Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017688.1 Corchorus olitorius cultivar O-4 contig17721, 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: 54627
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Found at i:2165 original size:13 final size:13
Alignment explanation
Indices: 2147--2171 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2137 ACTCTTTCTC
2147 TCTCTTCTCTTTA
1 TCTCTTCTCTTTA
2160 TCTCTTCTCTTT
1 TCTCTTCTCTTT
2172 TACTATCTTC
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:0.04, C:0.32, G:0.00, T:0.64
Consensus pattern (13 bp):
TCTCTTCTCTTTA
Found at i:15580 original size:27 final size:27
Alignment explanation
Indices: 15542--15647 Score: 131
Period size: 27 Copynumber: 3.9 Consensus size: 27
15532 GACCTGGTCT
* * *
15542 TGGCTGATCTTGGCCTGGTGGGAAGTG
1 TGGCTTATCTTGCCCTGGTGGAAAGTG
15569 TGGCTTATCTTGCCCTGGTGGAAAGTG
1 TGGCTTATCTTGCCCTGGTGGAAAGTG
* *
15596 TGGCTTATCTTGTCCTGGTGGAAAATG
1 TGGCTTATCTTGCCCTGGTGGAAAGTG
** * *
15623 TGGCAAATCATGCACTGGTGGAAAG
1 TGGCTTATCTTGCCCTGGTGGAAAG
15648 GCTGGCCAAT
Statistics
Matches: 68, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 68 1.00
ACGTcount: A:0.19, C:0.16, G:0.35, T:0.30
Consensus pattern (27 bp):
TGGCTTATCTTGCCCTGGTGGAAAGTG
Found at i:15698 original size:30 final size:30
Alignment explanation
Indices: 15663--15808 Score: 166
Period size: 30 Copynumber: 4.6 Consensus size: 30
15653 CCAATCACTA
15663 ACTGGTGGAGGTGGTGGCGGCGAATGATAT
1 ACTGGTGGAGGTGGTGGCGGCGAATGATAT
* *
15693 ACTGGTGGAGGAGGTGGAGGAGGTGGAGGCGAGTGATAT
1 ACTGGT---GGAGGT------GGTGGCGGCGAATGATAT
15732 ACTGGTGGAGGTGGTGGCGGCGAATGATAT
1 ACTGGTGGAGGTGGTGGCGGCGAATGATAT
* * *
15762 ACTGGTGGAGGAGGTGGTGGCGAGTGATAT
1 ACTGGTGGAGGTGGTGGCGGCGAATGATAT
15792 ACTGGTGGAGGTGGTGG
1 ACTGGTGGAGGTGGTGG
15809 TGAGCGTTTA
Statistics
Matches: 99, Mismatches: 8, Indels: 18
0.79 0.06 0.14
Matches are distributed among these distances:
30 65 0.66
33 6 0.06
36 6 0.06
39 22 0.22
ACGTcount: A:0.20, C:0.08, G:0.51, T:0.22
Consensus pattern (30 bp):
ACTGGTGGAGGTGGTGGCGGCGAATGATAT
Found at i:15710 original size:9 final size:9
Alignment explanation
Indices: 15696--15721 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
15686 ATGATATACT
15696 GGTGGAGGA
1 GGTGGAGGA
15705 GGTGGAGGA
1 GGTGGAGGA
15714 GGTGGAGG
1 GGTGGAGG
15722 CGAGTGATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.19, C:0.00, G:0.69, T:0.12
Consensus pattern (9 bp):
GGTGGAGGA
Found at i:15710 original size:39 final size:39
Alignment explanation
Indices: 15666--15778 Score: 136
Period size: 39 Copynumber: 3.1 Consensus size: 39
15656 ATCACTAACT
15666 GGTGGAGGTGGTGGCGGCGAATGATATACTGGTGGAGGA
1 GGTGGAGGTGGTGGCGGCGAATGATATACTGGTGGAGGA
* * *
15705 GGTGGAGGAGGTGGAGGCGAGTGATATAC---T------
1 GGTGGAGGTGGTGGCGGCGAATGATATACTGGTGGAGGA
15735 GGTGGAGGTGGTGGCGGCGAATGATATACTGGTGGAGGA
1 GGTGGAGGTGGTGGCGGCGAATGATATACTGGTGGAGGA
15774 GGTGG
1 GGTGG
15779 TGGCGAGTGA
Statistics
Matches: 59, Mismatches: 6, Indels: 18
0.71 0.07 0.22
Matches are distributed among these distances:
30 26 0.44
33 1 0.02
36 1 0.02
39 31 0.53
ACGTcount: A:0.20, C:0.07, G:0.52, T:0.20
Consensus pattern (39 bp):
GGTGGAGGTGGTGGCGGCGAATGATATACTGGTGGAGGA
Found at i:15809 original size:30 final size:30
Alignment explanation
Indices: 15705--15810 Score: 167
Period size: 30 Copynumber: 3.5 Consensus size: 30
15695 TGGTGGAGGA
*
15705 GGTGGAGGAGGTGGAGGCGAGTGATATACT
1 GGTGGAGGAGGTGGTGGCGAGTGATATACT
* * *
15735 GGTGGAGGTGGTGGCGGCGAATGATATACT
1 GGTGGAGGAGGTGGTGGCGAGTGATATACT
15765 GGTGGAGGAGGTGGTGGCGAGTGATATACT
1 GGTGGAGGAGGTGGTGGCGAGTGATATACT
*
15795 GGTGGAGGTGGTGGTG
1 GGTGGAGGAGGTGGTG
15811 AGCGTTTAGG
Statistics
Matches: 69, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 69 1.00
ACGTcount: A:0.19, C:0.07, G:0.52, T:0.23
Consensus pattern (30 bp):
GGTGGAGGAGGTGGTGGCGAGTGATATACT
Found at i:15823 original size:51 final size:50
Alignment explanation
Indices: 15767--15907 Score: 178
Period size: 48 Copynumber: 2.8 Consensus size: 50
15757 GATATACTGG
* * *
15767 TGGAGGAGGTGGTGGCGAGTGATATACTGGTGGAGGTGGTGGTGAGCGTT
1 TGGAGGAGGCGGTGGCGAGTGATACACTGGTGGAGGTGGTGGTGAACGTT
15817 T--AGGAGGCGGTGGCGAGTGATACACTGGTGGAGGTGGTGGTGGTGAACGTT
1 TGGAGGAGGCGGTGGCGAGTGATACACTGGTGGA---GGTGGTGGTGAACGTT
* * *
15868 TAGGAGGTGGCGGCGGCGAATGATACACTGGTGGAGGTGG
1 T-GGAGGAGGCGGTGGCGAGTGATACACTGGTGGAGGTGG
15908 CGGCGGCGAA
Statistics
Matches: 79, Mismatches: 6, Indels: 11
0.82 0.06 0.11
Matches are distributed among these distances:
48 29 0.37
50 1 0.01
51 21 0.27
54 28 0.35
ACGTcount: A:0.18, C:0.09, G:0.50, T:0.23
Consensus pattern (50 bp):
TGGAGGAGGCGGTGGCGAGTGATACACTGGTGGAGGTGGTGGTGAACGTT
Found at i:15852 original size:24 final size:24
Alignment explanation
Indices: 15777--15853 Score: 59
Period size: 24 Copynumber: 3.2 Consensus size: 24
15767 TGGAGGAGGT
*
15777 GGTGGCGAGTGATATACTGGTGGA
1 GGTGGCGAGTGATACACTGGTGGA
* * ** * *
15801 GGTGGTG-GTGA-GCGTTTAGGAGGC
1 GGTGGCGAGTGATAC-ACT-GGTGGA
15825 GGTGGCGAGTGATACACTGGTGGA
1 GGTGGCGAGTGATACACTGGTGGA
15849 GGTGG
1 GGTGG
15854 TGGTGGTGAA
Statistics
Matches: 36, Mismatches: 13, Indels: 8
0.63 0.23 0.14
Matches are distributed among these distances:
23 5 0.14
24 25 0.69
25 5 0.14
26 1 0.03
ACGTcount: A:0.17, C:0.09, G:0.51, T:0.23
Consensus pattern (24 bp):
GGTGGCGAGTGATACACTGGTGGA
Found at i:15880 original size:54 final size:53
Alignment explanation
Indices: 15768--15907 Score: 182
Period size: 54 Copynumber: 2.7 Consensus size: 53
15758 ATATACTGGT
* * *
15768 GGAGGAGGTGGTGGCGAGTGATATACTGGTGGA---GGTGGTGGTGAGCGTTTA
1 GGAGG-GGCGGTGGCGAGTGATACACTGGTGGAGGTGGTGGTGGTGAACGTTTA
15819 GGA--GGCGGTGGCGAGTGATACACTGGTGGAGGTGGTGGTGGTGAACGTTTA
1 GGAGGGGCGGTGGCGAGTGATACACTGGTGGAGGTGGTGGTGGTGAACGTTTA
* *
15870 GGAGGTGGCGGCGGCGAATGATACACTGGTGGAGGTGG
1 GGAGG-GGCGGTGGCGAGTGATACACTGGTGGAGGTGG
15908 CGGCGGCGAA
Statistics
Matches: 78, Mismatches: 5, Indels: 9
0.85 0.05 0.10
Matches are distributed among these distances:
48 25 0.32
51 23 0.29
54 30 0.38
ACGTcount: A:0.18, C:0.09, G:0.51, T:0.22
Consensus pattern (53 bp):
GGAGGGGCGGTGGCGAGTGATACACTGGTGGAGGTGGTGGTGGTGAACGTTTA
Found at i:15904 original size:30 final size:32
Alignment explanation
Indices: 15870--15942 Score: 114
Period size: 30 Copynumber: 2.3 Consensus size: 32
15860 TGAACGTTTA
15870 GGAGGTGGCGGCGGCGAATG-ATAC-ACTGGT
1 GGAGGTGGCGGCGGCGAATGAATACTACTGGT
15900 GGAGGTGGCGGCGGCGAATGATATACTACTGGT
1 GGAGGTGGCGGCGGCGAATGA-ATACTACTGGT
*
15933 GGAGGAGGCG
1 GGAGGTGGCG
15943 ATGGAGGCGG
Statistics
Matches: 39, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
30 20 0.51
32 4 0.10
33 15 0.38
ACGTcount: A:0.21, C:0.15, G:0.48, T:0.16
Consensus pattern (32 bp):
GGAGGTGGCGGCGGCGAATGAATACTACTGGT
Found at i:27674 original size:19 final size:21
Alignment explanation
Indices: 27650--27690 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
27640 AAAGGTGTCC
27650 ATATTGCA-TA-TATATATAT
1 ATATTGCAGTACTATATATAT
*
27669 ATATTGGAGTACTATATATAT
1 ATATTGCAGTACTATATATAT
27690 A
1 A
27691 GAATATTCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 7 0.37
20 2 0.11
21 10 0.53
ACGTcount: A:0.41, C:0.05, G:0.10, T:0.44
Consensus pattern (21 bp):
ATATTGCAGTACTATATATAT
Found at i:28004 original size:15 final size:16
Alignment explanation
Indices: 27972--28009 Score: 60
Period size: 15 Copynumber: 2.4 Consensus size: 16
27962 CTTGCTCTAC
27972 ATTTCATAACAAATTA
1 ATTTCATAACAAATTA
*
27988 ATTTCATAA-ATATTA
1 ATTTCATAACAAATTA
28003 ATTTCAT
1 ATTTCAT
28010 TAATTAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 12 0.57
16 9 0.43
ACGTcount: A:0.45, C:0.11, G:0.00, T:0.45
Consensus pattern (16 bp):
ATTTCATAACAAATTA
Found at i:36149 original size:21 final size:21
Alignment explanation
Indices: 36125--36171 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
36115 TCTTACAGGG
*
36125 AGGTTATAAAAAATCATAGGA
1 AGGTTACAAAAAATCATAGGA
** *
36146 AGGTTACAAAATTTTATAGGA
1 AGGTTACAAAAAATCATAGGA
36167 AGGTT
1 AGGTT
36172 TATTAATATT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.45, C:0.04, G:0.21, T:0.30
Consensus pattern (21 bp):
AGGTTACAAAAAATCATAGGA
Found at i:36195 original size:44 final size:44
Alignment explanation
Indices: 36146--36296 Score: 137
Period size: 44 Copynumber: 3.4 Consensus size: 44
36136 AATCATAGGA
* * *
36146 AGGTTA-CAAAATTTTATAGGAAGGTTTATTAATATTTCATAGTT
1 AGGTTATCAAAATTTCATAGGAA-GTTTATCAAAATTTCATAGTT
* * * *
36190 AGGTTATCTAAGTTTCATATGAAGTTTATCAAAATTTCATAGGT
1 AGGTTATCAAAATTTCATAGGAAGTTTATCAAAATTTCATAGTT
** * * *
36234 AAATTATCAAAATTTCATAGTGTAG-TTATCAAAATTTAATAAGAT
1 AGGTTATCAAAATTTCATAG-GAAGTTTATCAAAATTTCAT-AGTT
*
36279 A-GTTACCAAAATTTCATA
1 AGGTTATCAAAATTTCATA
36297 AAAATATTCA
Statistics
Matches: 87, Mismatches: 17, Indels: 6
0.79 0.15 0.05
Matches are distributed among these distances:
44 68 0.78
45 19 0.22
ACGTcount: A:0.40, C:0.08, G:0.13, T:0.40
Consensus pattern (44 bp):
AGGTTATCAAAATTTCATAGGAAGTTTATCAAAATTTCATAGTT
Found at i:36240 original size:22 final size:22
Alignment explanation
Indices: 36138--36296 Score: 114
Period size: 22 Copynumber: 7.2 Consensus size: 22
36128 TTATAAAAAA
36138 TCATAGG-AAGGTTA-CAAAATT
1 TCATAGGTAA-GTTATCAAAATT
* * *
36159 TTATAGG-AAGGTTTATTAATATT
1 TCATAGGTAA-G-TTATCAAAATT
* * * *
36182 TCATAGTTAGGTTATCTAAGTT
1 TCATAGGTAAGTTATCAAAATT
*
36204 TCATATG-AAGTTTATCAAAATT
1 TCATAGGTAAG-TTATCAAAATT
*
36226 TCATAGGTAAATTATCAAAATT
1 TCATAGGTAAGTTATCAAAATT
36248 TCATAGTGT-AGTTATCAAAATT
1 TCATAG-GTAAGTTATCAAAATT
* * *
36270 TAATAAG-ATAGTTACCAAAATT
1 TCATAGGTA-AGTTATCAAAATT
36292 TCATA
1 TCATA
36297 AAAATATTCA
Statistics
Matches: 108, Mismatches: 22, Indels: 15
0.74 0.15 0.10
Matches are distributed among these distances:
21 13 0.12
22 79 0.73
23 15 0.14
24 1 0.01
ACGTcount: A:0.40, C:0.08, G:0.13, T:0.39
Consensus pattern (22 bp):
TCATAGGTAAGTTATCAAAATT
Found at i:36607 original size:31 final size:31
Alignment explanation
Indices: 36569--36734 Score: 114
Period size: 31 Copynumber: 5.5 Consensus size: 31
36559 CTTGACTAAT
*
36569 TGCTCAAATGAGGGCCTAACATTTATCAAAA
1 TGCTCAAATAAGGGCCTAACATTTATCAAAA
** * **
36600 TGCTCAAATAAGGGATTGATC-TTT-T-AATT
1 TGCTCAAATAAGGGCCT-AACATTTATCAAAA
* *
36629 TGGTCAAATAAGGGCCTAATA-TTATCAAAAA
1 TGCTCAAATAAGGGCCTAACATTTATC-AAAA
* * * **
36660 TGCTCAAATCATGGCCTGATC-TTT-T-AATT
1 TGCTCAAATAAGGGCCT-AACATTTATCAAAA
*
36689 TGATCAAATAAGGGCCTAACA-TTATCGAAAA
1 TGCTCAAATAAGGGCCTAACATTTATC-AAAA
36720 TGCTCAAATAAGGGC
1 TGCTCAAATAAGGGC
36735 TTGATCTTTT
Statistics
Matches: 97, Mismatches: 27, Indels: 22
0.66 0.18 0.15
Matches are distributed among these distances:
28 7 0.07
29 34 0.35
30 1 0.01
31 50 0.52
32 5 0.05
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.30
Consensus pattern (31 bp):
TGCTCAAATAAGGGCCTAACATTTATCAAAA
Found at i:36660 original size:60 final size:60
Alignment explanation
Indices: 36572--36794 Score: 313
Period size: 60 Copynumber: 3.7 Consensus size: 60
36562 GACTAATTGC
*
36572 TCAAATGAGGGCCTAACATTTATC-AAAATGCTCAAATAAGGGATTGATCTTTTAATTTGG
1 TCAAATAAGGGCCTAACA-TTATCGAAAATGCTCAAATAAGGGATTGATCTTTTAATTTGG
* * * * ** *
36632 TCAAATAAGGGCCTAATATTATCAAAAATGCTCAAATCATGGCCTGATCTTTTAATTTGA
1 TCAAATAAGGGCCTAACATTATCGAAAATGCTCAAATAAGGGATTGATCTTTTAATTTGG
*
36692 TCAAATAAGGGCCTAACATTATCGAAAATGCTCAAATAAGGGCTTGATCTTTTAATTTGG
1 TCAAATAAGGGCCTAACATTATCGAAAATGCTCAAATAAGGGATTGATCTTTTAATTTGG
* * * *
36752 CCAAATAAAGGCCTAACGTTATTGAAAATGCTCAAATAAGGGA
1 TCAAATAAGGGCCTAACATTATCGAAAATGCTCAAATAAGGGA
36795 CTGACGTCAG
Statistics
Matches: 144, Mismatches: 18, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
59 5 0.03
60 139 0.97
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.30
Consensus pattern (60 bp):
TCAAATAAGGGCCTAACATTATCGAAAATGCTCAAATAAGGGATTGATCTTTTAATTTGG
Found at i:36705 original size:29 final size:29
Alignment explanation
Indices: 36600--36765 Score: 111
Period size: 29 Copynumber: 5.6 Consensus size: 29
36590 TTTATCAAAA
**
36600 TGCTCAAATAAGGGATTGATCTTTTAATT
1 TGCTCAAATAAGGGCCTGATCTTTTAATT
* * * * **
36629 TGGTCAAATAAGGGCCTAATATTATCAAAAA
1 TGCTCAAATAAGGGCCTGATCTT-T-TAATT
* *
36660 TGCTCAAATCATGGCCTGATCTTTTAATT
1 TGCTCAAATAAGGGCCTGATCTTTTAATT
* * * **
36689 TGATCAAATAAGGGCCT-AACATTATCGAAAA
1 TGCTCAAATAAGGGCCTGATC-TT-T-TAATT
*
36720 TGCTCAAATAAGGGCTTGATCTTTTAATT
1 TGCTCAAATAAGGGCCTGATCTTTTAATT
*
36749 TGGC-CAAATAAAGGCCT
1 T-GCTCAAATAAGGGCCT
36766 AACGTTATTG
Statistics
Matches: 99, Mismatches: 31, Indels: 14
0.69 0.22 0.10
Matches are distributed among these distances:
28 2 0.02
29 50 0.51
30 6 0.06
31 39 0.39
32 2 0.02
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.33
Consensus pattern (29 bp):
TGCTCAAATAAGGGCCTGATCTTTTAATT
Found at i:36785 original size:120 final size:120
Alignment explanation
Indices: 36572--36788 Score: 346
Period size: 120 Copynumber: 1.8 Consensus size: 120
36562 GACTAATTGC
* *
36572 TCAAATGAGGGCCTAACATTTATCAAAATGCTCAAATAAGGGATTGATCTTTTAATTTGGTCAAA
1 TCAAATAAGGGCCTAACATTTATCAAAATGCTCAAATAAGGGATTGATCTTTTAATTTGGCCAAA
* *
36637 TAAGGGCCTAATATTATCAAAAATGCTCAAATCATGGCCTGATCTTTTAATTTGA
66 TAAAGGCCTAACATTATCAAAAATGCTCAAATCATGGCCTGATCTTTTAATTTGA
*
36692 TCAAATAAGGGCCTAACA-TTATCGAAAATGCTCAAATAAGGGCTTGATCTTTTAATTTGGCCAA
1 TCAAATAAGGGCCTAACATTTATC-AAAATGCTCAAATAAGGGATTGATCTTTTAATTTGGCCAA
* **
36756 ATAAAGGCCTAACGTTATTGAAAATGCTCAAAT
65 ATAAAGGCCTAACATTATCAAAAATGCTCAAAT
36789 AAGGGACTGA
Statistics
Matches: 88, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
119 5 0.06
120 83 0.94
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.31
Consensus pattern (120 bp):
TCAAATAAGGGCCTAACATTTATCAAAATGCTCAAATAAGGGATTGATCTTTTAATTTGGCCAAA
TAAAGGCCTAACATTATCAAAAATGCTCAAATCATGGCCTGATCTTTTAATTTGA
Found at i:36870 original size:31 final size:31
Alignment explanation
Indices: 36825--36999 Score: 123
Period size: 31 Copynumber: 5.8 Consensus size: 31
36815 GCAGTTTTCG
*
36825 ACGTCAGGCCCTTATTTGAGCATTTTGGCAA
1 ACGTTAGGCCCTTATTTGAGCATTTTGGCAA
** **
36856 ACGTTAGGTTCTTATTTG-GCCAAATT---AA
1 ACGTTAGGCCCTTATTTGAG-CATTTTGGCAA
* *
36884 AAGATTAGACCCTTATTTGAGCATTTTGGCAA
1 ACG-TTAGGCCCTTATTTGAGCATTTTGGCAA
**
36916 ACGTTAGGCCCTTATTTG-GCCAAATT---AA
1 ACGTTAGGCCCTTATTTGAG-CATTTTGGCAA
* * * **
36944 AAGATCAGACCCTTATTTGAGCATTTTTACAA
1 ACG-TTAGGCCCTTATTTGAGCATTTTGGCAA
*
36976 ATGTTAGGCCCTTATTTGAGCATT
1 ACGTTAGGCCCTTATTTGAGCATT
37000 AGCCTATACA
Statistics
Matches: 109, Mismatches: 23, Indels: 24
0.70 0.15 0.15
Matches are distributed among these distances:
28 8 0.07
29 33 0.30
30 4 0.04
31 56 0.51
32 8 0.07
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.35
Consensus pattern (31 bp):
ACGTTAGGCCCTTATTTGAGCATTTTGGCAA
Found at i:36898 original size:29 final size:29
Alignment explanation
Indices: 36866--36962 Score: 99
Period size: 29 Copynumber: 3.3 Consensus size: 29
36856 ACGTTAGGTT
36866 CTTATTTGGCCAAATTAAAAGATTAGACC
1 CTTATTTGGCCAAATTAAAAGATTAGACC
** * *
36895 CTTATTTGAG-CATTTTGGCAAACG-TTAGGCC
1 CTTATTTG-GCCAAATT---AAAAGATTAGACC
*
36926 CTTATTTGGCCAAATTAAAAGATCAGACC
1 CTTATTTGGCCAAATTAAAAGATTAGACC
36955 CTTATTTG
1 CTTATTTG
36963 AGCATTTTTA
Statistics
Matches: 53, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
28 4 0.08
29 25 0.47
30 2 0.04
31 18 0.34
32 4 0.08
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (29 bp):
CTTATTTGGCCAAATTAAAAGATTAGACC
Found at i:36906 original size:60 final size:60
Alignment explanation
Indices: 36828--36993 Score: 269
Period size: 60 Copynumber: 2.8 Consensus size: 60
36818 GTTTTCGACG
* **
36828 TCAGGCCCTTATTTGAGCATTTTGGCAAACGTTAGGTTCTTATTTGGCCAAATTAAAAGA
1 TCAGACCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGA
*
36888 TTAGACCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGA
1 TCAGACCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGA
** *
36948 TCAGACCCTTATTTGAGCATTTTTACAAATGTTAGGCCCTTATTTG
1 TCAGACCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTG
36994 AGCATTAGCC
Statistics
Matches: 98, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
60 98 1.00
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (60 bp):
TCAGACCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGA
Found at i:38049 original size:33 final size:33
Alignment explanation
Indices: 38006--38069 Score: 119
Period size: 33 Copynumber: 1.9 Consensus size: 33
37996 GTGACCTATA
*
38006 TCCACGAGCAGGAAGAGAGATTTTCTTATTTCT
1 TCCACCAGCAGGAAGAGAGATTTTCTTATTTCT
38039 TCCACCAGCAGGAAGAGAGATTTTCTTATTT
1 TCCACCAGCAGGAAGAGAGATTTTCTTATTT
38070 TTTGAGAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Consensus pattern (33 bp):
TCCACCAGCAGGAAGAGAGATTTTCTTATTTCT
Found at i:43202 original size:1 final size:1
Alignment explanation
Indices: 43196--43285 Score: 81
Period size: 1 Copynumber: 90.0 Consensus size: 1
43186 TAGCTTTCGT
* * * * * * * *
43196 AAAAAAAAAAAAAAAGAACAAAACAAAAAACAAAAAAAAAAAACAAAAAACAAAAAACAAAAAAC
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * *
43261 AAAAAACAAAAAACAAAAACAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
43286 CTGGTAGCTG
Statistics
Matches: 67, Mismatches: 22, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 67 1.00
ACGTcount: A:0.88, C:0.11, G:0.01, T:0.00
Consensus pattern (1 bp):
A
Found at i:43223 original size:14 final size:14
Alignment explanation
Indices: 43198--43285 Score: 135
Period size: 14 Copynumber: 6.4 Consensus size: 14
43188 GCTTTCGTAA
* *
43198 AAAAAAAAAAAAAG
1 AAAAAACAAAAAAC
43212 AACAAAACAAAAAAC
1 AA-AAAACAAAAAAC
43227 AAAAAA-AAAAAAC
1 AAAAAACAAAAAAC
43240 AAAAAACAAAAAAC
1 AAAAAACAAAAAAC
43254 AAAAAACAAAAAAC
1 AAAAAACAAAAAAC
43268 AAAAAAC-AAAAAC
1 AAAAAACAAAAAAC
43281 AAAAA
1 AAAAA
43286 CTGGTAGCTG
Statistics
Matches: 70, Mismatches: 2, Indels: 5
0.91 0.03 0.06
Matches are distributed among these distances:
13 24 0.34
14 34 0.49
15 12 0.17
ACGTcount: A:0.88, C:0.11, G:0.01, T:0.00
Consensus pattern (14 bp):
AAAAAACAAAAAAC
Found at i:43245 original size:27 final size:27
Alignment explanation
Indices: 43199--43285 Score: 140
Period size: 27 Copynumber: 3.2 Consensus size: 27
43189 CTTTCGTAAA
*
43199 AAAAAAAAAAAAGAACAAAACAAAAAAC
1 AAAAAAAAAAAACAA-AAAACAAAAAAC
43227 AAAAAAAAAAAACAAAAAACAAAAAAC
1 AAAAAAAAAAAACAAAAAACAAAAAAC
43254 AAAAAACAAAAAACAAAAAAC-AAAAAC
1 AAAAAA-AAAAAACAAAAAACAAAAAAC
43281 AAAAA
1 AAAAA
43286 CTGGTAGCTG
Statistics
Matches: 57, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
27 29 0.51
28 28 0.49
ACGTcount: A:0.87, C:0.11, G:0.01, T:0.00
Consensus pattern (27 bp):
AAAAAAAAAAAACAAAAAACAAAAAAC
Found at i:43280 original size:34 final size:33
Alignment explanation
Indices: 43196--43285 Score: 137
Period size: 34 Copynumber: 2.7 Consensus size: 33
43186 TAGCTTTCGT
*
43196 AAAAAAAAAA-AAAAAGAACAAAACAAAAAACAA
1 AAAAAAAAAACAAAAACAA-AAAACAAAAAACAA
43229 AAAAAAAAAACAAAAAACAAAAAACAAAAAACAA
1 AAAAAAAAAAC-AAAAACAAAAAACAAAAAACAA
43263 AAAACAAAAAACAAAAACAAAAA
1 AAAA-AAAAAACAAAAACAAAAA
43286 CTGGTAGCTG
Statistics
Matches: 53, Mismatches: 1, Indels: 5
0.90 0.02 0.08
Matches are distributed among these distances:
33 10 0.19
34 29 0.55
35 14 0.26
ACGTcount: A:0.88, C:0.11, G:0.01, T:0.00
Consensus pattern (33 bp):
AAAAAAAAAACAAAAACAAAAAACAAAAAACAA
Found at i:44113 original size:44 final size:44
Alignment explanation
Indices: 44048--44172 Score: 151
Period size: 44 Copynumber: 2.8 Consensus size: 44
44038 TGACAATCAA
* * * * *
44048 ACCAAAATTACATAGAAAGATTATCAAAATTTCGTAGTGTTGTT
1 ACCAAAATTTCATACAGAGATTATCAAAATTTCATAGTGTAGTT
* * *
44092 ACCAAATTTTCATATAGAGATTATCAAAACTTCATAGTGTAGTT
1 ACCAAAATTTCATACAGAGATTATCAAAATTTCATAGTGTAGTT
* * *
44136 ATCAAAATTTCATACAGAGGTTACCAAAATTTCATAG
1 ACCAAAATTTCATACAGAGATTATCAAAATTTCATAG
44173 GGAGGGAGGT
Statistics
Matches: 68, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
44 68 1.00
ACGTcount: A:0.41, C:0.14, G:0.12, T:0.34
Consensus pattern (44 bp):
ACCAAAATTTCATACAGAGATTATCAAAATTTCATAGTGTAGTT
Found at i:44177 original size:22 final size:22
Alignment explanation
Indices: 44048--44193 Score: 96
Period size: 22 Copynumber: 6.5 Consensus size: 22
44038 TGACAATCAA
* * *
44048 ACCAAAATTACATAGAAAGATT
1 ACCAAAATTTCATAGAGAGGTT
* * * **
44070 ATCAAAATTTCGTAGTGTTGTT
1 ACCAAAATTTCATAGAGAGGTT
* * *
44092 ACCAAATTTTCATATAGAGATT
1 ACCAAAATTTCATAGAGAGGTT
* * *
44114 ATCAAAACTTCATAGTGTA-GTT
1 ACCAAAATTTCATAGAG-AGGTT
* *
44136 ATCAAAATTTCATACAGAGGTT
1 ACCAAAATTTCATAGAGAGGTT
44158 ACCAAAATTTCATAGGGAGGGAGGTT
1 ACCAAAATTTCATA--GA--GAGGTT
44184 ACCAAAATTT
1 ACCAAAATTT
44194 GTGCTTATCA
Statistics
Matches: 91, Mismatches: 27, Indels: 8
0.72 0.21 0.06
Matches are distributed among these distances:
21 1 0.01
22 72 0.79
23 1 0.01
24 1 0.01
26 16 0.18
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.32
Consensus pattern (22 bp):
ACCAAAATTTCATAGAGAGGTT
Found at i:44264 original size:22 final size:23
Alignment explanation
Indices: 44217--44274 Score: 68
Period size: 22 Copynumber: 2.6 Consensus size: 23
44207 TTTCCTAAAG
* *
44217 AGGTTAAC-AAAATTTTATAGGG
1 AGGTTATCGAAAATTTTATAGGA
44239 AGGTTAT-GAAAATTTTAT-GGAA
1 AGGTTATCGAAAATTTTATAGG-A
44261 AGGTTATCGAAAAT
1 AGGTTATCGAAAAT
44275 ACATATAGAG
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
21 2 0.06
22 23 0.74
23 6 0.19
ACGTcount: A:0.41, C:0.03, G:0.22, T:0.33
Consensus pattern (23 bp):
AGGTTATCGAAAATTTTATAGGA
Found at i:44337 original size:22 final size:22
Alignment explanation
Indices: 44303--44546 Score: 158
Period size: 22 Copynumber: 11.1 Consensus size: 22
44293 AGTTTCATTC
* *
44303 TCATAGGGAGGTTATCAAAATT
1 TCATAGTGTGGTTATCAAAATT
*
44325 TCATGGTGTGGTTATCAAAATTT
1 TCATAGTGTGGTTATCAAAA-TT
* *
44348 TCATAGTGCGGTTA-C-CAATT
1 TCATAGTGTGGTTATCAAAATT
* * *
44368 TTATTTAGTGTGATTATTAAAATT
1 TCA--TAGTGTGGTTATCAAAATT
* * *
44392 TTATAG-GCAGATTATCAAAATT
1 TCATAGTG-TGGTTATCAAAATT
* * * * *
44414 TCACACTGAGATTATCGAAATT
1 TCATAGTGTGGTTATCAAAATT
* *
44436 TCATAGTGTGGTTACCCAAATT
1 TCATAGTGTGGTTATCAAAATT
* *
44458 TCATAGTGTGGTTATCGAATTT
1 TCATAGTGTGGTTATCAAAATT
* * *
44480 TCATAGGGAGGTTATCGAAATT
1 TCATAGTGTGGTTATCAAAATT
44502 TCATA-T-TAGGTTATC-AAATT
1 TCATAGTGT-GGTTATCAAAATT
* * *
44522 TGCAAAATGTGGTTATCAATATT
1 T-CATAGTGTGGTTATCAAAATT
44545 TC
1 TC
44547 TACGCTGGAG
Statistics
Matches: 177, Mismatches: 33, Indels: 24
0.76 0.14 0.10
Matches are distributed among these distances:
20 10 0.06
21 13 0.07
22 126 0.71
23 21 0.12
24 7 0.04
ACGTcount: A:0.32, C:0.11, G:0.18, T:0.39
Consensus pattern (22 bp):
TCATAGTGTGGTTATCAAAATT
Found at i:44963 original size:167 final size:166
Alignment explanation
Indices: 44634--45033 Score: 403
Period size: 167 Copynumber: 2.4 Consensus size: 166
44624 ATTACATTTA
* * * * * ** **
44634 AATAGAGTTTATTGTAAAGTGGACTCGCCAAATAAAGCTTTCTAAAAAGCCTAAAACCTCAACTT
1 AATAGAGCTAATTGGAAAGTGG-CTTGCCAAAAAAAAATTTCTTCAAAGCCTAAAACCTCAACTT
* *
44699 CCCGATTTAGCACGTTTGAGCGCCAAACCTTATTCTCAGGAAAATGCTCATTCCAAGTACATTAT
65 CACGATTTAGCACGTTTGAGCGCCAAACCTTATTCTCAGGAAAATGCTAATTCCAAGTACATTAT
* * * *
44764 TTGTGAAACCAACGTTCAAATGTTATGTTTCAGAGTG
130 TTGTGAAACCAACGCTCAAATGTCAGGTTTCAGAGTC
* * * *
44801 AGTA-AGCTAATTGGAAAGTGGGTTTGCCAACAAAAAAATTTCTTCAAAGCCTAAAACTTAAACT
1 AATAGAGCTAATTGGAAAGT-GGCTTGCCAA-AAAAAAATTTCTTCAAAGCCTAAAACCTCAACT
* ** * * * * *
44865 TCACGATTTTGCGTGTTTGTGCG-CAGAACGTTATTCT-TGAGAAAATGTTAATTCCGAA-TGCA
64 TCACGATTTAGCACGTTTGAGCGCCA-AACCTTATTCTCAG-GAAAATGCTAATTCC-AAGTACA
* * *
44927 TTATTTGTGTAACCATCGCTCATATGTCAGGTTTCAGAGTC
126 TTATTTGTGAAACCAACGCTCAAATGTCAGGTTTCAGAGTC
* * ** *
44968 AATAGAGCTCATTGGAAAGTGGCTTGCCAAACAAATTTTTCTTCAAAGGCTAAAACCTCAACTTC
1 AATAGAGCTAATTGGAAAGTGGCTTGCCAAAAAAAAATTTCTTCAAAGCCTAAAACCTCAACTTC
45033 A
66 A
45034 AAATTTTGTA
Statistics
Matches: 188, Mismatches: 39, Indels: 13
0.78 0.16 0.05
Matches are distributed among these distances:
166 51 0.27
167 121 0.64
168 16 0.09
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (166 bp):
AATAGAGCTAATTGGAAAGTGGCTTGCCAAAAAAAAATTTCTTCAAAGCCTAAAACCTCAACTTC
ACGATTTAGCACGTTTGAGCGCCAAACCTTATTCTCAGGAAAATGCTAATTCCAAGTACATTATT
TGTGAAACCAACGCTCAAATGTCAGGTTTCAGAGTC
Found at i:46316 original size:22 final size:22
Alignment explanation
Indices: 46275--46860 Score: 175
Period size: 22 Copynumber: 26.4 Consensus size: 22
46265 ACAATCAAAC
* *
46275 CAAAATTACATAGTAAGGTTAT
1 CAAAATTTCATAGTGAGGTTAT
* * *
46297 TAAAATTTCATAGTGTGGTTAC
1 CAAAATTTCATAGTGAGGTTAT
46319 CAAAATTTCATA-TGGAGGTTAT
1 CAAAATTTCATAGT-GAGGTTAT
* * *
46341 CAAAACTTCGTAGTGTA-ATTAT
1 CAAAATTTCATAGTG-AGGTTAT
** *
46363 CAAAATTTCATACAGAGGTTAC
1 CAAAATTTCATAGTGAGGTTAT
***
46385 CAAAATTTCATAAAAAAAGGTTAT
1 CAAAATTTCAT--AGTGAGGTTAT
* * *
46409 CAAAATCTCTTA-TGGAGATTAT
1 CAAAATTTCATAGT-GAGGTTAT
*
46431 CAAAATTTCATACG-AAGGTTAT
1 CAAAATTTCATA-GTGAGGTTAT
** * * *
46453 TGAAATTTTATAGTGTGATTAT
1 CAAAATTTCATAGTGAGGTTAT
* * *
46475 CAAAA-TTAATTAG-AACGTTAT
1 CAAAATTTCA-TAGTGAGGTTAT
**
46496 CAAAA-TT--T-GT--TCTTAT
1 CAAAATTTCATAGTGAGGTTAT
* *
46512 CAAAATTTCCCT-G-GATGGTTAA
1 CAAAATTT-CATAGTGA-GGTTAT
* **
46534 CAAAATTTCATAGGGAACTTAT
1 CAAAATTTCATAGTGAGGTTAT
* * *
46556 GAAAATATT-ATGGAGAGGTTAT
1 CAAAAT-TTCATAGTGAGGTTAT
* **
46578 CAAAATTACATA-TAGAGAATAT
1 CAAAATTTCATAGT-GAGGTTAT
* * *
46600 CACAATTTCATTCTTATAGGGAAGTTAT
1 CA-AA----ATT-TCATAGTGAGGTTAT
* * *
46628 CGAAATTTCATGGTGTGGTTAT
1 CAAAATTTCATAGTGAGGTTAT
* *
46650 CAAAATTTTCATAGTGCGATTA-
1 CAAAA-TTTCATAGTGAGGTTAT
* * * *
46672 C-CAATTTTATAAT-ATGATTAT
1 CAAAATTTCATAGTGA-GGTTAT
46693 CAAAATTTCATAGACAATGAGGTTAT
1 CAAAATTTCATAG----TGAGGTTAT
* * *
46719 CAAAACTTCATTGTGTGGTTAT
1 CAAAATTTCATAGTGAGGTTAT
* * *
46741 CAGAATTTCACAGTGTGGTTAT
1 CAAAATTTCATAGTGAGGTTAT
* * * *
46763 CAGAATTTCACATTGTGGTTAT
1 CAAAATTTCATAGTGAGGTTAT
* * *
46785 CAAATTTTCATAGGGAGGTAAAT
1 CAAAATTTCATAGTGAGGT-TAT
* * *
46808 CGAAATTTCACAATGAGGTTAT
1 CAAAATTTCATAGTGAGGTTAT
* ** *
46830 CAAATTTTCGCAGTGTGGTTAT
1 CAAAATTTCATAGTGAGGTTAT
*
46852 CAATATTTC
1 CAAAATTTC
46861 TACGTTGGAG
Statistics
Matches: 409, Mismatches: 114, Indels: 82
0.68 0.19 0.14
Matches are distributed among these distances:
16 9 0.02
17 3 0.01
18 1 0.00
20 14 0.03
21 23 0.06
22 270 0.66
23 40 0.10
24 17 0.04
26 17 0.04
27 6 0.01
28 9 0.02
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.36
Consensus pattern (22 bp):
CAAAATTTCATAGTGAGGTTAT
Found at i:46440 original size:68 final size:65
Alignment explanation
Indices: 46293--46451 Score: 169
Period size: 68 Copynumber: 2.4 Consensus size: 65
46283 CATAGTAAGG
* * * *** *
46293 TTATTAAAATTTCATAGTGTGGTTACCAAAATTTCATATGGAGGTTATCAAAACTTCGTAGTGTA
1 TTATCAAAATTTCATA-CGAGGTTACCAAAATTTCATAAAAAGGTTATCAAAACTTCGTAGTGGA
46358 A
65 A
*
46359 TTATCAAAATTTCATACAGAGGTTACCAAAATTTCATAAAAAAAGGTTATCAAAA-TCTCTTA-T
1 TTATCAAAATTTCATAC-GAGGTTACCAAAATTTCAT--AAAAAGGTTATCAAAACT-TCGTAGT
46422 GGAGA
62 GGA-A
46427 TTATCAAAATTTCATACGAAGGTTA
1 TTATCAAAATTTCATACG-AGGTTA
46452 TTGAAATTTT
Statistics
Matches: 79, Mismatches: 8, Indels: 10
0.81 0.08 0.10
Matches are distributed among these distances:
66 33 0.42
67 5 0.06
68 41 0.52
ACGTcount: A:0.40, C:0.12, G:0.14, T:0.35
Consensus pattern (65 bp):
TTATCAAAATTTCATACGAGGTTACCAAAATTTCATAAAAAGGTTATCAAAACTTCGTAGTGGAA
Found at i:53117 original size:53 final size:53
Alignment explanation
Indices: 53016--53127 Score: 129
Period size: 53 Copynumber: 2.1 Consensus size: 53
53006 ACAATCCAAT
* *
53016 AAATAATATAAGCAAAACTAAGCAAGATGTTAACATCAACTAATCAATAA-CA
1 AAATAATATAAGCAAAACTAAGCAAGATGCTAACATCAAATAATCAATAATCA
* * * * *
53068 AAATAAGTATGAGCAAAATTAAGCAAGGTGCTAATAT-AAATAATCCAATAATCT
1 AAATAA-TATAAGCAAAACTAAGCAAGATGCTAACATCAAATAAT-CAATAATCA
53122 AAATAA
1 AAATAA
53128 AATCTAAGCA
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
52 12 0.24
53 31 0.62
54 7 0.14
ACGTcount: A:0.54, C:0.12, G:0.10, T:0.23
Consensus pattern (53 bp):
AAATAATATAAGCAAAACTAAGCAAGATGCTAACATCAAATAATCAATAATCA
Found at i:53672 original size:41 final size:41
Alignment explanation
Indices: 53609--53693 Score: 111
Period size: 41 Copynumber: 2.1 Consensus size: 41
53599 TATGAAACCC
* *
53609 AAACCCTAACAAACAATATAAACCCTAAGTGAGAT-GAAAG
1 AAACCCTAAAAAACAATATAAACCCTAAGTGAGATAAAAAG
*
53649 AAACCCTCAAAAAACACAT-TAAACCCTAGGTGAGATAAAAAG
1 AAACCCT-AAAAAACA-ATATAAACCCTAAGTGAGATAAAAAG
53691 AAA
1 AAA
53694 AAAACATGAA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
40 7 0.18
41 23 0.59
42 9 0.23
ACGTcount: A:0.54, C:0.20, G:0.12, T:0.14
Consensus pattern (41 bp):
AAACCCTAAAAAACAATATAAACCCTAAGTGAGATAAAAAG
Done.