Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1232
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: 125048
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:3091 original size:9 final size:10
Alignment explanation
Indices: 3065--3117 Score: 70
Period size: 10 Copynumber: 5.1 Consensus size: 10
3055 ATATAGTTTC
*
3065 TCAAAAAAAC
1 TCAAAAAAAA
3075 TCGAAAAAAAA
1 TC-AAAAAAAA
*
3086 TTAAAAAAAA
1 TCAAAAAAAA
3096 TCAAAAAAAAA
1 TC-AAAAAAAA
3107 TCAAAAAAAA
1 TCAAAAAAAA
3117 T
1 T
3118 TTGGTTTCCA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
10 20 0.53
11 18 0.47
ACGTcount: A:0.75, C:0.09, G:0.02, T:0.13
Consensus pattern (10 bp):
TCAAAAAAAA
Found at i:3093 original size:21 final size:21
Alignment explanation
Indices: 3065--3117 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
3055 ATATAGTTTC
* *
3065 TCAAAAAAACTCGAAAAAAAA
1 TCAAAAAAAATCAAAAAAAAA
*
3086 TTAAAAAAAATCAAAAAAAAA
1 TCAAAAAAAATCAAAAAAAAA
3107 TCAAAAAAAAT
1 TCAAAAAAAAT
3118 TTGGTTTCCA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.75, C:0.09, G:0.02, T:0.13
Consensus pattern (21 bp):
TCAAAAAAAATCAAAAAAAAA
Found at i:8086 original size:22 final size:22
Alignment explanation
Indices: 8056--8099 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
8046 TTTGGTATTT
8056 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
8078 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
8100 TGGTTCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.05, G:0.36, T:0.25
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:12313 original size:17 final size:17
Alignment explanation
Indices: 12288--12342 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
12278 TCTCTTTTCA
*
12288 TTCTCTTTTTTTGAATT
1 TTCTTTTTTTTTGAATT
* *
12305 TTCTTTTTTTTTTCATTT
1 TTC-TTTTTTTTTGAATT
* *
12323 TTCTTTTCTTTTGTATT
1 TTCTTTTTTTTTGAATT
12340 TTC
1 TTC
12343 GCTCTTTTCT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 16 0.53
18 14 0.47
ACGTcount: A:0.07, C:0.13, G:0.04, T:0.76
Consensus pattern (17 bp):
TTCTTTTTTTTTGAATT
Found at i:12316 original size:18 final size:18
Alignment explanation
Indices: 12293--12334 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
12283 TTTCATTCTC
*
12293 TTTTTTTGAATTTTCTTT
1 TTTTTTTCAATTTTCTTT
*
12311 TTTTTTTCATTTTTCTTT
1 TTTTTTTCAATTTTCTTT
12329 TCTTTT
1 T-TTTT
12335 GTATTTTCGC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 17 0.81
19 4 0.19
ACGTcount: A:0.07, C:0.10, G:0.02, T:0.81
Consensus pattern (18 bp):
TTTTTTTCAATTTTCTTT
Found at i:14579 original size:11 final size:12
Alignment explanation
Indices: 14544--14578 Score: 70
Period size: 12 Copynumber: 2.9 Consensus size: 12
14534 AAACCGTATG
14544 CAATTTTTTTTT
1 CAATTTTTTTTT
14556 CAATTTTTTTTT
1 CAATTTTTTTTT
14568 CAATTTTTTTT
1 CAATTTTTTTT
14579 CGAACTCTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.17, C:0.09, G:0.00, T:0.74
Consensus pattern (12 bp):
CAATTTTTTTTT
Found at i:14922 original size:22 final size:22
Alignment explanation
Indices: 14892--14935 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
14882 TTTGGTATTT
14892 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
14914 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
14936 TGGTTCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.05, G:0.36, T:0.25
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:19767 original size:23 final size:21
Alignment explanation
Indices: 19736--19779 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 21
19726 AAGGGCATAA
*
19736 AATGCTCTTTAAAGACTCCTTTT
1 AATGATCTTT-AAG-CTCCTTTT
19759 AATGATCTTTAAGCTCCTTTT
1 AATGATCTTTAAGCTCCTTTT
19780 TTTAACAGCC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 8 0.40
22 3 0.15
23 9 0.45
ACGTcount: A:0.25, C:0.20, G:0.09, T:0.45
Consensus pattern (21 bp):
AATGATCTTTAAGCTCCTTTT
Found at i:19930 original size:21 final size:23
Alignment explanation
Indices: 19885--19931 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
19875 TCACCTGCAA
* *
19885 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
19908 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
19929 TAA
1 TAA
19932 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:20853 original size:20 final size:20
Alignment explanation
Indices: 20817--20895 Score: 65
Period size: 20 Copynumber: 4.0 Consensus size: 20
20807 GAGCTAATAA
*
20817 TGAGCT-GAATGAGCTGAAT
1 TGAGCTCGAATAAGCTGAAT
**
20836 TGAGCTCGTGTAAGCTGACA-
1 TGAGCTCGAATAAGCTGA-AT
* *
20856 TGAGCTCGAATAAGATGACT
1 TGAGCTCGAATAAGCTGAAT
*
20876 TGAGCTC-AAGTGAGCTGAAT
1 TGAGCTCGAA-TAAGCTGAAT
20896 CGCATGGAGA
Statistics
Matches: 46, Mismatches: 10, Indels: 7
0.73 0.16 0.11
Matches are distributed among these distances:
19 8 0.17
20 37 0.80
21 1 0.02
ACGTcount: A:0.30, C:0.15, G:0.29, T:0.25
Consensus pattern (20 bp):
TGAGCTCGAATAAGCTGAAT
Found at i:20892 original size:40 final size:39
Alignment explanation
Indices: 20816--20893 Score: 93
Period size: 40 Copynumber: 2.0 Consensus size: 39
20806 AGAGCTAATA
* * **
20816 ATGAGCTGAATGAGCTGAATTGAGCTCGTGTAAGCTGAC
1 ATGAGCTGAATAAGATGAATTGAGCTCAAGTAAGCTGAC
* *
20855 ATGAGCTCGAATAAGATGACTTGAGCTCAAGTGAGCTGA
1 ATGAGCT-GAATAAGATGAATTGAGCTCAAGTAAGCTGA
20894 ATCGCATGGA
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
39 7 0.22
40 25 0.78
ACGTcount: A:0.31, C:0.15, G:0.29, T:0.24
Consensus pattern (39 bp):
ATGAGCTGAATAAGATGAATTGAGCTCAAGTAAGCTGAC
Found at i:32449 original size:13 final size:11
Alignment explanation
Indices: 32428--32461 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
32418 TAGTAGTTTC
*
32428 TTCAAAAAAATT
1 TTCAAAAAAA-A
32440 TTCAAAAAAAA
1 TTCAAAAAAAA
32451 TTCAAAAAAAA
1 TTCAAAAAAAA
32462 AATTGGTTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.68, C:0.09, G:0.00, T:0.24
Consensus pattern (11 bp):
TTCAAAAAAAA
Found at i:32525 original size:14 final size:14
Alignment explanation
Indices: 32506--32556 Score: 93
Period size: 14 Copynumber: 3.6 Consensus size: 14
32496 TCAAGTTGAA
32506 AAAAAAAATTCGTG
1 AAAAAAAATTCGTG
32520 AAAAAAAATTCGTG
1 AAAAAAAATTCGTG
32534 AAAAAAAAATTCGTG
1 -AAAAAAAATTCGTG
32549 AAAAAAAA
1 AAAAAAAA
32557 GAAGAAGCTA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
14 22 0.61
15 14 0.39
ACGTcount: A:0.65, C:0.06, G:0.12, T:0.18
Consensus pattern (14 bp):
AAAAAAAATTCGTG
Found at i:32525 original size:15 final size:15
Alignment explanation
Indices: 32505--32556 Score: 97
Period size: 15 Copynumber: 3.5 Consensus size: 15
32495 ATCAAGTTGA
32505 AAAAAAAAATTCGTG
1 AAAAAAAAATTCGTG
32520 -AAAAAAAATTCGTG
1 AAAAAAAAATTCGTG
32534 AAAAAAAAATTCGTG
1 AAAAAAAAATTCGTG
32549 AAAAAAAA
1 AAAAAAAA
32557 GAAGAAGCTA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
14 14 0.39
15 22 0.61
ACGTcount: A:0.65, C:0.06, G:0.12, T:0.17
Consensus pattern (15 bp):
AAAAAAAAATTCGTG
Found at i:36617 original size:11 final size:11
Alignment explanation
Indices: 36601--36630 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
36591 GGAAATTTGA
36601 AAAAAAAATTC
1 AAAAAAAATTC
36612 AAAAAAAATTC
1 AAAAAAAATTC
36623 AAAAAAAA
1 AAAAAAAA
36631 AATTTTGAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.80, C:0.07, G:0.00, T:0.13
Consensus pattern (11 bp):
AAAAAAAATTC
Found at i:37617 original size:18 final size:18
Alignment explanation
Indices: 37561--37620 Score: 66
Period size: 18 Copynumber: 3.2 Consensus size: 18
37551 AGTGCGAGCG
37561 AGAAAAAGAAATCAAAAGAAA
1 AGAAAAAGAAATC--AA-AAA
* **
37582 AGAAAAAGAGATTGAAAA
1 AGAAAAAGAAATCAAAAA
37600 AGAAAAAGAAATCAAAAA
1 AGAAAAAGAAATCAAAAA
37618 AGA
1 AGA
37621 GAGTGAGGTC
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
18 21 0.64
19 1 0.03
21 11 0.33
ACGTcount: A:0.73, C:0.03, G:0.17, T:0.07
Consensus pattern (18 bp):
AGAAAAAGAAATCAAAAA
Found at i:39677 original size:16 final size:16
Alignment explanation
Indices: 39656--39687 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
39646 TAATGTGTTT
39656 TGCTGCTGTTGTTTAA
1 TGCTGCTGTTGTTTAA
39672 TGCTGCTGTTGTTTAA
1 TGCTGCTGTTGTTTAA
39688 ATGCAGAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.12, G:0.25, T:0.50
Consensus pattern (16 bp):
TGCTGCTGTTGTTTAA
Found at i:40012 original size:72 final size:73
Alignment explanation
Indices: 39874--40021 Score: 183
Period size: 72 Copynumber: 2.0 Consensus size: 73
39864 GCAGGTACAT
* * * *
39874 GGACGGCATTTAAAGAAAAGGTGGCTGCTGCATTTTTCCAAAGCTGCCGAATTTATTGAGTGCAT
1 GGACGGCATTTAAAGAAAAGGTGGCTGCTGCATTTTTCCAAACCAGCCAAATTTAGTGAGTGCAT
39939 GGGACTTG
66 GGGACTTG
* * * * * *
39947 GGACGGCATTTAAAGCGAAA-GTTGCTGTTGTA-TTTTCCCAACCAGCCAAATTTAGTGTGTGCA
1 GGACGGCATTTAAAG-AAAAGGTGGCTGCTGCATTTTTCCAAACCAGCCAAATTTAGTGAGTGCA
40010 TGGGACTTG
65 TGGGACTTG
40019 GGA
1 GGA
40022 TAGCATTAAA
Statistics
Matches: 64, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
72 37 0.58
73 24 0.38
74 3 0.05
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.29
Consensus pattern (73 bp):
GGACGGCATTTAAAGAAAAGGTGGCTGCTGCATTTTTCCAAACCAGCCAAATTTAGTGAGTGCAT
GGGACTTG
Found at i:42002 original size:20 final size:20
Alignment explanation
Indices: 41979--42025 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
41969 AGGTTAAGAT
*
41979 TGAGCTGAATTGAGCTTGAA
1 TGAGCTGAATTGAGCTCGAA
* * *
41999 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAA
42019 TGAGCTG
1 TGAGCTG
42026 GAAACGAGCT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.23, C:0.13, G:0.34, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAA
Found at i:49900 original size:23 final size:22
Alignment explanation
Indices: 49849--49900 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
49839 CCTCGTCTTT
*
49849 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
49871 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
49894 TTCTTTT
1 TTCTTTT
49901 TCAATTTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:53573 original size:11 final size:12
Alignment explanation
Indices: 53553--53590 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
53543 AATGGAAACT
53553 AAATTTTTTTTC
1 AAATTTTTTTTC
53565 AAATTTTTTTT-
1 AAATTTTTTTTC
*
53576 GAATTTTTTTTC
1 AAATTTTTTTTC
53588 AAA
1 AAA
53591 GAAACTACTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
11 10 0.43
12 13 0.57
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (12 bp):
AAATTTTTTTTC
Found at i:67937 original size:20 final size:20
Alignment explanation
Indices: 67914--67967 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
67904 AACTAAGAAG
67914 GAGCTGAATGAGCTAAGGA-T
1 GAGCTGAATGAGCT-AGGATT
* *
67934 GAGCTCAATGAGCTATGATT
1 GAGCTGAATGAGCTAGGATT
*
67954 GACCTGAATGAGCT
1 GAGCTGAATGAGCT
67968 TGAAGTAGAG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 3 0.10
20 26 0.90
ACGTcount: A:0.31, C:0.15, G:0.30, T:0.24
Consensus pattern (20 bp):
GAGCTGAATGAGCTAGGATT
Found at i:75736 original size:24 final size:24
Alignment explanation
Indices: 75712--75758 Score: 76
Period size: 25 Copynumber: 1.9 Consensus size: 24
75702 AAACTACTTC
75712 TAAAGAAAACTCAAGAGAGAATTCT
1 TAAAGAAAACTCAA-AGAGAATTCT
*
75737 TAGAGAAAACTCAAAGAGAATT
1 TAAAGAAAACTCAAAGAGAATT
75759 TTCACTCAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.53, C:0.11, G:0.17, T:0.19
Consensus pattern (24 bp):
TAAAGAAAACTCAAAGAGAATTCT
Found at i:80977 original size:3 final size:3
Alignment explanation
Indices: 80969--81008 Score: 55
Period size: 3 Copynumber: 13.3 Consensus size: 3
80959 ATATGTAGGT
*
80969 ATA ATA ATA ATA TATA AT- ATA ATA ATA AAA ATA ATA ATA A
1 ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA A
81009 CAAAATTAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 2 0.06
3 28 0.85
4 3 0.09
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:80992 original size:15 final size:12
Alignment explanation
Indices: 80971--81022 Score: 52
Period size: 12 Copynumber: 4.1 Consensus size: 12
80961 ATGTAGGTAT
80971 AATAATAATATATA
1 AATAATAATA-A-A
80985 ATATAATAATAAA
1 A-ATAATAATAAA
80998 AATAATAATAACA
1 AATAATAATAA-A
*
81011 AA-ATTAATAAA
1 AATAATAATAAA
81022 A
1 A
81023 TAGACTAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
11 2 0.06
12 17 0.49
13 5 0.14
14 2 0.06
15 9 0.26
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (12 bp):
AATAATAATAAA
Found at i:81491 original size:21 final size:21
Alignment explanation
Indices: 81465--81540 Score: 102
Period size: 21 Copynumber: 3.7 Consensus size: 21
81455 AATCATATCT
81465 TCTAAGATTGTATATATCATA
1 TCTAAGATTGTATATATCATA
**
81486 TCTAAGATTACATATATCATA
1 TCTAAGATTGTATATATCATA
* *
81507 TCTAGGATTG--CATATCATA
1 TCTAAGATTGTATATATCATA
81526 TCTAAGATTGTATAT
1 TCTAAGATTGTATAT
81541 CCTCGAAAAT
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
19 17 0.37
21 29 0.63
ACGTcount: A:0.37, C:0.12, G:0.11, T:0.41
Consensus pattern (21 bp):
TCTAAGATTGTATATATCATA
Found at i:81500 original size:19 final size:20
Alignment explanation
Indices: 81444--81534 Score: 85
Period size: 21 Copynumber: 4.3 Consensus size: 20
81434 ATTAAATCTT
*
81444 TAAGATTACAAAATCATATCTTC
1 TAAGATTACAATATCATA---TC
**
81467 TAAGATTGTATATATCATATC
1 TAAGATTACA-ATATCATATC
81488 TAAGATTACATATATCATATC
1 TAAGATTACA-ATATCATATC
* *
81509 TAGGATTGC-ATATCATATC
1 TAAGATTACAATATCATATC
81528 TAAGATT
1 TAAGATT
81535 GTATATCCTC
Statistics
Matches: 59, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
19 16 0.27
21 28 0.47
23 8 0.14
24 7 0.12
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (20 bp):
TAAGATTACAATATCATATC
Found at i:81535 original size:19 final size:19
Alignment explanation
Indices: 81478--81541 Score: 83
Period size: 19 Copynumber: 3.3 Consensus size: 19
81468 AAGATTGTAT
*
81478 ATATCATATCTAAGATTAC
1 ATATCATATCTAAGATTGC
*
81497 ATATATCATATCTAGGATTGC
1 --ATATCATATCTAAGATTGC
*
81518 ATATCATATCTAAGATTGT
1 ATATCATATCTAAGATTGC
81537 ATATC
1 ATATC
81542 CTCGAAAATT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
19 22 0.56
21 17 0.44
ACGTcount: A:0.38, C:0.14, G:0.09, T:0.39
Consensus pattern (19 bp):
ATATCATATCTAAGATTGC
Found at i:82010 original size:132 final size:132
Alignment explanation
Indices: 81826--82353 Score: 912
Period size: 132 Copynumber: 4.0 Consensus size: 132
81816 GACGATAAGA
* * *
81826 CTTGCTGGCTTAAATCTACTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTCGATCTGCTC
1 CTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTTGATCTGCTC
* *
81891 CCCTACTGCTTAGGGATATAAGATCTACAATCTTCAACCTACTCCGCTGCTGCTCAGGGAGACAA
66 CACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCGCTGCTGCTCAGGGAGACAA
81956 GG
131 GG
* * *
81958 CTTGGTGCCTTAAATCTGCTTCCCACTATCTTCGAAAGATAAGATTTTCCGTCTTTGATCTGCTC
1 CTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTTGATCTGCTC
* *
82023 CACTACTGCTTAGGGATATAAGATCTACAATCTTCAACCTACTCCGCTGCTGCTCAGGGACACAA
66 CACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCGCTGCTGCTCAGGGAGACAA
82088 GG
131 GG
*
82090 CTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCATCTTTGATCTGCTC
1 CTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTTGATCTGCTC
* *
82155 CACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTAATCCGCTGCTGCTCATGGAGACAA
66 CACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCGCTGCTGCTCAGGGAGACAA
82220 GG
131 GG
* *
82222 CTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTTGATCTGTTT
1 CTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTTGATCTGCTC
*
82287 CACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCGCTGCTACTCAGGGAGACAA
66 CACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCGCTGCTGCTCAGGGAGACAA
82352 GG
131 GG
82354 TGATGTGACC
Statistics
Matches: 374, Mismatches: 22, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
132 374 1.00
ACGTcount: A:0.25, C:0.26, G:0.19, T:0.30
Consensus pattern (132 bp):
CTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTTGATCTGCTC
CACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCGCTGCTGCTCAGGGAGACAA
GG
Found at i:82174 original size:44 final size:44
Alignment explanation
Indices: 81862--82310 Score: 113
Period size: 44 Copynumber: 10.2 Consensus size: 44
81852 TATCTTGGAA
* ** *
81862 AGATAAGATTTGCCGTCTTCGATCTGCTCCCCTACTGCTTAGGG
1 AGATAAGATTTGCCATCTTTAATCTGCTCCACTACTGCTTAGGG
* * * * * * * * * *
81906 ATATAAGATCTACAATCTTCAACCTACTCCGCTGCTGCTCAGGG
1 AGATAAGATTTGCCATCTTTAATCTGCTCCACTACTGCTTAGGG
* ** **** * * **
81950 AGACAAGGCTTGGTGCCTTAAATCTGCTTCCCACTA-T-CTTCGAA
1 AGATAAGATTTGCCATCTTTAATCTGC-T-CCACTACTGCTTAGGG
* * *
81994 AGATAAGATTTTCCGTCTTTGATCTGCTCCACTACTGCTTAGGG
1 AGATAAGATTTGCCATCTTTAATCTGCTCCACTACTGCTTAGGG
* * * * * * * * * *
82038 ATATAAGATCTACAATCTTCAACCTACTCCGCTGCTGCTCAGGG
1 AGATAAGATTTGCCATCTTTAATCTGCTCCACTACTGCTTAGGG
* * ** **** * *
82082 ACACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTA-T-CTT-GGAA
1 AGATAAGATTTGCCATCTTTAATCTGC-T-CCACTACTGCTTAGG-G
*
82126 AGATAAGATTTGCCATCTTTGATCTGCTCCACTACTGCTTAGGG
1 AGATAAGATTTGCCATCTTTAATCTGCTCCACTACTGCTTAGGG
* * * * * ** * * * *
82170 AGATAAGATCTACAATCTTCAACCTAATCCGCTGCTGCTCATGG
1 AGATAAGATTTGCCATCTTTAATCTGCTCCACTACTGCTTAGGG
* ** **** * *
82214 AGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTA-T-CTT-GGAA
1 AGATAAGATTTGCCATCTTTAATCTGC-T-CCACTACTGCTTAGG-G
* * * *
82258 AGATAAGATTTGCCGTCTTTGATCTGTTTCACTACTGCTTAGGG
1 AGATAAGATTTGCCATCTTTAATCTGCTCCACTACTGCTTAGGG
82302 AGATAAGAT
1 AGATAAGAT
82311 CTACAATCTT
Statistics
Matches: 266, Mismatches: 123, Indels: 32
0.63 0.29 0.08
Matches are distributed among these distances:
42 17 0.06
43 9 0.03
44 218 0.82
45 10 0.04
46 12 0.05
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.31
Consensus pattern (44 bp):
AGATAAGATTTGCCATCTTTAATCTGCTCCACTACTGCTTAGGG
Found at i:85216 original size:56 final size:55
Alignment explanation
Indices: 85104--85217 Score: 149
Period size: 55 Copynumber: 2.1 Consensus size: 55
85094 TGCTTTTATT
* * * * *
85104 AATGCCGTCCATGCATGGTGAATATCTCATTTAATTCATGTTTTGCTTCCCTTTA
1 AATGCCGTCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCACATTA
*
85159 AATGCCGTTCCATACATGG-GAACATTTCATTTAATTCATGTCTTTGCTGCACATTA
1 AATGCCG-TCCATACATGGTGAACATCTCATTTAATTCATGT-TTTGCTGCACATTA
85215 AAT
1 AAT
85218 CAGCAAGCAG
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
55 27 0.53
56 24 0.47
ACGTcount: A:0.25, C:0.21, G:0.14, T:0.39
Consensus pattern (55 bp):
AATGCCGTCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCACATTA
Found at i:85866 original size:20 final size:20
Alignment explanation
Indices: 85841--85895 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
85831 ACGAGTTAAA
* *
85841 TTGAGCTTGAATGAGCTGAC
1 TTGAGCTCGAATGAGCTAAC
*
85861 TTGAGCACGAATGAGCTAAC
1 TTGAGCTCGAATGAGCTAAC
85881 TTGAGCTCGAATGAG
1 TTGAGCTCGAATGAG
85896 TTGAACCACA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.25
Consensus pattern (20 bp):
TTGAGCTCGAATGAGCTAAC
Found at i:87230 original size:12 final size:12
Alignment explanation
Indices: 87215--87277 Score: 60
Period size: 12 Copynumber: 5.2 Consensus size: 12
87205 TCAAGCTCTC
87215 TTTCAATTTCTT
1 TTTCAATTTCTT
*
87227 TTTCCACTCTTTCTT
1 TTT-CA--ATTTCTT
87242 TTTC---TTCTT
1 TTTCAATTTCTT
87251 TTTCAATTTCTT
1 TTTCAATTTCTT
*
87263 TTTCAATCTCTT
1 TTTCAATTTCTT
87275 TTT
1 TTT
87278 GCTTTTCACT
Statistics
Matches: 43, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
9 9 0.21
12 22 0.51
13 2 0.05
14 1 0.02
15 9 0.21
ACGTcount: A:0.11, C:0.22, G:0.00, T:0.67
Consensus pattern (12 bp):
TTTCAATTTCTT
Found at i:88268 original size:26 final size:27
Alignment explanation
Indices: 88229--88289 Score: 88
Period size: 26 Copynumber: 2.3 Consensus size: 27
88219 CAATCACTCT
* * *
88229 TTTTTTTTTCAATTTCGATTTTTTTTC
1 TTTTTTTTTCAATTCCGAATTTTTTTA
88256 TTTTTTTTT-AATTCCGAATTTTTTTA
1 TTTTTTTTTCAATTCCGAATTTTTTTA
88282 TTTTTTTT
1 TTTTTTTT
88290 CTTCAATACT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
26 22 0.71
27 9 0.29
ACGTcount: A:0.13, C:0.08, G:0.03, T:0.75
Consensus pattern (27 bp):
TTTTTTTTTCAATTCCGAATTTTTTTA
Found at i:88276 original size:27 final size:26
Alignment explanation
Indices: 88229--88289 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 26
88219 CAATCACTCT
*
88229 TTTTTTTTTCAATTTCGATTTTTTT-
1 TTTTTTTTTCAATTCCGATTTTTTTA
*
88254 TCTTTTTTTTTAATTCCGAATTTTTTTA
1 T-TTTTTTTTCAATTCCG-ATTTTTTTA
88282 TTTTTTTT
1 TTTTTTTT
88290 CTTCAATACT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
25 1 0.03
26 14 0.45
27 15 0.48
28 1 0.03
ACGTcount: A:0.13, C:0.08, G:0.03, T:0.75
Consensus pattern (26 bp):
TTTTTTTTTCAATTCCGATTTTTTTA
Found at i:88352 original size:13 final size:13
Alignment explanation
Indices: 88334--88389 Score: 71
Period size: 13 Copynumber: 4.5 Consensus size: 13
88324 GAATACAAAC
*
88334 TTTTTTTTTGAAT
1 TTTTTTTTTCAAT
*
88347 TTTTTTTTTCAAA
1 TTTTTTTTTCAAT
*
88360 TTTTTTTTTCAAG
1 TTTTTTTTTCAAT
88373 TTTTTTTTT--AT
1 TTTTTTTTTCAAT
88384 TTTTTT
1 TTTTTT
88390 ACAATACCGT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
11 7 0.18
13 32 0.82
ACGTcount: A:0.14, C:0.04, G:0.04, T:0.79
Consensus pattern (13 bp):
TTTTTTTTTCAAT
Found at i:88388 original size:12 final size:12
Alignment explanation
Indices: 88334--88389 Score: 60
Period size: 12 Copynumber: 4.6 Consensus size: 12
88324 GAATACAAAC
*
88334 TTTTTTTTTGAA
1 TTTTTTTTTTAA
88346 TTTTTTTTTTCAAA
1 TTTTTTTTTT--AA
*
88360 TTTTTTTTTCAA
1 TTTTTTTTTTAA
*
88372 GTTTTTTTTT-A
1 TTTTTTTTTTAA
88383 TTTTTTT
1 TTTTTTT
88390 ACAATACCGT
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
11 7 0.19
12 19 0.51
14 11 0.30
ACGTcount: A:0.14, C:0.04, G:0.04, T:0.79
Consensus pattern (12 bp):
TTTTTTTTTTAA
Found at i:90393 original size:132 final size:132
Alignment explanation
Indices: 90154--90438 Score: 489
Period size: 132 Copynumber: 2.2 Consensus size: 132
90144 TGGTCGTATC
* * *
90154 ACAAGGCTTGCTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTCGAT
1 ACAAGGCTTGGTGGCTTAAATCTCCTTCCCACTATCTTCGAAAGATAAGATTTGCCGTCTTCGAT
* * * *
90219 CTGCTCCCCTACTACTTAGGGATATAAGATCTACAATTTTCAACCTACTCCGCTGCTGCTCAGGG
66 CTGCTCCACTACTACTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCGCTGCTGCTCAGGA
90284 AG
131 AG
*
90286 ACAAGGCTTGGTGGCTTAAATCTCCTTCCCACTATCTTCGAAAGATAAGATTTGCCGTCTTTGAT
1 ACAAGGCTTGGTGGCTTAAATCTCCTTCCCACTATCTTCGAAAGATAAGATTTGCCGTCTTCGAT
*
90351 CTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCGCTGCTGCTCAGGA
66 CTGCTCCACTACTACTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCGCTGCTGCTCAGGA
90416 AG
131 AG
90418 ACAAGGCTTGGTGGCTTAAAT
1 ACAAGGCTTGGTGGCTTAAAT
90439 TCAAATGAGC
Statistics
Matches: 144, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
132 144 1.00
ACGTcount: A:0.25, C:0.26, G:0.20, T:0.30
Consensus pattern (132 bp):
ACAAGGCTTGGTGGCTTAAATCTCCTTCCCACTATCTTCGAAAGATAAGATTTGCCGTCTTCGAT
CTGCTCCACTACTACTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCGCTGCTGCTCAGGA
AG
Found at i:91195 original size:23 final size:22
Alignment explanation
Indices: 91143--91195 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
91133 TCCACGTCTT
*
91143 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTGCTTCTTTTTCTAA
91165 -TTCATTTTCGCTTCTTTCTTC-AA
1 TTTC-TTTT-GCTTCTTT-TTCTAA
91188 TTTCTTTT
1 TTTCTTTT
91196 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 4 0.15
23 13 0.50
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.04, T:0.68
Consensus pattern (22 bp):
TTTCTTTTGCTTCTTTTTCTAA
Found at i:92565 original size:16 final size:17
Alignment explanation
Indices: 92536--92577 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
92526 TTTTTTAAAT
92536 TTTTATTGAATTTTGTA-
1 TTTT-TTGAATTTTGTAC
* *
92553 TTTTTTGATTTTTTTAC
1 TTTTTTGAATTTTGTAC
92570 TTTTTTGA
1 TTTTTTGA
92578 CTGATTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 10 0.45
17 12 0.55
ACGTcount: A:0.17, C:0.02, G:0.10, T:0.71
Consensus pattern (17 bp):
TTTTTTGAATTTTGTAC
Found at i:94989 original size:18 final size:17
Alignment explanation
Indices: 94966--95006 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
94956 CTTTTTCTTC
94966 TTTTTTTCACGAAAATTT
1 TTTTTTTCACG-AAATTT
94984 TTTTTTTCACGAAATTT
1 TTTTTTTCACGAAATTT
95001 TTTTTT
1 TTTTTT
95007 CAACTTGATA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 12 0.52
18 11 0.48
ACGTcount: A:0.22, C:0.10, G:0.05, T:0.63
Consensus pattern (17 bp):
TTTTTTTCACGAAATTT
Found at i:95066 original size:12 final size:12
Alignment explanation
Indices: 95049--95106 Score: 89
Period size: 12 Copynumber: 4.7 Consensus size: 12
95039 GAAACCAAAT
95049 TTTTTTTTTCAA
1 TTTTTTTTTCAA
95061 TTTTTTTTTCAA
1 TTTTTTTTTCAA
*
95073 TTTTTTTTTGAA
1 TTTTTTTTTCAA
95085 TTTTTTTTTCAAAA
1 TTTTTTTTTC--AA
95099 TTTTTTTT
1 TTTTTTTT
95107 GAAGAAACTA
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
12 32 0.76
14 10 0.24
ACGTcount: A:0.17, C:0.05, G:0.02, T:0.76
Consensus pattern (12 bp):
TTTTTTTTTCAA
Found at i:96138 original size:21 final size:23
Alignment explanation
Indices: 96093--96139 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
96083 TCACCTGCAA
* *
96093 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
96116 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
96137 TAA
1 TAA
96140 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:96887 original size:13 final size:13
Alignment explanation
Indices: 96869--96921 Score: 63
Period size: 13 Copynumber: 4.2 Consensus size: 13
96859 ATAGTAGTTT
96869 CTCGAAAAAAAAA
1 CTCGAAAAAAAAA
96882 CTCG-AAAAAAAA
1 CTCGAAAAAAAAA
* *
96894 TTCAAAAAAAAAA
1 CTCGAAAAAAAAA
* *
96907 TTTGAAAAAAAAA
1 CTCGAAAAAAAAA
96920 CT
1 CT
96922 AGTTTCCATT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
12 10 0.29
13 24 0.71
ACGTcount: A:0.68, C:0.11, G:0.06, T:0.15
Consensus pattern (13 bp):
CTCGAAAAAAAAA
Found at i:96979 original size:13 final size:13
Alignment explanation
Indices: 96961--96993 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
96951 ATCAAGTTGT
*
96961 AAAAAAATTTTGA
1 AAAAAAATTGTGA
96974 AAAAAAATTGTGA
1 AAAAAAATTGTGA
96987 AAAAAAA
1 AAAAAAA
96994 GAGAGCTAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.70, C:0.00, G:0.09, T:0.21
Consensus pattern (13 bp):
AAAAAAATTGTGA
Found at i:97951 original size:16 final size:18
Alignment explanation
Indices: 97930--97975 Score: 60
Period size: 16 Copynumber: 2.6 Consensus size: 18
97920 AAAAGAAACC
97930 GAAAAAGAAAAAA-ATT-
1 GAAAAAGAAAAAAGATTG
97946 GAAAAAGAGAAAAAGATTG
1 GAAAAAGA-AAAAAGATTG
*
97965 GAGAAAGAAAA
1 GAAAAAGAAAA
97976 GAAAGAGTGC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
16 8 0.31
17 5 0.19
18 6 0.23
19 7 0.27
ACGTcount: A:0.70, C:0.00, G:0.22, T:0.09
Consensus pattern (18 bp):
GAAAAAGAAAAAAGATTG
Found at i:97956 original size:18 final size:17
Alignment explanation
Indices: 97931--97975 Score: 54
Period size: 18 Copynumber: 2.6 Consensus size: 17
97921 AAAGAAACCG
97931 AAAAAGAAAAAAATTGA
1 AAAAAGAAAAAAATTGA
* *
97948 AAAAGAGAAAAAGATTGG
1 AAAA-AGAAAAAAATTGA
*
97966 AGAAAGAAAA
1 AAAAAGAAAA
97976 GAAAGAGTGC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 10 0.42
18 14 0.58
ACGTcount: A:0.71, C:0.00, G:0.20, T:0.09
Consensus pattern (17 bp):
AAAAAGAAAAAAATTGA
Found at i:104764 original size:23 final size:23
Alignment explanation
Indices: 104727--104789 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
104717 AATTTGGTTT
**
104727 ATTTCGTACCAAAAATTCCATACC
1 ATTTCGTACC-AAAACCCCATACC
104751 ATTTCGTACCAAAACCCCATACC
1 ATTTCGTACCAAAACCCCATACC
104774 ATTTCGTACCAAAACC
1 ATTTCGTACCAAAACC
104790 AACTCCATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
23 27 0.73
24 10 0.27
ACGTcount: A:0.37, C:0.33, G:0.05, T:0.25
Consensus pattern (23 bp):
ATTTCGTACCAAAACCCCATACC
Found at i:106636 original size:13 final size:13
Alignment explanation
Indices: 106603--106652 Score: 66
Period size: 13 Copynumber: 3.9 Consensus size: 13
106593 TAGTAGTTTC
* *
106603 TTCAAAAAAGAAT
1 TTCAAAAAAAAAA
*
106616 TTCGAAAAAAAAA
1 TTCAAAAAAAAAA
106629 TTC-AAAAAAAAA
1 TTCAAAAAAAAAA
106641 TTCAAAAAAAAA
1 TTCAAAAAAAAA
106653 TTTGGTTTCC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
12 12 0.36
13 21 0.64
ACGTcount: A:0.70, C:0.08, G:0.04, T:0.18
Consensus pattern (13 bp):
TTCAAAAAAAAAA
Found at i:106637 original size:11 final size:12
Alignment explanation
Indices: 106603--106654 Score: 77
Period size: 12 Copynumber: 4.2 Consensus size: 12
106593 TAGTAGTTTC
*
106603 TTCAAAAAAGAAT
1 TTCAAAAAA-AAA
106616 TTCGAAAAAAAAA
1 TTC-AAAAAAAAA
106629 TTCAAAAAAAAA
1 TTCAAAAAAAAA
106641 TTCAAAAAAAAA
1 TTCAAAAAAAAA
106653 TT
1 TT
106655 TGGTTTCCAT
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
12 23 0.62
13 8 0.22
14 6 0.16
ACGTcount: A:0.67, C:0.08, G:0.04, T:0.21
Consensus pattern (12 bp):
TTCAAAAAAAAA
Found at i:106709 original size:13 final size:13
Alignment explanation
Indices: 106691--106726 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
106681 GGATATCAAG
106691 TTGAAAAAAAAAT
1 TTGAAAAAAAAAT
106704 TTG-AAAAAAAAT
1 TTGAAAAAAAAAT
106716 TGTGAAAAAAA
1 T-TGAAAAAAA
106727 TTCGTGAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 10 0.48
13 5 0.24
14 6 0.29
ACGTcount: A:0.67, C:0.00, G:0.11, T:0.22
Consensus pattern (13 bp):
TTGAAAAAAAAAT
Found at i:106712 original size:12 final size:13
Alignment explanation
Indices: 106695--106740 Score: 69
Period size: 12 Copynumber: 3.6 Consensus size: 13
106685 ATCAAGTTGA
106695 AAAAAAAATT-TG
1 AAAAAAAATTGTG
106707 AAAAAAAATTGTG
1 AAAAAAAATTGTG
106720 -AAAAAAATTCGTG
1 AAAAAAAATT-GTG
106733 AAAAAAAA
1 AAAAAAAA
106741 GAAGAAGCTA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
12 19 0.61
13 5 0.16
14 7 0.23
ACGTcount: A:0.67, C:0.02, G:0.11, T:0.20
Consensus pattern (13 bp):
AAAAAAAATTGTG
Found at i:110691 original size:19 final size:19
Alignment explanation
Indices: 110660--110701 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
110650 ACTCAAATTC
* *
110660 ACGATCGAGCAAA-CACTA
1 ACGATCGAACAAATCACAA
110678 ACGACTCGAACAAATCACAA
1 ACGA-TCGAACAAATCACAA
110698 ACGA
1 ACGA
110702 GTTCGTATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 4 0.20
19 8 0.40
20 8 0.40
ACGTcount: A:0.48, C:0.29, G:0.14, T:0.10
Consensus pattern (19 bp):
ACGATCGAACAAATCACAA
Found at i:110894 original size:12 final size:12
Alignment explanation
Indices: 110867--110913 Score: 58
Period size: 14 Copynumber: 3.6 Consensus size: 12
110857 TCAAGTTGAA
110867 AAAAAAATTCGTTG
1 AAAAAAATT-G-TG
110881 AAAAAAATTGTG
1 AAAAAAATTGTG
110893 AAAAAAAAATTGTG
1 --AAAAAAATTGTG
110907 AAAAAAA
1 AAAAAAA
110914 GAAGAAGCTA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
12 9 0.29
13 1 0.03
14 21 0.68
ACGTcount: A:0.64, C:0.02, G:0.13, T:0.21
Consensus pattern (12 bp):
AAAAAAATTGTG
Found at i:111905 original size:19 final size:17
Alignment explanation
Indices: 111854--111906 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 17
111844 AAAAGAAACC
*
111854 GAAAAAGAAACAAAAATT
1 GAAAAAGAAA-AAAGATT
111872 GAAAAAGAGAAAAAGATT
1 GAAAAAGA-AAAAAGATT
*
111890 GGAGAAAGAAAGAAAGA
1 -GAAAAAGAAA-AAAGA
111907 GTGCAGAAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
18 16 0.53
19 14 0.47
ACGTcount: A:0.68, C:0.02, G:0.23, T:0.08
Consensus pattern (17 bp):
GAAAAAGAAAAAAGATT
Found at i:114499 original size:11 final size:11
Alignment explanation
Indices: 114483--114525 Score: 68
Period size: 11 Copynumber: 3.8 Consensus size: 11
114473 GTAGTTTCTC
114483 AAAAAAAATCA
1 AAAAAAAATCA
*
114494 AAAAAAATTCA
1 AAAAAAAATCA
114505 AAAAAAAATTCA
1 AAAAAAAA-TCA
114517 AAAAAAAAT
1 AAAAAAAAT
114526 TTGGTTTCCA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
11 18 0.62
12 11 0.38
ACGTcount: A:0.79, C:0.07, G:0.00, T:0.14
Consensus pattern (11 bp):
AAAAAAAATCA
Found at i:114500 original size:12 final size:12
Alignment explanation
Indices: 114483--114526 Score: 74
Period size: 12 Copynumber: 3.8 Consensus size: 12
114473 GTAGTTTCTC
114483 AAAAAAAA-TC-
1 AAAAAAAATTCA
114493 AAAAAAAATTCA
1 AAAAAAAATTCA
114505 AAAAAAAATTCA
1 AAAAAAAATTCA
114517 AAAAAAAATT
1 AAAAAAAATT
114527 TGGTTTCCAT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
10 8 0.25
11 2 0.06
12 22 0.69
ACGTcount: A:0.77, C:0.07, G:0.00, T:0.16
Consensus pattern (12 bp):
AAAAAAAATTCA
Found at i:119121 original size:15 final size:16
Alignment explanation
Indices: 119096--119126 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
119086 CATTCTGCAT
119096 TTAAACAACAGCAGCA
1 TTAAACAACAGCAGCA
119112 TTAAAC-ACAGCAGCA
1 TTAAACAACAGCAGCA
119127 AAACACATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.48, C:0.26, G:0.13, T:0.13
Consensus pattern (16 bp):
TTAAACAACAGCAGCA
Found at i:120051 original size:11 final size:11
Alignment explanation
Indices: 120035--120083 Score: 75
Period size: 11 Copynumber: 4.6 Consensus size: 11
120025 AGTTTCTCGA
*
120035 AAAAAAAACTC
1 AAAAAAAATTC
120046 AAAAAAAATT-
1 AAAAAAAATTC
120056 -AAAAAAATTC
1 AAAAAAAATTC
120066 AAAAAAAATTC
1 AAAAAAAATTC
120077 AAAAAAA
1 AAAAAAA
120084 TTTTTTTGGT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
9 9 0.26
11 26 0.74
ACGTcount: A:0.78, C:0.08, G:0.00, T:0.14
Consensus pattern (11 bp):
AAAAAAAATTC
Found at i:120061 original size:20 final size:21
Alignment explanation
Indices: 120036--120083 Score: 80
Period size: 20 Copynumber: 2.3 Consensus size: 21
120026 GTTTCTCGAA
120036 AAAAAAACTCAAAAAAAATT-
1 AAAAAAACTCAAAAAAAATTC
*
120056 AAAAAAATTCAAAAAAAATTC
1 AAAAAAACTCAAAAAAAATTC
120077 AAAAAAA
1 AAAAAAA
120084 TTTTTTTGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
20 19 0.73
21 7 0.27
ACGTcount: A:0.77, C:0.08, G:0.00, T:0.15
Consensus pattern (21 bp):
AAAAAAACTCAAAAAAAATTC
Found at i:120145 original size:12 final size:13
Alignment explanation
Indices: 120125--120176 Score: 88
Period size: 14 Copynumber: 4.0 Consensus size: 13
120115 TGGATACAAG
120125 TTGTGAAAAAAAA
1 TTGTGAAAAAAAA
120138 TT-TGAAAAAAAA
1 TTGTGAAAAAAAA
120150 TTGTGAAAAAAAAA
1 TTGTG-AAAAAAAA
120164 TTGTGAAAAAAAA
1 TTGTGAAAAAAAA
120177 AGAGAGCTAG
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
12 12 0.32
13 12 0.32
14 13 0.35
ACGTcount: A:0.63, C:0.00, G:0.13, T:0.23
Consensus pattern (13 bp):
TTGTGAAAAAAAA
Found at i:120153 original size:25 final size:27
Alignment explanation
Indices: 120125--120176 Score: 90
Period size: 26 Copynumber: 2.0 Consensus size: 27
120115 TGGATACAAG
120125 TTGTG-AAAAAAAATT-TGAAAAAAAA
1 TTGTGAAAAAAAAATTGTGAAAAAAAA
120150 TTGTGAAAAAAAAATTGTGAAAAAAAA
1 TTGTGAAAAAAAAATTGTGAAAAAAAA
120177 AGAGAGCTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
25 5 0.20
26 10 0.40
27 10 0.40
ACGTcount: A:0.63, C:0.00, G:0.13, T:0.23
Consensus pattern (27 bp):
TTGTGAAAAAAAAATTGTGAAAAAAAA
Found at i:122421 original size:20 final size:20
Alignment explanation
Indices: 122375--122421 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
122365 AGCTCGTTTC
*
122375 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* * *
122395 CAACTCATTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
122415 CAGCTCA
1 CAGCTCA
122422 ATCTTAACCT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.34, G:0.13, T:0.23
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:124456 original size:72 final size:73
Alignment explanation
Indices: 124380--124527 Score: 192
Period size: 72 Copynumber: 2.0 Consensus size: 73
124370 TTTAATGCTA
* * *
124380 TCCCAAGTCCCATGCACACACTAAATTCGGCTG-GTTGGGAAAATACAACAG-CAACTTTCGCTT
1 TCCCAAGTCCCATGCACACAATAAATTCGGCAGCGTTGGAAAAATACAACAGCCAACTTT-GCTT
124443 TAAATGCCG
65 TAAATGCCG
* * * * * *
124452 TCCCAAGTCCCATGCACTCAATAAATTCGGCAGCTTTGGAAAAATGCAGCAGCCACCTTTTCTTT
1 TCCCAAGTCCCATGCACACAATAAATTCGGCAGCGTTGGAAAAATACAACAGCCAACTTTGCTTT
124517 AAATGCCG
66 AAATGCCG
124525 TCC
1 TCC
124528 ATGTACCTGC
Statistics
Matches: 65, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
72 30 0.46
73 29 0.45
74 6 0.09
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.25
Consensus pattern (73 bp):
TCCCAAGTCCCATGCACACAATAAATTCGGCAGCGTTGGAAAAATACAACAGCCAACTTTGCTTT
AAATGCCG
Found at i:124735 original size:16 final size:16
Alignment explanation
Indices: 124714--124745 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
124704 CATTCTGCAT
124714 TTAAACAACAGCAGCA
1 TTAAACAACAGCAGCA
124730 TTAAACAACAGCAGCA
1 TTAAACAACAGCAGCA
124746 AAACACATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.25, G:0.12, T:0.12
Consensus pattern (16 bp):
TTAAACAACAGCAGCA
Done.