATGCGAA
56077 TTTATTTTCG
Statistics
Matches: 123, Mismatches: 10, Indels: 35
0.73 0.06 0.21
Matches are distributed among these distances:
14 25 0.20
16 13 0.11
17 13 0.11
19 61 0.50
20 10 0.08
21 1 0.01
ACGTcount: A:0.46, C:0.18, G:0.23, T:0.13
Consensus pattern (17 bp):
ATCGCAATGCGAAATGA
Found at i:55964 original size:14 final size:14
Alignment explanation
Indices: 55945--56001 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
55935 GCGAAATGAA
55945 AATCGCAATGAGAG
1 AATCGCAATGAGAG
*
55959 AATCGCAATGCGAAATGAA
1 AATCGCAAT--G--A-GAG
*
55978 AATCGCAACGAGAG
1 AATCGCAATGAGAG
55992 AATCGCAATG
1 AATCGCAATG
56002 CGAAATGAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
14 20 0.59
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
19 10 0.29
ACGTcount: A:0.44, C:0.18, G:0.25, T:0.14
Consensus pattern (14 bp):
AATCGCAATGAGAG
Found at i:55964 original size:33 final size:33
Alignment explanation
Indices: 55927--56051 Score: 223
Period size: 33 Copynumber: 3.8 Consensus size: 33
55917 AAAAATGACT
*
55927 ATCGCAATGCGAAATGAAAATCGCAATGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
55960 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
55993 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
56026 ATCGCAAAGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
56052 AGCGAAATGA
Statistics
Matches: 89, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 89 1.00
ACGTcount: A:0.46, C:0.18, G:0.24, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:56015 original size:52 final size:51
Alignment explanation
Indices: 55959--56076 Score: 130
Period size: 52 Copynumber: 2.3 Consensus size: 51
55949 GCAATGAGAG
* * * *
55959 AATCGCAATGCGAAAT-GAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAACGCGAAATCGAAAAGCGAAACGA-A-AATCGCAAAGCGAAATGAA
* * * *
56011 AATCGCAACGAGGGAATCGCAAAGCGAAATGAAAATCGCAAAGCGAAATGAA
1 AATCGCAACG-CGAAATCGAAAAGCGAAACGAAAATCGCAAAGCGAAATGAA
56063 AATCGCAACGCGAA
1 AATCGCAACGCGAA
56077 TTTATTTTCG
Statistics
Matches: 54, Mismatches: 10, Indels: 5
0.78 0.14 0.07
Matches are distributed among these distances:
51 2 0.04
52 37 0.69
53 5 0.09
54 10 0.19
ACGTcount: A:0.47, C:0.19, G:0.24, T:0.11
Consensus pattern (51 bp):
AATCGCAACGCGAAATCGAAAAGCGAAACGAAAATCGCAAAGCGAAATGAA
Found at i:56235 original size:14 final size:14
Alignment explanation
Indices: 56216--56252 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
56206 CATCAATTAA
56216 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
56230 ACAAATCATCTTTT
1 ACAAATCAACTTTT
56244 ACAAATCAA
1 ACAAATCAA
56253 TTAAACAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:58101 original size:33 final size:33
Alignment explanation
Indices: 58055--58149 Score: 127
Period size: 33 Copynumber: 2.8 Consensus size: 33
58045 AAAAATGACT
* *
58055 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
*
58088 ATCGCAACACGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
* **
58121 ATCGTAACGCGAAACCAAAAATCGCAACG
1 ATCGCAACGCGAAA-TGAAAATCGCAACG
58150 CGATTATAGT
Statistics
Matches: 54, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
33 42 0.78
34 12 0.22
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.09
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:58111 original size:19 final size:19
Alignment explanation
Indices: 58055--58114 Score: 67
Period size: 19 Copynumber: 3.4 Consensus size: 19
58045 AAAAATGACT
*
58055 ATCGCAACGCGAAATGAAA
1 ATCGCAACACGAAATGAAA
*
58074 ATCGC-A-ACG--A-GAGA
1 ATCGCAACACGAAATGAAA
58088 ATCGCAACACGAAATGAAA
1 ATCGCAACACGAAATGAAA
58107 ATCGCAAC
1 ATCGCAAC
58115 GACAAAATCG
Statistics
Matches: 33, Mismatches: 3, Indels: 10
0.72 0.07 0.22
Matches are distributed among these distances:
14 8 0.24
15 2 0.06
16 3 0.09
17 2 0.06
18 2 0.06
19 16 0.48
ACGTcount: A:0.47, C:0.23, G:0.20, T:0.10
Consensus pattern (19 bp):
ATCGCAACACGAAATGAAA
Found at i:58196 original size:33 final size:34
Alignment explanation
Indices: 58159--58247 Score: 108
Period size: 38 Copynumber: 2.5 Consensus size: 34
58149 GCGATTATAG
58159 TTTCGCGTTGCGATTTTGT-CGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTGTCCGTTGCGATTTTCA
*
58192 TTTCGCGTTGCGATTTTCCTTTCCCGTTGCGATTTTCA
1 TTTCGCGTTGCGA-TTT--TGT-CCGTTGCGATTTTCA
*
58230 TTCTCTCGTTGCGATTTT
1 TT-TCGCGTTGCGATTTT
58248 CATTTCAACC
Statistics
Matches: 48, Mismatches: 2, Indels: 9
0.81 0.03 0.15
Matches are distributed among these distances:
33 13 0.27
34 3 0.06
36 3 0.06
38 19 0.40
39 10 0.21
ACGTcount: A:0.08, C:0.22, G:0.20, T:0.49
Consensus pattern (34 bp):
TTTCGCGTTGCGATTTTGTCCGTTGCGATTTTCA
Found at i:58241 original size:20 final size:19
Alignment explanation
Indices: 58177--58253 Score: 118
Period size: 19 Copynumber: 4.0 Consensus size: 19
58167 TGCGATTTTG
58177 TCGTTGCGATTTTCATTTC
1 TCGTTGCGATTTTCATTTC
* *
58196 GCGTTGCGATTTTCCTTTC
1 TCGTTGCGATTTTCATTTC
*
58215 CCGTTGCGATTTTCATTCTC
1 TCGTTGCGATTTTCATT-TC
58235 TCGTTGCGATTTTCATTTC
1 TCGTTGCGATTTTCATTTC
58254 AACCAAAAGA
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
19 34 0.65
20 18 0.35
ACGTcount: A:0.09, C:0.25, G:0.17, T:0.49
Consensus pattern (19 bp):
TCGTTGCGATTTTCATTTC
Found at i:58454 original size:94 final size:94
Alignment explanation
Indices: 58342--58706 Score: 467
Period size: 94 Copynumber: 4.1 Consensus size: 94
58332 ATGGATTGCA
* *
58342 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCAGAGTATTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
* *
58406 TTAGAAGAATTGGCAGCAAACGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
* * *
58435 TTACTTTCAACCAAAAGACAAAAAAAAAACAAATACTAACTTTACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
* * *
58500 TTAGCAGAATTGGCAGCAGCCGAGCAAGT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
*
58529 TTACTTTCAA-C------C---A-AAAGACAAATACTAACTTCACAATGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
58583 TTAGCAGAATTGGCAGCAACCGAATAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
*
58612 TTAC-TTCAACCAAAAGACAAAACAAAAGACAAATACTAACTTCACAGTGTT----AATAAACAG
1 TTACTTTCAACCAAAAGACAAAAC-AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAG
* *
58672 TTTAGCAGTATTGGCAGCAACCGAATAAAT
65 TTTAGCAGAATTGGCAGCAACCGAACAAAT
58702 TTACT
1 TTACT
58707 AAGCAATCTA
Statistics
Matches: 238, Mismatches: 20, Indels: 30
0.83 0.07 0.10
Matches are distributed among these distances:
82 5 0.02
83 68 0.29
84 1 0.00
87 1 0.00
89 1 0.00
90 41 0.17
92 1 0.00
93 5 0.02
94 115 0.48
ACGTcount: A:0.47, C:0.18, G:0.13, T:0.22
Consensus pattern (94 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
TTAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:58615 original size:83 final size:82
Alignment explanation
Indices: 58458--58632 Score: 278
Period size: 83 Copynumber: 2.1 Consensus size: 82
58448 AAAGACAAAA
* * * *
58458 AAAAAACAAATACTAACTTTACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAGCCGA
1 AAAAGACAAATACTAACTTCACAATGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGA
* *
58523 GCAAGTTTACTTTCAACC
66 ACAAATTTAC-TTCAACC
58541 AAAAGACAAATACTAACTTCACAATGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGA
1 AAAAGACAAATACTAACTTCACAATGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGA
*
58606 ATAAATTTACTTCAACC
66 ACAAATTTACTTCAACC
58623 AAAAGACAAA
1 AAAAGACAAA
58633 ACAAAAGACA
Statistics
Matches: 85, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
82 17 0.20
83 68 0.80
ACGTcount: A:0.45, C:0.19, G:0.14, T:0.22
Consensus pattern (82 bp):
AAAAGACAAATACTAACTTCACAATGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGA
ACAAATTTACTTCAACC
Found at i:58661 original size:177 final size:173
Alignment explanation
Indices: 58365--58695 Score: 511
Period size: 177 Copynumber: 1.9 Consensus size: 173
58355 AAGACAAAAC
* *
58365 AAAGACAAATACTAACTTCAGAGTATTAAAGAATACACAGTTTAGAAGAATTGGCAGCAAACGAA
1 AAAGACAAATACTAACTTCACAATATTAAAGAATACACAGTTTAGAAGAATTGGCAGCAAACGAA
* *
58430 CAAATTTACTTTCAACCAAAAGACAAAAAAAAAACAAATACTAACTTTACAGTGTTAAAGAATAC
66 CAAATTTACTTTCAACCAAAAGACAAAAAAAAAACAAATACTAACTTCACAGTGTT----AATAA
*
58495 ACAGTTTAGCAGAATTGGCAGCAGCCGAGCAAGTTTACTTTCAACCA
127 ACAGTTTAGCAGAATTGGCAGCAACCGAGCAAGTTTACTTTCAACCA
* * *
58542 AAAGACAAATACTAACTTCACAATGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAA
1 AAAGACAAATACTAACTTCACAATATTAAAGAATACACAGTTTAGAAGAATTGGCAGCAAACGAA
* *
58607 TAAATTTAC-TTCAACCAAAAGACAAAACAAAAGACAAATACTAACTTCACAGTGTTAATAAACA
66 CAAATTTACTTTCAACCAAAAGACAAAA-AAAAAACAAATACTAACTTCACAGTGTTAATAAACA
*
58671 GTTTAGCAGTATTGGCAGCAACCGA
130 GTTTAGCAGAATTGGCAGCAACCGA
58696 ATAAATTTAC
Statistics
Matches: 142, Mismatches: 11, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
173 30 0.21
176 18 0.13
177 94 0.66
ACGTcount: A:0.46, C:0.18, G:0.14, T:0.22
Consensus pattern (173 bp):
AAAGACAAATACTAACTTCACAATATTAAAGAATACACAGTTTAGAAGAATTGGCAGCAAACGAA
CAAATTTACTTTCAACCAAAAGACAAAAAAAAAACAAATACTAACTTCACAGTGTTAATAAACAG
TTTAGCAGAATTGGCAGCAACCGAGCAAGTTTACTTTCAACCA
Found at i:59135 original size:18 final size:18
Alignment explanation
Indices: 59112--59160 Score: 89
Period size: 18 Copynumber: 2.7 Consensus size: 18
59102 CGGGTCGATC
*
59112 AGGTGATTGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
59130 AGGTGATGGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
59148 AGGTGATGGCTCT
1 AGGTGATGGCTCT
59161 CGAAGTGGAG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.12, C:0.12, G:0.45, T:0.31
Consensus pattern (18 bp):
AGGTGATGGCTCTGGGTG
Found at i:60501 original size:19 final size:19
Alignment explanation
Indices: 60415--60521 Score: 98
Period size: 20 Copynumber: 5.8 Consensus size: 19
60405 TCTTTTGGTT
60415 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
* *
60434 GAGAATGAAAATCACAACGTG
1 GA-AATGAAAATCGCAACG-A
**
60455 GAAATGACTATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
60474 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
60488 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
**
60507 GAAACCAAAATCGCA
1 GAAATGAAAATCGCA
60522 TTGCGATTTT
Statistics
Matches: 70, Mismatches: 11, Indels: 14
0.74 0.12 0.15
Matches are distributed among these distances:
14 10 0.14
16 2 0.03
17 2 0.03
19 26 0.37
20 28 0.40
21 2 0.03
ACGTcount: A:0.48, C:0.20, G:0.21, T:0.11
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:60587 original size:20 final size:19
Alignment explanation
Indices: 60517--60588 Score: 64
Period size: 20 Copynumber: 4.0 Consensus size: 19
60507 GAAACCAAAA
*
60517 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
60536 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
60550 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
60569 TCCGCGTTGCGATTTTCATT
1 T-CGCGTTGCGATTTTCATT
60589 CTCGAAACTA
Statistics
Matches: 41, Mismatches: 6, Indels: 11
0.71 0.10 0.19
Matches are distributed among these distances:
14 10 0.24
16 2 0.05
17 3 0.07
19 11 0.27
20 15 0.37
ACGTcount: A:0.12, C:0.24, G:0.21, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:61162 original size:20 final size:20
Alignment explanation
Indices: 61135--61228 Score: 107
Period size: 20 Copynumber: 4.7 Consensus size: 20
61125 CGATAGTCAG
61135 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* * *
61155 ATTTGCATTGCGATTTTCCT
1 ATTCGCATTGCGATTTACGT
* *
61175 AATTCGTATTGCGATTTACTT
1 -ATTCGCATTGCGATTTACGT
* * *
61196 AATCACGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
61216 ATTCGCATTGCGA
1 ATTCGCATTGCGA
61229 ATTATGAAAA
Statistics
Matches: 58, Mismatches: 15, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
20 42 0.72
21 16 0.28
ACGTcount: A:0.21, C:0.19, G:0.18, T:0.41
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:61207 original size:41 final size:40
Alignment explanation
Indices: 61135--61228 Score: 107
Period size: 41 Copynumber: 2.3 Consensus size: 40
61125 CGATAGTCAG
* ** *
61135 ATTCGCATTGCGATTTACGTATTTGCATTGCGATTTTCCT
1 ATTCGCATTGCGATTTACGTAATCACATTGCGATTTACCT
* * * *
61175 AATTCGTATTGCGATTTACTTAATCACGTTGCGATTTACGT
1 -ATTCGCATTGCGATTTACGTAATCACATTGCGATTTACCT
61216 ATTCGCATTGCGA
1 ATTCGCATTGCGA
61229 ATTATGAAAA
Statistics
Matches: 44, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
40 12 0.27
41 32 0.73
ACGTcount: A:0.21, C:0.19, G:0.18, T:0.41
Consensus pattern (40 bp):
ATTCGCATTGCGATTTACGTAATCACATTGCGATTTACCT
Found at i:61249 original size:21 final size:21
Alignment explanation
Indices: 61225--61292 Score: 93
Period size: 21 Copynumber: 3.3 Consensus size: 21
61215 TATTCGCATT
*
61225 GCGAATTATGAAAATCGCAAC
1 GCGAATTACGAAAATCGCAAC
* *
61246 GCGAA-TACGTAAATCGCAAT
1 GCGAATTACGAAAATCGCAAC
*
61266 GCGAATTAGGAAAATCGCAAC
1 GCGAATTACGAAAATCGCAAC
61287 GCGAAT
1 GCGAAT
61293 CTGGGAAATC
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
20 17 0.43
21 23 0.57
ACGTcount: A:0.41, C:0.19, G:0.22, T:0.18
Consensus pattern (21 bp):
GCGAATTACGAAAATCGCAAC
Found at i:61269 original size:41 final size:41
Alignment explanation
Indices: 61218--61311 Score: 136
Period size: 41 Copynumber: 2.3 Consensus size: 41
61208 ATTTACGTAT
* * *
61218 TCGCATTGCGAATTATGAAAATCGCAACGCGAATAC-GTAAA
1 TCGCAATGCGAATTAGGAAAATCGCAACGCGAAT-CGGGAAA
61259 TCGCAATGCGAATTAGGAAAATCGCAACGCGAATCTGGGAAA
1 TCGCAATGCGAATTAGGAAAATCGCAACGCGAATC-GGGAAA
61301 TCGCAATGCGA
1 TCGCAATGCGA
61312 TAGTCAGAAT
Statistics
Matches: 48, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
40 1 0.02
41 32 0.67
42 15 0.31
ACGTcount: A:0.37, C:0.20, G:0.23, T:0.19
Consensus pattern (41 bp):
TCGCAATGCGAATTAGGAAAATCGCAACGCGAATCGGGAAA
Found at i:61301 original size:21 final size:21
Alignment explanation
Indices: 61234--61311 Score: 81
Period size: 21 Copynumber: 3.8 Consensus size: 21
61224 TGCGAATTAT
61234 GAAAATCGCAACGCGAATAC--
1 GAAAATCGCAACGCGAAT-CTG
* *
61254 GTAAATCGCAATGCGAAT-TAG
1 GAAAATCGCAACGCGAATCT-G
61275 GAAAATCGCAACGCGAATCTG
1 GAAAATCGCAACGCGAATCTG
* *
61296 GGAAATCGCAATGCGA
1 GAAAATCGCAACGCGA
61312 TAGTCAGAAT
Statistics
Matches: 48, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
20 16 0.33
21 31 0.65
22 1 0.02
ACGTcount: A:0.40, C:0.21, G:0.24, T:0.15
Consensus pattern (21 bp):
GAAAATCGCAACGCGAATCTG
Found at i:62715 original size:192 final size:193
Alignment explanation
Indices: 62336--62689 Score: 484
Period size: 192 Copynumber: 1.8 Consensus size: 193
62326 ATATATGGTG
62336 ACGTTATGCATAATCATCATTCATAATATTATTAGGTAACAATATATTATGTCACTAAAAATGTG
1 ACGTTATGCATAATCATCATTCATAATATTATTAGGTAACAATATATTATGTCACTAAAAATGTG
* *
62401 ACAATATCTTTTTCATCACATATAAGTTGATTTTAATGCATTATTTGTGACAATATAAACTATCA
66 ACAATATCTCTTTCATCACATATAAGTTGATTTTAATGCATTATCTGTGACAATATAAACTATCA
* ** * * *
62466 ATAATGAAATCTTATTTAATTTAGTGGCGTAACCAACTGACATAGAATATAAATTATAAAGCA
131 ATAACGAAATCTTACATAATTTAGAGACATAACCAACTGACATAGAATATAAATTATAAAGCA
* * * *
62529 ACGTTATGCATAGA-CGTCATTCATAATATTATTATGTAAC-ATTTA-TATTGTCACTAAAAATT
1 ACGTTATGCATA-ATCATCATTCATAATATTATTAGGTAACAATATATTA-TGTCACTAAAAATG
* * * *
62591 TGACAATATCTCTTTCGTCACATATAGGTT-ATTTTTAATGTATTATCTGTGACGATATAAA-TC
64 TGACAATATCTCTTTCATCACATATAAGTTGA-TTTTAATGCATTATCTGTGACAATATAAACT-
*
62654 ATCAATAACGAAATTTTACATAATTTAGAGACATAA
127 ATCAATAACGAAATCTTACATAATTTAGAGACATAA
62690 TTAGTTGTCA
Statistics
Matches: 140, Mismatches: 17, Indels: 9
0.84 0.10 0.05
Matches are distributed among these distances:
191 4 0.03
192 99 0.71
193 36 0.26
194 1 0.01
ACGTcount: A:0.39, C:0.13, G:0.10, T:0.38
Consensus pattern (193 bp):
ACGTTATGCATAATCATCATTCATAATATTATTAGGTAACAATATATTATGTCACTAAAAATGTG
ACAATATCTCTTTCATCACATATAAGTTGATTTTAATGCATTATCTGTGACAATATAAACTATCA
ATAACGAAATCTTACATAATTTAGAGACATAACCAACTGACATAGAATATAAATTATAAAGCA
Found at i:65502 original size:233 final size:233
Alignment explanation
Indices: 65095--65563 Score: 902
Period size: 233 Copynumber: 2.0 Consensus size: 233
65085 CAATTCTGGG
65095 TACTGTGAGGGTGTCAATCATTCACCACACGTAATCGACTCTAAACCCTTTCAAAATGAATTTCT
1 TACTGTGAGGGTGTCAATCATTCACCACACGTAATCGACTCTAAACCCTTTCAAAATGAATTTCT
65160 GGTAACATGCAGATCAATTTTGTCTTTTTAAAAGAATTTTATAAAAAAAATCTTTAAAAAACGTT
66 GGTAACATGCAGATCAATTTTGTCTTTTTAAAAGAATTTTATAAAAAAAATCTTTAAAAAACGTT
65225 TTTAGGCATTTAACCTACCTAACCCAAAGGTCGATGGCGACTCCATATTTTTTATAACATTTCAA
131 TTTAGGCATTTAACCTACCTAACCCAAAGGTCGATGGCGACTCCATATTTTTTATAACATTTCAA
*
65290 AACCCGTCAAATGCGGCCCAAAAAAAGCCGTTAAGAAA
196 AACCCGTCAAATGCGGCCCAAAAAAAGCCGTTAAAAAA
* *
65328 TACTGTGATGGTGTCAATCATTCCCCACACGTAATCGACTCTAAACCCTTTCAAAATGAATTTCT
1 TACTGTGAGGGTGTCAATCATTCACCACACGTAATCGACTCTAAACCCTTTCAAAATGAATTTCT
65393 GGTAACATGCAGATCAATTTTGTCTTTTTAAAAGAATTTTATAAAAAAAATCTTTAAAAAACGTT
66 GGTAACATGCAGATCAATTTTGTCTTTTTAAAAGAATTTTATAAAAAAAATCTTTAAAAAACGTT
65458 TTTAGGCATTTAACCTACCTAACCCAAAGGTCGATGGCGACTCCATATTTTTTATAACATTTCAA
131 TTTAGGCATTTAACCTACCTAACCCAAAGGTCGATGGCGACTCCATATTTTTTATAACATTTCAA
*
65523 AACCCGTCTAATGCGGCCCAAAAAAAGCCGTTAAAAAA
196 AACCCGTCAAATGCGGCCCAAAAAAAGCCGTTAAAAAA
65561 TAC
1 TAC
65564 ATTTATATAA
Statistics
Matches: 232, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
233 232 1.00
ACGTcount: A:0.36, C:0.20, G:0.13, T:0.30
Consensus pattern (233 bp):
TACTGTGAGGGTGTCAATCATTCACCACACGTAATCGACTCTAAACCCTTTCAAAATGAATTTCT
GGTAACATGCAGATCAATTTTGTCTTTTTAAAAGAATTTTATAAAAAAAATCTTTAAAAAACGTT
TTTAGGCATTTAACCTACCTAACCCAAAGGTCGATGGCGACTCCATATTTTTTATAACATTTCAA
AACCCGTCAAATGCGGCCCAAAAAAAGCCGTTAAAAAA
Found at i:70366 original size:14 final size:15
Alignment explanation
Indices: 70338--70374 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
70328 TATTTTGAAT
70338 TTCAAAATGATTTTA
1 TTCAAAATGATTTTA
70353 TTCAAAAT-ATTTTA
1 TTCAAAATGATTTTA
*
70367 TTAAAAAT
1 TTCAAAAT
70375 CAATAAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 13 0.62
15 8 0.38
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (15 bp):
TTCAAAATGATTTTA
Found at i:74295 original size:19 final size:19
Alignment explanation
Indices: 74268--74321 Score: 72
Period size: 19 Copynumber: 2.8 Consensus size: 19
74258 ATTTGTTTTA
* *
74268 TTTATTATTATTATTTTGT
1 TTTATTATTATTATTATAT
*
74287 TTTAATATTATTATTATAT
1 TTTATTATTATTATTATAT
*
74306 TATATTATTATTATTA
1 TTTATTATTATTATTA
74322 AATAAATAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (19 bp):
TTTATTATTATTATTATAT
Found at i:74295 original size:22 final size:22
Alignment explanation
Indices: 74259--74321 Score: 81
Period size: 22 Copynumber: 2.8 Consensus size: 22
74249 TTTTATTTCA
74259 TTTGTTTTATTTATTATTATTAT
1 TTTGTTTTA-TTATTATTATTAT
*
74282 TTTGTTTTAATATTATTATTAT
1 TTTGTTTTATTATTATTATTAT
* * *
74304 ATTATATTATTATTATTA
1 TTTGTTTTATTATTATTA
74322 AATAAATAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
22 26 0.74
23 9 0.26
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (22 bp):
TTTGTTTTATTATTATTATTAT
Found at i:74342 original size:3 final size:3
Alignment explanation
Indices: 74269--74321 Score: 60
Period size: 3 Copynumber: 19.0 Consensus size: 3
74259 TTTGTTTTAT
* *
74269 TTA TTA TTA TTA TT- TTG TT- TTA ATA TTA TTA TTA -TA TTA -TA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
74313 TTA TTA TTA
1 TTA TTA TTA
74322 AATAAATAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
2 8 0.18
3 36 0.82
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:75681 original size:16 final size:16
Alignment explanation
Indices: 75640--75682 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
75630 TTATTTGCAA
75640 TATTATTTTATTATTAT
1 TATTA-TTTATTATTAT
*
75657 TACTT-TTTATTATTCT
1 TA-TTATTTATTATTAT
75673 TATTATTTAT
1 TATTATTTAT
75683 ATAAATAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
15 2 0.09
16 17 0.74
17 2 0.09
18 2 0.09
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.70
Consensus pattern (16 bp):
TATTATTTATTATTAT
Found at i:75888 original size:20 final size:18
Alignment explanation
Indices: 75858--75905 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
75848 TAAATATCTT
*
75858 ATTTTTAAATTATATATTA
1 ATTTTTTAATTAT-TATTA
*
75877 ATTGTTTTAATTATTATTT
1 ATT-TTTTAATTATTATTA
75896 ATTTTTTAAT
1 ATTTTTTAAT
75906 ATCAAAAAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 7 0.27
19 10 0.38
20 9 0.35
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (18 bp):
ATTTTTTAATTATTATTA
Done.