Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005751.1 Hibiscus syriacus cultivar Beakdansim tig00013454_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: 121156
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:799 original size:14 final size:14
Alignment explanation
Indices: 782--810 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
772 ATTACTCCTA
782 AGAAAGAAAAAAAG
1 AGAAAGAAAAAAAG
796 AGAAAGAAAAAAAG
1 AGAAAGAAAAAAAG
810 A
1 A
811 AAAAATTAAA
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:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (14 bp):
AGAAAGAAAAAAAG
Found at i:805 original size:12 final size:12
Alignment explanation
Indices: 781--890 Score: 64
Period size: 13 Copynumber: 8.5 Consensus size: 12
771 AATTACTCCT
781 AAGAAAGAAAAAA
1 AAGAAAG-AAAAA
794 AGAGAAAGAAAAA
1 A-AGAAAGAAAAA
*
807 AAGAAAAAATTAAA
1 AAGAAAGAA--AAA
*
821 AATGAAA-ATGAAA
1 AA-GAAAGA-AAAA
*
834 ATGAAAAGAAAAA
1 AAG-AAAGAAAAA
*
847 GAACAAA-AAAAA
1 -AAGAAAGAAAAA
859 ATA-AAAGAACAAA
1 A-AGAAAGAA-AAA
872 AAGTAAAGAAAAA
1 AAG-AAAGAAAAA
885 AAGAAA
1 AAGAAA
891 AAGAAAATAA
Statistics
Matches: 78, Mismatches: 6, Indels: 27
0.70 0.05 0.24
Matches are distributed among these distances:
11 4 0.05
12 20 0.26
13 30 0.38
14 20 0.26
15 4 0.05
ACGTcount: A:0.78, C:0.02, G:0.14, T:0.06
Consensus pattern (12 bp):
AAGAAAGAAAAA
Found at i:813 original size:6 final size:6
Alignment explanation
Indices: 781--897 Score: 55
Period size: 6 Copynumber: 19.2 Consensus size: 6
771 AATTACTCCT
* * **
781 AAGAAA GAA-AAA AAGAGA AAGAAA AA-AAG AA-AAA ATTAAA AATGAAA
1 AAGAAA -AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AA-GAAA
* * * * *
828 ATGAAA ATG-AA AAGAAA AAGAACA AAAAAA AATAAAA GAACAAA AAGTAAA
1 AAGAAA AAGAAA AAGAAA AAGAA-A AAGAAA AA-GAAA -AAGAAA AAG-AAA
879 GAA-AAA AAGAAA AAGAAA A
1 -AAGAAA AAGAAA AAGAAA A
898 TAAAATGAAG
Statistics
Matches: 88, Mismatches: 12, Indels: 21
0.73 0.10 0.17
Matches are distributed among these distances:
5 15 0.17
6 48 0.55
7 21 0.24
8 4 0.05
ACGTcount: A:0.79, C:0.02, G:0.14, T:0.06
Consensus pattern (6 bp):
AAGAAA
Found at i:858 original size:18 final size:18
Alignment explanation
Indices: 837--884 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 18
827 AATGAAAATG
837 AAAAGAAAAAGAACAAAA
1 AAAAGAAAAAGAACAAAA
855 AAAA-ATAAAAGAACAAAA
1 AAAAGA-AAAAGAACAAAA
873 AGTAAAGAAAAA
1 A--AAAGAAAAA
885 AAGAAAAAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
17 1 0.04
18 17 0.65
20 7 0.27
21 1 0.04
ACGTcount: A:0.81, C:0.04, G:0.10, T:0.04
Consensus pattern (18 bp):
AAAAGAAAAAGAACAAAA
Found at i:859 original size:14 final size:13
Alignment explanation
Indices: 837--897 Score: 50
Period size: 13 Copynumber: 4.5 Consensus size: 13
827 AATGAAAATG
*
837 AAAAGAAAAAGAA
1 AAAAAAAAAAGAA
* *
850 CAAAAAAAAATAA
1 AAAAAAAAAAGAA
* *
863 AAGAACAAAAAGTA
1 AA-AAAAAAAAGAA
*
877 AAGAAAAAAAGAA
1 AAAAAAAAAAGAA
890 AAAGAAAA
1 AAA-AAAA
898 TAAAATGAAG
Statistics
Matches: 35, Mismatches: 11, Indels: 3
0.71 0.22 0.06
Matches are distributed among these distances:
13 21 0.60
14 14 0.40
ACGTcount: A:0.82, C:0.03, G:0.11, T:0.03
Consensus pattern (13 bp):
AAAAAAAAAAGAA
Found at i:2197 original size:131 final size:133
Alignment explanation
Indices: 1912--2402 Score: 535
Period size: 131 Copynumber: 3.8 Consensus size: 133
1902 AAGATAAACT
* * **
1912 GATTAACATTTCCAATGGAGAGTTTATGATAAGAAGAACTCATTTGATAGAGGGAGAAGAAGTTC
1 GATTAACATTTCCAATGGAGAGTTTATAATGAGAAGAACTCATCCGATAGAGGGAGAAGAAGTTC
* * *
1977 GTACTTAGAAGAACTTGTTCAACCTTTGCTCGATTCACGACATTT-GAATCA-TGAAACCTCACT
66 GTA-TAAGAAGAACTTGTTCAACATTTGCTCGATTCACGACATTTCAAATCAGT-AAACCTCACT
2040 TGAGG
129 TGAGG
* * * * *
2045 GATTAAAATTTCCAATTGAGAGTTTGTAATGAGAAGAACTCGTCCGATAGA-GGAGAA-AAATTC
1 GATTAACATTTCCAATGGAGAGTTTATAATGAGAAGAACTCATCCGATAGAGGGAGAAGAAGTTC
* *
2108 GTATAAGAAGAACTTGTTCAACATTTGCTCGAATCACGACATTTCAAATCAGTAAACCTCACTTA
66 GTATAAGAAGAACTTGTTCAACATTTGCTCGATTCACGACATTTCAAATCAGTAAACCTCACTTG
2173 AGG
131 AGG
* * * *
2176 GTTTAATATTTCCAATTGAGAG-TT-TAATGAGAAGAACTCATCCAATAGAGGGAGAAGAAGTTC
1 GATTAACATTTCCAATGGAGAGTTTATAATGAGAAGAACTCATCCGATAGAGGGAGAAGAAGTTC
* * * * * *
2239 GTAATGAGAAGAA-TTGTTCAACATTTTCTCCATTTAC-ATCATTTCAAATCAGCAACACCTCGC
66 GT-ATAAGAAGAACTTGTTCAACATTTGCTCGATTCACGA-CATTTCAAATCAGTAA-ACCTCAC
2302 TTGA-G
128 TTGAGG
* * *
2307 GATTAACATTTCCAATGGAGAGTTCATAATGAGATGAACTTATCCG--AGA---AGAAG-AGTTC
1 GATTAACATTTCCAATGGAGAGTTTATAATGAGAAGAACTCATCCGATAGAGGGAGAAGAAGTTC
* * * * *
2366 ATATTGAGAAGAACTTGTTTAACCTTTGCTTGATTCA
66 GTA-TAAGAAGAACTTGTTCAACATTTGCTCGATTCA
2403 TGGTCTTTTG
Statistics
Matches: 306, Mismatches: 41, Indels: 27
0.82 0.11 0.07
Matches are distributed among these distances:
126 1 0.00
127 15 0.05
128 22 0.07
129 23 0.08
130 47 0.15
131 112 0.37
132 26 0.08
133 60 0.20
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.30
Consensus pattern (133 bp):
GATTAACATTTCCAATGGAGAGTTTATAATGAGAAGAACTCATCCGATAGAGGGAGAAGAAGTTC
GTATAAGAAGAACTTGTTCAACATTTGCTCGATTCACGACATTTCAAATCAGTAAACCTCACTTG
AGG
Found at i:2621 original size:22 final size:22
Alignment explanation
Indices: 2596--2650 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
2586 ACCCCATTTA
*
2596 CAAACTAACCTCAAGCCCAACC
1 CAAACCAACCTCAAGCCCAACC
*
2618 CAAACCAACCTCAAGCCCATCC
1 CAAACCAACCTCAAGCCCAACC
*
2640 GAAACCAACCT
1 CAAACCAACCT
2651 AAATACCCAA
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:0.40, C:0.45, G:0.05, T:0.09
Consensus pattern (22 bp):
CAAACCAACCTCAAGCCCAACC
Found at i:2679 original size:17 final size:18
Alignment explanation
Indices: 2641--2679 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
2631 AGCCCATCCG
*
2641 AAACCAACCTAAATACCC
1 AAACCAACATAAATACCC
2659 AAACCAACATAAATA-CC
1 AAACCAACATAAATACCC
2676 AAAC
1 AAAC
2680 TCGGCCCGGG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.56, C:0.33, G:0.00, T:0.10
Consensus pattern (18 bp):
AAACCAACATAAATACCC
Found at i:7721 original size:45 final size:45
Alignment explanation
Indices: 7656--7965 Score: 397
Period size: 45 Copynumber: 6.9 Consensus size: 45
7646 ATGGGATGCC
**
7656 ATAGTTGAAATGTATATGGGTACGCTATCAACAGAAAAGTATACT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
* *
7701 TTAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATGCT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
* * * * *
7746 AAAGTTGAAATGCATATGGGTGCATCATCAACA-AGAAAGTATGCT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGA-AAAGTATACT
* * * * * *
7791 AGAGTTGAAATGCATATGGGTGCATTATCAACAGAAGAGCATGCT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
* *
7836 AGAGTTGAAATGTATATGTGTACATTATCAACAGAAAAGTATACT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
* *
7881 ATGGTTGAAATATATATGGGTACATTATCAACAGAAAAGTATACT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
* * * *
7926 ATAGTTGAAATGCATAAGGGTTCATCATCAACAGAAAAGT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGT
7966 TGTTATTGTT
Statistics
Matches: 234, Mismatches: 29, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
44 1 0.00
45 232 0.99
46 1 0.00
ACGTcount: A:0.40, C:0.11, G:0.21, T:0.28
Consensus pattern (45 bp):
ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
Found at i:7998 original size:90 final size:90
Alignment explanation
Indices: 7658--8003 Score: 332
Period size: 90 Copynumber: 3.8 Consensus size: 90
7648 GGGATGCCAT
* * * * *
7658 AGTTGAAATGTATATGGGTAC-GCTATCAACAGAAAAGTATACTTTAGTTGAAATGTAT-ATGG-
1 AGTTGAAATGCATATGGGTACATC-ATCAACAGAAAAGTATGCTATAGTTGAAATGCATAATGGT
7720 GTACATTATCAACAGAAAAGTATGCTAA
65 GT--ATTATCAACAGAAAAGTATGCTAA
* *
7748 AGTTGAAATGCATATGGGTGCATCATCAACA-AGAAAGTATGCTAGAGTTGAAATGCAT-ATGGG
1 AGTTGAAATGCATATGGGTACATCATCAACAGA-AAAGTATGCTATAGTTGAAATGCATAAT-GG
* * * *
7811 TGCATTATCAACAGAAGAGCATGCTAG
64 TGTATTATCAACAGAAAAGTATGCTAA
* * * * *
7838 AGTTGAAATGTATATGTGTACATTATCAACAGAAAAGTATACTATGGTTGAAAT--ATATATGG-
1 AGTTGAAATGCATATGGGTACATCATCAACAGAAAAGTATGCTATAGTTGAAATGCATA-ATGGT
* *
7900 GTACATTATCAACAGAAAAGTATACTAT
65 GT--ATTATCAACAGAAAAGTATGCTAA
* * * * *
7928 AGTTGAAATGCATAAGGGTTCATCATCAACAGAAAAGT-TGTTATTGTTTAAAGTGCATAATGGT
1 AGTTGAAATGCATATGGGTACATCATCAACAGAAAAGTATGCTATAGTTGAAA-TGCATAATGGT
*
7992 GTATTATAAACA
65 GTATTATCAACA
8004 TAAATGGAAG
Statistics
Matches: 210, Mismatches: 33, Indels: 26
0.78 0.12 0.10
Matches are distributed among these distances:
88 3 0.01
89 13 0.06
90 180 0.86
91 8 0.04
92 6 0.03
ACGTcount: A:0.39, C:0.10, G:0.21, T:0.30
Consensus pattern (90 bp):
AGTTGAAATGCATATGGGTACATCATCAACAGAAAAGTATGCTATAGTTGAAATGCATAATGGTG
TATTATCAACAGAAAAGTATGCTAA
Found at i:14055 original size:96 final size:94
Alignment explanation
Indices: 13927--14139 Score: 259
Period size: 96 Copynumber: 2.2 Consensus size: 94
13917 TGGTATGGAA
* **
13927 ACCATGGTGAGGGTATCGATACCAGGAAACATCGAA-CTTAATTTTGATATCGATACCGAAGGGA
1 ACCATGGTGAGGGTATCGATACTAGGAAACATCGAATC-TAATTTTGATATCGATA-CGAAAAG-
* *
13991 GGGAATTGATACCATAACATAGTAGTATCGAT
63 GGGAATCGATACCATAACAGAGTAGTATCGAT
** * *
14023 ACCATGGTGAGGGTATCGATACTAGGCTACATCGAATCTAATTTTGGTATCGATACTAAAAGGGG
1 ACCATGGTGAGGGTATCGATACTAGGAAACATCGAATCTAATTTTGATATCGATACGAAAAGGGG
* * *
14088 TATCGATACCATAATAGAGTAGTATTGAT
66 AATCGATACCATAACAGAGTAGTATCGAT
*
14117 ACCATAGT-AGGGGTATCGATACT
1 ACCATGGTGA-GGGTATCGATACT
14140 GAAGGGCCAG
Statistics
Matches: 102, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
93 1 0.01
94 47 0.46
95 4 0.04
96 49 0.48
97 1 0.01
ACGTcount: A:0.34, C:0.15, G:0.24, T:0.27
Consensus pattern (94 bp):
ACCATGGTGAGGGTATCGATACTAGGAAACATCGAATCTAATTTTGATATCGATACGAAAAGGGG
AATCGATACCATAACAGAGTAGTATCGAT
Found at i:14137 original size:20 final size:20
Alignment explanation
Indices: 14068--14138 Score: 74
Period size: 22 Copynumber: 3.5 Consensus size: 20
14058 ATCTAATTTT
*
14068 GGTATCGATA-C-TAAAAGG
1 GGTATCGATACCATAATAGG
14086 GGTATCGATACCATAATAGAG
1 GGTATCGATACCATAATAG-G
* * *
14107 TAGTATTGATACCATAGTAGG
1 -GGTATCGATACCATAATAGG
14128 GGTATCGATAC
1 GGTATCGATAC
14139 TGAAGGGCCA
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
18 10 0.23
19 1 0.02
20 14 0.33
21 2 0.05
22 16 0.37
ACGTcount: A:0.35, C:0.13, G:0.25, T:0.27
Consensus pattern (20 bp):
GGTATCGATACCATAATAGG
Found at i:14639 original size:45 final size:45
Alignment explanation
Indices: 14590--14894 Score: 324
Period size: 45 Copynumber: 6.8 Consensus size: 45
14580 GATGCCATAT
* * ** **
14590 TTGAAATGTATATGGGTACACTATCAAAAGAAAAACATACTTTAG
1 TTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACTAGAG
* *
14635 TTGAAATGTATATGGGTACATTATCAACATAAAAGTATGCTAGAG
1 TTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACTAGAG
* * ** *
14680 TTGAAATGCATATGGATGTATTATCAACAGAAAAGTATGCTAGAG
1 TTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACTAGAG
* * * * * *
14725 TTGAAATGCATAGGGGTGCATTATCAACAGAAGAGCATGCTAGAG
1 TTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACTAGAG
* *
14770 TTGAAATGTATATGGGTACATTATCAACAGAAATGTATACCATG-G
1 TTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACTA-GAG
* * * *
14815 TTGAAATGTATATGAGTACATTATCAATAAAAAAGTATACTACAG
1 TTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACTAGAG
* * * * *
14860 TTGAAATGCATATGGGTGCATCATAAATAGAAAAG
1 TTGAAATGTATATGGGTACATTATCAACAGAAAAG
14895 ATGTTATAGT
Statistics
Matches: 220, Mismatches: 38, Indels: 4
0.84 0.15 0.02
Matches are distributed among these distances:
45 219 1.00
46 1 0.00
ACGTcount: A:0.41, C:0.10, G:0.20, T:0.29
Consensus pattern (45 bp):
TTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACTAGAG
Found at i:23717 original size:20 final size:22
Alignment explanation
Indices: 23692--23731 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
23682 TTTCGTAAGA
23692 ATATGC-CAT-AAATTCCAGAT
1 ATATGCGCATAAAATTCCAGAT
*
23712 ATATGCGGATAAAATTCCAG
1 ATATGCGCATAAAATTCCAG
23732 CACCGCCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
21 2 0.12
22 9 0.53
ACGTcount: A:0.40, C:0.17, G:0.15, T:0.28
Consensus pattern (22 bp):
ATATGCGCATAAAATTCCAGAT
Found at i:24641 original size:9 final size:9
Alignment explanation
Indices: 24627--24684 Score: 55
Period size: 9 Copynumber: 6.1 Consensus size: 9
24617 TATCAAGCCT
*
24627 AAGAAACAA
1 AAGAAAAAA
24636 AAGAAAAAA
1 AAGAAAAAA
24645 GAA-AAAAAA
1 -AAGAAAAAA
24654 AAGAAAAAA
1 AAGAAAAAA
*
24663 AAGTAGTAGAAA
1 AAG-A--AAAAA
24675 AAGAAAAAA
1 AAGAAAAAA
24684 A
1 A
24685 TGAGGGTTCA
Statistics
Matches: 41, Mismatches: 3, Indels: 10
0.76 0.06 0.19
Matches are distributed among these distances:
8 2 0.05
9 28 0.68
10 3 0.07
11 1 0.02
12 7 0.17
ACGTcount: A:0.81, C:0.02, G:0.14, T:0.03
Consensus pattern (9 bp):
AAGAAAAAA
Found at i:24655 original size:11 final size:11
Alignment explanation
Indices: 24634--24664 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
24624 CCTAAGAAAC
24634 AAAAGAAAAAAG
1 AAAA-AAAAAAG
24646 AAAAAAAAAAG
1 AAAAAAAAAAG
24657 AAAAAAAA
1 AAAAAAAA
24665 GTAGTAGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 15 0.79
12 4 0.21
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:25871 original size:135 final size:135
Alignment explanation
Indices: 25628--26205 Score: 581
Period size: 135 Copynumber: 4.3 Consensus size: 135
25618 TGATAAACCA
* * * * * *
25628 ATTAACATTTCCAATAGAGATTTCATAATAATAAGAACTCATCCGATAGAGGGAGAAGAAGTTCG
1 ATTAACATTTCCAATAGAGAGTTCATAATGAGAAGAACTCATCCGATAAAGGAAGAAAAAGTTCG
* * *
25693 TAATGAGAAGAACTTGTTCAACCTTTACTCGATTCACGATATTTTGAACCAGTGAA-ACCTCACT
66 TAATGAGAAGAACTTGTTCAACCTTTGCTCGATTCACGACATTTTGAATCAGT-AACACCTCACT
25757 TGAGGG
130 TGAGGG
* * *
25763 ATTAACATTTCCAATGGAGAGTTCGTAATGAGAAGAACTCATCTGATAAAGGAAGAAAAAGTTCG
1 ATTAACATTTCCAATAGAGAGTTCATAATGAGAAGAACTCATCCGATAAAGGAAGAAAAAGTTCG
* * * * ** * * *
25828 TAATAAGAATAACTTGTTAAACCTTTGCTCGATTCATGGTA-TTTGAAATTAGCAAAACCTCACT
66 TAATGAGAAGAACTTGTTCAACCTTTGCTCGATTCACGACATTTTG-AATCAGTAACACCTCACT
25892 TGAGGG
130 TGAGGG
* * * * ** * *
25898 ATTAATATTTCCAATAGAGAGTTCATAATGAGAAGAA-TAAATCTGATAGAGGGTGAAAAAATTT
1 ATTAACATTTCCAATAGAGAGTTCATAATGAGAAGAACT-CATCCGATAAAGGAAGAAAAAGTTC
* * ** **
25962 GTAATGAGAAGAACTTGTTCAGCCTTTGCTCGATTCACGACATTTCGAATCAGTAATGCCTTGCT
65 GTAATGAGAAGAACTTGTTCAACCTTTGCTCGATTCACGACATTTTGAATCAGTAACACCTCACT
*
26027 TTAGGG
130 TGAGGG
* * * * * * * *
26033 TTTAGCATTTCCAAT-GAAGATTTCTTAATGAGATGAACTCATCCGATTGAGGGAA-AAGAAGTT
1 ATTAACATTTCCAATAG-AGAGTTCATAATGAGAAGAACTCATCCGA-TAAAGGAAGAAAAAGTT
* * * * * *
26096 AGTAATGAGAAGAAATTGTTCAATCTTTTCTCGATTCACGACATTTTGAATCAGCAACACCTTAC
64 CGTAATGAGAAGAACTTGTTCAACCTTTGCTCGATTCACGACATTTTGAATCAGTAACACCTCAC
*
26161 TCGAGGG
129 TTGAGGG
* * * *
26168 ATCAACATTTCCAGTAGAAAGTTCATGATGAGAAGAAC
1 ATTAACATTTCCAATAGAGAGTTCATAATGAGAAGAAC
26206 CCGCAGCTTG
Statistics
Matches: 357, Mismatches: 78, Indels: 16
0.79 0.17 0.04
Matches are distributed among these distances:
134 8 0.02
135 341 0.96
136 8 0.02
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.29
Consensus pattern (135 bp):
ATTAACATTTCCAATAGAGAGTTCATAATGAGAAGAACTCATCCGATAAAGGAAGAAAAAGTTCG
TAATGAGAAGAACTTGTTCAACCTTTGCTCGATTCACGACATTTTGAATCAGTAACACCTCACTT
GAGGG
Found at i:26131 original size:270 final size:270
Alignment explanation
Indices: 25628--26205 Score: 669
Period size: 270 Copynumber: 2.1 Consensus size: 270
25618 TGATAAACCA
* * * * * *
25628 ATTAACATTTCCAATAGAGATTTCATAATAATAAGAACTCATCCGATAGAGGGAGAAGAAGTTCG
1 ATTAACATTTCCAATAGAGAGTTCATAATGAGAAGAACTAATCCGATAGAGGGAGAAAAAATTCG
* *
25693 TAATGAGAAGAACTTGTTCAACCTTTACTCGATTCACGATATTTTGAACCAGTGAAACCTCACTT
66 TAATGAGAAGAACTTGTTCAACCTTTACTCGATTCACGACATTTCGAACCAGTGAAACCTCACTT
* *
25758 GAGGGATTAACATTTCCAATGGAGAGTTCGTAATGAGAAGAACTCATCTGATAAAGGAAGAAAAA
131 GAGGGATTAACATTTCCAATGAAGAGTTCGTAATGAGAAGAACTCATCCGATAAAGGAAGAAAAA
* * * * ** *
25823 GTTCGTAATAAGAATAACTTGTTAAACCTTTGCTCGATTCATGGTA-TTTGAAATTAGCAAAACC
196 GTTAGTAATAAGAAGAAATTGTTAAACCTTTGCTCGATTCACGACATTTTG-AATCAGCAAAACC
*
25887 TCACTTGAGGG
260 TCACTCGAGGG
* * * *
25898 ATTAATATTTCCAATAGAGAGTTCATAATGAGAAGAA-TAAATCTGATAGAGGGTGAAAAAATTT
1 ATTAACATTTCCAATAGAGAGTTCATAATGAGAAGAACT-AATCCGATAGAGGGAGAAAAAATTC
* * * * **
25962 GTAATGAGAAGAACTTGTTCAGCCTTTGCTCGATTCACGACATTTCGAATCAGT-AATGCCTTGC
65 GTAATGAGAAGAACTTGTTCAACCTTTACTCGATTCACGACATTTCGAACCAGTGAA-ACCTCAC
* * * * * * * *
26026 TTTAGGGTTTAGCATTTCCAATGAAGATTTCTTAATGAGATGAACTCATCCGATTGAGGGAA-AA
129 TTGAGGGATTAACATTTCCAATGAAGAGTTCGTAATGAGAAGAACTCATCCGA-TAAAGGAAGAA
* * * * * *
26090 GAAGTTAGTAATGAGAAGAAATTGTTCAATCTTTTCTCGATTCACGACATTTTGAATCAGCAACA
193 AAAGTTAGTAATAAGAAGAAATTGTTAAACCTTTGCTCGATTCACGACATTTTGAATCAGCAAAA
*
26155 CCTTACTCGAGGG
258 CCTCACTCGAGGG
* * * *
26168 ATCAACATTTCCAGTAGAAAGTTCATGATGAGAAGAAC
1 ATTAACATTTCCAATAGAGAGTTCATAATGAGAAGAAC
26206 CCGCAGCTTG
Statistics
Matches: 255, Mismatches: 48, Indels: 9
0.82 0.15 0.03
Matches are distributed among these distances:
269 3 0.01
270 242 0.95
271 10 0.04
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.29
Consensus pattern (270 bp):
ATTAACATTTCCAATAGAGAGTTCATAATGAGAAGAACTAATCCGATAGAGGGAGAAAAAATTCG
TAATGAGAAGAACTTGTTCAACCTTTACTCGATTCACGACATTTCGAACCAGTGAAACCTCACTT
GAGGGATTAACATTTCCAATGAAGAGTTCGTAATGAGAAGAACTCATCCGATAAAGGAAGAAAAA
GTTAGTAATAAGAAGAAATTGTTAAACCTTTGCTCGATTCACGACATTTTGAATCAGCAAAACCT
CACTCGAGGG
Found at i:26420 original size:18 final size:18
Alignment explanation
Indices: 26353--26408 Score: 112
Period size: 18 Copynumber: 3.1 Consensus size: 18
26343 CTCAAGCCCA
26353 ACCCAAACCAACCTAAAT
1 ACCCAAACCAACCTAAAT
26371 ACCCAAACCAACCTAAAT
1 ACCCAAACCAACCTAAAT
26389 ACCCAAACCAACCTAAAT
1 ACCCAAACCAACCTAAAT
26407 AC
1 AC
26409 TAAACCCGAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 38 1.00
ACGTcount: A:0.50, C:0.39, G:0.00, T:0.11
Consensus pattern (18 bp):
ACCCAAACCAACCTAAAT
Found at i:27581 original size:107 final size:109
Alignment explanation
Indices: 27398--27600 Score: 252
Period size: 107 Copynumber: 1.9 Consensus size: 109
27388 CCAAATCTTT
* ** * *
27398 TATTTTCCCTTTTCTTTGTGTGCTTTGTAATTTTTGGGTTATTCATATTTTGGCCCCTCTAACTT
1 TATTTTCCATTTTCTTTGCATGCTTTGTAATTTTTAGGTTATTCATATTTTGGCCCCTATAACTT
*
27463 TAGCGTATTTTTTCA-TTCTGGTCATATGTAGGATTTAAAACTGC
66 TAGCGTATTTTTACACTT-TGGTCATATGTAGGATTTAAAACTGC
* * * *
27507 TATTTTCCATTTTC-TTGCATGCTTTGT-ATTTTTAGGTTATTC-TCTGTTTGGTCCTTATAAGT
1 TATTTTCCATTTTCTTTGCATGCTTTGTAATTTTTAGGTTATTCATAT-TTTGGCCCCTATAACT
* *
27569 TTAGCGTGTTTTTACACTTTGGTCATGTGTAG
65 TTAGCGTATTTTTACACTTTGGTCATATGTAG
27601 TGACTTTTTA
Statistics
Matches: 80, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
106 2 0.03
107 52 0.65
108 13 0.16
109 13 0.16
ACGTcount: A:0.16, C:0.15, G:0.17, T:0.52
Consensus pattern (109 bp):
TATTTTCCATTTTCTTTGCATGCTTTGTAATTTTTAGGTTATTCATATTTTGGCCCCTATAACTT
TAGCGTATTTTTACACTTTGGTCATATGTAGGATTTAAAACTGC
Found at i:30253 original size:23 final size:23
Alignment explanation
Indices: 30223--30267 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
30213 TTTGCAGTTG
30223 TAACTTTTACAAGTGGGATTTGT
1 TAACTTTTACAAGTGGGATTTGT
30246 TAACTTTTACAAGTGGGATTTG
1 TAACTTTTACAAGTGGGATTTG
30268 AATTATAGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.27, C:0.09, G:0.22, T:0.42
Consensus pattern (23 bp):
TAACTTTTACAAGTGGGATTTGT
Found at i:30877 original size:3 final size:3
Alignment explanation
Indices: 30871--30919 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
30861 TTTACTCATT
30871 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
30919 T
1 T
30920 ATAAAATAAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:34862 original size:15 final size:15
Alignment explanation
Indices: 34826--34864 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
34816 AATTTACATG
34826 TTTACATTT-GCATA
1 TTTACATTTGGCATA
*
34840 TTTACATTTGGCATC
1 TTTACATTTGGCATA
*
34855 TTTGCATTTG
1 TTTACATTTG
34865 TATTTTTATG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 9 0.41
15 13 0.59
ACGTcount: A:0.21, C:0.15, G:0.13, T:0.51
Consensus pattern (15 bp):
TTTACATTTGGCATA
Found at i:37760 original size:2 final size:2
Alignment explanation
Indices: 37753--37810 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
37743 TTATCCTTTA
37753 AT AT AT AT AT 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 AT AT AT AT AT
37795 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
37811 CCTTTGTTGT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:38124 original size:23 final size:23
Alignment explanation
Indices: 38097--38141 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
38087 TATTATACTC
38097 ATCCAGCAAAGAAAGAAAAAAAA
1 ATCCAGCAAAGAAAGAAAAAAAA
*
38120 ATCCAGCAAAGAAAGGAAAAAA
1 ATCCAGCAAAGAAAGAAAAAAA
38142 GAAAAAAGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.67, C:0.13, G:0.16, T:0.04
Consensus pattern (23 bp):
ATCCAGCAAAGAAAGAAAAAAAA
Found at i:38147 original size:7 final size:7
Alignment explanation
Indices: 38135--38207 Score: 51
Period size: 7 Copynumber: 10.0 Consensus size: 7
38125 GCAAAGAAAG
38135 GAAAAAA
1 GAAAAAA
38142 GAAAAAAGA
1 G-AAAAA-A
38151 GGAAAAAA
1 -GAAAAAA
38159 GAAAAAA
1 GAAAAAA
**
38166 -AGGAAA
1 GAAAAAA
38172 GAAATAGAA
1 GAAA-A-AA
*
38181 AAAAAAA
1 GAAAAAA
*
38188 CAAAAAA
1 GAAAAAA
38195 G-AAAAA
1 GAAAAAA
38201 GAAAAAA
1 GAAAAAA
38208 ATTAAATCAA
Statistics
Matches: 52, Mismatches: 7, Indels: 14
0.71 0.10 0.19
Matches are distributed among these distances:
6 10 0.19
7 22 0.42
8 8 0.15
9 11 0.21
10 1 0.02
ACGTcount: A:0.81, C:0.01, G:0.16, T:0.01
Consensus pattern (7 bp):
GAAAAAA
Found at i:38155 original size:17 final size:16
Alignment explanation
Indices: 38131--38200 Score: 77
Period size: 17 Copynumber: 4.1 Consensus size: 16
38121 TCCAGCAAAG
38131 AAAGGAAAAAAGAAAA
1 AAAGGAAAAAAGAAAA
38147 AAGAGGAAAAAAGAAAA
1 AA-AGGAAAAAAGAAAA
38164 AAAGGAAAGAAATAGAAAAA
1 AAAGG-AA-AAA-AG-AAAA
**
38184 AAAACAAAAAAGAAAA
1 AAAGGAAAAAAGAAAA
38200 A
1 A
38201 GAAAAAAATT
Statistics
Matches: 47, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
16 10 0.21
17 20 0.43
18 6 0.13
19 4 0.09
20 7 0.15
ACGTcount: A:0.80, C:0.01, G:0.17, T:0.01
Consensus pattern (16 bp):
AAAGGAAAAAAGAAAA
Found at i:40743 original size:94 final size:94
Alignment explanation
Indices: 40456--40820 Score: 513
Period size: 94 Copynumber: 4.0 Consensus size: 94
40446 AACAAATGCC
40456 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCG
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCG
40521 AAAAACCAATCATTGGACTTGAAAGATGA
66 AAAAACCAATCATTGGACTTGAAAGATGA
*
40550 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTAAGTTATCTGATCTGG--T--T-T--A----G
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCG
* * * * * *
40604 TAAAATCAATCATTGAATTTGGAAGAGGA
66 AAAAACCAATCATTGGACTTGAAAGATGA
40633 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCG
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCG
40698 AAAAACCAATCATTGGACTTGAAAGATGA
66 AAAAACCAATCATTGGACTTGAAAGATGA
* * * *
40727 ATGTGCTCATAGCATCTTCTGGAAGTGTTATTTGAGTTATCTGATCTGGTTCGGTAGGAACCAC-
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCG
* * *
40791 -AGAACCAATCATTGGAATTAAAAGATGA
66 AAAAACCAATCATTGGACTTGAAAGATGA
40819 AT
1 AT
40821 TGTATGATCG
Statistics
Matches: 239, Mismatches: 21, Indels: 24
0.84 0.07 0.08
Matches are distributed among these distances:
83 72 0.30
85 1 0.00
87 2 0.01
88 1 0.00
89 1 0.00
90 2 0.01
92 28 0.12
94 132 0.55
ACGTcount: A:0.29, C:0.15, G:0.22, T:0.34
Consensus pattern (94 bp):
ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCG
AAAAACCAATCATTGGACTTGAAAGATGA
Found at i:40752 original size:177 final size:177
Alignment explanation
Indices: 40456--40777 Score: 626
Period size: 177 Copynumber: 1.8 Consensus size: 177
40446 AACAAATGCC
40456 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCG
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCG
*
40521 AAAAACCAATCATTGGACTTGAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTAAG
66 AAAAACCAATCATTGGACTTGAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTATTTAAG
40586 TTATCTGATCTGGTTTAGTAAAATCAATCATTGAATTTGGAAGAGGA
131 TTATCTGATCTGGTTTAGTAAAATCAATCATTGAATTTGGAAGAGGA
40633 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCG
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCG
*
40698 AAAAACCAATCATTGGACTTGAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTATTTGAG
66 AAAAACCAATCATTGGACTTGAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTATTTAAG
40763 TTATCTGATCTGGTT
131 TTATCTGATCTGGTT
40778 CGGTAGGAAC
Statistics
Matches: 143, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
177 143 1.00
ACGTcount: A:0.27, C:0.15, G:0.22, T:0.36
Consensus pattern (177 bp):
ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCG
AAAAACCAATCATTGGACTTGAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTATTTAAG
TTATCTGATCTGGTTTAGTAAAATCAATCATTGAATTTGGAAGAGGA
Found at i:41713 original size:24 final size:23
Alignment explanation
Indices: 41670--41714 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
41660 GTTCATAATG
*
41670 AGAAGAATTCATCTGAAGAAGGA
1 AGAAGAATTCATATGAAGAAGGA
41693 AGAAGAAATTCATAATG-AGAAG
1 AGAAG-AATTCAT-ATGAAGAAG
41715 AATTTGTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 5 0.26
24 12 0.63
25 2 0.11
ACGTcount: A:0.51, C:0.07, G:0.24, T:0.18
Consensus pattern (23 bp):
AGAAGAATTCATATGAAGAAGGA
Found at i:41722 original size:113 final size:114
Alignment explanation
Indices: 41504--42188 Score: 828
Period size: 113 Copynumber: 6.0 Consensus size: 114
41494 TAGCAAAGAT
* * *
41504 TCAAATCCATCATTTGATGGATTAGCATTTTCCAATTCGAGTTCATAATGAGAAGAACTCATCAT
1 TCAAATCCATCACTTGATGGATCAGC-TTTTCCAGTTCGAGTTCATAATGAGAAGAACT--TCAT
* * * *
41569 TTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTTAACCTTTTGC
63 CTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTAC
41621 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAA-TTCATCTG
1 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTTCATCTG
* * *
41685 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTTAACCTTTTGC
66 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTAC
41734 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAA-TTCATCTG
1 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTTCATCTG
* *
41798 AATAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTAT
66 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTAC
* * * **** * *
41847 TCAAATTCATCACTTGATGGATCAACATTTCCAGAGAAAGTTCATAATAATAAGAACTT-ATCTG
1 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTTCATCTG
*
41911 AAG-AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTAT
66 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTAC
* * * **** *
41959 TCAAATTCATCACTTGATGGATCAACATTTCCAGAGAAAGTTCATAATAAGAAGAACTT-ATCTG
1 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTTCATCTG
* * * *
42023 AAG-AGGAAGAAGAAGTTCACAATGAGAAGAGCCTGTTCAACCTTTTAC
66 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTAC
* **
42071 AT-AATTTTATCACATAT-ATGTTAGCATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAACT
1 -TCAAATCCATCAC-T-TGATG---G-ATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAACT
* * * * *
42134 CATCATCTGAAAAAGAAAGAAGAAGTTCATAATGAGAAGAGCTTATTCAACCTTT
59 --TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTT
42189 GGAATGACTC
Statistics
Matches: 517, Mismatches: 39, Indels: 20
0.90 0.07 0.03
Matches are distributed among these distances:
112 160 0.31
113 222 0.43
114 3 0.01
115 1 0.00
116 30 0.06
117 55 0.11
119 1 0.00
120 7 0.01
121 38 0.07
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.31
Consensus pattern (114 bp):
TCAAATCCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTTCATCTG
AAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTAC
Found at i:42424 original size:3 final size:3
Alignment explanation
Indices: 42418--42459 Score: 57
Period size: 3 Copynumber: 14.0 Consensus size: 3
42408 TTTACTCATT
* * *
42418 TTA TTA TTA TTA TTA TAA TTA TTA TTA TAA TAA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
42460 AAAAAATAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:42440 original size:15 final size:15
Alignment explanation
Indices: 42420--42459 Score: 71
Period size: 15 Copynumber: 2.7 Consensus size: 15
42410 TACTCATTTT
*
42420 ATTATTATTATTATA
1 ATTATTATTATAATA
42435 ATTATTATTATAATA
1 ATTATTATTATAATA
42450 ATTATTATTA
1 ATTATTATTA
42460 AAAAAATAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
ATTATTATTATAATA
Found at i:51152 original size:34 final size:30
Alignment explanation
Indices: 51114--51182 Score: 86
Period size: 30 Copynumber: 2.2 Consensus size: 30
51104 TCGATATAAC
*
51114 AATTTAAGGCAAAATGGTTTTTGGACTTGAATTG
1 AATTTAA--CAAAAT-GTATTTGGACTT-AATTG
51148 AATTT-ACAAAATGTATTTGGACTTAATTG
1 AATTTAACAAAATGTATTTGGACTTAATTG
51177 AATTTA
1 AATTTA
51183 TTCAAAATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
29 10 0.30
30 11 0.33
31 6 0.18
33 1 0.03
34 5 0.15
ACGTcount: A:0.36, C:0.06, G:0.17, T:0.41
Consensus pattern (30 bp):
AATTTAACAAAATGTATTTGGACTTAATTG
Found at i:51190 original size:31 final size:31
Alignment explanation
Indices: 51123--51182 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
51113 CAATTTAAGG
*
51123 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTATTTGGACTTGAATTGAATTTA
51154 CAAAAT-GTATTTGGACTT-AATTGAATTTA
1 CAAAATGGTATTTGGACTTGAATTGAATTTA
51183 TTCAAAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.35, C:0.07, G:0.17, T:0.42
Consensus pattern (31 bp):
CAAAATGGTATTTGGACTTGAATTGAATTTA
Found at i:51424 original size:21 final size:21
Alignment explanation
Indices: 51391--51430 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
51381 TTTTTTGCAG
*
51391 AAAATCATTCCCAAACGGCTCC
1 AAAATCA-TCCCCAACGGCTCC
51413 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
51431 AGATATGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 2 0.12
22 4 0.24
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:53625 original size:37 final size:37
Alignment explanation
Indices: 53575--53649 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
53565 CAAAGTTTAC
53575 GCTTATAATGGAATGAAAATGCAAGAGAAAAGAATAA
1 GCTTATAATGGAATGAAAATGCAAGAGAAAAGAATAA
53612 GCTTATAATGGAATGAAAATGCAAGAGAAAAGAATAA
1 GCTTATAATGGAATGAAAATGCAAGAGAAAAGAATAA
53649 G
1 G
53650 TTGTGATGTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.53, C:0.05, G:0.23, T:0.19
Consensus pattern (37 bp):
GCTTATAATGGAATGAAAATGCAAGAGAAAAGAATAA
Found at i:58666 original size:21 final size:19
Alignment explanation
Indices: 58641--58685 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
58631 TTTTACTCGT
58641 TTTTGGCTTGATTGGATGTTG
1 TTTTGGCTTGA-T-GATGTTG
* *
58662 TTTTGGGTTGATGTTGTTG
1 TTTTGGCTTGATGATGTTG
58681 TTTTG
1 TTTTG
58686 TTGCTCATGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 11 0.50
20 1 0.05
21 10 0.45
ACGTcount: A:0.07, C:0.02, G:0.33, T:0.58
Consensus pattern (19 bp):
TTTTGGCTTGATGATGTTG
Found at i:58914 original size:19 final size:19
Alignment explanation
Indices: 58890--58982 Score: 95
Period size: 19 Copynumber: 5.0 Consensus size: 19
58880 CCGAACTGGT
58890 CTGACCCGTTGACTTTGAC
1 CTGACCCGTTGACTTTGAC
58909 CTGACCCGTTGAC-TTGAAC
1 CTGACCCGTTGACTTTG-AC
58928 C-GACCCGTTGACTTTGA-
1 CTGACCCGTTGACTTTGAC
* * * *
58945 TTGATCTC-TTGATTTTAAC
1 CTGA-CCCGTTGACTTTGAC
*
58964 CTGACCCATTGACTTTGAC
1 CTGACCCGTTGACTTTGAC
58983 AAGAGTTGAC
Statistics
Matches: 60, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
18 27 0.45
19 33 0.55
ACGTcount: A:0.19, C:0.28, G:0.18, T:0.34
Consensus pattern (19 bp):
CTGACCCGTTGACTTTGAC
Found at i:58932 original size:18 final size:18
Alignment explanation
Indices: 58890--58941 Score: 79
Period size: 18 Copynumber: 2.8 Consensus size: 18
58880 CCGAACTGGT
58890 CTGACCCGTTGACTTTGAC
1 CTGACCCGTTGAC-TTGAC
58909 CTGACCCGTTGACTTGAAC
1 CTGACCCGTTGACTTG-AC
58928 C-GACCCGTTGACTT
1 CTGACCCGTTGACTT
58942 TGATTGATCT
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
18 16 0.50
19 16 0.50
ACGTcount: A:0.17, C:0.33, G:0.21, T:0.29
Consensus pattern (18 bp):
CTGACCCGTTGACTTGAC
Found at i:58970 original size:37 final size:38
Alignment explanation
Indices: 58890--58982 Score: 111
Period size: 37 Copynumber: 2.5 Consensus size: 38
58880 CCGAACTGGT
58890 CTGACCCGTTGACTTTGACCTGACCCGTTGACTTGAAC
1 CTGACCCGTTGACTTTGACCTGACCCGTTGACTTGAAC
* * * *
58928 C-GACCCGTTGACTTTGA-TTGATCTC-TTGATTTTAAC
1 CTGACCCGTTGACTTTGACCTGA-CCCGTTGACTTGAAC
*
58964 CTGACCCATTGACTTTGAC
1 CTGACCCGTTGACTTTGAC
58983 AAGAGTTGAC
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
36 13 0.28
37 33 0.70
38 1 0.02
ACGTcount: A:0.19, C:0.28, G:0.18, T:0.34
Consensus pattern (38 bp):
CTGACCCGTTGACTTTGACCTGACCCGTTGACTTGAAC
Found at i:62533 original size:39 final size:39
Alignment explanation
Indices: 62478--62644 Score: 171
Period size: 39 Copynumber: 4.3 Consensus size: 39
62468 CCGATGATTT
62478 TTTTACAAACA-A-GAAAATAAATCCAACGATTTATTTCC
1 TTTTACAAA-ATAGGAAAATAAATCCAACGATTTATTTCC
* * * * *
62516 TTTTATAAAATAGGAAAATAAATTCTACTATTTATTTTC
1 TTTTACAAAATAGGAAAATAAATCCAACGATTTATTTCC
* ** * *
62555 TTTTACATACCA-AAAAATAAATCCAATGATTTATTTCC
1 TTTTACAAAATAGGAAAATAAATCCAACGATTTATTTCC
* * *
62593 TTTTACAAGATAGGAAAATAAATCCAATGATTTATTTAC
1 TTTTACAAAATAGGAAAATAAATCCAACGATTTATTTCC
62632 TTTTA-AAAGATAG
1 TTTTACAAA-ATAG
62645 AATTATATAA
Statistics
Matches: 103, Mismatches: 22, Indels: 7
0.78 0.17 0.05
Matches are distributed among these distances:
37 1 0.01
38 39 0.38
39 63 0.61
ACGTcount: A:0.43, C:0.13, G:0.07, T:0.38
Consensus pattern (39 bp):
TTTTACAAAATAGGAAAATAAATCCAACGATTTATTTCC
Found at i:62626 original size:77 final size:77
Alignment explanation
Indices: 62478--62636 Score: 223
Period size: 77 Copynumber: 2.1 Consensus size: 77
62468 CCGATGATTT
* *
62478 TTTTACAAACAAGAAAATAAATCCAACGATTTATTTCCTTTTATAAAATAGGAAAATAAATTCTA
1 TTTTACAAACAAGAAAATAAATCCAACGATTTATTTCCTTTTACAAAATAGGAAAATAAATTCCA
* *
62543 CTATTTATTTTC
66 ATATTTATTTAC
* * *
62555 TTTTACATACCAA-AAAATAAATCCAATGATTTATTTCCTTTTACAAGATAGGAAAATAAA-TCC
1 TTTTACA-AACAAGAAAATAAATCCAACGATTTATTTCCTTTTACAAAATAGGAAAATAAATTCC
62618 AATGATTTATTTAC
65 AAT-ATTTATTTAC
62632 TTTTA
1 TTTTA
62637 AAAGATAGAA
Statistics
Matches: 73, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
76 4 0.05
77 65 0.89
78 4 0.05
ACGTcount: A:0.42, C:0.13, G:0.06, T:0.39
Consensus pattern (77 bp):
TTTTACAAACAAGAAAATAAATCCAACGATTTATTTCCTTTTACAAAATAGGAAAATAAATTCCA
ATATTTATTTAC
Found at i:62962 original size:58 final size:58
Alignment explanation
Indices: 62684--62974 Score: 252
Period size: 58 Copynumber: 5.0 Consensus size: 58
62674 TTATTTCTTT
* * * * *
62684 ATTCAAGATTCATGAGAAAATAAATTTAACAATTTATTTCCTT-TAACAAA-ATAGAATC
1 ATTCAAGATTCTTAAGAAAATAAATTCAACAATTTATTT--TTCTTACAAAGTTAGAATC
** * * * *
62742 ATTTTAGATTCTCAAGAAAATAAAGTT-AACAATTTATTTCTTTTTA-AAGGATAGAATC
1 ATTCAAGATTCTTAAGAAAATAAA-TTCAACAATTTATTT-TTCTTACAAAGTTAGAATC
* * * * * *
62800 ATCCATAG-TTCTGAAGAAAATAATTTCGACAATTTATTTTCCTTACAAAGTTAAAATC
1 ATTCA-AGATTCTTAAGAAAATAAATTCAACAATTTATTTTTCTTACAAAGTTAGAATC
* * **
62858 ATTCAAGATT-TCTAAGGAAATAAATTCTACAATTTATTTCCCTTACAAAGTTAGAATC
1 ATTCAAGATTCT-TAAGAAAATAAATTCAACAATTTATTTTTCTTACAAAGTTAGAATC
* * * * *
62916 ATTTAAGATTCTTAAAAAAATAAATTCAATAATTTATTTTTATTACAAACTTAGAATC
1 ATTCAAGATTCTTAAGAAAATAAATTCAACAATTTATTTTTCTTACAAAGTTAGAATC
62974 A
1 A
62975 ACGAAAGATT
Statistics
Matches: 190, Mismatches: 34, Indels: 18
0.79 0.14 0.07
Matches are distributed among these distances:
57 14 0.07
58 171 0.90
59 5 0.03
ACGTcount: A:0.43, C:0.12, G:0.08, T:0.37
Consensus pattern (58 bp):
ATTCAAGATTCTTAAGAAAATAAATTCAACAATTTATTTTTCTTACAAAGTTAGAATC
Found at i:63163 original size:45 final size:44
Alignment explanation
Indices: 63104--63246 Score: 180
Period size: 45 Copynumber: 3.2 Consensus size: 44
63094 AACAAATAGA
* * *
63104 AATCAAAAGGAATTAGTCCTTTGATTTTAATTTTCACAATCCAAT
1 AATCAAAAGGAATTAATCCTTTGATTTTACTTTTGACAA-CCAAT
* *
63149 AATCGAAAA-GAATTAATCATTTGATATTACTTTTGACAACACAAT
1 AATC-AAAAGGAATTAATCCTTTGATTTTACTTTTGACAAC-CAAT
* *
63194 AATCAAAAGGAACTAATCCTTTGATTGTACTTTTGACAACCCAAT
1 AATCAAAAGGAATTAATCCTTTGATTTTACTTTTGACAA-CCAAT
63239 AATCAAAA
1 AATCAAAA
63247 TCCTTGGAGT
Statistics
Matches: 85, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
44 5 0.06
45 75 0.88
46 5 0.06
ACGTcount: A:0.42, C:0.16, G:0.09, T:0.33
Consensus pattern (44 bp):
AATCAAAAGGAATTAATCCTTTGATTTTACTTTTGACAACCAAT
Found at i:63473 original size:13 final size:13
Alignment explanation
Indices: 63455--63480 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
63445 ATAAAATAAC
63455 AATAATATCATGA
1 AATAATATCATGA
63468 AATAATATCATGA
1 AATAATATCATGA
63481 TTAATGCACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.08, G:0.08, T:0.31
Consensus pattern (13 bp):
AATAATATCATGA
Found at i:66301 original size:19 final size:19
Alignment explanation
Indices: 66279--66331 Score: 61
Period size: 23 Copynumber: 2.6 Consensus size: 19
66269 TTAATTTTTA
*
66279 AAATCATATTATTTATTTG
1 AAATAATATTATTTATTTG
66298 AAATAATATGAATTATTTATTTG
1 AAAT-A-AT--ATTATTTATTTG
66321 AAATAATATTA
1 AAATAATATTA
66332 CTTTTAAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
19 8 0.28
21 4 0.14
22 1 0.03
23 16 0.55
ACGTcount: A:0.45, C:0.02, G:0.06, T:0.47
Consensus pattern (19 bp):
AAATAATATTATTTATTTG
Found at i:66316 original size:23 final size:23
Alignment explanation
Indices: 66286--66329 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
66276 TTAAAATCAT
66286 ATTATTTATTTGAAATAATATGA
1 ATTATTTATTTGAAATAATATGA
66309 ATTATTTATTTGAAATAATAT
1 ATTATTTATTTGAAATAATAT
66330 TACTTTTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (23 bp):
ATTATTTATTTGAAATAATATGA
Found at i:71157 original size:220 final size:221
Alignment explanation
Indices: 70772--71215 Score: 710
Period size: 220 Copynumber: 2.0 Consensus size: 221
70762 GCTCCTGCCA
* * * * *
70772 TGAAATGTAAGCAATAGTTTTTCTTGTGTTTTCTTACATTCTCATTTTCACTAAAGATTCAGCAT
1 TGAAATGTAAGAAATAGTTTTTCCTGTG--TTCTTACATTCTCAGTCTCACTAAAGATGCAGCAT
* * **
70837 GCAGGTAAACGAAAAATATGATGAAGCCTACATTAATATCTTTTTTAATGACTTTGCTTTTGAAA
64 GCAGGTAAACGAAAAACATGATGAAGCCTACATTAATATATTTTTTAATGACTTTGCGATTGAAA
* * *
70902 ATTTATATAAAGCCCATTCTTTATGTGCTTGAATTTGGGTACATTATTTTGAACTCAGTTCTTAT
129 ATTTATATAAAGCCCATTCTTTATGTGCTTGAATTTGGGTACAATATTTTAAACTCAGCTCTTAT
70967 GATGGATGCTATTATCATCTGTAGCTAT
194 GATGGATGCTATTATCATCTGTAGCTAT
70995 TGAAATGTAAGAAATAGTTTTTCCTGTG-TCTTACATTCTCAGTCTCACTAAAGATGCAGCATGC
1 TGAAATGTAAGAAATAGTTTTTCCTGTGTTCTTACATTCTCAGTCTCACTAAAGATGCAGCATGC
* * * * *
71059 AGGTATAGGAAAAACATTATGAAGCCTACTTTAATATATTTTTTAATGACTTTGCGATTGAAATT
66 AGGTAAACGAAAAACATGATGAAGCCTACATTAATATATTTTTTAATGACTTTGCGATTGAAAAT
71124 TTATATAAAGCCCATTCTTTATGTGCTTGAATTTGGGTACAATATTTTAAACTCAGCTCTTATGA
131 TTATATAAAGCCCATTCTTTATGTGCTTGAATTTGGGTACAATATTTTAAACTCAGCTCTTATGA
71189 TGGATGCTATTATCATCTGTAGCTAT
196 TGGATGCTATTATCATCTGTAGCTAT
71215 T
1 T
71216 AAGCAGCGAA
Statistics
Matches: 204, Mismatches: 17, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
220 178 0.87
223 26 0.13
ACGTcount: A:0.30, C:0.14, G:0.15, T:0.40
Consensus pattern (221 bp):
TGAAATGTAAGAAATAGTTTTTCCTGTGTTCTTACATTCTCAGTCTCACTAAAGATGCAGCATGC
AGGTAAACGAAAAACATGATGAAGCCTACATTAATATATTTTTTAATGACTTTGCGATTGAAAAT
TTATATAAAGCCCATTCTTTATGTGCTTGAATTTGGGTACAATATTTTAAACTCAGCTCTTATGA
TGGATGCTATTATCATCTGTAGCTAT
Found at i:76935 original size:26 final size:26
Alignment explanation
Indices: 76879--76931 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 26
76869 CTGGATGATG
* * *
76879 CAGATGTTGTCAATATGGTATATATG
1 CAGATGTTGTCAATATGGGAGATATC
*
76905 CAGATGTTGTCAATATGGGGGA-ATC
1 CAGATGTTGTCAATATGGGAGATATC
76930 CA
1 CA
76932 AGATTAAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
25 4 0.17
26 19 0.83
ACGTcount: A:0.30, C:0.11, G:0.26, T:0.32
Consensus pattern (26 bp):
CAGATGTTGTCAATATGGGAGATATC
Found at i:80913 original size:256 final size:258
Alignment explanation
Indices: 80483--80979 Score: 671
Period size: 256 Copynumber: 1.9 Consensus size: 258
80473 CTGGAGGGAC
* *
80483 TTACTAAGTAAGAAACTTTCGAAATTGTTTTCTTACTTTTAAAAAAAATCAATTTTTAGAAAAGA
1 TTACTAAGTAAGAAACTTTCGAAATCGTTTTCTTACTTTT--AAAAAATCAATTTTCAGAAAAGA
* *
80548 TTTAAATGAGAAATTTTGAAAATCGCTTTCTCATTTTTCAAAAATCATGTGAAAACATCCCGCCT
64 TTTAAATGAGAAATTTAGAAAATCGCTTTCTCATTTTTCAAAAATCATGTGAAAACATCCCGCCC
* * * * *
80613 GAAGGTCTTATGGATGACCTGAATGGCTTATAAACTTGCTCGAAAGGCTTATAGATGA-CCGAAG
129 GAAGGTCTTATGGATGACCCGAATGGCTTACAAACTTACTCGAAAGACTTATAGATGACCCAAAG
*
80677 GATTTAAGAAACATGCTC-AAAAGACTTACTGATGGCCTGAAAGACTTACCAATTTTGGAAATAG
194 GATTTAAGAAACATGCTCGAAAA-ACTTACTGATGGCCCGAAAGACTTACCAATTTTGGAAATAG
80741 T
258 T
* * * * *
80742 TTACTAGGTAAGAAACTTTGGAAATCGTTTTCTTACTTTT-CAAAATCAATTTTCATAATAGATT
1 TTACTAAGTAAGAAACTTTCGAAATCGTTTTCTTACTTTTAAAAAATCAATTTTCAGAAAAGATT
* * * *
80806 TAAATGAGAAACTTTAG-AAATTGTTTTCTCATTTTTCAAAAATCATGTGAAAACCTCCTGCCCG
66 TAAATGAGAAA-TTTAGAAAATCGCTTTCTCATTTTTCAAAAATCATGTGAAAACATCCCGCCCG
* * *
80870 AAGGTCTTATGGATGGCCCGAA-GGACTTACCATCTTACTCGAAAGACTTATAGATGACCCAAAG
130 AAGGTCTTATGGATGACCCGAATGG-CTTACAAACTTACTCGAAAGACTTATAGATGACCCAAAG
* ** * *
80934 GATTTAAGCATTATGCTCGAAAAACTTAGTGATGGCCCGAATGACT
194 GATTTAAGAAACATGCTCGAAAAACTTACTGATGGCCCGAAAGACT
80980 GACTAAGTAA
Statistics
Matches: 207, Mismatches: 27, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
255 2 0.01
256 120 0.58
257 44 0.21
258 4 0.02
259 37 0.18
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.32
Consensus pattern (258 bp):
TTACTAAGTAAGAAACTTTCGAAATCGTTTTCTTACTTTTAAAAAATCAATTTTCAGAAAAGATT
TAAATGAGAAATTTAGAAAATCGCTTTCTCATTTTTCAAAAATCATGTGAAAACATCCCGCCCGA
AGGTCTTATGGATGACCCGAATGGCTTACAAACTTACTCGAAAGACTTATAGATGACCCAAAGGA
TTTAAGAAACATGCTCGAAAAACTTACTGATGGCCCGAAAGACTTACCAATTTTGGAAATAGT
Found at i:92027 original size:22 final size:22
Alignment explanation
Indices: 92002--92043 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
91992 TGTAATATAA
92002 TTTAATATAAGATGTATTATCC
1 TTTAATATAAGATGTATTATCC
* * *
92024 TTTAGTATTAGATTTATTAT
1 TTTAATATAAGATGTATTAT
92044 TTTAGTATGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.33, C:0.05, G:0.10, T:0.52
Consensus pattern (22 bp):
TTTAATATAAGATGTATTATCC
Found at i:92150 original size:51 final size:51
Alignment explanation
Indices: 92037--92151 Score: 158
Period size: 51 Copynumber: 2.3 Consensus size: 51
92027 AGTATTAGAT
* * ** * *
92037 TTATTATTTTAGTATGAATTAAGATAGGGTTAAAACATTATCTTTGGTTTA
1 TTATTATTTTATTAGGAATTAAGATAGAATCAAAACATTATCTTTAGTTTA
* *
92088 TTATTATTTTATTAGGAATTAGGATAGAATCAAAATATTATCTTTAGTTTA
1 TTATTATTTTATTAGGAATTAAGATAGAATCAAAACATTATCTTTAGTTTA
92139 TTATTATTTTATT
1 TTATTATTTTATT
92152 CAATAGTTAC
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
51 56 1.00
ACGTcount: A:0.34, C:0.03, G:0.12, T:0.50
Consensus pattern (51 bp):
TTATTATTTTATTAGGAATTAAGATAGAATCAAAACATTATCTTTAGTTTA
Found at i:96833 original size:22 final size:22
Alignment explanation
Indices: 96805--96859 Score: 103
Period size: 22 Copynumber: 2.5 Consensus size: 22
96795 GTGAGCATTG
96805 AAATACTCTTAATCATTAACTT
1 AAATACTCTTAATCATTAACTT
96827 AAATACTCTTAATCATTAACTT
1 AAATACTCTTAATCATTAACTT
96849 AAATAC-CTTAA
1 AAATACTCTTAA
96860 AGTTACGATA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 5 0.15
22 28 0.85
ACGTcount: A:0.44, C:0.18, G:0.00, T:0.38
Consensus pattern (22 bp):
AAATACTCTTAATCATTAACTT
Found at i:100191 original size:21 final size:22
Alignment explanation
Indices: 100157--100204 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 22
100147 GAATATTTGA
*
100157 ATTTTATGTGTTTTC-ATA-TT
1 ATTTTATGAGTTTTCTATACTT
100177 ATTTTGATGAGTTTTCTATACTT
1 ATTTT-ATGAGTTTTCTATACTT
100200 ATTTT
1 ATTTT
100205 TTTGCATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 5 0.21
21 9 0.38
22 3 0.12
23 7 0.29
ACGTcount: A:0.21, C:0.06, G:0.10, T:0.62
Consensus pattern (22 bp):
ATTTTATGAGTTTTCTATACTT
Found at i:102743 original size:22 final size:22
Alignment explanation
Indices: 102718--102766 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 22
102708 ACCGGTTCCA
*
102718 ACCCGACCCGACCCGTTGAC-CG
1 ACCCGACCCGA-CAGTTGACGCG
102740 ACCCGACCCGACAGTTGACGCG
1 ACCCGACCCGACAGTTGACGCG
102762 ACCCG
1 ACCCG
102767 TTAACCCGAC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 7 0.28
22 18 0.72
ACGTcount: A:0.20, C:0.47, G:0.24, T:0.08
Consensus pattern (22 bp):
ACCCGACCCGACAGTTGACGCG
Found at i:102792 original size:7 final size:7
Alignment explanation
Indices: 102780--102820 Score: 64
Period size: 7 Copynumber: 5.9 Consensus size: 7
102770 ACCCGACCCG
102780 ACCGTTA
1 ACCGTTA
*
102787 ACCGTTG
1 ACCGTTA
102794 ACCGTTA
1 ACCGTTA
*
102801 ACCATTA
1 ACCGTTA
102808 ACCGTTA
1 ACCGTTA
102815 ACCGTT
1 ACCGTT
102821 GATCGGGTGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.27, C:0.29, G:0.15, T:0.29
Consensus pattern (7 bp):
ACCGTTA
Found at i:102868 original size:29 final size:29
Alignment explanation
Indices: 102825--102899 Score: 107
Period size: 29 Copynumber: 2.6 Consensus size: 29
102815 ACCGTTGATC
*
102825 GGGTGCTATTTTAGTAATTAATTCGAAATA
1 GGGTGCTATTTTAGTAATTAATT-GAAAAA
*
102855 -GGTGCTATTTTAGTAATTAATTTAAAAA
1 GGGTGCTATTTTAGTAATTAATTGAAAAA
*
102883 GGGTGCTATTTTTGTAA
1 GGGTGCTATTTTAGTAA
102900 AATGGTTGAC
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
28 4 0.10
29 37 0.90
ACGTcount: A:0.32, C:0.05, G:0.20, T:0.43
Consensus pattern (29 bp):
GGGTGCTATTTTAGTAATTAATTGAAAAA
Found at i:104230 original size:17 final size:19
Alignment explanation
Indices: 104205--104243 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
104195 ATATCTGTAT
104205 TATTAATATTT-TGTTCTA
1 TATTAATATTTATGTTCTA
104223 TATT-ATATTTAATGTTCTA
1 TATTAATATTT-ATGTTCTA
104242 TA
1 TA
104244 ATTGTTAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.32
18 4 0.21
19 9 0.47
ACGTcount: A:0.31, C:0.05, G:0.05, T:0.59
Consensus pattern (19 bp):
TATTAATATTTATGTTCTA
Found at i:116647 original size:18 final size:18
Alignment explanation
Indices: 116624--116660 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
116614 AATCGGAGGG
116624 TTCTCTATACCTCGAGCC
1 TTCTCTATACCTCGAGCC
116642 TTCTCTATACCTCGAGCC
1 TTCTCTATACCTCGAGCC
116660 T
1 T
116661 CGTAACTCAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.16, C:0.38, G:0.11, T:0.35
Consensus pattern (18 bp):
TTCTCTATACCTCGAGCC
Done.