Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008138.1 Hibiscus syriacus cultivar Beakdansim tig00110694_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: 3838456
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 17 of 18
Found at i:3468111 original size:39 final size:38
Alignment explanation
Indices: 3467990--3468170 Score: 145
Period size: 39 Copynumber: 4.7 Consensus size: 38
3467980 AGGACTTGCG
* *
3467990 GTAAGGACTTACCCTGAGCACAAA-ATCGA-GAAGCCTAC
1 GTAAGGACTTACCCTGAGCACAAAGCT-GAGGAA-CCTGC
* * * * *
3468028 GATAAGGACTTA-CCTGAGCACAACGCCGGGGAGCCAGC
1 G-TAAGGACTTACCCTGAGCACAAAGCTGAGGAACCTGC
* *
3468066 AATAAGGACTTACCCTGAGCACAAAGCTGAGGAACTTGC
1 -GTAAGGACTTACCCTGAGCACAAAGCTGAGGAACCTGC
* *
3468105 TGTAAGGATTTACCCTGAGCACAAAGCTGAGGAGCCTATG-
1 -GTAAGGACTTACCCTGAGCACAAAGCTGAGGAACC--TGC
* * *
3468145 GTAAGCACTTTCCCTGAGCAAAAAGC
1 GTAAGGACTTACCCTGAGCACAAAGC
3468171 CAAGGAGCAT
Statistics
Matches: 113, Mismatches: 23, Indels: 13
0.76 0.15 0.09
Matches are distributed among these distances:
38 26 0.23
39 85 0.75
41 2 0.02
ACGTcount: A:0.33, C:0.25, G:0.25, T:0.17
Consensus pattern (38 bp):
GTAAGGACTTACCCTGAGCACAAAGCTGAGGAACCTGC
Found at i:3469068 original size:17 final size:17
Alignment explanation
Indices: 3469046--3469088 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
3469036 TTGCGCCTCG
*
3469046 AATTTAGTTAAAATTTC
1 AATTTAGTCAAAATTTC
3469063 AATTTAGTCAAAATTTC
1 AATTTAGTCAAAATTTC
3469080 AATTTAGTC
1 AATTTAGTC
3469089 CTCGAAAGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.40, C:0.09, G:0.07, T:0.44
Consensus pattern (17 bp):
AATTTAGTCAAAATTTC
Found at i:3471148 original size:21 final size:22
Alignment explanation
Indices: 3471124--3471164 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
3471114 TTCATCCAGT
3471124 TTCTTTCCAT-TTTCTCTTTCA
1 TTCTTTCCATGTTTCTCTTTCA
**
3471145 TTCTTTGTATGTTTCTCTTT
1 TTCTTTCCATGTTTCTCTTT
3471165 TAAATTGACT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.07, C:0.22, G:0.05, T:0.66
Consensus pattern (22 bp):
TTCTTTCCATGTTTCTCTTTCA
Found at i:3475761 original size:3 final size:3
Alignment explanation
Indices: 3475746--3475806 Score: 54
Period size: 3 Copynumber: 19.3 Consensus size: 3
3475736 TGCCTACAGA
*
3475746 AAT AAT -AT AAAT AAT -AT AAAT AAA AAT AAT AATT AACT AAT AAT AATT
1 AAT AAT AAT -AAT AAT AAT -AAT AAT AAT AAT AA-T AA-T AAT AAT AA-T
3475794 AAT AAT AAT AAT A
1 AAT AAT AAT AAT A
3475807 GCAAGATCTT
Statistics
Matches: 49, Mismatches: 3, Indels: 12
0.77 0.05 0.19
Matches are distributed among these distances:
2 4 0.08
3 32 0.65
4 13 0.27
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:3475789 original size:14 final size:13
Alignment explanation
Indices: 3475746--3475805 Score: 70
Period size: 13 Copynumber: 4.7 Consensus size: 13
3475736 TGCCTACAGA
*
3475746 AATAAT-ATAAAT
1 AATAATAATTAAT
* *
3475758 AAT-ATAAATAAA
1 AATAATAATTAAT
3475770 AATAATAATTAACT
1 AATAATAATTAA-T
3475784 AATAATAATTAAT
1 AATAATAATTAAT
3475797 AATAATAAT
1 AATAATAAT
3475806 AGCAAGATCT
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
11 2 0.05
12 9 0.22
13 17 0.43
14 12 0.30
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (13 bp):
AATAATAATTAAT
Found at i:3476341 original size:132 final size:131
Alignment explanation
Indices: 3476109--3476572 Score: 452
Period size: 132 Copynumber: 3.5 Consensus size: 131
3476099 TTCATTATTA
* * * * * * * *
3476109 CTCAGGGAAGATCAAATTTGAAAAAAG-GATATGCTCCACTGCTCTTCA-GGTATATCAGATCTA
1 CTCAGGGAAGATCAAATATGGAGAAAGAGATCTGCTCCGCTGCTCTTTAGGGTAGATCAGATCTG
* * * * ** * * *
3476172 AAAATGTTGAATAATTCCACTACCTT-TT-AGGGAAGATTGAATCGAGGCAGACTCGTTCCACTG
66 GAAATGTTGATTCACTCCA-T-TGTTCTTCAAGGAAGATTGAATCAAGGCAGACTTGTTCCACTG
3476235 CTC
129 CTC
* * * *
3476238 CTCAGGGAAGATCAAATCTAGAGAAAGTAGATCTGCTCCGCTGCACTTTAGGTTAGATCAGATCT
1 CTCAGGGAAGATCAAATATGGAGAAAG-AGATCTGCTCCGCTGCTCTTTAGGGTAGATCAGATCT
* *
3476303 GGAAATGTTGATTCATTCCATTGTTCTTCAAGGAAGATTGAATCAAGGCAAACTTGTTCCACTGC
65 GGAAATGTTGATTCACTCCATTGTTCTTCAAGGAAGATTGAATCAAGGCAGACTTGTTCCACTGC
3476368 TC
130 TC
* * * * * *
3476370 CTTAGAGAAGATCAAATATGGAAAAAGGGTATCTGCTCCGCTACTCTTTAGGGTAAATCAGATCT
1 CTCAGGGAAGATCAAATATGGAGAAAGAG-ATCTGCTCCGCTGCTCTTTAGGGTAGATCAGATCT
* * * * * * * **
3476435 AGAAACGTTGATTCACTCCATTTTTTTTCAA-GATAGATTTAATCAAGGTAGATTTAATCCACTG
65 GGAAATGTTGATTCACTCCATTGTTCTTCAAGGA-AGATTGAATCAAGGCAGACTTGTTCCACTG
3476499 CTC
129 CTC
* * ** *
3476502 TTCAGGGAAGATCAAATATGGAGAAAGAGGATCTGTTATGCTGCTCTTTAGGGTAGATCATATCT
1 CTCAGGGAAGATCAAATATGGAGAAAGA-GATCTGCTCCGCTGCTCTTTAGGGTAGATCAGATCT
3476567 GGAAAT
65 GGAAAT
3476573 TAAACATTAC
Statistics
Matches: 273, Mismatches: 54, Indels: 13
0.80 0.16 0.04
Matches are distributed among these distances:
129 23 0.08
130 2 0.01
131 23 0.08
132 224 0.82
133 1 0.00
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Consensus pattern (131 bp):
CTCAGGGAAGATCAAATATGGAGAAAGAGATCTGCTCCGCTGCTCTTTAGGGTAGATCAGATCTG
GAAATGTTGATTCACTCCATTGTTCTTCAAGGAAGATTGAATCAAGGCAGACTTGTTCCACTGCT
C
Found at i:3476480 original size:15 final size:15
Alignment explanation
Indices: 3476462--3476493 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
3476452 CCATTTTTTT
3476462 TCAAGATAGATTTAA
1 TCAAGATAGATTTAA
*
3476477 TCAAGGTAGATTTAA
1 TCAAGATAGATTTAA
3476492 TC
1 TC
3476494 CACTGCTCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.41, C:0.09, G:0.16, T:0.34
Consensus pattern (15 bp):
TCAAGATAGATTTAA
Found at i:3477181 original size:41 final size:41
Alignment explanation
Indices: 3477121--3477227 Score: 119
Period size: 42 Copynumber: 2.6 Consensus size: 41
3477111 GCCCGAAGGT
* * *
3477121 CTTATGGATGACCCGAATGACTTA-TCATCTTGCTTTAAAGA
1 CTTAT-GATGACCCAAATGACTTAGTCATCATGCTTGAAAGA
3477162 CTTATAGATGACCCAAATGA-TATAGTCATCATGCTTGAAAGA
1 CTTAT-GATGACCCAAATGACT-TAGTCATCATGCTTGAAAGA
* *
3477204 CTTACTGATGGCCCAAAGGACTTA
1 CTTA-TGATGACCCAAATGACTTA
3477228 CTTAGTAAGA
Statistics
Matches: 56, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
40 1 0.02
41 20 0.36
42 33 0.59
43 2 0.04
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.30
Consensus pattern (41 bp):
CTTATGATGACCCAAATGACTTAGTCATCATGCTTGAAAGA
Found at i:3477372 original size:179 final size:177
Alignment explanation
Indices: 3477049--3477419 Score: 476
Period size: 179 Copynumber: 2.1 Consensus size: 177
3477039 TTTTTGAAAA
* * * * *
3477049 TACTAAATGAGAAACTTTGAAAATTACTTTCTCATTTTTCAAAAATCCTTTGAAAACATAATGCC
1 TACTAAGTAAGAAACTTTGAAAATCACTTTCTCATTTTTCAAAAATCATGTGAAAACATAATGCC
* * * **
3477114 CGAAGGTCTTATGGATGACCCGAATGACTTATCATCTTGCTTTAAAGACTTATAGATGACCCAAA
66 CAAAGGTCTTATAGATGACCCGAATGACTTATCACCTTGCTCAAAAGACTTATAGATGACCCAAA
* * *
3477179 TGATATAGTCATCATGCTTGAAAGACTTACTGATGGCCC-AAAGGACT
131 GGATATAATCATCATGCTTGAAAGACTTAATGATGGCCCGAAA-GACT
* * * *
3477226 TACTTAGTAAGAAACTTTGGAAATCATTTTCTCATTTATTTCAAAAATCATGTGAAAACATCATG
1 TACTAAGTAAGAAACTTTGAAAATCACTTTCTCA-TT-TTTCAAAAATCATGTGAAAACATAATG
* * * *
3477291 CCTAAAGGTCTTATAGATGGCCCGAA-GAACTTATCACCTTGCTCAAAATACTTATAGATGACCT
64 CCCAAAGGTCTTATAGATGACCCGAATG-ACTTATCACCTTGCTCAAAAGACTTATAGATGACCC
** *
3477355 GCAGGATTTAATCATCATGCTTGAAAGACTTAATGATGGCCCGAAAGACT
128 AAAGGATATAATCATCATGCTTGAAAGACTTAATGATGGCCCGAAAGACT
3477405 TACTAAGTAAGAAAC
1 TACTAAGTAAGAAAC
3477420 CTTAAAAAAT
Statistics
Matches: 165, Mismatches: 25, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
177 28 0.17
178 3 0.02
179 131 0.79
180 3 0.02
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.30
Consensus pattern (177 bp):
TACTAAGTAAGAAACTTTGAAAATCACTTTCTCATTTTTCAAAAATCATGTGAAAACATAATGCC
CAAAGGTCTTATAGATGACCCGAATGACTTATCACCTTGCTCAAAAGACTTATAGATGACCCAAA
GGATATAATCATCATGCTTGAAAGACTTAATGATGGCCCGAAAGACT
Found at i:3485578 original size:6 final size:7
Alignment explanation
Indices: 3485559--3485583 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
3485549 GTGTAGGACC
3485559 TATTTTT
1 TATTTTT
3485566 TATTTTT
1 TATTTTT
3485573 TATTTTT
1 TATTTTT
3485580 TATT
1 TATT
3485584 ATTAATATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (7 bp):
TATTTTT
Found at i:3487624 original size:20 final size:20
Alignment explanation
Indices: 3487599--3487647 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
3487589 TTTTCCGAAT
3487599 TCGCAACACGAATCTGTAAA
1 TCGCAACACGAATCTGTAAA
* * *
3487619 TCGCAACGCGAATTTGTAAT
1 TCGCAACACGAATCTGTAAA
3487639 TCGCAACAC
1 TCGCAACAC
3487648 ATAAGTCAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.35, C:0.27, G:0.16, T:0.22
Consensus pattern (20 bp):
TCGCAACACGAATCTGTAAA
Found at i:3488239 original size:19 final size:20
Alignment explanation
Indices: 3488211--3488254 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
3488201 GAAACTTATT
*
3488211 ATTTTTATTTT-GCGTTACG
1 ATTTTCATTTTCGCGTTACG
* *
3488230 ATTTTCATTTTCTCGTTGCG
1 ATTTTCATTTTCGCGTTACG
3488250 ATTTT
1 ATTTT
3488255 AAGTTTTAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 10 0.48
20 11 0.52
ACGTcount: A:0.14, C:0.14, G:0.14, T:0.59
Consensus pattern (20 bp):
ATTTTCATTTTCGCGTTACG
Found at i:3491920 original size:41 final size:40
Alignment explanation
Indices: 3491847--3491948 Score: 107
Period size: 41 Copynumber: 2.5 Consensus size: 40
3491837 GCGAATTCGA
* * *
3491847 AAATCGAGTTACGATTTTCCAAATTCACGTTGTAAATTCAG
1 AAATCGAGTTGCGAATTT-GAAATTCACGTTGTAAATTCAG
* * **
3491888 AAATCGAGTTGCGAATTTGAAATTCAGTGTTGTGAATTTGG
1 AAATCGAGTTGCGAATTTGAAATTCA-CGTTGTAAATTCAG
3491929 AAATCGTA-TTGCGAATTTGA
1 AAATCG-AGTTGCGAATTTGA
3491949 CTTGTGTTGT
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
40 7 0.13
41 44 0.85
42 1 0.02
ACGTcount: A:0.32, C:0.12, G:0.21, T:0.35
Consensus pattern (40 bp):
AAATCGAGTTGCGAATTTGAAATTCACGTTGTAAATTCAG
Found at i:3491946 original size:20 final size:20
Alignment explanation
Indices: 3491887--3491947 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
3491877 TGTAAATTCA
3491887 GAAATCG-AGTTGCGAATTT-
1 GAAATCGTA-TTGCGAATTTG
* *
3491906 GAAATTCAGTGTTGTGAATTTG
1 GAAA-TC-GTATTGCGAATTTG
3491928 GAAATCGTATTGCGAATTTG
1 GAAATCGTATTGCGAATTTG
3491948 ACTTGTGTTG
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
19 4 0.12
20 14 0.41
21 12 0.35
22 4 0.12
ACGTcount: A:0.30, C:0.08, G:0.26, T:0.36
Consensus pattern (20 bp):
GAAATCGTATTGCGAATTTG
Found at i:3491978 original size:38 final size:40
Alignment explanation
Indices: 3491888--3492028 Score: 98
Period size: 40 Copynumber: 3.5 Consensus size: 40
3491878 GTAAATTCAG
**
3491888 AAATCG-AGTTGCGAATTTGAAATTCAGTGTTGTGAATTTGG
1 AAATCGCA-TTGCGAATTTGAAATT-AGTGTTGTGAATTTAC
* *
3491929 AAATCGTATTGCGAATTTG-ACTT-GTGTTGTGAA-TTAC
1 AAATCGCATTGCGAATTTGAAATTAGTGTTGTGAATTTAC
* * **
3491966 AAATTCGCATTGCG-ATTT-ACATATTCGCGTTACG-ATTTAC
1 AAA-TCGCATTGCGAATTTGA-A-ATTAGTGTTGTGAATTTAC
*
3492006 ATATTCGCATTGCGAATTTGAAA
1 A-AATCGCATTGCGAATTTGAAA
3492029 ACCGCATTGC
Statistics
Matches: 81, Mismatches: 9, Indels: 21
0.73 0.08 0.19
Matches are distributed among these distances:
37 9 0.11
38 20 0.25
39 3 0.04
40 24 0.30
41 23 0.28
42 2 0.02
ACGTcount: A:0.29, C:0.13, G:0.21, T:0.38
Consensus pattern (40 bp):
AAATCGCATTGCGAATTTGAAATTAGTGTTGTGAATTTAC
Found at i:3491991 original size:20 final size:20
Alignment explanation
Indices: 3491962--3492020 Score: 91
Period size: 20 Copynumber: 3.0 Consensus size: 20
3491952 GTGTTGTGAA
*
3491962 TTACAAATTCGCATTGCGAT
1 TTACATATTCGCATTGCGAT
* *
3491982 TTACATATTCGCGTTACGAT
1 TTACATATTCGCATTGCGAT
3492002 TTACATATTCGCATTGCGA
1 TTACATATTCGCATTGCGA
3492021 ATTTGAAAAC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.27, C:0.20, G:0.15, T:0.37
Consensus pattern (20 bp):
TTACATATTCGCATTGCGAT
Found at i:3492071 original size:21 final size:21
Alignment explanation
Indices: 3492010--3492123 Score: 151
Period size: 21 Copynumber: 5.5 Consensus size: 21
3492000 ATTTACATAT
3492010 TCGCATTGCGAATTT-GAAAA
1 TCGCATTGCGAATTTGGAAAA
*
3492030 CCGCATTGCGAATTT-GAAAA
1 TCGCATTGCGAATTTGGAAAA
*
3492050 TCGCGTTGCGAATTTGGAAAA
1 TCGCATTGCGAATTTGGAAAA
* *
3492071 TCGCAATGCGAATTCGGAAAA
1 TCGCATTGCGAATTTGGAAAA
* *
3492092 TCGCAATGCGAATTCGGAAAA
1 TCGCATTGCGAATTTGGAAAA
*
3492113 TCGCAATGCGA
1 TCGCATTGCGA
3492124 TTTACATATT
Statistics
Matches: 87, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
20 32 0.37
21 55 0.63
ACGTcount: A:0.34, C:0.18, G:0.24, T:0.24
Consensus pattern (21 bp):
TCGCATTGCGAATTTGGAAAA
Found at i:3493855 original size:20 final size:20
Alignment explanation
Indices: 3493830--3493881 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
3493820 GATTGAAGTA
*
3493830 GTATCGATACTGATGTGT-AG
1 GTATCGATACTGA-GAGTAAG
*
3493850 GTATCGATACCGAGAGTAAG
1 GTATCGATACTGAGAGTAAG
*
3493870 GTACCGATACTG
1 GTATCGATACTG
3493882 TAATTGAAGA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 3 0.11
20 24 0.89
ACGTcount: A:0.29, C:0.15, G:0.29, T:0.27
Consensus pattern (20 bp):
GTATCGATACTGAGAGTAAG
Found at i:3494366 original size:15 final size:15
Alignment explanation
Indices: 3494346--3494400 Score: 58
Period size: 15 Copynumber: 3.7 Consensus size: 15
3494336 ATTTTATTAG
*
3494346 TATGTGAATGTGTTA
1 TATGTGAATATGTTA
*
3494361 TATGTGAATATGTTC
1 TATGTGAATATGTTA
* *
3494376 TACGTGGAA-ATGTTT
1 TATGT-GAATATGTTA
3494391 TATGTGAATA
1 TATGTGAATA
3494401 AAAGATACTT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
14 3 0.09
15 27 0.82
16 3 0.09
ACGTcount: A:0.29, C:0.04, G:0.24, T:0.44
Consensus pattern (15 bp):
TATGTGAATATGTTA
Found at i:3494582 original size:24 final size:24
Alignment explanation
Indices: 3494555--3494602 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
3494545 ATAAATATAT
* *
3494555 GTGGCACTTCAGTGCATATTCTAC
1 GTGGCACATCAGTGCAAATTCTAC
3494579 GTGGCACATCAGTGCAAATTCTAC
1 GTGGCACATCAGTGCAAATTCTAC
3494603 ATGGTAGTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.29
Consensus pattern (24 bp):
GTGGCACATCAGTGCAAATTCTAC
Found at i:3501157 original size:15 final size:15
Alignment explanation
Indices: 3501137--3501218 Score: 101
Period size: 15 Copynumber: 5.5 Consensus size: 15
3501127 TTATTAGTAA
*
3501137 GTGAATATGTTATAT
1 GTGAATATGTTCTAT
*
3501152 GTGAATATGTTCTAC
1 GTGAATATGTTCTAT
* *
3501167 GTAAAAATGTTCTAT
1 GTGAATATGTTCTAT
*
3501182 GTGAAAATGTTCTAT
1 GTGAATATGTTCTAT
* *
3501197 GTGAATGTATTCTAT
1 GTGAATATGTTCTAT
3501212 GTGAATA
1 GTGAATA
3501219 AAAGATACTT
Statistics
Matches: 57, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 57 1.00
ACGTcount: A:0.33, C:0.06, G:0.20, T:0.41
Consensus pattern (15 bp):
GTGAATATGTTCTAT
Found at i:3501405 original size:24 final size:24
Alignment explanation
Indices: 3501369--3501420 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
3501359 TCGGGGCAAA
* * *
3501369 TCTATGTGGCACTTCGGTGCATAT
1 TCTACGTGACACTTCGGTGCACAT
3501393 TCTACGTGACACTTCGGTGCACAT
1 TCTACGTGACACTTCGGTGCACAT
3501417 TCTA
1 TCTA
3501421 TGCGGCAGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.19, C:0.25, G:0.21, T:0.35
Consensus pattern (24 bp):
TCTACGTGACACTTCGGTGCACAT
Found at i:3503061 original size:19 final size:19
Alignment explanation
Indices: 3503037--3503084 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
3503027 CGAAATTGGG
*
3503037 TATCGATACTGAAGTATAA
1 TATCGATACCGAAGTATAA
3503056 TATCGATACCGAAGTATAA
1 TATCGATACCGAAGTATAA
3503075 TATCGATACC
1 TATCGATACC
3503085 ATAGTGTAGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.40, C:0.17, G:0.15, T:0.29
Consensus pattern (19 bp):
TATCGATACCGAAGTATAA
Found at i:3503834 original size:23 final size:22
Alignment explanation
Indices: 3503800--3503875 Score: 91
Period size: 23 Copynumber: 3.5 Consensus size: 22
3503790 GAGTCGAGGG
*
3503800 TTCTACGCGGTCCTTCGGGACAA
1 TTCTACGTGGTCCTTCGGGAC-A
3503823 TTCTACGTGGTCCTTCGGGACA
1 TTCTACGTGGTCCTTCGGGACA
* * *
3503845 -TCTATGTGGTCTTTTGGGACA
1 TTCTACGTGGTCCTTCGGGACA
*
3503866 TTCTATGTGG
1 TTCTACGTGG
3503876 CACCTCAATG
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
21 18 0.38
22 10 0.21
23 20 0.42
ACGTcount: A:0.14, C:0.22, G:0.28, T:0.36
Consensus pattern (22 bp):
TTCTACGTGGTCCTTCGGGACA
Found at i:3503873 original size:22 final size:22
Alignment explanation
Indices: 3503808--3503875 Score: 93
Period size: 21 Copynumber: 3.1 Consensus size: 22
3503798 GGTTCTACGC
*
3503808 GGTCCTTCGGGACAATTCTACGT
1 GGTCCTTCGGGAC-ATTCTATGT
3503831 GGTCCTTCGGGACA-TCTATGT
1 GGTCCTTCGGGACATTCTATGT
* *
3503852 GGTCTTTTGGGACATTCTATGT
1 GGTCCTTCGGGACATTCTATGT
3503874 GG
1 GG
3503876 CACCTCAATG
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
21 18 0.44
22 10 0.24
23 13 0.32
ACGTcount: A:0.15, C:0.21, G:0.29, T:0.35
Consensus pattern (22 bp):
GGTCCTTCGGGACATTCTATGT
Found at i:3507566 original size:19 final size:20
Alignment explanation
Indices: 3507528--3507566 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
3507518 CCTTTCATTC
*
3507528 CTTATTTCCTTATCACATAA
1 CTTATTTCCATATCACATAA
*
3507548 CTTATTT-CATATCATATAA
1 CTTATTTCCATATCACATAA
3507567 TCATATAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.33, C:0.21, G:0.00, T:0.46
Consensus pattern (20 bp):
CTTATTTCCATATCACATAA
Found at i:3512221 original size:57 final size:56
Alignment explanation
Indices: 3512119--3512225 Score: 133
Period size: 57 Copynumber: 1.9 Consensus size: 56
3512109 GGATACACTA
** * **
3512119 AAGGATACCTAGTGTATATGGTGGGTACGACCTTAAGTGCCATACGAGACTGTACTT
1 AAGGATACCTAGTACATATAGTGGACACGACCTTAAGTGCCATACG-GACTGTACTT
* **
3512176 AAGGATACCTAGTACATATAGTGGACACGACCTTATGTGTTATACGGACT
1 AAGGATACCTAGTACATATAGTGGACACGACCTTAAGTGCCATACGGACT
3512226 ATGGTGGACA
Statistics
Matches: 42, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
56 4 0.10
57 38 0.90
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.28
Consensus pattern (56 bp):
AAGGATACCTAGTACATATAGTGGACACGACCTTAAGTGCCATACGGACTGTACTT
Found at i:3514811 original size:56 final size:57
Alignment explanation
Indices: 3514702--3514812 Score: 163
Period size: 56 Copynumber: 2.0 Consensus size: 57
3514692 TATGCACATA
*
3514702 CCATGCATCGATGCACTGAGGATTTTATGAAAACATCGAATGCATTTGATGCATCAG
1 CCATGCATCGATGCACTGAGGATTTTATGAAAACATCGAATGCACTTGATGCATCAG
** *
3514759 CCATGCATCGATGCACTTTGGCTATTT-TG-AAACATCGAATGCACTTGATGCATC
1 CCATGCATCGATGCACTGAGGAT-TTTATGAAAACATCGAATGCACTTGATGCATC
3514813 GATGCACTAT
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
56 24 0.49
57 22 0.45
58 3 0.06
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.30
Consensus pattern (57 bp):
CCATGCATCGATGCACTGAGGATTTTATGAAAACATCGAATGCACTTGATGCATCAG
Found at i:3520925 original size:33 final size:33
Alignment explanation
Indices: 3520883--3520949 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
3520873 CCTAGTACAA
* *
3520883 ATGGTGGACACGACCTTATGTGTCATACGGATT
1 ATGGTGGACACAACCTTATGTGTCATACGAATT
3520916 ATGGTGGACACAACCTTATGTGTCATACGAATT
1 ATGGTGGACACAACCTTATGTGTCATACGAATT
3520949 A
1 A
3520950 GCACTACAGT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.30
Consensus pattern (33 bp):
ATGGTGGACACAACCTTATGTGTCATACGAATT
Found at i:3521034 original size:20 final size:20
Alignment explanation
Indices: 3521009--3521051 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
3520999 TATATTGGGC
* *
3521009 TATTGTCTATTGTTTATGGT
1 TATTGTCTATGGTATATGGT
3521029 TATTGTCTATGGTATATGGT
1 TATTGTCTATGGTATATGGT
3521049 TAT
1 TAT
3521052 GGAATAATGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.19, C:0.05, G:0.21, T:0.56
Consensus pattern (20 bp):
TATTGTCTATGGTATATGGT
Found at i:3521118 original size:46 final size:45
Alignment explanation
Indices: 3521057--3521155 Score: 153
Period size: 46 Copynumber: 2.2 Consensus size: 45
3521047 GTTATGGAAT
* * *
3521057 AATGGCAAGTGTATTGGTAAAATAAGCTTACGAGCTTATGATATTA
1 AATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGAGA-TA
*
3521103 AATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGGATA
1 AATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGAGATA
3521148 AATGGTAA
1 AATGGTAA
3521156 AAGATTTTAT
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
45 10 0.20
46 39 0.80
ACGTcount: A:0.38, C:0.07, G:0.23, T:0.31
Consensus pattern (45 bp):
AATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGAGATA
Found at i:3523242 original size:23 final size:22
Alignment explanation
Indices: 3523216--3523285 Score: 86
Period size: 23 Copynumber: 3.1 Consensus size: 22
3523206 GGTTCTGTGC
3523216 GGTCCTTCGGGACAATTCTACGT
1 GGTCCTTCGGGAC-ATTCTACGT
*
3523239 GGTCCTTCGGGACATGTCTACGC
1 GGTCCTTCGGGACAT-TCTACGT
* * *
3523262 GGTTCTTTGGGACATTCTATGT
1 GGTCCTTCGGGACATTCTACGT
3523284 GG
1 GG
3523286 CACCTCATTG
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
22 9 0.22
23 32 0.78
ACGTcount: A:0.14, C:0.23, G:0.30, T:0.33
Consensus pattern (22 bp):
GGTCCTTCGGGACATTCTACGT
Found at i:3534012 original size:14 final size:14
Alignment explanation
Indices: 3533989--3534022 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
3533979 ACTATGCTGG
3533989 GAATTGTTGTTTGA
1 GAATTGTTGTTTGA
*
3534003 GAATTTTTGTTTGA
1 GAATTGTTGTTTGA
3534017 GAATTG
1 GAATTG
3534023 AAATGAGTGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.24, C:0.00, G:0.26, T:0.50
Consensus pattern (14 bp):
GAATTGTTGTTTGA
Found at i:3535177 original size:48 final size:46
Alignment explanation
Indices: 3535066--3535187 Score: 138
Period size: 48 Copynumber: 2.6 Consensus size: 46
3535056 GTAACCATGG
*
3535066 AAATAAGCTTATGAGCTTACGGAATAATGGCAAGTATATTGAAAAAA
1 AAATAAGCTTATGAGCTTATGGAATAATGGCAAGTATATTG-AAAAA
* * * **
3535113 AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATTTTG-GTAA
1 AAATAAGCTTATGAGCTTATGGAA--T-AATGGCAAGTATATTGAAAAA
*
3535161 AAATAAGCTTATGAGCTTATGGGATAA
1 AAATAAGCTTATGAGCTTATGGAATAA
3535188 AAGGTAAGAA
Statistics
Matches: 64, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
45 2 0.03
46 1 0.02
47 22 0.34
48 24 0.38
49 1 0.02
50 14 0.22
ACGTcount: A:0.42, C:0.07, G:0.20, T:0.30
Consensus pattern (46 bp):
AAATAAGCTTATGAGCTTATGGAATAATGGCAAGTATATTGAAAAA
Found at i:3535567 original size:22 final size:22
Alignment explanation
Indices: 3535542--3535594 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
3535532 AAAGGGGTAC
*
3535542 CGATTCTCCTGCTTCAGGGAAT
1 CGATTCTCCTGCTACAGGGAAT
*
3535564 CGATTCCCCTGCTACAGGGAAT
1 CGATTCTCCTGCTACAGGGAAT
*
3535586 CAATTCTCC
1 CGATTCTCC
3535595 CACTGTTCAC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.21, C:0.32, G:0.19, T:0.28
Consensus pattern (22 bp):
CGATTCTCCTGCTACAGGGAAT
Found at i:3540463 original size:13 final size:13
Alignment explanation
Indices: 3540445--3540483 Score: 78
Period size: 13 Copynumber: 3.0 Consensus size: 13
3540435 AAGAAAGTCA
3540445 ACGGTCAACGGTC
1 ACGGTCAACGGTC
3540458 ACGGTCAACGGTC
1 ACGGTCAACGGTC
3540471 ACGGTCAACGGTC
1 ACGGTCAACGGTC
3540484 GGGTCGGGTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.23, C:0.31, G:0.31, T:0.15
Consensus pattern (13 bp):
ACGGTCAACGGTC
Found at i:3540466 original size:20 final size:20
Alignment explanation
Indices: 3540441--3540483 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 20
3540431 GTCAAAGAAA
3540441 GTCAACGGTCAACGGTCACG
1 GTCAACGGTCAACGGTCACG
3540461 GTCAACGGTC-ACGGTCAACG
1 GTCAACGGTCAACGGTC-ACG
3540481 GTC
1 GTC
3540484 GGGTCGGGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.23, C:0.30, G:0.30, T:0.16
Consensus pattern (20 bp):
GTCAACGGTCAACGGTCACG
Found at i:3540495 original size:17 final size:17
Alignment explanation
Indices: 3540473--3540547 Score: 132
Period size: 17 Copynumber: 4.4 Consensus size: 17
3540463 CAACGGTCAC
*
3540473 GGTCAACGGTCGGGTCG
1 GGTCAACAGTCGGGTCG
*
3540490 GGTCAACGGTCGGGTCG
1 GGTCAACAGTCGGGTCG
3540507 GGTCAACAGTCGGGTCG
1 GGTCAACAGTCGGGTCG
3540524 GGTCAACAGTCGGGTCG
1 GGTCAACAGTCGGGTCG
3540541 GGTCAAC
1 GGTCAAC
3540548 CCGGTTCAGA
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
17 57 1.00
ACGTcount: A:0.16, C:0.24, G:0.43, T:0.17
Consensus pattern (17 bp):
GGTCAACAGTCGGGTCG
Found at i:3540500 original size:7 final size:7
Alignment explanation
Indices: 3540441--3540483 Score: 72
Period size: 7 Copynumber: 6.4 Consensus size: 7
3540431 GTCAAAGAAA
3540441 GTCAACG
1 GTCAACG
3540448 GTCAACG
1 GTCAACG
3540455 GTC-ACG
1 GTCAACG
3540461 GTCAACG
1 GTCAACG
3540468 GTC-ACG
1 GTCAACG
3540474 GTCAACG
1 GTCAACG
3540481 GTC
1 GTC
3540484 GGGTCGGGTC
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
6 12 0.35
7 22 0.65
ACGTcount: A:0.23, C:0.30, G:0.30, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:3542916 original size:14 final size:14
Alignment explanation
Indices: 3542897--3542930 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
3542887 ACTATGCTGG
3542897 GAATTGTTGTTTGA
1 GAATTGTTGTTTGA
3542911 GAATTGTTGTTTGA
1 GAATTGTTGTTTGA
3542925 GAATTG
1 GAATTG
3542931 AAATGAGTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.24, C:0.00, G:0.29, T:0.47
Consensus pattern (14 bp):
GAATTGTTGTTTGA
Found at i:3552261 original size:96 final size:96
Alignment explanation
Indices: 3552086--3552269 Score: 253
Period size: 96 Copynumber: 1.9 Consensus size: 96
3552076 TAACCAGTAG
* *
3552086 ATTCCATGATCCATAAATCAGGAACAATCATATTTTCCAGTGAAAATAGGAAACCAGATAACACA
1 ATTCCATGATCCATAAATCAGGAACAATCATATTTTCCAGTGAAAACAGGAAACCAGAGAACACA
**
3552151 TTTCAGGTAACCATAGTTCATAAACTCGTAT
66 TACCAGGTAACCATAGTTCATAAACTCGTAT
* * * * *
3552182 ATTCCATGATCCATAAATCAGGAACTTAT-ATATTTTCTAGTGAAAACATGTAACCAGAGAACAT
1 ATTCCATGATCCATAAATCAGGAAC-AATCATATTTTCCAGTGAAAACAGGAAACCAGAGAACAC
* *
3552246 ATACCATGTAGCCATAGTTCATAA
65 ATACCAGGTAACCATAGTTCATAA
3552270 GCCAATAAAT
Statistics
Matches: 76, Mismatches: 11, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
96 74 0.97
97 2 0.03
ACGTcount: A:0.40, C:0.19, G:0.12, T:0.28
Consensus pattern (96 bp):
ATTCCATGATCCATAAATCAGGAACAATCATATTTTCCAGTGAAAACAGGAAACCAGAGAACACA
TACCAGGTAACCATAGTTCATAAACTCGTAT
Found at i:3559147 original size:14 final size:14
Alignment explanation
Indices: 3559128--3559160 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
3559118 ATGTCAACAG
*
3559128 GTTGACTCTAACGA
1 GTTGACTCAAACGA
3559142 GTTGACTCAAACGA
1 GTTGACTCAAACGA
3559156 GTTGA
1 GTTGA
3559161 ATCAGTTTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.27
Consensus pattern (14 bp):
GTTGACTCAAACGA
Found at i:3561389 original size:34 final size:34
Alignment explanation
Indices: 3561343--3561407 Score: 80
Period size: 34 Copynumber: 1.9 Consensus size: 34
3561333 AGGGGTTTTG
* *
3561343 GTTCTATCTTAGCCTGCT-AAAAGCTAGGGAGAAT
1 GTTCTATCTTAGCCCG-TGAAAAACTAGGGAGAAT
3561377 GTTCTAGT-TTAGCCCGTGAAAAACTAGGGAG
1 GTTCTA-TCTTAGCCCGTGAAAAACTAGGGAG
3561408 TTGTAAAGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
33 1 0.04
34 25 0.93
35 1 0.04
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.28
Consensus pattern (34 bp):
GTTCTATCTTAGCCCGTGAAAAACTAGGGAGAAT
Found at i:3564264 original size:34 final size:34
Alignment explanation
Indices: 3564225--3564289 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 34
3564215 AAGGGGTTTT
* *
3564225 GGTTCTA-TATTAGCCTGCTAAAATCTAGGGAAAA
1 GGTTCTAGT-TTAGCCCGCTAAAAACTAGGGAAAA
*
3564259 GGTTCTAGTTTAGCCCGTTAAAAACTAGGGA
1 GGTTCTAGTTTAGCCCGCTAAAAACTAGGGA
3564290 GTTGTAAAGG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
34 26 0.96
35 1 0.04
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.29
Consensus pattern (34 bp):
GGTTCTAGTTTAGCCCGCTAAAAACTAGGGAAAA
Found at i:3571238 original size:15 final size:15
Alignment explanation
Indices: 3571226--3571260 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
3571216 TGAAAATTTC
3571226 TAAAATAAAAATTAT
1 TAAAATAAAAATTAT
3571241 TAAAATAAAAATTA-
1 TAAAATAAAAATTAT
3571255 TAAAAT
1 TAAAAT
3571261 TACAATAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 6 0.30
15 14 0.70
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
TAAAATAAAAATTAT
Found at i:3571312 original size:29 final size:29
Alignment explanation
Indices: 3571252--3571351 Score: 86
Period size: 29 Copynumber: 3.6 Consensus size: 29
3571242 AAAATAAAAA
** *
3571252 TTATA-AAATTACAATAAAATTTTTAATAT
1 TTATATAAATTACAATAAAA-TTCAAATTT
3571281 TTATATAAATTACAATAAAATTCAAATTT
1 TTATATAAATTACAATAAAATTCAAATTT
* *
3571310 TTA-AT--ATTACAAT-AAATACCAAAATTA
1 TTATATAAATTACAATAAAAT-TC-AAATTT
3571337 TT-TATAAATTACAAT
1 TTATATAAATTACAAT
3571352 CAAAGAAAAA
Statistics
Matches: 60, Mismatches: 5, Indels: 12
0.78 0.06 0.16
Matches are distributed among these distances:
25 4 0.07
26 9 0.15
27 9 0.15
28 2 0.03
29 22 0.37
30 14 0.23
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (29 bp):
TTATATAAATTACAATAAAATTCAAATTT
Found at i:3571332 original size:26 final size:29
Alignment explanation
Indices: 3571284--3571351 Score: 81
Period size: 26 Copynumber: 2.4 Consensus size: 29
3571274 TTAATATTTA
*
3571284 TATAAATTACAATAAAATTC-AAATT-TT
1 TATAAATTACAATAAAATCCAAAATTATT
*
3571311 TA-ATATTACAAT-AAATACCAAAATTATT
1 TATAAATTACAATAAAAT-CCAAAATTATT
3571339 TATAAATTACAAT
1 TATAAATTACAAT
3571352 CAAAGAAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
25 4 0.12
26 10 0.29
27 7 0.21
28 4 0.12
29 9 0.26
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (29 bp):
TATAAATTACAATAAAATCCAAAATTATT
Found at i:3572912 original size:64 final size:64
Alignment explanation
Indices: 3572844--3573022 Score: 225
Period size: 64 Copynumber: 2.8 Consensus size: 64
3572834 TGGAACACTT
** * * **
3572844 AGTGCATCGGTGCACCAAGTGTGCATCGATGCATAAAATGCATTCGATGTTTGAA-AATAGCCTG
1 AGTGCATCGGTGCATAAAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAATAA-AACCCA
** * *
3572908 AGTGCATCGGTGCATTGATTGTGCATCGATGCATGAAATGCATTCGATGTTTTAATAAAACCCA
1 AGTGCATCGGTGCATAAAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAATAAAACCCA
* * *
3572972 AGTGCATCGATGCATAAAGAGTGCATCGATGCATGAAATGCATTTGATGTT
1 AGTGCATCGGTGCATAAAGTGTGCATCGATGCATGAAATGCATTCGATGTT
3573023 CAATTTATTC
Statistics
Matches: 99, Mismatches: 15, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
64 97 0.98
65 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.29
Consensus pattern (64 bp):
AGTGCATCGGTGCATAAAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAATAAAACCCA
Found at i:3573455 original size:20 final size:20
Alignment explanation
Indices: 3573430--3573471 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
3573420 ATTTCGCCCC
3573430 CTTTAAAACATTTTACACTT
1 CTTTAAAACATTTTACACTT
3573450 CTTTAAAACATTTTACACTT
1 CTTTAAAACATTTTACACTT
3573470 CT
1 CT
3573472 CCCCCTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.33, C:0.21, G:0.00, T:0.45
Consensus pattern (20 bp):
CTTTAAAACATTTTACACTT
Found at i:3581470 original size:64 final size:63
Alignment explanation
Indices: 3581402--3581580 Score: 200
Period size: 64 Copynumber: 2.8 Consensus size: 63
3581392 TGGAACACTC
* * * ***
3581402 AGTGCATCGGTGCACCAAGTGTGCATCGATGCATAAAATGCATTCGATGTTTGAA-AATAGCTTG
1 AGTGCATCGGTGCA-TAAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAATAA-AACCCA
* *
3581466 AGTGCATCGGTGCAT-TGCTTGTGCATCGATGCATGAAATGCATTCGATGTTTTAATAAAACCCA
1 AGTGCATCGGTGCATAAG--TGTGCATCGATGCATGAAATGCATTCGATGTTTGAATAAAACCCA
** *
3581530 AGTGCATCAATGCATAGAGAGTGCATCGATGCATGAAATGCATTCGATGTT
1 AGTGCATCGGTGCATA-AGTGTGCATCGATGCATGAAATGCATTCGATGTT
3581581 CAATTTATTC
Statistics
Matches: 98, Mismatches: 12, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
62 1 0.01
64 94 0.96
65 2 0.02
66 1 0.01
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.29
Consensus pattern (63 bp):
AGTGCATCGGTGCATAAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAATAAAACCCA
Found at i:3583633 original size:16 final size:16
Alignment explanation
Indices: 3583608--3583642 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
3583598 CAAACGAATC
3583608 TTTAAAATTTAATATT
1 TTTAAAATTTAATATT
* *
3583624 TTTAACATTTTATATT
1 TTTAAAATTTAATATT
3583640 TTT
1 TTT
3583643 TATTGTTTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (16 bp):
TTTAAAATTTAATATT
Found at i:3583678 original size:20 final size:21
Alignment explanation
Indices: 3583655--3583693 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
3583645 TTGTTTTCTA
*
3583655 AATATTTTA-AGTAATTATTT
1 AATATTTTAGAATAATTATTT
3583675 AATATTTTAGAATAATTAT
1 AATATTTTAGAATAATTAT
3583694 GTATTGTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (21 bp):
AATATTTTAGAATAATTATTT
Found at i:3583719 original size:30 final size:30
Alignment explanation
Indices: 3583679--3583735 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
3583669 TTATTTAATA
* * *
3583679 TTTTAGAATAATTATGTATTGTTTTATGAT
1 TTTTAAAATAATTATGTAATATTTTATGAT
*
3583709 TTTTAAAATAATTGTGTAATATTTTAT
1 TTTTAAAATAATTATGTAATATTTTAT
3583736 ACTTAAAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.33, C:0.00, G:0.11, T:0.56
Consensus pattern (30 bp):
TTTTAAAATAATTATGTAATATTTTATGAT
Found at i:3585927 original size:13 final size:14
Alignment explanation
Indices: 3585911--3585947 Score: 58
Period size: 13 Copynumber: 2.7 Consensus size: 14
3585901 TGTTTCACGT
3585911 AAAATGTTTTCC-G
1 AAAATGTTTTCCGG
*
3585924 AAAATATTTTCCGG
1 AAAATGTTTTCCGG
3585938 AAAATGTTTT
1 AAAATGTTTT
3585948 GATGGAAAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 11 0.52
14 10 0.48
ACGTcount: A:0.35, C:0.11, G:0.14, T:0.41
Consensus pattern (14 bp):
AAAATGTTTTCCGG
Found at i:3586153 original size:24 final size:23
Alignment explanation
Indices: 3586109--3586154 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 23
3586099 GAATTTAATA
3586109 TTAATAAAATATTTTAATATTATT
1 TTAATAAAATA-TTTAATATTATT
3586133 TTAATCAAAATA-TTAATTATTA
1 TTAAT-AAAATATTTAA-TATTA
3586155 AAATATTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 4 0.20
24 10 0.50
25 6 0.30
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (23 bp):
TTAATAAAATATTTAATATTATT
Found at i:3586201 original size:26 final size:24
Alignment explanation
Indices: 3586139--3586201 Score: 60
Period size: 23 Copynumber: 2.6 Consensus size: 24
3586129 TATTTTAATC
3586139 AAAATAT-TAATTATTAAAATATTT
1 AAAATATAT-ATTATTAAAATATTT
*
3586163 AAAATATAT-TTATTAATAT-TTCT
1 AAAATATATATTATTAAAATATT-T
3586186 AATAATATAATATTAT
1 AA-AATAT-ATATTAT
3586202 ATTTTTAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
22 2 0.06
23 12 0.36
24 12 0.36
25 3 0.09
26 4 0.12
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (24 bp):
AAAATATATATTATTAAAATATTT
Found at i:3586203 original size:22 final size:23
Alignment explanation
Indices: 3586173--3586219 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
3586163 AAAATATATT
3586173 TATTAATATTTCTAATAATATAA
1 TATTAATATTTCTAATAATATAA
* *
3586196 TATT-ATATTTTTAATATTATAA
1 TATTAATATTTCTAATAATATAA
3586218 TA
1 TA
3586220 AAATAATCTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 18 0.82
23 4 0.18
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (23 bp):
TATTAATATTTCTAATAATATAA
Found at i:3586232 original size:32 final size:32
Alignment explanation
Indices: 3586167--3586246 Score: 92
Period size: 32 Copynumber: 2.5 Consensus size: 32
3586157 ATATTTAAAA
* *
3586167 TATATTTATTAATATTTCTAATAATATAATAT
1 TATATTTATTAATATTTATAATAAAATAATAT
3586199 TATATTT-TTAATA-TTATAATAAAATAATCTAT
1 TATATTTATTAATATTTATAATAAAATAA--TAT
*
3586231 TATATTATAATAATAT
1 TATATT-TATTAATAT
3586247 AAGATATTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
30 12 0.30
31 6 0.15
32 16 0.40
33 1 0.03
34 5 0.12
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (32 bp):
TATATTTATTAATATTTATAATAAAATAATAT
Found at i:3586233 original size:18 final size:18
Alignment explanation
Indices: 3586210--3586244 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3586200 ATATTTTTAA
3586210 TATTATAATAAAATAATC
1 TATTATAATAAAATAATC
* *
3586228 TATTATATTATAATAAT
1 TATTATAATAAAATAAT
3586245 ATAAGATATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (18 bp):
TATTATAATAAAATAATC
Found at i:3586238 original size:23 final size:23
Alignment explanation
Indices: 3586209--3586257 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
3586199 TATATTTTTA
**
3586209 ATATTATAATAAAATAATCTATT
1 ATATTATAATAAAATAAGATATT
*
3586232 ATATTATAATAATATAAGATATT
1 ATATTATAATAAAATAAGATATT
3586255 ATA
1 ATA
3586258 CTTTTATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (23 bp):
ATATTATAATAAAATAAGATATT
Found at i:3586380 original size:27 final size:27
Alignment explanation
Indices: 3586300--3586380 Score: 69
Period size: 27 Copynumber: 3.0 Consensus size: 27
3586290 AAATAAATTT
*
3586300 ATATTATTTAT-TAATTTCATAGAAATA
1 ATATTATTTATAT-ATTTCATATAAATA
* * *
3586327 ATATTA-TTAAAT-TATTAATAATGAATA
1 ATATTATTTATATAT-TTCAT-ATAAATA
*
3586354 ATATTATTTATATATTTCATATTAATA
1 ATATTATTTATATATTTCATATAAATA
3586381 TAAAAAATAA
Statistics
Matches: 42, Mismatches: 7, Indels: 10
0.71 0.12 0.17
Matches are distributed among these distances:
25 1 0.02
26 7 0.17
27 24 0.57
28 9 0.21
29 1 0.02
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.49
Consensus pattern (27 bp):
ATATTATTTATATATTTCATATAAATA
Found at i:3587353 original size:14 final size:14
Alignment explanation
Indices: 3587334--3587383 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
3587324 AAGTCAACAG
3587334 GTTGACTC-AGACGA
1 GTTGACTCGA-ACGA
*
3587348 GTTGACTCGAATGA
1 GTTGACTCGAACGA
* *
3587362 GTTGACTTGAATGA
1 GTTGACTCGAACGA
3587376 GTTGACTC
1 GTTGACTC
3587384 AGTTCGGGTT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
14 31 0.97
15 1 0.03
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (14 bp):
GTTGACTCGAACGA
Found at i:3589825 original size:15 final size:15
Alignment explanation
Indices: 3589805--3589838 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
3589795 ATAAAAGTTA
3589805 CAATGATTATTTAGT
1 CAATGATTATTTAGT
3589820 CAATGATTATTTAGT
1 CAATGATTATTTAGT
3589835 CAAT
1 CAAT
3589839 TGTTAGAGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.35, C:0.09, G:0.12, T:0.44
Consensus pattern (15 bp):
CAATGATTATTTAGT
Found at i:3592329 original size:60 final size:60
Alignment explanation
Indices: 3592226--3592340 Score: 135
Period size: 60 Copynumber: 1.9 Consensus size: 60
3592216 ACGTTTTAGT
* * *
3592226 CTCTCATTCTAAATTGACCTCTAAACTGTTAAGTATTCTAATTTTATTTTTAAACAATGA
1 CTCTCATTCTAAATTGACCTCCAAACTGTTAAGTATTCTAATTTCATTCTTAAACAATGA
* * * *
3592286 CTCTTATTCTAAATTGATCC-CCAAACTTTTAAATTGTTC-AATTTCATTCTTAAAC
1 CTCTCATTCTAAATTGA-CCTCCAAACTGTT-AAGTATTCTAATTTCATTCTTAAAC
3592341 TATCAATATA
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
60 38 0.83
61 8 0.17
ACGTcount: A:0.32, C:0.19, G:0.05, T:0.43
Consensus pattern (60 bp):
CTCTCATTCTAAATTGACCTCCAAACTGTTAAGTATTCTAATTTCATTCTTAAACAATGA
Found at i:3596034 original size:32 final size:31
Alignment explanation
Indices: 3595993--3596114 Score: 91
Period size: 32 Copynumber: 3.8 Consensus size: 31
3595983 CCTAAGGTGA
* *
3595993 CCTTGGGTAGGCTTTGAGGCCCCAAGGCATTT
1 CCTTGGGTAGGCTCTGAGGCCCCAAGGCA-CT
* * * * *
3596025 CCTTGGGTAGACTCTAAGACCCCCAGGTACT
1 CCTTGGGTAGGCTCTGAGGCCCCAAGGCACT
* * *
3596056 CCATTGGGTAGGCTCTGAGGCCCTAGGGTACT
1 CC-TTGGGTAGGCTCTGAGGCCCCAAGGCACT
* * * *
3596088 CTATTAGGTAGGCTCTCAGGCTCCAAG
1 C-CTTGGGTAGGCTCTGAGGCCCCAAG
3596115 ATACTCCCTT
Statistics
Matches: 69, Mismatches: 19, Indels: 4
0.75 0.21 0.04
Matches are distributed among these distances:
31 3 0.04
32 66 0.96
ACGTcount: A:0.19, C:0.27, G:0.29, T:0.25
Consensus pattern (31 bp):
CCTTGGGTAGGCTCTGAGGCCCCAAGGCACT
Found at i:3596120 original size:32 final size:32
Alignment explanation
Indices: 3596052--3596134 Score: 87
Period size: 32 Copynumber: 2.6 Consensus size: 32
3596042 GACCCCCAGG
* * * *
3596052 TACTCCATTGGGTAGGCTCTGAGGCCCTAGGG
1 TACTCCATTAGGTAGGCTCTCAGGCCCTAAGA
*
3596084 TACTCTATTAGGTAGGCTCTCAGGCTCC-AAGA
1 TACTCCATTAGGTAGGCTCTCAGGC-CCTAAGA
* *
3596116 TACTCCCTTAGGTTGGCTC
1 TACTCCATTAGGTAGGCTC
3596135 CTACGCCCAA
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
32 40 0.95
33 2 0.05
ACGTcount: A:0.18, C:0.27, G:0.27, T:0.29
Consensus pattern (32 bp):
TACTCCATTAGGTAGGCTCTCAGGCCCTAAGA
Found at i:3600876 original size:15 final size:15
Alignment explanation
Indices: 3600858--3600887 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3600848 CCACGGTGCT
*
3600858 CCCGGAATCCTGCGC
1 CCCGAAATCCTGCGC
3600873 CCCGAAATCCTGCGC
1 CCCGAAATCCTGCGC
3600888 GATTGTGATA
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:0.17, C:0.47, G:0.23, T:0.13
Consensus pattern (15 bp):
CCCGAAATCCTGCGC
Found at i:3604350 original size:15 final size:15
Alignment explanation
Indices: 3604330--3604381 Score: 104
Period size: 15 Copynumber: 3.5 Consensus size: 15
3604320 TGAGACATTA
3604330 CCCGCCCCGCATCCG
1 CCCGCCCCGCATCCG
3604345 CCCGCCCCGCATCCG
1 CCCGCCCCGCATCCG
3604360 CCCGCCCCGCATCCG
1 CCCGCCCCGCATCCG
3604375 CCCGCCC
1 CCCGCCC
3604382 AACTAAATAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 37 1.00
ACGTcount: A:0.06, C:0.69, G:0.19, T:0.06
Consensus pattern (15 bp):
CCCGCCCCGCATCCG
Found at i:3604954 original size:32 final size:32
Alignment explanation
Indices: 3604918--3604994 Score: 136
Period size: 32 Copynumber: 2.4 Consensus size: 32
3604908 GGTGTGGGGA
*
3604918 TGGATTTGAAAATGTACTCGCGTGGGCGGGTG
1 TGGATTTGAAAATGTACCCGCGTGGGCGGGTG
*
3604950 TGGATTTGAAAATGTACCCTCGTGGGCGGGTG
1 TGGATTTGAAAATGTACCCGCGTGGGCGGGTG
3604982 TGGATTTGAAAAT
1 TGGATTTGAAAAT
3604995 TTGTACCCAT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 43 1.00
ACGTcount: A:0.22, C:0.12, G:0.36, T:0.30
Consensus pattern (32 bp):
TGGATTTGAAAATGTACCCGCGTGGGCGGGTG
Found at i:3605738 original size:181 final size:181
Alignment explanation
Indices: 3605208--3605867 Score: 855
Period size: 181 Copynumber: 3.6 Consensus size: 181
3605198 CGATACAAAT
*
3605208 AAAAATGTATCGATCCATAACAATATAATAGGTAAAAATATGACAAAACCGGTTTCATTATGACA
1 AAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGG-TTCATTATGACA
**
3605273 AAACCGGTAAAGCGCTACCGGATATGTTGAAAGTATCGATTAGATTGTAAT-T-AGTATCGACAC
65 AAACCGGTAAAGCGCTACCGGATATGTTGAAAGTATCGA-TACCTT-TAATATAAGTATCGACAC
* * **
3605336 TTTTGGAATTTAAAAGAGAAGCAGTAATAGCGTCAATAAAGTGTCGATAC-AAA
128 TTTTGGAATTTAAAAGAGAAGCAGTAATAGCGCCTATAAAGTGTCGATACTTTA
* * * *
3605389 TAAAAATATATTGATCCATAATAATATAACAGGGAAAAAATATGACAAAACCGGGTTCATTATGA
1 -AAAAATGTATCGATCCATAACAATATAACA-GGTAAAAATATGACAAAACC-GGTTCATTATGA
* ** * * * * * *
3605454 AAAAACCGGTAAATTGATATCGGATATGTTGAATGTCTTGATACCATTGAA-ATAAGTATCGACA
63 CAAAACCGGTAAAGCGCTACCGGATATGTTGAAAGTATCGATACC-TTTAATATAAGTATCGACA
*
3605518 CTTTTGGAATTTAAAAGAGAAACAGTAATAGCGCCTATAAAGTGTCGATACTTTA
127 CTTTTGGAATTTAAAAGAGAAGCAGTAATAGCGCCTATAAAGTGTCGATACTTTA
* *
3605573 AAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAGCAGGTATCATTATGACA
1 AAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGT-TCATTATGACA
3605638 AAACCGGTAAAGCGCTACCGGATATGTTGAAAGTATCGATA-CTTTAATATAAGTATCGACACTT
65 AAACCGGTAAAGCGCTACCGGATATGTTGAAAGTATCGATACCTTTAATATAAGTATCGACACTT
** *
3605702 TTGGAATTTAAAAGAGAAGTTGTAATAGCACCTATAAAGTGTCGATACTTTA
130 TTGGAATTTAAAAGAGAAGCAGTAATAGCGCCTATAAAGTGTCGATACTTTA
* * * ** *
3605754 TAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGATAAAACCGGTCTCAAAATGATA
1 AAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGT-TCATTATGACA
* * * * * *
3605819 AAACTGGTAAAGAGCTATCGGATATATTAAAAGTGTCGATA-CTTTAATA
65 AAACCGGTAAAGCGCTACCGGATATGTTGAAAGTATCGATACCTTTAATA
3605868 AGTACGCGTA
Statistics
Matches: 415, Mismatches: 55, Indels: 17
0.85 0.11 0.03
Matches are distributed among these distances:
180 4 0.01
181 167 0.40
182 92 0.22
183 149 0.36
184 3 0.01
ACGTcount: A:0.43, C:0.13, G:0.17, T:0.28
Consensus pattern (181 bp):
AAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGTTCATTATGACAA
AACCGGTAAAGCGCTACCGGATATGTTGAAAGTATCGATACCTTTAATATAAGTATCGACACTTT
TGGAATTTAAAAGAGAAGCAGTAATAGCGCCTATAAAGTGTCGATACTTTA
Found at i:3608292 original size:66 final size:66
Alignment explanation
Indices: 3608164--3608292 Score: 152
Period size: 66 Copynumber: 2.0 Consensus size: 66
3608154 GGGGAAGTGG
* ** * *
3608164 GTGGAAAAATAGATGGAGTGATGAAAGAAGTTGAGGTGTTGAGGGGTGAACTTAAGATGGTGACG
1 GTGGAAAAATAGATGGAATGATGAAAGAAGTTGAGGAATTGAGGAGTGAACTTAAGAGGGTGACG
3608229 T
66 T
* * * * *
3608230 GTGGAAAAATTGATGGAATGGTGAAGGAAGTT-ATGGAATTGAGGAGTGAACTTATGGGGGTGA
1 GTGGAAAAATAGATGGAATGATGAAAGAAGTTGA-GGAATTGAGGAGTGAACTTAAGAGGGTGA
3608293 AGGGGGTGGT
Statistics
Matches: 52, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
65 1 0.02
66 51 0.98
ACGTcount: A:0.33, C:0.02, G:0.40, T:0.25
Consensus pattern (66 bp):
GTGGAAAAATAGATGGAATGATGAAAGAAGTTGAGGAATTGAGGAGTGAACTTAAGAGGGTGACG
T
Found at i:3608454 original size:158 final size:158
Alignment explanation
Indices: 3608257--3608576 Score: 534
Period size: 158 Copynumber: 2.0 Consensus size: 158
3608247 ATGGTGAAGG
**
3608257 AAGTTATGGAATTGAGGAGTGAACTTATGGGGGTGAAGGGGGTGGTTGATAAAAAGTGGGATGAA
1 AAGTTATGGAATTGAGGAGTGAACTTACAGGGGTGAAGGGGGTGGTTGATAAAAAGTGGGATGAA
* * *
3608322 TGGG-AAAAATGAAGGGTGAAATAAATGTGATGAAGAGCTATGTAGAGGAAAAATACGATGAATT
66 -GGGAAAAAATAAAGGGTGAAATAAATGCGAAGAAGAGCTATGTAGAGGAAAAATACGATGAATT
*
3608386 GAAAAAATATGAAGAACTAAAGATGGAGA
130 GAAAAAATATGAAGAACAAAAGATGGAGA
* *
3608415 AAGTTGTGGAATTGAGGAGTTAACTTACAGGGGTGAAGGGGGTGGTTGATAAAAAGTGGGATGAA
1 AAGTTATGGAATTGAGGAGTGAACTTACAGGGGTGAAGGGGGTGGTTGATAAAAAGTGGGATGAA
*
3608480 GGGAAAAAATAAAGGGTGAAATAAATGCGAAGAAGAGCTATGTATAGGAAAAATACGATGAATTG
66 GGGAAAAAATAAAGGGTGAAATAAATGCGAAGAAGAGCTATGTAGAGGAAAAATACGATGAATTG
*
3608545 AAAAAATATGAAGAACAAAAGATGGAGG
131 AAAAAATATGAAGAACAAAAGATGGAGA
3608573 AAGT
1 AAGT
3608577 GAGGAGGAAG
Statistics
Matches: 151, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
157 3 0.02
158 148 0.98
ACGTcount: A:0.43, C:0.03, G:0.33, T:0.21
Consensus pattern (158 bp):
AAGTTATGGAATTGAGGAGTGAACTTACAGGGGTGAAGGGGGTGGTTGATAAAAAGTGGGATGAA
GGGAAAAAATAAAGGGTGAAATAAATGCGAAGAAGAGCTATGTAGAGGAAAAATACGATGAATTG
AAAAAATATGAAGAACAAAAGATGGAGA
Found at i:3611407 original size:21 final size:21
Alignment explanation
Indices: 3611381--3611425 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
3611371 GATTATTTCC
3611381 CTTCTCAATCACCCATGGATG
1 CTTCTCAATCACCCATGGATG
*
3611402 CTTCTCAATCACCCATTGATG
1 CTTCTCAATCACCCATGGATG
3611423 CTT
1 CTT
3611426 TTCGACATTG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.22, C:0.33, G:0.11, T:0.33
Consensus pattern (21 bp):
CTTCTCAATCACCCATGGATG
Found at i:3613161 original size:171 final size:171
Alignment explanation
Indices: 3612871--3613212 Score: 558
Period size: 171 Copynumber: 2.0 Consensus size: 171
3612861 TATACCAGTT
* * * * * *
3612871 TTATGAGAAAATAGGTCTACATAATGTATCGACATTTTTTAAATTTGTGTCGATATTTTTTGTTC
1 TTATAAGAAAATAGGTCTACATAATGTATCAACACTTTTTAAATTTGTGTCGATACTTATTGTCC
**
3612936 AGAATGAATAACAAACTAGGTGCATGCATAAAGTGTCGATACATTTAAAATTGTATCGATCCCAA
66 AGAATGAATAACAAACTAGGTGCACACATAAAGTGTCGATACATTTAAAATTGTATCGATCCCAA
* * *
3613001 AAACATCGAAACTGATAATTATAACGTAATAGGTAAATTTA
131 AAACATCAAAACCGATAATTACAACGTAATAGGTAAATTTA
3613042 TTATAAGAAAATAGGTCTACATAATGTATCAACACTTTTTAAATTTGTGTCGATACTTATTGTCC
1 TTATAAGAAAATAGGTCTACATAATGTATCAACACTTTTTAAATTTGTGTCGATACTTATTGTCC
* *
3613107 AGAATGAATGACAAACTAGGTGCACACATAAAGTGTCGATACATTTAAAATTGTATCGATCCCAG
66 AGAATGAATAACAAACTAGGTGCACACATAAAGTGTCGATACATTTAAAATTGTATCGATCCCAA
*
3613172 AAACATCAAAACCGATAATTACAATGTAATAGGTAAATTTA
131 AAACATCAAAACCGATAATTACAACGTAATAGGTAAATTTA
3613213 CAATGTAACC
Statistics
Matches: 157, Mismatches: 14, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
171 157 1.00
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.33
Consensus pattern (171 bp):
TTATAAGAAAATAGGTCTACATAATGTATCAACACTTTTTAAATTTGTGTCGATACTTATTGTCC
AGAATGAATAACAAACTAGGTGCACACATAAAGTGTCGATACATTTAAAATTGTATCGATCCCAA
AAACATCAAAACCGATAATTACAACGTAATAGGTAAATTTA
Found at i:3613468 original size:200 final size:198
Alignment explanation
Indices: 3613042--3614097 Score: 1548
Period size: 199 Copynumber: 5.3 Consensus size: 198
3613032 GGTAAATTTA
* *
3613042 TTATAAGAAAATAGGTCTACATAATGTATCAACACTTTTTAAATTTGTGTCGATACTTATTGTCC
1 TTATGAGAAAATAGGTCTACATAATGTATCGACACTTTTTAAATTTGTGTCGATACTT-TTGTCC
*
3613107 AGAATGAATGACAAACTAGGTGCACACATAAAGTGTCGATACATTTAAAATTGTATCGATCCCAG
65 AGAATGAATGACAAACTAGGTGCACGCATAAAGTGTCGATACATTTAAAATTGTATCGATCCCAG
* * ** *
3613172 AAACATCAAAACCGATAATTACAATGTAATAGGTAAATTTACAATGTAACCTATATAAATATACT
130 AAACATCGAAACCGATAATTATAATGTAATAGGTAAATTTACAATGTAACCGGTATAAATATACC
*
3613237 GGTT
195 AGTT
*
3613241 TTATGAGAAAATAGGTCTACATAATGTATTGACACTTTTTAAATTTGTGTCGATACTATTTGTCC
1 TTATGAGAAAATAGGTCTACATAATGTATCGACACTTTTTAAATTTGTGTCGATACT-TTTGTCC
* * *
3613306 AGAATAAATGACAAACTAGGTGCACGCATAAAGTGTCGATACATTTATTAAA-AGTATCGATCCT
65 AGAATGAATGACAAACTAGGTGCACGCATAAAGTGTCGATACATTTA--AAATTGTATCGATCCC
* *
3613370 AGAAACATCGAAACTGATAATTATAATGTAATAGGTAAATTTAAAATGTAACCGGTATAAATATA
128 AGAAACATCGAAACCGATAATTATAATGTAATAGGTAAATTTACAATGTAACCGGTATAAATATA
3613435 CC-GATT
193 CCAG-TT
*
3613441 TTATGAGAAAATAGGTCTACATAATGTATCGACACTTTTTAAATTTGTGTCGATACCTTTTTTCC
1 TTATGAGAAAATAGGTCTACATAATGTATCGACACTTTTTAAATTTGTGTCGATA-CTTTTGTCC
* * *
3613506 AAAATGAATGACAAACTAGGTGCACGCATAAAATGTCGATACATTTAAAATTGTATCGATCCCAA
65 AGAATGAATGACAAACTAGGTGCACGCATAAAGTGTCGATACATTTAAAATTGTATCGATCCCAG
* * *
3613571 AAACATCGAAACCGATAATTATAATGTAATAGGTAAATTTACATTATAACCGGTATAAATATATC
130 AAACATCGAAACCGATAATTATAATGTAATAGGTAAATTTACAATGTAACCGGTATAAATATACC
3613636 AGTT
195 AGTT
* * *
3613640 TTATGAGAAAATAGGTCTACATAATGTATCAACACTTTTTTAAATTTGTGTTGATACTTTTTGTA
1 TTATGAGAAAATAGGTCTACATAATGTATCGACAC-TTTTTAAATTTGTGTCGATAC-TTTTGTC
*
3613705 CAGAATGAATGACAAACTAAGTGCACGCATAAAGTGTCGATA-ATTTAAAATTGTATCGATCCCA
64 CAGAATGAATGACAAACTAGGTGCACGCATAAAGTGTCGATACATTTAAAATTGTATCGATCCCA
* * * * * * *
3613769 TAAACATCAAAACCGATAATTATAATGTAATAAGTAAATTTATACTATAACCTGTATAAATATAC
129 GAAACATCGAAACCGATAATTATAATGTAATAGGTAAATTTACAATGTAACCGGTATAAATATAC
3613834 CAGTT
194 CAGTT
* *
3613839 TTATGAGAAAATAGGTATACATAATGTTTCGACACTTTTTAAATTTGTGTCGATA-TATTTGTCC
1 TTATGAGAAAATAGGTCTACATAATGTATCGACACTTTTTAAATTTGTGTCGATACT-TTTGTCC
* * *
3613903 AGAATAAATGACAAACTAGGTGCATGCATAACGTGTCGATACACTTATTAAAA--GTATCGATCC
65 AGAATGAATGACAAACTAGGTGCACGCATAAAGTGTCGATACA--T-TTAAAATTGTATCGATCC
* * *
3613966 TAGAAACATTGAAACCAATAATTATAATGTAATAGGTAAATTTACAATGTAACCGGTATAAATAT
127 CAGAAACATCGAAACCGATAATTATAATGTAATAGGTAAATTTACAATGTAACCGGTATAAATAT
*
3614031 ACTAGTT
192 ACCAGTT
* * * *
3614038 TTATGAGAAAACATGTCTACATAATGTATCGACACTTTTTAAATTTGTGTTGATATTTTT
1 TTATGAGAAAATAGGTCTACATAATGTATCGACACTTTTTAAATTTGTGTCGATACTTTT
3614098 TTAAAATTAC
Statistics
Matches: 776, Mismatches: 66, Indels: 30
0.89 0.08 0.03
Matches are distributed among these distances:
196 1 0.00
197 43 0.06
198 23 0.03
199 455 0.59
200 243 0.31
201 11 0.01
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.34
Consensus pattern (198 bp):
TTATGAGAAAATAGGTCTACATAATGTATCGACACTTTTTAAATTTGTGTCGATACTTTTGTCCA
GAATGAATGACAAACTAGGTGCACGCATAAAGTGTCGATACATTTAAAATTGTATCGATCCCAGA
AACATCGAAACCGATAATTATAATGTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCA
GTT
Found at i:3616897 original size:24 final size:23
Alignment explanation
Indices: 3616859--3616911 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 23
3616849 TTTCATGTTC
3616859 ATTTCATATTTAATTGGAGTTTGA
1 ATTT-ATATTTAATTGGAGTTTGA
*
3616883 ATTTATATTTCAATTTGAGTTTGA
1 ATTTATATTT-AATTGGAGTTTGA
3616907 ATTTA
1 ATTTA
3616912 AATATAAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 6 0.22
24 21 0.78
ACGTcount: A:0.30, C:0.04, G:0.13, T:0.53
Consensus pattern (23 bp):
ATTTATATTTAATTGGAGTTTGA
Found at i:3616921 original size:24 final size:24
Alignment explanation
Indices: 3616870--3616922 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
3616860 TTTCATATTT
* * * *
3616870 AATTGGAGTTTGAATTTATATTTC
1 AATTTGAGTTTGAATTTAAATATA
3616894 AATTTGAGTTTGAATTTAAATATA
1 AATTTGAGTTTGAATTTAAATATA
3616918 AATTT
1 AATTT
3616923 CGGCTCCACT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.36, C:0.02, G:0.13, T:0.49
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATA
Found at i:3618767 original size:199 final size:199
Alignment explanation
Indices: 3618364--3619723 Score: 1892
Period size: 199 Copynumber: 6.8 Consensus size: 199
3618354 AATAGGTAAA
*
3618364 CATAAAGTATCGAT-CATTTTTAAAATTGTATCGATCCC-AAAACATCGAAACCGATAATTATAA
1 CATAAAGTGTCGATACA--TTTAAAATTGTATCGATCCCAAAAACATCGAAACCGATAATTATAA
*
3618427 TGTAATAGGTAAATTTACAATGTAACCGGTAGAAATATACCA-G-TTAATTAGAAAATAGATCAA
64 TGTAATAGGTAAATTTACAATGTAACCGGTAGAAATATA-CATGTTTAATTAGAAAATAGGTCAA
* * * **
3618490 CATAATGTATCAACACTTTCTAAATTTGTATCGATACTTTTTGTTCAGAATGAATATCCAACGAG
128 CATAATGTATCGACACTTTCTAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAACGAG
3618555 GTGCACG
193 GTGCACG
*
3618562 CATAAAGTGTCGATACATTTAAAATTGTATCGATCCCAAAAACATCGAAACCGATAATTACAATG
1 CATAAAGTGTCGATACATTTAAAATTGTATCGATCCCAAAAACATCGAAACCGATAATTATAATG
* * *
3618627 TAATAGGTAAATTTACAATGTAACCGGTAGAAATATACATGTTTTATGAGAAAATAGGTCTACAT
66 TAATAGGTAAATTTACAATGTAACCGGTAGAAATATACATGTTTAATTAGAAAATAGGTCAACAT
*
3618692 AATGTATCGACACTTTCTAAATTTGTGTCGATA-TGTTTTGTCTAGAATGAATGCCCAACGAGGT
131 AATGTATCGACACTTTCTAAATTTGTGTCGATACT-TTTTGTCCAGAATGAATGCCCAACGAGGT
3618756 GCACG
195 GCACG
*
3618761 CATAAAGTGTCGATACATTTAAAATTGTATCGATCCCAAAAACATCGAAACCTATAATTATAATG
1 CATAAAGTGTCGATACATTTAAAATTGTATCGATCCCAAAAACATCGAAACCGATAATTATAATG
* * * * * *
3618826 TAATAGGTAAATTTACAATATAACCAGTAGAAATATACAGGCATT-ATGAGAAAATAGGTCCACA
66 TAATAGGTAAATTTACAATGTAACCGGTAGAAATATACATG-TTTAATTAGAAAATAGGTCAACA
*
3618890 TAATGTATCGACACTTTCTAAATTTGTGTCGATACTTTTTGTCCATAATGAATGCCCAACGAGGT
130 TAATGTATCGACACTTTCTAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAACGAGGT
3618955 GCACG
195 GCACG
** * ** *
3618960 CATAAAGTGTCGATACATTTAAAATTGTATCGATATCAAAACCATCGAAACTTATAATTATACTG
1 CATAAAGTGTCGATACATTTAAAATTGTATCGATCCCAAAAACATCGAAACCGATAATTATAATG
* * * *
3619025 TAATAGGTAAATTTACAATGTAACCGATAGAAATATAC-TAGTTTTATGAGAAAATAGGTCCACA
66 TAATAGGTAAATTTACAATGTAACCGGTAGAAATATACAT-GTTTAATTAGAAAATAGGTCAACA
* * *
3619089 TAATGTATCGACACTTTTTAAATTTGTGTCGATACTTTTTGTCCACAATGAATGCCCAAAGAGGT
130 TAATGTATCGACACTTTCTAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAACGAGGT
*
3619154 GCATG
195 GCACG
* * *
3619159 CATAAAGTGTCGATACATTTAAAATTGTATCGATCCCAAAAACATCGAATCTGATAATTATAATT
1 CATAAAGTGTCGATACATTTAAAATTGTATCGATCCCAAAAACATCGAAACCGATAATTATAATG
*
3619224 TAATATGTAAATTTACAATGTAACCGGTAGAAATATACCA-G-TTAATTAGAAAATAGGTCAACA
66 TAATAGGTAAATTTACAATGTAACCGGTAGAAATATA-CATGTTTAATTAGAAAATAGGTCAACA
* * * * *
3619287 TAATGTATCGATACTTT-TTAATTTGTGTCGATACTTTTTGTCCATAATGAATGTCAAACGA-GT
130 TAATGTATCGACACTTTCTAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAACGAGGT
3619350 GCACG
195 GCACG
* * *
3619355 CATAAAGTGTCGTTACATTTATTAAA-AGTATCGATCCAAAAAACATCGAAACTC-ATAATTATA
1 CATAAAGTGTCGATACATTTA--AAATTGTATCGATCCCAAAAACATCGAAAC-CGATAATTATA
* * * *
3619418 ATGTAATAGGTAAATATACAATGTAACCGGTAGAAATAT--ATCGGTTAATTAGAAAATATGCCA
63 ATGTAATAGGTAAATTTACAATGTAACCGGTAGAAATATACAT-GTTTAATTAGAAAATAGGTCA
* *
3619481 ACATAATGTATCGATACATTT-TAAAATTT-TGTCGATACTTTTTGTCCAGAATGAATGCCAAAC
127 ACATAATGTATCGACAC-TTTCT-AAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAC
*
3619544 GAGGTGCACA
190 GAGGTGCACG
* * *
3619554 CATAAAGTGTCGATACATTTATTAATAGTATCGATCCCAAAAACACCGAAACAC-ATAATTATAA
1 CATAAAGTGTCGATACATTTA-AAATTGTATCGATCCCAAAAACATCGAAAC-CGATAATTATAA
** **
3619618 TGTAATAGGTAAATTTACAATGTAACCGGTAGAAATATACCGGTTTAATTAGAAAATAATTCAAC
64 TGTAATAGGTAAATTTACAATGTAACCGGTAGAAATATACATGTTTAATTAGAAAATAGGTCAAC
* * *
3619683 ATAATGTATCGACACTTTTTAAATTTGTATCGATATTTTTT
129 ATAATGTATCGACACTTTCTAAATTTGTGTCGATACTTTTT
3619724 TAAAATTATG
Statistics
Matches: 1054, Mismatches: 83, Indels: 48
0.89 0.07 0.04
Matches are distributed among these distances:
194 1 0.00
196 27 0.03
197 163 0.15
198 159 0.15
199 654 0.62
200 50 0.05
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.32
Consensus pattern (199 bp):
CATAAAGTGTCGATACATTTAAAATTGTATCGATCCCAAAAACATCGAAACCGATAATTATAATG
TAATAGGTAAATTTACAATGTAACCGGTAGAAATATACATGTTTAATTAGAAAATAGGTCAACAT
AATGTATCGACACTTTCTAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAACGAGGTG
CACG
Found at i:3622093 original size:23 final size:23
Alignment explanation
Indices: 3622067--3622117 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
3622057 TAAGTAATTA
**
3622067 ACCTATTTTATTATATAAGCGCT
1 ACCTATTACATTATATAAGCGCT
*
3622090 ACCTATTACGTTATATAAGCGCT
1 ACCTATTACATTATATAAGCGCT
3622113 ACCTA
1 ACCTA
3622118 ATATGTTATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.31, C:0.22, G:0.10, T:0.37
Consensus pattern (23 bp):
ACCTATTACATTATATAAGCGCT
Found at i:3622125 original size:23 final size:23
Alignment explanation
Indices: 3622077--3622126 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
3622067 ACCTATTTTA
*
3622077 TTATATAAGCGCTACCTATTACG
1 TTATATAAGCGCTACCTAATACG
*
3622100 TTATATAAGCGCTACCTAATATG
1 TTATATAAGCGCTACCTAATACG
3622123 TTAT
1 TTAT
3622127 TGTGCTTGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.32, C:0.18, G:0.12, T:0.38
Consensus pattern (23 bp):
TTATATAAGCGCTACCTAATACG
Found at i:3622191 original size:158 final size:158
Alignment explanation
Indices: 3621922--3622455 Score: 825
Period size: 158 Copynumber: 3.4 Consensus size: 158
3621912 ATCAGCTTTA
* * * * *
3621922 ATAATGCGCAACCTATTACGTTACATAAGCTCTACCTAATATGTTATTATGCTTGATAATATTTC
1 ATAA-GCGCTACCTATTACGTTATATAAGCGCTACCTAATATGTTATTGTGCTTGATAATGTTTC
* * * * * *
3621987 CATTAAATAACCGGTTATGCTATCATTGGTAACATTTTAGGTGTTTACCTAATATGTTGTAATAA
65 CAGTAAATAACCGGATATGTTATCCTTGGTAACATTTTAAGCGTTTACCTAATATGTTGTAATAA
3622052 CAAATTAAGTAATTAACCTATTTTATTAT
130 CAAATTAAGTAATTAACCTATTTTATTAT
*
3622081 ATAAGCGCTACCTATTACGTTATATAAGCGCTACCTAATATGTTATTGTGCTTGATAATGTTTCT
1 ATAAGCGCTACCTATTACGTTATATAAGCGCTACCTAATATGTTATTGTGCTTGATAATGTTTCC
*
3622146 AGTAAATAACCGGATATGTTATCCTTGGTAACATTTTATGCGTTTACCTAATATGTTGTAATAAC
66 AGTAAATAACCGGATATGTTATCCTTGGTAACATTTTAAGCGTTTACCTAATATGTTGTAATAAC
3622211 AAATTAAGTAATTAACCTATTTTATTAT
131 AAATTAAGTAATTAACCTATTTTATTAT
*
3622239 ATAAGCGCTACTTATTACGTTATATAAGCGCTACCTAATATGTTATTGTGCTTGATAATGTTTCC
1 ATAAGCGCTACCTATTACGTTATATAAGCGCTACCTAATATGTTATTGTGCTTGATAATGTTTCC
* ** * *
3622304 AGTAATTAATTGGCTATGTTATTCTTGGTAACATTTTAAGCGTTTACCTAATATGTTGTAATAAC
66 AGTAAATAACCGGATATGTTATCCTTGGTAACATTTTAAGCGTTTACCTAATATGTTGTAATAAC
* * *
3622369 AAATTAAGCAATTAAGCTATATTATTAT
131 AAATTAAGTAATTAACCTATTTTATTAT
* * * *
3622397 ATAAGCGCTACCTATTACATTATATAAGCTCTATCTAATATGTTATTGTACTTGATAAT
1 ATAAGCGCTACCTATTACGTTATATAAGCGCTACCTAATATGTTATTGTGCTTGATAAT
3622456 ATTTTCGGTT
Statistics
Matches: 347, Mismatches: 28, Indels: 1
0.92 0.07 0.00
Matches are distributed among these distances:
158 343 0.99
159 4 0.01
ACGTcount: A:0.33, C:0.14, G:0.13, T:0.41
Consensus pattern (158 bp):
ATAAGCGCTACCTATTACGTTATATAAGCGCTACCTAATATGTTATTGTGCTTGATAATGTTTCC
AGTAAATAACCGGATATGTTATCCTTGGTAACATTTTAAGCGTTTACCTAATATGTTGTAATAAC
AAATTAAGTAATTAACCTATTTTATTAT
Found at i:3622283 original size:23 final size:23
Alignment explanation
Indices: 3622235--3622284 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
3622225 ACCTATTTTA
* *
3622235 TTATATAAGCGCTACTTATTACG
1 TTATATAAGCGCTACCTAATACG
*
3622258 TTATATAAGCGCTACCTAATATG
1 TTATATAAGCGCTACCTAATACG
3622281 TTAT
1 TTAT
3622285 TGTGCTTGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.40
Consensus pattern (23 bp):
TTATATAAGCGCTACCTAATACG
Found at i:3622442 original size:23 final size:23
Alignment explanation
Indices: 3622392--3622436 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
3622382 AAGCTATATT
*
3622392 ATTATATAAGCGCTACCTATTAC
1 ATTATATAAGCGCTACCTAATAC
* *
3622415 ATTATATAAGCTCTATCTAATA
1 ATTATATAAGCGCTACCTAATA
3622437 TGTTATTGTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.38, C:0.18, G:0.07, T:0.38
Consensus pattern (23 bp):
ATTATATAAGCGCTACCTAATAC
Found at i:3625854 original size:21 final size:22
Alignment explanation
Indices: 3625819--3625862 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
3625809 TTTAATTATT
3625819 TGTTTATATCTTATTTTTGTCA
1 TGTTTATATCTTATTTTTGTCA
* *
3625841 TGTTT-TATTTTATTTTTTTCA
1 TGTTTATATCTTATTTTTGTCA
3625862 T
1 T
3625863 AATTTTTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.16, C:0.07, G:0.07, T:0.70
Consensus pattern (22 bp):
TGTTTATATCTTATTTTTGTCA
Found at i:3633373 original size:10 final size:10
Alignment explanation
Indices: 3633358--3633432 Score: 66
Period size: 10 Copynumber: 8.7 Consensus size: 10
3633348 CATTTAATAA
3633358 ATAAACGAAC
1 ATAAACGAAC
3633368 ATAAACGAAC
1 ATAAACGAAC
3633378 ----ACGAAC
1 ATAAACGAAC
3633384 ATAAACGAAC
1 ATAAACGAAC
3633394 ----ACGAAC
1 ATAAACGAAC
3633400 ATAAACGAAC
1 ATAAACGAAC
3633410 ----ACGAAC
1 ATAAACGAAC
3633416 ATAAACGAAC
1 ATAAACGAAC
3633426 ATAAACG
1 ATAAACG
3633433 TTGGAGACCC
Statistics
Matches: 53, Mismatches: 0, Indels: 24
0.69 0.00 0.31
Matches are distributed among these distances:
6 18 0.34
10 35 0.66
ACGTcount: A:0.57, C:0.23, G:0.12, T:0.08
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:3633383 original size:16 final size:16
Alignment explanation
Indices: 3633362--3633426 Score: 130
Period size: 16 Copynumber: 4.1 Consensus size: 16
3633352 TAATAAATAA
3633362 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
3633378 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
3633394 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
3633410 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
3633426 A
1 A
3633427 TAAACGTTGG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 49 1.00
ACGTcount: A:0.57, C:0.25, G:0.12, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:3634258 original size:24 final size:24
Alignment explanation
Indices: 3634228--3634302 Score: 105
Period size: 24 Copynumber: 3.1 Consensus size: 24
3634218 TATTGGGTTA
* *
3634228 AACATAAATGAATGAACATAAACG
1 AACATAACTGAACGAACATAAACG
* *
3634252 AATATAACCGAACGAACATAAACG
1 AACATAACTGAACGAACATAAACG
*
3634276 AACATAACTGAACGAACATAACCG
1 AACATAACTGAACGAACATAAACG
3634300 AAC
1 AAC
3634303 GTTCACGAAC
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 44 1.00
ACGTcount: A:0.55, C:0.20, G:0.12, T:0.13
Consensus pattern (24 bp):
AACATAACTGAACGAACATAAACG
Found at i:3634265 original size:14 final size:14
Alignment explanation
Indices: 3634248--3634303 Score: 66
Period size: 14 Copynumber: 4.3 Consensus size: 14
3634238 AATGAACATA
*
3634248 AACGAATATAACCG
1 AACGAACATAACCG
3634262 AACGAACAT-A---
1 AACGAACATAACCG
*
3634272 AACGAACATAACTG
1 AACGAACATAACCG
3634286 AACGAACATAACCG
1 AACGAACATAACCG
3634300 AACG
1 AACG
3634304 TTCACGAACA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
10 9 0.25
11 1 0.03
13 1 0.03
14 25 0.69
ACGTcount: A:0.52, C:0.23, G:0.14, T:0.11
Consensus pattern (14 bp):
AACGAACATAACCG
Found at i:3636069 original size:322 final size:327
Alignment explanation
Indices: 3635533--3636128 Score: 839
Period size: 322 Copynumber: 1.8 Consensus size: 327
3635523 ATTTTCTCCA
* *
3635533 TTACACTTTTAAGTGTATTTATCTTTATATTTTTTTAAATTTTTTAATAATAAAAATATTATCAT
1 TTACACTTTTAAGTGCATTTATCGTTATA--TTTTTAAATTTTTTAATAATAAAAATATTATCAT
* * * *
3635598 TTTACAAAAATTAAAAAAAAAATCAAACTCCCACTCCCCGCGTTGTCCCTCTCCCCCCATCCTCC
64 TTTACAAAAATT--AAAAAAAATCAAACTCCCACTCCCCGCGTCGTACCTATCCCCCCATCCACC
*
3635663 ACCTCTGACGGCGAAGGGTCACCATCGATCATGTTTTGTTTGGAGTAGGACAAGAAATTCAATGG
127 ACCTCTGACGACGAAGGGTCACCATCGATCATGTTTTGTTTGGAGTAGGACAAGAAATTCAATGG
*
3635728 CGGCGGTCGCGTAATGTATGGACG-CTGTAGCTATCAAAA-TCGTCAGAAAACAACAACGAAAAC
192 CGGCGGTCGCGTAATGTATGAACGACTGTAGCTATCAAAAGTCGTCA-AAAACAACAACGAAAAC
*
3635791 CTAGAAATTTGACGAACGATTTGGTGTCTAAAGAATTTTTTACTAAAGATAGGAGCATAACACAT
256 CTAGAAATTCGACGAACGATTTGGTGTCTAAAGAATTTTTTACTAAAGATAGGAGCATAACACAT
3635856 TCTTTCG
321 TCTTTCG
* *
3635863 TTACACTTTTAGGTGCATTTATCGTTATA-TTTTAAA-TTTTTAATAATAAAAATATTATCTTTT
1 TTACACTTTTAAGTGCATTTATCGTTATATTTTTAAATTTTTTAATAATAAAAATATTATCATTT
* * *
3635926 TA-TAAAA-T-AAAAAAATCAAACTCCCCCTCCCCTCGTCGTACCTATCCCTCCCATCCACCACC
66 TACAAAAATTAAAAAAAATCAAACTCCCACTCCCCGCGTCGTACCTATCCC-CCCATCCACCACC
* * * * * *
3635988 TCTGACGACGAAGGGTCACGA-CTGATCGTGTTTTGTTTGGAGTAGGATAAGGAATTCATTGGTG
130 TCTGACGACGAAGGGTCACCATC-GATCATGTTTTGTTTGGAGTAGGACAAGAAATTCAATGGCG
* * ** * *
3636052 GCGGTCGTGTAATGTATGAACGACTGTAGCTGTCAAAAGTTTTGAAAAACAGCAACGAAAACCTA
194 GCGGTCGCGTAATGTATGAACGACTGTAGCTATCAAAAGTCGTCAAAAACAACAACGAAAACCTA
3636117 GAAATTCGACGA
259 GAAATTCGACGA
3636129 CCCTTCGTGG
Statistics
Matches: 236, Mismatches: 26, Indels: 15
0.85 0.09 0.05
Matches are distributed among these distances:
321 36 0.15
322 87 0.37
323 44 0.19
324 4 0.02
325 4 0.02
326 28 0.12
327 7 0.03
330 26 0.11
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Consensus pattern (327 bp):
TTACACTTTTAAGTGCATTTATCGTTATATTTTTAAATTTTTTAATAATAAAAATATTATCATTT
TACAAAAATTAAAAAAAATCAAACTCCCACTCCCCGCGTCGTACCTATCCCCCCATCCACCACCT
CTGACGACGAAGGGTCACCATCGATCATGTTTTGTTTGGAGTAGGACAAGAAATTCAATGGCGGC
GGTCGCGTAATGTATGAACGACTGTAGCTATCAAAAGTCGTCAAAAACAACAACGAAAACCTAGA
AATTCGACGAACGATTTGGTGTCTAAAGAATTTTTTACTAAAGATAGGAGCATAACACATTCTTT
CG
Found at i:3636333 original size:21 final size:22
Alignment explanation
Indices: 3636295--3636335 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
3636285 TTTTTTTATG
* *
3636295 TTTTTTATAATTATAATATTAA
1 TTTTTTATAAATAAAATATTAA
3636317 TTTTTT-TAAATAAAATATT
1 TTTTTTATAAATAAAATATT
3636336 TTTTGAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (22 bp):
TTTTTTATAAATAAAATATTAA
Found at i:3637662 original size:26 final size:26
Alignment explanation
Indices: 3637594--3637662 Score: 129
Period size: 26 Copynumber: 2.7 Consensus size: 26
3637584 TTTTATCCCC
*
3637594 TAAAATTTTATAAGTTATCTCTTACT
1 TAAAATTTTATAAGTTCTCTCTTACT
3637620 TAAAATTTTATAAGTTCTCTCTTACT
1 TAAAATTTTATAAGTTCTCTCTTACT
3637646 TAAAATTTTATAAGTTC
1 TAAAATTTTATAAGTTC
3637663 ATCCCTCCTA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 42 1.00
ACGTcount: A:0.35, C:0.12, G:0.04, T:0.49
Consensus pattern (26 bp):
TAAAATTTTATAAGTTCTCTCTTACT
Found at i:3637709 original size:40 final size:40
Alignment explanation
Indices: 3637654--3637733 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
3637644 CTTAAAATTT
3637654 TATAAGTTCATCCCTCCTAACATAAAATATTGTATTTGTC
1 TATAAGTTCATCCCTCCTAACATAAAATATTGTATTTGTC
3637694 TATAAGTTCATCCCTCCTAACATAAAATATTGTATTTGTC
1 TATAAGTTCATCCCTCCTAACATAAAATATTGTATTTGTC
3637734 CCTGCTTGTG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.33, C:0.20, G:0.07, T:0.40
Consensus pattern (40 bp):
TATAAGTTCATCCCTCCTAACATAAAATATTGTATTTGTC
Found at i:3639597 original size:59 final size:58
Alignment explanation
Indices: 3639497--3639613 Score: 150
Period size: 59 Copynumber: 2.0 Consensus size: 58
3639487 TGACTATAAA
* *
3639497 TCTCATTTTAAATTGTCCTTAAACTTTTAAATATTTCAATTTCA-TCCTCAAACTATGAC
1 TCTCATTTTAAATTGTCCTCAAACTTTGAAATATTTCAATTTCATTCCT-AAACT-TGAC
*
3639556 TCTCATTTTAAATTAGTCCTCAAAGTTTGAACAT-TTT-AATTTCATTCCTAAACTTGAC
1 TCTCATTTTAAATT-GTCCTCAAACTTTGAA-ATATTTCAATTTCATTCCTAAACTTGAC
3639614 CCAATTTCAT
Statistics
Matches: 52, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
58 4 0.08
59 26 0.50
60 20 0.38
61 2 0.04
ACGTcount: A:0.32, C:0.20, G:0.05, T:0.44
Consensus pattern (58 bp):
TCTCATTTTAAATTGTCCTCAAACTTTGAAATATTTCAATTTCATTCCTAAACTTGAC
Found at i:3644088 original size:2 final size:2
Alignment explanation
Indices: 3644081--3644111 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3644071 ATTCTAAGTA
3644081 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3644112 AAATTCTTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3644158 original size:2 final size:2
Alignment explanation
Indices: 3644151--3644178 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3644141 ATATAATTAG
3644151 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
3644179 ATTTTGTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3645152 original size:3 final size:3
Alignment explanation
Indices: 3645144--3645200 Score: 73
Period size: 3 Copynumber: 19.0 Consensus size: 3
3645134 CAGTTTGCTT
*
3645144 TTA TTA TTA TTA TTA TTA TTTA TT- TTA TTA TTA TTA -TA TTA TACA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA T-TA
3645189 TTA TTA TTA TTA
1 TTA TTA TTA TTA
3645201 AATAAATATT
Statistics
Matches: 48, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
2 4 0.08
3 39 0.81
4 5 0.10
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:3645174 original size:24 final size:23
Alignment explanation
Indices: 3645142--3645200 Score: 82
Period size: 24 Copynumber: 2.5 Consensus size: 23
3645132 TTCAGTTTGC
**
3645142 TTTTATTATTATTATTATTATTTA
1 TTTTATTATTATTA-TATTATACA
3645166 TTTTATTATTATTATATTATACA
1 TTTTATTATTATTATATTATACA
3645189 TTATTATTATTA
1 TT-TTATTATTA
3645201 AATAAATATT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
23 9 0.28
24 23 0.72
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (23 bp):
TTTTATTATTATTATATTATACA
Found at i:3646899 original size:2 final size:2
Alignment explanation
Indices: 3646892--3646937 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
3646882 ATAAATATCT
3646892 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
3646934 TA TA
1 TA TA
3646938 AATTAATAGA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3649850 original size:47 final size:44
Alignment explanation
Indices: 3649771--3649869 Score: 153
Period size: 47 Copynumber: 2.2 Consensus size: 44
3649761 TGCATTTACA
*
3649771 TTTTGCATCTTTGCATTATTTCATATTCATACTTTTATGTTTGC
1 TTTTGCATCTTTGCATTATTTCATATTCATACTTTTATGTTCGC
*
3649815 TTTTGCATCTTTGCATTTTTATTTCCTATTCATACTTTTATGTTCGC
1 TTTTGCATCTTTGCA---TTATTTCATATTCATACTTTTATGTTCGC
3649862 TTTTGCAT
1 TTTTGCAT
3649870 TGCACAGTTT
Statistics
Matches: 50, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
44 15 0.30
47 35 0.70
ACGTcount: A:0.16, C:0.17, G:0.09, T:0.58
Consensus pattern (44 bp):
TTTTGCATCTTTGCATTATTTCATATTCATACTTTTATGTTCGC
Found at i:3651612 original size:8 final size:8
Alignment explanation
Indices: 3651583--3651621 Score: 60
Period size: 8 Copynumber: 4.8 Consensus size: 8
3651573 CTTGAAGAAA
3651583 AAAAAAGG
1 AAAAAAGG
*
3651591 AGAAAAGG
1 AAAAAAGG
3651599 AAAAAAGG
1 AAAAAAGG
3651607 AAAAAAAGG
1 -AAAAAAGG
3651616 AAAAAA
1 AAAAAA
3651622 TTAAACTAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
8 20 0.71
9 8 0.29
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (8 bp):
AAAAAAGG
Found at i:3652111 original size:32 final size:32
Alignment explanation
Indices: 3652075--3652136 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
3652065 TCTGGAAATA
*
3652075 AGAAGTATCTCTACGAGATGAGCATAACAACG
1 AGAAGTATCTCTACAAGATGAGCATAACAACG
* *
3652107 AGAAGTATCTTTACAATATGAGCATAACAA
1 AGAAGTATCTCTACAAGATGAGCATAACAA
3652137 TCATTTTTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.44, C:0.16, G:0.18, T:0.23
Consensus pattern (32 bp):
AGAAGTATCTCTACAAGATGAGCATAACAACG
Found at i:3656145 original size:22 final size:22
Alignment explanation
Indices: 3656119--3656173 Score: 110
Period size: 22 Copynumber: 2.5 Consensus size: 22
3656109 ATCTACCCTC
3656119 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
3656141 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
3656163 TTCAAAGATGA
1 TTCAAAGATGA
3656174 AAGCTTTATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.38
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Found at i:3656954 original size:50 final size:50
Alignment explanation
Indices: 3656879--3656976 Score: 187
Period size: 50 Copynumber: 2.0 Consensus size: 50
3656869 CTTCGGGAGT
3656879 TTTTTGATCTTAAAGCCTCAAGGTCATCTGTAAGACCTACAGTGCATGGC
1 TTTTTGATCTTAAAGCCTCAAGGTCATCTGTAAGACCTACAGTGCATGGC
*
3656929 TTTTTGATCTTAAAGCCTCAGGGTCATCTGTAAGACCTACAGTGCATG
1 TTTTTGATCTTAAAGCCTCAAGGTCATCTGTAAGACCTACAGTGCATG
3656977 ATGTTTTCAA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 47 1.00
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.33
Consensus pattern (50 bp):
TTTTTGATCTTAAAGCCTCAAGGTCATCTGTAAGACCTACAGTGCATGGC
Found at i:3657017 original size:73 final size:73
Alignment explanation
Indices: 3656927--3657191 Score: 485
Period size: 73 Copynumber: 3.6 Consensus size: 73
3656917 ACAGTGCATG
3656927 GCTTTTTGATCTTAAAGCCTCAGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGC
1 GCTTTTTGATCTTAAAGCCTCAGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGC
3656992 CTTTGGGA
66 CTTTGGGA
* *
3657000 GCTTTTTGATCTTAAAGCCTAAGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAAC
1 GCTTTTTGATCTTAAAGCCTCAGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGC
*
3657065 CTTTGGAA
66 CTTTGGGA
3657073 GCTTTTTGATCTTAAAGCCTCAGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGC
1 GCTTTTTGATCTTAAAGCCTCAGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGC
*
3657138 CTTCGGGA
66 CTTTGGGA
*
3657146 GCTTTTTGATCTTAAAGCCTCAGGGTTATCTGTAAGACCTACAGTG
1 GCTTTTTGATCTTAAAGCCTCAGGGTCATCTGTAAGACCTACAGTG
3657192 AAAGATGATA
Statistics
Matches: 184, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
73 184 1.00
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.33
Consensus pattern (73 bp):
GCTTTTTGATCTTAAAGCCTCAGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGC
CTTTGGGA
Found at i:3657380 original size:3 final size:3
Alignment explanation
Indices: 3657372--3657428 Score: 114
Period size: 3 Copynumber: 19.0 Consensus size: 3
3657362 CAGTTTGCTT
3657372 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3657420 TTA TTA TTA
1 TTA TTA TTA
3657429 AATAAATATT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:3658743 original size:11 final size:11
Alignment explanation
Indices: 3658727--3658752 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
3658717 TAAATTAGTA
3658727 ATTTAATTATT
1 ATTTAATTATT
3658738 ATTTAATTATT
1 ATTTAATTATT
3658749 ATTT
1 ATTT
3658753 TAGTTATATA
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:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (11 bp):
ATTTAATTATT
Found at i:3666594 original size:23 final size:22
Alignment explanation
Indices: 3666523--3666603 Score: 92
Period size: 23 Copynumber: 3.6 Consensus size: 22
3666513 ACACTTAACA
3666523 GTGCATCGATGCATCCCTTTGAAT
1 GTGCATCGATGCA-CCC-TTGAAT
* * *
3666547 GTGCATCGATACA-CCATGAAG
1 GTGCATCGATGCACCCTTGAAT
*
3666568 GTGCACCGATGCACGCCTTGAAT
1 GTGCATCGATGCAC-CCTTGAAT
3666591 GTGCATCGATGCA
1 GTGCATCGATGCA
3666604 TCGGTCGGGT
Statistics
Matches: 47, Mismatches: 8, Indels: 5
0.78 0.13 0.08
Matches are distributed among these distances:
21 15 0.32
22 2 0.04
23 18 0.38
24 12 0.26
ACGTcount: A:0.25, C:0.26, G:0.25, T:0.25
Consensus pattern (22 bp):
GTGCATCGATGCACCCTTGAAT
Found at i:3675222 original size:23 final size:23
Alignment explanation
Indices: 3675152--3675233 Score: 80
Period size: 23 Copynumber: 3.6 Consensus size: 23
3675142 CACTTAACAA
*
3675152 TGCATCAATGCATC-CCTTTGAATG
1 TGCATCGATGCA-CACC-TTGAATG
* *
3675176 TGCATCGAT--ACACCATGAAGG
1 TGCATCGATGCACACCTTGAATG
* *
3675197 TGCACCGATGCACGCCTTGAATG
1 TGCATCGATGCACACCTTGAATG
3675220 TGCATCGATGCACA
1 TGCATCGATGCACA
3675234 AGGTCATGCA
Statistics
Matches: 46, Mismatches: 9, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
21 14 0.30
22 3 0.07
23 21 0.46
24 8 0.17
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.24
Consensus pattern (23 bp):
TGCATCGATGCACACCTTGAATG
Found at i:3678018 original size:65 final size:65
Alignment explanation
Indices: 3677913--3678072 Score: 159
Period size: 65 Copynumber: 2.5 Consensus size: 65
3677903 GAATAAATTG
* * *
3677913 AACATCGAATGCATTTCATGCACCAATGCA-CATACTATGCATCAAAGCAC-TCATAG-T-TTTA
1 AACATCGAATGCATTTCATGCATCGATGCACCATACCATGCATCAAAGCACGT-A-AGCTATTT-
3677974 TGAA
63 TG-A
* * * * * *
3677978 AACATCGAATGCATTTGATGCATCGATGCACCA-GCCATGCATCGATGTACGTAGGCTATTTTGA
1 AACATCGAATGCATTTCATGCATCGATGCACCATACCATGCATCAAAGCACGTAAGCTATTTTGA
*
3678042 AACATCGAATGCATTTTATGCATCGATGCAC
1 AACATCGAATGCATTTCATGCATCGATGCAC
3678073 TCTTAGTGCA
Statistics
Matches: 81, Mismatches: 10, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
64 32 0.40
65 43 0.53
66 6 0.07
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.28
Consensus pattern (65 bp):
AACATCGAATGCATTTCATGCATCGATGCACCATACCATGCATCAAAGCACGTAAGCTATTTTGA
Found at i:3689189 original size:20 final size:20
Alignment explanation
Indices: 3689160--3689198 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3689150 ATTTTACCAC
*
3689160 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGATCCTAA
*
3689180 ATGCATCTATATGATCCTA
1 ATGCAACTATATGATCCTA
3689199 TATGAGCTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.23, G:0.10, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGATCCTAA
Found at i:3697663 original size:29 final size:29
Alignment explanation
Indices: 3697604--3697753 Score: 137
Period size: 29 Copynumber: 5.3 Consensus size: 29
3697594 CATTTTACAC
* *
3697604 AAATAGCA-CTTTTT--AAATAATTACCA
1 AAATAGCACCTTTTTCGAATTAATTCCCA
3697630 AAATAGCACCTTTTTCGAATTAATTCCCA
1 AAATAGCACCTTTTTCGAATTAATTCCCA
* **
3697659 AAATAGAACCAATTTCGAATTAATTCCCA
1 AAATAGCACCTTTTTCGAATTAATTCCCA
* * ** *
3697688 GAATATCACCTTTTTC-AAAAATATTACCA
1 AAATAGCACCTTTTTCGAATTA-ATTCCCA
** *
3697717 AAATAGCACCCATTTCGAATTAATTCCCC
1 AAATAGCACCTTTTTCGAATTAATTCCCA
*
3697746 GAATAGCA
1 AAATAGCA
3697754 ATAACGAATT
Statistics
Matches: 97, Mismatches: 22, Indels: 7
0.77 0.17 0.06
Matches are distributed among these distances:
26 8 0.08
27 6 0.06
28 3 0.03
29 77 0.79
30 3 0.03
ACGTcount: A:0.41, C:0.22, G:0.07, T:0.31
Consensus pattern (29 bp):
AAATAGCACCTTTTTCGAATTAATTCCCA
Found at i:3697698 original size:58 final size:58
Alignment explanation
Indices: 3697621--3697753 Score: 169
Period size: 58 Copynumber: 2.3 Consensus size: 58
3697611 ACTTTTTAAA
* * * * *
3697621 TAATTACCAAAATAGCACCTTTTTC-GAATTAATTCCCAAAATAGAACCAATTTCGAAT
1 TAATTCCCAGAATAGCACCTTTTTCAAAAAT-ATTACCAAAATAGAACCAATTTCGAAT
* * *
3697679 TAATTCCCAGAATATCACCTTTTTCAAAAATATTACCAAAATAGCACCCATTTCGAAT
1 TAATTCCCAGAATAGCACCTTTTTCAAAAATATTACCAAAATAGAACCAATTTCGAAT
*
3697737 TAATTCCCCGAATAGCA
1 TAATTCCCAGAATAGCA
3697754 ATAACGAATT
Statistics
Matches: 64, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
58 61 0.95
59 3 0.05
ACGTcount: A:0.40, C:0.23, G:0.07, T:0.30
Consensus pattern (58 bp):
TAATTCCCAGAATAGCACCTTTTTCAAAAATATTACCAAAATAGAACCAATTTCGAAT
Found at i:3697819 original size:17 final size:17
Alignment explanation
Indices: 3697789--3697832 Score: 79
Period size: 17 Copynumber: 2.5 Consensus size: 17
3697779 ACCGGTCAAC
3697789 GGTCAACGGGTCGGGTCG
1 GGTCAAC-GGTCGGGTCG
3697807 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
3697824 GGTCAACGG
1 GGTCAACGG
3697833 GTAAACGGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 19 0.73
18 7 0.27
ACGTcount: A:0.14, C:0.23, G:0.48, T:0.16
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:3697867 original size:10 final size:10
Alignment explanation
Indices: 3697847--3697882 Score: 56
Period size: 11 Copynumber: 3.6 Consensus size: 10
3697837 ACGGGTCGTG
3697847 ACCGGTC-AA
1 ACCGGTCAAA
3697856 ACCGGTCAAA
1 ACCGGTCAAA
3697866 ACCGGTTCAAA
1 ACCGG-TCAAA
3697877 ACCGGT
1 ACCGGT
3697883 TTTCAGCGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 7 0.28
10 8 0.32
11 10 0.40
ACGTcount: A:0.33, C:0.31, G:0.22, T:0.14
Consensus pattern (10 bp):
ACCGGTCAAA
Found at i:3703806 original size:29 final size:28
Alignment explanation
Indices: 3703756--3703894 Score: 95
Period size: 29 Copynumber: 4.9 Consensus size: 28
3703746 CATTTTACAC
** *
3703756 AAATAGCA-CTTTTTTAAATAATTACCA
1 AAATAGCACCTTTTCGAATTAATTACCA
*
3703783 AAATAGCACCCTTTTCGAATTAATT-CTTA
1 AAATAGCA-CCTTTTCGAATTAATTAC-CA
*
3703812 AAATAGCACCAATTTT-GAATTAATTCCCA
1 AAATAGCACC--TTTTCGAATTAATTACCA
* * * ** **
3703841 GAATATCACTTTTTTAAAAAATATTACCA
1 AAATAGCACCTTTTCGAATTA-ATTACCA
3703870 AAATAGCACCTATTTCGAATTAATT
1 AAATAGCACCT-TTTCGAATTAATT
3703895 CCCCGAATAG
Statistics
Matches: 84, Mismatches: 19, Indels: 16
0.71 0.16 0.13
Matches are distributed among these distances:
27 12 0.14
28 6 0.07
29 55 0.65
30 11 0.13
ACGTcount: A:0.41, C:0.17, G:0.06, T:0.36
Consensus pattern (28 bp):
AAATAGCACCTTTTCGAATTAATTACCA
Found at i:3703931 original size:28 final size:29
Alignment explanation
Indices: 3703867--3703931 Score: 78
Period size: 28 Copynumber: 2.3 Consensus size: 29
3703857 AAAAATATTA
***
3703867 CCAAAATAGCACCTATTTCGAATTAATTC
1 CCAAAATAGCACCTAAACCGAATTAATTC
**
3703896 CCCGAATAGCA-CTAAACCGAATTAATTC
1 CCAAAATAGCACCTAAACCGAATTAATTC
3703924 CCAAAATA
1 CCAAAATA
3703932 ACACGTCAAC
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
28 20 0.69
29 9 0.31
ACGTcount: A:0.42, C:0.26, G:0.08, T:0.25
Consensus pattern (29 bp):
CCAAAATAGCACCTAAACCGAATTAATTC
Found at i:3703967 original size:12 final size:12
Alignment explanation
Indices: 3703967--3703992 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3703957 TCAACGGTCG
3703967 GGTCGGGTCAAC
1 GGTCGGGTCAAC
3703979 GGTCGGGTCAAC
1 GGTCGGGTCAAC
3703991 GG
1 GG
3703993 GTAAACAGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.23, G:0.46, T:0.15
Consensus pattern (12 bp):
GGTCGGGTCAAC
Found at i:3703970 original size:17 final size:17
Alignment explanation
Indices: 3703948--3703987 Score: 80
Period size: 17 Copynumber: 2.4 Consensus size: 17
3703938 CAACGGTCAA
3703948 CGGGTCGGGTCAACGGT
1 CGGGTCGGGTCAACGGT
3703965 CGGGTCGGGTCAACGGT
1 CGGGTCGGGTCAACGGT
3703982 CGGGTC
1 CGGGTC
3703988 AACGGGTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.10, C:0.25, G:0.47, T:0.17
Consensus pattern (17 bp):
CGGGTCGGGTCAACGGT
Found at i:3706141 original size:20 final size:20
Alignment explanation
Indices: 3706112--3706150 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3706102 ATTTCACCAC
*
3706112 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGATCCTAA
*
3706132 ATGCATCTATATGATCCTA
1 ATGCAACTATATGATCCTA
3706151 TATGAGCTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.23, G:0.10, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGATCCTAA
Found at i:3716028 original size:21 final size:20
Alignment explanation
Indices: 3715981--3716033 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 20
3715971 CCGGCTAAGT
3715981 TCGGGTCGGTCTGAATAATA
1 TCGGGTCGGTCTGAATAATA
*
3716001 TCAGGTCGGGTCTGAATAATA
1 TCGGGTC-GGTCTGAATAATA
*
3716022 TTGGGTCAGGTC
1 TCGGGTC-GGTC
3716034 GGGTATCGGG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 6 0.21
21 22 0.79
ACGTcount: A:0.23, C:0.15, G:0.32, T:0.30
Consensus pattern (20 bp):
TCGGGTCGGTCTGAATAATA
Done.