Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007695.1 Hibiscus syriacus cultivar Beakdansim tig00109903_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: 87041
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:587 original size:30 final size:30
Alignment explanation
Indices: 553--623 Score: 79
Period size: 32 Copynumber: 2.3 Consensus size: 30
543 TACAATATTA
*
553 TTTATATATCCCTAATTTTTTTGTTAACAT
1 TTTATATATCCCTAATCTTTTTGTTAACAT
**
583 TTTATATACATCGTTAATCTTTTTGTTAACAT
1 TTTATAT--ATCCCTAATCTTTTTGTTAACAT
* *
615 GTCATATAT
1 TTTATATAT
624 ATATATATTA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
30 9 0.26
32 25 0.74
ACGTcount: A:0.28, C:0.13, G:0.06, T:0.54
Consensus pattern (30 bp):
TTTATATATCCCTAATCTTTTTGTTAACAT
Found at i:5108 original size:2 final size:2
Alignment explanation
Indices: 5101--5125 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5091 TTTTTAAAAC
5101 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
5126 CCCCCATCCG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5313 original size:24 final size:24
Alignment explanation
Indices: 5286--5392 Score: 97
Period size: 24 Copynumber: 4.5 Consensus size: 24
5276 AAACGGAGAT
*
5286 ATCAGAAATCAAAACATAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * *
5310 ATCAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * * * *
5334 GTTAGGAATCAGAACAGATTTCAG
1 ATCAGAAATCAAAACAGAATTCAG
** * *
5358 ATCAGATGTCAAAACATAATTCAA
1 ATCAGAAATCAAAACAGAATTCAG
5382 ATCAGAAATCA
1 ATCAGAAATCA
5393 GATAAAATAT
Statistics
Matches: 62, Mismatches: 21, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
24 62 1.00
ACGTcount: A:0.48, C:0.17, G:0.14, T:0.21
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATTCAG
Found at i:5392 original size:48 final size:48
Alignment explanation
Indices: 5286--5394 Score: 119
Period size: 48 Copynumber: 2.3 Consensus size: 48
5276 AAACGGAGAT
* * * *
5286 ATCAGAAATCAAAACATAATTCAGATCAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
* * * * * * *
5334 GTTAGGAATCAGAACAGATTTCAGATCAGATGTCAAAACATAATTCAA
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
5382 ATCAGAAATCAGA
1 ATCAGAAATCAGA
5395 TAAAATATTC
Statistics
Matches: 47, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.48, C:0.17, G:0.15, T:0.21
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
Found at i:6495 original size:26 final size:26
Alignment explanation
Indices: 6466--6518 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
6456 TCAGTTTTAT
* *
6466 TCCATTCATTTCAGAGCTTGGGGATA
1 TCCAATCATTCCAGAGCTTGGGGATA
* *
6492 TCCAATCATTCCTGAGCTTGGTGATA
1 TCCAATCATTCCAGAGCTTGGGGATA
6518 T
1 T
6519 TCTTGGGTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.36
Consensus pattern (26 bp):
TCCAATCATTCCAGAGCTTGGGGATA
Found at i:9693 original size:32 final size:31
Alignment explanation
Indices: 9620--9716 Score: 131
Period size: 31 Copynumber: 3.1 Consensus size: 31
9610 GTCCTGAAGG
* * *
9620 ACCTATCCATATGTTCCGAAGAACATAGGTA
1 ACCTGTCCATATGTCCCGAAGGACATAGGTA
9651 ACCTGTCCATATGTCCCGAAGGACATAGGTA
1 ACCTGTCCATATGTCCCGAAGGACATAGGTA
* * *
9682 ATCCTGTCCATATGTCTCGAATGACATATGTA
1 A-CCTGTCCATATGTCCCGAAGGACATAGGTA
9714 ACC
1 ACC
9717 CTCGACTCTT
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
31 31 0.53
32 28 0.47
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.27
Consensus pattern (31 bp):
ACCTGTCCATATGTCCCGAAGGACATAGGTA
Found at i:14353 original size:32 final size:32
Alignment explanation
Indices: 14298--14436 Score: 171
Period size: 32 Copynumber: 4.4 Consensus size: 32
14288 TCTATATGTT
*
14298 CCGAAGAACAT-CGATAA-CATGTCCATATATC
1 CCGAAGAACATATG-TAATCATGTCCATATATC
* * *
14329 CCGGAGAACATATGTAATCATGTCCATATGTT
1 CCGAAGAACATATGTAATCATGTCCATATATC
14361 CCGAAGAACAT-TGGTAA-CATGTCCATATATC
1 CCGAAGAACATAT-GTAATCATGTCCATATATC
*
14392 CCGAAGGACATATGTAATCATGTCCATATATC
1 CCGAAGAACATATGTAATCATGTCCATATATC
14424 CCGAATG-ACATAT
1 CCGAA-GAACATAT
14437 ATAAACCTCG
Statistics
Matches: 94, Mismatches: 8, Indels: 11
0.83 0.07 0.10
Matches are distributed among these distances:
31 40 0.43
32 53 0.56
33 1 0.01
ACGTcount: A:0.35, C:0.22, G:0.16, T:0.27
Consensus pattern (32 bp):
CCGAAGAACATATGTAATCATGTCCATATATC
Found at i:14369 original size:63 final size:63
Alignment explanation
Indices: 14291--14420 Score: 224
Period size: 63 Copynumber: 2.1 Consensus size: 63
14281 GAACCTATCT
*
14291 ATATGTTCCGAAGAACATCGATAACATGTCCATATATCCCGGAGAACATATGTAATCATGTCC
1 ATATGTTCCGAAGAACATCGATAACATGTCCATATATCCCGAAGAACATATGTAATCATGTCC
* * *
14354 ATATGTTCCGAAGAACATTGGTAACATGTCCATATATCCCGAAGGACATATGTAATCATGTCC
1 ATATGTTCCGAAGAACATCGATAACATGTCCATATATCCCGAAGAACATATGTAATCATGTCC
14417 ATAT
1 ATAT
14421 ATCCCGAATG
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
63 63 1.00
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.28
Consensus pattern (63 bp):
ATATGTTCCGAAGAACATCGATAACATGTCCATATATCCCGAAGAACATATGTAATCATGTCC
Found at i:15503 original size:19 final size:19
Alignment explanation
Indices: 15479--15515 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
15469 CTATTCATAG
15479 TGTACCGATACACCCTGCA
1 TGTACCGATACACCCTGCA
15498 TGTACCGATACACCCTGC
1 TGTACCGATACACCCTGC
15516 CCAGAGTAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.24, C:0.38, G:0.16, T:0.22
Consensus pattern (19 bp):
TGTACCGATACACCCTGCA
Found at i:18386 original size:23 final size:24
Alignment explanation
Indices: 18342--18386 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 24
18332 AATCCGACCC
**
18342 AACCCGATCCCGAATTTAAAAAAA
1 AACCCGATCCCGAATACAAAAAAA
*
18366 AACCCGA-CCCGAATACCAAAA
1 AACCCGATCCCGAATACAAAAA
18387 GATTAATGAG
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 11 0.61
24 7 0.39
ACGTcount: A:0.49, C:0.31, G:0.09, T:0.11
Consensus pattern (24 bp):
AACCCGATCCCGAATACAAAAAAA
Found at i:20038 original size:20 final size:23
Alignment explanation
Indices: 20009--20061 Score: 58
Period size: 21 Copynumber: 2.4 Consensus size: 23
19999 TTTCAAAATA
*
20009 ATTTTCAAA-GCTAAATAT-TAT
1 ATTTTAAAAGGCTAAATATATAT
*
20030 -TTTTAAAAGGTTAAATATATAT
1 ATTTTAAAAGGCTAAATATATAT
20052 ATATTTAAAA
1 AT-TTTAAAA
20062 TTATATAGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
20 7 0.27
21 8 0.31
22 3 0.12
23 1 0.04
24 7 0.27
ACGTcount: A:0.47, C:0.04, G:0.06, T:0.43
Consensus pattern (23 bp):
ATTTTAAAAGGCTAAATATATAT
Found at i:20052 original size:82 final size:82
Alignment explanation
Indices: 19966--20126 Score: 304
Period size: 82 Copynumber: 2.0 Consensus size: 82
19956 ATAACTTATA
19966 ATATATATTTAAAATTATATAGTATATAATGTTTTTCAAAATAATTTTCAAAGCTAAATATTATT
1 ATATATATTTAAAATTATATAGTATATAATGTTTTTCAAAATAATTTTCAAAGCTAAATATTATT
*
20031 TTTAAAAGGTTAAATAT
66 TTCAAAAGGTTAAATAT
*
20048 ATATATATTTAAAATTATATAGTATATAATGTTTTTCAAAATAATTTTCAAAGCTACATATTATT
1 ATATATATTTAAAATTATATAGTATATAATGTTTTTCAAAATAATTTTCAAAGCTAAATATTATT
20113 TTCAAAAGGTTAAA
66 TTCAAAAGGTTAAA
20127 ACTAAAATGT
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
82 77 1.00
ACGTcount: A:0.45, C:0.05, G:0.06, T:0.44
Consensus pattern (82 bp):
ATATATATTTAAAATTATATAGTATATAATGTTTTTCAAAATAATTTTCAAAGCTAAATATTATT
TTCAAAAGGTTAAATAT
Found at i:20234 original size:38 final size:35
Alignment explanation
Indices: 20166--20251 Score: 109
Period size: 38 Copynumber: 2.3 Consensus size: 35
20156 AAAACTATAT
*
20166 TATTTTCAAAACTATATATATAATATTTTTCAAAGC
1 TATTTT-AAAACTATATATATAATATTTTTCAAAAC
20202 TATTTTAAAACTATATAATATTTAATATTTTTCAAAAC
1 TATTTTAAAACTATAT-ATA--TAATATTTTTCAAAAC
*
20240 TGTTTTTAAAAC
1 T-ATTTTAAAAC
20252 GTAATGTATC
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
35 10 0.23
36 9 0.20
38 16 0.36
39 9 0.20
ACGTcount: A:0.42, C:0.09, G:0.02, T:0.47
Consensus pattern (35 bp):
TATTTTAAAACTATATATATAATATTTTTCAAAAC
Found at i:22980 original size:67 final size:67
Alignment explanation
Indices: 22871--23007 Score: 238
Period size: 67 Copynumber: 2.0 Consensus size: 67
22861 CTATATCCAA
* *
22871 AAAATCATTATTTTTATTCAATTTAGACCATGCAGAGTTCACTTAAAACAATCCACAATTAATCT
1 AAAATCATTATTTTTATTCAATTTAGACCATGCAGAGGTCACTTAAAACAATCCACAACTAATCT
22936 AC
66 AC
*
22938 AAAATTATTATTTTTATTCAATTTAGACCATGCAGAGGTCACTTAAAACAATCCACAACTAATCT
1 AAAATCATTATTTTTATTCAATTTAGACCATGCAGAGGTCACTTAAAACAATCCACAACTAATCT
*
23003 GC
66 AC
23005 AAA
1 AAA
23008 CTTTTTTAAA
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
67 66 1.00
ACGTcount: A:0.41, C:0.19, G:0.07, T:0.33
Consensus pattern (67 bp):
AAAATCATTATTTTTATTCAATTTAGACCATGCAGAGGTCACTTAAAACAATCCACAACTAATCT
AC
Found at i:25018 original size:31 final size:29
Alignment explanation
Indices: 24961--25032 Score: 81
Period size: 31 Copynumber: 2.4 Consensus size: 29
24951 CTTTTTCATT
* * *
24961 TAAGTATTTAAATTATTTTTTTGTCAAAA
1 TAAGTATTAAAATTAATTTTTAGTCAAAA
24990 TAAGTACTTAAAATTAAATTTTTAGTCAAAA
1 TAAGTA-TTAAAATT-AATTTTTAGTCAAAA
*
25021 TAGGTATCTAAA
1 TAAGTAT-TAAA
25033 GTATTCAATT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
29 6 0.17
30 8 0.22
31 22 0.61
ACGTcount: A:0.43, C:0.06, G:0.08, T:0.43
Consensus pattern (29 bp):
TAAGTATTAAAATTAATTTTTAGTCAAAA
Found at i:25102 original size:20 final size:20
Alignment explanation
Indices: 25077--25114 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
25067 TTTGGTTCAC
*
25077 GGAATATAAGATTACCAGTG
1 GGAATAAAAGATTACCAGTG
25097 GGAATAAAAGATTACCAG
1 GGAATAAAAGATTACCAG
25115 AGAATAGGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.11, G:0.24, T:0.21
Consensus pattern (20 bp):
GGAATAAAAGATTACCAGTG
Found at i:25119 original size:18 final size:19
Alignment explanation
Indices: 25078--25120 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
25068 TTGGTTCACG
* *
25078 GAATATAAGATTACCAGTGG
1 GAATAAAAGATTACCAG-GA
25098 GAATAAAAGATTACCA-GA
1 GAATAAAAGATTACCAGGA
25116 GAATA
1 GAATA
25121 GGATTATTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 6 0.29
20 15 0.71
ACGTcount: A:0.49, C:0.09, G:0.21, T:0.21
Consensus pattern (19 bp):
GAATAAAAGATTACCAGGA
Found at i:30888 original size:14 final size:15
Alignment explanation
Indices: 30857--30889 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
30847 TATTTTTGAA
30857 AAAATTATTGTCTTT
1 AAAATTATTGTCTTT
*
30872 AAAATTATT-TGTTT
1 AAAATTATTGTCTTT
30886 AAAA
1 AAAA
30890 ATATAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.48
Consensus pattern (15 bp):
AAAATTATTGTCTTT
Found at i:34320 original size:2 final size:2
Alignment explanation
Indices: 34315--34371 Score: 107
Period size: 2 Copynumber: 29.0 Consensus size: 2
34305 ATATAAAGAA
34315 AT AT AT AT 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 AT AT AT AT
34357 AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT
34372 GGTTAGAGCA
Statistics
Matches: 54, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 53 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:34900 original size:12 final size:11
Alignment explanation
Indices: 34879--34909 Score: 53
Period size: 12 Copynumber: 2.7 Consensus size: 11
34869 ATGGGGTCGG
34879 AATGAAATCCA
1 AATGAAATCCA
34890 AATGCAAATCCA
1 AATG-AAATCCA
34902 AATGAAAT
1 AATGAAAT
34910 GTTTAATTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 8 0.42
12 11 0.58
ACGTcount: A:0.55, C:0.16, G:0.10, T:0.19
Consensus pattern (11 bp):
AATGAAATCCA
Found at i:38746 original size:33 final size:33
Alignment explanation
Indices: 38709--38774 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
38699 AAAAACAAAG
38709 TATGGGTACCTATTTAGACCATAAAACCTTTTT
1 TATGGGTACCTATTTAGACCATAAAACCTTTTT
38742 TATGGGTACCTATTTAGACCATAAAACCTTTTT
1 TATGGGTACCTATTTAGACCATAAAACCTTTTT
38775 GCACTACATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.30, C:0.18, G:0.12, T:0.39
Consensus pattern (33 bp):
TATGGGTACCTATTTAGACCATAAAACCTTTTT
Found at i:48192 original size:17 final size:17
Alignment explanation
Indices: 48170--48208 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
48160 TGACTTTGAC
48170 CCAAAAAATCAAAATTT
1 CCAAAAAATCAAAATTT
48187 CCAAAAAATCAAAATTT
1 CCAAAAAATCAAAATTT
48204 CCAAA
1 CCAAA
48209 TATCATATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.59, C:0.21, G:0.00, T:0.21
Consensus pattern (17 bp):
CCAAAAAATCAAAATTT
Found at i:54669 original size:68 final size:69
Alignment explanation
Indices: 54584--54715 Score: 221
Period size: 68 Copynumber: 1.9 Consensus size: 69
54574 ATGATTATAG
* *
54584 TGTTGGTTTTCGTTTGCTTTGTAAAACTTCCATTTTTTT-AATGATGTTGAACGCTCCATTTATA
1 TGTTGGTTTTCATTTGCTTTGTAAAACTTCCATTTTTTTAAATGATGATGAACGCTCCATTTATA
54648 GATT
66 GATT
* *
54652 TGTTGGTTTTCATTTGCTTTGTAAAACTTCCATTTTTTTAAATGGTGATGAACGTTCCATTTAT
1 TGTTGGTTTTCATTTGCTTTGTAAAACTTCCATTTTTTTAAATGATGATGAACGCTCCATTTAT
54716 TATAGATTTG
Statistics
Matches: 59, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
68 38 0.64
69 21 0.36
ACGTcount: A:0.21, C:0.13, G:0.16, T:0.50
Consensus pattern (69 bp):
TGTTGGTTTTCATTTGCTTTGTAAAACTTCCATTTTTTTAAATGATGATGAACGCTCCATTTATA
GATT
Found at i:57238 original size:159 final size:155
Alignment explanation
Indices: 56987--57420 Score: 459
Period size: 152 Copynumber: 2.8 Consensus size: 155
56977 AAAAAATGAG
* * * ** * *
56987 GTGATATATCACTGATAA-GAAAAATGACATTTTGAATTCAGATATCACTGAAATGTCA-TTTAA
1 GTGATATATCAATGA-AAGGAAAAAAGACGTTTTTCATTCAGATATCACTGAAAAGTCATTTTGA
*
57050 GGTGATATATCACTGAAAAGTCATTGTGAAATTATTATGATAGGATTTGATCAATTATTATTAAA
65 GGTGATATATCACTGAAAAGTCATGGTGAAATTATTATGATAGGATTTGATCAATTATTATTAAA
* * *
57115 TAAGCAATGAAAAGATCAGAAGTT-A
130 TAAACAATAAAAAGATCAGAAATTAA
* * * * *
57140 GATGGTATATCAATGAAAAGGAAAAAAAAGATGTTTTTCCATTCCGATATCACTAAAAAATCATT
1 G-TGATATATCAATG-AAAGG--AAAAAAGACGTTTTT-CATTCAGATATCACTGAAAAGTCATT
*
57205 TTGAGGTGATATATCACTGAAAAATCATGGTGAAATTATTATGATAGTG-TTTGATC-A--ATTA
61 TTGAGGTGATATATCACTGAAAAGTCATGGTGAAATTATTATGATAG-GATTTGATCAATTATTA
* * *
57266 TTAAATAAACACTAAAAAGTTTAGAAATTAA
125 TTAAATAAACAATAAAAAGATCAGAAATTAA
* * * * * * *
57297 GTGATATATCAATGAAAGGAAAACATACGTTTTTCATTCAGGTATCATTGAAAGGTAATTGTGAG
1 GTGATATATCAATGAAAGGAAAAAAGACGTTTTTCATTCAGATATCACTGAAAAGTCATTTTGAG
* * * * * *
57362 GTGATATATTACTTAAAAGTCATGGCGAAATTATTATGATAGAATCTGACCAATTATTA
66 GTGATATATCACTGAAAAGTCATGGTGAAATTATTATGATAGGATTTGATCAATTATTA
57421 AATATGGTCA
Statistics
Matches: 229, Mismatches: 39, Indels: 24
0.78 0.13 0.08
Matches are distributed among these distances:
152 66 0.29
153 14 0.06
154 13 0.06
155 11 0.05
156 39 0.17
157 13 0.06
158 20 0.09
159 52 0.23
160 1 0.00
ACGTcount: A:0.41, C:0.09, G:0.16, T:0.33
Consensus pattern (155 bp):
GTGATATATCAATGAAAGGAAAAAAGACGTTTTTCATTCAGATATCACTGAAAAGTCATTTTGAG
GTGATATATCACTGAAAAGTCATGGTGAAATTATTATGATAGGATTTGATCAATTATTATTAAAT
AAACAATAAAAAGATCAGAAATTAA
Found at i:57579 original size:30 final size:30
Alignment explanation
Indices: 57519--57596 Score: 111
Period size: 30 Copynumber: 2.6 Consensus size: 30
57509 CTGAACTGAG
*
57519 GTGATATATCACTGAAAAGTTAAAAAATAAA
1 GTGATATATCACT-AAAAATTAAAAAATAAA
* *
57550 GTGATATATCACTAAAAATTCATAAATAAA
1 GTGATATATCACTAAAAATTAAAAAATAAA
*
57580 ATGATATATCACTAAAA
1 GTGATATATCACTAAAA
57597 TGATTCTCTG
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
30 30 0.70
31 13 0.30
ACGTcount: A:0.54, C:0.09, G:0.09, T:0.28
Consensus pattern (30 bp):
GTGATATATCACTAAAAATTAAAAAATAAA
Found at i:57597 original size:16 final size:16
Alignment explanation
Indices: 57546--57600 Score: 53
Period size: 16 Copynumber: 3.6 Consensus size: 16
57536 AGTTAAAAAA
*
57546 TAAAGTGATATATCAC
1 TAAAATGATATATCAC
* *
57562 TAAAA--AT-TCATAAA
1 TAAAATGATAT-ATCAC
57576 TAAAATGATATATCAC
1 TAAAATGATATATCAC
57592 TAAAATGAT
1 TAAAATGAT
57601 TCTCTGCCCT
Statistics
Matches: 30, Mismatches: 5, Indels: 8
0.70 0.12 0.19
Matches are distributed among these distances:
13 1 0.03
14 10 0.33
16 18 0.60
17 1 0.03
ACGTcount: A:0.53, C:0.09, G:0.07, T:0.31
Consensus pattern (16 bp):
TAAAATGATATATCAC
Found at i:59870 original size:32 final size:27
Alignment explanation
Indices: 59841--59898 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
59831 AATCCGACCT
* *
59841 GACCCGAAAGATATATACCCTCCACCC
1 GACCTGAAAAATATATACCCTCCACCC
* *
59868 GACTTGAAAAATATATACCCTTCACCC
1 GACCTGAAAAATATATACCCTCCACCC
59895 GACC
1 GACC
59899 CGAACCTGAC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.34, C:0.36, G:0.10, T:0.19
Consensus pattern (27 bp):
GACCTGAAAAATATATACCCTCCACCC
Found at i:59884 original size:27 final size:27
Alignment explanation
Indices: 59846--59897 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
59836 GACCTGACCC
*
59846 GAAAGATATATACCCTCCACCCGACTT
1 GAAAAATATATACCCTCCACCCGACTT
*
59873 GAAAAATATATACCCTTCACCCGAC
1 GAAAAATATATACCCTCCACCCGAC
59898 CCGAACCTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.37, C:0.33, G:0.10, T:0.21
Consensus pattern (27 bp):
GAAAAATATATACCCTCCACCCGACTT
Found at i:63048 original size:4 final size:4
Alignment explanation
Indices: 63039--63067 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
63029 ATGTTAGAGA
63039 AAAT AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT A
63068 CTAAATCAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:63136 original size:6 final size:6
Alignment explanation
Indices: 63114--63260 Score: 55
Period size: 6 Copynumber: 22.7 Consensus size: 6
63104 GGAAAAACAT
* * * *
63114 ATAAAA ATAGTAAA ATAAAA ATAAAA ATAGATAA ACAATAA AGACAA ATCAAA
1 ATAAAA ATA--AAA ATAAAA ATAAAA ATA-A-AA ATAA-AA ATAAAA ATAAAA
** * *
63167 GGAAAA AT-AAA ACAAAA ATAAAAA ACAAAA ATAAAA ATAATGATA ATAAAA
1 ATAAAA ATAAAA ATAAAA AT-AAAA ATAAAA ATAAAA ATAA--A-A ATAAAA
** * *
63218 ATATTGA ATAAACA AAAAAA TATATAAA AT-AAA ATAATA ATAA
1 ATA-AAA ATAAA-A ATAAAA -ATA-AAA ATAAAA ATAAAA ATAA
63261 TAAGATGTAA
Statistics
Matches: 105, Mismatches: 22, Indels: 28
0.68 0.14 0.18
Matches are distributed among these distances:
5 9 0.09
6 51 0.49
7 26 0.25
8 14 0.13
9 5 0.05
ACGTcount: A:0.73, C:0.04, G:0.05, T:0.18
Consensus pattern (6 bp):
ATAAAA
Found at i:63193 original size:13 final size:13
Alignment explanation
Indices: 63175--63203 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
63165 AAGGAAAAAT
63175 AAAACAAAAATAA
1 AAAACAAAAATAA
63188 AAAACAAAAATAA
1 AAAACAAAAATAA
63201 AAA
1 AAA
63204 TAATGATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.86, C:0.07, G:0.00, T:0.07
Consensus pattern (13 bp):
AAAACAAAAATAA
Found at i:63251 original size:17 final size:17
Alignment explanation
Indices: 63231--63308 Score: 54
Period size: 16 Copynumber: 4.5 Consensus size: 17
63221 TTGAATAAAC
*
63231 AAAAAAATATATAAAAT
1 AAAAAAATATATAAGAT
*
63248 AAAATAATAATAATAAGAT
1 AAAAAAAT-AT-ATAAGAT
* *
63267 GTAAACAATA-ATAATGAT
1 -AAAAAAATATATAA-GAT
*
63285 -AAAAAATATAT-ACAT
1 AAAAAAATATATAAGAT
63300 AAAAAAATA
1 AAAAAAATA
63309 AAACAAAAAC
Statistics
Matches: 49, Mismatches: 6, Indels: 13
0.72 0.09 0.19
Matches are distributed among these distances:
15 2 0.04
16 16 0.33
17 13 0.27
18 5 0.10
19 7 0.14
20 6 0.12
ACGTcount: A:0.69, C:0.03, G:0.04, T:0.24
Consensus pattern (17 bp):
AAAAAAATATATAAGAT
Found at i:63938 original size:13 final size:13
Alignment explanation
Indices: 63920--63952 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
63910 TGTGTGTGTG
63920 TTTGGTTTTGATA-
1 TTTGGTTTT-ATAC
63933 TTTGGTTTTATAC
1 TTTGGTTTTATAC
63946 TTTGGTT
1 TTTGGTT
63953 GGTTGATGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 3 0.16
13 16 0.84
ACGTcount: A:0.12, C:0.03, G:0.21, T:0.64
Consensus pattern (13 bp):
TTTGGTTTTATAC
Found at i:64534 original size:38 final size:39
Alignment explanation
Indices: 64455--64743 Score: 264
Period size: 38 Copynumber: 7.6 Consensus size: 39
64445 AAAACAATTC
* * *
64455 AAAAAC-ATATAATATAT-TAATTTCTAAAATAT-TTTTA
1 AAAAACTATATATTATATATATTTTCCAAAA-ATGTTTTA
* * * *
64492 AAAAATTATATATTTTATGTATTTTCCAAAAACGTTTTA
1 AAAAACTATATATTATATATATTTTCCAAAAATGTTTTA
*
64531 AAAAACTATATAATATATATATTTT-CAAAAATGTTTTA
1 AAAAACTATATATTATATATATTTTCCAAAAATGTTTTA
*
64569 AAAAACTATATATTATATATA-TTTCC-AAAATGTTTTC
1 AAAAACTATATATTATATATATTTTCCAAAAATGTTTTA
* * *
64606 AAAAACTATATAATATATAAATGTTTTC-AAAATGTTTT-
1 AAAAACTATATATTATATATAT-TTTCCAAAAATGTTTTA
* *
64644 CAAAACTATATATTATATAAAATTTT-CAAAAATGTTTT-
1 AAAAACTATATATTATAT-ATATTTTCCAAAAATGTTTTA
* * *
64682 CAAAACTATATATTGTATA-AGTTTT-C-AAAATGAATTT-
1 AAAAACTATATATTATATATA-TTTTCCAAAAATG-TTTTA
* *
64719 AAAAACTATATAGTACATATATTTT
1 AAAAACTATATATTATATATATTTT
64744 ATAAATATAT
Statistics
Matches: 217, Mismatches: 24, Indels: 22
0.83 0.09 0.08
Matches are distributed among these distances:
36 7 0.03
37 66 0.30
38 90 0.41
39 54 0.25
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.43
Consensus pattern (39 bp):
AAAAACTATATATTATATATATTTTCCAAAAATGTTTTA
Found at i:64623 original size:75 final size:74
Alignment explanation
Indices: 64452--64743 Score: 306
Period size: 75 Copynumber: 3.9 Consensus size: 74
64442 TGAAAAACAA
* * * * *
64452 TTCAAAAAC-ATATAATATAT-TAATTTCTAAAATATTTTTAAAAAATTATATATTTTATGTATT
1 TTCAAAAACTATATAATATATATATTTTC-AAAAT-GTTTT-AAAAACTATATATTATATATATT
*
64515 TTCCAAAAACGTT
63 TTCC-AAAATGTT
*
64528 TTAAAAAACTATATAATATATATATTTTCAAAAATGTTTTAAAAAACTATATATTATATATA-TT
1 TTCAAAAACTATATAATATATATATTTTC-AAAATGTTTT-AAAAACTATATATTATATATATTT
64592 TCCAAAATGTT
64 TCCAAAATGTT
* * *
64603 TTCAAAAACTATATAATATATAAATGTTTTCAAAATGTTTTCAAAACTATATATTATATAAAATT
1 TTCAAAAACTATATAATATAT--ATATTTTCAAAATGTTTTAAAAACTATATATTATAT-ATATT
*
64668 TTCAAAAATGTT
63 TTCCAAAATGTT
* * * * *
64680 TTC-AAAACTATATATTGTATA-AGTTTTCAAAATGAATTTAAAAACTATATAGTACATATATTT
1 TTCAAAAACTATATAATATATATA-TTTTCAAAATG-TTTTAAAAACTATATATTATATATATTT
64743 T
64 T
64744 ATAAATATAT
Statistics
Matches: 187, Mismatches: 21, Indels: 18
0.83 0.09 0.08
Matches are distributed among these distances:
74 18 0.10
75 62 0.33
76 40 0.21
77 56 0.30
78 11 0.06
ACGTcount: A:0.46, C:0.08, G:0.04, T:0.43
Consensus pattern (74 bp):
TTCAAAAACTATATAATATATATATTTTCAAAATGTTTTAAAAACTATATATTATATATATTTTC
CAAAATGTT
Found at i:64640 original size:11 final size:11
Alignment explanation
Indices: 64624--64648 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
64614 TATAATATAT
64624 AAATGTTTTCA
1 AAATGTTTTCA
64635 AAATGTTTTCA
1 AAATGTTTTCA
64646 AAA
1 AAA
64649 CTATATATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (11 bp):
AAATGTTTTCA
Found at i:64822 original size:39 final size:37
Alignment explanation
Indices: 64748--64837 Score: 103
Period size: 39 Copynumber: 2.4 Consensus size: 37
64738 TATTTTATAA
64748 ATATATTATATA-GTTTTCAAAAATGTTTTAAAAACT
1 ATATATTATATATGTTTTCAAAAATGTTTTAAAAACT
**
64784 ATATATTATATATGTATTTTCAAAAATCG-TTTGCAAACT
1 ATATATTATATATG--TTTTCAAAAAT-GTTTTAAAAACT
64823 ATAATATATATATAT
1 AT-ATAT-TATATAT
64838 ATATATATAT
Statistics
Matches: 46, Mismatches: 2, Indels: 7
0.84 0.04 0.13
Matches are distributed among these distances:
36 12 0.26
37 1 0.02
39 21 0.46
40 5 0.11
41 7 0.15
ACGTcount: A:0.43, C:0.07, G:0.06, T:0.44
Consensus pattern (37 bp):
ATATATTATATATGTTTTCAAAAATGTTTTAAAAACT
Found at i:64833 original size:2 final size:2
Alignment explanation
Indices: 64822--64868 Score: 78
Period size: 2 Copynumber: 24.0 Consensus size: 2
64812 GTTTGCAAAC
*
64822 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA AA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
64863 TA TA TA
1 TA TA TA
64869 AATAAAATAA
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:64834 original size:95 final size:95
Alignment explanation
Indices: 64651--64858 Score: 233
Period size: 95 Copynumber: 2.1 Consensus size: 95
64641 TTTCAAAACT
* *
64651 ATATATTATATAAAATTTTCAAAAATGTTTTCAAAACTATATATTGTATAAGTTTTCAAAATGAA
1 ATATATTATAT--AATTTTCAAAAATGTTTTAAAAACTATATATTATATAAGTTTTCAAAATG-A
*
64716 TTTAAAAACTATATAGTACATATAT-TTTATAA
63 TTTAAAAACTATATAGTACATATATATATATAA
* *
64748 ATATATTATATAGTTTTCAAAAATGTTTTAAAAACTATATATTATATATGTATTTTCAAAAATCG
1 ATATATTATATAATTTTCAAAAATGTTTTAAAAACTATATATTATATAAG--TTTTC-AAAAT-G
** * *
64813 -TTTGCAAACTATAATA-TATATATATATATATAT
62 ATTTAAAAACTAT-ATAGTACATATATATATATAA
64846 ATATATATATATA
1 ATATAT-TATATA
64859 TAAATATATA
Statistics
Matches: 95, Mismatches: 9, Indels: 12
0.82 0.08 0.10
Matches are distributed among these distances:
95 35 0.37
97 34 0.36
98 19 0.20
99 7 0.07
ACGTcount: A:0.46, C:0.06, G:0.05, T:0.44
Consensus pattern (95 bp):
ATATATTATATAATTTTCAAAAATGTTTTAAAAACTATATATTATATAAGTTTTCAAAATGATTT
AAAAACTATATAGTACATATATATATATAA
Found at i:65567 original size:84 final size:84
Alignment explanation
Indices: 65479--66259 Score: 650
Period size: 84 Copynumber: 9.4 Consensus size: 84
65469 GTTTGCCTCT
* * * * ** * * * *
65479 GAGCTGAGTGTAATCGAAATCGAAGGTCTTCGGTTGGCAGATAACTTTTCTTGACTTAGGATATA
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATG
* *
65544 CTGTAAATAATATGCCTTG
66 CTGTAAATGATGTGCCTTG
* * * * *
65563 GAGCTGAGCGTAGTCGAACTTGAAGGTCTTTTGG-TGACAGATAACCCTTCTAGCCTTGAGTTAT
1 GAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTAT
* **
65627 GCTGTAAATAATGTGCCCTCA
65 GCTGTAAATGATGTG-CCTTG
* * ** * * **
65648 AATCTGAATGTAATCGAACTCGAGGGTC--T--TTGGCAGATAACCCTTCTCGACTTAAACTATG
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATG
* * *
65709 CTATAAATGATGTGCTTTA
66 CTGTAAATGATGTGCCTTG
* * * *
65728 GAGCTGAGCGTAGTCCAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGAGTTAATTTATA
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATG
* *
65793 CTGCAAATGATATGCCTTG
66 CTGTAAATGATGTGCCTTG
** * * * * *
65812 GAGCTGAGCGTAGTCGAACTTAAAGGTCTTTTGG-TGACAGATAACCCTTTTAGCCTTGAGTTAT
1 GAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTAT
* *
65876 ACTGTAAATGATGTGCCCTCG
65 GCTGTAAATGATGTG-CCTTG
* * * * * * * * *
65897 AATCTGAGTGTAATCAAACTTGAGGGTC--T--TTGGCAGATAGCCCTTCTCGACTTAAGCTATG
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATG
** * *
65958 CTACAAATGATGTGCATTA
66 CTGTAAATGATGTGCCTTG
* * * * * *
65977 GAGTTGAGCGTAGTCGAACTCAAAAGTCTTTGGTTGACAGATAACCCTTCACGACTAAAGTTATG
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATG
* * *
66042 TTGCAAATGATATGCCTTG
66 CTGTAAATGATGTGCCTTG
* * * * * *
66061 GAGCTGAGTGTAGTCGAACTCGAAGGTCTTTTGG-AGACAGATAACCCTTCTAGCCTTGAGTTAT
1 GAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTAT
*
66125 GCTGTAAATGATGTGCCCTCG
65 GCTGTAAATGATGTG-CCTTG
* * * * * * * * *
66146 AAGCTGAGTGCAATCGAACTCGAAGGTCTTCGATTGGTAGATAGCTCTTCTCGACTTAA-TATAT
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGT-TAT
*
66210 GCTGCAAATGATGTGCCTTG
65 GCTGTAAATGATGTGCCTTG
66230 GAGCTGAGCGTAGTCGAACTCGAAGGTCTT
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTT
66260 GGCTGATAGA
Statistics
Matches: 543, Mismatches: 136, Indels: 36
0.76 0.19 0.05
Matches are distributed among these distances:
80 44 0.08
81 72 0.13
82 4 0.01
84 297 0.55
85 126 0.23
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.31
Consensus pattern (84 bp):
GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATG
CTGTAAATGATGTGCCTTG
Found at i:65755 original size:165 final size:168
Alignment explanation
Indices: 65480--66259 Score: 622
Period size: 165 Copynumber: 4.7 Consensus size: 168
65470 TTTGCCTCTG
* * * * * ** * *
65480 AGCTGAGTGTAATCGAAATCGAAGGTC-TTCGGTTGGCAGATAACTTTTCTTGACTTAGGA-TAT
1 AGCTGAGCGTAATCGAACTCAAAGGTCTTTTGG-TGACAGATAACCCTTCTCGACTTA-AATTAT
* * * * *
65543 ACTGTAAATAATATGCCTTGGAGCTGAGCGTAGTCGAACTTGAAGGTCTTTTGGTGACAGATAAC
64 GCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACAGATAAC
* * * *
65608 CCTTCTAGCCTTGAGTTATGCTGTAAATAATGTGCCCTCAA
129 CCTTCTAGACTTAAGTTATGCTGCAAATGATGTG-CCTCAA
* ** * * *
65649 ATCTGAATGTAATCGAACTCGAGGGTC-TTT-G-G-CAGATAACCCTTCTCGACTTAAACTATGC
1 AGCTGAGCGTAATCGAACTCAAAGGTCTTTTGGTGACAGATAACCCTTCTCGACTTAAATTATGC
** * * * *
65710 TATAAATGATGTGCTTTAGAGCTGAGCGTAGTCCAACTCGAAGGTC-TTTGGTTGGCAGATAACC
66 TGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGG-TGACAGATAACC
* * * * * ***
65774 CTTCTCGAGTTAATTTATACTGCAAATGATATGCCTTGG
130 CTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTCAA
* * * * * * * *
65813 AGCTGAGCGTAGTCGAACTTAAAGGTCTTTTGGTGACAGATAACCCTTTTAGCCTTGAGTTATAC
1 AGCTGAGCGTAATCGAACTCAAAGGTCTTTTGGTGACAGATAACCCTTCTCGACTTAAATTATGC
* * * * * * * * * *
65878 TGTAAATGATGTGCCCTCGAATCTGAGTGTAATCAAACTTGAGGGTC-TTT-G-G-CAGATAGCC
66 TGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACAGATAACC
* * * * * *
65939 CTTCTCGACTTAAGCTATGCTACAAATGATGTGCATTAG
130 CTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTCAA
* * * *
65978 AGTTGAGCGTAGTCGAACTCAAAAGTC-TTTGGTTGACAGATAACCCTTCACGAC-TAAAGTTAT
1 AGCTGAGCGTAATCGAACTCAAAGGTCTTTTGG-TGACAGATAACCCTTCTCGACTTAAA-TTAT
* * * *
66041 GTTGCAAATGATATGCCTTGGAGCTGAGTGTAGTCGAACTCGAAGGTCTTTTGGAGACAGATAAC
64 GCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACAGATAAC
* * * *
66106 CCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGA
129 CCTTCTAGACTTAAGTTATGCTGCAAATGATGTG-CCTCAA
* * * * *
66147 AGCTGAGTGCAATCGAACTCGAAGGTCTTCGATTGGT---AGATAGCTCTTCTCGACTT-AATAT
1 AGCTGAGCGTAATCGAACTCAAAGGTCTT---TTGGTGACAGATAACCCTTCTCGACTTAAAT-T
66208 ATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTT
62 ATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTT
66260 GGCTGATAGA
Statistics
Matches: 484, Mismatches: 107, Indels: 40
0.77 0.17 0.06
Matches are distributed among these distances:
164 62 0.13
165 197 0.41
166 4 0.01
167 2 0.00
168 72 0.15
169 140 0.29
170 2 0.00
172 1 0.00
173 4 0.01
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.31
Consensus pattern (168 bp):
AGCTGAGCGTAATCGAACTCAAAGGTCTTTTGGTGACAGATAACCCTTCTCGACTTAAATTATGC
TGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACAGATAACCC
TTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTCAA
Found at i:65924 original size:249 final size:249
Alignment explanation
Indices: 65479--66259 Score: 1105
Period size: 249 Copynumber: 3.1 Consensus size: 249
65469 GTTTGCCTCT
* * * * ** * * *
65479 GAGCTGAGTGTAATCGAAATCGAAGGTCTTCGGTTGGCAGATAACTTTTCTTGACTTAGGATATA
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATA
* *
65544 CTGTAAATAATATGCCTTGGAGCTGAGCGTAGTCGAACTTGAAGGTCTTTTGGTGACAGATAACC
66 CTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTTGAAGGTCTTTTGGTGACAGATAACC
* * *
65609 CTTCTAGCCTTGAGTTATGCTGTAAATAATGTGCCCTCAAATCTGAATGTAATCGAACTCGAGGG
131 CTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAATCTGAGTGTAATCGAACTCGAGGG
* * *
65674 TCTTTGGCAGATAACCCTTCTCGACTTAAACTATGCTATAAATGATGTGCTTTA
196 TCTTTGGCAGATAGCCCTTCTCGACTTAAACTATGCTACAAATGATGTGCATTA
* * *
65728 GAGCTGAGCGTAGTCCAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGAGTTAATTTATA
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATA
*
65793 CTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTTAAAGGTCTTTTGGTGACAGATAACC
66 CTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTTGAAGGTCTTTTGGTGACAGATAACC
* * * *
65858 CTTTTAGCCTTGAGTTATACTGTAAATGATGTGCCCTCGAATCTGAGTGTAATCAAACTTGAGGG
131 CTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAATCTGAGTGTAATCGAACTCGAGGG
*
65923 TCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTACAAATGATGTGCATTA
196 TCTTTGGCAGATAGCCCTTCTCGACTTAAACTATGCTACAAATGATGTGCATTA
* * * * * * *
65977 GAGTTGAGCGTAGTCGAACTCAAAAGTCTTTGGTTGACAGATAACCCTTCACGACTAAAGTTATG
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATA
* * * *
66042 TTGCAAATGATATGCCTTGGAGCTGAGTGTAGTCGAACTCGAAGGTCTTTTGGAGACAGATAACC
66 CTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTTGAAGGTCTTTTGGTGACAGATAACC
* * *
66107 CTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGCAATCGAACTCGAAGG
131 CTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAATCTGAGTGTAATCGAACTCGAGGG
* * * * *
66172 TCTTCGATTGGTAGATAGCTCTTCTCGACTTAATA-TATGCTGCAAATGATGTGCCTTG
196 TC-T---TTGGCAGATAGCCCTTCTCGACTTAA-ACTATGCTACAAATGATGTGCATTA
66230 GAGCTGAGCGTAGTCGAACTCGAAGGTCTT
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTT
66260 GGCTGATAGA
Statistics
Matches: 470, Mismatches: 57, Indels: 6
0.88 0.11 0.01
Matches are distributed among these distances:
249 398 0.85
250 1 0.00
253 71 0.15
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.31
Consensus pattern (249 bp):
GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATA
CTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTTGAAGGTCTTTTGGTGACAGATAACC
CTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAATCTGAGTGTAATCGAACTCGAGGG
TCTTTGGCAGATAGCCCTTCTCGACTTAAACTATGCTACAAATGATGTGCATTA
Found at i:71429 original size:17 final size:17
Alignment explanation
Indices: 71407--71439 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
71397 ATGTTAGAGA
71407 AAATAAATAAAT-AAAAT
1 AAAT-AATAAATCAAAAT
71424 AAATAATAAATCAAAA
1 AAATAATAAATCAAAA
71440 GAACGAGAAA
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:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (17 bp):
AAATAATAAATCAAAAT
Found at i:72926 original size:13 final size:14
Alignment explanation
Indices: 72903--72936 Score: 52
Period size: 13 Copynumber: 2.4 Consensus size: 14
72893 TATATATTAT
72903 ATATATTTTCAAAA
1 ATATATTTTCAAAA
72917 ATAT-TTTTCAAAA
1 ATATATTTTCAAAA
72930 ACTATAT
1 A-TATAT
72937 AATATATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 10 0.56
14 7 0.39
15 1 0.06
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.44
Consensus pattern (14 bp):
ATATATTTTCAAAA
Found at i:72960 original size:11 final size:11
Alignment explanation
Indices: 72944--72968 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
72934 TATAATATAT
72944 AAATGTTTTCA
1 AAATGTTTTCA
72955 AAATGTTTTCA
1 AAATGTTTTCA
72966 AAA
1 AAA
72969 ATATATATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (11 bp):
AAATGTTTTCA
Found at i:73004 original size:37 final size:38
Alignment explanation
Indices: 72768--73136 Score: 367
Period size: 37 Copynumber: 9.9 Consensus size: 38
72758 AATGAAAAAA
* *
72768 TTCAAAAAC-ATATAATATATTAA-TTTCTAAAATAT-TT
1 TTCAAAAACTATATATTATATAAATTTTC-AAAA-ATGTT
* * *** *
72805 TTTAAAAATTATATATTATACGTATTTTCCAAAAACGTT
1 TTCAAAAACTATATATTATATAAATTTT-CAAAAATGTT
* *
72844 TTAAAAAACTATATAATATATATATATTTTCAAAAATGTT
1 TTCAAAAACTATAT-AT-TATATAAATTTTCAAAAATGTT
* * *
72884 TTAAAAAACTATATATTATATATATTTTCAAAAATATTT
1 TTCAAAAACTATATATTATATAAATTTTCAAAAAT-GTT
*
72923 TTCAAAAACTATATAATATATAAATGTTTTC-AAAATGTT
1 TTCAAAAACTATATATTATATAAA--TTTTCAAAAATGTT
72962 TTCAAAAA-TATATATTATATAAATTTTCAAAAATGTT
1 TTCAAAAACTATATATTATATAAATTTTCAAAAATGTT
*
72999 TTC-AAAACTATATATTATATAAGTTTTC-AAAATGATT
1 TTCAAAAACTATATATTATATAAATTTTCAAAAATG-TT
*
73036 TT-AAAAACTATATATTATATATA-TTT--AAAATGTT
1 TTCAAAAACTATATATTATATAAATTTTCAAAAATGTT
*
73070 TT-AAAAA-TATATA-TATAT-AGTTTTCAAAAATGTT
1 TTCAAAAACTATATATTATATAAATTTTCAAAAATGTT
73104 TT-AAAAACTATATA-TATATACATATTTTCAAAA
1 TTCAAAAACTATATATTATATA-A-ATTTTCAAAA
73137 TCGTTTGCAA
Statistics
Matches: 288, Mismatches: 24, Indels: 39
0.82 0.07 0.11
Matches are distributed among these distances:
32 8 0.03
33 6 0.02
34 24 0.08
35 17 0.06
36 18 0.06
37 60 0.21
38 53 0.18
39 56 0.19
40 31 0.11
41 15 0.05
ACGTcount: A:0.47, C:0.07, G:0.03, T:0.43
Consensus pattern (38 bp):
TTCAAAAACTATATATTATATAAATTTTCAAAAATGTT
Found at i:73158 original size:39 final size:40
Alignment explanation
Indices: 73074--73167 Score: 106
Period size: 39 Copynumber: 2.4 Consensus size: 40
73064 AATGTTTTAA
*
73074 AAATATATATATATAGTTTTCAAAAATGTTTTAAAAACTAT
1 AAATATATATACATA-TTTTCAAAAATGTTTTAAAAACTAT
**
73115 --ATATATATACATATTTTC-AAAATCG-TTTGCAAACTAT
1 AAATATATATACATATTTTCAAAAAT-GTTTTAAAAACTAT
*
73152 AAATATATATAGATAT
1 AAATATATATACATAT
73168 ATATATAAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
37 15 0.33
38 6 0.13
39 25 0.54
ACGTcount: A:0.47, C:0.07, G:0.05, T:0.40
Consensus pattern (40 bp):
AAATATATATACATATTTTCAAAAATGTTTTAAAAACTAT
Done.