Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 135709677
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: 135709677
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 350 characters in sequence are not A, C, G, or T
File 415 of 438
Found at i:128802505 original size:15 final size:15
Alignment explanation
Indices: 128802487--128802515 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
128802477 CTAAAAACTC
128802487 TAAACTACTAAACCT
1 TAAACTACTAAACCT
128802502 TAAACTACTAAACC
1 TAAACTACTAAACC
128802516 CTAATTTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.28, G:0.00, T:0.24
Consensus pattern (15 bp):
TAAACTACTAAACCT
Found at i:128802791 original size:17 final size:17
Alignment explanation
Indices: 128802769--128802827 Score: 91
Period size: 17 Copynumber: 3.5 Consensus size: 17
128802759 CCTTAAAAAA
128802769 CACTAAAAATCCTAAAC
1 CACTAAAAATCCTAAAC
*
128802786 CACTAAAAATACTAAAC
1 CACTAAAAATCCTAAAC
*
128802803 CACCAAAAATCCTAAAC
1 CACTAAAAATCCTAAAC
*
128802820 CAGTAAAA
1 CACTAAAA
128802828 CCTTAACCCT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 37 1.00
ACGTcount: A:0.56, C:0.27, G:0.02, T:0.15
Consensus pattern (17 bp):
CACTAAAAATCCTAAAC
Found at i:128803359 original size:3 final size:3
Alignment explanation
Indices: 128803293--128803344 Score: 70
Period size: 3 Copynumber: 17.7 Consensus size: 3
128803283 TGGAAACCTA
* * *
128803293 TAT T-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TGT TGT TGT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
128803340 TAT TA
1 TAT TA
128803345 CCTTTTGATA
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
2 2 0.04
3 44 0.96
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:128804337 original size:49 final size:49
Alignment explanation
Indices: 128804284--128804382 Score: 189
Period size: 49 Copynumber: 2.0 Consensus size: 49
128804274 AGACAGAAAA
*
128804284 GACCAGTACATCATCACTAACAACAAGTTGTTACCATATTGGAAAAGCG
1 GACCAGTACATCATCACTAACAACAAATTGTTACCATATTGGAAAAGCG
128804333 GACCAGTACATCATCACTAACAACAAATTGTTACCATATTGGAAAAGCG
1 GACCAGTACATCATCACTAACAACAAATTGTTACCATATTGGAAAAGCG
128804382 G
1 G
128804383 GTTATCTGGA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.39, C:0.22, G:0.16, T:0.22
Consensus pattern (49 bp):
GACCAGTACATCATCACTAACAACAAATTGTTACCATATTGGAAAAGCG
Found at i:128808445 original size:16 final size:17
Alignment explanation
Indices: 128808414--128808446 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
128808404 TTCATAAGTA
128808414 TATATCAATCATTTCAT
1 TATATCAATCATTTCAT
128808431 TATATCAAT-ATTTCAT
1 TATATCAATCATTTCAT
128808447 GCACCATCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.36, C:0.15, G:0.00, T:0.48
Consensus pattern (17 bp):
TATATCAATCATTTCAT
Found at i:128808790 original size:46 final size:46
Alignment explanation
Indices: 128808728--128809097 Score: 519
Period size: 46 Copynumber: 8.0 Consensus size: 46
128808718 TTATCTTTGA
* * * * *
128808728 CATGATGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCA-TTTCATAT
* * *
128808774 CATGTTGCCATGGTGTCTTTCAACCATGGTCTTATTCATTTCATGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATAT
* * * * *
128808820 CACGCTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCCTGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATAT
* *
128808866 CATGTTGCCATGATATCTTTCAACCATGGTCTTATTCATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATAT
*
128808912 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATAT
*
128808958 CAAGTTGCCATGGTATCTTTCAACCATGGTCTTA-TACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACT-CATTTCATAT
* *
128809004 CAAGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATAT
* *
128809050 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATAT
128809096 CA
1 CA
128809098 GAGAGCACAC
Statistics
Matches: 301, Mismatches: 20, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
45 4 0.01
46 297 0.99
ACGTcount: A:0.22, C:0.24, G:0.14, T:0.40
Consensus pattern (46 bp):
CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATAT
Found at i:128819149 original size:24 final size:24
Alignment explanation
Indices: 128819117--128819162 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
128819107 TGATTTAACT
*
128819117 TAATCGAACATGTTCATGAACATA
1 TAATCGAACATGTTCACGAACATA
*
128819141 TAATTGAACATGTTCACGAACA
1 TAATCGAACATGTTCACGAACA
128819163 ATGTTAATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.41, C:0.17, G:0.13, T:0.28
Consensus pattern (24 bp):
TAATCGAACATGTTCACGAACATA
Found at i:128819383 original size:24 final size:24
Alignment explanation
Indices: 128819337--128819394 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
128819327 TCATTAATAA
* * *
128819337 ATAAACGAGTCAATAAACGAACTT
1 ATAAACAAGCCAATAAACAAACTT
*
128819361 ATAAACAAGCCAATAAATAAACTT
1 ATAAACAAGCCAATAAACAAACTT
*
128819385 TTAAACAAGC
1 ATAAACAAGC
128819395 TTGTTCGTGA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.53, C:0.17, G:0.09, T:0.21
Consensus pattern (24 bp):
ATAAACAAGCCAATAAACAAACTT
Found at i:128828716 original size:2 final size:2
Alignment explanation
Indices: 128828709--128828735 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
128828699 AAGATATTCT
128828709 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
128828736 TTAATAAACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:128829259 original size:2 final size:2
Alignment explanation
Indices: 128829252--128829288 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
128829242 TTTCCAAATT
128829252 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
128829289 GTTTTATAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:128838396 original size:96 final size:96
Alignment explanation
Indices: 128838230--128838423 Score: 300
Period size: 96 Copynumber: 2.0 Consensus size: 96
128838220 GTGTCCGAGG
* * * * *
128838230 AAGTCTGTTATCGATGGGAATGATCGAGCAGATACAGAGCCCAAGAAGCTTGGTTCGAGCAAGGG
1 AAGTCTGTCATCGAAGGGAACGATCGAGCAGACACAGAGCCCAAGAAGCTTGGTTCAAGCAAGGG
128838295 AAAAGCCGAAGCCAAGAGGGCAAAGAGGAGC
66 AAAAGCCGAAGCCAAGAGGGCAAAGAGGAGC
*
128838326 AAGTCTGTCATCGAAGGGAACGATGGAGCAGACA-AGGAGCCCAAGAAGCTTGGTTCAAGCAAGG
1 AAGTCTGTCATCGAAGGGAACGATCGAGCAGACACA-GAGCCCAAGAAGCTTGGTTCAAGCAAGG
* *
128838390 GTAAAGCCGAAGCCAAGAGGGCTAAGAGGAGC
65 GAAAAGCCGAAGCCAAGAGGGCAAAGAGGAGC
128838422 AA
1 AA
128838424 AAAGAAGCGA
Statistics
Matches: 89, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
95 1 0.01
96 88 0.99
ACGTcount: A:0.36, C:0.18, G:0.34, T:0.12
Consensus pattern (96 bp):
AAGTCTGTCATCGAAGGGAACGATCGAGCAGACACAGAGCCCAAGAAGCTTGGTTCAAGCAAGGG
AAAAGCCGAAGCCAAGAGGGCAAAGAGGAGC
Found at i:128847306 original size:24 final size:24
Alignment explanation
Indices: 128847273--128847327 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
128847263 AACTTTCAAA
* * * *
128847273 AATAATAAAATTAATTTTTTAAAT
1 AATAAAAAAATAAATTATTAAAAT
*
128847297 TATAAAAAAATAAATTATTAAAAT
1 AATAAAAAAATAAATTATTAAAAT
128847321 AATAAAA
1 AATAAAA
128847328 TTATATTTTA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (24 bp):
AATAAAAAAATAAATTATTAAAAT
Found at i:128847320 original size:45 final size:46
Alignment explanation
Indices: 128847271--128847358 Score: 126
Period size: 45 Copynumber: 1.9 Consensus size: 46
128847261 TTAACTTTCA
*
128847271 AAAATAATAAAATTAATTTTTTA-AATTATAAAAAAATA-AATTATT
1 AAAATAATAAAATT-ATATTTTACAATTATAAAAAAATACAATTATT
* *
128847316 AAAATAATAAAATTATATTTTACTATTATAAAAATATACAATT
1 AAAATAATAAAATTATATTTTACAATTATAAAAAAATACAATT
128847359 TAATTTTAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
44 7 0.18
45 27 0.71
46 4 0.11
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (46 bp):
AAAATAATAAAATTATATTTTACAATTATAAAAAAATACAATTATT
Found at i:128847358 original size:29 final size:30
Alignment explanation
Indices: 128847310--128847366 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
128847300 AAAAAAATAA
*
128847310 ATTATTAAAATAATAAAA-TTATATTTTACT
1 ATTATAAAAATAATAAAATTTA-ATTTTACT
*
128847340 ATTATAAAAAT-ATACAATTTAATTTTA
1 ATTATAAAAATAATAAAATTTAATTTTA
128847367 ATCTCTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 11 0.46
30 13 0.54
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.46
Consensus pattern (30 bp):
ATTATAAAAATAATAAAATTTAATTTTACT
Found at i:128851331 original size:17 final size:17
Alignment explanation
Indices: 128851309--128851349 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
128851299 TATTTTCTTT
128851309 CAAAGTTAACTAATAGA
1 CAAAGTTAACTAATAGA
**
128851326 CAAAGTTGGCTAATAGA
1 CAAAGTTAACTAATAGA
*
128851343 TAAAGTT
1 CAAAGTT
128851350 GGAGAAGAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.46, C:0.10, G:0.17, T:0.27
Consensus pattern (17 bp):
CAAAGTTAACTAATAGA
Found at i:128851350 original size:17 final size:17
Alignment explanation
Indices: 128851318--128851351 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
128851308 TCAAAGTTAA
128851318 CTAATAGACAAAGTTGG
1 CTAATAGACAAAGTTGG
*
128851335 CTAATAGATAAAGTTGG
1 CTAATAGACAAAGTTGG
128851352 AGAAGAAAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.41, C:0.09, G:0.24, T:0.26
Consensus pattern (17 bp):
CTAATAGACAAAGTTGG
Found at i:128857959 original size:50 final size:50
Alignment explanation
Indices: 128857884--128857983 Score: 182
Period size: 50 Copynumber: 2.0 Consensus size: 50
128857874 ACACGGTTCA
* *
128857884 GGGCTTTTTACACAGTTCGGTCACACGACCACGTGTCCCTATAAGAATTT
1 GGGCTTTCTACACAGTCCGGTCACACGACCACGTGTCCCTATAAGAATTT
128857934 GGGCTTTCTACACAGTCCGGTCACACGACCACGTGTCCCTATAAGAATTT
1 GGGCTTTCTACACAGTCCGGTCACACGACCACGTGTCCCTATAAGAATTT
128857984 ATAATTTTGA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 48 1.00
ACGTcount: A:0.24, C:0.28, G:0.20, T:0.28
Consensus pattern (50 bp):
GGGCTTTCTACACAGTCCGGTCACACGACCACGTGTCCCTATAAGAATTT
Found at i:128862804 original size:3 final size:3
Alignment explanation
Indices: 128862796--128862853 Score: 116
Period size: 3 Copynumber: 19.3 Consensus size: 3
128862786 TAAGGAGTAT
128862796 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
128862844 TAA TAA TAA T
1 TAA TAA TAA T
128862854 GATGATGATG
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:128862858 original size:3 final size:3
Alignment explanation
Indices: 128862852--128862880 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
128862842 AATAATAATA
128862852 ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
128862881 TAAAAAGTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.31, T:0.34
Consensus pattern (3 bp):
ATG
Found at i:128863275 original size:12 final size:11
Alignment explanation
Indices: 128863250--128863291 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
128863240 AGTTAAATAT
128863250 TATTTTATTAA
1 TATTTTATTAA
*
128863261 TATTTTTTTAGA
1 TATTTTATTA-A
*
128863273 TA-TTTATTAT
1 TATTTTATTAA
128863283 TATTTTATT
1 TATTTTATT
128863292 TAGAAAAATG
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
10 2 0.08
11 21 0.81
12 3 0.12
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:128863281 original size:22 final size:23
Alignment explanation
Indices: 128863253--128863295 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
128863243 TAAATATTAT
128863253 TTTATTAATATTTT-TTTAGATA
1 TTTATTAATATTTTATTTAGATA
*
128863275 TTTATTATTATTTTATTTAGA
1 TTTATTAATATTTTATTTAGA
128863296 AAAATGGTAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (23 bp):
TTTATTAATATTTTATTTAGATA
Found at i:128863474 original size:16 final size:16
Alignment explanation
Indices: 128863453--128863491 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
128863443 GTTTGGTTCA
*
128863453 CTGTAATGGAATAGGG
1 CTGTAATGGAATAGAG
*
128863469 CTGTAATTGAATAGAG
1 CTGTAATGGAATAGAG
128863485 CTGTAAT
1 CTGTAAT
128863492 CAGTAATTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.33, C:0.08, G:0.28, T:0.31
Consensus pattern (16 bp):
CTGTAATGGAATAGAG
Found at i:128863561 original size:44 final size:46
Alignment explanation
Indices: 128863477--128863565 Score: 130
Period size: 44 Copynumber: 2.0 Consensus size: 46
128863467 GGCTGTAATT
*
128863477 GAATAGAGCTGTAATCAGTAATTCAGCTGTTTGGTTGAATGGAATG
1 GAATAGAACTGTAATCAGTAATTCAGCTGTTTGGTTGAATGGAATG
*
128863523 GAATAGAACTGTAAT-AGT-ATTCTTG-TGTTTGGTTGAATGGAAT
1 GAATAGAACTGTAATCAGTAATTC-AGCTGTTTGGTTGAATGGAAT
128863566 AATGTTGTAA
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
44 22 0.55
45 4 0.10
46 14 0.35
ACGTcount: A:0.30, C:0.07, G:0.27, T:0.36
Consensus pattern (46 bp):
GAATAGAACTGTAATCAGTAATTCAGCTGTTTGGTTGAATGGAATG
Found at i:128863751 original size:58 final size:54
Alignment explanation
Indices: 128863669--128863791 Score: 140
Period size: 58 Copynumber: 2.2 Consensus size: 54
128863659 TTTTAATAAG
* * *
128863669 ATTATTATTGAAAATAATTTAATAAAAATAATAAATAATTTAATCATATT-TTAACATA
1 ATTATTATT-AAAATAATTCAAT-AAAA-AAT--ATAATTTAATAACATTCTTAACATA
* *
128863727 TTTATTATTAAATATAATTCAATAAAAAATATAATTTAATAACATTCTTAATATA
1 ATTATTATTAAA-ATAATTCAATAAAAAATATAATTTAATAACATTCTTAACATA
128863782 ATTATTATTA
1 ATTATTATTA
128863792 TATGAATTAA
Statistics
Matches: 57, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
54 14 0.25
55 16 0.28
56 3 0.05
57 7 0.12
58 17 0.30
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.44
Consensus pattern (54 bp):
ATTATTATTAAAATAATTCAATAAAAAATATAATTTAATAACATTCTTAACATA
Found at i:128863758 original size:17 final size:17
Alignment explanation
Indices: 128863736--128863768 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
128863726 ATTTATTATT
128863736 AAATATAATTCAATAAA
1 AAATATAATTCAATAAA
*
128863753 AAATATAATTTAATAA
1 AAATATAATTCAATAA
128863769 CATTCTTAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (17 bp):
AAATATAATTCAATAAA
Found at i:128871741 original size:3 final size:3
Alignment explanation
Indices: 128871733--128871802 Score: 131
Period size: 3 Copynumber: 23.0 Consensus size: 3
128871723 TCCTCATTCA
128871733 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
128871781 ATT ATT ATT ATT ATT ATCT ATT
1 ATT ATT ATT ATT ATT AT-T ATT
128871803 TATTCTGTTG
Statistics
Matches: 66, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
3 63 0.95
4 3 0.05
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:128873098 original size:6 final size:6
Alignment explanation
Indices: 128873080--128873149 Score: 81
Period size: 6 Copynumber: 11.8 Consensus size: 6
128873070 TTATCTTTGT
* * *
128873080 TTTTTA TTTTT- TTTATT- TTTTTA TTTTTA TCTTTA TCTTTA TCTTTA
1 TTTTTA TTTTTA TTT-TTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA
*
128873127 TTTTTA TTTTTA TATTTA TTTTT
1 TTTTTA TTTTTA TTTTTA TTTTT
128873150 TTATATTTTA
Statistics
Matches: 58, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
5 5 0.09
6 53 0.91
ACGTcount: A:0.16, C:0.04, G:0.00, T:0.80
Consensus pattern (6 bp):
TTTTTA
Found at i:128873112 original size:36 final size:38
Alignment explanation
Indices: 128873069--128873143 Score: 100
Period size: 38 Copynumber: 2.0 Consensus size: 38
128873059 ATTGAGTCTA
* * *
128873069 TTTATCTTTGT-TTTTTATTT-TTTTTATTTTTTTATT
1 TTTATCTTTATCTTTATATTTATTTTTATTTTTATATT
*
128873105 TTTATCTTTATCTTTATCTTTATTTTTATTTTTATATT
1 TTTATCTTTATCTTTATATTTATTTTTATTTTTATATT
128873143 T
1 T
128873144 ATTTTTTTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
36 10 0.30
37 7 0.21
38 16 0.48
ACGTcount: A:0.15, C:0.05, G:0.01, T:0.79
Consensus pattern (38 bp):
TTTATCTTTATCTTTATATTTATTTTTATTTTTATATT
Found at i:128873114 original size:12 final size:12
Alignment explanation
Indices: 128873069--128873145 Score: 68
Period size: 12 Copynumber: 6.4 Consensus size: 12
128873059 ATTGAGTCTA
*
128873069 TTTATCTTTGTTT
1 TTTATCTTT-ATT
128873082 TTTAT-TTT-TT
1 TTTATCTTTATT
* *
128873092 TTATTTTTTTATT
1 TT-TATCTTTATT
*
128873105 TTTATCTTTATC
1 TTTATCTTTATT
128873117 TTTATCTTTATT
1 TTTATCTTTATT
* *
128873129 TTTATTTTTATA
1 TTTATCTTTATT
128873141 TTTAT
1 TTTAT
128873146 TTTTTTATAT
Statistics
Matches: 54, Mismatches: 7, Indels: 7
0.79 0.10 0.10
Matches are distributed among these distances:
10 4 0.07
11 2 0.04
12 39 0.72
13 9 0.17
ACGTcount: A:0.16, C:0.05, G:0.01, T:0.78
Consensus pattern (12 bp):
TTTATCTTTATT
Found at i:128873145 original size:36 final size:35
Alignment explanation
Indices: 128873067--128873158 Score: 93
Period size: 36 Copynumber: 2.7 Consensus size: 35
128873057 CCATTGAGTC
* *
128873067 TATTTATCTTTGTTTTTTATTTTTTTTATTTTTTTA
1 TATTTATCTTTATTTTATATTTTTTTTA-TTTTTTA
* *
128873103 TTTTTATCTTTATCTTTATCTTTATTTTTA-TTTTTA
1 TATTTATCTTTAT-TTTATATTT-TTTTTATTTTTTA
128873139 TATTTA--TTT-TTTTATATTTT
1 TATTTATCTTTATTTTATATTTT
128873159 AAACTTTATT
Statistics
Matches: 48, Mismatches: 6, Indels: 9
0.76 0.10 0.14
Matches are distributed among these distances:
31 1 0.02
32 8 0.17
33 1 0.02
34 3 0.06
36 22 0.46
37 7 0.15
38 6 0.12
ACGTcount: A:0.16, C:0.04, G:0.01, T:0.78
Consensus pattern (35 bp):
TATTTATCTTTATTTTATATTTTTTTTATTTTTTA
Found at i:128876293 original size:80 final size:79
Alignment explanation
Indices: 128876146--128876375 Score: 379
Period size: 80 Copynumber: 2.9 Consensus size: 79
128876136 AAAATTTTTA
*
128876146 AGATTCTAGAGAATATGCTCATCAATTTAGAAGCAAGAAAATAGTAGATGAAAGTGGACAAAATG
1 AGATTCTAGAGAATATGCTCATCAATTTAGAAGCAAGAAAATAGTAGATGAAAGTGGAGAAAATG
128876211 AGAAGATGAAGTAG
66 AGAAGATGAAGTAG
* * *
128876225 AGATTTTAGAGAACATGCTCATCAATTTAGAAGCGAAGAAAATAGTAGATGAAAGTGGGGAAAAT
1 AGATTCTAGAGAATATGCTCATCAATTTAGAAGC-AAGAAAATAGTAGATGAAAGTGGAGAAAAT
128876290 GAGAAGATGAAGTAG
65 GAGAAGATGAAGTAG
* * **
128876305 AGATTCTAGAGAATATGCTCATCAATTTAGAAACAAGAAAATGGTATTTGAAAGTGGAGAAAATG
1 AGATTCTAGAGAATATGCTCATCAATTTAGAAGCAAGAAAATAGTAGATGAAAGTGGAGAAAATG
128876370 AGAAGA
66 AGAAGA
128876376 AAAAATGAAG
Statistics
Matches: 139, Mismatches: 11, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
79 65 0.47
80 74 0.53
ACGTcount: A:0.46, C:0.07, G:0.25, T:0.22
Consensus pattern (79 bp):
AGATTCTAGAGAATATGCTCATCAATTTAGAAGCAAGAAAATAGTAGATGAAAGTGGAGAAAATG
AGAAGATGAAGTAG
Found at i:128876998 original size:19 final size:20
Alignment explanation
Indices: 128876962--128876999 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
128876952 CACGAATAGT
128876962 AGGGAAAGAAAGAAGAAAAA
1 AGGGAAAGAAAGAAGAAAAA
128876982 AGGGAAAGAAA-AAGAAAA
1 AGGGAAAGAAAGAAGAAAA
128877000 GGAAAATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (20 bp):
AGGGAAAGAAAGAAGAAAAA
Found at i:128878051 original size:2 final size:2
Alignment explanation
Indices: 128878046--128878077 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
128878036 AAAACATGAA
128878046 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
128878078 GAATTGCTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:128883660 original size:19 final size:19
Alignment explanation
Indices: 128883632--128883709 Score: 61
Period size: 19 Copynumber: 4.1 Consensus size: 19
128883622 TGAAAACAAT
128883632 AGAAATATTATAAAATTTTA
1 AGAAA-ATTATAAAATTTTA
** *
128883652 AGAAAATTATAAAAAATTG
1 AGAAAATTATAAAATTTTA
* *
128883671 AG-AATTTATAAAATTTATT
1 AGAAAATTATAAAATTT-TA
*
128883690 A-AATATTATAAAATATTTA
1 AGAAAATTATAAAAT-TTTA
128883709 A
1 A
128883710 ATATATTAAA
Statistics
Matches: 45, Mismatches: 10, Indels: 7
0.73 0.16 0.11
Matches are distributed among these distances:
18 11 0.24
19 27 0.60
20 7 0.16
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.38
Consensus pattern (19 bp):
AGAAAATTATAAAATTTTA
Found at i:128883685 original size:9 final size:10
Alignment explanation
Indices: 128883634--128883730 Score: 75
Period size: 10 Copynumber: 10.3 Consensus size: 10
128883624 AAAACAATAG
128883634 AAATATTATA
1 AAATATTATA
128883644 AAAT-TT-TA
1 AAATATTATA
*
128883652 AGAAAATTATA
1 A-AATATTATA
* *
128883663 AAAAATT-GA
1 AAATATTATA
*
128883672 GAAT-TTATA
1 AAATATTATA
*
128883681 AAAT-TTATT
1 AAATATTATA
128883690 AAATATTATA
1 AAATATTATA
128883700 AAATATT-TA
1 AAATATTATA
128883709 AATATATTA-A
1 AA-ATATTATA
128883719 AAA-ATTATA
1 AAATATTATA
128883728 AAA
1 AAA
128883731 GGAATTATAA
Statistics
Matches: 71, Mismatches: 8, Indels: 17
0.74 0.08 0.18
Matches are distributed among these distances:
8 9 0.13
9 28 0.39
10 31 0.44
11 3 0.04
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (10 bp):
AAATATTATA
Found at i:128883725 original size:8 final size:9
Alignment explanation
Indices: 128883654--128883824 Score: 53
Period size: 10 Copynumber: 17.4 Consensus size: 9
128883644 AAATTTTAAG
128883654 AAAATTATAA
1 AAAATTAT-A
*
128883664 AAAATT-GA
1 AAAATTATA
* *
128883672 GAATTTATA
1 AAAATTATA
*
128883681 AAATTTATTA
1 AAAATTA-TA
*
128883691 AATATTATA
1 AAAATTATA
128883700 AAATATT-TA
1 AAA-ATTATA
128883709 AATATATTA-A
1 AA-A-ATTATA
128883719 AAAATTATAA
1 AAAATTAT-A
128883729 AAGGAATTATA
1 AA--AATTATA
*
128883740 AAAAGTATA
1 AAAATTATA
*
128883749 AGAAAGTATA
1 A-AAATTATA
* *
128883759 TATATGCGTATTA
1 AAAAT---TA-TA
128883772 AAATGATTA-A
1 AAA--ATTATA
128883782 AAAATTTATA
1 AAAA-TTATA
*
128883792 AAACTTATTA
1 AAAATTA-TA
*
128883802 AAAAGTTACA
1 AAAA-TTATA
128883812 AAAATTATA
1 AAAATTATA
128883821 AAAA
1 AAAA
128883825 GAAAATTAAG
Statistics
Matches: 123, Mismatches: 18, Indels: 41
0.68 0.10 0.23
Matches are distributed among these distances:
8 10 0.08
9 39 0.32
10 53 0.43
11 6 0.05
12 10 0.08
13 3 0.02
15 2 0.02
ACGTcount: A:0.58, C:0.02, G:0.06, T:0.34
Consensus pattern (9 bp):
AAAATTATA
Found at i:128883801 original size:30 final size:29
Alignment explanation
Indices: 128883767--128883823 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 29
128883757 TATATATGCG
*
128883767 TATTAAAATGATTA-AAAAATTTATAAAACT
1 TATTAAAAAG-TTACAAAAA-TTATAAAACT
128883797 TATTAAAAAGTTACAAAAATTATAAAA
1 TATTAAAAAGTTACAAAAATTATAAAA
128883824 AGAAAATTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 11 0.44
30 14 0.56
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.33
Consensus pattern (29 bp):
TATTAAAAAGTTACAAAAATTATAAAACT
Found at i:128884121 original size:20 final size:21
Alignment explanation
Indices: 128884098--128884154 Score: 59
Period size: 19 Copynumber: 2.8 Consensus size: 21
128884088 AAGCTTTTAG
128884098 AAATTATTAAAATATTATA-A
1 AAATTATTAAAATATTATAGA
128884118 AAATGTA--AAAA-ATTATAGA
1 AAAT-TATTAAAATATTATAGA
*
128884137 AAATTATATAAATTATTA
1 AAATTAT-TAAAATATTA
128884155 AAAGATTAGA
Statistics
Matches: 30, Mismatches: 1, Indels: 10
0.73 0.02 0.24
Matches are distributed among these distances:
18 8 0.27
19 9 0.30
20 4 0.13
21 5 0.17
22 4 0.13
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.37
Consensus pattern (21 bp):
AAATTATTAAAATATTATAGA
Found at i:128884132 original size:18 final size:19
Alignment explanation
Indices: 128884105--128884140 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
128884095 TAGAAATTAT
*
128884105 TAAAATATTATA-AAAATG
1 TAAAAAATTATAGAAAATG
128884123 TAAAAAATTATAGAAAAT
1 TAAAAAATTATAGAAAAT
128884141 TATATAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.31
Consensus pattern (19 bp):
TAAAAAATTATAGAAAATG
Found at i:128884139 original size:10 final size:9
Alignment explanation
Indices: 128884098--128884162 Score: 60
Period size: 10 Copynumber: 6.7 Consensus size: 9
128884088 AAGCTTTTAG
128884098 AAATTATTAA
1 AAATTA-TAA
128884108 AATATTATAA
1 AA-ATTATAA
128884118 AAATGTA-AA
1 AAAT-TATAA
128884127 AAATTATAGA
1 AAATTATA-A
*
128884137 AAATTATAT
1 AAATTATAA
128884146 AAATTATTAA
1 AAATTA-TAA
128884156 AAGATTA
1 AA-ATTA
128884163 GAAATTACTA
Statistics
Matches: 47, Mismatches: 2, Indels: 11
0.78 0.03 0.18
Matches are distributed among these distances:
8 2 0.04
9 15 0.32
10 22 0.47
11 8 0.17
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (9 bp):
AAATTATAA
Found at i:128887398 original size:2 final size:2
Alignment explanation
Indices: 128887391--128887420 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
128887381 TTCGACTTTT
128887391 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
128887421 GGAAAACGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:128891907 original size:16 final size:16
Alignment explanation
Indices: 128891888--128891919 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
128891878 TTTTATTTAT
*
128891888 AATAAATTTTAAAAAA
1 AATAAAATTTAAAAAA
128891904 AATAAAATTTAAAAAA
1 AATAAAATTTAAAAAA
128891920 TAGTCACTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (16 bp):
AATAAAATTTAAAAAA
Found at i:128896396 original size:33 final size:33
Alignment explanation
Indices: 128896359--128896426 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
128896349 TTAACTCGGT
128896359 TTAGCTTAATCTACTTAGCTCGGGGGGGTTGAA
1 TTAGCTTAATCTACTTAGCTCGGGGGGGTTGAA
128896392 TTAGCTTAATCTACTTAGCTCGGGGGGGTTGAA
1 TTAGCTTAATCTACTTAGCTCGGGGGGGTTGAA
128896425 TT
1 TT
128896427 GTAAACTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.21, C:0.15, G:0.29, T:0.35
Consensus pattern (33 bp):
TTAGCTTAATCTACTTAGCTCGGGGGGGTTGAA
Found at i:128898794 original size:35 final size:35
Alignment explanation
Indices: 128898767--128898932 Score: 172
Period size: 35 Copynumber: 4.6 Consensus size: 35
128898757 CATGGCAAAG
*
128898767 TGTGAAATGTAGGTATGGTATCATCCATACTGAGT
1 TGTGAAATGTAGGTATGGTATCATCCATACTGAGC
*
128898802 TGTGAAATGTAGGTATGGTATTATCCATACTGAGC
1 TGTGAAATGTAGGTATGGTATCATCCATACTGAGC
*
128898837 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGT
1 TGTGAAATGTAGGTATGG---TATC--ATCCATACTGAGC
** * * * *
128898877 TAAGAAATGTAGGTATGGCAT-TTCCCATACCGAGT
1 TGTGAAATGTAGGTATGGTATCAT-CCATACTGAGC
**
128898912 TGAAAAATGTAGGTATGGTAT
1 TGTGAAATGTAGGTATGGTAT
128898933 TTCAATGAGG
Statistics
Matches: 113, Mismatches: 12, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
34 1 0.01
35 79 0.70
37 2 0.02
38 3 0.03
40 28 0.25
ACGTcount: A:0.31, C:0.11, G:0.25, T:0.33
Consensus pattern (35 bp):
TGTGAAATGTAGGTATGGTATCATCCATACTGAGC
Found at i:128898886 original size:75 final size:75
Alignment explanation
Indices: 128898767--128898937 Score: 221
Period size: 75 Copynumber: 2.4 Consensus size: 75
128898757 CATGGCAAAG
** *
128898767 TGTGAAATGTAGGTATGG---TATC--ATCCATACTGAGTTGTGAAATGTAGGTATGGTATTAT-
1 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATT-TC
*
128898826 CCATACTGAGC
65 CCATACCGAGC
128898837 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
1 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
*
128898902 CATACCGAGT
66 CATACCGAGC
**
128898912 TGAAAAATGTAGGTATGGTATT-TCAA
1 TGTGAAATGTAGGTATGGTATTATCAA
128898938 TGAGGAAAAC
Statistics
Matches: 88, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
70 18 0.20
73 4 0.05
74 5 0.06
75 61 0.69
ACGTcount: A:0.32, C:0.11, G:0.24, T:0.33
Consensus pattern (75 bp):
TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
CATACCGAGC
Found at i:128906228 original size:35 final size:35
Alignment explanation
Indices: 128906201--128906366 Score: 172
Period size: 35 Copynumber: 4.6 Consensus size: 35
128906191 CATGGCAAAG
*
128906201 TGTGAAATGTAGGTATGGTATCATCCATACTGAGT
1 TGTGAAATGTAGGTATGGTATCATCCATACTGAGC
*
128906236 TGTGAAATGTAGGTATGGTATTATCCATACTGAGC
1 TGTGAAATGTAGGTATGGTATCATCCATACTGAGC
*
128906271 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGT
1 TGTGAAATGTAGGTATGG---TATC--ATCCATACTGAGC
** * * * *
128906311 TAAGAAATGTAGGTATGGCAT-TTCCCATACCGAGT
1 TGTGAAATGTAGGTATGGTATCAT-CCATACTGAGC
**
128906346 TGAAAAATGTAGGTATGGTAT
1 TGTGAAATGTAGGTATGGTAT
128906367 TTCAATGAGG
Statistics
Matches: 113, Mismatches: 12, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
34 1 0.01
35 79 0.70
37 2 0.02
38 3 0.03
40 28 0.25
ACGTcount: A:0.31, C:0.11, G:0.25, T:0.33
Consensus pattern (35 bp):
TGTGAAATGTAGGTATGGTATCATCCATACTGAGC
Found at i:128906320 original size:75 final size:75
Alignment explanation
Indices: 128906201--128906371 Score: 221
Period size: 75 Copynumber: 2.4 Consensus size: 75
128906191 CATGGCAAAG
** *
128906201 TGTGAAATGTAGGTATGG---TATC--ATCCATACTGAGTTGTGAAATGTAGGTATGGTATTAT-
1 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATT-TC
*
128906260 CCATACTGAGC
65 CCATACCGAGC
128906271 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
1 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
*
128906336 CATACCGAGT
66 CATACCGAGC
**
128906346 TGAAAAATGTAGGTATGGTATT-TCAA
1 TGTGAAATGTAGGTATGGTATTATCAA
128906372 TGAGGAAAAC
Statistics
Matches: 88, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
70 18 0.20
73 4 0.05
74 5 0.06
75 61 0.69
ACGTcount: A:0.32, C:0.11, G:0.24, T:0.33
Consensus pattern (75 bp):
TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
CATACCGAGC
Found at i:128911842 original size:48 final size:49
Alignment explanation
Indices: 128911781--128911878 Score: 162
Period size: 48 Copynumber: 2.0 Consensus size: 49
128911771 GATTCAAAAG
* *
128911781 AACTGTTTTCAAAAAATCTGGATGATTTGAGAAAG-ATGTAGTTTACTA
1 AACTATTTTCAAAAAATCTGGATGATTTGAGAAAGTATGTAGTTCACTA
*
128911829 AACTATTTTCAAAAAATCTGGATGATTTGAGAAAGTATGTGGTTCACTA
1 AACTATTTTCAAAAAATCTGGATGATTTGAGAAAGTATGTAGTTCACTA
128911878 A
1 A
128911879 GTCTCCGGCA
Statistics
Matches: 46, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
48 34 0.74
49 12 0.26
ACGTcount: A:0.38, C:0.09, G:0.18, T:0.35
Consensus pattern (49 bp):
AACTATTTTCAAAAAATCTGGATGATTTGAGAAAGTATGTAGTTCACTA
Found at i:128915319 original size:26 final size:26
Alignment explanation
Indices: 128915289--128915370 Score: 155
Period size: 26 Copynumber: 3.2 Consensus size: 26
128915279 TGAAATTCCC
128915289 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
128915315 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
128915341 ATCATGAAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
128915367 ATCA
1 ATCA
128915371 ATTTGTATCA
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 55 1.00
ACGTcount: A:0.37, C:0.27, G:0.06, T:0.30
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:128922295 original size:26 final size:26
Alignment explanation
Indices: 128922265--128922372 Score: 198
Period size: 26 Copynumber: 4.2 Consensus size: 26
128922255 TGAAATTCCC
128922265 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
128922291 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
128922317 ATCATGAAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
128922343 ATCATGGAACATTTACCTAACTCATT
1 ATCATGGAACATTTACCTAACCCATT
128922369 ATCA
1 ATCA
128922373 ATTTGTATCA
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 79 1.00
ACGTcount: A:0.36, C:0.26, G:0.06, T:0.31
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:128934700 original size:21 final size:22
Alignment explanation
Indices: 128934653--128934733 Score: 62
Period size: 21 Copynumber: 3.7 Consensus size: 22
128934643 AATACTAGGG
*
128934653 TAATAATATGAAAA-AAAAACTATT
1 TAAT-ATAT-AAAATAAAAA-TAAT
** *
128934677 TAATATATATGAT-AAAATAGT
1 TAATATATAAAATAAAAATAAT
128934698 TAA-ATATAAAATAAAAATAAT
1 TAATATATAAAATAAAAATAAT
*
128934719 TAATAT-TAAATTAAA
1 TAATATATAAAATAAA
128934734 TTTGAAAGTA
Statistics
Matches: 47, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
20 7 0.15
21 24 0.51
22 8 0.17
23 4 0.09
24 4 0.09
ACGTcount: A:0.62, C:0.01, G:0.04, T:0.33
Consensus pattern (22 bp):
TAATATATAAAATAAAAATAAT
Found at i:128934723 original size:20 final size:21
Alignment explanation
Indices: 128934690--128934729 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
128934680 TATATATGAT
*
128934690 AAAATAGTTAAATATAAAATA
1 AAAATAATTAAATATAAAATA
*
128934711 AAAATAATT-AATATTAAAT
1 AAAATAATTAAATATAAAAT
128934730 TAAATTTGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.33
Consensus pattern (21 bp):
AAAATAATTAAATATAAAATA
Found at i:128938808 original size:46 final size:44
Alignment explanation
Indices: 128938708--128938813 Score: 131
Period size: 44 Copynumber: 2.4 Consensus size: 44
128938698 TGTCTTTGAC
** * * * *
128938708 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTGAATCCTATCTCCAAAGCCATATATAAT
*
128938752 ATGGACTTACATGGCTGAATCCTATCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTGAATCCTATCTCCAAAGCCATA--TATAAT
128938798 ATGGACTTACATGGCT
1 ATGGACTTACATGGCT
128938814 CATTTCTGTT
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
44 32 0.60
46 21 0.40
ACGTcount: A:0.30, C:0.22, G:0.14, T:0.34
Consensus pattern (44 bp):
ATGGACTTACATGGCTGAATCCTATCTCCAAAGCCATATATAAT
Found at i:128942207 original size:40 final size:38
Alignment explanation
Indices: 128942163--128942261 Score: 123
Period size: 36 Copynumber: 2.6 Consensus size: 38
128942153 GGCAAAGTGT
*
128942163 GAAATGTAGGTATGGTATTATCAAATCCATACTGAGTT-AA
1 GAAATGTAGGTATGGTATT-TC-AA-CCATACCGAGTTAAA
*
128942203 GAAATGTAGGTATGGCATTTC--CCATACCGAGTTAAA
1 GAAATGTAGGTATGGTATTTCAACCATACCGAGTTAAA
*
128942239 AAAATGTAGGTATGGTATTTCAA
1 GAAATGTAGGTATGGTATTTCAA
128942262 TGAGGAAAAC
Statistics
Matches: 52, Mismatches: 4, Indels: 8
0.81 0.06 0.12
Matches are distributed among these distances:
35 11 0.21
36 21 0.40
39 2 0.04
40 18 0.35
ACGTcount: A:0.36, C:0.11, G:0.21, T:0.31
Consensus pattern (38 bp):
GAAATGTAGGTATGGTATTTCAACCATACCGAGTTAAA
Found at i:128949659 original size:35 final size:36
Alignment explanation
Indices: 128949613--128949683 Score: 108
Period size: 36 Copynumber: 2.0 Consensus size: 36
128949603 ATTATCAAAT
* *
128949613 CCATACTGAGTT-AAGAAATGTAGGTATGGCATTTC
1 CCATACCGAGTTAAAAAAATGTAGGTATGGCATTTC
*
128949648 CCATACCGAGTTAAAAAAATGTAGGTATGGTATTTC
1 CCATACCGAGTTAAAAAAATGTAGGTATGGCATTTC
128949684 AATGAGGAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
35 11 0.34
36 21 0.66
ACGTcount: A:0.34, C:0.14, G:0.21, T:0.31
Consensus pattern (36 bp):
CCATACCGAGTTAAAAAAATGTAGGTATGGCATTTC
Found at i:128951753 original size:47 final size:46
Alignment explanation
Indices: 128951679--128951775 Score: 108
Period size: 47 Copynumber: 2.1 Consensus size: 46
128951669 TATCCATGTG
* * *
128951679 ACAAAAAATGACGTTGTAACGAGCCTAAATTTATTA-AGGAATTTTA
1 ACAAAAAATGACATTGTAACGAGCCTAAATTTAATAGA-GAATTTAA
* *
128951725 ACAAAAATATGACATTGTAATG-GACCTAAGTTTAATAGAGAATTTAA
1 ACAAAAA-ATGACATTGTAACGAG-CCTAAATTTAATAGAGAATTTAA
128951772 ACAA
1 ACAA
128951776 TGTTAACAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
46 8 0.19
47 34 0.79
48 1 0.02
ACGTcount: A:0.46, C:0.10, G:0.14, T:0.29
Consensus pattern (46 bp):
ACAAAAAATGACATTGTAACGAGCCTAAATTTAATAGAGAATTTAA
Found at i:128953521 original size:38 final size:38
Alignment explanation
Indices: 128953474--128953577 Score: 136
Period size: 38 Copynumber: 2.7 Consensus size: 38
128953464 ATTGTTGAAT
* * *
128953474 CAAATACATGCTAAACATGTCTACTATTGCTGTTAAAC
1 CAAATACATGTTAAGCATGTCTACTATTACTGTTAAAC
* ** *
128953512 CAAAAACATGTTAAGCATGTCTACTGCTACTGTTGAAC
1 CAAATACATGTTAAGCATGTCTACTATTACTGTTAAAC
*
128953550 CAAATACATGTTAAGCATGTTTACTATT
1 CAAATACATGTTAAGCATGTCTACTATT
128953578 TTTGTACTGT
Statistics
Matches: 55, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
38 55 1.00
ACGTcount: A:0.36, C:0.19, G:0.12, T:0.33
Consensus pattern (38 bp):
CAAATACATGTTAAGCATGTCTACTATTACTGTTAAAC
Found at i:128959096 original size:2 final size:2
Alignment explanation
Indices: 128959089--128959122 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
128959079 CCCTTTTTAA
128959089 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
128959123 TACTAGTTTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:128964364 original size:53 final size:53
Alignment explanation
Indices: 128964283--128964433 Score: 214
Period size: 53 Copynumber: 2.8 Consensus size: 53
128964273 CTTACACGGT
* *
128964283 TCACATATCATACCGAAGCCATATCCCAGAC-ATGGTCTTATACGGAATCACATTA
1 TCACAT-T-ATACCGATGCCATAGCCCAG-CTATGGTCTTATACGGAATCACATTA
*
128964338 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAGTCACATTA
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
** *
128964391 TCACATTGCACCGATGCCATAGCCCAGCTATGGTCTTAAACGG
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGG
128964434 GCACACTTGT
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
52 1 0.01
53 81 0.91
54 1 0.01
55 6 0.07
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.26
Consensus pattern (53 bp):
TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
Found at i:128968707 original size:86 final size:86
Alignment explanation
Indices: 128968598--128968768 Score: 220
Period size: 86 Copynumber: 2.0 Consensus size: 86
128968588 GTTTCATCTA
* *
128968598 CAAATAGTGTGGTTCGATTATGAAACAAGTGACATTTTATTTAATCTGCAAAAAATGTTGTGCAC
1 CAAATAGTGTGGTTCGATCATGAAACAAGTGACAATTTATTTAATCTGC-AAAAATGTTGTGCAC
* * * *
128968663 TCATAACAAGTGGCAATAACTG
65 CCACAACAAGTGACAACAACTG
* * * *
128968685 CAAATA-TGTGGTTC-AGTCATGAACCAAGTGGCAATTTGTTTAATCTGCAAATATGTTGTGCAC
1 CAAATAGTGTGGTTCGA-TCATGAAACAAGTGACAATTTATTTAATCTGCAAAAATGTTGTGCAC
128968748 CCACAACAAGTGACAACAACT
65 CCACAACAAGTGACAACAACT
128968769 ATAAATCAAT
Statistics
Matches: 73, Mismatches: 10, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
85 32 0.44
86 35 0.48
87 6 0.08
ACGTcount: A:0.36, C:0.17, G:0.18, T:0.29
Consensus pattern (86 bp):
CAAATAGTGTGGTTCGATCATGAAACAAGTGACAATTTATTTAATCTGCAAAAATGTTGTGCACC
CACAACAAGTGACAACAACTG
Found at i:128970645 original size:53 final size:53
Alignment explanation
Indices: 128970489--128970654 Score: 221
Period size: 53 Copynumber: 3.1 Consensus size: 53
128970479 GACGAAAAAT
* **
128970489 ATGTGATAAGTGTG-C-CCGTTTAAGACCATAGCTGGGCTATGGCATCGGTGCA
1 ATGTGATAA-TGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTATA
128970541 ATGTGATAATGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTATA
1 ATGTGATAATGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTATA
* * *
128970594 ATGTGATAATGTGATTCCGTATAAGACCAT-GTCTGGGATATGGCTTCGGTATGA
1 ATGTGATAATGTGACTCCGTATAAGACCATAG-CTGGGCTATGGCATCGGTAT-A
128970648 TATGTGA
1 -ATGTGA
128970655 ACCGTGTAAG
Statistics
Matches: 103, Mismatches: 6, Indels: 7
0.89 0.05 0.06
Matches are distributed among these distances:
51 4 0.04
52 11 0.11
53 81 0.79
54 1 0.01
55 6 0.06
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (53 bp):
ATGTGATAATGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTATA
Found at i:128972827 original size:17 final size:19
Alignment explanation
Indices: 128972791--128972829 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
128972781 TAGCATTTAA
*
128972791 TTTTAGAATATATATCTAT
1 TTTTAAAATATATATCTAT
128972810 TTTTAAAATATA-AT-TAT
1 TTTTAAAATATATATCTAT
128972827 TTT
1 TTT
128972830 ACTGATTTCG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 6 0.32
18 2 0.11
19 11 0.58
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (19 bp):
TTTTAAAATATATATCTAT
Found at i:128977958 original size:18 final size:18
Alignment explanation
Indices: 128977935--128978023 Score: 97
Period size: 18 Copynumber: 4.9 Consensus size: 18
128977925 TCATCGGTAT
*
128977935 TAATCAATTATTCAGTAG
1 TAATCAATTATTCAGTAA
*
128977953 TAATCATTTATTCAGTAA
1 TAATCAATTATTCAGTAA
* * ** *
128977971 CAGTCGTTTATTTAGTAA
1 TAATCAATTATTCAGTAA
*
128977989 CAATCAATTATTCAGTAA
1 TAATCAATTATTCAGTAA
*
128978007 TAATCAGTTATTCAGTA
1 TAATCAATTATTCAGTA
128978024 CCTTTATTTA
Statistics
Matches: 59, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 59 1.00
ACGTcount: A:0.37, C:0.12, G:0.10, T:0.40
Consensus pattern (18 bp):
TAATCAATTATTCAGTAA
Found at i:128978383 original size:20 final size:20
Alignment explanation
Indices: 128978358--128978397 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
128978348 TTTCATTTTC
128978358 AATCAGTATATATT-TCAATT
1 AATCAG-ATATATTCTCAATT
128978378 AATCAGATATATTCTCAATT
1 AATCAGATATATTCTCAATT
128978398 CAATATATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.40, C:0.12, G:0.05, T:0.42
Consensus pattern (20 bp):
AATCAGATATATTCTCAATT
Found at i:128978405 original size:16 final size:15
Alignment explanation
Indices: 128978365--128978414 Score: 55
Period size: 15 Copynumber: 3.0 Consensus size: 15
128978355 TTCAATCAGT
128978365 ATATATTTCAATTAATCA
1 ATATATTTCAA-T--TCA
128978383 GATATATTCTCAATTCA
1 -ATATATT-TCAATTCA
128978400 ATATATTTCAATTCA
1 ATATATTTCAATTCA
128978415 CTTTAACAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
15 8 0.27
16 7 0.23
17 3 0.10
19 8 0.27
20 4 0.13
ACGTcount: A:0.40, C:0.14, G:0.02, T:0.44
Consensus pattern (15 bp):
ATATATTTCAATTCA
Found at i:128979607 original size:4 final size:4
Alignment explanation
Indices: 128979598--128979631 Score: 50
Period size: 4 Copynumber: 8.0 Consensus size: 4
128979588 CACAATTGTC
128979598 TTTA TTTA TTTA TTTAA TTTA TTTAA TTTA TTTA
1 TTTA TTTA TTTA TTT-A TTTA TTT-A TTTA TTTA
128979632 ATTAATATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
4 20 0.71
5 8 0.29
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (4 bp):
TTTA
Found at i:128979619 original size:9 final size:9
Alignment explanation
Indices: 128979598--128979634 Score: 67
Period size: 9 Copynumber: 4.2 Consensus size: 9
128979588 CACAATTGTC
128979598 TTTATTT-A
1 TTTATTTAA
128979606 TTTATTTAA
1 TTTATTTAA
128979615 TTTATTTAA
1 TTTATTTAA
128979624 TTTATTTAA
1 TTTATTTAA
128979633 TT
1 TT
128979635 AATATAAAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
8 7 0.25
9 21 0.75
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (9 bp):
TTTATTTAA
Found at i:128979619 original size:13 final size:13
Alignment explanation
Indices: 128979598--128979637 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
128979588 CACAATTGTC
128979598 TTTATTTATTT-A
1 TTTATTTATTTAA
128979610 TTTAATTTATTTAA
1 TTT-ATTTATTTAA
*
128979624 TTTATTTAATTAA
1 TTTATTTATTTAA
128979637 T
1 T
128979638 ATAAAAGAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
12 3 0.12
13 18 0.72
14 4 0.16
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
TTTATTTATTTAA
Found at i:128981011 original size:12 final size:12
Alignment explanation
Indices: 128980996--128981024 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
128980986 GTGAGTAAAG
128980996 AAGATAAATGGA
1 AAGATAAATGGA
128981008 AAGAT-AATGGA
1 AAGATAAATGGA
128981019 AAGATA
1 AAGATA
128981025 GAACGTGGCG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.59, C:0.00, G:0.24, T:0.17
Consensus pattern (12 bp):
AAGATAAATGGA
Found at i:128985117 original size:12 final size:12
Alignment explanation
Indices: 128985102--128985130 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
128985092 GTAAATAAAG
128985102 AAGATAAATGGA
1 AAGATAAATGGA
128985114 AAGAT-AATGGA
1 AAGATAAATGGA
128985125 AAGATA
1 AAGATA
128985131 GAACGTGGCG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.59, C:0.00, G:0.24, T:0.17
Consensus pattern (12 bp):
AAGATAAATGGA
Found at i:128988127 original size:34 final size:34
Alignment explanation
Indices: 128988089--128988273 Score: 244
Period size: 34 Copynumber: 5.4 Consensus size: 34
128988079 AGCATGTCTT
* * * * *
128988089 TTGCTACTTTAATGATTTGTTAGAAGCATATGAA
1 TTGCTACTGTATTGATCTGTTACAAGCATATTAA
* * * *
128988123 TTGCTACCGTATTGATATGTTATAAGCATATTCA
1 TTGCTACTGTATTGATCTGTTACAAGCATATTAA
* * *
128988157 TTGTTACTGTATTGATCTATTATAAGCATATTAA
1 TTGCTACTGTATTGATCTGTTACAAGCATATTAA
*
128988191 TTGCTACTGTATTGATCTATTACAAGCATATTAA
1 TTGCTACTGTATTGATCTGTTACAAGCATATTAA
128988225 TTGCTACTGTATTGATCTGTTACAAGCATATTAA
1 TTGCTACTGTATTGATCTGTTACAAGCATATTAA
*
128988259 TTGCTACCGTATTGA
1 TTGCTACTGTATTGA
128988274 AATGTTCATG
Statistics
Matches: 135, Mismatches: 16, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 135 1.00
ACGTcount: A:0.30, C:0.13, G:0.15, T:0.42
Consensus pattern (34 bp):
TTGCTACTGTATTGATCTGTTACAAGCATATTAA
Found at i:128989009 original size:13 final size:14
Alignment explanation
Indices: 128988991--128989031 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 14
128988981 ATTCCAAATA
128988991 CAGATA-ACAGAAT
1 CAGATATACAGAAT
*
128989004 CAGATATGCAGAAT
1 CAGATATACAGAAT
*
128989018 -AGATATACTGAAT
1 CAGATATACAGAAT
128989031 C
1 C
128989032 TTACCTCCAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
13 17 0.74
14 6 0.26
ACGTcount: A:0.46, C:0.15, G:0.17, T:0.22
Consensus pattern (14 bp):
CAGATATACAGAAT
Found at i:128993533 original size:3 final size:3
Alignment explanation
Indices: 128993510--128993609 Score: 78
Period size: 3 Copynumber: 32.7 Consensus size: 3
128993500 GAAAGGAAAT
* * * * * *
128993510 ATA ATT ATA ATA GTG ATA ATA ATA AAA ATA ATA ACA ATA AT- ACA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* *
128993557 ATA ATA CATTA ATA ACA ACA ATA ATA AT- ATA CATTA ATA ATA ATA ATA
1 ATA ATA -A-TA ATA ATA ATA ATA ATA ATA ATA -A-TA ATA ATA ATA ATA
128993605 ATA AT
1 ATA AT
128993610 TAATTAATTA
Statistics
Matches: 77, Mismatches: 14, Indels: 12
0.75 0.14 0.12
Matches are distributed among these distances:
2 3 0.04
3 66 0.86
4 4 0.05
5 4 0.05
ACGTcount: A:0.61, C:0.06, G:0.02, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:128993574 original size:28 final size:26
Alignment explanation
Indices: 128993538--128993617 Score: 96
Period size: 25 Copynumber: 3.2 Consensus size: 26
128993528 ATAATAAAAA
128993538 TAATAACAATAATACAATAATAATACAT
1 TAATAACAATAATA-AATAAT-ATACAT
*
128993566 TAATAACAACAAT-AATAATATACAT
1 TAATAACAATAATAAATAATATACAT
*
128993591 TAATAATAATAAT-AATAAT-TA-AT
1 TAATAACAATAATAAATAATATACAT
128993614 TAAT
1 TAAT
128993618 TAATCTTACT
Statistics
Matches: 49, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
23 6 0.12
24 2 0.04
25 23 0.47
26 6 0.12
28 12 0.24
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (26 bp):
TAATAACAATAATAAATAATATACAT
Found at i:128993600 original size:19 final size:19
Alignment explanation
Indices: 128993510--128993613 Score: 81
Period size: 20 Copynumber: 5.5 Consensus size: 19
128993500 GAAAGGAAAT
* *
128993510 ATAATT-ATAATAGTGATA
1 ATAATTAATAATAATAATA
* *
128993528 ATAA-TAAAAATAATAACA
1 ATAATTAATAATAATAATA
*
128993546 ATAATACAATAATAATACATTA
1 ATAAT-TAATAATAATA-A-TA
* *
128993568 ATAA-CAACAATAATAAT-
1 ATAATTAATAATAATAATA
128993585 ATACATTAATAATAATAATA
1 ATA-ATTAATAATAATAATA
128993605 ATAATTAAT
1 ATAATTAAT
128993614 TAATTAATCT
Statistics
Matches: 68, Mismatches: 10, Indels: 15
0.73 0.11 0.16
Matches are distributed among these distances:
17 4 0.06
18 18 0.26
19 18 0.26
20 22 0.32
21 1 0.01
22 5 0.07
ACGTcount: A:0.61, C:0.06, G:0.02, T:0.32
Consensus pattern (19 bp):
ATAATTAATAATAATAATA
Found at i:128993601 original size:31 final size:29
Alignment explanation
Indices: 128993525--128993602 Score: 86
Period size: 31 Copynumber: 2.6 Consensus size: 29
128993515 TATAATAGTG
* *
128993525 ATAATAATAAAAATAATAACAATAATACA
1 ATAATAATAATAATAACAACAATAATACA
128993554 ATAATAATACATTAATAACAACAATAATA-A
1 ATAATAATA-A-TAATAACAACAATAATACA
128993584 TATACATTAATAATAATAA
1 -ATA-A-TAATAATAATAA
128993603 TAATAATTAA
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
29 9 0.21
30 2 0.05
31 24 0.57
32 2 0.05
33 5 0.12
ACGTcount: A:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (29 bp):
ATAATAATAATAATAACAACAATAATACA
Found at i:128994831 original size:28 final size:27
Alignment explanation
Indices: 128994790--128994863 Score: 75
Period size: 24 Copynumber: 2.8 Consensus size: 27
128994780 TCTGTCTTTG
* *
128994790 CTAT-TGTTTTTTTTTTTGTTTTTTGAA
1 CTATCTGTTTCTTTTTTT-TTTCTTGAA
128994817 CTATCTGTTTC---TTTTTTTCTTGAA
1 CTATCTGTTTCTTTTTTTTTTCTTGAA
128994841 CTATCTGTTTCTTTCTCTTTTTT
1 CTATCTGTTTCTTT-T-TTTTTT
128994864 TATTGATTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
24 19 0.49
25 4 0.10
27 4 0.10
28 6 0.15
29 6 0.15
ACGTcount: A:0.09, C:0.14, G:0.08, T:0.69
Consensus pattern (27 bp):
CTATCTGTTTCTTTTTTTTTTCTTGAA
Found at i:128994844 original size:24 final size:23
Alignment explanation
Indices: 128994808--128994854 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 23
128994798 TTTTTTTTTG
128994808 TTTTTTGAACTATCTGTTTCTTT
1 TTTTTTGAACTATCTGTTTCTTT
128994831 TTTTCTTGAACTATCTGTTTCTTT
1 TTTT-TTGAACTATCTGTTTCTTT
128994855 CTCTTTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 4 0.17
24 19 0.83
ACGTcount: A:0.13, C:0.15, G:0.09, T:0.64
Consensus pattern (23 bp):
TTTTTTGAACTATCTGTTTCTTT
Found at i:129004656 original size:60 final size:59
Alignment explanation
Indices: 129004543--129004659 Score: 148
Period size: 60 Copynumber: 1.9 Consensus size: 59
129004533 AACTAGGCTT
*
129004543 TAGCCCATATCAATATTAATCTAGGTCATAGCCCCTTACAGTATCAGAGTATATTGGGCC
1 TAGCCCATATCAATATTAATCTAGGTCATAGCCCATTACAG-ATCAGAGTATATTGGGCC
* * *
129004603 TAGCCCATATCAATATTAATCTGGGTCGTATCCCTATTACA-AGTC-GAGATATATTGG
1 TAGCCCATATCAATATTAATCTAGGTCATAGCCC-ATTACAGA-TCAGAG-TATATTGG
129004660 ACCTTTCCCA
Statistics
Matches: 50, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
59 4 0.08
60 41 0.82
61 5 0.10
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (59 bp):
TAGCCCATATCAATATTAATCTAGGTCATAGCCCATTACAGATCAGAGTATATTGGGCC
Found at i:129006157 original size:15 final size:16
Alignment explanation
Indices: 129006116--129006164 Score: 55
Period size: 16 Copynumber: 3.0 Consensus size: 16
129006106 GGTTATAGGG
129006116 GAAAAGAAGAAGAGAAA
1 GAAAAGAAGAAGA-AAA
* *
129006133 GTAGATGAAG-AGAAAA
1 G-AAAAGAAGAAGAAAA
129006149 GAAAAGAAGAAGAAAA
1 GAAAAGAAGAAGAAAA
129006165 AACTGAATCC
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
15 6 0.23
16 10 0.38
17 4 0.15
18 6 0.23
ACGTcount: A:0.67, C:0.00, G:0.29, T:0.04
Consensus pattern (16 bp):
GAAAAGAAGAAGAAAA
Found at i:129008229 original size:18 final size:18
Alignment explanation
Indices: 129008204--129008250 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 18
129008194 TATTAAAAAA
129008204 TAATTAAAATAATATT-T
1 TAATTAAAATAATATTAT
129008221 TATATT-AAATAAATATTAT
1 TA-ATTAAAAT-AATATTAT
*
129008240 TAATGAAAATA
1 TAATTAAAATA
129008251 TTGCTAACAT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
17 6 0.24
18 12 0.48
19 7 0.28
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (18 bp):
TAATTAAAATAATATTAT
Found at i:129030187 original size:2 final size:2
Alignment explanation
Indices: 129030180--129030233 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
129030170 AACAGTGACA
129030180 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
129030222 GT GT GT GT GT GT
1 GT GT GT GT GT GT
129030234 AAAGACAAAG
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:129035139 original size:26 final size:27
Alignment explanation
Indices: 129035091--129035150 Score: 88
Period size: 26 Copynumber: 2.3 Consensus size: 27
129035081 TTTATTTTTC
*
129035091 TTTTTAATTTTTATGAATTTTTTAT-A
1 TTTTTAATTTTTATGAATGTTTTATAA
129035117 TTATTTAATTTTT-TGAATGTTTTATAA
1 TT-TTTAATTTTTATGAATGTTTTATAA
129035144 TTTTTAA
1 TTTTTAA
129035151 ATGGGTTAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
26 18 0.58
27 13 0.42
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (27 bp):
TTTTTAATTTTTATGAATGTTTTATAA
Found at i:129035149 original size:9 final size:8
Alignment explanation
Indices: 129035091--129035148 Score: 53
Period size: 9 Copynumber: 6.5 Consensus size: 8
129035081 TTTATTTTTC
129035091 TTTTTAAT
1 TTTTTAAT
129035099 TTTTATGAAT
1 TTTT-T-AAT
129035109 TTTTTATAT
1 TTTTTA-AT
*
129035118 TATTTAAT
1 TTTTTAAT
129035126 TTTTTGAAT
1 TTTTT-AAT
129035135 GTTTTATAAT
1 -TTTT-TAAT
129035145 TTTT
1 TTTT
129035149 AAATGGGTTA
Statistics
Matches: 42, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
8 11 0.26
9 16 0.38
10 14 0.33
11 1 0.02
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.69
Consensus pattern (8 bp):
TTTTTAAT
Found at i:129039720 original size:21 final size:20
Alignment explanation
Indices: 129039690--129039728 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
129039680 AAATACTAAA
129039690 AAATTTATTA-AGAAAATAAT
1 AAATTTATTATA-AAAATAAT
129039710 AAATATTATTATAAAAATA
1 AAAT-TTATTATAAAAATA
129039729 TTTTTTTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 4 0.24
21 12 0.71
22 1 0.06
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (20 bp):
AAATTTATTATAAAAATAAT
Found at i:129045377 original size:11 final size:11
Alignment explanation
Indices: 129045363--129045396 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
129045353 ATATCTAAAT
*
129045363 AATAATAACAA
1 AATAATAGCAA
129045374 AATAATAGCAA
1 AATAATAGCAA
*
129045385 TATAATAGCAA
1 AATAATAGCAA
129045396 A
1 A
129045397 TTAGTAGTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.65, C:0.09, G:0.06, T:0.21
Consensus pattern (11 bp):
AATAATAGCAA
Found at i:129046919 original size:22 final size:21
Alignment explanation
Indices: 129046885--129046925 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
129046875 TATTAAGTTT
* *
129046885 TTAATTGAGTTTATGTTATAAG
1 TTAAGTGACTTTAT-TTATAAG
129046907 TTAAGTGACTTTATTTATA
1 TTAAGTGACTTTATTTATA
129046926 TTTTGAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.32, C:0.02, G:0.15, T:0.51
Consensus pattern (21 bp):
TTAAGTGACTTTATTTATAAG
Found at i:129047062 original size:18 final size:16
Alignment explanation
Indices: 129047020--129047070 Score: 57
Period size: 18 Copynumber: 3.0 Consensus size: 16
129047010 TTGAGATTTG
129047020 AGATTTTATAATTTTCT
1 AGATTTTATAATTTT-T
* *
129047037 AAAATTTAATATATTTTT
1 -AGATTTTATA-ATTTTT
129047055 AGATTTTATAATTTTT
1 AGATTTTATAATTTTT
129047071 TGTAATTTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
16 6 0.21
17 8 0.29
18 9 0.32
19 5 0.18
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.59
Consensus pattern (16 bp):
AGATTTTATAATTTTT
Found at i:129047071 original size:18 final size:18
Alignment explanation
Indices: 129047020--129047071 Score: 54
Period size: 17 Copynumber: 2.9 Consensus size: 18
129047010 TTGAGATTTG
*
129047020 AGATTTTATAATTTTCTA
1 AGATTTTATAATTTTTTA
* *
129047038 AAATTTAAT-ATATTTTT-
1 AGATTTTATAAT-TTTTTA
129047055 AGATTTTATAATTTTTT
1 AGATTTTATAATTTTTT
129047072 GTAATTTTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 5
0.73 0.14 0.14
Matches are distributed among these distances:
17 14 0.52
18 13 0.48
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.60
Consensus pattern (18 bp):
AGATTTTATAATTTTTTA
Found at i:129054762 original size:2 final size:2
Alignment explanation
Indices: 129054757--129054812 Score: 103
Period size: 2 Copynumber: 28.0 Consensus size: 2
129054747 TATATATCAT
*
129054757 CA CA CA CA CA CA CA CA CA AA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
129054799 CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA
129054813 TATATATATA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:129054817 original size:2 final size:2
Alignment explanation
Indices: 129054812--129054870 Score: 109
Period size: 2 Copynumber: 29.5 Consensus size: 2
129054802 ACACACACAC
129054812 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
129054854 AT AT AT AT AT TT AT AT A
1 AT AT AT AT AT AT AT AT A
129054871 CCATCACATT
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:129057616 original size:3 final size:3
Alignment explanation
Indices: 129057608--129057652 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
129057598 ATTGTTTGAT
129057608 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
129057653 CTTTCTCTGT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
TCA
Found at i:129059136 original size:72 final size:72
Alignment explanation
Indices: 129059022--129059201 Score: 258
Period size: 72 Copynumber: 2.5 Consensus size: 72
129059012 AACAAATTTT
* * *
129059022 ATATCC-AAAATCAAACATAAACCACTATTGATAAAACTAGATTACA-AATAAA-AATGTATAAC
1 ATATCCAAAAATCAAACATAAACAACTATTGATAAAACAAGATTACACAA-AAATAA-GTAGAAC
129059084 ATAAATTCA
64 ATAAATTCA
*
129059093 ATATCCAAAAACCAAACATAAACAACTATTGATAAAACAAGATTACACAAAAATAAGTAGAACAT
1 ATATCCAAAAATCAAACATAAACAACTATTGATAAAACAAGATTACACAAAAATAAGTAGAACAT
**
129059158 AAATTTG
66 AAATTCA
*
129059165 ATATCCAAAAATCAAATATAAACAACTATTGATAAAA
1 ATATCCAAAAATCAAACATAAACAACTATTGATAAAA
129059202 ACTAGTTTAG
Statistics
Matches: 98, Mismatches: 8, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
71 6 0.06
72 88 0.90
73 4 0.04
ACGTcount: A:0.57, C:0.15, G:0.05, T:0.23
Consensus pattern (72 bp):
ATATCCAAAAATCAAACATAAACAACTATTGATAAAACAAGATTACACAAAAATAAGTAGAACAT
AAATTCA
Found at i:129070992 original size:20 final size:21
Alignment explanation
Indices: 129070950--129070994 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 21
129070940 GTTAAAATTC
*
129070950 TTAAAAGATTTAAAAGATTCT
1 TTAAAAGATTTAAAAGATCCT
**
129070971 TTAAAAGA-TTACGAGATCCT
1 TTAAAAGATTTAAAAGATCCT
129070991 TTAA
1 TTAA
129070995 TATTACAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 13 0.62
21 8 0.38
ACGTcount: A:0.44, C:0.09, G:0.11, T:0.36
Consensus pattern (21 bp):
TTAAAAGATTTAAAAGATCCT
Found at i:129071464 original size:18 final size:20
Alignment explanation
Indices: 129071427--129071466 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
129071417 GGGAATAAAG
*
129071427 TATACATAATAAAATTAAAA
1 TATACATAATAAAATCAAAA
129071447 TATACA-AAT-AAATCAAAA
1 TATACATAATAAAATCAAAA
129071465 TA
1 TA
129071467 AAACTTTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 10 0.53
19 3 0.16
20 6 0.32
ACGTcount: A:0.65, C:0.07, G:0.00, T:0.28
Consensus pattern (20 bp):
TATACATAATAAAATCAAAA
Found at i:129073925 original size:15 final size:15
Alignment explanation
Indices: 129073860--129073932 Score: 68
Period size: 15 Copynumber: 5.3 Consensus size: 15
129073850 AGACAACGCC
*
129073860 CAGCAGCAACAGCAG
1 CAGCAGCAACAACAG
*
129073875 CAGCAGCCAC-A-AG
1 CAGCAGCAACAACAG
129073888 -AGCAGCAACAACA-
1 CAGCAGCAACAACAG
129073901 -AG-AGCAACAACAG
1 CAGCAGCAACAACAG
* *
129073914 CAGCAGCCACAACCG
1 CAGCAGCAACAACAG
129073929 CAGC
1 CAGC
129073933 TGCCGCGAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
12 18 0.38
13 5 0.10
14 3 0.06
15 22 0.46
ACGTcount: A:0.42, C:0.36, G:0.22, T:0.00
Consensus pattern (15 bp):
CAGCAGCAACAACAG
Found at i:129073995 original size:18 final size:18
Alignment explanation
Indices: 129073961--129073999 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
129073951 AACTGGTCAA
*
129073961 GGTTAAGAAAGTAGTGGT
1 GGTTAAGAAAGAAGTGGT
129073979 GGTTAAG-AAGAAGGTGGT
1 GGTTAAGAAAGAA-GTGGT
129073997 GGT
1 GGT
129074000 GGGAGCAGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.31, C:0.00, G:0.44, T:0.26
Consensus pattern (18 bp):
GGTTAAGAAAGAAGTGGT
Found at i:129088422 original size:178 final size:178
Alignment explanation
Indices: 129088123--129088477 Score: 649
Period size: 178 Copynumber: 2.0 Consensus size: 178
129088113 CCTTTTTTTC
* *
129088123 TTTTTCAATCTTTTAACTTTGTTTATTTGCTCCAATTTTACTGTTGGGTGCATCCTGCTTAACGT
1 TTTTTCAATCTTTTAACGTTGTTTATTTGCTCCAATTTTACTGTTGGGTGCATCCTGCGTAACGT
129088188 GAAAACATGACATTTTTGTACCCCAAAAAAGCATGACACATTTCTGGTTCAAACCGAGATTGATA
66 GAAAACATGACATTTTTGTACCCCAAAAAAGCATGACACATTTCTGGTTCAAACCGAGATTGATA
* *
129088253 TAGCTATGTCCCCTGATTTACCACTTTGTGCATCAGTGACAGTGACTT
131 TAGCTATGTCCCCCGATTTACCACTCTGTGCATCAGTGACAGTGACTT
*
129088301 TTTTTCAATCTTTTAACGTTGTTTATTTGCT-CATTTTTACTGTTGGGTGCATCCTGCGTAACGT
1 TTTTTCAATCTTTTAACGTTGTTTATTTGCTCCAATTTTACTGTTGGGTGCATCCTGCGTAACGT
129088365 GAAAACATGACATTTTTGTACCCCAAAAAAAGCATGACACATTTCTGGTTCAAACCGAGATTGAT
66 GAAAACATGACATTTTTGTACCCC-AAAAAAGCATGACACATTTCTGGTTCAAACCGAGATTGAT
129088430 ATAGCTATGTCCCCCGATTTACCACTCTGTGCATCAGTGACAGTGACT
130 ATAGCTATGTCCCCCGATTTACCACTCTGTGCATCAGTGACAGTGACT
129088478 GGATGAAAAG
Statistics
Matches: 171, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
177 55 0.32
178 116 0.68
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.37
Consensus pattern (178 bp):
TTTTTCAATCTTTTAACGTTGTTTATTTGCTCCAATTTTACTGTTGGGTGCATCCTGCGTAACGT
GAAAACATGACATTTTTGTACCCCAAAAAAGCATGACACATTTCTGGTTCAAACCGAGATTGATA
TAGCTATGTCCCCCGATTTACCACTCTGTGCATCAGTGACAGTGACTT
Found at i:129092908 original size:16 final size:16
Alignment explanation
Indices: 129092886--129092956 Score: 88
Period size: 16 Copynumber: 4.4 Consensus size: 16
129092876 GTTTGATTCG
*
129092886 CTGTAATAGAATAGAA
1 CTGTAATGGAATAGAA
* *
129092902 TTGTAATGGAATAGAG
1 CTGTAATGGAATAGAA
* *
129092918 TTGTAATGGAATAGAG
1 CTGTAATGGAATAGAA
*
129092934 CTGTAATGGAATAAAA
1 CTGTAATGGAATAGAA
129092950 CTGTAAT
1 CTGTAAT
129092957 TAGTAATTTA
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 49 1.00
ACGTcount: A:0.42, C:0.04, G:0.24, T:0.30
Consensus pattern (16 bp):
CTGTAATGGAATAGAA
Found at i:129102841 original size:12 final size:12
Alignment explanation
Indices: 129102824--129102848 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
129102814 TTTGTAAAGA
129102824 TAATGCATAAAT
1 TAATGCATAAAT
129102836 TAATGCATAAAT
1 TAATGCATAAAT
129102848 T
1 T
129102849 TGGTACCTGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.08, G:0.08, T:0.36
Consensus pattern (12 bp):
TAATGCATAAAT
Found at i:129106996 original size:29 final size:29
Alignment explanation
Indices: 129106964--129107028 Score: 112
Period size: 29 Copynumber: 2.2 Consensus size: 29
129106954 ATATTTTTCT
*
129106964 TCACTTATATTTAAAATGTTACGTTTTAG
1 TCACTTATATTTAAAATATTACGTTTTAG
*
129106993 TCACTTATGTTTAAAATATTACGTTTTAG
1 TCACTTATATTTAAAATATTACGTTTTAG
129107022 TCACTTA
1 TCACTTA
129107029 CGTTATCATT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.31, C:0.12, G:0.09, T:0.48
Consensus pattern (29 bp):
TCACTTATATTTAAAATATTACGTTTTAG
Found at i:129107029 original size:15 final size:15
Alignment explanation
Indices: 129106982--129107032 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
129106972 ATTTAAAATG
129106982 TTACGTTTTAGTCAC
1 TTACGTTTTAGTCAC
* * *
129106997 TTATGTTTAAAAT-A-
1 TTACGTTT-TAGTCAC
129107011 TTACGTTTTAGTCAC
1 TTACGTTTTAGTCAC
129107026 TTACGTT
1 TTACGTT
129107033 ATCATTTTGT
Statistics
Matches: 27, Mismatches: 6, Indels: 6
0.69 0.15 0.15
Matches are distributed among these distances:
13 2 0.07
14 8 0.30
15 15 0.56
16 2 0.07
ACGTcount: A:0.25, C:0.14, G:0.12, T:0.49
Consensus pattern (15 bp):
TTACGTTTTAGTCAC
Found at i:129107480 original size:27 final size:28
Alignment explanation
Indices: 129107448--129107501 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
129107438 TAACAAGTTC
*
129107448 AATTAATTAGTT-TGAGTTATCAAATTT
1 AATTAATTAATTATGAGTTATCAAATTT
*
129107475 AATTAATTAATTATGAGTTATGAAATT
1 AATTAATTAATTATGAGTTATCAAATT
129107502 CAAGTAACCA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 11 0.46
28 13 0.54
ACGTcount: A:0.41, C:0.02, G:0.11, T:0.46
Consensus pattern (28 bp):
AATTAATTAATTATGAGTTATCAAATTT
Found at i:129108220 original size:19 final size:19
Alignment explanation
Indices: 129108196--129108243 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 19
129108186 TATCATGTTA
129108196 TATTTTTCTA-TTTTTCTAT
1 TATTTTT-TATTTTTTCTAT
129108215 TATTTTTTATTTTTTCTAT
1 TATTTTTTATTTTTTCTAT
129108234 T-TTATTTTAT
1 TATT-TTTTAT
129108244 GTCATGTTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
18 4 0.15
19 23 0.85
ACGTcount: A:0.17, C:0.06, G:0.00, T:0.77
Consensus pattern (19 bp):
TATTTTTTATTTTTTCTAT
Found at i:129113731 original size:2 final size:2
Alignment explanation
Indices: 129113724--129113756 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
129113714 GGGCGTTACA
129113724 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
129113757 GCATTATAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:129116260 original size:20 final size:20
Alignment explanation
Indices: 129116235--129116300 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 20
129116225 ACGAGCTTCC
129116235 GTTAACTCATATGAGTTTCA
1 GTTAACTCATATGAGTTTCA
* *
129116255 GTTAAC-CATTTTGGGGTTTCA
1 GTTAACTCA-TAT-GAGTTTCA
*
129116276 GTTCAACTC-TGATGAGCTTCA
1 GTT-AACTCAT-ATGAGTTTCA
129116297 GTTA
1 GTTA
129116301 GCCTTCAGGA
Statistics
Matches: 36, Mismatches: 5, Indels: 10
0.71 0.10 0.20
Matches are distributed among these distances:
19 2 0.06
20 9 0.25
21 20 0.56
22 4 0.11
23 1 0.03
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (20 bp):
GTTAACTCATATGAGTTTCA
Found at i:129116390 original size:39 final size:39
Alignment explanation
Indices: 129116291--129116391 Score: 139
Period size: 39 Copynumber: 2.6 Consensus size: 39
129116281 ACTCTGATGA
* * *
129116291 GCTTCAGTTAGCCTTCAGGATTCTGTTTAACACTTGTGT
1 GCTTCAGTTAGCCTTCAGGCTTCCGTTTAACACTTATGT
*
129116330 GCTTCAGTTAGCCTTCAGGCTTCCGTTTAGCACTTATGT
1 GCTTCAGTTAGCCTTCAGGCTTCCGTTTAACACTTATGT
* * *
129116369 GCTTCAGCTAGACTTCGGGCTTC
1 GCTTCAGTTAGCCTTCAGGCTTC
129116392 AGATCACGAT
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 55 1.00
ACGTcount: A:0.16, C:0.25, G:0.22, T:0.38
Consensus pattern (39 bp):
GCTTCAGTTAGCCTTCAGGCTTCCGTTTAACACTTATGT
Found at i:129117093 original size:13 final size:12
Alignment explanation
Indices: 129117075--129117116 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 12
129117065 GAGTTTTTTT
129117075 AAAATAATAATAA
1 AAAATAA-AATAA
129117088 AAAAT-AAATAAA
1 AAAATAAAAT-AA
129117100 AAAATAAAAATAA
1 AAAAT-AAAATAA
129117113 AAAA
1 AAAA
129117117 ATAACTATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
11 3 0.12
12 8 0.31
13 11 0.42
14 4 0.15
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (12 bp):
AAAATAAAATAA
Found at i:129117118 original size:14 final size:14
Alignment explanation
Indices: 129117075--129117120 Score: 62
Period size: 14 Copynumber: 3.5 Consensus size: 14
129117065 GAGTTTTTTT
*
129117075 AAAATAATAAT-AA
1 AAAATAAAAATAAA
129117088 AAAAT--AAATAAA
1 AAAATAAAAATAAA
129117100 AAAATAAAAATAAA
1 AAAATAAAAATAAA
129117114 AAAATAA
1 AAAATAA
129117121 CTATATTATG
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
11 3 0.10
12 7 0.24
13 5 0.17
14 14 0.48
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (14 bp):
AAAATAAAAATAAA
Found at i:129122506 original size:3 final size:3
Alignment explanation
Indices: 129122498--129122529 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
129122488 TCTAAAATTT
129122498 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
129122530 TTTTTCTCTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:129123312 original size:21 final size:21
Alignment explanation
Indices: 129123286--129123329 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
129123276 CAGAAAAAAG
129123286 TTATGTACTAAAATTTGATCA
1 TTATGTACTAAAATTTGATCA
129123307 TTATGTACTAAAATTTGATCA
1 TTATGTACTAAAATTTGATCA
129123328 TT
1 TT
129123330 CTGCATAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.36, C:0.09, G:0.09, T:0.45
Consensus pattern (21 bp):
TTATGTACTAAAATTTGATCA
Found at i:129123340 original size:21 final size:21
Alignment explanation
Indices: 129123286--129123339 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
129123276 CAGAAAAAAG
*
129123286 TTATGTACTAAAATTTGATCA
1 TTATGCACTAAAATTTGATCA
*
129123307 TTATGTACTAAAATTTGATCA
1 TTATGCACTAAAATTTGATCA
*
129123328 TTCTGCA-TAAAA
1 TTATGCACTAAAA
129123340 AATAATAGGT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 5 0.16
21 26 0.84
ACGTcount: A:0.39, C:0.11, G:0.09, T:0.41
Consensus pattern (21 bp):
TTATGCACTAAAATTTGATCA
Found at i:129124160 original size:4 final size:4
Alignment explanation
Indices: 129124153--129124199 Score: 85
Period size: 4 Copynumber: 11.8 Consensus size: 4
129124143 CCCTTCGTAC
*
129124153 GTAT GTAT GTAT GTAT GTAT GTAT GGAT GTAT GTAT GTAT GTAT GTA
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTA
129124200 CATGTGTGTG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 41 1.00
ACGTcount: A:0.26, C:0.00, G:0.28, T:0.47
Consensus pattern (4 bp):
GTAT
Found at i:129131161 original size:20 final size:20
Alignment explanation
Indices: 129131119--129131161 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
129131109 AAAAAAAAAA
* *
129131119 AACATCATATAAAATTACAC
1 AACATAATATAAAATAACAC
129131139 AACATAATA-AAAATAACATC
1 AACATAATATAAAATAACA-C
129131159 AAC
1 AAC
129131162 GAACCCATGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.60, C:0.19, G:0.00, T:0.21
Consensus pattern (20 bp):
AACATAATATAAAATAACAC
Found at i:129131638 original size:22 final size:21
Alignment explanation
Indices: 129131613--129131665 Score: 61
Period size: 23 Copynumber: 2.4 Consensus size: 21
129131603 AATTTTATTT
*
129131613 TTTATAAAGTTTATAATTTAAA
1 TTTATAAAATTTATAATTT-AA
*
129131635 TTTAGTAAAATTTTTAATTTAA
1 TTTA-TAAAATTTATAATTTAA
129131657 TTTAATAAA
1 TTT-ATAAA
129131666 TTAATACAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 13 0.48
23 14 0.52
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (21 bp):
TTTATAAAATTTATAATTTAA
Found at i:129133108 original size:25 final size:25
Alignment explanation
Indices: 129133080--129133165 Score: 81
Period size: 25 Copynumber: 3.5 Consensus size: 25
129133070 ATATTGATAA
* *
129133080 ATATTAATGAAAAGAAACGCAAAGC
1 ATATAAATTAAAAGAAACGCAAAGC
**
129133105 ATATAAATTAAAA-ATATTG-ATAA--
1 ATATAAATTAAAAGA-AACGCA-AAGC
*
129133128 ATATTAATTAAAAGAAACGCAAAGC
1 ATATAAATTAAAAGAAACGCAAAGC
129133153 ATATAAATTAAAA
1 ATATAAATTAAAA
129133166 AGCCATTATC
Statistics
Matches: 47, Mismatches: 8, Indels: 12
0.70 0.12 0.18
Matches are distributed among these distances:
23 16 0.34
24 4 0.09
25 27 0.57
ACGTcount: A:0.59, C:0.07, G:0.09, T:0.24
Consensus pattern (25 bp):
ATATAAATTAAAAGAAACGCAAAGC
Found at i:129133134 original size:48 final size:48
Alignment explanation
Indices: 129133058--129133166 Score: 200
Period size: 48 Copynumber: 2.3 Consensus size: 48
129133048 TTGGGTGTTT
*
129133058 TATAGATTAAAAATATTGATAAATATTAATGAAAAGAAACGCAAAGCA
1 TATAAATTAAAAATATTGATAAATATTAATGAAAAGAAACGCAAAGCA
*
129133106 TATAAATTAAAAATATTGATAAATATTAATTAAAAGAAACGCAAAGCA
1 TATAAATTAAAAATATTGATAAATATTAATGAAAAGAAACGCAAAGCA
129133154 TATAAATTAAAAA
1 TATAAATTAAAAA
129133167 GCCATTATCC
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
48 59 1.00
ACGTcount: A:0.59, C:0.06, G:0.09, T:0.27
Consensus pattern (48 bp):
TATAAATTAAAAATATTGATAAATATTAATGAAAAGAAACGCAAAGCA
Found at i:129133136 original size:23 final size:23
Alignment explanation
Indices: 129133063--129133140 Score: 70
Period size: 23 Copynumber: 3.3 Consensus size: 23
129133053 TGTTTTATAG
129133063 ATTAAAAATATTGATAAATATTA
1 ATTAAAAATATTGATAAATATTA
* ** *
129133086 ATGAAAAGA-AACGCA-AAGCATATAA
1 ATTAAAA-ATATTG-ATAA--ATATTA
129133111 ATTAAAAATATTGATAAATATTA
1 ATTAAAAATATTGATAAATATTA
129133134 ATTAAAA
1 ATTAAAA
129133141 GAAACGCAAA
Statistics
Matches: 41, Mismatches: 8, Indels: 12
0.67 0.13 0.20
Matches are distributed among these distances:
23 22 0.54
24 4 0.10
25 15 0.37
ACGTcount: A:0.59, C:0.04, G:0.08, T:0.29
Consensus pattern (23 bp):
ATTAAAAATATTGATAAATATTA
Found at i:129134499 original size:45 final size:45
Alignment explanation
Indices: 129134260--129134519 Score: 265
Period size: 45 Copynumber: 5.8 Consensus size: 45
129134250 AACAATTAGG
* * * *
129134260 ATATACATATAGGAGGTACTATGTATCAGTGTTGGCTATCATGTC
1 ATATACATACAGCAGGTACTATGTATCGGTGTTGGCTATCATGCC
* * * * *
129134305 ATATACATATAGTAGGTACTACGTATCGATGTCGGCTATCATGCC
1 ATATACATACAGCAGGTACTATGTATCGGTGTTGGCTATCATGCC
* * * * *
129134350 ATATACATACAGCAAGTACTATGTATCGGTATCGACTTTCATGCC
1 ATATACATACAGCAGGTACTATGTATCGGTGTTGGCTATCATGCC
* * * *
129134395 ATATAAATACAGCAGGTACTATATATCAGTGTTGGCTATCATACC
1 ATATACATACAGCAGGTACTATGTATCGGTGTTGGCTATCATGCC
* * * *
129134440 ATATACATACAACAGGTATTATGTATCGGTGTTGGCTTTTATGCC
1 ATATACATACAGCAGGTACTATGTATCGGTGTTGGCTATCATGCC
*
129134485 ATATAAGCATA-A-CAGGTAATATGTA-CGGGTGTTGG
1 ATAT-A-CATACAGCAGGTACTATGTATC-GGTGTTGG
129134520 TTATTTTGCC
Statistics
Matches: 180, Mismatches: 32, Indels: 6
0.83 0.15 0.03
Matches are distributed among these distances:
44 1 0.01
45 173 0.96
46 2 0.01
47 4 0.02
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.33
Consensus pattern (45 bp):
ATATACATACAGCAGGTACTATGTATCGGTGTTGGCTATCATGCC
Found at i:129136963 original size:46 final size:44
Alignment explanation
Indices: 129136859--129136966 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
129136849 TGTCTTTGAC
** * * *
129136859 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
129136903 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
129136949 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
129136967 TTTCGTTCTG
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Done.