Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014105.1 Corchorus olitorius cultivar O-4 contig14138, 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: 43906
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:9429 original size:42 final size:43
Alignment explanation
Indices: 9371--9455 Score: 145
Period size: 42 Copynumber: 2.0 Consensus size: 43
9361 AGTCCATATA
* *
9371 CATGTCGGATACCAACCCGAACCCAAAATCTTAGACTGATGGT
1 CATGTCGGACACCAACCCGAACCCAAAATCCTAGACTGATGGT
9414 CATGTC-GACACCAACCCGAACCCAAAATCCTAGACTGATGGT
1 CATGTCGGACACCAACCCGAACCCAAAATCCTAGACTGATGGT
9456 TTCTTAGGTC
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
42 34 0.85
43 6 0.15
ACGTcount: A:0.33, C:0.31, G:0.18, T:0.19
Consensus pattern (43 bp):
CATGTCGGACACCAACCCGAACCCAAAATCCTAGACTGATGGT
Found at i:10235 original size:22 final size:22
Alignment explanation
Indices: 10125--10238 Score: 77
Period size: 22 Copynumber: 5.2 Consensus size: 22
10115 ATTTTTTATG
* *
10125 ACCTCCTTATGAAATTTTGATA
1 ACCTTCTTATGAAATTTTAATA
* *
10147 ATCTTCCTATGAAATTTTAATA
1 ACCTTCTTATGAAATTTTAATA
** ** * *
10169 ACGATAGTATGAAATTTCAAGA
1 ACCTTCTTATGAAATTTTAATA
* * **
10191 ATCTTTTTAT-AAATTTCTTTTA
1 ACCTTCTTATGAAATTT-TAATA
*
10213 ACCTTCTTATGAAATTTTATTA
1 ACCTTCTTATGAAATTTTAATA
10235 ACCT
1 ACCT
10239 CCCTAAGGAA
Statistics
Matches: 67, Mismatches: 23, Indels: 4
0.71 0.24 0.04
Matches are distributed among these distances:
21 6 0.09
22 55 0.82
23 6 0.09
ACGTcount: A:0.34, C:0.14, G:0.07, T:0.45
Consensus pattern (22 bp):
ACCTTCTTATGAAATTTTAATA
Found at i:10272 original size:22 final size:22
Alignment explanation
Indices: 10220--10659 Score: 244
Period size: 22 Copynumber: 19.9 Consensus size: 22
10210 TTAACCTTCT
*
10220 TATGAAATTTT-ATTAACCTCCC
1 TATGAAATTTTGA-TAACCTCAC
* * *
10242 TAAGGAATTTTGAAAACCTCAC
1 TATGAAATTTTGATAACCTCAC
* * ***
10264 TATGAAATTATGATAACTTTTG
1 TATGAAATTTTGATAACCTCAC
* *
10286 AATGAAATTTTGATAACCAGCAC
1 TATGAAATTTTGATAACC-TCAC
* *
10309 TATGAGATATTGATAACCTCCATTCC
1 TATGAAATTTTGATAACCT-CA---C
* * **
10335 ATAT-AATATATTGATAACCACGT
1 -TATGAA-ATTTTGATAACCTCAC
* * *
10358 TATGAAAATTTAAAAACCTC-C
1 TATGAAATTTTGATAACCTCAC
* *
10379 ATATGAAATTGTGATAACCTCGC
1 -TATGAAATTTTGATAACCTCAC
10402 TATGAAATTTTGATAAACCTTC-C
1 TATGAAATTTTGAT-AACC-TCAC
* *
10425 TATAAAATTTTGATAAACCTCCC
1 TATGAAATTTTGAT-AACCTCAC
* *
10448 TGTAAAATTTTGATAACCTC-C
1 TATGAAATTTTGATAACCTCAC
*
10469 TTATGAAATCTTGATAA-CT-AC
1 -TATGAAATTTTGATAACCTCAC
*
10490 ----AAATTTTGATAACCTCCC
1 TATGAAATTTTGATAACCTCAC
** *
10508 TATGATTTTTTGATAACCTCAT
1 TATGAAATTTTGATAACCTCAC
* * *
10530 TATGAAATTTTGTTAATCTCCC
1 TATGAAATTTTGATAACCTCAC
* *
10552 TATGAAATTTTGATCTACAT-AC
1 TATGAAATTTTGAT-AACCTCAC
* *
10574 TATAAAATTTTGATAACCCTC-T
1 TATGAAATTTTGATAA-CCTCAC
* *
10596 TATGAAATTTTGA-AAACTAAAC
1 TATGAAATTTTGATAACCT-CAC
*
10618 TATGAAATTTTGATAACATTCA-
1 TATGAAATTTTGATAAC-CTCAC
*
10640 TATGAAATTTTGATATCCTC
1 TATGAAATTTTGATAACCTC
10660 CATAATAAAA
Statistics
Matches: 316, Mismatches: 73, Indels: 59
0.71 0.16 0.13
Matches are distributed among these distances:
16 11 0.03
17 2 0.01
18 1 0.00
20 2 0.01
21 9 0.03
22 207 0.66
23 63 0.20
24 3 0.01
26 3 0.01
27 15 0.05
ACGTcount: A:0.37, C:0.17, G:0.09, T:0.37
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTCAC
Found at i:10793 original size:22 final size:22
Alignment explanation
Indices: 10760--10924 Score: 99
Period size: 22 Copynumber: 7.6 Consensus size: 22
10750 AATCACATTT
*
10760 TGAAAATTTGATAACCTCTTTA
1 TGAAATTTTGATAACCTCTTTA
* *
10782 TCAAATTTTGATAACCTCTCTA
1 TGAAATTTTGATAACCTCTTTA
* * * *
10804 T-AAA-TTTGTTGACCCCTCTA
1 TGAAATTTTGATAACCTCTTTA
* * * *
10824 TGAAATTTTGATAATCACATCA
1 TGAAATTTTGATAACCTCTTTA
* *
10846 TGTAATTTTGATAACCTCGCTT-
1 TGAAATTTTGATAACCTC-TTTA
* ** **
10868 TCAAATTTTGATAACAACACTA
1 TGAAATTTTGATAACCTCTTTA
10890 TGAAATTTTGATAA--TCTTCCTA
1 TGAAATTTTGATAACCTCTT--TA
10912 T-AAATTTTGATAA
1 TGAAATTTTGATAA
10925 TCTGATCTCT
Statistics
Matches: 109, Mismatches: 28, Indels: 13
0.73 0.19 0.09
Matches are distributed among these distances:
20 15 0.14
21 19 0.17
22 74 0.68
23 1 0.01
ACGTcount: A:0.35, C:0.16, G:0.08, T:0.41
Consensus pattern (22 bp):
TGAAATTTTGATAACCTCTTTA
Found at i:10879 original size:44 final size:44
Alignment explanation
Indices: 10821--10926 Score: 121
Period size: 44 Copynumber: 2.4 Consensus size: 44
10811 GTTGACCCCT
*
10821 CTATGAAATTTTGATAATC-ACA-TCATGTAATTTTGATAA-CCTC
1 CTAT-AAATTTTGATAATCAACACT-ATGAAATTTTGATAATCCTC
* *
10864 GCTTTCAAATTTTGATAA-CAACACTATGAAATTTTGATAATCTTC
1 -CTAT-AAATTTTGATAATCAACACTATGAAATTTTGATAATCCTC
10909 CTATAAATTTTGATAATC
1 CTATAAATTTTGATAATC
10927 TGATCTCTTT
Statistics
Matches: 53, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
43 13 0.25
44 36 0.68
45 4 0.08
ACGTcount: A:0.36, C:0.15, G:0.08, T:0.41
Consensus pattern (44 bp):
CTATAAATTTTGATAATCAACACTATGAAATTTTGATAATCCTC
Found at i:10925 original size:21 final size:23
Alignment explanation
Indices: 10821--10927 Score: 100
Period size: 22 Copynumber: 4.9 Consensus size: 23
10811 GTTGACCCCT
10821 CTATGAAATTTTGATAATC-ACA
1 CTATGAAATTTTGATAATCTACA
* * *
10843 -TCATGTAATTTTGATAACCT-CG
1 CT-ATGAAATTTTGATAATCTACA
* * *
10865 CTTTCAAATTTTGATAA-CAACA
1 CTATGAAATTTTGATAATCTACA
*
10887 CTATGAAATTTTGATAATCTTC-
1 CTATGAAATTTTGATAATCTACA
10909 CTAT-AAATTTTGATAATCT
1 CTATGAAATTTTGATAATCT
10928 GATCTCTTTG
Statistics
Matches: 68, Mismatches: 12, Indels: 11
0.75 0.13 0.12
Matches are distributed among these distances:
21 17 0.25
22 48 0.71
23 3 0.04
ACGTcount: A:0.36, C:0.15, G:0.08, T:0.41
Consensus pattern (23 bp):
CTATGAAATTTTGATAATCTACA
Found at i:10957 original size:66 final size:66
Alignment explanation
Indices: 10780--10985 Score: 149
Period size: 65 Copynumber: 3.2 Consensus size: 66
10770 ATAACCTCTT
* * * * * ** *
10780 TATCAAATTTTGATAACCTCTCTAT-AAATTT-GTTGACCCCTCTATGAAATTTTGATAATC-AC
1 TATCAAATTTTGATAACATCGCTTTCAAATTTCGATAACAACTCTATGAAATTTTGATAATCTTC
*
10842 A
66 C
** * * *
10843 TCATGTAATTTTGATAACCTCGCTTTCAAATTTTGATAACAACACTATGAAATTTTGATAATCTT
1 T-ATCAAATTTTGATAACATCGCTTTCAAATTTCGATAACAACTCTATGAAATTTTGATAATCTT
10908 CC
65 CC
* * ** *
10910 TAT-AAATTTTGATAATCTGATCTCTTTGAAATTTCGAT-AC-ACTCTATGGGA-TTTGATAACC
1 TATCAAATTTTGATAA-C--ATCGCTTTCAAATTTCGATAACAACTCTATGAAATTTTGATAATC
10971 TT-C
63 TTCC
10974 TATCAAATTTTG
1 TATCAAATTTTG
10986 GAACTCCTTA
Statistics
Matches: 115, Mismatches: 20, Indels: 14
0.77 0.13 0.09
Matches are distributed among these distances:
63 1 0.01
64 24 0.21
65 36 0.31
66 35 0.30
67 4 0.03
68 15 0.13
ACGTcount: A:0.32, C:0.17, G:0.10, T:0.41
Consensus pattern (66 bp):
TATCAAATTTTGATAACATCGCTTTCAAATTTCGATAACAACTCTATGAAATTTTGATAATCTTC
C
Found at i:11037 original size:22 final size:22
Alignment explanation
Indices: 11022--11081 Score: 86
Period size: 22 Copynumber: 2.7 Consensus size: 22
11012 ATAACCTTCA
11022 AATGAAATTTTGATAACCACAC
1 AATGAAATTTTGATAACCACAC
*
11044 TAA-AAAATTTTGATAACCACAC
1 -AATGAAATTTTGATAACCACAC
*
11066 TATGAAATTTTGATAA
1 AATGAAATTTTGATAA
11082 TCTCCCTGTA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
21 1 0.03
22 30 0.91
23 2 0.06
ACGTcount: A:0.47, C:0.13, G:0.08, T:0.32
Consensus pattern (22 bp):
AATGAAATTTTGATAACCACAC
Found at i:11249 original size:28 final size:27
Alignment explanation
Indices: 11161--11261 Score: 123
Period size: 27 Copynumber: 3.7 Consensus size: 27
11151 AGGGTCACCT
*
11161 AGGGGGATTTTGGGTCATTTGCATGTTC
1 AGGGGCATTTT-GGTCATTTGCATGTTC
* *
11189 AGGGGCATTTTAGTCATTTGCATGTCC
1 AGGGGCATTTTGGTCATTTGCATGTTC
**
11216 AGGGGCATTTTGGTCATTTTGCACATTC
1 AGGGGCATTTTGGTCA-TTTGCATGTTC
*
11244 AAGGGCA-TTTGGTCATTT
1 AGGGGCATTTTGGTCATTT
11262 TAAGCTCACT
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
26 3 0.05
27 37 0.58
28 24 0.38
ACGTcount: A:0.18, C:0.15, G:0.29, T:0.39
Consensus pattern (27 bp):
AGGGGCATTTTGGTCATTTGCATGTTC
Found at i:13432 original size:41 final size:41
Alignment explanation
Indices: 13375--13461 Score: 138
Period size: 41 Copynumber: 2.1 Consensus size: 41
13365 TATTTCCATT
* * *
13375 TTCAATATAGTCCCTGATTTAGGGTAACATTTGTTAATTGA
1 TTCAACATAGTCCCTGAGTTAGGGTAACATTTATTAATTGA
*
13416 TTCAACATAGTCCCTGAGTTAGGGTAATATTTATTAATTGA
1 TTCAACATAGTCCCTGAGTTAGGGTAACATTTATTAATTGA
13457 TTCAA
1 TTCAA
13462 TTTCGCCCCT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.31, C:0.13, G:0.16, T:0.40
Consensus pattern (41 bp):
TTCAACATAGTCCCTGAGTTAGGGTAACATTTATTAATTGA
Found at i:13479 original size:41 final size:41
Alignment explanation
Indices: 13375--13479 Score: 113
Period size: 41 Copynumber: 2.6 Consensus size: 41
13365 TATTTCCATT
* * * *
13375 TTCAATATAGTCCCTGATTTAGGGTAACATTTGTTAATTGA
1 TTCAACATAGCCCCTGGTTTAGGGTAACATTTATTAATTGA
* *
13416 TTCAACATAGTCCCTGAG-TTAGGGTAATATTTATTAATTGA
1 TTCAACATAGCCCCTG-GTTTAGGGTAACATTTATTAATTGA
** *
13457 TTCAATTTCGCCCCTGGTTTAGG
1 TTCAACATAGCCCCTGGTTTAGG
13480 ATTTTATTTT
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
40 1 0.02
41 53 0.98
ACGTcount: A:0.27, C:0.15, G:0.18, T:0.40
Consensus pattern (41 bp):
TTCAACATAGCCCCTGGTTTAGGGTAACATTTATTAATTGA
Found at i:25753 original size:112 final size:103
Alignment explanation
Indices: 25607--25824 Score: 249
Period size: 102 Copynumber: 2.0 Consensus size: 103
25597 GGAACTTACA
* * * *
25607 TTATTTTCTCAATAGTTTAATCAACTAAAGTGGACTTCTTGATACTTTGTCCCTTTGTTTCTTTG
1 TTATCTTCTCAATAGTTTAATCAACTAAAGTGGA---C-T--TACTTTG----TATGTGTCTTTC
* *
25672 TTTCTTTTGTCTTTTAAGGGTACAATTAGCATTGTTTAGAATATTC-T
56 TTTCTTTTGTCTTTTAAGGGTACAATTAACATTATTTAGAATATTCAT
* * * *
25719 TTATCTTCTCAATAGTTTATTTAACTAAATTGGACTTACTTTGTATGTGTCTTTCTTTTTTTTGT
1 TTATCTTCTCAATAGTTTAATCAACTAAAGTGGACTTACTTTGTATGTGTCTTTCTTTCTTTTGT
25784 CTTTTAAGGGTACAATTAACATTATTTAGAATATTCAT
66 CTTTTAAGGGTACAATTAACATTATTTAGAATATTCAT
25822 TTA
1 TTA
25825 CTTTTAATTA
Statistics
Matches: 95, Mismatches: 10, Indels: 11
0.82 0.09 0.09
Matches are distributed among these distances:
102 52 0.55
103 4 0.04
106 7 0.07
108 1 0.01
109 1 0.01
112 30 0.32
ACGTcount: A:0.24, C:0.13, G:0.12, T:0.51
Consensus pattern (103 bp):
TTATCTTCTCAATAGTTTAATCAACTAAAGTGGACTTACTTTGTATGTGTCTTTCTTTCTTTTGT
CTTTTAAGGGTACAATTAACATTATTTAGAATATTCAT
Found at i:34246 original size:41 final size:42
Alignment explanation
Indices: 34201--34281 Score: 155
Period size: 42 Copynumber: 2.0 Consensus size: 42
34191 AATTCGAATG
34201 TGAGTTTTGATTAACC-TTTTTTTTATTATGTAAAAACAATC
1 TGAGTTTTGATTAACCTTTTTTTTTATTATGTAAAAACAATC
34242 TGAGTTTTGATTAACCTTTTTTTTTATTATGTAAAAACAA
1 TGAGTTTTGATTAACCTTTTTTTTTATTATGTAAAAACAA
34282 AATAAAAAGT
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
41 16 0.41
42 23 0.59
ACGTcount: A:0.32, C:0.09, G:0.10, T:0.49
Consensus pattern (42 bp):
TGAGTTTTGATTAACCTTTTTTTTTATTATGTAAAAACAATC
Found at i:34910 original size:22 final size:22
Alignment explanation
Indices: 34868--34943 Score: 98
Period size: 22 Copynumber: 3.4 Consensus size: 22
34858 AAATGAAATT
* *
34868 TTGATAACCAACACTATGAGATG
1 TTGATAACC-TCAATATGAGATG
34891 TTGATAACCTCAATATGAGATG
1 TTGATAACCTCAATATGAGATG
* * *
34913 TTAATAACCTCAATATGATATA
1 TTGATAACCTCAATATGAGATG
34935 TTGATAACC
1 TTGATAACC
34944 ACGTTATGAA
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
22 38 0.81
23 9 0.19
ACGTcount: A:0.39, C:0.16, G:0.13, T:0.32
Consensus pattern (22 bp):
TTGATAACCTCAATATGAGATG
Found at i:35008 original size:22 final size:22
Alignment explanation
Indices: 34974--35029 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
34964 CCTCCATATG
* *
34974 AATTGTTAGTAATCACACCCTGA
1 AATTGTGA-TAATCACACCATGA
* *
34997 AATTTTGATAATCACACTATGA
1 AATTGTGATAATCACACCATGA
35019 AATTGTGATAA
1 AATTGTGATAA
35030 CCTTGCTATG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 22 0.79
23 6 0.21
ACGTcount: A:0.39, C:0.14, G:0.12, T:0.34
Consensus pattern (22 bp):
AATTGTGATAATCACACCATGA
Found at i:35032 original size:66 final size:66
Alignment explanation
Indices: 34860--35032 Score: 154
Period size: 66 Copynumber: 2.6 Consensus size: 66
34850 TAACTTCCAA
* *
34860 ATGAAATTTTGATAACCAACACTATGAGA-TGTTGATAACCTCAATATGAGATGTTAATAACCTC
1 ATGAAATTTTGATAACC-ACACTATGAAATTG-TGATAACCTCAATATGAGATGTTAATAACCAC
*
34924 AAT
64 AAC
* * ** * * * * *
34927 ATGATATATTGATAACCACGTTATGAAAATT-TAAAAACCTCCATATGA-ATTGTTAGTAATCAC
1 ATGAAATTTTGATAACCACACTATG-AAATTGTGATAACCTCAATATGAGA-TGTTAATAACCAC
*
34990 ACC
64 AAC
* *
34993 CTGAAATTTTGATAATCACACTATGAAATTGTGATAACCT
1 ATGAAATTTTGATAACCACACTATGAAATTGTGATAACCT
35033 TGCTATGAAA
Statistics
Matches: 81, Mismatches: 21, Indels: 9
0.73 0.19 0.08
Matches are distributed among these distances:
65 6 0.07
66 57 0.70
67 17 0.21
68 1 0.01
ACGTcount: A:0.40, C:0.16, G:0.12, T:0.32
Consensus pattern (66 bp):
ATGAAATTTTGATAACCACACTATGAAATTGTGATAACCTCAATATGAGATGTTAATAACCACAA
C
Found at i:35038 original size:22 final size:23
Alignment explanation
Indices: 35013--35119 Score: 112
Period size: 23 Copynumber: 4.7 Consensus size: 23
35003 GATAATCACA
* * *
35013 CTATGAAATTGTGAT-AACCTTG
1 CTATAAAATTTTGATAAACCTTC
* *
35035 CTATGAAATTTTGATAAACCGTC
1 CTATAAAATTTTGATAAACCTTC
*
35058 CTATAAAATTTTGATAAACCTCC
1 CTATAAAATTTTGATAAACCTTC
35081 CTATAAAATTTTGAT-AACC-TC
1 CTATAAAATTTTGATAAACCTTC
* *
35102 CTTATGAAATCTTGATAA
1 C-TATAAAATTTTGATAA
35120 CTACAAATTT
Statistics
Matches: 73, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
21 2 0.03
22 30 0.41
23 41 0.56
ACGTcount: A:0.36, C:0.17, G:0.10, T:0.36
Consensus pattern (23 bp):
CTATAAAATTTTGATAAACCTTC
Found at i:35061 original size:23 final size:22
Alignment explanation
Indices: 34994--35119 Score: 123
Period size: 22 Copynumber: 5.6 Consensus size: 22
34984 AATCACACCC
* *
34994 TGAAATTTTGATAATCAC-ACTA
1 TGAAATTTTGATAAAC-CTCCTA
* *
35016 TGAAATTGTGAT-AACCTTGCTA
1 TGAAATTTTGATAAACC-TCCTA
35038 TGAAATTTTGATAAACCGTCCTA
1 TGAAATTTTGATAAACC-TCCTA
*
35061 TAAAATTTTGATAAACCTCCCTA
1 TGAAATTTTGATAAACCT-CCTA
*
35084 TAAAATTTTGAT-AACCTCCTTA
1 TGAAATTTTGATAAACCTCC-TA
*
35106 TGAAATCTTGATAA
1 TGAAATTTTGATAA
35120 CTACAAATTT
Statistics
Matches: 89, Mismatches: 9, Indels: 11
0.82 0.08 0.10
Matches are distributed among these distances:
20 1 0.01
21 4 0.04
22 43 0.48
23 41 0.46
ACGTcount: A:0.37, C:0.16, G:0.10, T:0.37
Consensus pattern (22 bp):
TGAAATTTTGATAAACCTCCTA
Found at i:35238 original size:22 final size:21
Alignment explanation
Indices: 35213--35282 Score: 77
Period size: 22 Copynumber: 3.2 Consensus size: 21
35203 ACATACTACA
35213 AAATTTTGATAACCATCTTATG
1 AAATTTTGATAACCATC-TATG
* * *
35235 AAATTTTGAAAACTAAACTATG
1 AAATTTTGATAAC-CATCTATG
*
35257 AAATTTTGATAACCTTCATATG
1 AAATTTTGATAACCATC-TATG
35279 AAAT
1 AAAT
35283 CTTAATATCC
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
21 1 0.03
22 36 0.92
23 2 0.05
ACGTcount: A:0.43, C:0.11, G:0.09, T:0.37
Consensus pattern (21 bp):
AAATTTTGATAACCATCTATG
Found at i:35502 original size:22 final size:21
Alignment explanation
Indices: 35389--35625 Score: 86
Period size: 22 Copynumber: 10.8 Consensus size: 21
35379 GAAATACCAC
* *
35389 TATGAAATTTTGGTAATCAAAT
1 TATGAAATTTTGATAATC-ACT
* * * *
35411 TTTGAAAATTTGATAAACTCTT
1 TATGAAATTTTGATAATCAC-T
* * *
35433 TAAGAAATTTTGATAACCTCT
1 TATGAAATTTTGATAATCACT
* * * * * *
35454 CCATAAAATTTTGTTGACCCCT
1 -TATGAAATTTTGATAATCACT
35476 CTATGAAATTTTGATAATCACAT
1 -TATGAAATTTTGATAATCAC-T
* * *
35499 TATGTAATTATT-ATAACCTCGT
1 TATGAAATT-TTGATAATCAC-T
* * *
35521 TTTCAAATTTTGATAA-CAATAT
1 TATGAAATTTTGATAATC-A-CT
* *
35543 TATGAAATTTTGATAATCTTCC
1 TATGAAATTTTGATAATC-ACT
35565 TAT-AAATTTTGATAATTCGATCT
1 TATGAAATTTTGATAA-TC-A-CT
*
35588 CTATGAAATTTCGATAATCACT
1 -TATGAAATTTTGATAATCACT
*
35610 CTATGAGA-TTTGATAA
1 -TATGAAATTTTGATAA
35626 CCTTCTATCA
Statistics
Matches: 160, Mismatches: 43, Indels: 25
0.70 0.19 0.11
Matches are distributed among these distances:
21 23 0.14
22 115 0.72
23 6 0.04
24 5 0.03
25 11 0.07
ACGTcount: A:0.36, C:0.13, G:0.10, T:0.42
Consensus pattern (21 bp):
TATGAAATTTTGATAATCACT
Found at i:35694 original size:22 final size:21
Alignment explanation
Indices: 35677--35804 Score: 62
Period size: 22 Copynumber: 5.9 Consensus size: 21
35667 TTATAACCTT
35677 CATATGAAATTTTGATAACCA
1 CATATGAAATTTTGATAACCA
** *
35698 CACTAAAAAATTTTGATAACCTC
1 CA-TATGAAATTTTGATAACC-A
** * * *
35721 CCCATAAAATATT-AGTAACCTC
1 CATATGAAATTTTGA-TAACC-A
* *
35743 CTTATGAAATTTTGTTAACCA
1 CATATGAAATTTTGATAACCA
*
35764 CACTATGAAATTGTT-ATAACCT
1 CA-TATGAAATT-TTGATAACCA
* *
35786 CGCTATGACATTTTGATAA
1 C-ATATGAAATTTTGATAA
35805 TCTCTTTGAT
Statistics
Matches: 81, Mismatches: 18, Indels: 15
0.71 0.16 0.13
Matches are distributed among these distances:
21 6 0.07
22 72 0.89
23 3 0.04
ACGTcount: A:0.38, C:0.19, G:0.09, T:0.34
Consensus pattern (21 bp):
CATATGAAATTTTGATAACCA
Found at i:35860 original size:19 final size:21
Alignment explanation
Indices: 35822--35861 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
35812 GATAACTTTT
35822 CTATAAAATTGTGATAATAACA
1 CTATAAAATTGT-ATAATAACA
35844 CTATAAAATT-T-TAATAAC
1 CTATAAAATTGTATAATAAC
35862 CTTCCTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.39
21 1 0.06
22 10 0.56
ACGTcount: A:0.50, C:0.10, G:0.05, T:0.35
Consensus pattern (21 bp):
CTATAAAATTGTATAATAACA
Found at i:35918 original size:22 final size:21
Alignment explanation
Indices: 35889--36019 Score: 100
Period size: 22 Copynumber: 6.0 Consensus size: 21
35879 CTAACATGAT
*
35889 CCTATGAAATTTTGGTAACCA
1 CCTATGAAATTTTGATAACCA
*
35910 CACTATGAAATTTTGATAACCTT
1 C-CTATGAAATTTTGATAACC-A
* * **
35933 CCCATTAAATTTTGATAACTT
1 CCTATGAAATTTTGATAACCA
*
35954 CCTTATGAAATTTTGGTAACCA
1 CC-TATGAAATTTTGATAACCA
* * *
35976 CACTATGGAATTTTAATAACCT
1 C-CTATGAAATTTTGATAACCA
* * *
35998 CCTCATGAGATTATAATAACCA
1 CCT-ATGAAATTTTGATAACCA
36020 TCTTATGTAC
Statistics
Matches: 87, Mismatches: 18, Indels: 9
0.76 0.16 0.08
Matches are distributed among these distances:
21 6 0.07
22 79 0.91
23 2 0.02
ACGTcount: A:0.35, C:0.19, G:0.10, T:0.36
Consensus pattern (21 bp):
CCTATGAAATTTTGATAACCA
Found at i:36017 original size:66 final size:66
Alignment explanation
Indices: 35841--36017 Score: 196
Period size: 66 Copynumber: 2.7 Consensus size: 66
35831 TGTGATAATA
* * ** * *
35841 ACACTATAAAATTTTAATAACCTTCCTAAAAAATTTTACTAACATGATCC-TATGAAATTTTGGT
1 ACACTATGAAATTTTAATAACCTTCCCATGAAATTATAATAAC-T--TCCTTATGAAATTTTGGT
35905 AACC
63 AACC
* * * *
35909 ACACTATGAAATTTTGATAACCTTCCCATTAAATTTTGATAACTTCCTTATGAAATTTTGGTAAC
1 ACACTATGAAATTTTAATAACCTTCCCATGAAATTATAATAACTTCCTTATGAAATTTTGGTAAC
35974 C
66 C
* *
35975 ACACTATGGAATTTTAATAACC-TCCTCATGAGATTATAATAAC
1 ACACTATGAAATTTTAATAACCTTCC-CATGAAATTATAATAAC
36018 CATCTTATGT
Statistics
Matches: 94, Mismatches: 13, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
65 6 0.06
66 51 0.54
67 1 0.01
68 36 0.38
ACGTcount: A:0.38, C:0.18, G:0.08, T:0.36
Consensus pattern (66 bp):
ACACTATGAAATTTTAATAACCTTCCCATGAAATTATAATAACTTCCTTATGAAATTTTGGTAAC
C
Found at i:36067 original size:22 final size:22
Alignment explanation
Indices: 35891--36067 Score: 74
Period size: 22 Copynumber: 7.9 Consensus size: 22
35881 AACATGATCC
* *
35891 TATGAAATTTTGGTAACCA-CAC
1 TATGAAATTTTGATAACCATC-T
* *
35913 TATGAAATTTTGATAACCTTCC
1 TATGAAATTTTGATAACCATCT
* * *
35935 CATTAAATTTTGATAA-CTTCCT
1 TATGAAATTTTGATAACCAT-CT
* *
35957 TATGAAATTTTGGTAACCA-CAC
1 TATGAAATTTTGATAACCATC-T
* *
35979 TATGGAATTTTAATAACC-TCCT
1 TATGAAATTTTGATAACCAT-CT
* * * *
36001 CATGAGATTATAATAACCATCT
1 TATGAAATTTTGATAACCATCT
* * ***
36023 TATGTACTTCAAAAAAATAACCATCT
1 TATGAAATT----TTGATAACCATCT
36049 TATGAAATTTTGATAACCA
1 TATGAAATTTTGATAACCA
36068 CACAAAGACA
Statistics
Matches: 116, Mismatches: 28, Indels: 22
0.70 0.17 0.13
Matches are distributed among these distances:
21 4 0.03
22 89 0.77
23 4 0.03
26 19 0.16
ACGTcount: A:0.37, C:0.18, G:0.09, T:0.36
Consensus pattern (22 bp):
TATGAAATTTTGATAACCATCT
Found at i:36271 original size:20 final size:20
Alignment explanation
Indices: 36233--36271 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
36223 TATTGACATT
36233 TAAAAAATTGAAATTAAAAG
1 TAAAAAATTGAAATTAAAAG
*
36253 TAAAATATT-AAATTCAAAA
1 TAAAAAATTGAAATT-AAAA
36272 AATAATAGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.64, C:0.03, G:0.05, T:0.28
Consensus pattern (20 bp):
TAAAAAATTGAAATTAAAAG
Found at i:39831 original size:27 final size:27
Alignment explanation
Indices: 39789--39849 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 27
39779 TCCTCATTAT
* *
39789 AGGGGTAAAATCGTAATTTTA-CCAATC
1 AGGGGTAAAATAGTAAATTTATCC-ATC
*
39816 AGGGGTAATATAGTAAATTTATCCATC
1 AGGGGTAAAATAGTAAATTTATCCATC
*
39843 ACGGGTA
1 AGGGGTA
39850 TTTTGGTAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
27 27 0.93
28 2 0.07
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.30
Consensus pattern (27 bp):
AGGGGTAAAATAGTAAATTTATCCATC
Found at i:43354 original size:25 final size:24
Alignment explanation
Indices: 43326--43388 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
43316 GTGGATTGTA
*
43326 AAATAAATTGAATAATTAAGACATT
1 AAATAAATTGAAGAATTAA-ACATT
*
43351 AAATAAATTTAAGAATTAAACATT
1 AAATAAATTGAAGAATTAAACATT
* *
43375 AAAAAAATTCAAGA
1 AAATAAATTGAAGA
43389 CTGACCCAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
24 17 0.50
25 17 0.50
ACGTcount: A:0.60, C:0.05, G:0.06, T:0.29
Consensus pattern (24 bp):
AAATAAATTGAAGAATTAAACATT
Done.