Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001420.1 Kokia drynarioides strain JFW-HI SEQ_112917, 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: 98498
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.35
Warning! 59 characters in sequence are not A, C, G, or T
Found at i:10 original size:2 final size:2
Alignment explanation
Indices: 4--36 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1 AAA
4 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
37 ATGTTGTCAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:781 original size:15 final size:16
Alignment explanation
Indices: 763--813 Score: 54
Period size: 15 Copynumber: 3.3 Consensus size: 16
753 CAAATACAAA
763 TATAATTATAAATAA-
1 TATAATTATAAATAAC
*
778 TATATATT-TAAATAAT
1 TATA-ATTATAAATAAC
*
794 TATAACTA-AAATAAC
1 TATAATTATAAATAAC
809 TATAA
1 TATAA
814 CCACACATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
15 24 0.77
16 7 0.23
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (16 bp):
TATAATTATAAATAAC
Found at i:1192 original size:27 final size:27
Alignment explanation
Indices: 1156--1209 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
1146 GCTAATGATT
*
1156 AAAAAAGTACTAATAATTGAGTGACTA
1 AAAAAAGTACTAATAATTGAGCGACTA
1183 AAAAAAGTACTAATAATTGAGCGACTA
1 AAAAAAGTACTAATAATTGAGCGACTA
1210 CTAGTGTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.52, C:0.09, G:0.15, T:0.24
Consensus pattern (27 bp):
AAAAAAGTACTAATAATTGAGCGACTA
Found at i:3230 original size:24 final size:23
Alignment explanation
Indices: 3198--3242 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
3188 GATAGTAAAA
*
3198 TATAATTTTATCATTTTATTAATT
1 TATAATTTTATAATTTT-TTAATT
*
3222 TATATTTTTATAATTTTTTAA
1 TATAATTTTATAATTTTTTAA
3243 ATGTTAAACC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (23 bp):
TATAATTTTATAATTTTTTAATT
Found at i:6414 original size:21 final size:23
Alignment explanation
Indices: 6388--6429 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
6378 AAAAATATAA
6388 TATTACCTT-T-AAAATAATTTT
1 TATTACCTTATAAAAATAATTTT
*
6409 TATTACTTTATAAAAATAATT
1 TATTACCTTATAAAAATAATT
6430 ATTTTAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 8 0.44
22 1 0.06
23 9 0.50
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (23 bp):
TATTACCTTATAAAAATAATTTT
Found at i:6431 original size:20 final size:21
Alignment explanation
Indices: 6375--6432 Score: 57
Period size: 20 Copynumber: 2.8 Consensus size: 21
6365 TATATAAAAA
*
6375 TATAAAAATATAATATTACCTT
1 TATAAAAATA-ATTATTACCTT
**
6397 TA-AAATAATTTTTATTA-CTT
1 TATAAA-AATAATTATTACCTT
6417 TATAAAAATAATTATT
1 TATAAAAATAATTATT
6433 TTAATAATTT
Statistics
Matches: 29, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
20 13 0.45
21 11 0.38
22 5 0.17
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.47
Consensus pattern (21 bp):
TATAAAAATAATTATTACCTT
Found at i:7169 original size:16 final size:16
Alignment explanation
Indices: 7148--7193 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 16
7138 CTATATCTAA
7148 TAATATAATAAATTAT
1 TAATATAATAAATTAT
7164 T-A-AT-ATAAATTAT
1 TAATATAATAAATTAT
* *
7177 TATTTTAATAAATTAT
1 TAATATAATAAATTAT
7193 T
1 T
7194 TAACATTCCA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
13 10 0.40
14 2 0.08
15 2 0.08
16 11 0.44
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TAATATAATAAATTAT
Found at i:7274 original size:15 final size:15
Alignment explanation
Indices: 7254--7313 Score: 57
Period size: 15 Copynumber: 3.7 Consensus size: 15
7244 AACATTCAAT
7254 ATAAATATTTTAATA
1 ATAAATATTTTAATA
*
7269 ATAAATATTGATTACAATT
1 ATAAATATT--TT--AATA
*
7288 ATAAATATATTAATA
1 ATAAATATTTTAATA
*
7303 ATAAATGTTTT
1 ATAAATATTTT
7314 GTAGTATAGA
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
15 21 0.58
17 4 0.11
19 11 0.31
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.45
Consensus pattern (15 bp):
ATAAATATTTTAATA
Found at i:7875 original size:13 final size:13
Alignment explanation
Indices: 7857--7881 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
7847 TTTTAAATCA
7857 TATTGTTTTCTTT
1 TATTGTTTTCTTT
7870 TATTGTTTTCTT
1 TATTGTTTTCTT
7882 AAAAAGCAAA
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:0.08, C:0.08, G:0.08, T:0.76
Consensus pattern (13 bp):
TATTGTTTTCTTT
Found at i:10151 original size:6 final size:6
Alignment explanation
Indices: 10130--10216 Score: 58
Period size: 6 Copynumber: 14.8 Consensus size: 6
10120 TAAAATTAGG
** **
10130 TTTAAA TTTATT TTTAAA TTTAAA TTTAAGA --TAAA TTTAAA TTTATCTT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAA-A TTTAAA TTTAAA TTTA--AA
**
10179 TTTAAA TTTAAA TTT-GC TTTAAA TTT--A TTTAAA TTTAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAA
10217 TCAAATTTGA
Statistics
Matches: 61, Mismatches: 12, Indels: 16
0.69 0.13 0.18
Matches are distributed among these distances:
4 5 0.08
5 6 0.10
6 45 0.74
7 1 0.02
8 4 0.07
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (6 bp):
TTTAAA
Found at i:10201 original size:17 final size:17
Alignment explanation
Indices: 10130--10205 Score: 71
Period size: 17 Copynumber: 4.2 Consensus size: 17
10120 TAAAATTAGG
*
10130 TTTAAATTTATTTTTAAA
1 TTTAAATTTA-CTTTAAA
***
10148 TTTAAATTTAAGATAAA
1 TTTAAATTTACTTTAAA
10165 TTTAAATTTATCTTTTTAAA
1 TTTAAATTTA-C--TTTAAA
*
10185 TTTAAATTTGCTTTAAA
1 TTTAAATTTACTTTAAA
10202 TTTA
1 TTTA
10206 TTTAAATTTA
Statistics
Matches: 48, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
17 24 0.50
18 10 0.21
19 1 0.02
20 13 0.27
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (17 bp):
TTTAAATTTACTTTAAA
Found at i:11922 original size:29 final size:28
Alignment explanation
Indices: 11889--12215 Score: 323
Period size: 29 Copynumber: 11.2 Consensus size: 28
11879 CGAAAATTAT
*
11889 ATTTTTACTCCTGAACTTCCAAAAATTCC
1 ATTTTTAC-CCTAAACTTCCAAAAATTCC
* *
11918 ATTTTGACCCCAAAACTTCCAAAAATTCC
1 ATTTTTA-CCCTAAACTTCCAAAAATTCC
11947 ATTTTTACCCCTAAACTTCCAAAAATTCC
1 ATTTTTA-CCCTAAACTTCCAAAAATTCC
*
11976 ATTTTAACCCTAAAACTTCCAAAAATTCC
1 ATTTTTACCCT-AAACTTCCAAAAATTCC
* *
12005 ATTTTTACCCCCAAACTTCCAAAAATTTC
1 ATTTTTA-CCCTAAACTTCCAAAAATTCC
* * *
12034 ATTTTTGACCTCGAAACTTTCAAAAATTAC
1 ATTTTT-ACC-CTAAACTTCCAAAAATTCC
* * *
12064 AATTTTACCCCCAAGCTTCC-AAAATTCC
1 ATTTTTA-CCCTAAACTTCCAAAAATTCC
*
12092 ATTTTTGACACTAAAACTTCCAAAAATTCC
1 ATTTTT-ACCCT-AAACTTCCAAAAATTCC
** *
12122 AAATTTACCCCTAAACTTCCAAAAATTCT
1 ATTTTTA-CCCTAAACTTCCAAAAATTCC
* * *
12151 ATTTTTACCCTCGAGCTTTCAAAAATTCC
1 ATTTTTACCCT-AAACTTCCAAAAATTCC
* *
12180 ATTTTTTACCTCGAAACTTTCAAAAATTACC
1 A-TTTTTACC-CTAAACTTCCAAAAATT-CC
12211 ATTTT
1 ATTTT
12216 GCCCCCGAAT
Statistics
Matches: 250, Mismatches: 34, Indels: 27
0.80 0.11 0.09
Matches are distributed among these distances:
28 22 0.09
29 156 0.62
30 68 0.27
31 4 0.02
ACGTcount: A:0.35, C:0.27, G:0.03, T:0.35
Consensus pattern (28 bp):
ATTTTTACCCTAAACTTCCAAAAATTCC
Found at i:11951 original size:58 final size:58
Alignment explanation
Indices: 11889--12337 Score: 376
Period size: 58 Copynumber: 7.7 Consensus size: 58
11879 CGAAAATTAT
* *
11889 ATTTTTACTCCTGAACTTCCAAAAATTCCATTTTGACCCCAAAACTTCCAAAAATTCC
1 ATTTTTACCCCTAAACTTCCAAAAATTCCATTTTGACCCCAAAACTTCCAAAAATTCC
* *
11947 ATTTTTACCCCTAAACTTCCAAAAATTCCATTTTAACCCTAAAACTTCCAAAAATTCC
1 ATTTTTACCCCTAAACTTCCAAAAATTCCATTTTGACCCCAAAACTTCCAAAAATTCC
* * * * * *
12005 ATTTTTACCCCCAAACTTCCAAAAATTTCATTTTTGACCTCGAAACTTTCAAAAATTAC
1 ATTTTTACCCCTAAACTTCCAAAAATTCCA-TTTTGACCCCAAAACTTCCAAAAATTCC
* * * * *
12064 AATTTTACCCCCAAGCTTCC-AAAATTCCATTTTTGACACTAAAACTTCCAAAAATTCC
1 ATTTTTACCCCTAAACTTCCAAAAATTCCA-TTTTGACCCCAAAACTTCCAAAAATTCC
** * * * * *
12122 AAATTTACCCCTAAACTTCCAAAAATTCTATTTTTACCCTC-GAGCTTTCAAAAATTCC
1 ATTTTTACCCCTAAACTTCCAAAAATTCCATTTTGACCC-CAAAACTTCCAAAAATTCC
* * * ** *
12180 ATTTTTTACCTCGAAACTTTCAAAAATTACCATTTTG-CCCCCGAA-TGTCCAAAAACTCC
1 A-TTTTTACCCCTAAACTTCCAAAAATT-CCATTTTGACCCCAAAACT-TCCAAAAATTCC
* ** * * * * ** *
12239 ATTTTCGACGTCGAAAC-TCTCAAAATTATCC-TTTT-ACCCCCAAATTTATAAAAATTTC
1 ATTTT-TACCCCTAAACTTC-CAAAAAT-TCCATTTTGACCCCAAAACTTCCAAAAATTCC
*
12297 ATTTTTAACCCC-AAACTTTCCCAAAATTACCATTTT-ACCCC
1 ATTTTT-ACCCCTAAAC-TTCCAAAAATT-CCATTTTGACCCC
12338 TCGGGTATCC
Statistics
Matches: 319, Mismatches: 55, Indels: 33
0.78 0.14 0.08
Matches are distributed among these distances:
57 5 0.02
58 193 0.61
59 114 0.36
60 7 0.02
ACGTcount: A:0.35, C:0.28, G:0.03, T:0.34
Consensus pattern (58 bp):
ATTTTTACCCCTAAACTTCCAAAAATTCCATTTTGACCCCAAAACTTCCAAAAATTCC
Found at i:12138 original size:146 final size:146
Alignment explanation
Indices: 11902--12243 Score: 451
Period size: 146 Copynumber: 2.3 Consensus size: 146
11892 TTTACTCCTG
* * *
11902 AACTTCCAAAAATT-CCATTTTGACCCCAAAACTTCCAAAAATTCCATTTTTACCCCTAAACTTC
1 AACTTTCAAAAATTACCATTTT-ACCCCCAAACTTCCAAAAATTCCATTTTTACCACTAAACTTC
*
11966 CAAAAATTCCATTTTAACCCTAAAACTTCCAAAAATTCCATTTTTACCCCCAAACTTCCAAAAAT
65 CAAAAATTCCAATTTAACCCTAAAACTTCCAAAAATTCCATTTTTACCCCCAAACTTCCAAAAAT
*
12031 TTCATTTTTGACCTCGA
130 TCCATTTTTGACCTCGA
* *
12048 AACTTTCAAAAATTACAATTTTACCCCCAAGCTTCC-AAAATTCCATTTTTGA-CACTAAAACTT
1 AACTTTCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATTCCATTTTT-ACCACT-AAACTT
* * * * * *
12111 CCAAAAATTCCAAATTTACCCCT-AAACTTCCAAAAATTCTATTTTTACCCTCGAGCTTTCAAAA
64 CCAAAAATTCC-AATTTAACCCTAAAACTTCCAAAAATTCCATTTTTACCCCCAAACTTCCAAAA
*
12175 ATTCCATTTTTTACCTCGA
128 ATTCCATTTTTGACCTCGA
* * *
12194 AACTTTCAAAAATTACCATTTTGCCCCCGAA-TGTCCAAAAACTCCATTTT
1 AACTTTCAAAAATTACCATTTTACCCCCAAACT-TCCAAAAATTCCATTTT
12244 CGACGTCGAA
Statistics
Matches: 171, Mismatches: 19, Indels: 11
0.85 0.09 0.05
Matches are distributed among these distances:
145 18 0.11
146 126 0.74
147 27 0.16
ACGTcount: A:0.36, C:0.28, G:0.03, T:0.33
Consensus pattern (146 bp):
AACTTTCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATTCCATTTTTACCACTAAACTTCC
AAAAATTCCAATTTAACCCTAAAACTTCCAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATT
CCATTTTTGACCTCGA
Found at i:12233 original size:59 final size:58
Alignment explanation
Indices: 12170--12337 Score: 169
Period size: 59 Copynumber: 2.9 Consensus size: 58
12160 CTCGAGCTTT
* * * *
12170 CAAAAATTCCATTTTTTACCTCGAAACTTTCAAAAATTACCATTTTGCCCCCGAATGTC
1 CAAAAATTCCATTTTTAACCTCGAAACTTTC-AAAATTACCATTTTACCCCCAAATGTA
* ** * * *
12229 CAAAAACTCCATTTTCGACGTCGAAACTCTCAAAATTATCC-TTTTACCCCCAAATTTA
1 CAAAAATTCCATTTTTAACCTCGAAACTTTCAAAATTA-CCATTTTACCCCCAAATGTA
* * *
12287 TAAAAATTTCATTTTTAACC-CCAAACTTTCCCAAAATTACCATTTTACCCC
1 CAAAAATTCCATTTTTAACCTCGAAACTTT--CAAAATTACCATTTTACCCC
12338 TCGGGTATCC
Statistics
Matches: 88, Mismatches: 17, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
57 7 0.08
58 36 0.41
59 45 0.51
ACGTcount: A:0.34, C:0.29, G:0.04, T:0.33
Consensus pattern (58 bp):
CAAAAATTCCATTTTTAACCTCGAAACTTTCAAAATTACCATTTTACCCCCAAATGTA
Found at i:12336 original size:29 final size:27
Alignment explanation
Indices: 11902--12337 Score: 286
Period size: 29 Copynumber: 15.0 Consensus size: 27
11892 TTTACTCCTG
11902 AACTTCCAAAAATTCCATTTTGACCCCAA
1 AACTTCCAAAAATTCCATTTT-ACCCC-A
11931 AACTTCCAAAAATTCCATTTTTACCCCTA
1 AACTTCCAAAAATTCCA-TTTTACCCC-A
*
11960 AACTTCCAAAAATTCCATTTTAACCCTAA
1 AACTTCCAAAAATTCCATTTT-ACCC-CA
11989 AACTTCCAAAAATTCCATTTTTACCCCCA
1 AACTTCCAAAAATTCCA-TTTTA-CCCCA
* *
12018 AACTTCCAAAAATTTCATTTTTGACCTCGA
1 AACTTCCAAAAATTCCA-TTTT-ACC-CCA
* *
12048 AACTTTCAAAAATTACAATTTTACCCCCA
1 AACTTCCAAAAATT-CCATTTTA-CCCCA
* **
12077 AGCTTCC-AAAATTCCATTTTTGACACTAA
1 AACTTCCAAAAATTCCA-TTTT-AC-CCCA
*
12106 AACTTCCAAAAATTCCAAATTTACCCCTA
1 AACTTCCAAAAATTCC-ATTTTACCCC-A
* *
12135 AACTTCCAAAAATTCTATTTTTACCCTCG
1 AACTTCCAAAAATTCCA-TTTTACCC-CA
* * *
12164 AGCTTTCAAAAATTCCATTTTTTACCTCGA
1 AACTTCCAAAAATTCCA--TTTTACC-CCA
* * *
12194 AACTTTCAAAAATTACCATTTTGCCCCCG
1 AACTTCCAAAAATT-CCATTTT-ACCCCA
* * *
12223 AA-TGTCCAAAAACTCCATTTTCGACGTCGA
1 AACT-TCCAAAAATTCCATTTT--AC-CCCA
*
12253 AAC-TCTCAAAATTATCC-TTTTACCCCCA
1 AACTTC-CAAAAAT-TCCATTTTA-CCCCA
* ** *
12281 AATTTATAAAAATTTCATTTTTAACCCCA
1 AACTTCCAAAAATTCCA-TTTT-ACCCCA
*
12310 AACTTTCCCAAAATTACCATTTTACCCC
1 AAC-TTCCAAAAATT-CCATTTTACCCC
12338 TCGGGTATCC
Statistics
Matches: 323, Mismatches: 50, Indels: 68
0.73 0.11 0.15
Matches are distributed among these distances:
27 4 0.01
28 35 0.11
29 180 0.56
30 93 0.29
31 11 0.03
ACGTcount: A:0.35, C:0.28, G:0.03, T:0.33
Consensus pattern (27 bp):
AACTTCCAAAAATTCCATTTTACCCCA
Found at i:15854 original size:58 final size:59
Alignment explanation
Indices: 15792--16351 Score: 359
Period size: 58 Copynumber: 9.6 Consensus size: 59
15782 CTTCGAAAAC
* * * * *
15792 AAAATGGTAATTTTTGGAAGGTTCGGAGTCAAAAACGAAA-TTTTAGACGTCCAAGGGT
1 AAAATGGTAATTTTTGGAAGGTTCGGGGTTAAAAATGAAATTTTTAGACATCCGAGGGT
* * * *
15850 AAAATGGTGATTTTTGGAAAGTTCGGGGTTAAAAATGGAA--TTTAGACATCCGGGGGT
1 AAAATGGTAATTTTTGGAAGGTTCGGGGTTAAAAATGAAATTTTTAGACATCCGAGGGT
* ** *
15907 AAAATGGTAA-TTTTGGAAAGTTTAGGGTTAAAAATGAAATTTTTAGACATTCGAGGGAT
1 AAAATGGTAATTTTTGGAAGGTTCGGGGTTAAAAATGAAATTTTTAGACATCCGAGGG-T
* *
15966 AAAATGATAA-TTTTGGAAGGATTCGGGGTTAAAAATGAAATTTTTAGACATTCGAGGGT
1 AAAATGGTAATTTTTGGAAGG-TTCGGGGTTAAAAATGAAATTTTTAGACATCCGAGGGT
* * * * * * **
16025 AAAAGGGTAATTTTTGGAAAGTTTGAGG-TCAAAAT-ATAATTTTT-GAAAAGT-TTAGGGGT
1 AAAATGGTAATTTTTGGAAGGTTCGGGGTTAAAAATGA-AATTTTTAG-ACA-TCCGA-GGGT
* ** ** * * * * **
16084 AAAATTGTAATTTTTGGAAAATTCAAGGTT-AAAATG-GAGTTTTGGAAAGT-TTAGGGT
1 AAAATGGTAATTTTTGGAAGGTTCGGGGTTAAAAATGAAATTTTTAGACA-TCCGAGGGT
* * * *
16141 AAAAT-GTAATTTTT-GAAGGATTTGGGGTTAAAAATGGAATTTTTAGACATTCG-GGTT
1 AAAATGGTAATTTTTGGAAGG-TTCGGGGTTAAAAATGAAATTTTTAGACATCCGAGGGT
* ** ** * * * * * ** *
16198 AAAATGGTAATTTTTGAAAATTTTAGGG-TCAAAATGTATTTTTTGGAAAGTTTGGGGGT
1 AAAATGGTAATTTTTGGAAGGTTCGGGGTTAAAAATGAAATTTTTAGACA-TCCGAGGGT
* * * * *
16257 AAAAT-GTAACTTTT-GAAGGATTTGGGGTT-AAAATGAATTTTTTAGACATTCG-GAGT
1 AAAATGGTAATTTTTGGAAGG-TTCGGGGTTAAAAATGAAATTTTTAGACATCCGAGGGT
* *
16313 AAAATGGTAATTTTTGGAAAGTTCGGGGTCAAAATATGA
1 AAAATGGTAATTTTTGGAAGGTTCGGGGTTAAAA-ATGA
16352 TTCATGGGCA
Statistics
Matches: 404, Mismatches: 72, Indels: 51
0.77 0.14 0.10
Matches are distributed among these distances:
55 3 0.01
56 49 0.12
57 85 0.21
58 140 0.35
59 82 0.20
60 45 0.11
ACGTcount: A:0.36, C:0.04, G:0.26, T:0.34
Consensus pattern (59 bp):
AAAATGGTAATTTTTGGAAGGTTCGGGGTTAAAAATGAAATTTTTAGACATCCGAGGGT
Found at i:15953 original size:115 final size:116
Alignment explanation
Indices: 15792--16346 Score: 426
Period size: 115 Copynumber: 4.8 Consensus size: 116
15782 CTTCGAAAAC
* * * * * * *
15792 AAAATGGTAATTTTTGGAAGGTTCGGAGTCAAAAACGAAA-TTTTAGACGTCCAAGGGTAAAATG
1 AAAATGGTAATTTTTGGAAAGTTTGGGGTTAAAAATGAAATTTTTAGACATTC--GGGTAAAATG
* * * *
15856 GTGATTTTTGGAAAGTTCGGGGTTAAAAATGGA-ATTTAGACA-TCCGGGGGT
64 GTAATTTTTGGAAAGTTCGGGGTTAAAAATGGATATTTAGAAAGTTCGAGGGT
*
15907 AAAATGGTAA-TTTTGGAAAGTTTAGGGTTAAAAATGAAATTTTTAGACATTCGAGGGATAAAAT
1 AAAATGGTAATTTTTGGAAAGTTTGGGGTTAAAAATGAAATTTTTAGACATTC--GGG-TAAAAT
* * * * *
15971 GATAA-TTTTGGAAGGATTCGGGGTTAAAAATGAAATTTTTAGACA-TTCGAGGGT
63 GGTAATTTTTGGAAAG-TTCGGGGTTAAAAATG-GATATTTAGAAAGTTCGAGGGT
* * * * *
16025 AAAAGGGTAATTTTTGGAAAGTTTGAGG-TCAAAAT-ATAATTTTT-GAAAAGTTTAGGGGTAAA
1 AAAATGGTAATTTTTGGAAAGTTTGGGGTTAAAAATGA-AATTTTTAG-ACA--TT-CGGGTAAA
* * ** * *
16087 ATTGTAATTTTTGGAAAATTCAAGGTT-AAAATGGAGT-TTTGGAAAGTT-TAGGGT
61 ATGGTAATTTTTGGAAAGTTCGGGGTTAAAAATGGA-TATTTAGAAAGTTCGAGGGT
* *
16141 AAAAT-GTAATTTTT-GAAGGATTTGGGGTTAAAAATGGAATTTTTAGACATTCGGGTTAAAATG
1 AAAATGGTAATTTTTGGAAAG-TTTGGGGTTAAAAATGAAATTTTTAGACATTCGGG-TAAAATG
* * ** * * * * * *
16204 GTAATTTTTGAAAATTTTAGGG-TCAAAATGTATTTTTTGGAAAGTTTGGGGGT
64 GTAATTTTTGGAAAGTTCGGGGTTAAAAATGGA-TATTTAGAAAGTTCGAGGGT
* * *
16257 AAAAT-GTAACTTTT-GAAGGATTTGGGGTT-AAAATGAATTTTTTAGACATTCGGAGTAAAATG
1 AAAATGGTAATTTTTGGAAAG-TTTGGGGTTAAAAATGAAATTTTTAGACATTCGG-GTAAAATG
*
16319 GTAATTTTTGGAAAGTTCGGGGTCAAAA
64 GTAATTTTTGGAAAGTTCGGGGTTAAAA
16347 TATGATTCAT
Statistics
Matches: 359, Mismatches: 57, Indels: 47
0.78 0.12 0.10
Matches are distributed among these distances:
113 4 0.01
114 61 0.17
115 106 0.30
116 92 0.26
117 13 0.04
118 55 0.15
119 26 0.07
120 2 0.01
ACGTcount: A:0.35, C:0.05, G:0.26, T:0.34
Consensus pattern (116 bp):
AAAATGGTAATTTTTGGAAAGTTTGGGGTTAAAAATGAAATTTTTAGACATTCGGGTAAAATGGT
AATTTTTGGAAAGTTCGGGGTTAAAAATGGATATTTAGAAAGTTCGAGGGT
Found at i:16337 original size:29 final size:29
Alignment explanation
Indices: 15846--16347 Score: 240
Period size: 29 Copynumber: 17.3 Consensus size: 29
15836 AGACGTCCAA
*
15846 GGGTAAAATGGTGATTTTTGGAAAGTTCG
1 GGGTAAAATGGTAATTTTTGGAAAGTTCG
* * *
15875 GGGTTAAAAATGG-AA--TTTAGACA-TCCGG
1 GGG-T-AAAATGGTAATTTTTGGAAAGTTC-G
*
15903 GGGTAAAATGGTAA-TTTTGGAAAGTTTAG
1 GGGTAAAATGGTAATTTTTGGAAAG-TTCG
* * * *
15932 GGTTAAAAAT-GAAATTTTTAGACA-TTCG
1 GGGT-AAAATGGTAATTTTTGGAAAGTTCG
* *
15960 AGGGATAAAATGATAA-TTTTGGAAGGATTCG
1 -GGG-TAAAATGGTAATTTTTGGAAAG-TTCG
* * *
15991 GGGTTAAAAAT-GAAATTTTTAGACA-TTCG
1 GGG-T-AAAATGGTAATTTTTGGAAAGTTCG
* *
16020 AGGGTAAAAGGGTAATTTTTGGAAAGTTTG
1 -GGGTAAAATGGTAATTTTTGGAAAGTTCG
* * * *
16050 AGGTCAAAAT-ATAATTTTTGAAAAGTTTAG
1 GGGT-AAAATGGTAATTTTTGGAAAG-TTCG
* * *
16080 GGGTAAAATTGTAATTTTTGGAAAATTCAA
1 GGGTAAAATGGTAATTTTTGGAAAGTTC-G
* * **
16110 GGTTAAAATGG--AGTTTTGGAAAGTTTA
1 GGGTAAAATGGTAATTTTTGGAAAGTTCG
* *
16137 GGGTAAAAT-GTAATTTTT-GAAGGATTTG
1 GGGTAAAATGGTAATTTTTGGAAAG-TTCG
* *
16165 GGGTTAAAAATGG-AATTTTTAGACA-TTCG
1 GGG-T-AAAATGGTAATTTTTGGAAAGTTCG
* * * **
16194 GGTTAAAATGGTAATTTTTGAAAATTTTA
1 GGGTAAAATGGTAATTTTTGGAAAGTTCG
* *
16223 GGGTCAAAAT-GTATTTTTTGGAAAGTTTGG
1 GGGT-AAAATGGTAATTTTTGGAAAG-TTCG
* * *
16253 GGGTAAAAT-GTAACTTTT-GAAGGATTTG
1 GGGTAAAATGGTAATTTTTGGAAAG-TTCG
* *
16281 GGGTTAAAAT-G-AATTTTTTAGACA-TTCG
1 GGG-TAAAATGGTAA-TTTTTGGAAAGTTCG
*
16309 GAGTAAAATGGTAATTTTTGGAAAGTTCG
1 GGGTAAAATGGTAATTTTTGGAAAGTTCG
16338 GGGTCAAAAT
1 GGGT-AAAAT
16348 ATGATTCATG
Statistics
Matches: 354, Mismatches: 78, Indels: 81
0.69 0.15 0.16
Matches are distributed among these distances:
26 8 0.02
27 31 0.09
28 82 0.23
29 117 0.33
30 91 0.26
31 25 0.07
ACGTcount: A:0.35, C:0.04, G:0.26, T:0.35
Consensus pattern (29 bp):
GGGTAAAATGGTAATTTTTGGAAAGTTCG
Found at i:17354 original size:14 final size:14
Alignment explanation
Indices: 17335--17364 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
17325 TTGGGCCCAA
17335 TTTGTAATTGGACT
1 TTTGTAATTGGACT
*
17349 TTTGTATTTGGACT
1 TTTGTAATTGGACT
17363 TT
1 TT
17365 ATTTAAATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.17, C:0.07, G:0.20, T:0.57
Consensus pattern (14 bp):
TTTGTAATTGGACT
Found at i:17383 original size:6 final size:6
Alignment explanation
Indices: 17372--17427 Score: 50
Period size: 6 Copynumber: 9.7 Consensus size: 6
17362 TTTATTTAAA
17372 TAAATT TAAATT TAAATT TATAA-- TAAATT TAAATTT TCAAA-- -AAATT
1 TAAATT TAAATT TAAATT TA-AATT TAAATT TAAA-TT T-AAATT TAAATT
17418 TAAATT TAAA
1 TAAATT TAAA
17428 ATACTTAATT
Statistics
Matches: 42, Mismatches: 0, Indels: 16
0.72 0.00 0.28
Matches are distributed among these distances:
3 3 0.07
4 2 0.05
5 2 0.05
6 27 0.64
7 5 0.12
8 3 0.07
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.45
Consensus pattern (6 bp):
TAAATT
Found at i:17400 original size:17 final size:17
Alignment explanation
Indices: 17378--17430 Score: 72
Period size: 17 Copynumber: 3.1 Consensus size: 17
17368 TAAATAAATT
17378 TAAATTTAAATTTATAA
1 TAAATTTAAATTTATAA
17395 TAAATTTAAATTT-TCAA
1 TAAATTTAAATTTAT-AA
* *
17412 AAAATTTAAATTTAAAA
1 TAAATTTAAATTTATAA
17429 TA
1 TA
17431 CTTAATTTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
16 1 0.03
17 30 0.97
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (17 bp):
TAAATTTAAATTTATAA
Found at i:17400 original size:23 final size:22
Alignment explanation
Indices: 17365--17407 Score: 77
Period size: 23 Copynumber: 1.9 Consensus size: 22
17355 TTTGGACTTT
17365 ATTTAAATAAATTTAAATTTAA
1 ATTTAAATAAATTTAAATTTAA
17387 ATTTATAATAAATTTAAATTT
1 ATTTA-AATAAATTTAAATTT
17408 TCAAAAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
ATTTAAATAAATTTAAATTTAA
Found at i:23732 original size:31 final size:31
Alignment explanation
Indices: 23694--23812 Score: 86
Period size: 31 Copynumber: 3.9 Consensus size: 31
23684 TTAATATAAT
23694 ATTTGGTAATTAAACTTGACATTTTTTCTTA
1 ATTTGGTAATTAAACTTGACATTTTTTCTTA
* *
23725 ATTTGGT-ATCTAAA-TT--TATTTTTGGTC-CA
1 ATTTGGTAAT-TAAACTTGACATTTTT--TCTTA
* * * * *
23754 ATTTGGTACTCAAACTTAATAATTTTTCTTA
1 ATTTGGTAATTAAACTTGACATTTTTTCTTA
**
23785 ATTTGGTACCTAAACTTGACACTTTTTT
1 ATTTGGTAATTAAACTTGACA-TTTTTT
23813 TTATGTTGAT
Statistics
Matches: 68, Mismatches: 11, Indels: 17
0.71 0.11 0.18
Matches are distributed among these distances:
28 6 0.09
29 11 0.16
30 11 0.16
31 29 0.43
32 11 0.16
ACGTcount: A:0.28, C:0.13, G:0.10, T:0.50
Consensus pattern (31 bp):
ATTTGGTAATTAAACTTGACATTTTTTCTTA
Found at i:23929 original size:25 final size:23
Alignment explanation
Indices: 23892--23937 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 23
23882 CCTAATTTTT
23892 TTAATATTAATTTGTTAAGCATAGC
1 TTAATATTAATTT-TTAA-CATAGC
23917 TTAATATCT-ATTTTTAACATA
1 TTAATAT-TAATTTTTAACATA
23938 AATATTCTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 4 0.20
24 4 0.20
25 11 0.55
26 1 0.05
ACGTcount: A:0.37, C:0.09, G:0.07, T:0.48
Consensus pattern (23 bp):
TTAATATTAATTTTTAACATAGC
Found at i:24139 original size:59 final size:58
Alignment explanation
Indices: 24053--24212 Score: 171
Period size: 59 Copynumber: 2.7 Consensus size: 58
24043 TGAATCTTAA
* * *
24053 AAAAAAAGCTTT-GGTATCAAACTAGGAAAAAATGTCAAGTTCATGTACCAAATTGGAT
1 AAAAAAAG-TTTAGGTACCAAATTAGGAAAAAATGTCAAGTTCAGGTACCAAATTGGAT
* * * * *
24111 CCAAAAAAGTTTAGGTACCAAATTAGGAAAAAATGTTAGGTTAAGGTACCAAATTGGGT
1 -AAAAAAAGTTTAGGTACCAAATTAGGAAAAAATGTCAAGTTCAGGTACCAAATTGGAT
** * *
24170 AATAAAAAAATTAAGTACCAAATTA-AAAAAAATGTCAAGTTCA
1 AA-AAAAAGTTTAGGTACCAAATTAGGAAAAAATGTCAAGTTCA
24213 AATATCAAAT
Statistics
Matches: 83, Mismatches: 16, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
58 18 0.22
59 65 0.78
ACGTcount: A:0.48, C:0.11, G:0.16, T:0.25
Consensus pattern (58 bp):
AAAAAAAGTTTAGGTACCAAATTAGGAAAAAATGTCAAGTTCAGGTACCAAATTGGAT
Found at i:28312 original size:19 final size:18
Alignment explanation
Indices: 28269--28331 Score: 51
Period size: 18 Copynumber: 3.5 Consensus size: 18
28259 TTTAACTAAT
28269 TGTTTTA-AACATTTATAA
1 TGTTTTATAACATTT-TAA
**
28287 TACTTTATAACATTTTAA
1 TGTTTTATAACATTTTAA
*
28305 CTGTTTTAT-ATATTTTAAA
1 -TGTTTTATAACATTTT-AA
28324 T-TTTTATA
1 TGTTTTATA
28332 TAATTTTATT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
17 6 0.17
18 15 0.42
19 15 0.42
ACGTcount: A:0.35, C:0.06, G:0.03, T:0.56
Consensus pattern (18 bp):
TGTTTTATAACATTTTAA
Found at i:28330 original size:17 final size:19
Alignment explanation
Indices: 28298--28339 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
28288 ACTTTATAAC
*
28298 ATTTTAACTGTTTTATAT-
1 ATTTTAAATGTTTTATATA
28316 ATTTTAAAT-TTTTATATA
1 ATTTTAAATGTTTTATATA
28334 ATTTTA
1 ATTTTA
28340 TTTAATTTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (19 bp):
ATTTTAAATGTTTTATATA
Found at i:35650 original size:29 final size:29
Alignment explanation
Indices: 35592--35652 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
35582 TTTTTTTAAC
* *
35592 AAAATTATGTGATTAGGCTATTTTCTCAA
1 AAAATTATGTGATTAGGATATTTTCACAA
35621 AAAATTAT-TAGATTAGGATGATTTT-ACAA
1 AAAATTATGT-GATTAGGAT-ATTTTCACAA
35650 AAA
1 AAA
35653 TATGTCCATC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 1 0.04
29 22 0.79
30 5 0.18
ACGTcount: A:0.43, C:0.07, G:0.13, T:0.38
Consensus pattern (29 bp):
AAAATTATGTGATTAGGATATTTTCACAA
Found at i:36567 original size:21 final size:21
Alignment explanation
Indices: 36542--36590 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
36532 AATAACATTA
*
36542 AATAAAAATA-TAGTAATTAAT
1 AATAAAAATATTAAT-ATTAAT
*
36563 AATAATAATATTAATATTAAT
1 AATAAAAATATTAATATTAAT
36584 AATAAAA
1 AATAAAA
36591 TAAAAGAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 21 0.88
22 3 0.12
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (21 bp):
AATAAAAATATTAATATTAAT
Found at i:36575 original size:15 final size:15
Alignment explanation
Indices: 36557--36587 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
36547 AAATATAGTA
36557 ATTAATAATAATAAT
1 ATTAATAATAATAAT
*
36572 ATTAATATTAATAAT
1 ATTAATAATAATAAT
36587 A
1 A
36588 AAATAAAAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
ATTAATAATAATAAT
Found at i:37793 original size:29 final size:29
Alignment explanation
Indices: 37760--37972 Score: 111
Period size: 29 Copynumber: 7.4 Consensus size: 29
37750 AATTTATCTA
*
37760 AAAATTACATTTTTACCCTTAAAATTTAC
1 AAAATTACATTTTTACCCTTAAACTTTAC
** ** *
37789 AAAATT-CTATTTAAACCC-TAATTTTTCC
1 AAAATTAC-ATTTTTACCCTTAAACTTTAC
***
37817 AAAATTACATTTTTACCCCCGAACTTT-C
1 AAAATTACATTTTTACCCTTAAACTTTAC
* * * *
37845 TAAAATTTCA-TTTAACCTCGATT--TCTCTA-
1 -AAAATTACATTTTTACC-C--TTAAACTTTAC
* *
37874 AAAATTACATTTTTACCCATAAACTTTCC
1 AAAATTACATTTTTACCCTTAAACTTTAC
* * **
37903 AAAATTTCATTTTGA-CCTTAATTTTCTA-
1 AAAATTACATTTTTACCCTTAAACTT-TAC
* *
37931 AAAATTACATTTTTACCCTCAAACTTTCC
1 AAAATTACATTTTTACCCTTAAACTTTAC
*
37960 AAAATTTCATTTT
1 AAAATTACATTTT
37973 CGACCCCGTT
Statistics
Matches: 133, Mismatches: 36, Indels: 30
0.67 0.18 0.15
Matches are distributed among these distances:
26 1 0.01
28 62 0.47
29 70 0.53
ACGTcount: A:0.35, C:0.21, G:0.01, T:0.42
Consensus pattern (29 bp):
AAAATTACATTTTTACCCTTAAACTTTAC
Found at i:37828 original size:28 final size:29
Alignment explanation
Indices: 37760--37828 Score: 70
Period size: 28 Copynumber: 2.4 Consensus size: 29
37750 AATTTATCTA
**
37760 AAAATTACATTTTTACCCTTAAAATTTAC
1 AAAATTACATTTAAACCCTTAAAATTTAC
** *
37789 AAAATT-CTATTTAAACCC-TAATTTTTCC
1 AAAATTAC-ATTTAAACCCTTAAAATTTAC
37817 AAAATTACATTT
1 AAAATTACATTT
37829 TTACCCCCGA
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
28 18 0.55
29 15 0.45
ACGTcount: A:0.41, C:0.17, G:0.00, T:0.42
Consensus pattern (29 bp):
AAAATTACATTTAAACCCTTAAAATTTAC
Found at i:37925 original size:114 final size:113
Alignment explanation
Indices: 37644--38109 Score: 431
Period size: 114 Copynumber: 4.1 Consensus size: 113
37634 TAAACTTCCC
* * * * **
37644 AAAAATTACATTTTCACCCTAAACTATCTAAAATTCCATTTTGACCCGATTTTTCCAAAAATTAC
1 AAAAATTACATTTTTACCCTAAACTTTCCAAAATTCTATTTTGACCTAATTTTTCC-AAAATTAC
** * * * * *
37709 ATTTTTATACCCGAACTTCCCAAAATTCCATTTTTGATCTCAATTTATCT
65 ATTTTTACCCCCGAACTTTCCAAAATTTCA-TTTTGACCTCGATTTTTCT
* * **
37759 AAAAATTACATTTTTACCCTTAAAATTTACAAAATTCTATTTAAACCCTAATTTTTCCAAAATTA
1 AAAAATTACATTTTTACCC-TAAACTTTCCAAAATTCTATTTTGA-CCTAATTTTTCCAAAATTA
* * *
37824 CATTTTTACCCCCGAACTTTCTAAAATTTCA-TTTAACCTCGATTTCTCT
64 CATTTTTACCCCCGAACTTTCCAAAATTTCATTTTGACCTCGATTTTTCT
*
37873 AAAAATTACATTTTTACCCATAAACTTTCCAAAATT-TCATTTTGACCTTAA-TTTTCTAAAAAT
1 AAAAATTACATTTTTACCC-TAAACTTTCCAAAATTCT-ATTTTGACC-TAATTTTTC-CAAAAT
* * * * *
37936 TACATTTTTACCCTCAAACTTTCCAAAATTTCATTTTCGACCCCGTTTTTTCC
62 TACATTTTTACCCCCGAACTTTCCAAAATTTCATTTT-GACCTCGATTTTTCT
* ** *** **
37989 AAAAATTATATTTTT-CCCCGAACTTTTTGAAATTCTATTTTTGACC-ATATTTTTTTAGAAATT
1 AAAAATTACATTTTTACCCTAAACTTTCCAAAATTCTA-TTTTGACCTA-ATTTTTCCA-AAATT
* * * *
38052 ACATTTTTACCCTCGAACTTTCTAAAGTTTCATTTTTA-CTCCGATTTTTCT
63 ACATTTTTACCCCCGAACTTTCCAAAATTTCATTTTGACCT-CGATTTTTCT
38103 AAAAATT
1 AAAAATT
38110 TCTATTTTAC
Statistics
Matches: 290, Mismatches: 48, Indels: 27
0.79 0.13 0.07
Matches are distributed among these distances:
113 10 0.03
114 120 0.41
115 75 0.26
116 75 0.26
117 10 0.03
ACGTcount: A:0.33, C:0.21, G:0.03, T:0.43
Consensus pattern (113 bp):
AAAAATTACATTTTTACCCTAAACTTTCCAAAATTCTATTTTGACCTAATTTTTCCAAAATTACA
TTTTTACCCCCGAACTTTCCAAAATTTCATTTTGACCTCGATTTTTCT
Found at i:38072 original size:115 final size:113
Alignment explanation
Indices: 37817--38135 Score: 338
Period size: 115 Copynumber: 2.8 Consensus size: 113
37807 TAATTTTTCC
* * *
37817 AAAATTACATTTTTACCCCCGAACTTTCTAAAATTTCA-TTTAACCTCGATTTCTCTAAAAATTA
1 AAAATTACATTTTTACCCTCGAACTTTCTAAAATTTCATTTTAACCCCGATTTTTCTAAAAATTA
* ** *** *
37881 CATTTTTACCCATAAACTTTCCAAAATTTCATTTTGACCTTAATTTTCTA
66 TATTTTT-CCC-CGAACTTTTTGAAATTTCATTTTGACCATAATTTTCTA
* * * * *
37931 AAAATTACATTTTTACCCTCAAACTTTCCAAAATTTCATTTTCGACCCCGTTTTTTCCAAAAATT
1 AAAATTACATTTTTACCCTCGAACTTTCTAAAATTTCATTTT-AACCCCGATTTTTCTAAAAATT
* *
37996 ATATTTTTCCCCGAACTTTTTGAAA-TTCTATTTTTGACCATATTTTTTTA
65 ATATTTTTCCCCGAACTTTTTGAAATTTC-A-TTTTGACCATAATTTTCTA
* * * *
38046 GAAATTACATTTTTACCCTCGAACTTTCTAAAGTTTCATTTTTACTCCGATTTTTCTAAAAATTT
1 AAAATTACATTTTTACCCTCGAACTTTCTAAAATTTCATTTTAACCCCGATTTTTCTAAAAA-TT
* * *
38111 CTATTTTACCTTCGAA-TTTTTGAAA
65 ATATTTTTCC-CCGAACTTTTTGAAA
38136 ATTCCGCTTT
Statistics
Matches: 171, Mismatches: 28, Indels: 11
0.81 0.13 0.05
Matches are distributed among these distances:
113 3 0.02
114 61 0.36
115 79 0.46
116 28 0.16
ACGTcount: A:0.30, C:0.20, G:0.04, T:0.45
Consensus pattern (113 bp):
AAAATTACATTTTTACCCTCGAACTTTCTAAAATTTCATTTTAACCCCGATTTTTCTAAAAATTA
TATTTTTCCCCGAACTTTTTGAAATTTCATTTTGACCATAATTTTCTA
Found at i:38099 original size:58 final size:57
Alignment explanation
Indices: 37644--38126 Score: 385
Period size: 57 Copynumber: 8.4 Consensus size: 57
37634 TAAACTTCCC
* * * * *
37644 AAAAATTACATTTTCACCCT-AAACTATCTAAAATTCCATTTTGACCCGATTTTTCC
1 AAAAATTACATTTTTACCCTCGAACTTTCTAAAATTTCATTTTGACCCGATTTTTCT
* * * * * * *
37700 AAAAATTACATTTTTATACC-CGAACTTCCCAAAATTCCATTTTTGATCTCAATTTATCT
1 AAAAATTACATTTTTA-CCCTCGAACTTTCTAAAATTTCA-TTTTGA-CCCGATTTTTCT
** * ** *
37759 AAAAATTACATTTTTACCCTTAAAATTTAC-AAAA-TTCTATTTAAACCCTAATTTTTC-
1 AAAAATTACATTTTTACCCTCGAACTTT-CTAAAATTTC-ATTTTGACCC-GATTTTTCT
* * * *
37816 CAAAATTACATTTTTACCCCCGAACTTTCTAAAATTTCA-TTTAACCTCGATTTCTCT
1 AAAAATTACATTTTTACCCTCGAACTTTCTAAAATTTCATTTTGACC-CGATTTTTCT
* * ** *
37873 AAAAATTACATTTTTACCCAT-AAACTTTCCAAAATTTCATTTTGACCTTAATTTTCT
1 AAAAATTACATTTTTACCC-TCGAACTTTCTAAAATTTCATTTTGACCCGATTTTTCT
* * * *
37930 AAAAATTACATTTTTACCCTCAAACTTTCCAAAATTTCATTTTCGACCCCGTTTTTTCC
1 AAAAATTACATTTTTACCCTCGAACTTTCTAAAATTTCATTTT-GA-CCCGATTTTTCT
* * * ** *
37989 AAAAATTATATTTTT-CCC-CGAACTTTTTGAAA-TTCTATTTTTGACCATATTTTTTT
1 AAAAATTACATTTTTACCCTCGAACTTTCTAAAATTTC-A-TTTTGACCCGATTTTTCT
* * *
38045 AGAAATTACATTTTTACCCTCGAACTTTCTAAAGTTTCATTTTTACTCCGATTTTTCT
1 AAAAATTACATTTTTACCCTCGAACTTTCTAAAATTTCATTTTGAC-CCGATTTTTCT
* *
38103 AAAAATTTC-TATTTTACCTTCGAA
1 AAAAATTACAT-TTTTACCCTCGAA
38127 TTTTTGAAAA
Statistics
Matches: 339, Mismatches: 64, Indels: 46
0.76 0.14 0.10
Matches are distributed among these distances:
56 52 0.15
57 151 0.45
58 78 0.23
59 57 0.17
60 1 0.00
ACGTcount: A:0.32, C:0.21, G:0.04, T:0.43
Consensus pattern (57 bp):
AAAAATTACATTTTTACCCTCGAACTTTCTAAAATTTCATTTTGACCCGATTTTTCT
Found at i:38111 original size:29 final size:30
Alignment explanation
Indices: 37809--38131 Score: 121
Period size: 29 Copynumber: 11.2 Consensus size: 30
37799 TTAAACCCTA
* * *
37809 ATTTTTC-CAAAATTACATTTTTACCCCCG
1 ATTTTTCTAAAAATTTCATTTTTACCCTCG
** *
37838 AACTTTCT-AAAATTTCA--TTTAACCTCG
1 ATTTTTCTAAAAATTTCATTTTTACCCTCG
* * *
37865 ATTTCTCTAAAAATTACATTTTTACCCAT-A
1 ATTTTTCTAAAAATTTCATTTTTACCC-TCG
** * * *
37895 AACTTTC-CAAAATTTCATTTTGA-CCT-T
1 ATTTTTCTAAAAATTTCATTTTTACCCTCG
* * *
37922 AATTTTCTAAAAATTACATTTTTACCCTCA
1 ATTTTTCTAAAAATTTCATTTTTACCCTCG
** * *
37952 AACTTTC-CAAAATTTCATTTTCGACCC-CG
1 ATTTTTCTAAAAATTTCATTTT-TACCCTCG
* *
37981 TTTTTTCCAAAAATTAT-ATTTTT-CCC-CG
1 ATTTTTCTAAAAATT-TCATTTTTACCCTCG
* * *
38009 AACTTTT-T-GAAA-TTCTATTTTTGACCAT--
1 -ATTTTTCTAAAAATTTC-ATTTTT-ACCCTCG
* * *
38037 ATTTTTTTAGAAATTACATTTTTACCCTCG
1 ATTTTTCTAAAAATTTCATTTTTACCCTCG
** * *
38067 AACTTTCT-AAAGTTTCATTTTTACTC-CG
1 ATTTTTCTAAAAATTTCATTTTTACCCTCG
*
38095 ATTTTTCTAAAAATTTC-TATTTTACCTTCG
1 ATTTTTCTAAAAATTTCAT-TTTTACCCTCG
38125 AATTTTT
1 -ATTTTT
38132 GAAAATTCCG
Statistics
Matches: 215, Mismatches: 53, Indels: 50
0.68 0.17 0.16
Matches are distributed among these distances:
25 1 0.00
26 1 0.00
27 34 0.16
28 42 0.20
29 89 0.41
30 40 0.19
31 8 0.04
ACGTcount: A:0.29, C:0.21, G:0.04, T:0.46
Consensus pattern (30 bp):
ATTTTTCTAAAAATTTCATTTTTACCCTCG
Found at i:49730 original size:201 final size:192
Alignment explanation
Indices: 49229--49815 Score: 755
Period size: 201 Copynumber: 3.0 Consensus size: 192
49219 AACTCAAGGT
* * *
49229 TCAATACGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATAGTGAGAAGTAGGGCGAAGCAAT
1 TCAATGCGAGCAAATCTTCGAA-CCCAGCTTCCTGATGAGATACTGAGAAGCA-GGCGAAGCAAT
* * * * *
49294 AAAAAGGTTAGCTTCTTGATGAGAT-TTGAGAAGTGGACCAAATTCGTCTTCCTAATAAGGTATA
64 AAAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGGTACA
*
49358 GAGAAGCGGATTGAAACAAGTGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGTATACCAAC
129 GAGAAGCGGATTGAAACAAGCGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGTATACCAAC
* *
49422 TCAATGCGAGCAAATCTTCGAACCACAGCTTCCTAATGAGATACTGAAAAGCAGAGCGAAGCAAT
1 TCAATGCGAGCAAATCTTCGAACC-CAGCTTCCTGATGAGATACTGAGAAGCAG-GCGAAGCAAT
* * *
49487 AAAAAGGTTAGCTTCCTGATGAGACACTAAGAAGTGGACCAAATTCATCTTCCTGATGAGGTACA
64 AAAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGGTACA
* * * *
49552 GAGAAGCGGATTGAAACAAACGGGGCGGTTATCTTCCTGTTGAGATACAGAGAAGTATACCAAC
129 GAGAAGCGGATTGAAACAAGCGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGTATACCAAC
* * *
49616 TCAGGGCTCGATGTGAGTAAATCTTCGAATCCCAGCTTCTTGATGAGATACTGAGAAGCAGGTCG
1 TCA-------ATGCGAGCAAATCTTCGAA-CCCAGCTTCCTGATGAGATACTGAGAAGCAGG-CG
* * * **
49681 AAGCAATAAAATGGTTAGCTTCCTGATGAAATACTGAGAAGTAGACCAAATTCGTCTTTTTGATG
57 AAGCAATAAAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATG
* * * *
49746 AGGTACAGAGAAGCGGAATGAAACAAGCGATGCGGTCATATTCCTGATAAGATACTA-AGAAGTA
122 AGGTACAGAGAAGCGGATTGAAACAAGCGAGGCGGTCATCTTCCTGATGAGATAC-AGAGAAGTA
*
49810 GACCAA
186 TACCAA
49816 ATTAACGACA
Statistics
Matches: 341, Mismatches: 40, Indels: 18
0.85 0.10 0.05
Matches are distributed among these distances:
192 3 0.01
193 78 0.23
194 95 0.28
200 1 0.00
201 161 0.47
202 3 0.01
ACGTcount: A:0.35, C:0.18, G:0.24, T:0.23
Consensus pattern (192 bp):
TCAATGCGAGCAAATCTTCGAACCCAGCTTCCTGATGAGATACTGAGAAGCAGGCGAAGCAATAA
AAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGGTACAGA
GAAGCGGATTGAAACAAGCGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGTATACCAAC
Found at i:50183 original size:18 final size:17
Alignment explanation
Indices: 50127--50216 Score: 81
Period size: 17 Copynumber: 5.2 Consensus size: 17
50117 ACTCATTTTA
**
50127 AAATTTATTTTAAGGTT
1 AAATTTATTTTAAATTT
* *
50144 AAATTTATTTTGAATAT
1 AAATTTATTTTAAATTT
*
50161 AAATTTGTTTTCAAATTT
1 AAATTTATTTT-AAATTT
***
50179 AAATTTAAAATAAATTT
1 AAATTTATTTTAAATTT
*
50196 AGATTTATATTTAAATTT
1 AAATTTAT-TTTAAATTT
50214 AAA
1 AAA
50217 ACTTATTATA
Statistics
Matches: 55, Mismatches: 16, Indels: 3
0.74 0.22 0.04
Matches are distributed among these distances:
17 35 0.64
18 20 0.36
ACGTcount: A:0.43, C:0.01, G:0.06, T:0.50
Consensus pattern (17 bp):
AAATTTATTTTAAATTT
Found at i:50184 original size:6 final size:6
Alignment explanation
Indices: 50173--50216 Score: 54
Period size: 6 Copynumber: 7.5 Consensus size: 6
50163 ATTTGTTTTC
* * *
50173 AAATTT AAATTT AAA-AT AAATTT AGATTT ATATTT AAATTT AAA
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAA
50217 ACTTATTATA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
5 4 0.12
6 28 0.88
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (6 bp):
AAATTT
Found at i:50191 original size:29 final size:29
Alignment explanation
Indices: 50142--50217 Score: 84
Period size: 29 Copynumber: 2.6 Consensus size: 29
50132 TATTTTAAGG
* * *
50142 TTAAATTT-ATTTTGAATATAAATTT-GTT
1 TTAAATTTAAATTT-AAAATAAATTTAGAT
50170 TTCAAATTTAAATTTAAAATAAATTTAGAT
1 TT-AAATTTAAATTTAAAATAAATTTAGAT
*
50200 TTATATTTAAATTTAAAA
1 TTAAATTTAAATTTAAAA
50218 CTTATTATAA
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
28 2 0.05
29 31 0.76
30 8 0.20
ACGTcount: A:0.45, C:0.01, G:0.04, T:0.50
Consensus pattern (29 bp):
TTAAATTTAAATTTAAAATAAATTTAGAT
Found at i:52193 original size:29 final size:29
Alignment explanation
Indices: 52154--52265 Score: 81
Period size: 29 Copynumber: 3.8 Consensus size: 29
52144 TACCTCGATT
*
52154 TTTCCAAAAATTACATTTTGACACCTGAAC
1 TTTCCTAAAATTACATTTTGAC-CCTGAAC
*
52184 TTTCC-AAAA-TACTATTTTGACCCCG-A-
1 TTTCCTAAAATTAC-ATTTTGACCCTGAAC
* *
52210 TTTCTCTTAAAATTACATTTTTACCCTCAAAC
1 TTTC-C-TAAAATTACATTTTGACCCT-GAAC
* *
52242 -TTCCCAAAATTTCATTTTTGACCC
1 TTTCCTAAAATTACA-TTTTGACCC
52266 CGATTTTTTT
Statistics
Matches: 66, Mismatches: 7, Indels: 18
0.73 0.08 0.20
Matches are distributed among these distances:
26 4 0.06
27 2 0.03
28 6 0.09
29 33 0.50
30 17 0.26
31 4 0.06
ACGTcount: A:0.31, C:0.26, G:0.04, T:0.38
Consensus pattern (29 bp):
TTTCCTAAAATTACATTTTGACCCTGAAC
Found at i:52201 original size:59 final size:59
Alignment explanation
Indices: 52098--52296 Score: 185
Period size: 58 Copynumber: 3.4 Consensus size: 59
52088 CCTAAACTTC
* * * *
52098 CCAAAAATTATATTTTCACCCCCAAACTTT-CAAAA-ACTCCATTTTTTACCTCGATTTTT
1 CCAAAAATTACATTTTCA-CCCTAAACTTTCCAAAATACT-CATTTTTGACCCCGATTTTT
* * *
52157 CCAAAAATTACATTTTGACACCTGAACTTTCCAAAATACT-A-TTTTGACCCCGATTTCT
1 CCAAAAATTACATTTTCAC-CCTAAACTTTCCAAAATACTCATTTTTGACCCCGATTTTT
** * * *
52215 CTTAAAATTACATTTTTACCCTCAAACTTCCCAAAAT-TTCATTTTTGACCCCGATTTTTT
1 CCAAAAATTACATTTTCACCCT-AAACTTTCCAAAATACTCATTTTTGACCCCGA-TTTTT
*
52275 TCAAAAATTACCATTTT-ACCCT
1 CCAAAAATTA-CATTTTCACCCT
52297 TGGATTTCTA
Statistics
Matches: 115, Mismatches: 17, Indels: 15
0.78 0.12 0.10
Matches are distributed among these distances:
57 4 0.03
58 44 0.38
59 37 0.32
60 21 0.18
61 9 0.08
ACGTcount: A:0.32, C:0.26, G:0.04, T:0.39
Consensus pattern (59 bp):
CCAAAAATTACATTTTCACCCTAAACTTTCCAAAATACTCATTTTTGACCCCGATTTTT
Found at i:54718 original size:2 final size:2
Alignment explanation
Indices: 54711--54741 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
54701 AAATAAAATA
54711 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
54742 AAAAGTGAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:55429 original size:15 final size:16
Alignment explanation
Indices: 55409--55438 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
55399 AAAAAATATA
55409 AAAATAT-AAATTATT
1 AAAATATAAAATTATT
55424 AAAATATAAAATTAT
1 AAAATATAAAATTAT
55439 ATTTTTACAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
AAAATATAAAATTATT
Found at i:60842 original size:25 final size:23
Alignment explanation
Indices: 60811--60859 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 23
60801 ATATCGAATT
60811 TTAAAATCTAGAAAAAGTAATAGAA
1 TTAAAAT-T-GAAAAAGTAATAGAA
*
60836 TTAAAATTTAAAAAGTAATAGAA
1 TTAAAATTGAAAAAGTAATAGAA
60859 T
1 T
60860 AAGCCCAGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 15 0.65
24 1 0.04
25 7 0.30
ACGTcount: A:0.59, C:0.02, G:0.10, T:0.29
Consensus pattern (23 bp):
TTAAAATTGAAAAAGTAATAGAA
Found at i:63325 original size:13 final size:14
Alignment explanation
Indices: 63309--63337 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
63299 ATATTGAAAA
63309 TTAAG-TATAGAAT
1 TTAAGTTATAGAAT
63322 TTAAGTTATAGAAT
1 TTAAGTTATAGAAT
63336 TT
1 TT
63338 GTTTGGTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.33
14 10 0.67
ACGTcount: A:0.41, C:0.00, G:0.14, T:0.45
Consensus pattern (14 bp):
TTAAGTTATAGAAT
Found at i:66584 original size:23 final size:21
Alignment explanation
Indices: 66501--66577 Score: 84
Period size: 23 Copynumber: 3.5 Consensus size: 21
66491 ATTATATTGT
*
66501 TGTTTTG-GTGTTTTTTTTAC
1 TGTTTTGATTGTTTTTTTTAC
*
66521 TGTTTTGATTGATTTTTTTTTGC
1 TGTTTTGATTG--TTTTTTTTAC
*
66544 TGTTTTTGAGTTGTTTTTTTTAT
1 TG-TTTTGA-TTGTTTTTTTTAC
66567 TGTTTTGATTG
1 TGTTTTGATTG
66578 CTATTTTCGT
Statistics
Matches: 48, Mismatches: 4, Indels: 9
0.79 0.07 0.15
Matches are distributed among these distances:
20 7 0.15
21 5 0.10
22 6 0.12
23 21 0.44
24 6 0.12
25 3 0.06
ACGTcount: A:0.08, C:0.03, G:0.19, T:0.70
Consensus pattern (21 bp):
TGTTTTGATTGTTTTTTTTAC
Found at i:66596 original size:46 final size:44
Alignment explanation
Indices: 66503--66605 Score: 116
Period size: 46 Copynumber: 2.3 Consensus size: 44
66493 TATATTGTTG
* * ** *
66503 TTTTGGTGTTTTTTTTACTGTTTTGATTGATTTTTTTTTGCTGT
1 TTTTGTTGTTTTTTTTACTGTTTTGATTGATATTTTCGTGCTAT
* * *
66547 TTTTGAGTTGTTTTTTTTATTGTTTTGATTGCTATTTTCGTGTTAT
1 TTTT--GTTGTTTTTTTTACTGTTTTGATTGATATTTTCGTGCTAT
66593 TTTTGTTGTTTTT
1 TTTTGTTGTTTTT
66606 GTTGTTGCTA
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
44 13 0.27
46 36 0.73
ACGTcount: A:0.08, C:0.04, G:0.17, T:0.71
Consensus pattern (44 bp):
TTTTGTTGTTTTTTTTACTGTTTTGATTGATATTTTCGTGCTAT
Found at i:66602 original size:12 final size:12
Alignment explanation
Indices: 66569--66682 Score: 80
Period size: 12 Copynumber: 9.8 Consensus size: 12
66559 TTTTTTATTG
*
66569 TTTTGATTGCTAT
1 TTTTG-TTGTTAT
*
66582 TTTCG-TGTTAT
1 TTTTGTTGTTAT
66593 TTTTGTTGTT-T
1 TTTTGTTGTTAT
*
66604 TTGTTGTTGCTAT
1 TT-TTGTTGTTAT
66617 TTTTGTTGTT-T
1 TTTTGTTGTTAT
*
66628 TTAATGTTG----
1 TT-TTGTTGTTAT
**
66637 TTTTACTGTTAT
1 TTTTGTTGTTAT
*
66649 TTTTGTTGTTGT
1 TTTTGTTGTTAT
*
66661 TTTGGTTGTTAT
1 TTTTGTTGTTAT
66673 TTTTGTTGTT
1 TTTTGTTGTT
66683 TGGATGTTAT
Statistics
Matches: 78, Mismatches: 15, Indels: 17
0.71 0.14 0.15
Matches are distributed among these distances:
8 3 0.04
9 2 0.03
11 15 0.19
12 51 0.65
13 7 0.09
ACGTcount: A:0.08, C:0.04, G:0.19, T:0.69
Consensus pattern (12 bp):
TTTTGTTGTTAT
Found at i:66617 original size:24 final size:23
Alignment explanation
Indices: 66557--66682 Score: 89
Period size: 24 Copynumber: 5.5 Consensus size: 23
66547 TTTTGAGTTG
* * *
66557 TTTTTTTTATTGTTTTGATTGCTA
1 TTTTTGTTGTTGTTTTG-TTGTTA
* * *
66581 TTTTCG-TGTT-ATTT-TTGTTG
1 TTTTTGTTGTTGTTTTGTTGTTA
*
66601 TTTTTGTTGTTGCTATTT-TTGTTG
1 TTTTTGTTGTTG-T-TTTGTTGTTA
** **
66625 TTTTTAATGTTGTTTTACTGTTA
1 TTTTTGTTGTTGTTTTGTTGTTA
66648 TTTTTGTTGTTGTTTTGGTTGTTA
1 TTTTTGTTGTTGTTTT-GTTGTTA
66672 TTTTTGTTGTT
1 TTTTTGTTGTT
66683 TGGATGTTAT
Statistics
Matches: 80, Mismatches: 16, Indels: 12
0.74 0.15 0.11
Matches are distributed among these distances:
20 9 0.11
21 4 0.05
22 6 0.08
23 22 0.28
24 39 0.49
ACGTcount: A:0.08, C:0.03, G:0.18, T:0.71
Consensus pattern (23 bp):
TTTTTGTTGTTGTTTTGTTGTTA
Found at i:66627 original size:56 final size:56
Alignment explanation
Indices: 66537--66683 Score: 165
Period size: 56 Copynumber: 2.6 Consensus size: 56
66527 GATTGATTTT
* * * *
66537 TTTTTGCTGTTTTTG-AGTTGTTTTTTTTATTGTTTTGATTGCTATTTT-CGTGTTA
1 TTTTTGTTGTTTTTGTAGTTGTTATTTTTGTTGTTTTGAATGCTATTTTAC-TGTTA
* * * * *
66592 TTTTTGTTGTTTTTGTTGTTGCTATTTTTGTTGTTTTTAATGTTGTTTTACTGTTA
1 TTTTTGTTGTTTTTGTAGTTGTTATTTTTGTTGTTTTGAATGCTATTTTACTGTTA
*
66648 TTTTTGTTGTTGTTT-TGGTTGTTATTTTTGTTGTTT
1 TTTTTGTTGTT-TTTGTAGTTGTTATTTTTGTTGTTT
66684 GGATGTTATT
Statistics
Matches: 78, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
55 14 0.18
56 60 0.77
57 4 0.05
ACGTcount: A:0.07, C:0.03, G:0.19, T:0.70
Consensus pattern (56 bp):
TTTTTGTTGTTTTTGTAGTTGTTATTTTTGTTGTTTTGAATGCTATTTTACTGTTA
Found at i:66646 original size:23 final size:23
Alignment explanation
Indices: 66620--66663 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
66610 TTGCTATTTT
*
66620 TGTTGTTTTTAATGTTGTTTTAC
1 TGTTATTTTTAATGTTGTTTTAC
**
66643 TGTTATTTTTGTTGTTGTTTT
1 TGTTATTTTTAATGTTGTTTT
66664 GGTTGTTATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.09, C:0.02, G:0.18, T:0.70
Consensus pattern (23 bp):
TGTTATTTTTAATGTTGTTTTAC
Found at i:66670 original size:44 final size:45
Alignment explanation
Indices: 66596--66696 Score: 109
Period size: 44 Copynumber: 2.2 Consensus size: 45
66586 GTGTTATTTT
* * *
66596 TGTTGTTTTTGTTGTTGCTATTTTTGTTGTT-TTTAATGTTGTTT-TA
1 TGTTATTTTTGTTGTTG--ATTTTGGTTGTTATTT-ATGTTGTTTGGA
*
66642 CTGTTATTTTTGTTGTTG-TTTTGGTTGTTATTTTTGTTGTTTGGA
1 -TGTTATTTTTGTTGTTGATTTTGGTTGTTATTTATGTTGTTTGGA
66687 TGTTATTTTT
1 TGTTATTTTT
66697 TTATGCGTTT
Statistics
Matches: 48, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
44 28 0.58
45 4 0.08
47 16 0.33
ACGTcount: A:0.08, C:0.02, G:0.21, T:0.69
Consensus pattern (45 bp):
TGTTATTTTTGTTGTTGATTTTGGTTGTTATTTATGTTGTTTGGA
Found at i:66690 original size:20 final size:21
Alignment explanation
Indices: 66654--66696 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 21
66644 GTTATTTTTG
*
66654 TTGTTGTTTTGGTTGTTATTT
1 TTGTTGTTTTGGATGTTATTT
66675 TTGTTG-TTTGGATGTTATTT
1 TTGTTGTTTTGGATGTTATTT
66695 TT
1 TT
66697 TTATGCGTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 15 0.71
21 6 0.29
ACGTcount: A:0.07, C:0.00, G:0.23, T:0.70
Consensus pattern (21 bp):
TTGTTGTTTTGGATGTTATTT
Found at i:66697 original size:21 final size:22
Alignment explanation
Indices: 66643--66697 Score: 69
Period size: 21 Copynumber: 2.5 Consensus size: 22
66633 GTTGTTTTAC
*
66643 TGTTATTTTTGTTGTTGTTTTGGT
1 TGTTA-TTTT-TTGTTGTTTTGGA
66667 TGTTA-TTTTTGTTG-TTTGGA
1 TGTTATTTTTTGTTGTTTTGGA
66687 TGTTATTTTTT
1 TGTTATTTTTT
66698 TATGCGTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
20 10 0.34
21 11 0.38
22 3 0.10
24 5 0.17
ACGTcount: A:0.07, C:0.00, G:0.22, T:0.71
Consensus pattern (22 bp):
TGTTATTTTTTGTTGTTTTGGA
Found at i:70175 original size:15 final size:16
Alignment explanation
Indices: 70155--70184 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
70145 TTTTAATTAT
70155 TTTATA-TTTGGAAAC
1 TTTATATTTTGGAAAC
70170 TTTATATTTTGGAAA
1 TTTATATTTTGGAAA
70185 ATTATCTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.33, C:0.03, G:0.13, T:0.50
Consensus pattern (16 bp):
TTTATATTTTGGAAAC
Found at i:72379 original size:31 final size:31
Alignment explanation
Indices: 72329--72393 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 31
72319 ATGTGCATGA
*
72329 TTAAATCAAAAATAAAATTTTAAGTATATAT
1 TTAAATCAAAAATAAAATTTCAAGTATATAT
* * * * *
72360 TTAAATCACAATTAGAATTTCATGTATATGT
1 TTAAATCAAAAATAAAATTTCAAGTATATAT
72391 TTA
1 TTA
72394 CACCAAATTA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.46, C:0.06, G:0.06, T:0.42
Consensus pattern (31 bp):
TTAAATCAAAAATAAAATTTCAAGTATATAT
Found at i:73571 original size:6 final size:6
Alignment explanation
Indices: 73560--73598 Score: 60
Period size: 6 Copynumber: 6.3 Consensus size: 6
73550 AAATAATAAG
*
73560 AATTAA AATTAA AATTAA AATTAA AATTATT AATTAA AA
1 AATTAA AATTAA AATTAA AATTAA AATTA-A AATTAA AA
73599 AGAATTGGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
6 25 0.83
7 5 0.17
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (6 bp):
AATTAA
Found at i:78058 original size:20 final size:20
Alignment explanation
Indices: 78033--78095 Score: 56
Period size: 20 Copynumber: 3.0 Consensus size: 20
78023 ACAAAAAGAT
78033 TCAAAATAATTTTTAAAAAA
1 TCAAAATAATTTTTAAAAAA
* * *
78053 TCAAAA-CATTTATAAAAATT
1 TCAAAATAATTTTTAAAAA-A
*
78073 TCAAAATTTATCTTTTAAAAAA
1 TCAAAA-TAAT-TTTTAAAAAA
78095 T
1 T
78096 TATAAAAATT
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
19 10 0.30
20 12 0.36
22 3 0.09
23 8 0.24
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (20 bp):
TCAAAATAATTTTTAAAAAA
Found at i:85391 original size:12 final size:12
Alignment explanation
Indices: 85374--85401 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
85364 TCTTTAGTTC
85374 ACAAGGATAATG
1 ACAAGGATAATG
85386 ACAAGGATAATG
1 ACAAGGATAATG
85398 ACAA
1 ACAA
85402 ATTTGCATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.54, C:0.11, G:0.21, T:0.14
Consensus pattern (12 bp):
ACAAGGATAATG
Found at i:87229 original size:15 final size:16
Alignment explanation
Indices: 87199--87232 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
87189 AAATACCATT
87199 TTTATCATTTTAATAA
1 TTTATCATTTTAATAA
*
87215 TTTAT-ATTTTTATAA
1 TTTATCATTTTAATAA
87230 TTT
1 TTT
87233 TTTTAATGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTATCATTTTAATAA
Found at i:88655 original size:16 final size:17
Alignment explanation
Indices: 88636--88669 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
88626 TAAAAATAAA
*
88636 ATTAGATAAAAT-TTTT
1 ATTAGAAAAAATATTTT
88652 ATTAGAAAAAATATTTT
1 ATTAGAAAAAATATTTT
88669 A
1 A
88670 CTCTTTGATC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (17 bp):
ATTAGAAAAAATATTTT
Found at i:89638 original size:21 final size:22
Alignment explanation
Indices: 89594--89638 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
89584 TTTTTAAAAA
* *
89594 TAATATAAAATAATTACTACAC
1 TAATATAAAAAAATTACTAAAC
*
89616 TAATA-AAAAAAATTATTAAAC
1 TAATATAAAAAAATTACTAAAC
89637 TA
1 TA
89639 TTTAAAAGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.60, C:0.09, G:0.00, T:0.31
Consensus pattern (22 bp):
TAATATAAAAAAATTACTAAAC
Done.