Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008154.1 Corchorus capsularis cultivar CVL-1 contig08175, 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: 79029
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Found at i:2497 original size:68 final size:68
Alignment explanation
Indices: 2388--2906 Score: 443
Period size: 66 Copynumber: 7.7 Consensus size: 68
2378 GGAAAGATTA
* *
2388 ATTTTGTTTTCCCAAAAATACCCTTTCGGCGGAAGGGTCATTTTCGTCTTTCCGCATTTTAGTTT
1 ATTTTGTTTTCCCAAAAATACCCTTTCGGTGGAAGGGTCATTTTCGTCTTTCCGCATTTAAGTTT
2453 AGT
66 AGT
* *
2456 ATTTTGTTTTCCCAAAAATACCCTTTTGGTGGAAGGGTCATTTCCGTCTTTCCGCATTTAAGTTT
1 ATTTTGTTTTCCCAAAAATACCCTTTCGGTGGAAGGGTCATTTTCGTCTTTCCGCATTTAAGTTT
*
2521 AGC
66 AGT
** **
2524 ATTTTGTTTTTTTCAAAAATACCCTTTCGGTGGAAGGGTCATTTTCGTCTTTTTGCATTTAAGTT
1 ATTTTG-TTTTCCCAAAAATACCCTTTCGGTGGAAGGGTCATTTTCGTCTTTCCGCATTTAAGTT
*
2589 TAAT
65 TAGT
* * * * * *
2593 ATTTTCTTTTCCAAAAAAATACCCTTTCGGTGGAAGGGTCAATTTCGTCTTT-TGCATTTAGGTA
1 ATTTTGTTTTCC-CAAAAATACCCTTTCGGTGGAAGGGTCATTTTCGTCTTTCCGCATTTAAGTT
*
2657 TGGT
65 TAGT
* ** * ** * * *
2661 ATTCT-CATTCCCAAAAATATCCTTTCGGTCAAAGGGTCAGTATT-GTCTTT-TGCATTCAAGTT
1 ATTTTGTTTTCCCAAAAATACCCTTTCGGTGGAAGGGTCA-TTTTCGTCTTTCCGCATTTAAGTT
2723 TAGT
65 TAGT
* ** * ** * *
2727 ATTCT-CATTCCCAAAAACACCCTTTCGGTCAAAGGGTCAGTATT-GTCTCTT--GCATTCAAGT
1 ATTTTGTTTTCCCAAAAATACCCTTTCGGTGGAAGGGTCA-TTTTCGTCT-TTCCGCATTTAAGT
2788 TTAGT
64 TTAGT
* ** * * * * * *
2793 ATTCT-CATTCCCAAGAATACCCTTTCGGT-CAAGGGTCAGTATT-GTCTTT-TGTATTCAAGTT
1 ATTTTGTTTTCCCAAAAATACCCTTTCGGTGGAAGGGTCA-TTTTCGTCTTTCCGCATTTAAGTT
2854 TAGT
65 TAGT
** * * * * *
2858 ATTTTCATTT-CCAAAAATACCCTTCCAGTCGAAGGATCATTTTTGTCTT
1 ATTTTGTTTTCCCAAAAATACCCTTTCGGTGGAAGGGTCATTTTCGTCTT
2907 GTGCATCTAA
Statistics
Matches: 393, Mismatches: 50, Indels: 18
0.85 0.11 0.04
Matches are distributed among these distances:
64 2 0.01
65 54 0.14
66 144 0.37
67 8 0.02
68 89 0.23
69 96 0.24
ACGTcount: A:0.23, C:0.19, G:0.16, T:0.41
Consensus pattern (68 bp):
ATTTTGTTTTCCCAAAAATACCCTTTCGGTGGAAGGGTCATTTTCGTCTTTCCGCATTTAAGTTT
AGT
Found at i:2709 original size:66 final size:66
Alignment explanation
Indices: 2396--2963 Score: 429
Period size: 66 Copynumber: 8.5 Consensus size: 66
2386 TAATTTTGTT
* * * **
2396 TTCCCAAAAATACCCTTTCGG-CGGAAGGGTCA-TTTTCGTCTTTCCGCATTTTAGTTTAGTATT
1 TTCCCAAAAATACCCTTTCGGTC-AAAGGGTCAGTATT-GTCTTT-TGCATTCAAGTTTAGTATT
* **
2459 TTGTT
63 CT-CA
* ** * * *
2464 TTCCCAAAAATACCCTTTTGGTGGAAGGGTCA-T-TTCCGTCTTTCCGCATTTAAGTTTAGCATT
1 TTCCCAAAAATACCCTTTCGGTCAAAGGGTCAGTATT--GTCTTT-TGCATTCAAGTTTAG--TA
* **
2527 TTGTTT
61 TTCTCA
** ** * * * *
2533 TTTTCAAAAATACCCTTTCGGTGGAAGGGTCA-TTTTCGTCTTTTTGCATTTAAGTTTAATATTT
1 TTCCCAAAAATACCCTTTCGGTCAAAGGGTCAGTATT-GTC-TTTTGCATTCAAGTTTAGTATTC
*
2597 TCTT
64 TC-A
* ** * * * * *
2601 TTCCAAAAAAATACCCTTTCGGTGGAAGGGTCAAT-TTCGTCTTTTGCATTTAGGTATGGTATTC
1 TTCC-CAAAAATACCCTTTCGGTCAAAGGGTCAGTATT-GTCTTTTGCATTCAAGTTTAGTATTC
2665 TCA
64 TCA
*
2668 TTCCCAAAAATATCCTTTCGGTCAAAGGGTCAGTATTGTCTTTTGCATTCAAGTTTAGTATTCTC
1 TTCCCAAAAATACCCTTTCGGTCAAAGGGTCAGTATTGTCTTTTGCATTCAAGTTTAGTATTCTC
2733 A
66 A
* *
2734 TTCCCAAAAACACCCTTTCGGTCAAAGGGTCAGTATTGTCTCTTGCATTCAAGTTTAGTATTCTC
1 TTCCCAAAAATACCCTTTCGGTCAAAGGGTCAGTATTGTCTTTTGCATTCAAGTTTAGTATTCTC
2799 A
66 A
* * *
2800 TTCCCAAGAATACCCTTTCGGTC-AAGGGTCAGTATTGTCTTTTGTATTCAAGTTTAGTATTTTC
1 TTCCCAAAAATACCCTTTCGGTCAAAGGGTCAGTATTGTCTTTTGCATTCAAGTTTAGTATTCTC
2864 A
66 A
* * * * * * * *
2865 TTTCCAAAAATACCCTTCCAGTCGAAGGATCATTTTTGTCTTGTGCA-TCTAAGTTTACG--TTC
1 TTCCCAAAAATACCCTTTCGGTCAAAGGGTCAGTATTGTCTTTTGCATTC-AAGTTTA-GTATTC
*
2927 -AA
64 TCA
* * * *
2929 TTTCCAAAAATGCCCCTTCGGTGAAAGGGGTCAGT
1 TTCCCAAAAATACCCTTTCGGTCAAA-GGGTCAGT
2964 TTCTTCATTT
Statistics
Matches: 428, Mismatches: 58, Indels: 31
0.83 0.11 0.06
Matches are distributed among these distances:
64 21 0.05
65 68 0.16
66 159 0.37
67 13 0.03
68 75 0.18
69 82 0.19
70 10 0.02
ACGTcount: A:0.24, C:0.20, G:0.17, T:0.40
Consensus pattern (66 bp):
TTCCCAAAAATACCCTTTCGGTCAAAGGGTCAGTATTGTCTTTTGCATTCAAGTTTAGTATTCTC
A
Found at i:2904 original size:131 final size:130
Alignment explanation
Indices: 2396--2921 Score: 477
Period size: 131 Copynumber: 3.9 Consensus size: 130
2386 TAATTTTGTT
* * **
2396 TTCCCAAAAATACCCTTTCGG-CGGAAGGGTCA-TTTTCGTCTTTCCGCATTTTAGTTTAGTATT
1 TTCCCAAAAATACCCTTTCGGTC--AAGGGTCAGTATT-GTCTTT-TGCATTCAAGTTTAGTATT
** * * * *
2459 TTGTTTTCCCAAAAATACCCTTTTGGTGGAAGGGTC-ATTTCCGTCTTTCCGCATTTAAGTTTAG
62 TTCATTT-CCAAAAATACCCTTTCGGTCGAAGGGTCAATTT-TGTCTTT--GCATTCAAGTTTAG
* * **
2523 CATTTTGTTT
123 --TATTCTCA
** * * * *
2533 TTTTCAAAAATACCCTTTCGGTGGAAGGGTCA-TTTTCGTCTTTTTGCATTTAAGTTTAATATTT
1 TTCCCAAAAATACCCTTTCGGT-CAAGGGTCAGTATT-GTC-TTTTGCATTCAAGTTTAGTATTT
* * * * * * *
2597 TCTTTTCCAAAAAAATACCCTTTCGGTGGAAGGGTCAATTTCGTCTTTTGCATTTAGGTATGGTA
63 TCATTTCC--AAAAATACCCTTTCGGTCGAAGGGTCAATTTTGTC-TTTGCATTCAAGTTTAGTA
2662 TTCTCA
125 TTCTCA
* *
2668 TTCCCAAAAATATCCTTTCGGTCAAAGGGTCAGTATTGTCTTTTGCATTCAAGTTTAGTATTCTC
1 TTCCCAAAAATACCCTTTCGGTC-AAGGGTCAGTATTGTCTTTTGCATTCAAGTTTAGTATTTTC
* * * * *
2733 ATTCCCAAAAACACCCTTTCGGTCAAAGGGTCAGTATTGTCTCTTGCATTCAAGTTTAGTATTCT
65 ATTTCCAAAAATACCCTTTCGGTCGAAGGGTCAATTTTGTCT-TTGCATTCAAGTTTAGTATTCT
2798 CA
129 CA
* *
2800 TTCCCAAGAATACCCTTTCGGTCAAGGGTCAGTATTGTCTTTTGTATTCAAGTTTAGTATTTTCA
1 TTCCCAAAAATACCCTTTCGGTCAAGGGTCAGTATTGTCTTTTGCATTCAAGTTTAGTATTTTCA
* * * *
2865 TTTCCAAAAATACCCTTCCAGTCGAAGGATCATTTTTGTCTTGTGCA-TCTAAGTTTA
66 TTTCCAAAAATACCCTTTCGGTCGAAGGGTCAATTTTGTCTT-TGCATTC-AAGTTTA
2922 CGTTCAATTT
Statistics
Matches: 330, Mismatches: 47, Indels: 30
0.81 0.12 0.07
Matches are distributed among these distances:
130 3 0.01
131 85 0.26
132 70 0.21
134 26 0.08
135 34 0.10
136 5 0.02
137 68 0.21
138 32 0.10
139 7 0.02
ACGTcount: A:0.23, C:0.20, G:0.16, T:0.41
Consensus pattern (130 bp):
TTCCCAAAAATACCCTTTCGGTCAAGGGTCAGTATTGTCTTTTGCATTCAAGTTTAGTATTTTCA
TTTCCAAAAATACCCTTTCGGTCGAAGGGTCAATTTTGTCTTTGCATTCAAGTTTAGTATTCTCA
Found at i:2960 original size:131 final size:130
Alignment explanation
Indices: 2661--2963 Score: 344
Period size: 131 Copynumber: 2.3 Consensus size: 130
2651 TAGGTATGGT
* * *
2661 ATTCTCATTCCCAAAAATATCCTTTCGGTCAAAGGGTCAGTATTGTCTTTTGCATTCAAGTTTAG
1 ATTCTAATTCCCAAAAATACCCCTTCGGT-AAAGGGTCAGTATTGTCTTTTGCATTCAAGTTTAG
* * *
2726 TATTCTCATTCCCAAAAACACCCTTTCGGTCAAAGGGTCAGTATTGTCTCTTGCATTCAAGTTTA
65 TATTCTCATTCCCAAAAACACCCTTCCAGTCAAAGGATCAGTATTGTCTCTTGCATTCAAGTTTA
2791 G
130 G
* * * * *
2792 TATTCTCATTCCCAAGAATACCCTTTCGGTCAAGGGTCAGTATTGTCTTTTGTATTCAAGTTTAG
1 -ATTCTAATTCCCAAAAATACCCCTTCGGTAAAGGGTCAGTATTGTCTTTTGCATTCAAGTTTAG
* * * * * *
2857 TATTTTCATTTCCAAAAATACCCTTCCAGTCGAAGGATCATTTTTGTCT-TGTGCA-TCTAAGTT
65 TATTCTCATTCCCAAAAACACCCTTCCAGTCAAAGGATCAGTATTGTCTCT-TGCATTC-AAGTT
2920 TACG
128 TA-G
* *
2924 -TTC-AATTTCCAAAAATGCCCCTTCGGTGAAAGGGGTCAGT
1 ATTCTAATTCCCAAAAATACCCCTTCGGT-AAA-GGGTCAGT
2964 TTCTTCATTT
Statistics
Matches: 147, Mismatches: 19, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
129 19 0.13
130 8 0.05
131 92 0.63
132 28 0.19
ACGTcount: A:0.25, C:0.21, G:0.16, T:0.37
Consensus pattern (130 bp):
ATTCTAATTCCCAAAAATACCCCTTCGGTAAAGGGTCAGTATTGTCTTTTGCATTCAAGTTTAGT
ATTCTCATTCCCAAAAACACCCTTCCAGTCAAAGGATCAGTATTGTCTCTTGCATTCAAGTTTAG
Found at i:4530 original size:39 final size:40
Alignment explanation
Indices: 4455--4537 Score: 132
Period size: 39 Copynumber: 2.1 Consensus size: 40
4445 TTATCATGAT
* *
4455 ATTCATTTGTATATGTTCATGCATCGATCATACATTATCC
1 ATTCATTTGTATATGTTCATGCATCCATCATACATTATAC
*
4495 ATTCATTTGTATATG-TCATGCATCCATCATGCATTATAC
1 ATTCATTTGTATATGTTCATGCATCCATCATACATTATAC
4534 ATTC
1 ATTC
4538 CATCGTATAT
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
39 25 0.62
40 15 0.38
ACGTcount: A:0.28, C:0.20, G:0.10, T:0.42
Consensus pattern (40 bp):
ATTCATTTGTATATGTTCATGCATCCATCATACATTATAC
Found at i:4546 original size:39 final size:40
Alignment explanation
Indices: 4455--4547 Score: 118
Period size: 39 Copynumber: 2.4 Consensus size: 40
4445 TTATCATGAT
* * *
4455 ATTCATTTGTATATGTTCATGCATCGATCATACATTATCC
1 ATTCATTCGTATATGTTCATGCATCCATCATACATTATAC
* *
4495 ATTCATTTGTATATG-TCATGCATCCATCATGCATTATAC
1 ATTCATTCGTATATGTTCATGCATCCATCATACATTATAC
4534 ATTCCA-TCGTATAT
1 ATT-CATTCGTATAT
4548 ATGATCATGC
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
39 31 0.65
40 17 0.35
ACGTcount: A:0.28, C:0.20, G:0.10, T:0.42
Consensus pattern (40 bp):
ATTCATTCGTATATGTTCATGCATCCATCATACATTATAC
Found at i:5888 original size:14 final size:13
Alignment explanation
Indices: 5839--5901 Score: 65
Period size: 14 Copynumber: 4.8 Consensus size: 13
5829 TCAAAATAAG
*
5839 AAATGTTTTTCAA
1 AAATGGTTTTCAA
* *
5852 AAATTGTTTTTAA
1 AAATGGTTTTCAA
*
5865 GAAAAGGTTTTCAA
1 -AAATGGTTTTCAA
5879 AAATGAGTTTTCAA
1 AAATG-GTTTTCAA
5893 AAA-GGTTTT
1 AAATGGTTTT
5902 ATGTTTTTAA
Statistics
Matches: 41, Mismatches: 7, Indels: 5
0.77 0.13 0.09
Matches are distributed among these distances:
12 5 0.12
13 15 0.37
14 21 0.51
ACGTcount: A:0.40, C:0.05, G:0.14, T:0.41
Consensus pattern (13 bp):
AAATGGTTTTCAA
Found at i:5889 original size:27 final size:27
Alignment explanation
Indices: 5835--5901 Score: 75
Period size: 27 Copynumber: 2.5 Consensus size: 27
5825 ACTATCAAAA
* * *
5835 TAAGAAATGTTTTTCAAAAATTGTTTT
1 TAAGAAAAGGTTTTCAAAAATTGGTTT
5862 TAAGAAAAGGTTTTCAAAAA-TGAGTTT
1 TAAGAAAAGGTTTTCAAAAATTG-GTTT
*
5889 TCA-AAAAGGTTTT
1 TAAGAAAAGGTTTT
5902 ATGTTTTTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
26 12 0.34
27 23 0.66
ACGTcount: A:0.40, C:0.04, G:0.15, T:0.40
Consensus pattern (27 bp):
TAAGAAAAGGTTTTCAAAAATTGGTTT
Found at i:8424 original size:54 final size:54
Alignment explanation
Indices: 8330--8772 Score: 523
Period size: 54 Copynumber: 8.2 Consensus size: 54
8320 TCTAGTGCGG
* * *
8330 TCAAGAAAGTTTCCAGTGTTATTAAGTCTATCTTCTAGTGATCCAGTGCGGTCAA
1 TCAAGAAAGTTTCCAGTGGT-TTAAGTTTATCTTCAAGTGATCCAGTGCGGTCAA
* * *
8385 TTAAGAAAGTTTACAGTGGTTTAAGTTTATCTTCAAGTGATCCAGTACGGTCAA
1 TCAAGAAAGTTTCCAGTGGTTTAAGTTTATCTTCAAGTGATCCAGTGCGGTCAA
* *
8439 TCAAGAAAGTTTCCAGTGGTTTAAGTTTATCTTCAAGTGAACCAGTGTGGTCAA
1 TCAAGAAAGTTTCCAGTGGTTTAAGTTTATCTTCAAGTGATCCAGTGCGGTCAA
* * * * * * **
8493 TCAAGCAAGTTTACAATGGTCTAAGTTTGTCTTCAAGTGATCCAGTGCGATCGT
1 TCAAGAAAGTTTCCAGTGGTTTAAGTTTATCTTCAAGTGATCCAGTGCGGTCAA
* * * *
8547 TCAA-AAAGTTTTCCAGTGGTTCAAATTTATTTTCAAGTGATCCAGTGCGGTCAG
1 TCAAGAAAG-TTTCCAGTGGTTTAAGTTTATCTTCAAGTGATCCAGTGCGGTCAA
*
8601 TCAA-AAAGTTTCTAGTGGTTTAAGTTTATCTTCAAGTGATCCAGTGCGGTCAA
1 TCAAGAAAGTTTCCAGTGGTTTAAGTTTATCTTCAAGTGATCCAGTGCGGTCAA
* * * * * * * **
8654 TCAAGCAAGTTTACAATGGTCTAAGTTTGTCTTCAAGTGATCTAGTGCGTTCGT
1 TCAAGAAAGTTTCCAGTGGTTTAAGTTTATCTTCAAGTGATCCAGTGCGGTCAA
* ** * *
8708 TCAA-AAAGTTTCCAGTGGTTTAAATTTATCTTCAAGTGATTTAGTGCAGTCAG
1 TCAAGAAAGTTTCCAGTGGTTTAAGTTTATCTTCAAGTGATCCAGTGCGGTCAA
*
8761 TCAAGGAAGTTT
1 TCAAGAAAGTTT
8773 TTAGTAATTT
Statistics
Matches: 326, Mismatches: 59, Indels: 7
0.83 0.15 0.02
Matches are distributed among these distances:
53 89 0.27
54 220 0.67
55 17 0.05
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.35
Consensus pattern (54 bp):
TCAAGAAAGTTTCCAGTGGTTTAAGTTTATCTTCAAGTGATCCAGTGCGGTCAA
Found at i:8503 original size:108 final size:107
Alignment explanation
Indices: 8330--8772 Score: 521
Period size: 107 Copynumber: 4.1 Consensus size: 107
8320 TCTAGTGCGG
* * * *
8330 TCAAGAAAGTTTCCAGTGTTATTAAGTCTATCTTCTAGTGATCCAGTGCGGTCAATTAAGAAAGT
1 TCAAGAAAGTTTCCAGTGGT-TTAAGTTTATCTTCAAGTGATCCAGTGCGGTCAATCAA-AAAGT
*
8395 TTACAGTGGTTTAAGTTTATCTTCAAGTGATCCAGTACGGTCAA
64 TTACAGTGGTTTAAGTTTATCTTCAAGTGATCCAGTGCGGTCAA
* * *
8439 TCAAGAAAGTTTCCAGTGGTTTAAGTTTATCTTCAAGTGAACCAGTGTGGTCAATCAAGCAAGTT
1 TCAAGAAAGTTTCCAGTGGTTTAAGTTTATCTTCAAGTGATCCAGTGCGGTCAATCAA-AAAGTT
* * * * **
8504 TACAATGGTCTAAGTTTGTCTTCAAGTGATCCAGTGCGATCGT
65 TACAGTGGTTTAAGTTTATCTTCAAGTGATCCAGTGCGGTCAA
* * * *
8547 TCAA-AAAGTTTTCCAGTGGTTCAAATTTATTTTCAAGTGATCCAGTGCGGTCAGTCAAAAAGTT
1 TCAAGAAAG-TTTCCAGTGGTTTAAGTTTATCTTCAAGTGATCCAGTGCGGTCAATCAAAAAGTT
8611 T-CTAGTGGTTTAAGTTTATCTTCAAGTGATCCAGTGCGGTCAA
65 TAC-AGTGGTTTAAGTTTATCTTCAAGTGATCCAGTGCGGTCAA
* * * * * * * **
8654 TCAAGCAAGTTTACAATGGTCTAAGTTTGTCTTCAAGTGATCTAGTGCGTTCGTTCAAAAAGTTT
1 TCAAGAAAGTTTCCAGTGGTTTAAGTTTATCTTCAAGTGATCCAGTGCGGTCAATCAAAAAGTTT
* * ** * *
8719 CCAGTGGTTTAAATTTATCTTCAAGTGATTTAGTGCAGTCAG
66 ACAGTGGTTTAAGTTTATCTTCAAGTGATCCAGTGCGGTCAA
*
8761 TCAAGGAAGTTT
1 TCAAGAAAGTTT
8773 TTAGTAATTT
Statistics
Matches: 285, Mismatches: 45, Indels: 10
0.84 0.13 0.03
Matches are distributed among these distances:
106 1 0.00
107 139 0.49
108 126 0.44
109 19 0.07
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.35
Consensus pattern (107 bp):
TCAAGAAAGTTTCCAGTGGTTTAAGTTTATCTTCAAGTGATCCAGTGCGGTCAATCAAAAAGTTT
ACAGTGGTTTAAGTTTATCTTCAAGTGATCCAGTGCGGTCAA
Found at i:8635 original size:161 final size:161
Alignment explanation
Indices: 8360--8799 Score: 625
Period size: 161 Copynumber: 2.7 Consensus size: 161
8350 ATTAAGTCTA
* * * * *
8360 TCTTCTAGTGATCCAGTGCGGTCAATT-AAGAAAGTTTACAGTGGTTTAAGTTTATCTTCAAGTG
1 TCTTCAAGTGATCCAGTGCGATC-GTTCAA-AAAGTTTCCAGTGGTTTAAATTTATCTTCAAGTG
* * * *
8424 ATCCAGTACGGTCAATCAAGAAAGTTTCCAGTGGTTTAAGTTTATCTTCAAGTGAACCAGTGTGG
64 ATCCAGTGCGGTCAGTCAAGAAAGTTTCTAGTGGTTTAAGTTTATCTTCAAGTGAACCAGTGCGG
8489 TCAATCAAGCAAGTTTACAATGGTCTAAGTTTG
129 TCAATCAAGCAAGTTTACAATGGTCTAAGTTTG
* *
8522 TCTTCAAGTGATCCAGTGCGATCGTTCAAAAAGTTTTCCAGTGGTTCAAATTTATTTTCAAGTGA
1 TCTTCAAGTGATCCAGTGCGATCGTTCAAAAAG-TTTCCAGTGGTTTAAATTTATCTTCAAGTGA
*
8587 TCCAGTGCGGTCAGTCAA-AAAGTTTCTAGTGGTTTAAGTTTATCTTCAAGTGATCCAGTGCGGT
65 TCCAGTGCGGTCAGTCAAGAAAGTTTCTAGTGGTTTAAGTTTATCTTCAAGTGAACCAGTGCGGT
8651 CAATCAAGCAAGTTTACAATGGTCTAAGTTTG
130 CAATCAAGCAAGTTTACAATGGTCTAAGTTTG
* *
8683 TCTTCAAGTGATCTAGTGCGTTCGTTCAAAAAGTTTCCAGTGGTTTAAATTTATCTTCAAGTGAT
1 TCTTCAAGTGATCCAGTGCGATCGTTCAAAAAGTTTCCAGTGGTTTAAATTTATCTTCAAGTGAT
** * * * ** * *
8748 TTAGTGCAGTCAGTCAAGGAAGTTTTTAGTAATTT-GGGTTATCTTCAAGTGA
66 CCAGTGCGGTCAGTCAAGAAAGTTTCTAGTGGTTTAAGTTTATCTTCAAGTGA
8800 TTCGGGTAAT
Statistics
Matches: 250, Mismatches: 25, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
160 59 0.24
161 125 0.50
162 66 0.26
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.36
Consensus pattern (161 bp):
TCTTCAAGTGATCCAGTGCGATCGTTCAAAAAGTTTCCAGTGGTTTAAATTTATCTTCAAGTGAT
CCAGTGCGGTCAGTCAAGAAAGTTTCTAGTGGTTTAAGTTTATCTTCAAGTGAACCAGTGCGGTC
AATCAAGCAAGTTTACAATGGTCTAAGTTTG
Found at i:9207 original size:91 final size:89
Alignment explanation
Indices: 8966--9194 Score: 332
Period size: 91 Copynumber: 2.5 Consensus size: 89
8956 AATGTTTTAA
* * * * *
8966 CGGTGGATCAAGTTAATGTGGTGCATAATTTCTTTAAAGATGGAATTCGGTGAGCTCGGTGCAGC
1 CGGTGAATCAAGTTAATGCGGTGCATTATTTCTTCAAAG-TGG-ATTCGGTGAGCTCGGTGCAAC
*
9031 ATATTCTCAAACAGTTCAGGATGATT
64 ACATTCTCAAACAGTTCAGGATGATT
*
9057 CGGTGAATCAATTTAATGCGGTGCATTATTTCTTCAAGAGTGGATTCGGTGAGCTCGGTGCAACA
1 CGGTGAATCAAGTTAATGCGGTGCATTATTTCTTCAA-AGTGGATTCGGTGAGCTCGGTGCAACA
*
9122 CATTTTCAAACAAGTTCAGGATGATT
65 CATTCTCAAAC-AGTTCAGGATGATT
*
9148 CGGTGAGTCAAGTTAATGCGGTGCATTATTTCTTCAAAGTTGGATTC
1 CGGTGAATCAAGTTAATGCGGTGCATTATTTCTTCAAAG-TGGATTC
9195 AGATAACTCG
Statistics
Matches: 125, Mismatches: 10, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
90 32 0.26
91 91 0.73
92 2 0.02
ACGTcount: A:0.27, C:0.15, G:0.25, T:0.33
Consensus pattern (89 bp):
CGGTGAATCAAGTTAATGCGGTGCATTATTTCTTCAAAGTGGATTCGGTGAGCTCGGTGCAACAC
ATTCTCAAACAGTTCAGGATGATT
Found at i:9217 original size:35 final size:35
Alignment explanation
Indices: 9178--9457 Score: 438
Period size: 35 Copynumber: 8.0 Consensus size: 35
9168 GTGCATTATT
*
9178 TCTTCAAAGTTGGATTCAGATAACTCGGTGTAGCA
1 TCTTCAAAGTTGGATTCAGATGACTCGGTGTAGCA
9213 TCTTCAAAGTTGGATTCAGATGACTCGGTGTAGCA
1 TCTTCAAAGTTGGATTCAGATGACTCGGTGTAGCA
*
9248 TCTTCAAAGGTGGATTCAGATGACTCGGTGTAGCA
1 TCTTCAAAGTTGGATTCAGATGACTCGGTGTAGCA
* *
9283 TCTTCAAAGTTGGAATCAGTTGACTCGGTGTAGCA
1 TCTTCAAAGTTGGATTCAGATGACTCGGTGTAGCA
*
9318 TCTTCAAAGTTGGATTCAGGTGACTCGGTGTAGCA
1 TCTTCAAAGTTGGATTCAGATGACTCGGTGTAGCA
*
9353 TCTTCAATA-CTGGATTCAGATGACTCGGTGTAGCA
1 TCTTCAA-AGTTGGATTCAGATGACTCGGTGTAGCA
* *
9388 TCTTCAAAGTTGAATTCAGATGACTTGGTGTAGCA
1 TCTTCAAAGTTGGATTCAGATGACTCGGTGTAGCA
* *
9423 TCTTCAAAGTTGGATTC-GGTGAGCTCGGTGCAGCA
1 TCTTCAAAGTTGGATTCAGATGA-CTCGGTGTAGCA
9458 AATTTTCAAA
Statistics
Matches: 226, Mismatches: 16, Indels: 6
0.91 0.06 0.02
Matches are distributed among these distances:
34 5 0.02
35 220 0.97
36 1 0.00
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.31
Consensus pattern (35 bp):
TCTTCAAAGTTGGATTCAGATGACTCGGTGTAGCA
Found at i:12880 original size:66 final size:66
Alignment explanation
Indices: 12578--13141 Score: 453
Period size: 66 Copynumber: 8.4 Consensus size: 66
12568 TAATTTTGTT
* * * *
12578 TTCCCAAAAATACCCTTTCGGTGGAAGGGTCATTTTCGTCTTTCCGCATTTTAGTTTAGTATTTT
1 TTCCCAAAAATACCCTTTCGGTGAAAGGGTCATTTTCGTCTTT-TGCATTTAAGTTTAGTATTCT
**
12643 GTT
65 -CA
* * * * * *
12646 TTCCCAAAATTACCCTTTCGGTGGAAGGGTCATTTCCGTCTTTTTGCACTTAACTTTAGCATTTT
1 TTCCCAAAAATACCCTTTCGGTGAAAGGGTCATTTTCGTC-TTTTGCATTTAAGTTTAG--TATT
* **
12711 GTTT
63 CTCA
* * * *
12715 TTTCCAAAAATACCCTTTCGGTGGAAA-GGTCATTTTCATCTTTTTGCATTTAAGTTTAATATTT
1 TTCCCAAAAATACCCTTTCGGT-GAAAGGGTCATTTTCGTC-TTTTGCATTTAAGTTTAGTATTC
*
12779 TCTT
64 TC-A
* * * * * *
12783 TTCCAAAAAAAATACCCTTTCGATGGAAGGGTCATTTTCGTCTTTTGCATTTAGGTATGGTATTC
1 TTCC--CAAAAATACCCTTTCGGTGAAAGGGTCATTTTCGTCTTTTGCATTTAAGTTTAGTATTC
12848 TCA
64 TCA
* * *
12851 TTCCCAAAAATACCCTTTCGGTCAAAGGGTCAGTATT-GTCTTTTGCATTCAAGTTTAGTATTCT
1 TTCCCAAAAATACCCTTTCGGTGAAAGGGTCA-TTTTCGTCTTTTGCATTTAAGTTTAGTATTCT
12915 CA
65 CA
* * * * *
12917 TTCCCAAAAACACCCTTTCGGTCAAAGGGTCAGTATT-GTCTCTTGCATTCAAGTTTAGTATTCT
1 TTCCCAAAAATACCCTTTCGGTGAAAGGGTCA-TTTTCGTCTTTTGCATTTAAGTTTAGTATTCT
12981 CA
65 CA
* * * * * *
12983 TTCCCAAGAATACCCTTTCGGTCAAAGGGTCAGTATT-GTCTTTTGTATTCAAGTTTAGTATTTT
1 TTCCCAAAAATACCCTTTCGGTGAAAGGGTCA-TTTTCGTCTTTTGCATTTAAGTTTAGTATTCT
13047 CA
65 CA
* * * * * * * *
13049 TTTCCAAAAAT-GCCATTCTGGTCG-AATGATCATTTTTGTCTTGTGCATCTAAGTTTACG--TT
1 TTCCCAAAAATACCCTTTC-GGT-GAAAGGGTCATTTTCGTCTTTTGCATTTAAGTTTA-GTATT
*
13110 C-AA
63 CTCA
* * *
13113 TTTCCAAAAATGCCCCTTCGGTGAAAGGG
1 TTCCCAAAAATACCCTTTCGGTGAAAGGG
13142 GCCAGTTTCT
Statistics
Matches: 417, Mismatches: 64, Indels: 34
0.81 0.12 0.07
Matches are distributed among these distances:
63 1 0.00
64 18 0.04
65 15 0.04
66 208 0.50
67 8 0.02
68 57 0.14
69 75 0.18
70 35 0.08
ACGTcount: A:0.24, C:0.20, G:0.16, T:0.40
Consensus pattern (66 bp):
TTCCCAAAAATACCCTTTCGGTGAAAGGGTCATTTTCGTCTTTTGCATTTAAGTTTAGTATTCTC
A
Found at i:34046 original size:19 final size:18
Alignment explanation
Indices: 34025--34059 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
34015 AAAATTTAAA
*
34025 AAAAATCTAAAATACAAT
1 AAAAATCTAAAAAACAAT
34043 AAAAATCTAAAAAACAA
1 AAAAATCTAAAAAACAA
34060 AGCCAAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.71, C:0.11, G:0.00, T:0.17
Consensus pattern (18 bp):
AAAAATCTAAAAAACAAT
Found at i:34281 original size:22 final size:22
Alignment explanation
Indices: 34232--34281 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
34222 TGTATCTGTG
*
34232 TGGTTATCGAATTTTATAATGA
1 TGGTTATCAAATTTTATAATGA
*
34254 -GGTTATCAAATTTTCATAGT-A
1 TGGTTATCAAATTTT-ATAATGA
34275 TGGTTAT
1 TGGTTAT
34282 TTGTATTAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
21 14 0.58
22 10 0.42
ACGTcount: A:0.30, C:0.06, G:0.18, T:0.46
Consensus pattern (22 bp):
TGGTTATCAAATTTTATAATGA
Found at i:39244 original size:2 final size:2
Alignment explanation
Indices: 39237--39265 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
39227 ACATACATAC
39237 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 A
39266 ATACTCAAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:41552 original size:39 final size:39
Alignment explanation
Indices: 41482--41558 Score: 100
Period size: 39 Copynumber: 2.0 Consensus size: 39
41472 CCTCGTGCAC
* * *
41482 AATTAAACAGGGGTGCCGCTCGGGGCACTCAGTCGTCAG
1 AATTAAACAGGGGGGCCGCTCCGGGCACTCAGCCGTCAG
* * *
41521 AATTGAACAGGGGGGCCGCTCCTGGCCCTCAGCCGTCA
1 AATTAAACAGGGGGGCCGCTCCGGGCACTCAGCCGTCA
41559 AACGAGGGAG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
39 32 1.00
ACGTcount: A:0.21, C:0.30, G:0.32, T:0.17
Consensus pattern (39 bp):
AATTAAACAGGGGGGCCGCTCCGGGCACTCAGCCGTCAG
Found at i:41605 original size:117 final size:117
Alignment explanation
Indices: 41236--41634 Score: 381
Period size: 118 Copynumber: 3.4 Consensus size: 117
41226 GATCTAGACA
* * * ** * * * * *
41236 CTCGTGCTCAATTAAACAGGGGGGGCCACTCATGGCCCTCTGCCGTCAAAATTAAAC-AGGGCGC
1 CTCGTGCACAATTAAACA-GGGGTGCCGCTCGGGGCACTCAGCTGTCAAAATTAAACAAGGGGGA
* ** * * * *
41300 CATTTTTGGCGCTCAACCGTCCAAACGAGGGGAGTCTCATGGCGAGACGTGTGTC
65 CACTCCTGGCCCTCAGCCGT-CAAACGA-GGGAGTCTCATGGCGAGACGAGCGTC
* * * *
41355 TTCGTGCACAATTAAACA-AGGTCGCCGCTCGAGGCACTGAGCTGTCAAAATTAAACAAGGGGGA
1 CTCGTGCACAATTAAACAGGGGT-GCCGCTCGGGGCACTCAGCTGTCAAAATTAAACAAGGGGGA
* * * * * * * *
41419 CATTCTTGGTCCTTAGCCGTCTGAACAAGGGAGTCTCGTGGCGAGACGCGCGTC
65 CACTCCTGGCCCTCAGCCGTC-AAACGAGGGAGTCTCATGGCGAGACGAGCGTC
* * * *
41473 CTCGTGCACAATTAAACAGGGGTGCCGCTCGGGGCACTCAG-TCGTCAGAATTGAACAGGGGGGC
1 CTCGTGCACAATTAAACAGGGGTGCCGCTCGGGGCACTCAGCT-GTCAAAATTAAACAAGGGGGA
* * * *
41537 CGCTCCTGGCCCTCAGCCGTCAAACGAGGGAGTCTCTTGACGAGACGAACGTC
65 CACTCCTGGCCCTCAGCCGTCAAACGAGGGAGTCTCATGGCGAGACGAGCGTC
*
41590 CTCGTGCACAATTAAACAGGGGTGCCGCTCGGGGCACTTAGCTGT
1 CTCGTGCACAATTAAACAGGGGTGCCGCTCGGGGCACTCAGCTGT
41635 GTGATGGGTG
Statistics
Matches: 231, Mismatches: 43, Indels: 14
0.80 0.15 0.05
Matches are distributed among these distances:
117 71 0.31
118 117 0.51
119 43 0.19
ACGTcount: A:0.23, C:0.27, G:0.30, T:0.20
Consensus pattern (117 bp):
CTCGTGCACAATTAAACAGGGGTGCCGCTCGGGGCACTCAGCTGTCAAAATTAAACAAGGGGGAC
ACTCCTGGCCCTCAGCCGTCAAACGAGGGAGTCTCATGGCGAGACGAGCGTC
Found at i:43741 original size:26 final size:27
Alignment explanation
Indices: 43692--43744 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 27
43682 TATTTTTTTG
*
43692 AAATAAACGTATATATTAATATTATTA
1 AAATAAACATATATATTAATATTATTA
*
43719 AAATAAACATAT-TATTAGTATTATTA
1 AAATAAACATATATATTAATATTATTA
43745 GAACTGTCGA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 13 0.54
27 11 0.46
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.42
Consensus pattern (27 bp):
AAATAAACATATATATTAATATTATTA
Found at i:43949 original size:16 final size:16
Alignment explanation
Indices: 43844--43977 Score: 96
Period size: 16 Copynumber: 8.4 Consensus size: 16
43834 CTCGCCCGAT
43844 CCGAGACCCGAATGAC
1 CCGAGACCCGAATGAC
43860 CCGCA-ACCC-AGATGAC
1 CCG-AGACCCGA-ATGAC
*
43876 CCAAGACCCGAATGAC
1 CCGAGACCCGAATGAC
* * *
43892 CCGTAGTCCAG-ATGAG
1 CCG-AGACCCGAATGAC
* *
43908 CCGAAACCCCAATGAC
1 CCGAGACCCGAATGAC
*
43924 CTGTAG-CCCGAATGAC
1 CCG-AGACCCGAATGAC
** *
43940 CCGAGACCCGTTTAAC
1 CCGAGACCCGAATGAC
* *
43956 CCGAAACCCGAATAAC
1 CCGAGACCCGAATGAC
43972 CCGAGA
1 CCGAGA
43978 AGTTAACCCG
Statistics
Matches: 89, Mismatches: 21, Indels: 16
0.71 0.17 0.13
Matches are distributed among these distances:
15 7 0.08
16 74 0.83
17 8 0.09
ACGTcount: A:0.32, C:0.37, G:0.21, T:0.10
Consensus pattern (16 bp):
CCGAGACCCGAATGAC
Found at i:44843 original size:21 final size:22
Alignment explanation
Indices: 44807--44848 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
44797 TTTCGAGAAC
*
44807 CTTTTTATAAT-TTTTTTTAAT
1 CTTTTTATAATATTTTGTTAAT
*
44828 CTTTTTATGATATTTTGTTAA
1 CTTTTTATAATATTTTGTTAA
44849 CCTCCATAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.24, C:0.05, G:0.05, T:0.67
Consensus pattern (22 bp):
CTTTTTATAATATTTTGTTAAT
Found at i:44936 original size:23 final size:21
Alignment explanation
Indices: 44900--44949 Score: 64
Period size: 23 Copynumber: 2.3 Consensus size: 21
44890 TAACTTCCCA
*
44900 ATATGAAATTTTGATAACCAAC
1 ATATGAAATGTTGATAACC-AC
*
44922 ACTATGAGATGTTGATAACCAC
1 A-TATGAAATGTTGATAACCAC
44944 ATATGA
1 ATATGA
44950 TGATAACCAC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 5 0.20
22 4 0.16
23 16 0.64
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (21 bp):
ATATGAAATGTTGATAACCAC
Found at i:45023 original size:22 final size:22
Alignment explanation
Indices: 44998--45088 Score: 101
Period size: 22 Copynumber: 4.1 Consensus size: 22
44988 GAATTATTAG
* *
44998 TAATCACACTCTGAAATTTTGA
1 TAATCATACTATGAAATTTTGA
*
45020 TAATCATACTATGAAATTATGA
1 TAATCATACTATGAAATTTTGA
* *
45042 TAACCTTACTATGAAATTTTGA
1 TAATCATACTATGAAATTTTGA
* * *
45064 TAAATCTTCCTATAAAATTTTGA
1 T-AATCATACTATGAAATTTTGA
45087 TA
1 TA
45089 TAAACCTCCC
Statistics
Matches: 59, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
22 40 0.68
23 19 0.32
ACGTcount: A:0.40, C:0.13, G:0.08, T:0.40
Consensus pattern (22 bp):
TAATCATACTATGAAATTTTGA
Found at i:45100 original size:25 final size:25
Alignment explanation
Indices: 45050--45113 Score: 87
Period size: 25 Copynumber: 2.6 Consensus size: 25
45040 GATAACCTTA
* * *
45050 CTATGAAATTTTG--ATAAATCTTC
1 CTATAAAATTTTGATATAAACCTCC
45073 CTATAAAATTTTGATATAAACCTCC
1 CTATAAAATTTTGATATAAACCTCC
45098 CTATAAAATTTTGATA
1 CTATAAAATTTTGATA
45114 ACTTTCTTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
23 12 0.33
25 24 0.67
ACGTcount: A:0.39, C:0.14, G:0.06, T:0.41
Consensus pattern (25 bp):
CTATAAAATTTTGATATAAACCTCC
Found at i:45191 original size:22 final size:22
Alignment explanation
Indices: 44743--45259 Score: 96
Period size: 22 Copynumber: 23.7 Consensus size: 22
44733 TTTATGATCC
44743 CATTATGAAATTTTGATAACCTT
1 CATTATGAAATTTTGATAACC-T
*
44766 C-TTATGAAATTTTAATAA--T
1 CATTATGAAATTTTGATAACCT
* * * *
44785 GATACTATGGAATTTCGAGAACCT
1 CAT--TATGAAATTTTGATAACCT
** * ** *
44809 TTTTAT-AATTTTTTTTAATCT
1 CATTATGAAATTTTGATAACCT
** * *
44830 TTTTATGATATTTTGTTAACCT
1 CATTATGAAATTTTGATAACCT
* * *
44852 CCA-TAAGAAATTTTGAAAATCT
1 -CATTATGAAATTTTGATAACCT
* * *
44874 CAATATTAAATTTTGATAACTTCC
1 CATTATGAAATTTTGATAAC--CT
* *
44898 CAATATGAAATTTTGATAACCAA
1 CATTATGAAATTTTGATAACC-T
* * * *
44921 CACTATGAGATGTTGATAACCA
1 CATTATGAAATTTTGATAACCT
*
44943 CA-TATG--A---TGATAACCA
1 CATTATGAAATTTTGATAACCT
* ** *
44959 CGTTATGGAAATTTAAAAAACCT
1 CATTAT-GAAATTTTGATAACCT
* *
44982 CCA-TATG-AATTATT-AGTAATCA
1 -CATTATGAAATT-TTGA-TAACCT
* *
45004 CACTCTGAAATTTTGATAA--T
1 CATTATGAAATTTTGATAACCT
*
45024 CATACTATGAAATTATGATAACCT
1 CAT--TATGAAATTTTGATAACCT
* * *
45048 TACTATGAAATTTTGATAAATCTT
1 CATTATGAAATTTTGAT-AA-CCT
* *
45072 C-CTATAAAATTTTGATATAAACCT
1 CATTATGAAATTTTG--AT-AACCT
** * *
45096 CCCTATAAAATTTTGATAACTTT
1 CATTATGAAATTTTGATAAC-CT
* *
45119 C-TTATGAGATCTTGATAA---
1 CATTATGAAATTTTGATAACCT
* *
45137 C--TA-CAAATTTTAATAACCT
1 CATTATGAAATTTTGATAACCT
** **
45156 CCCTATGATTTTTTGATAACCT
1 CATTATGAAATTTTGATAACCT
* * *
45178 CATTATGAAATTTTGTTGATCT
1 CATTATGAAATTTTGATAACCT
** * * *
45200 CCCTATGAAATTTTGGTTTACAT
1 CATTATGAAATTTT-GATAACCT
*
45223 -ACTATGAAATTTTGATAACCCT
1 CATTATGAAATTTTGATAA-CCT
45245 C-TTATGAAATTTTGA
1 CATTATGAAATTTTGA
45260 AAAGTAAACT
Statistics
Matches: 363, Mismatches: 88, Indels: 87
0.67 0.16 0.16
Matches are distributed among these distances:
16 19 0.05
17 5 0.01
18 2 0.01
19 3 0.01
20 4 0.01
21 32 0.09
22 195 0.54
23 55 0.15
24 30 0.08
25 18 0.05
ACGTcount: A:0.36, C:0.14, G:0.09, T:0.40
Consensus pattern (22 bp):
CATTATGAAATTTTGATAACCT
Found at i:45371 original size:11 final size:11
Alignment explanation
Indices: 45349--45384 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
45339 GTTTCCGGTT
45349 TTTTGTTTTTTG
1 TTTTG-TTTTTG
45361 TTTTGTTTTTG
1 TTTTGTTTTTG
*
45372 CTTTGTTTTTG
1 TTTTGTTTTTG
45383 TT
1 TT
45385 ACGCTGTCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 17 0.77
12 5 0.23
ACGTcount: A:0.00, C:0.03, G:0.17, T:0.81
Consensus pattern (11 bp):
TTTTGTTTTTG
Found at i:46169 original size:11 final size:11
Alignment explanation
Indices: 46153--46183 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
46143 CCAATAAGAG
46153 AAAAAAAATGA
1 AAAAAAAATGA
46164 AAAAAAAATGA
1 AAAAAAAATGA
46175 AAGAAAAAA
1 AA-AAAAAA
46184 AGCCAAAGCC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.68
12 6 0.32
ACGTcount: A:0.84, C:0.00, G:0.10, T:0.06
Consensus pattern (11 bp):
AAAAAAAATGA
Found at i:46633 original size:34 final size:34
Alignment explanation
Indices: 46590--46668 Score: 133
Period size: 34 Copynumber: 2.3 Consensus size: 34
46580 CTAATCATAT
*
46590 TATGAAATTTTGATAACCTTCC-CAGAAATATCGC
1 TATGAAATTTTGATAACC-TCCTCAGAAATATCAC
46624 TATGAAATTTTGATAACCTCCTCAGAAATATCAC
1 TATGAAATTTTGATAACCTCCTCAGAAATATCAC
46658 TATGAAATTTT
1 TATGAAATTTT
46669 TGTAATCACA
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
33 3 0.07
34 40 0.93
ACGTcount: A:0.37, C:0.18, G:0.10, T:0.35
Consensus pattern (34 bp):
TATGAAATTTTGATAACCTCCTCAGAAATATCAC
Found at i:46719 original size:44 final size:44
Alignment explanation
Indices: 46657--46850 Score: 148
Period size: 44 Copynumber: 4.4 Consensus size: 44
46647 AGAAATATCA
* *
46657 CTATGAAATTTTTG-TAATCACATTTTGAAAATTTGATAATCTCT
1 CTATGAAA-TTTTGATAATCACATTATGAAAATTTGATAACCTCT
* * * * *
46701 TTATGAAATTTTGATAATCTC-TGTAT-AAAATTTTGTTGACCCCT
1 CTATGAAATTTTGATAATCACAT-TATGAAAA-TTTGATAACCTCT
* * * *
46745 CTATGAAATTCTGATAATCACATTATGTAATTTTGATAACCTCG
1 CTATGAAATTTTGATAATCACATTATGAAAATTTGATAACCTCT
* * * * * *
46789 CTTTGAAATTTCGATAA-CAAAACTATGAAATTTTGATAATCT-T
1 CTATGAAATTTTGATAATC-ACATTATGAAAATTTGATAACCTCT
46832 CCTAT-AAATTTTGATAATC
1 -CTATGAAATTTTGATAATC
46851 TGATCTCTAT
Statistics
Matches: 116, Mismatches: 26, Indels: 16
0.73 0.16 0.10
Matches are distributed among these distances:
43 22 0.19
44 91 0.78
45 3 0.03
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.42
Consensus pattern (44 bp):
CTATGAAATTTTGATAATCACATTATGAAAATTTGATAACCTCT
Found at i:46836 original size:22 final size:22
Alignment explanation
Indices: 46657--46926 Score: 132
Period size: 22 Copynumber: 12.5 Consensus size: 22
46647 AGAAATATCA
*
46657 CTATGAAATTTTTG-TAATCACAT
1 CTATGAAA-TTTTGATAATCTC-T
* *
46680 -TTTGAAAATTTGATAATCTCT
1 CTATGAAATTTTGATAATCTCT
*
46701 TTATGAAATTTTGATAATCTCT
1 CTATGAAATTTTGATAATCTCT
* * * * * *
46723 GTATAAAATTTTGTTGACCCCT
1 CTATGAAATTTTGATAATCTCT
* *
46745 CTATGAAATTCTGATAATCACAT
1 CTATGAAATTTTGATAATCTC-T
* * *
46768 -TATGTAATTTTGATAACCTCG
1 CTATGAAATTTTGATAATCTCT
* * ***
46789 CTTTGAAATTTCGATAA-CAAAA
1 CTATGAAATTTTGATAATC-TCT
46811 CTATGAAATTTTGATAATCT-T
1 CTATGAAATTTTGATAATCTCT
46832 CCTAT-AAATTTTGATAATCTGATCT
1 -CTATGAAATTTTGATAATC---TCT
** *
46857 CTATGAAATTTCAATAATCACT
1 CTATGAAATTTTGATAATCTCT
* *
46879 C--TGAGA-TTTGATAACCT-T
1 CTATGAAATTTTGATAATCTCT
* * *
46897 CTTTCAAATTTTGATACTC-CT
1 CTATGAAATTTTGATAATCTCT
46918 -TATGAAATT
1 CTATGAAATT
46927 GAGACTTTTA
Statistics
Matches: 184, Mismatches: 47, Indels: 35
0.69 0.18 0.13
Matches are distributed among these distances:
18 2 0.01
19 7 0.04
20 14 0.08
21 29 0.16
22 112 0.61
23 2 0.01
24 5 0.03
25 13 0.07
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.42
Consensus pattern (22 bp):
CTATGAAATTTTGATAATCTCT
Found at i:47130 original size:30 final size:31
Alignment explanation
Indices: 47095--47159 Score: 87
Period size: 30 Copynumber: 2.1 Consensus size: 31
47085 TGACAATTTA
* *
47095 GAAATATGTTTTAAAAA-AAAAGTACAATTG
1 GAAATATATTTTAAAAATAAAAGTACAATAG
**
47125 GAAATATATTTTAAAAATAAGGGTACAATAG
1 GAAATATATTTTAAAAATAAAAGTACAATAG
47156 GAAA
1 GAAA
47160 ACATAAAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 16 0.53
31 14 0.47
ACGTcount: A:0.54, C:0.03, G:0.15, T:0.28
Consensus pattern (31 bp):
GAAATATATTTTAAAAATAAAAGTACAATAG
Found at i:47359 original size:16 final size:16
Alignment explanation
Indices: 47340--47405 Score: 53
Period size: 16 Copynumber: 4.2 Consensus size: 16
47330 TAGACTCGGG
*
47340 ACCCGAATGAACCAAA
1 ACCCGAATGAACCGAA
* * *
47356 ACCCGTATGACCCGGA
1 ACCCGAATGAACCGAA
* * *
47372 ACCCAAATGACCCGGA
1 ACCCGAATGAACCGAA
*
47388 ACCCGAAT-AACCCAA
1 ACCCGAATGAACCGAA
47403 ACC
1 ACC
47406 AGATAATCCG
Statistics
Matches: 40, Mismatches: 10, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
15 7 0.17
16 33 0.82
ACGTcount: A:0.39, C:0.38, G:0.15, T:0.08
Consensus pattern (16 bp):
ACCCGAATGAACCGAA
Found at i:47722 original size:20 final size:21
Alignment explanation
Indices: 47697--47750 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 21
47687 ATGGGAGTTC
* *
47697 AAGGAGAGAGAAAGAGAGA-A
1 AAGGAGAGAGAAAGAAAAAGA
47717 AAGGAGAGA-AAAGAAAAAGA
1 AAGGAGAGAGAAAGAAAAAGA
*
47737 AAGGAGAAAGAAAG
1 AAGGAGAGAGAAAG
47751 GGATAGAAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
19 7 0.24
20 18 0.62
21 4 0.14
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (21 bp):
AAGGAGAGAGAAAGAAAAAGA
Found at i:51317 original size:24 final size:24
Alignment explanation
Indices: 51289--51336 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
51279 TATATATCAG
51289 CTAAATGTGTGCATATGATAATTT
1 CTAAATGTGTGCATATGATAATTT
51313 CTAAATGTGTGCATATGATAATTT
1 CTAAATGTGTGCATATGATAATTT
51337 GTTATAATAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.33, C:0.08, G:0.17, T:0.42
Consensus pattern (24 bp):
CTAAATGTGTGCATATGATAATTT
Found at i:56025 original size:2 final size:2
Alignment explanation
Indices: 56018--56061 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
56008 AGGCATCCGA
56018 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
56060 TC
1 TC
56062 CATGTTTGTG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:58940 original size:21 final size:21
Alignment explanation
Indices: 58889--58940 Score: 50
Period size: 21 Copynumber: 2.5 Consensus size: 21
58879 AACTCATCTT
* *
58889 GATGATATGAAGTCCTTTGAA
1 GATGATTTGAAGACCTTTGAA
* * * *
58910 GATCAATTGAAGACTTTTGGA
1 GATGATTTGAAGACCTTTGAA
58931 GATGATTTGA
1 GATGATTTGA
58941 GCAAGAAAGC
Statistics
Matches: 23, Mismatches: 8, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.33, C:0.08, G:0.25, T:0.35
Consensus pattern (21 bp):
GATGATTTGAAGACCTTTGAA
Found at i:64846 original size:10 final size:10
Alignment explanation
Indices: 64813--64846 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
64803 CCTTAGCAAC
*
64813 AAAATACAGA
1 AAAATACAAA
*
64823 AAAATACCAA
1 AAAATACAAA
64833 AAAATACAAA
1 AAAATACAAA
64843 AAAA
1 AAAA
64847 AAAGAAAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.76, C:0.12, G:0.03, T:0.09
Consensus pattern (10 bp):
AAAATACAAA
Done.