Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A02
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: 100057689
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3589301 characters in sequence are not A, C, G, or T
File 173 of 295
Found at i:59201721 original size:16 final size:16
Alignment explanation
Indices: 59201667--59201721 Score: 51
Period size: 16 Copynumber: 3.3 Consensus size: 16
59201657 ATTCATTATG
59201667 AAATGGTTGATCTTGT
1 AAATGGTTGATCTTGT
*
59201683 AAATTGTATTGCAT-TAT-T
1 AAA-TG-GTTG-ATCT-TGT
59201701 AAATGGTTGATCTTGT
1 AAATGGTTGATCTTGT
59201717 AAATG
1 AAATG
59201722 ATATTGCACT
Statistics
Matches: 31, Mismatches: 2, Indels: 12
0.69 0.04 0.27
Matches are distributed among these distances:
15 3 0.10
16 13 0.42
17 4 0.13
18 8 0.26
19 3 0.10
ACGTcount: A:0.31, C:0.05, G:0.20, T:0.44
Consensus pattern (16 bp):
AAATGGTTGATCTTGT
Found at i:59203108 original size:21 final size:21
Alignment explanation
Indices: 59203080--59203122 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
59203070 TTACATGGCC
59203080 TGTTCACAAGGCCGTGT-CCT
1 TGTTCACAAGGCCGTGTGCCT
* *
59203100 TGTTACACACGGGCGTGTGCCT
1 TGTT-CACAAGGCCGTGTGCCT
59203122 T
1 T
59203123 AGCCACACGG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 4 0.21
21 11 0.58
22 4 0.21
ACGTcount: A:0.14, C:0.28, G:0.28, T:0.30
Consensus pattern (21 bp):
TGTTCACAAGGCCGTGTGCCT
Found at i:59208501 original size:43 final size:42
Alignment explanation
Indices: 59208454--59208621 Score: 228
Period size: 42 Copynumber: 4.0 Consensus size: 42
59208444 CATAGTATCG
* * *
59208454 TATCGATGCCAGTAGCCCAGCTATGGTCTTACATGTAATCTCA
1 TATCGATGCCA-TAGCCCAGATATGGTCTTACACGAAATCTCA
* * *
59208497 TATCGATGCCAATAGCCTAGCTATGATCTTACACGAAATCTCA
1 TATCGATGCC-ATAGCCCAGATATGGTCTTACACGAAATCTCA
** *
59208540 TATCGATGCCATATACCAAATATGGTCTTACACGAAATCTCA
1 TATCGATGCCATAGCCCAGATATGGTCTTACACGAAATCTCA
*
59208582 TATCGATGCCATATCCCAGATATGGTCTTACACGAAATCT
1 TATCGATGCCATAGCCCAGATATGGTCTTACACGAAATCT
59208622 TAGTAACCCT
Statistics
Matches: 112, Mismatches: 12, Indels: 3
0.88 0.09 0.02
Matches are distributed among these distances:
42 64 0.57
43 47 0.42
44 1 0.01
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.29
Consensus pattern (42 bp):
TATCGATGCCATAGCCCAGATATGGTCTTACACGAAATCTCA
Found at i:59211774 original size:11 final size:11
Alignment explanation
Indices: 59211758--59211783 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
59211748 GCATTAACAT
59211758 ATTTAATTATA
1 ATTTAATTATA
59211769 ATTTAATTATA
1 ATTTAATTATA
59211780 ATTT
1 ATTT
59211784 TTAAGATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (11 bp):
ATTTAATTATA
Found at i:59211777 original size:24 final size:25
Alignment explanation
Indices: 59211724--59211777 Score: 58
Period size: 24 Copynumber: 2.2 Consensus size: 25
59211714 ACTAAATAAA
59211724 AATTAAAAATTTATATATATAATTG
1 AATTAAAAATTTATATATATAATTG
* * *
59211749 CATTAACATATTTA-AT-TATAATTT
1 AATTAA-AAATTTATATATATAATTG
59211773 AATTA
1 AATTA
59211778 TAATTTTTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
24 11 0.46
25 7 0.29
26 6 0.25
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (25 bp):
AATTAAAAATTTATATATATAATTG
Found at i:59213420 original size:36 final size:36
Alignment explanation
Indices: 59213348--59213417 Score: 97
Period size: 36 Copynumber: 1.9 Consensus size: 36
59213338 ATGATTAAAC
* *
59213348 AATTTAATAATATATATAGTAAAAAATGTAAAAATT
1 AATTTAATAATATAAATAGTAAAAAATATAAAAATT
59213384 AATTTAATAATATAAATAGTATATAAAA-ATAAAA
1 AATTTAATAATATAAATAGTA-A-AAAATATAAAA
59213418 TTATTACTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
36 20 0.67
37 6 0.20
38 4 0.13
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.34
Consensus pattern (36 bp):
AATTTAATAATATAAATAGTAAAAAATATAAAAATT
Found at i:59215601 original size:42 final size:43
Alignment explanation
Indices: 59215501--59215616 Score: 146
Period size: 43 Copynumber: 2.7 Consensus size: 43
59215491 AGCTCGTACA
* *
59215501 ATGCCAACGTCCCAGAC-GTGGTCTTACATGTAATCAAATATCG
1 ATGCCAACGTCCCAGACAG-GGTCTTACACGAAATCAAATATCG
* ** *
59215544 ATGTCATTGTCCCAGACAGGGTCATACACGAAATCAAATA-CG
1 ATGCCAACGTCCCAGACAGGGTCTTACACGAAATCAAATATCG
*
59215586 ATGCCAACGTCCCAGACATGGTCTTACACGA
1 ATGCCAACGTCCCAGACAGGGTCTTACACGA
59215617 TAACACATAC
Statistics
Matches: 61, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
42 28 0.46
43 32 0.52
44 1 0.02
ACGTcount: A:0.32, C:0.27, G:0.19, T:0.22
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACAGGGTCTTACACGAAATCAAATATCG
Found at i:59223194 original size:43 final size:43
Alignment explanation
Indices: 59223130--59223235 Score: 114
Period size: 43 Copynumber: 2.5 Consensus size: 43
59223120 GCACGTACAT
*
59223130 CGTGGTCTTACA--TATCATCAAATATCGATGCC-ACTATCCCAAA
1 CGTGGTCTTACACGTA-AATCAAATAT-GATGCCAAC-ATCCCAAA
* *
59223173 CAG-GGTCTTACACG-AAATCAAATATGATGCCAACGTCCCAGA
1 C-GTGGTCTTACACGTAAATCAAATATGATGCCAACATCCCAAA
59223215 CGTGGTCTTACACGTAAATCA
1 CGTGGTCTTACACGTAAATCA
59223236 TAAGTCGGCA
Statistics
Matches: 54, Mismatches: 3, Indels: 12
0.78 0.04 0.17
Matches are distributed among these distances:
41 1 0.02
42 24 0.44
43 27 0.50
44 2 0.04
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.25
Consensus pattern (43 bp):
CGTGGTCTTACACGTAAATCAAATATGATGCCAACATCCCAAA
Found at i:59223222 original size:42 final size:44
Alignment explanation
Indices: 59223146--59223235 Score: 116
Period size: 42 Copynumber: 2.1 Consensus size: 44
59223136 CTTACATATC
59223146 ATCAAATATCGATGCCACTATCCCAAACAGGGTCTTACACG-AA
1 ATCAAATATCGATGCCACTATCCCAAACAGGGTCTTACACGTAA
* *
59223189 ATCAAATAT-GATGCCAAC-GTCCCAGAC-GTGGTCTTACACGTAA
1 ATCAAATATCGATGCC-ACTATCCCAAACAG-GGTCTTACACGTAA
59223232 ATCA
1 ATCA
59223236 TAAGTCGGCA
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
41 1 0.02
42 24 0.57
43 17 0.40
ACGTcount: A:0.36, C:0.27, G:0.16, T:0.22
Consensus pattern (44 bp):
ATCAAATATCGATGCCACTATCCCAAACAGGGTCTTACACGTAA
Found at i:59229527 original size:7 final size:7
Alignment explanation
Indices: 59229515--59229540 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
59229505 GTTGAATGTA
59229515 GGCTTTG
1 GGCTTTG
59229522 GGCTTTG
1 GGCTTTG
59229529 GGCTTTG
1 GGCTTTG
59229536 GGCTT
1 GGCTT
59229541 GTGGAGTAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.00, C:0.15, G:0.42, T:0.42
Consensus pattern (7 bp):
GGCTTTG
Found at i:59230392 original size:34 final size:34
Alignment explanation
Indices: 59230348--59230417 Score: 131
Period size: 34 Copynumber: 2.1 Consensus size: 34
59230338 ATTATGCAAT
59230348 TGTTACTGTAATGGGCTAAGGCCCACACTGATAC
1 TGTTACTGTAATGGGCTAAGGCCCACACTGATAC
*
59230382 TGTTATTGTAATGGGCTAAGGCCCACACTGATAC
1 TGTTACTGTAATGGGCTAAGGCCCACACTGATAC
59230416 TG
1 TG
59230418 GACTTTACTG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.29
Consensus pattern (34 bp):
TGTTACTGTAATGGGCTAAGGCCCACACTGATAC
Found at i:59247254 original size:42 final size:41
Alignment explanation
Indices: 59247146--59247254 Score: 112
Period size: 44 Copynumber: 2.6 Consensus size: 41
59247136 TTCCGATATG
* * * *
59247146 TGATTTTGTGTAAGACCAC-GTCTGGGACATTGGTATCGTTT
1 TGATTTTGTGTAAGACC-CTGTCTGAGACATCGGCATCGTTA
* *
59247187 TGAGATTTACGTGTAAGACCATGTCTGAGACATCGGCATCGTATA
1 T--GATTT-TGTGTAAGACCCTGTCTGAGACATCGGCATCGT-TA
59247232 TGATTTTGTGTAAGACCCTGTCT
1 TGATTTTGTGTAAGACCCTGTCT
59247255 AGGACAGTGG
Statistics
Matches: 55, Mismatches: 8, Indels: 9
0.76 0.11 0.12
Matches are distributed among these distances:
41 1 0.02
42 15 0.27
43 10 0.18
44 27 0.49
45 2 0.04
ACGTcount: A:0.23, C:0.17, G:0.25, T:0.36
Consensus pattern (41 bp):
TGATTTTGTGTAAGACCCTGTCTGAGACATCGGCATCGTTA
Found at i:59247267 original size:42 final size:39
Alignment explanation
Indices: 59247146--59247268 Score: 104
Period size: 42 Copynumber: 2.9 Consensus size: 39
59247136 TTCCGATATG
* *
59247146 TGATTTTGTGTAAGACCAC-GTCTGGGACATTGGTATCGTTT
1 TGATTTTGTGTAAGACC-CTGTCT-GGACA-TGGCATCGTTA
* *
59247187 TGAGATTTACGTGTAAGACCATGTCTGAGACATCGGCATCGTATA
1 T--GATTT-TGTGTAAGACCCTGTCTG-GACAT-GGCATCGT-TA
59247232 TGATTTTGTGTAAGACCCTGTCTAGGACAGTGGCATC
1 TGATTTTGTGTAAGACCCTGTCT-GGACA-TGGCATC
59247269 AATATTTGAT
Statistics
Matches: 67, Mismatches: 6, Indels: 17
0.74 0.07 0.19
Matches are distributed among these distances:
41 1 0.01
42 25 0.37
43 14 0.21
44 25 0.37
45 2 0.03
ACGTcount: A:0.24, C:0.17, G:0.26, T:0.33
Consensus pattern (39 bp):
TGATTTTGTGTAAGACCCTGTCTGGACATGGCATCGTTA
Found at i:59255515 original size:21 final size:21
Alignment explanation
Indices: 59255440--59255505 Score: 69
Period size: 21 Copynumber: 3.0 Consensus size: 21
59255430 GTCTTGAATT
*
59255440 TGTTAGATATTGAATTTATTG
1 TGTTAGATATTGAATTTATTA
* *
59255461 TGTTTTAAGCTTGTTGAATTTATTA
1 TG--TT-AG-ATATTGAATTTATTA
59255486 TGTTAGATATTGAATTTATT
1 TGTTAGATATTGAATTTATT
59255506 TGGTTGGATA
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
21 14 0.39
22 2 0.06
23 4 0.11
24 2 0.06
25 14 0.39
ACGTcount: A:0.27, C:0.02, G:0.17, T:0.55
Consensus pattern (21 bp):
TGTTAGATATTGAATTTATTA
Found at i:59256804 original size:29 final size:29
Alignment explanation
Indices: 59256765--59256821 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
59256755 CAGTATATGT
*
59256765 AAAAACAATTTAAAGTATAAATTTATTAA
1 AAAAACAATTTAAAATATAAATTTATTAA
*
59256794 AAAAAGAATTTAAAATATAAATTTATTA
1 AAAAACAATTTAAAATATAAATTTATTA
59256822 GTATATATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.35
Consensus pattern (29 bp):
AAAAACAATTTAAAATATAAATTTATTAA
Found at i:59256831 original size:20 final size:20
Alignment explanation
Indices: 59256808--59256847 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
59256798 AGAATTTAAA
*
59256808 ATATAAATTTATTAGTATAT
1 ATATAAATTTATTAATATAT
59256828 ATATAAATTTATTAATATAT
1 ATATAAATTTATTAATATAT
59256848 GTAAAAACAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (20 bp):
ATATAAATTTATTAATATAT
Found at i:59256845 original size:16 final size:17
Alignment explanation
Indices: 59256801--59256847 Score: 51
Period size: 20 Copynumber: 2.6 Consensus size: 17
59256791 TAAAAAAAGA
*
59256801 ATTTAAAATATAAATTT
1 ATTTAATATATAAATTT
59256818 ATTAGTATATATATAAATTT
1 ATT--TA-ATATATAAATTT
59256838 A-TTAATATAT
1 ATTTAATATAT
59256848 GTAAAAACAG
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
16 6 0.23
17 5 0.19
19 3 0.12
20 12 0.46
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (17 bp):
ATTTAATATATAAATTT
Found at i:59256845 original size:18 final size:19
Alignment explanation
Indices: 59256808--59256852 Score: 65
Period size: 20 Copynumber: 2.4 Consensus size: 19
59256798 AGAATTTAAA
59256808 ATATAAATTTATTAGTATAT
1 ATATAAATTTATTAG-ATAT
59256828 ATATAAATTTATTA-ATAT
1 ATATAAATTTATTAGATAT
*
59256846 ATGTAAA
1 ATATAAA
59256853 AACAGCTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 10 0.42
20 14 0.58
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (19 bp):
ATATAAATTTATTAGATAT
Found at i:59271339 original size:55 final size:53
Alignment explanation
Indices: 59271252--59271506 Score: 229
Period size: 55 Copynumber: 4.8 Consensus size: 53
59271242 ATTAGGGTTT
*
59271252 AAGGATACCATGTAAGACCATGCCAAGGCATGGAAATTGGTAAGGTTTCTAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGG-AATTGGTAA-GTTTCTAAGGC
* * * * * *
59271307 AAGGAAATCATGTAAGACCATGTCAAGACATGGCATTGATAAGTTACTATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGAATTGGTAAGTT--TCTAAGGC
* * * * * *
59271362 AAAGG-TCCCATGTAAGACCATGCCAAGGCATCGCATTAGTGAG-TTCATAAGGC
1 -AAGGATACCATGTAAGACCATGCCAAGACATGGAATTGGTAAGTTTC-TAAGGC
*
59271415 AAGGATACCATGTAAGACCATGTCAAGACATGGCAA-TGGTAAGTTTC-AA---
1 AAGGATACCATGTAAGACCATGCCAAGACATGG-AATTGGTAAGTTTCTAAGGC
* * *
59271464 AAGGATACCACGTAAGACCATGACAAGTCATGGCAA-TGGTAAG
1 AAGGATACCATGTAAGACCATGCCAAGACATGG-AATTGGTAAG
59271507 GTACCCACGT
Statistics
Matches: 166, Mismatches: 27, Indels: 20
0.78 0.13 0.09
Matches are distributed among these distances:
49 40 0.24
52 7 0.04
53 38 0.23
54 12 0.07
55 65 0.39
56 4 0.02
ACGTcount: A:0.37, C:0.18, G:0.24, T:0.21
Consensus pattern (53 bp):
AAGGATACCATGTAAGACCATGCCAAGACATGGAATTGGTAAGTTTCTAAGGC
Found at i:59271458 original size:108 final size:110
Alignment explanation
Indices: 59271259--59271459 Score: 300
Period size: 108 Copynumber: 1.8 Consensus size: 110
59271249 TTTAAGGATA
* * *
59271259 CCATGTAAGACCATGCCAAGGCATGGAAATTGGTAAGGTTTCTAAGGCAAGGAAATCATGTAAGA
1 CCATGTAAGACCATGCCAAGGCATCGAAATTAGTAAGGTTTCTAAGGCAAGGAAACCATGTAAGA
*
59271324 CCATGTCAAGACATGGCATTGATAAGTTACTATAAGGCAAAGGTC
66 CCATGTCAAGACATGGCAATGATAAGTTACTATAAGGCAAAGGTC
* * *
59271369 CCATGTAAGACCATGCCAAGGCATCG-CATTAGTGA-G-TTCATAAGGCAAGGATACCATGTAAG
1 CCATGTAAGACCATGCCAAGGCATCGAAATTAGTAAGGTTTC-TAAGGCAAGGAAACCATGTAAG
*
59271431 ACCATGTCAAGACATGGCAATGGTAAGTT
65 ACCATGTCAAGACATGGCAATGATAAGTT
59271460 TCAAAAGGAT
Statistics
Matches: 82, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
107 3 0.04
108 48 0.59
109 6 0.07
110 25 0.30
ACGTcount: A:0.35, C:0.18, G:0.24, T:0.22
Consensus pattern (110 bp):
CCATGTAAGACCATGCCAAGGCATCGAAATTAGTAAGGTTTCTAAGGCAAGGAAACCATGTAAGA
CCATGTCAAGACATGGCAATGATAAGTTACTATAAGGCAAAGGTC
Found at i:59271717 original size:16 final size:16
Alignment explanation
Indices: 59271696--59271726 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
59271686 ATAAATTTGA
59271696 TTAAGTAAGTAAGTAT
1 TTAAGTAAGTAAGTAT
*
59271712 TTAAGTAAGTGAGTA
1 TTAAGTAAGTAAGTA
59271727 AGTGAAGAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.23, T:0.35
Consensus pattern (16 bp):
TTAAGTAAGTAAGTAT
Found at i:59276277 original size:33 final size:35
Alignment explanation
Indices: 59276235--59276319 Score: 102
Period size: 40 Copynumber: 2.3 Consensus size: 35
59276225 TCCCGAAGGC
59276235 AGTGATTTTAT-GTT-ACCCGAAGGCATTTATGCT
1 AGTGATTTTATCGTTAACCCGAAGGCATTTATGCT
*
59276268 AGTGATTTTATCCGGGTTAAGACCCGAAGGCATTTGTGCT
1 AGTGATTTTAT-C--GTT-A-ACCCGAAGGCATTTATGCT
59276308 AGTGATTTTATC
1 AGTGATTTTATC
59276320 CGGGCTAAGA
Statistics
Matches: 44, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
33 11 0.25
37 3 0.07
39 1 0.02
40 29 0.66
ACGTcount: A:0.24, C:0.15, G:0.24, T:0.38
Consensus pattern (35 bp):
AGTGATTTTATCGTTAACCCGAAGGCATTTATGCT
Found at i:59276308 original size:40 final size:40
Alignment explanation
Indices: 59276249--59276446 Score: 249
Period size: 40 Copynumber: 5.0 Consensus size: 40
59276239 ATTTTATGTT
* * *
59276249 ACCCGAAGGCATTTATGCTAGTGATTTTATCCGGGTTAAG
1 ACCCGAAGGCATTTGTGCTAGTGATTATATCCGGGCTAAG
*
59276289 ACCCGAAGGCATTTGTGCTAGTGATTTTATCCGGGCTAAG
1 ACCCGAAGGCATTTGTGCTAGTGATTATATCCGGGCTAAG
*
59276329 ACCCGAAGGCATTTGTGCGAGTTGA-TATATCCGGGCTAAG
1 ACCCGAAGGCATTTGTGCTAG-TGATTATATCCGGGCTAAG
* * * *
59276369 ACCCGAAGGCATTTGTGCGAGTTG-CTATACCCGGGTTAAG
1 ACCCGAAGGCATTTGTGCTAG-TGATTATATCCGGGCTAAG
* * *
59276409 ACCCGAAGGCAATTGTGCTTGTGGTTATATCC-GGCTAA
1 ACCCGAAGGCATTTGTGCTAGTGATTATATCCGGGCTAA
59276447 ATTCCGAAGA
Statistics
Matches: 143, Mismatches: 12, Indels: 7
0.88 0.07 0.04
Matches are distributed among these distances:
39 7 0.05
40 133 0.93
41 3 0.02
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (40 bp):
ACCCGAAGGCATTTGTGCTAGTGATTATATCCGGGCTAAG
Found at i:59284408 original size:40 final size:40
Alignment explanation
Indices: 59284349--59284600 Score: 330
Period size: 40 Copynumber: 6.3 Consensus size: 40
59284339 CATTTGAATG
*
59284349 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
* * *
59284389 TTATCCGGGTTAAGACCCGAAGGCATTTATGCTAGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
* *
59284429 TTATCCGGGTTAAGACCCGAAGGCATTTGTGCTAGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
* *
59284469 TTATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGA-T
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGATT
* *
59284509 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGATT
* * * * *
59284549 ATACCCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
59284589 ATATCC-GGCTAA
1 ATATCCGGGCTAA
59284601 ATTCCGAAGA
Statistics
Matches: 193, Mismatches: 16, Indels: 7
0.89 0.07 0.03
Matches are distributed among these distances:
39 7 0.04
40 183 0.95
41 3 0.02
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.29
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
Found at i:59288021 original size:6 final size:6
Alignment explanation
Indices: 59288003--59288084 Score: 62
Period size: 6 Copynumber: 13.3 Consensus size: 6
59287993 AAGAAGCATT
* *
59288003 ATCAGA A-CTAGA ATCAGA ATCAGA ATCAGA ATTAG- GTGACAGA ATCAGA
1 ATCAGA ATC-AGA ATCAGA ATCAGA ATCAGA ATCAGA AT--CAGA ATCAGA
* *
59288052 ATCAGT ATCAGGTA A-CAGA ATCAAA ATCAGA AT
1 ATCAGA ATCA-G-A ATCAGA ATCAGA ATCAGA AT
59288085 GTGAATGCAA
Statistics
Matches: 60, Mismatches: 8, Indels: 16
0.71 0.10 0.19
Matches are distributed among these distances:
5 4 0.07
6 48 0.80
7 6 0.10
8 2 0.03
ACGTcount: A:0.48, C:0.15, G:0.18, T:0.20
Consensus pattern (6 bp):
ATCAGA
Found at i:59288048 original size:25 final size:25
Alignment explanation
Indices: 59288017--59288084 Score: 100
Period size: 25 Copynumber: 2.7 Consensus size: 25
59288007 GAACTAGAAT
* *
59288017 CAGAATCAGAATCAGAATTAGGTGA
1 CAGAATCAGAATCAGAATCAGGTAA
*
59288042 CAGAATCAGAATCAGTATCAGGTAA
1 CAGAATCAGAATCAGAATCAGGTAA
*
59288067 CAGAATCAAAATCAGAAT
1 CAGAATCAGAATCAGAAT
59288085 GTGAATGCAA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 38 1.00
ACGTcount: A:0.47, C:0.15, G:0.19, T:0.19
Consensus pattern (25 bp):
CAGAATCAGAATCAGAATCAGGTAA
Found at i:59288516 original size:27 final size:27
Alignment explanation
Indices: 59288487--59288708 Score: 320
Period size: 27 Copynumber: 8.2 Consensus size: 27
59288477 GGGCAAAATG
* * * *
59288487 GTAATTTTACCCCACAAGGGTATCTCG
1 GTAATTCTACCCTACAAGGGTATTTCA
59288514 GTAATTCTACCCTACAAGGGTATTTCA
1 GTAATTCTACCCTACAAGGGTATTTCA
* *
59288541 GTAATTCTACCATACAGGGGTATTTCA
1 GTAATTCTACCCTACAAGGGTATTTCA
**
59288568 GTAATTCTACCCTAC-AGTGGTATTTTG
1 GTAATTCTACCCTACAAG-GGTATTTCA
* *
59288595 GTAATTCTATCCTACAAGGGTATTTTA
1 GTAATTCTACCCTACAAGGGTATTTCA
*
59288622 GTAATTCTACCCTACAATGGTATTTCA
1 GTAATTCTACCCTACAAGGGTATTTCA
59288649 GTAATTCTACCCTACAAGGGTATTTCA
1 GTAATTCTACCCTACAAGGGTATTTCA
*
59288676 GTAATTCTATCCTACAAGGGTATTTCA
1 GTAATTCTACCCTACAAGGGTATTTCA
59288703 GTAATT
1 GTAATT
59288709 TTTTTACATT
Statistics
Matches: 176, Mismatches: 17, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
26 1 0.01
27 173 0.98
28 2 0.01
ACGTcount: A:0.28, C:0.20, G:0.16, T:0.36
Consensus pattern (27 bp):
GTAATTCTACCCTACAAGGGTATTTCA
Found at i:59288753 original size:27 final size:27
Alignment explanation
Indices: 59288719--59288957 Score: 352
Period size: 27 Copynumber: 8.8 Consensus size: 27
59288709 TTTTTACATT
59288719 GAGGGTAAAATGGTAATTCTATAAATC
1 GAGGGTAAAATGGTAATTCTATAAATC
* *
59288746 GAGGGTAAGACGGTAATTCTATAAATC
1 GAGGGTAAAATGGTAATTCTATAAATC
* *
59288773 GAGGGTAAAACGGTAATTCTGTAAATC
1 GAGGGTAAAATGGTAATTCTATAAATC
*
59288800 GAGGGTAAAATAGTAATTCTATAAATC
1 GAGGGTAAAATGGTAATTCTATAAATC
* * *
59288827 GAGGGTAAAACGATAATTCTGTAAATC
1 GAGGGTAAAATGGTAATTCTATAAATC
*
59288854 GAGGGTAAAATGGTAATTCTGTAAATC
1 GAGGGTAAAATGGTAATTCTATAAATC
*
59288881 GAGGGTAAAAATAGTAATTCTATAAATC
1 GAGGGT-AAAATGGTAATTCTATAAATC
* * *
59288909 GAGGGTAAAACGATAATTCTGTAAATC
1 GAGGGTAAAATGGTAATTCTATAAATC
59288936 GAGGGTAAAATGGTAATTCTAT
1 GAGGGTAAAATGGTAATTCTAT
59288958 CTTACAGGAG
Statistics
Matches: 189, Mismatches: 22, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
27 164 0.87
28 25 0.13
ACGTcount: A:0.40, C:0.09, G:0.23, T:0.28
Consensus pattern (27 bp):
GAGGGTAAAATGGTAATTCTATAAATC
Found at i:59288828 original size:81 final size:81
Alignment explanation
Indices: 59288719--59288955 Score: 420
Period size: 81 Copynumber: 2.9 Consensus size: 81
59288709 TTTTTACATT
* * * * *
59288719 GAGGGTAAAATGGTAATTCTATAAATCGAGGGTAAGACGGTAATTCTATAAATCGAGGGTAAAAC
1 GAGGGTAAAATAGTAATTCTATAAATCGAGGGTAAAACGATAATTCTGTAAATCGAGGGTAAAAT
59288784 GGTAATTCTGTAAATC
66 GGTAATTCTGTAAATC
59288800 GAGGGTAAAATAGTAATTCTATAAATCGAGGGTAAAACGATAATTCTGTAAATCGAGGGTAAAAT
1 GAGGGTAAAATAGTAATTCTATAAATCGAGGGTAAAACGATAATTCTGTAAATCGAGGGTAAAAT
59288865 GGTAATTCTGTAAATC
66 GGTAATTCTGTAAATC
59288881 GAGGGTAAAAATAGTAATTCTATAAATCGAGGGTAAAACGATAATTCTGTAAATCGAGGGTAAAA
1 GAGGGT-AAAATAGTAATTCTATAAATCGAGGGTAAAACGATAATTCTGTAAATCGAGGGTAAAA
59288946 TGGTAATTCT
65 TGGTAATTCT
59288956 ATCTTACAGG
Statistics
Matches: 150, Mismatches: 5, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
81 82 0.55
82 68 0.45
ACGTcount: A:0.40, C:0.09, G:0.23, T:0.28
Consensus pattern (81 bp):
GAGGGTAAAATAGTAATTCTATAAATCGAGGGTAAAACGATAATTCTGTAAATCGAGGGTAAAAT
GGTAATTCTGTAAATC
Found at i:59288997 original size:27 final size:27
Alignment explanation
Indices: 59288967--59289116 Score: 160
Period size: 27 Copynumber: 5.6 Consensus size: 27
59288957 TCTTACAGGA
59288967 GTATTTCAGTAATTTTACAAATCGAGG
1 GTATTTCAGTAATTTTACAAATCGAGG
*
59288994 GTATTTCAGTAATTTTGCAAA-CTGAGG
1 GTATTTCAGTAATTTTACAAATC-GAGG
**
59289021 GTATTTTTGTAATTTTACAAATCGAGG
1 GTATTTCAGTAATTTTACAAATCGAGG
* ** * *
59289048 ATATTTGGGTAATTTTATAAATCGGGG
1 GTATTTCAGTAATTTTACAAATCGAGG
* * * *
59289075 GTACTTT-GGTAGTTTTACAAGTTGAGG
1 GTA-TTTCAGTAATTTTACAAATCGAGG
59289102 GTATTTCAGTAATTT
1 GTATTTCAGTAATTT
59289117 GGTAAACTAA
Statistics
Matches: 102, Mismatches: 17, Indels: 8
0.80 0.13 0.06
Matches are distributed among these distances:
26 4 0.04
27 94 0.92
28 4 0.04
ACGTcount: A:0.29, C:0.08, G:0.22, T:0.41
Consensus pattern (27 bp):
GTATTTCAGTAATTTTACAAATCGAGG
Found at i:59291625 original size:43 final size:42
Alignment explanation
Indices: 59291534--59291657 Score: 142
Period size: 42 Copynumber: 2.9 Consensus size: 42
59291524 AATACCGTAC
* * *
59291534 CAATGCCATATCCTAGATATGGTCTTACATGTAATCTCGTAT
1 CAATGCCATATCCCAGATATGGTCTTACACGTAATCTCATAT
* * * *
59291576 CGATGCCAATAGCCCAGCTATGGTGTTACACG-AAGTCTCATAT
1 CAATGCC-ATATCCCAGATATGGTCTTACACGTAA-TCTCATAT
* *
59291619 CAATGCCATATCCCATATATGGTCTTACACGTTATCTCA
1 CAATGCCATATCCCAGATATGGTCTTACACGTAATCTCA
59291658 ATAACCCTAA
Statistics
Matches: 66, Mismatches: 13, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
42 33 0.50
43 33 0.50
ACGTcount: A:0.28, C:0.25, G:0.15, T:0.31
Consensus pattern (42 bp):
CAATGCCATATCCCAGATATGGTCTTACACGTAATCTCATAT
Found at i:59305333 original size:19 final size:19
Alignment explanation
Indices: 59305309--59305345 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
59305299 TCCTCAAGTA
59305309 AAATCCTCAACTCACAATT
1 AAATCCTCAACTCACAATT
59305328 AAATCCTCAACTCACAAT
1 AAATCCTCAACTCACAAT
59305346 AAAAACAAAT
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:0.43, C:0.32, G:0.00, T:0.24
Consensus pattern (19 bp):
AAATCCTCAACTCACAATT
Found at i:59307173 original size:17 final size:17
Alignment explanation
Indices: 59307153--59307195 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
59307143 AAGAAATGCT
*
59307153 AAAATAAAAATAAAATG
1 AAAATAAAAACAAAATG
* *
59307170 AAAAGAAAAACAAATTG
1 AAAATAAAAACAAAATG
59307187 AAAACTAAA
1 AAAA-TAAA
59307196 TGGACTCGAA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 18 0.86
18 3 0.14
ACGTcount: A:0.74, C:0.05, G:0.07, T:0.14
Consensus pattern (17 bp):
AAAATAAAAACAAAATG
Found at i:59308878 original size:10 final size:10
Alignment explanation
Indices: 59308865--59308893 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
59308855 GAAAAAGAGA
59308865 AAAAGTGAAG
1 AAAAGTGAAG
59308875 AAAAGTGAAG
1 AAAAGTGAAG
59308885 AAAAG-GAAG
1 AAAAGTGAAG
59308894 GAGAAAGAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 4 0.21
10 15 0.79
ACGTcount: A:0.62, C:0.00, G:0.31, T:0.07
Consensus pattern (10 bp):
AAAAGTGAAG
Found at i:59312182 original size:14 final size:15
Alignment explanation
Indices: 59312163--59312192 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
59312153 ATATTTAACT
59312163 TGTTCTTAATT-ATG
1 TGTTCTTAATTCATG
59312177 TGTTCTTAATTCATG
1 TGTTCTTAATTCATG
59312192 T
1 T
59312193 TTTAATATTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.20, C:0.10, G:0.13, T:0.57
Consensus pattern (15 bp):
TGTTCTTAATTCATG
Found at i:59326453 original size:30 final size:30
Alignment explanation
Indices: 59326413--59326470 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
59326403 CACGGCCATG
*
59326413 ACACATGGGCATATGGTAT-ACCCGTGTGTC
1 ACACACGGGCATATGG-ATCACCCGTGTGTC
*
59326443 ACACACGGGCATGTGGATCACCCGTGTG
1 ACACACGGGCATATGGATCACCCGTGTG
59326471 GAAGTGCCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 2 0.08
30 23 0.92
ACGTcount: A:0.22, C:0.26, G:0.29, T:0.22
Consensus pattern (30 bp):
ACACACGGGCATATGGATCACCCGTGTGTC
Found at i:59330667 original size:46 final size:46
Alignment explanation
Indices: 59330617--59330789 Score: 192
Period size: 46 Copynumber: 3.7 Consensus size: 46
59330607 TGGTTGAGCA
*
59330617 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * * * *
59330663 TCCGAGCTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A--CG
* *
59330710 TCCGAACTTGTTGAGTTGAGTCCGAGTTCATTTATGGATGCAAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
*
59330756 -CCTGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCC-GAACTCGTTGAGTTGAGTCCGAGTTCACTTA
59330790 GGGGCGGGTT
Statistics
Matches: 104, Mismatches: 15, Indels: 16
0.77 0.11 0.12
Matches are distributed among these distances:
43 6 0.06
45 5 0.05
46 57 0.55
47 27 0.26
48 3 0.03
50 6 0.06
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.31
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:59330773 original size:93 final size:93
Alignment explanation
Indices: 59330614--59330784 Score: 299
Period size: 93 Copynumber: 1.8 Consensus size: 93
59330604 GGATGGTTGA
*
59330614 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGTCCGAGCTCGTTGAGT
59330679 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* *
59330707 GCATCCGAACTTGTTGAGTTGAGTCCGAGTTCATTTATGGATGCAAACG-CCTGAGCTCGTTGAG
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGTCC-GAGCTCGTTGAG
59330771 TTGAGTCCGAGTTC
65 TTGAGTCCGAGTTC
59330785 ACTTAGGGGC
Statistics
Matches: 74, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
92 2 0.03
93 72 0.97
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.30
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGTCCGAGCTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:59347343 original size:15 final size:15
Alignment explanation
Indices: 59347325--59347355 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
59347315 CTCAGTCTAA
59347325 GAAATCTAAAGAGAT
1 GAAATCTAAAGAGAT
*
59347340 GAAATCTAATGAGAT
1 GAAATCTAAAGAGAT
59347355 G
1 G
59347356 GATTCTCGTT
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:0.48, C:0.06, G:0.23, T:0.23
Consensus pattern (15 bp):
GAAATCTAAAGAGAT
Found at i:59355279 original size:48 final size:48
Alignment explanation
Indices: 59355207--59355472 Score: 227
Period size: 48 Copynumber: 5.5 Consensus size: 48
59355197 CATTTGGGTG
* * * *
59355207 ATATGTGCGCTAGTGTAAGACCATGTCTAGGACATGGCAT-TGACCACA
1 ATATGTGAGCTAGTGTAAGACCATGTCTGGGACATGGCGTCAG-CCACA
* * * *
59355255 TTATGTGTGCCAGTGTAAGGCCATGTCTGGGACATGGCGTCAGCCACA
1 ATATGTGAGCTAGTGTAAGACCATGTCTGGGACATGGCGTCAGCCACA
* *** *
59355303 ATATGAGAGCTAGTGTAAGACCATGTCTGGGACATGAAATCAG-CATTA
1 ATATGTGAGCTAGTGTAAGACCATGTCTGGGACATGGCGTCAGCCA-CA
* * * **
59355351 ATATGTGCA-TTAGTGTAAGACCATGTCTGGGACATGGCATC-GGCATTG
1 ATATGTG-AGCTAGTGTAAGACCATGTCTGGGACATGGCGTCAGCCA-CA
* * * * *
59355399 AGATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATC-GACCTCG
1 ATATGTGAGCTAGTGTAAGACCATGTCTGGGACATGGCGTCAG-CCACA
* *
59355447 ACATGTGAGCCAGTGTAAGACCATGT
1 ATATGTGAGCTAGTGTAAGACCATGT
59355473 TTGGAAGAAG
Statistics
Matches: 182, Mismatches: 30, Indels: 12
0.81 0.13 0.05
Matches are distributed among these distances:
47 4 0.02
48 175 0.96
49 3 0.02
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.25
Consensus pattern (48 bp):
ATATGTGAGCTAGTGTAAGACCATGTCTGGGACATGGCGTCAGCCACA
Found at i:59355488 original size:96 final size:94
Alignment explanation
Indices: 59355215--59355472 Score: 286
Period size: 96 Copynumber: 2.7 Consensus size: 94
59355205 TGATATGTGC
* * * * *
59355215 GCTAGTGTAAGACCATGTCTAGGACATGGCATTGACCACATTATGTGTGCCAGTGTAAGGCCATG
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGACCTCA-TATGTGAGCCAGTGTAAGACCATG
* *
59355280 TCTGGGACATGGCGTCAGCCACAATATGAGA
65 TCTGGGACATGGCATC-GCCACAAGATGAGA
** * * **
59355311 GCTAGTGTAAGACCATGTCTGGGACATGAAATC-AGCATTAATATGTGCA-TTAGTGTAAGACCA
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGA-C-CTCATATGTG-AGCCAGTGTAAGACCA
* **
59355374 TGTCTGGGACATGGCATCGGCATTGAGATGAGA
63 TGTCTGGGACATGGCATCGCCA-CAAGATGAGA
*
59355407 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGACCTCGACATGTGAGCCAGTGTAAGACCATG
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGACCTC-ATATGTGAGCCAGTGTAAGACCATG
59355472 T
65 T
59355473 TTGGAAGAAG
Statistics
Matches: 132, Mismatches: 23, Indels: 14
0.78 0.14 0.08
Matches are distributed among these distances:
95 6 0.05
96 124 0.94
97 2 0.02
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.24
Consensus pattern (94 bp):
GCTAGTGTAAGACCATGTCTGGGACATGGCATCGACCTCATATGTGAGCCAGTGTAAGACCATGT
CTGGGACATGGCATCGCCACAAGATGAGA
Found at i:59363776 original size:29 final size:29
Alignment explanation
Indices: 59363715--59363804 Score: 128
Period size: 29 Copynumber: 3.1 Consensus size: 29
59363705 CACATACCTG
*
59363715 TATATGGCCCACTAGGCCC-AATCACATT
1 TATATGGCCCATTAGGCCCAAATCACATT
*
59363743 TATATCGCCCATTAGGCCCAAATCACATT
1 TATATGGCCCATTAGGCCCAAATCACATT
* * *
59363772 TATATGGCCCATCAGGCCCAATTTACATT
1 TATATGGCCCATTAGGCCCAAATCACATT
59363801 TATA
1 TATA
59363805 GTCATGCTCA
Statistics
Matches: 55, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
28 17 0.31
29 38 0.69
ACGTcount: A:0.30, C:0.29, G:0.12, T:0.29
Consensus pattern (29 bp):
TATATGGCCCATTAGGCCCAAATCACATT
Found at i:59365025 original size:29 final size:29
Alignment explanation
Indices: 59364944--59365058 Score: 119
Period size: 29 Copynumber: 4.0 Consensus size: 29
59364934 TACAAACATG
*
59364944 CATATGGCCCACTAGGCCCAA-TCTTATT
1 CATATGGCCCACTAGGCCCAATTCATATT
* *
59364972 CAAATGGCCCATCT-GGCCCAGTTCATATT
1 CATATGGCCCA-CTAGGCCCAATTCATATT
* **
59365001 -ATTATGGCCCACTAGGTCCAATTCACCTT
1 CA-TATGGCCCACTAGGCCCAATTCATATT
* *
59365030 CATATGGCCCATTAGGCCCAAATCATATT
1 CATATGGCCCACTAGGCCCAATTCATATT
59365059 ATACTCATGC
Statistics
Matches: 69, Mismatches: 13, Indels: 9
0.76 0.14 0.10
Matches are distributed among these distances:
28 19 0.28
29 49 0.71
30 1 0.01
ACGTcount: A:0.26, C:0.30, G:0.15, T:0.29
Consensus pattern (29 bp):
CATATGGCCCACTAGGCCCAATTCATATT
Found at i:59365056 original size:58 final size:57
Alignment explanation
Indices: 59364946--59365060 Score: 144
Period size: 58 Copynumber: 2.0 Consensus size: 57
59364936 CAAACATGCA
* **
59364946 TATGGCCCACTAGGCCCAATCTTATTCAAATGGCCCATCTGGCCCAGTTCATATTAT
1 TATGGCCCACTAGGCCCAATCTCATTCAAATGGCCCATCTGGCCCAAATCATATTAT
* *
59365003 TATGGCCCACTAGGTCCAAT-TCACCTTCATATGGCCCAT-TAGGCCCAAATCATATTAT
1 TATGGCCCACTAGGCCCAATCTCA--TTCAAATGGCCCATCT-GGCCCAAATCATATTAT
59365061 ACTCATGCTC
Statistics
Matches: 50, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
56 2 0.04
57 20 0.40
58 28 0.56
ACGTcount: A:0.26, C:0.30, G:0.15, T:0.30
Consensus pattern (57 bp):
TATGGCCCACTAGGCCCAATCTCATTCAAATGGCCCATCTGGCCCAAATCATATTAT
Found at i:59365306 original size:24 final size:23
Alignment explanation
Indices: 59365273--59365323 Score: 75
Period size: 24 Copynumber: 2.2 Consensus size: 23
59365263 CGTAGCCCAA
*
59365273 CTTTCGACTTTTTAGCATTTTGG
1 CTTTCGACTTTTTAGCATTTCGG
*
59365296 CTTTCTGACTTTTTGGCATTTCGG
1 CTTTC-GACTTTTTAGCATTTCGG
59365320 CTTT
1 CTTT
59365324 TGCTGATTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 5 0.20
24 20 0.80
ACGTcount: A:0.10, C:0.20, G:0.18, T:0.53
Consensus pattern (23 bp):
CTTTCGACTTTTTAGCATTTCGG
Found at i:59372618 original size:29 final size:30
Alignment explanation
Indices: 59372555--59372658 Score: 101
Period size: 29 Copynumber: 3.6 Consensus size: 30
59372545 TATATACATG
* **
59372555 CATATGGCCCA-CTAGGCCCAA-TCTTATT
1 CATATGGCTCATCTAGGCCCAATTCAAATT
*
59372583 CAAATGGCTCATCT-GGCCCAATTCAAATT
1 CATATGGCTCATCTAGGCCCAATTCAAATT
* * **
59372612 CTTATGGCCCA-CTAGGCCCAATTCACCTT
1 CATATGGCTCATCTAGGCCCAATTCAAATT
59372641 CATATGGCTCAT-TAGGCC
1 CATATGGCTCATCTAGGCC
59372659 AAAATCATAT
Statistics
Matches: 61, Mismatches: 11, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
28 18 0.30
29 43 0.70
ACGTcount: A:0.25, C:0.32, G:0.15, T:0.28
Consensus pattern (30 bp):
CATATGGCTCATCTAGGCCCAATTCAAATT
Found at i:59372756 original size:17 final size:17
Alignment explanation
Indices: 59372734--59372790 Score: 96
Period size: 17 Copynumber: 3.4 Consensus size: 17
59372724 GTCTATTATT
*
59372734 GGCCCAACAGCCCATCA
1 GGCCCAACAACCCATCA
*
59372751 GGCCCAATAACCCATCA
1 GGCCCAACAACCCATCA
59372768 GGCCCAACAACCCATCA
1 GGCCCAACAACCCATCA
59372785 GGCCCA
1 GGCCCA
59372791 TTTAGCCCAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
17 37 1.00
ACGTcount: A:0.32, C:0.46, G:0.16, T:0.07
Consensus pattern (17 bp):
GGCCCAACAACCCATCA
Found at i:59380947 original size:46 final size:46
Alignment explanation
Indices: 59380897--59381069 Score: 190
Period size: 46 Copynumber: 3.7 Consensus size: 46
59380887 TGGTTGAGCA
59380897 TCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
* * * * * *
59380943 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--AATGTAACTAGG
1 TCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--ATG
** *
59380988 CATCCGAACTTGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 --TCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
* *
59381036 ACCGATCTCATTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCATTGAGTTGAGTCCGAGTTCACTTA
59381070 GGGGCGGGTT
Statistics
Matches: 103, Mismatches: 17, Indels: 14
0.77 0.13 0.10
Matches are distributed among these distances:
43 5 0.05
45 4 0.04
46 58 0.56
47 28 0.27
48 4 0.04
50 4 0.04
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.31
Consensus pattern (46 bp):
TCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
Found at i:59381053 original size:93 final size:93
Alignment explanation
Indices: 59380894--59381064 Score: 288
Period size: 93 Copynumber: 1.8 Consensus size: 93
59380884 GGATGGTTGA
* *
59380894 GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGACCGAACTCATTGAGT
59380959 TGAGTCCGAGTTCGTGAAATGTAACTAG
66 TGAGTCCGAGTTCGTGAAATGTAACTAG
** * *
59380987 GCATCCGAACTTGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGACCGATCTCATTGAGT
1 GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGACCGAACTCATTGAGT
59381052 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
59381065 ACTTAGGGGC
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.30
Consensus pattern (93 bp):
GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGACCGAACTCATTGAGT
TGAGTCCGAGTTCGTGAAATGTAACTAG
Found at i:59383499 original size:29 final size:29
Alignment explanation
Indices: 59383438--59383527 Score: 137
Period size: 29 Copynumber: 3.1 Consensus size: 29
59383428 CACGTACTTG
*
59383438 TATATGGCCCACTAGGCCC-AATCACATT
1 TATATGGCCCATTAGGCCCAAATCACATT
*
59383466 TATATGGCCTATTAGGCCCAAATCACATT
1 TATATGGCCCATTAGGCCCAAATCACATT
* *
59383495 TATATGGCCCATCAGGCCCAATTCACATT
1 TATATGGCCCATTAGGCCCAAATCACATT
59383524 TATA
1 TATA
59383528 GTCATGCTTA
Statistics
Matches: 56, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
28 17 0.30
29 39 0.70
ACGTcount: A:0.30, C:0.28, G:0.13, T:0.29
Consensus pattern (29 bp):
TATATGGCCCATTAGGCCCAAATCACATT
Found at i:59383766 original size:16 final size:16
Alignment explanation
Indices: 59383745--59383783 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
59383735 TCAAACTTTT
* *
59383745 GGCTTTTCGGTATTTC
1 GGCTTTTCAGCATTTC
59383761 GGCTTTTCAGCATTTC
1 GGCTTTTCAGCATTTC
*
59383777 AGCTTTT
1 GGCTTTT
59383784 GCCGATCTAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.10, C:0.21, G:0.21, T:0.49
Consensus pattern (16 bp):
GGCTTTTCAGCATTTC
Found at i:59385007 original size:257 final size:257
Alignment explanation
Indices: 59384551--59385044 Score: 819
Period size: 257 Copynumber: 1.9 Consensus size: 257
59384541 AAATATATAT
*
59384551 ATAAATAAATAAAAATACACCTGCACTCCTCAATCAGCTTAAACTCAACAAGATAATTTCCCTTC
1 ATAAATAAATAAAAATACACCTACACTCCTCAATCAGCTTAAACTCAACAAGATAATTTCCCTTC
* * *
59384616 AAATTCTCCAATTTTATCACCATCATATTTACCCTTAACCCTCATCCTAATCCCCTTGATTTTAG
66 AAATTCTACAATTTTATCACCATCATATTTACACTTAACCCTCATCCTAATCCCATTGATTTTAG
* * * * *
59384681 CCAAAAATTCCAATTTGAATTGCATTCAAATTGCTTCCACCGTATAGCACTTGAGTAGCACAATT
131 CCAAAAATTCAAATTTGAATTGCATTCAAATTGCTTCCACCGTACAGCACTTGAATAGAAAAATT
* * *
59384746 AAATTCTCCCTTTTCGCGCGCCTCCACTCGAACTCCAAACCTAGAAATATATATATAAATAA
196 AAATTCTCCCTCTGCGCGCGCCTCCACTCAAACTCCAAACCTAGAAATATATATATAAATAA
**
59384808 ATAAATAAATAAAAATACACCTACACTCCTCAATC-GACTTAAACTCGTCAAGATAATTTCCCTT
1 ATAAATAAATAAAAATACACCTACACTCCTCAATCAG-CTTAAACTCAACAAGATAATTTCCCTT
*
59384872 CAAATTCTACAATTTTATCACCATCATATTTACACTTAATCCTCATCCTAATCCCATTGATTTTA
65 CAAATTCTACAATTTTATCACCATCATATTTACACTTAACCCTCATCCTAATCCCATTGATTTTA
*
59384937 GCCAAAAATTCAAATTTGAATTGCATTCAAATTGCTTCCACTGTACAGCACTTGAATAGAAAAAT
130 GCCAAAAATTCAAATTTGAATTGCATTCAAATTGCTTCCACCGTACAGCACTTGAATAGAAAAAT
*
59385002 TAAATTCTCCCTCTGCGCGCGCCTCCACTTAAACTCCAAACCT
195 TAAATTCTCCCTCTGCGCGCGCCTCCACTCAAACTCCAAACCT
59385045 CAAGGTTACT
Statistics
Matches: 219, Mismatches: 17, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
256 1 0.00
257 218 1.00
ACGTcount: A:0.35, C:0.27, G:0.07, T:0.31
Consensus pattern (257 bp):
ATAAATAAATAAAAATACACCTACACTCCTCAATCAGCTTAAACTCAACAAGATAATTTCCCTTC
AAATTCTACAATTTTATCACCATCATATTTACACTTAACCCTCATCCTAATCCCATTGATTTTAG
CCAAAAATTCAAATTTGAATTGCATTCAAATTGCTTCCACCGTACAGCACTTGAATAGAAAAATT
AAATTCTCCCTCTGCGCGCGCCTCCACTCAAACTCCAAACCTAGAAATATATATATAAATAA
Found at i:59387012 original size:15 final size:15
Alignment explanation
Indices: 59386989--59387018 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
59386979 TCAAAACTTC
59386989 TAATACAAAACATAT
1 TAATACAAAACATAT
*
59387004 TAATCCAAAACATAT
1 TAATACAAAACATAT
59387019 CTTTCATAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.17, G:0.00, T:0.27
Consensus pattern (15 bp):
TAATACAAAACATAT
Found at i:59402847 original size:39 final size:39
Alignment explanation
Indices: 59402795--59402875 Score: 128
Period size: 39 Copynumber: 2.1 Consensus size: 39
59402785 AGATACACAA
*
59402795 AGAACGAGTAAGAAGACGATACTCAACCCCCAA-CAAAAG
1 AGAACGAGCAAGAAGACGATACTCAACCCCCAATC-AAAG
*
59402834 AGAACGAGCAAGAATACGATACTCAACCCCCAATCAAAG
1 AGAACGAGCAAGAAGACGATACTCAACCCCCAATCAAAG
59402873 AGA
1 AGA
59402876 TGGCTGAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
39 38 0.97
40 1 0.03
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (39 bp):
AGAACGAGCAAGAAGACGATACTCAACCCCCAATCAAAG
Found at i:59403175 original size:20 final size:20
Alignment explanation
Indices: 59403150--59403201 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
59403140 TCAATGGCAT
59403150 TTCTGATGATTCCATTCATC
1 TTCTGATGATTCCATTCATC
* *
59403170 TTCTGATGATGCCATTCGTC
1 TTCTGATGATTCCATTCATC
*
59403190 TTC-GATTATTCC
1 TTCTGATGATTCC
59403202 CTTTTTCATT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 7 0.25
20 21 0.75
ACGTcount: A:0.17, C:0.25, G:0.13, T:0.44
Consensus pattern (20 bp):
TTCTGATGATTCCATTCATC
Found at i:59406583 original size:27 final size:27
Alignment explanation
Indices: 59406553--59406696 Score: 164
Period size: 27 Copynumber: 5.3 Consensus size: 27
59406543 TACTGAAATG
** *
59406553 CCCTCGATTTGTAGAATTACCATTTTA
1 CCCTCGATTTACAAAATTACCATTTTA
* * * *
59406580 CCCTCGATTTATAGAATTACCGTTTCA
1 CCCTCGATTTACAAAATTACCATTTTA
* * *
59406607 CCCTTGATTTACAAAATTACCGTTTCA
1 CCCTCGATTTACAAAATTACCATTTTA
*
59406634 CCCTCAATTTACAAAATTACCATTTTA
1 CCCTCGATTTACAAAATTACCATTTTA
*
59406661 CCCTC-AGTCTACAAAATTACCATTTTA
1 CCCTCGA-TTTACAAAATTACCATTTTA
59406688 CCCTCGATT
1 CCCTCGATT
59406697 GTGAAATTAC
Statistics
Matches: 103, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
26 1 0.01
27 101 0.98
28 1 0.01
ACGTcount: A:0.29, C:0.27, G:0.07, T:0.37
Consensus pattern (27 bp):
CCCTCGATTTACAAAATTACCATTTTA
Found at i:59406762 original size:27 final size:27
Alignment explanation
Indices: 59406728--59406876 Score: 191
Period size: 27 Copynumber: 5.6 Consensus size: 27
59406718 TGTAGGATAG
59406728 AATTACCAAAATACCCCTAGTTTGTAA
1 AATTACCAAAATACCCCTAGTTTGTAA
*
59406755 AATAACCAAAATACCCCTAGTTTGTAA
1 AATTACCAAAATACCCCTAGTTTGTAA
59406782 AATTACC--AATACCCCTAGTTTGTAA
1 AATTACCAAAATACCCCTAGTTTGTAA
* *
59406807 AATTACTAAAATA-CCCTCAATTTGTAA
1 AATTACCAAAATACCCCT-AGTTTGTAA
**
59406834 AATTACCAAAATACCCCT-GATTTACAA
1 AATTACCAAAATACCCCTAG-TTTGTAA
59406861 AATTA-CAGAAATACCC
1 AATTACCA-AAATACCC
59406877 TTGACTTTTT
Statistics
Matches: 108, Mismatches: 8, Indels: 12
0.84 0.06 0.09
Matches are distributed among these distances:
25 24 0.22
26 6 0.06
27 74 0.69
28 4 0.04
ACGTcount: A:0.43, C:0.23, G:0.06, T:0.28
Consensus pattern (27 bp):
AATTACCAAAATACCCCTAGTTTGTAA
Found at i:59406807 original size:52 final size:53
Alignment explanation
Indices: 59406728--59406851 Score: 180
Period size: 52 Copynumber: 2.3 Consensus size: 53
59406718 TGTAGGATAG
*
59406728 AATTACCAAAATACCCCTAGTTTGTAAAATAACCAAAATACCC-CTAGTTTGTAA
1 AATTACC-AAATACCCCTAGTTTGTAAAATAACCAAAATACCCTC-AATTTGTAA
* *
59406782 AATTACC-AATACCCCTAGTTTGTAAAATTACTAAAATACCCTCAATTTGTAA
1 AATTACCAAATACCCCTAGTTTGTAAAATAACCAAAATACCCTCAATTTGTAA
59406834 AATTACCAAAATACCCCT
1 AATTACC-AAATACCCCT
59406852 GATTTACAAA
Statistics
Matches: 64, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
52 47 0.73
53 1 0.02
54 16 0.25
ACGTcount: A:0.42, C:0.23, G:0.06, T:0.29
Consensus pattern (53 bp):
AATTACCAAATACCCCTAGTTTGTAAAATAACCAAAATACCCTCAATTTGTAA
Found at i:59406939 original size:27 final size:27
Alignment explanation
Indices: 59406695--59406942 Score: 177
Period size: 27 Copynumber: 9.2 Consensus size: 27
59406685 TTACCCTCGA
* *
59406695 TTGTGAAATTACTGAAATACCCCT-GT
1 TTGTAAAATTACTAAAATACCCCTAGT
** * *
59406721 AGGATAGAATTACCAAAATACCCCTAGT
1 TTG-TAAAATTACTAAAATACCCCTAGT
* *
59406749 TTGTAAAATAACCAAAATACCCCTAGT
1 TTGTAAAATTACTAAAATACCCCTAGT
*
59406776 TTGTAAAATTAC--CAATACCCCTAGT
1 TTGTAAAATTACTAAAATACCCCTAGT
*
59406801 TTGTAAAATTACTAAAATA-CCCTCAAT
1 TTGTAAAATTACTAAAATACCCCT-AGT
*
59406828 TTGTAAAATTACCAAAATACCCCT-GAT
1 TTGTAAAATTACTAAAATACCCCTAG-T
** * *
59406855 TTACAAAATTAC-AGAAATACCCTTGACT
1 TTGTAAAATTACTA-AAATACCCCT-AGT
* ** *
59406883 TTTTAGAAATTA-TAGAAATACCATTGGT
1 TTGTA-AAATTACTA-AAATACCCCTAGT
** * *
59406911 TTACAAAATTACTGAAATACCCTTAGT
1 TTGTAAAATTACTAAAATACCCCTAGT
59406938 TTGTA
1 TTGTA
59406943 GATTTACCAA
Statistics
Matches: 177, Mismatches: 32, Indels: 25
0.76 0.14 0.11
Matches are distributed among these distances:
25 24 0.14
26 6 0.03
27 114 0.64
28 16 0.09
29 17 0.10
ACGTcount: A:0.40, C:0.19, G:0.10, T:0.31
Consensus pattern (27 bp):
TTGTAAAATTACTAAAATACCCCTAGT
Found at i:59407035 original size:27 final size:27
Alignment explanation
Indices: 59406993--59407057 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 27
59406983 ACCCCCAATA
* * *
59406993 GGTAAAAAGACTGTAA-AGCCTCTGTAG
1 GGTAAAATGACCGTAATACCCT-TGTAG
* *
59407020 GGTAAAGTGACCGTAATACCCTTGTAT
1 GGTAAAATGACCGTAATACCCTTGTAG
59407047 GGTAAAATGAC
1 GGTAAAATGAC
59407058 GAATATGCCC
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
27 27 0.87
28 4 0.13
ACGTcount: A:0.35, C:0.15, G:0.25, T:0.25
Consensus pattern (27 bp):
GGTAAAATGACCGTAATACCCTTGTAG
Found at i:59407949 original size:24 final size:24
Alignment explanation
Indices: 59407867--59407949 Score: 78
Period size: 25 Copynumber: 3.4 Consensus size: 24
59407857 AGGAAGTGTT
* * * *
59407867 AAAAGGGCTCTGCCCTAATTTACC
1 AAAAGGGCTTTGCCCCAGTTTATC
*
59407891 GAAAAGGGCTTTGCCCCGGTTTATC
1 -AAAAGGGCTTTGCCCCAGTTTATC
*
59407916 AGAAAGGGCTTTGCCCCAG-TTATT
1 A-AAAGGGCTTTGCCCCAGTTTATC
59407940 AAAAGAGGCT
1 AAAAG-GGCT
59407950 AGGCCTCCAG
Statistics
Matches: 49, Mismatches: 7, Indels: 5
0.80 0.11 0.08
Matches are distributed among these distances:
23 4 0.08
24 10 0.20
25 35 0.71
ACGTcount: A:0.28, C:0.23, G:0.24, T:0.25
Consensus pattern (24 bp):
AAAAGGGCTTTGCCCCAGTTTATC
Found at i:59408143 original size:42 final size:42
Alignment explanation
Indices: 59408084--59408175 Score: 148
Period size: 42 Copynumber: 2.2 Consensus size: 42
59408074 TAGTCTCCCC
* * *
59408084 AAATGGGCTTGCATACATTCATTGACATTACATGTGATATTT
1 AAATGGGCTTGCATACATCCATTGACATTACATGTGACATTG
*
59408126 AAATGGTCTTGCATACATCCATTGACATTACATGTGACATTG
1 AAATGGGCTTGCATACATCCATTGACATTACATGTGACATTG
59408168 AAATGGGC
1 AAATGGGC
59408176 CTAAGGGCCA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (42 bp):
AAATGGGCTTGCATACATCCATTGACATTACATGTGACATTG
Found at i:59408234 original size:31 final size:31
Alignment explanation
Indices: 59408199--59408345 Score: 233
Period size: 31 Copynumber: 4.8 Consensus size: 31
59408189 CGTTTACATT
*
59408199 AAAAGGCTTAGGCCCAGTGATATGATTTATG
1 AAAAGGCTTCGGCCCAGTGATATGATTTATG
* *
59408230 AAAAGGCTCCGGCCCAATGATATGATTTATG
1 AAAAGGCTTCGGCCCAGTGATATGATTTATG
*
59408261 AAAAGGCTTCAGCCCAGTGATATGATTTATG
1 AAAAGGCTTCGGCCCAGTGATATGATTTATG
59408292 AAAAGGCTTCGGCCCAGTGATATGATTTATG
1 AAAAGGCTTCGGCCCAGTGATATGATTTATG
* *
59408323 GAAAGGCTTCGGTCCAGT-ATATG
1 AAAAGGCTTCGGCCCAGTGATATG
59408346 TCAAGACTAC
Statistics
Matches: 107, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
30 5 0.05
31 102 0.95
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.28
Consensus pattern (31 bp):
AAAAGGCTTCGGCCCAGTGATATGATTTATG
Found at i:59409281 original size:13 final size:13
Alignment explanation
Indices: 59409263--59409289 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
59409253 TTGAAACTGA
59409263 GAAACTAGCACGG
1 GAAACTAGCACGG
59409276 GAAACTAGCACGG
1 GAAACTAGCACGG
59409289 G
1 G
59409290 CGTGCGACAT
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:0.37, C:0.22, G:0.33, T:0.07
Consensus pattern (13 bp):
GAAACTAGCACGG
Found at i:59410464 original size:8 final size:8
Alignment explanation
Indices: 59410451--59410484 Score: 59
Period size: 8 Copynumber: 4.1 Consensus size: 8
59410441 TTGTTTTTTT
59410451 AAAAAAAC
1 AAAAAAAC
59410459 AAAAAAAC
1 AAAAAAAC
59410467 AAAAAAAAC
1 -AAAAAAAC
59410476 AAAAAAAC
1 AAAAAAAC
59410484 A
1 A
59410485 CTATGTATAC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
8 17 0.68
9 8 0.32
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (8 bp):
AAAAAAAC
Found at i:59410465 original size:9 final size:9
Alignment explanation
Indices: 59410451--59410482 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
59410441 TTGTTTTTTT
59410451 AAAAAAAC-
1 AAAAAAACA
59410459 AAAAAAACA
1 AAAAAAACA
59410468 AAAAAAACA
1 AAAAAAACA
59410477 AAAAAA
1 AAAAAA
59410483 CACTATGTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 8 0.35
9 15 0.65
ACGTcount: A:0.91, C:0.09, G:0.00, T:0.00
Consensus pattern (9 bp):
AAAAAAACA
Found at i:59410473 original size:17 final size:17
Alignment explanation
Indices: 59410451--59410484 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
59410441 TTGTTTTTTT
59410451 AAAAAAACAAAAAAACA
1 AAAAAAACAAAAAAACA
59410468 AAAAAAACAAAAAAACA
1 AAAAAAACAAAAAAACA
59410485 CTATGTATAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (17 bp):
AAAAAAACAAAAAAACA
Found at i:59411743 original size:13 final size:13
Alignment explanation
Indices: 59411710--59411743 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
59411700 AATATTTAAC
*
59411710 TTGTTCTTAATTA
1 TTGTTTTTAATTA
59411723 TGTGTTTTTAATTA
1 T-TGTTTTTAATTA
59411737 TTGTTTT
1 TTGTTTT
59411744 AATATCCCAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.18, C:0.03, G:0.12, T:0.68
Consensus pattern (13 bp):
TTGTTTTTAATTA
Found at i:59422554 original size:40 final size:40
Alignment explanation
Indices: 59422449--59422540 Score: 148
Period size: 40 Copynumber: 2.3 Consensus size: 40
59422439 GAGATTCAAA
** * *
59422449 ATAGCTTCGGCTATAAATAGGACTAAGTGTGGGAAATGGT
1 ATAGCTTCGGCTATAAATAACACTAACTGTGCGAAATGGT
59422489 ATAGCTTCGGCTATAAATAACACTAACTGTGCGAAATGGT
1 ATAGCTTCGGCTATAAATAACACTAACTGTGCGAAATGGT
59422529 ATAGCTTCGGCT
1 ATAGCTTCGGCT
59422541 GCATGAGGCA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 48 1.00
ACGTcount: A:0.32, C:0.15, G:0.25, T:0.28
Consensus pattern (40 bp):
ATAGCTTCGGCTATAAATAACACTAACTGTGCGAAATGGT
Found at i:59425806 original size:16 final size:16
Alignment explanation
Indices: 59425785--59425822 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
59425775 TCGGCAAATC
59425785 CTGAAAAGCCGAAAAG
1 CTGAAAAGCCGAAAAG
*
59425801 CTGAAATGCCGAAAAG
1 CTGAAAAGCCGAAAAG
59425817 CTGAAA
1 CTGAAA
59425823 GTTTGGCTAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.47, C:0.18, G:0.24, T:0.11
Consensus pattern (16 bp):
CTGAAAAGCCGAAAAG
Found at i:59429306 original size:16 final size:16
Alignment explanation
Indices: 59429285--59429319 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
59429275 ATCACTGGCT
*
59429285 TCTACAGGATTGGAGC
1 TCTACAAGATTGGAGC
59429301 TCTACAAGATTGGAGC
1 TCTACAAGATTGGAGC
59429317 TCT
1 TCT
59429320 GTTCTTTAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.29
Consensus pattern (16 bp):
TCTACAAGATTGGAGC
Found at i:59431352 original size:21 final size:20
Alignment explanation
Indices: 59431328--59431367 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
59431318 CATGTATTTT
59431328 AATGATTGATGATAGATTACG
1 AATGATTGATGATAG-TTACG
*
59431349 AATGTTTGATGATAGTTAC
1 AATGATTGATGATAGTTAC
59431368 ACAAGTTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.35, C:0.05, G:0.23, T:0.38
Consensus pattern (20 bp):
AATGATTGATGATAGTTACG
Found at i:59431375 original size:20 final size:21
Alignment explanation
Indices: 59431333--59431375 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
59431323 ATTTTAATGA
*
59431333 TTGATGATAGATTACGAATGT
1 TTGATGATAGATTACGAAAGT
59431354 TTGATGATAG-TTAC-ACAAGT
1 TTGATGATAGATTACGA-AAGT
59431374 TT
1 TT
59431376 TGTTAAGTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 1 0.05
20 9 0.45
21 10 0.50
ACGTcount: A:0.33, C:0.07, G:0.21, T:0.40
Consensus pattern (21 bp):
TTGATGATAGATTACGAAAGT
Found at i:59431992 original size:48 final size:48
Alignment explanation
Indices: 59431915--59432052 Score: 163
Period size: 47 Copynumber: 2.9 Consensus size: 48
59431905 TTGGAGTAAC
* *
59431915 ATTGATTTGGCTTTGGGCCATAATATTGGCACTTAGGGTGCGAG-TTAA
1 ATTGATTTGGCTTCGGGCCATGATATTGGCACTTAGGGTGCGAGCTT-A
* * * * *
59431963 ATTGATTTGGCTTCGGGTCATGATGTTGGCACTT-CGGTGCAAGCTTT
1 ATTGATTTGGCTTCGGGCCATGATATTGGCACTTAGGGTGCGAGCTTA
* * *
59432010 ATTGATTTGGCTTCAGGCCATGATATTGACACTTAGGATGCGA
1 ATTGATTTGGCTTCGGGCCATGATATTGGCACTTAGGGTGCGA
59432053 AACTTTCGAG
Statistics
Matches: 74, Mismatches: 14, Indels: 4
0.80 0.15 0.04
Matches are distributed among these distances:
47 37 0.50
48 37 0.50
ACGTcount: A:0.21, C:0.15, G:0.28, T:0.36
Consensus pattern (48 bp):
ATTGATTTGGCTTCGGGCCATGATATTGGCACTTAGGGTGCGAGCTTA
Found at i:59434791 original size:22 final size:23
Alignment explanation
Indices: 59434766--59434808 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
59434756 TATTCCTATA
*
59434766 TGGAGTGTAG-GGCTGGATGGAG
1 TGGAGTGTAGAGGATGGATGGAG
59434788 TGGAGTGTAGAGGATGGATGG
1 TGGAGTGTAGAGGATGGATGG
59434809 GTAGGACTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.21, C:0.02, G:0.53, T:0.23
Consensus pattern (23 bp):
TGGAGTGTAGAGGATGGATGGAG
Found at i:59434905 original size:34 final size:33
Alignment explanation
Indices: 59434841--59434912 Score: 83
Period size: 34 Copynumber: 2.2 Consensus size: 33
59434831 TGTTACTATT
59434841 ACTGTAATGGGCTAAAGCCCACACTATTACTGAG
1 ACTGTAATGGGCTAAAGCCCACACTATTACT-AG
* * * *
59434875 ACTGTATTGGGCTAAGGCTCTA-ACTGTTACTAG
1 ACTGTAATGGGCTAAAGC-CCACACTATTACTAG
59434908 ACTGT
1 ACTGT
59434913 TACTGAAACA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
33 7 0.21
34 24 0.73
35 2 0.06
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.29
Consensus pattern (33 bp):
ACTGTAATGGGCTAAAGCCCACACTATTACTAG
Found at i:59436460 original size:18 final size:18
Alignment explanation
Indices: 59436437--59436479 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
59436427 TATTTGAAAG
59436437 TTAAATTTAGTGAATTAA
1 TTAAATTTAGTGAATTAA
59436455 TTAAATTTAGTGAATTAA
1 TTAAATTTAGTGAATTAA
*
59436473 TTGAATT
1 TTAAATT
59436480 ATGTTAAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.47
Consensus pattern (18 bp):
TTAAATTTAGTGAATTAA
Found at i:59441307 original size:68 final size:64
Alignment explanation
Indices: 59441190--59441340 Score: 160
Period size: 68 Copynumber: 2.3 Consensus size: 64
59441180 ATACAGATAG
* * * * *
59441190 TATGTAGCTAGGTCACATGTATGGTGCTAAGTGCACATCATGTGTACAAGAGAGCTACAAGACAT
1 TATGTAGCTAGGTCGCATGGATGATACTAAGTGCACACCATGTGTACAAGAGAGCTAC--GACA-
59441255 TA
63 TA
* * * **
59441257 TGATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAG-ACAAGAGAGCTACGGGAT
1 T-ATGTAGCTAGGTCGCATGGATGATACTAAGTGCACACCATGT-GTACAAGAGAGCTACGACAT
59441321 A
64 A
59441322 TATGTAGCTAGGTCGCATG
1 TATGTAGCTAGGTCGCATG
59441341 TGTAGTACAA
Statistics
Matches: 72, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
64 18 0.25
65 3 0.04
66 2 0.03
67 1 0.01
68 47 0.65
69 1 0.01
ACGTcount: A:0.30, C:0.16, G:0.28, T:0.26
Consensus pattern (64 bp):
TATGTAGCTAGGTCGCATGGATGATACTAAGTGCACACCATGTGTACAAGAGAGCTACGACATA
Found at i:59447438 original size:26 final size:26
Alignment explanation
Indices: 59447403--59447454 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
59447393 AATGTGAAAG
*
59447403 GGGGTTGCTATGTGCTGATTCCCCGA
1 GGGGTTGCTAAGTGCTGATTCCCCGA
59447429 GGGGTTGCTAAGTGCTGATTCCCCGA
1 GGGGTTGCTAAGTGCTGATTCCCCGA
59447455 TTCAGCGGTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.13, C:0.23, G:0.35, T:0.29
Consensus pattern (26 bp):
GGGGTTGCTAAGTGCTGATTCCCCGA
Found at i:59447472 original size:103 final size:105
Alignment explanation
Indices: 59447220--59447486 Score: 432
Period size: 105 Copynumber: 2.6 Consensus size: 105
59447210 TTGTATATAA
** *
59447220 AGGGGTTGCTGTGTGCTGATTCCCCGATTCATTGGTGGTGCTATGTGCG-TGATCCACCATATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGAT-ATCCACCATATCT
59447284 TTGAAATGTGAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
65 TTGAAATGTGAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
* *
59447325 AGGGGTTGCTAAGTGATGATTCCCCGGTTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
59447390 TGAAATGTG-AAAGGGGGTTGCTATGTGCTGATT-CCCCG
66 TGAAATGTGAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
** *
59447428 AGGGGTTGCTAAGTGCTGATTCCCCGATTCAGCGGTGGTGCTAAGTGCGAGATCCACCA
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCA
59447487 ATAACGGTTA
Statistics
Matches: 151, Mismatches: 10, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
103 59 0.39
104 24 0.16
105 67 0.44
106 1 0.01
ACGTcount: A:0.19, C:0.20, G:0.31, T:0.30
Consensus pattern (105 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
TGAAATGTGAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
Found at i:59451304 original size:13 final size:13
Alignment explanation
Indices: 59451286--59451314 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
59451276 CCATAAATTA
59451286 CATGGGTAATAAT
1 CATGGGTAATAAT
59451299 CATGGGTAATAAT
1 CATGGGTAATAAT
59451312 CAT
1 CAT
59451315 CGATCTAAAA
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:0.38, C:0.10, G:0.21, T:0.31
Consensus pattern (13 bp):
CATGGGTAATAAT
Found at i:59456938 original size:11 final size:10
Alignment explanation
Indices: 59456886--59456940 Score: 51
Period size: 11 Copynumber: 5.5 Consensus size: 10
59456876 CATGAGATTT
59456886 TGATAT-ACA
1 TGATATGACA
*
59456895 TGATTTGACA
1 TGATATGACA
*
59456905 TGATATACACA
1 TGATAT-GACA
*
59456916 TGATATG-TA
1 TGATATGACA
59456925 TGATATGCACA
1 TGATATG-ACA
59456936 TGATA
1 TGATA
59456941 AATTCATATA
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
9 13 0.36
10 8 0.22
11 15 0.42
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.35
Consensus pattern (10 bp):
TGATATGACA
Found at i:59457064 original size:24 final size:25
Alignment explanation
Indices: 59456988--59457057 Score: 113
Period size: 25 Copynumber: 2.8 Consensus size: 25
59456978 GAGGAAGTGC
* * *
59456988 AAAAGGGCTATGCCCTAGTTTATCG
1 AAAAGGGCTTTGCCCCAGTTTATCA
59457013 AAAAGGGCTTTGCCCCAGTTTATCA
1 AAAAGGGCTTTGCCCCAGTTTATCA
59457038 AAAAGGGCTTTGCCCCAGTT
1 AAAAGGGCTTTGCCCCAGTT
59457058 ATTAAAAGAG
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 42 1.00
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTTATCA
Found at i:59457070 original size:24 final size:24
Alignment explanation
Indices: 59456987--59457084 Score: 85
Period size: 25 Copynumber: 4.0 Consensus size: 24
59456977 AGAGGAAGTG
* *
59456987 CAAAAG-GGCTATGCCCTAGTTTAT
1 CAAAAGAGGCTTTGCCCCAG-TTAT
59457011 CGAAAAG-GGCTTTGCCCCAGTTTAT
1 C-AAAAGAGGCTTTGCCCCAG-TTAT
59457036 CAAAA-AGGGCTTTGCCCCAGTTAT
1 CAAAAGA-GGCTTTGCCCCAGTTAT
* **
59457060 TAAAAGAGGCTAGGCCTCCAGTTAT
1 CAAAAGAGGCTTTGCC-CCAGTTAT
59457085 ATGATAAAGC
Statistics
Matches: 64, Mismatches: 5, Indels: 9
0.82 0.06 0.12
Matches are distributed among these distances:
24 20 0.31
25 44 0.69
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (24 bp):
CAAAAGAGGCTTTGCCCCAGTTAT
Found at i:59457081 original size:50 final size:50
Alignment explanation
Indices: 59456988--59457082 Score: 113
Period size: 50 Copynumber: 1.9 Consensus size: 50
59456978 GAGGAAGTGC
* **
59456988 AAAAGGGCTATGCCCTAGTTTATCGAAAAGGGCTTTGCCCCAGTTTATCA
1 AAAAGGGCTATGCCCCAGTTTATCGAAAAGGGCTAGGCCCCAGTTTATCA
* *
59457038 AAAAGGGCTTTGCCCCAG-TTAT-TAAAAGAGGCTAGGCCTCCAGTT
1 AAAAGGGCTATGCCCCAGTTTATCGAAAAG-GGCTAGGCC-CCAGTT
59457083 ATATGATAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
48 5 0.13
49 11 0.29
50 22 0.58
ACGTcount: A:0.28, C:0.22, G:0.23, T:0.26
Consensus pattern (50 bp):
AAAAGGGCTATGCCCCAGTTTATCGAAAAGGGCTAGGCCCCAGTTTATCA
Found at i:59457337 original size:31 final size:31
Alignment explanation
Indices: 59457279--59457354 Score: 107
Period size: 31 Copynumber: 2.5 Consensus size: 31
59457269 CGTTTACAGT
* *
59457279 AAAAGGCTTTGGCCTAGTGATAGGAATAATG
1 AAAAGGCTTTGGCCCAGTGACAGGAATAATG
* * *
59457310 AAAATGCTTCGGCCCAGTGACATGAATAATG
1 AAAAGGCTTTGGCCCAGTGACAGGAATAATG
59457341 AAAAGGCTTTGGCC
1 AAAAGGCTTTGGCC
59457355 TAGTATATGT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.34, C:0.16, G:0.26, T:0.24
Consensus pattern (31 bp):
AAAAGGCTTTGGCCCAGTGACAGGAATAATG
Found at i:59464866 original size:11 final size:10
Alignment explanation
Indices: 59464834--59464888 Score: 60
Period size: 11 Copynumber: 5.5 Consensus size: 10
59464824 CATGAGATTT
59464834 TGATAT-ACA
1 TGATATGACA
*
59464843 TGATTTGACA
1 TGATATGACA
59464853 TGATATGCACA
1 TGATATG-ACA
*
59464864 TGATATG-TA
1 TGATATGACA
59464873 TGATATGCACA
1 TGATATG-ACA
59464884 TGATA
1 TGATA
59464889 AATTCATATA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
9 13 0.34
10 9 0.24
11 16 0.42
ACGTcount: A:0.36, C:0.11, G:0.18, T:0.35
Consensus pattern (10 bp):
TGATATGACA
Found at i:59465007 original size:24 final size:25
Alignment explanation
Indices: 59464936--59465005 Score: 95
Period size: 25 Copynumber: 2.8 Consensus size: 25
59464926 AAGGAAGTGC
* * *
59464936 AAAAGGGCTATGCCCCAGTTTACCG
1 AAAAGGGCTTTGCCCCAGTTTATCA
*
59464961 AAAAGGGCTTTACCCCAGTTTATCA
1 AAAAGGGCTTTGCCCCAGTTTATCA
*
59464986 AAAAGAGCTTTGCCCCAGTT
1 AAAAGGGCTTTGCCCCAGTT
59465006 ATTAAAAGAG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTTATCA
Found at i:59465262 original size:31 final size:31
Alignment explanation
Indices: 59465227--59465306 Score: 124
Period size: 31 Copynumber: 2.6 Consensus size: 31
59465217 CGTTTACAGT
*
59465227 AAAAGGCTTCGGCCCAGTGATAGGAATAATG
1 AAAAGGCTTCGGCCCAGTGACAGGAATAATG
* *
59465258 AAAAGGCTTCGGCCTAGTGACATGAATAATG
1 AAAAGGCTTCGGCCCAGTGACAGGAATAATG
*
59465289 CAAAGGCTTCGGCCCAGT
1 AAAAGGCTTCGGCCCAGT
59465307 ATATGTTGAG
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.33, C:0.20, G:0.28, T:0.20
Consensus pattern (31 bp):
AAAAGGCTTCGGCCCAGTGACAGGAATAATG
Found at i:59467616 original size:28 final size:29
Alignment explanation
Indices: 59467579--59467699 Score: 154
Period size: 29 Copynumber: 4.2 Consensus size: 29
59467569 TACATATATG
* * *
59467579 CATATAGCCCACTAGG-CCTAATCTCATT
1 CATATAGCCCATTAGGCCCAAATCACATT
* *
59467607 CATATGGCCCATTAGGCCCAAATCATATT
1 CATATAGCCCATTAGGCCCAAATCACATT
* *
59467636 CGTATGGCCCATTAGGCCCAAATCACATT
1 CATATAGCCCATTAGGCCCAAATCACATT
* *
59467665 CTTACAGCCCATTAGGCCCAAATCACATT
1 CATATAGCCCATTAGGCCCAAATCACATT
59467694 CATATA
1 CATATA
59467700 CATGCTTTCA
Statistics
Matches: 80, Mismatches: 12, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
28 14 0.17
29 66 0.82
ACGTcount: A:0.31, C:0.31, G:0.12, T:0.26
Consensus pattern (29 bp):
CATATAGCCCATTAGGCCCAAATCACATT
Found at i:59469321 original size:29 final size:29
Alignment explanation
Indices: 59469197--59469320 Score: 151
Period size: 29 Copynumber: 4.3 Consensus size: 29
59469187 AAGTCTGCAT
* * *
59469197 ACATGCATATGGCCCACTAAGCCC-AATC
1 ACATTCATATGGCCCATTAGGCCCAAATC
* * *
59469225 TCATTCATATGGCCCATTAGGTCCAAATA
1 ACATTCATATGGCCCATTAGGCCCAAATC
* *
59469254 ATATTCGTATGGCCCATTAGGCCCAAATC
1 ACATTCATATGGCCCATTAGGCCCAAATC
* *
59469283 ACATTCATACGGCCCATTAGGCCCGAATC
1 ACATTCATATGGCCCATTAGGCCCAAATC
59469312 ACATTCATA
1 ACATTCATA
59469321 CACATGCTTT
Statistics
Matches: 80, Mismatches: 15, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
28 19 0.24
29 61 0.76
ACGTcount: A:0.31, C:0.30, G:0.15, T:0.25
Consensus pattern (29 bp):
ACATTCATATGGCCCATTAGGCCCAAATC
Found at i:59469555 original size:16 final size:16
Alignment explanation
Indices: 59469530--59469588 Score: 73
Period size: 16 Copynumber: 3.7 Consensus size: 16
59469520 GTAGCTAAAC
*
59469530 TTTCGGCTTTTCGGCA
1 TTTCAGCTTTTCGGCA
* * *
59469546 TTTCAACTTTTTGGTA
1 TTTCAGCTTTTCGGCA
*
59469562 TTCCAGCTTTTCGGCA
1 TTTCAGCTTTTCGGCA
59469578 TTTCAGCTTTT
1 TTTCAGCTTTT
59469589 ACCGATCTAC
Statistics
Matches: 34, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.12, C:0.22, G:0.17, T:0.49
Consensus pattern (16 bp):
TTTCAGCTTTTCGGCA
Found at i:59473875 original size:29 final size:29
Alignment explanation
Indices: 59473786--59473900 Score: 124
Period size: 29 Copynumber: 4.0 Consensus size: 29
59473776 CATGCATATG
* * **
59473786 GCCCACTAGGCCC-AATCTCATTCATATG
1 GCCCATTAGGCCCAAATCACATTCATACA
* ** * **
59473814 GCCCATTAGGTCCAAATCATTTTCGTATG
1 GCCCATTAGGCCCAAATCACATTCATACA
59473843 GCCCATTAGGCCCAAATCACATTCATACA
1 GCCCATTAGGCCCAAATCACATTCATACA
*
59473872 GCCCATTAGGCCCGAATCACATTCATACA
1 GCCCATTAGGCCCAAATCACATTCATACA
59473901 CATGCTTTCA
Statistics
Matches: 73, Mismatches: 13, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
28 11 0.15
29 62 0.85
ACGTcount: A:0.29, C:0.32, G:0.14, T:0.25
Consensus pattern (29 bp):
GCCCATTAGGCCCAAATCACATTCATACA
Found at i:59473881 original size:58 final size:57
Alignment explanation
Indices: 59473782--59473890 Score: 155
Period size: 58 Copynumber: 1.9 Consensus size: 57
59473772 CATACATGCA
* ** *
59473782 TATGGCCCACTAGGCCCAATCTCATTCATATGGCCCATTAGGTCCAAATCATTTTCG
1 TATGGCCCACTAGGCCCAATCACATTCATACAGCCCATTAGGCCCAAATCATTTTCG
* *
59473839 TATGGCCCATTAGGCCCAAATCACATTCATACAGCCCATTAGGCCCGAATCA
1 TATGGCCCACTAGGCCC-AATCACATTCATACAGCCCATTAGGCCCAAATCA
59473891 CATTCATACA
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
57 16 0.36
58 29 0.64
ACGTcount: A:0.28, C:0.31, G:0.16, T:0.26
Consensus pattern (57 bp):
TATGGCCCACTAGGCCCAATCACATTCATACAGCCCATTAGGCCCAAATCATTTTCG
Found at i:59474133 original size:16 final size:16
Alignment explanation
Indices: 59474108--59474166 Score: 82
Period size: 16 Copynumber: 3.7 Consensus size: 16
59474098 GTAGCCAAAC
59474108 TTTCAGCTTTTCGGCA
1 TTTCAGCTTTTCGGCA
* * *
59474124 TTTCAACTTTTTGGTA
1 TTTCAGCTTTTCGGCA
*
59474140 TTCCAGCTTTTCGGCA
1 TTTCAGCTTTTCGGCA
59474156 TTTCAGCTTTT
1 TTTCAGCTTTT
59474167 GCCGATCTAC
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.14, C:0.22, G:0.15, T:0.49
Consensus pattern (16 bp):
TTTCAGCTTTTCGGCA
Found at i:59476979 original size:14 final size:14
Alignment explanation
Indices: 59476960--59476989 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
59476950 CAGATAAAGA
59476960 GTGGGAGAGTTTGC
1 GTGGGAGAGTTTGC
59476974 GTGGGAGAGTTTGC
1 GTGGGAGAGTTTGC
59476988 GT
1 GT
59476990 ACCGAAGGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.13, C:0.07, G:0.50, T:0.30
Consensus pattern (14 bp):
GTGGGAGAGTTTGC
Found at i:59479886 original size:27 final size:27
Alignment explanation
Indices: 59479856--59479907 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
59479846 CCCATACTGA
59479856 TAAAATGACT-ATTATACCCCTATGAGG
1 TAAAATGACTGA-TATACCCCTATGAGG
*
59479883 TAAAATGACTGATATGCCCCTATGA
1 TAAAATGACTGATATACCCCTATGA
59479908 TTTGTATGAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
27 22 0.96
28 1 0.04
ACGTcount: A:0.37, C:0.19, G:0.15, T:0.29
Consensus pattern (27 bp):
TAAAATGACTGATATACCCCTATGAGG
Found at i:59480217 original size:34 final size:34
Alignment explanation
Indices: 59480179--59480244 Score: 98
Period size: 34 Copynumber: 1.9 Consensus size: 34
59480169 CTATTACTGT
59480179 TATTGTAATGGGCTAAAGCCC-ACACTGTTACTAA
1 TATTGTAATGGGCTAAAGCCCTA-ACTGTTACTAA
* *
59480213 TATTGTATTGGGCTAAGGCCCTAACTGTTACT
1 TATTGTAATGGGCTAAAGCCCTAACTGTTACT
59480245 GGACTGTTAC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 28 0.97
35 1 0.03
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (34 bp):
TATTGTAATGGGCTAAAGCCCTAACTGTTACTAA
Found at i:59481501 original size:34 final size:34
Alignment explanation
Indices: 59481446--59481536 Score: 112
Period size: 34 Copynumber: 2.7 Consensus size: 34
59481436 AACAGTGTTG
* *
59481446 AACAGTCTGGGCCTAAGCCCATGT-CAGTAGCAAT
1 AACAGTGTGGGCCTTAGCCCAT-TACAGTAGCAAT
** * *
59481480 GTCAGTGTGGGCCTTATCCCATTACAGTAGTAAT
1 AACAGTGTGGGCCTTAGCCCATTACAGTAGCAAT
59481514 AACAGTGTGGGCCTTAGCCCATT
1 AACAGTGTGGGCCTTAGCCCATT
59481537 TTAGTACAGT
Statistics
Matches: 47, Mismatches: 9, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
33 1 0.02
34 46 0.98
ACGTcount: A:0.25, C:0.24, G:0.24, T:0.26
Consensus pattern (34 bp):
AACAGTGTGGGCCTTAGCCCATTACAGTAGCAAT
Found at i:59484024 original size:46 final size:45
Alignment explanation
Indices: 59483957--59484129 Score: 206
Period size: 46 Copynumber: 3.8 Consensus size: 45
59483947 AACCCGCCCC
*
59483957 TAAGTGAACTCGAACTCAACTCAACGAGCTCGGACGTTCGCATCCA
1 TAAGTGAACTCGAACTCAACTCAACGAGTTCGGAC-TTCGCATCCA
* * *
59484003 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA-TAC-CTAGTTACA
1 TAAGTGAACTCGAACTCAACTCAACGAGTTCGGACTTCGC-A--TCCA
*** *
59484049 TCTCTCGAACTCAAACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGT-GAACTCGAACTCAACTCAACGAGTTCGGAC-TTCGCATCCA
59484096 TAAGTGAACTCGAACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGAACTCAACTCAACGAGTTCGGA
59484130 TGCTCAACCA
Statistics
Matches: 105, Mismatches: 15, Indels: 14
0.78 0.11 0.10
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
46 65 0.62
47 32 0.30
49 3 0.03
50 1 0.01
ACGTcount: A:0.32, C:0.28, G:0.18, T:0.22
Consensus pattern (45 bp):
TAAGTGAACTCGAACTCAACTCAACGAGTTCGGACTTCGCATCCA
Found at i:59484071 original size:93 final size:93
Alignment explanation
Indices: 59483962--59484130 Score: 302
Period size: 93 Copynumber: 1.8 Consensus size: 93
59483952 GCCCCTAAGT
* * *
59483962 GAACTCGAACTCAACTCAACGAGCTCGGACGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCAAACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGAACTCAACTCAA
59484027 CGAGTTCGGATACCTAGTTACATCTCTC
66 CGAGTTCGGATACCTAGTTACATCTCTC
*
59484055 GAACTCAAACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGAACTCAACTCAA
1 GAACTCAAACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGAACTCAACTCAA
59484120 CGAGTTCGGAT
66 CGAGTTCGGAT
59484131 GCTCAACCAT
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.31, C:0.29, G:0.18, T:0.22
Consensus pattern (93 bp):
GAACTCAAACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGAACTCAACTCAA
CGAGTTCGGATACCTAGTTACATCTCTC
Found at i:59488230 original size:119 final size:118
Alignment explanation
Indices: 59488042--59488255 Score: 374
Period size: 119 Copynumber: 1.8 Consensus size: 118
59488032 ACGGTATTCC
*
59488042 GTGTAGTATGAACCTATTAAGGATTAGCATAGGTATGTAAATGTATATTATGAGCTTAAATTTGA
1 GTGTAGTATGAACCTATTAAGGATTAGCACAGGTATGTAAATGTATATTATGAGCTTAAATTTGA
59488107 AGAAGTTACAAAGTTTGTATATAAGCTTATTATTGAGTATTCAATAGTATTTT
66 AGAAGTTACAAAGTTTGTATATAAGCTTATTATTGAGTATTCAATAGTATTTT
* * * *
59488160 GTGTATGTATGAACCTGTTAAGGATTGGTACAGGTATGTACATGTATATTATGAGCTTAAATTTG
1 GTGTA-GTATGAACCTATTAAGGATTAGCACAGGTATGTAAATGTATATTATGAGCTTAAATTTG
59488225 AAGAAGTTACAAAGTTTGTATATAAGCTTAT
65 AAGAAGTTACAAAGTTTGTATATAAGCTTAT
59488256 AAATAAGTAG
Statistics
Matches: 90, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
118 5 0.06
119 85 0.94
ACGTcount: A:0.35, C:0.07, G:0.20, T:0.39
Consensus pattern (118 bp):
GTGTAGTATGAACCTATTAAGGATTAGCACAGGTATGTAAATGTATATTATGAGCTTAAATTTGA
AGAAGTTACAAAGTTTGTATATAAGCTTATTATTGAGTATTCAATAGTATTTT
Found at i:59489309 original size:6 final size:6
Alignment explanation
Indices: 59489279--59489403 Score: 69
Period size: 6 Copynumber: 20.3 Consensus size: 6
59489269 AAGAAACATT
* * *
59489279 ATCAGA A-CTAGA ATCAAA ATGAGA ATCAGA ATCAGA ATCAG- GTGACAGA
1 ATCAGA ATC-AGA ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA AT--CAGA
* * * * * *
59489328 ATCAGA ATTAAA ATCAGA ATCAGA ATTAGGTG AT-AGG ATCAGA ATCAGT
1 ATCAGA ATCAGA ATCAGA ATCAGA ATCA-G-A ATCAGA ATCAGA ATCAGA
*
59489377 ATCAGGTA A-CAGA ATCAGA ACCAGA AT
1 ATCA-G-A ATCAGA ATCAGA ATCAGA AT
59489404 GTGAATGCAA
Statistics
Matches: 91, Mismatches: 17, Indels: 22
0.70 0.13 0.17
Matches are distributed among these distances:
5 7 0.08
6 71 0.78
7 9 0.10
8 4 0.04
ACGTcount: A:0.47, C:0.14, G:0.20, T:0.19
Consensus pattern (6 bp):
ATCAGA
Found at i:59489368 original size:25 final size:25
Alignment explanation
Indices: 59489339--59489403 Score: 76
Period size: 25 Copynumber: 2.6 Consensus size: 25
59489329 TCAGAATTAA
* * *
59489339 AATCAGAATCAGAATTAGGTGATAG
1 AATCAGAATCAGAATCAGGTAACAG
* *
59489364 GATCAGAATCAGTATCAGGTAACAG
1 AATCAGAATCAGAATCAGGTAACAG
*
59489389 AATCAGAACCAGAAT
1 AATCAGAATCAGAAT
59489404 GTGAATGCAA
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.45, C:0.14, G:0.22, T:0.20
Consensus pattern (25 bp):
AATCAGAATCAGAATCAGGTAACAG
Found at i:59489369 original size:37 final size:37
Alignment explanation
Indices: 59489288--59489372 Score: 116
Period size: 37 Copynumber: 2.3 Consensus size: 37
59489278 TATCAGAACT
* * *
59489288 AGAATCAAAATGAGAATCAGAATCAGAATCAGGTGAC
1 AGAATCAGAATTAAAATCAGAATCAGAATCAGGTGAC
* *
59489325 AGAATCAGAATTAAAATCAGAATCAGAATTAGGTGAT
1 AGAATCAGAATTAAAATCAGAATCAGAATCAGGTGAC
*
59489362 AGGATCAGAAT
1 AGAATCAGAAT
59489373 CAGTATCAGG
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 42 1.00
ACGTcount: A:0.48, C:0.11, G:0.21, T:0.20
Consensus pattern (37 bp):
AGAATCAGAATTAAAATCAGAATCAGAATCAGGTGAC
Found at i:59489618 original size:28 final size:27
Alignment explanation
Indices: 59489525--59489656 Score: 133
Period size: 27 Copynumber: 4.9 Consensus size: 27
59489515 TGGCTGCTAG
* *
59489525 AACAGATATTGTGACAGAGTCACCAGA
1 AACAGATATTGTGGCAGAGCCACCAGA
* * * *
59489552 TATAGACATTGTGGTAGAGCCACCAG-
1 AACAGATATTGTGGCAGAGCCACCAGA
* *
59489578 AACAGATATTTGTGGCATAGCCGCCAGA
1 AACAGATA-TTGTGGCAGAGCCACCAGA
59489606 AACAGAATATTGTGGCAGAGCCACCA-A
1 AACAG-ATATTGTGGCAGAGCCACCAGA
* *
59489633 AATCAGATAATGTGGCAAAGCCAC
1 AA-CAGATATTGTGGCAGAGCCAC
59489657 TTAACAGAAT
Statistics
Matches: 85, Mismatches: 16, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
26 5 0.06
27 54 0.64
28 23 0.27
29 3 0.04
ACGTcount: A:0.37, C:0.20, G:0.23, T:0.19
Consensus pattern (27 bp):
AACAGATATTGTGGCAGAGCCACCAGA
Found at i:59489809 original size:27 final size:27
Alignment explanation
Indices: 59489779--59489830 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
59489769 AGTCGTCAAC
*
59489779 AAATATGTTAGGCAC-ATAGCCATAGGT
1 AAATACGTTAGGCACGA-AGCCATAGGT
*
59489806 AAATACGTTTGGCACGAAGCCATAG
1 AAATACGTTAGGCACGAAGCCATAG
59489831 TCAAGATGGC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 21 0.95
28 1 0.05
ACGTcount: A:0.37, C:0.17, G:0.23, T:0.23
Consensus pattern (27 bp):
AAATACGTTAGGCACGAAGCCATAGGT
Found at i:59489862 original size:22 final size:22
Alignment explanation
Indices: 59489814--59489872 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 22
59489804 GTAAATACGT
*
59489814 TTGGCACGAAGCCATAGTCAAG
1 TTGGCACAAAGCCATAGTCAAG
* * * *
59489836 ATGGCACAAAGCCATATTTAGG
1 TTGGCACAAAGCCATAGTCAAG
*
59489858 TTGGCACAGAGCCAT
1 TTGGCACAAAGCCAT
59489873 CGATAACGGG
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.32, C:0.22, G:0.25, T:0.20
Consensus pattern (22 bp):
TTGGCACAAAGCCATAGTCAAG
Found at i:59490497 original size:27 final size:27
Alignment explanation
Indices: 59490218--59490501 Score: 345
Period size: 27 Copynumber: 10.5 Consensus size: 27
59490208 TACCCCACGA
* * *
59490218 GGGTATCTCGATAATTCTACCCTACAG
1 GGGTATTTCGGTAATTCTACCTTACAG
* * * *
59490245 GGGTATTTCAGTATTTCTACCCTACAA
1 GGGTATTTCGGTAATTCTACCTTACAG
*
59490272 GGGTATTTCGGTAATACTATCC-TACAG
1 GGGTATTTCGGTAATTCTA-CCTTACAG
* *
59490299 GGGTATTTCAGTAATTCTACCCTACAG
1 GGGTATTTCGGTAATTCTACCTTACAG
*
59490326 GGGTATTTTGGTAATTCTACCTTACAG
1 GGGTATTTCGGTAATTCTACCTTACAG
*
59490353 GGGTATTTCAGTAATTCTACCTTACAGG
1 GGGTATTTCGGTAATTCTACCTTACA-G
**
59490381 GGGTATTTTAGTAATTCTACCTTACAG
1 GGGTATTTCGGTAATTCTACCTTACAG
*
59490408 GGGTATTTCGGTAATTCTACTTTACAG
1 GGGTATTTCGGTAATTCTACCTTACAG
* * * *
59490435 GAGCATTTCAGTAATTCTACCTTATAG
1 GGGTATTTCGGTAATTCTACCTTACAG
* *
59490462 GGGTATTTTGGTAATTCTACCTTACAA
1 GGGTATTTCGGTAATTCTACCTTACAG
*
59490489 GGGTATTTTGGTA
1 GGGTATTTCGGTA
59490502 CTTTTTCTAA
Statistics
Matches: 223, Mismatches: 31, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
26 2 0.01
27 193 0.87
28 28 0.13
ACGTcount: A:0.25, C:0.18, G:0.20, T:0.37
Consensus pattern (27 bp):
GGGTATTTCGGTAATTCTACCTTACAG
Found at i:59490518 original size:27 final size:27
Alignment explanation
Indices: 59490458--59490559 Score: 118
Period size: 27 Copynumber: 3.8 Consensus size: 27
59490448 ATTCTACCTT
** *
59490458 ATAG-GGGTATTTTGGTAATTCTACCTT
1 ATAGAGGGTATTTTGGTAATT-TTGCTA
* * *
59490485 ACA-AGGGTATTTTGGTACTTTTTCTA
1 ATAGAGGGTATTTTGGTAATTTTGCTA
59490511 ATAGAGGGTATTTTGGTAATTTTGCTA
1 ATAGAGGGTATTTTGGTAATTTTGCTA
*
59490538 ATCGAGGGTATTTTGGTAATTT
1 ATAGAGGGTATTTTGGTAATTT
59490560 GGTAAACTAA
Statistics
Matches: 64, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
26 5 0.08
27 59 0.92
ACGTcount: A:0.24, C:0.08, G:0.24, T:0.45
Consensus pattern (27 bp):
ATAGAGGGTATTTTGGTAATTTTGCTA
Found at i:59492219 original size:22 final size:23
Alignment explanation
Indices: 59492189--59492232 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
59492179 GATTTATGAG
*
59492189 AATGAATGCTTTATGTT-TGATA
1 AATGAATGCTATATGTTGTGATA
*
59492211 AATGTATGCTATATGTTGTGAT
1 AATGAATGCTATATGTTGTGAT
59492233 TTGATCGATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.30, C:0.05, G:0.20, T:0.45
Consensus pattern (23 bp):
AATGAATGCTATATGTTGTGATA
Found at i:59493232 original size:50 final size:50
Alignment explanation
Indices: 59493157--59493257 Score: 202
Period size: 50 Copynumber: 2.0 Consensus size: 50
59493147 TGCTCGAGAC
59493157 TATGTTTCTACTGAAGAAATCATGTGCAAATGGTTCATTGATGGGTTGAA
1 TATGTTTCTACTGAAGAAATCATGTGCAAATGGTTCATTGATGGGTTGAA
59493207 TATGTTTCTACTGAAGAAATCATGTGCAAATGGTTCATTGATGGGTTGAA
1 TATGTTTCTACTGAAGAAATCATGTGCAAATGGTTCATTGATGGGTTGAA
59493257 T
1 T
59493258 GAGGATATTA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.30, C:0.10, G:0.24, T:0.37
Consensus pattern (50 bp):
TATGTTTCTACTGAAGAAATCATGTGCAAATGGTTCATTGATGGGTTGAA
Found at i:59495199 original size:27 final size:27
Alignment explanation
Indices: 59495134--59495201 Score: 118
Period size: 27 Copynumber: 2.5 Consensus size: 27
59495124 ATAGGCTAAT
*
59495134 ATTACTGAAATACCCCTGTAGGGTAGA
1 ATTACTGAAATGCCCCTGTAGGGTAGA
*
59495161 ATTACTGAAATGCCCTTGTAGGGTAGA
1 ATTACTGAAATGCCCCTGTAGGGTAGA
59495188 ATTACTGAAATGCC
1 ATTACTGAAATGCC
59495202 TTTGGTTTAC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.28
Consensus pattern (27 bp):
ATTACTGAAATGCCCCTGTAGGGTAGA
Found at i:59495217 original size:27 final size:26
Alignment explanation
Indices: 59495187--59495245 Score: 91
Period size: 26 Copynumber: 2.2 Consensus size: 26
59495177 TGTAGGGTAG
* *
59495187 AATTACTGAAATGCCTTTGGTTTACAA
1 AATTACTG-AATACCCTTGGTTTACAA
59495214 AATTACTGAATACCCTTGGTTTACAA
1 AATTACTGAATACCCTTGGTTTACAA
59495240 AATTAC
1 AATTAC
59495246 CAAAATATCC
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
26 22 0.73
27 8 0.27
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.36
Consensus pattern (26 bp):
AATTACTGAATACCCTTGGTTTACAA
Found at i:59495555 original size:27 final size:27
Alignment explanation
Indices: 59495222--59495573 Score: 273
Period size: 27 Copynumber: 13.1 Consensus size: 27
59495212 AAAATTACTG
* **
59495222 AATACCCTTGGTTTACAAAATTACCAA
1 AATACCCTTGATTTGTAAAATTACCAA
* * *
59495249 AATATCCTTGATTAGCAAAATTACCAA
1 AATACCCTTGATTTGTAAAATTACCAA
*
59495276 AATA-CCTCTGGTTTGTAAAATTACCAA
1 AATACCCT-TGATTTGTAAAATTACCAA
* * * * *
59495303 AGTACCCCTAATTTGTGAAATTACCGA
1 AATACCCTTGATTTGTAAAATTACCAA
* ** * *
59495330 AATACCCTCGACCTGTAAAATTATCGA
1 AATACCCTTGATTTGTAAAATTACCAA
** * *
59495357 AATACCCTCAACTTATAAAATTACCAA
1 AATACCCTTGATTTGTAAAATTACCAA
* *
59495384 AATACCCTCGATTTGAAAAATTACCAA
1 AATACCCTTGATTTGTAAAATTACCAA
* * *
59495411 AATACCCTTAATTTG-GAAATTATCAA
1 AATACCCTTGATTTGTAAAATTACCAA
*
59495437 AATACCCTTGATTTGGAAAATTA-CAGA
1 AATACCCTTGATTTGTAAAATTACCA-A
* ** *
59495464 AATACCCCTGATTTAAAAAATTACAAA
1 AATACCCTTGATTTGTAAAATTACCAA
**
59495491 AATACCCTTGGCCTT-TAAAATTA-CAGA
1 AATACCCTT-GATTTGTAAAATTACCA-A
* * * *
59495518 ATTACCATTGGTTTGCAAAATTACCAA
1 AATACCCTTGATTTGTAAAATTACCAA
* * *
59495545 AATACCCTTGGTTTGTAGATTTACCAA
1 AATACCCTTGATTTGTAAAATTACCAA
59495572 AA
1 AA
59495574 CACTCTTGTA
Statistics
Matches: 261, Mismatches: 55, Indels: 18
0.78 0.16 0.05
Matches are distributed among these distances:
26 32 0.12
27 221 0.85
28 8 0.03
ACGTcount: A:0.41, C:0.20, G:0.09, T:0.30
Consensus pattern (27 bp):
AATACCCTTGATTTGTAAAATTACCAA
Found at i:59496216 original size:8 final size:8
Alignment explanation
Indices: 59496203--59496228 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
59496193 ATCGATGGCT
59496203 TTGTGCCA
1 TTGTGCCA
59496211 TTGTGCCA
1 TTGTGCCA
59496219 TTGTGCCA
1 TTGTGCCA
59496227 TT
1 TT
59496229 CTGCTTACTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.12, C:0.23, G:0.23, T:0.42
Consensus pattern (8 bp):
TTGTGCCA
Found at i:59503090 original size:16 final size:16
Alignment explanation
Indices: 59503069--59503101 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
59503059 ATAAATTACA
59503069 TAGTGAAACAAATGAT
1 TAGTGAAACAAATGAT
*
59503085 TAGTGAAACAAGTGAT
1 TAGTGAAACAAATGAT
59503101 T
1 T
59503102 TTTATTTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.45, C:0.06, G:0.21, T:0.27
Consensus pattern (16 bp):
TAGTGAAACAAATGAT
Found at i:59503324 original size:40 final size:40
Alignment explanation
Indices: 59503269--59503358 Score: 171
Period size: 40 Copynumber: 2.2 Consensus size: 40
59503259 TATGTGCATA
59503269 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
1 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
*
59503309 GCATTGGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
1 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
59503349 GCATTCGTGC
1 GCATTCGTGC
59503359 TAGTTGTTAC
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 48 1.00
ACGTcount: A:0.21, C:0.20, G:0.31, T:0.28
Consensus pattern (40 bp):
GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
Found at i:59506136 original size:27 final size:27
Alignment explanation
Indices: 59506096--59506207 Score: 129
Period size: 27 Copynumber: 4.1 Consensus size: 27
59506086 AGGAAGCGTC
*
59506096 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCACAATTATCTGAT
* *
59506123 CTGGTCGCTCTGCCACATATT-TCTGTT
1 CTGGTGGCTCTGCCACA-ATTATCTGAT
*
59506150 CTGGTGGCTCTGCCACGATTATCTGTAT
1 CTGGTGGCTCTGCCACAATTATCTG-AT
* * *
59506178 CTGGTGACTCTGTCAC-ATTATCTGTT
1 CTGGTGGCTCTGCCACAATTATCTGAT
59506204 CTGG
1 CTGG
59506208 CAGCCATGCT
Statistics
Matches: 73, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
26 8 0.11
27 47 0.64
28 18 0.25
ACGTcount: A:0.15, C:0.25, G:0.22, T:0.38
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACAATTATCTGAT
Found at i:59506202 original size:54 final size:54
Alignment explanation
Indices: 59506096--59506207 Score: 156
Period size: 54 Copynumber: 2.1 Consensus size: 54
59506086 AGGAAGCGTC
*
59506096 CTGGTGGCTATGCCACAATTATCTGATCTGGTCGCTCTGCCACATATTTCTGTT
1 CTGGTGGCTATGCCACAATTATCTGATCTGGTCGCTCTGCCACATATATCTGTT
* * *
59506150 CTGGTGGCTCTGCCACGATTATCTGTATCTGGT-GACTCTGTCACAT-TATCTGTT
1 CTGGTGGCTATGCCACAATTATCTG-ATCTGGTCG-CTCTGCCACATATATCTGTT
59506204 CTGG
1 CTGG
59506208 CAGCCATGCT
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
54 35 0.67
55 17 0.33
ACGTcount: A:0.15, C:0.25, G:0.22, T:0.38
Consensus pattern (54 bp):
CTGGTGGCTATGCCACAATTATCTGATCTGGTCGCTCTGCCACATATATCTGTT
Done.