Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr1
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: 37323695
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.32
Warning! 1370832 characters in sequence are not A, C, G, or T
File 68 of 93
Found at i:26114412 original size:16 final size:16
Alignment explanation
Indices: 26114391--26114421 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
26114381 TTGAGGCTGT
26114391 AGGGATGGTGGTAAGC
1 AGGGATGGTGGTAAGC
26114407 AGGGATGGTGGTAAG
1 AGGGATGGTGGTAAG
26114422 AGTCCCGCCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.26, C:0.03, G:0.52, T:0.19
Consensus pattern (16 bp):
AGGGATGGTGGTAAGC
Found at i:26121362 original size:21 final size:22
Alignment explanation
Indices: 26121336--26121376 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
26121326 CCTAGGTTGA
*
26121336 AAAATTCAAGGGAA-AAGTGTG
1 AAAATTCAAGGAAACAAGTGTG
26121357 AAAATTCAAGGAAACAAGTG
1 AAAATTCAAGGAAACAAGTG
26121377 AAAAAAAAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.51, C:0.07, G:0.24, T:0.17
Consensus pattern (22 bp):
AAAATTCAAGGAAACAAGTGTG
Found at i:26121377 original size:20 final size:21
Alignment explanation
Indices: 26121336--26121380 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
26121326 CCTAGGTTGA
*
26121336 AAAATTCAAGGGAAAAGTGTG
1 AAAATTCAAGGGAAAAGAGTG
26121357 AAAATTCAA-GGAAACA-AGTG
1 AAAATTCAAGGGAAA-AGAGTG
26121377 AAAA
1 AAAA
26121381 AAAAGGTAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.56, C:0.07, G:0.22, T:0.16
Consensus pattern (21 bp):
AAAATTCAAGGGAAAAGAGTG
Found at i:26121381 original size:21 final size:20
Alignment explanation
Indices: 26121333--26121381 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
26121323 AACCCTAGGT
*
26121333 TGAAAAATTCAAGGGAAAAG
1 TGAAAAATTCAAGGAAAAAG
*
26121353 TGTGAAAATTCAAGGAAACAAG
1 TG-AAAAATTCAAGGAAA-AAG
26121375 TGAAAAA
1 TGAAAAA
26121382 AAAGGTAAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 2 0.08
21 17 0.71
22 5 0.21
ACGTcount: A:0.55, C:0.06, G:0.22, T:0.16
Consensus pattern (20 bp):
TGAAAAATTCAAGGAAAAAG
Found at i:26121738 original size:389 final size:387
Alignment explanation
Indices: 26121010--26121789 Score: 1508
Period size: 389 Copynumber: 2.0 Consensus size: 387
26121000 TGAAAAATTT
26121010 TAATTTCGACATTTTTTCAAGGATAAGGGCAAAATAGACATTTTGCCACCCAAGGGCAAAATTGG
1 TAATTTCGACATTTTTTCAAGGATAAGGGCAAAATAGACATTTTGCCACCCAAGGGCAAAATTGG
26121075 AATTTTACACCACCCAACACTTGTCCAGCACATGGATTTTACCCAATATTATCATGGATAATTGA
66 AATTTTACACCACCCAACACTTGTCCAGCACATGGATTTTACCCAATATTATCATGGATAATTGA
*
26121140 GAAAATTTAAGTGGTAGAGAGAGATTGCTTAATGGGTAAGTATGACACTTGGACCAATGGAATTG
131 GAAAATTTAAGTGGTAGAGAGAGATTGCTTAATGGGTAAGTATGACACTTAGACCAATGGAATTG
26121205 TGACACATGGCAAATTTTTGTCCATTTAATATTTTCCTTTATAAAGCCAATTTGAACTCTTCCAC
196 TGACACATGGCAAATTTTTGTCCATTTAATATTTTCCTTTATAAAGCCAATTTGAACTCTTCCAC
26121270 ATTCATTCTTATGGCCGGCCAAAGTAAAAACAAAGGAAGAAAAGAAAGAACAAAACCCTAGGTTG
261 ATTCATTCTTATGGCCGGCCAAAGTAAAAACAAAGGAAGAAAAGAAAGAACAAAACCCTAGGTTG
26121335 AAAAATTCAAGGGAAAAGTGTGAAAATTCAAGGAAACAAGTGAAAAAAAAGGTAAGATTTTTC
326 AAAAATTCAAGGGAAAAGTGTGAAAATTCAAGGAAACAAGTGAAAAAAAAGG-AAGATTTTTC
26121398 TAATTTCGACATTTTTTTCAAGGATAAGGGCAAAATAGACATTTTGCCACCCAAGGGCAAAATTG
1 TAATTTCGACA-TTTTTTCAAGGATAAGGGCAAAATAGACATTTTGCCACCCAAGGGCAAAATTG
26121463 GAATTTTACACCACCCAACACTTGTCCAGCACATGGATTTTACCCAATATTATCATGGATAATTG
65 GAATTTTACACCACCCAACACTTGTCCAGCACATGGATTTTACCCAATATTATCATGGATAATTG
*
26121528 AGAAAATTTAAGTGGTGGAGAGAGATTGCTTAATGGGTAAGTATGACACTTAGACCAATGGAATT
130 AGAAAATTTAAGTGGTAGAGAGAGATTGCTTAATGGGTAAGTATGACACTTAGACCAATGGAATT
26121593 GTGACACATGGCAAATTTTTGTCCATTTAATATTTTCCTTTATAAAGCCAATTTGAACTCTTCCA
195 GTGACACATGGCAAATTTTTGTCCATTTAATATTTTCCTTTATAAAGCCAATTTGAACTCTTCCA
*
26121658 CATTCATTCTTATGGCCGGCCAAAGTAAGAACAAAGGAAGAAAAGAAAGAACAAAACCCTAGGTT
260 CATTCATTCTTATGGCCGGCCAAAGTAAAAACAAAGGAAGAAAAGAAAGAACAAAACCCTAGGTT
26121723 GAAAAATTCAAGGGAAAAGTGTGAAAATTCAAGGAAACAAGTGAAAAAAAAGGAAGATTTTTC
325 GAAAAATTCAAGGGAAAAGTGTGAAAATTCAAGGAAACAAGTGAAAAAAAAGGAAGATTTTTC
26121786 -AATT
1 TAATT
26121790 AAGCTTGAGA
Statistics
Matches: 388, Mismatches: 3, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
387 4 0.01
388 21 0.05
389 363 0.94
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.27
Consensus pattern (387 bp):
TAATTTCGACATTTTTTCAAGGATAAGGGCAAAATAGACATTTTGCCACCCAAGGGCAAAATTGG
AATTTTACACCACCCAACACTTGTCCAGCACATGGATTTTACCCAATATTATCATGGATAATTGA
GAAAATTTAAGTGGTAGAGAGAGATTGCTTAATGGGTAAGTATGACACTTAGACCAATGGAATTG
TGACACATGGCAAATTTTTGTCCATTTAATATTTTCCTTTATAAAGCCAATTTGAACTCTTCCAC
ATTCATTCTTATGGCCGGCCAAAGTAAAAACAAAGGAAGAAAAGAAAGAACAAAACCCTAGGTTG
AAAAATTCAAGGGAAAAGTGTGAAAATTCAAGGAAACAAGTGAAAAAAAAGGAAGATTTTTC
Found at i:26121751 original size:21 final size:22
Alignment explanation
Indices: 26121725--26121765 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
26121715 CCTAGGTTGA
*
26121725 AAAATTCAAGGGAA-AAGTGTG
1 AAAATTCAAGGAAACAAGTGTG
26121746 AAAATTCAAGGAAACAAGTG
1 AAAATTCAAGGAAACAAGTG
26121766 AAAAAAAAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.51, C:0.07, G:0.24, T:0.17
Consensus pattern (22 bp):
AAAATTCAAGGAAACAAGTGTG
Found at i:26121766 original size:20 final size:21
Alignment explanation
Indices: 26121725--26121769 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
26121715 CCTAGGTTGA
*
26121725 AAAATTCAAGGGAAAAGTGTG
1 AAAATTCAAGGGAAAAGAGTG
26121746 AAAATTCAA-GGAAACA-AGTG
1 AAAATTCAAGGGAAA-AGAGTG
26121766 AAAA
1 AAAA
26121770 AAAAGGAAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.56, C:0.07, G:0.22, T:0.16
Consensus pattern (21 bp):
AAAATTCAAGGGAAAAGAGTG
Found at i:26121770 original size:21 final size:20
Alignment explanation
Indices: 26121722--26121770 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
26121712 AACCCTAGGT
*
26121722 TGAAAAATTCAAGGGAAAAG
1 TGAAAAATTCAAGGAAAAAG
*
26121742 TGTGAAAATTCAAGGAAACAAG
1 TG-AAAAATTCAAGGAAA-AAG
26121764 TGAAAAA
1 TGAAAAA
26121771 AAAGGAAGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 2 0.08
21 17 0.71
22 5 0.21
ACGTcount: A:0.55, C:0.06, G:0.22, T:0.16
Consensus pattern (20 bp):
TGAAAAATTCAAGGAAAAAG
Found at i:26127270 original size:31 final size:31
Alignment explanation
Indices: 26127224--26127286 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
26127214 ATATGTATTG
* *
26127224 TAGCATTGTGTTATTGTTTGTTGCTTAAAAT
1 TAGCATTGTATTATTGATTGTTGCTTAAAAT
*
26127255 TAGCGTTGTATTATTGATTGTTGCTTAAAAT
1 TAGCATTGTATTATTGATTGTTGCTTAAAAT
26127286 T
1 T
26127287 TCATCAATAC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.24, C:0.06, G:0.19, T:0.51
Consensus pattern (31 bp):
TAGCATTGTATTATTGATTGTTGCTTAAAAT
Found at i:26128975 original size:2 final size:2
Alignment explanation
Indices: 26128970--26129005 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
26128960 GAGAGTAAAA
26128970 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
26129006 GATGTTTTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:26134845 original size:30 final size:30
Alignment explanation
Indices: 26134810--26134868 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
26134800 ATATGGTTTT
* *
26134810 AATGGGATTGTGATAACTACTCATTATCTG
1 AATGGGATTATGATAACTACCCATTATCTG
*
26134840 AATGGGATTATGATAATTACCCATTATCT
1 AATGGGATTATGATAACTACCCATTATCT
26134869 TTGAAATTCC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.37
Consensus pattern (30 bp):
AATGGGATTATGATAACTACCCATTATCTG
Found at i:26135716 original size:47 final size:47
Alignment explanation
Indices: 26135658--26135791 Score: 196
Period size: 47 Copynumber: 2.9 Consensus size: 47
26135648 TTTTAGTTTG
* *
26135658 TAGTCTAGACCAAAATAAAGAATATTGGGTTTTGTCTTTTATACAAT
1 TAGTCTGGACCAAAATAAAGAATATTGAGTTTTGTCTTTTATACAAT
* * * *
26135705 TAGTCTGGACCATAATAAAAAATATTGAGTTTTATTTTTTATACAAT
1 TAGTCTGGACCAAAATAAAGAATATTGAGTTTTGTCTTTTATACAAT
* *
26135752 TAGTTTGGACCAAAATAAAGAATGTTGAGTTTTGTCTTTT
1 TAGTCTGGACCAAAATAAAGAATATTGAGTTTTGTCTTTT
26135792 TATGCTATCA
Statistics
Matches: 75, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
47 75 1.00
ACGTcount: A:0.35, C:0.09, G:0.15, T:0.41
Consensus pattern (47 bp):
TAGTCTGGACCAAAATAAAGAATATTGAGTTTTGTCTTTTATACAAT
Found at i:26145586 original size:21 final size:21
Alignment explanation
Indices: 26145560--26145600 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
26145550 AACAAAAAGT
26145560 TTCTCGCTACAGCAAGATTCA
1 TTCTCGCTACAGCAAGATTCA
*
26145581 TTCTCGCTGCAGCAAGATTC
1 TTCTCGCTACAGCAAGATTC
26145601 TCGGCCAGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.24, C:0.29, G:0.17, T:0.29
Consensus pattern (21 bp):
TTCTCGCTACAGCAAGATTCA
Found at i:26145823 original size:2 final size:2
Alignment explanation
Indices: 26145811--26145950 Score: 138
Period size: 2 Copynumber: 66.0 Consensus size: 2
26145801 ACCATATACC
*
26145811 AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * *
26145853 AT AT AT AT AT AT ACT AT ACT ACT ACT ACT AC CT -T AC CT ACT ACT
1 AT AT AT AT AT AT A-T AT A-T A-T A-T A-T AT AT AT AT AT A-T A-T
*
26145897 ACT ACT AN AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 A-T A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
26145941 AT AT AT AT AT
1 AT AT AT AT AT
26145951 CAATCATCAT
Statistics
Matches: 123, Mismatches: 11, Indels: 8
0.87 0.08 0.06
Matches are distributed among these distances:
1 1 0.01
2 98 0.80
3 24 0.20
ACGTcount: A:0.44, C:0.09, G:0.01, T:0.45
Consensus pattern (2 bp):
AT
Found at i:26146055 original size:42 final size:42
Alignment explanation
Indices: 26145991--26146115 Score: 160
Period size: 42 Copynumber: 3.0 Consensus size: 42
26145981 CATCTCGTAT
* * * *
26145991 GCAACAGCTTATGCGCATTCCCACTCGCATATAGCCGGGTCA
1 GCAACGGCTTATGTGCACTCCCACTCGCACATAGCCGGGTCA
* * * *
26146033 GCAACGGTTTATGTGTACTCCCACTCGCACATAGTCGAGTCA
1 GCAACGGCTTATGTGCACTCCCACTCGCACATAGCCGGGTCA
* *
26146075 GCAACGGCTTATGTGCACTCCTACTCGCACATAGCTGGGTC
1 GCAACGGCTTATGTGCACTCCCACTCGCACATAGCCGGGTC
26146116 CACATCAACA
Statistics
Matches: 69, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 69 1.00
ACGTcount: A:0.22, C:0.31, G:0.22, T:0.24
Consensus pattern (42 bp):
GCAACGGCTTATGTGCACTCCCACTCGCACATAGCCGGGTCA
Found at i:26151975 original size:23 final size:22
Alignment explanation
Indices: 26151941--26151985 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
26151931 ATGGATGTTG
*
26151941 ATATATTTATGGTACTTTGCTA
1 ATATATTCATGGTACTTTGCTA
*
26151963 ATATGATTCATGGTATTTTGCTA
1 ATAT-ATTCATGGTACTTTGCTA
26151986 CTGATAATTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.27, C:0.09, G:0.16, T:0.49
Consensus pattern (22 bp):
ATATATTCATGGTACTTTGCTA
Found at i:26153395 original size:11 final size:11
Alignment explanation
Indices: 26153381--26153408 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
26153371 AAGCCATTGT
26153381 AAAGCTTGGTG
1 AAAGCTTGGTG
26153392 AAAGCTTGGTG
1 AAAGCTTGGTG
26153403 AAAGCT
1 AAAGCT
26153409 GATGAATTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.32, C:0.11, G:0.32, T:0.25
Consensus pattern (11 bp):
AAAGCTTGGTG
Found at i:26154028 original size:30 final size:30
Alignment explanation
Indices: 26153993--26154054 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 30
26153983 TGATATGGTT
* *
26153993 TTAATGGGATTGTGATAACTACCCATTATC
1 TTAATGGAATTATGATAACTACCCATTATC
* *
26154023 TTAATGGAATTATGATAATTACCCATTTTC
1 TTAATGGAATTATGATAACTACCCATTATC
26154053 TT
1 TT
26154055 TGAAATTCCC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.42
Consensus pattern (30 bp):
TTAATGGAATTATGATAACTACCCATTATC
Found at i:26159315 original size:20 final size:20
Alignment explanation
Indices: 26159270--26159307 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
26159260 TTTTGGCCCC
26159270 ATTTGACTTATTGGAGTATA
1 ATTTGACTTATTGGAGTATA
26159290 ATTTGACTTATTGGAGTA
1 ATTTGACTTATTGGAGTA
26159308 AGATTTGAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.29, C:0.05, G:0.21, T:0.45
Consensus pattern (20 bp):
ATTTGACTTATTGGAGTATA
Found at i:26159697 original size:30 final size:32
Alignment explanation
Indices: 26159663--26159726 Score: 78
Period size: 32 Copynumber: 2.1 Consensus size: 32
26159653 CCCTAGAGAG
*
26159663 AGAAAATCAA-AGAAAAA-GTGTGAATTTTCA
1 AGAAAATCAAGAGAAAAAGGTATGAATTTTCA
* * *
26159693 AGAAAATTAAGTGAAAAAGGTATGATTTTTCA
1 AGAAAATCAAGAGAAAAAGGTATGAATTTTCA
26159725 AG
1 AG
26159727 CTTAGTTTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 9 0.32
31 6 0.21
32 13 0.46
ACGTcount: A:0.50, C:0.05, G:0.19, T:0.27
Consensus pattern (32 bp):
AGAAAATCAAGAGAAAAAGGTATGAATTTTCA
Found at i:26163474 original size:5 final size:5
Alignment explanation
Indices: 26163439--26163473 Score: 61
Period size: 5 Copynumber: 7.0 Consensus size: 5
26163429 CCCCAAGTCC
*
26163439 AGTTA AGTTA AGTTA AGTTA AGTTA AGTTA GGTTA
1 AGTTA AGTTA AGTTA AGTTA AGTTA AGTTA AGTTA
26163474 GATTGAATAG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.37, C:0.00, G:0.23, T:0.40
Consensus pattern (5 bp):
AGTTA
Found at i:26177575 original size:35 final size:35
Alignment explanation
Indices: 26177536--26177649 Score: 165
Period size: 35 Copynumber: 3.3 Consensus size: 35
26177526 ATCATGCAAT
* *
26177536 AACCCTCACAATGGTTTTTAACAAGATCAATCACA
1 AACCCTCACAATGGTTTTTAACAAGCTCAACCACA
*** *
26177571 AACCCTCACAATGGTTTTTAAGGGGCTCAACCTCA
1 AACCCTCACAATGGTTTTTAACAAGCTCAACCACA
26177606 AACCCTCACAATGGTTTTTAACAAGCTCAACCACA
1 AACCCTCACAATGGTTTTTAACAAGCTCAACCACA
*
26177641 AATCCTCAC
1 AACCCTCAC
26177650 TAACTTTTCA
Statistics
Matches: 68, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 68 1.00
ACGTcount: A:0.35, C:0.30, G:0.11, T:0.25
Consensus pattern (35 bp):
AACCCTCACAATGGTTTTTAACAAGCTCAACCACA
Found at i:26179031 original size:2 final size:2
Alignment explanation
Indices: 26179024--26179048 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
26179014 AATGCATGTA
26179024 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
26179049 ATCTATACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:26179127 original size:44 final size:43
Alignment explanation
Indices: 26179052--26179187 Score: 157
Period size: 44 Copynumber: 3.1 Consensus size: 43
26179042 TGTGTGTATC
*
26179052 TATACATACATATATATAT-ATATACATACACACACACACACATA
1 TATACATACATATATATATCATATAC--ACACACACACACACACA
*
26179096 TATACATACATATATATGTGCATATACACACACACACACACACA
1 TATACATACATATATATAT-CATATACACACACACACACACACA
* * * * * *
26179140 TATATATATATATACATACACACACACACACACACACACACACA
1 TATACATACATATATATA-TCATATACACACACACACACACACA
26179184 TATA
1 TATA
26179188 TATGTATGTA
Statistics
Matches: 80, Mismatches: 9, Indels: 6
0.84 0.09 0.06
Matches are distributed among these distances:
44 74 0.93
46 6 0.08
ACGTcount: A:0.49, C:0.26, G:0.01, T:0.24
Consensus pattern (43 bp):
TATACATACATATATATATCATATACACACACACACACACACA
Found at i:26179162 original size:2 final size:2
Alignment explanation
Indices: 26179157--26179183 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
26179147 ATATATACAT
26179157 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
26179184 TATATATGTA
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:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:26179190 original size:4 final size:4
Alignment explanation
Indices: 26179183--26179253 Score: 61
Period size: 4 Copynumber: 17.8 Consensus size: 4
26179173 ACACACACAC
* * * * * *
26179183 ATAT ATAT GTAT GTAT GTAT GTAT GTAT ATAT ATAT ATAA ATAT ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
* * *
26179231 ATTT GTAT ATAC ATAT ATAT ATA
1 ATAT ATAT ATAT ATAT ATAT ATA
26179254 AGCAAATTGT
Statistics
Matches: 57, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
4 57 1.00
ACGTcount: A:0.42, C:0.01, G:0.08, T:0.48
Consensus pattern (4 bp):
ATAT
Found at i:26179226 original size:10 final size:10
Alignment explanation
Indices: 26179183--26179253 Score: 61
Period size: 10 Copynumber: 7.1 Consensus size: 10
26179173 ACACACACAC
*
26179183 ATATATATGT
1 ATATATATAT
* *
26179193 ATGTATGTAT
1 ATATATATAT
* *
26179203 GTATGTATAT
1 ATATATATAT
*
26179213 ATATATATAA
1 ATATATATAT
26179223 ATATATATAT
1 ATATATATAT
* * *
26179233 TTGTATATAC
1 ATATATATAT
26179243 ATATATATAT
1 ATATATATAT
26179253 A
1 A
26179254 AGCAAATTGT
Statistics
Matches: 44, Mismatches: 17, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
10 44 1.00
ACGTcount: A:0.42, C:0.01, G:0.08, T:0.48
Consensus pattern (10 bp):
ATATATATAT
Found at i:26179359 original size:2 final size:2
Alignment explanation
Indices: 26179340--26179405 Score: 62
Period size: 2 Copynumber: 33.5 Consensus size: 2
26179330 TCCAAAGTAC
* * * * *
26179340 AT AT AC AT AT AT AC AT AT AT AT A- AT AT TT AT GT AT AT AT GT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
26179381 AA AT AT AT AT AT GT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
26179406 AGCAAAATAT
Statistics
Matches: 49, Mismatches: 14, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
1 1 0.02
2 48 0.98
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (2 bp):
AT
Found at i:26187758 original size:13 final size:13
Alignment explanation
Indices: 26187740--26187764 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
26187730 ATTTTTAAAA
26187740 ATTTTATAAAATT
1 ATTTTATAAAATT
26187753 ATTTTATAAAAT
1 ATTTTATAAAAT
26187765 CTCATTTTCC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
ATTTTATAAAATT
Found at i:26188884 original size:19 final size:20
Alignment explanation
Indices: 26188855--26188894 Score: 73
Period size: 19 Copynumber: 2.0 Consensus size: 20
26188845 TCACTTCTAA
26188855 ACTTCAAATCATACTCCAAT
1 ACTTCAAATCATACTCCAAT
26188875 ACTT-AAATCATACTCCAAT
1 ACTTCAAATCATACTCCAAT
26188894 A
1 A
26188895 AGTCAAATGG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.42, C:0.28, G:0.00, T:0.30
Consensus pattern (20 bp):
ACTTCAAATCATACTCCAAT
Found at i:26190660 original size:35 final size:34
Alignment explanation
Indices: 26190577--26190663 Score: 115
Period size: 34 Copynumber: 2.6 Consensus size: 34
26190567 CTCATATCCA
26190577 CCTC-AAAATCAA-CAGCCAAGCTGCTCTATTCTT
1 CCTCAAAAAT-AAGCAGCCAAGCTGCTCTATTCTT
* * *
26190610 CCTCAAAAATCAGCAGCTAAGCTGCTTTATTCTT
1 CCTCAAAAATAAGCAGCCAAGCTGCTCTATTCTT
26190644 CCTCCAAAAATAAGCAGCCA
1 CCT-CAAAAATAAGCAGCCA
26190664 CAACTGCTTC
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
33 5 0.11
34 27 0.59
35 14 0.30
ACGTcount: A:0.33, C:0.31, G:0.10, T:0.25
Consensus pattern (34 bp):
CCTCAAAAATAAGCAGCCAAGCTGCTCTATTCTT
Found at i:26193356 original size:22 final size:22
Alignment explanation
Indices: 26193289--26193343 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
26193279 TTTGAATAAG
*
26193289 AATTTTTCATCTTATACATGAA
1 AATTTTTCATCTTATAAATGAA
26193311 AATTTTTCATCTTATAAATGAA
1 AATTTTTCATCTTATAAATGAA
26193333 AATTTTTCATC
1 AATTTTTCATC
26193344 ATTCAATATA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.36, C:0.13, G:0.04, T:0.47
Consensus pattern (22 bp):
AATTTTTCATCTTATAAATGAA
Found at i:26193357 original size:23 final size:22
Alignment explanation
Indices: 26193283--26193361 Score: 88
Period size: 22 Copynumber: 3.5 Consensus size: 22
26193273 ATTATCTTTG
*
26193283 AATAAGAATTTTTCATCTTATA
1 AATAAAAATTTTTCATCTTATA
* *
26193305 CATGAAAATTTTTCATCTTATA
1 AATAAAAATTTTTCATCTTATA
*
26193327 AATGAAAATTTTTCATCATTCA-A
1 AATAAAAATTTTTCATC-TT-ATA
*
26193350 TATAAAAATTTT
1 AATAAAAATTTT
26193362 CATGCTGAGG
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
22 35 0.71
23 13 0.27
24 1 0.02
ACGTcount: A:0.42, C:0.10, G:0.04, T:0.44
Consensus pattern (22 bp):
AATAAAAATTTTTCATCTTATA
Found at i:26195422 original size:19 final size:20
Alignment explanation
Indices: 26195395--26195440 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
26195385 AGGAGACAAG
*
26195395 ATAAAATTTTTA-GAATAAA
1 ATAATATTTTTATGAATAAA
*
26195414 ATAATA-TTTTATTAATAAA
1 ATAATATTTTTATGAATAAA
26195433 ATAATATT
1 ATAATATT
26195441 AAAATATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 5 0.22
19 17 0.74
20 1 0.04
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.43
Consensus pattern (20 bp):
ATAATATTTTTATGAATAAA
Found at i:26205266 original size:15 final size:15
Alignment explanation
Indices: 26205246--26205285 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
26205236 AAGATATTTT
26205246 GATTTTAAAGCATTA
1 GATTTTAAAGCATTA
* *
26205261 GATTTTAAAGCTTTT
1 GATTTTAAAGCATTA
*
26205276 GGTTTTAAAG
1 GATTTTAAAG
26205286 TTGTTTTAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.33, C:0.05, G:0.17, T:0.45
Consensus pattern (15 bp):
GATTTTAAAGCATTA
Found at i:26205369 original size:5 final size:5
Alignment explanation
Indices: 26205329--26205368 Score: 53
Period size: 5 Copynumber: 8.0 Consensus size: 5
26205319 CCCCAAGTCC
* * *
26205329 AGTTA AGTGA AGATA AGTTA AGTTA AGTTA AGTTA GGTTA
1 AGTTA AGTTA AGTTA AGTTA AGTTA AGTTA AGTTA AGTTA
26205369 GATTGAATAG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.40, C:0.00, G:0.25, T:0.35
Consensus pattern (5 bp):
AGTTA
Found at i:26208427 original size:28 final size:27
Alignment explanation
Indices: 26208380--26208432 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
26208370 AATGCTCTGG
* *
26208380 GGGTGCAAAATTACCGTTTTGCCCCTA
1 GGGTGCAAAATTACAGTTTTACCCCTA
*
26208407 GGGTGGCAAAATTACATTTTTACCCC
1 GGGT-GCAAAATTACAGTTTTACCCC
26208433 AAAAACTAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 4 0.18
28 18 0.82
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.30
Consensus pattern (27 bp):
GGGTGCAAAATTACAGTTTTACCCCTA
Found at i:26208637 original size:19 final size:19
Alignment explanation
Indices: 26208613--26208650 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
26208603 CTGTCAAACC
*
26208613 CTCAAATTATACTCCAATA
1 CTCAAATCATACTCCAATA
26208632 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
26208651 AGTTAAATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.42, C:0.29, G:0.00, T:0.29
Consensus pattern (19 bp):
CTCAAATCATACTCCAATA
Found at i:26209041 original size:31 final size:31
Alignment explanation
Indices: 26209006--26209068 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
26208996 ACACCACTCA
*
26209006 TTTACAAAAAATATTTACTTGCTATATTACT
1 TTTACAAAAAATATTTACTTGCTATACTACT
*
26209037 TTTACAAAAAATATTTACTTGTTATACTACT
1 TTTACAAAAAATATTTACTTGCTATACTACT
26209068 T
1 T
26209069 ATCTAGAGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.38, C:0.13, G:0.03, T:0.46
Consensus pattern (31 bp):
TTTACAAAAAATATTTACTTGCTATACTACT
Found at i:26217558 original size:19 final size:21
Alignment explanation
Indices: 26217536--26217575 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
26217526 AAAGTAACTA
26217536 CAAGA-CCCT-AAACAAAAAT
1 CAAGACCCCTAAAACAAAAAT
26217555 CAAGACCCCTAAAACAAAAAT
1 CAAGACCCCTAAAACAAAAAT
26217576 AGGGGAACAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.26
20 4 0.21
21 10 0.53
ACGTcount: A:0.57, C:0.28, G:0.05, T:0.10
Consensus pattern (21 bp):
CAAGACCCCTAAAACAAAAAT
Found at i:26243290 original size:54 final size:54
Alignment explanation
Indices: 26243232--26243340 Score: 123
Period size: 54 Copynumber: 2.0 Consensus size: 54
26243222 TTTTTCGATG
* *
26243232 TGGGTTTGT-GGGTTTTTTTCCCT-ACTTCTTTGTCTCATTTAATCTTTTTTGGTT
1 TGGGTTTGTAAGGTTTTTTTCCCTCACTTCTTTGTCTCATTT-A-CTTTTTTAGTT
* ** * *
26243286 TGGGTTTTTAAGGTTTTTTTTTCTCGCTTTTTTGTCTCATTTACTTTTTTAGTT
1 TGGGTTTGTAAGGTTTTTTTCCCTCACTTCTTTGTCTCATTTACTTTTTTAGTT
26243340 T
1 T
26243341 TTGTTAGCTT
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
54 19 0.41
55 12 0.26
56 15 0.33
ACGTcount: A:0.08, C:0.13, G:0.17, T:0.62
Consensus pattern (54 bp):
TGGGTTTGTAAGGTTTTTTTCCCTCACTTCTTTGTCTCATTTACTTTTTTAGTT
Found at i:26244702 original size:35 final size:35
Alignment explanation
Indices: 26244663--26244763 Score: 150
Period size: 34 Copynumber: 2.9 Consensus size: 35
26244653 GAGGTTGTGC
* *
26244663 TTGATCTTGTGAAAGGCAAGTTGTAAAGGTTACTT
1 TTGATCTTGCGAAAAGCAAGTTGTAAAGGTTACTT
26244698 TTGATCTTGCGAAAAGC-AGTTGTAAAGGTTACTT
1 TTGATCTTGCGAAAAGCAAGTTGTAAAGGTTACTT
* * *
26244732 TTGATCTTGCAAAAAGCATGTTATAAAGGTTA
1 TTGATCTTGCGAAAAGCAAGTTGTAAAGGTTA
26244764 TGCTTGACAC
Statistics
Matches: 60, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
34 33 0.55
35 27 0.45
ACGTcount: A:0.32, C:0.10, G:0.23, T:0.36
Consensus pattern (35 bp):
TTGATCTTGCGAAAAGCAAGTTGTAAAGGTTACTT
Found at i:26252254 original size:21 final size:21
Alignment explanation
Indices: 26252229--26252270 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
26252219 TCTTTTTGAA
*
26252229 AAAGCATATAATT-AAGGGGAG
1 AAAGCATA-AATTCAAAGGGAG
26252250 AAAGCATAAATTCAAAGGGAG
1 AAAGCATAAATTCAAAGGGAG
26252271 CTTTACCTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.50, C:0.07, G:0.26, T:0.17
Consensus pattern (21 bp):
AAAGCATAAATTCAAAGGGAG
Found at i:26253761 original size:35 final size:35
Alignment explanation
Indices: 26253683--26253763 Score: 94
Period size: 35 Copynumber: 2.3 Consensus size: 35
26253673 TAGTGTCTTA
*
26253683 GTAAAGGTTACATCTGATCTTGTAAAAGGCAAGTT
1 GTAAAGGTTACATCTGATCTTGAAAAAGGCAAGTT
* *
26253718 GTAGAGGTTATGAT-TGATCTTGAAAAAGGCATA-TT
1 GTAAAGGTTA-CATCTGATCTTGAAAAAGGCA-AGTT
*
26253753 TTAAAGGTTAC
1 GTAAAGGTTAC
26253764 GCGTGACCCT
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
35 35 0.92
36 3 0.08
ACGTcount: A:0.35, C:0.09, G:0.23, T:0.33
Consensus pattern (35 bp):
GTAAAGGTTACATCTGATCTTGAAAAAGGCAAGTT
Found at i:26255320 original size:20 final size:20
Alignment explanation
Indices: 26255291--26255341 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 20
26255281 ACTCTTCTTA
26255291 AAGTAAATTAAAAC-AAAAT
1 AAGTAAATTAAAACTAAAAT
26255310 AAGTAAAATT-AAACTAAAAT
1 AAGT-AAATTAAAACTAAAAT
*
26255330 AACTTAAATTAA
1 AA-GTAAATTAA
26255342 CTATTCAACA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
19 8 0.30
20 17 0.63
21 2 0.07
ACGTcount: A:0.65, C:0.06, G:0.04, T:0.25
Consensus pattern (20 bp):
AAGTAAATTAAAACTAAAAT
Found at i:26261150 original size:29 final size:30
Alignment explanation
Indices: 26261085--26261150 Score: 107
Period size: 29 Copynumber: 2.2 Consensus size: 30
26261075 ATTCTCATAA
*
26261085 CAATATTCTATATAAACTCATTTGCTATAN
1 CAATATTCTATATAAACTCATTTGCTATAT
26261115 CAATATTCTATAT-AACTCATTTGCTATAT
1 CAATATTCTATATAAACTCATTTGCTATAT
*
26261144 CATTATT
1 CAATATT
26261151 GAAATCTTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
29 21 0.62
30 13 0.38
ACGTcount: A:0.35, C:0.17, G:0.03, T:0.44
Consensus pattern (30 bp):
CAATATTCTATATAAACTCATTTGCTATAT
Found at i:26263034 original size:22 final size:22
Alignment explanation
Indices: 26263008--26263051 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
26262998 TTTAAATTGA
26263008 CTTTAAAACCAAAAACTCTTAT
1 CTTTAAAACCAAAAACTCTTAT
*
26263030 CTTTAAAACCAAAAGCTCTTAT
1 CTTTAAAACCAAAAACTCTTAT
26263052 ACAAATAGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.43, C:0.23, G:0.02, T:0.32
Consensus pattern (22 bp):
CTTTAAAACCAAAAACTCTTAT
Found at i:26276560 original size:88 final size:88
Alignment explanation
Indices: 26276411--26276582 Score: 292
Period size: 88 Copynumber: 2.0 Consensus size: 88
26276401 TTTTAGCTGA
*
26276411 TTCTCTTAGCTTTCCAATGGGTCAAGAATCTCATTAATTTGGCTTTTGTAGCTCAATTTATCCTT
1 TTCTCTTAGCTTTCCAATGGATCAAGAATCTCATTAATTTGGCTTTTGTAGCTCAATTTATCCTT
*
26276476 GAAATGCTGCAACATGTACCCCG
66 AAAATGCTGCAACATGTACCCCG
*
26276499 TTCTCTTAGCTTTCCAATGGATCAAGAATCTCATTAA-TTGGACTTTTGTGGCTCAATTTATCCT
1 TTCTCTTAGCTTTCCAATGGATCAAGAATCTCATTAATTTGG-CTTTTGTAGCTCAATTTATCCT
*
26276563 TAAAATGCTGTAACATGTAC
65 TAAAATGCTGCAACATGTAC
26276583 AAATGAAGCC
Statistics
Matches: 79, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
87 4 0.05
88 75 0.95
ACGTcount: A:0.26, C:0.21, G:0.15, T:0.38
Consensus pattern (88 bp):
TTCTCTTAGCTTTCCAATGGATCAAGAATCTCATTAATTTGGCTTTTGTAGCTCAATTTATCCTT
AAAATGCTGCAACATGTACCCCG
Found at i:26277322 original size:22 final size:21
Alignment explanation
Indices: 26277292--26277345 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
26277282 TTTTTTTGGG
* *
26277292 TTTTGTTTTTTTCTCCTGCTTT
1 TTTTTTTTTTTTCTCCTG-TGT
**
26277314 TTTTTTTTTTTTCTTTTGTGT
1 TTTTTTTTTTTTCTCCTGTGT
26277335 TTTTTTTTTTT
1 TTTTTTTTTTT
26277346 CGTCTTTATC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
21 13 0.46
22 15 0.54
ACGTcount: A:0.00, C:0.09, G:0.07, T:0.83
Consensus pattern (21 bp):
TTTTTTTTTTTTCTCCTGTGT
Found at i:26280864 original size:28 final size:29
Alignment explanation
Indices: 26280823--26280882 Score: 68
Period size: 30 Copynumber: 2.1 Consensus size: 29
26280813 GTCTATGGGC
*
26280823 AATTTTTCAGTTTT-TGGGGCAAAAATGT
1 AATTTTTCAGTTTTAGGGGGCAAAAATGT
* * *
26280851 AATTTTTGATTTTTACGGGGGCAAAAGTGT
1 AATTTTTCAGTTTTA-GGGGGCAAAAATGT
26280881 AA
1 AA
26280883 ATATCAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
28 12 0.46
30 14 0.54
ACGTcount: A:0.30, C:0.07, G:0.23, T:0.40
Consensus pattern (29 bp):
AATTTTTCAGTTTTAGGGGGCAAAAATGT
Found at i:26290071 original size:19 final size:19
Alignment explanation
Indices: 26290047--26290084 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
26290037 CTGCCAAACC
*
26290047 CTCAAATTATACTCCAATA
1 CTCAAATCATACTCCAATA
26290066 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
26290085 AGTTAAATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.42, C:0.29, G:0.00, T:0.29
Consensus pattern (19 bp):
CTCAAATCATACTCCAATA
Found at i:26295524 original size:19 final size:19
Alignment explanation
Indices: 26295486--26295526 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
26295476 AAATTTAGAA
** *
26295486 TAAAATAATATTTTATTAT
1 TAAAATAATATTAAAATAT
26295505 TAAAATAATATTAAAATAT
1 TAAAATAATATTAAAATAT
26295524 TAA
1 TAA
26295527 TATTTTATTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
TAAAATAATATTAAAATAT
Found at i:26296421 original size:91 final size:92
Alignment explanation
Indices: 26296262--26296499 Score: 284
Period size: 92 Copynumber: 2.6 Consensus size: 92
26296252 TTTTTCTTCC
* * * ** *
26296262 ATTTTAAGGGTGAGATGAACACCTTTAGCTGCTGATTTTTGAAGTTTGAAATGAGCAGCTTTGGC
1 ATTTTGAGGGTGAGATGAGCAGCTTTAGCTGCTGA-TTTTGAAGGCTGAAATGAGCAACTTTGGC
* *
26296327 TACTAATTTTTTAGGT-TTTGGCT-ATCG
65 TACTAATTTTTGAGGTCTTTGGCTGCT-G
* *
26296354 ATTTTGAGGGTGAGAGGAGCAGCTTTAGTTGCTGATTTTGAAGGCTGAAATGAGCAACTTTGGCT
1 ATTTTGAGGGTGAGATGAGCAGCTTTAGCTGCTGATTTTGAAGGCTGAAATGAGCAACTTTGGCT
* *
26296419 ACTGATTTTTGAGGTCTTTTGCTGCTG
66 ACTAATTTTTGAGGTCTTTGGCTGCTG
* * * *
26296446 GTTTTGAGGGTGAAATGAGCAGCTTTGGCTG-TCGATTTTTAAGGCTGAAATGAG
1 ATTTTGAGGGTGAGATGAGCAGCTTTAGCTGCT-GATTTTGAAGGCTGAAATGAG
26296500 GAGTTTAAGC
Statistics
Matches: 125, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
91 41 0.33
92 83 0.66
93 1 0.01
ACGTcount: A:0.23, C:0.11, G:0.29, T:0.37
Consensus pattern (92 bp):
ATTTTGAGGGTGAGATGAGCAGCTTTAGCTGCTGATTTTGAAGGCTGAAATGAGCAACTTTGGCT
ACTAATTTTTGAGGTCTTTGGCTGCTG
Found at i:26296437 original size:23 final size:22
Alignment explanation
Indices: 26296411--26296454 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 22
26296401 AAATGAGCAA
*
26296411 CTTTGGCTACTGATTTTTGAGGT
1 CTTTGGCTACTG-GTTTTGAGGT
* *
26296434 CTTTTGCTGCTGGTTTTGAGG
1 CTTTGGCTACTGGTTTTGAGG
26296455 GTGAAATGAG
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 8 0.44
23 10 0.56
ACGTcount: A:0.09, C:0.14, G:0.30, T:0.48
Consensus pattern (22 bp):
CTTTGGCTACTGGTTTTGAGGT
Found at i:26297935 original size:63 final size:63
Alignment explanation
Indices: 26297835--26298001 Score: 227
Period size: 63 Copynumber: 2.7 Consensus size: 63
26297825 GGATGTAACC
*
26297835 GTGCATGTGCGGAGTGGGCAGTGCACATGCCGGTTGAATGATGAGGTT-TAGATAGTTAC-ACCC
1 GTGCATGTGCGGAGTGGGCAGTGCACATGCCGGTTGAATGATGAGGTTGT-GATAATTACTA--C
26297898 A
63 A
* *
26297899 -TGCATGTGCGGAGTGGGCAGTGCACATGCCGGTTGAATGACGATGTTGTGATAATTACTACA
1 GTGCATGTGCGGAGTGGGCAGTGCACATGCCGGTTGAATGATGAGGTTGTGATAATTACTACA
* *
26297961 GTGCATATGCAGAGTGGGCAGTGCACATGCCGG-T-AATGATG
1 GTGCATGTGCGGAGTGGGCAGTGCACATGCCGGTTGAATGATG
26298002 CATATGAGCT
Statistics
Matches: 94, Mismatches: 6, Indels: 9
0.86 0.06 0.08
Matches are distributed among these distances:
61 6 0.06
62 3 0.03
63 83 0.88
64 2 0.02
ACGTcount: A:0.24, C:0.17, G:0.34, T:0.25
Consensus pattern (63 bp):
GTGCATGTGCGGAGTGGGCAGTGCACATGCCGGTTGAATGATGAGGTTGTGATAATTACTACA
Found at i:26315445 original size:36 final size:35
Alignment explanation
Indices: 26315398--26315607 Score: 129
Period size: 36 Copynumber: 5.7 Consensus size: 35
26315388 TAATCGTGCA
* * * *
26315398 TGTGCAGTGTGGGAGTGCACATAACGGTGAGAGTGG
1 TGTGCGGTGTGGGAGTGCACATGATGGTGACA-TGG
* * * * *
26315434 TGTGCGGTGTGGGAATGCACACGATGATGATATTGCCA
1 TGTGCGGTGTGGGAGTGCACATGATGGTGACA-TG--G
* *
26315472 TGTGCGGTGTGAGAGTGCACATGATGGGGACATGG
1 TGTGCGGTGTGGGAGTGCACATGATGGTGACATGG
* * *
26315507 TGTGCGGTGT-GGAGTGCACACGATGATGATGATATATGCCA
1 TGTGCGGTGTGGGAGTG--CAC-ATGATGGTG--ACATG--G
* *
26315548 TGTGCGGTGTGGGAGTGCACATGATGGT-A-TTAGCTA
1 TGTGCGGTGTGGGAGTGCACATGATGGTGACAT-G--G
26315584 TGTGCGGTGTGGGAGTGCACATGA
1 TGTGCGGTGTGGGAGTGCACATGA
26315608 GCTGAGTTGC
Statistics
Matches: 139, Mismatches: 24, Indels: 22
0.75 0.13 0.12
Matches are distributed among these distances:
34 5 0.04
35 11 0.08
36 58 0.42
37 9 0.06
38 26 0.19
39 11 0.08
40 3 0.02
41 10 0.07
42 6 0.04
ACGTcount: A:0.21, C:0.13, G:0.40, T:0.26
Consensus pattern (35 bp):
TGTGCGGTGTGGGAGTGCACATGATGGTGACATGG
Found at i:26315558 original size:76 final size:74
Alignment explanation
Indices: 26315396--26315574 Score: 245
Period size: 76 Copynumber: 2.4 Consensus size: 74
26315386 TATAATCGTG
* * * * *
26315396 CATGTGCAGTGTGGGAGTGCACATAACGGTGAGAGTGGTGTGCGGTGTGGGAATGCACACGATGA
1 CATGTGCGGTGTGGGAGTGCACATGATGGGGACAGTGGTGTGCGGTGTGGGAATGCACACGATGA
26315461 TGATATTGC
66 TGATATTGC
* *
26315470 CATGTGCGGTGTGAGAGTGCACATGATGGGGACA-TGGTGTGCGGTGT-GGAGTGCACACGATGA
1 CATGTGCGGTGTGGGAGTGCACATGATGGGGACAGTGGTGTGCGGTGTGGGAATGCACAC---GA
26315533 TGATGATATATGC
63 TGATGATAT-TGC
26315546 CATGTGCGGTGTGGGAGTGCACATGATGG
1 CATGTGCGGTGTGGGAGTGCACATGATGG
26315575 TATTAGCTAT
Statistics
Matches: 93, Mismatches: 8, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
72 10 0.11
73 13 0.14
74 28 0.30
75 11 0.12
76 31 0.33
ACGTcount: A:0.22, C:0.13, G:0.40, T:0.25
Consensus pattern (74 bp):
CATGTGCGGTGTGGGAGTGCACATGATGGGGACAGTGGTGTGCGGTGTGGGAATGCACACGATGA
TGATATTGC
Found at i:26315701 original size:2 final size:2
Alignment explanation
Indices: 26315689--26315753 Score: 100
Period size: 2 Copynumber: 34.0 Consensus size: 2
26315679 TGTATGTTTA
*
26315689 AT AT AT CT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
26315730 -T AT -T AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
26315754 TAACTTCANC
Statistics
Matches: 58, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
1 3 0.05
2 55 0.95
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:26315847 original size:2 final size:2
Alignment explanation
Indices: 26315835--26315895 Score: 72
Period size: 2 Copynumber: 31.0 Consensus size: 2
26315825 TGTATGTTTA
*
26315835 AT AT AT CT AT AT AT AT AT AT AT AT AT AT AT AT AT ACT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT
* *
26315877 TT AT GT A- AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
26315896 GAATTCTTGT
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
1 2 0.04
2 47 0.94
3 1 0.02
ACGTcount: A:0.44, C:0.03, G:0.02, T:0.51
Consensus pattern (2 bp):
AT
Found at i:26315859 original size:146 final size:141
Alignment explanation
Indices: 26315617--26315895 Score: 495
Period size: 146 Copynumber: 1.9 Consensus size: 141
26315607 AGCTGAGTTG
26315617 CGGATGGCAGTTGTGTGCGTTGAGTCATGTTGACTAGTTGGGAATGACCTTGATGTGTTGGATGT
1 CGGATGGCAGTTGTGTGCGTTGAGTCATGTTGACTAGTTGGGAATGACCTTGATGTGTTGGATGT
26315682 ATGTTTAATATATCTATATATATATATATATATATATATATATATTATTATTATATATATATATA
66 ATGTTTAATATATCTATATATATATATATATATATATATATA-ATTA-TATT-TATATA-ATATA
26315747 TATATATTAACTTCA
127 TATATATTAACTTCA
26315762 NCGGATGGCAGTTGTGTGCGTTGAGTCATGTTGACTAGTTGGGAATGACCTTGATGTGTTGGATG
1 -CGGATGGCAGTTGTGTGCGTTGAGTCATGTTGACTAGTTGGGAATGACCTTGATGTGTTGGATG
* *
26315827 TATGTTTAATATATCTATATATATATATATATATATATATATACTTATATTTATGTAATATATAT
65 TATGTTTAATATATCTATATATATATATATATATATATATATAATTATATTTATATAATATATAT
26315892 ATAT
130 ATAT
26315896 GAATTCTTGT
Statistics
Matches: 131, Mismatches: 2, Indels: 4
0.96 0.01 0.03
Matches are distributed among these distances:
142 12 0.09
143 5 0.04
144 4 0.03
145 3 0.02
146 107 0.82
ACGTcount: A:0.31, C:0.07, G:0.18, T:0.44
Consensus pattern (141 bp):
CGGATGGCAGTTGTGTGCGTTGAGTCATGTTGACTAGTTGGGAATGACCTTGATGTGTTGGATGT
ATGTTTAATATATCTATATATATATATATATATATATATATAATTATATTTATATAATATATATA
TATTAACTTCA
Found at i:26325466 original size:46 final size:47
Alignment explanation
Indices: 26325377--26325467 Score: 121
Period size: 46 Copynumber: 2.0 Consensus size: 47
26325367 CACGTTCGTT
* **
26325377 ATTTATTTTTTGTCAGAGAGAATCCACGTTCTTCAACTGACGGTCTC
1 ATTTATTTTTGGTCAGAGAGAATCCACGTTCTTCAACAAACGGTCTC
* * *
26325424 ATTTATTTTTGGTCAGAG-GAGTCCATGTTCTTCACCAAACGGTC
1 ATTTATTTTTGGTCAGAGAGAATCCACGTTCTTCAACAAACGGTC
26325468 AGTGGAGCCA
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
46 21 0.55
47 17 0.45
ACGTcount: A:0.23, C:0.21, G:0.19, T:0.37
Consensus pattern (47 bp):
ATTTATTTTTGGTCAGAGAGAATCCACGTTCTTCAACAAACGGTCTC
Found at i:26326036 original size:2 final size:2
Alignment explanation
Indices: 26326029--26326063 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
26326019 ATGCTCCCTC
26326029 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
26326064 GTTTAATACA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:26335136 original size:3 final size:3
Alignment explanation
Indices: 26335124--26335164 Score: 66
Period size: 3 Copynumber: 14.0 Consensus size: 3
26335114 CATATATTCA
*
26335124 TAT T-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TGT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
26335165 ATGTCCATTA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 2 0.06
3 33 0.94
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:26336353 original size:38 final size:38
Alignment explanation
Indices: 26336282--26336354 Score: 103
Period size: 38 Copynumber: 1.9 Consensus size: 38
26336272 CAATTTATAA
*
26336282 CTTATTAACACAATTAACATAATTGATAAGATTAACAG
1 CTTATTAACACAATTAACATAATTGAAAAGATTAACAG
* *
26336320 CTTATTGATACAATTAACATAATT-AAAATGATTAA
1 CTTATTAACACAATTAACATAATTGAAAA-GATTAA
26336355 ATTAAAATAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
37 3 0.10
38 28 0.90
ACGTcount: A:0.48, C:0.11, G:0.07, T:0.34
Consensus pattern (38 bp):
CTTATTAACACAATTAACATAATTGAAAAGATTAACAG
Found at i:26337772 original size:19 final size:20
Alignment explanation
Indices: 26337750--26337788 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
26337740 AATATTTAAA
*
26337750 AAAACTTTTCAAT-TATTTT
1 AAAACTTTTAAATATATTTT
*
26337769 AAAATTTTTAAATATATTTT
1 AAAACTTTTAAATATATTTT
26337789 TATTTTTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (20 bp):
AAAACTTTTAAATATATTTT
Found at i:26338811 original size:24 final size:23
Alignment explanation
Indices: 26338753--26338811 Score: 57
Period size: 24 Copynumber: 2.5 Consensus size: 23
26338743 AAACTTCATC
*
26338753 TATAAT-TATAAAATATATAAAT
1 TATAATATATTAAATATATAAAT
* * *
26338775 TATGTATAGATTAAATATATGAAT
1 TAT-AATATATTAAATATATAAAT
26338799 ATATAATATATTA
1 -TATAATATATTA
26338812 CTTTATTATA
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
22 3 0.11
23 2 0.07
24 20 0.71
25 3 0.11
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (23 bp):
TATAATATATTAAATATATAAAT
Found at i:26346534 original size:50 final size:50
Alignment explanation
Indices: 26346459--26346568 Score: 202
Period size: 50 Copynumber: 2.2 Consensus size: 50
26346449 CTCTTTATCT
*
26346459 GATTTTATGTCCAGTATTGGAAGGTTGAAAATGATGTAAGTAATGAATTG
1 GATTTTATGTCCAGTATTGGAAGGTTGAAAATGATGTAAGTAATGAATTA
26346509 GATTTTATGTCCAGTATTGGAAGGTTGAAAATGATGTAAGTAATGAATTA
1 GATTTTATGTCCAGTATTGGAAGGTTGAAAATGATGTAAGTAATGAATTA
26346559 GATTATTATG
1 GATT-TTATG
26346569 AAGTGTTGTT
Statistics
Matches: 58, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
50 53 0.91
51 5 0.09
ACGTcount: A:0.35, C:0.04, G:0.25, T:0.37
Consensus pattern (50 bp):
GATTTTATGTCCAGTATTGGAAGGTTGAAAATGATGTAAGTAATGAATTA
Found at i:26365623 original size:23 final size:23
Alignment explanation
Indices: 26365571--26365624 Score: 56
Period size: 24 Copynumber: 2.3 Consensus size: 23
26365561 AGAATAATAC
* * *
26365571 ATATAAAGGAATATAAATATATAT
1 ATATAAA-TAATATAAATAAAAAT
26365595 ATATAAATAATATAACATAAAAAT
1 ATATAAATAATATAA-ATAAAAAT
26365619 A-ATAAA
1 ATATAAA
26365625 ACTTGCATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
23 12 0.46
24 14 0.54
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.30
Consensus pattern (23 bp):
ATATAAATAATATAAATAAAAAT
Found at i:26365732 original size:22 final size:22
Alignment explanation
Indices: 26365690--26365745 Score: 60
Period size: 24 Copynumber: 2.5 Consensus size: 22
26365680 TGAAGTCCAT
26365690 ATAAAAAATATATATATATAAA
1 ATAAAAAATATATATATATAAA
*
26365712 ATAAAATAATA-ATAGTAATAAAAA
1 ATAAAA-AATATATA-T-ATATAAA
*
26365736 ATACAAAATA
1 ATAAAAAATA
26365746 CCATGATATT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
22 9 0.31
23 9 0.31
24 11 0.38
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.27
Consensus pattern (22 bp):
ATAAAAAATATATATATATAAA
Found at i:26366037 original size:24 final size:24
Alignment explanation
Indices: 26365987--26366037 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
26365977 GATAAAATGA
****
26365987 AAAAAATAAAAAAAAAATATTTTT
1 AAAAAATAAAAAAAAAATAAGCAT
*
26366011 AAAAAATAAAAATAAAATAAGCAT
1 AAAAAATAAAAAAAAAATAAGCAT
26366035 AAA
1 AAA
26366038 CTTCACAAAC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.75, C:0.02, G:0.02, T:0.22
Consensus pattern (24 bp):
AAAAAATAAAAAAAAAATAAGCAT
Found at i:26367024 original size:23 final size:23
Alignment explanation
Indices: 26366998--26367043 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
26366988 ACCAAAAATG
*
26366998 ATTTTTTCATAATTTTTAGAGTA
1 ATTTTTCCATAATTTTTAGAGTA
*
26367021 ATTTTTCCATAATTTTTTGAGTA
1 ATTTTTCCATAATTTTTAGAGTA
26367044 CGTTTGCTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.28, C:0.07, G:0.09, T:0.57
Consensus pattern (23 bp):
ATTTTTCCATAATTTTTAGAGTA
Found at i:26367152 original size:16 final size:16
Alignment explanation
Indices: 26367118--26367151 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
26367108 GAAACCAAAA
26367118 TTTAGATTTTGAATTT
1 TTTAGATTTTGAATTT
26367134 TTTAGATTTTG-ATTT
1 TTTAGATTTTGAATTT
26367149 TTT
1 TTT
26367152 TGATATTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 7 0.39
16 11 0.61
ACGTcount: A:0.21, C:0.00, G:0.12, T:0.68
Consensus pattern (16 bp):
TTTAGATTTTGAATTT
Found at i:26369772 original size:2 final size:2
Alignment explanation
Indices: 26369767--26369812 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
26369757 TTTTTTGCAT
26369767 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
26369809 TA TA
1 TA TA
26369813 AAGTACACAC
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:26369969 original size:2 final size:2
Alignment explanation
Indices: 26369926--26369950 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
26369916 CAAGTACGGN
26369926 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 T
26369951 TAAGTAGTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:26376739 original size:19 final size:19
Alignment explanation
Indices: 26376715--26376752 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
26376705 ACTTCTAAAC
26376715 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
26376734 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
26376753 AGTCAAATGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.32, G:0.00, T:0.26
Consensus pattern (19 bp):
CTCAAATCATACTCCAATA
Found at i:26377121 original size:21 final size:20
Alignment explanation
Indices: 26377095--26377146 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
26377085 ATTACAAAGG
26377095 GTATCGATAGATTTCTTGCAT
1 GTATCGATAGA-TTCTTGCAT
* * *
26377116 GTATCGATACATTCTAGAAT
1 GTATCGATAGATTCTTGCAT
*
26377136 GTATCAATAGA
1 GTATCGATAGA
26377147 ATTGTTGCAG
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 16 0.62
21 10 0.38
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (20 bp):
GTATCGATAGATTCTTGCAT
Found at i:26378393 original size:2 final size:2
Alignment explanation
Indices: 26378386--26378418 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
26378376 TACATACATA
*
26378386 TG TG TG TG TG TG TG TG TG TG TG TG TG TA TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
26378419 TAAGTTATCC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.03, C:0.00, G:0.45, T:0.52
Consensus pattern (2 bp):
TG
Found at i:26384052 original size:48 final size:48
Alignment explanation
Indices: 26383981--26384095 Score: 194
Period size: 48 Copynumber: 2.4 Consensus size: 48
26383971 AAACCAAAGG
26383981 ATGAGCAGAGAGATCAATCTGCAGAAGCTGCAAAAAATTCTTGGAAGA
1 ATGAGCAGAGAGATCAATCTGCAGAAGCTGCAAAAAATTCTTGGAAGA
* *
26384029 ATGAGCAGAGAGATCGATCTGCAGAAGCTGCGAAAAATTCTTGGAAGA
1 ATGAGCAGAGAGATCAATCTGCAGAAGCTGCAAAAAATTCTTGGAAGA
* *
26384077 CTGAGCAGAGAGATAAATC
1 ATGAGCAGAGAGATCAATC
26384096 ATAATTGGAA
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
48 62 1.00
ACGTcount: A:0.40, C:0.15, G:0.27, T:0.18
Consensus pattern (48 bp):
ATGAGCAGAGAGATCAATCTGCAGAAGCTGCAAAAAATTCTTGGAAGA
Found at i:26390396 original size:6 final size:6
Alignment explanation
Indices: 26390385--26390414 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
26390375 AAAGCAATGC
26390385 CTGGCA CTGGCA CTGGCA CTGGCA CTGGCA
1 CTGGCA CTGGCA CTGGCA CTGGCA CTGGCA
26390415 GGCAACACAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.33, G:0.33, T:0.17
Consensus pattern (6 bp):
CTGGCA
Found at i:26396503 original size:22 final size:22
Alignment explanation
Indices: 26396478--26396521 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
26396468 TATCCACTCT
26396478 TAGTGGGTAAAGGTTTTTGACG
1 TAGTGGGTAAAGGTTTTTGACG
26396500 TAGTGGGTAAAGGTTTTTGACG
1 TAGTGGGTAAAGGTTTTTGACG
26396522 GGTAAAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.23, C:0.05, G:0.36, T:0.36
Consensus pattern (22 bp):
TAGTGGGTAAAGGTTTTTGACG
Found at i:26412356 original size:12 final size:12
Alignment explanation
Indices: 26412339--26412389 Score: 66
Period size: 12 Copynumber: 4.2 Consensus size: 12
26412329 GCTCTACTTA
26412339 AAGAAGATGAAG
1 AAGAAGATGAAG
*
26412351 AAGAAGATGACG
1 AAGAAGATGAAG
* *
26412363 AAGATGATGGAG
1 AAGAAGATGAAG
*
26412375 AAGGAGATGAAG
1 AAGAAGATGAAG
26412387 AAG
1 AAG
26412390 CATCAGCAGA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 32 1.00
ACGTcount: A:0.51, C:0.02, G:0.37, T:0.10
Consensus pattern (12 bp):
AAGAAGATGAAG
Found at i:26412906 original size:17 final size:19
Alignment explanation
Indices: 26412884--26412920 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
26412874 GAAGGGTTAG
26412884 GTTGGG-AA-GGTGCGGGT
1 GTTGGGCAATGGTGCGGGT
*
26412901 GTTGGGCAATGGTGCTGGT
1 GTTGGGCAATGGTGCGGGT
26412920 G
1 G
26412921 CTGGTGCTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 6 0.35
18 2 0.12
19 9 0.53
ACGTcount: A:0.11, C:0.08, G:0.54, T:0.27
Consensus pattern (19 bp):
GTTGGGCAATGGTGCGGGT
Found at i:26437204 original size:33 final size:33
Alignment explanation
Indices: 26437167--26437259 Score: 132
Period size: 33 Copynumber: 2.8 Consensus size: 33
26437157 ATCTAAACTC
** * *
26437167 ATACAAAATAGTTCATGACTGCCCAACTAGCAT
1 ATACAAAATAACTCATGACTACACAACTAGCAT
* *
26437200 ATACAAAGTAACTCATGACTATACAACTAGCAT
1 ATACAAAATAACTCATGACTACACAACTAGCAT
26437233 ATACAAAATAACTCATGACTACACAAC
1 ATACAAAATAACTCATGACTACACAAC
26437260 AAAGTGACTT
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 52 1.00
ACGTcount: A:0.45, C:0.24, G:0.09, T:0.23
Consensus pattern (33 bp):
ATACAAAATAACTCATGACTACACAACTAGCAT
Found at i:26438215 original size:14 final size:14
Alignment explanation
Indices: 26438194--26438262 Score: 77
Period size: 14 Copynumber: 4.8 Consensus size: 14
26438184 AGTATTAGAG
26438194 GAAAGAAAAAAAAA
1 GAAAGAAAAAAAAA
* *
26438208 GCAAGAAAAAAGAA
1 GAAAGAAAAAAAAA
26438222 GAAAGGAAAAATAAAA
1 GAAA-GAAAAA-AAAA
*
26438238 GAAA-AAAAAGAAA
1 GAAAGAAAAAAAAA
26438251 GTAAAGAAAAAA
1 G-AAAGAAAAAA
26438263 GAAAAAAAGT
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
13 4 0.09
14 23 0.51
15 11 0.24
16 7 0.16
ACGTcount: A:0.78, C:0.01, G:0.17, T:0.03
Consensus pattern (14 bp):
GAAAGAAAAAAAAA
Found at i:26438259 original size:29 final size:28
Alignment explanation
Indices: 26438194--26438262 Score: 88
Period size: 29 Copynumber: 2.4 Consensus size: 28
26438184 AGTATTAGAG
26438194 GAAAGAAAAAAAAAGCAAGAAAAAAGAA
1 GAAAGAAAAAAAAAGCAAGAAAAAAGAA
26438222 GAAAGGAAAAATAAAAG-AA-AAAAAAGAAA
1 GAAA-GAAAAA-AAAAGCAAGAAAAAAG-AA
26438251 GTAAAGAAAAAA
1 G-AAAGAAAAAA
26438263 GAAAAAAAGT
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
28 12 0.32
29 17 0.46
30 8 0.22
ACGTcount: A:0.78, C:0.01, G:0.17, T:0.03
Consensus pattern (28 bp):
GAAAGAAAAAAAAAGCAAGAAAAAAGAA
Found at i:26438284 original size:25 final size:25
Alignment explanation
Indices: 26438210--26438270 Score: 88
Period size: 25 Copynumber: 2.4 Consensus size: 25
26438200 AAAAAAAAGC
*
26438210 AAGAAAAAAGAAGAAAGGAAA-AATAA
1 AAGAAAAAA-AAGAAAGTAAAGAA-AA
26438236 AAGAAAAAAAAGAAAGTAAAGAAAA
1 AAGAAAAAAAAGAAAGTAAAGAAAA
26438261 AAGAAAAAAA
1 AAGAAAAAAA
26438271 GTAATTTAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
25 22 0.67
26 11 0.33
ACGTcount: A:0.80, C:0.00, G:0.16, T:0.03
Consensus pattern (25 bp):
AAGAAAAAAAAGAAAGTAAAGAAAA
Found at i:26438967 original size:7 final size:7
Alignment explanation
Indices: 26438955--26439008 Score: 81
Period size: 7 Copynumber: 7.6 Consensus size: 7
26438945 AAAGGAATAG
26438955 AAAAGAA
1 AAAAGAA
26438962 AAAAGAA
1 AAAAGAA
26438969 AAAAGAA
1 AAAAGAA
26438976 AAAAGAA
1 AAAAGAA
26438983 AAAAGAGA
1 AAAAGA-A
*
26438991 AATAGAA
1 AAAAGAA
*
26438998 AAATGAA
1 AAAAGAA
26439005 AAAA
1 AAAA
26439009 AAGGATAATT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
7 36 0.86
8 6 0.14
ACGTcount: A:0.81, C:0.00, G:0.15, T:0.04
Consensus pattern (7 bp):
AAAAGAA
Found at i:26438981 original size:21 final size:22
Alignment explanation
Indices: 26438956--26439008 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
26438946 AAGGAATAGA
26438956 AAAGAAAAAAGAAAAAAGA-AA
1 AAAGAAAAAAGAAAAAAGAGAA
*
26438977 AAAGAAAAAAGAGAAATAGA-AA
1 AAAGAAAAAAGA-AAAAAGAGAA
*
26438999 AATGAAAAAA
1 AAAGAAAAAA
26439009 AAGGATAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
21 12 0.41
22 17 0.59
ACGTcount: A:0.81, C:0.00, G:0.15, T:0.04
Consensus pattern (22 bp):
AAAGAAAAAAGAAAAAAGAGAA
Found at i:26440472 original size:12 final size:12
Alignment explanation
Indices: 26440447--26440482 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
26440437 CTTGCTTCCT
*
26440447 ATACAATACATAC
1 ATAC-ATACGTAC
26440460 ATACATACGTAC
1 ATACATACGTAC
26440472 ATACATACGTA
1 ATACATACGTA
26440483 TATGTGTGTG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 18 0.82
13 4 0.18
ACGTcount: A:0.47, C:0.22, G:0.06, T:0.25
Consensus pattern (12 bp):
ATACATACGTAC
Found at i:26443323 original size:15 final size:15
Alignment explanation
Indices: 26443303--26443332 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
26443293 TATTTATTAA
26443303 TAATTAATAAATATT
1 TAATTAATAAATATT
*
26443318 TAATTAATTAATATT
1 TAATTAATAAATATT
26443333 GAATATTGTT
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TAATTAATAAATATT
Found at i:26449356 original size:17 final size:17
Alignment explanation
Indices: 26449334--26449373 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
26449324 ATTGAGAGTA
26449334 AACTTAATTAATAATAT
1 AACTTAATTAATAATAT
26449351 AACTTAATTAATAATAT
1 AACTTAATTAATAATAT
26449368 -ACTTAA
1 AACTTAA
26449374 AATGTAACAC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 6 0.26
17 17 0.74
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (17 bp):
AACTTAATTAATAATAT
Found at i:26449943 original size:28 final size:30
Alignment explanation
Indices: 26449902--26449964 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 30
26449892 TCTATGGGCA
* *
26449902 AATTTTTCAGTTTT-TGG-GGCAAAAATGT
1 AATTTTTCACTTTTACGGAGGCAAAAATGT
* *
26449930 AATTTTTGACTTTTACGGAGGCAAAAGTGT
1 AATTTTTCACTTTTACGGAGGCAAAAATGT
26449960 AATTT
1 AATTT
26449965 CAAAAAATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 12 0.41
29 2 0.07
30 15 0.52
ACGTcount: A:0.30, C:0.08, G:0.21, T:0.41
Consensus pattern (30 bp):
AATTTTTCACTTTTACGGAGGCAAAAATGT
Found at i:26451106 original size:13 final size:13
Alignment explanation
Indices: 26451088--26451112 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
26451078 AGAGAAATTG
26451088 TGATTTTATAAAA
1 TGATTTTATAAAA
26451101 TGATTTTATAAA
1 TGATTTTATAAA
26451113 TTTTTTGAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TGATTTTATAAAA
Found at i:26454812 original size:4 final size:4
Alignment explanation
Indices: 26454795--26454861 Score: 107
Period size: 4 Copynumber: 16.8 Consensus size: 4
26454785 GGAGAGGACA
* * *
26454795 TATG TATA TATG TATG TATG TATG TATG TATG TATG TGTG TATA TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
26454843 TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TAT
26454862 AAGAGTTAGA
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
4 57 1.00
ACGTcount: A:0.27, C:0.00, G:0.22, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:26462220 original size:2 final size:2
Alignment explanation
Indices: 26462208--26462239 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
26462198 AGGAATTACA
*
26462208 AG AG AG GG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
26462240 TATNCCTACG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (2 bp):
AG
Found at i:26462279 original size:2 final size:2
Alignment explanation
Indices: 26462267--26462298 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
26462257 AAAGTAACTA
*
26462267 AG AG AG GG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
26462299 TCTATGTAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (2 bp):
AG
Found at i:26463734 original size:17 final size:17
Alignment explanation
Indices: 26463699--26463752 Score: 51
Period size: 17 Copynumber: 3.1 Consensus size: 17
26463689 AAATATTAAT
26463699 AAATTATATTAA-TATTAA
1 AAATT-TATTAATTA-TAA
26463717 ATAA-TTATTAATTATAA
1 A-AATTTATTAATTATAA
26463734 AAATTTATCTAATT-TAA
1 AAATTTAT-TAATTATAA
26463751 AA
1 AA
26463753 TAAAAATAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
16 2 0.06
17 19 0.59
18 9 0.28
19 2 0.06
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (17 bp):
AAATTTATTAATTATAA
Found at i:26463874 original size:30 final size:30
Alignment explanation
Indices: 26463834--26463903 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 30
26463824 GAGTAGAATC
* *
26463834 AAACTTTTATA-TTTATATTTTAAATTAAAT
1 AAACTCTTATACTTT-TATTTTAAATCAAAT
* *
26463864 AAACTCTTATACTTTTATTTTGAGTCAAAT
1 AAACTCTTATACTTTTATTTTAAATCAAAT
*
26463894 AAATTCTTAT
1 AAACTCTTAT
26463904 CACTAACTAT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
30 31 0.91
31 3 0.09
ACGTcount: A:0.39, C:0.09, G:0.03, T:0.50
Consensus pattern (30 bp):
AAACTCTTATACTTTTATTTTAAATCAAAT
Found at i:26464016 original size:34 final size:33
Alignment explanation
Indices: 26463958--26464051 Score: 109
Period size: 34 Copynumber: 2.8 Consensus size: 33
26463948 TGTGTGACAC
*
26463958 TAATATAATATGCTAACATATCATAATTGATGA
1 TAATATAATATGCTAACATATCATAATTAATGA
* *
26463991 TAATATAATAATGTTTACATATCATAATTAATGA
1 TAATATAAT-ATGCTAACATATCATAATTAATGA
* * *
26464025 TAACATGAA-ATGCTAACTTAACATAAT
1 TAATAT-AATATGCTAACATATCATAAT
26464052 AACTTGTAGA
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
33 23 0.45
34 26 0.51
35 2 0.04
ACGTcount: A:0.47, C:0.10, G:0.07, T:0.36
Consensus pattern (33 bp):
TAATATAATATGCTAACATATCATAATTAATGA
Found at i:26464030 original size:20 final size:20
Alignment explanation
Indices: 26463971--26464030 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 20
26463961 TATAATATGC
*
26463971 TAACATATCATAATTGATGA
1 TAACATATCATAATTAATGA
*
26463991 T---A-AT-ATAA-TAATGT
1 TAACATATCATAATTAATGA
*
26464005 TTACATATCATAATTAATGA
1 TAACATATCATAATTAATGA
26464025 TAACAT
1 TAACAT
26464031 GAAATGCTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 12
0.65 0.09 0.26
Matches are distributed among these distances:
14 5 0.17
15 4 0.13
16 2 0.07
17 2 0.07
18 2 0.07
19 4 0.13
20 11 0.37
ACGTcount: A:0.47, C:0.08, G:0.07, T:0.38
Consensus pattern (20 bp):
TAACATATCATAATTAATGA
Found at i:26467071 original size:55 final size:55
Alignment explanation
Indices: 26466976--26467082 Score: 164
Period size: 55 Copynumber: 1.9 Consensus size: 55
26466966 ATTCAGAATC
*
26466976 TCAAACAGCATCACAATCTTATGAGAAAAAGTCTTCAAACAAACTCAAGACATTT
1 TCAAACAGCATCACAATCTTATGAGAAAAAGTCTTAAAACAAACTCAAGACATTT
*
26467031 TCAAACAGCATTCACAATCTTGA-GAGAAACA-TCTTAAAACAAACTCAAGACA
1 TCAAACAGCA-TCACAATCTT-ATGAGAAAAAGTCTTAAAACAAACTCAAGACA
26467083 GAAAAGGGGG
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
55 30 0.62
56 17 0.35
57 1 0.02
ACGTcount: A:0.47, C:0.22, G:0.09, T:0.21
Consensus pattern (55 bp):
TCAAACAGCATCACAATCTTATGAGAAAAAGTCTTAAAACAAACTCAAGACATTT
Found at i:26467522 original size:2 final size:2
Alignment explanation
Indices: 26467515--26467542 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
26467505 GCATGTGCAT
26467515 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
26467543 ACCTCAAGGA
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:26472250 original size:3 final size:3
Alignment explanation
Indices: 26472242--26472271 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
26472232 TCAAACTTTC
26472242 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
26472272 ACGGAAGAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:26475775 original size:2 final size:2
Alignment explanation
Indices: 26475768--26475792 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
26475758 AGACTTAGCC
26475768 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
26475793 ATAAATAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:26483165 original size:37 final size:38
Alignment explanation
Indices: 26483124--26483200 Score: 129
Period size: 37 Copynumber: 2.1 Consensus size: 38
26483114 AACCCGAGAG
* *
26483124 TATACAAATTTAGAGACTAATCTAAA-GAGAGTACATA
1 TATACAAATTTAGAGACTAAACCAAAGGAGAGTACATA
26483161 TATACAAATTTAGAGACTAAACCAAAGGAGAGTACATA
1 TATACAAATTTAGAGACTAAACCAAAGGAGAGTACATA
26483199 TA
1 TA
26483201 ACCATTCAAC
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
37 24 0.65
38 13 0.35
ACGTcount: A:0.49, C:0.12, G:0.14, T:0.25
Consensus pattern (38 bp):
TATACAAATTTAGAGACTAAACCAAAGGAGAGTACATA
Found at i:26484937 original size:30 final size:30
Alignment explanation
Indices: 26484903--26484961 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
26484893 GAAATTTCGA
* *
26484903 AGATAATGGGTAATTATCATAATCCCATTC
1 AGATAATGAGTAATTATCACAATCCCATTC
*
26484933 AGATAATGAGTAGTTATCACAATCCCATT
1 AGATAATGAGTAATTATCACAATCCCATT
26484962 AAAACCATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.37, C:0.17, G:0.14, T:0.32
Consensus pattern (30 bp):
AGATAATGAGTAATTATCACAATCCCATTC
Found at i:26490341 original size:48 final size:47
Alignment explanation
Indices: 26490289--26490396 Score: 126
Period size: 48 Copynumber: 2.3 Consensus size: 47
26490279 AAACATGCTC
* * *
26490289 AACCCAATATTGTATACTCTGGTCCAGACTAATAGCATAAAAAGACAA
1 AACCCAATATTCTATAATCTGATCCAGACTAATAGCAT-AAAAGACAA
* * * * *
26490337 AACCCAATATTCTTTAATCTGATCCAGAGTAATTGTATAAAAGATAA
1 AACCCAATATTCTATAATCTGATCCAGACTAATAGCATAAAAGACAA
*
26490384 AACCCAACATTCT
1 AACCCAATATTCT
26490397 TTATCCTGGT
Statistics
Matches: 51, Mismatches: 9, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
47 20 0.39
48 31 0.61
ACGTcount: A:0.43, C:0.20, G:0.10, T:0.27
Consensus pattern (47 bp):
AACCCAATATTCTATAATCTGATCCAGACTAATAGCATAAAAGACAA
Found at i:26492059 original size:2 final size:2
Alignment explanation
Indices: 26492052--26492097 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
26492042 TCTGGGTATT
*
26492052 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A- AG GG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
26492093 AG AG A
1 AG AG A
26492098 ATGTTTCTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:26496444 original size:21 final size:20
Alignment explanation
Indices: 26496420--26496458 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
26496410 TAACCTAAAA
*
26496420 GTATCTATACATTTCTCAAAT
1 GTATCAATACATTT-TCAAAT
*
26496441 GTATCAATAGATTTTCAA
1 GTATCAATACATTTTCAA
26496459 CAGAATGCTC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.36, C:0.15, G:0.08, T:0.41
Consensus pattern (20 bp):
GTATCAATACATTTTCAAAT
Found at i:26500044 original size:38 final size:39
Alignment explanation
Indices: 26499958--26500060 Score: 147
Period size: 38 Copynumber: 2.6 Consensus size: 39
26499948 TCCCGGCTCA
*
26499958 TGTACATCCCCCCACATCGTGCACATAGCCGGCACCATCG
1 TGTACATCCCCCCACATCGTGCACATAGCAGG-ACCATCG
* *
26499998 TGTGCATCCCCCCACATCGTGCACA-ATCAGTG-CCATCG
1 TGTACATCCCCCCACATCGTGCACATAGCAG-GACCATCG
26500036 TGTACATCCCCCCACATCGTGCACA
1 TGTACATCCCCCCACATCGTGCACA
26500061 CGAGCACTAT
Statistics
Matches: 58, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
38 30 0.52
39 3 0.05
40 25 0.43
ACGTcount: A:0.22, C:0.42, G:0.17, T:0.19
Consensus pattern (39 bp):
TGTACATCCCCCCACATCGTGCACATAGCAGGACCATCG
Found at i:26500053 original size:19 final size:19
Alignment explanation
Indices: 26499958--26500056 Score: 74
Period size: 19 Copynumber: 5.1 Consensus size: 19
26499948 TCCCGGCTCA
26499958 TGTACATCCCCCCACATCG
1 TGTACATCCCCCCACATCG
* * **
26499977 TGCACATAGCCGGCACCATCG
1 TGTACAT-CCCCCCA-CATCG
*
26499998 TGTGCATCCCCCCACATCG
1 TGTACATCCCCCCACATCG
* ****
26500017 TGCACAATCAGTGC-CATCG
1 TGTAC-ATCCCCCCACATCG
26500036 TGTACATCCCCCCACATCG
1 TGTACATCCCCCCACATCG
26500055 TG
1 TG
26500057 CACACGAGCA
Statistics
Matches: 56, Mismatches: 20, Indels: 8
0.67 0.24 0.10
Matches are distributed among these distances:
18 4 0.07
19 30 0.54
20 12 0.21
21 10 0.18
ACGTcount: A:0.21, C:0.41, G:0.17, T:0.20
Consensus pattern (19 bp):
TGTACATCCCCCCACATCG
Found at i:26503915 original size:20 final size:20
Alignment explanation
Indices: 26503871--26503908 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
26503861 TTTTGGCCCC
26503871 ATTTGACTTATTGGAGTATA
1 ATTTGACTTATTGGAGTATA
26503891 ATTTGACTTATTGGAGTA
1 ATTTGACTTATTGGAGTA
26503909 AGATTTGTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.29, C:0.05, G:0.21, T:0.45
Consensus pattern (20 bp):
ATTTGACTTATTGGAGTATA
Found at i:26512127 original size:19 final size:19
Alignment explanation
Indices: 26512103--26512141 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
26512093 AACATTAAAA
26512103 ACAAAACCAAGAGAATAAG
1 ACAAAACCAAGAGAATAAG
26512122 ACAAAACCAAGAGAATAAG
1 ACAAAACCAAGAGAATAAG
26512141 A
1 A
26512142 GAATAACAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.64, C:0.15, G:0.15, T:0.05
Consensus pattern (19 bp):
ACAAAACCAAGAGAATAAG
Found at i:26526662 original size:2 final size:2
Alignment explanation
Indices: 26526655--26526720 Score: 123
Period size: 2 Copynumber: 33.0 Consensus size: 2
26526645 AAACCACTTT
*
26526655 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TN 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
26526697 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
26526721 AAGGTGAAAA
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:26531961 original size:15 final size:15
Alignment explanation
Indices: 26531941--26531975 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
26531931 GAAAGCAGCA
26531941 AATAACAACTTGAAT
1 AATAACAACTTGAAT
26531956 AATAACAACTTGAAT
1 AATAACAACTTGAAT
26531971 AATAA
1 AATAA
26531976 TAATAATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.57, C:0.11, G:0.06, T:0.26
Consensus pattern (15 bp):
AATAACAACTTGAAT
Found at i:26537380 original size:28 final size:27
Alignment explanation
Indices: 26537342--26537399 Score: 82
Period size: 29 Copynumber: 2.1 Consensus size: 27
26537332 AGACTATCTT
*
26537342 TTTAATTTC-AAAAATATGATTTTCTA
1 TTTAATTTCAAAAAACATGATTTTCTA
26537368 TTTAATATATCAAAAAACATGATTTTCTA
1 TTTAAT-T-TCAAAAAACATGATTTTCTA
26537397 TTT
1 TTT
26537400 CTACTAGTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
26 6 0.21
27 1 0.04
28 2 0.07
29 19 0.68
ACGTcount: A:0.40, C:0.09, G:0.03, T:0.48
Consensus pattern (27 bp):
TTTAATTTCAAAAAACATGATTTTCTA
Found at i:26539580 original size:21 final size:22
Alignment explanation
Indices: 26539527--26539580 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 22
26539517 CCTACAAACG
*
26539527 CATAAAACTAAATCAATACTAA
1 CATAAAACTAAAGCAATACTAA
*
26539549 -ACTAAAA-TAAAGCAAT-TTAA
1 CA-TAAAACTAAAGCAATACTAA
26539569 CATAAAACTAAA
1 CATAAAACTAAA
26539581 ATAAAACAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
20 8 0.30
21 14 0.52
22 5 0.19
ACGTcount: A:0.61, C:0.15, G:0.02, T:0.22
Consensus pattern (22 bp):
CATAAAACTAAAGCAATACTAA
Found at i:26539610 original size:20 final size:20
Alignment explanation
Indices: 26539567--26539625 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 20
26539557 AAAGCAATTT
*
26539567 AACATAAAACTAAAATAAAAC
1 AACAT-AAATTAAAATAAAAC
* **
26539588 AACTTAAATTAAAATAACTC
1 AACATAAATTAAAATAAAAC
* *
26539608 AACATAATTTAAACTAAA
1 AACATAAATTAAAATAAA
26539626 TTAAGAAAAA
Statistics
Matches: 30, Mismatches: 8, Indels: 1
0.77 0.21 0.03
Matches are distributed among these distances:
20 26 0.87
21 4 0.13
ACGTcount: A:0.63, C:0.14, G:0.00, T:0.24
Consensus pattern (20 bp):
AACATAAATTAAAATAAAAC
Found at i:26540568 original size:2 final size:2
Alignment explanation
Indices: 26540525--26540549 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
26540515 TTTATGAACT
26540525 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 T
26540550 GTAAATATTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:26563692 original size:2 final size:2
Alignment explanation
Indices: 26563685--26563720 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
26563675 GAACTACAAC
26563685 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
26563721 GCATTGCAGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.