Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021573.1 Corchorus olitorius cultivar O-4 contig21606, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 47652
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.31
Found at i:856 original size:439 final size:436
Alignment explanation
Indices: 12--1043 Score: 1206
Period size: 439 Copynumber: 2.4 Consensus size: 436
2 AATAGATTGT
* * ** * *
12 CAATCGAAATAACAAAATTTCAAAAGCATTTTTTTAGAATTGAAACATAAAAATTAGCCTTTGAG
1 CAATCAAAATCACAAAATTTCGGAAGCATTTTTTTAGAATTAAAACATAAAAATTAGCTTTTGAG
* * * * * *
77 TATTTCATGAAAGTTCTAAATCATAAAATTACCTTTTAATAGACACCTGAAGT-ACCTTAATTGG
66 TACTTCATGAAAGTTGTAGATCATGAAATTACCTTTTAATAGACACATGAA-TCACCTTAATCGG
* * * *
141 ATAAATAGAATAAAGAAAAAAAAAATGAAGCGTGAAATCGAGTAAGATATAATTTGTAAAGGATT
130 ATAAATAGAACAAAGAAAAAAAAAATAAAGCGTGAAATCGAGTAAGATAGAATTTGTAAAGGACT
* * * * * *
206 AAGTAGAATAAAATAAAAAAGTATGGGAGTGATTTGATAACTAATTCAAATAAGAATATATTTGT
195 AAATAGAATAAAATAAAAAAGTATAGGAGTCATTTGATAAATAATCCAAATAAGAAAATATTTGT
* *
271 TAATAGAGATCTTAAAACATATAAATTCCCTTTTGAACCCTTCATGAAACTCGTAGATCAAATTA
260 TAATAGAGATCTTAAAACATAAAAATTCCCTTTTGAACCCTTCACGAAACTCGTAGATCAAATTA
* * * * * * * *
336 ACTTTCGGGTTATTCATGAAAGTAGTAGATCATACAATAACCTTTTAACCGACACCTGAATAACT
325 ACTTTCGGATCATTCATAAAAATAGCAAATCATACAATAACCATTTAACCGACACCTCAATAACT
* * * * * * *
401 TTAATTGGATATGTGGATC-GAAAATTATATGGTATTAAATTGACCAA
390 TCAATCGGACATGTGGA-CAAAAAATTATACGATATTAAATTAACCAA
* * * *
448 CAATCAAAA-CGACCAAATTTTGTAAGCATTTTTTTTA-AATTAAAACATAAAAATTTGCTTTTG
1 CAATCAAAATC-ACAAAATTTCGGAAGCA-TTTTTTTAGAATTAAAACATAAAAATTAGCTTTTG
* * * *
511 AGTCCTTCATGAAAGTTGTAGATCATGAAATTACCTTTTGATAGACAAATGAATCAACTTAATCG
64 AGTACTTCATGAAAGTTGTAGATCATGAAATTACCTTTTAATAGACACATGAATCACCTTAATCG
* *
576 GACAAATAGAACAAAGATTAAAAAAAATAAAGC-TGAAA-CGTTAGATTAAGATAGAATTTGTAA
129 GATAAATAGAACAAAGA-AAAAAAAAATAAAGCGTGAAATCG--AG--TAAGATAGAATTTGTAA
* * *
639 AGGACTAAATAGTATAAAGTAGAAAAGTATTAGG-GTCATTTGATAAATAATCCAAATAAGAAAA
189 AGGACTAAATAGAATAAAATAAAAAAGTA-TAGGAGTCATTTGATAAATAATCCAAATAAGAAAA
* * * *
703 TGTTTGTTAATGGAGATCTTGAAACATAAAAATTCCCTTTTGAACCCTTTACGAAACTCGTAGAT
253 TATTTGTTAATAGAGATCTTAAAACATAAAAATTCCCTTTTGAACCCTTCACGAAACTCGTAGAT
* * * * *
768 CAAATTTAGCTTTCGGATCCTT-ATAAAAATCGCAAATCATGCAATAACCATTTAACCGACACTT
318 CAAA-TTAACTTTCGGATCATTCATAAAAATAGCAAATCATACAATAACCATTTAACCGACACCT
**
832 CAATAACTTCAATCGGACATGTGGACAAAAAATTATACGATATTAAATTAACCGG
382 CAATAACTTCAATCGGACATGTGGACAAAAAATTATACGATATTAAATTAACCAA
** * * *
887 CAATCAAAATCACAAAATTTCGGAAGCA-TTTTTTAGAACCAAAACATTAAAATTGGCTTTTAAG
1 CAATCAAAATCACAAAATTTCGGAAGCATTTTTTTAGAATTAAAACATAAAAATTAGCTTTTGAG
* * * *
951 TTCTT-ATTGAAAATTGTAGATCATGAAATAACCTTTTAATAGACACTTGAATCACCTTAATCGG
66 TACTTCA-TGAAAGTTGTAGATCATGAAATTACCTTTTAATAGACACATGAATCACCTTAATCGG
1015 ATAAATAGAA-AAA-AAAATACAAAAATAAA
130 ATAAATAGAACAAAGAAAA-A-AAAAATAAA
1044 AGTCAACTCG
Statistics
Matches: 501, Mismatches: 79, Indels: 31
0.82 0.13 0.05
Matches are distributed among these distances:
435 5 0.01
436 119 0.24
437 43 0.09
438 88 0.18
439 229 0.46
440 17 0.03
ACGTcount: A:0.44, C:0.13, G:0.13, T:0.30
Consensus pattern (436 bp):
CAATCAAAATCACAAAATTTCGGAAGCATTTTTTTAGAATTAAAACATAAAAATTAGCTTTTGAG
TACTTCATGAAAGTTGTAGATCATGAAATTACCTTTTAATAGACACATGAATCACCTTAATCGGA
TAAATAGAACAAAGAAAAAAAAAATAAAGCGTGAAATCGAGTAAGATAGAATTTGTAAAGGACTA
AATAGAATAAAATAAAAAAGTATAGGAGTCATTTGATAAATAATCCAAATAAGAAAATATTTGTT
AATAGAGATCTTAAAACATAAAAATTCCCTTTTGAACCCTTCACGAAACTCGTAGATCAAATTAA
CTTTCGGATCATTCATAAAAATAGCAAATCATACAATAACCATTTAACCGACACCTCAATAACTT
CAATCGGACATGTGGACAAAAAATTATACGATATTAAATTAACCAA
Found at i:8535 original size:21 final size:21
Alignment explanation
Indices: 8485--8578 Score: 100
Period size: 22 Copynumber: 4.3 Consensus size: 21
8475 CTCCAATGTA
*
8485 GAAATATTGATAACCACACTGT
1 GAAAT-TTGATAACCACACTAT
* *
8507 GAAAATTTGATAACCTCATTAT
1 G-AAATTTGATAACCACACTAT
* *
8529 GAAATTTCAATAACCTC-CTAT
1 GAAATTT-GATAACCACACTAT
8550 GAAAATTTGATAACCACACTAT
1 G-AAATTTGATAACCACACTAT
8572 GAAATTT
1 GAAATTT
8579 CGACTTATTG
Statistics
Matches: 61, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
21 23 0.38
22 34 0.56
23 4 0.07
ACGTcount: A:0.41, C:0.17, G:0.10, T:0.32
Consensus pattern (21 bp):
GAAATTTGATAACCACACTAT
Found at i:8639 original size:22 final size:22
Alignment explanation
Indices: 8591--8637 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 22
8581 ACTTATTGTG
*
8591 AAATTTTGATAATCTCCTTATA
1 AAATTTTGATAATCACCTTATA
*
8613 AAATTTTTATAATCACACTATATA
1 AAATTTTGATAATCAC-CT-TATA
8637 A
1 A
8638 TTGGTAACCG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 14 0.67
23 2 0.10
24 5 0.24
ACGTcount: A:0.43, C:0.13, G:0.02, T:0.43
Consensus pattern (22 bp):
AAATTTTGATAATCACCTTATA
Found at i:8839 original size:26 final size:23
Alignment explanation
Indices: 8810--8869 Score: 68
Period size: 22 Copynumber: 2.5 Consensus size: 23
8800 TGATAAGCAT
8810 AAATTTTGATAAATTCCCTCCCTATG
1 AAATTTTGATAAA---CCTCCCTATG
* *
8836 AAATTTT-ATTAACCTTCCTATG
1 AAATTTTGATAAACCTCCCTATG
8858 AAATTTTGATAA
1 AAATTTTGATAA
8870 CCAAACTATA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
22 16 0.53
23 3 0.10
25 4 0.13
26 7 0.23
ACGTcount: A:0.35, C:0.17, G:0.07, T:0.42
Consensus pattern (23 bp):
AAATTTTGATAAACCTCCCTATG
Found at i:8858 original size:22 final size:21
Alignment explanation
Indices: 8830--8980 Score: 86
Period size: 22 Copynumber: 6.9 Consensus size: 21
8820 AAATTCCCTC
8830 CCTATGAAATTTTATTAACCTT
1 CCTATGAAATTTTA-TAACCTT
**
8852 CCTATGAAATTTTGATAACCAA
1 CCTATGAAATTTT-ATAACCTT
* * * *
8874 ACTATAAAATTTCGATAACTTT
1 CCTATGAAATTT-TATAACCTT
* * *
8896 CGTATAAAATTTTGTTAACCTT
1 CCTATGAAATTTT-ATAACCTT
* *
8918 CCTAGGAAATTTTAATAATCTT
1 CCTATGAAATTTT-ATAACCTT
** **
8940 TTTATGAAAATTTGGTAACCTT
1 CCTATG-AAATTTTATAACCTT
**
8962 TGTATGAAATTTTGATAAC
1 CCTATGAAATTTT-ATAAC
8981 TACACAATGA
Statistics
Matches: 96, Mismatches: 28, Indels: 10
0.72 0.21 0.07
Matches are distributed among these distances:
21 6 0.06
22 83 0.86
23 7 0.07
ACGTcount: A:0.36, C:0.13, G:0.09, T:0.42
Consensus pattern (21 bp):
CCTATGAAATTTTATAACCTT
Found at i:8928 original size:44 final size:43
Alignment explanation
Indices: 8880--8981 Score: 107
Period size: 44 Copynumber: 2.3 Consensus size: 43
8870 CCAAACTATA
* *
8880 AAATTTCGATAACTTTCGTAT-AAAATTTTGTTAACCTTCCTAGG
1 AAATTTTGATAACTTT-GTATGAAAA-TTTGGTAACCTTCCTAGG
* * ** *
8924 AAATTTTAATAATCTTTTTATGAAAATTTGGTAACCTTTGTATG
1 AAATTTTGATAA-CTTTGTATGAAAATTTGGTAACCTTCCTAGG
8968 AAATTTTGATAACT
1 AAATTTTGATAACT
8982 ACACAATGAA
Statistics
Matches: 48, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
43 2 0.04
44 38 0.79
45 8 0.17
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.44
Consensus pattern (43 bp):
AAATTTTGATAACTTTGTATGAAAATTTGGTAACCTTCCTAGG
Found at i:8990 original size:22 final size:22
Alignment explanation
Indices: 8964--9046 Score: 87
Period size: 22 Copynumber: 3.8 Consensus size: 22
8954 GTAACCTTTG
8964 TATGAAATTTTGATAACTACAC
1 TATGAAATTTTGATAACTACAC
* * * *
8986 AATGAAGTTTTGATAATTTTCA-
1 TATGAAATTTTGATAA-CTACAC
* * *
9008 TATGAAATTTTGGTGACAACAC
1 TATGAAATTTTGATAACTACAC
9030 TATGAAATTTTGATAAC
1 TATGAAATTTTGATAAC
9047 CTTCTCATGT
Statistics
Matches: 46, Mismatches: 13, Indels: 4
0.73 0.21 0.06
Matches are distributed among these distances:
21 2 0.04
22 41 0.89
23 3 0.07
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.39
Consensus pattern (22 bp):
TATGAAATTTTGATAACTACAC
Found at i:9061 original size:44 final size:43
Alignment explanation
Indices: 8942--9065 Score: 122
Period size: 44 Copynumber: 2.8 Consensus size: 43
8932 ATAATCTTTT
* * * * *
8942 TATGAAAATTTGGTAACCTTTGTATGAAATTTTGATAACTACAC
1 TATGAAATTTTGATAACC-TTCTATGAAATTTTGGTAACAACAC
* * ** *
8986 AATGAAGTTTTGATAATTTTCATATGAAATTTTGGTGACAACAC
1 TATGAAATTTTGATAACCTTC-TATGAAATTTTGGTAACAACAC
*
9030 TATGAAATTTTGATAACCTTCTCATGTAATTTTGGT
1 TATGAAATTTTGATAACCTTCT-ATGAAATTTTGGT
9066 TTGATTGTCA
Statistics
Matches: 63, Mismatches: 15, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
43 3 0.05
44 60 0.95
ACGTcount: A:0.34, C:0.10, G:0.15, T:0.41
Consensus pattern (43 bp):
TATGAAATTTTGATAACCTTCTATGAAATTTTGGTAACAACAC
Found at i:9313 original size:30 final size:29
Alignment explanation
Indices: 9251--9313 Score: 83
Period size: 29 Copynumber: 2.1 Consensus size: 29
9241 CGTTAATGGT
* *
9251 CAAATAAGCTCATGAACTTCAATTTGGAC
1 CAAATAAGCCCATGAACTCCAATTTGGAC
9280 CAAATAAGCCCATGAACTACCAATTTTGG-C
1 CAAATAAGCCCATGAACT-CCAA-TTTGGAC
9310 CAAA
1 CAAA
9314 ATTACCCTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
29 17 0.57
30 8 0.27
31 5 0.17
ACGTcount: A:0.40, C:0.24, G:0.13, T:0.24
Consensus pattern (29 bp):
CAAATAAGCCCATGAACTCCAATTTGGAC
Found at i:12591 original size:22 final size:22
Alignment explanation
Indices: 12544--12604 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 22
12534 TTGAATATTT
* *
12544 TTATGAAATTTTGATAACTACC
1 TTATGGAATTTTGATAACCACC
* *
12566 TTAT-TACATTTTGATAACCACG
1 TTATGGA-ATTTTGATAACCACC
12588 TTATGGAATTTTGATAA
1 TTATGGAATTTTGATAA
12605 TTTACCTATG
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
21 1 0.03
22 31 0.94
23 1 0.03
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.43
Consensus pattern (22 bp):
TTATGGAATTTTGATAACCACC
Found at i:12644 original size:22 final size:23
Alignment explanation
Indices: 12618--12669 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
12608 ACCTATGAAA
*
12618 TATGAAACTTTGAT-AACCTAAC
1 TATGAAACTTTAATAAACCTAAC
* **
12640 TATGAAATTTTAATAAACCTTCC
1 TATGAAACTTTAATAAACCTAAC
12663 TATGAAA
1 TATGAAA
12670 TTCTGTAACC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
22 12 0.48
23 13 0.52
ACGTcount: A:0.42, C:0.15, G:0.08, T:0.35
Consensus pattern (23 bp):
TATGAAACTTTAATAAACCTAAC
Found at i:12665 original size:23 final size:21
Alignment explanation
Indices: 12630--12701 Score: 65
Period size: 21 Copynumber: 3.4 Consensus size: 21
12620 TGAAACTTTG
** *
12630 ATAACCTAACTATGAAATTTT
1 ATAACCTTCCTATGAAATTCT
12651 AATAAACCTTCCTATGAAATTCT
1 -AT-AACCTTCCTATGAAATTCT
* * *
12674 GTAACCTTCCTAAGAAATT-A
1 ATAACCTTCCTATGAAATTCT
12694 ATAACCTT
1 ATAACCTT
12702 TCTGTGAGAT
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
20 7 0.17
21 16 0.38
22 3 0.07
23 16 0.38
ACGTcount: A:0.40, C:0.19, G:0.06, T:0.35
Consensus pattern (21 bp):
ATAACCTTCCTATGAAATTCT
Found at i:13524 original size:16 final size:16
Alignment explanation
Indices: 13502--13533 Score: 55
Period size: 16 Copynumber: 1.9 Consensus size: 16
13492 GTGACTAGGA
13502 AAAAAAAGAAGAAAAAG
1 AAAAAAA-AAGAAAAAG
13519 AAAAAAAAAGAAAAA
1 AAAAAAAAAGAAAAA
13534 AAGAAAGCCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAGAAAAAG
Found at i:13525 original size:19 final size:18
Alignment explanation
Indices: 13501--13539 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 18
13491 GGTGACTAGG
13501 AAAAAAAAGAAGAAAAAGA
1 AAAAAAAAGAA-AAAAAGA
13520 AAAAAAAAGAAAAAAAGA
1 AAAAAAAAGAAAAAAAGA
13538 AA
1 AA
13540 GCCATTGGGC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (18 bp):
AAAAAAAAGAAAAAAAGA
Found at i:13526 original size:10 final size:10
Alignment explanation
Indices: 13501--13535 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
13491 GGTGACTAGG
13501 AAAAAAAAG-
1 AAAAAAAAGA
*
13510 AAGAAAAAGA
1 AAAAAAAAGA
13520 AAAAAAAAGA
1 AAAAAAAAGA
13530 AAAAAA
1 AAAAAA
13536 GAAAGCCATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 8 0.35
10 15 0.65
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (10 bp):
AAAAAAAAGA
Found at i:13715 original size:18 final size:18
Alignment explanation
Indices: 13674--13716 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
13664 CCAAATGTTG
*
13674 GAAAAGAAAAGAAAAATAA
1 GAAAA-AAAAGAAAAAGAA
* *
13693 AAAAAAAAAGAAATAGAA
1 GAAAAAAAAGAAAAAGAA
13711 GAAAAA
1 GAAAAA
13717 GAATAAGGAA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.81, C:0.00, G:0.14, T:0.05
Consensus pattern (18 bp):
GAAAAAAAAGAAAAAGAA
Found at i:13729 original size:13 final size:13
Alignment explanation
Indices: 13681--13736 Score: 60
Period size: 13 Copynumber: 4.2 Consensus size: 13
13671 TTGGAAAAGA
*
13681 AAAGAAAAATAA-
1 AAAGAAAAAGAAT
*
13693 AAAAAAAAAGAAAT
1 AAAGAAAAAG-AAT
13707 AGAAGAAAAAGAAT
1 A-AAGAAAAAGAAT
*
13721 AAGGAAAAAGAAT
1 AAAGAAAAAGAAT
13734 AAA
1 AAA
13737 ATATATATAT
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
12 8 0.22
13 15 0.42
14 5 0.14
15 8 0.22
ACGTcount: A:0.79, C:0.00, G:0.14, T:0.07
Consensus pattern (13 bp):
AAAGAAAAAGAAT
Found at i:14728 original size:27 final size:27
Alignment explanation
Indices: 14661--14728 Score: 75
Period size: 27 Copynumber: 2.5 Consensus size: 27
14651 TTAAGATGTC
* * *
14661 AAAATTACTGTTTTGCCCTTGGTTGGCT
1 AAAATTAC-GTTTTACCCCTGGTTGACT
*
14689 AAAATTACCTTTTACCCCTGGTTGACT
1 AAAATTACGTTTTACCCCTGGTTGACT
14716 -AAATTACAGTTTT
1 AAAATTAC-GTTTT
14729 GCTCTTAAAC
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
26 7 0.21
27 19 0.56
28 8 0.24
ACGTcount: A:0.25, C:0.19, G:0.15, T:0.41
Consensus pattern (27 bp):
AAAATTACGTTTTACCCCTGGTTGACT
Found at i:15132 original size:13 final size:12
Alignment explanation
Indices: 15114--15158 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 12
15104 ATTTTATTAC
15114 TGTTTTACTAAAT
1 TGTTTTA-TAAAT
15127 TGTTTTATAAAT
1 TGTTTTATAAAT
*
15139 GGTTTTAAATAAAT
1 TGTTTT--ATAAAT
15153 TGTTTT
1 TGTTTT
15159 GGGTGCATGA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
12 10 0.36
13 7 0.25
14 11 0.39
ACGTcount: A:0.31, C:0.02, G:0.11, T:0.56
Consensus pattern (12 bp):
TGTTTTATAAAT
Found at i:20578 original size:74 final size:73
Alignment explanation
Indices: 20436--20584 Score: 262
Period size: 74 Copynumber: 2.0 Consensus size: 73
20426 GTTTTGTATT
* *
20436 ATCCAGTTCAGTCCTAGAGAATGTGCAAATACATGGCTTCCAACGTATTATACAGTATATACAGA
1 ATCCAGTTCAATCCTAGAGAATGTGCAAATACATAGCTTCCAACGTATTATACAGTATATACAGA
20501 TATGCACG
66 TATGCACG
*
20509 ATCCAGTTCAATCCTAGAGAATGTGCAAATACATTAGCTTCCAACGTATTATATAGTATATACAG
1 ATCCAGTTCAATCCTAGAGAATGTGCAAATACA-TAGCTTCCAACGTATTATACAGTATATACAG
20574 ATATGCACG
65 ATATGCACG
20583 AT
1 AT
20585 TGAATGTGCG
Statistics
Matches: 72, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
73 32 0.44
74 40 0.56
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.29
Consensus pattern (73 bp):
ATCCAGTTCAATCCTAGAGAATGTGCAAATACATAGCTTCCAACGTATTATACAGTATATACAGA
TATGCACG
Found at i:20706 original size:17 final size:17
Alignment explanation
Indices: 20684--20718 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
20674 AAAGCAAACA
20684 AATCTCTAATTTCAACT
1 AATCTCTAATTTCAACT
20701 AATCTCTAATTTCAACT
1 AATCTCTAATTTCAACT
20718 A
1 A
20719 TAACTACCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.37, C:0.23, G:0.00, T:0.40
Consensus pattern (17 bp):
AATCTCTAATTTCAACT
Found at i:23078 original size:65 final size:64
Alignment explanation
Indices: 22974--23104 Score: 253
Period size: 65 Copynumber: 2.0 Consensus size: 64
22964 TCATTTCTGC
22974 GTATTCTGCCGACAACAGATTCCAAAAGATAGAACCAGCATACTTGCCATGACTAAATTCCAAAA
1 GTATTCTGCCGACAACAGATTCCAAAAGATAGAACCAGCATACTTG-CATGACTAAATTCCAAAA
23039 GTATTCTGCCGACAACAGATTCCAAAAGATAGAACCAGCATACTTGCATGACTAAATTCCAAAA
1 GTATTCTGCCGACAACAGATTCCAAAAGATAGAACCAGCATACTTGCATGACTAAATTCCAAAA
23103 GT
1 GT
23105 TGAAGGTCAA
Statistics
Matches: 66, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
64 20 0.30
65 46 0.70
ACGTcount: A:0.40, C:0.24, G:0.15, T:0.22
Consensus pattern (64 bp):
GTATTCTGCCGACAACAGATTCCAAAAGATAGAACCAGCATACTTGCATGACTAAATTCCAAAA
Found at i:28584 original size:33 final size:33
Alignment explanation
Indices: 28542--28609 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
28532 ACACATTTTT
*
28542 TAGGGTATACTTTTTTAATATTAAATAAATTCA
1 TAGGGTATACTTTTTTAATATCAAATAAATTCA
28575 TAGGGTATACTTTTTTAATATCAAATAAATTCA
1 TAGGGTATACTTTTTTAATATCAAATAAATTCA
28608 TA
1 TA
28610 ATTTAATTTA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.40, C:0.07, G:0.09, T:0.44
Consensus pattern (33 bp):
TAGGGTATACTTTTTTAATATCAAATAAATTCA
Found at i:29360 original size:28 final size:28
Alignment explanation
Indices: 29329--29405 Score: 111
Period size: 28 Copynumber: 2.8 Consensus size: 28
29319 TTAGGATCAA
*
29329 CTAGGGGCATTTCAGTCATTTTCAAAAT
1 CTAGGGGCATTTTAGTCATTTTCAAAAT
* * *
29357 CTAGGGGCATTTTAGTCATTTGCACATT
1 CTAGGGGCATTTTAGTCATTTTCAAAAT
29385 C-AGGGGCATTTTAGTCATTTT
1 CTAGGGGCATTTTAGTCATTTT
29406 AAGTTCAGGG
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
27 19 0.43
28 25 0.57
ACGTcount: A:0.23, C:0.17, G:0.21, T:0.39
Consensus pattern (28 bp):
CTAGGGGCATTTTAGTCATTTTCAAAAT
Found at i:29427 original size:26 final size:26
Alignment explanation
Indices: 29383--29435 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
29373 CATTTGCACA
**
29383 TTCAGGGGCATTTTAGTCATTTTAAG
1 TTCAGGGGCACGTTAGTCATTTTAAG
*
29409 TTCAGGGGCACGTTGGTCATTTTAAG
1 TTCAGGGGCACGTTAGTCATTTTAAG
29435 T
1 T
29436 CCACTTTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.21, C:0.13, G:0.26, T:0.40
Consensus pattern (26 bp):
TTCAGGGGCACGTTAGTCATTTTAAG
Found at i:40480 original size:77 final size:77
Alignment explanation
Indices: 40353--40559 Score: 308
Period size: 77 Copynumber: 2.7 Consensus size: 77
40343 CCCATGAGGC
* *
40353 CATATGCCGTATCACGACAACCAAAGTATCACATGGCTACAAAGGTCTCCACCGCCACGTAATGG
1 CATATGCCGTTTCACGGCAACCAAAGTATCACATGGCTACAAAGGTCTCCACCGCCACGTAATGG
40418 CATAAAAACCTT
66 CATAAAAACCTT
40430 CATATGCCGTTTCACGGCAACCAAAGTATCACATGGCTACAAAGGTCTCCACCGCCACGTAATGG
1 CATATGCCGTTTCACGGCAACCAAAGTATCACATGGCTACAAAGGTCTCCACCGCCACGTAATGG
** *
40495 CATAAGGATCTT
66 CATAAAAACCTT
* ** * *
40507 CATATGCCGTATT-ACAGCAACCAAAACATCATATGGCTACAAAGCTCTCCACC
1 CATATGCCGT-TTCACGGCAACCAAAGTATCACATGGCTACAAAGGTCTCCACC
40560 ACCATGTTGC
Statistics
Matches: 119, Mismatches: 10, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
77 117 0.98
78 2 0.02
ACGTcount: A:0.33, C:0.30, G:0.16, T:0.21
Consensus pattern (77 bp):
CATATGCCGTTTCACGGCAACCAAAGTATCACATGGCTACAAAGGTCTCCACCGCCACGTAATGG
CATAAAAACCTT
Found at i:41659 original size:37 final size:37
Alignment explanation
Indices: 41616--41778 Score: 209
Period size: 37 Copynumber: 4.3 Consensus size: 37
41606 TGCGATAGCA
*
41616 CTCTTTACCGCAGAGCTCTCCTTACCGTGGTAGCACC
1 CTCTTTACCGCAGAGCTCTCCTTACCGCGGTAGCACC
*
41653 CTCTTTACTGCAGAGCTCTCCTTACCGCGGTAGCACC
1 CTCTTTACCGCAGAGCTCTCCTTACCGCGGTAGCACC
* * *
41690 CTCTCTACCGCAGAGCTCCCCTTACTGCGGTAGCACC
1 CTCTTTACCGCAGAGCTCTCCTTACCGCGGTAGCACC
* * ** *
41727 CTCTTTACCGCGACAACACTCTCCTCGCTGCGGTAGCACC
1 CTCTTTACCGC-A-GA-GCTCTCCTTACCGCGGTAGCACC
41767 CTCTTTACCGCA
1 CTCTTTACCGCA
41779 CAACTCCTCT
Statistics
Matches: 111, Mismatches: 12, Indels: 4
0.87 0.09 0.03
Matches are distributed among these distances:
37 78 0.70
38 1 0.01
39 2 0.02
40 30 0.27
ACGTcount: A:0.17, C:0.40, G:0.18, T:0.25
Consensus pattern (37 bp):
CTCTTTACCGCAGAGCTCTCCTTACCGCGGTAGCACC
Found at i:41700 original size:20 final size:20
Alignment explanation
Indices: 41675--41777 Score: 72
Period size: 20 Copynumber: 5.3 Consensus size: 20
41665 GAGCTCTCCT
41675 TACCGCGGTAGCACCCTCTC
1 TACCGCGGTAGCACCCTCTC
* *
41695 TACCGCAG-AGCTCCC-CT-
1 TACCGCGGTAGCACCCTCTC
* *
41712 TACTGCGGTAGCACCCTCTT
1 TACCGCGGTAGCACCCTCTC
** * *
41732 TACCGCGACAACACTCTC-C
1 TACCGCGGTAGCACCCTCTC
*
41751 T-CGCTGCGGTAGCACCCTCTT
1 TAC-C-GCGGTAGCACCCTCTC
41772 TACCGC
1 TACCGC
41778 ACAACTCCTC
Statistics
Matches: 60, Mismatches: 16, Indels: 14
0.67 0.18 0.16
Matches are distributed among these distances:
17 6 0.10
18 9 0.15
19 10 0.17
20 32 0.53
21 2 0.03
22 1 0.02
ACGTcount: A:0.17, C:0.43, G:0.18, T:0.22
Consensus pattern (20 bp):
TACCGCGGTAGCACCCTCTC
Found at i:42579 original size:75 final size:75
Alignment explanation
Indices: 42456--42596 Score: 237
Period size: 75 Copynumber: 1.9 Consensus size: 75
42446 ACAGCTGTGG
* * * *
42456 AGATTTGCGGCAGTAGGTAGTGGGAGCCACGACACCTTATTAAGAAAAAAAACAAAGAATGGCTT
1 AGATTTGCGGCAGTAGGTAGCGGAAGCCACGACACATTATTAAAAAAAAAAACAAAGAATGGCTT
42521 ACAACAACGA
66 ACAACAACGA
*
42531 AGATTTGCGGCAGTAGGTAGCGGAAGTCACGACACATTATTAAAAAAAAAAACAAAGAATGGCTT
1 AGATTTGCGGCAGTAGGTAGCGGAAGCCACGACACATTATTAAAAAAAAAAACAAAGAATGGCTT
42596 A
66 A
42597 GAGATTTGCG
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
75 61 1.00
ACGTcount: A:0.43, C:0.16, G:0.23, T:0.18
Consensus pattern (75 bp):
AGATTTGCGGCAGTAGGTAGCGGAAGCCACGACACATTATTAAAAAAAAAAACAAAGAATGGCTT
ACAACAACGA
Found at i:42680 original size:16 final size:16
Alignment explanation
Indices: 42637--42696 Score: 74
Period size: 16 Copynumber: 4.0 Consensus size: 16
42627 TGGAGATTTG
42637 CGACATAAGTGAGCTA
1 CGACATAAGTGAGCTA
*
42653 CTAC---AG-GAGCTA
1 CGACATAAGTGAGCTA
42665 CGACATAAGTGAGCTA
1 CGACATAAGTGAGCTA
*
42681 CAACATAAGTGAGCTA
1 CGACATAAGTGAGCTA
42697 TGGCAAACAA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
12 9 0.24
13 2 0.05
15 2 0.05
16 24 0.65
ACGTcount: A:0.38, C:0.20, G:0.23, T:0.18
Consensus pattern (16 bp):
CGACATAAGTGAGCTA
Found at i:42738 original size:16 final size:16
Alignment explanation
Indices: 42716--42978 Score: 152
Period size: 16 Copynumber: 16.1 Consensus size: 16
42706 ATAGATTACG
42716 GCACCCAAGCAATGCC
1 GCACCCAAGCAATGCC
* *
42732 ACACCCAAGTAAATGCC
1 GCACCCAAG-CAATGCC
42749 GCACCCAAGCAATGCC
1 GCACCCAAGCAATGCC
*
42765 ACACCCAAGCGAATGCC
1 GCACCCAAGC-AATGCC
**
42782 GTGCCCGAA--AGATGCC
1 GCACCC-AAGCA-ATGCC
* * *
42798 ACACCCAAGTAAATGCT
1 GCACCCAAG-CAATGCC
* *
42815 GCGCCCAAGCAATGAC
1 GCACCCAAGCAATGCC
* * **
42831 ACACCTAAGCAATTTC
1 GCACCCAAGCAATGCC
* **
42847 TCACCCAAGCGGTGCC
1 GCACCCAAGCAATGCC
* *
42863 GTATCCAAGCAATGCC
1 GCACCCAAGCAATGCC
*
42879 GCACCCAAGCGATGCC
1 GCACCCAAGCAATGCC
* *
42895 GCACCCAAGTAAATGTC
1 GCACCCAAG-CAATGCC
* ** *
42912 GCGCCCAAGTGATACC
1 GCACCCAAGCAATGCC
* *
42928 GCACCCAAGCGATGTC
1 GCACCCAAGCAATGCC
* * **
42944 GCGCCCAAGCGATGTT
1 GCACCCAAGCAATGCC
*
42960 GCACCCAAGTAAATGCC
1 GCACCCAAG-CAATGCC
42977 GC
1 GC
42979 GCCCTAGTGA
Statistics
Matches: 183, Mismatches: 55, Indels: 17
0.72 0.22 0.07
Matches are distributed among these distances:
15 3 0.02
16 126 0.69
17 51 0.28
18 3 0.02
ACGTcount: A:0.30, C:0.37, G:0.21, T:0.13
Consensus pattern (16 bp):
GCACCCAAGCAATGCC
Found at i:42758 original size:33 final size:33
Alignment explanation
Indices: 42719--43023 Score: 199
Period size: 33 Copynumber: 9.3 Consensus size: 33
42709 GATTACGGCA
* *
42719 CCCAAGCAATGCCACACCCAAGTAAATGCCGCA
1 CCCAAGCAATGCCGCACCCAAGTAAATGCCGCG
* ** *
42752 CCCAAGCAATGCCACACCCAAGCGAATGCCGTG
1 CCCAAGCAATGCCGCACCCAAGTAAATGCCGCG
* *
42785 CCCGAA--AGATGCCACACCCAAGTAAATGCTGCG
1 CCC-AAGCA-ATGCCGCACCCAAGTAAATGCCGCG
* * * * ** * *
42818 CCCAAGCAATGACACACCTAAG-CAATTTCTCA
1 CCCAAGCAATGCCGCACCCAAGTAAATGCCGCG
** * * * *
42850 CCCAAGCGGTGCCGTATCCAAG-CAATGCCGCA
1 CCCAAGCAATGCCGCACCCAAGTAAATGCCGCG
* *
42882 CCCAAGCGATGCCGCACCCAAGTAAATGTCGCG
1 CCCAAGCAATGCCGCACCCAAGTAAATGCCGCG
** * ** *
42915 CCCAAGTGATACCGCACCCAAG-CGATGTCGCG
1 CCCAAGCAATGCCGCACCCAAGTAAATGCCGCG
* **
42947 CCCAAGCGATGTTGCACCCAAGTAAATGCCGCG
1 CCCAAGCAATGCCGCACCCAAGTAAATGCCGCG
* ** * *
42980 CCCTAGTGATGTCGCACCCTAGTAAATGCCGCTG
1 CCCAAGCAATGCCGCACCCAAGTAAATGCCGC-G
43014 -CCAAGCAATG
1 CCCAAGCAATG
43024 AAGAGACGCC
Statistics
Matches: 215, Mismatches: 50, Indels: 14
0.77 0.18 0.05
Matches are distributed among these distances:
32 74 0.34
33 137 0.64
34 4 0.02
ACGTcount: A:0.30, C:0.36, G:0.21, T:0.14
Consensus pattern (33 bp):
CCCAAGCAATGCCGCACCCAAGTAAATGCCGCG
Found at i:42937 original size:65 final size:65
Alignment explanation
Indices: 42867--42998 Score: 183
Period size: 65 Copynumber: 2.0 Consensus size: 65
42857 GGTGCCGTAT
*
42867 CCAAGCAATGCCGCACCCAAGCGATGCCGCACCCAAGTAAATGTCGCGCCCAAGTGATACCGCAC
1 CCAAGCAATGCCGCACCCAAGCGATGCCGCACCCAAGTAAATGCCGCGCCCAAGTGATACCGCAC
* * * ** * **
42932 CCAAGCGATGTCGCGCCCAAGCGATGTTGCACCCAAGTAAATGCCGCGCCCTAGTGATGTCGCAC
1 CCAAGCAATGCCGCACCCAAGCGATGCCGCACCCAAGTAAATGCCGCGCCCAAGTGATACCGCAC
42997 CC
1 CC
42999 TAGTAAATGC
Statistics
Matches: 58, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
65 58 1.00
ACGTcount: A:0.26, C:0.37, G:0.23, T:0.14
Consensus pattern (65 bp):
CCAAGCAATGCCGCACCCAAGCGATGCCGCACCCAAGTAAATGCCGCGCCCAAGTGATACCGCAC
Found at i:43002 original size:16 final size:16
Alignment explanation
Indices: 42878--42998 Score: 98
Period size: 16 Copynumber: 7.4 Consensus size: 16
42868 CAAGCAATGC
* *
42878 CGCACCCAAGCGATGC
1 CGCACCCAAGTGATGT
*
42894 CGCACCCAAGTAAATGT
1 CGCACCCAAGT-GATGT
* **
42911 CGCGCCCAAGTGATAC
1 CGCACCCAAGTGATGT
*
42927 CGCACCCAAGCGATGT
1 CGCACCCAAGTGATGT
* *
42943 CGCGCCCAAGCGATGT
1 CGCACCCAAGTGATGT
* * *
42959 TGCACCCAAGTAAATGC
1 CGCACCCAAGT-GATGT
* *
42976 CGCGCCCTAGTGATGT
1 CGCACCCAAGTGATGT
42992 CGCACCC
1 CGCACCC
42999 TAGTAAATGC
Statistics
Matches: 80, Mismatches: 23, Indels: 4
0.75 0.21 0.04
Matches are distributed among these distances:
16 56 0.70
17 24 0.30
ACGTcount: A:0.25, C:0.37, G:0.24, T:0.14
Consensus pattern (16 bp):
CGCACCCAAGTGATGT
Found at i:43050 original size:24 final size:24
Alignment explanation
Indices: 43014--43099 Score: 82
Period size: 24 Copynumber: 3.6 Consensus size: 24
43004 AATGCCGCTG
* *
43014 CCAAGCAATGAAGAGACGCCACAC
1 CCAAGCAAGGAAGAGATGCCACAC
* **** *
43038 CCAAGCAAGGAAGAAATGATGTAG
1 CCAAGCAAGGAAGAGATGCCACAC
* *
43062 TCAAGCAATGAAGAGATGCCACAC
1 CCAAGCAAGGAAGAGATGCCACAC
43086 CCAAGCAAGGAAGA
1 CCAAGCAAGGAAGA
43100 AATGATGTAG
Statistics
Matches: 44, Mismatches: 18, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
24 44 1.00
ACGTcount: A:0.44, C:0.23, G:0.24, T:0.08
Consensus pattern (24 bp):
CCAAGCAAGGAAGAGATGCCACAC
Found at i:43067 original size:48 final size:48
Alignment explanation
Indices: 43013--43118 Score: 194
Period size: 48 Copynumber: 2.2 Consensus size: 48
43003 AAATGCCGCT
43013 GCCAAGCAATGAAGAGACGCCACACCCAAGCAAGGAAGAAATGATGTA
1 GCCAAGCAATGAAGAGACGCCACACCCAAGCAAGGAAGAAATGATGTA
* *
43061 GTCAAGCAATGAAGAGATGCCACACCCAAGCAAGGAAGAAATGATGTA
1 GCCAAGCAATGAAGAGACGCCACACCCAAGCAAGGAAGAAATGATGTA
43109 GCCAAGCAAT
1 GCCAAGCAAT
43119 CATGAAATGT
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
48 55 1.00
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (48 bp):
GCCAAGCAATGAAGAGACGCCACACCCAAGCAAGGAAGAAATGATGTA
Found at i:43113 original size:24 final size:24
Alignment explanation
Indices: 43038--43117 Score: 88
Period size: 24 Copynumber: 3.3 Consensus size: 24
43028 GACGCCACAC
43038 CCAAGCAAGGAAGAAATGATGTAG
1 CCAAGCAAGGAAGAAATGATGTAG
* * * **** *
43062 TCAAGCAATGAAGAGATGCCACAC
1 CCAAGCAAGGAAGAAATGATGTAG
43086 CCAAGCAAGGAAGAAATGATGTAG
1 CCAAGCAAGGAAGAAATGATGTAG
43110 CCAAGCAA
1 CCAAGCAA
43118 TCATGAAATG
Statistics
Matches: 40, Mismatches: 16, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.45, C:0.19, G:0.25, T:0.11
Consensus pattern (24 bp):
CCAAGCAAGGAAGAAATGATGTAG
Found at i:43333 original size:50 final size:50
Alignment explanation
Indices: 43274--43405 Score: 131
Period size: 50 Copynumber: 2.6 Consensus size: 50
43264 TGAGATGCGG
* * * *
43274 CATCAGAAGTTTGTGACATAAGACATGAGATGCGGCGTCAAACATTACGA
1 CATCAGAAGTCTATGACATAAGACATGAGATACAGCGTCAAACATTACGA
* * * * * *
43324 CATCAGAAGTCTATGGCATATGGCATGAGATACAGCGTCAGACATTATGG
1 CATCAGAAGTCTATGACATAAGACATGAGATACAGCGTCAAACATTACGA
* * *
43374 CATCAGACACT-TATGGCGTAAGACATGAGATA
1 CATCAGA-AGTCTATGACATAAGACATGAGATA
43406 TGGCATAAGA
Statistics
Matches: 67, Mismatches: 14, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
50 65 0.97
51 2 0.03
ACGTcount: A:0.35, C:0.18, G:0.24, T:0.23
Consensus pattern (50 bp):
CATCAGAAGTCTATGACATAAGACATGAGATACAGCGTCAAACATTACGA
Found at i:43389 original size:16 final size:15
Alignment explanation
Indices: 43363--43450 Score: 86
Period size: 16 Copynumber: 5.4 Consensus size: 15
43353 ATACAGCGTC
*
43363 AGACATTATGGCATC
1 AGACATTATGGCATA
*
43378 AGACACTTATGGCGTA
1 AGACA-TTATGGCATA
43394 AGACATGAGATATGGCATA
1 AGACAT----TATGGCATA
*
43413 AGATACTTATGGCATA
1 AGACA-TTATGGCATA
43429 AGACATTTATGGCATA
1 AGACA-TTATGGCATA
43445 AGACAT
1 AGACAT
43451 GAGATGCGAC
Statistics
Matches: 61, Mismatches: 6, Indels: 12
0.77 0.08 0.15
Matches are distributed among these distances:
15 7 0.11
16 41 0.67
19 12 0.20
20 1 0.02
ACGTcount: A:0.38, C:0.15, G:0.22, T:0.26
Consensus pattern (15 bp):
AGACATTATGGCATA
Found at i:43439 original size:51 final size:51
Alignment explanation
Indices: 43368--43539 Score: 191
Period size: 51 Copynumber: 3.3 Consensus size: 51
43358 GCGTCAGACA
* * **
43368 TTATGGCATCAGACACTTATGGCGTAAGACATGAGATATGGCATAAGATAC
1 TTATGGCATAAGACATTTATGGCGTAAGACATGAGATGCGGCATAAGATAC
* * * *
43419 TTATGGCATAAGACATTTATGGCATAAGACATGAGATGCGACATCAGACAC
1 TTATGGCATAAGACATTTATGGCGTAAGACATGAGATGCGGCATAAGATAC
* ** * * *
43470 TTATGGCACAAGACATGAGATGCGGCGTAAGACATGCGATGCAGCATAAGATAT
1 TTATGGCATAAGACAT-TTAT--GGCGTAAGACATGAGATGCGGCATAAGATAC
43524 TTATGGCATAAGACAT
1 TTATGGCATAAGACAT
43540 GAGATGCAAC
Statistics
Matches: 99, Mismatches: 19, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
51 58 0.59
52 2 0.02
54 39 0.39
ACGTcount: A:0.36, C:0.16, G:0.24, T:0.24
Consensus pattern (51 bp):
TTATGGCATAAGACATTTATGGCGTAAGACATGAGATGCGGCATAAGATAC
Found at i:43503 original size:35 final size:35
Alignment explanation
Indices: 43425--43503 Score: 113
Period size: 35 Copynumber: 2.3 Consensus size: 35
43415 ATACTTATGG
* *
43425 CATAAGACATTTATGGCATAAGACATGAGATGCGA
1 CATAAGACACTTATGGCACAAGACATGAGATGCGA
* *
43460 CATCAGACACTTATGGCACAAGACATGAGATGCGG
1 CATAAGACACTTATGGCACAAGACATGAGATGCGA
*
43495 CGTAAGACA
1 CATAAGACA
43504 TGCGATGCAG
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.38, C:0.19, G:0.24, T:0.19
Consensus pattern (35 bp):
CATAAGACACTTATGGCACAAGACATGAGATGCGA
Found at i:43519 original size:19 final size:19
Alignment explanation
Indices: 43479--43547 Score: 63
Period size: 19 Copynumber: 3.8 Consensus size: 19
43469 CTTATGGCAC
* *
43479 AAGACATGAGATGCGGCGT
1 AAGACATGAGATGCAGCAT
*
43498 AAGACATGCGATGCAGCAT
1 AAGACATGAGATGCAGCAT
* **
43517 AAGATAT-TTATG--GCAT
1 AAGACATGAGATGCAGCAT
43533 AAGACATGAGATGCA
1 AAGACATGAGATGCA
43548 ACACCAGATA
Statistics
Matches: 38, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
16 10 0.26
17 3 0.08
18 3 0.08
19 22 0.58
ACGTcount: A:0.38, C:0.14, G:0.28, T:0.20
Consensus pattern (19 bp):
AAGACATGAGATGCAGCAT
Found at i:43536 original size:35 final size:35
Alignment explanation
Indices: 43497--43685 Score: 159
Period size: 35 Copynumber: 5.4 Consensus size: 35
43487 AGATGCGGCG
*
43497 TAAGACATGCGATGCAGCATAAGATATTTATGGCA
1 TAAGACATGAGATGCAGCATAAGATATTTATGGCA
* ** *
43532 TAAGACATGAGATGCAACACCAGATATTTATGGCG
1 TAAGACATGAGATGCAGCATAAGATATTTATGGCA
* *
43567 TAAGACATGAGATGC-GACATTAGACATTTATGGCA
1 TAAGACATGAGATGCAG-CATAAGATATTTATGGCA
* * * *** * * *
43602 TCAGACATTAAATATGGCACAAGACATTTATGCCA
1 TAAGACATGAGATGCAGCATAAGATATTTATGGCA
* * * *
43637 TTAGACATGAGATGC-GACAT-AGACATATATGGCG
1 TAAGACATGAGATGCAG-CATAAGATATTTATGGCA
43671 TAAGACATGAGATGC
1 TAAGACATGAGATGC
43686 GGCGCACACA
Statistics
Matches: 123, Mismatches: 28, Indels: 7
0.78 0.18 0.04
Matches are distributed among these distances:
34 26 0.21
35 96 0.78
36 1 0.01
ACGTcount: A:0.38, C:0.16, G:0.22, T:0.24
Consensus pattern (35 bp):
TAAGACATGAGATGCAGCATAAGATATTTATGGCA
Found at i:43609 original size:16 final size:16
Alignment explanation
Indices: 43588--43644 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 16
43578 ATGCGACATT
43588 AGACATTTATGGCATC
1 AGACATTTATGGCATC
43604 AGACATTAAATATGGCA-C
1 AGACATT---TATGGCATC
* *
43622 AAGACATTTATGCCATT
1 -AGACATTTATGGCATC
43639 AGACAT
1 AGACAT
43645 GAGATGCGAC
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
16 19 0.56
18 1 0.03
19 14 0.41
ACGTcount: A:0.39, C:0.18, G:0.16, T:0.28
Consensus pattern (16 bp):
AGACATTTATGGCATC
Found at i:43618 original size:89 final size:86
Alignment explanation
Indices: 43377--43628 Score: 288
Period size: 89 Copynumber: 2.9 Consensus size: 86
43367 ATTATGGCAT
** * *
43377 CAGACACTTATGGCGTAAGACATGAGATATGGCATAAGATACTTATGGCATAAGACATTTATGGC
1 CAGACACTTATGGCGTAAGACATGAGATGCGGCATAAGACATTTATGGCATAAGACATTTATGGC
* *
43442 ATAAGACATGAGATGCGACAT
66 ATAAGACATGAGATGCAACAC
** * ** *
43463 CAGACACTTATGGCACAAGACATGAGATGCGGCGTAAGACATGCGATGCAGCATAAGATATTTAT
1 CAGACACTTATGGCGTAAGACATGAGATGCGGCATAAGACAT-TTATG--GCATAAGACATTTAT
43528 GGCATAAGACATGAGATGCAACAC
63 GGCATAAGACATGAGATGCAACAC
* * * * *
43552 CAGATATTTATGGCGTAAGACATGAGATGCGACATTAGACATTTATGGCATCAGACATTAAATAT
1 CAGACACTTATGGCGTAAGACATGAGATGCGGCATAAGACATTTATGGCATAAGACATT---TAT
*
43617 GGCACAAGACAT
63 GGCATAAGACAT
43629 TTATGCCATT
Statistics
Matches: 136, Mismatches: 24, Indels: 9
0.80 0.14 0.05
Matches are distributed among these distances:
86 45 0.33
87 3 0.02
88 3 0.02
89 85 0.62
ACGTcount: A:0.37, C:0.17, G:0.23, T:0.23
Consensus pattern (86 bp):
CAGACACTTATGGCGTAAGACATGAGATGCGGCATAAGACATTTATGGCATAAGACATTTATGGC
ATAAGACATGAGATGCAACAC
Found at i:43631 original size:70 final size:70
Alignment explanation
Indices: 43493--43680 Score: 200
Period size: 70 Copynumber: 2.7 Consensus size: 70
43483 CATGAGATGC
* * * * * * *
43493 GGCGTAAGACATGCGATGC-AGCATAAGATATTTATGGCATAAGACATGAGATGCAACACCAGAT
1 GGCGTAAGACATGAGATGCGA-CATTAGACATTTATGGCATAAGACATGAAATACAACACAAGAC
43557 ATTTAT
65 ATTTAT
* * ***
43563 GGCGTAAGACATGAGATGCGACATTAGACATTTATGGCATCAGACATTAAATATGGCACAAGACA
1 GGCGTAAGACATGAGATGCGACATTAGACATTTATGGCATAAGACATGAAATACAACACAAGACA
43628 TTTAT
66 TTTAT
* * * * *
43633 GCCATTAGACATGAGATGCGACA-TAGACATATATGGCGTAAGACATGA
1 GGCGTAAGACATGAGATGCGACATTAGACATTTATGGCATAAGACATGA
43681 GATGCGGCGC
Statistics
Matches: 98, Mismatches: 19, Indels: 3
0.82 0.16 0.03
Matches are distributed among these distances:
69 21 0.21
70 76 0.78
71 1 0.01
ACGTcount: A:0.37, C:0.16, G:0.23, T:0.24
Consensus pattern (70 bp):
GGCGTAAGACATGAGATGCGACATTAGACATTTATGGCATAAGACATGAAATACAACACAAGACA
TTTAT
Found at i:44038 original size:27 final size:26
Alignment explanation
Indices: 44008--44095 Score: 104
Period size: 27 Copynumber: 3.3 Consensus size: 26
43998 TAGCCAAAGA
*
44008 TGCCGCAACAACCCAAAATTGCAAAAT
1 TGCCGCAA-AACCAAAAATTGCAAAAT
44035 TGCCGCAAATACCAAAAATTGCAAAAT
1 TGCCGCAAA-ACCAAAAATTGCAAAAT
* * *
44062 TGCCGCAAGTACCTAAAATTGCACAAT
1 TGCCGCAA-AACCAAAAATTGCAAAAT
*
44089 TGTCGCA
1 TGCCGCA
44096 GCTAGCCAAA
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
26 1 0.02
27 53 0.98
ACGTcount: A:0.41, C:0.26, G:0.14, T:0.19
Consensus pattern (26 bp):
TGCCGCAAAACCAAAAATTGCAAAAT
Found at i:44106 original size:27 final size:26
Alignment explanation
Indices: 44022--44107 Score: 100
Period size: 27 Copynumber: 3.2 Consensus size: 26
44012 GCAACAACCC
*
44022 AAAATTGCAAAATTGCCGCAAATACCA
1 AAAATTGCAAAATTGCCGC-AGTACCA
*
44049 AAAATTGCAAAATTGCCGCAAGTACCT
1 AAAATTGCAAAATTGCCGC-AGTACCA
* *
44076 AAAATTGCACAATTGTCGCAGCTAGCCA
1 AAAATTGCAAAATTGCCGCAG-TA-CCA
44104 AAAA
1 AAAA
44108 AAAAACACAG
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
26 2 0.04
27 44 0.85
28 6 0.12
ACGTcount: A:0.44, C:0.22, G:0.14, T:0.20
Consensus pattern (26 bp):
AAAATTGCAAAATTGCCGCAGTACCA
Found at i:46617 original size:77 final size:77
Alignment explanation
Indices: 46508--46713 Score: 297
Period size: 77 Copynumber: 2.7 Consensus size: 77
46498 CCGATGAGGC
46508 CATATGCCGTATCACGG-AACCAAAGTATCACATGGCTACAAAGGTCTCCACCGCCACATAATGG
1 CATATGCCGTATCACGGCAACCAAAGTATCACATGGCTACAAAGGTCTCCACCGCCACATAATGG
*
46572 CATAAAAACCTT
66 CATAAAAACCAT
* *
46584 CATATACCGTATCACGGCAACCAAAGTATCACATGGCTACAAAGGTCTCCACCGCCACGTAATGG
1 CATATGCCGTATCACGGCAACCAAAGTATCACATGGCTACAAAGGTCTCCACCGCCACATAATGG
** *
46649 CATAAGGATCAT
66 CATAAAAACCAT
* * ** * *
46661 CATATGCCGTATTACAGCAACCAAAACATCATATGGCTACAAAGCTCTCCACC
1 CATATGCCGTATCACGGCAACCAAAGTATCACATGGCTACAAAGGTCTCCACC
46714 ACCATGTTGC
Statistics
Matches: 116, Mismatches: 13, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
76 16 0.14
77 100 0.86
ACGTcount: A:0.35, C:0.30, G:0.16, T:0.20
Consensus pattern (77 bp):
CATATGCCGTATCACGGCAACCAAAGTATCACATGGCTACAAAGGTCTCCACCGCCACATAATGG
CATAAAAACCAT
Found at i:47431 original size:28 final size:28
Alignment explanation
Indices: 47354--47459 Score: 106
Period size: 28 Copynumber: 3.7 Consensus size: 28
47344 GGATCACCTA
*
47354 GGGGCATTTTGGTCA-TTTTCAAAATATTC
1 GGGGCATTTTGGTCATTTTTC-ACAT-TTC
*
47383 TAGGGGCATTTTTGTCATTTTTCACATTTC
1 --GGGGCATTTTGGTCATTTTTCACATTTC
* * * **
47413 GGGGCATTTTGGTCGTTTTGCACGTTAA
1 GGGGCATTTTGGTCATTTTTCACATTTC
47441 GGGGCATTTTGGTCATTTT
1 GGGGCATTTTGGTCATTTT
47460 AGGTTCACTT
Statistics
Matches: 65, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
28 40 0.62
30 3 0.05
31 17 0.26
32 5 0.08
ACGTcount: A:0.17, C:0.14, G:0.25, T:0.44
Consensus pattern (28 bp):
GGGGCATTTTGGTCATTTTTCACATTTC
Done.