Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000172.1 Hibiscus syriacus cultivar Beakdansim tig00000303_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: 137261
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Found at i:2668 original size:20 final size:20
Alignment explanation
Indices: 2644--2770 Score: 155
Period size: 20 Copynumber: 6.3 Consensus size: 20
2634 AAATTCAGTG
* *
2644 TTGCGACAGTCAGAATCGCG
1 TTGCGATAGTCAGAATCGCA
* *
2664 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCGCA
*
2684 TTGCGATAATCAGAATCGCA
1 TTGCGATAGTCAGAATCGCA
*
2704 TTGCGATTGTCAGAATCGCA
1 TTGCGATAGTCAGAATCGCA
* *
2724 TTGCGATTGTCATAATCGCA
1 TTGCGATAGTCAGAATCGCA
* * *
2744 TTGCGATTGCCATAATCGCA
1 TTGCGATAGTCAGAATCGCA
2764 TTGCGAT
1 TTGCGAT
2771 TTACATATTC
Statistics
Matches: 98, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 98 1.00
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.29
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCGCA
Found at i:2771 original size:20 final size:20
Alignment explanation
Indices: 2697--2829 Score: 167
Period size: 20 Copynumber: 6.7 Consensus size: 20
2687 CGATAATCAG
* *
2697 AATCGCATTGCGATTGTCAG
1 AATCGCATTGCGATTGACAT
*
2717 AATCGCATTGCGATTGTCAT
1 AATCGCATTGCGATTGACAT
*
2737 AATCGCATTGCGATTGCCAT
1 AATCGCATTGCGATTGACAT
*
2757 AATCGCATTGCGATTTACAT
1 AATCGCATTGCGATTGACAT
* * *
2777 ATTCACATTGCGATTTACAT
1 AATCGCATTGCGATTGACAT
* *
2797 ATTCGCATTGCGATTTACAT
1 AATCGCATTGCGATTGACAT
*
2817 ATTCGCATTGCGA
1 AATCGCATTGCGA
2830 ATTCGGAAAA
Statistics
Matches: 106, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 106 1.00
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.35
Consensus pattern (20 bp):
AATCGCATTGCGATTGACAT
Found at i:2771 original size:40 final size:39
Alignment explanation
Indices: 2657--2829 Score: 177
Period size: 40 Copynumber: 4.3 Consensus size: 39
2647 CGACAGTCAG
* * * * * *
2657 AATCGCGTTGCGATAGTCAGAATCTCGTTGCGATAATCAG
1 AATCGCATTGCGATTGTCAGAATCGCATTGCGAT-TTCAT
2697 AATCGCATTGCGATTGTCAGAATCGCATTGCGATTGTCAT
1 AATCGCATTGCGATTGTCAGAATCGCATTGCGATT-TCAT
* *
2737 AATCGCATTGCGATTGCCATAATCGCATTGCGATTTACAT
1 AATCGCATTGCGATTGTCAGAATCGCATTGCGATTT-CAT
* * * *
2777 ATTCACATTGCGATT-TACATATTCGCATTGCGATTTACAT
1 AATCGCATTGCGATTGT-CAGAATCGCATTGCGATTT-CAT
*
2817 ATTCGCATTGCGA
1 AATCGCATTGCGA
2830 ATTCGGAAAA
Statistics
Matches: 117, Mismatches: 13, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
39 1 0.01
40 116 0.99
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.33
Consensus pattern (39 bp):
AATCGCATTGCGATTGTCAGAATCGCATTGCGATTTCAT
Found at i:2852 original size:21 final size:21
Alignment explanation
Indices: 2826--2871 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
2816 TATTCGCATT
*
2826 GCGAATTCGGAAAATTGCAAC
1 GCGAATTCGGAAAATCGCAAC
* *
2847 GCGAATTTGGAAAATCGCAAT
1 GCGAATTCGGAAAATCGCAAC
2868 GCGA
1 GCGA
2872 TAGTCAGATC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.17, G:0.26, T:0.20
Consensus pattern (21 bp):
GCGAATTCGGAAAATCGCAAC
Found at i:3054 original size:14 final size:13
Alignment explanation
Indices: 3033--3067 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
3023 ATTTTCTCTA
3033 AAAATAAACAAAT
1 AAAATAAACAAAT
*
3046 AACAATAAATAAAT
1 AA-AATAAACAAAT
3060 AAAATAAA
1 AAAATAAA
3068 TTAGAAAAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.77, C:0.06, G:0.00, T:0.17
Consensus pattern (13 bp):
AAAATAAACAAAT
Found at i:3572 original size:26 final size:24
Alignment explanation
Indices: 3543--3620 Score: 61
Period size: 26 Copynumber: 3.0 Consensus size: 24
3533 TATAATATCG
3543 TATAAATAAAACAAAATAATAAGAAA
1 TATAAATAAAACAAAATAA-AA-AAA
*
3569 TAT-AATAAGAATAAAATAAAAAAA
1 TATAAATAA-AACAAAATAAAAAAA
*
3593 TA-AATATAAATATAAATAATAAAAAAA
1 TATAA-ATAAA-A-CAA-AATAAAAAAA
3620 T
1 T
3621 GATTAAATTA
Statistics
Matches: 44, Mismatches: 2, Indels: 11
0.77 0.04 0.19
Matches are distributed among these distances:
24 7 0.16
25 12 0.27
26 14 0.32
27 11 0.25
ACGTcount: A:0.73, C:0.01, G:0.03, T:0.23
Consensus pattern (24 bp):
TATAAATAAAACAAAATAAAAAAA
Found at i:3613 original size:19 final size:18
Alignment explanation
Indices: 3544--3620 Score: 60
Period size: 15 Copynumber: 4.6 Consensus size: 18
3534 ATAATATCGT
*
3544 ATAAATAAAACA-AAATA
1 ATAAATAAAATATAAATA
*
3561 AT-AA-GAAATAT-AATA
1 ATAAATAAAATATAAATA
* *
3576 A-GAATAAAATA-AAAAA
1 ATAAATAAAATATAAATA
3592 ATAAATATAAATATAAATA
1 ATAAATA-AAATATAAATA
3611 ATAAA-AAAAT
1 ATAAATAAAAT
3621 GATTAAATTA
Statistics
Matches: 47, Mismatches: 6, Indels: 14
0.70 0.09 0.21
Matches are distributed among these distances:
15 11 0.23
16 11 0.23
17 10 0.21
18 6 0.13
19 9 0.19
ACGTcount: A:0.74, C:0.01, G:0.03, T:0.22
Consensus pattern (18 bp):
ATAAATAAAATATAAATA
Found at i:3786 original size:29 final size:29
Alignment explanation
Indices: 3753--3818 Score: 132
Period size: 29 Copynumber: 2.3 Consensus size: 29
3743 TAATTATAAA
3753 ACACGCGGATCCTTCCCGTGTCAGGGTCG
1 ACACGCGGATCCTTCCCGTGTCAGGGTCG
3782 ACACGCGGATCCTTCCCGTGTCAGGGTCG
1 ACACGCGGATCCTTCCCGTGTCAGGGTCG
3811 ACACGCGG
1 ACACGCGG
3819 GTCACCAGTC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.15, C:0.35, G:0.32, T:0.18
Consensus pattern (29 bp):
ACACGCGGATCCTTCCCGTGTCAGGGTCG
Found at i:4746 original size:3 final size:3
Alignment explanation
Indices: 4732--4768 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
4722 TGTGTTAGTT
4732 TAA TAA -AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
4769 CAATATATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:4778 original size:2 final size:2
Alignment explanation
Indices: 4771--4818 Score: 71
Period size: 2 Copynumber: 24.0 Consensus size: 2
4761 TAATAATACA
*
4771 AT AT AT AT AT AT AT AT AT AT AT AT GAT AT AT AT A- AT AT AT AA
1 AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT
4813 AT AT AT
1 AT AT AT
4819 GTTTATTTCG
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
1 1 0.02
2 39 0.93
3 2 0.05
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (2 bp):
AT
Found at i:5040 original size:18 final size:19
Alignment explanation
Indices: 4991--5040 Score: 93
Period size: 19 Copynumber: 2.7 Consensus size: 19
4981 AGAGAAGCGA
4991 AAAAGGAAATTTGAGATCG
1 AAAAGGAAATTTGAGATCG
5010 AAAAGGAAATTTGAGATCG
1 AAAAGGAAATTTGAGATCG
5029 AAAAGG-AATTTG
1 AAAAGGAAATTTG
5041 GGGTTTAGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
18 6 0.19
19 25 0.81
ACGTcount: A:0.48, C:0.04, G:0.26, T:0.22
Consensus pattern (19 bp):
AAAAGGAAATTTGAGATCG
Found at i:5209 original size:30 final size:30
Alignment explanation
Indices: 5175--5243 Score: 84
Period size: 31 Copynumber: 2.3 Consensus size: 30
5165 GGCCGGTTAC
5175 GTTGGGGACCATATTGCAAACAGACTAAAT
1 GTTGGGGACCATATTGCAAACAGACTAAAT
*** *
5205 GTTGGGGGATTGTATTGCAAACAGACTTAAT
1 GTT-GGGGACCATATTGCAAACAGACTAAAT
*
5236 GTTAGGGA
1 GTTGGGGA
5244 ATGTATTGTA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
30 7 0.21
31 26 0.79
ACGTcount: A:0.32, C:0.12, G:0.29, T:0.28
Consensus pattern (30 bp):
GTTGGGGACCATATTGCAAACAGACTAAAT
Found at i:5213 original size:31 final size:31
Alignment explanation
Indices: 5178--5238 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
5168 CGGTTACGTT
5178 GGGGACCATATTGCAAACAGACTAAATGTTG
1 GGGGACCATATTGCAAACAGACTAAATGTTG
*** *
5209 GGGGATTGTATTGCAAACAGACTTAATGTT
1 GGGGACCATATTGCAAACAGACTAAATGTT
5239 AGGGAATGTA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (31 bp):
GGGGACCATATTGCAAACAGACTAAATGTTG
Found at i:5251 original size:30 final size:31
Alignment explanation
Indices: 5186--5251 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 31
5176 TTGGGGACCA
* *
5186 TATTGCAAACAGACTAAATGTTGGGGGATTG
1 TATTGCAAACAGACTAAATGTTGAGGGAATG
*
5217 TATTGCAAACAGACTTAATGTT-AGGGAATG
1 TATTGCAAACAGACTAAATGTTGAGGGAATG
5247 TATTG
1 TATTG
5252 TAAATTTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
30 11 0.34
31 21 0.66
ACGTcount: A:0.33, C:0.09, G:0.26, T:0.32
Consensus pattern (31 bp):
TATTGCAAACAGACTAAATGTTGAGGGAATG
Found at i:9524 original size:14 final size:14
Alignment explanation
Indices: 9505--9536 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
9495 CGTTCGTGAA
9505 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
9519 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
9533 CGTT
1 CGTT
9537 TATGTTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.06, C:0.16, G:0.28, T:0.50
Consensus pattern (14 bp):
CGTTCGGTTATGTT
Found at i:10024 original size:16 final size:16
Alignment explanation
Indices: 10005--10069 Score: 103
Period size: 16 Copynumber: 4.1 Consensus size: 16
9995 CCAACGTTTA
*
10005 TGTTCGTTTATGTTTG
1 TGTTCGTTTATGTTCG
*
10021 TGTTCATTTATGTTCG
1 TGTTCGTTTATGTTCG
*
10037 TGTTCGTTTATATTCG
1 TGTTCGTTTATGTTCG
10053 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
10069 T
1 T
10070 TTATTTATTA
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 44 1.00
ACGTcount: A:0.09, C:0.11, G:0.22, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:16237 original size:14 final size:14
Alignment explanation
Indices: 16202--16228 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
16192 CAAACTCTGA
16202 AGGCACCTTACTTC
1 AGGCACCTTACTTC
16216 AGGCACCTTACTT
1 AGGCACCTTACTT
16229 TGGGCACCTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.33, G:0.15, T:0.30
Consensus pattern (14 bp):
AGGCACCTTACTTC
Found at i:21082 original size:42 final size:42
Alignment explanation
Indices: 21023--21106 Score: 159
Period size: 42 Copynumber: 2.0 Consensus size: 42
21013 TACCAGATTG
*
21023 AAGAAGTAAAAGACACTAAGCCTTGGTACTACGATATTTTGC
1 AAGAAGTAAAAGACACTAAGCCTTGGTACTACGACATTTTGC
21065 AAGAAGTAAAAGACACTAAGCCTTGGTACTACGACATTTTGC
1 AAGAAGTAAAAGACACTAAGCCTTGGTACTACGACATTTTGC
21107 TGTATATCAA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.38, C:0.18, G:0.19, T:0.25
Consensus pattern (42 bp):
AAGAAGTAAAAGACACTAAGCCTTGGTACTACGACATTTTGC
Found at i:22470 original size:17 final size:17
Alignment explanation
Indices: 22450--22482 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
22440 AAAAAATTGA
22450 AAAAGAGAAAAA-AGAAT
1 AAAAGA-AAAAAGAGAAT
22467 AAAAGAAAAAAGAGAA
1 AAAAGAAAAAAGAGAA
22483 AGAACAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (17 bp):
AAAAGAAAAAAGAGAAT
Found at i:26011 original size:13 final size:13
Alignment explanation
Indices: 25993--26017 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
25983 TATTTTCTTC
25993 TTATTTTATTTAT
1 TTATTTTATTTAT
26006 TTATTTTATTTA
1 TTATTTTATTTA
26018 CTATTTTTAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
TTATTTTATTTAT
Found at i:36247 original size:13 final size:13
Alignment explanation
Indices: 36229--36253 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
36219 TATTTTCTTC
36229 TTATTTTATTTAT
1 TTATTTTATTTAT
36242 TTATTTTATTTA
1 TTATTTTATTTA
36254 CTGTTTTTAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
TTATTTTATTTAT
Found at i:41201 original size:21 final size:21
Alignment explanation
Indices: 41177--41222 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
41167 CCTAAATTGA
41177 GAAAAGA-AAAAAGAAAAAGAG
1 GAAAAGAGAAAAA-AAAAAGAG
* *
41198 GAAAAGAGAATAAAAGAAGAG
1 GAAAAGAGAAAAAAAAAAGAG
41219 GAAA
1 GAAA
41223 TAAGGTGGGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.72, C:0.00, G:0.26, T:0.02
Consensus pattern (21 bp):
GAAAAGAGAAAAAAAAAAGAG
Found at i:42155 original size:105 final size:105
Alignment explanation
Indices: 41973--42750 Score: 1295
Period size: 105 Copynumber: 7.4 Consensus size: 105
41963 AGGTTTTACC
41973 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
42038 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
42078 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
42143 ACGAAGGGACCGCTGGTTGTCAACAAATATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
42183 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
42248 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
42288 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
42353 ACGAAGGGACCGCTGGTTGTCAACAAATATTTCTCAATGT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
*
42393 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTGAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
42458 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
* * ***
42498 CAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAGTACAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
** ** *
42563 ACGAAGGGACCGCTGACTGTCAACCGACAACTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAAC-ATTTCTCAATTT
* * *
42604 CAAGAGCCAATTTCAACTTCACAACGAATGATATTGGACTCCGGACAACACAAGTTCAACTTCAC
1 C-AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
* * * * *
42669 GACGAAGGGACCGTTAGTTGTCAACAAACAATTTCCCAGTTC
65 GACGAAGGGACCGCTGGTTGTCAACAAAC-ATTTCTCAATTT
* * * *
42711 CAGAACCAGTTTCAACTTCACAGCGGAGGATATTGGACTC
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
42751 GGAACAATAC
Statistics
Matches: 632, Mismatches: 39, Indels: 3
0.94 0.06 0.00
Matches are distributed among these distances:
105 496 0.78
106 46 0.07
107 90 0.14
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.23
Consensus pattern (105 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
Found at i:43276 original size:15 final size:15
Alignment explanation
Indices: 43256--43288 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
43246 AAACACATAT
43256 TTTA-TTATTTTATTA
1 TTTATTTATTTT-TTA
43271 TTTATTTATTTTTTA
1 TTTATTTATTTTTTA
43286 TTT
1 TTT
43289 CATGTTTCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTATTTATTTTTTA
Found at i:48859 original size:50 final size:48
Alignment explanation
Indices: 48774--48870 Score: 167
Period size: 50 Copynumber: 2.0 Consensus size: 48
48764 TGTGGAAGAG
*
48774 TTTTGGTTTAGGTTGTGGATGCTTGTCTGTGGCAAACTTTCTTTCATT
1 TTTTGGTTTAGGTTGTGGATACTTGTCTGTGGCAAACTTTCTTTCATT
48822 TTTTGGTTTTAGGTTGTGGATACTTTGTCTGTGGCAAACTTTCTTTCAT
1 TTTTGG-TTTAGGTTGTGGATAC-TTGTCTGTGGCAAACTTTCTTTCAT
48871 CTACACGTAC
Statistics
Matches: 46, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
48 6 0.13
49 15 0.33
50 25 0.54
ACGTcount: A:0.13, C:0.12, G:0.24, T:0.51
Consensus pattern (48 bp):
TTTTGGTTTAGGTTGTGGATACTTGTCTGTGGCAAACTTTCTTTCATT
Found at i:65355 original size:32 final size:33
Alignment explanation
Indices: 65314--65391 Score: 97
Period size: 33 Copynumber: 2.4 Consensus size: 33
65304 TTTAAATAGT
* *
65314 TATTATTTTTTA-TATTAAT-ATATTTATGTAAA
1 TATTATTTTTTATTA-AAATAATATTTATATAAA
*
65346 TATTATTTTTTATTAAAATAATATTTATATAAT
1 TATTATTTTTTATTAAAATAATATTTATATAAA
65379 TATTATTTATTTA
1 TATTATTT-TTTA
65392 GAATTATTAA
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
32 15 0.38
33 21 0.52
34 4 0.10
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.60
Consensus pattern (33 bp):
TATTATTTTTTATTAAAATAATATTTATATAAA
Found at i:67141 original size:21 final size:21
Alignment explanation
Indices: 67111--67158 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
67101 GTAGGGGTAC
* *
67111 ATGCCCAGCCCTCCACTTCAT
1 ATGCCAAGCCCACCACTTCAT
* *
67132 ATGCCAAGCCCACCAGTTTAT
1 ATGCCAAGCCCACCACTTCAT
67153 ATGCCA
1 ATGCCA
67159 TCTCCGCAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.40, G:0.12, T:0.23
Consensus pattern (21 bp):
ATGCCAAGCCCACCACTTCAT
Found at i:67192 original size:21 final size:22
Alignment explanation
Indices: 67165--67255 Score: 118
Period size: 21 Copynumber: 4.3 Consensus size: 22
67155 GCCATCTCCG
* *
67165 CAGGGTTACATTCCGAGCCCG-
1 CAGGGTTACATGCCTAGCCCGC
* *
67186 TAGGGTTACATTCCTAGCCCGC
1 CAGGGTTACATGCCTAGCCCGC
67208 CA-GGTTACATGCCTAGCCCGC
1 CAGGGTTACATGCCTAGCCCGC
67229 CA-GGTTACATGCCTAGCCCG-
1 CAGGGTTACATGCCTAGCCCGC
67249 CAGGGTT
1 CAGGGTT
67256 TTATACCATA
Statistics
Matches: 64, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
20 2 0.03
21 61 0.95
22 1 0.02
ACGTcount: A:0.19, C:0.33, G:0.26, T:0.22
Consensus pattern (22 bp):
CAGGGTTACATGCCTAGCCCGC
Found at i:67836 original size:33 final size:34
Alignment explanation
Indices: 67777--67873 Score: 133
Period size: 33 Copynumber: 2.9 Consensus size: 34
67767 TAAATGTTTT
*
67777 AAAATACAAATTATATTATTCGAAATTTAAAATA
1 AAAATAAAAATTATATTATTCGAAATTTAAAATA
* * *
67811 AAAATAAAAATAATATTATTC-AAATTTAAATTT
1 AAAATAAAAATTATATTATTCGAAATTTAAAATA
* *
67844 AAAATATAAATTATAGTATTCGAAATTTAA
1 AAAATAAAAATTATATTATTCGAAATTTAA
67874 CATTAAATTT
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
33 28 0.51
34 27 0.49
ACGTcount: A:0.56, C:0.04, G:0.03, T:0.37
Consensus pattern (34 bp):
AAAATAAAAATTATATTATTCGAAATTTAAAATA
Found at i:67880 original size:34 final size:33
Alignment explanation
Indices: 67775--67880 Score: 133
Period size: 34 Copynumber: 3.2 Consensus size: 33
67765 GATAAATGTT
*
67775 TTAAAATACAAATTATATTATTCGAAATTTAAAA
1 TTAAAATAAAAATTATATTATTCGAAATTT-AAA
* *
67809 TAAAAATAAAAATAATATTATTC-AAATTTAAA
1 TTAAAATAAAAATTATATTATTCGAAATTTAAA
* *
67841 TTTAAAATATAAATTATAGTATTCGAAATTTAACA
1 -TTAAAATAAAAATTATATTATTCGAAATTTAA-A
67876 TTAAA
1 TTAAA
67881 TTTCAACTTA
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
32 3 0.05
33 25 0.40
34 33 0.53
35 1 0.02
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.38
Consensus pattern (33 bp):
TTAAAATAAAAATTATATTATTCGAAATTTAAA
Found at i:68494 original size:128 final size:128
Alignment explanation
Indices: 68266--68768 Score: 961
Period size: 128 Copynumber: 3.9 Consensus size: 128
68256 AGTTATTCAA
* *
68266 ACTGATATATCTAGTGTCCTCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
1 ACTGATATATCTAGTGTCCCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCT
68331 GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGT
66 GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGT
68394 ACTGATATATCTAGTGTCCCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCT
1 ACTGATATATCTAGTGTCCCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCT
68459 GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGT
66 GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGT
*
68522 ACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
1 ACTGATATATCTAGTGTCCCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCT
*
68587 GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCGTGTGAATAGTGAAATAATAGGT
66 GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGT
*
68650 ACTGATATATCTAGTGTCCCCGAGAGACATGAATGACATAATAGGGCAATGATAACATATTCTCT
1 ACTGATATATCTAGTGTCCCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCT
68715 GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAA
66 GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAA
68769 CCGATTATAG
Statistics
Matches: 368, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
128 368 1.00
ACGTcount: A:0.32, C:0.20, G:0.25, T:0.23
Consensus pattern (128 bp):
ACTGATATATCTAGTGTCCCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCT
GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGT
Found at i:68849 original size:8 final size:8
Alignment explanation
Indices: 68836--68876 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
68826 TCACAATCTT
68836 TCAAATTC
1 TCAAATTC
68844 TCAAATTC
1 TCAAATTC
* *
68852 CCAAACTC
1 TCAAATTC
68860 T-AAATTC
1 TCAAATTC
68867 TCAAATTC
1 TCAAATTC
68875 TC
1 TC
68877 TAAAAATGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.37, C:0.29, G:0.00, T:0.34
Consensus pattern (8 bp):
TCAAATTC
Found at i:76434 original size:34 final size:34
Alignment explanation
Indices: 76377--76442 Score: 96
Period size: 34 Copynumber: 1.9 Consensus size: 34
76367 TAACTTATAT
*
76377 TAAGAATATTTAAAAATAATGTAATTTTTCTTAC
1 TAAGAATATATAAAAATAATGTAATTTTTCTTAC
** *
76411 TAAGAATATATAAATTTATTGTAATTTTTCTT
1 TAAGAATATATAAAAATAATGTAATTTTTCTT
76443 CAAATATGTG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.41, C:0.05, G:0.06, T:0.48
Consensus pattern (34 bp):
TAAGAATATATAAAAATAATGTAATTTTTCTTAC
Found at i:84944 original size:22 final size:22
Alignment explanation
Indices: 84916--84960 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
84906 TTAACCGATC
84916 GAATCGGTCCGACCGGTCGGAA
1 GAATCGGTCCGACCGGTCGGAA
84938 GAATCGGTCCGACCGGTCGGAA
1 GAATCGGTCCGACCGGTCGGAA
84960 G
1 G
84961 TACCGGACGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.22, C:0.27, G:0.38, T:0.13
Consensus pattern (22 bp):
GAATCGGTCCGACCGGTCGGAA
Found at i:85020 original size:23 final size:22
Alignment explanation
Indices: 84985--85027 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
84975 ATAATTATTT
84985 AAAAAATTAAATAAAAAATACC
1 AAAAAATTAAATAAAAAATACC
*
85007 AAAAATATTTAATAAAAAATA
1 AAAAA-ATTAAATAAAAAATA
85028 ATTTTTTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.72, C:0.05, G:0.00, T:0.23
Consensus pattern (22 bp):
AAAAAATTAAATAAAAAATACC
Found at i:87691 original size:34 final size:35
Alignment explanation
Indices: 87629--87713 Score: 127
Period size: 34 Copynumber: 2.5 Consensus size: 35
87619 TCCCCCCAGG
**
87629 GGGAACAGATTCCCCTTAGGGGGTATCGATTCCCC
1 GGGAACAGATTCCCCCCAGGGGGTATCGATTCCCC
*
87664 GGGAATAGATTCCCCCCA-GGGGTATCGATTCCCC
1 GGGAACAGATTCCCCCCAGGGGGTATCGATTCCCC
*
87698 GGGTACAGATTCCCCC
1 GGGAACAGATTCCCCC
87714 TGCATGATTT
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
34 30 0.67
35 15 0.33
ACGTcount: A:0.20, C:0.32, G:0.27, T:0.21
Consensus pattern (35 bp):
GGGAACAGATTCCCCCCAGGGGGTATCGATTCCCC
Found at i:87851 original size:21 final size:21
Alignment explanation
Indices: 87825--87866 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
87815 ATTTGAATAT
87825 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTATCGATTCCC
87846 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTATCGATTCCC
87867 CCCATTCTGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.19, G:0.29, T:0.29
Consensus pattern (21 bp):
TATGAAGGGGTATCGATTCCC
Found at i:87928 original size:21 final size:21
Alignment explanation
Indices: 87895--87934 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
87885 TTTTTGCAGA
*
87895 AAAATCATTCCCAAACGGCTCC
1 AAAATCA-TCCCCAACGGCTCC
87917 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
87935 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:88188 original size:34 final size:32
Alignment explanation
Indices: 88149--88218 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
88139 TTTTGTAAAG
*
88149 GGGAAAGGTTCTAGCTAATCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTAATCCCG-G-AAAAACTA
* *
88183 GGGAAAGGTTCTAGTTTATCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTAATCCCGGAAAAACTA
88215 GGGA
1 GGGA
88219 GTTTGTAAGG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 11 0.33
33 1 0.03
34 21 0.64
ACGTcount: A:0.33, C:0.16, G:0.29, T:0.23
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTAATCCCGGAAAAACTA
Found at i:91204 original size:20 final size:20
Alignment explanation
Indices: 91179--91238 Score: 77
Period size: 20 Copynumber: 3.0 Consensus size: 20
91169 ATCAGATTGT
91179 CCAGGGGGTACAGATTCCCC
1 CCAGGGGGTACAGATTCCCC
* *
91199 CCAGGGGGAACAAATTCCCC
1 CCAGGGGGTACAGATTCCCC
*
91219 CTAGGGGGTATC-GATTCCCC
1 CCAGGGGGTA-CAGATTCCCC
91239 GGGAACAGAT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
20 33 0.97
21 1 0.03
ACGTcount: A:0.22, C:0.33, G:0.28, T:0.17
Consensus pattern (20 bp):
CCAGGGGGTACAGATTCCCC
Found at i:91266 original size:34 final size:35
Alignment explanation
Indices: 91204--91288 Score: 127
Period size: 34 Copynumber: 2.5 Consensus size: 35
91194 TCCCCCCAGG
* *
91204 GGGAACAAATTCCCCCTAGGGGGTATCGATTCCCC
1 GGGAACAGATTCCCCCCAGGGGGTATCGATTCCCC
*
91239 GGGAACAGATTCCCCCCA-GGGGTATCGATTCCTC
1 GGGAACAGATTCCCCCCAGGGGGTATCGATTCCCC
*
91273 GGGTACAGATTCCCCC
1 GGGAACAGATTCCCCC
91289 TGCATGGTTT
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
34 30 0.65
35 16 0.35
ACGTcount: A:0.21, C:0.33, G:0.26, T:0.20
Consensus pattern (35 bp):
GGGAACAGATTCCCCCCAGGGGGTATCGATTCCCC
Found at i:91427 original size:21 final size:21
Alignment explanation
Indices: 91401--91442 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
91391 ATTTGAATAT
* *
91401 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCAATTCCC
91422 TATGAAGGGGTACCAATTCCC
1 TATGAAGGGGTACCAATTCCC
91443 CCCATTCTAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.26
Consensus pattern (21 bp):
TATGAAGGGGTACCAATTCCC
Found at i:91764 original size:34 final size:32
Alignment explanation
Indices: 91725--91794 Score: 77
Period size: 34 Copynumber: 2.1 Consensus size: 32
91715 TTTTGTAAAG
* *
91725 GGGAAAGGTTTTAGCTAATCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTAATCCCG-G-AAAAACTA
* * *
91759 GGGAAATGTTCTAGTTTATCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTAATCCCGGAAAAACTA
91791 GGGA
1 GGGA
91795 GTTTGTAAGG
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
32 11 0.35
33 1 0.03
34 19 0.61
ACGTcount: A:0.33, C:0.14, G:0.27, T:0.26
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTAATCCCGGAAAAACTA
Found at i:93739 original size:23 final size:23
Alignment explanation
Indices: 93713--93757 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
93703 CACCACAGCT
*
93713 CGTATAATTGCACCGAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCG
*
93736 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAATTGCACCGAAGTGCC
93758 ATATAATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCG
Found at i:93999 original size:151 final size:149
Alignment explanation
Indices: 93736--94041 Score: 558
Period size: 151 Copynumber: 2.0 Consensus size: 149
93726 CGAAGTGCCG
*
93736 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTATTCCTTAAGAAT
1 CGTAGAATTACACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTATTCCTTAAGAAT
*
93801 CATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACGTGTTCCACAGAATATA
66 CATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCACAG-A-ATA
93866 TATATATATCCCGAAGGACCA
129 TATATATATCCCGAAGGACCA
*
93887 CGTAGAATTACACCGTAGTGCCATATAATAATGTCCATAAGGACCATATATTATTCCTTAAGAAT
1 CGTAGAATTACACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTATTCCTTAAGAAT
93952 CATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCACAGAATATA
66 CATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCACAGAATATA
*
94017 TATATATCCCGAAGGACCG
131 TATATATCCCGAAGGACCA
94036 CGTAGA
1 CGTAGA
94042 CCCTCGACTC
Statistics
Matches: 151, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
149 29 0.19
150 1 0.01
151 121 0.80
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.29
Consensus pattern (149 bp):
CGTAGAATTACACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTATTCCTTAAGAAT
CATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCACAGAATATA
TATATATCCCGAAGGACCA
Found at i:95498 original size:64 final size:66
Alignment explanation
Indices: 95400--95524 Score: 202
Period size: 64 Copynumber: 1.9 Consensus size: 66
95390 TAATGAAGAT
*
95400 ATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATG-TTTGTATTTAATGGG
1 ATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAATGGG
95464 G
66 G
*
95465 ATGCATCGATGCACT-C-CTTATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAA
1 ATGCATCGATGCACTACAC-CATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAA
95525 ATTCATGCAT
Statistics
Matches: 56, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
63 1 0.02
64 30 0.54
65 25 0.45
ACGTcount: A:0.27, C:0.21, G:0.17, T:0.35
Consensus pattern (66 bp):
ATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAATGGG
G
Found at i:95533 original size:64 final size:64
Alignment explanation
Indices: 95400--95542 Score: 193
Period size: 64 Copynumber: 2.2 Consensus size: 64
95390 TAATGAAGAT
* *
95400 ATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATGTTTGTATTTAATGGGG
1 ATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATGTTTCTATTTAAT-GGC
*
95465 ATGCATCGATGCACT-C-CTTATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAAAT-
1 ATGCATCGATGCACTACAC-CATGCATCGATGCATAAATCCTATTCGATG-TTTCTATTT-AATG
*
95527 TC
63 GC
95529 ATGCATCGATGCAC
1 ATGCATCGATGCAC
95543 CTTAAACAAT
Statistics
Matches: 71, Mismatches: 4, Indels: 7
0.87 0.05 0.09
Matches are distributed among these distances:
63 1 0.01
64 44 0.62
65 23 0.32
66 3 0.04
ACGTcount: A:0.27, C:0.22, G:0.17, T:0.34
Consensus pattern (64 bp):
ATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATGTTTCTATTTAATGGC
Found at i:99001 original size:154 final size:146
Alignment explanation
Indices: 98748--99047 Score: 496
Period size: 154 Copynumber: 2.0 Consensus size: 146
98738 TTCAAAATTT
98748 GATGAATGATCTATTTGGAGCTATTTAAGGAGGTTGTTCTTGTATTTTTGATGATATTCTTACAG
1 GATGAATGATCTATTTGGAGCTATTTAAGGAGGTTGTTCTTGTATTTTTGATGATATTCTTACAG
98813 TGTAGTATGGCAGAACAAACAACATTTGGAATTGTGTTGGAGATTTTGTTGAAG-ATCATTTATA
66 TGTAGTATGGCAGAACAAACAACATTTGGAATTGTGTTGGAGATTTTGTTGAAGAATCATTTATA
98877 TGCC-AAAAGAGTAAA
131 TGCCAAAAAGAGTAAA
98892 GATGAATGATCTATTTGGAGCTTATTTAAGGAGGTTTGTTCTTGTATTTTTTGATGATATTCTGG
1 GATGAATGATCTATTTGGAGC-TATTTAAGGAGG-TTGTTCTTGTA-TTTTTGATGATATTC---
98957 TTTACAGTGCTAGTATGGCAGAACACAAACAACATTTGGAATTGTGTTGGAGATTTTGTTGAAGA
60 -TTACAGTG-TAGTATGGCAG-A-ACAAACAACATTTGGAATTGTGTTGGAGATTTTGTTGAAGA
99022 ATCATTTATATGCCAAAAAGAGTAAA
121 ATCATTTATATGCCAAAAAGAGTAAA
99048 TATTTTTTTG
Statistics
Matches: 144, Mismatches: 0, Indels: 12
0.92 0.00 0.08
Matches are distributed among these distances:
144 21 0.15
145 12 0.08
146 11 0.08
147 15 0.10
151 8 0.06
152 11 0.08
153 1 0.01
154 40 0.28
155 14 0.10
156 11 0.08
ACGTcount: A:0.31, C:0.09, G:0.23, T:0.38
Consensus pattern (146 bp):
GATGAATGATCTATTTGGAGCTATTTAAGGAGGTTGTTCTTGTATTTTTGATGATATTCTTACAG
TGTAGTATGGCAGAACAAACAACATTTGGAATTGTGTTGGAGATTTTGTTGAAGAATCATTTATA
TGCCAAAAAGAGTAAA
Found at i:105407 original size:2 final size:2
Alignment explanation
Indices: 105402--105436 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
105392 GAACTATATA
105402 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
105437 CGAACCACAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:106637 original size:50 final size:50
Alignment explanation
Indices: 106578--106690 Score: 154
Period size: 50 Copynumber: 2.3 Consensus size: 50
106568 TTAGCAGAAA
* * * *
106578 AGCGCGCCCCCTGCACCGCGGTATATGCTGATTTGGCGCCACGTGGGTAT
1 AGCGCGCCCCCTGCACCGCGATATACGCTGATCTGGCGCCACGTGGATAT
* * * *
106628 AGCGCGCCCCCTGCCCCGCGATATACGGTTATCTGGCGTCACGTGGATAT
1 AGCGCGCCCCCTGCACCGCGATATACGCTGATCTGGCGCCACGTGGATAT
106678 AGCGCGCCCCCTG
1 AGCGCGCCCCCTG
106691 ATCCACGCTA
Statistics
Matches: 55, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
50 55 1.00
ACGTcount: A:0.14, C:0.35, G:0.30, T:0.20
Consensus pattern (50 bp):
AGCGCGCCCCCTGCACCGCGATATACGCTGATCTGGCGCCACGTGGATAT
Found at i:107133 original size:111 final size:111
Alignment explanation
Indices: 106934--107155 Score: 383
Period size: 111 Copynumber: 2.0 Consensus size: 111
106924 TGGAAATCAT
*
106934 ATATCTCTACACTTTGCTGATACGATAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGATAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
* * *
106999 TATTTAGTTGATTTATTATATGCATGATTATTATATTAAGAATTAA
66 TAATTAGTTGATTCATTATATGCATGATTATTAGATTAAGAATTAA
*
107045 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGATAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
107110 TAATTAGTTGATTCATT-TAATGCATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTCATTAT-ATGCATGATTATTAGATTAAGAATTAA
107156 TTTTGTAATT
Statistics
Matches: 105, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
110 1 0.01
111 104 0.99
ACGTcount: A:0.36, C:0.09, G:0.10, T:0.45
Consensus pattern (111 bp):
ATATCTCGACACTTTGCTGATACGATAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
TAATTAGTTGATTCATTATATGCATGATTATTAGATTAAGAATTAA
Found at i:112887 original size:50 final size:50
Alignment explanation
Indices: 112810--112936 Score: 146
Period size: 50 Copynumber: 2.5 Consensus size: 50
112800 CCCTACGTGG
* * * * *
112810 CGTATAGCGCGGATCAGGGGGCACGCTATACCCACGTGGCGCCAGATCAC
1 CGTATAACGCGGAGCAGGGGGCGCGCTATACCCACGTGGCACCAAATCAC
* * * *
112860 CGTATATCGCGGGGCAGGGGGCGCGCTATACTCACGTGGCACCAAATCAG
1 CGTATAACGCGGAGCAGGGGGCGCGCTATACCCACGTGGCACCAAATCAC
* * *
112910 CATATAACGCGGTGCAAGGGGCGCGCT
1 CGTATAACGCGGAGCAGGGGGCGCGCT
112937 TTTCTGCTAA
Statistics
Matches: 65, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
50 65 1.00
ACGTcount: A:0.22, C:0.29, G:0.34, T:0.15
Consensus pattern (50 bp):
CGTATAACGCGGAGCAGGGGGCGCGCTATACCCACGTGGCACCAAATCAC
Found at i:113848 original size:18 final size:17
Alignment explanation
Indices: 113825--113874 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 17
113815 GAAGAAGAAG
113825 AAGAAAAAAAGAAAATGA
1 AAGAAAAAAAGAAAAT-A
*
113843 AAGAAAGAAAGAAAAATA
1 AAGAAAAAAAG-AAAATA
113861 AA-AAATAAAAGAAA
1 AAGAAA-AAAAGAAA
113875 GAAAAAAGAG
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
17 6 0.21
18 17 0.61
19 5 0.18
ACGTcount: A:0.80, C:0.00, G:0.14, T:0.06
Consensus pattern (17 bp):
AAGAAAAAAAGAAAATA
Found at i:113854 original size:26 final size:26
Alignment explanation
Indices: 113791--113878 Score: 85
Period size: 26 Copynumber: 3.5 Consensus size: 26
113781 CACTTGAACA
* * *
113791 AAAAAAAAGAAAGAAAAATAGTAAGA-
1 AAAAGAAAGAAAGAAAAATA-AAAAAT
*
113817 AGAAG-AAG-AAGAAAAA-AAGAAAAT
1 AAAAGAAAGAAAGAAAAATAA-AAAAT
*
113841 GAAAGAAAGAAAGAAAAATAAAAAAT
1 AAAAGAAAGAAAGAAAAATAAAAAAT
113867 AAAAGAAAGAAA
1 AAAAGAAAGAAA
113879 AAAGAGGGAG
Statistics
Matches: 50, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
23 4 0.08
24 11 0.22
25 6 0.12
26 27 0.54
27 2 0.04
ACGTcount: A:0.77, C:0.00, G:0.17, T:0.06
Consensus pattern (26 bp):
AAAAGAAAGAAAGAAAAATAAAAAAT
Found at i:113907 original size:13 final size:13
Alignment explanation
Indices: 113874--113906 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
113864 AATAAAAGAA
113874 AGAAAAAAGAGGG
1 AGAAAAAAGAGGG
*
113887 AGGAAAAAGA-GG
1 AGAAAAAAGAGGG
113899 AGAAAAAA
1 AGAAAAAA
113907 AAAGAAATGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
12 9 0.50
13 9 0.50
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (13 bp):
AGAAAAAAGAGGG
Found at i:113935 original size:13 final size:14
Alignment explanation
Indices: 113905--113939 Score: 54
Period size: 13 Copynumber: 2.5 Consensus size: 14
113895 GAGGAGAAAA
113905 AAAAAGAAATGAAGG
1 AAAAAG-AATGAAGG
113920 AAAAAGAATG-AGG
1 AAAAAGAATGAAGG
113933 AAAAAGA
1 AAAAAGA
113940 GAGGATAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 10 0.50
14 4 0.20
15 6 0.30
ACGTcount: A:0.69, C:0.00, G:0.26, T:0.06
Consensus pattern (14 bp):
AAAAAGAATGAAGG
Found at i:118088 original size:22 final size:21
Alignment explanation
Indices: 118054--118096 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
118044 GGAATTGTTT
118054 TTTTTAATATTTTAAAATAATA
1 TTTTTAATATTTTAAAA-AATA
* *
118076 TTTTTACTTTTTTAAAAAATA
1 TTTTTAATATTTTAAAAAATA
118097 AATTTTCTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (21 bp):
TTTTTAATATTTTAAAAAATA
Found at i:119607 original size:46 final size:46
Alignment explanation
Indices: 119556--119651 Score: 133
Period size: 46 Copynumber: 2.1 Consensus size: 46
119546 ATTATTTTTT
*
119556 ATTTTCATTGA-GAGCATCCATTCATGCTTATAATGCA-CCATTATGC
1 ATTTTCATTGATGA-CATCCATTCATGCTGATAATGCACCCA-TATGC
* *
119602 ATTTTCATTTATGACATCCTTTCATGCTGATAATGCACCCATATGC
1 ATTTTCATTGATGACATCCATTCATGCTGATAATGCACCCATATGC
119648 ATTT
1 ATTT
119652 CAATTATGGC
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
46 40 0.89
47 5 0.11
ACGTcount: A:0.27, C:0.22, G:0.11, T:0.40
Consensus pattern (46 bp):
ATTTTCATTGATGACATCCATTCATGCTGATAATGCACCCATATGC
Found at i:120053 original size:55 final size:55
Alignment explanation
Indices: 119993--120221 Score: 293
Period size: 55 Copynumber: 4.2 Consensus size: 55
119983 CTATTAATAT
* * * **
119993 GGAAATTTATACACTTAGTATGAATTTCCT-AGTTTTGTACATAAAGTGCCCATAC
1 GGAAATTCATCCACTTAGTATGAATTTCTTAAG-TTTACACATAAAGTGCCCATAC
* * * *
120048 AGAAATTCATCAACTTAGTATGAATTTTTTAAGTTTACACATAAAGTG-ACATAC
1 GGAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCCATAC
* * * *
120102 GAAAATTCATCCACTTAGTATCAATTTTTTAAGTTTACACATAAAGTGCCTATAC
1 GGAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCCATAC
*
120157 GGAAATTCATCCACTTAGTATAAATTTCTTAAGTTTAC-CAATAAAGTGCCCATAC
1 GGAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACAC-ATAAAGTGCCCATAC
120212 GGAAATTCAT
1 GGAAATTCAT
120222 AAACAAATTA
Statistics
Matches: 152, Mismatches: 19, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
54 50 0.33
55 100 0.66
56 2 0.01
ACGTcount: A:0.37, C:0.17, G:0.12, T:0.35
Consensus pattern (55 bp):
GGAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCCATAC
Found at i:120432 original size:36 final size:36
Alignment explanation
Indices: 120385--120471 Score: 138
Period size: 36 Copynumber: 2.4 Consensus size: 36
120375 ACAAAGTTGA
* *
120385 TTACTCGGGTACTTGGCCTTTGCCTTTCGTTTTTTT
1 TTACTCGGGTACTTGGCCTTTGCCTTTCATTTTGTT
120421 TTACTCGGGTACTTGGCCTTTGCCTTTCATTTTGTT
1 TTACTCGGGTACTTGGCCTTTGCCTTTCATTTTGTT
* *
120457 TGACTCGGGAACTTG
1 TTACTCGGGTACTTG
120472 ATTTTGATCT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 47 1.00
ACGTcount: A:0.09, C:0.22, G:0.22, T:0.47
Consensus pattern (36 bp):
TTACTCGGGTACTTGGCCTTTGCCTTTCATTTTGTT
Found at i:124566 original size:20 final size:20
Alignment explanation
Indices: 124517--124572 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
124507 TTAGCATCGA
* *
124517 TACTGTTCACACAGTATTAG
1 TACTATTCATACAGTATTAG
*
124537 TACTATTCATACAGTATTGG
1 TACTATTCATACAGTATTAG
*
124557 TACTATTCATATAGTA
1 TACTATTCATACAGTA
124573 CTATTCATAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.39
Consensus pattern (20 bp):
TACTATTCATACAGTATTAG
Found at i:133107 original size:61 final size:61
Alignment explanation
Indices: 133019--133133 Score: 178
Period size: 61 Copynumber: 1.9 Consensus size: 61
133009 AAAGGTGGAT
* *
133019 ACGACCTTATGTATCATGTCCGGATTAGCACTATAGCGTAAGCTTAGTGTAGGTGGTGGGC
1 ACGACCTTATGTATCATATCCGGATTAGCACTATAGCGTAAGCTTAGTGCAGGTGGTGGGC
* *
133080 ACGACCTTATGTGT-ATTATCCGGATTAGCACTATGGCGTAAGCTTAGTGCAGGT
1 ACGACCTTATGTATCA-TATCCGGATTAGCACTATAGCGTAAGCTTAGTGCAGGT
133134 TTAGCACTAC
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
60 1 0.02
61 48 0.98
ACGTcount: A:0.23, C:0.18, G:0.28, T:0.30
Consensus pattern (61 bp):
ACGACCTTATGTATCATATCCGGATTAGCACTATAGCGTAAGCTTAGTGCAGGTGGTGGGC
Found at i:133796 original size:22 final size:22
Alignment explanation
Indices: 133765--133806 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
133755 CACTGTTCAT
* *
133765 GTACTATTCATCACTGTTTACG
1 GTACTATTCACCACTATTTACG
*
133787 GTACTGTTCACCACTATTTA
1 GTACTATTCACCACTATTTA
133807 AAAAATATTT
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:0.24, C:0.24, G:0.12, T:0.40
Consensus pattern (22 bp):
GTACTATTCACCACTATTTACG
Found at i:136923 original size:12 final size:12
Alignment explanation
Indices: 136906--136948 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
136896 TACATTGTTC
136906 ACTGTTCACGGT
1 ACTGTTCACGGT
*
136918 ACTGTTCA--TT
1 ACTGTTCACGGT
*
136928 AATGTTCACGGT
1 ACTGTTCACGGT
136940 ACTGTTCAC
1 ACTGTTCAC
136949 CACTATTTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
10 8 0.32
12 17 0.68
ACGTcount: A:0.21, C:0.23, G:0.19, T:0.37
Consensus pattern (12 bp):
ACTGTTCACGGT
Done.