Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013795.1 Corchorus olitorius cultivar O-4 contig13828, 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: 56544
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Found at i:5906 original size:3 final size:3
Alignment explanation
Indices: 5900--5960 Score: 113
Period size: 3 Copynumber: 20.3 Consensus size: 3
5890 CTTTTTAACC
*
5900 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT ACT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
5948 TCT TCT TCT TCT T
1 TCT TCT TCT TCT T
5961 TTTTTTTTTG
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.02, C:0.33, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:6510 original size:25 final size:22
Alignment explanation
Indices: 6475--6539 Score: 60
Period size: 25 Copynumber: 2.8 Consensus size: 22
6465 CAAGGGTACG
*
6475 TTCTTTCTTTTCTTTCTTCATCTTC
1 TTCTTTTTTTTCTTTCTT--TC-TC
*
6500 TTCTTTTTTTTCCCTCTCTTTCTC
1 TTCTTTTTTTT--CTTTCTTTCTC
6524 TT-TTTTTTTTCTTTCT
1 TTCTTTTTTTTCTTTCT
6540 CTAGAACAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
21 5 0.14
23 8 0.23
24 4 0.11
25 12 0.34
27 6 0.17
ACGTcount: A:0.02, C:0.26, G:0.00, T:0.72
Consensus pattern (22 bp):
TTCTTTTTTTTCTTTCTTTCTC
Found at i:7228 original size:24 final size:22
Alignment explanation
Indices: 7201--7249 Score: 53
Period size: 24 Copynumber: 2.1 Consensus size: 22
7191 AATCCTACGA
*
7201 TTTAATCTTCGTTTCTTTTCTTTT
1 TTTAATATTCGTTT-TTTT-TTTT
* *
7225 TTTATTATTTGTTTTTTTTTTT
1 TTTAATATTCGTTTTTTTTTTT
7247 TTT
1 TTT
7250 GGTAATGGCA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 7 0.32
23 4 0.18
24 11 0.50
ACGTcount: A:0.08, C:0.08, G:0.04, T:0.80
Consensus pattern (22 bp):
TTTAATATTCGTTTTTTTTTTT
Found at i:22823 original size:7 final size:7
Alignment explanation
Indices: 22811--22860 Score: 70
Period size: 7 Copynumber: 7.4 Consensus size: 7
22801 TGTGCGGGCA
22811 CTACTAT
1 CTACTAT
22818 CTACTA-
1 CTACTAT
22824 -T-CTAT
1 CTACTAT
22829 CTATCTAT
1 CTA-CTAT
22837 CTACTAT
1 CTACTAT
22844 CTACTAT
1 CTACTAT
22851 CTACTAT
1 CTACTAT
22858 CTA
1 CTA
22861 ATAAAATCAC
Statistics
Matches: 39, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
4 3 0.08
5 1 0.03
6 1 0.03
7 27 0.69
8 7 0.18
ACGTcount: A:0.28, C:0.28, G:0.00, T:0.44
Consensus pattern (7 bp):
CTACTAT
Found at i:22830 original size:4 final size:4
Alignment explanation
Indices: 22814--22860 Score: 66
Period size: 4 Copynumber: 12.8 Consensus size: 4
22804 GCGGGCACTA
22814 CTAT CTA- CTAT CTAT CTAT CTAT CTA- CTAT CTA- CTAT CTA- CTAT
1 CTAT CTAT CTAT CTAT CTAT CTAT CTAT CTAT CTAT CTAT CTAT CTAT
22858 CTA
1 CTA
22861 ATAAAATCAC
Statistics
Matches: 39, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
3 12 0.31
4 27 0.69
ACGTcount: A:0.28, C:0.28, G:0.00, T:0.45
Consensus pattern (4 bp):
CTAT
Found at i:23963 original size:22 final size:22
Alignment explanation
Indices: 23914--24050 Score: 109
Period size: 22 Copynumber: 6.1 Consensus size: 22
23904 GATCTCCATA
23914 TGATAACACTTCCTTAT-AAACTTT
1 TGATAACA-TTCC-TATGAAA-TTT
23938 TGATAACATTCCTATGAAATTT
1 TGATAACATTCCTATGAAATTT
* *
23960 TGATAATGA-TACTATGAAATTT
1 TGATAA-CATTCCTATGAAATTT
* * *
23982 CGAAAACATTCCTATCAAATTT
1 TGATAACATTCCTATGAAATTT
** *
24004 CAATAACATCCCTATGAAATTT
1 TGATAACATTCCTATGAAATTT
* * *
24026 TGTTAACCTCCCTAT-AGAATTT
1 TGATAACATTCCTATGA-AATTT
24048 TGA
1 TGA
24051 AAACTACTAT
Statistics
Matches: 93, Mismatches: 16, Indels: 10
0.78 0.13 0.08
Matches are distributed among these distances:
21 2 0.02
22 75 0.81
23 8 0.09
24 8 0.09
ACGTcount: A:0.36, C:0.18, G:0.08, T:0.38
Consensus pattern (22 bp):
TGATAACATTCCTATGAAATTT
Found at i:24218 original size:23 final size:23
Alignment explanation
Indices: 24185--24275 Score: 121
Period size: 23 Copynumber: 4.0 Consensus size: 23
24175 AATTGTAATG
*
24185 ACCTCGATATAAAATTTTGATAA
1 ACCTCCATATAAAATTTTGATAA
* *
24208 ACATTCATATAAAATTTTGATAA
1 ACCTCCATATAAAATTTTGATAA
*
24231 ACCTCCCTATAAAATTTTGAT-A
1 ACCTCCATATAAAATTTTGATAA
* *
24253 ACCTCCTTATGAAATTTTGATAA
1 ACCTCCATATAAAATTTTGATAA
24276 TCACAAATTT
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
22 20 0.34
23 39 0.66
ACGTcount: A:0.41, C:0.15, G:0.07, T:0.37
Consensus pattern (23 bp):
ACCTCCATATAAAATTTTGATAA
Found at i:24258 original size:22 final size:22
Alignment explanation
Indices: 23935--24998 Score: 280
Period size: 22 Copynumber: 48.6 Consensus size: 22
23925 CCTTATAAAC
* *
23935 TTTTGATAACATTCCTATGAAA
1 TTTTGATAACCTCCCTATGAAA
** *
23957 TTTTGATAATGAT-ACTATGAAA
1 TTTTGATAA-CCTCCCTATGAAA
* * * * *
23979 TTTCGAAAACATTCCTATCAAA
1 TTTTGATAACCTCCCTATGAAA
** *
24001 TTTCAATAACATCCCTATGAAA
1 TTTTGATAACCTCCCTATGAAA
*
24023 TTTTGTTAACCTCCCTAT-AGAA
1 TTTTGATAACCTCCCTATGA-AA
* * *
24045 TTTTGA-AAACT-ACTATAAAA
1 TTTTGATAACCTCCCTATGAAA
* * * *
24065 TTCT-ATTAATCTCCATTTGAAA
1 TTTTGA-TAACCTCCCTATGAAA
* * * * *
24087 TGTTGGTAAGCACACTATGATAA
1 TTTTGATAACCTCCCTATGA-AA
*
24110 TTTTTTATAACCTCCCTATGAAA
1 -TTTTGATAACCTCCCTATGAAA
* * * * * *
24133 TATT-AGTGATCACACTGTGAAA
1 TTTTGA-TAACCTCCCTATGAAA
* * *
24155 TTTTAATAACCACACTATGAAA
1 TTTTGATAACCTCCCTATGAAA
* * * ** *
24177 TTGTAATGACCTCGATATAAAA
1 TTTTGATAACCTCCCTATGAAA
* * * *
24199 TTTTGATAAACATTCATATAAAA
1 TTTTGAT-AACCTCCCTATGAAA
*
24222 TTTTGATAAACCTCCCTATAAAA
1 TTTTGAT-AACCTCCCTATGAAA
*
24245 TTTTGATAACCTCCTTATGAAA
1 TTTTGATAACCTCCCTATGAAA
*
24267 TTTTGATAA--T--C-A-CAAA
1 TTTTGATAACCTCCCTATGAAA
* * *
24283 TTTCGATAACCTCCATAT-AAT
1 TTTTGATAACCTCCCTATGAAA
* * **
24304 TTTTCAATAACTTCATTATGAAA
1 TTTT-GATAACCTCCCTATGAAA
**
24327 TTTTTTTAACCTCCCTATGAAA
1 TTTTGATAACCTCCCTATGAAA
*
24349 TTTTGATAA-C-CCCTATAAAA
1 TTTTGATAACCTCCCTATGAAA
* * * **
24369 TTCT-AAAAACTAAACTATGAAA
1 TTTTGATAACCT-CCCTATGAAA
*
24391 TTTTGATATCCTCCCTATGAAA
1 TTTTGATAACCTCCCTATGAAA
*
24413 TTTTGGTAATCC-CCCT-TCGAAA
1 TTTTGATAA-CCTCCCTAT-GAAA
* * * *
24435 TTTTAATAACCTTCATACGAAA
1 TTTTGATAACCTCCCTATGAAA
* * * ** *
24457 TTTTGGTCA-TTGCACAAATGCAAT
1 TTTTGATAACCT-C-CCTATG-AAA
* *
24481 TTTTGATAACCTCACTTTGAAA
1 TTTTGATAACCTCCCTATGAAA
***
24503 -TACCAT-A-CT--CTA--AAA
1 TTTTGATAACCTCCCTATGAAA
* ** **
24518 TTTGGATAACAACATTATGAAA
1 TTTTGATAACCTCCCTATGAAA
* * * *
24540 TTTCGATAACCTTCTTAAGAAA
1 TTTTGATAACCTCCCTATGAAA
*
24562 TTTCGATAACCTCCCTATGAAA
1 TTTTGATAACCTCCCTATGAAA
* *
24584 GTTTGCTAACCT--CTATGAAA
1 TTTTGATAACCTCCCTATGAAA
* *
24604 TTTTGATAATCAT-ACTATGAAA
1 TTTTGATAA-CCTCCCTATGAAA
*
24626 -TTTGA-AACCTCCATATGAAA
1 TTTTGATAACCTCCCTATGAAA
* * **
24646 TTTTAATAACCACAATATGAAAA
1 TTTTGATAACCTCCCTATG-AAA
* * *
24669 TTTTTCATAACCTCACT-GGAAAA
1 -TTTTGATAACCTCCCTATG-AAA
* *
24692 TTTTGATAACCT-TCAATGAAA
1 TTTTGATAACCTCCCTATGAAA
* *
24713 TTTTGATAACCT-TCAATGAAA
1 TTTTGATAACCTCCCTATGAAA
* * *
24734 TTTTGATAA-TTACAT-TGTAAAA
1 TTTTGATAACCTCCCTATG--AAA
* *
24756 TTTTGATAACCTTCCTATGCAA
1 TTTTGATAACCTCCCTATGAAA
* * * *
24778 TTTTGGTAATCTGATCTCTATGAAT
1 TTTTGATAA-C--CTCCCTATGAAA
* *
24803 TTTTGATAA-CTACTCTATGAGA
1 TTTTGATAACCT-CCCTATGAAA
** *
24825 TTTTGAT-TGCTTCCTGATGAAA
1 TTTTGATAACCTCCCT-ATGAAA
* ***
24847 TTTTGATAACATTTGTATGAAA
1 TTTTGATAACCTCCCTATGAAA
* * **
24869 TTTAGAATTTTGTAACATTACTATGAAA
1 TTTTG-A-----TAACCTCCCTATGAAA
* **
24897 TTTTGGTAACCAT-ATTATGAAA
1 TTTTGATAACC-TCCCTATGAAA
* * * *
24919 TCTTTAATAATCTCCTTATAAAA
1 T-TTTGATAACCTCCCTATGAAA
* *
24942 TTTTGATAACCACACTATGAAA
1 TTTTGATAACCTCCCTATGAAA
* * *
24964 TTCTGATAACCTCGCTATGGAA
1 TTTTGATAACCTCCCTATGAAA
24986 TTTTGATAACCTC
1 TTTTGATAACCTC
24999 TTTGATAGCC
Statistics
Matches: 766, Mismatches: 207, Indels: 138
0.69 0.19 0.12
Matches are distributed among these distances:
15 3 0.00
16 14 0.02
17 4 0.01
18 1 0.00
19 8 0.01
20 53 0.07
21 75 0.10
22 440 0.57
23 95 0.12
24 39 0.05
25 16 0.02
28 18 0.02
ACGTcount: A:0.36, C:0.16, G:0.09, T:0.38
Consensus pattern (22 bp):
TTTTGATAACCTCCCTATGAAA
Found at i:24622 original size:42 final size:42
Alignment explanation
Indices: 24576--24831 Score: 133
Period size: 42 Copynumber: 5.8 Consensus size: 42
24566 GATAACCTCC
*
24576 CTATGAAAGTTTGCTAACCTCTATGAAATTTTGATAATCATA
1 CTATGAAATTTTGCTAACCTCTATGAAATTTTGATAATCATA
* * * *
24618 CTATGAAA-TTTG-AAACCTCCATATGAAATTTTAATAACCACA
1 CTATGAAATTTTGCTAACCT-C-TATGAAATTTTGATAATCATA
* * * *
24660 ATATGAAAATTTTTCATAACCTC-ACTGGAAAATTTTGATAA-CCTT
1 CTATG-AAATTTTGC-TAACCTCTA-T-G-AAATTTTGATAATCATA
* * * * *
24705 CAATGAAATTTTGATAACCTTCAATGAAATTTTGATAATTACA
1 CTATGAAATTTTGCTAACC-TCTATGAAATTTTGATAATCATA
* * * * * * *
24748 TTGTAAAATTTTGATAACCTTCCTATGCAATTTTGGTAATCTGATCT
1 CTATGAAATTTTGCTAACC-T-CTATGAAATTTTGATAATC--AT-A
* * *
24795 CTATGAATTTTTGATAACTACTCTATGAGATTTTGAT
1 CTATGAAATTTTGCTAAC--CTCTATGAAATTTTGAT
24832 TGCTTCCTGA
Statistics
Matches: 160, Mismatches: 36, Indels: 31
0.70 0.16 0.14
Matches are distributed among these distances:
40 5 0.03
41 5 0.03
42 42 0.26
43 27 0.17
44 29 0.18
45 7 0.04
46 17 0.11
47 26 0.16
48 1 0.01
49 1 0.01
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.39
Consensus pattern (42 bp):
CTATGAAATTTTGCTAACCTCTATGAAATTTTGATAATCATA
Found at i:24665 original size:64 final size:65
Alignment explanation
Indices: 24523--24742 Score: 157
Period size: 64 Copynumber: 3.4 Consensus size: 65
24513 TAAAATTTGG
* * * * *
24523 ATAACAACATTATGAAATTTCGATAACCTTCTTAAGAAATTTCGATAACCTCCCTATGAAAGTTT
1 ATAACCACA-TATGAAATTTTGATAACATACTTAAGAAATTTCGATAACCTCCATATGAAAGTTT
*
24588 G
65 A
* * * *
24589 CTAACCTC-TATGAAATTTTGATAATCATAC-TATGAAATTT-GA-AACCTCCATATGAAATTTT
1 ATAACCACATATGAAATTTTGATAA-CATACTTAAGAAATTTCGATAACCTCCATATGAAAGTTT
24650 A
65 A
* * ** * * *
24651 ATAACCACAATATGAAAATTTTTCATAACCTCACTGGA-AAATTTTGATAACCTTCA-ATGAAAT
1 ATAACCAC-ATATG-AAA-TTTTGATAACAT-ACTTAAGAAATTTCGATAACCTCCATATGAAAG
*
24714 TTTG
62 TTTA
*
24718 ATAACCTTCA-ATGAAATTTTGATAA
1 ATAACC-ACATATGAAATTTTGATAA
24743 TTACATTGTA
Statistics
Matches: 123, Mismatches: 21, Indels: 22
0.74 0.13 0.13
Matches are distributed among these distances:
62 23 0.19
63 2 0.02
64 36 0.29
65 11 0.09
66 24 0.20
67 19 0.15
68 8 0.07
ACGTcount: A:0.40, C:0.16, G:0.09, T:0.35
Consensus pattern (65 bp):
ATAACCACATATGAAATTTTGATAACATACTTAAGAAATTTCGATAACCTCCATATGAAAGTTTA
Found at i:24887 original size:28 final size:29
Alignment explanation
Indices: 24845--24899 Score: 85
Period size: 28 Copynumber: 1.9 Consensus size: 29
24835 TTCCTGATGA
**
24845 AATTTTGATAACATTTGTATGAAATTTAG
1 AATTTTGATAACATTACTATGAAATTTAG
24874 AATTTTG-TAACATTACTATGAAATTT
1 AATTTTGATAACATTACTATGAAATTT
24900 TGGTAACCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 17 0.71
29 7 0.29
ACGTcount: A:0.38, C:0.05, G:0.11, T:0.45
Consensus pattern (29 bp):
AATTTTGATAACATTACTATGAAATTTAG
Found at i:25027 original size:22 final size:22
Alignment explanation
Indices: 24999--25344 Score: 119
Period size: 22 Copynumber: 15.3 Consensus size: 22
24989 TGATAACCTC
*
24999 TTTGATAGCCTCCCTATGAAAT
1 TTTGATAACCTCCCTATGAAAT
* *
25021 TTTGATAACCACACTATGAAAT
1 TTTGATAACCTCCCTATGAAAT
* * *
25043 TTTGATAACTTTCATATGAAAT
1 TTTGATAACCTCCCTATGAAAT
* *
25065 TTTAATAACCTAATCCATATGAAAT
1 TTTGATAACC---TCCCTATGAAAT
* *
25090 TTTGATAACCACTCTATGAAAT
1 TTTGATAACCTCCCTATGAAAT
* * ** *
25112 TTTAATAATCT-TTTAATGCCACAAAAAAA
1 TTTGATAACCTCCCT-ATG-------AAAT
* * *
25141 TTTGATAACCTTCTTTTGAAAT
1 TTTGATAACCTCCCTATGAAAT
* *
25163 TTTAATAACATAATCCCTAT-AAAT
1 TTTGATAAC---CTCCCTATGAAAT
* * * * *
25187 TTTGACAATCACTCGATGAAAT
1 TTTGATAACCTCCCTATGAAAT
* *
25209 TTTTATAACCTTCAC-ATGAAAT
1 TTTGATAACC-TCCCTATGAAAT
* * *
25231 TTTGGTAACCGCACTATGAAAT
1 TTTGATAACCTCCCTATGAAAT
* * **** *
25253 TTGGGTAACCAAAATATGAATT
1 TTTGATAACCTCCCTATGAAAT
*
25275 TTTGATAACCTCCCTATAAAAT
1 TTTGATAACCTCCCTATGAAAT
* **
25297 TTAG-TAA-CTGTACTATGAAA-
1 TTTGATAACCT-CCCTATGAAAT
*
25317 TTTGATAACCTCCTTATGAAAT
1 TTTGATAACCTCCCTATGAAAT
*
25339 TCTGAT
1 TTTGAT
25345 TACCACACAA
Statistics
Matches: 235, Mismatches: 67, Indels: 44
0.68 0.19 0.13
Matches are distributed among these distances:
20 5 0.02
21 29 0.12
22 149 0.63
23 2 0.01
24 10 0.04
25 24 0.10
29 14 0.06
30 2 0.01
ACGTcount: A:0.37, C:0.16, G:0.09, T:0.37
Consensus pattern (22 bp):
TTTGATAACCTCCCTATGAAAT
Found at i:25066 original size:78 final size:78
Alignment explanation
Indices: 24930--25075 Score: 213
Period size: 78 Copynumber: 1.9 Consensus size: 78
24920 CTTTAATAAT
* * * *
24930 CTCCTTATAAAATTTTGATAACCACACTATGAAATTCTGATAACCTCGCTATGGAATTTTGATAA
1 CTCCCTATAAAATTTTGATAACCACACTATGAAATTCTGATAACCTCGATATGAAATTTTAATAA
24995 CCTCTTTGATAGC
66 CCTCTTTGATAGC
* * *
25008 CTCCCTATGAAATTTTGATAACCACACTATGAAATTTTGATAACTTTC-ATATGAAATTTTAATA
1 CTCCCTATAAAATTTTGATAACCACACTATGAAATTCTGATAAC-CTCGATATGAAATTTTAATA
25072 ACCT
65 ACCT
25076 AATCCATATG
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
78 58 0.97
79 2 0.03
ACGTcount: A:0.34, C:0.19, G:0.10, T:0.37
Consensus pattern (78 bp):
CTCCCTATAAAATTTTGATAACCACACTATGAAATTCTGATAACCTCGATATGAAATTTTAATAA
CCTCTTTGATAGC
Found at i:25098 original size:47 final size:46
Alignment explanation
Indices: 25035--25217 Score: 152
Period size: 47 Copynumber: 3.8 Consensus size: 46
25025 ATAACCACAC
* *
25035 TATGAAATTTTGATAACTTTCATATGAAATTTTAATAACCTAATCCA
1 TATGAAATTTTGATAACATTC-TATGAAATTTTAATAACATAATCCA
* *
25082 TATGAAATTTTGATAACCACTCTATGAAATTTTAATAATCTTTTAATGCCA
1 TATGAAATTTTGATAA-CATTCTATGAAATTTTAATAA-C--ATAAT-CCA
* ** * * * *
25133 CAAAAAAATTTGATAACCTTCTTTTGAAATTTTAATAACATAATCCC
1 TATGAAATTTTGATAACATTC-TATGAAATTTTAATAACATAATCCA
* * * *
25180 TAT-AAATTTTGACAATCACTCGATGAAATTTTTATAAC
1 TATGAAATTTTGATAA-CATTCTATGAAATTTTAATAAC
25218 CTTCACATGA
Statistics
Matches: 108, Mismatches: 21, Indels: 15
0.75 0.15 0.10
Matches are distributed among these distances:
46 24 0.22
47 38 0.35
48 8 0.07
50 8 0.07
51 30 0.28
ACGTcount: A:0.40, C:0.14, G:0.07, T:0.39
Consensus pattern (46 bp):
TATGAAATTTTGATAACATTCTATGAAATTTTAATAACATAATCCA
Found at i:25334 original size:21 final size:20
Alignment explanation
Indices: 25275--25344 Score: 61
Period size: 21 Copynumber: 3.3 Consensus size: 20
25265 AATATGAATT
*
25275 TTTGATAACCTCCCTATAAAA
1 TTTGATAACCT-CCTATGAAA
* *
25296 TTT-AGTAACTGTACTATGAAA
1 TTTGA-TAAC-CTCCTATGAAA
25317 TTTGATAACCTCCTTATGAAA
1 TTTGATAACCTCC-TATGAAA
25338 TTCTGAT
1 TT-TGAT
25345 TACCACACAA
Statistics
Matches: 39, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
20 3 0.08
21 30 0.77
22 6 0.15
ACGTcount: A:0.34, C:0.17, G:0.10, T:0.39
Consensus pattern (20 bp):
TTTGATAACCTCCTATGAAA
Found at i:25927 original size:11 final size:10
Alignment explanation
Indices: 25897--25921 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
25887 GGCAAGTGAG
25897 AAAAGACAAA
1 AAAAGACAAA
25907 AAAAGACAAA
1 AAAAGACAAA
25917 AAAAG
1 AAAAG
25922 TTCAAATGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.80, C:0.08, G:0.12, T:0.00
Consensus pattern (10 bp):
AAAAGACAAA
Found at i:26063 original size:22 final size:22
Alignment explanation
Indices: 26013--26055 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
26003 TAATTTTCCT
**
26013 CATGAAAACTTGATAATCTCAC
1 CATGAAAGTTTGATAATCTCAC
*
26035 CATGAAAGTTTGATTATCTCA
1 CATGAAAGTTTGATAATCTCA
26056 TTATGAAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.37, C:0.19, G:0.12, T:0.33
Consensus pattern (22 bp):
CATGAAAGTTTGATAATCTCAC
Found at i:26739 original size:20 final size:21
Alignment explanation
Indices: 26696--26753 Score: 91
Period size: 20 Copynumber: 2.8 Consensus size: 21
26686 TAGTGTCTGA
26696 GGTTATCAAAATTTCACTGTGT
1 GGTTATCAAAATTTCAC-GTGT
26718 GGTTATCAAAATTTCA-GTGT
1 GGTTATCAAAATTTCACGTGT
*
26738 GGTTATCAAATTTTCA
1 GGTTATCAAAATTTCA
26754 TAGGGAGGTT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
20 19 0.54
22 16 0.46
ACGTcount: A:0.29, C:0.12, G:0.17, T:0.41
Consensus pattern (21 bp):
GGTTATCAAAATTTCACGTGT
Found at i:26744 original size:42 final size:42
Alignment explanation
Indices: 26696--26775 Score: 108
Period size: 42 Copynumber: 1.9 Consensus size: 42
26686 TAGTGTCTGA
* *
26696 GGTTATCAAAATTTCACT-GTGTGGTTATCAAAATTTCAGTGT
1 GGTTATCAAAATTTCA-TAGGGAGGTTATCAAAATTTCAGTGT
* *
26738 GGTTATCAAATTTTCATAGGGAGGTTATCGAAATTTCA
1 GGTTATCAAAATTTCATAGGGAGGTTATCAAAATTTCA
26776 TAATGAGATT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
41 1 0.03
42 32 0.97
ACGTcount: A:0.30, C:0.11, G:0.20, T:0.39
Consensus pattern (42 bp):
GGTTATCAAAATTTCATAGGGAGGTTATCAAAATTTCAGTGT
Found at i:26777 original size:22 final size:22
Alignment explanation
Indices: 26693--26817 Score: 105
Period size: 22 Copynumber: 5.8 Consensus size: 22
26683 TTATAGTGTC
26693 TGAGGTTATCAAAATTTCACT-G
1 TGAGGTTATCAAAATTTCA-TAG
*
26715 TGTGGTTATCAAAATTTC--AG
1 TGAGGTTATCAAAATTTCATAG
* *
26735 TGTGGTTATCAAATTTTCATAG
1 TGAGGTTATCAAAATTTCATAG
* * *
26757 GGAGGTTATCGAAATTTCATAA
1 TGAGGTTATCAAAATTTCATAG
* ** *
26779 TGAGATTATC-ATTTTTCACAG
1 TGAGGTTATCAAAATTTCATAG
* *
26800 TGTGGTTATCAATATTTC
1 TGAGGTTATCAAAATTTC
26818 TACATTGGAG
Statistics
Matches: 83, Mismatches: 16, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
20 18 0.22
21 15 0.18
22 50 0.60
ACGTcount: A:0.30, C:0.11, G:0.18, T:0.41
Consensus pattern (22 bp):
TGAGGTTATCAAAATTTCATAG
Found at i:26788 original size:64 final size:65
Alignment explanation
Indices: 26694--26816 Score: 144
Period size: 64 Copynumber: 1.9 Consensus size: 65
26684 TATAGTGTCT
* * *
26694 GAGGTTATCAAAATTTCACTGTGTGGTTATCAAAATTT-CAGTGTGGTTATCAA-ATTTTCATAG
1 GAGGTTATCAAAATTTCACTATGAGATTATC-AAATTTACAGTGTGGTTATCAATATTTTCATAG
26757 G
65 G
* **
26758 GAGGTTATCGAAATTTCA-TAATGAGATTATCATTTTTCACAGTGTGGTTATCAATATTT
1 GAGGTTATCAAAATTTCACT-ATGAGATTATCAAATTT-ACAGTGTGGTTATCAATATTT
26817 CTACATTGGA
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
63 5 0.10
64 25 0.51
65 15 0.31
66 4 0.08
ACGTcount: A:0.30, C:0.11, G:0.19, T:0.41
Consensus pattern (65 bp):
GAGGTTATCAAAATTTCACTATGAGATTATCAAATTTACAGTGTGGTTATCAATATTTTCATAGG
Found at i:30116 original size:18 final size:17
Alignment explanation
Indices: 30090--30123 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
30080 ACTTTGTCTC
30090 ACATGAGCATGGCAATTA
1 ACATGAGCATGG-AATTA
*
30108 ACATTAGCATGGAATT
1 ACATGAGCATGGAATT
30124 CAAATATGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.26
Consensus pattern (17 bp):
ACATGAGCATGGAATTA
Found at i:51547 original size:163 final size:164
Alignment explanation
Indices: 51277--51678 Score: 673
Period size: 163 Copynumber: 2.5 Consensus size: 164
51267 GACTATATAT
* * * *
51277 GGAAAACATCTCATTGGGGGGATGTTCGTCCTCTTTATTAGTTATACGGGGATACCAGTTTAGGT
1 GGAAAACGTCTCATT-AGGGGACGTTCGTCCTCTTTATTAGTTATACGGGGACACCAGTTTAGGT
*
51342 ATTCAACCG-TTGTAGAGGGAAAATGTCTCAGTAGGGGACGTTCGTCCTCTTTACTAGTTATACG
65 GTTCAACCGTTTGTAGAGGGAAAATGTCTCAGTAGGGGACGTTCGTCCTCTTTACTAGTTATACG
*
51406 GGGACACCATTTTAGGTGTTCAACCATTT-TAGAG
130 GGGACACCAGTTTAGGTGTTCAACCATTTGTAGAG
51440 GGAAAACGTCTCATTAGGGGACGTTCGTCCTCTTTATTAGTTATACGGGGACACCAGTTTAGGTG
1 GGAAAACGTCTCATTAGGGGACGTTCGTCCTCTTTATTAGTTATACGGGGACACCAGTTTAGGTG
* *
51505 TTCAACCGTTTGTAGAGGGAAAATGTCTCATTAGGGGACGTTCGTCCTCTTTATTAGTTATACGG
66 TTCAACCGTTTGTAGAGGGAAAATGTCTCAGTAGGGGACGTTCGTCCTCTTTACTAGTTATACGG
*
51570 GGACACCAGTTTAGGTGTTCAACCGTTTGTAGAG
131 GGACACCAGTTTAGGTGTTCAACCATTTGTAGAG
* * *
51604 GAAAAACGTCTTATTAGGGGACGTTCGTCCTCTTTATTAGTTATACGGGGACACCAATTTAGGTG
1 GGAAAACGTCTCATTAGGGGACGTTCGTCCTCTTTATTAGTTATACGGGGACACCAGTTTAGGTG
51669 TTCAACCGTT
66 TTCAACCGTT
51679 ATTTAAGCTA
Statistics
Matches: 225, Mismatches: 12, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
162 54 0.24
163 94 0.42
164 77 0.34
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.33
Consensus pattern (164 bp):
GGAAAACGTCTCATTAGGGGACGTTCGTCCTCTTTATTAGTTATACGGGGACACCAGTTTAGGTG
TTCAACCGTTTGTAGAGGGAAAATGTCTCAGTAGGGGACGTTCGTCCTCTTTACTAGTTATACGG
GGACACCAGTTTAGGTGTTCAACCATTTGTAGAG
Found at i:51556 original size:82 final size:82
Alignment explanation
Indices: 51277--51678 Score: 655
Period size: 82 Copynumber: 4.9 Consensus size: 82
51267 GACTATATAT
* * * *
51277 GGAAAACATCTCATTGGGGGGATGTTCGTCCTCTTTATTAGTTATACGGGGATACCAGTTTAGGT
1 GGAAAACGTCTCATT-AGGGGACGTTCGTCCTCTTTATTAGTTATACGGGGACACCAGTTTAGGT
*
51342 ATTCAACCG-TTGTAGAG
65 GTTCAACCGTTTGTAGAG
* * * *
51359 GGAAAATGTCTCAGTAGGGGACGTTCGTCCTCTTTACTAGTTATACGGGGACACCATTTTAGGTG
1 GGAAAACGTCTCATTAGGGGACGTTCGTCCTCTTTATTAGTTATACGGGGACACCAGTTTAGGTG
*
51424 TTCAACCATTT-TAGAG
66 TTCAACCGTTTGTAGAG
51440 GGAAAACGTCTCATTAGGGGACGTTCGTCCTCTTTATTAGTTATACGGGGACACCAGTTTAGGTG
1 GGAAAACGTCTCATTAGGGGACGTTCGTCCTCTTTATTAGTTATACGGGGACACCAGTTTAGGTG
51505 TTCAACCGTTTGTAGAG
66 TTCAACCGTTTGTAGAG
*
51522 GGAAAATGTCTCATTAGGGGACGTTCGTCCTCTTTATTAGTTATACGGGGACACCAGTTTAGGTG
1 GGAAAACGTCTCATTAGGGGACGTTCGTCCTCTTTATTAGTTATACGGGGACACCAGTTTAGGTG
51587 TTCAACCGTTTGTAGAG
66 TTCAACCGTTTGTAGAG
* * *
51604 GAAAAACGTCTTATTAGGGGACGTTCGTCCTCTTTATTAGTTATACGGGGACACCAATTTAGGTG
1 GGAAAACGTCTCATTAGGGGACGTTCGTCCTCTTTATTAGTTATACGGGGACACCAGTTTAGGTG
51669 TTCAACCGTT
66 TTCAACCGTT
51679 ATTTAAGCTA
Statistics
Matches: 298, Mismatches: 20, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
81 127 0.43
82 171 0.57
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.33
Consensus pattern (82 bp):
GGAAAACGTCTCATTAGGGGACGTTCGTCCTCTTTATTAGTTATACGGGGACACCAGTTTAGGTG
TTCAACCGTTTGTAGAG
Done.