Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021283.1 Corchorus olitorius cultivar O-4 contig21316, 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: 82995
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:108 original size:29 final size:28
Alignment explanation
Indices: 66--121 Score: 85
Period size: 29 Copynumber: 2.0 Consensus size: 28
56 GTTATTCCAC
*
66 GTTCTTTAGCGTTCTTGAAGATTAGAAAT
1 GTTCTTGAGCGTTCTTGAA-ATTAGAAAT
*
95 GTTCTTGAGTGTTCTTGAAATTAGAAA
1 GTTCTTGAGCGTTCTTGAAATTAGAAA
122 GTTTGAAGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 8 0.32
29 17 0.68
ACGTcount: A:0.29, C:0.09, G:0.21, T:0.41
Consensus pattern (28 bp):
GTTCTTGAGCGTTCTTGAAATTAGAAAT
Found at i:376 original size:36 final size:36
Alignment explanation
Indices: 329--398 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
319 TTCAATAACC
* *
329 TTACATCTTTTGTGATTTTGGTTATCATATTTCTTA
1 TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
*
365 TTACATTTTTTGTAATTTTGATTATCATATTTCT
1 TTACATCTTTTGTAATTTTGATTATCATATTTCT
399 CCAAAATTTC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.21, C:0.10, G:0.09, T:0.60
Consensus pattern (36 bp):
TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
Found at i:1304 original size:209 final size:202
Alignment explanation
Indices: 908--1306 Score: 699
Period size: 209 Copynumber: 1.9 Consensus size: 202
898 GCTTAATAAC
908 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
1 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
* *
973 GATACAACACATTATTATTATATATAAAACTATACCAAAAAAAAGTAGTTGAACATTAGTGGTTG
66 GATACAACACATTATTATTATATATAAAACTATACCAAAAAAAAATAGTTGAACATTAGTGGTTA
1038 ATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAAATT
131 ATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAAATT
1103 CGATTTA
196 CGATTTA
*
1110 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAATAAAGTTGTAGTGAATAA
1 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
*
1175 GATACAACACATTACTATTATAATATATATAGAACTATACCAAAAAAAAAAATAGTTGAACATTA
66 GATACAACACA-T--TATTAT--TATATATAAAACTATACC--AAAAAAAAATAGTTGAACATTA
1240 GTGGTTAATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATT
124 GTGGTTAATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATT
1305 AA
189 AA
1307 GATCCGATTT
Statistics
Matches: 186, Mismatches: 4, Indels: 7
0.94 0.02 0.04
Matches are distributed among these distances:
202 75 0.40
203 1 0.01
205 6 0.03
207 17 0.09
209 87 0.47
ACGTcount: A:0.46, C:0.08, G:0.11, T:0.36
Consensus pattern (202 bp):
TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
GATACAACACATTATTATTATATATAAAACTATACCAAAAAAAAATAGTTGAACATTAGTGGTTA
ATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAAATT
CGATTTA
Found at i:1492 original size:39 final size:40
Alignment explanation
Indices: 1433--1513 Score: 121
Period size: 39 Copynumber: 2.0 Consensus size: 40
1423 ATACCTAAGA
*
1433 ATTTAATTAATGTAGTTATTTCAGTTATTATA-GTATTAC
1 ATTTAATTAATGTAGTTATTTCAGTTATTATATATATTAC
*
1472 ATTTAATTAATGTAAG-TATTTTAGTTATTATATATATTAC
1 ATTTAATTAATGT-AGTTATTTCAGTTATTATATATATTAC
1512 AT
1 AT
1514 AGGAATTAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
39 28 0.74
40 10 0.26
ACGTcount: A:0.36, C:0.04, G:0.09, T:0.52
Consensus pattern (40 bp):
ATTTAATTAATGTAGTTATTTCAGTTATTATATATATTAC
Found at i:1773 original size:2 final size:2
Alignment explanation
Indices: 1761--1798 Score: 58
Period size: 2 Copynumber: 18.5 Consensus size: 2
1751 AGTTTAGACT
*
1761 TA TA TA GTA TA TA GA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1799 TTAGTAGTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
2 31 0.94
3 2 0.06
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (2 bp):
TA
Found at i:2037 original size:16 final size:16
Alignment explanation
Indices: 1996--2038 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
1986 CGGTCTCGGA
* *
1996 TCGGGTTGGGGTAGTT
1 TCGGGTTCGGGTACTT
* *
2012 TCTGGCTCGGGTACTT
1 TCGGGTTCGGGTACTT
2028 TCGGGTTCGGG
1 TCGGGTTCGGG
2039 ATGTTAACTT
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.05, C:0.16, G:0.44, T:0.35
Consensus pattern (16 bp):
TCGGGTTCGGGTACTT
Found at i:8076 original size:2 final size:2
Alignment explanation
Indices: 8069--8107 Score: 57
Period size: 2 Copynumber: 21.0 Consensus size: 2
8059 ATAAAATCTC
8069 AT AT AT AT A- AT -T AT A- AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
8108 TTAATAAAGG
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
1 3 0.09
2 31 0.91
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:8773 original size:3 final size:3
Alignment explanation
Indices: 8765--8807 Score: 61
Period size: 3 Copynumber: 14.7 Consensus size: 3
8755 CTTCAAAATA
* *
8765 AAT AAT AAT AAT AAT AAT AAT AAT -AC AAT AAT AAT AAA AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
8808 ATAAATAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
2 1 0.03
3 34 0.97
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:8824 original size:20 final size:20
Alignment explanation
Indices: 8759--8815 Score: 71
Period size: 23 Copynumber: 2.8 Consensus size: 20
8749 TAGGTCCTTC
8759 AAAATAAAT-AATAATAATA
1 AAAATAAATAAATAATAATA
*
8778 ATAATAATAATACAATAATAATA
1 AAAAT-A-AATA-AATAATAATA
8801 AAAATAAATAAATAA
1 AAAATAAATAAATAA
8816 AAACAAAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
19 4 0.12
20 6 0.19
21 7 0.22
22 1 0.03
23 14 0.44
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (20 bp):
AAAATAAATAAATAATAATA
Found at i:10360 original size:4 final size:4
Alignment explanation
Indices: 10351--10377 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
10341 TAATCTAAAA
10351 GAGG GAGG GAGG GAGG GAGG GAGG GAG
1 GAGG GAGG GAGG GAGG GAGG GAGG GAG
10378 AAGGCAAGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.74, T:0.00
Consensus pattern (4 bp):
GAGG
Found at i:10966 original size:42 final size:43
Alignment explanation
Indices: 10914--11007 Score: 138
Period size: 45 Copynumber: 2.2 Consensus size: 43
10904 AGTGTATTAC
*
10914 CTAA-ATTCTA-CTCCATCTCTAGGTAATTCATCAAAATAAAG
1 CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAG
10955 CTAATATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAG
1 CTAATATTCTA--CCTCCATCTCTAGATAATTCATCAAAATAAAG
*
11000 TTAATATT
1 CTAATATT
11008 AATTGTTGCT
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
41 4 0.09
42 6 0.13
45 37 0.79
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.35
Consensus pattern (43 bp):
CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAG
Found at i:14654 original size:19 final size:19
Alignment explanation
Indices: 14626--14671 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
14616 AGGGAAAAGC
*
14626 AAAAGCATCAGTCCATGTA
1 AAAAGAATCAGTCCATGTA
*
14645 AAAAGAATCAGTTCATGTA
1 AAAAGAATCAGTCCATGTA
14664 AAAAGAAT
1 AAAAGAAT
14672 TGATATAAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.50, C:0.13, G:0.15, T:0.22
Consensus pattern (19 bp):
AAAAGAATCAGTCCATGTA
Found at i:15531 original size:163 final size:163
Alignment explanation
Indices: 15237--15535 Score: 483
Period size: 163 Copynumber: 1.8 Consensus size: 163
15227 GGAACATCAC
*
15237 TTATCAGAACTCAATGGCCAAATTACACACAAAGACAATGGATCTGAAGAAAACACGTTAGGCTT
1 TTATCAGAACTCAATGGCCAAATTACACACAAAGACAATGGATCTAAAGAAAACACGTTAGGCTT
* * *
15302 AAGGGATATTTCAGTAATCAACCACGTGAGAATAGACCAAAACGAGGCGATAAGGTCACTCCACA
66 AAGGGATATTTCAGTAATCAACCACATGAGAAAAGACCAAAACGAGGCGAAAAGGTCACTCCACA
15367 TTAAAATTTAGTAAATTTTCGTGGAAATGGCAT
131 TTAAAATTTAGTAAATTTTCGTGGAAATGGCAT
* * *
15400 TTATTAGAACTCAATGGCCAAATTACACACAAAGACAATGGATCTAAAGAAAACATGTTAGGTTT
1 TTATCAGAACTCAATGGCCAAATTACACACAAAGACAATGGATCTAAAGAAAACACGTTAGGCTT
* * * *
15465 AGGGGATATTTCAGTAATCAACCACATTAGAAAAGACCAAAACGGGGCGAAAAGGT-TCTCCCAC
66 AAGGGATATTTCAGTAATCAACCACATGAGAAAAGACCAAAACGAGGCGAAAAGGTCACT-CCAC
15529 ATTAAAA
130 ATTAAAA
15536 ATTGTTGGGA
Statistics
Matches: 124, Mismatches: 11, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
162 2 0.02
163 122 0.98
ACGTcount: A:0.41, C:0.18, G:0.18, T:0.23
Consensus pattern (163 bp):
TTATCAGAACTCAATGGCCAAATTACACACAAAGACAATGGATCTAAAGAAAACACGTTAGGCTT
AAGGGATATTTCAGTAATCAACCACATGAGAAAAGACCAAAACGAGGCGAAAAGGTCACTCCACA
TTAAAATTTAGTAAATTTTCGTGGAAATGGCAT
Found at i:15591 original size:2 final size:2
Alignment explanation
Indices: 15578--15635 Score: 80
Period size: 2 Copynumber: 28.0 Consensus size: 2
15568 TATCCAAATA
* *
15578 AT AT AT AGT AT AT AT AGT GT GT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT A-T AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT
15622 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
15636 TGTTATGGAT
Statistics
Matches: 52, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
2 49 0.94
3 3 0.06
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (2 bp):
AT
Found at i:17358 original size:30 final size:30
Alignment explanation
Indices: 16794--17356 Score: 754
Period size: 30 Copynumber: 18.8 Consensus size: 30
16784 TTTACTCTCT
*
16794 AATTGACACCAGAAGTTGTCATGATCTTGC
1 AATTGACACCAGAAGTTGTCATGGTCTTGC
*
16824 AATTGACACCAGAAGTTGTCATGGTCTTAC
1 AATTGACACCAGAAGTTGTCATGGTCTTGC
* ** *
16854 AAATGACACCAGAAGTT-T-ATTCTACTTAC
1 AATTGACACCAGAAGTTGTCATGGT-CTTGC
*
16883 AATTGACACCAGAAGTTGTCATGGTCTTAC
1 AATTGACACCAGAAGTTGTCATGGTCTTGC
* *
16913 AAATGACACCAGAAGTTGTCATGGTCTTAC
1 AATTGACACCAGAAGTTGTCATGGTCTTGC
* *
16943 AAATGACACCAGAAGTTGTCATGGTCTTAC
1 AATTGACACCAGAAGTTGTCATGGTCTTGC
* * *
16973 AAATGACACCAGAAGTTGTCATGATCTTAC
1 AATTGACACCAGAAGTTGTCATGGTCTTGC
17003 AATTGACACCAGAAGTTGTCATGGTCTTGC
1 AATTGACACCAGAAGTTGTCATGGTCTTGC
17033 AATTGACACCAGAAGTTGTCATGGTCTTGC
1 AATTGACACCAGAAGTTGTCATGGTCTTGC
*
17063 AATTGACACCAGAAGTTGTCATGGTCTTAC
1 AATTGACACCAGAAGTTGTCATGGTCTTGC
*
17093 AATTGACACCAGAAGTTGTCAATGATCTTGC
1 AATTGACACCAGAAGTTGTC-ATGGTCTTGC
* *
17124 AATTGACACCAGAAGTTGTCATGCTCCTGC
1 AATTGACACCAGAAGTTGTCATGGTCTTGC
* * * *
17154 AGTTGACACCAGAACTTGTCATGCTCCTGC
1 AATTGACACCAGAAGTTGTCATGGTCTTGC
* *
17184 AATTGACACCAGAAGTTGTCATGCTATTGC
1 AATTGACACCAGAAGTTGTCATGGTCTTGC
** *
17214 AATTGACACCAGAAGTTGTCATACTGTTGC
1 AATTGACACCAGAAGTTGTCATGGTCTTGC
* * *
17244 AAATGACACCATAAGTTGTCATGCTCTTGC
1 AATTGACACCAGAAGTTGTCATGGTCTTGC
* *
17274 AATTGACACCAGAAGTTGCCATGCTCTTGC
1 AATTGACACCAGAAGTTGTCATGGTCTTGC
* *
17304 AATTGACACCAGAAGTTGTCATGATAATT-C
1 AATTGACACCAGAAGTTGTCATGGT-CTTGC
* *
17334 ACTTGACACCAAAAGTTGTCATG
1 AATTGACACCAGAAGTTGTCATG
17357 ATTTTACCTT
Statistics
Matches: 490, Mismatches: 38, Indels: 10
0.91 0.07 0.02
Matches are distributed among these distances:
28 3 0.01
29 22 0.04
30 432 0.88
31 33 0.07
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29
Consensus pattern (30 bp):
AATTGACACCAGAAGTTGTCATGGTCTTGC
Found at i:24497 original size:30 final size:28
Alignment explanation
Indices: 24462--24537 Score: 82
Period size: 28 Copynumber: 2.6 Consensus size: 28
24452 CTACCTATCT
*
24462 AAAAAAGCCTTATTGTTTATT-CTAAAAGAA
1 AAAAAAGCCTTATTGTGTATTAC--AAA-AA
** *
24492 AAAAAAAACTTATTGTGTATTACCAAAA
1 AAAAAAGCCTTATTGTGTATTACAAAAA
24520 AAAAAAGCCTTATTGTGT
1 AAAAAAGCCTTATTGTGT
24538 GCCAACAAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
28 18 0.46
29 2 0.05
30 18 0.46
31 1 0.03
ACGTcount: A:0.47, C:0.11, G:0.11, T:0.32
Consensus pattern (28 bp):
AAAAAAGCCTTATTGTGTATTACAAAAA
Found at i:24546 original size:28 final size:26
Alignment explanation
Indices: 24490--24550 Score: 68
Period size: 28 Copynumber: 2.3 Consensus size: 26
24480 ATTCTAAAAG
** *
24490 AAAAAAAAAACTTATTGTGTATTACC
1 AAAAAAAAAACTTATTGTGTACCAAC
*
24516 AAAAAAAAAAGCCTTATTGTGTGCCAAC
1 AAAAAAAAAA--CTTATTGTGTACCAAC
24544 AAAAAAA
1 AAAAAAA
24551 CTACCACAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 10 0.34
28 19 0.66
ACGTcount: A:0.54, C:0.13, G:0.10, T:0.23
Consensus pattern (26 bp):
AAAAAAAAAACTTATTGTGTACCAAC
Found at i:29411 original size:97 final size:93
Alignment explanation
Indices: 29207--29545 Score: 567
Period size: 97 Copynumber: 3.6 Consensus size: 93
29197 ATATGACATG
29207 ACTGAATGCCTTATATACAGACTGGGCCTCTCCACCTATTGACAATTGACTTTAGGTTGGATGCT
1 ACTGAATGCCTTATATACAGACTGGGCCTCTCCACCTATTGACAATTGACTTTAGGTTGGATGCT
29272 TGACAGGTATGACATATTTTGATAGACAGA
66 TGACAGGTATGACATATTTTGATAG--AGA
29302 ACTGAATGCCTTATATACAGACTGGGCCTCTCCACCTATTGACAATTGACTTTATAGGTTGGATG
1 ACTGAATGCCTTATATACAGACTGGGCCTCTCCACCTATTGACAATTGAC-TT-TAGGTTGGATG
29367 CTTGACAGGTATGACATATTTTGATAGATTGA
64 CTTGACAGGTATGACATATTTTGATAGA--GA
*
29399 ACTGAATGCCTTATATACAGACTAGGCCTCTCCACCTATTGACAATTGACTTTAGGTTGGATGCT
1 ACTGAATGCCTTATATACAGACTGGGCCTCTCCACCTATTGACAATTGACTTTAGGTTGGATGCT
*
29464 TGACAAGTATGACATATTTTGAT--AG-
66 TGACAGGTATGACATATTTTGATAGAGA
* *
29489 ACTGAATGCCTTATATACAGATTGGGCATCTCCACCTATTGACAATTGACTTTAGGT
1 ACTGAATGCCTTATATACAGACTGGGCCTCTCCACCTATTGACAATTGACTTTAGGT
29546 GAAGCATATA
Statistics
Matches: 235, Mismatches: 5, Indels: 13
0.93 0.02 0.05
Matches are distributed among these distances:
90 54 0.23
91 1 0.00
93 1 0.00
95 86 0.37
96 4 0.02
97 89 0.38
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Consensus pattern (93 bp):
ACTGAATGCCTTATATACAGACTGGGCCTCTCCACCTATTGACAATTGACTTTAGGTTGGATGCT
TGACAGGTATGACATATTTTGATAGAGA
Found at i:39493 original size:78 final size:78
Alignment explanation
Indices: 39393--39619 Score: 339
Period size: 79 Copynumber: 2.9 Consensus size: 78
39383 AAAATATCAG
* *
39393 AAATTCTTGAAACCAACAAAAGCATTTAGCAAGACATGACAAGAAAAGAGAATAAAATGTTTCTT
1 AAATACTTGAAACCAACAAAAGCATTTAGCAAGACATGACAAGAAAAGAGAATAAAAAGTTTCTT
39458 TCCAAATATATAA
66 TCCAAATATATAA
* * * * *
39471 AAATATTTGAAACCAACAAAAGCATTTAGCGAGACATGACAAGAAATGAGAGTAAAAGGTTTCTT
1 AAATACTTGAAACCAACAAAAGCATTTAGCAAGACATGACAAGAAAAGAGAATAAAAAGTTTCTT
* *
39536 TCCAAAATATCTGA
66 TCC-AAATATATAA
*
39550 ATATACTTGAAACCAACAAAAGCATTTAGCAAGACATGACAAGAAAAGAGAGA-AAAAAGTTTCT
1 AAATACTTGAAACCAACAAAAGCATTTAGCAAGACATGACAAGAAAAGAGA-ATAAAAAGTTTCT
39614 TTCCAA
65 TTCCAA
39620 GAAAAAATAA
Statistics
Matches: 133, Mismatches: 14, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
78 64 0.48
79 69 0.52
ACGTcount: A:0.48, C:0.15, G:0.14, T:0.23
Consensus pattern (78 bp):
AAATACTTGAAACCAACAAAAGCATTTAGCAAGACATGACAAGAAAAGAGAATAAAAAGTTTCTT
TCCAAATATATAA
Found at i:39585 original size:79 final size:78
Alignment explanation
Indices: 39382--39619 Score: 352
Period size: 78 Copynumber: 3.0 Consensus size: 78
39372 TCTGATTCAA
* * *
39382 CAAAATATCAGAAATTCTTGAAACCAACAAAAGCATTTAGCAAGACATGACAAGAAAAGAGAATA
1 CAAAATATCTGAAATACTTGAAACCAACAAAAGCATTTAGCAAGACATGACAAGAAAAGAGAGTA
*
39447 AAATGTTTCTTTC
66 AAAAGTTTCTTTC
** * * *
39460 CAAATATAT-AAAAATATTTGAAACCAACAAAAGCATTTAGCGAGACATGACAAGAAATGAGAGT
1 CAAA-ATATCTGAAATACTTGAAACCAACAAAAGCATTTAGCAAGACATGACAAGAAAAGAGAGT
*
39524 AAAAGGTTTCTTTC
65 AAAAAGTTTCTTTC
*
39538 CAAAATATCTGAATATACTTGAAACCAACAAAAGCATTTAGCAAGACATGACAAGAAAAGAGAGA
1 CAAAATATCTGAA-ATACTTGAAACCAACAAAAGCATTTAGCAAGACATGACAAGAAAAGAGAGT
39603 AAAAAGTTTCTTTC
65 AAAAAGTTTCTTTC
39617 CAA
1 CAA
39620 GAAAAAATAA
Statistics
Matches: 143, Mismatches: 14, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
77 4 0.03
78 72 0.50
79 67 0.47
ACGTcount: A:0.49, C:0.15, G:0.14, T:0.23
Consensus pattern (78 bp):
CAAAATATCTGAAATACTTGAAACCAACAAAAGCATTTAGCAAGACATGACAAGAAAAGAGAGTA
AAAAGTTTCTTTC
Found at i:43377 original size:17 final size:17
Alignment explanation
Indices: 43355--43387 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
43345 CAAGCCGAGC
43355 TCGAGTATCGAA-TCAAA
1 TCGAGT-TCGAACTCAAA
43372 TCGAGTTCGAACTCAA
1 TCGAGTTCGAACTCAA
43388 TGATGCTTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.36, C:0.21, G:0.18, T:0.24
Consensus pattern (17 bp):
TCGAGTTCGAACTCAAA
Found at i:53829 original size:479 final size:479
Alignment explanation
Indices: 52932--53890 Score: 1909
Period size: 479 Copynumber: 2.0 Consensus size: 479
52922 ACGGTTTCCA
52932 TTGGGCGGTCCTATATTATTCTTGTGAAATACTCTACACAGCACATATGACTTCTCCACCCAAAT
1 TTGGGCGGTCCTATATTATTCTTGTGAAATACTCTACACAGCACATATGACTTCTCCACCCAAAT
*
52997 GAGTGAAAAAGAATAACGGGAAAAAGGAGAAAGACATTTCTCAGATTAGTTTCAGAAAATGAATG
66 GAGTGAAAAAGAATAACGGGAAAAAGGAGAAAGACATTTCGCAGATTAGTTTCAGAAAATGAATG
53062 GTAAAAATTGGTTATTGAGAAAATAGTAGCACTTCTAAACATAAGGGATTCAGAGTACTAACAAG
131 GTAAAAATTGGTTATTGAGAAAATAGTAGCACTTCTAAACATAAGGGATTCAGAGTACTAACAAG
53127 TAACAACCATATTGACTCAAGTCCTAAATCTACTTAACTCAAGCTAATTTAACAGTACACTTAAG
196 TAACAACCATATTGACTCAAGTCCTAAATCTACTTAACTCAAGCTAATTTAACAGTACACTTAAG
53192 TTATTAACTATATAAAATTAAAAACATCATAGCACATGACATCCCAGATCACATTTTCTCCAATT
261 TTATTAACTATATAAAATTAAAAACATCATAGCACATGACATCCCAGATCACATTTTCTCCAATT
53257 TCCTAAATTTTCACGGCCACCAGATGAATAACCCATTTTATTGAAACCAAAGCAGTTCTTCGGTC
326 TCCTAAATTTTCACGGCCACCAGATGAATAACCCATTTTATTGAAACCAAAGCAGTTCTTCGGTC
53322 AGTTCTTCAGTTCAATCAGACCAATGCAGCATCGTCCATCATTAAAGCCAAAATGGACTAAATAT
391 AGTTCTTCAGTTCAATCAGACCAATGCAGCATCGTCCATCATTAAAGCCAAAATGGACTAAATAT
53387 TTCATGTTAAACATCTATACCTTC
456 TTCATGTTAAACATCTATACCTTC
53411 TTGGGCGGTCCTATATTATTCTTGTGAAATACTCTACACAGCACATATGACTTCTCCACCCAAAT
1 TTGGGCGGTCCTATATTATTCTTGTGAAATACTCTACACAGCACATATGACTTCTCCACCCAAAT
53476 GAGTGAAAAAGAATAACGGGAAAAAGGAGAAAGACATTTCGCAGATTAGTTTCAGAAAATGAATG
66 GAGTGAAAAAGAATAACGGGAAAAAGGAGAAAGACATTTCGCAGATTAGTTTCAGAAAATGAATG
53541 GTAAAAATTGGTTATTGAGAAAATAGTAGCACTTCTAAACATAAGGGATTCAGAGTACTAACAAG
131 GTAAAAATTGGTTATTGAGAAAATAGTAGCACTTCTAAACATAAGGGATTCAGAGTACTAACAAG
53606 TAACAACCATATTGACTCAAGTCCTAAATCTACTTAACTCAAGCTAATTTAACAGTACACTTAAG
196 TAACAACCATATTGACTCAAGTCCTAAATCTACTTAACTCAAGCTAATTTAACAGTACACTTAAG
53671 TTATTAACTATATAAAATTAAAAACATCATAGCACATGACATCCCAGATCACATTTTCTCCAATT
261 TTATTAACTATATAAAATTAAAAACATCATAGCACATGACATCCCAGATCACATTTTCTCCAATT
53736 TCCTAAATTTTCACGGCCACCAGATGAATAACCCATTTTATTGAAACCAAAGCAGTTCTTCGGTC
326 TCCTAAATTTTCACGGCCACCAGATGAATAACCCATTTTATTGAAACCAAAGCAGTTCTTCGGTC
53801 AGTTCTTCAGTTCAATCAGACCAATGCAGCATCGTCCATCATTAAAGCCAAAATGGACTAAATAT
391 AGTTCTTCAGTTCAATCAGACCAATGCAGCATCGTCCATCATTAAAGCCAAAATGGACTAAATAT
53866 TTCATGTTAAACATCTATACCTTC
456 TTCATGTTAAACATCTATACCTTC
53890 T
1 T
53891 AGTCATCAAA
Statistics
Matches: 479, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
479 479 1.00
ACGTcount: A:0.38, C:0.20, G:0.14, T:0.29
Consensus pattern (479 bp):
TTGGGCGGTCCTATATTATTCTTGTGAAATACTCTACACAGCACATATGACTTCTCCACCCAAAT
GAGTGAAAAAGAATAACGGGAAAAAGGAGAAAGACATTTCGCAGATTAGTTTCAGAAAATGAATG
GTAAAAATTGGTTATTGAGAAAATAGTAGCACTTCTAAACATAAGGGATTCAGAGTACTAACAAG
TAACAACCATATTGACTCAAGTCCTAAATCTACTTAACTCAAGCTAATTTAACAGTACACTTAAG
TTATTAACTATATAAAATTAAAAACATCATAGCACATGACATCCCAGATCACATTTTCTCCAATT
TCCTAAATTTTCACGGCCACCAGATGAATAACCCATTTTATTGAAACCAAAGCAGTTCTTCGGTC
AGTTCTTCAGTTCAATCAGACCAATGCAGCATCGTCCATCATTAAAGCCAAAATGGACTAAATAT
TTCATGTTAAACATCTATACCTTC
Found at i:56513 original size:14 final size:14
Alignment explanation
Indices: 56496--56525 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
56486 TCACGATAAG
56496 TAATTTCGTTTGAT
1 TAATTTCGTTTGAT
56510 TAATTTCGTTTGAT
1 TAATTTCGTTTGAT
56524 TA
1 TA
56526 TATTAAGAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.23, C:0.07, G:0.13, T:0.57
Consensus pattern (14 bp):
TAATTTCGTTTGAT
Found at i:58690 original size:20 final size:20
Alignment explanation
Indices: 58657--58695 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
58647 CATAAATGAA
*
58657 ATTTTCAGAAATTATTATTT
1 ATTTTCAGAAATTAGTATTT
58677 ATTTTCA-AATATTAGTATT
1 ATTTTCAGAA-ATTAGTATT
58696 GAATTCGGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.36, C:0.05, G:0.05, T:0.54
Consensus pattern (20 bp):
ATTTTCAGAAATTAGTATTT
Found at i:60835 original size:220 final size:219
Alignment explanation
Indices: 60433--60846 Score: 523
Period size: 220 Copynumber: 1.9 Consensus size: 219
60423 TACTTTTCGA
60433 ATATATTTCTTAAATGCCATTGTTTAGACTTTTATAGTTTTACTCAACTAAAAACTCTATTTTTA
1 ATATATTTCTTAAATGCCATTGTTTAGACTTTTATAGTTTTACTCAACTAAAAACTCTATTTTTA
* *
60498 TTTAATTAAATATAATATCCTTATAACTATTTAATTTTTACCATTTTACTATTTTAATTAAAAAT
66 TTTAACTAAATATAATATCCTTATAACTATTTAATTTTTACCATTTAACTATTTT-ATTAAAAAT
* * ** **** *** *
60563 ATTATATATATTAGAATTTTTTAAATATATTTTTATAGTTTTACTCAACTAAAAGCTCTATTTTT
130 ATTATATATATTACAA-TCTAAAAATATATTTTTATAGAAAAAAAAAACTAAAAACTCTATTTTT
60628 GGCAAAAAAAAAAAACTAAAAACTCT
194 GGCAAAAAAAAAAAACTAAAAACTCT
*
60654 ATAT-TTTCTTAAATGCCATTGTTTAGACTTTTATAGTTTTACTCAATTAAAAACTCTATTTTTA
1 ATATATTTCTTAAATGCCATTGTTTAGACTTTTATAGTTTTACTCAACTAAAAACTCTATTTTTA
* * *
60718 TTTAACTAAATCTTATATCCTTATAACTATTTAATTTTTACCATTTAACTA-TTT-TTAAATATA
66 TTTAACTAAATATAATATCCTTATAACTATTTAATTTTTACCATTTAACTATTTTATTAAAAATA
* * * *
60781 CTTTTATAGTTTTACTCAA-CTAAAAACTCTATTTTT-TGGCAAAAAAAAAACTAAAAACTCTAT
131 -TTATATA-TATTA--CAATCTAAAAA-TATATTTTTATAG-AAAAAAAAAACTAAAAACTCTAT
60844 TTT
190 TTT
60847 ATTTAATTAA
Statistics
Matches: 165, Mismatches: 22, Indels: 13
0.82 0.11 0.06
Matches are distributed among these distances:
217 8 0.05
218 6 0.04
219 13 0.08
220 132 0.80
221 6 0.04
ACGTcount: A:0.38, C:0.12, G:0.04, T:0.46
Consensus pattern (219 bp):
ATATATTTCTTAAATGCCATTGTTTAGACTTTTATAGTTTTACTCAACTAAAAACTCTATTTTTA
TTTAACTAAATATAATATCCTTATAACTATTTAATTTTTACCATTTAACTATTTTATTAAAAATA
TTATATATATTACAATCTAAAAATATATTTTTATAGAAAAAAAAAACTAAAAACTCTATTTTTGG
CAAAAAAAAAAAACTAAAAACTCT
Found at i:64926 original size:12 final size:12
Alignment explanation
Indices: 64909--64934 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
64899 TCTCTTCATA
64909 ATCAAGCATGTC
1 ATCAAGCATGTC
64921 ATCAAGCATGTC
1 ATCAAGCATGTC
64933 AT
1 AT
64935 AAGATTGTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.23, G:0.15, T:0.27
Consensus pattern (12 bp):
ATCAAGCATGTC
Found at i:65048 original size:43 final size:43
Alignment explanation
Indices: 64980--65064 Score: 118
Period size: 43 Copynumber: 2.0 Consensus size: 43
64970 TATAAATTAC
64980 CTATAGACAAGAATTATTGACAAAATTAGAACTCTAAACCTTA
1 CTATAGACAAGAATTATTGACAAAATTAGAACTCTAAACCTTA
* * * *
65023 CTATCGACAA-AAGTTATTGATAAAATTCGGACTCTAAACCTT
1 CTATAGACAAGAA-TTATTGACAAAATTAGAACTCTAAACCTT
65065 TCAAACAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
42 2 0.05
43 35 0.95
ACGTcount: A:0.42, C:0.18, G:0.11, T:0.29
Consensus pattern (43 bp):
CTATAGACAAGAATTATTGACAAAATTAGAACTCTAAACCTTA
Done.