Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008310.1 Hibiscus syriacus cultivar Beakdansim tig00111000_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: 3887810
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 15
Found at i:2290587 original size:1 final size:1
Alignment explanation
Indices: 2290583--2290612 Score: 51
Period size: 1 Copynumber: 30.0 Consensus size: 1
2290573 TTTTTTTTAC
*
2290583 AAAAAAAAAAAAAAAAAACAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
2290613 CACAAAAGCC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.97, C:0.03, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:2290605 original size:14 final size:14
Alignment explanation
Indices: 2290583--2290619 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
2290573 TTTTTTTTAC
2290583 AAAAA-AAAAAAAA
1 AAAAACAAAAAAAA
2290596 AAAAACAAAAAAAA
1 AAAAACAAAAAAAA
*
2290610 AAACACAAAA
1 AAAAACAAAA
2290620 GCCAAAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 5 0.23
14 17 0.77
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (14 bp):
AAAAACAAAAAAAA
Found at i:2290613 original size:12 final size:12
Alignment explanation
Indices: 2290583--2290619 Score: 58
Period size: 12 Copynumber: 3.1 Consensus size: 12
2290573 TTTTTTTTAC
2290583 AAAAAAA-AAAA
1 AAAAAAACAAAA
2290594 AAAAAAACAAAA
1 AAAAAAACAAAA
2290606 AAAAAAACACAAA
1 AAAAAAACA-AAA
2290619 A
1 A
2290620 GCCAAAATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 7 0.29
12 13 0.54
13 4 0.17
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (12 bp):
AAAAAAACAAAA
Found at i:2300960 original size:366 final size:366
Alignment explanation
Indices: 2300283--2301019 Score: 1269
Period size: 366 Copynumber: 2.0 Consensus size: 366
2300273 CTTCTTTGAG
* *
2300283 TCTTCTTTAAGATACTATCCTCACAACCATCCCCTTTGTTTTATAAACCATAACCATAGCCATAT
1 TCTTATTTAAGATACTATCCTCACAACCATCCCCTTTGTTTCATAAACCATAACCATAGCCATAT
*
2300348 CAACCATCTTCCGCTTCCATCTCTCAATTAAACAGCCCACCTAATCACCCACACATCTACCACCC
66 CAACCATCTTCCGCTTCCATCTCTCAATTAAACAGCCCAACTAATCACCCACACATCTACCACCC
2300413 TTAACCATTCTGTTTTGAGCCATTCACTTTGCAGGTTGTTTTGCTTCCTTCCTAAATCCACAATT
131 TTAACCATTCTGTTTTGAGCCATTCACTTTGCAGGTTGTTTTGCTTCCTTCCTAAATCCACAATT
* * *
2300478 ATTTTGTTAAGGTAACAAAAGAGCCTTACATCACTGGTGGGATCAATTGGTGAGTTCAAGAAGAT
196 AGTTTGTCAAGGTAACAAAAGAGCCTTACATCACTGGTGGGATCAATTGGTGAGTTCAAGAAGAC
*
2300543 GAAATGATGAACGTCCCATCACTACGTGGGAAGAAATGAAGGCTATTATGAGGAAAAGGTTCGTG
261 GAAATGATGAACGTCCCATCACTACGTGGGAAGAAATAAAGGCTATTATGAGGAAAAGGTTCGTG
* * *
2300608 CCTACTCACTATCACAGAGATCTCTATCATAAGTTACAATA
326 CCTACTCACCATCACAGAGATCTCTATCATAAGCTACAAAA
2300649 TCTTATTTAAGATACTATCCTCACAACCATCCCCTTTGTTTCATAAACCATAACCATAGCCATAT
1 TCTTATTTAAGATACTATCCTCACAACCATCCCCTTTGTTTCATAAACCATAACCATAGCCATAT
* * * * *
2300714 CAACCATCTTTCTCTTCTATCTCTCAATTAAACAGCCCAACTAATCACCCATACGTCTACCACCC
66 CAACCATCTTCCGCTTCCATCTCTCAATTAAACAGCCCAACTAATCACCCACACATCTACCACCC
*
2300779 TTAACCATTCTGTTTTGAGCCATTCACTTTGCAGGTT-TTTTGGCTTCCTTCCTAGATCCACAAT
131 TTAACCATTCTGTTTTGAGCCATTCACTTTGCAGGTTGTTTT-GCTTCCTTCCTAAATCCACAAT
* * *
2300843 TAGTTTGTCAAGGTAATAGAAGAGCCTTACATCATTGGTGGGATCAATTGGTGAGTTCAAGAAGA
195 TAGTTTGTCAAGGTAACAAAAGAGCCTTACATCACTGGTGGGATCAATTGGTGAGTTCAAGAAGA
*
2300908 CGAAATGGTGAACGTCCCATCACTACGTGGGAAGAAATAAAGGCTATTATGAGGAAAAGGTTCGT
260 CGAAATGATGAACGTCCCATCACTACGTGGGAAGAAATAAAGGCTATTATGAGGAAAAGGTTCGT
*
2300973 GCCTACTCACCATCATAGAGATCTCTATCATAAGCTACAAAA
325 GCCTACTCACCATCACAGAGATCTCTATCATAAGCTACAAAA
2301015 TCTTA
1 TCTTA
2301020 AACAAGGGAG
Statistics
Matches: 349, Mismatches: 21, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
365 4 0.01
366 345 0.99
ACGTcount: A:0.31, C:0.25, G:0.14, T:0.30
Consensus pattern (366 bp):
TCTTATTTAAGATACTATCCTCACAACCATCCCCTTTGTTTCATAAACCATAACCATAGCCATAT
CAACCATCTTCCGCTTCCATCTCTCAATTAAACAGCCCAACTAATCACCCACACATCTACCACCC
TTAACCATTCTGTTTTGAGCCATTCACTTTGCAGGTTGTTTTGCTTCCTTCCTAAATCCACAATT
AGTTTGTCAAGGTAACAAAAGAGCCTTACATCACTGGTGGGATCAATTGGTGAGTTCAAGAAGAC
GAAATGATGAACGTCCCATCACTACGTGGGAAGAAATAAAGGCTATTATGAGGAAAAGGTTCGTG
CCTACTCACCATCACAGAGATCTCTATCATAAGCTACAAAA
Found at i:2307980 original size:20 final size:22
Alignment explanation
Indices: 2307955--2307994 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
2307945 GTGTAAGACC
2307955 TATGAGCT-A-AAATGAATGCA
1 TATGAGCTAACAAATGAATGCA
2307975 TATGAGCTAACAAATGAATG
1 TATGAGCTAACAAATGAATG
2307995 ATTAAGCATG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 8 0.44
21 1 0.06
22 9 0.50
ACGTcount: A:0.45, C:0.10, G:0.20, T:0.25
Consensus pattern (22 bp):
TATGAGCTAACAAATGAATGCA
Found at i:2318592 original size:26 final size:26
Alignment explanation
Indices: 2318556--2318630 Score: 77
Period size: 26 Copynumber: 3.0 Consensus size: 26
2318546 ATTCTTTATT
2318556 TTATTTCATTTCATTTCTTATCTTTA
1 TTATTTCATTTCATTTCTTATCTTTA
*
2318582 TTATTTCATTT-A-TTCTT-CCTTTA
1 TTATTTCATTTCATTTCTTATCTTTA
* *
2318605 TTA-ATCATCTTCCTTTTCTTATCTTT
1 TTATTTCAT-TT-CATTTCTTATCTTT
2318631 GTTGCAGCCA
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
22 4 0.10
23 10 0.25
24 5 0.12
25 1 0.03
26 16 0.40
27 4 0.10
ACGTcount: A:0.17, C:0.19, G:0.00, T:0.64
Consensus pattern (26 bp):
TTATTTCATTTCATTTCTTATCTTTA
Found at i:2328025 original size:19 final size:20
Alignment explanation
Indices: 2328001--2328043 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
2327991 TGCATTTATC
*
2328001 TTCATT-AAAATTATGTATT
1 TTCATTAAAAATCATGTATT
*
2328020 TTCATTAAAAATCATGTGTT
1 TTCATTAAAAATCATGTATT
2328040 TTCA
1 TTCA
2328044 AAGGGGTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.35, C:0.09, G:0.07, T:0.49
Consensus pattern (20 bp):
TTCATTAAAAATCATGTATT
Found at i:2328481 original size:23 final size:23
Alignment explanation
Indices: 2328451--2328528 Score: 70
Period size: 21 Copynumber: 3.2 Consensus size: 23
2328441 CTCTATCCCT
2328451 TCTTTATTTCATTTCATTTCTTA
1 TCTTTATTTCATTTCATTTCTTA
* *
2328474 TCTTTA-TT-ATTTCATTTATTCT
1 TCTTTATTTCATTTCATTTCTT-A
2328496 TCCTTTATTAATCATCTTCATTTTCTTA
1 T-CTTTATT--TCAT-TTCA-TTTCTTA
2328524 TCTTT
1 TCTTT
2328529 GTTGCAGCCA
Statistics
Matches: 43, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
21 11 0.26
22 3 0.07
23 11 0.26
24 1 0.02
26 1 0.02
27 6 0.14
28 5 0.12
29 5 0.12
ACGTcount: A:0.18, C:0.18, G:0.00, T:0.64
Consensus pattern (23 bp):
TCTTTATTTCATTTCATTTCTTA
Found at i:2328487 original size:26 final size:26
Alignment explanation
Indices: 2328454--2328528 Score: 86
Period size: 26 Copynumber: 3.0 Consensus size: 26
2328444 TATCCCTTCT
2328454 TTATTTCATTTCATTTCTTATCTTTA
1 TTATTTCATTTCATTTCTTATCTTTA
*
2328480 TTATTTCATTT-A-TTCTT-CCTTTA
1 TTATTTCATTTCATTTCTTATCTTTA
*
2328503 TTA-ATCATCTTCATTTTCTTATCTTT
1 TTATTTCAT-TTCA-TTTCTTATCTTT
2328529 GTTGCAGCCA
Statistics
Matches: 41, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
22 4 0.10
23 10 0.24
24 6 0.15
25 1 0.02
26 16 0.39
27 4 0.10
ACGTcount: A:0.19, C:0.17, G:0.00, T:0.64
Consensus pattern (26 bp):
TTATTTCATTTCATTTCTTATCTTTA
Found at i:2330245 original size:24 final size:23
Alignment explanation
Indices: 2330216--2330271 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 23
2330206 CTCGCTTTCC
2330216 CTTTTTGAACTTCTTT-TTCTTTCTT
1 CTTTTTGAA-TT-TTTCTTC-TTCTT
2330241 CTTTTCTGAATTTTTCTTCTTCTT
1 CTTTT-TGAATTTTTCTTCTTCTT
2330265 CTTTTTG
1 CTTTTTG
2330272 TCTTTTCTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
23 2 0.07
24 13 0.45
25 10 0.34
26 4 0.14
ACGTcount: A:0.07, C:0.20, G:0.05, T:0.68
Consensus pattern (23 bp):
CTTTTTGAATTTTTCTTCTTCTT
Found at i:2330284 original size:21 final size:22
Alignment explanation
Indices: 2330229--2330285 Score: 66
Period size: 22 Copynumber: 2.6 Consensus size: 22
2330219 TTTGAACTTC
2330229 TTTTTC-TTTCTTCTTTTCTGAA
1 TTTTTCTTTTCTTCTTTTCTG-A
2330251 TTTTTCTTCTTCTTCTTTT-TG-
1 TTTTTCTT-TTCTTCTTTTCTGA
2330272 TCTTTTCTTTTCTT
1 T-TTTTCTTTTCTT
2330286 TTACTTTGTA
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
21 6 0.19
22 13 0.41
23 3 0.09
24 10 0.31
ACGTcount: A:0.04, C:0.19, G:0.04, T:0.74
Consensus pattern (22 bp):
TTTTTCTTTTCTTCTTTTCTGA
Found at i:2330285 original size:24 final size:24
Alignment explanation
Indices: 2330216--2330269 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 24
2330206 CTCGCTTTCC
*
2330216 CTTTT-TGAACTTCTTTTTCTTTCTT
1 CTTTTCTGAA-TTTTTTTTC-TTCTT
*
2330241 CTTTTCTGAATTTTTCTTCTTCTT
1 CTTTTCTGAATTTTTTTTCTTCTT
2330265 CTTTT
1 CTTTT
2330270 TGTCTTTTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
24 10 0.38
25 12 0.46
26 4 0.15
ACGTcount: A:0.07, C:0.20, G:0.04, T:0.69
Consensus pattern (24 bp):
CTTTTCTGAATTTTTTTTCTTCTT
Found at i:2330536 original size:19 final size:20
Alignment explanation
Indices: 2330508--2330547 Score: 73
Period size: 19 Copynumber: 2.0 Consensus size: 20
2330498 GAATAATAAT
2330508 ATAAGTAATGAAATGAAATA
1 ATAAGTAATGAAATGAAATA
2330528 ATAAG-AATGAAATGAAATA
1 ATAAGTAATGAAATGAAATA
2330547 A
1 A
2330548 AGAAAGGATA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.62, C:0.00, G:0.15, T:0.23
Consensus pattern (20 bp):
ATAAGTAATGAAATGAAATA
Found at i:2333579 original size:26 final size:27
Alignment explanation
Indices: 2333533--2333583 Score: 70
Period size: 26 Copynumber: 1.9 Consensus size: 27
2333523 AAAGAAATTG
*
2333533 AAGCACTCCAAAAGAATAAGAAAAGTC
1 AAGCACTCCAAAAGAAGAAGAAAAGTC
2333560 AAGCACT-CAGAAA-AAGAAGAAAAG
1 AAGCACTCCA-AAAGAAGAAGAAAAG
2333584 AAAAGTAAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 12 0.55
27 10 0.45
ACGTcount: A:0.59, C:0.16, G:0.18, T:0.08
Consensus pattern (27 bp):
AAGCACTCCAAAAGAAGAAGAAAAGTC
Found at i:2333596 original size:13 final size:14
Alignment explanation
Indices: 2333571--2333602 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
2333561 AGCACTCAGA
2333571 AAAAG-AAGAAAAG
1 AAAAGTAAGAAAAG
2333584 AAAAGTAAG-AAAG
1 AAAAGTAAGAAAAG
2333597 AAAAGT
1 AAAAGT
2333603 TAAAAGCACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 15 0.83
14 3 0.17
ACGTcount: A:0.72, C:0.00, G:0.22, T:0.06
Consensus pattern (14 bp):
AAAAGTAAGAAAAG
Found at i:2337783 original size:26 final size:27
Alignment explanation
Indices: 2337737--2337787 Score: 70
Period size: 26 Copynumber: 1.9 Consensus size: 27
2337727 AAAGAAATTG
*
2337737 AAGCACTCCAAAAGAATAAGAAAAGTC
1 AAGCACTCCAAAAGAAGAAGAAAAGTC
2337764 AAGCACT-CAGAAA-AAGAAGAAAAG
1 AAGCACTCCA-AAAGAAGAAGAAAAG
2337788 AAAAGTAAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 12 0.55
27 10 0.45
ACGTcount: A:0.59, C:0.16, G:0.18, T:0.08
Consensus pattern (27 bp):
AAGCACTCCAAAAGAAGAAGAAAAGTC
Found at i:2337800 original size:13 final size:14
Alignment explanation
Indices: 2337775--2337806 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
2337765 AGCACTCAGA
2337775 AAAAG-AAGAAAAG
1 AAAAGTAAGAAAAG
2337788 AAAAGTAAG-AAAG
1 AAAAGTAAGAAAAG
2337801 AAAAGT
1 AAAAGT
2337807 TAAAAGCACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 15 0.83
14 3 0.17
ACGTcount: A:0.72, C:0.00, G:0.22, T:0.06
Consensus pattern (14 bp):
AAAAGTAAGAAAAG
Found at i:2341934 original size:26 final size:27
Alignment explanation
Indices: 2341888--2341938 Score: 70
Period size: 26 Copynumber: 1.9 Consensus size: 27
2341878 AAAGAAATTG
*
2341888 AAGCACTCCAAAAGAATAAGAAAAGTC
1 AAGCACTCCAAAAGAAGAAGAAAAGTC
2341915 AAGCACT-CAGAAA-AAGAAGAAAAG
1 AAGCACTCCA-AAAGAAGAAGAAAAG
2341939 AAAAGTAAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 12 0.55
27 10 0.45
ACGTcount: A:0.59, C:0.16, G:0.18, T:0.08
Consensus pattern (27 bp):
AAGCACTCCAAAAGAAGAAGAAAAGTC
Found at i:2341951 original size:13 final size:14
Alignment explanation
Indices: 2341926--2341957 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
2341916 AGCACTCAGA
2341926 AAAAG-AAGAAAAG
1 AAAAGTAAGAAAAG
2341939 AAAAGTAAG-AAAG
1 AAAAGTAAGAAAAG
2341952 AAAAGT
1 AAAAGT
2341958 TAAAAGCACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 15 0.83
14 3 0.17
ACGTcount: A:0.72, C:0.00, G:0.22, T:0.06
Consensus pattern (14 bp):
AAAAGTAAGAAAAG
Found at i:2347730 original size:15 final size:15
Alignment explanation
Indices: 2347710--2347745 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
2347700 ATTATTAGCT
*
2347710 TTATAATATATGTTA
1 TTATAATATATATTA
2347725 TTATAATATATATTA
1 TTATAATATATATTA
*
2347740 TGATAA
1 TTATAA
2347746 GAATATTAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (15 bp):
TTATAATATATATTA
Found at i:2351988 original size:15 final size:15
Alignment explanation
Indices: 2351968--2352003 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
2351958 ATTATTAGCT
*
2351968 TTATAATATATGTTA
1 TTATAATATATATTA
2351983 TTATAATATATATTA
1 TTATAATATATATTA
*
2351998 TGATAA
1 TTATAA
2352004 GAATATTAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (15 bp):
TTATAATATATATTA
Found at i:2355952 original size:26 final size:27
Alignment explanation
Indices: 2355906--2355956 Score: 70
Period size: 26 Copynumber: 1.9 Consensus size: 27
2355896 AAAGAAATTG
*
2355906 AAGCACTCCAAAAGAATAAGAAAAGTC
1 AAGCACTCCAAAAGAAGAAGAAAAGTC
2355933 AAGCACT-CAGAAA-AAGAAGAAAAG
1 AAGCACTCCA-AAAGAAGAAGAAAAG
2355957 AAAAGTAAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 12 0.55
27 10 0.45
ACGTcount: A:0.59, C:0.16, G:0.18, T:0.08
Consensus pattern (27 bp):
AAGCACTCCAAAAGAAGAAGAAAAGTC
Found at i:2355969 original size:13 final size:14
Alignment explanation
Indices: 2355944--2355975 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
2355934 AGCACTCAGA
2355944 AAAAG-AAGAAAAG
1 AAAAGTAAGAAAAG
2355957 AAAAGTAAG-AAAG
1 AAAAGTAAGAAAAG
2355970 AAAAGT
1 AAAAGT
2355976 TAAAAGCACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 15 0.83
14 3 0.17
ACGTcount: A:0.72, C:0.00, G:0.22, T:0.06
Consensus pattern (14 bp):
AAAAGTAAGAAAAG
Found at i:2360102 original size:26 final size:27
Alignment explanation
Indices: 2360056--2360106 Score: 70
Period size: 26 Copynumber: 1.9 Consensus size: 27
2360046 AAAGAAATTG
*
2360056 AAGCACTCCAAAAGAATAAGAAAAGTC
1 AAGCACTCCAAAAGAAGAAGAAAAGTC
2360083 AAGCACT-CAGAAA-AAGAAGAAAAG
1 AAGCACTCCA-AAAGAAGAAGAAAAG
2360107 AAAAGTAAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 12 0.55
27 10 0.45
ACGTcount: A:0.59, C:0.16, G:0.18, T:0.08
Consensus pattern (27 bp):
AAGCACTCCAAAAGAAGAAGAAAAGTC
Found at i:2360119 original size:13 final size:14
Alignment explanation
Indices: 2360094--2360125 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
2360084 AGCACTCAGA
2360094 AAAAG-AAGAAAAG
1 AAAAGTAAGAAAAG
2360107 AAAAGTAAG-AAAG
1 AAAAGTAAGAAAAG
2360120 AAAAGT
1 AAAAGT
2360126 TAAAATCACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 15 0.83
14 3 0.17
ACGTcount: A:0.72, C:0.00, G:0.22, T:0.06
Consensus pattern (14 bp):
AAAAGTAAGAAAAG
Found at i:2369847 original size:54 final size:54
Alignment explanation
Indices: 2369759--2369907 Score: 190
Period size: 54 Copynumber: 2.8 Consensus size: 54
2369749 CTATGTGTAC
* *
2369759 TATCGGCACTAAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAAAGACCG
1 TATCGGCACTAAGTGTGCAACCCACAAAATTCATAATAAGTTTATGAAAGACCA
** * ** *
2369813 TATCTTCACTAAGTGTGCAACCCATAAAATTCATAATGTGTTTATGAACGACCA
1 TATCGGCACTAAGTGTGCAACCCACAAAATTCATAATAAGTTTATGAAAGACCA
* ** *
2369867 TATCGGCACTAAGTGTGCAACCTACGGAATTTATAATAAGT
1 TATCGGCACTAAGTGTGCAACCCACAAAATTCATAATAAGT
2369908 GATACAAGCA
Statistics
Matches: 78, Mismatches: 17, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
54 78 1.00
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.28
Consensus pattern (54 bp):
TATCGGCACTAAGTGTGCAACCCACAAAATTCATAATAAGTTTATGAAAGACCA
Found at i:2371823 original size:15 final size:15
Alignment explanation
Indices: 2371812--2371840 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2371802 ACTCAAAAAG
2371812 AAGAAAAGCAAAGAA
1 AAGAAAAGCAAAGAA
2371827 AAGAAAAG-AAAGAA
1 AAGAAAAGCAAAGAA
2371841 GTTGAAGCAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.76, C:0.03, G:0.21, T:0.00
Consensus pattern (15 bp):
AAGAAAAGCAAAGAA
Found at i:2378914 original size:22 final size:21
Alignment explanation
Indices: 2378888--2378929 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
2378878 TGGCTACAGA
2378888 ATTGATGGTCTTGATGGATGAT
1 ATTGATGGTCTTGAT-GATGAT
*
2378910 ATTGATGGTGTTGATGATGA
1 ATTGATGGTCTTGATGATGA
2378930 AATGGAGATG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.24, C:0.02, G:0.33, T:0.40
Consensus pattern (21 bp):
ATTGATGGTCTTGATGATGAT
Found at i:2389048 original size:16 final size:16
Alignment explanation
Indices: 2389029--2389094 Score: 64
Period size: 16 Copynumber: 4.0 Consensus size: 16
2389019 TTCTTTTTGA
2389029 CTTTTTGACTTTTCTT
1 CTTTTTGACTTTTCTT
2389045 CTTTTT--CTTTTCTTT
1 CTTTTTGACTTTTC-TT
*
2389060 CTTTTTGAATTTGTTTCTT
1 CTTTTTG-A-CT-TTTCTT
*
2389079 CTTTTTGTCTTTTCTT
1 CTTTTTGACTTTTCTT
2389095 TTCTTTTTAT
Statistics
Matches: 41, Mismatches: 3, Indels: 12
0.73 0.05 0.21
Matches are distributed among these distances:
14 6 0.15
15 8 0.20
16 12 0.29
17 1 0.02
19 10 0.24
20 4 0.10
ACGTcount: A:0.05, C:0.17, G:0.06, T:0.73
Consensus pattern (16 bp):
CTTTTTGACTTTTCTT
Found at i:2389056 original size:14 final size:15
Alignment explanation
Indices: 2389037--2389065 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2389027 GACTTTTTGA
2389037 CTTTTC-TTCTTTTT
1 CTTTTCTTTCTTTTT
2389051 CTTTTCTTTCTTTTT
1 CTTTTCTTTCTTTTT
2389066 GAATTTGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (15 bp):
CTTTTCTTTCTTTTT
Found at i:2392064 original size:19 final size:18
Alignment explanation
Indices: 2392024--2392070 Score: 58
Period size: 20 Copynumber: 2.5 Consensus size: 18
2392014 ATTGGAGTGC
*
2392024 AAAAAGAAAGAAAAAGAC
1 AAAAAGAAAGAAAAAGAA
*
2392042 AAAAAGAATAGAAAAATAAA
1 AAAAAGAA-AGAAAAA-GAA
2392062 AAAAAGAAA
1 AAAAAGAAA
2392071 AAGAATTCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 8 0.32
19 8 0.32
20 9 0.36
ACGTcount: A:0.81, C:0.02, G:0.13, T:0.04
Consensus pattern (18 bp):
AAAAAGAAAGAAAAAGAA
Found at i:2392064 original size:26 final size:26
Alignment explanation
Indices: 2392023--2392092 Score: 77
Period size: 26 Copynumber: 2.6 Consensus size: 26
2392013 AATTGGAGTG
2392023 CAAAAAGAAAGAAAAAGACAAAAAGAATA
1 CAAAAA-AAA-AAAAA-ACAAAAAGAATA
* * * *
2392052 GAAAAATAAAAAAAAGAAAAAGAATT
1 CAAAAAAAAAAAAAACAAAAAGAATA
2392078 CAAAAAAAAAAAAAA
1 CAAAAAAAAAAAAAA
2392093 ACAAGCCAAG
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
26 23 0.66
27 5 0.14
28 2 0.06
29 5 0.14
ACGTcount: A:0.80, C:0.04, G:0.10, T:0.06
Consensus pattern (26 bp):
CAAAAAAAAAAAAAACAAAAAGAATA
Found at i:2397862 original size:23 final size:23
Alignment explanation
Indices: 2397806--2397876 Score: 66
Period size: 24 Copynumber: 3.3 Consensus size: 23
2397796 AGTTATTATC
2397806 ATAATAACTATA-TATATA-AT-
1 ATAATAACTATAGTATATATATG
2397826 AT-AT-A-TATATGTATATATATG
1 ATAATAACTATA-GTATATATATG
*
2397847 ATAATAACTATAGTATAACATATG
1 ATAATAACTATAGTAT-ATATATG
2397871 A-AATAA
1 ATAATAA
2397877 GAAAAATTAG
Statistics
Matches: 42, Mismatches: 1, Indels: 13
0.75 0.02 0.23
Matches are distributed among these distances:
17 4 0.10
18 1 0.02
19 8 0.19
20 4 0.10
21 2 0.05
22 2 0.05
23 10 0.24
24 11 0.26
ACGTcount: A:0.52, C:0.04, G:0.06, T:0.38
Consensus pattern (23 bp):
ATAATAACTATAGTATATATATG
Found at i:2403894 original size:32 final size:33
Alignment explanation
Indices: 2403833--2403899 Score: 77
Period size: 32 Copynumber: 2.1 Consensus size: 33
2403823 ACAAAATTAA
* *
2403833 AAGAAAGAAATGATTAAAATGGAATATGGA-AG
1 AAGAAAGAAATGATTAAAATAGAAAATGGATAG
2403865 AAGAAAGGAAATGA-TAAGAA-AGAAAATGGATAG
1 AAGAAA-GAAATGATTAA-AATAGAAAATGGATAG
2403898 AA
1 AA
2403900 ATGTTATTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
32 17 0.57
33 13 0.43
ACGTcount: A:0.60, C:0.00, G:0.25, T:0.15
Consensus pattern (33 bp):
AAGAAAGAAATGATTAAAATAGAAAATGGATAG
Found at i:2414195 original size:16 final size:16
Alignment explanation
Indices: 2414165--2414213 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
2414155 AAGTAATGAA
2414165 AATAAGAAAAGATGAAAG
1 AATAAG-AAA-ATGAAAG
*
2414183 AATAAGAAAATGAAAT
1 AATAAGAAAATGAAAG
*
2414199 AGTAAGACAAATGAA
1 AATAAGA-AAATGAA
2414214 GATAACTTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 12 0.43
17 10 0.36
18 6 0.21
ACGTcount: A:0.65, C:0.02, G:0.18, T:0.14
Consensus pattern (16 bp):
AATAAGAAAATGAAAG
Found at i:2414426 original size:6 final size:6
Alignment explanation
Indices: 2414415--2414458 Score: 54
Period size: 6 Copynumber: 7.2 Consensus size: 6
2414405 GATGTAGGAG
*
2414415 TCTTTT TC-TTT TCTTTT TGTTTT TCTTCTT TCTTTT TCTCTTT T
1 TCTTTT TCTTTT TCTTTT TCTTTT TCTT-TT TCTTTT TCT-TTT T
2414459 TTTGTTGCTT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
5 5 0.15
6 18 0.55
7 10 0.30
ACGTcount: A:0.00, C:0.18, G:0.02, T:0.80
Consensus pattern (6 bp):
TCTTTT
Found at i:2414438 original size:12 final size:12
Alignment explanation
Indices: 2414415--2414458 Score: 54
Period size: 13 Copynumber: 3.6 Consensus size: 12
2414405 GATGTAGGAG
2414415 TCTTTTTC-TTT
1 TCTTTTTCTTTT
*
2414426 TCTTTTTGTTTT
1 TCTTTTTCTTTT
2414438 TCTTCTTTCTTTT
1 TCTT-TTTCTTTT
2414451 TCTCTTTT
1 TCT-TTTT
2414459 TTTGTTGCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 7 0.25
12 7 0.25
13 13 0.46
14 1 0.04
ACGTcount: A:0.00, C:0.18, G:0.02, T:0.80
Consensus pattern (12 bp):
TCTTTTTCTTTT
Found at i:2414445 original size:15 final size:15
Alignment explanation
Indices: 2414419--2414464 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
2414409 TAGGAGTCTT
*
2414419 TTTCTTTTCTTTTTG
1 TTTCTCTTCTTTTTG
*
2414434 TTTTTCTTCTTTCTT-
1 TTTCTCTTCTTT-TTG
2414449 TTTCTCTT-TTTTTG
1 TTTCTCTTCTTTTTG
2414463 TT
1 TT
2414465 GCTTTTGTTG
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
13 2 0.08
14 5 0.19
15 17 0.65
16 2 0.08
ACGTcount: A:0.00, C:0.15, G:0.04, T:0.80
Consensus pattern (15 bp):
TTTCTCTTCTTTTTG
Found at i:2414871 original size:33 final size:34
Alignment explanation
Indices: 2414834--2414900 Score: 82
Period size: 35 Copynumber: 2.0 Consensus size: 34
2414824 ATAAATGGTA
* *
2414834 ATGGAAG-GATGATGTTATTGGCGTGATATGGAG
1 ATGGAAGAGATGATGATATAGGCGTGATATGGAG
* *
2414867 ATGGAAGATGGTGATGATATAGGTGTGATATGGA
1 ATGGAAGA-GATGATGATATAGGCGTGATATGGA
2414901 AGATAGTGAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
33 7 0.25
35 21 0.75
ACGTcount: A:0.30, C:0.01, G:0.39, T:0.30
Consensus pattern (34 bp):
ATGGAAGAGATGATGATATAGGCGTGATATGGAG
Found at i:2422305 original size:957 final size:956
Alignment explanation
Indices: 2420426--2422344 Score: 3250
Period size: 957 Copynumber: 2.0 Consensus size: 956
2420416 GGGAGGAAAG
** *
2420426 CCAAGGAAGACTTAGTCCGTCTTTCCCGCCTATCCCTCCCGCAAGAGAGGACTCGTTCTGGCTTT
1 CCAAGGAAGACTTAGTCCACCTTTCCCGCCTATCCCTCCCGCAACAGAGGACTCGTTCTGGCTTT
2420491 AAAGAGCCTCTTTTTTAGCAGTCTCATCCATAAGAGAAGATTGACCATCTCTTCTTCCAAGCTTC
66 AAAGAGCCTCTTTTTTAGCAGTCTCATCCATAAGAGAAGATTGACCATCTCTTCTTCCAAGCTTC
*
2420556 TTTCTTCTCGGCGTAACGAAAGAACTAGATGAGGAGAGGCCTCAGGTTTCAAATCCCTACCCTAC
131 TTTCTTCTCGGCATAACGAAAGAACTAGATGAGGAGAGGCCTCAGGTTTCAAATCCCTACCCTAC
*
2420621 ACCTTACGAGGGCGCCCTAGCCAAATTCAATCCCAAGGGGCCTTTTCAACTAGAAAAAAAGTCGT
196 ACCTTACGAGGGCGCCCTAGCCAAATTCAATCCCAAGGGGCCTTTTCAACTAGAAAAAAAGTCGC
* *
2420686 CATAGTCTTCGTTCCTGCTTTCAACGAGATTCTTAGCTGCATCAGCTTGTAAAACTTTCTCTCCT
261 CACAGTCTTCGTTCCTGCTTTCAACGAGATTCTTAGATGCATCAGCTTGTAAAACTTTCTCTCCT
2420751 TCACCAGGAAAGGGAGAGCGCGGACAAAGTACCAGACGATTTAGGAATAATTTTGGGTAAGAAGA
326 TCACCAGGAAAGGGAGAGCGCGGACAAAGTACCAGACGATTTAGGAATAATTTTGGGTAAGAAGA
** ** *
2420816 GCGTACGAGAAGAGTAAGCAGACGATGTCGATAGAAGACGATTATTGGGATCTTCTCAAAGTCAA
391 GCGTACGAGAAGAGTAAGCAGACGATGTCGATAGAAGACGATTAGCGAAACCTTCTCAAAGTCAA
* *
2420881 AGAAAGAGAGGAATGAGCTAAAGAATGGGTATGCCCAGCCCATGGAATTAGATGTCGAATGAGTA
456 AGAAAGAGAAGAATGAGCTAAACAATGGGTATGCCCAGCCCATGGAATTAGATGTCGAATGAGTA
* * * *
2420946 CGATTTTGAGCAAAAAGAGAGAAGAGAAAGAAAGGATGGACATCTATCGCTACCGTGATGACGCA
521 CGATTTCGAGCAAAAAGAGAGAAAAGAAAGAAAGGATAGACATCTATCGCTACCGTGATAACGCA
* *
2421011 GTTGAGTATTCATTCGATCCACCACCTGAGGCCAGGTCGATCAAACCTATTCATTTTGGGGTTCG
586 GTTGAGTATTCATTCGATCCACCACCTGAGGCCAGGCCGATCAAACCTAATCATTTTGGGGTTCG
*
2421076 ATCCAGCAAGTGATCCATAAGCACCAGTAGAAGCAAAAGCATATCCAGAAGCCGATACCAACAGT
651 ATCCAGCAAGTGATCCATAAGCACCAGTAGAAGCAAAAGCATATCCAGAAGCCGATACCAACAGC
*
2421141 AGTAAAAAAGACCCCCGCTAATAGAAAAAGAGGCATATATGCCGATGATAACGAGAGTAGTACCA
716 AGTAAAAAAGACCCCCGCTAATAGAAAAAGAGGCATATATGCCGATGATAACGAGAGCAGTACCA
* *
2421206 ATAACACCAATAGCATCCCTTCCAGTTCCCTTTACTAGGTTGGGGAGCCATCACCAGGGTCGATG
781 ATAACACCAATAGCATCCCTTCCAGTTCCCTTTACTAGGTTAGGGAGCCATCACCAGGGCCGATG
*
2421271 ATCCAACCCCATACCAAGATGCCCTTATGAAGGTGCGAGATTAGCGTAGGCTATCTCCCTCATGA
846 ATCCAACCCCATACCAAGATACCCTTATGAAGGTGCGAGATTAGCGTAGGCTATCTCCCTCATGA
2421336 GTGTTGAGCGACTACTTTTACTTTCCCATCCTCCTGGAGAAGTCAC
911 GTGTTGAGCGACTACTTTTACTTTCCCATCCTCCTGGAGAAGTCAC
* * *
2421382 CCAAGGAAGACTTAGTCCACCTTTCTC-CCTATCCCTCTCGCAACAGATGACTCGTTCTGGCTTT
1 CCAAGGAAGACTTAGTCCACCTTTCCCGCCTATCCCTCCCGCAACAGAGGACTCGTTCTGGCTTT
2421446 AAAGAGCCTCTTTTTTAGCAGTCTCATCCATAAGAGAAGATTGACCATCTCTTCTTCCAAGCTTC
66 AAAGAGCCTCTTTTTTAGCAGTCTCATCCATAAGAGAAGATTGACCATCTCTTCTTCCAAGCTTC
2421511 TTTCTTCTCGGCATAACGAAAGAACTAGATGAGGAGAGGCCTCAGGTTTCAAATCCCTACCCTAC
131 TTTCTTCTCGGCATAACGAAAGAACTAGATGAGGAGAGGCCTCAGGTTTCAAATCCCTACCCTAC
* *
2421576 GCCTTACGAGGGCGCCCTAGCCAAATTCAATTCCAAGGGGCCTTTTCAACTAGAAAAAAAAAGTC
196 ACCTTACGAGGGCGCCCTAGCCAAATTCAATCCCAAGGGGCCTTTTCAACTAG--AAAAAAAGTC
* *
2421641 GCCACAGTCTTCGTTTCTGCTTTCAATGAGATTCTTAGATGCATCAGCTTGTAAAACTTTCTCAT
259 GCCACAGTCTTCGTTCCTGCTTTCAACGAGATTCTTAGATGCATCAGCTTGTAAAACTTTCTC-T
* * * * **
2421706 -CTTCACCAGGAAAGGGAGAGCGTGGACAAGGTACCAGATGATTTGGGAATGCTTTTGGGTAAGA
323 CCTTCACCAGGAAAGGGAGAGCGCGGACAAAGTACCAGACGATTTAGGAATAATTTTGGGTAAGA
2421770 AGAGCGTACGAGAAGAGTAAGCAGACGATGTCGATAGAAGACGATTAGCGAAACCTTCTCAAAGT
388 AGAGCGTACGAGAAGAGTAAGCAGACGATGTCGATAGAAGACGATTAGCGAAACCTTCTCAAAGT
* *
2421835 CAACGAAAGAGAAGAATGAGCTAAACAATGGGTATGCCCAGCGCATGGAATTAGATGTCGAATGA
453 CAAAGAAAGAGAAGAATGAGCTAAACAATGGGTATGCCCAGCCCATGGAATTAGATGTCGAATGA
* * * *
2421900 GTACGATTTCGAGTATAAAGAGAGAAAAGCAAGAAAGGTTAGACATCTATCGCTACCGTGATAAC
518 GTACGATTTCGAGCAAAAAGAGAGAAAAGAAAGAAAGGATAGACATCTATCGCTACCGTGATAAC
*
2421965 GCAGTTGAGTATTCATTCGATCCACCACCTGAGGCCAGGCCGATCAAACCTAATCGTTTTGGGGT
583 GCAGTTGAGTATTCATTCGATCCACCACCTGAGGCCAGGCCGATCAAACCTAATCATTTTGGGGT
* * ** *
2422030 TTGATCTAGCAAGTGATCCATAAGCACCAGTAGAAGCAAAAGCATATCCAGAAGTTGATACCAAT
648 TCGATCCAGCAAGTGATCCATAAGCACCAGTAGAAGCAAAAGCATATCCAGAAGCCGATACCAAC
** *
2422095 AGCAGTAGGGAAAGA-CCCTGCTAATAGAAAAAGAGGCATATATGCCGATGATAACGAGAGCAGT
713 AGCAGTA-AAAAAGACCCCCGCTAATAGAAAAAGAGGCATATATGCCGATGATAACGAGAGCAGT
* *
2422159 ACCGATAGCACCAATAGCATCCCTTCCAGTTCCCTTTACTAGGTTAGGGAGCCATCACCAGGGCC
777 ACCAATAACACCAATAGCATCCCTTCCAGTTCCCTTTACTAGGTTAGGGAGCCATCACCAGGGCC
* *
2422224 GATGATCCAACCCCATACCAAGATACCCTTATGGAGGTGCGTGATTAGCGTAGGCTATCTCCCTC
842 GATGATCCAACCCCATACCAAGATACCCTTATGAAGGTGCGAGATTAGCGTAGGCTATCTCCCTC
* *
2422289 GTGAGTGTTGAGCGACTACTTTTACTTTCCCATCCTCCTGGATAAGTCAC
907 ATGAGTGTTGAGCGACTACTTTTACTTTCCCATCCTCCTGGAGAAGTCAC
2422339 CCAAGG
1 CCAAGG
2422345 CGAAGACCAT
Statistics
Matches: 900, Mismatches: 59, Indels: 7
0.93 0.06 0.01
Matches are distributed among these distances:
955 214 0.24
956 24 0.03
957 656 0.73
958 6 0.01
ACGTcount: A:0.31, C:0.23, G:0.22, T:0.24
Consensus pattern (956 bp):
CCAAGGAAGACTTAGTCCACCTTTCCCGCCTATCCCTCCCGCAACAGAGGACTCGTTCTGGCTTT
AAAGAGCCTCTTTTTTAGCAGTCTCATCCATAAGAGAAGATTGACCATCTCTTCTTCCAAGCTTC
TTTCTTCTCGGCATAACGAAAGAACTAGATGAGGAGAGGCCTCAGGTTTCAAATCCCTACCCTAC
ACCTTACGAGGGCGCCCTAGCCAAATTCAATCCCAAGGGGCCTTTTCAACTAGAAAAAAAGTCGC
CACAGTCTTCGTTCCTGCTTTCAACGAGATTCTTAGATGCATCAGCTTGTAAAACTTTCTCTCCT
TCACCAGGAAAGGGAGAGCGCGGACAAAGTACCAGACGATTTAGGAATAATTTTGGGTAAGAAGA
GCGTACGAGAAGAGTAAGCAGACGATGTCGATAGAAGACGATTAGCGAAACCTTCTCAAAGTCAA
AGAAAGAGAAGAATGAGCTAAACAATGGGTATGCCCAGCCCATGGAATTAGATGTCGAATGAGTA
CGATTTCGAGCAAAAAGAGAGAAAAGAAAGAAAGGATAGACATCTATCGCTACCGTGATAACGCA
GTTGAGTATTCATTCGATCCACCACCTGAGGCCAGGCCGATCAAACCTAATCATTTTGGGGTTCG
ATCCAGCAAGTGATCCATAAGCACCAGTAGAAGCAAAAGCATATCCAGAAGCCGATACCAACAGC
AGTAAAAAAGACCCCCGCTAATAGAAAAAGAGGCATATATGCCGATGATAACGAGAGCAGTACCA
ATAACACCAATAGCATCCCTTCCAGTTCCCTTTACTAGGTTAGGGAGCCATCACCAGGGCCGATG
ATCCAACCCCATACCAAGATACCCTTATGAAGGTGCGAGATTAGCGTAGGCTATCTCCCTCATGA
GTGTTGAGCGACTACTTTTACTTTCCCATCCTCCTGGAGAAGTCAC
Found at i:2427099 original size:21 final size:21
Alignment explanation
Indices: 2427058--2427099 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
2427048 TGAGCTATGG
* *
2427058 CTTTGAAGTAAGGTGCCTTGA
1 CTTTGAAGTAAGCTGCATTGA
2427079 CTTTGAAGTAAAGCT-CATTGA
1 CTTTGAAGT-AAGCTGCATTGA
2427100 TTCTTAATTG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.29, C:0.14, G:0.24, T:0.33
Consensus pattern (21 bp):
CTTTGAAGTAAGCTGCATTGA
Found at i:2430511 original size:47 final size:45
Alignment explanation
Indices: 2430444--2430569 Score: 173
Period size: 47 Copynumber: 2.8 Consensus size: 45
2430434 TATAAAATCT
2430444 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* * *
2430489 CTTACCATTTAAATTCCATAAGCTCGAAAGCTTATTTTACCCATATA
1 CTTACCATTT--ATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* * *
2430536 CTTGCCA-TTATTCTAAAAGCTCGTAAGCTTATTT
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTT
2430570 GTATGCTTAC
Statistics
Matches: 72, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
44 22 0.31
45 10 0.14
46 2 0.03
47 38 0.53
ACGTcount: A:0.32, C:0.22, G:0.08, T:0.38
Consensus pattern (45 bp):
CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
Found at i:2430778 original size:59 final size:59
Alignment explanation
Indices: 2430679--2430805 Score: 182
Period size: 59 Copynumber: 2.2 Consensus size: 59
2430669 GTAGTGCTAT
* * **
2430679 CCGAATATGACACATAAGGTCGTGTCCACCATCTGTACTAGGTATCCTTAAGTACAGTC
1 CCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTAAGTACAGTC
* ** *
2430738 CCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTTAGTGTATTC
1 CCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTAAGTACAGTC
2430797 CCGAATATG
1 CCGAATATG
2430806 CAGCCTACTG
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
59 60 1.00
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.28
Consensus pattern (59 bp):
CCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTAAGTACAGTC
Found at i:2435503 original size:6 final size:6
Alignment explanation
Indices: 2435492--2435516 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
2435482 ACACTTATAT
2435492 CATGAC CATGAC CATGAC CATGAC C
1 CATGAC CATGAC CATGAC CATGAC C
2435517 TATGGTCTCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.36, G:0.16, T:0.16
Consensus pattern (6 bp):
CATGAC
Found at i:2437313 original size:47 final size:45
Alignment explanation
Indices: 2437246--2437370 Score: 173
Period size: 47 Copynumber: 2.8 Consensus size: 45
2437236 TATAAAATCC
2437246 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* * *
2437291 CTTACCATTTAAATTCCATAAGCTCGAAAGCTTATTTTACCCATATA
1 CTTACCATTT--ATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* *
2437338 CTTGCCA-TTATTCCAAAAGCT-GTAAGCTTATTT
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTT
2437371 GTATGCTTAC
Statistics
Matches: 72, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
43 11 0.15
44 11 0.15
45 10 0.14
46 2 0.03
47 38 0.53
ACGTcount: A:0.32, C:0.22, G:0.08, T:0.38
Consensus pattern (45 bp):
CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
Found at i:2437580 original size:59 final size:59
Alignment explanation
Indices: 2437479--2437607 Score: 177
Period size: 59 Copynumber: 2.2 Consensus size: 59
2437469 CGTAGTGCTA
* * * * **
2437479 TCCCGAATATGACACATAAGGTCGTGTCGATCATCTGTACTAGGTATCCTTAAGTATAG
1 TCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTAAGTATAG
* * *
2437538 TCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCTTTTAGTATAT
1 TCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTAAGTATAG
2437597 TCCCGAATATG
1 TCCCGAATATG
2437608 CAGCCTGTTG
Statistics
Matches: 61, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
59 61 1.00
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.30
Consensus pattern (59 bp):
TCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTAAGTATAG
Found at i:2444234 original size:28 final size:26
Alignment explanation
Indices: 2444203--2444265 Score: 67
Period size: 25 Copynumber: 2.4 Consensus size: 26
2444193 AAGAAAAATC
*
2444203 AGAAAAGAAAGTGAAGCACTCAAAAGA
1 AGAAAAGAAA-TCAAGCACTCAAAAGA
*
2444230 A-AGAAA-AAATCCAGCACTCAAAAGA
1 AGA-AAAGAAATCAAGCACTCAAAAGA
2444255 AGAAAAAGAAA
1 AG-AAAAGAAA
2444266 AGAAAAGAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
25 15 0.50
26 7 0.23
27 8 0.27
ACGTcount: A:0.63, C:0.13, G:0.17, T:0.06
Consensus pattern (26 bp):
AGAAAAGAAATCAAGCACTCAAAAGA
Found at i:2455328 original size:54 final size:54
Alignment explanation
Indices: 2455264--2455440 Score: 264
Period size: 54 Copynumber: 3.3 Consensus size: 54
2455254 GCATCAATAA
* *
2455264 GTTTATGAACGACCGTATCGGCACTAAATGTGCAACCCACGGAATTCATAATGT
1 GTTTATGAACGACCGTATCGGCACTAAGTGTGCAACCCACAGAATTCATAATGT
* * *
2455318 GTTTATGAACGACCGTATCGACACTAAGTGTGTAACCCATAGAATTCATAATGT
1 GTTTATGAACGACCGTATCGGCACTAAGTGTGCAACCCACAGAATTCATAATGT
* * **
2455372 GTTTATGAACGACCATATCGGCACTAAGTGTGCAACCCACAGAATTTATAATAA
1 GTTTATGAACGACCGTATCGGCACTAAGTGTGCAACCCACAGAATTCATAATGT
*
2455426 GTTTATAAACGACCG
1 GTTTATGAACGACCG
2455441 ATCAACACAA
Statistics
Matches: 109, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 109 1.00
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.27
Consensus pattern (54 bp):
GTTTATGAACGACCGTATCGGCACTAAGTGTGCAACCCACAGAATTCATAATGT
Found at i:2461664 original size:23 final size:23
Alignment explanation
Indices: 2461638--2461681 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
2461628 GATTCCCCTG
*
2461638 GGGGAATCGGTTCCCCTTCAAAA
1 GGGGAATCAGTTCCCCTTCAAAA
2461661 GGGGAATCAGTTCCCCTTCAA
1 GGGGAATCAGTTCCCCTTCAA
2461682 GGGGGTATCG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.25, C:0.27, G:0.25, T:0.23
Consensus pattern (23 bp):
GGGGAATCAGTTCCCCTTCAAAA
Found at i:2466395 original size:19 final size:21
Alignment explanation
Indices: 2466352--2466403 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 21
2466342 GAAACCCCTT
*
2466352 TGAAAATATATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
2466373 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
2466392 TGAAGATACATG
1 TGAAAATACATG
2466404 CTCTTGGCTG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 13 0.45
20 4 0.14
21 12 0.41
ACGTcount: A:0.46, C:0.04, G:0.13, T:0.37
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:2466767 original size:16 final size:16
Alignment explanation
Indices: 2466746--2466785 Score: 80
Period size: 16 Copynumber: 2.5 Consensus size: 16
2466736 CAACTTGTCA
2466746 TGAAAGGTCACATTTG
1 TGAAAGGTCACATTTG
2466762 TGAAAGGTCACATTTG
1 TGAAAGGTCACATTTG
2466778 TGAAAGGT
1 TGAAAGGT
2466786 AACCTTTCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.33, C:0.10, G:0.28, T:0.30
Consensus pattern (16 bp):
TGAAAGGTCACATTTG
Found at i:2470771 original size:19 final size:18
Alignment explanation
Indices: 2470747--2470797 Score: 59
Period size: 19 Copynumber: 2.8 Consensus size: 18
2470737 TTTGAACTTC
2470747 TTTTTCTTTTCTTTTCTGA
1 TTTTTCTTTTCTTTTCT-A
* * *
2470766 TTTTTCTCTTCTTTTGTC
1 TTTTTCTTTTCTTTTCTA
2470784 TTTTTC-TTTCTTTT
1 TTTTTCTTTTCTTTT
2470798 TGCACTCCAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
17 7 0.25
18 6 0.21
19 15 0.54
ACGTcount: A:0.02, C:0.18, G:0.04, T:0.76
Consensus pattern (18 bp):
TTTTTCTTTTCTTTTCTA
Found at i:2471092 original size:19 final size:20
Alignment explanation
Indices: 2471046--2471094 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
2471036 TAATAAAGGT
2471046 AATAATAAT-ATAAGTAATGA
1 AATAA-AATAATAAGTAATGA
2471066 AA-ATAAATAATAAG-AATGA
1 AATA-AAATAATAAGTAATGA
2471085 AATAAAATAA
1 AATAAAATAA
2471095 AGAAAGGATA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
19 17 0.65
20 9 0.35
ACGTcount: A:0.67, C:0.00, G:0.08, T:0.24
Consensus pattern (20 bp):
AATAAAATAATAAGTAATGA
Found at i:2471548 original size:19 final size:20
Alignment explanation
Indices: 2471507--2471557 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
2471497 GAAACCCCTT
*
2471507 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
*
2471527 TGAAAATACATTA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
2471546 TGAAGATACATG
1 TGAAAATACATG
2471558 CTCTTGGCCG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
19 15 0.56
20 12 0.44
ACGTcount: A:0.43, C:0.06, G:0.14, T:0.37
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:2472493 original size:30 final size:31
Alignment explanation
Indices: 2472454--2472513 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
2472444 ACATGTTGTC
**
2472454 ATGATATCTAAATGATATGCAAACATAATAA
1 ATGATATCTAAAACATATGCAAACATAATAA
* *
2472485 ATGA-ATCTAAAACTTATGTAAACATAATA
1 ATGATATCTAAAACATATGCAAACATAATA
2472514 TAAAGCTAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.52, C:0.10, G:0.08, T:0.30
Consensus pattern (31 bp):
ATGATATCTAAAACATATGCAAACATAATAA
Found at i:2474651 original size:2 final size:2
Alignment explanation
Indices: 2474644--2474677 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2474634 TAACTATGAA
2474644 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2474678 GTGTGTGTAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2477453 original size:24 final size:24
Alignment explanation
Indices: 2477421--2477477 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
2477411 CTTGGCTTGC
2477421 TTTA-TCTTTTA-AATTTCTTTTCT
1 TTTATTCTTTTATAATTT-TTTTCT
*
2477444 TTTATTCTTTTATGATTTTTTTCT
1 TTTATTCTTTTATAATTTTTTTCT
2477468 TTT-TTCTTTT
1 TTTATTCTTTT
2477478 TGCACTCCAA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
23 11 0.35
24 16 0.52
25 4 0.13
ACGTcount: A:0.12, C:0.11, G:0.02, T:0.75
Consensus pattern (24 bp):
TTTATTCTTTTATAATTTTTTTCT
Found at i:2477768 original size:21 final size:21
Alignment explanation
Indices: 2477729--2477768 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2477719 AAGGAAGATT
*
2477729 AATGAAATGATAAAGATAAAG
1 AATGAAATGATAAAAATAAAG
2477750 AATGAAATGA-AATAAATAA
1 AATGAAATGATAA-AAATAA
2477769 TGGATAGAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.65, C:0.00, G:0.15, T:0.20
Consensus pattern (21 bp):
AATGAAATGATAAAAATAAAG
Found at i:2477816 original size:22 final size:21
Alignment explanation
Indices: 2477791--2477831 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
2477781 GCTGCGGAAT
2477791 TGATGGTCTTGATTGATGAAGA
1 TGATGGTCTTGA-TGATGAAGA
*
2477813 TGATGGTGTTGATGATGAA
1 TGATGGTCTTGATGATGAA
2477832 ATGGAGATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.27, C:0.02, G:0.34, T:0.37
Consensus pattern (21 bp):
TGATGGTCTTGATGATGAAGA
Found at i:2493701 original size:17 final size:17
Alignment explanation
Indices: 2493679--2493715 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
2493669 TTCCATTCAA
2493679 TCTATACCATAACCATT
1 TCTATACCATAACCATT
*
2493696 TCTATACCCTAACCATT
1 TCTATACCATAACCATT
2493713 TCT
1 TCT
2493716 TTTAAGCCGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.30, C:0.32, G:0.00, T:0.38
Consensus pattern (17 bp):
TCTATACCATAACCATT
Found at i:2502702 original size:14 final size:13
Alignment explanation
Indices: 2502683--2502723 Score: 55
Period size: 14 Copynumber: 3.1 Consensus size: 13
2502673 AGATACTACA
2502683 TTTCCATCACCAT
1 TTTCCATCACCAT
2502696 CTTTCCATCACCAT
1 -TTTCCATCACCAT
* *
2502710 TCTCTATCACCAT
1 TTTCCATCACCAT
2502723 T
1 T
2502724 CACACCTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 12 0.48
14 13 0.52
ACGTcount: A:0.22, C:0.39, G:0.00, T:0.39
Consensus pattern (13 bp):
TTTCCATCACCAT
Found at i:2502720 original size:13 final size:13
Alignment explanation
Indices: 2502681--2502724 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
2502671 TAAGATACTA
2502681 CATT-TCCATCAC
1 CATTCTCCATCAC
*
2502693 CATCTTTCCATCAC
1 CAT-TCTCCATCAC
*
2502707 CATTCTCTATCAC
1 CATTCTCCATCAC
2502720 CATTC
1 CATTC
2502725 ACACCTATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
12 3 0.11
13 14 0.50
14 11 0.39
ACGTcount: A:0.23, C:0.41, G:0.00, T:0.36
Consensus pattern (13 bp):
CATTCTCCATCAC
Found at i:2503129 original size:16 final size:16
Alignment explanation
Indices: 2503110--2503153 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
2503100 GTGATCCAAC
* * *
2503110 AAGAAGAAAAAGAAAG
1 AAGAAAAAAAACAAAA
2503126 AAGAAAAAAAACAAAA
1 AAGAAAAAAAACAAAA
2503142 AAGAAAAGAAAA
1 AAGAAAA-AAAA
2503154 GACTCCTACA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
16 20 0.83
17 4 0.17
ACGTcount: A:0.82, C:0.02, G:0.16, T:0.00
Consensus pattern (16 bp):
AAGAAAAAAAACAAAA
Found at i:2506333 original size:21 final size:21
Alignment explanation
Indices: 2506307--2506347 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
2506297 CCATCTCTAT
*
2506307 TTCATCATCAACTCCATCAAC
1 TTCATCATCAACACCATCAAC
2506328 TTCATCATCAACACCATCAA
1 TTCATCATCAACACCATCAA
2506348 TTTCGTAGCC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.37, C:0.37, G:0.00, T:0.27
Consensus pattern (21 bp):
TTCATCATCAACACCATCAAC
Found at i:2528714 original size:27 final size:27
Alignment explanation
Indices: 2528683--2528736 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
2528673 TGATCCAAAT
2528683 GGATTTCTCGGTAATGATCAGAGATCC
1 GGATTTCTCGGTAATGATCAGAGATCC
* *
2528710 GGATTTCTCGGTCATGGTCAGAGATCC
1 GGATTTCTCGGTAATGATCAGAGATCC
2528737 CGTGAAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.30
Consensus pattern (27 bp):
GGATTTCTCGGTAATGATCAGAGATCC
Found at i:2531525 original size:19 final size:19
Alignment explanation
Indices: 2531501--2531543 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
2531491 ATAAAGTTTC
*
2531501 TAGCTGACCCCCGAGCTCA
1 TAGCTGACCCCAGAGCTCA
* *
2531520 TAGCTGACCCTAGAGGTCA
1 TAGCTGACCCCAGAGCTCA
2531539 TAGCT
1 TAGCT
2531544 AACATGAGCT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.23, C:0.33, G:0.23, T:0.21
Consensus pattern (19 bp):
TAGCTGACCCCAGAGCTCA
Found at i:2536575 original size:17 final size:17
Alignment explanation
Indices: 2536553--2536585 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2536543 ATCCTACCCT
2536553 TATACCATAACCATTTC
1 TATACCATAACCATTTC
*
2536570 TATACCCTAACCATTT
1 TATACCATAACCATTT
2536586 GTTTAAAGTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.33, C:0.30, G:0.00, T:0.36
Consensus pattern (17 bp):
TATACCATAACCATTTC
Found at i:2544578 original size:23 final size:24
Alignment explanation
Indices: 2544551--2544595 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
2544541 TTTTATAAGA
2544551 CTACCCTT-TATTTTTTACTCTTT
1 CTACCCTTCTATTTTTTACTCTTT
* *
2544574 CTACCTTTCTATTTTTTCCTCT
1 CTACCCTTCTATTTTTTACTCT
2544596 ACACTAACAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 7 0.37
24 12 0.63
ACGTcount: A:0.11, C:0.29, G:0.00, T:0.60
Consensus pattern (24 bp):
CTACCCTTCTATTTTTTACTCTTT
Found at i:2547960 original size:14 final size:14
Alignment explanation
Indices: 2547941--2547970 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
2547931 TTTGGAGTGC
2547941 AAAAAGAAAAAGAA
1 AAAAAGAAAAAGAA
2547955 AAAAAGAAAAAGAA
1 AAAAAGAAAAAGAA
2547969 AA
1 AA
2547971 GACTCCTACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (14 bp):
AAAAAGAAAAAGAA
Found at i:2550235 original size:19 final size:20
Alignment explanation
Indices: 2550208--2550251 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
2550198 AGCATTTATC
*
2550208 TTCAAT-AAAATTATGTATT
1 TTCAATAAAAATCATGTATT
* *
2550227 TTCATTAAAAATCATGTGTT
1 TTCAATAAAAATCATGTATT
2550247 TTCAA
1 TTCAA
2550252 AAGGGTTTCA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.39, C:0.09, G:0.07, T:0.45
Consensus pattern (20 bp):
TTCAATAAAAATCATGTATT
Found at i:2551061 original size:6 final size:6
Alignment explanation
Indices: 2551050--2551085 Score: 54
Period size: 6 Copynumber: 5.8 Consensus size: 6
2551040 TAAAAGCAAC
*
2551050 AAAAAG AAAAAG AAAGAAG AAAAAA AAAAAG AAAAA
1 AAAAAG AAAAAG AAA-AAG AAAAAG AAAAAG AAAAA
2551086 AAAGACTCCT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
6 21 0.78
7 6 0.22
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:2551074 original size:15 final size:14
Alignment explanation
Indices: 2551050--2551088 Score: 51
Period size: 16 Copynumber: 2.6 Consensus size: 14
2551040 TAAAAGCAAC
2551050 AAAAAGAAAAAGAAAG
1 AAAAA-AAAAA-AAAG
2551066 AAGAAAAAAAAAAAG
1 AA-AAAAAAAAAAAG
2551081 AAAAAAAA
1 AAAAAAAA
2551089 GACTCCTACA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 6 0.27
15 6 0.27
16 7 0.32
17 3 0.14
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAAAAG
Found at i:2551081 original size:12 final size:12
Alignment explanation
Indices: 2551050--2551088 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
2551040 TAAAAGCAAC
2551050 AAAAAGAAAAAGA
1 AAAAAGAAAAA-A
*
2551063 AAGAAGAAAAAA
1 AAAAAGAAAAAA
2551075 AAAAAGAAAAAA
1 AAAAAGAAAAAA
2551087 AA
1 AA
2551089 GACTCCTACA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
12 14 0.58
13 10 0.42
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (12 bp):
AAAAAGAAAAAA
Found at i:2554338 original size:19 final size:20
Alignment explanation
Indices: 2554314--2554356 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
2554304 AGCATTTATC
*
2554314 TTCATT-AAAATTATGTATT
1 TTCATTAAAAATCATGTATT
*
2554333 TTCATTAAAAATCATGTGTT
1 TTCATTAAAAATCATGTATT
2554353 TTCA
1 TTCA
2554357 AAGGGGTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.35, C:0.09, G:0.07, T:0.49
Consensus pattern (20 bp):
TTCATTAAAAATCATGTATT
Found at i:2570844 original size:6 final size:6
Alignment explanation
Indices: 2570833--2570875 Score: 61
Period size: 6 Copynumber: 7.2 Consensus size: 6
2570823 GATGTAGGAG
*
2570833 TCTTTT TC-TTT TCTTTT TATTTT TCTTCTT TCTTTT TCTTTT T
1 TCTTTT TCTTTT TCTTTT TCTTTT TCTT-TT TCTTTT TCTTTT T
2570876 TTGTTGCTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
5 5 0.15
6 22 0.67
7 6 0.18
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.81
Consensus pattern (6 bp):
TCTTTT
Found at i:2583005 original size:24 final size:25
Alignment explanation
Indices: 2582959--2583013 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 25
2582949 ACAGTTATGC
*
2582959 CACTTGAAGTTCAAAAAGATGTG-T
1 CACTTGAAGTGCAAAAAGATGTGAT
* * *
2582983 CACTTGAAGTGCCACAAGTTGTGAT
1 CACTTGAAGTGCAAAAAGATGTGAT
2583008 CA-TTGA
1 CACTTGA
2583014 GGCTCCAAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
24 23 0.88
25 3 0.12
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (25 bp):
CACTTGAAGTGCAAAAAGATGTGAT
Found at i:2585702 original size:23 final size:23
Alignment explanation
Indices: 2585675--2585728 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
2585665 AAAAATCAGA
*
2585675 AAAGAAAGTAAAGCACTCAAAAG
1 AAAGAAAATAAAGCACTCAAAAG
**
2585698 AAAGAAAAATCTAGCACTCAAAAG
1 AAAG-AAAATAAAGCACTCAAAAG
2585722 -AAGAAAA
1 AAAGAAAA
2585729 AACAAAGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 4 0.15
23 7 0.26
24 16 0.59
ACGTcount: A:0.63, C:0.13, G:0.15, T:0.09
Consensus pattern (23 bp):
AAAGAAAATAAAGCACTCAAAAG
Found at i:2590232 original size:22 final size:21
Alignment explanation
Indices: 2590206--2590246 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
2590196 GGCTGGGAAA
2590206 TTGATGGTCTTGATGGATGATG
1 TTGATGGTCTTGAT-GATGATG
*
2590228 TTGATGGTGTTGATGATGA
1 TTGATGGTCTTGATGATGA
2590247 AATGGAGATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.20, C:0.02, G:0.37, T:0.41
Consensus pattern (21 bp):
TTGATGGTCTTGATGATGATG
Found at i:2594601 original size:24 final size:24
Alignment explanation
Indices: 2594569--2594621 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
2594559 AAAATCTGCA
*
2594569 AAGAAAAGTCAAGCACTCCAAAAG
1 AAGAAAAGTCAAGCACTCAAAAAG
2594593 AAGAAAAGTCAAGCACTCAAAAAG
1 AAGAAAAGTCAAGCACTCAAAAAG
2594617 AAGAA
1 AAGAA
2594622 GAAAAAGAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.58, C:0.17, G:0.17, T:0.08
Consensus pattern (24 bp):
AAGAAAAGTCAAGCACTCAAAAAG
Found at i:2595890 original size:24 final size:21
Alignment explanation
Indices: 2595856--2595898 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
2595846 TCCACAAGAC
*
2595856 ATGTCCTTTGACATTTCAAAGG
1 ATGTCCTTTGA-AATTCAAAGG
2595878 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
2595899 AGAATGTGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 10 0.56
24 4 0.22
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.35
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAAGG
Found at i:2600090 original size:24 final size:24
Alignment explanation
Indices: 2600063--2600117 Score: 101
Period size: 24 Copynumber: 2.3 Consensus size: 24
2600053 TAAATCAGCA
*
2600063 AAGAAAAGTCAAGCACTCCAAAAG
1 AAGAAAAGTCAAGCACTCAAAAAG
2600087 AAGAAAAGTCAAGCACTCAAAAAG
1 AAGAAAAGTCAAGCACTCAAAAAG
2600111 AAGAAAA
1 AAGAAAA
2600118 AAGAAAAGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.60, C:0.16, G:0.16, T:0.07
Consensus pattern (24 bp):
AAGAAAAGTCAAGCACTCAAAAAG
Found at i:2602899 original size:30 final size:31
Alignment explanation
Indices: 2602863--2602922 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
2602853 CTTAGCTTTA
**
2602863 TATTATGTTTACATATGTTTTAGAT-TCATT
1 TATTATGTTTACATATCATTTAGATATCATT
*
2602893 TATTATGTTTGCATATCATTTAGATATCAT
1 TATTATGTTTACATATCATTTAGATATCAT
2602923 GGCAGCATGT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.28, C:0.08, G:0.10, T:0.53
Consensus pattern (31 bp):
TATTATGTTTACATATCATTTAGATATCATT
Found at i:2603878 original size:20 final size:19
Alignment explanation
Indices: 2603820--2603889 Score: 95
Period size: 19 Copynumber: 3.6 Consensus size: 19
2603810 CGGCCAAGAG
2603820 CATGTATCTTCATTAAAAT
1 CATGTATCTTCATTAAAAT
*
2603839 CATGTATCTTAATTAAAAT
1 CATGTATCTTCATTAAAAT
* *
2603858 CATGTATTTTCATCAAAAAT
1 CATGTATCTTCAT-TAAAAT
*
2603878 CATGTATTTTCA
1 CATGTATCTTCA
2603890 AAGGGGTTTC
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
19 29 0.63
20 17 0.37
ACGTcount: A:0.37, C:0.14, G:0.06, T:0.43
Consensus pattern (19 bp):
CATGTATCTTCATTAAAAT
Found at i:2605021 original size:24 final size:21
Alignment explanation
Indices: 2604987--2605029 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
2604977 TGCACAAGAT
*
2604987 ATGTCCTTTGACATTTCAAAGG
1 ATGTCCTTTGA-AATTCAAAGG
2605009 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
2605030 AGAATGAGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 10 0.56
24 4 0.22
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.35
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAAGG
Found at i:2615354 original size:18 final size:18
Alignment explanation
Indices: 2615333--2615371 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
2615323 CTTTAACCTT
2615333 ACAACAATTACCACGACA
1 ACAACAATTACCACGACA
* *
2615351 ACAACATTTGCCACGACA
1 ACAACAATTACCACGACA
2615369 ACA
1 ACA
2615372 CCATTCATAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.46, C:0.33, G:0.08, T:0.13
Consensus pattern (18 bp):
ACAACAATTACCACGACA
Found at i:2617002 original size:22 final size:21
Alignment explanation
Indices: 2616976--2617016 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
2616966 GGCTGCGGAA
2616976 TTGATGGTCTTGATGGATGATG
1 TTGATGGTCTTGAT-GATGATG
*
2616998 TTGATGGTGTTGATGATGA
1 TTGATGGTCTTGATGATGA
2617017 AATGGAGATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.20, C:0.02, G:0.37, T:0.41
Consensus pattern (21 bp):
TTGATGGTCTTGATGATGATG
Found at i:2618271 original size:23 final size:23
Alignment explanation
Indices: 2618245--2618289 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
2618235 TAACTATAGA
*
2618245 TATAATAT-ATATATGATAATAAT
1 TATAATATAACATATGA-AATAAT
*
2618268 TATAGTATAACATATGAAATAA
1 TATAATATAACATATGAAATAA
2618290 GCAAAGTTAG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.53, C:0.02, G:0.07, T:0.38
Consensus pattern (23 bp):
TATAATATAACATATGAAATAAT
Found at i:2619920 original size:25 final size:26
Alignment explanation
Indices: 2619892--2619949 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
2619882 TCAACTTTTC
*
2619892 TTTTCTTCTT-TTTCTG-AGTGCTTGA
1 TTTTCTTCTTCTTT-TGTAGTGCTTCA
2619917 TTTTCTTCTTCTTTTGTAGTGCTTCA
1 TTTTCTTCTTCTTTTGTAGTGCTTCA
*
2619943 ATTTCTT
1 TTTTCTT
2619950 TTGCTGATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 12 0.41
26 17 0.59
ACGTcount: A:0.09, C:0.17, G:0.12, T:0.62
Consensus pattern (26 bp):
TTTTCTTCTTCTTTTGTAGTGCTTCA
Found at i:2628354 original size:15 final size:14
Alignment explanation
Indices: 2628307--2628353 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
2628297 GTGCTTCAAC
*
2628307 TTTTCTCTTCTTTA
1 TTTTCTTTTCTTTA
*
2628321 TTTTCTTTTCGTTTC
1 TTTTCTTTTC-TTTA
2628336 TTTTCTTTTTCTTT-
1 TTTTC-TTTTCTTTA
2628350 TTTT
1 TTTT
2628354 TGAGTGCTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
14 13 0.45
15 11 0.38
16 5 0.17
ACGTcount: A:0.02, C:0.17, G:0.02, T:0.79
Consensus pattern (14 bp):
TTTTCTTTTCTTTA
Found at i:2628396 original size:23 final size:24
Alignment explanation
Indices: 2628343--2628396 Score: 76
Period size: 23 Copynumber: 2.3 Consensus size: 24
2628333 TTCTTTTCTT
*
2628343 TTTCTTTTTTTTGAGTGCTTTCAA
1 TTTCTTTCTTTTGAGTGCTTTCAA
*
2628367 TTT-TTTCTTTTGAGTGCTTT-GA
1 TTTCTTTCTTTTGAGTGCTTTCAA
2628389 TTTCTTTC
1 TTTCTTTC
2628397 CTGGATTTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
22 4 0.15
23 20 0.74
24 3 0.11
ACGTcount: A:0.09, C:0.13, G:0.13, T:0.65
Consensus pattern (24 bp):
TTTCTTTCTTTTGAGTGCTTTCAA
Found at i:2628445 original size:3 final size:3
Alignment explanation
Indices: 2628437--2628463 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
2628427 TTTTGTATTT
2628437 TTG TTG TTG TTG TTG TTG TTG TTG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG
2628464 CATGTTTGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.33, T:0.67
Consensus pattern (3 bp):
TTG
Found at i:2641982 original size:28 final size:28
Alignment explanation
Indices: 2641958--2642009 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
2641948 TTAATTTTGG
2641958 TTTTTTGGTTTTTTCTCTTTTATTTGCC
1 TTTTTTGGTTTTTTCTCTTTTATTTGCC
*
2641986 TTTTTTGTTTTTTTC-CTTTT-TTTG
1 TTTTTTGGTTTTTTCTCTTTTATTTG
2642010 ATGAAAACAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 4 0.17
27 5 0.22
28 14 0.61
ACGTcount: A:0.02, C:0.12, G:0.10, T:0.77
Consensus pattern (28 bp):
TTTTTTGGTTTTTTCTCTTTTATTTGCC
Found at i:2648830 original size:5 final size:5
Alignment explanation
Indices: 2648820--2648861 Score: 52
Period size: 5 Copynumber: 8.8 Consensus size: 5
2648810 TTTGTAATAA
* *
2648820 AAAAT AAAAT -AAA- AAAAT AAAAG AAAAG AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
2648862 AGGCACAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
4 6 0.18
5 27 0.82
ACGTcount: A:0.83, C:0.00, G:0.05, T:0.12
Consensus pattern (5 bp):
AAAAT
Found at i:2648840 original size:20 final size:19
Alignment explanation
Indices: 2648815--2648862 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 19
2648805 TACTATTTGT
2648815 AATAAAAAATAA-AATAAAAA
1 AATAAAAAA-AAGAA-AAAAA
*
2648835 AATAAAAGAAAAGAAAATAA
1 AATAAAA-AAAAGAAAAAAA
2648855 AATAAAAA
1 AATAAAAA
2648863 GGCACAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 1 0.04
20 20 0.80
21 4 0.16
ACGTcount: A:0.83, C:0.00, G:0.04, T:0.12
Consensus pattern (19 bp):
AATAAAAAAAAGAAAAAAA
Found at i:2653110 original size:24 final size:21
Alignment explanation
Indices: 2653075--2653117 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
2653065 GGCACATTAT
*
2653075 TTTGAATTTCAAGAGGTACATCC
1 TTTGAATGTCAA-AGG-ACATCC
2653098 TTTGAAATGTCAAAGGACAT
1 TTTG-AATGTCAAAGGACAT
2653118 GTCTTGTGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 7 0.39
24 7 0.39
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.33
Consensus pattern (21 bp):
TTTGAATGTCAAAGGACATCC
Found at i:2664514 original size:19 final size:20
Alignment explanation
Indices: 2664478--2664520 Score: 70
Period size: 19 Copynumber: 2.2 Consensus size: 20
2664468 GAAACCCCTT
2664478 TGAAAACACATGAATTTTAA
1 TGAAAACACATGAATTTTAA
*
2664498 TGAAAATACAT-AATTTTAA
1 TGAAAACACATGAATTTTAA
2664517 TGAA
1 TGAA
2664521 GATAAATGCT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 12 0.55
20 10 0.45
ACGTcount: A:0.51, C:0.07, G:0.09, T:0.33
Consensus pattern (20 bp):
TGAAAACACATGAATTTTAA
Found at i:2672278 original size:13 final size:13
Alignment explanation
Indices: 2672262--2672291 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
2672252 CTGTTGACCC
*
2672262 GACCCGATCCGTT
1 GACCCGACCCGTT
2672275 GACCCGACCCGTT
1 GACCCGACCCGTT
2672288 GACC
1 GACC
2672292 GACGTTGACT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.17, C:0.43, G:0.23, T:0.17
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:2675179 original size:32 final size:31
Alignment explanation
Indices: 2675142--2675229 Score: 81
Period size: 32 Copynumber: 2.8 Consensus size: 31
2675132 ATCATTCTCG
*
2675142 GGTAGGCCCTATGGCCCTAAGATGTGTTCTTA
1 GGTAGGCCCTATGGCCCTAAGATGT-ATCTTA
* * * * *
2675174 GGTAGGCCCCACGGCCCCAAAATCTATCTTA
1 GGTAGGCCCTATGGCCCTAAGATGTATCTTA
2675205 GGTA-GCCTCTCAT-GCCCTAAGATGT
1 GGTAGGCC-CT-ATGGCCCTAAGATGT
2675230 CCCCTTAGGT
Statistics
Matches: 43, Mismatches: 11, Indels: 5
0.73 0.19 0.08
Matches are distributed among these distances:
30 3 0.07
31 19 0.44
32 21 0.49
ACGTcount: A:0.22, C:0.28, G:0.24, T:0.26
Consensus pattern (31 bp):
GGTAGGCCCTATGGCCCTAAGATGTATCTTA
Found at i:2680091 original size:32 final size:31
Alignment explanation
Indices: 2680017--2680093 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 31
2680007 CTAATGTGAC
* * *
2680017 TCTTAGGTAGGCTCTGCGGCGCTGAGATCAT
1 TCTTAGGTAGGCCCTGCGGCCCTAAGATCAT
** **
2680048 TCTCGGGTAGGCCCTGCGGCCCTAAGATGTGT
1 TCTTAGGTAGGCCCTGCGGCCCTAAGAT-CAT
2680080 TCTTAGGTAGGCCC
1 TCTTAGGTAGGCCC
2680094 CATGGCCCCG
Statistics
Matches: 36, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
31 23 0.64
32 13 0.36
ACGTcount: A:0.14, C:0.26, G:0.32, T:0.27
Consensus pattern (31 bp):
TCTTAGGTAGGCCCTGCGGCCCTAAGATCAT
Found at i:2682787 original size:19 final size:19
Alignment explanation
Indices: 2682765--2682805 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
2682755 TTGAGTGTAT
2682765 TTTGCAACTTT-TTCTTTTC
1 TTTG-AACTTTCTTCTTTTC
*
2682784 TTTGAATTTTCTTCTTTTC
1 TTTGAACTTTCTTCTTTTC
2682803 TTT
1 TTT
2682806 TCTTTTGCAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.10, C:0.17, G:0.05, T:0.68
Consensus pattern (19 bp):
TTTGAACTTTCTTCTTTTC
Found at i:2683700 original size:19 final size:20
Alignment explanation
Indices: 2683662--2683704 Score: 70
Period size: 19 Copynumber: 2.2 Consensus size: 20
2683652 GAAACCCCTT
*
2683662 TGAAAATACATGATTTTTAA
1 TGAAAATACATGAATTTTAA
2683682 TGAAAATACAT-AATTTTAA
1 TGAAAATACATGAATTTTAA
2683701 TGAA
1 TGAA
2683705 GATAAATGCT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 11 0.50
20 11 0.50
ACGTcount: A:0.49, C:0.05, G:0.09, T:0.37
Consensus pattern (20 bp):
TGAAAATACATGAATTTTAA
Found at i:2686342 original size:31 final size:29
Alignment explanation
Indices: 2686301--2686377 Score: 93
Period size: 29 Copynumber: 2.6 Consensus size: 29
2686291 AACTTGATGA
2686301 AGCATTTGGAAGACACATACAGATTAGTGG
1 AGCATTTGGAAGACACA-ACAGATTAGTGG
** *
2686331 AGCATTTTGGAAGACA-AACATCTTGGTGG
1 AGCA-TTTGGAAGACACAACAGATTAGTGG
*
2686360 AGCATTTGGGAGACACAA
1 AGCATTTGGAAGACACAA
2686378 ACAACTCACA
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
28 10 0.24
29 15 0.37
30 5 0.12
31 11 0.27
ACGTcount: A:0.35, C:0.14, G:0.27, T:0.23
Consensus pattern (29 bp):
AGCATTTGGAAGACACAACAGATTAGTGG
Found at i:2687199 original size:2 final size:2
Alignment explanation
Indices: 2687192--2687223 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2687182 CTTGAAAGTA
2687192 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2687224 TATGAAAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2694233 original size:19 final size:19
Alignment explanation
Indices: 2694203--2694239 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
2694193 GAATAATAAT
2694203 ATAAGTAATGAAATGAAAAA
1 ATAAGTAATGAAAT-AAAAA
2694223 ATAAG-AATGAAATAAAA
1 ATAAGTAATGAAATAAAA
2694240 TAAAGAAAGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 8 0.47
20 5 0.29
ACGTcount: A:0.68, C:0.00, G:0.14, T:0.19
Consensus pattern (19 bp):
ATAAGTAATGAAATAAAAA
Found at i:2694296 original size:45 final size:45
Alignment explanation
Indices: 2694246--2694335 Score: 144
Period size: 45 Copynumber: 2.0 Consensus size: 45
2694236 AAAATAAAGA
2694246 AAGGATAGAGATGGCTGCAGAATTCATGAAAGAGATGGATGATGT
1 AAGGATAGAGATGGCTGCAGAATTCATGAAAGAGATGGATGATGT
* * * *
2694291 AAGGATAGGGATGGCTGCGGAATTGATGGAAGAGATGGATGATGT
1 AAGGATAGAGATGGCTGCAGAATTCATGAAAGAGATGGATGATGT
2694336 TGATGATGAA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.34, C:0.06, G:0.38, T:0.22
Consensus pattern (45 bp):
AAGGATAGAGATGGCTGCAGAATTCATGAAAGAGATGGATGATGT
Found at i:2701911 original size:9 final size:9
Alignment explanation
Indices: 2701897--2701925 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
2701887 CCTTTCACAT
2701897 ACCTTTTCA
1 ACCTTTTCA
2701906 ACCTTTTCA
1 ACCTTTTCA
2701915 ACCTTTTCA
1 ACCTTTTCA
2701924 AC
1 AC
2701926 TTTGGCCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.24, C:0.34, G:0.00, T:0.41
Consensus pattern (9 bp):
ACCTTTTCA
Found at i:2705447 original size:31 final size:30
Alignment explanation
Indices: 2705408--2705490 Score: 98
Period size: 29 Copynumber: 2.8 Consensus size: 30
2705398 AGCTTGATGA
2705408 AGCATTTGGAAGACACATACAGCTTAGTGG
1 AGCATTTGGAAGACACATACAGCTTAGTGG
* * *
2705438 AGCCTTTTGGAAGACA-A-ACCGCTTGGTGG
1 AG-CATTTGGAAGACACATACAGCTTAGTGG
* *
2705467 AGCATTTGGGAGACGCATACAGCT
1 AGCATTTGGAAGACACATACAGCT
2705491 CACAATGAAT
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
28 10 0.23
29 13 0.30
30 8 0.19
31 12 0.28
ACGTcount: A:0.29, C:0.19, G:0.29, T:0.23
Consensus pattern (30 bp):
AGCATTTGGAAGACACATACAGCTTAGTGG
Found at i:2711938 original size:26 final size:27
Alignment explanation
Indices: 2711909--2711963 Score: 71
Period size: 25 Copynumber: 2.1 Consensus size: 27
2711899 TTATTTCTTT
*
2711909 CTTTTCTTTTCTTCTT-TTTCT-GAGTG
1 CTTTTATTTTCTTCTTCTTT-TGGAGTG
2711935 C-TTTATTTTCTTCTTCTTTTGGAGTG
1 CTTTTATTTTCTTCTTCTTTTGGAGTG
2711961 CTT
1 CTT
2711964 CAATTTCTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
25 14 0.56
26 10 0.40
27 1 0.04
ACGTcount: A:0.05, C:0.18, G:0.13, T:0.64
Consensus pattern (27 bp):
CTTTTATTTTCTTCTTCTTTTGGAGTG
Found at i:2711947 original size:25 final size:26
Alignment explanation
Indices: 2711915--2711972 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
2711905 CTTTCTTTTC
*
2711915 TTTTCTTCTT-TTTCT-GAGTGCTTTA
1 TTTTCTTCTTCTTT-TGGAGTGCTTCA
2711940 TTTTCTTCTTCTTTTGGAGTGCTTCA
1 TTTTCTTCTTCTTTTGGAGTGCTTCA
*
2711966 ATTTCTT
1 TTTTCTT
2711973 TTGCTGTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 11 0.38
26 18 0.62
ACGTcount: A:0.09, C:0.17, G:0.12, T:0.62
Consensus pattern (26 bp):
TTTTCTTCTTCTTTTGGAGTGCTTCA
Found at i:2722630 original size:11 final size:11
Alignment explanation
Indices: 2722614--2722652 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
2722604 AAACTTTAGC
2722614 TTTTTTGTTTT
1 TTTTTTGTTTT
**
2722625 TTTTTTCCTTT
1 TTTTTTGTTTT
2722636 TTTTTTGTTTT
1 TTTTTTGTTTT
2722647 TTTTTT
1 TTTTTT
2722653 AAAATAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.00, C:0.05, G:0.05, T:0.90
Consensus pattern (11 bp):
TTTTTTGTTTT
Found at i:2728105 original size:19 final size:20
Alignment explanation
Indices: 2728077--2728116 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
2728067 GGATAATAAT
2728077 ATAAGTAATGAAAAGAAATA
1 ATAAGTAATGAAAAGAAATA
*
2728097 ATAAG-AATGAAATGAAATA
1 ATAAGTAATGAAAAGAAATA
2728116 A
1 A
2728117 GGATGTGATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.65, C:0.00, G:0.15, T:0.20
Consensus pattern (20 bp):
ATAAGTAATGAAAAGAAATA
Found at i:2734767 original size:23 final size:23
Alignment explanation
Indices: 2734725--2734783 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
2734715 TTTCTTACTT
2734725 TTTCTTCTTTTCGAGTGCTTTCAA
1 TTTCTTCTTTT-GAGTGCTTTCAA
* *
2734749 TTTCTTCTTTTGAGTGCTTTTAT
1 TTTCTTCTTTTGAGTGCTTTCAA
2734772 TTTCTT-TTTTGA
1 TTTCTTCTTTTGA
2734784 TTTTTTTCTT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
22 6 0.18
23 16 0.48
24 11 0.33
ACGTcount: A:0.10, C:0.15, G:0.12, T:0.63
Consensus pattern (23 bp):
TTTCTTCTTTTGAGTGCTTTCAA
Found at i:2736574 original size:17 final size:17
Alignment explanation
Indices: 2736552--2736602 Score: 59
Period size: 17 Copynumber: 3.0 Consensus size: 17
2736542 AATTAAGAGT
2736552 TAGTTT-ATTAAATGAAC
1 TAGTTTAATT-AATGAAC
* *
2736569 TAGTTTGATGAATGAAC
1 TAGTTTAATTAATGAAC
*
2736586 TACTTTAATTAATGAAC
1 TAGTTTAATTAATGAAC
2736603 CAACTTTATT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
17 27 0.93
18 2 0.07
ACGTcount: A:0.39, C:0.08, G:0.14, T:0.39
Consensus pattern (17 bp):
TAGTTTAATTAATGAAC
Found at i:2736636 original size:17 final size:17
Alignment explanation
Indices: 2736614--2736679 Score: 53
Period size: 17 Copynumber: 3.8 Consensus size: 17
2736604 AACTTTATTC
2736614 AATGAACTAGATGCATG
1 AATGAACTAGATGCATG
* * *
2736631 AATGAAGTAGCT-TATTG
1 AATGAACTAGATGCA-TG
* * *
2736648 AATGATCTAATATGCATA
1 AATGAACT-AGATGCATG
2736666 AATGAACTAGATGC
1 AATGAACTAGATGC
2736680 TTTTAATGCA
Statistics
Matches: 35, Mismatches: 11, Indels: 6
0.67 0.21 0.12
Matches are distributed among these distances:
16 1 0.03
17 23 0.66
18 10 0.29
19 1 0.03
ACGTcount: A:0.41, C:0.11, G:0.20, T:0.29
Consensus pattern (17 bp):
AATGAACTAGATGCATG
Found at i:2737784 original size:8 final size:8
Alignment explanation
Indices: 2737758--2737805 Score: 53
Period size: 8 Copynumber: 5.8 Consensus size: 8
2737748 ATAGATTAAT
2737758 GAAAT-AA
1 GAAATAAA
2737765 GAAATGAAA
1 GAAAT-AAA
2737774 GAAATAAA
1 GAAATAAA
2737782 GAAATGATAA
1 GAAAT-A-AA
2737792 GAAATAAA
1 GAAATAAA
*
2737800 GGAATA
1 GAAATA
2737806 GAATGGTTAT
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
7 5 0.14
8 15 0.42
9 9 0.25
10 7 0.19
ACGTcount: A:0.67, C:0.00, G:0.19, T:0.15
Consensus pattern (8 bp):
GAAATAAA
Found at i:2737785 original size:17 final size:18
Alignment explanation
Indices: 2737742--2737800 Score: 77
Period size: 17 Copynumber: 3.2 Consensus size: 18
2737732 TAAAATTATG
2737742 AAAGAAATAGATTAATGAAAT
1 AAAGAAAT-GA-TAA-GAAAT
2737763 -AAGAAATGA-AAGAAAT
1 AAAGAAATGATAAGAAAT
2737779 AAAGAAATGATAAGAAAT
1 AAAGAAATGATAAGAAAT
2737797 AAAG
1 AAAG
2737801 GAATAGAATG
Statistics
Matches: 36, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
16 5 0.14
17 11 0.31
18 11 0.31
19 2 0.06
20 7 0.19
ACGTcount: A:0.66, C:0.00, G:0.17, T:0.17
Consensus pattern (18 bp):
AAAGAAATGATAAGAAAT
Found at i:2740730 original size:35 final size:36
Alignment explanation
Indices: 2740656--2740724 Score: 93
Period size: 36 Copynumber: 1.9 Consensus size: 36
2740646 TTTCAAAAAG
*
2740656 CTTTTCTTCATTTGAATTTTCCACTAAACGTTCAAC
1 CTTTTCTTCATTTGAATTTTCCACCAAACGTTCAAC
* * * *
2740692 CTTTTCTTTATTTGATTTTTCCTCCAAATGTTC
1 CTTTTCTTCATTTGAATTTTCCACCAAACGTTC
2740725 TCCTTTAATT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 28 1.00
ACGTcount: A:0.20, C:0.23, G:0.06, T:0.51
Consensus pattern (36 bp):
CTTTTCTTCATTTGAATTTTCCACCAAACGTTCAAC
Found at i:2741965 original size:6 final size:6
Alignment explanation
Indices: 2741946--2741980 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
2741936 TGATAATGGA
* *
2741946 ATGGTG AAGGTG ATGATG ATGGTG ATGGTG ATGGT
1 ATGGTG ATGGTG ATGGTG ATGGTG ATGGTG ATGGT
2741981 TTAAGAAGTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.23, C:0.00, G:0.46, T:0.31
Consensus pattern (6 bp):
ATGGTG
Found at i:2746105 original size:54 final size:55
Alignment explanation
Indices: 2745950--2746117 Score: 207
Period size: 55 Copynumber: 3.0 Consensus size: 55
2745940 ATTACCAAAT
* * *
2745950 GGCACTAAGTGTGCAAAAACTTAAGAAA-TCTATATTAAGTGTATGAATTTCTGTATG
1 GGCACTATGTGTGC-TAAAC-TAAGAAATTC-ATACTAAGTGTATGAATTTCTGTATG
* *
2746007 GGCACTTTGTGTGCTAAACTAAGAAATTCATACTAAGTGCATGAATTTCTGTATG
1 GGCACTATGTGTGCTAAACTAAGAAATTCATACTAAGTGTATGAATTTCTGTATG
* * *
2746062 GGCAGTATGTGTGC-GAACTAAGAAATTCATTCTAAGTGTATGAATTT-TCGTATG
1 GGCACTATGTGTGCTAAACTAAGAAATTCATACTAAGTGTATGAATTTCT-GTATG
2746116 GG
1 GG
2746118 AAATATATGT
Statistics
Matches: 99, Mismatches: 10, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
53 1 0.01
54 37 0.37
55 43 0.43
56 6 0.06
57 12 0.12
ACGTcount: A:0.32, C:0.12, G:0.22, T:0.34
Consensus pattern (55 bp):
GGCACTATGTGTGCTAAACTAAGAAATTCATACTAAGTGTATGAATTTCTGTATG
Found at i:2746440 original size:68 final size:68
Alignment explanation
Indices: 2746327--2746521 Score: 284
Period size: 68 Copynumber: 2.9 Consensus size: 68
2746317 AAAAGATTAA
2746327 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGTTAACT-TCC
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGTTAACTGT-C
2746391 TTTG
65 TTTG
* * * * * *
2746395 AGGCCTAACTGTGCTTTTCACAGAAATGTGTCATTTATGCAAGTTAGATGAAAGGCTAAGTGTCT
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGTTAACTGTCT
2746460 TTG
66 TTG
* * * *
2746463 AGGCCTAACTGTGCATTTGATAGAAAGGTGTCAATTATTCCAGTTAGATGAACGGTTAA
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGTTAA
2746522 ATATCGTTTA
Statistics
Matches: 111, Mismatches: 15, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
68 110 0.99
69 1 0.01
ACGTcount: A:0.29, C:0.15, G:0.24, T:0.32
Consensus pattern (68 bp):
AGGCCTAACTGTGCATTTGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGTTAACTGTCT
TTG
Done.