Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 135709677
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: 135709677
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 350 characters in sequence are not A, C, G, or T
File 176 of 438
Found at i:54268794 original size:130 final size:130
Alignment explanation
Indices: 54268561--54268820 Score: 520
Period size: 130 Copynumber: 2.0 Consensus size: 130
54268551 ACATCAGTGC
54268561 TTTGGATTCTGAGGTTCCGTCTGTTAAAGATATCAGAACAGTTAAGGACTTTCTGAACGTCTTTC
1 TTTGGATTCTGAGGTTCCGTCTGTTAAAGATATCAGAACAGTTAAGGACTTTCTGAACGTCTTTC
54268626 TCGATGAGCTACCTGGGTTACCTCCAAACTGTGAAGTTGATTTTGGGATTGATCTCCTACTTGGT
66 TCGATGAGCTACCTGGGTTACCTCCAAACTGTGAAGTTGATTTTGGGATTGATCTCCTACTTGGT
54268691 TTTGGATTCTGAGGTTCCGTCTGTTAAAGATATCAGAACAGTTAAGGACTTTCTGAACGTCTTTC
1 TTTGGATTCTGAGGTTCCGTCTGTTAAAGATATCAGAACAGTTAAGGACTTTCTGAACGTCTTTC
54268756 TCGATGAGCTACCTGGGTTACCTCCAAACTGTGAAGTTGATTTTGGGATTGATCTCCTACTTGGT
66 TCGATGAGCTACCTGGGTTACCTCCAAACTGTGAAGTTGATTTTGGGATTGATCTCCTACTTGGT
54268821 ATAGCTCTTG
Statistics
Matches: 130, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
130 130 1.00
ACGTcount: A:0.22, C:0.18, G:0.23, T:0.36
Consensus pattern (130 bp):
TTTGGATTCTGAGGTTCCGTCTGTTAAAGATATCAGAACAGTTAAGGACTTTCTGAACGTCTTTC
TCGATGAGCTACCTGGGTTACCTCCAAACTGTGAAGTTGATTTTGGGATTGATCTCCTACTTGGT
Found at i:54279272 original size:27 final size:28
Alignment explanation
Indices: 54279242--54279311 Score: 106
Period size: 27 Copynumber: 2.5 Consensus size: 28
54279232 ATAATAAGTC
*
54279242 CGCACACTTAGTGCTATATAATC-AGCT
1 CGCACACTTAGTGCTATATAATCAAACT
* *
54279269 CGCACACATAGTGCTATATAATCAAATT
1 CGCACACTTAGTGCTATATAATCAAACT
54279297 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
54279312 GTACAAATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
27 22 0.58
28 16 0.42
ACGTcount: A:0.31, C:0.26, G:0.14, T:0.29
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:54287195 original size:27 final size:28
Alignment explanation
Indices: 54287165--54287234 Score: 106
Period size: 27 Copynumber: 2.5 Consensus size: 28
54287155 ATAATAAGTC
*
54287165 CGCACACTTAGTGCTATATAATC-AGCT
1 CGCACACTTAGTGCTATATAATCAAACT
* *
54287192 CGCACACATAGTGCTATATAATCAAATT
1 CGCACACTTAGTGCTATATAATCAAACT
54287220 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
54287235 GTACAAATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
27 22 0.58
28 16 0.42
ACGTcount: A:0.31, C:0.26, G:0.14, T:0.29
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:54294100 original size:20 final size:19
Alignment explanation
Indices: 54294077--54294133 Score: 53
Period size: 20 Copynumber: 2.9 Consensus size: 19
54294067 CATTACAAAT
54294077 ATATCTTATCATATACATAA
1 ATATCTTATCATATACAT-A
* * *
54294097 ATATCATATCA-AAACATT
1 ATATCTTATCATATACATA
54294115 ATATGCTTATACATATACA
1 ATAT-CTTAT-CATATACA
54294134 AATGTCGAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
18 4 0.14
19 9 0.31
20 12 0.41
21 4 0.14
ACGTcount: A:0.46, C:0.16, G:0.02, T:0.37
Consensus pattern (19 bp):
ATATCTTATCATATACATA
Found at i:54306385 original size:10 final size:10
Alignment explanation
Indices: 54306370--54306395 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
54306360 AAACACCAAG
54306370 AGTTTGAATA
1 AGTTTGAATA
54306380 AGTTTGAATA
1 AGTTTGAATA
54306390 AGTTTG
1 AGTTTG
54306396 TTGTTAGCCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.35, C:0.00, G:0.23, T:0.42
Consensus pattern (10 bp):
AGTTTGAATA
Found at i:54306597 original size:19 final size:18
Alignment explanation
Indices: 54306570--54306608 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
54306560 GGTTTTGATG
*
54306570 TTTTGCTCTTCAATTCATT
1 TTTTACTCTTC-ATTCATT
*
54306589 TTTTACTCTTCTTTCATT
1 TTTTACTCTTCATTCATT
54306607 TT
1 TT
54306609 ATTTTCTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.13, C:0.21, G:0.03, T:0.64
Consensus pattern (18 bp):
TTTTACTCTTCATTCATT
Found at i:54307343 original size:8 final size:8
Alignment explanation
Indices: 54307326--54307382 Score: 69
Period size: 8 Copynumber: 7.1 Consensus size: 8
54307316 AATTACAAAG
54307326 GCTGAAAA
1 GCTGAAAA
*
54307334 GCTAAAAA
1 GCTGAAAA
*
54307342 GCTGAAAG
1 GCTGAAAA
54307350 GCTGAAAA
1 GCTGAAAA
*
54307358 GATGAAAA
1 GCTGAAAA
* *
54307366 ACTGAAAG
1 GCTGAAAA
54307374 GCTGAAAA
1 GCTGAAAA
54307382 G
1 G
54307383 TCAAAAAGTG
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
8 39 1.00
ACGTcount: A:0.51, C:0.11, G:0.26, T:0.12
Consensus pattern (8 bp):
GCTGAAAA
Found at i:54307354 original size:24 final size:24
Alignment explanation
Indices: 54307322--54307390 Score: 97
Period size: 24 Copynumber: 2.9 Consensus size: 24
54307312 GTGAAATTAC
54307322 AAAGGCTGAAAAG-CTAAAAAGCTG
1 AAAGGCTGAAAAGTC-AAAAAGCTG
*
54307346 AAAGGCTGAAAAGATGAAAAA-CTG
1 AAAGGCTGAAAAG-TCAAAAAGCTG
54307370 AAAGGCTGAAAAGTCAAAAAG
1 AAAGGCTGAAAAGTCAAAAAG
54307391 TGGGTTGACG
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
23 6 0.15
24 29 0.73
25 5 0.12
ACGTcount: A:0.54, C:0.10, G:0.25, T:0.12
Consensus pattern (24 bp):
AAAGGCTGAAAAGTCAAAAAGCTG
Found at i:54307558 original size:73 final size:73
Alignment explanation
Indices: 54307439--54307657 Score: 350
Period size: 73 Copynumber: 3.0 Consensus size: 73
54307429 TGGCAAGTCG
**
54307439 TGTAACAAAACATGG-TCGTGTGGAAAACGAGATGGCCATGGGCGTTTCCATGAGCCGAAACCAT
1 TGTAACAAAACATGGCT-GTGTGGTCAACGAGATGGCCATGGGCGTTTCCATGAGCCGAAACCAT
54307503 ACTGGGCCA
65 ACTGGGCCA
54307512 TGTAACAAAACATGGCTGTGTGGTCAACGAGATGGCCATGGGCGTTTCCATGAGCCGAAACCATA
1 TGTAACAAAACATGGCTGTGTGGTCAACGAGATGGCCATGGGCGTTTCCATGAGCCGAAACCATA
54307577 CTGGGCCA
66 CTGGGCCA
* * * * **
54307585 TGTCACAAAACATGACCGTGTGGTCAACGAGATGGCCATGGGCGTTTCCATGAGCCAAAAAGATA
1 TGTAACAAAACATGGCTGTGTGGTCAACGAGATGGCCATGGGCGTTTCCATGAGCCGAAACCATA
54307650 CTGGGCCA
66 CTGGGCCA
54307658 CGTAGGCCCA
Statistics
Matches: 137, Mismatches: 8, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
73 136 0.99
74 1 0.01
ACGTcount: A:0.29, C:0.23, G:0.28, T:0.20
Consensus pattern (73 bp):
TGTAACAAAACATGGCTGTGTGGTCAACGAGATGGCCATGGGCGTTTCCATGAGCCGAAACCATA
CTGGGCCA
Found at i:54307957 original size:27 final size:27
Alignment explanation
Indices: 54307927--54307980 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
54307917 AAATGATCGG
*
54307927 AATACCCCCATAGGGTAAAATGACTGT
1 AATACCCCCATAAGGTAAAATGACTGT
* **
54307954 AATACCTCTGTAAGGTAAAATGACTGT
1 AATACCCCCATAAGGTAAAATGACTGT
54307981 TTTGCCCTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.26
Consensus pattern (27 bp):
AATACCCCCATAAGGTAAAATGACTGT
Found at i:54307999 original size:27 final size:27
Alignment explanation
Indices: 54307969--54308078 Score: 125
Period size: 27 Copynumber: 4.1 Consensus size: 27
54307959 CTCTGTAAGG
*
54307969 TAAAATGACTGTTTTGCCCTTATGTGT
1 TAAAATGACTGTTTTGCCCTTATGTGA
* *
54307996 TAAAATGAC-GATTTTTCCCTTATGTGG
1 TAAAATGACTG-TTTTGCCCTTATGTGA
* **
54308023 TAAAATGACTGTTTTGCCCCTAACTGA
1 TAAAATGACTGTTTTGCCCTTATGTGA
*
54308050 TAAAATGAATGTTTTGACCC-TATGTGA
1 TAAAATGACTGTTTTG-CCCTTATGTGA
54308077 TA
1 TA
54308079 TATGTTTATA
Statistics
Matches: 70, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
26 1 0.01
27 65 0.93
28 4 0.06
ACGTcount: A:0.28, C:0.15, G:0.17, T:0.39
Consensus pattern (27 bp):
TAAAATGACTGTTTTGCCCTTATGTGA
Found at i:54315381 original size:40 final size:39
Alignment explanation
Indices: 54315216--54315399 Score: 138
Period size: 40 Copynumber: 4.6 Consensus size: 39
54315206 AAATTGAATG
* * *
54315216 ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAAT--T
1 ATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCAAATCGT
* * * * * *
54315256 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-T
* * * * *
54315296 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATC-GT
*
54315336 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
* * *
54315375 GATATCCGGGTTAAGTCCCGTAGGC
1 -ATATCCGGGCTAAGACCCGAAGGC
54315400 CTTGGTGCGG
Statistics
Matches: 113, Mismatches: 26, Indels: 10
0.76 0.17 0.07
Matches are distributed among these distances:
37 4 0.04
38 2 0.02
39 3 0.03
40 104 0.92
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (39 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
Found at i:54315424 original size:80 final size:81
Alignment explanation
Indices: 54315256--54315444 Score: 186
Period size: 80 Copynumber: 2.4 Consensus size: 81
54315246 GCTGGAAATT
* * * *
54315256 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCTACATCCGGGCTAAGACCCGAAGGCA
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
*
54315321 TTCGTGCGAGTCATTC
66 TTCGTGCGAGTCATCC
* * * * * *
54315337 -TATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-TGATATCCGGGTTAAGTCCCGTAGGC
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCT-ACATCCGGGCTAAGACCCGAAGGC
* * * *
54315400 CTTGGTGCGGGTTA-CC
65 ATTCGTGCGAGTCATCC
* * *
54315416 ATAACCGGGCTATGTCCCGAAGGCGATTG
1 ATAACCGGGCTAAGACCCGAAGGCAATTG
54315445 ATCGAGTAGC
Statistics
Matches: 86, Mismatches: 20, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
79 2 0.02
80 84 0.98
ACGTcount: A:0.23, C:0.24, G:0.30, T:0.23
Consensus pattern (81 bp):
ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
TTCGTGCGAGTCATCC
Found at i:54322671 original size:40 final size:39
Alignment explanation
Indices: 54322506--54322689 Score: 138
Period size: 40 Copynumber: 4.6 Consensus size: 39
54322496 AAATTGAATG
* * *
54322506 ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAAT--T
1 ATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCAAATCGT
* * * * * *
54322546 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-T
* * * * *
54322586 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATC-GT
*
54322626 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
* * *
54322665 GATATCCGGGTTAAGTCCCGTAGGC
1 -ATATCCGGGCTAAGACCCGAAGGC
54322690 CTTGGTGCGG
Statistics
Matches: 113, Mismatches: 26, Indels: 10
0.76 0.17 0.07
Matches are distributed among these distances:
37 4 0.04
38 2 0.02
39 3 0.03
40 104 0.92
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (39 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
Found at i:54322714 original size:80 final size:81
Alignment explanation
Indices: 54322546--54322734 Score: 186
Period size: 80 Copynumber: 2.4 Consensus size: 81
54322536 GCTGGAAATT
* * * *
54322546 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCTACATCCGGGCTAAGACCCGAAGGCA
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
*
54322611 TTCGTGCGAGTCATTC
66 TTCGTGCGAGTCATCC
* * * * * *
54322627 -TATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-TGATATCCGGGTTAAGTCCCGTAGGC
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCT-ACATCCGGGCTAAGACCCGAAGGC
* * * *
54322690 CTTGGTGCGGGTTA-CC
65 ATTCGTGCGAGTCATCC
* * *
54322706 ATAACCGGGCTATGTCCCGAAGGCGATTG
1 ATAACCGGGCTAAGACCCGAAGGCAATTG
54322735 ATCGAGTAGC
Statistics
Matches: 86, Mismatches: 20, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
79 2 0.02
80 84 0.98
ACGTcount: A:0.23, C:0.24, G:0.30, T:0.23
Consensus pattern (81 bp):
ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
TTCGTGCGAGTCATCC
Found at i:54331723 original size:34 final size:34
Alignment explanation
Indices: 54331677--54331747 Score: 117
Period size: 34 Copynumber: 2.1 Consensus size: 34
54331667 GCCGAATGGC
*
54331677 TAATGTGAAATATATGTGTG-ATATGTATATGTGG
1 TAATATGAAATATATGTG-GAATATGTATATGTGG
54331711 TAATATGAAATATATGTGGAATATGTATATGTGG
1 TAATATGAAATATATGTGGAATATGTATATGTGG
54331745 TAA
1 TAA
54331748 AGCCGAATGG
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
33 1 0.03
34 34 0.97
ACGTcount: A:0.37, C:0.00, G:0.24, T:0.39
Consensus pattern (34 bp):
TAATATGAAATATATGTGGAATATGTATATGTGG
Found at i:54331744 original size:15 final size:15
Alignment explanation
Indices: 54331687--54331744 Score: 64
Period size: 15 Copynumber: 3.6 Consensus size: 15
54331677 TAATGTGAAA
54331687 TATATGTGTG-ATATG
1 TATATGTG-GAATATG
54331702 TATATGTGGTAATATG
1 TATATGTGG-AATATG
54331718 AAATATATGTGGAATATG
1 ---TATATGTGGAATATG
54331736 TATATGTGG
1 TATATGTGG
54331745 TAAAGCCGAA
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
14 1 0.03
15 17 0.45
16 5 0.13
18 6 0.16
19 9 0.24
ACGTcount: A:0.33, C:0.00, G:0.26, T:0.41
Consensus pattern (15 bp):
TATATGTGGAATATG
Found at i:54331768 original size:48 final size:48
Alignment explanation
Indices: 54331711--54332007 Score: 434
Period size: 48 Copynumber: 6.2 Consensus size: 48
54331701 GTATATGTGG
*
54331711 TAATATGAAATATATGTG-GAATATGTATATGTGGTAAAGCCGAATGGC
1 TAATGTGAAATATATGTGTG-ATATGTATATGTGGTAAAGCCGAATGGC
* **
54331759 TAATATGAAATATATGTGTGATATGTATATGTGGTAAAGCCGAGCGGC
1 TAATGTGAAATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGC
*
54331807 TAATGTGAAATATATGTGTGATATGTATATGTGGTAAAGCCGAAGGGC
1 TAATGTGAAATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGC
* * * * *
54331855 CAATGTGAAATATGTATGAGATATGTATATGTGGTAAAGTCGAATGGC
1 TAATGTGAAATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGC
* * * *
54331903 TAATGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATAGC
1 TAATGTGAAATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGC
* *
54331951 TAATATGAAATATATGTGTGATATGAATATGTGGTAAAGCCGAATGGC
1 TAATGTGAAATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGC
54331999 TAATGTGAA
1 TAATGTGAA
54332008 TGTTGTAACA
Statistics
Matches: 227, Mismatches: 21, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
48 226 1.00
49 1 0.00
ACGTcount: A:0.36, C:0.06, G:0.26, T:0.31
Consensus pattern (48 bp):
TAATGTGAAATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGC
Found at i:54332102 original size:37 final size:37
Alignment explanation
Indices: 54332052--54332159 Score: 162
Period size: 37 Copynumber: 2.9 Consensus size: 37
54332042 GGAAATATAT
54332052 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
*
54332089 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
* * * * *
54332126 TCCGAGTGAGACCTGATAACTTCGTGTGGAGATT
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATT
54332160 TCGTCTGAGC
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 65 1.00
ACGTcount: A:0.23, C:0.19, G:0.31, T:0.27
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
Found at i:54334732 original size:16 final size:16
Alignment explanation
Indices: 54334711--54334741 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
54334701 TCGGTAGATC
54334711 TCAAAATGCCGAAAAG
1 TCAAAATGCCGAAAAG
*
54334727 TCAAAATGCTGAAAA
1 TCAAAATGCCGAAAA
54334742 ACTGAAAGTT
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:0.52, C:0.16, G:0.16, T:0.16
Consensus pattern (16 bp):
TCAAAATGCCGAAAAG
Found at i:54335013 original size:29 final size:28
Alignment explanation
Indices: 54334964--54335024 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 28
54334954 ACATGTCTTG
*
54334964 GAATTGATTTAGGCCAGATGGGCCATAT
1 GAATTGATTTAAGCCAGATGGGCCATAT
54334992 GAATGTGATTTAAGCCTA-ATGGGCCATAT
1 GAAT-TGATTTAAGCC-AGATGGGCCATAT
54335021 GAAT
1 GAAT
54335025 AAGATTGGGC
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
28 4 0.13
29 25 0.83
30 1 0.03
ACGTcount: A:0.31, C:0.13, G:0.26, T:0.30
Consensus pattern (28 bp):
GAATTGATTTAAGCCAGATGGGCCATAT
Found at i:54335045 original size:28 final size:29
Alignment explanation
Indices: 54334981--54335049 Score: 86
Period size: 28 Copynumber: 2.4 Consensus size: 29
54334971 TTTAGGCCAG
**
54334981 ATGGGCCATATGAATGTGATTTAAGCCTA
1 ATGGGCCATATGAATAAGATTTAAGCCTA
**
54335010 ATGGGCCATATGAATAAGA-TTGGGCCTA
1 ATGGGCCATATGAATAAGATTTAAGCCTA
*
54335038 GTGGGCCATATG
1 ATGGGCCATATG
54335050 CATGTATGTA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
28 18 0.51
29 17 0.49
ACGTcount: A:0.29, C:0.14, G:0.29, T:0.28
Consensus pattern (29 bp):
ATGGGCCATATGAATAAGATTTAAGCCTA
Found at i:54338182 original size:40 final size:39
Alignment explanation
Indices: 54338137--54338344 Score: 202
Period size: 40 Copynumber: 5.2 Consensus size: 39
54338127 CGGAATACAA
*
54338137 CCGGATATAACCACATGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC
* * *
54338177 CCGGATAGAACGACTTGCACAAATGCCTTCGGGTATTAGC
1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC
* * *
54338217 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC
* ** *
54338257 CCGGATGTAGTCACTAGCAC-AATGGCCTTCGGGTCTTAAC
1 CCGGATATAACCACT-GCACAAAT-GCCTTCGGGTCTTAGC
* ** * * *
54338297 CTGGATATAATTACTAGCATAAATGTCTTCGGGACTTAGC
1 CCGGATATAACCACT-GCACAAATGCCTTCGGGTCTTAGC
54338337 CCGGATAT
1 CCGGATAT
54338345 CATTCAATTG
Statistics
Matches: 141, Mismatches: 24, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
39 4 0.03
40 134 0.95
41 3 0.02
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.26
Consensus pattern (39 bp):
CCGGATATAACCACTGCACAAATGCCTTCGGGTCTTAGC
Found at i:54338277 original size:80 final size:81
Alignment explanation
Indices: 54338137--54338342 Score: 231
Period size: 80 Copynumber: 2.6 Consensus size: 81
54338127 CGGAATACAA
* * *
54338137 CCGGATATAACCACATGCACGAATGCCTTCGGGTCTTAGCCCGGA-TAGAACGACTTGCACAAAT
1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATTAGAACGACTAGCAC-AAT
*
54338201 -GCCTTCGGGTATTAGC
65 GGCCTTCGGGTATTAAC
* *
54338217 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATGTAG-TC-ACTAGCACAAT
1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGAT-TAGAACGACTAGCACAAT
*
54338280 GGCCTTCGGGTCTTAAC
65 GGCCTTCGGGTATTAAC
* ** * ** * *
54338297 CTGGATATAATTACTAGCATAAATGTCTTCGGGACTTAGCCCGGAT
1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGAT
54338343 ATCATTCAAT
Statistics
Matches: 107, Mismatches: 16, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
79 3 0.03
80 100 0.93
81 1 0.01
82 3 0.03
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.26
Consensus pattern (81 bp):
CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATTAGAACGACTAGCACAATG
GCCTTCGGGTATTAAC
Found at i:54340934 original size:17 final size:17
Alignment explanation
Indices: 54340898--54340944 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
54340888 CATTGTCCCT
* *
54340898 AATGCACTAAC-ATTAA
1 AATGCAATAACAATAAA
*
54340914 AATGGAATAACAATAAA
1 AATGCAATAACAATAAA
*
54340931 AATGCAATGACAAT
1 AATGCAATAACAAT
54340945 GTTCACTAAC
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
16 9 0.36
17 16 0.64
ACGTcount: A:0.55, C:0.13, G:0.11, T:0.21
Consensus pattern (17 bp):
AATGCAATAACAATAAA
Found at i:54344719 original size:46 final size:45
Alignment explanation
Indices: 54344669--54344844 Score: 187
Period size: 46 Copynumber: 3.8 Consensus size: 45
54344659 TGGTTGAGCA
54344669 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG-GAATG
* * *
54344715 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGGAA-T--G
*
54344760 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG-GAATG
* * * * *
54344808 CCCGAGCTCGTTGAGTTGAGTCCAATTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
54344845 GCGGGTTACA
Statistics
Matches: 109, Mismatches: 12, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 61 0.56
47 29 0.27
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.21, C:0.20, G:0.28, T:0.30
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGGAATG
Found at i:54346260 original size:47 final size:48
Alignment explanation
Indices: 54346191--54346312 Score: 135
Period size: 47 Copynumber: 2.6 Consensus size: 48
54346181 GCCAATGCCG
* * *
54346191 TGTCCCAGACACGGTCTTACACTGGCTTA-TATCAC-AAGTCAAAGCCA
1 TGTCCCAGACATGGTCTTACACTGGCTTAGCATCACGAAGCCAAAG-CA
* * * *
54346238 TGTCCCAGACATGGTCTTACACTGAC-TAGCATCTCGTAGCCAATGCA
1 TGTCCCAGACATGGTCTTACACTGGCTTAGCATCACGAAGCCAAAGCA
*
54346285 TGTCACAGACAT-GTCTTACACTGGCTTA
1 TGTCCCAGACATGGTCTTACACTGGCTTA
54346313 CGTCTCAAGG
Statistics
Matches: 63, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
46 14 0.22
47 43 0.68
48 6 0.10
ACGTcount: A:0.27, C:0.29, G:0.18, T:0.26
Consensus pattern (48 bp):
TGTCCCAGACATGGTCTTACACTGGCTTAGCATCACGAAGCCAAAGCA
Found at i:54346330 original size:46 final size:46
Alignment explanation
Indices: 54346191--54346400 Score: 160
Period size: 46 Copynumber: 4.5 Consensus size: 46
54346181 GCCAATGCCG
* ** * * * *
54346191 TGTCCCAGACACGGTCTTACACTGGCTTA-TATCACAAGTCAAAGCCA
1 TGTCCCAGACATGGTCTTACACTGGC-TACCGTCTCAAGCCGATG-CA
* * * * *
54346238 TGTCCCAGACATGGTCTTACACTGACTAGCATCTCGTAGCCAATGCA
1 TGTCCCAGACATGGTCTTACACTGGCTACCGTCTC-AAGCCGATGCA
*
54346285 TGTCACAGACAT-GTCTTACACTGGCTTA-CGTCTCAAGGCCGATGCA
1 TGTCCCAGACATGGTCTTACACTGGC-TACCGTCTCAA-GCCGATGCA
* * * *
54346331 TGTCCCGGACA-CGTCTTACACTAG-TACTCGTCTCAATACCGATGCCA
1 TGTCCCAGACATGGTCTTACACTGGCTAC-CGTCTCAA-GCCGATG-CA
54346378 TGTCCCAGACATGGTCTTACACT
1 TGTCCCAGACATGGTCTTACACT
54346401 AGCTCTCACA
Statistics
Matches: 135, Mismatches: 19, Indels: 17
0.79 0.11 0.10
Matches are distributed among these distances:
44 2 0.01
45 1 0.01
46 61 0.45
47 55 0.41
48 16 0.12
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.26
Consensus pattern (46 bp):
TGTCCCAGACATGGTCTTACACTGGCTACCGTCTCAAGCCGATGCA
Found at i:54356811 original size:47 final size:47
Alignment explanation
Indices: 54356707--54356920 Score: 142
Period size: 47 Copynumber: 4.6 Consensus size: 47
54356697 AGGTGCCGAT
* * *
54356707 GCCATGTCCCAGACACGGTCTTACACTGGCTTATATCTCAAGTCGAA
1 GCCATGTCCCAGACATGGTCTTACACTGACTTATATCTCAAGTCCAA
* **
54356754 GCCATATCCCAGACATGGTCTTACACTGAC-TATCATCTTGTAG-CCAA
1 GCCATGTCCCAGACATGGTCTTACACTGACTTAT-ATC-TCAAGTCCAA
** * * *
54356801 -CGCATGTCCCAGACAT-GTCTTACACT-AGCTTACGTCTCGAGGCCGAT
1 GC-CATGTCCCAGACATGGTCTTACACTGA-CTTATATCTCAAGTCC-AA
* * *
54356848 G-CATGTCCCAGAAAT-GTCTTACACTAGCAC-T-TGTCTCAA-TACCGAT
1 GCCATGTCCCAGACATGGTCTTACACT-G-ACTTATATCTCAAGT-CC-AA
*
54356894 GCCATGTCCCAGGCATGGTCTTACACT
1 GCCATGTCCCAGACATGGTCTTACACT
54356921 AGCTCTCACA
Statistics
Matches: 135, Mismatches: 18, Indels: 27
0.75 0.10 0.15
Matches are distributed among these distances:
45 4 0.03
46 54 0.40
47 62 0.46
48 14 0.10
49 1 0.01
ACGTcount: A:0.25, C:0.30, G:0.18, T:0.27
Consensus pattern (47 bp):
GCCATGTCCCAGACATGGTCTTACACTGACTTATATCTCAAGTCCAA
Found at i:54356852 original size:46 final size:46
Alignment explanation
Indices: 54356701--54356924 Score: 172
Period size: 46 Copynumber: 4.8 Consensus size: 46
54356691 GGGGTAAGGT
* * * *
54356701 GCCGATGCCATGTCCCAGACACGGTCTTACACTGGCTTATATCTCAA
1 GCCGATGCCATGTCCCAGACA-TGTCTTACACTAGCTTACATCTCGA
* * * *
54356748 GTCGAAGCCATATCCCAGACATGGTCTTACACT-GAC-TATCATCTTGTA
1 GCCGATGCCATGTCCCAGACAT-GTCTTACACTAG-CTTA-CATCTCG-A
* * *
54356796 GCCAACG-CATGTCCCAGACATGTCTTACACTAGCTTACGTCTCGA
1 GCCGATGCCATGTCCCAGACATGTCTTACACTAGCTTACATCTCGA
* * *
54356841 GGCCGATG-CATGTCCCAGAAATGTCTTACACTAGC--ACTTGTCTCAA
1 -GCCGATGCCATGTCCCAGACATGTCTTACACTAGCTTAC--ATCTCGA
* *
54356887 TACCGATGCCATGTCCCAGGCATGGTCTTACACTAGCT
1 -GCCGATGCCATGTCCCAGACAT-GTCTTACACTAGCT
54356925 CTCACAAATG
Statistics
Matches: 144, Mismatches: 21, Indels: 22
0.77 0.11 0.12
Matches are distributed among these distances:
44 2 0.01
45 1 0.01
46 62 0.43
47 61 0.42
48 18 0.12
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.26
Consensus pattern (46 bp):
GCCGATGCCATGTCCCAGACATGTCTTACACTAGCTTACATCTCGA
Found at i:54359361 original size:18 final size:17
Alignment explanation
Indices: 54359328--54359365 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
54359318 AACAAACTTG
54359328 AATAAAAATAATAATAA
1 AATAAAAATAATAATAA
*
54359345 AATAAAATTACATAATAA
1 AATAAAAATA-ATAATAA
54359363 AAT
1 AAT
54359366 TCATAAGAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (17 bp):
AATAAAAATAATAATAA
Found at i:54374573 original size:40 final size:40
Alignment explanation
Indices: 54374529--54374695 Score: 167
Period size: 40 Copynumber: 4.2 Consensus size: 40
54374519 TCGAATATAA
54374529 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * * * *
54374569 CCGGATAGAATAACTCGCACGAATGCCTTCAGGCCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * *
54374609 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
54374649 CCGGATATAATTTCCAGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
54374688 CCGGATAT
1 CCGGATAT
54374696 CATTCAATTT
Statistics
Matches: 103, Mismatches: 23, Indels: 3
0.80 0.18 0.02
Matches are distributed among these distances:
39 14 0.14
40 89 0.86
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:54377530 original size:87 final size:85
Alignment explanation
Indices: 54377373--54377537 Score: 222
Period size: 87 Copynumber: 1.9 Consensus size: 85
54377363 AGCTATCTGG
** * *
54377373 TACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACGTAGTAGCCTG
1 TACACATAGTAGCCTGCACTTAGTACTACACACACGACCAATTATCAGGTACACATAGTAGCCTG
*
54377438 TACTTAGTACTACCATTTGA
66 CACTTAGTACTACCATTTGA
* * * * *
54377458 TACACGTAGTAGCCTGTACTTAGTACTACACACATGATCGAAGTTATCAGGTACGCATAGTAGCC
1 TACACATAGTAGCCTGCACTTAGTACTACACACACGA-CCAA-TTATCAGGTACACATAGTAGCC
54377523 TGCACTTAGTACTAC
64 TGCACTTAGTACTAC
54377538 ACATGCGACC
Statistics
Matches: 68, Mismatches: 10, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
85 32 0.47
86 3 0.04
87 33 0.49
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.28
Consensus pattern (85 bp):
TACACATAGTAGCCTGCACTTAGTACTACACACACGACCAATTATCAGGTACACATAGTAGCCTG
CACTTAGTACTACCATTTGA
Found at i:54377937 original size:35 final size:35
Alignment explanation
Indices: 54377886--54377952 Score: 116
Period size: 35 Copynumber: 1.9 Consensus size: 35
54377876 ATATTTCATA
*
54377886 ATAACAATCTTCATATCATATAAATAACATTAATG
1 ATAACAATCATCATATCATATAAATAACATTAATG
*
54377921 ATAATAATCATCATATCATATAAATAACATTA
1 ATAACAATCATCATATCATATAAATAACATTA
54377953 TATTACTTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.51, C:0.13, G:0.01, T:0.34
Consensus pattern (35 bp):
ATAACAATCATCATATCATATAAATAACATTAATG
Found at i:54377955 original size:19 final size:19
Alignment explanation
Indices: 54377898--54377955 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 19
54377888 AACAATCTTC
54377898 ATATCATATAAATAACATT
1 ATATCATATAAATAACATT
* *
54377917 A-AT--GAT-AATAATCATC
1 ATATCATATAAATAA-CATT
54377933 ATATCATATAAATAACATT
1 ATATCATATAAATAACATT
54377952 ATAT
1 ATAT
54377956 TACTTAAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 10
0.68 0.09 0.23
Matches are distributed among these distances:
15 5 0.17
16 6 0.20
17 2 0.07
18 2 0.07
19 10 0.33
20 5 0.17
ACGTcount: A:0.52, C:0.10, G:0.02, T:0.36
Consensus pattern (19 bp):
ATATCATATAAATAACATT
Found at i:54380283 original size:15 final size:16
Alignment explanation
Indices: 54380254--54380285 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
54380244 AACAGAGAAG
54380254 CCAAGAATAAAGAAAT
1 CCAAGAATAAAGAAAT
54380270 CCAAG-ATAAAGAAAT
1 CCAAGAATAAAGAAAT
54380285 C
1 C
54380286 AATGATACGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.59, C:0.16, G:0.12, T:0.12
Consensus pattern (16 bp):
CCAAGAATAAAGAAAT
Found at i:54390982 original size:40 final size:40
Alignment explanation
Indices: 54390938--54391039 Score: 134
Period size: 40 Copynumber: 2.5 Consensus size: 40
54390928 TCGCACGATT
* * * *
54390938 GCCTTCGGGTCTTAACCCGGATTTGGT-AACTTGCACAAAG
1 GCCTTCGGGTCTTAGCCCGGATAT-ATCAACTCGCACAAAG
* *
54390978 GCCTTCGGGTCTTAGCCCGGATATATCAACTCGCACGAAT
1 GCCTTCGGGTCTTAGCCCGGATATATCAACTCGCACAAAG
54391018 GCCTTCGGGTCTTAGCCCGGAT
1 GCCTTCGGGTCTTAGCCCGGAT
54391040 GTAATACTAG
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
39 1 0.02
40 54 0.98
ACGTcount: A:0.20, C:0.28, G:0.25, T:0.26
Consensus pattern (40 bp):
GCCTTCGGGTCTTAGCCCGGATATATCAACTCGCACAAAG
Found at i:54393283 original size:30 final size:29
Alignment explanation
Indices: 54393172--54393327 Score: 214
Period size: 30 Copynumber: 5.5 Consensus size: 29
54393162 GACAAGATTG
* * * * *
54393172 GCACTAAGTGTGCGGGTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGCTGAAAA-TATATA
54393202 GCACTAAGTGTGCGAG-TG---ATATATA
1 GCACTAAGTGTGCGAGCTGAAAATATATA
54393227 GCACTAAGTGTGCGAGCTG-AAATATATA
1 GCACTAAGTGTGCGAGCTGAAAATATATA
54393255 GCACTAAGTGTGCGAGCTGAAAATTATATA
1 GCACTAAGTGTGCGAGCTGAAAA-TATATA
54393285 GCACTAAGTGTGCGAGCTGAAAATATATA
1 GCACTAAGTGTGCGAGCTGAAAATATATA
54393314 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
54393328 GATTCACTAT
Statistics
Matches: 117, Mismatches: 4, Indels: 11
0.89 0.03 0.08
Matches are distributed among these distances:
25 20 0.17
26 3 0.03
28 26 0.22
29 24 0.21
30 44 0.38
ACGTcount: A:0.33, C:0.14, G:0.26, T:0.26
Consensus pattern (29 bp):
GCACTAAGTGTGCGAGCTGAAAATATATA
Found at i:54393295 original size:58 final size:54
Alignment explanation
Indices: 54393172--54393327 Score: 206
Period size: 58 Copynumber: 2.8 Consensus size: 54
54393162 GACAAGATTG
* * * * *
54393172 GCACTAAGTGTGCGGGTTTAAAATTGTACAGCACTAAGTGTGCGAGTGATATATA
1 GCACTAAGTGTGCGAGCTGAAAA-TATATAGCACTAAGTGTGCGAGTGATATATA
54393227 GCACTAAGTGTGCGAGCTG-AAATATATAGCACTAAGTGTGCGAGCTGAAAATTATATA
1 GCACTAAGTGTGCGAGCTGAAAATATATAGCACTAAGTGTGCGAG-TG---A-TATATA
54393285 GCACTAAGTGTGCGAGCTGAAAATATATAGCACTAAGTGTGCG
1 GCACTAAGTGTGCGAGCTGAAAATATATAGCACTAAGTGTGCG
54393328 GATTCACTAT
Statistics
Matches: 90, Mismatches: 5, Indels: 8
0.87 0.05 0.08
Matches are distributed among these distances:
53 20 0.22
54 5 0.06
55 16 0.18
57 1 0.01
58 25 0.28
59 23 0.26
ACGTcount: A:0.33, C:0.14, G:0.26, T:0.26
Consensus pattern (54 bp):
GCACTAAGTGTGCGAGCTGAAAATATATAGCACTAAGTGTGCGAGTGATATATA
Found at i:54401179 original size:59 final size:58
Alignment explanation
Indices: 54401063--54401223 Score: 250
Period size: 59 Copynumber: 2.7 Consensus size: 58
54401053 GACAAGATTG
* * * * *
54401063 GCACTAAGTGTGCGGGTTTAAAATTGTACAGCACTAAGTGTGCGAACTGAAAATATATA
1 GCACTAAGTGTGCGAGCTGAAAA-TATATAGCACTAAGTGTGCGAACTGAAAATATATA
*
54401122 GCACTAAGTGTGCGAGCTGAAAATATATAGCACTAAGTGTGCGAGCTGAAAATTATATA
1 GCACTAAGTGTGCGAGCTGAAAATATATAGCACTAAGTGTGCGAACTGAAAA-TATATA
54401181 GCACTAAGTGTGCGAGCTGAAAATATATAGCACTAAGTGTGCG
1 GCACTAAGTGTGCGAGCTGAAAATATATAGCACTAAGTGTGCG
54401224 GATTCACTAT
Statistics
Matches: 95, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
58 26 0.27
59 69 0.73
ACGTcount: A:0.35, C:0.14, G:0.25, T:0.25
Consensus pattern (58 bp):
GCACTAAGTGTGCGAGCTGAAAATATATAGCACTAAGTGTGCGAACTGAAAATATATA
Found at i:54401212 original size:88 final size:88
Alignment explanation
Indices: 54401063--54401223 Score: 268
Period size: 88 Copynumber: 1.8 Consensus size: 88
54401053 GACAAGATTG
* * * *
54401063 GCACTAAGTGTGCGGGTTTAAAATTGTACAGCACTAAGTGTGCGAACTGAAAATATATAGCACTA
1 GCACTAAGTGTGCGAGCTGAAAATTATACAGCACTAAGTGTGCGAACTGAAAATATATAGCACTA
54401128 AGTGTGCGAGCTGAAAATATATA
66 AGTGTGCGAGCTGAAAATATATA
* *
54401151 GCACTAAGTGTGCGAGCTGAAAATTATATAGCACTAAGTGTGCGAGCTGAAAATATATAGCACTA
1 GCACTAAGTGTGCGAGCTGAAAATTATACAGCACTAAGTGTGCGAACTGAAAATATATAGCACTA
54401216 AGTGTGCG
66 AGTGTGCG
54401224 GATTCACTAT
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
88 67 1.00
ACGTcount: A:0.35, C:0.14, G:0.25, T:0.25
Consensus pattern (88 bp):
GCACTAAGTGTGCGAGCTGAAAATTATACAGCACTAAGTGTGCGAACTGAAAATATATAGCACTA
AGTGTGCGAGCTGAAAATATATA
Found at i:54401235 original size:29 final size:29
Alignment explanation
Indices: 54401063--54401223 Score: 250
Period size: 29 Copynumber: 5.5 Consensus size: 29
54401053 GACAAGATTG
* * * * *
54401063 GCACTAAGTGTGCGGGTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGCTGAAAA-TATATA
*
54401093 GCACTAAGTGTGCGAACTGAAAATATATA
1 GCACTAAGTGTGCGAGCTGAAAATATATA
54401122 GCACTAAGTGTGCGAGCTGAAAATATATA
1 GCACTAAGTGTGCGAGCTGAAAATATATA
54401151 GCACTAAGTGTGCGAGCTGAAAATTATATA
1 GCACTAAGTGTGCGAGCTGAAAA-TATATA
54401181 GCACTAAGTGTGCGAGCTGAAAATATATA
1 GCACTAAGTGTGCGAGCTGAAAATATATA
54401210 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
54401224 GATTCACTAT
Statistics
Matches: 123, Mismatches: 7, Indels: 3
0.92 0.05 0.02
Matches are distributed among these distances:
29 75 0.61
30 48 0.39
ACGTcount: A:0.35, C:0.14, G:0.25, T:0.25
Consensus pattern (29 bp):
GCACTAAGTGTGCGAGCTGAAAATATATA
Found at i:54407344 original size:40 final size:39
Alignment explanation
Indices: 54407176--54407346 Score: 159
Period size: 40 Copynumber: 4.3 Consensus size: 39
54407166 AGAAATTGAA
* *
54407176 TGATATCCGGGCTAAGCCCCGAAGACAATTATGCTG-AAAT-
1 TGATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCAAATG
* * * * *
54407216 TTATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTAG
1 TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAAT-G
* *
54407256 CT-ATATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTG
1 -TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAA-ATG
* *
54407296 TTAAATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG
1 TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAAT-G
54407336 TGATATCCGGG
1 TGATATCCGGG
54407347 TAAAGTCCCG
Statistics
Matches: 107, Mismatches: 17, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
37 2 0.02
38 4 0.04
39 4 0.04
40 95 0.89
41 2 0.02
ACGTcount: A:0.28, C:0.22, G:0.26, T:0.24
Consensus pattern (39 bp):
TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATG
Found at i:54409588 original size:20 final size:20
Alignment explanation
Indices: 54409565--54409602 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
54409555 TGTATTCATA
54409565 AAATTTTAGAATTTTTCAGC
1 AAATTTTAGAATTTTTCAGC
**
54409585 AAATTTTTTAATTTTTCA
1 AAATTTTAGAATTTTTCA
54409603 TTTTAGTCCC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.08, G:0.05, T:0.53
Consensus pattern (20 bp):
AAATTTTAGAATTTTTCAGC
Found at i:54417835 original size:95 final size:98
Alignment explanation
Indices: 54417655--54417879 Score: 289
Period size: 95 Copynumber: 2.3 Consensus size: 98
54417645 CATTAAAGTT
* * *
54417655 GATGCCATGTCCCAGGCATGGTCTTACACTGACTCTCGTATATCGAGGCCGATGCCATGTCTCAA
1 GATGCCATGTCCCAGACATGGTCTTACACTGAC-CACG-ATATCGAAGCCGATGCCATGTCTCAA
* *
54417720 GCATGGTCTTACACTGGCTCTCATCTATCG-GTGCC
64 GCATGGTCTTACACTAGCTCTCATATATCGAG-GCC
* * *
54417755 GATGCCATGTCCCACACATGGTCTTACACTGA-CAC-ATATC-AAGCCGATGTCATGTC-CTAGA
1 GATGCCATGTCCCAGACATGGTCTTACACTGACCACGATATCGAAGCCGATGCCATGTCTCAAG-
*
54417816 CATGGTCTTACACTAGCTCTCATATCTCGAGGCC
65 CATGGTCTTACACTAGCTCTCATATATCGAGGCC
*
54417850 AATGCCATGTCCCAGACATGGTCTTACACT
1 GATGCCATGTCCCAGACATGGTCTTACACT
54417880 AGCTATCATA
Statistics
Matches: 112, Mismatches: 11, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
94 3 0.03
95 71 0.63
96 6 0.05
98 2 0.02
100 30 0.27
ACGTcount: A:0.23, C:0.30, G:0.20, T:0.27
Consensus pattern (98 bp):
GATGCCATGTCCCAGACATGGTCTTACACTGACCACGATATCGAAGCCGATGCCATGTCTCAAGC
ATGGTCTTACACTAGCTCTCATATATCGAGGCC
Found at i:54417893 original size:50 final size:49
Alignment explanation
Indices: 54417655--54417890 Score: 259
Period size: 50 Copynumber: 4.8 Consensus size: 49
54417645 CATTAAAGTT
* *
54417655 GATGCCATGTCCCAGGCATGGTCTTACACTGACTCTCGTATATCGAGGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTG-CTCTCATATATCGAGGCC
* *
54417705 GATGCCATGTCTCA-AGCATGGTCTTACACTGGCTCTCATCTATCG-GTGCC
1 GATGCCATGTCCCAGA-CATGGTCTTACACT-GCTCTCATATATCGAG-GCC
* * * *
54417755 GATGCCATGTCCCACACATGGTCTTACACTG---ACACATATC-AAGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTGCTCTCATATATCGAGGCC
* * *
54417800 GATGTCATGTCCTAGACATGGTCTTACACTAGCTCTCATATCTCGAGGCC
1 GATGCCATGTCCCAGACATGGTCTTACACT-GCTCTCATATATCGAGGCC
* *
54417850 AATGCCATGTCCCAGACATGGTCTTACACTAGCTATCATAT
1 GATGCCATGTCCCAGACATGGTCTTACACT-GCTCTCATAT
54417891 CTCCCTAGCA
Statistics
Matches: 156, Mismatches: 20, Indels: 20
0.80 0.10 0.10
Matches are distributed among these distances:
45 30 0.19
46 7 0.04
49 8 0.05
50 109 0.70
51 2 0.01
ACGTcount: A:0.23, C:0.30, G:0.19, T:0.28
Consensus pattern (49 bp):
GATGCCATGTCCCAGACATGGTCTTACACTGCTCTCATATATCGAGGCC
Found at i:54419661 original size:40 final size:40
Alignment explanation
Indices: 54419616--54419782 Score: 158
Period size: 40 Copynumber: 4.2 Consensus size: 40
54419606 CGGAATATAA
*
54419616 CCGGATATAACCA-TGTGCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCACT-AGCACAAATGCCTTCGGGTCTTAGC
* ** * *
54419656 CCGGATAGAATGACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC
* * * *
54419696 CCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC
*** * * * *
54419736 CCGGATATAATTTCCAGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC
54419775 CCGGATAT
1 CCGGATAT
54419783 CATTCAATTT
Statistics
Matches: 103, Mismatches: 23, Indels: 3
0.80 0.18 0.02
Matches are distributed among these distances:
39 13 0.13
40 89 0.86
41 1 0.01
ACGTcount: A:0.23, C:0.27, G:0.23, T:0.26
Consensus pattern (40 bp):
CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:54427657 original size:40 final size:40
Alignment explanation
Indices: 54427612--54427779 Score: 158
Period size: 40 Copynumber: 4.2 Consensus size: 40
54427602 CGGAATATAA
*
54427612 CCGGATATAACCA-TGTGCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCACT-AGCACAAATGCCTTCGGGTCTTAGC
* ** * *
54427652 CCGGATAGAATGACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC
* * * *
54427692 CCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC
*** * * * * *
54427732 CCGGATATAATTTCCAGCATAATTGTCTTCGGGGCTTAGC
1 CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC
54427772 CCGGATAT
1 CCGGATAT
54427780 CATTCAATTT
Statistics
Matches: 103, Mismatches: 24, Indels: 2
0.80 0.19 0.02
Matches are distributed among these distances:
40 102 0.99
41 1 0.01
ACGTcount: A:0.23, C:0.27, G:0.24, T:0.26
Consensus pattern (40 bp):
CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:54427762 original size:80 final size:80
Alignment explanation
Indices: 54427628--54427777 Score: 196
Period size: 80 Copynumber: 1.9 Consensus size: 80
54427618 ATAACCATGT
* *
54427628 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATGACTCGCACGAATGCCTTCGGGTCTTAGCC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGACTCGCACGAATGCCTTCGGGGCTTAGCC
54427693 CGGATGTAGCCACTA
66 CGGATGTAGCCACTA
* * ** * *
54427708 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTC-CAGCA-TAATTGTCTTCGGGGCTTAG
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGACTC-GCACGAA-TGCCTTCGGGGCTTAG
54427771 CCCGGAT
64 CCCGGAT
54427778 ATCATTCAAT
Statistics
Matches: 60, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
79 3 0.05
80 57 0.95
ACGTcount: A:0.22, C:0.27, G:0.25, T:0.26
Consensus pattern (80 bp):
GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGACTCGCACGAATGCCTTCGGGGCTTAGCC
CGGATGTAGCCACTA
Found at i:54431819 original size:34 final size:34
Alignment explanation
Indices: 54431743--54431811 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
54431733 TTATGAGTAC
54431743 AAATAATGATCGACTAGGCTTGGGCTATGATGAA
1 AAATAATGATCGACTAGGCTTGGGCTATGATGAA
54431777 AAATAATGATCGACTAGGCTTGGGCTATGATGAA
1 AAATAATGATCGACTAGGCTTGGGCTATGATGAA
54431811 A
1 A
54431812 TTGAATGAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.36, C:0.12, G:0.26, T:0.26
Consensus pattern (34 bp):
AAATAATGATCGACTAGGCTTGGGCTATGATGAA
Found at i:54433637 original size:13 final size:13
Alignment explanation
Indices: 54433621--54433646 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
54433611 TTAATTTATT
54433621 ATTGTCTTGTTAA
1 ATTGTCTTGTTAA
54433634 ATTGTCTTGTTAA
1 ATTGTCTTGTTAA
54433647 CTGTTGTAAT
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:0.23, C:0.08, G:0.15, T:0.54
Consensus pattern (13 bp):
ATTGTCTTGTTAA
Found at i:54435692 original size:2 final size:2
Alignment explanation
Indices: 54435685--54435717 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
54435675 GTGTAACATG
54435685 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
54435718 ACTAAATAGT
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:54436594 original size:17 final size:18
Alignment explanation
Indices: 54436559--54436597 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 18
54436549 TTTGTTGGAA
54436559 TTATGTTAACATATAAGT
1 TTATGTTAACATATAAGT
54436577 TTATGTTAA-A-AGTAAGT
1 TTATGTTAACATA-TAAGT
54436594 TTAT
1 TTAT
54436598 ATCCTTTCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 1 0.05
17 10 0.50
18 9 0.45
ACGTcount: A:0.38, C:0.03, G:0.13, T:0.46
Consensus pattern (18 bp):
TTATGTTAACATATAAGT
Found at i:54438779 original size:17 final size:16
Alignment explanation
Indices: 54438753--54438784 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
54438743 TAAATTAGAA
54438753 ATGAAAATAATTAAAG
1 ATGAAAATAATTAAAG
54438769 ATGATAAATAATTAAA
1 ATGA-AAATAATTAAA
54438785 TAGAAATATC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.62, C:0.00, G:0.09, T:0.28
Consensus pattern (16 bp):
ATGAAAATAATTAAAG
Found at i:54442685 original size:27 final size:28
Alignment explanation
Indices: 54442629--54442703 Score: 75
Period size: 27 Copynumber: 2.8 Consensus size: 28
54442619 GGAGGAAGTG
*
54442629 TACTG-TACT-GTTGGCTCTGCCACATAA
1 TACTGTTACTGGTT-GCTTTGCCACATAA
*
54442656 TACTGTTACTGGTTGCTTTGCCACA-GA
1 TACTGTTACTGGTTGCTTTGCCACATAA
* **
54442683 TACTGTTGCTGGCAGCTTTGC
1 TACTGTTACTGGTTGCTTTGC
54442704 TATGATATTA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
27 24 0.59
28 14 0.34
29 3 0.07
ACGTcount: A:0.17, C:0.24, G:0.23, T:0.36
Consensus pattern (28 bp):
TACTGTTACTGGTTGCTTTGCCACATAA
Found at i:54448334 original size:16 final size:17
Alignment explanation
Indices: 54448309--54448346 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
54448299 TGGGTTTTGG
* *
54448309 TTTTGTTTTTCTTTTCT
1 TTTTGTTTTTCTCTACT
54448326 TTTTG-TTTTCTCTACT
1 TTTTGTTTTTCTCTACT
54448342 TTTTG
1 TTTTG
54448347 CATTTTTGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.03, C:0.13, G:0.08, T:0.76
Consensus pattern (17 bp):
TTTTGTTTTTCTCTACT
Found at i:54449714 original size:27 final size:28
Alignment explanation
Indices: 54449642--54449707 Score: 100
Period size: 28 Copynumber: 2.4 Consensus size: 28
54449632 GAAGTAAGTG
54449642 TACTG-TACTGGTGGCTTTGCCACATAA
1 TACTGTTACTGGTGGCTTTGCCACATAA
* *
54449669 TACTATTACTGGTGGCTTTGCCACA-GA
1 TACTGTTACTGGTGGCTTTGCCACATAA
54449696 TACTGTTACTGG
1 TACTGTTACTGG
54449708 CAGCTTTACA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
27 16 0.46
28 19 0.54
ACGTcount: A:0.21, C:0.21, G:0.23, T:0.35
Consensus pattern (28 bp):
TACTGTTACTGGTGGCTTTGCCACATAA
Found at i:54450129 original size:36 final size:36
Alignment explanation
Indices: 54450082--54450153 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
54450072 TCGTTTTGGG
54450082 TTTAAATTATGTAATAAGGCCTCATTAATTTTCTAT
1 TTTAAATTATGTAATAAGGCCTCATTAATTTTCTAT
*
54450118 TTTAAATTATGTAATAAGGCTTCATTAATTTTCTAT
1 TTTAAATTATGTAATAAGGCCTCATTAATTTTCTAT
54450154 CTTTTTATTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.33, C:0.10, G:0.08, T:0.49
Consensus pattern (36 bp):
TTTAAATTATGTAATAAGGCCTCATTAATTTTCTAT
Found at i:54453981 original size:3 final size:3
Alignment explanation
Indices: 54453973--54454045 Score: 96
Period size: 3 Copynumber: 24.7 Consensus size: 3
54453963 ATGAATTAAA
* *
54453973 TAT TAT TA- TAT TA- TAT TAT TAT AAT GTAT TAT TGT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT
*
54454017 TAT TAT TAT TAT TAT TAA TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
54454046 ACTAATATAT
Statistics
Matches: 61, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
2 4 0.07
3 55 0.90
4 2 0.03
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:54456331 original size:20 final size:20
Alignment explanation
Indices: 54456306--54456364 Score: 100
Period size: 20 Copynumber: 3.0 Consensus size: 20
54456296 TGTATCCATT
54456306 AAATTTTATAATTTTTCATC
1 AAATTTTATAATTTTTCATC
54456326 AAATTTTATAATTTTTCATC
1 AAATTTTATAATTTTTCATC
* *
54456346 AAATTTTACAACTTTTCAT
1 AAATTTTATAATTTTTCAT
54456365 TTTAGTCCCT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.36, C:0.12, G:0.00, T:0.53
Consensus pattern (20 bp):
AAATTTTATAATTTTTCATC
Found at i:54462381 original size:28 final size:28
Alignment explanation
Indices: 54462349--54462411 Score: 117
Period size: 28 Copynumber: 2.2 Consensus size: 28
54462339 TATAGGTAGA
*
54462349 GACACGGGCATGTGTCTCAGCCGTGTGT
1 GACACGGGCATGTGTCTCAGCAGTGTGT
54462377 GACACGGGCATGTGTCTCAGCAGTGTGT
1 GACACGGGCATGTGTCTCAGCAGTGTGT
54462405 GACACGG
1 GACACGG
54462412 TCAGATGATA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.17, C:0.24, G:0.37, T:0.22
Consensus pattern (28 bp):
GACACGGGCATGTGTCTCAGCAGTGTGT
Found at i:54463966 original size:16 final size:16
Alignment explanation
Indices: 54463945--54463977 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
54463935 AAATGGCTAG
54463945 GAATTTAATTAGTTAA
1 GAATTTAATTAGTTAA
54463961 GAATTTAATTAGTTAA
1 GAATTTAATTAGTTAA
54463977 G
1 G
54463978 GGATTTATGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.15, T:0.42
Consensus pattern (16 bp):
GAATTTAATTAGTTAA
Found at i:54471445 original size:26 final size:26
Alignment explanation
Indices: 54471416--54471483 Score: 82
Period size: 26 Copynumber: 2.6 Consensus size: 26
54471406 AGATTTCGAC
*
54471416 CCACATCTCGTGTGAGCAGACCCATT
1 CCACAACTCGTGTGAGCAGACCCATT
* * * *
54471442 CCACAACTCATGTGTGCATACCTATT
1 CCACAACTCGTGTGAGCAGACCCATT
*
54471468 TCACAACTCGTGTGAG
1 CCACAACTCGTGTGAG
54471484 GAACTATGTA
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.25, C:0.31, G:0.18, T:0.26
Consensus pattern (26 bp):
CCACAACTCGTGTGAGCAGACCCATT
Found at i:54478545 original size:25 final size:24
Alignment explanation
Indices: 54478511--54478561 Score: 75
Period size: 25 Copynumber: 2.1 Consensus size: 24
54478501 AAAATACAGA
*
54478511 TCTTTATGAGCATCCTGATATAGGC
1 TCTTTATGAGCATCCTGACAT-GGC
*
54478536 TCTTTATGAGCTTCCTGACATGGC
1 TCTTTATGAGCATCCTGACATGGC
54478560 TC
1 TC
54478562 GCATGAACAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 5 0.21
25 19 0.79
ACGTcount: A:0.20, C:0.24, G:0.20, T:0.37
Consensus pattern (24 bp):
TCTTTATGAGCATCCTGACATGGC
Found at i:54490542 original size:9 final size:9
Alignment explanation
Indices: 54490528--54490556 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
54490518 GAAAGCCAAG
54490528 TAAATCGAC
1 TAAATCGAC
54490537 TAAATCGAC
1 TAAATCGAC
54490546 TAAATCGAC
1 TAAATCGAC
54490555 TA
1 TA
54490557 GTCGCCACAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.45, C:0.21, G:0.10, T:0.24
Consensus pattern (9 bp):
TAAATCGAC
Found at i:54499098 original size:30 final size:30
Alignment explanation
Indices: 54499043--54499202 Score: 222
Period size: 29 Copynumber: 5.5 Consensus size: 30
54499033 ATGGTGAATC
54499043 CGCACACTTAGTGCTATAT-ATTTTCAGCT
1 CGCACACTTAGTGCTATATAATTTTCAGCT
54499072 CGCACACTTAGTGCTATATAATTTTCAGCT
1 CGCACACTTAGTGCTATATAATTTTCAGCT
54499102 CGCACACTTAGTGCTATAT-ATTTTCAGCT
1 CGCACACTTAGTGCTATATAATTTTCAGCT
*
54499131 CGCACACTTAGTGCTATATAA---TCAAACT
1 CGCACACTTAGTGCTATATAATTTTC-AGCT
* * * * *
54499159 CGCACACTTAGTGCTGTACAATTTTAAACC
1 CGCACACTTAGTGCTATATAATTTTCAGCT
54499189 CGCACACTTAGTGC
1 CGCACACTTAGTGC
54499203 CAATCTTGTC
Statistics
Matches: 120, Mismatches: 5, Indels: 11
0.88 0.04 0.08
Matches are distributed among these distances:
27 2 0.02
28 22 0.18
29 48 0.40
30 47 0.39
31 1 0.01
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.33
Consensus pattern (30 bp):
CGCACACTTAGTGCTATATAATTTTCAGCT
Found at i:54499135 original size:59 final size:57
Alignment explanation
Indices: 54499043--54499202 Score: 223
Period size: 59 Copynumber: 2.8 Consensus size: 57
54499033 ATGGTGAATC
*
54499043 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATTTTC-AGCT
1 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAA---TCAAACT
54499102 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATCAAACT
* * * * *
54499159 CGCACACTTAGTGCTGTACAATTTTAAACCCGCACACTTAGTGC
1 CGCACACTTAGTGCTATA-TATTTTCAGCTCGCACACTTAGTGC
54499203 CAATCTTGTC
Statistics
Matches: 93, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
56 2 0.02
57 20 0.22
58 21 0.23
59 50 0.54
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.33
Consensus pattern (57 bp):
CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATCAAACT
Found at i:54506868 original size:30 final size:30
Alignment explanation
Indices: 54506813--54506972 Score: 222
Period size: 29 Copynumber: 5.5 Consensus size: 30
54506803 TATGTGAATC
54506813 CGCACACTTAGTGCTATAT-ATTTTCAGCT
1 CGCACACTTAGTGCTATATAATTTTCAGCT
54506842 CGCACACTTAGTGCTATATAATTTTCAGCT
1 CGCACACTTAGTGCTATATAATTTTCAGCT
54506872 CGCACACTTAGTGCTATAT-ATTTTCAGCT
1 CGCACACTTAGTGCTATATAATTTTCAGCT
*
54506901 CGCACACTTAGTGCTATATAA---TCAAACT
1 CGCACACTTAGTGCTATATAATTTTC-AGCT
* * * * *
54506929 CGCACACTTAGTGCTGTACAATTTTAAACC
1 CGCACACTTAGTGCTATATAATTTTCAGCT
54506959 CGCACACTTAGTGC
1 CGCACACTTAGTGC
54506973 CAATCTTGTC
Statistics
Matches: 120, Mismatches: 5, Indels: 11
0.88 0.04 0.08
Matches are distributed among these distances:
27 2 0.02
28 22 0.18
29 48 0.40
30 47 0.39
31 1 0.01
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.33
Consensus pattern (30 bp):
CGCACACTTAGTGCTATATAATTTTCAGCT
Found at i:54506905 original size:59 final size:57
Alignment explanation
Indices: 54506813--54506972 Score: 223
Period size: 59 Copynumber: 2.8 Consensus size: 57
54506803 TATGTGAATC
*
54506813 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATTTTC-AGCT
1 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAA---TCAAACT
54506872 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATCAAACT
* * * * *
54506929 CGCACACTTAGTGCTGTACAATTTTAAACCCGCACACTTAGTGC
1 CGCACACTTAGTGCTATA-TATTTTCAGCTCGCACACTTAGTGC
54506973 CAATCTTGTC
Statistics
Matches: 93, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
56 2 0.02
57 20 0.22
58 21 0.23
59 50 0.54
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.33
Consensus pattern (57 bp):
CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATCAAACT
Found at i:54509083 original size:21 final size:20
Alignment explanation
Indices: 54509039--54509084 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
54509029 GTGGTTCGGG
*
54509039 AAACTTTAAAAATTTTTACA
1 AAACTTTAAAAATTTTCACA
* *
54509059 AAACTTTGAAAATTTTGCACT
1 AAACTTTAAAAATTTT-CACA
54509080 AAACT
1 AAACT
54509085 GGGGACACAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 15 0.68
21 7 0.32
ACGTcount: A:0.46, C:0.13, G:0.04, T:0.37
Consensus pattern (20 bp):
AAACTTTAAAAATTTTCACA
Found at i:54514379 original size:17 final size:18
Alignment explanation
Indices: 54514337--54514385 Score: 50
Period size: 17 Copynumber: 2.8 Consensus size: 18
54514327 AGTTGAAAAG
54514337 GAGCATGATTGTCATACTT
1 GAGCATGA-TGTCATACTT
*
54514356 G-GCCATGATG-CATTCTT
1 GAG-CATGATGTCATACTT
54514373 GAGCATGAT-TCAT
1 GAGCATGATGTCAT
54514386 GCTTCTTGCA
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
17 16 0.62
18 4 0.15
19 6 0.23
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.35
Consensus pattern (18 bp):
GAGCATGATGTCATACTT
Found at i:54515273 original size:40 final size:40
Alignment explanation
Indices: 54515207--54515357 Score: 155
Period size: 40 Copynumber: 3.8 Consensus size: 40
54515197 AAATTGAATG
* * *
54515207 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* * ***
54515246 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* *
54515286 ACATCCGGGCTAAGACCCGAAGGC-ATTCGTGC-GAGTTATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-GTAATT
* *
54515326 CTATCCGGGCTAAGACCCGAAGGCATTTGTGC
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGC
54515358 ACTGATTATA
Statistics
Matches: 91, Mismatches: 17, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
39 16 0.18
40 73 0.80
41 2 0.02
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
Found at i:54518585 original size:39 final size:39
Alignment explanation
Indices: 54518521--54518662 Score: 117
Period size: 40 Copynumber: 3.6 Consensus size: 39
54518511 AATTTGAATG
* * *
54518521 ATATCCGGGCTAAG-CCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCGAAGGCAATTATGCTAGAAACT
* * ***
54518559 ATATCCGGGTTAAGACCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCGAAGGCAATTATGCTAGAAACT
* * ** *
54518598 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTTATT
1 ATATCCGGGCTAAGA-CCGAAGGCAATT-ATGCTAGAAACT
*
54518638 CTATCCGGGCTAAGACCCGAAGGCA
1 ATATCCGGGCTAAGA-CCGAAGGCA
54518663 TTTGTGCACT
Statistics
Matches: 86, Mismatches: 14, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
38 13 0.15
39 34 0.40
40 39 0.45
ACGTcount: A:0.28, C:0.22, G:0.27, T:0.23
Consensus pattern (39 bp):
ATATCCGGGCTAAGACCGAAGGCAATTATGCTAGAAACT
Found at i:54518683 original size:40 final size:40
Alignment explanation
Indices: 54518556--54518685 Score: 149
Period size: 40 Copynumber: 3.3 Consensus size: 40
54518546 TATGCTGGAA
* * * *
54518556 ATTATATCCGGGTTAAGA-CCGAAGGCAATTGTGCTAGTG
1 ATTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGATTG
** *
54518595 GCTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTT-
1 ATTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGA-TTG
*
54518635 ATTCTATCCGGGCTAAGACCCGAAGGCATTTGTGC-ACTTG
1 ATTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGA-TTG
54518675 ATTATATCCGG
1 ATTATATCCGG
54518686 TTATATTCCG
Statistics
Matches: 75, Mismatches: 13, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
39 18 0.24
40 56 0.75
41 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.27
Consensus pattern (40 bp):
ATTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGATTG
Found at i:54525623 original size:17 final size:18
Alignment explanation
Indices: 54525581--54525629 Score: 50
Period size: 17 Copynumber: 2.8 Consensus size: 18
54525571 AGTTGAAAAG
54525581 GAGCATGATTGTCATACTT
1 GAGCATGA-TGTCATACTT
*
54525600 G-GCCATGATG-CATTCTT
1 GAG-CATGATGTCATACTT
54525617 GAGCATGAT-TCAT
1 GAGCATGATGTCAT
54525630 GCTTCTTGCA
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
17 16 0.62
18 4 0.15
19 6 0.23
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.35
Consensus pattern (18 bp):
GAGCATGATGTCATACTT
Found at i:54526515 original size:40 final size:40
Alignment explanation
Indices: 54526449--54526599 Score: 155
Period size: 40 Copynumber: 3.8 Consensus size: 40
54526439 AAATTGAATG
* * *
54526449 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* * ***
54526488 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* *
54526528 ACATCCGGGCTAAGACCCGAAGGC-ATTCGTGC-GAGTTATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-GTAATT
* *
54526568 CTATCCGGGCTAAGACCCGAAGGCATTTGTGC
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGC
54526600 ACTTGATTAT
Statistics
Matches: 91, Mismatches: 17, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
39 16 0.18
40 73 0.80
41 2 0.02
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
Found at i:54526613 original size:40 final size:40
Alignment explanation
Indices: 54526485--54526615 Score: 149
Period size: 40 Copynumber: 3.3 Consensus size: 40
54526475 TATGCTGGAA
* * * *
54526485 ATTATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTG
1 ATTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGATTG
** * *
54526525 GCTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTT-
1 ATTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGA-TTG
*
54526565 ATTCTATCCGGGCTAAGACCCGAAGGCATTTGTGC-ACTTG
1 ATTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGA-TTG
54526605 ATTATATCCGG
1 ATTATATCCGG
54526616 TTATATTCCG
Statistics
Matches: 74, Mismatches: 15, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
39 3 0.04
40 70 0.95
41 1 0.01
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.26
Consensus pattern (40 bp):
ATTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGATTG
Found at i:54528588 original size:40 final size:40
Alignment explanation
Indices: 54528543--54528710 Score: 149
Period size: 40 Copynumber: 4.2 Consensus size: 40
54528533 CGGAATATAA
54528543 CCGGATATAACCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* *** * **
54528583 CCGGATAGAATGTCTCGCACGTATGCCTTCGGGTCTTAGC
1 CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC
* * * *
54528623 CCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC
*** * * * * *
54528663 CCGGATATAATTTCCAGCATAATTGTCTTCGGGGCTTAGC
1 CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC
54528703 CCGGATAT
1 CCGGATAT
54528711 CATTCAATTT
Statistics
Matches: 100, Mismatches: 27, Indels: 2
0.78 0.21 0.02
Matches are distributed among these distances:
39 1 0.01
40 99 0.99
ACGTcount: A:0.22, C:0.27, G:0.24, T:0.27
Consensus pattern (40 bp):
CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:54528693 original size:80 final size:80
Alignment explanation
Indices: 54528559--54528708 Score: 198
Period size: 80 Copynumber: 1.9 Consensus size: 80
54528549 ATAACCACGT
* * *
54528559 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATGTCTCGCACGTATGCCTTCGGGTCTTAGCC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGTCTCGCACATATGCCTTCGGGGCTTAGCC
54528624 CGGATGTAGCCACTA
66 CGGATGTAGCCACTA
* * *
54528639 GCACAATTGCCTTCGGGTCTTAACCCGGATATAAT-T-TC-CAGCATAATTGTCTTCGGGGCTTA
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGTCTCGCA-CAT-A-TGCCTTCGGGGCTTA
54528701 GCCCGGAT
63 GCCCGGAT
54528709 ATCATTCAAT
Statistics
Matches: 61, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
77 2 0.03
78 4 0.07
79 2 0.03
80 53 0.87
ACGTcount: A:0.21, C:0.27, G:0.25, T:0.27
Consensus pattern (80 bp):
GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGTCTCGCACATATGCCTTCGGGGCTTAGCC
CGGATGTAGCCACTA
Found at i:54541871 original size:47 final size:48
Alignment explanation
Indices: 54541801--54541932 Score: 185
Period size: 47 Copynumber: 2.8 Consensus size: 48
54541791 CTCAATCGAT
* *
54541801 AAGTACCTATACCATGGCCTGTAGCCAAATCAAGGTAACTTATC-CCG
1 AAGTACCTATACCATGGCCTGTAGCCAAATCAAGGTAACTCATCTCCA
* * *
54541848 GAGTACCTATACCACGGCCTGTAGCCAAATCAAGGTAACTCCTCTCCA
1 AAGTACCTATACCATGGCCTGTAGCCAAATCAAGGTAACTCATCTCCA
* * *
54541896 AAATACCTATACCATGGCCCGTAGCCGAATCAAGGTA
1 AAGTACCTATACCATGGCCTGTAGCCAAATCAAGGTA
54541933 TAACTCGCAC
Statistics
Matches: 74, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
47 40 0.54
48 34 0.46
ACGTcount: A:0.32, C:0.30, G:0.17, T:0.21
Consensus pattern (48 bp):
AAGTACCTATACCATGGCCTGTAGCCAAATCAAGGTAACTCATCTCCA
Found at i:54548955 original size:40 final size:40
Alignment explanation
Indices: 54548877--54549098 Score: 331
Period size: 40 Copynumber: 5.6 Consensus size: 40
54548867 AAACCAAGTA
* * * *
54548877 CCTTCGGGAATTAG-CCGGATATAGCT-ACTTGCATAAATG
1 CCTTCGGGACTTAGCCCGGTTATAG-TAACTCGCACAAATG
*
54548916 CCTTCGGGATTTAGCCCGGTTATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
* * *
54548956 CCTTCGGGACTTAGCCCGGATCTAGTAACTCGTACAAATG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
54548996 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
* *
54549036 CCTTCGGGACTTAGCTCGGTTATAGTAACTTGCACAAATG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
54549076 CCTTCGGGACTTAGCCCGGTTAT
1 CCTTCGGGACTTAGCCCGGTTAT
54549099 CATCCGAATA
Statistics
Matches: 167, Mismatches: 14, Indels: 3
0.91 0.08 0.02
Matches are distributed among these distances:
39 14 0.08
40 153 0.92
ACGTcount: A:0.24, C:0.25, G:0.23, T:0.27
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
Found at i:54555016 original size:43 final size:43
Alignment explanation
Indices: 54554910--54555072 Score: 143
Period size: 43 Copynumber: 3.7 Consensus size: 43
54554900 GATCATGAAT
**
54554910 TTTAGTGGCGCTTTTTCT-AAAAACGCCGCTAATGGTCCTGGTC
1 TTTAGTGGCGCTTTTT-TAAAAAACGCCGCTAAAAGTCCTGGTC
* * * *
54554953 ATTCGCGGCGCTTTTTTAAAAAACACCGCTAAAAGTCCTGGTC
1 TTTAGTGGCGCTTTTTTAAAAAACGCCGCTAAAAGTCCTGGTC
* * * * *
54554996 TTTAGTGGTG-TTTTTATAAAAAGCGTCGCTAAAAGTCATGATC
1 TTTAGTGGCGCTTTTT-TAAAAAACGCCGCTAAAAGTCCTGGTC
* *
54555039 TTTAGCGGC-CTTTTTTTCAAACAAACGCCACTAA
1 TTTAGTGGCGC-TTTTTT-AAA-AAACGCCGCTAA
54555073 TTTTCCCAGT
Statistics
Matches: 94, Mismatches: 20, Indels: 10
0.76 0.16 0.08
Matches are distributed among these distances:
42 6 0.06
43 71 0.76
44 8 0.09
45 9 0.10
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.33
Consensus pattern (43 bp):
TTTAGTGGCGCTTTTTTAAAAAACGCCGCTAAAAGTCCTGGTC
Found at i:54556275 original size:14 final size:15
Alignment explanation
Indices: 54556244--54556276 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
54556234 GGCTTGTGGG
*
54556244 TTTTTTAAAATATTC
1 TTTTTTAAAATATGC
54556259 TTTTTTAAAA-ATGC
1 TTTTTTAAAATATGC
54556273 TTTT
1 TTTT
54556277 ATGGTCTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.30, C:0.06, G:0.03, T:0.61
Consensus pattern (15 bp):
TTTTTTAAAATATGC
Found at i:54559061 original size:12 final size:12
Alignment explanation
Indices: 54559044--54559069 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
54559034 GTCATCCTCC
54559044 TCATCAGATTCA
1 TCATCAGATTCA
54559056 TCATCAGATTCA
1 TCATCAGATTCA
54559068 TC
1 TC
54559070 CCTCGATCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.27, G:0.08, T:0.35
Consensus pattern (12 bp):
TCATCAGATTCA
Found at i:54560597 original size:40 final size:40
Alignment explanation
Indices: 54560530--54560701 Score: 215
Period size: 40 Copynumber: 4.3 Consensus size: 40
54560520 ACCCAAGTAT
*
54560530 CTTCGGGAT-TTAG-CCGGATATAACAACTCGCACAAATGC
1 CTTCGGG-TCTTAGCCCGGATATAGCAACTCGCACAAATGC
54560569 CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
* * * *
54560609 CTTCGGGTCTTAGCCTGGATATAATC-ACTAGCATAAATGC
1 CTTCGGGTCTTAGCCCGGATAT-AGCAACTCGCACAAATGC
* * * *
54560649 CTTCGGGACATAGCCCGGATATAGCAACTTGCACGAATGC
1 CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
*
54560689 CTTCGGATCTTAG
1 CTTCGGGTCTTAG
54560702 TCCAGTTATC
Statistics
Matches: 114, Mismatches: 15, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
38 1 0.01
39 13 0.11
40 98 0.86
41 2 0.02
ACGTcount: A:0.27, C:0.26, G:0.22, T:0.25
Consensus pattern (40 bp):
CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
Found at i:54560663 original size:80 final size:79
Alignment explanation
Indices: 54560530--54560701 Score: 240
Period size: 80 Copynumber: 2.2 Consensus size: 79
54560520 ACCCAAGTAT
* * *
54560530 CTTCGGGAT-TTAGCCGGATATAACAACTCGCACAAATGCCTTCGGGTCTTAGCCCGGATATAGC
1 CTTCGGG-TCTTAGCCGGATATAACAACTAGCACAAATGCCTTCGGGACATAGCCCGGATATAGC
54560594 AACTCGCACAAATGC
65 AACTCGCACAAATGC
*
54560609 CTTCGGGTCTTAGCCTGGATATAATC-ACTAGCATAAATGCCTTCGGGACATAGCCCGGATATAG
1 CTTCGGGTCTTAGCC-GGATATAA-CAACTAGCACAAATGCCTTCGGGACATAGCCCGGATATAG
* *
54560673 CAACTTGCACGAATGC
64 CAACTCGCACAAATGC
*
54560689 CTTCGGATCTTAG
1 CTTCGGGTCTTAG
54560702 TCCAGTTATC
Statistics
Matches: 83, Mismatches: 7, Indels: 5
0.87 0.07 0.05
Matches are distributed among these distances:
78 1 0.01
79 13 0.16
80 68 0.82
81 1 0.01
ACGTcount: A:0.27, C:0.26, G:0.22, T:0.25
Consensus pattern (79 bp):
CTTCGGGTCTTAGCCGGATATAACAACTAGCACAAATGCCTTCGGGACATAGCCCGGATATAGCA
ACTCGCACAAATGC
Found at i:54563152 original size:40 final size:39
Alignment explanation
Indices: 54562940--54563149 Score: 313
Period size: 40 Copynumber: 5.4 Consensus size: 39
54562930 AAACCAAGTA
* *
54562940 CCTTCGGGATTTAGCCGGATATAGCT-ACTCGCTCAAATG
1 CCTTCGGGACTTAGCCGGATATAG-TAACTCGCACAAATG
54562979 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCAC-AATG
1 CCTTCGGGACTTAG-CCGGATATAGTAACTCGCACAAATG
54563018 CCTTCGGGACTTAG-CGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCGGATATAGTAACTCGCACAAATG
54563056 CC-TCGGGACTTAGCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCGGATATAGTAACTCGCACAAATG
* *
54563094 CCTTCGGGACTTAGCCCGGA-ATTAGTCACTAGCACAAATG
1 CCTTCGGGACTTAG-CCGGATA-TAGTAACTCGCACAAATG
54563134 CCTTCGGGACTTAGCC
1 CCTTCGGGACTTAGCC
54563150 CGGTTACCAT
Statistics
Matches: 160, Mismatches: 4, Indels: 14
0.90 0.02 0.08
Matches are distributed among these distances:
37 30 0.19
38 32 0.20
39 46 0.29
40 52 0.32
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.24
Consensus pattern (39 bp):
CCTTCGGGACTTAGCCGGATATAGTAACTCGCACAAATG
Found at i:54570996 original size:40 final size:40
Alignment explanation
Indices: 54570937--54571113 Score: 272
Period size: 40 Copynumber: 4.5 Consensus size: 40
54570927 AAACCAAGTA
* *
54570937 CCTTC-GGATTTAG-CCGGATATAGCT-ACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
54570975 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
54571015 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
54571055 CCTTCGGGACTTAGCCCGGA-ATTAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
54571095 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
54571114 TTACCATCGA
Statistics
Matches: 131, Mismatches: 4, Indels: 6
0.93 0.03 0.04
Matches are distributed among these distances:
38 5 0.04
39 9 0.07
40 117 0.89
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:54579300 original size:40 final size:40
Alignment explanation
Indices: 54579242--54579396 Score: 190
Period size: 40 Copynumber: 3.9 Consensus size: 40
54579232 ATCTTGGGAT
*
54579242 TTAG-CCGGATATAACAACTCGCACAAATGCCTTCGGGTC
1 TTAGCCCGGATATAGCAACTCGCACAAATGCCTTCGGGTC
54579281 TTAGCCCGGATATAGCAACT-GCACAAACTGCCTTCGGGTC
1 TTAGCCCGGATATAGCAACTCGCACAAA-TGCCTTCGGGTC
* * * *
54579321 TTAGCCCGGATATAATC-ACTAGCATAAATGCCTTCGGGAC
1 TTAGCCCGGATAT-AGCAACTCGCACAAATGCCTTCGGGTC
* * * *
54579361 ATAGCCCAGATATAGCAACTCACACGAATGCCTTCG
1 TTAGCCCGGATATAGCAACTCGCACAAATGCCTTCG
54579397 TATCTTAGTC
Statistics
Matches: 100, Mismatches: 11, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
39 13 0.13
40 79 0.79
41 8 0.08
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.23
Consensus pattern (40 bp):
TTAGCCCGGATATAGCAACTCGCACAAATGCCTTCGGGTC
Found at i:54582320 original size:9 final size:9
Alignment explanation
Indices: 54582306--54582433 Score: 121
Period size: 9 Copynumber: 13.6 Consensus size: 9
54582296 ATGTATTAGT
54582306 TAAGTTATG
1 TAAGTTATG
54582315 TAAGTTGTTATG
1 TAA---GTTATG
*
54582327 TACGTTATG
1 TAAGTTATG
*
54582336 TGAGTTATG
1 TAAGTTATG
*
54582345 TAAATTATG
1 TAAGTTATG
54582354 TAAGTTATG
1 TAAGTTATG
*
54582363 TGAGTTATG
1 TAAGTTATG
54582372 TAAGTTGTTATG
1 TAA---GTTATG
*
54582384 TAAATTATG
1 TAAGTTATG
*
54582393 TAAGTTATA
1 TAAGTTATG
*
54582402 TGAGTTATG
1 TAAGTTATG
54582411 TAAGTTATG
1 TAAGTTATG
* *
54582420 TAATTTATT
1 TAAGTTATG
54582429 TAAGT
1 TAAGT
54582434 AATGATCAAT
Statistics
Matches: 96, Mismatches: 17, Indels: 12
0.77 0.14 0.10
Matches are distributed among these distances:
9 79 0.82
12 17 0.18
ACGTcount: A:0.31, C:0.01, G:0.21, T:0.47
Consensus pattern (9 bp):
TAAGTTATG
Found at i:54582433 original size:57 final size:57
Alignment explanation
Indices: 54582306--54582433 Score: 175
Period size: 57 Copynumber: 2.2 Consensus size: 57
54582296 ATGTATTAGT
** * *
54582306 TAAGTTATGTAAGTTGTTATGTACGTTATGTGAGTTATGTAAATTATGTAAGTTATG
1 TAAGTTATGTAAGTTGTTATGTAAATTATGTAAGTTATATAAATTATGTAAGTTATG
* * *
54582363 TGAGTTATGTAAGTTGTTATGTAAATTATGTAAGTTATATGAGTTATGTAAGTTATG
1 TAAGTTATGTAAGTTGTTATGTAAATTATGTAAGTTATATAAATTATGTAAGTTATG
* *
54582420 TAATTTATTTAAGT
1 TAAGTTATGTAAGT
54582434 AATGATCAAT
Statistics
Matches: 61, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
57 61 1.00
ACGTcount: A:0.31, C:0.01, G:0.21, T:0.47
Consensus pattern (57 bp):
TAAGTTATGTAAGTTGTTATGTAAATTATGTAAGTTATATAAATTATGTAAGTTATG
Found at i:54583273 original size:23 final size:23
Alignment explanation
Indices: 54583247--54583296 Score: 91
Period size: 23 Copynumber: 2.2 Consensus size: 23
54583237 GTTCAAGTTT
54583247 ATTTAAAGGGCTGCAATTCATAC
1 ATTTAAAGGGCTGCAATTCATAC
*
54583270 ATTTAATGGGCTGCAATTCATAC
1 ATTTAAAGGGCTGCAATTCATAC
54583293 ATTT
1 ATTT
54583297 GATTAATGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (23 bp):
ATTTAAAGGGCTGCAATTCATAC
Found at i:54586256 original size:3 final size:3
Alignment explanation
Indices: 54586248--54586309 Score: 124
Period size: 3 Copynumber: 20.7 Consensus size: 3
54586238 TTTCTTTCTT
54586248 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
54586296 TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TT
54586310 TCCTATTAAT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:54588074 original size:50 final size:49
Alignment explanation
Indices: 54588010--54588139 Score: 181
Period size: 50 Copynumber: 2.6 Consensus size: 49
54588000 AAAATTGTGA
**
54588010 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATTAGA-TGGTGAGG
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGACT-GT-AGG
* *
54588060 TCACGTGTGTAGTACTAAGTGCAGGCTACTACTTGTACCAGACTGTTGG
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGACTGTAGG
* *
54588109 TCGCATGTGTAGTACTAAGTGCAGGCTACTA
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTA
54588140 TGCATACCAG
Statistics
Matches: 73, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
49 31 0.42
50 41 0.56
51 1 0.01
ACGTcount: A:0.24, C:0.18, G:0.28, T:0.30
Consensus pattern (49 bp):
TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGACTGTAGG
Found at i:54588137 original size:49 final size:50
Alignment explanation
Indices: 54587953--54588139 Score: 175
Period size: 50 Copynumber: 3.7 Consensus size: 50
54587943 ATGATCTATT
* * * * * * * *
54587953 GTGAGGTCGCATGTGCAGTAGTAAGTGCAGACTACTATGCGTACCCGAAAATT
1 GTGAGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTA-CC--AGATG
* **
54588006 GTGA--TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATTAGATG
1 GTGAGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATG
* *
54588054 GTGAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACTTGTACCAGACT-
1 GTGAGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGA-TG
* *
54588104 GT-TGGTCGCATGTGTAGTACTAAGTGCAGGCTACTA
1 GTGAGGTCACATGTGTAGTACTAAGTGCAGGCTACTA
54588140 TGCATACCAG
Statistics
Matches: 114, Mismatches: 17, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
48 7 0.06
49 31 0.27
50 41 0.36
51 31 0.27
53 4 0.04
ACGTcount: A:0.25, C:0.18, G:0.29, T:0.28
Consensus pattern (50 bp):
GTGAGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATG
Found at i:54589630 original size:12 final size:11
Alignment explanation
Indices: 54589608--54589649 Score: 52
Period size: 12 Copynumber: 3.8 Consensus size: 11
54589598 TTTTACATTA
54589608 ATATC-TATAT
1 ATATCATATAT
54589618 ATA-CATATAT
1 ATATCATATAT
54589628 ATATCAATATAT
1 ATATC-ATATAT
54589640 ATATCCATAT
1 ATAT-CATAT
54589650 GAAATTTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
9 1 0.04
10 11 0.39
11 1 0.04
12 14 0.50
13 1 0.04
ACGTcount: A:0.45, C:0.12, G:0.00, T:0.43
Consensus pattern (11 bp):
ATATCATATAT
Found at i:54589896 original size:36 final size:36
Alignment explanation
Indices: 54589854--54589922 Score: 111
Period size: 36 Copynumber: 1.9 Consensus size: 36
54589844 TTGTCTATAG
* *
54589854 TTTAGGGTTTTATGGTTTAGAATTCAAGGTTTAATA
1 TTTAGGGTTTTAAGGTTTACAATTCAAGGTTTAATA
*
54589890 TTTAGGGTTTTAAGGTTTACAATTTAAGGTTTA
1 TTTAGGGTTTTAAGGTTTACAATTCAAGGTTTA
54589923 TGACTAGAGA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.28, C:0.03, G:0.22, T:0.48
Consensus pattern (36 bp):
TTTAGGGTTTTAAGGTTTACAATTCAAGGTTTAATA
Found at i:54589904 original size:22 final size:22
Alignment explanation
Indices: 54589879--54589921 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
54589869 TTTAGAATTC
*
54589879 AAGGTTTA-ATATTTAGGGTTTT
1 AAGGTTTACA-ATTTAAGGTTTT
54589901 AAGGTTTACAATTTAAGGTTT
1 AAGGTTTACAATTTAAGGTTT
54589922 ATGACTAGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 18 0.95
23 1 0.05
ACGTcount: A:0.30, C:0.02, G:0.21, T:0.47
Consensus pattern (22 bp):
AAGGTTTACAATTTAAGGTTTT
Found at i:54593497 original size:40 final size:39
Alignment explanation
Indices: 54593329--54593499 Score: 159
Period size: 40 Copynumber: 4.3 Consensus size: 39
54593319 AGAAATTGAA
* *
54593329 TGATATCCGGGCTAAGCCCCGAAGACAATTATGCTG-AAAT-
1 TGATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCAAATG
* * * * *
54593369 TTATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTAG
1 TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAAT-G
* *
54593409 CT-ATATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTG
1 -TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAA-ATG
* *
54593449 TTAAATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG
1 TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAAT-G
54593489 TGATATCCGGG
1 TGATATCCGGG
54593500 TAAAGTCCCG
Statistics
Matches: 107, Mismatches: 17, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
37 2 0.02
38 4 0.04
39 4 0.04
40 95 0.89
41 2 0.02
ACGTcount: A:0.28, C:0.22, G:0.26, T:0.24
Consensus pattern (39 bp):
TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATG
Found at i:54601537 original size:40 final size:39
Alignment explanation
Indices: 54601369--54601539 Score: 159
Period size: 40 Copynumber: 4.3 Consensus size: 39
54601359 AGAAATTGAA
* *
54601369 TGATATCCGGGCTAAGCCCCGAAGACAATTATGCTG-AAAT-
1 TGATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCAAATG
* * * * *
54601409 TTATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTAG
1 TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAAT-G
* *
54601449 CT-ATATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTG
1 -TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAA-ATG
* *
54601489 TTAAATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG
1 TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAAT-G
54601529 TGATATCCGGG
1 TGATATCCGGG
54601540 TAAAGTCCCG
Statistics
Matches: 107, Mismatches: 17, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
37 2 0.02
38 4 0.04
39 4 0.04
40 95 0.89
41 2 0.02
ACGTcount: A:0.28, C:0.22, G:0.26, T:0.24
Consensus pattern (39 bp):
TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATG
Found at i:54603780 original size:20 final size:20
Alignment explanation
Indices: 54603757--54603794 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
54603747 TGTATTCATA
54603757 AAATTTTAGAATTTTTCAGC
1 AAATTTTAGAATTTTTCAGC
**
54603777 AAATTTTTTAATTTTTCA
1 AAATTTTAGAATTTTTCA
54603795 TTTTAGTCCC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.08, G:0.05, T:0.53
Consensus pattern (20 bp):
AAATTTTAGAATTTTTCAGC
Found at i:54610924 original size:40 final size:40
Alignment explanation
Indices: 54610876--54611187 Score: 341
Period size: 40 Copynumber: 7.8 Consensus size: 40
54610866 GAATACACAT
*
54610876 CACCGGCACGAATGCCCTTCGGGATTTAGCCC-GATTATAA
1 CACCGGCACGAATGCCCTTCGGGACTTAGCCCGGA-TATAA
* * * *
54610916 CATCGGCACGAATACCCTTCGGGATTTAGCCCAGATATAA
1 CACCGGCACGAATGCCCTTCGGGACTTAGCCCGGATATAA
* *
54610956 CACCGGCACGAATGCCCTTCGGGACTTAGCCCGGATACAT
1 CACCGGCACGAATGCCCTTCGGGACTTAGCCCGGATATAA
** *
54610996 CACTAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
1 CACCGGCACGAATGCCCTTCGGGACTTAGCCCGGATATAA
* *
54611036 CACCGGCACGAATGCCCTTCGGGACTTAGCCCGGATACAT
1 CACCGGCACGAATGCCCTTCGGGACTTAGCCCGGATATAA
** * * *
54611076 CACTAGCACGAATGCTCTTCGAGACTTAGCCCGGATATAT
1 CACCGGCACGAATGCCCTTCGGGACTTAGCCCGGATATAA
** *
54611116 CACTAGCACGATTG-CCTTCGGG-CTTAGCCCGGAATTAGTAA
1 CACCGGCACGAATGCCCTTCGGGACTTAGCCCGG-A-TA-TAA
*
54611157 C-TC-GCAC-AATTG-CCTTCGGGACTTAGCCCGG
1 CACCGGCACGAA-TGCCCTTCGGGACTTAGCCCGG
54611188 TTATCATCCG
Statistics
Matches: 236, Mismatches: 30, Indels: 12
0.85 0.11 0.04
Matches are distributed among these distances:
38 11 0.05
39 21 0.09
40 199 0.84
41 5 0.02
ACGTcount: A:0.25, C:0.30, G:0.23, T:0.22
Consensus pattern (40 bp):
CACCGGCACGAATGCCCTTCGGGACTTAGCCCGGATATAA
Found at i:54611016 original size:80 final size:80
Alignment explanation
Indices: 54610876--54611187 Score: 386
Period size: 80 Copynumber: 3.9 Consensus size: 80
54610866 GAATACACAT
* * * * * *
54610876 CACCGGCACGAATGCCCTTCGGGATTTAGCCC-GAT-TATAACATCGGCACGAATACCCTTCGGG
1 CACCGGCACGAATGCCCTTCGGGACTTAGCCCGGATACATCAC-T-AGCACGAATGCTCTTCGGG
* *
54610939 ATTTAGCCCAGATATAA
64 ACTTAGCCCGGATATAA
54610956 CACCGGCACGAATGCCCTTCGGGACTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGGAC
1 CACCGGCACGAATGCCCTTCGGGACTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGGAC
54611021 TTAGCCCGGATATAA
66 TTAGCCCGGATATAA
*
54611036 CACCGGCACGAATGCCCTTCGGGACTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGAGAC
1 CACCGGCACGAATGCCCTTCGGGACTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGGAC
*
54611101 TTAGCCCGGATATAT
66 TTAGCCCGGATATAA
** * * * *
54611116 CACTAGCACGATTG-CCTTCGGG-CTTAGCCCGGAATTA-GTAACTCGCAC-AATTGC-CTTCGG
1 CACCGGCACGAATGCCCTTCGGGACTTAGCCCGG-A-TACATCACTAGCACGAA-TGCTCTTCGG
54611176 GACTTAGCCCGG
63 GACTTAGCCCGG
54611188 TTATCATCCG
Statistics
Matches: 210, Mismatches: 17, Indels: 12
0.88 0.07 0.05
Matches are distributed among these distances:
78 29 0.14
79 20 0.10
80 153 0.73
81 4 0.02
82 4 0.02
ACGTcount: A:0.25, C:0.30, G:0.23, T:0.22
Consensus pattern (80 bp):
CACCGGCACGAATGCCCTTCGGGACTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGGAC
TTAGCCCGGATATAA
Found at i:54611085 original size:120 final size:120
Alignment explanation
Indices: 54610872--54611187 Score: 403
Period size: 120 Copynumber: 2.6 Consensus size: 120
54610862 GCCCGAATAC
** * *
54610872 ACATCACCGGCACGAATGCCCTTCGGGATTTAGCCC-GATTATAACATCGGCACGAATACCCTTC
1 ACATCACTAGCACGAATG-CCTTCGGGACTTAGCCCGGATTATAACATCGGCACGAATGCCCTTC
* * * * *
54610936 GGGATTTAGCCCAGATATAACACCGGCACGAATGCCCTTCGGGACTTAGCCCGGAT
65 GGGACTTAGCCCGGATACAACACCAGCACGAATGCCCTTCGAGACTTAGCCCGGAT
*
54610992 ACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGA-TATAACACCGGCACGAATGCCCTTC
1 ACATCACTAGCACGAATGC-CTTCGGGACTTAGCCCGGATTATAACATCGGCACGAATGCCCTTC
* * *
54611056 GGGACTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGAGACTTAGCCCGGAT
65 GGGACTTAGCCCGGATACAACACCAGCACGAATGCCCTTCGAGACTTAGCCCGGAT
* *
54611112 ATATCACTAGCACGATTGCCTTCGGG-CTTAGCCCGGAATTAGTAAC-TC-GCAC-AATTG-CCT
1 ACATCACTAGCACGAATGCCTTCGGGACTTAGCCCGG-ATTA-TAACATCGGCACGAA-TGCCCT
54611172 TCGGGACTTAGCCCGG
63 TCGGGACTTAGCCCGG
54611188 TTATCATCCG
Statistics
Matches: 174, Mismatches: 16, Indels: 14
0.85 0.08 0.07
Matches are distributed among these distances:
118 31 0.18
119 15 0.09
120 122 0.70
121 6 0.03
ACGTcount: A:0.25, C:0.30, G:0.23, T:0.22
Consensus pattern (120 bp):
ACATCACTAGCACGAATGCCTTCGGGACTTAGCCCGGATTATAACATCGGCACGAATGCCCTTCG
GGACTTAGCCCGGATACAACACCAGCACGAATGCCCTTCGAGACTTAGCCCGGAT
Found at i:54613682 original size:48 final size:48
Alignment explanation
Indices: 54613630--54613757 Score: 186
Period size: 48 Copynumber: 2.7 Consensus size: 48
54613620 CGTATTGCAC
* *
54613630 ATTAGCCATTCGGCTTTACCA-AGTATACATCTCTCATACATATTTCAT
1 ATTAGCCATTCGGCTTTACCACA-TATACATATCTCATACATATCTCAT
* *
54613678 ATTAGCCATTTGGCTTTACCACATATACATATCTCATACATGTCTCAT
1 ATTAGCCATTCGGCTTTACCACATATACATATCTCATACATATCTCAT
* *
54613726 ATTAGCCATTCGGCTTTACCACACATATATAT
1 ATTAGCCATTCGGCTTTACCACATATACATAT
54613758 ATTTACCTTG
Statistics
Matches: 72, Mismatches: 7, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
48 71 0.99
49 1 0.01
ACGTcount: A:0.30, C:0.25, G:0.09, T:0.37
Consensus pattern (48 bp):
ATTAGCCATTCGGCTTTACCACATATACATATCTCATACATATCTCAT
Found at i:54617386 original size:40 final size:40
Alignment explanation
Indices: 54617338--54617649 Score: 341
Period size: 40 Copynumber: 7.8 Consensus size: 40
54617328 GAATACACAT
*
54617338 CACCGGCACGAATGCCCTTCGGGATTTAGCCC-GATTATAA
1 CACCGGCACGAATGCCCTTCGGGACTTAGCCCGGA-TATAA
* * * *
54617378 CATCGGCACGAATACCCTTCGGGATTTAGCCCAGATATAA
1 CACCGGCACGAATGCCCTTCGGGACTTAGCCCGGATATAA
* *
54617418 CACCGGCACGAATGCCCTTCGGGACTTAGCCCGGATACAT
1 CACCGGCACGAATGCCCTTCGGGACTTAGCCCGGATATAA
** *
54617458 CACTAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
1 CACCGGCACGAATGCCCTTCGGGACTTAGCCCGGATATAA
* *
54617498 CACCGGCACGAATGCCCTTCGGGACTTAGCCCGGATACAT
1 CACCGGCACGAATGCCCTTCGGGACTTAGCCCGGATATAA
** * * *
54617538 CACTAGCACGAATGCTCTTCGAGACTTAGCCCGGATATAT
1 CACCGGCACGAATGCCCTTCGGGACTTAGCCCGGATATAA
** *
54617578 CACTAGCACGATTG-CCTTCGGG-CTTAGCCCGGAATTAGTAA
1 CACCGGCACGAATGCCCTTCGGGACTTAGCCCGG-A-TA-TAA
*
54617619 C-TC-GCAC-AATTG-CCTTCGGGACTTAGCCCGG
1 CACCGGCACGAA-TGCCCTTCGGGACTTAGCCCGG
54617650 TTATCATCCG
Statistics
Matches: 236, Mismatches: 30, Indels: 12
0.85 0.11 0.04
Matches are distributed among these distances:
38 11 0.05
39 21 0.09
40 199 0.84
41 5 0.02
ACGTcount: A:0.25, C:0.30, G:0.23, T:0.22
Consensus pattern (40 bp):
CACCGGCACGAATGCCCTTCGGGACTTAGCCCGGATATAA
Found at i:54617478 original size:80 final size:80
Alignment explanation
Indices: 54617338--54617649 Score: 386
Period size: 80 Copynumber: 3.9 Consensus size: 80
54617328 GAATACACAT
* * * * * *
54617338 CACCGGCACGAATGCCCTTCGGGATTTAGCCC-GAT-TATAACATCGGCACGAATACCCTTCGGG
1 CACCGGCACGAATGCCCTTCGGGACTTAGCCCGGATACATCAC-T-AGCACGAATGCTCTTCGGG
* *
54617401 ATTTAGCCCAGATATAA
64 ACTTAGCCCGGATATAA
54617418 CACCGGCACGAATGCCCTTCGGGACTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGGAC
1 CACCGGCACGAATGCCCTTCGGGACTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGGAC
54617483 TTAGCCCGGATATAA
66 TTAGCCCGGATATAA
*
54617498 CACCGGCACGAATGCCCTTCGGGACTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGAGAC
1 CACCGGCACGAATGCCCTTCGGGACTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGGAC
*
54617563 TTAGCCCGGATATAT
66 TTAGCCCGGATATAA
** * * * *
54617578 CACTAGCACGATTG-CCTTCGGG-CTTAGCCCGGAATTA-GTAACTCGCAC-AATTGC-CTTCGG
1 CACCGGCACGAATGCCCTTCGGGACTTAGCCCGG-A-TACATCACTAGCACGAA-TGCTCTTCGG
54617638 GACTTAGCCCGG
63 GACTTAGCCCGG
54617650 TTATCATCCG
Statistics
Matches: 210, Mismatches: 17, Indels: 12
0.88 0.07 0.05
Matches are distributed among these distances:
78 29 0.14
79 20 0.10
80 153 0.73
81 4 0.02
82 4 0.02
ACGTcount: A:0.25, C:0.30, G:0.23, T:0.22
Consensus pattern (80 bp):
CACCGGCACGAATGCCCTTCGGGACTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGGAC
TTAGCCCGGATATAA
Found at i:54617547 original size:120 final size:120
Alignment explanation
Indices: 54617334--54617649 Score: 403
Period size: 120 Copynumber: 2.6 Consensus size: 120
54617324 GCCCGAATAC
** * *
54617334 ACATCACCGGCACGAATGCCCTTCGGGATTTAGCCC-GATTATAACATCGGCACGAATACCCTTC
1 ACATCACTAGCACGAATG-CCTTCGGGACTTAGCCCGGATTATAACATCGGCACGAATGCCCTTC
* * * * *
54617398 GGGATTTAGCCCAGATATAACACCGGCACGAATGCCCTTCGGGACTTAGCCCGGAT
65 GGGACTTAGCCCGGATACAACACCAGCACGAATGCCCTTCGAGACTTAGCCCGGAT
*
54617454 ACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGA-TATAACACCGGCACGAATGCCCTTC
1 ACATCACTAGCACGAATGC-CTTCGGGACTTAGCCCGGATTATAACATCGGCACGAATGCCCTTC
* * *
54617518 GGGACTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGAGACTTAGCCCGGAT
65 GGGACTTAGCCCGGATACAACACCAGCACGAATGCCCTTCGAGACTTAGCCCGGAT
* *
54617574 ATATCACTAGCACGATTGCCTTCGGG-CTTAGCCCGGAATTAGTAAC-TC-GCAC-AATTG-CCT
1 ACATCACTAGCACGAATGCCTTCGGGACTTAGCCCGG-ATTA-TAACATCGGCACGAA-TGCCCT
54617634 TCGGGACTTAGCCCGG
63 TCGGGACTTAGCCCGG
54617650 TTATCATCCG
Statistics
Matches: 174, Mismatches: 16, Indels: 14
0.85 0.08 0.07
Matches are distributed among these distances:
118 31 0.18
119 15 0.09
120 122 0.70
121 6 0.03
ACGTcount: A:0.25, C:0.30, G:0.23, T:0.22
Consensus pattern (120 bp):
ACATCACTAGCACGAATGCCTTCGGGACTTAGCCCGGATTATAACATCGGCACGAATGCCCTTCG
GGACTTAGCCCGGATACAACACCAGCACGAATGCCCTTCGAGACTTAGCCCGGAT
Found at i:54620140 original size:48 final size:48
Alignment explanation
Indices: 54620088--54620215 Score: 186
Period size: 48 Copynumber: 2.7 Consensus size: 48
54620078 CGTATTGCAC
* *
54620088 ATTAGCCATTCGGCTTTACCA-AGTATACATCTCTCATACATATTTCAT
1 ATTAGCCATTCGGCTTTACCACA-TATACATATCTCATACATATCTCAT
* *
54620136 ATTAGCCATTTGGCTTTACCACATATACATATCTCATACATGTCTCAT
1 ATTAGCCATTCGGCTTTACCACATATACATATCTCATACATATCTCAT
* *
54620184 ATTAGCCATTCGGCTTTACCACACATATATAT
1 ATTAGCCATTCGGCTTTACCACATATACATAT
54620216 ATTTACCTTG
Statistics
Matches: 72, Mismatches: 7, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
48 71 0.99
49 1 0.01
ACGTcount: A:0.30, C:0.25, G:0.09, T:0.37
Consensus pattern (48 bp):
ATTAGCCATTCGGCTTTACCACATATACATATCTCATACATATCTCAT
Found at i:54623841 original size:40 final size:39
Alignment explanation
Indices: 54623797--54624065 Score: 328
Period size: 40 Copynumber: 6.8 Consensus size: 39
54623787 TACACATCAC
* *
54623797 CGGCACGAATGCCCTTCGGGATTTAGCCCGGTTATAACA
1 CGGCACGAATGCCCTTCGGGACTTAGCCCGGATATAACA
* *
54623836 TCGGCACGAATACCCTTCGGGATTTAGCCCGGATATAACA
1 -CGGCACGAATGCCCTTCGGGACTTAGCCCGGATATAACA
* *
54623876 CCGGCACGAATGCCCTTCGGGACTTAGCCCGGATACATCA
1 -CGGCACGAATGCCCTTCGGGACTTAGCCCGGATATAACA
* *
54623916 CTAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAACA
1 C-GGCACGAATGCCCTTCGGGACTTAGCCCGGATATAACA
* *
54623956 CCGGCACGAATGCCCTTCGGGACTTAGCCCGGATACATCA
1 -CGGCACGAATGCCCTTCGGGACTTAGCCCGGATATAACA
* * *
54623996 CTAGCACGAATGCTCTTC-GGACTTAGCCCGGATATATCA
1 C-GGCACGAATGCCCTTCGGGACTTAGCCCGGATATAACA
* *
54624035 CTAGCACGATTG-CCTTCGGG-CTTAGCCCGGA
1 C-GGCACGAATGCCCTTCGGGACTTAGCCCGGA
54624066 ATTAGTAACT
Statistics
Matches: 205, Mismatches: 20, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
38 15 0.07
39 35 0.17
40 154 0.75
41 1 0.00
ACGTcount: A:0.24, C:0.30, G:0.24, T:0.22
Consensus pattern (39 bp):
CGGCACGAATGCCCTTCGGGACTTAGCCCGGATATAACA
Found at i:54623934 original size:80 final size:80
Alignment explanation
Indices: 54623794--54624065 Score: 399
Period size: 80 Copynumber: 3.4 Consensus size: 80
54623784 GAATACACAT
* * * * * * *
54623794 CACCGGCACGAATGCCCTTCGGGATTTAGCCCGGTTATAACA-TCGGCACGAATACCCTTCGGGA
1 CACCGGCACGAATGCCCTTCGGGACTTAGCCCGGATACATCACT-AGCACGAATGCTCTTCGGGA
*
54623858 TTTAGCCCGGATATAA
65 CTTAGCCCGGATATAA
54623874 CACCGGCACGAATGCCCTTCGGGACTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGGAC
1 CACCGGCACGAATGCCCTTCGGGACTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGGAC
54623939 TTAGCCCGGATATAA
66 TTAGCCCGGATATAA
54623954 CACCGGCACGAATGCCCTTCGGGACTTAGCCCGGATACATCACTAGCACGAATGCTCTTC-GGAC
1 CACCGGCACGAATGCCCTTCGGGACTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGGAC
*
54624018 TTAGCCCGGATATAT
66 TTAGCCCGGATATAA
** *
54624033 CACTAGCACGATTG-CCTTCGGG-CTTAGCCCGGA
1 CACCGGCACGAATGCCCTTCGGGACTTAGCCCGGA
54624066 ATTAGTAACT
Statistics
Matches: 179, Mismatches: 12, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
77 11 0.06
78 8 0.04
79 29 0.16
80 130 0.73
81 1 0.01
ACGTcount: A:0.24, C:0.31, G:0.24, T:0.21
Consensus pattern (80 bp):
CACCGGCACGAATGCCCTTCGGGACTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGGAC
TTAGCCCGGATATAA
Found at i:54624003 original size:120 final size:118
Alignment explanation
Indices: 54623790--54624065 Score: 392
Period size: 120 Copynumber: 2.3 Consensus size: 118
54623780 GCCCGAATAC
** * * *
54623790 ACATCACCGGCACGAATGCCCTTCGGGATTTAGCCCGGTTATAACATCGGCACGAATACCCTTCG
1 ACATCACTAGCACGAATG-CCTTCGGGACTTAGCCCGGATATAACACCGGCACGAATACCCTTCG
* * *
54623855 GGATTTAGCCCGGATATAACACCGGCACGAATGCCCTTCGGGACTTAGCCCGGAT
65 GGACTTAGCCCGGATACAACACCAGCACGAATGCCCTTC-GGACTTAGCCCGGAT
*
54623910 ACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAACACCGGCACGAATGCCCTTCG
1 ACATCACTAGCACGAATGC-CTTCGGGACTTAGCCCGGATATAACACCGGCACGAATACCCTTCG
* * *
54623975 GGACTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGACTTAGCCCGGAT
65 GGACTTAGCCCGGATACAACACCAGCACGAATGCCCTTCGGACTTAGCCCGGAT
* *
54624029 ATATCACTAGCACGATTGCCTTCGGG-CTTAGCCCGGA
1 ACATCACTAGCACGAATGCCTTCGGGACTTAGCCCGGA
54624066 ATTAGTAACT
Statistics
Matches: 141, Mismatches: 14, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
117 11 0.08
118 7 0.05
119 33 0.23
120 90 0.64
ACGTcount: A:0.24, C:0.31, G:0.24, T:0.21
Consensus pattern (118 bp):
ACATCACTAGCACGAATGCCTTCGGGACTTAGCCCGGATATAACACCGGCACGAATACCCTTCGG
GACTTAGCCCGGATACAACACCAGCACGAATGCCCTTCGGACTTAGCCCGGAT
Found at i:54624092 original size:39 final size:38
Alignment explanation
Indices: 54623849--54624103 Score: 193
Period size: 40 Copynumber: 6.5 Consensus size: 38
54623839 GCACGAATAC
* **
54623849 CCTTCGGGATTTAGCCCGGATATA-ACACCGGCACGAA-TG
1 CCTTC-GGACTTAGCCCGGATATATA-ACTAGCAC-AATTG
* *
54623888 CCCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA-TG
1 -CCTTC-GGACTTAGCCCGGATATATAACTAGCAC-AATTG
**
54623928 CTCTTCGGGACTTAGCCCGGATATA-ACACCGGCACGAA-TG
1 C-CTTC-GGACTTAGCCCGGATATATA-ACTAGCAC-AATTG
* *
54623968 CCCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA-TG
1 -CCTTC-GGACTTAGCCCGGATATATAACTAGCAC-AATTG
* *
54624008 CTCTTCGGACTTAGCCCGGATATATCACTAGCACGATTG
1 C-CTTCGGACTTAGCCCGGATATATAACTAGCACAATTG
*
54624047 CCTTCGGGCTTAGCCCGGA-ATTAGTAACTCA-CACAATTG
1 CCTTCGGACTTAGCCCGGATA-TA-TAACT-AGCACAATTG
54624086 CCTTCGGACTTAGCCCGG
1 CCTTCGGACTTAGCCCGG
54624104 TTATCATCCG
Statistics
Matches: 186, Mismatches: 19, Indels: 21
0.82 0.08 0.09
Matches are distributed among these distances:
37 1 0.01
38 20 0.11
39 60 0.32
40 104 0.56
41 1 0.01
ACGTcount: A:0.24, C:0.31, G:0.23, T:0.22
Consensus pattern (38 bp):
CCTTCGGACTTAGCCCGGATATATAACTAGCACAATTG
Found at i:54626593 original size:48 final size:48
Alignment explanation
Indices: 54626541--54626668 Score: 186
Period size: 48 Copynumber: 2.7 Consensus size: 48
54626531 CGTATTGCAC
* *
54626541 ATTAGCCATTCGGCTTTACCA-AGTATACATCTCTCATACATATTTCAT
1 ATTAGCCATTCGGCTTTACCACA-TATACATATCTCATACATATCTCAT
* *
54626589 ATTAGCCATTTGGCTTTACCACATATACATATCTCATACATGTCTCAT
1 ATTAGCCATTCGGCTTTACCACATATACATATCTCATACATATCTCAT
* *
54626637 ATTAGCCATTCGGCTTTACCACACATATATAT
1 ATTAGCCATTCGGCTTTACCACATATACATAT
54626669 ATTTACCTTG
Statistics
Matches: 72, Mismatches: 7, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
48 71 0.99
49 1 0.01
ACGTcount: A:0.30, C:0.25, G:0.09, T:0.37
Consensus pattern (48 bp):
ATTAGCCATTCGGCTTTACCACATATACATATCTCATACATATCTCAT
Found at i:54631146 original size:48 final size:48
Alignment explanation
Indices: 54631095--54631432 Score: 622
Period size: 48 Copynumber: 7.0 Consensus size: 48
54631085 CATCTGCTAC
* *
54631095 ATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATAC
1 ATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATAT
*
54631143 ATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATAT
1 ATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATAT
54631191 ATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATAT
1 ATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATAT
54631239 ATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATAT
1 ATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATAT
*
54631287 ATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATAC
1 ATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATAT
* *
54631335 ATATTTCACACTAGCCATTTGGCTTTACCACATATACATATCTCATAT
1 ATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATAT
54631383 ATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATAT
1 ATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATAT
54631431 AT
1 AT
54631433 CAATTTCAGC
Statistics
Matches: 282, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
48 282 1.00
ACGTcount: A:0.31, C:0.26, G:0.06, T:0.36
Consensus pattern (48 bp):
ATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATAT
Found at i:54637600 original size:21 final size:18
Alignment explanation
Indices: 54637559--54637601 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 18
54637549 TTTTAGCTTG
54637559 AATTCTTATGAAATCGGA
1 AATTCTTATGAAATCGGA
*
54637577 AATTCATTCATGAATTCGGGA
1 AATTC-TT-ATGAAATC-GGA
54637598 AATT
1 AATT
54637602 TTTTTTAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 5 0.24
19 2 0.10
20 7 0.33
21 7 0.33
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.35
Consensus pattern (18 bp):
AATTCTTATGAAATCGGA
Found at i:54639084 original size:47 final size:47
Alignment explanation
Indices: 54639027--54639370 Score: 589
Period size: 47 Copynumber: 7.3 Consensus size: 47
54639017 GTATGAGATA
54639027 TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTG
1 TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTG
* * *
54639074 TATATATGTGACAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
1 TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTG
54639121 TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTG
1 TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTG
* * * *
54639168 CATATATGAGATAAGGCCTAATGGCCAATGTGATGAATGTGAACGTG
1 TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTG
54639215 TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTG
1 TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTG
*
54639262 CATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTG
1 TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTG
* *
54639309 TATATATGTGATAAGGCCGAGTGGCCAATGTGATGGATGTGAAAGTG
1 TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTG
*
54639356 TATAAATGTGATAAG
1 TATATATGTGATAAG
54639371 TCCCGAAGGG
Statistics
Matches: 278, Mismatches: 19, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 278 1.00
ACGTcount: A:0.34, C:0.09, G:0.30, T:0.27
Consensus pattern (47 bp):
TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTG
Found at i:54644631 original size:23 final size:23
Alignment explanation
Indices: 54644605--54644658 Score: 108
Period size: 23 Copynumber: 2.3 Consensus size: 23
54644595 TATCCCCACA
54644605 TGGAGTGTAAGGCTGGACGAGAG
1 TGGAGTGTAAGGCTGGACGAGAG
54644628 TGGAGTGTAAGGCTGGACGAGAG
1 TGGAGTGTAAGGCTGGACGAGAG
54644651 TGGAGTGT
1 TGGAGTGT
54644659 GGAGGATACA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.24, C:0.07, G:0.48, T:0.20
Consensus pattern (23 bp):
TGGAGTGTAAGGCTGGACGAGAG
Found at i:54652652 original size:2 final size:2
Alignment explanation
Indices: 54652645--54652681 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
54652635 GACATCACTA
54652645 AT 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 AT A
54652682 GTTTATAGAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:54653305 original size:3 final size:3
Alignment explanation
Indices: 54653297--54653362 Score: 69
Period size: 3 Copynumber: 21.7 Consensus size: 3
54653287 GCCTGTTCTA
* * * * *
54653297 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAC AAC AAC AACC AAC
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT
*
54653343 ATT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AA
54653363 CAACAACAAC
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
3 55 0.95
4 3 0.05
ACGTcount: A:0.65, C:0.09, G:0.00, T:0.26
Consensus pattern (3 bp):
AAT
Done.