Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032248.1 Gossypioides kirkii chromosome KI_06
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: 60359545
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 900 characters in sequence are not A, C, G, or T
File 55 of 193
Found at i:17096784 original size:29 final size:29
Alignment explanation
Indices: 17096742--17096826 Score: 107
Period size: 29 Copynumber: 2.9 Consensus size: 29
17096732 ATGGGGGTAT
*
17096742 CATGTCTACATTTGTAACTGTATCTATAC
1 CATGTCTGCATTTGTAACTGTATCTATAC
* *
17096771 CATGTCTGCATTTGTAACTGTCTCTATAT
1 CATGTCTGCATTTGTAACTGTATCTATAC
* * * *
17096800 CATGTCTGGATCTATAACTATATCTAT
1 CATGTCTGCATTTGTAACTGTATCTAT
17096827 GACATGTTTG
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 48 1.00
ACGTcount: A:0.26, C:0.20, G:0.12, T:0.42
Consensus pattern (29 bp):
CATGTCTGCATTTGTAACTGTATCTATAC
Found at i:17096832 original size:29 final size:29
Alignment explanation
Indices: 17096742--17096853 Score: 100
Period size: 29 Copynumber: 3.9 Consensus size: 29
17096732 ATGGGGGTAT
* * *
17096742 CATGTCTACATTTGTAACTGTATCTATAC
1 CATGTCTGCATCTATAACTGTATCTATAC
* * * *
17096771 CATGTCTGCATTTGTAACTGTCTCTATAT
1 CATGTCTGCATCTATAACTGTATCTATAC
* *
17096800 CATGTCTGGATCTATAACTATATCTATGA-
1 CATGTCTGCATCTATAACTGTATCTAT-AC
* * *
17096829 CATGTTTGTATCTATAATTGTATCT
1 CATGTCTGCATCTATAACTGTATCT
17096854 TATTATATCT
Statistics
Matches: 70, Mismatches: 12, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
29 69 0.99
30 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.12, T:0.44
Consensus pattern (29 bp):
CATGTCTGCATCTATAACTGTATCTATAC
Found at i:17097982 original size:19 final size:17
Alignment explanation
Indices: 17097949--17097997 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 17
17097939 TTAAAAAAAG
17097949 TATAAAA-ATAAAATATA
1 TATAAAATATAAAA-ATA
* *
17097966 TTTAAAATTTAAAAATA
1 TATAAAATATAAAAATA
17097983 TATAAAATATAAAAA
1 TATAAAATATAAAAA
17097998 GTCATAACAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
17 22 0.81
18 5 0.19
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
TATAAAATATAAAAATA
Found at i:17102489 original size:21 final size:21
Alignment explanation
Indices: 17102465--17102507 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
17102455 CCAAGATAGA
*
17102465 AATAAAAAGTAAGAGTATGTG
1 AATAAAAAGCAAGAGTATGTG
* * *
17102486 AATATAGAGCAGGAGTATGTG
1 AATAAAAAGCAAGAGTATGTG
17102507 A
1 A
17102508 CTCAAGATGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.47, C:0.02, G:0.28, T:0.23
Consensus pattern (21 bp):
AATAAAAAGCAAGAGTATGTG
Found at i:17104080 original size:20 final size:21
Alignment explanation
Indices: 17104043--17104094 Score: 56
Period size: 20 Copynumber: 2.5 Consensus size: 21
17104033 GTATCAGTTT
*
17104043 ATTTATATTAAGTGTAAATA-G
1 ATTTA-ATTAAGTGTAAAAATG
17104064 ATTTAATTAAGAT-TAAAAATG
1 ATTTAATTAAG-TGTAAAAATG
17104085 A-TTAATTAAG
1 ATTTAATTAAG
17104095 GCTTAATGAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
20 20 0.71
21 8 0.29
ACGTcount: A:0.48, C:0.00, G:0.12, T:0.40
Consensus pattern (21 bp):
ATTTAATTAAGTGTAAAAATG
Found at i:17120482 original size:60 final size:56
Alignment explanation
Indices: 17120375--17120621 Score: 252
Period size: 52 Copynumber: 4.6 Consensus size: 56
17120365 TTCGTGTATG
* * * * *
17120375 ATACTCATGATGACACAGAGTCATCGGACC-CTTAATTCGCAATAGGATTCATTTCCTTT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAA-AGGATTCA-TT-C-TT
* *
17120434 AATACTCACGATAACACATAGTCATCGGACCTCATAATCCTTAAAGGATTCA----T
1 -ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCATTCTT
* *
17120487 ACACTCACGATGACACATAGTCATCGAACCTCATAATCCGTAAAGG----ATTCTT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCATTCTT
17120539 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGG----ATTCTT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCATTCTT
*
17120591 ATACTCACGATGACA-AGTAGTCATTGGACCT
1 ATACTCACGATGACACA-TAGTCATCGGACCT
17120622 TTTCATTTAC
Statistics
Matches: 167, Mismatches: 14, Indels: 20
0.83 0.07 0.10
Matches are distributed among these distances:
48 1 0.01
51 1 0.01
52 121 0.72
53 1 0.01
60 35 0.21
61 8 0.05
ACGTcount: A:0.33, C:0.25, G:0.15, T:0.28
Consensus pattern (56 bp):
ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCATTCTT
Found at i:17120518 original size:52 final size:52
Alignment explanation
Indices: 17120435--17120621 Score: 304
Period size: 52 Copynumber: 3.6 Consensus size: 52
17120425 ATTTCCTTTA
* * *
17120435 ATACTCACGATAACACATAGTCATCGGACCTCATAATCCTTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCTT
* *
17120487 ACACTCACGATGACACATAGTCATCGAACCTCATAATCCGTAAAGGATTCTT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCTT
17120539 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCTT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCTT
*
17120591 ATACTCACGATGACA-AGTAGTCATTGGACCT
1 ATACTCACGATGACACA-TAGTCATCGGACCT
17120622 TTTCATTTAC
Statistics
Matches: 126, Mismatches: 8, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
51 1 0.01
52 125 0.99
ACGTcount: A:0.34, C:0.25, G:0.14, T:0.26
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCTT
Found at i:17123026 original size:29 final size:29
Alignment explanation
Indices: 17122984--17123041 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
17122974 TAAAGTATCT
17122984 CATTTGCAAAATTTTAATGGATTGAATTA
1 CATTTGCAAAATTTTAATGGATTGAATTA
17123013 CATTTGCAAAATTTTAATGGATTGAATTA
1 CATTTGCAAAATTTTAATGGATTGAATTA
17123042 GAGGTGTTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.38, C:0.07, G:0.14, T:0.41
Consensus pattern (29 bp):
CATTTGCAAAATTTTAATGGATTGAATTA
Found at i:17123359 original size:18 final size:16
Alignment explanation
Indices: 17123328--17123361 Score: 50
Period size: 18 Copynumber: 2.0 Consensus size: 16
17123318 TAATGTGTTC
17123328 TAAATTAGATAATATA
1 TAAATTAGATAATATA
17123344 TAAATATAGCATAATATA
1 TAAAT-TAG-ATAATATA
17123362 ATGTATTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 3 0.19
18 8 0.50
ACGTcount: A:0.56, C:0.03, G:0.06, T:0.35
Consensus pattern (16 bp):
TAAATTAGATAATATA
Found at i:17123601 original size:35 final size:35
Alignment explanation
Indices: 17123550--17123619 Score: 122
Period size: 35 Copynumber: 2.0 Consensus size: 35
17123540 TTAATAGATT
*
17123550 TATTGCATTTATGATTAAAAAACAAAATAAAGACA
1 TATTGCATTTAAGATTAAAAAACAAAATAAAGACA
*
17123585 TATTGCATTTAAGATTAAAAAACAAAATAAGGACA
1 TATTGCATTTAAGATTAAAAAACAAAATAAAGACA
17123620 GAGGATGAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.54, C:0.09, G:0.10, T:0.27
Consensus pattern (35 bp):
TATTGCATTTAAGATTAAAAAACAAAATAAAGACA
Found at i:17125764 original size:23 final size:24
Alignment explanation
Indices: 17125732--17125776 Score: 83
Period size: 23 Copynumber: 1.9 Consensus size: 24
17125722 AACAAGCTCA
17125732 TTTATTGACTCGTTTATTTATTCG
1 TTTATTGACTCGTTTATTTATTCG
17125756 TTTA-TGACTCGTTTATTTATT
1 TTTATTGACTCGTTTATTTATT
17125777 AATGATATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
23 17 0.81
24 4 0.19
ACGTcount: A:0.18, C:0.11, G:0.11, T:0.60
Consensus pattern (24 bp):
TTTATTGACTCGTTTATTTATTCG
Found at i:17125769 original size:11 final size:12
Alignment explanation
Indices: 17125732--17125772 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
17125722 AACAAGCTCA
17125732 TTTATTGACTCG
1 TTTATTGACTCG
* *
17125744 TTTATTTATTCG
1 TTTATTGACTCG
17125756 TTTA-TGACTCG
1 TTTATTGACTCG
17125767 TTTATT
1 TTTATT
17125773 TATTAATGAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
11 9 0.38
12 15 0.62
ACGTcount: A:0.17, C:0.12, G:0.12, T:0.59
Consensus pattern (12 bp):
TTTATTGACTCG
Found at i:17126803 original size:18 final size:19
Alignment explanation
Indices: 17126775--17126812 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
17126765 GTTGGATTCT
*
17126775 AATATATATATATATTTAA
1 AATATATATATATAATTAA
17126794 AATA-ATATATATAATTAA
1 AATATATATATATAATTAA
17126812 A
1 A
17126813 TAAAATTCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
AATATATATATATAATTAA
Found at i:17126816 original size:22 final size:22
Alignment explanation
Indices: 17126774--17126818 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
17126764 TGTTGGATTC
**
17126774 TAATATATATATATATTTAAAA
1 TAATATATATATATAAATAAAA
17126796 TAATATATATA-ATTAAATAAAA
1 TAATATATATATA-TAAATAAAA
17126818 T
1 T
17126819 TCTAAAAAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 1 0.05
22 19 0.95
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
TAATATATATATATAAATAAAA
Found at i:17126862 original size:15 final size:16
Alignment explanation
Indices: 17126842--17126894 Score: 56
Period size: 16 Copynumber: 3.3 Consensus size: 16
17126832 TTTTTATTTT
17126842 ATAAAAAAACAT-AAA
1 ATAAAAAAACATCAAA
*
17126857 ATAAAAAAA-AGTGAAA
1 ATAAAAAAACA-TCAAA
*
17126873 ATACAAAAACTATCAAA
1 ATAAAAAAAC-ATCAAA
17126890 ATAAA
1 ATAAA
17126895 TTCAAAAACA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
14 1 0.03
15 10 0.32
16 11 0.35
17 8 0.26
18 1 0.03
ACGTcount: A:0.74, C:0.08, G:0.04, T:0.15
Consensus pattern (16 bp):
ATAAAAAAACATCAAA
Found at i:17137330 original size:21 final size:21
Alignment explanation
Indices: 17137306--17137353 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
17137296 TTAATATATG
17137306 TAATTTTCATAATTTCA-TCAC
1 TAATTTT-ATAATTTCATTCAC
*
17137327 TAATCTTTATCATTTCATTCAC
1 TAAT-TTTATAATTTCATTCAC
17137349 -AATTT
1 TAATTT
17137354 ATCTTTACAC
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
20 2 0.08
21 15 0.62
22 7 0.29
ACGTcount: A:0.31, C:0.19, G:0.00, T:0.50
Consensus pattern (21 bp):
TAATTTTATAATTTCATTCAC
Found at i:17137623 original size:22 final size:20
Alignment explanation
Indices: 17137595--17137673 Score: 77
Period size: 22 Copynumber: 3.6 Consensus size: 20
17137585 AGAAGGCATC
17137595 GAAGTGCAAATCACTAAGCACT
1 GAAGTGCAAA-CA-TAAGCACT
*
17137617 GAAGTGCAAAACAATAGGCACT
1 GAAGTGC-AAAC-ATAAGCACT
*
17137639 GAAGTGCAGAACGATAAGCACC
1 GAAGTGCA-AAC-ATAAGCACT
17137661 GAAGTGCGAAACA
1 GAAGTGC-AAACA
17137674 AAAAATGCCT
Statistics
Matches: 49, Mismatches: 4, Indels: 9
0.79 0.06 0.15
Matches are distributed among these distances:
21 2 0.04
22 42 0.86
23 5 0.10
ACGTcount: A:0.43, C:0.20, G:0.24, T:0.13
Consensus pattern (20 bp):
GAAGTGCAAACATAAGCACT
Found at i:17139152 original size:11 final size:11
Alignment explanation
Indices: 17139135--17139178 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
17139125 AATCATTTAA
17139135 TAATAAAATAT
1 TAATAAAATAT
* *
17139146 TACTAAAAATCT
1 TAAT-AAAATAT
17139158 TAATAAAATAT
1 TAATAAAATAT
*
17139169 TAATTAAATA
1 TAATAAAATA
17139179 ACAGTTTTCT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
11 18 0.67
12 9 0.33
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (11 bp):
TAATAAAATAT
Found at i:17142030 original size:13 final size:13
Alignment explanation
Indices: 17142012--17142064 Score: 63
Period size: 13 Copynumber: 4.1 Consensus size: 13
17142002 AGTTTAGCAT
17142012 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
*
17142025 TGCTTTTAAAAAG
1 TGCTTTTGAAAAG
**
17142038 TG-TGGTGAAAAAG
1 TGCTTTTG-AAAAG
17142051 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
17142064 T
1 T
17142065 TTGGTTTAAG
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
12 2 0.06
13 27 0.84
14 3 0.09
ACGTcount: A:0.34, C:0.06, G:0.25, T:0.36
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:17142055 original size:26 final size:26
Alignment explanation
Indices: 17142020--17142069 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
17142010 ATTGCTTTTG
17142020 AAAAGTGCTTTTAAAAAGTGTGGTGA
1 AAAAGTGCTTTTAAAAAGTGTGGTGA
* *
17142046 AAAAGTGCTTTTGAAAAGTTTGGT
1 AAAAGTGCTTTTAAAAAGTGTGGT
17142070 TTAAGATTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.36, C:0.04, G:0.26, T:0.34
Consensus pattern (26 bp):
AAAAGTGCTTTTAAAAAGTGTGGTGA
Found at i:17143252 original size:18 final size:18
Alignment explanation
Indices: 17143229--17143293 Score: 112
Period size: 18 Copynumber: 3.6 Consensus size: 18
17143219 GGAAGGAGTA
17143229 GCATACTGGCTCGTTAGG
1 GCATACTGGCTCGTTAGG
*
17143247 GCATACTGACTCGTTAGG
1 GCATACTGGCTCGTTAGG
*
17143265 GCATACTGGCTCGTTAGA
1 GCATACTGGCTCGTTAGG
17143283 GCATACTGGCT
1 GCATACTGGCT
17143294 TGTAGGACCA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 44 1.00
ACGTcount: A:0.20, C:0.23, G:0.29, T:0.28
Consensus pattern (18 bp):
GCATACTGGCTCGTTAGG
Found at i:17144478 original size:23 final size:22
Alignment explanation
Indices: 17144452--17144557 Score: 62
Period size: 21 Copynumber: 4.9 Consensus size: 22
17144442 TATATGAAAT
*
17144452 ATTAATTTTAAATATTTCTAAGA
1 ATTAATTTTAAATATTTATAA-A
* *
17144475 ATTAATATTAATTATTTATAAA
1 ATTAATTTTAAATATTTATAAA
* *
17144497 ATTTAA--TTAGAT-TATAT-AA
1 A-TTAATTTTAAATATTTATAAA
* *
17144516 ACTATATTTTAAATATTTA-AAT
1 ATTA-ATTTTAAATATTTATAAA
*
17144538 A-TAATCATTAAATATTTATA
1 ATTAAT-TTTAAATATTTATA
17144558 TTTAAATATT
Statistics
Matches: 64, Mismatches: 11, Indels: 17
0.70 0.12 0.18
Matches are distributed among these distances:
18 2 0.03
19 4 0.06
20 6 0.09
21 22 0.34
22 8 0.12
23 22 0.34
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.48
Consensus pattern (22 bp):
ATTAATTTTAAATATTTATAAA
Found at i:17144564 original size:14 final size:14
Alignment explanation
Indices: 17144527--17144569 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
17144517 CTATATTTTA
17144527 AATATTTAAATA-T
1 AATATTTAAATATT
17144540 AATCA-TTAAATATT
1 AAT-ATTTAAATATT
*
17144554 TATATTTAAATATT
1 AATATTTAAATATT
17144568 AA
1 AA
17144570 CACAGTTGTC
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
13 11 0.44
14 14 0.56
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (14 bp):
AATATTTAAATATT
Found at i:17146455 original size:72 final size:72
Alignment explanation
Indices: 17146272--17146460 Score: 317
Period size: 72 Copynumber: 2.6 Consensus size: 72
17146262 AACAAATTTT
* * *
17146272 ATATCC-AAAATCAAATATAAACAACTATTGATAAAACTAAATTACACATAAATAAGTAGAACAT
1 ATATCCAAAAACCAAACATAAACAACTATTGATAAAACTAGATTACACATAAATAAGTAGAACAT
17146336 AAATTCA
66 AAATTCA
*
17146343 ATATCCAAAAACCAAACATAAACAACTATTGGTAAAACTAGATTACACATAAATAAGTAGAACAT
1 ATATCCAAAAACCAAACATAAACAACTATTGATAAAACTAGATTACACATAAATAAGTAGAACAT
17146408 AAATTCA
66 AAATTCA
* *
17146415 ATATCCAAAAACCAAACATAAACAACTACTGATAAAACTAGTTTAC
1 ATATCCAAAAACCAAACATAAACAACTATTGATAAAACTAGATTAC
17146461 CATTGTTGTT
Statistics
Matches: 110, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
71 6 0.05
72 104 0.95
ACGTcount: A:0.54, C:0.17, G:0.05, T:0.23
Consensus pattern (72 bp):
ATATCCAAAAACCAAACATAAACAACTATTGATAAAACTAGATTACACATAAATAAGTAGAACAT
AAATTCA
Found at i:17149489 original size:12 final size:11
Alignment explanation
Indices: 17149460--17149493 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
17149450 AGAGAGATTT
17149460 TGGAAGAAAAA
1 TGGAAGAAAAA
*
17149471 AGGAAGAAGAAA
1 TGGAAGAA-AAA
17149483 TGGAAGAAAAA
1 TGGAAGAAAAA
17149494 ATGAAAATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.65, C:0.00, G:0.29, T:0.06
Consensus pattern (11 bp):
TGGAAGAAAAA
Found at i:17149495 original size:12 final size:12
Alignment explanation
Indices: 17149460--17149496 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
17149450 AGAGAGATTT
17149460 TGGAAGAAAAAA
1 TGGAAGAAAAAA
*
17149472 -GGAAGAAGAAA
1 TGGAAGAAAAAA
17149483 TGGAAGAAAAAA
1 TGGAAGAAAAAA
17149495 TG
1 TG
17149497 AAAATAAAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
11 10 0.45
12 12 0.55
ACGTcount: A:0.62, C:0.00, G:0.30, T:0.08
Consensus pattern (12 bp):
TGGAAGAAAAAA
Found at i:17149616 original size:19 final size:18
Alignment explanation
Indices: 17149577--17149622 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 18
17149567 TAAAAGCAGT
17149577 GAAGAAAATGGAAAAAAG
1 GAAGAAAATGGAAAAAAG
* *
17149595 GAAGAAAAATGGAAGAAGG
1 GAAG-AAAATGGAAAAAAG
*
17149614 GAAGGAAAT
1 GAAGAAAAT
17149623 AAAAGAGAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 8 0.33
19 16 0.67
ACGTcount: A:0.61, C:0.00, G:0.33, T:0.07
Consensus pattern (18 bp):
GAAGAAAATGGAAAAAAG
Found at i:17150892 original size:30 final size:30
Alignment explanation
Indices: 17150858--17150918 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
17150848 TCGAATTGTA
17150858 TAATTCATATTCGAGTTAAACCGAAAAACT
1 TAATTCATATTCGAGTTAAACCGAAAAACT
** * * *
17150888 TAATTTTTATTCGAGTTTATCCGAATAACT
1 TAATTCATATTCGAGTTAAACCGAAAAACT
17150918 T
1 T
17150919 GATTAACTCA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.39
Consensus pattern (30 bp):
TAATTCATATTCGAGTTAAACCGAAAAACT
Found at i:17152337 original size:21 final size:21
Alignment explanation
Indices: 17152313--17152360 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
17152303 CTAATAGATG
17152313 TAATTTTCATAATTTCA-TCAC
1 TAATTTT-ATAATTTCATTCAC
*
17152334 TAATATTTATCATTTCATTCAC
1 TAAT-TTTATAATTTCATTCAC
17152356 -AATTT
1 TAATTT
17152361 ATCTTTACAC
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
20 2 0.08
21 15 0.62
22 7 0.29
ACGTcount: A:0.33, C:0.17, G:0.00, T:0.50
Consensus pattern (21 bp):
TAATTTTATAATTTCATTCAC
Found at i:17154135 original size:12 final size:11
Alignment explanation
Indices: 17154106--17154148 Score: 50
Period size: 12 Copynumber: 3.7 Consensus size: 11
17154096 AATAATTTAA
17154106 TAATAAAATAT
1 TAATAAAATAT
* *
17154117 TACTAAAAATCT
1 TAAT-AAAATAT
17154129 TAATAAAATAT
1 TAATAAAATAT
17154140 TAATTAAAA
1 TAA-TAAAA
17154149 AATATTTTCT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
11 12 0.46
12 14 0.54
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (11 bp):
TAATAAAATAT
Found at i:17156594 original size:31 final size:30
Alignment explanation
Indices: 17156546--17156603 Score: 98
Period size: 31 Copynumber: 1.9 Consensus size: 30
17156536 GAATTGAATC
*
17156546 AAATCAAAATTTCATGTATACAATTGCTCA
1 AAATCAAAAGTTCATGTATACAATTGCTCA
17156576 AAATCACAAAGTTCATGTATACAATTGC
1 AAATCA-AAAGTTCATGTATACAATTGC
17156604 ACATTAAACC
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
30 6 0.23
31 20 0.77
ACGTcount: A:0.43, C:0.17, G:0.09, T:0.31
Consensus pattern (30 bp):
AAATCAAAAGTTCATGTATACAATTGCTCA
Found at i:17171376 original size:20 final size:20
Alignment explanation
Indices: 17171351--17171447 Score: 95
Period size: 20 Copynumber: 4.8 Consensus size: 20
17171341 GTCTAAAGCA
17171351 ATACTAAAATTTTTAATGTG
1 ATACTAAAATTTTTAATGTG
* * *
17171371 ATACTAATATTTTTAACGCG
1 ATACTAAAATTTTTAATGTG
* *
17171391 AAATTAAAATTTTTAATGTG
1 ATACTAAAATTTTTAATGTG
* * * * *
17171411 ATGCCAAAATCTCTAATGTA
1 ATACTAAAATTTTTAATGTG
*
17171431 ATACCAAAATTTTTAAT
1 ATACTAAAATTTTTAAT
17171448 AACATTTCAT
Statistics
Matches: 59, Mismatches: 18, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 59 1.00
ACGTcount: A:0.41, C:0.10, G:0.08, T:0.40
Consensus pattern (20 bp):
ATACTAAAATTTTTAATGTG
Found at i:17171893 original size:24 final size:25
Alignment explanation
Indices: 17171861--17171912 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 25
17171851 AAAATTATAT
*
17171861 AATAAAGTACATTTCG-TATACCAA
1 AATAAAGTACATTTCGATATACAAA
* * *
17171885 AATACAGTATATTTTGATATACAAA
1 AATAAAGTACATTTCGATATACAAA
17171910 AAT
1 AAT
17171913 TTTAACCAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
24 13 0.57
25 10 0.43
ACGTcount: A:0.48, C:0.12, G:0.08, T:0.33
Consensus pattern (25 bp):
AATAAAGTACATTTCGATATACAAA
Found at i:17178373 original size:51 final size:51
Alignment explanation
Indices: 17178297--17178450 Score: 256
Period size: 51 Copynumber: 3.0 Consensus size: 51
17178287 ATAGCATAAG
* *
17178297 GGCTACTATGCGCTTC-CTGTAAAATAGATTGCCTTAACTTAACATTATTAT
1 GGCTACTATGCGCTTCTC-GTAAAATAGATTGCCTTAACTCAACATCATTAT
* *
17178348 GGCTACTATGTGCTTCTCGTAAAATAGATTACCTTAACTCAACATCATTAT
1 GGCTACTATGCGCTTCTCGTAAAATAGATTGCCTTAACTCAACATCATTAT
17178399 GGCTACTATGCGCTTCTCGTAAAATAGATTGCCTTAACTCAACATCATTAT
1 GGCTACTATGCGCTTCTCGTAAAATAGATTGCCTTAACTCAACATCATTAT
17178450 G
1 G
17178451 CACACAGATC
Statistics
Matches: 96, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
51 95 0.99
52 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.14, T:0.35
Consensus pattern (51 bp):
GGCTACTATGCGCTTCTCGTAAAATAGATTGCCTTAACTCAACATCATTAT
Found at i:17187879 original size:51 final size:51
Alignment explanation
Indices: 17187772--17187881 Score: 132
Period size: 51 Copynumber: 2.2 Consensus size: 51
17187762 TCAGATAAGG
* * *
17187772 AAATATAATTTAATTATTATTAAAAAAAGAGTTTTAGATAAATAATAATTA
1 AAATAGAATTTAATTATTATTAAAAAAAGAGTTTTAAATAAACAATAATTA
** * *
17187823 AAATAGAATTTAATTATTATTATTTAAAAGAGTTTTAAATTAACGATAATT-
1 AAATAGAATTTAATTATTATTA-AAAAAAGAGTTTTAAATAAACAATAATTA
*
17187874 TAATAGAA
1 AAATAGAA
17187882 ATTATTAGTT
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
51 28 0.56
52 22 0.44
ACGTcount: A:0.52, C:0.01, G:0.07, T:0.40
Consensus pattern (51 bp):
AAATAGAATTTAATTATTATTAAAAAAAGAGTTTTAAATAAACAATAATTA
Found at i:17191492 original size:21 final size:21
Alignment explanation
Indices: 17191462--17191524 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 21
17191452 AAAATTTAGG
*
17191462 TACAATGGTTGCTTGGGTGGC
1 TACAAAGGTTGCTTGGGTGGC
* ** *
17191483 TACAAGGGTTGCTTGGACGAC
1 TACAAAGGTTGCTTGGGTGGC
*
17191504 TACAAAGGTTACTTGGGTGGC
1 TACAAAGGTTGCTTGGGTGGC
17191525 AAGGTAAGGA
Statistics
Matches: 33, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.21, C:0.16, G:0.35, T:0.29
Consensus pattern (21 bp):
TACAAAGGTTGCTTGGGTGGC
Found at i:17200762 original size:24 final size:24
Alignment explanation
Indices: 17200727--17200939 Score: 201
Period size: 24 Copynumber: 8.9 Consensus size: 24
17200717 ACAAGTTCAT
17200727 TACGTTTACGCTCGTCAGCTTATA
1 TACGTTTACGCTCGTCAGCTTATA
* * **
17200751 TACGTTTGCGCTCATCAGCTTGCA
1 TACGTTTACGCTCGTCAGCTTATA
* * *
17200775 CACGTTTAAGCTCGTCAGCTCATA
1 TACGTTTACGCTCGTCAGCTTATA
** **
17200799 TACGTTTACGCTCACCAGCTTGCA
1 TACGTTTACGCTCGTCAGCTTATA
* * *
17200823 CACGTTTACTCTCGTCAGTTTATA
1 TACGTTTACGCTCGTCAGCTTATA
* * **
17200847 TACATTTACGCTCGCCAGCTTGCA
1 TACGTTTACGCTCGTCAGCTTATA
* * * *
17200871 CACATTTATGCTCGTCAACTTATA
1 TACGTTTACGCTCGTCAGCTTATA
* *
17200895 TACTTTTACGCTCGTTAGCTTATA
1 TACGTTTACGCTCGTCAGCTTATA
*
17200919 TACATTTACGCTCGTCAGCTT
1 TACGTTTACGCTCGTCAGCTT
17200940 GCACATGTTT
Statistics
Matches: 144, Mismatches: 45, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
24 144 1.00
ACGTcount: A:0.22, C:0.28, G:0.15, T:0.36
Consensus pattern (24 bp):
TACGTTTACGCTCGTCAGCTTATA
Found at i:17200780 original size:48 final size:48
Alignment explanation
Indices: 17200728--17200939 Score: 253
Period size: 48 Copynumber: 4.4 Consensus size: 48
17200718 CAAGTTCATT
* *
17200728 ACGTTTACGCTCGTCAGCTTATATACGTTTGCGCTCATCAGCTTGCAC
1 ACGTTTACGCTCGTCAGCTTATATACGTTTACGCTCACCAGCTTGCAC
* *
17200776 ACGTTTAAGCTCGTCAGCTCATATACGTTTACGCTCACCAGCTTGCAC
1 ACGTTTACGCTCGTCAGCTTATATACGTTTACGCTCACCAGCTTGCAC
* * * *
17200824 ACGTTTACTCTCGTCAGTTTATATACATTTACGCTCGCCAGCTTGCAC
1 ACGTTTACGCTCGTCAGCTTATATACGTTTACGCTCACCAGCTTGCAC
* * * * *** ** *
17200872 ACATTTATGCTCGTCAACTTATATACTTTTACGCTCGTTAGCTTATAT
1 ACGTTTACGCTCGTCAGCTTATATACGTTTACGCTCACCAGCTTGCAC
*
17200920 ACATTTACGCTCGTCAGCTT
1 ACGTTTACGCTCGTCAGCTT
17200940 GCACATGTTT
Statistics
Matches: 141, Mismatches: 23, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
48 141 1.00
ACGTcount: A:0.22, C:0.28, G:0.15, T:0.35
Consensus pattern (48 bp):
ACGTTTACGCTCGTCAGCTTATATACGTTTACGCTCACCAGCTTGCAC
Found at i:17201434 original size:21 final size:21
Alignment explanation
Indices: 17201410--17201453 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
17201400 ATAACACCCA
17201410 ATTTAAACATCATCACA-AATT
1 ATTTAAAC-TCATCACATAATT
*
17201431 ATTTCAACTCATCACATAATT
1 ATTTAAACTCATCACATAATT
17201452 AT
1 AT
17201454 CTCAAACAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.43, C:0.20, G:0.00, T:0.36
Consensus pattern (21 bp):
ATTTAAACTCATCACATAATT
Found at i:17201444 original size:20 final size:21
Alignment explanation
Indices: 17201419--17201458 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
17201409 AATTTAAACA
*
17201419 TCATCACA-AATTATTTCAAC
1 TCATCACATAATTATCTCAAC
17201439 TCATCACATAATTATCTCAA
1 TCATCACATAATTATCTCAA
17201459 ACAATCAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.40, C:0.25, G:0.00, T:0.35
Consensus pattern (21 bp):
TCATCACATAATTATCTCAAC
Found at i:17201591 original size:4 final size:4
Alignment explanation
Indices: 17201566--17201724 Score: 277
Period size: 4 Copynumber: 39.5 Consensus size: 4
17201556 TACTAAAATC
17201566 CTTT CATTT CATTT CATTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT C-TT
1 CTTT C-TTT C-TTT C-TTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT
17201616 -TTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT
1 CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT
17201663 CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT
1 CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT
17201711 CTTT CTTT CTTT CT
1 CTTT CTTT CTTT CT
17201725 CCTTTATTTT
Statistics
Matches: 152, Mismatches: 0, Indels: 6
0.96 0.00 0.04
Matches are distributed among these distances:
3 4 0.03
4 134 0.88
5 14 0.09
ACGTcount: A:0.02, C:0.25, G:0.00, T:0.74
Consensus pattern (4 bp):
CTTT
Found at i:17213872 original size:116 final size:116
Alignment explanation
Indices: 17213668--17213879 Score: 257
Period size: 116 Copynumber: 1.8 Consensus size: 116
17213658 TATCCAGGGA
* * * * * *
17213668 TGTATCGATAGAAGTACAGGGTAGGAGAGAGGTTGTTATCTGATATTGGTTATATCGGTAGTTGA
1 TGTATCGATAAAAGTACAGGGCAGGAGAGAGGTTGATATCTGATATAGGTTATACCGGTAGATGA
* ** *
17213733 ATAGCAAGTGTCGGTAGTTATGTAATTAGAAGTATCAGTATTTTGCATGTT
66 ATACCAAGTGTCGAAAGTCATGTAATTAGAAGTATCAGTATTTTGCATGTT
* *
17213784 TGTATCGGTAAAAGTACAGGGCAGGAGAGAGGTTGCATA-CTGACT-TAGGTTGTACCGGTAGAT
1 TGTATCGATAAAAGTACAGGGCAGGAGAGAGGTTG-ATATCTGA-TATAGGTTATACCGGTAGAT
* * *
17213847 GAATACCTAGTTTCGAAAGTCATGTATTTAGAA
64 GAATACCAAGTGTCGAAAGTCATGTAATTAGAA
17213880 ATACCGATAG
Statistics
Matches: 79, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
116 76 0.96
117 3 0.04
ACGTcount: A:0.30, C:0.09, G:0.28, T:0.33
Consensus pattern (116 bp):
TGTATCGATAAAAGTACAGGGCAGGAGAGAGGTTGATATCTGATATAGGTTATACCGGTAGATGA
ATACCAAGTGTCGAAAGTCATGTAATTAGAAGTATCAGTATTTTGCATGTT
Found at i:17219620 original size:21 final size:20
Alignment explanation
Indices: 17219575--17219626 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
17219565 TGTGCTAGTT
*
17219575 CTACCGATACAAGTATGATTT
1 CTACCGATACAAGTATGA-TA
17219596 CTACCGATACAAGTCATGCA-A
1 CTACCGATACAAGT-ATG-ATA
17219617 CTACCGATAC
1 CTACCGATAC
17219627 CAAAAACTCC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
21 24 0.86
22 3 0.11
23 1 0.04
ACGTcount: A:0.35, C:0.27, G:0.13, T:0.25
Consensus pattern (20 bp):
CTACCGATACAAGTATGATA
Found at i:17224632 original size:17 final size:17
Alignment explanation
Indices: 17224610--17224665 Score: 60
Period size: 17 Copynumber: 3.2 Consensus size: 17
17224600 ACAAACTCAG
17224610 AAAATTAGAAAATATTA
1 AAAATTAGAAAATATTA
17224627 AAAATT-GTAAAATAAATTA
1 AAAATTAG-AAAAT--ATTA
* *
17224646 AATATTAAAAAATATTA
1 AAAATTAGAAAATATTA
17224663 AAA
1 AAA
17224666 TCTACTTCAT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
16 1 0.03
17 17 0.53
19 14 0.44
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (17 bp):
AAAATTAGAAAATATTA
Found at i:17224690 original size:35 final size:35
Alignment explanation
Indices: 17224651--17224732 Score: 123
Period size: 35 Copynumber: 2.4 Consensus size: 35
17224641 AATTAAATAT
17224651 TAAAAAATATTAAAATCTACTTCATTGAAATTGTA
1 TAAAAAATATTAAAATCTACTTCATTGAAATTGTA
* *
17224686 TAAAAAATATTAAACTTTACTTCATTGAAATTGTA
1 TAAAAAATATTAAAATCTACTTCATTGAAATTGTA
*
17224721 -AAATAA-ATTAAA
1 TAAAAAATATTAAA
17224733 TATTAAAATA
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
33 6 0.14
34 5 0.11
35 33 0.75
ACGTcount: A:0.51, C:0.07, G:0.05, T:0.37
Consensus pattern (35 bp):
TAAAAAATATTAAAATCTACTTCATTGAAATTGTA
Found at i:17224739 original size:7 final size:7
Alignment explanation
Indices: 17224727--17224765 Score: 62
Period size: 7 Copynumber: 5.6 Consensus size: 7
17224717 TGTAAAATAA
17224727 ATTAAAT
1 ATTAAAT
17224734 ATTAAAAT
1 ATT-AAAT
17224742 ATTAAAT
1 ATTAAAT
17224749 ATTAAAT
1 ATTAAAT
17224756 ATTAAA-
1 ATTAAAT
17224762 ATTA
1 ATTA
17224766 TTTTAAGTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
6 4 0.13
7 20 0.65
8 7 0.23
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (7 bp):
ATTAAAT
Found at i:17224786 original size:22 final size:22
Alignment explanation
Indices: 17224761--17224809 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 22
17224751 TAAATATTAA
17224761 AATTATTTTAAGT-TTTGACATC
1 AATTATTTTAAGTATTTGA-ATC
*
17224783 AATTATTTTAAGTATTTGAATT
1 AATTATTTTAAGTATTTGAATC
17224805 AATTA
1 AATTA
17224810 AATTGTATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 20 0.80
23 5 0.20
ACGTcount: A:0.37, C:0.04, G:0.08, T:0.51
Consensus pattern (22 bp):
AATTATTTTAAGTATTTGAATC
Found at i:17224981 original size:16 final size:16
Alignment explanation
Indices: 17224949--17224978 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
17224939 TATTTTGAGA
17224949 TTAAAAATTATATAAT
1 TTAAAAATTATATAAT
17224965 TTAAAAA-TATATAA
1 TTAAAAATTATATAA
17224979 ATTACTTCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
TTAAAAATTATATAAT
Found at i:17229014 original size:33 final size:33
Alignment explanation
Indices: 17228952--17229014 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
17228942 TTAGTATTTA
* *
17228952 ATTTTTTTATTTAATTTGGTTCTTCAATTTGGT
1 ATTTTTTTATTTAATTTGGTTCCTAAATTTGGT
17228985 ATTTTTTT-TTTAATTTGGTATCCTAAATTT
1 ATTTTTTTATTTAATTTGGT-TCCTAAATTT
17229015 ATTAAATATT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
32 11 0.41
33 16 0.59
ACGTcount: A:0.21, C:0.06, G:0.10, T:0.63
Consensus pattern (33 bp):
ATTTTTTTATTTAATTTGGTTCCTAAATTTGGT
Found at i:17230647 original size:18 final size:19
Alignment explanation
Indices: 17230611--17230648 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
17230601 TAATGGCAAA
17230611 ATAATAAAAATACATTAAT
1 ATAATAAAAATACATTAAT
*
17230630 ATAATAAACATA-ATTAAT
1 ATAATAAAAATACATTAAT
17230648 A
1 A
17230649 ACACAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (19 bp):
ATAATAAAAATACATTAAT
Found at i:17230905 original size:22 final size:21
Alignment explanation
Indices: 17230877--17230929 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
17230867 AGGCAAAAAT
*
17230877 ATAAATAACATA-AAAATAACAA
1 ATAAATAAAATACAAAA-AAC-A
*
17230899 ATAAATAAAATACATAAAACA
1 ATAAATAAAATACAAAAAACA
17230920 ATAAATAAAA
1 ATAAATAAAA
17230930 GAAAATAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 11 0.39
22 14 0.50
23 3 0.11
ACGTcount: A:0.74, C:0.08, G:0.00, T:0.19
Consensus pattern (21 bp):
ATAAATAAAATACAAAAAACA
Found at i:17230978 original size:14 final size:13
Alignment explanation
Indices: 17230879--17230966 Score: 63
Period size: 14 Copynumber: 6.5 Consensus size: 13
17230869 GCAAAAATAT
17230879 AAATAACATAAAAA
1 AAATAA-ATAAAAA
* * *
17230893 TAACAAATAAATA
1 AAATAAATAAAAA
*
17230906 AAATACAT-AAAA
1 AAATAAATAAAAA
*
17230918 CAATAAATAAAAGA
1 AAATAAATAAAA-A
17230932 AAATAAA-AGAAAA
1 AAATAAATA-AAAA
*
17230945 AATGTAAATAATAAA
1 AA-ATAAATAA-AAA
17230960 AAATAAA
1 AAATAAA
17230967 AAACAATAAA
Statistics
Matches: 56, Mismatches: 12, Indels: 12
0.70 0.15 0.15
Matches are distributed among these distances:
12 9 0.16
13 18 0.32
14 23 0.41
15 6 0.11
ACGTcount: A:0.75, C:0.05, G:0.03, T:0.17
Consensus pattern (13 bp):
AAATAAATAAAAA
Found at i:17231237 original size:13 final size:13
Alignment explanation
Indices: 17231174--17231237 Score: 51
Period size: 13 Copynumber: 4.9 Consensus size: 13
17231164 ACAACTAGAT
*
17231174 AAATAAACA-AAA
1 AAATAAAAATAAA
17231186 AAATAAAAATGAAA
1 AAATAAAAAT-AAA
***
17231200 TGCT-AAAATAAA
1 AAATAAAAATAAA
*
17231212 CAAATAAATATAAA
1 -AAATAAAAATAAA
17231226 AAATAAAAATAA
1 AAATAAAAATAA
17231238 TTGGGATTAG
Statistics
Matches: 39, Mismatches: 9, Indels: 7
0.71 0.16 0.13
Matches are distributed among these distances:
12 11 0.28
13 17 0.44
14 11 0.28
ACGTcount: A:0.75, C:0.05, G:0.03, T:0.17
Consensus pattern (13 bp):
AAATAAAAATAAA
Found at i:17231288 original size:16 final size:16
Alignment explanation
Indices: 17231253--17231295 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
17231243 ATTAGGCATG
*
17231253 AAAATAAAT-GACAAA
1 AAAATAAATAAACAAA
*
17231268 TAAATAAATAAACAAA
1 AAAATAAATAAACAAA
*
17231284 AAAATCAATAAA
1 AAAATAAATAAA
17231296 TTAAATGTCA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.74, C:0.07, G:0.02, T:0.16
Consensus pattern (16 bp):
AAAATAAATAAACAAA
Found at i:17231594 original size:23 final size:23
Alignment explanation
Indices: 17231542--17231585 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
17231532 TATGTCACAA
*
17231542 AAAAAAATCTCTAAATATTGTAT
1 AAAAAAATCTCTAAATATTATAT
*
17231565 AAAAAAATCTCTAAATCTTAT
1 AAAAAAATCTCTAAATATTAT
17231586 TCCAAAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.52, C:0.11, G:0.02, T:0.34
Consensus pattern (23 bp):
AAAAAAATCTCTAAATATTATAT
Found at i:17231763 original size:22 final size:22
Alignment explanation
Indices: 17231732--17231773 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
17231722 AAGGCAGCTG
* *
17231732 TTAGGTTTTTTCATTTTTGAGT
1 TTAGGGTTTTTCACTTTTGAGT
*
17231754 TTAGGGTTTTTTACTTTTGA
1 TTAGGGTTTTTCACTTTTGA
17231774 ATTTTGTAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.14, C:0.05, G:0.19, T:0.62
Consensus pattern (22 bp):
TTAGGGTTTTTCACTTTTGAGT
Found at i:17232000 original size:35 final size:35
Alignment explanation
Indices: 17231956--17232026 Score: 83
Period size: 36 Copynumber: 2.0 Consensus size: 35
17231946 TTTTTACAAC
* *
17231956 TTTTAATTTTTTAA-ATAATTGTT-TCACTAATTTT
1 TTTTAATTTTATAATATAATTATTATCACT-ATTTT
*
17231990 TTTTGAATTTTATAATATAGTTATTATCACTATTTT
1 TTTT-AATTTTATAATATAATTATTATCACTATTTT
17232026 T
1 T
17232027 GAAATCTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
34 4 0.13
35 9 0.29
36 13 0.42
37 5 0.16
ACGTcount: A:0.30, C:0.06, G:0.04, T:0.61
Consensus pattern (35 bp):
TTTTAATTTTATAATATAATTATTATCACTATTTT
Found at i:17233184 original size:54 final size:54
Alignment explanation
Indices: 17233109--17233219 Score: 152
Period size: 54 Copynumber: 2.1 Consensus size: 54
17233099 CGAGAATTTG
** * * * *
17233109 AAAAAAAATTTGGTCGTGGCCATTGCATGGTCGACACCCCCTTTTTTATTTGAC
1 AAAAAAAATTTGGTCGTGGCCATACCATGGCCGACACCCCCCTCTTTATCTGAC
17233163 AAAAAAAATTTGGT-GTTGGCCATACCATGGCCGACACCCCCCTCTTTATCTGAC
1 AAAAAAAATTTGGTCG-TGGCCATACCATGGCCGACACCCCCCTCTTTATCTGAC
17233217 AAA
1 AAA
17233220 TTTTTTTTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
53 1 0.02
54 49 0.98
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.29
Consensus pattern (54 bp):
AAAAAAAATTTGGTCGTGGCCATACCATGGCCGACACCCCCCTCTTTATCTGAC
Found at i:17233325 original size:60 final size:59
Alignment explanation
Indices: 17233244--17233670 Score: 264
Period size: 59 Copynumber: 7.2 Consensus size: 59
17233234 TGACCATGTA
* *
17233244 ATGATCGACACCCCTTTTTGTCAGATAAAAAATTCAAAATTTTGGGTGTTGGCCATTGC
1 ATGACCGACACCCCTTTTTGTCAGATAAAAAATTCAAATTTTTGGGTGTTGGCCATTGC
* * ** *
17233303 ATGACCGACAATCCCTTTTTGTCTA-ATAAAAAAATCAAATTTTTTAGTGTTGGTCATTGC
1 ATGACCGAC-ACCCCTTTTTGTC-AGATAAAAAATTCAAATTTTTGGGTGTTGGCCATTGC
* * *
17233363 ATGGCCGACACCCCTTTTTATCTGAATAAAAAATT-AAATTTTTGGGTGTTGGCCA-TGCC
1 ATGACCGACACCCCTTTTTGTCAG-ATAAAAAATTCAAATTTTTGGGTGTTGGCCATTG-C
* * * ** ** *
17233422 ATGATCGACACCCCTTTTT-TCAGATAAAAAATTTAATTTTTTTTTGTGTTGGTTA-TAC
1 ATGACCGACACCCCTTTTTGTCAGATAAAAAATTCAA-ATTTTTGGGTGTTGGCCATTGC
** * * * * * **
17233480 AATGGTCGACACCTCTTTTTTTATCTGGTAAAAAAAT--AATTTTTTTGTGTTGGCCA-TGC
1 -ATGACCGACACC-C-CTTTTTGTCAGATAAAAAATTCAAATTTTTGGGTGTTGGCCATTGC
** * * * * * **
17233539 AATGGTCGACACACCTTTTTTATCTGGTAAAAAATT-AATTTTTTTTGTGTTGGCCATTGC
1 -ATGACCGACAC-CCCTTTTTGTCAGATAAAAAATTCAAATTTTTGGGTGTTGGCCATTGC
** * * * * **
17233599 ATGGTCGACACCCCCTTTTTTATCTGGTAAAAAA-TCAATTTTTTTTGTGTTGGCCA-TGC
1 ATGACCGACA-CCCC-TTTTTGTCAGATAAAAAATTCAAATTTTTGGGTGTTGGCCATTGC
17233658 AATGACCGACACC
1 -ATGACCGACACC
17233671 AACTTTCTCT
Statistics
Matches: 312, Mismatches: 38, Indels: 36
0.81 0.10 0.09
Matches are distributed among these distances:
57 10 0.03
58 28 0.09
59 145 0.46
60 112 0.36
61 6 0.02
62 11 0.04
ACGTcount: A:0.27, C:0.18, G:0.16, T:0.39
Consensus pattern (59 bp):
ATGACCGACACCCCTTTTTGTCAGATAAAAAATTCAAATTTTTGGGTGTTGGCCATTGC
Found at i:17233513 original size:118 final size:116
Alignment explanation
Indices: 17233222--17233670 Score: 415
Period size: 119 Copynumber: 3.8 Consensus size: 116
17233212 CTGACAAATT
** * * * * * * *
17233222 TTTTTTTTGTGTTGACCA-TGTAATGATCGACACCCCTTTTTGTCAGATAAAAAATTCAAAATTT
1 TTTTTTTTGTGTTGGTCATTG-CATGGTCGACACCCTTTTTTATCTGGTAAAAAATT-AAATTTT
* * *
17233286 TGGGTGTTGGCCATTGC-ATGACCGACAATCCCTTTTTGTCTA-ATAAAAAAATCAA
64 TGGGTGTTGGCCA-TGCAATGACCGAC-ACCCCTTTTTATC-AGAT-AAAAAATTAA
* * * * *
17233341 ATTTTTTAGTGTTGGTCATTGCATGGCCGACACCCCTTTTTATCTGAATAAAAAATTAAATTTTT
1 TTTTTTTTGTGTTGGTCATTGCATGGTCGACACCCTTTTTTATCTG-GTAAAAAATTAAATTTTT
* *
17233406 GGGTGTTGGCCATGCCATGATCGACACCCCTTTTT-TCAGATAAAAAATTTAA
65 GGGTGTTGGCCATGCAATGACCGACACCCCTTTTTATCAGATAAAAAA-TTAA
* * *
17233458 TTTTTTTTTGTGTTGGTTA-TACAATGGTCGACACCTCTTTTTTTATCTGGTAAAAAAAT-AATT
1 -TTTTTTTTGTGTTGGTCATTGC-ATGGTCGACACC-C-TTTTTTATCTGGTAAAAAATTAAATT
** ** * * *
17233521 TTTTTGTGTTGGCCATGCAATGGTCGACACACCTTTTTTATCTGGTAAAAAATTAA
62 TTTGGGTGTTGGCCATGCAATGACCGACAC-CCCTTTTTATCAGATAAAAAATTAA
* * *
17233577 TTTTTTTTGTGTTGGCCATTGCATGGTCGACACCCCCTTTTTTATCTGGTAAAAAATCAATTTTT
1 TTTTTTTTGTGTTGGTCATTGCATGGTCGACA--CCCTTTTTTATCTGGTAAAAAATTAAATTTT
**
17233642 TTTGTGTTGGCCATGCAATGACCGACACC
64 TGGGTGTTGGCCATGCAATGACCGACACC
17233671 AACTTTCTCT
Statistics
Matches: 279, Mismatches: 36, Indels: 31
0.81 0.10 0.09
Matches are distributed among these distances:
116 7 0.03
117 9 0.03
118 114 0.41
119 115 0.41
120 34 0.12
ACGTcount: A:0.27, C:0.17, G:0.16, T:0.40
Consensus pattern (116 bp):
TTTTTTTTGTGTTGGTCATTGCATGGTCGACACCCTTTTTTATCTGGTAAAAAATTAAATTTTTG
GGTGTTGGCCATGCAATGACCGACACCCCTTTTTATCAGATAAAAAATTAA
Found at i:17233532 original size:177 final size:179
Alignment explanation
Indices: 17233329--17233651 Score: 435
Period size: 177 Copynumber: 1.8 Consensus size: 179
17233319 TTTTGTCTAA
*
17233329 TAAAAAAATCAAATTTTTTAGTGTTGGTCATTGC-ATGGCCGACAC-CCCTTTTTATCTGAATAA
1 TAAAAAAAT-AAATTTTTTAGTGTTGGCCA-TGCAATGGCCGACACACCCTTTTTATCTG-ATAA
17233392 AAAATTAAATTTTTGGGTGTTGGCCA-TGCCATGATCGACA-CCCC-TTTTT-TCAGATAAAAAA
63 AAAATTAAATTTTTGGGTGTTGGCCATTG-CATGATCGACACCCCCTTTTTTATCAGATAAAAAA
*
17233453 TTTAATTTTTTTTTGTGTTGGTTATACAATGGTCGACACCTCTTTTTTTATCTGG
127 -TCAA-TTTTTTTTGTGTTGGTTATACAATGGTCGACACCTCTTTTTTTATCTGG
* * * *
17233508 TAAAAAAAT-AATTTTTTTGTGTTGGCCATGCAATGGTCGACACACCTTTTTTATCTGGTAAAAA
1 TAAAAAAATAAATTTTTTAGTGTTGGCCATGCAATGGCCGACACACCCTTTTTATCTGATAAAAA
* ** * * *
17233572 ATTAATTTTTTTTGTGTTGGCCATTGCATGGTCGACACCCCCTTTTTTATCTGGTAAAAAATCAA
66 ATTAAATTTTTGGGTGTTGGCCATTGCATGATCGACACCCCCTTTTTTATCAGATAAAAAATCAA
17233637 TTTTTTTTGTGTTGG
131 TTTTTTTTGTGTTGG
17233652 CCATGCAATG
Statistics
Matches: 126, Mismatches: 12, Indels: 13
0.83 0.08 0.09
Matches are distributed among these distances:
176 3 0.02
177 63 0.50
178 33 0.26
179 17 0.13
180 10 0.08
ACGTcount: A:0.27, C:0.15, G:0.16, T:0.42
Consensus pattern (179 bp):
TAAAAAAATAAATTTTTTAGTGTTGGCCATGCAATGGCCGACACACCCTTTTTATCTGATAAAAA
ATTAAATTTTTGGGTGTTGGCCATTGCATGATCGACACCCCCTTTTTTATCAGATAAAAAATCAA
TTTTTTTTGTGTTGGTTATACAATGGTCGACACCTCTTTTTTTATCTGG
Found at i:17235033 original size:20 final size:20
Alignment explanation
Indices: 17235008--17235045 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
17234998 TTTTTTTAAA
*
17235008 TTCGAAAATATAAAAAACAT
1 TTCGAAAATAGAAAAAACAT
17235028 TTCGAAAATAGAAAAAAC
1 TTCGAAAATAGAAAAAAC
17235046 TATTATAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.61, C:0.11, G:0.08, T:0.21
Consensus pattern (20 bp):
TTCGAAAATAGAAAAAACAT
Found at i:17236107 original size:22 final size:22
Alignment explanation
Indices: 17236089--17236160 Score: 83
Period size: 22 Copynumber: 3.3 Consensus size: 22
17236079 GCAGAATTGG
17236089 GGTGTTGGTGAGCTGGAATTTC
1 GGTGTTGGTGAGCTGGAATTTC
* * *
17236111 GGTTTTAGTGAGTTGGAATTTC
1 GGTGTTGGTGAGCTGGAATTTC
* *
17236133 GGT-TTAGGTAAGCTGGAATTTG
1 GGTGTT-GGTGAGCTGGAATTTC
17236155 GGTGTT
1 GGTGTT
17236161 CCAATATTAT
Statistics
Matches: 41, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
21 2 0.05
22 37 0.90
23 2 0.05
ACGTcount: A:0.17, C:0.06, G:0.38, T:0.40
Consensus pattern (22 bp):
GGTGTTGGTGAGCTGGAATTTC
Found at i:17236335 original size:35 final size:35
Alignment explanation
Indices: 17236295--17236403 Score: 111
Period size: 35 Copynumber: 3.2 Consensus size: 35
17236285 AAATATTAAA
17236295 ATTTGATAAATAATGTATTGTCAAATCAAAACATT
1 ATTTGATAAATAATGTATTGTCAAATCAAAACATT
** * ***
17236330 ATTTGATAAAATTTTTTATT-T-AAATGTTAA-A--
1 ATTTGAT-AAATAATGTATTGTCAAATCAAAACATT
*
17236361 ATTTGATAAATAATGTATTGTCAAATCAACACATT
1 ATTTGATAAATAATGTATTGTCAAATCAAAACATT
17236396 ATTTGATA
1 ATTTGATA
17236404 TAAATTAAAA
Statistics
Matches: 55, Mismatches: 13, Indels: 12
0.69 0.16 0.15
Matches are distributed among these distances:
30 9 0.16
31 8 0.15
32 5 0.09
33 2 0.04
34 6 0.11
35 16 0.29
36 9 0.16
ACGTcount: A:0.43, C:0.06, G:0.08, T:0.42
Consensus pattern (35 bp):
ATTTGATAAATAATGTATTGTCAAATCAAAACATT
Found at i:17236345 original size:66 final size:66
Alignment explanation
Indices: 17236268--17236409 Score: 239
Period size: 66 Copynumber: 2.1 Consensus size: 66
17236258 TTGAAATATA
17236268 ATAATAATTTTTAATTTAAATATTAAAATTTGATAAATAATGTATTGTCAAATCAAAACATTATT
1 ATAA-AATTTTTAATTTAAATATTAAAATTTGATAAATAATGTATTGTCAAATCAAAACATTATT
17236333 TG
65 TG
* * *
17236335 ATAAAATTTTTTATTTAAATGTTAAAATTTGATAAATAATGTATTGTCAAATCAACACATTATTT
1 ATAAAATTTTTAATTTAAATATTAAAATTTGATAAATAATGTATTGTCAAATCAAAACATTATTT
17236400 G
66 G
17236401 ATATAAATT
1 ATA-AAATT
17236410 AAAATATAAT
Statistics
Matches: 71, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
66 62 0.87
67 9 0.13
ACGTcount: A:0.45, C:0.05, G:0.06, T:0.44
Consensus pattern (66 bp):
ATAAAATTTTTAATTTAAATATTAAAATTTGATAAATAATGTATTGTCAAATCAAAACATTATTT
G
Found at i:17236468 original size:12 final size:11
Alignment explanation
Indices: 17236434--17236473 Score: 57
Period size: 11 Copynumber: 3.7 Consensus size: 11
17236424 ATATTTTTTA
17236434 TTTAAA-TAAT
1 TTTAAATTAAT
17236444 TTTAAATTAAT
1 TTTAAATTAAT
17236455 TTTAAATGTAA-
1 TTTAAAT-TAAT
17236466 TTTAAATT
1 TTTAAATT
17236474 TCAACTTCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
10 7 0.25
11 18 0.64
12 3 0.11
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (11 bp):
TTTAAATTAAT
Found at i:17236577 original size:11 final size:12
Alignment explanation
Indices: 17236556--17236603 Score: 51
Period size: 12 Copynumber: 3.7 Consensus size: 12
17236546 AACATGTACC
17236556 TTAATTTTCAAA
1 TTAATTTTCAAA
*
17236568 TTAATTTCAACTTAAA
1 TTAATTT----TCAAA
17236584 TTAATTTTCAAA
1 TTAATTTTCAAA
17236596 TTAATTTT
1 TTAATTTT
17236604 TACACAAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
12 19 0.63
16 11 0.37
ACGTcount: A:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (12 bp):
TTAATTTTCAAA
Found at i:17236601 original size:16 final size:16
Alignment explanation
Indices: 17236565--17236599 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
17236555 CTTAATTTTC
*
17236565 AAATTAATTTCAACTT
1 AAATTAATTTCAAATT
17236581 AAATTAATTTTCAAATT
1 AAATTAA-TTTCAAATT
17236598 AA
1 AA
17236600 TTTTTACACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.43
Consensus pattern (16 bp):
AAATTAATTTCAAATT
Found at i:17236612 original size:28 final size:28
Alignment explanation
Indices: 17236556--17236612 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
17236546 AACATGTACC
**
17236556 TTAATTTTCAAATTAATTTCAACTTAAA
1 TTAATTTTCAAATTAATTTCAACACAAA
**
17236584 TTAATTTTCAAATTAATTTTTACACAAA
1 TTAATTTTCAAATTAATTTCAACACAAA
17236612 T
1 T
17236613 ATTCTTCATG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.42, C:0.11, G:0.00, T:0.47
Consensus pattern (28 bp):
TTAATTTTCAAATTAATTTCAACACAAA
Found at i:17239470 original size:13 final size:12
Alignment explanation
Indices: 17239437--17239483 Score: 51
Period size: 13 Copynumber: 3.8 Consensus size: 12
17239427 TTATTTTTGT
*
17239437 TTATTTCTTAAAA
1 TTATTT-TTAATA
*
17239450 TTAATTTTAATTA
1 TTATTTTTAA-TA
17239463 TTATTTTTAATA
1 TTATTTTTAATA
17239475 -TATTTTTAA
1 TTATTTTTAA
17239484 CTTGTCGATA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
11 9 0.30
12 6 0.20
13 15 0.50
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (12 bp):
TTATTTTTAATA
Found at i:17242669 original size:77 final size:76
Alignment explanation
Indices: 17242571--17242721 Score: 203
Period size: 77 Copynumber: 2.0 Consensus size: 76
17242561 TTTCGAATCG
* *
17242571 AATCAAGTTTTACTCGCTCTAATATAGATTTAACTTACCTCTTACAAACCAAATTGAATTAAAAC
1 AATCAAGTTTTACTCACTCTAATATAGATTTAACTTA-ATCTTACAAACCAAATTGAATTAAAAC
17242636 AAATCCATTATA
65 AAATCCATTATA
* * * * * ***
17242648 AATCGAGTTTTACTCACTCTAATGTAGATTTAACTTAATCTTACAGATCAAATTGGATTAGGGCA
1 AATCAAGTTTTACTCACTCTAATATAGATTTAACTTAATCTTACAAACCAAATTGAATTAAAACA
17242713 AATCCATTA
66 AATCCATTA
17242722 CACTAATTAT
Statistics
Matches: 64, Mismatches: 10, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
76 30 0.47
77 34 0.53
ACGTcount: A:0.38, C:0.18, G:0.09, T:0.34
Consensus pattern (76 bp):
AATCAAGTTTTACTCACTCTAATATAGATTTAACTTAATCTTACAAACCAAATTGAATTAAAACA
AATCCATTATA
Found at i:17243077 original size:30 final size:29
Alignment explanation
Indices: 17243035--17243113 Score: 97
Period size: 30 Copynumber: 2.7 Consensus size: 29
17243025 TTTTAAATAA
*
17243035 TAAAAAT-AAAAAATATACTTTAATTTCT
1 TAAAAATAAAAAAATATAATTTAATTTCT
* *
17243063 TAAAAATAATAAAAATTTAATTTAATTTTT
1 TAAAAATAA-AAAAATATAATTTAATTTCT
17243093 TAAAATTATAAAAAAATATAA
1 TAAAA--ATAAAAAAATATAA
17243114 ATTATTAAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
28 7 0.16
29 1 0.02
30 22 0.51
31 9 0.21
32 4 0.09
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (29 bp):
TAAAAATAAAAAAATATAATTTAATTTCT
Found at i:17243710 original size:11 final size:11
Alignment explanation
Indices: 17243662--17243716 Score: 51
Period size: 10 Copynumber: 5.1 Consensus size: 11
17243652 TTAACCTTTT
*
17243662 AAAATTAT-TA
1 AAAATTATAAA
*
17243672 AAAATCAT-AA
1 AAAATTATAAA
*
17243682 AAAGTTATAAA
1 AAAATTATAAA
*
17243693 TAAAATTTTAAA
1 -AAAATTATAAA
17243705 AAAATTATAAA
1 AAAATTATAAA
17243716 A
1 A
17243717 TTTTTATTAA
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
10 14 0.39
11 13 0.36
12 9 0.25
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (11 bp):
AAAATTATAAA
Found at i:17245082 original size:12 final size:12
Alignment explanation
Indices: 17245052--17245090 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
17245042 TCAGCCTCAG
17245052 CTGCTTCACCTT
1 CTGCTTCACCTT
17245064 CAT-CTTCACCTT
1 C-TGCTTCACCTT
*
17245076 CTGCTTCCCCTT
1 CTGCTTCACCTT
17245088 CTG
1 CTG
17245091 GTTCTGGCTC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
11 1 0.04
12 22 0.92
13 1 0.04
ACGTcount: A:0.08, C:0.44, G:0.08, T:0.41
Consensus pattern (12 bp):
CTGCTTCACCTT
Found at i:17246182 original size:3 final size:3
Alignment explanation
Indices: 17246174--17246199 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
17246164 GGCTTCTGGT
17246174 TCA TCA TCA TCA TCA TCA TCA TCA TC
1 TCA TCA TCA TCA TCA TCA TCA TCA TC
17246200 CTCTGCTTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.35, G:0.00, T:0.35
Consensus pattern (3 bp):
TCA
Found at i:17248617 original size:102 final size:102
Alignment explanation
Indices: 17248431--17248886 Score: 664
Period size: 102 Copynumber: 4.5 Consensus size: 102
17248421 CTATCAATTC
* * * *
17248431 ATGGCACCCGGTGCCTAGCGGATATACCGCGATATGTGAGCCCAGCTCTAGTTGGATTATCCAAC
1 ATGGCACCCAGTGCCTAGCGGATAAACCGCGATATGTGAGCCCAGCTCTGGTTGGATTAACCAAC
* * *
17248496 GATTTGCGCCCAACACTAGTTAGATAAA-TCGACGGTT
66 GGTTTGCGCCCAACGCTAGTCAGATAAACT-GACGGTT
* * *
17248533 ATGGCACCCAATGCCTAGCGGATAAACCGCGATATGTGAGCCCAGCTCTGGTTGGATTAACTAAT
1 ATGGCACCCAGTGCCTAGCGGATAAACCGCGATATGTGAGCCCAGCTCTGGTTGGATTAACCAAC
* * *
17248598 GGTTTGTGTCCAGCGCTAGTCAGATAAACTGACGGTT
66 GGTTTGCGCCCAACGCTAGTCAGATAAACTGACGGTT
* *
17248635 ATGGCACCCAGTGCTTAGCGGATAAACTGCGATATGTGAGCCCAGCTCTGGTTGGATTAACCAAC
1 ATGGCACCCAGTGCCTAGCGGATAAACCGCGATATGTGAGCCCAGCTCTGGTTGGATTAACCAAC
* *
17248700 GGTTTGCGTCCAGCGCTAGTCAGATAAACTGACGGTT
66 GGTTTGCGCCCAACGCTAGTCAGATAAACTGACGGTT
* *
17248737 ATGGCACCCAATGCTTAGCGGATAAACCGCGATATGTGAGCCCAGCTCTGGTTGGATTAACCAAC
1 ATGGCACCCAGTGCCTAGCGGATAAACCGCGATATGTGAGCCCAGCTCTGGTTGGATTAACCAAC
* *
17248802 GTTTTGCGCCCAACGCTAGTCAAATAAACTGACGGTT
66 GGTTTGCGCCCAACGCTAGTCAGATAAACTGACGGTT
* * * *
17248839 ATGGTACCCAGTGCCTAGCGGATAAACCGCAAGA-GTGAGTCCAGCTCT
1 ATGGCACCCAGTGCCTAGCGGATAAACCGCGATATGTGAGCCCAGCTCT
17248887 AGTCAATTAA
Statistics
Matches: 322, Mismatches: 31, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
101 13 0.04
102 308 0.96
103 1 0.00
ACGTcount: A:0.26, C:0.25, G:0.26, T:0.24
Consensus pattern (102 bp):
ATGGCACCCAGTGCCTAGCGGATAAACCGCGATATGTGAGCCCAGCTCTGGTTGGATTAACCAAC
GGTTTGCGCCCAACGCTAGTCAGATAAACTGACGGTT
Found at i:17248735 original size:33 final size:34
Alignment explanation
Indices: 17248607--17248739 Score: 92
Period size: 33 Copynumber: 3.9 Consensus size: 34
17248597 TGGTTTGTGT
*
17248607 CCAGCGCTAGTCAGATAAACTGACGGTTATGGCAC
1 CCAGCGCTAGTCAGATAAACTGACGGTTAT-GCGC
* * * * *
17248642 CCAGTGCTTAG-CGGATAAACTG-CGATATGTGAGC
1 CCAGCGC-TAGTCAGATAAACTGACGGT-TATGCGC
* * ** * ** *
17248676 CCAGCTCTGGTTGGATTAACCAACGGTT-TGCGT
1 CCAGCGCTAGTCAGATAAACTGACGGTTATGCGC
17248709 CCAGCGCTAGTCAGATAAACTGACGGTTATG
1 CCAGCGCTAGTCAGATAAACTGACGGTTATG
17248740 GCACCCAATG
Statistics
Matches: 70, Mismatches: 23, Indels: 11
0.67 0.22 0.11
Matches are distributed among these distances:
33 26 0.37
34 20 0.29
35 21 0.30
36 3 0.04
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24
Consensus pattern (34 bp):
CCAGCGCTAGTCAGATAAACTGACGGTTATGCGC
Found at i:17249513 original size:136 final size:136
Alignment explanation
Indices: 17249206--17249578 Score: 637
Period size: 136 Copynumber: 2.8 Consensus size: 136
17249196 TTCTTGCTCT
* *
17249206 ATATATATAACAATTCAAATCTTTCATTAATCCTTTTTATTCAACTCATTTCAACAATCCAAAAT
1 ATATATATAACAATTCAAATATTTCATTAATCCTTTGTATTCAACTCATTTCAACAATCCAAAAT
* *
17249271 GTTCAATATAATTCACATGGCAAAAAGC----ATTTATTTATTTATTTCCAGCCACCAAATATGC
66 GTTCAATATAATTCACATAGCAAAAAGCATTTATTTATTTATTTATTTCCAACCACCAAATATGC
*
17249332 ATATCG
131 ATATCA
17249338 ATATATATAACAATTCAAATATTTCATTAATCCTTTGTATTCAACTCATTTCAACAATCCAAAAT
1 ATATATATAACAATTCAAATATTTCATTAATCCTTTGTATTCAACTCATTTCAACAATCCAAAAT
*
17249403 GTTCAATATAATTCACATAGCAAAAAACATTTATTTATTTATTTATTTCCAACCACCAAATATGC
66 GTTCAATATAATTCACATAGCAAAAAGCATTTATTTATTTATTTATTTCCAACCACCAAATATGC
*
17249468 ATATTA
131 ATATCA
*
17249474 ATATATATAAAAATTCAAATATTTCATTAATCCTTTGTATTCAACTCATTTCAACAATCCAAAAT
1 ATATATATAACAATTCAAATATTTCATTAATCCTTTGTATTCAACTCATTTCAACAATCCAAAAT
*
17249539 GTTCAATATAATTCACATAACAAAAAGCATTTATTTATTT
66 GTTCAATATAATTCACATAGCAAAAAGCATTTATTTATTT
17249579 TTGTTAATGT
Statistics
Matches: 227, Mismatches: 10, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
132 89 0.39
136 138 0.61
ACGTcount: A:0.40, C:0.18, G:0.04, T:0.38
Consensus pattern (136 bp):
ATATATATAACAATTCAAATATTTCATTAATCCTTTGTATTCAACTCATTTCAACAATCCAAAAT
GTTCAATATAATTCACATAGCAAAAAGCATTTATTTATTTATTTATTTCCAACCACCAAATATGC
ATATCA
Found at i:17256651 original size:102 final size:102
Alignment explanation
Indices: 17256353--17256654 Score: 453
Period size: 102 Copynumber: 3.0 Consensus size: 102
17256343 TTCTCAATTC
** * * * * *
17256353 ATGGCACCCGGTGCCTAGCGGATATACCGCGGTATGTGAGCCCAGCTCTAGTTGGATTATCCAAT
1 ATGGCACCCAATGCCTAGCGGATAAACCGCGATATGTGAGCCCAGCTCTGGTTGGATTAACCAAC
* * *
17256418 GATTTGCGTCC-AACGCTAGTCGGATAAACCGACGGTT
66 GATTTGCG-CCTAGCGCTAGTCAGATAAACTGACGGTT
*
17256455 ATGGCACCCAATGCCTAGCGGATAAACCGCGATATGTGAGCCCAACTCTGGTTGGATTAACCAAC
1 ATGGCACCCAATGCCTAGCGGATAAACCGCGATATGTGAGCCCAGCTCTGGTTGGATTAACCAAC
*
17256520 GGTTTGCGCCTAGCGCTAGTCAGATAAACTGACGGTT
66 GATTTGCGCCTAGCGCTAGTCAGATAAACTGACGGTT
* *
17256557 ATGGCACCTAATGCCTAGCGGATAAACCGCGATATGTGAGCCCAGCTTTGGTTGGATTAACCAAC
1 ATGGCACCCAATGCCTAGCGGATAAACCGCGATATGTGAGCCCAGCTCTGGTTGGATTAACCAAC
*
17256622 GTTTTGCGCCTAGCGCTAGTCAGATAAACTGAC
66 GATTTGCGCCTAGCGCTAGTCAGATAAACTGAC
17256655 AAACATTTAA
Statistics
Matches: 183, Mismatches: 16, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
101 2 0.01
102 181 0.99
ACGTcount: A:0.25, C:0.25, G:0.26, T:0.24
Consensus pattern (102 bp):
ATGGCACCCAATGCCTAGCGGATAAACCGCGATATGTGAGCCCAGCTCTGGTTGGATTAACCAAC
GATTTGCGCCTAGCGCTAGTCAGATAAACTGACGGTT
Found at i:17256885 original size:15 final size:15
Alignment explanation
Indices: 17256865--17256895 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
17256855 TACGAACTTA
*
17256865 CCGAAGTACGATTGT
1 CCGAAGCACGATTGT
17256880 CCGAAGCACGATTGT
1 CCGAAGCACGATTGT
17256895 C
1 C
17256896 ACTTAAGCCG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.26, C:0.26, G:0.26, T:0.23
Consensus pattern (15 bp):
CCGAAGCACGATTGT
Found at i:17257208 original size:132 final size:132
Alignment explanation
Indices: 17256971--17257339 Score: 650
Period size: 132 Copynumber: 2.8 Consensus size: 132
17256961 TTCTTGCTCT
* *
17256971 ATATATATAACAATTCAAATCTTTCATTAATCCTTTTTATTCAACTCATTTCAACAATCCAAAAT
1 ATATATATAACAATTCAAATATTTCATTAATCCTTTGTATTCAACTCATTTCAACAATCCAAAAT
17257036 GTTCAATATAATTCACAT-GGCAAAAAGCATTTATTTATTTATTTCCAGCCACCAAATATGCATA
66 GTTCAATATAATTCACATAGG-AAAAAGCATTTATTTATTTATTTCCAGCCACCAAATATGCATA
*
17257100 TCG
130 TCA
17257103 ATATATATAACAATTCAAATATTTCATTAATCCTTTGTATTCAACTCATTTCAACAATCCAAAAT
1 ATATATATAACAATTCAAATATTTCATTAATCCTTTGTATTCAACTCATTTCAACAATCCAAAAT
*
17257168 GTTCAATATAATTTACATAGGAAAAAGCATTTATTTATTTATTTCCAGCCACCAAATATGCATAT
66 GTTCAATATAATTCACATAGGAAAAAGCATTTATTTATTTATTTCCAGCCACCAAATATGCATAT
*
17257233 TA
131 CA
*
17257235 ATATATATAAAAATTCAAATATTTCATTAATCCTTTGTATTCAACTCATTTCAACAATCCAAAAT
1 ATATATATAACAATTCAAATATTTCATTAATCCTTTGTATTCAACTCATTTCAACAATCCAAAAT
* *
17257300 GTTCAATATAATTCAAATAGCAAAAAGCATTTATTTATTT
66 GTTCAATATAATTCACATAGGAAAAAGCATTTATTTATTT
17257340 TTGTTAACGG
Statistics
Matches: 227, Mismatches: 9, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
132 225 0.99
133 2 0.01
ACGTcount: A:0.40, C:0.17, G:0.05, T:0.38
Consensus pattern (132 bp):
ATATATATAACAATTCAAATATTTCATTAATCCTTTGTATTCAACTCATTTCAACAATCCAAAAT
GTTCAATATAATTCACATAGGAAAAAGCATTTATTTATTTATTTCCAGCCACCAAATATGCATAT
CA
Found at i:17259878 original size:25 final size:22
Alignment explanation
Indices: 17259850--17259908 Score: 57
Period size: 21 Copynumber: 2.6 Consensus size: 22
17259840 GGGCAAAGGT
*
17259850 TAATAAATACTATGTTATGATAAAG
1 TAATAAATA-TAT-ATAT-ATAAAG
*
17259875 TAATATATATATATATATAAAG
1 TAATAAATATATATATATAAAG
*
17259897 -AATAAAAATATA
1 TAATAAATATATA
17259909 ATACGTATTA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
21 10 0.33
22 6 0.20
23 3 0.10
24 3 0.10
25 8 0.27
ACGTcount: A:0.56, C:0.02, G:0.07, T:0.36
Consensus pattern (22 bp):
TAATAAATATATATATATAAAG
Found at i:17259944 original size:17 final size:19
Alignment explanation
Indices: 17259883--17259970 Score: 60
Period size: 19 Copynumber: 4.6 Consensus size: 19
17259873 AGTAATATAT
17259883 ATATATATATAAAGAATAAA-
1 ATATATA-AT-AAGAATAAAG
* *
17259903 A-ATATAATACGTATTAGAA-
1 ATATATAATAAG-AATA-AAG
17259922 ATATATAA-AA-AATAAAG
1 ATATATAATAAGAATAAAG
*
17259939 ATATATAATAAGAATAAAA
1 ATATATAATAAGAATAAAG
17259958 ATAATCATAATAA
1 AT-AT-ATAATAA
17259971 TATATGTATA
Statistics
Matches: 55, Mismatches: 5, Indels: 15
0.73 0.07 0.20
Matches are distributed among these distances:
16 2 0.04
17 13 0.24
18 7 0.13
19 17 0.31
20 9 0.16
21 7 0.13
ACGTcount: A:0.64, C:0.02, G:0.06, T:0.28
Consensus pattern (19 bp):
ATATATAATAAGAATAAAG
Found at i:17261875 original size:17 final size:17
Alignment explanation
Indices: 17261836--17261878 Score: 61
Period size: 16 Copynumber: 2.6 Consensus size: 17
17261826 ATAATTTAAC
*
17261836 ATAAAAATTTATTATTA
1 ATAAAATTTTATTATTA
*
17261853 AT-AAATTTTCTTATTA
1 ATAAAATTTTATTATTA
17261869 ATAAAATTTT
1 ATAAAATTTT
17261879 GATATAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 14 0.61
17 9 0.39
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (17 bp):
ATAAAATTTTATTATTA
Found at i:17265969 original size:1 final size:1
Alignment explanation
Indices: 17265963--17265987 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
17265953 CTGTTTTAAC
17265963 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
17265988 CCTCTGGCCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:17269105 original size:3 final size:3
Alignment explanation
Indices: 17269097--17269131 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
17269087 AGTTAACAAT
17269097 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
17269132 GAGGAGGAGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:17269226 original size:3 final size:3
Alignment explanation
Indices: 17269218--17269253 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
17269208 TCTACCGTTC
*
17269218 TCT TCT TCT TAT TCT TCT T-T TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
17269254 TTATTGCCCA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.03, C:0.28, G:0.00, T:0.69
Consensus pattern (3 bp):
TCT
Found at i:17269240 original size:17 final size:17
Alignment explanation
Indices: 17269215--17269255 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
17269205 CTCTCTACCG
*
17269215 TTCTCTTCTTCTTATTC
1 TTCTTTTCTTCTTATTC
*
17269232 TTCTTTTCTTCTTCTTC
1 TTCTTTTCTTCTTATTC
17269249 TTCTTTT
1 TTCTTTT
17269256 ATTGCCCAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.02, C:0.27, G:0.00, T:0.71
Consensus pattern (17 bp):
TTCTTTTCTTCTTATTC
Found at i:17269754 original size:96 final size:96
Alignment explanation
Indices: 17269590--17269877 Score: 549
Period size: 96 Copynumber: 3.0 Consensus size: 96
17269580 TGAATTCTCG
* *
17269590 ATAGTCTAAATAGGTACTTTTATGAGAAAGGAAAATTTAAGTTAAGAACTTGGAATTGTATAATG
1 ATAGTCTAAATAGGTACTTTTACGAGAAAGGAAAAATTAAGTTAAGAACTTGGAATTGTATAATG
17269655 GTAATGAAATAAATGGATAGAAAGGATATAA
66 GTAATGAAATAAATGGATAGAAAGGATATAA
17269686 ATAGTCTAAATAGGTACTTTTACGAGAAAGGAAAAATTAAGTTAAGAACTTGGAATTGTATAATG
1 ATAGTCTAAATAGGTACTTTTACGAGAAAGGAAAAATTAAGTTAAGAACTTGGAATTGTATAATG
17269751 GTAATGAAATAAATGGATAGAAAGGATATAA
66 GTAATGAAATAAATGGATAGAAAGGATATAA
*
17269782 ATAGTCTAAATAGGTACTTTTACAAGAAAGGAAAAATTAAGTTAAGAACTTGGAATTGTATAATG
1 ATAGTCTAAATAGGTACTTTTACGAGAAAGGAAAAATTAAGTTAAGAACTTGGAATTGTATAATG
17269847 GTAATGAAATAAATGGATAGAAAGGATATAA
66 GTAATGAAATAAATGGATAGAAAGGATATAA
17269878 CTTATAAAAA
Statistics
Matches: 189, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
96 189 1.00
ACGTcount: A:0.47, C:0.04, G:0.20, T:0.29
Consensus pattern (96 bp):
ATAGTCTAAATAGGTACTTTTACGAGAAAGGAAAAATTAAGTTAAGAACTTGGAATTGTATAATG
GTAATGAAATAAATGGATAGAAAGGATATAA
Found at i:17285789 original size:33 final size:32
Alignment explanation
Indices: 17285725--17285789 Score: 78
Period size: 32 Copynumber: 2.0 Consensus size: 32
17285715 ATATTTATGT
* * *
17285725 CTTAAATTGAAAATGATTTTTATATAGGGGAG
1 CTTAAATTCAAAATGATTTTTATAAAAGGGAG
17285757 CTTAAATTCAAAATG-TATTTTATTAAAAGGGAG
1 CTTAAATTCAAAATGAT-TTTTA-TAAAAGGGAG
17285790 TAATCTATTC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
31 1 0.04
32 19 0.68
33 8 0.29
ACGTcount: A:0.40, C:0.05, G:0.18, T:0.37
Consensus pattern (32 bp):
CTTAAATTCAAAATGATTTTTATAAAAGGGAG
Found at i:17288633 original size:16 final size:16
Alignment explanation
Indices: 17288612--17288648 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
17288602 CATTAAAAAT
17288612 AACTAAATAAACTAAC
1 AACTAAATAAACTAAC
* *
17288628 AACTAATTTAACTAAC
1 AACTAAATAAACTAAC
17288644 AACTA
1 AACTA
17288649 CCAGCATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.57, C:0.19, G:0.00, T:0.24
Consensus pattern (16 bp):
AACTAAATAAACTAAC
Found at i:17290424 original size:19 final size:20
Alignment explanation
Indices: 17290400--17290441 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
17290390 AATTTTTTAG
17290400 TTTTTA-TAAACTTATAATT
1 TTTTTAGTAAACTTATAATT
**
17290419 TTTTTAGTATTCTTATAATT
1 TTTTTAGTAAACTTATAATT
17290439 TTT
1 TTT
17290442 AAATTATTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.64
Consensus pattern (20 bp):
TTTTTAGTAAACTTATAATT
Found at i:17290449 original size:20 final size:20
Alignment explanation
Indices: 17290410--17290449 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
17290400 TTTTTATAAA
**
17290410 CTTATAATTTTTTTAGTATT
1 CTTATAATTTTTAAAGTATT
*
17290430 CTTATAATTTTTAAATTATT
1 CTTATAATTTTTAAAGTATT
17290450 AATTGACATG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.30, C:0.05, G:0.03, T:0.62
Consensus pattern (20 bp):
CTTATAATTTTTAAAGTATT
Found at i:17290765 original size:20 final size:20
Alignment explanation
Indices: 17290735--17290784 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
17290725 ATTAACATGA
*
17290735 GTTATATTAAGTA-TAAATAGG
1 GTTA-ATTAAG-ACTAAAAAGG
*
17290756 TTTAATTAAGACTAAAAAGG
1 GTTAATTAAGACTAAAAAGG
17290776 GTTAATTAA
1 GTTAATTAA
17290785 AGCTTAATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.46, C:0.02, G:0.16, T:0.36
Consensus pattern (20 bp):
GTTAATTAAGACTAAAAAGG
Found at i:17294565 original size:18 final size:19
Alignment explanation
Indices: 17294529--17294566 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
17294519 ATTGAATTAA
*
17294529 TCGATTAAATCGATTTAAT
1 TCGATTAAATCGATCTAAT
*
17294548 TCGATT-AATTGATCTAAT
1 TCGATTAAATCGATCTAAT
17294566 T
1 T
17294567 TGATCAGAGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.45
Consensus pattern (19 bp):
TCGATTAAATCGATCTAAT
Found at i:17300994 original size:8 final size:8
Alignment explanation
Indices: 17300981--17301023 Score: 61
Period size: 8 Copynumber: 5.2 Consensus size: 8
17300971 GAAGAAAGCT
17300981 AGAGAATG
1 AGAGAATG
17300989 AGAGAATG
1 AGAGAATG
17300997 AGAGAATG
1 AGAGAATG
17301005 AGAGAAATG
1 AGAG-AATG
17301014 A-AGGAATG
1 AGA-GAATG
17301022 AG
1 AG
17301024 GGATGATTTG
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
8 26 0.81
9 6 0.19
ACGTcount: A:0.51, C:0.00, G:0.37, T:0.12
Consensus pattern (8 bp):
AGAGAATG
Found at i:17315054 original size:86 final size:86
Alignment explanation
Indices: 17314936--17315097 Score: 261
Period size: 86 Copynumber: 1.9 Consensus size: 86
17314926 GTCCATATTA
* * * *
17314936 CCACTCACGATGCTGCTTACACAAGCTGTCAAGAATCCGCAACATATGCAAGATCTCAGGCATTG
1 CCACTCACGATGCTGCTCACACAAGCTATCAAGAATCCACAACATATGCAAGATCTCAGCCATTG
17315001 GAGGGTCCATATATGTAACAC
66 GAGGGTCCATATATGTAACAC
* * *
17315022 CCACTCTCGATGCTGCTCACACAAGCTATCAAGGATCCACAACATATGCAAGATCTTAGCCATTG
1 CCACTCACGATGCTGCTCACACAAGCTATCAAGAATCCACAACATATGCAAGATCTCAGCCATTG
17315087 GAGGGTCCATA
66 GAGGGTCCATA
17315098 CAGTCAGTAT
Statistics
Matches: 69, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
86 69 1.00
ACGTcount: A:0.31, C:0.28, G:0.19, T:0.22
Consensus pattern (86 bp):
CCACTCACGATGCTGCTCACACAAGCTATCAAGAATCCACAACATATGCAAGATCTCAGCCATTG
GAGGGTCCATATATGTAACAC
Found at i:17333790 original size:19 final size:20
Alignment explanation
Indices: 17333743--17333790 Score: 50
Period size: 19 Copynumber: 2.5 Consensus size: 20
17333733 TTGATAATTC
17333743 TTAA-TATTA-AATTATAAA
1 TTAATTATTATAATTATAAA
*
17333761 TTAAATT-TTATAATT-TATA
1 TT-AATTATTATAATTATAAA
17333780 TTAATTATTAT
1 TTAATTATTAT
17333791 CAAGAGTTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
18 6 0.24
19 14 0.56
20 5 0.20
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TTAATTATTATAATTATAAA
Found at i:17334452 original size:16 final size:16
Alignment explanation
Indices: 17334431--17334471 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
17334421 ATTTATCTTC
17334431 TAATTT-TTAAATTATT
1 TAATTTATTAAATT-TT
*
17334447 TAATTTATTAACTTTT
1 TAATTTATTAAATTTT
17334463 TAATTTATT
1 TAATTTATT
17334472 TTAAATTGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 17 0.74
17 6 0.26
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.63
Consensus pattern (16 bp):
TAATTTATTAAATTTT
Found at i:17334489 original size:26 final size:24
Alignment explanation
Indices: 17334431--17334489 Score: 64
Period size: 26 Copynumber: 2.3 Consensus size: 24
17334421 ATTTATCTTC
*
17334431 TAATTTTTAAATTATTTAATTTAT
1 TAATTTTTAAATTATTTAAATTAT
* *
17334455 TAACTTTTTAATTTATTTTAAATTGT
1 TAA-TTTTTAAATTA-TTTAAATTAT
17334481 TAATATTTT
1 TAAT-TTTT
17334490 TACTAATTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
24 3 0.10
25 11 0.38
26 15 0.52
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.63
Consensus pattern (24 bp):
TAATTTTTAAATTATTTAAATTAT
Found at i:17335389 original size:21 final size:21
Alignment explanation
Indices: 17335363--17335414 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
17335353 CAACAGCAAG
*
17335363 CTGAAGAAGAATAAGAAGACC
1 CTGAAGAAGAAGAAGAAGACC
* *
17335384 CTGAAGAAGAAGAAGAGGATC
1 CTGAAGAAGAAGAAGAAGACC
*
17335405 CTGAATAAGA
1 CTGAAGAAGA
17335415 TCTTGTGGAG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.50, C:0.12, G:0.27, T:0.12
Consensus pattern (21 bp):
CTGAAGAAGAAGAAGAAGACC
Found at i:17336160 original size:7 final size:7
Alignment explanation
Indices: 17336148--17336174 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
17336138 GTAAGGGGAC
17336148 CGAAAAT
1 CGAAAAT
17336155 CGAAAAT
1 CGAAAAT
17336162 CGAAAAT
1 CGAAAAT
17336169 CGAAAA
1 CGAAAA
17336175 CTTCTTAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.59, C:0.15, G:0.15, T:0.11
Consensus pattern (7 bp):
CGAAAAT
Found at i:17360729 original size:22 final size:22
Alignment explanation
Indices: 17360701--17360748 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
17360691 ATTTAACAAT
17360701 CAATAACATACACAAGCTAAGA
1 CAATAACATACACAAGCTAAGA
*
17360723 CAATAACATACATAAGCTAAGA
1 CAATAACATACACAAGCTAAGA
17360745 CAAT
1 CAAT
17360749 TGCATTAATC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.54, C:0.21, G:0.08, T:0.17
Consensus pattern (22 bp):
CAATAACATACACAAGCTAAGA
Found at i:17362340 original size:26 final size:26
Alignment explanation
Indices: 17362300--17362466 Score: 185
Period size: 26 Copynumber: 6.5 Consensus size: 26
17362290 CTTTGAAGAA
17362300 ATACTGAACTAGCTCGTAAGAGCAAT
1 ATACTGAACTAGCTCGTAAGAGCAAT
* * *
17362326 ATACTGTACTGGCTCGTAAGAGCGAT
1 ATACTGAACTAGCTCGTAAGAGCAAT
* *
17362352 ATACTGTACTAGCTCGTAAGAGTGAA-
1 ATACTGAACTAGCTCGTAAGAG-CAAT
*
17362378 ATACTGAACTGGCTCGTAAGAGCAAT
1 ATACTGAACTAGCTCGTAAGAGCAAT
* * * * * * *
17362404 ATATTGTATTGGCTCGTAAGATCGAC
1 ATACTGAACTAGCTCGTAAGAGCAAT
*
17362430 ATACTAAACTAGCTCGTAAGAGCAAT
1 ATACTGAACTAGCTCGTAAGAGCAAT
17362456 ATACTG-ACTAG
1 ATACTGAACTAG
17362467 GATTGTATGA
Statistics
Matches: 115, Mismatches: 24, Indels: 5
0.80 0.17 0.03
Matches are distributed among these distances:
25 7 0.06
26 107 0.93
27 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.26
Consensus pattern (26 bp):
ATACTGAACTAGCTCGTAAGAGCAAT
Found at i:17362382 original size:52 final size:52
Alignment explanation
Indices: 17362300--17362466 Score: 205
Period size: 52 Copynumber: 3.2 Consensus size: 52
17362290 CTTTGAAGAA
* * * *
17362300 ATACTGAACTAGCTCGTAAGAG-CAATATACTGTACTGGCTCGTAAGAGCGAT
1 ATACTGTACTAGCTCGTAAGAGTGAA-ATACTGAACTGGCTCGTAAGAGCAAT
17362352 ATACTGTACTAGCTCGTAAGAGTGAAATACTGAACTGGCTCGTAAGAGCAAT
1 ATACTGTACTAGCTCGTAAGAGTGAAATACTGAACTGGCTCGTAAGAGCAAT
* * * * * *
17362404 ATATTGTATTGGCTCGTAAGA-TCGACATACTAAACTAGCTCGTAAGAGCAAT
1 ATACTGTACTAGCTCGTAAGAGT-GAAATACTGAACTGGCTCGTAAGAGCAAT
17362456 ATACTG-ACTAG
1 ATACTGTACTAG
17362467 GATTGTATGA
Statistics
Matches: 100, Mismatches: 13, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
51 4 0.04
52 94 0.94
53 2 0.02
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.26
Consensus pattern (52 bp):
ATACTGTACTAGCTCGTAAGAGTGAAATACTGAACTGGCTCGTAAGAGCAAT
Found at i:17362434 original size:78 final size:78
Alignment explanation
Indices: 17362297--17362451 Score: 247
Period size: 78 Copynumber: 2.0 Consensus size: 78
17362287 AGACTTTGAA
* **
17362297 GAAATACTGAACTAGCTCGTAAGAGCAATATACTGTACTGGCTCGTAAGAGCGATATACTGTACT
1 GAAATACTGAACTAGCTCGTAAGAGCAATATACTGTACTGGCTCGTAAGAGCGACATACTAAACT
17362362 AGCTCGTAAGAGT
66 AGCTCGTAAGAGT
* * * *
17362375 GAAATACTGAACTGGCTCGTAAGAGCAATATATTGTATTGGCTCGTAAGATCGACATACTAAACT
1 GAAATACTGAACTAGCTCGTAAGAGCAATATACTGTACTGGCTCGTAAGAGCGACATACTAAACT
17362440 AGCTCGTAAGAG
66 AGCTCGTAAGAG
17362452 CAATATACTG
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
78 70 1.00
ACGTcount: A:0.34, C:0.17, G:0.23, T:0.26
Consensus pattern (78 bp):
GAAATACTGAACTAGCTCGTAAGAGCAATATACTGTACTGGCTCGTAAGAGCGACATACTAAACT
AGCTCGTAAGAGT
Found at i:17383323 original size:30 final size:30
Alignment explanation
Indices: 17383287--17383350 Score: 128
Period size: 30 Copynumber: 2.1 Consensus size: 30
17383277 GGAAGAAATG
17383287 CTTTCAATCCTGAAGCACAGCCACGACGCC
1 CTTTCAATCCTGAAGCACAGCCACGACGCC
17383317 CTTTCAATCCTGAAGCACAGCCACGACGCC
1 CTTTCAATCCTGAAGCACAGCCACGACGCC
17383347 CTTT
1 CTTT
17383351 ATAGAGGTCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.25, C:0.39, G:0.16, T:0.20
Consensus pattern (30 bp):
CTTTCAATCCTGAAGCACAGCCACGACGCC
Found at i:17386654 original size:34 final size:34
Alignment explanation
Indices: 17386611--17386680 Score: 97
Period size: 34 Copynumber: 2.1 Consensus size: 34
17386601 GTAGGTGTAA
* *
17386611 TTTAATTGTCACCACAT-TCCCTTTGTCATTGCAT
1 TTTAATTGTCACCACATCTACATTT-TCATTGCAT
*
17386645 TTTAATTGTCACTACATCTACATTTTCATTGCAT
1 TTTAATTGTCACCACATCTACATTTTCATTGCAT
17386679 TT
1 TT
17386681 CCATGTGACA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
34 27 0.84
35 5 0.16
ACGTcount: A:0.23, C:0.23, G:0.07, T:0.47
Consensus pattern (34 bp):
TTTAATTGTCACCACATCTACATTTTCATTGCAT
Found at i:17388938 original size:3 final size:3
Alignment explanation
Indices: 17388932--17388981 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
17388922 AAAAATGATA
17388932 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
17388980 TT
1 TT
17388982 TACACGGTTG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:17389681 original size:26 final size:26
Alignment explanation
Indices: 17389623--17389811 Score: 193
Period size: 26 Copynumber: 7.3 Consensus size: 26
17389613 AATTATATAT
* *
17389623 TGTACTAGCTCGTAAGAGCGAAATAA
1 TGTACTGGCTCGTAAGAGCGAAATAC
* * * * *
17389649 TGAACTGGCTTGTAAGAGTGATATAT
1 TGTACTGGCTCGTAAGAGCGAAATAC
* * *
17389675 TGTACTGGCTAGTAAGAGCAAAATAT
1 TGTACTGGCTCGTAAGAGCGAAATAC
* * *
17389701 TGTACTAGCTTGTAAGGGCGAAATAC
1 TGTACTGGCTCGTAAGAGCGAAATAC
*
17389727 TGAACTGGCTCGTAAGAGCGAAATAC
1 TGTACTGGCTCGTAAGAGCGAAATAC
* * *
17389753 TGTACTGGCTTGTAAGAACGACATAC
1 TGTACTGGCTCGTAAGAGCGAAATAC
*
17389779 TGAACTGGCTCGTAAGAGC-AATATAC
1 TGTACTGGCTCGTAAGAGCGAA-ATAC
17389805 TG-ACTGG
1 TGTACTGG
17389812 GATCGTATGA
Statistics
Matches: 134, Mismatches: 28, Indels: 3
0.81 0.17 0.02
Matches are distributed among these distances:
25 6 0.04
26 128 0.96
ACGTcount: A:0.33, C:0.15, G:0.25, T:0.26
Consensus pattern (26 bp):
TGTACTGGCTCGTAAGAGCGAAATAC
Found at i:17389757 original size:78 final size:78
Alignment explanation
Indices: 17389619--17389797 Score: 232
Period size: 78 Copynumber: 2.3 Consensus size: 78
17389609 GTGTAATTAT
* * * *
17389619 ATATTGTACTAGCTCGTAAGAGCGAAATAATGAACTGGCTTGTAAGAGTGATATATTGTACTGGC
1 ATATTGTACTAGCTCGTAAGAGCGAAATAATGAACTGGCTCGTAAGAGCGAAATACTGTACTGGC
17389684 TAGTAAGAGCAAA
66 TAGTAAGAGCAAA
* * *
17389697 ATATTGTACTAGCTTGTAAGGGCGAAATACTGAACTGGCTCGTAAGAGCGAAATACTGTACTGGC
1 ATATTGTACTAGCTCGTAAGAGCGAAATAATGAACTGGCTCGTAAGAGCGAAATACTGTACTGGC
* * * *
17389762 TTGTAAGAACGAC
66 TAGTAAGAGCAAA
* * *
17389775 ATACTGAACTGGCTCGTAAGAGC
1 ATATTGTACTAGCTCGTAAGAGC
17389798 AATATACTGA
Statistics
Matches: 85, Mismatches: 16, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
78 85 1.00
ACGTcount: A:0.34, C:0.15, G:0.25, T:0.26
Consensus pattern (78 bp):
ATATTGTACTAGCTCGTAAGAGCGAAATAATGAACTGGCTCGTAAGAGCGAAATACTGTACTGGC
TAGTAAGAGCAAA
Found at i:17389805 original size:52 final size:52
Alignment explanation
Indices: 17389630--17389811 Score: 224
Period size: 52 Copynumber: 3.5 Consensus size: 52
17389620 TATTGTACTA
* * * * * *
17389630 GCTCGTAAGAGCGAAATAATGAACTGGCTTGTAAGAGTGATATATTGTACTG
1 GCTCGTAAGAGCGAAATACTGTACTGGCTTGTAAGAGCGAAATACTGAACTG
* * * * *
17389682 GCTAGTAAGAGCAAAATATTGTACTAGCTTGTAAGGGCGAAATACTGAACTG
1 GCTCGTAAGAGCGAAATACTGTACTGGCTTGTAAGAGCGAAATACTGAACTG
* *
17389734 GCTCGTAAGAGCGAAATACTGTACTGGCTTGTAAGAACGACATACTGAACTG
1 GCTCGTAAGAGCGAAATACTGTACTGGCTTGTAAGAGCGAAATACTGAACTG
17389786 GCTCGTAAGAGC-AATATACTG-ACTGG
1 GCTCGTAAGAGCGAA-ATACTGTACTGG
17389812 GATCGTATGA
Statistics
Matches: 112, Mismatches: 17, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
51 7 0.06
52 105 0.94
ACGTcount: A:0.34, C:0.15, G:0.26, T:0.25
Consensus pattern (52 bp):
GCTCGTAAGAGCGAAATACTGTACTGGCTTGTAAGAGCGAAATACTGAACTG
Found at i:17389823 original size:26 final size:27
Alignment explanation
Indices: 17389632--17389833 Score: 87
Period size: 26 Copynumber: 7.7 Consensus size: 27
17389622 TTGTACTAGC
* * *
17389632 TCGTAAGAGCGAA-ATAATGAACTGGC
1 TCGTAAGAGCTAATATACTGAACTGGA
* * * * *
17389658 TTGTAAGAG-TGATATATTGTACTGGC
1 TCGTAAGAGCTAATATACTGAACTGGA
* * * * * *
17389684 TAGTAAGAGC-AAAATATTGTACTAGC
1 TCGTAAGAGCTAATATACTGAACTGGA
* * * *
17389710 TTGTAAGGGCGAA-ATACTGAACTGGC
1 TCGTAAGAGCTAATATACTGAACTGGA
* * *
17389736 TCGTAAGAGCGAA-ATACTGTACTGGC
1 TCGTAAGAGCTAATATACTGAACTGGA
* * * * *
17389762 TTGTAAGAAC-GACATACTGAACTGGC
1 TCGTAAGAGCTAATATACTGAACTGGA
17389788 TCGTAAGAGC-AATATACTG-ACTGGGA
1 TCGTAAGAGCTAATATACTGAACT-GGA
* *
17389814 TCGTATGAGCTAATTTACTG
1 TCGTAAGAGCTAATATACTG
17389834 GAAGACTAGA
Statistics
Matches: 142, Mismatches: 28, Indels: 11
0.78 0.15 0.06
Matches are distributed among these distances:
25 5 0.04
26 127 0.89
27 10 0.07
ACGTcount: A:0.33, C:0.15, G:0.25, T:0.27
Consensus pattern (27 bp):
TCGTAAGAGCTAATATACTGAACTGGA
Found at i:17394392 original size:17 final size:17
Alignment explanation
Indices: 17394352--17394389 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
17394342 TATCTACAAG
*
17394352 TTAAATATTAAATTTAA
1 TTAAATATTAAATCTAA
*
17394369 TTTAATATTAAATCT-A
1 TTAAATATTAAATCTAA
17394385 TTAAA
1 TTAAA
17394390 ATAATATTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
16 5 0.28
17 13 0.72
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (17 bp):
TTAAATATTAAATCTAA
Found at i:17394742 original size:19 final size:19
Alignment explanation
Indices: 17394718--17394757 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
17394708 CGATCTCGAT
* *
17394718 TTTTTTTTCTCGAGCTCAA
1 TTTTTTATCTCAAGCTCAA
*
17394737 TTTTTTATCTCAAGTTCAA
1 TTTTTTATCTCAAGCTCAA
17394756 TT
1 TT
17394758 ACTCTTTGAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.20, C:0.17, G:0.07, T:0.55
Consensus pattern (19 bp):
TTTTTTATCTCAAGCTCAA
Found at i:17394828 original size:9 final size:9
Alignment explanation
Indices: 17394808--17394838 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
17394798 AATATATCAT
17394808 ATTAATTTTA
1 ATTAA-TTTA
17394818 ATTAATTTA
1 ATTAATTTA
17394827 ATTAATTTA
1 ATTAATTTA
17394836 ATT
1 ATT
17394839 TTATTTGATC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 16 0.76
10 5 0.24
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (9 bp):
ATTAATTTA
Found at i:17399828 original size:26 final size:25
Alignment explanation
Indices: 17399789--17399860 Score: 81
Period size: 25 Copynumber: 2.8 Consensus size: 25
17399779 TCGTGCGACC
* *
17399789 TAGATCCGCGAGCTCTCCTTGCAAGT
1 TAGATCCGCAAGCTCCCCTTG-AAGT
*
17399815 TAGATCCGTAAGCTCCCCTTGAAGT
1 TAGATCCGCAAGCTCCCCTTGAAGT
* * *
17399840 TAGGTCCACAAGCTCCTCTTG
1 TAGATCCGCAAGCTCCCCTTG
17399861 TTGTCCTCTC
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
25 21 0.54
26 18 0.46
ACGTcount: A:0.21, C:0.31, G:0.21, T:0.28
Consensus pattern (25 bp):
TAGATCCGCAAGCTCCCCTTGAAGT
Found at i:17401512 original size:17 final size:17
Alignment explanation
Indices: 17401490--17401529 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
17401480 AAAATTAAAC
17401490 TTTTAAATAGTTTTT-AT
1 TTTTAAA-AGTTTTTAAT
*
17401507 TTTTAAAGGTTTTTAAT
1 TTTTAAAAGTTTTTAAT
17401524 TTTTAA
1 TTTTAA
17401530 GAATCAATAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 6 0.29
17 15 0.71
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.62
Consensus pattern (17 bp):
TTTTAAAAGTTTTTAAT
Found at i:17401806 original size:4 final size:4
Alignment explanation
Indices: 17401797--17401829 Score: 59
Period size: 4 Copynumber: 8.5 Consensus size: 4
17401787 ATTTCTTTTG
17401797 GGGT GGGT GGGT GGGT GGGT GGGT -GGT GGGT GG
1 GGGT GGGT GGGT GGGT GGGT GGGT GGGT GGGT GG
17401830 ATGCAGTGCA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.11
4 25 0.89
ACGTcount: A:0.00, C:0.00, G:0.76, T:0.24
Consensus pattern (4 bp):
GGGT
Found at i:17401995 original size:35 final size:35
Alignment explanation
Indices: 17401955--17402021 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
17401945 AATTTTATCT
*
17401955 TTTTAAATTTTT-AAATTAATAAAAATAAAATTATA
1 TTTT-AATTTTTAAAAATAATAAAAATAAAATTATA
*
17401990 TTTTAATTTTTAAAAATAATAAAAATTAAATT
1 TTTTAATTTTTAAAAATAATAAAAATAAAATT
17402022 TGATTGTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 7 0.24
35 22 0.76
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (35 bp):
TTTTAATTTTTAAAAATAATAAAAATAAAATTATA
Done.