Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr3
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: 26558743
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1281270 characters in sequence are not A, C, G, or T
File 38 of 79
Found at i:12401825 original size:20 final size:21
Alignment explanation
Indices: 12401797--12401839 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 21
12401787 AAGTCCAAGT
12401797 AAAACTTAAAATAAAAA-TAA
1 AAAACTTAAAATAAAAATTAA
* **
12401817 AAAATTTAATTTAAAAATTAA
1 AAAACTTAAAATAAAAATTAA
12401838 AA
1 AA
12401840 GAATAATTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (21 bp):
AAAACTTAAAATAAAAATTAA
Found at i:12404044 original size:16 final size:18
Alignment explanation
Indices: 12404005--12404044 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
12403995 AATATTTATA
12404005 TTATTTTTATATAATATT
1 TTATTTTTATATAATATT
*
12404023 TAATTTTTATAT-AT-TT
1 TTATTTTTATATAATATT
12404039 TTATTT
1 TTATTT
12404045 ACTGAATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 7 0.35
17 2 0.10
18 11 0.55
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (18 bp):
TTATTTTTATATAATATT
Found at i:12407349 original size:17 final size:17
Alignment explanation
Indices: 12407329--12407436 Score: 65
Period size: 17 Copynumber: 6.4 Consensus size: 17
12407319 CCAAACATCT
*
12407329 ATTCATATGAAATAACA
1 ATTCATACGAAATAACA
* * *
12407346 ATTCTTACCAAATGACA
1 ATTCATACGAAATAACA
** * * *
12407363 GCTCATGCAAAATAATA
1 ATTCATACGAAATAACA
* *
12407380 ATTCATATGAAATATCA
1 ATTCATACGAAATAACA
*
12407397 GTTCATACCG-AATAACA
1 ATTCATA-CGAAATAACA
* *
12407414 ATTCATGCAAAATAACA
1 ATTCATACGAAATAACA
*
12407431 GTTCAT
1 ATTCAT
12407437 GCTCCATCAT
Statistics
Matches: 64, Mismatches: 25, Indels: 4
0.69 0.27 0.04
Matches are distributed among these distances:
16 1 0.02
17 62 0.97
18 1 0.02
ACGTcount: A:0.45, C:0.18, G:0.08, T:0.29
Consensus pattern (17 bp):
ATTCATACGAAATAACA
Found at i:12407389 original size:51 final size:51
Alignment explanation
Indices: 12407329--12407428 Score: 137
Period size: 51 Copynumber: 2.0 Consensus size: 51
12407319 CCAAACATCT
* * *
12407329 ATTCATATGAAATAACAATTCTTACCAAATGACAGCTCATGCAAAATAATA
1 ATTCATATGAAATAACAATTCATACCAAATAACAACTCATGCAAAATAATA
* * * *
12407380 ATTCATATGAAATATCAGTTCATACCGAATAACAATTCATGCAAAATAA
1 ATTCATATGAAATAACAATTCATACCAAATAACAACTCATGCAAAATAA
12407429 CAGTTCATGC
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
51 42 1.00
ACGTcount: A:0.47, C:0.17, G:0.08, T:0.28
Consensus pattern (51 bp):
ATTCATATGAAATAACAATTCATACCAAATAACAACTCATGCAAAATAATA
Found at i:12423740 original size:21 final size:21
Alignment explanation
Indices: 12423714--12423765 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
12423704 TATTTTTAAA
12423714 ATTTTTA-AAAATATGTATATT
1 ATTTTTATAAAATATGTA-ATT
* *
12423735 ATTTTTATATAATATTTAATT
1 ATTTTTATAAAATATGTAATT
12423756 ATTTTATATA
1 ATTTT-TATA
12423766 TAATCATCTG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
21 15 0.56
22 12 0.44
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (21 bp):
ATTTTTATAAAATATGTAATT
Found at i:12423748 original size:22 final size:21
Alignment explanation
Indices: 12423714--12423769 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 21
12423704 TATTTTTAAA
*
12423714 ATTTTTA-AAAATATGTATATT
1 ATTTTTATATAATATGTA-ATT
*
12423735 ATTTTTATATAATATTTAATT
1 ATTTTTATATAATATGTAATT
12423756 ATTTTATATATAAT
1 ATTTT-TATATAAT
12423770 CATCTGAACA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
21 15 0.48
22 16 0.52
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (21 bp):
ATTTTTATATAATATGTAATT
Found at i:12424199 original size:15 final size:17
Alignment explanation
Indices: 12424178--12424218 Score: 59
Period size: 15 Copynumber: 2.5 Consensus size: 17
12424168 AGACATTTTA
12424178 AAAATTATAAAAAT-AT
1 AAAATTATAAAAATGAT
*
12424194 -AAATTATTAAAATGAT
1 AAAATTATAAAAATGAT
12424210 AAAATTATA
1 AAAATTATA
12424219 TTTTTTACTA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 12 0.57
16 2 0.10
17 7 0.33
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (17 bp):
AAAATTATAAAAATGAT
Found at i:12435474 original size:45 final size:45
Alignment explanation
Indices: 12435401--12435496 Score: 110
Period size: 45 Copynumber: 2.2 Consensus size: 45
12435391 GAATGAATAG
12435401 AAAAT-GAGAAATGAGAAACATTTAGAAATG-AT-TATGGTTTTCTCC
1 AAAATGGAGAAATGAGAAACATTTAGAAATGAATGTA-GG-TTTC-CC
* * *
12435446 AAAATGGAGAAATGA-AATCTTTTGGAAATGAATGTAGGTTTCCC
1 AAAATGGAGAAATGAGAAACATTTAGAAATGAATGTAGGTTTCCC
12435490 AAAATGG
1 AAAATGG
12435497 TAATGGAAAT
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
44 9 0.20
45 21 0.47
46 13 0.29
47 2 0.04
ACGTcount: A:0.42, C:0.08, G:0.21, T:0.29
Consensus pattern (45 bp):
AAAATGGAGAAATGAGAAACATTTAGAAATGAATGTAGGTTTCCC
Found at i:12439285 original size:12 final size:12
Alignment explanation
Indices: 12439268--12439292 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
12439258 GTTACACCTC
12439268 ATTATTTATGTT
1 ATTATTTATGTT
12439280 ATTATTTATGTT
1 ATTATTTATGTT
12439292 A
1 A
12439293 ACTTGTGCAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.28, C:0.00, G:0.08, T:0.64
Consensus pattern (12 bp):
ATTATTTATGTT
Found at i:12440232 original size:21 final size:21
Alignment explanation
Indices: 12440208--12440247 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
12440198 ACGGTTTGTT
*
12440208 CACACGGCCATGTGACCCATC
1 CACAAGGCCATGTGACCCATC
*
12440229 CACAAGGCTATGTGACCCA
1 CACAAGGCCATGTGACCCA
12440248 CTCACATGAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.28, C:0.38, G:0.20, T:0.15
Consensus pattern (21 bp):
CACAAGGCCATGTGACCCATC
Found at i:12440253 original size:21 final size:20
Alignment explanation
Indices: 12440207--12440253 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
12440197 CACGGTTTGT
*
12440207 TCACACGGCCATGTGACCCA
1 TCACAAGGCCATGTGACCCA
*
12440227 TCCACAAGGCTATGTGACCCA
1 T-CACAAGGCCATGTGACCCA
12440248 CTCACA
1 -TCACA
12440254 TGACCAAGCG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 1 0.04
21 21 0.91
22 1 0.04
ACGTcount: A:0.28, C:0.38, G:0.17, T:0.17
Consensus pattern (20 bp):
TCACAAGGCCATGTGACCCA
Found at i:12440853 original size:90 final size:91
Alignment explanation
Indices: 12440738--12440905 Score: 259
Period size: 91 Copynumber: 1.9 Consensus size: 91
12440728 TGTTGTTAAA
* ** *
12440738 AAAATGTTATAAATTATATTTATAAA-AAAA-TAAAACATAACTTTAATAATAAAATAAAGTTAG
1 AAAATGTTATAAATTATATTAATAAAGAAAACT-AAACATAACTACAATAATAAAATAAAGCTAG
12440801 TGGAAGAAAACCAAAATAATTAACAAC
65 TGGAAGAAAACCAAAATAATTAACAAC
* *
12440828 AAAATGTTATAAATTATATTAATAAAGAAAACTAAACATAACTACAATAATATAATTAAGCTAGT
1 AAAATGTTATAAATTATATTAATAAAGAAAACTAAACATAACTACAATAATAAAATAAAGCTAGT
12440893 GGAAGAAAACCAA
66 GGAAGAAAACCAA
12440906 GAAAAAGCTA
Statistics
Matches: 70, Mismatches: 6, Indels: 3
0.89 0.08 0.04
Matches are distributed among these distances:
90 25 0.36
91 44 0.63
92 1 0.01
ACGTcount: A:0.58, C:0.08, G:0.08, T:0.27
Consensus pattern (91 bp):
AAAATGTTATAAATTATATTAATAAAGAAAACTAAACATAACTACAATAATAAAATAAAGCTAGT
GGAAGAAAACCAAAATAATTAACAAC
Found at i:12446414 original size:18 final size:18
Alignment explanation
Indices: 12446391--12446433 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
12446381 CCCACGCCAG
12446391 AAAAAATAAAATATATGT
1 AAAAAATAAAATATATGT
* *
12446409 AAAAAATAAAATATTTTT
1 AAAAAATAAAATATATGT
12446427 AAAAAAT
1 AAAAAAT
12446434 TAATTCAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (18 bp):
AAAAAATAAAATATATGT
Found at i:12446996 original size:19 final size:18
Alignment explanation
Indices: 12446956--12446997 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
12446946 CTCATTTACT
*
12446956 TTTTTTATATTTTTATAG
1 TTTTTTATATTTTAATAG
12446974 TTTTTTATAATTATTAATA-
1 TTTTTTAT-ATT-TTAATAG
12446993 TTTTT
1 TTTTT
12446998 ATGATTTTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 8 0.38
19 8 0.38
20 5 0.24
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.71
Consensus pattern (18 bp):
TTTTTTATATTTTAATAG
Found at i:12457755 original size:266 final size:266
Alignment explanation
Indices: 12457281--12457812 Score: 938
Period size: 266 Copynumber: 2.0 Consensus size: 266
12457271 ATTGGCCTAT
*
12457281 CCCGATCATCAAGCATCTGAGCAACAAGAGGATTAACATTCGGAGCTCCTAGATTAAGTTGCTCA
1 CCCGATCATCAAACATCTGAGCAACAAGAGGATTAACATTCGGAGCTCCTAGATTAAGTTGCTCA
12457346 TTCATAGTAGGTGGATTGTTACCATCTTGATTCATTGCTTTTTGTCCTCTTCTCCTTCTTAGCAA
66 TTCATAGTAGGTGGATTGTTACCATCTTGATTCATTGCTTTTTGTCCTCTTCTCCTTCTTAGCAA
*
12457411 TGTCCTTTCAATTTCTGGACCTAAAGGATAGAGCCCTTCAGTAGGAGTTCCTCTACGCATACAGC
131 TGTCCTTTCAATTTCTGGACCTAAAGGATAGAGCCCTTCAGCAGGAGTTCCTCTACGCATACAGC
* *
12457476 TACTAATAGACCTATTGAGTTCACGAAACAAAAAAATTAGCAACTGAAACTATAAAAATTGTAAT
196 TACTAATAGACCTATTGAGATCACGAAACAAAAAAATTAGCAACTAAAACTATAAAAATTGTAAT
12457541 AACAAA
261 AACAAA
12457547 CCCGATCATCAAACATCTGAGCAACAAGAGGATTAACATTCGGAGCTCCTAGATTAAGTTGCTCA
1 CCCGATCATCAAACATCTGAGCAACAAGAGGATTAACATTCGGAGCTCCTAGATTAAGTTGCTCA
*
12457612 TTCATAGTAGGTGGATTGTTACCATCTTGATTCATTGCTTTTTGTTCTCTTCTCCTTCTTAGCAA
66 TTCATAGTAGGTGGATTGTTACCATCTTGATTCATTGCTTTTTGTCCTCTTCTCCTTCTTAGCAA
* * * * * *
12457677 TTTCCTTTCAATTTCTGGATCTAAAGGATAGAGGCCTTTAGCAGGAGTTCTTTTACGCATACAGC
131 TGTCCTTTCAATTTCTGGACCTAAAGGATAGAGCCCTTCAGCAGGAGTTCCTCTACGCATACAGC
* * *
12457742 TAGTAATAGACCTATTGAGATCATGAAACAAAAAAATTAGCAATTAAAACTATAAAAATTGTAAT
196 TACTAATAGACCTATTGAGATCACGAAACAAAAAAATTAGCAACTAAAACTATAAAAATTGTAAT
12457807 AACAAA
261 AACAAA
12457813 AACTAAAGTT
Statistics
Matches: 252, Mismatches: 14, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
266 252 1.00
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.32
Consensus pattern (266 bp):
CCCGATCATCAAACATCTGAGCAACAAGAGGATTAACATTCGGAGCTCCTAGATTAAGTTGCTCA
TTCATAGTAGGTGGATTGTTACCATCTTGATTCATTGCTTTTTGTCCTCTTCTCCTTCTTAGCAA
TGTCCTTTCAATTTCTGGACCTAAAGGATAGAGCCCTTCAGCAGGAGTTCCTCTACGCATACAGC
TACTAATAGACCTATTGAGATCACGAAACAAAAAAATTAGCAACTAAAACTATAAAAATTGTAAT
AACAAA
Found at i:12462663 original size:45 final size:45
Alignment explanation
Indices: 12462590--12462675 Score: 127
Period size: 45 Copynumber: 1.9 Consensus size: 45
12462580 GCGTTTTCAT
* * *
12462590 ATGATGCCATAGCGTCTTTCACCAATGGTCTTATTCATTTTTATC
1 ATGACGCCATAACATCTTTCACCAATGGTCTTATTCATTTTTATC
* *
12462635 ATGACGCCATAACATCTTTCAGCTATGGTCTTATTCATTTT
1 ATGACGCCATAACATCTTTCACCAATGGTCTTATTCATTTT
12462676 CATAATAACA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 36 1.00
ACGTcount: A:0.23, C:0.22, G:0.13, T:0.42
Consensus pattern (45 bp):
ATGACGCCATAACATCTTTCACCAATGGTCTTATTCATTTTTATC
Found at i:12464541 original size:21 final size:20
Alignment explanation
Indices: 12464513--12464551 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
12464503 CTAACTGGCA
* *
12464513 AAATAAATGTTTAATTTTTC
1 AAATAAATGGTCAATTTTTC
12464533 AAATAAAATGGTCAATTTT
1 AAAT-AAATGGTCAATTTT
12464552 GATCCAAGTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.44, C:0.05, G:0.08, T:0.44
Consensus pattern (20 bp):
AAATAAATGGTCAATTTTTC
Found at i:12464765 original size:22 final size:19
Alignment explanation
Indices: 12464737--12464778 Score: 57
Period size: 22 Copynumber: 2.1 Consensus size: 19
12464727 TTATAACAAC
12464737 TAATATATAATTATATTTATTA
1 TAATATAT-ATTA-A-TTATTA
12464759 TAATATATATTAATTATTA
1 TAATATATATTAATTATTA
12464778 T
1 T
12464779 CAACTTGGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 7 0.35
20 1 0.05
21 4 0.20
22 8 0.40
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
TAATATATATTAATTATTA
Found at i:12464769 original size:16 final size:15
Alignment explanation
Indices: 12464737--12464775 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
12464727 TTATAACAAC
12464737 TAATATATAATTATAT
1 TAAT-TATAATTATAT
*
12464753 TTATTATAATATATAT
1 TAATTATAAT-TATAT
12464769 TAATTAT
1 TAATTAT
12464776 TATCAACTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
TAATTATAATTATAT
Found at i:12466950 original size:26 final size:27
Alignment explanation
Indices: 12466920--12467006 Score: 97
Period size: 27 Copynumber: 3.3 Consensus size: 27
12466910 GCACAAATCA
*
12466920 GTCA-TTTACCCTCTAGGGGCATTACG
1 GTCATTTTACCCTCTAGGGGTATTACG
* *
12466946 GTCATTTTACCTTAC-AGGGGTATTTCG
1 GTCATTTTACCCT-CTAGGGGTATTACG
* * *
12466973 GTCATTTTAACCTATAAGGGTATTACG
1 GTCATTTTACCCTCTAGGGGTATTACG
12467000 GTCATTT
1 GTCATTT
12467007 AACAACCTTT
Statistics
Matches: 50, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
26 4 0.08
27 45 0.90
28 1 0.02
ACGTcount: A:0.22, C:0.20, G:0.21, T:0.38
Consensus pattern (27 bp):
GTCATTTTACCCTCTAGGGGTATTACG
Found at i:12466964 original size:27 final size:28
Alignment explanation
Indices: 12466934--12467006 Score: 98
Period size: 27 Copynumber: 2.7 Consensus size: 28
12466924 TTTACCCTCT
*
12466934 AGGGGCATTACGGTCATTTT-ACCT-TA
1 AGGGGTATTACGGTCATTTTAACCTATA
*
12466960 CAGGGGTATTTCGGTCATTTTAACCTATA
1 -AGGGGTATTACGGTCATTTTAACCTATA
12466989 A-GGGTATTACGGTCATTT
1 AGGGGTATTACGGTCATTT
12467007 AACAACCTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
27 34 0.83
28 5 0.12
29 2 0.05
ACGTcount: A:0.23, C:0.16, G:0.23, T:0.37
Consensus pattern (28 bp):
AGGGGTATTACGGTCATTTTAACCTATA
Found at i:12468425 original size:23 final size:24
Alignment explanation
Indices: 12468377--12468426 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
12468367 TTTTCGAATT
* * *
12468377 TCCTTGATTTTCTCCCCAATCTCC
1 TCCTTGATTTCCTCCACAAACTCC
12468401 TCCTTGATTTCCTCCACAAAC-CC
1 TCCTTGATTTCCTCCACAAACTCC
12468424 TCC
1 TCC
12468427 AAGACCAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 5 0.22
24 18 0.78
ACGTcount: A:0.16, C:0.44, G:0.04, T:0.36
Consensus pattern (24 bp):
TCCTTGATTTCCTCCACAAACTCC
Found at i:12474760 original size:23 final size:22
Alignment explanation
Indices: 12474735--12474777 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
12474725 GTTTAAATTT
12474735 TAATTAAT-TAA--AATTAACA
1 TAATTAATATAATTAATTAACA
12474754 TAATTAATCATAATTAATTAACA
1 TAATTAAT-ATAATTAATTAACA
12474777 T
1 T
12474778 TAAGTGTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
19 8 0.40
21 3 0.15
23 9 0.45
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (22 bp):
TAATTAATATAATTAATTAACA
Found at i:12483012 original size:20 final size:20
Alignment explanation
Indices: 12482987--12483053 Score: 59
Period size: 20 Copynumber: 3.5 Consensus size: 20
12482977 TCTTCCAAAA
12482987 TATCGATACCTGTGATGGTG
1 TATCGATACCTGTGATGGTG
* * ***
12483007 TATCGATATCT-TCCA--AAA
1 TATCGATACCTGT-GATGGTG
12483025 TATCGATACCTGTGATGGTG
1 TATCGATACCTGTGATGGTG
12483045 TATCGATAC
1 TATCGATAC
12483054 TTACATAGTT
Statistics
Matches: 33, Mismatches: 10, Indels: 8
0.65 0.20 0.16
Matches are distributed among these distances:
18 11 0.33
19 2 0.06
20 20 0.61
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.34
Consensus pattern (20 bp):
TATCGATACCTGTGATGGTG
Found at i:12483020 original size:38 final size:38
Alignment explanation
Indices: 12482975--12483052 Score: 156
Period size: 38 Copynumber: 2.1 Consensus size: 38
12482965 TACCGATACT
12482975 TATCTTCCAAAATATCGATACCTGTGATGGTGTATCGA
1 TATCTTCCAAAATATCGATACCTGTGATGGTGTATCGA
12483013 TATCTTCCAAAATATCGATACCTGTGATGGTGTATCGA
1 TATCTTCCAAAATATCGATACCTGTGATGGTGTATCGA
12483051 TA
1 TA
12483053 CTTACATAGT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (38 bp):
TATCTTCCAAAATATCGATACCTGTGATGGTGTATCGA
Found at i:12486863 original size:33 final size:33
Alignment explanation
Indices: 12486820--12486917 Score: 124
Period size: 33 Copynumber: 3.0 Consensus size: 33
12486810 TAGTCTATTG
* *
12486820 GGACAATAAACATAGAATGGAGATAGTCCACTA
1 GGACAATAAACAAAGAATAGAGATAGTCCACTA
* * * * * *
12486853 GGGCAGTAAACACATAACAGAGATAGCCCACTA
1 GGACAATAAACAAAGAATAGAGATAGTCCACTA
12486886 GGACAATAAACAAAGAATAGAGATAGTCCACT
1 GGACAATAAACAAAGAATAGAGATAGTCCACT
12486918 CTGAAAGTAA
Statistics
Matches: 52, Mismatches: 13, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
33 52 1.00
ACGTcount: A:0.46, C:0.18, G:0.20, T:0.15
Consensus pattern (33 bp):
GGACAATAAACAAAGAATAGAGATAGTCCACTA
Found at i:12490300 original size:21 final size:20
Alignment explanation
Indices: 12490276--12490322 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
12490266 AGATGCAGGT
12490276 AGGATGAAAGAGATAAGAAGA
1 AGGATGAAAGAGA-AAGAAGA
*
12490297 AGGA--AAAGAGAACGAAGA
1 AGGATGAAAGAGAAAGAAGA
12490315 AGG-TGAAA
1 AGGATGAAA
12490323 CGTTGCCAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
18 9 0.39
19 10 0.43
21 4 0.17
ACGTcount: A:0.57, C:0.02, G:0.34, T:0.06
Consensus pattern (20 bp):
AGGATGAAAGAGAAAGAAGA
Found at i:12490313 original size:18 final size:19
Alignment explanation
Indices: 12490282--12490317 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
12490272 AGGTAGGATG
12490282 AAAGAGATAAGAAGAAGGA
1 AAAGAGATAAGAAGAAGGA
*
12490301 AAAGAGA-ACGAAGAAGG
1 AAAGAGATAAGAAGAAGG
12490318 TGAAACGTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.61, C:0.03, G:0.33, T:0.03
Consensus pattern (19 bp):
AAAGAGATAAGAAGAAGGA
Found at i:12491977 original size:11 final size:11
Alignment explanation
Indices: 12491961--12491985 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
12491951 GTGATGCTAT
12491961 GTTCAATGGTG
1 GTTCAATGGTG
12491972 GTTCAATGGTG
1 GTTCAATGGTG
12491983 GTT
1 GTT
12491986 GAGTTTGGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.08, G:0.36, T:0.40
Consensus pattern (11 bp):
GTTCAATGGTG
Found at i:12493069 original size:21 final size:21
Alignment explanation
Indices: 12493045--12493086 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
12493035 ACCATGATCG
12493045 TATGGTAATGATAATGAATTA
1 TATGGTAATGATAATGAATTA
*
12493066 TATGGTAATGATGATGAATTA
1 TATGGTAATGATAATGAATTA
12493087 AGTGTTACGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.21, T:0.38
Consensus pattern (21 bp):
TATGGTAATGATAATGAATTA
Found at i:12497111 original size:51 final size:50
Alignment explanation
Indices: 12496968--12497313 Score: 310
Period size: 51 Copynumber: 6.9 Consensus size: 50
12496958 GTGAAGTTGC
*
12496968 TAGGTCACGTGTGTAGTACTATGTGCAGG-TACTACGTGTACCGAA-ATGA
1 TAGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGAATA-GA
* * * *
12497017 TAGGTCGCACGTGTAGTATTATGTGCAGGCTACT--GTGCATACCGAATAGCT
1 TAGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTG--TACCGAATAG-A
* * * *
12497068 TCGATCACGTGTGTAGTATTATGTGCAGGCTACTACGTGTACCGAA-ATGA
1 TAGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGAATA-GA
* *
12497118 TAGGTCGCATGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGAAT-GA
1 TAGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACC-GAATAGA
** * * * *
12497168 TAGGTCGTATGTCTAGTACTATGTGCAGGCTACTATGTGTACCGGATAGCT
1 TAGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGAATAG-A
* * *** * * *
12497219 TCGATCACGCATGTAATACTATGTGCAGGCTACTACGTGTATCGGAT-GAA
1 TAGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGAATAG-A
* * *
12497269 AATGGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGAACCG
1 TA-GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCG
12497314 GGTATCATTT
Statistics
Matches: 240, Mismatches: 44, Indels: 24
0.78 0.14 0.08
Matches are distributed among these distances:
48 3 0.01
49 28 0.12
50 95 0.40
51 111 0.46
53 3 0.01
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.30
Consensus pattern (50 bp):
TAGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGAATAGA
Found at i:12497161 original size:101 final size:100
Alignment explanation
Indices: 12496972--12497154 Score: 321
Period size: 101 Copynumber: 1.8 Consensus size: 100
12496962 AGTTGCTAGG
*
12496972 TCACGTGTGTAGTACTATGTGCAGGTACTACGTGTACCGAAATGATAGGTCGCACGTGTAGTATT
1 TCACGTGTGTAGTACTATGTGCAGGTACTACGTGTACCGAAATGATAGGTCGCACGTGTAGTACT
*
12497037 ATGTGCAGGCTACTGTGCATACCGAATAGCTTCGA
66 ATGTGCAGGCTACTATGCATACCGAATAGCTTCGA
* *
12497072 TCACGTGTGTAGTATTATGTGCAGGCTACTACGTGTACCGAAATGATAGGTCGCATGTGTAGTAC
1 TCACGTGTGTAGTACTATGTGCAGG-TACTACGTGTACCGAAATGATAGGTCGCACGTGTAGTAC
12497137 TATGTGCAGGCTACTATG
65 TATGTGCAGGCTACTATG
12497155 TGTACCGGAA
Statistics
Matches: 78, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
100 24 0.31
101 54 0.69
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.30
Consensus pattern (100 bp):
TCACGTGTGTAGTACTATGTGCAGGTACTACGTGTACCGAAATGATAGGTCGCACGTGTAGTACT
ATGTGCAGGCTACTATGCATACCGAATAGCTTCGA
Found at i:12497242 original size:151 final size:151
Alignment explanation
Indices: 12496968--12497314 Score: 482
Period size: 151 Copynumber: 2.3 Consensus size: 151
12496958 GTGAAGTTGC
* * * *
12496968 TAGGTCACGTGTGTAGTACTATGTGCAGG-TACTACGTGTACCGAAATGATAGGTCGCACGTGTA
1 TAGGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGAATGATAGGTCGCACGTCTA
* * ** * *
12497032 GTATTATGTGCAGGCTACTGTGCATACCGAATAGCTTCGATCACGTGTGTAGTATTATGTGCAGG
66 GTACTATGTGCAGGCTACTATGCATACCGAATAGCTTCGATCACGCATGTAATACTATGTGCAGG
12497097 CTACTACGTGTACCGAAATG-A
131 CTACTACGTGTACCG-AATGAA
* * *
12497118 TAGGTCGCATGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGAATGATAGGTCGTATGTCTA
1 TAGGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGAATGATAGGTCGCACGTCTA
** *
12497183 GTACTATGTGCAGGCTACTATGTGTACCGGATAGCTTCGATCACGCATGTAATACTATGTGCAGG
66 GTACTATGTGCAGGCTACTATGCATACCGAATAGCTTCGATCACGCATGTAATACTATGTGCAGG
* *
12497248 CTACTACGTGTATCGGATGAA
131 CTACTACGTGTACCGAATGAA
* *
12497269 AATGGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGAACCGG
1 TA-GGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACCGG
12497315 GTATCATTTA
Statistics
Matches: 173, Mismatches: 21, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
150 30 0.17
151 102 0.59
152 41 0.24
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.30
Consensus pattern (151 bp):
TAGGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGAATGATAGGTCGCACGTCTA
GTACTATGTGCAGGCTACTATGCATACCGAATAGCTTCGATCACGCATGTAATACTATGTGCAGG
CTACTACGTGTACCGAATGAA
Found at i:12497961 original size:17 final size:16
Alignment explanation
Indices: 12497939--12497972 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
12497929 AGATAATTCA
*
12497939 TTTTAATTTTTCAAATT
1 TTTTAATATTT-AAATT
12497956 TTTTAATATTTAAATT
1 TTTTAATATTTAAATT
12497972 T
1 T
12497973 ACATTATATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTTAATATTTAAATT
Found at i:12514503 original size:7 final size:7
Alignment explanation
Indices: 12514492--12514526 Score: 61
Period size: 7 Copynumber: 5.0 Consensus size: 7
12514482 TTGAGAGGTT
12514492 GGATGAG
1 GGATGAG
*
12514499 AGATGAG
1 GGATGAG
12514506 GGATGAG
1 GGATGAG
12514513 GGATGAG
1 GGATGAG
12514520 GGATGAG
1 GGATGAG
12514527 CTCTTATTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.54, T:0.14
Consensus pattern (7 bp):
GGATGAG
Found at i:12520811 original size:17 final size:17
Alignment explanation
Indices: 12520789--12520822 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
12520779 ATACAACCTC
*
12520789 TTTTTTTTATGCACGAA
1 TTTTTTTAATGCACGAA
*
12520806 TTTTTTTAATTCACGAA
1 TTTTTTTAATGCACGAA
12520823 CCTAATTTGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.26, C:0.12, G:0.09, T:0.53
Consensus pattern (17 bp):
TTTTTTTAATGCACGAA
Found at i:12532086 original size:53 final size:53
Alignment explanation
Indices: 12532006--12532112 Score: 205
Period size: 53 Copynumber: 2.0 Consensus size: 53
12531996 TTACAATTTT
*
12532006 TAATTATTTTCCAAAGTCAGAATAGGGGATTCCGAAATCAGTTCAACCCTGCC
1 TAATTATTTTCCAAAGTCAGAACAGGGGATTCCGAAATCAGTTCAACCCTGCC
12532059 TAATTATTTTCCAAAGTCAGAACAGGGGATTCCGAAATCAGTTCAACCCTGCC
1 TAATTATTTTCCAAAGTCAGAACAGGGGATTCCGAAATCAGTTCAACCCTGCC
12532112 T
1 T
12532113 CACTAAAATT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.28
Consensus pattern (53 bp):
TAATTATTTTCCAAAGTCAGAACAGGGGATTCCGAAATCAGTTCAACCCTGCC
Found at i:12532312 original size:16 final size:16
Alignment explanation
Indices: 12532291--12532322 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
12532281 ATTTTGTTGC
*
12532291 TAATTTTACTTTTTCA
1 TAATTTCACTTTTTCA
12532307 TAATTTCACTTTTTCA
1 TAATTTCACTTTTTCA
12532323 CTTTCAATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.16, G:0.00, T:0.59
Consensus pattern (16 bp):
TAATTTCACTTTTTCA
Found at i:12532510 original size:46 final size:43
Alignment explanation
Indices: 12532452--12532544 Score: 107
Period size: 46 Copynumber: 2.1 Consensus size: 43
12532442 GACAGATACA
* *
12532452 TGGTGGATTCAGCACACAGCAACCACCCTTTGTAATCAATGATAT
1 TGGTGGATTCAGCACACAACAACCA-CC-TTATAATCAATGATAT
* *
12532497 CTGGTGGGA-TCAGCACATAACAACCACCTTATAATTAATGATAT
1 -TGGT-GGATTCAGCACACAACAACCACCTTATAATCAATGATAT
12532541 TGGT
1 TGGT
12532545 TCACATAGTA
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
43 4 0.10
44 14 0.33
45 2 0.05
46 19 0.45
47 3 0.07
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.28
Consensus pattern (43 bp):
TGGTGGATTCAGCACACAACAACCACCTTATAATCAATGATAT
Found at i:12551649 original size:66 final size:66
Alignment explanation
Indices: 12551543--12551670 Score: 195
Period size: 66 Copynumber: 1.9 Consensus size: 66
12551533 TTATTACATT
*
12551543 AATGTCGCTGCATGAGTTAATTCCAGATTGCGTCCAGAATTGTCGCCGCACCTAACAGATGTCTG
1 AATGTCGCTGCATGAGTTAATTCCAGATTGCGTCCAGAATTGTCACCGCACCTAACAGATGTCTG
12551608 C
66 C
* * * *
12551609 AATGTCGCTGCAT-AGGTTAATTCCATATTGTGTCCAGAATTGTCATCGCACCTAATAGATGT
1 AATGTCGCTGCATGA-GTTAATTCCAGATTGCGTCCAGAATTGTCACCGCACCTAACAGATGT
12551671 TCGAATAAGA
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
65 1 0.02
66 55 0.98
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30
Consensus pattern (66 bp):
AATGTCGCTGCATGAGTTAATTCCAGATTGCGTCCAGAATTGTCACCGCACCTAACAGATGTCTG
C
Found at i:12555010 original size:12 final size:13
Alignment explanation
Indices: 12554986--12555014 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
12554976 GGGCTATAAC
12554986 TATTGCATTTATT
1 TATTGCATTTATT
12554999 TATTGC-TTTATT
1 TATTGCATTTATT
12555011 TATT
1 TATT
12555015 CATGTGTTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.21, C:0.07, G:0.07, T:0.66
Consensus pattern (13 bp):
TATTGCATTTATT
Found at i:12586204 original size:33 final size:33
Alignment explanation
Indices: 12586034--12586210 Score: 165
Period size: 33 Copynumber: 5.4 Consensus size: 33
12586024 TGTCCCGACA
* * * *
12586034 GACTTACCTTGTTCTGTATTTACTGTCCCAGCG
1 GACTTACCCTGTTCTGTGTTTACTATCCCAGTG
* * * *
12586067 GACTTACCCTATTTTATGTTTATTATCCCAGTG
1 GACTTACCCTGTTCTGTGTTTACTATCCCAGTG
* * * *
12586100 GACTTACTCTGTTTTGTGTTTACTATCCTAGCG
1 GACTTACCCTGTTCTGTGTTTACTATCCCAGTG
* ** *
12586133 AACTTACTTTGTTCTTTGTTTACTATCCCAGTG
1 GACTTACCCTGTTCTGTGTTTACTATCCCAGTG
* * *
12586166 GACTTACCCTATTCTGTGTTTACTGTCCCAATG
1 GACTTACCCTGTTCTGTGTTTACTATCCCAGTG
* *
12586199 AACTTACTCTGT
1 GACTTACCCTGT
12586211 GGTTGCCATG
Statistics
Matches: 114, Mismatches: 30, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
33 114 1.00
ACGTcount: A:0.18, C:0.24, G:0.15, T:0.44
Consensus pattern (33 bp):
GACTTACCCTGTTCTGTGTTTACTATCCCAGTG
Found at i:12586206 original size:66 final size:66
Alignment explanation
Indices: 12586034--12586208 Score: 208
Period size: 66 Copynumber: 2.7 Consensus size: 66
12586024 TGTCCCGACA
* * * * *
12586034 GACTTACCTTGTTCTGTATTTACTGTCCCAGCGGACTTACCCTATTTTATGTTTATTATCCCAGT
1 GACTTACCCTGTTCTGTGTTTACTGTCCCAGCGAACTTACTCTATTTTATGTTTACTATCCCAGT
12586099 G
66 G
* * * * * *
12586100 GACTTACTCTGTTTTGTGTTTACTATCCTAGCGAACTTACTTTGTTCTT-TGTTTACTATCCCAG
1 GACTTACCCTGTTCTGTGTTTACTGTCCCAGCGAACTTACTCTATT-TTATGTTTACTATCCCAG
12586164 TG
65 TG
* **
12586166 GACTTACCCTATTCTGTGTTTACTGTCCCAATGAACTTACTCT
1 GACTTACCCTGTTCTGTGTTTACTGTCCCAGCGAACTTACTCT
12586209 GTGGTTGCCA
Statistics
Matches: 89, Mismatches: 19, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
66 87 0.98
67 2 0.02
ACGTcount: A:0.18, C:0.24, G:0.14, T:0.43
Consensus pattern (66 bp):
GACTTACCCTGTTCTGTGTTTACTGTCCCAGCGAACTTACTCTATTTTATGTTTACTATCCCAGT
G
Found at i:12587975 original size:50 final size:50
Alignment explanation
Indices: 12587806--12588097 Score: 216
Period size: 50 Copynumber: 5.9 Consensus size: 50
12587796 GATAATAACA
* * *
12587806 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA--TGTT-TC-CTGTAC
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTTATCTC-G--G
* * * * ** * * *
12587855 TGCCAATGCCATATCCCAGATATGGTCTTACATAGGAGTTCTCATATTGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTTATCTCGG
* * * ** * *
12587905 TGTCC-ATGTCATGTCTCAGACATGGTCTTACGGGGGACCTCTCATCTCGC
1 TG-CCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTTATCTCGG
* * *
12587955 TGCCAACGCCATATCCCAGACATGGTCCTACATGGGACCTCTTACCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTTATCTCGG
* * * * *
12588005 TGTCAATGCCATGTCCTAGACATGCTCTTACATGGGACCTCTTATCTTGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTTATCTCGG
* ** * **
12588055 TGCCAACACCATGTTGCAGACACGGTCTTACATAAGACCTCTT
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTT
12588098 TACCCAAATG
Statistics
Matches: 188, Mismatches: 49, Indels: 11
0.76 0.20 0.04
Matches are distributed among these distances:
49 35 0.19
50 147 0.78
51 4 0.02
52 2 0.01
ACGTcount: A:0.22, C:0.28, G:0.21, T:0.29
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTTATCTCGG
Found at i:12587981 original size:100 final size:100
Alignment explanation
Indices: 12587854--12588096 Score: 254
Period size: 100 Copynumber: 2.4 Consensus size: 100
12587844 GTTTCCTGTA
* * ** * * * *
12587854 CTGCCAATGCCATATCCCAGATATGGTCTTACATAGGAGTTCTCATATTGGTGTCCATGTCATGT
1 CTGCCAACGCCATATCCCAGACATGGTCTTACATAGGACCTCTCACATCGGTGTCAATGCCATGT
* *
12587919 -CTCAGACATGGTCTTACGGGGGACCTCTCATCTCG
66 CCT-AGACATGCTCTTACAGGGGACCTCTCATCTCG
* * * *
12587954 CTGCCAACGCCATATCCCAGACATGGTCCTACATGGGACCTCTTACCTCGGTGTCAATGCCATGT
1 CTGCCAACGCCATATCCCAGACATGGTCTTACATAGGACCTCTCACATCGGTGTCAATGCCATGT
* * *
12588019 CCTAGACATGCTCTTACATGGGACCTCTTATCTTG
66 CCTAGACATGCTCTTACAGGGGACCTCTCATCTCG
* * * ** * *
12588054 GTGCCAACACCATGTTGCAGACACGGTCTTACATAAGACCTCT
1 CTGCCAACGCCATATCCCAGACATGGTCTTACATAGGACCTCT
12588097 TTACCCAAAT
Statistics
Matches: 116, Mismatches: 26, Indels: 2
0.81 0.18 0.01
Matches are distributed among these distances:
100 114 0.98
101 2 0.02
ACGTcount: A:0.22, C:0.29, G:0.20, T:0.28
Consensus pattern (100 bp):
CTGCCAACGCCATATCCCAGACATGGTCTTACATAGGACCTCTCACATCGGTGTCAATGCCATGT
CCTAGACATGCTCTTACAGGGGACCTCTCATCTCG
Found at i:12594628 original size:50 final size:50
Alignment explanation
Indices: 12594553--12594794 Score: 247
Period size: 50 Copynumber: 4.8 Consensus size: 50
12594543 TTTCTTGTAC
* * * ** *
12594553 TGCCAATGCCATATCCTAGATATGGTCTTACATGGGAGTTCTCATATTGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* *
12594603 TGCCCATGCCATGTCCCAGACATGGTCTT--ATGGGGAACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAT-GGG-ACCTCTCATATCGG
* * *
12594653 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGATCTC-CTATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC-ATATCGG
* * * * * *
12594703 TGCCAACGCCATGTCCTAGACATGGTATTACATGGGACCTCTTATCTCAG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
** * *
12594753 TGCCAATGCCATGTTGCAGACACGGTCTTACATGAGACCTCT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
12594795 TTACCCAAAT
Statistics
Matches: 163, Mismatches: 23, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
48 2 0.01
49 4 0.02
50 152 0.93
51 3 0.02
52 2 0.01
ACGTcount: A:0.22, C:0.28, G:0.22, T:0.28
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
Found at i:12594726 original size:100 final size:98
Alignment explanation
Indices: 12594553--12594786 Score: 274
Period size: 100 Copynumber: 2.3 Consensus size: 98
12594543 TTTCTTGTAC
* * * * *
12594553 TGCCAATGCCATATCCTAGATATGGTCTTACATGGGAGTTCTCATATTGGTGCCCATGCCATGTC
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAG-TCTCATATTGGTGCCAACGCCATGTC
* *
12594618 CCAGACATGGTCTT-ATGGGGAACCTCTCATCTCGG
65 CCAGACATGGTATTAAT-GGG-ACCTCTCATCTCAG
* *
12594653 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGA-TCTCCTATCTCGGTGCCAACGCCATGT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGTCTCATAT-T-GGTGCCAACGCCATGT
* *
12594717 CCTAGACATGGTATTACATGGGACCTCTTATCTCAG
64 CCCAGACATGGTATTA-ATGGGACCTCTCATCTCAG
** *
12594753 TGCCAATGCCATGTTGCAGACACGGTCTTACATG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATG
12594787 AGACCTCTTT
Statistics
Matches: 115, Mismatches: 15, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
98 7 0.06
99 1 0.01
100 102 0.89
101 3 0.03
102 2 0.02
ACGTcount: A:0.22, C:0.28, G:0.22, T:0.28
Consensus pattern (98 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGTCTCATATTGGTGCCAACGCCATGTCC
CAGACATGGTATTAATGGGACCTCTCATCTCAG
Found at i:12600920 original size:125 final size:126
Alignment explanation
Indices: 12600698--12600948 Score: 495
Period size: 125 Copynumber: 2.0 Consensus size: 126
12600688 TCCACTTAGT
12600698 ATCTGCACTACTCACTGGTCGATGAACTAAAGAACTATATGACATCCGCACCGTGAACCTCATCT
1 ATCTGCACTACTCACTGGTCGATGAACTAAAGAACTATATGACATCCGCACCGTGAACCTCATCT
12600763 TGTAATCCCAAATCCAATTAGGTGAGTTGCCTATATCAAACTTTTAAAAA-GGAATTTTTA
66 TGTAATCCCAAATCCAATTAGGTGAGTTGCCTATATCAAACTTTTAAAAATGGAATTTTTA
12600823 ATCTGCACTACTCACTGGTCGATGAACTAAAGAACTATATGACATCCGCACCGTGAACCTCATCT
1 ATCTGCACTACTCACTGGTCGATGAACTAAAGAACTATATGACATCCGCACCGTGAACCTCATCT
12600888 TGTAATCCCAAATCCAATTAGGTGAGTTGCCTATATCAAACTTTTAAAAATGGAATTTTTA
66 TGTAATCCCAAATCCAATTAGGTGAGTTGCCTATATCAAACTTTTAAAAATGGAATTTTTA
12600949 TTATTTTTTT
Statistics
Matches: 125, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
125 115 0.92
126 10 0.08
ACGTcount: A:0.33, C:0.22, G:0.14, T:0.30
Consensus pattern (126 bp):
ATCTGCACTACTCACTGGTCGATGAACTAAAGAACTATATGACATCCGCACCGTGAACCTCATCT
TGTAATCCCAAATCCAATTAGGTGAGTTGCCTATATCAAACTTTTAAAAATGGAATTTTTA
Found at i:12614770 original size:16 final size:15
Alignment explanation
Indices: 12614736--12614776 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 15
12614726 GGTGATAATA
12614736 ATTAATATATAATTAT
1 ATTAAT-TATAATTAT
*
12614752 ATTTATTATAATGTAT
1 ATTAATTATAAT-TAT
12614768 ATTAATTAT
1 ATTAATTAT
12614777 TATCAACTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
15 6 0.27
16 16 0.73
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
ATTAATTATAATTAT
Found at i:12615297 original size:41 final size:41
Alignment explanation
Indices: 12615234--12615320 Score: 102
Period size: 41 Copynumber: 2.1 Consensus size: 41
12615224 CGACGAACCT
* * * **
12615234 GCTCGCACACTAGCCTTGCTGCCTTTGCACGCATCATACCA
1 GCTCGCACACCAGCCCTACTGCCCCTGCACGCATCATACCA
* * *
12615275 GCTCGCGCACCAGCCCTACTGCCCCTGCACGCATCATCCCT
1 GCTCGCACACCAGCCCTACTGCCCCTGCACGCATCATACCA
12615316 GCTCG
1 GCTCG
12615321 TGCCTTGCTT
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.16, C:0.45, G:0.18, T:0.21
Consensus pattern (41 bp):
GCTCGCACACCAGCCCTACTGCCCCTGCACGCATCATACCA
Found at i:12618874 original size:27 final size:27
Alignment explanation
Indices: 12618822--12618907 Score: 95
Period size: 28 Copynumber: 3.2 Consensus size: 27
12618812 ATAGTCATAC
* *
12618822 ATAACATA-GAGCAT-ACGGTCATTTT
1 ATAACATAGGGGCATAACAGTCATTTT
12618847 ATAACATAGGGGCATAACAGTCATTTT
1 ATAACATAGGGGCATAACAGTCATTTT
** * *
12618874 ACCACGTAGGAGGCATAACACTCATTTT
1 ATAACATAGG-GGCATAACAGTCATTTT
12618902 ATAACA
1 ATAACA
12618908 GAGGTCTACT
Statistics
Matches: 49, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
25 8 0.16
26 5 0.10
27 17 0.35
28 19 0.39
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.28
Consensus pattern (27 bp):
ATAACATAGGGGCATAACAGTCATTTT
Found at i:12622109 original size:20 final size:20
Alignment explanation
Indices: 12622084--12622122 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
12622074 AACTATTTCT
12622084 TTCAAATTAAGTTAAAAATA
1 TTCAAATTAAGTTAAAAATA
*
12622104 TTCAAATTAAGTTGAAAAT
1 TTCAAATTAAGTTAAAAAT
12622123 GATGATATCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.51, C:0.05, G:0.08, T:0.36
Consensus pattern (20 bp):
TTCAAATTAAGTTAAAAATA
Found at i:12634312 original size:4 final size:4
Alignment explanation
Indices: 12634303--12634358 Score: 112
Period size: 4 Copynumber: 14.0 Consensus size: 4
12634293 TATGAATGTG
12634303 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
12634351 ATAC ATAC
1 ATAC ATAC
12634359 CAACAGTGTA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 52 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAC
Found at i:12635173 original size:75 final size:76
Alignment explanation
Indices: 12635071--12635230 Score: 304
Period size: 75 Copynumber: 2.1 Consensus size: 76
12635061 TGAAAGTGAA
*
12635071 AAATTAAAAATAACTAATAACAAAAATCAATAATTTTCATCTATTGTATATAATTTTAATTAATA
1 AAATAAAAAATAACTAATAACAAAAATCAATAATTTTCATCTATTGTATATAATTTTAATTAATA
12635136 TTATT-ATAAT
66 TTATTAATAAT
12635146 AAATAAAAAATAACTAATAACAAAAATCAATAATTTTCATCTATTGTATATAATTTTAATTAATA
1 AAATAAAAAATAACTAATAACAAAAATCAATAATTTTCATCTATTGTATATAATTTTAATTAATA
12635211 TTATTAATAAT
66 TTATTAATAAT
12635222 AAATAAAAA
1 AAATAAAAA
12635231 CCCTTAATGT
Statistics
Matches: 83, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
75 69 0.83
76 14 0.17
ACGTcount: A:0.54, C:0.06, G:0.01, T:0.39
Consensus pattern (76 bp):
AAATAAAAAATAACTAATAACAAAAATCAATAATTTTCATCTATTGTATATAATTTTAATTAATA
TTATTAATAAT
Found at i:12644819 original size:27 final size:27
Alignment explanation
Indices: 12644789--12644844 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
12644779 CAAAATAATT
12644789 TTCAAAAT-TTGA-AAATAATTTTTAAAA
1 TTCAAAATATTGATAAA-AA-TTTTAAAA
*
12644816 TTCAAAATATTTATAAAAATTTTAAAA
1 TTCAAAATATTGATAAAAATTTTAAAA
12644843 TT
1 TT
12644845 TTCATTTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
27 18 0.69
28 5 0.19
29 3 0.12
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.43
Consensus pattern (27 bp):
TTCAAAATATTGATAAAAATTTTAAAA
Found at i:12644824 original size:19 final size:20
Alignment explanation
Indices: 12644778--12644843 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
12644768 TAACAAAAGA
*
12644778 TCAAAATAATTTTCAAAATT
1 TCAAAATAATTTTTAAAATT
*
12644798 TGAAAATAATTTTTAAAA-T
1 TCAAAATAATTTTTAAAATT
*
12644817 TCAAAAT-ATTTATAAAAATT
1 TCAAAATAATTT-TTAAAATT
*
12644837 TTAAAAT
1 TCAAAAT
12644844 TTTCATTTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
18 4 0.10
19 12 0.31
20 23 0.59
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.41
Consensus pattern (20 bp):
TCAAAATAATTTTTAAAATT
Found at i:12645689 original size:14 final size:15
Alignment explanation
Indices: 12645659--12645691 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
12645649 TTAAATCATC
12645659 TTATTTTTATATAAT
1 TTATTTTTATATAAT
*
12645674 TTATTTTTTTAT-AT
1 TTATTTTTATATAAT
12645688 TTAT
1 TTAT
12645692 GCAAAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (15 bp):
TTATTTTTATATAAT
Found at i:12648510 original size:45 final size:45
Alignment explanation
Indices: 12648404--12648666 Score: 185
Period size: 45 Copynumber: 5.8 Consensus size: 45
12648394 TGGCTTGAAG
* * * * * **
12648404 GAAATGATTAAGACCATAGTTGAAAGATATTATGGCACTA-TACCG
1 GAAATGAGTAAGACCATAGTTGAAAGACACTATGGCACCACGA-TT
* * * *
12648449 GGAAT-AGATAATACCATAGTTGAAAGACACTATGACACCA-TATT
1 GAAATGAG-TAAGACCATAGTTGAAAGACACTATGGCACCACGATT
* * * *
12648493 AGAAATGAGTAAGACCATAGCTGAAAGATATTATGGCATCACGATT
1 -GAAATGAGTAAGACCATAGTTGAAAGACACTATGGCACCACGATT
** * * * * *
12648539 -CTATCGAGTAAGACTATAGCTGAAAGACGCTATGGCATCACGAAT
1 GAAAT-GAGTAAGACCATAGTTGAAAGACACTATGGCACCACGATT
* * * *
12648584 CAAA-GAAATAAGACCATAGTTGAAAGACACTATGGCAACACGATGG
1 GAAATG-AGTAAGACCATAGTTGAAAGACACTATGGCACCACGAT-T
* *
12648630 GAAATGAATAAGACCATGGTTGAAAGACACTATGGCA
1 GAAATGAGTAAGACCATAGTTGAAAGACACTATGGCA
12648667 TCAAGACGAG
Statistics
Matches: 174, Mismatches: 35, Indels: 17
0.77 0.15 0.08
Matches are distributed among these distances:
44 4 0.02
45 130 0.75
46 39 0.22
47 1 0.01
ACGTcount: A:0.41, C:0.16, G:0.21, T:0.22
Consensus pattern (45 bp):
GAAATGAGTAAGACCATAGTTGAAAGACACTATGGCACCACGATT
Found at i:12648656 original size:46 final size:45
Alignment explanation
Indices: 12648589--12648711 Score: 156
Period size: 46 Copynumber: 2.7 Consensus size: 45
12648579 CGAATCAAAG
* * * *
12648589 AAATAAGACCATAGTTGAAAGACACTATGGCAACACGATGGGAAAT
1 AAATAAGACCATGGTTGAAAGACACTATGGCAACAAGACGAG-AAT
* *
12648635 GAATAAGACCATGGTTGAAAGACACTATGGCATCAAGACGAGAAT
1 AAATAAGACCATGGTTGAAAGACACTATGGCAACAAGACGAGAAT
* * *
12648680 AAATAAGACCGTGGTTGAAAGAGACCATGGCA
1 AAATAAGACCATGGTTGAAAGACACTATGGCA
12648712 CCCTCCGATC
Statistics
Matches: 67, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
45 31 0.46
46 36 0.54
ACGTcount: A:0.43, C:0.15, G:0.24, T:0.17
Consensus pattern (45 bp):
AAATAAGACCATGGTTGAAAGACACTATGGCAACAAGACGAGAAT
Found at i:12648700 original size:45 final size:45
Alignment explanation
Indices: 12648559--12648711 Score: 166
Period size: 45 Copynumber: 3.4 Consensus size: 45
12648549 AGACTATAGC
* * *
12648559 TGAAAGACGCTATGGCATCACGAATC-A-AAGAAATAAGACCATAGT
1 TGAAAGACACTATGGCATCACG-A-CGAGAATAAATAAGACCATGGT
* * * *
12648604 TGAAAGACACTATGGCAACACGATGGGAAATGAATAAGACCATGGT
1 TGAAAGACACTATGGCATCACGACGAG-AATAAATAAGACCATGGT
* *
12648650 TGAAAGACACTATGGCATCAAGACGAGAATAAATAAGACCGTGGT
1 TGAAAGACACTATGGCATCACGACGAGAATAAATAAGACCATGGT
* *
12648695 TGAAAGAGACCATGGCA
1 TGAAAGACACTATGGCA
12648712 CCCTCCGATC
Statistics
Matches: 90, Mismatches: 15, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
44 1 0.01
45 51 0.57
46 38 0.42
ACGTcount: A:0.42, C:0.16, G:0.24, T:0.17
Consensus pattern (45 bp):
TGAAAGACACTATGGCATCACGACGAGAATAAATAAGACCATGGT
Found at i:12651807 original size:15 final size:15
Alignment explanation
Indices: 12651787--12651815 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
12651777 TAAACATCAA
12651787 GAATCATACAAAATG
1 GAATCATACAAAATG
12651802 GAATCATACAAAAT
1 GAATCATACAAAAT
12651816 CATGCATTGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.14, G:0.10, T:0.21
Consensus pattern (15 bp):
GAATCATACAAAATG
Found at i:12662375 original size:41 final size:40
Alignment explanation
Indices: 12662313--12662450 Score: 159
Period size: 41 Copynumber: 3.4 Consensus size: 40
12662303 AATGAGATAT
* * *
12662313 TAGCTAGCTTTGTGCCAGTGTATATTATCAGGTTTTGTGTC
1 TAGCAAGCTTTGTG-CAGTGTATATTATCAGGCTTTGTGCC
* *
12662354 TAGCAAGCTTTGTGTCGGTGTATATTATTAGGCTTTGTGCC
1 TAGCAAGCTTTGTG-CAGTGTATATTATCAGGCTTTGTGCC
* * * **
12662395 TAGCAGGCTTTGTGCTAGTGTATATTATCAAGCCTTAAGCC
1 TAGCAAGCTTTGTGC-AGTGTATATTATCAGGCTTTGTGCC
12662436 TAGCAAGCTTTGTGC
1 TAGCAAGCTTTGTGC
12662451 CGGTGAATTA
Statistics
Matches: 82, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
40 1 0.01
41 81 0.99
ACGTcount: A:0.20, C:0.17, G:0.25, T:0.39
Consensus pattern (40 bp):
TAGCAAGCTTTGTGCAGTGTATATTATCAGGCTTTGTGCC
Found at i:12668143 original size:21 final size:21
Alignment explanation
Indices: 12668117--12668159 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
12668107 CTTAACGGGA
12668117 TAGCTGACGTGGCCAGTTAAC
1 TAGCTGACGTGGCCAGTTAAC
* *
12668138 TAGCTGATGTGGCTAGTTAAC
1 TAGCTGACGTGGCCAGTTAAC
12668159 T
1 T
12668160 TGCCACGTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.23, C:0.19, G:0.28, T:0.30
Consensus pattern (21 bp):
TAGCTGACGTGGCCAGTTAAC
Found at i:12669268 original size:3 final size:3
Alignment explanation
Indices: 12669260--12669338 Score: 69
Period size: 3 Copynumber: 28.0 Consensus size: 3
12669250 CATTTTCTCA
* *
12669260 TCT TCT TCT TC- TCT TCT TCT T-T TCT TCT TCT TCT TCT CCA T-T TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
* * * *
12669305 TC- TCT TAT TCT TCT TTT TTT TC- TCT TCC TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
12669339 ACTACCCAGT
Statistics
Matches: 61, Mismatches: 10, Indels: 10
0.75 0.12 0.12
Matches are distributed among these distances:
2 9 0.15
3 52 0.85
ACGTcount: A:0.03, C:0.32, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:12669274 original size:8 final size:8
Alignment explanation
Indices: 12669263--12669297 Score: 52
Period size: 8 Copynumber: 4.2 Consensus size: 8
12669253 TTTCTCATCT
12669263 TCTTCTTC
1 TCTTCTTC
12669271 TCTTCTTC
1 TCTTCTTC
*
12669279 TTTTCTTC
1 TCTTCTTC
12669287 TTCTTCTTC
1 -TCTTCTTC
12669296 TC
1 TC
12669298 CATTTCTTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
8 17 0.71
9 7 0.29
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (8 bp):
TCTTCTTC
Found at i:12669274 original size:11 final size:11
Alignment explanation
Indices: 12669260--12669338 Score: 72
Period size: 11 Copynumber: 7.1 Consensus size: 11
12669250 CATTTTCTCA
12669260 TCTTCTTCTTC
1 TCTTCTTCTTC
*
12669271 TCTTCTTCTTT
1 TCTTCTTCTTC
12669282 TCTTCTTCTTC
1 TCTTCTTCTTC
*
12669293 TTCTCCATTTCTTC
1 -TCTTC--TTCTTC
*
12669307 TCTTATTCTTC
1 TCTTCTTCTTC
*
12669318 T-TT-TTTTTC
1 TCTTCTTCTTC
*
12669327 TCTTCCTCTTC
1 TCTTCTTCTTC
12669338 T
1 T
12669339 ACTACCCAGT
Statistics
Matches: 55, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
9 6 0.11
10 4 0.07
11 32 0.58
12 4 0.07
13 3 0.05
14 6 0.11
ACGTcount: A:0.03, C:0.32, G:0.00, T:0.66
Consensus pattern (11 bp):
TCTTCTTCTTC
Found at i:12669277 original size:14 final size:14
Alignment explanation
Indices: 12669254--12669338 Score: 68
Period size: 14 Copynumber: 6.1 Consensus size: 14
12669244 TCCTTCCATT
*
12669254 TTCTCATCTTCTTC
1 TTCTCTTCTTCTTC
12669268 TTCTCTTCTTCTT-
1 TTCTCTTCTTCTTC
12669281 TTCTTCTTCTTCTTC
1 TTC-TCTTCTTCTTC
*
12669296 TCCAT-TTCTTC-TC
1 TTC-TCTTCTTCTTC
* * *
12669309 TTATTCTTCTTTTTT
1 TT-CTCTTCTTCTTC
*
12669324 TTCTCTTCCTCTTC
1 TTCTCTTCTTCTTC
12669338 T
1 T
12669339 ACTACCCAGT
Statistics
Matches: 55, Mismatches: 11, Indels: 10
0.72 0.14 0.13
Matches are distributed among these distances:
13 7 0.13
14 42 0.76
15 6 0.11
ACGTcount: A:0.04, C:0.32, G:0.00, T:0.65
Consensus pattern (14 bp):
TTCTCTTCTTCTTC
Found at i:12669294 original size:25 final size:25
Alignment explanation
Indices: 12669254--12669319 Score: 80
Period size: 25 Copynumber: 2.6 Consensus size: 25
12669244 TCCTTCCATT
* *
12669254 TTCTCATCTTCTTCTTCT-CTTCTTC
1 TTCTCTTCTTCTTCTTCTCCAT-TTC
*
12669279 TTTTCTTCTTCTTCTTCTCCATTTC
1 TTCTCTTCTTCTTCTTCTCCATTTC
*
12669304 TTCTCTTATTCTTCTT
1 TTCTCTTCTTCTTCTT
12669320 TTTTTTCTCT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
25 33 0.94
26 2 0.06
ACGTcount: A:0.05, C:0.32, G:0.00, T:0.64
Consensus pattern (25 bp):
TTCTCTTCTTCTTCTTCTCCATTTC
Found at i:12682524 original size:24 final size:24
Alignment explanation
Indices: 12682479--12682536 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 24
12682469 GTTTAATTAC
** *
12682479 TTTTAATTTAATTTCATAAATTTA
1 TTTTAATTTAACATAATAAATTTA
* *
12682503 TTTTAATTTAACATAATGAATTTT
1 TTTTAATTTAACATAATAAATTTA
*
12682527 TTTTATTTTA
1 TTTTAATTTA
12682537 GTTTTTTAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.60
Consensus pattern (24 bp):
TTTTAATTTAACATAATAAATTTA
Found at i:12682868 original size:59 final size:59
Alignment explanation
Indices: 12682730--12682871 Score: 162
Period size: 59 Copynumber: 2.4 Consensus size: 59
12682720 ACAAGTTTAG
* *
12682730 GTATTAAATTGGACTAAAAAAAAGCTTAGATACCAAATTAAGAAAAAGTATCAAGTTCAA
1 GTATCAAATTGGAC-AAAAAAAAGCTTAGATACCAAATTAAGAAAAAGTATCAAATTCAA
* * * * * *
12682790 GTA-CTAATTTAGG-CAAAAAAAAGCTTAGGTGCCAAATTACGAAAAAGTGTCAAATTCAT
1 GTATC-AAATT-GGACAAAAAAAAGCTTAGATACCAAATTAAGAAAAAGTATCAAATTCAA
12682849 GTATCAAATTGGACCAAAAAAAA
1 GTATCAAATTGGA-CAAAAAAAA
12682872 TTAAGTACCA
Statistics
Matches: 68, Mismatches: 9, Indels: 10
0.78 0.10 0.11
Matches are distributed among these distances:
58 2 0.03
59 46 0.68
60 18 0.26
61 2 0.03
ACGTcount: A:0.49, C:0.12, G:0.15, T:0.24
Consensus pattern (59 bp):
GTATCAAATTGGACAAAAAAAAGCTTAGATACCAAATTAAGAAAAAGTATCAAATTCAA
Found at i:12702154 original size:22 final size:23
Alignment explanation
Indices: 12702115--12702161 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
12702105 CACGTTAGCT
12702115 AACAAATATATAAATAT-AAATA
1 AACAAATATATAAATATAAAATA
*
12702137 AACAAATAT-TCAAGTATAAAATA
1 AACAAATATAT-AAATATAAAATA
12702160 AA
1 AA
12702162 ATAAATTGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 1 0.05
22 14 0.64
23 7 0.32
ACGTcount: A:0.66, C:0.06, G:0.02, T:0.26
Consensus pattern (23 bp):
AACAAATATATAAATATAAAATA
Found at i:12709619 original size:17 final size:18
Alignment explanation
Indices: 12709591--12709624 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
12709581 TCATAAGCAA
12709591 TTAAACAATTCAATAACG
1 TTAAACAATTCAATAACG
12709609 TTAAA-AATTCAATAAC
1 TTAAACAATTCAATAAC
12709625 AAGCCGAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.53, C:0.15, G:0.03, T:0.29
Consensus pattern (18 bp):
TTAAACAATTCAATAACG
Found at i:12719792 original size:30 final size:30
Alignment explanation
Indices: 12719756--12719815 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
12719746 CACGGTCTAG
*
12719756 CACATGGCCATGTGTCCAGACCGTGTGGCT
1 CACATGGCCATGTGTCCAGACCATGTGGCT
* * * *
12719786 CACATGGTCGTGTGTCTAGCCCATGTGGCT
1 CACATGGCCATGTGTCCAGACCATGTGGCT
12719816 TCTTAAATAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.15, C:0.28, G:0.30, T:0.27
Consensus pattern (30 bp):
CACATGGCCATGTGTCCAGACCATGTGGCT
Found at i:12721742 original size:85 final size:85
Alignment explanation
Indices: 12721580--12721778 Score: 237
Period size: 85 Copynumber: 2.4 Consensus size: 85
12721570 GAATGTTGGA
* * * * *
12721580 AATAAATCCCGAAATAGAA-TTATTTGA--TTAAGTTTTCATTTGGAAACAAATCAAGATTAAAT
1 AATAAATCCCGAAACAGAATTTATTTAATTTTAAGTATTCATTTGGAAAAAAATCAAGATGAAAT
*
12721642 AAAATCTGTTAAACGAAAGT
66 AAAATCTGTTAAACGAAAGG
*
12721662 AATAAATCCCGAAACAGAATTTATTTAATTTTAA-TATTCGTTTGGAAAAAAATCAAAGATGAAA
1 AATAAATCCCGAAACAGAATTTATTTAATTTTAAGTATTCATTTGGAAAAAAATC-AAGATGAAA
* **
12721726 TAAAATCTGTTGAACGACGGG
65 TAAAATCTGTTAAACGAAAGG
* *
12721747 AATAAA-CCACGAAACAGATTTTATTCAATTTT
1 AATAAATCC-CGAAACAGAATTTATTTAATTTT
12721779 TATTTTTATT
Statistics
Matches: 100, Mismatches: 12, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
82 18 0.18
83 7 0.07
84 19 0.19
85 56 0.56
ACGTcount: A:0.45, C:0.11, G:0.13, T:0.31
Consensus pattern (85 bp):
AATAAATCCCGAAACAGAATTTATTTAATTTTAAGTATTCATTTGGAAAAAAATCAAGATGAAAT
AAAATCTGTTAAACGAAAGG
Found at i:12722408 original size:20 final size:20
Alignment explanation
Indices: 12722383--12722420 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
12722373 TTAAATGAGC
*
12722383 AATTAAATCAATTTGATTAA
1 AATTAAATCAAATTGATTAA
12722403 AATTAAATCAAATTGATT
1 AATTAAATCAAATTGATT
12722421 GGAATCAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.39
Consensus pattern (20 bp):
AATTAAATCAAATTGATTAA
Found at i:12722430 original size:20 final size:20
Alignment explanation
Indices: 12722387--12722436 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
12722377 ATGAGCAATT
* *
12722387 AAATCAATTTGATTAAAATT
1 AAATCAAATTGATTAAAATC
**
12722407 AAATCAAATTGATTGGAATC
1 AAATCAAATTGATTAAAATC
*
12722427 AAATAAAATT
1 AAATCAAATT
12722437 ATGATATATG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.52, C:0.06, G:0.08, T:0.34
Consensus pattern (20 bp):
AAATCAAATTGATTAAAATC
Found at i:12722646 original size:32 final size:34
Alignment explanation
Indices: 12722610--12722698 Score: 137
Period size: 32 Copynumber: 2.6 Consensus size: 34
12722600 TTCAAATTTA
12722610 AAATTAAAATAGAGTTATTAAATGAGAA-A-ATT
1 AAATTAAAATAGAGTTATTAAATGAGAATATATT
12722642 AAATTAAAATAGAGTTATTAAATGAGAATAGTTTATT
1 AAATTAAAATAGAGTTATTAAATGAGAATA---TATT
12722679 AAATTAAAATAGAGTTATTA
1 AAATTAAAATAGAGTTATTA
12722699 CTTAATTAGA
Statistics
Matches: 52, Mismatches: 0, Indels: 5
0.91 0.00 0.09
Matches are distributed among these distances:
32 28 0.54
33 1 0.02
37 23 0.44
ACGTcount: A:0.53, C:0.00, G:0.12, T:0.35
Consensus pattern (34 bp):
AAATTAAAATAGAGTTATTAAATGAGAATATATT
Found at i:12722703 original size:18 final size:19
Alignment explanation
Indices: 12722639--12722698 Score: 86
Period size: 19 Copynumber: 3.2 Consensus size: 19
12722629 AAATGAGAAA
12722639 ATTAAATTAAAATAGAGTT
1 ATTAAATTAAAATAGAGTT
* * *
12722658 ATTAAATGAGAATAG-TTT
1 ATTAAATTAAAATAGAGTT
12722676 ATTAAATTAAAATAGAGTT
1 ATTAAATTAAAATAGAGTT
12722695 ATTA
1 ATTA
12722699 CTTAATTAGA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
18 15 0.44
19 19 0.56
ACGTcount: A:0.50, C:0.00, G:0.12, T:0.38
Consensus pattern (19 bp):
ATTAAATTAAAATAGAGTT
Found at i:12723042 original size:27 final size:27
Alignment explanation
Indices: 12723007--12723058 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
12722997 CATTTTAGTC
*
12723007 CTTTTGCACCATTGGTGCCGCCAATCT
1 CTTTGGCACCATTGGTGCCGCCAATCT
*
12723034 CTTTGGCACCTTTGGTGCCGCCAAT
1 CTTTGGCACCATTGGTGCCGCCAAT
12723059 GTGATTCGCC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.13, C:0.33, G:0.21, T:0.33
Consensus pattern (27 bp):
CTTTGGCACCATTGGTGCCGCCAATCT
Found at i:12723133 original size:27 final size:27
Alignment explanation
Indices: 12723103--12723172 Score: 90
Period size: 27 Copynumber: 2.6 Consensus size: 27
12723093 TTTTTGTTTT
12723103 TTTAGTATATTTTGGTAAAT-AAAAAAA
1 TTTA-TATATTTTGGTAAATAAAAAAAA
12723130 TTTATA-ATATTTGGTAAATAAAAAAAA
1 TTTATATAT-TTTGGTAAATAAAAAAAA
*
12723157 GTTATAATATTTTGGT
1 TTTAT-ATATTTTGGT
12723173 TATTTTTTAT
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
25 2 0.05
26 12 0.32
27 15 0.39
28 7 0.18
29 2 0.05
ACGTcount: A:0.46, C:0.00, G:0.11, T:0.43
Consensus pattern (27 bp):
TTTATATATTTTGGTAAATAAAAAAAA
Found at i:12723148 original size:26 final size:27
Alignment explanation
Indices: 12723113--12723168 Score: 96
Period size: 27 Copynumber: 2.1 Consensus size: 27
12723103 TTTAGTATAT
*
12723113 TTTGGTAAAT-AAAAAAATTTATAATA
1 TTTGGTAAATAAAAAAAAGTTATAATA
12723139 TTTGGTAAATAAAAAAAAGTTATAATA
1 TTTGGTAAATAAAAAAAAGTTATAATA
12723166 TTT
1 TTT
12723169 TGGTTATTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
26 10 0.36
27 18 0.64
ACGTcount: A:0.52, C:0.00, G:0.09, T:0.39
Consensus pattern (27 bp):
TTTGGTAAATAAAAAAAAGTTATAATA
Found at i:12726070 original size:29 final size:29
Alignment explanation
Indices: 12726037--12726092 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
12726027 ACTCACTATA
* *
12726037 TTGTATTTAAATAAGTCCTTAACTTATTT
1 TTGTAGTTAAATAAGCCCTTAACTTATTT
12726066 TTGTAGTTAAATAAGCCCTTAACTTAT
1 TTGTAGTTAAATAAGCCCTTAACTTAT
12726093 GGTTTTTACT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.32, C:0.12, G:0.09, T:0.46
Consensus pattern (29 bp):
TTGTAGTTAAATAAGCCCTTAACTTATTT
Found at i:12727554 original size:5 final size:6
Alignment explanation
Indices: 12727537--12727561 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
12727527 AAAAACGAAT
12727537 ATAAAA ATAAAA ATAAAA ATAAAA A
1 ATAAAA ATAAAA ATAAAA ATAAAA A
12727562 CTTTTTCACC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
ATAAAA
Found at i:12728374 original size:19 final size:20
Alignment explanation
Indices: 12728347--12728384 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
12728337 TAAATACATC
12728347 TATTCTATTT-TATCACATTA
1 TATTCTATTTAT-TCACATTA
12728367 TATT-TATTTATTCACATT
1 TATTCTATTTATTCACATT
12728385 CTTTTATATG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.29, C:0.13, G:0.00, T:0.58
Consensus pattern (20 bp):
TATTCTATTTATTCACATTA
Found at i:12728676 original size:19 final size:20
Alignment explanation
Indices: 12728649--12728686 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
12728639 TAAATACATC
12728649 TATTCTATTT-TATCACATTA
1 TATTCTATTTAT-TCACATTA
12728669 TATT-TATTTATTCACATT
1 TATTCTATTTATTCACATT
12728687 CTTTTATATG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.29, C:0.13, G:0.00, T:0.58
Consensus pattern (20 bp):
TATTCTATTTATTCACATTA
Found at i:12728686 original size:302 final size:303
Alignment explanation
Indices: 12728131--12728735 Score: 1203
Period size: 302 Copynumber: 2.0 Consensus size: 303
12728121 ATTTGCCCCA
12728131 AATTTCTGTTTTAAAGTTCAATTTAGCCATTTTATTTGTTATTTTTGCTATTTTATTATCAAATT
1 AATTTCTGTTTTAAAGTTCAATTTAGCCATTTTATTTGTTATTTTTGCTATTTTATTATCAAATT
12728196 AATTAATTTAATCTTATTATTACTATTATTATTTTCCTTTTTTTATTCATTTACTTGTTATTATT
66 AATTAATTTAATCTTATTATTACTATTATTATTTTCCTTTTTTTATTCATTTACTTGTTATTATT
12728261 ATCATATTATTAAATTAATTAGTTTTGCATTATTATATCTATTATATTTGTTTTCATATTTATTT
131 ATCATATTATTAAATTAATTAGTTTTGCATTATTATATCTATTATATTTGTTTTCATATTTATTT
12728326 ACCTAATATTTTAAATACATCTATTCTATTTTATCACATTATATTTATTTATTCACATTCTTTTA
196 ACCTAATATTTTAAATACATCTATTCTATTTTATCACATTATATTTATTTATTCACATTCTTTTA
12728391 TATGATTACAAACCTTAGATTATTCATTATTTTTTATTTTTAT
261 TATGATTACAAACCTTAGATTATTCATTATTTTTTATTTTTAT
12728434 AATTTCTG-TTTAAAGTTCAATTTAGCCATTTTATTTGTTATTTTTGCTATTTTATTATCAAATT
1 AATTTCTGTTTTAAAGTTCAATTTAGCCATTTTATTTGTTATTTTTGCTATTTTATTATCAAATT
12728498 AATTAATTTAATCTTATTATTACTATTATTATTTTCCTTTTTTTATTCATTTACTTGTTATTATT
66 AATTAATTTAATCTTATTATTACTATTATTATTTTCCTTTTTTTATTCATTTACTTGTTATTATT
12728563 ATCATATTATTAAATTAATTAGTTTTGCATTATTATATCTATTATATTTGTTTTCATATTTATTT
131 ATCATATTATTAAATTAATTAGTTTTGCATTATTATATCTATTATATTTGTTTTCATATTTATTT
12728628 ACCTAATATTTTAAATACATCTATTCTATTTTATCACATTATATTTATTTATTCACATTCTTTTA
196 ACCTAATATTTTAAATACATCTATTCTATTTTATCACATTATATTTATTTATTCACATTCTTTTA
12728693 TATGATTACAAACCTTAGATTATTCATTATTTTTTATTTTTAT
261 TATGATTACAAACCTTAGATTATTCATTATTTTTTATTTTTAT
12728736 TATCATTCAT
Statistics
Matches: 302, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
302 294 0.97
303 8 0.03
ACGTcount: A:0.29, C:0.10, G:0.04, T:0.57
Consensus pattern (303 bp):
AATTTCTGTTTTAAAGTTCAATTTAGCCATTTTATTTGTTATTTTTGCTATTTTATTATCAAATT
AATTAATTTAATCTTATTATTACTATTATTATTTTCCTTTTTTTATTCATTTACTTGTTATTATT
ATCATATTATTAAATTAATTAGTTTTGCATTATTATATCTATTATATTTGTTTTCATATTTATTT
ACCTAATATTTTAAATACATCTATTCTATTTTATCACATTATATTTATTTATTCACATTCTTTTA
TATGATTACAAACCTTAGATTATTCATTATTTTTTATTTTTAT
Found at i:12733427 original size:50 final size:50
Alignment explanation
Indices: 12733311--12733554 Score: 249
Period size: 50 Copynumber: 4.9 Consensus size: 50
12733301 GAATATAACA
* * * * ** * * * *
12733311 TGCCAAAGCTATGTCCCAAACATAGTCTTACATGGGATGTTTCTTGTA-C
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGAACTCTCATCTAGG
* * * * * *
12733360 TGCCAATGCCATATCCCAGATATGGTCTTACATGAGAATTCTCATATAGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGAACTCTCATCTAGG
* * * *
12733410 TGCCCATGCCATGTCCCAGACATGGTCTTAC-GGGGAACCTCTCATCTTGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGAA-CTCTCATCTAGG
* * *
12733460 TGCCAACGCCATGTCCCATACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGAACTCTCATCTAGG
*
12733510 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGAACTCTCAT
12733555 AATCTTAATT
Statistics
Matches: 164, Mismatches: 28, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
49 40 0.24
50 120 0.73
51 4 0.02
ACGTcount: A:0.23, C:0.29, G:0.20, T:0.28
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGAACTCTCATCTAGG
Found at i:12733583 original size:56 final size:50
Alignment explanation
Indices: 12733360--12733554 Score: 257
Period size: 50 Copynumber: 3.9 Consensus size: 50
12733350 TTTCTTGTAC
* * * * ** * *
12733360 TGCCAATGCCATATCCCAGATATGGTCTTACATGAGAATTCTCATATAGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTTGG
* * *
12733410 TGCCCATGCCATGTCCCAGACATGGTCTTAC-GGGGAACCTCTCATCTTGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGG-ACCTCTCATCTTGG
* *
12733460 TGCCAACGCCATGTCCCATACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTTGG
12733510 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT
12733555 AATCTTAATT
Statistics
Matches: 128, Mismatches: 15, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
49 2 0.02
50 123 0.96
51 3 0.02
ACGTcount: A:0.23, C:0.30, G:0.21, T:0.27
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTTGG
Found at i:12733589 original size:56 final size:50
Alignment explanation
Indices: 12733310--12733607 Score: 217
Period size: 50 Copynumber: 5.9 Consensus size: 50
12733300 TGAATATAAC
* * * * * *
12733310 ATGCCAAAGCTATGTCCCAAACATAGTCTTACATGGGA--TGT-TTCTTG
1 ATGCCAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATCTCG
* * * * * ** * *
12733357 TACTGCCAATGCCATATCCCAGATATGGTCTTACATGAGAATTCTCATATAG
1 -A-TGCCAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATCTCG
* * * * * *
12733409 GTGCCCATGCCATGTCCCAGACATGGTCTTAC-GGGGAACCTCTCATCTTG
1 ATGCCAACGCCATGTCCCAAACATGGTCTTACATGGG-ACCTCTCATCTCG
* *
12733459 GTGCCAACGCCATGTCCCATACATGGTCTTACATGGGACCTCTCATCTCG
1 ATGCCAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATCTCG
* * **
12733509 GTGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAATCTTAATT
1 ATGCCAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCTC---ATC-T--CG
* * *
12733565 ATGCCAATGCCATGTCCCAAACATGGTCTTACATTGGATCTCT
1 ATGCCAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCT
12733608 TTACCCAAAT
Statistics
Matches: 204, Mismatches: 34, Indels: 16
0.80 0.13 0.06
Matches are distributed among these distances:
48 1 0.00
49 32 0.16
50 121 0.59
51 5 0.02
52 3 0.01
53 3 0.01
54 1 0.00
56 38 0.19
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.29
Consensus pattern (50 bp):
ATGCCAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATCTCG
Found at i:12741097 original size:44 final size:44
Alignment explanation
Indices: 12741048--12741593 Score: 471
Period size: 44 Copynumber: 12.4 Consensus size: 44
12741038 ATCATATTCT
* * * * *
12741048 TGAAGTTGCAGCGGAGTATATTGAAGTTGTAAATCTTATCTTCC
1 TGAAGTTGCAGTGGAGCAGATTGAAGTTATAAATCTTATCTCCC
* ** *
12741092 TGAAGTTGCAATGGAGCAGATTGAAGACATAAATCTTATCTCCT
1 TGAAGTTGCAGTGGAGCAGATTGAAGTTATAAATCTTATCTCCC
* * * * * *
12741136 TAAAATTACAATGGAGCAGATTTAAGTTATAGATCTTATCTCCC
1 TGAAGTTGCAGTGGAGCAGATTGAAGTTATAAATCTTATCTCCC
* * * ** * *
12741180 TGAGGTCGTAGTGGAGCAGATTGAAGACACAAATCTTATCTCCT
1 TGAAGTTGCAGTGGAGCAGATTGAAGTTATAAATCTTATCTCCC
* * * *
12741224 TGAAGTTGCAGCGGAGCAGATTGAAGTTACAAGTATTATCTCCC
1 TGAAGTTGCAGTGGAGCAGATTGAAGTTATAAATCTTATCTCCC
* * *
12741268 TGAAGTTGCAGTGGAGCAGACTGAAAATTACAAATCTTATCTCCC
1 TGAAGTTGCAGTGGAGCAGATTG-AAGTTATAAATCTTATCTCCC
* * *
12741313 TGAAGTTACATTGGAGCAGATTGAAGTTATAGATCTTATCTCCC
1 TGAAGTTGCAGTGGAGCAGATTGAAGTTATAAATCTTATCTCCC
* * ** * * *
12741357 TGAGGTCGCAGTGGAGCAGATTGAAGACACAAACCTCATCTCCC
1 TGAAGTTGCAGTGGAGCAGATTGAAGTTATAAATCTTATCTCCC
* * * * *
12741401 TGAAGTTACAGTGAAGCAGATTGAAATTACAAGTCTTATCTCCC
1 TGAAGTTGCAGTGGAGCAGATTGAAGTTATAAATCTTATCTCCC
* * * * * *
12741445 TAAAGTTGCAATGGAGCAGACTGAAAGTTACAAATATTGTCTCCC
1 TGAAGTTGCAGTGGAGCAGATTG-AAGTTATAAATCTTATCTCCC
* * * * * *
12741490 TAAAGTTGTAGTGGAGCAGATTGAAGCTATAAGTCTTGTCTCCT
1 TGAAGTTGCAGTGGAGCAGATTGAAGTTATAAATCTTATCTCCC
* * *** * * * **
12741534 TGAAATTACAGTGGAATGGATCGAAGCTACACGTCTTATCTCCC
1 TGAAGTTGCAGTGGAGCAGATTGAAGTTATAAATCTTATCTCCC
*
12741578 TAAAGTTGCAGTGGAG
1 TGAAGTTGCAGTGGAG
12741594 TGGGTCGAAG
Statistics
Matches: 397, Mismatches: 103, Indels: 4
0.79 0.20 0.01
Matches are distributed among these distances:
44 322 0.81
45 75 0.19
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.29
Consensus pattern (44 bp):
TGAAGTTGCAGTGGAGCAGATTGAAGTTATAAATCTTATCTCCC
Found at i:12741351 original size:177 final size:177
Alignment explanation
Indices: 12741046--12741520 Score: 646
Period size: 177 Copynumber: 2.7 Consensus size: 177
12741036 ATATCATATT
* * ** * *
12741046 CTTGAAGTTGCAGCGGAGTATATTGAAGTTGTAAATCTTATCTTCCTGAAGTTGCAATGGAGCAG
1 CTTGAAGTTGCAGCGGAGCAGATTGAAGTTACAAGTCTTATCTCCCTGAAGTTGCAATGGAGCAG
* * * * * * *
12741111 ATTGAAGA-CATAAATCTTATCTCCTTAAAATTACAATGGAGCAGATTTAAGTTATAGATCTTAT
66 ACTGAAAATTACAAATCTTATCTCCCTAAAGTTACAATGGAGCAGATTGAAGTTATAGATCTTAT
* * *
12741175 CTCCCTGAGGTCGTAGTGGAGCAGATTGAAGACACAAATCTTATCTC
131 CTCCCTGAGGTCGCAGTGGAGCAGATTGAAGACACAAACCTCATCTC
* *
12741222 CTTGAAGTTGCAGCGGAGCAGATTGAAGTTACAAGTATTATCTCCCTGAAGTTGCAGTGGAGCAG
1 CTTGAAGTTGCAGCGGAGCAGATTGAAGTTACAAGTCTTATCTCCCTGAAGTTGCAATGGAGCAG
* *
12741287 ACTGAAAATTACAAATCTTATCTCCCTGAAGTTACATTGGAGCAGATTGAAGTTATAGATCTTAT
66 ACTGAAAATTACAAATCTTATCTCCCTAAAGTTACAATGGAGCAGATTGAAGTTATAGATCTTAT
12741352 CTCCCTGAGGTCGCAGTGGAGCAGATTGAAGACACAAACCTCATCTC
131 CTCCCTGAGGTCGCAGTGGAGCAGATTGAAGACACAAACCTCATCTC
* * * * * *
12741399 CCTGAAGTTACAGTGAAGCAGATTGAAATTACAAGTCTTATCTCCCTAAAGTTGCAATGGAGCAG
1 CTTGAAGTTGCAGCGGAGCAGATTGAAGTTACAAGTCTTATCTCCCTGAAGTTGCAATGGAGCAG
* * * ** * *
12741464 ACTGAAAGTTACAAATATTGTCTCCCTAAAGTTGTAGTGGAGCAGATTGAAGCTATA
66 ACTGAAAATTACAAATCTTATCTCCCTAAAGTTACAATGGAGCAGATTGAAGTTATA
12741521 AGTCTTGTCT
Statistics
Matches: 262, Mismatches: 36, Indels: 1
0.88 0.12 0.00
Matches are distributed among these distances:
176 63 0.24
177 199 0.76
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.29
Consensus pattern (177 bp):
CTTGAAGTTGCAGCGGAGCAGATTGAAGTTACAAGTCTTATCTCCCTGAAGTTGCAATGGAGCAG
ACTGAAAATTACAAATCTTATCTCCCTAAAGTTACAATGGAGCAGATTGAAGTTATAGATCTTAT
CTCCCTGAGGTCGCAGTGGAGCAGATTGAAGACACAAACCTCATCTC
Found at i:12741577 original size:177 final size:177
Alignment explanation
Indices: 12741083--12741590 Score: 536
Period size: 177 Copynumber: 2.9 Consensus size: 177
12741073 GTTGTAAATC
* * * * * * * * * *
12741083 TTATCTTCCTGAAGTTGCAATGGAGCAGATTGAAGA-CATAAATCTTATCTCCTTAAAATTACAA
1 TTATCTCCCTAAAGTTGCAATGGAGCAGACTGAAAATTACAAATATTATCTCCCTAAAGTTACAG
* * ** ** * *
12741147 TGGAGCAGATTTAAGTTATAGATCTTATCTCCCTGAGGTCGTAGTGGAGCAGATTGAAGACACAA
66 TGGAGCAGATTGAAGCTATAGATCTTATCTCCCTGAAATCACAGTGGAACAGATCGAAGACACAA
* * * *
12741212 ATCTTATCTCCTTGAAGTTGCAGCGGAGCAGATTGAAGTTACAAGTA
131 ATCTTATCTCCCTGAAGTTGCAGTGAAGCAGATTGAAATTACAAGTA
* * * * *
12741259 TTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAAATTACAAATCTTATCTCCCTGAAGTTACAT
1 TTATCTCCCTAAAGTTGCAATGGAGCAGACTGAAAATTACAAATATTATCTCCCTAAAGTTACAG
* ** * * *
12741324 TGGAGCAGATTGAAGTTATAGATCTTATCTCCCTGAGGTCGCAGTGGAGCAGATTGAAGACACAA
66 TGGAGCAGATTGAAGCTATAGATCTTATCTCCCTGAAATCACAGTGGAACAGATCGAAGACACAA
* * * *
12741389 ACCTCATCTCCCTGAAGTTACAGTGAAGCAGATTGAAATTACAAGTC
131 ATCTTATCTCCCTGAAGTTGCAGTGAAGCAGATTGAAATTACAAGTA
* * **
12741436 TTATCTCCCTAAAGTTGCAATGGAGCAGACTGAAAGTTACAAATATTGTCTCCCTAAAGTTGTAG
1 TTATCTCCCTAAAGTTGCAATGGAGCAGACTGAAAATTACAAATATTATCTCCCTAAAGTTACAG
* * * **
12741501 TGGAGCAGATTGAAGCTATA-AGTCTTGTCTCCTTGAAATTACAGTGGAATGGATCGAAG-CTAC
66 TGGAGCAGATTGAAGCTATAGA-TCTTATCTCCCTGAAATCACAGTGGAACAGATCGAAGAC-AC
** *
12741564 ACGTCTTATCTCCCTAAAGTTGCAGTG
129 AAATCTTATCTCCCTGAAGTTGCAGTG
12741591 GAGTGGGTCG
Statistics
Matches: 283, Mismatches: 46, Indels: 5
0.85 0.14 0.01
Matches are distributed among these distances:
176 34 0.12
177 249 0.88
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (177 bp):
TTATCTCCCTAAAGTTGCAATGGAGCAGACTGAAAATTACAAATATTATCTCCCTAAAGTTACAG
TGGAGCAGATTGAAGCTATAGATCTTATCTCCCTGAAATCACAGTGGAACAGATCGAAGACACAA
ATCTTATCTCCCTGAAGTTGCAGTGAAGCAGATTGAAATTACAAGTA
Found at i:12741829 original size:16 final size:18
Alignment explanation
Indices: 12741798--12741833 Score: 58
Period size: 16 Copynumber: 2.1 Consensus size: 18
12741788 GCCCAAACAG
12741798 AAACCTAAAGACAAAAAA
1 AAACCTAAAGACAAAAAA
12741816 AAACC-AAA-ACAAAAAA
1 AAACCTAAAGACAAAAAA
12741832 AA
1 AA
12741834 TTATAACAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 10 0.56
17 3 0.17
18 5 0.28
ACGTcount: A:0.78, C:0.17, G:0.03, T:0.03
Consensus pattern (18 bp):
AAACCTAAAGACAAAAAA
Found at i:12743009 original size:3 final size:3
Alignment explanation
Indices: 12742982--12743046 Score: 51
Period size: 3 Copynumber: 21.0 Consensus size: 3
12742972 TAAACCTTAG
* * * *
12742982 ATT ATT CATT ATTT ATT ATT TTT ATT ATC ATT CA-T ATT ATT CTC ATT
1 ATT ATT -ATT A-TT ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT ATT
*
12743029 ATT ATT AGT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT
12743047 TTTAAAACCA
Statistics
Matches: 48, Mismatches: 10, Indels: 8
0.73 0.15 0.12
Matches are distributed among these distances:
2 1 0.02
3 40 0.83
4 7 0.15
ACGTcount: A:0.29, C:0.08, G:0.02, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:12746537 original size:19 final size:18
Alignment explanation
Indices: 12746495--12746537 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
12746485 AATTTTTTAT
12746495 ATAAAAATATTTAAAATA
1 ATAAAAATATTTAAAATA
*
12746513 ACAAAAACTATTTTAAAA-A
1 ATAAAAA-TA-TTTAAAATA
12746532 ATAAAA
1 ATAAAA
12746538 TAAAACTGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 6 0.29
19 8 0.38
20 7 0.33
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.28
Consensus pattern (18 bp):
ATAAAAATATTTAAAATA
Found at i:12755856 original size:54 final size:53
Alignment explanation
Indices: 12755761--12755863 Score: 127
Period size: 54 Copynumber: 1.9 Consensus size: 53
12755751 AGTGATTATC
* * * *
12755761 TTAATATTAAATTTAATTTAATCTTTATCTACAATTCTATTATTTTAATAAGAT
1 TTAAGATTAAATTTAATTTAATATTTATCTACAA-TATATTATATTAATAAGAT
*
12755815 TTAAGATTAAATTTAATTTAATATTTATCTTGATAA-ATATTATATTAAT
1 TTAAGATTAAATTTAATTTAATATTTATC-T-ACAATATATTATATTAAT
12755864 TTAATATTAA
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
54 38 0.90
55 1 0.02
56 3 0.07
ACGTcount: A:0.41, C:0.05, G:0.03, T:0.51
Consensus pattern (53 bp):
TTAAGATTAAATTTAATTTAATATTTATCTACAATATATTATATTAATAAGAT
Found at i:12760826 original size:9 final size:9
Alignment explanation
Indices: 12760814--12760838 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
12760804 TAGTAAAAAG
12760814 TTGAAAATT
1 TTGAAAATT
12760823 TTGAAAATT
1 TTGAAAATT
12760832 TTGAAAA
1 TTGAAAA
12760839 CAGGGGTCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.12, T:0.40
Consensus pattern (9 bp):
TTGAAAATT
Found at i:12762241 original size:50 final size:50
Alignment explanation
Indices: 12762136--12762268 Score: 167
Period size: 50 Copynumber: 2.7 Consensus size: 50
12762126 TTACTGAGGT
* * * *
12762136 TATGAGAGGTCCCACGTAAGACCATGTCTGGGACATGGCGTTGGTACCGA
1 TATGAGAGGTCCCACGTAAGACCATGTCTGGGACATGGCATGGGCACCAA
* *
12762186 GATGAGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCAA
1 TATGAGAGGTCCCACGTAAGACCATGTCTGGGACATGGCATGGGCACCAA
** * * *
12762236 TATGAGAACTCTCATGTAAGACCATATCTGGGA
1 TATGAGAGGTCCCACGTAAGACCATGTCTGGGA
12762269 TATGACATTT
Statistics
Matches: 70, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
50 70 1.00
ACGTcount: A:0.27, C:0.23, G:0.29, T:0.21
Consensus pattern (50 bp):
TATGAGAGGTCCCACGTAAGACCATGTCTGGGACATGGCATGGGCACCAA
Found at i:12763554 original size:121 final size:122
Alignment explanation
Indices: 12763405--12763647 Score: 479
Period size: 121 Copynumber: 2.0 Consensus size: 122
12763395 AAAATTTTAT
12763405 GGTAAGAAGATACGTGAGTCTAGTTTTAGGGAAAATTTATGGATCTAAATTTTGAGTTTTGTAAC
1 GGTAAGAAGATACGTGAGTCTAGTTTTAGGGAAAATTTATGGATCTAAATTTTGAGTTTTGTAAC
12763470 TCGAGTTATAATTAAATTAGTGACTATCACACAAGTGGACAGTTTTATTGTGAATAG
66 TCGAGTTATAATTAAATTAGTGACTATCACACAAGTGGACAGTTTTATTGTGAATAG
12763527 GGTAAGAAGA-ACGTGAGTCTAGTTTTAGGGAAAATTTATGGATCTAAATTTTGAGTTTTGTAAC
1 GGTAAGAAGATACGTGAGTCTAGTTTTAGGGAAAATTTATGGATCTAAATTTTGAGTTTTGTAAC
12763591 TCGAGTTATAATTAAATTAGTGACTATCACACAAGTGGACAGTTTTATTGTGAATAG
66 TCGAGTTATAATTAAATTAGTGACTATCACACAAGTGGACAGTTTTATTGTGAATAG
12763648 TGAAATAAAT
Statistics
Matches: 121, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
121 111 0.92
122 10 0.08
ACGTcount: A:0.34, C:0.08, G:0.22, T:0.36
Consensus pattern (122 bp):
GGTAAGAAGATACGTGAGTCTAGTTTTAGGGAAAATTTATGGATCTAAATTTTGAGTTTTGTAAC
TCGAGTTATAATTAAATTAGTGACTATCACACAAGTGGACAGTTTTATTGTGAATAG
Found at i:12769224 original size:22 final size:22
Alignment explanation
Indices: 12769207--12769251 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
12769197 CATGAATGAT
12769207 TTTAATTGGAAGCATGAACAAC
1 TTTAATTGGAAGCATGAACAAC
12769229 TTTAATTGGAAGCATGAACAAC
1 TTTAATTGGAAGCATGAACAAC
12769251 T
1 T
12769252 GAGGCACAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.40, C:0.13, G:0.18, T:0.29
Consensus pattern (22 bp):
TTTAATTGGAAGCATGAACAAC
Found at i:12785025 original size:23 final size:22
Alignment explanation
Indices: 12784968--12785017 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 22
12784958 TTCTCTCTTA
12784968 TAGGGTTAAGGTTTTTAATTTT
1 TAGGGTTAAGGTTTTTAATTTT
* *
12784990 TAAGGTTATGGTTTTTAATATTT
1 TAGGGTTAAGGTTTTTAAT-TTT
12785013 TAGGG
1 TAGGG
12785018 GTAGGGTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
22 17 0.71
23 7 0.29
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (22 bp):
TAGGGTTAAGGTTTTTAATTTT
Found at i:12791328 original size:20 final size:20
Alignment explanation
Indices: 12791303--12791343 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
12791293 TTACGTATCC
12791303 TCCACTCTTGCTACTGGTGG
1 TCCACTCTTGCTACTGGTGG
12791323 TCCACTCTTGCTACTGGTGG
1 TCCACTCTTGCTACTGGTGG
12791343 T
1 T
12791344 TGAGCCGATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.10, C:0.29, G:0.24, T:0.37
Consensus pattern (20 bp):
TCCACTCTTGCTACTGGTGG
Found at i:12797580 original size:16 final size:16
Alignment explanation
Indices: 12797559--12797606 Score: 73
Period size: 16 Copynumber: 3.1 Consensus size: 16
12797549 AAGATTAGAG
12797559 AAAGAAGTGAAGATGA
1 AAAGAAGTGAAGATGA
12797575 AAAGAAGTGAAGATGA
1 AAAGAAGTGAAGATGA
*
12797591 AAGGAA--GAAGATGA
1 AAAGAAGTGAAGATGA
12797605 AA
1 AA
12797607 TAGGGGATAA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
14 10 0.32
16 21 0.68
ACGTcount: A:0.58, C:0.00, G:0.31, T:0.10
Consensus pattern (16 bp):
AAAGAAGTGAAGATGA
Found at i:12804673 original size:51 final size:50
Alignment explanation
Indices: 12804554--12804939 Score: 341
Period size: 51 Copynumber: 7.6 Consensus size: 50
12804544 TCGATACATG
* * *
12804554 TAGTAGCATTCACATAGTACTACACACGTGATCAAG-TTTTACGGTTCACA
1 TAGTAGCCTTCACATAGTACTACACACGTGACCAAGCTTTT-CGGTACACA
*
12804604 TAGTAGCCTTCACATAGTACTACACACGTGGCCAAAGCTTTTCGGTACACA
1 TAGTAGCCTTCACATAGTACTACACACGTGACC-AAGCTTTTCGGTACACA
* * * * * **
12804655 TAGTAGCCTTCACTTAGTACTACACATGTGACC-ATCATTTATCGATTCATG
1 TAGTAGCCTTCACATAGTACTACACACGTGACCAAGC-TTT-TCGGTACACA
* *
12804706 TAGTAGCCTTCACACAGTACTACACACGTGACCAAAACTTTTCGGTACACA
1 TAGTAGCCTTCACATAGTACTACACACGTGACC-AAGCTTTTCGGTACACA
* * * * * * * *
12804757 TAGTAGCCTTTACTTAGTACAACACATGTGACC-ATCATTTATCGATTCACG
1 TAGTAGCCTTCACATAGTACTACACACGTGACCAAGC-TTT-TCGGTACACA
* * *
12804808 TAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTCTT-AGTACACG
1 TAGTAGCCTTCACATAGTACTACACACGTGACC-AAGCTT-TTCGGTACACA
* * ** * * * *
12804859 TTGTAGCCTTCACTTAGTACTACACATTTGACC-ATCATTTATCGATTCACG
1 TAGTAGCCTTCACATAGTACTACACACGTGACCAAGC-TTT-TCGGTACACA
*
12804910 TAGTAGCCTTCACACAGTACTACACACGTG
1 TAGTAGCCTTCACATAGTACTACACACGTG
12804940 TTCATCGATA
Statistics
Matches: 270, Mismatches: 52, Indels: 27
0.77 0.15 0.08
Matches are distributed among these distances:
49 7 0.03
50 39 0.14
51 209 0.77
52 10 0.04
53 5 0.02
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.29
Consensus pattern (50 bp):
TAGTAGCCTTCACATAGTACTACACACGTGACCAAGCTTTTCGGTACACA
Found at i:12804730 original size:102 final size:102
Alignment explanation
Indices: 12804554--12804939 Score: 578
Period size: 102 Copynumber: 3.8 Consensus size: 102
12804544 TCGATACATG
* * * * *** * *
12804554 TAGTAGCATTCACATAGTACTACACACGTGATCAAGTTTTA-CGGTTCACATAGTAGCCTTCACA
1 TAGTAGCCTTCACTTAGTACTACACATGTGACCATCATTTATCGATTCACGTAGTAGCCTTCACA
* *
12804618 TAGTACTACACACGTGGCCAAAGCTTTTCGGTACACA
66 CAGTACTACACACGTGACCAAAGCTTTTCGGTACACA
*
12804655 TAGTAGCCTTCACTTAGTACTACACATGTGACCATCATTTATCGATTCATGTAGTAGCCTTCACA
1 TAGTAGCCTTCACTTAGTACTACACATGTGACCATCATTTATCGATTCACGTAGTAGCCTTCACA
*
12804720 CAGTACTACACACGTGACCAAAACTTTTCGGTACACA
66 CAGTACTACACACGTGACCAAAGCTTTTCGGTACACA
* *
12804757 TAGTAGCCTTTACTTAGTACAACACATGTGACCATCATTTATCGATTCACGTAGTAGCCTTCACA
1 TAGTAGCCTTCACTTAGTACTACACATGTGACCATCATTTATCGATTCACGTAGTAGCCTTCACA
* *
12804822 CAGTACTACACACGTGACCAAAGCTTCTT-AGTACACG
66 CAGTACTACACACGTGACCAAAGCTT-TTCGGTACACA
* *
12804859 TTGTAGCCTTCACTTAGTACTACACATTTGACCATCATTTATCGATTCACGTAGTAGCCTTCACA
1 TAGTAGCCTTCACTTAGTACTACACATGTGACCATCATTTATCGATTCACGTAGTAGCCTTCACA
12804924 CAGTACTACACACGTG
66 CAGTACTACACACGTG
12804940 TTCATCGATA
Statistics
Matches: 260, Mismatches: 23, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
101 34 0.13
102 224 0.86
103 2 0.01
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.29
Consensus pattern (102 bp):
TAGTAGCCTTCACTTAGTACTACACATGTGACCATCATTTATCGATTCACGTAGTAGCCTTCACA
CAGTACTACACACGTGACCAAAGCTTTTCGGTACACA
Found at i:12806127 original size:11 final size:12
Alignment explanation
Indices: 12806099--12806131 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
12806089 GCCCAAACGT
12806099 CGAAATTTTCGAA
1 CGAAATTTTC-AA
12806112 CGAAATTTTC-A
1 CGAAATTTTCAA
12806123 CGAAATTTT
1 CGAAATTTT
12806132 TCTGTGAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 10 0.50
13 10 0.50
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.36
Consensus pattern (12 bp):
CGAAATTTTCAA
Found at i:12813332 original size:551 final size:551
Alignment explanation
Indices: 12812292--12813387 Score: 1836
Period size: 551 Copynumber: 2.0 Consensus size: 551
12812282 AATTTTTTAA
*
12812292 ATTATAATTTAACATAACAAATCATGCAGAAGAGAAAAACCCCAAAACATTATCCAAAGTTCACA
1 ATTATAATTTAACATAACAAATCATGCAGAAAAGAAAAACCCCAAAACATTATCCAAAGTTCACA
*** *
12812357 AATCAAAAATTTGAACCAAAGTCCCAAAAATAAAGTCCATAAAGCATGAACACAAACTAAAATGT
66 AATCAAAAATCCAAACCAAAGTCCCAAAAATAAAGTCCATAAAGCATGAACAAAAACTAAAATGT
*
12812422 CCAATACCACTACTTGTAAGGTTTTCCAAAAAATAACCAAGAGTACCTTCGTAGCCAAGCCCATC
131 CCAATACCACTACTTGCAAGGTTTTCCAAAAAATAACCAAGAGTACCTTCGTAGCCAAGCCCATC
* * * * *
12812487 CTAGTCTCGATTATCTGAAATCAAAGTTTAAGGGCGTGAGCTTAAAAATGCTCAATGTAGGTCTT
196 CTAGTCCCGATTATCTAAAATCAAAGTTTAAGGGCGTAAGATTAAAAAGGCTCAATGTAGGTCTT
* *
12812552 AAATAACAATTATTTCACAAAAATAATTCATTATAACATCATATTAATCAGCCCATAACATATAT
261 AAATAACAATTAGTTCACAAAAACAATTCATTATAACATCATATTAATCAGCCCATAACATATAT
*
12812617 AAATTACTCAATTATAAATCAAATATGGCAGATTGTGTAATGACGTAATTAATACAACATTTTTA
326 AAATTACTCAATTATAAATCAAATATGGCAAATTGTGTAATGACGTAATTAATACAACATTTTTA
** * *
12812682 GAATACAATACAGTTATTAGAACTTAAATCCTACCTAACTCCGCTACACGCCACATAGAGTTCCC
391 GAATACAATACAAATATTAGAACTTAAATCCTACCCAACTCCGCTACACGCCACACAGAGTTCCC
* * *
12812747 TATAACTCATCCAACCAATAACACACCAAAATGTGATCTAACCACCAGAAATTGTAGATTTACTG
456 CATAACTCATCCAACCAATAACACACCAAAATGTGATCCAACCACCAGAAATTATAGATTTACTG
*
12812812 CCAAATACATAATATTGT-GACAAGAAAAAC
521 CCAAATACATAATATTATGGACAAGAAAAAC
* *
12812842 ATTATAATTTAACATAACAAATCATGCAGAAAAGAAAAACCCCAAAACATTATCCAAATTTCGCA
1 ATTATAATTTAACATAACAAATCATGCAGAAAAGAAAAACCCCAAAACATTATCCAAAGTTCACA
* *
12812907 AATCAAAAATCCAAACCAAAGTCCCAAAATTAAAGTCCATAAAGCATGAACAAAAACTAAAATTT
66 AATCAAAAATCCAAACCAAAGTCCCAAAAATAAAGTCCATAAAGCATGAACAAAAACTAAAATGT
* *
12812972 CCAATACCACTACTTGCAAGGTTTTTTCAAAAAATAATCAAGAGTACCTTCGTAGCCAAGCCCAT
131 CCAATACCACTACTTGCAAGG-TTTTCCAAAAAATAACCAAGAGTACCTTCGTAGCCAAGCCCAT
12813037 CCTAGTCCCGATTATCTAAAATCAAAGTTTAAGGAG-GTAAGATTAAAAAGGCTCAATGTAGGTC
195 CCTAGTCCCGATTATCTAAAATCAAAGTTTAAGG-GCGTAAGATTAAAAAGGCTCAATGTAGGTC
*
12813101 TTAAATAACAATTAGTTCACAAAAACAATTCATTATAACATCATATTAATCAGTCCATAACATAT
259 TTAAATAACAATTAGTTCACAAAAACAATTCATTATAACATCATATTAATCAGCCCATAACATAT
*
12813166 ATAAATTACTCAATTATAAATCAAATATGGCAAATTGTGTAATGACGTATTTAATACAACATTTT
324 ATAAATTACTCAATTATAAATCAAATATGGCAAATTGTGTAATGACGTAATTAATACAACATTTT
* *
12813231 TAGAATACAATACAAATATTAGAACTTAAATCCTACCCAACTCCGTTACACGCCATACAGAGTTC
389 TAGAATACAATACAAATATTAGAACTTAAATCCTACCCAACTCCGCTACACGCCACACAGAGTTC
* * *
12813296 CCCATAACTCATCCAACTAATAACACACCAAAATGTGGTCCAACCACCAGAAATTATGGATTTAC
454 CCCATAACTCATCCAACCAATAACACACCAAAATGTGATCCAACCACCAGAAATTATAGATTTAC
*
12813361 TGCCAGATACATAATATTATGGACAAG
519 TGCCAAATACATAATATTATGGACAAG
12813388 CCACCAGAAA
Statistics
Matches: 507, Mismatches: 36, Indels: 4
0.93 0.07 0.01
Matches are distributed among these distances:
550 141 0.28
551 359 0.71
552 7 0.01
ACGTcount: A:0.43, C:0.20, G:0.10, T:0.26
Consensus pattern (551 bp):
ATTATAATTTAACATAACAAATCATGCAGAAAAGAAAAACCCCAAAACATTATCCAAAGTTCACA
AATCAAAAATCCAAACCAAAGTCCCAAAAATAAAGTCCATAAAGCATGAACAAAAACTAAAATGT
CCAATACCACTACTTGCAAGGTTTTCCAAAAAATAACCAAGAGTACCTTCGTAGCCAAGCCCATC
CTAGTCCCGATTATCTAAAATCAAAGTTTAAGGGCGTAAGATTAAAAAGGCTCAATGTAGGTCTT
AAATAACAATTAGTTCACAAAAACAATTCATTATAACATCATATTAATCAGCCCATAACATATAT
AAATTACTCAATTATAAATCAAATATGGCAAATTGTGTAATGACGTAATTAATACAACATTTTTA
GAATACAATACAAATATTAGAACTTAAATCCTACCCAACTCCGCTACACGCCACACAGAGTTCCC
CATAACTCATCCAACCAATAACACACCAAAATGTGATCCAACCACCAGAAATTATAGATTTACTG
CCAAATACATAATATTATGGACAAGAAAAAC
Found at i:12819652 original size:11 final size:11
Alignment explanation
Indices: 12819636--12819683 Score: 62
Period size: 11 Copynumber: 4.4 Consensus size: 11
12819626 GATGATGATG
12819636 ATTTTAAAATC
1 ATTTTAAAATC
12819647 ATTTTAATAAT-
1 ATTTTAA-AATC
* *
12819658 TTTTTAAAATA
1 ATTTTAAAATC
12819669 ATTTTAAAATC
1 ATTTTAAAATC
12819680 ATTT
1 ATTT
12819684 GTTGATATAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
10 3 0.09
11 26 0.81
12 3 0.09
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (11 bp):
ATTTTAAAATC
Found at i:12823815 original size:16 final size:16
Alignment explanation
Indices: 12823794--12823827 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
12823784 AAGAACATAG
12823794 AAAATGAAACAAAGGA
1 AAAATGAAACAAAGGA
*
12823810 AAAATGAAATAAAGGA
1 AAAATGAAACAAAGGA
12823826 AA
1 AA
12823828 TTTAAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.71, C:0.03, G:0.18, T:0.09
Consensus pattern (16 bp):
AAAATGAAACAAAGGA
Found at i:12825933 original size:5 final size:5
Alignment explanation
Indices: 12825925--12825958 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
12825915 AGTTAAATAT
12825925 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
12825959 TATCACACAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTA
Found at i:12827265 original size:5 final size:5
Alignment explanation
Indices: 12827255--12827279 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
12827245 GGGGTAGGAC
12827255 ATGAT ATGAT ATGAT ATGAT ATGAT
1 ATGAT ATGAT ATGAT ATGAT ATGAT
12827280 TCGTATACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.20, T:0.40
Consensus pattern (5 bp):
ATGAT
Found at i:12834013 original size:9 final size:9
Alignment explanation
Indices: 12833984--12834020 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
12833974 TGAGTTTTCG
12833984 AATTCGAAT
1 AATTCGAAT
*
12833993 AACTCGAAT
1 AATTCGAAT
12834002 AATTCGAAT
1 AATTCGAAT
*
12834011 AATTCAAAT
1 AATTCGAAT
12834020 A
1 A
12834021 TCAAACTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.49, C:0.14, G:0.08, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:12834835 original size:5 final size:5
Alignment explanation
Indices: 12834825--12834850 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
12834815 TTCGAAAATT
12834825 TTCGA TTCGA TTCGA TTCGA TTCGA T
1 TTCGA TTCGA TTCGA TTCGA TTCGA T
12834851 CGAATGCTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (5 bp):
TTCGA
Found at i:12836199 original size:3 final size:3
Alignment explanation
Indices: 12836191--12836249 Score: 118
Period size: 3 Copynumber: 19.7 Consensus size: 3
12836181 TGATTTTGGT
12836191 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
12836239 TTA TTA TTA TT
1 TTA TTA TTA TT
12836250 TTTGCCTCTG
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:12836870 original size:19 final size:19
Alignment explanation
Indices: 12836846--12836886 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
12836836 TTATTAATAA
*
12836846 ATTTATTGTTACTATTATT
1 ATTTATTATTACTATTATT
**
12836865 ATTTATTATTGGTATTATT
1 ATTTATTATTACTATTATT
12836884 ATT
1 ATT
12836887 ACACTTATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.27, C:0.02, G:0.07, T:0.63
Consensus pattern (19 bp):
ATTTATTATTACTATTATT
Found at i:12842085 original size:24 final size:25
Alignment explanation
Indices: 12842058--12842112 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
12842048 ATTTTTAATC
12842058 GTTAA-CCGAACCGAAATTTTTTCG
1 GTTAATCCGAACCGAAATTTTTTCG
* ***
12842082 GTTAATTCGGTTCGAAATTTTTTCG
1 GTTAATCCGAACCGAAATTTTTTCG
12842107 GTTAAT
1 GTTAAT
12842113 TTGGTCGGTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
24 5 0.19
25 21 0.81
ACGTcount: A:0.25, C:0.15, G:0.18, T:0.42
Consensus pattern (25 bp):
GTTAATCCGAACCGAAATTTTTTCG
Found at i:12842183 original size:9 final size:9
Alignment explanation
Indices: 12842169--12842226 Score: 82
Period size: 9 Copynumber: 6.4 Consensus size: 9
12842159 TTTGGTTAAA
12842169 AATTAACCG
1 AATTAACCG
*
12842178 AATTAACCT
1 AATTAACCG
12842187 AATT-ACCTG
1 AATTAACC-G
12842196 AATTAACCG
1 AATTAACCG
*
12842205 AATTACCCG
1 AATTAACCG
12842214 AATTAACCG
1 AATTAACCG
12842223 AATT
1 AATT
12842227 GAATCACTAC
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
8 3 0.07
9 37 0.86
10 3 0.07
ACGTcount: A:0.41, C:0.22, G:0.09, T:0.28
Consensus pattern (9 bp):
AATTAACCG
Found at i:12843759 original size:25 final size:25
Alignment explanation
Indices: 12843728--12843780 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
12843718 AATTTTTTAT
* **
12843728 TTTTATAATTTTATTTTTTTAAATA
1 TTTTATAATTATAAATTTTTAAATA
*
12843753 TTTTATAATTATAAATTTTTGAATA
1 TTTTATAATTATAAATTTTTAAATA
12843778 TTT
1 TTT
12843781 GGAAAAATGT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (25 bp):
TTTTATAATTATAAATTTTTAAATA
Found at i:12850756 original size:88 final size:88
Alignment explanation
Indices: 12850645--12850810 Score: 332
Period size: 88 Copynumber: 1.9 Consensus size: 88
12850635 TCTGATTCGG
12850645 AGGGTGAATTAGCTATTAACTAACCAATTATTACCTCCCGACCTCTAACTGATTAATTAATGATT
1 AGGGTGAATTAGCTATTAACTAACCAATTATTACCTCCCGACCTCTAACTGATTAATTAATGATT
12850710 GATACTCGCTTATAACTTCTGAT
66 GATACTCGCTTATAACTTCTGAT
12850733 AGGGTGAATTAGCTATTAACTAACCAATTATTACCTCCCGACCTCTAACTGATTAATTAATGATT
1 AGGGTGAATTAGCTATTAACTAACCAATTATTACCTCCCGACCTCTAACTGATTAATTAATGATT
12850798 GATACTCGCTTAT
66 GATACTCGCTTAT
12850811 CTCTCGACCT
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
88 78 1.00
ACGTcount: A:0.32, C:0.20, G:0.13, T:0.35
Consensus pattern (88 bp):
AGGGTGAATTAGCTATTAACTAACCAATTATTACCTCCCGACCTCTAACTGATTAATTAATGATT
GATACTCGCTTATAACTTCTGAT
Found at i:12859486 original size:55 final size:55
Alignment explanation
Indices: 12859403--12859508 Score: 176
Period size: 55 Copynumber: 1.9 Consensus size: 55
12859393 TCGTTGGATG
* * *
12859403 ATAAATCATCACTTTTAATTTGATTAGTGCTTATGAATAATTAATTTGCAAGATA
1 ATAAATCATCACTTTTAATTAGAATAGTGCTCATGAATAATTAATTTGCAAGATA
*
12859458 ATAAATCATCACTTTTAATTAGAATAGTGCTCATTAATAATTAATTTGCAA
1 ATAAATCATCACTTTTAATTAGAATAGTGCTCATGAATAATTAATTTGCAA
12859509 TCTGTAATTT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
55 47 1.00
ACGTcount: A:0.40, C:0.10, G:0.09, T:0.41
Consensus pattern (55 bp):
ATAAATCATCACTTTTAATTAGAATAGTGCTCATGAATAATTAATTTGCAAGATA
Done.