Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold60
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: 3815296
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 18690 characters in sequence are not A, C, G, or T
File 20 of 21
Found at i:3629284 original size:19 final size:19
Alignment explanation
Indices: 3629257--3629293 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
3629247 ATTATGTTAG
*
3629257 TATTTTTTAAAAGTAATAA
1 TATTATTTAAAAGTAATAA
*
3629276 TATTATTTAAATGTAATA
1 TATTATTTAAAAGTAATA
3629294 TTAGTTTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (19 bp):
TATTATTTAAAAGTAATAA
Found at i:3629539 original size:18 final size:18
Alignment explanation
Indices: 3629516--3629569 Score: 65
Period size: 19 Copynumber: 2.9 Consensus size: 18
3629506 AGTTTAACAA
3629516 TTTAAAATAATTAAAATT
1 TTTAAAATAATTAAAATT
3629534 TTTAAAAATAATTAAACA-T
1 TTT-AAAATAATTAAA-ATT
* *
3629553 TATAATATAATTAAAAT
1 TTTAAAATAATTAAAAT
3629570 AAAATTTTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
17 1 0.03
18 14 0.45
19 15 0.48
20 1 0.03
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (18 bp):
TTTAAAATAATTAAAATT
Found at i:3629885 original size:19 final size:19
Alignment explanation
Indices: 3629845--3629902 Score: 82
Period size: 19 Copynumber: 3.0 Consensus size: 19
3629835 AATAATAAAA
3629845 AATATTATTATATTTA-TAAT
1 AATATTATT-T-TTTATTAAT
3629865 AATATTATTTTTTATTAAT
1 AATATTATTTTTTATTAAT
*
3629884 AATATAATTTTTTATTAAT
1 AATATTATTTTTTATTAAT
3629903 TTTAAAGAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
18 4 0.11
19 23 0.64
20 9 0.25
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
AATATTATTTTTTATTAAT
Found at i:3631080 original size:10 final size:10
Alignment explanation
Indices: 3631052--3631081 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
3631042 TTTTATTCGT
*
3631052 TATATATATA
1 TATATATACA
3631062 TATATATACA
1 TATATATACA
3631072 TATATATACA
1 TATATATACA
3631082 CTGCAATTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (10 bp):
TATATATACA
Found at i:3631381 original size:2 final size:2
Alignment explanation
Indices: 3631374--3631398 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3631364 ATTACTCATC
3631374 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
3631399 TCATGAATAT
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:3632118 original size:2 final size:2
Alignment explanation
Indices: 3632111--3632135 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3632101 CTTATACGTG
3632111 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
3632136 TTGTTCAAGA
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:3632452 original size:4 final size:4
Alignment explanation
Indices: 3632439--3632474 Score: 54
Period size: 4 Copynumber: 8.8 Consensus size: 4
3632429 CTAGCTACTA
*
3632439 TTAT TATAT TTAT TTAT TTAT TTAT TTAT CTAT TTA
1 TTAT T-TAT TTAT TTAT TTAT TTAT TTAT TTAT TTA
3632475 CAGCTCCAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
4 25 0.86
5 4 0.14
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (4 bp):
TTAT
Found at i:3635023 original size:2 final size:2
Alignment explanation
Indices: 3635016--3635050 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3635006 TACGCTGTGA
3635016 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3635051 ACCATCAGCA
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3638547 original size:15 final size:15
Alignment explanation
Indices: 3638524--3638567 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
3638514 AAAATTTTAA
*
3638524 ATATAAATATAATAT
1 ATATTAATATAATAT
*
3638539 ATATTAATATCATAT
1 ATATTAATATAATAT
* *
3638554 ATTTTTATATAATA
1 ATATTAATATAATA
3638568 AAATTTAATG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (15 bp):
ATATTAATATAATAT
Found at i:3648424 original size:17 final size:17
Alignment explanation
Indices: 3648402--3648435 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
3648392 AATTATAAGT
3648402 GCAGTCCTACACTAGGC
1 GCAGTCCTACACTAGGC
3648419 GCAGTCCTACACTAGGC
1 GCAGTCCTACACTAGGC
3648436 CATGTTGTCT
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:0.24, C:0.35, G:0.24, T:0.18
Consensus pattern (17 bp):
GCAGTCCTACACTAGGC
Found at i:3653266 original size:3 final size:3
Alignment explanation
Indices: 3653253--3653301 Score: 80
Period size: 3 Copynumber: 16.0 Consensus size: 3
3653243 GAATGCTAGT
*
3653253 TAA TGAA TAA TAA TAA CAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
3653299 TAA
1 TAA
3653302 AATCAACTAC
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
3 40 0.93
4 3 0.07
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:3655580 original size:30 final size:29
Alignment explanation
Indices: 3655543--3655658 Score: 142
Period size: 30 Copynumber: 3.9 Consensus size: 29
3655533 TTATATAGTA
* *
3655543 GTGCACTAGTCCTTAATTTAAAGGACAAT
1 GTGCACTAGTCCTTAATTTAAGGGATAAT
* * *
3655572 GATGCACTAGTCTTTAATTCAAGGGATAGT
1 G-TGCACTAGTCCTTAATTTAAGGGATAAT
* *
3655602 GGTGCACTAGTCCTTAATCTAAGGGATAGAA
1 -GTGCACTAGTCCTTAATTTAAGGGATA-AT
3655633 GTGCACTAGTCCTTAATTTAAGGGAT
1 GTGCACTAGTCCTTAATTTAAGGGAT
3655659 TTAAATTAGT
Statistics
Matches: 73, Mismatches: 11, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
29 1 0.01
30 71 0.97
31 1 0.01
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.31
Consensus pattern (29 bp):
GTGCACTAGTCCTTAATTTAAGGGATAAT
Found at i:3655609 original size:60 final size:60
Alignment explanation
Indices: 3655537--3655658 Score: 165
Period size: 60 Copynumber: 2.0 Consensus size: 60
3655527 TTTAAATTAT
* * *
3655537 ATAGTAGTGCACTAGTCCTTAATTTAAAGGACA-ATGATGCACTAGTCTTTAATTCAAGGG
1 ATAGTAGTGCACTAGTCCTTAATCTAAAGGACAGAAG-TGCACTAGTCCTTAATTCAAGGG
* * * *
3655597 ATAGTGGTGCACTAGTCCTTAATCTAAGGGATAGAAGTGCACTAGTCCTTAATTTAAGGG
1 ATAGTAGTGCACTAGTCCTTAATCTAAAGGACAGAAGTGCACTAGTCCTTAATTCAAGGG
3655657 AT
1 AT
3655659 TTAAATTAGT
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
60 52 0.96
61 2 0.04
ACGTcount: A:0.32, C:0.15, G:0.22, T:0.31
Consensus pattern (60 bp):
ATAGTAGTGCACTAGTCCTTAATCTAAAGGACAGAAGTGCACTAGTCCTTAATTCAAGGG
Found at i:3655884 original size:31 final size:33
Alignment explanation
Indices: 3655829--3655892 Score: 87
Period size: 31 Copynumber: 2.0 Consensus size: 33
3655819 AAGAACCTGA
** *
3655829 GAATATTTTTTTTTCTGTTCAGCCTTCATTGCT
1 GAATATTTTTTTTTCTAATCAGCCTTAATTGCT
3655862 GAAT-TTTTTTTTTCTAAT-AGCCTTAATTGCT
1 GAATATTTTTTTTTCTAATCAGCCTTAATTGCT
3655893 ACCTTTCAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 12 0.43
32 12 0.43
33 4 0.14
ACGTcount: A:0.19, C:0.16, G:0.11, T:0.55
Consensus pattern (33 bp):
GAATATTTTTTTTTCTAATCAGCCTTAATTGCT
Found at i:3660486 original size:30 final size:30
Alignment explanation
Indices: 3660447--3660509 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
3660437 ATTTAAATTA
*
3660447 GATAATGGTGCACTAGTCTTTAATCTAAGG
1 GATAATGGTGCACTAGTCATTAATCTAAGG
* *
3660477 GATAGTGGTGCACTAGTCATTAATTTAAGG
1 GATAATGGTGCACTAGTCATTAATCTAAGG
3660507 GAT
1 GAT
3660510 TTAAATTAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.30, C:0.11, G:0.25, T:0.33
Consensus pattern (30 bp):
GATAATGGTGCACTAGTCATTAATCTAAGG
Found at i:3668739 original size:2 final size:2
Alignment explanation
Indices: 3668727--3668763 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
3668717 ATCGGAGAAT
*
3668727 GA GA GA CA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
3668764 GAGGAGGAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.03, G:0.49, T:0.00
Consensus pattern (2 bp):
GA
Found at i:3669700 original size:26 final size:27
Alignment explanation
Indices: 3669655--3669705 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
3669645 TGTTTTATTG
3669655 GTTTGATTTATAAATCTTATTTAATGA
1 GTTTGATTTATAAATCTTATTTAATGA
*
3669682 GTTTGGTTTATAAAT-TTATTTAAT
1 GTTTGATTTATAAATCTTATTTAAT
3669706 AAATTTTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 9 0.39
27 14 0.61
ACGTcount: A:0.31, C:0.02, G:0.12, T:0.55
Consensus pattern (27 bp):
GTTTGATTTATAAATCTTATTTAATGA
Found at i:3670783 original size:3 final size:3
Alignment explanation
Indices: 3670775--3670805 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
3670765 GTTGGGTACA
3670775 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
3670806 TTTGATTAGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:3670905 original size:2 final size:2
Alignment explanation
Indices: 3670898--3670927 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3670888 ATGATTAAAT
3670898 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
3670928 CAATACATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3675485 original size:3 final size:3
Alignment explanation
Indices: 3675477--3675522 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
3675467 TTAGATTGTT
3675477 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
3675523 GTGGACCATC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:3678925 original size:2 final size:2
Alignment explanation
Indices: 3678918--3678948 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3678908 AAAGTAAAAG
3678918 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3678949 GATTTGAAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3679544 original size:2 final size:2
Alignment explanation
Indices: 3679537--3679574 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
3679527 TTGATTAATA
*
3679537 AT AT AT AT AG 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
3679575 TCTTTCTGAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3682505 original size:10 final size:9
Alignment explanation
Indices: 3682472--3682503 Score: 64
Period size: 9 Copynumber: 3.6 Consensus size: 9
3682462 ACATGAGAGT
3682472 AAAAAGAAA
1 AAAAAGAAA
3682481 AAAAAGAAA
1 AAAAAGAAA
3682490 AAAAAGAAA
1 AAAAAGAAA
3682499 AAAAA
1 AAAAA
3682504 AGCCAAATTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (9 bp):
AAAAAGAAA
Found at i:3683056 original size:2 final size:2
Alignment explanation
Indices: 3683049--3683079 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
3683039 GATGCAAACC
*
3683049 CT CT CT CT CT CT TT 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 C
3683080 GGTTTTGCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
CT
Found at i:3685107 original size:34 final size:34
Alignment explanation
Indices: 3685069--3685271 Score: 352
Period size: 34 Copynumber: 6.0 Consensus size: 34
3685059 AAATATCTTA
* * * * *
3685069 CTCACCTAACACATTACCTAACACATCTAATATT
1 CTCACCAAATACATCACCTAACACACCTAACATT
3685103 CTCACCAAATACATCACCTAACACACCTAACATT
1 CTCACCAAATACATCACCTAACACACCTAACATT
*
3685137 CTCATCAAATACATCACCTAACACACCTAACATT
1 CTCACCAAATACATCACCTAACACACCTAACATT
3685171 CTCACCAAATACATCACCTAACACACCTAACATT
1 CTCACCAAATACATCACCTAACACACCTAACATT
3685205 CTCACCAAATACATCACCTAACACACCTAACATT
1 CTCACCAAATACATCACCTAACACACCTAACATT
3685239 CTCACCAAATACATCACCTAACACACCTAACAT
1 CTCACCAAATACATCACCTAACACACCTAACAT
3685272 GCTTCACCTA
Statistics
Matches: 162, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
34 162 1.00
ACGTcount: A:0.41, C:0.37, G:0.00, T:0.22
Consensus pattern (34 bp):
CTCACCAAATACATCACCTAACACACCTAACATT
Found at i:3685189 original size:25 final size:25
Alignment explanation
Indices: 3685160--3685261 Score: 80
Period size: 25 Copynumber: 4.4 Consensus size: 25
3685150 TCACCTAACA
3685160 CACCTAACATTCTCACCAAATACAT
1 CACCTAACATTCTCACCAAATACAT
*
3685185 CACCTAACA----CACCTAACATTC-T
1 CACCTAACATTCTCACC-AA-ATACAT
* *
3685207 CACC-AA-ATACATCACC-TA-ACA-
1 CACCTAACATTC-TCACCAAATACAT
3685228 CACCTAACATTCTCACCAAATACAT
1 CACCTAACATTCTCACCAAATACAT
3685253 CACCTAACA
1 CACCTAACA
3685262 CACCTAACAT
Statistics
Matches: 59, Mismatches: 5, Indels: 26
0.66 0.06 0.29
Matches are distributed among these distances:
20 1 0.02
21 11 0.19
22 15 0.25
23 7 0.12
24 3 0.05
25 22 0.37
ACGTcount: A:0.41, C:0.38, G:0.00, T:0.21
Consensus pattern (25 bp):
CACCTAACATTCTCACCAAATACAT
Found at i:3688236 original size:13 final size:13
Alignment explanation
Indices: 3688218--3688243 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3688208 CATAAAGTGC
3688218 TGTATCGATACAT
1 TGTATCGATACAT
3688231 TGTATCGATACAT
1 TGTATCGATACAT
3688244 AAGTTTTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3688259 original size:32 final size:33
Alignment explanation
Indices: 3688197--3688261 Score: 105
Period size: 32 Copynumber: 2.0 Consensus size: 33
3688187 TTTTAACGAT
3688197 TTGTATCGATACATAAAGTGCTGTATCGATACA
1 TTGTATCGATACATAAAGTGCTGTATCGATACA
**
3688230 TTGTATCGATACAT-AAGTTTTGTATCGATACA
1 TTGTATCGATACATAAAGTGCTGTATCGATACA
3688262 ATTTAAGCTA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 16 0.53
33 14 0.47
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.37
Consensus pattern (33 bp):
TTGTATCGATACATAAAGTGCTGTATCGATACA
Found at i:3696345 original size:222 final size:222
Alignment explanation
Indices: 3695955--3696399 Score: 845
Period size: 222 Copynumber: 2.0 Consensus size: 222
3695945 TTAGTGCTCT
3695955 CTGGAGAAATGATTGATGCGGCCATTAAGAGTGGTAGGATGTCTGCCGGAAAAGCAACCGGCTTG
1 CTGGAGAAATGATTGATGCGGCCATTAAGAGTGGTAGGATGTCTGCCGGAAAAGCAACCGGCTTG
*
3696020 AGTAAAAAGCCTGTTGCTAAGAAAAAAGAAGGAGAAACCAATACCATAAGTTATGCTGGCTCATC
66 AGCAAAAAGCCTGTTGCTAAGAAAAAAGAAGGAGAAACCAATACCATAAGTTATGCTGGCTCATC
3696085 TCAGCCAAGACAGCGTCGGCCACCTAGCCCTCATTACCAAAACACACCATATTCCTACCCCTTTA
131 TCAGCCAAGACAGCGTCGGCCACCTAGCCCTCATTACCAAAACACACCATATTCCTACCCCTTTA
3696150 CAATCCCTTCTCAGCCGATTTATGCCA
196 CAATCCCTTCTCAGCCGATTTATGCCA
*
3696177 CTGGAGAAATGATTGATGCGGCCATTAAGAGTGGTAGGATGTCTGCCGGAAAAGCAACTGGCTTG
1 CTGGAGAAATGATTGATGCGGCCATTAAGAGTGGTAGGATGTCTGCCGGAAAAGCAACCGGCTTG
*
3696242 AGCAAAAAGCCTGTTGCTAAGAAAAAAGAAGGAGAAACCAATACCATAAGTTATGTTGGCTCATC
66 AGCAAAAAGCCTGTTGCTAAGAAAAAAGAAGGAGAAACCAATACCATAAGTTATGCTGGCTCATC
* *
3696307 TCAGCCAAGACAGCGTCGGCCACCTAGCGCTTATTACCAAAACACACCATATTCCTACCCCTTTA
131 TCAGCCAAGACAGCGTCGGCCACCTAGCCCTCATTACCAAAACACACCATATTCCTACCCCTTTA
3696372 CAATCCCTTCTCAGCCGATTTATGCCA
196 CAATCCCTTCTCAGCCGATTTATGCCA
3696399 C
1 C
3696400 AACTATAACC
Statistics
Matches: 218, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
222 218 1.00
ACGTcount: A:0.32, C:0.26, G:0.20, T:0.22
Consensus pattern (222 bp):
CTGGAGAAATGATTGATGCGGCCATTAAGAGTGGTAGGATGTCTGCCGGAAAAGCAACCGGCTTG
AGCAAAAAGCCTGTTGCTAAGAAAAAAGAAGGAGAAACCAATACCATAAGTTATGCTGGCTCATC
TCAGCCAAGACAGCGTCGGCCACCTAGCCCTCATTACCAAAACACACCATATTCCTACCCCTTTA
CAATCCCTTCTCAGCCGATTTATGCCA
Found at i:3702466 original size:9 final size:9
Alignment explanation
Indices: 3702453--3702518 Score: 66
Period size: 9 Copynumber: 7.4 Consensus size: 9
3702443 TAATAATAAT
3702453 AAAAAAACA
1 AAAAAAACA
3702462 GAAAAAAA-A
1 -AAAAAAACA
*
3702471 CAAAACAA-A
1 -AAAAAAACA
3702480 AAAAAAACA
1 AAAAAAACA
3702489 AAAAAAACA
1 AAAAAAACA
3702498 AAAAAAA-A
1 AAAAAAACA
* *
3702506 ACAACAACA
1 AAAAAAACA
3702515 AAAA
1 AAAA
3702519 GGGTCCAGAT
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
8 12 0.25
9 29 0.60
10 7 0.15
ACGTcount: A:0.86, C:0.12, G:0.02, T:0.00
Consensus pattern (9 bp):
AAAAAAACA
Found at i:3702469 original size:11 final size:11
Alignment explanation
Indices: 3702453--3702518 Score: 60
Period size: 11 Copynumber: 5.6 Consensus size: 11
3702443 TAATAATAAT
*
3702453 AAAAAAACAGA
1 AAAAAAACACA
3702464 AAAAAAACAAAACA
1 AAAAAAAC---ACA
*
3702478 AAAAAAAAACA
1 AAAAAAACACA
*
3702489 AAAAAAACAAA
1 AAAAAAACACA
3702500 AAAAAAACAACA
1 AAAAAAAC-ACA
*
3702512 ACAAAAA
1 AAAAAAA
3702519 GGGTCCAGAT
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
11 28 0.62
12 8 0.18
14 9 0.20
ACGTcount: A:0.86, C:0.12, G:0.02, T:0.00
Consensus pattern (11 bp):
AAAAAAACACA
Found at i:3702491 original size:25 final size:24
Alignment explanation
Indices: 3702453--3702518 Score: 87
Period size: 25 Copynumber: 2.6 Consensus size: 24
3702443 TAATAATAAT
* *
3702453 AAAAAAACAGAAAAAAAACAAAACA
1 AAAAAAAAACAAAAAAAACAAAA-A
3702478 AAAAAAAAACAAAAAAAACAAAAA
1 AAAAAAAAACAAAAAAAACAAAAA
3702502 AAAAACAACAACAAAAA
1 AAAAA-AA-AACAAAAA
3702519 GGGTCCAGAT
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
24 6 0.16
25 23 0.62
26 8 0.22
ACGTcount: A:0.86, C:0.12, G:0.02, T:0.00
Consensus pattern (24 bp):
AAAAAAAAACAAAAAAAACAAAAA
Found at i:3702495 original size:20 final size:20
Alignment explanation
Indices: 3702463--3702509 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
3702453 AAAAAAACAG
*
3702463 AAAAA-AAACAAAACAAAAA
1 AAAAACAAAAAAAACAAAAA
3702482 AAAAACAAAAAAAACAAAAA
1 AAAAACAAAAAAAACAAAAA
3702502 AAAAACAA
1 AAAAACAA
3702510 CAACAAAAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
19 5 0.19
20 21 0.81
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (20 bp):
AAAAACAAAAAAAACAAAAA
Found at i:3702517 original size:16 final size:16
Alignment explanation
Indices: 3702456--3702509 Score: 76
Period size: 16 Copynumber: 3.4 Consensus size: 16
3702446 TAATAATAAA
*
3702456 AAAACAGAAAAAAAAC
1 AAAACAAAAAAAAAAC
3702472 AAAACAAAAAAAAAAC
1 AAAACAAAAAAAAAAC
3702488 AAAA-AAAACAAAAAA-
1 AAAACAAAA-AAAAAAC
3702503 AAAACAA
1 AAAACAA
3702510 CAACAAAAAG
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
15 8 0.23
16 27 0.77
ACGTcount: A:0.87, C:0.11, G:0.02, T:0.00
Consensus pattern (16 bp):
AAAACAAAAAAAAAAC
Found at i:3702518 original size:1 final size:1
Alignment explanation
Indices: 3702453--3702506 Score: 54
Period size: 1 Copynumber: 54.0 Consensus size: 1
3702443 TAATAATAAT
* * * * * *
3702453 AAAAAAACAGAAAAAAAACAAAACAAAAAAAAAACAAAAAAAACAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
3702507 CAACAACAAA
Statistics
Matches: 41, Mismatches: 12, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 41 1.00
ACGTcount: A:0.89, C:0.09, G:0.02, T:0.00
Consensus pattern (1 bp):
A
Found at i:3702518 original size:16 final size:16
Alignment explanation
Indices: 3702464--3702518 Score: 65
Period size: 17 Copynumber: 3.3 Consensus size: 16
3702454 AAAAAACAGA
*
3702464 AAAAAAACAAAACAAA
1 AAAAAAACAAAACAAC
*
3702480 AAAAAAACAAAAAAAAC
1 AAAAAAAC-AAAACAAC
*
3702497 AAAAAAAAAACAACAAC
1 AAAAAAACAA-AACAAC
3702514 AAAAA
1 AAAAA
3702519 GGGTCCAGAT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
16 10 0.30
17 23 0.70
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (16 bp):
AAAAAAACAAAACAAC
Found at i:3703996 original size:29 final size:29
Alignment explanation
Indices: 3703957--3704015 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
3703947 TCACCCTTCA
3703957 AAAGCCCACAAGTCAGTGGCATCTTTTTC
1 AAAGCCCACAAGTCAGTGGCATCTTTTTC
3703986 AAAGCCCACAAGTCAGTGGCATCTTTTTC
1 AAAGCCCACAAGTCAGTGGCATCTTTTTC
3704015 A
1 A
3704016 TCAGTGGCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.27
Consensus pattern (29 bp):
AAAGCCCACAAGTCAGTGGCATCTTTTTC
Found at i:3704068 original size:30 final size:30
Alignment explanation
Indices: 3704030--3704117 Score: 97
Period size: 30 Copynumber: 3.0 Consensus size: 30
3704020 TGGCAACCTT
*
3704030 CAAAGCCCACAAATCAGTGGCACCCTTTTC
1 CAAAGCCCACAAATCAGTGGCACTCTTTTC
* * * *
3704060 CGAAGCCCACAAGTCGGTGGCA-TATTTTC
1 CAAAGCCCACAAATCAGTGGCACTCTTTTC
* * *
3704089 CAAAGTCCACAACTCCGTGGCACTCTTTT
1 CAAAGCCCACAAATCAGTGGCACTCTTTT
3704118 TCTTTTGTAA
Statistics
Matches: 47, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
29 23 0.49
30 24 0.51
ACGTcount: A:0.26, C:0.33, G:0.17, T:0.24
Consensus pattern (30 bp):
CAAAGCCCACAAATCAGTGGCACTCTTTTC
Found at i:3704098 original size:29 final size:29
Alignment explanation
Indices: 3704030--3704110 Score: 81
Period size: 29 Copynumber: 2.8 Consensus size: 29
3704020 TGGCAACCTT
* * **
3704030 CAAAGCCCACAAATCAGTGGCACCCTTTTC
1 CAAAGCCCACAACTCCGTGGCA-TATTTTC
* * *
3704060 CGAAGCCCACAAGTCGGTGGCATATTTTC
1 CAAAGCCCACAACTCCGTGGCATATTTTC
*
3704089 CAAAGTCCACAACTCCGTGGCA
1 CAAAGCCCACAACTCCGTGGCA
3704111 CTCTTTTTCT
Statistics
Matches: 42, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
29 23 0.55
30 19 0.45
ACGTcount: A:0.28, C:0.33, G:0.19, T:0.20
Consensus pattern (29 bp):
CAAAGCCCACAACTCCGTGGCATATTTTC
Found at i:3704169 original size:34 final size:35
Alignment explanation
Indices: 3704095--3704169 Score: 107
Period size: 35 Copynumber: 2.2 Consensus size: 35
3704085 TTTCCAAAGT
* *
3704095 CCACAACTCCGTGGCACTCTTTTTCTTTTGTAAGC
1 CCACAACTCCGTAGCACTCTTTTTCCTTTGTAAGC
* *
3704130 TCACAATTCCGTAGCACTCTTTTTCCTTT-TAAGC
1 CCACAACTCCGTAGCACTCTTTTTCCTTTGTAAGC
3704164 CCACAA
1 CCACAA
3704170 GTTAGTGGCA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
34 10 0.29
35 25 0.71
ACGTcount: A:0.21, C:0.32, G:0.11, T:0.36
Consensus pattern (35 bp):
CCACAACTCCGTAGCACTCTTTTTCCTTTGTAAGC
Found at i:3704186 original size:34 final size:35
Alignment explanation
Indices: 3704095--3704186 Score: 98
Period size: 35 Copynumber: 2.7 Consensus size: 35
3704085 TTTCCAAAGT
* * *
3704095 CCACAACTCCGTGGCACTCTTTTTCTTTTGTAAGC
1 CCACAATTCAGTGGCACTCTTTTTCCTTTGTAAGC
* * *
3704130 TCACAATTCCGTAGCACTCTTTTTCCTTT-TAAGC
1 CCACAATTCAGTGGCACTCTTTTTCCTTTGTAAGC
*
3704164 CCACAAGTT-AGTGGCACCCTTTT
1 CCACAA-TTCAGTGGCACTCTTTT
3704187 CAAAAGCCCA
Statistics
Matches: 48, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
34 21 0.44
35 27 0.56
ACGTcount: A:0.20, C:0.30, G:0.13, T:0.37
Consensus pattern (35 bp):
CCACAATTCAGTGGCACTCTTTTTCCTTTGTAAGC
Found at i:3704228 original size:28 final size:28
Alignment explanation
Indices: 3704160--3704311 Score: 164
Period size: 28 Copynumber: 5.3 Consensus size: 28
3704150 TTTTCCTTTT
* *
3704160 AAGCCCACAAGTTAGTGGCACCCTTTTCAA
1 AAGCCCACAAGTCAGTGGCAACC-TTT-AA
3704190 AAGCCCACAAGTCAGTGGCAACCTTTAA
1 AAGCCCACAAGTCAGTGGCAACCTTTAA
* *
3704218 AAGCCCACAAGTCAGTAGCAATCTTTAA
1 AAGCCCACAAGTCAGTGGCAACCTTTAA
* * *
3704246 AAGCCCACAAGTCAATGACAACCTTCAA
1 AAGCCCACAAGTCAGTGGCAACCTTTAA
* *
3704274 AAGCACACAAGT-TGAT-GCAAACCTTTCAA
1 AAGCCCACAAGTCAG-TGGC-AACCTTT-AA
3704303 AAGCCCACA
1 AAGCCCACA
3704312 CAAGTTGGTG
Statistics
Matches: 104, Mismatches: 15, Indels: 7
0.83 0.12 0.06
Matches are distributed among these distances:
27 1 0.01
28 69 0.66
29 13 0.12
30 21 0.20
ACGTcount: A:0.38, C:0.29, G:0.14, T:0.18
Consensus pattern (28 bp):
AAGCCCACAAGTCAGTGGCAACCTTTAA
Found at i:3704397 original size:49 final size:48
Alignment explanation
Indices: 3704331--3704669 Score: 311
Period size: 49 Copynumber: 7.0 Consensus size: 48
3704321 GGCGTCTTCT
* *
3704331 TTTAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTTATT
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CTTTATC
* *
3704380 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC-----C
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACTTTATC
* * *
3704423 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGCCACCTTCATC
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CTTTATC
* *
3704472 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC-----C
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACTTTATC
*
3704515 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTAGCACATTTTCCATC
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC--TTT--ATC
* * * *
3704567 TTTAAATTCAATGTAGCTGGCCTTGAATCAGCATATTGACATCCTTTTTCTCATC
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA--C---TT-T-ATC
* * * * *
3704622 TTTAAGCCCAATATCGTTGGCCGTGAATCAACATATTGGCATCTTTAT
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CTTTAT
3704670 TACTTTTCTC
Statistics
Matches: 240, Mismatches: 31, Indels: 38
0.78 0.10 0.12
Matches are distributed among these distances:
43 77 0.32
44 1 0.00
48 2 0.01
49 78 0.32
50 1 0.00
51 2 0.01
52 37 0.15
54 2 0.01
55 39 0.16
56 1 0.00
ACGTcount: A:0.26, C:0.24, G:0.16, T:0.34
Consensus pattern (48 bp):
TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACTTTATC
Found at i:3704442 original size:43 final size:44
Alignment explanation
Indices: 3704380--3704556 Score: 232
Period size: 43 Copynumber: 4.0 Consensus size: 44
3704370 CATCTTTATT
* *
3704380 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC-C
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACTC
* *
3704423 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGCCACCTTCATC
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA----C-TC
* *
3704472 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC-C
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACTC
*
3704515 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTAGCAC
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC
3704557 ATTTTCCATC
Statistics
Matches: 117, Mismatches: 11, Indels: 12
0.84 0.08 0.09
Matches are distributed among these distances:
43 77 0.66
45 1 0.01
47 1 0.01
49 38 0.32
ACGTcount: A:0.27, C:0.25, G:0.18, T:0.30
Consensus pattern (44 bp):
TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACTC
Found at i:3704488 original size:92 final size:92
Alignment explanation
Indices: 3704331--3704613 Score: 431
Period size: 92 Copynumber: 3.0 Consensus size: 92
3704321 GGCGTCTTCT
* * * *
3704331 TTTAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTTATTTTTAAGTCCAATGTAG
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGCCATCTTCATCTTTAAGTCCAATGTAG
3704396 CTGGCCTTGAATCAGCACATTGGCACC
66 CTGGCCTTGAATCAGCACATTGGCACC
* *
3704423 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGCCACCTTCATCTTTAAGTCCAATGTAG
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGCCATCTTCATCTTTAAGTCCAATGTAG
3704488 CTGGCCTTGAATCAGCACATTGGCACC
66 CTGGCCTTGAATCAGCACATTGGCACC
* * *
3704515 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTAGCACATTTTCCATCTTTAAATTCAATG
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATT-GC-CATCTT-CATCTTTAAGTCCAATG
* *
3704580 TAGCTGGCCTTGAATCAGCATATTGACATCC
63 TAGCTGGCCTTGAATCAGCACATTGGCA-CC
3704611 TTT
1 TTT
3704614 TTCTCATCTT
Statistics
Matches: 174, Mismatches: 13, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
92 122 0.70
93 2 0.01
94 4 0.02
95 41 0.24
96 5 0.03
ACGTcount: A:0.27, C:0.24, G:0.17, T:0.33
Consensus pattern (92 bp):
TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGCCATCTTCATCTTTAAGTCCAATGTAG
CTGGCCTTGAATCAGCACATTGGCACC
Found at i:3704649 original size:55 final size:54
Alignment explanation
Indices: 3704514--3704664 Score: 173
Period size: 55 Copynumber: 2.8 Consensus size: 54
3704504 ACATTGGCAC
3704514 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATT-AGCA--CATTTTCCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGA-CATCCATTTTCCAT
* * * *
3704566 CTTTAAATTCAATGTAGCTGGCCTTGAATCAGCATATTGACATCCTTTTTCTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGACATCCATTTTC-CAT
* * * * * *
3704621 CTTTAAGCCCAATATCGTTGGCCGTGAATCAACATATTGGCATC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGACATC
3704665 TTTATTACTT
Statistics
Matches: 82, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
52 37 0.45
53 1 0.01
54 6 0.07
55 38 0.46
ACGTcount: A:0.27, C:0.23, G:0.15, T:0.35
Consensus pattern (54 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGACATCCATTTTCCAT
Found at i:3705337 original size:32 final size:34
Alignment explanation
Indices: 3705272--3705338 Score: 93
Period size: 32 Copynumber: 2.0 Consensus size: 34
3705262 AATTTCAACG
* *
3705272 ATTATTATCGATACATAAAGTGTTGTATTGATAC
1 ATTATTATCAATACATAAAGTGTTGTATCGATAC
*
3705306 ATTA-TATCAATACAT-AAGTTTTGTATCGATAC
1 ATTATTATCAATACATAAAGTGTTGTATCGATAC
3705338 A
1 A
3705339 ATTTAAGCTA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
32 16 0.53
33 10 0.33
34 4 0.13
ACGTcount: A:0.37, C:0.10, G:0.12, T:0.40
Consensus pattern (34 bp):
ATTATTATCAATACATAAAGTGTTGTATCGATAC
Found at i:3710650 original size:34 final size:34
Alignment explanation
Indices: 3710611--3710779 Score: 257
Period size: 34 Copynumber: 5.0 Consensus size: 34
3710601 AAATATCTTA
* * * *
3710611 CTCACCTAACACATTACCTAACACACCTAATATT
1 CTCACCAAATACATCACCTAACACACCTAACATT
* * * *
3710645 TTCACCAAATACATTACCTAACACATCTAATATT
1 CTCACCAAATACATCACCTAACACACCTAACATT
3710679 CTCACCAAATACATCACCTAACACACCTAACATT
1 CTCACCAAATACATCACCTAACACACCTAACATT
*
3710713 CTCATCAAATACATCACCTAACACACCTAACATT
1 CTCACCAAATACATCACCTAACACACCTAACATT
3710747 CTCACCAAATACATCACCTAACACACCTAACAT
1 CTCACCAAATACATCACCTAACACACCTAACAT
3710780 GCTTCACCTA
Statistics
Matches: 125, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
34 125 1.00
ACGTcount: A:0.41, C:0.35, G:0.00, T:0.24
Consensus pattern (34 bp):
CTCACCAAATACATCACCTAACACACCTAACATT
Found at i:3714031 original size:3 final size:3
Alignment explanation
Indices: 3714016--3714050 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
3714006 CTTTCTCTCA
* *
3714016 AAG AAG AAA AAG AAG AAG AAG AAG ATG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
3714051 TAGATGAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.69, C:0.00, G:0.29, T:0.03
Consensus pattern (3 bp):
AAG
Found at i:3725742 original size:21 final size:21
Alignment explanation
Indices: 3725719--3725848 Score: 138
Period size: 21 Copynumber: 6.2 Consensus size: 21
3725709 TCTCCTACAT
*
3725719 CATCCCCTGGTTACAGCCC-A
1 CATCTCCTGGTTACAGCCCTA
* *
3725739 TCATCTCCAGGATACAGTCCCT-
1 -CATCTCCTGGTTACAG-CCCTA
*
3725761 CATCTCCTGGTTACAGTCCTA
1 CATCTCCTGGTTACAGCCCTA
* *
3725782 CCTCTCCTGGTTACAGTCCTA
1 CATCTCCTGGTTACAGCCCTA
* *
3725803 CCTCTCCTGGTTACAGTCCTA
1 CATCTCCTGGTTACAGCCCTA
* *
3725824 CATCTCCTGGTTATAGCCCCA
1 CATCTCCTGGTTACAGCCCTA
3725845 CATC
1 CATC
3725849 ACCTACTTAC
Statistics
Matches: 95, Mismatches: 11, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
20 3 0.03
21 89 0.94
22 3 0.03
ACGTcount: A:0.18, C:0.38, G:0.14, T:0.29
Consensus pattern (21 bp):
CATCTCCTGGTTACAGCCCTA
Found at i:3725788 original size:42 final size:42
Alignment explanation
Indices: 3725718--3725884 Score: 151
Period size: 42 Copynumber: 4.0 Consensus size: 42
3725708 TTCTCCTACA
* *
3725718 TCATCCCCTGGTTACAG-CCCATCATCTCCAGGATACAGTCCC
1 TCATCTCCTGGTTACAGTCCTA-CATCTCCAGGATACAGTCCC
* * *
3725760 TCATCTCCTGGTTACAGTCCTACCTCTCCTGGTTACAGT-CC
1 TCATCTCCTGGTTACAGTCCTACATCTCCAGGATACAGTCCC
* * * * *
3725801 TACCTCTCCTGGTTACAGTCCTACATCTCCTGGTTATAGCCCC
1 T-CATCTCCTGGTTACAGTCCTACATCTCCAGGATACAGTCCC
* * ** *
3725844 ACATCACCTACTTACAGTCCTAGC-TCACCAGGATACAGTCC
1 TCATCTCCTGGTTACAGTCCTA-CATCTCCAGGATACAGTCC
3725885 AACAAGTCCA
Statistics
Matches: 102, Mismatches: 19, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
41 3 0.03
42 93 0.91
43 6 0.06
ACGTcount: A:0.20, C:0.38, G:0.14, T:0.28
Consensus pattern (42 bp):
TCATCTCCTGGTTACAGTCCTACATCTCCAGGATACAGTCCC
Found at i:3725859 original size:63 final size:62
Alignment explanation
Indices: 3725742--3725884 Score: 169
Period size: 63 Copynumber: 2.3 Consensus size: 62
3725732 CAGCCCATCA
* * * * **
3725742 TCTCCAGGATACAGTCCCTCATCTCCTGGTTACAGTCCTACCTCTCCTGGTTACAGTCCTACC
1 TCTCCAGGATACAGT-CCTCATCTCCTGGTTACAGCCCCACATCACCTACTTACAGTCCTACC
* * * *
3725805 TCTCCTGGTTACAGTCCTACATCTCCTGGTTATAGCCCCACATCACCTACTTACAGTCCTAGC
1 TCTCCAGGATACAGTCCT-CATCTCCTGGTTACAGCCCCACATCACCTACTTACAGTCCTACC
*
3725868 TCACCAGGATACAGTCC
1 TCTCCAGGATACAGTCC
3725885 AACAAGTCCA
Statistics
Matches: 66, Mismatches: 13, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
62 3 0.05
63 63 0.95
ACGTcount: A:0.20, C:0.37, G:0.14, T:0.29
Consensus pattern (62 bp):
TCTCCAGGATACAGTCCTCATCTCCTGGTTACAGCCCCACATCACCTACTTACAGTCCTACC
Found at i:3725949 original size:21 final size:21
Alignment explanation
Indices: 3725931--3726301 Score: 126
Period size: 21 Copynumber: 17.7 Consensus size: 21
3725921 TTCTCCTACC
* *
3725931 TCACCAAGCTATAGCCCTACC
1 TCACCAAGCTATAGCCCAACA
* * * *
3725952 TCTCCAAGTTACAGCCCCACA
1 TCACCAAGCTATAGCCCAACA
* * * *
3725973 TCTCCAAGTTACAGCCCCACA
1 TCACCAAGCTATAGCCCAACA
* * * *
3725994 TCTCCAAGTTACAGCCCCACA
1 TCACCAAGCTATAGCCCAACA
* * * *
3726015 TCTCCCAGCTATAGTCCAACT
1 TCACCAAGCTATAGCCCAACA
* * *
3726036 TCACCTAGCTACAGCCCAACT
1 TCACCAAGCTATAGCCCAACA
* *
3726057 TCACC-CGTATATAGCCCAACA
1 TCACCAAG-CTATAGCCCAACA
*
3726078 TCACC-AGCATATAGCCCAACT
1 TCACCAAGC-TATAGCCCAACA
* *
3726099 TCACC-TGCGTATAGCCCTACA
1 TCACCAAGC-TATAGCCCAACA
* ** * *
3726120 TCTCCATCCTACAGCCCAACC
1 TCACCAAGCTATAGCCCAACA
** * *
3726141 TCACCATCCTACAGCCCTACA
1 TCACCAAGCTATAGCCCAACA
* ** * *
3726162 TCTCCATCCTACAGCCCAACC
1 TCACCAAGCTATAGCCCAACA
**
3726183 TCACCATCCTATAGTCCC-ACA
1 TCACCAAGCTATAG-CCCAACA
* * * * *
3726204 TCTCC-ATCATACAGCCCTACT
1 TCACCAAGC-TATAGCCCAACA
* *
3726225 TCACC-AGCTTATAGCCCCACT
1 TCACCAAGC-TATAGCCCAACA
* ** * * *
3726246 TCTCCTGGGTACAGCCCAACC
1 TCACCAAGCTATAGCCCAACA
*
3726267 TCACCAAGTTATAGTCCC-ACA
1 TCACCAAGCTATAG-CCCAACA
3726288 TCACCAAGCTATAG
1 TCACCAAGCTATAG
3726302 TCCTACCTCT
Statistics
Matches: 279, Mismatches: 63, Indels: 16
0.78 0.18 0.04
Matches are distributed among these distances:
20 5 0.02
21 265 0.95
22 9 0.03
ACGTcount: A:0.27, C:0.42, G:0.09, T:0.21
Consensus pattern (21 bp):
TCACCAAGCTATAGCCCAACA
Found at i:3726050 original size:63 final size:64
Alignment explanation
Indices: 3725982--3726146 Score: 153
Period size: 63 Copynumber: 2.6 Consensus size: 64
3725972 ATCTCCAAGT
* * * *
3725982 TACAGCCCCACATCTCCAAGT-TACAGCCCCACATCTCCCAGC-TATAGTCCAACTTCACCTAGC
1 TACAGCCCAACATCTCCAAGTATACAGCCCAACATC-ACCAGCATATAGCCCAACTTCACCT-GC
3726045 -
64 G
* * * *
3726045 TACAGCCCAACTTCACC-CGTATATAGCCCAACATCACCAGCATATAGCCCAACTTCACCTGCG
1 TACAGCCCAACATCTCCAAGTATACAGCCCAACATCACCAGCATATAGCCCAACTTCACCTGCG
* * * *
3726108 TATAGCCCTACATCTCC-A-TCCTACAGCCCAACCTCACCA
1 TACAGCCCAACATCTCCAAGT-ATACAGCCCAACATCACCA
3726147 TCCTACAGCC
Statistics
Matches: 82, Mismatches: 16, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
62 10 0.12
63 72 0.88
ACGTcount: A:0.28, C:0.42, G:0.09, T:0.20
Consensus pattern (64 bp):
TACAGCCCAACATCTCCAAGTATACAGCCCAACATCACCAGCATATAGCCCAACTTCACCTGCG
Found at i:3726132 original size:84 final size:85
Alignment explanation
Indices: 3726044--3726289 Score: 214
Period size: 84 Copynumber: 2.9 Consensus size: 85
3726034 CTTCACCTAG
* * * *
3726044 CTACAGCCCAACTTCACCCGT-ATATAGCCCAACATCACCAGCATATAGCCCAACTTCACC-TGC
1 CTACAGCCCAACTTCACCCATCATACAGCCCAACATCACCAGCATACAGCCCAACCTCACCAT-C
*
3726107 GTATAG-CCCTACATCTCCATC
65 CTATAGTCCC-ACATCTCCATC
* * * * * *
3726128 CTACAGCCCAACCTCA-CCATCCTACAGCCCTACATCTCCATCCTACAGCCCAACCTCACCATCC
1 CTACAGCCCAACTTCACCCATCATACAGCCCAACATCACCAGCATACAGCCCAACCTCACCATCC
3726192 TATAGTCCCACATCTCCATC
66 TATAGTCCCACATCTCCATC
* * * * * * * * * ** ***
3726212 ATACAGCCCTACTTCA-CCAGCTTATAGCCCCACTTCTCCTGGGTACAGCCCAACCTCACCAAGT
1 CTACAGCCCAACTTCACCCATCATACAGCCCAACATCACCAGCATACAGCCCAACCTCACCATCC
3726276 TATAGTCCCACATC
66 TATAGTCCCACATC
3726290 ACCAAGCTAT
Statistics
Matches: 133, Mismatches: 26, Indels: 6
0.81 0.16 0.04
Matches are distributed among these distances:
83 3 0.02
84 126 0.95
85 4 0.03
ACGTcount: A:0.27, C:0.43, G:0.09, T:0.22
Consensus pattern (85 bp):
CTACAGCCCAACTTCACCCATCATACAGCCCAACATCACCAGCATACAGCCCAACCTCACCATCC
TATAGTCCCACATCTCCATC
Found at i:3726230 original size:42 final size:42
Alignment explanation
Indices: 3726066--3726272 Score: 213
Period size: 42 Copynumber: 4.9 Consensus size: 42
3726056 TTCACCCGTA
* * * * * *
3726066 TATAGCCCAACATCACCAGCATATAGCCCAACTTCACC-TGCG
1 TATAGCCCTACATCTCCATCATACAGCCCAACCTCACCAT-CC
*
3726108 TATAGCCCTACATCTCCATCCTACAGCCCAACCTCACCATCC
1 TATAGCCCTACATCTCCATCATACAGCCCAACCTCACCATCC
* *
3726150 TACAGCCCTACATCTCCATCCTACAGCCCAACCTCACCATCC
1 TATAGCCCTACATCTCCATCATACAGCCCAACCTCACCATCC
* * * *
3726192 TATAGTCCC-ACATCTCCATCATACAGCCCTACTTCACCAGCT
1 TATAG-CCCTACATCTCCATCATACAGCCCAACCTCACCATCC
* * **
3726234 TATAGCCCCACTTCTCC-TGGGTACAGCCCAACCTCACCA
1 TATAGCCCTACATCTCCAT-CATACAGCCCAACCTCACCA
3726273 AGTTATAGTC
Statistics
Matches: 142, Mismatches: 19, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
41 4 0.03
42 134 0.94
43 4 0.03
ACGTcount: A:0.27, C:0.44, G:0.08, T:0.21
Consensus pattern (42 bp):
TATAGCCCTACATCTCCATCATACAGCCCAACCTCACCATCC
Found at i:3726279 original size:42 final size:42
Alignment explanation
Indices: 3725928--3726289 Score: 175
Period size: 42 Copynumber: 8.6 Consensus size: 42
3725918 GTATTCTCCT
* * *** *
3725928 ACCTCACCAAGCTATAG-CCCTACCTCTCCAAGTTACAGCCCC
1 ACCTCACCAAGTTATAGTCCC-ACATCTCCATCATACAGCCCA
* * * * *** *
3725970 ACATCTCCAAGTTACAGCCCCACATCTCCAAGTTACAGCCCC
1 ACCTCACCAAGTTATAGTCCCACATCTCCATCATACAGCCCA
* * * * * * * *
3726012 ACATCTCCCAGCTATAGTCCAACTTCACCTAGC-TACAGCCCA
1 ACCTCACCAAGTTATAGTCCCACATCTCC-ATCATACAGCCCA
* * * * *
3726054 ACTTCACC-CGTATATAG-CCCAACATCACCAGCATATAGCCCA
1 ACCTCACCAAGT-TATAGTCCC-ACATCTCCATCATACAGCCCA
* * * *
3726096 ACTTCACC-TGCGTATAG-CCCTACATCTCCATCCTACAGCCCA
1 ACCTCACCAAG-TTATAGTCCC-ACATCTCCATCATACAGCCCA
*** * *
3726138 ACCTCACCATCCTACAG-CCCTACATCTCCATCCTACAGCCCA
1 ACCTCACCAAGTTATAGTCCC-ACATCTCCATCATACAGCCCA
*** *
3726180 ACCTCACCATCCTATAGTCCCACATCTCCATCATACAGCCCT
1 ACCTCACCAAGTTATAGTCCCACATCTCCATCATACAGCCCA
* * * **
3726222 ACTTCACC-AGCTTATAGCCCCACTTCTCC-TGGGTACAGCCCA
1 ACCTCACCAAG-TTATAGTCCCACATCTCCAT-CATACAGCCCA
3726264 ACCTCACCAAGTTATAGTCCCACATC
1 ACCTCACCAAGTTATAGTCCCACATC
3726290 ACCAAGCTAT
Statistics
Matches: 261, Mismatches: 48, Indels: 22
0.79 0.15 0.07
Matches are distributed among these distances:
41 7 0.03
42 244 0.93
43 10 0.04
ACGTcount: A:0.27, C:0.43, G:0.09, T:0.21
Consensus pattern (42 bp):
ACCTCACCAAGTTATAGTCCCACATCTCCATCATACAGCCCA
Found at i:3726315 original size:21 final size:21
Alignment explanation
Indices: 3726264--3726321 Score: 80
Period size: 21 Copynumber: 2.8 Consensus size: 21
3726254 GTACAGCCCA
3726264 ACCTCACCAAGTTATAGTCCC
1 ACCTCACCAAGTTATAGTCCC
* * *
3726285 ACATCACCAAGCTATAGTCCT
1 ACCTCACCAAGTTATAGTCCC
*
3726306 ACCTCTCCAAGTTATA
1 ACCTCACCAAGTTATA
3726322 ATCCGCAGTC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.31, C:0.34, G:0.09, T:0.26
Consensus pattern (21 bp):
ACCTCACCAAGTTATAGTCCC
Found at i:3726346 original size:42 final size:41
Alignment explanation
Indices: 3726254--3726347 Score: 100
Period size: 42 Copynumber: 2.2 Consensus size: 41
3726244 CTTCTCCTGG
* *
3726254 GTACAGCCCAACCTCACCAAGTTATAGTCCCACATCACCAA
1 GTACAGTCCAACCTCACCAAGTTATAATCCCACATCACCAA
* * * *
3726295 GCTATAGTCCTACCTCTCCAAGTTATAATCCGCA-GTCAGCCAA
1 G-TACAGTCCAACCTCACCAAGTTATAATCC-CACATCA-CCAA
3726338 GTACAGTCCA
1 GTACAGTCCA
3726348 TCTTTGGCGT
Statistics
Matches: 42, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
41 1 0.02
42 34 0.81
43 7 0.17
ACGTcount: A:0.31, C:0.35, G:0.13, T:0.21
Consensus pattern (41 bp):
GTACAGTCCAACCTCACCAAGTTATAATCCCACATCACCAA
Found at i:3731474 original size:2 final size:2
Alignment explanation
Indices: 3731461--3731495 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
3731451 GTCTTAAGTT
* *
3731461 TC TC TT TC TC TC TC TA TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
3731496 GTCACACATA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.03, C:0.43, G:0.00, T:0.54
Consensus pattern (2 bp):
TC
Found at i:3733484 original size:2 final size:2
Alignment explanation
Indices: 3733477--3733507 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3733467 GCATGGGCGA
3733477 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
3733508 GTGTTGGGGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:3734149 original size:2 final size:2
Alignment explanation
Indices: 3734144--3734171 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3734134 TTTTAATCAC
3734144 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
3734172 TTGTGTTTAC
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:3741114 original size:18 final size:17
Alignment explanation
Indices: 3741086--3741134 Score: 64
Period size: 18 Copynumber: 2.9 Consensus size: 17
3741076 GTGATCAACG
*
3741086 AATGAATAAGAAAAAAA
1 AATGAAAAAGAAAAAAA
*
3741103 AATTGAAGAAGAAAAAAA
1 AA-TGAAAAAGAAAAAAA
3741121 AA-GAAAAAGAAAAA
1 AATGAAAAAGAAAAA
3741135 TACCAATCGA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 11 0.38
17 2 0.07
18 16 0.55
ACGTcount: A:0.78, C:0.00, G:0.14, T:0.08
Consensus pattern (17 bp):
AATGAAAAAGAAAAAAA
Found at i:3743310 original size:6 final size:6
Alignment explanation
Indices: 3743297--3743331 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
3743287 AAACATGAAC
* *
3743297 ACAAAT ACATAT ACAAAT ACACAT ACAAAT ACAAA
1 ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAA
3743332 AGGAGCTTGA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.63, C:0.20, G:0.00, T:0.17
Consensus pattern (6 bp):
ACAAAT
Found at i:3744177 original size:2 final size:2
Alignment explanation
Indices: 3744170--3744195 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3744160 GAACTTGAAT
3744170 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
3744196 AAGGGATCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3745089 original size:4 final size:4
Alignment explanation
Indices: 3745074--3745104 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
3745064 GCGACTGAGT
*
3745074 AATA AGTA AATA AATA AATA AATA AATA AAT
1 AATA AATA AATA AATA AATA AATA AATA AAT
3745105 TATTTTCGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (4 bp):
AATA
Found at i:3745439 original size:2 final size:2
Alignment explanation
Indices: 3745432--3745460 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3745422 TTCTGCAGAG
3745432 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3745461 CAATTTTGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3746776 original size:3 final size:3
Alignment explanation
Indices: 3746768--3746800 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
3746758 TGAATCAGGC
3746768 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
3746801 TTGTGGCAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:3747143 original size:30 final size:30
Alignment explanation
Indices: 3747109--3747166 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
3747099 CATTCCATTA
*
3747109 GCATAAAGGAATGGAAATTACATAAAAATT
1 GCATAAAGGAATAGAAATTACATAAAAATT
3747139 GCATAAAGGAATAGAAATTACATAAAAA
1 GCATAAAGGAATAGAAATTACATAAAAA
3747167 CTAACTTTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.57, C:0.07, G:0.16, T:0.21
Consensus pattern (30 bp):
GCATAAAGGAATAGAAATTACATAAAAATT
Found at i:3747470 original size:3 final size:3
Alignment explanation
Indices: 3747462--3747492 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
3747452 ATAAAGATTC
*
3747462 AAT AAT AAT AAT AAT AAT AAT AAT ATT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
3747493 TATTAATATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:3747509 original size:3 final size:3
Alignment explanation
Indices: 3747501--3747539 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
3747491 TATATTAATA
*
3747501 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAG TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
3747540 ATATGATAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:3747793 original size:2 final size:2
Alignment explanation
Indices: 3747786--3747813 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3747776 TGGACAGATC
3747786 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
3747814 TCCAACGTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3749840 original size:27 final size:27
Alignment explanation
Indices: 3749790--3749863 Score: 94
Period size: 27 Copynumber: 2.7 Consensus size: 27
3749780 AAACAGCATG
*
3749790 CCACCATTTTTGACAAATAAAAAGAAA
1 CCACCATTTTTGACAAACAAAAAGAAA
* * * *
3749817 CCACCATTTTTTATAAACATAAAGTAA
1 CCACCATTTTTGACAAACAAAAAGAAA
*
3749844 CCACAATTTTTGACAAACAA
1 CCACCATTTTTGACAAACAA
3749864 TGGTGGTTTT
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.47, C:0.20, G:0.05, T:0.27
Consensus pattern (27 bp):
CCACCATTTTTGACAAACAAAAAGAAA
Found at i:3751772 original size:21 final size:21
Alignment explanation
Indices: 3751734--3751775 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3751724 ATCTGTTGAA
* **
3751734 ACTCCACCTGTTTTGGAGTAT
1 ACTCCACCTGCTGCGGAGTAT
3751755 ACTCCACCTGCTGCGGAGTAT
1 ACTCCACCTGCTGCGGAGTAT
3751776 TACTTGTCCG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.19, C:0.29, G:0.21, T:0.31
Consensus pattern (21 bp):
ACTCCACCTGCTGCGGAGTAT
Found at i:3754472 original size:13 final size:13
Alignment explanation
Indices: 3754439--3754484 Score: 51
Period size: 13 Copynumber: 3.6 Consensus size: 13
3754429 GAATAAATTG
3754439 AAGAGGGATAC--
1 AAGAGGGATACTT
*
3754450 AAGAGAGGATGCTT
1 AAGAG-GGATACTT
3754464 AAGAGGGATACTT
1 AAGAGGGATACTT
*
3754477 GAGAGGGA
1 AAGAGGGA
3754485 GGAGGGAGCC
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
11 5 0.17
12 5 0.17
13 14 0.48
14 5 0.17
ACGTcount: A:0.39, C:0.07, G:0.39, T:0.15
Consensus pattern (13 bp):
AAGAGGGATACTT
Found at i:3754537 original size:307 final size:307
Alignment explanation
Indices: 3753983--3754597 Score: 1142
Period size: 307 Copynumber: 2.0 Consensus size: 307
3753973 TGATACCAAC
*
3753983 TGTGGTGGAACTAACGGATATTCCACCTACAATCTATTGGAAAAATAAAGACAATAAAAGAAGAA
1 TGTGGTGGAACTAACGGATATTCCACCTACAATCTATTGAAAAAATAAAGACAATAAAAGAAGAA
*
3754048 ACACAACACGAAAGATTTAACGAGGTTCGACCAACTTATACCTACGTCATCGGACACCACCAATT
66 ACACAACACCAAAGATTTAACGAGGTTCGACCAACTTATACCTACGTCATCGGACACCACCAATT
* *
3754113 CTATTATGAGAATGAATTGAAGAGGGATACAAGAGAGGATGTTTAAGAGGGATACTTGAGAGGGA
131 CTATTATGAGAATAAATTGAAGAGGGATACAAGAGAGGATGCTTAAGAGGGATACTTGAGAGGGA
3754178 GGAGGGAGCCTCTATTTATAGGCTCCATCCTCCCCATTTTACAATAAAAATTAGCCACAAATTTT
196 GGAGGGAGCCTCTATTTATAGGCTCCATCCTCCCCATTTTACAATAAAAATTAGCCACAAATTTT
3754243 GACAAACAACATGCCACCATTTTTGACAAATAAAAAGAAACCACCAT
261 GACAAACAACATGCCACCATTTTTGACAAATAAAAAGAAACCACCAT
* *
3754290 TGTGGTGGAAC-AAGTGGATATTCCACCTACAATTTATTGAAAAAATAAAGACAATAAAAGAAGA
1 TGTGGTGGAACTAA-CGGATATTCCACCTACAATCTATTGAAAAAATAAAGACAATAAAAGAAGA
*
3754354 AACACAACACCAAAGATTTAACGAGGTTCGACCAACTTATACCTACGTCCTCGGACACCACCAAT
65 AACACAACACCAAAGATTTAACGAGGTTCGACCAACTTATACCTACGTCATCGGACACCACCAAT
3754419 TCTATTATGAGAATAAATTGAAGAGGGATACAAGAGAGGATGCTTAAGAGGGATACTTGAGAGGG
130 TCTATTATGAGAATAAATTGAAGAGGGATACAAGAGAGGATGCTTAAGAGGGATACTTGAGAGGG
*
3754484 AGGAGGGAGCCTCTATTTATAGGCTCTATCCTCCCCATTTTACAATAAAAATTAGCCACAAATTT
195 AGGAGGGAGCCTCTATTTATAGGCTCCATCCTCCCCATTTTACAATAAAAATTAGCCACAAATTT
3754549 TGACAAACAACATGCCACCATTTTTGACAAATAAAAAGAAACCACCAT
260 TGACAAACAACATGCCACCATTTTTGACAAATAAAAAGAAACCACCAT
3754597 T
1 T
3754598 TTTGACAAAC
Statistics
Matches: 299, Mismatches: 8, Indels: 2
0.97 0.03 0.01
Matches are distributed among these distances:
306 2 0.01
307 297 0.99
ACGTcount: A:0.40, C:0.19, G:0.18, T:0.23
Consensus pattern (307 bp):
TGTGGTGGAACTAACGGATATTCCACCTACAATCTATTGAAAAAATAAAGACAATAAAAGAAGAA
ACACAACACCAAAGATTTAACGAGGTTCGACCAACTTATACCTACGTCATCGGACACCACCAATT
CTATTATGAGAATAAATTGAAGAGGGATACAAGAGAGGATGCTTAAGAGGGATACTTGAGAGGGA
GGAGGGAGCCTCTATTTATAGGCTCCATCCTCCCCATTTTACAATAAAAATTAGCCACAAATTTT
GACAAACAACATGCCACCATTTTTGACAAATAAAAAGAAACCACCAT
Found at i:3754601 original size:27 final size:27
Alignment explanation
Indices: 3754563--3754636 Score: 112
Period size: 27 Copynumber: 2.7 Consensus size: 27
3754553 AAACAACATG
*
3754563 CCACCATTTTTGACAAATAAAAAGAAA
1 CCACCATTTTTGACAAACAAAAAGAAA
* *
3754590 CCACCATTTTTGACAAACACAAAGTAA
1 CCACCATTTTTGACAAACAAAAAGAAA
*
3754617 CCACAATTTTTGACAAACAA
1 CCACCATTTTTGACAAACAA
3754637 TGGGTGGTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.47, C:0.23, G:0.07, T:0.23
Consensus pattern (27 bp):
CCACCATTTTTGACAAACAAAAAGAAA
Found at i:3755832 original size:50 final size:50
Alignment explanation
Indices: 3755764--3755951 Score: 268
Period size: 50 Copynumber: 3.8 Consensus size: 50
3755754 GGTAAAAAGT
* * * * * * * *
3755764 ACCTTTGATAATAAAGAGAGGTGGTCGTAATTGTTAAAGATTTTTCACTA
1 ACCTTTGACAATAGAGAGAGGTGGCCATAATTGTTGACGATTCTTCACCA
* *
3755814 ACTTTTGACAATAGAGAGAGGTGGCCGTAATTGTTGACGATTCTTCACCA
1 ACCTTTGACAATAGAGAGAGGTGGCCATAATTGTTGACGATTCTTCACCA
*
3755864 ACCTTTGACAATAGAGGGAGGTGGCCATAATTGTTGACGATTCTTCACCA
1 ACCTTTGACAATAGAGAGAGGTGGCCATAATTGTTGACGATTCTTCACCA
*
3755914 ACCTTTGACAATAGAGAGAGGTGGTCATAATTGTTGAC
1 ACCTTTGACAATAGAGAGAGGTGGCCATAATTGTTGAC
3755952 TCTAAGTATA
Statistics
Matches: 125, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
50 125 1.00
ACGTcount: A:0.30, C:0.15, G:0.23, T:0.31
Consensus pattern (50 bp):
ACCTTTGACAATAGAGAGAGGTGGCCATAATTGTTGACGATTCTTCACCA
Found at i:3760259 original size:50 final size:50
Alignment explanation
Indices: 3760202--3760334 Score: 221
Period size: 50 Copynumber: 2.7 Consensus size: 50
3760192 AAAGTACCTC
*
3760202 TGACAATAGAGAGAGGTGGCCGTAATTGTTGACGATTCTTCACCAACATT
1 TGACAATAGAGAGAGGTGGCCATAATTGTTGACGATTCTTCACCAACATT
* * *
3760252 TGACAATAGAGGGAGGTGGCTATAATTGTTGACGATTCTTCACCAACCTT
1 TGACAATAGAGAGAGGTGGCCATAATTGTTGACGATTCTTCACCAACATT
*
3760302 TGACAATAGAGAGAGGTGGTCATAATTGTTGAC
1 TGACAATAGAGAGAGGTGGCCATAATTGTTGAC
3760335 TCTAAGTATA
Statistics
Matches: 76, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
50 76 1.00
ACGTcount: A:0.30, C:0.16, G:0.26, T:0.29
Consensus pattern (50 bp):
TGACAATAGAGAGAGGTGGCCATAATTGTTGACGATTCTTCACCAACATT
Found at i:3770585 original size:2 final size:2
Alignment explanation
Indices: 3770578--3770610 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3770568 TTATTAACAG
3770578 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3770611 CTTTTTTACG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3770815 original size:13 final size:13
Alignment explanation
Indices: 3770797--3770824 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
3770787 CTATTCATTC
3770797 ATATATATATAAT
1 ATATATATATAAT
3770810 ATATATATATAAT
1 ATATATATATAAT
3770823 AT
1 AT
3770825 TACTACAGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
ATATATATATAAT
Found at i:3771812 original size:2 final size:2
Alignment explanation
Indices: 3771807--3771847 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
3771797 TAATCAAGTG
3771807 TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA T
3771848 CATGAGAAAC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3775396 original size:2 final size:2
Alignment explanation
Indices: 3775389--3775419 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3775379 CATAGGTGGT
3775389 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
3775420 GAACTAACTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:3775631 original size:2 final size:2
Alignment explanation
Indices: 3775624--3775658 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3775614 CAGATGATAA
3775624 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3775659 ATCATGAATT
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3784967 original size:2 final size:2
Alignment explanation
Indices: 3784962--3784990 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3784952 TAATCAAGTG
3784962 TA 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 TA T
3784991 CATGAGAAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3789480 original size:28 final size:28
Alignment explanation
Indices: 3789444--3789506 Score: 108
Period size: 28 Copynumber: 2.2 Consensus size: 28
3789434 TAAATACCAC
*
3789444 TTTTTGTATTTGTCAAATATGGTGATTT
1 TTTTTGTATTTGTCAAATATGGTGATTA
*
3789472 TTTTTGTATTTGTCAAATATGGTGGTTA
1 TTTTTGTATTTGTCAAATATGGTGATTA
3789500 TTTTTGT
1 TTTTTGT
3789507 TTGTAAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.19, C:0.03, G:0.19, T:0.59
Consensus pattern (28 bp):
TTTTTGTATTTGTCAAATATGGTGATTA
Found at i:3789539 original size:24 final size:26
Alignment explanation
Indices: 3789480--3789539 Score: 70
Period size: 24 Copynumber: 2.4 Consensus size: 26
3789470 TTTTTTTGTA
* * *
3789480 TTTGTCAAATATGGTGGTTATTTTTG
1 TTTGTCAAAAATAGTGGTTATTGTTG
*
3789506 TTTGTAAAAAATAGTGG-T-TTGTTG
1 TTTGTCAAAAATAGTGGTTATTGTTG
3789530 TTTGTCAAAA
1 TTTGTCAAAA
3789540 TTGATGGCTA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
24 14 0.48
25 1 0.03
26 14 0.48
ACGTcount: A:0.27, C:0.03, G:0.22, T:0.48
Consensus pattern (26 bp):
TTTGTCAAAAATAGTGGTTATTGTTG
Found at i:3789634 original size:13 final size:13
Alignment explanation
Indices: 3789618--3789659 Score: 68
Period size: 13 Copynumber: 3.3 Consensus size: 13
3789608 TCTTGTATCC
*
3789618 CTCTTAAGCATCT
1 CTCTCAAGCATCT
3789631 CTCTCAAGCATCT
1 CTCTCAAGCATCT
3789644 CTCTCAAGCATC-
1 CTCTCAAGCATCT
3789656 CTCT
1 CTCT
3789660 TTTGTATCCC
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
12 4 0.14
13 24 0.86
ACGTcount: A:0.21, C:0.38, G:0.07, T:0.33
Consensus pattern (13 bp):
CTCTCAAGCATCT
Found at i:3789676 original size:26 final size:26
Alignment explanation
Indices: 3789604--3789676 Score: 78
Period size: 26 Copynumber: 2.8 Consensus size: 26
3789594 CTCCCTAATC
3789604 CCTCTCTTGTATCCCTCTT-AAGCAT
1 CCTCTCTTGTATCCCTCTTCAAGCAT
** * *
3789629 CTCTCTCAAGCATCTCTC-TCAAGCAT
1 C-CTCTCTTGTATCCCTCTTCAAGCAT
*
3789655 CCTCTTTTGTATCCCTCTTCAA
1 CCTCTCTTGTATCCCTCTTCAA
3789677 TTCTTTCTCA
Statistics
Matches: 36, Mismatches: 9, Indels: 5
0.72 0.18 0.10
Matches are distributed among these distances:
25 13 0.36
26 23 0.64
ACGTcount: A:0.18, C:0.37, G:0.07, T:0.38
Consensus pattern (26 bp):
CCTCTCTTGTATCCCTCTTCAAGCAT
Found at i:3794086 original size:28 final size:28
Alignment explanation
Indices: 3794054--3794108 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
3794044 CAAATGCTAC
*
3794054 CCTTTGTATTTGTCAAATATGGTGGTTT
1 CCTTTATATTTGTCAAATATGGTGGTTT
3794082 CCTTTATATTTGTCAAATATGGTGGTT
1 CCTTTATATTTGTCAAATATGGTGGTT
3794109 ATTTTTGTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.20, C:0.11, G:0.20, T:0.49
Consensus pattern (28 bp):
CCTTTATATTTGTCAAATATGGTGGTTT
Found at i:3794469 original size:12 final size:12
Alignment explanation
Indices: 3794452--3794478 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
3794442 TTGTAGTTGC
3794452 TGAGGAAAGTGG
1 TGAGGAAAGTGG
3794464 TGAGGAAAGTGG
1 TGAGGAAAGTGG
3794476 TGA
1 TGA
3794479 ATTTGGGTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.33, C:0.00, G:0.48, T:0.19
Consensus pattern (12 bp):
TGAGGAAAGTGG
Found at i:3796037 original size:2 final size:2
Alignment explanation
Indices: 3796032--3796058 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3796022 TATATATATA
3796032 TG 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 TG T
3796059 CTAATTCAAT
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:3796570 original size:2 final size:2
Alignment explanation
Indices: 3796563--3796598 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
3796553 TATGTATGTG
3796563 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
3796599 ACGTTACATA
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):
TA
Found at i:3797133 original size:16 final size:16
Alignment explanation
Indices: 3797112--3797142 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3797102 GAATCTTGGT
*
3797112 AGAGGCCTCTCCTTAC
1 AGAGGCCTCTACTTAC
3797128 AGAGGCCTCTACTTA
1 AGAGGCCTCTACTTA
3797143 TCATCTAATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.32, G:0.19, T:0.26
Consensus pattern (16 bp):
AGAGGCCTCTACTTAC
Found at i:3797420 original size:20 final size:21
Alignment explanation
Indices: 3797374--3797431 Score: 66
Period size: 20 Copynumber: 2.9 Consensus size: 21
3797364 AGCGTTGTTT
* *
3797374 AAATAATACAAATGTA-TTAT
1 AAATAATACAAATATATTTAA
* *
3797394 AATTAATA-AAATTTATTTAA
1 AAATAATACAAATATATTTAA
3797414 AAATAATACAAATATATT
1 AAATAATACAAATATATT
3797432 ATTAACATAT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
19 6 0.19
20 17 0.55
21 8 0.26
ACGTcount: A:0.57, C:0.03, G:0.02, T:0.38
Consensus pattern (21 bp):
AAATAATACAAATATATTTAA
Found at i:3798753 original size:4 final size:4
Alignment explanation
Indices: 3798744--3798814 Score: 63
Period size: 4 Copynumber: 17.8 Consensus size: 4
3798734 TAAATATATT
* * * * *
3798744 TTTC TTTC TTTC CTT- TTTC TTTT TTCTC TTTC TTTT TTTT TTTC TTCC
1 TTTC TTTC TTTC TTTC TTTC TTTC TT-TC TTTC TTTC TTTC TTTC TTTC
* *
3798792 TTTC TTTT TTTC TTTC TTAC TTT
1 TTTC TTTC TTTC TTTC TTTC TTT
3798815 TTCAGCTGAA
Statistics
Matches: 53, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
3 2 0.04
4 48 0.91
5 3 0.06
ACGTcount: A:0.01, C:0.21, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTC
Found at i:3798761 original size:16 final size:14
Alignment explanation
Indices: 3798742--3798817 Score: 77
Period size: 13 Copynumber: 5.4 Consensus size: 14
3798732 CATAAATATA
3798742 TTTTTCTTTCTTTCC
1 TTTTTCTTTCTTT-C
3798757 TTTTTCTTT-TTTC
1 TTTTTCTTTCTTTC
*
3798770 TCTTTCTTT-TTT-
1 TTTTTCTTTCTTTC
*
3798782 TTTTTCTTCCTTTC
1 TTTTTCTTTCTTTC
*
3798796 TTTTTTTCTTTCTTAC
1 --TTTTTCTTTCTTTC
3798812 TTTTTC
1 TTTTTC
3798818 AGCTGAATGC
Statistics
Matches: 52, Mismatches: 5, Indels: 9
0.79 0.08 0.14
Matches are distributed among these distances:
12 7 0.13
13 15 0.29
14 9 0.17
15 9 0.17
16 12 0.23
ACGTcount: A:0.01, C:0.21, G:0.00, T:0.78
Consensus pattern (14 bp):
TTTTTCTTTCTTTC
Found at i:3798780 original size:19 final size:19
Alignment explanation
Indices: 3798742--3798814 Score: 85
Period size: 20 Copynumber: 3.6 Consensus size: 19
3798732 CATAAATATA
3798742 TTTTTCTTTCTTTCCTTTTTCT
1 TTTTTC-TTCTTT-CTTTTT-T
3798764 TTTTTC-TCTTTCTTTTTT
1 TTTTTCTTCTTTCTTTTTT
3798782 TTTTTCTTCCTTTCTTTTTT
1 TTTTTCTT-CTTTCTTTTTT
*
3798802 TCTTTCTTACTTT
1 TTTTTCTT-CTTT
3798815 TTCAGCTGAA
Statistics
Matches: 47, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
18 7 0.15
19 7 0.15
20 27 0.57
22 6 0.13
ACGTcount: A:0.01, C:0.21, G:0.00, T:0.78
Consensus pattern (19 bp):
TTTTTCTTCTTTCTTTTTT
Found at i:3799705 original size:20 final size:20
Alignment explanation
Indices: 3799680--3799719 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
3799670 CTACTGCCTT
3799680 GTTGAGTTCTTGGTAAATTC
1 GTTGAGTTCTTGGTAAATTC
3799700 GTTGAGTTCTTGGTAAATTC
1 GTTGAGTTCTTGGTAAATTC
3799720 TCTGTTTGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.20, C:0.10, G:0.25, T:0.45
Consensus pattern (20 bp):
GTTGAGTTCTTGGTAAATTC
Found at i:3805358 original size:3 final size:3
Alignment explanation
Indices: 3805350--3805382 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
3805340 AAGCCAAAAA
*
3805350 ATT ATT ATT ATT ATT ATT GTT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
3805383 TGCCTTTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:3807904 original size:7 final size:7
Alignment explanation
Indices: 3807892--3808146 Score: 194
Period size: 7 Copynumber: 36.4 Consensus size: 7
3807882 TATGCAGCTT
3807892 GTTTGGG
1 GTTTGGG
*
3807899 GTTTGGA
1 GTTTGGG
* *
3807906 GTTTAGA
1 GTTTGGG
3807913 GTTTGGG
1 GTTTGGG
* *
3807920 GTTAGAG
1 GTTTGGG
*
3807927 GTTGGGG
1 GTTTGGG
*
3807934 GTTCGGG
1 GTTTGGG
*
3807941 GTTTTGG
1 GTTTGGG
*
3807948 GTTCGGG
1 GTTTGGG
*
3807955 GTTTTGG
1 GTTTGGG
3807962 GTTTGGG
1 GTTTGGG
**
3807969 GTTAAGG
1 GTTTGGG
*
3807976 GTTAGGG
1 GTTTGGG
3807983 GTTTAGGG
1 GTTT-GGG
*
3807991 G-TTAGG
1 GTTTGGG
3807997 GTTTGGG
1 GTTTGGG
3808004 GTTTGGG
1 GTTTGGG
3808011 GTTTAGGG
1 GTTT-GGG
3808019 G-TTGGG
1 GTTTGGG
*
3808025 GGTTGGG
1 GTTTGGG
*
3808032 GTTAGGG
1 GTTTGGG
*
3808039 GTTTAGG
1 GTTTGGG
3808046 G-TTGGG
1 GTTTGGG
*
3808052 GTTTAGG
1 GTTTGGG
**
3808059 GTTTAAG
1 GTTTGGG
3808066 GTTTGGG
1 GTTTGGG
3808073 GTTTGGGG
1 GTTT-GGG
3808081 GTTTGGAG
1 GTTTGG-G
3808089 G-TTGGG
1 GTTTGGG
*
3808095 GTTAGGG
1 GTTTGGG
*
3808102 GTTAGGG
1 GTTTGGG
*
3808109 GTTTAGG
1 GTTTGGG
*
3808116 ATTTGGG
1 GTTTGGG
**
3808123 GTTTTAG
1 GTTTGGG
* *
3808130 GTTTCGA
1 GTTTGGG
3808137 GTTTGGG
1 GTTTGGG
3808144 GTT
1 GTT
3808147 GAACCCGAAA
Statistics
Matches: 196, Mismatches: 44, Indels: 16
0.77 0.17 0.06
Matches are distributed among these distances:
6 14 0.07
7 165 0.84
8 17 0.09
ACGTcount: A:0.09, C:0.01, G:0.51, T:0.39
Consensus pattern (7 bp):
GTTTGGG
Found at i:3808188 original size:15 final size:15
Alignment explanation
Indices: 3808148--3810651 Score: 918
Period size: 15 Copynumber: 158.8 Consensus size: 15
3808138 TTTGGGGTTG
3808148 AACCCGAAACTCCGAA
1 AACCCGAAAC-CCGAA
*
3808164 TA-CCGTAAACCCGAA
1 AACCCG-AAACCCGAA
3808179 AACCCGAAACCCGAA
1 AACCCGAAACCCGAA
** * *
3808194 CTCTCGCATAACCCGTA
1 AACCCG-A-AACCCGAA
3808211 AACCTCGAAATCCCGGAA
1 AACC-CGAAA-CCC-GAA
*
3808229 ATCGCCGCTAAACCCGAA
1 AAC-CCG--AAACCCGAA
3808247 AACCCGCCGCGAAAACCTCGAA
1 AA----CC-CG-AAACC-CGAA
3808269 AACCCGAAACCCCG-A
1 AACCCGAAA-CCCGAA
* *
3808284 AACCCGATACCCGGA
1 AACCCGAAACCCGAA
* *
3808299 ACCCCGAAACCCGAT
1 AACCCGAAACCCGAA
3808314 AACCTCGAAA-CCG-A
1 AACC-CGAAACCCGAA
*
3808328 ACCCCGAAA-CCG-A
1 AACCCGAAACCCGAA
3808341 AA-CCGAAACCCG-A
1 AACCCGAAACCCGAA
*
3808354 AACACGAAACCCGAA
1 AACCCGAAACCCGAA
*
3808369 AACCCGCAACCCGAA
1 AACCCGAAACCCGAA
* *
3808384 ACCCCGCAACCCCGAA
1 AACCCG-AAACCCGAA
*
3808400 AGCCCGAAACCCG-A
1 AACCCGAAACCCGAA
3808414 AACCCGAAACCCGAA
1 AACCCGAAACCCGAA
* *
3808429 CTTACTTCCGAAACCCGAC
1 --AAC--CCGAAACCCGAA
3808448 AACCCG-AACCCG--
1 AACCCGAAACCCGAA
3808460 AACCCGAAACCCG-A
1 AACCCGAAACCCGAA
3808474 AACCCGAAACCCG-A
1 AACCCGAAACCCGAA
*
3808488 AACCCGACCTACCCG-A
1 AACCCGA--AACCCGAA
3808504 AACGCCGAAACCCGAA
1 AAC-CCGAAACCCGAA
**
3808520 ATACCCGATATACCCGCT
1 A-ACCCGA-A-ACCCGAA
*
3808538 AACCC----CCTG-A
1 AACCCGAAACCCGAA
* *
3808548 AACCCGATACTCGAA
1 AACCCGAAACCCGAA
*
3808563 ATCCCGAAAACCCG--
1 AACCCG-AAACCCGAA
*
3808577 AACCCGAAACCTCG-C
1 AACCCGAAACC-CGAA
3808592 AACCCGAAACCCGTAA
1 AACCCGAAACCCG-AA
3808608 AACCCTGAAACCCG-A
1 AACCC-GAAACCCGAA
3808623 AACCCGAAACCCG-A
1 AACCCGAAACCCGAA
*
3808637 AACCCGGAAACCCG-C
1 AACCC-GAAACCCGAA
3808652 AACTCTCGATAA-CCG-A
1 AAC-C-CGA-AACCCGAA
3808668 AACCCGTAATA-CCGAA
1 AACCCG-AA-ACCCGAA
*
3808684 TACCTCGAAACCCGAA
1 AACC-CGAAACCCGAA
3808700 AACCCGAAACCCG-A
1 AACCCGAAACCCGAA
*
3808714 AACTCCGTAACCCCGAA
1 AAC-CCG-AAACCCGAA
* *
3808731 TACCTCGTTAAACCCGGA
1 AACC-CG--AAACCCGAA
3808749 AACCCGAAACCCGGAGGAA
1 AACCCGAAACCC----GAA
*
3808768 AACCCCCGAATTA-CCG-C
1 AA--CCCGAA--ACCCGAA
*
3808785 AACTCCGAAACCCG-G
1 AAC-CCGAAACCCGAA
*
3808800 AACCCGAATA-CCG-C
1 AACCCGAA-ACCCGAA
*
3808814 AACCTCGAAACCCGGGA
1 AACC-CGAAACCC-GAA
*
3808831 AACCGGAAACCCGAA
1 AACCCGAAACCCGAA
3808846 AACCCCG-AACCCGAA
1 AA-CCCGAAACCCGAA
3808861 AACCCGGAAACCCGAA
1 AACCC-GAAACCCGAA
3808877 AACCCGAAACCCG-A
1 AACCCGAAACCCGAA
3808891 AACGCCGAAAACCTCG-A
1 AAC-CCG-AAACC-CGAA
*
3808908 AACCCGAAACCCGAGTGT
1 AACCCGAAACCCGA---A
3808926 AACCCGAAACCCGAA
1 AACCCGAAACCCGAA
* * *
3808941 ATCCGGAAAACTCGCGTACG
1 AACCCG-AAAC-C-CG-A-A
3808961 AACCCGAAACCTCG-A
1 AACCCGAAACC-CGAA
*
3808976 AACCGGAAACCCGAA
1 AACCCGAAACCCGAA
*
3808991 ACCCCGAAACCCGGGAA
1 AACCCGAAACCC--GAA
*
3809008 ATCCCGAAA-CCGAA
1 AACCCGAAACCCGAA
3809022 AACCCGAATACCCG-A
1 AACCCGAA-ACCCGAA
*
3809037 AACCCGAAACCCGGA
1 AACCCGAAACCCGAA
3809052 AA-CCGAACTACCTCGGTAA
1 AACCCGAA--ACC-C-G-AA
*
3809071 ACCCCCGAAACCCGAA
1 A-ACCCGAAACCCGAA
3809087 AACCCGAAACCCG-A
1 AACCCGAAACCCGAA
*
3809101 AACCC-AACCCCG-A
1 AACCCGAAACCCGAA
*
3809114 AACACGAAACCCGAA
1 AACCCGAAACCCGAA
* * *
3809129 TACCAGAAACCCGGA
1 AACCCGAAACCCGAA
3809144 AACCCGAAA-CCG-A
1 AACCCGAAACCCGAA
3809157 AACCCGAAACCCG-A
1 AACCCGAAACCCGAA
*
3809171 AACCC--TA---GAA
1 AACCCGAAACCCGAA
3809181 AACCCTGTAAACCCG-A
1 AACCC-G-AAACCCGAA
*
3809197 AACCTCG-AACCCGGAG
1 AACC-CGAAACCC-GAA
*
3809213 AACCTCGAAACCCTGGA
1 AACC-CGAAACCC-GAA
*
3809230 AACCTCGGATAATCCCGGA
1 AACC-C-GA-AA-CCCGAA
*
3809249 AACCCGAAACCCGTA
1 AACCCGAAACCCGAA
3809264 AACCCGAAAAACCCG-A
1 AACCCG--AAACCCGAA
3809280 AACCTCTGAAA-CCGAA
1 AACC-C-GAAACCCGAA
** *
3809296 CTCCCGTTCAACCCG-A
1 AACCCG--AAACCCGAA
3809312 AA-CCGAAACCCG-A
1 AACCCGAAACCCGAA
*
3809325 AACCAGAAACTCCGAA
1 AACCCGAAAC-CCGAA
*
3809341 ATATCCCGAAA-CCGGA
1 A-A-CCCGAAACCCGAA
3809357 AACCCGAAACCCGAA
1 AACCCGAAACCCGAA
*
3809372 AACCCGGACACCCG-A
1 AACCC-GAAACCCGAA
3809387 AACCCGAAA-CCG-A
1 AACCCGAAACCCGAA
3809400 AACCCGAAA--C--A
1 AACCCGAAACCCGAA
3809411 AACCCTGGAAACCCGAA
1 AACCC--GAAACCCGAA
*
3809428 CA-CCGACAACCTCG-A
1 AACCCGA-AACC-CGAA
*
3809443 AACTCCGAAACCCGTAT
1 AAC-CCGAAACCCG-AA
3809460 AACCTCG-AACCCG-A
1 AACC-CGAAACCCGAA
*
3809474 AACCAGAAACCCGAGA
1 AACCCGAAACCCGA-A
3809490 ACCGACCCCGGAAATCTCCGAA
1 A---A-CCC-GAAA-C-CCGAA
3809512 ATAGCCCGATAACCGCG-A
1 A-A-CCCGA-AACC-CGAA
3809530 AACCTCGAAACTCCTGGAGA
1 AACC-CGAAAC-CC--GA-A
* *
3809550 ATCCCGAAAACCG-A
1 AACCCGAAACCCGAA
3809564 AACCCGAAACCCG-A
1 AACCCGAAACCCGAA
* *
3809578 AACCCGAACCCCGGTAC
1 AACCCGAAACCC-G-AA
* **
3809595 ATCCCGAGAATCCCGTC
1 AACCCGA-AA-CCCGAA
* *
3809612 AACCCGAAAACCGTA
1 AACCCGAAACCCGAA
* *
3809627 AA-CCGCAACCCGTA
1 AACCCGAAACCCGAA
3809641 AACCCGGAAACCCGAA
1 AACCC-GAAACCCGAA
*
3809657 CACCCGAAACTCCG-A
1 AACCCGAAAC-CCGAA
*
3809672 CACCCGGAAACCCTTGAA
1 AACCC-GAAACCC--GAA
* *
3809690 CACCTCGCTATACCCCG-A
1 AACC-CG--A-AACCCGAA
3809708 AACCCGAATAATCCCG--
1 AACCCG-A-AA-CCCGAA
*
3809724 AACCTCGACACCCGAA
1 AACC-CGAAACCCGAA
* *
3809740 GACCCGCAACCCGGTAA
1 AACCCGAAACCC-G-AA
* *
3809757 ACCCCGAAAACCCGTA
1 AACCCG-AAACCCGAA
3809773 AACCTCGAAACCCGAA
1 AACC-CGAAACCCGAA
* *
3809789 ATTCTCTCGAAACCCGAG
1 A-AC-C-CGAAACCCGAA
*
3809807 AACCCGAAACCCGGTA
1 AACCCGAAACCC-GAA
* *
3809823 AACCCGATACCTG-A
1 AACCCGAAACCCGAA
*
3809837 AACCCGAAATCCGAA
1 AACCCGAAACCCGAA
3809852 AA-CCGAAACCCGAA
1 AACCCGAAACCCGAA
*
3809866 AACCCGTAACCCCG-A
1 AACCCG-AAACCCGAA
3809881 AACCCGAAACTCCCG-A
1 AACCCGAAA--CCCGAA
3809897 AACTCTCGATTAACTTCTCG-A
1 AAC-C-CGA--AAC--C-CGAA
*
3809918 AACCCTGTAGACCCG-A
1 AACCC-G-AAACCCGAA
*
3809934 AACCCGTAACCCGTAA
1 AACCCGAAACCCG-AA
*
3809950 ATCCCGAAACCCG-A
1 AACCCGAAACCCGAA
3809964 AACCCTGGAAACCC--A
1 AACCC--GAAACCCGAA
* *
3809979 AACCAG-AA-CCGTA
1 AACCCGAAACCCGAA
3809992 AACCCGAAACCCG-A
1 AACCCGAAACCCGAA
*
3810006 AA-CCGAAACCCGAG
1 AACCCGAAACCCGAA
3810020 AACCCGAAACCCCG-A
1 AACCCGAAA-CCCGAA
3810035 AACCCGATAACCCG-A
1 AACCCGA-AACCCGAA
* * *
3810050 AACCCTAATCCGCGAT
1 AACCCGAAACC-CGAA
*
3810066 AACCCGCTAATCCCGAA
1 AACCCG--AAACCCGAA
3810083 AACCCCTTG-AACCCTG-A
1 AA-CCC--GAAACCC-GAA
3810100 AACCCGAAACCCGCGAA
1 AACCCGAAA-CC-CGAA
*
3810117 TACCCG-AACCCG-A
1 AACCCGAAACCCGAA
**
3810130 AACCCGCCACCCG-A
1 AACCCGAAACCCGAA
3810144 AACCCGAAACGCCGAA
1 AACCCGAAAC-CCGAA
*
3810160 TACCCGAAATCCCTGAA
1 AACCCGAAA-CCC-GAA
3810177 AACCCGAGAAGACCCG-A
1 AACCC--GAA-ACCCGAA
3810194 AACCCGAAATATCCCGGAA
1 AACCCG-AA-A-CCC-GAA
*
3810213 AACCCGAGACCCGAA
1 AACCCGAAACCCGAA
* *
3810228 ATCCGGCGTAAACGCG-A
1 AACC--CG-AAACCCGAA
3810245 AACCCGATAACCCG--
1 AACCCGA-AACCCGAA
3810259 AACCCGGAAACCCGAGGA
1 AACCC-GAAACCCGA--A
3810277 AACCCGGAAA-CCGAGA
1 AACCC-GAAACCCGA-A
3810293 AGACCGTCGGAAACGCCGAAA
1 A-ACC--C-GAAAC-CCG-AA
* *
3810314 ATACCCGCTAACCCG-C
1 A-ACCCG-AAACCCGAA
3810330 AACCCGAAACCCGAGA
1 AACCCGAAACCCGA-A
3810346 AACCGCGAAAACCCTTCGAA
1 AACC-CG-AAA-CC--CGAA
3810366 AACCCGAAACCCG-A
1 AACCCGAAACCCGAA
*
3810380 AACCCTGATAATTCCTGAA
1 AACCC-GA-AA--CCCGAA
*
3810399 TATCGCCGAAACCCTG-A
1 -AAC-CCGAAACCC-GAA
3810416 AACCCGAAACCCTGAA
1 AACCCGAAACCC-GAA
* *
3810432 GACGCCGACACCTCGATA
1 AAC-CCGAAACC-CGA-A
*
3810450 TACCCGAAACCCG-A
1 AACCCGAAACCCGAA
3810464 AA-CCGAGAACCCGAA
1 AACCCGA-AACCCGAA
3810479 ACACCGCGTAAACCCG-A
1 A-ACC-CG-AAACCCGAA
3810496 AACCCTGAAA-CCG-A
1 AACCC-GAAACCCGAA
* * *
3810510 ACCGCCGGAACCCCGGA
1 AAC-CC-GAAACCCGAA
* *
3810527 ACCCCGAAACCCGAG
1 AACCCGAAACCCGAA
*
3810542 AACCCGCAATCCCG-A
1 AACCCG-AAACCCGAA
*
3810557 AACCCGAAACCCGGGAG
1 AACCCGAAACCC--GAA
* * *
3810574 ACCCCGAAGCCTCGGA
1 AACCCGAAACC-CGAA
*
3810590 CACCCGAAACCTCTGAA
1 AACCCGAAACC-C-GAA
*
3810607 ACCCCGAAACCCG-A
1 AACCCGAAACCCGAA
*
3810621 AACCTCGTAAACGCCGGA
1 AACC-CG-AAAC-CCGAA
3810639 AACCGCGAAACCC
1 AACC-CGAAACCC
3810652 AGAACCCCGA
Statistics
Matches: 1959, Mismatches: 228, Indels: 602
0.70 0.08 0.22
Matches are distributed among these distances:
9 1 0.00
10 11 0.01
11 11 0.01
12 16 0.01
13 102 0.05
14 342 0.17
15 462 0.24
16 395 0.20
17 263 0.13
18 164 0.08
19 88 0.04
20 39 0.02
21 45 0.02
22 15 0.01
23 5 0.00
ACGTcount: A:0.38, C:0.39, G:0.16, T:0.07
Consensus pattern (15 bp):
AACCCGAAACCCGAA
Found at i:3808445 original size:33 final size:31
Alignment explanation
Indices: 3808268--3810050 Score: 256
Period size: 31 Copynumber: 55.7 Consensus size: 31
3808258 AAAACCTCGA
3808268 AAACCCGAAACCCCGAAACCCG-A--TACCCGG
1 AAACCCGAAA-CCCGAAACCCGAACCTACCC-G
* *
3808298 AACCCCGAAACCCGATAACCTCGAAACCGAACCCCG
1 AAACCCGAAACCCGA-AACC-CG-AACC-TA-CCCG
*
3808334 AAA-CCGAAA-CCGAAACCCGAA---ACACG
1 AAACCCGAAACCCGAAACCCGAACCTACCCG
* *
3808360 AAACCCGAAAACCCGCAACCCGAAAC--CCCG
1 AAACCCG-AAACCCGAAACCCGAACCTACCCG
*
3808390 CAACCCCGAAAGCCCGAAACCCGAA---ACCCG
1 -AAACCCGAAA-CCCGAAACCCGAACCTACCCG
*
3808420 AAACCCGAACTTACTTCCGAAACCCG-A-CAACCCG
1 AAACCCGAA---AC--CCGAAACCCGAACCTACCCG
3808454 -AACCCG-AACCCGAAACCCGAA---ACCCG
1 AAACCCGAAACCCGAAACCCGAACCTACCCG
*
3808480 AAACCCGAAACCCGACCTACCCGAA---ACGCCG
1 AAACCCGAAACCCGA--AACCCGAACCTAC-CCG
3808511 AAACCCGAAATACCCGATATACCCGCTAACC--CCCTG
1 AAACCCG-AA-ACCCGA-A-ACCCG--AACCTACCC-G
* * *
3808547 AAACCCGATACTCGAAATCCCGAA--AACCCG
1 AAACCCGAAACCCGAAA-CCCGAACCTACCCG
*
3808577 -AACCCGAAACCTCGCAACCCGAA---ACCCG
1 AAACCCGAAACC-CGAAACCCGAACCTACCCG
3808605 TAAAACCCTGAAACCCGAAACCCGAA---ACCCG
1 --AAACCC-GAAACCCGAAACCCGAACCTACCCG
* *
3808636 AAACCCGGAAACCCGCAACTCTCGATAACCGAAACCCG
1 AAACCC-GAAACCCGAAAC-C-CG--AACC--TACCCG
*
3808674 TAATA-CCGAATACCTCGAAACCCGAA--AACCCG
1 -AA-ACCCGAA-ACC-CGAAACCCGAACCTACCCG
*
3808706 AAACCCGAAACTCCGTAACCCCGAA--TACCTCG
1 AAACCCGAAAC-CCG-AAACCCGAACCTACC-CG
3808738 TTAAACCCGGAAACCCGAAACCCGGAGGAAAACC--CCCG
1 --AAACCC-GAAACCCGAAACCC----G--AACCTACCCG
* *
3808776 AATTA-CCGCAACTCCGAAACCCGGA---ACCCG
1 AA--ACCCGAAAC-CCGAAACCCGAACCTACCCG
* *
3808806 AATA-CCGCAACCTCGAAACCCGGGAA---ACCGG
1 AA-ACCCGAAACC-CGAAACCC--GAACCTACCCG
*
3808837 AAACCCGAAAACCCCG-AACCCGAA--AACCCGG
1 AAACCCG-AAA-CCCGAAACCCGAACCTACCC-G
3808868 AAACCCGAAAACCCGAAACCCGAA---ACGCCG
1 AAACCCG-AAACCCGAAACCCGAACCTAC-CCG
***
3808898 AAAACCTCGAAACCCGAAACCCGAGTGTAACCCG
1 -AAACC-CGAAACCCGAAACCCGAACCT-ACCCG
* * **
3808932 AAACCCGAAATCCGGAAAACTCGCGTACGAACCCG
1 AAACCCGAAA-CCCG-AAAC-C-CGAACCTACCCG
* *
3808967 AAACCTCGAAACCGGAAACCCGAAAC--CCCG
1 AAACC-CGAAACCCGAAACCCGAACCTACCCG
3808997 AAACCCGGGAAATCCCGAAA-CCGAAAACCCGAATACCCG
1 AAACCC--GAAA-CCCGAAACCCG--AA-CC---TACCCG
3809036 AAACCCGAAACCCGGAAA-CCGAA-CTACCTCGG
1 AAACCCGAAACCC-GAAACCCGAACCTACC-C-G
3809068 TAAACCCCCGAAACCCGAAAACCCGAA---ACCCG
1 -AAA--CCCGAAACCCG-AAACCCGAACCTACCCG
* *
3809100 AAACCC-AACCCCGAAACACGAA---ACCCG
1 AAACCCGAAACCCGAAACCCGAACCTACCCG
*
3809127 AATACCAGAAACCCGGAAACCCGAA---A-CCG
1 AA-ACCCGAAACCC-GAAACCCGAACCTACCCG
*
3809156 AAACCCGAAACCCGAAACCCTAGAA--AACCCTG
1 AAACCCGAAACCCGAAACCC--GAACCTACCC-G
* **
3809188 TAAACCCGAAACCTCG-AACCCGGA-GAACCTCG
1 -AAACCCGAAACC-CGAAACCCGAACCTACC-CG
3809220 AAACCCTGGAAACCTCGGATAATCCCGGAA---ACCCG
1 AAACCC--GAAACC-C-GA-AA-CCC-GAACCTACCCG
*
3809255 AAACCCGTAAACCCGAAAAACCCGAAACCT--CTG
1 AAACCCG-AAACCCG--AAACCCG-AACCTACCCG
* *
3809288 AAA-CCGAACTCCCGTTCAACCCGAA---A-CCG
1 AAACCCGAA-ACCCG--AAACCCGAACCTACCCG
* *
3809317 AAACCCGAAACCAGAAACTCCGAA-ATATCCCG
1 AAACCCGAAACCCGAAAC-CCGAACCTA-CCCG
* *
3809349 AAACCGGAAACCCGAAACCCGAA--AACCCGG
1 AAACCCGAAACCCGAAACCCGAACCTACCC-G
*
3809379 ACACCCGAAACCCGAAA-CCGAA---ACCCG
1 AAACCCGAAACCCGAAACCCGAACCTACCCG
3809406 AAA--C-AAACCCTGGAAACCCGAA-C-A-CCG
1 AAACCCGAAACCC--GAAACCCGAACCTACCCG
*
3809433 ACAACCTCGAAACTCCGAAACCCGTA--TAACCTCG
1 A-AACC-CGAAAC-CCGAAACCCGAACCT-ACC-CG
* *
3809467 -AACCCGAAACCAGAAACCCGAGAACCGACCCCGG
1 AAACCCGAAACCCGAAACCC--GAACCTA-CCC-G
3809501 AAATCTCCGAAATAGCCCGATAACCGCGAA---ACCTCG
1 AAA-C-CCG-AA-A-CCCGA-AACC-CGAACCTACC-CG
*
3809537 AAACTCCTGGAGAATCCCGAAAACCGAA---ACCCG
1 AAAC-CC--GA-AA-CCCGAAACCCGAACCTACCCG
* * *
3809570 AAACCCGAAACCCGAACCCCGGTACAT-CCCG
1 AAACCCGAAACCCGAAACCC-GAACCTACCCG
* *
3809601 AGAATCCCGTCAACCCGAAAACCGTAA---A-CCG
1 A-AA-CCCG-AAACCCGAAACCCG-AACCTACCCG
*
3809632 CAACCCGTAAACCCGGAAACCCGAA-C-ACCCG
1 AAACCCG-AAACCC-GAAACCCGAACCTACCCG
*
3809663 AAACTCCGACACCCGGAAACCCTTGAA-C-ACCTCG
1 AAAC-CCGAAACCC-GAAACCC--GAACCTACC-CG
*
3809697 CTATACCCCGAAACCCGAATAATCCCGAACCT---CG
1 --A-AACCCGAAACCCG-A-AA-CCCGAACCTACCCG
* * *
3809731 ACACCCGAAGACCCGCAACCCGGTAAAC--CCCG
1 AAACCCGAA-ACCCGAAACCC-G-AACCTACCCG
* *
3809763 AAAACCCGTAAACCTCGAAACCCGAAATTCT-CTCG
1 -AAACCCG-AAACC-CGAAACCCG-AA-CCTACCCG
*
3809798 AAACCCGAGAACCCGAAACCCGGTAAACCCGATACCTG
1 AAACCCGA-AACCCGAAACCC-G--AA-CC--TACCCG
* *
3809836 AAACCCGAAATCCGAAAACCGAA---ACCCG
1 AAACCCGAAACCCGAAACCCGAACCTACCCG
* *
3809864 AAAACCCGTAACCCCGAAACCCGAAACT-CCCG
1 -AAACCCG-AAACCCGAAACCCGAACCTACCCG
* *
3809896 AAACTCTCGATTAACTTCTCGAAACCCTGTA--GACCCG
1 AAAC-C-CGA--AAC--C-CGAAACCC-GAACCTACCCG
*
3809933 AAACCCGTAACCCGTAAATCCCGAA---ACCCG
1 AAACCCGAAACCCG-AAA-CCCGAACCTACCCG
*
3809963 AAACCCTGGAAACCC-AAACCAGAACCGTAAACCCG
1 AAACCC--GAAACCCGAAACCCGAACC-T--ACCCG
3809998 AAACCCGAAA-CCGAAACCCGAGA---ACCCG
1 AAACCCGAAACCCGAAACCCGA-ACCTACCCG
3810026 AAACCCCGAAACCCGATAACCCGAA
1 AAA-CCCGAAACCCGA-AACCCGAA
3810051 ACCCTAATCC
Statistics
Matches: 1388, Mismatches: 112, Indels: 506
0.69 0.06 0.25
Matches are distributed among these distances:
24 6 0.00
25 1 0.00
26 15 0.01
27 57 0.04
28 68 0.05
29 149 0.11
30 164 0.12
31 238 0.17
32 131 0.09
33 158 0.11
34 102 0.07
35 86 0.06
36 72 0.05
37 68 0.05
38 32 0.02
39 23 0.02
40 13 0.01
41 4 0.00
42 1 0.00
ACGTcount: A:0.38, C:0.39, G:0.15, T:0.07
Consensus pattern (31 bp):
AAACCCGAAACCCGAAACCCGAACCTACCCG
Found at i:3808459 original size:6 final size:7
Alignment explanation
Indices: 3808148--3810671 Score: 1226
Period size: 7 Copynumber: 320.1 Consensus size: 7
3808138 TTTGGGGTTG
3808148 AACCCGA
1 AACCCGA
3808155 AACTCCGA
1 AAC-CCGA
3808163 ATA-CCGTA
1 A-ACCCG-A
3808171 AACCCGAA
1 AACCCG-A
3808179 AACCCGA
1 AACCCGA
3808186 AACCCG-
1 AACCCGA
3808192 AACTCTCGCA
1 AAC-C-CG-A
3808202 TAACCCGTA
1 -AACCCG-A
3808211 AACCTCGA
1 AACC-CGA
3808219 AATCCCGGA
1 AA-CCC-GA
3808228 AATCGCCGCTA
1 AA-C-CCG--A
3808239 AACCCGAA
1 AACCCG-A
3808247 AACCCG-
1 AACCCGA
3808253 --CCGCGAA
1 AACC-CG-A
3808260 AACCTCGAA
1 AACC-CG-A
3808269 AACCCGA
1 AACCCGA
3808276 AACCCCGA
1 AA-CCCGA
3808284 AACCCGA
1 AACCCGA
*
3808291 TACCCGGA
1 AACCC-GA
*
3808299 ACCCCGA
1 AACCCGA
3808306 AACCCGA
1 AACCCGA
3808313 TAACCTCGA
1 -AACC-CGA
3808322 AA-CCGA
1 AACCCGA
*
3808328 ACCCCGA
1 AACCCGA
3808335 AA-CCGA
1 AACCCGA
3808341 AA-CCGA
1 AACCCGA
3808347 AACCCGA
1 AACCCGA
*
3808354 AACACGA
1 AACCCGA
3808361 AACCCGAA
1 AACCCG-A
*
3808369 AACCCGC
1 AACCCGA
3808376 AACCCGA
1 AACCCGA
3808383 AACCCCGCA
1 AA-CCCG-A
*
3808392 ACCCCGA
1 AACCCGA
3808399 AAGCCCGA
1 AA-CCCGA
3808407 AACCCGA
1 AACCCGA
3808414 AACCCGA
1 AACCCGA
3808421 AACCCGA
1 AACCCGA
3808428 ACTTACTTCCGA
1 A---AC--CCGA
3808440 AACCCGA
1 AACCCGA
3808447 CAACCCG-
1 -AACCCGA
3808454 AACCCG-
1 AACCCGA
3808460 AACCCGA
1 AACCCGA
3808467 AACCCGA
1 AACCCGA
3808474 AACCCGA
1 AACCCGA
3808481 AACCCGA
1 AACCCGA
3808488 AACCCGA
1 AACCCGA
*
3808495 CCTACCCGA
1 --AACCCGA
3808504 AACGCCGA
1 AAC-CCGA
3808512 AACCCGAA
1 AACCCG-A
3808520 ATACCCGA
1 A-ACCCGA
3808528 TATACCCGCTA
1 -A-ACCCG--A
*
3808539 ACCCCCTGA
1 A-ACCC-GA
3808548 AACCCGA
1 AACCCGA
* *
3808555 TACTCGA
1 AACCCGA
3808562 AATCCCGAA
1 AA-CCCG-A
3808571 AACCCG-
1 AACCCGA
3808577 AACCCGA
1 AACCCGA
*
3808584 AACCTCGC
1 AACC-CGA
3808592 AACCCGA
1 AACCCGA
3808599 AACCCGTAA
1 AACCCG--A
3808608 AACCCTGA
1 AACCC-GA
3808616 AACCCGA
1 AACCCGA
3808623 AACCCGA
1 AACCCGA
3808630 AACCCGA
1 AACCCGA
3808637 AACCCGGA
1 AACCC-GA
*
3808645 AACCCGC
1 AACCCGA
3808652 AACTCTCGA
1 AAC-C-CGA
3808661 TAA-CCGA
1 -AACCCGA
3808668 AACCCGTA
1 AACCCG-A
3808676 ATA-CCGA
1 A-ACCCGA
3808683 ATACCTCGA
1 A-ACC-CGA
3808692 AACCCGAA
1 AACCCG-A
3808700 AACCCGA
1 AACCCGA
3808707 AACCCGA
1 AACCCGA
3808714 AACTCCGTA
1 AAC-CCG-A
*
3808723 ACCCCGA
1 AACCCGA
3808730 ATACCTCGTTA
1 A-ACC-CG--A
3808741 AACCCGGA
1 AACCC-GA
3808749 AACCCGA
1 AACCCGA
3808756 AACCCGGAGGAA
1 AACCC----G-A
3808768 AACCCCCGA
1 AA--CCCGA
*
3808777 ATTA-CCGC
1 A--ACCCGA
3808785 AACTCCGA
1 AAC-CCGA
*
3808793 AACCCGG
1 AACCCGA
3808800 AACCCGA
1 AACCCGA
*
3808807 ATA-CCGC
1 A-ACCCGA
3808814 AACCTCGA
1 AACC-CGA
3808822 AACCCGGGA
1 AACCC--GA
*
3808831 AACCGGA
1 AACCCGA
3808838 AACCCGAA
1 AACCCG-A
3808846 AACCCCG-
1 AA-CCCGA
3808853 AACCCGAA
1 AACCCG-A
3808861 AACCCGGA
1 AACCC-GA
3808869 AACCCGAA
1 AACCCG-A
3808877 AACCCGA
1 AACCCGA
3808884 AACCCGA
1 AACCCGA
3808891 AACGCCGAA
1 AAC-CCG-A
3808900 AACCTCGA
1 AACC-CGA
3808908 AACCCGA
1 AACCCGA
3808915 AACCCGA
1 AACCCGA
3808922 GTGTAACCCGA
1 ----AACCCGA
3808933 AACCCGA
1 AACCCGA
*
3808940 AATCCGGAA
1 AA-CCCG-A
3808949 AACTCGCGTA
1 AAC-C-CG-A
3808959 CGAACCCGA
1 --AACCCGA
3808968 AACCTCGA
1 AACC-CGA
*
3808976 AACCGGA
1 AACCCGA
3808983 AACCCGA
1 AACCCGA
3808990 AACCCCGA
1 AA-CCCGA
3808998 AACCCGGGA
1 AACCC--GA
3809007 AATCCCGA
1 AA-CCCGA
3809015 AA-CCGAA
1 AACCCG-A
3809022 AACCCGA
1 AACCCGA
3809029 ATACCCGA
1 A-ACCCGA
3809037 AACCCGA
1 AACCCGA
3809044 AACCCGGA
1 AACCC-GA
3809052 AA-CCGA
1 AACCCGA
3809058 ACTACCTCGGTA
1 A--ACC-C-G-A
3809070 AACCCCCGA
1 AA--CCCGA
3809079 AACCCGAA
1 AACCCG-A
3809087 AACCCGA
1 AACCCGA
3809094 AACCCGA
1 AACCCGA
3809101 AACCC-A
1 AACCCGA
*
3809107 ACCCCGA
1 AACCCGA
*
3809114 AACACGA
1 AACCCGA
3809121 AACCCGA
1 AACCCGA
*
3809128 ATACCAGA
1 A-ACCCGA
3809136 AACCCGGA
1 AACCC-GA
3809144 AACCCGA
1 AACCCGA
3809151 AA-CCGA
1 AACCCGA
3809157 AACCCGA
1 AACCCGA
3809164 AACCCGA
1 AACCCGA
3809171 AACCCTAGAA
1 AACCC--G-A
3809181 AACCCTGTA
1 AACCC-G-A
3809190 AACCCGA
1 AACCCGA
3809197 AACCTCG-
1 AACC-CGA
3809204 AACCCGGA
1 AACCC-GA
3809212 GAACCTCGA
1 -AACC-CGA
3809221 AACCCTGGA
1 AACCC--GA
3809230 AACCTCGGA
1 AACC-C-GA
3809239 TAATCCCGGA
1 -AA-CCC-GA
3809249 AACCCGA
1 AACCCGA
3809256 AACCCGTA
1 AACCCG-A
3809264 AACCCGAAA
1 AACCCG--A
3809273 AACCCGA
1 AACCCGA
3809280 AACCTCTGA
1 AACC-C-GA
3809289 AA-CCGA
1 AACCCGA
* *
3809295 ACTCCCGTTC
1 A-ACCCG--A
3809305 AACCCGA
1 AACCCGA
3809312 AA-CCGA
1 AACCCGA
3809318 AACCCGA
1 AACCCGA
*
3809325 AACCAGA
1 AACCCGA
3809332 AACTCCGAA
1 AAC-CCG-A
3809341 ATATCCCGA
1 A-A-CCCGA
*
3809350 AACCGGA
1 AACCCGA
3809357 AACCCGA
1 AACCCGA
3809364 AACCCGAA
1 AACCCG-A
3809372 AACCCGGA
1 AACCC-GA
*
3809380 CACCCGA
1 AACCCGA
3809387 AACCCGA
1 AACCCGA
3809394 AA-CCGA
1 AACCCGA
3809400 AACCCGA
1 AACCCGA
3809407 AA--C-A
1 AACCCGA
3809411 AACCCTGGA
1 AACCC--GA
3809420 AACCCG-
1 AACCCGA
3809426 AACACCGA
1 AAC-CCGA
3809434 CAACCTCGA
1 -AACC-CGA
3809443 AACTCCGA
1 AAC-CCGA
3809451 AACCCGTA
1 AACCCG-A
3809459 TAACCTCG-
1 -AACC-CGA
3809467 AACCCGA
1 AACCCGA
*
3809474 AACCAGA
1 AACCCGA
3809481 AACCCGA
1 AACCCGA
3809488 GAA-CCG-
1 -AACCCGA
*
3809494 ACCCCGGA
1 AACCC-GA
3809502 AATCTCCGAA
1 AA-C-CCG-A
3809512 ATAGCCCGA
1 A-A-CCCGA
3809521 TAACCGCGA
1 -AACC-CGA
3809530 AACCTCGA
1 AACC-CGA
3809538 AACTCCTGGA
1 AAC-CC--GA
3809548 GAATCCCGA
1 -AA-CCCGA
*
3809557 AAACCGA
1 AACCCGA
3809564 AACCCGA
1 AACCCGA
3809571 AACCCGA
1 AACCCGA
3809578 AACCCGA
1 AACCCGA
*
3809585 ACCCCGGTA
1 AACCC-G-A
*
3809594 CATCCCGA
1 -AACCCGA
*
3809602 GAATCCCGTC
1 -AA-CCCG-A
3809612 AACCCGA
1 AACCCGA
*
3809619 AAACCGTA
1 AACCCG-A
*
3809627 AA-CCGC
1 AACCCGA
3809633 AACCCGTA
1 AACCCG-A
3809641 AACCCGGA
1 AACCC-GA
3809649 AACCCGA
1 AACCCGA
3809656 ACACCCGA
1 A-ACCCGA
3809664 AACTCCGA
1 AAC-CCGA
*
3809672 CACCCGGA
1 AACCC-GA
3809680 AACCCTTGA
1 AACCC--GA
3809689 ACACCTCGCTA
1 A-ACC-CG--A
*
3809700 TACCCCGA
1 -AACCCGA
3809708 AACCCGAA
1 AACCCG-A
3809716 TAATCCCG-
1 -AA-CCCGA
3809724 AACCTCGA
1 AACC-CGA
*
3809732 CACCCGA
1 AACCCGA
*
3809739 AGACCCGC
1 A-ACCCGA
3809747 AACCCGGTA
1 AACCC-G-A
3809756 AACCCCGAA
1 AA-CCCG-A
3809765 AACCCGTA
1 AACCCG-A
3809773 AACCTCGA
1 AACC-CGA
3809781 AACCCGA
1 AACCCGA
3809788 AATTCTCTCGA
1 AA--C-C-CGA
3809799 AACCCGA
1 AACCCGA
3809806 GAACCCGA
1 -AACCCGA
3809814 AACCCGGTA
1 AACCC-G-A
3809823 AACCCGA
1 AACCCGA
* *
3809830 TACCTGA
1 AACCCGA
3809837 AACCCGA
1 AACCCGA
*
3809844 AATCCGA
1 AACCCGA
*
3809851 AAACCGA
1 AACCCGA
3809858 AACCCGAA
1 AACCCG-A
3809866 AACCCGTA
1 AACCCG-A
*
3809874 ACCCCGA
1 AACCCGA
3809881 AACCCGA
1 AACCCGA
3809888 AACTCCCGA
1 AA--CCCGA
3809897 AACTCTCGA
1 AAC-C-CGA
3809906 TTAACTTCTCGA
1 --AAC--C-CGA
3809918 AACCCTGTA
1 AACCC-G-A
*
3809927 GACCCGA
1 AACCCGA
*
3809934 AACCCGT
1 AACCCGA
3809941 AACCCGTA
1 AACCCG-A
3809949 AATCCCGA
1 AA-CCCGA
3809957 AACCCGA
1 AACCCGA
3809964 AACCCTGGA
1 AACCC--GA
3809973 AACCC-A
1 AACCCGA
*
3809979 AACCAG-
1 AACCCGA
3809985 AA-CCGTA
1 AACCCG-A
3809992 AACCCGA
1 AACCCGA
3809999 AACCCGA
1 AACCCGA
3810006 AA-CCGA
1 AACCCGA
3810012 AACCCGA
1 AACCCGA
3810019 GAACCCGA
1 -AACCCGA
3810027 AACCCCGA
1 AA-CCCGA
3810035 AACCCGA
1 AACCCGA
3810042 TAACCCGA
1 -AACCCGA
*
3810050 AACCCTA
1 AACCCGA
*
3810057 ATCCGCGA
1 AACC-CGA
3810065 TAACCCGCTA
1 -AACCCG--A
*
3810075 ATCCCGAA
1 AACCCG-A
3810083 AACCCCTTG-
1 AA-CCC--GA
3810092 AACCCTGA
1 AACCC-GA
3810100 AACCCGA
1 AACCCGA
3810107 AACCCGCGA
1 AA-CC-CGA
3810116 ATACCCG-
1 A-ACCCGA
3810123 AACCCGA
1 AACCCGA
*
3810130 AACCCGC
1 AACCCGA
*
3810137 CACCCGA
1 AACCCGA
3810144 AACCCGA
1 AACCCGA
3810151 AACGCCGA
1 AAC-CCGA
3810159 ATACCCGA
1 A-ACCCGA
3810167 AATCCCTGAA
1 AA-CCC-G-A
3810177 AACCCGAGA
1 AACCC--GA
3810186 AGACCCGA
1 A-ACCCGA
3810194 AACCCGAA
1 AACCCG-A
3810202 ATATCCCGGAA
1 A-A-CCC-G-A
3810213 AACCCGA
1 AACCCGA
*
3810220 GACCCGA
1 AACCCGA
3810227 AATCCGGCGTA
1 AA-CC--CG-A
*
3810238 AACGCGA
1 AACCCGA
3810245 AACCCGA
1 AACCCGA
3810252 TAACCCG-
1 -AACCCGA
3810259 AACCCGGA
1 AACCC-GA
3810267 AACCCGAGGA
1 AACCC---GA
3810277 AACCCGGA
1 AACCC-GA
*
3810285 AACCGAGA
1 AACC-CGA
3810293 AGACCGTCGGA
1 A-ACC--C-GA
3810304 AACGCCGAAA
1 AAC-CCG--A
*
3810314 ATACCCGCT
1 A-ACCCG-A
*
3810323 AACCCGC
1 AACCCGA
3810330 AACCCGA
1 AACCCGA
3810337 AACCCGAGA
1 AACCC--GA
3810346 AACCGCGAA
1 AACC-CG-A
3810355 AACCCTTCGAA
1 AA-CC--CG-A
3810366 AACCCGA
1 AACCCGA
3810373 AACCCGA
1 AACCCGA
3810380 AACCCTGA
1 AACCC-GA
*
3810388 TAATTCCTGA
1 -AA--CCCGA
3810398 ATATCGCCGA
1 A-A-C-CCGA
3810408 AACCCTGA
1 AACCC-GA
3810416 AACCCGA
1 AACCCGA
3810423 AACCCTGA
1 AACCC-GA
3810431 AGACGCCGA
1 A-AC-CCGA
*
3810440 CACCTCGA
1 AACC-CGA
3810448 TATACCCGA
1 -A-ACCCGA
3810457 AACCCGA
1 AACCCGA
3810464 AA-CCGA
1 AACCCGA
3810470 GAACCCGAA
1 -AACCCG-A
3810479 ACACCGCGTA
1 A-ACC-CG-A
3810489 AACCCGA
1 AACCCGA
3810496 AACCCTGA
1 AACCC-GA
3810504 AA-CCGA
1 AACCCGA
*
3810510 ACCGCCGGA
1 AAC-CC-GA
*
3810519 ACCCCGGA
1 AACCC-GA
*
3810527 ACCCCGA
1 AACCCGA
3810534 AACCCGA
1 AACCCGA
3810541 GAACCCGCA
1 -AACCCG-A
*
3810550 ATCCCGA
1 AACCCGA
3810557 AACCCGA
1 AACCCGA
3810564 AACCCGGGA
1 AACCC--GA
*
3810573 GACCCCGA
1 -AACCCGA
*
3810581 AGCCTCGGA
1 AACC-C-GA
*
3810590 CACCCGA
1 AACCCGA
3810597 AACCTCTGA
1 AACC-C-GA
3810606 AACCCCGA
1 AA-CCCGA
3810614 AACCCGA
1 AACCCGA
3810621 AACCTCGTA
1 AACC-CG-A
3810630 AACGCCGGA
1 AAC-CC-GA
3810639 AACCGCGA
1 AACC-CGA
3810647 AACCCAGA
1 AACCC-GA
*
3810655 ACCCCGA
1 AACCCGA
3810662 GAACCTCGA
1 -AACC-CGA
3810671 A
1 A
3810672 GACTGGCGGA
Statistics
Matches: 2042, Mismatches: 147, Indels: 655
0.72 0.05 0.23
Matches are distributed among these distances:
4 5 0.00
5 6 0.00
6 120 0.06
7 752 0.37
8 595 0.29
9 333 0.16
10 140 0.07
11 65 0.03
12 23 0.01
14 3 0.00
ACGTcount: A:0.38, C:0.39, G:0.16, T:0.07
Consensus pattern (7 bp):
AACCCGA
Found at i:3809531 original size:87 final size:80
Alignment explanation
Indices: 3809305--3809580 Score: 190
Period size: 82 Copynumber: 3.3 Consensus size: 80
3809295 ACTCCCGTTC
* *
3809305 AACCCGAAACCGAAACCCGAAACCAGAAACTCCGAAATATCCCGAA-ACCGGA-AACC-CGAAAC
1 AACCCGAAACCGAAACCCGAAA-C--AAACCCCGGAA-A-CCCGAACACC-GACAACCGCGAAAC
* *
3809367 C-CGAAAACCCGGA-CACC-CG
60 CTCG-AAACCCGTATAACCTCG
* *
3809386 AAACCCGAAACCGAAACCCGAAACAAACCCTGGAAACCCGAACACCGACAACCTCGAAA-CTCCG
1 -AACCCGAAACCGAAACCCGAAACAAACCCCGGAAACCCGAACACCGACAACCGCGAAACCT-CG
3809450 AAACCCGTATAACCTCG
64 AAACCCGTATAACCTCG
** * *
3809467 AACCCGAAACCAGAAACCCGAGAACCGACCCCGGAAATCTCCGAAATAGCCCGATAACCGCGAAA
1 AACCCGAAACC-GAAACCCGA-AACAAACCCCGGAAA-C-CCG-AACA--CCGACAACCGCGAAA
* *
3809532 CCTCGAAACTCCTGGAGAATCC-CG
59 CCTCGAAAC-CC-GTATAA-CCTCG
*
3809556 AAAACCGAAACCCGAAACCCGAAAC
1 -AACCCGAAA-CCGAAACCCGAAAC
3809581 CCGAACCCCG
Statistics
Matches: 160, Mismatches: 14, Indels: 33
0.77 0.07 0.16
Matches are distributed among these distances:
77 8 0.05
78 9 0.06
79 21 0.13
80 16 0.10
81 12 0.08
82 34 0.21
83 1 0.01
84 3 0.02
85 3 0.02
87 19 0.12
88 4 0.03
89 9 0.06
90 19 0.12
91 2 0.01
ACGTcount: A:0.41, C:0.37, G:0.16, T:0.06
Consensus pattern (80 bp):
AACCCGAAACCGAAACCCGAAACAAACCCCGGAAACCCGAACACCGACAACCGCGAAACCTCGAA
ACCCGTATAACCTCG
Found at i:3809842 original size:23 final size:24
Alignment explanation
Indices: 3809798--3810054 Score: 85
Period size: 23 Copynumber: 10.9 Consensus size: 24
3809788 AATTCTCTCG
3809798 AAACCCGAGAACCCGAAACCCGGT
1 AAACCCGAGAACCCGAAACCCGGT
* *
3809822 AAACCCGA-TACCTGAAACCC-G-
1 AAACCCGAGAACCCGAAACCCGGT
* * *
3809843 AAATCCGA-AAACCGAAACCC-GA
1 AAACCCGAGAACCCGAAACCCGGT
*
3809865 AAACCCGTA-ACCCCGAAACCC-G-
1 AAACCCG-AGAACCCGAAACCCGGT
3809887 AAACTCCCGA-AACTCTCGATTAACTTCTC-G-
1 AAA--CCCGAGAAC-C-CGA--AAC--C-CGGT
3809917 AAACCCTGTAG-ACCCGAAACCC-GT
1 AAACCC-G-AGAACCCGAAACCCGGT
3809941 -AACCCGTA-AATCCCGAAACCC-G-
1 AAACCCG-AGAA-CCCGAAACCCGGT
*
3809963 AAACCCTG-GAAACCC-AAACCAGAACCGT
1 AAACCC-GAG-AACCCGAAACC----CGGT
3809991 AAACCCGA-AACCCGAAA-CC-G-
1 AAACCCGAGAACCCGAAACCCGGT
*
3810011 AAACCCGAGAACCCGAAACCCCG-
1 AAACCCGAGAACCCGAAACCCGGT
*
3810034 AAACCCGATAACCCGAAACCC
1 AAACCCGAGAACCCGAAACCC
3810055 TAATCCGCGA
Statistics
Matches: 190, Mismatches: 11, Indels: 65
0.71 0.04 0.24
Matches are distributed among these distances:
20 8 0.04
21 27 0.14
22 22 0.12
23 72 0.38
24 17 0.09
25 3 0.02
26 10 0.05
27 8 0.04
28 12 0.06
29 3 0.02
30 8 0.04
ACGTcount: A:0.39, C:0.39, G:0.14, T:0.08
Consensus pattern (24 bp):
AAACCCGAGAACCCGAAACCCGGT
Found at i:3810077 original size:18 final size:17
Alignment explanation
Indices: 3810030--3810087 Score: 54
Period size: 17 Copynumber: 3.6 Consensus size: 17
3810020 AACCCGAAAC
*
3810030 CCCG-AAACCCGATAA-
1 CCCGAAAACCCGCTAAT
3810045 CCCG-AAA-CC-CTAAT
1 CCCGAAAACCCGCTAAT
*
3810059 CCGCGATAACCCGCTAAT
1 CC-CGAAAACCCGCTAAT
3810077 CCCGAAAACCC
1 CCCGAAAACCC
3810088 CTTGAACCCT
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
13 3 0.09
14 4 0.11
15 9 0.26
16 2 0.06
17 10 0.29
18 7 0.20
ACGTcount: A:0.34, C:0.43, G:0.12, T:0.10
Consensus pattern (17 bp):
CCCGAAAACCCGCTAAT
Found at i:3810224 original size:26 final size:27
Alignment explanation
Indices: 3810161--3810229 Score: 81
Period size: 26 Copynumber: 2.6 Consensus size: 27
3810151 AACGCCGAAT
*
3810161 ACCCGAAATCCCTGAAA-A-CCCGAGAAG
1 ACCCGAAA-CCC-GAAATATCCCGAGAAA
3810188 ACCCGAAACCCGAAATATCCCG-GAAA
1 ACCCGAAACCCGAAATATCCCGAGAAA
*
3810214 ACCCGAGACCCGAAAT
1 ACCCGAAACCCGAAAT
3810230 CCGGCGTAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
25 4 0.11
26 22 0.58
27 12 0.32
ACGTcount: A:0.41, C:0.35, G:0.17, T:0.07
Consensus pattern (27 bp):
ACCCGAAACCCGAAATATCCCGAGAAA
Found at i:3810533 original size:38 final size:39
Alignment explanation
Indices: 3810451--3810545 Score: 106
Period size: 38 Copynumber: 2.4 Consensus size: 39
3810441 ACCTCGATAT
*
3810451 ACCCGAAACCCGAAACCGAGAACCCGAAACACCGCGTAA
1 ACCCGAAACCCGAAACCGAGAACCCGAAACACCGCGGAA
* *
3810490 ACCCGAAACCCTGAAACCGA-ACCGCCGGAAC-CC-CGGAA
1 ACCCGAAACCC-GAAACCGAGAAC-CCGAAACACCGCGGAA
*
3810528 CCCCGAAACCCGAGAACC
1 ACCCGAAACCCGA-AACC
3810546 CGCAATCCCG
Statistics
Matches: 49, Mismatches: 4, Indels: 7
0.82 0.07 0.12
Matches are distributed among these distances:
37 2 0.04
38 18 0.37
39 15 0.31
40 14 0.29
ACGTcount: A:0.37, C:0.42, G:0.19, T:0.02
Consensus pattern (39 bp):
ACCCGAAACCCGAAACCGAGAACCCGAAACACCGCGGAA
Found at i:3810581 original size:17 final size:17
Alignment explanation
Indices: 3810555--3810669 Score: 75
Period size: 16 Copynumber: 7.0 Consensus size: 17
3810545 CCGCAATCCC
3810555 GAAA-CCCGAAACC-CGG
1 GAAACCCCGAAACCTC-G
* *
3810571 GAGACCCCGAAGCCTCG
1 GAAACCCCGAAACCTCG
* *
3810588 GACA-CCCGAAACCTCT
1 GAAACCCCGAAACCTCG
3810604 GAAACCCCGAAACC-C-
1 GAAACCCCGAAACCTCG
*
3810619 GAAACCTCGTAAACGC-CG
1 GAAACCCCG-AAAC-CTCG
* *
3810637 GAAACCGCGAAACC-CA
1 GAAACCCCGAAACCTCG
3810653 G-AACCCCGAGAACCTCG
1 GAAACCCCGA-AACCTCG
3810670 AAGACTGGCG
Statistics
Matches: 80, Mismatches: 11, Indels: 15
0.75 0.10 0.14
Matches are distributed among these distances:
15 15 0.19
16 28 0.35
17 28 0.35
18 9 0.11
ACGTcount: A:0.34, C:0.40, G:0.21, T:0.05
Consensus pattern (17 bp):
GAAACCCCGAAACCTCG
Found at i:3810619 original size:24 final size:24
Alignment explanation
Indices: 3810594--3810671 Score: 72
Period size: 24 Copynumber: 3.2 Consensus size: 24
3810584 CTCGGACACC
3810594 CGAAACCTCTGAAACCCCGAAACC-
1 CGAAACCTC-GAAACCCCGAAACCG
*
3810618 CGAAACCTCGTAAACGCCGGAAACCG
1 CGAAACCTCG-AAAC-CCCGAAACCG
*
3810644 CGAAACC-C-AGAACCCCGAGAACCT
1 CGAAACCTCGA-AACCCCGA-AACCG
3810668 CGAA
1 CGAA
3810672 GACTGGCGGA
Statistics
Matches: 46, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
23 6 0.13
24 24 0.52
25 9 0.20
26 7 0.15
ACGTcount: A:0.37, C:0.38, G:0.18, T:0.06
Consensus pattern (24 bp):
CGAAACCTCGAAACCCCGAAACCG
Found at i:3811005 original size:16 final size:15
Alignment explanation
Indices: 3810984--3811067 Score: 77
Period size: 14 Copynumber: 5.5 Consensus size: 15
3810974 CGGGGATAGA
3810984 CCGAAACCGCGAAATC
1 CCGAAACC-CGAAATC
*
3811000 CCGAAACCCGAGGCAT-
1 CCGAAACCCGA--AATC
3811016 CCG-AACTCCGAAAATC
1 CCGAAAC-CCG-AAATC
3811032 CCGAAACCCGAAA-C
1 CCGAAACCCGAAATC
*
3811046 CCGCAACCCGAAA-C
1 CCGAAACCCGAAATC
3811060 CCGAAACC
1 CCGAAACC
3811068 TCGTAAACCG
Statistics
Matches: 58, Mismatches: 4, Indels: 14
0.76 0.05 0.18
Matches are distributed among these distances:
14 21 0.36
15 11 0.19
16 20 0.34
17 6 0.10
ACGTcount: A:0.37, C:0.42, G:0.17, T:0.05
Consensus pattern (15 bp):
CCGAAACCCGAAATC
Found at i:3811041 original size:7 final size:7
Alignment explanation
Indices: 3811031--3811067 Score: 65
Period size: 7 Copynumber: 5.3 Consensus size: 7
3811021 CTCCGAAAAT
3811031 CCCGAAA
1 CCCGAAA
3811038 CCCGAAA
1 CCCGAAA
*
3811045 CCCGCAA
1 CCCGAAA
3811052 CCCGAAA
1 CCCGAAA
3811059 CCCGAAA
1 CCCGAAA
3811066 CC
1 CC
3811068 TCGTAAACCG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.38, C:0.49, G:0.14, T:0.00
Consensus pattern (7 bp):
CCCGAAA
Found at i:3811311 original size:7 final size:7
Alignment explanation
Indices: 3811291--3811363 Score: 74
Period size: 8 Copynumber: 9.7 Consensus size: 7
3811281 AAACGCCGAT
3811291 AAACCCG
1 AAACCCG
3811298 TAAACCCG
1 -AAACCCG
3811306 AAACCCG
1 AAACCCG
*
3811313 CGAACCCG
1 -AAACCCG
3811321 AGAACCCG
1 A-AACCCG
*
3811329 AAACCGG
1 AAACCCG
*
3811336 AAGACCTG
1 AA-ACCCG
3811344 AGAACCCG
1 A-AACCCG
3811352 AAACCCG
1 AAACCCG
3811359 AAACC
1 AAACC
3811364 GGCAAGCCTC
Statistics
Matches: 56, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
7 25 0.45
8 30 0.54
9 1 0.02
ACGTcount: A:0.40, C:0.38, G:0.19, T:0.03
Consensus pattern (7 bp):
AAACCCG
Found at i:3811380 original size:30 final size:31
Alignment explanation
Indices: 3811292--3811365 Score: 98
Period size: 30 Copynumber: 2.4 Consensus size: 31
3811282 AACGCCGATA
* * *
3811292 AACCCGTAAACCCGAA-ACCCGCGAACCCGAG
1 AACCCG-AAACCGGAAGACCTGAGAACCCGAG
3811323 AACCCGAAACCGGAAGACCTGAGAACCCGA-
1 AACCCGAAACCGGAAGACCTGAGAACCCGAG
3811353 AACCCGAAACCGG
1 AACCCGAAACCGG
3811366 CAAGCCTCGA
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
30 21 0.54
31 18 0.46
ACGTcount: A:0.38, C:0.38, G:0.22, T:0.03
Consensus pattern (31 bp):
AACCCGAAACCGGAAGACCTGAGAACCCGAG
Found at i:3811465 original size:8 final size:7
Alignment explanation
Indices: 3811452--3811534 Score: 51
Period size: 8 Copynumber: 10.4 Consensus size: 7
3811442 GCCGTAAATC
3811452 CCCGAAGA
1 CCCGAA-A
3811460 CCCGAAA
1 CCCGAAA
3811467 CCCGAAA
1 CCCGAAA
3811474 GCCCGAAA
1 -CCCGAAA
3811482 GCTCCGAAAA
1 -C-CCG-AAA
3811492 CCGCGAAGA
1 CC-CGAA-A
3811501 CCCGATAA
1 CCCGA-AA
*
3811509 CCCCAAA
1 CCCGAAA
3811516 CGGCCCGAAA
1 ---CCCGAAA
3811526 CCC-AAA
1 CCCGAAA
3811532 CCC
1 CCC
3811535 CTAGAACCCC
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
6 6 0.09
7 13 0.20
8 26 0.41
9 10 0.16
10 9 0.14
ACGTcount: A:0.37, C:0.42, G:0.18, T:0.02
Consensus pattern (7 bp):
CCCGAAA
Found at i:3811505 original size:17 final size:15
Alignment explanation
Indices: 3811452--3811516 Score: 58
Period size: 17 Copynumber: 4.1 Consensus size: 15
3811442 GCCGTAAATC
*
3811452 CCCGAAGACCCGAAA
1 CCCGAAAACCCGAAA
*
3811467 CCCGAAAGCCCGAAA
1 CCCGAAAACCCGAAA
3811482 GCTCCGAAAACCGCGAAGA
1 -C-CCGAAAACC-CGAA-A
* *
3811501 CCCGATAACCCCAAA
1 CCCGAAAACCCGAAA
3811516 C
1 C
3811517 GGCCCGAAAC
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
15 15 0.37
16 4 0.10
17 16 0.39
18 5 0.12
19 1 0.02
ACGTcount: A:0.38, C:0.40, G:0.18, T:0.03
Consensus pattern (15 bp):
CCCGAAAACCCGAAA
Found at i:3811790 original size:8 final size:8
Alignment explanation
Indices: 3811777--3811899 Score: 62
Period size: 8 Copynumber: 15.0 Consensus size: 8
3811767 ACACCCCACG
3811777 AACCCCAA
1 AACCCCAA
*
3811785 AACCCCAG
1 AACCCCAA
3811793 AACCCC-A
1 AACCCCAA
3811800 AACGACCC--
1 AAC--CCCAA
3811808 AA-CCC-A
1 AACCCCAA
*
3811814 AACCCCCA
1 AACCCCAA
3811822 AACCCCAGA
1 AACCCCA-A
3811831 AACCCGCAGA
1 AACCC-CA-A
*
3811841 TAACCCC-C
1 -AACCCCAA
3811849 AACCCCAAA
1 AACCCC-AA
3811858 GAGACCCC-A
1 -A-ACCCCAA
3811867 AACGCCCAA
1 AAC-CCCAA
*
3811876 AACCCCGA
1 AACCCCAA
*
3811884 GACCCCAA
1 AACCCCAA
3811892 AACCCCAA
1 AACCCCAA
3811900 GAGCCCCCCA
Statistics
Matches: 92, Mismatches: 9, Indels: 28
0.71 0.07 0.22
Matches are distributed among these distances:
5 3 0.03
6 2 0.02
7 14 0.15
8 43 0.47
9 14 0.15
10 6 0.07
11 10 0.11
ACGTcount: A:0.41, C:0.50, G:0.08, T:0.01
Consensus pattern (8 bp):
AACCCCAA
Found at i:3812079 original size:8 final size:7
Alignment explanation
Indices: 3812061--3812150 Score: 63
Period size: 9 Copynumber: 11.1 Consensus size: 7
3812051 CTCCATGAAT
3812061 CCCCAAGA
1 CCCCAA-A
3812069 CCCCATAA
1 CCCCA-AA
3812077 CCCCAAA
1 CCCCAAA
3812084 CCGCCAGAA
1 CC-CCA-AA
3812093 CCCCTGAAA
1 CCCC--AAA
3812102 TCCCTCAAA
1 -CCC-CAAA
3812111 CCCCAAGCA
1 CCCCAA--A
3812120 CCCCAAA
1 CCCCAAA
3812127 CCCTCAAAA
1 CCC-C-AAA
3812136 CCCCAAA
1 CCCCAAA
*
3812143 CGCCAAA
1 CCCCAAA
3812150 C
1 C
3812151 GCCCCGACCC
Statistics
Matches: 70, Mismatches: 1, Indels: 23
0.74 0.01 0.24
Matches are distributed among these distances:
7 21 0.30
8 21 0.30
9 23 0.33
10 4 0.06
11 1 0.01
ACGTcount: A:0.38, C:0.50, G:0.07, T:0.06
Consensus pattern (7 bp):
CCCCAAA
Found at i:3812082 original size:16 final size:15
Alignment explanation
Indices: 3812061--3812148 Score: 63
Period size: 16 Copynumber: 5.4 Consensus size: 15
3812051 CTCCATGAAT
3812061 CCCCAAGACCCCATAA
1 CCCCAAGACCCCA-AA
3812077 CCCCAA-ACCGCCAGAA
1 CCCCAAGACC-CCA-AA
3812093 CCCCTGAA-ATCCCTCAAA
1 CCCC--AAGA-CCC-CAAA
3812111 CCCCAAGCACCCCAAA
1 CCCCAAG-ACCCCAAA
*
3812127 CCCTCAAAACCCCAAA
1 CCC-CAAGACCCCAAA
*
3812143 CGCCAA
1 CCCCAA
3812149 ACGCCCCGAC
Statistics
Matches: 61, Mismatches: 3, Indels: 17
0.75 0.04 0.21
Matches are distributed among these distances:
15 6 0.10
16 34 0.56
17 6 0.10
18 11 0.18
19 4 0.07
ACGTcount: A:0.38, C:0.50, G:0.07, T:0.06
Consensus pattern (15 bp):
CCCCAAGACCCCAAA
Done.