Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015694.1 Corchorus olitorius cultivar O-4 contig15727, 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: 50478
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:2946 original size:68 final size:67
Alignment explanation
Indices: 2874--3083 Score: 245
Period size: 68 Copynumber: 3.1 Consensus size: 67
2864 CTTTTTAATC
2874 TTGATAATCAAACGCCATATCAAATTTTGATAATCGCCCTATATTGTTGATAACTGCCCTTTGAG
1 TTGATAATCAAACG-CATATCAAATTTTGATAATCGCCCTATATTGTTGATAACTGCCCTTTGAG
2939 ATT
65 ATT
* * * * **
2942 TTGATAATC--TCG-AT-T-AGAATTTTGACAATTGTCCTATATAAT-TATGATAACCACCCTTT
1 TTGATAATCAAACGCATATCA-AATTTTGATAATCGCCCTATAT--TGT-TGATAACTGCCCTTT
*
3001 GTA-ATC
62 G-AGATT
3007 TTGATAATCAAACGTCATATCAAATTTTGATAATCGCCCTATATTGTTGATAACTGCCCTTTGAG
1 TTGATAATCAAACG-CATATCAAATTTTGATAATCGCCCTATATTGTTGATAACTGCCCTTTGAG
3072 ATT
65 ATT
3075 TTGATAATC
1 TTGATAATC
3084 TCGATTAGAA
Statistics
Matches: 115, Mismatches: 14, Indels: 26
0.74 0.09 0.17
Matches are distributed among these distances:
62 1 0.01
63 20 0.17
64 3 0.03
65 26 0.23
66 3 0.03
67 3 0.03
68 35 0.30
69 3 0.03
70 20 0.17
71 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.12, T:0.39
Consensus pattern (67 bp):
TTGATAATCAAACGCATATCAAATTTTGATAATCGCCCTATATTGTTGATAACTGCCCTTTGAGA
TT
Found at i:3011 original size:65 final size:66
Alignment explanation
Indices: 2896--3176 Score: 228
Period size: 65 Copynumber: 4.3 Consensus size: 66
2886 CGCCATATCA
* * **
2896 AATTTTGATAATCGCCCTATAT--TGT-TGATAACTGCCCTTTG-AGATTTTGATAATC-TCGAT
1 AATTTTGACAATTGCCCTATATAAT-TATGATAACCACCCTTTGTA-ATTTTGATAATCATCGAT
2956 TAG
64 TAG
* * *
2959 AATTTTGACAATTGTCCTATATAATTATGATAACCACCCTTTGTAATCTTGATAATCAAACGTCA
1 AATTTTGACAATTGCCCTATATAATTATGATAACCACCCTTTGTAATTTTGATAATC-ATCG--A
3024 TATCA-
63 T-T-AG
* * **
3029 AATTTTGATAATCGCCCTATAT--TGT-TGATAACTGCCCTTTG-AGATTTTGATAATC-TCGAT
1 AATTTTGACAATTGCCCTATATAAT-TATGATAACCACCCTTTGTA-ATTTTGATAATCATCGAT
3089 TAG
64 TAG
* * * * *
3092 AATTTTGACAATTGTCCTATATAATTATGATAACCATCCTTTATAATTTTAATAA-CTTCGATT-
1 AATTTTGACAATTGCCCTATATAATTATGATAACCACCCTTTGTAATTTTGATAATCATCGATTA
3155 G
66 G
*
3156 AGATTTTGACAACTGCCCTAT
1 A-ATTTTGACAATTGCCCTAT
3177 GAAATTTTAA
Statistics
Matches: 175, Mismatches: 24, Indels: 36
0.74 0.10 0.15
Matches are distributed among these distances:
62 1 0.01
63 39 0.22
64 7 0.04
65 71 0.41
66 4 0.02
67 3 0.02
68 26 0.15
69 3 0.02
70 20 0.11
71 1 0.01
ACGTcount: A:0.31, C:0.17, G:0.12, T:0.40
Consensus pattern (66 bp):
AATTTTGACAATTGCCCTATATAATTATGATAACCACCCTTTGTAATTTTGATAATCATCGATTA
G
Found at i:3093 original size:133 final size:133
Alignment explanation
Indices: 2855--3138 Score: 532
Period size: 133 Copynumber: 2.1 Consensus size: 133
2845 TGTATTTTTT
*
2855 ATAACCATCCTTTTTAATCTTGATAATCAAACGCCATATCAAATTTTGATAATCGCCCTATATTG
1 ATAACCATCCTTTATAATCTTGATAATCAAACGCCATATCAAATTTTGATAATCGCCCTATATTG
2920 TTGATAACTGCCCTTTGAGATTTTGATAATCTCGATTAGAATTTTGACAATTGTCCTATATAATT
66 TTGATAACTGCCCTTTGAGATTTTGATAATCTCGATTAGAATTTTGACAATTGTCCTATATAATT
2985 ATG
131 ATG
* * *
2988 ATAACCACCCTTTGTAATCTTGATAATCAAACGTCATATCAAATTTTGATAATCGCCCTATATTG
1 ATAACCATCCTTTATAATCTTGATAATCAAACGCCATATCAAATTTTGATAATCGCCCTATATTG
3053 TTGATAACTGCCCTTTGAGATTTTGATAATCTCGATTAGAATTTTGACAATTGTCCTATATAATT
66 TTGATAACTGCCCTTTGAGATTTTGATAATCTCGATTAGAATTTTGACAATTGTCCTATATAATT
3118 ATG
131 ATG
3121 ATAACCATCCTTTATAAT
1 ATAACCATCCTTTATAAT
3139 TTTAATAACT
Statistics
Matches: 146, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
133 146 1.00
ACGTcount: A:0.32, C:0.18, G:0.11, T:0.39
Consensus pattern (133 bp):
ATAACCATCCTTTATAATCTTGATAATCAAACGCCATATCAAATTTTGATAATCGCCCTATATTG
TTGATAACTGCCCTTTGAGATTTTGATAATCTCGATTAGAATTTTGACAATTGTCCTATATAATT
ATG
Found at i:3146 original size:22 final size:22
Alignment explanation
Indices: 3106--3147 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
3096 TTGACAATTG
*
3106 TCCTATATAATTATGATAACCA
1 TCCTATATAATTATAATAACCA
* *
3128 TCCTTTATAATTTTAATAAC
1 TCCTATATAATTATAATAAC
3148 TTCGATTGAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.38, C:0.17, G:0.02, T:0.43
Consensus pattern (22 bp):
TCCTATATAATTATAATAACCA
Found at i:3351 original size:22 final size:22
Alignment explanation
Indices: 3321--3373 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
3311 CATAAAGTGT
* * *
3321 TTATAAAAATTACGAAGGATAA
1 TTATCAAAATGACAAAGGATAA
**
3343 TTATCAAAATGACAAAGGATTG
1 TTATCAAAATGACAAAGGATAA
3365 TTATCAAAA
1 TTATCAAAA
3374 CCTCATAAGA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.51, C:0.08, G:0.13, T:0.28
Consensus pattern (22 bp):
TTATCAAAATGACAAAGGATAA
Found at i:5842 original size:26 final size:27
Alignment explanation
Indices: 5793--5844 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
5783 GAAATCATCC
*
5793 AAAAATTAATTTTAGTCTTTTTGAAAA
1 AAAAATTAATTTTAGTCTTGTTGAAAA
5820 AAAAATTAATTTTAGT-TTGTTGAAA
1 AAAAATTAATTTTAGTCTTGTTGAAA
5845 TTTTAGAGCC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 8 0.33
27 16 0.67
ACGTcount: A:0.44, C:0.02, G:0.10, T:0.44
Consensus pattern (27 bp):
AAAAATTAATTTTAGTCTTGTTGAAAA
Found at i:8212 original size:13 final size:13
Alignment explanation
Indices: 8194--8221 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
8184 TCTAGTGTTT
8194 CTGAATTATATAC
1 CTGAATTATATAC
8207 CTGAATTATATAC
1 CTGAATTATATAC
8220 CT
1 CT
8222 TTGACGTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.36, C:0.18, G:0.07, T:0.39
Consensus pattern (13 bp):
CTGAATTATATAC
Found at i:8316 original size:68 final size:68
Alignment explanation
Indices: 8207--8338 Score: 264
Period size: 68 Copynumber: 1.9 Consensus size: 68
8197 AATTATATAC
8207 CTGAATTATATACCTTTGACGTTATTGATACATGTGGCTTGGGTTTTAATTATCAATTTCAATAG
1 CTGAATTATATACCTTTGACGTTATTGATACATGTGGCTTGGGTTTTAATTATCAATTTCAATAG
8272 TTT
66 TTT
8275 CTGAATTATATACCTTTGACGTTATTGATACATGTGGCTTGGGTTTTAATTATCAATTTCAATA
1 CTGAATTATATACCTTTGACGTTATTGATACATGTGGCTTGGGTTTTAATTATCAATTTCAATA
8339 ATTAGCTTTT
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 64 1.00
ACGTcount: A:0.27, C:0.12, G:0.16, T:0.45
Consensus pattern (68 bp):
CTGAATTATATACCTTTGACGTTATTGATACATGTGGCTTGGGTTTTAATTATCAATTTCAATAG
TTT
Found at i:9952 original size:29 final size:30
Alignment explanation
Indices: 9910--9980 Score: 92
Period size: 29 Copynumber: 2.4 Consensus size: 30
9900 ACTTGTAGCG
* *
9910 TTTAGA-AGTTTTGCCCCTTGAACT-TCAAT
1 TTTAGACA-TTTTGCCCCCTAAACTCTCAAT
9939 TTTAGACATTTTGCCCCCTAAACTCTCAAT
1 TTTAGACATTTTGCCCCCTAAACTCTCAAT
*
9969 TTTAGACGTTTT
1 TTTAGACATTTT
9981 AATTTGCCTG
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
29 20 0.54
30 17 0.46
ACGTcount: A:0.24, C:0.23, G:0.11, T:0.42
Consensus pattern (30 bp):
TTTAGACATTTTGCCCCCTAAACTCTCAAT
Found at i:10901 original size:35 final size:32
Alignment explanation
Indices: 10862--10925 Score: 92
Period size: 32 Copynumber: 1.9 Consensus size: 32
10852 ACCAAATTGA
10862 ACCAAACCGATGACGACGTGGCATTGCCATGTTGG
1 ACCAAACCGAT---GACGTGGCATTGCCATGTTGG
*
10897 ACCAAATCGATGACGTGGCATTGCCATGT
1 ACCAAACCGATGACGTGGCATTGCCATGT
10926 GGGATTTTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 18 0.64
35 10 0.36
ACGTcount: A:0.27, C:0.25, G:0.27, T:0.22
Consensus pattern (32 bp):
ACCAAACCGATGACGTGGCATTGCCATGTTGG
Found at i:11064 original size:29 final size:30
Alignment explanation
Indices: 11002--11067 Score: 82
Period size: 29 Copynumber: 2.2 Consensus size: 30
10992 AAAGGGAGAT
* *
11002 GTCCAAAATTGAGAGTTCAGGACGCAAAAT
1 GTCCAAAATTGAGAGTTAAGGACGCAAAAC
*
11032 GTCCAAAATTGA-AGTTGAAGG-CGGAAAAC
1 GTCCAAAATTGAGAGTT-AAGGACGCAAAAC
11061 GTCCAAA
1 GTCCAAA
11068 TACTACAAGT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 17 0.53
30 15 0.47
ACGTcount: A:0.41, C:0.17, G:0.24, T:0.18
Consensus pattern (30 bp):
GTCCAAAATTGAGAGTTAAGGACGCAAAAC
Found at i:12551 original size:31 final size:31
Alignment explanation
Indices: 12513--12609 Score: 122
Period size: 31 Copynumber: 3.1 Consensus size: 31
12503 GATCATTTTC
* *
12513 AAATAAATAATATTTCGCGCACAAATGCATA
1 AAATAAATAATGTTTCGCGCACAAACGCATA
* *
12544 AAATAAATAATGTTTCGCGCACAAACACACA
1 AAATAAATAATGTTTCGCGCACAAACGCATA
* * * *
12575 AAATAATTAATGTTTCGTGTACAAACGCGTA
1 AAATAAATAATGTTTCGCGCACAAACGCATA
12606 AAAT
1 AAAT
12610 TGTGAAGTTG
Statistics
Matches: 56, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 56 1.00
ACGTcount: A:0.46, C:0.16, G:0.11, T:0.26
Consensus pattern (31 bp):
AAATAAATAATGTTTCGCGCACAAACGCATA
Found at i:13166 original size:22 final size:22
Alignment explanation
Indices: 13140--13320 Score: 138
Period size: 22 Copynumber: 8.3 Consensus size: 22
13130 TAAAATATCA
*
13140 ATAACTTCACTATGAAAATTTG
1 ATAACCTCACTATGAAAATTTG
* * * *
13162 ATAACCACATTGTGAAATTTTG
1 ATAACCTCACTATGAAAATTTG
* *
13184 ATAACCACACTATGAAATTTTG
1 ATAACCTCACTATGAAAATTTG
* * *
13206 ATAACCTCAGTGTGAAATTTTG
1 ATAACCTCACTATGAAAATTTG
* * *
13228 ATAATCTCCCTATGAAATTTTG
1 ATAACCTCACTATGAAAATTTG
*
13250 ATAA-TTACACTAT-AAAA-TTG
1 ATAACCT-CACTATGAAAATTTG
* * *
13270 GTAATCGCACTATGAAAATTTTG
1 ATAACCTCACTATGAAAA-TTTG
13293 ATAACCTC-CTCAT-AAAATTTTG
1 ATAACCTCACT-ATGAAAA-TTTG
13315 ATAACC
1 ATAACC
13321 AAACCATGAA
Statistics
Matches: 130, Mismatches: 23, Indels: 12
0.79 0.14 0.07
Matches are distributed among these distances:
20 12 0.09
21 8 0.06
22 100 0.77
23 10 0.08
ACGTcount: A:0.38, C:0.16, G:0.10, T:0.35
Consensus pattern (22 bp):
ATAACCTCACTATGAAAATTTG
Found at i:13195 original size:44 final size:44
Alignment explanation
Indices: 13147--13340 Score: 151
Period size: 44 Copynumber: 4.4 Consensus size: 44
13137 TCAATAACTT
*
13147 CACTATGAAAATTTGATAACCACATTGTGAAATTTTGATAACCA
1 CACTATGAAAATTTGATAACCACATTATGAAATTTTGATAACCA
* * * * * *
13191 CACTATGAAATTTTGATAACCTCAGTGTGAAATTTTGATAATCT
1 CACTATGAAAATTTGATAACCACATTATGAAATTTTGATAACCA
* * ** * * * * *
13235 CCCTATGAAATTTTGATAATTACACTAT-AAA-ATTGGTAATCG
1 CACTATGAAAATTTGATAACCACATTATGAAATTTTGATAACCA
* * * *
13277 CACTATGAAAATTTTGATAACCTCCTCATAAAATTTTGATAACCA
1 CACTATGAAAA-TTTGATAACCACATTATGAAATTTTGATAACCA
* *
13322 AACCATG-AAATTTCGATAA
1 CACTATGAAAATTT-GATAA
13341 ACTCCTAATT
Statistics
Matches: 118, Mismatches: 28, Indels: 8
0.77 0.18 0.05
Matches are distributed among these distances:
42 17 0.14
43 17 0.14
44 72 0.61
45 12 0.10
ACGTcount: A:0.39, C:0.16, G:0.11, T:0.34
Consensus pattern (44 bp):
CACTATGAAAATTTGATAACCACATTATGAAATTTTGATAACCA
Found at i:13332 original size:22 final size:22
Alignment explanation
Indices: 13284--13340 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
13274 TCGCACTATG
**
13284 AAAATTTTGATAACCTCCTCAT
1 AAAATTTTGATAACCAACTCAT
13306 AAAATTTTGATAACCAAAC-CAT
1 AAAATTTTGATAACC-AACTCAT
* *
13328 GAAATTTCGATAA
1 AAAATTTTGATAA
13341 ACTCCTAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
22 29 0.97
23 1 0.03
ACGTcount: A:0.44, C:0.18, G:0.07, T:0.32
Consensus pattern (22 bp):
AAAATTTTGATAACCAACTCAT
Found at i:13408 original size:22 final size:21
Alignment explanation
Indices: 13383--13459 Score: 73
Period size: 22 Copynumber: 3.5 Consensus size: 21
13373 CTCTCTATGT
13383 AATTTTGATAACCTCTCCATAA
1 AATTTTGATAACCTC-CCATAA
* * *
13405 AATTTTCATAGCCTCCCTATGA
1 AATTTTGATAACCTCCC-ATAA
* * *
13427 AATTTTGTTAACCTACCTAGAA
1 AATTTTGATAACCT-CCCATAA
13449 AATTTTGATAA
1 AATTTTGATAA
13460 GCACAAATTT
Statistics
Matches: 43, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
21 2 0.05
22 39 0.91
23 2 0.05
ACGTcount: A:0.35, C:0.19, G:0.08, T:0.38
Consensus pattern (21 bp):
AATTTTGATAACCTCCCATAA
Found at i:13498 original size:64 final size:64
Alignment explanation
Indices: 13404--13589 Score: 172
Period size: 64 Copynumber: 2.9 Consensus size: 64
13394 CCTCTCCATA
* * *
13404 AAATTTTCATAGCCT-C-CCTATGAAATTTTGTTAACCTACCTAGAAAATTTTGATAA-GCAC-
1 AAATTTTGATAACCTCCTCCTATGAAATTTTGTTAACCTACCTAGAAAATTTTGATAACACACT
* * *
13464 AAATTTTGATAACCTCCCTCTCTATGAAATTTTGTTTACCTTCTTATG-AAATTTTGATAACCAC
1 AAATTTTGATAACCT-CCTC-CTATGAAATTTTGTTAACCTACCTA-GAAAATTTTGATAA-CAC
13528 ACTAT
62 AC--T
* * *
13533 AAATTTTGATAACCT--TCGTATGAAATTTTGTTAACCTCCCTA-AGAAATTTCGATAAC
1 AAATTTTGATAACCTCCTCCTATGAAATTTTGTTAACCTACCTAGA-AAATTTTGATAAC
13590 TTTTATGTGA
Statistics
Matches: 103, Mismatches: 11, Indels: 20
0.77 0.08 0.15
Matches are distributed among these distances:
60 13 0.13
62 1 0.01
63 1 0.01
64 35 0.34
65 33 0.32
66 5 0.05
69 15 0.15
ACGTcount: A:0.33, C:0.19, G:0.09, T:0.38
Consensus pattern (64 bp):
AAATTTTGATAACCTCCTCCTATGAAATTTTGTTAACCTACCTAGAAAATTTTGATAACACACT
Found at i:13514 original size:22 final size:22
Alignment explanation
Indices: 13464--13693 Score: 141
Period size: 22 Copynumber: 10.4 Consensus size: 22
13454 TGATAAGCAC
13464 AAATTTTGATAACCTCCCTCTCTATG
1 AAATTTTGATAACCT---TC-CTATG
* * *
13490 AAATTTTGTTTACCTTCTTATG
1 AAATTTTGATAACCTTCCTATG
*
13512 AAATTTTGATAACC-ACACTAT-
1 AAATTTTGATAACCTTC-CTATG
*
13533 AAATTTTGATAACCTTCGTATG
1 AAATTTTGATAACCTTCCTATG
* * *
13555 AAATTTTGTTAACCTCCCTAAG
1 AAATTTTGATAACCTTCCTATG
* * ** *
13577 AAATTTCGATAACTTTTATGTG
1 AAATTTTGATAACCTTCCTATG
** **
13599 AAATTTTGGCAACCTTTGTATG
1 AAATTTTGATAACCTTCCTATG
* *
13621 AAATCTTGATAACC-CCCATATG
1 AAATTTTGATAACCTTCC-TATG
*
13643 AAATTTTTG-TAACAC--ACTATG
1 AAA-TTTTGATAAC-CTTCCTATG
13664 AAATTTT-ACTAACCTTCCTATG
1 AAATTTTGA-TAACCTTCCTATG
*
13686 TAATTTTG
1 AAATTTTG
13694 GTTTGATTGT
Statistics
Matches: 156, Mismatches: 37, Indels: 25
0.72 0.17 0.11
Matches are distributed among these distances:
20 5 0.03
21 29 0.19
22 102 0.65
23 7 0.04
26 13 0.08
ACGTcount: A:0.32, C:0.18, G:0.10, T:0.40
Consensus pattern (22 bp):
AAATTTTGATAACCTTCCTATG
Found at i:13555 original size:43 final size:43
Alignment explanation
Indices: 13485--13693 Score: 163
Period size: 43 Copynumber: 4.8 Consensus size: 43
13475 ACCTCCCTCT
* * *
13485 CTATGAAATTTTGTTTACCTTCTTATGAAATTTTGATAACCACA
1 CTATGAAATTTTGATAACCTTCATATGAAATTTTG-TAACCACA
* * *
13529 CTAT-AAATTTTGATAACCTTCGTATGAAATTTTGTTAACCTCC
1 CTATGAAATTTTGATAACCTTCATATGAAATTTTG-TAACCACA
* * * * * * ***
13572 CTAAGAAATTTCGATAACTTTTATGTGAAATTTTGGCAACCTTT
1 CTATGAAATTTTGATAACCTTCATATGAAATTTT-GTAACCACA
* * **
13616 GTATGAAATCTTGATAACCCCCATATGAAATTTTTGTAA-CACA
1 CTATGAAATTTTGATAACCTTCATATGAAA-TTTTGTAACCACA
* *
13659 CTATGAAATTTT-ACTAACCTTCCTATGTAATTTTG
1 CTATGAAATTTTGA-TAACCTTCATATGAAATTTTG
13694 GTTTGATTGT
Statistics
Matches: 127, Mismatches: 34, Indels: 10
0.74 0.20 0.06
Matches are distributed among these distances:
42 6 0.05
43 59 0.46
44 57 0.45
45 5 0.04
ACGTcount: A:0.32, C:0.17, G:0.11, T:0.41
Consensus pattern (43 bp):
CTATGAAATTTTGATAACCTTCATATGAAATTTTGTAACCACA
Found at i:14795 original size:3 final size:3
Alignment explanation
Indices: 14787--14811 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
14777 TTAAAAAAGG
14787 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
14812 ATTTAATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:17529 original size:23 final size:23
Alignment explanation
Indices: 17502--17545 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
17492 GTTGCTACAT
17502 AAAAGTACTT-ACTCTATTGGTAA
1 AAAAG-ACTTAACTCTATTGGTAA
*
17525 AAAAGATTTAACTCTATTGGT
1 AAAAGACTTAACTCTATTGGT
17546 TATGAAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 3 0.16
23 16 0.84
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.36
Consensus pattern (23 bp):
AAAAGACTTAACTCTATTGGTAA
Found at i:19821 original size:13 final size:13
Alignment explanation
Indices: 19803--19830 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
19793 ATCTTGTCCT
19803 AATAATAATAATA
1 AATAATAATAATA
19816 AATAATAATAATA
1 AATAATAATAATA
19829 AA
1 AA
19831 GTAAAGTTGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (13 bp):
AATAATAATAATA
Found at i:22533 original size:25 final size:25
Alignment explanation
Indices: 22499--22547 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
22489 CCAAACAATC
22499 TTGAGCACTCTCGCTCGGTCTCTAT
1 TTGAGCACTCTCGCTCGGTCTCTAT
22524 TTGAGCACTCTCGCTCGGTCTCTA
1 TTGAGCACTCTCGCTCGGTCTCTA
22548 CAAACTAATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.12, C:0.33, G:0.20, T:0.35
Consensus pattern (25 bp):
TTGAGCACTCTCGCTCGGTCTCTAT
Found at i:23044 original size:44 final size:44
Alignment explanation
Indices: 22981--23087 Score: 126
Period size: 45 Copynumber: 2.4 Consensus size: 44
22971 GGGAGCTTAT
* *
22981 CAATTGGTCCCGATATTAGCATTACATATA-CCGTCAGGATCCAA
1 CAATTGGTCTCGATATTAGCATTACATA-AGCCGTCAGGACCCAA
* * * * *
23025 CAATTGGTCTTGATATTAGCTTTGCTTAAGTTCGTCAGGACCCAA
1 CAATTGGTCTCGATATTAGCATTACATAAG-CCGTCAGGACCCAA
23070 CAATTGGTCTCGATATTA
1 CAATTGGTCTCGATATTA
23088 ATTTTATTAA
Statistics
Matches: 53, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
43 1 0.02
44 23 0.43
45 29 0.55
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (44 bp):
CAATTGGTCTCGATATTAGCATTACATAAGCCGTCAGGACCCAA
Found at i:23075 original size:45 final size:43
Alignment explanation
Indices: 23012--23136 Score: 151
Period size: 44 Copynumber: 2.8 Consensus size: 43
23002 TTACATATAC
*
23012 CGTCAGGATCCAACAATTGGTCTTGATATTAGCTTTGCTTAAGTT
1 CGTCAGGATCCAACAATTGGTCTTGATATTA-CTTTGATTAAG-T
* * * *
23057 CGTCAGGACCCAACAATTGGTCTCGATATTAATTTTATTAAGT
1 CGTCAGGATCCAACAATTGGTCTTGATATTACTTTGATTAAGT
* *
23100 CTGTCAGGATCAAACAATTGGTCCTGATATTAACTTT
1 C-GTCAGGATCCAACAATTGGTCTTGATATT-ACTTT
23137 AGAATTTATC
Statistics
Matches: 68, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
43 2 0.03
44 33 0.49
45 33 0.49
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (43 bp):
CGTCAGGATCCAACAATTGGTCTTGATATTACTTTGATTAAGT
Found at i:23503 original size:15 final size:15
Alignment explanation
Indices: 23483--23515 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
23473 ACAGTTTGTG
23483 TTTATTTTT-TTTATT
1 TTTATTTTTATTT-TT
23498 TTTATTTTTATTTTT
1 TTTATTTTTATTTTT
23513 TTT
1 TTT
23516 GTGTGCAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 14 0.82
16 3 0.18
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (15 bp):
TTTATTTTTATTTTT
Found at i:23937 original size:13 final size:13
Alignment explanation
Indices: 23919--23944 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
23909 GGGCTTTCTT
23919 TGGTGGCCCAAAA
1 TGGTGGCCCAAAA
23932 TGGTGGCCCAAAA
1 TGGTGGCCCAAAA
23945 ATCTTTAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.23, G:0.31, T:0.15
Consensus pattern (13 bp):
TGGTGGCCCAAAA
Found at i:24716 original size:18 final size:18
Alignment explanation
Indices: 24693--24763 Score: 80
Period size: 18 Copynumber: 4.1 Consensus size: 18
24683 CCAAATTATA
24693 AACTAAAATTATTGTTGT
1 AACTAAAATTATTGTTGT
*
24711 AACTAAAATATAAT-TT-T
1 AACTAAAAT-TATTGTTGT
24728 AGA-T--AATTATTGTTGT
1 A-ACTAAAATTATTGTTGT
24744 AACTAAAATTATTGTTGT
1 AACTAAAATTATTGTTGT
24762 AA
1 AA
24764 ATTTGGATGG
Statistics
Matches: 44, Mismatches: 2, Indels: 14
0.73 0.03 0.23
Matches are distributed among these distances:
14 3 0.07
15 6 0.14
16 3 0.07
17 3 0.07
18 26 0.59
19 3 0.07
ACGTcount: A:0.42, C:0.04, G:0.10, T:0.44
Consensus pattern (18 bp):
AACTAAAATTATTGTTGT
Found at i:25162 original size:78 final size:76
Alignment explanation
Indices: 25103--25270 Score: 203
Period size: 77 Copynumber: 2.2 Consensus size: 76
25093 TCTAATATAT
* * * *
25103 AAGTTTT-TTAATTAAAATTGTAAAATGGTAAAATAAAATAGTTATAAGGATATTATATTTAATT
1 AAGTTTTATTAAGTAAAA-AGTAAAATGGTAAAATAAAATAGTTATAAAGATATTATATTTAATA
25167 AAACAGAAATAG
65 AAACAGAAATAG
* * * *
25179 AGGTTTTAGTTGAGTAAAAAGTAAAATGGTAAAATAAAATAGTTATAAAGATATTAGATTTAATT
1 AAGTTTTA-TTAAGTAAAAAGTAAAATGGTAAAATAAAATAGTTATAAAGATATTATATTTAATA
* *
25244 AAATAAAAATAG
65 AAACAGAAATAG
*
25256 AATTTTTATTTAAGT
1 AAGTTTTA-TTAAGT
25271 GAAATTATAA
Statistics
Matches: 78, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
76 6 0.08
77 64 0.82
78 8 0.10
ACGTcount: A:0.49, C:0.01, G:0.13, T:0.37
Consensus pattern (76 bp):
AAGTTTTATTAAGTAAAAAGTAAAATGGTAAAATAAAATAGTTATAAAGATATTATATTTAATAA
AACAGAAATAG
Found at i:25292 original size:77 final size:77
Alignment explanation
Indices: 25122--25270 Score: 226
Period size: 77 Copynumber: 1.9 Consensus size: 77
25112 AATTAAAATT
* * * *
25122 GTAAAATGGTAAAATAAAATAGTTATAAGGATATTATATTTAATTAAACAGAAATAGAGGTTTTA
1 GTAAAATGGTAAAATAAAATAGTTATAAAGATATTAGATTTAATTAAACAAAAATAGAAGTTTTA
*
25187 GTTGAGTAAAAA
66 GTTAAGTAAAAA
* *
25199 GTAAAATGGTAAAATAAAATAGTTATAAAGATATTAGATTTAATTAAATAAAAATAGAATTTTTA
1 GTAAAATGGTAAAATAAAATAGTTATAAAGATATTAGATTTAATTAAACAAAAATAGAAGTTTTA
*
25264 TTTAAGT
66 GTTAAGT
25271 GAAATTATAA
Statistics
Matches: 64, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
77 64 1.00
ACGTcount: A:0.50, C:0.01, G:0.14, T:0.35
Consensus pattern (77 bp):
GTAAAATGGTAAAATAAAATAGTTATAAAGATATTAGATTTAATTAAACAAAAATAGAAGTTTTA
GTTAAGTAAAAA
Found at i:25550 original size:7 final size:7
Alignment explanation
Indices: 25538--25565 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
25528 CAGCCATGAC
25538 CCCATAG
1 CCCATAG
25545 CCCATAG
1 CCCATAG
25552 CCCATAG
1 CCCATAG
25559 CCCATAG
1 CCCATAG
25566 ATGAATCTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.29, C:0.43, G:0.14, T:0.14
Consensus pattern (7 bp):
CCCATAG
Found at i:27542 original size:27 final size:27
Alignment explanation
Indices: 27512--27567 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 27
27502 GGAGTGGGAA
27512 GAAAGTGCTGATAATAAGAAAAAGGAG
1 GAAAGTGCTGATAATAAGAAAAAGGAG
* * *
27539 GAAAGTGCTGATGATGAGAAAAGGGAG
1 GAAAGTGCTGATAATAAGAAAAAGGAG
27566 GA
1 GA
27568 CACTGTAGAG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.46, C:0.04, G:0.36, T:0.14
Consensus pattern (27 bp):
GAAAGTGCTGATAATAAGAAAAAGGAG
Found at i:31534 original size:24 final size:24
Alignment explanation
Indices: 31489--31537 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
31479 ATAAGTTTTC
* *
31489 TCAGTTTATACATTTTACTATATA
1 TCAGTTTATACAGTATACTATATA
31513 TCAGTTTATAGCAGTATA-TATATA
1 TCAGTTTATA-CAGTATACTATATA
31537 T
1 T
31538 ATATAATTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 17 0.77
25 5 0.23
ACGTcount: A:0.35, C:0.10, G:0.08, T:0.47
Consensus pattern (24 bp):
TCAGTTTATACAGTATACTATATA
Found at i:47152 original size:109 final size:109
Alignment explanation
Indices: 46961--47178 Score: 382
Period size: 109 Copynumber: 2.0 Consensus size: 109
46951 TATATATATA
* * * *
46961 TATTATTATTAATTGTGTGGTTTATTCAATTGAACTTATTAAATAAGCACACATACCAAATAATA
1 TATTATTATTAAATGTGTGGTTTATTCAATTAAACCTATTAAATAAGCACACATACCAAACAATA
47026 CAAAATGCAATGAACTATTGGATTTAAAGAAAAATACAAGCACC
66 CAAAATGCAATGAACTATTGGATTTAAAGAAAAATACAAGCACC
*
47070 TATTATTATTAAATGTGTTGTTTATTCAATTAAACCTATTAAATAAGCACACATACCAAACAATA
1 TATTATTATTAAATGTGTGGTTTATTCAATTAAACCTATTAAATAAGCACACATACCAAACAATA
*
47135 CAAAGTGCAATGAACTATTGGATTTAAAGAAAAATACAAGCACC
66 CAAAATGCAATGAACTATTGGATTTAAAGAAAAATACAAGCACC
47179 AAAATGACTA
Statistics
Matches: 103, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
109 103 1.00
ACGTcount: A:0.44, C:0.14, G:0.11, T:0.31
Consensus pattern (109 bp):
TATTATTATTAAATGTGTGGTTTATTCAATTAAACCTATTAAATAAGCACACATACCAAACAATA
CAAAATGCAATGAACTATTGGATTTAAAGAAAAATACAAGCACC
Found at i:49169 original size:35 final size:33
Alignment explanation
Indices: 49123--49196 Score: 94
Period size: 35 Copynumber: 2.2 Consensus size: 33
49113 AATTATGCCA
**
49123 TTTTTTTAAAAAAAAAACTACAACATTTTGTCT
1 TTTTTTTAAAAAAAAAAAGACAACATTTTGTCT
* *
49156 TTTTTATTGAAAAAAAAAAAGATAACGTTTTGTCT
1 TTTTT-TT-AAAAAAAAAAAGACAACATTTTGTCT
49191 TTTTTT
1 TTTTTT
49197 GAAATTACGC
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
33 5 0.14
34 3 0.09
35 27 0.77
ACGTcount: A:0.39, C:0.08, G:0.07, T:0.46
Consensus pattern (33 bp):
TTTTTTTAAAAAAAAAAAGACAACATTTTGTCT
Found at i:49907 original size:23 final size:24
Alignment explanation
Indices: 49870--49954 Score: 88
Period size: 23 Copynumber: 3.6 Consensus size: 24
49860 CGCGACCCGC
*
49870 GTCGCGACTCGGATCCATGGCCAG
1 GTCGCGACGCGGATCCATGGCCAG
* *
49894 GTCGCG-CGCGGATCGC--GACCCG
1 GTCGCGACGCGGATC-CATGGCCAG
*
49916 CGTCGCGACTCGGATCCATGGCCAG
1 -GTCGCGACGCGGATCCATGGCCAG
49941 GTCGCG-CGCGGATC
1 GTCGCGACGCGGATC
49955 GCGACCCGCC
Statistics
Matches: 49, Mismatches: 7, Indels: 11
0.73 0.10 0.16
Matches are distributed among these distances:
22 4 0.08
23 21 0.43
24 20 0.41
25 4 0.08
ACGTcount: A:0.13, C:0.36, G:0.36, T:0.14
Consensus pattern (24 bp):
GTCGCGACGCGGATCCATGGCCAG
Found at i:49917 original size:47 final size:47
Alignment explanation
Indices: 49860--49963 Score: 208
Period size: 47 Copynumber: 2.2 Consensus size: 47
49850 CAGGGTCGCG
49860 CGCGACCCGCGTCGCGACTCGGATCCATGGCCAGGTCGCGCGCGGAT
1 CGCGACCCGCGTCGCGACTCGGATCCATGGCCAGGTCGCGCGCGGAT
49907 CGCGACCCGCGTCGCGACTCGGATCCATGGCCAGGTCGCGCGCGGAT
1 CGCGACCCGCGTCGCGACTCGGATCCATGGCCAGGTCGCGCGCGGAT
49954 CGCGACCCGC
1 CGCGACCCGC
49964 CATGGTCCGT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 57 1.00
ACGTcount: A:0.12, C:0.40, G:0.36, T:0.12
Consensus pattern (47 bp):
CGCGACCCGCGTCGCGACTCGGATCCATGGCCAGGTCGCGCGCGGAT
Done.