Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D11
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: 73211361
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1690000 characters in sequence are not A, C, G, or T
File 49 of 240
Found at i:16739179 original size:21 final size:21
Alignment explanation
Indices: 16739150--16739200 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
16739140 TTTCGTTGAA
* *
16739150 CCTCAGCTTCTCTCGCTGCTG
1 CCTCTGCTTCTCTCGCTGCCG
*
16739171 CCTCTGCTTCTCTTGCTGCCG
1 CCTCTGCTTCTCTCGCTGCCG
*
16739192 CATCTGCTT
1 CCTCTGCTT
16739201 TAAGTTGTAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.04, C:0.41, G:0.18, T:0.37
Consensus pattern (21 bp):
CCTCTGCTTCTCTCGCTGCCG
Found at i:16742284 original size:3 final size:3
Alignment explanation
Indices: 16742265--16742357 Score: 82
Period size: 3 Copynumber: 30.3 Consensus size: 3
16742255 TTTAGCAACT
* * *
16742265 TTA TTAA TTA GTTA TTA TTA TTA TTA TAA TTA TTA TCT- TTA TTG TTC
1 TTA TT-A TTA -TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA
* * *
16742312 TTA TTA TTA TTA -TA TTCA TTA ATA TTA TTG TTA TTA TTA TTT TTA
1 TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA
16742357 T
1 T
16742358 ATTCACTTAT
Statistics
Matches: 73, Mismatches: 11, Indels: 12
0.76 0.11 0.12
Matches are distributed among these distances:
2 3 0.04
3 60 0.82
4 10 0.14
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:16742317 original size:33 final size:34
Alignment explanation
Indices: 16742277--16742362 Score: 108
Period size: 33 Copynumber: 2.6 Consensus size: 34
16742267 ATTAATTAGT
*
16742277 TATTATTATTATTATAATT-ATT-ATCTTTATTGT
1 TATTATTATTATTATAATTCATTAAT-ATTATTGT
*
16742310 TCTTATTATTATTAT-ATTCATTAATATTATTGT
1 TATTATTATTATTATAATTCATTAATATTATTGT
*
16742343 TATTATTATTTTTAT-ATTCA
1 TATTATTATTATTATAATTCA
16742363 CTTATGGAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
32 3 0.06
33 42 0.89
34 2 0.04
ACGTcount: A:0.30, C:0.05, G:0.02, T:0.63
Consensus pattern (34 bp):
TATTATTATTATTATAATTCATTAATATTATTGT
Found at i:16744032 original size:23 final size:23
Alignment explanation
Indices: 16743989--16744033 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
16743979 TGCTTTTATA
*
16743989 CCCTAAAACCCGAAGCTATTAAT
1 CCCTAAAACCCGAAACTATTAAT
*
16744012 CCCTATAACCCGTAAAC-ATTAA
1 CCCTAAAACCCG-AAACTATTAA
16744034 AATTAAAGGC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 16 0.84
24 3 0.16
ACGTcount: A:0.40, C:0.31, G:0.07, T:0.22
Consensus pattern (23 bp):
CCCTAAAACCCGAAACTATTAAT
Found at i:16745072 original size:40 final size:39
Alignment explanation
Indices: 16744995--16745113 Score: 121
Period size: 40 Copynumber: 3.0 Consensus size: 39
16744985 GCGCTTTTTG
* * * *
16744995 TAAAACGCCGCTAATGCTTGGTTTTAGCGGCGTTTTTTTA
1 TAAAACGCCGCTAATGCTCGATTTTAGTGGCG-TTTTTCA
** * *
16745035 TGTAACGCCGCTAATGCTCGATATTTTGTGGCGTTTTTCG
1 TAAAACGCCGCTAATGCTCGAT-TTTAGTGGCGTTTTTCA
**
16745075 TAAAATACCGCTAATGCTCGATTGTTAGTGGCGTTTTTC
1 TAAAACGCCGCTAATGCTCGATT-TTAGTGGCGTTTTTC
16745114 GCCCAAACGC
Statistics
Matches: 64, Mismatches: 13, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
39 1 0.02
40 55 0.86
41 8 0.12
ACGTcount: A:0.19, C:0.18, G:0.23, T:0.39
Consensus pattern (39 bp):
TAAAACGCCGCTAATGCTCGATTTTAGTGGCGTTTTTCA
Found at i:16750958 original size:3 final size:3
Alignment explanation
Indices: 16750950--16750974 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
16750940 ACCTCAAAAA
16750950 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
16750975 TATTCCTTGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:16752091 original size:13 final size:13
Alignment explanation
Indices: 16752073--16752098 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
16752063 AGGAATAATA
16752073 GCAGTTAACAGTT
1 GCAGTTAACAGTT
16752086 GCAGTTAACAGTT
1 GCAGTTAACAGTT
16752099 AAGGAAGTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (13 bp):
GCAGTTAACAGTT
Found at i:16755755 original size:21 final size:21
Alignment explanation
Indices: 16755729--16755769 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
16755719 AGACGAGCAA
* *
16755729 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
16755750 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
16755770 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:16768536 original size:14 final size:14
Alignment explanation
Indices: 16768517--16768564 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
16768507 TAGGAAAGTC
16768517 ATTTTTGCAGTGAA
1 ATTTTTGCAGTGAA
* *
16768531 ATTTTTGTCGGTCAA
1 ATTTTTG-CAGTGAA
*
16768546 TATTTTTGAAGTGAA
1 -ATTTTTGCAGTGAA
16768561 ATTT
1 ATTT
16768565 GGTCATATGA
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
14 11 0.41
15 9 0.33
16 7 0.26
ACGTcount: A:0.27, C:0.06, G:0.19, T:0.48
Consensus pattern (14 bp):
ATTTTTGCAGTGAA
Found at i:16769559 original size:75 final size:75
Alignment explanation
Indices: 16769449--16769742 Score: 369
Period size: 75 Copynumber: 3.9 Consensus size: 75
16769439 ACGCCTGCTG
* * * *
16769449 ATTTCTAAGATCTTCTAGGAGCCAGCTGTTGGTAAAAGAGACACCATTGGCTCCATTTTGAGAAG
1 ATTTCTAAGATCTTCTTGAAACCAACTGTTGGTAAAAGAGACACCATTGGCTCCATTTTGAGAAG
*
16769514 CTTGCTGATG
66 CTTGCTGATC
* * * * * *
16769524 ATTTCTAACATCTTCTTGCAACCAATTGTTTGTAAAAGAGGCACCATTGGCTCCTTTTTGAGAAG
1 ATTTCTAAGATCTTCTTGAAACCAACTGTTGGTAAAAGAGACACCATTGGCTCCATTTTGAGAAG
*
16769589 CTTGGTGATC
66 CTTGCTGATC
* *
16769599 ATTT-TGATGATCTTCTTGAAACCAACTGTTGGTAAAAGAGGA-ACCATTGGCTCCATTTCGAGA
1 ATTTCT-AAGATCTTCTTGAAACCAACTGTTGGTAAAAGA-GACACCATTGGCTCCATTTTGAGA
16769662 AGCTTGCTGATC
64 AGCTTGCTGATC
* * * * *
16769674 ATTTCTATGATCTTCTTGAAACCAATTGTAAGG-AAAAGAGGCACCATTAGCTCCATTTTGAGAA
1 ATTTCTAAGATCTTCTTGAAACCAACTGT-TGGTAAAAGAGACACCATTGGCTCCATTTTGAGAA
16769738 GCTTG
65 GCTTG
16769743 GTCTTGCTGA
Statistics
Matches: 189, Mismatches: 25, Indels: 10
0.84 0.11 0.04
Matches are distributed among these distances:
74 2 0.01
75 183 0.97
76 4 0.02
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.33
Consensus pattern (75 bp):
ATTTCTAAGATCTTCTTGAAACCAACTGTTGGTAAAAGAGACACCATTGGCTCCATTTTGAGAAG
CTTGCTGATC
Found at i:16769646 original size:150 final size:150
Alignment explanation
Indices: 16769474--16769744 Score: 436
Period size: 150 Copynumber: 1.8 Consensus size: 150
16769464 TAGGAGCCAG
* *
16769474 CTGTTGGTAAAAGAGACACCATTGGCTCCATTTTGAGAAGCTTGCTGATGATTTCTAACATCTTC
1 CTGTTGGTAAAAGAGACACCATTGGCTCCATTTCGAGAAGCTTGCTGATCATTTCTAACATCTTC
* ** * * *
16769539 TTGCAACCAATTGTTTGTAAAAGAGGCACCATTGGCTCCTTTTTGAGAAGCTTGGTGATCATTTT
66 TTGAAACCAATTGTAAGGAAAAGAGGCACCATTAGCTCCATTTTGAGAAGCTTGGTGATCATTTT
16769604 GATGATCTTCTTGAAACCAA
131 GATGATCTTCTTGAAACCAA
**
16769624 CTGTTGGTAAAAGAGGA-ACCATTGGCTCCATTTCGAGAAGCTTGCTGATCATTTCTATGATCTT
1 CTGTTGGTAAAAGA-GACACCATTGGCTCCATTTCGAGAAGCTTGCTGATCATTTCTAACATCTT
16769688 CTTGAAACCAATTGTAAGGAAAAGAGGCACCATTAGCTCCATTTTGAGAAGCTTGGT
65 CTTGAAACCAATTGTAAGGAAAAGAGGCACCATTAGCTCCATTTTGAGAAGCTTGGT
16769745 CTTGCTGAAA
Statistics
Matches: 110, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
150 108 0.98
151 2 0.02
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.33
Consensus pattern (150 bp):
CTGTTGGTAAAAGAGACACCATTGGCTCCATTTCGAGAAGCTTGCTGATCATTTCTAACATCTTC
TTGAAACCAATTGTAAGGAAAAGAGGCACCATTAGCTCCATTTTGAGAAGCTTGGTGATCATTTT
GATGATCTTCTTGAAACCAA
Found at i:16773376 original size:25 final size:24
Alignment explanation
Indices: 16773348--16773400 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 24
16773338 ATACCATAGG
* *
16773348 TAAAAATTATGTAAAAATATATTAA
1 TAAAAATCATGT-AAAATATATAAA
*
16773373 TAAAAAATCATGTAATATATATAAA
1 T-AAAAATCATGTAAAATATATAAA
16773398 TAA
1 TAA
16773401 GTGGTAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
24 2 0.08
25 12 0.50
26 10 0.42
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.34
Consensus pattern (24 bp):
TAAAAATCATGTAAAATATATAAA
Found at i:16784831 original size:19 final size:19
Alignment explanation
Indices: 16784807--16784844 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
16784797 TGCACTTTAC
16784807 AATCAGTAATTCAATGTAT
1 AATCAGTAATTCAATGTAT
16784826 AATCAGTAATTCAATGTAT
1 AATCAGTAATTCAATGTAT
16784845 CTTGACAAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.37
Consensus pattern (19 bp):
AATCAGTAATTCAATGTAT
Found at i:16789779 original size:43 final size:43
Alignment explanation
Indices: 16789681--16789791 Score: 111
Period size: 43 Copynumber: 2.6 Consensus size: 43
16789671 ATCTACGTGT
* * * * *
16789681 AAGACCATGTCTGGGACATTGGCATCGTATATGATTTACGTGT
1 AAGACCCTGTCTGGGACAGTGGCATCGGATATGATTTACATGC
*
16789724 AAGACCCTGTCTGGGACAGTGGCATCGAGATTTGA-TTACATGC
1 AAGACCCTGTCTGGGACAGTGGCATCG-GATATGATTTACATGC
*
16789767 AATA-CCTCGTCTGGGAC-GTAGGCAT
1 AAGACCCT-GTCTGGGACAGT-GGCAT
16789792 TGTACGATCT
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
42 5 0.09
43 48 0.83
44 5 0.09
ACGTcount: A:0.25, C:0.20, G:0.27, T:0.28
Consensus pattern (43 bp):
AAGACCCTGTCTGGGACAGTGGCATCGGATATGATTTACATGC
Found at i:16794235 original size:44 final size:44
Alignment explanation
Indices: 16794172--16794260 Score: 169
Period size: 44 Copynumber: 2.0 Consensus size: 44
16794162 TTTTTTAAAA
*
16794172 TGTTTAATTTGCCAGCAAGTTAAAGCTGAGCATCAAGTACCGTC
1 TGTTTAATTTGCCAGCAAGTTAAAGCCGAGCATCAAGTACCGTC
16794216 TGTTTAATTTGCCAGCAAGTTAAAGCCGAGCATCAAGTACCGTC
1 TGTTTAATTTGCCAGCAAGTTAAAGCCGAGCATCAAGTACCGTC
16794260 T
1 T
16794261 AGATTACTTC
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.29
Consensus pattern (44 bp):
TGTTTAATTTGCCAGCAAGTTAAAGCCGAGCATCAAGTACCGTC
Found at i:16797402 original size:43 final size:43
Alignment explanation
Indices: 16797342--16797494 Score: 220
Period size: 43 Copynumber: 3.6 Consensus size: 43
16797332 ATTTGAGATC
16797342 TACGTGTAAGACCATGTCTGGGACATTGGCATCGTATATGATT
1 TACGTGTAAGACCATGTCTGGGACATTGGCATCGTATATGATT
*
16797385 TATGTGTAAGACCATGTCTGGGACATTGGCATCGTATATGATT
1 TACGTGTAAGACCATGTCTGGGACATTGGCATCGTATATGATT
* * *
16797428 TACGTGTAAGACCCTGTCTGGGACAGTGGCATCGATATTTGA-T
1 TACGTGTAAGACCATGTCTGGGACATTGGCATCG-TATATGATT
* *
16797471 TACATGCAAGACC-TCGTCTGGGAC
1 TACGTGTAAGACCAT-GTCTGGGAC
16797495 GTAGGCATTG
Statistics
Matches: 101, Mismatches: 7, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
42 1 0.01
43 94 0.93
44 6 0.06
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.31
Consensus pattern (43 bp):
TACGTGTAAGACCATGTCTGGGACATTGGCATCGTATATGATT
Found at i:16803224 original size:23 final size:22
Alignment explanation
Indices: 16803172--16803224 Score: 54
Period size: 23 Copynumber: 2.4 Consensus size: 22
16803162 TCCTTGTCTT
*
16803172 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
* *
16803194 CTTATTTTCTCTTCTTTCTTC-AA
1 TTTCTTTTCT-TTCTTT-TTCTAA
16803217 TTTCTTTT
1 TTTCTTTT
16803225 TCACTTTTCT
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
22 7 0.29
23 14 0.58
24 3 0.12
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:16803238 original size:18 final size:18
Alignment explanation
Indices: 16803217--16803256 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
16803207 CTTTCTTCAA
* * *
16803217 TTTCTTTTTCACTTTTCT
1 TTTCTGTTTCACATTCCT
16803235 TTTCTGTTTCACATTCCT
1 TTTCTGTTTCACATTCCT
16803253 TTTC
1 TTTC
16803257 ACTCTCAATC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.07, C:0.25, G:0.03, T:0.65
Consensus pattern (18 bp):
TTTCTGTTTCACATTCCT
Found at i:16803320 original size:71 final size:71
Alignment explanation
Indices: 16803236--16803379 Score: 288
Period size: 71 Copynumber: 2.0 Consensus size: 71
16803226 CACTTTTCTT
16803236 TTCTGTTTCACATTCCTTTTCACTCTCAATCTTTTTTTGCTCTTTTTCATTCTCTTTTTCTTTTT
1 TTCTGTTTCACATTCCTTTTCACTCTCAATCTTTTTTTGCTCTTTTTCATTCTCTTTTTCTTTTT
16803301 TCTCAC
66 TCTCAC
16803307 TTCTGTTTCACATTCCTTTTCACTCTCAATCTTTTTTTGCTCTTTTTCATTCTCTTTTTCTTTTT
1 TTCTGTTTCACATTCCTTTTCACTCTCAATCTTTTTTTGCTCTTTTTCATTCTCTTTTTCTTTTT
16803372 TCTCAC
66 TCTCAC
16803378 TT
1 TT
16803380 GTTTTAACAA
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 73 1.00
ACGTcount: A:0.10, C:0.26, G:0.03, T:0.61
Consensus pattern (71 bp):
TTCTGTTTCACATTCCTTTTCACTCTCAATCTTTTTTTGCTCTTTTTCATTCTCTTTTTCTTTTT
TCTCAC
Found at i:16813962 original size:8 final size:8
Alignment explanation
Indices: 16813939--16813986 Score: 60
Period size: 8 Copynumber: 6.0 Consensus size: 8
16813929 TCACCTCTCA
*
16813939 CTCACTCA
1 CTCACTCT
16813947 CTCACTCT
1 CTCACTCT
16813955 CTCACTCT
1 CTCACTCT
*
16813963 CTCTCTCT
1 CTCACTCT
*
16813971 CTCTCTCT
1 CTCACTCT
*
16813979 CTCTCTCT
1 CTCACTCT
16813987 TTTCATTTCC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 38 1.00
ACGTcount: A:0.08, C:0.50, G:0.00, T:0.42
Consensus pattern (8 bp):
CTCACTCT
Found at i:16813964 original size:2 final size:2
Alignment explanation
Indices: 16813951--16813986 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
16813941 CACTCACTCA
*
16813951 CT CT CT CA CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
16813987 TTTCATTTCC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.03, C:0.50, G:0.00, T:0.47
Consensus pattern (2 bp):
CT
Found at i:16813966 original size:12 final size:12
Alignment explanation
Indices: 16813933--16813985 Score: 61
Period size: 12 Copynumber: 4.4 Consensus size: 12
16813923 CCCCCTTCAC
*
16813933 CTCTCACTCACT
1 CTCTCACTCTCT
*
16813945 CACTCACTCTCT
1 CTCTCACTCTCT
* *
16813957 CACTCTCTCTCT
1 CTCTCACTCTCT
*
16813969 CTCTCTCTCTCT
1 CTCTCACTCTCT
16813981 CTCTC
1 CTCTC
16813986 TTTTCATTTC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 37 1.00
ACGTcount: A:0.09, C:0.51, G:0.00, T:0.40
Consensus pattern (12 bp):
CTCTCACTCTCT
Found at i:16821537 original size:25 final size:24
Alignment explanation
Indices: 16821509--16821561 Score: 79
Period size: 25 Copynumber: 2.2 Consensus size: 24
16821499 ACATATCGCA
16821509 GCTCTTTATGAGCATCCCGATATAG
1 GCTCTTTATGAGCATCCCGATAT-G
* *
16821534 GCTCTTTATGAGCTTCCTGATATG
1 GCTCTTTATGAGCATCCCGATATG
16821558 GCTC
1 GCTC
16821562 GCTTGAACTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
24 5 0.19
25 21 0.81
ACGTcount: A:0.19, C:0.25, G:0.21, T:0.36
Consensus pattern (24 bp):
GCTCTTTATGAGCATCCCGATATG
Found at i:16826771 original size:24 final size:24
Alignment explanation
Indices: 16826731--16826790 Score: 61
Period size: 24 Copynumber: 2.5 Consensus size: 24
16826721 AATTTTTTTA
*
16826731 AAAAATT-TAAAAGAAAA-ATATAT
1 AAAAATTATAAAAGAAAAGAAAT-T
* *
16826754 AAAAATTATAATATAAAAGAAATT
1 AAAAATTATAAAAGAAAAGAAATT
*
16826778 ATAAATTATAAAA
1 AAAAATTATAAAA
16826791 ATAAATGTAT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
23 7 0.23
24 20 0.67
25 3 0.10
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.28
Consensus pattern (24 bp):
AAAAATTATAAAAGAAAAGAAATT
Found at i:16826778 original size:17 final size:16
Alignment explanation
Indices: 16826747--16826832 Score: 59
Period size: 16 Copynumber: 5.1 Consensus size: 16
16826737 TTAAAAGAAA
*
16826747 AATATATAAAAATTAT
1 AATATAAAAAAATTAT
16826763 AATATAAAAGAAATTAT
1 AATATAAAA-AAATTAT
* *
16826780 AAATTATAAAAATAAATGT
1 -AA-TATAAAAA-AATTAT
* *
16826799 -ATGTAAAAAAATTTAA
1 AATATAAAAAAA-TTAT
16826815 AATATTAAAAAAA-TAT
1 AATA-TAAAAAAATTAT
16826831 AA
1 AA
16826833 AATTCAAGTT
Statistics
Matches: 54, Mismatches: 9, Indels: 14
0.70 0.12 0.18
Matches are distributed among these distances:
15 2 0.04
16 20 0.37
17 10 0.19
18 11 0.20
19 11 0.20
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.31
Consensus pattern (16 bp):
AATATAAAAAAATTAT
Found at i:16833699 original size:6 final size:6
Alignment explanation
Indices: 16833688--16833713 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
16833678 CGCTTTTAAC
16833688 AAATAA AAATAA AAATAA AAATAA AA
1 AAATAA AAATAA AAATAA AAATAA AA
16833714 TCTTTACGTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAATAA
Found at i:16837485 original size:34 final size:34
Alignment explanation
Indices: 16837447--16837524 Score: 111
Period size: 34 Copynumber: 2.3 Consensus size: 34
16837437 CTATAGTGTT
*
16837447 ATTTGGTGTGATGGATGGATTCATTCATACGAAC
1 ATTTGGTGTGATGGATGGATTCACTCATACGAAC
* * * *
16837481 ATTTGATGTGTTGGATGGATTGACTCATACGAGC
1 ATTTGGTGTGATGGATGGATTCACTCATACGAAC
16837515 ATTTGGTGTG
1 ATTTGGTGTG
16837525 CTAGATAAAT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 38 1.00
ACGTcount: A:0.23, C:0.10, G:0.29, T:0.37
Consensus pattern (34 bp):
ATTTGGTGTGATGGATGGATTCACTCATACGAAC
Found at i:16840873 original size:15 final size:15
Alignment explanation
Indices: 16840846--16840932 Score: 76
Period size: 15 Copynumber: 6.0 Consensus size: 15
16840836 ATTGTTATTA
16840846 AATT-TTAATATAAT
1 AATTATTAATATAAT
*
16840860 AATTATTAAAATAAT
1 AATTATTAATATAAT
*
16840875 --TTAATAATA-AAT
1 AATTATTAATATAAT
* * *
16840887 AATAAATAATTTAAT
1 AATTATTAATATAAT
16840902 ATATT-TTAATATAAT
1 A-ATTATTAATATAAT
16840917 AATTATTAAATATAAT
1 AATTATT-AATATAAT
16840933 TTGATAAAAA
Statistics
Matches: 58, Mismatches: 8, Indels: 12
0.74 0.10 0.15
Matches are distributed among these distances:
12 3 0.05
13 7 0.12
14 14 0.24
15 24 0.41
16 10 0.17
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
AATTATTAATATAAT
Found at i:16840910 original size:57 final size:58
Alignment explanation
Indices: 16840847--16840991 Score: 188
Period size: 57 Copynumber: 2.4 Consensus size: 58
16840837 TTGTTATTAA
16840847 ATTTTAATATAATAATTATTAAAATAATTTAATAATAAAT-AATAAATAATTTAAT-AT
1 ATTTTAATATAATAATTATTAAAATAATTTAATAA-AAATAAATAAATAATTTAATAAT
* *
16840904 ATTTTAATATAATAATTATTAAATATAATTTGATAAAAATAAAAATATATAATTTAATAAT
1 ATTTTAATATAATAATTATTAAA-ATAATTTAATAAAAAT--AAATAAATAATTTAATAAT
*
16840965 ATTTTAAATATAATTA-TATCTAAAATA
1 ATTTT-AATATAATAATTAT-TAAAATA
16840992 TTTCAAATAT
Statistics
Matches: 78, Mismatches: 3, Indels: 10
0.86 0.03 0.11
Matches are distributed among these distances:
57 27 0.35
58 11 0.14
60 14 0.18
61 13 0.17
62 13 0.17
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (58 bp):
ATTTTAATATAATAATTATTAAAATAATTTAATAAAAATAAATAAATAATTTAATAAT
Found at i:16840939 original size:24 final size:24
Alignment explanation
Indices: 16840884--16840979 Score: 72
Period size: 24 Copynumber: 4.0 Consensus size: 24
16840874 TTTAATAATA
* * *
16840884 AATAATAAATAATTTAATATATTTT
1 AATAAT-AATTATTAAATATAATTT
16840909 AATATAATAATTATTAAATATAATTT
1 -A-ATAATAATTATTAAATATAATTT
* * **
16840935 GATAA-AAATAAAAATATATAATTT
1 AATAATAATTATTAA-ATATAATTT
16840959 AATAAT-ATT-TTAAATATAATT
1 AATAATAATTATTAAATATAATT
16840980 ATATCTAAAA
Statistics
Matches: 56, Mismatches: 11, Indels: 10
0.73 0.14 0.13
Matches are distributed among these distances:
22 8 0.14
23 8 0.14
24 19 0.34
26 16 0.29
27 5 0.09
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (24 bp):
AATAATAATTATTAAATATAATTT
Found at i:16841709 original size:55 final size:57
Alignment explanation
Indices: 16841591--16841713 Score: 216
Period size: 56 Copynumber: 2.2 Consensus size: 57
16841581 AAAAAAGTTG
*
16841591 TAATTATTATTTGAAAATTTTTATTTATAATATGTGAATTGACAAATTAATATATTT
1 TAATTATTATTTGAAAATTTTTATTTATAATATGTGAAATGACAAATTAATATATTT
16841648 TAATTATTATTTGAAAA-TTTTATTTATAATATGTGAAATGA-AAATTAATATATTT
1 TAATTATTATTTGAAAATTTTTATTTATAATATGTGAAATGACAAATTAATATATTT
16841703 TAATTA-TATTT
1 TAATTATTATTT
16841714 AATAATTCAA
Statistics
Matches: 65, Mismatches: 1, Indels: 3
0.94 0.01 0.04
Matches are distributed among these distances:
54 5 0.08
55 20 0.31
56 23 0.35
57 17 0.26
ACGTcount: A:0.41, C:0.01, G:0.07, T:0.51
Consensus pattern (57 bp):
TAATTATTATTTGAAAATTTTTATTTATAATATGTGAAATGACAAATTAATATATTT
Found at i:16841931 original size:36 final size:38
Alignment explanation
Indices: 16841888--16841970 Score: 145
Period size: 37 Copynumber: 2.3 Consensus size: 38
16841878 CTAATATATA
16841888 ATTATATAATTTA-TTTTTAATTTGAAATATATA-TTT
1 ATTATATAATTTATTTTTTAATTTGAAATATATATTTT
16841924 ATTATATAATTTATTTTTTAATTTGAAATATATATTTT
1 ATTATATAATTTATTTTTTAATTTGAAATATATATTTT
16841962 ATTAT-TAAT
1 ATTATATAAT
16841971 AAAATATTTA
Statistics
Matches: 45, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
36 13 0.29
37 24 0.53
38 8 0.18
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (38 bp):
ATTATATAATTTATTTTTTAATTTGAAATATATATTTT
Found at i:16841961 original size:19 final size:19
Alignment explanation
Indices: 16841902--16841962 Score: 65
Period size: 19 Copynumber: 3.3 Consensus size: 19
16841892 TATAATTTAT
16841902 TTTTAATTTGAAATATATA
1 TTTTAATTTGAAATATATA
* *
16841921 -TTT-ATTAT-ATAATTTATT
1 TTTTAATT-TGA-AATATATA
16841939 TTTTAATTTGAAATATATA
1 TTTTAATTTGAAATATATA
16841958 TTTTA
1 TTTTA
16841963 TTATTAATAA
Statistics
Matches: 33, Mismatches: 4, Indels: 10
0.70 0.09 0.21
Matches are distributed among these distances:
17 4 0.12
18 10 0.30
19 15 0.45
20 4 0.12
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (19 bp):
TTTTAATTTGAAATATATA
Found at i:16843574 original size:22 final size:25
Alignment explanation
Indices: 16843538--16843588 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 25
16843528 TTTACTTTTC
*
16843538 CCTATTGGTATTTAT-G-TTTTTGT
1 CCTATTGGTACTTATGGTTTTTTGT
16843561 CCTATT-GTACTTATGGTTTTTTGT
1 CCTATTGGTACTTATGGTTTTTTGT
16843585 CCTA
1 CCTA
16843589 GATTGACACC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 7 0.28
23 7 0.28
24 11 0.44
ACGTcount: A:0.14, C:0.14, G:0.16, T:0.57
Consensus pattern (25 bp):
CCTATTGGTACTTATGGTTTTTTGT
Found at i:16843797 original size:20 final size:21
Alignment explanation
Indices: 16843742--16843798 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 21
16843732 TTTCCCCTGT
* *
16843742 TCTTTGTCT-CTTCTCTCTCTC
1 TCTTTTTCTCCTT-TCTTTCTC
**
16843763 TCTTTTTCTTTTTTCTTTCTC
1 TCTTTTTCTCCTTTCTTTCTC
16843784 -CTTTTTCTCCTTTCT
1 TCTTTTTCTCCTTTCT
16843799 CTTTCATGAA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
20 13 0.43
21 15 0.50
22 2 0.07
ACGTcount: A:0.00, C:0.32, G:0.02, T:0.67
Consensus pattern (21 bp):
TCTTTTTCTCCTTTCTTTCTC
Found at i:16843866 original size:16 final size:16
Alignment explanation
Indices: 16843845--16843878 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
16843835 AATTTTCATT
16843845 ATTTTCTACCTCTTTC
1 ATTTTCTACCTCTTTC
*
16843861 ATTTTCTACCTTTTTC
1 ATTTTCTACCTCTTTC
16843877 AT
1 AT
16843879 CAGTTCATCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.15, C:0.26, G:0.00, T:0.59
Consensus pattern (16 bp):
ATTTTCTACCTCTTTC
Found at i:16860088 original size:18 final size:17
Alignment explanation
Indices: 16860042--16860084 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 17
16860032 TAATATCAAT
16860042 TAATAAAATATTATTAC
1 TAATAAAATATTATTAC
* *
16860059 TTATTAAAATATTATTAG
1 -TAATAAAATATTATTAC
16860077 TAATAAAA
1 TAATAAAA
16860085 ATATCATTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 7 0.32
18 15 0.68
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (17 bp):
TAATAAAATATTATTAC
Found at i:16865597 original size:10 final size:11
Alignment explanation
Indices: 16865565--16865591 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
16865555 AATTTGAAAT
16865565 TGAAAAAGGAG
1 TGAAAAAGGAG
16865576 TGAAAAAGGAG
1 TGAAAAAGGAG
16865587 TGAAA
1 TGAAA
16865592 TAGAGTAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.33, T:0.11
Consensus pattern (11 bp):
TGAAAAAGGAG
Found at i:16877751 original size:22 final size:23
Alignment explanation
Indices: 16877726--16877788 Score: 69
Period size: 22 Copynumber: 2.7 Consensus size: 23
16877716 AATAAAATTA
16877726 TATTAAAATTATTATTA-AATAT
1 TATTAAAATTATTATTAGAATAT
*
16877748 TATTAATAATTA-TATTAGTAATGT
1 TATTAA-AATTATTATTAG-AATAT
16877772 TATT-AAATTATATATTA
1 TATTAAAATTAT-TATTA
16877789 TTTTATTAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
22 16 0.46
23 6 0.17
24 13 0.37
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (23 bp):
TATTAAAATTATTATTAGAATAT
Found at i:16877787 original size:12 final size:11
Alignment explanation
Indices: 16877720--16877800 Score: 50
Period size: 12 Copynumber: 7.5 Consensus size: 11
16877710 CTTAATAATA
16877720 AAATTA-TATT
1 AAATTATTATT
16877730 AAAATTATTATT
1 -AAATTATTATT
16877742 AAA-TATTATT
1 AAATTATTATT
16877752 AATAATTA-TATT
1 -A-AATTATTATT
*
16877764 AGTAA-TGTTATT
1 A--AATTATTATT
16877776 AAATTATATATT
1 AAATTAT-TATT
16877788 --ATT-TTATT
1 AAATTATTATT
16877796 AAATT
1 AAATT
16877801 GTACTTAACA
Statistics
Matches: 58, Mismatches: 2, Indels: 21
0.72 0.02 0.26
Matches are distributed among these distances:
8 4 0.07
9 1 0.02
10 15 0.26
11 14 0.24
12 22 0.38
13 2 0.03
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (11 bp):
AAATTATTATT
Found at i:16877966 original size:43 final size:43
Alignment explanation
Indices: 16877917--16878000 Score: 114
Period size: 43 Copynumber: 2.0 Consensus size: 43
16877907 CTGAACAACT
* *
16877917 CAAAACTTACATAACCTAAATAACATACATAACTTACATAATA
1 CAAAACTCACATAACCTAAATAACATACACAACTTACATAATA
* ** *
16877960 CAAAACTCACATAACTTAAATCTCTTACACAACTTACATAA
1 CAAAACTCACATAACCTAAATAACATACACAACTTACATAA
16878001 CCTTCATAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 35 1.00
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.26
Consensus pattern (43 bp):
CAAAACTCACATAACCTAAATAACATACACAACTTACATAATA
Found at i:16878048 original size:19 final size:19
Alignment explanation
Indices: 16878024--16878174 Score: 62
Period size: 19 Copynumber: 8.5 Consensus size: 19
16878014 TTTAACTTAC
16878024 ATAACTTACATAATACATA
1 ATAACTTACATAATACATA
*
16878043 ATAACTTACA-ACTTACATA
1 ATAACTTACATA-ATACATA
* *
16878062 AT-ACAT-C-T-A-AC-TT
1 ATAACTTACATAATACATA
*
16878075 ACAACTTACATAATACAT-
1 ATAACTTACATAATACATA
* *
16878093 TTAACTTACA-ACTTACATA
1 ATAACTTACATA-ATACATA
*
16878112 AT-ACATT---T-A-ACTTA
1 ATAAC-TTACATAATACATA
* * *
16878126 CATAACTTACGTAATCCATC
1 -ATAACTTACATAATACATA
*
16878146 TTAACTTACATAATACATA
1 ATAACTTACATAATACATA
16878165 ATAACTTACA
1 ATAACTTACA
16878175 ACTTACATAA
Statistics
Matches: 93, Mismatches: 20, Indels: 38
0.62 0.13 0.25
Matches are distributed among these distances:
13 2 0.02
14 9 0.10
15 5 0.05
16 3 0.03
17 3 0.03
18 22 0.24
19 47 0.51
20 2 0.02
ACGTcount: A:0.45, C:0.21, G:0.01, T:0.34
Consensus pattern (19 bp):
ATAACTTACATAATACATA
Found at i:16878078 original size:25 final size:25
Alignment explanation
Indices: 16878005--16878184 Score: 219
Period size: 25 Copynumber: 7.2 Consensus size: 25
16877995 ACATAACCTT
16878005 CATAATACATTTAACTTACATAACTTA
1 CATAATACATTTAACTTAC--AACTTA
*
16878032 CATAATACATAATAACTTACAACTTA
1 CATAATACAT-TTAACTTACAACTTA
*
16878058 CATAATACATCTAACTTACAACTTA
1 CATAATACATTTAACTTACAACTTA
16878083 CATAATACATTTAACTTACAACTTA
1 CATAATACATTTAACTTACAACTTA
16878108 CATAATACATTTAACTTACATAACTTA
1 CATAATACATTTAACTTAC--AACTTA
* *
16878135 CGTAATCCA--T--CTT--AACTTA
1 CATAATACATTTAACTTACAACTTA
*
16878154 CATAATACATAATAACTTACAACTTA
1 CATAATACAT-TTAACTTACAACTTA
16878180 CATAA
1 CATAA
16878185 CATACATTAC
Statistics
Matches: 136, Mismatches: 7, Indels: 21
0.83 0.04 0.13
Matches are distributed among these distances:
19 13 0.10
22 1 0.01
23 3 0.02
24 3 0.02
25 58 0.43
26 27 0.20
27 23 0.17
28 8 0.06
ACGTcount: A:0.45, C:0.21, G:0.01, T:0.34
Consensus pattern (25 bp):
CATAATACATTTAACTTACAACTTA
Found at i:16878133 original size:9 final size:9
Alignment explanation
Indices: 16877920--16878347 Score: 194
Period size: 9 Copynumber: 49.8 Consensus size: 9
16877910 AACAACTCAA
16877920 AACTTACAT
1 AACTTACAT
* *
16877929 AACCTAAAT
1 AACTTACAT
*
16877938 AACATACAT
1 AACTTACAT
16877947 AACTTACAT
1 AACTTACAT
*
16877956 AA--TACAA
1 AACTTACAT
*
16877963 AACTCACAT
1 AACTTACAT
*
16877972 AACTTAAAT
1 AACTTACAT
** *
16877981 CTCTTACAC
1 AACTTACAT
16877990 AACTTACAT
1 AACTTACAT
16877999 AACCTT-CAT
1 AA-CTTACAT
16878008 AA--TACATTT
1 AACTTACA--T
16878017 AACTTACAT
1 AACTTACAT
16878026 AACTTACAT
1 AACTTACAT
*
16878035 AATACATA-AT
1 -A-ACTTACAT
16878045 AACTTAC--
1 AACTTACAT
16878052 AACTTACAT
1 AACTTACAT
16878061 AA--TACATCT
1 AACTTACA--T
16878070 AACTTAC--
1 AACTTACAT
16878077 AACTTACAT
1 AACTTACAT
16878086 AA--TACATTT
1 AACTTACA--T
16878095 AACTTAC--
1 AACTTACAT
16878102 AACTTACAT
1 AACTTACAT
16878111 AA--TACATTT
1 AACTTACA--T
16878120 AACTTACAT
1 AACTTACAT
*
16878129 AACTTACGT
1 AACTTACAT
* *
16878138 AA-TCCATCTT
1 AACT-TA-CAT
16878148 AACTTACAT
1 AACTTACAT
*
16878157 AATACATA-AT
1 -A-ACTTACAT
16878167 AACTTAC--
1 AACTTACAT
16878174 AACTTACAT
1 AACTTACAT
*
16878183 AACATACAT
1 AACTTACAT
* **
16878192 TACTTTGAT
1 AACTTACAT
16878201 AACTTACAT
1 AACTTACAT
16878210 AAC---C-T
1 AACTTACAT
16878215 -ACTTACAT
1 AACTTACAT
16878223 AACTTACAT
1 AACTTACAT
16878232 AACTTACAT
1 AACTTACAT
16878241 AACTTACAT
1 AACTTACAT
* *
16878250 TA--TACAC
1 AACTTACAT
*
16878257 AACTTACAC
1 AACTTACAT
16878266 AA--TACAT
1 AACTTACAT
*
16878273 TACTTACAT
1 AACTTACAT
*
16878282 AACGTAAAGCAT
1 AAC-T-TA-CAT
16878294 AA--TA-AT
1 AACTTACAT
16878300 AACTTACAT
1 AACTTACAT
*
16878309 AA--TACAC
1 AACTTACAT
16878316 AACTTACAT
1 AACTTACAT
* *
16878325 AGCTTACAC
1 AACTTACAT
16878334 AA--TACAT
1 AACTTACAT
16878341 AACTTAC
1 AACTTAC
16878348 CCGTGCAATT
Statistics
Matches: 315, Mismatches: 48, Indels: 112
0.66 0.10 0.24
Matches are distributed among these distances:
4 2 0.01
5 1 0.00
6 6 0.02
7 71 0.23
8 13 0.04
9 178 0.57
10 15 0.05
11 24 0.08
12 5 0.02
ACGTcount: A:0.45, C:0.22, G:0.01, T:0.32
Consensus pattern (9 bp):
AACTTACAT
Found at i:16878151 original size:103 final size:97
Alignment explanation
Indices: 16878025--16878242 Score: 225
Period size: 96 Copynumber: 2.2 Consensus size: 97
16878015 TTAACTTACA
* * *
16878025 TAACTTACATAA--TACATAATA-ACTTACAACTTACATAATACAT-CTAACTTACAACTTACAT
1 TAACTTACATAACTTACATAATACA-TAATAACTTACATAATACATAATAACTTACAACTTACAT
16878086 AATACATTTAACTTACAACTTACATAATACATT
65 AATACATTTAACTTACAACTTACATAATACATT
* * **
16878119 TAACTTACATAACTTACGTAATCCATCTTAACTTACATAATACATAATAACTTACAACTTACATA
1 TAACTTACATAACTTACATAATACATAATAACTTACATAATACATAATAACTTACAACTTACAT-
*
16878184 ACATACA-TT-ACTTTGATAACTTACATAACCTAC-TT
65 A-ATACATTTAAC-TT-ACAACTTACATAA--TACATT
16878219 ACATAACTTACATAACTTACATAA
1 ---TAACTTACATAACTTACATAA
16878243 CTTACATTAT
Statistics
Matches: 103, Mismatches: 8, Indels: 17
0.80 0.06 0.13
Matches are distributed among these distances:
94 12 0.12
96 24 0.23
97 20 0.19
98 5 0.05
99 17 0.17
100 2 0.02
101 3 0.03
103 20 0.19
ACGTcount: A:0.44, C:0.21, G:0.01, T:0.34
Consensus pattern (97 bp):
TAACTTACATAACTTACATAATACATAATAACTTACATAATACATAATAACTTACAACTTACATA
ATACATTTAACTTACAACTTACATAATACATT
Found at i:16878234 original size:31 final size:29
Alignment explanation
Indices: 16878147--16878244 Score: 100
Period size: 31 Copynumber: 3.5 Consensus size: 29
16878137 TAATCCATCT
16878147 TAACTTACATAA-TACATA-ATAACTTAC-
1 TAACTTACATAACTAC-TACATAACTTACA
* **
16878174 -AACTTACATAAC-A-TACATTACTTTGA
1 TAACTTACATAACTACTACATAACTTACA
16878200 TAACTTACATAACCTACTTACATAACTTACA
1 TAACTTACATAA-CTAC-TACATAACTTACA
16878231 TAACTTACATAACT
1 TAACTTACATAACT
16878245 TACATTATAC
Statistics
Matches: 57, Mismatches: 6, Indels: 13
0.75 0.08 0.17
Matches are distributed among these distances:
24 2 0.04
25 6 0.11
26 12 0.21
27 11 0.19
28 1 0.02
29 1 0.02
30 2 0.04
31 22 0.39
ACGTcount: A:0.44, C:0.21, G:0.01, T:0.34
Consensus pattern (29 bp):
TAACTTACATAACTACTACATAACTTACA
Found at i:16883844 original size:66 final size:65
Alignment explanation
Indices: 16883736--16883900 Score: 206
Period size: 66 Copynumber: 2.5 Consensus size: 65
16883726 GAGCAAATTA
* * * * *
16883736 CACAACTTAAAGCGGAGGCAACATCGAGAGAAGCTGATGTTCAA-AAAAGATATGAAGAACTCCA
1 CACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAG-TATGAAGAACTCCA
16883800 G
65 G
*
16883801 CTACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACGAAAGTATGAAGAACTCCA
1 C-ACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAGTATGAAGAACTCCA
16883866 G
65 G
* * * *
16883867 CAGCAGCTTAGAGCAGATGCGGCAGCAAGAGAAG
1 CA-CAACTTAAAGCAGATGCAGCAGCGAGAGAAG
16883901 TAGAGGCGGC
Statistics
Matches: 87, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
65 2 0.02
66 81 0.93
67 4 0.05
ACGTcount: A:0.40, C:0.19, G:0.27, T:0.14
Consensus pattern (65 bp):
CACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAGTATGAAGAACTCCAG
Found at i:16883911 original size:21 final size:21
Alignment explanation
Indices: 16883885--16883928 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
16883875 TAGAGCAGAT
16883885 GCGGCAGCAAGAGAAGTAGAG
1 GCGGCAGCAAGAGAAGTAGAG
** *
16883906 GCGGCAGGGAGAGAAGTATAG
1 GCGGCAGCAAGAGAAGTAGAG
16883927 GC
1 GC
16883929 TGCTAAGAGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.34, C:0.14, G:0.45, T:0.07
Consensus pattern (21 bp):
GCGGCAGCAAGAGAAGTAGAG
Found at i:16883959 original size:21 final size:21
Alignment explanation
Indices: 16883935--16883989 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
16883925 AGGCTGCTAA
16883935 GAGGGAAGCAGAGGCTAAAGC
1 GAGGGAAGCAGAGGCTAAAGC
** **
16883956 GAGGGAAATAGAGGCTGCAGC
1 GAGGGAAGCAGAGGCTAAAGC
16883977 GAGGGAAGCAGAG
1 GAGGGAAGCAGAG
16883990 CAGCGTTAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.36, C:0.13, G:0.45, T:0.05
Consensus pattern (21 bp):
GAGGGAAGCAGAGGCTAAAGC
Found at i:16884460 original size:43 final size:43
Alignment explanation
Indices: 16884413--16884504 Score: 141
Period size: 43 Copynumber: 2.1 Consensus size: 43
16884403 ACAAATGCCA
*
16884413 CTAAAGACCCT-GATCTATAGCGGCGCTTTTACCAAAAACGCCG
1 CTAAAGACCCTAG-TCTATAGCGGCGCTTATACCAAAAACGCCG
* *
16884456 CTAAAGACCCTAGTTTATAGCGGCGCTTATACCAAAAATGCCG
1 CTAAAGACCCTAGTCTATAGCGGCGCTTATACCAAAAACGCCG
16884499 CTAAAG
1 CTAAAG
16884505 GTATTACTCT
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
43 44 0.98
44 1 0.02
ACGTcount: A:0.33, C:0.27, G:0.18, T:0.22
Consensus pattern (43 bp):
CTAAAGACCCTAGTCTATAGCGGCGCTTATACCAAAAACGCCG
Found at i:16884521 original size:43 final size:42
Alignment explanation
Indices: 16884431--16884565 Score: 112
Period size: 43 Copynumber: 3.2 Consensus size: 42
16884421 CCTGATCTAT
* ** * *
16884431 AGCGGCGCTTTTACCAAAAACGCCGCTAAAGAC-CCTAGT-TTAT
1 AGCGGCGCTTATA-CAAAAACGCCGCTAAAG-CTATTACTCTT-C
* *
16884474 AGCGGCGCTTATACCAAAAATGCCGCTAAAGGTATTACTCTTC
1 AGCGGCGCTTATA-CAAAAACGCCGCTAAAGCTATTACTCTTC
* * * * *
16884517 AGCGGCGCTTCTACTAAAGCGCCGGTAAAGCTCTTACTCTTC
1 AGCGGCGCTTATACAAAAACGCCGCTAAAGCTATTACTCTTC
16884559 AGCGGCG
1 AGCGGCG
16884566 TTTGTGATAT
Statistics
Matches: 76, Mismatches: 14, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
42 30 0.39
43 44 0.58
44 2 0.03
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (42 bp):
AGCGGCGCTTATACAAAAACGCCGCTAAAGCTATTACTCTTC
Found at i:16884684 original size:22 final size:22
Alignment explanation
Indices: 16884656--16884699 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
16884646 CTGCGGCGCT
*
16884656 AAAAAGCGCCGCTAAAGGCCTA
1 AAAAAGCGCCGCTAAAAGCCTA
16884678 AAAAAGCGCCGCTAAAAGCCTA
1 AAAAAGCGCCGCTAAAAGCCTA
16884700 TTTTAGTGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.43, C:0.27, G:0.20, T:0.09
Consensus pattern (22 bp):
AAAAAGCGCCGCTAAAAGCCTA
Found at i:16886129 original size:16 final size:18
Alignment explanation
Indices: 16886103--16886135 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
16886093 TAAAAAAAAT
16886103 GTATAAAATATA-TACAG
1 GTATAAAATATACTACAG
16886120 GTAT-AAATATACTACA
1 GTATAAAATATACTACA
16886136 TAAAAAGATG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.52, C:0.09, G:0.09, T:0.30
Consensus pattern (18 bp):
GTATAAAATATACTACAG
Found at i:16886237 original size:25 final size:24
Alignment explanation
Indices: 16886158--16886237 Score: 63
Period size: 25 Copynumber: 3.2 Consensus size: 24
16886148 TATATATAGA
* * *
16886158 TATATTACAAAAAAAACCCATGCGAG
1 TATATTATATAAAAAA--CATGCGTG
* *
16886184 TATATTATAT-AAAAACATGCATATA
1 TATATTATATAAAAAACATGC--GTG
16886209 TATATTATATAAAAAACAATGCGTG
1 TATATTATATAAAAAAC-ATGCGTG
16886234 TATA
1 TATA
16886238 AATATAGAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 9
0.73 0.12 0.15
Matches are distributed among these distances:
23 5 0.12
25 20 0.47
26 14 0.33
27 4 0.09
ACGTcount: A:0.50, C:0.11, G:0.09, T:0.30
Consensus pattern (24 bp):
TATATTATATAAAAAACATGCGTG
Found at i:16887408 original size:17 final size:18
Alignment explanation
Indices: 16887381--16887414 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
16887371 ATTATGTAGT
16887381 GATTCAATACTTTAATTC
1 GATTCAATACTTTAATTC
16887399 GATT-AATACTTTAATT
1 GATTCAATACTTTAATT
16887415 TAGGTAATTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.35, C:0.12, G:0.06, T:0.47
Consensus pattern (18 bp):
GATTCAATACTTTAATTC
Found at i:16889397 original size:25 final size:25
Alignment explanation
Indices: 16889296--16889412 Score: 92
Period size: 25 Copynumber: 4.7 Consensus size: 25
16889286 CCATTATTTA
* * * *
16889296 GCTCTTATGAGCATCCCGTTAAATG
1 GCTCTCATGAGCTTCCCGATAATTG
*
16889321 GCTCTCATGAGCTTCCCGATATTTG
1 GCTCTCATGAGCTTCCCGATAATTG
* * ** *
16889346 GATTTCATGAGCTTTTCAATTAA-TG
1 GCTCTCATGAGCTTCCCGA-TAATTG
*
16889371 GCTCTCTTGAGCTTCCCGATAATTG
1 GCTCTCATGAGCTTCCCGATAATTG
** *
16889396 GCTAGCAAGAGCTTCCC
1 GCTCTCATGAGCTTCCC
16889413 TTTATACAAC
Statistics
Matches: 69, Mismatches: 21, Indels: 4
0.73 0.22 0.04
Matches are distributed among these distances:
24 3 0.04
25 64 0.93
26 2 0.03
ACGTcount: A:0.21, C:0.25, G:0.20, T:0.34
Consensus pattern (25 bp):
GCTCTCATGAGCTTCCCGATAATTG
Found at i:16891291 original size:24 final size:24
Alignment explanation
Indices: 16891264--16891322 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 24
16891254 CGAAAGAGCG
*
16891264 TCCTGTTA-ATAGCTCTCATGAGT
1 TCCTGTTATATAGCTCTCACGAGT
* *
16891287 ATCCTGATATTTAGCTCTCACGAGT
1 -TCCTGTTATATAGCTCTCACGAGT
*
16891312 TCCCGTTATAT
1 TCCTGTTATAT
16891323 GGTTGTTGCG
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
24 15 0.54
25 13 0.46
ACGTcount: A:0.22, C:0.24, G:0.15, T:0.39
Consensus pattern (24 bp):
TCCTGTTATATAGCTCTCACGAGT
Found at i:16891445 original size:25 final size:25
Alignment explanation
Indices: 16891417--16891481 Score: 78
Period size: 25 Copynumber: 2.6 Consensus size: 25
16891407 CTTATGAGTG
16891417 TCCCGA-TATATGGCTCTACGAAGCT
1 TCCCGATTA-ATGGCTCTACGAAGCT
* * *
16891442 TCCCAATTAATGGCTCTCCGGAGCT
1 TCCCGATTAATGGCTCTACGAAGCT
*
16891467 TCCCGATTAACGGCT
1 TCCCGATTAATGGCT
16891482 TGCTTGAACT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
25 32 0.94
26 2 0.06
ACGTcount: A:0.22, C:0.31, G:0.20, T:0.28
Consensus pattern (25 bp):
TCCCGATTAATGGCTCTACGAAGCT
Found at i:16891515 original size:49 final size:50
Alignment explanation
Indices: 16891462--16891570 Score: 125
Period size: 49 Copynumber: 2.2 Consensus size: 50
16891452 TGGCTCTCCG
** * **
16891462 GAGCTTCCCGATTA-ACGGCTTGCTTGAACTTTCCGATTACA-GCTCTTAT
1 GAGCTTCCCGATTACACGGCTCACATGAACTTTCC-ATTACAGGCTCACAT
*
16891511 GAGCTTCCC-ATTACACGGCTCACATGAGCTTTCCATTACATGGCTCACAT
1 GAGCTTCCCGATTACACGGCTCACATGAACTTTCCATTACA-GGCTCACAT
16891561 GAGCTTCCCG
1 GAGCTTCCCG
16891571 TGATATGGCT
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
48 10 0.20
49 25 0.50
50 15 0.30
ACGTcount: A:0.21, C:0.30, G:0.18, T:0.30
Consensus pattern (50 bp):
GAGCTTCCCGATTACACGGCTCACATGAACTTTCCATTACAGGCTCACAT
Found at i:16891523 original size:23 final size:24
Alignment explanation
Indices: 16891492--16891569 Score: 95
Period size: 25 Copynumber: 3.2 Consensus size: 24
16891482 TGCTTGAACT
* **
16891492 TTCCGATTACA-GCTCTTATGAGC
1 TTCCCATTACAGGCTCACATGAGC
16891515 TTCCCATTACACGGCTCACATGAGC
1 TTCCCATTACA-GGCTCACATGAGC
*
16891540 TTTCCATTACATGGCTCACATGAGC
1 TTCCCATTACA-GGCTCACATGAGC
16891565 TTCCC
1 TTCCC
16891570 GTGATATGGC
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
23 10 0.21
25 37 0.79
ACGTcount: A:0.22, C:0.32, G:0.15, T:0.31
Consensus pattern (24 bp):
TTCCCATTACAGGCTCACATGAGC
Found at i:16891581 original size:25 final size:25
Alignment explanation
Indices: 16891509--16891569 Score: 104
Period size: 25 Copynumber: 2.4 Consensus size: 25
16891499 TACAGCTCTT
*
16891509 ATGAGCTTCCCATTACACGGCTCAC
1 ATGAGCTTCCCATTACATGGCTCAC
*
16891534 ATGAGCTTTCCATTACATGGCTCAC
1 ATGAGCTTCCCATTACATGGCTCAC
16891559 ATGAGCTTCCC
1 ATGAGCTTCCC
16891570 GTGATATGGC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.23, C:0.33, G:0.16, T:0.28
Consensus pattern (25 bp):
ATGAGCTTCCCATTACATGGCTCAC
Found at i:16895499 original size:129 final size:130
Alignment explanation
Indices: 16895256--16895509 Score: 431
Period size: 129 Copynumber: 2.0 Consensus size: 130
16895246 TAAAATATTA
*
16895256 TTATTTTATAAAATAAATTATATTATTTTGAGAGTGTTATATTTTCTAAGCAAAAAATATAAAAA
1 TTATTTTATAAAATAAATTATATTATTTTGAGAGTGTTATATTTTCTAAACAAAAAATATAAAAA
* *
16895321 CAATAAGATTTAAATTTAAAACACTGTATTTTGATGATTTGTACTTTACCATTTCAACTAAATTT
66 CAATAAGATTTAAATTTAAAACACTGTATTTTGAAGATATGTACTTTACCATTTCAACTAAATTT
16895386 TTATTTTATAAAATAAATTATATTATTTTGAGAGTGTTATAATTTT-TAAACAAAAAATA-AAAA
1 TTATTTTATAAAATAAATTATATTATTTTGAGAGTGTTAT-ATTTTCTAAACAAAAAATATAAAA
* * *
16895449 ATAATTAGATTTAAATTTAAAACACTGTATTTTGAAGATATGTACTTTACCCTTTCAACTA
65 ACAATAAGATTTAAATTTAAAACACTGTATTTTGAAGATATGTACTTTACCATTTCAACTA
16895510 GATTCTTACT
Statistics
Matches: 117, Mismatches: 6, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
129 60 0.51
130 52 0.44
131 5 0.04
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (130 bp):
TTATTTTATAAAATAAATTATATTATTTTGAGAGTGTTATATTTTCTAAACAAAAAATATAAAAA
CAATAAGATTTAAATTTAAAACACTGTATTTTGAAGATATGTACTTTACCATTTCAACTAAATTT
Found at i:16912996 original size:24 final size:25
Alignment explanation
Indices: 16912948--16913009 Score: 74
Period size: 25 Copynumber: 2.5 Consensus size: 25
16912938 TTCAAATACA
*
16912948 ATTTTAGAATTTAGATTTTATTATT
1 ATTTTAGAATTTAGAATTTATTATT
*
16912973 ATTTTGGAATTT-GAATTTATTATTT
1 ATTTTAGAATTTAGAATTTATTA-TT
16912998 ATATTTA-AATTT
1 AT-TTTAGAATTT
16913010 TATTTTTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
24 9 0.28
25 20 0.62
26 3 0.09
ACGTcount: A:0.32, C:0.00, G:0.08, T:0.60
Consensus pattern (25 bp):
ATTTTAGAATTTAGAATTTATTATT
Found at i:16914711 original size:22 final size:22
Alignment explanation
Indices: 16914686--16914737 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
16914676 AAATAATAGC
16914686 ATATTAGA-AATTATATAATCTT
1 ATATTA-ATAATTATATAATCTT
* *
16914708 ATATTAATATTTATATAATTTT
1 ATATTAATAATTATATAATCTT
16914730 A-ATTAATA
1 ATATTAATA
16914738 TTTGAATAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
21 8 0.30
22 19 0.70
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (22 bp):
ATATTAATAATTATATAATCTT
Found at i:16914746 original size:21 final size:22
Alignment explanation
Indices: 16914696--16914740 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
16914686 ATATTAGAAA
16914696 TTATATAATCTTATATTAATAT
1 TTATATAATCTTATATTAATAT
*
16914718 TTATATAATTTTA-ATTAATAT
1 TTATATAATCTTATATTAATAT
16914739 TT
1 TT
16914741 GAATAAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (22 bp):
TTATATAATCTTATATTAATAT
Found at i:16918143 original size:21 final size:21
Alignment explanation
Indices: 16918117--16918163 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
16918107 TGAATTTATA
16918117 TTTTTTAGAATCATT-AATATT
1 TTTTTTAGAAT-ATTAAATATT
* *
16918138 TTTTTTATAATTTTAAATATT
1 TTTTTTAGAATATTAAATATT
16918159 TTTTT
1 TTTTT
16918164 ATAGTTTTGC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 2 0.09
21 21 0.91
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (21 bp):
TTTTTTAGAATATTAAATATT
Found at i:16918164 original size:20 final size:21
Alignment explanation
Indices: 16918132--16918171 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
16918122 TAGAATCATT
16918132 AATATTTTTTTTATAATTTTA
1 AATATTTTTTTTATAATTTTA
*
16918153 AATA-TTTTTTTATAGTTTT
1 AATATTTTTTTTATAATTTT
16918172 GCACTCATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (21 bp):
AATATTTTTTTTATAATTTTA
Found at i:16918328 original size:15 final size:16
Alignment explanation
Indices: 16918291--16918329 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
16918281 ATATTAATAC
*
16918291 TTTTTTA-ATTTTTAA
1 TTTTTTATATTTTGAA
16918306 TTTTTTATA-TTTGAA
1 TTTTTTATATTTTGAA
16918321 TTTTTTATA
1 TTTTTTATA
16918330 ACTTTTAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 21 0.95
16 1 0.05
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.72
Consensus pattern (16 bp):
TTTTTTATATTTTGAA
Found at i:16919868 original size:12 final size:12
Alignment explanation
Indices: 16919853--16919898 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
16919843 TAGCAACAAT
16919853 AACAGCAAAAAC
1 AACAGCAAAAAC
* *
16919865 AACAACAAAATC
1 AACAGCAAAAAC
*
16919877 AATAGCAAAAAC
1 AACAGCAAAAAC
*
16919889 AACACCAAAA
1 AACAGCAAAA
16919899 TATCAGGAAC
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.67, C:0.24, G:0.04, T:0.04
Consensus pattern (12 bp):
AACAGCAAAAAC
Found at i:16919883 original size:36 final size:36
Alignment explanation
Indices: 16919829--16919898 Score: 86
Period size: 36 Copynumber: 1.9 Consensus size: 36
16919819 AAAAAACCCA
* * * * *
16919829 AACAACAAAAAGAGTAGCAACAATAACAGCAAAAAC
1 AACAACAAAAACAATAGCAAAAACAACACCAAAAAC
*
16919865 AACAACAAAATCAATAGCAAAAACAACACCAAAA
1 AACAACAAAAACAATAGCAAAAACAACACCAAAA
16919899 TATCAGGAAC
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
36 28 1.00
ACGTcount: A:0.66, C:0.21, G:0.07, T:0.06
Consensus pattern (36 bp):
AACAACAAAAACAATAGCAAAAACAACACCAAAAAC
Found at i:16920221 original size:14 final size:14
Alignment explanation
Indices: 16920179--16920221 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
16920169 AGTAGTAAAA
*
16920179 ATAAATATATTATTT
1 ATAAA-ATATTATAT
*
16920194 ATAAAATGTTATAT
1 ATAAAATATTATAT
*
16920208 ATAAAATATCATAT
1 ATAAAATATTATAT
16920222 CACTTATTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
14 19 0.79
15 5 0.21
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (14 bp):
ATAAAATATTATAT
Found at i:16923529 original size:26 final size:26
Alignment explanation
Indices: 16923470--16923534 Score: 69
Period size: 26 Copynumber: 2.4 Consensus size: 26
16923460 CGTTTTAGGG
16923470 GTTAGGTTTTCTTTTCCTTTCATTTTTA
1 GTTAGG-TTT-TTTTCCTTTCATTTTTA
*
16923498 GATTAGGTTTTTTTCTTTTC-TTTTTAA
1 G-TTAGGTTTTTTTCCTTTCATTTTT-A
*
16923525 GTTAGATTTT
1 GTTAGGTTTT
16923535 AGTTTTGTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
26 13 0.39
27 11 0.33
28 4 0.12
29 5 0.15
ACGTcount: A:0.14, C:0.09, G:0.12, T:0.65
Consensus pattern (26 bp):
GTTAGGTTTTTTTCCTTTCATTTTTA
Found at i:16933644 original size:166 final size:166
Alignment explanation
Indices: 16933370--16933695 Score: 589
Period size: 166 Copynumber: 2.0 Consensus size: 166
16933360 CCAACAGCAG
*
16933370 ACAATTTTAGCTTTTTGCCGAATCCCATTTTCTGCGTTTCAGATACACACCTGGTTTTGTTTGAT
1 ACAATTTTAGCTTTTCGCCGAATCCCATTTTCTGCGTTTCAGATACACACCTGGTTTTGTTTGAT
*
16933435 GCTAAAACAGTCCCCGAGCACTCCAAAGCCTATAATTGAACAAATAACACTAATTTAATCTCACA
66 GCTAAAACAGTCCCCGAGCACTCCAAAGCCTATAATTGAACAAAGAACACTAATTTAATCTCACA
16933500 TAACGTGATCCCAAATCGAACTCGTATCAATAGAAA
131 TAACGTGATCCCAAATCGAACTCGTATCAATAGAAA
*
16933536 ACAATTTTAGCTTTTCGTCGAATCCCATTTTCTGCGTTTCAGATACACACCTGGTTTTGTTTGAT
1 ACAATTTTAGCTTTTCGCCGAATCCCATTTTCTGCGTTTCAGATACACACCTGGTTTTGTTTGAT
** *
16933601 GCTAAAACAGTCTTCGAGCACTCCAAAGCCTATAATTGAACAAAGAGCACTAATTTAATCTCACA
66 GCTAAAACAGTCCCCGAGCACTCCAAAGCCTATAATTGAACAAAGAACACTAATTTAATCTCACA
*
16933666 TAATGTGATCCCAAATCGAACTCGTATCAA
131 TAACGTGATCCCAAATCGAACTCGTATCAA
16933696 GGTTTTAACC
Statistics
Matches: 153, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
166 153 1.00
ACGTcount: A:0.32, C:0.24, G:0.13, T:0.31
Consensus pattern (166 bp):
ACAATTTTAGCTTTTCGCCGAATCCCATTTTCTGCGTTTCAGATACACACCTGGTTTTGTTTGAT
GCTAAAACAGTCCCCGAGCACTCCAAAGCCTATAATTGAACAAAGAACACTAATTTAATCTCACA
TAACGTGATCCCAAATCGAACTCGTATCAATAGAAA
Found at i:16937415 original size:53 final size:53
Alignment explanation
Indices: 16937349--16937454 Score: 212
Period size: 53 Copynumber: 2.0 Consensus size: 53
16937339 AAGACAGTGG
16937349 AAAATAAATAGAGTAAGCATTTAATGCTTAGTAAGTTCGTATAACATAGAATT
1 AAAATAAATAGAGTAAGCATTTAATGCTTAGTAAGTTCGTATAACATAGAATT
16937402 AAAATAAATAGAGTAAGCATTTAATGCTTAGTAAGTTCGTATAACATAGAATT
1 AAAATAAATAGAGTAAGCATTTAATGCTTAGTAAGTTCGTATAACATAGAATT
16937455 TAACTTACCA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.45, C:0.08, G:0.15, T:0.32
Consensus pattern (53 bp):
AAAATAAATAGAGTAAGCATTTAATGCTTAGTAAGTTCGTATAACATAGAATT
Found at i:16937870 original size:52 final size:50
Alignment explanation
Indices: 16937806--16937915 Score: 141
Period size: 52 Copynumber: 2.1 Consensus size: 50
16937796 AATTCATATC
16937806 CGGGAATGCTCATATGAGCACAT-AAACAGGAAGCTCACTCTCGAGCCGTATAA
1 CGGGAA-GCTCATATGAGC-CATGAAACAGGAAGCTCA-T-TCGAGCCGTATAA
* * * *
16937859 CGGGAAGCTCATGTGAGCCATGTAACGGGAAGCTCATTCGAGCTGTATAA
1 CGGGAAGCTCATATGAGCCATGAAACAGGAAGCTCATTCGAGCCGTATAA
16937909 CGGGAAG
1 CGGGAAG
16937916 TTCAAGCAAG
Statistics
Matches: 52, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
50 19 0.37
51 4 0.08
52 23 0.44
53 6 0.12
ACGTcount: A:0.31, C:0.22, G:0.28, T:0.19
Consensus pattern (50 bp):
CGGGAAGCTCATATGAGCCATGAAACAGGAAGCTCATTCGAGCCGTATAA
Found at i:16937884 original size:25 final size:24
Alignment explanation
Indices: 16937806--16937895 Score: 81
Period size: 25 Copynumber: 3.5 Consensus size: 24
16937796 AATTCATATC
*
16937806 CGGGAATGCTCATATGAGCACATAAA
1 CGGGAA-GCTCATATGAGC-CATTAA
* * *
16937832 CAGGAAGCTCACTCTCGAGCCGTATAA
1 CGGGAAGCTCA-TAT-GAGCCAT-TAA
*
16937859 CGGGAAGCTCATGTGAGCCATGTAA
1 CGGGAAGCTCATATGAGCCAT-TAA
16937884 CGGGAAGCTCAT
1 CGGGAAGCTCAT
16937896 TCGAGCTGTA
Statistics
Matches: 53, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
25 26 0.49
26 11 0.21
27 16 0.30
ACGTcount: A:0.31, C:0.23, G:0.27, T:0.19
Consensus pattern (24 bp):
CGGGAAGCTCATATGAGCCATTAA
Found at i:16937901 original size:25 final size:26
Alignment explanation
Indices: 16937834--16937915 Score: 105
Period size: 25 Copynumber: 3.2 Consensus size: 26
16937824 CACATAAACA
16937834 GGAAGCTCACTCTCGAGCCGTATAACG
1 GGAAGCTCA-TCTCGAGCCGTATAACG
* * *
16937861 GGAAGCTCATGT-GAGCCATGTAACG
1 GGAAGCTCATCTCGAGCCGTATAACG
*
16937886 GGAAGCTCAT-TCGAGCTGTATAACG
1 GGAAGCTCATCTCGAGCCGTATAACG
16937911 GGAAG
1 GGAAG
16937916 TTCAAGCAAG
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
24 1 0.02
25 36 0.75
26 2 0.04
27 9 0.19
ACGTcount: A:0.28, C:0.22, G:0.30, T:0.20
Consensus pattern (26 bp):
GGAAGCTCATCTCGAGCCGTATAACG
Found at i:16939028 original size:27 final size:26
Alignment explanation
Indices: 16938998--16939219 Score: 194
Period size: 27 Copynumber: 8.3 Consensus size: 26
16938988 CCCAAAATAA
* *
16938998 GTAAAATAACCAAAATAACCCCATAGA
1 GTAAAATGACCAAAAT-ACCCCATAGG
* *
16939025 GTAAAATGACCGAAATACCCTATAGG
1 GTAAAATGACCAAAATACCCCATAGG
*
16939051 GTAAAATGACCAAAATACCCCCGTAGG
1 GTAAAATGACCAAAATA-CCCCATAGG
* * *
16939078 GTAAAAT-AACAGAAATACCCTAACAGG
1 GTAAAATGACCA-AAATACCC-CATAGG
* * * *
16939105 GGAAAATGATCGAAATACCCCTATAAG
1 GTAAAATGACCAAAATACCCC-ATAGG
* ** * *
16939132 GTAAAATAACTGAAATGCCCCCTAGG
1 GTAAAATGACCAAAATACCCCATAGG
*
16939158 ATAAAATGACCAAAATACCCCCCATAGG
1 GTAAAATGACCAAAATA--CCCCATAGG
*
16939186 GTAAAATGACCGAAATACCCCCATAGG
1 GTAAAATGACCAAAATA-CCCCATAGG
16939213 GTAAAAT
1 GTAAAAT
16939220 AACTGTTATG
Statistics
Matches: 156, Mismatches: 32, Indels: 14
0.77 0.16 0.07
Matches are distributed among these distances:
26 45 0.29
27 86 0.55
28 25 0.16
ACGTcount: A:0.45, C:0.22, G:0.16, T:0.17
Consensus pattern (26 bp):
GTAAAATGACCAAAATACCCCATAGG
Found at i:16939082 original size:53 final size:53
Alignment explanation
Indices: 16938998--16939219 Score: 246
Period size: 54 Copynumber: 4.1 Consensus size: 53
16938988 CCCAAAATAA
* * * * *
16938998 GTAAAATAACCAAAATAACCCCATAGAGTAAAATGACCGAAATACCCTATAGG
1 GTAAAATGACCAAAATACCCCCATAGGGTAAAATAACCGAAATACCCCATAGG
* * * *
16939051 GTAAAATGACCAAAATACCCCCGTAGGGTAAAATAACAGAAATACCCTAACAGG
1 GTAAAATGACCAAAATACCCCCATAGGGTAAAATAACCGAAATACCC-CATAGG
* * * * * * * *
16939105 GGAAAATGATCGAAATACCCCTATAAGGTAAAATAACTGAAATGCCCCCTAGG
1 GTAAAATGACCAAAATACCCCCATAGGGTAAAATAACCGAAATACCCCATAGG
* *
16939158 ATAAAATGACCAAAATACCCCCCATAGGGTAAAATGACCGAAATACCCCCATAGG
1 GTAAAATGACCAAAATA-CCCCCATAGGGTAAAATAACCGAAATA-CCCCATAGG
16939213 GTAAAAT
1 GTAAAAT
16939220 AACTGTTATG
Statistics
Matches: 136, Mismatches: 30, Indels: 4
0.80 0.18 0.02
Matches are distributed among these distances:
53 57 0.42
54 65 0.48
55 14 0.10
ACGTcount: A:0.45, C:0.22, G:0.16, T:0.17
Consensus pattern (53 bp):
GTAAAATGACCAAAATACCCCCATAGGGTAAAATAACCGAAATACCCCATAGG
Found at i:16942677 original size:27 final size:27
Alignment explanation
Indices: 16942646--16942948 Score: 333
Period size: 27 Copynumber: 11.3 Consensus size: 27
16942636 CCCTAAAATA
*
16942646 GGTAAAATAACCAAAATACCCCCATAG
1 GGTAAAATGACCAAAATACCCCCATAG
* *
16942673 GGTAAAATGACC-AAATA-TCTCATAG
1 GGTAAAATGACCAAAATACCCCCATAG
* **
16942698 GGTAAAATAACCAAAATACCCTTATAG
1 GGTAAAATGACCAAAATACCCCCATAG
* *
16942725 GGTAAAAT-AACAGAAATACGCCCATAG
1 GGTAAAATGACCA-AAATACCCCCATAG
* * *
16942752 GGTAAAATGACCGAAATGCCCTCATAG
1 GGTAAAATGACCAAAATACCCCCATAG
* *
16942779 GGTAAAATGACAAAAATACCCCCATAA
1 GGTAAAATGACCAAAATACCCCCATAG
* * * *
16942806 AGAAAAATGACCAAAATATCGCCATAG
1 GGTAAAATGACCAAAATACCCCCATAG
* *
16942833 GGTAAAATGACTAAAATACCCCTATAG
1 GGTAAAATGACCAAAATACCCCCATAG
** * *
16942860 AATAAAATGACTAAAATACCCTCATAG
1 GGTAAAATGACCAAAATACCCCCATAG
* * *
16942887 GGTAAAATAATCGAAATACCCCCATAG
1 GGTAAAATGACCAAAATACCCCCATAG
*
16942914 GGTAAAATGACCGAAATACCCCCATAG
1 GGTAAAATGACCAAAATACCCCCATAG
16942941 GGTAAAAT
1 GGTAAAAT
16942949 AATTGTTATA
Statistics
Matches: 227, Mismatches: 45, Indels: 8
0.81 0.16 0.03
Matches are distributed among these distances:
25 17 0.07
26 13 0.06
27 195 0.86
28 2 0.01
ACGTcount: A:0.47, C:0.20, G:0.15, T:0.18
Consensus pattern (27 bp):
GGTAAAATGACCAAAATACCCCCATAG
Found at i:16942823 original size:81 final size:81
Alignment explanation
Indices: 16942646--16942948 Score: 371
Period size: 81 Copynumber: 3.8 Consensus size: 81
16942636 CCCTAAAATA
* *
16942646 GGTAAAATAACCAAAATACCCCCATAGGGTAAAATGACC-AAATA-TCTCATAGGGTAAAATAAC
1 GGTAAAATAACCAAAATACCCCCATAGGGTAAAATGACCGAAATACCCTCATAGGGTAAAATGAC
* *
16942709 CAAAATACCCTTATAG
66 AAAAATACCCTCATAG
* *
16942725 GGTAAAATAA-CAGAAATACGCCCATAGGGTAAAATGACCGAAATGCCCTCATAGGGTAAAATGA
1 GGTAAAATAACCA-AAATACCCCCATAGGGTAAAATGACCGAAATACCCTCATAGGGTAAAATGA
* *
16942789 CAAAAATACCCCCATAA
65 CAAAAATACCCTCATAG
* * * * * ** **
16942806 AGAAAAATGACCAAAATATCGCCATAGGGTAAAATGACTAAAATACCC-CTATAGAATAAAATGA
1 GGTAAAATAACCAAAATACCCCCATAGGGTAAAATGACCGAAATACCCTC-ATAGGGTAAAATGA
*
16942870 CTAAAATACCCTCATAG
65 CAAAAATACCCTCATAG
* * *
16942887 GGTAAAATAATCGAAATACCCCCATAGGGTAAAATGACCGAAATACCCCCATAGGGTAAAAT
1 GGTAAAATAACCAAAATACCCCCATAGGGTAAAATGACCGAAATACCCTCATAGGGTAAAAT
16942949 AATTGTTATA
Statistics
Matches: 185, Mismatches: 33, Indels: 10
0.81 0.14 0.04
Matches are distributed among these distances:
78 2 0.01
79 35 0.19
80 5 0.03
81 140 0.76
82 3 0.02
ACGTcount: A:0.47, C:0.20, G:0.15, T:0.18
Consensus pattern (81 bp):
GGTAAAATAACCAAAATACCCCCATAGGGTAAAATGACCGAAATACCCTCATAGGGTAAAATGAC
AAAAATACCCTCATAG
Found at i:16951166 original size:21 final size:22
Alignment explanation
Indices: 16951126--16951167 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
16951116 TATATAATTC
*
16951126 ACATATACAACATTCAATTTAA
1 ACATATACAACATACAATTTAA
*
16951148 ACATATA-AATATACAATTTA
1 ACATATACAACATACAATTTA
16951168 GTTACACGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.52, C:0.14, G:0.00, T:0.33
Consensus pattern (22 bp):
ACATATACAACATACAATTTAA
Found at i:16956539 original size:23 final size:23
Alignment explanation
Indices: 16956512--16956587 Score: 134
Period size: 23 Copynumber: 3.3 Consensus size: 23
16956502 AATGTTATTG
16956512 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* *
16956535 TTCAGTGGTAGCTACGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
16956558 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
16956581 ATCAGTG
1 ATCAGTG
16956588 TGGTACTTAT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 49 1.00
ACGTcount: A:0.22, C:0.21, G:0.26, T:0.30
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:16966194 original size:16 final size:17
Alignment explanation
Indices: 16966154--16966195 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
16966144 AATCCAGTTC
16966154 GTGTTTTCAAAAAAGTCT
1 GTGTTTTCAAAAAAG-CT
* *
16966172 TTGTTTTCATAAAA-CT
1 GTGTTTTCAAAAAAGCT
16966188 GTGTTTTC
1 GTGTTTTC
16966196 CATCATGCAT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
16 9 0.43
18 12 0.57
ACGTcount: A:0.26, C:0.12, G:0.14, T:0.48
Consensus pattern (17 bp):
GTGTTTTCAAAAAAGCT
Found at i:16984691 original size:36 final size:33
Alignment explanation
Indices: 16984615--16984724 Score: 98
Period size: 33 Copynumber: 3.2 Consensus size: 33
16984605 ATTTTGTTCC
*
16984615 AAGTTTGTTGCAATAAATCTAATTTAAATTACA
1 AAGTTTGTTCCAATAAATCTAATTTAAATTACA
16984648 ACA-TTTGTTCCAATAAATCTCAA-TTAAATAAATACA
1 A-AGTTTGTTCCAATAAATCT-AATTTAAAT---TACA
* * * * *
16984684 AAGTTTGTTCAAACATATGTCATTTAAAATTACA
1 AAGTTTGTTCCAATAAATCTAATTT-AAATTACA
16984718 AAGTTTG
1 AAGTTTG
16984725 AATTTTCGCA
Statistics
Matches: 63, Mismatches: 6, Indels: 15
0.75 0.07 0.18
Matches are distributed among these distances:
33 23 0.37
34 14 0.22
35 2 0.03
36 20 0.32
37 4 0.06
ACGTcount: A:0.43, C:0.12, G:0.08, T:0.37
Consensus pattern (33 bp):
AAGTTTGTTCCAATAAATCTAATTTAAATTACA
Found at i:16986537 original size:22 final size:22
Alignment explanation
Indices: 16986512--16986562 Score: 52
Period size: 22 Copynumber: 2.3 Consensus size: 22
16986502 AAATAAATTA
*
16986512 AAAATAACATAAA-AATGAC-AAT
1 AAAATAAC-TAAATAAT-ACTAAC
*
16986534 AAAAAAACTAAATAATACTAAC
1 AAAATAACTAAATAATACTAAC
16986556 AAAATAA
1 AAAATAA
16986563 TTTATAATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
21 6 0.25
22 18 0.75
ACGTcount: A:0.71, C:0.10, G:0.02, T:0.18
Consensus pattern (22 bp):
AAAATAACTAAATAATACTAAC
Found at i:16990021 original size:97 final size:97
Alignment explanation
Indices: 16989855--16990050 Score: 392
Period size: 97 Copynumber: 2.0 Consensus size: 97
16989845 TTTAGGGACT
16989855 GTCTCAAAGTTTGGCATGTTACTTTAAAATAACTAGGTTGCCCACCAGAACTGTCATATAGAGAG
1 GTCTCAAAGTTTGGCATGTTACTTTAAAATAACTAGGTTGCCCACCAGAACTGTCATATAGAGAG
16989920 AAAAATTGTAGATTGGAGAAGAGATCACTTGG
66 AAAAATTGTAGATTGGAGAAGAGATCACTTGG
16989952 GTCTCAAAGTTTGGCATGTTACTTTAAAATAACTAGGTTGCCCACCAGAACTGTCATATAGAGAG
1 GTCTCAAAGTTTGGCATGTTACTTTAAAATAACTAGGTTGCCCACCAGAACTGTCATATAGAGAG
16990017 AAAAATTGTAGATTGGAGAAGAGATCACTTGG
66 AAAAATTGTAGATTGGAGAAGAGATCACTTGG
16990049 GT
1 GT
16990051 TTCTTGCTAA
Statistics
Matches: 99, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
97 99 1.00
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28
Consensus pattern (97 bp):
GTCTCAAAGTTTGGCATGTTACTTTAAAATAACTAGGTTGCCCACCAGAACTGTCATATAGAGAG
AAAAATTGTAGATTGGAGAAGAGATCACTTGG
Found at i:16995047 original size:43 final size:43
Alignment explanation
Indices: 16994999--16995086 Score: 176
Period size: 43 Copynumber: 2.0 Consensus size: 43
16994989 AATGTTTTAG
16994999 AAAAAGACACTTATCCTTGTTGAATTGATAAAATCTCAATTAT
1 AAAAAGACACTTATCCTTGTTGAATTGATAAAATCTCAATTAT
16995042 AAAAAGACACTTATCCTTGTTGAATTGATAAAATCTCAATTAT
1 AAAAAGACACTTATCCTTGTTGAATTGATAAAATCTCAATTAT
16995085 AA
1 AA
16995087 TCATAAATTT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.43, C:0.14, G:0.09, T:0.34
Consensus pattern (43 bp):
AAAAAGACACTTATCCTTGTTGAATTGATAAAATCTCAATTAT
Found at i:17004657 original size:10 final size:10
Alignment explanation
Indices: 17004608--17004655 Score: 53
Period size: 10 Copynumber: 4.9 Consensus size: 10
17004598 TAAATTCCTA
17004608 AAAGATAAAT
1 AAAGATAAAT
** *
17004618 AAATTTAATT
1 AAAGATAAAT
*
17004628 GAAGATAAAT
1 AAAGATAAAT
17004638 AAAGATAAAT
1 AAAGATAAAT
17004648 AAA-ATAAA
1 AAAGATAAA
17004656 ATCCTAAAAA
Statistics
Matches: 30, Mismatches: 8, Indels: 1
0.77 0.21 0.03
Matches are distributed among these distances:
9 5 0.17
10 25 0.83
ACGTcount: A:0.67, C:0.00, G:0.08, T:0.25
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:17007185 original size:22 final size:21
Alignment explanation
Indices: 17007112--17007199 Score: 56
Period size: 22 Copynumber: 4.1 Consensus size: 21
17007102 AACCACATAA
**
17007112 TTTGAATATA-TTTAA-AACT
1 TTTGAATATATTTTAATATTT
* *
17007131 TTTAAATATATCTTTTTATAATTT
1 TTTGAATATA--TTTTAAT-ATTT
17007155 TTTGAATAT-TTTATACATATTT
1 TTTGAATATATTT-TA-ATATTT
**
17007177 TTTTTATATATTTTAATATTT
1 TTTGAATATATTTTAATATTT
17007198 TT
1 TT
17007200 AATTTTAATT
Statistics
Matches: 53, Mismatches: 8, Indels: 14
0.71 0.11 0.19
Matches are distributed among these distances:
19 9 0.17
21 11 0.21
22 18 0.34
23 5 0.09
24 10 0.19
ACGTcount: A:0.33, C:0.03, G:0.02, T:0.61
Consensus pattern (21 bp):
TTTGAATATATTTTAATATTT
Found at i:17010783 original size:13 final size:14
Alignment explanation
Indices: 17010760--17010788 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
17010750 CTAATTTTAA
17010760 TATTATTAATATTT
1 TATTATTAATATTT
17010774 TATT-TTAATATTT
1 TATTATTAATATTT
17010787 TA
1 TA
17010789 AAAATACATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (14 bp):
TATTATTAATATTT
Found at i:17013759 original size:24 final size:24
Alignment explanation
Indices: 17013722--17013777 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 24
17013712 TATACAGAAT
* * *
17013722 CAAATGTATTTTCATAACCAGATA
1 CAAATGCATATTCAGAACCAGATA
* **
17013746 CAGATGCATATTCAGATTCAGATA
1 CAAATGCATATTCAGAACCAGATA
17013770 CAAATGCA
1 CAAATGCA
17013778 GACACAGGTC
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.41, C:0.18, G:0.12, T:0.29
Consensus pattern (24 bp):
CAAATGCATATTCAGAACCAGATA
Found at i:17019104 original size:21 final size:21
Alignment explanation
Indices: 17019078--17019121 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
17019068 CATACATCTG
17019078 AAATATCATAAGCATACACAC
1 AAATATCATAAGCATACACAC
17019099 AAATATCATAAGCATACACAC
1 AAATATCATAAGCATACACAC
17019120 AA
1 AA
17019122 CTAGGGGTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.55, C:0.23, G:0.05, T:0.18
Consensus pattern (21 bp):
AAATATCATAAGCATACACAC
Found at i:17021059 original size:46 final size:46
Alignment explanation
Indices: 17021009--17021097 Score: 169
Period size: 46 Copynumber: 1.9 Consensus size: 46
17020999 CATAGAATGA
17021009 GTTTGGCATAGAGAGAGACTCAAACCTAAGATCTAAGAGTTGAGAG
1 GTTTGGCATAGAGAGAGACTCAAACCTAAGATCTAAGAGTTGAGAG
*
17021055 GTTTGGCATAGAGAGAGACTCAAACCTAAGATTTAAGAGTTGA
1 GTTTGGCATAGAGAGAGACTCAAACCTAAGATCTAAGAGTTGA
17021098 CTGACCTCTC
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 42 1.00
ACGTcount: A:0.37, C:0.12, G:0.27, T:0.24
Consensus pattern (46 bp):
GTTTGGCATAGAGAGAGACTCAAACCTAAGATCTAAGAGTTGAGAG
Found at i:17024813 original size:22 final size:25
Alignment explanation
Indices: 17024788--17024839 Score: 76
Period size: 24 Copynumber: 2.2 Consensus size: 25
17024778 ATCAGAGTTG
17024788 ATGTAGACA-CTT-ATTTT-TTGAC
1 ATGTAGACATCTTAATTTTGTTGAC
17024810 ATGT-GACATCTTAATTTTGTTGAC
1 ATGTAGACATCTTAATTTTGTTGAC
17024834 ATGTAG
1 ATGTAG
17024840 CAATTGTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
21 4 0.15
22 7 0.27
23 5 0.19
24 9 0.35
25 1 0.04
ACGTcount: A:0.27, C:0.12, G:0.17, T:0.44
Consensus pattern (25 bp):
ATGTAGACATCTTAATTTTGTTGAC
Found at i:17025575 original size:69 final size:70
Alignment explanation
Indices: 17025433--17025585 Score: 190
Period size: 69 Copynumber: 2.2 Consensus size: 70
17025423 CTATTTTCAT
* * * *
17025433 AAAAAATTAATTTTAATCTCACATTAACTAGAGAATACTCATATAGCTCACTTTTTACTATTTTT
1 AAAAAATTAATTTTAATCTCACATTAACTAGAGAATACTCATATAGCTCAATTTTCACTAATTTC
17025498 ATTGA
66 ATTGA
* * *
17025503 AAAAAATT-ATTTTAATCTCTCATTGACTAGAGAATACTC-TCATAGTTCAATTCTTCACTAATT
1 AAAAAATTAATTTTAATCTCACATTAACTAGAGAATACTCAT-ATAGCTCAATT-TTCACTAATT
17025566 TCATT--
64 TCATTGA
17025571 -AAAAATTAATTTTAA
1 AAAAAATTAATTTTAA
17025586 CTAGAGAATA
Statistics
Matches: 73, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
67 7 0.10
68 8 0.11
69 38 0.52
70 20 0.27
ACGTcount: A:0.39, C:0.14, G:0.05, T:0.41
Consensus pattern (70 bp):
AAAAAATTAATTTTAATCTCACATTAACTAGAGAATACTCATATAGCTCAATTTTCACTAATTTC
ATTGA
Found at i:17028181 original size:67 final size:67
Alignment explanation
Indices: 17028095--17028263 Score: 184
Period size: 67 Copynumber: 2.5 Consensus size: 67
17028085 AGTGATAATT
* * * * * * *
17028095 TCTTCACCATTTTTCTTAAAAAAGTTAATTTTAATCT-CATATTGACTAGATAATACTCTTATAA
1 TCTTCACTATTTTTATTAAAAAA-TTAATTTTAATCTCCACACTGACTAAAGAATACTC-GATAA
17028159 CTCA
64 CTCA
*
17028163 -CTTCACTATTTTTATTAAAAAATTAATTTTAAT-TCCACACTGATTAAAGAATACTCGATAACT
1 TCTTCACTATTTTTATTAAAAAATTAATTTTAATCTCCACACTGACTAAAGAATACTCGATAACT
17028226 CA
66 CA
* *
17028228 CTTCTTCACTAGTTTCATTAAAAAA-TAATTTTAATC
1 --TCTTCACTATTTTTATTAAAAAATTAATTTTAATC
17028264 CCTCATTGGC
Statistics
Matches: 86, Mismatches: 10, Indels: 10
0.81 0.09 0.09
Matches are distributed among these distances:
65 9 0.10
66 27 0.31
67 30 0.35
68 20 0.23
ACGTcount: A:0.37, C:0.17, G:0.04, T:0.41
Consensus pattern (67 bp):
TCTTCACTATTTTTATTAAAAAATTAATTTTAATCTCCACACTGACTAAAGAATACTCGATAACT
CA
Found at i:17030379 original size:18 final size:19
Alignment explanation
Indices: 17030358--17030397 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
17030348 ACTAATAAAT
17030358 TTTAATATAAGAT-ATTTA
1 TTTAATATAAGATAATTTA
* *
17030376 TTTAATATTATATAATTTA
1 TTTAATATAAGATAATTTA
17030395 TTT
1 TTT
17030398 TTATTATCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (19 bp):
TTTAATATAAGATAATTTA
Found at i:17040995 original size:35 final size:35
Alignment explanation
Indices: 17040946--17041016 Score: 115
Period size: 35 Copynumber: 2.0 Consensus size: 35
17040936 GTCAATCTAG
*
17040946 AGGTAAAGATAGATGCCGAGACAAATGGCGGAGAT
1 AGGTAAAGACAGATGCCGAGACAAATGGCGGAGAT
* *
17040981 AGGTAAAGACAGATGCCGAGGCAAATGGTGGAGAT
1 AGGTAAAGACAGATGCCGAGACAAATGGCGGAGAT
17041016 A
1 A
17041017 CCGACCTTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.39, C:0.11, G:0.35, T:0.14
Consensus pattern (35 bp):
AGGTAAAGACAGATGCCGAGACAAATGGCGGAGAT
Found at i:17042658 original size:25 final size:24
Alignment explanation
Indices: 17042606--17042657 Score: 70
Period size: 26 Copynumber: 2.1 Consensus size: 24
17042596 TTGAATATTA
*
17042606 TTTAATATTTTTTATTTTATGTAAT
1 TTTAATAATTTTTATTTTA-GTAAT
17042631 TTTAATTAATTTTTATTTTA-TAAT
1 TTTAA-TAATTTTTATTTTAGTAAT
17042655 TTT
1 TTT
17042658 TTATAACAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 7 0.28
25 5 0.20
26 13 0.52
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (24 bp):
TTTAATAATTTTTATTTTAGTAAT
Found at i:17042659 original size:26 final size:26
Alignment explanation
Indices: 17042582--17042660 Score: 67
Period size: 26 Copynumber: 3.0 Consensus size: 26
17042572 AATGGTATGG
*
17042582 ATTAATTTTAATTTT-TGAATATTATTTA
1 ATTAATTTTTATTTTAT-AAT-TT-TTTA
*
17042610 A-TATTTTTTATTTTATGTAA--TTTTA
1 ATTAATTTTTATTTTA--TAATTTTTTA
17042635 ATTAATTTTTATTTTATAATTTTTTA
1 ATTAATTTTTATTTTATAATTTTTTA
17042661 TAACAGTTTG
Statistics
Matches: 42, Mismatches: 3, Indels: 14
0.71 0.05 0.24
Matches are distributed among these distances:
24 3 0.07
25 5 0.12
26 19 0.45
27 11 0.26
28 1 0.02
29 2 0.05
30 1 0.02
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.66
Consensus pattern (26 bp):
ATTAATTTTTATTTTATAATTTTTTA
Found at i:17044219 original size:18 final size:18
Alignment explanation
Indices: 17044196--17044230 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
17044186 GTCAGGTGCG
*
17044196 TATCCTAGCCCTTATATA
1 TATCCTAACCCTTATATA
17044214 TATCCTAACCCTTATAT
1 TATCCTAACCCTTATAT
17044231 GTTTCTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.29, C:0.29, G:0.03, T:0.40
Consensus pattern (18 bp):
TATCCTAACCCTTATATA
Found at i:17044687 original size:29 final size:28
Alignment explanation
Indices: 17044654--17044738 Score: 75
Period size: 29 Copynumber: 2.9 Consensus size: 28
17044644 GTACAAACTT
17044654 ATTTATATTGTTTTATTTAATAAAATAAA
1 ATTTATATT-TTTTATTTAATAAAATAAA
* * *
17044683 ATTTAT-TTTTAATATTTTAATAGTAAATTAT
1 ATTTATATTTT-TTA-TTTAATA--AAATAAA
*
17044714 TTTTATA-TTTTTATTTAATAAAATA
1 ATTTATATTTTTTATTTAATAAAATA
17044739 GAAGTTCTTT
Statistics
Matches: 45, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
27 6 0.13
28 4 0.09
29 20 0.44
30 2 0.04
31 13 0.29
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.56
Consensus pattern (28 bp):
ATTTATATTTTTTATTTAATAAAATAAA
Found at i:17044704 original size:24 final size:23
Alignment explanation
Indices: 17044677--17044724 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 23
17044667 TATTTAATAA
17044677 AATA-AAATTTATTTTTAATATTTT
1 AATAGAAA-TTATTTTT-ATATTTT
17044701 AATAGTAAATTATTTTTATATTTT
1 AATAG-AAATTATTTTTATATTTT
17044725 TATTTAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 11 0.50
25 8 0.36
26 3 0.14
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (23 bp):
AATAGAAATTATTTTTATATTTT
Found at i:17044763 original size:58 final size:59
Alignment explanation
Indices: 17044655--17044767 Score: 131
Period size: 58 Copynumber: 1.9 Consensus size: 59
17044645 TACAAACTTA
* * ****
17044655 TTTATATTGTTTTATTTAATAAAATAAAATTTATTTTTAATATTTTAATAGTAAATTATT
1 TTTATATTGTTTTATTTAATAAAATAAAAGTTATTTTGAATAAGGCAATAG-AAATTATT
* *
17044715 TTTATA-T-TTTTATTTAATAAAATAGAAGTTCTTTTGAATAAGGCAATAGAAAT
1 TTTATATTGTTTTATTTAATAAAATAAAAGTTATTTTGAATAAGGCAATAGAAAT
17044768 AATGCAACAT
Statistics
Matches: 45, Mismatches: 8, Indels: 3
0.80 0.14 0.05
Matches are distributed among these distances:
57 4 0.09
58 34 0.76
59 1 0.02
60 6 0.13
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.50
Consensus pattern (59 bp):
TTTATATTGTTTTATTTAATAAAATAAAAGTTATTTTGAATAAGGCAATAGAAATTATT
Found at i:17047767 original size:126 final size:126
Alignment explanation
Indices: 17047599--17048121 Score: 859
Period size: 126 Copynumber: 4.2 Consensus size: 126
17047589 TAACGCCAAA
* * * *
17047599 CAGGAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCATCAATTTTGTTGTCAGTGC
1 CAGGAACTACTGTAGAAAAAGAACGTCCACGTAGGAGCTTTTTTCATCAATTTTGCTGACAGTGC
* * * *
17047664 ATCTTGCTTGAAGTGTTTTTGACACTATTTGTTTAGAAGCGTCTTCTCAAAATTATTTTTT
66 ATCCTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAACCGTCTTCTCAAAATTATTTTTT
* * *
17047725 CAGGAGCTACTGTAGAAAAAGAATGTCCACGTATGAGCTTTTTTCATCAATTTTGCTGACAGTGC
1 CAGGAACTACTGTAGAAAAAGAACGTCCACGTAGGAGCTTTTTTCATCAATTTTGCTGACAGTGC
* * * *
17047790 ATCCTGCTTGAAGCATTTTTGACACTATTTTTTCAAAACTGTCTTCTCAAAATTATTTTTT
66 ATCCTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAACCGTCTTCTCAAAATTATTTTTT
* *
17047851 CAGGAACTACTGTAGAAAAAGAGCGTCCACATAGGAGC-TTTTTCATCAATTTTGCTGACAGTGC
1 CAGGAACTACTGTAGAAAAAGAACGTCCACGTAGGAGCTTTTTTCATCAATTTTGCTGACAGTGC
17047915 ATCCTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAACCGTCTTCTCAAAATTATTTTTT
66 ATCCTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAACCGTCTTCTCAAAATTATTTTTT
* *
17047976 CAGGAACTACTGTAGAAAAAGAACGTCCATGTAGGAGTTTTTTTCATCAATTTTGCTGACAGTGC
1 CAGGAACTACTGTAGAAAAAGAACGTCCACGTAGGAGCTTTTTTCATCAATTTTGCTGACAGTGC
*
17048041 ATCCTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAACCATCTTCTCAAAATTATTTTTT
66 ATCCTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAACCGTCTTCTCAAAATTATTTTTT
17048102 CAGGAACTACTGTAGAAAAA
1 CAGGAACTACTGTAGAAAAA
17048122 AAAATCCTTA
Statistics
Matches: 367, Mismatches: 29, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
125 117 0.32
126 250 0.68
ACGTcount: A:0.28, C:0.18, G:0.17, T:0.37
Consensus pattern (126 bp):
CAGGAACTACTGTAGAAAAAGAACGTCCACGTAGGAGCTTTTTTCATCAATTTTGCTGACAGTGC
ATCCTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAACCGTCTTCTCAAAATTATTTTTT
Found at i:17048043 original size:251 final size:252
Alignment explanation
Indices: 17047599--17048121 Score: 877
Period size: 251 Copynumber: 2.1 Consensus size: 252
17047589 TAACGCCAAA
* * * *
17047599 CAGGAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCATCAATTTTGTTGTCAGTGC
1 CAGGAACTACTGTAGAAAAAGAGCGTCCACATAGGAGCTTTTTTCATCAATTTTGCTGACAGTGC
* * * *
17047664 ATCTTGCTTGAAGTGTTTTTGACACTATTTGTTTAGAAGCGTCTTCTCAAAATTATTTTTTCAGG
66 ATCCTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAACCGTCTTCTCAAAATTATTTTTTCAGG
* * *
17047729 AGCTACTGTAGAAAAAGAATGTCCACGTATGAGCTTTTTTCATCAATTTTGCTGACAGTGCATCC
131 AACTACTGTAGAAAAAGAACGTCCACGTAGGAGCTTTTTTCATCAATTTTGCTGACAGTGCATCC
* **
17047794 TGCTTGAAGCATTTTTGACACTATTTTTTCAAAACTGTCTTCTCAAAATTATTTTTT
196 TGCTTGAAGCATTTTTGACACTATTTGTTCAAAACCATCTTCTCAAAATTATTTTTT
17047851 CAGGAACTACTGTAGAAAAAGAGCGTCCACATAGGAGC-TTTTTCATCAATTTTGCTGACAGTGC
1 CAGGAACTACTGTAGAAAAAGAGCGTCCACATAGGAGCTTTTTTCATCAATTTTGCTGACAGTGC
17047915 ATCCTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAACCGTCTTCTCAAAATTATTTTTTCAGG
66 ATCCTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAACCGTCTTCTCAAAATTATTTTTTCAGG
* *
17047980 AACTACTGTAGAAAAAGAACGTCCATGTAGGAGTTTTTTTCATCAATTTTGCTGACAGTGCATCC
131 AACTACTGTAGAAAAAGAACGTCCACGTAGGAGCTTTTTTCATCAATTTTGCTGACAGTGCATCC
* *
17048045 TGCTTGAAGCGTTTTTGACACTATTTGTTCAGAACCATCTTCTCAAAATTATTTTTT
196 TGCTTGAAGCATTTTTGACACTATTTGTTCAAAACCATCTTCTCAAAATTATTTTTT
17048102 CAGGAACTACTGTAGAAAAA
1 CAGGAACTACTGTAGAAAAA
17048122 AAAATCCTTA
Statistics
Matches: 253, Mismatches: 18, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
251 217 0.86
252 36 0.14
ACGTcount: A:0.28, C:0.18, G:0.17, T:0.37
Consensus pattern (252 bp):
CAGGAACTACTGTAGAAAAAGAGCGTCCACATAGGAGCTTTTTTCATCAATTTTGCTGACAGTGC
ATCCTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAACCGTCTTCTCAAAATTATTTTTTCAGG
AACTACTGTAGAAAAAGAACGTCCACGTAGGAGCTTTTTTCATCAATTTTGCTGACAGTGCATCC
TGCTTGAAGCATTTTTGACACTATTTGTTCAAAACCATCTTCTCAAAATTATTTTTT
Found at i:17048220 original size:34 final size:33
Alignment explanation
Indices: 17048178--17048280 Score: 134
Period size: 34 Copynumber: 3.1 Consensus size: 33
17048168 CACAAAGTTA
17048178 TTTTAAAAACTCTAAACCCTAATTTAATTAATT
1 TTTTAAAAACTCTAAACCCTAATTTAATTAATT
* * *
17048211 TTCTTAAAAACTCTACACCTTAATTTAATTTATT
1 TT-TTAAAAACTCTAAACCCTAATTTAATTAATT
* * *
17048245 TATTTAAAACCCCTAAAACCTAATTTAATTAATT
1 T-TTTAAAAACTCTAAACCCTAATTTAATTAATT
17048279 TT
1 TT
17048281 AAAAAAACAC
Statistics
Matches: 59, Mismatches: 9, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
33 3 0.05
34 55 0.93
35 1 0.02
ACGTcount: A:0.40, C:0.17, G:0.00, T:0.44
Consensus pattern (33 bp):
TTTTAAAAACTCTAAACCCTAATTTAATTAATT
Found at i:17054745 original size:6 final size:6
Alignment explanation
Indices: 17054726--17054759 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
17054716 AATCTGCGGA
*
17054726 TGAGAG TGATAG TGAGAG TGAGAG TGAGAG TGAG
1 TGAGAG TGAGAG TGAGAG TGAGAG TGAGAG TGAG
17054760 TGGGAGCGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.32, C:0.00, G:0.47, T:0.21
Consensus pattern (6 bp):
TGAGAG
Found at i:17056877 original size:5 final size:5
Alignment explanation
Indices: 17056862--17056892 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
17056852 TTTGATTCTG
17056862 TTTTA -TTTA TTTTA TTTTA TTTTA TTTTA TT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TT
17056893 CATTCATTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.16
5 21 0.84
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:17059929 original size:65 final size:67
Alignment explanation
Indices: 17059831--17059965 Score: 247
Period size: 66 Copynumber: 2.0 Consensus size: 67
17059821 TATCAACCTA
17059831 TTTTAAATTATAAATTTAATTTGAAT-AATTTTTTTATTAGTAAACAATAATTCGAATCAAATCA
1 TTTTAAATTATAAATTTAATTTGAATAAATTTTTTTATTAGTAAACAATAATTCGAATCAAATCA
17059895 AT
66 AT
*
17059897 TTTTAAATTATACA-TTAATTTGAATAAATTTTTTTATTAGTAAACAATAATTCGAATCAAATCA
1 TTTTAAATTATAAATTTAATTTGAATAAATTTTTTTATTAGTAAACAATAATTCGAATCAAATCA
17059961 AT
66 AT
17059963 TTT
1 TTT
17059966 ATTTGAAATT
Statistics
Matches: 67, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
65 11 0.16
66 56 0.84
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.46
Consensus pattern (67 bp):
TTTTAAATTATAAATTTAATTTGAATAAATTTTTTTATTAGTAAACAATAATTCGAATCAAATCA
AT
Found at i:17059967 original size:34 final size:34
Alignment explanation
Indices: 17059862--17059968 Score: 121
Period size: 34 Copynumber: 3.2 Consensus size: 34
17059852 TGAATAATTT
17059862 TTTTATTAGTAAACAATAATTCGAATCAAATCAA
1 TTTTATTAGTAAACAATAATTCGAATCAAATCAA
* * * * * **
17059896 TTTT-TAAATTATACATTAATTTGAAT-AAAT-TT
1 TTTTAT-TAGTAAACAATAATTCGAATCAAATCAA
17059928 TTTTATTAGTAAACAATAATTCGAATCAAATCAA
1 TTTTATTAGTAAACAATAATTCGAATCAAATCAA
17059962 TTTTATT
1 TTTTATT
17059969 TGAAATTATA
Statistics
Matches: 55, Mismatches: 14, Indels: 8
0.71 0.18 0.10
Matches are distributed among these distances:
32 19 0.35
33 10 0.18
34 26 0.47
ACGTcount: A:0.43, C:0.08, G:0.05, T:0.44
Consensus pattern (34 bp):
TTTTATTAGTAAACAATAATTCGAATCAAATCAA
Found at i:17060997 original size:14 final size:15
Alignment explanation
Indices: 17060978--17061010 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
17060968 GGGGCAAAGC
*
17060978 TAAAAAT-CTTGAAT
1 TAAAAATGCTTAAAT
17060992 TAAAAATGCTTAAAT
1 TAAAAATGCTTAAAT
17061007 TAAA
1 TAAA
17061011 TTATTAACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.55, C:0.06, G:0.06, T:0.33
Consensus pattern (15 bp):
TAAAAATGCTTAAAT
Found at i:17065710 original size:91 final size:91
Alignment explanation
Indices: 17065555--17066048 Score: 656
Period size: 91 Copynumber: 5.4 Consensus size: 91
17065545 TAATGATTGA
* * * * * *
17065555 AGGATGCCAGAGTGTCTTTCGACCATAGTTTTATTCAATTTTCGATATGATGT-CATAGTATCTT
1 AGGATGCCATAGTGTCTTTCAACCATGGTCTTATTC-ATTTTCGATATGATTTCCATAATATCTT
*
17065619 TCAACCATGGTCTTTTTCATTTTCAAT
65 TCAACCATGGTCTTATTCATTTTCAAT
* * *
17065646 AGGATGCCACAGTGTCTTTCAACCATGGTCTTATTCATTTTCGATAGGATTTCCATAATGTCTTT
1 AGGATGCCATAGTGTCTTTCAACCATGGTCTTATTCATTTTCGATATGATTTCCATAATATCTTT
*
17065711 CAACCATGGTCTTATTCATTTTCGAT
66 CAACCATGGTCTTATTCATTTTCAAT
* * * * * *
17065737 AGGATGCCATAGTGTCTTTCAACTATGGTCTTACTCACTTTCCGATATGATGT-CATAGTGTCTT
1 AGGATGCCATAGTGTCTTTCAACCATGGTCTTATTCA-TTTTCGATATGATTTCCATAATATCTT
*
17065801 TCAACCATGGTTTTATTCATTTTCCAAT
65 TCAACCATGGTCTTATTCATTTT-CAAT
* *
17065829 ATGATGCCATAGTGTCTTTCAACCATGGTCTTATTCATTTTCCGATATGA-TGCCATAATATCTT
1 AGGATGCCATAGTGTCTTTCAACCATGGTCTTATTCATTTT-CGATATGATTTCCATAATATCTT
17065893 TCAA-CATGGTCTTATTCATTTTCCAAT
65 TCAACCATGGTCTTATTCATTTT-CAAT
* *
17065920 ATGATGCCATAGTGTCTTTCAACCATGGTCTTATTCATTTTTCGATATGA-TGCCATAATATCTT
1 AGGATGCCATAGTGTCTTTCAACCATGGTCTTATTCA-TTTTCGATATGATTTCCATAATATCTT
*
17065984 TCAACCATGGTCTTATTCATTTTCGAT
65 TCAACCATGGTCTTATTCATTTTCAAT
* * * *
17066011 AGGCTGCCATAGTGTTTTTCAACTATGGTCTTACTCAT
1 AGGATGCCATAGTGTCTTTCAACCATGGTCTTATTCAT
17066049 CTGAATCATG
Statistics
Matches: 362, Mismatches: 34, Indels: 15
0.88 0.08 0.04
Matches are distributed among these distances:
90 15 0.04
91 255 0.70
92 92 0.25
ACGTcount: A:0.24, C:0.20, G:0.15, T:0.42
Consensus pattern (91 bp):
AGGATGCCATAGTGTCTTTCAACCATGGTCTTATTCATTTTCGATATGATTTCCATAATATCTTT
CAACCATGGTCTTATTCATTTTCAAT
Found at i:17065722 original size:46 final size:45
Alignment explanation
Indices: 17065557--17066088 Score: 647
Period size: 46 Copynumber: 11.7 Consensus size: 45
17065547 ATGATTGAAG
* * * *
17065557 GATGCCAGAGTGTCTTTCGACCATAGTTTTATTCAATTTTCGATAT
1 GATGCCATAGTGTCTTTCAACCATGGTCTTATTC-ATTTTCGATAT
* * * * *
17065603 GATGTCATAGTATCTTTCAACCATGGTCTTTTTCATTTTCAATAG
1 GATGCCATAGTGTCTTTCAACCATGGTCTTATTCATTTTCGATAT
* *
17065648 GATGCCACAGTGTCTTTCAACCATGGTCTTATTCATTTTCGATAG
1 GATGCCATAGTGTCTTTCAACCATGGTCTTATTCATTTTCGATAT
* * *
17065693 GATTTCCATAATGTCTTTCAACCATGGTCTTATTCATTTTCGATAG
1 GA-TGCCATAGTGTCTTTCAACCATGGTCTTATTCATTTTCGATAT
* * *
17065739 GATGCCATAGTGTCTTTCAACTATGGTCTTACTCACTTTCCGATAT
1 GATGCCATAGTGTCTTTCAACCATGGTCTTATTCA-TTTTCGATAT
* * *
17065785 GATGTCATAGTGTCTTTCAACCATGGTTTTATTCATTTTCCAATAT
1 GATGCCATAGTGTCTTTCAACCATGGTCTTATTCATTTT-CGATAT
17065831 GATGCCATAGTGTCTTTCAACCATGGTCTTATTCATTTTCCGATAT
1 GATGCCATAGTGTCTTTCAACCATGGTCTTATTCATTTT-CGATAT
* * *
17065877 GATGCCATAATATCTTTCAA-CATGGTCTTATTCATTTTCCAATAT
1 GATGCCATAGTGTCTTTCAACCATGGTCTTATTCATTTT-CGATAT
17065922 GATGCCATAGTGTCTTTCAACCATGGTCTTATTCATTTTTCGATAT
1 GATGCCATAGTGTCTTTCAACCATGGTCTTATTCA-TTTTCGATAT
* * *
17065968 GATGCCATAATATCTTTCAACCATGGTCTTATTCATTTTCGATAG
1 GATGCCATAGTGTCTTTCAACCATGGTCTTATTCATTTTCGATAT
* * * * *
17066013 GCTGCCATAGTGTTTTTCAACTATGGTCTTACTCA-TCT-GAATCAT
1 GATGCCATAGTGTCTTTCAACCATGGTCTTATTCATTTTCG-AT-AT
** * *
17066058 GATGCCATAACGTCTTTCAGCTATGGTCTTA
1 GATGCCATAGTGTCTTTCAACCATGGTCTTA
17066089 CTCGTTTGAA
Statistics
Matches: 425, Mismatches: 54, Indels: 15
0.86 0.11 0.03
Matches are distributed among these distances:
43 1 0.00
44 4 0.01
45 190 0.45
46 226 0.53
47 4 0.01
ACGTcount: A:0.24, C:0.20, G:0.15, T:0.41
Consensus pattern (45 bp):
GATGCCATAGTGTCTTTCAACCATGGTCTTATTCATTTTCGATAT
Found at i:17065810 original size:137 final size:135
Alignment explanation
Indices: 17065557--17066088 Score: 672
Period size: 137 Copynumber: 3.9 Consensus size: 135
17065547 ATGATTGAAG
* * * * * * *
17065557 GATGCCAGAGTGTCTTTCGACCATAGTTTTATTCAATTTTCGATATGATGTCATAGTATCTTTCA
1 GATGCCATAATGTCTTTCAACCATGGTCTTATTC-ATTTTCGATAGGATGCCATAGTATCTTTCA
* ** * * *
17065622 ACCATGGTCTTTTTCATTTTCAATAGGATGCCACAGTGTCTTTCAACCATGGTCTTATTCATTTT
65 ACTATGGTCTTACTCATTTCCAATATGATGCCATAGTGTCTTTCAACCATGGTCTTATTCATTTT
*
17065687 CGATAG
130 CGATAT
* *
17065693 GATTTCCATAATGTCTTTCAACCATGGTCTTATTCATTTTCGATAGGATGCCATAGTGTCTTTCA
1 GA-TGCCATAATGTCTTTCAACCATGGTCTTATTCATTTTCGATAGGATGCCATAGTATCTTTCA
* * *
17065758 ACTATGGTCTTACTCACTTTCCGATATGATGTCATAGTGTCTTTCAACCATGGTTTTATTCATTT
65 ACTATGGTCTTACTCA-TTTCCAATATGATGCCATAGTGTCTTTCAACCATGGTCTTATTCATTT
*
17065823 TCCAATAT
129 T-CGATAT
* * *
17065831 GATGCCATAGTGTCTTTCAACCATGGTCTTATTCATTTTCCGATATGATGCCATAATATCTTTCA
1 GATGCCATAATGTCTTTCAACCATGGTCTTATTCATTTT-CGATAGGATGCCATAGTATCTTTCA
*
17065896 AC-ATGGTCTTATTCATTTTCCAATATGATGCCATAGTGTCTTTCAACCATGGTCTTATTCATTT
65 ACTATGGTCTTACTCA-TTTCCAATATGATGCCATAGTGTCTTTCAACCATGGTCTTATTCA-TT
17065960 TTCGATAT
128 TTCGATAT
* * * *
17065968 GATGCCATAATATCTTTCAACCATGGTCTTATTCATTTTCGATAGGCTGCCATAGTGTTTTTCAA
1 GATGCCATAATGTCTTTCAACCATGGTCTTATTCATTTTCGATAGGATGCCATAGTATCTTTCAA
* * ** * *
17066033 CTATGGTCTTACTCATCT-GAATCATGATGCCATAACGTCTTTCAGCTATGGTCTTA
66 CTATGGTCTTACTCATTTCCAAT-ATGATGCCATAGTGTCTTTCAACCATGGTCTTA
17066089 CTCGTTTGAA
Statistics
Matches: 344, Mismatches: 45, Indels: 14
0.85 0.11 0.03
Matches are distributed among these distances:
135 3 0.01
136 95 0.28
137 212 0.62
138 34 0.10
ACGTcount: A:0.24, C:0.20, G:0.15, T:0.41
Consensus pattern (135 bp):
GATGCCATAATGTCTTTCAACCATGGTCTTATTCATTTTCGATAGGATGCCATAGTATCTTTCAA
CTATGGTCTTACTCATTTCCAATATGATGCCATAGTGTCTTTCAACCATGGTCTTATTCATTTTC
GATAT
Found at i:17065962 original size:23 final size:23
Alignment explanation
Indices: 17065936--17066006 Score: 56
Period size: 23 Copynumber: 3.1 Consensus size: 23
17065926 CCATAGTGTC
17065936 TTTCAACCATGGTCTTATTCATT
1 TTTCAACCATGGTCTTATTCATT
* * * * * *
17065959 TTTCGA-TATGATGCCATAAT-ATC
1 TTTCAACCATG--GTCTTATTCATT
17065982 TTTCAACCATGGTCTTATTCATT
1 TTTCAACCATGGTCTTATTCATT
17066005 TT
1 TT
17066007 CGATAGGCTG
Statistics
Matches: 32, Mismatches: 12, Indels: 8
0.62 0.23 0.15
Matches are distributed among these distances:
22 8 0.25
23 16 0.50
24 8 0.25
ACGTcount: A:0.24, C:0.20, G:0.10, T:0.46
Consensus pattern (23 bp):
TTTCAACCATGGTCTTATTCATT
Found at i:17071177 original size:68 final size:69
Alignment explanation
Indices: 17071047--17071181 Score: 191
Period size: 68 Copynumber: 2.0 Consensus size: 69
17071037 TGATTAAACT
* * * *
17071047 TAATCACTATAATATTAAATTAGTATAATATTTATAAAGATAAATATTAGATTAAATTTAATATT
1 TAATCACTATAATATTAAATTAATAAAATATCTATAAAGATAAATATTAAATTAAATTTAATATT
17071112 AAGA
66 AAGA
* * * *
17071116 TAATCACTTTAATATTAAATTAATAAAATA-CTATTAAGATAAGTATTAAATTTAATTTAATATT
1 TAATCACTATAATATTAAATTAATAAAATATCTATAAAGATAAATATTAAATTAAATTTAATATT
17071180 AA
66 AA
17071182 ACTATTAAAA
Statistics
Matches: 58, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
68 31 0.53
69 27 0.47
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.41
Consensus pattern (69 bp):
TAATCACTATAATATTAAATTAATAAAATATCTATAAAGATAAATATTAAATTAAATTTAATATT
AAGA
Found at i:17079572 original size:27 final size:28
Alignment explanation
Indices: 17079538--17079599 Score: 99
Period size: 28 Copynumber: 2.2 Consensus size: 28
17079528 AAAAATAACC
*
17079538 AAAATATTAT-AACTTTTTTTATTTACA
1 AAAATATTATAAAATTTTTTTATTTACA
*
17079565 AAAATATTATAAAATTTTTTTATTTACC
1 AAAATATTATAAAATTTTTTTATTTACA
17079593 AAAATAT
1 AAAATAT
17079600 ACAAAAAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
27 10 0.31
28 22 0.69
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.48
Consensus pattern (28 bp):
AAAATATTATAAAATTTTTTTATTTACA
Found at i:17079607 original size:29 final size:28
Alignment explanation
Indices: 17079551--17079607 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
17079541 ATATTATAAC
* *
17079551 TTTTTTTATTTACAAAAATATTATAAAA
1 TTTTTTTATTTACAAAAATATCAAAAAA
*
17079579 TTTTTTTATTTACCAAAATATACAAAAAA
1 TTTTTTTATTTACAAAAATAT-CAAAAAA
17079608 AACAAAAAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
28 20 0.80
29 5 0.20
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.46
Consensus pattern (28 bp):
TTTTTTTATTTACAAAAATATCAAAAAA
Done.