Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000002.1 Kokia drynarioides strain JFW-HI SEQ_130364, 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: 318400
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 9 characters in sequence are not A, C, G, or T
Found at i:48 original size:18 final size:18
Alignment explanation
Indices: 25--61 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
15 ACAATTCATA
25 TCACTTTCAATTCCAATT
1 TCACTTTCAATTCCAATT
* *
43 TCACTTTCACTTTCAATT
1 TCACTTTCAATTCCAATT
61 T
1 T
62 TGATCACAAA
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:0.24, C:0.27, G:0.00, T:0.49
Consensus pattern (18 bp):
TCACTTTCAATTCCAATT
Found at i:4792 original size:19 final size:20
Alignment explanation
Indices: 4763--4800 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
4753 TATCAATACT
4763 TTTCTTAAGGTATCGATATA
1 TTTCTTAAGGTATCGATATA
4783 TTTC-TAAGGTATCGATAT
1 TTTCTTAAGGTATCGATAT
4801 TTCTAATCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.29, C:0.11, G:0.16, T:0.45
Consensus pattern (20 bp):
TTTCTTAAGGTATCGATATA
Found at i:4802 original size:17 final size:18
Alignment explanation
Indices: 4763--4806 Score: 63
Period size: 17 Copynumber: 2.4 Consensus size: 18
4753 TATCAATACT
4763 TTTCTTAAGGTATCGATATA
1 TTTC-TAAGGTATCGA-ATA
4783 TTTCTAAGGTATCG-ATA
1 TTTCTAAGGTATCGAATA
4800 TTTCTAA
1 TTTCTAA
4807 TCCAACAGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 10 0.42
19 10 0.42
20 4 0.17
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.45
Consensus pattern (18 bp):
TTTCTAAGGTATCGAATA
Found at i:10133 original size:40 final size:40
Alignment explanation
Indices: 10078--10262 Score: 239
Period size: 40 Copynumber: 4.6 Consensus size: 40
10068 ACGCATATAG
* *
10078 TTCAGGCTACGGCCTAGCAGGTTTTGAGCCGTTGATG-TGA
1 TTCAGGCTACGGCCTAGCAGGCTTTGAGCCGGTGA-GATGA
**
10118 TTCAGGCTACGGCCTAGCAGGCTTTGAGCTAGTGAGATGA
1 TTCAGGCTACGGCCTAGCAGGCTTTGAGCCGGTGAGATGA
* * *
10158 TTCAAGCTACGACCTAGCAGGCTTTAAGCCGGTGATG-TGA
1 TTCAGGCTACGGCCTAGCAGGCTTTGAGCCGGTGA-GATGA
*
10198 TTCAGGCTACGGCCTAGCAGGCTTTGAGCTGGTGAGATGA
1 TTCAGGCTACGGCCTAGCAGGCTTTGAGCCGGTGAGATGA
* * *
10238 TTCAGGTTACGGCATAGTAGGCTTT
1 TTCAGGCTACGGCCTAGCAGGCTTT
10263 AGTTGGTGTT
Statistics
Matches: 126, Mismatches: 16, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
39 2 0.02
40 123 0.98
41 1 0.01
ACGTcount: A:0.21, C:0.20, G:0.31, T:0.28
Consensus pattern (40 bp):
TTCAGGCTACGGCCTAGCAGGCTTTGAGCCGGTGAGATGA
Found at i:10260 original size:80 final size:80
Alignment explanation
Indices: 10078--10263 Score: 291
Period size: 80 Copynumber: 2.3 Consensus size: 80
10068 ACGCATATAG
* * *
10078 TTCAGGCTACGGCCTAGCAGGTTTTGAGCCGTTGATGTGATTCAGGCTACGGCCTAGCAGGCTTT
1 TTCAGGCTACGGCCTAGCAGGCTTTAAGCCGGTGATGTGATTCAGGCTACGGCCTAGCAGGCTTT
10143 GAGCTAGTGAGATGA
66 GAGCTAGTGAGATGA
* *
10158 TTCAAGCTACGACCTAGCAGGCTTTAAGCCGGTGATGTGATTCAGGCTACGGCCTAGCAGGCTTT
1 TTCAGGCTACGGCCTAGCAGGCTTTAAGCCGGTGATGTGATTCAGGCTACGGCCTAGCAGGCTTT
*
10223 GAGCTGGTGAGATGA
66 GAGCTAGTGAGATGA
* * *
10238 TTCAGGTTACGGCATAGTAGGCTTTA
1 TTCAGGCTACGGCCTAGCAGGCTTTA
10264 GTTGGTGTTT
Statistics
Matches: 95, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
80 95 1.00
ACGTcount: A:0.22, C:0.20, G:0.31, T:0.27
Consensus pattern (80 bp):
TTCAGGCTACGGCCTAGCAGGCTTTAAGCCGGTGATGTGATTCAGGCTACGGCCTAGCAGGCTTT
GAGCTAGTGAGATGA
Found at i:15494 original size:26 final size:26
Alignment explanation
Indices: 15470--15552 Score: 121
Period size: 26 Copynumber: 3.2 Consensus size: 26
15460 GACCCTAGTT
*
15470 CAGTATATCGCTCTTACGAGTTAGTA
1 CAGTATATCGCTCTTACGAGTCAGTA
* * *
15496 CAATATATCGCTCTTACGAGCCAGTT
1 CAGTATATCGCTCTTACGAGTCAGTA
*
15522 CAGTATATCGCTCTTATGAGTCAGTA
1 CAGTATATCGCTCTTACGAGTCAGTA
15548 CAGTA
1 CAGTA
15553 ATTTCTTCAG
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 49 1.00
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.33
Consensus pattern (26 bp):
CAGTATATCGCTCTTACGAGTCAGTA
Found at i:22146 original size:26 final size:26
Alignment explanation
Indices: 22092--22189 Score: 133
Period size: 26 Copynumber: 3.7 Consensus size: 26
22082 TAGTAATTTA
* * *
22092 GCTCATACGAGCCCAATTCAGTATATC
1 GCTCTTACGAG-CCAGTACAGTATATC
22119 GCTCTTACGAGCCAGTACAGTATATC
1 GCTCTTACGAGCCAGTACAGTATATC
* *
22145 GCTCTTACGAGCCAGTTCATTATATC
1 GCTCTTACGAGCCAGTACAGTATATC
*
22171 ACTCTTACGAGCCAGTACA
1 GCTCTTACGAGCCAGTACA
22190 ATAATTTCTT
Statistics
Matches: 64, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
26 54 0.84
27 10 0.16
ACGTcount: A:0.28, C:0.29, G:0.16, T:0.28
Consensus pattern (26 bp):
GCTCTTACGAGCCAGTACAGTATATC
Found at i:27016 original size:26 final size:26
Alignment explanation
Indices: 26987--27058 Score: 92
Period size: 26 Copynumber: 2.8 Consensus size: 26
26977 GACAACTCCA
*
26987 GACATGTTCATGCAGCGATAATTTTG
1 GACATGTTCATGCAGCGACAATTTTG
*
27013 GACAAGTTTC-TGCAGCGACAATTTTG
1 GACATG-TTCATGCAGCGACAATTTTG
* *
27039 GACATGCTCATGCTGCGACA
1 GACATGTTCATGCAGCGACA
27059 TTAGTACTAA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
25 2 0.05
26 34 0.87
27 3 0.08
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.29
Consensus pattern (26 bp):
GACATGTTCATGCAGCGACAATTTTG
Found at i:28136 original size:17 final size:18
Alignment explanation
Indices: 28108--28175 Score: 61
Period size: 17 Copynumber: 3.9 Consensus size: 18
28098 TAACAAATGG
*
28108 AAATGTAATGACAATGCA
1 AAATGCAATGACAATGCA
* *
28126 AAA-GCAGTGACAAT-TA
1 AAATGCAATGACAATGCA
*
28142 AAATGTAATGACAATGC-
1 AAATGCAATGACAATGCA
**
28159 AAATGTGATGACAATGC
1 AAATGCAATGACAATGC
28176 TTACTAACAG
Statistics
Matches: 41, Mismatches: 7, Indels: 5
0.77 0.13 0.09
Matches are distributed among these distances:
16 4 0.10
17 34 0.83
18 3 0.07
ACGTcount: A:0.47, C:0.12, G:0.19, T:0.22
Consensus pattern (18 bp):
AAATGCAATGACAATGCA
Found at i:34745 original size:21 final size:21
Alignment explanation
Indices: 34690--34746 Score: 53
Period size: 21 Copynumber: 2.7 Consensus size: 21
34680 GCACTGCAGA
* * *
34690 TTGTTGTGGCTACATCTGATT
1 TTGTTGTGGATGCATCTGACT
* *
34711 TTGATGT-GACTGCATCTGGCT
1 TTGTTGTGGA-TGCATCTGACT
34732 TTGTTGTGGATGCAT
1 TTGTTGTGGATGCAT
34747 TTGAATCTGT
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
20 1 0.04
21 25 0.89
22 2 0.07
ACGTcount: A:0.14, C:0.14, G:0.28, T:0.44
Consensus pattern (21 bp):
TTGTTGTGGATGCATCTGACT
Found at i:37050 original size:26 final size:26
Alignment explanation
Indices: 37012--37086 Score: 62
Period size: 26 Copynumber: 2.9 Consensus size: 26
37002 TCATATAACG
* *
37012 ACAACTCTGGACATGTTCATGCAACA
1 ACAATTCTAGACATGTTCATGCAACA
* * * *
37038 ATAATTCTAGACAAGTTTC-TGTAGCA
1 ACAATTCTAGACATG-TTCATGCAACA
* *
37064 ACAATTCTGGACATGCTCATGCA
1 ACAATTCTAGACATGTTCATGCA
37087 GCGACATTAG
Statistics
Matches: 36, Mismatches: 11, Indels: 4
0.71 0.22 0.08
Matches are distributed among these distances:
25 2 0.06
26 31 0.86
27 3 0.08
ACGTcount: A:0.33, C:0.23, G:0.16, T:0.28
Consensus pattern (26 bp):
ACAATTCTAGACATGTTCATGCAACA
Found at i:41832 original size:26 final size:26
Alignment explanation
Indices: 41792--41867 Score: 116
Period size: 26 Copynumber: 2.9 Consensus size: 26
41782 TGAGAGCAAT
*
41792 TCTGGACATGCTCATACAGCGACAAC
1 TCTGGACATGCTCATGCAGCGACAAC
* * *
41818 TCTGGACATGTTCATGCAGCGATAAT
1 TCTGGACATGCTCATGCAGCGACAAC
41844 TCTGGACATGCTCATGCAGCGACA
1 TCTGGACATGCTCATGCAGCGACA
41868 TTAGTAGTAA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 44 1.00
ACGTcount: A:0.28, C:0.26, G:0.22, T:0.24
Consensus pattern (26 bp):
TCTGGACATGCTCATGCAGCGACAAC
Found at i:44066 original size:13 final size:13
Alignment explanation
Indices: 44048--44077 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
44038 CCCAACTATT
44048 TTTTATTATTTTA
1 TTTTATTATTTTA
*
44061 TTTTATTTTTTTA
1 TTTTATTATTTTA
44074 TTTT
1 TTTT
44078 TTTACATTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (13 bp):
TTTTATTATTTTA
Found at i:47343 original size:16 final size:16
Alignment explanation
Indices: 47322--47372 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
47312 GTGAATCTAG
47322 TTATTTTATTTTATTT
1 TTATTTTATTTTATTT
*
47338 TTATTTTTTCTTCTATTT
1 TTATTTTAT-TT-TATTT
*
47356 TT-TTTCATTATTATTT
1 TTATTTTATT-TTATTT
47372 T
1 T
47373 GTTTCTTTCT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
16 15 0.52
17 7 0.24
18 7 0.24
ACGTcount: A:0.16, C:0.06, G:0.00, T:0.78
Consensus pattern (16 bp):
TTATTTTATTTTATTT
Found at i:47457 original size:20 final size:19
Alignment explanation
Indices: 47434--47563 Score: 72
Period size: 20 Copynumber: 6.6 Consensus size: 19
47424 AATTTTTTCG
47434 TTTTTATTTTCATTTTCATT
1 TTTTTATTTTCATTTT-ATT
*
47454 TTTTTATTTTTATTTTATT
1 TTTTTATTTTCATTTTATT
* *
47473 TATTTTATTATGCATTGTATT
1 T-TTTTATT-TTCATTTTATT
*
47494 TTATTGT-TTTGTCA-GTTATT
1 TT-TT-TATTT-TCATTTTATT
*
47514 TTTCTATTTT--TTTTATCT
1 TTTTTATTTTCATTTTAT-T
* *
47532 CTTTATATTTTTA-TTTATT
1 -TTTTTATTTTCATTTTATT
47551 TATGTTTATTTTC
1 T-T-TTTATTTTC
47564 TTATTAGTTT
Statistics
Matches: 85, Mismatches: 12, Indels: 26
0.69 0.10 0.21
Matches are distributed among these distances:
17 4 0.05
18 4 0.05
19 19 0.22
20 42 0.49
21 15 0.18
22 1 0.01
ACGTcount: A:0.17, C:0.06, G:0.05, T:0.72
Consensus pattern (19 bp):
TTTTTATTTTCATTTTATT
Found at i:47463 original size:26 final size:25
Alignment explanation
Indices: 47425--47473 Score: 71
Period size: 26 Copynumber: 1.9 Consensus size: 25
47415 TATTTTATTA
*
47425 ATTTTTTCGTTTTTATTTTCATTTTC
1 ATTTTTTCATTTTTATTTT-ATTTTC
*
47451 ATTTTTTTATTTTTATTTTATTT
1 ATTTTTTCATTTTTATTTTATTT
47474 ATTTTATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 4 0.19
26 17 0.81
ACGTcount: A:0.14, C:0.06, G:0.02, T:0.78
Consensus pattern (25 bp):
ATTTTTTCATTTTTATTTTATTTTC
Found at i:47464 original size:15 final size:15
Alignment explanation
Indices: 47435--47478 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
47425 ATTTTTTCGT
*
47435 TTTTATTTTCATTTTCA
1 TTTTA-TTT-ATTTTTA
47452 TTTT-TTTATTTTTA
1 TTTTATTTATTTTTA
47466 TTTTATTTATTTT
1 TTTTATTTATTTT
47479 ATTATGCATT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
14 10 0.40
15 11 0.44
17 4 0.16
ACGTcount: A:0.16, C:0.05, G:0.00, T:0.80
Consensus pattern (15 bp):
TTTTATTTATTTTTA
Found at i:50503 original size:22 final size:23
Alignment explanation
Indices: 50458--50517 Score: 70
Period size: 22 Copynumber: 2.7 Consensus size: 23
50448 AATAAAATCA
*
50458 TATTTATATTTAAAACTTATATT
1 TATTTATATTTAAAACTTAGATT
* *
50481 TATTTA-ATTTAAAATTTGGATT
1 TATTTATATTTAAAACTTAGATT
50503 T-TTATATATTTAAAA
1 TATT-TATATTTAAAA
50518 AAATTGGATT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
21 2 0.06
22 16 0.50
23 14 0.44
ACGTcount: A:0.40, C:0.02, G:0.03, T:0.55
Consensus pattern (23 bp):
TATTTATATTTAAAACTTAGATT
Found at i:50541 original size:26 final size:25
Alignment explanation
Indices: 50491--50537 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
50481 TATTTAATTT
*
50491 AAAATTTGGATTTTTATATATTTAA
1 AAAAATTGGATTTTTATATATTTAA
50516 AAAAATTGGATTTTTATA-ATTT
1 AAAAATTGGATTTTTATATATTT
50538 TTAATTTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 4 0.19
25 17 0.81
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (25 bp):
AAAAATTGGATTTTTATATATTTAA
Found at i:51204 original size:39 final size:42
Alignment explanation
Indices: 51141--51239 Score: 100
Period size: 40 Copynumber: 2.5 Consensus size: 42
51131 ATTTTAAAAA
* * *
51141 ATATATATTTATATTATTTTAA-TTTAATATTTAATGATTTT
1 ATATATTTTTATATTATTTAAATTTTAATATTTAATGATCTT
* * *
51182 ATATATTTTTAT-TTA-TTAAATTTTTATATTTACTTATCTT
1 ATATATTTTTATATTATTTAAATTTTAATATTTAATGATCTT
*
51222 A-ATATTTTT-TAATATTTA
1 ATATATTTTTATATTATTTA
51240 TATTATAGTA
Statistics
Matches: 48, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
38 1 0.02
39 14 0.29
40 22 0.46
41 11 0.23
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.63
Consensus pattern (42 bp):
ATATATTTTTATATTATTTAAATTTTAATATTTAATGATCTT
Found at i:51578 original size:89 final size:88
Alignment explanation
Indices: 51462--51647 Score: 223
Period size: 89 Copynumber: 2.1 Consensus size: 88
51452 TTAAAGGTGT
* * * *
51462 AAAAAG-CCCTTAAACTTTTTCAAAAAAAGCAATTAAACCCCTCCTTTTTTTTTTACACTC-TTT
1 AAAAAGACCCTCAAAC-CTTTCCAAAAAAGCAATTAAACCCCTAC-TTTTTTTTTACACTCATTT
* *
51525 TAGGTATTTGAACTTTTAAAATGCATA
64 T--GTACTTAAACTTTTAAAATGCATA
* *
51552 AAAAAGACCCTCAAACCTTTCCAAAAAAGCAATTAAGCCTCTACTTTTTTTTTACACTCAATTTT
1 AAAAAGACCCTCAAACCTTTCCAAAAAAGCAATTAAACCCCTACTTTTTTTTTACACTC-ATTTT
* *
51617 GTACTTAAACTTTTAAACTGCATT
65 GTACTTAAACTTTTAAAATGCATA
51641 AAAAAGA
1 AAAAAGA
51648 TTCTCAGACT
Statistics
Matches: 83, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
89 42 0.51
90 29 0.35
91 12 0.14
ACGTcount: A:0.38, C:0.20, G:0.06, T:0.36
Consensus pattern (88 bp):
AAAAAGACCCTCAAACCTTTCCAAAAAAGCAATTAAACCCCTACTTTTTTTTTACACTCATTTTG
TACTTAAACTTTTAAAATGCATA
Found at i:51778 original size:17 final size:16
Alignment explanation
Indices: 51756--51792 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
51746 AAATTTTAAT
*
51756 AAAAAATTCAAATATTA
1 AAAAAATT-AAAAATTA
51773 AAAAAATTAAAAATTA
1 AAAAAATTAAAAATTA
51789 AAAA
1 AAAA
51793 TTAGAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.24
Consensus pattern (16 bp):
AAAAAATTAAAAATTA
Found at i:51793 original size:25 final size:25
Alignment explanation
Indices: 51753--51830 Score: 81
Period size: 24 Copynumber: 3.1 Consensus size: 25
51743 ATTAAATTTT
*
51753 AATA-AAAAATTCAAATATTAAAAA
1 AATATAAAAATTAAAATATTAAAAA
51777 AAT-TAAAAATTAAAA-ATTAGAAAA
1 AATATAAAAATTAAAATATTA-AAAA
* *
51801 AATATAAATATTGTAAAATATTATAAA
1 AATATAAA-AAT-TAAAATATTAAAAA
51828 AAT
1 AAT
51831 CATGTAAAAT
Statistics
Matches: 45, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
23 4 0.09
24 20 0.44
25 4 0.09
26 2 0.04
27 11 0.24
28 4 0.09
ACGTcount: A:0.67, C:0.01, G:0.03, T:0.29
Consensus pattern (25 bp):
AATATAAAAATTAAAATATTAAAAA
Found at i:51808 original size:18 final size:18
Alignment explanation
Indices: 51781--51848 Score: 52
Period size: 19 Copynumber: 3.7 Consensus size: 18
51771 TAAAAAAATT
51781 AAAAAT-TAAAAATTAG-A
1 AAAAATATAAAAATT-GTA
*
51798 AAAAATATAAATATTGTA
1 AAAAATATAAAAATTGTA
*
51816 AAATATTATAAAAATCATGT-
1 AAA-AATATAAAAAT--TGTA
*
51836 AAAATTATAAAAA
1 AAAAATATAAAAA
51849 AATATAGAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
17 7 0.16
18 11 0.26
19 19 0.44
20 3 0.07
21 3 0.07
ACGTcount: A:0.65, C:0.01, G:0.04, T:0.29
Consensus pattern (18 bp):
AAAAATATAAAAATTGTA
Found at i:51819 original size:10 final size:10
Alignment explanation
Indices: 51806--51886 Score: 51
Period size: 10 Copynumber: 8.2 Consensus size: 10
51796 GAAAAAATAT
*
51806 AAATATTGTA
1 AAATATTATA
51816 AAATATTATA
1 AAATATTATA
* *
51826 AAA-ATCATGT
1 AAATATTAT-A
51836 AAA-ATTATA
1 AAATATTATA
* *
51845 AAAAAATATA
1 AAATATTATA
* *
51855 GAAATA-CAAA
1 -AAATATTATA
51865 AAATATTATA
1 AAATATTATA
*
51875 AAATTTTATA
1 AAATATTATA
51885 AA
1 AA
51887 GTCCTAAGAA
Statistics
Matches: 55, Mismatches: 12, Indels: 8
0.73 0.16 0.11
Matches are distributed among these distances:
9 12 0.22
10 39 0.71
11 4 0.07
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (10 bp):
AAATATTATA
Found at i:51849 original size:21 final size:21
Alignment explanation
Indices: 51812--51851 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
51802 ATATAAATAT
*
51812 TGTAAAATATTATAAAAATCA
1 TGTAAAATATTAAAAAAATCA
51833 TGTAAAAT-TATAAAAAAAT
1 TGTAAAATAT-TAAAAAAAT
51852 ATAGAAATAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.60, C:0.03, G:0.05, T:0.33
Consensus pattern (21 bp):
TGTAAAATATTAAAAAAATCA
Found at i:52238 original size:20 final size:21
Alignment explanation
Indices: 52215--52293 Score: 60
Period size: 20 Copynumber: 4.0 Consensus size: 21
52205 TTAATAAATT
52215 TTAAATTTTTTAT-ATTTTTA
1 TTAAATTTTTTATAATTTTTA
* * *
52235 TTAAA-ATTTAATAATTTTTC
1 TTAAATTTTTTATAATTTTTA
* *
52255 TAAAATTTATTAT--TTTTTA
1 TTAAATTTTTTATAATTTTTA
* *
52274 -TAATTTTTTTCTAATTTTTA
1 TTAAATTTTTTATAATTTTTA
52294 ATACGAGCAA
Statistics
Matches: 43, Mismatches: 12, Indels: 8
0.68 0.19 0.13
Matches are distributed among these distances:
18 8 0.19
19 10 0.23
20 21 0.49
21 4 0.09
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (21 bp):
TTAAATTTTTTATAATTTTTA
Found at i:52252 original size:27 final size:26
Alignment explanation
Indices: 52192--52252 Score: 61
Period size: 27 Copynumber: 2.3 Consensus size: 26
52182 AAAAAAAATC
*
52192 TAATTTCTAATTTTTAATAAATTTTAA
1 TAATTT-TAATTTTTAATAAAATTTAA
* *
52219 -ATTTTTTATATTTTTATTAAAATTTAA
1 TA-ATTTTA-ATTTTTAATAAAATTTAA
52246 TAATTTT
1 TAATTTT
52253 TCTAAAATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
26 3 0.11
27 23 0.85
28 1 0.04
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.61
Consensus pattern (26 bp):
TAATTTTAATTTTTAATAAAATTTAA
Found at i:52271 original size:18 final size:19
Alignment explanation
Indices: 52223--52271 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
52213 TTTTAAATTT
*
52223 TTTA-TATTTTTATTAAAA
1 TTTATTATTTTTACTAAAA
*
52241 TTTAATAATTTTT-CTAAAA
1 TTT-ATTATTTTTACTAAAA
52260 TTTATTATTTTT
1 TTTATTATTTTT
52272 TATAATTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 11 0.42
19 9 0.35
20 6 0.23
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (19 bp):
TTTATTATTTTTACTAAAA
Found at i:52271 original size:19 final size:17
Alignment explanation
Indices: 52223--52272 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 17
52213 TTTTAAATTT
52223 TTTATATTTTTATTAAAA
1 TTTATATTTTT-TTAAAA
*
52241 TTTAATAATTTTTCTAAAA
1 TTT-AT-ATTTTTTTAAAA
52260 TTTATTATTTTTT
1 TTTA-TATTTTTT
52273 ATAATTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
18 10 0.37
19 11 0.41
20 6 0.22
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (17 bp):
TTTATATTTTTTTAAAA
Found at i:52419 original size:66 final size:64
Alignment explanation
Indices: 52349--52487 Score: 167
Period size: 66 Copynumber: 2.1 Consensus size: 64
52339 TTTTTCATTT
* * * *
52349 ATTTTGAAAGTTTAAGTATC-TAATTGAGTGAAAAATAAAGA-AATGG-CTTAATTGCTTTTTTG
1 ATTTTAAAAGTTTAAGTA-CGCAATTAAGTGAAAAA-AAA-ATAA-GGACTTAATT-ATTTTTTG
52411 ATGC
61 ATGC
*
52415 ATTTTAAAAGTTTAAGTACGCAATTAAGTGAAAAAAAAATAAGGACTTAATTATTTTTTTATGC
1 ATTTTAAAAGTTTAAGTACGCAATTAAGTGAAAAAAAAATAAGGACTTAATTATTTTTTGATGC
52479 ATTTTAAAA
1 ATTTTAAAA
52488 ATTAAGTGCT
Statistics
Matches: 65, Mismatches: 5, Indels: 8
0.83 0.06 0.10
Matches are distributed among these distances:
64 22 0.34
65 13 0.20
66 30 0.46
ACGTcount: A:0.41, C:0.06, G:0.14, T:0.39
Consensus pattern (64 bp):
ATTTTAAAAGTTTAAGTACGCAATTAAGTGAAAAAAAAATAAGGACTTAATTATTTTTTGATGC
Found at i:52517 original size:64 final size:65
Alignment explanation
Indices: 52370--52494 Score: 159
Period size: 64 Copynumber: 1.9 Consensus size: 65
52360 TTAAGTATCT
* * *
52370 AATTGAGTGAAAAATAAAGA-AATGG-CTTAATTGCTTTTTTGATGCATTTTAAAAGTTTAAGTA
1 AATTAAGTGAAAAA-AAA-ATAA-GGACTTAATTGATTTTTTGATGCATTTTAAAAGATTAAGTA
52433 CGC
63 CGC
*
52436 AATTAAGTGAAAAAAAAATAAGGACTTAATT-ATTTTTTTATGCATTTTAAAA-ATTAAGT
1 AATTAAGTGAAAAAAAAATAAGGACTTAATTGATTTTTTGATGCATTTTAAAAGATTAAGT
52495 GCTTAATTTA
Statistics
Matches: 53, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
63 6 0.11
64 22 0.42
65 12 0.23
66 13 0.25
ACGTcount: A:0.42, C:0.06, G:0.14, T:0.38
Consensus pattern (65 bp):
AATTAAGTGAAAAAAAAATAAGGACTTAATTGATTTTTTGATGCATTTTAAAAGATTAAGTACGC
Found at i:56900 original size:19 final size:19
Alignment explanation
Indices: 56876--56915 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
56866 TTGGTGGTAA
56876 TATTAGTCACTAATAAGTT
1 TATTAGTCACTAATAAGTT
56895 TATTAGTCACTAATAAGTT
1 TATTAGTCACTAATAAGTT
56914 TA
1 TA
56916 GTGCATATCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.42
Consensus pattern (19 bp):
TATTAGTCACTAATAAGTT
Found at i:87530 original size:2 final size:2
Alignment explanation
Indices: 87523--87547 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
87513 AGCTTTCAAT
87523 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
87548 TATATATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:92888 original size:28 final size:28
Alignment explanation
Indices: 92857--92910 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
92847 GAATGCCTTC
*
92857 ATGTGAAACCACCAAGAGAACTAACTTT
1 ATGTGAAACCACCAAGAGAACCAACTTT
92885 ATGTGAAACCACCAAGAGAACCAACT
1 ATGTGAAACCACCAAGAGAACCAACT
92911 CTAGGGTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.44, C:0.24, G:0.15, T:0.17
Consensus pattern (28 bp):
ATGTGAAACCACCAAGAGAACCAACTTT
Found at i:93316 original size:23 final size:23
Alignment explanation
Indices: 93286--93331 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
93276 CTAATCAAAG
93286 AAGTCGGGGGAGTTTGATTCATT
1 AAGTCGGGGGAGTTTGATTCATT
93309 AAGTCGGGGGAGTTTGATTCATT
1 AAGTCGGGGGAGTTTGATTCATT
93332 TTCATTCAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.22, C:0.09, G:0.35, T:0.35
Consensus pattern (23 bp):
AAGTCGGGGGAGTTTGATTCATT
Found at i:101061 original size:20 final size:21
Alignment explanation
Indices: 101025--101063 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
101015 CATTTTGTTA
*
101025 TTTACTTTTATTTGTTTCACT
1 TTTACTTTTAGTTGTTTCACT
101046 TTTACTTTT-GTTGTTTCA
1 TTTACTTTTAGTTGTTTCA
101064 AATTCCTTGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.13, C:0.13, G:0.08, T:0.67
Consensus pattern (21 bp):
TTTACTTTTAGTTGTTTCACT
Found at i:103993 original size:31 final size:30
Alignment explanation
Indices: 103958--104015 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 30
103948 AGTCACTTAG
103958 AAAAG-GAAAATGAGAAA-AAGAAAGAAAAAAT
1 AAAAGAGAAAA-GA-AAAGAAGAAA-AAAAAAT
103989 AAAAGAGAAAAGAAAAGAAGAAAAAAA
1 AAAAGAGAAAAGAAAAGAAGAAAAAAA
104016 TGTTTACTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
30 7 0.28
31 13 0.52
32 5 0.20
ACGTcount: A:0.78, C:0.00, G:0.19, T:0.03
Consensus pattern (30 bp):
AAAAGAGAAAAGAAAAGAAGAAAAAAAAAT
Found at i:103996 original size:24 final size:26
Alignment explanation
Indices: 103964--104012 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 26
103954 TTAGAAAAGG
103964 AAAATGAGAAAA-AGAAAGAA-AAAAT
1 AAAATGAGAAAAGA-AAAGAAGAAAAT
103989 AAAA-GAGAAAAGAAAAGAAGAAAA
1 AAAATGAGAAAAGAAAAGAAGAAAA
104013 AAATGTTTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 13 0.59
25 9 0.41
ACGTcount: A:0.78, C:0.00, G:0.18, T:0.04
Consensus pattern (26 bp):
AAAATGAGAAAAGAAAAGAAGAAAAT
Found at i:105758 original size:18 final size:19
Alignment explanation
Indices: 105721--105759 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
105711 TTATTGACAC
*
105721 TTTGTCTTTTCTTCTTATT
1 TTTGTCTTTACTTCTTATT
*
105740 TTTGT-TTTACTTTTTATT
1 TTTGTCTTTACTTCTTATT
105758 TT
1 TT
105760 CTTTATATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.08, C:0.10, G:0.05, T:0.77
Consensus pattern (19 bp):
TTTGTCTTTACTTCTTATT
Found at i:109080 original size:34 final size:34
Alignment explanation
Indices: 109042--109125 Score: 96
Period size: 34 Copynumber: 2.5 Consensus size: 34
109032 TGTTACAACG
*
109042 TTTGGTGTGTTAGTTGAACTAGCTCATACAAGCA
1 TTTGGTGTGTTAGATGAACTAGCTCATACAAGCA
* * * * * *
109076 TTTGGTGTGCTGGATGGATTGGCTCATACGAGCA
1 TTTGGTGTGTTAGATGAACTAGCTCATACAAGCA
*
109110 TCTGGTGTGTTAGATG
1 TTTGGTGTGTTAGATG
109126 GTTAATTGTG
Statistics
Matches: 40, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
34 40 1.00
ACGTcount: A:0.20, C:0.13, G:0.31, T:0.36
Consensus pattern (34 bp):
TTTGGTGTGTTAGATGAACTAGCTCATACAAGCA
Found at i:115789 original size:17 final size:17
Alignment explanation
Indices: 115769--115806 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
115759 AACTAGCAAG
115769 TAAAATGCAACGACAAC
1 TAAAATGCAACGACAAC
* *
115786 TAAAATGCAATGACAAT
1 TAAAATGCAACGACAAC
115803 TAAA
1 TAAA
115807 TGAGATGCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.55, C:0.16, G:0.11, T:0.18
Consensus pattern (17 bp):
TAAAATGCAACGACAAC
Found at i:119273 original size:24 final size:24
Alignment explanation
Indices: 119225--119271 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
119215 AAGAGTTGAT
*
119225 TTGTCAATGCAAATATAAAATAAA
1 TTGTCAAAGCAAATATAAAATAAA
*
119249 TTGTCAAAGCAAAT-TAAGATAAA
1 TTGTCAAAGCAAATATAAAATAAA
119272 ATGAATAGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 8 0.38
24 13 0.62
ACGTcount: A:0.53, C:0.09, G:0.11, T:0.28
Consensus pattern (24 bp):
TTGTCAAAGCAAATATAAAATAAA
Found at i:120686 original size:15 final size:15
Alignment explanation
Indices: 120656--120689 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
120646 TTTTATAATT
**
120656 AATTTTAATTTGATG
1 AATTTTAATTAAATG
120671 AATTTTAATTAAATG
1 AATTTTAATTAAATG
120686 AATT
1 AATT
120690 AAAAGTTAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (15 bp):
AATTTTAATTAAATG
Found at i:124206 original size:32 final size:32
Alignment explanation
Indices: 124142--124496 Score: 374
Period size: 32 Copynumber: 11.1 Consensus size: 32
124132 GTTGTGGGGA
* * * * *
124142 TGTTCACAAATTAATCGCTTTTACGAGAATAC
1 TGTTCACAGATTGATAGCTCTTACGAGCATAC
* * *
124174 TGTTCATAGATTGATAGCTCTTACAAGTATAC
1 TGTTCACAGATTGATAGCTCTTACGAGCATAC
*
124206 TGTTCACA-AGTTGACAGCTCTTACGAGCATAC
1 TGTTCACAGA-TTGATAGCTCTTACGAGCATAC
*
124238 TGTTCACAGATTGGTAGCTCTTACGAGCATAC
1 TGTTCACAGATTGATAGCTCTTACGAGCATAC
* * * * **
124270 TATTCATAGTTTGACAGCTCTTACGAGCATTT
1 TGTTCACAGATTGATAGCTCTTACGAGCATAC
* * *
124302 TGTTCATAGATTGACAGCTCTTACGAGCATAT
1 TGTTCACAGATTGATAGCTCTTACGAGCATAC
*
124334 TGTTCACAGATTGATAGCTCTTACGAGCATAT
1 TGTTCACAGATTGATAGCTCTTACGAGCATAC
* * * * *
124366 TGTTCACAGACTGACAGGTCTTACGA-TATAT
1 TGTTCACAGATTGATAGCTCTTACGAGCATAC
*
124397 TGTTCACAGATTGATAACTCTTACGAGCATAC
1 TGTTCACAGATTGATAGCTCTTACGAGCATAC
* * * *
124429 TATTCACAAATTGATAGCTCTTACAACCATAC
1 TGTTCACAGATTGATAGCTCTTACGAGCATAC
* * *
124461 AGTTCACAGATTGACAAG-TCCTACGAGCATAC
1 TGTTCACAGATTGA-TAGCTCTTACGAGCATAC
124493 TGTT
1 TGTT
124497 TACATGTTTA
Statistics
Matches: 271, Mismatches: 48, Indels: 8
0.83 0.15 0.02
Matches are distributed among these distances:
31 27 0.10
32 241 0.89
33 3 0.01
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.33
Consensus pattern (32 bp):
TGTTCACAGATTGATAGCTCTTACGAGCATAC
Found at i:137006 original size:32 final size:32
Alignment explanation
Indices: 136963--137441 Score: 310
Period size: 32 Copynumber: 15.0 Consensus size: 32
136953 GTTGTGGATA
* * *
136963 TGTTCACAGATTGATAGCTTTTACGAGCATAT
1 TGTTCAAAGATTGATAGCTCTTACGAGCATAC
* *
136995 TGTTCAAAGATTGATTGCT-ATACGAGCATAC
1 TGTTCAAAGATTGATAGCTCTTACGAGCATAC
* * *
137026 TGTTCATAGATTGACAGCTCTTACGAGCATAT
1 TGTTCAAAGATTGATAGCTCTTACGAGCATAC
* * ** * ** *
137058 TTTTCACAA-ACTGGCAGTTCTTATAAGCATAG
1 TGTTCA-AAGATTGATAGCTCTTACGAGCATAC
* * *
137090 TGTTTACAA-ATTGACAACTCTTACGAGCATAC
1 TGTTCA-AAGATTGATAGCTCTTACGAGCATAC
* * *
137122 TATT-AACAGATTGATAGCTCTTACGAGTATAT
1 TGTTCAA-AGATTGATAGCTCTTACGAGCATAC
* * *
137154 TGTTCACATG-TTGATAGCTTTTACGGGCATAC
1 TGTTCA-AAGATTGATAGCTCTTACGAGCATAC
* * *
137186 TATTCACAGATTGATAGCTCTTACGAGTATAC
1 TGTTCAAAGATTGATAGCTCTTACGAGCATAC
* * * * *
137218 TATTCACAGGTTGACAGCTCTTACGAGCACAC
1 TGTTCAAAGATTGATAGCTCTTACGAGCATAC
* * * ** *
137250 TGTTCATAGATTGACA--ACTTAC-AATATAT
1 TGTTCAAAGATTGATAGCTCTTACGAGCATAC
* *
137279 TGTTCATAGATTGATAGCTCTTACAAGCATAC
1 TGTTCAAAGATTGATAGCTCTTACGAGCATAC
* *
137311 TGTTCATAGATTGATAGCTCTTACAAGCATAC
1 TGTTCAAAGATTGATAGCTCTTACGAGCATAC
* ** * * *
137343 TATTCCTAGATTGACAACTCTTACAAGCATAC
1 TGTTCAAAGATTGATAGCTCTTACGAGCATAC
* * * * *
137375 TATTTACAGATTGATTAGCTCATACGAGCTTAC
1 TGTTCAAAGATTGA-TAGCTCTTACGAGCATAC
** * *
137408 TGTAT-ACTGATTGATCAACTCATACGAGCATAC
1 TGT-TCAAAGATTGAT-AGCTCTTACGAGCATAC
137441 T
1 T
137442 AGATACTGAT
Statistics
Matches: 358, Mismatches: 76, Indels: 25
0.78 0.17 0.05
Matches are distributed among these distances:
29 18 0.05
30 6 0.02
31 34 0.09
32 256 0.72
33 42 0.12
34 2 0.01
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (32 bp):
TGTTCAAAGATTGATAGCTCTTACGAGCATAC
Found at i:137144 original size:64 final size:64
Alignment explanation
Indices: 136963--137464 Score: 381
Period size: 64 Copynumber: 7.9 Consensus size: 64
136953 GTTGTGGATA
* * * * * * * *
136963 TGTTCACAGATTGATAGCTTTTACGAGCATATTGTTCAAAGATTGATTGCT-ATACGAGCATAC
1 TGTTCACAGATTGACAGCTCTTACGAGCATACTATTCACAGATTGATAGCTCTTACAAGCATAC
* * * * * ** * * *
137026 TGTTCATAGATTGACAGCTCTTACGAGCATATTTTTCACAAACTGGCAGTTCTTATAAGCATAG
1 TGTTCACAGATTGACAGCTCTTACGAGCATACTATTCACAGATTGATAGCTCTTACAAGCATAC
* * * * * * *
137090 TGTTTACAAATTGACAACTCTTACGAGCATACTATTAACAGATTGATAGCTCTTACGAGTATAT
1 TGTTCACAGATTGACAGCTCTTACGAGCATACTATTCACAGATTGATAGCTCTTACAAGCATAC
* * * * *
137154 TGTTCACATG-TTGATAGCTTTTACGGGCATACTATTCACAGATTGATAGCTCTTACGAGTATAC
1 TGTTCACA-GATTGACAGCTCTTACGAGCATACTATTCACAGATTGATAGCTCTTACAAGCATAC
* * * * * * * * *
137218 TATTCACAGGTTGACAGCTCTTACGAGCACACTGTTCATAGATTGACA--ACTTACAA-TATAT
1 TGTTCACAGATTGACAGCTCTTACGAGCATACTATTCACAGATTGATAGCTCTTACAAGCATAC
* * * * *
137279 TGTTCATAGATTGATAGCTCTTACAAGCATACTGTTCATAGATTGATAGCTCTTACAAGCATAC
1 TGTTCACAGATTGACAGCTCTTACGAGCATACTATTCACAGATTGATAGCTCTTACAAGCATAC
* * * * * * *
137343 TATTC-CTAGATTGACAACTCTTACAAGCATACTATTTACAGATTGATTAGCTCATACGAGCTTA
1 TGTTCAC-AGATTGACAGCTCTTACGAGCATACTATTCACAGATTGA-TAGCTCTTACAAGCATA
137407 C
64 C
* * * * *
137408 TGTAT-ACTGATTGATCAACTCATACGAGCATACTAGAT-ACTGATTGATTAGCTCTTA
1 TGT-TCACAGATTGA-CAGCTCTTACGAGCATACTA-TTCACAGATTGA-TAGCTCTTA
137465 TGATCATACT
Statistics
Matches: 350, Mismatches: 77, Indels: 21
0.78 0.17 0.05
Matches are distributed among these distances:
61 45 0.13
62 6 0.02
63 48 0.14
64 190 0.54
65 23 0.07
66 37 0.11
67 1 0.00
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (64 bp):
TGTTCACAGATTGACAGCTCTTACGAGCATACTATTCACAGATTGATAGCTCTTACAAGCATAC
Found at i:137330 original size:93 final size:93
Alignment explanation
Indices: 137188--137361 Score: 249
Period size: 93 Copynumber: 1.9 Consensus size: 93
137178 GGGCATACTA
* * * * *
137188 TTCACAGATTGATAGCTCTTACGAGTATACTATTCACAGGTTGACAGCTCTTACGAGCACACTGT
1 TTCACAGATTGATAGCTCTTACAAGCATACTATTCACAGATTGACAGCTCTTACAAGCACACTAT
137253 TCATAGATTGACAACTTACAATATATTG
66 TCATAGATTGACAACTTACAATATATTG
* * * * *
137281 TTCATAGATTGATAGCTCTTACAAGCATACTGTTCATAGATTGATAGCTCTTACAAGCATACTAT
1 TTCACAGATTGATAGCTCTTACAAGCATACTATTCACAGATTGACAGCTCTTACAAGCACACTAT
*
137346 TCCTAGATTGACAACT
66 TCATAGATTGACAACT
137362 CTTACAAGCA
Statistics
Matches: 70, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
93 70 1.00
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.33
Consensus pattern (93 bp):
TTCACAGATTGATAGCTCTTACAAGCATACTATTCACAGATTGACAGCTCTTACAAGCACACTAT
TCATAGATTGACAACTTACAATATATTG
Found at i:137386 original size:125 final size:127
Alignment explanation
Indices: 137076--137388 Score: 355
Period size: 125 Copynumber: 2.5 Consensus size: 127
137066 AACTGGCAGT
* * * * * * *
137076 TCTTATAAGCATAGTGTTTACAAATTGACAACTCTTACGAGCATACTATTAACAGATTGATAGCT
1 TCTTACAAGCATACTATTCACAGATTGACAACTCTTACGAGCATACTATTAACAGATTGACA-CA
* * **
137141 CTTACGAGTATATTGTTCACATGTTGATAGCTTTTACGGGCATACTATTCACAGATTGATAGC
65 CTTACGAATATATTGTTCACATGTTGATAGCTCTTACAAGCATACTATTCACAGATTGATAGC
* * * * * * * *
137204 TCTTACGAGTATACTATTCACAGGTTGACAGCTCTTACGAGCACACTGTTCATAGATTGACA-AC
1 TCTTACAAGCATACTATTCACAGATTGACAACTCTTACGAGCATACTATTAACAGATTGACACAC
* * *
137268 TTAC-AATATATTGTTCATA-GATTGATAGCTCTTACAAGCATACTGTTCATAGATTGATAGC
66 TTACGAATATATTGTTCACATG-TTGATAGCTCTTACAAGCATACTATTCACAGATTGATAGC
* *
137329 TCTTACAAGCATACTATTC-CTAGATTGACAACTCTTACAAGCATACTATTTACAGATTGA
1 TCTTACAAGCATACTATTCAC-AGATTGACAACTCTTACGAGCATACTATTAACAGATTGA
137389 TTAGCTCATA
Statistics
Matches: 152, Mismatches: 31, Indels: 7
0.80 0.16 0.04
Matches are distributed among these distances:
124 2 0.01
125 97 0.64
126 5 0.03
128 48 0.32
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.34
Consensus pattern (127 bp):
TCTTACAAGCATACTATTCACAGATTGACAACTCTTACGAGCATACTATTAACAGATTGACACAC
TTACGAATATATTGTTCACATGTTGATAGCTCTTACAAGCATACTATTCACAGATTGATAGC
Found at i:137430 original size:33 final size:33
Alignment explanation
Indices: 137351--137455 Score: 115
Period size: 33 Copynumber: 3.2 Consensus size: 33
137341 ACTATTCCTA
* * * * *
137351 GATTGA-CAACTCTTACAAGCATACTATTTACA
1 GATTGATCAACTCATACGAGCATACTGTATACT
* * *
137383 GATTGATTAGCTCATACGAGCTTACTGTATACT
1 GATTGATCAACTCATACGAGCATACTGTATACT
137416 GATTGATCAACTCATACGAGCATACTAG-ATACT
1 GATTGATCAACTCATACGAGCATACT-GTATACT
137449 GATTGAT
1 GATTGAT
137456 TAGCTCTTAT
Statistics
Matches: 60, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
32 6 0.10
33 53 0.88
34 1 0.02
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.32
Consensus pattern (33 bp):
GATTGATCAACTCATACGAGCATACTGTATACT
Found at i:137473 original size:33 final size:34
Alignment explanation
Indices: 137368--137475 Score: 123
Period size: 33 Copynumber: 3.3 Consensus size: 34
137358 AACTCTTACA
* *
137368 AGCATACTA-TTTACAGATTGATTAGCTCATACG
1 AGCATACTAGTATACTGATTGATTAGCTCATACG
* * *
137401 AGCTTACT-GTATACTGATTGATCAACTCATACG
1 AGCATACTAGTATACTGATTGATTAGCTCATACG
* *
137434 AGCATACTAG-ATACTGATTGATTAGCTCTTATG
1 AGCATACTAGTATACTGATTGATTAGCTCATACG
*
137467 ATCATACTA
1 AGCATACTA
137476 TGAAATTACA
Statistics
Matches: 62, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
33 61 0.98
34 1 0.02
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.34
Consensus pattern (34 bp):
AGCATACTAGTATACTGATTGATTAGCTCATACG
Found at i:143395 original size:24 final size:24
Alignment explanation
Indices: 143359--143404 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
143349 ACATTCATCC
* *
143359 AATTCATGCATTA-GCATTCAAAAG
1 AATTCAAGAATTACGCA-TCAAAAG
143383 AATTCAAGAATTACGCATCAAA
1 AATTCAAGAATTACGCATCAAA
143405 TGAAAAATTG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 16 0.84
25 3 0.16
ACGTcount: A:0.46, C:0.17, G:0.11, T:0.26
Consensus pattern (24 bp):
AATTCAAGAATTACGCATCAAAAG
Found at i:144070 original size:12 final size:12
Alignment explanation
Indices: 144039--144081 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
144029 CAATACTTTC
144039 TTCTTCTTCCTT
1 TTCTTCTTCCTT
* *
144051 CTCCTCTTCCTT
1 TTCTTCTTCCTT
* *
144063 TTCTTCTTTCTC
1 TTCTTCTTCCTT
144075 TTCTTCT
1 TTCTTCT
144082 CTTGCTCCTT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (12 bp):
TTCTTCTTCCTT
Found at i:170428 original size:21 final size:22
Alignment explanation
Indices: 170395--170437 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
170385 AAATGATATC
* *
170395 TAGTCCTTTAAAC-TAAGTTTT
1 TAGTCATTAAAACGTAAGTTTT
170416 TAGTCATTAAAACGTAAGTTTT
1 TAGTCATTAAAACGTAAGTTTT
170438 GAATAAAAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.44
Consensus pattern (22 bp):
TAGTCATTAAAACGTAAGTTTT
Found at i:171115 original size:23 final size:23
Alignment explanation
Indices: 171087--171552 Score: 536
Period size: 23 Copynumber: 20.7 Consensus size: 23
171077 CTTATATCTA
*
171087 TGCTTAAATATTAATGTGATTTA
1 TGCTTAAATATTAATGTGATTTG
* *
171110 TGCTTAAATATTAGTATGATTTG
1 TGCTTAAATATTAATGTGATTTG
*
171133 TGCTTAAATATTAATATGATTTG
1 TGCTTAAATATTAATGTGATTTG
* *
171156 TGCTTAAAAATTAATGTGATTTA
1 TGCTTAAATATTAATGTGATTTG
* *
171179 TGCATAAATATTAATGTAATTTG
1 TGCTTAAATATTAATGTGATTTG
*
171202 TGCTTAAATATTAATGTGATTTA
1 TGCTTAAATATTAATGTGATTTG
*
171225 TGCTTAAATATTAATATGATTTG
1 TGCTTAAATATTAATGTGATTTG
* * *
171248 TAC-TCAATACTAATGTGATTTG
1 TGCTTAAATATTAATGTGATTTG
*
171270 TGCTTAAATATTAATATGATTTG
1 TGCTTAAATATTAATGTGATTTG
* * **
171293 TGCTCAAATATTAATGCGATTCA
1 TGCTTAAATATTAATGTGATTTG
* * **
171316 TGGTTAAATATTAATGCGATTCA
1 TGCTTAAATATTAATGTGATTTG
* *
171339 TGCTTAAATATTAATGCGGTTTG
1 TGCTTAAATATTAATGTGATTTG
* *
171362 TGTTTAAATATTAATGTGA-TTA
1 TGCTTAAATATTAATGTGATTTG
*
171384 TGCTTAAATATTAATATGATTTG
1 TGCTTAAATATTAATGTGATTTG
*
171407 TGC-----T-CTAATGTGATTTG
1 TGCTTAAATATTAATGTGATTTG
*
171424 TGCTTAAATATTAATATGATTTG
1 TGCTTAAATATTAATGTGATTTG
* *
171447 TGCTCAAATA-TAATGTGATTTA
1 TGCTTAAATATTAATGTGATTTG
* * *
171469 TACATAAATATTAATGTGATTTA
1 TGCTTAAATATTAATGTGATTTG
*
171492 TGCTTAAATATTAATATGATTTG
1 TGCTTAAATATTAATGTGATTTG
* *
171515 TGCTCAAATATTAATGTGATTTA
1 TGCTTAAATATTAATGTGATTTG
171538 TGCTTAAATATTAAT
1 TGCTTAAATATTAAT
171553 AAATATTAAT
Statistics
Matches: 374, Mismatches: 60, Indels: 18
0.83 0.13 0.04
Matches are distributed among these distances:
17 14 0.04
18 1 0.00
22 55 0.15
23 304 0.81
ACGTcount: A:0.35, C:0.06, G:0.14, T:0.45
Consensus pattern (23 bp):
TGCTTAAATATTAATGTGATTTG
Found at i:171154 original size:46 final size:46
Alignment explanation
Indices: 171085--171612 Score: 543
Period size: 46 Copynumber: 11.5 Consensus size: 46
171075 TTCTTATATC
* * *
171085 TATGCTTAAATATTAATGTGATTTATGCTTAAATATTAGTATGATT
1 TATGCTTAAATATTAATGTGATTTGTGCTTAAATATTAATGTGATT
* * *
171131 TGTGCTTAAATATTAATATGATTTGTGCTTAAAAATTAATGTGATT
1 TATGCTTAAATATTAATGTGATTTGTGCTTAAATATTAATGTGATT
* *
171177 TATGCATAAATATTAATGTAATTTGTGCTTAAATATTAATGTGATT
1 TATGCTTAAATATTAATGTGATTTGTGCTTAAATATTAATGTGATT
* * * *
171223 TATGCTTAAATATTAATATGATTTGTAC-TCAATACTAATGTGATT
1 TATGCTTAAATATTAATGTGATTTGTGCTTAAATATTAATGTGATT
* * * *
171268 TGTGCTTAAATATTAATATGATTTGTGCTCAAATATTAATGCGATT
1 TATGCTTAAATATTAATGTGATTTGTGCTTAAATATTAATGTGATT
* * * ** * *
171314 CATGGTTAAATATTAATGCGATTCATGCTTAAATATTAATGCGGTT
1 TATGCTTAAATATTAATGTGATTTGTGCTTAAATATTAATGTGATT
* * * *
171360 TGTGTTTAAATATTAATGTGA-TTATGCTTAAATATTAATATGATT
1 TATGCTTAAATATTAATGTGATTTGTGCTTAAATATTAATGTGATT
* * *
171405 TGTGC-----T-CTAATGTGATTTGTGCTTAAATATTAATATGATT
1 TATGCTTAAATATTAATGTGATTTGTGCTTAAATATTAATGTGATT
* * * * *
171445 TGTGCTCAAATA-TAATGTGATTTATACATAAATATTAATGTGATT
1 TATGCTTAAATATTAATGTGATTTGTGCTTAAATATTAATGTGATT
* *
171490 TATGCTTAAATATTAATATGATTTGTGCTCAAATATTAATGTGATT
1 TATGCTTAAATATTAATGTGATTTGTGCTTAAATATTAATGTGATT
*
171536 TATGCTTAAATATTAATAAATATTAATGTGATTTGTGCTTAAATATTAATATGATT
1 TATGC--------T--TAAATATTAATGTGATTTGTGCTTAAATATTAATGTGATT
**
171592 TATTATTAAATATTAATGTGA
1 TATGCTTAAATATTAATGTGA
171613 AATTGTGAAA
Statistics
Matches: 404, Mismatches: 59, Indels: 38
0.81 0.12 0.08
Matches are distributed among these distances:
39 8 0.02
40 29 0.07
45 105 0.26
46 220 0.54
48 1 0.00
54 1 0.00
56 40 0.10
ACGTcount: A:0.35, C:0.06, G:0.14, T:0.45
Consensus pattern (46 bp):
TATGCTTAAATATTAATGTGATTTGTGCTTAAATATTAATGTGATT
Found at i:171326 original size:114 final size:115
Alignment explanation
Indices: 171085--171552 Score: 587
Period size: 114 Copynumber: 4.1 Consensus size: 115
171075 TTCTTATATC
* * * *
171085 TATGCTTAAATATTAATGTGATTTATGCTTAAATATTAGTATGATTTGTGCTTAAATATTAATAT
1 TATGCTTAAATATTAATGTGATTTATGCTTAAATATTAATATGATTTGTACATAAATATTAATGT
* * * * *
171150 GATTTGTGCTTAAAAATTAATGTGATTTATGCAT-AAATATTAATGTAATT
66 GATTTATGCTTAAATATTAATATGATTTGTGC-TCAAATATTAATGTGATT
* * *
171200 TGTGCTTAAATATTAATGTGATTTATGCTTAAATATTAATATGATTTGTAC-TCAATACTAATGT
1 TATGCTTAAATATTAATGTGATTTATGCTTAAATATTAATATGATTTGTACATAAATATTAATGT
* *
171264 GATTTGTGCTTAAATATTAATATGATTTGTGCTCAAATATTAATGCGATT
66 GATTTATGCTTAAATATTAATATGATTTGTGCTCAAATATTAATGTGATT
* * * * ** * ***
171314 CATGGTTAAATATTAATGCGATTCATGCTTAAATATTAATGCGGTTTGTGTTTAAATATTAATGT
1 TATGCTTAAATATTAATGTGATTTATGCTTAAATATTAATATGATTTGTACATAAATATTAATGT
171379 GA-TTATGCTTAAATATTAATATGATTTGTGCTC------TAATGTGATT
66 GATTTATGCTTAAATATTAATATGATTTGTGCTCAAATATTAATGTGATT
* * * * * *
171422 TGTGCTTAAATATTAATATGATTTGTGCTCAAATA-TAATGTGATTTATACATAAATATTAATGT
1 TATGCTTAAATATTAATGTGATTTATGCTTAAATATTAATATGATTTGTACATAAATATTAATGT
171486 GATTTATGCTTAAATATTAATATGATTTGTGCTCAAATATTAATGTGATT
66 GATTTATGCTTAAATATTAATATGATTTGTGCTCAAATATTAATGTGATT
171536 TATGCTTAAATATTAAT
1 TATGCTTAAATATTAAT
171553 AAATATTAAT
Statistics
Matches: 304, Mismatches: 40, Indels: 19
0.84 0.11 0.05
Matches are distributed among these distances:
107 25 0.08
108 67 0.22
113 1 0.00
114 150 0.49
115 61 0.20
ACGTcount: A:0.35, C:0.06, G:0.14, T:0.45
Consensus pattern (115 bp):
TATGCTTAAATATTAATGTGATTTATGCTTAAATATTAATATGATTTGTACATAAATATTAATGT
GATTTATGCTTAAATATTAATATGATTTGTGCTCAAATATTAATGTGATT
Found at i:171420 original size:17 final size:17
Alignment explanation
Indices: 171395--171427 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
171385 GCTTAAATAT
171395 TAATATGATTTGTGCTC
1 TAATATGATTTGTGCTC
*
171412 TAATGTGATTTGTGCT
1 TAATATGATTTGTGCT
171428 TAAATATTAA
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:0.21, C:0.09, G:0.21, T:0.48
Consensus pattern (17 bp):
TAATATGATTTGTGCTC
Found at i:171433 original size:40 final size:39
Alignment explanation
Indices: 171373--171451 Score: 140
Period size: 40 Copynumber: 2.0 Consensus size: 39
171363 GTTTAAATAT
171373 TAATGTGATTATGCTTAAATATTAATATGATTTGTGCTC
1 TAATGTGATTATGCTTAAATATTAATATGATTTGTGCTC
*
171412 TAATGTGATTTGTGCTTAAATATTAATATGATTTGTGCTC
1 TAATGTGA-TTATGCTTAAATATTAATATGATTTGTGCTC
171452 AAATATAATG
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
39 8 0.21
40 30 0.79
ACGTcount: A:0.29, C:0.08, G:0.16, T:0.47
Consensus pattern (39 bp):
TAATGTGATTATGCTTAAATATTAATATGATTTGTGCTC
Found at i:171434 original size:85 final size:85
Alignment explanation
Indices: 171339--171495 Score: 217
Period size: 85 Copynumber: 1.8 Consensus size: 85
171329 ATGCGATTCA
* * * * * *
171339 TGCTTAAATATTAATGCGGTTTGTGTTTAAATATTAATGTGA-TTATGCTTAAATATTAATATGA
1 TGCTTAAATATTAATACGATTTGTGCTCAAATA-TAATGTGATTTATACATAAATATTAATATGA
*
171403 TTTGTGCTCTAATGTGATTTG
65 TTTATGCTCTAATGTGATTTG
* *
171424 TGCTTAAATATTAATATGATTTGTGCTCAAATATAATGTGATTTATACATAAATATTAATGTGAT
1 TGCTTAAATATTAATACGATTTGTGCTCAAATATAATGTGATTTATACATAAATATTAATATGAT
171489 TTATGCT
66 TTATGCT
171496 TAAATATTAA
Statistics
Matches: 62, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
84 8 0.13
85 54 0.87
ACGTcount: A:0.32, C:0.06, G:0.15, T:0.46
Consensus pattern (85 bp):
TGCTTAAATATTAATACGATTTGTGCTCAAATATAATGTGATTTATACATAAATATTAATATGAT
TTATGCTCTAATGTGATTTG
Found at i:171559 original size:33 final size:33
Alignment explanation
Indices: 171520--171586 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
171510 ATTTGTGCTC
171520 AAATATTAATGTGATTTATGCTTAAATATTAAT
1 AAATATTAATGTGATTTATGCTTAAATATTAAT
*
171553 AAATATTAATGTGATTTGTGCTTAAATATTAAT
1 AAATATTAATGTGATTTATGCTTAAATATTAAT
171586 A
1 A
171587 TGATTTATTA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.42, C:0.03, G:0.10, T:0.45
Consensus pattern (33 bp):
AAATATTAATGTGATTTATGCTTAAATATTAAT
Found at i:171581 original size:23 final size:23
Alignment explanation
Indices: 171552--171612 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
171542 TAAATATTAA
* *
171552 TAAATATTAATGTGATTTGTGCT
1 TAAATATTAATGTGATTTATGAT
* *
171575 TAAATATTAATATGATTTATTAT
1 TAAATATTAATGTGATTTATGAT
171598 TAAATATTAATGTGA
1 TAAATATTAATGTGA
171613 AATTGTGAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.39, C:0.02, G:0.11, T:0.48
Consensus pattern (23 bp):
TAAATATTAATGTGATTTATGAT
Found at i:171582 original size:56 final size:56
Alignment explanation
Indices: 171496--171608 Score: 181
Period size: 56 Copynumber: 2.0 Consensus size: 56
171486 GATTTATGCT
* *
171496 TAAATATTAATATGATTTGTGCTCAAATATTAATGTGATTTATGCTTAAATATTAA
1 TAAATATTAATATGATTTGTGCTCAAATATTAATATGATTTATGATTAAATATTAA
* * *
171552 TAAATATTAATGTGATTTGTGCTTAAATATTAATATGATTTATTATTAAATATTAA
1 TAAATATTAATATGATTTGTGCTCAAATATTAATATGATTTATGATTAAATATTAA
171608 T
1 T
171609 GTGAAATTGT
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
56 52 1.00
ACGTcount: A:0.40, C:0.04, G:0.10, T:0.47
Consensus pattern (56 bp):
TAAATATTAATATGATTTGTGCTCAAATATTAATATGATTTATGATTAAATATTAA
Found at i:171716 original size:36 final size:36
Alignment explanation
Indices: 171668--171771 Score: 120
Period size: 36 Copynumber: 2.9 Consensus size: 36
171658 GACTGTTGTG
*
171668 AATATGTAGGTATATTCTTCATGCTATGTGACAGAA
1 AATATGTGGGTATATTCTTCATGCTATGTGACAGAA
* * *
171704 AATATGTGGGTATGA-TCTTCATGCCATATAACAGAA
1 AATATGTGGGTAT-ATTCTTCATGCTATGTGACAGAA
* * * *
171740 CATATGTGAGTATGTTTTTCATGCTATGTGAC
1 AATATGTGGGTATATTCTTCATGCTATGTGAC
171772 TGATTATATT
Statistics
Matches: 55, Mismatches: 11, Indels: 4
0.79 0.16 0.06
Matches are distributed among these distances:
36 54 0.98
37 1 0.02
ACGTcount: A:0.31, C:0.12, G:0.20, T:0.37
Consensus pattern (36 bp):
AATATGTGGGTATATTCTTCATGCTATGTGACAGAA
Found at i:173491 original size:21 final size:20
Alignment explanation
Indices: 173465--173533 Score: 52
Period size: 21 Copynumber: 3.2 Consensus size: 20
173455 ATGTTTAATG
173465 TTATATTCAATTTTTTATATA
1 TTATATTCAATTTTTT-TATA
*
173486 TTATA-TCTATTTAATTTTATA
1 TTATATTCAATTT--TTTTATA
173507 -TATATTCTAAATATTTTTTTATA
1 TTATATTC---A-ATTTTTTTATA
173530 TTAT
1 TTAT
173534 CATATATATA
Statistics
Matches: 38, Mismatches: 2, Indels: 13
0.72 0.04 0.25
Matches are distributed among these distances:
20 10 0.26
21 11 0.29
22 3 0.08
23 7 0.18
24 3 0.08
25 4 0.11
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.62
Consensus pattern (20 bp):
TTATATTCAATTTTTTTATA
Found at i:173521 original size:25 final size:25
Alignment explanation
Indices: 173467--173548 Score: 69
Period size: 25 Copynumber: 3.2 Consensus size: 25
173457 GTTTAATGTT
* * *
173467 ATATTCAATTTTTTATATATTATAT
1 ATATTTAATTTTATATATATTATAA
* *
173492 CTATTTAATTTTATATATATTCTAA
1 ATATTTAATTTTATATATATTATAA
*
173517 ATATTT--TTTTATATTATCATATATAT
1 ATATTTAATTTTATA-TAT-AT-TATAA
173543 ATATTT
1 ATATTT
173549 TGAATATATT
Statistics
Matches: 46, Mismatches: 8, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
23 7 0.15
24 3 0.07
25 27 0.59
26 9 0.20
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (25 bp):
ATATTTAATTTTATATATATTATAA
Found at i:177446 original size:84 final size:85
Alignment explanation
Indices: 177319--177485 Score: 293
Period size: 84 Copynumber: 2.0 Consensus size: 85
177309 ATTTCTGCTA
177319 TTTGAGCTTAGGTTCAACACAAGCTCAACGAATGCAAACCAGCTGACATCAATATCTAGTGATGT
1 TTTGAGCTTAGGTT-AACACAAGCTCAACGAATGCAAACCAGCTGACATCAATATCTAGTGATGT
177384 ATACTCATCATGGTTTTTCGG
65 ATACTCATCATGGTTTTTCGG
*
177405 TTTGAGCTTAGG-T-ACACAAGCTCCACGACATGCAAACCAGCTGACATCAATATCTAGTGATGT
1 TTTGAGCTTAGGTTAACACAAGCTCAACGA-ATGCAAACCAGCTGACATCAATATCTAGTGATGT
177468 ATACTCATCATGGTTTTT
65 ATACTCATCATGGTTTTT
177486 AGGCAATGGG
Statistics
Matches: 79, Mismatches: 1, Indels: 4
0.94 0.01 0.05
Matches are distributed among these distances:
83 14 0.18
84 52 0.66
85 1 0.01
86 12 0.15
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.31
Consensus pattern (85 bp):
TTTGAGCTTAGGTTAACACAAGCTCAACGAATGCAAACCAGCTGACATCAATATCTAGTGATGTA
TACTCATCATGGTTTTTCGG
Found at i:182817 original size:17 final size:17
Alignment explanation
Indices: 182775--182817 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
182765 AAAAGAACTA
*
182775 ACAAGTAAAATGCAACG
1 ACAACTAAAATGCAACG
* *
182792 ATAACTAAAATGCAATG
1 ACAACTAAAATGCAACG
*
182809 ACAATTAAA
1 ACAACTAAA
182818 TGAGATGCAT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.56, C:0.14, G:0.12, T:0.19
Consensus pattern (17 bp):
ACAACTAAAATGCAACG
Found at i:201711 original size:35 final size:35
Alignment explanation
Indices: 201657--201767 Score: 118
Period size: 35 Copynumber: 3.2 Consensus size: 35
201647 TATTGACTGT
* *
201657 TCCTTCGAGGCGAA-TCCATGTAAACGGTATATAGG
1 TCCTTCGAGGC-AACACCATGTAAATGGTATATAGG
** * *
201692 TCCTTCTG-GGTGACACCATGTAAATAGTATATAGC
1 TCCTTC-GAGGCAACACCATGTAAATGGTATATAGG
* *
201727 TCTTTCGAGGCAACACCATGTAAATGATATATAGG
1 TCCTTCGAGGCAACACCATGTAAATGGTATATAGG
201762 TCCTTC
1 TCCTTC
201768 AGGATAATAC
Statistics
Matches: 60, Mismatches: 13, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
34 2 0.03
35 57 0.95
36 1 0.02
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.30
Consensus pattern (35 bp):
TCCTTCGAGGCAACACCATGTAAATGGTATATAGG
Found at i:204530 original size:17 final size:17
Alignment explanation
Indices: 204504--204536 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
204494 TAACAAATGG
204504 AAATGCAATGACAATTA
1 AAATGCAATGACAATTA
*
204521 AAATGTAATGACAATT
1 AAATGCAATGACAATT
204537 GGGATGTGAT
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:0.52, C:0.09, G:0.12, T:0.27
Consensus pattern (17 bp):
AAATGCAATGACAATTA
Found at i:205948 original size:104 final size:103
Alignment explanation
Indices: 205768--205974 Score: 378
Period size: 104 Copynumber: 2.0 Consensus size: 103
205758 AGAGGGATTA
205768 ACAAATGAATCGAAGCATATTATTCCTAGGCTACTAGAATTCTCCCATAACCACTCCTCTTACGT
1 ACAAATGAATCGAAGCATATTATTCCTAGGCTACTAGAATTCTCCCATAACCACTCCTCTTACGT
205833 CGCACCAAGCACTTCTCGTCAGAAGCTGTTGTGCCCTTG
66 CGCACCAAGCAC-TCTCGTCAGAAGCTGTTGTGCCCTTG
* * *
205872 ACAAATGAATCGAAGCATATTATTCCTAGGCTACTAGAATTCTCCCTTAACCACTCCTTTTGCGT
1 ACAAATGAATCGAAGCATATTATTCCTAGGCTACTAGAATTCTCCCATAACCACTCCTCTTACGT
205937 CGCACCAAGCACTCTCGTCAGAAGCTGTTGTGCCCTTG
66 CGCACCAAGCACTCTCGTCAGAAGCTGTTGTGCCCTTG
205975 CTAGATCAGA
Statistics
Matches: 100, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
103 26 0.26
104 74 0.74
ACGTcount: A:0.26, C:0.29, G:0.16, T:0.29
Consensus pattern (103 bp):
ACAAATGAATCGAAGCATATTATTCCTAGGCTACTAGAATTCTCCCATAACCACTCCTCTTACGT
CGCACCAAGCACTCTCGTCAGAAGCTGTTGTGCCCTTG
Found at i:207298 original size:24 final size:24
Alignment explanation
Indices: 207262--207307 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
207252 ACATTCATTC
* *
207262 AATTCATGCATTA-GCATTCAAAAG
1 AATTCAAGAATTATGCA-TCAAAAG
207286 AATTCAAGAATTATGCATCAAA
1 AATTCAAGAATTATGCATCAAA
207308 TGAAAAATTG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 16 0.84
25 3 0.16
ACGTcount: A:0.46, C:0.15, G:0.11, T:0.28
Consensus pattern (24 bp):
AATTCAAGAATTATGCATCAAAAG
Found at i:207965 original size:12 final size:12
Alignment explanation
Indices: 207948--207978 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
207938 AATACTTTGT
207948 TCTTCTTCCTTC
1 TCTTCTTCCTTC
*
207960 TCTTCTTCCTTT
1 TCTTCTTCCTTC
207972 TCTTCTT
1 TCTTCTT
207979 TCTCTTCTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (12 bp):
TCTTCTTCCTTC
Found at i:217114 original size:18 final size:18
Alignment explanation
Indices: 217091--217125 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
217081 ATACATAAGA
217091 TTGCGTCAACATCTTTGG
1 TTGCGTCAACATCTTTGG
*
217109 TTGCGTCAACATTTTTG
1 TTGCGTCAACATCTTTG
217126 AAGGTCGGAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.20, G:0.20, T:0.43
Consensus pattern (18 bp):
TTGCGTCAACATCTTTGG
Found at i:217614 original size:21 final size:20
Alignment explanation
Indices: 217565--217614 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
217555 GCATTACAAA
217565 TTGTTGTGACTACATTAGAT
1 TTGTTGTGACTACATTAGAT
* * *
217585 TCTGATGTGACTGCATCTAGCT
1 T-TGTTGTGACTACAT-TAGAT
217607 TTGTTGTG
1 TTGTTGTG
217615 GATACATCTA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
20 1 0.04
21 18 0.75
22 5 0.21
ACGTcount: A:0.18, C:0.14, G:0.24, T:0.44
Consensus pattern (20 bp):
TTGTTGTGACTACATTAGAT
Found at i:231084 original size:15 final size:14
Alignment explanation
Indices: 231059--231109 Score: 54
Period size: 14 Copynumber: 3.7 Consensus size: 14
231049 TATGGGTGTT
231059 GAAAA-AGAAGAAG
1 GAAAAGAGAAGAAG
231072 AGAAAAGAGAAGAAG
1 -GAAAAGAGAAGAAG
*
231087 GAAGAGAAGAA-AAG
1 GAAAAG-AGAAGAAG
231101 GAAAA-AGAA
1 GAAAAGAGAA
231110 AATGAAGAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
12 4 0.12
14 17 0.52
15 12 0.36
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (14 bp):
GAAAAGAGAAGAAG
Found at i:231118 original size:21 final size:21
Alignment explanation
Indices: 231059--231118 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 21
231049 TATGGGTGTT
231059 GAAAAAGAAGAAG-AGAAAAGA
1 GAAAAAGAA-AAGAAGAAAAGA
* *
231080 GAAGAAGGAAGAGAAGAAAAG-
1 GAA-AAAGAAAAGAAGAAAAGA
231101 GAAAAAGAAAATGAAGAA
1 GAAAAAGAAAA-GAAGAA
231119 GATTTTGTGT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
20 6 0.19
21 14 0.44
22 12 0.38
ACGTcount: A:0.68, C:0.00, G:0.30, T:0.02
Consensus pattern (21 bp):
GAAAAAGAAAAGAAGAAAAGA
Found at i:237971 original size:29 final size:30
Alignment explanation
Indices: 237911--237971 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 30
237901 ACTAACTAAA
237911 TTAATTAACCTAAAAATATACTAATGAAAT
1 TTAATTAACCTAAAAATATACTAATGAAAT
* * *
237941 TTAATTAACCT-AAGATATCCTAATGGAAT
1 TTAATTAACCTAAAAATATACTAATGAAAT
237970 TT
1 TT
237972 CCTATTCCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 17 0.61
30 11 0.39
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.36
Consensus pattern (30 bp):
TTAATTAACCTAAAAATATACTAATGAAAT
Found at i:246071 original size:21 final size:21
Alignment explanation
Indices: 246047--246086 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
246037 AACATCCCAA
246047 AAATTAAAAGTCTTAAAAATT
1 AAATTAAAAGTCTTAAAAATT
*
246068 AAATTCAAAGTCTTAAAAA
1 AAATTAAAAGTCTTAAAAA
246087 AAATTGTTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.57, C:0.07, G:0.05, T:0.30
Consensus pattern (21 bp):
AAATTAAAAGTCTTAAAAATT
Found at i:254991 original size:26 final size:26
Alignment explanation
Indices: 254946--255029 Score: 89
Period size: 26 Copynumber: 3.2 Consensus size: 26
254936 TTACTACTAA
* *
254946 TGTCGCTACATGAGCATGTCCAGAAT
1 TGTCGCTGCATGAACATGTCCAGAAT
* *
254972 TGTCGCTGCA-GAAACTTGTCCATAAT
1 TGTCGCTGCATG-AACATGTCCAGAAT
* * *
254998 TATCGTTGCATGAACATGTCCAGAGT
1 TGTCGCTGCATGAACATGTCCAGAAT
255024 TGTCGC
1 TGTCGC
255030 CAGCATGTCC
Statistics
Matches: 45, Mismatches: 11, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
25 1 0.02
26 43 0.96
27 1 0.02
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.30
Consensus pattern (26 bp):
TGTCGCTGCATGAACATGTCCAGAAT
Found at i:259731 original size:55 final size:55
Alignment explanation
Indices: 259665--259818 Score: 218
Period size: 55 Copynumber: 2.8 Consensus size: 55
259655 TCGTTCAATT
* * * * *
259665 AGCATATCCAGAATTGCGTCCAGAATTGTCGCCACATCTAATAGCTCGTTGCATG
1 AGCATATCCAGAATTACGCCCAGAATTGTCGCCGCATCTGATAGCTCGCTGCATG
*** *
259720 AGCATATCCAGAATTACGCCCAGAATTGTCATTGCATCTGACAGCTCGCTGCATG
1 AGCATATCCAGAATTACGCCCAGAATTGTCGCCGCATCTGATAGCTCGCTGCATG
*
259775 AGCATATCTAGAATTACGCCCAGAATTGTCGCCGCATCTGATAG
1 AGCATATCCAGAATTACGCCCAGAATTGTCGCCGCATCTGATAG
259819 ATGTGTGGAT
Statistics
Matches: 85, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
55 85 1.00
ACGTcount: A:0.28, C:0.26, G:0.20, T:0.26
Consensus pattern (55 bp):
AGCATATCCAGAATTACGCCCAGAATTGTCGCCGCATCTGATAGCTCGCTGCATG
Found at i:262419 original size:23 final size:23
Alignment explanation
Indices: 262392--262450 Score: 100
Period size: 23 Copynumber: 2.6 Consensus size: 23
262382 ACAAATATAC
*
262392 GAACTATCGATACTTCTGAAATA
1 GAACTACCGATACTTCTGAAATA
*
262415 GAACTACCGATACTTCTGAAGTA
1 GAACTACCGATACTTCTGAAATA
262438 GAACTACCGATAC
1 GAACTACCGATAC
262451 CTATGATGCA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.37, C:0.22, G:0.15, T:0.25
Consensus pattern (23 bp):
GAACTACCGATACTTCTGAAATA
Found at i:263087 original size:41 final size:41
Alignment explanation
Indices: 262992--263248 Score: 288
Period size: 41 Copynumber: 6.2 Consensus size: 41
262982 GAGTCGTAGA
* * *
262992 TCTTCCTTTTAA-ACAATCTTATGCTC-TACT-GAGTCATAAG
1 TCTTCC-TTTAATATAATCTCATGCTCAT-CTCGAGTCATGAG
*
263032 TCTTCCTTTAAATATAATCTCATGCTCATCCCGAGTCATGAG
1 TCTTCCTTT-AATATAATCTCATGCTCATCTCGAGTCATGAG
* *
263074 TCTTCCTTTAATATAATCTCATGCTCATCTCGAGACATGAC
1 TCTTCCTTTAATATAATCTCATGCTCATCTCGAGTCATGAG
* * * *
263115 TCTTCCTTTAATATAATCTCATGCTCATTTTGAGTTACGAG
1 TCTTCCTTTAATATAATCTCATGCTCATCTCGAGTCATGAG
* * * * *
263156 T-TATCATTTAATATAATCTCATGATCATTTTGAGTCACGAG
1 TCT-TCCTTTAATATAATCTCATGCTCATCTCGAGTCATGAG
* *
263197 TCTTCCTTTAATATAATCTCATTCTCATCTCGAGACATGAG
1 TCTTCCTTTAATATAATCTCATGCTCATCTCGAGTCATGAG
263238 TCTTCCATTTA
1 TCTTCC-TTTA
263249 TACATCAAAT
Statistics
Matches: 187, Mismatches: 23, Indels: 12
0.84 0.10 0.05
Matches are distributed among these distances:
39 3 0.02
40 9 0.05
41 151 0.81
42 24 0.13
ACGTcount: A:0.27, C:0.23, G:0.11, T:0.40
Consensus pattern (41 bp):
TCTTCCTTTAATATAATCTCATGCTCATCTCGAGTCATGAG
Found at i:265975 original size:21 final size:21
Alignment explanation
Indices: 265951--265996 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
265941 CCCTGCTGTT
*
265951 GAGGAGGAAGT-TGATGTTGGA
1 GAGGAGGAAGTCTG-TGTTGAA
265972 GAGGAGGAAGTCTGTGTTGAA
1 GAGGAGGAAGTCTGTGTTGAA
265993 GAGG
1 GAGG
265997 TGAAAGAGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 21 0.91
22 2 0.09
ACGTcount: A:0.28, C:0.02, G:0.48, T:0.22
Consensus pattern (21 bp):
GAGGAGGAAGTCTGTGTTGAA
Found at i:266276 original size:18 final size:18
Alignment explanation
Indices: 266255--266297 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
266245 TCCAAGGATA
266255 AAAAGCATAGA-AAGGAAG
1 AAAAGCA-AGAGAAGGAAG
266273 AAAAG-AAGAGAAGGAAG
1 AAAAGCAAGAGAAGGAAG
266290 AAGAAGCA
1 AA-AAGCA
266298 CCATGTAGCA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 3 0.14
17 10 0.45
18 8 0.36
19 1 0.05
ACGTcount: A:0.63, C:0.05, G:0.30, T:0.02
Consensus pattern (18 bp):
AAAAGCAAGAGAAGGAAG
Found at i:268801 original size:20 final size:21
Alignment explanation
Indices: 268776--268831 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
268766 CTAGAGTTTT
*
268776 TAGTATCGGTATAAG-ATGAC
1 TAGTATCGGTAGAAGCATGAC
268796 TAGTATCGGTAGAAGCATGAC
1 TAGTATCGGTAGAAGCATGAC
* *
268817 TTGTATCGATAGAAG
1 TAGTATCGGTAGAAG
268832 TGACACTTGT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
20 14 0.44
21 18 0.56
ACGTcount: A:0.34, C:0.11, G:0.27, T:0.29
Consensus pattern (21 bp):
TAGTATCGGTAGAAGCATGAC
Found at i:272318 original size:22 final size:22
Alignment explanation
Indices: 272290--272335 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
272280 CAAAGTATAT
*
272290 TAATAAT-CCAAAATCAAAATAA
1 TAATAATAACAAAAT-AAAATAA
*
272312 TAATAATAATAAAATAAAATAA
1 TAATAATAACAAAATAAAATAA
272334 TA
1 TA
272336 TAAATTTGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.26
Consensus pattern (22 bp):
TAATAATAACAAAATAAAATAA
Found at i:273424 original size:14 final size:14
Alignment explanation
Indices: 273391--273424 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
273381 TTTCGAAAAA
273391 AGTCAACGATCAAC
1 AGTCAACGATCAAC
*
273405 AATCAACGATCAAC
1 AGTCAACGATCAAC
*
273419 TGTCAA
1 AGTCAA
273425 TGGTCAACGG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.44, C:0.26, G:0.12, T:0.18
Consensus pattern (14 bp):
AGTCAACGATCAAC
Found at i:277153 original size:31 final size:31
Alignment explanation
Indices: 277109--277216 Score: 98
Period size: 31 Copynumber: 3.5 Consensus size: 31
277099 TTCATATAAC
*
277109 ATTTGATACCTAAACTTGACATTTTTTTCTA
1 ATTTGGTACCTAAACTTGACATTTTTTTCTA
* * *
277140 ATTTGGTATCTAAACTT----TTTTTGGATCCA
1 ATTTGGTACCTAAACTTGACATTTTT--TTCTA
* * *
277169 ATTTGGTACCTGAACTTGACACTTTTTCCTA
1 ATTTGGTACCTAAACTTGACATTTTTTTCTA
*
277200 AGTTGGTACCTAAACTT
1 ATTTGGTACCTAAACTT
277217 TTTTTGGACC
Statistics
Matches: 59, Mismatches: 12, Indels: 12
0.71 0.14 0.14
Matches are distributed among these distances:
27 5 0.08
29 18 0.31
31 32 0.54
33 4 0.07
ACGTcount: A:0.26, C:0.18, G:0.12, T:0.44
Consensus pattern (31 bp):
ATTTGGTACCTAAACTTGACATTTTTTTCTA
Found at i:277206 original size:60 final size:60
Alignment explanation
Indices: 277109--277224 Score: 178
Period size: 60 Copynumber: 1.9 Consensus size: 60
277099 TTCATATAAC
* * * *
277109 ATTTGATACCTAAACTTGACATTTTTTTCTAATTTGGTATCTAAACTTTTTTTGGATCCA
1 ATTTGATACCTAAACTTGACACTTTTTCCTAAGTTGGTACCTAAACTTTTTTTGGATCCA
* *
277169 ATTTGGTACCTGAACTTGACACTTTTTCCTAAGTTGGTACCTAAACTTTTTTTGGA
1 ATTTGATACCTAAACTTGACACTTTTTCCTAAGTTGGTACCTAAACTTTTTTTGGA
277225 CCTAAACTTG
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
60 50 1.00
ACGTcount: A:0.25, C:0.16, G:0.13, T:0.46
Consensus pattern (60 bp):
ATTTGATACCTAAACTTGACACTTTTTCCTAAGTTGGTACCTAAACTTTTTTTGGATCCA
Found at i:277268 original size:48 final size:49
Alignment explanation
Indices: 277170--277270 Score: 125
Period size: 49 Copynumber: 2.1 Consensus size: 49
277160 TTGGATCCAA
* * *
277170 TTTGGTACCTGAACTTGACACTTTTTCCTAAGTTGGTACCTAAACTTTT
1 TTTGGTACCTAAACTTGACACTTTTTCCTAAGTTGATACCCAAACTTTT
* *
277219 TTTGG-ACCTAAACTTGACATTTTTTTCCTAA-TTCGATACCCAAGCTTTT
1 TTTGGTACCTAAACTTGACA-CTTTTTCCTAAGTT-GATACCCAAACTTTT
277268 TTT
1 TTT
277271 TAAGATTCAA
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
48 15 0.33
49 30 0.67
ACGTcount: A:0.23, C:0.21, G:0.12, T:0.45
Consensus pattern (49 bp):
TTTGGTACCTAAACTTGACACTTTTTCCTAAGTTGATACCCAAACTTTT
Found at i:277473 original size:31 final size:31
Alignment explanation
Indices: 277437--277571 Score: 93
Period size: 31 Copynumber: 4.4 Consensus size: 31
277427 TTAAAAAATA
277437 TTAGGTACCAAATTAAGAAAAAGAGTCAAGT
1 TTAGGTACCAAATTAAGAAAAAGAGTCAAGT
* * **
277468 TTAGGTACTAAATT-GGACCCCAA-A---AAGT
1 TTAGGTACCAAATTAAGA--AAAAGAGTCAAGT
* * **
277496 TTAAGTACCAATTTAA-AAAGAAGTTTCAAGT
1 TTAGGTACCAAATTAAGAAA-AAGAGTCAAGT
* *
277527 TTAGGTACCAAATTAGGAAAAAAGTGTCAAGT
1 TTAGGTACCAAATTAAG-AAAAAGAGTCAAGT
*
277559 TCAGGTACCAAAT
1 TTAGGTACCAAAT
277572 GTTATATTAA
Statistics
Matches: 78, Mismatches: 16, Indels: 19
0.69 0.14 0.17
Matches are distributed among these distances:
27 2 0.03
28 16 0.21
30 2 0.03
31 31 0.40
32 24 0.31
33 3 0.04
ACGTcount: A:0.44, C:0.13, G:0.18, T:0.26
Consensus pattern (31 bp):
TTAGGTACCAAATTAAGAAAAAGAGTCAAGT
Found at i:279464 original size:9 final size:9
Alignment explanation
Indices: 279452--279484 Score: 57
Period size: 9 Copynumber: 3.6 Consensus size: 9
279442 TATTTTTTGG
279452 TTTTTTTAT
1 TTTTTTTAT
279461 TTTTTTTAT
1 TTTTTTTAT
279470 TTTTTTTAT
1 TTTTTTTAT
279479 CTTTTT
1 -TTTTT
279485 CTTTATTTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 18 0.78
10 5 0.22
ACGTcount: A:0.09, C:0.03, G:0.00, T:0.88
Consensus pattern (9 bp):
TTTTTTTAT
Found at i:279466 original size:18 final size:19
Alignment explanation
Indices: 279444--279484 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
279434 ATTTTCTTTA
*
279444 TTTTTTGGTTTTTTTAT-T
1 TTTTTTAGTTTTTTTATCT
*
279462 TTTTTTATTTTTTTTATCT
1 TTTTTTAGTTTTTTTATCT
279481 TTTT
1 TTTT
279485 CTTTATTTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.07, C:0.02, G:0.05, T:0.85
Consensus pattern (19 bp):
TTTTTTAGTTTTTTTATCT
Found at i:285491 original size:29 final size:26
Alignment explanation
Indices: 285458--285510 Score: 70
Period size: 29 Copynumber: 1.9 Consensus size: 26
285448 TTCTAAATAT
*
285458 ATTAATTATCGCTTAATTAATATATTAAA
1 ATTAATTAT-G-TTAATCAAT-TATTAAA
285487 ATTAATTATGTTAATCAATTATTA
1 ATTAATTATGTTAATCAATTATTA
285511 TTTTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 5 0.22
27 8 0.35
28 1 0.04
29 9 0.39
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.47
Consensus pattern (26 bp):
ATTAATTATGTTAATCAATTATTAAA
Found at i:292317 original size:10 final size:10
Alignment explanation
Indices: 292302--292333 Score: 64
Period size: 10 Copynumber: 3.2 Consensus size: 10
292292 CTCTTTAAAA
292302 TGTGGAAACT
1 TGTGGAAACT
292312 TGTGGAAACT
1 TGTGGAAACT
292322 TGTGGAAACT
1 TGTGGAAACT
292332 TG
1 TG
292334 ACTTTCAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.28, C:0.09, G:0.31, T:0.31
Consensus pattern (10 bp):
TGTGGAAACT
Found at i:304556 original size:30 final size:29
Alignment explanation
Indices: 304516--304573 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
304506 AAAAAATGCA
* *
304516 TTACAAACAAACTGAAACAAACTAAATTGG
1 TTACAAACAAA-AGAAACAAAATAAATTGG
*
304546 TTACATACAAAAGAAACAAAATAAATTG
1 TTACAAACAAAAGAAACAAAATAAATTG
304574 CATGGATGAG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 15 0.60
30 10 0.40
ACGTcount: A:0.57, C:0.14, G:0.09, T:0.21
Consensus pattern (29 bp):
TTACAAACAAAAGAAACAAAATAAATTGG
Found at i:307225 original size:28 final size:29
Alignment explanation
Indices: 307194--307254 Score: 67
Period size: 28 Copynumber: 2.2 Consensus size: 29
307184 AATTTTCCTC
*
307194 TCTTTA-G-TTTAGTTTAGTGTTTC-TTTTT
1 TCTTTAGGTTTTAGTTT-GT-TTTCATTTTG
307222 TC-TTAGGTTTTAGTTTGTTTTCATTTTG
1 TCTTTAGGTTTTAGTTTGTTTTCATTTTG
307250 TCTTT
1 TCTTT
307255 CTTTCGAGAG
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
27 7 0.25
28 11 0.39
29 10 0.36
ACGTcount: A:0.10, C:0.08, G:0.15, T:0.67
Consensus pattern (29 bp):
TCTTTAGGTTTTAGTTTGTTTTCATTTTG
Found at i:309166 original size:16 final size:15
Alignment explanation
Indices: 309147--309186 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
309137 TTGTTAGTTT
309147 TTTATTTTATTATTCA
1 TTTATTTTATT-TTCA
*
309163 TTTATTTTATTTTTA
1 TTTATTTTATTTTCA
*
309178 TTAATTTTA
1 TTTATTTTA
309187 GTTGTGTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 11 0.50
16 11 0.50
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (15 bp):
TTTATTTTATTTTCA
Found at i:312069 original size:39 final size:39
Alignment explanation
Indices: 312026--312124 Score: 162
Period size: 39 Copynumber: 2.5 Consensus size: 39
312016 TTAAATAGGG
312026 TTTTAATGTGTCTTAGTTTGATACATATTTAATAGTTGT
1 TTTTAATGTGTCTTAGTTTGATACATATTTAATAGTTGT
* *
312065 TTTTAATGCGTCTTATTTTGATACATATTTAATAGTTGT
1 TTTTAATGTGTCTTAGTTTGATACATATTTAATAGTTGT
* *
312104 TTTTAAGGTGTCTAAGTTTGA
1 TTTTAATGTGTCTTAGTTTGA
312125 GACAAATTAA
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 54 1.00
ACGTcount: A:0.25, C:0.06, G:0.16, T:0.53
Consensus pattern (39 bp):
TTTTAATGTGTCTTAGTTTGATACATATTTAATAGTTGT
Found at i:312540 original size:10 final size:10
Alignment explanation
Indices: 312525--312558 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
312515 TCTAGCCTAG
312525 TCCATTCAGC
1 TCCATTCAGC
312535 TCCATTCAGC
1 TCCATTCAGC
*
312545 TCAATTTCAGC
1 TCCA-TTCAGC
312556 TCC
1 TCC
312559 TTACTTAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 13 0.62
11 8 0.38
ACGTcount: A:0.21, C:0.38, G:0.09, T:0.32
Consensus pattern (10 bp):
TCCATTCAGC
Found at i:315436 original size:11 final size:11
Alignment explanation
Indices: 315422--315505 Score: 52
Period size: 11 Copynumber: 7.7 Consensus size: 11
315412 GAGTGAGAAT
315422 GAAAAAGAAAA
1 GAAAAAGAAAA
*
315433 GAAAATTG-AAA
1 GAAAA-AGAAAA
*
315444 -AAAAAGAAAG
1 GAAAAAGAAAA
*
315454 GAAAAATG-AGA
1 GAAAAA-GAAAA
315465 G-AAAAG-AAA
1 GAAAAAGAAAA
**
315474 GAAAGTGAAAA
1 GAAAAAGAAAA
315485 GAAAGAGAGAAAA
1 GAAA-A-AGAAAA
315498 GAAAAAGA
1 GAAAAAGA
315506 TGAAAAGGAA
Statistics
Matches: 55, Mismatches: 10, Indels: 16
0.68 0.12 0.20
Matches are distributed among these distances:
9 5 0.09
10 13 0.24
11 25 0.45
12 3 0.05
13 9 0.16
ACGTcount: A:0.71, C:0.00, G:0.24, T:0.05
Consensus pattern (11 bp):
GAAAAAGAAAA
Found at i:315447 original size:21 final size:21
Alignment explanation
Indices: 315423--315490 Score: 68
Period size: 21 Copynumber: 3.3 Consensus size: 21
315413 AGTGAGAATG
*
315423 AAAAAGAAAAGAAAATTGAAA
1 AAAAAGAAAAGAAAAATGAAA
* *
315444 AAAAAGAAAGGAAAAATGAGA
1 AAAAAGAAAAGAAAAATGAAA
* *
315465 GAAAAG-AAAG-AAAGTGAAA
1 AAAAAGAAAAGAAAAATGAAA
*
315484 AGAAAGA
1 AAAAAGA
315491 GAGAAAAGAA
Statistics
Matches: 37, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
19 11 0.30
20 3 0.08
21 23 0.62
ACGTcount: A:0.72, C:0.00, G:0.22, T:0.06
Consensus pattern (21 bp):
AAAAAGAAAAGAAAAATGAAA
Found at i:315485 original size:15 final size:15
Alignment explanation
Indices: 315465--315519 Score: 55
Period size: 15 Copynumber: 3.9 Consensus size: 15
315455 AAAAATGAGA
315465 GAAAAGAAAGAAAGT
1 GAAAAGAAAGAAAGT
*
315480 GAAAAGAAAG--AGA
1 GAAAAGAAAGAAAGT
315493 GAAAAG-AA-AAAGAT
1 GAAAAGAAAGAAAG-T
*
315507 GAAAAGGAAGAAA
1 GAAAAGAAAGAAA
315520 AAGAGATAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
12 2 0.06
13 10 0.30
14 6 0.18
15 12 0.36
16 3 0.09
ACGTcount: A:0.69, C:0.00, G:0.27, T:0.04
Consensus pattern (15 bp):
GAAAAGAAAGAAAGT
Found at i:315500 original size:28 final size:28
Alignment explanation
Indices: 315440--315517 Score: 85
Period size: 27 Copynumber: 2.9 Consensus size: 28
315430 AAAGAAAATT
* *
315440 GAAAAAAAAGAAAG-G-AAA-AATGAGA
1 GAAAAGAAAGAAAGTGAAAAGAAAGAGA
315465 GAAAAGAAAGAAAGTGAAAAGAAAGAGA
1 GAAAAGAAAGAAAGTGAAAAGAAAGAGA
*
315493 GAAAAG-AA-AAAGATGAAAAGGAAGA
1 GAAAAGAAAGAAAG-TGAAAAGAAAGA
315518 AAAAGAGATA
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
25 13 0.28
26 5 0.11
27 16 0.35
28 12 0.26
ACGTcount: A:0.69, C:0.00, G:0.27, T:0.04
Consensus pattern (28 bp):
GAAAAGAAAGAAAGTGAAAAGAAAGAGA
Done.