Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016962.1 Corchorus olitorius cultivar O-4 contig16995, 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: 81018
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:3074 original size:56 final size:56
Alignment explanation
Indices: 2999--3112 Score: 210
Period size: 56 Copynumber: 2.0 Consensus size: 56
2989 TTTATTCTGT
*
2999 AGAATAATTAAGTAGAGATAGGGGGATAGAATTTATTATAACATTTATTGTGTGAA
1 AGAATAATTAAGTAAAGATAGGGGGATAGAATTTATTATAACATTTATTGTGTGAA
*
3055 AGAATAATTAAGTAAAGATAGGGGGATAGGATTTATTATAACATTTATTGTGTGAA
1 AGAATAATTAAGTAAAGATAGGGGGATAGAATTTATTATAACATTTATTGTGTGAA
3111 AG
1 AG
3113 GAAACGGATA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.41, C:0.02, G:0.24, T:0.33
Consensus pattern (56 bp):
AGAATAATTAAGTAAAGATAGGGGGATAGAATTTATTATAACATTTATTGTGTGAA
Found at i:3305 original size:2 final size:2
Alignment explanation
Indices: 3298--3406 Score: 122
Period size: 2 Copynumber: 56.0 Consensus size: 2
3288 TAATATGTAG
3298 TA TA TA TA TA TA TA TA TA -A TA -A TA -A TA -A TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
3335 TA TA TA TA TG TA TA TA TA TA TA TA GTA TA TA -A TA TA TA GTA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA -TA TA
* *
3378 TA GTA TA TG CA TA TA TA TA TA TA TA TA TA
1 TA -TA TA TA TA TA TA TA TA TA TA TA TA TA
3407 ACCCTATTAA
Statistics
Matches: 92, Mismatches: 6, Indels: 18
0.79 0.05 0.16
Matches are distributed among these distances:
1 6 0.07
2 80 0.87
3 6 0.07
ACGTcount: A:0.50, C:0.01, G:0.05, T:0.45
Consensus pattern (2 bp):
TA
Found at i:3367 original size:50 final size:49
Alignment explanation
Indices: 3290--3406 Score: 155
Period size: 50 Copynumber: 2.3 Consensus size: 49
3280 GTTTCAAATA
*
3290 ATATGTAGTATATATATATATATATAATA-ATAATAATATAATATATATAT
1 ATATGTA-TATATATATATATATATAATATATAAT-ATATAATATATACAT
* * *
3340 ATATGTATATATATATATAGTATATAATATATAGTATATAGTATATGCAT
1 ATATGTATATATATATATA-TATATAATATATAATATATAATATATACAT
*
3390 ATATATATATATATATA
1 ATATGTATATATATATA
3407 ACCCTATTAA
Statistics
Matches: 60, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
49 12 0.20
50 44 0.73
51 4 0.07
ACGTcount: A:0.49, C:0.01, G:0.06, T:0.44
Consensus pattern (49 bp):
ATATGTATATATATATATATATATAATATATAATATATAATATATACAT
Found at i:9861 original size:2 final size:2
Alignment explanation
Indices: 9854--9884 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
9844 AGCAGCCACA
9854 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
9885 ACAAAAGTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:11593 original size:293 final size:299
Alignment explanation
Indices: 11059--11647 Score: 1073
Period size: 293 Copynumber: 2.0 Consensus size: 299
11049 CACACATCCT
*
11059 CCATACTCCTGCCATCATATCATAGTGGAAGCTTGCTGCCCATTTAATTTGTAGTTTTGTATAGC
1 CCATACTCCTGCCATCATATCATAGTGGAAGCTCGCTGCCCATTTAATTTGTAG-TTTGTATAGC
*
11124 CTTTATGAGGGGTTTAACTCTCCTCTATTTATTGATTAAATCAAAATTTTGTAATTTCGTAATTA
65 CTATATGAGGGGTTTAACTCTCCTCTATTTATTGATTAAATCAAAATTTTGTAATTTCGTAATTA
*
11189 GAAGGATTAGGCCTAAAGGATAGATTTAGGCCTTATTTGCTCGTCCACACATAGATTTAGGTCCA
130 GAAGGATTAGGCCTAAAGGATAGATTTAGGCCTTATTTGCTCATCCACACATAGATTTAGGTCCA
11254 AAATGTCACAATTATGATGTTTAGGCATAAATTGATAAAACTTGCAAAATTTTAGGTCTTTAATT
195 AAATGTCACAATTATGATGTTTAGGCATAAATTGATAAAACTTGCAAAATTTTAGGTCTTTAATT
11319 ATAGAGTTTTTAGCCTTTCCATCCGATAAACTTTTCATAG
260 ATAGAGTTTTTAGCCTTTCCATCCGATAAACTTTTCATAG
11359 CCATACTCCTGCCATCATATCATAGTGGAAGCTCGCTGCCCATTTAATTTGTAG-TT-T-T-G-C
1 CCATACTCCTGCCATCATATCATAGTGGAAGCTCGCTGCCCATTTAATTTGTAGTTTGTATAGCC
* *
11419 -ATATGTGGGGTTTAACTCTCCTCTATTTATTGATTAAATCAAAATTTTGTTATTTCGTAATTAG
66 TATATGAGGGGTTTAACTCTCCTCTATTTATTGATTAAATCAAAATTTTGTAATTTCGTAATTAG
*
11483 AAGGATTAGGCCTAAAGGATAGATTTAGGCCTTATTTGCTCATCCACACTTAGATTTAGGTCCAA
131 AAGGATTAGGCCTAAAGGATAGATTTAGGCCTTATTTGCTCATCCACACATAGATTTAGGTCCAA
11548 AATGTCACAATTATGATGTTTAGGCATAAATTGATAAAACTTGCAAAATTTTAGGTCTTTAATTA
196 AATGTCACAATTATGATGTTTAGGCATAAATTGATAAAACTTGCAAAATTTTAGGTCTTTAATTA
11613 TAGAGTTTTTAGCCTTTCCATCCGATAAACTTTTC
261 TAGAGTTTTTAGCCTTTCCATCCGATAAACTTTTC
11648 CATGGAAAAG
Statistics
Matches: 283, Mismatches: 6, Indels: 7
0.96 0.02 0.02
Matches are distributed among these distances:
293 224 0.79
294 1 0.00
295 1 0.00
296 1 0.00
297 1 0.00
298 2 0.01
300 53 0.19
ACGTcount: A:0.29, C:0.17, G:0.16, T:0.38
Consensus pattern (299 bp):
CCATACTCCTGCCATCATATCATAGTGGAAGCTCGCTGCCCATTTAATTTGTAGTTTGTATAGCC
TATATGAGGGGTTTAACTCTCCTCTATTTATTGATTAAATCAAAATTTTGTAATTTCGTAATTAG
AAGGATTAGGCCTAAAGGATAGATTTAGGCCTTATTTGCTCATCCACACATAGATTTAGGTCCAA
AATGTCACAATTATGATGTTTAGGCATAAATTGATAAAACTTGCAAAATTTTAGGTCTTTAATTA
TAGAGTTTTTAGCCTTTCCATCCGATAAACTTTTCATAG
Found at i:12773 original size:42 final size:43
Alignment explanation
Indices: 12718--12811 Score: 120
Period size: 45 Copynumber: 2.2 Consensus size: 43
12708 AGTGCATTAT
*
12718 CTAA-ATTCTA-CTCCATCTCTAGGTAATTCATCAAAATAAAG
1 CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAG
* *
12759 CTAATATTTTACTCCTCCATCTTTAGATAATTCATCAAAATAAAG
1 CTAATATTCTA--CCTCCATCTCTAGATAATTCATCAAAATAAAG
*
12804 TTAATATT
1 CTAATATT
12812 AATTGTTGCT
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
41 4 0.09
42 5 0.11
45 36 0.80
ACGTcount: A:0.38, C:0.19, G:0.05, T:0.37
Consensus pattern (43 bp):
CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAG
Found at i:14586 original size:13 final size:13
Alignment explanation
Indices: 14568--14594 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
14558 GAATACCAAT
14568 ACTTGATCCTTGG
1 ACTTGATCCTTGG
14581 ACTTGATCCTTGG
1 ACTTGATCCTTGG
14594 A
1 A
14595 TATTCACGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.19, C:0.22, G:0.22, T:0.37
Consensus pattern (13 bp):
ACTTGATCCTTGG
Found at i:15960 original size:12 final size:12
Alignment explanation
Indices: 15943--15967 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
15933 TTTCGTTCTT
15943 AAAAAAAAAATA
1 AAAAAAAAAATA
15955 AAAAAAAAAATA
1 AAAAAAAAAATA
15967 A
1 A
15968 GTTGGCTTCG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (12 bp):
AAAAAAAAAATA
Found at i:16108 original size:2 final size:2
Alignment explanation
Indices: 16097--16135 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
16087 AATCACACAC
*
16097 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
16136 CTAGTTAAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:20689 original size:23 final size:22
Alignment explanation
Indices: 20656--20730 Score: 78
Period size: 23 Copynumber: 3.2 Consensus size: 22
20646 ATTACACCTT
20656 GTAAAAACAAGGGTGATGAAAA
1 GTAAAAACAAGGGTGATGAAAA
* * * *
20678 GTAAATGACAAGGTTGATCACAACTT
1 GTAAA-AACAAGGGTGATGA-AA--A
20704 GTAAAAACAAGGGTGATGAAAA
1 GTAAAAACAAGGGTGATGAAAA
20726 GTAAA
1 GTAAA
20731 CGATAGGGTT
Statistics
Matches: 41, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
22 10 0.24
23 11 0.27
24 4 0.10
25 11 0.27
26 5 0.12
ACGTcount: A:0.49, C:0.08, G:0.24, T:0.19
Consensus pattern (22 bp):
GTAAAAACAAGGGTGATGAAAA
Found at i:20724 original size:48 final size:48
Alignment explanation
Indices: 20653--20745 Score: 159
Period size: 48 Copynumber: 1.9 Consensus size: 48
20643 AAGATTACAC
*
20653 CTTGTAAAAACAAGGGTGATGAAAAGTAAATGACAAGGTTGATCACAA
1 CTTGTAAAAACAAGGGTGATGAAAAGTAAACGACAAGGTTGATCACAA
* *
20701 CTTGTAAAAACAAGGGTGATGAAAAGTAAACGATAGGGTTGATCA
1 CTTGTAAAAACAAGGGTGATGAAAAGTAAACGACAAGGTTGATCA
20746 AACAAGAGTT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
48 42 1.00
ACGTcount: A:0.44, C:0.10, G:0.25, T:0.22
Consensus pattern (48 bp):
CTTGTAAAAACAAGGGTGATGAAAAGTAAACGACAAGGTTGATCACAA
Found at i:25972 original size:13 final size:13
Alignment explanation
Indices: 25954--25978 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
25944 TTCAATGTTG
25954 TAAATATTATTTA
1 TAAATATTATTTA
25967 TAAATATTATTT
1 TAAATATTATTT
25979 GAAATTCTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TAAATATTATTTA
Found at i:26590 original size:26 final size:26
Alignment explanation
Indices: 26541--26590 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
26531 AAATATATGT
* *
26541 ATGAATTATAATCAATAAAAAAATGG
1 ATGAATTATAATAAACAAAAAAATGG
26567 ATGAATTA-AATAAACAAAAGAAAT
1 ATGAATTATAATAAACAAAA-AAAT
26591 TTCTCAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 9 0.43
26 12 0.57
ACGTcount: A:0.62, C:0.04, G:0.10, T:0.24
Consensus pattern (26 bp):
ATGAATTATAATAAACAAAAAAATGG
Found at i:26605 original size:31 final size:32
Alignment explanation
Indices: 26570--26643 Score: 80
Period size: 32 Copynumber: 2.3 Consensus size: 32
26560 AAAATGGATG
* **
26570 AATTAAATAAACAA-AAGAAAT-TTCTCAAAAA
1 AATTAAAAAAACAAGAA-AAATATTCAAAAAAA
*
26601 AATTATAAAAAAGAAGAAAAATATTCAAAAAAA
1 AATTA-AAAAAACAAGAAAAATATTCAAAAAAA
26634 AATTAAAAAA
1 AATTAAAAAA
26644 GAGAAAGTTG
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
31 5 0.14
32 16 0.44
33 15 0.42
ACGTcount: A:0.70, C:0.05, G:0.04, T:0.20
Consensus pattern (32 bp):
AATTAAAAAAACAAGAAAAATATTCAAAAAAA
Found at i:28495 original size:100 final size:100
Alignment explanation
Indices: 28322--28521 Score: 382
Period size: 100 Copynumber: 2.0 Consensus size: 100
28312 TTTGCATGTT
28322 TAAAAAGTTAGCTTACAAAGATTTATGGCAATAACAAGAGAAAATATTAAAACGAATCCATCTAA
1 TAAAAAGTTAGCTTACAAAGATTTATGGCAATAACAAGAGAAAATATTAAAACGAATCCATCTAA
28387 ATTGCATTTTTACTGCAATCTTATATAATTCAATC
66 ATTGCATTTTTACTGCAATCTTATATAATTCAATC
* *
28422 TAAAAAGTTAGCTTACAAAGATTTATGGCAATAGCAAGAGAAAATATTAAAACGAATCCATTTAA
1 TAAAAAGTTAGCTTACAAAGATTTATGGCAATAACAAGAGAAAATATTAAAACGAATCCATCTAA
28487 ATTGCATTTTTACTGCAATCTTATATAATTCAATC
66 ATTGCATTTTTACTGCAATCTTATATAATTCAATC
28522 AATTAATCAA
Statistics
Matches: 98, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
100 98 1.00
ACGTcount: A:0.43, C:0.14, G:0.10, T:0.33
Consensus pattern (100 bp):
TAAAAAGTTAGCTTACAAAGATTTATGGCAATAACAAGAGAAAATATTAAAACGAATCCATCTAA
ATTGCATTTTTACTGCAATCTTATATAATTCAATC
Found at i:29066 original size:15 final size:15
Alignment explanation
Indices: 29033--29075 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
29023 ATTTTACCAC
*
29033 TAATAATAATTATTA
1 TAATAATAATAATTA
29048 TAATAATAATAAGTT-
1 TAATAATAATAA-TTA
*
29063 TAATAATTATAAT
1 TAATAATAATAAT
29076 ATTAAGATGT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 1 0.04
15 22 0.88
16 2 0.08
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (15 bp):
TAATAATAATAATTA
Found at i:29075 original size:9 final size:9
Alignment explanation
Indices: 29035--29076 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
29025 TTTACCACTA
29035 ATAATAATT
1 ATAATAATT
* *
29044 ATTATAATA
1 ATAATAATT
29053 ATAATAAGTT
1 ATAATAA-TT
29063 -TAATAATT
1 ATAATAATT
29071 ATAATA
1 ATAATA
29077 TTAAGATGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
8 2 0.07
9 24 0.89
10 1 0.04
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (9 bp):
ATAATAATT
Found at i:29087 original size:24 final size:24
Alignment explanation
Indices: 29039--29089 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
29029 CCACTAATAA
* *
29039 TAATTATTATAATAATAATAAGTT
1 TAATAATTATAATAATAAGAAGTT
* *
29063 TAATAATTATAATATTAAGATGTT
1 TAATAATTATAATAATAAGAAGTT
29087 TAA
1 TAA
29090 CGTAAAAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.45
Consensus pattern (24 bp):
TAATAATTATAATAATAAGAAGTT
Found at i:35585 original size:3 final size:3
Alignment explanation
Indices: 35577--35614 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
35567 AAAGAGTTAC
35577 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
35615 AAAGAGAAAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:41982 original size:9 final size:9
Alignment explanation
Indices: 41968--41993 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
41958 TGAGGTATCT
41968 GATGATGGG
1 GATGATGGG
41977 GATGATGGG
1 GATGATGGG
41986 GATGATGG
1 GATGATGG
41994 TGACCTTTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.23, C:0.00, G:0.54, T:0.23
Consensus pattern (9 bp):
GATGATGGG
Found at i:47694 original size:20 final size:21
Alignment explanation
Indices: 47649--47714 Score: 62
Period size: 21 Copynumber: 3.1 Consensus size: 21
47639 AAGAATCAAG
* * *
47649 AAATCAGTATGATTCGTGCAA
1 AAATCAGCAAGATTCGAGCAA
47670 AAATCAGCAAGATTCGAGC-A
1 AAATCAGCAAGATTCGAGCAA
* * *
47690 AAATCCAGCAACAATCGATCAA
1 AAAT-CAGCAAGATTCGAGCAA
47712 AAA
1 AAA
47715 CCAGAGGAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
20 5 0.14
21 28 0.76
22 4 0.11
ACGTcount: A:0.47, C:0.20, G:0.15, T:0.18
Consensus pattern (21 bp):
AAATCAGCAAGATTCGAGCAA
Found at i:53504 original size:23 final size:21
Alignment explanation
Indices: 53478--53537 Score: 59
Period size: 23 Copynumber: 2.7 Consensus size: 21
53468 AATCCTGTAG
53478 AAAGAAACAAGAAAAA-TCAAAGC
1 AAAGAAA-AAGAAAAATTC-AA-C
*
53501 AAAGAGAAATCGAAAAATTCAAC
1 AAAGA-AAA-AGAAAAATTCAAC
53524 AAAGAAAAAGAAAA
1 AAAGAAAAAGAAAA
53538 GAAAAACGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
21 5 0.16
22 3 0.09
23 12 0.38
24 10 0.31
25 2 0.06
ACGTcount: A:0.70, C:0.10, G:0.13, T:0.07
Consensus pattern (21 bp):
AAAGAAAAAGAAAAATTCAAC
Found at i:54687 original size:15 final size:15
Alignment explanation
Indices: 54667--54698 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
54657 ACCATAGATC
54667 AAATAATTATTCCAT
1 AAATAATTATTCCAT
54682 AAATAATTATTCCAT
1 AAATAATTATTCCAT
54697 AA
1 AA
54699 CTATGATCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (15 bp):
AAATAATTATTCCAT
Found at i:63230 original size:34 final size:35
Alignment explanation
Indices: 63084--63250 Score: 187
Period size: 34 Copynumber: 4.7 Consensus size: 35
63074 TGAAAATTGA
* * *
63084 TGGGAACTTTCCCTAAATTGAAAAC-AAAAACCTGA
1 TGGGAACTTTCCC-AATTTAAAAACTAAAAACCTGG
*
63119 TGGGAACTCTCCCAATTTAAAAACTTTGAAAAA-CTGG
1 TGGGAACTTTCCCAATTTAAAAAC--T-AAAAACCTGG
* * * *
63156 TGGGAACCTTCCCAATTTTAAAACTTAAAAACTTGT
1 TGGGAACTTTCCCAATTTAAAAAC-TAAAAACCTGG
63192 TGGGAACTTTCCCAATTTAAAAACT-AAAACCTGG
1 TGGGAACTTTCCCAATTTAAAAACTAAAAACCTGG
*
63226 TGGGAACTTTCCCAATTTGAAAACT
1 TGGGAACTTTCCCAATTTAAAAACT
63251 TCGAAGACTG
Statistics
Matches: 113, Mismatches: 14, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
34 40 0.35
35 18 0.16
36 26 0.23
37 24 0.21
38 5 0.04
ACGTcount: A:0.38, C:0.20, G:0.14, T:0.28
Consensus pattern (35 bp):
TGGGAACTTTCCCAATTTAAAAACTAAAAACCTGG
Found at i:63290 original size:15 final size:16
Alignment explanation
Indices: 63265--63300 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
63255 AGACTGATTC
63265 TTGATTTTTTTGAATT
1 TTGATTTTTTTGAATT
* *
63281 TTGATTTTTTGGATTT
1 TTGATTTTTTTGAATT
63297 TTGA
1 TTGA
63301 AAGCTTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.17, C:0.00, G:0.17, T:0.67
Consensus pattern (16 bp):
TTGATTTTTTTGAATT
Found at i:64561 original size:2 final size:2
Alignment explanation
Indices: 64554--64578 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
64544 GAAAAATGTG
64554 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
64579 GCCCCTCTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:65722 original size:19 final size:18
Alignment explanation
Indices: 65698--65733 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
65688 TGAAGACCAT
65698 TTGAAGATAATTTGAAGAC
1 TTGAAGAT-ATTTGAAGAC
*
65717 TTGAAGATTTTTGAAGA
1 TTGAAGATATTTGAAGA
65734 ACTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.39, C:0.03, G:0.22, T:0.36
Consensus pattern (18 bp):
TTGAAGATATTTGAAGAC
Found at i:66349 original size:11 final size:11
Alignment explanation
Indices: 66333--66358 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
66323 AGATAATTTC
66333 TTTTCTTCTAG
1 TTTTCTTCTAG
66344 TTTTCTTCTAG
1 TTTTCTTCTAG
66355 TTTT
1 TTTT
66359 TTAGGCAAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.15, G:0.08, T:0.69
Consensus pattern (11 bp):
TTTTCTTCTAG
Found at i:70048 original size:2 final size:2
Alignment explanation
Indices: 70043--70071 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
70033 ATATATGTAT
70043 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
70072 TATATATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:80968 original size:2 final size:2
Alignment explanation
Indices: 80963--80994 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
80953 TCTTTTTTTC
80963 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
80995 ATAAGCACCC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.