Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015145.1 Kokia drynarioides strain JFW-HI SEQ_130189, 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: 283638
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 207 characters in sequence are not A, C, G, or T
Found at i:1675 original size:21 final size:22
Alignment explanation
Indices: 1651--1695 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
1641 AAAGTTTTAA
*
1651 TTATACATTTATCTA-TTTATT
1 TTATACATTTAACTATTTTATT
**
1672 TTATTTATTTAACTATTTTATT
1 TTATACATTTAACTATTTTATT
1694 TT
1 TT
1696 TCTTATGAAG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.27, C:0.07, G:0.00, T:0.67
Consensus pattern (22 bp):
TTATACATTTAACTATTTTATT
Found at i:12079 original size:25 final size:25
Alignment explanation
Indices: 12045--12092 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
12035 TTAAAGCTTA
12045 AAATTTCGAATCAAACTCAAACTTC
1 AAATTTCGAATCAAACTCAAACTTC
12070 AAATTTCGAATCAAACTCAAACT
1 AAATTTCGAATCAAACTCAAACT
12093 CGCTTCGATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.46, C:0.23, G:0.04, T:0.27
Consensus pattern (25 bp):
AAATTTCGAATCAAACTCAAACTTC
Found at i:12841 original size:6 final size:6
Alignment explanation
Indices: 12830--12854 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
12820 GACTGAGGGG
12830 AAAACC AAAACC AAAACC AAAACC A
1 AAAACC AAAACC AAAACC AAAACC A
12855 TTAACTATCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (6 bp):
AAAACC
Found at i:14306 original size:17 final size:18
Alignment explanation
Indices: 14274--14312 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
14264 ATTTAATTTA
*
14274 ATTTATTATTTATAAT-T
1 ATTTATTATTCATAATCT
*
14291 ATTTATTATTCGTAATCT
1 ATTTATTATTCATAATCT
14309 ATTT
1 ATTT
14313 CAGTTGAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.31, C:0.05, G:0.03, T:0.62
Consensus pattern (18 bp):
ATTTATTATTCATAATCT
Found at i:25297 original size:23 final size:23
Alignment explanation
Indices: 25270--25315 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
25260 TCAATTTAAA
*
25270 TTTTGGAGGCTAAAATTATATAT
1 TTTTGGAGGCAAAAATTATATAT
* *
25293 TTTTGGTGGCAAAAATTTTATAT
1 TTTTGGAGGCAAAAATTATATAT
25316 AAAATTATTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.33, C:0.04, G:0.17, T:0.46
Consensus pattern (23 bp):
TTTTGGAGGCAAAAATTATATAT
Found at i:27374 original size:20 final size:20
Alignment explanation
Indices: 27329--27376 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
27319 TCTAGCCTAA
*
27329 ACATCAACCAAACCACTCTC
1 ACATCAAACAAACCACTCTC
*
27349 ATATCAAACAAACCACTC-C
1 ACATCAAACAAACCACTCTC
27368 TACATCAAA
1 -ACATCAAA
27377 TATTGTTGGT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 1 0.04
20 23 0.96
ACGTcount: A:0.46, C:0.38, G:0.00, T:0.17
Consensus pattern (20 bp):
ACATCAAACAAACCACTCTC
Found at i:29357 original size:19 final size:21
Alignment explanation
Indices: 29333--29375 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
29323 GACAAGTATG
29333 TTTCTG-TTTTT-TTTTTTAA
1 TTTCTGTTTTTTATTTTTTAA
29352 TTTCTGTTTTTTATTTTTTAA
1 TTTCTGTTTTTTATTTTTTAA
29373 TTT
1 TTT
29376 AAATGCGTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 6 0.27
20 5 0.23
21 11 0.50
ACGTcount: A:0.12, C:0.05, G:0.05, T:0.79
Consensus pattern (21 bp):
TTTCTGTTTTTTATTTTTTAA
Found at i:37843 original size:2 final size:2
Alignment explanation
Indices: 37836--37863 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
37826 AACTTAGTAT
37836 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
37864 AAGGGAAGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:40160 original size:35 final size:34
Alignment explanation
Indices: 40121--40210 Score: 110
Period size: 35 Copynumber: 2.6 Consensus size: 34
40111 TAAGCTCCCC
* *
40121 TTTAAATTTATTTTAAGA-TTAAATTTGTTTAAAA
1 TTTAAATTTATTTTAA-ATTTAAATGTATTTAAAA
*
40155 TTTTAAATTTATTTTAAATTTAAATGTATTTTAAA
1 -TTTAAATTTATTTTAAATTTAAATGTATTTAAAA
*
40190 TTTAAATTTAAGTTTAAATTT
1 TTTAAATTT-ATTTTAAATTT
40211 GTTATCAAAT
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
34 10 0.20
35 39 0.80
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (34 bp):
TTTAAATTTATTTTAAATTTAAATGTATTTAAAA
Found at i:40162 original size:18 final size:17
Alignment explanation
Indices: 40121--40210 Score: 110
Period size: 17 Copynumber: 5.2 Consensus size: 17
40111 TAAGCTCCCC
40121 TTTAAATTTATTTTAAGA
1 TTTAAATTTATTTTAA-A
* *
40139 -TTAAATTTGTTTAAAA
1 TTTAAATTTATTTTAAA
40155 TTTTAAATTTATTTTAAA
1 -TTTAAATTTATTTTAAA
*
40173 TTTAAATGTATTTTAAA
1 TTTAAATTTATTTTAAA
*
40190 TTTAAATTTAAGTTTAAA
1 TTTAAATTT-ATTTTAAA
40208 TTT
1 TTT
40211 GTTATCAAAT
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
16 1 0.02
17 37 0.60
18 24 0.39
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:40176 original size:6 final size:6
Alignment explanation
Indices: 40156--40210 Score: 60
Period size: 6 Copynumber: 9.5 Consensus size: 6
40146 TGTTTAAAAT
* * * *
40156 TTTAAA TTT-AT TTTAAA TTTAAA TGT-AT TTTAAA TTTAAA TTTAAG
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
40202 TTTAAA TTT
1 TTTAAA TTT
40211 GTTATCAAAT
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
5 7 0.18
6 32 0.82
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (6 bp):
TTTAAA
Found at i:40233 original size:18 final size:17
Alignment explanation
Indices: 40156--40244 Score: 55
Period size: 17 Copynumber: 5.5 Consensus size: 17
40146 TGTTTAAAAT
* *
40156 TTTAAATTTATTTTAAA
1 TTTAAAATTATTATAAA
*
40173 TTT-AAATGTATTTTAAA
1 TTTAAAAT-TATTATAAA
*
40190 TTT--AA--ATT-TAAG
1 TTTAAAATTATTATAAA
* *
40202 TTTAAATTTGTTATCAAA
1 TTTAAAATTATTAT-AAA
*
40220 TTTAAAATTATTATGAA
1 TTTAAAATTATTATAAA
40237 TTTAAAAT
1 TTTAAAAT
40245 AAATAAAGTT
Statistics
Matches: 57, Mismatches: 8, Indels: 14
0.72 0.10 0.18
Matches are distributed among these distances:
12 6 0.11
13 3 0.05
14 1 0.02
16 7 0.12
17 26 0.46
18 14 0.25
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.52
Consensus pattern (17 bp):
TTTAAAATTATTATAAA
Found at i:40949 original size:3 final size:3
Alignment explanation
Indices: 40943--41003 Score: 52
Period size: 3 Copynumber: 20.3 Consensus size: 3
40933 ATTATATTAT
* * *
40943 TAA TAA TAT TTA T-A TAA TAA TAA TTAA TAT TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA
* * *
40988 TGA CAC TAA TAA TAA T
1 TAA TAA TAA TAA TAA T
41004 TTTTAATGAT
Statistics
Matches: 45, Mismatches: 11, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
2 2 0.04
3 40 0.89
4 3 0.07
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:40980 original size:19 final size:21
Alignment explanation
Indices: 40946--40988 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
40936 ATATTATTAA
40946 TAATATTTATATAATAATAAT
1 TAATATTTATATAATAATAAT
*
40967 TAATATTAATAATAATAATAAT
1 TAATATTTAT-ATAATAATAAT
40989 GACACTAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
TAATATTTATATAATAATAAT
Found at i:42104 original size:30 final size:29
Alignment explanation
Indices: 42068--42350 Score: 318
Period size: 30 Copynumber: 9.6 Consensus size: 29
42058 ATTGTTCAAC
42068 AATCCCATTTTTAACCCCAAAACTTCCAAA
1 AATCCCATTTTT-ACCCCAAAACTTCCAAA
42098 AATCCCATTTTTACCCCTAAAACTTCCAAA
1 AATCCCATTTTTACCCC-AAAACTTCCAAA
* ** **
42128 AATCCCATTTTAACCCTGAAACTTATAAA
1 AATCCCATTTTTACCCCAAAACTTCCAAA
** *
42157 AATCCCATTTTTACCCCCGAACTTCTAAA
1 AATCCCATTTTTACCCCAAAACTTCCAAA
*
42186 AATCTCATTTTTAACCCCAAAACTTCCAAA
1 AATCCCATTTTT-ACCCCAAAACTTCCAAA
*
42216 AATCCCATTTTTAACCTCAAAACTTCCAAA
1 AATCCCATTTTT-ACCCCAAAACTTCCAAA
* *
42246 AATCCCATTTTTACCCTC-GAACTTCTAAA
1 AATCCCATTTTTACCC-CAAAACTTCCAAA
* * *
42275 AATTCAATTTTTAACCCCAAAACTTTCAAA
1 AATCCCATTTTT-ACCCCAAAACTTCCAAA
** *
42305 AGAT-CCATTTTTACCCCCGAACTTCTAAA
1 A-ATCCCATTTTTACCCCAAAACTTCCAAA
*
42334 AGTCCCATTTTTACCCC
1 AATCCCATTTTTACCCC
42351 GAATTTTCCC
Statistics
Matches: 216, Mismatches: 30, Indels: 15
0.83 0.11 0.06
Matches are distributed among these distances:
28 1 0.00
29 99 0.46
30 114 0.53
31 2 0.01
ACGTcount: A:0.36, C:0.31, G:0.02, T:0.31
Consensus pattern (29 bp):
AATCCCATTTTTACCCCAAAACTTCCAAA
Found at i:42158 original size:59 final size:59
Alignment explanation
Indices: 42068--42350 Score: 342
Period size: 59 Copynumber: 4.8 Consensus size: 59
42058 ATTGTTCAAC
* *
42068 AATCCCATTTTTAACCCCAAAACTTCCAAAAATCCCATTTTTACCCCTAAAACTTCCAAA
1 AATCCCATTTTTAACCCCGAAACTTCTAAAAATCCCATTTTTACCCC-AAAACTTCCAAA
* * ** *
42128 AATCCCA-TTTTAACCCTGAAACTTATAAAAATCCCATTTTTACCCCCGAACTTCTAAA
1 AATCCCATTTTTAACCCCGAAACTTCTAAAAATCCCATTTTTACCCCAAAACTTCCAAA
* * * *
42186 AATCTCATTTTTAACCCCAAAACTTCCAAAAATCCCATTTTTAACCTCAAAACTTCCAAA
1 AATCCCATTTTTAACCCCGAAACTTCTAAAAATCCCATTTTT-ACCCCAAAACTTCCAAA
* * *
42246 AATCCCATTTTT-ACCCTCG-AACTTCTAAAAATTCAATTTTTAACCCCAAAACTTTCAAA
1 AATCCCATTTTTAACCC-CGAAACTTCTAAAAATCCCATTTTT-ACCCCAAAACTTCCAAA
* *
42305 AGAT-CCATTTTTACCCCCG-AACTTCTAAAAGTCCCATTTTTACCCC
1 A-ATCCCATTTTTAACCCCGAAACTTCTAAAAATCCCATTTTTACCCC
42351 GAATTTTCCC
Statistics
Matches: 191, Mismatches: 27, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
58 20 0.10
59 134 0.70
60 37 0.19
ACGTcount: A:0.36, C:0.31, G:0.02, T:0.31
Consensus pattern (59 bp):
AATCCCATTTTTAACCCCGAAACTTCTAAAAATCCCATTTTTACCCCAAAACTTCCAAA
Found at i:54639 original size:5 final size:5
Alignment explanation
Indices: 54571--54621 Score: 68
Period size: 5 Copynumber: 10.0 Consensus size: 5
54561 ATTTGAAAAT
*
54571 TTTTA TTTCA -TTTA TTTATTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA -TT-TTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
54622 AATTTTGGGT
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
4 3 0.07
5 32 0.78
6 3 0.07
7 3 0.07
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (5 bp):
TTTTA
Found at i:55084 original size:49 final size:49
Alignment explanation
Indices: 55031--55317 Score: 281
Period size: 49 Copynumber: 5.8 Consensus size: 49
55021 TTAGGATATA
* * * *
55031 AGATTTGCCGTTGCGGCTTCAATCTTTCCCTTTACGTCTTCGTGGTACT
1 AGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTTCGTGGTACT
* * *
55080 AGATTCGCCATTGCGGCTTAAATCTTTCCCTTCATG-CTTCTGAGGTACA
1 AGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTTC-GTGGTACT
* * * * * * * * *
55129 AGGTTCGTCGTTGCGACTTAAACCTTTTCCTCCCTTATCTTCATGGTACT
1 AGATTCGCCGTTGCGGCTTAAATCTTTCCCT-TCATGTCTTCGTGGTACT
* * *
55179 AGATTCGTCGTTGCGGCTTAAATCTTTCCCTTCATG-CTTCTGAGGTACA
1 AGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTTC-GTGGTACT
* * * ** *
55228 AGGTTCGCCCTTGCGACTTAAATCTTTCCCTTTGTATCTTCGTGGTACT
1 AGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTTCGTGGTACT
** *
55277 AGATTTTCCGTTGCGGCTTAAATCATTCCCTTCATGTCTTC
1 AGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTTC
55318 ATAGTAATGA
Statistics
Matches: 186, Mismatches: 47, Indels: 10
0.77 0.19 0.04
Matches are distributed among these distances:
48 8 0.04
49 136 0.73
50 38 0.20
51 4 0.02
ACGTcount: A:0.16, C:0.26, G:0.18, T:0.39
Consensus pattern (49 bp):
AGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTTCGTGGTACT
Found at i:55183 original size:99 final size:98
Alignment explanation
Indices: 55067--55317 Score: 369
Period size: 99 Copynumber: 2.5 Consensus size: 98
55057 TCCCTTTACG
*
55067 TCTTCGTGGTACTAGATTCGCCATTGCGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGG
1 TCTTCGTGGTACTAGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGG
* *
55132 TTCGTCGTTGCGACTTAAACCTTTTCCTCCCT-TA
66 TTCGCCCTTGCGACTTAAACC-TTTCC-CCCTGTA
* *
55166 TCTTCATGGTACTAGATTCGTCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGG
1 TCTTCGTGGTACTAGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGG
* **
55231 TTCGCCCTTGCGACTTAAATCTTTCCCTTTGTA
66 TTCGCCCTTGCGACTTAAACCTTTCCCCCTGTA
** *
55264 TCTTCGTGGTACTAGATTTTCCGTTGCGGCTTAAATCATTCCCTTCATGTCTTC
1 TCTTCGTGGTACTAGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATG-CTTC
55318 ATAGTAATGA
Statistics
Matches: 137, Mismatches: 13, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
97 2 0.01
98 51 0.37
99 84 0.61
ACGTcount: A:0.17, C:0.26, G:0.18, T:0.39
Consensus pattern (98 bp):
TCTTCGTGGTACTAGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGG
TTCGCCCTTGCGACTTAAACCTTTCCCCCTGTA
Found at i:55764 original size:18 final size:18
Alignment explanation
Indices: 55741--55775 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
55731 CAATTGTCAA
55741 ATAATTACAAGGAACAAG
1 ATAATTACAAGGAACAAG
*
55759 ATAATTACATGGAACAA
1 ATAATTACAAGGAACAA
55776 TATTAGATGC
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:0.54, C:0.11, G:0.14, T:0.20
Consensus pattern (18 bp):
ATAATTACAAGGAACAAG
Found at i:72679 original size:18 final size:18
Alignment explanation
Indices: 72658--72693 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
72648 TGTTTAGCAT
*
72658 TGCTTATGGCTCCAAAAG
1 TGCTTATGCCTCCAAAAG
*
72676 TGCTTCTGCCTCCAAAAG
1 TGCTTATGCCTCCAAAAG
72694 CACTTTTGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.28
Consensus pattern (18 bp):
TGCTTATGCCTCCAAAAG
Found at i:77452 original size:16 final size:16
Alignment explanation
Indices: 77414--77450 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
77404 AAAATATTGT
*
77414 ATTTTTAATTATATAC
1 ATTTTTAACTATATAC
77430 ATTTTTAACTATATA-
1 ATTTTTAACTATATAC
77445 ATTTTT
1 ATTTTT
77451 TATAAAATAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.59
Consensus pattern (16 bp):
ATTTTTAACTATATAC
Found at i:78311 original size:20 final size:20
Alignment explanation
Indices: 78283--78322 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
78273 TTAAATTATG
78283 TAAAAATTAACACGGATGGA
1 TAAAAATTAACACGGATGGA
* *
78303 TAAAGATTAACATGGATGGA
1 TAAAAATTAACACGGATGGA
78323 GCGGCAAATG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.47, C:0.07, G:0.23, T:0.23
Consensus pattern (20 bp):
TAAAAATTAACACGGATGGA
Found at i:78906 original size:49 final size:49
Alignment explanation
Indices: 78838--78935 Score: 196
Period size: 49 Copynumber: 2.0 Consensus size: 49
78828 AAATATAGAG
78838 ATTAAATCTCAAATTTGAGTGAAATACATGGATCAAAACTGAAATTTAA
1 ATTAAATCTCAAATTTGAGTGAAATACATGGATCAAAACTGAAATTTAA
78887 ATTAAATCTCAAATTTGAGTGAAATACATGGATCAAAACTGAAATTTAA
1 ATTAAATCTCAAATTTGAGTGAAATACATGGATCAAAACTGAAATTTAA
78936 TCATTCTTAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.47, C:0.10, G:0.12, T:0.31
Consensus pattern (49 bp):
ATTAAATCTCAAATTTGAGTGAAATACATGGATCAAAACTGAAATTTAA
Found at i:78923 original size:24 final size:24
Alignment explanation
Indices: 78846--78923 Score: 61
Period size: 24 Copynumber: 3.2 Consensus size: 24
78836 AGATTAAATC
78846 TCAAATTTGAGTGAAATACATGGA
1 TCAAATTTGAGTGAAATACATGGA
** * * * *
78870 TCAAAACTGAAATTTAAATTAAAT--C
1 TCAAATTTG--AGTGAAA-TACATGGA
78895 TCAAATTTGAGTGAAATACATGGA
1 TCAAATTTGAGTGAAATACATGGA
78919 TCAAA
1 TCAAA
78924 ACTGAAATTT
Statistics
Matches: 37, Mismatches: 12, Indels: 10
0.63 0.20 0.17
Matches are distributed among these distances:
22 4 0.11
23 5 0.14
24 12 0.32
25 7 0.19
26 5 0.14
27 4 0.11
ACGTcount: A:0.46, C:0.10, G:0.14, T:0.29
Consensus pattern (24 bp):
TCAAATTTGAGTGAAATACATGGA
Found at i:79761 original size:27 final size:27
Alignment explanation
Indices: 79707--79779 Score: 71
Period size: 27 Copynumber: 2.8 Consensus size: 27
79697 TTGAAAGTTA
* **
79707 AAAAATAAATATAAATT-ATTTTATTT
1 AAAAATAAATATTAATTAAAATTATTT
79733 AAGAAATAAATATTAATTAAAATTA-TT
1 AA-AAATAAATATTAATTAAAATTATTT
* *
79760 AAACATAAATAATAA-TAAAA
1 AAAAATAAATATTAATTAAAA
79780 CATCAAATAA
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
25 5 0.12
26 13 0.32
27 18 0.45
28 4 0.10
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.36
Consensus pattern (27 bp):
AAAAATAAATATTAATTAAAATTATTT
Found at i:98005 original size:30 final size:30
Alignment explanation
Indices: 97971--98274 Score: 192
Period size: 30 Copynumber: 10.2 Consensus size: 30
97961 ATTTTATTTA
* *
97971 AAAATTACACTTTGACCCTCAAAGTTTTCT
1 AAAATTACATTTTGACCCTCAAACTTTTCT
* * *
98001 AAAATCACAATTTAACACCT-AAACTTTTCT
1 AAAATTACATTTTGAC-CCTCAAACTTTTCT
* * * *
98031 AAAATTTCATTTTAACTCT-AAACTTTTTT
1 AAAATTACATTTTGACCCTCAAACTTTTCT
* * *
98060 AAAAATATCATTTTGA-CCTCAAACTATTCC
1 AAAATTA-CATTTTGACCCTCAAACTTTTCT
* *
98090 AAAATTTCATTTTGACCC-CTAAACTTTTCC
1 AAAATTACATTTTGACCCTC-AAACTTTTCT
* * * *
98120 AAAATCATATTTTAACCCTTAAACTTCTT-T
1 AAAATTACATTTTGACCCTCAAACTT-TTCT
* * * * *
98150 AGAATTATATTTTAACCCTCAAA-TTTCCA
1 AAAATTACATTTTGACCCTCAAACTTTTCT
* * * * *
98179 AAAATCACATTTTAACCC-CAAACCTTACC
1 AAAATTACATTTTGACCCTCAAACTTTTCT
* * * *
98208 AAAATCACATTTTAACCCCCAAACTTTCCT
1 AAAATTACATTTTGACCCTCAAACTTTTCT
* **
98238 AAAATTACATTTTGATCCTTGAA-TTTTCT
1 AAAATTACATTTTGACCCTCAAACTTTTCT
98267 CAAAATTA
1 -AAAATTA
98275 TGTTTTAACC
Statistics
Matches: 217, Mismatches: 46, Indels: 22
0.76 0.16 0.08
Matches are distributed among these distances:
28 5 0.02
29 70 0.32
30 137 0.63
31 5 0.02
ACGTcount: A:0.37, C:0.23, G:0.02, T:0.38
Consensus pattern (30 bp):
AAAATTACATTTTGACCCTCAAACTTTTCT
Found at i:98124 original size:59 final size:58
Alignment explanation
Indices: 98017--98132 Score: 137
Period size: 59 Copynumber: 2.0 Consensus size: 58
98007 ACAATTTAAC
* * * *
98017 ACCTAAACTTTTCTAAAATTTCATTTTAACTCTAAACTTTTTTAAAAAT-ATCATTTTG
1 ACCTAAACTATTCCAAAATTTCATTTTAACCCTAAACTTTTTCAAAAATCAT-ATTTTG
* *
98075 ACCTCAAACTATTCCAAAATTTCATTTTGACCCCTAAAC-TTTTCCAAAATCATATTTT
1 ACCT-AAACTATTCCAAAATTTCATTTT-AACCCTAAACTTTTTCAAAAATCATATTTT
98133 AACCCTTAAA
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
58 4 0.08
59 35 0.71
60 10 0.20
ACGTcount: A:0.35, C:0.21, G:0.02, T:0.42
Consensus pattern (58 bp):
ACCTAAACTATTCCAAAATTTCATTTTAACCCTAAACTTTTTCAAAAATCATATTTTG
Found at i:98263 original size:88 final size:89
Alignment explanation
Indices: 97971--98250 Score: 228
Period size: 89 Copynumber: 3.1 Consensus size: 89
97961 ATTTTATTTA
* * * * * * * * *
97971 AAAATTACACTTTGACCCTCAAAGTTTTCTAAAATCACAATTTAACACCTAAACTTTTCTAAAAT
1 AAAATTACATTTTAACCCTCAAA-TTTCCAAAAATCACATTTTAACCCCTAAACCTTACCAAAAT
** * * * *
98036 TTCATTTTAA-CTCTAAACTTTTTT
65 CACATTTTAACCCCCAAACTTCTCT
* * ** * * *
98060 AAAAATATCATTTTGA-CCTCAAACTATTCC-AAAATTTCATTTTGACCCCTAAACTTTTCCAAA
1 AAAATTA-CATTTTAACCCTCAAA-T-TTCCAAAAATCACATTTTAACCCCTAAACCTTACCAAA
* ** *
98123 ATCATATTTTAACCCTTAAACTTCTTT
63 ATCACATTTTAACCCCCAAACTTCTCT
* *
98150 AGAATTATATTTTAACCCTCAAATTTCCAAAAATCACATTTTAACCCC-AAACCTTACCAAAATC
1 AAAATTACATTTTAACCCTCAAATTTCCAAAAATCACATTTTAACCCCTAAACCTTACCAAAATC
98214 ACATTTTAACCCCCAAACTT-TCCT
66 ACATTTTAACCCCCAAACTTCT-CT
98238 AAAATTACATTTT
1 AAAATTACATTTT
98251 GATCCTTGAA
Statistics
Matches: 154, Mismatches: 31, Indels: 13
0.78 0.16 0.07
Matches are distributed among these distances:
87 1 0.01
88 47 0.31
89 73 0.47
90 33 0.21
ACGTcount: A:0.38, C:0.24, G:0.02, T:0.37
Consensus pattern (89 bp):
AAAATTACATTTTAACCCTCAAATTTCCAAAAATCACATTTTAACCCCTAAACCTTACCAAAATC
ACATTTTAACCCCCAAACTTCTCT
Found at i:99577 original size:32 final size:30
Alignment explanation
Indices: 99540--99611 Score: 74
Period size: 32 Copynumber: 2.3 Consensus size: 30
99530 CCGAGCCTGA
99540 GAAAAAAATGAACCT-ATAATAGATCCAAACCC
1 GAAAAAAATGAACCTAAT-ATA-ATCCAAA-CC
* * *
99572 GAAAAAATTTGACCCTAATCTAATCCAAACC
1 GAAAAAA-ATGAACCTAATATAATCCAAACC
99603 GAAAAAAAT
1 GAAAAAAAT
99612 CCAAATCTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
30 1 0.03
31 9 0.26
32 14 0.41
33 8 0.24
34 2 0.06
ACGTcount: A:0.53, C:0.21, G:0.08, T:0.18
Consensus pattern (30 bp):
GAAAAAAATGAACCTAATATAATCCAAACC
Found at i:103112 original size:21 final size:21
Alignment explanation
Indices: 103086--103130 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
103076 TGAGTTTTGG
103086 ACTATAGACTTTATAATACTT
1 ACTATAGACTTTATAATACTT
103107 ACTATAGACTTTATAATACTT
1 ACTATAGACTTTATAATACTT
103128 ACT
1 ACT
103131 TGTTTATTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.38, C:0.16, G:0.04, T:0.42
Consensus pattern (21 bp):
ACTATAGACTTTATAATACTT
Found at i:107920 original size:26 final size:26
Alignment explanation
Indices: 107891--107944 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
107881 ATATACAGAC
107891 ATGGAAGTGTCAGTCATAATCCACAA
1 ATGGAAGTGTCAGTCATAATCCACAA
107917 ATGGAAGTGTCAGTCATAATCCACAA
1 ATGGAAGTGTCAGTCATAATCCACAA
107943 AT
1 AT
107945 AACTGACAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.39, C:0.19, G:0.19, T:0.24
Consensus pattern (26 bp):
ATGGAAGTGTCAGTCATAATCCACAA
Found at i:113629 original size:7 final size:7
Alignment explanation
Indices: 113617--113654 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
113607 TTTAATAAAT
*
113617 ATTATAG
1 ATTATAA
113624 ATTATAA
1 ATTATAA
113631 ATTATAA
1 ATTATAA
113638 ATTATAA
1 ATTATAA
*
113645 ATTACAA
1 ATTATAA
113652 ATT
1 ATT
113655 TATTTTAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (7 bp):
ATTATAA
Found at i:123266 original size:21 final size:22
Alignment explanation
Indices: 123240--123281 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
123230 ACTCTGATAA
*
123240 CAGGAACTCTAG-AAATATATG
1 CAGGAACTCTAGTAAACATATG
123261 CAGGAACTCTAGTAAACATAT
1 CAGGAACTCTAGTAAACATAT
123282 CACATAACCC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.43, C:0.17, G:0.17, T:0.24
Consensus pattern (22 bp):
CAGGAACTCTAGTAAACATATG
Found at i:123529 original size:24 final size:24
Alignment explanation
Indices: 123483--123529 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
123473 TCACATAAAC
** *
123483 ATATTCACTATATTTTTATTTCAG
1 ATATTCACTATATTCATAATTCAG
*
123507 ATATTCACTTTATTCATAATTCA
1 ATATTCACTATATTCATAATTCA
123530 TAAAAATATA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.32, C:0.15, G:0.02, T:0.51
Consensus pattern (24 bp):
ATATTCACTATATTCATAATTCAG
Found at i:124299 original size:16 final size:16
Alignment explanation
Indices: 124274--124310 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
124264 GGAGATTTTC
*
124274 TTTTCTTTTTCTATCT
1 TTTTCCTTTTCTATCT
*
124290 TTTTCCTTTTCTTTCT
1 TTTTCCTTTTCTATCT
124306 TTTTC
1 TTTTC
124311 TCCCTCTCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.03, C:0.22, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTTCCTTTTCTATCT
Found at i:124495 original size:24 final size:24
Alignment explanation
Indices: 124467--124529 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
124457 AGAAATAATC
* *
124467 TTTCAGTTAAACTCTGTTTATTTG
1 TTTCAGTTAAACTCTATTTATTTA
*
124491 TTTCAATTAAACTCTATTTATTTA
1 TTTCAGTTAAACTCTATTTATTTA
* *
124515 TTTGAGTCAAACTCT
1 TTTCAGTTAAACTCT
124530 TATTATTCTA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.27, C:0.14, G:0.08, T:0.51
Consensus pattern (24 bp):
TTTCAGTTAAACTCTATTTATTTA
Found at i:126310 original size:24 final size:24
Alignment explanation
Indices: 126282--126344 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
126272 AGAAATAATC
*
126282 TTTCAGTTAAACTCTGTTTATTTA
1 TTTCAGTTAAACTCTATTTATTTA
* * *
126306 TTTCAATTAAACTTTATTTATTTG
1 TTTCAGTTAAACTCTATTTATTTA
*
126330 TTTGAGTTAAACTCT
1 TTTCAGTTAAACTCT
126345 TATTACTCTA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.27, C:0.11, G:0.08, T:0.54
Consensus pattern (24 bp):
TTTCAGTTAAACTCTATTTATTTA
Found at i:128754 original size:19 final size:19
Alignment explanation
Indices: 128692--128754 Score: 60
Period size: 19 Copynumber: 3.4 Consensus size: 19
128682 AAAAATATTT
* *
128692 AAAATTTTTTTTTAAAT-A
1 AAAATTTATTTTTATATAA
*
128710 AAAA-TTATTATTATA-AA
1 AAAATTTATTTTTATATAA
*
128727 AATATTTTATTTTTATATAA
1 AA-AATTTATTTTTATATAA
128747 AAAATTTA
1 AAAATTTA
128755 AATAAAATAA
Statistics
Matches: 35, Mismatches: 6, Indels: 7
0.73 0.12 0.15
Matches are distributed among these distances:
17 11 0.31
18 5 0.14
19 15 0.43
20 4 0.11
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
AAAATTTATTTTTATATAA
Found at i:131568 original size:14 final size:14
Alignment explanation
Indices: 131546--131581 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
131536 TCGCACCCAA
131546 ATAAAAATA-ATTT
1 ATAAAAATATATTT
131559 ATATAAAATATATTT
1 ATA-AAAATATATTT
131574 ATAAAAAT
1 ATAAAAAT
131582 TTAATAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 3 0.14
14 11 0.52
15 7 0.33
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
ATAAAAATATATTT
Found at i:134004 original size:11 final size:11
Alignment explanation
Indices: 133988--134012 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
133978 TTTTATCAAA
133988 TTTATATATTT
1 TTTATATATTT
133999 TTTATATATTT
1 TTTATATATTT
134010 TTT
1 TTT
134013 GTGACAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (11 bp):
TTTATATATTT
Found at i:141934 original size:17 final size:17
Alignment explanation
Indices: 141906--141948 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
141896 TAGATAGTAG
*
141906 AAATAAAAATAAATAAT
1 AAATATAAATAAATAAT
141923 GAAA-ATAAATAAATAAT
1 -AAATATAAATAAATAAT
141940 AAATATAAA
1 AAATATAAA
141949 CAAACGATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 3 0.13
17 17 0.74
18 3 0.13
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.23
Consensus pattern (17 bp):
AAATATAAATAAATAAT
Found at i:151508 original size:19 final size:19
Alignment explanation
Indices: 151484--151552 Score: 72
Period size: 19 Copynumber: 3.7 Consensus size: 19
151474 TTTTTTAGAG
151484 TTTATATATATTTAGATTA
1 TTTATATATATTTAGATTA
* *
151503 TTTATATATTTTTTGGA--A
1 TTTATATA-TATTTAGATTA
*
151521 TTTTTATATATTTA-ATTA
1 TTTATATATATTTAGATTA
151539 TTTCATATATATTT
1 TTT-ATATATATTT
151553 TTTAGAGTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
16 1 0.03
17 4 0.10
18 12 0.30
19 17 0.43
20 6 0.15
ACGTcount: A:0.32, C:0.01, G:0.04, T:0.62
Consensus pattern (19 bp):
TTTATATATATTTAGATTA
Found at i:151548 original size:39 final size:37
Alignment explanation
Indices: 151473--151568 Score: 122
Period size: 37 Copynumber: 2.5 Consensus size: 37
151463 ATTTTTAATG
*
151473 ATTTTTTAGAGTTTATATATATTTAGATTATTTATAT
1 ATTTTTTAGAATTTATATATATTTAGATTATTTATAT
* *
151510 ATTTTTTGGAATTTTTATATATTTA-ATTATTTCATATAT
1 ATTTTTTAGAATTTATATATATTTAGATTA-TT--TATAT
*
151549 ATTTTTTAGAGTTTATATAT
1 ATTTTTTAGAATTTATATAT
151569 TATAATTTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
36 4 0.08
37 24 0.48
39 22 0.44
ACGTcount: A:0.31, C:0.01, G:0.07, T:0.60
Consensus pattern (37 bp):
ATTTTTTAGAATTTATATATATTTAGATTATTTATAT
Found at i:151569 original size:37 final size:34
Alignment explanation
Indices: 151451--151579 Score: 113
Period size: 37 Copynumber: 3.6 Consensus size: 34
151441 CCTCGAAAAC
*
151451 GTTTATATA-TAAATT-TTTA-ATGATTTTTTAGA
1 GTTTATATATTTAATTATTTATAT-ATTTTTTAGA
*
151483 GTTTATATATATTTAGATTATTTATATATTTTTTGGAA
1 G-TT-TATATATTTA-ATTATTTATATATTTTTTAG-A
*
151521 TTTTTATATATTTAATTATTTCATATATATTTTTTAGA
1 -GTTTATATATTTAATTA-TT--TATATATTTTTTAGA
151559 GTTTATATATTATAATT-TTTA
1 GTTTATATATT-TAATTATTTA
151580 AAATTTCTTT
Statistics
Matches: 80, Mismatches: 5, Indels: 22
0.75 0.05 0.21
Matches are distributed among these distances:
32 1 0.01
33 2 0.03
34 8 0.10
35 2 0.03
36 9 0.11
37 34 0.43
38 11 0.14
39 13 0.16
ACGTcount: A:0.33, C:0.01, G:0.07, T:0.60
Consensus pattern (34 bp):
GTTTATATATTTAATTATTTATATATTTTTTAGA
Found at i:151604 original size:8 final size:8
Alignment explanation
Indices: 151591--151664 Score: 55
Period size: 8 Copynumber: 9.0 Consensus size: 8
151581 AATTTCTTTC
151591 TATTTTTA
1 TATTTTTA
151599 TATTTTT-
1 TATTTTTA
* *
151606 TAATATGTA
1 T-ATTTTTA
151615 TATTTTTA
1 TATTTTTA
*
151623 AATTATATTA
1 TATT-T-TTA
151633 T-TTTTCT-
1 TATTTT-TA
151640 TATTTTTA
1 TATTTTTA
151648 TATTTTTA
1 TATTTTTA
151656 TGATTTTTA
1 T-ATTTTTA
151665 AAAGTTTATA
Statistics
Matches: 52, Mismatches: 6, Indels: 15
0.71 0.08 0.21
Matches are distributed among these distances:
7 4 0.08
8 34 0.65
9 11 0.21
10 3 0.06
ACGTcount: A:0.27, C:0.01, G:0.03, T:0.69
Consensus pattern (8 bp):
TATTTTTA
Found at i:151636 original size:15 final size:15
Alignment explanation
Indices: 151596--151636 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
151586 CTTTCTATTT
151596 TTATATTTTTTAATA
1 TTATATTTTTTAATA
151611 TGTATA-TTTTTAA-A
1 T-TATATTTTTTAATA
151625 TTATATTATTTT
1 TTATATT-TTTT
151637 TCTTATTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
13 4 0.17
14 3 0.13
15 12 0.52
16 4 0.17
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (15 bp):
TTATATTTTTTAATA
Found at i:151651 original size:17 final size:17
Alignment explanation
Indices: 151631--151664 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
151621 TAAATTATAT
* *
151631 TATTTTTCTTATTTTTA
1 TATTTTTATGATTTTTA
151648 TATTTTTATGATTTTTA
1 TATTTTTATGATTTTTA
151665 AAAGTTTATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.21, C:0.03, G:0.03, T:0.74
Consensus pattern (17 bp):
TATTTTTATGATTTTTA
Found at i:156621 original size:27 final size:27
Alignment explanation
Indices: 156568--156621 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
156558 GTCAAGGTGA
**
156568 TTAACCATTTGCTCATTAAACTTTGAT
1 TTAACCATTTGCTCATTAAACCATGAT
* *
156595 TTAACCTTTTTCTCATTAAACCATGAT
1 TTAACCATTTGCTCATTAAACCATGAT
156622 CATTTTGTTG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.30, C:0.20, G:0.06, T:0.44
Consensus pattern (27 bp):
TTAACCATTTGCTCATTAAACCATGAT
Found at i:159626 original size:21 final size:23
Alignment explanation
Indices: 159597--159638 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
159587 GAGTCAGGTA
159597 CAAACAAGATCTTAAT-TTAAAC
1 CAAACAAGATCTTAATGTTAAAC
*
159619 CAAA-AAGATTTTAATGTTAA
1 CAAACAAGATCTTAATGTTAA
159639 CTAAATATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.50, C:0.12, G:0.07, T:0.31
Consensus pattern (23 bp):
CAAACAAGATCTTAATGTTAAAC
Found at i:177825 original size:24 final size:26
Alignment explanation
Indices: 177798--177845 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
177788 AGAGAAATGT
177798 AAATG-TGATATATGA-AG-TTATGAG
1 AAATGATGA-ATATGAGAGATTATGAG
177822 AAATGATGAATATGAGAGATTATG
1 AAATGATGAATATGAGAGATTATG
177846 CCCATGTAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 11 0.52
25 5 0.24
26 5 0.24
ACGTcount: A:0.44, C:0.00, G:0.25, T:0.31
Consensus pattern (26 bp):
AAATGATGAATATGAGAGATTATGAG
Found at i:177936 original size:22 final size:23
Alignment explanation
Indices: 177908--177963 Score: 87
Period size: 25 Copynumber: 2.4 Consensus size: 23
177898 ACGCTAGCGC
177908 GCTTCTGTT-CAGCACTGTGTGT
1 GCTTCTGTTCCAGCACTGTGTGT
177930 GCTTCTGTTACCCAGCACTGTGTGT
1 GCTTCTGTT--CCAGCACTGTGTGT
177955 GCTTCTGTT
1 GCTTCTGTT
177964 TCCCCAGCAC
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
22 9 0.29
25 22 0.71
ACGTcount: A:0.09, C:0.25, G:0.25, T:0.41
Consensus pattern (23 bp):
GCTTCTGTTCCAGCACTGTGTGT
Found at i:177950 original size:25 final size:26
Alignment explanation
Indices: 177917--177974 Score: 100
Period size: 25 Copynumber: 2.3 Consensus size: 26
177907 CGCTTCTGTT
177917 CAGCACTGTGTGTGCTTCTG-TTACC
1 CAGCACTGTGTGTGCTTCTGTTTACC
*
177942 CAGCACTGTGTGTGCTTCTGTTTCCC
1 CAGCACTGTGTGTGCTTCTGTTTACC
177968 CAGCACT
1 CAGCACT
177975 TATGTACCTC
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
25 20 0.65
26 11 0.35
ACGTcount: A:0.12, C:0.31, G:0.22, T:0.34
Consensus pattern (26 bp):
CAGCACTGTGTGTGCTTCTGTTTACC
Found at i:177986 original size:25 final size:26
Alignment explanation
Indices: 177917--177988 Score: 67
Period size: 25 Copynumber: 2.8 Consensus size: 26
177907 CGCTTCTGTT
* * * *
177917 CAGCACTGTGTGTGCTTCTG-TTACC
1 CAGCACTGTATGTACCTCTGTTTCCC
* * *
177942 CAGCACTGTGTGTGCTTCTGTTTCCC
1 CAGCACTGTATGTACCTCTGTTTCCC
177968 CAGCACT-TATGTACCTCTGTT
1 CAGCACTGTATGTACCTCTGTT
177989 AAGCACTTCG
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
25 31 0.74
26 11 0.26
ACGTcount: A:0.12, C:0.29, G:0.21, T:0.38
Consensus pattern (26 bp):
CAGCACTGTATGTACCTCTGTTTCCC
Found at i:179528 original size:21 final size:21
Alignment explanation
Indices: 179502--179577 Score: 98
Period size: 21 Copynumber: 3.6 Consensus size: 21
179492 AACAGTGCAG
179502 ACTTCTACCGATACAAGTGAC
1 ACTTCTACCGATACAAGTGAC
* *
179523 AGTTCTACCGATACAAGAGAC
1 ACTTCTACCGATACAAGTGAC
* * * *
179544 TCTTCTATCGAAACAAGTCAC
1 ACTTCTACCGATACAAGTGAC
179565 ACTTCTACCGATA
1 ACTTCTACCGATA
179578 TTAAAACCTC
Statistics
Matches: 44, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.34, C:0.28, G:0.13, T:0.25
Consensus pattern (21 bp):
ACTTCTACCGATACAAGTGAC
Found at i:183170 original size:6 final size:7
Alignment explanation
Indices: 183153--183178 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
183143 ATTTTCAAAA
183153 AAAAATT
1 AAAAATT
183160 AAAAATT
1 AAAAATT
183167 AAAAATT
1 AAAAATT
183174 AAAAA
1 AAAAA
183179 AATTTAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (7 bp):
AAAAATT
Found at i:184267 original size:22 final size:22
Alignment explanation
Indices: 184239--184281 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
184229 TGTTGTTGTT
*
184239 TTGTTACTATTTCGTTATTATA
1 TTGTTACGATTTCGTTATTATA
*
184261 TTGTTACGATTTTGTTATTAT
1 TTGTTACGATTTCGTTATTAT
184282 TGTTTGGATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.21, C:0.07, G:0.12, T:0.60
Consensus pattern (22 bp):
TTGTTACGATTTCGTTATTATA
Found at i:186866 original size:27 final size:27
Alignment explanation
Indices: 186810--186869 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
186800 CTTTCTAAAA
** * *
186810 AATAAATATTAAATAAGTTATTTTTTT
1 AATAAATATTAAATAAGTTAAATATCT
186837 AATAAATATTAAATATAG-TAAATATCT
1 AATAAATATTAAATA-AGTTAAATATCT
186864 AATAAA
1 AATAAA
186870 AATCTGTATC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 26 0.93
28 2 0.07
ACGTcount: A:0.53, C:0.02, G:0.03, T:0.42
Consensus pattern (27 bp):
AATAAATATTAAATAAGTTAAATATCT
Found at i:187809 original size:14 final size:14
Alignment explanation
Indices: 187790--187823 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
187780 AACCCAAAAC
187790 CAAAATAATAATAA
1 CAAAATAATAATAA
187804 CAAAATAATAATAA
1 CAAAATAATAATAA
*
187818 TAAAAT
1 CAAAAT
187824 GATGAAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.24
Consensus pattern (14 bp):
CAAAATAATAATAA
Found at i:188887 original size:13 final size:13
Alignment explanation
Indices: 188869--188896 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
188859 GTTTTTCAAA
188869 AAAGTCAACGGTC
1 AAAGTCAACGGTC
188882 AAAGTCAACGGTC
1 AAAGTCAACGGTC
188895 AA
1 AA
188897 TGGTTAACAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.43, C:0.21, G:0.21, T:0.14
Consensus pattern (13 bp):
AAAGTCAACGGTC
Found at i:198660 original size:30 final size:30
Alignment explanation
Indices: 198625--198696 Score: 74
Period size: 31 Copynumber: 2.4 Consensus size: 30
198615 TTTAGTATAT
*
198625 AAACTTTAATTTGGTGCAATTGTGCACATG
1 AAACTTTAATTTGGTGCAAATGTGCACATG
** * * *
198655 AAACTTTTGTTGCGGTTCAAATGTGTACATG
1 AAACTTTAATT-TGGTGCAAATGTGCACATG
198686 AAA-TTTAATTT
1 AAACTTTAATTT
198697 TGATTAATCA
Statistics
Matches: 32, Mismatches: 9, Indels: 3
0.73 0.20 0.07
Matches are distributed among these distances:
30 14 0.44
31 18 0.56
ACGTcount: A:0.31, C:0.11, G:0.18, T:0.40
Consensus pattern (30 bp):
AAACTTTAATTTGGTGCAAATGTGCACATG
Found at i:204028 original size:2 final size:2
Alignment explanation
Indices: 204021--204045 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
204011 TTACGCTGTT
204021 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
204046 TTAGAGAAAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:204219 original size:23 final size:24
Alignment explanation
Indices: 204193--204239 Score: 60
Period size: 26 Copynumber: 1.9 Consensus size: 24
204183 CTACTATTCA
*
204193 CGTTTGTA-TTTTTTATTTAATGT
1 CGTTTGAACTTTTTTATTTAATGT
204216 CGTTTGAAGCTTTTTTTATTTAAT
1 CGTTTGAA-C-TTTTTTATTTAAT
204240 AAATATATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 7 0.35
26 13 0.65
ACGTcount: A:0.19, C:0.06, G:0.13, T:0.62
Consensus pattern (24 bp):
CGTTTGAACTTTTTTATTTAATGT
Found at i:204485 original size:22 final size:22
Alignment explanation
Indices: 204419--204487 Score: 56
Period size: 22 Copynumber: 3.2 Consensus size: 22
204409 TTTGTATGTG
* *
204419 TATTTGAAATTATTATTTGAAA
1 TATTTGAAATAATTAATTGAAA
* *
204441 CATTTCACATATAA-TAA-TG--A
1 TATTTGA-A-ATAATTAATTGAAA
204461 TATTTGAAATAATTAATTGAAA
1 TATTTGAAATAATTAATTGAAA
204483 TATTT
1 TATTT
204488 TACATATAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 12
0.66 0.11 0.23
Matches are distributed among these distances:
18 4 0.11
19 4 0.11
20 8 0.23
22 13 0.37
23 3 0.09
24 3 0.09
ACGTcount: A:0.43, C:0.04, G:0.07, T:0.45
Consensus pattern (22 bp):
TATTTGAAATAATTAATTGAAA
Found at i:204722 original size:19 final size:19
Alignment explanation
Indices: 204698--204734 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
204688 TAAAATGTAT
204698 ATATTTATTATATAATTTC
1 ATATTTATTATATAATTTC
*
204717 ATATTTATTATTTAATTT
1 ATATTTATTATATAATTT
204735 TATAAATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (19 bp):
ATATTTATTATATAATTTC
Found at i:207508 original size:28 final size:28
Alignment explanation
Indices: 207472--207533 Score: 124
Period size: 28 Copynumber: 2.2 Consensus size: 28
207462 CCAATCAATT
207472 TAAATTTTAAACTTTTAAATGTGGTTAA
1 TAAATTTTAAACTTTTAAATGTGGTTAA
207500 TAAATTTTAAACTTTTAAATGTGGTTAA
1 TAAATTTTAAACTTTTAAATGTGGTTAA
207528 TAAATT
1 TAAATT
207534 ATAAGATTAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.40, C:0.03, G:0.10, T:0.47
Consensus pattern (28 bp):
TAAATTTTAAACTTTTAAATGTGGTTAA
Found at i:209025 original size:2 final size:2
Alignment explanation
Indices: 209018--209051 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
209008 TACTACAACC
* *
209018 AT AT AT AT AT AT AT AT AC AT AT GT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
209052 CAATCATCTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:216529 original size:38 final size:38
Alignment explanation
Indices: 216481--216566 Score: 106
Period size: 39 Copynumber: 2.2 Consensus size: 38
216471 AAATAAGTAT
216481 TAAATAATTATAA-AAATGTA-AAATA-TTATTTAAAATTA
1 TAAA-AATTATAAGAAAT-TATAAATAGTT-TTTAAAATTA
*
216519 TTAAGAATTATAAGAAATTATAAATAGTTTTTAAAATTA
1 -TAAAAATTATAAGAAATTATAAATAGTTTTTAAAATTA
216558 TAAAAATTA
1 TAAAAATTA
216567 ATTATGTTGG
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
38 18 0.43
39 22 0.52
40 2 0.05
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.40
Consensus pattern (38 bp):
TAAAAATTATAAGAAATTATAAATAGTTTTTAAAATTA
Found at i:216648 original size:11 final size:11
Alignment explanation
Indices: 216632--216695 Score: 58
Period size: 12 Copynumber: 5.6 Consensus size: 11
216622 CAATCTTTAA
216632 TTAAATTTATT
1 TTAAATTTATT
*
216643 TTAAATTTAAAT
1 TTAAATTT-ATT
**
216655 TT-AATTTAAA
1 TTAAATTTATT
*
216665 CTACAATTTATT
1 TTA-AATTTATT
216677 TTAAATTTAATT
1 TTAAATTT-ATT
216689 TTAAATT
1 TTAAATT
216696 GAGTTTAAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
10 3 0.07
11 18 0.42
12 22 0.51
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (11 bp):
TTAAATTTATT
Found at i:216652 original size:17 final size:17
Alignment explanation
Indices: 216632--216691 Score: 77
Period size: 17 Copynumber: 3.5 Consensus size: 17
216622 CAATCTTTAA
216632 TTAAATTTATTTTAAAT
1 TTAAATTTATTTTAAAT
*
216649 TTAAATTTAATTTAAA-
1 TTAAATTTATTTTAAAT
*
216665 CTACAATTTATTTTAAAT
1 TTA-AATTTATTTTAAAT
*
216683 TTAATTTTA
1 TTAAATTTA
216692 AATTGAGTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
16 2 0.06
17 32 0.89
18 2 0.06
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (17 bp):
TTAAATTTATTTTAAAT
Found at i:217367 original size:3 final size:3
Alignment explanation
Indices: 217359--217436 Score: 102
Period size: 3 Copynumber: 26.0 Consensus size: 3
217349 ATAATTCTAT
* * * *
217359 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TGA TGA TGA TAT
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
217407 TAA TAA TAA TAG TAT TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
217437 AAGTTGAAGG
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 68 1.00
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:218514 original size:29 final size:29
Alignment explanation
Indices: 218482--218639 Score: 139
Period size: 29 Copynumber: 5.5 Consensus size: 29
218472 AACTGTTCAT
*
218482 AAATTACATTTTTACCCTTAAACTTTCCA
1 AAATTACATTTTTACCCTTGAACTTTCCA
* * **
218511 AAATTCCATTTTTAACC-TGAACTTTTTGA
1 AAATTACATTTTTACCCTTGAAC-TTTCCA
*
218540 AAATTACA-TTTTACCCCTT-AATTTTCC-
1 AAATTACATTTTTA-CCCTTGAACTTTCCA
* *
218567 AAATT-CTATTTTTGA-CCTCGATCTTTCCAA
1 AAATTAC-ATTTTT-ACCCTTGAACTTTCC-A
* *
218597 AAATTACATTTTTACTCTCGAACTTTCCA
1 AAATTACATTTTTACCCTTGAACTTTCCA
218626 AAATTACATTTTTA
1 AAATTACATTTTTA
218640 TCCCGTTTTT
Statistics
Matches: 103, Mismatches: 15, Indels: 22
0.74 0.11 0.16
Matches are distributed among these distances:
26 1 0.01
27 9 0.09
28 22 0.21
29 47 0.46
30 23 0.22
31 1 0.01
ACGTcount: A:0.32, C:0.22, G:0.03, T:0.44
Consensus pattern (29 bp):
AAATTACATTTTTACCCTTGAACTTTCCA
Found at i:218626 original size:58 final size:58
Alignment explanation
Indices: 218482--218919 Score: 325
Period size: 58 Copynumber: 7.6 Consensus size: 58
218472 AACTGTTCAT
** * *
218482 AAATTA-CATTTTTACCCTTAAACTTTCCAAAATTCCATTTTTAACCT-GAACTTTTT--GA
1 AAATTACCA-TTTTACCCCCAAAC-TTCCAAAATTCCATTTTTGACCTCG-A-TTTTTCCAA
* ** * *
218540 AAATTA-CATTTTACCCCTTAATTTTCC-AAATTCTATTTTTGACCTCGATCTTTCCAA
1 AAATTACCATTTTACCCC-CAAACTTCCAAAATTCCATTTTTGACCTCGATTTTTCCAA
* * * * * *
218597 AAATTA-CATTTTTACTCTCGAACTTTCCAAAATTACATTTTT-ATCC-CGTTTTTTTCAA
1 AAATTACCA-TTTTACCCCCAAAC-TTCCAAAATTCCATTTTTGA-CCTCGATTTTTCCAA
* * * *
218655 AAATTACCATTTTACCCCCGAACTTCCAAAAATTCCATTTTTAACCTAGATTTTTCAAA
1 AAATTACCATTTTACCCCCAAACTTCC-AAAATTCCATTTTTGACCTCGATTTTTCCAA
**
218714 AAATTACCATTTTACCCATAAACTTCCAAAAATTCCA-TTTTGACAC-C-A-TTTTCCAA
1 AAATTACCATTTTACCCCCAAACTTCC-AAAATTCCATTTTTGAC-CTCGATTTTTCCAA
* * *
218770 AAATTACCATTTTACCCCCAAACTTCCAAAAACTCAATTTTTGACCTTGATTTTTCCAA
1 AAATTACCATTTTACCCCCAAACTTCC-AAAATTCCATTTTTGACCTCGATTTTTCCAA
*** * * *
218829 AAATTACCATTTTACCCCTGGA-TGTCTAAAATTCCGTTTTTGA-CTCCGAACTTTTCC-A
1 AAATTACCATTTTACCCCCAAACT-TCCAAAATTCCATTTTTGACCT-CG-ATTTTTCCAA
* *
218887 AAATTACCATTTTGCCCCCCAA-TGTCCAAAATT
1 AAATTACCATTTTACCCCCAAACT-TCCAAAATT
218920 ACTATTTTGC
Statistics
Matches: 310, Mismatches: 50, Indels: 40
0.77 0.12 0.10
Matches are distributed among these distances:
55 4 0.01
56 58 0.19
57 37 0.12
58 116 0.37
59 95 0.31
ACGTcount: A:0.32, C:0.25, G:0.04, T:0.39
Consensus pattern (58 bp):
AAATTACCATTTTACCCCCAAACTTCCAAAATTCCATTTTTGACCTCGATTTTTCCAA
Found at i:218684 original size:29 final size:29
Alignment explanation
Indices: 218652--218801 Score: 130
Period size: 29 Copynumber: 5.2 Consensus size: 29
218642 CCGTTTTTTT
*
218652 CAAAAATTACCATTTTACCCCCGAACTTC
1 CAAAAATTACCATTTTACCCCCAAACTTC
* * **
218681 CAAAAATT-CCATTTTTA-ACCTAGATTTTTC
1 CAAAAATTACCA-TTTTACCCCCA-A-ACTTC
* **
218711 AAAAAATTACCATTTTACCCATAAACTTC
1 CAAAAATTACCATTTTACCCCCAAACTTC
* **
218740 CAAAAATT-CCATTTTGA-CACC-ATTTTC
1 CAAAAATTACCATTTT-ACCCCCAAACTTC
218767 CAAAAATTACCATTTTACCCCCAAACTTC
1 CAAAAATTACCATTTTACCCCCAAACTTC
218796 CAAAAA
1 CAAAAA
218802 CTCAATTTTT
Statistics
Matches: 93, Mismatches: 19, Indels: 18
0.72 0.15 0.14
Matches are distributed among these distances:
27 13 0.14
28 23 0.25
29 35 0.38
30 16 0.17
31 6 0.06
ACGTcount: A:0.39, C:0.27, G:0.02, T:0.32
Consensus pattern (29 bp):
CAAAAATTACCATTTTACCCCCAAACTTC
Found at i:218684 original size:115 final size:114
Alignment explanation
Indices: 218482--218919 Score: 376
Period size: 115 Copynumber: 3.8 Consensus size: 114
218472 AACTGTTCAT
* *
218482 AAATTA-CATTTTTACCCTTAAACTTTCCAAAATTCCATTTTTAACCTGAACTTTTT-GAAAATT
1 AAATTACCATTTTTACCC-TAAACTTTCCAAAATTCCATTTTT-ACCCG-A-TTTTTCAAAAATT
* ** * * *
218545 A-CATTTTACCCCTTAATTTTCC-AAATTCTATTTTTGACCTCGATCTTTCCAA
62 ACCATTTTACCCC-CAAACTTCCAAAATTCAATTTTTGACCTAGATTTTTCCAA
* * * *
218597 AAATTA-CATTTTTACTCTCGAACTTTCCAAAATTACATTTTTATCCCGTTTTTTTCAAAAATTA
1 AAATTACCATTTTTACCCT-AAACTTTCCAAAATTCCATTTTTA-CCCG-ATTTTTCAAAAATTA
* * * *
218661 CCATTTTACCCCCGAACTTCCAAAAATTCCATTTTTAACCTAGATTTTTCAAA
63 CCATTTTACCCCCAAACTTCC-AAAATTCAATTTTTGACCTAGATTTTTCCAA
* *
218714 AAATTACCA-TTTTACCCATAAAC-TTCCAAAAATTCCATTTTGACACC-ATTTTCCAAAAATTA
1 AAATTACCATTTTTACCC-TAAACTTTCC-AAAATTCCATTTTTAC-CCGATTTTTCAAAAATTA
* *
218776 CCATTTTACCCCCAAACTTCCAAAAACTCAATTTTTGACCTTGATTTTTCCAA
63 CCATTTTACCCCCAAACTTCC-AAAATTCAATTTTTGACCTAGATTTTTCCAA
** * * * * *
218829 AAATTACCA-TTTTACCCCTGGA-TGTCTAAAATTCCGTTTTTGACTCCGAACTTTTCCAAAATT
1 AAATTACCATTTTTA-CCCTAAACTTTCCAAAATTCCATTTTT-AC-CCG-ATTTTTCAAAAATT
* *
218892 ACCATTTTGCCCCCCAA-TGTCCAAAATT
62 ACCATTTTACCCCCAAACT-TCCAAAATT
218920 ACTATTTTGC
Statistics
Matches: 266, Mismatches: 41, Indels: 31
0.79 0.12 0.09
Matches are distributed among these distances:
114 19 0.07
115 134 0.50
116 25 0.09
117 85 0.32
118 3 0.01
ACGTcount: A:0.32, C:0.25, G:0.04, T:0.39
Consensus pattern (114 bp):
AAATTACCATTTTTACCCTAAACTTTCCAAAATTCCATTTTTACCCGATTTTTCAAAAATTACCA
TTTTACCCCCAAACTTCCAAAATTCAATTTTTGACCTAGATTTTTCCAA
Found at i:218719 original size:59 final size:57
Alignment explanation
Indices: 218482--218846 Score: 316
Period size: 59 Copynumber: 6.3 Consensus size: 57
218472 AACTGTTCAT
** *
218482 AAATTA-CATTTTTACCCTTAAACTTTCCAAAATTCCATTTTTAACCTGAACTTTTT--GA
1 AAATTACCA-TTTTACCCCCAAAC-TTCCAAAATTCCATTTTTAACCTG-A-TTTTTCCAA
* ** * * *
218540 AAATTA-CATTTTACCCCTTAATTTTCC-AAATTCTATTTTTGACCTCGATCTTTCCAA
1 AAATTACCATTTTACCCC-CAAACTTCCAAAATTCCATTTTTAACCT-GATTTTTCCAA
* * * * * * * *
218597 AAATTA-CATTTTTACTCTCGAACTTTCCAAAATTACATTTTTATCCCGTTTTTTTCAA
1 AAATTACCA-TTTTACCCCCAAAC-TTCCAAAATTCCATTTTTAACCTGATTTTTCCAA
* *
218655 AAATTACCATTTTACCCCCGAACTTCCAAAAATTCCATTTTTAACCTAGATTTTTCAAA
1 AAATTACCATTTTACCCCCAAACTTCC-AAAATTCCATTTTTAACCT-GATTTTTCCAA
** *
218714 AAATTACCATTTTACCCATAAACTTCCAAAAATTCCATTTTGACACC--A-TTTTCCAA
1 AAATTACCATTTTACCCCCAAACTTCC-AAAATTCCATTTTTA-ACCTGATTTTTCCAA
* * *
218770 AAATTACCATTTTACCCCCAAACTTCCAAAAACTCAATTTTTGACCTTGATTTTTCCAA
1 AAATTACCATTTTACCCCCAAACTTCC-AAAATTCCATTTTTAACC-TGATTTTTCCAA
218829 AAATTACCATTTTACCCC
1 AAATTACCATTTTACCCC
218847 TGGATGTCTA
Statistics
Matches: 252, Mismatches: 40, Indels: 29
0.79 0.12 0.09
Matches are distributed among these distances:
55 7 0.03
56 61 0.24
57 28 0.11
58 65 0.26
59 88 0.35
60 3 0.01
ACGTcount: A:0.33, C:0.25, G:0.03, T:0.39
Consensus pattern (57 bp):
AAATTACCATTTTACCCCCAAACTTCCAAAATTCCATTTTTAACCTGATTTTTCCAA
Found at i:219692 original size:16 final size:15
Alignment explanation
Indices: 219661--219690 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
219651 TTTTCAAAAC
219661 GGATTTTTAACGTTT
1 GGATTTTTAACGTTT
219676 GGATTTTTAACGTTT
1 GGATTTTTAACGTTT
219691 TGTGGTGATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.07, G:0.20, T:0.53
Consensus pattern (15 bp):
GGATTTTTAACGTTT
Found at i:224328 original size:18 final size:19
Alignment explanation
Indices: 224305--224345 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
224295 GAATGAATTT
* *
224305 TTAATTACATAAATTT-AA
1 TTAATTAAAAAAATTTAAA
224323 TTAATTAAAAAAATTTAAA
1 TTAATTAAAAAAATTTAAA
224342 TTAA
1 TTAA
224346 GTAGACTTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (19 bp):
TTAATTAAAAAAATTTAAA
Found at i:224976 original size:29 final size:29
Alignment explanation
Indices: 224936--224996 Score: 97
Period size: 29 Copynumber: 2.1 Consensus size: 29
224926 CCAGAGCTAT
*
224936 TCTCCCTCTCCTCTTTT-TGCGTCCCCATC
1 TCTCCCTCTCCT-TTTTCTGCCTCCCCATC
224965 TCTCCCTCTCCTTTTTCTGCCTCCCCATC
1 TCTCCCTCTCCTTTTTCTGCCTCCCCATC
224994 TCT
1 TCT
224997 GCTTAACTCT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 4 0.13
29 26 0.87
ACGTcount: A:0.03, C:0.49, G:0.05, T:0.43
Consensus pattern (29 bp):
TCTCCCTCTCCTTTTTCTGCCTCCCCATC
Found at i:236398 original size:31 final size:31
Alignment explanation
Indices: 236360--236423 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
236350 TACTCTTGAC
236360 CAGATCAACACACGGGATTCTCAAACATATT
1 CAGATCAACACACGGGATTCTCAAACATATT
236391 CAGATCAACACACGGGATTCTCAAACATATT
1 CAGATCAACACACGGGATTCTCAAACATATT
236422 CA
1 CA
236424 TTCTCCTCTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.39, C:0.27, G:0.12, T:0.22
Consensus pattern (31 bp):
CAGATCAACACACGGGATTCTCAAACATATT
Found at i:240368 original size:45 final size:45
Alignment explanation
Indices: 240312--240415 Score: 181
Period size: 45 Copynumber: 2.3 Consensus size: 45
240302 TCTTATATGT
*
240312 GACTCATACATGCAAACTCGTAGAAGAAGATTCATAGATATGGTA
1 GACTCATACATGCAAACTCGTAGAAGAAGATTCATAGATATGGAA
*
240357 GACTCACACATGCAAACTCGTAGAAGAAGATTCATAGATATGGAA
1 GACTCATACATGCAAACTCGTAGAAGAAGATTCATAGATATGGAA
*
240402 AACTCATACATGCA
1 GACTCATACATGCA
240416 GATTCATAGA
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 55 1.00
ACGTcount: A:0.41, C:0.18, G:0.18, T:0.22
Consensus pattern (45 bp):
GACTCATACATGCAAACTCGTAGAAGAAGATTCATAGATATGGAA
Found at i:242870 original size:15 final size:16
Alignment explanation
Indices: 242849--242894 Score: 51
Period size: 15 Copynumber: 3.0 Consensus size: 16
242839 AGCAGGCGGT
242849 GATGGTGGTGGAGGGC
1 GATGGTGGTGGAGGGC
* *
242865 -ATGGTGGAGG-CGGC
1 GATGGTGGTGGAGGGC
*
242879 GACGGTGGTGGAGGGC
1 GATGGTGGTGGAGGGC
242895 TTTGCACGCA
Statistics
Matches: 23, Mismatches: 5, Indels: 4
0.72 0.16 0.12
Matches are distributed among these distances:
14 3 0.13
15 17 0.74
16 3 0.13
ACGTcount: A:0.13, C:0.11, G:0.61, T:0.15
Consensus pattern (16 bp):
GATGGTGGTGGAGGGC
Found at i:253254 original size:14 final size:15
Alignment explanation
Indices: 253235--253275 Score: 66
Period size: 15 Copynumber: 2.8 Consensus size: 15
253225 TCGGTGTCTT
253235 TTTTTAAATATT-AA
1 TTTTTAAATATTAAA
*
253249 TTTTTAAATTTTAAA
1 TTTTTAAATATTAAA
253264 TTTTTAAATATT
1 TTTTTAAATATT
253276 CGGTTAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 11 0.46
15 13 0.54
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
TTTTTAAATATTAAA
Found at i:253638 original size:21 final size:22
Alignment explanation
Indices: 253605--253645 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
253595 AAATTATCTT
253605 TATTATTTTAAAT-ATAAAATA
1 TATTATTTTAAATCATAAAATA
253626 TATT-TTTTAAAATCATAAAA
1 TATTATTTT-AAATCATAAAA
253646 ATTAAAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.22
21 8 0.44
22 6 0.33
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (22 bp):
TATTATTTTAAATCATAAAATA
Found at i:260395 original size:13 final size:11
Alignment explanation
Indices: 260368--260410 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
260358 AGGTAAATAT
260368 TATTTTATTAA
1 TATTTTATTAA
260379 TATTTTACTTAA
1 TATTTTA-TTAA
*
260391 -ATATTTATTAT
1 TAT-TTTATTAA
260402 TATTTTATT
1 TATTTTATT
260411 TAGAAAATGG
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
11 18 0.64
12 10 0.36
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:268361 original size:130 final size:130
Alignment explanation
Indices: 268128--268517 Score: 753
Period size: 130 Copynumber: 3.0 Consensus size: 130
268118 GGCTGCTTAC
268128 TCTAATCATAGCATTTCGGTTCCTATGATCCAAATCTCGTCAGCTTTGAGTTAGCATTTGATGTA
1 TCTAATCATAGCATTTCGGTTCCTATGATCCAAATCTCGTCAGCTTTGAGTTAGCATTTGATGTA
*
268193 CTACTCTTTGATTCAAAGCATGGAATTTGGGTTATGAATTAATGACTATCAATAAAGGAGGCAGA
66 CTACTCTTTGATTCAAAGCATGGAATTTGGGTTATGAATTTATGACTATCAATAAAGGAGGCAGA
268258 TCTAATCATAGCATTTCGGTTCCTATGATCCAAATCTCGTCAGCTTTGAGTTAGCATTTGATGTA
1 TCTAATCATAGCATTTCGGTTCCTATGATCCAAATCTCGTCAGCTTTGAGTTAGCATTTGATGTA
268323 CTACTCTTTGATTCAAAGCATGGAATTTGGGTTATGAATTTATGACTATCAATAAAGGAGGCAGA
66 CTACTCTTTGATTCAAAGCATGGAATTTGGGTTATGAATTTATGACTATCAATAAAGGAGGCAGA
*
268388 TCTAATCATAGCATTTCGGTTCCTATGATCCAAATCTCGTCAGCTTTGAGTTGGCATTTGATGTA
1 TCTAATCATAGCATTTCGGTTCCTATGATCCAAATCTCGTCAGCTTTGAGTTAGCATTTGATGTA
*
268453 CTACTCTTTGATTCAAAGCATGGAATTTGGGTTATGAATTTACGACTATCAATAAAGGAGGCAGA
66 CTACTCTTTGATTCAAAGCATGGAATTTGGGTTATGAATTTATGACTATCAATAAAGGAGGCAGA
268518 AAAGTGGAGA
Statistics
Matches: 257, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
130 257 1.00
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.35
Consensus pattern (130 bp):
TCTAATCATAGCATTTCGGTTCCTATGATCCAAATCTCGTCAGCTTTGAGTTAGCATTTGATGTA
CTACTCTTTGATTCAAAGCATGGAATTTGGGTTATGAATTTATGACTATCAATAAAGGAGGCAGA
Done.