Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007841.1 Corchorus capsularis cultivar CVL-1 contig07862, 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: 42600
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.34
Found at i:677 original size:15 final size:15
Alignment explanation
Indices: 639--682 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
629 CCGGGCCTGA
639 ACCCGAACCCGAAAAT
1 ACCCGAACCCG-AAAT
* *
655 ATCCGAACCCGAAGT
1 ACCCGAACCCGAAAT
670 ACCCGAACCCGAA
1 ACCCGAACCCGAA
683 CCCGCCCAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
15 15 0.60
16 10 0.40
ACGTcount: A:0.39, C:0.39, G:0.16, T:0.07
Consensus pattern (15 bp):
ACCCGAACCCGAAAT
Found at i:3750 original size:22 final size:21
Alignment explanation
Indices: 3724--3777 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 21
3714 GATAACCTCC
*
3724 ATATAGAATTTTAATAATTAT
1 ATATAGAATTTTAATAATGAT
* *
3745 ACTATA-AAGTTTTTATGATGAT
1 A-TATAGAA-TTTTAATAATGAT
3767 ATATAGAATTT
1 ATATAGAATTT
3778 CGAGAACCTC
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
21 10 0.37
22 17 0.63
ACGTcount: A:0.43, C:0.02, G:0.09, T:0.46
Consensus pattern (21 bp):
ATATAGAATTTTAATAATGAT
Found at i:3885 original size:22 final size:22
Alignment explanation
Indices: 3860--4044 Score: 76
Period size: 22 Copynumber: 8.5 Consensus size: 22
3850 CAACCTAATA
*
3860 AAATTTTGATAA-CTACCCTATG
1 AAATTTTGATAACCT-CCCGATG
3882 AAATTTTGATAACCTCCCGATG
1 AAATTTTGATAACCTCCCGATG
* * * * **
3904 AAATATTGGTAAGC-GCATATG
1 AAATTTTGATAACCTCCCGATG
* * *
3925 ATATTTTGATAACCTTCCGATA
1 AAATTTTGATAACCTCCCGATG
* * * ***
3947 AAATATTGATAATCACATTATG
1 AAATTTTGATAACCTCCCGATG
* * *
3969 AAAATCTGATAACCATACC-ATG
1 AAATTTTGATAACC-TCCCGATG
* * *
3991 AAATTGTG--AACCTCACTATG
1 AAATTTTGATAACCTCCCGATG
* * *
4011 AAATTTTTATAAACCTCCCTATA
1 AAATTTTGAT-AACCTCCCGATG
4034 AAATTTT-ATAA
1 AAATTTTGATAA
4045 AATTTTGATA
Statistics
Matches: 116, Mismatches: 40, Indels: 15
0.68 0.23 0.09
Matches are distributed among these distances:
19 2 0.02
20 13 0.11
21 16 0.14
22 66 0.57
23 19 0.16
ACGTcount: A:0.39, C:0.17, G:0.10, T:0.34
Consensus pattern (22 bp):
AAATTTTGATAACCTCCCGATG
Found at i:4157 original size:22 final size:21
Alignment explanation
Indices: 4039--4190 Score: 82
Period size: 22 Copynumber: 7.0 Consensus size: 21
4029 CTATAAAATT
*
4039 TTATAAAATTTTGATAACTTCC
1 TTAT-AAATTTTGATAACATCC
*
4061 ATT-TGAAATTTCGAT-A-A-CC
1 -TTAT-AAATTTTGATAACATCC
* *
4080 TCATGAAATTTTGAAAACCA-CC
1 TTAT-AAATTTTGATAA-CATCC
*
4102 TCATGAAATTTTGATAACCAT-C
1 TTAT-AAATTTTGATAA-CATCC
4124 TTATGAAATTTTGATAACATCC
1 TTAT-AAATTTTGATAACATCC
* * *
4146 CTATAAATTTTTTATAACCTCC
1 TTATAAA-TTTTGATAACATCC
* *
4168 TTATAAAATTTTGTTAACCTCC
1 TTAT-AAATTTTGATAACATCC
4190 T
1 T
4191 ACGAAATTTC
Statistics
Matches: 107, Mismatches: 14, Indels: 17
0.78 0.10 0.12
Matches are distributed among these distances:
18 1 0.01
19 12 0.11
20 1 0.01
21 7 0.07
22 81 0.76
23 5 0.05
ACGTcount: A:0.36, C:0.18, G:0.07, T:0.40
Consensus pattern (21 bp):
TTATAAATTTTGATAACATCC
Found at i:4198 original size:44 final size:44
Alignment explanation
Indices: 4039--4199 Score: 106
Period size: 44 Copynumber: 3.7 Consensus size: 44
4029 CTATAAAATT
* * * *
4039 TTATAAAATTTTGATAACTTCCATTTGAAA-TTTCGATAACC-TC
1 TTATAAAATTTTGATAACATCC-CTAGAAATTTTTGATAACCATC
* *
4082 --ATGAAATTTTGA-AA-ACCACCTCATGAAA-TTTTGATAACCATC
1 TTATAAAATTTTGATAACATC-CCT-A-GAAATTTTTGATAACCATC
* * *
4124 TTATGAAATTTTGATAACATCCCTATAAATTTTTTATAACC-TCC
1 TTATAAAATTTTGATAACATCCCTAGAAATTTTTGATAACCAT-C
* *
4168 TTATAAAATTTTGTTAACCT-CCTACGAAATTT
1 TTATAAAATTTTGATAACATCCCTA-GAAATTT
4200 CGATAAGAAC
Statistics
Matches: 94, Mismatches: 13, Indels: 21
0.73 0.10 0.16
Matches are distributed among these distances:
39 2 0.02
40 3 0.03
41 25 0.27
42 2 0.02
43 8 0.09
44 47 0.50
45 5 0.05
46 2 0.02
ACGTcount: A:0.36, C:0.17, G:0.07, T:0.40
Consensus pattern (44 bp):
TTATAAAATTTTGATAACATCCCTAGAAATTTTTGATAACCATC
Found at i:4328 original size:22 final size:21
Alignment explanation
Indices: 4303--4364 Score: 52
Period size: 22 Copynumber: 2.8 Consensus size: 21
4293 GTTAATCTCC
4303 CTATAAAATTTTGAAAACCACA
1 CTAT-AAATTTTGAAAACCACA
* ** * *
4325 CTATCAATTTTTGTTAATCTCA
1 CTAT-AAATTTTGAAAACCACA
4347 CTATAAATTTTGATAAAC
1 CTATAAATTTTGA-AAAC
4365 TCGTTATGAA
Statistics
Matches: 29, Mismatches: 10, Indels: 2
0.71 0.24 0.05
Matches are distributed among these distances:
21 7 0.24
22 22 0.76
ACGTcount: A:0.40, C:0.16, G:0.05, T:0.39
Consensus pattern (21 bp):
CTATAAATTTTGAAAACCACA
Found at i:4752 original size:22 final size:21
Alignment explanation
Indices: 4727--4775 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
4717 AAATTTTAGT
*
4727 AACCTCCCCGTAAAATTTTGAC
1 AACCTCCCCAT-AAATTTTGAC
* * *
4749 AACCTTCCCATGAATTTTGAT
1 AACCTCCCCATAAATTTTGAC
4770 AACCTC
1 AACCTC
4776 TTAATTCTTA
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
21 13 0.59
22 9 0.41
ACGTcount: A:0.31, C:0.31, G:0.08, T:0.31
Consensus pattern (21 bp):
AACCTCCCCATAAATTTTGAC
Found at i:5278 original size:10 final size:10
Alignment explanation
Indices: 5248--5285 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
5238 ATTATTTTAT
5248 ATATAGTATAG
1 ATATAG-ATAG
5259 ATA-A-ATAG
1 ATATAGATAG
5267 ATATAGATAG
1 ATATAGATAG
5277 ATATAGATA
1 ATATAGATA
5286 TACTTCTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
8 7 0.28
9 1 0.04
10 14 0.56
11 3 0.12
ACGTcount: A:0.53, C:0.00, G:0.16, T:0.32
Consensus pattern (10 bp):
ATATAGATAG
Found at i:15690 original size:38 final size:37
Alignment explanation
Indices: 15613--15708 Score: 104
Period size: 38 Copynumber: 2.6 Consensus size: 37
15603 AATTTGCCTT
* * *
15613 TTTATTTCCAACGTCCTATTTAATTTTGTCTTTTGTC
1 TTTATTTCCAACGTCATATTTAATTTTCTCTTTTATC
*
15650 TTTATTTCCAATCGTTATATTTAATTTTC-CTTTTTATC
1 TTTATTTCCAA-CGTCATATTTAATTTTCTC-TTTTATC
* * *
15688 TTTGTCTCCAACGTCCTATTT
1 TTTATTTCCAACGTCATATTT
15709 GGACTTAGCT
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
37 20 0.41
38 29 0.59
ACGTcount: A:0.18, C:0.20, G:0.06, T:0.56
Consensus pattern (37 bp):
TTTATTTCCAACGTCATATTTAATTTTCTCTTTTATC
Found at i:16056 original size:22 final size:22
Alignment explanation
Indices: 16031--16159 Score: 104
Period size: 22 Copynumber: 5.9 Consensus size: 22
16021 TTTCTCTATG
16031 TGGTTATCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAAGA
* * *
16053 TGGTTATTATAATTTCATGAGGA
1 TGGTTATCAAAATTTCAT-AAGA
*
16076 -GGTTATCAAAATTCCATAATG-
1 TGGTTATCAAAATTTCATAA-GA
* *
16097 TGGTTACCAAAATTTCATATGGA
1 TGGTTATCAAAATTTCATA-AGA
* *
16120 -AGTTATCAAAATTTCAT-AGTT
1 TGGTTATCAAAATTTCATAAG-A
* *
16141 TGGTTACCAAAATTACATA
1 TGGTTATCAAAATTTCATA
16160 GGATCAGGTT
Statistics
Matches: 82, Mismatches: 17, Indels: 15
0.72 0.15 0.13
Matches are distributed among these distances:
20 1 0.01
21 1 0.01
22 77 0.94
23 3 0.04
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.37
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAAGA
Found at i:16101 original size:44 final size:44
Alignment explanation
Indices: 16032--16159 Score: 152
Period size: 44 Copynumber: 2.9 Consensus size: 44
16022 TTCTCTATGT
** *
16032 GGTTATCAAAATTTCATAA-GATGGTTATTATAATTTCATGA-GGA
1 GGTTATCAAAATTTCATAATG-TGGTTACCAAAATTTCAT-ATGGA
*
16076 GGTTATCAAAATTCCATAATGTGGTTACCAAAATTTCATATGGA
1 GGTTATCAAAATTTCATAATGTGGTTACCAAAATTTCATATGGA
* * * *
16120 AGTTATCAAAATTTCATAGTTTGGTTACCAAAATTACATA
1 GGTTATCAAAATTTCATAATGTGGTTACCAAAATTTCATA
16160 GGATCAGGTT
Statistics
Matches: 73, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
43 1 0.01
44 71 0.97
45 1 0.01
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.37
Consensus pattern (44 bp):
GGTTATCAAAATTTCATAATGTGGTTACCAAAATTTCATATGGA
Found at i:16146 original size:66 final size:66
Alignment explanation
Indices: 16028--16159 Score: 151
Period size: 66 Copynumber: 2.0 Consensus size: 66
16018 TCTTTTCTCT
* * * * * *
16028 ATGTGGTTATCAAAATTTCATAAGATGGTTATTATAATTTCATGAGGAGGTTATCAAAATTCCAT
1 ATGTGGTTACCAAAATTTCATAAGATAGTTATCAAAATTTCATGAGGAGGTTACCAAAATTACAT
16093 A
66 A
* **
16094 ATGTGGTTACCAAAATTTCATATGGA-AGTTATCAAAATTTCAT-AGTTTGGTTACCAAAATTAC
1 ATGTGGTTACCAAAATTTCATA-AGATAGTTATCAAAATTTCATGAG-GAGGTTACCAAAATTAC
16157 ATA
64 ATA
16160 GGATCAGGTT
Statistics
Matches: 55, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
65 2 0.04
66 51 0.93
67 2 0.04
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.37
Consensus pattern (66 bp):
ATGTGGTTACCAAAATTTCATAAGATAGTTATCAAAATTTCATGAGGAGGTTACCAAAATTACAT
A
Found at i:16212 original size:22 final size:22
Alignment explanation
Indices: 16166--16214 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
16156 CATAGGATCA
* *
16166 GGTTATTGAAATTTCTTATGTT
1 GGTTATTGAAATTTCTTAGGGT
16188 GGTTATTGAAATTT-TATAGGGT
1 GGTTATTGAAATTTCT-TAGGGT
16210 GGTTA
1 GGTTA
16215 ATTATCACAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 1 0.04
22 23 0.96
ACGTcount: A:0.24, C:0.02, G:0.24, T:0.49
Consensus pattern (22 bp):
GGTTATTGAAATTTCTTAGGGT
Found at i:16275 original size:22 final size:21
Alignment explanation
Indices: 16250--16619 Score: 142
Period size: 22 Copynumber: 16.7 Consensus size: 21
16240 ATCAAAGAGA
*
16250 TTATCAAAATGTCATAGCGAGG
1 TTATCAAAATTTCATAG-GAGG
* *
16272 TTAT-AAGAATTTCGTAGTGTGG
1 TTATCAA-AATTTCATAG-GAGG
*
16294 TTAACAAAATTTCATTAGGAGG
1 TTATCAAAATTTCA-TAGGAGG
* *
16316 TTA-CTAATATTTCATGGGGAGG
1 TTATC-AAAATTTCAT-AGGAGG
* * *
16338 TTATCGAAATTTCTTATGAAGG
1 TTATCAAAATTTCATA-GGAGG
*
16360 TTATAAAAGTCTCAATTTCATA--AGG
1 TTAT-CAA-----AATTTCATAGGAGG
* * *
16385 AGTACCAAAATTTCATAGAAGG
1 -TTATCAAAATTTCATAGGAGG
*
16407 TTATC-AAATCTCATA-GAGTG
1 TTATCAAAATTTCATAGGAG-G
* *
16427 ATTATCGAAATTTCATAGAGATCAGA
1 -TTATCAAAATTTCATAG-G---AGG
* *
16453 TTATCAAAATTT-ATAGAAAGA
1 TTATCAAAATTTCATAG-GAGG
***
16474 TTATCAAAATTTCATAGTGTTA
1 TTATCAAAATTTCATAG-GAGG
*
16496 TTATCAAAATTTCAAAGCGAGG
1 TTATCAAAATTTCATAG-GAGG
* * * * *
16518 TTATCAAAAGTACATAATGTGA
1 TTATCAAAATTTCAT-AGGAGG
*
16540 TTATCAAAATTTCATAGAGGGG
1 TTATCAAAATTTCATAG-GAGG
* * * *
16562 TCAACAAAATTTTATAAAGAGG
1 TTATCAAAATTTCAT-AGGAGG
*
16584 TTATCAAAATTTCATAATGAGG
1 TTATCAAAATTTCAT-AGGAGG
*
16606 TTATCAAATTTTCA
1 TTATCAAAATTTCA
16620 AAATGTGATT
Statistics
Matches: 262, Mismatches: 58, Indels: 56
0.70 0.15 0.15
Matches are distributed among these distances:
19 2 0.01
20 19 0.07
21 28 0.11
22 170 0.65
23 9 0.03
24 6 0.02
25 16 0.06
26 2 0.01
27 2 0.01
28 8 0.03
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.34
Consensus pattern (21 bp):
TTATCAAAATTTCATAGGAGG
Found at i:16431 original size:21 final size:22
Alignment explanation
Indices: 16373--16643 Score: 168
Period size: 22 Copynumber: 12.4 Consensus size: 22
16363 TAAAAGTCTC
* *
16373 AATTTCATA-AG-GAGTACCAA
1 AATTTCATAGAGTGATTATCAA
16393 AATTTCATAGAAG-G-TTATC-A
1 AATTTCATAG-AGTGATTATCAA
* *
16413 AATCTCATAGAGTGATTATCGA
1 AATTTCATAGAGTGATTATCAA
16435 AATTTCATAGAGATCAGATTATCAA
1 AATTTCATAGAG-T--GATTATCAA
**
16460 AATTT-ATAGAAAGATTATCAA
1 AATTTCATAGAGTGATTATCAA
* *
16481 AATTTCATAGTGTTATTATCAA
1 AATTTCATAGAGTGATTATCAA
* * * *
16503 AATTTCAAAGCGAGGTTATCAA
1 AATTTCATAGAGTGATTATCAA
* *
16525 AAGTACATA-ATGTGATTATCAA
1 AATTTCATAGA-GTGATTATCAA
* * * *
16547 AATTTCATAGAGGGGTCAACAA
1 AATTTCATAGAGTGATTATCAA
* * * *
16569 AATTTTATAAAGAGGTTATCAA
1 AATTTCATAGAGTGATTATCAA
16591 AATTTCATA-A-TGAGGTTATCAA
1 AATTTCATAGAGTGA--TTATCAA
* *
16613 ATTTTCA-AAATGTGATTA-CAAA
1 AATTTCATAGA-GTGATTATC-AA
16635 AATTTCATA
1 AATTTCATA
16644 ACGGTATTTC
Statistics
Matches: 195, Mismatches: 38, Indels: 33
0.73 0.14 0.12
Matches are distributed among these distances:
19 2 0.01
20 21 0.11
21 25 0.13
22 123 0.63
23 3 0.02
24 8 0.04
25 13 0.07
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (22 bp):
AATTTCATAGAGTGATTATCAA
Found at i:16750 original size:20 final size:20
Alignment explanation
Indices: 16725--16776 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
16715 TTATGGAGTA
16725 ATCAAAATTTCAAGGAGGAT
1 ATCAAAATTTCAAGGAGGAT
*
16745 ATCAAAATTTCAGGGAGGAT
1 ATCAAAATTTCAAGGAGGAT
*
16765 ATCACAATTTCA
1 ATCAAAATTTCA
16777 TAGTTTAGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.42, C:0.13, G:0.17, T:0.27
Consensus pattern (20 bp):
ATCAAAATTTCAAGGAGGAT
Found at i:16813 original size:22 final size:21
Alignment explanation
Indices: 16725--17036 Score: 113
Period size: 22 Copynumber: 14.6 Consensus size: 21
16715 TTATGGAGTA
*
16725 ATCAAAATTTCA-AG-GAGGAT
1 ATCAAAATTTCATAGAG-GGTT
** *
16745 ATCAAAATTTCAGGGA-GGAT
1 ATCAAAATTTCATAGAGGGTT
* ***
16765 ATCACAATTTCATAGTTTAGTT
1 ATCAAAATTTCATAG-AGGGTT
*
16787 TTCAAAATTTCATAAGAGGGTT
1 ATCAAAATTTCAT-AGAGGGTT
* *
16809 ATCAAAATTTCATAGTA-TGTAG
1 ATCAAAATTTCATAG-AGGGT-T
*
16831 ATCAAAATTTCATAGGGAGGTT
1 ATCAAAATTTCATAGAG-GGTT
* * *
16853 AACAAAATTTCATAATAAGGTT
1 ATCAAAATTTCAT-AGAGGGTT
** *
16875 ATCAAAAAATCATAGGGAGGTT
1 ATCAAAATTTCATAGAG-GGTT
*
16897 ATCAAAATTT-GT--A--GTT
1 ATCAAAATTTCATAGAGGGTT
* ***
16913 ATCAAGATTTCATAAGAAATTT
1 ATCAAAATTTCAT-AGAGGGTT
* *
16935 ATCAAAATTTTATAGGGAGGTTT
1 ATCAAAATTTCATA--GAGGGTT
**
16958 ATCAAAAATTT-ATAGGAAGATTT
1 ATC-AAAATTTCATA-G-AGGGTT
* *
16981 ATCAAAATATCATAGCGAGGTT
1 ATCAAAATTTCATAGAG-GGTT
* * * *
17003 ATTACAATTTCATAGTGTGCTT
1 ATCAAAATTTCATAGAG-GGTT
17025 ATCAAAATTTCA
1 ATCAAAATTTCA
17037 GAGTGTGATT
Statistics
Matches: 217, Mismatches: 52, Indels: 44
0.69 0.17 0.14
Matches are distributed among these distances:
16 12 0.06
17 1 0.00
20 29 0.13
21 9 0.04
22 132 0.61
23 27 0.12
24 7 0.03
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.34
Consensus pattern (21 bp):
ATCAAAATTTCATAGAGGGTT
Found at i:16819 original size:44 final size:44
Alignment explanation
Indices: 16745--16906 Score: 138
Period size: 44 Copynumber: 3.7 Consensus size: 44
16735 CAAGGAGGAT
* * *
16745 ATCAAAATTTC--AGGGAGGATATCACAATTTCATAGT-T-TAG
1 ATCAAAATTTCATAGAGAGGTTATCAAAATTTCATAGTATGTAG
*
16785 TTTTCAAAATTTCATA-AGAGGGTTATCAAAATTTCATAGTATGTAG
1 --ATCAAAATTTCATAGAGA-GGTTATCAAAATTTCATAGTATGTAG
* * * * *
16831 ATCAAAATTTCATAGGGAGGTTAACAAAATTTCATAATAAGGT-T
1 ATCAAAATTTCATAGAGAGGTTATCAAAATTTCATAGT-ATGTAG
** *
16875 ATCAAAAAATCATAGGGAGGTTATCAAAATTT
1 ATCAAAATTTCATAGAGAGGTTATCAAAATTT
16907 GTAGTTATCA
Statistics
Matches: 100, Mismatches: 13, Indels: 12
0.80 0.10 0.10
Matches are distributed among these distances:
42 10 0.10
43 2 0.02
44 79 0.79
45 6 0.06
46 3 0.03
ACGTcount: A:0.41, C:0.10, G:0.16, T:0.33
Consensus pattern (44 bp):
ATCAAAATTTCATAGAGAGGTTATCAAAATTTCATAGTATGTAG
Found at i:16952 original size:60 final size:61
Alignment explanation
Indices: 16850--16964 Score: 151
Period size: 60 Copynumber: 1.9 Consensus size: 61
16840 TCATAGGGAG
* *
16850 GTTAACAAAATTTCATAATAAGGTTATCAAAAAATCATAGGGAGG-TTATCAAAATTTGTA
1 GTTAACAAAATTTCATAAGAAAGTTATCAAAAAATCATAGGGAGGTTTATCAAAATTTGTA
* * * ** *
16910 GTTATCAAGATTTCATAAGAAATTTATCAAAATTTTATAGGGAGGTTTATCAAAA
1 GTTAACAAAATTTCATAAGAAAGTTATCAAAAAATCATAGGGAGGTTTATCAAAA
16965 ATTTATAGGA
Statistics
Matches: 46, Mismatches: 8, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
60 37 0.80
61 9 0.20
ACGTcount: A:0.43, C:0.08, G:0.15, T:0.34
Consensus pattern (61 bp):
GTTAACAAAATTTCATAAGAAAGTTATCAAAAAATCATAGGGAGGTTTATCAAAATTTGTA
Found at i:16961 original size:23 final size:23
Alignment explanation
Indices: 16932--17002 Score: 88
Period size: 23 Copynumber: 3.1 Consensus size: 23
16922 TCATAAGAAA
16932 TTTATCAAAATTTTATAGGGAGG
1 TTTATCAAAATTTTATAGGGAGG
* * *
16955 TTTATCAAAAATTTATAGGAAGA
1 TTTATCAAAATTTTATAGGGAGG
* * *
16978 TTTATCAAAATATCATAGCGAGG
1 TTTATCAAAATTTTATAGGGAGG
17001 TT
1 TT
17003 ATTACAATTT
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.39, C:0.07, G:0.17, T:0.37
Consensus pattern (23 bp):
TTTATCAAAATTTTATAGGGAGG
Found at i:17139 original size:23 final size:22
Alignment explanation
Indices: 17085--17140 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
17075 TTTTCGTAAC
*
17085 GTGGTTATCAATATATCATATG
1 GTGGTTATCAACATATCATATG
* *
17107 GAGGTTATCAACATCTCATAGTG
1 GTGGTTATCAACATATCATA-TG
*
17130 TTGGTTATCAA
1 GTGGTTATCAA
17141 AATTTCATTG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 17 0.61
23 11 0.39
ACGTcount: A:0.30, C:0.12, G:0.20, T:0.38
Consensus pattern (22 bp):
GTGGTTATCAACATATCATATG
Found at i:17148 original size:23 final size:22
Alignment explanation
Indices: 17085--17148 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 22
17075 TTTTCGTAAC
*
17085 GTGGTTATCAATATATCATATG
1 GTGGTTATCAAAATATCATATG
* * *
17107 GAGGTTATCAACATCTCATAGTG
1 GTGGTTATCAAAATATCATA-TG
* *
17130 TTGGTTATCAAAATTTCAT
1 GTGGTTATCAAAATATCAT
17149 TGGGAAGTCA
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
22 17 0.50
23 17 0.50
ACGTcount: A:0.31, C:0.12, G:0.17, T:0.39
Consensus pattern (22 bp):
GTGGTTATCAAAATATCATATG
Found at i:17162 original size:45 final size:45
Alignment explanation
Indices: 17086--17171 Score: 102
Period size: 45 Copynumber: 1.9 Consensus size: 45
17076 TTTCGTAACG
* * * *
17086 TGGTTATCAATATATCATATGGAGGTTATCAACATCTCATAGTGT
1 TGGTTATCAAAATATCATATGGAAGTCATCAAAATCTCATAGTGT
* *
17131 TGGTTATCAAAATTTCAT-TGGGAAGTCATCAAAATTTCATA
1 TGGTTATCAAAATATCATAT-GGAAGTCATCAAAATCTCATA
17172 TTGAGGTCTT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
44 1 0.03
45 33 0.97
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.37
Consensus pattern (45 bp):
TGGTTATCAAAATATCATATGGAAGTCATCAAAATCTCATAGTGT
Found at i:17163 original size:22 final size:22
Alignment explanation
Indices: 17136--17213 Score: 79
Period size: 22 Copynumber: 3.5 Consensus size: 22
17126 AGTGTTGGTT
*
17136 ATCAAAATTTCATTGGGAAGTC
1 ATCAAAATTTCATTGGGAGGTC
*
17158 ATCAAAATTTCATAT-TGAGGTC
1 ATCAAAATTTCAT-TGGGAGGTC
* *
17180 TTCAAAATTTC-TTAGGGAGGTT
1 ATCAAAATTTCATT-GGGAGGTC
*
17202 AACAAAATTTCA
1 ATCAAAATTTCA
17214 CAAGAAGGTT
Statistics
Matches: 45, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
20 1 0.02
21 1 0.02
22 42 0.93
23 1 0.02
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35
Consensus pattern (22 bp):
ATCAAAATTTCATTGGGAGGTC
Found at i:17448 original size:2 final size:2
Alignment explanation
Indices: 17441--17466 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
17431 CTAAAACTAG
17441 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
17467 AGTTATCAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:17527 original size:22 final size:21
Alignment explanation
Indices: 17468--17583 Score: 106
Period size: 22 Copynumber: 5.2 Consensus size: 21
17458 ATATATATAA
* *
17468 GTTATCAAAATTTTAGAGTGTG
1 GTTATCAAAATTTCATAG-GTG
*
17490 GTTACCAAAATTTCATAGCGTG
1 GTTATCAAAATTTCATAG-GTG
17512 GTTATCAAAATTTCATAGGATCAG
1 GTTATCAAAATTTCATAGG-T--G
* *
17536 GTTATTAAAATTTCTTAGGTTG
1 GTTATCAAAATTTCATAGG-TG
**
17558 GTTATTGAAATTTCATAGGGTG
1 GTTATCAAAATTTCATA-GGTG
17580 GTTA
1 GTTA
17584 ATTATCACAA
Statistics
Matches: 80, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
21 1 0.01
22 58 0.73
23 2 0.03
24 19 0.24
ACGTcount: A:0.31, C:0.09, G:0.21, T:0.40
Consensus pattern (21 bp):
GTTATCAAAATTTCATAGGTG
Found at i:17644 original size:22 final size:21
Alignment explanation
Indices: 17619--17987 Score: 133
Period size: 22 Copynumber: 16.7 Consensus size: 21
17609 ATCAAAGAGA
*
17619 TTATCAAAATGTCATAGCGAGG
1 TTATCAAAATTTCATAG-GAGG
*
17641 TTAT-AAGAATTTCATAGTGTGG
1 TTATCAA-AATTTCATAG-GAGG
*
17663 TTAACAAAATTTCATTAGGAGG
1 TTATCAAAATTTCA-TAGGAGG
* *
17685 TTA-CTAATATTTCATGGGGAGG
1 TTATC-AAAATTTCAT-AGGAGG
* *
17707 TTATCAAAATTTCTTATGAAGG
1 TTATCAAAATTTCATA-GGAGG
*
17729 TTATAAAAGTCTCAATTTCATA--AGG
1 TTAT-CAA-----AATTTCATAGGAGG
* * * *
17754 AGTACCAAAATTTGATAGAAGG
1 -TTATCAAAATTTCATAGGAGG
* *
17776 TTGTC-AAATCTCATA-GAGTG
1 TTATCAAAATTTCATAGGAG-G
* *
17796 ATTATCGAAATTTCATAGAGATCAGA
1 -TTATCAAAATTTCATAG-G---AGG
*
17822 TTATCAAAATTT-ATAGGAAGA
1 TTATCAAAATTTCATAGG-AGG
* * **
17843 TTATCCAATTTTCATAGTGTTG
1 TTATCAAAATTTCATAG-GAGG
*
17865 TTATCAAAATTTCAAAGCGAGG
1 TTATCAAAATTTCATAG-GAGG
* * * *
17887 TTATCAAAATTACATAATGTGA
1 TTATCAAAATTTCAT-AGGAGG
* *
17909 TTATCAGAATTTCATAGAGGGG
1 TTATCAAAATTTCATAG-GAGG
* * * *
17931 TCA-CAAAATTTTATAAAGAGA
1 TTATCAAAATTTCAT-AGGAGG
*
17952 TTATCAAAATTTCATAAAGAGG
1 TTATCAAAATTTCAT-AGGAGG
*
17974 TTATCAAATTTTCA
1 TTATCAAAATTTCA
17988 AAATATGATT
Statistics
Matches: 258, Mismatches: 59, Indels: 60
0.68 0.16 0.16
Matches are distributed among these distances:
19 2 0.01
20 17 0.07
21 37 0.14
22 158 0.61
23 11 0.04
24 5 0.02
25 16 0.06
26 2 0.01
27 2 0.01
28 8 0.03
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.34
Consensus pattern (21 bp):
TTATCAAAATTTCATAGGAGG
Found at i:17999 original size:22 final size:22
Alignment explanation
Indices: 17781--18011 Score: 123
Period size: 22 Copynumber: 10.5 Consensus size: 22
17771 GAAGGTTGTC
* * * *
17781 AAATCTCATAGAGTGATTATCG
1 AAATTTCATAAAGAGATTATCA
*
17803 AAATTTCATAGAGATCAGATTATCA
1 AAATTTCATA-A-A-GAGATTATCA
* *
17828 AAATTT-AT-AGGAAGATTATCC
1 AAATTTCATAAAG-AGATTATCA
* ** *
17849 AATTTTCATAGTGTTG-TTATCA
1 AAATTTCATAAAG-AGATTATCA
* *
17871 AAATTTCA-AAGCGAGGTTATCA
1 AAATTTCATAA-AGAGATTATCA
* * *
17893 AAATTACATAATGTGATTATCA
1 AAATTTCATAAAGAGATTATCA
* * * * *
17915 GAATTTCATAGAGGGGTCA-CA
1 AAATTTCATAAAGAGATTATCA
*
17936 AAATTTTATAAAGAGATTATCA
1 AAATTTCATAAAGAGATTATCA
*
17958 AAATTTCATAAAGAGGTTATCA
1 AAATTTCATAAAGAGATTATCA
* * *
17980 AATTTTCA-AAATATGATTATAA
1 AAATTTCATAAAGA-GATTATCA
18002 AAATTTCATA
1 AAATTTCATA
18012 GTGGTATTTT
Statistics
Matches: 155, Mismatches: 42, Indels: 23
0.70 0.19 0.10
Matches are distributed among these distances:
21 34 0.22
22 100 0.65
23 5 0.03
24 3 0.02
25 13 0.08
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.35
Consensus pattern (22 bp):
AAATTTCATAAAGAGATTATCA
Found at i:18010 original size:44 final size:44
Alignment explanation
Indices: 17865--18011 Score: 140
Period size: 44 Copynumber: 3.4 Consensus size: 44
17855 CATAGTGTTG
* * * * *
17865 TTATCAAAATTTCA-AAGCGAGGTTATCAAAATTACATAATGTGA
1 TTATCAAAATTTCATAA-AGAGGTTATCAAATTTTCAAAATATGA
* * * * *
17909 TTATCAGAATTTCATAGAGGGGTCA-CAAAATTTT-ATAAAGA-GA
1 TTATCAAAATTTCATAAAGAGGTTATC-AAATTTTCA-AAATATGA
17952 TTATCAAAATTTCATAAAGAGGTTATCAAATTTTCAAAATATGA
1 TTATCAAAATTTCATAAAGAGGTTATCAAATTTTCAAAATATGA
*
17996 TTATAAAAATTTCATA
1 TTATCAAAATTTCATA
18012 GTGGTATTTT
Statistics
Matches: 81, Mismatches: 16, Indels: 12
0.74 0.15 0.11
Matches are distributed among these distances:
43 36 0.44
44 44 0.54
45 1 0.01
ACGTcount: A:0.44, C:0.10, G:0.12, T:0.34
Consensus pattern (44 bp):
TTATCAAAATTTCATAAAGAGGTTATCAAATTTTCAAAATATGA
Found at i:18118 original size:20 final size:20
Alignment explanation
Indices: 18093--18143 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
18083 TTATGGAATA
18093 ATCAAAATTTCAGAGAGGAT
1 ATCAAAATTTCAGAGAGGAT
*
18113 ATCAAAATTTCAGGGAGGAT
1 ATCAAAATTTCAGAGAGGAT
18133 ATCAAAATTTC
1 ATCAAAATTTC
18144 GTATGAAGGT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.43, C:0.12, G:0.18, T:0.27
Consensus pattern (20 bp):
ATCAAAATTTCAGAGAGGAT
Found at i:18269 original size:44 final size:44
Alignment explanation
Indices: 18093--18689 Score: 244
Period size: 44 Copynumber: 13.9 Consensus size: 44
18083 TTATGGAATA
* * ** *
18093 ATCAAAATTTCAGAGAG-GA-TATCAAAATTTC--AGGGAGGAT
1 ATCAAAATTTCATAGGGAGATTATCAAAATTTCATAATGAGGTT
* * * * * * * *
18133 ATCAAAATTTCGTATGAAGGTTGTCAAAATTTCCTAGTTTA-GTT
1 ATCAAAATTTCATAGGGAGATTATCAAAATTTCATA-ATGAGGTT
* * * * *
18177 TTCAAAATTTCATAAGAGG-G-TTATCAAAATTCCATAGT-ATGTAG
1 ATCAAAATTTCAT-AG-GGAGATTATCAAAATTTCATAATGAGGT-T
*
18221 ATCAAAATTTCATAGGGAGATTAACAAAATTTCATAATGAGGTT
1 ATCAAAATTTCATAGGGAGATTATCAAAATTTCATAATGAGGTT
** * *
18265 ATCAAAAAATCATAGGGAGGTTATCAAAA-TT--T-GT-A-GTT
1 ATCAAAATTTCATAGGGAGATTATCAAAATTTCATAATGAGGTT
* * * * *
18303 ATCAAGATTTCATA-AGAAATTATCAAAATTTTAT-AGGTAGGTTT
1 ATCAAAATTTCATAGGGAGATTATCAAAATTTCATAATG-AGG-TT
* * *
18347 ATCAAAATTTTATAGGAAGATTTATCAAAATTTCATAGTGAGGTT
1 ATCAAAATTTCATAGGGAGA-TTATCAAAATTTCATAATGAGGTT
* * * * * *
18392 ATCACAATTTCATAGTGTGATTATCAAAATTTCATAGTGTGATT
1 ATCAAAATTTCATAGGGAGATTATCAAAATTTCATAATGAGGTT
* * * * *
18436 A-CTAATAA-TTCATATGGAGATTTTTAAATTTTCATAATGTGGTT
1 ATC-AA-AATTTCATAGGGAGATTATCAAAATTTCATAATGAGGTT
* * * * * *
18480 ATC--AA--T-ATATGGAGGTTATCAACATCTCATAGTGTTGGTT
1 ATCAAAATTTCATAGGGAGATTATCAAAATTTCATAATG-AGGTT
* *
18520 ATCAAAATTTCATTGGGA-AGTTATCAAAATTTCATATTGAGGTCT
1 ATCAAAATTTCATAGGGAGA-TTATCAAAATTTCATAATGAGGT-T
* * * * **
18565 -TCAAAATTCCTTAGGGAGGTTAACCGAATTTCATAA-GAAGGTT
1 ATCAAAATTTCATAGGGAGATTATCAAAATTTCATAATG-AGGTT
* * *** * * * * *
18608 A-AAAAAATT-ATAAAAAGATTCTCGAAATTGCATAGT-ATCGTT
1 ATCAAAATTTCATAGGGAGATTATCAAAATTTCATAATGA-GGTT
* *
18650 ATTAAAATTTCATAGGGAAGGTTATCAAAATTTCATAATG
1 ATCAAAATTTCATAGGG-AGATTATCAAAATTTCATAATG
18690 GGGTCATAAA
Statistics
Matches: 405, Mismatches: 110, Indels: 78
0.68 0.19 0.13
Matches are distributed among these distances:
37 11 0.03
38 16 0.04
39 22 0.05
40 23 0.06
41 5 0.01
42 36 0.09
43 23 0.06
44 184 0.45
45 66 0.16
46 18 0.04
47 1 0.00
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (44 bp):
ATCAAAATTTCATAGGGAGATTATCAAAATTTCATAATGAGGTT
Found at i:18349 original size:23 final size:23
Alignment explanation
Indices: 18322--18428 Score: 114
Period size: 23 Copynumber: 4.7 Consensus size: 23
18312 TCATAAGAAA
*
18322 TTATCAAAATTTTATAGGTAGGT
1 TTATCAAAATTTCATAGGTAGGT
* * *
18345 TTATCAAAATTTTATAGGAAGAT
1 TTATCAAAATTTCATAGGTAGGT
18368 TTATCAAAATTTCATA-GTGAGG-
1 TTATCAAAATTTCATAGGT-AGGT
* *
18390 TTATCACAATTTCATA-GT-GTGA
1 TTATCAAAATTTCATAGGTAG-GT
18412 TTATCAAAATTTCATAG
1 TTATCAAAATTTCATAG
18429 TGTGATTACT
Statistics
Matches: 73, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
20 1 0.01
21 1 0.01
22 33 0.45
23 38 0.52
ACGTcount: A:0.37, C:0.08, G:0.14, T:0.40
Consensus pattern (23 bp):
TTATCAAAATTTCATAGGTAGGT
Found at i:18429 original size:22 final size:22
Alignment explanation
Indices: 18093--18560 Score: 191
Period size: 22 Copynumber: 21.9 Consensus size: 22
18083 TTATGGAATA
* *
18093 ATCAAAATTTCAGAGAG-GA-T
1 ATCAAAATTTCATAGTGAGATT
*
18113 ATCAAAATTTC--AGGGAGGA-T
1 ATCAAAATTTCATAGTGA-GATT
* *
18133 ATCAAAATTTCGTA-TGAAGGTT
1 ATCAAAATTTCATAGTG-AGATT
* * *
18155 GTCAAAATTTCCTAGTTTAG-TT
1 ATCAAAATTTCATAG-TGAGATT
* * *
18177 TTCAAAATTTCATA-AGAGGGTT
1 ATCAAAATTTCATAGTGA-GATT
* *
18199 ATCAAAATTCCATAGT-ATG-TAG
1 ATCAAAATTTCATAGTGA-GAT-T
*
18221 ATCAAAATTTCATAGGGAGATT
1 ATCAAAATTTCATAGTGAGATT
* * *
18243 AACAAAATTTCATAATGAGGTT
1 ATCAAAATTTCATAGTGAGATT
** * *
18265 ATCAAAAAATCATAGGGAGGTT
1 ATCAAAATTTCATAGTGAGATT
18287 ATCAAAA-TT--T-GT-AG-TT
1 ATCAAAATTTCATAGTGAGATT
* * *
18303 ATCAAGATTTCATA-AGAAATT
1 ATCAAAATTTCATAGTGAGATT
* *
18324 ATCAAAATTTTATAG-GTAGGTTT
1 ATCAAAATTTCATAGTG-A-GATT
*
18347 ATCAAAATTTTATAG-GAAGATTT
1 ATCAAAATTTCATAGTG-AGA-TT
*
18370 ATCAAAATTTCATAGTGAGGTT
1 ATCAAAATTTCATAGTGAGATT
* *
18392 ATCACAATTTCATAGTGTGATT
1 ATCAAAATTTCATAGTGAGATT
*
18414 ATCAAAATTTCATAGTGTGATT
1 ATCAAAATTTCATAGTGAGATT
18436 A-CTAATAA-TTCATA-TGGAGATT
1 ATC-AA-AATTTCATAGT-GAGATT
* * * * * *
18458 TTTAAATTTTCATAATGTGGTT
1 ATCAAAATTTCATAGTGAGATT
* *
18480 ATC--AATAT-AT-G-GAGGTT
1 ATCAAAATTTCATAGTGAGATT
* * * *
18497 ATCAACATCTCATAGTGTTGGTT
1 ATCAAAATTTCATAGTG-AGATT
* *
18520 ATCAAAATTTCATTGGGA-AGTT
1 ATCAAAATTTCATAGTGAGA-TT
*
18542 ATCAAAATTTCATATTGAG
1 ATCAAAATTTCATAGTGAG
18561 GTCTTCAAAA
Statistics
Matches: 341, Mismatches: 68, Indels: 75
0.70 0.14 0.15
Matches are distributed among these distances:
16 8 0.02
17 12 0.04
18 4 0.01
19 7 0.02
20 32 0.09
21 24 0.07
22 191 0.56
23 61 0.18
24 2 0.01
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.37
Consensus pattern (22 bp):
ATCAAAATTTCATAGTGAGATT
Found at i:18532 original size:23 final size:22
Alignment explanation
Indices: 18490--18686 Score: 87
Period size: 22 Copynumber: 9.0 Consensus size: 22
18480 ATCAATATAT
* *
18490 GGAGGTTATCAACATCTCATAG
1 GGAGGTTATCAAAATTTCATAG
** *
18512 TGTTGGTTATCAAAATTTCATTG
1 -GGAGGTTATCAAAATTTCATAG
* *
18535 GGAAGTTATCAAAATTTCATAT
1 GGAGGTTATCAAAATTTCATAG
* * *
18557 TGAGGTCT-TCAAAATTCCTTAG
1 GGAGGT-TATCAAAATTTCATAG
* ** *
18579 GGAGGTTAACCGAATTTCATAA
1 GGAGGTTATCAAAATTTCATAG
* * * *
18601 GAAGGTTA-AAAAAATT-ATAA
1 GGAGGTTATCAAAATTTCATAG
** * * * *
18621 AAAGATTCTCGAAATTGCATA-
1 GGAGGTTATCAAAATTTCATAG
* * *
18642 GTATCGTTATTAAAATTTCATAG
1 GGA-GGTTATCAAAATTTCATAG
18665 GGAAGGTTATCAAAATTTCATA
1 GG-AGGTTATCAAAATTTCATA
18687 ATGGGGTCAT
Statistics
Matches: 122, Mismatches: 45, Indels: 14
0.67 0.25 0.08
Matches are distributed among these distances:
20 9 0.07
21 10 0.08
22 67 0.55
23 35 0.29
24 1 0.01
ACGTcount: A:0.38, C:0.11, G:0.17, T:0.34
Consensus pattern (22 bp):
GGAGGTTATCAAAATTTCATAG
Found at i:21353 original size:21 final size:21
Alignment explanation
Indices: 21329--21369 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
21319 TAACAAAATT
21329 TCATAAAGAGGTTATAAAAAA
1 TCATAAAGAGGTTATAAAAAA
** *
21350 TCATATGGAGGTTATCAAAA
1 TCATAAAGAGGTTATAAAAA
21370 TTTCATATGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.49, C:0.07, G:0.17, T:0.27
Consensus pattern (21 bp):
TCATAAAGAGGTTATAAAAAA
Found at i:21369 original size:22 final size:22
Alignment explanation
Indices: 21299--21378 Score: 63
Period size: 22 Copynumber: 3.7 Consensus size: 22
21289 TACTAGGGTG
* * *
21299 TCAAAAAATTATAGGGAGATTA
1 TCAAAAAATCATATGGAGGTTA
* ** **
21321 ACAAAATTTCATAAAGAGGTTA
1 TCAAAAAATCATATGGAGGTTA
21343 T-AAAAAATCATATGGAGGTTA
1 TCAAAAAATCATATGGAGGTTA
**
21364 TCAAAATTTCATATG
1 TCAAAAAATCATATG
21379 AAGTTTTATT
Statistics
Matches: 43, Mismatches: 14, Indels: 2
0.73 0.24 0.03
Matches are distributed among these distances:
21 17 0.40
22 26 0.60
ACGTcount: A:0.47, C:0.07, G:0.15, T:0.30
Consensus pattern (22 bp):
TCAAAAAATCATATGGAGGTTA
Found at i:21590 original size:2 final size:2
Alignment explanation
Indices: 21583--21607 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
21573 TGGTTACCTC
21583 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 A
21608 CCATATAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:24710 original size:17 final size:17
Alignment explanation
Indices: 24688--24732 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 17
24678 TTTCTGATTT
24688 AATTTCTAAGTATTGTA
1 AATTTCTAAGTATTGTA
*
24705 AATTTCT--G-ATT-TT
1 AATTTCTAAGTATTGTA
24718 AATTTCTAAGTATTG
1 AATTTCTAAGTATTG
24733 AAAACCGCCT
Statistics
Matches: 23, Mismatches: 1, Indels: 8
0.72 0.03 0.25
Matches are distributed among these distances:
13 8 0.35
14 3 0.13
15 2 0.09
16 3 0.13
17 7 0.30
ACGTcount: A:0.31, C:0.07, G:0.11, T:0.51
Consensus pattern (17 bp):
AATTTCTAAGTATTGTA
Found at i:24715 original size:29 final size:30
Alignment explanation
Indices: 24676--24732 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
24666 AGCTAAGAGT
24676 AATTTCTGA-TTTAATTTCTAAGTATTGTA
1 AATTTCTGATTTTAATTTCTAAGTATTGTA
24705 AATTTCTGATTTTAATTTCTAAGTATTG
1 AATTTCTGATTTTAATTTCTAAGTATTG
24733 AAAACCGCCT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
29 9 0.33
30 18 0.67
ACGTcount: A:0.30, C:0.07, G:0.11, T:0.53
Consensus pattern (30 bp):
AATTTCTGATTTTAATTTCTAAGTATTGTA
Found at i:42253 original size:20 final size:22
Alignment explanation
Indices: 42214--42254 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 22
42204 GCTGGAATGT
*
42214 AAGTTTCTTCTGTTTTTTGTGC
1 AAGTTTCTTCTGTATTTTGTGC
42236 AAGTTT-TT-TGTATTTTGTG
1 AAGTTTCTTCTGTATTTTGTG
42255 GACATTACTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 10 0.56
21 2 0.11
22 6 0.33
ACGTcount: A:0.12, C:0.07, G:0.20, T:0.61
Consensus pattern (22 bp):
AAGTTTCTTCTGTATTTTGTGC
Done.