Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007142.1 Corchorus capsularis cultivar CVL-1 contig07163, 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: 39990
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:4755 original size:14 final size:13
Alignment explanation
Indices: 4726--4761 Score: 63
Period size: 13 Copynumber: 2.7 Consensus size: 13
4716 GTTTCATATC
4726 AAATCCAATTTGAA
1 AAAT-CAATTTGAA
4740 AAATCAATTTGAA
1 AAATCAATTTGAA
4753 AAATCAATT
1 AAATCAATT
4762 AATTTTGATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 18 0.82
14 4 0.18
ACGTcount: A:0.53, C:0.11, G:0.06, T:0.31
Consensus pattern (13 bp):
AAATCAATTTGAA
Found at i:5753 original size:107 final size:107
Alignment explanation
Indices: 5616--5862 Score: 359
Period size: 107 Copynumber: 2.3 Consensus size: 107
5606 GGTTTTTTTA
*
5616 TTATAGAGTTTTAGAAATAAAATATAAAACTAATTTCACTAAGTTTAGCCCCAAATTAAAATTTT
1 TTATAGGGTTTTAGAAATAAAATATAAAACTAATTTCACTAAGTTTAGCCCCAAATTAAAATTTT
* ** *
5681 ATTTTTATTCTAAGGGTAAATTTTAAAATTAATAATTTATTG
66 ATCTTTATTCTAAGGGTAAATTGCAAAATTAATAATATATTG
* * **
5723 TTATAGGGTTTTAGAAATAAAATACAAAACTGATTTCACTAAGTTTAGCCCCAAATTAATTTTTT
1 TTATAGGGTTTTAGAAATAAAATATAAAACTAATTTCACTAAGTTTAGCCCCAAATTAAAATTTT
* * *
5788 GTCTTTATTTTAAGGGTAAATTGCATAATTAATAATATATTG
66 ATCTTTATTCTAAGGGTAAATTGCAAAATTAATAATATATTG
* * *
5830 TTATAAGGTTTTATAAATAAAATATATAACTAA
1 TTATAGGGTTTTAGAAATAAAATATAAAACTAA
5863 ATCTTTACTT
Statistics
Matches: 123, Mismatches: 17, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
107 123 1.00
ACGTcount: A:0.41, C:0.08, G:0.10, T:0.41
Consensus pattern (107 bp):
TTATAGGGTTTTAGAAATAAAATATAAAACTAATTTCACTAAGTTTAGCCCCAAATTAAAATTTT
ATCTTTATTCTAAGGGTAAATTGCAAAATTAATAATATATTG
Found at i:6785 original size:31 final size:31
Alignment explanation
Indices: 6750--6809 Score: 104
Period size: 31 Copynumber: 1.9 Consensus size: 31
6740 ATGTTTTTCG
6750 ATTGTACCCTTATT-TTTAAAACATATTTCCA
1 ATTGTACCCTT-TTCTTTAAAACATATTTCCA
6781 ATTGTACCCTTTTCTTTAAAACATATTTC
1 ATTGTACCCTTTTCTTTAAAACATATTTC
6810 TAAATTGCCA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
30 2 0.07
31 26 0.93
ACGTcount: A:0.30, C:0.20, G:0.03, T:0.47
Consensus pattern (31 bp):
ATTGTACCCTTTTCTTTAAAACATATTTCCA
Found at i:7334 original size:22 final size:21
Alignment explanation
Indices: 7264--7371 Score: 99
Period size: 22 Copynumber: 5.0 Consensus size: 21
7254 TGTCTCTAAG
*
7264 TGGTTATCAAAATTTCACAAGA
1 TGGTTATCAAAATTTCA-TAGA
* *
7286 TGGTTATTATAATTTCATGAGA
1 TGGTTATCAAAATTTCAT-AGA
* *
7308 AGGTTATCAAAATTTCATAGTT
1 TGGTTATCAAAATTTCATAG-A
* * *
7330 TGGTTACCAAAATTCCATAGTG
1 TGGTTATCAAAATTTCATAG-A
*
7352 TGGTTACCAAAATTTCATAG
1 TGGTTATCAAAATTTCATAG
7372 GATCAGATTA
Statistics
Matches: 72, Mismatches: 12, Indels: 4
0.82 0.14 0.05
Matches are distributed among these distances:
21 2 0.03
22 70 0.97
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.37
Consensus pattern (21 bp):
TGGTTATCAAAATTTCATAGA
Found at i:7592 original size:22 final size:21
Alignment explanation
Indices: 7544--7850 Score: 133
Period size: 22 Copynumber: 13.8 Consensus size: 21
7534 AATGGGGATC
* *
7544 AGGTTATCAAAATTTTATAGTG
1 AGGTTATCAAAATTTCATAG-A
*
7566 TGGTTATCAAAATTTCATATGA
1 AGGTTATCAAAATTTCATA-GA
*
7588 AGGTTATAAAAGTCTCAATTTCATAG-
1 AGGTTAT-CAA-----AATTTCATAGA
* * *
7614 -GGAGTACCAAAATTTGATAGA
1 AGG-TTATCAAAATTTCATAGA
*
7635 AGGTTATC-AAATCTCATAG-
1 AGGTTATCAAAATTTCATAGA
*
7654 AGTGATTATCGAAATTTCATAGA
1 AG-G-TTATCAAAATTTCATAGA
7677 GATCGGATTATCAAAATTT-ATAGAA
1 -A--GG-TTATCAAAATTTCATAG-A
*
7702 AGATTATCAAAATTTCATAG-
1 AGGTTATCAAAATTTCATAGA
* * *
7722 TGTTGTTATCAAAATTTCAAAGCG
1 AG--GTTATCAAAATTTCATAG-A
*
7746 AGGTTATCAAAATTACATA-A
1 AGGTTATCAAAATTTCATAGA
* *
7766 TGTGATTATCAGAATTTCATAGA
1 AG-G-TTATCAAAATTTCATAGA
* * * * *
7789 GGGGTCAACAAAATTTTATAAA
1 -AGGTTATCAAAATTTCATAGA
* *
7811 GAGGTTATGAAAATTTCATAAA
1 -AGGTTATCAAAATTTCATAGA
*
7833 GAGGTTATCAAATTTTCA
1 -AGGTTATCAAAATTTCA
7851 AAATGTGATT
Statistics
Matches: 219, Mismatches: 39, Indels: 54
0.70 0.12 0.17
Matches are distributed among these distances:
19 2 0.01
20 21 0.10
21 21 0.10
22 131 0.60
23 5 0.02
24 8 0.04
25 18 0.08
26 3 0.01
27 1 0.00
28 9 0.04
ACGTcount: A:0.40, C:0.09, G:0.16, T:0.34
Consensus pattern (21 bp):
AGGTTATCAAAATTTCATAGA
Found at i:7662 original size:21 final size:23
Alignment explanation
Indices: 7621--7850 Score: 135
Period size: 22 Copynumber: 10.4 Consensus size: 23
7611 TAGGGAGTAC
* *
7621 CAAAATTTGATAGA-A-GGTTAT
1 CAAAATTTCATAGAGATGATTAT
*
7642 C-AAATCTCATAGAG-TGATTAT
1 CAAAATTTCATAGAGATGATTAT
*
7663 CGAAATTTCATAGAGATCGGATTAT
1 CAAAATTTCATAGAGAT--GATTAT
*
7688 CAAAATTT-ATAGA-AAGATTAT
1 CAAAATTTCATAGAGATGATTAT
* *
7709 CAAAATTTCATAGTGTTG-TTAT
1 CAAAATTTCATAGAGATGATTAT
* * *
7731 CAAAATTTCAAAGCGA-GGTTAT
1 CAAAATTTCATAGAGATGATTAT
*
7753 CAAAATTACATA-ATG-TGATTAT
1 CAAAATTTCATAGA-GATGATTAT
* * * * *
7775 CAGAATTTCATAGAG-GGGTCAA
1 CAAAATTTCATAGAGATGATTAT
* * *
7797 CAAAATTTTATAAAGA-GGTTAT
1 CAAAATTTCATAGAGATGATTAT
* * *
7819 GAAAATTTCATAAAGA-GGTTAT
1 CAAAATTTCATAGAGATGATTAT
*
7841 CAAATTTTCA
1 CAAAATTTCA
7851 AAATGTGATT
Statistics
Matches: 165, Mismatches: 31, Indels: 25
0.75 0.14 0.11
Matches are distributed among these distances:
20 10 0.06
21 22 0.13
22 111 0.67
23 4 0.02
24 5 0.03
25 13 0.08
ACGTcount: A:0.41, C:0.10, G:0.16, T:0.33
Consensus pattern (23 bp):
CAAAATTTCATAGAGATGATTAT
Found at i:7775 original size:44 final size:44
Alignment explanation
Indices: 7682--7866 Score: 162
Period size: 44 Copynumber: 4.2 Consensus size: 44
7672 ATAGAGATCG
* * * *
7682 GATTATCAAAATTT-ATAGAAAGATTATCAAAATTTCATAGTGTT
1 GATTATCAAAATTTCAAAGAGAGGTTATCAAAATTTCATAATG-T
* *
7726 G-TTATCAAAATTTCAAAGCGAGGTTATCAAAATTACATAATGT
1 GATTATCAAAATTTCAAAGAGAGGTTATCAAAATTTCATAATGT
* * * * * * * *
7769 GATTATCAGAATTTCATAGAGGGGTCAACAAAATTTTATAAAGA
1 GATTATCAAAATTTCAAAGAGAGGTTATCAAAATTTCATAATGT
* * * *
7813 GGTTATGAAAATTTCATAA-AGAGGTTATCAAATTTTCAAAATGT
1 GATTATCAAAATTTCA-AAGAGAGGTTATCAAAATTTCATAATGT
7857 GATTA-CAAAA
1 GATTATCAAAA
7867 ATCTCATAGT
Statistics
Matches: 108, Mismatches: 30, Indels: 7
0.74 0.21 0.05
Matches are distributed among these distances:
43 18 0.17
44 89 0.82
45 1 0.01
ACGTcount: A:0.43, C:0.09, G:0.15, T:0.34
Consensus pattern (44 bp):
GATTATCAAAATTTCAAAGAGAGGTTATCAAAATTTCATAATGT
Found at i:7801 original size:66 final size:66
Alignment explanation
Indices: 7703--7850 Score: 154
Period size: 66 Copynumber: 2.2 Consensus size: 66
7693 TTTATAGAAA
* ** * * *
7703 GATTATCAAAATTTCATAGTGTTGTTATCAAAATTTCA-AAGCGAGGTTATCAAAATTACATAAT
1 GATTATCAAAATTTCATAGAGGGGTCAACAAAATTTCATAA-AGAGGTTATCAAAATTACATAAT
7767 GT
65 GT
* * * * *
7769 GATTATCAGAATTTCATAGAGGGGTCAACAAAATTTTATAAAGAGGTTATGAAAATTTCATAAAG
1 GATTATCAAAATTTCATAGAGGGGTCAACAAAATTTCATAAAGAGGTTATCAAAATTACATAATG
*
7834 A
66 T
* *
7835 GGTTATCAAATTTTCA
1 GATTATCAAAATTTCA
7851 AAATGTGATT
Statistics
Matches: 66, Mismatches: 15, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
66 64 0.97
67 2 0.03
ACGTcount: A:0.41, C:0.09, G:0.16, T:0.34
Consensus pattern (66 bp):
GATTATCAAAATTTCATAGAGGGGTCAACAAAATTTCATAAAGAGGTTATCAAAATTACATAATG
T
Found at i:7917 original size:22 final size:21
Alignment explanation
Indices: 7888--8513 Score: 215
Period size: 22 Copynumber: 29.0 Consensus size: 21
7878 GTATTTCTGG
7888 GGAGGTTATCAAAATTTCATA
1 GGAGGTTATCAAAATTTCATA
* *
7909 GTATGGTTA-CCAAA--T--TA
1 GGA-GGTTATCAAAATTTCATA
* * *
7926 GGAAGGTTATTAAACTTTTATTA
1 GG-AGGTTATCAAAATTTCA-TA
*
7949 TGGA-GTAATCAAAATTTCA-A
1 -GGAGGTTATCAAAATTTCATA
*
7969 GGAGGATATCAAAATTTCATA
1 GGAGGTTATCAAAATTTCATA
* * *
7990 GTTTA-GTTTTCAAAATTTCACA
1 G--GAGGTTATCAAAATTTCATA
* *
8012 AGAGGGTTAACAAAATTTCATA
1 GGA-GGTTATCAAAATTTCATA
* * *
8034 GTATGTAGATCAAAATTTCATA
1 GGAGGT-TATCAAAATTTCATA
* *
8056 GGGAGATTAACAAAATTTCATAA
1 -GGAGGTTATCAAAATTTCAT-A
* * **
8079 TGAGATTATCAAAAAATCATA
1 GGAGGTTATCAAAATTTCATA
8100 GGGAGGTTATCAAAA-TT--T-
1 -GGAGGTTATCAAAATTTCATA
* *
8118 GTA-GTTATCAAGATTTCATAA
1 GGAGGTTATCAAAATTTCAT-A
* * *
8139 GAAAGTTATCAAAATTTTATA
1 GGAGGTTATCAAAATTTCATA
*
8160 GGGAGGTTTATCAAAATTTTATA
1 -GGAGG-TTATCAAAATTTCATA
*
8183 GGAAGATTTATCAAAATTTCATA
1 GG-AG-GTTATCAAAATTTCATA
*
8206 GCGAGGTTATCACAATTTCATA
1 G-GAGGTTATCAAAATTTCATA
* * *
8228 GTGTGATTATCAAAATTTCAGA
1 G-GAGGTTATCAAAATTTCATA
* *
8250 GTGTGATTA-CTAACAA-TTCATA
1 G-GAGGTTATC-AA-AATTTCATA
* * *
8272 TGGAGGTTTTTAAATTTTCATAA
1 -GGAGGTTATCAAAATTTCAT-A
* * * * *
8295 CGTGGTTATCAATATATCACA
1 GGAGGTTATCAAAATTTCATA
* * *
8316 CAGAGGTTATCAACATCTCATA
1 -GGAGGTTATCAAAATTTCATA
* * *
8338 GTGTTGGTAATCAAAATTTCATTG
1 G-G-AGGTTATCAAAATTTCA-TA
*
8362 GGAAGTTATCAAAATTTCATA
1 GGAGGTTATCAAAATTTCATA
* * *
8383 TTGAGGTCT-TCAAAATTCCTTA
1 -GGAGGT-TATCAAAATTTCATA
* * *
8405 GGGAAGTTAACCAAATTTCATAA
1 -GGAGGTTATCAAAATTTCAT-A
* **
8428 GAAGGTTAAAAAAATTT-ATAA
1 GGAGGTTATCAAAATTTCAT-A
** * * *
8449 AAAAGTTCTCAAAATTCCATA
1 GGAGGTTATCAAAATTTCATA
* * *
8470 GTATTGTTATTAAAATTTCATAA
1 GGA-GGTTATCAAAATTTCAT-A
**
8493 TAAGGTTATCAAAATTTCATA
1 GGAGGTTATCAAAATTTCATA
8514 ATGGGATCAT
Statistics
Matches: 444, Mismatches: 114, Indels: 94
0.68 0.17 0.14
Matches are distributed among these distances:
16 9 0.02
17 12 0.03
18 3 0.01
19 6 0.01
20 16 0.04
21 38 0.09
22 289 0.65
23 66 0.15
24 5 0.01
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.35
Consensus pattern (21 bp):
GGAGGTTATCAAAATTTCATA
Found at i:8173 original size:45 final size:44
Alignment explanation
Indices: 8121--8227 Score: 126
Period size: 45 Copynumber: 2.4 Consensus size: 44
8111 AAAATTTGTA
* *
8121 GTTATCAAGATTTCATAAGAA-AGTTATCAAAATTTTATAGGGAG
1 GTTATCAA-ATTTCATAAGAAGAGTTATCAAAATTTCATAGCGAG
* * *
8165 GTTTATCAAAATTTTATAGGAAGATTTATCAAAATTTCATAGCGAG
1 G-TTATC-AAATTTCATAAGAAGAGTTATCAAAATTTCATAGCGAG
8211 GTTATCACAATTTCATA
1 GTTATCA-AATTTCATA
8228 GTGTGATTAT
Statistics
Matches: 53, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
44 2 0.04
45 28 0.53
46 23 0.43
ACGTcount: A:0.39, C:0.09, G:0.15, T:0.36
Consensus pattern (44 bp):
GTTATCAAATTTCATAAGAAGAGTTATCAAAATTTCATAGCGAG
Found at i:8528 original size:22 final size:22
Alignment explanation
Indices: 8481--8528 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
8471 TATTGTTATT
* *
8481 AAAATTTCATAATAAGGTTATC
1 AAAATTTCATAATAAGGTCATA
*
8503 AAAATTTCATAAT-GGGATCATA
1 AAAATTTCATAATAAGG-TCATA
8525 AAAA
1 AAAA
8529 ATAATGTAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 2 0.09
22 20 0.91
ACGTcount: A:0.50, C:0.08, G:0.10, T:0.31
Consensus pattern (22 bp):
AAAATTTCATAATAAGGTCATA
Found at i:9092 original size:45 final size:45
Alignment explanation
Indices: 9025--9112 Score: 158
Period size: 45 Copynumber: 2.0 Consensus size: 45
9015 TGATTTGAAT
* *
9025 ATATTCAATCAAATATTGAAATCAAATCAATGAAATTTCCATTTA
1 ATATTCAATCAAATATTCAAATCAAATCAATGAAATTGCCATTTA
9070 ATATTCAATCAAATATTCAAATCAAATCAATGAAATTGCCATT
1 ATATTCAATCAAATATTCAAATCAAATCAATGAAATTGCCATT
9113 AACAATGAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.47, C:0.15, G:0.05, T:0.34
Consensus pattern (45 bp):
ATATTCAATCAAATATTCAAATCAAATCAATGAAATTGCCATTTA
Found at i:9094 original size:13 final size:12
Alignment explanation
Indices: 9025--9096 Score: 53
Period size: 12 Copynumber: 6.2 Consensus size: 12
9015 TGATTTGAAT
9025 ATATTCAATCAA
1 ATATTCAATCAA
*
9037 ATATTGAAATC-A
1 ATATT-CAATCAA
*
9049 A-A-TCAATGAA
1 ATATTCAATCAA
* **
9059 AT-TTCCATTTA
1 ATATTCAATCAA
9070 ATATTCAATCAA
1 ATATTCAATCAA
9082 ATATTCAAATCAA
1 ATATTC-AATCAA
9095 AT
1 AT
9097 CAATGAAATT
Statistics
Matches: 45, Mismatches: 9, Indels: 11
0.69 0.14 0.17
Matches are distributed among these distances:
9 3 0.07
10 3 0.07
11 8 0.18
12 19 0.42
13 12 0.27
ACGTcount: A:0.49, C:0.14, G:0.03, T:0.35
Consensus pattern (12 bp):
ATATTCAATCAA
Found at i:11763 original size:2 final size:2
Alignment explanation
Indices: 11756--11817 Score: 78
Period size: 2 Copynumber: 32.0 Consensus size: 2
11746 TACAGTTTTA
11756 AT AT AT AT AT AT AT AT GAT AT AT AT AT AT AT AT AT AT GAT A- AT
1 AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT -AT AT AT
11799 A- AT A- AT AT AT A- AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
11818 GATTTCACTT
Statistics
Matches: 54, Mismatches: 0, Indels: 12
0.82 0.00 0.18
Matches are distributed among these distances:
1 4 0.07
2 46 0.85
3 4 0.07
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (2 bp):
AT
Found at i:11790 original size:25 final size:23
Alignment explanation
Indices: 11754--11820 Score: 102
Period size: 21 Copynumber: 2.9 Consensus size: 23
11744 TCTACAGTTT
11754 TAATATATATATATATATGAT-A
1 TAATATATATATATATATGATAA
11776 T-ATATATATATATATATGATAA
1 TAATATATATATATATATGATAA
11798 TAATAATATATAATATATATGAT
1 TAAT-ATATAT-ATATATATGAT
11821 TTCACTTATG
Statistics
Matches: 41, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
21 19 0.46
22 3 0.07
23 2 0.05
24 6 0.15
25 11 0.27
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (23 bp):
TAATATATATATATATATGATAA
Found at i:12155 original size:26 final size:26
Alignment explanation
Indices: 12107--12161 Score: 69
Period size: 26 Copynumber: 2.1 Consensus size: 26
12097 TTAGTTTTTA
*
12107 TATATATAATTATTTTTTATTATTAT
1 TATATATAATTATTTTTTATTATAAT
12133 TATATATAATT-TTAGTTTT-TTATAAT
1 TATATATAATTATT--TTTTATTATAAT
12159 TAT
1 TAT
12162 TTTAGATTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
25 2 0.08
26 20 0.77
27 4 0.15
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.64
Consensus pattern (26 bp):
TATATATAATTATTTTTTATTATAAT
Found at i:12161 original size:29 final size:26
Alignment explanation
Indices: 12107--12162 Score: 76
Period size: 29 Copynumber: 2.0 Consensus size: 26
12097 TTAGTTTTTA
*
12107 TATATATAATTATTTTTTATTATTAT
1 TATATATAATTATTTTTTATAATTAT
12133 TATATATAATTTTAGTTTTTTATAATTAT
1 TATATATAA--TTA-TTTTTTATAATTAT
12162 T
1 T
12163 TTAGATTATT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 9 0.35
28 3 0.12
29 14 0.54
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (26 bp):
TATATATAATTATTTTTTATAATTAT
Found at i:12165 original size:19 final size:19
Alignment explanation
Indices: 12062--12201 Score: 79
Period size: 20 Copynumber: 6.8 Consensus size: 19
12052 TTTATTATTA
12062 TTATTATATATAATTTTAGT
1 TTATTATATAT-ATTTTAGT
* *
12082 TT-TTAGATTTTAATTTTAGTTT
1 TTATTATA-TAT-ATTTTAG--T
*
12104 TTATATATATAATTATTTTTTATT
1 TTAT-TATAT-A-TA--TTTTAGT
12128 ATTATTATATATAATTTTAGT
1 -TTATTATATAT-ATTTTAGT
* *
12149 TTTTTATA-ATTATTTTAGA
1 TTATTATATA-TATTTTAGT
12168 TTATTATATATAGTTTTAGT
1 TTATTATATATA-TTTTAGT
*
12188 TTATAAT-TATATTT
1 TTATTATATATATTT
12202 ATATATATGA
Statistics
Matches: 95, Mismatches: 11, Indels: 30
0.70 0.08 0.22
Matches are distributed among these distances:
18 3 0.03
19 25 0.26
20 33 0.35
21 6 0.06
22 4 0.04
23 4 0.04
24 10 0.11
25 5 0.05
26 5 0.05
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (19 bp):
TTATTATATATATTTTAGT
Found at i:12175 original size:67 final size:67
Alignment explanation
Indices: 12037--12179 Score: 218
Period size: 67 Copynumber: 2.1 Consensus size: 67
12027 AGAAACCGAC
*
12037 TTATATATATAATTATTTATTATTATTATTATATATAATTTTAGTTTTTAGATTTTAATTTTAGT
1 TTATATATATAATTATTTATTATTATTATTATATATAATTTTAGTTTTTAGATATTAATTTTAGT
*
12102 TT
66 TA
* *
12104 TTATATATATAATTATTTTTTATTATTATTATATATAATTTTAGTTTTT-TATAATT-ATTTTAG
1 TTATATATATAATTATTTATTATTATTATTATATATAATTTTAGTTTTTAGAT-ATTAATTTTAG
12167 ATTA
65 -TTA
12171 TTATATATA
1 TTATATATA
12180 GTTTTAGTTT
Statistics
Matches: 70, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
66 9 0.13
67 61 0.87
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.62
Consensus pattern (67 bp):
TTATATATATAATTATTTATTATTATTATTATATATAATTTTAGTTTTTAGATATTAATTTTAGT
TA
Found at i:12186 original size:20 final size:19
Alignment explanation
Indices: 12128--12201 Score: 71
Period size: 19 Copynumber: 3.8 Consensus size: 19
12118 ATTTTTTATT
12128 ATTATTATATATAATTTTAG
1 ATTATTATATAT-ATTTTAG
* *
12148 TTTTTTATA-ATTATTTTAG
1 ATTATTATATA-TATTTTAG
12167 ATTATTATATATAGTTTTAG
1 ATTATTATATATA-TTTTAG
* *
12187 TTTATAAT-TATATTT
1 ATTATTATATATATTT
12202 ATATATATGA
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
18 3 0.07
19 21 0.47
20 21 0.47
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (19 bp):
ATTATTATATATATTTTAG
Found at i:18456 original size:15 final size:15
Alignment explanation
Indices: 18432--18466 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
18422 GAGACAGCTC
*
18432 CTTCAGGTGACTTCT
1 CTTCAAGTGACTTCT
18447 CTTCAAGTGACTTCT
1 CTTCAAGTGACTTCT
18462 CTTCA
1 CTTCA
18467 TCGTCTTCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.17, C:0.29, G:0.14, T:0.40
Consensus pattern (15 bp):
CTTCAAGTGACTTCT
Found at i:18473 original size:24 final size:24
Alignment explanation
Indices: 18446--18502 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
18436 AGGTGACTTC
* *
18446 TCTTCAAGTGACTTC-TCTTCATCG
1 TCTTCAAGTGAC-TCGTCATCATCA
*
18470 TCTTCAAGTGGCTCGTCATCATCA
1 TCTTCAAGTGACTCGTCATCATCA
18494 TCTTCAAGT
1 TCTTCAAGT
18503 CTGTGCCATT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 2 0.07
24 27 0.93
ACGTcount: A:0.19, C:0.28, G:0.14, T:0.39
Consensus pattern (24 bp):
TCTTCAAGTGACTCGTCATCATCA
Found at i:25553 original size:2 final size:2
Alignment explanation
Indices: 25546--25600 Score: 59
Period size: 2 Copynumber: 30.5 Consensus size: 2
25536 AACACTCAGA
*
25546 AT AT AT AT -T AT AT -T AT AT -T AT AT -T AT AT CT A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
25583 AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT A
25601 AGAAACCATA
Statistics
Matches: 45, Mismatches: 2, Indels: 12
0.76 0.03 0.20
Matches are distributed among these distances:
1 6 0.13
2 39 0.87
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:25559 original size:5 final size:5
Alignment explanation
Indices: 25549--25600 Score: 61
Period size: 5 Copynumber: 9.8 Consensus size: 5
25539 ACTCAGAATA
25549 TATAT TATAT TATAT TATAT TATAT CTA-AT ATATAT ATATAT ATATAT
1 TATAT TATAT TATAT TATAT TATAT -TATAT -TATAT -TATAT -TATAT
25597 TATA
1 TATA
25601 AGAAACCATA
Statistics
Matches: 44, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
5 28 0.64
6 16 0.36
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (5 bp):
TATAT
Found at i:25564 original size:10 final size:11
Alignment explanation
Indices: 25546--25600 Score: 71
Period size: 10 Copynumber: 5.1 Consensus size: 11
25536 AACACTCAGA
25546 ATATATATTAT
1 ATATATATTAT
25557 AT-TATATTAT
1 ATATATATTAT
25567 AT-TATATCTA-
1 ATATATAT-TAT
25577 ATATATATATAT
1 ATATATAT-TAT
25589 ATATATATTAT
1 ATATATATTAT
25600 A
1 A
25601 AGAAACCATA
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
10 17 0.43
11 15 0.38
12 8 0.20
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (11 bp):
ATATATATTAT
Found at i:27641 original size:2 final size:2
Alignment explanation
Indices: 27634--27662 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
27624 AGATATCTAG
27634 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
27663 TTTTGAAAGG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:28072 original size:16 final size:16
Alignment explanation
Indices: 28026--28075 Score: 61
Period size: 15 Copynumber: 3.2 Consensus size: 16
28016 TTGTAGGGAG
28026 GAAAT-GGGAAGGAAA
1 GAAATGGGGAAGGAAA
*
28041 GAAGA-GGGG-CGGAAA
1 GAA-ATGGGGAAGGAAA
28056 GAAATGGGGAAGGAAA
1 GAAATGGGGAAGGAAA
28072 GAAA
1 GAAA
28076 CGCTTCCATT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
14 1 0.03
15 15 0.52
16 13 0.45
ACGTcount: A:0.50, C:0.02, G:0.44, T:0.04
Consensus pattern (16 bp):
GAAATGGGGAAGGAAA
Found at i:29375 original size:4 final size:4
Alignment explanation
Indices: 29368--29403 Score: 72
Period size: 4 Copynumber: 9.0 Consensus size: 4
29358 CAAGACAAAC
29368 AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA
1 AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA
29404 GAAACTACAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:35221 original size:12 final size:12
Alignment explanation
Indices: 35204--35367 Score: 169
Period size: 12 Copynumber: 14.0 Consensus size: 12
35194 AAGATATTCC
*
35204 CGTTCCTTAAGT
1 CGTTCCTGAAGT
***
35216 CGTTCCTGGCCT
1 CGTTCCTGAAGT
*
35228 CGTTCCTGACGT
1 CGTTCCTGAAGT
35240 CGTTCCTGCAAGT
1 CGTTCCTG-AAGT
35253 CGTTCCTGAAGT
1 CGTTCCTGAAGT
*
35265 CGTTCCTTAAGT
1 CGTTCCTGAAGT
* *
35277 CATTCCTTAAGT
1 CGTTCCTGAAGT
35289 CGTTCC-----T
1 CGTTCCTGAAGT
*
35296 CGTTCCTGACGT
1 CGTTCCTGAAGT
35308 CGTTCCTGAAGT
1 CGTTCCTGAAGT
35320 CGTTCCT-AGAGT
1 CGTTCCTGA-AGT
35332 CGTTCCTGAAGT
1 CGTTCCTGAAGT
*
35344 CGTTCCTTAAGT
1 CGTTCCTGAAGT
*
35356 CGTTCTTGAAGT
1 CGTTCCTGAAGT
35368 TAAAAAAAAA
Statistics
Matches: 130, Mismatches: 14, Indels: 16
0.81 0.09 0.10
Matches are distributed among these distances:
7 7 0.05
11 1 0.01
12 110 0.85
13 12 0.09
ACGTcount: A:0.14, C:0.28, G:0.21, T:0.37
Consensus pattern (12 bp):
CGTTCCTGAAGT
Found at i:35313 original size:43 final size:43
Alignment explanation
Indices: 35252--35338 Score: 131
Period size: 43 Copynumber: 2.0 Consensus size: 43
35242 TTCCTGCAAG
*
35252 TCGTTCCTGAAGTCGTTCCTTAAGTCATTCCTTA-AGTCGTTCC
1 TCGTTCCTGAAGTCGTTCCTGAAGTCATTCC-TAGAGTCGTTCC
* *
35295 TCGTTCCTGACGTCGTTCCTGAAGTCGTTCCTAGAGTCGTTCC
1 TCGTTCCTGAAGTCGTTCCTGAAGTCATTCCTAGAGTCGTTCC
35338 T
1 T
35339 GAAGTCGTTC
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
42 2 0.05
43 38 0.95
ACGTcount: A:0.14, C:0.29, G:0.20, T:0.38
Consensus pattern (43 bp):
TCGTTCCTGAAGTCGTTCCTGAAGTCATTCCTAGAGTCGTTCC
Found at i:35324 original size:55 final size:56
Alignment explanation
Indices: 35239--35350 Score: 174
Period size: 55 Copynumber: 2.0 Consensus size: 56
35229 GTTCCTGACG
*
35239 TCGTTCCTGCAAGTCGTTCCTGAAGTCGTTCCTTA-AGTCATTCCTTAAGTCGTTCC
1 TCGTTCCTGCAAGTCGTTCCTGAAGTCGTTCC-TAGAGTCATTCCTGAAGTCGTTCC
* *
35295 TCGTTCCTG-ACGTCGTTCCTGAAGTCGTTCCTAGAGTCGTTCCTGAAGTCGTTCC
1 TCGTTCCTGCAAGTCGTTCCTGAAGTCGTTCCTAGAGTCATTCCTGAAGTCGTTCC
35350 T
1 T
35351 TAAGTCGTTC
Statistics
Matches: 52, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
54 2 0.04
55 41 0.79
56 9 0.17
ACGTcount: A:0.14, C:0.29, G:0.21, T:0.37
Consensus pattern (56 bp):
TCGTTCCTGCAAGTCGTTCCTGAAGTCGTTCCTAGAGTCATTCCTGAAGTCGTTCC
Found at i:35344 original size:67 final size:68
Alignment explanation
Indices: 35225--35360 Score: 231
Period size: 67 Copynumber: 2.0 Consensus size: 68
35215 TCGTTCCTGG
*
35225 CCTCGTTCCTGACGTCGTTCCTGCAAGTCGTTCCTGAAGTCGTTCCTTAAGTCATTCCTTAAGTC
1 CCTCGTTCCTGACGTCGTTCCTGCAAGTCGTTCCTGAAGTCGTTCCTGAAGTCATTCCTTAAGTC
35290 GTT
66 GTT
*
35293 CCTCGTTCCTGACGTCGTTCCTG-AAGTCGTTCCT-AGAGTCGTTCCTGAAGTCGTTCCTTAAGT
1 CCTCGTTCCTGACGTCGTTCCTGCAAGTCGTTCCTGA-AGTCGTTCCTGAAGTCATTCCTTAAGT
35356 CGTT
65 CGTT
35360 C
1 C
35361 TTGAAGTTAA
Statistics
Matches: 65, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
66 1 0.02
67 41 0.63
68 23 0.35
ACGTcount: A:0.14, C:0.29, G:0.21, T:0.36
Consensus pattern (68 bp):
CCTCGTTCCTGACGTCGTTCCTGCAAGTCGTTCCTGAAGTCGTTCCTGAAGTCATTCCTTAAGTC
GTT
Found at i:38404 original size:24 final size:24
Alignment explanation
Indices: 38375--38441 Score: 89
Period size: 24 Copynumber: 2.8 Consensus size: 24
38365 TAGGCCATTG
38375 CAGCAGCCACCACCTCCTCCAGTT
1 CAGCAGCCACCACCTCCTCCAGTT
* ** *
38399 GAGCAGCCAGTACCTCATCCAGTT
1 CAGCAGCCACCACCTCCTCCAGTT
*
38423 CAGCATCCACCACCTCCTC
1 CAGCAGCCACCACCTCCTC
38442 TTGTTGAACA
Statistics
Matches: 34, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.22, C:0.46, G:0.13, T:0.18
Consensus pattern (24 bp):
CAGCAGCCACCACCTCCTCCAGTT
Done.