Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167915.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_18, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 20765110
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 90000 characters in sequence are not A, C, G, or T
File 12 of 117
Found at i:3461392 original size:24 final size:24
Alignment explanation
Indices: 3461356--3461402 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
3461346 ATTTTGGAGA
*
3461356 TGAGGAGGATGGTGTTGGTGGTGC
1 TGAGGAGGATGGTGGTGGTGGTGC
*
3461380 TGAGGAGGGTGGTGGTGGTGGTG
1 TGAGGAGGATGGTGGTGGTGGTG
3461403 GAGATGACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.11, C:0.02, G:0.60, T:0.28
Consensus pattern (24 bp):
TGAGGAGGATGGTGGTGGTGGTGC
Found at i:3462844 original size:23 final size:22
Alignment explanation
Indices: 3462794--3462844 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 22
3462784 ATAATTATTG
3462794 TAATAATGAGATTAAATATTAA
1 TAATAATGAGATTAAATATTAA
*
3462816 TTATAATAGAAGATTAAA-ATTAA
1 TAATAAT-G-AGATTAAATATTAA
3462839 TAATAA
1 TAATAA
3462845 AAAAATATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 6 0.24
23 11 0.44
24 8 0.32
ACGTcount: A:0.57, C:0.00, G:0.08, T:0.35
Consensus pattern (22 bp):
TAATAATGAGATTAAATATTAA
Found at i:3466728 original size:60 final size:60
Alignment explanation
Indices: 3466655--3466771 Score: 207
Period size: 60 Copynumber: 1.9 Consensus size: 60
3466645 TATGCTTTTA
* *
3466655 AGCAGAGCTATGCAAACTATAGGTGCTGAGAGTTTCAGACGTTAATATTGCAGTAAGGCT
1 AGCAGAGCTATGCAAACTATAGATGCTGAGAGTTTCAGACGTTAATATTACAGTAAGGCT
*
3466715 AGCAGAGCTATGCAAACTATCGATGCTGAGAGTTTCAGACGTTAATATTACAGTAAG
1 AGCAGAGCTATGCAAACTATAGATGCTGAGAGTTTCAGACGTTAATATTACAGTAAG
3466772 ACTTACTTCC
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
60 54 1.00
ACGTcount: A:0.33, C:0.15, G:0.25, T:0.26
Consensus pattern (60 bp):
AGCAGAGCTATGCAAACTATAGATGCTGAGAGTTTCAGACGTTAATATTACAGTAAGGCT
Found at i:3476029 original size:3 final size:3
Alignment explanation
Indices: 3476021--3476045 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
3476011 TTTTCTCGTT
3476021 GGA GGA GGA GGA GGA GGA GGA GGA G
1 GGA GGA GGA GGA GGA GGA GGA GGA G
3476046 ACAGCATCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.68, T:0.00
Consensus pattern (3 bp):
GGA
Found at i:3477472 original size:17 final size:20
Alignment explanation
Indices: 3477424--3477463 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
3477414 TCCAAATGAT
3477424 ATAATT-TA-AAATTTTAATA
1 ATAATTATATAAA-TTTAATA
3477443 ATAATTATATAAATTTAATA
1 ATAATTATATAAATTTAATA
3477463 A
1 A
3477464 AATAATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.32
20 10 0.53
21 3 0.16
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
ATAATTATATAAATTTAATA
Found at i:3477476 original size:20 final size:20
Alignment explanation
Indices: 3477430--3477474 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
3477420 TGATATAATT
* *
3477430 TAAAATTTTAATAATAATTA
1 TAAAAATTTAATAATAATAA
*
3477450 TATAAATTTAATAA-AATAA
1 TAAAAATTTAATAATAATAA
3477469 TAAAAA
1 TAAAAA
3477475 ATATATTTTA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
TAAAAATTTAATAATAATAA
Found at i:3477500 original size:30 final size:30
Alignment explanation
Indices: 3477466--3477525 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
3477456 TTTAATAAAA
*
3477466 TAATAAAAAATA-TATTTTATATTTTTATAT
1 TAATAAAAAATATTATTGTA-ATTTTTATAT
* *
3477496 TAATATAAATTATTATTGTAATTTTTATAT
1 TAATAAAAAATATTATTGTAATTTTTATAT
3477526 AAAATATAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 20 0.77
31 6 0.23
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (30 bp):
TAATAAAAAATATTATTGTAATTTTTATAT
Found at i:3480983 original size:43 final size:43
Alignment explanation
Indices: 3480922--3481008 Score: 138
Period size: 43 Copynumber: 2.0 Consensus size: 43
3480912 CATATATATA
* * *
3480922 TTGATGAATGAATCAGTTGATCATGACATGCAAATTAATTAAG
1 TTGATGAATGAATCAGTTGATCACGACATGCAAACTAACTAAG
*
3480965 TTGATGAATGAATCAGTTGATCACGACGTGCAAACTAACTAAG
1 TTGATGAATGAATCAGTTGATCACGACATGCAAACTAACTAAG
3481008 T
1 T
3481009 CACCATTATT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.30
Consensus pattern (43 bp):
TTGATGAATGAATCAGTTGATCACGACATGCAAACTAACTAAG
Found at i:3481652 original size:13 final size:13
Alignment explanation
Indices: 3481634--3481663 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
3481624 ATACTGATAA
*
3481634 AAACAAATCTATT
1 AAACAAATCTATC
3481647 AAACAAATCTATC
1 AAACAAATCTATC
3481660 AAAC
1 AAAC
3481664 TTTTTATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.57, C:0.20, G:0.00, T:0.23
Consensus pattern (13 bp):
AAACAAATCTATC
Found at i:3482157 original size:25 final size:26
Alignment explanation
Indices: 3482114--3482164 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
3482104 CCCGTATGTC
* *
3482114 TTTTAATTTATTTATTATATATTAAT
1 TTTTAATTTATTAAATATATATTAAT
*
3482140 TTTTAATTT-TTAAATATATCTTAAT
1 TTTTAATTTATTAAATATATATTAAT
3482165 GGGATTCTGT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 13 0.59
26 9 0.41
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (26 bp):
TTTTAATTTATTAAATATATATTAAT
Found at i:3482702 original size:3 final size:3
Alignment explanation
Indices: 3482694--3482752 Score: 104
Period size: 3 Copynumber: 20.3 Consensus size: 3
3482684 TTAACTTGTG
3482694 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-A ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
3482741 A-A ATA ATA ATA A
1 ATA ATA ATA ATA A
3482753 AAAGAATCTA
Statistics
Matches: 54, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
2 4 0.07
3 50 0.93
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:3494748 original size:13 final size:13
Alignment explanation
Indices: 3494724--3494760 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 13
3494714 TATTTATATA
3494724 TTTATT-AATAAT
1 TTTATTAAATAAT
3494736 TTTATTAAATAAT
1 TTTATTAAATAAT
*
3494749 TATA-TAAATAAT
1 TTTATTAAATAAT
3494761 ATATTTTATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 14 0.61
13 9 0.39
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (13 bp):
TTTATTAAATAAT
Found at i:3502288 original size:25 final size:25
Alignment explanation
Indices: 3502236--3502288 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
3502226 ATAATTAATG
* * *
3502236 TAATTATTATTAAAAAAATTTATTA
1 TAATTACTATTAAAAAAATCTATGA
*
3502261 TAATTACTATTAAAATAATCTATGA
1 TAATTACTATTAAAAAAATCTATGA
3502286 TAA
1 TAA
3502289 AAAATTTATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (25 bp):
TAATTACTATTAAAAAAATCTATGA
Found at i:3508625 original size:98 final size:97
Alignment explanation
Indices: 3508453--3508631 Score: 286
Period size: 98 Copynumber: 1.8 Consensus size: 97
3508443 AAGTCTTGAG
*
3508453 GTTGTGCTTTCGATTAAGGTTCCATTTGTTTCCTGGAGAAAATATATCCTCAGGAATAACGTGGA
1 GTTGTGCTTTCGATTAAGGTCCCATTTGTTTCCTGGAGAAAATATATCCTCAGGAATAACGTGGA
*
3508518 ATCGGAATTCACGAAAGGCGCTTTAGTTTTTAC
66 AGCGGAATTCAC-AAAGGCGCTTTAGTTTTTAC
* * * *
3508551 GTTGTGCTTTCGGTTACGGTCCCATTTGTTTCCTGGTGAAAATATATCCTCTGGAATAACGTGGA
1 GTTGTGCTTTCGATTAAGGTCCCATTTGTTTCCTGGAGAAAATATATCCTCAGGAATAACGTGGA
*
3508616 AGCGTAATTCACAAAG
66 AGCGGAATTCACAAAG
3508632 TCAACTTTCT
Statistics
Matches: 74, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
97 4 0.05
98 70 0.95
ACGTcount: A:0.26, C:0.17, G:0.23, T:0.34
Consensus pattern (97 bp):
GTTGTGCTTTCGATTAAGGTCCCATTTGTTTCCTGGAGAAAATATATCCTCAGGAATAACGTGGA
AGCGGAATTCACAAAGGCGCTTTAGTTTTTAC
Found at i:3511553 original size:9 final size:9
Alignment explanation
Indices: 3511539--3511564 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
3511529 TCTGAAGAAA
3511539 GTATGTCTG
1 GTATGTCTG
3511548 GTATGTCTG
1 GTATGTCTG
3511557 GTATGTCT
1 GTATGTCT
3511565 ATGCCTAAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.12, C:0.12, G:0.31, T:0.46
Consensus pattern (9 bp):
GTATGTCTG
Found at i:3523800 original size:2 final size:2
Alignment explanation
Indices: 3523793--3523825 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
3523783 GTTGGGATTT
*
3523793 GA GA GA GA GA GA GA GA GA GA AA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
3523826 GATGAAGCAG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
GA
Found at i:3525973 original size:14 final size:15
Alignment explanation
Indices: 3525944--3525977 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
3525934 AAATTTTATT
*
3525944 AATATTTTTATTAAA
1 AATATTTATATTAAA
3525959 AATATTTAT-TTAAA
1 AATATTTATATTAAA
3525973 AATAT
1 AATAT
3525978 AAATTTATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
AATATTTATATTAAA
Found at i:3527229 original size:26 final size:26
Alignment explanation
Indices: 3527187--3527237 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
3527177 CGAAAATATT
*
3527187 ATTTATTATTAATTAAAGTATAAAAAC
1 ATTTATTATTAATTAAAAT-TAAAAAC
*
3527214 ATTTTTTA-TAATTAAAATTAAAAA
1 ATTTATTATTAATTAAAATTAAAAA
3527238 ATTGAAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 6 0.27
26 9 0.41
27 7 0.32
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (26 bp):
ATTTATTATTAATTAAAATTAAAAAC
Found at i:3530701 original size:6 final size:6
Alignment explanation
Indices: 3530677--3530741 Score: 55
Period size: 6 Copynumber: 11.0 Consensus size: 6
3530667 AAATATTTTT
** * *
3530677 TATTATA TATTTA -ATTTTA TATTTA TAAATA TTTTTA TATTTA T-TTAA
1 TATT-TA TATTTA TA-TTTA TATTTA TATTTA TATTTA TATTTA TATTTA
3530725 T-TTTA TATTTA TATTTA
1 TATTTA TATTTA TATTTA
3530742 AAAATAATGT
Statistics
Matches: 47, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
5 9 0.19
6 33 0.70
7 5 0.11
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (6 bp):
TATTTA
Found at i:3530703 original size:18 final size:18
Alignment explanation
Indices: 3530671--3530742 Score: 85
Period size: 18 Copynumber: 4.1 Consensus size: 18
3530661 CATAAAAAAT
*
3530671 ATTTTTTATTATATATTTA
1 ATTTTATATT-TATATTTA
**
3530690 ATTTTATATTTATAAATA
1 ATTTTATATTTATATTTA
*
3530708 TTTTTATA-TT-TATTTA
1 ATTTTATATTTATATTTA
3530724 ATTTTATATTTATATTTA
1 ATTTTATATTTATATTTA
3530742 A
1 A
3530743 AAATAATGTT
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
16 11 0.25
17 4 0.09
18 20 0.45
19 9 0.20
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
ATTTTATATTTATATTTA
Found at i:3530727 original size:34 final size:36
Alignment explanation
Indices: 3530667--3530737 Score: 119
Period size: 34 Copynumber: 2.0 Consensus size: 36
3530657 TATACATAAA
3530667 AAATATTTTTTATTATATATTTAATTTTATATTTAT
1 AAATATTTTTTATTATATATTTAATTTTATATTTAT
*
3530703 AAATA-TTTTTA-TATTTATTTAATTTTATATTTAT
1 AAATATTTTTTATTATATATTTAATTTTATATTTAT
3530737 A
1 A
3530738 TTTAAAAATA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
34 23 0.68
35 6 0.18
36 5 0.15
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (36 bp):
AAATATTTTTTATTATATATTTAATTTTATATTTAT
Found at i:3530730 original size:16 final size:16
Alignment explanation
Indices: 3530674--3530736 Score: 72
Period size: 16 Copynumber: 3.8 Consensus size: 16
3530664 AAAAAATATT
*
3530674 TTTTATTATATATTTAA
1 TTTTA-TATTTATTTAA
* *
3530691 TTTTATATTTATAAATAT
1 TTTTATATTTAT--TTAA
3530709 TTTTATATTTATTTAA
1 TTTTATATTTATTTAA
3530725 TTTTATATTTAT
1 TTTTATATTTAT
3530737 ATTTAAAAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
16 20 0.51
17 5 0.13
18 14 0.36
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TTTTATATTTATTTAA
Found at i:3534926 original size:57 final size:57
Alignment explanation
Indices: 3534850--3535170 Score: 175
Period size: 57 Copynumber: 5.5 Consensus size: 57
3534840 AAATATATTC
*
3534850 TCAAC-TTTTCTTTAAAGTATATTTTTAAAATTTGACCTGCAAGA-AAAATTAATATTT
1 TCAACTTTTTC-TTAAAGTATATTTTTAAAATTTGACCTGCAA-ATAAAATTAATACTT
* * * * * *
3534907 TCAATTTTTTCTTAGAGTATATTTTTGAAATTTGATCTTCAAATAAAATTGATACTT
1 TCAACTTTTTCTTAAAGTATATTTTTAAAATTTGACCTGCAAATAAAATTAATACTT
* * * * ** ** * * *
3534964 TCAACTTTTTCTTAATGTATTTTTTTTGTTTGAAATTTTTATTTTTAGAGAAAATTAACACTT
1 TCAACTTTTTCTTAAAGTA----TATT-TTT-AAAATTTGACCTGCAAATAAAATTAATACTT
* * * * * * *
3535027 TCAACTTTTCCTTAAAGTTTTTTTTTTTTAAATTTGATCTTG-AAAAAAAATTGATACTT
1 TCAACTTTTTCTTAAAG--TATATTTTTAAAATTTGA-CCTGCAAATAAAATTAATACTT
* * * * * *
3535086 TCAAC-TTTTCTTTAAAATGTTTTTTTTTTAAATTTGATCTTCAAGA-AAAATTGATACTT
1 TCAACTTTTTC-TT-AAA-GTATATTTTTAAAATTTGACCTGCAA-ATAAAATTAATACTT
* *
3535145 TCAACTTTTTTTTAAAGTATTTTTTT
1 TCAACTTTTTCTTAAAGTATATTTTT
3535171 TAATTTTTAT
Statistics
Matches: 209, Mismatches: 38, Indels: 34
0.74 0.14 0.12
Matches are distributed among these distances:
56 1 0.00
57 67 0.32
58 13 0.06
59 66 0.32
60 13 0.06
61 8 0.04
62 3 0.01
63 37 0.18
65 1 0.00
ACGTcount: A:0.32, C:0.09, G:0.07, T:0.51
Consensus pattern (57 bp):
TCAACTTTTTCTTAAAGTATATTTTTAAAATTTGACCTGCAAATAAAATTAATACTT
Found at i:3535088 original size:59 final size:59
Alignment explanation
Indices: 3534850--3535171 Score: 283
Period size: 59 Copynumber: 5.5 Consensus size: 59
3534840 AAATATATTC
* * * * * * * * *
3534850 TCAACTTTTCTTTAAAG--TATATTTTTAAAATTTGACCTGCAAGAAAAATTAATATTT
1 TCAACTTTTCCTTAAAGTTTTTTTTTTTTAAATTTGATCTTCAAAAAAAATTGATACTT
* * * * * * *
3534907 TCAATTTTTTCTTAGAG--TATATTTTTGAAATTTGATCTTCAAATAAAATTGATACTT
1 TCAACTTTTCCTTAAAGTTTTTTTTTTTTAAATTTGATCTTCAAAAAAAATTGATACTT
* * * * * * * * *
3534964 TCAACTTTTTCTTAATGTATTTTTTTTGTTTGAAATTTTTATTTTTAGAGAAAATTAACACTT
1 TCAACTTTTCCTTAAAGT-TTTTTTTT-TTT-AAA-TTTGATCTTCAAAAAAAATTGATACTT
*
3535027 TCAACTTTTCCTTAAAGTTTTTTTTTTTTAAATTTGATCTTGAAAAAAAATTGATACTT
1 TCAACTTTTCCTTAAAGTTTTTTTTTTTTAAATTTGATCTTCAAAAAAAATTGATACTT
* * * *
3535086 TCAACTTTTCTTTAAAATGTTTTTTTTTTAAATTTGATCTTCAAGAAAAATTGATACTT
1 TCAACTTTTCCTTAAAGTTTTTTTTTTTTAAATTTGATCTTCAAAAAAAATTGATACTT
** *
3535145 TCAACTTTTTTTTAAAGTATTTTTTTT
1 TCAACTTTTCCTTAAAGTTTTTTTTTT
3535172 AATTTTTATT
Statistics
Matches: 218, Mismatches: 41, Indels: 10
0.81 0.15 0.04
Matches are distributed among these distances:
57 60 0.28
59 98 0.45
60 8 0.04
61 5 0.02
62 11 0.05
63 36 0.17
ACGTcount: A:0.32, C:0.09, G:0.07, T:0.52
Consensus pattern (59 bp):
TCAACTTTTCCTTAAAGTTTTTTTTTTTTAAATTTGATCTTCAAAAAAAATTGATACTT
Found at i:3535240 original size:22 final size:20
Alignment explanation
Indices: 3535208--3535252 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 20
3535198 AAACCTAAAG
3535208 AATGTTTAATTAAATAAATA
1 AATGTTTAATTAAATAAATA
* *
3535228 AATGATTTCAATTTAATCAATA
1 AATG-TTT-AATTAAATAAATA
3535250 AAT
1 AAT
3535253 AAATAAGTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 4 0.19
21 3 0.14
22 14 0.67
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.40
Consensus pattern (20 bp):
AATGTTTAATTAAATAAATA
Found at i:3535255 original size:4 final size:4
Alignment explanation
Indices: 3535246--3535305 Score: 59
Period size: 4 Copynumber: 15.0 Consensus size: 4
3535236 CAATTTAATC
* * * *
3535246 AATA AATA AATA AGTA AAAA AATAA AATA AATA AAT- AATA AGTA AACA
1 AATA AATA AATA AATA AATA AAT-A AATA AATA AATA AATA AATA AATA
*
3535294 AATA GATA AATA
1 AATA AATA AATA
3535306 GGATTAAAAA
Statistics
Matches: 44, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
3 3 0.07
4 37 0.84
5 4 0.09
ACGTcount: A:0.72, C:0.02, G:0.05, T:0.22
Consensus pattern (4 bp):
AATA
Found at i:3535270 original size:16 final size:15
Alignment explanation
Indices: 3535249--3535302 Score: 58
Period size: 15 Copynumber: 3.6 Consensus size: 15
3535239 TTTAATCAAT
3535249 AAATAAATAAGTAAAA
1 AAAT-AATAAGTAAAA
*
3535265 AAATAA-AA-TAAAT
1 AAATAATAAGTAAAA
*
3535278 AAATAATAAGTAAAC
1 AAATAATAAGTAAAA
3535293 AAATAGATAA
1 AAATA-ATAA
3535303 ATAGGATTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
13 10 0.30
14 4 0.12
15 11 0.33
16 8 0.24
ACGTcount: A:0.72, C:0.02, G:0.06, T:0.20
Consensus pattern (15 bp):
AAATAATAAGTAAAA
Found at i:3535296 original size:28 final size:28
Alignment explanation
Indices: 3535246--3535305 Score: 86
Period size: 28 Copynumber: 2.1 Consensus size: 28
3535236 CAATTTAATC
3535246 AATAAATAAATAAGTAAAAAAATAAAATA
1 AATAAATAAATAAGTAAAAAAAT-AAATA
* *
3535275 AATAAAT-AATAAGTAAACAAATAGATA
1 AATAAATAAATAAGTAAAAAAATAAATA
3535302 AATA
1 AATA
3535306 GGATTAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 8 0.28
28 14 0.48
29 7 0.24
ACGTcount: A:0.72, C:0.02, G:0.05, T:0.22
Consensus pattern (28 bp):
AATAAATAAATAAGTAAAAAAATAAATA
Found at i:3546134 original size:132 final size:132
Alignment explanation
Indices: 3545895--3546162 Score: 464
Period size: 132 Copynumber: 2.0 Consensus size: 132
3545885 TTGAGTTTTA
* *
3545895 TGTTAATGAGAGGTTAACTTTGTGTCAATAATTTACTCTTCCTCTTTAGGATTAGTGACTAAGCA
1 TGTTAATGAGAGGTTAACTCTGTGTCAATAATTTACTCTTCCTCTTTAGGATTAGTCACTAAGCA
* *
3545960 GTCTTTATGATTTGTATTCAGTAAGCATTCTTAGGAACATGGATTATAAGTGAATCTTCTGGTTG
66 GTCTTTATGATTTGTATTCAGTAAGCATTCTTAGGAAAATGGATTATAAGTGAATCTTCTGATTG
3546025 TT
131 TT
*
3546027 TGTTAATGAGAGGTTGACTCTGTGTCAATAATTTACTCTTCCTCTTTAGGATTAGTCACTAAGCA
1 TGTTAATGAGAGGTTAACTCTGTGTCAATAATTTACTCTTCCTCTTTAGGATTAGTCACTAAGCA
* * *
3546092 TTCTTTATGATTTGTATTCGGTAAGCGTTCTTAGGAAAATGGATTATAAGTGAATCTTCTGATTG
66 GTCTTTATGATTTGTATTCAGTAAGCATTCTTAGGAAAATGGATTATAAGTGAATCTTCTGATTG
3546157 TT
131 TT
3546159 TGTT
1 TGTT
3546163 TGTACTATGC
Statistics
Matches: 128, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
132 128 1.00
ACGTcount: A:0.26, C:0.12, G:0.20, T:0.42
Consensus pattern (132 bp):
TGTTAATGAGAGGTTAACTCTGTGTCAATAATTTACTCTTCCTCTTTAGGATTAGTCACTAAGCA
GTCTTTATGATTTGTATTCAGTAAGCATTCTTAGGAAAATGGATTATAAGTGAATCTTCTGATTG
TT
Found at i:3552770 original size:2 final size:2
Alignment explanation
Indices: 3552763--3552791 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3552753 TTGCTCTATT
3552763 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
3552792 TCGGTGAAGT
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:3563280 original size:2 final size:2
Alignment explanation
Indices: 3563273--3563315 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
3563263 TGATCCTTCC
* *
3563273 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA AA AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3563315 A
1 A
3563316 GAGAGAGACA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:3564953 original size:28 final size:27
Alignment explanation
Indices: 3564900--3564955 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 27
3564890 TTCATTTAAA
*
3564900 ATAAAAATTTATTTGAAAATGATAAAAT
1 ATAAAAAATTATTTGAAAAT-ATAAAAT
*
3564928 ATAAAAAATTATTTTGAAAA-ATTAAAT
1 ATAAAAAATTA-TTTGAAAATATAAAAT
3564955 A
1 A
3564956 ATTTAAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 7 0.28
28 10 0.40
29 8 0.32
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (27 bp):
ATAAAAAATTATTTGAAAATATAAAAT
Found at i:3571543 original size:21 final size:20
Alignment explanation
Indices: 3571496--3571543 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
3571486 CTAATATTTG
3571496 TTGATTTTATTTAAAAAAAT
1 TTGATTTTATTTAAAAAAAT
**
3571516 TAAATTTT-TTTAAAAAAAAAT
1 TTGATTTTATTT--AAAAAAAT
3571537 TTGATTT
1 TTGATTT
3571544 CAAATATTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
19 3 0.14
20 6 0.27
21 13 0.59
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (20 bp):
TTGATTTTATTTAAAAAAAT
Found at i:3574700 original size:36 final size:37
Alignment explanation
Indices: 3574574--3574700 Score: 148
Period size: 41 Copynumber: 3.4 Consensus size: 37
3574564 TAAAATCAAA
* *
3574574 ATAATACTTAAAATACTTTTACTTAATATTATTACAT
1 ATAAAACTTAAAATACTTTTACTTTATATTATTACAT
* *
3574611 ATGAAACTTGAAATACTTTTACTTAATATATATTATTACAT
1 ATAAAACTTAAAATACTTTTAC-T--T-TATATTATTACAT
* *
3574652 ATAAAAATTAAAATACTTTTA-TTTATATTATTATAT
1 ATAAAACTTAAAATACTTTTACTTTATATTATTACAT
*
3574688 ATAAAACCTAAAA
1 ATAAAACTTAAAA
3574701 GGTTGATTTA
Statistics
Matches: 76, Mismatches: 10, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
36 23 0.30
37 20 0.26
38 1 0.01
39 1 0.01
40 1 0.01
41 30 0.39
ACGTcount: A:0.46, C:0.09, G:0.02, T:0.43
Consensus pattern (37 bp):
ATAAAACTTAAAATACTTTTACTTTATATTATTACAT
Found at i:3590185 original size:23 final size:24
Alignment explanation
Indices: 3590154--3590199 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
3590144 ACAACCAACC
* *
3590154 TATACT-AAATTTGGCACCTTTAG
1 TATACTAAAAGTTAGCACCTTTAG
*
3590177 TATAGTAAAAGTTAGCACCTTTA
1 TATACTAAAAGTTAGCACCTTTA
3590200 CAGTAAAAAG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 5 0.26
24 14 0.74
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.37
Consensus pattern (24 bp):
TATACTAAAAGTTAGCACCTTTAG
Found at i:3590335 original size:15 final size:16
Alignment explanation
Indices: 3590309--3590338 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
3590299 GTGAATCAAC
3590309 TGTTTCTTTTCTTTAT
1 TGTTTCTTTTCTTTAT
3590325 TGTTT-TTTTCTTTA
1 TGTTTCTTTTCTTTA
3590339 GCAATCCAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.07, C:0.10, G:0.07, T:0.77
Consensus pattern (16 bp):
TGTTTCTTTTCTTTAT
Found at i:3595437 original size:19 final size:17
Alignment explanation
Indices: 3595415--3595478 Score: 58
Period size: 17 Copynumber: 3.7 Consensus size: 17
3595405 AATGAATAAC
3595415 AAAAATAATAATACATGCA
1 AAAAATAATAATACAT--A
* * *
3595434 AAAATTAGTAACACATA
1 AAAAATAATAATACATA
**
3595451 AAAAATAATAATATTTA
1 AAAAATAATAATACATA
3595468 AAAAA-AATAAT
1 AAAAATAATAAT
3595479 CAAACCTAAC
Statistics
Matches: 37, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
16 6 0.16
17 18 0.49
19 13 0.35
ACGTcount: A:0.66, C:0.06, G:0.03, T:0.25
Consensus pattern (17 bp):
AAAAATAATAATACATA
Found at i:3604564 original size:20 final size:20
Alignment explanation
Indices: 3604526--3604564 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
3604516 AAAAATTCTC
*
3604526 AATTCAATTTAATTTTTTTA
1 AATTCAATTTAATTATTTTA
* *
3604546 AATTTAATTTGATTATTTT
1 AATTCAATTTAATTATTTT
3604565 CAAGTTAGTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.62
Consensus pattern (20 bp):
AATTCAATTTAATTATTTTA
Found at i:3607290 original size:24 final size:24
Alignment explanation
Indices: 3607232--3607291 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
3607222 TCTTCTCGTA
* *
3607232 CTCATCTTCTTCTTCTACTTCTTC
1 CTCATCTTCTTCTTCTACTGCATC
* *
3607256 CTCAGCATCTTCTTCT-CTAGCATC
1 CTCATCTTCTTCTTCTACT-GCATC
3607280 CTCATCTTCTTC
1 CTCATCTTCTTC
3607292 ACCACCCCAG
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
23 2 0.07
24 27 0.93
ACGTcount: A:0.12, C:0.38, G:0.03, T:0.47
Consensus pattern (24 bp):
CTCATCTTCTTCTTCTACTGCATC
Found at i:3609844 original size:15 final size:15
Alignment explanation
Indices: 3609824--3609880 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
3609814 CATAAACATC
3609824 ATACATGCATGCATA
1 ATACATGCATGCATA
* *
3609839 ATACATGGATAGTAAACATC
1 ATACATGCAT-G----CATA
3609859 ATACATGCATGCATA
1 ATACATGCATGCATA
3609874 ATACATG
1 ATACATG
3609881 GATAGATGCA
Statistics
Matches: 33, Mismatches: 4, Indels: 10
0.70 0.09 0.21
Matches are distributed among these distances:
15 19 0.58
16 1 0.03
19 1 0.03
20 12 0.36
ACGTcount: A:0.42, C:0.18, G:0.14, T:0.26
Consensus pattern (15 bp):
ATACATGCATGCATA
Found at i:3609862 original size:35 final size:35
Alignment explanation
Indices: 3609816--3609885 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
3609806 CAATCCTACA
3609816 TAAACATCATACATGCATGCATAATACATGGATAG
1 TAAACATCATACATGCATGCATAATACATGGATAG
3609851 TAAACATCATACATGCATGCATAATACATGGATAG
1 TAAACATCATACATGCATGCATAATACATGGATAG
3609886 ATGCATTTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.43, C:0.17, G:0.14, T:0.26
Consensus pattern (35 bp):
TAAACATCATACATGCATGCATAATACATGGATAG
Found at i:3612886 original size:28 final size:28
Alignment explanation
Indices: 3612850--3612944 Score: 81
Period size: 28 Copynumber: 3.3 Consensus size: 28
3612840 TGTAAAATCT
3612850 TTTCATTATTGATATTACAAAATATATC
1 TTTCATTATTGATATTACAAAATATATC
*
3612878 TTTCTTTA-T-ATATGTAACTAGACAATCA-AT-
1 TTTCATTATTGATAT-T-AC-A-A-AAT-ATATC
*
3612908 TTTCATTATCGATATTACAAAATATATC
1 TTTCATTATTGATATTACAAAATATATC
*
3612936 TTTCTTTAT
1 TTTCATTAT
3612945 ATATGTAACT
Statistics
Matches: 53, Mismatches: 4, Indels: 20
0.69 0.05 0.26
Matches are distributed among these distances:
26 5 0.09
27 7 0.13
28 18 0.34
29 2 0.04
30 10 0.19
31 6 0.11
32 5 0.09
ACGTcount: A:0.36, C:0.13, G:0.04, T:0.47
Consensus pattern (28 bp):
TTTCATTATTGATATTACAAAATATATC
Found at i:3612939 original size:58 final size:58
Alignment explanation
Indices: 3612849--3612965 Score: 207
Period size: 58 Copynumber: 2.0 Consensus size: 58
3612839 TTGTAAAATC
* *
3612849 TTTTCATTATTGATATTACAAAATATATCTTTCTTTATATATGTAACTAGACAATCAA
1 TTTTCATTATCGATATTACAAAATATATCTTTCTTTATATATGTAACTAAACAATCAA
*
3612907 TTTTCATTATCGATATTACAAAATATATCTTTCTTTATATATGTAACTAAATAATCAA
1 TTTTCATTATCGATATTACAAAATATATCTTTCTTTATATATGTAACTAAACAATCAA
3612965 T
1 T
3612966 CATCCATGAA
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
58 56 1.00
ACGTcount: A:0.38, C:0.12, G:0.04, T:0.45
Consensus pattern (58 bp):
TTTTCATTATCGATATTACAAAATATATCTTTCTTTATATATGTAACTAAACAATCAA
Found at i:3630608 original size:14 final size:14
Alignment explanation
Indices: 3630571--3630608 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
3630561 ATCCAGGAAA
3630571 CAAGGAAGTGGGTT
1 CAAGGAAGTGGGTT
*
3630585 C-AGAATAGTGGGTT
1 CAAGGA-AGTGGGTT
3630599 CAAGGAAGTG
1 CAAGGAAGTG
3630609 AAACGTTTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 4
0.77 0.08 0.15
Matches are distributed among these distances:
13 3 0.15
14 14 0.70
15 3 0.15
ACGTcount: A:0.32, C:0.08, G:0.39, T:0.21
Consensus pattern (14 bp):
CAAGGAAGTGGGTT
Found at i:3634472 original size:16 final size:15
Alignment explanation
Indices: 3634433--3634488 Score: 60
Period size: 16 Copynumber: 3.6 Consensus size: 15
3634423 TTCATTTAAT
*
3634433 AAAAAAATATAAA-A
1 AAAAAAAAATAAACA
*
3634447 AAATAAAAAACAAAACA
1 AAA-AAAAAA-TAAACA
3634464 AAAACAAAAATAAACA
1 AAAA-AAAAATAAACA
3634480 AAAAAAAAA
1 AAAAAAAAA
3634489 GAACTCATTG
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
14 3 0.09
15 10 0.29
16 13 0.37
17 9 0.26
ACGTcount: A:0.86, C:0.07, G:0.00, T:0.07
Consensus pattern (15 bp):
AAAAAAAAATAAACA
Found at i:3634592 original size:19 final size:19
Alignment explanation
Indices: 3634570--3634620 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 19
3634560 TTGCTTTTTT
3634570 AATAAAAAATTAAAAAAG-A
1 AATAAAAAA-TAAAAAAGTA
3634589 AATAAAATAATAAAAAAGTA
1 AATAAAA-AATAAAAAAGTA
3634609 AA-AAAAAA-AAAA
1 AATAAAAAATAAAA
3634621 GAGAAAAGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
17 4 0.13
18 2 0.07
19 19 0.63
20 5 0.17
ACGTcount: A:0.82, C:0.00, G:0.04, T:0.14
Consensus pattern (19 bp):
AATAAAAAATAAAAAAGTA
Found at i:3634605 original size:27 final size:25
Alignment explanation
Indices: 3634569--3634620 Score: 77
Period size: 27 Copynumber: 2.0 Consensus size: 25
3634559 ATTGCTTTTT
*
3634569 TAATAAAAAATTAAAAAAGAAATAAAA
1 TAATAAAAAAGTAAAAAA-AAA-AAAA
3634596 TAATAAAAAAGTAAAAAAAAAAAAA
1 TAATAAAAAAGTAAAAAAAAAAAAA
3634621 GAGAAAAGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 4 0.17
26 3 0.12
27 17 0.71
ACGTcount: A:0.81, C:0.00, G:0.04, T:0.15
Consensus pattern (25 bp):
TAATAAAAAAGTAAAAAAAAAAAAA
Found at i:3636291 original size:6 final size:6
Alignment explanation
Indices: 3636282--3636309 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
3636272 TTAAAAAAAA
3636282 AAAACT AAAACT AAAACT AAAACT AAAA
1 AAAACT AAAACT AAAACT AAAACT AAAA
3636310 ATAGACAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.71, C:0.14, G:0.00, T:0.14
Consensus pattern (6 bp):
AAAACT
Found at i:3637453 original size:2 final size:2
Alignment explanation
Indices: 3637441--3637483 Score: 56
Period size: 2 Copynumber: 22.5 Consensus size: 2
3637431 AATTGCAATC
3637441 AT AT AT CAT AT AT A- AT AT -T AT AT -T AT AT AT AT AT AT AT AT
1 AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3637481 AT A
1 AT A
3637484 AAACTTAATA
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
1 3 0.08
2 32 0.86
3 2 0.05
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3637468 original size:17 final size:19
Alignment explanation
Indices: 3637441--3637482 Score: 61
Period size: 17 Copynumber: 2.3 Consensus size: 19
3637431 AATTGCAATC
3637441 ATATATCATATATA-ATAT
1 ATATATCATATATATATAT
*
3637459 -TATATTATATATATATAT
1 ATATATCATATATATATAT
3637477 ATATAT
1 ATATAT
3637483 AAAACTTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 12 0.57
18 4 0.19
19 5 0.24
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (19 bp):
ATATATCATATATATATAT
Found at i:3638641 original size:15 final size:16
Alignment explanation
Indices: 3638623--3638653 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3638613 TTATTTAAAA
3638623 TTAATT-TTTTATAAT
1 TTAATTCTTTTATAAT
3638638 TTAATTCTTTTATAAT
1 TTAATTCTTTTATAAT
3638654 ATTATTAGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (16 bp):
TTAATTCTTTTATAAT
Found at i:3639020 original size:22 final size:20
Alignment explanation
Indices: 3638974--3639025 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 20
3638964 TAAACATTTA
*
3638974 AAATTAATTT-TTTTCAAAT
1 AAATAAATTTATTTTCAAAT
*
3638993 AAATAAAATTTATTTTTAAATT
1 AAAT-AAATTTATTTTCAAA-T
*
3639015 ATATAAATTTA
1 AAATAAATTTA
3639026 CAAATATATA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 4 0.15
20 5 0.19
21 14 0.52
22 4 0.15
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (20 bp):
AAATAAATTTATTTTCAAAT
Found at i:3640081 original size:12 final size:12
Alignment explanation
Indices: 3640064--3640091 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
3640054 ATGTTAATAT
3640064 AAAAAAATTTAA
1 AAAAAAATTTAA
3640076 AAAAAAATTTAA
1 AAAAAAATTTAA
3640088 AAAA
1 AAAA
3640092 TTCTAAAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (12 bp):
AAAAAAATTTAA
Found at i:3640706 original size:21 final size:22
Alignment explanation
Indices: 3640669--3640715 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
3640659 TTCCAATTAT
*
3640669 AAATTTATAGATAAAAATAGTA
1 AAATTTACAGATAAAAATAGTA
3640691 AAATTTACAGATAAAAATAGTA
1 AAATTTACAGATAAAAATAGTA
3640713 AAA
1 AAA
3640716 GTGATTGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.62, C:0.02, G:0.09, T:0.28
Consensus pattern (22 bp):
AAATTTACAGATAAAAATAGTA
Found at i:3641102 original size:24 final size:24
Alignment explanation
Indices: 3641057--3641103 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
3641047 AAACAATTAT
**
3641057 ATTTTTTTAATATGGTACTTAAAA
1 ATTTTTTTAATATAATACTTAAAA
* *
3641081 ATTTTTTTAATCTAATATTTAAA
1 ATTTTTTTAATATAATACTTAAA
3641104 TTATATTTAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.53
Consensus pattern (24 bp):
ATTTTTTTAATATAATACTTAAAA
Found at i:3641266 original size:10 final size:9
Alignment explanation
Indices: 3641240--3641290 Score: 59
Period size: 9 Copynumber: 5.7 Consensus size: 9
3641230 GTTAATATAA
3641240 AAAAATTTT
1 AAAAATTTT
3641249 AAAAATTTT
1 AAAAATTTT
3641258 AAAAGATTTT
1 AAAA-ATTTT
* *
3641268 AAAAACTAT
1 AAAAATTTT
*
3641277 -AAAATTTC
1 AAAAATTTT
3641285 AAAAAT
1 AAAAAT
3641291 AAAAATAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
8 5 0.14
9 21 0.60
10 9 0.26
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (9 bp):
AAAAATTTT
Found at i:3641279 original size:19 final size:19
Alignment explanation
Indices: 3641239--3641280 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
3641229 CGTTAATATA
* *
3641239 AAAAAATTTTAAAAATTTT
1 AAAAAATTTTAAAAACTAT
*
3641258 AAAAGATTTTAAAAACTAT
1 AAAAAATTTTAAAAACTAT
3641277 AAAA
1 AAAA
3641281 TTTCAAAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.33
Consensus pattern (19 bp):
AAAAAATTTTAAAAACTAT
Found at i:3641303 original size:21 final size:24
Alignment explanation
Indices: 3641267--3641326 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 24
3641257 TAAAAGATTT
3641267 TAAAAACTATAAAATTTCAA-AAA
1 TAAAAACTATAAAATTTCAATAAA
3641290 TAAAAA-TA-AAAATTTCAATAAA
1 TAAAAACTATAAAATTTCAATAAA
* * *
3641312 AAAAAAATCTAAAAT
1 TAAAAACTATAAAAT
3641327 GCTATCGCTT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
21 10 0.31
22 10 0.31
23 7 0.22
24 5 0.16
ACGTcount: A:0.68, C:0.07, G:0.00, T:0.25
Consensus pattern (24 bp):
TAAAAACTATAAAATTTCAATAAA
Found at i:3641312 original size:23 final size:22
Alignment explanation
Indices: 3641267--3641326 Score: 68
Period size: 23 Copynumber: 2.6 Consensus size: 22
3641257 TAAAAGATTT
3641267 TAAAAACTATAAAATTTCAAAAA
1 TAAAAA-TATAAAATTTCAAAAA
3641290 TAAAAATA-AAAATTTCAATAAAA
1 TAAAAATATAAAATTTC-A-AAAA
* *
3641313 AAAAAATCTAAAAT
1 TAAAAATATAAAAT
3641327 GCTATCGCTT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
21 8 0.25
22 3 0.09
23 16 0.50
24 5 0.16
ACGTcount: A:0.68, C:0.07, G:0.00, T:0.25
Consensus pattern (22 bp):
TAAAAATATAAAATTTCAAAAA
Found at i:3642429 original size:10 final size:10
Alignment explanation
Indices: 3642414--3642469 Score: 62
Period size: 10 Copynumber: 5.7 Consensus size: 10
3642404 TTGCTTTTTG
3642414 ATTTTTTAAA
1 ATTTTTTAAA
*
3642424 ATTTTTTAGA
1 ATTTTTTAAA
*
3642434 A-TTTTTAAG
1 ATTTTTTAAA
3642443 ATTTCTTT-AA
1 ATTT-TTTAAA
*
3642453 ATTATTTAAA
1 ATTTTTTAAA
3642463 ATTTTTT
1 ATTTTTT
3642470 GAATATTTTG
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 10 0.27
10 24 0.65
11 3 0.08
ACGTcount: A:0.34, C:0.02, G:0.04, T:0.61
Consensus pattern (10 bp):
ATTTTTTAAA
Found at i:3642454 original size:29 final size:29
Alignment explanation
Indices: 3642413--3642468 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
3642403 ATTGCTTTTT
* *
3642413 GATTTTTTAAAATTTTTTAGAATTTTTAA
1 GATTTTTTAAAATTATTTAAAATTTTTAA
3642442 GATTTCTTT-AAATTATTTAAAATTTTT
1 GATTT-TTTAAAATTATTTAAAATTTTT
3642469 TGAATATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 21 0.88
30 3 0.12
ACGTcount: A:0.34, C:0.02, G:0.05, T:0.59
Consensus pattern (29 bp):
GATTTTTTAAAATTATTTAAAATTTTTAA
Found at i:3642461 original size:39 final size:39
Alignment explanation
Indices: 3642418--3642495 Score: 106
Period size: 39 Copynumber: 2.0 Consensus size: 39
3642408 TTTTTGATTT
3642418 TTTAAAATTTTTTAGAAT-TTTTAAGATTTCTTTA-AATTA
1 TTTAAAATTTTTT-GAATATTTTAA-ATTTCTTTAGAATTA
* *
3642457 TTTAAAATTTTTTGAATATTTTGAATTTTTTTAGAATTA
1 TTTAAAATTTTTTGAATATTTTAAATTTCTTTAGAATTA
3642496 AAAAAATAGA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
38 12 0.34
39 23 0.66
ACGTcount: A:0.35, C:0.01, G:0.06, T:0.58
Consensus pattern (39 bp):
TTTAAAATTTTTTGAATATTTTAAATTTCTTTAGAATTA
Found at i:3642487 original size:9 final size:9
Alignment explanation
Indices: 3642414--3642487 Score: 60
Period size: 9 Copynumber: 7.8 Consensus size: 9
3642404 TTGCTTTTTG
3642414 ATTTTTTAAA
1 ATTTTTT-AA
3642424 ATTTTTTAGA
1 ATTTTTTA-A
3642434 A-TTTTTAA
1 ATTTTTTAA
3642442 GATTTCTTTAA
1 -ATTT-TTTAA
*
3642453 ATTATTTAAA
1 ATT-TTTTAA
*
3642463 ATTTTTTGA
1 ATTTTTTAA
* *
3642472 ATATTTTGA
1 ATTTTTTAA
3642481 ATTTTTT
1 ATTTTTT
3642488 TAGAATTAAA
Statistics
Matches: 54, Mismatches: 5, Indels: 11
0.77 0.07 0.16
Matches are distributed among these distances:
8 1 0.02
9 26 0.48
10 21 0.39
11 6 0.11
ACGTcount: A:0.32, C:0.01, G:0.05, T:0.61
Consensus pattern (9 bp):
ATTTTTTAA
Found at i:3648119 original size:81 final size:81
Alignment explanation
Indices: 3647984--3648145 Score: 252
Period size: 81 Copynumber: 2.0 Consensus size: 81
3647974 GTCAGGGAAA
* *
3647984 TTATAATTCCCAAGAACGAAGGGACTTCTTTCAAGGAGAGCAGAGGAATTATATGCCACCTGAGC
1 TTATAATTCCCAAGAACGAAGGGACTCCTTTCAAGGAGAGCAGAGGAATTATATGCCACCTGAAC
3648049 AAAGGGATTTCAGAGG
66 AAAGGGATTTCAGAGG
* * * *
3648065 TTATAGTTCCCGAGAAGGAAGGGACTCCTTTCAAGGAGAGCAGAGGAATTATATGCCTCCTGAAC
1 TTATAATTCCCAAGAACGAAGGGACTCCTTTCAAGGAGAGCAGAGGAATTATATGCCACCTGAAC
* *
3648130 AAATGGATTTCCGAGG
66 AAAGGGATTTCAGAGG
3648146 AGATCATAGG
Statistics
Matches: 73, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
81 73 1.00
ACGTcount: A:0.33, C:0.18, G:0.27, T:0.23
Consensus pattern (81 bp):
TTATAATTCCCAAGAACGAAGGGACTCCTTTCAAGGAGAGCAGAGGAATTATATGCCACCTGAAC
AAAGGGATTTCAGAGG
Found at i:3648226 original size:36 final size:36
Alignment explanation
Indices: 3648179--3648360 Score: 106
Period size: 36 Copynumber: 5.1 Consensus size: 36
3648169 CACAAGGTGG
* * *
3648179 GAATTATGGGCAGGCACCAAGTTCTGGCTATGGACA
1 GAATTTTGGGCAGGCACCAAATCCTGGCTATGGACA
*** *
3648215 GAATTTTGGGCAGGGGGCAAATCCTGGCTATGGGCA
1 GAATTTTGGGCAGGCACCAAATCCTGGCTATGGACA
**
3648251 GAATTTTGGGCAAAGG-GTC-AATCCTGGCTATCAGG--A
1 GAATTTTGGGC--AGGCACCAAATCCTGGCTAT--GGACA
** * * * *
3648287 GAATTCCGGACAAGG-AGCAAATCCTGGTTATGGGCA
1 GAATTTTGGGC-AGGCACCAAATCCTGGCTATGGACA
* * *
3648323 GAATTCTGGGCAAGG-AGCAAATTCTGGCTATGGACA
1 GAATTTTGGGC-AGGCACCAAATCCTGGCTATGGACA
3648359 GA
1 GA
3648361 GTTATGGCCA
Statistics
Matches: 120, Mismatches: 19, Indels: 14
0.78 0.12 0.09
Matches are distributed among these distances:
34 2 0.02
35 5 0.04
36 106 0.88
37 2 0.02
38 5 0.04
ACGTcount: A:0.28, C:0.18, G:0.32, T:0.22
Consensus pattern (36 bp):
GAATTTTGGGCAGGCACCAAATCCTGGCTATGGACA
Found at i:3648345 original size:18 final size:18
Alignment explanation
Indices: 3648297--3648349 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
3648287 GAATTCCGGA
* *
3648297 CAAGGAGCAAATCCTGGT
1 CAAGGAGCAAATTCTGGG
* *
3648315 TATGG-GCAGAATTCTGGG
1 CAAGGAGCA-AATTCTGGG
3648333 CAAGGAGCAAATTCTGG
1 CAAGGAGCAAATTCTGG
3648350 CTATGGACAG
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
17 3 0.11
18 21 0.78
19 3 0.11
ACGTcount: A:0.30, C:0.17, G:0.32, T:0.21
Consensus pattern (18 bp):
CAAGGAGCAAATTCTGGG
Found at i:3648373 original size:36 final size:36
Alignment explanation
Indices: 3648202--3648382 Score: 145
Period size: 36 Copynumber: 5.0 Consensus size: 36
3648192 GCACCAAGTT
* * * *
3648202 CTGGCTATGGACAGAATTTTGGGCAGGGGGCAAATC
1 CTGGCTATGGACAGAATTATGGCCAAGGAGCAAATC
* * *
3648238 CTGGCTATGGGCAGAATTTTGGGCAAAGG-GTC-AATC
1 CTGGCTATGGACAGAATTAT-GGCCAAGGAG-CAAATC
** *
3648274 CTGGCTATCAGG--AGAATTCCGGACAAGGAGCAAATC
1 CTGGCTAT--GGACAGAATTATGGCCAAGGAGCAAATC
* * * * *
3648310 CTGGTTATGGGCAGAATTCTGGGCAAGGAGCAAATT
1 CTGGCTATGGACAGAATTATGGCCAAGGAGCAAATC
* *
3648346 CTGGCTATGGACAGAGTTATGGCCAAGGATCAAATC
1 CTGGCTATGGACAGAATTATGGCCAAGGAGCAAATC
3648382 C
1 C
3648383 CGGATATCGT
Statistics
Matches: 118, Mismatches: 19, Indels: 16
0.77 0.12 0.10
Matches are distributed among these distances:
34 2 0.02
35 7 0.06
36 101 0.86
37 6 0.05
38 2 0.02
ACGTcount: A:0.28, C:0.18, G:0.31, T:0.22
Consensus pattern (36 bp):
CTGGCTATGGACAGAATTATGGCCAAGGAGCAAATC
Found at i:3648373 original size:72 final size:72
Alignment explanation
Indices: 3648200--3648382 Score: 194
Period size: 72 Copynumber: 2.5 Consensus size: 72
3648190 AGGCACCAAG
* * * * *
3648200 TTCTGGCTATGGACAGAATTTTGGGCAGGGGGCAAATCCTGGCTATGGGCAGAATTTTGGGCAAA
1 TTCTGGCTATGGACAGAATTATGGACAAGGAGCAAATCCTGGCTATGGGCAGAATTCTGGGCAAA
3648265 GGGTCAA
66 GGGTCAA
* ** *
3648272 TCCTGGCTATCAGG--AGAATTCCGGACAAGGAGCAAATCCTGGTTATGGGCAGAATTCTGGGC-
1 TTCTGGCTAT--GGACAGAATTATGGACAAGGAGCAAATCCTGGCTATGGGCAGAATTCTGGGCA
3648334 AAGGAG-CAAA
64 AAGG-GTC-AA
* * *
3648344 TTCTGGCTATGGACAGAGTTATGGCCAAGGATCAAATCC
1 TTCTGGCTATGGACAGAATTATGGACAAGGAGCAAATCC
3648383 CGGATATCGT
Statistics
Matches: 91, Mismatches: 14, Indels: 12
0.78 0.12 0.10
Matches are distributed among these distances:
70 2 0.02
71 5 0.05
72 82 0.90
74 2 0.02
ACGTcount: A:0.28, C:0.18, G:0.31, T:0.23
Consensus pattern (72 bp):
TTCTGGCTATGGACAGAATTATGGACAAGGAGCAAATCCTGGCTATGGGCAGAATTCTGGGCAAA
GGGTCAA
Found at i:3648397 original size:72 final size:72
Alignment explanation
Indices: 3648297--3648433 Score: 159
Period size: 72 Copynumber: 1.9 Consensus size: 72
3648287 GAATTCCGGA
* * * * *
3648297 CAAGGAGCAAATCCTGGTTATGGGCAGAATTC-TGGGCAAGGAGCAAATTCTGGCTATGGACAGA
1 CAAGGAGCAAATCCCGGATATCGGCAGAA-CCATGGGCAAGGAGCAAATGCTGGCTATGGACAGA
3648361 GTTATGGC
65 GTTATGGC
* * * * * *
3648369 CAAGGATCAAATCCCGGATATCGTCAGAACCATGGGCCAGGAGCAACTGCTGGCTCTGGGCAGAG
1 CAAGGAGCAAATCCCGGATATCGGCAGAACCATGGGCAAGGAGCAAATGCTGGCTATGGACAGAG
3648434 AGCAAATCCT
Statistics
Matches: 53, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
71 1 0.02
72 52 0.98
ACGTcount: A:0.28, C:0.21, G:0.31, T:0.19
Consensus pattern (72 bp):
CAAGGAGCAAATCCCGGATATCGGCAGAACCATGGGCAAGGAGCAAATGCTGGCTATGGACAGAG
TTATGGC
Found at i:3658591 original size:2 final size:2
Alignment explanation
Indices: 3658586--3658622 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
3658576 TTTTTTGTTT
*
3658586 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3658623 TTATCCTTAT
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:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3659663 original size:26 final size:26
Alignment explanation
Indices: 3659612--3659663 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
3659602 GTATGGCTTT
* *
3659612 TTTTTTCCCCTTATTTTTATCTTTAA
1 TTTTGTCCCCTTATTTTTACCTTTAA
*
3659638 TTTTGTCCCCTT-TTTTTCCCTGTTAA
1 TTTTGTCCCCTTATTTTTACCT-TTAA
3659664 ATGTTTTCTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 7 0.32
26 15 0.68
ACGTcount: A:0.12, C:0.23, G:0.04, T:0.62
Consensus pattern (26 bp):
TTTTGTCCCCTTATTTTTACCTTTAA
Found at i:3662944 original size:15 final size:15
Alignment explanation
Indices: 3662924--3662956 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
3662914 AGATTAAAAT
3662924 TTTATTTATATT-TTA
1 TTTATTTAT-TTATTA
3662939 TTTATTTATTTATTA
1 TTTATTTATTTATTA
3662954 TTT
1 TTT
3662957 TAAATATAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 2 0.12
15 15 0.88
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTATTTATTTATTA
Found at i:3665117 original size:21 final size:22
Alignment explanation
Indices: 3665091--3665131 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
3665081 TATTCGCTCA
*
3665091 TAATTTTTATTATTT-CAATAT
1 TAATTTTTATAATTTACAATAT
3665112 TAATTTTTATAATTTACAAT
1 TAATTTTTATAATTTACAAT
3665132 TATCTTATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.59
Consensus pattern (22 bp):
TAATTTTTATAATTTACAATAT
Found at i:3665560 original size:31 final size:31
Alignment explanation
Indices: 3665490--3665565 Score: 91
Period size: 32 Copynumber: 2.4 Consensus size: 31
3665480 CACTAAATAT
* * * *
3665490 GATTTCACTTGGTAAAATATTAATGCATATTT
1 GATTTCATTTGATAAAATATTAAT-CATAATG
3665522 GATTTCATTTGATAAAATATTAAT-ATACATG
1 GATTTCATTTGATAAAATATTAATCATA-ATG
3665553 GATTTCATTTGAT
1 GATTTCATTTGAT
3665566 TTTAGTTGTA
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
30 3 0.08
31 14 0.36
32 22 0.56
ACGTcount: A:0.36, C:0.08, G:0.12, T:0.45
Consensus pattern (31 bp):
GATTTCATTTGATAAAATATTAATCATAATG
Found at i:3681805 original size:17 final size:16
Alignment explanation
Indices: 3681783--3681833 Score: 57
Period size: 17 Copynumber: 3.1 Consensus size: 16
3681773 ATCTTATTTA
*
3681783 ATTTTATATTTTAATAT
1 ATTTTA-ATTTTAAAAT
*
3681800 ATTTTAATTAATAAAAT
1 ATTTTAATT-TTAAAAT
*
3681817 ATTTTAAATTTAAAAT
1 ATTTTAATTTTAAAAT
3681833 A
1 A
3681834 AAATATAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
16 10 0.34
17 19 0.66
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
ATTTTAATTTTAAAAT
Found at i:3692461 original size:14 final size:14
Alignment explanation
Indices: 3692437--3692470 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
3692427 AGTTAAATCT
3692437 GATTGGATCATATTG
1 GATT-GATCATATTG
*
3692452 GATTGATCATATTT
1 GATTGATCATATTG
3692466 GATTG
1 GATTG
3692471 GATTTTGATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 14 0.78
15 4 0.22
ACGTcount: A:0.26, C:0.06, G:0.24, T:0.44
Consensus pattern (14 bp):
GATTGATCATATTG
Found at i:3699649 original size:36 final size:35
Alignment explanation
Indices: 3699609--3699705 Score: 94
Period size: 36 Copynumber: 2.8 Consensus size: 35
3699599 TTCATAAAAA
* *
3699609 TTCAAATTAGCAAGATATTTTAGATTTGCAAAATAT
1 TTCAAATTAGTAAGATATTTTAGATTTGC-AAAGAT
* *
3699645 TTCAAA-TATGTAAGAT-TTTTCAAATTTGCAAGGAT
1 TTCAAATTA-GTAAGATATTTT-AGATTTGCAAAGAT
*
3699680 TTC-AATTCGTAAGA-ATTTTAGATTTG
1 TTCAAATTAGTAAGATATTTTAGATTTG
3699706 TAAGAATTTT
Statistics
Matches: 51, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
33 6 0.12
34 12 0.24
35 14 0.27
36 19 0.37
ACGTcount: A:0.37, C:0.08, G:0.13, T:0.41
Consensus pattern (35 bp):
TTCAAATTAGTAAGATATTTTAGATTTGCAAAGAT
Found at i:3699710 original size:17 final size:17
Alignment explanation
Indices: 3699620--3699715 Score: 61
Period size: 17 Copynumber: 5.5 Consensus size: 17
3699610 TCAAATTAGC
* *
3699620 AAGATATTTTAGATTTGC
1 AAGA-ATTTTAAATTTGT
*
3699638 AA-AATATTTCAAATATGT
1 AAGAAT-TTT-AAATTTGT
* *
3699656 AAGATTTTTCAAATTTGC
1 AAGAATTTT-AAATTTGT
* * *
3699674 AAGGA-TTTCAATTCGT
1 AAGAATTTTAAATTTGT
*
3699690 AAGAATTTTAGATTTGT
1 AAGAATTTTAAATTTGT
3699707 AAGAATTTT
1 AAGAATTTT
3699716 CATTCTCAAG
Statistics
Matches: 59, Mismatches: 15, Indels: 9
0.71 0.18 0.11
Matches are distributed among these distances:
16 11 0.19
17 24 0.41
18 22 0.37
19 2 0.03
ACGTcount: A:0.38, C:0.06, G:0.14, T:0.43
Consensus pattern (17 bp):
AAGAATTTTAAATTTGT
Found at i:3699717 original size:34 final size:34
Alignment explanation
Indices: 3699620--3699717 Score: 94
Period size: 34 Copynumber: 2.8 Consensus size: 34
3699610 TCAAATTAGC
3699620 AAGATATTTTAGATTTGCAA-AATATTTCAAATATGT
1 AAGA-ATTTTAGATTTGCAAGAAT-TTTC-AATATGT
* * *
3699656 AAGATTTTTCAAATTTGCAAGGA-TTTCAAT-TCGT
1 AAGAATTTT-AGATTTGCAAGAATTTTCAATAT-GT
*
3699690 AAGAATTTTAGATTTGTAAGAATTTTCA
1 AAGAATTTTAGATTTGCAAGAATTTTCA
3699718 TTCTCAAGGA
Statistics
Matches: 51, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
33 11 0.22
34 18 0.35
35 8 0.16
36 13 0.25
37 1 0.02
ACGTcount: A:0.38, C:0.07, G:0.13, T:0.42
Consensus pattern (34 bp):
AAGAATTTTAGATTTGCAAGAATTTTCAATATGT
Found at i:3700059 original size:109 final size:108
Alignment explanation
Indices: 3699893--3700162 Score: 346
Period size: 109 Copynumber: 2.5 Consensus size: 108
3699883 CGTCCGATGC
* * * *
3699893 TTCTAATTTAAAAACTTTAGGA-TTT-CATCCAAAATTTTAAAGCTTCTCATTCGAGTTCAAAGA
1 TTCTCATTTAAAAAATTTAGGAGTTTACATCCAAAATTTCAAAGCTTCTCATTCAAGTTCAAAGA
* * * *
3699956 TTCACATTCGATAAATTTTAAAGTTTCACATCTAACTTTAAAGA
66 TCCACATTCGATAAATTTT-AAGTTTCACATATAAATTCAAAGA
** * *
3700000 TTCTCATTTAAAAAATTTATAAGTTTACATCCAAAATTTCAAAGCATCTTATTCAAGTTCAAAGA
1 TTCTCATTTAAAAAATTTAGGAGTTTACATCCAAAATTTCAAAGCTTCTCATTCAAGTTCAAAGA
* * *
3700065 TCCACATTTGATAAATTTTGAGTTTCACATATAAATTCAAAGG
66 TCCACATTCGATAAATTTTAAGTTTCACATATAAATTCAAAGA
* * *
3700108 TTTTCATTTAAAAAAATTTAGGGGTTTACATTCAAAATTTCAAAGCTTCTCATTC
1 TTCTCATTT-AAAAAATTTAGGAGTTTACATCCAAAATTTCAAAGCTTCTCATTC
3700163 TAAAACTCAA
Statistics
Matches: 138, Mismatches: 22, Indels: 4
0.84 0.13 0.02
Matches are distributed among these distances:
107 18 0.13
108 30 0.22
109 90 0.65
ACGTcount: A:0.38, C:0.15, G:0.09, T:0.39
Consensus pattern (108 bp):
TTCTCATTTAAAAAATTTAGGAGTTTACATCCAAAATTTCAAAGCTTCTCATTCAAGTTCAAAGA
TCCACATTCGATAAATTTTAAGTTTCACATATAAATTCAAAGA
Found at i:3700199 original size:27 final size:28
Alignment explanation
Indices: 3700148--3700200 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
3700138 TTCAAAATTT
*
3700148 CAAAGCTTCTCATTCTAAAACTCAAAGA
1 CAAAGATTCTCATTCTAAAACTCAAAGA
*
3700176 CAAAGATTTTCATT-TAAAACTCAAA
1 CAAAGATTCTCATTCTAAAACTCAAA
3700201 TATTCTTATC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 11 0.48
28 12 0.52
ACGTcount: A:0.45, C:0.21, G:0.06, T:0.28
Consensus pattern (28 bp):
CAAAGATTCTCATTCTAAAACTCAAAGA
Found at i:3700818 original size:79 final size:79
Alignment explanation
Indices: 3700674--3700819 Score: 202
Period size: 79 Copynumber: 1.8 Consensus size: 79
3700664 AGCTTCTTAG
* * * * * * * *
3700674 CACTAACTATTTTAAAATAAATTTCATCCATTAATCCTCATTATTTTCATTACTTAATCATAACT
1 CACTAACAATTTCAAAATAAATTCCATCCACTAATCCACATTAGTTTCATCACTTAATCACAACT
3700739 CACATGCCTCTTCA
66 CACATGCCTCTTCA
* *
3700753 CACTAACAATTTCAAAATAAATTCCATCCACTGATCCACATTAGTTTCATCACTTGATCACAACT
1 CACTAACAATTTCAAAATAAATTCCATCCACTAATCCACATTAGTTTCATCACTTAATCACAACT
3700818 CA
66 CA
3700820 TAGGCTTCTT
Statistics
Matches: 57, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
79 57 1.00
ACGTcount: A:0.36, C:0.26, G:0.03, T:0.36
Consensus pattern (79 bp):
CACTAACAATTTCAAAATAAATTCCATCCACTAATCCACATTAGTTTCATCACTTAATCACAACT
CACATGCCTCTTCA
Found at i:3701963 original size:21 final size:22
Alignment explanation
Indices: 3701922--3701973 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 22
3701912 AAATATTTTT
*
3701922 ATTGAATTTATGACTTAATTTA
1 ATTGAATTTATGAATTAATTTA
3701944 ATTG-ATTTAT-AATTATATTT-
1 ATTGAATTTATGAATTA-ATTTA
*
3701964 ATTAAATTTA
1 ATTGAATTTA
3701974 AGGTTAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
20 7 0.27
21 15 0.58
22 4 0.15
ACGTcount: A:0.38, C:0.02, G:0.06, T:0.54
Consensus pattern (22 bp):
ATTGAATTTATGAATTAATTTA
Found at i:3709507 original size:2 final size:2
Alignment explanation
Indices: 3709500--3709528 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3709490 TCCCTTCAAA
3709500 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
3709529 AAAGCAGAAA
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:3711811 original size:26 final size:26
Alignment explanation
Indices: 3711787--3711860 Score: 76
Period size: 28 Copynumber: 2.7 Consensus size: 26
3711777 CTATTAATTC
*
3711787 AATTTAATTTATTGATTTTTAAATTTA
1 AATTTAATATATT-ATTTTTAAATTTA
*
3711814 AATTTAATATATTATTTTAATATATTTA
1 AATTTAATATATTATTTT--TAAATTTA
* *
3711842 AATATAAAATAATTATTTT
1 AATTTAATAT-ATTATTTT
3711861 ATTTTGTAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
26 5 0.12
27 12 0.30
28 15 0.38
29 8 0.20
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.55
Consensus pattern (26 bp):
AATTTAATATATTATTTTTAAATTTA
Found at i:3711990 original size:22 final size:22
Alignment explanation
Indices: 3711964--3712007 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
3711954 CTAAATTTAA
3711964 TTTAAATCAAATAAAAAATTAT
1 TTTAAATCAAATAAAAAATTAT
* * *
3711986 TTTAAATTAAATCAAATATTAT
1 TTTAAATCAAATAAAAAATTAT
3712008 AATTATAAAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.41
Consensus pattern (22 bp):
TTTAAATCAAATAAAAAATTAT
Found at i:3713745 original size:18 final size:18
Alignment explanation
Indices: 3713732--3713766 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
3713722 GTTAAAAAAC
*
3713732 TAAATATAAATAAATAAA
1 TAAAAATAAATAAATAAA
3713750 TAAAAATAAA-AAATAAA
1 TAAAAATAAATAAATAAA
3713767 AGAAAGATGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (18 bp):
TAAAAATAAATAAATAAA
Found at i:3716185 original size:26 final size:28
Alignment explanation
Indices: 3716156--3716212 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 28
3716146 TGAGAATCGT
* *
3716156 AAAAATTTCGA-GTGATAAATTT-TTTA
1 AAAAATCTCGAGGTGAGAAATTTATTTA
*
3716182 AAAAATCTCTAGGTGAGAAATTTATTTA
1 AAAAATCTCGAGGTGAGAAATTTATTTA
3716210 AAA
1 AAA
3716213 TTATCCCGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 9 0.35
27 10 0.38
28 7 0.27
ACGTcount: A:0.46, C:0.05, G:0.12, T:0.37
Consensus pattern (28 bp):
AAAAATCTCGAGGTGAGAAATTTATTTA
Found at i:3716384 original size:48 final size:48
Alignment explanation
Indices: 3716296--3716389 Score: 111
Period size: 48 Copynumber: 2.0 Consensus size: 48
3716286 AAAAAAAGAA
*
3716296 TCTAAATAAACCCAAATGATGACAAATTTAGAAATCAAAAAGAAAATT
1 TCTAAATAAACCCAAATGATGACAAATTTAAAAATCAAAAAGAAAATT
** * *
3716344 TCTAAATTGACCCAAATGGTGA-AAATTTTGAAAAAT-AAAAATAAAA
1 TCTAAATAAACCCAAATGATGACAAA-TTT-AAAAATCAAAAAGAAAA
3716390 AATAAAAATA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
47 3 0.08
48 31 0.79
49 5 0.13
ACGTcount: A:0.55, C:0.11, G:0.10, T:0.24
Consensus pattern (48 bp):
TCTAAATAAACCCAAATGATGACAAATTTAAAAATCAAAAAGAAAATT
Found at i:3716392 original size:13 final size:13
Alignment explanation
Indices: 3716374--3716401 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
3716364 GAAAATTTTG
3716374 AAAAATAAAAATA
1 AAAAATAAAAATA
3716387 AAAAATAAAAATA
1 AAAAATAAAAATA
3716400 AA
1 AA
3716402 TTTCGACGAT
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:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (13 bp):
AAAAATAAAAATA
Found at i:3718272 original size:18 final size:18
Alignment explanation
Indices: 3718251--3718295 Score: 90
Period size: 18 Copynumber: 2.5 Consensus size: 18
3718241 ATATCTTTAA
3718251 AAATTATATCAATAATTT
1 AAATTATATCAATAATTT
3718269 AAATTATATCAATAATTT
1 AAATTATATCAATAATTT
3718287 AAATTATAT
1 AAATTATAT
3718296 AAATTTTGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.44
Consensus pattern (18 bp):
AAATTATATCAATAATTT
Found at i:3725278 original size:13 final size:14
Alignment explanation
Indices: 3725250--3725310 Score: 59
Period size: 14 Copynumber: 4.1 Consensus size: 14
3725240 ATTATATAAA
3725250 ATATTAAAATTTAT
1 ATATTAAAATTTAT
3725264 ATATTAAAATTATATT
1 ATATTAAAATT-TA-T
* *
3725280 TTATATAAAAATTAT
1 ATAT-TAAAATTTAT
* *
3725295 ATATCATAATTTAT
1 ATATTAAAATTTAT
3725309 AT
1 AT
3725311 CAATATAAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
14 20 0.53
15 6 0.16
16 6 0.16
17 6 0.16
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (14 bp):
ATATTAAAATTTAT
Found at i:3725290 original size:18 final size:18
Alignment explanation
Indices: 3725241--3725296 Score: 67
Period size: 18 Copynumber: 2.9 Consensus size: 18
3725231 TATATTTATA
*
3725241 TTATATAAAATATTAAAATT
1 TTATATAAAA-ATT-ATATT
*
3725261 TATATATTAAAATTATATT
1 T-TATATAAAAATTATATT
3725280 TTATATAAAAATTATAT
1 TTATATAAAAATTATAT
3725297 ATCATAATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
18 15 0.47
19 5 0.16
20 4 0.12
21 8 0.25
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
TTATATAAAAATTATATT
Found at i:3725411 original size:13 final size:13
Alignment explanation
Indices: 3725381--3725417 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
3725371 ATAATTATAA
3725381 ATCATATTAT-TT
1 ATCATATTATATT
*
3725393 -TTATATTATATT
1 ATCATATTATATT
3725405 ATCATATTATATT
1 ATCATATTATATT
3725418 TTAAATTATC
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
11 8 0.38
12 2 0.10
13 11 0.52
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.59
Consensus pattern (13 bp):
ATCATATTATATT
Found at i:3725427 original size:20 final size:21
Alignment explanation
Indices: 3725402--3725442 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3725392 TTTATATTAT
* *
3725402 ATTATCATA-TTATATTTTAA
1 ATTATCAAATTTATACTTTAA
3725422 ATTATCAAATTTATACTTTAA
1 ATTATCAAATTTATACTTTAA
3725443 CCGTCTCGCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.51
Consensus pattern (21 bp):
ATTATCAAATTTATACTTTAA
Found at i:3727480 original size:25 final size:25
Alignment explanation
Indices: 3727446--3727496 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
3727436 CTATTAATAC
3727446 TTCTTTTGGGTTAAACAACTTCATA
1 TTCTTTTGGGTTAAACAACTTCATA
3727471 TTCTTTTGGGTTAAACAACTTCATA
1 TTCTTTTGGGTTAAACAACTTCATA
3727496 T
1 T
3727497 CTCTAGTGTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.27, C:0.16, G:0.12, T:0.45
Consensus pattern (25 bp):
TTCTTTTGGGTTAAACAACTTCATA
Found at i:3729431 original size:14 final size:14
Alignment explanation
Indices: 3729412--3729452 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
3729402 TATAATAAAA
3729412 TATTTTAATTTATC
1 TATTTTAATTTATC
* *
3729426 TATTTTAATTTTTT
1 TATTTTAATTTATC
3729440 TATTTTAATTTAT
1 TATTTTAATTTAT
3729453 ATTAATTATT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (14 bp):
TATTTTAATTTATC
Found at i:3733420 original size:23 final size:23
Alignment explanation
Indices: 3733375--3733420 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
3733365 GTAAACAATT
*
3733375 AAATCAGCAAAAATTTTTAAAAA
1 AAATCAGCAAAAATTTGTAAAAA
*
3733398 AAATCAGCAAAGAGTTTGTAAAA
1 AAATCAGCAAA-AATTTGTAAAA
3733421 GTAAAATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.57, C:0.09, G:0.11, T:0.24
Consensus pattern (23 bp):
AAATCAGCAAAAATTTGTAAAAA
Found at i:3743904 original size:15 final size:15
Alignment explanation
Indices: 3743884--3743919 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
3743874 GGAAGGAACA
*
3743884 CAAAATATTCTTACC
1 CAAAATATTCATACC
*
3743899 CAAAATATTGATACC
1 CAAAATATTCATACC
3743914 CAAAAT
1 CAAAAT
3743920 CCATTAATCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.47, C:0.22, G:0.03, T:0.28
Consensus pattern (15 bp):
CAAAATATTCATACC
Found at i:3752404 original size:6 final size:5
Alignment explanation
Indices: 3752379--3752427 Score: 52
Period size: 5 Copynumber: 10.4 Consensus size: 5
3752369 AATGAGTAAA
*
3752379 TTTAT TTTAT TTTAT TTTAT TTT-T ATTT-T TTTAT CTTA- TTTA- TTTAT
1 TTTAT TTTAT TTTAT TTTAT TTTAT -TTTAT TTTAT TTTAT TTTAT TTTAT
3752426 TT
1 TT
3752428 ATTGCTATTA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
4 11 0.28
5 28 0.72
ACGTcount: A:0.18, C:0.02, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTAT
Found at i:3752423 original size:4 final size:4
Alignment explanation
Indices: 3752378--3752473 Score: 51
Period size: 4 Copynumber: 23.8 Consensus size: 4
3752368 AAATGAGTAA
*
3752378 ATTT ATTTT ATTTT ATTT -TATT -TTT ATTT TTTT ATCTT ATTT ATTT
1 ATTT A-TTT A-TTT ATTT AT-TT ATTT ATTT ATTT AT-TT ATTT ATTT
* * *
3752424 ATTT ATTGCT A-TT A-TT A-TT ATTT ATTA ATAT ATATT A-TT ATTT ATCT
1 ATTT ATT--T ATTT ATTT ATTT ATTT ATTT ATTT AT-TT ATTT ATTT ATTT
3752471 ATT
1 ATT
3752474 AATGTATATA
Statistics
Matches: 75, Mismatches: 8, Indels: 18
0.74 0.08 0.18
Matches are distributed among these distances:
3 14 0.19
4 43 0.57
5 16 0.21
6 2 0.03
ACGTcount: A:0.26, C:0.03, G:0.01, T:0.70
Consensus pattern (4 bp):
ATTT
Found at i:3752444 original size:23 final size:21
Alignment explanation
Indices: 3752378--3752556 Score: 88
Period size: 21 Copynumber: 8.3 Consensus size: 21
3752368 AAATGAGTAA
* *
3752378 ATTTATTTTATTTTATTTTATT
1 ATTTA-TTTATTATATATTATT
* *
3752400 -TTTATTT-TTTTATCTTATTT
1 ATTTATTTATTATATATTA-TT
*
3752420 ATTTATTTATTGCTATTATTATT
1 ATTTATTTATT-ATA-TATTATT
*
3752443 ATTTA-TTAATATATATTATT
1 ATTTATTTATTATATATTATT
* *
3752463 ATTTATCTATTAATGTATATAAATT
1 ATTTATTTATT-A--TATAT-TATT
3752488 -TTTA-TTATTA-ACTATTATCT
1 ATTTATTTATTATA-TATTAT-T
*
3752508 A-TTATTTATCTAT-TAATATAT
1 ATTTATTTAT-TATATATTAT-T
*
3752529 ATATATTTATTGATATATT-TT
1 ATTTATTTATT-ATATATTATT
3752550 ATTTATT
1 ATTTATT
3752557 ATTTATCTAT
Statistics
Matches: 123, Mismatches: 15, Indels: 39
0.69 0.08 0.22
Matches are distributed among these distances:
19 12 0.10
20 24 0.20
21 35 0.28
22 20 0.16
23 16 0.13
24 13 0.11
25 3 0.02
ACGTcount: A:0.31, C:0.03, G:0.02, T:0.64
Consensus pattern (21 bp):
ATTTATTTATTATATATTATT
Found at i:3752448 original size:10 final size:10
Alignment explanation
Indices: 3752378--3752572 Score: 81
Period size: 10 Copynumber: 19.4 Consensus size: 10
3752368 AAATGAGTAA
3752378 ATTTATT-TT
1 ATTTATTATT
3752387 ATTTTATT-TT
1 A-TTTATTATT
3752397 ATTT-TTATT
1 ATTTATTATT
3752406 -TTT-TTATCTT
1 ATTTATTA--TT
3752416 ATTTA-T-TT
1 ATTTATTATT
**
3752424 ATTTATTGCT
1 ATTTATTATT
3752434 A-TTATTATT
1 ATTTATTATT
*
3752443 ATTTATTAAT
1 ATTTATTATT
*
3752453 ATATATTATT
1 ATTTATTATT
3752463 ATTTATCTATT
1 ATTTAT-TATT
* *
3752474 AATGTA-TATAA
1 -ATTTATTAT-T
3752485 ATTT-TTATT
1 ATTTATTATT
* *
3752494 ATTAACTATT
1 ATTTATTATT
*
3752504 ATCTATTATTT
1 ATTTATTA-TT
* *
3752515 ATCTATTAAT
1 ATTTATTATT
*
3752525 ATATA-TA-T
1 ATTTATTATT
3752533 ATTTATTGATAT
1 ATTTATT-AT-T
3752545 ATTTTATTTATT
1 A-TTTA-TTATT
3752557 ATTTATCTATT
1 ATTTAT-TATT
3752568 CATTT
1 -ATTT
3752573 TTTTTGCTGA
Statistics
Matches: 144, Mismatches: 19, Indels: 43
0.70 0.09 0.21
Matches are distributed among these distances:
8 20 0.14
9 20 0.14
10 58 0.40
11 26 0.18
12 12 0.08
13 6 0.04
14 2 0.01
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.64
Consensus pattern (10 bp):
ATTTATTATT
Found at i:3752515 original size:48 final size:47
Alignment explanation
Indices: 3752445--3752567 Score: 148
Period size: 48 Copynumber: 2.6 Consensus size: 47
3752435 TTATTATTAT
*
3752445 TTATTAATATATATTATTATTTATCTATTAATGTATATAAATTTTTA
1 TTATTAATATATATTATTATTTATCTATTAATATATATAAATTTTTA
*
3752492 TTATTAACTAT-TATCTATTATTTATCTATTAATATATATATATTTATTGA
1 TTATTAA-TATATAT-TATTATTTATCTATTAATATATATAAATTT-TT-A
3752542 TATATT--T-TAT-TTATTATTTATCTATT
1 T-TATTAATATATATTATTATTTATCTATT
3752568 CATTTTTTTT
Statistics
Matches: 68, Mismatches: 2, Indels: 13
0.82 0.02 0.16
Matches are distributed among these distances:
46 15 0.22
47 12 0.18
48 33 0.49
49 2 0.03
50 2 0.03
51 4 0.06
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.59
Consensus pattern (47 bp):
TTATTAATATATATTATTATTTATCTATTAATATATATAAATTTTTA
Found at i:3752557 original size:46 final size:48
Alignment explanation
Indices: 3752445--3752567 Score: 141
Period size: 46 Copynumber: 2.6 Consensus size: 48
3752435 TTATTATTAT
*
3752445 TTATTAA-TA-TATATTATTATTTATCTATTAATGTATATAAATTTTTA
1 TTATTAACTATTAT-TTATTATTTATCTATTAATATATATAAATTTTTA
* *
3752492 TTATTAACTATTATCTATTATTTATCTATTAATATATAT--ATATTTA
1 TTATTAACTATTATTTATTATTTATCTATTAATATATATAAATTTTTA
*
3752538 TTGA-TATA-TTTTATTTATTATTTATCTATT
1 TT-ATTA-ACTATTATTTATTATTTATCTATT
3752568 CATTTTTTTT
Statistics
Matches: 67, Mismatches: 5, Indels: 9
0.83 0.06 0.11
Matches are distributed among these distances:
46 30 0.45
47 9 0.13
48 25 0.37
49 3 0.04
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.59
Consensus pattern (48 bp):
TTATTAACTATTATTTATTATTTATCTATTAATATATATAAATTTTTA
Found at i:3752861 original size:12 final size:11
Alignment explanation
Indices: 3752825--3752873 Score: 55
Period size: 11 Copynumber: 4.5 Consensus size: 11
3752815 TGAAATTTTT
*
3752825 TTTTTTCAAAA
1 TTTTTTGAAAA
**
3752836 -TTTTTGAAGT
1 TTTTTTGAAAA
3752846 TTTTTTGAAAAA
1 TTTTTTG-AAAA
3752858 TTTTTTGAAAA
1 TTTTTTGAAAA
3752869 TTTTT
1 TTTTT
3752874 CAGAATTCGA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
10 7 0.23
11 15 0.48
12 9 0.29
ACGTcount: A:0.31, C:0.02, G:0.08, T:0.59
Consensus pattern (11 bp):
TTTTTTGAAAA
Found at i:3753455 original size:63 final size:58
Alignment explanation
Indices: 3753363--3753531 Score: 171
Period size: 63 Copynumber: 2.8 Consensus size: 58
3753353 TTTAAATAAA
*
3753363 ATTTCAAAAAAATATTTATGAGAAAAAGTTGAAAGTATCAATTTTCCTGAAAAATAAAA-AG
1 ATTT-AAAAAAAAATTTA--AG-AAAAGTTGAAAGTATCAATTTTCCTGAAAAATAAAATAG
* * **
3753424 ATTTAAAAAATATATATTTTTAAGGAAAAGTTGAAAGTATCAATTTT-TTTAAAAATAAAATTTT
1 ATTTAAAAAA-A-A-A--TTTAA-GAAAAGTTGAAAGTATCAATTTTCCTGAAAAATAAAA-TAG
*
3753488 TTTTAAAAAAAAATTTAAGAAAAGTTGAAAGTATCAATTTTCCT
1 ATTTAAAAAAAAATTTAAGAAAAGTTGAAAGTATCAATTTTCCT
3753532 TGTATGAAAG
Statistics
Matches: 92, Mismatches: 7, Indels: 20
0.77 0.06 0.17
Matches are distributed among these distances:
58 23 0.25
59 6 0.07
60 6 0.07
61 6 0.07
62 12 0.13
63 25 0.27
64 10 0.11
65 4 0.04
ACGTcount: A:0.50, C:0.05, G:0.09, T:0.36
Consensus pattern (58 bp):
ATTTAAAAAAAAATTTAAGAAAAGTTGAAAGTATCAATTTTCCTGAAAAATAAAATAG
Found at i:3753490 original size:18 final size:17
Alignment explanation
Indices: 3753467--3753503 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 17
3753457 AAAGTATCAA
3753467 TTTTTTTAAAAATAAAAT
1 TTTTTTTAAAAA-AAAAT
3753485 TTTTTTTAAAAAAAAAT
1 TTTTTTTAAAAAAAAAT
3753502 TT
1 TT
3753504 AAGAAAAGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
TTTTTTTAAAAAAAAAT
Found at i:3756739 original size:15 final size:15
Alignment explanation
Indices: 3756716--3756747 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
3756706 TGCATACATG
*
3756716 CATTTTCATTCATTA
1 CATTCTCATTCATTA
3756731 CATTCTCATTCATTA
1 CATTCTCATTCATTA
3756746 CA
1 CA
3756748 CTTAATAAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.28, C:0.25, G:0.00, T:0.47
Consensus pattern (15 bp):
CATTCTCATTCATTA
Found at i:3764338 original size:142 final size:142
Alignment explanation
Indices: 3764080--3764367 Score: 540
Period size: 142 Copynumber: 2.0 Consensus size: 142
3764070 GGGAGGCTAG
3764080 CAAATTTAGAGGAGCTCTAAGTTATTAAGTGCATCATATGATTAAGTTTTCAAAAAAATCTTAAA
1 CAAATTTAGAGGAGCTCTAAGTTATTAAGTGCATCATATGATTAAGTTTTCAAAAAAATCTTAAA
*
3764145 ATGTGTTATCATGATTGTCTGATTGTTCATTTTTGGGCATTGTCTCCTTATGCTTATTTTTGTAA
66 ATGTGTTATCATGATTGTCTGATTGTTCATTTTTGGGCATTGTCTCATTATGCTTATTTTTGTAA
*
3764210 TTTTTTCTTGGC
131 TTCTTTCTTGGC
* *
3764222 CAAATTTAGAGGAGCTCTAAGTTATTAAGTGCATCATATGATTAAGTTTTCAAAAGAATCTTAAG
1 CAAATTTAGAGGAGCTCTAAGTTATTAAGTGCATCATATGATTAAGTTTTCAAAAAAATCTTAAA
3764287 ATGTGTTATCATGATTGTCTGATTGTTCATTTTTGGGCATTGTCTCATTATGCTTATTTTTGTAA
66 ATGTGTTATCATGATTGTCTGATTGTTCATTTTTGGGCATTGTCTCATTATGCTTATTTTTGTAA
3764352 TTCTTTCTTGGC
131 TTCTTTCTTGGC
3764364 CAAA
1 CAAA
3764368 GTTTGCCAAC
Statistics
Matches: 142, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
142 142 1.00
ACGTcount: A:0.27, C:0.12, G:0.17, T:0.44
Consensus pattern (142 bp):
CAAATTTAGAGGAGCTCTAAGTTATTAAGTGCATCATATGATTAAGTTTTCAAAAAAATCTTAAA
ATGTGTTATCATGATTGTCTGATTGTTCATTTTTGGGCATTGTCTCATTATGCTTATTTTTGTAA
TTCTTTCTTGGC
Found at i:3765124 original size:42 final size:42
Alignment explanation
Indices: 3765070--3765270 Score: 205
Period size: 42 Copynumber: 4.8 Consensus size: 42
3765060 ATGATCGTCA
*
3765070 AGGAGC-ATTTACTTTTTCAAAGTTG-TGATGCCTGTGTTTAG
1 AGGAGCAATTTACTTTTTCAAAGTTGTTGA-GCCTCTGTTTAG
* * *
3765111 AGGAGCAATTTAC-TTTCCAAAAGTGGTTGAGCCTCTGATTAG
1 AGGAGCAATTTACTTTTTC-AAAGTTGTTGAGCCTCTGTTTAG
* * * *
3765153 AGGAGCCATTTATTTTTTCAAAGTTGTGGTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTTCAAAGTTGTTGAGCCTCTGTTTAG
* *
3765195 AGGAGCAATTTACTTTTTAAAAGTAGTTGAGCCTCTAG-TTAG
1 AGGAGCAATTTACTTTTTCAAAGTTGTTGAGCCTCT-GTTTAG
** * *
3765237 AGGAGCCGTTTA-TTTTTCTAAAGTCGTTAAGCCT
1 AGGAGCAATTTACTTTTTC-AAAGTTGTTGAGCCT
3765271 TTGACTAAAT
Statistics
Matches: 132, Mismatches: 22, Indels: 11
0.80 0.13 0.07
Matches are distributed among these distances:
41 15 0.11
42 109 0.83
43 8 0.06
ACGTcount: A:0.25, C:0.14, G:0.23, T:0.38
Consensus pattern (42 bp):
AGGAGCAATTTACTTTTTCAAAGTTGTTGAGCCTCTGTTTAG
Found at i:3765210 original size:84 final size:84
Alignment explanation
Indices: 3765070--3765253 Score: 282
Period size: 84 Copynumber: 2.2 Consensus size: 84
3765060 ATGATCGTCA
* *
3765070 AGGAG-CATTTACTTTTTCAAAGTTGTGATGCCTGTGTTTAGAGGAGCAATTTACTTTCCAAAAG
1 AGGAGCCATTTATTTTTTCAAAGTTGTGATGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAAG
*
3765134 TGGTTGAGCCTCT-GATTAG
66 TAGTTGAGCCTCTAG-TTAG
* **
3765153 AGGAGCCATTTATTTTTTCAAAGTTGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTTAAAAG
1 AGGAGCCATTTATTTTTTCAAAGTTGTGATGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAAG
3765218 TAGTTGAGCCTCTAGTTAG
66 TAGTTGAGCCTCTAGTTAG
*
3765237 AGGAGCCGTTTATTTTT
1 AGGAGCCATTTATTTTT
3765254 CTAAAGTCGT
Statistics
Matches: 92, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
83 5 0.05
84 86 0.93
85 1 0.01
ACGTcount: A:0.24, C:0.14, G:0.23, T:0.39
Consensus pattern (84 bp):
AGGAGCCATTTATTTTTTCAAAGTTGTGATGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAAG
TAGTTGAGCCTCTAGTTAG
Found at i:3765290 original size:84 final size:84
Alignment explanation
Indices: 3765070--3765297 Score: 221
Period size: 84 Copynumber: 2.7 Consensus size: 84
3765060 ATGATCGTCA
* * * * ** * *
3765070 AGGAG-CATTTACTTTTTCAAAGTTGTGATGCCTGTGTTTAGAGGAGCAATTTACTTTCCAAAAG
1 AGGAGCCATTTATTTTTTCAAAGTCGTGAAGCCTCTGACTAAAGGAGCAATTTACTTTTCAAAAG
*
3765134 TGGTTGAGCCTCTGATTAG
66 TAGTTGAGCCTCTGATTAG
* ** ** * *
3765153 AGGAGCCATTTATTTTTTCAAAGTTGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTTAAAAG
1 AGGAGCCATTTATTTTTTCAAAGTCGTGAAGCCTCTGACTAAAGGAGCAATTTACTTTTCAAAAG
3765218 TAGTTGAGCCTCT-AGTTAG
66 TAGTTGAGCCTCTGA-TTAG
* * * * *
3765237 AGGAGCCGTTTA-TTTTTCTAAAGTCGTTAAGCCTTTGACTAAATGAGCCATTTA-TTTTCAA
1 AGGAGCCATTTATTTTTTC-AAAGTCGTGAAGCCTCTGACTAAAGGAGCAATTTACTTTTCAA
3765298 GGTCATGGAG
Statistics
Matches: 124, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
83 18 0.15
84 106 0.85
ACGTcount: A:0.26, C:0.14, G:0.21, T:0.38
Consensus pattern (84 bp):
AGGAGCCATTTATTTTTTCAAAGTCGTGAAGCCTCTGACTAAAGGAGCAATTTACTTTTCAAAAG
TAGTTGAGCCTCTGATTAG
Found at i:3765595 original size:4 final size:4
Alignment explanation
Indices: 3765549--3765662 Score: 65
Period size: 4 Copynumber: 27.5 Consensus size: 4
3765539 GTAAGCCCAT
* *
3765549 TTTA TTTTA TTTTA TTT- TTTAA TTTT TTGTA TCTTA GTTA TTTA TTTA
1 TTTA -TTTA -TTTA TTTA TTT-A TTTA TT-TA T-TTA TTTA TTTA TTTA
* * * *
3765597 TTTA TTGCTA -TTA -TTA TTTA TTAA TATA TTTA TTTA TTTA TTAA TATA
1 TTTA TT--TA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
*
3765645 TATTA -TTA TTTA TCTA TT
1 T-TTA TTTA TTTA TTTA TT
3765663 AATGTATATA
Statistics
Matches: 86, Mismatches: 14, Indels: 19
0.72 0.12 0.16
Matches are distributed among these distances:
3 11 0.13
4 53 0.62
5 19 0.22
6 3 0.03
ACGTcount: A:0.27, C:0.03, G:0.03, T:0.68
Consensus pattern (4 bp):
TTTA
Found at i:3765633 original size:20 final size:20
Alignment explanation
Indices: 3765605--3765657 Score: 90
Period size: 20 Copynumber: 2.6 Consensus size: 20
3765595 TATTTATTGC
3765605 TATTATTATTTATTAATATA
1 TATTATTATTTATTAATATA
3765625 T-TTATTTATTTATTAATATA
1 TATTA-TTATTTATTAATATA
3765645 TATTATTATTTAT
1 TATTATTATTTAT
3765658 CTATTAATGT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
19 3 0.10
20 25 0.81
21 3 0.10
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (20 bp):
TATTATTATTTATTAATATA
Found at i:3765647 original size:24 final size:24
Alignment explanation
Indices: 3765620--3765754 Score: 97
Period size: 24 Copynumber: 5.8 Consensus size: 24
3765610 TTATTTATTA
3765620 ATATATTTATTTATTTATTAATAT
1 ATATATTTATTTATTTATTAATAT
* *
3765644 ATAT-TATTATTTATCTATTAATGT
1 ATATAT-TTATTTATTTATTAATAT
*
3765668 ATATAAATT-TTTA-TTATTAACTAT
1 ATAT-ATTTATTTATTTATTAA-TAT
* *
3765692 -TATCTATTATTTATCTATTAATAT
1 ATATAT-TTATTTATTTATTAATAT
* *
3765716 ATATA--TATCT-TTTATTGATAT
1 ATATATTTATTTATTTATTAATAT
*
3765737 ATTTTATTTA-TTATTTAT
1 A-TATATTTATTTATTTAT
3765755 CTATTCATTT
Statistics
Matches: 85, Mismatches: 14, Indels: 24
0.69 0.11 0.20
Matches are distributed among these distances:
21 10 0.12
22 7 0.08
23 13 0.15
24 44 0.52
25 11 0.13
ACGTcount: A:0.35, C:0.04, G:0.01, T:0.60
Consensus pattern (24 bp):
ATATATTTATTTATTTATTAATAT
Found at i:3765671 original size:28 final size:28
Alignment explanation
Indices: 3765623--3765682 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
3765613 TTTATTAATA
* * *
3765623 TATTTATTTATTTATTAATATATATTAT
1 TATTTATCTATTAATTAATATAAATTAT
*
3765651 TATTTATCTATTAATGT-ATATAAATTTT
1 TATTTATCTATTAAT-TAATATAAATTAT
3765679 TATT
1 TATT
3765683 ATTAACTATT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 26 0.96
29 1 0.04
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.62
Consensus pattern (28 bp):
TATTTATCTATTAATTAATATAAATTAT
Found at i:3765681 original size:48 final size:49
Alignment explanation
Indices: 3765629--3765759 Score: 162
Period size: 48 Copynumber: 2.7 Consensus size: 49
3765619 AATATATTTA
*
3765629 TTTATTTATTAATATATATTATTATTTATCTATTAATGTATATAAAT-T
1 TTTATTTATTAATATATATTATTATTTATCTATTAATATATATAAATCT
*
3765677 TTTA-TTATTAACTAT-TATCTATTATTTATCTATTAATATATATATATCT
1 TTTATTTATTAA-TATATAT-TATTATTTATCTATTAATATATATAAATCT
* * *
3765726 TTTATTGATATATTTTAT-TTATTATTTATCTATT
1 TTTATTTAT-TAATATATATTATTATTTATCTATT
3765760 CATTTTTTTT
Statistics
Matches: 72, Mismatches: 5, Indels: 11
0.82 0.06 0.12
Matches are distributed among these distances:
47 10 0.14
48 33 0.46
49 20 0.28
50 6 0.08
51 3 0.04
ACGTcount: A:0.34, C:0.05, G:0.02, T:0.60
Consensus pattern (49 bp):
TTTATTTATTAATATATATTATTATTTATCTATTAATATATATAAATCT
Found at i:3766478 original size:6 final size:6
Alignment explanation
Indices: 3766467--3766498 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
3766457 CATTCTAAGG
3766467 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TT
3766499 ATTGATTAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTAT
Found at i:3766555 original size:13 final size:13
Alignment explanation
Indices: 3766528--3766569 Score: 59
Period size: 13 Copynumber: 3.2 Consensus size: 13
3766518 CTTAGTATTC
3766528 TTTATTTTATTTAT
1 TTTA-TTTATTTAT
3766542 TTTA-TTATTTTAT
1 TTTATTTA-TTTAT
3766555 TTTATTTATTTAT
1 TTTATTTATTTAT
3766568 TT
1 TT
3766570 AAATGATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
12 3 0.12
13 16 0.62
14 7 0.27
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (13 bp):
TTTATTTATTTAT
Done.