Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023251.1 Corchorus olitorius cultivar O-4 contig23284, 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: 80496
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:534 original size:125 final size:127
Alignment explanation
Indices: 302--556 Score: 383
Period size: 125 Copynumber: 2.0 Consensus size: 127
292 ATTTAAGAAA
*
302 TATATTTACAAAATTCTAATATATATAAGTTTTTAAAATAAAATAGTAAAATGGTAAAAATAAAA
1 TATATTTAAAAAATTCTAATATATATAAGTTTTTAAAATAAAATAGTAAAATGGTAAAAAT---A
*
367 TAGGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAA
63 CA-GTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAA
432 T
127 T
* *
433 TATATTTAAAAAATTCTAATATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAAT-C
1 TATATTTAAAAAATTCT-A-ATATATATAAGTTTTTAAAATAAAATAGTAAAATGGTAAAAATAC
*
497 A-TA-AA-GATATTAGATTTAATTAAATAAAATTAGAGTTTTTAGTTGAGTAAAACTATAAAA
64 AGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAA
557 GTTTAAACAA
Statistics
Matches: 117, Mismatches: 5, Indels: 10
0.89 0.04 0.08
Matches are distributed among these distances:
125 54 0.46
126 2 0.02
127 2 0.02
129 1 0.01
131 16 0.14
132 1 0.01
133 41 0.35
ACGTcount: A:0.51, C:0.02, G:0.10, T:0.37
Consensus pattern (127 bp):
TATATTTAAAAAATTCTAATATATATAAGTTTTTAAAATAAAATAGTAAAATGGTAAAAATACAG
TATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAT
Found at i:6878 original size:2 final size:2
Alignment explanation
Indices: 6871--6903 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
6861 GATAGCATGA
6871 AT AT 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 AT AT A
6904 ATTGATTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:8828 original size:19 final size:18
Alignment explanation
Indices: 8806--8847 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
8796 AGTATAATTA
8806 AGAAAAAAAAAGAAAAAGG
1 AGAAAAAAAAA-AAAAAGG
*
8825 AGAAAAAAAAAACAAAGG
1 AGAAAAAAAAAAAAAAGG
8843 -GAAAA
1 AGAAAA
8848 CAAACGGAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.23
18 6 0.27
19 11 0.50
ACGTcount: A:0.79, C:0.02, G:0.19, T:0.00
Consensus pattern (18 bp):
AGAAAAAAAAAAAAAAGG
Found at i:8916 original size:17 final size:18
Alignment explanation
Indices: 8888--8922 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
8878 AGGATCAAAT
8888 AAAAGAGAAAACAAGAAA
1 AAAAGAGAAAACAAGAAA
8906 AAAAGAG-AAACAAGAAA
1 AAAAGAGAAAACAAGAAA
8923 CATCTTCCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.77, C:0.06, G:0.17, T:0.00
Consensus pattern (18 bp):
AAAAGAGAAAACAAGAAA
Found at i:26586 original size:10 final size:10
Alignment explanation
Indices: 26571--26605 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
26561 TTGCATGATT
26571 TATAATAAAA
1 TATAATAAAA
26581 TATAATAAATA
1 TATAATAAA-A
*
26592 TATAATATAA
1 TATAATAAAA
26602 TATA
1 TATA
26606 TAGTAGATCC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 14 0.61
11 9 0.39
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (10 bp):
TATAATAAAA
Found at i:26851 original size:3 final size:3
Alignment explanation
Indices: 26845--26902 Score: 86
Period size: 3 Copynumber: 20.3 Consensus size: 3
26835 ATAATACAAT
*
26845 TTA TTA TTA TTA TTA TTA TTA TTA GTA TTA TT- TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
26892 -TA TTA -TA TTA T
1 TTA TTA TTA TTA T
26903 ATATATATAT
Statistics
Matches: 50, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
2 6 0.12
3 44 0.88
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:28681 original size:13 final size:13
Alignment explanation
Indices: 28663--28687 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28653 TTAGAATTCC
28663 AAATAATATTTAT
1 AAATAATATTTAT
28676 AAATAATATTTA
1 AAATAATATTTA
28688 GAACATTGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
AAATAATATTTAT
Found at i:29565 original size:21 final size:22
Alignment explanation
Indices: 29525--29565 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
29515 GACAAACTCG
*
29525 TAACCCGAATAACCCGAGAAGA
1 TAACCCGAATAACCCAAGAAGA
*
29547 TAACCCG-ATGACCCAAGAA
1 TAACCCGAATAACCCAAGAA
29566 TATTATAAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.44, C:0.29, G:0.17, T:0.10
Consensus pattern (22 bp):
TAACCCGAATAACCCAAGAAGA
Found at i:30616 original size:23 final size:23
Alignment explanation
Indices: 30573--30616 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
30563 TAATATTTTT
*
30573 AATTAAAATAGTAAAATGATAAA
1 AATTAAAATAGTAAAAGGATAAA
*
30596 AATT-AAATAGTTATAAGGATA
1 AATTAAAATAG-TAAAAGGATA
30617 TTATATTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 6 0.33
23 12 0.67
ACGTcount: A:0.59, C:0.00, G:0.11, T:0.30
Consensus pattern (23 bp):
AATTAAAATAGTAAAAGGATAAA
Found at i:31569 original size:22 final size:23
Alignment explanation
Indices: 31534--31578 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
31524 TTTTTTATGG
* *
31534 CTTTCTTATGAAATTTTGATAAC
1 CTTTCTTATAAAATTTTAATAAC
31557 CTTTC-TATAAAATTTTAATAAC
1 CTTTCTTATAAAATTTTAATAAC
31579 GATATATGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.36, C:0.13, G:0.04, T:0.47
Consensus pattern (23 bp):
CTTTCTTATAAAATTTTAATAAC
Found at i:31725 original size:45 final size:44
Alignment explanation
Indices: 31667--32067 Score: 122
Period size: 44 Copynumber: 8.8 Consensus size: 44
31657 AAGACCTCAT
* * *
31667 TATGAAATTTTGATAACTTCCCA-ATGAAATTTTGATAACCAACAC
1 TATGAAATGTTGATAACCT-CCATATGAAATATTGATAACC-ACAC
* * *
31712 TATGAGATGTTGATAACCTCCATATGATATATTGATAACCACAT
1 TATGAAATGTTGATAACCTCCATATGAAATATTGATAACCACAC
* * * * *
31756 TATGAAAAT-TTAAAAACCTCCATAT-AGAT-TGTTAGTAATCACAC
1 TATG-AAATGTTGATAACCTCCATATGAAATAT-TGA-TAACCACAC
* * * *
31800 TCTGAAATATTGATAA--TCACACTATG-AA-ATTGTAGTAACCTCAT
1 TATGAAATGTTGATAACCTC-CA-TATGAAATATTG-A-TAACCACAC
* * * * * * *
31844 TGTGAAATTTTGATACACCTTCC-TATAAAATTTTGATAAAGCTCCC
1 TATGAAATGTTGATA-ACC-TCCATATGAAATATTGAT-AACCACAC
* * * * ** *
31890 TATAAAATTTTGATAACCTCCTTATGAAATCTTGATATGATTTTTTGATAAC
1 TATGAAATGTTGATAACCTCCATATGAAATATTGATA--A-----CCA-CAC
* * * * * *
31942 TCATGAAATTTTGTTAATCTCCCTATGAAATTTTGATCTA-CACAC
1 T-ATGAAATGTTGATAACCTCCATATGAAATATTGAT-AACCACAC
* * * * * *
31987 TATGAAATTTTGATAACC-CTCTTATGAAATTTTGAAAACTAAAC
1 TATGAAATGTTGATAACCTC-CATATGAAATATTGATAACCACAC
* * *
32031 TATGAAATTTTGATAACCTTCATATGAAATTTTGATA
1 TATGAAATGTTGATAACCTCCATATGAAATATTGATA
32068 TCCTCCCTGA
Statistics
Matches: 270, Mismatches: 55, Indels: 63
0.70 0.14 0.16
Matches are distributed among these distances:
42 3 0.01
43 14 0.05
44 134 0.50
45 57 0.21
46 23 0.09
47 4 0.01
48 2 0.01
52 3 0.01
53 30 0.11
ACGTcount: A:0.37, C:0.15, G:0.10, T:0.37
Consensus pattern (44 bp):
TATGAAATGTTGATAACCTCCATATGAAATATTGATAACCACAC
Found at i:31746 original size:22 final size:22
Alignment explanation
Indices: 31614--31926 Score: 132
Period size: 22 Copynumber: 14.1 Consensus size: 22
31604 ATTATTTTTT
* *
31614 TAACCTTCTTATGAAATTTT-A
1 TAACCTCCATATGAAATTTTGA
* * *
31635 TTAACCTCCCTAAGGAATTTTGA
1 -TAACCTCCATATGAAATTTTGA
31658 -AGACCT-CATTATGAAATTTTGA
1 TA-ACCTCCA-TATGAAATTTTGA
*
31680 TAACTTCCCA-ATGAAATTTTGA
1 TAACCT-CCATATGAAATTTTGA
** * *
31702 TAACCAACACTATGAGATGTTGA
1 TAACCTCCA-TATGAAATTTTGA
* *
31725 TAACCTCCATATGATATATTGA
1 TAACCTCCATATGAAATTTTGA
* * *
31747 TAACC-ACATTATGAAAATTTAA
1 TAACCTCCA-TATGAAATTTTGA
* *
31769 AAACCTCCATAT-AGATTGTT-A
1 TAACCTCCATATGAAATT-TTGA
* *
31790 GTAA--TCACACTCTGAAATATTGA
1 -TAACCTC-CA-TATGAAATTTTGA
*
31813 TAA--TCACACTATGAAATTGT-A
1 TAACCTC-CA-TATGAAATTTTGA
*
31834 GTAACCT-CATTGTGAAATTTTGA
1 -TAACCTCCA-TATGAAATTTTGA
*
31857 TACACCTTCC-TATAAAATTTTGA
1 TA-ACC-TCCATATGAAATTTTGA
* * *
31880 TAAAGCTCCCTATAAAATTTTGA
1 T-AACCTCCATATGAAATTTTGA
* *
31903 TAACCTCCTTATGAAATCTTGA
1 TAACCTCCATATGAAATTTTGA
31925 TA
1 TA
31927 TGATTTTTTG
Statistics
Matches: 223, Mismatches: 43, Indels: 50
0.71 0.14 0.16
Matches are distributed among these distances:
20 2 0.01
21 13 0.06
22 145 0.65
23 57 0.26
24 5 0.02
25 1 0.00
ACGTcount: A:0.37, C:0.17, G:0.10, T:0.35
Consensus pattern (22 bp):
TAACCTCCATATGAAATTTTGA
Found at i:31874 original size:23 final size:22
Alignment explanation
Indices: 31848--31926 Score: 88
Period size: 23 Copynumber: 3.5 Consensus size: 22
31838 CCTCATTGTG
31848 AAATTTTGATACACCTTCCTATA
1 AAATTTTGATA-ACCTTCCTATA
* *
31871 AAATTTTGATAAAGCTCCCTATA
1 AAATTTTGAT-AACCTTCCTATA
*
31894 AAATTTTGATAACC-TCCTTATG
1 AAATTTTGATAACCTTCC-TATA
*
31916 AAATCTTGATA
1 AAATTTTGATA
31927 TGATTTTTTG
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
21 2 0.04
22 16 0.33
23 29 0.60
24 1 0.02
ACGTcount: A:0.37, C:0.18, G:0.08, T:0.38
Consensus pattern (22 bp):
AAATTTTGATAACCTTCCTATA
Found at i:31970 original size:22 final size:22
Alignment explanation
Indices: 31944--32086 Score: 102
Period size: 22 Copynumber: 6.6 Consensus size: 22
31934 TTGATAACTC
*
31944 ATGAAATTTTGTTAATCTCCCT
1 ATGAAATTTTGATAATCTCCCT
* * *
31966 ATGAAATTTTGAT-CTACACACT
1 ATGAAATTTTGATAAT-CTCCCT
31988 ATGAAATTTTGATAA-C-CCTCTT
1 ATGAAATTTTGATAATCTCC-C-T
* **
32010 ATGAAATTTTGA-AAACTAAACT
1 ATGAAATTTTGATAATCT-CCCT
* * *
32032 ATGAAATTTTGATAACCTTCAT
1 ATGAAATTTTGATAATCTCCCT
32054 ATGAAATTTTGAT-ATCCTCCC-
1 ATGAAATTTTGATAAT-CTCCCT
32075 -TGAAATTTTGAT
1 ATGAAATTTTGAT
32087 TATTCCATAA
Statistics
Matches: 97, Mismatches: 15, Indels: 20
0.73 0.11 0.15
Matches are distributed among these distances:
20 13 0.13
21 6 0.06
22 73 0.75
23 5 0.05
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.40
Consensus pattern (22 bp):
ATGAAATTTTGATAATCTCCCT
Found at i:32013 original size:44 final size:41
Alignment explanation
Indices: 31939--32066 Score: 141
Period size: 44 Copynumber: 2.9 Consensus size: 41
31929 ATTTTTTGAT
*
31939 AACTCATGAAATTTTGTTAATCTCC-CTATGAAATTTTGATCTA
1 AACT-ATGAAATTTTGATAA-C-CCTCTATGAAATTTTGATCTA
*
31982 CACACTATGAAATTTTGATAACCCTCTTATGAAATTTTGAAAACTA
1 -A-ACTATGAAATTTTGATAACCCTC-TATGAAATTTTG--ATCTA
*
32028 AACTATGAAATTTTGATAACCTTCATATGAAATTTTGAT
1 AACTATGAAATTTTGATAACCCTC-TATGAAATTTTGAT
32067 ATCCTCCCTG
Statistics
Matches: 74, Mismatches: 5, Indels: 12
0.81 0.05 0.13
Matches are distributed among these distances:
42 3 0.04
43 2 0.03
44 61 0.82
45 4 0.05
46 4 0.05
ACGTcount: A:0.37, C:0.15, G:0.09, T:0.39
Consensus pattern (41 bp):
AACTATGAAATTTTGATAACCCTCTATGAAATTTTGATCTA
Found at i:32217 original size:22 final size:22
Alignment explanation
Indices: 32168--32293 Score: 123
Period size: 22 Copynumber: 5.7 Consensus size: 22
32158 AAAATACCAC
* * *
32168 TATGAAATTTTGGTAATCACATT
1 TATGAAATTTTGATAACCTC-TT
*
32191 T-TGAAAATTTGATAACCTCTT
1 TATGAAATTTTGATAACCTCTT
32212 TATGAAATTTTGATAACCT-TT
1 TATGAAATTTTGATAACCTCTT
* * * *
32233 CTATAAAATTTTGCTGACCCCTT
1 -TATGAAATTTTGATAACCTCTT
*
32256 TATGAAATTTTGATAACCTCGCT
1 TATGAAATTTTGATAACCTC-TT
32279 T-TGAAATTTTGATAA
1 TATGAAATTTTGATAA
32294 GAAAACTATG
Statistics
Matches: 85, Mismatches: 14, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
21 5 0.06
22 75 0.88
23 5 0.06
ACGTcount: A:0.33, C:0.13, G:0.11, T:0.43
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTCTT
Found at i:32286 original size:44 final size:44
Alignment explanation
Indices: 32190--32293 Score: 136
Period size: 44 Copynumber: 2.4 Consensus size: 44
32180 GTAATCACAT
* * **
32190 TTTGAAAATTTGATAACCTCTTTATGAAATTTTGATAACCTTTC
1 TTTGAAATTTTGATAACCCCTTTATGAAATTTTGATAACCTCGC
* * * *
32234 TATAAAATTTTGCTGACCCCTTTATGAAATTTTGATAACCTCGC
1 TTTGAAATTTTGATAACCCCTTTATGAAATTTTGATAACCTCGC
32278 TTTGAAATTTTGATAA
1 TTTGAAATTTTGATAA
32294 GAAAACTATG
Statistics
Matches: 48, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
44 48 1.00
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.43
Consensus pattern (44 bp):
TTTGAAATTTTGATAACCCCTTTATGAAATTTTGATAACCTCGC
Found at i:32308 original size:66 final size:66
Alignment explanation
Indices: 32166--32317 Score: 155
Period size: 66 Copynumber: 2.3 Consensus size: 66
32156 CAAAAATACC
* * **
32166 ACTATGAAATTTTGGTAATCACATTTTGAAAATTTGATAACCTCTTTATGAAATTTTGATAACCT
1 ACTATGAAATTTTGCTAATCACATTTTGAAAATTTGATAACCTCCTTATGAAATTTTGATAACAA
*
32231 T
66 A
* * * * * * *
32232 TCTATAAAATTTTGCTGA-CCCCTTTATGAAATTTTGATAACCTCGCTT-TGAAATTTTGATAAG
1 ACTATGAAATTTTGCTAATCACATTT-TGAAAATTTGATAACCTC-CTTATGAAATTTTGATAAC
32295 AAA
64 AAA
*
32298 ACTATGAAATTTTGATAATC
1 ACTATGAAATTTTGCTAATC
32318 CGATCTCTAT
Statistics
Matches: 67, Mismatches: 16, Indels: 5
0.76 0.18 0.06
Matches are distributed among these distances:
65 5 0.07
66 59 0.88
67 3 0.04
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.41
Consensus pattern (66 bp):
ACTATGAAATTTTGCTAATCACATTTTGAAAATTTGATAACCTCCTTATGAAATTTTGATAACAA
A
Found at i:32350 original size:22 final size:24
Alignment explanation
Indices: 32299--32360 Score: 76
Period size: 25 Copynumber: 2.6 Consensus size: 24
32289 GATAAGAAAA
32299 CTATGAAATTTTGATAATCCGATCT
1 CTATGAAA-TTTGATAATCCGATCT
32324 CTATGAAATTTCGATAAT-C-A-CT
1 CTATGAAATTT-GATAATCCGATCT
*
32346 CTATGAGATTTGATA
1 CTATGAAATTTGATA
32361 GCCTTCTATC
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
21 4 0.11
22 12 0.34
23 1 0.03
24 4 0.11
25 14 0.40
ACGTcount: A:0.34, C:0.15, G:0.13, T:0.39
Consensus pattern (24 bp):
CTATGAAATTTGATAATCCGATCT
Found at i:32651 original size:68 final size:67
Alignment explanation
Indices: 32545--32724 Score: 174
Period size: 68 Copynumber: 2.7 Consensus size: 67
32535 TGATAATTTC
* * * * *
32545 TTTGATAACCTTTC-TATAAAATTGTGATAAC-CACACTATGAAATTTCAG-TAACCTTCCTAAG
1 TTTGATAA-CTTCCATATGAAATTTTGATAACTTACACTATGAAATTT-AGATAACCTTCCCAAG
32607 AAAT
64 AAAT
* * * * *
32611 TTTGGTAACCTGATCC-TATGAAATTTTGGTAA-TTACACTATGAAATTTTGATAACTTTCCCAT
1 TTTGATAA-CT--TCCATATGAAATTTTGATAACTTACACTATGAAATTTAGATAACCTTCCCAA
32674 GAAAT
63 GAAAT
*
32679 TTTGATAACTTCCATATGAAATTTTGATAACTTCCA-TATGAAATTT
1 TTTGATAACTTCCATATGAAATTTTGATAACTTACACTATGAAATTT
32725 TGGTAACCAC
Statistics
Matches: 95, Mismatches: 13, Indels: 12
0.79 0.11 0.10
Matches are distributed among these distances:
65 3 0.03
66 35 0.37
67 7 0.07
68 50 0.53
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.39
Consensus pattern (67 bp):
TTTGATAACTTCCATATGAAATTTTGATAACTTACACTATGAAATTTAGATAACCTTCCCAAGAA
AT
Found at i:32798 original size:22 final size:22
Alignment explanation
Indices: 32545--32799 Score: 182
Period size: 22 Copynumber: 11.5 Consensus size: 22
32535 TGATAATTTC
* * *
32545 TTTGATAACCTTTCTATAAAAT
1 TTTGATAACCATCCTATGAAAT
*
32567 TGTGATAACCA-CACTATGAAA-
1 TTTGATAACCATC-CTATGAAAT
* * *
32588 TTTCAGTAACCTTCCTAAGAAAT
1 TTTGA-TAACCATCCTATGAAAT
*
32611 TTTGGTAACCTGATCCTATGAAAT
1 TTTGATAACC--ATCCTATGAAAT
* **
32635 TTTGGTAATTA-CACTATGAAAT
1 TTTGATAACCATC-CTATGAAAT
** *
32657 TTTGATAACTTTCCCATGAAAT
1 TTTGATAACCATCCTATGAAAT
*
32679 TTTGATAA-CTTCCATATGAAAT
1 TTTGATAACCATCC-TATGAAAT
*
32701 TTTGATAA-CTTCCATATGAAAT
1 TTTGATAACCATCC-TATGAAAT
* *
32723 TTTGGTAACCA-CACTATGGAAT
1 TTTGATAACCATC-CTATGAAAT
*
32745 TTTGATAACC-TCCTCATAAAAT
1 TTTGATAACCATCCT-ATGAAAT
* * *
32767 TATAATAACCATCTTATGAAAT
1 TTTGATAACCATCCTATGAAAT
32789 TTTGATAACCA
1 TTTGATAACCA
32800 CATAGAGACA
Statistics
Matches: 187, Mismatches: 32, Indels: 28
0.76 0.13 0.11
Matches are distributed among these distances:
21 10 0.05
22 149 0.80
23 10 0.05
24 18 0.10
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.37
Consensus pattern (22 bp):
TTTGATAACCATCCTATGAAAT
Found at i:33274 original size:13 final size:13
Alignment explanation
Indices: 33238--33276 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 13
33228 TCTAAATTGA
33238 AATTTT-ATAATT
1 AATTTTAATAATT
33250 AATTTTTAAATAATT
1 AA-TTTT-AATAATT
33265 AATTTTAATAAT
1 AATTTTAATAAT
33277 GTCAATTTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
12 2 0.08
13 10 0.42
14 4 0.17
15 8 0.33
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
AATTTTAATAATT
Found at i:33284 original size:15 final size:14
Alignment explanation
Indices: 33244--33276 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
33234 TTGAAATTTT
33244 ATAATTAATTTTTAA
1 ATAATTAA-TTTTAA
33259 ATAATTAATTTT-A
1 ATAATTAATTTTAA
33272 ATAAT
1 ATAAT
33277 GTCAATTTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 6 0.33
14 4 0.22
15 8 0.44
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
ATAATTAATTTTAA
Found at i:34780 original size:17 final size:17
Alignment explanation
Indices: 34758--34793 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
34748 ATACAAAGAG
34758 CTATCTAGTATAACAAA
1 CTATCTAGTATAACAAA
* *
34775 CTATCTGGTATAACGAA
1 CTATCTAGTATAACAAA
34792 CT
1 CT
34794 TTACAAATCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.39, C:0.19, G:0.11, T:0.31
Consensus pattern (17 bp):
CTATCTAGTATAACAAA
Found at i:36288 original size:178 final size:178
Alignment explanation
Indices: 35989--36311 Score: 508
Period size: 178 Copynumber: 1.8 Consensus size: 178
35979 AAATTATGTA
* *
35989 ATATTAAGTAGACCGTCTATTTCCATTAACCGAAACAACTAATTCTTTGGAAGCATTTTTTATAC
1 ATATTAAGTAGACCGTCTATTCCCATTAACCGAAACAACTAATTCTTTGGAAGCATTTTTGATAC
36054 CTTGAACAATAAATTTAGTTTTCGAGTCCCTCATGAAAGTTGTAGATCATGGAACAAACTTTCAA
66 CTTGAACAATAAATTTAGTTTTCGAGTCCCTCATGAAAGTTGTAGATCATGGAACAAACTTTCAA
*
36119 GAGACACTTGAATCATCTCAATTAGACAACTGAAGCAAAAGTTATATG
131 GAGACACTTAAATCATCTCAATTAGACAACTGAAGCAAAAGTTATATG
* *
36167 ATATTAAGTGGACCGTCTATTCCCGTTAACCGAAACAA-TAAATT-TTTCGGAAGCATTTTTGAT
1 ATATTAAGTAGACCGTCTATTCCCATTAACCGAAACAACT-AATTCTTT-GGAAGCATTTTTGAT
* * *
36230 A-CTTGAAACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAGATCATGGAACAATCTTT
64 ACCTTG-AACAATAAATTTAGTTTTCGAGTCCCTCATGAAAGTTGTAGATCATGGAACAAACTTT
* *
36294 TAATAGACACTTAAATCA
128 CAAGAGACACTTAAATCA
36312 CCTTAATCGG
Statistics
Matches: 132, Mismatches: 10, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
177 8 0.06
178 124 0.94
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (178 bp):
ATATTAAGTAGACCGTCTATTCCCATTAACCGAAACAACTAATTCTTTGGAAGCATTTTTGATAC
CTTGAACAATAAATTTAGTTTTCGAGTCCCTCATGAAAGTTGTAGATCATGGAACAAACTTTCAA
GAGACACTTAAATCATCTCAATTAGACAACTGAAGCAAAAGTTATATG
Found at i:36351 original size:178 final size:177
Alignment explanation
Indices: 35979--36361 Score: 504
Period size: 178 Copynumber: 2.1 Consensus size: 177
35969 ACATAAGTGC
* *
35979 AAATTATGTAATATTAAGTAGACCGTCTATTTCCATTAACCGAAACAACTAATTCTTTGGAAGCA
1 AAATTATATAATATTAAGTAGACCGTCTATTCCCATTAACCGAAACAACTAATTCTTTGGAAGCA
*
36044 TTTTTTATACCTTGAACAATAAATTTAGTTTTCGAGTCCCTCATGAAAGTTGTAGATCATGGAAC
66 TTTTTGATACCTTGAACAATAAATTTAGTTTTCGAGTCCCTCATGAAAGTTGTAGATCATGGAAC
* * * *
36109 AAACTTTCAAGAGACACTTGAATCATCTCAATTAGACAACTGAAGCA
131 AAACTTTCAAGAGACACTTAAATCACCTCAATCAGACAACAGAAGCA
* * *
36156 AAAGTTATATGATATTAAGTGGACCGTCTATTCCCGTTAACCGAAACAA-TAAATT-TTTCGGAA
1 AAA-TTATATAATATTAAGTAGACCGTCTATTCCCATTAACCGAAACAACT-AATTCTTT-GGAA
* *
36219 GCATTTTTGATA-CTTGAAACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAGATCATG
63 GCATTTTTGATACCTTG-AACAATAAATTTAGTTTTCGAGTCCCTCATGAAAGTTGTAGATCATG
* * * * * *
36283 GAACAATCTTTTAATAGACACTTAAATCACCTTAATCGGATAATCAGAGAG-A
127 GAACAAACTTTCAAGAGACACTTAAATCACCTCAATCAGACAA-CAGA-AGCA
*
36335 AAATTATATAATATTAAAATAGACCGT
1 AAATTATATAATATT-AAGTAGACCGT
36362 TTAACCAAAC
Statistics
Matches: 178, Mismatches: 21, Indels: 12
0.84 0.10 0.06
Matches are distributed among these distances:
177 11 0.06
178 149 0.84
179 16 0.09
180 2 0.01
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (177 bp):
AAATTATATAATATTAAGTAGACCGTCTATTCCCATTAACCGAAACAACTAATTCTTTGGAAGCA
TTTTTGATACCTTGAACAATAAATTTAGTTTTCGAGTCCCTCATGAAAGTTGTAGATCATGGAAC
AAACTTTCAAGAGACACTTAAATCACCTCAATCAGACAACAGAAGCA
Found at i:38276 original size:16 final size:17
Alignment explanation
Indices: 38251--38290 Score: 64
Period size: 16 Copynumber: 2.4 Consensus size: 17
38241 TAAATTACTT
*
38251 ACTAATTAAATAAACAA
1 ACTAAATAAATAAACAA
38268 A-TAAATAAATAAACAA
1 ACTAAATAAATAAACAA
38284 ACTAAAT
1 ACTAAAT
38291 CCACACTCCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 15 0.71
17 6 0.29
ACGTcount: A:0.68, C:0.10, G:0.00, T:0.23
Consensus pattern (17 bp):
ACTAAATAAATAAACAA
Found at i:54969 original size:3 final size:3
Alignment explanation
Indices: 54963--54999 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
54953 TGGGTTGTGT
54963 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
55000 GAGATCCAAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:59615 original size:28 final size:28
Alignment explanation
Indices: 59550--59621 Score: 92
Period size: 27 Copynumber: 2.6 Consensus size: 28
59540 TTGAGAGCCC
* **
59550 AAAACCTAACCCTTATTTTTTTTTGCCA
1 AAAACCTAACCCTTATTTTTTTATAACA
**
59578 AAAA-AAAACCCTTATTTTTTTATAACA
1 AAAACCTAACCCTTATTTTTTTATAACA
59605 AAAACCTAACCCTTATT
1 AAAACCTAACCCTTATT
59622 GAAGTTAGTT
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
27 22 0.61
28 14 0.39
ACGTcount: A:0.39, C:0.22, G:0.01, T:0.38
Consensus pattern (28 bp):
AAAACCTAACCCTTATTTTTTTATAACA
Found at i:67546 original size:16 final size:16
Alignment explanation
Indices: 67522--67566 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
67512 ACTCTTTTTA
*
67522 TTTAAAAAATACTTT-
1 TTTAAAAAATAATTTC
67537 TTTCAAAAAATAATTTC
1 TTT-AAAAAATAATTTC
67554 TTTAAAAAA-AATT
1 TTTAAAAAATAATT
67567 GAAAAAATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
15 7 0.26
16 17 0.63
17 3 0.11
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.42
Consensus pattern (16 bp):
TTTAAAAAATAATTTC
Found at i:67808 original size:19 final size:18
Alignment explanation
Indices: 67774--67810 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
67764 CTTTTTTTTG
*
67774 AAAAATAGAAAAAAGGAA
1 AAAAAAAGAAAAAAGGAA
67792 AAAAAAAGAAAAGAAGGAA
1 AAAAAAAGAAAA-AAGGAA
67811 TAATCAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.78, C:0.00, G:0.19, T:0.03
Consensus pattern (18 bp):
AAAAAAAGAAAAAAGGAA
Found at i:67890 original size:16 final size:18
Alignment explanation
Indices: 67865--67898 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
67855 TTAAAAACCG
67865 AAAATCA-TTTTTTGAAA
1 AAAATCATTTTTTTGAAA
67882 AAAAT-ATTTTTTTGAAA
1 AAAATCATTTTTTTGAAA
67899 TTTTTTGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 1 0.06
17 15 0.94
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.44
Consensus pattern (18 bp):
AAAATCATTTTTTTGAAA
Found at i:68273 original size:23 final size:24
Alignment explanation
Indices: 68228--68274 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
68218 TATAAATGCT
* * *
68228 AATATATACTTGACTTGGCTAAAA
1 AATATATACTAGAATTGGATAAAA
68252 AATATATA-TAGAATTGGATAAAA
1 AATATATACTAGAATTGGATAAAA
68275 CAAAAACATG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.49, C:0.06, G:0.13, T:0.32
Consensus pattern (24 bp):
AATATATACTAGAATTGGATAAAA
Found at i:74543 original size:45 final size:46
Alignment explanation
Indices: 74468--74562 Score: 120
Period size: 45 Copynumber: 2.1 Consensus size: 46
74458 ATCCAAATGG
* * * ** * *
74468 CAATAGTCTGATACGTAAATGGTTGGAGACCTGAGATACAAAAGTC
1 CAATAGTCCGATACATAAATGGTTGAAGACCCAAAATACAAAAATC
74514 CAAT-GTCCGATACATAAATGGTTGAAGACCCAAAATACAAAAATC
1 CAATAGTCCGATACATAAATGGTTGAAGACCCAAAATACAAAAATC
74559 CAAT
1 CAAT
74563 TTAGTAAATG
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
45 38 0.90
46 4 0.10
ACGTcount: A:0.42, C:0.18, G:0.18, T:0.22
Consensus pattern (46 bp):
CAATAGTCCGATACATAAATGGTTGAAGACCCAAAATACAAAAATC
Found at i:75540 original size:21 final size:24
Alignment explanation
Indices: 75496--75575 Score: 66
Period size: 21 Copynumber: 3.5 Consensus size: 24
75486 TATCTTAGAT
75496 ATAATATATATTACTAAATAAATA
1 ATAATATATATTACTAAATAAATA
*
75520 ATAA-ATATATT-TTAAAT-AAT-
1 ATAATATATATTACTAAATAAATA
*
75540 A-AATA-ATGAGTT-CAAAATAAATAA
1 ATAATATAT-A-TTACTAAATAAAT-A
75564 ATAATATATATT
1 ATAATATATATT
75576 TAATTACTAA
Statistics
Matches: 45, Mismatches: 3, Indels: 16
0.70 0.05 0.25
Matches are distributed among these distances:
19 4 0.09
20 3 0.07
21 9 0.20
22 8 0.18
23 7 0.16
24 7 0.16
25 5 0.11
26 2 0.04
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.38
Consensus pattern (24 bp):
ATAATATATATTACTAAATAAATA
Found at i:76159 original size:74 final size:75
Alignment explanation
Indices: 76064--76215 Score: 297
Period size: 74 Copynumber: 2.0 Consensus size: 75
76054 CATGGTGTAG
76064 TTATTTTCTTTTTTATTAAGGTTAAAAATGTGATTTCAATTTCCATTTCAAAAATTTTGTTAAAT
1 TTATTTTCTTTTTTATTAAGGTTAAAAATGTGATTTCAATTTCCATTTCAAAAATTTTGTTAAAT
76129 ATTTATTTAC
66 ATTTATTTAC
76139 TTATTTTC-TTTTTATTAAGGTTAAAAATGTGATTTCAATTTCCATTTCAAAAATTTTGTTAAAT
1 TTATTTTCTTTTTTATTAAGGTTAAAAATGTGATTTCAATTTCCATTTCAAAAATTTTGTTAAAT
76203 ATTTATTTAC
66 ATTTATTTAC
76213 TTA
1 TTA
76216 ATCATAATTA
Statistics
Matches: 77, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
74 69 0.90
75 8 0.10
ACGTcount: A:0.32, C:0.08, G:0.07, T:0.53
Consensus pattern (75 bp):
TTATTTTCTTTTTTATTAAGGTTAAAAATGTGATTTCAATTTCCATTTCAAAAATTTTGTTAAAT
ATTTATTTAC
Found at i:76582 original size:53 final size:52
Alignment explanation
Indices: 76451--76608 Score: 230
Period size: 53 Copynumber: 3.0 Consensus size: 52
76441 TTTGTCTTTG
* *
76451 TATGAGTTGTAAATTTGTCATTACCTC-ATTAAAT-CACTTGTAATTTTGTTTTA
1 TATGAGTTGTAAATTTGTCATTACATCAATT-AATGC-CTTGTAAATTTG-TTTA
*
76504 TATGAGTTGTAAATTTGTCAATACATGCAATTAATGCCTTGTAAATTTGTTTA
1 TATGAGTTGTAAATTTGTCATTACAT-CAATTAATGCCTTGTAAATTTGTTTA
76557 TATGAGTTGTAAATTTGTCATTACATACAATTAATGCCTTGTAAATTTGTTT
1 TATGAGTTGTAAATTTGTCATTACAT-CAATTAATGCCTTGTAAATTTGTTT
76609 TTATCTCATT
Statistics
Matches: 97, Mismatches: 5, Indels: 6
0.90 0.05 0.06
Matches are distributed among these distances:
53 78 0.80
54 15 0.15
55 4 0.04
ACGTcount: A:0.30, C:0.10, G:0.13, T:0.46
Consensus pattern (52 bp):
TATGAGTTGTAAATTTGTCATTACATCAATTAATGCCTTGTAAATTTGTTTA
Found at i:77545 original size:57 final size:57
Alignment explanation
Indices: 77470--77588 Score: 220
Period size: 57 Copynumber: 2.1 Consensus size: 57
77460 ATTTAATAAT
77470 TTTCCCACGTTAACCAAACATGGTAATCTTATTCCCACAAAAACAAAAAAATTATAC
1 TTTCCCACGTTAACCAAACATGGTAATCTTATTCCCACAAAAACAAAAAAATTATAC
* *
77527 TTTCTCACGTTAATCAAACATGGTAATCTTATTCCCACAAAAACAAAAAAATTATAC
1 TTTCCCACGTTAACCAAACATGGTAATCTTATTCCCACAAAAACAAAAAAATTATAC
77584 TTTCC
1 TTTCC
77589 GACTAAAATA
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
57 59 1.00
ACGTcount: A:0.42, C:0.24, G:0.05, T:0.29
Consensus pattern (57 bp):
TTTCCCACGTTAACCAAACATGGTAATCTTATTCCCACAAAAACAAAAAAATTATAC
Found at i:79049 original size:28 final size:28
Alignment explanation
Indices: 79007--79070 Score: 92
Period size: 28 Copynumber: 2.3 Consensus size: 28
78997 AAATTGAACG
* *
79007 CTTTGAAAACGTGATGGTAACTTTCCTA
1 CTTTGAAAACGTGATGGGAACTTTCCCA
*
79035 CTTTGAAAACTTGATGGGAACTTTCCCA
1 CTTTGAAAACGTGATGGGAACTTTCCCA
*
79063 ATTTGAAA
1 CTTTGAAA
79071 GAAGCTAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.34
Consensus pattern (28 bp):
CTTTGAAAACGTGATGGGAACTTTCCCA
Done.