Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023022.1 Corchorus olitorius cultivar O-4 contig23055, 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: 40309
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:475 original size:21 final size:20
Alignment explanation
Indices: 451--503 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
441 TATAAAATGC
451 ATATGGATTTTGTGCCACTTT
1 ATAT-GATTTTGTGCCACTTT
* *
472 ATATAAATTTTGTGCCCCTTT
1 ATAT-GATTTTGTGCCACTTT
*
493 ATGTGATTTTG
1 ATATGATTTTG
504 ATTAGTTTGT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 6 0.22
21 21 0.78
ACGTcount: A:0.21, C:0.13, G:0.17, T:0.49
Consensus pattern (20 bp):
ATATGATTTTGTGCCACTTT
Found at i:3997 original size:26 final size:27
Alignment explanation
Indices: 3954--4019 Score: 75
Period size: 26 Copynumber: 2.5 Consensus size: 27
3944 GAGAGGAAAA
*
3954 GAAAAAGAAAA-ATGAAGAAAAGAA-TT
1 GAAAAAGAAAAGATAAAG-AAAGAAGTT
3980 GAAAAAGAAAAGA-AAAGAAAGAAGTT
1 GAAAAAGAAAAGATAAAGAAAGAAGTT
*
4006 GAAAATGCAAAAGA
1 GAAAAAG-AAAAGA
4020 CGGAGGAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
25 6 0.17
26 22 0.63
27 7 0.20
ACGTcount: A:0.68, C:0.02, G:0.21, T:0.09
Consensus pattern (27 bp):
GAAAAAGAAAAGATAAAGAAAGAAGTT
Found at i:5410 original size:54 final size:54
Alignment explanation
Indices: 5352--5504 Score: 177
Period size: 55 Copynumber: 2.8 Consensus size: 54
5342 AGCCAGTGTG
*
5352 GTCTTTCATAGAAGTTTTTAGAAATCTA-AGTTGATCTTCAGATGACCCTGTGCA
1 GTCTTTCATAGAAGTTTTTAGAGATC-AGAGTTGATCTTCAGATGACCCTGTGCA
* * * * *
5406 GTCTTTCATAAGAAGCTTTCA-ATGATCAGAGTTGATCTTAAGTTGACCCTGTGCG
1 GTCTTTCAT-AGAAGTTTTTAGA-GATCAGAGTTGATCTTCAGATGACCCTGTGCA
* * *
5461 GTCTTTCAAAGAAGTTTTTAGAGATCATAGTTGATC-CCAGATGA
1 GTCTTTCATAGAAGTTTTTAGAGATCAGAGTTGATCTTCAGATGA
5505 TCTAGTGCGG
Statistics
Matches: 82, Mismatches: 13, Indels: 9
0.79 0.12 0.09
Matches are distributed among these distances:
53 5 0.06
54 33 0.40
55 44 0.54
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.35
Consensus pattern (54 bp):
GTCTTTCATAGAAGTTTTTAGAGATCAGAGTTGATCTTCAGATGACCCTGTGCA
Found at i:5453 original size:55 final size:54
Alignment explanation
Indices: 5334--5496 Score: 159
Period size: 54 Copynumber: 3.0 Consensus size: 54
5324 GTACAGATGT
* * ** * * * *
5334 TTAAGATGAGCCAGTGTGGTCTTTCATAGAAGTTTTTAGAAATCTA-AGTTGATC
1 TTAAGATGACCCTGTGCAGTCTTTCAAAGAAGCTTTCAGAGATC-AGAGTTGATC
*
5388 TTCAGATGACCCTGTGCAGTCTTTCATAAGAAGCTTTCA-ATGATCAGAGTTGATC
1 TTAAGATGACCCTGTGCAGTCTTTCA-AAGAAGCTTTCAGA-GATCAGAGTTGATC
* * * * *
5443 TTAAGTTGACCCTGTGCGGTCTTTCAAAGAAGTTTTTAGAGATCATAGTTGATC
1 TTAAGATGACCCTGTGCAGTCTTTCAAAGAAGCTTTCAGAGATCAGAGTTGATC
5497 CCAGATGATC
Statistics
Matches: 90, Mismatches: 15, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
54 46 0.51
55 44 0.49
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.36
Consensus pattern (54 bp):
TTAAGATGACCCTGTGCAGTCTTTCAAAGAAGCTTTCAGAGATCAGAGTTGATC
Found at i:5566 original size:35 final size:35
Alignment explanation
Indices: 5525--6190 Score: 932
Period size: 35 Copynumber: 19.2 Consensus size: 35
5515 TCGTTCCAAT
*
5525 AAGTTTTCGATGATCAGAGTTGATCTCCTTTCAAG
1 AAGTTTTCGATGATCAGAGTTGATCTCATTTCAAG
* *
5560 AAGTTTTCGTTGATCAGAGTGGATCTCATTTCAAG
1 AAGTTTTCGATGATCAGAGTTGATCTCATTTCAAG
* * * *
5595 AATTTTTCGTTGATCAGAGTGGATCTCGTTTCAAG
1 AAGTTTTCGATGATCAGAGTTGATCTCATTTCAAG
* * *
5630 AAGTTTT-TATGATCAGAGTTGATATCGTTTCAAG
1 AAGTTTTCGATGATCAGAGTTGATCTCATTTCAAG
* *
5664 AAGTTTT-TATGATCAGAGTTGATCTCCTTTCAAG
1 AAGTTTTCGATGATCAGAGTTGATCTCATTTCAAG
5698 AAGTTTTCGATGATCAGAGTTGATCTCATTTCAAG
1 AAGTTTTCGATGATCAGAGTTGATCTCATTTCAAG
* * * *
5733 AAGTTTT-TAAGATCAGAGTTGATCTCGTTTTAAG
1 AAGTTTTCGATGATCAGAGTTGATCTCATTTCAAG
* * *
5767 AAGTTTTCGGTGATCAGAGTTGATCACATTTTAAG
1 AAGTTTTCGATGATCAGAGTTGATCTCATTTCAAG
*
5802 AAGTTTT-GATGATCAGAGTTGATCGCATTTCAAG
1 AAGTTTTCGATGATCAGAGTTGATCTCATTTCAAG
* * *
5836 AAGTTTTTGATGATCAGAGTTGATCACATTTTAAG
1 AAGTTTTCGATGATCAGAGTTGATCTCATTTCAAG
* *
5871 AAGTTTT-GATGATCAGGGTTGATCGCATTTCAAG
1 AAGTTTTCGATGATCAGAGTTGATCTCATTTCAAG
*
5905 AAGTTTTCGATGATCAGAGTTGATCTCATTTTAAG
1 AAGTTTTCGATGATCAGAGTTGATCTCATTTCAAG
*
5940 AAGTTTTCGATGATCAGAGTTGATCGCATTTCAAG
1 AAGTTTTCGATGATCAGAGTTGATCTCATTTCAAG
*
5975 AAGTTTTCGATGATTAGAGTTGATCTCATTTCAAG
1 AAGTTTTCGATGATCAGAGTTGATCTCATTTCAAG
*
6010 AAGTTTT-GATGATCATAGTTGATCTCATTTCAAG
1 AAGTTTTCGATGATCAGAGTTGATCTCATTTCAAG
*
6044 AAGTTTTCGATGATCAGAGTTGATCTCGTTTCAAG
1 AAGTTTTCGATGATCAGAGTTGATCTCATTTCAAG
* *
6079 AAGTTTTCGATGATTAAAGTTGATCTCATTTCAAG
1 AAGTTTTCGATGATCAGAGTTGATCTCATTTCAAG
** * *
6114 AAGTTTTTTATGATCAGAGTTGATCTCCTTTTAAG
1 AAGTTTTCGATGATCAGAGTTGATCTCATTTCAAG
* *
6149 AAGTTTTTG-TCGATCAGAGTTTATCTCATTTCAAG
1 AAGTTTTCGAT-GATCAGAGTTGATCTCATTTCAAG
6184 AAGTTTT
1 AAGTTTT
6191 TTTTTACGCA
Statistics
Matches: 570, Mismatches: 55, Indels: 12
0.89 0.09 0.02
Matches are distributed among these distances:
34 187 0.33
35 383 0.67
ACGTcount: A:0.28, C:0.12, G:0.21, T:0.39
Consensus pattern (35 bp):
AAGTTTTCGATGATCAGAGTTGATCTCATTTCAAG
Found at i:5711 original size:69 final size:69
Alignment explanation
Indices: 5525--6190 Score: 931
Period size: 69 Copynumber: 9.6 Consensus size: 69
5515 TCGTTCCAAT
* * *
5525 AAGTTTTCGATGATCAGAGTTGATCTCCTTTCAAGAAGTTTTCGTTGATCAGAGTGGATCTCATT
1 AAGTTTT-GATGATCAGAGTTGATCTCATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCATT
5590 TCAAG
65 TCAAG
* * * * * * *
5595 AATTTTTCGTTGATCAGAGTGGATCTCGTTTCAAGAAGTTTT-TATGATCAGAGTTGATATCGTT
1 AAGTTTT-GATGATCAGAGTTGATCTCATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCATT
5659 TCAAG
65 TCAAG
* *
5664 AAGTTTTTATGATCAGAGTTGATCTCCTTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCATTT
1 AAGTTTTGATGATCAGAGTTGATCTCATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCATTT
5729 CAAG
66 CAAG
* * * * * *
5733 AAGTTTTTAAGATCAGAGTTGATCTCGTTTTAAGAAGTTTTCGGTGATCAGAGTTGATCACATTT
1 AAGTTTTGATGATCAGAGTTGATCTCATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCATTT
*
5798 TAAG
66 CAAG
* * *
5802 AAGTTTTGATGATCAGAGTTGATCGCATTTCAAGAAGTTTTTGATGATCAGAGTTGATCACATTT
1 AAGTTTTGATGATCAGAGTTGATCTCATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCATTT
*
5867 TAAG
66 CAAG
* *
5871 AAGTTTTGATGATCAGGGTTGATCGCATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCATTT
1 AAGTTTTGATGATCAGAGTTGATCTCATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCATTT
*
5936 TAAG
66 CAAG
* *
5940 AAGTTTTCGATGATCAGAGTTGATCGCATTTCAAGAAGTTTTCGATGATTAGAGTTGATCTCATT
1 AAGTTTT-GATGATCAGAGTTGATCTCATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCATT
6005 TCAAG
65 TCAAG
* *
6010 AAGTTTTGATGATCATAGTTGATCTCATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCGTTT
1 AAGTTTTGATGATCAGAGTTGATCTCATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCATTT
6075 CAAG
66 CAAG
* * ** *
6079 AAGTTTTCGATGATTAAAGTTGATCTCATTTCAAGAAGTTTTTTATGATCAGAGTTGATCTCCTT
1 AAGTTTT-GATGATCAGAGTTGATCTCATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCATT
*
6144 TTAAG
65 TCAAG
*
6149 AAGTTTTTG-TCGATCAGAGTTTATCTCATTTCAAGAAGTTTT
1 AAG-TTTTGAT-GATCAGAGTTGATCTCATTTCAAGAAGTTTT
6191 TTTTTACGCA
Statistics
Matches: 542, Mismatches: 49, Indels: 10
0.90 0.08 0.02
Matches are distributed among these distances:
68 30 0.06
69 316 0.58
70 192 0.35
71 4 0.01
ACGTcount: A:0.28, C:0.12, G:0.21, T:0.39
Consensus pattern (69 bp):
AAGTTTTGATGATCAGAGTTGATCTCATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCATTT
CAAG
Found at i:5868 original size:104 final size:105
Alignment explanation
Indices: 5525--6190 Score: 941
Period size: 104 Copynumber: 6.4 Consensus size: 105
5515 TCGTTCCAAT
* * * *
5525 AAGTTTTCGATGATCAGAGTTGATCTCCTTTCAAGAAGTTTTCGTTGATCAGAGTGGATCTCATT
1 AAGTTTTTGATGATCAGAGTTGATCTCATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCATT
* * * *
5590 TCAAGAATTTTTCGTTGATCAGAGTGGATCTCGTTTCAAG
66 TCAAGAAGTTTTCGATGATCAGAGTTGATCTCATTTCAAG
* * * *
5630 AAGTTTTT-ATGATCAGAGTTGATATCGTTTCAAGAAGTTTT-TATGATCAGAGTTGATCTCCTT
1 AAGTTTTTGATGATCAGAGTTGATCTCATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCATT
5693 TCAAGAAGTTTTCGATGATCAGAGTTGATCTCATTTCAAG
66 TCAAGAAGTTTTCGATGATCAGAGTTGATCTCATTTCAAG
* * * * *
5733 AAGTTTTT-AAGATCAGAGTTGATCTCGTTTTAAGAAGTTTTCGGTGATCAGAGTTGATCACATT
1 AAGTTTTTGATGATCAGAGTTGATCTCATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCATT
* *
5797 TTAAGAAGTTTT-GATGATCAGAGTTGATCGCATTTCAAG
66 TCAAGAAGTTTTCGATGATCAGAGTTGATCTCATTTCAAG
* * * *
5836 AAGTTTTTGATGATCAGAGTTGATCACATTTTAAGAAGTTTT-GATGATCAGGGTTGATCGCATT
1 AAGTTTTTGATGATCAGAGTTGATCTCATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCATT
*
5900 TCAAGAAGTTTTCGATGATCAGAGTTGATCTCATTTTAAG
66 TCAAGAAGTTTTCGATGATCAGAGTTGATCTCATTTCAAG
* * *
5940 AAGTTTTCGATGATCAGAGTTGATCGCATTTCAAGAAGTTTTCGATGATTAGAGTTGATCTCATT
1 AAGTTTTTGATGATCAGAGTTGATCTCATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCATT
*
6005 TCAAGAAGTTTT-GATGATCATAGTTGATCTCATTTCAAG
66 TCAAGAAGTTTTCGATGATCAGAGTTGATCTCATTTCAAG
* * * *
6044 AAGTTTTCGATGATCAGAGTTGATCTCGTTTCAAGAAGTTTTCGATGATTAAAGTTGATCTCATT
1 AAGTTTTTGATGATCAGAGTTGATCTCATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCATT
** * *
6109 TCAAGAAGTTTTTTATGATCAGAGTTGATCTCCTTTTAAG
66 TCAAGAAGTTTTCGATGATCAGAGTTGATCTCATTTCAAG
*
6149 AAGTTTTTG-TCGATCAGAGTTTATCTCATTTCAAGAAGTTTT
1 AAGTTTTTGAT-GATCAGAGTTGATCTCATTTCAAGAAGTTTT
6191 TTTTTACGCA
Statistics
Matches: 508, Mismatches: 47, Indels: 12
0.90 0.08 0.02
Matches are distributed among these distances:
103 156 0.31
104 254 0.50
105 98 0.19
ACGTcount: A:0.28, C:0.12, G:0.21, T:0.39
Consensus pattern (105 bp):
AAGTTTTTGATGATCAGAGTTGATCTCATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCATT
TCAAGAAGTTTTCGATGATCAGAGTTGATCTCATTTCAAG
Found at i:8493 original size:25 final size:22
Alignment explanation
Indices: 8459--8538 Score: 74
Period size: 22 Copynumber: 3.5 Consensus size: 22
8449 TGACAAGTGG
*
8459 TTATCGAAATTTCATAGAGATCAGA
1 TTATCAAAATTT-ATAGAGA--AGA
8484 TTATCAAAATTTATA-AGAAGA
1 TTATCAAAATTTATAGAGAAGA
* **
8505 TTATCAAAATTTTATAGTG-TTA
1 TTATCAAAA-TTTATAGAGAAGA
8527 TTATCAAAATTT
1 TTATCAAAATTT
8539 CAAAGCGAGG
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
21 15 0.31
22 16 0.33
23 4 0.08
24 3 0.06
25 11 0.22
ACGTcount: A:0.42, C:0.07, G:0.10, T:0.40
Consensus pattern (22 bp):
TTATCAAAATTTATAGAGAAGA
Found at i:8649 original size:22 final size:22
Alignment explanation
Indices: 8599--8650 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
8589 GGGGTCAACT
* *
8599 AAATTTT-ATAGATAGGTTATC
1 AAATTTTCATAAAGAGGTTATC
*
8620 AAAATTTCATAAAGAGGTTATC
1 AAATTTTCATAAAGAGGTTATC
8642 AAATTTTCA
1 AAATTTTCA
8651 AAATGTGATT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
21 6 0.23
22 20 0.77
ACGTcount: A:0.42, C:0.08, G:0.12, T:0.38
Consensus pattern (22 bp):
AAATTTTCATAAAGAGGTTATC
Found at i:8667 original size:44 final size:44
Alignment explanation
Indices: 8482--8674 Score: 146
Period size: 44 Copynumber: 4.4 Consensus size: 44
8472 ATAGAGATCA
* * *
8482 GATTATCAAAATTT-AT-AAGAAGATTATCAAAATTTTATAGTGT
1 GATTATCAAAATTTCATAAAG-AGGTTATCAAAATTTTAAAATGT
* * * ** *
8525 TATTATCAAAATTTCA-AAGCGAGGCTATCAAAATTACATAATGT
1 GATTATCAAAATTTCATAA-AGAGGTTATCAAAATTTTAAAATGT
* * * * * * *
8569 GATTATTAAAATTTCATAGAGGGGTCAACTAAATTTTATAGATAG-
1 GATTATCAAAATTTCATAAAGAGGTTATCAAAATTTTA-AAAT-GT
8614 G-TTATCAAAATTTCATAAAGAGGTTATC-AAATTTTCAAAATGT
1 GATTATCAAAATTTCATAAAGAGGTTATCAAAATTTT-AAAATGT
*
8657 GATTACCAAAATTTCATA
1 GATTATCAAAATTTCATA
8675 GTGGCATTTC
Statistics
Matches: 114, Mismatches: 27, Indels: 17
0.72 0.17 0.11
Matches are distributed among these distances:
42 1 0.01
43 24 0.21
44 83 0.73
45 5 0.04
46 1 0.01
ACGTcount: A:0.42, C:0.09, G:0.12, T:0.36
Consensus pattern (44 bp):
GATTATCAAAATTTCATAAAGAGGTTATCAAAATTTTAAAATGT
Found at i:8803 original size:22 final size:21
Alignment explanation
Indices: 8775--8933 Score: 114
Period size: 22 Copynumber: 7.5 Consensus size: 21
8765 TCAGGCAGGA
8775 TATCAAAATTTCATATGAAGGT
1 TATCAAAATTTCATATG-AGGT
*
8797 TATCAAAATTTCATAGTTTA-GT
1 TATCAAAATTTCATA--TGAGGT
* * * *
8819 TTTCAAAATTTCTTAGGGAGAT
1 TATCAAAATTTCATA-TGAGGT
*
8841 TAACAAAATTTCATAATGAGGT
1 TATCAAAATTTCAT-ATGAGGT
** *
8863 TATCAAAAAATCATAGGGAGGT
1 TATCAAAATTTCATA-TGAGGT
*
8885 TATCAAAA-TT--TGT-A-GT
1 TATCAAAATTTCATATGAGGT
*
8901 TATCAAGATTTCATAATGAGGT
1 TATCAAAATTTCAT-ATGAGGT
8923 TATCAAAATTT
1 TATCAAAATTT
8934 TATAGGAAAA
Statistics
Matches: 104, Mismatches: 22, Indels: 22
0.70 0.15 0.15
Matches are distributed among these distances:
16 9 0.09
17 3 0.03
19 2 0.02
20 1 0.01
21 4 0.04
22 82 0.79
23 2 0.02
24 1 0.01
ACGTcount: A:0.40, C:0.09, G:0.14, T:0.37
Consensus pattern (21 bp):
TATCAAAATTTCATATGAGGT
Found at i:8829 original size:44 final size:43
Alignment explanation
Indices: 8775--8938 Score: 149
Period size: 44 Copynumber: 3.9 Consensus size: 43
8765 TCAGGCAGGA
* *
8775 TATCAAAATTTCATATGAAGGTTATCAAAATTTCATAGTTTAGT
1 TATCAAAATTTCATAGGGAGGTTATCAAAATTTCATAG-TTAGT
* * * * * *
8819 TTTCAAAATTTCTTAGGGAGATTAACAAAATTTCATAATGAGGT
1 TATCAAAATTTCATAGGGAGGTTATCAAAATTTCATAGTTA-GT
**
8863 TATCAAAAAATCATAGGGAGGTTATCAAAA-TT--T-G-TAGT
1 TATCAAAATTTCATAGGGAGGTTATCAAAATTTCATAGTTAGT
* ** *
8901 TATCAAGATTTCATAATGAGGTTATCAAAATTTTATAG
1 TATCAAAATTTCATAGGGAGGTTATCAAAATTTCATAG
8939 GAAAAAATTT
Statistics
Matches: 94, Mismatches: 21, Indels: 12
0.74 0.17 0.09
Matches are distributed among these distances:
38 27 0.29
39 3 0.03
41 2 0.02
42 1 0.01
43 4 0.04
44 57 0.61
ACGTcount: A:0.40, C:0.09, G:0.15, T:0.37
Consensus pattern (43 bp):
TATCAAAATTTCATAGGGAGGTTATCAAAATTTCATAGTTAGT
Found at i:8891 original size:66 final size:60
Alignment explanation
Indices: 8778--8930 Score: 148
Period size: 66 Copynumber: 2.5 Consensus size: 60
8768 GGCAGGATAT
** ** *
8778 CAAAATTTCAT-ATGAAGGTTATCAAAATTTCATAGTTTAGTTTTCAAAATTTCTTAGGGAGATT
1 CAAAATTTCATAATG-AGGTTATCAAAAAATCATAGTGGAGTTATCAAAA--T-TT--GGAG-TT
8842 AA
59 AA
* *
8844 CAAAATTTCATAATGAGGTTATCAAAAAATCATAG-GGAGGTTATCAAAATTTGTAGTTAT
1 CAAAATTTCATAATGAGGTTATCAAAAAATCATAGTGGA-GTTATCAAAATTTGGAGTTAA
*
8904 CAAGATTTCATAATGAGGTTATCAAAA
1 CAAAATTTCATAATGAGGTTATCAAAA
8931 TTTTATAGGA
Statistics
Matches: 77, Mismatches: 8, Indels: 10
0.81 0.08 0.11
Matches are distributed among these distances:
60 29 0.38
61 3 0.04
63 2 0.03
64 1 0.01
65 1 0.01
66 38 0.49
67 3 0.04
ACGTcount: A:0.41, C:0.09, G:0.15, T:0.35
Consensus pattern (60 bp):
CAAAATTTCATAATGAGGTTATCAAAAAATCATAGTGGAGTTATCAAAATTTGGAGTTAA
Found at i:11133 original size:2 final size:2
Alignment explanation
Indices: 11117--11149 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
11107 AAATGAGCAC
*
11117 AT AT AT TT AT A- AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
11150 TAATATTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:12058 original size:57 final size:57
Alignment explanation
Indices: 11987--12102 Score: 196
Period size: 57 Copynumber: 2.0 Consensus size: 57
11977 TTTATTTTGT
* * *
11987 AGAATAATTAAGTAGAGATAGGGGGGATATGATTTGTTATAACATTTATTGCGTGAA
1 AGAATAATTAAGTAGAGATAGGGGGGATAGGATTTATTACAACATTTATTGCGTGAA
*
12044 AGAATAATTAAGTAGAGATAGGGGGGATAGGATTTATTACAACATTTATTGTGTGAA
1 AGAATAATTAAGTAGAGATAGGGGGGATAGGATTTATTACAACATTTATTGCGTGAA
12101 AG
1 AG
12103 GGAAACAGAT
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
57 55 1.00
ACGTcount: A:0.38, C:0.03, G:0.27, T:0.32
Consensus pattern (57 bp):
AGAATAATTAAGTAGAGATAGGGGGGATAGGATTTATTACAACATTTATTGCGTGAA
Found at i:19066 original size:14 final size:14
Alignment explanation
Indices: 19033--19065 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
19023 AAACGGTGCA
19033 GTTTTTGCTTTTTT
1 GTTTTTGCTTTTTT
*
19047 GCTTTTGCTTTTTT
1 GTTTTTGCTTTTTT
19061 -TTTTT
1 GTTTTT
19066 TTTTGGGTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
13 4 0.24
14 13 0.76
ACGTcount: A:0.00, C:0.09, G:0.12, T:0.79
Consensus pattern (14 bp):
GTTTTTGCTTTTTT
Found at i:19832 original size:15 final size:16
Alignment explanation
Indices: 19809--19841 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
19799 ATATTATTAG
19809 TATATAATAATAATTC
1 TATATAATAATAATTC
*
19825 TATA-AATAATACTTC
1 TATATAATAATAATTC
19840 TA
1 TA
19842 AAGATACTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.48, C:0.09, G:0.00, T:0.42
Consensus pattern (16 bp):
TATATAATAATAATTC
Found at i:21365 original size:21 final size:19
Alignment explanation
Indices: 21320--21377 Score: 80
Period size: 19 Copynumber: 2.9 Consensus size: 19
21310 CTGTTTGGCA
21320 ACTGTACAGATGAGATTAC
1 ACTGTACAGATGAGATTAC
* *
21339 ACTGTACAGATTAGATTAGGT
1 ACTGTACAGATGAGATTA--C
21360 ACTGTACAGATGAGATTA
1 ACTGTACAGATGAGATTA
21378 TTAGAGCAGC
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 17 0.50
21 17 0.50
ACGTcount: A:0.36, C:0.12, G:0.22, T:0.29
Consensus pattern (19 bp):
ACTGTACAGATGAGATTAC
Found at i:23734 original size:20 final size:19
Alignment explanation
Indices: 23704--23756 Score: 52
Period size: 19 Copynumber: 2.7 Consensus size: 19
23694 CTTATGGAGT
*
23704 TTATCACAATTTTATAGTTAA
1 TTATCA-AATTTTAT-GGTAA
* *
23725 TTATCAAATTATATGGTGA
1 TTATCAAATTTTATGGTAA
*
23744 TTATCAAAATTTA
1 TTATCAAATTTTA
23757 ATAGGGTAGT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
19 14 0.52
20 7 0.26
21 6 0.22
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.45
Consensus pattern (19 bp):
TTATCAAATTTTATGGTAA
Found at i:23847 original size:2 final size:2
Alignment explanation
Indices: 23840--23866 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
23830 CTAAAACTAG
23840 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
23867 GTTTTAATGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:29749 original size:19 final size:19
Alignment explanation
Indices: 29725--29761 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
29715 GTACAATACC
29725 TAATCTAATCTGTACAGTG
1 TAATCTAATCTGTACAGTG
*
29744 TAATCTCATCTGTACAGT
1 TAATCTAATCTGTACAGT
29762 TGCTAAACAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.38
Consensus pattern (19 bp):
TAATCTAATCTGTACAGTG
Done.