Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008467.1 Hibiscus syriacus cultivar Beakdansim tig00111281_pilon, 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: 88319
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32
Found at i:2184 original size:16 final size:15
Alignment explanation
Indices: 2162--2200 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
2152 GAAATCATTG
2162 AAAAATTATATATAAA
1 AAAAATTATATA-AAA
* *
2178 TAAAATTATGTAAAA
1 AAAAATTATATAAAA
2193 AAAAATTA
1 AAAAATTA
2201 GAGATGGGGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (15 bp):
AAAAATTATATAAAA
Found at i:2196 original size:14 final size:15
Alignment explanation
Indices: 2162--2200 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
2152 GAAATCATTG
2162 AAAAATTATATATAA
1 AAAAATTATATATAA
* *
2177 ATAAAATTATGTAAAA
1 A-AAAATTATATATAA
2193 AAAAATTA
1 AAAAATTA
2201 GAGATGGGGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (15 bp):
AAAAATTATATATAA
Found at i:2435 original size:41 final size:40
Alignment explanation
Indices: 2369--2510 Score: 110
Period size: 41 Copynumber: 3.5 Consensus size: 40
2359 TGCGAAAACA
*
2369 AAATTCGCGTTGCGAA-TTCAGAAATCGAGTTGCGAATTTG
1 AAATTCGCGTTGCGAATTTGA-AAATCGAGTTGCGAATTTG
* **
2409 AAATTCAGTGTTGCGAATTTGAAAATCGCA-ACGCGAATTTGG
1 AAATTC-GCGTTGCGAATTTGAAAATCG-AGTTGCGAATTT-G
* *** *
2451 AAAATCGCAACGCGAATTTGAAAA-CTGAGTTGCGAAATTG
1 AAATTCGCGTTGCGAATTTGAAAATC-GAGTTGCGAATTTG
* * *
2491 GAGTTCGTGTTGCGAATTTG
1 AAATTCGCGTTGCGAATTTG
2511 TTGGTCATTT
Statistics
Matches: 77, Mismatches: 19, Indels: 12
0.71 0.18 0.11
Matches are distributed among these distances:
40 22 0.29
41 45 0.58
42 10 0.13
ACGTcount: A:0.32, C:0.14, G:0.25, T:0.29
Consensus pattern (40 bp):
AAATTCGCGTTGCGAATTTGAAAATCGAGTTGCGAATTTG
Found at i:2455 original size:21 final size:20
Alignment explanation
Indices: 2421--2474 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 20
2411 ATTCAGTGTT
2421 GCGAATTTGAAAATCGCAAC
1 GCGAATTTGAAAATCGCAAC
2441 GCGAATTTGGAAAATCGCAAC
1 GCGAATTT-GAAAATCGCAAC
2462 GCGAATTTGAAAA
1 GCGAATTTGAAAA
2475 CTGAGTTGCG
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 13 0.39
21 20 0.61
ACGTcount: A:0.41, C:0.17, G:0.22, T:0.20
Consensus pattern (20 bp):
GCGAATTTGAAAATCGCAAC
Found at i:2684 original size:7 final size:7
Alignment explanation
Indices: 2669--2895 Score: 136
Period size: 7 Copynumber: 32.1 Consensus size: 7
2659 TTTCGTCTAG
*
2669 TATAGTA
1 TATATTA
2676 TATATTA
1 TATATTA
*
2683 TAGTA-CA
1 TA-TATTA
2690 TATA-T-
1 TATATTA
*
2695 TATAGTA
1 TATATTA
2702 TATATTA
1 TATATTA
2709 TCATATTA
1 T-ATATTA
* *
2717 CATAGTA
1 TATATTA
2724 TATATTA
1 TATATTA
2731 TAGTATTA
1 TA-TATTA
2739 TATATTA
1 TATATTA
*
2746 TAT-GTA
1 TATATTA
2752 GTATATTA
1 -TATATTA
*
2760 TATAATA
1 TATATTA
2767 TATATTA
1 TATATTA
2774 TATA-TA
1 TATATTA
*
2780 TTATCTTA
1 -TATATTA
2788 TTATATTA
1 -TATATTA
2796 TATATTA
1 TATATTA
2803 TTATGGTATTA
1 -TA---TATTA
2814 TATATTA
1 TATATTA
*
2821 TATAATA
1 TATATTA
2828 TATATTA
1 TATATTA
2835 TAT-TT-
1 TATATTA
2840 TAGTATTA
1 TA-TATTA
*
2848 TGT-TTA
1 TATATTA
2854 T-T-TGT-
1 TATAT-TA
*
2859 TATGTTA
1 TATATTA
2866 TATATTA
1 TATATTA
2873 TAT-TTA
1 TATATTA
2879 TATTATTTA
1 TA-TA-TTA
*
2888 TTTATTA
1 TATATTA
2895 T
1 T
2896 TTTGATTTTA
Statistics
Matches: 178, Mismatches: 19, Indels: 46
0.73 0.08 0.19
Matches are distributed among these distances:
5 9 0.05
6 22 0.12
7 105 0.59
8 31 0.17
9 4 0.02
10 2 0.01
11 5 0.03
ACGTcount: A:0.37, C:0.02, G:0.06, T:0.55
Consensus pattern (7 bp):
TATATTA
Found at i:2694 original size:14 final size:12
Alignment explanation
Indices: 2669--2845 Score: 106
Period size: 12 Copynumber: 14.7 Consensus size: 12
2659 TTTCGTCTAG
2669 TATAGTATATAT
1 TATAGTATATAT
2681 TATAGTACATATAT
1 TATAGT--ATATAT
2695 TATAGTATATAT
1 TATAGTATATAT
2707 TATCA-TAT-TA-
1 TAT-AGTATATAT
*
2717 CATAGTATATAT
1 TATAGTATATAT
2729 TATAGTATTATATAT
1 TATAG---TATATAT
2744 TATATGTAGTATAT
1 TATA-GTA-TATAT
2758 TATA-TA-ATAT
1 TATAGTATATAT
2768 ATATTA-TATATAT
1 -TA-TAGTATATAT
**
2781 TATCTTATTATAT
1 TATAGTA-TATAT
2794 TATA-TAT-TAT
1 TATAGTATATAT
*
2804 TATGGTAT-TA-
1 TATAGTATATAT
* *
2814 TATATTATATAA
1 TATAGTATATAT
2826 TATA-TATTATAT
1 TATAGTA-TATAT
*
2838 TTTAGTAT
1 TATAGTAT
2846 TATGTTTATT
Statistics
Matches: 135, Mismatches: 9, Indels: 42
0.73 0.05 0.23
Matches are distributed among these distances:
9 1 0.01
10 21 0.16
11 17 0.13
12 46 0.34
13 17 0.13
14 21 0.16
15 11 0.08
16 1 0.01
ACGTcount: A:0.40, C:0.02, G:0.06, T:0.52
Consensus pattern (12 bp):
TATAGTATATAT
Found at i:2747 original size:5 final size:5
Alignment explanation
Indices: 2676--2838 Score: 73
Period size: 5 Copynumber: 34.2 Consensus size: 5
2666 TAGTATAGTA
* * * * *
2676 TATAT TATAG TACA- TATAT TATAG TATA- TATTAT CATAT TACA- TAGTA-
1 TATAT TATAT TATAT TATAT TATAT TATAT TA-TAT TATAT TATAT TA-TAT
* * * *
2724 TATAT TATAG TAT-T ATATAT TATA- TGTAG TATAT TATAT AATA- TATAT
1 TATAT TATAT TATAT -TATAT TATAT TATAT TATAT TATAT TATAT TATAT
* **
2772 TATA- TATAT TAT-C T-TAT TATAT TATA- TATTAT TATGG TAT-T ATATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TA-TAT TATAT TATAT -TATAT
*
2819 TATAT AATA- TATAT TATAT T
1 TATAT TATAT TATAT TATAT T
2839 TTAGTATTAT
Statistics
Matches: 119, Mismatches: 22, Indels: 34
0.68 0.13 0.19
Matches are distributed among these distances:
3 1 0.01
4 26 0.22
5 87 0.73
6 5 0.04
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.52
Consensus pattern (5 bp):
TATAT
Found at i:2847 original size:52 final size:52
Alignment explanation
Indices: 2700--2875 Score: 153
Period size: 52 Copynumber: 3.2 Consensus size: 52
2690 TATATTATAG
* * *
2700 TATATATTATCATATTACATAGTATATATTATAGTATTATATATTA-TATGTAGTATAT
1 TATATATTAT-ATAATATATA-T-TATATTTTAGTATTATATATTATTATG--G--TAT
* *
2758 TATATAATATATATTATATATATTATCTTATTA-TATTATATATTATTATGGTAT
1 TATAT-AT-TATATAATATATATTATATT-TTAGTATTATATATTATTATGGTAT
* *
2812 TATATATTATATAATATATATTATATTTTAGTATTATGT-TTATT-TGTTATGT
1 TATATATTATATAATATATATTATATTTTAGTATTATATATTATTATGGTA--T
2864 TATATATTATAT
1 TATATATTATAT
2876 TTATATTATT
Statistics
Matches: 102, Mismatches: 9, Indels: 20
0.78 0.07 0.15
Matches are distributed among these distances:
50 4 0.04
51 8 0.08
52 38 0.37
53 2 0.02
54 8 0.08
56 1 0.01
57 17 0.17
58 12 0.12
59 9 0.09
60 3 0.03
ACGTcount: A:0.38, C:0.02, G:0.06, T:0.55
Consensus pattern (52 bp):
TATATATTATATAATATATATTATATTTTAGTATTATATATTATTATGGTAT
Found at i:5347 original size:17 final size:17
Alignment explanation
Indices: 5325--5357 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
5315 TTTTCTCTCA
5325 CTTTTTTGT-TTTATTTT
1 CTTTTTT-TATTTATTTT
5342 CTTTTTTTATTTATTT
1 CTTTTTTTATTTATTT
5358 GCATCATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 1 0.07
17 14 0.93
ACGTcount: A:0.09, C:0.06, G:0.03, T:0.82
Consensus pattern (17 bp):
CTTTTTTTATTTATTTT
Found at i:10920 original size:14 final size:15
Alignment explanation
Indices: 10895--10926 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
10885 AAATATAACC
10895 ACATACAATATAGAA
1 ACATACAATATAGAA
10910 ACATA-AATATAGAA
1 ACATACAATATAGAA
10924 ACA
1 ACA
10927 ATCACAGTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.62, C:0.12, G:0.06, T:0.19
Consensus pattern (15 bp):
ACATACAATATAGAA
Found at i:13798 original size:24 final size:24
Alignment explanation
Indices: 13753--13798 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
13743 CCATTTCCAT
* *
13753 CATCATCTTCATATTCATCTTCGC
1 CATCATCTTCATATCCACCTTCGC
13777 CATCATCTTCAGT-TCCACCTTC
1 CATCATCTTCA-TATCCACCTTC
13799 AGTCTTAGCC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 18 0.95
25 1 0.05
ACGTcount: A:0.20, C:0.37, G:0.04, T:0.39
Consensus pattern (24 bp):
CATCATCTTCATATCCACCTTCGC
Found at i:19546 original size:571 final size:563
Alignment explanation
Indices: 18429--19557 Score: 1890
Period size: 571 Copynumber: 2.0 Consensus size: 563
18419 ATCAAAAGCA
18429 CTGATGCCAGTTGTTGGGAAATAAACCGAGTACGAGTAATTTCCATATAACCAGATCAATGAGAA
1 CTGATGCCAGTTGTTGGGAAATAAACCGAGTACGAGTAATTTCCATATAACCAGATCAATGAGAA
18494 TGCAAAATAAAAGCGGAAAAATAATACCCGAAATTGATAACGGAGTTCAACCAATTATGCCTACA
66 TGCAAAATAAAAGCGGAAAAATAATACCCGAAATTGATAACGGAGTTCAACCAATTATGCCTACA
* *
18559 TCTCCGGACTGCTGCAGATCTTTTACTGAAGAAAGAAAATTTACAGGTGTTTACAAAACACTCAC
131 TCTCCGGACTGCTGCAGATCGTTTACTGAAGAAAGAAAATTTACAGCTGTTTACAAAACACTCAC
*
18624 TACTCACAAGAAAGCACTCTAGTATTGGGAGAAAGAAATGATTTGGGATGATTTTGAAGCTAAAT
196 TACTCACAAGAAAGCACTCTAGTATTAGGAGAAAGAAATGATTTGGGATGATTTTGAAGCTAAAT
*
18689 GGGTTAGAGTATTTATAGTTGAAGCTTAAGGACTAATCTTGTAAATACCCTAAAGTGTGCAGGGA
261 GGGTTAGAGTATTTATAGTTGAAGCTTAAGGACTAATCTTGTAAATACCCTAAAGTATGCAGGGA
* * *
18754 ATAAAATGCAATTTCTCTAAATAAAAATTAAATGCACTGAATTCGATGCCCAATACACAGAATTC
326 ATAAAATGCAATTTCTCCAAATAAAAATAAAATACACTGAATTCGATGCCCAATACACAGAATTC
*
18819 GGCGCCCCAATTCTTGATTTTAAACGCCCCTCATCTTTGACTTTACAACAGGTTCGAGCACTAGC
391 GGCACCCCAATTCTTGATTTTAAA----CCTCA-C--T--CTTTACAACAGGTTCGAGCACTAGC
* *
18884 GACTGTAAAAGGATGATTGAACGTTCATTTGTTAAATAGTATAGAGTATTTAAAACAAATACTAC
447 GACTGCAAAAGGATGATTGAACGTTCATTTGTCAAATAGTATAGAGTATTTAAAACAAATACTAC
* *
18949 TTTATAATCATCTTAGCTTAATAAAAAAATCCATAAAAATGATTAGAATAGG
512 ATTATAATCACCTTAGCTTAATAAAAAAATCCATAAAAATGATTAGAATAGG
* * *
19001 CTGATGCCAGTTGTTGGGAAATAAACCGAGTACGAGTAATTTCCATATAAGCATATTAATGAGAA
1 CTGATGCCAGTTGTTGGGAAATAAACCGAGTACGAGTAATTTCCATATAACCAGATCAATGAGAA
* *
19066 TGCAAAATAAAAGCGGAAAAATAATACCCG-AATTGATAACGGAGTTCAGCCAATTATGCCTACG
66 TGCAAAATAAAAGCGGAAAAATAATACCCGAAATTGATAACGGAGTTCAACCAATTATGCCTACA
* *
19130 TCTCCGGACTGCTGCAGATCGTTTACTGAAGAGAGAAAATTTACAGCTGTTTACAAAACACTCAT
131 TCTCCGGACTGCTGCAGATCGTTTACTGAAGAAAGAAAATTTACAGCTGTTTACAAAACACTCAC
*
19195 TACTCACAAGAAAGCTCTCTAGTATTAGGAGAAAGAAATGATTTGGGATGATTTTGAAGCTAAAT
196 TACTCACAAGAAAGCACTCTAGTATTAGGAGAAAGAAATGATTTGGGATGATTTTGAAGCTAAAT
*
19260 GGGTTAGAGTATTTATAGTTGAAGCTTAAGGACTAATCTTGTAATTACCCTAAAGTATGCAGGGA
261 GGGTTAGAGTATTTATAGTTGAAGCTTAAGGACTAATCTTGTAAATACCCTAAAGTATGCAGGGA
* * *
19325 CTAAAATGTAATTT-TCCCAAATAAAAATAAAATACACTGAATTTGATGCCCAATACACAGAATT
326 ATAAAATGCAATTTCT-CCAAATAAAAATAAAATACACTGAATTCGATGCCCAATACACAGAATT
19389 CGGCACCCCAATTCTTGATTTTAAA-CTC-C-CTTTACAACAGGTTCGAGCACTAGCGACTGCAA
390 CGGCACCCCAATTCTTGATTTTAAACCTCACTCTTTACAACAGGTTCGAGCACTAGCGACTGCAA
19451 AAGGATGATTGAACGTTCATTTGTCAAATAGTATAGAGTATTTAAAACAAATACTACATTATAAT
455 AAGGATGATTGAACGTTCATTTGTCAAATAGTATAGAGTATTTAAAACAAATACTACATTATAAT
* * *
19516 CACCTTAGTTTAATAAAAAAATTCATAAAAACGATTAGAATA
520 CACCTTAGCTTAATAAAAAAATCCATAAAAATGATTAGAATA
19558 TGATAGATGG
Statistics
Matches: 529, Mismatches: 27, Indels: 15
0.93 0.05 0.03
Matches are distributed among these distances:
559 133 0.25
564 1 0.00
566 3 0.01
570 1 0.00
571 299 0.57
572 92 0.17
ACGTcount: A:0.38, C:0.16, G:0.17, T:0.28
Consensus pattern (563 bp):
CTGATGCCAGTTGTTGGGAAATAAACCGAGTACGAGTAATTTCCATATAACCAGATCAATGAGAA
TGCAAAATAAAAGCGGAAAAATAATACCCGAAATTGATAACGGAGTTCAACCAATTATGCCTACA
TCTCCGGACTGCTGCAGATCGTTTACTGAAGAAAGAAAATTTACAGCTGTTTACAAAACACTCAC
TACTCACAAGAAAGCACTCTAGTATTAGGAGAAAGAAATGATTTGGGATGATTTTGAAGCTAAAT
GGGTTAGAGTATTTATAGTTGAAGCTTAAGGACTAATCTTGTAAATACCCTAAAGTATGCAGGGA
ATAAAATGCAATTTCTCCAAATAAAAATAAAATACACTGAATTCGATGCCCAATACACAGAATTC
GGCACCCCAATTCTTGATTTTAAACCTCACTCTTTACAACAGGTTCGAGCACTAGCGACTGCAAA
AGGATGATTGAACGTTCATTTGTCAAATAGTATAGAGTATTTAAAACAAATACTACATTATAATC
ACCTTAGCTTAATAAAAAAATCCATAAAAATGATTAGAATAGG
Found at i:19581 original size:15 final size:15
Alignment explanation
Indices: 19561--19596 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
19551 TAGAATATGA
19561 TAGATGGAGTTTCTT
1 TAGATGGAGTTTCTT
19576 TAGATGGAGTTTCTT
1 TAGATGGAGTTTCTT
*
19591 TGGATG
1 TAGATG
19597 AACAAAAGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.19, C:0.06, G:0.31, T:0.44
Consensus pattern (15 bp):
TAGATGGAGTTTCTT
Found at i:20126 original size:23 final size:23
Alignment explanation
Indices: 20100--20149 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
20090 TTCCTCCAAA
20100 TACCCCTCCTTTTTCCATCTAAT
1 TACCCCTCCTTTTTCCATCTAAT
20123 TACCCCTCCTTTTTCCATCTAAT
1 TACCCCTCCTTTTTCCATCTAAT
20146 TACC
1 TACC
20150 ATTCATACCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.18, C:0.40, G:0.00, T:0.42
Consensus pattern (23 bp):
TACCCCTCCTTTTTCCATCTAAT
Found at i:20909 original size:16 final size:16
Alignment explanation
Indices: 20888--20936 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
20878 AATATTTTAT
20888 AAATTTTAATAATAAA
1 AAATTTTAATAATAAA
20904 AAATTTTAATAA-AATA
1 AAATTTTAATAATAA-A
* *
20920 ATATCTT-ATAATAAA
1 AAATTTTAATAATAAA
20935 AA
1 AA
20937 CTTATTTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
15 8 0.29
16 20 0.71
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (16 bp):
AAATTTTAATAATAAA
Found at i:21086 original size:2 final size:2
Alignment explanation
Indices: 21079--21127 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
21069 AAATCACGAC
21079 TA TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA TA
21121 TA TA TA T
1 TA TA TA T
21128 GCGTGAAAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:22231 original size:44 final size:45
Alignment explanation
Indices: 22183--22293 Score: 108
Period size: 44 Copynumber: 2.6 Consensus size: 45
22173 CCATCTTCAT
* **
22183 TATTCAATCACATTATACCTCTTTTGATT-TATTTAATTCA-AAAA
1 TATTCAATCACATTATACCTCTTTTGATTAAAAATAA-TCATAAAA
** * *
22227 TATTCGTTAACATTATACCTCTATT-ATTAAAAATAATCATAAAA
1 TATTCAATCACATTATACCTCTTTTGATTAAAAATAATCATAAAA
22271 TA---AATCACATTATACCTCTTTTG
1 TATTCAATCACATTATACCTCTTTTG
22294 GTTACTCTCT
Statistics
Matches: 53, Mismatches: 11, Indels: 8
0.74 0.15 0.11
Matches are distributed among these distances:
41 16 0.30
43 6 0.11
44 31 0.58
ACGTcount: A:0.39, C:0.16, G:0.03, T:0.42
Consensus pattern (45 bp):
TATTCAATCACATTATACCTCTTTTGATTAAAAATAATCATAAAA
Found at i:24779 original size:3 final size:3
Alignment explanation
Indices: 24771--24875 Score: 151
Period size: 3 Copynumber: 35.0 Consensus size: 3
24761 TTCATTTAAA
** *
24771 ATT ATT ATT ATT AAA ATT ATT ATT ATT ATT ATT AGT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
24819 ATT ATT ATT ATT ATT ATT ATT ATTT ATT A-T ATT ATT A-T ATT ATAT
1 ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT AT-T
24864 ATT ATT ATT ATT
1 ATT ATT ATT ATT
24876 TAATAAATAA
Statistics
Matches: 92, Mismatches: 6, Indels: 8
0.87 0.06 0.08
Matches are distributed among these distances:
2 4 0.04
3 82 0.89
4 6 0.07
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:24888 original size:18 final size:18
Alignment explanation
Indices: 24770--24888 Score: 55
Period size: 18 Copynumber: 6.3 Consensus size: 18
24760 TTTCATTTAA
24770 AATTATTATTATTA-AAAT
1 AATTATTA-TATTATAAAT
* * *
24788 TATTATTATTATTATTAGT
1 AATTATTA-TATTATAAAT
*
24807 -ATTATTATTATTATTATTAT
1 AATTATTA-TATTA-TA-AAT
* * *
24827 TATTATTATTATTATTTATT
1 AATTATTA-TATTA-TAAAT
*
24847 ATATTATTATATTATATAT
1 A-ATTATTATATTATAAAT
*
24866 TATTATTAT-TTAATAAAT
1 AATTATTATATT-ATAAAT
24884 AATTA
1 AATTA
24889 CAAAACTGGA
Statistics
Matches: 79, Mismatches: 16, Indels: 12
0.74 0.15 0.11
Matches are distributed among these distances:
17 2 0.03
18 43 0.54
19 5 0.06
20 7 0.09
21 22 0.28
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (18 bp):
AATTATTATATTATAAAT
Found at i:26939 original size:17 final size:17
Alignment explanation
Indices: 26917--26956 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
26907 TAGGTCAAAT
26917 TTTTTATATATTTATTA
1 TTTTTATATATTTATTA
* *
26934 TTTTTATATTTTTTTTA
1 TTTTTATATATTTATTA
26951 TATTTT
1 T-TTTT
26957 CTTATTAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 16 0.80
18 4 0.20
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTTTATATATTTATTA
Found at i:31274 original size:2 final size:2
Alignment explanation
Indices: 31267--31339 Score: 139
Period size: 2 Copynumber: 37.0 Consensus size: 2
31257 TTATCCTTTA
31267 AT AT AT AT AT AT AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
31308 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
31340 CCTTTGTTAT
Statistics
Matches: 70, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 69 0.99
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:33784 original size:114 final size:115
Alignment explanation
Indices: 33584--33921 Score: 579
Period size: 114 Copynumber: 2.9 Consensus size: 115
33574 TGCCATATTA
33584 CTCATGGTAGAAATAAGGAGGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
1 CTCATGGTAGAAATAAGGAGGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
33649 ATTTGGTATGAACTCCAAAATCAATCATTGGATTTGAAAGATGAA-TTTG
66 ATTTGGTATGAACTCCAAAATCAATCATTGGATTTGAAAGATGAATTTTG
33698 CTCATGGTAGAAATAAGGAGGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
1 CTCATGGTAGAAATAAGGAGGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
33763 ATTTGGTATGAACTCCAAAATCAATCATTGGATTTGAAAGATGAATTTTG
66 ATTTGGTATGAACTCCAAAATCAATCATTGGATTTGAAAGATGAATTTTG
* * *
33813 CTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
1 CTCATGGTAGAAATAAGGAGGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
* * * * * * *
33878 ATTTGGTAAGAACTACAGAACCAATCATTAGAATTAAAAGATGA
66 ATTTGGTATGAACTCCAAAATCAATCATTGGATTTGAAAGATGA
33922 GCTGCATGAT
Statistics
Matches: 213, Mismatches: 10, Indels: 1
0.95 0.04 0.00
Matches are distributed among these distances:
114 110 0.52
115 103 0.48
ACGTcount: A:0.33, C:0.14, G:0.21, T:0.33
Consensus pattern (115 bp):
CTCATGGTAGAAATAAGGAGGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
ATTTGGTATGAACTCCAAAATCAATCATTGGATTTGAAAGATGAATTTTG
Found at i:36067 original size:52 final size:52
Alignment explanation
Indices: 35910--36075 Score: 251
Period size: 52 Copynumber: 3.2 Consensus size: 52
35900 ACTTCAATAA
35910 TTACGAACATCTGAACAGAAACCATGAAAGGATGAATGTGTTGTCAAATGTT
1 TTACGAACATCTGAACAGAAACCATGAAAGGATGAATGTGTTGTCAAATGTT
*
35962 TTACGAACATCTAAACAGAAACCACATGAAAGGATGAATGTGTTGTCAAATGTT
1 TTACGAACATCTGAACAGAAA-C-CATGAAAGGATGAATGTGTTGTCAAATGTT
* * *** *
36016 TTACGAACATCTGAACAGAAGCCAGGAAAGGATGAATGCACTATCAAATGTT
1 TTACGAACATCTGAACAGAAACCATGAAAGGATGAATGTGTTGTCAAATGTT
36068 TTACGAAC
1 TTACGAAC
36076 CTGCTATTCT
Statistics
Matches: 104, Mismatches: 8, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
52 53 0.51
53 2 0.02
54 49 0.47
ACGTcount: A:0.40, C:0.16, G:0.20, T:0.25
Consensus pattern (52 bp):
TTACGAACATCTGAACAGAAACCATGAAAGGATGAATGTGTTGTCAAATGTT
Found at i:36299 original size:22 final size:22
Alignment explanation
Indices: 36270--36324 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
36260 ATCTACACTC
*
36270 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGACAGATTCTCTT
*
36292 TTTAAAGATGACAGATTCTCTT
1 TTCAAAGATGACAGATTCTCTT
36314 TTCAAAGATGA
1 TTCAAAGATGA
36325 AAACTTTATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.38
Consensus pattern (22 bp):
TTCAAAGATGACAGATTCTCTT
Found at i:36988 original size:112 final size:113
Alignment explanation
Indices: 36723--37387 Score: 831
Period size: 112 Copynumber: 6.0 Consensus size: 113
36713 GCAAAGTTCA
** * **
36723 AATCCATCATTCAATGGATCAACA-TTCCAG-GTCGAGTTCATAATGAGAAGAACTCATCTGAAG
1 AATCCATCATTTGATGGATCATCATTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTGAAG
* * * * **
36786 AAGAAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCA
65 AAGGAAGAAGAAGTTCATAATAAGAAGAATTTGTTCAACCTTTTACTTG
* * * * *
36835 AATCCATCATTCGATGGATTGA-CATTTCTATAG-AAGTTCATAATGAGAAGAACTCATATGAAG
1 AATCCATCATTTGATGGA-TCATCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
*
36898 AAGGAAGAA-AAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACTTG
65 AAGGAAGAAGAAGTTCATAATAAGAAGAATTTGTTCAACCTTTTACTTG
*
36946 AATCCATCATTTGATGGATCATCATTTCCAGAGAAAGTTCATAATGAGAAG-ACTTATCT---GA
1 AATCCATCATTTGATGGATCATCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
37007 A-GAAGAAGAAGTTCATAATAAGAAGAATTTGTTCAACCTTTTACTTG
66 AGGAAGAAGAAGTTCATAATAAGAAGAATTTGTTCAACCTTTTACTTG
* *
37054 AATCTATTATTTGATGGATCATCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTGATGGATCATCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
*
37119 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTGT-C-TG
66 AGGAAGAAGAAGTTCATAATAAGAAGAATTTGTTCAACCTTT-TACTTG
* * * *
37166 AATTCATC-CTTGATGGATTAT--TTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAG
1 AATCCATCATTTGATGGATCATCATTT-CCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
* * **
37228 AAGGAAGAAGTTCATAATTCATAATAAGAAGAATTTGTTCAACCTTTTGCTCA
65 AAGGAAGAAG---A-AGTTCATAATAAGAAGAATTTGTTCAACCTTTTACTTG
* * * * *
37281 AATCCATCACTTGATGGAACAGCTTTTCTAGAG-AAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTGATGGATCATCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
*
37345 AGGAAGAAGAAGTTCATAATAAGAAGAATTTGTTCAACTTTTT
66 AGGAAGAAGAAGTTCATAATAAGAAGAATTTGTTCAACCTTTT
37388 GCATAATTCT
Statistics
Matches: 491, Mismatches: 40, Indels: 44
0.85 0.07 0.08
Matches are distributed among these distances:
107 6 0.01
108 90 0.18
109 10 0.02
110 48 0.10
111 78 0.16
112 113 0.23
113 49 0.10
114 33 0.07
115 7 0.01
116 49 0.10
117 5 0.01
118 3 0.01
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.30
Consensus pattern (113 bp):
AATCCATCATTTGATGGATCATCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
AGGAAGAAGAAGTTCATAATAAGAAGAATTTGTTCAACCTTTTACTTG
Found at i:37890 original size:76 final size:75
Alignment explanation
Indices: 37790--38270 Score: 846
Period size: 76 Copynumber: 6.4 Consensus size: 75
37780 ACTATTTCCC
* *
37790 TCATCTATAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGAGAGCTTTTTGATGTTCTTA
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTT-TTA
37855 AAGCCTTCGGG
65 AAGCCTTCGGG
37866 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGC-TTTTGATGTTTTCA
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTT-A
37930 AAGCCTTCGGG
65 AAGCCTTCGGG
*
37941 TCATCTGTAAGTCCTTCAGTGCATGA--TTTCC-AAAAGCCTTCGGGAGC-TTTTGATATTTTAA
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTAA
38002 AGCCTTCGGG
66 AGCCTTCGGG
38012 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTCTTA
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTT-TTA
38077 AAGCCTTCGGG
65 AAGCCTTCGGG
*
38088 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATATTTTTA
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGAT-GTTTTA
38153 AAGCCTTCGGG
65 AAGCCTTCGGG
38164 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTT-A
38229 AAGCCTTCGGG
65 AAGCCTTCGGG
38240 TCATCTGTAAGTCCTTCAGTGCATGATGTTT
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTT
38271 TCAACATTTC
Statistics
Matches: 391, Mismatches: 6, Indels: 16
0.95 0.01 0.04
Matches are distributed among these distances:
71 38 0.10
72 27 0.07
73 10 0.03
74 18 0.05
75 61 0.16
76 235 0.60
77 2 0.01
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.36
Consensus pattern (75 bp):
TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTAA
AGCCTTCGGG
Found at i:38408 original size:3 final size:3
Alignment explanation
Indices: 38402--38520 Score: 175
Period size: 3 Copynumber: 39.0 Consensus size: 3
38392 TTCATTTAAA
** *
38402 ATT ATT ATT AAA ATT ATT ATT ATT ATT ATT ATT AGT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
38450 ATT AGT ATT ATT ATT ATT ATT ATT ATT ATT ATTT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT
*
38496 ATT AAT ATT ATAT ATT ATT ATT ATT
1 ATT ATT ATT AT-T ATT ATT ATT ATT
38521 TAATAAATAA
Statistics
Matches: 104, Mismatches: 10, Indels: 4
0.88 0.08 0.03
Matches are distributed among these distances:
3 98 0.94
4 6 0.06
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:45618 original size:112 final size:112
Alignment explanation
Indices: 45496--45958 Score: 737
Period size: 112 Copynumber: 4.1 Consensus size: 112
45486 TTGTCGGTTT
** *
45496 GTGTCGATACTTTATAAAAATATATTAATCTATAACAATATAACAGGTAAAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
* * *
45561 GATCTATAAATGACAAAACATGTAAAGCGCTATCGGATATATTGAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
* * * *
45608 GTGTCGATACTTTATAAAAATATATTGATCCATAATAATATAACAAGTAAAAAAATGACAAAATC
1 GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
* ** *
45673 GGTCTATAAATTACAAAACAGGTAAAGCGCTATTGGATATATTAAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
* *
45720 GTGTCGATAATTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
45785 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
* * *
45832 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAATAGGTAAAAAAATTACAAAACC
1 GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
* *
45897 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATGTTGATA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
45944 GTGTCGATACTTTAT
1 GTGTCGATACTTTAT
45959 TATAAGTATC
Statistics
Matches: 326, Mismatches: 25, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
112 326 1.00
ACGTcount: A:0.46, C:0.13, G:0.14, T:0.27
Consensus pattern (112 bp):
GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
Found at i:46136 original size:182 final size:182
Alignment explanation
Indices: 45829--46281 Score: 728
Period size: 182 Copynumber: 2.5 Consensus size: 182
45819 GGATATATTG
* * *
45829 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAATAGGTAAAAAAATTACAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
** * * * *
45894 ACCGGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATGTTGATAGTGTCGATACTTTAT
66 ACCGGTCTCGAAATGACAAAACCGGTAAAGAGCTACCAGATATGTTGAAAGTGTCGATACTTTAT
* * * *
45959 TATAAGTATCGACACTTTTGGAATTTAAATGAGAAGAAGTTATAG-AGCTAAT
131 TATAAGTATCAACACTTTTGGAATTTAAAAGAAAAGAAGTTATAGCA-CCAAT
*
46011 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGAAAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
* *
46076 ATCAGTCTCGAAATGACAAAACCGGTAAAGAGCTACCAGATATGTTGAAAGTGTCGATACTTTAT
66 ACCGGTCTCGAAATGACAAAACCGGTAAAGAGCTACCAGATATGTTGAAAGTGTCGATACTTTAT
46141 TATAAGTATCAACACTTTTGGAATTTAAAAGAAAAGAAGTTATAGCACCAAT
131 TATAAGTATCAACACTTTTGGAATTTAAAAGAAAAGAAGTTATAGCACCAAT
*
46193 AAAGTGTCGATACTTTATAAAAATGTATCAATCCATAACAATATAACAGGTAAAAATATGACAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
*
46258 ACCGGTCTCGAAATGATAAAACCG
66 ACCGGTCTCGAAATGACAAAACCG
46282 ATAGTAAAAA
Statistics
Matches: 249, Mismatches: 21, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
182 248 1.00
183 1 0.00
ACGTcount: A:0.44, C:0.13, G:0.16, T:0.27
Consensus pattern (182 bp):
AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
ACCGGTCTCGAAATGACAAAACCGGTAAAGAGCTACCAGATATGTTGAAAGTGTCGATACTTTAT
TATAAGTATCAACACTTTTGGAATTTAAAAGAAAAGAAGTTATAGCACCAAT
Found at i:46734 original size:23 final size:23
Alignment explanation
Indices: 46705--46752 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
46695 AAATAGATCA
*
46705 ATATAAGCGCTACCTATTACATT
1 ATATAAGCGCTACCTAATACATT
* *
46728 ATATAAGCGTTACCTAATATATT
1 ATATAAGCGCTACCTAATACATT
46751 AT
1 AT
46753 TGTACTTGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.38, C:0.17, G:0.08, T:0.38
Consensus pattern (23 bp):
ATATAAGCGCTACCTAATACATT
Found at i:47516 original size:22 final size:22
Alignment explanation
Indices: 47491--47585 Score: 63
Period size: 22 Copynumber: 4.2 Consensus size: 22
47481 TACAACATAG
47491 AAATTAAATGAAT-ATAATAAAT
1 AAATTAAAT-AATAATAATAAAT
*
47513 AAA-TACAATAATAATAATTAAT
1 AAATTA-AATAATAATAATAAAT
* *
47535 AATATTAATTATTAAAGTTAATAAAT
1 AA-ATTAAATAAT-AA--TAATAAAT
*
47561 -AATTAAA-ATATAATAATATAT
1 AAATTAAATA-ATAATAATAAAT
47582 AAAT
1 AAAT
47586 ATAGTAATTA
Statistics
Matches: 57, Mismatches: 7, Indels: 18
0.70 0.09 0.22
Matches are distributed among these distances:
21 12 0.21
22 19 0.33
23 8 0.14
24 10 0.18
25 1 0.02
26 7 0.12
ACGTcount: A:0.61, C:0.01, G:0.02, T:0.36
Consensus pattern (22 bp):
AAATTAAATAATAATAATAAAT
Found at i:47587 original size:16 final size:15
Alignment explanation
Indices: 47501--47593 Score: 62
Period size: 13 Copynumber: 6.7 Consensus size: 15
47491 AAATTAAATG
47501 AATATAATAA-ATA-
1 AATATAATAATATAT
*
47514 AATACAATAATA-AT
1 AATATAATAATATAT
47528 AAT-TAATAATAT-T
1 AATATAATAATATAT
*
47541 AAT-TATTAA-AGT-T
1 AATATAATAATA-TAT
*
47554 AATA-AATAAT-TAA
1 AATATAATAATATAT
47567 AATATAATAATATAT
1 AATATAATAATATAT
*
47582 AAATATAGTAAT
1 -AATATAATAAT
47594 TAAAATCGAT
Statistics
Matches: 63, Mismatches: 7, Indels: 17
0.72 0.08 0.20
Matches are distributed among these distances:
12 2 0.03
13 39 0.62
14 10 0.16
15 2 0.03
16 10 0.16
ACGTcount: A:0.60, C:0.01, G:0.02, T:0.37
Consensus pattern (15 bp):
AATATAATAATATAT
Found at i:50972 original size:64 final size:65
Alignment explanation
Indices: 50884--51036 Score: 193
Period size: 65 Copynumber: 2.4 Consensus size: 65
50874 TACACTAGGG
* * * * *
50884 GTGCATCGGTACACTAATTACATTCAATGTTTC-AAAGAGCCAGGAGTGCATCGATGCATGGAC-
1 GTGCATCGGTACACAAAATGCATTCAATGTTTCAAAAGAGCCAAGAGTGCATCGATGCATAG-CT
50947 T
65 T
* * **
50948 GTGCATCGGTACACAAAATGCATTCGATGTTTCAAAATATTCAAGAGTGCATCGATGCATAGCTT
1 GTGCATCGGTACACAAAATGCATTCAATGTTTCAAAAGAGCCAAGAGTGCATCGATGCATAGCTT
*
51013 CTGCATCGGTACACAAAATGCATT
1 GTGCATCGGTACACAAAATGCATT
51037 TGAAATGGGT
Statistics
Matches: 77, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
64 30 0.39
65 47 0.61
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.27
Consensus pattern (65 bp):
GTGCATCGGTACACAAAATGCATTCAATGTTTCAAAAGAGCCAAGAGTGCATCGATGCATAGCTT
Found at i:51381 original size:21 final size:21
Alignment explanation
Indices: 51357--51404 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
51347 AAACATTTAA
51357 GAAAATTTTAAGATTTTCTTT
1 GAAAATTTTAAGATTTTCTTT
51378 GAAAATTTTAAGATTTTCTTT
1 GAAAATTTTAAGATTTTCTTT
51399 GAAAAT
1 GAAAAT
51405 CATTTTTGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.38, C:0.04, G:0.10, T:0.48
Consensus pattern (21 bp):
GAAAATTTTAAGATTTTCTTT
Found at i:53711 original size:21 final size:22
Alignment explanation
Indices: 53656--53729 Score: 69
Period size: 23 Copynumber: 3.3 Consensus size: 22
53646 CATAGCAGAG
53656 TGCATCGATGCACATTCAAGGAA
1 TGCATCGATGCACATTCAAGG-A
* * *
53679 TGCATCGGTGCACCTTCATGG-
1 TGCATCGATGCACATTCAAGGA
* *
53700 TGTATCGATGCACATTTAAGGGA
1 TGCATCGATGCACATTCAA-GGA
*
53723 TGTATCG
1 TGCATCG
53730 GTTCACTCTC
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
21 14 0.34
22 2 0.05
23 25 0.61
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.28
Consensus pattern (22 bp):
TGCATCGATGCACATTCAAGGA
Found at i:53730 original size:44 final size:43
Alignment explanation
Indices: 53654--53754 Score: 123
Period size: 44 Copynumber: 2.3 Consensus size: 43
53644 TGCATAGCAG
*
53654 AGTGCATCGATGCACATTCAAGGAATGCATCGGTGCAC-CTTCAT
1 AGTGTATCGATGCACATTCAAGGAATGCATCGGTGCACTC-TC-T
* * * * *
53698 GGTGTATCGATGCACATTTAAGGGATGTATCGGTTCACTCTCT
1 AGTGTATCGATGCACATTCAAGGAATGCATCGGTGCACTCTCT
53741 AGTGTATCGATGCA
1 AGTGTATCGATGCA
53755 TGAAGCACAA
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
43 14 0.29
44 34 0.69
45 1 0.02
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.30
Consensus pattern (43 bp):
AGTGTATCGATGCACATTCAAGGAATGCATCGGTGCACTCTCT
Found at i:54514 original size:14 final size:14
Alignment explanation
Indices: 54495--54523 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
54485 GCAAGCTAAA
54495 GCTAGAGTCTATAG
1 GCTAGAGTCTATAG
54509 GCTAGAGTCTATAG
1 GCTAGAGTCTATAG
54523 G
1 G
54524 ATACCAAAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.14, G:0.31, T:0.28
Consensus pattern (14 bp):
GCTAGAGTCTATAG
Found at i:57823 original size:116 final size:117
Alignment explanation
Indices: 57604--57824 Score: 286
Period size: 116 Copynumber: 1.9 Consensus size: 117
57594 CTTTTAAATC
**
57604 GAAATTTTCTTTTTCAATACTTTCAAATTTCATTTTTGAAAGCTATAAATCCTTCTTCAATTTTT
1 GAAATTTTCTTTTTCAATACTTTCAAATTTCATTTTTGAAAGCTATAAATCCTTCTTCAACATTT
* * *
57669 CATTTTGATTTTCAAAATCCATTTTAGTTTTTAGAAGAAGTTTGTTTAATTT
66 CATTTTGATTTTCAAAATCCATTTTAGCTTTCAAAAGAAGTTTGTTTAATTT
* * * * * *
57721 GAAATTTT-TTTTTCAA-AGTTTTCATATTTTATTTTTGAAAGCTCTAACTCCTTTTTCAACATT
1 GAAATTTTCTTTTTCAATA-CTTTCAAATTTCATTTTTGAAAGCTATAAATCCTTCTTCAACATT
* *
57784 TCATTTTGATTTTCCAAGT-CAGTTTTAGCTTTCAAAAGAAG
65 TCATTTTGATTTTCAAAATCCA-TTTTAGCTTTCAAAAGAAG
57825 ATCATTTTTA
Statistics
Matches: 89, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
115 3 0.03
116 78 0.88
117 8 0.09
ACGTcount: A:0.29, C:0.13, G:0.09, T:0.50
Consensus pattern (117 bp):
GAAATTTTCTTTTTCAATACTTTCAAATTTCATTTTTGAAAGCTATAAATCCTTCTTCAACATTT
CATTTTGATTTTCAAAATCCATTTTAGCTTTCAAAAGAAGTTTGTTTAATTT
Found at i:59230 original size:64 final size:65
Alignment explanation
Indices: 59137--59292 Score: 201
Period size: 65 Copynumber: 2.4 Consensus size: 65
59127 TACACTAGGG
* * * * *
59137 GTGCATCGGTACACTAATTACATTGGATGTTTC-AAAGAGCC-AGAAGTGCATCGATGCAT-GGT
1 GTGCATCGGTACACAAAATGCATTCGATGTTTCAAAAGAGCCAAG-AGTGCATCGATGCATAGCT
59199 CT
65 -T
* **
59201 GTGCATCGGTACACAAAATGCATTCGATGTTTCAAAATATTCAAGAGTGCATCGATGCATAGCTT
1 GTGCATCGGTACACAAAATGCATTCGATGTTTCAAAAGAGCCAAGAGTGCATCGATGCATAGCTT
59266 GTGCATCGGTACACAAAATGCATTCGA
1 GTGCATCGGTACACAAAATGCATTCGA
59293 AATGGGTGTG
Statistics
Matches: 81, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
64 29 0.36
65 48 0.59
66 4 0.05
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (65 bp):
GTGCATCGGTACACAAAATGCATTCGATGTTTCAAAAGAGCCAAGAGTGCATCGATGCATAGCTT
Found at i:69890 original size:43 final size:43
Alignment explanation
Indices: 69692--69933 Score: 143
Period size: 43 Copynumber: 5.6 Consensus size: 43
69682 GCTAAAGTTT
* ** * *
69692 GCGGCGTTTTTCAACAAAAAACGCCGCAATAGGT-TACAACATATA
1 GCGGCGTTTATC-AC-AAAAACGCCGCAATAGGTGT-TGATATTTA
* * *
69737 GCGGCGATTGT-TCA-ACAAACGCCGCAAAAGGTATTGATATTTA
1 GCGGCG-TT-TATCACAAAAACGCCGCAATAGGTGTTGATATTTA
***
69780 GCGGCGTTTATCATTTAAACGCCGCAATAGGTGTTGATATTTA
1 GCGGCGTTTATCACAAAAACGCCGCAATAGGTGTTGATATTTA
* * ** * * * * *
69823 ACGGCATTTGGCAGACAAATGCCGCAATAGTTGTTGATGTTTA
1 GCGGCGTTTATCACAAAAACGCCGCAATAGGTGTTGATATTTA
* * * * *
69866 GCGGCGTTT-TCTACAAAAACGCCGCAGTAGATTTTTATTTTTA
1 GCGGCGTTTATC-ACAAAAACGCCGCAATAGGTGTTGATATTTA
* *
69909 CCGGCGTTT-TTATCAAAAACGCCGC
1 GCGGCGTTTATCA-CAAAAACGCCGC
69934 TAACTGTATG
Statistics
Matches: 157, Mismatches: 33, Indels: 16
0.76 0.16 0.08
Matches are distributed among these distances:
41 1 0.01
42 7 0.04
43 136 0.87
44 1 0.01
45 7 0.04
46 4 0.03
47 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.29
Consensus pattern (43 bp):
GCGGCGTTTATCACAAAAACGCCGCAATAGGTGTTGATATTTA
Found at i:70335 original size:21 final size:21
Alignment explanation
Indices: 70271--70400 Score: 100
Period size: 21 Copynumber: 6.2 Consensus size: 21
70261 TGATATATTA
* * * *
70271 CTTCTCTCTGTTCTGCCGTTG
1 CTTCTCTCTCTGCTTCCGCTG
* * *
70292 CCTCTCTCTGTGCTGCCGCTG
1 CTTCTCTCTCTGCTTCCGCTG
70313 CTTCTCTCTCTGCTTCCGCTG
1 CTTCTCTCTCTGCTTCCGCTG
* **
70334 CTGCTCTAGCTGCTTCCGCTG
1 CTTCTCTCTCTGCTTCCGCTG
* * **
70355 CTGCTATAGCTGCTTCCGCTG
1 CTTCTCTCTCTGCTTCCGCTG
* *
70376 CTGCTCTCTCTGTTTCC-CTTG
1 CTTCTCTCTCTGCTTCCGC-TG
70397 CTTC
1 CTTC
70401 ATTTTCCGCT
Statistics
Matches: 93, Mismatches: 15, Indels: 2
0.85 0.14 0.02
Matches are distributed among these distances:
20 1 0.01
21 92 0.99
ACGTcount: A:0.02, C:0.38, G:0.19, T:0.40
Consensus pattern (21 bp):
CTTCTCTCTCTGCTTCCGCTG
Found at i:70353 original size:42 final size:42
Alignment explanation
Indices: 70302--70382 Score: 117
Period size: 42 Copynumber: 1.9 Consensus size: 42
70292 CCTCTCTCTG
* * **
70302 TGCTGCCGCTGCTTCTCTCTCTGCTTCCGCTGCTGCTCTAGC
1 TGCTGCCGCTGCTGCTATAGCTGCTTCCGCTGCTGCTCTAGC
*
70344 TGCTTCCGCTGCTGCTATAGCTGCTTCCGCTGCTGCTCT
1 TGCTGCCGCTGCTGCTATAGCTGCTTCCGCTGCTGCTCT
70383 CTCTGTTTCC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.04, C:0.38, G:0.22, T:0.36
Consensus pattern (42 bp):
TGCTGCCGCTGCTGCTATAGCTGCTTCCGCTGCTGCTCTAGC
Found at i:78338 original size:21 final size:21
Alignment explanation
Indices: 78312--78351 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
78302 CGAAACATCA
78312 TTCGTGTTCAGTAAAAAACAT
1 TTCGTGTTCAGTAAAAAACAT
78333 TTCGTGTTCAGTAAAAAAC
1 TTCGTGTTCAGTAAAAAAC
78352 TAATTGCTCG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.33
Consensus pattern (21 bp):
TTCGTGTTCAGTAAAAAACAT
Found at i:79188 original size:83 final size:83
Alignment explanation
Indices: 79064--79290 Score: 247
Period size: 83 Copynumber: 2.7 Consensus size: 83
79054 ACTATATGTG
* * * * * * *
79064 TAATATATTGCGGCGTTTTTTGTCAAAACGCCGCCAATTTACCGCTCTATTACGGCGTTTTGACT
1 TAATCTATTGAGGCGTTTGTGGTAAAAACGCCGCCAATTTACCACTATATTACGGCGTTTTGACT
*
79129 CAATCGCCGCAAAATTTA
66 AAATCGCCGCAAAATTTA
* * * * * * *
79147 TACTCTATTGTGGCGTTTGTGGTAAAAATGCTGCCAGTTTACCACTATATTGCGGCGTTTTGGCT
1 TAATCTATTGAGGCGTTTGTGGTAAAAACGCCGCCAATTTACCACTATATTACGGCGTTTTGACT
79212 AAATCGCCGCAAAATTTA
66 AAATCGCCGCAAAATTTA
* * * * * ** *
79230 TAATCTATTGAAGCGTTTGTGATATAAACGCCGCTAATTTAGCACCCTATTGCGGCGTTTT
1 TAATCTATTGAGGCGTTTGTGGTAAAAACGCCGCCAATTTACCACTATATTACGGCGTTTT
79291 TCTAAAAACG
Statistics
Matches: 118, Mismatches: 26, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
83 118 1.00
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.35
Consensus pattern (83 bp):
TAATCTATTGAGGCGTTTGTGGTAAAAACGCCGCCAATTTACCACTATATTACGGCGTTTTGACT
AAATCGCCGCAAAATTTA
Found at i:79300 original size:41 final size:43
Alignment explanation
Indices: 79255--79349 Score: 108
Period size: 41 Copynumber: 2.3 Consensus size: 43
79245 TTTGTGATAT
* * *
79255 AAACGCCGCTAATTTAG-C-ACCCTATTGCGGCGTTTTT-CTAA
1 AAACGCCGCTAATAT-GTCAACCATATTGCAGCGTTTTTACTAA
**
79296 AAACGCCGC-AATATGTCAATTATATTGCAGCGTTTTTACTAA
1 AAACGCCGCTAATATGTCAACCATATTGCAGCGTTTTTACTAA
79338 AAACGCCGCTAA
1 AAACGCCGCTAA
79350 AGTATCAATT
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
39 1 0.02
40 5 0.11
41 24 0.53
42 13 0.29
43 2 0.04
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.29
Consensus pattern (43 bp):
AAACGCCGCTAATATGTCAACCATATTGCAGCGTTTTTACTAA
Found at i:79306 original size:83 final size:83
Alignment explanation
Indices: 79088--79290 Score: 262
Period size: 83 Copynumber: 2.4 Consensus size: 83
79078 GTTTTTTGTC
* * * *
79088 AAAACGCCGCCAATTTACCGCTCTATTACGGCGTTTTGACTCAATCGCCGCAAAATTTATACTCT
1 AAAACGCCGCCAATTTACCACTCTATTGCGGCGTTTTGACTAAATCGCCGCAAAATTTATAATCT
** *
79153 ATTGTGGCGTTTGTGGTA
66 ATTGAAGCGTTTGTGATA
* * * * *
79171 AAAATGCTGCCAGTTTACCACTATATTGCGGCGTTTTGGCTAAATCGCCGCAAAATTTATAATCT
1 AAAACGCCGCCAATTTACCACTCTATTGCGGCGTTTTGACTAAATCGCCGCAAAATTTATAATCT
79236 ATTGAAGCGTTTGTGATA
66 ATTGAAGCGTTTGTGATA
* * * *
79254 TAAACGCCGCTAATTTAGCACCCTATTGCGGCGTTTT
1 AAAACGCCGCCAATTTACCACTCTATTGCGGCGTTTT
79291 TCTAAAAACG
Statistics
Matches: 100, Mismatches: 20, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
83 100 1.00
ACGTcount: A:0.26, C:0.22, G:0.19, T:0.33
Consensus pattern (83 bp):
AAAACGCCGCCAATTTACCACTCTATTGCGGCGTTTTGACTAAATCGCCGCAAAATTTATAATCT
ATTGAAGCGTTTGTGATA
Found at i:81295 original size:23 final size:23
Alignment explanation
Indices: 81251--81295 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
81241 TATTTAAGAT
* *
81251 ATTTTTTTAAATAAAAATTAATG
1 ATTTTTATAAATAAAAAGTAATG
81274 ATTTTTATAAA-AATAAAGTAAT
1 ATTTTTATAAATAA-AAAGTAAT
81296 CATTGACACA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 2 0.11
23 17 0.89
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.44
Consensus pattern (23 bp):
ATTTTTATAAATAAAAAGTAATG
Found at i:86663 original size:2 final size:2
Alignment explanation
Indices: 86656--86685 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
86646 AATAAAAACA
86656 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
86686 GTGTTTACAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.