Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003589.1 Hibiscus syriacus cultivar Beakdansim tig00007570_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: 119437
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:7406 original size:26 final size:26
Alignment explanation
Indices: 7336--7399 Score: 110
Period size: 26 Copynumber: 2.5 Consensus size: 26
7326 CTCGACGAGC
* *
7336 ATCGCTGAGCACCGCTAATGATAAGT
1 ATCGTTGAGCACCACTAATGATAAGT
7362 ATCGTTGAGCACCACTAATGATAAGT
1 ATCGTTGAGCACCACTAATGATAAGT
7388 ATCGTTGAGCAC
1 ATCGTTGAGCAC
7400 TATTAATTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.25
Consensus pattern (26 bp):
ATCGTTGAGCACCACTAATGATAAGT
Found at i:13607 original size:16 final size:16
Alignment explanation
Indices: 13586--13617 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
13576 AAAGTATTTC
*
13586 ATATATTGTTAGGATT
1 ATATATTGCTAGGATT
13602 ATATATTGCTAGGATT
1 ATATATTGCTAGGATT
13618 GATTAAAGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.31, C:0.03, G:0.19, T:0.47
Consensus pattern (16 bp):
ATATATTGCTAGGATT
Found at i:16134 original size:106 final size:105
Alignment explanation
Indices: 15908--16175 Score: 367
Period size: 106 Copynumber: 2.5 Consensus size: 105
15898 GGAGGTCATA
* * * *
15908 AAAATATATTCTT-AGTGGCAAACAAATTTATCACAATTTCTATTGATAATAGCGTTGAACACTT
1 AAAATATATT-TTCAGTGTCAAACAAATTCATCACAATTTCTATTGATAATAGTGTCGAACACTT
*
15972 GGTCACTAAAAAATATTTAGAGTGACAACATTGATGGTCAC
65 GGTCACTAAAAAATACTTAGAGTGACAACATTGATGGTCAC
* * * * * *
16013 AAAATATATCTTCAGTGTCAAACAAATTCATCAAAATTTCCATTGAAAATTGTGTCGAACATTTG
1 AAAATATATTTTCAGTGTCAAACAAATTCATCACAATTTCTATTGATAATAGTGTCGAACACTTG
*
16078 GTCACTAAATATATACTTAGAGTGACAACATTGATGGTCAC
66 GTCACTAAA-AAATACTTAGAGTGACAACATTGATGGTCAC
* * * *
16119 AAAATATGTTTTCAGTGTCGAACAAGTTCATCACAATTTATATTGATAATAGTGTCG
1 AAAATATATTTTCAGTGTCAAACAAATTCATCACAATTTCTATTGATAATAGTGTCG
16176 GCTAGATGGT
Statistics
Matches: 140, Mismatches: 21, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
104 2 0.01
105 61 0.44
106 77 0.55
ACGTcount: A:0.38, C:0.15, G:0.14, T:0.33
Consensus pattern (105 bp):
AAAATATATTTTCAGTGTCAAACAAATTCATCACAATTTCTATTGATAATAGTGTCGAACACTTG
GTCACTAAAAAATACTTAGAGTGACAACATTGATGGTCAC
Found at i:17347 original size:20 final size:20
Alignment explanation
Indices: 17322--17368 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
17312 TCTCTGGCTC
*
17322 AAAGGATCGAT-CCCTTAGGA
1 AAAGGATCGATCCCCTT-GAA
17342 AAAGGATCGATCCCCTTGAA
1 AAAGGATCGATCCCCTTGAA
17362 AAAGGAT
1 AAAGGAT
17369 ATATCCCTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 20 0.80
21 5 0.20
ACGTcount: A:0.38, C:0.19, G:0.23, T:0.19
Consensus pattern (20 bp):
AAAGGATCGATCCCCTTGAA
Found at i:17376 original size:19 final size:19
Alignment explanation
Indices: 17322--17378 Score: 60
Period size: 20 Copynumber: 2.9 Consensus size: 19
17312 TCTCTGGCTC
* *
17322 AAAGGATCGATCCCTTAGGA
1 AAAGGATAGATCCCTT-GAA
*
17342 AAAGGATCGATCCCCTTGAA
1 AAAGGATAGAT-CCCTTGAA
*
17362 AAAGGATATATCCCTTG
1 AAAGGATAGATCCCTTG
17379 GATTCTAGTA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
19 6 0.18
20 22 0.67
21 5 0.15
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.23
Consensus pattern (19 bp):
AAAGGATAGATCCCTTGAA
Found at i:18491 original size:15 final size:16
Alignment explanation
Indices: 18462--18502 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
18452 ATTTAAAATA
*
18462 TAATATTCT-TAC-TT
1 TAATATTATATACTTT
18476 TAATATTATATACTTT
1 TAATATTATATACTTT
18492 TCAATATTATA
1 T-AATATTATA
18503 ATAGTTTCTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
14 8 0.35
15 3 0.13
16 3 0.13
17 9 0.39
ACGTcount: A:0.37, C:0.10, G:0.00, T:0.54
Consensus pattern (16 bp):
TAATATTATATACTTT
Found at i:19873 original size:23 final size:23
Alignment explanation
Indices: 19842--19887 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
19832 ATTTTAATCC
* *
19842 TTATGTTA-TTATTGTATATTACT
1 TTATATTATTTATT-TAGATTACT
19865 TTATATTATTTATTTAGATTACT
1 TTATATTATTTATTTAGATTACT
19888 ATATGCGTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.28, C:0.04, G:0.07, T:0.61
Consensus pattern (23 bp):
TTATATTATTTATTTAGATTACT
Found at i:20044 original size:3 final size:3
Alignment explanation
Indices: 20036--20066 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
20026 TTTTGGTGCT
20036 TTA TTA TTA TTA -TA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
20067 TTTCCTTTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:20055 original size:14 final size:14
Alignment explanation
Indices: 20036--20062 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
20026 TTTTGGTGCT
20036 TTATTATTATTATA
1 TTATTATTATTATA
20050 TTATTATTATTAT
1 TTATTATTATTAT
20063 TATTTTTCCT
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:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TTATTATTATTATA
Found at i:20107 original size:2 final size:2
Alignment explanation
Indices: 20102--20174 Score: 146
Period size: 2 Copynumber: 36.5 Consensus size: 2
20092 GTTTTTTTCT
20102 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
20144 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
20175 TATCCGTGTT
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 71 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:30129 original size:7 final size:7
Alignment explanation
Indices: 30119--30178 Score: 104
Period size: 7 Copynumber: 8.7 Consensus size: 7
30109 TAAGTTGAAA
*
30119 AAAAGAA
1 AAAAGAT
30126 AAAAGAT
1 AAAAGAT
30133 AAAAGAT
1 AAAAGAT
30140 AAAAGAT
1 AAAAGAT
30147 AAAAGAT
1 AAAAGAT
30154 AAAAGAT
1 AAAAGAT
30161 AAAAGAT
1 AAAAGAT
30168 AAAAGA-
1 AAAAGAT
30174 AAAAG
1 AAAAG
30179 GGAAAGGGAA
Statistics
Matches: 52, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
6 5 0.10
7 47 0.90
ACGTcount: A:0.75, C:0.00, G:0.15, T:0.10
Consensus pattern (7 bp):
AAAAGAT
Found at i:30261 original size:8 final size:7
Alignment explanation
Indices: 30244--30290 Score: 51
Period size: 8 Copynumber: 6.4 Consensus size: 7
30234 CCCTAAATTG
30244 AAAAAG-
1 AAAAAGA
30250 AAAAAGA
1 AAAAAGA
30257 GAAAAAGAA
1 -AAAAAG-A
30266 AAAAAGA
1 AAAAAGA
*
30273 ACAAGAGA
1 A-AAAAGA
30281 AAAAAGA
1 AAAAAGA
30288 AAA
1 AAA
30291 GAAAAATAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
6 6 0.17
7 10 0.29
8 18 0.51
9 1 0.03
ACGTcount: A:0.81, C:0.02, G:0.17, T:0.00
Consensus pattern (7 bp):
AAAAAGA
Found at i:30262 original size:14 final size:13
Alignment explanation
Indices: 30243--30296 Score: 65
Period size: 15 Copynumber: 3.9 Consensus size: 13
30233 GCCCTAAATT
30243 GAAAAAGAAAAAGA
1 GAAAAAGAAAAA-A
30257 GAAAAAGAAAAAAA
1 GAAAAAG-AAAAAA
30271 GAACAAGAGAAAAAA
1 GAA-AA-AGAAAAAA
30286 G-AAAAGAAAAA
1 GAAAAAGAAAAA
30297 TAAGGTGAGT
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
12 7 0.19
13 2 0.05
14 12 0.32
15 14 0.38
16 2 0.05
ACGTcount: A:0.80, C:0.02, G:0.19, T:0.00
Consensus pattern (13 bp):
GAAAAAGAAAAAA
Found at i:30271 original size:22 final size:23
Alignment explanation
Indices: 30244--30290 Score: 78
Period size: 22 Copynumber: 2.1 Consensus size: 23
30234 CCCTAAATTG
30244 AAAAAGAAAAAGAG-AAAAAGAA
1 AAAAAGAAAAAGAGAAAAAAGAA
*
30266 AAAAAGAACAAGAGAAAAAAGAA
1 AAAAAGAAAAAGAGAAAAAAGAA
30289 AA
1 AA
30291 GAAAAATAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 13 0.57
23 10 0.43
ACGTcount: A:0.81, C:0.02, G:0.17, T:0.00
Consensus pattern (23 bp):
AAAAAGAAAAAGAGAAAAAAGAA
Found at i:31584 original size:99 final size:99
Alignment explanation
Indices: 31412--31599 Score: 270
Period size: 99 Copynumber: 1.9 Consensus size: 99
31402 ATTTCAGAAC
*
31412 CAATTTCAACTTCACAACGAAGGATATTGGACCCAAGACAACACAAGCTCAACTTCACGACGAAG
1 CAATTTCAACTTCACAACGAAGGATATTAGACCCAAGACAACACAAGCTCAACTTCACGACGAAG
*
31477 GGGCGGCTTATTGTCAACAAATAACTTTTAGAGT
66 GGGCGGCTTACTGTCAACAAATAACTTTTAGAGT
* * * * * * *
31511 CAATTTTAACTTCACAACGAAGGATATTAGACTCGATG-CATCACAAGCTCAACTTTATGGCGAA
1 CAATTTCAACTTCACAACGAAGGATATTAGAC-CCAAGACAACACAAGCTCAACTTCACGACGAA
*
31575 GGGGTGGCTTACTGTCAACAAATAA
65 GGGGCGGCTTACTGTCAACAAATAA
31600 TTTCCCAGTT
Statistics
Matches: 78, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
99 75 0.96
100 3 0.04
ACGTcount: A:0.36, C:0.22, G:0.19, T:0.24
Consensus pattern (99 bp):
CAATTTCAACTTCACAACGAAGGATATTAGACCCAAGACAACACAAGCTCAACTTCACGACGAAG
GGGCGGCTTACTGTCAACAAATAACTTTTAGAGT
Found at i:33590 original size:2 final size:2
Alignment explanation
Indices: 33583--33659 Score: 154
Period size: 2 Copynumber: 38.5 Consensus size: 2
33573 TATAATTATG
33583 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
33625 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
33660 TTTTTTTCTA
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 75 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:34805 original size:118 final size:119
Alignment explanation
Indices: 34597--34829 Score: 441
Period size: 118 Copynumber: 2.0 Consensus size: 119
34587 TTTAGTTTCT
34597 ACTTGTTGATACACATTGCATAATATTAATGAAAATATAACATAAACTATTTGATATCAGTTCTA
1 ACTTGTTGATACACATTGCATAATATTAATGAAAATATAACATAAACTATTTGATATCAGTTCTA
34662 GACTATCATGAAGAAGTAATACAATACAAACGAGGAATTCTA-AAAAAAATGCC
66 GACTATCATGAAGAAGTAATACAATACAAACGAGGAATTCTATAAAAAAATGCC
34715 ACTTGTTGATACACATTGCATAATATTAATGAAAATATAACATAAACTATTTGATATCAGTTCTA
1 ACTTGTTGATACACATTGCATAATATTAATGAAAATATAACATAAACTATTTGATATCAGTTCTA
* *
34780 GACTATCATGATGATGTAATACAATACAAACGAGGAATTCTATAAAAAAA
66 GACTATCATGAAGAAGTAATACAATACAAACGAGGAATTCTATAAAAAAA
34830 AATGCCGCAG
Statistics
Matches: 112, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
118 105 0.94
119 7 0.06
ACGTcount: A:0.45, C:0.13, G:0.12, T:0.30
Consensus pattern (119 bp):
ACTTGTTGATACACATTGCATAATATTAATGAAAATATAACATAAACTATTTGATATCAGTTCTA
GACTATCATGAAGAAGTAATACAATACAAACGAGGAATTCTATAAAAAAATGCC
Found at i:35562 original size:37 final size:38
Alignment explanation
Indices: 35504--35828 Score: 308
Period size: 38 Copynumber: 8.8 Consensus size: 38
35494 TTTGCAAACG
*
35504 TTTGAAAATACGTATATAATATATAGTTTCTAAAAACA-T
1 TTTGAAAATA--TATATAATATATAGTTTTTAAAAACATT
35543 TTTGAAAATATATATAATATAT-GATTTTTAAAACACA--
1 TTTGAAAATATATATAATATATAG-TTTTTAAAA-ACATT
*
35580 TTTGAAAAT-TATATAATATATAGTTTTT-AAAATATT
1 TTTGAAAATATATATAATATATAGTTTTTAAAAACATT
* * * *
35616 TTAGAAAAAAAATATAATATATAGTTTTTAAAATCATT
1 TTTGAAAATATATATAATATATAGTTTTTAAAAACATT
*
35654 TTTGAAAACT-TATATAATATATAGTTTTTGAAAACATT
1 TTTGAAAA-TATATATAATATATAGTTTTTAAAAACATT
* * *
35692 TTTGAAAACT-TATATAATATATATTTTTTGAAAATATT
1 TTTGAAAA-TATATATAATATATAGTTTTTAAAAACATT
*
35730 TTTG---A-A-A-AT--TATATAGTTTTTAAAAAATATT
1 TTTGAAAATATATATAATATATAGTTTTT-AAAAACATT
*
35761 TTTGAAAATTTATATATAATATATAGTTTTTAAAAAAATAT
1 TTTGAAAA--TATATATAATATATAGTTTTTAAAAACAT-T
* *
35802 TTT-AAAA-ATTTATATTATATAGTTTTT
1 TTTGAAAATATATATAATATATAGTTTTT
35829 TTTACAAAAA
Statistics
Matches: 246, Mismatches: 19, Indels: 44
0.80 0.06 0.14
Matches are distributed among these distances:
30 11 0.04
31 12 0.05
32 2 0.01
33 1 0.00
34 3 0.01
35 4 0.02
36 25 0.10
37 67 0.27
38 82 0.33
39 12 0.05
40 11 0.04
41 16 0.07
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.46
Consensus pattern (38 bp):
TTTGAAAATATATATAATATATAGTTTTTAAAAACATT
Found at i:35564 original size:73 final size:72
Alignment explanation
Indices: 35477--35719 Score: 219
Period size: 73 Copynumber: 3.3 Consensus size: 72
35467 TTTTATATAT
* * ** *
35477 ATATATATTATATATA-ATTTGCAAACGTTTGAAAATACGTATATAATATATAGTTTCTAAAAAC
1 ATATATATAATATATAGTTTTAAAAACATTTGAAAATAC-TATATAATATATAGTTT-TAAAAAC
35541 ATTTTGAAA
64 ATTTTGAAA
* * *
35550 ATATATATAATATATGATTTTTAAAACACATTTGAAAAT--TATATAATATATAGTTTTTAAAAT
1 ATATATATAATATAT-AGTTTTAAAA-ACATTTGAAAATACTATATAATATATAGTTTTAAAAAC
35613 ATTTTAGAAA
64 ATTTT-GAAA
* * * *
35623 AAAAATATAATATATAGTTTTTAAAATCATTTTTG-AAA-ACTTATATAATATATAGTTTTTGAA
1 ATATATATAATATATAG-TTTTAAAAACA--TTTGAAAATAC-TATATAATATATAG-TTTTAAA
35686 AACATTTTTGAAA
61 AACA-TTTTGAAA
*
35699 ACT-TATATAATATATATTTTT
1 A-TATATATAATATATAGTTTT
35720 TGAAAATATT
Statistics
Matches: 141, Mismatches: 16, Indels: 24
0.78 0.09 0.13
Matches are distributed among these distances:
72 13 0.09
73 59 0.42
74 5 0.04
75 23 0.16
76 37 0.26
77 4 0.03
ACGTcount: A:0.46, C:0.05, G:0.06, T:0.44
Consensus pattern (72 bp):
ATATATATAATATATAGTTTTAAAAACATTTGAAAATACTATATAATATATAGTTTTAAAAACAT
TTTGAAA
Found at i:35593 original size:38 final size:36
Alignment explanation
Indices: 35516--35828 Score: 300
Period size: 37 Copynumber: 8.5 Consensus size: 36
35506 TGAAAATACG
*
35516 TATATAATATATAGTTTCTAAAAACA-TTTTGAAAAT
1 TATATAATATATAGTTT-TTAAAACATTTTTGAAAAT
**
35552 ATATATAATATAT-GATTTTTAAAACACATTTGAAAAT
1 -TATATAATATATAG-TTTTTAAAACATTTTTGAAAAT
* * *
35589 TATATAATATATAGTTTTTAAAATATTTTAGAAAAAA
1 TATATAATATATAGTTTTTAAAACATTTTTG-AAAAT
*
35626 AATATAATATATAGTTTTTAAAATCATTTTTGAAAACT
1 TATATAATATATAGTTTTTAAAA-CATTTTTGAAAA-T
35664 TATATAATATATAGTTTTTGAAAACATTTTTGAAAACT
1 TATATAATATATAGTTTTT-AAAACATTTTTGAAAA-T
* *
35702 TATATAATATATATTTTTTGAAAATATTTTTGAAAAT
1 TATATAATATATAGTTTTT-AAAACATTTTTGAAAAT
* ** *
35739 TATAT-A-GT-T--TTTAAAAAATATTTTTGAAAATTT
1 TATATAATATATAGTTTTTAAAACATTTTTGAAAA--T
* *
35772 ATATATAATATATAGTTTTTAAAAAAATATTTTAAAAAT
1 -TATATAATATATAGTTTTT-AAAACAT-TTTTGAAAAT
*
35811 T-TATATTATATAGTTTTT
1 TATATAATATATAGTTTTT
35829 TTTACAAAAA
Statistics
Matches: 236, Mismatches: 23, Indels: 34
0.81 0.08 0.12
Matches are distributed among these distances:
31 16 0.07
32 3 0.01
33 1 0.00
34 6 0.03
35 2 0.01
36 35 0.15
37 78 0.33
38 73 0.31
39 8 0.03
40 6 0.03
41 8 0.03
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46
Consensus pattern (36 bp):
TATATAATATATAGTTTTTAAAACATTTTTGAAAAT
Found at i:35757 original size:31 final size:31
Alignment explanation
Indices: 35709--35777 Score: 104
Period size: 31 Copynumber: 2.2 Consensus size: 31
35699 ACTTATATAA
**
35709 TATATATTTTTTGAAAATATTTTTGAAAA-T
1 TATATATTTTTAAAAAATATTTTTGAAAATT
35739 TATATAGTTTTTAAAAAATATTTTTGAAAATT
1 TATATA-TTTTTAAAAAATATTTTTGAAAATT
35771 TATATAT
1 TATATAT
35778 AATATATAGT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
30 6 0.17
31 22 0.63
32 7 0.20
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (31 bp):
TATATATTTTTAAAAAATATTTTTGAAAATT
Found at i:35838 original size:42 final size:42
Alignment explanation
Indices: 35739--35847 Score: 127
Period size: 41 Copynumber: 2.6 Consensus size: 42
35729 TTTTGAAAAT
* *
35739 TATATAGTTTTT-AAAAAATATTTTTGAAAATTTATATATAA
1 TATATAGTTTTTAAAAAAATACTTTTAAAAATTTATATATAA
35780 TATATAGTTTTTAAAAAAATA-TTTTAAAAATTTATAT-T-A
1 TATATAGTTTTTAAAAAAATACTTTTAAAAATTTATATATAA
**
35819 TATAGTTTTTTTTACAAAAAAATACTTTT
1 TATA-TAGTTTTT--AAAAAAATACTTTT
35848 TTATATTTAT
Statistics
Matches: 60, Mismatches: 3, Indels: 8
0.85 0.04 0.11
Matches are distributed among these distances:
39 5 0.08
40 7 0.12
41 27 0.45
42 17 0.28
43 4 0.07
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.50
Consensus pattern (42 bp):
TATATAGTTTTTAAAAAAATACTTTTAAAAATTTATATATAA
Found at i:35839 original size:41 final size:42
Alignment explanation
Indices: 35739--35816 Score: 133
Period size: 41 Copynumber: 1.9 Consensus size: 42
35729 TTTTGAAAAT
*
35739 TATATAGTTTTT-AAAAAATATTTTTGAAAATTTATATATAA
1 TATATAGTTTTTAAAAAAATATTTTTAAAAATTTATATATAA
35780 TATATAGTTTTTAAAAAAATA-TTTTAAAAATTTATAT
1 TATATAGTTTTTAAAAAAATATTTTTAAAAATTTATAT
35817 TATATAGTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
41 27 0.77
42 8 0.23
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (42 bp):
TATATAGTTTTTAAAAAAATATTTTTAAAAATTTATATATAA
Found at i:35872 original size:15 final size:17
Alignment explanation
Indices: 35854--35895 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
35844 TTTTTTATAT
35854 TTATTATTA-TTATTA-
1 TTATTATTATTTATTAC
35869 TTATTTATTTATTTATTAC
1 TTA-TTA-TTATTTATTAC
35888 TTATTATT
1 TTATTATT
35896 TTTTTTGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
15 3 0.13
16 3 0.13
17 5 0.22
18 9 0.39
19 3 0.13
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (17 bp):
TTATTATTATTTATTAC
Found at i:37320 original size:15 final size:14
Alignment explanation
Indices: 37299--37366 Score: 66
Period size: 14 Copynumber: 4.7 Consensus size: 14
37289 TAAATTTTAT
37299 TTTATTTTTTTTCA
1 TTTATTTTTTTTCA
37313 TATTATTTTTATTTCA
1 T-TTATTTTT-TTTCA
***
37329 TTTAACATTTTTCA
1 TTTATTTTTTTTCA
*
37343 TTTCTTTTTATTT-A
1 TTTATTTTT-TTTCA
37357 TTTATTTTTT
1 TTTATTTTTT
37367 ATATCCCTTT
Statistics
Matches: 43, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
13 1 0.02
14 20 0.47
15 16 0.37
16 6 0.14
ACGTcount: A:0.19, C:0.07, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTATTTTTTTTCA
Found at i:37694 original size:21 final size:21
Alignment explanation
Indices: 37643--37695 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
37633 ATTATGACTA
37643 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
**
37664 TCGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
37685 TCGCAATGCGA
1 TCGCAATGCGA
37696 ATAAGTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:37750 original size:20 final size:20
Alignment explanation
Indices: 37725--37839 Score: 124
Period size: 20 Copynumber: 5.7 Consensus size: 20
37715 AATTGGGAAA
*
37725 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
37745 ATCGCAACGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
*
37766 ATCACAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
37786 TTCGCAACGCGATACTTACT
1 ATCGCAACGCGATACTGACT
*
37806 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
37826 TTCGCAACGAGATA
1 ATCGCAACGCGATA
37840 ATACATAATC
Statistics
Matches: 81, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
19 2 0.02
20 63 0.78
21 14 0.17
22 2 0.02
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:37825 original size:40 final size:40
Alignment explanation
Indices: 37723--37859 Score: 168
Period size: 41 Copynumber: 3.4 Consensus size: 40
37713 CGAATTGGGA
* *
37723 AAATCGCAATGCGATACTGACTATCGCAACGCGATAATAC
1 AAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
* *
37763 AAAATCACAACGCGATACTGACTTTCGCAACGCGATACTTAC
1 -AAATCGCAACGCGATACTGACTTTCGCAACGCGATA-ATAC
** *
37805 -TTTCGCAACGCGATACTGACTTTCGCAACGAGATAATAC
1 AAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
*
37844 ATAATCGCAATGCGAT
1 A-AATCGCAACGCGAT
37860 TTTCAAAGCG
Statistics
Matches: 81, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
39 3 0.04
40 31 0.38
41 44 0.54
42 3 0.04
ACGTcount: A:0.35, C:0.26, G:0.17, T:0.23
Consensus pattern (40 bp):
AAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
Found at i:38054 original size:22 final size:22
Alignment explanation
Indices: 38026--38069 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
38016 CACTCTCTCA
*
38026 CCCATCTCCGATGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
38048 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
38070 TATCTCCATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.20, C:0.43, G:0.16, T:0.20
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:38385 original size:20 final size:20
Alignment explanation
Indices: 38331--38389 Score: 82
Period size: 20 Copynumber: 3.0 Consensus size: 20
38321 TTTATTCTCT
* **
38331 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATTGTCATTTTCG
38351 CGTTGCGATTGTCATTTTCG
1 CGTTGCGATTGTCATTTTCG
*
38371 TGTTGCGATTGTCATTTTC
1 CGTTGCGATTGTCATTTTC
38390 AGAAACTATT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.15, C:0.19, G:0.24, T:0.42
Consensus pattern (20 bp):
CGTTGCGATTGTCATTTTCG
Found at i:39727 original size:18 final size:18
Alignment explanation
Indices: 39706--39753 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
39696 TCCACTTCGG
*
39706 GAGCCATCACCTCACTCA
1 GAGCCATCACCTCACCCA
*
39724 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
*
39742 GGGCCATCACCT
1 GAGCCATCACCT
39754 GATCGACCCG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.25, C:0.44, G:0.15, T:0.17
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:40330 original size:19 final size:20
Alignment explanation
Indices: 40276--40342 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
40266 TAGTTTACTT
* *
40276 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
40296 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
40316 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
40335 TCGCAACG
1 TCGCAACG
40343 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:40350 original size:14 final size:14
Alignment explanation
Indices: 40331--40420 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
40321 ATGCGAAATG
40331 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
40345 AAAATCGCAATGCGAAATG
1 AAAATCGCAA--CG--A-C
40364 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
40378 AAAATCGCAATGCGAAATG
1 AAAATCGCAA--CG--A-C
40397 AAAATCGCAACGAC
1 AAAATCGCAACGAC
40411 AAAATCGCAA
1 AAAATCGCAA
40421 TGCGAAATGA
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
14 30 0.48
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 20 0.32
ACGTcount: A:0.50, C:0.22, G:0.17, T:0.11
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:40357 original size:33 final size:33
Alignment explanation
Indices: 40315--40439 Score: 250
Period size: 33 Copynumber: 3.8 Consensus size: 33
40305 GGAAATGGCT
40315 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
40348 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
40381 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
40414 ATCGCAATGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
40440 TGCGATTTGT
Statistics
Matches: 92, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 92 1.00
ACGTcount: A:0.48, C:0.21, G:0.18, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:40369 original size:19 final size:19
Alignment explanation
Indices: 40315--40444 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
40305 GGAAATGGCT
40315 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
40334 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
40348 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
40367 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
40381 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
40400 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
40414 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
40433 ATCGCAATGCGA
1 ATCGCAATGCGA
40445 TTTGTGTTTC
Statistics
Matches: 90, Mismatches: 6, Indels: 30
0.71 0.05 0.24
Matches are distributed among these distances:
14 30 0.33
15 3 0.03
16 6 0.07
17 6 0.07
18 3 0.03
19 42 0.47
ACGTcount: A:0.47, C:0.21, G:0.19, T:0.13
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:40532 original size:19 final size:19
Alignment explanation
Indices: 40470--40574 Score: 102
Period size: 19 Copynumber: 5.4 Consensus size: 19
40460 TCGATTTTGT
*
40470 CGTTGTGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
* *
40489 CATTACGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
40508 CATTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
***
40527 CGTTGCGATAGCCATTTTCG
1 CGTTGCGATTTTCA-TTTCG
** *
40547 CGTTGCGATAGTCATTTTCA
1 CGTTGCGATTTTCA-TTTCG
40567 CGTTGCGA
1 CGTTGCGA
40575 AAGTAAGTTT
Statistics
Matches: 75, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
19 44 0.59
20 31 0.41
ACGTcount: A:0.16, C:0.21, G:0.20, T:0.43
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:40547 original size:20 final size:20
Alignment explanation
Indices: 40522--40574 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
40512 GCGATTTTCA
40522 TTTCGCGTTGCGATAGCCAT
1 TTTCGCGTTGCGATAGCCAT
*
40542 TTTCGCGTTGCGATAGTCAT
1 TTTCGCGTTGCGATAGCCAT
*
40562 TTTCACGTTGCGA
1 TTTCGCGTTGCGA
40575 AAGTAAGTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.15, C:0.23, G:0.25, T:0.38
Consensus pattern (20 bp):
TTTCGCGTTGCGATAGCCAT
Found at i:40976 original size:21 final size:20
Alignment explanation
Indices: 40950--41018 Score: 66
Period size: 21 Copynumber: 3.4 Consensus size: 20
40940 CTGTCATCCC
40950 TCAAGAGTCCCCTCCAATCGT
1 TCAAGAGTCCCCTCC-ATCGT
* * **
40971 TCAAGAGGCCCCTATCATCCC
1 TCAAGAGTCCCCT-CCATCGT
* *
40992 TCAAGAGTCCCCCCCACCGT
1 TCAAGAGTCCCCTCCATCGT
41012 TCAAGAG
1 TCAAGAG
41019 GCCACTGTCA
Statistics
Matches: 37, Mismatches: 10, Indels: 3
0.74 0.20 0.06
Matches are distributed among these distances:
20 10 0.27
21 26 0.70
22 1 0.03
ACGTcount: A:0.25, C:0.41, G:0.16, T:0.19
Consensus pattern (20 bp):
TCAAGAGTCCCCTCCATCGT
Found at i:41030 original size:41 final size:42
Alignment explanation
Indices: 40940--41030 Score: 139
Period size: 41 Copynumber: 2.2 Consensus size: 42
40930 CCCGACTCAC
* *
40940 CTGTCATCCCTCAAGAGTCCCCTCCAATCGTTCAAGAGGCCC
1 CTGTCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCA
* *
40982 CTATCATCCCTCAAGAGTCCCC-CCCACCGTTCAAGAGGCCA
1 CTGTCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCA
41023 CTGTCATC
1 CTGTCATC
41031 GTTGAAGAGG
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
41 23 0.52
42 21 0.48
ACGTcount: A:0.22, C:0.42, G:0.15, T:0.21
Consensus pattern (42 bp):
CTGTCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCA
Found at i:42641 original size:19 final size:19
Alignment explanation
Indices: 42617--42662 Score: 92
Period size: 19 Copynumber: 2.4 Consensus size: 19
42607 GCAACGAGAG
42617 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
42636 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
42655 AATCGCAA
1 AATCGCAA
42663 CGAAAAAATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.48, C:0.17, G:0.20, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:42724 original size:20 final size:20
Alignment explanation
Indices: 42701--42756 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
42691 TCGCATTGCG
*
42701 ATTTTCTCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
*
42721 ATTTTCGCGTTGCGATAGTC
1 ATTTTCGCGTTGCGATAGCC
42741 ATTTTCGCGTTGCGAT
1 ATTTTCGCGTTGCGAT
42757 TTCCCCGTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.14, C:0.21, G:0.23, T:0.41
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:43116 original size:21 final size:21
Alignment explanation
Indices: 43090--43145 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
43080 ATAGTCAGTA
43090 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
43111 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
*
43132 TCACATTGCGATTT
1 TCGCATTGCGATTT
43146 ACTTATTCGT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.23, C:0.23, G:0.14, T:0.39
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:43204 original size:21 final size:22
Alignment explanation
Indices: 43156--43204 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
43146 ACTTATTCGT
43156 ATTGC-AAATTGGGAAAATCGC
1 ATTGCGAAATTGGGAAAATCGC
**
43177 AACGCGAAATT-GGAAAATCGC
1 ATTGCGAAATTGGGAAAATCGC
43198 ATTGCGA
1 ATTGCGA
43205 TAGTCATAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 18 0.78
22 5 0.22
ACGTcount: A:0.39, C:0.16, G:0.24, T:0.20
Consensus pattern (22 bp):
ATTGCGAAATTGGGAAAATCGC
Found at i:48097 original size:20 final size:21
Alignment explanation
Indices: 48072--48113 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
48062 TGTCTGACTG
*
48072 AGATTATATTAATA-ATTTAA
1 AGATTAAATTAATATATTTAA
*
48092 AGATTAAATTAGTATATTTAA
1 AGATTAAATTAATATATTTAA
48113 A
1 A
48114 ACCTATAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (21 bp):
AGATTAAATTAATATATTTAA
Found at i:59575 original size:22 final size:20
Alignment explanation
Indices: 59536--59576 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
59526 CTTGATAAAA
*
59536 ATTCAACTCGGGTTGACTCG
1 ATTCAACTCGGCTTGACTCG
59556 ATTCGAACTCGAGCTTGACTC
1 ATTC-AACTCG-GCTTGACTC
59577 AAGACCTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 6 0.33
22 8 0.44
ACGTcount: A:0.22, C:0.27, G:0.22, T:0.29
Consensus pattern (20 bp):
ATTCAACTCGGCTTGACTCG
Found at i:59758 original size:44 final size:44
Alignment explanation
Indices: 59703--59786 Score: 125
Period size: 44 Copynumber: 1.9 Consensus size: 44
59693 AAATAATTAC
59703 TAATTTACTAATAGATAATAAAAAATGA-TAAATTACTAATCTAT
1 TAATTTACTAATAGATAATAAAAAAT-ATTAAATTACTAATCTAT
* * *
59747 TAATTTTCTAATAGATAATTAAATATATTAAATTACTAAT
1 TAATTTACTAATAGATAATAAAAAATATTAAATTACTAAT
59787 TAATCATTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
43 1 0.03
44 35 0.97
ACGTcount: A:0.50, C:0.06, G:0.04, T:0.40
Consensus pattern (44 bp):
TAATTTACTAATAGATAATAAAAAATATTAAATTACTAATCTAT
Found at i:60066 original size:27 final size:28
Alignment explanation
Indices: 60036--60088 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
60026 ACAACAAATT
*
60036 TTTTTAACAAG-AACAAGTCGAGCAAAA
1 TTTTTAACAAGCAACAAGTCAAGCAAAA
* *
60063 TTTTTAACTAGCAACGAGTCAAGCAA
1 TTTTTAACAAGCAACAAGTCAAGCAA
60089 CAAATTATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 10 0.45
28 12 0.55
ACGTcount: A:0.43, C:0.17, G:0.15, T:0.25
Consensus pattern (28 bp):
TTTTTAACAAGCAACAAGTCAAGCAAAA
Found at i:60839 original size:6 final size:6
Alignment explanation
Indices: 60828--60855 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
60818 CTAAAATATA
60828 ATAATT ATAATT ATAATT ATAATT ATAA
1 ATAATT ATAATT ATAATT ATAATT ATAA
60856 AGAGTTATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (6 bp):
ATAATT
Found at i:60912 original size:2 final size:2
Alignment explanation
Indices: 60907--60936 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
60897 AATGACACAC
60907 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
60937 TAGCTTAACC
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
Found at i:64766 original size:20 final size:20
Alignment explanation
Indices: 64741--64794 Score: 83
Period size: 20 Copynumber: 2.7 Consensus size: 20
64731 GACCAACAAA
64741 TTCGCAACGCGAATTCCAAT
1 TTCGCAACGCGAATTCCAAT
*
64761 TTCGCAAC-CCAATTTCCAAT
1 TTCGCAACGCGAA-TTCCAAT
64781 TTCGCAACGCGAAT
1 TTCGCAACGCGAAT
64795 ATGTAAATCG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 3 0.10
20 24 0.80
21 3 0.10
ACGTcount: A:0.30, C:0.31, G:0.13, T:0.26
Consensus pattern (20 bp):
TTCGCAACGCGAATTCCAAT
Found at i:64841 original size:20 final size:20
Alignment explanation
Indices: 64818--64929 Score: 91
Period size: 20 Copynumber: 5.2 Consensus size: 20
64808 TACGATTTTC
*
64818 CAAATTCGTAACGCGAAAGT
1 CAAATTCGCAACGCGAAAGT
* *
64838 CAAATTCACAATGCGAAAGT
1 CAAATTCGCAACGCGAAAGT
* *
64858 CAAATTTGTAAATCACAACAC-AGAAGT
1 CAAA----T---TCGCAACGCGA-AAGT
*
64885 CAAATTCGCAACGCGATAGT
1 CAAATTCGCAACGCGAAAGT
64905 CAAATTCGCAACGCGAAAGT
1 CAAATTCGCAACGCGAAAGT
64925 CAAAT
1 CAAAT
64930 GTTTTTACGC
Statistics
Matches: 74, Mismatches: 9, Indels: 18
0.73 0.09 0.18
Matches are distributed among these distances:
20 55 0.74
21 1 0.01
23 1 0.01
24 1 0.01
26 1 0.01
27 15 0.20
ACGTcount: A:0.43, C:0.21, G:0.16, T:0.20
Consensus pattern (20 bp):
CAAATTCGCAACGCGAAAGT
Found at i:65082 original size:22 final size:22
Alignment explanation
Indices: 65057--65107 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
65047 CTACGGCGAC
*
65057 ATCCGTCCCCATCTCCGACGAA
1 ATCCGTCCCCATCTCCGACAAA
*
65079 ATCCGTCCCCATTTCCGACAAA
1 ATCCGTCCCCATCTCCGACAAA
65101 ATCCGTC
1 ATCCGTC
65108 TATCTCCATC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.24, C:0.43, G:0.12, T:0.22
Consensus pattern (22 bp):
ATCCGTCCCCATCTCCGACAAA
Found at i:67593 original size:42 final size:42
Alignment explanation
Indices: 67546--67668 Score: 140
Period size: 42 Copynumber: 2.9 Consensus size: 42
67536 GCCTAATGCA
* * *
67546 CCTATCATCATTCAAGAGGCGCCTCCTACCGTTCAAGAGGCC
1 CCTATCATCATTCAAGAAGCCCCTCCCACCGTTCAAGAGGCC
67588 CCTATCATCA-TCGAAGAAGCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCATTC-AAGAAGCCCCTCCCACCGTTCAAGAGGCC
* * ** * * *
67630 CCTGTCATCGTTCAAGTGGTCCCGCCCGCCGTTCAAGAG
1 CCTATCATCATTCAAGAAGCCCCTCCCACCGTTCAAGAG
67669 CCTGATTCAT
Statistics
Matches: 69, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
41 2 0.03
42 65 0.94
43 2 0.03
ACGTcount: A:0.22, C:0.37, G:0.20, T:0.20
Consensus pattern (42 bp):
CCTATCATCATTCAAGAAGCCCCTCCCACCGTTCAAGAGGCC
Found at i:67625 original size:21 final size:21
Alignment explanation
Indices: 67556--67668 Score: 84
Period size: 21 Copynumber: 5.4 Consensus size: 21
67546 CCTATCATCA
* *
67556 TTCAAGAGGCGCCTCCTACCG
1 TTCAAGAGGCCCCTCCCACCG
** *
67577 TTCAAGAGGCCCCTATCATC-
1 TTCAAGAGGCCCCTCCCACCG
* *
67597 ATCGAAGAAGCCCCTCCCACCG
1 TTC-AAGAGGCCCCTCCCACCG
** *
67619 TTCAAGAGGCCCCTGTCATCG
1 TTCAAGAGGCCCCTCCCACCG
* * * *
67640 TTCAAGTGGTCCCGCCCGCCG
1 TTCAAGAGGCCCCTCCCACCG
67661 TTCAAGAG
1 TTCAAGAG
67669 CCTGATTCAT
Statistics
Matches: 67, Mismatches: 23, Indels: 4
0.71 0.24 0.04
Matches are distributed among these distances:
20 2 0.03
21 63 0.94
22 2 0.03
ACGTcount: A:0.21, C:0.37, G:0.22, T:0.19
Consensus pattern (21 bp):
TTCAAGAGGCCCCTCCCACCG
Found at i:69078 original size:47 final size:51
Alignment explanation
Indices: 69027--69130 Score: 126
Period size: 52 Copynumber: 2.1 Consensus size: 51
69017 TTTGTTCCAA
69027 TTGATGAGGAAATAAG-A-T-TTATTTT-TTGATTAATTGATTTGTAAAAG
1 TTGATGAGGAAATAAGAATTATTATTTTCTTGATTAATTGATTTGTAAAAG
** * * *
69074 TTGATTTGTAAATAAGAATTATTTTTTTGCTTGTTTAATTGATTTGTAAAAG
1 TTGATGAGGAAATAAGAATTATTATTTT-CTTGATTAATTGATTTGTAAAAG
69126 TTGAT
1 TTGAT
69131 TTGTTGTTTC
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
47 13 0.28
48 1 0.02
49 1 0.02
50 6 0.13
52 26 0.55
ACGTcount: A:0.33, C:0.01, G:0.17, T:0.49
Consensus pattern (51 bp):
TTGATGAGGAAATAAGAATTATTATTTTCTTGATTAATTGATTTGTAAAAG
Found at i:69220 original size:20 final size:20
Alignment explanation
Indices: 69194--69261 Score: 102
Period size: 20 Copynumber: 3.4 Consensus size: 20
69184 GTTGAAGGTA
69194 CAAATTCGCAACGCGAAAGT
1 CAAATTCGCAACGCGAAAGT
* *
69214 TAAATTCGCAACGCAAAAGT
1 CAAATTCGCAACGCGAAAGT
69234 CAAATAT-GCAACGCGAAAGT
1 CAAAT-TCGCAACGCGAAAGT
69254 CAAATTCG
1 CAAATTCG
69262 TAACACAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
19 1 0.02
20 40 0.95
21 1 0.02
ACGTcount: A:0.43, C:0.22, G:0.18, T:0.18
Consensus pattern (20 bp):
CAAATTCGCAACGCGAAAGT
Found at i:69330 original size:34 final size:34
Alignment explanation
Indices: 69292--69365 Score: 107
Period size: 34 Copynumber: 2.2 Consensus size: 34
69282 GATAATCAAA
69292 TTCGCAACGCA-ATTTTCG-GTTTGCGAATTTGACT
1 TTCGCAACGCATA-TTTCGTG-TTGCGAATTTGACT
*
69326 TTCGCAACGCTTATTTCGTGTTGCGAATTTGACT
1 TTCGCAACGCATATTTCGTGTTGCGAATTTGACT
69360 TTCGCA
1 TTCGCA
69366 TTGATCGCAA
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
34 35 0.95
35 2 0.05
ACGTcount: A:0.19, C:0.22, G:0.20, T:0.39
Consensus pattern (34 bp):
TTCGCAACGCATATTTCGTGTTGCGAATTTGACT
Found at i:69596 original size:39 final size:39
Alignment explanation
Indices: 69542--69628 Score: 165
Period size: 39 Copynumber: 2.2 Consensus size: 39
69532 TCAAGTTGTA
69542 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
*
69581 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGCTTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
69620 GATTTTGAT
1 GATTTTGAT
69629 GAGCATCGGA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 47 1.00
ACGTcount: A:0.17, C:0.15, G:0.21, T:0.47
Consensus pattern (39 bp):
GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
Found at i:70393 original size:25 final size:25
Alignment explanation
Indices: 70346--70395 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
70336 ATTATTTTTC
* * *
70346 CAAATAATGTACGCATAACAATGTT
1 CAAATAATATACCCACAACAATGTT
*
70371 CAAATAATATACCCACAATAATGTT
1 CAAATAATATACCCACAACAATGTT
70396 TAATTGATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.46, C:0.18, G:0.08, T:0.28
Consensus pattern (25 bp):
CAAATAATATACCCACAACAATGTT
Found at i:70509 original size:20 final size:20
Alignment explanation
Indices: 70486--70547 Score: 97
Period size: 20 Copynumber: 3.1 Consensus size: 20
70476 AATAAGCGTT
70486 GCGATAGTCAAATTCGCAAC
1 GCGATAGTCAAATTCGCAAC
* * *
70506 GCGAAAGTTAAATTCGCTAC
1 GCGATAGTCAAATTCGCAAC
70526 GCGATAGTCAAATTCGCAAC
1 GCGATAGTCAAATTCGCAAC
70546 GC
1 GC
70548 TTATTTCGCG
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.34, C:0.24, G:0.21, T:0.21
Consensus pattern (20 bp):
GCGATAGTCAAATTCGCAAC
Found at i:70577 original size:34 final size:34
Alignment explanation
Indices: 70539--70644 Score: 167
Period size: 34 Copynumber: 3.1 Consensus size: 34
70529 ATAGTCAAAT
* *
70539 TCGCAACGCTTATTTCGCGTTTCAAATTTGACTA
1 TCGCAACGCTTATTTCGCGTTGCGAATTTGACTA
*
70573 TCGCAACGCTTATTTCACGTTGCGAATTTGACTA
1 TCGCAACGCTTATTTCGCGTTGCGAATTTGACTA
* *
70607 CCGCAACGCTTATTTCGCGTTGCGAATTTGACTT
1 TCGCAACGCTTATTTCGCGTTGCGAATTTGACTA
70641 TCGC
1 TCGC
70645 GTTGATCGCA
Statistics
Matches: 65, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 65 1.00
ACGTcount: A:0.21, C:0.25, G:0.18, T:0.36
Consensus pattern (34 bp):
TCGCAACGCTTATTTCGCGTTGCGAATTTGACTA
Found at i:73223 original size:24 final size:24
Alignment explanation
Indices: 73196--73245 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
73186 CCATCACATC
*
73196 ATCAAAATCCGAGTATTGATCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
73220 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
73244 AT
1 AT
73246 TAAATTTCGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.38, C:0.18, G:0.20, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:74181 original size:19 final size:19
Alignment explanation
Indices: 74154--74204 Score: 93
Period size: 19 Copynumber: 2.7 Consensus size: 19
74144 ACTAAAACTT
*
74154 GTTGTGAATTTGAAATTCA
1 GTTGCGAATTTGAAATTCA
74173 GTTGCGAATTTGAAATTCA
1 GTTGCGAATTTGAAATTCA
74192 GTTGCGAATTTGA
1 GTTGCGAATTTGA
74205 CTTTCGTGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.29, C:0.08, G:0.24, T:0.39
Consensus pattern (19 bp):
GTTGCGAATTTGAAATTCA
Found at i:74240 original size:20 final size:20
Alignment explanation
Indices: 74193--74243 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
74183 TGAAATTCAG
* **
74193 TTGCGAATTTGACTTTCGTG
1 TTGCGAATTTGACTATCGCA
*
74213 TTGAGAATTTGACTATCGCA
1 TTGCGAATTTGACTATCGCA
74233 TTGCGAATTTG
1 TTGCGAATTTG
74244 GAACGCGAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.22, C:0.14, G:0.24, T:0.41
Consensus pattern (20 bp):
TTGCGAATTTGACTATCGCA
Found at i:74253 original size:13 final size:13
Alignment explanation
Indices: 74235--74259 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
74225 CTATCGCATT
74235 GCGAATTTGGAAC
1 GCGAATTTGGAAC
74248 GCGAATTTGGAA
1 GCGAATTTGGAA
74260 AAACGCAACG
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:0.32, C:0.12, G:0.32, T:0.24
Consensus pattern (13 bp):
GCGAATTTGGAAC
Found at i:74275 original size:21 final size:21
Alignment explanation
Indices: 74245--74288 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
74235 GCGAATTTGG
* *
74245 AACGCGAATTTGGAAAAACGC
1 AACGCAAATTTAGAAAAACGC
*
74266 AACGCAAATTTAGAAAATCGC
1 AACGCAAATTTAGAAAAACGC
74287 AA
1 AA
74289 TGTGATTTAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.48, C:0.18, G:0.18, T:0.16
Consensus pattern (21 bp):
AACGCAAATTTAGAAAAACGC
Found at i:74350 original size:20 final size:19
Alignment explanation
Indices: 74303--74373 Score: 81
Period size: 20 Copynumber: 3.6 Consensus size: 19
74293 ATTTACATAT
74303 TCGCGTTGCGAAATTGGAA
1 TCGCGTTGCGAAATTGGAA
* *
74322 ACTGAGTTGCGAAATTGGAA
1 TC-GCGTTGCGAAATTGGAA
*
74342 TTCGCGTTGCG-AATTTGAGA
1 -TCGCGTTGCGAAATTGGA-A
74362 TCGCGTTGCGAA
1 TCGCGTTGCGAA
74374 TTTGTTGGTC
Statistics
Matches: 43, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
19 17 0.40
20 25 0.58
21 1 0.02
ACGTcount: A:0.25, C:0.15, G:0.31, T:0.28
Consensus pattern (19 bp):
TCGCGTTGCGAAATTGGAA
Found at i:87910 original size:27 final size:27
Alignment explanation
Indices: 87840--87912 Score: 78
Period size: 27 Copynumber: 2.7 Consensus size: 27
87830 TCCAAATCAT
87840 AAGGGTA-TTTGAGTCATTTTAGTACTC
1 AAGGGTATTTTG-GTCATTTTAGTACTC
* * **
87867 AATGTTATTTTATTCATTTTAG-AGCTC
1 AAGGGTATTTTGGTCATTTTAGTA-CTC
87894 AAGGGTATTTTGGTCATTT
1 AAGGGTATTTTGGTCATTT
87913 CATTTGGTCT
Statistics
Matches: 36, Mismatches: 8, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
26 1 0.03
27 32 0.89
28 3 0.08
ACGTcount: A:0.25, C:0.10, G:0.19, T:0.47
Consensus pattern (27 bp):
AAGGGTATTTTGGTCATTTTAGTACTC
Found at i:89621 original size:20 final size:20
Alignment explanation
Indices: 89598--89641 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
89588 AGTAGTATTA
* * *
89598 ATACCTAGAGGTTAGTATCG
1 ATACCCAGAGGTCAGTACCG
*
89618 ATACCCATAGGTCAGTACCG
1 ATACCCAGAGGTCAGTACCG
89638 ATAC
1 ATAC
89642 TGATGGGCTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.25
Consensus pattern (20 bp):
ATACCCAGAGGTCAGTACCG
Found at i:93533 original size:21 final size:21
Alignment explanation
Indices: 93509--93553 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
93499 AAATGATGTA
*
93509 AAATATGCTAAAAATAAAT-CT
1 AAATATGATAAAAA-AAATGCT
*
93530 AAATATGATTAAAAAAATGCT
1 AAATATGATAAAAAAAATGCT
93551 AAA
1 AAA
93554 GTATAAGCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.60, C:0.07, G:0.07, T:0.27
Consensus pattern (21 bp):
AAATATGATAAAAAAAATGCT
Found at i:94398 original size:17 final size:17
Alignment explanation
Indices: 94376--94408 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
94366 TTTGCTTATC
94376 TAAATGTCATGGAAAGA
1 TAAATGTCATGGAAAGA
*
94393 TAAATGTCATGTAAAG
1 TAAATGTCATGGAAAG
94409 TTAGAATAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.06, G:0.21, T:0.27
Consensus pattern (17 bp):
TAAATGTCATGGAAAGA
Found at i:96987 original size:20 final size:20
Alignment explanation
Indices: 96962--96999 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
96952 GTTGTTGAGA
96962 CTTATGGTATCGATACTAAG
1 CTTATGGTATCGATACTAAG
96982 CTTATGGTATCGATACTA
1 CTTATGGTATCGATACTA
97000 CTATGTGAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.37
Consensus pattern (20 bp):
CTTATGGTATCGATACTAAG
Found at i:101150 original size:9 final size:9
Alignment explanation
Indices: 101120--101200 Score: 63
Period size: 10 Copynumber: 8.3 Consensus size: 9
101110 GGGTCAGTCG
*
101120 GGTCAAACT
1 GGTCAAACC
*
101129 GGTTCATACC
1 GG-TCAAACC
101139 GGTCAAACC
1 GGTCAAACC
*
101148 GGTTCGAACC
1 GG-TCAAACC
*
101158 AGTCGAAACC
1 GGTC-AAACC
101168 GGTCAGAACC
1 GGTCA-AACC
*
101178 GGTTGAAAACC
1 GG-T-CAAACC
101189 GGTCAAACC
1 GGTCAAACC
101198 GGT
1 GGT
101201 TTCCAGCCCT
Statistics
Matches: 57, Mismatches: 9, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
9 21 0.37
10 28 0.49
11 7 0.12
12 1 0.02
ACGTcount: A:0.30, C:0.27, G:0.26, T:0.17
Consensus pattern (9 bp):
GGTCAAACC
Found at i:101198 original size:20 final size:21
Alignment explanation
Indices: 101163--101201 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
101153 GAACCAGTCG
101163 AAACCGGTCAGAACCGGTTGA
1 AAACCGGTCAGAACCGGTTGA
101184 AAACCGGTCA-AACCGGTT
1 AAACCGGTCAGAACCGGTT
101202 TCCAGCCCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.33, C:0.26, G:0.26, T:0.15
Consensus pattern (21 bp):
AAACCGGTCAGAACCGGTTGA
Found at i:107664 original size:19 final size:19
Alignment explanation
Indices: 107642--107681 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
107632 CGGTCAACGA
107642 TCGGGTCAATCGGGTCAGG
1 TCGGGTCAATCGGGTCAGG
* *
107661 TCGGGTCAGTCGGGTCGGG
1 TCGGGTCAATCGGGTCAGG
107680 TC
1 TC
107682 AGACCGGTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.10, C:0.23, G:0.45, T:0.23
Consensus pattern (19 bp):
TCGGGTCAATCGGGTCAGG
Found at i:107690 original size:9 final size:9
Alignment explanation
Indices: 107678--107767 Score: 63
Period size: 9 Copynumber: 9.3 Consensus size: 9
107668 AGTCGGGTCG
*
107678 GGTCAGACC
1 GGTCAAACC
*
107687 GGTCAAACT
1 GGTCAAACC
*
107696 GGTTCATACC
1 GG-TCAAACC
107706 GGTCAAACC
1 GGTCAAACC
* *
107715 GATTCGAACC
1 G-GTCAAACC
*
107725 AGTCGAAACC
1 GGTC-AAACC
107735 GGTCAGAACC
1 GGTCA-AACC
*
107745 GGTTGGAAACC
1 GG-T-CAAACC
107756 GGTCAAACC
1 GGTCAAACC
107765 GGT
1 GGT
107768 TTCCAGCCCT
Statistics
Matches: 62, Mismatches: 13, Indels: 12
0.71 0.15 0.14
Matches are distributed among these distances:
9 27 0.44
10 27 0.44
11 7 0.11
12 1 0.02
ACGTcount: A:0.29, C:0.28, G:0.27, T:0.17
Consensus pattern (9 bp):
GGTCAAACC
Found at i:107743 original size:20 final size:21
Alignment explanation
Indices: 107720--107764 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
107710 AAACCGATTC
107720 GAACCAG-TCGAAACCGGTCA
1 GAACCAGTTCGAAACCGGTCA
* *
107740 GAACCGGTTGGAAACCGGTCA
1 GAACCAGTTCGAAACCGGTCA
107761 -AACC
1 GAACC
107765 GGTTTCCAGC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 10 0.45
21 12 0.55
ACGTcount: A:0.33, C:0.29, G:0.27, T:0.11
Consensus pattern (21 bp):
GAACCAGTTCGAAACCGGTCA
Found at i:107766 original size:20 final size:21
Alignment explanation
Indices: 107729--107768 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
107719 CGAACCAGTC
107729 GAAACCGGTCAGAACCGGTTG
1 GAAACCGGTCAGAACCGGTTG
107750 GAAACCGGTCA-AACCGGTT
1 GAAACCGGTCAGAACCGGTT
107769 TCCAGCCCTC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.30, C:0.25, G:0.30, T:0.15
Consensus pattern (21 bp):
GAAACCGGTCAGAACCGGTTG
Found at i:108787 original size:18 final size:18
Alignment explanation
Indices: 108760--108831 Score: 69
Period size: 17 Copynumber: 4.0 Consensus size: 18
108750 ATTAAATGAT
*
108760 ATAATAAATATAATAATA
1 ATAATTAATATAATAATA
*
108778 ATAATTAATA-AATATTA
1 ATAATTAATATAATAATA
*
108795 ATTATTAA-AT-ATAATAA
1 ATAATTAATATAATAAT-A
108812 ATAATTCAAATATAATAATA
1 ATAATT--AATATAATAATA
108832 TAAATATAGT
Statistics
Matches: 43, Mismatches: 5, Indels: 10
0.74 0.09 0.17
Matches are distributed among these distances:
16 5 0.12
17 19 0.44
18 9 0.21
19 2 0.05
20 3 0.07
21 5 0.12
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (18 bp):
ATAATTAATATAATAATA
Found at i:108828 original size:23 final size:22
Alignment explanation
Indices: 108758--108837 Score: 60
Period size: 23 Copynumber: 3.5 Consensus size: 22
108748 AAATTAAATG
*
108758 ATATAATAAAT-ATAATAATAATA
1 ATATAATAAATAATTA-AAT-ATA
*
108781 AT-TAATAAAT-ATTAATTATTAA
1 ATATAATAAATAATTAAATA-T-A
108803 ATATAATAAATAATTCAAATATA
1 ATATAATAAATAATT-AAATATA
108826 ATA-ATATAAATA
1 ATATA-ATAAATA
108838 TAGTAATTAA
Statistics
Matches: 48, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
20 1 0.02
21 3 0.06
22 15 0.31
23 21 0.44
24 4 0.08
25 4 0.08
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (22 bp):
ATATAATAAATAATTAAATATA
Found at i:108830 original size:14 final size:13
Alignment explanation
Indices: 108749--108878 Score: 62
Period size: 14 Copynumber: 9.8 Consensus size: 13
108739 GAAACGTATA
108749 AATTAAATGAT-AT
1 AATTAAAT-ATAAT
108762 AA-TAAATATAAT
1 AATTAAATATAAT
*
108774 AA-T-AATA-ATT
1 AATTAAATATAAT
108784 AA-TAAATATTAAT
1 AATTAAATA-TAAT
*
108797 TATTAAATATAATAAAT
1 AATT-AA-AT-AT-AAT
108814 AATTCAAATATAAT
1 AATT-AAATATAAT
*
108828 AATATAAATATAGT
1 AAT-TAAATATAAT
108842 AATTAAA-ATAGAT
1 AATTAAATATA-AT
*
108855 ATTTTAAA-A-AAT
1 A-ATTAAATATAAT
108867 AATTATAATATA
1 AATTA-AATATA
108879 TTTTGTAAAT
Statistics
Matches: 93, Mismatches: 9, Indels: 29
0.71 0.07 0.22
Matches are distributed among these distances:
10 5 0.05
11 13 0.14
12 18 0.19
13 13 0.14
14 25 0.27
15 5 0.05
16 5 0.05
17 9 0.10
ACGTcount: A:0.59, C:0.01, G:0.02, T:0.38
Consensus pattern (13 bp):
AATTAAATATAAT
Found at i:108942 original size:20 final size:20
Alignment explanation
Indices: 108919--108959 Score: 66
Period size: 19 Copynumber: 2.0 Consensus size: 20
108909 TACGTGTAAA
108919 TAATAAATATAATTA-ATAAT
1 TAAT-AATATAATTATATAAT
108939 TAATAATATAATTATATAAT
1 TAATAATATAATTATATAAT
108959 T
1 T
108960 TTGAAATTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
TAATAATATAATTATATAAT
Found at i:114798 original size:25 final size:24
Alignment explanation
Indices: 114770--114841 Score: 99
Period size: 24 Copynumber: 3.0 Consensus size: 24
114760 TAACAAACTT
* *
114770 GAAAAGGAGAGGGGCTGAAACAGTG
1 GAAAAGGA-AGGAGCAGAAACAGTG
*
114795 GAAAAGGAAGGATCAGAAACAGTG
1 GAAAAGGAAGGAGCAGAAACAGTG
*
114819 GAAAAGGAAGGATCAGAAACAGT
1 GAAAAGGAAGGAGCAGAAACAGT
114842 TTCCAAATAC
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
24 36 0.82
25 8 0.18
ACGTcount: A:0.47, C:0.08, G:0.36, T:0.08
Consensus pattern (24 bp):
GAAAAGGAAGGAGCAGAAACAGTG
Found at i:114817 original size:24 final size:24
Alignment explanation
Indices: 114786--114841 Score: 112
Period size: 24 Copynumber: 2.3 Consensus size: 24
114776 GAGAGGGGCT
114786 GAAACAGTGGAAAAGGAAGGATCA
1 GAAACAGTGGAAAAGGAAGGATCA
114810 GAAACAGTGGAAAAGGAAGGATCA
1 GAAACAGTGGAAAAGGAAGGATCA
114834 GAAACAGT
1 GAAACAGT
114842 TTCCAAATAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.50, C:0.09, G:0.32, T:0.09
Consensus pattern (24 bp):
GAAACAGTGGAAAAGGAAGGATCA
Found at i:115039 original size:23 final size:23
Alignment explanation
Indices: 115013--115060 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
115003 ATAAAGTACA
*
115013 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
115036 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
115059 AT
1 AT
115061 TTACCTATTT
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:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:115830 original size:23 final size:23
Alignment explanation
Indices: 115800--115860 Score: 81
Period size: 21 Copynumber: 2.7 Consensus size: 23
115790 CAATAGCCAC
115800 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
115823 TACCTATTACA-T-TATAAGCGC
1 TACCTATTACATTATATAAACGA
*
115844 TACCTATTACATCATAT
1 TACCTATTACATTATAT
115861 GTTTACCTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
21 18 0.55
22 1 0.03
23 14 0.42
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.36
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:116316 original size:39 final size:39
Alignment explanation
Indices: 116262--116344 Score: 148
Period size: 39 Copynumber: 2.1 Consensus size: 39
116252 GTTGTAGATA
*
116262 TTGATTTCCTTTTGCTTGGCATCATATGAGATTTGGATT
1 TTGATTTCCTTTTGCTTGGCACCATATGAGATTTGGATT
*
116301 TTGATTTCCTTTTGCTTGGCACCATATGAGCTTTGGATT
1 TTGATTTCCTTTTGCTTGGCACCATATGAGATTTGGATT
116340 TTGAT
1 TTGAT
116345 GAGCATCGGA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.17, C:0.14, G:0.20, T:0.48
Consensus pattern (39 bp):
TTGATTTCCTTTTGCTTGGCACCATATGAGATTTGGATT
Found at i:116623 original size:18 final size:18
Alignment explanation
Indices: 116600--116636 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
116590 CGAAATATAT
116600 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
116618 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
116636 A
1 A
116637 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:117055 original size:25 final size:25
Alignment explanation
Indices: 117021--117071 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
117011 TTTTTCCAAA
*
117021 TAATGTACCCATAACAATGTTCAAT
1 TAATGTACCCACAACAATGTTCAAT
*
117046 TAATGTACCCACAACAATGTTTAAT
1 TAATGTACCCACAACAATGTTCAAT
117071 T
1 T
117072 GATTTGTTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.39, C:0.20, G:0.08, T:0.33
Consensus pattern (25 bp):
TAATGTACCCACAACAATGTTCAAT
Found at i:117359 original size:21 final size:22
Alignment explanation
Indices: 117334--117385 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
117324 ACACTTTACA
*
117334 ATATAACCACTACCTATTACATT
1 ATATAAACA-TACCTATTACATT
117357 ATATAAACGATACCTATTACATT
1 ATATAAAC-ATACCTATTACATT
117380 ATATAA
1 ATATAA
117386 GGGCTACCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (22 bp):
ATATAAACATACCTATTACATT
Found at i:117370 original size:23 final size:23
Alignment explanation
Indices: 117344--117406 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
117334 ATATAACCAC
117344 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
117367 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
117390 TACCTATTACATCATAT
1 TACCTATTACATTATAT
117407 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Done.