Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007967.1 Hibiscus syriacus cultivar Beakdansim tig00110402_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: 2476418
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 11
Found at i:401436 original size:18 final size:18
Alignment explanation
Indices: 401387--401438 Score: 59
Period size: 21 Copynumber: 2.7 Consensus size: 18
401377 TTAACTAATC
401387 TATTATTTTAATAAATAA
1 TATTATTTTAATAAATAA
* *
401405 TAAAATATTATTAATTAATAA
1 T--ATTATT-TTAATAAATAA
401426 TATTATTTTAATA
1 TATTATTTTAATA
401439 CAAAAAAACC
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
18 6 0.22
19 5 0.19
20 5 0.19
21 11 0.41
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TATTATTTTAATAAATAA
Found at i:401598 original size:72 final size:73
Alignment explanation
Indices: 401519--401653 Score: 218
Period size: 72 Copynumber: 1.9 Consensus size: 73
401509 ATTTTTTAGT
* * *
401519 GAGCTTAACGAGCAACGAGTCGAGTTGAGCATC-AAATTTTTTTAACGAGCACAAGTCGAGCATA
1 GAGCTTAACGAGCAACGAGTCGAGTCGAGCAGCAAAAATTTTTTAACGAGCACAAGTCGAGCATA
401583 ATTTTAAC
66 ATTTTAAC
**
401591 GAGCTTAACGAGCAACGAGTCGAGTCGAGCAGCAAAAATTTTTTAACGAGCATGAGTCGAGCA
1 GAGCTTAACGAGCAACGAGTCGAGTCGAGCAGCAAAAATTTTTTAACGAGCACAAGTCGAGCA
401654 CTACCCAACT
Statistics
Matches: 57, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
72 31 0.54
73 26 0.46
ACGTcount: A:0.35, C:0.19, G:0.24, T:0.23
Consensus pattern (73 bp):
GAGCTTAACGAGCAACGAGTCGAGTCGAGCAGCAAAAATTTTTTAACGAGCACAAGTCGAGCATA
ATTTTAAC
Found at i:401921 original size:15 final size:15
Alignment explanation
Indices: 401901--401973 Score: 62
Period size: 15 Copynumber: 5.1 Consensus size: 15
401891 CTAGAACTTC
401901 CTTCCCATTTGAAAA
1 CTTCCCATTTGAAAA
*
401916 CTTCCCATTCGAAAA
1 CTTCCCATTTGAAAA
* * ** *
401931 C-ACGC-GCT-AGAA
1 CTTCCCATTTGAAAA
*
401943 CTTCCCGTTTGAAAA
1 CTTCCCATTTGAAAA
401958 CTTCCCATTTGAAAA
1 CTTCCCATTTGAAAA
401973 C
1 C
401974 ACGCGCCAGA
Statistics
Matches: 42, Mismatches: 13, Indels: 6
0.69 0.21 0.10
Matches are distributed among these distances:
12 4 0.10
13 2 0.05
14 3 0.07
15 33 0.79
ACGTcount: A:0.32, C:0.30, G:0.11, T:0.27
Consensus pattern (15 bp):
CTTCCCATTTGAAAA
Found at i:401960 original size:42 final size:42
Alignment explanation
Indices: 401882--402000 Score: 166
Period size: 42 Copynumber: 2.7 Consensus size: 42
401872 TGTGAGAGAC
*
401882 AAACACGCGCTAGAACTTCCTTCCCATTTGAAAACTTCCCATTCGA
1 AAACACGCGCTAGAA----CTTCCCGTTTGAAAACTTCCCATTCGA
*
401928 AAACACGCGCTAGAACTTCCCGTTTGAAAACTTCCCATTTGA
1 AAACACGCGCTAGAACTTCCCGTTTGAAAACTTCCCATTCGA
* *
401970 AAACACGCGCCAGAACTTCCCGTTTAAAAAC
1 AAACACGCGCTAGAACTTCCCGTTTGAAAAC
402001 GAAACGAGTT
Statistics
Matches: 69, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
42 54 0.78
46 15 0.22
ACGTcount: A:0.33, C:0.31, G:0.13, T:0.24
Consensus pattern (42 bp):
AAACACGCGCTAGAACTTCCCGTTTGAAAACTTCCCATTCGA
Found at i:403586 original size:90 final size:92
Alignment explanation
Indices: 403410--403590 Score: 276
Period size: 90 Copynumber: 2.0 Consensus size: 92
403400 GCATGCATGC
* * * * *
403410 ATGTATGTCTTTCATTGTTTGGTAAGGTGTTTTGGAGTCGGTTGTGTAGTTTTGATTTTTTGATG
1 ATGTATGTCTTTCATTATTTGGTAAGGTGTCTTGGAATCGGTTGTGTAGTTTCGACTTTTTGATG
*
403475 CTAATATGAATCTCAATATATGTATGT
66 CTAATATGAATCTCAAGATATGTATGT
* *
403502 ATGTATGTCTTTCATTATTTGGTAAGGTG-CTTGGAATTGGTTTTGTAG-TTCGACTTTTTGATG
1 ATGTATGTCTTTCATTATTTGGTAAGGTGTCTTGGAATCGGTTGTGTAGTTTCGACTTTTTGATG
403565 CTAATATGAATCTCAAGATATGTATG
66 CTAATATGAATCTCAAGATATGTATG
403591 AATTTAGGTA
Statistics
Matches: 81, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
90 38 0.47
91 15 0.19
92 28 0.35
ACGTcount: A:0.22, C:0.08, G:0.23, T:0.47
Consensus pattern (92 bp):
ATGTATGTCTTTCATTATTTGGTAAGGTGTCTTGGAATCGGTTGTGTAGTTTCGACTTTTTGATG
CTAATATGAATCTCAAGATATGTATGT
Found at i:405928 original size:122 final size:122
Alignment explanation
Indices: 405711--405933 Score: 410
Period size: 122 Copynumber: 1.8 Consensus size: 122
405701 GACGATCATT
*
405711 ACAAAAAGATGAGTTTAAAAATATGAATTGTCAGGTGACTACTTTGTAATTTTTAATAATCGAGG
1 ACAAAAAGATGAGTTTAAAAATATGAATTGTCAGGTGACTACTTTATAATTTTTAATAATCGAGG
*
405776 TACTCAACAAAATAATATCTTATAATTAAAAGATCAGACGATCATTTATTTTTTAAC
66 TACTCAACAAAACAATATCTTATAATTAAAAGATCAGACGATCATTTATTTTTTAAC
405833 ACAAAAAGATGAGTTTAAAAATATGAATTGTCAGGTGACTACTTTATAATTTTTAATAATCGAGG
1 ACAAAAAGATGAGTTTAAAAATATGAATTGTCAGGTGACTACTTTATAATTTTTAATAATCGAGG
* *
405898 TACTCAACAGAACAATATTTTATAATTAAAAGATCA
66 TACTCAACAAAACAATATCTTATAATTAAAAGATCA
405934 CTTTATAATT
Statistics
Matches: 97, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
122 97 1.00
ACGTcount: A:0.43, C:0.10, G:0.13, T:0.34
Consensus pattern (122 bp):
ACAAAAAGATGAGTTTAAAAATATGAATTGTCAGGTGACTACTTTATAATTTTTAATAATCGAGG
TACTCAACAAAACAATATCTTATAATTAAAAGATCAGACGATCATTTATTTTTTAAC
Found at i:406057 original size:8 final size:8
Alignment explanation
Indices: 406023--406120 Score: 59
Period size: 8 Copynumber: 13.0 Consensus size: 8
406013 ATCTCTAAAA
*
406023 TATACTAT
1 TATAATAT
406031 TAATAAT-T
1 T-ATAATAT
*
406039 T-TAATAA
1 TATAATAT
406046 TATAATAT
1 TATAATAT
406054 TAT-AT-T
1 TATAATAT
* *
406060 TTTAGTAT
1 TATAATAT
406068 TATAATAT
1 TATAATAT
*
406076 TATATTAT
1 TATAATAT
406084 TATAATA-
1 TATAATAT
406091 -ATAATA-
1 TATAATAT
406097 -ATAATAT
1 TATAATAT
**
406104 TATCTTAT
1 TATAATAT
406112 TAATAATAT
1 T-ATAATAT
406121 ATTATTTATT
Statistics
Matches: 69, Mismatches: 13, Indels: 15
0.71 0.13 0.15
Matches are distributed among these distances:
6 19 0.28
7 4 0.06
8 37 0.54
9 9 0.13
ACGTcount: A:0.46, C:0.02, G:0.01, T:0.51
Consensus pattern (8 bp):
TATAATAT
Found at i:406071 original size:22 final size:22
Alignment explanation
Indices: 406021--406132 Score: 100
Period size: 22 Copynumber: 4.8 Consensus size: 22
406011 AAATCTCTAA
* *
406021 AATATACTATTAATAATTTTAAT
1 AATATAATATT-ATATTTTTAAT
*
406044 AATATAATATTATATTTTTAGT
1 AATATAATATTATATTTTTAAT
*
406066 ATTATAATATTATATTATTATAAT
1 AATATAATATTATATT-TT-TAAT
*
406090 AATAATAATAATATTATCTTATTAAT
1 AAT-ATAATATTA-TAT-TT-TTAAT
*
406116 AATATATTATT-TATTTT
1 AATATAATATTATATTTT
406133 GTTTATCAAT
Statistics
Matches: 74, Mismatches: 9, Indels: 14
0.76 0.09 0.14
Matches are distributed among these distances:
21 1 0.01
22 26 0.35
23 15 0.20
24 5 0.07
25 14 0.19
26 11 0.15
27 2 0.03
ACGTcount: A:0.45, C:0.02, G:0.01, T:0.53
Consensus pattern (22 bp):
AATATAATATTATATTTTTAAT
Found at i:406106 original size:20 final size:19
Alignment explanation
Indices: 406065--406125 Score: 56
Period size: 20 Copynumber: 3.3 Consensus size: 19
406055 ATATTTTTAG
*
406065 TATTATAAT-ATTAT-AT-
1 TATTATAATAATAATAATA
406081 TATTATAATAATAATAATAA
1 TATTATAATAATAATAAT-A
** *
406101 TATTATCTTATTAATAATA
1 TATTATAATAATAATAATA
406120 TATTAT
1 TATTAT
406126 TTATTTTGTT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
16 9 0.24
17 4 0.11
18 2 0.05
19 7 0.19
20 15 0.41
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.51
Consensus pattern (19 bp):
TATTATAATAATAATAATA
Found at i:406391 original size:20 final size:20
Alignment explanation
Indices: 406363--406415 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
406353 ACCGTTGATA
*
406363 TTCTTTATTTTCTATTTCTT
1 TTCTTTATTTTCTATTTATT
* * * *
406383 TTCTATATTGTATCTTTATT
1 TTCTTTATTTTCTATTTATT
406403 TTCTTTATTTTCT
1 TTCTTTATTTTCT
406416 TTTTTTCAAT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.13, C:0.13, G:0.02, T:0.72
Consensus pattern (20 bp):
TTCTTTATTTTCTATTTATT
Found at i:406409 original size:9 final size:9
Alignment explanation
Indices: 406363--406422 Score: 59
Period size: 9 Copynumber: 6.3 Consensus size: 9
406353 ACCGTTGATA
406363 TTCTTTATT
1 TTCTTTATT
*
406372 TTCTATTTCTT
1 TTC--TTTATT
*
406383 TTCTATATT
1 TTCTTTATT
406392 GTATCTTTATT
1 -T-TCTTTATT
406403 TTCTTTATT
1 TTCTTTATT
406412 TTCTTT-TT
1 TTCTTTATT
406420 TTC
1 TTC
406423 AATAAGTTTG
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
8 5 0.12
9 21 0.49
10 2 0.05
11 15 0.35
ACGTcount: A:0.12, C:0.13, G:0.02, T:0.73
Consensus pattern (9 bp):
TTCTTTATT
Found at i:406483 original size:23 final size:22
Alignment explanation
Indices: 406441--406494 Score: 63
Period size: 23 Copynumber: 2.4 Consensus size: 22
406431 TGCATGTGTT
*
406441 GCACGTTTTCATCTGCCTTTATG
1 GCACGTTTTCATATGCCTTT-TG
* *
406464 GCACGTTTTCTTATGTCTTTTG
1 GCACGTTTTCATATGCCTTTTG
*
406486 GCATGTTTT
1 GCACGTTTT
406495 TCGGTTCTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
22 10 0.37
23 17 0.63
ACGTcount: A:0.11, C:0.20, G:0.19, T:0.50
Consensus pattern (22 bp):
GCACGTTTTCATATGCCTTTTG
Found at i:406511 original size:28 final size:28
Alignment explanation
Indices: 406480--406540 Score: 86
Period size: 28 Copynumber: 2.2 Consensus size: 28
406470 TTTCTTATGT
* * *
406480 CTTTTGGCATGTTTTTCGGTTCTTTTAC
1 CTTTTGACATATTTTTCGGTTCTTTGAC
*
406508 CTTTTGACATATTTTTTGGTTCTTTGAC
1 CTTTTGACATATTTTTCGGTTCTTTGAC
406536 CTTTT
1 CTTTT
406541 TTATTTATCT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.10, C:0.16, G:0.15, T:0.59
Consensus pattern (28 bp):
CTTTTGACATATTTTTCGGTTCTTTGAC
Found at i:406914 original size:13 final size:13
Alignment explanation
Indices: 406896--406921 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
406886 TTAATTTACG
406896 ATTTTGATTGTAA
1 ATTTTGATTGTAA
406909 ATTTTGATTGTAA
1 ATTTTGATTGTAA
406922 TTTGAGATAT
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:0.00, G:0.15, T:0.54
Consensus pattern (13 bp):
ATTTTGATTGTAA
Found at i:409544 original size:47 final size:48
Alignment explanation
Indices: 409481--409571 Score: 166
Period size: 47 Copynumber: 1.9 Consensus size: 48
409471 CTCGTGAGTA
*
409481 GCTCGAACTCGATTTGATCAAAATTTGATAAACGCTCAAATTGAGTTG
1 GCTCGAACTCGATTTGATCAAAATTCGATAAACGCTCAAATTGAGTTG
409529 GCTCG-ACTCGATTTGATCAAAATTCGATAAACGCTCAAATTGA
1 GCTCGAACTCGATTTGATCAAAATTCGATAAACGCTCAAATTGA
409572 ATTCGCGAGC
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
47 37 0.88
48 5 0.12
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.30
Consensus pattern (48 bp):
GCTCGAACTCGATTTGATCAAAATTCGATAAACGCTCAAATTGAGTTG
Found at i:409755 original size:18 final size:18
Alignment explanation
Indices: 409705--409757 Score: 52
Period size: 21 Copynumber: 2.7 Consensus size: 18
409695 TTAACTAATC
409705 TATTATTTTTAATAAATAA
1 TATTA-TTTTAATAAATAA
* *
409724 TAAAATATTATTAATTAATAA
1 T--ATTATT-TTAATAAATAA
409745 TATTATTTTAATA
1 TATTATTTTAATA
409758 CAAAAAAACC
Statistics
Matches: 27, Mismatches: 4, Indels: 7
0.71 0.11 0.18
Matches are distributed among these distances:
18 5 0.19
19 6 0.22
20 2 0.07
21 14 0.52
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TATTATTTTAATAAATAA
Found at i:409865 original size:21 final size:21
Alignment explanation
Indices: 409839--409882 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
409829 TTTTTTTAGT
409839 GAGCTTAACGAGCAACGAGTC
1 GAGCTTAACGAGCAACGAGTC
409860 GAGCTTAACGAGCAACGAGTC
1 GAGCTTAACGAGCAACGAGTC
409881 GA
1 GA
409883 ATTGAGCAGC
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:0.34, C:0.23, G:0.30, T:0.14
Consensus pattern (21 bp):
GAGCTTAACGAGCAACGAGTC
Found at i:410256 original size:15 final size:15
Alignment explanation
Indices: 410236--410266 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
410226 CTAGAACTTC
*
410236 CTTCCCATTTGAAAA
1 CTTCCCATTCGAAAA
410251 CTTCCCATTCGAAAA
1 CTTCCCATTCGAAAA
410266 C
1 C
410267 ACGCGCTAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.32, C:0.32, G:0.06, T:0.29
Consensus pattern (15 bp):
CTTCCCATTCGAAAA
Found at i:410295 original size:42 final size:42
Alignment explanation
Indices: 410236--410335 Score: 173
Period size: 42 Copynumber: 2.4 Consensus size: 42
410226 CTAGAACTTC
*
410236 CTTCCCATTTGAAAACTTCCCATTCGAAAACACGCGCTAGAA
1 CTTCCCATTTGAAAACTTCCCATTCGAAAACACGCGCCAGAA
*
410278 CTTCCCGTTTGAAAACTTCCCATTCGAAAACACGCGCCAGAA
1 CTTCCCATTTGAAAACTTCCCATTCGAAAACACGCGCCAGAA
*
410320 CTTCCCATTTAAAAAC
1 CTTCCCATTTGAAAAC
410336 GAAACGAGTT
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 54 1.00
ACGTcount: A:0.33, C:0.32, G:0.11, T:0.24
Consensus pattern (42 bp):
CTTCCCATTTGAAAACTTCCCATTCGAAAACACGCGCCAGAA
Found at i:414298 original size:47 final size:48
Alignment explanation
Indices: 414235--414328 Score: 172
Period size: 47 Copynumber: 2.0 Consensus size: 48
414225 CTCGTGAGTA
*
414235 GCTCGAACTCGATTTGATCAAAATTTGATAAACGCTCAAATTGAGTTG
1 GCTCGAACTCGATTTGATCAAAATTCGATAAACGCTCAAATTGAGTTG
414283 GCTCG-ACTCGATTTGATCAAAATTCGATAAACGCTCAAATTGAGTT
1 GCTCGAACTCGATTTGATCAAAATTCGATAAACGCTCAAATTGAGTT
414329 CGCGAGCAGC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
47 40 0.89
48 5 0.11
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (48 bp):
GCTCGAACTCGATTTGATCAAAATTCGATAAACGCTCAAATTGAGTTG
Found at i:414508 original size:18 final size:18
Alignment explanation
Indices: 414458--414510 Score: 52
Period size: 21 Copynumber: 2.7 Consensus size: 18
414448 TTAACTAATC
414458 TATTATTTTTAATAAATAA
1 TATTA-TTTTAATAAATAA
* *
414477 TAAAATATTATTAATTAATAA
1 T--ATTATT-TTAATAAATAA
414498 TATTATTTTAATA
1 TATTATTTTAATA
414511 CAAAAAACCC
Statistics
Matches: 27, Mismatches: 4, Indels: 7
0.71 0.11 0.18
Matches are distributed among these distances:
18 5 0.19
19 6 0.22
20 2 0.07
21 14 0.52
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TATTATTTTAATAAATAA
Found at i:414617 original size:21 final size:21
Alignment explanation
Indices: 414591--414634 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
414581 TTTTTTTAGT
414591 GAGCTTAACGAGCAACGAGTC
1 GAGCTTAACGAGCAACGAGTC
414612 GAGCTTAACGAGCAACGAGTC
1 GAGCTTAACGAGCAACGAGTC
414633 GA
1 GA
414635 ATTGAGCAGC
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:0.34, C:0.23, G:0.30, T:0.14
Consensus pattern (21 bp):
GAGCTTAACGAGCAACGAGTC
Found at i:415006 original size:15 final size:15
Alignment explanation
Indices: 414986--415058 Score: 62
Period size: 15 Copynumber: 5.1 Consensus size: 15
414976 CTAGAACTTC
414986 CTTCCCATTTGAAAA
1 CTTCCCATTTGAAAA
*
415001 CTTCCCATTCGAAAA
1 CTTCCCATTTGAAAA
* * ** *
415016 C-ACGC-GCT-AGAA
1 CTTCCCATTTGAAAA
*
415028 CTTCCCGTTTGAAAA
1 CTTCCCATTTGAAAA
415043 CTTCCCATTTGAAAA
1 CTTCCCATTTGAAAA
415058 C
1 C
415059 ACGCGCCAGA
Statistics
Matches: 42, Mismatches: 13, Indels: 6
0.69 0.21 0.10
Matches are distributed among these distances:
12 4 0.10
13 2 0.05
14 3 0.07
15 33 0.79
ACGTcount: A:0.32, C:0.30, G:0.11, T:0.27
Consensus pattern (15 bp):
CTTCCCATTTGAAAA
Found at i:415045 original size:42 final size:42
Alignment explanation
Indices: 414986--415085 Score: 164
Period size: 42 Copynumber: 2.4 Consensus size: 42
414976 CTAGAACTTC
* *
414986 CTTCCCATTTGAAAACTTCCCATTCGAAAACACGCGCTAGAA
1 CTTCCCGTTTGAAAACTTCCCATTCGAAAACACGCGCCAGAA
*
415028 CTTCCCGTTTGAAAACTTCCCATTTGAAAACACGCGCCAGAA
1 CTTCCCGTTTGAAAACTTCCCATTCGAAAACACGCGCCAGAA
*
415070 CTTCCCGTTTAAAAAC
1 CTTCCCGTTTGAAAAC
415086 GAAACGAGTT
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 54 1.00
ACGTcount: A:0.32, C:0.31, G:0.12, T:0.25
Consensus pattern (42 bp):
CTTCCCGTTTGAAAACTTCCCATTCGAAAACACGCGCCAGAA
Found at i:416201 original size:35 final size:35
Alignment explanation
Indices: 416162--416230 Score: 138
Period size: 35 Copynumber: 2.0 Consensus size: 35
416152 TTTGTACGGT
416162 TTGTAACTTGATATTGTTTAAGTAAAGTTTCGGGA
1 TTGTAACTTGATATTGTTTAAGTAAAGTTTCGGGA
416197 TTGTAACTTGATATTGTTTAAGTAAAGTTTCGGG
1 TTGTAACTTGATATTGTTTAAGTAAAGTTTCGGG
416231 TTTGAGTCAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.28, C:0.06, G:0.23, T:0.43
Consensus pattern (35 bp):
TTGTAACTTGATATTGTTTAAGTAAAGTTTCGGGA
Found at i:423647 original size:8 final size:8
Alignment explanation
Indices: 423634--423661 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
423624 CGGTTCGTTG
423634 CAACGGTA
1 CAACGGTA
423642 CAACGGTA
1 CAACGGTA
423650 CAACGGTA
1 CAACGGTA
423658 CAAC
1 CAAC
423662 CATTAAGATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.39, C:0.29, G:0.21, T:0.11
Consensus pattern (8 bp):
CAACGGTA
Found at i:426899 original size:157 final size:157
Alignment explanation
Indices: 426613--426955 Score: 499
Period size: 157 Copynumber: 2.2 Consensus size: 157
426603 CCTAATTTCA
* * * *** *
426613 TTATTTCTTCAATTTC-TCCTTCATTTTAAGTCAATTTTTACCAAATTTGAAACACATACTCCTA
1 TTATTTCTTCAA-TTCATCATTTATTTTAAATCCGCTTTTACCAAATTTGAAACACATACTCATA
*
426677 AACCATAGTAAAATACATGTGTACTTTAAATTCCTCTATTTGATAACAACTTTTTTATTTTTCAG
65 AACCATAGTAAAATACATGTGTACTTTAAATTCCTCTATTTGATAACAAATTTTTTATTTTTCAG
*
426742 TTTAGTCCTTCAATTTTTCATAATCTCC
130 TTTAGTCATTCAATTTTTCATAATCTCC
* ** *
426770 TTATTTCTTGAATTCATCATTTATTTTAAATCCGCTTTTACCAAATTTGAGTCACATGCTCATAA
1 TTATTTCTTCAATTCATCATTTATTTTAAATCCGCTTTTACCAAATTTGAAACACATACTCATAA
* * *
426835 ACTATAGTATAATACATGTGTACTTTAAATTCCTCTTTTTGATAACAAATTTTTTATTTTTCAGT
66 ACCATAGTAAAATACATGTGTACTTTAAATTCCTCTATTTGATAACAAATTTTTTATTTTTCAGT
426900 TTAGTCATTCAATTTTTCATAATCTCC
131 TTAGTCATTCAATTTTTCATAATCTCC
** *
426927 TTATTTCTTCAATTTGTGATTTATTTTAA
1 TTATTTCTTCAATTCATCATTTATTTTAA
426956 GTCTTTTTTT
Statistics
Matches: 165, Mismatches: 20, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
156 3 0.02
157 162 0.98
ACGTcount: A:0.29, C:0.17, G:0.06, T:0.48
Consensus pattern (157 bp):
TTATTTCTTCAATTCATCATTTATTTTAAATCCGCTTTTACCAAATTTGAAACACATACTCATAA
ACCATAGTAAAATACATGTGTACTTTAAATTCCTCTATTTGATAACAAATTTTTTATTTTTCAGT
TTAGTCATTCAATTTTTCATAATCTCC
Found at i:427239 original size:13 final size:13
Alignment explanation
Indices: 427223--427260 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
427213 TTATATATCA
427223 TATATATATTATG
1 TATATATATTATG
427236 TATATATA-TATTG
1 TATATATATTA-TG
*
427249 TATAAATATTAT
1 TATATATATTAT
427261 TATTATTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
12 2 0.09
13 18 0.82
14 2 0.09
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (13 bp):
TATATATATTATG
Found at i:427252 original size:11 final size:11
Alignment explanation
Indices: 427206--427260 Score: 51
Period size: 11 Copynumber: 5.0 Consensus size: 11
427196 CAAAATAAAC
*
427206 ATATATTTTAT
1 ATATATATTAT
427217 ATATCATA-TAT
1 ATAT-ATATTAT
427228 ATAT-TATGTAT
1 ATATATAT-TAT
*
427239 ATATATATTGT
1 ATATATATTAT
*
427250 ATAAATATTAT
1 ATATATATTAT
427261 TATTATTTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
9 2 0.06
11 29 0.81
12 5 0.14
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.53
Consensus pattern (11 bp):
ATATATATTAT
Found at i:428686 original size:20 final size:22
Alignment explanation
Indices: 428663--428712 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
428653 TTCCCTTTAC
428663 TTATTTTCTATATTT-T-ACCT
1 TTATTTTCTATATTTATGACCT
* *
428683 TTATTTT-TATTTTTATGACGT
1 TTATTTTCTATATTTATGACCT
428704 TTATTTTCT
1 TTATTTTCT
428713 TTATCCATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
19 6 0.24
20 8 0.32
21 10 0.40
22 1 0.04
ACGTcount: A:0.18, C:0.10, G:0.04, T:0.68
Consensus pattern (22 bp):
TTATTTTCTATATTTATGACCT
Found at i:432870 original size:95 final size:94
Alignment explanation
Indices: 432736--432921 Score: 275
Period size: 95 Copynumber: 2.0 Consensus size: 94
432726 TATAATATTA
*
432736 TATATATACAATAAAGCTTGAGTTATCCCTCTAGAGCAATTGGTTAAACACCCCGACTTTATGGA
1 TATATATACAATAAAGCTTGAGATATCCCTCTAGAGCAATTGGTTAAACACCCCGACTTTATGGA
* *
432801 TAATATTCAGCTAGCCTGATAAAGGTGAT
66 TAAGATTCAGCTAACCTGATAAAGGTGAT
* * * * *
432830 TATACTATACAATAAAGCTTGAGATGTCCCTCTA-AGGCAATTGGTTAAACGCTCTGGCTTTATG
1 TATA-TATACAATAAAGCTTGAGATATCCCTCTAGA-GCAATTGGTTAAACACCCCGACTTTATG
432894 GATAAGATTCAGCTAACCTGATAAAGGT
64 GATAAGATTCAGCTAACCTGATAAAGGT
432922 ATTTACATAT
Statistics
Matches: 82, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
94 5 0.06
95 77 0.94
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (94 bp):
TATATATACAATAAAGCTTGAGATATCCCTCTAGAGCAATTGGTTAAACACCCCGACTTTATGGA
TAAGATTCAGCTAACCTGATAAAGGTGAT
Found at i:434469 original size:35 final size:36
Alignment explanation
Indices: 434230--434331 Score: 113
Period size: 33 Copynumber: 2.9 Consensus size: 36
434220 TAATTTACTC
*
434230 AAAACAAAGTTTTGTCTCTCTTGAGAC-GATTTCTCTT
1 AAAACAAA-TTTTGTCTCTCTTGAGACAG-TTTCTATT
* *
434267 AAAA-AAA--TTGTCTCTCTTGAGACATTTTCTCTT
1 AAAACAAATTTTGTCTCTCTTGAGACAGTTTCTATT
* *
434300 AATACAAATTTTGTCTCTCTTGAGATAGTTTC
1 AAAACAAATTTTGTCTCTCTTGAGACAGTTTC
434332 CCTTGAAACA
Statistics
Matches: 57, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
33 27 0.47
34 3 0.05
36 23 0.40
37 4 0.07
ACGTcount: A:0.28, C:0.18, G:0.12, T:0.42
Consensus pattern (36 bp):
AAAACAAATTTTGTCTCTCTTGAGACAGTTTCTATT
Found at i:434516 original size:36 final size:36
Alignment explanation
Indices: 434230--434343 Score: 137
Period size: 36 Copynumber: 3.2 Consensus size: 36
434220 TAATTTACTC
434230 AAAACAAAGTTTTGTCTCTCTTGAGAC-GATTTCTCTT
1 AAAACAAA-TTTTGTCTCTCTTGAGACAG-TTTCTCTT
*
434267 AAAA-AAA--TTGTCTCTCTTGAGACATTTTCTCTT
1 AAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTT
* * *
434300 AATACAAATTTTGTCTCTCTTGAGATAGTTTCCCTT
1 AAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTT
*
434336 GAAACAAA
1 AAAACAAA
434344 AATATTTGAA
Statistics
Matches: 66, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
33 27 0.41
34 3 0.05
36 32 0.48
37 4 0.06
ACGTcount: A:0.31, C:0.18, G:0.11, T:0.39
Consensus pattern (36 bp):
AAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTT
Found at i:434583 original size:36 final size:36
Alignment explanation
Indices: 434531--434653 Score: 194
Period size: 36 Copynumber: 3.4 Consensus size: 36
434521 TTGAATCTAT
* *
434531 TTTC-CTTAAAACAAATTTCGTCTCCCTTGAGACAG
1 TTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACAG
* *
434566 TTTCTTTTAAAACAAATTTTGTCTCTCTTGAGACAT
1 TTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACAG
434602 TTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACAG
1 TTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACAG
*
434638 TTTCTCTTGAAACAAA
1 TTTCTCTTAAAACAAA
434654 ATCTTTGAAT
Statistics
Matches: 80, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
35 4 0.05
36 76 0.95
ACGTcount: A:0.29, C:0.20, G:0.10, T:0.41
Consensus pattern (36 bp):
TTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACAG
Found at i:434585 original size:101 final size:100
Alignment explanation
Indices: 434436--434617 Score: 292
Period size: 101 Copynumber: 1.8 Consensus size: 100
434426 ACATTTTCTA
* * * *
434436 TTAAAAAATTTTTGTCTCTCTTGAGACATTTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACAG
1 TTAAAAAAATTTCGTCTCCCTTGAGACAGTTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACAG
434501 TTTCCCTTAAAACAAAATCTTTGAATCTATTTTCC
66 TTTCCCTTAAAACAAAATCTTTGAATCTATTTTCC
*
434536 TTAAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTAAAACAAATTTTGTCTCTCTTGAGACA
1 TTAAAA-AAATTTCGTCTCCCTTGAGACAGTTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACA
* *
434601 TTTTCTCTTAAAACAAA
65 GTTTCCCTTAAAACAAA
434618 TTTTGTCTCT
Statistics
Matches: 74, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
100 6 0.08
101 68 0.92
ACGTcount: A:0.31, C:0.19, G:0.08, T:0.41
Consensus pattern (100 bp):
TTAAAAAAATTTCGTCTCCCTTGAGACAGTTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACAG
TTTCCCTTAAAACAAAATCTTTGAATCTATTTTCC
Found at i:434590 original size:137 final size:137
Alignment explanation
Indices: 434400--434816 Score: 653
Period size: 137 Copynumber: 3.1 Consensus size: 137
434390 ACAGTTTCTT
* * * *
434400 TTAAAACAAATTTTATCTCTCTTGAGACATTTTCTATTAAAA-AATTTTTGTCTCTCTTGAGACA
1 TTAAAACAAATTTCATCTCCCTTGAGACAATTTCTTTTAAAACAATTTTTGTCTCTCTTGAGACA
* *
434464 TTTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTAAAACAAAATCTTTGAATCT
66 TTTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATAT
434529 ATTTTCC
131 ATTTTCC
* * *
434536 TTAAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTAAAACAAATTTTGTCTCTCTTGAGACA
1 TTAAAACAAATTTCATCTCCCTTGAGACAATTTCTTTTAAAACAATTTTTGTCTCTCTTGAGACA
*
434601 TTTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAAATCTTTGAATAT
66 TTTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATAT
*
434666 GTTTTCC
131 ATTTTCC
* * * *
434673 TTGAAACAAATTTCATCTCCATTAAGACAATTTTTTTTAAAACAATTTTTGTCTCTCTTGAGACA
1 TTAAAACAAATTTCATCTCCCTTGAGACAATTTCTTTTAAAACAATTTTTGTCTCTCTTGAGACA
*
434738 TTTTCTCTT--AA-AAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATTT
66 TTTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATAT
*
434800 ATTTCCC
131 ATTTTCC
434807 TTAAAACAAA
1 TTAAAACAAA
434817 AAACCTTGAG
Statistics
Matches: 258, Mismatches: 22, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
134 63 0.24
135 2 0.01
136 37 0.14
137 156 0.60
ACGTcount: A:0.31, C:0.18, G:0.08, T:0.42
Consensus pattern (137 bp):
TTAAAACAAATTTCATCTCCCTTGAGACAATTTCTTTTAAAACAATTTTTGTCTCTCTTGAGACA
TTTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATAT
ATTTTCC
Found at i:434624 original size:173 final size:173
Alignment explanation
Indices: 434230--434653 Score: 694
Period size: 172 Copynumber: 2.5 Consensus size: 173
434220 TAATTTACTC
434230 AAAACAAAGTTTTGTCTCTCTTGAGACGA-TTTCTCTTAAAAAAA--TTGTCTCTCTTGAGACAT
1 AAAACAAA-TTTTGTCTCTCTTGAGAC-ATTTTCTCTTAAAAAAATTTTGTCTCTCTTGAGACAT
* * *
434292 TTTCTCTTAATACAAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAAATATTTGAATCT
64 TTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTAAAACAAAAATATTTGAATCT
* *
434357 GTTTTCCTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTT
129 ATTTTCCTTAAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTT
* * *
434402 AAAACAAATTTTATCTCTCTTGAGACATTTTCTATTAAAAAATTTTTGTCTCTCTTGAGACATTT
1 AAAACAAATTTTGTCTCTCTTGAGACATTTTCTCTTAAAAAAATTTTGTCTCTCTTGAGACATTT
*
434467 TCTCTTAAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTAAAAC-AAAATCTTTGAATCTAT
66 TCTCTTAAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTAAAACAAAAATATTTGAATCTAT
434531 TTTCCTTAAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTT
131 TTTCCTTAAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTT
*
434574 AAAACAAATTTTGTCTCTCTTGAGACATTTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACAGT
1 AAAACAAATTTTGTCTCTCTTGAGACATTTTCTCTTAAAA-AAATTTTGTCTCTCTTGAGACATT
*
434639 TTCTCTTGAAACAAA
65 TTCTCTTAAAACAAA
434654 ATCTTTGAAT
Statistics
Matches: 234, Mismatches: 14, Indels: 7
0.92 0.05 0.03
Matches are distributed among these distances:
170 1 0.00
171 30 0.13
172 103 0.44
173 100 0.43
ACGTcount: A:0.30, C:0.19, G:0.10, T:0.41
Consensus pattern (173 bp):
AAAACAAATTTTGTCTCTCTTGAGACATTTTCTCTTAAAAAAATTTTGTCTCTCTTGAGACATTT
TCTCTTAAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTAAAACAAAAATATTTGAATCTAT
TTTCCTTAAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTT
Found at i:434849 original size:32 final size:32
Alignment explanation
Indices: 434812--434914 Score: 93
Period size: 37 Copynumber: 3.1 Consensus size: 32
434802 TTCCCTTAAA
*
434812 ACAAAAAACCTTGAGACA-GTTTCTCTTGAAAC
1 ACAAAAAACCTTGA-AAATGTTTCTCTTGAAAC
* *
434844 AC-AAAAGCCTTTAAAATTGTTTCTCTTGAAAC
1 ACAAAAAACCTTGAAAA-TGTTTCTCTTGAAAC
*
434876 ACAAAAAAAAAACCTTTGAAAATGTTCCTCTTGAAAC
1 AC----AAAAAACC-TTGAAAATGTTTCTCTTGAAAC
434913 AC
1 AC
434915 CAAACCTTCG
Statistics
Matches: 57, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
30 2 0.04
31 9 0.16
32 18 0.32
37 22 0.39
38 6 0.11
ACGTcount: A:0.43, C:0.20, G:0.10, T:0.27
Consensus pattern (32 bp):
ACAAAAAACCTTGAAAATGTTTCTCTTGAAAC
Found at i:435477 original size:2 final size:2
Alignment explanation
Indices: 435465--435512 Score: 64
Period size: 2 Copynumber: 25.0 Consensus size: 2
435455 CAAAATAAAC
* *
435465 AT AT AT TT AT AT AT -T AT AT AT AT AT AT -T AT GT 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
435505 AT AT AT AT
1 AT AT AT AT
435513 TGTATAAATA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
1 2 0.05
2 38 0.95
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (2 bp):
AT
Found at i:435487 original size:17 final size:16
Alignment explanation
Indices: 435465--435532 Score: 75
Period size: 17 Copynumber: 4.1 Consensus size: 16
435455 CAAAATAAAC
*
435465 ATATATTTATA-TATT
1 ATATATATATATTATT
435480 ATATATATATATTATGT
1 ATATATATATATTAT-T
435497 ATATATATATATATATT
1 ATATATATATAT-TATT
* *
435514 GTATAAATATTATTATT
1 ATATATATA-TATTATT
435531 AT
1 AT
435533 TTTATTAAAC
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
15 10 0.22
16 3 0.07
17 26 0.58
18 6 0.13
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (16 bp):
ATATATATATATTATT
Found at i:435488 original size:13 final size:13
Alignment explanation
Indices: 435466--435512 Score: 69
Period size: 13 Copynumber: 3.7 Consensus size: 13
435456 AAAATAAACA
*
435466 TATATTTATATAT
1 TATATATATATAT
435479 TATATATATATAT
1 TATATATATATAT
*
435492 TATGTATATATA-
1 TATATATATATAT
435504 TATATATAT
1 TATATATAT
435513 TGTATAAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
12 8 0.26
13 23 0.74
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (13 bp):
TATATATATATAT
Found at i:435516 original size:19 final size:18
Alignment explanation
Indices: 435465--435523 Score: 77
Period size: 17 Copynumber: 3.3 Consensus size: 18
435455 CAAAATAAAC
*
435465 ATATATTTATATAT-TAT
1 ATATATATATATATGTAT
435482 ATATATATAT-TATGTAT
1 ATATATATATATATGTAT
435499 ATATATATATATATTGTAT
1 ATATATATATATA-TGTAT
*
435518 AAATAT
1 ATATAT
435524 TATTATTATT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
16 3 0.08
17 22 0.59
18 2 0.05
19 10 0.27
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (18 bp):
ATATATATATATATGTAT
Found at i:436902 original size:13 final size:14
Alignment explanation
Indices: 436886--436915 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
436876 TTTTTTCATC
436886 TTTATTTTATTA-T
1 TTTATTTTATTACT
436899 TTTATTTTATTACT
1 TTTATTTTATTACT
436913 TTT
1 TTT
436916 TCCCTTTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTATTTTATTACT
Found at i:436940 original size:25 final size:24
Alignment explanation
Indices: 436899--436950 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 24
436889 ATTTTATTAT
*
436899 TTTATTTTATTACTTTTTCCCTTTA
1 TTTATTTTATTAC-TTTTACCTTTA
*
436924 TTTATTTTCTATA-TTTTACCTTTA
1 TTTATTTTAT-TACTTTTACCTTTA
436948 TTT
1 TTT
436951 TTATCACGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 13 0.54
25 9 0.38
26 2 0.08
ACGTcount: A:0.17, C:0.13, G:0.00, T:0.69
Consensus pattern (24 bp):
TTTATTTTATTACTTTTACCTTTA
Found at i:436993 original size:15 final size:16
Alignment explanation
Indices: 436975--437018 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
436965 TTCTTTATCA
436975 TTATTT-TCTTTACTT
1 TTATTTATCTTTACTT
* *
436990 TTATTTACCTTTACCT
1 TTATTTATCTTTACTT
437006 TTACTTTATCTTT
1 TTA-TTTATCTTT
437019 TTCATTTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 6 0.25
16 10 0.42
17 8 0.33
ACGTcount: A:0.16, C:0.18, G:0.00, T:0.66
Consensus pattern (16 bp):
TTATTTATCTTTACTT
Found at i:441213 original size:24 final size:24
Alignment explanation
Indices: 441180--441227 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
441170 TAATTTAGTG
*
441180 ATAAATTTAGAATGTTCAAAAGTT
1 ATAAAATTAGAATGTTCAAAAGTT
441204 ATAAAATTAGAATGTTCAAAAGTT
1 ATAAAATTAGAATGTTCAAAAGTT
441228 TACGAACTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.48, C:0.04, G:0.12, T:0.35
Consensus pattern (24 bp):
ATAAAATTAGAATGTTCAAAAGTT
Found at i:441282 original size:84 final size:84
Alignment explanation
Indices: 441122--441283 Score: 209
Period size: 84 Copynumber: 1.9 Consensus size: 84
441112 ATCTGGGGAC
* * * * * *
441122 AAAATTGGAATATTCAAAAGTTTAAGGACTAATTTAGAAAGAGGGTGATAATTTAGTGATAAATT
1 AAAATTAGAATATTCAAAAGTTTAAGAACTAATATAGAAAGAGAGTCATAATTTAGGGATAAATT
* *
441187 TAGAATGTTCAAAAGTTAT
66 GAGAATATTCAAAAGTTAT
* * *
441206 AAAATTAGAATGTTCAAAAGTTTACGAACTAATATAGAATGAGAGTCATAATTTAGGGATGAAAT
1 AAAATTAGAATATTCAAAAGTTTAAGAACTAATATAGAAAGAGAGTCATAATTTAGGGAT-AAAT
441271 TGA-AATATTCAAA
65 TGAGAATATTCAAA
441284 TGTTTAGTGA
Statistics
Matches: 66, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
84 60 0.91
85 6 0.09
ACGTcount: A:0.46, C:0.05, G:0.18, T:0.31
Consensus pattern (84 bp):
AAAATTAGAATATTCAAAAGTTTAAGAACTAATATAGAAAGAGAGTCATAATTTAGGGATAAATT
GAGAATATTCAAAAGTTAT
Found at i:443340 original size:19 final size:19
Alignment explanation
Indices: 443311--443347 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
443301 ATATTTATAA
443311 ATATTAAAA-TTTTAAAAT
1 ATATTAAAATTTTTAAAAT
443329 ATATTCAAAATTTTTAAAA
1 ATATT-AAAATTTTTAAAA
443348 ATACTCATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 4 0.24
20 8 0.47
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (19 bp):
ATATTAAAATTTTTAAAAT
Found at i:448429 original size:2 final size:2
Alignment explanation
Indices: 448422--448468 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
448412 TCAAGAAAGT
448422 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
448464 TA TA T
1 TA TA T
448469 TCTCATAGCT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:449611 original size:67 final size:67
Alignment explanation
Indices: 449503--449640 Score: 188
Period size: 67 Copynumber: 2.1 Consensus size: 67
449493 TTAAAGAATT
* ** * *
449503 AACGACGATCTAAGCTGGACGTTAAGTTGTTAACTGTGATATGATAAAAT-TTGATCTTAAAATC
1 AACGACGATCTAAGCTAGACGTTAAACTGCTAACTGTGATATGATAAAATCTT-ATCCTAAAATC
449567 TCA
65 TCA
* * *
449570 AACGACGGTCTAAGTTAGACGTTAAACTGCTGACTGTGATATGATAAAATCTTATCCTAAAATCT
1 AACGACGATCTAAGCTAGACGTTAAACTGCTAACTGTGATATGATAAAATCTTATCCTAAAATCT
449635 CA
66 CA
449637 AACG
1 AACG
449641 TAATCAATAG
Statistics
Matches: 62, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
67 60 0.97
68 2 0.03
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.30
Consensus pattern (67 bp):
AACGACGATCTAAGCTAGACGTTAAACTGCTAACTGTGATATGATAAAATCTTATCCTAAAATCT
CA
Found at i:451377 original size:25 final size:25
Alignment explanation
Indices: 451343--451393 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
451333 ATTGGTCCCC
* *
451343 CCGTCCCCGTCCCCGTTTAAAAAAT
1 CCGTACCCGTCCCCGCTTAAAAAAT
451368 CCGTACCCGTCCCCGCTTAAAAAAT
1 CCGTACCCGTCCCCGCTTAAAAAAT
451393 C
1 C
451394 GCGGGGATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.25, C:0.41, G:0.12, T:0.22
Consensus pattern (25 bp):
CCGTACCCGTCCCCGCTTAAAAAAT
Found at i:451506 original size:2 final size:2
Alignment explanation
Indices: 451499--451601 Score: 106
Period size: 2 Copynumber: 53.5 Consensus size: 2
451489 TCGGGTCGGG
* * * *
451499 TA TA TA TA TA TA TA TT TA AA T- TA AA TA TA TA AA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
451539 TA TA TA TA TA TA TA TA TA TT TA AA T- TA AA TA TA TA AA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
451580 -A TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
451602 TTAATTTAAA
Statistics
Matches: 81, Mismatches: 16, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
1 4 0.05
2 77 0.95
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:451557 original size:44 final size:44
Alignment explanation
Indices: 451499--451671 Score: 248
Period size: 44 Copynumber: 4.0 Consensus size: 44
451489 TCGGGTCGGG
451499 TATATATATATATATTTAAATTAAATATATAAATATTATATATA
1 TATATATATATATATTTAAATTAAATATATAAATATTATATATA
*
451543 TATATATATATATATTTAAATTAAATATATAAATATAATATATA
1 TATATATATATATATTTAAATTAAATATATAAATATTATATATA
* *
451587 TATATATATATATATTTAATTTAAAT-TA-AATTTATTA-ATAT-
1 TATATATATATATATTTAAATTAAATATATAA-ATATTATATATA
* *
451628 TATATATATAT-TAATTTAAATTAAATTTATTAATATTATATATA
1 TATATATATATAT-ATTTAAATTAAATATATAAATATTATATATA
451672 AATAAATAAT
Statistics
Matches: 116, Mismatches: 7, Indels: 12
0.86 0.05 0.09
Matches are distributed among these distances:
40 1 0.01
41 23 0.20
42 13 0.11
43 11 0.09
44 68 0.59
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (44 bp):
TATATATATATATATTTAAATTAAATATATAAATATTATATATA
Found at i:451686 original size:36 final size:36
Alignment explanation
Indices: 451608--451679 Score: 117
Period size: 36 Copynumber: 2.0 Consensus size: 36
451598 ATATTTAATT
* * *
451608 TAAATTAAATTTATTAATATTATATATATATTAATT
1 TAAATTAAATTTATTAATATTATATATAAATAAATA
451644 TAAATTAAATTTATTAATATTATATATAAATAAATA
1 TAAATTAAATTTATTAATATTATATATAAATAAATA
451680 ATAATTATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (36 bp):
TAAATTAAATTTATTAATATTATATATAAATAAATA
Found at i:451844 original size:29 final size:30
Alignment explanation
Indices: 451775--451849 Score: 116
Period size: 30 Copynumber: 2.5 Consensus size: 30
451765 CCCATCCTCG
* *
451775 TCCCGTCCCCGTTTATCATAAACGATTTTT
1 TCCCGTCCCCGTTTAACATAAACAATTTTT
*
451805 TACCGTCCCCGTTTAACATAAACAATTTTT
1 TCCCGTCCCCGTTTAACATAAACAATTTTT
451835 TCCCGT-CCCGTTTAA
1 TCCCGTCCCCGTTTAA
451850 TTCAATTTTC
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
29 9 0.22
30 32 0.78
ACGTcount: A:0.23, C:0.31, G:0.09, T:0.37
Consensus pattern (30 bp):
TCCCGTCCCCGTTTAACATAAACAATTTTT
Found at i:454940 original size:30 final size:30
Alignment explanation
Indices: 454906--454974 Score: 102
Period size: 30 Copynumber: 2.3 Consensus size: 30
454896 TATCCAAACT
**
454906 ATAGGTGTCCAATTAAAAGACTTTTCACAA
1 ATAGGTGTCCAACCAAAAGACTTTTCACAA
* *
454936 ATAGGTGTTCAACCAAAAGACTTTTTACAA
1 ATAGGTGTCCAACCAAAAGACTTTTCACAA
454966 ATAGGTGTC
1 ATAGGTGTC
454975 AAAACTTTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.30
Consensus pattern (30 bp):
ATAGGTGTCCAACCAAAAGACTTTTCACAA
Found at i:455534 original size:13 final size:13
Alignment explanation
Indices: 455516--455540 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
455506 TAGAAATATA
455516 AATTTTTTTTAAT
1 AATTTTTTTTAAT
455529 AATTTTTTTTAA
1 AATTTTTTTTAA
455541 AAAAATTCAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
AATTTTTTTTAAT
Found at i:462337 original size:443 final size:443
Alignment explanation
Indices: 461347--462916 Score: 2638
Period size: 443 Copynumber: 3.6 Consensus size: 443
461337 TTTTAAAAAA
** * * *
461347 ATTAAGTTCGGATCAGATTAGGTTGGGTTTTTAAAAATATGTTT-GAGTCGAATCGGGTTTATGA
1 ATTAAGTTCATATCATATTAGGTCGGGTTTTTAAAAATATGTTTAG-GTCGAATTGGGTTTATGA
* ** *
461411 TGAAAAATATTCGATCCGACCCGGTCGGAAAAATAATATAAATTTATCTTATATAGTTAGAGATA
65 TGAAAAATATTTGATCCGACCCGACCGGAAAAATAATATAAATTTACCTTATATAGTTAGAGATA
* * * *
461476 ATTGTAATAATAACAATCTATGTATTATTTTTTTAATTAGATTCCTATTCTTATTGAAGAAAAAT
130 ATTGTAATAATAACAATCTATATATTATTTTTTTAATTAGATTCCTATTTTTATTAAATAAAAAT
* * * * * *
461541 AATATTTTTATAAATATA-TTATTTTAGGTCGGGTCTTTCGGATTTTGATTTTATCTTAAAAAGT
195 AATATTATTATAAATATATTTATTTCAGGTCGAGTCTTTCGAATTTGGATTTTAGCTTAAAAAGT
* *
461605 C--G---GG-TCGAATCCGGTGAAGTCACCCTTAAATTCAGGTCAAATCGGATTTCAAGTGAATG
260 CGGGTCAGGTTCGGATCCGGTGAAGTCACCCTTAAATTCGGGTCAAATCGGATTTCAAGTGAATG
* * *
461664 ATATATATTTTCATGCCGGGTTAAACAAAAATCTGATCCAACCTGACTTGACTCATGTTCATCCC
325 ATATATATTTTCATGCCGAGTTAAACAAAAATCTGATCCAACCCGACTTGACTTATGTTCAT-CC
461729 TAATTATAATTCTACAAAGTTAGCAACTCTTTATTTAAATAAAAAAAATACTCACT
389 TAATTATAATTCTACAAAGTTAGCAACTCTTTATTTAAAT-AAAAAAATACTCACT
461785 ATTAAGTTCATATCATATTAGGTCGGGTTTTTAAAAATATGTTTAGGTCGAATTGGGTTTATGAT
1 ATTAAGTTCATATCATATTAGGTCGGGTTTTTAAAAATATGTTTAGGTCGAATTGGGTTTATGAT
* *
461850 GAAAAATATTTGATCCGTCCCGACCGGAAAAATAATATAAATTTACCTTATATAGTTAGGGATAA
66 GAAAAATATTTGATCCGACCCGACCGGAAAAATAATATAAATTTACCTTATATAGTTAGAGATAA
461915 TTGTAATAATAACAATCTATATATTATTTTTTTAATTAGATTCCTATTTTTATTAAATAAAAATA
131 TTGTAATAATAACAATCTATATATTATTTTTTTAATTAGATTCCTATTTTTATTAAATAAAAATA
*
461980 ATATTATTATAAATATATTTATTTCAGGTCGAGTATTTCGAATTTGGATTTTAGCTTAAAAAGTC
196 ATATTATTATAAATATATTTATTTCAGGTCGAGTCTTTCGAATTTGGATTTTAGCTTAAAAAGTC
462045 GGGTCAGGTTCGGATCCGGTGAAGTCACCCTTAAATTCGGGTCAAATCGGATTTCAAGTGAATGA
261 GGGTCAGGTTCGGATCCGGTGAAGTCACCCTTAAATTCGGGTCAAATCGGATTTCAAGTGAATGA
462110 TATATATTTTCATGCCGAGTTAAACAAAAATCTGATCCAACCCGACTTGACTTATGTTCATCCTA
326 TATATATTTTCATGCCGAGTTAAACAAAAATCTGATCCAACCCGACTTGACTTATGTTCATCCTA
462175 ATTATAATTCTACAAAGTTAGCAACTCTTTATTTAAATAAAAAAATACTCACT
391 ATTATAATTCTACAAAGTTAGCAACTCTTTATTTAAATAAAAAAATACTCACT
462228 ATTAAGTTCATATCATATTAGGTCGGGTTTTTAAAAATATGTTTAGGTCGAATTGGGTTTATGAT
1 ATTAAGTTCATATCATATTAGGTCGGGTTTTTAAAAATATGTTTAGGTCGAATTGGGTTTATGAT
* * * *
462293 GAAAAATATTTGATCCGTCCCGATCGGAAAAATAATAGAAATTTACCTTATATAGTTAGGGATAA
66 GAAAAATATTTGATCCGACCCGACCGGAAAAATAATATAAATTTACCTTATATAGTTAGAGATAA
462358 TTGTAATAATAACAATCTATATATTATTTTTTTAATTAGATTCCTATTTTTATTAAATAAAAATA
131 TTGTAATAATAACAATCTATATATTATTTTTTTAATTAGATTCCTATTTTTATTAAATAAAAATA
462423 ATATTATTATAAATATATTTATTTCAGGTCGAGTCTTTCGAATTTGGATTTTAGCTTAAAAAGTC
196 ATATTATTATAAATATATTTATTTCAGGTCGAGTCTTTCGAATTTGGATTTTAGCTTAAAAAGTC
462488 GGGTCAGGTTCGGATCCGGTGAAGTCACCCTTAAATTCGGGTCAAATCGGATTTCAAGTGAATGA
261 GGGTCAGGTTCGGATCCGGTGAAGTCACCCTTAAATTCGGGTCAAATCGGATTTCAAGTGAATGA
462553 TATATATTTTCATGCCGAGTTAAACAAAAATCTGATCCAACCCGACTTGACTTATGTTCATCCTA
326 TATATATTTTCATGCCGAGTTAAACAAAAATCTGATCCAACCCGACTTGACTTATGTTCATCCTA
*
462618 ATTATAATTCTACAAAGTTAGCAACTCTTTATTTAAATAAAAAAAGACTCACT
391 ATTATAATTCTACAAAGTTAGCAACTCTTTATTTAAATAAAAAAATACTCACT
*
462671 ATTAAGTTCATATCATATTAGGTCGGGTTTTTAAAAATATGTTTAGGTCAAATTGGGTTTATGAT
1 ATTAAGTTCATATCATATTAGGTCGGGTTTTTAAAAATATGTTTAGGTCGAATTGGGTTTATGAT
* * *
462736 GAAAAATATTGGATCCGACCCTACCGGAAATATAATATAAATTTACCTTATATAGTTAGAGATAA
66 GAAAAATATTTGATCCGACCCGACCGGAAAAATAATATAAATTTACCTTATATAGTTAGAGATAA
* * *
462801 TTGTAATAATAACAATCTATGTATTA-TTTTTTAATTAGATTCTTATTTTTATTGAATAAAAATA
131 TTGTAATAATAACAATCTATATATTATTTTTTTAATTAGATTCCTATTTTTATTAAATAAAAATA
* * * * *
462865 ATATTTTTATAAATATATTTATTTTACGTCGGGTCTGTT-GGATTTGGATTTT
196 ATATTATTATAAATATATTTATTTCAGGTCGAGTCT-TTCGAATTTGGATTTT
462917 TTCAAGATTT
Statistics
Matches: 1076, Mismatches: 47, Indels: 14
0.95 0.04 0.01
Matches are distributed among these distances:
438 194 0.18
439 42 0.04
441 1 0.00
442 80 0.07
443 603 0.56
444 44 0.04
445 112 0.10
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (443 bp):
ATTAAGTTCATATCATATTAGGTCGGGTTTTTAAAAATATGTTTAGGTCGAATTGGGTTTATGAT
GAAAAATATTTGATCCGACCCGACCGGAAAAATAATATAAATTTACCTTATATAGTTAGAGATAA
TTGTAATAATAACAATCTATATATTATTTTTTTAATTAGATTCCTATTTTTATTAAATAAAAATA
ATATTATTATAAATATATTTATTTCAGGTCGAGTCTTTCGAATTTGGATTTTAGCTTAAAAAGTC
GGGTCAGGTTCGGATCCGGTGAAGTCACCCTTAAATTCGGGTCAAATCGGATTTCAAGTGAATGA
TATATATTTTCATGCCGAGTTAAACAAAAATCTGATCCAACCCGACTTGACTTATGTTCATCCTA
ATTATAATTCTACAAAGTTAGCAACTCTTTATTTAAATAAAAAAATACTCACT
Found at i:475069 original size:23 final size:23
Alignment explanation
Indices: 475043--475090 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
475033 ATAAAGTACA
*
475043 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
475066 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
475089 AT
1 AT
475091 TTACCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:475497 original size:21 final size:22
Alignment explanation
Indices: 475472--475520 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 22
475462 ACACTTTACA
*
475472 ATATAACCACTACCTATTACATT
1 ATATAAACA-TACCTATTACATT
475495 ATATAAACGATACCTATTACATT
1 ATATAAAC-ATACCTATTACATT
475518 ATA
1 ATA
475521 GGGCTACCTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 23 0.96
24 1 0.04
ACGTcount: A:0.43, C:0.20, G:0.02, T:0.35
Consensus pattern (22 bp):
ATATAAACATACCTATTACATT
Found at i:475998 original size:39 final size:39
Alignment explanation
Indices: 475944--476069 Score: 234
Period size: 39 Copynumber: 3.2 Consensus size: 39
475934 TCAAGTTGTA
475944 GATTTTGATTTCCTTTTGCTTGGCATCATATGAGATTTG
1 GATTTTGATTTCCTTTTGCTTGGCATCATATGAGATTTG
475983 GATTTTGATTTCCTTTTGCTTGGCATCATATGAGATTTG
1 GATTTTGATTTCCTTTTGCTTGGCATCATATGAGATTTG
* *
476022 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGCTTTG
1 GATTTTGATTTCCTTTTGCTTGGCATCATATGAGATTTG
476061 GATTTTGAT
1 GATTTTGAT
476070 GAGCATCGGA
Statistics
Matches: 85, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 85 1.00
ACGTcount: A:0.17, C:0.13, G:0.21, T:0.48
Consensus pattern (39 bp):
GATTTTGATTTCCTTTTGCTTGGCATCATATGAGATTTG
Found at i:476352 original size:18 final size:18
Alignment explanation
Indices: 476329--476365 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
476319 CGAAATATAT
476329 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
476347 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
476365 A
1 A
476366 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:476642 original size:25 final size:25
Alignment explanation
Indices: 476614--476664 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
476604 TTAATCCAAA
*
476614 TAATGTACCCATAACAATGTTCAAT
1 TAATGTACCCACAACAATGTTCAAT
*
476639 TAATGTACCCACAACAATGTTTAAT
1 TAATGTACCCACAACAATGTTCAAT
476664 T
1 T
476665 GATTTGTTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.39, C:0.20, G:0.08, T:0.33
Consensus pattern (25 bp):
TAATGTACCCACAACAATGTTCAAT
Found at i:476954 original size:21 final size:22
Alignment explanation
Indices: 476929--476980 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
476919 ACACTTTACA
*
476929 ATATAACCACTACCTATTACATT
1 ATATAAACA-TACCTATTACATT
476952 ATATAAACGATACCTATTACATT
1 ATATAAAC-ATACCTATTACATT
476975 ATATAA
1 ATATAA
476981 GGGCTACCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (22 bp):
ATATAAACATACCTATTACATT
Found at i:476965 original size:23 final size:23
Alignment explanation
Indices: 476939--477001 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
476929 ATATAACCAC
476939 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
476962 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
476985 TACCTATTACATCATAT
1 TACCTATTACATTATAT
477002 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:477385 original size:21 final size:22
Alignment explanation
Indices: 477360--477411 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
477350 ACACTTTACA
*
477360 ATATAACCACTACCTATTACATT
1 ATATAAACA-TACCTATTACATT
477383 ATATAAACGATACCTATTACATT
1 ATATAAAC-ATACCTATTACATT
477406 ATATAA
1 ATATAA
477412 GGGCTACCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (22 bp):
ATATAAACATACCTATTACATT
Found at i:477396 original size:23 final size:23
Alignment explanation
Indices: 477370--477432 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
477360 ATATAACCAC
477370 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
477393 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
477416 TACCTATTACATCATAT
1 TACCTATTACATTATAT
477433 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:477495 original size:431 final size:427
Alignment explanation
Indices: 476696--477531 Score: 1600
Period size: 431 Copynumber: 1.9 Consensus size: 427
476686 TTTGAATTAT
476696 TTGATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATAT
1 TTGATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATAT
*
476761 TTAGAATTTTTAATTTAATAATATATATCGTAACGTAAAAAATAAATCATTATACGCCTATAATT
66 TTAGAATTTTTAATTTAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATT
476826 ACTAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAA
131 ACTAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAA
476891 AGTATGGACACTTTTATAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACATTATAT
196 AGTATGGACACTTTTATAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACATTATAT
476956 AAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGTTTACCTATTATATTGAA
261 AAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGTTTACCTATTATATTGAA
*
477021 AGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTATGTAATTTATGTTTCAA
326 AGTGTACATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTATGTAATTTATGTTTCAA
477086 TTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATA
391 TTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATA
* *
477123 TTGATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTTATATTTTATAAAATATTAT
1 TTGATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATAT
477188 TTAGAATTTTTAATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATA
66 TTAGAATTTTTAATTTAATAAT-ATATAT--CGTAACGTAAAAAATAAATCATTAGACGCCTATA
477253 ATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGA
128 ATTACT-AATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGA
477318 AAAAAGTATGGACACTTTTATAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACATT
192 AAAAAGTATGGACACTTTTATAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACATT
477383 ATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGTTTACCTATTATAT
257 ATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGTTTACCTATTATAT
477448 TGAAAGTGTACATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTATGTAATTTATGTT
322 TGAAAGTGTACATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTATGTAATTTATGTT
477513 TCAATTTTTTTAACAGTGT
387 TCAATTTTTTTAACAGTGT
477532 ACTGCGAATT
Statistics
Matches: 401, Mismatches: 4, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
427 85 0.21
428 6 0.01
430 39 0.10
431 271 0.68
ACGTcount: A:0.39, C:0.13, G:0.08, T:0.40
Consensus pattern (427 bp):
TTGATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATAT
TTAGAATTTTTAATTTAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATT
ACTAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAA
AGTATGGACACTTTTATAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACATTATAT
AAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGTTTACCTATTATATTGAA
AGTGTACATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTATGTAATTTATGTTTCAA
TTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATA
Found at i:480587 original size:22 final size:23
Alignment explanation
Indices: 480556--480598 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
480546 TTCCACAGTG
480556 AAAAAAGTATAGACAC-TTTTAT
1 AAAAAAGTATAGACACATTTTAT
* *
480578 AAAAAGGTATCGACACATTTT
1 AAAAAAGTATAGACACATTTT
480599 TATACCGGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.30
Consensus pattern (23 bp):
AAAAAAGTATAGACACATTTTAT
Found at i:480909 original size:183 final size:183
Alignment explanation
Indices: 480594--481105 Score: 875
Period size: 183 Copynumber: 2.8 Consensus size: 183
480584 GTATCGACAC
480594 ATTTTTATACCGGTTATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAA
1 ATTTTTATACCGGTTATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAA
* *
480659 TGTCGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGAACATAAAGTACCAACAC
66 TGTCGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACAC
480724 AATATTAGAAAGTGTCGATAAAGGTTGTAGACCTATTCGCTCATAAAACCGGT
131 AATATTAGAAAGTGTCGATAAAGGTTGTAGACCTATTCGCTCATAAAACCGGT
*
480777 ATTTTTATACCGGTTATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCAATGTGTAAA
1 ATTTTTATACCGGTTATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAA
480842 TGTCGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACAC
66 TGTCGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACAC
*
480907 AATATTAGAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGT
131 AATATTAGAAAGTGTCGATAAAGGTTGTAGACCTATTCGCTCATAAAACCGGT
* * *
480960 ATATTTATACCGGTTATATTACAAAATCATCTATTACATTATAAATCTGGGTTCCGATGTTTTTT
1 ATTTTTATACCGGTTATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATG---TGT
* * * *
481025 CAA--TCGACACTTTTTTAAATGGTATCGACACATTTTTCTTTCATTCTGGACATAAAGTACAGA
63 AAATGTCGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGA
*
481088 CACAATATTAAAAAGTGT
128 CACAATATTAGAAAGTGT
481106 GAAAACTTTG
Statistics
Matches: 313, Mismatches: 13, Indels: 5
0.95 0.04 0.02
Matches are distributed among these distances:
183 235 0.75
184 74 0.24
186 4 0.01
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.36
Consensus pattern (183 bp):
ATTTTTATACCGGTTATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAA
TGTCGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACAC
AATATTAGAAAGTGTCGATAAAGGTTGTAGACCTATTCGCTCATAAAACCGGT
Found at i:482311 original size:3 final size:3
Alignment explanation
Indices: 482303--482377 Score: 78
Period size: 3 Copynumber: 25.0 Consensus size: 3
482293 ACTTGTTTGG
* * * **
482303 ATC ATC ATC TTC ATC ATC ATC ATC ATC ATC GTC ATC ATC TTC ATC GCC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
* * *
482351 AGC TTC ATC GTC ATC ATC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC
482378 GTCAGCTTCA
Statistics
Matches: 57, Mismatches: 15, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.25, C:0.35, G:0.05, T:0.35
Consensus pattern (3 bp):
ATC
Found at i:484553 original size:199 final size:199
Alignment explanation
Indices: 483851--484624 Score: 1489
Period size: 199 Copynumber: 3.9 Consensus size: 199
483841 TATTTAAATT
483851 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
1 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
483916 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
66 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
483981 ATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCATTCTGGGA
131 ATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCATTCTGGGA
484046 AAAA
196 AAAA
484050 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
1 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
*
484115 TAATTGTACCAGTTAGATTG-AAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
66 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
484179 ATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCATTCTGGG-
131 ATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCATTCTGGGA
484243 AAAA
196 AAAA
484247 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
1 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
484312 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
66 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
*
484377 ATCGACACTTTTTATATATGGATCGATACTTTATGGGTGCACCTTGTTTTCCATTCATTCTGGGA
131 ATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCATTCTGGGA
484442 AAAA
196 AAAA
484446 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
1 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
484511 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
66 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
* *
484576 ATTGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTT
131 ATCGACAC-TTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTT
484625 GGCCATATTG
Statistics
Matches: 566, Mismatches: 6, Indels: 5
0.98 0.01 0.01
Matches are distributed among these distances:
197 88 0.16
198 215 0.38
199 225 0.40
200 38 0.07
ACGTcount: A:0.30, C:0.16, G:0.17, T:0.37
Consensus pattern (199 bp):
AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
ATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCATTCTGGGA
AAAA
Found at i:484789 original size:19 final size:19
Alignment explanation
Indices: 484743--484791 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
484733 TTATATTCAC
*
484743 ATACAAAAATATAAATCGT
1 ATACAAAATTATAAATCGT
*
484762 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
484781 ATACAAAATTA
1 ATACAAAATTA
484792 ACTCGACATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.57, C:0.10, G:0.02, T:0.31
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:486621 original size:33 final size:33
Alignment explanation
Indices: 486584--486649 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
486574 CATCTTAATA
*
486584 TCACCCCTTAACACCCCAACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
* *
486617 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
486650 CCATCTATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.23, C:0.48, G:0.00, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCCCAACTTCTTTCACCACT
Found at i:486723 original size:21 final size:21
Alignment explanation
Indices: 486683--486747 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
486673 CCCCTTATTC
* *
486683 CTCTCGAGTGTATCTTCGACT
1 CTCTCGAGTTTCTCTTCGACT
*
486704 CTCTCGAGTTTCTCTACGACT
1 CTCTCGAGTTTCTCTTCGACT
* *
486725 -TGATCAAGTTTCTCTTCGACT
1 CT-CTCGAGTTTCTCTTCGACT
486746 CT
1 CT
486748 TGATTGTCTT
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
20 1 0.03
21 34 0.94
22 1 0.03
ACGTcount: A:0.15, C:0.29, G:0.15, T:0.40
Consensus pattern (21 bp):
CTCTCGAGTTTCTCTTCGACT
Found at i:488998 original size:17 final size:18
Alignment explanation
Indices: 488976--489018 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
488966 ATATATCCGG
488976 TATCATT-TTACCGGTTT
1 TATCATTGTTACCGGTTT
488993 TATCATTTTGTTACCGGTTT
1 TATCA--TTGTTACCGGTTT
489013 TATCAT
1 TATCAT
489019 ATTTTTACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
17 5 0.22
18 1 0.04
19 2 0.09
20 15 0.65
ACGTcount: A:0.19, C:0.16, G:0.12, T:0.53
Consensus pattern (18 bp):
TATCATTGTTACCGGTTT
Found at i:489008 original size:20 final size:20
Alignment explanation
Indices: 488981--489027 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
488971 TCCGGTATCA
488981 TTTTACCGGTTTTATCAT-T
1 TTTTACCGGTTTTATCATAT
489000 TTGTTACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCATAT
489021 TTTTACC
1 TTTTACC
489028 TGTTATATCG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.55
Consensus pattern (20 bp):
TTTTACCGGTTTTATCATAT
Found at i:489174 original size:20 final size:20
Alignment explanation
Indices: 489148--489193 Score: 76
Period size: 20 Copynumber: 2.3 Consensus size: 20
489138 CACTTTTAAA
489148 TTTACCGGTTTTATCAT-TT
1 TTTACCGGTTTTATCATATT
489167 TGTTACCGGTTTTATCATATT
1 T-TTACCGGTTTTATCATATT
489188 TTTACC
1 TTTACC
489194 TGGTATATCG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.54
Consensus pattern (20 bp):
TTTACCGGTTTTATCATATT
Found at i:489675 original size:228 final size:227
Alignment explanation
Indices: 489259--489706 Score: 790
Period size: 228 Copynumber: 2.0 Consensus size: 227
489249 TTAAAACTGC
489259 TTTTAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATA
1 TTTTAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATA
**
489324 TTAATTTAATAATTTAATTTACACAAATTATATTTGATTGTTTTGATATTTTATAAAATATTATT
66 TTAATTTAATAATTTAATTTACACAAAAAATATTTGATTGTTTTGATATTTTATAAAATATTATT
* *
489389 TAGAATTTAAATTTAACAATATTAACCAAATATAATAATAAATATGTTTTCAACAGTGAAATAAG
131 TAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATATTTTCAACAGTGAAATAAG
*
489454 TATGGACACTTTTATAAAAATGATATATACTT
196 TATGGACACTTTTATAAAAAGGATATATACTT
*
489486 TTTTGAAAGTTATGTAATTTATGTTTCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAAT
1 TTTT-AAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAAT
*
489551 ATTAATTTAATAATTTCATTTACACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTA
65 ATTAATTTAATAATTTAATTTACACAAAAAA-TATTTGATTGTTTTGATATTTTATAAAATATTA
* *
489616 TTTAGATTTTAAATTTAACAATATTAACTAAAGATAATAATAAATATATTTTC-ACAGTGAAATA
129 TTTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATATTTTCAACAGTGAAATA
489680 AGTATGGACACTTTTATAAAAAGGATA
194 AGTATGGACACTTTTATAAAAAGGATA
489707 GATAATTTAC
Statistics
Matches: 210, Mismatches: 9, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
227 4 0.02
228 124 0.59
229 82 0.39
ACGTcount: A:0.40, C:0.07, G:0.08, T:0.45
Consensus pattern (227 bp):
TTTTAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATA
TTAATTTAATAATTTAATTTACACAAAAAATATTTGATTGTTTTGATATTTTATAAAATATTATT
TAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATATTTTCAACAGTGAAATAAG
TATGGACACTTTTATAAAAAGGATATATACTT
Found at i:490464 original size:11 final size:12
Alignment explanation
Indices: 490422--490467 Score: 58
Period size: 12 Copynumber: 3.9 Consensus size: 12
490412 ATTATTTAAA
*
490422 CGGGTATTGGGC
1 CGGGTATTGGGT
**
490434 CAAGTATTGGGT
1 CGGGTATTGGGT
490446 CGGGTATTGGGT
1 CGGGTATTGGGT
490458 C-GGTATTGGG
1 CGGGTATTGGG
490468 CTGGGAATCG
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
11 9 0.31
12 20 0.69
ACGTcount: A:0.13, C:0.11, G:0.46, T:0.30
Consensus pattern (12 bp):
CGGGTATTGGGT
Found at i:490543 original size:24 final size:25
Alignment explanation
Indices: 490487--490543 Score: 66
Period size: 24 Copynumber: 2.3 Consensus size: 25
490477 GGGCCGGGTA
490487 TATATATATTTAAATTAAATATATAT
1 TATAT-TATTTAAATTAAATATATAT
*
490513 T-TTTTATTTAAATTAAAT-T-TAT
1 TATATTATTTAAATTAAATATATAT
490535 TAATATTAT
1 T-ATATTAT
490544 ATATATATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
22 4 0.15
23 1 0.04
24 19 0.70
25 2 0.07
26 1 0.04
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (25 bp):
TATATTATTTAAATTAAATATATAT
Found at i:490605 original size:13 final size:12
Alignment explanation
Indices: 490574--490610 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
490564 TTTTAATATT
*
490574 TATCGGGTCGGG
1 TATCGGGGCGGG
490586 TATCGGGGCGGG
1 TATCGGGGCGGG
490598 TAATCGGGGCGGG
1 T-ATCGGGGCGGG
490611 GATTACCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 12 0.52
13 11 0.48
ACGTcount: A:0.11, C:0.16, G:0.54, T:0.19
Consensus pattern (12 bp):
TATCGGGGCGGG
Found at i:490632 original size:6 final size:6
Alignment explanation
Indices: 490621--490649 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
490611 GATTACCAAA
490621 CCCGTC CCCGTC CCCGTC CCCGTC CCCGT
1 CCCGTC CCCGTC CCCGTC CCCGTC CCCGT
490650 TTAAAATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.66, G:0.17, T:0.17
Consensus pattern (6 bp):
CCCGTC
Found at i:490678 original size:6 final size:6
Alignment explanation
Indices: 490667--490691 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
490657 AAATGGGTTT
490667 TCCCCG TCCCCG TCCCCG TCCCCG T
1 TCCCCG TCCCCG TCCCCG TCCCCG T
490692 TTAAAATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.64, G:0.16, T:0.20
Consensus pattern (6 bp):
TCCCCG
Found at i:490684 original size:42 final size:42
Alignment explanation
Indices: 490625--490736 Score: 224
Period size: 42 Copynumber: 2.7 Consensus size: 42
490615 ACCAAACCCG
490625 TCCCCGTCCCCGTCCCCGTCCCCGTTTAAAATAAATGGGTTT
1 TCCCCGTCCCCGTCCCCGTCCCCGTTTAAAATAAATGGGTTT
490667 TCCCCGTCCCCGTCCCCGTCCCCGTTTAAAATAAATGGGTTT
1 TCCCCGTCCCCGTCCCCGTCCCCGTTTAAAATAAATGGGTTT
490709 TCCCCGTCCCCGTCCCCGTCCCCGTTTA
1 TCCCCGTCCCCGTCCCCGTCCCCGTTTA
490737 TTATCCCCGA
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 70 1.00
ACGTcount: A:0.13, C:0.43, G:0.16, T:0.28
Consensus pattern (42 bp):
TCCCCGTCCCCGTCCCCGTCCCCGTTTAAAATAAATGGGTTT
Found at i:490720 original size:6 final size:6
Alignment explanation
Indices: 490709--490733 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
490699 AAATGGGTTT
490709 TCCCCG TCCCCG TCCCCG TCCCCG T
1 TCCCCG TCCCCG TCCCCG TCCCCG T
490734 TTATTATCCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.64, G:0.16, T:0.20
Consensus pattern (6 bp):
TCCCCG
Found at i:491487 original size:21 final size:21
Alignment explanation
Indices: 491462--491509 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
491452 AGTTTATACT
491462 TATATACTACTATGCATAAAC
1 TATATACTACTATGCATAAAC
*
491483 TATATACTACTATGTATAAAC
1 TATATACTACTATGCATAAAC
491504 TATATA
1 TATATA
491510 TGGTTTAGGG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.44, C:0.15, G:0.04, T:0.38
Consensus pattern (21 bp):
TATATACTACTATGCATAAAC
Found at i:492102 original size:11 final size:11
Alignment explanation
Indices: 492086--492246 Score: 58
Period size: 11 Copynumber: 14.7 Consensus size: 11
492076 ACTAATGAAC
492086 TATATAAATTA
1 TATATAAATTA
*
492097 TATATAAACTA
1 TATATAAATTA
492108 -A-ATAAATTA
1 TATATAAATTA
492117 TATAGT---TTA
1 TATA-TAAATTA
* *
492126 CATATGAATTA
1 TATATAAATTA
492137 TATATATAA--A
1 TATATA-AATTA
* *
492147 CTA-ATGAACTA
1 -TATATAAATTA
492158 --TATAAATTA
1 TATATAAATTA
* *
492167 TATCTAAACTA
1 TATATAAATTA
492178 TATATGAAA-TA
1 TATAT-AAATTA
492189 TATATAAACTAATGAA
1 TATATAAA-T--T--A
492205 CTATATAAATTA
1 -TATATAAATTA
* *
492217 TATCTAAACTA
1 TATATAAATTA
492228 TATATGAAA-TA
1 TATAT-AAATTA
492239 TATATAAA
1 TATATAAA
492247 CTGTATAGTT
Statistics
Matches: 114, Mismatches: 14, Indels: 45
0.66 0.08 0.26
Matches are distributed among these distances:
8 1 0.01
9 21 0.18
10 11 0.10
11 59 0.52
12 10 0.09
14 2 0.02
16 2 0.02
17 8 0.07
ACGTcount: A:0.52, C:0.06, G:0.04, T:0.38
Consensus pattern (11 bp):
TATATAAATTA
Found at i:492112 original size:20 final size:20
Alignment explanation
Indices: 492083--492120 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
492073 TAAACTAATG
*
492083 AACTATATAAATTATATATA
1 AACTAAATAAATTATATATA
492103 AACTAAATAAATTATATA
1 AACTAAATAAATTATATA
492121 GTTTACATAT
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:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (20 bp):
AACTAAATAAATTATATATA
Found at i:492157 original size:50 final size:48
Alignment explanation
Indices: 492103--492248 Score: 184
Period size: 50 Copynumber: 2.9 Consensus size: 48
492093 ATTATATATA
* ***
492103 AACTAAATAAATTATATAGTTTACATATGAATTATATATATAAACTAATG
1 AACTATATAAATTATATAAACTACATATGAA--ATATATATAAACTAATG
*
492153 AACTATATAAATTATATCTAAACTATATATGAAATATATATAAACTAATG
1 AACTATATAAATTATA--TAAACTACATATGAAATATATATAAACTAATG
*
492203 AACTATATAAATTATATCTAAACTATATATGAAATATATATAAACT
1 AACTATATAAATTATA--TAAACTACATATGAAATATATATAAACT
492249 GTATAGTTTA
Statistics
Matches: 89, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
50 78 0.88
52 11 0.12
ACGTcount: A:0.51, C:0.08, G:0.04, T:0.37
Consensus pattern (48 bp):
AACTATATAAATTATATAAACTACATATGAAATATATATAAACTAATG
Found at i:492190 original size:22 final size:22
Alignment explanation
Indices: 492156--492423 Score: 84
Period size: 22 Copynumber: 11.2 Consensus size: 22
492146 ACTAATGAAC
*
492156 TATATAAATTATATCTAAACTA
1 TATATAAATTATATATAAACTA
492178 TATATGAAA-TATATATAAACTAATGAA
1 TATAT-AAATTATATATAAAC---T--A
*
492205 CTATATAAATTATATCTAAACTA
1 -TATATAAATTATATATAAACTA
492228 TATATGAAA-TATATATAAACTGTA
1 TATAT-AAATTATATATAAAC--TA
* * *
492252 TAGTTTATATTTATATACTATA-TA
1 TA-TATA-AATTATATA-TAAACTA
492276 TAATTATAAATTATATAT--ACTA
1 T-A-TATAAATTATATATAAACTA
* * ** *
492298 TGTATAAGTTATATTATTTATTA
1 TATATAAATTATA-TATAAACTA
* **
492321 -ACATAAACCATATAT--ACTA
1 TATATAAATTATATATAAACTA
*
492340 TATGTAAACTATATATATAAACTATA
1 TATATAAA-T-TATATATAAAC--TA
*
492366 TATACTATATAGTTTATATATGAACTA
1 TATA-TA-A-A--TTATATATAAACTA
492393 TATATAAAAATTATATATATAAACTA
1 TATAT--AAA-T-TATATATAAACTA
492419 TATAT
1 TATAT
492424 TATAGTTTAT
Statistics
Matches: 186, Mismatches: 26, Indels: 64
0.67 0.09 0.23
Matches are distributed among these distances:
19 3 0.02
20 15 0.08
21 7 0.04
22 46 0.25
23 11 0.06
24 18 0.10
25 11 0.06
26 30 0.16
27 16 0.09
28 17 0.09
29 11 0.06
30 1 0.01
ACGTcount: A:0.48, C:0.07, G:0.04, T:0.42
Consensus pattern (22 bp):
TATATAAATTATATATAAACTA
Found at i:492190 original size:70 final size:69
Alignment explanation
Indices: 492057--492192 Score: 218
Period size: 70 Copynumber: 1.9 Consensus size: 69
492047 AACTATATAT
*
492057 ATATGAGTTATATATATAAACTAATGAACTATATAAATTATATATAAACTAAATAAATTATATAG
1 ATATGAATTATATATATAAACTAATGAACTATATAAATTATATATAAACTAAATAAA-TATATAG
492122 TTTAC
65 TTTAC
*
492127 ATATGAATTATATATATAAACTAATGAACTATATAAATTATATCTAAACTATATATGAAATATAT
1 ATATGAATTATATATATAAACTAATGAACTATATAAATTATATATAAACTA-A-AT-AAATATAT
492192 A
63 A
492193 TAAACTAATG
Statistics
Matches: 61, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
70 49 0.80
71 1 0.02
72 8 0.13
73 3 0.05
ACGTcount: A:0.51, C:0.06, G:0.05, T:0.38
Consensus pattern (69 bp):
ATATGAATTATATATATAAACTAATGAACTATATAAATTATATATAAACTAAATAAATATATAGT
TTAC
Found at i:492253 original size:11 final size:11
Alignment explanation
Indices: 492156--492253 Score: 75
Period size: 11 Copynumber: 9.4 Consensus size: 11
492146 ACTAATGAAC
*
492156 TATATAAATTA
1 TATATAAACTA
*
492167 TATCTAAACTA
1 TATATAAACTA
492178 TATATGAAA-TA
1 TATAT-AAACTA
492189 TATATAAAC--
1 TATATAAACTA
*
492198 TA-ATGAAC--
1 TATATAAACTA
*
492206 TATATAAATTA
1 TATATAAACTA
*
492217 TATCTAAACTA
1 TATATAAACTA
492228 TATATGAAA-TA
1 TATAT-AAACTA
*
492239 TATATAAACTG
1 TATATAAACTA
492250 TATA
1 TATA
492254 GTTTATATTT
Statistics
Matches: 70, Mismatches: 10, Indels: 14
0.74 0.11 0.15
Matches are distributed among these distances:
8 7 0.10
9 6 0.09
10 6 0.09
11 45 0.64
12 6 0.09
ACGTcount: A:0.51, C:0.07, G:0.04, T:0.38
Consensus pattern (11 bp):
TATATAAACTA
Found at i:492354 original size:2 final size:2
Alignment explanation
Indices: 492330--492515 Score: 91
Period size: 2 Copynumber: 91.5 Consensus size: 2
492320 AACATAAACC
* * *
492330 AT AT AT ACT AT AT GT AA ACT AT AT AT AT AA ACT AT AT AT ACT AT
1 AT AT AT A-T AT AT AT AT A-T AT AT AT AT AT A-T AT AT AT A-T AT
* * * *
492374 AT AGT TT AT AT AT GA- ACT AT AT AT AA AA AT -T AT AT AT AT AA
1 AT A-T AT AT AT AT -AT A-T AT AT AT AT AT AT AT AT AT AT AT AT
* *
492415 ACT AT AT AT -T AT AGT TT AT AT AT AT AT A- AT AT AGT TT AT AT
1 A-T AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT A-T AT AT AT
* * *
492456 TT AT AT A- AT AT AT AT AT AT AC AT AT AT A- AT AT A- AGT AT AC
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT
* *
492496 AT -T AT AA AT AT AT AC AT AT A
1 AT AT AT AT AT AT AT AT AT AT A
492516 GTGCTACCCC
Statistics
Matches: 139, Mismatches: 26, Indels: 38
0.68 0.13 0.19
Matches are distributed among these distances:
1 8 0.06
2 118 0.85
3 13 0.09
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.44
Consensus pattern (2 bp):
AT
Found at i:492360 original size:13 final size:13
Alignment explanation
Indices: 492338--492423 Score: 91
Period size: 13 Copynumber: 6.4 Consensus size: 13
492328 CCATATATAC
*
492338 TATATGTAAACTA
1 TATATATAAACTA
492351 TATATATAAACTA
1 TATATATAAACTA
* *
492364 TATATACTATATAGTT
1 TATATA-TA-A-ACTA
*
492380 TATATATGAACTA
1 TATATATAAACTA
* *
492393 TATATAAAAATTA
1 TATATATAAACTA
492406 TATATATAAACTA
1 TATATATAAACTA
492419 TATAT
1 TATAT
492424 TATAGTTTAT
Statistics
Matches: 59, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
13 46 0.78
14 3 0.05
15 2 0.03
16 8 0.14
ACGTcount: A:0.49, C:0.06, G:0.03, T:0.42
Consensus pattern (13 bp):
TATATATAAACTA
Found at i:492447 original size:13 final size:13
Alignment explanation
Indices: 492349--492515 Score: 88
Period size: 13 Copynumber: 12.9 Consensus size: 13
492339 ATATGTAAAC
492349 TATATATATA-AA
1 TATATATATATAA
492361 CTATATATACTAT-A
1 -TATATATA-TATAA
*
492375 TAGTTTATATATGAA
1 TA-TATATATAT-AA
*
492390 CTATATATA-AAAA
1 -TATATATATATAA
492403 T-TATATATATAA
1 TATATATATATAA
492415 -ACTATATAT-T-A
1 TA-TATATATATAA
*
492426 TAGTTTATATAT-A
1 TA-TATATATATAA
*
492439 TATA-ATATAGT-T
1 TATATATATA-TAA
*
492451 TATATTTATATAA
1 TATATATATATAA
492464 TATATATATATACA
1 TATATATATATA-A
492478 TATATA-ATATAA
1 TATATATATATAA
*
492490 GTATACAT-TATAAA
1 -TATATATATAT-AA
*
492504 TATATACATATA
1 TATATATATATA
492516 GTGCTACCCC
Statistics
Matches: 121, Mismatches: 14, Indels: 38
0.70 0.08 0.22
Matches are distributed among these distances:
11 12 0.10
12 20 0.17
13 60 0.50
14 21 0.17
15 6 0.05
16 2 0.02
ACGTcount: A:0.49, C:0.04, G:0.03, T:0.44
Consensus pattern (13 bp):
TATATATATATAA
Found at i:495405 original size:17 final size:18
Alignment explanation
Indices: 495378--495534 Score: 128
Period size: 18 Copynumber: 8.9 Consensus size: 18
495368 ATTATTAGAC
*
495378 ATTTCATAGTTATAAGAT-
1 ATTT-ATAGTTATCAGATG
*
495396 ATTTATAGTTATTAGATG
1 ATTTATAGTTATCAGATG
495414 ATTT-TCAGTTATCAGAT-
1 ATTTAT-AGTTATCAGATG
*
495431 ATTTATAGTTATTAGATG
1 ATTTATAGTTATCAGATG
*
495449 ATTT-TCAGTTATCATAT-
1 ATTTAT-AGTTATCAGATG
* *
495466 ATTTACAGTTATGAGATG
1 ATTTATAGTTATCAGATG
** *
495484 ATTTCCAGTTATCATATG
1 ATTTATAGTTATCAGATG
* **
495502 -TTTACAGTTATTGGATG
1 ATTTATAGTTATCAGATG
*
495519 TTTTATAGTTATCAGA
1 ATTTATAGTTATCAGA
495535 CTTAGATTAA
Statistics
Matches: 113, Mismatches: 18, Indels: 16
0.77 0.12 0.11
Matches are distributed among these distances:
17 54 0.48
18 59 0.52
ACGTcount: A:0.31, C:0.07, G:0.15, T:0.47
Consensus pattern (18 bp):
ATTTATAGTTATCAGATG
Found at i:495424 original size:35 final size:35
Alignment explanation
Indices: 495385--495534 Score: 194
Period size: 35 Copynumber: 4.3 Consensus size: 35
495375 GACATTTCAT
* *
495385 AGTTATAAGATATTTATAGTTATTAGATGATTTTC
1 AGTTATCAGATATTTACAGTTATTAGATGATTTTC
*
495420 AGTTATCAGATATTTATAGTTATTAGATGATTTTC
1 AGTTATCAGATATTTACAGTTATTAGATGATTTTC
* * *
495455 AGTTATCATATATTTACAGTTATGAGATGATTTCC
1 AGTTATCAGATATTTACAGTTATTAGATGATTTTC
* * * *
495490 AGTTATCATATGTTTACAGTTATTGGATG-TTTTAT
1 AGTTATCAGATATTTACAGTTATTAGATGATTTT-C
495525 AGTTATCAGA
1 AGTTATCAGA
495535 CTTAGATTAA
Statistics
Matches: 103, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
34 3 0.03
35 100 0.97
ACGTcount: A:0.31, C:0.07, G:0.15, T:0.47
Consensus pattern (35 bp):
AGTTATCAGATATTTACAGTTATTAGATGATTTTC
Found at i:495529 original size:70 final size:70
Alignment explanation
Indices: 495357--495534 Score: 214
Period size: 70 Copynumber: 2.5 Consensus size: 70
495347 AATGAATTCT
* ** * * * * *
495357 ATATGTTTACAATTATTAGACATTTCATAGTTATAAGATATTTATAGTTATTAGATGATTTTCAG
1 ATATGTTTACAGTTATTAGATGTTTTATAGTTATCAGATATTTACAGTTATGAGATGATTTCCAG
495422 TTATC
66 TTATC
* * * * *
495427 AGATATTTATAGTTATTAGATGATTTT-CAGTTATCATATATTTACAGTTATGAGATGATTTCCA
1 ATATGTTTACAGTTATTAGATG-TTTTATAGTTATCAGATATTTACAGTTATGAGATGATTTCCA
495491 GTTATC
65 GTTATC
*
495497 ATATGTTTACAGTTATTGGATGTTTTATAGTTATCAGA
1 ATATGTTTACAGTTATTAGATGTTTTATAGTTATCAGA
495535 CTTAGATTAA
Statistics
Matches: 87, Mismatches: 19, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
69 4 0.05
70 80 0.92
71 3 0.03
ACGTcount: A:0.32, C:0.07, G:0.14, T:0.47
Consensus pattern (70 bp):
ATATGTTTACAGTTATTAGATGTTTTATAGTTATCAGATATTTACAGTTATGAGATGATTTCCAG
TTATC
Found at i:496735 original size:19 final size:19
Alignment explanation
Indices: 496711--496768 Score: 64
Period size: 19 Copynumber: 2.9 Consensus size: 19
496701 TAAACTTATA
496711 TATACATATATAATATAAG
1 TATACATATATAATATAAG
*
496730 TATACAT-TATACTTATAAG
1 TATACATATATA-ATATAAG
*
496749 TATATAATATATAAGTATAA
1 TATA-CATATATAA-TATAA
496769 AGTACATATA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
18 4 0.12
19 17 0.53
20 2 0.06
21 9 0.28
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.40
Consensus pattern (19 bp):
TATACATATATAATATAAG
Found at i:496915 original size:44 final size:45
Alignment explanation
Indices: 496867--496953 Score: 158
Period size: 45 Copynumber: 2.0 Consensus size: 45
496857 CAAAATTTCA
*
496867 AGCTGAAATTAAAAGCAATT-AAATAAGATAAAGGATTAAATTAT
1 AGCTGAAATTAAAAGCAATTAAAATAAGATAAAGGAATAAATTAT
496911 AGCTGAAATTAAAAGCAATTAAAATAAGATAAAGGAATAAATT
1 AGCTGAAATTAAAAGCAATTAAAATAAGATAAAGGAATAAATT
496954 GAAATAATTT
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
44 20 0.49
45 21 0.51
ACGTcount: A:0.56, C:0.05, G:0.14, T:0.25
Consensus pattern (45 bp):
AGCTGAAATTAAAAGCAATTAAAATAAGATAAAGGAATAAATTAT
Found at i:497535 original size:107 final size:105
Alignment explanation
Indices: 497344--497535 Score: 305
Period size: 105 Copynumber: 1.8 Consensus size: 105
497334 CATTTCTTAT
* * *
497344 TTTTTTTAGATCTAACGCATAAAATAAGCATTGTTCATCAGGAAAAAAACTCTGGAATCCTTCAC
1 TTTTTTTAGATCTAACCCAAAAAATAAGCATTGTTCATCAGGAAAAAAACTCTAGAATCCTTCAC
497409 CTTCTCGACTCCTCATCTTCGAAAAAAAATCGTTAATTTC
66 CTTCTCGACTCCTCATCTTCGAAAAAAAATCGTTAATTTC
*
497449 TTTTTTTAGATCTAACCCAAAAAATAAGCATTGTTCATCCGGAAAAAAATTCTCTAGAAT-CTTC
1 TTTTTTTAGATCTAACCCAAAAAATAAGCATTGTTCATCAGGAAAAAAA--CTCTAGAATCCTTC
*
497513 TACCTTCTTGACTCCTCATCTTC
64 -ACCTTCTCGACTCCTCATCTTC
497536 TATAGTTCCA
Statistics
Matches: 79, Mismatches: 5, Indels: 4
0.90 0.06 0.05
Matches are distributed among these distances:
105 46 0.58
106 4 0.05
107 29 0.37
ACGTcount: A:0.33, C:0.23, G:0.09, T:0.35
Consensus pattern (105 bp):
TTTTTTTAGATCTAACCCAAAAAATAAGCATTGTTCATCAGGAAAAAAACTCTAGAATCCTTCAC
CTTCTCGACTCCTCATCTTCGAAAAAAAATCGTTAATTTC
Found at i:498766 original size:36 final size:37
Alignment explanation
Indices: 498694--498778 Score: 93
Period size: 36 Copynumber: 2.3 Consensus size: 37
498684 AAAAACTAAT
*
498694 GTTTATTATTTGTTTTTCTATTTGCTAATTGTTTATTG
1 GTTT-TTATATGTTTTTCTATTTGCTAATTGTTTATTG
* *
498732 GTTTTTATATGTTTTT-TATTTTCT-ATTTTCTTATTG
1 GTTTTTATATGTTTTTCTATTTGCTAATTGT-TTATTG
* *
498768 TTTTTTGTATG
1 GTTTTTATATG
498779 CATTATATGT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
35 4 0.10
36 22 0.54
37 11 0.27
38 4 0.10
ACGTcount: A:0.14, C:0.05, G:0.12, T:0.69
Consensus pattern (37 bp):
GTTTTTATATGTTTTTCTATTTGCTAATTGTTTATTG
Found at i:498809 original size:20 final size:18
Alignment explanation
Indices: 498786--498836 Score: 59
Period size: 20 Copynumber: 2.7 Consensus size: 18
498776 ATGCATTATA
498786 TGTTTTTATTTTATATTTTC
1 TGTTTTTATTTT-TA-TTTC
*
498806 TGTTTTTATATTTTATTTG
1 TGTTTTTAT-TTTTATTTC
498825 T-TTTTTATTTTT
1 TGTTTTTATTTTT
498837 TTTATTTTCT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
17 4 0.14
18 7 0.24
19 4 0.14
20 11 0.38
21 3 0.10
ACGTcount: A:0.14, C:0.02, G:0.06, T:0.78
Consensus pattern (18 bp):
TGTTTTTATTTTTATTTC
Found at i:498833 original size:16 final size:16
Alignment explanation
Indices: 498806--498850 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
498796 TTATATTTTC
498806 TGTTTTTATATTTTATT
1 TGTTTTT-TATTTTATT
*
498823 TGTTTTTTATTTTTTT
1 TGTTTTTTATTTTATT
* *
498839 TATTTTCTATTT
1 TGTTTTTTATTT
498851 GTTTTTTTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
16 18 0.72
17 7 0.28
ACGTcount: A:0.13, C:0.02, G:0.04, T:0.80
Consensus pattern (16 bp):
TGTTTTTTATTTTATT
Found at i:499015 original size:51 final size:51
Alignment explanation
Indices: 498954--499070 Score: 198
Period size: 51 Copynumber: 2.3 Consensus size: 51
498944 AGGACTTTGA
*
498954 ATTAGCTGATTCTTATATTGTTTTATGTTTTTATTTGTTGATGGGAAGGAT
1 ATTAGTTGATTCTTATATTGTTTTATGTTTTTATTTGTTGATGGGAAGGAT
* *
499005 ATTAGTTGATTCTTATATTGTTTTCTGTTTTTATTTGTTGATGTGAAGGAT
1 ATTAGTTGATTCTTATATTGTTTTATGTTTTTATTTGTTGATGGGAAGGAT
*
499056 ATTGGTTGATTCTTA
1 ATTAGTTGATTCTTA
499071 ATGTTAATGT
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 62 1.00
ACGTcount: A:0.21, C:0.04, G:0.21, T:0.55
Consensus pattern (51 bp):
ATTAGTTGATTCTTATATTGTTTTATGTTTTTATTTGTTGATGGGAAGGAT
Found at i:499109 original size:31 final size:32
Alignment explanation
Indices: 499040--499117 Score: 113
Period size: 32 Copynumber: 2.5 Consensus size: 32
499030 TGTTTTTATT
* * *
499040 TGTTGATGTGAAGGATATTGGTTGATTCTTAA
1 TGTTAATGTGAATGATATTAGTTGATTCTTAA
499072 TGTTAATGTGAATGATATTAGTTGATTCTT-A
1 TGTTAATGTGAATGATATTAGTTGATTCTTAA
*
499103 TGTTAATATGAATGA
1 TGTTAATGTGAATGA
499118 CTTTGAATTA
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
31 15 0.36
32 27 0.64
ACGTcount: A:0.29, C:0.03, G:0.23, T:0.45
Consensus pattern (32 bp):
TGTTAATGTGAATGATATTAGTTGATTCTTAA
Found at i:499159 original size:13 final size:13
Alignment explanation
Indices: 499141--499224 Score: 52
Period size: 13 Copynumber: 6.5 Consensus size: 13
499131 AATTATTATA
*
499141 TTGTTTTTTGTTT
1 TTGTTTTTTATTT
499154 TTGTTTTTTATTT
1 TTGTTTTTTATTT
*
499167 TT-TTTATTA-TT
1 TTGTTTTTTATTT
* *
499178 TAG-TTTCTATTT
1 TTGTTTTTTATTT
499190 TT-TTATTTT-TTT
1 TTGTT-TTTTATTT
*
499202 GTTATTTATTTATTT
1 -TTGTTT-TTTATTT
499217 TATGTTTT
1 T-TGTTTT
499225 CTGTTATTTA
Statistics
Matches: 54, Mismatches: 8, Indels: 17
0.68 0.10 0.22
Matches are distributed among these distances:
11 7 0.13
12 13 0.24
13 20 0.37
14 7 0.13
15 7 0.13
ACGTcount: A:0.12, C:0.01, G:0.07, T:0.80
Consensus pattern (13 bp):
TTGTTTTTTATTT
Found at i:499190 original size:22 final size:23
Alignment explanation
Indices: 499165--499250 Score: 68
Period size: 25 Copynumber: 3.7 Consensus size: 23
499155 TGTTTTTTAT
499165 TTTTTTTATTATTTAGTT-TCTA
1 TTTTTTTATTATTTAGTTATCTA
* * *
499187 TTTTTTTATTTTTTTGTTATTTA
1 TTTTTTTATTATTTAGTTATCTA
* *
499210 TTTATTTTATGT-TTTCTGTTATTTA
1 TTT-TTTTAT-TATTT-AGTTATCTA
*
499235 TTTATTTATTTATTTA
1 TTTTTTTA-TTATTTA
499251 TTTTTGTTTA
Statistics
Matches: 53, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
22 16 0.30
23 6 0.11
24 14 0.26
25 17 0.32
ACGTcount: A:0.17, C:0.02, G:0.05, T:0.76
Consensus pattern (23 bp):
TTTTTTTATTATTTAGTTATCTA
Found at i:499198 original size:8 final size:8
Alignment explanation
Indices: 499157--499255 Score: 53
Period size: 8 Copynumber: 12.5 Consensus size: 8
499147 TTTGTTTTTG
499157 TTTTTTAT
1 TTTTTTAT
499165 TTTTTT-T
1 TTTTTTAT
*
499172 ATTATTTA-
1 -TTTTTTAT
* *
499180 GTTTCTAT
1 TTTTTTAT
499188 TTTTTTAT
1 TTTTTTAT
*
499196 TTTTTT-G
1 TTTTTTAT
*
499203 TTATTTAT
1 TTTTTTAT
499211 TTATTTTAT
1 TT-TTTTAT
* *
499220 GTTTTCT-G
1 -TTTTTTAT
*
499228 TTATTTAT
1 TTTTTTAT
*
499236 TTATTTAT
1 TTTTTTAT
*
499244 TTATTTAT
1 TTTTTTAT
499252 TTTT
1 TTTT
499256 GTTTATATTT
Statistics
Matches: 68, Mismatches: 16, Indels: 14
0.69 0.16 0.14
Matches are distributed among these distances:
7 14 0.21
8 44 0.65
9 8 0.12
10 2 0.03
ACGTcount: A:0.16, C:0.02, G:0.04, T:0.78
Consensus pattern (8 bp):
TTTTTTAT
Found at i:499212 original size:4 final size:4
Alignment explanation
Indices: 499185--499253 Score: 63
Period size: 4 Copynumber: 17.2 Consensus size: 4
499175 ATTTAGTTTC
* * *
499185 TATT TTTT TATT T-TT T-TGT TATT TATT TATTT TATG T-TT TCTGT TATT
1 TATT TATT TATT TATT TAT-T TATT TATT TA-TT TATT TATT TAT-T TATT
499233 TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT T
499254 TTGTTTATAT
Statistics
Matches: 55, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
3 6 0.11
4 41 0.75
5 8 0.15
ACGTcount: A:0.17, C:0.01, G:0.04, T:0.77
Consensus pattern (4 bp):
TATT
Found at i:499217 original size:25 final size:25
Alignment explanation
Indices: 499133--499241 Score: 93
Period size: 25 Copynumber: 4.4 Consensus size: 25
499123 AATTAGCTAA
* *
499133 TTATTATATTGTTTTTTGTTTTTGTTTT
1 TTATT-TATT-TTTATT-TTTTTGTTAT
* *
499161 TTATTT-TTTTTATTATTTAGTT-T
1 TTATTTATTTTTATTTTTTTGTTAT
*
499184 CTA-TT-TTTTTATTTTTTTGTTAT
1 TTATTTATTTTTATTTTTTTGTTAT
*
499207 TTATTTA-TTTTATGTTTTCTGTTAT
1 TTATTTATTTTTAT-TTTTTTGTTAT
499232 TTATTTATTT
1 TTATTTATTT
499242 ATTTATTTAT
Statistics
Matches: 68, Mismatches: 8, Indels: 12
0.77 0.09 0.14
Matches are distributed among these distances:
22 16 0.24
23 6 0.09
24 14 0.21
25 22 0.32
26 4 0.06
27 1 0.01
28 5 0.07
ACGTcount: A:0.15, C:0.02, G:0.06, T:0.77
Consensus pattern (25 bp):
TTATTTATTTTTATTTTTTTGTTAT
Found at i:501678 original size:2 final size:2
Alignment explanation
Indices: 501671--501713 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
501661 AAAAATATTA
*
501671 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
501713 A
1 A
501714 AAAATAATTA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:502656 original size:19 final size:19
Alignment explanation
Indices: 502615--502664 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
502605 ATAACCAACG
* **
502615 AATTCGCAACGCGATTTCA
1 AATTCGCAACACGAACTCA
502634 AATTCGCAACACGAACTCCA
1 AATTCGCAACACGAACT-CA
*
502654 ATTTCGCAACA
1 AATTCGCAACA
502665 TAGTTTCCAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 14 0.54
20 12 0.46
ACGTcount: A:0.36, C:0.30, G:0.12, T:0.22
Consensus pattern (19 bp):
AATTCGCAACACGAACTCA
Found at i:502766 original size:13 final size:13
Alignment explanation
Indices: 502748--502774 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
502738 AGGTGAACAC
502748 GGTTGCGAAATTG
1 GGTTGCGAAATTG
502761 GGTTGCGAAATTG
1 GGTTGCGAAATTG
502774 G
1 G
502775 CGAATTCGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.07, G:0.41, T:0.30
Consensus pattern (13 bp):
GGTTGCGAAATTG
Found at i:502839 original size:66 final size:65
Alignment explanation
Indices: 502756--502923 Score: 223
Period size: 66 Copynumber: 2.6 Consensus size: 65
502746 ACGGTTGCGA
* * *
502756 AATTGGGTTGCGAAATTGGCGAATTCGAGTTGCGGATTTTTCCTACAGTGTTTCCCCTATATCAG
1 AATTGAGTTGCGAAATTGACGAATTCGAGTTGCGGATTTTTCCTACAGTGTTT-ACCTATATCAG
502821 T
65 T
* * * *
502822 AATTGAGTCGCGAAATTGACGAATTCGAGTTGCGGATTTTTTCTACCGTGTTTACCTATATCGGT
1 AATTGAGTTGCGAAATTGACGAATTCGAGTTGCGGATTTTTCCTACAGTGTTTACCTATATCAGT
* * *
502887 AATTGAGTTGCGAAA-T-CCGAATTTGAGTTGCGAATTT
1 AATTGAGTTGCGAAATTGACGAATTCGAGTTGCGGATTT
502924 GAAAACTGAA
Statistics
Matches: 91, Mismatches: 11, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
63 18 0.20
64 1 0.01
65 24 0.26
66 48 0.53
ACGTcount: A:0.24, C:0.16, G:0.24, T:0.36
Consensus pattern (65 bp):
AATTGAGTTGCGAAATTGACGAATTCGAGTTGCGGATTTTTCCTACAGTGTTTACCTATATCAGT
Found at i:502959 original size:22 final size:22
Alignment explanation
Indices: 502913--502986 Score: 107
Period size: 22 Copynumber: 3.5 Consensus size: 22
502903 CCGAATTTGA
* *
502913 GTTGCGAATTTGA-AAACT-GA
1 GTTGCGAATTTGAGAAATTCGC
*
502933 ATTGCGAATTTGAGAAATTCGC
1 GTTGCGAATTTGAGAAATTCGC
502955 GTTGCGAATTTGAGAAATTCGC
1 GTTGCGAATTTGAGAAATTCGC
502977 GTTGCGAATT
1 GTTGCGAATT
502987 CATTGGTTAT
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
20 12 0.25
21 4 0.08
22 32 0.67
ACGTcount: A:0.30, C:0.12, G:0.26, T:0.32
Consensus pattern (22 bp):
GTTGCGAATTTGAGAAATTCGC
Found at i:503074 original size:15 final size:15
Alignment explanation
Indices: 503054--503088 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
503044 TTTTCGGTCA
503054 CTAAAGTTATTTTCT
1 CTAAAGTTATTTTCT
503069 CTAAAGTTATTTTCT
1 CTAAAGTTATTTTCT
503084 CTAAA
1 CTAAA
503089 ATTAAAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.31, C:0.14, G:0.06, T:0.49
Consensus pattern (15 bp):
CTAAAGTTATTTTCT
Found at i:509090 original size:21 final size:20
Alignment explanation
Indices: 509065--509126 Score: 88
Period size: 21 Copynumber: 3.0 Consensus size: 20
509055 TAAAAATTAT
509065 CTAAAACATTATTATTTTTAC
1 CTAAAACATTATT-TTTTTAC
*
509086 CTAAAACATTAATGTTTTTAC
1 CTAAAACATT-ATTTTTTTAC
509107 CTAAAACATTAATTTTTTTA
1 CTAAAACATT-ATTTTTTTA
509127 ACATTTCCGG
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
21 36 0.95
22 2 0.05
ACGTcount: A:0.39, C:0.13, G:0.02, T:0.47
Consensus pattern (20 bp):
CTAAAACATTATTTTTTTAC
Found at i:509442 original size:16 final size:15
Alignment explanation
Indices: 509418--509447 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
509408 ATAAAATATA
509418 AATTTAATTATTAAT
1 AATTTAATTATTAAT
509433 AATTTAAATTATTAA
1 AATTT-AATTATTAA
509448 ATCATTCTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
AATTTAATTATTAAT
Done.