Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 97507971
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: 97507971
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 232 characters in sequence are not A, C, G, or T
File 137 of 328
Found at i:39819048 original size:75 final size:76
Alignment explanation
Indices: 39818878--39819158 Score: 458
Period size: 76 Copynumber: 3.7 Consensus size: 76
39818868 AAATCGACAA
* *
39818878 TACCTCAGCGTGCCCTGAGGCTCAACTCACCTTTCACAATATGAGTTGATTTTTTTTGACAAA-C
1 TACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTGA-AAAGC
*
39818942 ATAAATTGAAAT
65 AGAAATTGAAAT
* *
39818954 TACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGTAATATGAGTTGA-TTTTTTTGAAAAGCA
1 TACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTGAAAAGCA
39819018 GAAATTGAAAT
66 GAAATTGAAAT
* *
39819029 TACCTCAGCATGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTGAAAAGCA
1 TACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTGAAAAGCA
*
39819094 GAAATTGAAAA
66 GAAATTGAAAT
*
39819105 TACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTTT
1 TACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
39819159 GAAAAACATA
Statistics
Matches: 192, Mismatches: 11, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
74 3 0.02
75 68 0.35
76 121 0.63
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.31
Consensus pattern (76 bp):
TACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTGAAAAGCA
GAAATTGAAAT
Found at i:39819140 original size:151 final size:149
Alignment explanation
Indices: 39818861--39819175 Score: 463
Period size: 151 Copynumber: 2.1 Consensus size: 149
39818851 GCAGAAATTG
* * * *
39818861 AAAATAGAAATCGACAA-TACCTCAGCGTGCCCTGAGGCTCAACTCACCTTTCACAATATGAGTT
1 AAAACAGAAATTGA-AATTACCTCAGCATGCCCTGAGGCTCAACTCACCTCTCACAATATGAGTT
* * *
39818925 GATTTTTTTTGACAAACATAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCG
65 GATTTTTTTTGACAAACAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCG
* *
39818990 TAATATGAGTTGATTTTTTTGA
130 CAATATGAGCTGA--TTTTTGA
* * *
39819012 AAAGCAGAAATTGAAATTACCTCAGCATGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTG
1 AAAACAGAAATTGAAATTACCTCAGCATGCCCTGAGGCTCAACTCACCTCTCACAATATGAGTTG
39819077 ATTTTTTTTGA-AAAGCAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCG
66 ATTTTTTTTGACAAA-CAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCG
39819141 CAATATGAGCTGATTTTTGA
130 CAATATGAGCTGATTTTTGA
*
39819161 AAAACATAAATTGAA
1 AAAACAGAAATTGAA
39819176 GAAAATAGAA
Statistics
Matches: 148, Mismatches: 14, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
149 20 0.14
150 5 0.03
151 123 0.83
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.30
Consensus pattern (149 bp):
AAAACAGAAATTGAAATTACCTCAGCATGCCCTGAGGCTCAACTCACCTCTCACAATATGAGTTG
ATTTTTTTTGACAAACAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGC
AATATGAGCTGATTTTTGA
Found at i:39827513 original size:12 final size:12
Alignment explanation
Indices: 39827481--39827516 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
39827471 TGGGATATGC
39827481 AATGTATGAATG
1 AATGTATGAATG
**
39827493 AATACATGAATG
1 AATGTATGAATG
39827505 AATGTATGAATG
1 AATGTATGAATG
39827517 TCAAAATGTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.44, C:0.03, G:0.22, T:0.31
Consensus pattern (12 bp):
AATGTATGAATG
Found at i:39831095 original size:16 final size:15
Alignment explanation
Indices: 39831074--39831121 Score: 69
Period size: 16 Copynumber: 3.1 Consensus size: 15
39831064 GATGTGAATA
39831074 ATAAAATATATAAAAT
1 ATAAAATAT-TAAAAT
39831090 ATAAAATATTAAAAT
1 ATAAAATATTAAAAT
*
39831105 ATCAAAATATTAGAAT
1 AT-AAAATATTAAAAT
39831121 A
1 A
39831122 ATAATAATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
15 8 0.27
16 22 0.73
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (15 bp):
ATAAAATATTAAAAT
Found at i:39831104 original size:8 final size:8
Alignment explanation
Indices: 39831070--39831121 Score: 61
Period size: 8 Copynumber: 6.5 Consensus size: 8
39831060 CAATGATGTG
*
39831070 AATAATAA
1 AATATTAA
39831078 AATATATAA
1 AATAT-TAA
39831087 AATA-TAA
1 AATATTAA
39831094 AATATTAA
1 AATATTAA
*
39831102 AATATCAA
1 AATATTAA
*
39831110 AATATTAG
1 AATATTAA
39831118 AATA
1 AATA
39831122 ATAATAATTA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
7 7 0.18
8 24 0.63
9 7 0.18
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (8 bp):
AATATTAA
Found at i:39831121 original size:24 final size:24
Alignment explanation
Indices: 39831069--39831125 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
39831059 ACAATGATGT
*
39831069 GAATAATAAAATATATAAAATATA
1 GAATAATAAAATATACAAAATATA
* *
39831093 AAATATTAAAATAT-CAAAATATTA
1 GAATAATAAAATATACAAAATA-TA
39831117 GAATAATAA
1 GAATAATAA
39831126 TAATTAATAT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
23 6 0.22
24 21 0.78
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.30
Consensus pattern (24 bp):
GAATAATAAAATATACAAAATATA
Found at i:39831387 original size:27 final size:25
Alignment explanation
Indices: 39831352--39831413 Score: 79
Period size: 25 Copynumber: 2.5 Consensus size: 25
39831342 ACATGTAGAA
*
39831352 AAAAAATATATAAATAATATAATAT
1 AAAAGATATATAAATAATATAATAT
* * *
39831377 TAAAGATATATAAATAAAATAGTAT
1 AAAAGATATATAAATAATATAATAT
*
39831402 AAAATATATATA
1 AAAAGATATATA
39831414 TACGTAATAT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (25 bp):
AAAAGATATATAAATAATATAATAT
Found at i:39831394 original size:14 final size:13
Alignment explanation
Indices: 39831354--39831404 Score: 52
Period size: 14 Copynumber: 3.9 Consensus size: 13
39831344 ATGTAGAAAA
39831354 AAAATATATAAAT
1 AAAATATATAAAT
* *
39831367 AATATA-AT-ATT
1 AAAATATATAAAT
39831378 AAAGATATATAAAT
1 AAA-ATATATAAAT
39831392 AAAATAGTATAAA
1 AAAATA-TATAAA
39831405 ATATATATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
11 4 0.13
12 5 0.17
13 10 0.33
14 11 0.37
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (13 bp):
AAAATATATAAAT
Found at i:39831414 original size:27 final size:27
Alignment explanation
Indices: 39831326--39831415 Score: 69
Period size: 25 Copynumber: 3.4 Consensus size: 27
39831316 TATAATTAAG
* * *
39831326 ATATATACATAAGATAACAT-GTAGAAA
1 ATATATATATAA-ATAAAATAGTATAAA
* * * * *
39831353 AAAAATATATAAATAATATAATAT-TA
1 ATATATATATAAATAAAATAGTATAAA
*
39831379 A-AGATATATAAATAAAATAGTATAAA
1 ATATATATATAAATAAAATAGTATAAA
39831405 ATATATATATA
1 ATATATATATA
39831416 CGTAATATAG
Statistics
Matches: 48, Mismatches: 12, Indels: 6
0.73 0.18 0.09
Matches are distributed among these distances:
25 19 0.40
26 10 0.21
27 19 0.40
ACGTcount: A:0.61, C:0.02, G:0.06, T:0.31
Consensus pattern (27 bp):
ATATATATATAAATAAAATAGTATAAA
Found at i:39832007 original size:30 final size:30
Alignment explanation
Indices: 39831971--39832084 Score: 176
Period size: 30 Copynumber: 3.8 Consensus size: 30
39831961 TAGGTACAAG
* * *
39831971 TGGTGGTGGAGAAGGTGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAAGAGTGGCTAGTGGAGT
39832001 TGGTGGTGG-AAAAGAGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAAGAGTGGCTAGTGGAGT
* *
39832030 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAAGAGTGGCTAGTGGAGT
39832060 TGGTGGTGGAAAAAGAGTGGCTAGT
1 TGGTGGTGGAAAAAGAGTGGCTAGT
39832085 TGAGAAAAGT
Statistics
Matches: 76, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
29 26 0.34
30 50 0.66
ACGTcount: A:0.22, C:0.04, G:0.49, T:0.25
Consensus pattern (30 bp):
TGGTGGTGGAAAAAGAGTGGCTAGTGGAGT
Found at i:39832063 original size:59 final size:60
Alignment explanation
Indices: 39831971--39832084 Score: 212
Period size: 59 Copynumber: 1.9 Consensus size: 60
39831961 TAGGTACAAG
*
39831971 TGGTGGTGGAGAAGGTGTGGCTAGTGGAGTTGGTGGTGG-AAAAGAGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGTTGGTGGTGGAAAAAGAGTGGCTAGTGGAGT
39832030 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGTTGGTGGTGGAAAAAGAGTGGCTAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGTTGGTGGTGGAAAAAGAGTGGCTAGT
39832085 TGAGAAAAGT
Statistics
Matches: 53, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
59 38 0.72
60 15 0.28
ACGTcount: A:0.22, C:0.04, G:0.49, T:0.25
Consensus pattern (60 bp):
TGGTGGTGGAAAAGGTGTGGCTAGTGGAGTTGGTGGTGGAAAAAGAGTGGCTAGTGGAGT
Found at i:39836303 original size:20 final size:21
Alignment explanation
Indices: 39836260--39836305 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
39836250 ACTGTTTTGT
39836260 TATGGG-CCAACTGTATTGAA
1 TATGGGCCCAACTGTATTGAA
*
39836280 -ATGGGCCCAACTGTGTT-AA
1 TATGGGCCCAACTGTATTGAA
39836299 TATGGGC
1 TATGGGC
39836306 AAGACCCAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.28
Consensus pattern (21 bp):
TATGGGCCCAACTGTATTGAA
Found at i:39841268 original size:9 final size:8
Alignment explanation
Indices: 39841251--39841333 Score: 58
Period size: 9 Copynumber: 9.4 Consensus size: 8
39841241 ATTAGAAAAC
39841251 AAATATAA
1 AAATATAA
39841259 AAATAGTAA
1 AAATA-TAA
39841268 AATATATAA
1 AA-ATATAA
*
39841277 AAATTGTAA
1 AAA-TATAA
*
39841286 AATTTTATAA
1 AA--ATATAA
39841296 AAATCATAA
1 AAAT-ATAA
*
39841305 AAGTTATAA
1 AA-ATATAA
*
39841314 AATATATAG
1 AA-ATATAA
39841323 AAATATAA
1 AAATATAA
39841331 AAA
1 AAA
39841334 ATTATAGAAT
Statistics
Matches: 59, Mismatches: 9, Indels: 14
0.72 0.11 0.17
Matches are distributed among these distances:
8 15 0.25
9 34 0.58
10 10 0.17
ACGTcount: A:0.64, C:0.01, G:0.05, T:0.30
Consensus pattern (8 bp):
AAATATAA
Found at i:39841276 original size:18 final size:18
Alignment explanation
Indices: 39841231--39841335 Score: 76
Period size: 18 Copynumber: 5.7 Consensus size: 18
39841221 AAAAAAATTT
*
39841231 AATAT-TAAAAATTAGAAA
1 AATATATAAAAA-TAGTAA
*
39841249 ACAAATATAAAAATAGTAA
1 A-ATATATAAAAATAGTAA
*
39841268 AATATATAAAAATTGTAA
1 AATATATAAAAATAGTAA
*
39841286 AATTTTATAAAAATCA-TAA
1 AA-TATATAAAAAT-AGTAA
39841305 AAGT-TATAAAATATA-TAGA
1 AA-TATATAAAA-ATAGTA-A
39841324 AATATA-AAAAAT
1 AATATATAAAAAT
39841336 TATAGAATTT
Statistics
Matches: 73, Mismatches: 7, Indels: 15
0.77 0.07 0.16
Matches are distributed among these distances:
17 2 0.03
18 33 0.45
19 32 0.44
20 6 0.08
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.30
Consensus pattern (18 bp):
AATATATAAAAATAGTAA
Found at i:39841453 original size:11 final size:11
Alignment explanation
Indices: 39841437--39841469 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
39841427 AGAAGCATTT
*
39841437 TATAATTTTTC
1 TATAATTTTTA
39841448 TATAATTTTTA
1 TATAATTTTTA
39841459 T-TAATTTTTA
1 TATAATTTTTA
39841469 T
1 T
39841470 TTTTATCATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
10 10 0.48
11 11 0.52
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (11 bp):
TATAATTTTTA
Found at i:39841635 original size:18 final size:17
Alignment explanation
Indices: 39841601--39841634 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
39841591 GATTTTTATA
39841601 AAAAAATTCTAATTTTT
1 AAAAAATTCTAATTTTT
39841618 AAAAAATTCTAATTTTT
1 AAAAAATTCTAATTTTT
39841635 TTTATATTTT
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:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (17 bp):
AAAAAATTCTAATTTTT
Found at i:39841677 original size:21 final size:22
Alignment explanation
Indices: 39841653--39841700 Score: 64
Period size: 20 Copynumber: 2.3 Consensus size: 22
39841643 TTTATTGAAA
*
39841653 TTTAATAATTTTTTTTCT--TT
1 TTTAATAATTTTCTTTCTAATT
*
39841673 TTTTATAATTTTCTTTCTAATT
1 TTTAATAATTTTCTTTCTAATT
39841695 TTTAAT
1 TTTAAT
39841701 GAAAGCTGGG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 16 0.70
22 7 0.30
ACGTcount: A:0.23, C:0.06, G:0.00, T:0.71
Consensus pattern (22 bp):
TTTAATAATTTTCTTTCTAATT
Found at i:39842553 original size:20 final size:20
Alignment explanation
Indices: 39842528--39842566 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
39842518 ATTGTATATA
*
39842528 TTAATTATAATATTTTAAAT
1 TTAATTATAAAATTTTAAAT
*
39842548 TTAATTTTAAAATTTTAAA
1 TTAATTATAAAATTTTAAA
39842567 AACAAAGTTA
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:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TTAATTATAAAATTTTAAAT
Found at i:39846911 original size:6 final size:6
Alignment explanation
Indices: 39846900--39846924 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
39846890 AAAAGATGTT
39846900 AACTAA AACTAA AACTAA AACTAA A
1 AACTAA AACTAA AACTAA AACTAA A
39846925 TCTATAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.68, C:0.16, G:0.00, T:0.16
Consensus pattern (6 bp):
AACTAA
Found at i:39850640 original size:29 final size:29
Alignment explanation
Indices: 39850606--39850710 Score: 86
Period size: 29 Copynumber: 3.6 Consensus size: 29
39850596 TACTCGATTT
* * *
39850606 CGCACACTTAGTGCCATGCGATTTAAGCC
1 CGCACACTTAGTGCCATACCATTCAAGCC
** * * *
39850635 CGCACACACAGTGCCATACCCTTCGAGCT
1 CGCACACTTAGTGCCATACCATTCAAGCC
* * *
39850664 CGCACACTTAGTGCCATA-TATTTCCAGCA
1 CGCACACTTAGTGCCATACCA-TTCAAGCC
*
39850693 TGCACACTTAGTGCCATA
1 CGCACACTTAGTGCCATA
39850711 TATTTCCAGC
Statistics
Matches: 60, Mismatches: 15, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
29 60 1.00
ACGTcount: A:0.26, C:0.33, G:0.17, T:0.24
Consensus pattern (29 bp):
CGCACACTTAGTGCCATACCATTCAAGCC
Found at i:39850698 original size:58 final size:59
Alignment explanation
Indices: 39850644--39850766 Score: 178
Period size: 58 Copynumber: 2.1 Consensus size: 59
39850634 CCGCACACAC
* *
39850644 AGTGCCATACCCTTCGAGC-TCGCACACTTAGTGCCATATATTTCCAGCATGCACACTT
1 AGTGCCATACACTTCCAGCATCGCACACTTAGTGCCATATATTTCCAGCATGCACACTT
* * * *
39850702 AGTGCCATATATTTCCAGCAT-GCACACTCAGTGCCATATTTTTCCAGCATGCACACTT
1 AGTGCCATACACTTCCAGCATCGCACACTTAGTGCCATATATTTCCAGCATGCACACTT
39850760 AGTGCCA
1 AGTGCCA
39850767 ATCTCGTCAC
Statistics
Matches: 58, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
58 57 0.98
59 1 0.02
ACGTcount: A:0.25, C:0.31, G:0.15, T:0.28
Consensus pattern (59 bp):
AGTGCCATACACTTCCAGCATCGCACACTTAGTGCCATATATTTCCAGCATGCACACTT
Found at i:39850711 original size:29 final size:29
Alignment explanation
Indices: 39850665--39850766 Score: 186
Period size: 29 Copynumber: 3.5 Consensus size: 29
39850655 CTTCGAGCTC
39850665 GCACACTTAGTGCCATATATTTCCAGCAT
1 GCACACTTAGTGCCATATATTTCCAGCAT
39850694 GCACACTTAGTGCCATATATTTCCAGCAT
1 GCACACTTAGTGCCATATATTTCCAGCAT
* *
39850723 GCACACTCAGTGCCATATTTTTCCAGCAT
1 GCACACTTAGTGCCATATATTTCCAGCAT
39850752 GCACACTTAGTGCCA
1 GCACACTTAGTGCCA
39850767 ATCTCGTCAC
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 70 1.00
ACGTcount: A:0.26, C:0.29, G:0.15, T:0.29
Consensus pattern (29 bp):
GCACACTTAGTGCCATATATTTCCAGCAT
Found at i:39854901 original size:9 final size:9
Alignment explanation
Indices: 39854889--39854917 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
39854879 TTATAATAAA
39854889 TAATTAACT
1 TAATTAACT
39854898 TAATTAACT
1 TAATTAACT
39854907 TAATTAA-T
1 TAATTAACT
39854915 TAA
1 TAA
39854918 ACAAAACATG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 4 0.20
9 16 0.80
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (9 bp):
TAATTAACT
Found at i:39858410 original size:45 final size:45
Alignment explanation
Indices: 39858360--39858484 Score: 164
Period size: 45 Copynumber: 2.8 Consensus size: 45
39858350 AATTAGTCAA
* *
39858360 ACCATAGCTGAAAGATATTATGGCACCATGATAAAAATGAGTAAG
1 ACCATAGCTGAAAGATACTATGGCACCATGATAAAAATAAGTAAG
* * *
39858405 ACCATAGCT-AAATGATGCTATGGCATCATGATAGAAATAAGTAAG
1 ACCATAGCTGAAA-GATACTATGGCACCATGATAAAAATAAGTAAG
* *
39858450 ACCATAGCTGAAAGACACTATGGCAGCAT-ATAAAA
1 ACCATAGCTGAAAGATACTATGGCACCATGATAAAA
39858485 GCACCTCATA
Statistics
Matches: 69, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
44 8 0.12
45 58 0.84
46 3 0.04
ACGTcount: A:0.44, C:0.15, G:0.19, T:0.22
Consensus pattern (45 bp):
ACCATAGCTGAAAGATACTATGGCACCATGATAAAAATAAGTAAG
Found at i:39865724 original size:20 final size:21
Alignment explanation
Indices: 39865699--39865738 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
39865689 CTCTTGAAAC
*
39865699 AGGGC-ACACGCCCGTGTGGA
1 AGGGCAACACGCCCATGTGGA
39865719 AGGGCAACACGCCCATGTGG
1 AGGGCAACACGCCCATGTGG
39865739 CCACTATGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.23, C:0.30, G:0.38, T:0.10
Consensus pattern (21 bp):
AGGGCAACACGCCCATGTGGA
Found at i:39866979 original size:46 final size:46
Alignment explanation
Indices: 39866774--39867088 Score: 183
Period size: 47 Copynumber: 6.6 Consensus size: 46
39866764 GTATAATGCC
* * *
39866774 GATGCCATGTCCCAGACATGGTCTTACACTGGC-TCACCCATCAAGTC-
1 GATGCCATGTCCCAGACAT-GTCTTACACTGGCTTCA--TATCGAGGCT
* * * ** * * *
39866821 AATGCCATGTTCCAGACATGGTCTTACATTAACTATCGAAATTGAGGTT
1 GATGCCATGTCCCAGACAT-GTCTTACACTGGCT-TC-ATATCGAGGCT
* * * * * * *
39866870 GACGTCATGTTCCTGACATGGTCTTACACTAGCTCTCACATATCCG-TGCC
1 GATGCCATGTCCCAGACAT-GTCTTACACTGGCT-T--CATAT-CGAGGCT
* *
39866920 GATGCCATGTCCCAGACATGTCTTGCACTGGCTTACATCTCGAGGCT
1 GATGCCATGTCCCAGACATGTCTTACACTGGCTT-CATATCGAGGCT
* * * * *
39866967 GATG-CATGTCCCAAACATGTCTTACACTAGCTCTCGTATCAATGCT
1 GATGCCATGTCCCAGACATGTCTTACACTGGCT-TCATATCGAGGCT
*
39867013 GATGCCATGTCCCAGACATGGTCTTACACTGGCTTTCATAAT-GTGGCT
1 GATGCCATGTCCCAGACAT-GTCTTACACTGGC-TTCAT-ATCGAGGCT
** *
39867061 GATG-CATGTCAAAGACATGCCTTACACT
1 GATGCCATGTCCCAGACATGTCTTACACT
39867089 AGCACACAAA
Statistics
Matches: 208, Mismatches: 47, Indels: 27
0.74 0.17 0.10
Matches are distributed among these distances:
46 48 0.23
47 65 0.31
48 27 0.13
49 46 0.22
50 20 0.10
51 2 0.01
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.29
Consensus pattern (46 bp):
GATGCCATGTCCCAGACATGTCTTACACTGGCTTCATATCGAGGCT
Found at i:39867062 original size:94 final size:94
Alignment explanation
Indices: 39866884--39867091 Score: 260
Period size: 94 Copynumber: 2.2 Consensus size: 94
39866874 TCATGTTCCT
** *
39866884 GACATGGTCTTACACTAGCTCTCACATATCCGTGCCGATGCCATGTCCCAGACATGTCTTGCACT
1 GACAT-GTCTTACACTAGCTCT-ACATATCAATGCCGATGCCATGTCCCAGACATGTCTTACACT
* *
39866949 GGCTTACATCTCGAGGCTGATGCATGTCCCAA
64 GGCTTACATATCGAGGCTGATGCATGT-CAAA
* *
39866981 -ACATGTCTTACACTAGCTCT-CGTATCAATGCTGATGCCATGTCCCAGACATGGTCTTACACTG
1 GACATGTCTTACACTAGCTCTACATATCAATGCCGATGCCATGTCCCAGACAT-GTCTTACACTG
* *
39867044 GCTTTCATAAT-GTGGCTGATGCATGTCAAA
65 GCTTACAT-ATCGAGGCTGATGCATGTCAAA
*
39867074 GACATGCCTTACACTAGC
1 GACATGTCTTACACTAGC
39867092 ACACAAATAA
Statistics
Matches: 98, Mismatches: 10, Indels: 9
0.84 0.09 0.08
Matches are distributed among these distances:
93 30 0.31
94 47 0.48
95 17 0.17
96 4 0.04
ACGTcount: A:0.24, C:0.28, G:0.20, T:0.28
Consensus pattern (94 bp):
GACATGTCTTACACTAGCTCTACATATCAATGCCGATGCCATGTCCCAGACATGTCTTACACTGG
CTTACATATCGAGGCTGATGCATGTCAAA
Found at i:39867069 original size:47 final size:47
Alignment explanation
Indices: 39866875--39867091 Score: 176
Period size: 46 Copynumber: 4.6 Consensus size: 47
39866865 AGGTTGACGT
* * * *
39866875 CATGTTCCTGACATGGTCTTACACTAGCTCTCACATATCCGTGCCGATGC
1 CATGTCCCAGACAT-GTCTTACACTAGCTCTCATA-AT-CGTGCTGATGC
* * * *
39866925 CATGTCCCAGACATGTCTTGCACTGGCT-TACAT-CTCGAGGCTGATG-
1 CATGTCCCAGACATGTCTTACACTAGCTCT-CATAATCG-TGCTGATGC
* * *
39866971 CATGTCCCAAACATGTCTTACACTAGCTCTCGT-ATCAATGCTGATGC
1 CATGTCCCAGACATGTCTTACACTAGCTCTCATAATC-GTGCTGATGC
* *
39867018 CATGTCCCAGACATGGTCTTACACTGGCTTTCATAAT-GTGGCTGATG-
1 CATGTCCCAGACAT-GTCTTACACTAGCTCTCATAATCGT-GCTGATGC
** *
39867065 CATGTCAAAGACATGCCTTACACTAGC
1 CATGTCCCAGACATGTCTTACACTAGC
39867092 ACACAAATAA
Statistics
Matches: 135, Mismatches: 24, Indels: 20
0.75 0.13 0.11
Matches are distributed among these distances:
46 49 0.36
47 34 0.25
48 24 0.18
49 16 0.12
50 12 0.09
ACGTcount: A:0.23, C:0.29, G:0.19, T:0.29
Consensus pattern (47 bp):
CATGTCCCAGACATGTCTTACACTAGCTCTCATAATCGTGCTGATGC
Found at i:39876617 original size:47 final size:49
Alignment explanation
Indices: 39876544--39876896 Score: 184
Period size: 47 Copynumber: 7.4 Consensus size: 49
39876534 GGGTATAATA
*
39876544 TCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATC-CATCAA-G
1 TCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCAAATCAAGG
* * *
39876591 TCGATGCCATGTCCCAGACATAGTCTTACAATGACT-ATCGAAATCAAGG
1 TCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATC-AAATCAAGG
* * * * *
39876640 TCGACGCCATGTCTCAGACATGGTTTTACACTAGCTC-TCATATATC-CGTG
1 TCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCA-A-ATCAAG-G
* * * * * * * *
39876690 CCAATACCATGTCCTAGACATGGTCTTACACTGACACATC---TCGTAGC
1 TCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCAAATC-AAGG
* * ** *
39876737 T-GATG-CATGTCCTAGACAT-GTCTTACACTGGCTTA-CATCTCGAGG
1 TCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCAAATCAAGG
* * * ** *** * *
39876782 CCGATG-TATGTCCCAGAC-TTGTCTTACACTAACTC-TCGTCTTAATG
1 TCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCAAATCAAGG
* * * * *
39876828 CCGATGCCAAGTCCTAGGCATGGTCTTACACTGGCTC-TCATAAT-ATGG
1 TCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCA-AATCAAGG
*
39876876 CCGATG-CATGTCCCAGACATG
1 TCGATGCCATGTCCCAGACATG
39876897 CCTTATACTA
Statistics
Matches: 230, Mismatches: 57, Indels: 38
0.71 0.18 0.12
Matches are distributed among these distances:
43 1 0.00
44 13 0.06
45 17 0.07
46 47 0.20
47 53 0.23
48 31 0.13
49 35 0.15
50 31 0.13
51 2 0.01
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.28
Consensus pattern (49 bp):
TCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCAAATCAAGG
Found at i:39876793 original size:46 final size:44
Alignment explanation
Indices: 39876697--39876860 Score: 143
Period size: 46 Copynumber: 3.6 Consensus size: 44
39876687 GTGCCAATAC
*
39876697 CATGTCCTAGACATGGTCTTACACTGACACATCTCGTAGCTGATG
1 CATGTCCTAGACAT-GTCTTACACTGACACATCTCGTAGCCGATG
*
39876742 CATGTCCTAGACATGTCTTACACTGGCTTACATCTCG-AGGCCGATG
1 CATGTCCTAGACATGTCTTACACTGAC--ACATCTCGTA-GCCGATG
* * * * * *
39876788 TATGTCCCAGACTTGTCTTACACTAACTC-TCGTCTTAATGCCGATG
1 CATGTCCTAGACATGTCTTACACTGACACATC-TCGT-A-GCCGATG
* *
39876834 CCAAGTCCTAGGCATGGTCTTACACTG
1 -CATGTCCTAGACAT-GTCTTACACTG
39876861 GCTCTCATAA
Statistics
Matches: 95, Mismatches: 16, Indels: 13
0.77 0.13 0.10
Matches are distributed among these distances:
43 2 0.02
44 15 0.16
45 15 0.16
46 44 0.46
47 9 0.09
48 10 0.11
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.30
Consensus pattern (44 bp):
CATGTCCTAGACATGTCTTACACTGACACATCTCGTAGCCGATG
Found at i:39877300 original size:30 final size:30
Alignment explanation
Indices: 39877244--39877300 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
39877234 CATAATTAGG
* *
39877244 CAAAATGATCATTTTGCCCTTAGACTTTCA
1 CAAAATGACCATTTTCCCCTTAGACTTTCA
39877274 CAAAATGACCATTTTACCCCTT-GACTT
1 CAAAATGACCATTTT-CCCCTTAGACTT
39877301 GAAAATTGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 19 0.79
31 5 0.21
ACGTcount: A:0.30, C:0.26, G:0.09, T:0.35
Consensus pattern (30 bp):
CAAAATGACCATTTTCCCCTTAGACTTTCA
Found at i:39880258 original size:93 final size:93
Alignment explanation
Indices: 39880146--39880316 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
39880136 GCCCATAAGT
* *
39880146 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
39880211 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
*
39880239 GAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
39880304 CGAGTTCGGATGC
66 CGAGTTCGGATGC
39880317 TCAACCATCC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.27, C:0.30, G:0.22, T:0.20
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:39880332 original size:46 final size:46
Alignment explanation
Indices: 39880138--39880318 Score: 233
Period size: 46 Copynumber: 3.9 Consensus size: 46
39880128 TGTAACCCGC
* * *
39880138 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
* *
39880184 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACG-CTCG---CAT
* *
39880234 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
*
39880277 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTC
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTC
39880319 AACCATCCTA
Statistics
Matches: 116, Mismatches: 12, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
43 3 0.03
44 1 0.01
45 2 0.02
46 72 0.62
47 32 0.28
48 2 0.02
49 1 0.01
50 3 0.03
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
Found at i:39882727 original size:30 final size:30
Alignment explanation
Indices: 39882683--39882771 Score: 101
Period size: 30 Copynumber: 3.0 Consensus size: 30
39882673 CAAAGATAAC
39882683 AAGAAAACC-GAATAAAGAAATCCAAGATA
1 AAGAAAACCAGAATAAAGAAATCCAAGATA
* *
39882712 GAGAAACCCAGAATAAAGAAATCC-AGAATA
1 AAGAAAACCAGAATAAAGAAATCCAAG-ATA
* * * *
39882742 AAGAGATCCAGGATAAAGAAACCCAAGATA
1 AAGAAAACCAGAATAAAGAAATCCAAGATA
39882772 CGATACTATG
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
29 9 0.18
30 39 0.78
31 2 0.04
ACGTcount: A:0.57, C:0.16, G:0.17, T:0.10
Consensus pattern (30 bp):
AAGAAAACCAGAATAAAGAAATCCAAGATA
Found at i:39882731 original size:15 final size:15
Alignment explanation
Indices: 39882683--39882762 Score: 92
Period size: 15 Copynumber: 5.4 Consensus size: 15
39882673 CAAAGATAAC
*
39882683 AAGAAAACC-GAATA
1 AAGAAATCCAGAATA
39882697 AAGAAATCCA-AGATA
1 AAGAAATCCAGA-ATA
* *
39882712 GAGAAACCCAGAATA
1 AAGAAATCCAGAATA
39882727 AAGAAATCCAGAATA
1 AAGAAATCCAGAATA
* *
39882742 AAGAGATCCAGGATA
1 AAGAAATCCAGAATA
39882757 AAGAAA
1 AAGAAA
39882763 CCCAAGATAC
Statistics
Matches: 55, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
14 9 0.16
15 45 0.82
16 1 0.02
ACGTcount: A:0.59, C:0.14, G:0.17, T:0.10
Consensus pattern (15 bp):
AAGAAATCCAGAATA
Found at i:39882771 original size:15 final size:15
Alignment explanation
Indices: 39882694--39882771 Score: 79
Period size: 15 Copynumber: 5.2 Consensus size: 15
39882684 AGAAAACCGA
39882694 ATAAAGAAATCCAAG
1 ATAAAGAAATCCAAG
* *
39882709 ATAGAGAAA-CCCAG
1 ATAAAGAAATCCAAG
39882723 AATAAAGAAATCC-AG
1 -ATAAAGAAATCCAAG
* *
39882738 AATAAAGAGATCCAGG
1 -ATAAAGAAATCCAAG
*
39882754 ATAAAGAAACCCAAG
1 ATAAAGAAATCCAAG
39882769 ATA
1 ATA
39882772 CGATACTATG
Statistics
Matches: 52, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
14 4 0.08
15 45 0.87
16 3 0.06
ACGTcount: A:0.56, C:0.15, G:0.17, T:0.12
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:39885794 original size:93 final size:93
Alignment explanation
Indices: 39885682--39885853 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
39885672 GCCCATAAGT
* *
39885682 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
39885747 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
*
39885775 GAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
39885840 CGAGTTCGGATGCC
66 CGAGTTCGGATGCC
39885854 AACCATCCTA
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.27, C:0.30, G:0.22, T:0.20
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:39885849 original size:46 final size:46
Alignment explanation
Indices: 39885674--39885849 Score: 232
Period size: 46 Copynumber: 3.8 Consensus size: 46
39885664 TGTAACCCGC
* * *
39885674 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
* *
39885720 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACG-CTCG---CAT
* *
39885770 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
39885813 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
39885850 TGCCAACCAT
Statistics
Matches: 112, Mismatches: 11, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
43 3 0.03
44 1 0.01
45 2 0.02
46 68 0.61
47 32 0.29
48 2 0.02
49 1 0.01
50 3 0.03
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.20
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
Found at i:39889943 original size:18 final size:19
Alignment explanation
Indices: 39889916--39889957 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
39889906 TGAGAAAATT
*
39889916 ATTTAATTAA-GAAATTTA
1 ATTTAATTAATGAAATTAA
* *
39889934 ATTTAGTTAATTAAATTAA
1 ATTTAATTAATGAAATTAA
39889953 ATTTA
1 ATTTA
39889958 TTTAGGGAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (19 bp):
ATTTAATTAATGAAATTAA
Found at i:39891208 original size:11 final size:11
Alignment explanation
Indices: 39891182--39891214 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
39891172 AAATAAATCA
*
39891182 TATATAT-ATA
1 TATATATGATT
39891192 TATATATGATT
1 TATATATGATT
39891203 TATATATGATT
1 TATATATGATT
39891214 T
1 T
39891215 TCACTTTAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
10 7 0.33
11 14 0.67
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (11 bp):
TATATATGATT
Found at i:39893278 original size:23 final size:22
Alignment explanation
Indices: 39893243--39893322 Score: 97
Period size: 23 Copynumber: 3.5 Consensus size: 22
39893233 ATTGAATCAC
*
39893243 ATAGGTTTGCATAATAGTTCAT
1 ATAGGTTCGCATAATAGTTCAT
*
39893265 ATAGGATTCGCATAATAGTTCAC
1 ATAGG-TTCGCATAATAGTTCAT
* *
39893288 ATAAGGTTCGCATACTAATTCAT
1 AT-AGGTTCGCATAATAGTTCAT
39893311 ATAGGATTCGCA
1 ATAGG-TTCGCA
39893323 CATTAAATCA
Statistics
Matches: 50, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
22 8 0.16
23 39 0.78
24 3 0.06
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Consensus pattern (22 bp):
ATAGGTTCGCATAATAGTTCAT
Found at i:39893334 original size:46 final size:45
Alignment explanation
Indices: 39893226--39893334 Score: 137
Period size: 46 Copynumber: 2.4 Consensus size: 45
39893216 CACATGAGGG
* * *
39893226 TTCGCATATTGAATCACATAGGTTTGCATAATAGTTCATATAGGA
1 TTCGCATATTAAATCACATAGGTTCGCATAATAATTCATATAGGA
* ** *
39893271 TTCGCATAATAGTTCACATAAGGTTCGCATACTAATTCATATAGGA
1 TTCGCATATTAAATCACAT-AGGTTCGCATAATAATTCATATAGGA
*
39893317 TTCGCACATTAAATCACA
1 TTCGCATATTAAATCACA
39893335 GACTAAATTT
Statistics
Matches: 52, Mismatches: 11, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
45 15 0.29
46 37 0.71
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (45 bp):
TTCGCATATTAAATCACATAGGTTCGCATAATAATTCATATAGGA
Found at i:39895209 original size:20 final size:21
Alignment explanation
Indices: 39895180--39895256 Score: 69
Period size: 19 Copynumber: 4.0 Consensus size: 21
39895170 TATTTTTAAG
39895180 AAAATGTTAATAA-TATTATTT
1 AAAATGTTAA-AATTATTATTT
39895201 AAAAT-TTAAAATTATTA-TT
1 AAAATGTTAAAATTATTATTT
* **
39895220 --AATGTTAAAATTAATAGAT
1 AAAATGTTAAAATTATTATTT
39895239 -AAAT-TTAAAATTATTATT
1 AAAATGTTAAAATTATTATT
39895257 AATGAATTTT
Statistics
Matches: 47, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
17 3 0.06
18 11 0.23
19 16 0.34
20 12 0.26
21 5 0.11
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (21 bp):
AAAATGTTAAAATTATTATTT
Found at i:39901815 original size:2 final size:2
Alignment explanation
Indices: 39901808--39901835 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
39901798 AGGAGATAAT
39901808 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
39901836 AATATTGGGA
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:39901896 original size:4 final size:4
Alignment explanation
Indices: 39901887--39901911 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
39901877 ACTGTCACAA
39901887 ACAT ACAT ACAT ACAT ACAT ACAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT A
39901912 TTATGCATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:39910446 original size:21 final size:21
Alignment explanation
Indices: 39910420--39910468 Score: 98
Period size: 21 Copynumber: 2.3 Consensus size: 21
39910410 TGACAGGTGT
39910420 AGAGTGAGGAAAAGAAATGAA
1 AGAGTGAGGAAAAGAAATGAA
39910441 AGAGTGAGGAAAAGAAATGAA
1 AGAGTGAGGAAAAGAAATGAA
39910462 AGAGTGA
1 AGAGTGA
39910469 AGTTTTTGTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.55, C:0.00, G:0.35, T:0.10
Consensus pattern (21 bp):
AGAGTGAGGAAAAGAAATGAA
Found at i:39915429 original size:64 final size:64
Alignment explanation
Indices: 39915348--39915527 Score: 168
Period size: 67 Copynumber: 2.8 Consensus size: 64
39915338 AGACATTATG
* *
39915348 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * * * * *
39915412 ATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACATCGTGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
39915477 AA
63 AA
* * * *
39915479 ACTG--GCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-GTACAAGA
1 A-TGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAG-ACAAGA
39915528 AGCCGAACTA
Statistics
Matches: 90, Mismatches: 21, Indels: 11
0.74 0.17 0.09
Matches are distributed among these distances:
62 1 0.01
63 13 0.14
64 21 0.23
65 8 0.09
66 16 0.18
67 29 0.32
68 2 0.02
ACGTcount: A:0.29, C:0.17, G:0.30, T:0.24
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:39916617 original size:2 final size:2
Alignment explanation
Indices: 39916610--39916636 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
39916600 TCATGACATG
39916610 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
39916637 GACTAGTCTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:39921954 original size:37 final size:37
Alignment explanation
Indices: 39921901--39921991 Score: 155
Period size: 37 Copynumber: 2.4 Consensus size: 37
39921891 TTATTACGAA
39921901 GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG
1 GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG
*
39921938 GTCTTACCCGGTCATAATCTCCACACGTAGTCATCGG
1 GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG
*
39921975 GTCTCACCCGGAACATA
1 GTCTTACCCGG-ACATA
39921992 TTCCAAGTTT
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
37 46 0.92
38 4 0.08
ACGTcount: A:0.24, C:0.33, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG
Found at i:39922229 original size:47 final size:47
Alignment explanation
Indices: 39922087--39922303 Score: 301
Period size: 47 Copynumber: 4.5 Consensus size: 47
39922077 TTTTACATTA
39922087 GCCATTAGGCCTTATCACATATATATACACTTTCACATTCACCACATCG
1 GCCATTAGGCCTTATCAC--ATATATACACTTTCACATTCACCACATCG
*
39922136 GCCATTAGGCCTCATCACATATACATACACTTTCACATTCACCACATCG
1 GCCATTAGGCCTTATCACATAT--ATACACTTTCACATTCACCACATCG
* *
39922185 GCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATTG
1 GCCATTAGGCCTTATCACATATATACACTTTCACATTCACCACATCG
* * * *
39922232 GCCA-TACGGCCTTATCACACATATGCACTTTCACATTCATCACATTG
1 GCCATTA-GGCCTTATCACATATATACACTTTCACATTCACCACATCG
* *
39922279 GCCATTCGGCCTTATCACACATATA
1 GCCATTAGGCCTTATCACATATATA
39922304 TGTATATCAT
Statistics
Matches: 156, Mismatches: 8, Indels: 10
0.90 0.05 0.06
Matches are distributed among these distances:
46 2 0.01
47 90 0.58
48 1 0.01
49 63 0.40
ACGTcount: A:0.29, C:0.31, G:0.09, T:0.30
Consensus pattern (47 bp):
GCCATTAGGCCTTATCACATATATACACTTTCACATTCACCACATCG
Found at i:39922304 original size:96 final size:97
Alignment explanation
Indices: 39922081--39922304 Score: 312
Period size: 96 Copynumber: 2.3 Consensus size: 97
39922071 CATATATTTT
* *
39922081 ACATTAGCCATTAGGCCTTATCACATATATATACACTTTCACATTCACCACATCGGCCATTAGGC
1 ACATTGGCCATTAGGCCTTATCACACATATATACACTTTCACATTCACCACATCGGCCATTAGGC
*
39922146 CTCATCACATATACATACACTTTCACATTCACC
66 CTCATCACACATA-ATACACTTTCACATTCACC
* * *
39922179 ACATCGGCCATTAGGCCTTAT--CACATATATACACTTTCACATTCATCACATTGGCCA-TACGG
1 ACATTGGCCATTAGGCCTTATCACACATATATACACTTTCACATTCACCACATCGGCCATTA-GG
* * *
39922241 CCTTATCACACAT-ATGCACTTTCACATTCATC
65 CCTCATCACACATAATACACTTTCACATTCACC
*
39922273 ACATTGGCCATTCGGCCTTATCACACATATAT
1 ACATTGGCCATTAGGCCTTATCACACATATAT
39922305 GTATATCATA
Statistics
Matches: 112, Mismatches: 11, Indels: 8
0.85 0.08 0.06
Matches are distributed among these distances:
94 36 0.32
95 2 0.02
96 55 0.49
98 19 0.17
ACGTcount: A:0.30, C:0.31, G:0.09, T:0.30
Consensus pattern (97 bp):
ACATTGGCCATTAGGCCTTATCACACATATATACACTTTCACATTCACCACATCGGCCATTAGGC
CTCATCACACATAATACACTTTCACATTCACC
Found at i:39925451 original size:29 final size:29
Alignment explanation
Indices: 39925415--39925722 Score: 553
Period size: 29 Copynumber: 10.6 Consensus size: 29
39925405 TGTTGAAAAA
*
39925415 CTCGCACACACAGTGCCTCAATTACTGAT
1 CTCGCACACATAGTGCCTCAATTACTGAT
39925444 CTCGCACACATAGTGCCTCAATTACTGAT
1 CTCGCACACATAGTGCCTCAATTACTGAT
39925473 CTCGCACACATAGTGCCTCAATTACTGAT
1 CTCGCACACATAGTGCCTCAATTACTGAT
39925502 CTCGCACACATAGTGCCTCAATTACTGAT
1 CTCGCACACATAGTGCCTCAATTACTGAT
39925531 CTCGCACACATAGTGCCTCAATTACTGAT
1 CTCGCACACATAGTGCCTCAATTACTGAT
39925560 CTCGCACACACATAGTGCCTCAATTACTGAT
1 CTCG--CACACATAGTGCCTCAATTACTGAT
*
39925591 CTCGCATACATAGTGCCTCAATTACTGAT
1 CTCGCACACATAGTGCCTCAATTACTGAT
*
39925620 CTCGCACACATAGTGCCTCAATTATTGAT
1 CTCGCACACATAGTGCCTCAATTACTGAT
*
39925649 CTCACACACATAGTGCCTCAATTACTGAT
1 CTCGCACACATAGTGCCTCAATTACTGAT
*
39925678 CTCGCACACATAGTGCCTCGATTACTGAT
1 CTCGCACACATAGTGCCTCAATTACTGAT
39925707 CTCGCACACATAGTGC
1 CTCGCACACATAGTGC
39925723 TCGGTTAACG
Statistics
Matches: 269, Mismatches: 8, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
29 240 0.89
31 29 0.11
ACGTcount: A:0.28, C:0.31, G:0.14, T:0.27
Consensus pattern (29 bp):
CTCGCACACATAGTGCCTCAATTACTGAT
Found at i:39925577 original size:147 final size:145
Alignment explanation
Indices: 39925415--39925722 Score: 553
Period size: 147 Copynumber: 2.1 Consensus size: 145
39925405 TGTTGAAAAA
39925415 CTCGCACACACAGTGCCTCAATTACTGATCTCGCACACATAGTGCCTCAATTACTGATCTCGCAC
1 CTCGCACACACAGTGCCTCAATTACTGATCTCGCACACATAGTGCCTCAATTACTGATCTCGCAC
*
39925480 ACATAGTGCCTCAATTACTGATCTCGCACACATAGTGCCTCAATTACTGATCTCGCACACATAGT
66 ACATAGTGCCTCAATTACTGATCTCACACACATAGTGCCTCAATTACTGATCTCGCACACATAGT
39925545 GCCTCAATTACTGAT
131 GCCTCAATTACTGAT
*
39925560 CTCGCACACACATAGTGCCTCAATTACTGATCTCGCATACATAGTGCCTCAATTACTGATCTCGC
1 CTCGCACACAC--AGTGCCTCAATTACTGATCTCGCACACATAGTGCCTCAATTACTGATCTCGC
*
39925625 ACACATAGTGCCTCAATTATTGATCTCACACACATAGTGCCTCAATTACTGATCTCGCACACATA
64 ACACATAGTGCCTCAATTACTGATCTCACACACATAGTGCCTCAATTACTGATCTCGCACACATA
*
39925690 GTGCCTCGATTACTGAT
129 GTGCCTCAATTACTGAT
*
39925707 CTCGCACACATAGTGC
1 CTCGCACACACAGTGC
39925723 TCGGTTAACG
Statistics
Matches: 156, Mismatches: 5, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
145 16 0.10
147 140 0.90
ACGTcount: A:0.28, C:0.31, G:0.14, T:0.27
Consensus pattern (145 bp):
CTCGCACACACAGTGCCTCAATTACTGATCTCGCACACATAGTGCCTCAATTACTGATCTCGCAC
ACATAGTGCCTCAATTACTGATCTCACACACATAGTGCCTCAATTACTGATCTCGCACACATAGT
GCCTCAATTACTGAT
Found at i:39927860 original size:37 final size:37
Alignment explanation
Indices: 39927807--39927897 Score: 155
Period size: 37 Copynumber: 2.4 Consensus size: 37
39927797 TTATTACGAA
39927807 GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG
1 GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG
*
39927844 GTCTTACCCGGTCATAATCTCCACACGTAGTCATCGG
1 GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG
*
39927881 GTCTCACCCGGAACATA
1 GTCTTACCCGG-ACATA
39927898 TTCCAAGTTT
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
37 46 0.92
38 4 0.08
ACGTcount: A:0.24, C:0.33, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG
Found at i:39928048 original size:49 final size:49
Alignment explanation
Indices: 39927993--39928212 Score: 320
Period size: 49 Copynumber: 4.5 Consensus size: 49
39927983 TTTTACATTA
39927993 GCCATTAGGCCTTATCACATATATATACACTTTCACATTCACCACATCG
1 GCCATTAGGCCTTATCACATATATATACACTTTCACATTCACCACATCG
*
39928042 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
1 GCCATTAGGCCTTATCACATATATATACACTTTCACATTCACCACATCG
* * *
39928091 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCATCACATTG
1 GCCATTAGGCCTTATCACATATATATACACTTTCACATTCACCACATCG
* * * *
39928140 GCCA-TACGGCCTTATCAC--ACATATGCACTTTCACATTCATCACATTG
1 GCCATTA-GGCCTTATCACATATATATACACTTTCACATTCACCACATCG
* *
39928187 GCCATTCGGCCTTATCACACATATAT
1 GCCATTAGGCCTTATCACATATATAT
39928213 GTATATCATA
Statistics
Matches: 159, Mismatches: 8, Indels: 8
0.91 0.05 0.05
Matches are distributed among these distances:
47 41 0.26
48 3 0.02
49 115 0.72
ACGTcount: A:0.30, C:0.31, G:0.09, T:0.30
Consensus pattern (49 bp):
GCCATTAGGCCTTATCACATATATATACACTTTCACATTCACCACATCG
Found at i:39931591 original size:28 final size:28
Alignment explanation
Indices: 39931551--39931620 Score: 97
Period size: 28 Copynumber: 2.5 Consensus size: 28
39931541 ATGAAAATTT
** *
39931551 CACTAAGCATGCGAGTTTGGTTAAT-GAG
1 CACTAAGTGTGCGAGTTTGATT-ATCGAG
39931579 CACTAAGTGTGCGAGTTTGATTATCGAG
1 CACTAAGTGTGCGAGTTTGATTATCGAG
39931607 CACTAAGTGTGCGA
1 CACTAAGTGTGCGA
39931621 AGGAAAATAT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
27 2 0.05
28 36 0.95
ACGTcount: A:0.27, C:0.16, G:0.29, T:0.29
Consensus pattern (28 bp):
CACTAAGTGTGCGAGTTTGATTATCGAG
Found at i:39948212 original size:2 final size:2
Alignment explanation
Indices: 39948205--39948231 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
39948195 AATCATATTC
39948205 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 A
39948232 ACATATTACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:39950112 original size:44 final size:43
Alignment explanation
Indices: 39949976--39950124 Score: 142
Period size: 44 Copynumber: 3.5 Consensus size: 43
39949966 CAACGCCAAC
* * * * *
39949976 GTCCTAGACGTGGTCTTACATGTTATCACATATCGATGTCACT
1 GTCCCAGACATGGTCTTACAAGTAATTACATATCGATGTCACT
* * * * *
39950019 GTCCCAGACAGGGTCTTACACG-AACT-CATATACAATGCCGA-T
1 GTCCCAGACATGGTCTTACAAGTAATTACATAT-CGATGTC-ACT
*
39950061 GTCCCAGACATGGTCTTACAAGTAAATTACAAATCGATGTCACT
1 GTCCCAGACATGGTCTTACAAGT-AATTACATATCGATGTCACT
*
39950105 GTCCCAGACGTGGTCTTACA
1 GTCCCAGACATGGTCTTACA
39950125 CGAAATCACA
Statistics
Matches: 84, Mismatches: 16, Indels: 11
0.76 0.14 0.10
Matches are distributed among these distances:
41 5 0.06
42 27 0.32
43 20 0.24
44 28 0.33
45 4 0.05
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.28
Consensus pattern (43 bp):
GTCCCAGACATGGTCTTACAAGTAATTACATATCGATGTCACT
Found at i:39962499 original size:22 final size:22
Alignment explanation
Indices: 39962474--39962518 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
39962464 AAAAAAATTG
39962474 TAGGAATATTCTGTAAATATTT
1 TAGGAATATTCTGTAAATATTT
* *
39962496 TAGGAATATTTTGTAGATATTT
1 TAGGAATATTCTGTAAATATTT
39962518 T
1 T
39962519 TTTTATTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.33, C:0.02, G:0.16, T:0.49
Consensus pattern (22 bp):
TAGGAATATTCTGTAAATATTT
Found at i:39967099 original size:22 final size:22
Alignment explanation
Indices: 39967071--39967115 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
39967061 AGGGGGAGTG
39967071 TAGGAATATTCTGTAAATATTT
1 TAGGAATATTCTGTAAATATTT
* *
39967093 TAGGAATATTTTGTAGATATTT
1 TAGGAATATTCTGTAAATATTT
39967115 T
1 T
39967116 TTTTATTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.33, C:0.02, G:0.16, T:0.49
Consensus pattern (22 bp):
TAGGAATATTCTGTAAATATTT
Found at i:39969322 original size:3 final size:3
Alignment explanation
Indices: 39969316--39969355 Score: 62
Period size: 3 Copynumber: 13.3 Consensus size: 3
39969306 GATAATAATG
* *
39969316 ACA ACA ACA ACA ACA ACA ACA ATA ACA ATA ACA ACA ACA A
1 ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA A
39969356 AACTAAGCAC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.68, C:0.28, G:0.00, T:0.05
Consensus pattern (3 bp):
ACA
Found at i:39971251 original size:31 final size:31
Alignment explanation
Indices: 39971202--39971275 Score: 94
Period size: 31 Copynumber: 2.4 Consensus size: 31
39971192 CAAAAAAAAA
* * * *
39971202 TTTAACAGCTCAATGACTTAAATAAAATTTT
1 TTTAATAGTTCAAAGACTTAAATAAAAATTT
39971233 TTTAATAGTTCAAAGACTTAAATAAAAATTT
1 TTTAATAGTTCAAAGACTTAAATAAAAATTT
* *
39971264 TTGAATAATTCA
1 TTTAATAGTTCA
39971276 GTAACCAAAT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.45, C:0.09, G:0.07, T:0.39
Consensus pattern (31 bp):
TTTAATAGTTCAAAGACTTAAATAAAAATTT
Found at i:39971903 original size:45 final size:45
Alignment explanation
Indices: 39971852--39971937 Score: 136
Period size: 45 Copynumber: 1.9 Consensus size: 45
39971842 AGATATTTTG
* *
39971852 TTAAGAGTTTAATTAATATTTGATTTATCTATATTTAGTTAGTTA
1 TTAAGAGTTTAACTAATATTTGATGTATCTATATTTAGTTAGTTA
* *
39971897 TTAAGAGTTTAACTAATATTTTATGTATCTTTATTTAGTTA
1 TTAAGAGTTTAACTAATATTTGATGTATCTATATTTAGTTA
39971938 AATAAATGGT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 37 1.00
ACGTcount: A:0.33, C:0.03, G:0.10, T:0.53
Consensus pattern (45 bp):
TTAAGAGTTTAACTAATATTTGATGTATCTATATTTAGTTAGTTA
Found at i:39977656 original size:25 final size:25
Alignment explanation
Indices: 39977624--39977684 Score: 79
Period size: 25 Copynumber: 2.4 Consensus size: 25
39977614 TTTCTTATCC
*
39977624 CAATTTTACCCCTA-AATTTTTTTGA
1 CAATTTTACCCCCATAA-TTTTTTGA
39977649 CAATTTTACCCCCATAATTTTTTGA
1 CAATTTTACCCCCATAATTTTTTGA
**
39977674 TGATTTTACCC
1 CAATTTTACCC
39977685 TTGGTAAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
25 30 0.94
26 2 0.06
ACGTcount: A:0.26, C:0.23, G:0.05, T:0.46
Consensus pattern (25 bp):
CAATTTTACCCCCATAATTTTTTGA
Found at i:39977873 original size:12 final size:12
Alignment explanation
Indices: 39977843--39977880 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
39977833 TGCAAATGTA
39977843 TCATTTCTC-TTT
1 TCATTTC-CATTT
39977855 CTCATTTCCATTT
1 -TCATTTCCATTT
39977868 TCATTTCCATTT
1 TCATTTCCATTT
39977880 T
1 T
39977881 GAGAAAATCA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 14 0.58
13 10 0.42
ACGTcount: A:0.13, C:0.26, G:0.00, T:0.61
Consensus pattern (12 bp):
TCATTTCCATTT
Found at i:39978606 original size:40 final size:40
Alignment explanation
Indices: 39978561--39978640 Score: 142
Period size: 40 Copynumber: 2.0 Consensus size: 40
39978551 GTCATGCATA
* *
39978561 CATAGTTTGTCATCCACTCATGATTCAGGTATGGCACACT
1 CATAGTTTGTCATCCACTCATGATTCAAGTATGACACACT
39978601 CATAGTTTGTCATCCACTCATGATTCAAGTATGACACACT
1 CATAGTTTGTCATCCACTCATGATTCAAGTATGACACACT
39978641 ATGAACATTA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.28, C:0.25, G:0.15, T:0.33
Consensus pattern (40 bp):
CATAGTTTGTCATCCACTCATGATTCAAGTATGACACACT
Found at i:39983753 original size:48 final size:48
Alignment explanation
Indices: 39983645--39983836 Score: 163
Period size: 48 Copynumber: 4.0 Consensus size: 48
39983635 GTCATTAGGG
* * * * * * *
39983645 GATACATTGATTTAGCTTCGGGCCATAATATTAGCTCTTCGGGTGC-A
1 GATACATTGATTTGGCTTTGAGCCATGATATCAGCACTTCAGGTGCGA
* * * * * * *
39983692 AATTGCATAGATTTGGCTTCGAGACATGATATCAGCACTTCGGGTGTGA
1 GA-TACATTGATTTGGCTTTGAGCCATGATATCAGCACTTCAGGTGCGA
* * * * *
39983741 GCTTCATTGATTTGGCTTTGGGCCATGATATTAGAACTTCAGGTGCGA
1 GATACATTGATTTGGCTTTGAGCCATGATATCAGCACTTCAGGTGCGA
* *
39983789 GATACATTGAGTTGGCTTTGAGCCATGATATGAGCACTT-AGTGTGCGA
1 GATACATTGATTTGGCTTTGAGCCATGATATCAGCACTTCAG-GTGCGA
39983837 TATTCCTGAG
Statistics
Matches: 115, Mismatches: 27, Indels: 5
0.78 0.18 0.03
Matches are distributed among these distances:
47 3 0.03
48 111 0.97
49 1 0.01
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.33
Consensus pattern (48 bp):
GATACATTGATTTGGCTTTGAGCCATGATATCAGCACTTCAGGTGCGA
Found at i:39983816 original size:96 final size:96
Alignment explanation
Indices: 39983649--39983827 Score: 225
Period size: 96 Copynumber: 1.9 Consensus size: 96
39983639 TTAGGGGATA
** * * *
39983649 CATTGATTTAGCTTCGGGCCATAATATTAGCTCTTCGGGTGCAAATTGCATAGATTTGGCTTCGA
1 CATTGATTTAGCTTCGGGCCATAATATTAGAACTTCAGGTGCAAATTACATAGAGTTGGCTTCGA
39983714 GACATGATATCAGCACTTCGGGTGTGAGCTT
66 GACATGATATCAGCACTTCGGGTGTGAGCTT
* * * * * *
39983745 CATTGATTTGGCTTTGGGCCATGATATTAGAACTTCAGGTGCGAGA-TACATTGAGTTGGCTTTG
1 CATTGATTTAGCTTCGGGCCATAATATTAGAACTTCAGGTGC-AAATTACATAGAGTTGGCTTCG
* *
39983809 AGCCATGATATGAGCACTT
65 AGACATGATATCAGCACTT
39983828 AGTGTGCGAT
Statistics
Matches: 69, Mismatches: 13, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
96 67 0.97
97 2 0.03
ACGTcount: A:0.23, C:0.17, G:0.26, T:0.34
Consensus pattern (96 bp):
CATTGATTTAGCTTCGGGCCATAATATTAGAACTTCAGGTGCAAATTACATAGAGTTGGCTTCGA
GACATGATATCAGCACTTCGGGTGTGAGCTT
Found at i:39991001 original size:48 final size:48
Alignment explanation
Indices: 39990919--39991055 Score: 132
Period size: 48 Copynumber: 2.9 Consensus size: 48
39990909 GGGATACATT
* * * * * *
39990919 GATTTGGCTCCGGGCCATGATATTAGCTCCTCGGGTGCGAG-TTGCATA
1 GATTTGGCTTCAGGACATGATATCAGCACTTCGGGTGCGAGCTT-CATA
* * * *
39990967 GATTTGGCTTCAGGATATGATATCGGCACTTCGGGTTCGAGCTTCATT
1 GATTTGGCTTCAGGACATGATATCAGCACTTCGGGTGCGAGCTTCATA
* * * *
39991015 GATTTGGCTTCGGGCCATGATATTAGCACTTCAGGTGCGAG
1 GATTTGGCTTCAGGACATGATATCAGCACTTCGGGTGCGAG
39991056 ATAAATTCAG
Statistics
Matches: 71, Mismatches: 17, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
48 69 0.97
49 2 0.03
ACGTcount: A:0.18, C:0.20, G:0.30, T:0.31
Consensus pattern (48 bp):
GATTTGGCTTCAGGACATGATATCAGCACTTCGGGTGCGAGCTTCATA
Found at i:39991083 original size:96 final size:96
Alignment explanation
Indices: 39990915--39991093 Score: 225
Period size: 96 Copynumber: 1.9 Consensus size: 96
39990905 TTAGGGGATA
* * * ** * *
39990915 CATTGATTTGGCTCCGGGCCATGATATTAGCTCCTCGGGTGCGAGTTGCATAGATTTGGCTTCAG
1 CATTGATTTGGCTCCGGGCCATGATATTAGCACCTCAGGTGCGAGATAAATACAGTTGGCTTCAG
*
39990980 GATATGATATCG-GCACTTCGGGTTCGAGCTT
66 GACATGATAT-GAGCACTTCGGGTTCGAGCTT
* * * *
39991011 CATTGATTTGGCTTCGGGCCATGATATTAGCACTTCAGGTGCGAGATAAATTCAGTTGGCTTCGG
1 CATTGATTTGGCTCCGGGCCATGATATTAGCACCTCAGGTGCGAGATAAATACAGTTGGCTTCAG
*
39991076 GCCATGATATGAGCACTT
66 GACATGATATGAGCACTT
39991094 AGTGTGCAAG
Statistics
Matches: 69, Mismatches: 13, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
95 1 0.01
96 68 0.99
ACGTcount: A:0.20, C:0.20, G:0.28, T:0.32
Consensus pattern (96 bp):
CATTGATTTGGCTCCGGGCCATGATATTAGCACCTCAGGTGCGAGATAAATACAGTTGGCTTCAG
GACATGATATGAGCACTTCGGGTTCGAGCTT
Found at i:39996096 original size:24 final size:24
Alignment explanation
Indices: 39996040--39996098 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 24
39996030 AGAAAGAAAC
*
39996040 AAAAAGAAAATCTATTCTAAAAAG
1 AAAAAGAAAATCTAATCTAAAAAG
*
39996064 AAAAGAGAAAA-CTTAATCTAAAAAT
1 AAAA-AGAAAATC-TAATCTAAAAAG
39996089 AAAAAGAAAA
1 AAAAAGAAAA
39996099 GAAAAGGAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
24 11 0.35
25 20 0.65
ACGTcount: A:0.68, C:0.07, G:0.08, T:0.17
Consensus pattern (24 bp):
AAAAAGAAAATCTAATCTAAAAAG
Found at i:39999135 original size:17 final size:18
Alignment explanation
Indices: 39999115--39999158 Score: 56
Period size: 17 Copynumber: 2.5 Consensus size: 18
39999105 CCAAAAATAA
39999115 TAATATTATAA-TAAATT
1 TAATATTATAATTAAATT
*
39999132 TAATATT-TAATTTAATT
1 TAATATTATAATTAAATT
39999149 TAATACTTAT
1 TAATA-TTAT
39999159 CCTGATAGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
16 3 0.13
17 17 0.74
18 2 0.09
19 1 0.04
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (18 bp):
TAATATTATAATTAAATT
Found at i:39999203 original size:68 final size:69
Alignment explanation
Indices: 39999131--39999258 Score: 204
Period size: 68 Copynumber: 1.9 Consensus size: 69
39999121 TATAATAAAT
* * *
39999131 TTAATATTTAATTTAATTTAATACTTATCCTGAT-AGTATTTTATTAATTTAATATTAAATTGAT
1 TTAATATTAAATTTAATATAATACTTATCCTGATAAGTATTATATTAATTTAATATTAAATTGAT
39999195 TATC
66 TATC
* *
39999199 TTAATATTAAATTTAATATAATATTTATCTTGATAAGTATTATATTAATTTAATATTAAA
1 TTAATATTAAATTTAATATAATACTTATCCTGATAAGTATTATATTAATTTAATATTAAA
39999259 GTGAACTCTT
Statistics
Matches: 54, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
68 30 0.56
69 24 0.44
ACGTcount: A:0.41, C:0.04, G:0.04, T:0.52
Consensus pattern (69 bp):
TTAATATTAAATTTAATATAATACTTATCCTGATAAGTATTATATTAATTTAATATTAAATTGAT
TATC
Found at i:40008082 original size:27 final size:26
Alignment explanation
Indices: 40008042--40008151 Score: 132
Period size: 27 Copynumber: 4.1 Consensus size: 26
40008032 AGGAAGCATC
*
40008042 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCAC-ATTATCTGAT
*
40008069 CTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTCTGCCACAT-TATCTGAT
40008096 CTGGTGGCTCTGCCACGATTAT-TGTAT
1 CTGGTGGCTCTGCCAC-ATTATCTG-AT
* * *
40008123 CTGGTGACTCTGTCACATTATCTGTT
1 CTGGTGGCTCTGCCACATTATCTGAT
40008149 CTG
1 CTG
40008152 ACATCCATGC
Statistics
Matches: 73, Mismatches: 6, Indels: 9
0.83 0.07 0.10
Matches are distributed among these distances:
26 13 0.18
27 58 0.79
28 2 0.03
ACGTcount: A:0.16, C:0.24, G:0.23, T:0.37
Consensus pattern (26 bp):
CTGGTGGCTCTGCCACATTATCTGAT
Found at i:40008125 original size:54 final size:53
Alignment explanation
Indices: 40008042--40008151 Score: 159
Period size: 54 Copynumber: 2.1 Consensus size: 53
40008032 AGGAAGCATC
*
40008042 CTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACAT-TATCTGTT
* * *
40008096 CTGGTGGCTCTGCCACGATTAT-TGTATCTGGTGACTCTGTCACATTATCTGTT
1 CTGGTGGCTATGCCACAATTATCTG-ATCTGGTGACTCTGCCACATTATCTGTT
40008149 CTG
1 CTG
40008152 ACATCCATGC
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
53 13 0.25
54 38 0.75
ACGTcount: A:0.16, C:0.24, G:0.23, T:0.37
Consensus pattern (53 bp):
CTGGTGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACATTATCTGTT
Found at i:40011545 original size:12 final size:11
Alignment explanation
Indices: 40011508--40011584 Score: 63
Period size: 12 Copynumber: 7.0 Consensus size: 11
40011498 TATGTCTTTC
40011508 AAAATAAAA-A
1 AAAATAAAATA
*
40011518 AATAATAAAATT
1 AA-AATAAAATA
40011530 AAAATGAAAATA
1 AAAAT-AAAATA
*
40011542 AAAATCAAAAGA
1 AAAAT-AAAATA
*
40011554 AAAAGAAAA-A
1 AAAATAAAATA
40011564 TAAAAT-AAAT-
1 -AAAATAAAATA
40011574 AAAATAAAATA
1 AAAATAAAATA
40011585 GGAGGATTCA
Statistics
Matches: 54, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
9 5 0.09
10 10 0.19
11 18 0.33
12 21 0.39
ACGTcount: A:0.78, C:0.01, G:0.04, T:0.17
Consensus pattern (11 bp):
AAAATAAAATA
Found at i:40011575 original size:4 final size:5
Alignment explanation
Indices: 40011508--40011584 Score: 57
Period size: 6 Copynumber: 14.2 Consensus size: 5
40011498 TATGTCTTTC
* * *
40011508 AAAAT AAAAA AATAAT AAAATT AAAAT GAAAAT AAAAAT CAAAAGA AAAAGA
1 AAAAT AAAAT AA-AAT AAAA-T AAAAT -AAAAT -AAAAT -AAAA-T AAAA-T
40011560 AAAAT AAAAT -AAAT AAAAT AAAAT A
1 AAAAT AAAAT AAAAT AAAAT AAAAT A
40011585 GGAGGATTCA
Statistics
Matches: 61, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
4 4 0.07
5 24 0.39
6 33 0.54
ACGTcount: A:0.78, C:0.01, G:0.04, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:40023644 original size:29 final size:29
Alignment explanation
Indices: 40023611--40023742 Score: 165
Period size: 29 Copynumber: 4.6 Consensus size: 29
40023601 GTGACGAGAT
*
40023611 TGGCACTAAGTGTGCGTGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAAAATA
*
40023640 TGGCACTAAGTGTGCGTGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAAAATA
* *
40023669 AGGCACTAAGTGTGCATGCTGGAAAAATA
1 TGGCACTAAGTGTGCGTGCTGGAAAAATA
* * **
40023698 TGACACTATGTGTGCAAGCTGGAAAAATA
1 TGGCACTAAGTGTGCGTGCTGGAAAAATA
* **
40023727 CGGCACTGGGTGTGCG
1 TGGCACTAAGTGTGCG
40023743 AGCTCGAAGG
Statistics
Matches: 91, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 91 1.00
ACGTcount: A:0.30, C:0.15, G:0.31, T:0.24
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGTGCTGGAAAAATA
Found at i:40031533 original size:13 final size:13
Alignment explanation
Indices: 40031515--40031540 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
40031505 CTCGGCAGGA
40031515 ACACGCCCGTGTG
1 ACACGCCCGTGTG
40031528 ACACGCCCGTGTG
1 ACACGCCCGTGTG
40031541 CGATTGCTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.38, G:0.31, T:0.15
Consensus pattern (13 bp):
ACACGCCCGTGTG
Found at i:40041257 original size:3 final size:3
Alignment explanation
Indices: 40041244--40041298 Score: 103
Period size: 3 Copynumber: 18.7 Consensus size: 3
40041234 CTTATTTAGT
40041244 TTA TT- 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
40041291 TTA TTA TT
1 TTA TTA TT
40041299 TTTACTTTTA
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 49 0.96
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:40042791 original size:89 final size:89
Alignment explanation
Indices: 40042685--40042926 Score: 299
Period size: 89 Copynumber: 2.7 Consensus size: 89
40042675 TACGTACCAC
* *
40042685 TATCTGATCTGGCAGTTTTTACTGCACGTCTATACCGCGGTTTACCGCATTGCACAGTACAGCTT
1 TATCTGATCTGGCAGTTTATACTGCATGTCTATACCGCGGTTTACCGCATTGCACAGTACAGCTT
* *
40042750 ATACGCTAGCCTTGCTGCGTAATA
66 ATACGCTAGCCTTGCTACATAATA
* * * ** *
40042774 TATCTGATCTGGGAGTTTATACTGCATGTCTATATCGCGGTCTT-CCGTATTATACAGTACAGCC
1 TATCTGATCTGGCAGTTTATACTGCATGTCTATACCGCGGT-TTACCGCATTGCACAGTACAGCT
*
40042838 TATATGCTAGCCTTGCTACATAATA
65 TATACGCTAGCCTTGCTACATAATA
* * * * * *
40042863 TATTTGATCTGGCAGTTCATACTGCATGTCTGTACCGCAGTCTACTGCATTGCACCA-TACAGCT
1 TATCTGATCTGGCAGTTTATACTGCATGTCTATACCGCGGTTTACCGCATTGCA-CAGTACAGCT
40042927 CAGTAATAGC
Statistics
Matches: 127, Mismatches: 23, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
88 1 0.01
89 122 0.96
90 4 0.03
ACGTcount: A:0.23, C:0.24, G:0.19, T:0.34
Consensus pattern (89 bp):
TATCTGATCTGGCAGTTTATACTGCATGTCTATACCGCGGTTTACCGCATTGCACAGTACAGCTT
ATACGCTAGCCTTGCTACATAATA
Found at i:40046347 original size:43 final size:43
Alignment explanation
Indices: 40046267--40046620 Score: 460
Period size: 43 Copynumber: 8.2 Consensus size: 43
40046257 AGGATTTCTT
* * *
40046267 ATATCTGATTACGTGTAAGACCACATCTAGGATGTTGGCATCG
1 ATATGTGATTACGTGTAAGACCACGTCTAGGACGTTGGCATCG
* *
40046310 ATATGTGATTACGTGTAAGATCACGTCTGGGACGTTGGCATCG
1 ATATGTGATTACGTGTAAGACCACGTCTAGGACGTTGGCATCG
* * *
40046353 ATATGTGATTAAGT-TGAAGACCACGTCTCGTACGTTGGCATCG
1 ATATGTGATTACGTGT-AAGACCACGTCTAGGACGTTGGCATCG
* *
40046396 ATATGTGATT-CTGTGTAAGACCATGTCTGGGACGTTGGCATCG
1 ATATGTGATTAC-GTGTAAGACCACGTCTAGGACGTTGGCATCG
*
40046439 ATATGTGATTACGTGTAAGACCACGTCAAGGACGTTGGCATCG
1 ATATGTGATTACGTGTAAGACCACGTCTAGGACGTTGGCATCG
* ** *
40046482 ATATGTGATTATGTGTAAGACCATTTCTGGGACGTTGGCATCG
1 ATATGTGATTACGTGTAAGACCACGTCTAGGACGTTGGCATCG
* * * *
40046525 ATATGTGATTACGTGTAAGACCACATCTAGAACTTTAGCATCG
1 ATATGTGATTACGTGTAAGACCACGTCTAGGACGTTGGCATCG
* * * **
40046568 ATATGTGATTATGAGTAAGACCACGTTTAATACGTTGGCATCG
1 ATATGTGATTACGTGTAAGACCACGTCTAGGACGTTGGCATCG
40046611 ATATGTGATT
1 ATATGTGATT
40046621 CCAATATGTG
Statistics
Matches: 271, Mismatches: 36, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
42 1 0.00
43 268 0.99
44 2 0.01
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.31
Consensus pattern (43 bp):
ATATGTGATTACGTGTAAGACCACGTCTAGGACGTTGGCATCG
Found at i:40046654 original size:56 final size:56
Alignment explanation
Indices: 40046580--40046813 Score: 301
Period size: 56 Copynumber: 4.2 Consensus size: 56
40046570 ATGTGATTAT
40046580 GAGTAAGACCACGTTTAATACGTTGGCATCGATATGTGATTCCAATATGTGTGTTC
1 GAGTAAGACCACGTTTAATACGTTGGCATCGATATGTGATTCCAATATGTGTGTTC
* *
40046636 GAGTAAGACCATGTTTAATACGTTGGCATCGATATGTGATTCTAATATGTGTGTGT-
1 GAGTAAGACCACGTTTAATACGTTGGCATCGATATGTGATTCCAATATGTGTGT-TC
* ** * * *
40046692 GAGTAAGACCACATTTAATACGTTCCCAACGATATGTGATTCCGATATGTATGTTC
1 GAGTAAGACCACGTTTAATACGTTGGCATCGATATGTGATTCCAATATGTGTGTTC
* * * * * *
40046748 GAGTAAGAACATGTTTAATACGTTGGCATTGATAGGTGATTTCGATATGTGT-TTAC
1 GAGTAAGACCACGTTTAATACGTTGGCATCGATATGTGATTCCAATATGTGTGTT-C
*
40046804 GAGAAAGACC
1 GAGTAAGACC
40046814 CTATTTGGGA
Statistics
Matches: 153, Mismatches: 22, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
55 3 0.02
56 149 0.97
57 1 0.01
ACGTcount: A:0.29, C:0.14, G:0.23, T:0.34
Consensus pattern (56 bp):
GAGTAAGACCACGTTTAATACGTTGGCATCGATATGTGATTCCAATATGTGTGTTC
Found at i:40046812 original size:112 final size:111
Alignment explanation
Indices: 40046565--40046813 Score: 345
Period size: 112 Copynumber: 2.2 Consensus size: 111
40046555 AACTTTAGCA
* * ** *
40046565 TCGATATGTGATTATGAGTAAGACCACGTTTAATACGTTGGCATCGATATGTGATTCCAATATGT
1 TCGATATGTGTTTATGAGTAAGACCACATTTAATACGTTCCCAACGATATGTGATTCCAATATGT
* * *
40046630 GTGTTCGAGTAAGACCATGTTTAATACGTTGGCATCGATATGTGAT
66 ATGTTCGAGTAAGAACATGTTTAATACGTTGGCATCGATAGGTGAT
* * * *
40046676 TCTAATATGTGTGTGTGAGTAAGACCACATTTAATACGTTCCCAACGATATGTGATTCCGATATG
1 TC-GATATGTGTTTATGAGTAAGACCACATTTAATACGTTCCCAACGATATGTGATTCCAATATG
*
40046741 TATGTTCGAGTAAGAACATGTTTAATACGTTGGCATTGATAGGTGATT
65 TATGTTCGAGTAAGAACATGTTTAATACGTTGGCATCGATAGGTGA-T
* *
40046789 TCGATATGTGTTTACGAGAAAGACC
1 TCGATATGTGTTTATGAGTAAGACC
40046814 CTATTTGGGA
Statistics
Matches: 118, Mismatches: 18, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
111 2 0.02
112 113 0.96
113 3 0.03
ACGTcount: A:0.29, C:0.14, G:0.23, T:0.35
Consensus pattern (111 bp):
TCGATATGTGTTTATGAGTAAGACCACATTTAATACGTTCCCAACGATATGTGATTCCAATATGT
ATGTTCGAGTAAGAACATGTTTAATACGTTGGCATCGATAGGTGAT
Found at i:40050220 original size:47 final size:48
Alignment explanation
Indices: 40050164--40050291 Score: 145
Period size: 47 Copynumber: 2.6 Consensus size: 48
40050154 AGGGTATAAT
*
40050164 GCCGATGCCATGTCCCAGATATGGTCTTACACTGGCTCATC-C-AT-CAA
1 GCCGATGCCATGTCCCAGA-ATGGTCTTACACTAGCTC-TCACAATCCAA
* * * * *
40050211 GTCGATGCCATGTCCCAAACATGGCCTTACATTAGCTCTCACATATCCAT
1 GCCGATGCCATGTCCCAGA-ATGGTCTTACACTAGCTCTCACA-ATCCAA
40050261 GCCGATGCCATGTCCCAGAATGGTCTTACAC
1 GCCGATGCCATGTCCCAGAATGGTCTTACAC
40050292 AGACACATCT
Statistics
Matches: 66, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
46 2 0.03
47 33 0.50
49 12 0.18
50 19 0.29
ACGTcount: A:0.24, C:0.32, G:0.18, T:0.26
Consensus pattern (48 bp):
GCCGATGCCATGTCCCAGAATGGTCTTACACTAGCTCTCACAATCCAA
Found at i:40053927 original size:40 final size:40
Alignment explanation
Indices: 40053883--40054096 Score: 261
Period size: 40 Copynumber: 5.3 Consensus size: 40
40053873 CTAACGGGGT
* * * *
40053883 TAAGTCCCGAAGACATGTGTGCTAGTGACTAATTCCGGGC
1 TAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCCGGGC
*
40053923 TAAGTCCCGAAGGCATTTGTGCGAGTTACAAATTCCGGGC
1 TAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCCGGGC
*
40053963 TAAGTCCCGAAGGCATTGGTGCGAGTTACTAATTCCGGGC
1 TAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCCGGGC
* * *
40054003 TAAGTCCGGAAGGCATTTGTACGAGTTTCT-ATATCCGGGC
1 TAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT-TCCGGGC
* * * * *
40054043 TAAGACCCGAAGGCATTTATGCTAGTGAC-CATATCCGGGC
1 TAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT-TCCGGGC
*
40054083 TAAGACCCGAAGGC
1 TAAGTCCCGAAGGC
40054097 CTTGTGTGAG
Statistics
Matches: 154, Mismatches: 18, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
39 2 0.01
40 152 0.99
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.24
Consensus pattern (40 bp):
TAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCCGGGC
Found at i:40064680 original size:25 final size:24
Alignment explanation
Indices: 40064639--40064708 Score: 72
Period size: 25 Copynumber: 2.9 Consensus size: 24
40064629 GATTATGTAG
40064639 AAAGAATAAAGAAATGAAAAAAAAA
1 AAAGAA-AAAGAAATGAAAAAAAAA
* * *
40064664 AAAGAAAGAGAATATGAAGAAAAAC
1 AAAGAAAAAGAA-ATGAAAAAAAAA
*
40064689 AAAGAAAAGGAAA--AAAAAAA
1 AAAGAAAAAGAAATGAAAAAAA
40064709 GTGTTCATTC
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
22 6 0.16
24 6 0.16
25 26 0.68
ACGTcount: A:0.77, C:0.01, G:0.16, T:0.06
Consensus pattern (24 bp):
AAAGAAAAAGAAATGAAAAAAAAA
Found at i:40065900 original size:29 final size:29
Alignment explanation
Indices: 40065867--40065931 Score: 112
Period size: 29 Copynumber: 2.2 Consensus size: 29
40065857 GTGACGAGAT
*
40065867 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAAAATA
40065896 TGGCACTAAGTGTGCATGCTGGAAAAATA
1 TGGCACTAAGTGTGCATGCTGGAAAAATA
*
40065925 CGGCACT
1 TGGCACT
40065932 GGGTGTGCGA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.31, C:0.17, G:0.28, T:0.25
Consensus pattern (29 bp):
TGGCACTAAGTGTGCATGCTGGAAAAATA
Found at i:40072576 original size:25 final size:24
Alignment explanation
Indices: 40072535--40072597 Score: 72
Period size: 25 Copynumber: 2.5 Consensus size: 24
40072525 GATTATGTAG
40072535 AAAGAATAAAGAAATGAAAAAAAAA
1 AAAGAA-AAAGAAATGAAAAAAAAA
* * *
40072560 AAAGAAAGAGAATATGAAGAAAAAC
1 AAAGAAAAAGAA-ATGAAAAAAAAA
*
40072585 AAAGAAAAGGAAA
1 AAAGAAAAAGAAA
40072598 AAAAAAGTGT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
24 6 0.19
25 26 0.81
ACGTcount: A:0.75, C:0.02, G:0.17, T:0.06
Consensus pattern (24 bp):
AAAGAAAAAGAAATGAAAAAAAAA
Found at i:40073795 original size:29 final size:29
Alignment explanation
Indices: 40073762--40073826 Score: 112
Period size: 29 Copynumber: 2.2 Consensus size: 29
40073752 GTGACGAGAT
*
40073762 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAAAATA
40073791 TGGCACTAAGTGTGCATGCTGGAAAAATA
1 TGGCACTAAGTGTGCATGCTGGAAAAATA
*
40073820 CGGCACT
1 TGGCACT
40073827 GGGTGTGCGA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.31, C:0.17, G:0.28, T:0.25
Consensus pattern (29 bp):
TGGCACTAAGTGTGCATGCTGGAAAAATA
Found at i:40077039 original size:93 final size:93
Alignment explanation
Indices: 40076880--40077050 Score: 288
Period size: 93 Copynumber: 1.8 Consensus size: 93
40076870 GGATGGTTGA
* * *
40076880 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATGTCCGAACTGGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAACGCCCGAACTCGTTGAGT
40076945 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* * *
40076973 GCATCCGAACTCGTTGAGTTGAGTTCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAACGCCCGAACTCGTTGAGT
40077038 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
40077051 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:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:40077053 original size:46 final size:46
Alignment explanation
Indices: 40076884--40077055 Score: 190
Period size: 46 Copynumber: 3.7 Consensus size: 46
40076874 GGTTGAGCAT
* * *
40076884 CCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATGT
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
* * * *
40076930 CCGAACTGGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGGC
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAC---GC
*
40076975 ATCCGAACTCGTTGAGTTGAGTTCGAGTTCACTTATGGATGCGAACGC
1 --CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
*
40077023 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
40077056 GGGGCGGGTT
Statistics
Matches: 103, Mismatches: 14, Indels: 18
0.76 0.10 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
45 2 0.02
46 58 0.56
47 26 0.25
48 4 0.04
50 4 0.04
51 3 0.03
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.28
Consensus pattern (46 bp):
CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
Found at i:40084118 original size:93 final size:93
Alignment explanation
Indices: 40083959--40084129 Score: 306
Period size: 93 Copynumber: 1.8 Consensus size: 93
40083949 GGATGGTTGA
* *
40083959 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAACGCCCGAACTCGTTGAGT
40084024 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* *
40084052 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAACGCCCGAACTCGTTGAGT
40084117 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
40084130 ACTTAGGGGC
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.21, C:0.22, G:0.29, T:0.27
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:40084132 original size:46 final size:46
Alignment explanation
Indices: 40083963--40084134 Score: 208
Period size: 46 Copynumber: 3.7 Consensus size: 46
40083953 GGTTGAGCAT
* * *
40083963 CCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATGT
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
* * *
40084009 CCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGGC
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAC---GC
40084054 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1 --CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
*
40084102 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
40084135 GGGGCGGGTT
Statistics
Matches: 107, Mismatches: 10, Indels: 18
0.79 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
45 2 0.02
46 60 0.56
47 28 0.26
48 4 0.04
50 4 0.04
51 3 0.03
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.28
Consensus pattern (46 bp):
CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
Found at i:40091180 original size:46 final size:46
Alignment explanation
Indices: 40091034--40091203 Score: 199
Period size: 46 Copynumber: 3.7 Consensus size: 46
40091024 GGTTGAGCAT
* *
40091034 CCGAACTCGTTGAGTTGAGTCCGAGTTCAC-TATGGATGCGAATGT
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
* * *
40091079 CCGAACTCGTTGAGTTGAGT-CGAGTTC-GTGA--GATG-TAACTAGGC
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAC---GC
40091123 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1 --CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
*
40091171 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
40091204 GGGGCGGGTT
Statistics
Matches: 105, Mismatches: 9, Indels: 21
0.78 0.07 0.16
Matches are distributed among these distances:
41 2 0.02
42 4 0.04
44 9 0.09
45 20 0.19
46 52 0.50
47 7 0.07
48 4 0.04
50 4 0.04
51 3 0.03
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.28
Consensus pattern (46 bp):
CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
Found at i:40099910 original size:34 final size:33
Alignment explanation
Indices: 40099831--40099925 Score: 82
Period size: 34 Copynumber: 2.8 Consensus size: 33
40099821 TTTGTTTGCA
* *
40099831 TACTGTTTTGAAATGGGCTAAGGCCTAGATTGC
1 TACTGTTCTGAAATGGGCTAAGGCCTAGACTGC
** * * *
40099864 CGCTGATACTGAAATGGGCTCAGGCCTAGACTGT
1 TACTG-TTCTGAAATGGGCTAAGGCCTAGACTGC
*
40099898 TACTGTTGCTGAAAGAGGGGCTAAGGCC
1 TACTGTT-CTG-AA-ATGGGCTAAGGCC
40099926 CCTAACTGAA
Statistics
Matches: 46, Mismatches: 12, Indels: 5
0.73 0.19 0.08
Matches are distributed among these distances:
33 4 0.09
34 29 0.63
35 2 0.04
36 11 0.24
ACGTcount: A:0.24, C:0.19, G:0.31, T:0.26
Consensus pattern (33 bp):
TACTGTTCTGAAATGGGCTAAGGCCTAGACTGC
Found at i:40103067 original size:45 final size:45
Alignment explanation
Indices: 40102914--40103171 Score: 264
Period size: 45 Copynumber: 5.9 Consensus size: 45
40102904 ATATCAAACA
* ** * *
40102914 ATGCCAACGTCCCAGACGTGGTCTTACATGCTATCTCATAT-T-G
1 ATGCCAACGTCCCAGACGTGGTCTTACACGAAAACACATATATCG
* *
40102957 ATGCC-ACTATCCCAGACAG-GGTCTTACACG-AATCA-A-ATAT-G
1 ATGCCAAC-GTCCCAGAC-GTGGTCTTACACGAAAACACATATATCG
* * * * * * *
40102998 ATGCCGATGT-CCAAACATGGTCTTACTCGTAACCACATATATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGAAAACACATATATCG
* *
40103042 ATGCCAACGTCCCAGACGTAGTCTTACACGAAAACACATATATCA
1 ATGCCAACGTCCCAGACGTGGTCTTACACGAAAACACATATATCG
* * *
40103087 ATGCCAATGTCCCAGACGTGGTCTTACACAAAAAAACATATATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGAAAACACATATATCG
40103132 ATGCCAACGTCCCAGACGTGGTCTTACACGAAAACACATA
1 ATGCCAACGTCCCAGACGTGGTCTTACACGAAAACACATA
40103172 GCAAAGTCCT
Statistics
Matches: 178, Mismatches: 27, Indels: 18
0.80 0.12 0.08
Matches are distributed among these distances:
40 17 0.10
41 13 0.07
42 7 0.04
43 27 0.15
44 10 0.06
45 104 0.58
ACGTcount: A:0.33, C:0.28, G:0.16, T:0.23
Consensus pattern (45 bp):
ATGCCAACGTCCCAGACGTGGTCTTACACGAAAACACATATATCG
Found at i:40106996 original size:15 final size:15
Alignment explanation
Indices: 40106972--40107002 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
40106962 ATGAACATAT
*
40106972 TTTTATATTTTTTTA
1 TTTTAAATTTTTTTA
40106987 TTTTAAATTTTTTTA
1 TTTTAAATTTTTTTA
40107002 T
1 T
40107003 AATTTGTTCC
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:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTTAAATTTTTTTA
Found at i:40111315 original size:11 final size:11
Alignment explanation
Indices: 40111299--40111323 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
40111289 TTTAGCTGAT
40111299 GAAAATGAAGA
1 GAAAATGAAGA
40111310 GAAAATGAAGA
1 GAAAATGAAGA
40111321 GAA
1 GAA
40111324 TTCTAGATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.64, C:0.00, G:0.28, T:0.08
Consensus pattern (11 bp):
GAAAATGAAGA
Found at i:40112717 original size:19 final size:18
Alignment explanation
Indices: 40112693--40112762 Score: 60
Period size: 19 Copynumber: 4.1 Consensus size: 18
40112683 TTTTAAATTT
40112693 TTATGTATATTATGTACTG
1 TTATGTATATTATGTA-TG
40112712 TTATG-----TATGTATG
1 TTATGTATATTATGTATG
* *
40112725 TTATGTATGTTATGTGTTG
1 TTATGTATATTATGT-ATG
*
40112744 TTATGCATATTATGTATG
1 TTATGTATATTATGTATG
40112762 T
1 T
40112763 ATACTTGTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 13
0.71 0.07 0.22
Matches are distributed among these distances:
13 7 0.17
14 6 0.15
18 8 0.20
19 20 0.49
ACGTcount: A:0.23, C:0.03, G:0.20, T:0.54
Consensus pattern (18 bp):
TTATGTATATTATGTATG
Found at i:40112730 original size:32 final size:32
Alignment explanation
Indices: 40112693--40112765 Score: 87
Period size: 32 Copynumber: 2.3 Consensus size: 32
40112683 TTTTAAATTT
40112693 TTATGTATATTATGTACTGTTATG-TATGTATG
1 TTATGTATATTATGTACTGTTATGATAT-TATG
* **
40112725 TTATGTATGTTATGTGTTGTTATGCATATTATG
1 TTATGTATATTATGTACTGTTATG-ATATTATG
40112758 -TATGTATA
1 TTATGTATA
40112766 CTTGTTTGTT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
32 28 0.80
33 4 0.11
34 3 0.09
ACGTcount: A:0.25, C:0.03, G:0.19, T:0.53
Consensus pattern (32 bp):
TTATGTATATTATGTACTGTTATGATATTATG
Found at i:40117578 original size:28 final size:28
Alignment explanation
Indices: 40117540--40117646 Score: 160
Period size: 28 Copynumber: 3.8 Consensus size: 28
40117530 GAATCATTCG
* *
40117540 ATATTTTGCACACTAAGTGTCATTCTCA
1 ATATTTCGCACACTAAGTGCCATTCTCA
*
40117568 ATATCTCGCACACTAAGTGCCATTCTCA
1 ATATTTCGCACACTAAGTGCCATTCTCA
*
40117596 ATATTTCGTACACTAAGTGCCATTCTCA
1 ATATTTCGCACACTAAGTGCCATTCTCA
* *
40117624 ATATTTCGTACACTAAGTACCAT
1 ATATTTCGCACACTAAGTGCCAT
40117647 ATTTGATTGC
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 73 1.00
ACGTcount: A:0.30, C:0.25, G:0.10, T:0.35
Consensus pattern (28 bp):
ATATTTCGCACACTAAGTGCCATTCTCA
Found at i:40121128 original size:40 final size:40
Alignment explanation
Indices: 40121074--40121295 Score: 270
Period size: 40 Copynumber: 5.6 Consensus size: 40
40121064 TATAACCACC
* * * *
40121074 CGCAC-AAGGCCTTCGGGTCTTAGCCCGG-ATATGGTCACT
1 CGCACAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTAACT
* * * *
40121113 AGCATAAATGCCTTCGGGTCTTAGCCCGG-ATATAGAAACT
1 CGCACAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTAACT
40121153 CGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACT
1 CGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACT
* *
40121193 CGCACCAATGCCTTCGGGACTTAGCCCGGAATTTGTAACT
1 CGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACT
*
40121233 CGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTCACT
1 CGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACT
* * * *
40121273 AGCACACATGTCTTCAGGACTTA
1 CGCACAAATGCCTTCGGGACTTA
40121296 ACCCCGTTAG
Statistics
Matches: 162, Mismatches: 19, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
39 3 0.02
40 157 0.97
41 2 0.01
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (40 bp):
CGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACT
Found at i:40129956 original size:39 final size:38
Alignment explanation
Indices: 40129912--40129996 Score: 100
Period size: 39 Copynumber: 2.2 Consensus size: 38
40129902 CGGATTTAGT
*
40129912 CGGATATAACCACTCA-CACAAGGCCTTCGGGTCTTAGCC
1 CGGATATAACCACT-AGCAAAAGGCCTTC-GGTCTTAGCC
*** *
40129951 CGGATATGGTCACTAGCAAAATGCCTTCGGTCTTAGCC
1 CGGATATAACCACTAGCAAAAGGCCTTCGGTCTTAGCC
40129989 CGGATATA
1 CGGATATA
40129997 GAAACTCGTA
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
38 18 0.46
39 21 0.54
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (38 bp):
CGGATATAACCACTAGCAAAAGGCCTTCGGTCTTAGCC
Found at i:40130012 original size:39 final size:39
Alignment explanation
Indices: 40129934--40130141 Score: 207
Period size: 38 Copynumber: 5.5 Consensus size: 39
40129924 CTCACACAAG
* * * *
40129934 GCCTTCGGGTCTTAGCCCGGATATGGTCACTAGCA-AAAT
1 GCCTTC-GGACTTAGCCCGGATATAGTAACTCGCACAAAT
* * *
40129973 GCCTTCGGTCTTAGCCCGGATATAGAAACTCGTACAAAT
1 GCCTTCGGACTTAGCCCGGATATAGTAACTCGCACAAAT
* *
40130012 GCCTTCGGACTTAGCCCGAAT-TAGTAACTCGCACCAA-
1 GCCTTCGGACTTAGCCCGGATATAGTAACTCGCACAAAT
*
40130049 GCCTTCGGGACTTAG-CCGGA-ATTGTAACTCGCACAAAT
1 GCCTTC-GGACTTAGCCCGGATATAGTAACTCGCACAAAT
* * *
40130087 GCCTTCGGACTTAGCCCGAAT-TAGTCACTAGCAC-AAT
1 GCCTTCGGACTTAGCCCGGATATAGTAACTCGCACAAAT
*
40130124 GTCTTCGGGACTTA-CCCG
1 GCCTTC-GGACTTAGCCCG
40130142 TTAGTATCTG
Statistics
Matches: 144, Mismatches: 18, Indels: 16
0.81 0.10 0.09
Matches are distributed among these distances:
37 44 0.31
38 71 0.49
39 29 0.20
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (39 bp):
GCCTTCGGACTTAGCCCGGATATAGTAACTCGCACAAAT
Found at i:40130090 original size:75 final size:77
Alignment explanation
Indices: 40129934--40130141 Score: 246
Period size: 75 Copynumber: 2.7 Consensus size: 77
40129924 CTCACACAAG
* * * * * *
40129934 GCCTTCGGGTCTTAGCCCGGATATGGTCACTAGCAAAATGCCTTC-GGTCTTAGCCCGGATATAG
1 GCCTTC-GGACTTAGCCCGAAT-TAGTAACTAGCACAATGCCTTCGGGACTTAGCCCGGATATAG
*
40129998 AAACTCGTACAAAT
64 AAACTCGCACAAAT
* * *
40130012 GCCTTCGGACTTAGCCCGAATTAGTAACTCGCACCAA-GCCTTCGGGACTTAG-CCGGA-ATTGT
1 GCCTTCGGACTTAGCCCGAATTAGTAACTAGCA-CAATGCCTTCGGGACTTAGCCCGGATATAGA
40130074 AACTCGCACAAAT
65 AACTCGCACAAAT
* *
40130087 GCCTTCGGACTTAGCCCGAATTAGTCACTAGCACAATGTCTTCGGGACTTA-CCCG
1 GCCTTCGGACTTAGCCCGAATTAGTAACTAGCACAATGCCTTCGGGACTTAGCCCG
40130142 TTAGTATCTG
Statistics
Matches: 113, Mismatches: 13, Indels: 11
0.82 0.09 0.08
Matches are distributed among these distances:
74 3 0.03
75 62 0.55
76 20 0.18
77 22 0.19
78 6 0.05
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (77 bp):
GCCTTCGGACTTAGCCCGAATTAGTAACTAGCACAATGCCTTCGGGACTTAGCCCGGATATAGAA
ACTCGCACAAAT
Found at i:40134888 original size:40 final size:40
Alignment explanation
Indices: 40134803--40134953 Score: 134
Period size: 40 Copynumber: 3.8 Consensus size: 40
40134793 AATTGAATGA
* * *
40134803 TATCCGGGCTAA-ATCCCGAAGACAATTATGCTG-GAAATTA-
1 TATCCGGGCTAAGA-CCCGAAGGCAATTGTGC-GAGACA-TAC
* * *
40134843 TATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGC-TAC
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGC--GAGACATAC
*
40134884 -ATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGACATTC
1 TATCCGGGCTAAGACCCGAAGGCAATT-GTGCGAGACATAC
*
40134923 TATCCGGGCTAAGACCCGAAGGCATTTGTGC
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGC
40134954 ACATGGTTAT
Statistics
Matches: 92, Mismatches: 11, Indels: 16
0.77 0.09 0.13
Matches are distributed among these distances:
38 3 0.03
39 5 0.05
40 79 0.86
41 4 0.04
42 1 0.01
ACGTcount: A:0.27, C:0.24, G:0.26, T:0.23
Consensus pattern (40 bp):
TATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGACATAC
Found at i:40134967 original size:40 final size:40
Alignment explanation
Indices: 40134840--40134969 Score: 138
Period size: 40 Copynumber: 3.2 Consensus size: 40
40134830 ATGCTGGAAA
* * * *
40134840 TTATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATGG
* * * **
40134880 CTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGA-CA
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGA-ATGG
*
40134920 TTCTATCCGGGCTAAGACCCGAAGGCATTTGTGC-ACATGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGA-ATGG
40134960 TTATATCCGG
1 TTATATCCGG
40134970 TTATGTTCCG
Statistics
Matches: 71, Mismatches: 17, Indels: 4
0.77 0.18 0.04
Matches are distributed among these distances:
39 2 0.03
40 69 0.97
ACGTcount: A:0.25, C:0.24, G:0.28, T:0.24
Consensus pattern (40 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATGG
Found at i:40139259 original size:2 final size:2
Alignment explanation
Indices: 40139252--40139285 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
40139242 AATGATAATG
40139252 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
40139286 CTTCGAATGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40139681 original size:2 final size:2
Alignment explanation
Indices: 40139669--40139701 Score: 57
Period size: 2 Copynumber: 16.0 Consensus size: 2
40139659 GCTAAGTAAA
40139669 AT AT CAT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT
40139702 GTTATGAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 28 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:40142923 original size:47 final size:47
Alignment explanation
Indices: 40142835--40142931 Score: 126
Period size: 48 Copynumber: 2.0 Consensus size: 47
40142825 TTTTTATTAC
40142835 TTTCATATTTTGTTTGCTCTTTATTTTCTAAGCCTTTTCTTTATTTTA
1 TTTCATATTTTGTTTGCTCTTTATTTTC-AAGCCTTTTCTTTATTTTA
* * *
40142883 TTTCATGTTTTGTTTGTTCTTTATCATTTC-GGCC-TTTCTTTATTTTA
1 TTTCATATTTTGTTTGCTCTTTAT--TTTCAAGCCTTTTCTTTATTTTA
40142930 TT
1 TT
40142932 AGTGCAAATA
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
47 15 0.34
48 25 0.57
50 4 0.09
ACGTcount: A:0.12, C:0.14, G:0.08, T:0.65
Consensus pattern (47 bp):
TTTCATATTTTGTTTGCTCTTTATTTTCAAGCCTTTTCTTTATTTTA
Found at i:40150972 original size:25 final size:25
Alignment explanation
Indices: 40150943--40150992 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
40150933 TCTGATCTGG
40150943 CAGTTTAACTACACTCTGGTGGCAT
1 CAGTTTAACTACACTCTGGTGGCAT
*
40150968 CAGTTTAACTACACTTTGGTGGCAT
1 CAGTTTAACTACACTCTGGTGGCAT
40150993 TGTCCACAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.34
Consensus pattern (25 bp):
CAGTTTAACTACACTCTGGTGGCAT
Found at i:40151582 original size:17 final size:16
Alignment explanation
Indices: 40151547--40151578 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
40151537 AATTGGGTTG
*
40151547 AAAAAATTATTTAATT
1 AAAAAATTAATTAATT
40151563 AAAAAATTAATTAATT
1 AAAAAATTAATTAATT
40151579 TAAATTAACT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
AAAAAATTAATTAATT
Found at i:40154714 original size:20 final size:20
Alignment explanation
Indices: 40154689--40154735 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
40154679 ATTTATTTTT
*
40154689 TAATTATTAAAAACTT-TAAA
1 TAATTAATAAAAA-TTATAAA
*
40154709 TAATTAATCAAAATTATAAA
1 TAATTAATAAAAATTATAAA
40154729 TAATTAA
1 TAATTAA
40154736 CAAATCAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 2 0.08
20 22 0.92
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.38
Consensus pattern (20 bp):
TAATTAATAAAAATTATAAA
Found at i:40155018 original size:21 final size:21
Alignment explanation
Indices: 40154994--40155055 Score: 60
Period size: 21 Copynumber: 3.0 Consensus size: 21
40154984 AATTTTAAAA
40154994 TTAAATATTATTTACAATTTT
1 TTAAATATTATTTACAATTTT
40155015 TTAAATAATT-TTCT-CAA-TTT
1 TTAAAT-ATTATT-TACAATTTT
*
40155035 TT-AATAATATTTACATATTTT
1 TTAAATATTATTTACA-ATTTT
40155056 AATGTTTTAT
Statistics
Matches: 34, Mismatches: 1, Indels: 12
0.72 0.02 0.26
Matches are distributed among these distances:
18 3 0.09
19 7 0.21
20 6 0.18
21 14 0.41
22 4 0.12
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.56
Consensus pattern (21 bp):
TTAAATATTATTTACAATTTT
Found at i:40155084 original size:21 final size:22
Alignment explanation
Indices: 40155060--40155114 Score: 69
Period size: 21 Copynumber: 2.6 Consensus size: 22
40155050 TATTTTAATG
*
40155060 TTTTATAATTTTTAATA-ACTT
1 TTTTATAATTTTTAAAATACTT
* *
40155081 TTTTACAA-TTTTAAAATATTT
1 TTTTATAATTTTTAAAATACTT
40155102 TTTTATAATTTTT
1 TTTTATAATTTTT
40155115 TAGTCTAATC
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
20 7 0.25
21 17 0.61
22 4 0.14
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.64
Consensus pattern (22 bp):
TTTTATAATTTTTAAAATACTT
Found at i:40155115 original size:10 final size:10
Alignment explanation
Indices: 40155055--40155116 Score: 52
Period size: 10 Copynumber: 6.0 Consensus size: 10
40155045 TTACATATTT
*
40155055 TAATGTTTTA
1 TAATTTTTTA
*
40155065 TAATTTTTAA
1 TAATTTTTTA
40155075 TAACTTTTTTA
1 TAA-TTTTTTA
* **
40155086 CAATTTTAAAA
1 TAATTTT-TTA
*
40155097 TATTTTTTTA
1 TAATTTTTTA
40155107 TAATTTTTTA
1 TAATTTTTTA
40155117 GTCTAATCAG
Statistics
Matches: 39, Mismatches: 11, Indels: 4
0.72 0.20 0.07
Matches are distributed among these distances:
10 25 0.64
11 14 0.36
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.61
Consensus pattern (10 bp):
TAATTTTTTA
Found at i:40156097 original size:30 final size:30
Alignment explanation
Indices: 40156063--40156122 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
40156053 AAGCTCTTTG
40156063 GGGGTATTGGGTATTGTTAAAGAAAATTGT
1 GGGGTATTGGGTATTGTTAAAGAAAATTGT
40156093 GGGGTATTGGGTATTGTTAAAGAAAATTGT
1 GGGGTATTGGGTATTGTTAAAGAAAATTGT
40156123 TCTCTTTTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.30, C:0.00, G:0.33, T:0.37
Consensus pattern (30 bp):
GGGGTATTGGGTATTGTTAAAGAAAATTGT
Found at i:40164008 original size:42 final size:42
Alignment explanation
Indices: 40163962--40164048 Score: 111
Period size: 42 Copynumber: 2.1 Consensus size: 42
40163952 TATTAATTTA
* * * * *
40163962 ATATTAATACGATATATTATATTTAATTTAATATTTGTCTAG
1 ATATTAATACGAGATATTAAATTAAATTAAATATTTATCTAG
* *
40164004 ATATTAATATGAGATATTAAATTAAATTAAATATTTATTTAG
1 ATATTAATACGAGATATTAAATTAAATTAAATATTTATCTAG
40164046 ATA
1 ATA
40164049 ATATTTTATT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.47
Consensus pattern (42 bp):
ATATTAATACGAGATATTAAATTAAATTAAATATTTATCTAG
Found at i:40165588 original size:3 final size:3
Alignment explanation
Indices: 40165580--40165624 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
40165570 TAAATATGTA
40165580 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
40165625 GGTTTTATAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Done.