Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012927.1 Corchorus olitorius cultivar O-4 contig12960, 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: 89822
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:7776 original size:3 final size:3
Alignment explanation
Indices: 7728--7762 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
7718 TAATTCAGTA
7728 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
7763 CTACAAAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:14273 original size:4 final size:4
Alignment explanation
Indices: 14266--14295 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
14256 TTGCTTGCTC
*
14266 CTTT CTTT CTTT CGTT CTTT CTTT CTTT CT
1 CTTT CTTT CTTT CTTT CTTT CTTT CTTT CT
14296 CTCTCTCTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.00, C:0.27, G:0.03, T:0.70
Consensus pattern (4 bp):
CTTT
Found at i:16324 original size:51 final size:51
Alignment explanation
Indices: 16253--16355 Score: 127
Period size: 51 Copynumber: 2.0 Consensus size: 51
16243 TATTTCTGAA
* **
16253 AGAGAAACACGAATACAGTGTTTTTATGTCCGGAGACAAGAT-TGAAACAAG
1 AGAGAAACACGAAAACAGTGTTTGGATGTCCGGAGACAAGATCT-AAACAAG
* * * *
16304 AGAGAAACACTAAAAGAGTGTTTGGGTGTCCTGAGACAAGATCTAAACAAG
1 AGAGAAACACGAAAACAGTGTTTGGATGTCCGGAGACAAGATCTAAACAAG
16355 A
1 A
16356 AAAATATGAA
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
51 43 0.98
52 1 0.02
ACGTcount: A:0.42, C:0.14, G:0.24, T:0.20
Consensus pattern (51 bp):
AGAGAAACACGAAAACAGTGTTTGGATGTCCGGAGACAAGATCTAAACAAG
Found at i:19657 original size:27 final size:27
Alignment explanation
Indices: 19619--19677 Score: 82
Period size: 27 Copynumber: 2.2 Consensus size: 27
19609 TTTGCTAATC
* * **
19619 AACTTTTCCTACTCCTTTACATTACCA
1 AACTGTTCCTACTCCTTAACAACACCA
19646 AACTGTTCCTACTCCTTAACAACACCA
1 AACTGTTCCTACTCCTTAACAACACCA
19673 AACTG
1 AACTG
19678 AAGGCAATTC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.31, C:0.34, G:0.03, T:0.32
Consensus pattern (27 bp):
AACTGTTCCTACTCCTTAACAACACCA
Found at i:21843 original size:18 final size:19
Alignment explanation
Indices: 21793--21844 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 19
21783 CACTCTTCAA
21793 CGCAGAGC-TCT-TCTTAC
1 CGCAGAGCTTCTCTCTTAC
*
21810 CGCGGTAGCATTCTCT-TTAC
1 CGCAG-AGC-TTCTCTCTTAC
21830 CGCAGAGCTTCTCTC
1 CGCAGAGCTTCTCTC
21845 ACTGCAAAGC
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
17 4 0.14
18 9 0.32
19 3 0.11
20 11 0.39
21 1 0.04
ACGTcount: A:0.15, C:0.35, G:0.19, T:0.31
Consensus pattern (19 bp):
CGCAGAGCTTCTCTCTTAC
Found at i:21844 original size:20 final size:18
Alignment explanation
Indices: 21793--21877 Score: 59
Period size: 19 Copynumber: 4.7 Consensus size: 18
21783 CACTCTTCAA
21793 CGCAGAGCTCT-TCTTAC
1 CGCAGAGCTCTCTCTTAC
*
21810 CGCGGTAGCAT-TCTCTTTAC
1 CGCAG-AGC-TCTCTC-TTAC
*
21830 CGCAGAGCT-TCTCTCAC
1 CGCAGAGCTCTCTCTTAC
* * * *
21847 TGCAAAGCACCCTCTCTAC
1 CGCAGAGCTCTCTCT-TAC
21866 CGCAGAGCTCTC
1 CGCAGAGCTCTC
21878 ATTACAGCGG
Statistics
Matches: 50, Mismatches: 12, Indels: 10
0.69 0.17 0.14
Matches are distributed among these distances:
17 13 0.26
18 13 0.26
19 16 0.32
20 8 0.16
ACGTcount: A:0.19, C:0.38, G:0.18, T:0.26
Consensus pattern (18 bp):
CGCAGAGCTCTCTCTTAC
Found at i:21872 original size:73 final size:74
Alignment explanation
Indices: 21793--21949 Score: 196
Period size: 73 Copynumber: 2.1 Consensus size: 74
21783 CACTCTTCAA
* *
21793 CGCAGAGCTCTTC-TTACCGCGGTAGCATTC-TCTTTACCGCAGAGCT-TCTCTCACTGCAAAGC
1 CGCAGAGCTCTTCATTACAGCGGTAGCA-CCGTCTTTACCGCAGAGCTCTC-CTCACTGCAAAGC
21855 ACCCTCTCTAC
64 ACCCTCTCTAC
* **
21866 CGCAGAGCTC-TCATTACAGCGGTAGCACCGTCTTTACCGCAGAGCTCTCCTTACTGCGTAGCAC
1 CGCAGAGCTCTTCATTACAGCGGTAGCACCGTCTTTACCGCAGAGCTCTCCTCACTGCAAAGCAC
*
21930 CCTCTTTAC
66 CCTCTCTAC
* *
21939 TGCAAAGCTCT
1 CGCAGAGCTCT
21950 CCATACAAAG
Statistics
Matches: 72, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
72 3 0.04
73 67 0.93
74 2 0.03
ACGTcount: A:0.20, C:0.36, G:0.18, T:0.27
Consensus pattern (74 bp):
CGCAGAGCTCTTCATTACAGCGGTAGCACCGTCTTTACCGCAGAGCTCTCCTCACTGCAAAGCAC
CCTCTCTAC
Found at i:21936 original size:36 final size:37
Alignment explanation
Indices: 21793--21951 Score: 171
Period size: 36 Copynumber: 4.4 Consensus size: 37
21783 CACTCTTCAA
* * **
21793 CGCAGAGCTCTTCTTACCGCGGTAGCATTCTCTTTAC
1 CGCAGAGCTCTCCTTACTGCGGTAGCACCCTCTTTAC
* ** *
21830 CGCAGAGCT-TCTCTCACTGC-AAAGCACCCTCTCTAC
1 CGCAGAGCTCTC-CTTACTGCGGTAGCACCCTCTTTAC
* * *
21866 CGCAGAGCTCTCATTACAGCGGTAGCACCGTCTTTAC
1 CGCAGAGCTCTCCTTACTGCGGTAGCACCCTCTTTAC
21903 CGCAGAGCTCTCCTTACTGC-GTAGCACCCTCTTTAC
1 CGCAGAGCTCTCCTTACTGCGGTAGCACCCTCTTTAC
* *
21939 TGCAAAGCTCTCC
1 CGCAGAGCTCTCC
21952 ATACAAAGCA
Statistics
Matches: 99, Mismatches: 20, Indels: 7
0.79 0.16 0.06
Matches are distributed among these distances:
36 52 0.53
37 47 0.47
ACGTcount: A:0.19, C:0.36, G:0.18, T:0.26
Consensus pattern (37 bp):
CGCAGAGCTCTCCTTACTGCGGTAGCACCCTCTTTAC
Found at i:26165 original size:25 final size:23
Alignment explanation
Indices: 26132--26184 Score: 61
Period size: 25 Copynumber: 2.2 Consensus size: 23
26122 ATGTTGTGTC
* * *
26132 AAAACCTTTTATTTATGTTTCTTTT
1 AAAATCTTTTACTT-TGTTT-TTTG
26157 AAAATCTTTTACTTTGTTTTTTG
1 AAAATCTTTTACTTTGTTTTTTG
26180 AAAAT
1 AAAAT
26185 TCCCATTTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 8 0.32
24 5 0.20
25 12 0.48
ACGTcount: A:0.28, C:0.09, G:0.06, T:0.57
Consensus pattern (23 bp):
AAAATCTTTTACTTTGTTTTTTG
Found at i:27592 original size:5 final size:5
Alignment explanation
Indices: 27584--27612 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
27574 AGTCCAAACG
27584 GAAAA GAAAA GAAAA -AAAA GAAAA GAAAA
1 GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA
27613 AGGCCCAAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 19 0.83
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (5 bp):
GAAAA
Found at i:27604 original size:14 final size:14
Alignment explanation
Indices: 27585--27613 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
27575 GTCCAAACGG
27585 AAAAGAAAAGAAAA
1 AAAAGAAAAGAAAA
27599 AAAAGAAAAGAAAA
1 AAAAGAAAAGAAAA
27613 A
1 A
27614 GGCCCAAGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (14 bp):
AAAAGAAAAGAAAA
Found at i:34436 original size:53 final size:52
Alignment explanation
Indices: 34327--34464 Score: 204
Period size: 53 Copynumber: 2.6 Consensus size: 52
34317 TCAAAATTTC
* * *
34327 CAAATTGGGAAAGTTCCCAACAAGTTTTCAAAGTGTTCGATTTAGATCTTTT
1 CAAAGTGGGAAAGTTCCCATCAAGTTTTCAAAGTGTTCAATTTAGATCTTTT
* *
34379 CAAAGTGGGAAATTTCCCATCAAGTTTTCAATAGTGTTCAATTTAGGTCTTTT
1 CAAAGTGGGAAAGTTCCCATCAAGTTTTCAA-AGTGTTCAATTTAGATCTTTT
* *
34432 CAAAGTGGGAAAGTTCTCATCAGGTTTTCAAAG
1 CAAAGTGGGAAAGTTCCCATCAAGTTTTCAAAG
34465 CGTCAAACAA
Statistics
Matches: 77, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
52 30 0.39
53 47 0.61
ACGTcount: A:0.30, C:0.15, G:0.19, T:0.36
Consensus pattern (52 bp):
CAAAGTGGGAAAGTTCCCATCAAGTTTTCAAAGTGTTCAATTTAGATCTTTT
Found at i:36269 original size:2 final size:2
Alignment explanation
Indices: 36262--36307 Score: 83
Period size: 2 Copynumber: 22.5 Consensus size: 2
36252 GAAGATCATC
36262 AT AT AT AT CAT AT AT AT AT 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
36305 AT A
1 AT A
36308 ATGATAACAA
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 41 0.95
3 2 0.05
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:37019 original size:140 final size:140
Alignment explanation
Indices: 36805--37086 Score: 537
Period size: 140 Copynumber: 2.0 Consensus size: 140
36795 CTAATTGTGC
*
36805 ATCTTTTTGGAAATATGATTGACCGAAATTATGGATTAATAATTGCTTAGTTTTAACATTACTAT
1 ATCTTATTGGAAATATGATTGACCGAAATTATGGATTAATAATTGCTTAGTTTTAACATTACTAT
* *
36870 ATTAGGAGTTAACCCCTTGATTTTAGTATATCTCAAATTAATTATCAATGTCAATTTTTTTTAAC
66 ATTAGGAGTTAACCCCTTGATTTTAGTAAATCTCAAATTAATTATCAATGTCAATTTCTTTTAAC
36935 GAAATTACAA
131 GAAATTACAA
36945 ATCTTATTGGAAATATGATTGACCGAAATTATGGATTAATAATTGCTTAGTTTTAACATTACTAT
1 ATCTTATTGGAAATATGATTGACCGAAATTATGGATTAATAATTGCTTAGTTTTAACATTACTAT
37010 ATTAGGAGTTAACCCCTTGATTTTAGTAAATCTCAAATTAATTATCAATGTCAATTTCTTTTAAC
66 ATTAGGAGTTAACCCCTTGATTTTAGTAAATCTCAAATTAATTATCAATGTCAATTTCTTTTAAC
37075 GAAATTACAA
131 GAAATTACAA
37085 AT
1 AT
37087 GTCAAATTGA
Statistics
Matches: 139, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
140 139 1.00
ACGTcount: A:0.36, C:0.12, G:0.11, T:0.41
Consensus pattern (140 bp):
ATCTTATTGGAAATATGATTGACCGAAATTATGGATTAATAATTGCTTAGTTTTAACATTACTAT
ATTAGGAGTTAACCCCTTGATTTTAGTAAATCTCAAATTAATTATCAATGTCAATTTCTTTTAAC
GAAATTACAA
Found at i:51104 original size:22 final size:21
Alignment explanation
Indices: 51057--51130 Score: 69
Period size: 22 Copynumber: 3.5 Consensus size: 21
51047 GCTTACAAGA
51057 TTAC-AAAAATTTTAATAAAGG
1 TTACTAAAAATTTTAAT-AAGG
*
51078 CTACTAAAAATTTTAATAAGGG
1 TTACTAAAAATTTTAATAA-GG
* ** *
51100 TTACTGAAACGTTTAGTAAGG
1 TTACTAAAAATTTTAATAAGG
*
51121 TTACTTAAAA
1 TTACTAAAAA
51131 GCTTATTAAC
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
21 15 0.35
22 28 0.65
ACGTcount: A:0.45, C:0.08, G:0.14, T:0.34
Consensus pattern (21 bp):
TTACTAAAAATTTTAATAAGG
Found at i:51622 original size:85 final size:86
Alignment explanation
Indices: 51520--51697 Score: 259
Period size: 85 Copynumber: 2.1 Consensus size: 86
51510 TAAGATGACT
* * * *
51520 AAAAATCTGAAATGAGGTTATTGAATAAATTTAAGAAAACTATTTAAAAAGCTGTTAAGTTTATT
1 AAAAATCTGAAACGAGGTGATTGAATAAATTTAAGAAAACTATTTAAAAAGCTGTTAACTTTAAT
* *
51585 G-ACAATTTATAAACTTACCA
66 GAAAAATTTATAAACTTACAA
* * *
51605 AAAAATCTTAAACGAGGTGATTGAATAAATTTATGAAAACTATTTAAAAAGCTTTTAACTTTAAT
1 AAAAATCTGAAACGAGGTGATTGAATAAATTTAAGAAAACTATTTAAAAAGCTGTTAACTTTAAT
51670 GAAAAATTTATAAACTTACAA
66 GAAAAATTTATAAACTTACAA
51691 AGAAAAT
1 A-AAAAT
51698 TTACAAGGTT
Statistics
Matches: 82, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
85 59 0.72
86 18 0.22
87 5 0.06
ACGTcount: A:0.48, C:0.08, G:0.11, T:0.33
Consensus pattern (86 bp):
AAAAATCTGAAACGAGGTGATTGAATAAATTTAAGAAAACTATTTAAAAAGCTGTTAACTTTAAT
GAAAAATTTATAAACTTACAA
Found at i:51868 original size:21 final size:21
Alignment explanation
Indices: 51815--51868 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 21
51805 GAAGAACTTA
51815 ATAAGGTTAC-AAAAAGTTTT
1 ATAAGGTTACTAAAAAGTTTT
* *
51835 ATTA--TTATTAAAAA-TATTT
1 ATAAGGTTACTAAAAAGT-TTT
51854 ATAAGGTTACTAAAA
1 ATAAGGTTACTAAAA
51869 TTAGTAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 7
0.70 0.11 0.19
Matches are distributed among these distances:
18 4 0.15
19 11 0.42
20 3 0.12
21 8 0.31
ACGTcount: A:0.48, C:0.04, G:0.09, T:0.39
Consensus pattern (21 bp):
ATAAGGTTACTAAAAAGTTTT
Found at i:56839 original size:2 final size:2
Alignment explanation
Indices: 56834--56879 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
56824 CCTTGCTTTG
56834 AT AT AT AT AT AT AT AT AT 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
56876 AT AT
1 AT AT
56880 TGACTACAAG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:57801 original size:26 final size:27
Alignment explanation
Indices: 57740--57803 Score: 78
Period size: 26 Copynumber: 2.4 Consensus size: 27
57730 ATATTGATCA
57740 AAGGTTACT-AAAATTTCTAAGAATGC
1 AAGGTTACTAAAAATTTCTAAGAATGC
* * *
57766 AAAGTCACTAAAAATTTC-AAGAATGT
1 AAGGTTACTAAAAATTTCTAAGAATGC
*
57792 GAGGTTACTAAA
1 AAGGTTACTAAA
57804 TTTATGTAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
26 23 0.74
27 8 0.26
ACGTcount: A:0.45, C:0.11, G:0.16, T:0.28
Consensus pattern (27 bp):
AAGGTTACTAAAAATTTCTAAGAATGC
Found at i:59706 original size:198 final size:200
Alignment explanation
Indices: 59266--60325 Score: 1507
Period size: 198 Copynumber: 5.3 Consensus size: 200
59256 TTGGCACAAA
* ** *
59266 AACTTCTTAACCCGTTTATAAAGTCCAAAATTTACGCTGACAGTGTATTGTATAATAATCCTATA
1 AACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTGTATAATAATCCTATA
* *
59331 AGAAAATTTATACAATACACCGTCAGTGGAGTTTAGTAGACTGCACGTGCGGGGTATAACTTTAA
66 AGAAAAATTATACAATACACCGTCAGTGGAGTTTAGCAGACTGCACGTGC----TATAA-TTTAA
* *
59396 GGGTTGACATGTGTACCCTTAGGGAATATGTATTAATATTAAATA--T--TTAATCATGAAATGG
126 GGGTTGACATGTGTCCCCTTAGGGAATATGTATTAATATTAAATATTTAATTAATTATGAAATGG
59457 GGTATGTGTC
191 GGTATGTGTC
* *
59467 AACTTCTTAACCCGTTTATGGAGTTCAAAATTTACACTGACAGTGTATTGTATAATAATCCTATA
1 AACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTGTATAATAATCCTATA
* *
59532 AGAAAAATTATACAATAC-CCGTCAGTGGATTTTAGCAGACTGCACGTGCAAT-ATTTAAGGGTT
66 AGAAAAATTATACAATACACCGTCAGTGGAGTTTAGCAGACTGCACGTGCTATAATTTAAGGGTT
*
59595 GACATGTGTCCCCTCAGGGAATATGTATTAATATTAAATATTTAATTAATTATGAAATGGGGTAT
131 GACATGTGTCCCCTTAGGGAATATGTATTAATATTAAATATTTAATTAATTATGAAATGGGGTAT
59660 GTGTC
196 GTGTC
* * *
59665 AACTTCTTAACTCGCTCATGGAGTCCAAAATTTATACTGACAGTGTATTGTATAATAATCCTATA
1 AACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTGTATAATAATCCTATA
*
59730 AGAAAATTTATACAATACACCGTCAGTGGAGTTTAGCAGACTGCACGTGCGGGGTATAACTTTAA
66 AGAAAAATTATACAATACACCGTCAGTGGAGTTTAGCAGACTGCACGTGC----TATAA-TTTAA
* *
59795 GGGTTGACATGTGTACCCTTAGGGAATATGTATTAATATTAAATA--T--TTAATCATGAAATGG
126 GGGTTGACATGTGTCCCCTTAGGGAATATGTATTAATATTAAATATTTAATTAATTATGAAATGG
59856 GGTATGTGTC
191 GGTATGTGTC
* * * * *
59866 AACTTCTTAACCCACTTAAGGAGTCCAAAAATTACATTGACAGTGTATTGTATAATAATCATATA
1 AACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTGTATAATAATCCTATA
* * * * ****
59931 AAAAAAATTATACAATACACTGTCAGTGGAGTTTAGAATACTGCACGTGC-GGGGTTTAAGGGTT
66 AGAAAAATTATACAATACACCGTCAGTGGAGTTTAGCAGACTGCACGTGCTATAATTTAAGGGTT
* * ** *
59995 GACATGTCTCCTCTTAGGGAATATGTATTAATATTTCATATTTAATTAATTATGAAATAGGGTAT
131 GACATGTGTCCCCTTAGGGAATATGTATTAATATTAAATATTTAATTAATTATGAAATGGGGTAT
60060 GTGTC
196 GTGTC
* *
60065 AACTTCTTAACCCGATTATGGAGTTCAAAATTTACACTGACAGTGTATTGTATAATAATCCTATA
1 AACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTGTATAATAATCCTATA
* * **
60130 A-AAAAATTATACAATACACGGTCAGTGGAGTTTAGTAGACTGCACGTGC-ATGGTTTAAGGGTT
66 AGAAAAATTATACAATACACCGTCAGTGGAGTTTAGCAGACTGCACGTGCTATAATTTAAGGGTT
* *
60193 GACATGTGTCCTCTTAGGGAATATGTATTAATATCAAATATTTAATTAATTATGAAATGGGGTAT
131 GACATGTGTCCCCTTAGGGAATATGTATTAATATTAAATATTTAATTAATTATGAAATGGGGTAT
60258 GTGTC
196 GTGTC
* *
60263 AACTTCTTAACCCGCTTATGGAGTCCACAATTTACATTGACAGTGTATTTGTATAATAATCCT
1 AACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTA-TTGTATAATAATCCT
60326 TATTATAAGC
Statistics
Matches: 776, Mismatches: 67, Indels: 34
0.88 0.08 0.04
Matches are distributed among these distances:
194 48 0.06
195 46 0.06
196 3 0.00
197 1 0.00
198 266 0.34
199 127 0.16
200 29 0.04
201 204 0.26
203 3 0.00
204 1 0.00
205 48 0.06
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.34
Consensus pattern (200 bp):
AACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTGTATAATAATCCTATA
AGAAAAATTATACAATACACCGTCAGTGGAGTTTAGCAGACTGCACGTGCTATAATTTAAGGGTT
GACATGTGTCCCCTTAGGGAATATGTATTAATATTAAATATTTAATTAATTATGAAATGGGGTAT
GTGTC
Found at i:60142 original size:399 final size:399
Alignment explanation
Indices: 59266--60323 Score: 1646
Period size: 399 Copynumber: 2.7 Consensus size: 399
59256 TTGGCACAAA
* ** *
59266 AACTTCTTAACCCGTTTATAAAGTCCAAAATTTACGCTGACAGTGTATTGTATAATAATCCTATA
1 AACTTCTTAACCCGATTATGGAGTCCAAAATTTACACTGACAGTGTATTGTATAATAATCCTATA
59331 AGAAAATTTATACAATACACCGTCAGTGGAGTTTAGTAGACTGCACGTGCGGGGTATAACTTTAA
66 AGAAAATTTATACAATACACCGTCAGTGGAGTTTAGTAGACTGCACGTGCGGGGTATAACTTTAA
59396 GGGTTGACATGTGTACCCTTAGGGAATATGTATTAATATTAAATATTTAATCATGAAATGGGGTA
131 GGGTTGACATGTGTACCCTTAGGGAATATGTATTAATATTAAATATTTAATCATGAAATGGGGTA
* * *
59461 TGTGTCAACTTCTTAACCCGTTTATGGAGTTCAAAATTTACACTGACAGTGTATTGTATAATAAT
196 TGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACATTGACAGTGTATTGTATAATAAT
* * * * *
59526 CCTATAAGAAAAATTATACAATACCCGTCAGTGGATTTTAGCAGACTGCACGTGCAATATTTAAG
261 CATATAAAAAAAATTATACAATACCCGTCAGTGGAGTTTAGAAGACTGCACGTGCAAGATTTAAG
* *
59591 GGTTGACATGTGTCCCCTCAGGGAATATGTATTAATATTAAATATTTAATTAATTATGAAATGGG
326 GGTTGACATGTCTCCCCTCAGGGAATATGTATTAATATTAAATATTTAATTAATTATGAAATAGG
59656 GTATGTGTC
391 GTATGTGTC
* * * *
59665 AACTTCTTAACTCGCTCATGGAGTCCAAAATTTATACTGACAGTGTATTGTATAATAATCCTATA
1 AACTTCTTAACCCGATTATGGAGTCCAAAATTTACACTGACAGTGTATTGTATAATAATCCTATA
*
59730 AGAAAATTTATACAATACACCGTCAGTGGAGTTTAGCAGACTGCACGTGCGGGGTATAACTTTAA
66 AGAAAATTTATACAATACACCGTCAGTGGAGTTTAGTAGACTGCACGTGCGGGGTATAACTTTAA
59795 GGGTTGACATGTGTACCCTTAGGGAATATGTATTAATATTAAATATTTAATCATGAAATGGGGTA
131 GGGTTGACATGTGTACCCTTAGGGAATATGTATTAATATTAAATATTTAATCATGAAATGGGGTA
* * *
59860 TGTGTCAACTTCTTAACCCACTTAAGGAGTCCAAAAATTACATTGACAGTGTATTGTATAATAAT
196 TGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACATTGACAGTGTATTGTATAATAAT
* * ** *
59925 CATATAAAAAAAATTATACAATACACTGTCAGTGGAGTTTAGAATACTGCACGTGCGGGGTTTAA
261 CATATAAAAAAAATTATACAATAC-CCGTCAGTGGAGTTTAGAAGACTGCACGTGCAAGATTTAA
* * **
59990 GGGTTGACATGTCTCCTCTTAGGGAATATGTATTAATATTTCATATTTAATTAATTATGAAATAG
325 GGGTTGACATGTCTCCCCTCAGGGAATATGTATTAATATTAAATATTTAATTAATTATGAAATAG
60055 GGTATGTGTC
390 GGTATGTGTC
*
60065 AACTTCTTAACCCGATTATGGAGTTCAAAATTTACACTGACAGTGTATTGTATAATAATCCTATA
1 AACTTCTTAACCCGATTATGGAGTCCAAAATTTACACTGACAGTGTATTGTATAATAATCCTATA
* * **
60130 A-AAAAATTATACAATACACGGTCAGTGGAGTTTAGTAGACTGCACGTGC-----AT-GGTTTAA
66 AGAAAATTTATACAATACACCGTCAGTGGAGTTTAGTAGACTGCACGTGCGGGGTATAACTTTAA
* *
60188 GGGTTGACATGTGT-CCTCTTAGGGAATATGTATTAATATCAAATATTTAATTAATTATGAAATG
131 GGGTTGACATGTGTACC-CTTAGGGAATATGTATTAATATTAAATA--T--TTAATCATGAAATG
*
60252 GGGTATGTGTCAACTTCTTAACCCGCTTATGGAGTCCACAATTTACATTGACAGTGTATTTGTAT
191 GGGTATGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACATTGACAGTGTA-TTGTAT
60317 AATAATC
255 AATAATC
60324 CTTATTATAA
Statistics
Matches: 606, Mismatches: 46, Indels: 15
0.91 0.07 0.02
Matches are distributed among these distances:
392 2 0.00
393 46 0.08
394 2 0.00
395 1 0.00
397 67 0.11
398 13 0.02
399 313 0.52
400 162 0.27
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.34
Consensus pattern (399 bp):
AACTTCTTAACCCGATTATGGAGTCCAAAATTTACACTGACAGTGTATTGTATAATAATCCTATA
AGAAAATTTATACAATACACCGTCAGTGGAGTTTAGTAGACTGCACGTGCGGGGTATAACTTTAA
GGGTTGACATGTGTACCCTTAGGGAATATGTATTAATATTAAATATTTAATCATGAAATGGGGTA
TGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACATTGACAGTGTATTGTATAATAAT
CATATAAAAAAAATTATACAATACCCGTCAGTGGAGTTTAGAAGACTGCACGTGCAAGATTTAAG
GGTTGACATGTCTCCCCTCAGGGAATATGTATTAATATTAAATATTTAATTAATTATGAAATAGG
GTATGTGTC
Found at i:66636 original size:18 final size:18
Alignment explanation
Indices: 66602--66636 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
66592 AAGGGATCCA
*
66602 AACTTTCTGTTGCAATTT
1 AACTTTCTGTTACAATTT
*
66620 AACTTTCTGTTATAATT
1 AACTTTCTGTTACAATT
66637 ATGTCTTAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.14, G:0.09, T:0.51
Consensus pattern (18 bp):
AACTTTCTGTTACAATTT
Found at i:75685 original size:14 final size:14
Alignment explanation
Indices: 75666--75694 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
75656 GTTTCTGTCC
75666 AAGAACATTAGGAT
1 AAGAACATTAGGAT
75680 AAGAACATTAGGAT
1 AAGAACATTAGGAT
75694 A
1 A
75695 GTTGCATGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.52, C:0.07, G:0.21, T:0.21
Consensus pattern (14 bp):
AAGAACATTAGGAT
Found at i:78398 original size:199 final size:199
Alignment explanation
Indices: 77930--78934 Score: 1359
Period size: 199 Copynumber: 5.1 Consensus size: 199
77920 AATCACTTTG
* *
77930 TATAATTTTTCTTATAGGATTATTATAC-ATACACTTTTCAGTGTAAATTTTGGACTTCATAAGC
1 TATAATTTTTCTTATAGGATTATTATACAATACAC-TGTCAGTGTAAATTTTGGACTCCATAAGC
* *
77994 GGGTTAAGAAGTTGATACATACCCCATTTCATAATCAATTAAATATTTAATATTAATACATATTC
65 GGGTTAAGAAGTTGACACATACCCCATTTCATAATTAATTAAATATTTAATATTAATACATATTC
* ** * *
78059 CTTAA-GGG------GTCAACCCTTAAACCCTTCACGTGCAGTCTGCTAAATTCGACTGACGGTG
130 CCTAAGGGGACACATGTCAACCCTTAAACCCCGCACGTGCAGTCTGCTAAACTCCACTGACGGTG
78117 TATAGTA
195 TAT--TA
* * * * *
78124 TAAATATTTTTCTTATAAGATTATTATACAATACACTGTTATTGTAAATTTTGGACTCCATAAAC
1 TATA-ATTTTTCTTATAGGATTATTATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAGC
* *
78189 GGGTTAAGAAGTTGACATATAACCCATTTCATAATTAATTAAATATTTAATATTAATACATATTC
65 GGGTTAAGAAGTTGACACATACCCCATTTCATAATTAATTAAATATTTAATATTAATACATATTC
* *
78254 CCTAAGGGGACACATGTCAACCCTCAAACCCCGCACGTGCAGTCTGCTAAGA-TCCACTGATGGT
130 CCTAAGGGGACACATGTCAACCCTTAAACCCCGCACGTGCAGTCTGCTAA-ACTCCACTGACGGT
78318 GTATTA
194 GTATTA
* * * *
78324 TATAATTCTTCTTATAGGATTATTATAAAACACGCTGTCAGTGTAAATTTTGGACTCCATAAGCG
1 TATAATTTTTCTTATAGGATTATTATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAGCG
* * * *
78389 GGTTAAGAAGTTGACACATACCTCATTTCATAATAAATTCAATATTGAATATTAATACATATTCC
66 GGTTAAGAAGTTGACACATACCCCATTTCATAATTAATTAAATATTTAATATTAATACATATTCC
* * ** * * *
78454 GTAGGGGGACACATGTCAACCCTTAAACCTTGCACGTGCAATCTGCTAAACTCGATTGACGGTGT
131 CTAAGGGGACACATGTCAACCCTTAAACCCCGCACGTGCAGTCTGCTAAACTCCACTGACGGTGT
78519 A-TA
196 ATTA
* * *
78522 GTGTAATTTTTCTTATAGGATTATTATACAATACACTTTCAGTGTAAATTTTGAACTCCATAAGC
1 -TATAATTTTTCTTATAGGATTATTATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAGC
*
78587 GGGTTAAGAAGTTGACACATACCCCATTTCATAATTAATAAAATATTTAATATTAATACATATTC
65 GGGTTAAGAAGTTGACACATACCCCATTTCATAATTAATTAAATATTTAATATTAATACATATTC
* * *
78652 CCTAAGGGGAAACATGTCAACCCTTAAACCTCGCACGTGCAGTCTGCTAAAATCCACTGACGGTG
130 CCTAAGGGGACACATGTCAACCCTTAAACCCCGCACGTGCAGTCTGCTAAACTCCACTGACGGTG
*
78717 TATTG
195 TATTA
** * *
78722 TATAATTTTTCTTATAGGATTATTATACAATACGTTGTCAGTGTAAATTTTGGA-T-TATAAGCA
1 TATAATTTTTCTTATAGGATTATTATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAGCG
* *
78785 GGTTAAGAAGTTGACACATACCCCATTTCATAATTAATAAAATATTTAATATTAATACATATTCA
66 GGTTAAGAAGTTGACACATACCCCATTTCATAATTAATTAAATATTTAATATTAATACATATTCC
* * * * * * * **
78850 CTAAGGGCAGACATGTCAACCCTTAAACCCCACACGTCCAGTCTACTAAACTCCAATGATGGCAT
131 CTAAGGGGACACATGTCAACCCTTAAACCCCGCACGTGCAGTCTGCTAAACTCCACTGACGGTGT
*
78915 ATTG
196 ATTA
78919 TATAATTTTTCTTATA
1 TATAATTTTTCTTATA
78935 ATAAACTGAT
Statistics
Matches: 717, Mismatches: 81, Indels: 23
0.87 0.10 0.03
Matches are distributed among these distances:
194 3 0.00
195 112 0.16
196 9 0.01
197 144 0.20
198 4 0.01
199 392 0.55
200 6 0.01
202 46 0.06
203 1 0.00
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Consensus pattern (199 bp):
TATAATTTTTCTTATAGGATTATTATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAGCG
GGTTAAGAAGTTGACACATACCCCATTTCATAATTAATTAAATATTTAATATTAATACATATTCC
CTAAGGGGACACATGTCAACCCTTAAACCCCGCACGTGCAGTCTGCTAAACTCCACTGACGGTGT
ATTA
Found at i:78964 original size:24 final size:25
Alignment explanation
Indices: 78922--78977 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 25
78912 CATATTGTAT
*
78922 AATTTTTCTTATAATAAACTGATAA
1 AATTTTTCTTATAAAAAACTGATAA
* *
78947 AATTTTTGTTA-AAAAAACTTATAA
1 AATTTTTCTTATAAAAAACTGATAA
*
78971 AGTTTTT
1 AATTTTT
78978 TAGTAACTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
24 17 0.63
25 10 0.37
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.46
Consensus pattern (25 bp):
AATTTTTCTTATAAAAAACTGATAA
Found at i:79059 original size:20 final size:20
Alignment explanation
Indices: 78995--79059 Score: 51
Period size: 20 Copynumber: 3.2 Consensus size: 20
78985 TTTCACTCAT
* *
78995 TTTTAGTGACCTCATTAAGTA
1 TTTTAGTGACTTTATTAAG-A
* * **
79016 TTATAGTAACTTT-TTAATTT
1 TTTTAGTGACTTTATTAA-GA
79036 TTTTAGTGACTTTATTAAGA
1 TTTTAGTGACTTTATTAAGA
79056 TTTT
1 TTTT
79060 TAGAAATTGT
Statistics
Matches: 32, Mismatches: 10, Indels: 5
0.68 0.21 0.11
Matches are distributed among these distances:
20 19 0.59
21 13 0.41
ACGTcount: A:0.28, C:0.08, G:0.11, T:0.54
Consensus pattern (20 bp):
TTTTAGTGACTTTATTAAGA
Found at i:79059 original size:21 final size:21
Alignment explanation
Indices: 78993--79062 Score: 63
Period size: 21 Copynumber: 3.4 Consensus size: 21
78983 ACTTTCACTC
* *
78993 ATTTTTAGTGACCTCATTAAG
1 ATTTTTAGTGACTTTATTAAG
* * *
79014 -TATTATAGTAACTTT-TTAAT
1 AT-TTTTAGTGACTTTATTAAG
*
79034 TTTTTTAGTGACTTTATTAAG
1 ATTTTTAGTGACTTTATTAAG
79055 ATTTTTAG
1 ATTTTTAG
79063 AAATTGTTGT
Statistics
Matches: 37, Mismatches: 9, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
20 16 0.43
21 21 0.57
ACGTcount: A:0.29, C:0.07, G:0.11, T:0.53
Consensus pattern (21 bp):
ATTTTTAGTGACTTTATTAAG
Found at i:84555 original size:21 final size:22
Alignment explanation
Indices: 84517--84557 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
84507 TTCCCCAATT
*
84517 AAAAAAAGATAAATGAAAAAGG
1 AAAAAAAGATAAAAGAAAAAGG
*
84539 AAAAAAGGA-AAAAGAAAAA
1 AAAAAAAGATAAAAGAAAAA
84558 ACACTTGAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.78, C:0.00, G:0.17, T:0.05
Consensus pattern (22 bp):
AAAAAAAGATAAAAGAAAAAGG
Done.