Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13
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: 46006518
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2011935 characters in sequence are not A, C, G, or T
File 132 of 141
Found at i:42484846 original size:2 final size:2
Alignment explanation
Indices: 42484839--42484866 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
42484829 TCCTCAGGTA
42484839 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
42484867 ACACTCACCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:42487123 original size:21 final size:20
Alignment explanation
Indices: 42487093--42487132 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
42487083 TGTACGGTTC
42487093 AAAAAATCTAAAATCTAAAAG
1 AAAAAATCTAAAAT-TAAAAG
* *
42487114 AAAAATTCTAATATTAAAA
1 AAAAAATCTAAAATTAAAA
42487133 TGTGAGGTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.65, C:0.07, G:0.03, T:0.25
Consensus pattern (20 bp):
AAAAAATCTAAAATTAAAAG
Found at i:42493152 original size:7 final size:7
Alignment explanation
Indices: 42493140--42493169 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
42493130 TCTTCACACC
42493140 TTCAGCT
1 TTCAGCT
42493147 TTCAGCT
1 TTCAGCT
42493154 TTCAGCT
1 TTCAGCT
42493161 TTCAGCT
1 TTCAGCT
42493168 TT
1 TT
42493170 TGAAGTGGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.13, C:0.27, G:0.13, T:0.47
Consensus pattern (7 bp):
TTCAGCT
Found at i:42494604 original size:3 final size:3
Alignment explanation
Indices: 42494596--42494633 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
42494586 AAAAACAAAA
42494596 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
42494634 ATTGATCAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:42494759 original size:77 final size:78
Alignment explanation
Indices: 42494631--42494786 Score: 305
Period size: 77 Copynumber: 2.0 Consensus size: 78
42494621 ATTATTATTA
42494631 TTAATTGATCAATTATAACATCATATCTCATCACCGACAACCATCTTTTTCCTTTGTTTAGAATT
1 TTAATTGATCAATTATAACATCATATCTCATCACCGACAACCATCTTTTTCCTTTGTTTAGAATT
42494696 TCATAATAAGCTT
66 TCATAATAAGCTT
42494709 TTAATTGATC-ATTATAACATCATATCTCATCACCGACAACCATCTTTTTCCTTTGTTTAGAATT
1 TTAATTGATCAATTATAACATCATATCTCATCACCGACAACCATCTTTTTCCTTTGTTTAGAATT
42494773 TCATAATAAGCTT
66 TCATAATAAGCTT
42494786 T
1 T
42494787 ACCTTATACG
Statistics
Matches: 78, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
77 68 0.87
78 10 0.13
ACGTcount: A:0.31, C:0.21, G:0.06, T:0.42
Consensus pattern (78 bp):
TTAATTGATCAATTATAACATCATATCTCATCACCGACAACCATCTTTTTCCTTTGTTTAGAATT
TCATAATAAGCTT
Found at i:42500083 original size:24 final size:24
Alignment explanation
Indices: 42500055--42500103 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
42500045 AACTTTGTAT
*
42500055 TAATTTTTCTCTCTTTTATTTTTC
1 TAATTTTTCTCTCTTTCATTTTTC
42500079 TAATTTTTCTCTCTTTCATTTTTC
1 TAATTTTTCTCTCTTTCATTTTTC
42500103 T
1 T
42500104 TCATATAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.12, C:0.18, G:0.00, T:0.69
Consensus pattern (24 bp):
TAATTTTTCTCTCTTTCATTTTTC
Found at i:42504694 original size:87 final size:89
Alignment explanation
Indices: 42504532--42504694 Score: 222
Period size: 87 Copynumber: 1.9 Consensus size: 89
42504522 ATTTTTAGGA
* * * * * *
42504532 GAGTTAAAAGTATAATTTTACTATATTTTAATTTATAATTTTTTTTATTTAGGAGAGGACTGAAT
1 GAGTTAAAAGTATAATTTTACGATATATTAATTTATAAGTTTCTCTATTTAGAAGAGGACTGAAT
* *
42504597 TGATATTTTTTTTTTGTTTTTGAG
66 TGAAAGTTTTTTTTTGTTTTTGAG
* *
42504621 GAGTTAAAA-TGTAATTTTACGATATATTAATTTAT-AGTTTCTCTATTTATAAGAGGACTGAAT
1 GAGTTAAAAGTATAATTTTACGATATATTAATTTATAAGTTTCTCTATTTAGAAGAGGACTGAAT
42504684 TGAAAGTTTTT
66 TGAAAGTTTTT
42504695 CATCTTGGTC
Statistics
Matches: 64, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
87 32 0.50
88 23 0.36
89 9 0.14
ACGTcount: A:0.32, C:0.04, G:0.15, T:0.50
Consensus pattern (89 bp):
GAGTTAAAAGTATAATTTTACGATATATTAATTTATAAGTTTCTCTATTTAGAAGAGGACTGAAT
TGAAAGTTTTTTTTTGTTTTTGAG
Found at i:42511456 original size:18 final size:17
Alignment explanation
Indices: 42511430--42511463 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
42511420 CATTTTGTTG
42511430 TCATCATATATTATAAGT
1 TCATCATATA-TATAAGT
*
42511448 TCATTATATATATAAG
1 TCATCATATATATAAG
42511464 GTGTTCCGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.41, C:0.09, G:0.06, T:0.44
Consensus pattern (17 bp):
TCATCATATATATAAGT
Found at i:42512398 original size:14 final size:14
Alignment explanation
Indices: 42512379--42512406 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
42512369 CTATTAATAC
42512379 TGTTAAATTTATTT
1 TGTTAAATTTATTT
42512393 TGTTAAATTTATTT
1 TGTTAAATTTATTT
42512407 CATACCAACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.00, G:0.07, T:0.64
Consensus pattern (14 bp):
TGTTAAATTTATTT
Found at i:42516500 original size:31 final size:31
Alignment explanation
Indices: 42516456--42516514 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
42516446 TTAGTCCTAT
*
42516456 TTTTTCATATTAGTCCCTAAATTTGATATCC
1 TTTTTCATATTAGTCCCTAAACTTGATATCC
42516487 TTTTTCA-ATTTAGTCCCTAAACTTGATA
1 TTTTTCATA-TTAGTCCCTAAACTTGATA
42516515 ACATGGCATT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 1 0.04
31 25 0.96
ACGTcount: A:0.27, C:0.19, G:0.07, T:0.47
Consensus pattern (31 bp):
TTTTTCATATTAGTCCCTAAACTTGATATCC
Found at i:42519839 original size:13 final size:13
Alignment explanation
Indices: 42519821--42519847 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
42519811 TAGTAGGGGA
42519821 TAATTTGTTTAAT
1 TAATTTGTTTAAT
42519834 TAATTTGTTTAAT
1 TAATTTGTTTAAT
42519847 T
1 T
42519848 TTGAAATTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (13 bp):
TAATTTGTTTAAT
Found at i:42526295 original size:131 final size:133
Alignment explanation
Indices: 42526105--42526368 Score: 496
Period size: 131 Copynumber: 2.0 Consensus size: 133
42526095 ATTATATTTC
42526105 CAAATGCTAAATATCAAACACATGGGCCCTACATTTTCCCGCCTCTTTTCTAATCAACTTATTGG
1 CAAATGCTAAATATCAAACACATGGGCCCTACATTTTCCCGCCTCTTTTCTAATCAACTTATTGG
42526170 CTGGTGGGTTTGTTGGTTGAATATATTTTTCCAATTATTTTAGTCGCTATTACTTAATTCAATTT
66 CTGGTGGGTTTGTTGGTTGAATATATTTTTCCAATTATTTTAGTCGCTATTACTTAATTCAATTT
42526235 TAT
131 TAT
42526238 CAAATGCT-AA-ATCAAACACATGGGCCCTACATTTTCCCGCCTCTTTTCTAATCAACTTATTGG
1 CAAATGCTAAATATCAAACACATGGGCCCTACATTTTCCCGCCTCTTTTCTAATCAACTTATTGG
**
42526301 CTGGTGGGTTTGTTGGTTGAATATATTTTTTTAATTATTTTAGTCGCTATTACTTAATTCAATTT
66 CTGGTGGGTTTGTTGGTTGAATATATTTTTCCAATTATTTTAGTCGCTATTACTTAATTCAATTT
42526366 TAT
131 TAT
42526369 TTTTAAATAT
Statistics
Matches: 129, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
131 119 0.92
132 2 0.02
133 8 0.06
ACGTcount: A:0.25, C:0.18, G:0.14, T:0.43
Consensus pattern (133 bp):
CAAATGCTAAATATCAAACACATGGGCCCTACATTTTCCCGCCTCTTTTCTAATCAACTTATTGG
CTGGTGGGTTTGTTGGTTGAATATATTTTTCCAATTATTTTAGTCGCTATTACTTAATTCAATTT
TAT
Found at i:42528222 original size:125 final size:125
Alignment explanation
Indices: 42528000--42528881 Score: 1658
Period size: 125 Copynumber: 7.1 Consensus size: 125
42527990 TCTGATGTTT
* * * * * *
42528000 TGTGATGCTAACGAGTGTGCTCGATTTTTAATTTTCG-TCGTTCTTTTGTTTTTATGGAGTATTC
1 TGTGATGCTAAGGAGTGTGCTTGATTTCTAATTTTTGTTC-TTCTTTTGTTTTCATGGAGTATTT
* * * *
42528064 TTGCTACAATTTTTTGGAGTTTTTAGGTTGTCTATGTTAAGGTATGATCTTACATTTAAGG
65 TTGCTACAATGTTTCGGAGTTTCTAGGTTGTCTATGTTAAGGGATGATCTTACATTTAAGG
42528125 TGTGATGCTAAGGAGTGTGCTTGATTTCTAATTTTTGTTCTTCTTTTGTTTTCATGGAGTATTTT
1 TGTGATGCTAAGGAGTGTGCTTGATTTCTAATTTTTGTTCTTCTTTTGTTTTCATGGAGTATTTT
42528190 TGCTACAATGTTTCGGAGTTTCTAGGTTGTCTATGTTAAGGGATGATCTTACATTTAAGG
66 TGCTACAATGTTTCGGAGTTTCTAGGTTGTCTATGTTAAGGGATGATCTTACATTTAAGG
42528250 TGTGATGCTAAGGAGTGTGCTTGATTTCTAATTTTTGTTCTTCTTTTGTTTTCATGGAGTATTTT
1 TGTGATGCTAAGGAGTGTGCTTGATTTCTAATTTTTGTTCTTCTTTTGTTTTCATGGAGTATTTT
42528315 TGCTACAATGTTTCGGAGTTTCTAGGTTGTCTATGTTAAGGGATGATCTTACATTTAAGG
66 TGCTACAATGTTTCGGAGTTTCTAGGTTGTCTATGTTAAGGGATGATCTTACATTTAAGG
42528375 TGTGATGCTAAGGAGTGTGCTTGATTTCTAATTTTTGTTCTTCTTTTGTTTTCATGGAGTATTTT
1 TGTGATGCTAAGGAGTGTGCTTGATTTCTAATTTTTGTTCTTCTTTTGTTTTCATGGAGTATTTT
42528440 TGCTACAATGTTTCGGAGTTTCTAGGTTGTCTATGTTAAGGGATGATCTTACATTTAAGG
66 TGCTACAATGTTTCGGAGTTTCTAGGTTGTCTATGTTAAGGGATGATCTTACATTTAAGG
42528500 TGTGATGCTAAGGAGTGTGCTTGATTTCTAATTTTTGTTCTTCTTTTGTTTTCATGGAGTATTTT
1 TGTGATGCTAAGGAGTGTGCTTGATTTCTAATTTTTGTTCTTCTTTTGTTTTCATGGAGTATTTT
42528565 TGCTACAATGTTTCGGAGTTTCTAGGTTGTCTATGTTAAGGGATGATCTTACATTTAAGG
66 TGCTACAATGTTTCGGAGTTTCTAGGTTGTCTATGTTAAGGGATGATCTTACATTTAAGG
42528625 TGTGATGCTAAGGAGTGTGCTTGATTTCTAATTTTTGTTCTTCTTTTGTTTTCATGGAGTATTTT
1 TGTGATGCTAAGGAGTGTGCTTGATTTCTAATTTTTGTTCTTCTTTTGTTTTCATGGAGTATTTT
42528690 TGCTACAATGTTTCGGAGTTTCTAGGTTGTCTATGTTAAGGGATGATCTTACATTTAAGG
66 TGCTACAATGTTTCGGAGTTTCTAGGTTGTCTATGTTAAGGGATGATCTTACATTTAAGG
42528750 TGTGATGCTAAGGAGTGTGCTTGATTTCTAATTTTTGTTCTTCTTTTGTTTTCATGGAGTATTTT
1 TGTGATGCTAAGGAGTGTGCTTGATTTCTAATTTTTGTTCTTCTTTTGTTTTCATGGAGTATTTT
42528815 TGCTACAATGTTTCGGAGTTTCTAGGTTGTCTATGTTAAGGGATGATCTTACATTTAAGG
66 TGCTACAATGTTTCGGAGTTTCTAGGTTGTCTATGTTAAGGGATGATCTTACATTTAAGG
42528875 TGTGATG
1 TGTGATG
42528882 TATAATTTTT
Statistics
Matches: 746, Mismatches: 10, Indels: 2
0.98 0.01 0.00
Matches are distributed among these distances:
125 744 1.00
126 2 0.00
ACGTcount: A:0.19, C:0.10, G:0.23, T:0.47
Consensus pattern (125 bp):
TGTGATGCTAAGGAGTGTGCTTGATTTCTAATTTTTGTTCTTCTTTTGTTTTCATGGAGTATTTT
TGCTACAATGTTTCGGAGTTTCTAGGTTGTCTATGTTAAGGGATGATCTTACATTTAAGG
Found at i:42530726 original size:125 final size:124
Alignment explanation
Indices: 42530504--42530917 Score: 490
Period size: 125 Copynumber: 3.2 Consensus size: 124
42530494 TCTGATGTTT
* *
42530504 TGTGATGCTAACGAGTGTGCTCGATTTTTAATTTTCG-TCGTTCTTTTGTTTTTATGGAGTATTC
1 TGTGATGCTAAGGAGTGTGCTCGA-TTTTAATTTTTGTTC-TTCTTTTGTTTTTATGGAGTATTC
* * *
42530568 TTGCTACAATTTTTTGGAGTTTTTAGGTTGTCTATGTTAAGGTATGATCTTACATTTAAGG
64 TTGCTACAATGTTTCGGAGTTTCTAGGTTGTCTATGTTAAGGTATGATCTTACATTTAAGG
* * *
42530629 TGTGATGCTAAGGAGTGTGCTTGATTTCTAATTTTTGTTCTTCTTTTGTTTTCATGGAGTATTTT
1 TGTGATGCTAAGGAGTGTGCTCGATTT-TAATTTTTGTTCTTCTTTTGTTTTTATGGAGTATTCT
*
42530694 TGCTACAATGTTTCGGAGTTTCTAGGTTGTCTATGTTAAGGGATGATCTTACATTTAAGG
65 TGCTACAATGTTTCGGAGTTTCTAGGTTGTCTATGTTAAGGTATGATCTTACATTTAAGG
* ** * *
42530754 TGTGATGCTAAGGAGTGCT-CGTTGTTATTTTGTTTTTACTCTATTATTGAGCTTGGTTGTTTTT
1 TGTGATGCTAAGGAGTG-TGC-TCG--ATTTT-AATTT--T-TGTTCTT---CTT--TTGTTTTT
* * * * *
42530818 ACGGAGTATTCTTGCTATAATGTTTCGGAGTTTCTATGTTGTCTACGTTAAGGTATGATCTTGCA
53 ATGGAGTATTCTTGCTACAATGTTTCGGAGTTTCTAGGTTGTCTATGTTAAGGTATGATCTTACA
42530883 TTTAAGG
118 TTTAAGG
*
42530890 TGCGATGCTAAGGAGTGTGCTCGATTTT
1 TGTGATGCTAAGGAGTGTGCTCGATTTT
42530918 TTATTTTCGT
Statistics
Matches: 250, Mismatches: 23, Indels: 24
0.84 0.08 0.08
Matches are distributed among these distances:
124 3 0.01
125 127 0.51
126 6 0.02
127 1 0.00
128 7 0.03
130 1 0.00
131 5 0.02
133 5 0.02
134 3 0.01
135 3 0.01
136 89 0.36
ACGTcount: A:0.19, C:0.11, G:0.23, T:0.47
Consensus pattern (124 bp):
TGTGATGCTAAGGAGTGTGCTCGATTTTAATTTTTGTTCTTCTTTTGTTTTTATGGAGTATTCTT
GCTACAATGTTTCGGAGTTTCTAGGTTGTCTATGTTAAGGTATGATCTTACATTTAAGG
Found at i:42539680 original size:53 final size:52
Alignment explanation
Indices: 42539634--42539737 Score: 163
Period size: 52 Copynumber: 2.0 Consensus size: 52
42539624 TTTTTTAAGG
42539634 AATTAAACATAATTTTTTTCATTTTTAAGGGGCTAAAGAGAAATTTTACTATA
1 AATTAAACATAA-TTTTTTCATTTTTAAGGGGCTAAAGAGAAATTTTACTATA
* ** *
42539687 TATTAATTATTATTTTTTCATTTTTAAGGGGCTAAAGAGAAATTTTACTAT
1 AATTAAACATAATTTTTTCATTTTTAAGGGGCTAAAGAGAAATTTTACTAT
42539738 TTATTAATTT
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
52 39 0.83
53 8 0.17
ACGTcount: A:0.37, C:0.07, G:0.12, T:0.45
Consensus pattern (52 bp):
AATTAAACATAATTTTTTCATTTTTAAGGGGCTAAAGAGAAATTTTACTATA
Found at i:42539715 original size:52 final size:52
Alignment explanation
Indices: 42539647--42539746 Score: 191
Period size: 52 Copynumber: 1.9 Consensus size: 52
42539637 TAAACATAAT
42539647 TTTTTTCATTTTTAAGGGGCTAAAGAGAAATTTTACTATATATTAATTATTA
1 TTTTTTCATTTTTAAGGGGCTAAAGAGAAATTTTACTATATATTAATTATTA
*
42539699 TTTTTTCATTTTTAAGGGGCTAAAGAGAAATTTTACTATTTATTAATT
1 TTTTTTCATTTTTAAGGGGCTAAAGAGAAATTTTACTATATATTAATT
42539747 TATAATTTCT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 47 1.00
ACGTcount: A:0.33, C:0.06, G:0.12, T:0.49
Consensus pattern (52 bp):
TTTTTTCATTTTTAAGGGGCTAAAGAGAAATTTTACTATATATTAATTATTA
Found at i:42544082 original size:11 final size:11
Alignment explanation
Indices: 42544068--42544092 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
42544058 AATTACAATT
42544068 AATCAATTCAC
1 AATCAATTCAC
42544079 AATCAATTCAC
1 AATCAATTCAC
42544090 AAT
1 AAT
42544093 TAACATACAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.48, C:0.24, G:0.00, T:0.28
Consensus pattern (11 bp):
AATCAATTCAC
Found at i:42549582 original size:107 final size:108
Alignment explanation
Indices: 42549323--42549632 Score: 484
Period size: 108 Copynumber: 2.9 Consensus size: 108
42549313 AAAATTCAAG
* * * * * * * * *
42549323 AGGATATTTGGCAATTTGGTT-AA-ACGAGAAATCGAAACCCAGCATCTTAGAGCACGTTCCTCG
1 AGGATATTTAGCTATTTGGTTGAACAAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTCTCG
*
42549386 AATTTCCAAATGCAAAACATTGCCTTATTTTGTAATTTTTGAA
66 AATTTCCAAACGCAAAACATTGCCTTATTTTGTAATTTTTGAA
42549429 AGGAATATTTAGCT-TTTGGTTGAACAAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTCTC
1 AGG-ATATTTAGCTATTTGGTTGAACAAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTCTC
42549493 GAATTTCCAAACGCAAAACATTGCCTTATTTTGT-ATTTTTGAA
65 GAATTTCCAAACGCAAAACATTGCCTTATTTTGTAATTTTTGAA
42549536 AGGATATTTAGCTATTTGGTTGAACAAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTCTCG
1 AGGATATTTAGCTATTTGGTTGAACAAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTCTCG
42549601 AATTTCCCAAACGCAAAACATTGCCTTATTTT
66 AATTT-CCAAACGCAAAACATTGCCTTATTTT
42549633 NNNNNNNNNN
Statistics
Matches: 189, Mismatches: 10, Indels: 8
0.91 0.05 0.04
Matches are distributed among these distances:
106 20 0.11
107 78 0.41
108 91 0.48
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Consensus pattern (108 bp):
AGGATATTTAGCTATTTGGTTGAACAAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTCTCG
AATTTCCAAACGCAAAACATTGCCTTATTTTGTAATTTTTGAA
Found at i:42550410 original size:3 final size:3
Alignment explanation
Indices: 42550402--42550444 Score: 59
Period size: 3 Copynumber: 14.3 Consensus size: 3
42550392 ATATAAAAGC
* * *
42550402 AAT AAT AAT AAA AAT AAT AAA AAT AAT AAT AAC AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
42550445 TGAAATTTAT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (3 bp):
AAT
Found at i:42552691 original size:11 final size:11
Alignment explanation
Indices: 42552675--42552699 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
42552665 AATTACAATT
42552675 AATCAATTCAC
1 AATCAATTCAC
42552686 AATCAATTCAC
1 AATCAATTCAC
42552697 AAT
1 AAT
42552700 AAACATACAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.48, C:0.24, G:0.00, T:0.28
Consensus pattern (11 bp):
AATCAATTCAC
Found at i:42552943 original size:43 final size:43
Alignment explanation
Indices: 42552861--42552944 Score: 107
Period size: 43 Copynumber: 2.0 Consensus size: 43
42552851 CCGTGTAGAC
* * *
42552861 ATTCAAAGTTGAGACACACGACCGTGTGTCTGCCCGTGTGTAT
1 ATTCAAAGTTAAGACACACGACCGTGTGACTGCCAGTGTGTAT
* *
42552904 ATTCAAA-TTAAGATCACATGACCGTGTGACTGCTAGTGTGT
1 ATTCAAAGTTAAGA-CACACGACCGTGTGACTGCCAGTGTGT
42552945 GCATTTTTTG
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
42 5 0.14
43 30 0.86
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.30
Consensus pattern (43 bp):
ATTCAAAGTTAAGACACACGACCGTGTGACTGCCAGTGTGTAT
Found at i:42556237 original size:38 final size:38
Alignment explanation
Indices: 42556178--42556253 Score: 116
Period size: 38 Copynumber: 2.0 Consensus size: 38
42556168 ATTCCTTACT
*
42556178 TCGACAGGGTACAAATATTTAAATTTAATATTTCAAAA
1 TCGACAGGGTAAAAATATTTAAATTTAATATTTCAAAA
* * *
42556216 TCGACTGGGTAAAAATGTTTAAATTTGATATTTCAAAA
1 TCGACAGGGTAAAAATATTTAAATTTAATATTTCAAAA
42556254 AAGAGTAGAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.42, C:0.09, G:0.13, T:0.36
Consensus pattern (38 bp):
TCGACAGGGTAAAAATATTTAAATTTAATATTTCAAAA
Found at i:42562325 original size:8 final size:8
Alignment explanation
Indices: 42562312--42562342 Score: 62
Period size: 8 Copynumber: 3.9 Consensus size: 8
42562302 AAATGTCAAG
42562312 TAAATATT
1 TAAATATT
42562320 TAAATATT
1 TAAATATT
42562328 TAAATATT
1 TAAATATT
42562336 TAAATAT
1 TAAATAT
42562343 GATAATTCCG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (8 bp):
TAAATATT
Found at i:42567785 original size:15 final size:17
Alignment explanation
Indices: 42567743--42567788 Score: 57
Period size: 15 Copynumber: 3.0 Consensus size: 17
42567733 CGAATTACTA
42567743 ATTA-TTATAAATAATT
1 ATTATTTATAAATAATT
42567759 ATTATTT-T-AATAATT
1 ATTATTTATAAATAATT
42567774 -TT-TTTATAAATAATT
1 ATTATTTATAAATAATT
42567789 CTCTTAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
13 3 0.11
14 3 0.11
15 14 0.52
16 5 0.19
17 2 0.07
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
ATTATTTATAAATAATT
Found at i:42570103 original size:20 final size:20
Alignment explanation
Indices: 42570075--42570113 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
42570065 CAAGGTAATA
42570075 TATTATATT-ATTTTTATTTT
1 TATTATATTCA-TTTTATTTT
*
42570095 TATTTTATTCATTTTATTT
1 TATTATATTCATTTTATTT
42570114 CTCTGTTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 16 0.94
21 1 0.06
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (20 bp):
TATTATATTCATTTTATTTT
Found at i:42570362 original size:13 final size:13
Alignment explanation
Indices: 42570344--42570368 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
42570334 AACACATATA
42570344 ATTAAAAAAATTG
1 ATTAAAAAAATTG
42570357 ATTAAAAAAATT
1 ATTAAAAAAATT
42570369 ATCTATTTAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (13 bp):
ATTAAAAAAATTG
Found at i:42575074 original size:1 final size:1
Alignment explanation
Indices: 42575068--42575102 Score: 70
Period size: 1 Copynumber: 35.0 Consensus size: 1
42575058 GCAACTTTCC
42575068 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
42575103 AAAAAAAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:42575288 original size:25 final size:27
Alignment explanation
Indices: 42575254--42575305 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 27
42575244 TAAAGAACTC
42575254 AATGTG-AAAAGAAAAATAAC-TCAAA
1 AATGTGAAAAAGAAAAATAACTTCAAA
*
42575279 AATGTTAAAAAGAAAAATAACTTCAAA
1 AATGTGAAAAAGAAAAATAACTTCAAA
42575306 CAGGTTTCCA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 5 0.21
26 14 0.58
27 5 0.21
ACGTcount: A:0.63, C:0.08, G:0.10, T:0.19
Consensus pattern (27 bp):
AATGTGAAAAAGAAAAATAACTTCAAA
Found at i:42577264 original size:33 final size:33
Alignment explanation
Indices: 42577222--42577286 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
42577212 ATGTGTATAT
*
42577222 AATAAAACCCTGTTTAGTTAACAATGGAAGTTC
1 AATAAAACCCTATTTAGTTAACAATGGAAGTTC
*
42577255 AATAAAACCCTATTTGGTTAACAATGGAAGTT
1 AATAAAACCCTATTTAGTTAACAATGGAAGTT
42577287 TAATGACTTC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.14, G:0.15, T:0.31
Consensus pattern (33 bp):
AATAAAACCCTATTTAGTTAACAATGGAAGTTC
Found at i:42579185 original size:103 final size:105
Alignment explanation
Indices: 42579049--42579326 Score: 386
Period size: 103 Copynumber: 2.6 Consensus size: 105
42579039 GACATTAAAC
* *
42579049 CCCACTGAAAAATAAGTAAAGAAGCAGTGATCTGAAAACTAAAACAGAGATGAAAAAGGCAAAGA
1 CCCACTGAAATAGAAG-AAAGAAGCAGTGATCTGAAAACTAAAACAGAGATGAAAAAGGCAAAGA
42579114 CAAACTTGTTCTAAAGTTGAAAACCCAAAAAAC-AAAAAAA
65 CAAACTTGTTCTAAAGTTGAAAACCCAAAAAACAAAAAAAA
* * *
42579154 CCCGCTGAAATAGAA-AAAGAAGCAGTGATCTGAAAACTAAAACAGAGATGAAAAAAGCAAAGAT
1 CCCACTGAAATAGAAGAAAGAAGCAGTGATCTGAAAACTAAAACAGAGATGAAAAAGGCAAAGAC
42579218 AAACTTGTTCTAAAGTTGAAAACCCAAAAAACAAAAAAAAA
66 AAACTTGTTCTAAAGTTGAAAACCCAAAAAAC-AAAAAAAA
* * * * *
42579259 CCCACTGAAATAGAAGTAGATAAGCA-TAGATCAGAAAACTAAAA-AGGACATG-AAAAGGAAAA
1 CCCACTGAAATAGAAG-AAAGAAGCAGT-GATCTGAAAACTAAAACA-GAGATGAAAAAGGCAAA
42579321 GACAAA
63 GACAAA
42579327 GTTGAAGTAA
Statistics
Matches: 154, Mismatches: 13, Indels: 11
0.87 0.07 0.06
Matches are distributed among these distances:
103 79 0.51
105 33 0.21
106 15 0.10
107 27 0.18
ACGTcount: A:0.56, C:0.14, G:0.16, T:0.14
Consensus pattern (105 bp):
CCCACTGAAATAGAAGAAAGAAGCAGTGATCTGAAAACTAAAACAGAGATGAAAAAGGCAAAGAC
AAACTTGTTCTAAAGTTGAAAACCCAAAAAACAAAAAAAA
Found at i:42579537 original size:21 final size:21
Alignment explanation
Indices: 42579503--42579543 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
42579493 AAATATATAT
42579503 ATATATAAATCATAAAAATTA
1 ATATATAAATCATAAAAATTA
*
42579524 ATATA-AAATACATATAAATT
1 ATATATAAAT-CATAAAAATT
42579544 GTGATATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (21 bp):
ATATATAAATCATAAAAATTA
Found at i:42588125 original size:165 final size:166
Alignment explanation
Indices: 42587841--42588172 Score: 657
Period size: 165 Copynumber: 2.0 Consensus size: 166
42587831 TATATATATA
42587841 TATACCCAACTCAGTGACTTTATAAGGAGCACACACCATTGCTTGGTGGAGAGGTTCATGATTAT
1 TATACCCAACTCAGTGACTTTATAAGGAGCACACACCATTGCTTGGTGGAGAGGTTCATGATTAT
42587906 GGTTAATGAAGATTATAAAATAGTATTTGTTTTGAATTCATGAAAAGAAGTAGGGTCGGAGTATG
66 GGTTAATGAAGATTATAAAATAGTATTTGTTTTGAATTCATGAAAAGAAGTAGGGTCGGAGTATG
42587971 GAATGATAAAAAGATCAATTTGAATTTTGTATCACT
131 GAATGATAAAAAGATCAATTTGAATTTTGTATCACT
42588007 TATACCCAACT-AGTGACTTTATAAGGAGCACACACCATTGCTTGGTGGAGAGGTTCATGATTAT
1 TATACCCAACTCAGTGACTTTATAAGGAGCACACACCATTGCTTGGTGGAGAGGTTCATGATTAT
42588071 GGTTAATGAAGATTATAAAATAGTATTTGTTTTGAATTCATGAAAAGAAGTAGGGTCGGAGTATG
66 GGTTAATGAAGATTATAAAATAGTATTTGTTTTGAATTCATGAAAAGAAGTAGGGTCGGAGTATG
42588136 GAATGATAAAAAGATCAATTTGAATTTTGTATCACT
131 GAATGATAAAAAGATCAATTTGAATTTTGTATCACT
42588172 T
1 T
42588173 TTGCTTTTTT
Statistics
Matches: 166, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
165 155 0.93
166 11 0.07
ACGTcount: A:0.35, C:0.11, G:0.22, T:0.33
Consensus pattern (166 bp):
TATACCCAACTCAGTGACTTTATAAGGAGCACACACCATTGCTTGGTGGAGAGGTTCATGATTAT
GGTTAATGAAGATTATAAAATAGTATTTGTTTTGAATTCATGAAAAGAAGTAGGGTCGGAGTATG
GAATGATAAAAAGATCAATTTGAATTTTGTATCACT
Found at i:42593089 original size:123 final size:124
Alignment explanation
Indices: 42592949--42593195 Score: 487
Period size: 123 Copynumber: 2.0 Consensus size: 124
42592939 ATTTTTTCAA
42592949 TATATATTTATAAAATTTTGGAAAAATATTTTATAAATATTTTGTATTTTTGTAACTTTTAGAGG
1 TATATATTTATAAAATTTTGGAAAAATATTTTATAAATATTTTGTATTTTTGTAACTTTTAGAGG
42593014 AACCAACTTGCACATTTTCGAACTATCAAAGACCTAAGGAGTATTTACATAAATTTATT
66 AACCAACTTGCACATTTTCGAACTATCAAAGACCTAAGGAGTATTTACATAAATTTATT
42593073 TATATATTTA-AAAATTTTGGAAAAATATTTTATAAATATTTTGTATTTTTGTAACTTTTAGAGG
1 TATATATTTATAAAATTTTGGAAAAATATTTTATAAATATTTTGTATTTTTGTAACTTTTAGAGG
42593137 AACCAACTTGCACATTTTCGAACTATCAAAGACCTAAGGAGTATTTACATAAATTTATT
66 AACCAACTTGCACATTTTCGAACTATCAAAGACCTAAGGAGTATTTACATAAATTTATT
42593196 ATTTGAGTTA
Statistics
Matches: 123, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
123 113 0.92
124 10 0.08
ACGTcount: A:0.38, C:0.10, G:0.11, T:0.42
Consensus pattern (124 bp):
TATATATTTATAAAATTTTGGAAAAATATTTTATAAATATTTTGTATTTTTGTAACTTTTAGAGG
AACCAACTTGCACATTTTCGAACTATCAAAGACCTAAGGAGTATTTACATAAATTTATT
Found at i:42596849 original size:18 final size:19
Alignment explanation
Indices: 42596826--42596868 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 19
42596816 CATTTTCCTA
42596826 TAATTAATTTAAAATT-TT
1 TAATTAATTTAAAATTATT
*
42596844 TAATT-ATTTAAAGTTATT
1 TAATTAATTTAAAATTATT
42596862 TAATTAA
1 TAATTAA
42596869 AAAATCAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 9 0.41
18 12 0.55
19 1 0.05
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (19 bp):
TAATTAATTTAAAATTATT
Found at i:42614714 original size:13 final size:13
Alignment explanation
Indices: 42614696--42614721 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
42614686 ACATCCTTAT
42614696 TGTCTGGTATAAA
1 TGTCTGGTATAAA
42614709 TGTCTGGTATAAA
1 TGTCTGGTATAAA
42614722 CAATTACCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.08, G:0.23, T:0.38
Consensus pattern (13 bp):
TGTCTGGTATAAA
Found at i:42623309 original size:21 final size:20
Alignment explanation
Indices: 42623279--42623318 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
42623269 TTTAGTAAAA
42623279 ATTTAAAGAAACATATTATAT
1 ATTTAAAGAAA-ATATTATAT
* *
42623300 ATTTAGAGAAAATGTTATA
1 ATTTAAAGAAAATATTATA
42623319 AATAATTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.50, C:0.03, G:0.10, T:0.38
Consensus pattern (20 bp):
ATTTAAAGAAAATATTATAT
Found at i:42632717 original size:22 final size:21
Alignment explanation
Indices: 42632692--42632734 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
42632682 AGTTCTTTTA
42632692 CTTTAA-TTTATCAAAAATGTGT
1 CTTTAATTTTA-CAAAAA-GTGT
*
42632714 CTTTTATTTTACAAAAAGTGT
1 CTTTAATTTTACAAAAAGTGT
42632735 AGGTACGATT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 4 0.21
22 11 0.58
23 4 0.21
ACGTcount: A:0.35, C:0.09, G:0.09, T:0.47
Consensus pattern (21 bp):
CTTTAATTTTACAAAAAGTGT
Found at i:42632724 original size:23 final size:21
Alignment explanation
Indices: 42632693--42632734 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 21
42632683 GTTCTTTTAC
42632693 TTTAATTTATCAAAAATGTGTCT
1 TTTAATTTA-CAAAAA-GTGTCT
*
42632716 TTTATTTTACAAAAAGTGT
1 TTTAATTTACAAAAAGTGT
42632735 AGGTACGATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 6 0.33
23 8 0.44
ACGTcount: A:0.36, C:0.07, G:0.10, T:0.48
Consensus pattern (21 bp):
TTTAATTTACAAAAAGTGTCT
Found at i:42633331 original size:13 final size:13
Alignment explanation
Indices: 42633313--42633339 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
42633303 TTGACGCACT
42633313 AAAAATTTAATAA
1 AAAAATTTAATAA
42633326 AAAAATTTAATAA
1 AAAAATTTAATAA
42633339 A
1 A
42633340 TTATTAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (13 bp):
AAAAATTTAATAA
Found at i:42639643 original size:21 final size:22
Alignment explanation
Indices: 42639603--42639643 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
42639593 TTATAATTGA
* *
42639603 TAAAATTTTAAATTAATAATGG
1 TAAAATTCTAAATAAATAATGG
42639625 TAAAATTCTAAA-AAATAAT
1 TAAAATTCTAAATAAATAAT
42639644 AAAAATGTGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.56, C:0.02, G:0.05, T:0.37
Consensus pattern (22 bp):
TAAAATTCTAAATAAATAATGG
Found at i:42643278 original size:6 final size:6
Alignment explanation
Indices: 42643267--42643293 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
42643257 GCGTTTCAAT
42643267 TAATTA TAATTA TAATTA TAATTA TAA
1 TAATTA TAATTA TAATTA TAATTA TAA
42643294 AATTTTGAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
TAATTA
Found at i:42651576 original size:31 final size:28
Alignment explanation
Indices: 42651539--42651596 Score: 73
Period size: 31 Copynumber: 2.0 Consensus size: 28
42651529 TATTATTTTT
42651539 AAGCCAC-TGAATTATTCTAAAGTTTTTATTC
1 AAGCCACTTG-ATTA-T-TAAA-TTTTTATTC
42651570 AAGCCACTTGATTATTAAATTTTTATT
1 AAGCCACTTGATTATTAAATTTTTATT
42651597 TTTTTAATAG
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
28 8 0.31
29 4 0.15
30 1 0.04
31 11 0.42
32 2 0.08
ACGTcount: A:0.33, C:0.14, G:0.09, T:0.45
Consensus pattern (28 bp):
AAGCCACTTGATTATTAAATTTTTATTC
Found at i:42659070 original size:21 final size:21
Alignment explanation
Indices: 42659046--42659090 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
42659036 TTTTTATTAA
*
42659046 TATGATTATTT-ATATTAATAT
1 TATGATT-TTTGATACTAATAT
*
42659067 TATGATTTTTGTTACTAATAT
1 TATGATTTTTGATACTAATAT
42659088 TAT
1 TAT
42659091 TTTCGTTAGG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 3 0.14
21 18 0.86
ACGTcount: A:0.33, C:0.02, G:0.07, T:0.58
Consensus pattern (21 bp):
TATGATTTTTGATACTAATAT
Found at i:42659092 original size:18 final size:18
Alignment explanation
Indices: 42659031--42659093 Score: 65
Period size: 18 Copynumber: 3.5 Consensus size: 18
42659021 TTTACACTAT
42659031 TATTATTTTTATTAAT-A
1 TATTATTTTTATTAATAA
* *
42659048 TGATTATTTATATTAATAT
1 T-ATTATTTTTATTAATAA
* * *
42659067 TATGATTTTTGTTACTAA
1 TATTATTTTTATTAATAA
42659085 TATTATTTT
1 TATTATTTT
42659094 CGTTAGGATC
Statistics
Matches: 36, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
17 1 0.03
18 34 0.94
19 1 0.03
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.62
Consensus pattern (18 bp):
TATTATTTTTATTAATAA
Found at i:42661404 original size:94 final size:94
Alignment explanation
Indices: 42661296--42661490 Score: 372
Period size: 94 Copynumber: 2.1 Consensus size: 94
42661286 GAATCCATCG
*
42661296 CTTTTTTCTCTAAAAAAGTGTCAACCCCATACTAGAAAGGTTTAGGAAGATGATTAATGATTATA
1 CTTTTTTCTCTAAAAAAGTGTCAACCCCAAACTAGAAAGGTTTAGGAAGATGATTAATGATTATA
42661361 TTTGCATTGATTTTTGTTGGTTTAATTAA
66 TTTGCATTGATTTTTGTTGGTTTAATTAA
42661390 CTTTTTTCTCTAAAAAAGTGTCAACCCCAAACTAGAAAGGTTTAGGAAGATGATTAATGATTATA
1 CTTTTTTCTCTAAAAAAGTGTCAACCCCAAACTAGAAAGGTTTAGGAAGATGATTAATGATTATA
*
42661455 TTTGTATTGATTTTTGTTGGTTTAATTAA
66 TTTGCATTGATTTTTGTTGGTTTAATTAA
42661484 CTTTTTT
1 CTTTTTT
42661491 TTTAACCAGT
Statistics
Matches: 99, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
94 99 1.00
ACGTcount: A:0.31, C:0.10, G:0.15, T:0.43
Consensus pattern (94 bp):
CTTTTTTCTCTAAAAAAGTGTCAACCCCAAACTAGAAAGGTTTAGGAAGATGATTAATGATTATA
TTTGCATTGATTTTTGTTGGTTTAATTAA
Found at i:42664293 original size:36 final size:36
Alignment explanation
Indices: 42664246--42664316 Score: 117
Period size: 36 Copynumber: 2.0 Consensus size: 36
42664236 ACCGGAACAG
42664246 ACATGATGTTGCCACCTTACC-GTGAGGATCTCCAAA
1 ACATGATGTTGCCACCTT-CCTGTGAGGATCTCCAAA
*
42664282 ACATGATGTTGCGACCTTCCTGTGAGGATCTCCAA
1 ACATGATGTTGCCACCTTCCTGTGAGGATCTCCAA
42664317 GGTTTCGGAG
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
35 2 0.06
36 31 0.94
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.27
Consensus pattern (36 bp):
ACATGATGTTGCCACCTTCCTGTGAGGATCTCCAAA
Found at i:42664335 original size:18 final size:18
Alignment explanation
Indices: 42664312--42664371 Score: 77
Period size: 18 Copynumber: 3.3 Consensus size: 18
42664302 TGTGAGGATC
42664312 TCCAAGGTTTCGGAGAAA
1 TCCAAGGTTTCGGAGAAA
* * *
42664330 TCCAAGGTCTC-AAGGAAG
1 TCCAAGGTTTCGGA-GAAA
42664348 TCCAAGGTTTCGGAGAAA
1 TCCAAGGTTTCGGAGAAA
42664366 TCCAAG
1 TCCAAG
42664372 TCGAACATCT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
17 1 0.03
18 32 0.94
19 1 0.03
ACGTcount: A:0.33, C:0.20, G:0.27, T:0.20
Consensus pattern (18 bp):
TCCAAGGTTTCGGAGAAA
Found at i:42665287 original size:18 final size:19
Alignment explanation
Indices: 42665261--42665296 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
42665251 TTGAATTACA
42665261 AATAATTACAC-AAAAATC
1 AATAATTACACTAAAAATC
*
42665279 AATATTTACACTAAAAAT
1 AATAATTACACTAAAAAT
42665297 TGAAAAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.58, C:0.14, G:0.00, T:0.28
Consensus pattern (19 bp):
AATAATTACACTAAAAATC
Found at i:42667248 original size:43 final size:43
Alignment explanation
Indices: 42667188--42667301 Score: 158
Period size: 43 Copynumber: 2.7 Consensus size: 43
42667178 TGTCCAAGAC
* **
42667188 ATGGTCTTACATGGAAATCTCGTATCGATGCCAATAGCCCAGCT
1 ATGGTCTTACA-CGAAATCTCAAATCGATGCCAATAGCCCAGCT
* * *
42667232 ATGGTCTTATACGAAATCTCAAATCGATGGCAATAGCCGAGCT
1 ATGGTCTTACACGAAATCTCAAATCGATGCCAATAGCCCAGCT
42667275 ATGGTCTTACACG-AATCTCAAATCGAT
1 ATGGTCTTACACGAAATCTCAAATCGAT
42667302 ATTGGAACAT
Statistics
Matches: 63, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
42 14 0.22
43 39 0.62
44 10 0.16
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.27
Consensus pattern (43 bp):
ATGGTCTTACACGAAATCTCAAATCGATGCCAATAGCCCAGCT
Found at i:42672775 original size:54 final size:55
Alignment explanation
Indices: 42672716--42672824 Score: 202
Period size: 55 Copynumber: 2.0 Consensus size: 55
42672706 AAGCATTATC
42672716 GTACATCAATATTCGTTAAATAATCCA-AAAACAAGGAATAAAGAGAAAAATATA
1 GTACATCAATATTCGTTAAATAATCCACAAAACAAGGAATAAAGAGAAAAATATA
*
42672770 GTACATCAATATTCGTTATATAATCCACAAAACAAGGAATAAAGAGAAAAATATA
1 GTACATCAATATTCGTTAAATAATCCACAAAACAAGGAATAAAGAGAAAAATATA
42672825 CTCGTTATCT
Statistics
Matches: 53, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
54 26 0.49
55 27 0.51
ACGTcount: A:0.54, C:0.12, G:0.11, T:0.23
Consensus pattern (55 bp):
GTACATCAATATTCGTTAAATAATCCACAAAACAAGGAATAAAGAGAAAAATATA
Found at i:42674792 original size:36 final size:36
Alignment explanation
Indices: 42674745--42674815 Score: 117
Period size: 36 Copynumber: 2.0 Consensus size: 36
42674735 ACCGGAACAG
42674745 ACATGATGTTGCCACCTTACC-GTGAGGATCTCCAAA
1 ACATGATGTTGCCACCTT-CCTGTGAGGATCTCCAAA
*
42674781 ACATGATGTTGCGACCTTCCTGTGAGGATCTCCAA
1 ACATGATGTTGCCACCTTCCTGTGAGGATCTCCAA
42674816 GGTTTCGGAG
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
35 2 0.06
36 31 0.94
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.27
Consensus pattern (36 bp):
ACATGATGTTGCCACCTTCCTGTGAGGATCTCCAAA
Found at i:42674834 original size:18 final size:18
Alignment explanation
Indices: 42674811--42674870 Score: 77
Period size: 18 Copynumber: 3.3 Consensus size: 18
42674801 TGTGAGGATC
42674811 TCCAAGGTTTCGGAGAAA
1 TCCAAGGTTTCGGAGAAA
* * *
42674829 TCCAAGGTCTC-AAGGAAG
1 TCCAAGGTTTCGGA-GAAA
42674847 TCCAAGGTTTCGGAGAAA
1 TCCAAGGTTTCGGAGAAA
42674865 TCCAAG
1 TCCAAG
42674871 TCGAACATCT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
17 1 0.03
18 32 0.94
19 1 0.03
ACGTcount: A:0.33, C:0.20, G:0.27, T:0.20
Consensus pattern (18 bp):
TCCAAGGTTTCGGAGAAA
Found at i:42688596 original size:72 final size:73
Alignment explanation
Indices: 42688466--42688611 Score: 285
Period size: 72 Copynumber: 2.0 Consensus size: 73
42688456 GTTCCAGGCC
42688466 TTGGTATGCAATCATCTTTTTGGATTTTTTTTTTTAAATACAGATGTTCTCATCTATTAATATGG
1 TTGGTATGCAATCATCTTTTTGGATTTTTTTTTTTAAATACAGATGTTCTCATCTATTAATATGG
42688531 TATTTATA
66 TATTTATA
42688539 TTGGTATGCAATCATCTTTTTGGA-TTTTTTTTTTAAATACAGATGTTCTCATCTATTAATATGG
1 TTGGTATGCAATCATCTTTTTGGATTTTTTTTTTTAAATACAGATGTTCTCATCTATTAATATGG
42688603 TATTTATA
66 TATTTATA
42688611 T
1 T
42688612 GAGTTTTTTT
Statistics
Matches: 73, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
72 49 0.67
73 24 0.33
ACGTcount: A:0.26, C:0.10, G:0.12, T:0.52
Consensus pattern (73 bp):
TTGGTATGCAATCATCTTTTTGGATTTTTTTTTTTAAATACAGATGTTCTCATCTATTAATATGG
TATTTATA
Found at i:42691701 original size:55 final size:55
Alignment explanation
Indices: 42691635--42691744 Score: 195
Period size: 55 Copynumber: 2.0 Consensus size: 55
42691625 AAACATTATC
42691635 GTACATCAATATTCGTTA-AGTAATCCACAAAACAAGGAATAAAGAGAAAAATATA
1 GTACATCAATATTCGTTATA-TAATCCACAAAACAAGGAATAAAGAGAAAAATATA
*
42691690 GTACATCAATATTCGTTATATAATCCACAAAACAAGGAATAAAGGGAAAAATATA
1 GTACATCAATATTCGTTATATAATCCACAAAACAAGGAATAAAGAGAAAAATATA
42691745 CTAGTTATCT
Statistics
Matches: 53, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
55 52 0.98
56 1 0.02
ACGTcount: A:0.52, C:0.13, G:0.13, T:0.23
Consensus pattern (55 bp):
GTACATCAATATTCGTTATATAATCCACAAAACAAGGAATAAAGAGAAAAATATA
Found at i:42692207 original size:25 final size:26
Alignment explanation
Indices: 42692178--42692231 Score: 92
Period size: 26 Copynumber: 2.1 Consensus size: 26
42692168 TTGTAGAATA
42692178 CTTAAAG-AAATCAGGCCAAGAAAAT
1 CTTAAAGAAAATCAGGCCAAGAAAAT
*
42692203 CTTAAAGAAAATCAGGCTAAGAAAAT
1 CTTAAAGAAAATCAGGCCAAGAAAAT
42692229 CTT
1 CTT
42692232 CCTTAGTATG
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
25 7 0.26
26 20 0.74
ACGTcount: A:0.50, C:0.15, G:0.15, T:0.20
Consensus pattern (26 bp):
CTTAAAGAAAATCAGGCCAAGAAAAT
Found at i:42698605 original size:51 final size:51
Alignment explanation
Indices: 42698488--42698703 Score: 346
Period size: 51 Copynumber: 4.3 Consensus size: 51
42698478 CTTACGTATG
* * *
42698488 ATCACTTATCACTTGTCATTGATCAGATAAGTGTAGCT-AAGCTACCACTT
1 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTGAAGCTACTACTT
*
42698538 ATCACTTGCCACTTGTCACTGATCAGATAAGTGTAGCTGAAGCTACTACTT
1 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTGAAGCTACTACTT
* *
42698589 ATCACTTGTCATTTGTCACTGATTAGATAAGTGTAGCTGAAGCTACTACTT
1 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTGAAGCTACTACTT
42698640 ATCACTT-TCCACTTGTCACTGATCAGATAAGTGTAGCTGAAGCTACTACTT
1 ATCACTTGT-CACTTGTCACTGATCAGATAAGTGTAGCTGAAGCTACTACTT
*
42698691 ATCACTTATCACT
1 ATCACTTGTCACT
42698704 GATCAGAAGT
Statistics
Matches: 154, Mismatches: 9, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
50 36 0.23
51 117 0.76
52 1 0.01
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.34
Consensus pattern (51 bp):
ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTGAAGCTACTACTT
Found at i:42701201 original size:6 final size:6
Alignment explanation
Indices: 42701194--42701228 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
42701184 AAACCCCCAT
* *
42701194 TGCCAT TGCCAT TGCCAC TGCCAC TGCCAC TGCCA
1 TGCCAC TGCCAC TGCCAC TGCCAC TGCCAC TGCCA
42701229 AGTAACAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.17, C:0.43, G:0.17, T:0.23
Consensus pattern (6 bp):
TGCCAC
Found at i:42701207 original size:12 final size:12
Alignment explanation
Indices: 42701190--42701228 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
42701180 TGTGAAACCC
*
42701190 CCATTGCCATTG
1 CCATTGCCACTG
42701202 CCATTGCCACTG
1 CCATTGCCACTG
*
42701214 CCACTGCCACTG
1 CCATTGCCACTG
42701226 CCA
1 CCA
42701229 AGTAACAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.18, C:0.44, G:0.15, T:0.23
Consensus pattern (12 bp):
CCATTGCCACTG
Found at i:42704552 original size:22 final size:23
Alignment explanation
Indices: 42704527--42704576 Score: 61
Period size: 21 Copynumber: 2.3 Consensus size: 23
42704517 TTATAGAAAT
42704527 TAAAAGATAA-TGAAAATTTA-AA
1 TAAAA-ATAATTGAAAATTTATAA
*
42704549 T-AAAATAATTTAAAATTTATAA
1 TAAAAATAATTGAAAATTTATAA
42704571 TAAAAA
1 TAAAAA
42704577 AAGGGAGAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
20 4 0.17
21 12 0.50
22 4 0.17
23 4 0.17
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAAAATAATTGAAAATTTATAA
Found at i:42705461 original size:14 final size:14
Alignment explanation
Indices: 42705439--42705474 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
42705429 TAATATTTTA
*
42705439 TAATAAATTAGATT
1 TAATTAATTAGATT
42705453 TAATTAATTAGATT
1 TAATTAATTAGATT
42705467 TAA-TAATT
1 TAATTAATT
42705475 TTAAAATATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 5 0.24
14 16 0.76
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (14 bp):
TAATTAATTAGATT
Found at i:42709206 original size:2 final size:2
Alignment explanation
Indices: 42709199--42709226 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
42709189 TTCTCAACAT
42709199 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
42709227 CATTTTTCGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:42713252 original size:17 final size:17
Alignment explanation
Indices: 42713227--42713268 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
42713217 GAGAATTACG
*
42713227 ATTACAAATACAATATA
1 ATTATAAATACAATATA
42713244 ATTATAAATACAATATA
1 ATTATAAATACAATATA
*
42713261 AATATAAA
1 ATTATAAA
42713269 AATATGTCCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.31
Consensus pattern (17 bp):
ATTATAAATACAATATA
Found at i:42716763 original size:12 final size:12
Alignment explanation
Indices: 42716746--42716771 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
42716736 ATTTAAGGGT
42716746 TGGGAGGGGCTA
1 TGGGAGGGGCTA
42716758 TGGGAGGGGCTA
1 TGGGAGGGGCTA
42716770 TG
1 TG
42716772 AGTAGTTCTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.08, G:0.58, T:0.19
Consensus pattern (12 bp):
TGGGAGGGGCTA
Found at i:42717530 original size:79 final size:79
Alignment explanation
Indices: 42717399--42717558 Score: 311
Period size: 79 Copynumber: 2.0 Consensus size: 79
42717389 AATTTTTATT
42717399 TTGAAAATTTTTATATTTCTTAGAATTATTTAAAATAAATTTTTAAAATGTATTTTTATTTTTAA
1 TTGAAAATTTTTATATTTCTTAGAATTATTTAAAATAAATTTTTAAAATGTATTTTTATTTTTAA
*
42717464 AACTTAAGAGTTTG
66 AACTTAAAAGTTTG
42717478 TTGAAAATTTTTATATTTCTTAGAATTATTTAAAATAAATTTTTAAAATGTATTTTTATTTTTAA
1 TTGAAAATTTTTATATTTCTTAGAATTATTTAAAATAAATTTTTAAAATGTATTTTTATTTTTAA
42717543 AACTTAAAAGTTTG
66 AACTTAAAAGTTTG
42717557 TT
1 TT
42717559 CATATTTTCA
Statistics
Matches: 80, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
79 80 1.00
ACGTcount: A:0.38, C:0.03, G:0.07, T:0.53
Consensus pattern (79 bp):
TTGAAAATTTTTATATTTCTTAGAATTATTTAAAATAAATTTTTAAAATGTATTTTTATTTTTAA
AACTTAAAAGTTTG
Found at i:42720463 original size:14 final size:15
Alignment explanation
Indices: 42720441--42720517 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
42720431 CAATCAAACA
42720441 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
42720455 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
42720470 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
42720490 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
* *
42720504 ACGGAAAA-CATTTT
1 CCAGAAAATCATTTT
42720518 ACTGGCTATC
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 22 0.44
15 14 0.28
16 1 0.02
18 1 0.02
19 3 0.06
20 9 0.18
ACGTcount: A:0.43, C:0.16, G:0.09, T:0.32
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:42720482 original size:20 final size:20
Alignment explanation
Indices: 42720457--42720496 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
42720447 AATATTTTCC
*
42720457 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
42720477 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
42720497 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:42720502 original size:34 final size:35
Alignment explanation
Indices: 42720445--42720511 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
42720435 CAAACACCAG
*
42720445 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
42720480 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
42720512 CATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:42720518 original size:14 final size:14
Alignment explanation
Indices: 42720480--42720519 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
42720470 ACAGAAAAGT
*
42720480 AAAACATTTTCCAG
1 AAAACATTTTACAG
* *
42720494 AAATCATTTTACGG
1 AAAACATTTTACAG
42720508 AAAACATTTTAC
1 AAAACATTTTAC
42720520 TGGCTATCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:42730967 original size:16 final size:15
Alignment explanation
Indices: 42730938--42730966 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
42730928 TAGTAAATTA
42730938 TTAAAAATTATATAT
1 TTAAAAATTATATAT
42730953 TTAAAAA-TATATAT
1 TTAAAAATTATATAT
42730967 ACTAATTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TTAAAAATTATATAT
Found at i:42734140 original size:16 final size:16
Alignment explanation
Indices: 42734118--42734150 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
42734108 AAAATTATTT
*
42734118 TAAAAATTAA-AAAAA
1 TAAAAAATAATAAAAA
42734133 TAAAAAATAATAAAAA
1 TAAAAAATAATAAAAA
42734149 TA
1 TA
42734151 TTTATTATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (16 bp):
TAAAAAATAATAAAAA
Found at i:42735684 original size:30 final size:29
Alignment explanation
Indices: 42735650--42735707 Score: 71
Period size: 30 Copynumber: 2.0 Consensus size: 29
42735640 GTTTATAATT
*
42735650 TTTTTAAAGGACTAAATCAAAATTTTATCG
1 TTTTTAAAGGACAAAAT-AAAATTTTATCG
* * *
42735680 TTTTTTAAGGCCAAAATATAATTTTATC
1 TTTTTAAAGGACAAAATAAAATTTTATC
42735708 TATACTAACT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 10 0.42
30 14 0.58
ACGTcount: A:0.38, C:0.10, G:0.09, T:0.43
Consensus pattern (29 bp):
TTTTTAAAGGACAAAATAAAATTTTATCG
Found at i:42740993 original size:17 final size:17
Alignment explanation
Indices: 42740971--42741004 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
42740961 TTTTACTTAT
*
42740971 CTTTTGATGATGTTTTG
1 CTTTTGATGATCTTTTG
42740988 CTTTTGATGATCTTTTG
1 CTTTTGATGATCTTTTG
42741005 AAATTCACTC
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:0.12, C:0.09, G:0.21, T:0.59
Consensus pattern (17 bp):
CTTTTGATGATCTTTTG
Found at i:42744801 original size:120 final size:120
Alignment explanation
Indices: 42744588--42744827 Score: 471
Period size: 120 Copynumber: 2.0 Consensus size: 120
42744578 ATTGAATTTA
*
42744588 GGCCGGACCGAGGTGTATAAATCCTCATCTAAGCTCAGCCTTTGTCTGGTTGGGCCTACCAGACA
1 GGCCGAACCGAGGTGTATAAATCCTCATCTAAGCTCAGCCTTTGTCTGGTTGGGCCTACCAGACA
42744653 GAACAAGCTATCCAATCCTTAGACAAGTCTAATCCTTATATATGTTCAAATTATT
66 GAACAAGCTATCCAATCCTTAGACAAGTCTAATCCTTATATATGTTCAAATTATT
42744708 GGCCGAACCGAGGTGTATAAATCCTCATCTAAGCTCAGCCTTTGTCTGGTTGGGCCTACCAGACA
1 GGCCGAACCGAGGTGTATAAATCCTCATCTAAGCTCAGCCTTTGTCTGGTTGGGCCTACCAGACA
42744773 GAACAAGCTATCCAATCCTTAGACAAGTCTAATCCTTATATATGTTCAAATTATT
66 GAACAAGCTATCCAATCCTTAGACAAGTCTAATCCTTATATATGTTCAAATTATT
42744828 TTTGTATTTC
Statistics
Matches: 119, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
120 119 1.00
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (120 bp):
GGCCGAACCGAGGTGTATAAATCCTCATCTAAGCTCAGCCTTTGTCTGGTTGGGCCTACCAGACA
GAACAAGCTATCCAATCCTTAGACAAGTCTAATCCTTATATATGTTCAAATTATT
Found at i:42751837 original size:19 final size:19
Alignment explanation
Indices: 42751797--42751846 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
42751787 TTAAATTTAG
**
42751797 AAATTAAATTACACTTAAA
1 AAATTAAATTACACAAAAA
*
42751816 AAATTAAATTACAAAAATAA
1 AAATTAAATTACACAAA-AA
42751836 AAATATAAATT
1 AAAT-TAAATT
42751847 CTCGAAAGAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
19 14 0.54
20 6 0.23
21 6 0.23
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (19 bp):
AAATTAAATTACACAAAAA
Found at i:42756983 original size:93 final size:93
Alignment explanation
Indices: 42756824--42757014 Score: 364
Period size: 93 Copynumber: 2.1 Consensus size: 93
42756814 GATTTATGGT
42756824 TTTACAGTGTCTTCTCATTATTCTTCGGTGGTAAAAGCATCATGGAGACCTTTATATTAAAATAT
1 TTTACAGTGTCTTCTCATTATTCTTCGGTGGTAAAAGCATCATGGAGACCTTTATATTAAAATAT
*
42756889 ACTAAGATTTAAATTGTATTTTGTCTCC
66 ACTAAGATTTAAATTGCATTTTGTCTCC
*
42756917 TTTACAGTGTCTTCTCATTATTCTTCGGTGGTAAAAGCATCATGGAGGCCTTTATATTAAAATAT
1 TTTACAGTGTCTTCTCATTATTCTTCGGTGGTAAAAGCATCATGGAGACCTTTATATTAAAATAT
42756982 ACTAAGATTTAAATTGCATTTTGTCTCC
66 ACTAAGATTTAAATTGCATTTTGTCTCC
42757010 TTTAC
1 TTTAC
42757015 TGAACAAATA
Statistics
Matches: 96, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
93 96 1.00
ACGTcount: A:0.28, C:0.16, G:0.14, T:0.42
Consensus pattern (93 bp):
TTTACAGTGTCTTCTCATTATTCTTCGGTGGTAAAAGCATCATGGAGACCTTTATATTAAAATAT
ACTAAGATTTAAATTGCATTTTGTCTCC
Found at i:42760935 original size:29 final size:26
Alignment explanation
Indices: 42760901--42760955 Score: 67
Period size: 29 Copynumber: 2.0 Consensus size: 26
42760891 TTATAGGGGC
42760901 TGGATC-ATGTTAGTACCTCTATTATTAAA
1 TGGATCAAT-TTAGT-CC-CTA-TATTAAA
42760930 TGGATCAATTTAGTCCCTATATTAAA
1 TGGATCAATTTAGTCCCTATATTAAA
42760956 AAGAATCAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
26 7 0.28
27 3 0.12
28 2 0.08
29 11 0.44
30 2 0.08
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.40
Consensus pattern (26 bp):
TGGATCAATTTAGTCCCTATATTAAA
Found at i:42765796 original size:55 final size:57
Alignment explanation
Indices: 42765730--42765842 Score: 169
Period size: 56 Copynumber: 2.0 Consensus size: 57
42765720 CTTAATCTGC
*
42765730 AAAACTATAAATATCCA-TTT-TCATGAGACTCTTCTCATTCATCAATC-ACCTTCTT
1 AAAACTATAAATATCCATTTTCTCAT-AAACTCTTCTCATTCATCAATCGACCTTCTT
* *
42765785 AAAACTATAAATATCCATTTTCTCATAAATTCTTCTCATTCATCAATCGACTTTCTT
1 AAAACTATAAATATCCATTTTCTCATAAACTCTTCTCATTCATCAATCGACCTTCTT
42765842 A
1 A
42765843 CCAAACAATA
Statistics
Matches: 52, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
55 17 0.33
56 23 0.44
57 12 0.23
ACGTcount: A:0.34, C:0.24, G:0.03, T:0.40
Consensus pattern (57 bp):
AAAACTATAAATATCCATTTTCTCATAAACTCTTCTCATTCATCAATCGACCTTCTT
Found at i:42768188 original size:20 final size:20
Alignment explanation
Indices: 42768152--42768190 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
42768142 TTTATCATTC
*
42768152 TAATAATTTTTTTATATAAT
1 TAATAATTTTTTAATATAAT
42768172 TAAT-ATTTTTTAAATATAA
1 TAATAATTTTTT-AATATAA
42768191 ATCATGTAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
TAATAATTTTTTAATATAAT
Found at i:42768668 original size:30 final size:31
Alignment explanation
Indices: 42768627--42768685 Score: 102
Period size: 30 Copynumber: 1.9 Consensus size: 31
42768617 ATCAAAAATT
42768627 TATTTTAAAAATTAAAAAAAATTAAAAAAAG
1 TATTTTAAAAATTAAAAAAAATTAAAAAAAG
*
42768658 TATTTT-AAAATTAAAAAAATTTAAAAAA
1 TATTTTAAAAATTAAAAAAAATTAAAAAA
42768686 TAAATATATT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
30 21 0.78
31 6 0.22
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (31 bp):
TATTTTAAAAATTAAAAAAAATTAAAAAAAG
Found at i:42773673 original size:28 final size:28
Alignment explanation
Indices: 42773633--42773692 Score: 111
Period size: 28 Copynumber: 2.1 Consensus size: 28
42773623 ATATTTTTAT
42773633 TTATACACATGTATTTACCGAAAGTAAA
1 TTATACACATGTATTTACCGAAAGTAAA
*
42773661 TTATACACATGTATTTATCGAAAGTAAA
1 TTATACACATGTATTTACCGAAAGTAAA
42773689 TTAT
1 TTAT
42773693 TTATTTTTTG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.42, C:0.12, G:0.10, T:0.37
Consensus pattern (28 bp):
TTATACACATGTATTTACCGAAAGTAAA
Found at i:42776336 original size:21 final size:20
Alignment explanation
Indices: 42776312--42776361 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
42776302 TTCAATTTTT
42776312 TTTATTTTTTAAACTATTTCA
1 TTTATTTTTTAAACTATTT-A
* **
42776333 TTTATTATTTTTATTTATTTA
1 TTTATT-TTTTAAACTATTTA
42776354 TTTATTTT
1 TTTATTTT
42776362 CAATTTTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 2 0.08
21 13 0.52
22 10 0.40
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.72
Consensus pattern (20 bp):
TTTATTTTTTAAACTATTTA
Found at i:42776358 original size:18 final size:18
Alignment explanation
Indices: 42776326--42776361 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
42776316 TTTTTTAAAC
42776326 TATTTCATTTATTATTTT
1 TATTTCATTTATTATTTT
42776344 TATTT-ATTTATTTATTTT
1 TATTTCATTTA-TTATTTT
42776362 CAATTTTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.75
Consensus pattern (18 bp):
TATTTCATTTATTATTTT
Found at i:42776548 original size:16 final size:15
Alignment explanation
Indices: 42776533--42776579 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
42776523 TTTAGATTAT
42776533 TTATTATTTATGTTA
1 TTATTATTTATGTTA
*
42776548 TTATTATATATTGTTA
1 TTATTATTTA-TGTTA
* *
42776564 TTGTTATTTATATTA
1 TTATTATTTATGTTA
42776579 T
1 T
42776580 CATTTTCATA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
15 14 0.52
16 13 0.48
ACGTcount: A:0.28, C:0.00, G:0.06, T:0.66
Consensus pattern (15 bp):
TTATTATTTATGTTA
Found at i:42776629 original size:22 final size:22
Alignment explanation
Indices: 42776590--42776631 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
42776580 CATTTTCATA
* *
42776590 ATTATTATTTATGCATATTAAT
1 ATTATGATTTATGAATATTAAT
*
42776612 ATTATGATTTATTAATATTA
1 ATTATGATTTATGAATATTA
42776632 TTGCTATACT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.55
Consensus pattern (22 bp):
ATTATGATTTATGAATATTAAT
Found at i:42778694 original size:22 final size:24
Alignment explanation
Indices: 42778643--42778695 Score: 83
Period size: 23 Copynumber: 2.2 Consensus size: 24
42778633 ATATAAGTAT
42778643 AAGAACAAACCCTGTTTGGTAGAAA
1 AAGAA-AAACCCTGTTTGGTAGAAA
42778668 AAGAAAAA-CCTGTTTGGTAG-AA
1 AAGAAAAACCCTGTTTGGTAGAAA
42778690 AAGAAA
1 AAGAAA
42778696 CGAACCTTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
22 8 0.29
23 12 0.43
24 3 0.11
25 5 0.18
ACGTcount: A:0.49, C:0.11, G:0.21, T:0.19
Consensus pattern (24 bp):
AAGAAAAACCCTGTTTGGTAGAAA
Found at i:42782236 original size:52 final size:53
Alignment explanation
Indices: 42782136--42782236 Score: 123
Period size: 52 Copynumber: 1.9 Consensus size: 53
42782126 ATAAAAATAA
* * * * *
42782136 ATGTATTTCTTTCTTTCAGAGTTTCACATGTATAGTTGCATGAAATTAATTTG
1 ATGTATTTCATTCTTTCAAAGTTTCACATGTATAATTACACGAAATTAATTTG
* * *
42782189 ATGTATTT-ATTCTTTTAAAGTTTCATATGTATAATTACACGAGATTAA
1 ATGTATTTCATTCTTTCAAAGTTTCACATGTATAATTACACGAAATTAA
42782237 AGTTTATGTA
Statistics
Matches: 40, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
52 32 0.80
53 8 0.20
ACGTcount: A:0.31, C:0.10, G:0.13, T:0.47
Consensus pattern (53 bp):
ATGTATTTCATTCTTTCAAAGTTTCACATGTATAATTACACGAAATTAATTTG
Found at i:42785968 original size:5 final size:5
Alignment explanation
Indices: 42785958--42786004 Score: 64
Period size: 5 Copynumber: 10.0 Consensus size: 5
42785948 AAACCCTTCC
*
42785958 TCTTT TCTTT TCTTT TCTTT TCTTT T-TTT T-TTT T-TTT GCTTT TCTTT
1 TCTTT TCTTT TCTTT TCTTT TCTTT TCTTT TCTTT TCTTT TCTTT TCTTT
42786005 GTTGTTGTTG
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
4 11 0.28
5 28 0.72
ACGTcount: A:0.00, C:0.15, G:0.02, T:0.83
Consensus pattern (5 bp):
TCTTT
Found at i:42785990 original size:22 final size:22
Alignment explanation
Indices: 42785960--42786004 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
42785950 ACCCTTCCTC
42785960 TTTTCTTTTCTTTT-CTTTTCTT
1 TTTTCTTTT-TTTTGCTTTTCTT
*
42785982 TTTTTTTTTTTTTGCTTTTCTT
1 TTTTCTTTTTTTTGCTTTTCTT
42786004 T
1 T
42786005 GTTGTTGTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 4 0.19
22 17 0.81
ACGTcount: A:0.00, C:0.13, G:0.02, T:0.84
Consensus pattern (22 bp):
TTTTCTTTTTTTTGCTTTTCTT
Found at i:42798542 original size:22 final size:22
Alignment explanation
Indices: 42798492--42798543 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 22
42798482 CTCTTATAAA
*
42798492 ATAT-TATAAAATATTTGATAT
1 ATATATATAAAATATGTGATAT
* *
42798513 AAAAATATAAAATATG-GTATAT
1 ATATATATAAAATATGTG-ATAT
42798535 ATATATATA
1 ATATATATA
42798544 TATAATATTA
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
21 3 0.12
22 21 0.88
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.40
Consensus pattern (22 bp):
ATATATATAAAATATGTGATAT
Found at i:42806808 original size:17 final size:17
Alignment explanation
Indices: 42806772--42806816 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 17
42806762 CCGATATAAT
* *
42806772 AAATATATTT-ATTTTT
1 AAATATTTTTAATTTTA
*
42806788 AAATTTTTTTAATTTTA
1 AAATATTTTTAATTTTA
42806805 AAATATTTTTAA
1 AAATATTTTTAA
42806817 AATACTTTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
16 8 0.33
17 16 0.67
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
AAATATTTTTAATTTTA
Found at i:42807185 original size:19 final size:19
Alignment explanation
Indices: 42807161--42807198 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
42807151 ATGATTTTTT
42807161 AAAAATT-TAAAATATATTA
1 AAAAATTATAAAAT-TATTA
42807180 AAAAATTATAAAATTATTA
1 AAAAATTATAAAATTATTA
42807199 TAAAGTTACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (19 bp):
AAAAATTATAAAATTATTA
Found at i:42807211 original size:19 final size:20
Alignment explanation
Indices: 42807169--42807211 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
42807159 TTAAAAATTT
*
42807169 AAAATATATTAAAAAATTAT
1 AAAATATATTAAAAAATTAC
* *
42807189 AAAAT-TATTATAAAGTTAC
1 AAAATATATTAAAAAATTAC
42807208 AAAA
1 AAAA
42807212 AAATAATTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (20 bp):
AAAATATATTAAAAAATTAC
Found at i:42815124 original size:18 final size:17
Alignment explanation
Indices: 42815098--42815136 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
42815088 TCATTGTGCA
*
42815098 TAATCTCTATTTTAATAC
1 TAATCTCTACTTTAAT-C
*
42815116 TAATTTCTACTTTAATC
1 TAATCTCTACTTTAATC
42815133 TAAT
1 TAAT
42815137 AAGAAAAGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.33, C:0.15, G:0.00, T:0.51
Consensus pattern (17 bp):
TAATCTCTACTTTAATC
Found at i:42816638 original size:29 final size:31
Alignment explanation
Indices: 42816587--42816648 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 31
42816577 TGTCTATATC
*
42816587 TTTATAATTTTTAAAGGATTAAA-T-CAATT
1 TTTATAATTTTTAAAGGACTAAAGTACAATT
** *
42816616 TTTATAATTTTTAGGGGGCTAAAGTACAATT
1 TTTATAATTTTTAAAGGACTAAAGTACAATT
42816647 TT
1 TT
42816649 ACCTTTACTA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 19 0.70
30 1 0.04
31 7 0.26
ACGTcount: A:0.35, C:0.05, G:0.13, T:0.47
Consensus pattern (31 bp):
TTTATAATTTTTAAAGGACTAAAGTACAATT
Found at i:42818265 original size:12 final size:12
Alignment explanation
Indices: 42818248--42818280 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
42818238 TTTTTATATA
*
42818248 TTATTTATTTAT
1 TTATTTATCTAT
42818260 TTATTTATCTAT
1 TTATTTATCTAT
42818272 TTA-TTATCT
1 TTATTTATCT
42818281 CTTACCCTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 6 0.30
12 14 0.70
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.70
Consensus pattern (12 bp):
TTATTTATCTAT
Found at i:42824369 original size:11 final size:11
Alignment explanation
Indices: 42824353--42824381 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
42824343 ACATGCCTTG
42824353 GCCAATCATGT
1 GCCAATCATGT
42824364 GCCAATCATGT
1 GCCAATCATGT
42824375 GCCAATC
1 GCCAATC
42824382 TCGAACTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.28, C:0.31, G:0.17, T:0.24
Consensus pattern (11 bp):
GCCAATCATGT
Found at i:42830474 original size:21 final size:20
Alignment explanation
Indices: 42830450--42830493 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
42830440 ATTAGGACTC
* *
42830450 TTTTTCTTTTTTATTCATAAA
1 TTTTGCTTTGTTA-TCATAAA
*
42830471 TTTTGCTTTGTTATCTTAAA
1 TTTTGCTTTGTTATCATAAA
42830491 TTT
1 TTT
42830494 AAGCAAAGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.20, C:0.09, G:0.05, T:0.66
Consensus pattern (20 bp):
TTTTGCTTTGTTATCATAAA
Found at i:42841339 original size:40 final size:40
Alignment explanation
Indices: 42841284--42841391 Score: 189
Period size: 40 Copynumber: 2.7 Consensus size: 40
42841274 TAAGAAGGTG
* * *
42841284 ATTGATGAATAAGAAGAGTTACAGAGAAATTGGATATTTT
1 ATTGATGAATGAGAAGAGTTACAGAGAAAATGGATATTTA
42841324 ATTGATGAATGAGAAGAGTTACAGAGAAAATGGATATTTA
1 ATTGATGAATGAGAAGAGTTACAGAGAAAATGGATATTTA
42841364 ATTGATGAATGAGAAGAGTTACAGAGAA
1 ATTGATGAATGAGAAGAGTTACAGAGAA
42841392 GATAGGTATT
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 65 1.00
ACGTcount: A:0.44, C:0.03, G:0.25, T:0.28
Consensus pattern (40 bp):
ATTGATGAATGAGAAGAGTTACAGAGAAAATGGATATTTA
Found at i:42846807 original size:28 final size:28
Alignment explanation
Indices: 42846765--42846820 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
42846755 ACTGTCTTAA
* *
42846765 CAACTACTGATGTGACATTAAATCAAAT
1 CAACGACTGACGTGACATTAAATCAAAT
*
42846793 CAACGACTGACGTGACATTAAATTAAAT
1 CAACGACTGACGTGACATTAAATCAAAT
42846821 AAAATTTTGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.43, C:0.18, G:0.12, T:0.27
Consensus pattern (28 bp):
CAACGACTGACGTGACATTAAATCAAAT
Found at i:42863941 original size:21 final size:19
Alignment explanation
Indices: 42863893--42863941 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 19
42863883 AAAATTAGGG
*
42863893 ATTTTATAATTTTTTAAATA
1 ATTTTA-AATTTTTTAAAAA
42863913 ATTGTTAAATTTTTTTAATAAA
1 ATT-TTAAA-TTTTTTAA-AAA
42863935 ATTTTAA
1 ATTTTAA
42863942 TAATATTTGA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 5 0.20
21 15 0.60
22 5 0.20
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (19 bp):
ATTTTAAATTTTTTAAAAA
Found at i:42875287 original size:24 final size:24
Alignment explanation
Indices: 42875251--42875302 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
42875241 TTTAAAATTT
* *
42875251 TATAAAATTTTAAAATGATAAAAA
1 TATAAAATATTAAAATAATAAAAA
* *
42875275 TATAAACTATTAAAATAATAAAAT
1 TATAAAATATTAAAATAATAAAAA
42875299 TATA
1 TATA
42875303 TTTTTATTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.35
Consensus pattern (24 bp):
TATAAAATATTAAAATAATAAAAA
Found at i:42875923 original size:121 final size:122
Alignment explanation
Indices: 42875705--42875925 Score: 417
Period size: 121 Copynumber: 1.8 Consensus size: 122
42875695 GTTATTTCTG
42875705 GGTTCAGCTAGAAAAAAGTGGGTAGAGATTTAGAAAGAAATGGAGAGAGAAATAAGCTAAACAAA
1 GGTTCAGCTA-AAAAAAGTGGGTAGAGATTTAGAAAGAAATGGAGAGAGAAATAAGCTAAACAAA
42875770 TTTGTTTGTTAGTTTAATAAATTAATAAAAATATTTCAAATTAAATTAAATATTATAT
65 TTTGTTTGTTAGTTTAATAAATTAATAAAAATATTTCAAATTAAATTAAATATTATAT
42875828 GGTTCAGCT-AAAAAAGTGGGTAGAGATTTAGAAAGAAATGGAGAGAGAAATAAGCTAAACAAAT
1 GGTTCAGCTAAAAAAAGTGGGTAGAGATTTAGAAAGAAATGGAGAGAGAAATAAGCTAAACAAAT
*
42875892 TTGTTTGTTAGTTTAATAAATTAATATAAATATT
66 TTGTTTGTTAGTTTAATAAATTAATAAAAATATT
42875926 ACCATATACA
Statistics
Matches: 97, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
121 88 0.91
123 9 0.09
ACGTcount: A:0.46, C:0.04, G:0.19, T:0.31
Consensus pattern (122 bp):
GGTTCAGCTAAAAAAAGTGGGTAGAGATTTAGAAAGAAATGGAGAGAGAAATAAGCTAAACAAAT
TTGTTTGTTAGTTTAATAAATTAATAAAAATATTTCAAATTAAATTAAATATTATAT
Found at i:42877428 original size:24 final size:24
Alignment explanation
Indices: 42877399--42877450 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
42877389 TTTAAAATTT
* *
42877399 TATAAAATTTTAAAATGATAAAAA
1 TATAAAATATTAAAATAATAAAAA
* *
42877423 TATAAACTATTAAAATAATAAAAT
1 TATAAAATATTAAAATAATAAAAA
42877447 TATA
1 TATA
42877451 TTTTTATTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.35
Consensus pattern (24 bp):
TATAAAATATTAAAATAATAAAAA
Found at i:42877855 original size:226 final size:226
Alignment explanation
Indices: 42877461--42877912 Score: 904
Period size: 226 Copynumber: 2.0 Consensus size: 226
42877451 TTTTTATTAT
42877461 CTTAAAAATACAAAATTTAATTTTACTTTCCCTTTAAAATAAATTTTTTGACTTCCACCTGGGTG
1 CTTAAAAATACAAAATTTAATTTTACTTTCCCTTTAAAATAAATTTTTTGACTTCCACCTGGGTG
42877526 AGAGTGGAGCTAAAATATCTTAAAGCATGGGCCTCATACATGGATGGAATTTGCTGTGTCCATTG
66 AGAGTGGAGCTAAAATATCTTAAAGCATGGGCCTCATACATGGATGGAATTTGCTGTGTCCATTG
42877591 CCTCTTTAGGGTAATAGACTTGAATCTTACGTATTTCCCTTTCTGTCTAACCCTACTCATATATC
131 CCTCTTTAGGGTAATAGACTTGAATCTTACGTATTTCCCTTTCTGTCTAACCCTACTCATATATC
42877656 TGAGCAACAAGGCAGTAAAAAGGTTTTGAGA
196 TGAGCAACAAGGCAGTAAAAAGGTTTTGAGA
42877687 CTTAAAAATACAAAATTTAATTTTACTTTCCCTTTAAAATAAATTTTTTGACTTCCACCTGGGTG
1 CTTAAAAATACAAAATTTAATTTTACTTTCCCTTTAAAATAAATTTTTTGACTTCCACCTGGGTG
42877752 AGAGTGGAGCTAAAATATCTTAAAGCATGGGCCTCATACATGGATGGAATTTGCTGTGTCCATTG
66 AGAGTGGAGCTAAAATATCTTAAAGCATGGGCCTCATACATGGATGGAATTTGCTGTGTCCATTG
42877817 CCTCTTTAGGGTAATAGACTTGAATCTTACGTATTTCCCTTTCTGTCTAACCCTACTCATATATC
131 CCTCTTTAGGGTAATAGACTTGAATCTTACGTATTTCCCTTTCTGTCTAACCCTACTCATATATC
42877882 TGAGCAACAAGGCAGTAAAAAGGTTTTGAGA
196 TGAGCAACAAGGCAGTAAAAAGGTTTTGAGA
42877913 ATGACAGGTG
Statistics
Matches: 226, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
226 226 1.00
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.35
Consensus pattern (226 bp):
CTTAAAAATACAAAATTTAATTTTACTTTCCCTTTAAAATAAATTTTTTGACTTCCACCTGGGTG
AGAGTGGAGCTAAAATATCTTAAAGCATGGGCCTCATACATGGATGGAATTTGCTGTGTCCATTG
CCTCTTTAGGGTAATAGACTTGAATCTTACGTATTTCCCTTTCTGTCTAACCCTACTCATATATC
TGAGCAACAAGGCAGTAAAAAGGTTTTGAGA
Found at i:42878795 original size:29 final size:29
Alignment explanation
Indices: 42878741--42878796 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
42878731 AATTTAAAAA
* *
42878741 TATTTTTAAAATACTTTTTATTTGTTTTT
1 TATTTTTAAAATAATTTTTATGTGTTTTT
42878770 TATTTTTAAAATAATTTTT-TGGTGTTT
1 TATTTTTAAAATAATTTTTAT-GTGTTT
42878797 ATTAAAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 1 0.04
29 23 0.96
ACGTcount: A:0.25, C:0.02, G:0.07, T:0.66
Consensus pattern (29 bp):
TATTTTTAAAATAATTTTTATGTGTTTTT
Found at i:42886652 original size:3 final size:3
Alignment explanation
Indices: 42886630--42886694 Score: 85
Period size: 3 Copynumber: 21.7 Consensus size: 3
42886620 AGCCTCACCT
* * * *
42886630 TCA TCA CCA TCA TCA CCA TCA TCA CCA TCA TTA TCA TCA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
*
42886678 CCA TCA TCA TCA TCA TC
1 TCA TCA TCA TCA TCA TC
42886695 TGAGTCTCCT
Statistics
Matches: 52, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.32, C:0.38, G:0.00, T:0.29
Consensus pattern (3 bp):
TCA
Found at i:42891954 original size:2 final size:2
Alignment explanation
Indices: 42891947--42891971 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
42891937 CTCGCCGGTA
42891947 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
42891972 GCTATTTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:42894649 original size:130 final size:130
Alignment explanation
Indices: 42894416--42894670 Score: 456
Period size: 130 Copynumber: 2.0 Consensus size: 130
42894406 TTTCAGATGT
*
42894416 AATATCACTGATATGCATTTCATGTGTCGGTGATAACTAGTTTCGATAAACATAAATGTTAGCAA
1 AATATCACTGATACGCATTTCATGTGTCGGTGATAACTAGTTTCGATAAACATAAATGTTAGCAA
*
42894481 TTCCAAAGGACACTAACAATAATATGGACTTAGATTTGCTTGGTTGTCTCCCCTTTACAACTAAC
66 TTCCAAAGGACACTAACAATAATATGAACTTAGATTTGCTTGGTTGTCTCCCCTTTACAACTAAC
* *
42894546 AATATCACTGATACGCATTTCGTGTGTCGGTGATAACTAGTTTCGATAAACGTAAATGTTAGCAA
1 AATATCACTGATACGCATTTCATGTGTCGGTGATAACTAGTTTCGATAAACATAAATGTTAGCAA
* *
42894611 TTTCAAAGGACACTAACAATAATCTGAACTTAGATTTGCTTGGTTGTCTCCCCTTTACAA
66 TTCCAAAGGACACTAACAATAATATGAACTTAGATTTGCTTGGTTGTCTCCCCTTTACAA
42894671 TCTAGAGATG
Statistics
Matches: 119, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
130 119 1.00
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.33
Consensus pattern (130 bp):
AATATCACTGATACGCATTTCATGTGTCGGTGATAACTAGTTTCGATAAACATAAATGTTAGCAA
TTCCAAAGGACACTAACAATAATATGAACTTAGATTTGCTTGGTTGTCTCCCCTTTACAACTAAC
Found at i:42897680 original size:29 final size:29
Alignment explanation
Indices: 42897602--42897723 Score: 87
Period size: 29 Copynumber: 4.3 Consensus size: 29
42897592 TTAAAATATG
* * * *
42897602 TAATTTATAAAAATTCTA-ATACGTTTTTT
1 TAATTT-TAAATATTTTATATAAGTTTTAT
42897631 TAATTTTAAATATTTTATATAAGTTTTAT
1 TAATTTTAAATATTTTATATAAGTTTTAT
* *
42897660 TAATTTATAATTCTTTT-TATAA--TTTAT
1 TAATTT-TAAATATTTTATATAAGTTTTAT
* *
42897687 TAGATTTT-TATATTTT-TATATACTTTTA-
1 TA-ATTTTAAATATTTTATATA-AGTTTTAT
42897715 TAATTTTAA
1 TAATTTTAA
42897724 TAAGTATATA
Statistics
Matches: 76, Mismatches: 10, Indels: 15
0.75 0.10 0.15
Matches are distributed among these distances:
26 9 0.12
27 14 0.18
28 15 0.20
29 30 0.39
30 8 0.11
ACGTcount: A:0.35, C:0.03, G:0.02, T:0.59
Consensus pattern (29 bp):
TAATTTTAAATATTTTATATAAGTTTTAT
Found at i:42897696 original size:18 final size:17
Alignment explanation
Indices: 42897673--42897721 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 17
42897663 TTTATAATTC
42897673 TTTTTATAATTTATTAGA
1 TTTTTATAATTT-TTAGA
*
42897691 TTTTTAT-ATTTTTATA
1 TTTTTATAATTTTTAGA
42897707 TACTTTTATAATTTT
1 T--TTTTATAATTTT
42897722 AATAAGTATA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
16 5 0.19
17 4 0.15
18 13 0.48
19 5 0.19
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (17 bp):
TTTTTATAATTTTTAGA
Found at i:42897721 original size:19 final size:19
Alignment explanation
Indices: 42897634--42897721 Score: 60
Period size: 20 Copynumber: 4.6 Consensus size: 19
42897624 GTTTTTTTAA
*
42897634 TTTTA-AATATTTTATATAAG
1 TTTTATAAT-TTTTATAT-AC
* *
42897654 TTTTATTAATTTATA-ATTC
1 TTTTA-TAATTTTTATATAC
*
42897673 TTTTTATAATTTATTAGAT--
1 -TTTTATAATTT-TTATATAC
42897692 TTTTAT-ATTTTTATATAC
1 TTTTATAATTTTTATATAC
42897710 TTTTATAATTTT
1 TTTTATAATTTT
42897722 AATAAGTATA
Statistics
Matches: 55, Mismatches: 5, Indels: 17
0.71 0.06 0.22
Matches are distributed among these distances:
16 5 0.09
17 4 0.07
18 12 0.22
19 11 0.20
20 14 0.25
21 6 0.11
22 3 0.05
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (19 bp):
TTTTATAATTTTTATATAC
Found at i:42898690 original size:17 final size:17
Alignment explanation
Indices: 42898668--42898701 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
42898658 TTAATCCTTG
*
42898668 AAGTACTCATATCAATC
1 AAGTACTCACATCAATC
*
42898685 AAGTACTTACATCAATC
1 AAGTACTCACATCAATC
42898702 TATTCATTAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.41, C:0.24, G:0.06, T:0.29
Consensus pattern (17 bp):
AAGTACTCACATCAATC
Found at i:42907468 original size:14 final size:14
Alignment explanation
Indices: 42907449--42907494 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
42907439 ATACGCAAGC
42907449 TATCATAACTTGTT
1 TATCATAACTTGTT
* *
42907463 TATCATGA-TT-TC
1 TATCATAACTTGTT
42907475 TATCATAACTTGTT
1 TATCATAACTTGTT
42907489 TATCAT
1 TATCAT
42907495 GATTTTTCTT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
12 8 0.31
13 4 0.15
14 14 0.54
ACGTcount: A:0.28, C:0.15, G:0.07, T:0.50
Consensus pattern (14 bp):
TATCATAACTTGTT
Found at i:42907484 original size:26 final size:26
Alignment explanation
Indices: 42907448--42907499 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
42907438 GATACGCAAG
42907448 CTATCATAACTTGTTTATCATGATTT
1 CTATCATAACTTGTTTATCATGATTT
42907474 CTATCATAACTTGTTTATCATGATTT
1 CTATCATAACTTGTTTATCATGATTT
42907500 TTCTTTCTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.27, C:0.15, G:0.08, T:0.50
Consensus pattern (26 bp):
CTATCATAACTTGTTTATCATGATTT
Found at i:42910209 original size:3 final size:3
Alignment explanation
Indices: 42910201--42910250 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
42910191 ATCGAGGAAA
42910201 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
42910249 AA
1 AA
42910251 AGCGACCCTT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:42912996 original size:18 final size:18
Alignment explanation
Indices: 42912973--42913011 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
42912963 AGATTTATCA
42912973 TTTATTTTAAATATATAT
1 TTTATTTTAAATATATAT
* *
42912991 TTTATTTTTATTATATAT
1 TTTATTTTAAATATATAT
42913009 TTT
1 TTT
42913012 CTCGTATCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (18 bp):
TTTATTTTAAATATATAT
Found at i:42920847 original size:13 final size:13
Alignment explanation
Indices: 42920825--42920856 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
42920815 TATTTTGCTG
*
42920825 AAAGACAAAGAAA
1 AAAGAAAAAGAAA
42920838 AAAGAAAAAGAAA
1 AAAGAAAAAGAAA
42920851 AAAGAA
1 AAAGAA
42920857 GGGCCCACGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.81, C:0.03, G:0.16, T:0.00
Consensus pattern (13 bp):
AAAGAAAAAGAAA
Found at i:42921501 original size:17 final size:17
Alignment explanation
Indices: 42921469--42921501 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
42921459 ATATTTAATA
*
42921469 TATATTTGATTGAAAAG
1 TATATTTGATTAAAAAG
42921486 TATATTTGATTAAAAA
1 TATATTTGATTAAAAA
42921502 TAAAAATATA
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:0.45, C:0.00, G:0.12, T:0.42
Consensus pattern (17 bp):
TATATTTGATTAAAAAG
Found at i:42924383 original size:234 final size:234
Alignment explanation
Indices: 42923851--42924526 Score: 835
Period size: 234 Copynumber: 2.9 Consensus size: 234
42923841 TTTGAATTTA
* * *
42923851 TTAGGTTAACATGTATGAGGAGTAAAAACTTCTTTTCATCCATTTTCTCGGTAAACAAACGGGAA
1 TTAGGTTTACATGTATGAGTAGT-AAAACTTCTTTTCATCCGTTTTCTCGGTAAACAAACGGGAA
* ** ** **** * * *
42923916 TTTGATCTTAAAGATCCTTAAGCTTACAAGTCA-AAAGTTT-CATCTGT-TTTCCTTCTTTTTTT
65 TTTGATCTTAAAGATCCTTAAGCTTACATGTCATGTA-TTTGCA-AAGTCTAAATTTCATCTGTT
* * * *
42923978 TTTTTTTTTTGCTTGATCTGTTG-TTGGTTGGTGAAAAAGTGAAGGAAAAGTTGCGGAAAATGAA
128 TTTCTTTTTGGTTTGATCTGTTGTTTGGTTGGTGAGAAAGTGAAGGAAAAGTTGCGGAAAATGAA
* *
42924042 TTTGAATTTATTAATTGATGTAACATTAAAATATAAATTATGATG
193 TTTGAA--T-TTAATTGATGTAAAATTAAAATATAAATTACGATG
* *
42924087 TTAGGTTTACATGTATGAGTAGTAAAAGCTTCTTTTCATCCGTTTTCTCGATAAATAAACGGGAA
1 TTAGGTTTACATGTATGAGTAGTAAAA-CTTCTTTTCATCCGTTTTCTCGGTAAACAAACGGGAA
* * * *
42924152 TTTGATCTTAAAGGTCTTTAAGCTTATATGATTATGTATTTGCAAAGTCTAAATTTCATCTGTTT
65 TTTGATCTTAAAGATCCTTAAGCTTACATG-TCATGTATTTGCAAAGTCTAAATTTCATCTGTTT
* **
42924217 TTCTTTTTGGTTTGATCTGTTGTTTGGTTGGTGAGAAAGTGAAGGGAAAGTTGCGGAATTTGAAT
129 TTCTTTTTGGTTTGATCTGTTGTTTGGTTGGTGAGAAAGTGAAGGAAAAGTTGCGGAAAATGAAT
*
42924282 TTGAATTT-ATTGATGTAAAATTAAAATATGAA-TACGATG
194 TTGAATTTAATTGATGTAAAATTAAAATATAAATTACGATG
* *
42924321 TTAGGTTTACATGTATGAGTAGTAAATACTTCTTGTCATCCGTTTTCTCGGTCAACAAACGGGAA
1 TTAGGTTTACATGTATGAGTAGTAAA-ACTTCTTTTCATCCGTTTTCTCGGTAAACAAACGGGAA
* * * * *
42924386 TTTGATCTTAAAGATCCTTAAGCTTGCATGGTCATGTTTTTGCGAAGTCAAAATTTCATCTGCTT
65 TTTGATCTTAAAGATCCTTAAGCTTACAT-GTCATGTATTTGCAAAGTCTAAATTTCATCTGTTT
* * *
42924451 TTCTTTTTGGTTTGATCTGTTTTTTGGTTGGTGAGAAAGTGAATGAAAAGTTGCTGAAAATGAA-
129 TTCTTTTTGGTTTGATCTGTTGTTTGGTTGGTGAGAAAGTGAAGGAAAAGTTGCGGAAAATGAAT
*
42924515 TTGAATTGAATT
194 TTGAATTTAATT
42924527 TGTTGGTTGA
Statistics
Matches: 380, Mismatches: 51, Indels: 20
0.84 0.11 0.04
Matches are distributed among these distances:
233 7 0.02
234 180 0.47
235 28 0.07
236 83 0.22
237 8 0.02
238 31 0.08
239 43 0.11
ACGTcount: A:0.29, C:0.10, G:0.20, T:0.41
Consensus pattern (234 bp):
TTAGGTTTACATGTATGAGTAGTAAAACTTCTTTTCATCCGTTTTCTCGGTAAACAAACGGGAAT
TTGATCTTAAAGATCCTTAAGCTTACATGTCATGTATTTGCAAAGTCTAAATTTCATCTGTTTTT
CTTTTTGGTTTGATCTGTTGTTTGGTTGGTGAGAAAGTGAAGGAAAAGTTGCGGAAAATGAATTT
GAATTTAATTGATGTAAAATTAAAATATAAATTACGATG
Found at i:42929363 original size:96 final size:99
Alignment explanation
Indices: 42929043--42930180 Score: 1371
Period size: 105 Copynumber: 11.2 Consensus size: 99
42929033 AAAGAAAAAT
*
42929043 AAGAAGAAGAAGAAGAGCAATGAGAATGTA-GATGCTATTGAGGCTATTGCTGTTGCTGTTGTTG
1 AAGAAGAAGAAGAAGAGCAATGAAAATG-AGGATGCTATTGAGGCTA------TTGCTGTTGTTG
* *
42929107 ATAGTGCAATTGATGTAGGGAGTAATGAAATT-----GAA-
59 ATGGTGCAATTGATGTAGGGAGTGATGAAATTGAAAAGAAG
*
42929142 AAGAAGAAGAAGAAGAGCAATGAAAATGAGGATGCTATTGAGGCAATTGCTGTTGTTGATGGTGC
1 AAGAAGAAGAAGAAGAGCAATGAAAATGAGGATGCTATTGAGGCTATTGCTGTTGTTGATGGTGC
42929207 AATTGATGTAGGGAGTGATGAAATT-----GAA-
66 AATTGATGTAGGGAGTGATGAAATTGAAAAGAAG
42929235 AAGAAGAAGAAGAAGAGCAATGAAAATGAGGATGCTATTGAGGCTATTGCTGTTGTTGATGGTGC
1 AAGAAGAAGAAGAAGAGCAATGAAAATGAGGATGCTATTGAGGCTATTGCTGTTGTTGATGGTGC
42929300 AATTGATGTAGGGAGTGATGAAATTGAAAAGAAG
66 AATTGATGTAGGGAGTGATGAAATTGAAAAGAAG
*
42929334 -A-AA-AAGAAGAAGAGCAATGAAAATGAGGATGCTATTGAGGCAATTGCTGTTGTTGATGGTGC
1 AAGAAGAAGAAGAAGAGCAATGAAAATGAGGATGCTATTGAGGCTATTGCTGTTGTTGATGGTGC
42929396 AATTGATGTAGGGAGTGATGAAATTGAAAAGAAG
66 AATTGATGTAGGGAGTGATGAAATTGAAAAGAAG
* * *
42929430 AAAAAGAAGAAGAAGAAGAAGAACAAAGAGAATGAGGAGGCTATTGAGGCTGATGCTGTTGCTGT
1 ---AAGAAGAAGAAGAAG-AG--CAATGAAAATGAGGATGCTATTGAGGCT-A-----TTGCTGT
* *
42929495 TGTTGATAGTGCAATTGATGCAGGGAGTGATGAAATTGAAAAGAAG
54 TGTTGATGGTGCAATTGATGTAGGGAGTGATGAAATTGAAAAGAAG
* * * ** * *
42929541 AAAAAGAAGAAGAAGAAGAAGAACAAAGAGAATGAGGAGGCTAAAGAGGCTATTTCCGTTGTTGA
1 ---AAGAAGAAGAAGAAG-AG--CAATGAAAATGAGGATGCTATTGAGGCTATTGCTGTTGTTGA
42929606 TGGTGCAATTGATGTAGGGAGTGATGAAATTGAAAAGAAG
60 TGGTGCAATTGATGTAGGGAGTGATGAAATTGAAAAGAAG
*
42929646 AAAAAGAAGAAGAAGAAGAAGGGCAATGAAAATGAGGATGCTGTTGAGGCTATTGCTGTTGTTGA
1 ---AAGAAGAAGAAGAAG-A--GCAATGAAAATGAGGATGCTATTGAGGCTATTGCTGTTGTTGA
*
42929711 TGGTGCAATTGATGAAGGGAGTGATGAAATTGAAAAGAAGAAAAAG
60 TGGTGCAATTGATGTAGGGAGTGATGAAATTG--AA-AAG---AAG
42929757 AAGAAGAAGAAGAAGAGCAATGAAAATGAGGATGCTATTGAGGCTATTGCTGTTGTTGATGGTGC
1 AAGAAGAAGAAGAAGAGCAATGAAAATGAGGATGCTATTGAGGCTATTGCTGTTGTTGATGGTGC
42929822 AATTGATGTAGGGAGTGATGAAATTGAAAAGAAG
66 AATTGATGTAGGGAGTGATGAAATTGAAAAGAAG
* * * * * * *
42929856 AAAAAGAAGAAGAAGAACAAAGAGAATGAGGAGGCTATT---GCTGTTGCTGTTGTTGATAGTGC
1 AAGAAGAAGAAGAAGAGCAATGAAAATGAGGATGCTATTGAGGCTATTGCTGTTGTTGATGGTGC
* *
42929918 AATTGACGCAGGGAGTGATGAAATTGAAAAGAAGAAAAAG
66 AATTGATGTAGGGAGTGATGAAATTG--AA-AAG---AAG
* * *
42929958 AAGAAGAAGAAGAAGAAGAACAAAGAGAATGAGGAGGCTATTGAGGCTATTGCTGTTGTTGATGG
1 AAGAAGAAGAAGAAG-AG--CAATGAAAATGAGGATGCTATTGAGGCTATTGCTGTTGTTGATGG
42930023 TGCAATTGATGTAGGGAGTGATGAAATTGAAAAGAAGAAAAAG
63 TGCAATTGATGTAGGGAGTGATGAAATTG--AA-AAG---AAG
42930066 AAGAAGAAGAAGAAGAGCAATGAAAATGAGGATGCTATTGAGGCTATTGCTGTTGTTGATGGTGC
1 AAGAAGAAGAAGAAGAGCAATGAAAATGAGGATGCTATTGAGGCTATTGCTGTTGTTGATGGTGC
*
42930131 AATTGATGTAGAGAGTGATGAAATTGAAAAGAAG
66 AATTGATGTAGGGAGTGATGAAATTGAAAAGAAG
42930165 ACA-AAGAAGAAGAAGA
1 A-AGAAGAAGAAGAAGA
42930181 AGAAGAAGAA
Statistics
Matches: 948, Mismatches: 48, Indels: 86
0.88 0.04 0.08
Matches are distributed among these distances:
93 134 0.14
96 137 0.14
97 2 0.00
98 7 0.01
99 99 0.10
100 2 0.00
101 2 0.00
102 32 0.03
103 7 0.01
105 323 0.34
106 1 0.00
107 6 0.01
108 92 0.10
110 1 0.00
111 103 0.11
ACGTcount: A:0.41, C:0.05, G:0.32, T:0.22
Consensus pattern (99 bp):
AAGAAGAAGAAGAAGAGCAATGAAAATGAGGATGCTATTGAGGCTATTGCTGTTGTTGATGGTGC
AATTGATGTAGGGAGTGATGAAATTGAAAAGAAG
Done.