Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012658.1 Corchorus olitorius cultivar O-4 contig12691, 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: 90455
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:12 original size:2 final size:2
Alignment explanation
Indices: 6--41 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1 GGTCG
6 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
42 GTTTTTTTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:424 original size:1 final size:1
Alignment explanation
Indices: 418--442 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
408 GTTTGAGTTT
418 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
443 TCAACCCTGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:6400 original size:5 final size:5
Alignment explanation
Indices: 6390--6416 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
6380 CTCCTACATA
6390 ATTTT ATTTT ATTTT ATTTT ATTTT AT
1 ATTTT ATTTT ATTTT ATTTT ATTTT AT
6417 GTGGTTGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (5 bp):
ATTTT
Found at i:9708 original size:24 final size:24
Alignment explanation
Indices: 9676--9727 Score: 104
Period size: 24 Copynumber: 2.2 Consensus size: 24
9666 AACTCCACTG
9676 ATAATGTATGATAGTGTATTATAC
1 ATAATGTATGATAGTGTATTATAC
9700 ATAATGTATGATAGTGTATTATAC
1 ATAATGTATGATAGTGTATTATAC
9724 ATAA
1 ATAA
9728 ACTGATAAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.40, C:0.04, G:0.15, T:0.40
Consensus pattern (24 bp):
ATAATGTATGATAGTGTATTATAC
Found at i:10941 original size:29 final size:29
Alignment explanation
Indices: 10882--10942 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 29
10872 TATGGTACAG
* **
10882 ATTTGGATTTAGTGATTCTGGCCCATTAA
1 ATTTGGATTTACTGATTCTGGCCCAACAA
10911 ATTT-GATTTACTGATTCTGGCCCAGACAA
1 ATTTGGATTTACTGATTCTGGCCCA-ACAA
10940 ATT
1 ATT
10943 GGGCTTTCTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 19 0.68
29 9 0.32
ACGTcount: A:0.26, C:0.16, G:0.18, T:0.39
Consensus pattern (29 bp):
ATTTGGATTTACTGATTCTGGCCCAACAA
Found at i:17916 original size:23 final size:23
Alignment explanation
Indices: 17887--17934 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
17877 TCCCTAGGGG
17887 ACACATGTCACCCTTCTAAAC-CC
1 ACACATG-CACCCTTCTAAACACC
**
17910 ACACATGCAGTCTTCTAAACACC
1 ACACATGCACCCTTCTAAACACC
17933 AC
1 AC
17935 TGACGGTGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 11 0.50
23 11 0.50
ACGTcount: A:0.33, C:0.40, G:0.06, T:0.21
Consensus pattern (23 bp):
ACACATGCACCCTTCTAAACACC
Found at i:24587 original size:33 final size:33
Alignment explanation
Indices: 24527--24597 Score: 81
Period size: 33 Copynumber: 2.2 Consensus size: 33
24517 CCGAAAACTG
* * * *
24527 GGACAACTGCGTCATTACCATCTTCTCCGGCCA
1 GGACTACTGCGTCATGACCATCATCTCCAGCCA
*
24560 GGACTACTGCGTCAGTGA-CATCATCTCCAGTCA
1 GGACTACTGCGTCA-TGACCATCATCTCCAGCCA
24593 GGACT
1 GGACT
24598 GCCGTTGCAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
33 30 0.94
34 2 0.06
ACGTcount: A:0.23, C:0.32, G:0.21, T:0.24
Consensus pattern (33 bp):
GGACTACTGCGTCATGACCATCATCTCCAGCCA
Found at i:28512 original size:2 final size:2
Alignment explanation
Indices: 28505--28531 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
28495 CAGTAACATA
28505 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 A
28532 ATTTAACTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:36177 original size:2 final size:2
Alignment explanation
Indices: 36170--36216 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
36160 TCATAAAATC
36170 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
36212 AT AT A
1 AT AT A
36217 CGTCACAAAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:38939 original size:36 final size:36
Alignment explanation
Indices: 38871--38943 Score: 101
Period size: 36 Copynumber: 2.0 Consensus size: 36
38861 GCCTAATATT
* ** *
38871 TGCCAAAATGCTTAAATAAGGGTTTGGCATCCAAAA
1 TGCCAAAATGCTAAAATAAGGGCCTAGCATCCAAAA
*
38907 TGCCAAAATGCTAAAATAAGGGCCTAGTATCCAAAA
1 TGCCAAAATGCTAAAATAAGGGCCTAGCATCCAAAA
38943 T
1 T
38944 TCTCACACGT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.41, C:0.18, G:0.18, T:0.23
Consensus pattern (36 bp):
TGCCAAAATGCTAAAATAAGGGCCTAGCATCCAAAA
Found at i:39127 original size:60 final size:59
Alignment explanation
Indices: 38975--39132 Score: 192
Period size: 59 Copynumber: 2.7 Consensus size: 59
38965 ACGTCAGGCT
* * * * *
38975 CTTATTTGAGCATTTTCGATAACATTATGCCCTTATTTGGTCAAATTAAAAGATCGGGC
1 CTTATTTGAGCATTTTCGATAACATTAAGCTCTTATTTGGCCAAATTAAAAGACCGGCC
* * * *
39034 CTTAGTTGAGTATTTTCGATAACGTTAATCTCTTATTTGGCCAAATTAAAAGACCGAGCC
1 CTTATTTGAGCATTTTCGATAACATTAAGCTCTTATTTGGCCAAATTAAAAGACCG-GCC
* *
39094 CTTATTTGAGCATTTTGGCA-AACATTAGGCTCTTATTTG
1 CTTATTTGAGCATTTTCG-ATAACATTAAGCTCTTATTTG
39133 AGCAATTAAC
Statistics
Matches: 82, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
59 48 0.59
60 33 0.40
61 1 0.01
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (59 bp):
CTTATTTGAGCATTTTCGATAACATTAAGCTCTTATTTGGCCAAATTAAAAGACCGGCC
Found at i:61245 original size:19 final size:19
Alignment explanation
Indices: 61221--61278 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 19
61211 CTGTTTAGCA
61221 ACTGTACAGATGAGATTAC
1 ACTGTACAGATGAGATTAC
* * *
61240 ACTGTACAGATTAGAATAGAT
1 ACTGTACAGATGAG-AT-TAC
61261 ACTGTACAGATGAGATTA
1 ACTGTACAGATGAGATTA
61279 TTAGAGCAGC
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
19 14 0.44
20 4 0.12
21 14 0.44
ACGTcount: A:0.40, C:0.12, G:0.21, T:0.28
Consensus pattern (19 bp):
ACTGTACAGATGAGATTAC
Found at i:70860 original size:2 final size:2
Alignment explanation
Indices: 70853--70881 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
70843 TTACCTAAAC
70853 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 A
70882 GATAAGATAC
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:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:74949 original size:33 final size:31
Alignment explanation
Indices: 74886--74950 Score: 78
Period size: 33 Copynumber: 2.0 Consensus size: 31
74876 TTTTGCAATG
**
74886 ACATAATAATTTTTTTTTTTGGTAGAACATA
1 ACATAATAATTTTTTTTTTTGCAAGAACATA
74917 ACATAATAATATTTCTTTTTTTGCAATG-ACATA
1 ACATAATAAT-TTT-TTTTTTTGCAA-GAACATA
74950 A
1 A
74951 TAATTTCTGC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
31 10 0.34
32 3 0.10
33 15 0.52
34 1 0.03
ACGTcount: A:0.37, C:0.09, G:0.08, T:0.46
Consensus pattern (31 bp):
ACATAATAATTTTTTTTTTTGCAAGAACATA
Found at i:89082 original size:51 final size:51
Alignment explanation
Indices: 89008--89218 Score: 271
Period size: 51 Copynumber: 4.1 Consensus size: 51
88998 ATATTATGTT
* * * * * * *
89008 TAAAAAAATTTAGTAATTAGGAGACTGATGAGAGCTATCTCTCTAAACATT
1 TAAAAAATTTTAGTAATTAGGAGACCGATGGGAGCTGTCTCCCCAAACATC
* * * *
89059 TAAAAAGTTTTAGTCATTAGGAGACTGATGGGAGTTGTCTCCCCAAACATC
1 TAAAAAATTTTAGTAATTAGGAGACCGATGGGAGCTGTCTCCCCAAACATC
* * *
89110 TAAAAAGTTTTAGTAATTAGGAGACCAATGGGAGCTGTCTCCCCAAATATC
1 TAAAAAATTTTAGTAATTAGGAGACCGATGGGAGCTGTCTCCCCAAACATC
*
89161 TAAAAAATTTTAGTAATTAGGAGACCGATGGGAGCTGTCTCCCCTAACAAT-
1 TAAAAAATTTTAGTAATTAGGAGACCGATGGGAGCTGTCTCCCCAAAC-ATC
89212 TAAAAAA
1 TAAAAAA
89219 GTGACTGATG
Statistics
Matches: 141, Mismatches: 18, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
51 139 0.99
52 2 0.01
ACGTcount: A:0.37, C:0.16, G:0.18, T:0.28
Consensus pattern (51 bp):
TAAAAAATTTTAGTAATTAGGAGACCGATGGGAGCTGTCTCCCCAAACATC
Found at i:89326 original size:38 final size:38
Alignment explanation
Indices: 89183--89476 Score: 151
Period size: 38 Copynumber: 7.6 Consensus size: 38
89173 GTAATTAGGA
* * * *
89183 GACCGATGGGAGCTGTCTCCCCTAACAATTAA-AAAAGT
1 GACCGATGAGAGCTGTCT-CTCAAACATTTAATAAAAGT
* * *
89221 GACTGATGAGAGGTGTCTCTCCAAACAATTAA-AAAAGT
1 GACCGATGAGAGCTGTCTCT-CAAACATTTAATAAAAGT
* * * * *
89259 GTCCAATGAGAG-TCGTCTTTCCAAACATTTAATTAAAGA
1 GACCGATGAGAGCT-GTCTCT-CAAACATTTAATAAAAGT
* *
89298 GACCGATGGGAGCTGTCTCTCTAACATTTAAATACAAAAGT
1 GACCGATGAGAGCTGTCTCTCAAACATTT-AAT--AAAAGT
*
89339 GACCGATAAGAGCTGTCTCTCGAAACATTTAATTGAAAAAATGT
1 GACCGATGAGAGCTGTCTCTC-AAACATTTAA-T---AAAA-GT
* **
89383 GA-C--TGA-AGCTAGCTCTCTCAAA-A---AAAAAAAAA
1 GACCGATGAGAGCT-G-TCTCTCAAACATTTAATAAAAGT
* * * *
89415 GACCGATGAGAACTATCTCTCCAAACAATATATTAAAAAGT
1 GACCGATGAGAGCTGTCTCT-CAAAC-ATTTAAT-AAAAGT
89456 GACCGATGAGAGCTGTCTCTC
1 GACCGATGAGAGCTGTCTCTC
89477 CAAATATCTA
Statistics
Matches: 197, Mismatches: 35, Indels: 46
0.71 0.13 0.17
Matches are distributed among these distances:
32 2 0.01
33 5 0.03
34 5 0.03
35 7 0.04
36 3 0.02
37 5 0.03
38 64 0.32
39 21 0.11
40 8 0.04
41 53 0.27
42 14 0.07
43 6 0.03
44 4 0.02
ACGTcount: A:0.38, C:0.19, G:0.18, T:0.24
Consensus pattern (38 bp):
GACCGATGAGAGCTGTCTCTCAAACATTTAATAAAAGT
Found at i:89654 original size:42 final size:39
Alignment explanation
Indices: 89549--89804 Score: 275
Period size: 38 Copynumber: 6.4 Consensus size: 39
89539 AAATTTAGTA
* *
89549 ATTAAAGAAGTGACCGATGAGAGCTATCTCTCCACACATTT
1 ATTAAAAAAGTGACCGATGAGAGCTATCTCTCCAAACA--T
89590 AATTAAAAAAAGTGACCGATGAGAGCTATCTCTCCAAACATTT
1 -ATT-AAAAAAGTGACCGATGAGAGCTATCTCTCCAAACA--T
**
89633 ACTTAAAAAAGTGACCGATGAGAGCCGTCTCTCCAAACA-
1 A-TTAAAAAAGTGACCGATGAGAGCTATCTCTCCAAACAT
* *
89672 ATTAAAAAAGTGACCGATGAAAGCTATCTCTTCAAACAAT
1 ATTAAAAAAGTGACCGATGAGAGCTATCTCTCCAAAC-AT
* * * * *
89712 AAATTAAAAAAGTGGCTGATGGGAGCTGTCTCCCCAAACAT
1 --ATTAAAAAAGTGACCGATGAGAGCTATCTCTCCAAACAT
* * *
89753 -CTAAAAAAGTGACCAATGAGAGCTGTCTCTCCAAACA-
1 ATTAAAAAAGTGACCGATGAGAGCTATCTCTCCAAACAT
89790 ATTAAAAAAGTGACC
1 ATTAAAAAAGTGACC
89805 AACATAAAAA
Statistics
Matches: 185, Mismatches: 22, Indels: 18
0.82 0.10 0.08
Matches are distributed among these distances:
38 76 0.41
39 2 0.01
41 2 0.01
42 67 0.36
43 38 0.21
ACGTcount: A:0.40, C:0.21, G:0.16, T:0.23
Consensus pattern (39 bp):
ATTAAAAAAGTGACCGATGAGAGCTATCTCTCCAAACAT
Found at i:89708 original size:80 final size:77
Alignment explanation
Indices: 89549--89804 Score: 282
Period size: 80 Copynumber: 3.2 Consensus size: 77
89539 AAATTTAGTA
* * *
89549 ATTAAAGAAGTGACCGATGAGAGCTATCTCTCCACACATTTAATTAAAAAAAGTGACCGATGAGA
1 ATTAAAAAAGTGACCGATGAGAGCTGTCTCTCCA-A-A--CAATT-AAAAAAGTGACCGATGAGA
89614 GCTATCTCTCCAAACATTT
61 GCTATCTCTCCAAACA--T
* *
89633 ACTTAAAAAAGTGACCGATGAGAGCCGTCTCTCCAAACAATTAAAAAAGTGACCGATGAAAGCTA
1 A-TTAAAAAAGTGACCGATGAGAGCTGTCTCTCCAAACAATTAAAAAAGTGACCGATGAGAGCTA
*
89698 TCTCTTCAAACAAT
65 TCTCTCCAAAC-AT
* * * * *
89712 AAATTAAAAAAGTGGCTGATGGGAGCTGTCTCCCCAAAC-ATCTAAAAAAGTGACCAATGAGAGC
1 --ATTAAAAAAGTGACCGATGAGAGCTGTCTCTCCAAACAAT-TAAAAAAGTGACCGATGAGAGC
*
89776 TGTCTCTCCAAACA-
63 TATCTCTCCAAACAT
89790 ATTAAAAAAGTGACC
1 ATTAAAAAAGTGACC
89805 AACATAAAAA
Statistics
Matches: 150, Mismatches: 17, Indels: 18
0.81 0.09 0.10
Matches are distributed among these distances:
76 13 0.09
79 4 0.03
80 94 0.63
81 6 0.04
83 1 0.01
84 2 0.01
85 30 0.20
ACGTcount: A:0.40, C:0.21, G:0.16, T:0.23
Consensus pattern (77 bp):
ATTAAAAAAGTGACCGATGAGAGCTGTCTCTCCAAACAATTAAAAAAGTGACCGATGAGAGCTAT
CTCTCCAAACAT
Found at i:89860 original size:41 final size:41
Alignment explanation
Indices: 89814--89973 Score: 211
Period size: 41 Copynumber: 4.0 Consensus size: 41
89804 CAACATAAAA
* *
89814 AAAAAGTGATCGATGAGAGCTGTCTCTCCAAACATTTAATT
1 AAAAAGTGACCGATGAGAGCTGTCTCTCCAAACAATTAATT
* *
89855 AAAAAGTGACCGATGAGAGTTATCTCTCCAAACAATTAATT
1 AAAAAGTGACCGATGAGAGCTGTCTCTCCAAACAATTAATT
* * *
89896 AAAAAAGTGACCTATGGGAGCTGTCTCCCCAAAC-ATCT-A--
1 -AAAAAGTGACCGATGAGAGCTGTCTCTCCAAACAAT-TAATT
89935 AAAAAGTGACCGATGAGAGCTGTCTCTCCAAACAATTAA
1 AAAAAGTGACCGATGAGAGCTGTCTCTCCAAACAATTAA
89974 AAAAGTTACC
Statistics
Matches: 103, Mismatches: 12, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
38 31 0.30
39 3 0.03
41 40 0.39
42 29 0.28
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (41 bp):
AAAAAGTGACCGATGAGAGCTGTCTCTCCAAACAATTAATT
Found at i:89934 original size:179 final size:180
Alignment explanation
Indices: 89637--90075 Score: 680
Period size: 179 Copynumber: 2.5 Consensus size: 180
89627 ACATTTACTT
* * *
89637 AAAAAAGTGACCGATGAGAGCCGTCTCTCCAAACAATT-A--AAAAAGTGACCGATGAAAGCTAT
1 AAAAAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATTAAAAAGTGACCGATGAGAGCTAT
* *
89699 CTCTTCAAACAATAAATTAAAAAAGTGGCTGATGGGAGCTGTCTCCCCAAACATCTAAAAAAGTG
66 CTCTCCAAACAATAAATTAAAAAAGTGCCTGATGGGAGCTGTCTCCCCAAACATCTAAAAAAGTG
89764 ACCAATGAGAGCTGTCTCTCCAAACAATTAAAAAAGTGACCAACATAAA-
131 ACCAATGAGAGCTGTCTCTCCAAACAATTAAAAAAGTGACCAACATAAAC
* *
89813 AAAAAAGTGATCGATGAGAGCTGTCTCTCCAAACATTTAATTAAAAAGTGACCGATGAGAGTTAT
1 AAAAAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATTAAAAAGTGACCGATGAGAGCTAT
*
89878 CTCTCCAAACAATTAATTAAAAAAGTGACCT-ATGGGAGCTGTCTCCCCAAACATCTAAAAAAGT
66 CTCTCCAAACAATAAATTAAAAAAGTG-CCTGATGGGAGCTGTCTCCCCAAACATCTAAAAAAGT
* *
89942 GACCGATGAGAGCTGTCTCTCCAAACAATTAAAAAAGTTACCAACATAAAC
130 GACCAATGAGAGCTGTCTCTCCAAACAATTAAAAAAGTGACCAACATAAAC
* * *
89993 AAAAAAGTGACCAATGAGAGCTGTCTCTCCAAACATTTAATTCAAAAGTGACCGATGAGGGC--T
1 AAAAAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATTAAAAAGTGACCGATGAGAGCTAT
*
90056 CTCT--AAACATTAAATTAAAA
66 CTCTCCAAACAATAAATTAAAA
90076 GATAAGAGCT
Statistics
Matches: 241, Mismatches: 17, Indels: 10
0.90 0.06 0.04
Matches are distributed among these distances:
176 49 0.20
177 1 0.00
178 5 0.02
179 127 0.53
180 59 0.24
ACGTcount: A:0.42, C:0.20, G:0.16, T:0.22
Consensus pattern (180 bp):
AAAAAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATTAAAAAGTGACCGATGAGAGCTAT
CTCTCCAAACAATAAATTAAAAAAGTGCCTGATGGGAGCTGTCTCCCCAAACATCTAAAAAAGTG
ACCAATGAGAGCTGTCTCTCCAAACAATTAAAAAAGTGACCAACATAAAC
Found at i:89955 original size:38 final size:39
Alignment explanation
Indices: 89813--89979 Score: 196
Period size: 38 Copynumber: 4.2 Consensus size: 39
89803 CCAACATAAA
*
89813 AAAAAAGTGATCGATGAGAGCTGTCTCTCCAAAC-ATTT
1 AAAAAAGTGACCGATGAGAGCTGTCTCTCCAAACAATTT
* *
89851 AATTAAAAAGTGACCGATGAGAGTTATCTCTCCAAACAATTAATT
1 -A--AAAAAGTGACCGATGAGAGCTGTCTCTCCAAACAA-T--TT
* * * *
89896 AAAAAAGTGACCTATGGGAGCTGTCTCCCCAAAC-ATCT
1 AAAAAAGTGACCGATGAGAGCTGTCTCTCCAAACAATTT
89934 AAAAAAGTGACCGATGAGAGCTGTCTCTCCAAACAA-TT
1 AAAAAAGTGACCGATGAGAGCTGTCTCTCCAAACAATTT
89972 AAAAAAGT
1 AAAAAAGT
89980 TACCAACATA
Statistics
Matches: 108, Mismatches: 13, Indels: 15
0.79 0.10 0.11
Matches are distributed among these distances:
38 41 0.38
39 2 0.02
40 1 0.01
41 31 0.29
42 29 0.27
43 1 0.01
44 1 0.01
45 2 0.02
ACGTcount: A:0.40, C:0.19, G:0.17, T:0.24
Consensus pattern (39 bp):
AAAAAAGTGACCGATGAGAGCTGTCTCTCCAAACAATTT
Found at i:90096 original size:32 final size:33
Alignment explanation
Indices: 90053--90178 Score: 105
Period size: 32 Copynumber: 3.7 Consensus size: 33
90043 ACCGATGAGG
*
90053 GCTCTCTAAACATTAAATTAAAAGATAAGAGCT
1 GCTCTCCAAACATTAAATTAAAAGATAAGAGCT
* *
90086 G-TCTCCAAACATTTAATTCAAAAG-TGACCGATGAG-G
1 GCTCTCCAAACATTAAATT-AAAAGAT-A---A-GAGCT
* *
90122 GCTCTCTAAACTTTAAATTAAAAGATAAGAGCT
1 GCTCTCCAAACATTAAATTAAAAGATAAGAGCT
* *
90155 GTCTCTCCAAACATTTAACTAAAA
1 G-CTCTCCAAACATTAAATTAAAA
90179 AAAAGTGACT
Statistics
Matches: 72, Mismatches: 11, Indels: 19
0.71 0.11 0.19
Matches are distributed among these distances:
32 19 0.26
33 9 0.12
34 18 0.25
36 8 0.11
37 18 0.25
ACGTcount: A:0.41, C:0.18, G:0.13, T:0.28
Consensus pattern (33 bp):
GCTCTCCAAACATTAAATTAAAAGATAAGAGCT
Found at i:90103 original size:69 final size:70
Alignment explanation
Indices: 90009--90172 Score: 294
Period size: 69 Copynumber: 2.3 Consensus size: 70
89999 GTGACCAATG
90009 AGAGCTGTCTCTCCAAACATTTAATTCAAAAGTGACCGATGAGGGCTCTCTAAACATTAAATTAA
1 AGAGCTG-CTCTCCAAACATTTAATTCAAAAGTGACCGATGAGGGCTCTCTAAACATTAAATTAA
90074 AAGATA
65 AAGATA
*
90080 AGAGCTG-TCTCCAAACATTTAATTCAAAAGTGACCGATGAGGGCTCTCTAAACTTTAAATTAAA
1 AGAGCTGCTCTCCAAACATTTAATTCAAAAGTGACCGATGAGGGCTCTCTAAACATTAAATTAAA
90144 AGATA
66 AGATA
90149 AGAGCTGTCTCTCCAAACATTTAA
1 AGAGCTG-CTCTCCAAACATTTAA
90173 CTAAAAAAAA
Statistics
Matches: 90, Mismatches: 1, Indels: 4
0.95 0.01 0.04
Matches are distributed among these distances:
69 68 0.76
71 22 0.24
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.27
Consensus pattern (70 bp):
AGAGCTGCTCTCCAAACATTTAATTCAAAAGTGACCGATGAGGGCTCTCTAAACATTAAATTAAA
AGATA
Found at i:90203 original size:42 final size:44
Alignment explanation
Indices: 90149--90386 Score: 242
Period size: 42 Copynumber: 5.6 Consensus size: 44
90139 TTAAAAGATA
* * *
90149 AGAGCTGTCTCTCCAAACATTTAACTAAAAAAAAGTGACTGATG
1 AGAGCTATCTCTCCAAACATTTAAATAAAAAAAAGTGACCGATG
*
90193 AGAG-T-TCTCTCCAAACA-TTAAAT-AAAAAAAGTGACTGATG
1 AGAGCTATCTCTCCAAACATTTAAATAAAAAAAAGTGACCGATG
* *
90233 AGAGCTATCTCTCCAAACATTTAAAAAAAAAAAAACTGACCGATG
1 AGAGCTATCTCTCCAAACATTT-AAATAAAAAAAAGTGACCGATG
* * * *
90278 AGAGCCATCTTTCCAAACATTT-ACT-TAAAAAAGTGACCGATG
1 AGAGCTATCTCTCCAAACATTTAAATAAAAAAAAGTGACCGATG
* * * *
90320 AGAGCTATCTCTCCGAACAATT-AAT-TAAAAAAGTGACCTATG
1 AGAGCTATCTCTCCAAACATTTAAATAAAAAAAAGTGACCGATG
* * *
90362 GGAGCTGTGTC-CACAAACATTTAAA
1 AGAGCTATCTCTC-CAAACATTTAAA
90387 GGTGTGACCA
Statistics
Matches: 166, Mismatches: 21, Indels: 15
0.82 0.10 0.07
Matches are distributed among these distances:
40 21 0.13
41 7 0.04
42 90 0.54
43 6 0.04
44 7 0.04
45 35 0.21
ACGTcount: A:0.42, C:0.19, G:0.15, T:0.24
Consensus pattern (44 bp):
AGAGCTATCTCTCCAAACATTTAAATAAAAAAAAGTGACCGATG
Found at i:90350 original size:87 final size:85
Alignment explanation
Indices: 90149--90351 Score: 255
Period size: 87 Copynumber: 2.4 Consensus size: 85
90139 TTAAAAGATA
* * * * *
90149 AGAGCTGTCTCTCCAAACATTTAACT-AAAAAAAAGTGACTGATGAGAGTTCTCTCCAAACATTA
1 AGAGCTATCTCTCCAAACATTTAAATAAAAAAAAACTGACCGATGAGAGATCTCTCCAAACATTA
*
90213 AATAAAAAAAGTGACTGATG
66 AATAAAAAAAGTGACCGATG
* *
90233 AGAGCTATCTCTCCAAACATTTAAAAAAAAAAAAACTGACCGATGAGAGCCATCTTTCCAAACAT
1 AGAGCTATCTCTCCAAACATTTAAATAAAAAAAAACTGACCGATGAGAG--ATCTCTCCAAACAT
* * *
90298 TTACTTAAAAAAGTGACCGATG
64 TAAATAAAAAAAGTGACCGATG
* * *
90320 AGAGCTATCTCTCCGAACAATTAATTAAAAAA
1 AGAGCTATCTCTCCAAACATTTAAATAAAAAA
90352 GTGACCTATG
Statistics
Matches: 101, Mismatches: 15, Indels: 3
0.85 0.13 0.03
Matches are distributed among these distances:
84 23 0.23
85 20 0.20
87 58 0.57
ACGTcount: A:0.44, C:0.19, G:0.13, T:0.24
Consensus pattern (85 bp):
AGAGCTATCTCTCCAAACATTTAAATAAAAAAAAACTGACCGATGAGAGATCTCTCCAAACATTA
AATAAAAAAAGTGACCGATG
Found at i:90395 original size:38 final size:38
Alignment explanation
Indices: 90352--90424 Score: 94
Period size: 38 Copynumber: 1.9 Consensus size: 38
90342 AATTAAAAAA
* * * *
90352 GTGACCTATGGGAGCTGTGTC-CACAAACATTTAAAGGT
1 GTGACCAATGAGAGCTGTCTCTC-CAAACACTTAAAGGT
90390 GTGACCAATGAGAGCTGTCTCTCCAAACACTTAAA
1 GTGACCAATGAGAGCTGTCTCTCCAAACACTTAAA
90425 AAGTGACCAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
38 29 0.97
39 1 0.03
ACGTcount: A:0.32, C:0.22, G:0.22, T:0.25
Consensus pattern (38 bp):
GTGACCAATGAGAGCTGTCTCTCCAAACACTTAAAGGT
Done.