Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr12
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: 101062743
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 4026412 characters in sequence are not A, C, G, or T
File 138 of 297
Found at i:47472445 original size:23 final size:23
Alignment explanation
Indices: 47472415--47472491 Score: 138
Period size: 23 Copynumber: 3.4 Consensus size: 23
47472405 ATGATGAATA
47472415 GTAAGCTCTATTGAGCTGAAACG
1 GTAAGCTCTATTGAGCTGAAACG
47472438 GTAAGCTCTATTGAGCTGAAACG
1 GTAAGCTCTATTGAGCTGAAACG
*
47472461 GTAAGCTCTATTGAGCTG-AACA
1 GTAAGCTCTATTGAGCTGAAACG
47472483 GTAAGCTCT
1 GTAAGCTCT
47472492 TACGAGCTGA
Statistics
Matches: 53, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
22 12 0.23
23 41 0.77
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.27
Consensus pattern (23 bp):
GTAAGCTCTATTGAGCTGAAACG
Found at i:47476491 original size:19 final size:18
Alignment explanation
Indices: 47476469--47476507 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
47476459 GAGAATTTAG
*
47476469 AATGGCAAAGAAGATAGAA
1 AATGGC-AAGAAGAAAGAA
*
47476488 AATGGCGAGAAGAAAGAA
1 AATGGCAAGAAGAAAGAA
47476506 AA
1 AA
47476508 GATGTGAATG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.59, C:0.05, G:0.28, T:0.08
Consensus pattern (18 bp):
AATGGCAAGAAGAAAGAA
Found at i:47486977 original size:74 final size:74
Alignment explanation
Indices: 47486856--47487003 Score: 287
Period size: 74 Copynumber: 2.0 Consensus size: 74
47486846 ACTACTTTTT
*
47486856 GGAAAAACGATTGAATTAAGATAATACCTAAGGAAAAATCCACCTAGACTTCACTTGTTATTTGA
1 GGAAAAACGATTGAATTAAGACAATACCTAAGGAAAAATCCACCTAGACTTCACTTGTTATTTGA
47486921 CTCTGAATC
66 CTCTGAATC
47486930 GGAAAAACGATTGAATTAAGACAATACCTAAGGAAAAATCCACCTAGACTTCACTTGTTATTTGA
1 GGAAAAACGATTGAATTAAGACAATACCTAAGGAAAAATCCACCTAGACTTCACTTGTTATTTGA
47486995 CTCTGAATC
66 CTCTGAATC
47487004 AGACGATTTA
Statistics
Matches: 73, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
74 73 1.00
ACGTcount: A:0.39, C:0.18, G:0.15, T:0.28
Consensus pattern (74 bp):
GGAAAAACGATTGAATTAAGACAATACCTAAGGAAAAATCCACCTAGACTTCACTTGTTATTTGA
CTCTGAATC
Found at i:47521817 original size:19 final size:19
Alignment explanation
Indices: 47521789--47521827 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
47521779 AGAGCGAAAG
47521789 AAATGAG-AAACGGGCCAA
1 AAATGAGAAAACGGGCCAA
*
47521807 AAATGGAGAAAATGGGCCAA
1 AAAT-GAGAAAACGGGCCAA
47521827 A
1 A
47521828 GTACGAAATC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 4 0.22
19 3 0.17
20 11 0.61
ACGTcount: A:0.51, C:0.13, G:0.28, T:0.08
Consensus pattern (19 bp):
AAATGAGAAAACGGGCCAA
Found at i:47530326 original size:93 final size:93
Alignment explanation
Indices: 47530213--47530384 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
47530203 CGCCCATAAG
* *
47530213 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
47530278 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
*
47530306 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
47530371 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
47530385 TCAACCATCC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:47530381 original size:46 final size:46
Alignment explanation
Indices: 47530206--47530381 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
47530196 TGTAACCCGC
* * *
47530206 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
47530252 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
47530302 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
47530345 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
47530382 TGCTCAACCA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 63 0.57
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:47534862 original size:304 final size:304
Alignment explanation
Indices: 47534313--47534920 Score: 1216
Period size: 304 Copynumber: 2.0 Consensus size: 304
47534303 ATCCATAGAT
47534313 TGAGTTAATACAACCATAGAGTGTAAATTAGAGACAAGTCTCGTCTATTCAATCTAGGGATTAGA
1 TGAGTTAATACAACCATAGAGTGTAAATTAGAGACAAGTCTCGTCTATTCAATCTAGGGATTAGA
47534378 CGTTATTAGTCTTGAAAAGGGATAATAACATAACTTAGGGATCTCAACAGAACAAGCTGAATGAA
66 CGTTATTAGTCTTGAAAAGGGATAATAACATAACTTAGGGATCTCAACAGAACAAGCTGAATGAA
47534443 TAAATCATCCGATTCGGAGCCAGAATAACAAGTAAAGTCTAGGTGGATTTTTCCTTAGGTATTGT
131 TAAATCATCCGATTCGGAGCCAGAATAACAAGTAAAGTCTAGGTGGATTTTTCCTTAGGTATTGT
47534508 CTTAAGTCAATCGATTTTCCCCAAAAGCAATTCCTCAATTCTTTTCTTTGTGAGTTCTTAGTTTA
196 CTTAAGTCAATCGATTTTCCCCAAAAGCAATTCCTCAATTCTTTTCTTTGTGAGTTCTTAGTTTA
47534573 GATAATTAGTTAATCAAAACAAAACCTCCTTATTCTTAGGCTAG
261 GATAATTAGTTAATCAAAACAAAACCTCCTTATTCTTAGGCTAG
47534617 TGAGTTAATACAACCATAGAGTGTAAATTAGAGACAAGTCTCGTCTATTCAATCTAGGGATTAGA
1 TGAGTTAATACAACCATAGAGTGTAAATTAGAGACAAGTCTCGTCTATTCAATCTAGGGATTAGA
47534682 CGTTATTAGTCTTGAAAAGGGATAATAACATAACTTAGGGATCTCAACAGAACAAGCTGAATGAA
66 CGTTATTAGTCTTGAAAAGGGATAATAACATAACTTAGGGATCTCAACAGAACAAGCTGAATGAA
47534747 TAAATCATCCGATTCGGAGCCAGAATAACAAGTAAAGTCTAGGTGGATTTTTCCTTAGGTATTGT
131 TAAATCATCCGATTCGGAGCCAGAATAACAAGTAAAGTCTAGGTGGATTTTTCCTTAGGTATTGT
47534812 CTTAAGTCAATCGATTTTCCCCAAAAGCAATTCCTCAATTCTTTTCTTTGTGAGTTCTTAGTTTA
196 CTTAAGTCAATCGATTTTCCCCAAAAGCAATTCCTCAATTCTTTTCTTTGTGAGTTCTTAGTTTA
47534877 GATAATTAGTTAATCAAAACAAAACCTCCTTATTCTTAGGCTAG
261 GATAATTAGTTAATCAAAACAAAACCTCCTTATTCTTAGGCTAG
47534921 ATAATAAAAA
Statistics
Matches: 304, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
304 304 1.00
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.32
Consensus pattern (304 bp):
TGAGTTAATACAACCATAGAGTGTAAATTAGAGACAAGTCTCGTCTATTCAATCTAGGGATTAGA
CGTTATTAGTCTTGAAAAGGGATAATAACATAACTTAGGGATCTCAACAGAACAAGCTGAATGAA
TAAATCATCCGATTCGGAGCCAGAATAACAAGTAAAGTCTAGGTGGATTTTTCCTTAGGTATTGT
CTTAAGTCAATCGATTTTCCCCAAAAGCAATTCCTCAATTCTTTTCTTTGTGAGTTCTTAGTTTA
GATAATTAGTTAATCAAAACAAAACCTCCTTATTCTTAGGCTAG
Found at i:47535569 original size:4 final size:4
Alignment explanation
Indices: 47535560--47535584 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
47535550 AAAGTATACA
47535560 TGTT TGTT TGTT TGTT TGTT TGTT T
1 TGTT TGTT TGTT TGTT TGTT TGTT T
47535585 TTTCTTGTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.00, C:0.00, G:0.24, T:0.76
Consensus pattern (4 bp):
TGTT
Found at i:47545763 original size:4 final size:4
Alignment explanation
Indices: 47545740--47545777 Score: 53
Period size: 4 Copynumber: 10.0 Consensus size: 4
47545730 CAAGAGAAAG
*
47545740 TAAA TTAA TAAA T-AA T-AA TAAA TAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
47545778 ATTAATTTCC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
3 6 0.19
4 25 0.81
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (4 bp):
TAAA
Found at i:47546224 original size:23 final size:23
Alignment explanation
Indices: 47546198--47546243 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
47546188 TCCCTATTCA
47546198 AGACTGTACTTGTTATTCTGGCT
1 AGACTGTACTTGTTATTCTGGCT
47546221 AGACTGTACTTGTTATTCTGGCT
1 AGACTGTACTTGTTATTCTGGCT
47546244 CCGAATCGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.17, C:0.17, G:0.22, T:0.43
Consensus pattern (23 bp):
AGACTGTACTTGTTATTCTGGCT
Found at i:47549734 original size:31 final size:31
Alignment explanation
Indices: 47549694--47549839 Score: 213
Period size: 31 Copynumber: 4.7 Consensus size: 31
47549684 TTAATCTTGA
*
47549694 CATAT-ACTGGGCCGAAGCCTTCTCATAAAT
1 CATATCACTGGGCCGAAGCCTTTTCATAAAT
* *
47549724 CATATCACTGGGCCAAAGCCTTTCCATAAAT
1 CATATCACTGGGCCGAAGCCTTTTCATAAAT
47549755 CATATCACTGGGCCGAAGCCTTTTCATAAAT
1 CATATCACTGGGCCGAAGCCTTTTCATAAAT
* *
47549786 CATATCACTCGGCCAAAGCCTTTTCATAAAT
1 CATATCACTGGGCCGAAGCCTTTTCATAAAT
* * *
47549817 CATTTCACTGCGCTGAAGCCTTT
1 CATATCACTGGGCCGAAGCCTTT
47549840 ACTGTAAACG
Statistics
Matches: 103, Mismatches: 12, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
30 5 0.05
31 98 0.95
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (31 bp):
CATATCACTGGGCCGAAGCCTTTTCATAAAT
Found at i:47549910 original size:42 final size:42
Alignment explanation
Indices: 47549863--47549996 Score: 259
Period size: 42 Copynumber: 3.2 Consensus size: 42
47549853 TGGCCCTTAG
*
47549863 GCCCATTTCAATATCACATGTAATGTCAATGGATGTATGCAA
1 GCCCATTTCAATATCACATGTAATGTCAATGAATGTATGCAA
47549905 GCCCATTTCAATATCACATGTAATGTCAATGAATGTATGCAA
1 GCCCATTTCAATATCACATGTAATGTCAATGAATGTATGCAA
47549947 GCCCATTTCAATATCACATGTAATGTCAATGAATGTATGCAA
1 GCCCATTTCAATATCACATGTAATGTCAATGAATGTATGCAA
47549989 GCCCATTT
1 GCCCATTT
47549997 GGGGAGACTA
Statistics
Matches: 91, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
42 91 1.00
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.31
Consensus pattern (42 bp):
GCCCATTTCAATATCACATGTAATGTCAATGAATGTATGCAA
Found at i:47550172 original size:25 final size:25
Alignment explanation
Indices: 47550144--47550213 Score: 106
Period size: 25 Copynumber: 2.8 Consensus size: 25
47550134 CTCTTTTAAT
47550144 AACTGGGGCAAAGCCC-TTTCTGATA
1 AACTGGGGCAAAGCCCTTTTC-GATA
*
47550169 AACTGGGGCAAAGCCCTTTTCGGTA
1 AACTGGGGCAAAGCCCTTTTCGATA
*
47550194 AACTGGGGCAGAGCCCTTTT
1 AACTGGGGCAAAGCCCTTTT
47550214 AGCACTTCCT
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
25 38 0.90
26 4 0.10
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.24
Consensus pattern (25 bp):
AACTGGGGCAAAGCCCTTTTCGATA
Found at i:47551171 original size:27 final size:27
Alignment explanation
Indices: 47551141--47551248 Score: 103
Period size: 27 Copynumber: 3.9 Consensus size: 27
47551131 GTAAATCTAC
47551141 AAACCAAGGGTATTTCAGTAATTTTGT
1 AAACCAAGGGTATTTCAGTAATTTTGT
*
47551168 AAACCAATGGTATTTCTA-TAATTTT-T
1 AAACCAAGGGTATTTC-AGTAATTTTGT
* *
47551194 AGAAAGTCAAGGGTATTTCTGTAATTTTGT
1 --AAA-CCAAGGGTATTTCAGTAATTTTGT
* * **
47551224 AAATCAGGGGTATTTTGGTAATTTT
1 AAACCAAGGGTATTTCAGTAATTTT
47551249 ACAAATTGAG
Statistics
Matches: 68, Mismatches: 7, Indels: 12
0.78 0.08 0.14
Matches are distributed among these distances:
26 1 0.01
27 41 0.60
28 7 0.10
29 18 0.26
30 1 0.01
ACGTcount: A:0.31, C:0.08, G:0.19, T:0.42
Consensus pattern (27 bp):
AAACCAAGGGTATTTCAGTAATTTTGT
Found at i:47551254 original size:27 final size:27
Alignment explanation
Indices: 47551190--47551354 Score: 176
Period size: 27 Copynumber: 6.1 Consensus size: 27
47551180 TTTCTATAAT
* *
47551190 TTTTAGAAAGTCAAGGGTATTTCT-GTAA
1 TTTTACAAA-TCAGGGGTATTT-TGGTAA
**
47551218 TTTTGTAAATCAGGGGTATTTTGGTAA
1 TTTTACAAATCAGGGGTATTTTGGTAA
*
47551245 TTTTACAAAT-TGAGGGTATTTTGGTAA
1 TTTTACAAATCAG-GGGTATTTTGGTAA
* * * *
47551272 TTTCACAAACCAGTGGTATTTCGGTAA
1 TTTTACAAATCAGGGGTATTTTGGTAA
47551299 TTTTACAAA-CTAGGGGTATTTTGGTAA
1 TTTTACAAATC-AGGGGTATTTTGGTAA
47551326 TTTTACAAA-CTAGGGGTATTTTGGTAA
1 TTTTACAAATC-AGGGGTATTTTGGTAA
47551353 TT
1 TT
47551355 CTATCCTACA
Statistics
Matches: 119, Mismatches: 14, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
26 3 0.03
27 108 0.91
28 8 0.07
ACGTcount: A:0.29, C:0.08, G:0.22, T:0.41
Consensus pattern (27 bp):
TTTTACAAATCAGGGGTATTTTGGTAA
Found at i:47551290 original size:54 final size:54
Alignment explanation
Indices: 47551228--47551387 Score: 198
Period size: 54 Copynumber: 3.0 Consensus size: 54
47551218 TTTTGTAAAT
*
47551228 CAGGGGTATTTTGGTAATTTTACAAA-TTGAGGGTATTTTGGTAATTTCACAAAC
1 CAGGGGTATTTTGGTAATTTTACAAACTAG-GGGTATTTTGGTAATTTCACAAAC
* * *
47551282 CAGTGGTATTTCGGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTACAAAC
1 CAGGGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGGTAATTTCACAAAC
* * ** **
47551336 TAGGGGTATTTTGGTAATTCTATCCTAC-AGGGGTATTTCAGTAATTTCACAA
1 CAGGGGTATTTTGGTAATTTTA-CAAACTAGGGGTATTTTGGTAATTTCACAA
47551388 TCGAGGGTAA
Statistics
Matches: 91, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
54 86 0.95
55 5 0.05
ACGTcount: A:0.29, C:0.11, G:0.21, T:0.39
Consensus pattern (54 bp):
CAGGGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGGTAATTTCACAAAC
Found at i:47551321 original size:81 final size:81
Alignment explanation
Indices: 47551205--47551354 Score: 232
Period size: 81 Copynumber: 1.9 Consensus size: 81
47551195 GAAAGTCAAG
* ** *
47551205 GGTATTTCTGTAATTTTGTAAATCAGGGGTATTTTGGTAATTTTACAAA-TTGAGGGTATTTTGG
1 GGTATTTCGGTAATTTTACAAATCAGGGGTATTTTGGTAATTTTACAAACTAG-GGGTATTTTGG
47551269 TAATTTCACAAACCAGT
65 TAATTTCACAAACCAGT
47551286 GGTATTTCGGTAATTTTACAAA-CTAGGGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGG
1 GGTATTTCGGTAATTTTACAAATC-AGGGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGG
47551350 TAATT
65 TAATT
47551355 CTATCCTACA
Statistics
Matches: 63, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
80 1 0.02
81 60 0.95
82 2 0.03
ACGTcount: A:0.28, C:0.08, G:0.22, T:0.42
Consensus pattern (81 bp):
GGTATTTCGGTAATTTTACAAATCAGGGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGGT
AATTTCACAAACCAGT
Found at i:47551371 original size:81 final size:81
Alignment explanation
Indices: 47551204--47551387 Score: 223
Period size: 81 Copynumber: 2.3 Consensus size: 81
47551194 AGAAAGTCAA
* ** *
47551204 GGGTATTTCTGTAATTTTGTAAATCAGGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTTGG
1 GGGTATTTCAGTAATTTTACAAATCAGGGGTATTTTGGTAATTTTACAAATAGAGGGTATTTTGG
47551269 TAATTTCACAAACCAG
66 TAATTTCACAAACCAG
* *
47551285 TGGTATTTCGGTAATTTTACAAA-CTAGGGGTATTTTGGTAATTTTACAAACTAG-GGGTATTTT
1 GGGTATTTCAGTAATTTTACAAATC-AGGGGTATTTTGGTAATTTTACAAA-TAGAGGGTATTTT
**
47551348 GGTAA-TTCTATCCTA-CAG
64 GGTAATTTC-A-CAAACCAG
*
47551366 GGGTATTTCAGTAATTTCACAA
1 GGGTATTTCAGTAATTTTACAA
47551388 TCGAGGGTAA
Statistics
Matches: 89, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
80 4 0.04
81 81 0.91
82 4 0.04
ACGTcount: A:0.28, C:0.10, G:0.21, T:0.40
Consensus pattern (81 bp):
GGGTATTTCAGTAATTTTACAAATCAGGGGTATTTTGGTAATTTTACAAATAGAGGGTATTTTGG
TAATTTCACAAACCAG
Found at i:47551394 original size:27 final size:26
Alignment explanation
Indices: 47551225--47551394 Score: 130
Period size: 27 Copynumber: 6.3 Consensus size: 26
47551215 TAATTTTGTA
*
47551225 AATCAGGGGTATTTTGGTAATTTTAC
1 AATCAGGGGTATTTTGGTAATTTCAC
*
47551251 AAAT-TGAGGGTATTTTGGTAATTTCAC
1 -AATCAG-GGGTATTTTGGTAATTTCAC
* * * *
47551278 AAACCAGTGGTATTTCGGTAATTTTAC
1 -AATCAGGGGTATTTTGGTAATTTCAC
* *
47551305 AAACTAGGGGTATTTTGGTAATTTTAC
1 AATC-AGGGGTATTTTGGTAATTTCAC
*
47551332 AAACTAGGGGTATTTTGGTAA-TTCTATC
1 AATC-AGGGGTATTTTGGTAATTTC-A-C
* **
47551360 -CTACAGGGGTATTTCAGTAATTTCAC
1 AAT-CAGGGGTATTTTGGTAATTTCAC
47551386 AATCGAGGG
1 AATC-AGGG
47551395 TAAAACGGTA
Statistics
Matches: 118, Mismatches: 16, Indels: 18
0.78 0.11 0.12
Matches are distributed among these distances:
26 8 0.07
27 104 0.88
28 6 0.05
ACGTcount: A:0.29, C:0.11, G:0.22, T:0.38
Consensus pattern (26 bp):
AATCAGGGGTATTTTGGTAATTTCAC
Found at i:47551420 original size:27 final size:27
Alignment explanation
Indices: 47551386--47551583 Score: 288
Period size: 27 Copynumber: 7.3 Consensus size: 27
47551376 GTAATTTCAC
*
47551386 AATCGAGGGTAAAACGGTAATTTTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
* * *
47551413 AATTGAGGGTAAAATGGTAATTTTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
47551440 AATCGAGGGTAAAACGGTAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
* *
47551467 AATCGAGGGTAAAATGGTAATTCTATA
1 AATCGAGGGTAAAACGGTAATTCTGTA
*
47551494 AATCGAGGGTAAAACGGTAATTTTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
* *
47551521 AATCGAGGGTGAAACGGTAATTCTATA
1 AATCGAGGGTAAAACGGTAATTCTGTA
* **
47551548 AATCGAGGGTAAAATGGTAATTCTACA
1 AATCGAGGGTAAAACGGTAATTCTGTA
47551575 AATCGAGGG
1 AATCGAGGG
47551584 CATTTCAGTA
Statistics
Matches: 155, Mismatches: 16, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 155 1.00
ACGTcount: A:0.38, C:0.08, G:0.26, T:0.28
Consensus pattern (27 bp):
AATCGAGGGTAAAACGGTAATTCTGTA
Found at i:47551496 original size:81 final size:81
Alignment explanation
Indices: 47551386--47551583 Score: 324
Period size: 81 Copynumber: 2.4 Consensus size: 81
47551376 GTAATTTCAC
* * * * *
47551386 AATCGAGGGTAAAACGGTAATTTTGTAAATTGAGGGTAAAATGGTAATTTTGTAAATCGAGGGTA
1 AATCGAGGGTAAAATGGTAATTCTATAAATCGAGGGTAAAACGGTAATTTTGTAAATCGAGGGTA
*
47551451 AAACGGTAATTCTGTA
66 AAACGGTAATTCTATA
*
47551467 AATCGAGGGTAAAATGGTAATTCTATAAATCGAGGGTAAAACGGTAATTTTGTAAATCGAGGGTG
1 AATCGAGGGTAAAATGGTAATTCTATAAATCGAGGGTAAAACGGTAATTTTGTAAATCGAGGGTA
47551532 AAACGGTAATTCTATA
66 AAACGGTAATTCTATA
*
47551548 AATCGAGGGTAAAATGGTAATTCTACAAATCGAGGG
1 AATCGAGGGTAAAATGGTAATTCTATAAATCGAGGG
47551584 CATTTCAGTA
Statistics
Matches: 109, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
81 109 1.00
ACGTcount: A:0.38, C:0.08, G:0.26, T:0.28
Consensus pattern (81 bp):
AATCGAGGGTAAAATGGTAATTCTATAAATCGAGGGTAAAACGGTAATTTTGTAAATCGAGGGTA
AAACGGTAATTCTATA
Found at i:47553901 original size:31 final size:31
Alignment explanation
Indices: 47553863--47553972 Score: 220
Period size: 31 Copynumber: 3.5 Consensus size: 31
47553853 TTTAACGGTT
47553863 ACTGGGCCGAAGCCTTTTCATAAATCATATC
1 ACTGGGCCGAAGCCTTTTCATAAATCATATC
47553894 ACTGGGCCGAAGCCTTTTCATAAATCATATC
1 ACTGGGCCGAAGCCTTTTCATAAATCATATC
47553925 ACTGGGCCGAAGCCTTTTCATAAATCATATC
1 ACTGGGCCGAAGCCTTTTCATAAATCATATC
47553956 ACTGGGCCGAAGCCTTT
1 ACTGGGCCGAAGCCTTT
47553973 ACTGTAAACG
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 79 1.00
ACGTcount: A:0.27, C:0.26, G:0.18, T:0.28
Consensus pattern (31 bp):
ACTGGGCCGAAGCCTTTTCATAAATCATATC
Found at i:47554043 original size:42 final size:42
Alignment explanation
Indices: 47553996--47554087 Score: 148
Period size: 42 Copynumber: 2.2 Consensus size: 42
47553986 TGGCCCTTAG
* ** *
47553996 GCCCATTTCAATATCACATGTAATGTCAATGGATGTATGCAA
1 GCCCATTTCAATATCACATGAAATACCAATGAATGTATGCAA
47554038 GCCCATTTCAATATCACATGAAATACCAATGAATGTATGCAA
1 GCCCATTTCAATATCACATGAAATACCAATGAATGTATGCAA
47554080 GCCCATTT
1 GCCCATTT
47554088 GGGGAGACTA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.35, C:0.22, G:0.14, T:0.29
Consensus pattern (42 bp):
GCCCATTTCAATATCACATGAAATACCAATGAATGTATGCAA
Found at i:47554262 original size:25 final size:25
Alignment explanation
Indices: 47554234--47554303 Score: 104
Period size: 25 Copynumber: 2.8 Consensus size: 25
47554224 CTCTTTTAAT
*
47554234 AACTGGGGCAAAGCCCTTTTTGATA
1 AACTGGGGCAAAGCCCTTTTCGATA
*
47554259 AACTGGGGCAAAGCCCTTTTCGGTA
1 AACTGGGGCAAAGCCCTTTTCGATA
* *
47554284 AACTGGGGTAGAGCCCTTTT
1 AACTGGGGCAAAGCCCTTTT
47554304 AGCACTTCCT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 41 1.00
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.27
Consensus pattern (25 bp):
AACTGGGGCAAAGCCCTTTTCGATA
Found at i:47555175 original size:27 final size:27
Alignment explanation
Indices: 47555113--47555190 Score: 88
Period size: 27 Copynumber: 2.9 Consensus size: 27
47555103 GGGCATATTC
47555113 GTCATTTTACCATACAGGGGTATTACG
1 GTCATTTTACCATACAGGGGTATTACG
* *
47555140 GTCACTTTACCCTACAGGGGCT-TTACG
1 GTCATTTTACCATACAGGGG-TATTACG
* *
47555167 GTCTTTTTACC-TAATAGGGGTATT
1 GTCATTTTACCAT-ACAGGGGTATT
47555191 TTAGTCATTT
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
26 2 0.05
27 40 0.93
28 1 0.02
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.36
Consensus pattern (27 bp):
GTCATTTTACCATACAGGGGTATTACG
Found at i:47555261 original size:27 final size:27
Alignment explanation
Indices: 47555231--47555338 Score: 103
Period size: 27 Copynumber: 3.9 Consensus size: 27
47555221 GTAAATCTAC
47555231 AAACCAAGGGTATTTCAGTAATTTTGT
1 AAACCAAGGGTATTTCAGTAATTTTGT
*
47555258 AAACCAATGGTATTTCTA-TAATTTT-T
1 AAACCAAGGGTATTTC-AGTAATTTTGT
* *
47555284 AAAAAGTCAAGGGTATTTCTGTAATTTTGT
1 --AAA-CCAAGGGTATTTCAGTAATTTTGT
* * **
47555314 AAATCAGGGGTATTTTGGTAATTTT
1 AAACCAAGGGTATTTCAGTAATTTT
47555339 ACAAATTGAG
Statistics
Matches: 68, Mismatches: 7, Indels: 12
0.78 0.08 0.14
Matches are distributed among these distances:
26 1 0.01
27 41 0.60
28 7 0.10
29 18 0.26
30 1 0.01
ACGTcount: A:0.32, C:0.08, G:0.18, T:0.42
Consensus pattern (27 bp):
AAACCAAGGGTATTTCAGTAATTTTGT
Found at i:47555380 original size:54 final size:54
Alignment explanation
Indices: 47555211--47555504 Score: 261
Period size: 54 Copynumber: 5.4 Consensus size: 54
47555201 CATCCTACAA
* * * * * * ** *
47555211 GGGTGTTTTGGTAAATCTACAAACCAAGGGTATTTCAGTAATTTTGTAAACCAA
1 GGGTATTTTGGTAATTTTACAAACTAGGGGTATTTCGGTAATTTTACAAACCAG
* * * * * * ** *
47555265 TGGTATTTCT-ATAATTTTTAAAAAGTCAAGGGTATTTCTGTAATTTTGTAAATCAG
1 GGGTATTT-TGGTAA-TTTTACAAACT-AGGGGTATTTCGGTAATTTTACAAACCAG
* *
47555321 GGGTATTTTGGTAATTTTACAAA-TTGAGGGTATTTCGGTAATTTCACAAACCAG
1 GGGTATTTTGGTAATTTTACAAACTAG-GGGTATTTCGGTAATTTTACAAACCAG
* * *
47555375 TGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTACAAACTAG
1 GGGTATTTTGGTAATTTTACAAACTAGGGGTATTTCGGTAATTTTACAAACCAG
* * **
47555429 GGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGGTAATTCTATCCTA-CAG
1 GGGTATTTTGGTAATTTTACAAACTAGGGGTATTTCGGTAATTTTA-CAAACCAG
* *
47555483 GGGTATTTTAGTAATTTCACAA
1 GGGTATTTTGGTAATTTTACAA
47555505 TCGAGGGTAA
Statistics
Matches: 200, Mismatches: 33, Indels: 14
0.81 0.13 0.06
Matches are distributed among these distances:
54 144 0.72
55 20 0.10
56 36 0.18
ACGTcount: A:0.30, C:0.10, G:0.20, T:0.40
Consensus pattern (54 bp):
GGGTATTTTGGTAATTTTACAAACTAGGGGTATTTCGGTAATTTTACAAACCAG
Found at i:47555511 original size:27 final size:27
Alignment explanation
Indices: 47555294--47555504 Score: 250
Period size: 27 Copynumber: 7.8 Consensus size: 27
47555284 AAAAAGTCAA
**
47555294 GGGTATTTCT-GTAATTTTGTAAA-TCAG
1 GGGTATTT-TGGTAATTTTACAAACT-AG
*
47555321 GGGTATTTTGGTAATTTTACAAA-TTG
1 GGGTATTTTGGTAATTTTACAAACTAG
* * *
47555347 AGGGTATTTCGGTAATTTCACAAACCAG
1 -GGGTATTTTGGTAATTTTACAAACTAG
*
47555375 TGGTATTTTGGTAATTTTACAAACTAG
1 GGGTATTTTGGTAATTTTACAAACTAG
47555402 GGGTATTTTGGTAATTTTACAAACTAG
1 GGGTATTTTGGTAATTTTACAAACTAG
47555429 GGGTATTTTGGTAATTTTACAAACTAG
1 GGGTATTTTGGTAATTTTACAAACTAG
* **
47555456 GGGTATTTTGGTAATTCTATCCTAC-AG
1 GGGTATTTTGGTAATTTTA-CAAACTAG
* *
47555483 GGGTATTTTAGTAATTTCACAA
1 GGGTATTTTGGTAATTTTACAA
47555505 TCGAGGGTAA
Statistics
Matches: 160, Mismatches: 20, Indels: 9
0.85 0.11 0.05
Matches are distributed among these distances:
26 3 0.02
27 153 0.96
28 4 0.03
ACGTcount: A:0.28, C:0.09, G:0.21, T:0.41
Consensus pattern (27 bp):
GGGTATTTTGGTAATTTTACAAACTAG
Found at i:47555537 original size:27 final size:27
Alignment explanation
Indices: 47555503--47555594 Score: 123
Period size: 27 Copynumber: 3.4 Consensus size: 27
47555493 GTAATTTCAC
47555503 AATCGAGGGTAAAACGATAATTTTGTA
1 AATCGAGGGTAAAACGATAATTTTGTA
* *
47555530 AA-CTGAGGGTAAAATGGTAATTTTGTA
1 AATC-GAGGGTAAAACGATAATTTTGTA
* * *
47555557 AATCGAAGGTAAAACGATAATTCTATA
1 AATCGAGGGTAAAACGATAATTTTGTA
47555584 AATCGAGGGTA
1 AATCGAGGGTA
47555595 CTTTGGTAAT
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
26 1 0.02
27 53 0.96
28 1 0.02
ACGTcount: A:0.41, C:0.08, G:0.23, T:0.28
Consensus pattern (27 bp):
AATCGAGGGTAAAACGATAATTTTGTA
Found at i:47557984 original size:42 final size:42
Alignment explanation
Indices: 47557933--47558037 Score: 147
Period size: 42 Copynumber: 2.5 Consensus size: 42
47557923 TAGTCCCGCT
* * *
47557933 ATGGTCTTACACGAAGTCTCATATTGATGCCATATCCTAGAA
1 ATGGTCTTACACGAAATCTCATATCGATGCCATATCCCAGAA
* * *
47557975 ATGTTCTTACACGAAATCTCATATCGATGTCATATCCCAGAT
1 ATGGTCTTACACGAAATCTCATATCGATGCCATATCCCAGAA
*
47558017 ATGGTCTTACACAAAATCTCA
1 ATGGTCTTACACGAAATCTCA
47558038 ATAACCCTAA
Statistics
Matches: 55, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 55 1.00
ACGTcount: A:0.32, C:0.23, G:0.13, T:0.31
Consensus pattern (42 bp):
ATGGTCTTACACGAAATCTCATATCGATGCCATATCCCAGAA
Found at i:47565023 original size:21 final size:20
Alignment explanation
Indices: 47564982--47565024 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
47564972 ATTTCCCATG
*
47564982 TTGGCCCATTTTCTCTATTT
1 TTGGCCCATTTTCACTATTT
* *
47565002 TTGGCCCGTTTTTCACTCTTT
1 TTGGCCC-ATTTTCACTATTT
47565023 TT
1 TT
47565025 ACTTTCCTGT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.07, C:0.26, G:0.12, T:0.56
Consensus pattern (20 bp):
TTGGCCCATTTTCACTATTT
Found at i:47566996 original size:7 final size:7
Alignment explanation
Indices: 47566980--47567010 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
47566970 ATGAATAAAG
47566980 ATAA-AA
1 ATAATAA
47566986 ATAATAA
1 ATAATAA
47566993 ATAATAA
1 ATAATAA
47567000 ATAATAA
1 ATAATAA
47567007 ATAA
1 ATAA
47567011 AAAGTCTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 4 0.17
7 20 0.83
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (7 bp):
ATAATAA
Found at i:47579112 original size:17 final size:17
Alignment explanation
Indices: 47579090--47579131 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
47579080 ATCACCAGTT
*
47579090 TGAACTTAGACAATCAA
1 TGAACTAAGACAATCAA
*
47579107 TTAACTAAGACAATCAA
1 TGAACTAAGACAATCAA
47579124 TGAACTAA
1 TGAACTAA
47579132 CATTTGTTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.50, C:0.17, G:0.10, T:0.24
Consensus pattern (17 bp):
TGAACTAAGACAATCAA
Found at i:47582415 original size:168 final size:168
Alignment explanation
Indices: 47582137--47582474 Score: 676
Period size: 168 Copynumber: 2.0 Consensus size: 168
47582127 ATTTTGCTCG
47582137 ATTTTTTATGATTTCTATGTTTTTATGATCGTTGTTATGTGTTCTAGCTAGCCCATGCTTAAATT
1 ATTTTTTATGATTTCTATGTTTTTATGATCGTTGTTATGTGTTCTAGCTAGCCCATGCTTAAATT
47582202 TATGAAATTGTTGATGATTTGATGAGATTCCATTGATGAATTCATGATTTTTGTGATGTTAAATG
66 TATGAAATTGTTGATGATTTGATGAGATTCCATTGATGAATTCATGATTTTTGTGATGTTAAATG
47582267 GTGAAATATGAAAGCTTGGTGATAGATATTCATGTTTT
131 GTGAAATATGAAAGCTTGGTGATAGATATTCATGTTTT
47582305 ATTTTTTATGATTTCTATGTTTTTATGATCGTTGTTATGTGTTCTAGCTAGCCCATGCTTAAATT
1 ATTTTTTATGATTTCTATGTTTTTATGATCGTTGTTATGTGTTCTAGCTAGCCCATGCTTAAATT
47582370 TATGAAATTGTTGATGATTTGATGAGATTCCATTGATGAATTCATGATTTTTGTGATGTTAAATG
66 TATGAAATTGTTGATGATTTGATGAGATTCCATTGATGAATTCATGATTTTTGTGATGTTAAATG
47582435 GTGAAATATGAAAGCTTGGTGATAGATATTCATGTTTT
131 GTGAAATATGAAAGCTTGGTGATAGATATTCATGTTTT
47582473 AT
1 AT
47582475 AAAGTGCTTT
Statistics
Matches: 170, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
168 170 1.00
ACGTcount: A:0.26, C:0.08, G:0.20, T:0.46
Consensus pattern (168 bp):
ATTTTTTATGATTTCTATGTTTTTATGATCGTTGTTATGTGTTCTAGCTAGCCCATGCTTAAATT
TATGAAATTGTTGATGATTTGATGAGATTCCATTGATGAATTCATGATTTTTGTGATGTTAAATG
GTGAAATATGAAAGCTTGGTGATAGATATTCATGTTTT
Found at i:47583257 original size:47 final size:47
Alignment explanation
Indices: 47583119--47583250 Score: 167
Period size: 47 Copynumber: 2.8 Consensus size: 47
47583109 GTACGAATGA
* **
47583119 TACCTTGATTTGGCTACTGGCCATGGTATAGGTATTCAAAGAGGAGT
1 TACCTTGATTTGGCTACTGGCCATGGTATAGGTACTCAAAGATAAGT
* * ***
47583166 TACCTT-AGTTTGGCTACAGGCCATGGTATAGATACTCCGGGATAAGT
1 TACCTTGA-TTTGGCTACTGGCCATGGTATAGGTACTCAAAGATAAGT
*
47583213 TACCTTGATTTGGCTACTGGTCATGGTATAGGTACTCA
1 TACCTTGATTTGGCTACTGGCCATGGTATAGGTACTCA
47583251 TCGATAAAAG
Statistics
Matches: 71, Mismatches: 12, Indels: 4
0.82 0.14 0.05
Matches are distributed among these distances:
46 1 0.01
47 69 0.97
48 1 0.01
ACGTcount: A:0.24, C:0.17, G:0.26, T:0.33
Consensus pattern (47 bp):
TACCTTGATTTGGCTACTGGCCATGGTATAGGTACTCAAAGATAAGT
Found at i:47585189 original size:24 final size:26
Alignment explanation
Indices: 47585160--47585209 Score: 77
Period size: 24 Copynumber: 2.0 Consensus size: 26
47585150 AGTTCATGCA
47585160 ATATTAAAGC-ATTTAA-ATACAAAT
1 ATATTAAAGCTATTTAACATACAAAT
47585184 ATATTAAAGCTTATTTAACATACAAA
1 ATATTAAAGC-TATTTAACATACAAA
47585210 CTTACCTCGG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 10 0.43
26 6 0.26
27 7 0.30
ACGTcount: A:0.52, C:0.10, G:0.04, T:0.34
Consensus pattern (26 bp):
ATATTAAAGCTATTTAACATACAAAT
Found at i:47591434 original size:57 final size:56
Alignment explanation
Indices: 47591373--47591505 Score: 144
Period size: 57 Copynumber: 2.3 Consensus size: 56
47591363 ATCATTATTC
* * *
47591373 ACATTTTGACAATATAAATATCTGCAC-TAAGAGACATTATGGC-ATCACCTATAAATT
1 ACATTTAGACAACATAAATA--TGCACATAAGAGACATTATGACAAT-ACCTATAAATT
* * *
47591430 ACATTTAGGCAACATAAATATGCACATTAAGAGACATTTTGACAATAGCTATAAATT
1 ACATTTAGACAACATAAATATGCACA-TAAGAGACATTATGACAATACCTATAAATT
* *
47591487 ACATTAAGACAGCATAAAT
1 ACATTTAGACAACATAAAT
47591506 TTAGAAATAA
Statistics
Matches: 64, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
55 5 0.08
57 57 0.89
58 2 0.03
ACGTcount: A:0.44, C:0.16, G:0.11, T:0.29
Consensus pattern (56 bp):
ACATTTAGACAACATAAATATGCACATAAGAGACATTATGACAATACCTATAAATT
Found at i:47593107 original size:68 final size:63
Alignment explanation
Indices: 47593035--47593182 Score: 158
Period size: 63 Copynumber: 2.3 Consensus size: 63
47593025 GAGTGCGCAT
*
47593035 CATGTGTACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTC-GCATGGGTGATACT-ATGTG
1 CATGTGTACAAGAGAGCTAC--GACA-TA-AAT-TAGCTAGGTCAG-ATGGGTGATACTGA-GTG
47593098 TACAC
59 TACAC
* * * *
47593103 CATGTAG-ACAAGAGAGCTACGAGATAAATTGGCTAGGTCAGATGGGTGGTACTGAGTGTTCAC
1 CATGT-GTACAAGAGAGCTACGACATAAATTAGCTAGGTCAGATGGGTGATACTGAGTGTACAC
47593166 CATGTGTACAAGAGAGC
1 CATGTGTACAAGAGAGC
47593183 CGATATGAGT
Statistics
Matches: 71, Mismatches: 5, Indels: 13
0.80 0.06 0.15
Matches are distributed among these distances:
62 1 0.01
63 42 0.59
64 4 0.06
65 2 0.03
66 3 0.04
68 18 0.25
69 1 0.01
ACGTcount: A:0.31, C:0.16, G:0.29, T:0.24
Consensus pattern (63 bp):
CATGTGTACAAGAGAGCTACGACATAAATTAGCTAGGTCAGATGGGTGATACTGAGTGTACAC
Found at i:47595937 original size:45 final size:45
Alignment explanation
Indices: 47595873--47595963 Score: 182
Period size: 45 Copynumber: 2.0 Consensus size: 45
47595863 AAAAGTCTAG
47595873 ACATTACTAGCCAAATAGAAAATTGCAACAAGTAATAACTTGAAA
1 ACATTACTAGCCAAATAGAAAATTGCAACAAGTAATAACTTGAAA
47595918 ACATTACTAGCCAAATAGAAAATTGCAACAAGTAATAACTTGAAA
1 ACATTACTAGCCAAATAGAAAATTGCAACAAGTAATAACTTGAAA
47595963 A
1 A
47595964 TATTTTTGTT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.52, C:0.15, G:0.11, T:0.22
Consensus pattern (45 bp):
ACATTACTAGCCAAATAGAAAATTGCAACAAGTAATAACTTGAAA
Found at i:47595962 original size:24 final size:24
Alignment explanation
Indices: 47595890--47595964 Score: 61
Period size: 24 Copynumber: 3.2 Consensus size: 24
47595880 TAGCCAAATA
47595890 GAAAATTGCAACAAGTAATAACTT
1 GAAAATTGCAACAAGTAATAACTT
* ** *
47595914 GAAAA---CATTACTAGCCA-AA-TA
1 GAAAATTGCA--ACAAGTAATAACTT
47595935 GAAAATTGCAACAAGTAATAACTT
1 GAAAATTGCAACAAGTAATAACTT
47595959 GAAAAT
1 GAAAAT
47595965 ATTTTTGTTT
Statistics
Matches: 36, Mismatches: 8, Indels: 14
0.62 0.14 0.24
Matches are distributed among these distances:
21 8 0.22
22 7 0.19
23 7 0.19
24 14 0.39
ACGTcount: A:0.52, C:0.13, G:0.12, T:0.23
Consensus pattern (24 bp):
GAAAATTGCAACAAGTAATAACTT
Found at i:47604234 original size:117 final size:120
Alignment explanation
Indices: 47604099--47604331 Score: 364
Period size: 117 Copynumber: 2.0 Consensus size: 120
47604089 TTTAATTTTT
*
47604099 TTTATAATTTTATAAAATTTTAAATTAATAATAATAAATTTATACTTTCAACTCTTTAAAAATGA
1 TTTATAATTTTATAAAATTTTAAATTAATAATAATAAATTTATACTTTCAACTCTTTAAAAATAA
*
47604164 T-AAAAAATTAATTTAAT-TTTTAAAAACTATAAAGATATAAACTATTAAATTAG
66 TGAAAAAATTAATTTAATCTTTTAAAAACTATAAAAATATAAACTATTAAATTAG
* * *
47604217 TTTATAA-TTTATAAAATTTTAAATTAATAATGATAATTTTATACTTTGAACTCTTTAAAAATAA
1 TTTATAATTTTATAAAATTTTAAATTAATAATAATAAATTTATACTTTCAACTCTTTAAAAATAA
** * *
47604281 TGAAAATTTTAATTTAATCTTTTAAAAATTATAAAAATATAAATTATTAAA
66 TGAAAAAATTAATTTAATCTTTTAAAAACTATAAAAATATAAACTATTAAA
47604332 ATAATAAAAT
Statistics
Matches: 104, Mismatches: 9, Indels: 3
0.90 0.08 0.03
Matches are distributed among these distances:
117 54 0.52
118 21 0.20
119 29 0.28
ACGTcount: A:0.49, C:0.04, G:0.03, T:0.44
Consensus pattern (120 bp):
TTTATAATTTTATAAAATTTTAAATTAATAATAATAAATTTATACTTTCAACTCTTTAAAAATAA
TGAAAAAATTAATTTAATCTTTTAAAAACTATAAAAATATAAACTATTAAATTAG
Found at i:47604308 original size:31 final size:33
Alignment explanation
Indices: 47604233--47604318 Score: 88
Period size: 31 Copynumber: 2.6 Consensus size: 33
47604223 ATTTATAAAA
*
47604233 TTTTAAATTAATAATGATAATTTTATACTTTGAAC
1 TTTTAAA--AATAATGAAAATTTTATACTTTGAAC
47604268 TCTTTAAAAATAATGAAAATTTTA-A-TTT-AATC
1 T-TTTAAAAATAATGAAAATTTTATACTTTGAA-C
* *
47604300 TTTTAAAAATTATAAAAAT
1 TTTTAAAAATAATGAAAAT
47604319 ATAAATTATT
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
31 18 0.39
32 5 0.11
33 1 0.02
34 15 0.33
35 1 0.02
36 6 0.13
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (33 bp):
TTTTAAAAATAATGAAAATTTTATACTTTGAAC
Found at i:47604326 original size:15 final size:17
Alignment explanation
Indices: 47604305--47604345 Score: 59
Period size: 15 Copynumber: 2.5 Consensus size: 17
47604295 TAATCTTTTA
47604305 AAAATTATAAAAAT-AT
1 AAAATTATAAAAATAAT
*
47604321 -AAATTATTAAAATAAT
1 AAAATTATAAAAATAAT
47604337 AAAATTATA
1 AAAATTATA
47604346 TTTTTACAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 12 0.57
16 2 0.10
17 7 0.33
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
AAAATTATAAAAATAAT
Found at i:47607509 original size:27 final size:27
Alignment explanation
Indices: 47607479--47607532 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
47607469 ATCCCTATGA
47607479 ATCAAACGAGCAAGAAAGTGACCACTC
1 ATCAAACGAGCAAGAAAGTGACCACTC
47607506 ATCAAACGAGCAAGAAAGTGACCACTC
1 ATCAAACGAGCAAGAAAGTGACCACTC
47607533 TTCCGCTCGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.44, C:0.26, G:0.19, T:0.11
Consensus pattern (27 bp):
ATCAAACGAGCAAGAAAGTGACCACTC
Found at i:47610973 original size:48 final size:46
Alignment explanation
Indices: 47610860--47610977 Score: 139
Period size: 46 Copynumber: 2.5 Consensus size: 46
47610850 TATGTGAGCC
*
47610860 AGTGTAAGACATGTCTGGGACATGCATCGACATTGAGAAGAGAGCT
1 AGTGTAAGACATGTCTGGGACATGCATCGACATTGAGAAGAAAGCT
* * * *
47610906 ATTGTAAGATATGTCTGGGACATGCATCGAC-TTCGGGATATACAAGCT
1 AGTGTAAGACATGTCTGGGACATGCATCGACATT-GAGA-AGA-AAGCT
* *
47610954 AGTGTAAGACCTGTATGGGACATG
1 AGTGTAAGACATGTCTGGGACATG
47610978 GCGTCAACTT
Statistics
Matches: 60, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
45 2 0.03
46 32 0.53
47 2 0.03
48 24 0.40
ACGTcount: A:0.31, C:0.15, G:0.29, T:0.25
Consensus pattern (46 bp):
AGTGTAAGACATGTCTGGGACATGCATCGACATTGAGAAGAAAGCT
Found at i:47612155 original size:28 final size:28
Alignment explanation
Indices: 47612115--47612178 Score: 101
Period size: 28 Copynumber: 2.3 Consensus size: 28
47612105 CACGGGCTAA
*
47612115 GACACGAGCGTGTCATGGCCGTGTGAGG
1 GACACGAGCGTGTCATGGCAGTGTGAGG
*
47612143 GACACGGGCGTGTCATGGCAGTGTGAGG
1 GACACGAGCGTGTCATGGCAGTGTGAGG
*
47612171 GATACGAG
1 GACACGAG
47612179 TATGTGCCAG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.20, C:0.19, G:0.44, T:0.17
Consensus pattern (28 bp):
GACACGAGCGTGTCATGGCAGTGTGAGG
Found at i:47613810 original size:25 final size:25
Alignment explanation
Indices: 47613782--47613833 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
47613772 TGTATTGCTT
47613782 GCAAAAAGGCAAAATCAATGATCCA
1 GCAAAAAGGCAAAATCAATGATCCA
*
47613807 GCAAAAAGGCGAAATCAATGATCCA
1 GCAAAAAGGCAAAATCAATGATCCA
47613832 GC
1 GC
47613834 CACATGGACT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.48, C:0.21, G:0.19, T:0.12
Consensus pattern (25 bp):
GCAAAAAGGCAAAATCAATGATCCA
Found at i:47615089 original size:13 final size:13
Alignment explanation
Indices: 47615057--47615091 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
47615047 TGTTAAATGT
47615057 GCTTATTAATTAA
1 GCTTATTAATTAA
47615070 G-TCTATTAATTAA
1 GCT-TATTAATTAA
47615083 GCTTATTAA
1 GCTTATTAA
47615092 GTTGTTTTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
12 1 0.05
13 18 0.90
14 1 0.05
ACGTcount: A:0.37, C:0.09, G:0.09, T:0.46
Consensus pattern (13 bp):
GCTTATTAATTAA
Found at i:47616566 original size:21 final size:21
Alignment explanation
Indices: 47616528--47616577 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 21
47616518 TTAAGCAAAG
47616528 ATATAAAATTATTTAAAA-TAA
1 ATAT-AAATTATTTAAAAGTAA
*
47616549 ATATAAATTCTTTAAAAAGTAA
1 ATATAAATTATTT-AAAAGTAA
*
47616571 AAATAAA
1 ATATAAA
47616578 AAAGTATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 8 0.32
21 8 0.32
22 9 0.36
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (21 bp):
ATATAAATTATTTAAAAGTAA
Found at i:47620246 original size:29 final size:29
Alignment explanation
Indices: 47620204--47620259 Score: 112
Period size: 29 Copynumber: 1.9 Consensus size: 29
47620194 AAATTTCGAG
47620204 TCAAATTGAGTCGAGTTAACGAATCCTAC
1 TCAAATTGAGTCGAGTTAACGAATCCTAC
47620233 TCAAATTGAGTCGAGTTAACGAATCCT
1 TCAAATTGAGTCGAGTTAACGAATCCT
47620260 GTTATTTATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.29
Consensus pattern (29 bp):
TCAAATTGAGTCGAGTTAACGAATCCTAC
Found at i:47621638 original size:31 final size:31
Alignment explanation
Indices: 47621601--47621661 Score: 122
Period size: 31 Copynumber: 2.0 Consensus size: 31
47621591 AGGGGGGAAA
47621601 AAAGAAAACAAAATTCTTCCATTATTTTCTG
1 AAAGAAAACAAAATTCTTCCATTATTTTCTG
47621632 AAAGAAAACAAAATTCTTCCATTATTTTCT
1 AAAGAAAACAAAATTCTTCCATTATTTTCT
47621662 TTCAAATTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.05, T:0.36
Consensus pattern (31 bp):
AAAGAAAACAAAATTCTTCCATTATTTTCTG
Found at i:47622256 original size:11 final size:11
Alignment explanation
Indices: 47622242--47622271 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
47622232 TGTTATTTTT
*
47622242 ATGAGTTTTGG
1 ATGAGCTTTGG
47622253 ATGAGCTTTGG
1 ATGAGCTTTGG
47622264 ATGAGCTT
1 ATGAGCTT
47622272 GAATAATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.20, C:0.07, G:0.33, T:0.40
Consensus pattern (11 bp):
ATGAGCTTTGG
Found at i:47625370 original size:18 final size:17
Alignment explanation
Indices: 47625336--47625370 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
47625326 CGATCAATTG
*
47625336 GGGCATGTGGGCCACAC
1 GGGCATGTGGCCCACAC
47625353 GGGCATGTGAGCCCACAC
1 GGGCATGTG-GCCCACAC
47625371 AAGTGAACCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.20, C:0.31, G:0.37, T:0.11
Consensus pattern (17 bp):
GGGCATGTGGCCCACAC
Found at i:47625503 original size:55 final size:55
Alignment explanation
Indices: 47625388--47625504 Score: 137
Period size: 55 Copynumber: 2.1 Consensus size: 55
47625378 CCACACGGGT
** ** *
47625388 GTGTGGGATTCTGGGCCAGGCTGTGTGATTCACACAACCAAGGCCATTTTAGGGC
1 GTGTGGGATTCTAAGCCAGGCCATGTGATCCACACAACCAAGGCCATTTTAGGGC
* * * *
47625443 ATGTGGGATTCTAAGCCAGGCCATGTGATCCATACAGCCAAGGCTATTTT-GGGCC
1 GTGTGGGATTCTAAGCCAGGCCATGTGATCCACACAACCAAGGCCATTTTAGGG-C
47625498 GTGTGGG
1 GTGTGGG
47625505 CCCACACGGG
Statistics
Matches: 51, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
54 3 0.06
55 48 0.94
ACGTcount: A:0.21, C:0.21, G:0.32, T:0.26
Consensus pattern (55 bp):
GTGTGGGATTCTAAGCCAGGCCATGTGATCCACACAACCAAGGCCATTTTAGGGC
Found at i:47626829 original size:45 final size:45
Alignment explanation
Indices: 47626760--47626849 Score: 162
Period size: 45 Copynumber: 2.0 Consensus size: 45
47626750 ATATACTTCA
*
47626760 CCACTTTGAGTTCGGGATCGGCTTTGGACACTAATTCAACGATCT
1 CCACCTTGAGTTCGGGATCGGCTTTGGACACTAATTCAACGATCT
*
47626805 CCACCTTGAGTTCGGGATCGGCTTTGGATACTAATTCAACGATCT
1 CCACCTTGAGTTCGGGATCGGCTTTGGACACTAATTCAACGATCT
47626850 GACTTTAACA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.22, C:0.24, G:0.22, T:0.31
Consensus pattern (45 bp):
CCACCTTGAGTTCGGGATCGGCTTTGGACACTAATTCAACGATCT
Found at i:47628258 original size:21 final size:19
Alignment explanation
Indices: 47628227--47628274 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 19
47628217 TTTCGTTCTC
47628227 CTTTCTTTTTC-TTTCTATT
1 CTTTCTTTTTCGTTTCT-TT
47628246 CTTTCTCTGTTTCGTTTCTTT
1 CTTTCT-T-TTTCGTTTCTTT
*
47628267 GTTTCTTT
1 CTTTCTTT
47628275 CCCTTTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
19 7 0.28
20 2 0.08
21 11 0.44
22 5 0.20
ACGTcount: A:0.02, C:0.21, G:0.06, T:0.71
Consensus pattern (19 bp):
CTTTCTTTTTCGTTTCTTT
Found at i:47628322 original size:5 final size:5
Alignment explanation
Indices: 47628312--47628380 Score: 97
Period size: 5 Copynumber: 14.2 Consensus size: 5
47628302 ATTCTTTAAT
* * *
47628312 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TACAA TACAA TACAA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
47628362 TATAA TATAA T-T-A TATAA T
1 TATAA TATAA TATAA TATAA T
47628381 TATATTTTAT
Statistics
Matches: 60, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
3 2 0.03
4 2 0.03
5 56 0.93
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (5 bp):
TATAA
Found at i:47635230 original size:16 final size:16
Alignment explanation
Indices: 47635196--47635232 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
47635186 AATTTTATTT
**
47635196 TAATAATAAATTTTTA
1 TAATAATAAATTTAAA
47635212 TAATAATAAATTTAAA
1 TAATAATAAATTTAAA
47635228 TAATA
1 TAATA
47635233 TTCTTCACAT
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:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
TAATAATAAATTTAAA
Found at i:47636604 original size:29 final size:29
Alignment explanation
Indices: 47636562--47636620 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
47636552 TCCGACATTG
47636562 GTATGTCGGGAGGCGGTCAATAATCCGTC
1 GTATGTCGGGAGGCGGTCAATAATCCGTC
47636591 GTATGTCGGGAGGCGGTCAATAATCCGTC
1 GTATGTCGGGAGGCGGTCAATAATCCGTC
47636620 G
1 G
47636621 GGACGATAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.20, C:0.20, G:0.36, T:0.24
Consensus pattern (29 bp):
GTATGTCGGGAGGCGGTCAATAATCCGTC
Found at i:47642017 original size:25 final size:25
Alignment explanation
Indices: 47641989--47642038 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 25
47641979 ATGTACATTT
47641989 TAAA-TATTTTTAAAAATAATTAATA
1 TAAATTATTTTTAAAAATAA-TAATA
*
47642014 TAAATTATTTTTAAAATTAATAATA
1 TAAATTATTTTTAAAAATAATAATA
47642039 CATGATTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 9 0.39
26 14 0.61
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (25 bp):
TAAATTATTTTTAAAAATAATAATA
Found at i:47642050 original size:26 final size:26
Alignment explanation
Indices: 47641993--47642053 Score: 72
Period size: 26 Copynumber: 2.4 Consensus size: 26
47641983 ACATTTTAAA
*
47641993 TATTTTTAAAAATAATTAATATAAAT
1 TATTTTTAAAAATAATTAATACAAAT
* *
47642019 TATTTTTAAAATTAA-TAATACATGAT
1 TATTTTTAAAAATAATTAATACA-AAT
47642045 T-TTTTTAAA
1 TATTTTTAAA
47642054 GTTTAAATAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
25 14 0.45
26 17 0.55
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.49
Consensus pattern (26 bp):
TATTTTTAAAAATAATTAATACAAAT
Found at i:47648614 original size:23 final size:22
Alignment explanation
Indices: 47648562--47648614 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
47648552 TCCTCGTCTT
*
47648562 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
47648584 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
47648607 TTTCTTTT
1 TTTCTTTT
47648615 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:47650803 original size:24 final size:24
Alignment explanation
Indices: 47650776--47650827 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
47650766 TTAGTAAGTC
*
47650776 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
47650800 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
47650824 AAAT
1 AAAT
47650828 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:47652772 original size:24 final size:24
Alignment explanation
Indices: 47652745--47652796 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
47652735 TTAGTAAGTC
*
47652745 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
47652769 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
47652793 AAAT
1 AAAT
47652797 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:47653969 original size:37 final size:38
Alignment explanation
Indices: 47653913--47653991 Score: 142
Period size: 37 Copynumber: 2.1 Consensus size: 38
47653903 AATTGAAACT
47653913 TTTCAAAAATAATTACACTCTCTTCCTCCCCATAATTC
1 TTTCAAAAATAATTACACTCTCTTCCTCCCCATAATTC
*
47653951 TTTC-AAAATAATTTCACTCTCTTCCTCCCCATAATTC
1 TTTCAAAAATAATTACACTCTCTTCCTCCCCATAATTC
47653988 TTTC
1 TTTC
47653992 TTCTGATGAA
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
37 36 0.90
38 4 0.10
ACGTcount: A:0.28, C:0.32, G:0.00, T:0.41
Consensus pattern (38 bp):
TTTCAAAAATAATTACACTCTCTTCCTCCCCATAATTC
Found at i:47656590 original size:31 final size:31
Alignment explanation
Indices: 47656546--47656615 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 31
47656536 AACGGTCAGT
** *
47656546 GACCAAAAGAGAAAACTTCAAATATTTGGGC
1 GACCAAAAGAGAAAAAGTCAAATAGTTGGGC
* *
47656577 GACC-AAAGAAGAAAAAGTCAAGTAGTTGGGT
1 GACCAAAAG-AGAAAAAGTCAAATAGTTGGGC
47656608 GACCAAAA
1 GACCAAAA
47656616 AAAAAATTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
30 4 0.12
31 25 0.78
32 3 0.09
ACGTcount: A:0.47, C:0.14, G:0.23, T:0.16
Consensus pattern (31 bp):
GACCAAAAGAGAAAAAGTCAAATAGTTGGGC
Found at i:47657719 original size:41 final size:41
Alignment explanation
Indices: 47657608--47657951 Score: 521
Period size: 41 Copynumber: 8.4 Consensus size: 41
47657598 CGTTTTAACA
* * * *
47657608 AAAACGTCGCTAAAAA-CAGAGCAATAGCGGCGTTTTTTTGTT
1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCG--CTTTTGGT
* * * * *
47657650 AAAACACTGCTAAAAA-CAGAACAATAGCGGCGTTTTTGGT
1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGT
47657690 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGT
1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGT
*
47657731 AAAACGCCGCTAAAAACCAAAGCATTAGCGGCGCTTTTGGT
1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGT
*
47657772 AAAACGCCGCAAAAAACCAGAGCATTAGCGGCGCTTTTGGT
1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGT
47657813 AAAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGT
1 -AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGT
*
47657855 AAAACGCCGCAAAAAACCAGAGCATTAGCGGCGCTTTTGGT
1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGT
* *
47657896 AAAACGCTGCTAAAAACCAGAGCATTTGCGGCGCTTTTGGT
1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGT
47657937 AAAACGCCGCTAAAA
1 AAAACGCCGCTAAAA
47657952 GTCATATAAC
Statistics
Matches: 281, Mismatches: 19, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
40 21 0.07
41 192 0.68
42 68 0.24
ACGTcount: A:0.35, C:0.22, G:0.23, T:0.20
Consensus pattern (41 bp):
AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGT
Found at i:47657840 original size:124 final size:123
Alignment explanation
Indices: 47657608--47657951 Score: 530
Period size: 124 Copynumber: 2.8 Consensus size: 123
47657598 CGTTTTAACA
* * * * * *
47657608 AAAACGTCGCTAAAAA-CAGAGCAATAGCGGCGTTTTTTTGTTAAAACACTGCTAAAAA-CAGAA
1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCG--CTTTTGGTAAAACGCTGCTAAAAACCAGAG
* *
47657671 CAATAGCGGCGTTTTTGGTAAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGT
64 CATTAGCGGCGCTTTTGGTAAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGT
* * *
47657731 AAAACGCCGCTAAAAACCAAAGCATTAGCGGCGCTTTTGGTAAAACGCCGCAAAAAACCAGAGCA
1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGTAAAACGCTGCTAAAAACCAGAGCA
47657796 TTAGCGGCGCTTTTGGTAAAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGT
66 TTAGCGGCGCTTTTGGT-AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGT
*
47657855 AAAACGCCGCAAAAAACCAGAGCATTAGCGGCGCTTTTGGTAAAACGCTGCTAAAAACCAGAGCA
1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGTAAAACGCTGCTAAAAACCAGAGCA
*
47657920 TTTGCGGCGCTTTTGGTAAAACGCCGCTAAAA
66 TTAGCGGCGCTTTTGGTAAAACGCCGCTAAAA
47657952 GTCATATAAC
Statistics
Matches: 202, Mismatches: 16, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
122 19 0.09
123 51 0.25
124 132 0.65
ACGTcount: A:0.35, C:0.22, G:0.23, T:0.20
Consensus pattern (123 bp):
AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGTAAAACGCTGCTAAAAACCAGAGCA
TTAGCGGCGCTTTTGGTAAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGT
Found at i:47658275 original size:15 final size:15
Alignment explanation
Indices: 47658252--47658305 Score: 51
Period size: 15 Copynumber: 3.7 Consensus size: 15
47658242 TATTTTAAGT
*
47658252 TTTATGGATTATGGG
1 TTTAGGGATTATGGG
47658267 TTTAGGGATTAT-GG
1 TTTAGGGATTATGGG
*
47658281 TTTAAGGG-TTAGGGG
1 TTT-AGGGATTATGGG
*
47658296 TCTA-GGATTA
1 TTTAGGGATTA
47658306 AGAGTTTATA
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
13 2 0.06
14 12 0.36
15 19 0.58
ACGTcount: A:0.22, C:0.02, G:0.35, T:0.41
Consensus pattern (15 bp):
TTTAGGGATTATGGG
Found at i:47658278 original size:22 final size:21
Alignment explanation
Indices: 47658253--47658307 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
47658243 ATTTTAAGTT
*
47658253 TTATGGATTATGGGTTTAGGGA
1 TTATGGATTAAGGG-TTAGGGA
* *
47658275 TTATGGTTTAAGGGTTAGGGG
1 TTATGGATTAAGGGTTAGGGA
47658296 TCTA-GGATTAAG
1 T-TATGGATTAAG
47658308 AGTTTATATT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
21 14 0.50
22 14 0.50
ACGTcount: A:0.24, C:0.02, G:0.36, T:0.38
Consensus pattern (21 bp):
TTATGGATTAAGGGTTAGGGA
Found at i:47658458 original size:14 final size:14
Alignment explanation
Indices: 47658441--47658479 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
47658431 ATCATTATAG
*
47658441 TTTAGGGTTTATTA
1 TTTAGGGTTTATGA
*
47658455 TTTAGGGTATATGA
1 TTTAGGGTTTATGA
*
47658469 TTAAGGGTTTA
1 TTTAGGGTTTA
47658480 AGGTTTATGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.49
Consensus pattern (14 bp):
TTTAGGGTTTATGA
Found at i:47658607 original size:22 final size:22
Alignment explanation
Indices: 47658582--47658639 Score: 57
Period size: 22 Copynumber: 2.7 Consensus size: 22
47658572 AGGTTTAATG
*
47658582 GTTTATATTTTA-GGATTTTAGA
1 GTTTATATTTTAGGGA-TTAAGA
* * *
47658604 GTTTAGAGTTTAGGGATTAAGG
1 GTTTATATTTTAGGGATTAAGA
47658626 GTTTATA-TTTAGGG
1 GTTTATATTTTAGGG
47658640 TATATGATTA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
21 7 0.23
22 20 0.67
23 3 0.10
ACGTcount: A:0.26, C:0.00, G:0.28, T:0.47
Consensus pattern (22 bp):
GTTTATATTTTAGGGATTAAGA
Found at i:47658647 original size:178 final size:179
Alignment explanation
Indices: 47658444--47658808 Score: 723
Period size: 178 Copynumber: 2.0 Consensus size: 179
47658434 ATTATAGTTT
47658444 AGGGTTTATTATTTAGGGTATATGATTAAGGGTTTAAGGTTTATGAGTTTCTATTTTAAGGTTTA
1 AGGGTTTATTATTTAGGGTATATGATTAAGGGTTTAAGGTTTATGAGTTTCTATTTTAAGGTTTA
47658509 TGTATTATGGTTTAAGGGTTGGGGTTTAAAGTTTAAGGGTTAGGGGTTATGGGTTATGGGTTTAG
66 TGTATTATGGTTTAAGGGTTGGGGTTTAAAGTTTAAGGGTTAGGGGTTATGGGTTATGGGTTTAG
47658574 GTTTAATGGTTTATATTTTAGGATTTTAGAGTTTAGAGTTTAGGGATTA
131 GTTTAATGGTTTATATTTTAGGATTTTAGAGTTTAGAGTTTAGGGATTA
47658623 AGGGTTTA-TATTTAGGGTATATGATTAAGGGTTTAAGGTTTATGAGTTTCTATTTTAAGGTTTA
1 AGGGTTTATTATTTAGGGTATATGATTAAGGGTTTAAGGTTTATGAGTTTCTATTTTAAGGTTTA
47658687 TGTATTATGGTTTAAGGGTTGGGGTTTAAAGTTTAAGGGTTAGGGGTTATGGGTTATGGGTTTAG
66 TGTATTATGGTTTAAGGGTTGGGGTTTAAAGTTTAAGGGTTAGGGGTTATGGGTTATGGGTTTAG
47658752 GTTTAATGGTTTATATTTTAGGATTTTAGAGTTTAGAGTTTAGGGATTA
131 GTTTAATGGTTTATATTTTAGGATTTTAGAGTTTAGAGTTTAGGGATTA
47658801 AGGGTTTA
1 AGGGTTTA
47658809 GATTAATTAG
Statistics
Matches: 186, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
178 178 0.96
179 8 0.04
ACGTcount: A:0.24, C:0.01, G:0.30, T:0.45
Consensus pattern (179 bp):
AGGGTTTATTATTTAGGGTATATGATTAAGGGTTTAAGGTTTATGAGTTTCTATTTTAAGGTTTA
TGTATTATGGTTTAAGGGTTGGGGTTTAAAGTTTAAGGGTTAGGGGTTATGGGTTATGGGTTTAG
GTTTAATGGTTTATATTTTAGGATTTTAGAGTTTAGAGTTTAGGGATTA
Found at i:47659148 original size:19 final size:19
Alignment explanation
Indices: 47659104--47659148 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
47659094 AACAACATTG
* *
47659104 ATAACAAATAAAAATGACAT
1 ATAA-AAATAAAAATAAAAT
*
47659124 ACAAAAATAAAAATAAAAT
1 ATAAAAATAAAAATAAAAT
47659143 ATAAAA
1 ATAAAA
47659149 TAGGGATTAG
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 18 0.86
20 3 0.14
ACGTcount: A:0.73, C:0.07, G:0.02, T:0.18
Consensus pattern (19 bp):
ATAAAAATAAAAATAAAAT
Found at i:47664765 original size:43 final size:43
Alignment explanation
Indices: 47664652--47664813 Score: 184
Period size: 43 Copynumber: 3.8 Consensus size: 43
47664642 GGTTATATTT
* * * * * *
47664652 TTTAGCGGCGTTTATGTGAAAAGCGTCGCTAACGGTC-TGTTC
1 TTTAGCGGCGTTTGTGGGAAAAACGCCGCTAAAGGTCATGGTC
* * * *
47664694 TATAGCGGCGTTTGT-GAAAAAAGTGCCGCTAAAAGTCATGGTC
1 TTTAGCGGCGTTTGTGGGAAAAA-CGCCGCTAAAGGTCATGGTC
*
47664737 TTTAGCAGCGTTTGTGGGAAAAACGCCGCTAAAGGTCATGGTC
1 TTTAGCGGCGTTTGTGGGAAAAACGCCGCTAAAGGTCATGGTC
* *
47664780 TTTAGCGGCGTTTGCGAGAAAAACGCCGCTAAAG
1 TTTAGCGGCGTTTGTGGGAAAAACGCCGCTAAAG
47664814 ACAAGGACCT
Statistics
Matches: 99, Mismatches: 18, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
41 4 0.04
42 23 0.23
43 66 0.67
44 6 0.06
ACGTcount: A:0.26, C:0.19, G:0.29, T:0.27
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGGGAAAAACGCCGCTAAAGGTCATGGTC
Found at i:47664826 original size:43 final size:42
Alignment explanation
Indices: 47664652--47664834 Score: 181
Period size: 43 Copynumber: 4.3 Consensus size: 42
47664642 GGTTATATTT
* * * * * *
47664652 TTTAGCGGCGTTTATGTGAAAAGCGTCGCTAACGGTC-TGTTC
1 TTTAGCGGCGTTTGTGAGAAAAACGCCGCTAA-AGTCATGGTC
* *
47664694 TATAGCGGCGTTTGTGA-AAAAAGTGCCGCTAAAAGTCATGGTC
1 TTTAGCGGCGTTTGTGAGAAAAA-CGCCGCT-AAAGTCATGGTC
* *
47664737 TTTAGCAGCGTTTGTGGGAAAAACGCCGCTAAAGGTCATGGTC
1 TTTAGCGGCGTTTGTGAGAAAAACGCCGCTAAA-GTCATGGTC
* * * *
47664780 TTTAGCGGCGTTTGCGAGAAAAACGCCGCTAAAGACAAGGACC
1 TTTAGCGGCGTTTGTGAGAAAAACGCCGCTAAAGTCATGG-TC
47664823 TTTAGCGGCGTT
1 TTTAGCGGCGTT
47664835 GCATATAGCG
Statistics
Matches: 117, Mismatches: 18, Indels: 11
0.80 0.12 0.08
Matches are distributed among these distances:
41 4 0.03
42 30 0.26
43 78 0.67
44 5 0.04
ACGTcount: A:0.26, C:0.19, G:0.29, T:0.26
Consensus pattern (42 bp):
TTTAGCGGCGTTTGTGAGAAAAACGCCGCTAAAGTCATGGTC
Found at i:47664826 original size:86 final size:85
Alignment explanation
Indices: 47664652--47664834 Score: 208
Period size: 85 Copynumber: 2.1 Consensus size: 85
47664642 GGTTATATTT
* * * * * *
47664652 TTTAGCGGCGTTTATGTGAAAAGCGTCGCTAACGGTCTGTTCTATAGCGGCGTTTGTGAAAAAAG
1 TTTAGCGGCGTTTATGGGAAAAACGCCGCTAAAGGTCTGGTCTATAGCGGCGTTTGCGAAAAAAG
* * * *
47664717 TGCCGCTAAAAGTCATGGTC
66 CGCCGCTAAAAGACAAGGCC
* * *
47664737 TTTAGCAGCGTTTGTGGGAAAAACGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGCGAGAAAA
1 TTTAGCGGCGTTTATGGGAAAAACGCCGCTAAAGGTC-TGGTCTATAGCGGCGTTTGCGA-AAAA
47664802 A-CGCCGCT-AAAGACAAGGACC
64 AGCGCCGCTAAAAGACAAGG-CC
47664823 TTTAGCGGCGTT
1 TTTAGCGGCGTT
47664835 GCATATAGCG
Statistics
Matches: 81, Mismatches: 14, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
85 39 0.48
86 37 0.46
87 5 0.06
ACGTcount: A:0.26, C:0.19, G:0.29, T:0.26
Consensus pattern (85 bp):
TTTAGCGGCGTTTATGGGAAAAACGCCGCTAAAGGTCTGGTCTATAGCGGCGTTTGCGAAAAAAG
CGCCGCTAAAAGACAAGGCC
Found at i:47673024 original size:20 final size:20
Alignment explanation
Indices: 47672999--47673038 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
47672989 TGTCATTAAG
47672999 TTAACAAAAACTTCACAAAC
1 TTAACAAAAACTTCACAAAC
47673019 TTAACAAAAACTTCACAAAC
1 TTAACAAAAACTTCACAAAC
47673039 ACGCTGAGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.55, C:0.25, G:0.00, T:0.20
Consensus pattern (20 bp):
TTAACAAAAACTTCACAAAC
Found at i:47686528 original size:13 final size:11
Alignment explanation
Indices: 47686497--47686526 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
47686487 GACAGATTTC
47686497 TTAAAAATATT
1 TTAAAAATATT
47686508 TTAAAAATATT
1 TTAAAAATATT
47686519 TTATAAAA
1 TTA-AAAA
47686527 ATTGTTTTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.78
12 4 0.22
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (11 bp):
TTAAAAATATT
Found at i:47686989 original size:14 final size:14
Alignment explanation
Indices: 47686962--47687040 Score: 52
Period size: 14 Copynumber: 5.4 Consensus size: 14
47686952 TGAATATTTT
* *
47686962 TAATAATATGTAAA
1 TAATATTATTTAAA
47686976 TAATATTATTTAAA
1 TAATATTATTTAAA
* *
47686990 AAATTATTATTAAAA
1 TAA-TATTATTTAAA
*
47687005 TAAAATTGAACTATTAAA
1 TAATATT--A-T-TTAAA
*
47687023 TAAT-TTATTAAAA
1 TAATATTATTTAAA
47687036 TAATA
1 TAATA
47687041 AATTATATTA
Statistics
Matches: 50, Mismatches: 9, Indels: 12
0.70 0.13 0.17
Matches are distributed among these distances:
13 8 0.16
14 18 0.36
15 13 0.26
16 1 0.02
17 3 0.06
18 7 0.14
ACGTcount: A:0.56, C:0.01, G:0.03, T:0.41
Consensus pattern (14 bp):
TAATATTATTTAAA
Found at i:47687061 original size:16 final size:16
Alignment explanation
Indices: 47687016--47687064 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
47687006 AAAATTGAAC
47687016 TATTAAATAATTTATTA
1 TATT-AATAATTTATTA
**
47687033 -A--AATAATAAATTA
1 TATTAATAATTTATTA
47687046 TATTAATAATTTATTA
1 TATTAATAATTTATTA
47687062 TAT
1 TAT
47687065 GACTTAATAT
Statistics
Matches: 25, Mismatches: 4, Indels: 7
0.69 0.11 0.19
Matches are distributed among these distances:
13 10 0.40
14 1 0.04
16 14 0.56
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
TATTAATAATTTATTA
Found at i:47696692 original size:39 final size:39
Alignment explanation
Indices: 47696638--47696715 Score: 138
Period size: 39 Copynumber: 2.0 Consensus size: 39
47696628 TTTTTTGATT
*
47696638 TCTCTAAATTTTAGGGTCAAGTTGTAAATATAAAAAATA
1 TCTCTAAACTTTAGGGTCAAGTTGTAAATATAAAAAATA
*
47696677 TCTCTAAACTTTAGGGTCAAGTTGTAAATATGAAAAATA
1 TCTCTAAACTTTAGGGTCAAGTTGTAAATATAAAAAATA
47696716 ATGACCCATG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.42, C:0.09, G:0.14, T:0.35
Consensus pattern (39 bp):
TCTCTAAACTTTAGGGTCAAGTTGTAAATATAAAAAATA
Found at i:47696961 original size:17 final size:16
Alignment explanation
Indices: 47696908--47696965 Score: 57
Period size: 17 Copynumber: 3.6 Consensus size: 16
47696898 TAATCACTTT
47696908 AATATTAAATT-AATA
1 AATATTAAATTAAATA
* *
47696923 AA-ATGATATTAAGATA
1 AATATTAAATTAA-ATA
*
47696939 AGTATTAAATTAAATTA
1 AATATTAAATTAAA-TA
47696956 AATATTAAAT
1 AATATTAAAT
47696966 CTATTAAAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
14 6 0.18
15 3 0.09
16 5 0.15
17 19 0.58
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (16 bp):
AATATTAAATTAAATA
Found at i:47698229 original size:16 final size:17
Alignment explanation
Indices: 47698201--47698236 Score: 65
Period size: 16 Copynumber: 2.2 Consensus size: 17
47698191 AAATCACACC
47698201 ATTAATGTCACAAATGA
1 ATTAATGTCACAAATGA
47698218 ATTAAT-TCACAAATGA
1 ATTAATGTCACAAATGA
47698234 ATT
1 ATT
47698237 TAGAATTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.47, C:0.11, G:0.08, T:0.33
Consensus pattern (17 bp):
ATTAATGTCACAAATGA
Found at i:47699902 original size:26 final size:26
Alignment explanation
Indices: 47699873--47699926 Score: 92
Period size: 26 Copynumber: 2.1 Consensus size: 26
47699863 TCCTTATAGT
47699873 CTCTTTGTGAGCTTCCTGATTA-ATGG
1 CTCTTTGTGAGCTTCCTG-TTATATGG
47699899 CTCTTTGTGAGCTTCCTGTTATATGG
1 CTCTTTGTGAGCTTCCTGTTATATGG
47699925 CT
1 CT
47699927 TAAGAGAGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
25 3 0.11
26 24 0.89
ACGTcount: A:0.13, C:0.20, G:0.22, T:0.44
Consensus pattern (26 bp):
CTCTTTGTGAGCTTCCTGTTATATGG
Found at i:47706957 original size:56 final size:56
Alignment explanation
Indices: 47706871--47707046 Score: 343
Period size: 56 Copynumber: 3.1 Consensus size: 56
47706861 ACAAGGGATG
*
47706871 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
47706927 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
47706983 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
47707039 ATGGGCAA
1 ATGGGCAA
47707047 TAAACTAATA
Statistics
Matches: 119, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
56 119 1.00
ACGTcount: A:0.45, C:0.09, G:0.23, T:0.23
Consensus pattern (56 bp):
ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
Found at i:47719874 original size:48 final size:47
Alignment explanation
Indices: 47719818--47719915 Score: 178
Period size: 48 Copynumber: 2.1 Consensus size: 47
47719808 TTCGCCAATT
*
47719818 AAGCACAAATACAAGGAAAACACTTGAACGAATAAAAAAATACAATGA
1 AAGCACAAATACAAGGAAAACACTTAAACGAAT-AAAAAATACAATGA
47719866 AAGCACAAATACAAGGAAAACACTTAAACGAATAAAAAATACAATGA
1 AAGCACAAATACAAGGAAAACACTTAAACGAATAAAAAATACAATGA
47719913 AAG
1 AAG
47719916 TTCACAAGTG
Statistics
Matches: 49, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
47 17 0.35
48 32 0.65
ACGTcount: A:0.61, C:0.14, G:0.12, T:0.12
Consensus pattern (47 bp):
AAGCACAAATACAAGGAAAACACTTAAACGAATAAAAAATACAATGA
Found at i:47722525 original size:18 final size:18
Alignment explanation
Indices: 47722511--47722548 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
47722501 GATCACATGT
47722511 CCGTGTACTATCACACGG
1 CCGTGTACTATCACACGG
47722529 CCGTGTACTATCACACGG
1 CCGTGTACTATCACACGG
47722547 CC
1 CC
47722549 TACCATACAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.21, C:0.37, G:0.21, T:0.21
Consensus pattern (18 bp):
CCGTGTACTATCACACGG
Found at i:47727997 original size:60 final size:60
Alignment explanation
Indices: 47727929--47728048 Score: 240
Period size: 60 Copynumber: 2.0 Consensus size: 60
47727919 TTGTGATCCC
47727929 GTTGAACTTCTTAATATCCAAATTTTTTATTGTGTGATAAACCGTAATTTATACATATTT
1 GTTGAACTTCTTAATATCCAAATTTTTTATTGTGTGATAAACCGTAATTTATACATATTT
47727989 GTTGAACTTCTTAATATCCAAATTTTTTATTGTGTGATAAACCGTAATTTATACATATTT
1 GTTGAACTTCTTAATATCCAAATTTTTTATTGTGTGATAAACCGTAATTTATACATATTT
47728049 TTATCCCATG
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 60 1.00
ACGTcount: A:0.32, C:0.12, G:0.10, T:0.47
Consensus pattern (60 bp):
GTTGAACTTCTTAATATCCAAATTTTTTATTGTGTGATAAACCGTAATTTATACATATTT
Found at i:47728362 original size:13 final size:13
Alignment explanation
Indices: 47728344--47728382 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
47728334 TAGGTAATCA
*
47728344 CACATGGGCGTGT
1 CACATGGGCATGT
47728357 CACATGGGCATGT
1 CACATGGGCATGT
*
47728370 CACACGGGCATGT
1 CACATGGGCATGT
47728383 AACACAGGCC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.21, C:0.26, G:0.33, T:0.21
Consensus pattern (13 bp):
CACATGGGCATGT
Found at i:47734354 original size:14 final size:12
Alignment explanation
Indices: 47734325--47734359 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
47734315 TTTAAAATTT
47734325 TTTTATTTTTTA
1 TTTTATTTTTTA
47734337 TTTTATGTTTTTA
1 TTTTAT-TTTTTA
47734350 CTTTTATTTT
1 -TTTTATTTT
47734360 ATTTTAAGAC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 6 0.29
13 9 0.43
14 6 0.29
ACGTcount: A:0.14, C:0.03, G:0.03, T:0.80
Consensus pattern (12 bp):
TTTTATTTTTTA
Found at i:47734755 original size:20 final size:20
Alignment explanation
Indices: 47734732--47734771 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
47734722 AGCTCATTCA
47734732 TCATTCAGGAAGTTTCACTT
1 TCATTCAGGAAGTTTCACTT
47734752 TCATTCAGGAAGTTTCACTT
1 TCATTCAGGAAGTTTCACTT
47734772 CTCTCCCTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.20, G:0.15, T:0.40
Consensus pattern (20 bp):
TCATTCAGGAAGTTTCACTT
Found at i:47740369 original size:40 final size:38
Alignment explanation
Indices: 47740286--47740373 Score: 106
Period size: 40 Copynumber: 2.3 Consensus size: 38
47740276 GTCCAACCCA
*
47740286 ACACACCATGTAGGGATAAAATCGACCCACCTATCCCT
1 ACACACCATATAGGGATAAAATCGACCCACCTATCCCT
* * *
47740324 GCACACCATATATGGGGATAAAATCGACCCGTCC-ATCCTT
1 ACACACCATATA--GGGATAAAATCGACCC-ACCTATCCCT
47740364 ACACACCATA
1 ACACACCATA
47740374 AGGTACTGCA
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
38 10 0.24
40 30 0.71
41 2 0.05
ACGTcount: A:0.34, C:0.33, G:0.14, T:0.19
Consensus pattern (38 bp):
ACACACCATATAGGGATAAAATCGACCCACCTATCCCT
Found at i:47751552 original size:40 final size:40
Alignment explanation
Indices: 47751508--47751769 Score: 337
Period size: 39 Copynumber: 6.7 Consensus size: 40
47751498 GCTCCTCGTT
* *
47751508 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGT-ATCTCGCA
* * *
47751548 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
47751588 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
47751627 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
47751666 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
* *
47751705 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCA-CTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGA-ATTAGT-ATC-TCGCA
47751746 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
47751770 CATCATTCAA
Statistics
Matches: 205, Mismatches: 9, Indels: 17
0.89 0.04 0.07
Matches are distributed among these distances:
38 2 0.01
39 128 0.62
40 64 0.31
41 11 0.05
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
Found at i:47759781 original size:40 final size:40
Alignment explanation
Indices: 47759722--47759809 Score: 117
Period size: 40 Copynumber: 2.2 Consensus size: 40
47759712 ATCCAACCCA
*
47759722 ACACACCATGTA--GGGATAAAATCGACCCACCCATCCCT
1 ACACACCATATATGGGGATAAAATCGACCCACCCATCCCT
* ** *
47759760 GCACACCATATATGGGGATAAAATCGACCCGTCCATTCCT
1 ACACACCATATATGGGGATAAAATCGACCCACCCATCCCT
47759800 ACACACCATA
1 ACACACCATA
47759810 AGGTACTGCA
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
38 10 0.24
40 32 0.76
ACGTcount: A:0.34, C:0.34, G:0.14, T:0.18
Consensus pattern (40 bp):
ACACACCATATATGGGGATAAAATCGACCCACCCATCCCT
Found at i:47761648 original size:8 final size:8
Alignment explanation
Indices: 47761637--47761669 Score: 57
Period size: 8 Copynumber: 4.1 Consensus size: 8
47761627 AATTTAGCCC
47761637 TCACATTT
1 TCACATTT
47761645 TCACATTT
1 TCACATTT
47761653 TCACATTT
1 TCACATTT
*
47761661 TAACATTT
1 TCACATTT
47761669 T
1 T
47761670 AGTCCATATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.27, C:0.21, G:0.00, T:0.52
Consensus pattern (8 bp):
TCACATTT
Found at i:47762732 original size:49 final size:48
Alignment explanation
Indices: 47762536--47762755 Score: 173
Period size: 49 Copynumber: 4.6 Consensus size: 48
47762526 CATCGAGGCT
** * **
47762536 GATGCCATGTCCCAGACAGGTCTTACACCGGCTCTCACTTATCTTTGTT
1 GATGCCATGTCCCAGACAGGTCTTACACTAGCTCTCAC-TATCTGTGCC
* * * * **
47762585 GATGCCATGTCCCAGACAGGTCTTACGCTA--ACACAC-CTC-AAGCC
1 GATGCCATGTCCCAGACAGGTCTTACACTAGCTCTCACTATCTGTGCC
* * * * *
47762629 AATGCCATGTCCTAAACAGGTCTTACACTAGCT-TGCA-TATCTTGAGGCT
1 GATGCCATGTCCCAGACAGGTCTTACACTAGCTCT-CACTATC-TG-TGCC
47762678 GATGCCATGTCCCAGACAGGTCTTACACTAGCTCTCACTTATCTGTGCC
1 GATGCCATGTCCCAGACAGGTCTTACACTAGCTCTCAC-TATCTGTGCC
* * * *
47762727 CATGCCCTATCCCAGACAGATCTTACACT
1 GATGCCATGTCCCAGACAGGTCTTACACT
47762756 GACACACATT
Statistics
Matches: 132, Mismatches: 29, Indels: 20
0.73 0.16 0.11
Matches are distributed among these distances:
44 27 0.20
45 2 0.02
46 4 0.03
47 4 0.03
49 88 0.67
50 3 0.02
51 4 0.03
ACGTcount: A:0.24, C:0.32, G:0.17, T:0.27
Consensus pattern (48 bp):
GATGCCATGTCCCAGACAGGTCTTACACTAGCTCTCACTATCTGTGCC
Found at i:47773491 original size:129 final size:129
Alignment explanation
Indices: 47773127--47773577 Score: 622
Period size: 129 Copynumber: 3.5 Consensus size: 129
47773117 AACGAAAAAC
* ** * * * * * * *
47773127 CGAAACCCAACACGGTAGGACACGATTCCTCGAATTTCCAAACATTGAACATTGCCTCGCTTTAG
1 CGAAACCCAGCACAATAGGGCACTATTCCCCGAATTTCCAAACATCGAATATTGCCTTGTTTTAG
* * * *
47773192 CATTT--AGAAAACACGAGCAAAATTCCAAAGGAATATTTGATTATTTTGAACAAACGGAGAAAT
66 CATTTGGAAAAAACACGAGTAAAATTCTAAAGGAATATTCGATTATTTTGAACAAACGG-GAAAT
** * *
47773255 CGAAACCCAGCACAATAGGGCACTATTCCCTAAATTTCTAAACATCGAATATTGCCTTGTTTTAA
1 CGAAACCCAGCACAATAGGGCACTATTCCCCGAATTTCCAAACATCGAATATTGCCTTGTTTTAG
* *
47773320 CATTTGG-AAAAACACGAGTAAAATTCTAAAGGAGTATTCGATTATTTTAAACAAACGGGAAAT
66 CATTTGGAAAAAACACGAGTAAAATTCTAAAGGAATATTCGATTATTTTGAACAAACGGGAAAT
* *
47773383 CGAAACCCAGCACGATAGGGCACTATTCCCCGAATTTCCAAACATCGAATATTGCATTGTTTTAG
1 CGAAACCCAGCACAATAGGGCACTATTCCCCGAATTTCCAAACATCGAATATTGCCTTGTTTTAG
*
47773448 CGTTTGGAAAAAACACGAGTAAAATTCTAAAGGAATATTCGATTATTTTGAACAAACGGGAAAT
66 CATTTGGAAAAAACACGAGTAAAATTCTAAAGGAATATTCGATTATTTTGAACAAACGGGAAAT
* *
47773512 CGAAACCCAGCACAATAGGGCCCTATTCCCCGCATTTCCAAACATC-AGATATTGCCTTTGTTTT
1 CGAAACCCAGCACAATAGGGCACTATTCCCCGAATTTCCAAACATCGA-ATATTGCC-TTGTTTT
47773576 AG
64 AG
47773578 TGAATCTTCA
Statistics
Matches: 285, Mismatches: 33, Indels: 8
0.87 0.10 0.02
Matches are distributed among these distances:
128 127 0.45
129 149 0.52
130 9 0.03
ACGTcount: A:0.37, C:0.21, G:0.16, T:0.26
Consensus pattern (129 bp):
CGAAACCCAGCACAATAGGGCACTATTCCCCGAATTTCCAAACATCGAATATTGCCTTGTTTTAG
CATTTGGAAAAAACACGAGTAAAATTCTAAAGGAATATTCGATTATTTTGAACAAACGGGAAAT
Found at i:47775913 original size:1 final size:1
Alignment explanation
Indices: 47775907--47775942 Score: 54
Period size: 1 Copynumber: 36.0 Consensus size: 1
47775897 TATAATTTGG
**
47775907 TTTTTTTTTTTTTTTTTTTTTTTTTGGTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
47775943 GGTTGTTGGG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:0.00, C:0.00, G:0.06, T:0.94
Consensus pattern (1 bp):
T
Found at i:47775943 original size:11 final size:11
Alignment explanation
Indices: 47775912--47775946 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
47775902 TTTGGTTTTT
**
47775912 TTTTTTTTTTT
1 TTTTTTTTTGG
47775923 TTTTTTTTTGG
1 TTTTTTTTTGG
47775934 TTTTTTTTTGG
1 TTTTTTTTTGG
47775945 TT
1 TT
47775947 GTTGGGCCCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (11 bp):
TTTTTTTTTGG
Found at i:47776512 original size:176 final size:176
Alignment explanation
Indices: 47776244--47776979 Score: 916
Period size: 176 Copynumber: 4.2 Consensus size: 176
47776234 TGTGATTTTT
* * * * *
47776244 AGCCTGTTACCCTACTGCTTAGGGGGTCAAGGCTCACCGTCTTTGATCTATTCCACTGCAACTTC
1 AGCCTGTTACCCTACTACTTAGGGGGTTAAGGCTCGCCGTCTTTGATCTGTTCCACTGCAGCTTC
* * *
47776309 TA-GGAGGCAAGATCTGCAATCTTCAGCCCGTTACCCTACTACTTAGGGGGTTAAGGCTTGCTTC
66 -AGGGAGACAAGATCGGCAATCTTCAGCCTGTTACCCTACTACTTAGGGGGTTAAGGCTTGCTTC
*
47776373 TTCGATTTGCTCCACTACTGTTTAGGGAGGCAAGATCTACAATCTTC
130 TTCGATTTGCTCCACTACTGTTTAGGGAGACAAGATCTACAATCTTC
**
47776420 ATTCTGTTACCCTACTACTTAGGGGGTTAAGGCTCGCCGTCTTTGATCTGTTCCACTGCAGCTTC
1 AGCCTGTTACCCTACTACTTAGGGGGTTAAGGCTCGCCGTCTTTGATCTGTTCCACTGCAGCTTC
* **
47776485 AGGGAGACAAGATCGGCAATCTTCAGCCTATTACCCTACTACTTAGTAGGTTAAGGCTTGCTTCT
66 AGGGAGACAAGATCGGCAATCTTCAGCCTGTTACCCTACTACTTAGGGGGTTAAGGCTTGCTTCT
* * * *
47776550 TCGATTTTCTCCACTACTATTTAGGGGGACAAGATCTACAATCTTT
131 TCGATTTGCTCCACTACTGTTTAGGGAGACAAGATCTACAATCTTC
**
47776596 AGCCTGTTA-CC--CTACTTAGGGGGTTAAGGCTCGTTGTCTTTGATCTGTTCCACTGCAGCTTC
1 AGCCTGTTACCCTACTACTTAGGGGGTTAAGGCTCGCCGTCTTTGATCTGTTCCACTGCAGCTTC
* *
47776658 AGAGAGAAAAGATCTGG-AATCTTCAGCCTGTTACCCTACTACTTAGGGGGTTAAGGCTTGCTTC
66 AGGGAGACAAGATC-GGCAATCTTCAGCCTGTTACCCTACTACTTAGGGGGTTAAGGCTTGCTTC
* * *
47776722 TTTGATTTGCTCCACTACTGTTTAGGGAGACAAGATTTACAATCTTT
130 TTCGATTTGCTCCACTACTGTTTAGGGAGACAAGATCTACAATCTTC
* * * ** * **
47776769 AGCCTATTACACTACTACTTAGGGGGTTAAGGCTTGCTTTCTTCGATCTGTTCCACT--ATTATT
1 AGCCTGTTACCCTACTACTTAGGGGGTTAAGGCTCGCCGTCTTTGATCTGTTCCACTGCA-GCTT
* * ** * * * *
47776832 TAGGGAGACAATATCTACAATCTTCAGCCTGTTACCTTACTACTTAGGGGGTTAAAGCTCGCCGT
65 CAGGGAGACAAGATCGGCAATCTTCAGCCTGTTACCCTACTACTTAGGGGGTTAAGGCTTG-CTT
* * * *
47776897 CTTTGATCTG-T--TCTACTGTAACTTCAGGGAGACAAGATCTGCAATCTTC
129 CTTCGATTTGCTCCACTACTGT---TT-AGGGAGACAAGATCTACAATCTTC
*
47776946 AGCCTATTACCCTACTACTTAGGGGGTTAAGGCT
1 AGCCTGTTACCCTACTACTTAGGGGGTTAAGGCT
47776980 TGCTTCTTCA
Statistics
Matches: 492, Mismatches: 56, Indels: 23
0.86 0.10 0.04
Matches are distributed among these distances:
173 162 0.33
174 4 0.01
175 57 0.12
176 215 0.44
177 54 0.11
ACGTcount: A:0.22, C:0.24, G:0.21, T:0.33
Consensus pattern (176 bp):
AGCCTGTTACCCTACTACTTAGGGGGTTAAGGCTCGCCGTCTTTGATCTGTTCCACTGCAGCTTC
AGGGAGACAAGATCGGCAATCTTCAGCCTGTTACCCTACTACTTAGGGGGTTAAGGCTTGCTTCT
TCGATTTGCTCCACTACTGTTTAGGGAGACAAGATCTACAATCTTC
Found at i:47777181 original size:64 final size:63
Alignment explanation
Indices: 47777079--47777269 Score: 301
Period size: 64 Copynumber: 3.0 Consensus size: 63
47777069 CTGTATGGCT
* * *
47777079 ATGCTTATGTCAAATGACTAGGATGCTATGCTCAAAATGAATTAAATGCTCCTAACTAGATGTG
1 ATGCTTATGTCAAATAATTAGGATGCTATG-ACAAAATGAATTAAATGCTCCTAACTAGATGTG
47777143 ATGCTTATGTCAAATAATTAGGATGCTATGACAGAAATGAATTAAATGCTCCTAACTAGATGTG
1 ATGCTTATGTCAAATAATTAGGATGCTATGACA-AAATGAATTAAATGCTCCTAACTAGATGTG
* * *
47777207 ATGCTTATGTTAAATAATTAGGATGTTATGATCAAAATGAATCAAATGCTCCTAACTAGATGT
1 ATGCTTATGTCAAATAATTAGGATGCTATGA-CAAAATGAATTAAATGCTCCTAACTAGATGT
47777270 ATTATGAATG
Statistics
Matches: 119, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
63 2 0.02
64 115 0.97
65 2 0.02
ACGTcount: A:0.37, C:0.13, G:0.18, T:0.32
Consensus pattern (63 bp):
ATGCTTATGTCAAATAATTAGGATGCTATGACAAAATGAATTAAATGCTCCTAACTAGATGTG
Found at i:47779643 original size:90 final size:91
Alignment explanation
Indices: 47779486--47779670 Score: 338
Period size: 90 Copynumber: 2.1 Consensus size: 91
47779476 GAGCTAGGCT
* *
47779486 TTGA-TCTTTACCTCTTTTCTTCTCTTAGGTTCGCGATGTCCATTGCCCCTTTTTAAGGTAGGAT
1 TTGACTCTTTACCTCTTTTCTTCTCTTAGGTTCACGATGTCCATTGCCCCTTTGTAAGGTAGGAT
47779550 CTATTTCTCATCTTGTTCTACCAT-C
66 CTATTTCTCATCTTGTTCTACCATCC
47779575 TTGACTCTTTACCTCTTTTCTTCTCTTAGGTTCACGATGTCCATTGCCCCTTTGTAAGGTAGGAT
1 TTGACTCTTTACCTCTTTTCTTCTCTTAGGTTCACGATGTCCATTGCCCCTTTGTAAGGTAGGAT
47779640 CTATTTCTCATCTTGTTCTACCATCC
66 CTATTTCTCATCTTGTTCTACCATCC
47779666 TTGAC
1 TTGAC
47779671 AAATCAGGAG
Statistics
Matches: 92, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
89 4 0.04
90 82 0.89
91 6 0.07
ACGTcount: A:0.15, C:0.26, G:0.14, T:0.45
Consensus pattern (91 bp):
TTGACTCTTTACCTCTTTTCTTCTCTTAGGTTCACGATGTCCATTGCCCCTTTGTAAGGTAGGAT
CTATTTCTCATCTTGTTCTACCATCC
Found at i:47782984 original size:128 final size:128
Alignment explanation
Indices: 47782731--47783180 Score: 668
Period size: 128 Copynumber: 3.5 Consensus size: 128
47782721 AACAAAAAAC
* * * * * * * * *
47782731 CGAAACCCAGAACGGTAGGGCACGATTCCTCAAATTTCCAAACATTGAACATTGCCTCGCTTTAG
1 CGAAACCCAGCACGATAGGGCACTATTCCCCGAATTTCCAAACATCGAATATTGCCTTGTTTTAG
* * ** * * *
47782796 CATTTAG-AAAACACGAGCGAAATTCCAAAGGAATATTCGATTATTTTGGACAAACGGGGAAAT
66 CGTTTGGAAAAACACGAGTAAAATTCTAAAGGAATATTTGATTATTTTGAACAAAC-GGGAAAT
47782859 CGAAACCCAGCACGATAGGGCACTATTCCCCGAATTTCCAAACATCGAATATTGCCTTGTTTTAG
1 CGAAACCCAGCACGATAGGGCACTATTCCCCGAATTTCCAAACATCGAATATTGCCTTGTTTTAG
47782924 CGTTTGGAAAAACACGAGTAAAATTCTAAAGGAATATTTGATTATTTTGAACAAACGGGAAAT
66 CGTTTGGAAAAACACGAGTAAAATTCTAAAGGAATATTTGATTATTTTGAACAAACGGGAAAT
* *
47782987 CGAAACACAGCACGATAAGGCACTATTCCCCGAATTTCCAAACATCGAATATTGCCTTGTTTTAG
1 CGAAACCCAGCACGATAGGGCACTATTCCCCGAATTTCCAAACATCGAATATTGCCTTGTTTTAG
*
47783052 CGTTTGGAAAAACACGAGTAAAATTCTAAAGGAATATTTGATTATTTTAAACAAACGGGAAAT
66 CGTTTGGAAAAACACGAGTAAAATTCTAAAGGAATATTTGATTATTTTGAACAAACGGGAAAT
* * * *
47783115 CGAAACCCAGCACGATAGGGCCCTATTCCCTGCATTTCCAAACATCGGATATTGCCTTTGTTTTA
1 CGAAACCCAGCACGATAGGGCACTATTCCCCGAATTTCCAAACATCGAATATTGCC-TTGTTTTA
47783180 G
65 G
47783181 TGAATCTTCA
Statistics
Matches: 295, Mismatches: 25, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
128 243 0.82
129 52 0.18
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (128 bp):
CGAAACCCAGCACGATAGGGCACTATTCCCCGAATTTCCAAACATCGAATATTGCCTTGTTTTAG
CGTTTGGAAAAACACGAGTAAAATTCTAAAGGAATATTTGATTATTTTGAACAAACGGGAAAT
Found at i:47789221 original size:28 final size:28
Alignment explanation
Indices: 47789158--47789280 Score: 176
Period size: 28 Copynumber: 4.4 Consensus size: 28
47789148 ATATTAAGTC
*
47789158 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
47789185 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
47789213 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
47789241 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
47789270 CGCACACTTAG
1 CGCACACTTAG
47789281 CGCCAATCTC
Statistics
Matches: 87, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
27 22 0.25
28 49 0.56
29 16 0.18
ACGTcount: A:0.33, C:0.28, G:0.12, T:0.26
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:47798910 original size:24 final size:24
Alignment explanation
Indices: 47798883--47798932 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
47798873 TGGTTTAGGG
*
47798883 TTAGGGTTTAGTGGTTTAAG-GTTT
1 TTAGGGTTGAG-GGTTTAAGTGTTT
*
47798907 TTAGGGTTGAGGGTTTTAGTGTTT
1 TTAGGGTTGAGGGTTTAAGTGTTT
47798931 TT
1 TT
47798933 TAAGGGAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 7 0.30
24 16 0.70
ACGTcount: A:0.14, C:0.00, G:0.34, T:0.52
Consensus pattern (24 bp):
TTAGGGTTGAGGGTTTAAGTGTTT
Found at i:47799291 original size:126 final size:125
Alignment explanation
Indices: 47799051--47799358 Score: 485
Period size: 126 Copynumber: 2.4 Consensus size: 125
47799041 ATTAACTATT
* *
47799051 AATTACGAAAAAAAGCTCCCACGTGGACGCTCTTTTGCTACAGTAGTATCTG-AAAAATAATTTT
1 AATTACG-AAAAAAGCTCCTACATGGACGCTCTTTTGCTACAGTAGTATCTGAAAAAATAATTTT
* * * *
47799115 GAGAAGATGTTCTGGAACGAATAGTGTCAAAAACGCTTCAAGAAGAATGCACTGTCAGCAA
65 GAGAAGATGTTCTGGAACAAACAATGTCAAAAACGCTTCAAGAAGAATGCACTGTCAACAA
47799176 AATTACAGAAAAAAGCTCCTACATGGACGCTCTTTTGCTACAGTAGTATCTGAAAAAATAATTTT
1 AATTAC-GAAAAAAGCTCCTACATGGACGCTCTTTTGCTACAGTAGTATCTGAAAAAATAATTTT
* *
47799241 GAGAAGATGTTTCT-GAACAAACAATGTCAAAAATGCTTCAAGAAGGATGCACTGTCAACAA
65 GAGAAGATG-TTCTGGAACAAACAATGTCAAAAACGCTTCAAGAAGAATGCACTGTCAACAA
*
47799302 AATTACGGAAAAAAGCTCCTAAATGGACGCTCTTTTGCTACAGTAGTATCTGAAAAA
1 AATTAC-GAAAAAAGCTCCTACATGGACGCTCTTTTGCTACAGTAGTATCTGAAAAA
47799359 GCCTTAGACT
Statistics
Matches: 170, Mismatches: 10, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
125 48 0.28
126 118 0.69
127 4 0.02
ACGTcount: A:0.39, C:0.17, G:0.18, T:0.26
Consensus pattern (125 bp):
AATTACGAAAAAAGCTCCTACATGGACGCTCTTTTGCTACAGTAGTATCTGAAAAAATAATTTTG
AGAAGATGTTCTGGAACAAACAATGTCAAAAACGCTTCAAGAAGAATGCACTGTCAACAA
Found at i:47802442 original size:38 final size:39
Alignment explanation
Indices: 47802400--47802481 Score: 96
Period size: 39 Copynumber: 2.1 Consensus size: 39
47802390 CTAAAAATAT
* *
47802400 TAAAAA-TATTGCCGT-ATTCAAAATAACATTTATTTTAA
1 TAAAAATTATTGCC-TAATTCAAAAGAACATTTATTGTAA
* * *
47802438 TAAAAATTATTGGCTAATTTAAAAGAACATTTATTGTAT
1 TAAAAATTATTGCCTAATTCAAAAGAACATTTATTGTAA
47802477 TAAAA
1 TAAAA
47802482 TTAAAAAAGT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
38 7 0.19
39 30 0.81
ACGTcount: A:0.46, C:0.07, G:0.07, T:0.39
Consensus pattern (39 bp):
TAAAAATTATTGCCTAATTCAAAAGAACATTTATTGTAA
Found at i:47802558 original size:15 final size:15
Alignment explanation
Indices: 47802538--47802569 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
47802528 TATTAATTAA
*
47802538 AACTATATAAATAAT
1 AACTATAAAAATAAT
47802553 AACTATAAAAATAAT
1 AACTATAAAAATAAT
47802568 AA
1 AA
47802570 AATATTGGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.66, C:0.06, G:0.00, T:0.28
Consensus pattern (15 bp):
AACTATAAAAATAAT
Found at i:47802764 original size:132 final size:129
Alignment explanation
Indices: 47802435--47802811 Score: 575
Period size: 132 Copynumber: 2.9 Consensus size: 129
47802425 ACATTTATTT
* * *
47802435 TAATAAAAATTATTGGCTAATTTAAAAGAACATTTATTGTATTAAAATT--AAAAAAGTAAAGTA
1 TAATAAAAAATATTGGCTAATTTAAAAGAACATTTATTTTAATAAAATTAAAAAAAAGTAAAGTA
* *
47802498 CAATTAAAATATTAAAAAAAACTTTTATTTTATTAATTAAAACTATATAAATAATAACTATAAAA
66 CAATTAAAATATT-AAAAAAACTTTTATTTTATTAATTGAAACTATATAAA-AATAAATATAAAA
47802563 A
129 A
*
47802564 TAAT--AAAATATTGGCAAATTTAAAAGAACATTTATTTTAATAAAATTAAAAAAAAGTAAAGTA
1 TAATAAAAAATATTGGCTAATTTAAAAGAACATTTATTTTAATAAAATTAAAAAAAAGTAAAGTA
*
47802627 TAATTAAAATATTAAAAAAACTTTTATTTTATTAATTGAAACTATATAAAAATTAAATATAAAAA
66 CAATTAAAATATTAAAAAAACTTTTATTTTATTAATTGAAACTATATAAAAA-TAAATATAAAAA
* *
47802692 TAATAAAAAAAATATTGCCTAATTTAAAAGAATATTTATTTTAATAAAATTAAAAAAAAGTAAAG
1 TAAT--AAAAAATATTGGCTAATTTAAAAGAACATTTATTTTAATAAAATTAAAAAAAAGTAAAG
47802757 TACAATTAAAATATTAAAAACAACTTTTATTTTATT-ATATGAAACTATATAAAAA
64 TACAATTAAAATATTAAAAA-AACTTTTATTTTATTAAT-TGAAACTATATAAAAA
47802812 AATTCTACAA
Statistics
Matches: 228, Mismatches: 11, Indels: 14
0.90 0.04 0.06
Matches are distributed among these distances:
127 41 0.18
128 51 0.22
129 30 0.13
132 75 0.33
133 31 0.14
ACGTcount: A:0.56, C:0.04, G:0.05, T:0.35
Consensus pattern (129 bp):
TAATAAAAAATATTGGCTAATTTAAAAGAACATTTATTTTAATAAAATTAAAAAAAAGTAAAGTA
CAATTAAAATATTAAAAAAACTTTTATTTTATTAATTGAAACTATATAAAAATAAATATAAAAA
Found at i:47802940 original size:21 final size:22
Alignment explanation
Indices: 47802915--47802967 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
47802905 TGGTTCAGCT
*
47802915 TCCGGCGAGGG-TTGTGGTTGC
1 TCCGGCGAGGGATTGTGGTTCC
*
47802936 TCCGGTG-GGGATTGTGGTTCC
1 TCCGGCGAGGGATTGTGGTTCC
47802957 TCCGGCAGAGG
1 TCCGGC-GAGG
47802968 ATCTGGTTGT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
20 3 0.12
21 20 0.77
22 1 0.04
23 2 0.08
ACGTcount: A:0.08, C:0.21, G:0.45, T:0.26
Consensus pattern (22 bp):
TCCGGCGAGGGATTGTGGTTCC
Found at i:47805069 original size:11 final size:10
Alignment explanation
Indices: 47805038--47805088 Score: 57
Period size: 11 Copynumber: 4.7 Consensus size: 10
47805028 TTAACAAAAA
47805038 TTGAGAGAAAT
1 TTGAGAG-AAT
47805049 TTGAGAGAAT
1 TTGAGAGAAT
47805059 TTGGAGAGAAT
1 TT-GAGAGAAT
*
47805070 TTAGATAGAAT
1 TT-GAGAGAAT
47805081 TGTGAGAG
1 T-TGAGAG
47805089 GACTATTGTG
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
10 5 0.14
11 29 0.83
12 1 0.03
ACGTcount: A:0.39, C:0.00, G:0.31, T:0.29
Consensus pattern (10 bp):
TTGAGAGAAT
Found at i:47805087 original size:22 final size:21
Alignment explanation
Indices: 47805038--47805088 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 21
47805028 TTAACAAAAA
47805038 TTGAGAGAAATTTGAGAGAAT
1 TTGAGAGAAATTTGAGAGAAT
*
47805059 TTG-GAGAGAATTTAGATAGAAT
1 TTGAGAGA-AATTT-GAGAGAAT
47805081 TGTGAGAG
1 T-TGAGAG
47805089 GACTATTGTG
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 4 0.16
21 8 0.32
22 8 0.32
23 2 0.08
24 3 0.12
ACGTcount: A:0.39, C:0.00, G:0.31, T:0.29
Consensus pattern (21 bp):
TTGAGAGAAATTTGAGAGAAT
Found at i:47806265 original size:26 final size:26
Alignment explanation
Indices: 47806236--47806328 Score: 100
Period size: 26 Copynumber: 3.6 Consensus size: 26
47806226 CTTGAACCGA
47806236 TGTTTATTTAGCAGGCATTGAGCCAG
1 TGTTTATTTAGCAGGCATTGAGCCAG
* *
47806262 TG-TTATTTAGTAGGCCTTGAGCC-G
1 TGTTTATTTAGCAGGCATTGAGCCAG
* *
47806286 ATGTTTATTTAGCAGGCTTTGAGCAAG
1 -TGTTTATTTAGCAGGCATTGAGCCAG
* * *
47806313 TGATTAATTAGTAGGC
1 TGTTTATTTAGCAGGC
47806329 TTTAACCCGA
Statistics
Matches: 56, Mismatches: 8, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
24 1 0.02
25 21 0.38
26 33 0.59
27 1 0.02
ACGTcount: A:0.24, C:0.13, G:0.27, T:0.37
Consensus pattern (26 bp):
TGTTTATTTAGCAGGCATTGAGCCAG
Found at i:47806300 original size:51 final size:52
Alignment explanation
Indices: 47806219--47806353 Score: 175
Period size: 51 Copynumber: 2.6 Consensus size: 52
47806209 ATATTGGAAA
* * *
47806219 AGTAAGCCTTGAACCGATGTTTATTTAGCAGGCATTGAGCCAGTG-TTATTT
1 AGTAGGCCTTGAACCGATGTTTATTTAGCAGGCATTGAGCAAGTGATTAATT
* *
47806270 AGTAGGCCTTGAGCCGATGTTTATTTAGCAGGCTTTGAGCAAGTGATTAATT
1 AGTAGGCCTTGAACCGATGTTTATTTAGCAGGCATTGAGCAAGTGATTAATT
* * *
47806322 AGTAGG-CTTTAACCCGATATATATTTAGCAGG
1 AGTAGGCCTTGAA-CCGATGTTTATTTAGCAGG
47806354 TACTATGTAC
Statistics
Matches: 73, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
51 45 0.62
52 28 0.38
ACGTcount: A:0.27, C:0.15, G:0.24, T:0.34
Consensus pattern (52 bp):
AGTAGGCCTTGAACCGATGTTTATTTAGCAGGCATTGAGCAAGTGATTAATT
Found at i:47806347 original size:52 final size:51
Alignment explanation
Indices: 47806240--47806353 Score: 147
Period size: 52 Copynumber: 2.2 Consensus size: 51
47806230 AACCGATGTT
* * * * * *
47806240 TATTTAGCAGGCATTGAGCCAGTGTTATTTAGTAGGCCTTGAGCCGATGTT
1 TATTTAGCAGGCATTGAGCAAGTGTTAATTAGTAGGCCTTAACCCGATATA
* *
47806291 TATTTAGCAGGCTTTGAGCAAGTGATTAATTAGTAGGCTTTAACCCGATATA
1 TATTTAGCAGGCATTGAGCAAGTG-TTAATTAGTAGGCCTTAACCCGATATA
47806343 TATTTAGCAGG
1 TATTTAGCAGG
47806354 TACTATGTAC
Statistics
Matches: 54, Mismatches: 8, Indels: 1
0.86 0.13 0.02
Matches are distributed among these distances:
51 22 0.41
52 32 0.59
ACGTcount: A:0.26, C:0.14, G:0.25, T:0.35
Consensus pattern (51 bp):
TATTTAGCAGGCATTGAGCAAGTGTTAATTAGTAGGCCTTAACCCGATATA
Found at i:47807964 original size:19 final size:19
Alignment explanation
Indices: 47807940--47807979 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
47807930 TGTGCTATTG
*
47807940 TAAATTCATAGGCATAACT
1 TAAATTCATAGACATAACT
**
47807959 TAAATTTGTAGACATAACT
1 TAAATTCATAGACATAACT
47807978 TA
1 TA
47807980 CACAATTTCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.42, C:0.12, G:0.10, T:0.35
Consensus pattern (19 bp):
TAAATTCATAGACATAACT
Found at i:47809426 original size:9 final size:9
Alignment explanation
Indices: 47809412--47809437 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
47809402 AGAACTCATG
47809412 TTTTGCAAC
1 TTTTGCAAC
47809421 TTTTGCAAC
1 TTTTGCAAC
47809430 TTTTGCAA
1 TTTTGCAA
47809438 TTTAGTCCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.23, C:0.19, G:0.12, T:0.46
Consensus pattern (9 bp):
TTTTGCAAC
Found at i:47816866 original size:30 final size:30
Alignment explanation
Indices: 47816830--47816891 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
47816820 GAGAGACTAA
47816830 GTAAGCCTTCTTCCAGATGATGAATGAGTG
1 GTAAGCCTTCTTCCAGATGATGAATGAGTG
*
47816860 GTAAGCCTTCTTCTAGATGATGAATGAGTG
1 GTAAGCCTTCTTCCAGATGATGAATGAGTG
47816890 GT
1 GT
47816892 TTACAGAGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.26, C:0.15, G:0.27, T:0.32
Consensus pattern (30 bp):
GTAAGCCTTCTTCCAGATGATGAATGAGTG
Found at i:47824426 original size:40 final size:39
Alignment explanation
Indices: 47824382--47824486 Score: 122
Period size: 39 Copynumber: 2.6 Consensus size: 39
47824372 AGTGACCATA
*
47824382 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGACTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
* *
47824422 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACT-AT
1 TCCGGACTAAGCCCGAAGGCATTTGTGCGAGATACTAAT
* * *
47824460 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGACTAAG-CCCGAAGGCATTTG
47824487 AACGAGTAGC
Statistics
Matches: 58, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
38 2 0.03
39 32 0.55
40 24 0.41
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25
Consensus pattern (39 bp):
TCCGGACTAAGCCCGAAGGCATTTGTGCGAGATACTAAT
Done.