Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012941.1 Corchorus olitorius cultivar O-4 contig12974, 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: 24826
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Found at i:2776 original size:166 final size:163
Alignment explanation
Indices: 2437--2756 Score: 464
Period size: 166 Copynumber: 1.9 Consensus size: 163
2427 CCTCTCCCAG
2437 ACGCCGCTATATATTATAGGCGTAGAGTTGGAAAATTTCTTTGTTTTAGGAGGAGGGAATTTTTC
1 ACGCCGCTATATATTATAGGCGTAGAGTTGGAAAATTTCTTTGTTTTAGGAGGAGGGAATTTTTC
* * * *
2502 CCTCCAAAAAAAGGAGAAAAAACATTTCTCCCTCCATATATTAAAATAGCGGCGTTTCCTTTTCT
66 CCTCCAAAAAAAGGAGAAAAAAAATTTCTCCCTCCATATATTAAAATACCGGCGTTTCCTTATCA
** * *
2567 CGACGCCACTAATTGGCGGCGTCTGATGTCCAA
131 AAACGCCACTAAATGGCAGCGTCTGATGTCCAA
* * * *
2600 ATGCCGCTATATATTATAGGTGTAGAGTTGTAAACTTTCTTTGTTTTAGTG-GAGAGGGAATTTT
1 ACGCCGCTATATATTATAGGCGTAGAGTTGGAAAATTTCTTTGTTTTAG-GAG-GAGGGAATTTT
*
2664 TCCCTCCAAAAAAAGGAGAAAAAAAAAATTTCTCCCTCCATATATTAAAATACCGGCGTCTTTC-
64 TCCCTCCAAAAAAAGGAG--AAAAAAAATTTCTCCCTCCATATATTAAAATACCGGCGT-TTCCT
2728 TATCAAAACGCCACTAAATGGCAGCGTCT
126 TATCAAAACGCCACTAAATGGCAGCGTCT
2757 TCGTTTCAAA
Statistics
Matches: 139, Mismatches: 13, Indels: 7
0.87 0.08 0.04
Matches are distributed among these distances:
163 46 0.33
164 30 0.22
166 60 0.43
167 3 0.02
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (163 bp):
ACGCCGCTATATATTATAGGCGTAGAGTTGGAAAATTTCTTTGTTTTAGGAGGAGGGAATTTTTC
CCTCCAAAAAAAGGAGAAAAAAAATTTCTCCCTCCATATATTAAAATACCGGCGTTTCCTTATCA
AAACGCCACTAAATGGCAGCGTCTGATGTCCAA
Found at i:3446 original size:22 final size:22
Alignment explanation
Indices: 3405--3446 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
3395 GACAAACCCG
*
3405 TAACCCGAATGACCCGAGAAAA
1 TAACCCGAATGACCCAAGAAAA
* *
3427 TAACCCGGATGATCCAAGAA
1 TAACCCGAATGACCCAAGAA
3447 TTTTATAAAT
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:0.43, C:0.26, G:0.19, T:0.12
Consensus pattern (22 bp):
TAACCCGAATGACCCAAGAAAA
Found at i:8901 original size:13 final size:14
Alignment explanation
Indices: 8869--8906 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
8859 AATCTGTAAA
*
8869 ATTTAAAAAATGTC
1 ATTTAAAAAATATC
*
8883 ATTTAAGAAATAT-
1 ATTTAAAAAATATC
8896 ATTTAAAAAAT
1 ATTTAAAAAAT
8907 TCTAATATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.55, C:0.03, G:0.05, T:0.37
Consensus pattern (14 bp):
ATTTAAAAAATATC
Found at i:9146 original size:123 final size:126
Alignment explanation
Indices: 8893--9146 Score: 381
Period size: 123 Copynumber: 2.0 Consensus size: 126
8883 ATTTAAGAAA
*
8893 TATATTTAAAAAATTCTAATATATATAATTTTTTTAATTAAAATTGTAAAATGGTAAAATAAAAT
1 TATATTTAAAAAATTCTAATATATATAATTTTTTTAATTAAAATAGTAAAATGGT--AATAAAAT
* *
8958 AGGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTTAGTAAAACTGTAAAAG
64 --GTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAG
*
9023 TATATTTAAAAAATTCTAATATATAT-ATGTTTTTTGATTAAAATAGTAAAATGGT-A-AAAAT-
1 TATATTTAAAAAATTCTAATATATATAAT-TTTTTTAATTAAAATAGTAAAATGGTAATAAAATG
* *
9084 TATAAGGATATTAGATTTAATTAAATAAAAATAGGGTTTTTAGTTGAGTAAAACTATTAAAG
65 TATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAG
9146 T
1 T
9147 TTAAACAATG
Statistics
Matches: 117, Mismatches: 6, Indels: 9
0.89 0.05 0.07
Matches are distributed among these distances:
123 59 0.50
126 5 0.04
127 1 0.01
129 2 0.02
130 50 0.43
ACGTcount: A:0.47, C:0.02, G:0.11, T:0.40
Consensus pattern (126 bp):
TATATTTAAAAAATTCTAATATATATAATTTTTTTAATTAAAATAGTAAAATGGTAATAAAATGT
ATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAG
Found at i:9834 original size:31 final size:31
Alignment explanation
Indices: 9796--9857 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
9786 TATGTTAGAC
*
9796 AAATAAGGATATAATAGGCATTTCAAAAGTT
1 AAATAAGGATACAATAGGCATTTCAAAAGTT
* **
9827 AAATAAGGGTACAATAGGTGTTTCAAAAGTT
1 AAATAAGGATACAATAGGCATTTCAAAAGTT
9858 TTACAAAACT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.45, C:0.06, G:0.19, T:0.29
Consensus pattern (31 bp):
AAATAAGGATACAATAGGCATTTCAAAAGTT
Found at i:10626 original size:2 final size:2
Alignment explanation
Indices: 10621--10661 Score: 66
Period size: 2 Copynumber: 20.5 Consensus size: 2
10611 AATAATAGTA
10621 AT AT AT AT ACT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
10662 CTAAATATTA
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 1 0.03
2 34 0.92
3 2 0.05
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:10638 original size:10 final size:11
Alignment explanation
Indices: 10621--10669 Score: 66
Period size: 10 Copynumber: 4.5 Consensus size: 11
10611 AATAATAGTA
10621 ATATATATACT
1 ATATATATACT
10632 AATATATATA-T
1 -ATATATATACT
10643 ATATATATA-T
1 ATATATATACT
10653 ATATATATACT
1 ATATATATACT
*
10664 AAATAT
1 ATATAT
10670 TATTTGAAAC
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
10 19 0.54
11 7 0.20
12 9 0.26
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (11 bp):
ATATATATACT
Found at i:14754 original size:14 final size:14
Alignment explanation
Indices: 14735--14764 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
14725 CTTTATATAC
14735 ATTTTATTTTACAT
1 ATTTTATTTTACAT
*
14749 ATTTTATTTTATAT
1 ATTTTATTTTACAT
14763 AT
1 AT
14765 ATAATATAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (14 bp):
ATTTTATTTTACAT
Found at i:16937 original size:9 final size:9
Alignment explanation
Indices: 16923--16947 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
16913 AGTTACACTT
16923 TTTTTTTGG
1 TTTTTTTGG
16932 TTTTTTTGG
1 TTTTTTTGG
16941 TTTTTTT
1 TTTTTTT
16948 TTTTTTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (9 bp):
TTTTTTTGG
Found at i:18402 original size:20 final size:21
Alignment explanation
Indices: 18377--19044 Score: 115
Period size: 22 Copynumber: 30.6 Consensus size: 21
18367 AAATTTTAAA
18377 TTTGATAA-TCACTATAAAAT
1 TTTGATAACTCACTATAAAAT
18397 TTTGATAACCTC-CATATAAAAT
1 TTTGATAA-CTCAC-TATAAAAT
* *
18419 TTTGATAATTACACTATAAAGT
1 TTTGATAACT-CACTATAAAAT
* * * *
18441 TTTTATGACGAT-ACCATAGAAT
1 TTTGATAAC--TCACTATAAAAT
* * *
18463 TTCGAGAACCTC-CATATGAAAT
1 TTTGATAA-CTCAC-TATAAAAT
* *
18485 TTTGTTAACTTCCCTATAAAAT
1 TTTGATAAC-TCACTATAAAAT
* *
18507 TTTG-TCACACTCCCTTTAAAAT
1 TTTGAT-A-ACTCACTATAAAAT
* * *
18529 TTTAATAA-TTACCTAATGAAAT
1 TTTGATAACTCA-CT-ATAAAAT
*
18551 TTTGATAAC-CACCCTATGAAAT
1 TTTGATAACTCA--CTATAAAAT
* * **
18573 TTTGATAACCTCCCAACGAAAT
1 TTTGATAA-CTCACTATAAAAT
* * * *
18595 GTTGGTAAGCGCACATTATGAAAT
1 TTTGATAA-CTCAC--TATAAAAT
*
18619 TTTGATAACCTTCA-GATAAAAT
1 TTTGATAA-C-TCACTATAAAAT
* * * *
18641 ATCGGTAA-TCACATTATGAAAT
1 TTTGATAACTCAC--TATAAAAT
* *
18663 TTTGATAAACAT-ACCATGAAAT
1 TTTGAT-AAC-TCACTATAAAAT
* *
18685 TGTGATACCTCACTATGAAAAT
1 TTTGATAACTCACTAT-AAAAT
* *
18707 TTT-ATAAACCTCCCTATCAAAT
1 TTTGAT-AA-CTCACTATAAAAT
* *
18729 TTTGATAACCTC-CATTTGAAAT
1 TTTGATAA-CTCAC-TATAAAAT
*
18751 TTTGATAACCTCA-T-GAAAA-
1 TTTGATAA-CTCACTATAAAAT
* *
18770 TTTGAAAAC-CACCTCATGAAAT
1 TTTGATAACTCA-CT-ATAAAAT
*
18792 TTTGATAAC-CATCTTATGAAAT
1 TTTGATAACTCA-C-TATAAAAT
*
18814 TTTGATAACATCCCTATAAACAT
1 TTTGATAAC-TCACTATAAA-AT
*
18837 TTT-ATAAC-CTC-ATAAAAT
1 TTTGATAACTCACTATAAAAT
* ** *
18855 TTTGTTAACCTC-CTATGGATT
1 TTTGATAA-CTCACTATAAAAT
* ** * *
18876 TTTTATAAGAACACTATTAAAG
1 TTTGATAA-CTCACTATAAAAT
* * * *
18898 TTTGATAACACCCAATGAAAT
1 TTTGATAACTCACTATAAAAT
*
18919 TTTGATAATTAACTACACCATAAAAT
1 TTTG---A-TAACT-CACTATAAAAT
*** *
18945 TACAATAACTTGC-CTATGAAAT
1 TTTGATAAC-T-CACTATAAAAT
* *
18967 TTTGTTAATCTCCCTATAAAAT
1 TTTGATAA-CTCACTATAAAAT
* *
18989 TTTGAAAAC-CATTCTATCAAAT
1 TTTGATAACTCA--CTATAAAAT
*
19011 TTTGTTAATCTCACTAT-AAAT
1 TTTGATAA-CTCACTATAAAAT
19032 TTTGATAAACTCA
1 TTTGAT-AACTCA
19045 TCATGAAATT
Statistics
Matches: 471, Mismatches: 113, Indels: 127
0.66 0.16 0.18
Matches are distributed among these distances:
17 2 0.00
18 6 0.01
19 19 0.04
20 18 0.04
21 61 0.13
22 295 0.63
23 33 0.07
24 21 0.04
25 7 0.01
26 9 0.02
ACGTcount: A:0.38, C:0.17, G:0.08, T:0.36
Consensus pattern (21 bp):
TTTGATAACTCACTATAAAAT
Found at i:18417 original size:22 final size:22
Alignment explanation
Indices: 18389--18867 Score: 167
Period size: 22 Copynumber: 22.0 Consensus size: 22
18379 TGATAATCAC
18389 TATAAAATTTTGATAACCTCCA
1 TATAAAATTTTGATAACCTCCA
* *
18411 TATAAAATTTTGATAA-TTACA
1 TATAAAATTTTGATAACCTCCA
* * * *
18432 CTATAAAGTTTTTATGACGATACC-
1 -TATAAAATTTTGATAAC-CT-CCA
* * *
18456 -ATAGAATTTCGAGAACCTCCA
1 TATAAAATTTTGATAACCTCCA
* * * *
18477 TATGAAATTTTGTTAACTTCCC
1 TATAAAATTTTGATAACCTCCA
* *
18499 TATAAAATTTTG-TCACACTCCC
1 TATAAAATTTTGATAAC-CTCCA
* * *
18521 TTTAAAATTTTAATAA-TTACC-
1 TATAAAATTTTGATAACCT-CCA
* * *
18542 TAATGAAATTTTGATAACCACCC
1 T-ATAAAATTTTGATAACCTCCA
*
18565 TATGAAATTTTGATAACCTCCCA
1 TATAAAATTTTGATAACCT-CCA
** * * * *
18588 -ACGAAATGTTGGTAAGCGCACA
1 TATAAAATTTTGATAACCTC-CA
* *
18610 TTATGAAATTTTGATAACCTTCA
1 -TATAAAATTTTGATAACCTCCA
* * * *
18633 GATAAAATATCGGTAA--TCACA
1 TATAAAATTTTGATAACCTC-CA
* *
18654 TTATGAAATTTTGATAAACATACC-
1 -TATAAAATTTTGAT-AACCT-CCA
* *
18678 -ATGAAATTGTGAT-ACCT-CA
1 TATAAAATTTTGATAACCTCCA
*
18697 CTATGAAAATTTT-ATAAACCTCCC
1 -TAT-AAAATTTTGAT-AACCTCCA
*
18721 TATCAAATTTTGATAACCTCCA
1 TATAAAATTTTGATAACCTCCA
* *
18743 TTTGAAATTTTGATAACCT-CA
1 TATAAAATTTTGATAACCTCCA
* * *
18764 T-GAAAA-TTTGAAAACCACC-
1 TATAAAATTTTGATAACCTCCA
* *
18783 TCATGAAATTTTGATAACCAT-CT
1 T-ATAAAATTTTGATAACC-TCCA
* * *
18806 TATGAAATTTTGATAACATCCC
1 TATAAAATTTTGATAACCTCCA
18828 TATAAACATTTT-ATAACCT-C-
1 TATAAA-ATTTTGATAACCTCCA
*
18848 -ATAAAATTTTGTTAACCTCC
1 TATAAAATTTTGATAACCTCC
18868 TATGGATTTT
Statistics
Matches: 338, Mismatches: 79, Indels: 82
0.68 0.16 0.16
Matches are distributed among these distances:
18 6 0.02
19 21 0.06
20 11 0.03
21 24 0.07
22 233 0.69
23 24 0.07
24 15 0.04
25 3 0.01
26 1 0.00
ACGTcount: A:0.38, C:0.18, G:0.09, T:0.35
Consensus pattern (22 bp):
TATAAAATTTTGATAACCTCCA
Found at i:18594 original size:44 final size:43
Alignment explanation
Indices: 18543--19503 Score: 243
Period size: 44 Copynumber: 21.9 Consensus size: 43
18533 ATAATTACCT
18543 AATGAAATTTTGATAACCACCCTATGAAATTTTGATAACCTCCC
1 AATGAAATTTTGATAACCACCCTATGAAATTTTGATAACCT-CC
* * * ** *
18587 AACGAAATGTTGGTAAGCGCACATTATGAAATTTTGATAACCTTC
1 AATGAAATTTTGATAA-C-CACCCTATGAAATTTTGATAACCTCC
* * * * * ** *
18632 AGATAAAATATCGGTAATCACATTATGAAATTTTGATAAACATACC
1 A-ATGAAATTTTGATAACCACCCTATGAAATTTTGAT-AACCT-CC
* * *
18678 -ATGAAATTGTGAT-ACCTCACTATGAAAATTTT-ATAAACCTCCC
1 AATGAAATTTTGATAACCACCCTATG-AAATTTTGAT-AACCT-CC
* * * * *
18721 TATCAAATTTTGATAACCTCCATTTGAAATTTTGATAACCT-C
1 AATGAAATTTTGATAACCACCCTATGAAATTTTGATAACCTCC
* * *
18763 -ATGAAAATTTGAAAACCA-CCTCATGAAATTTTGATAACCATCT
1 AATGAAATTTTGATAACCACCCT-ATGAAATTTTGATAACC-TCC
* *
18806 TATGAAATTTTGATAA-CATCCCTATAAACATTTT-ATAACCT-C
1 AATGAAATTTTGATAACCA-CCCTATGAA-ATTTTGATAACCTCC
* * * * * * ***
18848 -ATAAAATTTTGTTAACC-TCCTATGGATTTTTTATAAGAACAC
1 AATGAAATTTTGATAACCACCCTATGAAATTTTGATAACCTC-C
* * * * *
18890 TATTAAAGTTTGATAA-CACCCAATGAAATTTTGATAATTAACTACAC
1 AATGAAATTTTGATAACCACCCTATGAAATTTTGAT-A--ACCT-C-C
* * *** *** * *
18937 CATAAAATTACAATAACTTGCCTATGAAATTTTGTTAATCTCCC
1 AATGAAATTTTGATAACCACCCTATGAAATTTTGATAACCT-CC
* * * ** * * *
18981 TATAAAATTTTGAAAACCATTCTATCAAATTTTGTTAATCTCAC
1 AATGAAATTTTGATAACCACCCTATGAAATTTTGATAACCTC-C
* * * * *
19025 TAT-AAATTTTGATAA--ACTCATCATGAAATTTT-AGTTACCACAA
1 AATGAAATTTTGATAACCAC-CCT-ATGAAATTTTGA-TAACCTC-C
* * * * ***
19068 AATTAAAATTTGATAACCTCTCCCTCTGAAA-TACCAT-A--T--
1 AATGAAATTTTGATAA-C-CACCCTATGAAATTTTGATAACCTCC
* * * *
19107 TATAAAATTTTGATAACCACACTATGAAATTTTGATAATCTCCC
1 AATGAAATTTTGATAACCACCCTATGAAATTTTGATAACCT-CC
** * * * *
19151 TCTGAAATTTCGATAACCTCCCCATGAAATTTTGTTAACCT-C
1 AATGAAATTTTGATAACCACCCTATGAAATTTTGATAACCTCC
* * * ** * * **
19193 TATGAAATTGTGATTATTACACTATGAAATTTTGGTAA-CGAC
1 AATGAAATTTTGATAACCACCCTATGAAATTTTGATAACCTCC
* * * * *
19235 ACTTGAAATTTTGATAAGCTCACTCTATCTCACTATGCAATTTTTATAAGCACAC
1 A-ATGAAATTTTGAT-A----AC-C-A-C-C-CTATGAAATTTTGATAACCTC-C
* * * * * *
19290 TATGAAATTTTGATAATCTCCATATAAAATTTCGATAATCGC-CC
1 AATGAAATTTTGATAACCACCCTATGAAATTTTGATAA-C-CTCC
* * **
19334 AATGAAATTTTGTTAACCTCCCTATGAAATTTTGATAACC-AG
1 AATGAAATTTTGATAACCACCCTATGAAATTTTGATAACCTCC
* * * **
19376 AGTATGAAATTTT-AGTAATCTCCCTGTGAAATTCCGATAACCTTCC
1 A--ATGAAATTTTGA-TAACCACCCTATGAAATTTTGATAACC-TCC
* * * * *
19422 CATG-AATTTCGATAACCTCCTTATGAAATTTTAATAACCTCC
1 AATGAAATTTTGATAACCACCCTATGAAATTTTGATAACCTCC
*
19464 ACATGAAATTTTGATAA-CATCCTTATGAAATTTTGATAAC
1 A-ATGAAATTTTGATAACCA-CCCTATGAAATTTTGATAAC
19504 ATCCCTAACT
Statistics
Matches: 671, Mismatches: 177, Indels: 138
0.68 0.18 0.14
Matches are distributed among these distances:
37 9 0.01
38 4 0.01
39 18 0.03
40 12 0.02
41 46 0.07
42 41 0.06
43 114 0.17
44 286 0.43
45 33 0.05
46 43 0.06
47 16 0.02
48 17 0.03
49 1 0.00
50 1 0.00
51 1 0.00
53 15 0.02
54 13 0.02
55 1 0.00
ACGTcount: A:0.37, C:0.18, G:0.09, T:0.36
Consensus pattern (43 bp):
AATGAAATTTTGATAACCACCCTATGAAATTTTGATAACCTCC
Found at i:18648 original size:46 final size:44
Alignment explanation
Indices: 18565--18670 Score: 124
Period size: 46 Copynumber: 2.4 Consensus size: 44
18555 ATAACCACCC
* * *
18565 TATGAAATTTTGATAACCTCCCAACGAAATGTTGGTAAGCGCACAT
1 TATGAAATTTTGATAACCTCCCAACAAAATATCGGTAA--GCACAT
* * *
18611 TATGAAATTTTGATAACCT-TCAGATAAAATATCGGTAATCACAT
1 TATGAAATTTTGATAACCTCCCA-ACAAAATATCGGTAAGCACAT
18655 TATGAAATTTTGATAA
1 TATGAAATTTTGATAA
18671 ACATACCATG
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
44 21 0.40
45 2 0.04
46 30 0.57
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.33
Consensus pattern (44 bp):
TATGAAATTTTGATAACCTCCCAACAAAATATCGGTAAGCACAT
Found at i:18812 original size:63 final size:67
Alignment explanation
Indices: 18544--18822 Score: 190
Period size: 66 Copynumber: 4.2 Consensus size: 67
18534 TAATTACCTA
* * * * * *
18544 ATGAAATTTTGATAACC-ACCCTATGAAATTTTGAT-AACCTCCCAACGAAATGTTGGTAAGCGC
1 ATGAAATTTTGATAACCTA--CTATGAAAATTTGATAAACCACCCTATGAAATTTTGATAA-C-C
*
18607 ACA-TT
62 ATACTT
* * * * * ** *
18612 ATGAAATTTTGATAACCTTCAGAT-AAAATATCGGT-AATCACATTATGAAATTTTGATAAACAT
1 ATGAAATTTTGATAACCTAC-TATGAAAAT-TTGATAAACCACCCTATGAAATTTTGATAACCAT
*
18675 AC-C
64 ACTT
* * * * *
18678 ATGAAATTGTGAT-ACCTCACTATGAAAATTTTATAAACCTCCCTATCAAATTTTGATAACC-TC
1 ATGAAATTTTGATAACCT-ACTATGAAAATTTGATAAACCACCCTATGAAATTTTGATAACCATA
18741 CATT
65 C-TT
18745 -TGAAATTTTGATAACCT-C-ATGAAAATTTGA-AAACCA-CCTCATGAAATTTTGATAACCAT-
1 ATGAAATTTTGATAACCTACTATGAAAATTTGATAAACCACCCT-ATGAAATTTTGATAACCATA
18804 CTT
65 CTT
18807 ATGAAATTTTGATAAC
1 ATGAAATTTTGATAAC
18823 ATCCCTATAA
Statistics
Matches: 164, Mismatches: 34, Indels: 31
0.72 0.15 0.14
Matches are distributed among these distances:
62 5 0.03
63 37 0.23
64 12 0.07
65 11 0.07
66 52 0.32
67 9 0.05
68 38 0.23
ACGTcount: A:0.38, C:0.18, G:0.11, T:0.33
Consensus pattern (67 bp):
ATGAAATTTTGATAACCTACTATGAAAATTTGATAAACCACCCTATGAAATTTTGATAACCATAC
TT
Found at i:19033 original size:21 final size:22
Alignment explanation
Indices: 18958--19061 Score: 81
Period size: 22 Copynumber: 4.7 Consensus size: 22
18948 AATAACTTGC
* *
18958 CTATGAAATTTTGTTAATCTCC
1 CTATGAAATTTTGTTAAACTCA
* *
18980 CTATAAAATTTTG-AAAAC-CA
1 CTATGAAATTTTGTTAAACTCA
* *
19000 TTCTATCAAATTTTGTTAATCTCA
1 --CTATGAAATTTTGTTAAACTCA
*
19024 CTAT-AAATTTTGATAAACTCA
1 CTATGAAATTTTGTTAAACTCA
19045 -TCATGAAATTTTAGTTA
1 CT-ATGAAATTTT-GTTA
19062 CCACAAAATT
Statistics
Matches: 65, Mismatches: 10, Indels: 13
0.74 0.11 0.15
Matches are distributed among these distances:
20 2 0.03
21 20 0.31
22 35 0.54
23 6 0.09
24 2 0.03
ACGTcount: A:0.37, C:0.14, G:0.07, T:0.42
Consensus pattern (22 bp):
CTATGAAATTTTGTTAAACTCA
Found at i:19136 original size:22 final size:22
Alignment explanation
Indices: 19111--19251 Score: 117
Period size: 22 Copynumber: 6.5 Consensus size: 22
19101 CCATATTATA
19111 AAATTTTGATAACCACACTATG
1 AAATTTTGATAACCACACTATG
* * * *
19133 AAATTTTGATAATCTCCCTCTG
1 AAATTTTGATAACCACACTATG
* * * *
19155 AAATTTCGATAACCTCCCCATG
1 AAATTTTGATAACCACACTATG
* *
19177 AAATTTTGTTAA-C-CTCTATG
1 AAATTTTGATAACCACACTATG
* * **
19197 AAATTGTGATTATTACACTATG
1 AAATTTTGATAACCACACTATG
* *
19219 AAATTTTGGTAACGACACT-TG
1 AAATTTTGATAACCACACTATG
19240 AAATTTTGATAA
1 AAATTTTGATAA
19252 GCTCACTCTA
Statistics
Matches: 94, Mismatches: 23, Indels: 5
0.77 0.19 0.04
Matches are distributed among these distances:
20 14 0.15
21 14 0.15
22 66 0.70
ACGTcount: A:0.35, C:0.17, G:0.11, T:0.37
Consensus pattern (22 bp):
AAATTTTGATAACCACACTATG
Found at i:19480 original size:65 final size:66
Alignment explanation
Indices: 19335--19503 Score: 173
Period size: 65 Copynumber: 2.6 Consensus size: 66
19325 TAATCGCCCA
* * * * *
19335 ATGAAATTTTGTTAACCTCCCTATGAAATTTTGATAACCAGAGTATGAAATTTTAGTAATCTCCC
1 ATGAAATTTTGATAACCTCCCTATGAAATTTCGATAACCACAGTATGAAATTTTAATAACCTCCC
19400 T
66 T
* ** * **
19401 GTGAAATTCCGATAACCTTCCC-ATG-AATTTCGATAACCTCCTTATGAAATTTTAATAACCTCC
1 ATGAAATTTTGATAACC-TCCCTATGAAATTTCGATAACCACAGTATGAAATTTTAATAACCTCC
19464 AC-
65 -CT
* * *
19466 ATGAAATTTTGATAACATCCTTATGAAATTTTGATAAC
1 ATGAAATTTTGATAACCTCCCTATGAAATTTCGATAAC
19504 ATCCCTAACT
Statistics
Matches: 82, Mismatches: 17, Indels: 8
0.77 0.16 0.07
Matches are distributed among these distances:
64 3 0.04
65 47 0.57
66 28 0.34
67 4 0.05
ACGTcount: A:0.34, C:0.19, G:0.11, T:0.36
Consensus pattern (66 bp):
ATGAAATTTTGATAACCTCCCTATGAAATTTCGATAACCACAGTATGAAATTTTAATAACCTCCC
T
Found at i:19503 original size:22 final size:22
Alignment explanation
Indices: 19261--19510 Score: 161
Period size: 22 Copynumber: 11.4 Consensus size: 22
19251 AGCTCACTCT
* * *
19261 ATCTCACTATGCAATTTTTATA
1 ATCTCCCTATGAAATTTTGATA
* * *
19283 AGCACACTATGAAATTTTGATA
1 ATCTCCCTATGAAATTTTGATA
* * *
19305 ATCTCCATATAAAATTTCGATA
1 ATCTCCCTATGAAATTTTGATA
* * *
19327 ATCGCCCAATGAAATTTTGTTA
1 ATCTCCCTATGAAATTTTGATA
*
19349 ACCTCCCTATGAAATTTTGATA
1 ATCTCCCTATGAAATTTTGATA
* ****
19371 ACCAGAGTATGAAATTTT-AGTA
1 ATCTCCCTATGAAATTTTGA-TA
* **
19393 ATCTCCCTGTGAAATTCCGATA
1 ATCTCCCTATGAAATTTTGATA
* *
19415 ACCTTCCC-ATG-AATTTCGATA
1 ATC-TCCCTATGAAATTTTGATA
* * *
19436 ACCTCCTTATGAAATTTTAATA
1 ATCTCCCTATGAAATTTTGATA
*
19458 ACCTCCAC-ATGAAATTTTGATA
1 ATCTCC-CTATGAAATTTTGATA
*
19480 A-CATCCTTATGAAATTTTGATA
1 ATC-TCCCTATGAAATTTTGATA
19502 A-CATCCCTA
1 ATC-TCCCTA
19511 ACTACACTAT
Statistics
Matches: 178, Mismatches: 42, Indels: 16
0.75 0.18 0.07
Matches are distributed among these distances:
20 3 0.02
21 17 0.10
22 153 0.86
23 5 0.03
ACGTcount: A:0.35, C:0.20, G:0.10, T:0.36
Consensus pattern (22 bp):
ATCTCCCTATGAAATTTTGATA
Found at i:19540 original size:21 final size:22
Alignment explanation
Indices: 19515--19646 Score: 74
Period size: 21 Copynumber: 6.0 Consensus size: 22
19505 TCCCTAACTA
*
19515 CACTATAAAATTTTAATATCCT
1 CACTATAAAATTTTAATAACCT
* * **
19537 -ACTATTAAAGTTTGGTAACCT
1 CACTATAAAATTTTAATAACCT
* *
19558 CACTATAAAATTTTGATAACCA
1 CACTATAAAATTTTAATAACCT
* *
19580 CA-TGTAAAATTTTGAGA-AAACT
1 CACTATAAAATTTT-A-ATAACCT
* * *
19602 ACATTATAAAATTTTAGTAACCA
1 -CACTATAAAATTTTAATAACCT
* * *
19625 CACAAT-GAATTTTGATAACCT
1 CACTATAAAATTTTAATAACCT
19646 C
1 C
19647 CAAAATTAAA
Statistics
Matches: 81, Mismatches: 23, Indels: 13
0.69 0.20 0.11
Matches are distributed among these distances:
21 38 0.47
22 26 0.32
23 7 0.09
24 10 0.12
ACGTcount: A:0.42, C:0.16, G:0.08, T:0.35
Consensus pattern (22 bp):
CACTATAAAATTTTAATAACCT
Found at i:19562 original size:22 final size:22
Alignment explanation
Indices: 19515--19578 Score: 67
Period size: 22 Copynumber: 3.0 Consensus size: 22
19505 TCCCTAACTA
* * *
19515 CACTATAAAATTTTAATATCCT
1 CACTATAAAAGTTTGATAACCT
* *
19537 -ACTATTAAAGTTTGGTAACCT
1 CACTATAAAAGTTTGATAACCT
*
19558 CACTATAAAATTTTGATAACC
1 CACTATAAAAGTTTGATAACC
19579 ACATGTAAAA
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
21 16 0.48
22 17 0.52
ACGTcount: A:0.39, C:0.17, G:0.06, T:0.38
Consensus pattern (22 bp):
CACTATAAAAGTTTGATAACCT
Found at i:19567 original size:249 final size:249
Alignment explanation
Indices: 19111--19576 Score: 549
Period size: 249 Copynumber: 1.9 Consensus size: 249
19101 CCATATTATA
*
19111 AAATTTTGATAACCACACTATGAAATTTTGATAATCTCCCTCTGAAATTTCGATAACCTCCCCAT
1 AAATTTTGATAACCACACTATGAAATTTTGATAATCTCCCTCTGAAATTCCGATAACCTCCCCAT
* * * * * *
19176 GAAATTTTGTTAACCTCTATGAAATTGTGATTATTACACTATGAAATTTTGGTAACGACACTTGA
66 GAAATTTCGATAACCTCTATGAAATTGTAATAACTACACTATGAAATTTTGATAACGACACTTGA
* ** * *
19241 AATTTTGATAAGCTCACTCTATCTCACTATGCAATTTTTATAAGCACACTATGAAATTTTGATAA
131 AATTTTGATAAGCTCACTCTAACTCACTATAAAATTTTAATAAGCACACTATGAAAGTTTGATAA
*
19306 TCTCCATATAAAATTTCGATAATCGCCCAATGAAATTTTGTTAACCTCCCTATG
196 CCTCCATATAAAATTTCGATAATCGCCCAATGAAATTTTGTTAACCTCCCTATG
* * * *
19360 AAATTTTGATAACCAGAGTATGAAATTTT-AGTAATCTCCCTGTGAAATTCCGATAACCTTCCCA
1 AAATTTTGATAACCACACTATGAAATTTTGA-TAATCTCCCTCTGAAATTCCGATAACCTCCCCA
* *
19424 TG-AATTTCGATAACCTCCTTATGAAATTTTAATAACCTCCAC-ATGAAATTTTGATAAC-ATC-
65 TGAAATTTCGATAACCT-C-TATGAAATTGTAATAA-CTACACTATGAAATTTTGATAACGA-CA
* *
19485 CTTATGAAATTTTGATAA-CATC-C-CTAACTACACTATAAAATTTTAAT-ATC-CTACTATTAA
126 C-T-TGAAATTTTGATAAGC-TCACTCTAACT-CACTATAAAATTTTAATAAGCAC-ACTATGAA
* *
19545 AGTTTGGTAACCT-CACTATAAAATTTTGATAA
186 AGTTTGATAACCTCCA-TATAAAATTTCGATAA
19577 CCACATGTAA
Statistics
Matches: 183, Mismatches: 23, Indels: 22
0.80 0.10 0.10
Matches are distributed among these distances:
248 16 0.09
249 101 0.55
250 46 0.25
251 20 0.11
ACGTcount: A:0.35, C:0.19, G:0.10, T:0.36
Consensus pattern (249 bp):
AAATTTTGATAACCACACTATGAAATTTTGATAATCTCCCTCTGAAATTCCGATAACCTCCCCAT
GAAATTTCGATAACCTCTATGAAATTGTAATAACTACACTATGAAATTTTGATAACGACACTTGA
AATTTTGATAAGCTCACTCTAACTCACTATAAAATTTTAATAAGCACACTATGAAAGTTTGATAA
CCTCCATATAAAATTTCGATAATCGCCCAATGAAATTTTGTTAACCTCCCTATG
Found at i:19981 original size:14 final size:15
Alignment explanation
Indices: 19952--19988 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
19942 TTCGTACTTT
*
19952 TATATATAGTATAGA
1 TATAGATAGTATAGA
19967 TATAGATAG-ATAGA
1 TATAGATAGTATAGA
19981 TATAGATA
1 TATAGATA
19989 TATTTCTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 13 0.62
15 8 0.38
ACGTcount: A:0.49, C:0.00, G:0.16, T:0.35
Consensus pattern (15 bp):
TATAGATAGTATAGA
Found at i:22281 original size:30 final size:31
Alignment explanation
Indices: 22221--22281 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
22211 GAGTTTTGTA
22221 AAACTTTTGAATCGTCTATTATACCCTTATT
1 AAACTTTTGAATCGTCTATTATACCCTTATT
22252 AAACTTTTGAATCGTCTATTATA-CCTTATT
1 AAACTTTTGAATCGTCTATTATACCCTTATT
22282 TTTCAAATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 7 0.23
31 23 0.77
ACGTcount: A:0.30, C:0.18, G:0.07, T:0.46
Consensus pattern (31 bp):
AAACTTTTGAATCGTCTATTATACCCTTATT
Found at i:22428 original size:93 final size:93
Alignment explanation
Indices: 22317--22494 Score: 311
Period size: 93 Copynumber: 1.9 Consensus size: 93
22307 TTGTTTAAAT
22317 TTTTATAGTTTTAATCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAACTA
1 TTTTATAGTTTTAATCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAACTA
* *
22382 TTTTGTTTTTACCATTTTACCATTTTAC
66 TTTTATTTTTACCATATTACCATTTTAC
* * *
22410 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATTCTTATACCTA
1 TTTTATAGTTTTAATCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAACTA
22475 TTTTATTTTTACCATATTAC
66 TTTTATTTTTACCATATTAC
22495 TAATTTAATT
Statistics
Matches: 80, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 80 1.00
ACGTcount: A:0.33, C:0.14, G:0.02, T:0.52
Consensus pattern (93 bp):
TTTTATAGTTTTAATCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAACTA
TTTTATTTTTACCATATTACCATTTTAC
Done.