Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 132263754
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: 132263754
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 372 characters in sequence are not A, C, G, or T
File 171 of 433
Found at i:53247792 original size:25 final size:25
Alignment explanation
Indices: 53247764--53247840 Score: 63
Period size: 25 Copynumber: 3.2 Consensus size: 25
53247754 AGTGGCCAAC
53247764 GTGATGAATGTGAAAGTGTATATAT
1 GTGATGAATGTGAAAGTGTATATAT
* * ***
53247789 GTGAT-AAGGCCG-AA-TGGCCA-AT
1 GTGATGAATG-TGAAAGTGTATATAT
*
53247811 GTGATGAATGTGAAAGTATATATAT
1 GTGATGAATGTGAAAGTGTATATAT
53247836 GTGAT
1 GTGAT
53247841 AGGGCCGAGC
Statistics
Matches: 36, Mismatches: 11, Indels: 10
0.63 0.19 0.18
Matches are distributed among these distances:
22 8 0.22
23 8 0.22
24 7 0.19
25 13 0.36
ACGTcount: A:0.35, C:0.05, G:0.29, T:0.31
Consensus pattern (25 bp):
GTGATGAATGTGAAAGTGTATATAT
Found at i:53254662 original size:53 final size:54
Alignment explanation
Indices: 53254536--53254662 Score: 141
Period size: 53 Copynumber: 2.4 Consensus size: 54
53254526 CTACTAAGGA
* * * *
53254536 TACATGGGAACCTTTCCTTTTGAAACTTACCATTTCCATGTCTTGACATGGCCT
1 TACATGGGATCCTTTCCTTATGAAACTCACCATTTCCATGCCTTGACATGGCCT
* * * * *
53254590 TACGTGGTATCCTTGCCTTATG-AACTCACCATTGT-CATGCCTTGGCATGGTCT
1 TACATGGGATCCTTTCCTTATGAAACTCACCATT-TCCATGCCTTGACATGGCCT
*
53254643 TACATGGGATCTTTTCCTTA
1 TACATGGGATCCTTTCCTTA
53254663 CTATTTATCA
Statistics
Matches: 59, Mismatches: 13, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
53 41 0.69
54 18 0.31
ACGTcount: A:0.20, C:0.25, G:0.17, T:0.38
Consensus pattern (54 bp):
TACATGGGATCCTTTCCTTATGAAACTCACCATTTCCATGCCTTGACATGGCCT
Found at i:53255249 original size:19 final size:19
Alignment explanation
Indices: 53255225--53255267 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
53255215 TACCTATGGA
53255225 AACATCAAATTCCCACTCT
1 AACATCAAATTCCCACTCT
53255244 AACATCAAATTCCCACTCT
1 AACATCAAATTCCCACTCT
53255263 AACAT
1 AACAT
53255268 GTACTTATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.40, C:0.35, G:0.00, T:0.26
Consensus pattern (19 bp):
AACATCAAATTCCCACTCT
Found at i:53258458 original size:5 final size:5
Alignment explanation
Indices: 53258450--53258476 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
53258440 CAAAAATAAA
53258450 ATTTT ATTTT ATTTT ATTTT ATTTT AT
1 ATTTT ATTTT ATTTT ATTTT ATTTT AT
53258477 GATTGGCATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (5 bp):
ATTTT
Found at i:53262634 original size:292 final size:292
Alignment explanation
Indices: 53262075--53262661 Score: 1059
Period size: 292 Copynumber: 2.0 Consensus size: 292
53262065 GCTAAGCTCT
* *
53262075 TCGCCTTTGCAAGCTCTGTCAAATAGAACGACAATTTCTTTCAGCTTAAGAATCTCAACTAATAG
1 TCGCCTTTGCAAACTCTGTCAAATAGAACGACAAATTCTTTCAGCTTAAGAATCTCAACTAATAG
* *
53262140 TCTGATTTCTTCATTCAATCCATCTTCGAAGCTTTTACACATTATAGCCTCGGAAGAAACACATT
66 TCTGATTTCTTCATTCAATCCATCTTCGAACCTTTTACACATTATAGCCTCAGAAGAAACACATT
* *
53262205 CACGAGTATGTTTGCTAAGTCGTATAAACTCTCTTTCGTATTCTGTTACCGACATACGGCCCTAT
131 CACGAGCATGTTTGCTAAGTCGTACAAACTCTCTTTCGTATTCTGTTACCGACATACGGCCCTAT
* *
53262270 TTCAATTCAAGAAATTTCTTTCATTTCTGATCAATGAACCTTTGACTGATGTATTTCTTTATAAA
196 TTCAATTCAAGAAATTCCTTTCATTTCTGATCAATGAACCTTTGACTAATGTATTTCTTTATAAA
53262335 TTCAACTTGAAAGAACTCCCAAGTAACTCTTTC
261 TTCAACTTGAAAGAACT-CCAAGTAACTCTTTC
53262368 TCGCCTTTGCAAACTCTGTCAAATAGAACGACAAATTCTTTCAGCTTAAGAATCTCAACTAATAG
1 TCGCCTTTGCAAACTCTGTCAAATAGAACGACAAATTCTTTCAGCTTAAGAATCTCAACTAATAG
53262433 TCTGATTTCTTCATTCAATCCATCTTCGAACCTTTTACACATTATAGCCTCAGAAGAAACACATT
66 TCTGATTTCTTCATTCAATCCATCTTCGAACCTTTTACACATTATAGCCTCAGAAGAAACACATT
* *
53262498 -ACGAGCATGTTTGCTAAGTCGTACAAACTCTTTTTCGTATTCTGTTACCGACATACGGCCCTGT
131 CACGAGCATGTTTGCTAAGTCGTACAAACTCTCTTTCGTATTCTGTTACCGACATACGGCCCTAT
53262562 TTCAATTCAAGAAATTCCTTTCATTTCTGATCAATGAACCTTTGACTAATGTATTTCTTTATAAA
196 TTCAATTCAAGAAATTCCTTTCATTTCTGATCAATGAACCTTTGACTAATGTATTTCTTTATAAA
*
53262627 TTCAACTTGAAAGAACTCCTAGTAACTCTTTC
261 TTCAACTTGAAAGAACTCCAAGTAACTCTTTC
53262659 TCG
1 TCG
53262662 AGGAACTACG
Statistics
Matches: 283, Mismatches: 11, Indels: 2
0.96 0.04 0.01
Matches are distributed among these distances:
291 17 0.06
292 140 0.49
293 126 0.45
ACGTcount: A:0.30, C:0.23, G:0.12, T:0.36
Consensus pattern (292 bp):
TCGCCTTTGCAAACTCTGTCAAATAGAACGACAAATTCTTTCAGCTTAAGAATCTCAACTAATAG
TCTGATTTCTTCATTCAATCCATCTTCGAACCTTTTACACATTATAGCCTCAGAAGAAACACATT
CACGAGCATGTTTGCTAAGTCGTACAAACTCTCTTTCGTATTCTGTTACCGACATACGGCCCTAT
TTCAATTCAAGAAATTCCTTTCATTTCTGATCAATGAACCTTTGACTAATGTATTTCTTTATAAA
TTCAACTTGAAAGAACTCCAAGTAACTCTTTC
Found at i:53264931 original size:37 final size:36
Alignment explanation
Indices: 53264881--53264967 Score: 147
Period size: 37 Copynumber: 2.3 Consensus size: 36
53264871 TACGAAGTCT
53264881 TACCCGGACATAATCTCCACACGTAGTCATCGGGTC
1 TACCCGGACATAATCTCCACACGTAGTCATCGGGTC
53264917 GTACCCGGACATAATCTCCACACGTAGTCATCGGGTC
1 -TACCCGGACATAATCTCCACACGTAGTCATCGGGTC
53264954 TCACCCGGAACATA
1 T-ACCCGG-ACATA
53264968 TTTCCAAATT
Statistics
Matches: 48, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
36 1 0.02
37 42 0.88
38 5 0.10
ACGTcount: A:0.26, C:0.33, G:0.20, T:0.21
Consensus pattern (36 bp):
TACCCGGACATAATCTCCACACGTAGTCATCGGGTC
Found at i:53265113 original size:49 final size:49
Alignment explanation
Indices: 53265042--53265289 Score: 451
Period size: 49 Copynumber: 5.0 Consensus size: 49
53265032 ACATATATAG
*
53265042 ATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATAT
1 ATATACATTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATAT
53265091 ATATACATTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATAT
1 ATATACATTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATAT
53265140 ATATACATTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATAT
1 ATATACATTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATAT
*
53265189 ATATACATTTTCGCATTCATCACATCGGCCATTAGGCCTTATCACATAT
1 ATATACATTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATAT
* *
53265238 ATATACATTTTCACATTCATCACATCAGCCATTAGGCCTTATATACATAT
1 ATATACATTTTCACATTCATCACATCGGCCATTAGGCCTTAT-CACATAT
53265288 AT
1 AT
53265290 TATTATGTAC
Statistics
Matches: 193, Mismatches: 5, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
49 185 0.96
50 8 0.04
ACGTcount: A:0.31, C:0.26, G:0.08, T:0.35
Consensus pattern (49 bp):
ATATACATTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATAT
Found at i:53287444 original size:34 final size:34
Alignment explanation
Indices: 53287367--53287446 Score: 92
Period size: 34 Copynumber: 2.4 Consensus size: 34
53287357 TATTGAAATG
* *
53287367 GGCTATGGCCCACATTGATACTGGTACTGTATTG
1 GGCTAAGGCCCACATTGATACTGGTACTGTATTC
*
53287401 GGCTAAGGCCCACATTGATATTGCG-ACTG-ATATC
1 GGCTAAGGCCCACATTGATACTG-GTACTGTAT-TC
*
53287435 GGCTTAGGCCCA
1 GGCTAAGGCCCA
53287447 GACTGTTCAA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
33 2 0.05
34 37 0.93
35 1 0.03
ACGTcount: A:0.23, C:0.24, G:0.26, T:0.28
Consensus pattern (34 bp):
GGCTAAGGCCCACATTGATACTGGTACTGTATTC
Found at i:53288087 original size:24 final size:24
Alignment explanation
Indices: 53288009--53288113 Score: 70
Period size: 24 Copynumber: 4.2 Consensus size: 24
53287999 TGTTACATCC
*
53288009 TGAGCTGATGAACAATAAGCTC-TA
1 TGAGCTGA-GAACAGTAAGCTCTTA
* *
53288033 TCGAGCT-AGAAATAGTAAGCTCTGA
1 T-GAGCTGAG-AACAGTAAGCTCTTA
** *
53288058 CAAGCTGAGAAGAGTAAGCTCTTA
1 TGAGCTGAGAACAGTAAGCTCTTA
* * *
53288082 TGAGCTGATATATCGGTAAGCTCATA
1 TGAGCTGAGA-A-CAGTAAGCTCTTA
53288108 TGAGCT
1 TGAGCT
53288114 ACGGTGAGTC
Statistics
Matches: 62, Mismatches: 13, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
23 1 0.02
24 36 0.58
25 9 0.15
26 16 0.26
ACGTcount: A:0.34, C:0.16, G:0.24, T:0.26
Consensus pattern (24 bp):
TGAGCTGAGAACAGTAAGCTCTTA
Found at i:53289113 original size:17 final size:17
Alignment explanation
Indices: 53289091--53289127 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
53289081 GGACATCCAT
53289091 TTAAAATTCTATAGCAA
1 TTAAAATTCTATAGCAA
* *
53289108 TTAAAATTCTTTAGCTA
1 TTAAAATTCTATAGCAA
53289125 TTA
1 TTA
53289128 GAACATCACT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.41, C:0.11, G:0.05, T:0.43
Consensus pattern (17 bp):
TTAAAATTCTATAGCAA
Found at i:53291851 original size:80 final size:81
Alignment explanation
Indices: 53291706--53291884 Score: 231
Period size: 80 Copynumber: 2.2 Consensus size: 81
53291696 GCTACTCGTT
* *
53291706 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGGACTTAACCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
* *
53291771 ATTTAGTAAC-TCGCA
66 ATATAGTAACTTAGCA
**
53291786 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCACAAATGCCTTC-GGATCTTAGTCC
1 CAAATGCCTTCGGGACTTAACCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC
**
53291849 GGATATAGTCGCTTAGCA
64 GGATATAGTAACTTAGCA
*
53291867 CAAA-GCCTTTGGGACTTA
1 CAAATGCCTTCGGGACTTA
53291885 GCTCGGACAT
Statistics
Matches: 87, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
79 3 0.03
80 74 0.85
81 10 0.11
ACGTcount: A:0.27, C:0.26, G:0.21, T:0.26
Consensus pattern (81 bp):
CAAATGCCTTCGGGACTTAACCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
ATATAGTAACTTAGCA
Found at i:53291885 original size:40 final size:40
Alignment explanation
Indices: 53291706--53291838 Score: 232
Period size: 40 Copynumber: 3.3 Consensus size: 40
53291696 GCTACTCGTT
* *
53291706 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
53291746 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
53291786 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
53291826 CAAATGCCTTCGG
1 CAAATGCCTTCGG
53291839 ATCTTAGTCC
Statistics
Matches: 90, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
40 88 0.98
41 2 0.02
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:53294626 original size:18 final size:18
Alignment explanation
Indices: 53294603--53294641 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
53294593 TTTAACTTGG
53294603 CATAATTAAGTACTTAAA
1 CATAATTAAGTACTTAAA
53294621 CATAATTAAGTACTTAAA
1 CATAATTAAGTACTTAAA
53294639 CAT
1 CAT
53294642 CATCAAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.49, C:0.13, G:0.05, T:0.33
Consensus pattern (18 bp):
CATAATTAAGTACTTAAA
Found at i:53295564 original size:49 final size:49
Alignment explanation
Indices: 53295500--53295609 Score: 168
Period size: 49 Copynumber: 2.3 Consensus size: 49
53295490 CACATAGCAA
*
53295500 GATGCCAATA-CCATATCCCAAATATGGTCTTACATAGGATCACATATC
1 GATGCCAATAGCCATATCCCAAATATAGTCTTACATAGGATCACATATC
* * * *
53295548 GATGCAAATAGCCATATCCCAGATATAGTCTTACATGGGATCATATATC
1 GATGCCAATAGCCATATCCCAAATATAGTCTTACATAGGATCACATATC
53295597 GATGCCAATAGCC
1 GATGCCAATAGCC
53295610 CAGCTATGGT
Statistics
Matches: 55, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
48 9 0.16
49 46 0.84
ACGTcount: A:0.35, C:0.24, G:0.15, T:0.26
Consensus pattern (49 bp):
GATGCCAATAGCCATATCCCAAATATAGTCTTACATAGGATCACATATC
Found at i:53295622 original size:43 final size:44
Alignment explanation
Indices: 53295516--53295625 Score: 114
Period size: 49 Copynumber: 2.4 Consensus size: 44
53295506 AATACCATAT
*
53295516 CCCAAATATGGTCTTACATAGGATCACATATCGATGCAAATAGCCATA
1 CCCAGATATGGTCTTACATAGGATCACATATCGATGCAAATAG----A
* * * *
53295564 TCCCAGATATAGTCTTACATGGGATCATATATCGATGCCAATAG-
1 -CCCAGATATGGTCTTACATAGGATCACATATCGATGCAAATAGA
*
53295608 CCCAGCTATGGTCTTACA
1 CCCAGATATGGTCTTACA
53295626 CGATGTCTCA
Statistics
Matches: 54, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
43 16 0.30
49 38 0.70
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.27
Consensus pattern (44 bp):
CCCAGATATGGTCTTACATAGGATCACATATCGATGCAAATAGA
Found at i:53295665 original size:42 final size:42
Alignment explanation
Indices: 53295558--53295665 Score: 121
Period size: 43 Copynumber: 2.5 Consensus size: 42
53295548 GATGCAAATA
* *
53295558 GCCATATCCCAGATATAGTCTTACATGGGATCATATATCGAT
1 GCCATATCCCAGATATGGTCTTACACGGGATCATATATCGAT
* * * *
53295600 GCCAATAGCCCAGCTATGGTCTTACACGATG-TC-TCATATGGAT
1 GCC-ATATCCCAGATATGGTCTTACACG-GGATCAT-ATATCGAT
53295643 GCCATATCCCAGATATGGTCTTA
1 GCCATATCCCAGATATGGTCTTA
53295666 TACAAAGTCT
Statistics
Matches: 55, Mismatches: 8, Indels: 6
0.80 0.12 0.09
Matches are distributed among these distances:
42 22 0.40
43 32 0.58
44 1 0.02
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.30
Consensus pattern (42 bp):
GCCATATCCCAGATATGGTCTTACACGGGATCATATATCGAT
Found at i:53295676 original size:42 final size:43
Alignment explanation
Indices: 53295592--53295676 Score: 109
Period size: 42 Copynumber: 2.0 Consensus size: 43
53295582 ATGGGATCAT
* * *
53295592 ATATCGATGCCAATAGCCCAGCTATGGTCTTACACGATGTCTC
1 ATATCGATGCCAATAGCCCAGATATGGTCTTACACAAAGTCTC
* * *
53295635 ATATGGATGCC-ATATCCCAGATATGGTCTTATACAAAGTCTC
1 ATATCGATGCCAATAGCCCAGATATGGTCTTACACAAAGTCTC
53295677 TTTTTTTGAA
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
42 26 0.72
43 10 0.28
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.29
Consensus pattern (43 bp):
ATATCGATGCCAATAGCCCAGATATGGTCTTACACAAAGTCTC
Found at i:53299657 original size:49 final size:49
Alignment explanation
Indices: 53299594--53299907 Score: 194
Period size: 49 Copynumber: 6.6 Consensus size: 49
53299584 ACATCTAAGT
*
53299594 CGATGCCATGTCCCAAACAGGTCTTACACTGACTTTCATATATCGAG-GC
1 CGATGCCATGTCCCAAACAGGTCTTACACTGACTCTCATATATCG-GTGC
* * * * * *
53299643 CGATGCCATATCCCAGACAGGTCTTACATTGGCTCTCATCTATCGGTGT
1 CGATGCCATGTCCCAAACAGGTCTTACACTGACTCTCATATATCGGTGC
* * **
53299692 CGATGCCATGTCCCAAACAGGTCTTACACTGA----CACATGTC-AAGC
1 CGATGCCATGTCCCAAACAGGTCTTACACTGACTCTCATATATCGGTGC
* * * *
53299736 TGATGCCATGTCCCAGACAAGTCTTACACT-AGC-CTGCATATCTCGAG-GC
1 CGATGCCATGTCCCAAACAGGTCTTACACTGA-CTCT-CATATATCG-GTGC
* * * * ** *
53299785 CGATG-CATGTCCCAGACATGTCTCACACT-AGCTCTCATCT-T-AATGT
1 CGATGCCATGTCCCAAACAGGTCTTACACTGA-CTCTCATATATCGGTGC
* * * *
53299831 CGGTGCCCTGTCCCAGACATGGTCTTACACTGGCTCTCATA-AT--GTGGC
1 CGATGCCATGTCCCAAACA-GGTCTTACACTGACTCTCATATATCGGT-GC
* *
53299879 CGATG-CATGTCCCAGACATGTCTTACACT
1 CGATGCCATGTCCCAAACAGGTCTTACACT
53299908 AGCACACATC
Statistics
Matches: 209, Mismatches: 41, Indels: 33
0.74 0.14 0.12
Matches are distributed among these distances:
43 1 0.00
44 28 0.13
45 5 0.02
46 15 0.07
47 26 0.12
48 58 0.28
49 76 0.36
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.27
Consensus pattern (49 bp):
CGATGCCATGTCCCAAACAGGTCTTACACTGACTCTCATATATCGGTGC
Found at i:53299888 original size:142 final size:145
Alignment explanation
Indices: 53299546--53299910 Score: 395
Period size: 142 Copynumber: 2.6 Consensus size: 145
53299536 ATGCCGATGC
*** * * *
53299546 CGATGCCATGTTTAAAACATGGTCTTACACTGGCTCACACATCTAAGTCGATGCCATGTCCCAAA
1 CGATGCCATGTCCCAAACATGGTCTTACACTGGCTCACATATCT-AGCCGATGCCATGTCCCAGA
* * * * * *
53299611 CAGGTCTTACACT-GACTTTCATATATCGAGGCCGATGCCATATCCCAGACAGGTCTTACATTGG
65 CAAGTCTTACACTAG-CCTGCATATATCGAGGCCGATGCCATATCCCAGACAGGTCTCACACTAG
**
53299675 CTCTCATCTATCGGTGT
129 CTCTCATCTATCAATGT
* * * *
53299692 CGATGCCATGTCCCAAACA-GGTCTTACACT-G-ACACATGTCAAGCTGATGCCATGTCCCAGAC
1 CGATGCCATGTCCCAAACATGGTCTTACACTGGCTCACATATCTAGCCGATGCCATGTCCCAGAC
* * *
53299754 AAGTCTTACACTAGCCTGCATATCTCGAGGCCGATG-CATGTCCCAGACATGTCTCACACTAGCT
66 AAGTCTTACACTAGCCTGCATATATCGAGGCCGATGCCATATCCCAGACAGGTCTCACACTAGCT
53299818 CTCATCT-T-AATGT
131 CTCATCTATCAATGT
* * * * * *
53299831 CGGTGCCCTGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTGGCCGATG-CATGTCCCAGA
1 CGATGCCATGTCCCAAACATGGTCTTACACTGGCTCACAT-ATCTAGCCGATGCCATGTCCCAGA
*
53299895 CATGTCTTACACTAGC
65 CAAGTCTTACACTAGC
53299911 ACACATCCAT
Statistics
Matches: 182, Mismatches: 32, Indels: 14
0.80 0.14 0.06
Matches are distributed among these distances:
139 19 0.10
140 12 0.07
141 31 0.17
142 78 0.43
143 14 0.08
144 1 0.01
145 11 0.06
146 16 0.09
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.27
Consensus pattern (145 bp):
CGATGCCATGTCCCAAACATGGTCTTACACTGGCTCACATATCTAGCCGATGCCATGTCCCAGAC
AAGTCTTACACTAGCCTGCATATATCGAGGCCGATGCCATATCCCAGACAGGTCTCACACTAGCT
CTCATCTATCAATGT
Found at i:53299889 original size:94 final size:95
Alignment explanation
Indices: 53299739--53299910 Score: 251
Period size: 94 Copynumber: 1.8 Consensus size: 95
53299729 GTCAAGCTGA
*
53299739 TGCCATGTCCCAGACAAGTCTTACACTAGCCTGCATATCTCGAGGCCGATGCATGTCCCAGACAT
1 TGCCATGTCCCAGACAAGTCTTACACTAGCCTGCATATATCGAGGCCGATGCATGTCCCAGACAT
53299804 GTCTCACACTAGCTCTCATCTTAATGTCGG
66 GTCTCACACTAGCTCTCATCTTAATGTCGG
* * * *
53299834 TGCCCTGTCCCAGACATGGTCTTACACTGGCTCT-CATA-AT-GTGGCCGATGCATGTCCCAGAC
1 TGCCATGTCCCAGACA-AGTCTTACACTAGC-CTGCATATATCGAGGCCGATGCATGTCCCAGAC
*
53299896 ATGTCTTACACTAGC
64 ATGTCTCACACTAGC
53299911 ACACATCCAT
Statistics
Matches: 69, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
94 35 0.51
95 16 0.23
96 16 0.23
97 2 0.03
ACGTcount: A:0.22, C:0.31, G:0.20, T:0.27
Consensus pattern (95 bp):
TGCCATGTCCCAGACAAGTCTTACACTAGCCTGCATATATCGAGGCCGATGCATGTCCCAGACAT
GTCTCACACTAGCTCTCATCTTAATGTCGG
Found at i:53300604 original size:20 final size:18
Alignment explanation
Indices: 53300567--53300617 Score: 59
Period size: 20 Copynumber: 2.7 Consensus size: 18
53300557 CTATAGCAAC
53300567 TCACAATTT-CAATTATT
1 TCACAATTTACAATTATT
53300584 TCACACATTTACAACTTATT
1 TCACA-ATTTACAA-TTATT
*
53300604 TTACAACTTTACAA
1 TCACAA-TTTACAA
53300618 AATAGCCATT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
17 5 0.17
18 4 0.14
19 4 0.14
20 16 0.55
ACGTcount: A:0.37, C:0.22, G:0.00, T:0.41
Consensus pattern (18 bp):
TCACAATTTACAATTATT
Found at i:53306556 original size:29 final size:29
Alignment explanation
Indices: 53306523--53306625 Score: 152
Period size: 29 Copynumber: 3.6 Consensus size: 29
53306513 CCTTCGAGCT
** * *
53306523 CGCACACCCAGTGCCGTATTTTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
*
53306552 TGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
53306581 CGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
*
53306610 CACACACTTAGTGCCA
1 CGCACACTTAGTGCCA
53306626 ATCTCGTCAC
Statistics
Matches: 67, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 67 1.00
ACGTcount: A:0.26, C:0.33, G:0.15, T:0.26
Consensus pattern (29 bp):
CGCACACTTAGTGCCATATATTTCCAGCA
Found at i:53306557 original size:58 final size:58
Alignment explanation
Indices: 53306494--53306625 Score: 156
Period size: 58 Copynumber: 2.3 Consensus size: 58
53306484 AATTTAAGCC
* * * * * *
53306494 CGCACACATAGTGCCATACCCTTCGAGCTCGCACACCCAGTGCCGTATTTTTCCAGCA
1 CGCACACTTAGTGCCATACACTTCCAGCACGCACACCCAGTGCCATATATTTCCAGCA
* * * **
53306552 TGCACACTTAGTGCCATATATTTCCAGCACGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATACACTTCCAGCACGCACACCCAGTGCCATATATTTCCAGCA
*
53306610 CACACACTTAGTGCCA
1 CGCACACTTAGTGCCA
53306626 ATCTCGTCAC
Statistics
Matches: 61, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
58 61 1.00
ACGTcount: A:0.26, C:0.34, G:0.15, T:0.25
Consensus pattern (58 bp):
CGCACACTTAGTGCCATACACTTCCAGCACGCACACCCAGTGCCATATATTTCCAGCA
Found at i:53311993 original size:42 final size:42
Alignment explanation
Indices: 53311876--53312073 Score: 134
Period size: 43 Copynumber: 4.7 Consensus size: 42
53311866 ATGCCAAAAA
* * * * *
53311876 CCATATCCCAGATTTGGTCTTATATG-GGATCACATACCGATG
1 CCATATCCCAGATATGGTCTTATACGAAG-TCTCATATCGATG
* * * * * * *
53311918 CCAATAGCCCAGCTATGGTCTGACACCATGTCTCAAATCGATG
1 CC-ATATCCCAGATATGGTCTTATACGAAGTCTCATATCGATG
* * *
53311961 ACATATCCCAGATATGGTCTTATACGAAGTCTCATTTTCGAAG
1 CCATATCCCAGATATGGTCTTATACGAAGTCTCA-TATCGATG
* * * * *
53312004 CCA-AGTCCCAAACT-TGGTCTTACACGAAAT-TGCATGTCAATG
1 CCATA-TCCCAGA-TATGGTCTTATACGAAGTCT-CATATCGATG
53312046 CCATATCCCAGATATGGTCTTATACGAA
1 CCATATCCCAGATATGGTCTTATACGAA
53312074 ATCCCAATAA
Statistics
Matches: 118, Mismatches: 30, Indels: 16
0.72 0.18 0.10
Matches are distributed among these distances:
41 1 0.01
42 57 0.48
43 58 0.49
44 2 0.02
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.28
Consensus pattern (42 bp):
CCATATCCCAGATATGGTCTTATACGAAGTCTCATATCGATG
Found at i:53312074 original size:42 final size:43
Alignment explanation
Indices: 53311962--53312076 Score: 123
Period size: 42 Copynumber: 2.7 Consensus size: 43
53311952 AAATCGATGA
* *
53311962 CATATCCCAGATATGGTCTTATACGAAGTCTCATTTTCGAAGC
1 CATATCCCAGATATGGTCTTATACGAAATCTCATTGTCGAAGC
* *
53312005 CA-AGTCCCAAACT-TGGTCTTACACGAAAT-TGCA-TGTC-AATGC
1 CATA-TCCCAGA-TATGGTCTTATACGAAATCT-CATTGTCGAA-GC
53312047 CATATCCCAGATATGGTCTTATACGAAATC
1 CATATCCCAGATATGGTCTTATACGAAATC
53312077 CCAATAACCC
Statistics
Matches: 59, Mismatches: 6, Indels: 14
0.75 0.08 0.18
Matches are distributed among these distances:
41 3 0.05
42 30 0.51
43 25 0.42
44 1 0.02
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.30
Consensus pattern (43 bp):
CATATCCCAGATATGGTCTTATACGAAATCTCATTGTCGAAGC
Found at i:53323318 original size:22 final size:22
Alignment explanation
Indices: 53323249--53323332 Score: 77
Period size: 22 Copynumber: 3.9 Consensus size: 22
53323239 TATATACTAT
53323249 TTTG-TCTTTTAAACAGTAATTTA
1 TTTGATCTTTTAAACA-T-ATTTA
* **
53323272 TCTGATCTTTTCTACATA---A
1 TTTGATCTTTTAAACATATTTA
53323291 TTTGATCTTTTAAACATATTTA
1 TTTGATCTTTTAAACATATTTA
**
53323313 TTTGATCTTTTCTACATATT
1 TTTGATCTTTTAAACATATT
53323333 AAGTCACTTA
Statistics
Matches: 49, Mismatches: 8, Indels: 9
0.74 0.12 0.14
Matches are distributed among these distances:
19 16 0.33
22 20 0.41
23 4 0.08
24 9 0.18
ACGTcount: A:0.27, C:0.13, G:0.06, T:0.54
Consensus pattern (22 bp):
TTTGATCTTTTAAACATATTTA
Found at i:53323319 original size:41 final size:42
Alignment explanation
Indices: 53323249--53323330 Score: 132
Period size: 41 Copynumber: 2.0 Consensus size: 42
53323239 TATATACTAT
53323249 TTTGTCTTTTAAACAGTAATTTATCTGATCTTTTCTACATAA
1 TTTGTCTTTTAAACAGTAATTTATCTGATCTTTTCTACATAA
*
53323291 TTTGATCTTTTAAACA-T-ATTTATTTGATCTTTTCTACATA
1 TTTG-TCTTTTAAACAGTAATTTATCTGATCTTTTCTACATA
53323331 TTAAGTCACT
Statistics
Matches: 38, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
41 22 0.58
42 5 0.13
43 11 0.29
ACGTcount: A:0.28, C:0.13, G:0.06, T:0.52
Consensus pattern (42 bp):
TTTGTCTTTTAAACAGTAATTTATCTGATCTTTTCTACATAA
Found at i:53345400 original size:28 final size:28
Alignment explanation
Indices: 53345368--53345423 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
53345358 TAATTACTCG
53345368 TTGTATATCTCTTGTGAGAAAAGCTGAA
1 TTGTATATCTCTTGTGAGAAAAGCTGAA
53345396 TTGTATATCTCTTGTGAGAAAAGCTGAA
1 TTGTATATCTCTTGTGAGAAAAGCTGAA
53345424 AGGAGAAAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.32, C:0.11, G:0.21, T:0.36
Consensus pattern (28 bp):
TTGTATATCTCTTGTGAGAAAAGCTGAA
Found at i:53345440 original size:21 final size:21
Alignment explanation
Indices: 53345414--53345453 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
53345404 CTCTTGTGAG
*
53345414 AAAAGCTGAAAGGAGAAAACT
1 AAAAGCTAAAAGGAGAAAACT
53345435 AAAAGCTAAAAGGAGAAAA
1 AAAAGCTAAAAGGAGAAAA
53345454 GTCTTTTGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.62, C:0.07, G:0.23, T:0.07
Consensus pattern (21 bp):
AAAAGCTAAAAGGAGAAAACT
Found at i:53346192 original size:37 final size:36
Alignment explanation
Indices: 53346109--53346181 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
53346099 CCTTTTAAAT
53346109 AACAGTCTTTTATCAAAAAAGAAGGAAAAAAAATTA
1 AACAGTCTTTTATCAAAAAAGAAGGAAAAAAAATTA
53346145 AACAGTCTTTTATCAAAAAAGAAGGAAAAAAAATTA
1 AACAGTCTTTTATCAAAAAAGAAGGAAAAAAAATTA
53346181 A
1 A
53346182 CTATCCCTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.59, C:0.08, G:0.11, T:0.22
Consensus pattern (36 bp):
AACAGTCTTTTATCAAAAAAGAAGGAAAAAAAATTA
Found at i:53354702 original size:3 final size:3
Alignment explanation
Indices: 53354694--53354741 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
53354684 TCAGAAACAC
53354694 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
53354742 CAGTACTAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:53355538 original size:26 final size:26
Alignment explanation
Indices: 53355502--53355553 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
53355492 TTTTGTGCCT
53355502 TTACGCCTAAAAGGTTGTAATGTTTG
1 TTACGCCTAAAAGGTTGTAATGTTTG
53355528 TTACGCCTAAAAGGTTGTAATGTTTG
1 TTACGCCTAAAAGGTTGTAATGTTTG
53355554 ATGTCCTTGA
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:0.12, G:0.23, T:0.38
Consensus pattern (26 bp):
TTACGCCTAAAAGGTTGTAATGTTTG
Found at i:53357359 original size:20 final size:20
Alignment explanation
Indices: 53357334--53357373 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
53357324 CTTAGATGAG
*
53357334 TTGTAAGATATTTTGTTATT
1 TTGTAAGATATTTTATTATT
*
53357354 TTGTAAGGTATTTTATTATT
1 TTGTAAGATATTTTATTATT
53357374 AACTTATAAA
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:0.25, C:0.00, G:0.15, T:0.60
Consensus pattern (20 bp):
TTGTAAGATATTTTATTATT
Found at i:53365001 original size:2 final size:2
Alignment explanation
Indices: 53364994--53365028 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
53364984 AGAATTCAGA
*
53364994 TC TC TC TC TC TC TC TC TC TC TC TC TC TG TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
53365029 ATTTTCAACT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.46, G:0.03, T:0.51
Consensus pattern (2 bp):
TC
Found at i:53372649 original size:18 final size:16
Alignment explanation
Indices: 53372626--53372664 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 16
53372616 TATTTTATGC
*
53372626 AAAAGAAAGGAAATAAAT
1 AAAAGAAA-GAAA-AAAA
53372644 AAAAGAAAGAAAAAAA
1 AAAAGAAAGAAAAAAA
53372660 AAAAG
1 AAAAG
53372665 GGTAATGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 8 0.40
17 4 0.20
18 8 0.40
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.05
Consensus pattern (16 bp):
AAAAGAAAGAAAAAAA
Found at i:53373532 original size:14 final size:14
Alignment explanation
Indices: 53373513--53373543 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
53373503 GAATGACCGA
53373513 ATGAGCAATAGGTT
1 ATGAGCAATAGGTT
53373527 ATGAGCAATAGGTT
1 ATGAGCAATAGGTT
53373541 ATG
1 ATG
53373544 TATGGATGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.35, C:0.06, G:0.29, T:0.29
Consensus pattern (14 bp):
ATGAGCAATAGGTT
Found at i:53374159 original size:40 final size:39
Alignment explanation
Indices: 53374104--53374309 Score: 254
Period size: 40 Copynumber: 5.2 Consensus size: 39
53374094 TGAATGATAC
* * *
53374104 CCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTG-TTATAT
*
53374144 CCGGGCTAAGACCCGAAGGCA-TTGTGCGAGTTTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGTTATAT
53374182 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAG-TGTTATAT
* * *
53374222 CCGGGCTAAGACCCGAAGGCATTTGTGAGAGTTGCTATAC
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAG-TGTTATAT
* * * **
53374262 CCGGGTTAAGACCCGAAGGCAATTATGCTTGTGGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGT-GTTATAT
53374302 CC-GGCTAA
1 CCGGGCTAA
53374310 ATTCCGAAGA
Statistics
Matches: 146, Mismatches: 17, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
38 27 0.18
39 23 0.16
40 96 0.66
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (39 bp):
CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGTTATAT
Found at i:53374233 original size:78 final size:80
Alignment explanation
Indices: 53374100--53374309 Score: 293
Period size: 78 Copynumber: 2.7 Consensus size: 80
53374090 CATTTGAATG
*
53374100 ATACCCGGGCTAAGTCCCGAAGGCATTTATGCTAG-TGATTATATCCGGGCTAAGACCCGAAGGC
1 ATACCCGGGCTAAGACCCGAAGGCATTTATGCTAGTTG-TTATATCCGGGCTAAGACCCGAAGGC
* *
53374164 A-TTGTGCGAGTT-TT
65 ATTTGTGAGAGTTGCT
* * *
53374178 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATATCCGGGCTAAGACCCGAAGGCA
1 ATACCCGGGCTAAGACCCGAAGGCATTTATGCTAGTTGTTATATCCGGGCTAAGACCCGAAGGCA
53374243 TTTGTGAGAGTTGCT
66 TTTGTGAGAGTTGCT
* * * *
53374258 ATACCCGGGTTAAGACCCGAAGGCAATTATGCTTGTGGTTATATCC-GGCTAA
1 ATACCCGGGCTAAGACCCGAAGGCATTTATGCTAGTTGTTATATCCGGGCTAA
53374310 ATTCCGAAGA
Statistics
Matches: 116, Mismatches: 13, Indels: 5
0.87 0.10 0.04
Matches are distributed among these distances:
78 58 0.50
79 18 0.16
80 40 0.34
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (80 bp):
ATACCCGGGCTAAGACCCGAAGGCATTTATGCTAGTTGTTATATCCGGGCTAAGACCCGAAGGCA
TTTGTGAGAGTTGCT
Found at i:53381194 original size:21 final size:21
Alignment explanation
Indices: 53381168--53381209 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
53381158 AATCCCCGAC
53381168 ACCAAGTCTGTAAGTATCTTT
1 ACCAAGTCTGTAAGTATCTTT
53381189 ACCAAGTCTGTAAGTATCTTT
1 ACCAAGTCTGTAAGTATCTTT
53381210 CTGTTCTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (21 bp):
ACCAAGTCTGTAAGTATCTTT
Found at i:53391216 original size:13 final size:13
Alignment explanation
Indices: 53391198--53391229 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
53391188 CACATGACTA
53391198 ATTTCATATAGCC
1 ATTTCATATAGCC
*
53391211 ATTTCATATATCC
1 ATTTCATATAGCC
53391224 ATTTCA
1 ATTTCA
53391230 ATTTACACAT
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:0.31, C:0.22, G:0.03, T:0.44
Consensus pattern (13 bp):
ATTTCATATAGCC
Found at i:53392762 original size:33 final size:33
Alignment explanation
Indices: 53392725--53392791 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
53392715 TTTTGATTTG
53392725 AAATCGAGTTAACTTTAAGGGATGAATTTGTCA
1 AAATCGAGTTAACTTTAAGGGATGAATTTGTCA
53392758 AAATCGAGTTAACTTTAAGGGATGAATTTGTCA
1 AAATCGAGTTAACTTTAAGGGATGAATTTGTCA
53392791 A
1 A
53392792 TCTTGATATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.37, C:0.09, G:0.21, T:0.33
Consensus pattern (33 bp):
AAATCGAGTTAACTTTAAGGGATGAATTTGTCA
Found at i:53393624 original size:68 final size:68
Alignment explanation
Indices: 53393552--53393687 Score: 272
Period size: 68 Copynumber: 2.0 Consensus size: 68
53393542 AACAATTAAG
53393552 TCCTTAAATTCAAAATTGATTAAAGTCACTTTACAAAATGTTCCTATTTTGCTAACAAGTTCATG
1 TCCTTAAATTCAAAATTGATTAAAGTCACTTTACAAAATGTTCCTATTTTGCTAACAAGTTCATG
53393617 AAT
66 AAT
53393620 TCCTTAAATTCAAAATTGATTAAAGTCACTTTACAAAATGTTCCTATTTTGCTAACAAGTTCATG
1 TCCTTAAATTCAAAATTGATTAAAGTCACTTTACAAAATGTTCCTATTTTGCTAACAAGTTCATG
53393685 AAT
66 AAT
53393688 CTACCATCAA
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 68 1.00
ACGTcount: A:0.37, C:0.16, G:0.09, T:0.38
Consensus pattern (68 bp):
TCCTTAAATTCAAAATTGATTAAAGTCACTTTACAAAATGTTCCTATTTTGCTAACAAGTTCATG
AAT
Found at i:53394796 original size:23 final size:22
Alignment explanation
Indices: 53394759--53394834 Score: 73
Period size: 23 Copynumber: 3.3 Consensus size: 22
53394749 TCAAGTCAAG
*
53394759 TTGTCTTCCACAATTTTAGGGAT
1 TTGT-TTCCATAATTTTAGGGAT
* *
53394782 TTGTTTGCC-TAAATTGTAGGCAT
1 TTGTTT-CCAT-AATTTTAGGGAT
*
53394805 TTGTCTTCCATAATTTTAAGGAT
1 TTGT-TTCCATAATTTTAGGGAT
53394828 TTGTTTC
1 TTGTTTC
53394835 TTTTATCTAA
Statistics
Matches: 43, Mismatches: 6, Indels: 9
0.74 0.10 0.16
Matches are distributed among these distances:
22 5 0.12
23 35 0.81
24 3 0.07
ACGTcount: A:0.21, C:0.14, G:0.17, T:0.47
Consensus pattern (22 bp):
TTGTTTCCATAATTTTAGGGAT
Found at i:53398756 original size:40 final size:39
Alignment explanation
Indices: 53398712--53398811 Score: 137
Period size: 40 Copynumber: 2.5 Consensus size: 39
53398702 TATATATATA
*
53398712 TATATATGGCACTTAGTGTGTGATTCAAGAAAGCTTCGGC
1 TATATATGACACTTAGTGTGTGATTC-AGAAAGCTTCGGC
* * * *
53398752 TATATATGACACTTACTGTGCGATTCGGAATAGCTTCAGC
1 TATATATGACACTTAGTGTGTGATTCAGAA-AGCTTCGGC
53398792 TATATATGACACTTAGTGTG
1 TATATATGACACTTAGTGTG
53398812 GAGACCGAGA
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
39 3 0.06
40 50 0.94
ACGTcount: A:0.28, C:0.16, G:0.22, T:0.34
Consensus pattern (39 bp):
TATATATGACACTTAGTGTGTGATTCAGAAAGCTTCGGC
Found at i:53398834 original size:40 final size:40
Alignment explanation
Indices: 53398712--53398851 Score: 122
Period size: 40 Copynumber: 3.5 Consensus size: 40
53398702 TATATATATA
* * ** *
53398712 TATATATGGCACTTAGTGTGTGATTCAAGAA-AGCTTCGGC
1 TATATATGACACTTAGTGTGCGAGAC-CGAATAGCTTCGGC
* ** * *
53398752 TATATATGACACTTACTGTGCGATTCGGAATAGCTTCAGC
1 TATATATGACACTTAGTGTGCGAGACCGAATAGCTTCGGC
*
53398792 TATATATGACACTTAGTGTG-GAGACCGAGATAGTTTCGGC
1 TATATATGACACTTAGTGTGCGAGACCGA-ATAGCTTCGGC
* * *
53398832 TATGTAAGGCACTTAGTGTG
1 TATATATGACACTTAGTGTG
53398852 TGAAATTATA
Statistics
Matches: 84, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
39 8 0.10
40 76 0.90
ACGTcount: A:0.27, C:0.16, G:0.25, T:0.32
Consensus pattern (40 bp):
TATATATGACACTTAGTGTGCGAGACCGAATAGCTTCGGC
Found at i:53404203 original size:10 final size:10
Alignment explanation
Indices: 53404190--53404245 Score: 67
Period size: 10 Copynumber: 5.5 Consensus size: 10
53404180 TAAATTTTTT
53404190 TAAAAAATTA
1 TAAAAAATTA
53404200 TAAAAAATTA
1 TAAAAAATTA
**
53404210 TTGAAAATTA
1 TAAAAAATTA
*
53404220 TAAAAAATTC
1 TAAAAAATTA
*
53404230 TAAAATATGTA
1 TAAAAAAT-TA
53404241 TAAAA
1 TAAAA
53404246 TATTTTGTTA
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
10 32 0.84
11 6 0.16
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (10 bp):
TAAAAAATTA
Found at i:53409207 original size:20 final size:19
Alignment explanation
Indices: 53409171--53409221 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
53409161 AAAGGGCTAT
*
53409171 TTGTAAA-GTTGTAAAATAA
1 TTGTAAATG-TGTGAAATAA
53409190 GTTGTAAATGTGTGAAATAA
1 -TTGTAAATGTGTGAAATAA
53409210 TTG-AAAT-TGTGA
1 TTGTAAATGTGTGA
53409222 GTTGCTATAG
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
17 5 0.17
18 4 0.14
19 3 0.10
20 16 0.55
21 1 0.03
ACGTcount: A:0.41, C:0.00, G:0.22, T:0.37
Consensus pattern (19 bp):
TTGTAAATGTGTGAAATAA
Found at i:53410027 original size:48 final size:46
Alignment explanation
Indices: 53409869--53410041 Score: 161
Period size: 46 Copynumber: 3.7 Consensus size: 46
53409859 TGATATGTGT
** * * * *
53409869 GCTAGTGTAAGACATGCCTGGGATATGCATCGGCCAT--ATTATGAGA
1 GCTAGTGTAAGACATGTTTGGGACATGCATCGG-CATCGA-GAAGAAA
* * * * *
53409915 GCCAGTGTAAGACATGTATGGGACATGCATCGGCATTGAGACGAGA
1 GCTAGTGTAAGACATGTTTGGGACATGCATCGGCATCGAGAAGAAA
* *
53409961 GCTAGTGTAAGACATGTTTGGGACATGCATCGGCCTCGAGATATACAA
1 GCTAGTGTAAGACATGTTTGGGACATGCATCGGCATCGAGA-AGA-AA
*
53410009 GCTAGTGTAAGACCTGTTTGGGACATAGCATCG
1 GCTAGTGTAAGACATGTTTGGGACAT-GCATCG
53410042 ACACCGATAG
Statistics
Matches: 108, Mismatches: 14, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
45 3 0.03
46 71 0.66
47 2 0.02
48 26 0.24
49 6 0.06
ACGTcount: A:0.28, C:0.18, G:0.29, T:0.24
Consensus pattern (46 bp):
GCTAGTGTAAGACATGTTTGGGACATGCATCGGCATCGAGAAGAAA
Found at i:53410068 original size:49 final size:48
Alignment explanation
Indices: 53409872--53410139 Score: 210
Period size: 49 Copynumber: 5.6 Consensus size: 48
53409862 TATGTGTGCT
** *
53409872 AGTGTAAGACATGCCTGGGATATGCATCGG-C-C-ATATTATGAGAGCC
1 AGTGTAAGACATGTTTGGGACATGCATCGGCCTCGATA-TATGAGAGCC
* * * * * *
53409918 AGTGTAAGACATGTATGGGACATGCATCGGCATTG--AGACGAGAGCT
1 AGTGTAAGACATGTTTGGGACATGCATCGGCCTCGATATATGAGAGCC
* * *
53409964 AGTGTAAGACATGTTTGGGACATGCATCGGCCTCGAGATAT-ACAAGCT
1 AGTGTAAGACATGTTTGGGACATGCATCGGCCTCGATATATGA-GAGCC
* *
53410012 AGTGTAAGACCTGTTTGGGACATAGCATCGACAC-CGATAGT-TGAGAGCC
1 AGTGTAAGACATGTTTGGGACAT-GCATCGGC-CTCGATA-TATGAGAGCC
* * * ** * *
53410061 AGTGTAAGACCTGTCTAGGACACCACATCGGCCTCGATATATGAAAGTC
1 AGTGTAAGACATGTTTGGGACA-TGCATCGGCCTCGATATATGAGAGCC
* *
53410110 AGTGTCAGACTTGTTTGGGACATGGCATCG
1 AGTGTAAGACATGTTTGGGACAT-GCATCG
53410140 ACTTTGATGT
Statistics
Matches: 176, Mismatches: 32, Indels: 25
0.76 0.14 0.11
Matches are distributed among these distances:
46 66 0.38
47 2 0.01
48 30 0.17
49 75 0.43
50 3 0.02
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.24
Consensus pattern (48 bp):
AGTGTAAGACATGTTTGGGACATGCATCGGCCTCGATATATGAGAGCC
Found at i:53410082 original size:97 final size:98
Alignment explanation
Indices: 53409957--53410141 Score: 241
Period size: 98 Copynumber: 1.9 Consensus size: 98
53409947 GCATTGAGAC
* * * **
53409957 GAGAGCTAGTGTAAGACATGTTTGGGACA-TGCATCGGCCTCGAGATAT-ACAAG-CTAGTGTAA
1 GAGAGCCAGTGTAAGACATGTCTAGGACACCACATCGGCCTCGAGATATGA-AAGTC-AGTGTAA
53410019 GACCTGTTTGGGACATAGCATCGACACCGATAGTT
64 GACCTGTTTGGGACATAGCATCGACACCGATAGTT
* * *
53410054 GAGAGCCAGTGTAAGACCTGTCTAGGACACCACATCGGCCTCGATATATGAAAGTCAGTGTCAGA
1 GAGAGCCAGTGTAAGACATGTCTAGGACACCACATCGGCCTCGAGATATGAAAGTCAGTGTAAGA
* *
53410119 CTTGTTTGGGACATGGCATCGAC
66 CCTGTTTGGGACATAGCATCGAC
53410142 TTTGATGTGC
Statistics
Matches: 75, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
97 25 0.33
98 48 0.64
99 2 0.03
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.24
Consensus pattern (98 bp):
GAGAGCCAGTGTAAGACATGTCTAGGACACCACATCGGCCTCGAGATATGAAAGTCAGTGTAAGA
CCTGTTTGGGACATAGCATCGACACCGATAGTT
Found at i:53420737 original size:16 final size:17
Alignment explanation
Indices: 53420707--53420739 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
53420697 TCCACAAAGG
53420707 GAATGTAAGTAGCACTT
1 GAATGTAAGTAGCACTT
53420724 GAATGTAA-TAGCACTT
1 GAATGTAAGTAGCACTT
53420740 AGGTCGGGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.36, C:0.12, G:0.21, T:0.30
Consensus pattern (17 bp):
GAATGTAAGTAGCACTT
Found at i:53422242 original size:19 final size:19
Alignment explanation
Indices: 53422220--53422260 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
53422210 AACACCCTTT
*
53422220 ACCTCCTTAAAT-CTCTTAA
1 ACCTCCTCAAATAC-CTTAA
53422239 ACCTCCTCAAATACCTTAA
1 ACCTCCTCAAATACCTTAA
53422258 ACC
1 ACC
53422261 CTAACACATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 19 0.95
20 1 0.05
ACGTcount: A:0.34, C:0.37, G:0.00, T:0.29
Consensus pattern (19 bp):
ACCTCCTCAAATACCTTAA
Found at i:53428066 original size:21 final size:20
Alignment explanation
Indices: 53428034--53428072 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
53428024 AAAGGGACCC
53428034 TAAAACTTAAACCCTAAAAT
1 TAAAACTTAAACCCTAAAAT
53428054 TAAAACTTTAAACCCTAAA
1 TAAAAC-TTAAACCCTAAA
53428073 CCCTAAACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.54, C:0.21, G:0.00, T:0.26
Consensus pattern (20 bp):
TAAAACTTAAACCCTAAAAT
Found at i:53428082 original size:21 final size:22
Alignment explanation
Indices: 53428030--53428079 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 22
53428020 AGGGAAAGGG
53428030 ACCCTAAAAC-TTAAACCCTAA
1 ACCCTAAAACTTTAAACCCTAA
**
53428051 A-ATTAAAACTTTAAACCCTAA
1 ACCCTAAAACTTTAAACCCTAA
53428072 ACCCTAAA
1 ACCCTAAA
53428080 CTTGAAGATG
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
20 6 0.26
21 13 0.57
22 4 0.17
ACGTcount: A:0.50, C:0.28, G:0.00, T:0.22
Consensus pattern (22 bp):
ACCCTAAAACTTTAAACCCTAA
Found at i:53435468 original size:58 final size:57
Alignment explanation
Indices: 53435344--53435468 Score: 137
Period size: 58 Copynumber: 2.2 Consensus size: 57
53435334 ACTCCTACAT
* * *
53435344 ACATGCATATGACCCACTTGGCCCAATCTCATTTATAAGGCGCATCAGGCCCAATTC
1 ACATGCATATGACCCACTAGGCCCAATCTCATTTATAAGGCCCATCAGGCCCAAATC
* * * *
53435401 ACATTCATATGGCCCA-TCAGGCCCAAT-TCATATTCATATGGCCCATTAGGCCCAAATC
1 ACATGCATATGACCCACT-AGGCCCAATCTCAT-TT-ATAAGGCCCATCAGGCCCAAATC
*
53435459 AGATGCATAT
1 ACATGCATAT
53435469 TCATGCTCAC
Statistics
Matches: 56, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
56 5 0.09
57 24 0.43
58 27 0.48
ACGTcount: A:0.30, C:0.30, G:0.15, T:0.26
Consensus pattern (57 bp):
ACATGCATATGACCCACTAGGCCCAATCTCATTTATAAGGCCCATCAGGCCCAAATC
Found at i:53435472 original size:35 final size:29
Alignment explanation
Indices: 53435363--53435455 Score: 127
Period size: 29 Copynumber: 3.2 Consensus size: 29
53435353 TGACCCACTT
* *
53435363 GGCCCAATCTCAT-TT-ATAAGGCGCATCA
1 GGCCCAAT-TCATATTCATATGGCCCATCA
*
53435391 GGCCCAATTCACATTCATATGGCCCATCA
1 GGCCCAATTCATATTCATATGGCCCATCA
*
53435420 GGCCCAATTCATATTCATATGGCCCATTA
1 GGCCCAATTCATATTCATATGGCCCATCA
53435449 GGCCCAA
1 GGCCCAA
53435456 ATCAGATGCA
Statistics
Matches: 58, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
27 3 0.05
28 10 0.17
29 45 0.78
ACGTcount: A:0.28, C:0.31, G:0.16, T:0.25
Consensus pattern (29 bp):
GGCCCAATTCATATTCATATGGCCCATCA
Found at i:53435699 original size:8 final size:8
Alignment explanation
Indices: 53435686--53435721 Score: 54
Period size: 8 Copynumber: 4.5 Consensus size: 8
53435676 ACTTTTGCCT
53435686 TTTCGGCA
1 TTTCGGCA
*
53435694 TTTCGGCT
1 TTTCGGCA
*
53435702 TTTCGGCT
1 TTTCGGCA
53435710 TTTCGGCA
1 TTTCGGCA
53435718 TTTC
1 TTTC
53435722 AGCTTTTTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.06, C:0.25, G:0.22, T:0.47
Consensus pattern (8 bp):
TTTCGGCA
Found at i:53435705 original size:16 final size:16
Alignment explanation
Indices: 53435686--53435728 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
53435676 ACTTTTGCCT
* *
53435686 TTTCGGCATTTCGGCT
1 TTTCGGCTTTTCGGCA
53435702 TTTCGGCTTTTCGGCA
1 TTTCGGCTTTTCGGCA
*
53435718 TTTCAGCTTTT
1 TTTCGGCTTTT
53435729 TCTGATTCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.07, C:0.23, G:0.21, T:0.49
Consensus pattern (16 bp):
TTTCGGCTTTTCGGCA
Found at i:53438115 original size:29 final size:29
Alignment explanation
Indices: 53438014--53438107 Score: 179
Period size: 29 Copynumber: 3.2 Consensus size: 29
53438004 GTGACGAGAT
53438014 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
53438043 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
53438072 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
*
53438101 CGGCACT
1 TGGCACT
53438108 GGGTGTGCGA
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 64 1.00
ACGTcount: A:0.30, C:0.16, G:0.28, T:0.27
Consensus pattern (29 bp):
TGGCACTAAGTGTGCATGCTGGAAATATA
Found at i:53438132 original size:58 final size:58
Alignment explanation
Indices: 53438010--53438144 Score: 175
Period size: 58 Copynumber: 2.3 Consensus size: 58
53438000 TACGGTGACG
* *
53438010 AGAT-TGGCACTAAGTGTGCATGCTGGAAATATATGGCACTAAGTGTGCATGCTGGAA
1 AGATATGGCACTAAGTGTGCATGCTGGAAATATACGGCACTAAGTGTGCATGCTCGAA
* **
53438067 ATATATGGCACTAAGTGTGCATGCTGGAAATATACGGCACTGGGTGTGCGA-GCTCGAA
1 AGATATGGCACTAAGTGTGCATGCTGGAAATATACGGCACTAAGTGTGC-ATGCTCGAA
* * *
53438125 GGGTATGGCACTATGTGTGC
1 AGATATGGCACTAAGTGTGC
53438145 GGGCTTAAAT
Statistics
Matches: 67, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
57 3 0.04
58 63 0.94
59 1 0.01
ACGTcount: A:0.27, C:0.16, G:0.32, T:0.26
Consensus pattern (58 bp):
AGATATGGCACTAAGTGTGCATGCTGGAAATATACGGCACTAAGTGTGCATGCTCGAA
Found at i:53445965 original size:29 final size:29
Alignment explanation
Indices: 53445864--53445957 Score: 179
Period size: 29 Copynumber: 3.2 Consensus size: 29
53445854 GTGACGAGAT
53445864 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
53445893 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
53445922 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
*
53445951 CGGCACT
1 TGGCACT
53445958 GGGTGTGCGA
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 64 1.00
ACGTcount: A:0.30, C:0.16, G:0.28, T:0.27
Consensus pattern (29 bp):
TGGCACTAAGTGTGCATGCTGGAAATATA
Found at i:53445982 original size:58 final size:58
Alignment explanation
Indices: 53445860--53445994 Score: 175
Period size: 58 Copynumber: 2.3 Consensus size: 58
53445850 TACGGTGACG
* *
53445860 AGAT-TGGCACTAAGTGTGCATGCTGGAAATATATGGCACTAAGTGTGCATGCTGGAA
1 AGATATGGCACTAAGTGTGCATGCTGGAAATATACGGCACTAAGTGTGCATGCTCGAA
* **
53445917 ATATATGGCACTAAGTGTGCATGCTGGAAATATACGGCACTGGGTGTGCGA-GCTCGAA
1 AGATATGGCACTAAGTGTGCATGCTGGAAATATACGGCACTAAGTGTGC-ATGCTCGAA
* * *
53445975 GGGTATGGCACTATGTGTGC
1 AGATATGGCACTAAGTGTGC
53445995 GGGCTTAAAT
Statistics
Matches: 67, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
57 3 0.04
58 63 0.94
59 1 0.01
ACGTcount: A:0.27, C:0.16, G:0.32, T:0.26
Consensus pattern (58 bp):
AGATATGGCACTAAGTGTGCATGCTGGAAATATACGGCACTAAGTGTGCATGCTCGAA
Found at i:53454030 original size:28 final size:28
Alignment explanation
Indices: 53453993--53454075 Score: 98
Period size: 28 Copynumber: 2.9 Consensus size: 28
53453983 ACCCCTACAT
*
53453993 ATATGCATATGGCCCACTTGGCCCAATCTC
1 ATATTCATATGGCCCA-TTGGCCCAAT-TC
*
53454023 AT-TT-ATATGGCCCATCAGGCCCAATTC
1 ATATTCATATGGCCCAT-TGGCCCAATTC
53454050 ATATTCATATGGCCCATTAGGCCCAA
1 ATATTCATATGGCCCATT-GGCCCAA
53454076 ATCACATGCA
Statistics
Matches: 46, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
27 5 0.11
28 20 0.43
29 19 0.41
30 2 0.04
ACGTcount: A:0.27, C:0.30, G:0.16, T:0.28
Consensus pattern (28 bp):
ATATTCATATGGCCCATTGGCCCAATTC
Found at i:53454087 original size:29 final size:29
Alignment explanation
Indices: 53453995--53454088 Score: 102
Period size: 29 Copynumber: 3.3 Consensus size: 29
53453985 CCCTACATAT
*
53453995 ATGCATATGGCCCACTT-GGCCC-AATCTC
1 ATGCATATGGCCCA-TTAGGCCCAAATCAC
** * * *
53454023 ATTTATATGGCCCATCAGGCCCAATTCAT
1 ATGCATATGGCCCATTAGGCCCAAATCAC
*
53454052 ATTCATATGGCCCATTAGGCCCAAATCAC
1 ATGCATATGGCCCATTAGGCCCAAATCAC
53454081 ATGCATAT
1 ATGCATAT
53454089 TCATGCTCAC
Statistics
Matches: 53, Mismatches: 11, Indels: 3
0.79 0.16 0.04
Matches are distributed among these distances:
27 1 0.02
28 17 0.32
29 35 0.66
ACGTcount: A:0.28, C:0.30, G:0.15, T:0.28
Consensus pattern (29 bp):
ATGCATATGGCCCATTAGGCCCAAATCAC
Found at i:53457294 original size:28 final size:28
Alignment explanation
Indices: 53457233--53457330 Score: 108
Period size: 28 Copynumber: 3.5 Consensus size: 28
53457223 TCACAAATTG
** * *
53457233 GCACTAAGTGTGCGGGTTCAAATTATACA
1 GCACTAAGTGTGCAAGTTC-GATTATATA
*
53457262 GCACTAAGTGTGCAAGTTTGATTATATA
1 GCACTAAGTGTGCAAGTTCGATTATATA
* *
53457290 GCACTAAGTGTGCGAGTTCGACTAT-TAA
1 GCACTAAGTGTGCAAGTTCGATTATAT-A
53457318 GCACTAAGTGTGC
1 GCACTAAGTGTGC
53457331 GGGCTTATTG
Statistics
Matches: 60, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
27 1 0.02
28 43 0.72
29 16 0.27
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.30
Consensus pattern (28 bp):
GCACTAAGTGTGCAAGTTCGATTATATA
Found at i:53464500 original size:22 final size:21
Alignment explanation
Indices: 53464465--53464505 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
53464455 GATTATGCCA
53464465 TTTTCTCCTCTTTTGTCTTTCT
1 TTTTCTCCTCTTTTG-CTTTCT
53464487 TTTTCTCCAT-TTTTGCTTT
1 TTTTCTCC-TCTTTTGCTTT
53464506 TAGTTTTTGG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 4 0.22
22 13 0.72
23 1 0.06
ACGTcount: A:0.02, C:0.24, G:0.05, T:0.68
Consensus pattern (21 bp):
TTTTCTCCTCTTTTGCTTTCT
Found at i:53465736 original size:27 final size:27
Alignment explanation
Indices: 53465662--53465736 Score: 114
Period size: 27 Copynumber: 2.8 Consensus size: 27
53465652 CTGAGCTGAA
* *
53465662 ACCCCTATGGGGTAAAATGACCGTAAT
1 ACCCCTATAGGGTAAAATGATCGTAAT
*
53465689 GCCCCTATAGGGTAAAATGATCGTAAT
1 ACCCCTATAGGGTAAAATGATCGTAAT
*
53465716 ACCCCTATATGGTAAAATGAT
1 ACCCCTATAGGGTAAAATGAT
53465737 GATTATGCCC
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.25
Consensus pattern (27 bp):
ACCCCTATAGGGTAAAATGATCGTAAT
Found at i:53465929 original size:27 final size:27
Alignment explanation
Indices: 53465872--53465931 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 27
53465862 ATGGAAGAAG
*
53465872 TACTG-TACTGGTGACTATGTCACATT
1 TACTGTTACTGGTGACTATGCCACATT
* * * *
53465898 CACTGTTACTGGTGGCTTTGCCATATT
1 TACTGTTACTGGTGACTATGCCACATT
53465925 TACTGTT
1 TACTGTT
53465932 TCTAGCAACT
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
26 4 0.15
27 23 0.85
ACGTcount: A:0.18, C:0.20, G:0.20, T:0.42
Consensus pattern (27 bp):
TACTGTTACTGGTGACTATGCCACATT
Found at i:53467635 original size:39 final size:40
Alignment explanation
Indices: 53467579--53467736 Score: 176
Period size: 39 Copynumber: 4.0 Consensus size: 40
53467569 GTATGTGGCC
* *
53467579 ATTGTGCGAATTGTGATATCCGGGCTAAG-CCCGAAGGCA
1 ATTGTGCGAGTTATGATATCCGGGCTAAGTCCCGAAGGCA
* * *
53467618 AATGTGCGAGATATGATATCCGGGCTAAG-CCCGAAGGCG
1 ATTGTGCGAGTTATGATATCCGGGCTAAGTCCCGAAGGCA
* * * *
53467657 ATTGTGCGAGTTGTGATATCCAGGTTAAGTCCCGAAGGTA
1 ATTGTGCGAGTTATGATATCCGGGCTAAGTCCCGAAGGCA
* * * * *
53467697 TTTGTGCGGGTTATCATAACCGGGCTATGTCCCGAAGGCA
1 ATTGTGCGAGTTATGATATCCGGGCTAAGTCCCGAAGGCA
53467737 TTTGAACGAG
Statistics
Matches: 97, Mismatches: 21, Indels: 1
0.82 0.18 0.01
Matches are distributed among these distances:
39 58 0.60
40 39 0.40
ACGTcount: A:0.25, C:0.20, G:0.31, T:0.25
Consensus pattern (40 bp):
ATTGTGCGAGTTATGATATCCGGGCTAAGTCCCGAAGGCA
Found at i:53467721 original size:79 final size:79
Alignment explanation
Indices: 53467579--53467735 Score: 199
Period size: 79 Copynumber: 2.0 Consensus size: 79
53467569 GTATGTGGCC
* * *
53467579 ATTGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAATGTGCGAGATATGATATCCGGGCT
1 ATTGTGCGAATTGTGATATCCAGGCTAAGCCCGAAGGCAAATGTGCGAGATATCATAACCGGGCT
53467644 AAG-CCCGAAGGCG
66 AAGTCCCGAAGGCG
* * * ** * *
53467657 ATTGTGCGAGTTGTGATATCCAGGTTAAGTCCCGAAGGTATTTGTGCGGGTTATCATAACCGGGC
1 ATTGTGCGAATTGTGATATCCAGGCTAAG-CCCGAAGGCAAATGTGCGAGATATCATAACCGGGC
*
53467722 TATGTCCCGAAGGC
65 TAAGTCCCGAAGGC
53467736 ATTTGAACGA
Statistics
Matches: 66, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
78 26 0.39
79 31 0.47
80 9 0.14
ACGTcount: A:0.24, C:0.20, G:0.31, T:0.25
Consensus pattern (79 bp):
ATTGTGCGAATTGTGATATCCAGGCTAAGCCCGAAGGCAAATGTGCGAGATATCATAACCGGGCT
AAGTCCCGAAGGCG
Found at i:53469344 original size:27 final size:28
Alignment explanation
Indices: 53469280--53469332 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
53469270 ATTACACTGT
*
53469280 ACTGATACTGTATTGGGCTTAAGGCCAC
1 ACTGATACTGTATAGGGCTTAAGGCCAC
*
53469308 ACTGTTACTGTATAGGGC-TAAGGCC
1 ACTGATACTGTATAGGGCTTAAGGCC
53469333 CAGACTATAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 7 0.30
28 16 0.70
ACGTcount: A:0.25, C:0.21, G:0.26, T:0.28
Consensus pattern (28 bp):
ACTGATACTGTATAGGGCTTAAGGCCAC
Found at i:53469350 original size:33 final size:33
Alignment explanation
Indices: 53469308--53469371 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
53469298 TTAAGGCCAC
* *
53469308 ACTGTTACTGTATAGGGCTAAGGCCCAGACTAT
1 ACTGATACTGAATAGGGCTAAGGCCCAGACTAT
*
53469341 ACTGATACTGAATAGGGCTCAGGCCCAGACT
1 ACTGATACTGAATAGGGCTAAGGCCCAGACT
53469372 GTTACTGTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.28, C:0.23, G:0.25, T:0.23
Consensus pattern (33 bp):
ACTGATACTGAATAGGGCTAAGGCCCAGACTAT
Found at i:53470968 original size:34 final size:32
Alignment explanation
Indices: 53470878--53470975 Score: 83
Period size: 34 Copynumber: 3.0 Consensus size: 32
53470868 TTGATTGCAT
* *
53470878 ACTGTACTGATT-CTGTAATGGGCTTAGGCCCC
1 ACTGTACTG-TTACTGTAAAGGGCTAAGGCCCC
* * * *
53470910 ACTGGTATTGTTATTG-AAATGGGCTCAGGCCCAG
1 ACT-GTACTGTTACTGTAAA-GGGCTAAGGCCC-C
53470944 ACTGCTACTGTTACTGTAAAGGGCTAAGGCCC
1 ACTG-TACTGTTACTGTAAAGGGCTAAGGCCC
53470976 TAACTGATAT
Statistics
Matches: 52, Mismatches: 8, Indels: 10
0.74 0.11 0.14
Matches are distributed among these distances:
32 7 0.13
33 19 0.37
34 23 0.44
35 3 0.06
ACGTcount: A:0.22, C:0.22, G:0.27, T:0.29
Consensus pattern (32 bp):
ACTGTACTGTTACTGTAAAGGGCTAAGGCCCC
Found at i:53474594 original size:21 final size:21
Alignment explanation
Indices: 53474569--53474626 Score: 82
Period size: 21 Copynumber: 2.8 Consensus size: 21
53474559 AACTGTTGTT
53474569 GAAAAGGAAGTTGCTGCT-ACA
1 GAAAAGGAAGTTGCTGCTGA-A
*
53474590 GAAAAGGAAGTTGTTGCTGAA
1 GAAAAGGAAGTTGCTGCTGAA
*
53474611 GAAAAAGAAGTTGCTG
1 GAAAAGGAAGTTGCTG
53474627 AAAATGAGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
21 32 0.97
22 1 0.03
ACGTcount: A:0.40, C:0.09, G:0.31, T:0.21
Consensus pattern (21 bp):
GAAAAGGAAGTTGCTGCTGAA
Found at i:53477817 original size:80 final size:80
Alignment explanation
Indices: 53477733--53477881 Score: 183
Period size: 80 Copynumber: 1.9 Consensus size: 80
53477723 TATGGTAACC
* * * *
53477733 CGCACCAAGGCCTACGGGACTTAACCCGGATATCA-CGATTTGCACAAATGCCTTCGGGTCTTAG
1 CGCACCAAGGCCTACGGGACTTAACCCGGATAT-AGCCACTAGCACAAATGCCTTCGGGTCTTAA
53477797 CCCGGATAGAATGACT
65 CCCGGATAGAATGACT
* * * * * * *
53477813 CGCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
53477878 CCGG
66 CCGG
53477882 TTATAATTTC
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
79 1 0.02
80 56 0.98
ACGTcount: A:0.23, C:0.30, G:0.25, T:0.22
Consensus pattern (80 bp):
CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
CCGGATAGAATGACT
Found at i:53477823 original size:40 final size:38
Alignment explanation
Indices: 53477774--53477881 Score: 128
Period size: 40 Copynumber: 2.7 Consensus size: 38
53477764 ATCACGATTT
*
53477774 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATG-ACTC
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGAT-GAA-GCACTA
*
53477814 GCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTA
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATGAAG-CACTA
*
53477854 GCACAATTGCCTTCGGGTCTTAACCCGG
1 GCACAA-TGCCTTCGGGTCTTAGCCCGG
53477882 TTATAATTTC
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
38 1 0.02
39 4 0.07
40 56 0.92
ACGTcount: A:0.21, C:0.30, G:0.26, T:0.23
Consensus pattern (38 bp):
GCACAATGCCTTCGGGTCTTAGCCCGGATGAAGCACTA
Found at i:53485934 original size:80 final size:80
Alignment explanation
Indices: 53485850--53485998 Score: 183
Period size: 80 Copynumber: 1.9 Consensus size: 80
53485840 TATGGTAACC
* * * *
53485850 CGCACCAAGGCCTACGGGACTTAACCCGGATATCA-CGATTTGCACAAATGCCTTCGGGTCTTAG
1 CGCACCAAGGCCTACGGGACTTAACCCGGATAT-AGCCACTAGCACAAATGCCTTCGGGTCTTAA
53485914 CCCGGATAGAATGACT
65 CCCGGATAGAATGACT
* * * * * * *
53485930 CGCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
53485995 CCGG
66 CCGG
53485999 TTATAATTTC
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
79 1 0.02
80 56 0.98
ACGTcount: A:0.23, C:0.30, G:0.25, T:0.22
Consensus pattern (80 bp):
CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
CCGGATAGAATGACT
Found at i:53485940 original size:40 final size:38
Alignment explanation
Indices: 53485891--53485998 Score: 128
Period size: 40 Copynumber: 2.7 Consensus size: 38
53485881 ATCACGATTT
*
53485891 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATG-ACTC
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGAT-GAA-GCACTA
*
53485931 GCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTA
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATGAAG-CACTA
*
53485971 GCACAATTGCCTTCGGGTCTTAACCCGG
1 GCACAA-TGCCTTCGGGTCTTAGCCCGG
53485999 TTATAATTTC
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
38 1 0.02
39 4 0.07
40 56 0.92
ACGTcount: A:0.21, C:0.30, G:0.26, T:0.23
Consensus pattern (38 bp):
GCACAATGCCTTCGGGTCTTAGCCCGGATGAAGCACTA
Found at i:53492028 original size:124 final size:124
Alignment explanation
Indices: 53491806--53492030 Score: 326
Period size: 124 Copynumber: 1.8 Consensus size: 124
53491796 GAATTATGTG
* * * * * * *
53491806 AAATGAAATATGGATGTGTATTGATTATTGATTTATGTGTGTATGAGTATTTGAATGATACCCGG
1 AAATGAAATATGAATGTCTAATGATTATTGATGTATGTGTGCATGAGCAATTGAATGATACCCGG
* **
53491871 GCTAAGTCCCGAAGGCGATTATGCTAGTGATTATATTTGTGTTTGAGCCTTAGTAACGA
66 GCTAAGTCCCGAAGACGATTATGCTAGAAATTATATTTGTGTTTGAGCCTTAGTAACGA
*
53491930 AAATGAAATATGAATGTCTAATGATTATTGATGTATGTGTGCATGAGCAATTGAATGATATCCGG
1 AAATGAAATATGAATGTCTAATGATTATTGATGTATGTGTGCATGAGCAATTGAATGATACCCGG
*
53491995 GCTAAGTCCCGAAGACG-TTATTGCTGGAAATTATAT
66 GCTAAGTCCCGAAGACGATTA-TGCTAGAAATTATAT
53492031 CCGGGTTAAG
Statistics
Matches: 88, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
123 3 0.03
124 85 0.97
ACGTcount: A:0.31, C:0.10, G:0.24, T:0.35
Consensus pattern (124 bp):
AAATGAAATATGAATGTCTAATGATTATTGATGTATGTGTGCATGAGCAATTGAATGATACCCGG
GCTAAGTCCCGAAGACGATTATGCTAGAAATTATATTTGTGTTTGAGCCTTAGTAACGA
Found at i:53492152 original size:40 final size:40
Alignment explanation
Indices: 53492025--53492154 Score: 165
Period size: 40 Copynumber: 3.2 Consensus size: 40
53492015 TTGCTGGAAA
* * *
53492025 TTATATCCGGGTTAAGACCCGAAGGCAATT-GTGCTAGCGG
1 TTATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTGG
* * *
53492065 CTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCG
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTGG
*
53492105 TTCTATCCGGGCTAAGACCCGAAGGCATTCGTGC-ACGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGA-GTGG
53492145 TTATATCCGG
1 TTATATCCGG
53492155 TTGTATTCCG
Statistics
Matches: 77, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
39 4 0.05
40 73 0.95
ACGTcount: A:0.22, C:0.25, G:0.29, T:0.23
Consensus pattern (40 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTGG
Found at i:53495956 original size:18 final size:19
Alignment explanation
Indices: 53495918--53495958 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
53495908 TGGTTCATGT
53495918 TTTCAATCTCATATCTCAA
1 TTTCAATCTCATATCTCAA
53495937 TTTCAATTCTCA-AT-TCAA
1 TTTCAA-TCTCATATCTCAA
53495955 TTTC
1 TTTC
53495959 TCATTTCTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 8 0.38
20 5 0.24
ACGTcount: A:0.29, C:0.24, G:0.00, T:0.46
Consensus pattern (19 bp):
TTTCAATCTCATATCTCAA
Found at i:53496147 original size:21 final size:21
Alignment explanation
Indices: 53496121--53496205 Score: 80
Period size: 21 Copynumber: 4.0 Consensus size: 21
53496111 TGATCAGTAT
*
53496121 ACGACACATAAAGTGCCTAAA
1 ACGACACACAAAGTGCCTAAA
* * * *
53496142 ACGACACACGAGGTGCCTGAT
1 ACGACACACAAAGTGCCTAAA
* *
53496163 ACGACACACGAGGTGCCTGAAA
1 ACGACACACAAAGTGCCT-AAA
*
53496185 TACGACACATAAAGTGCCTAA
1 -ACGACACACAAAGTGCCTAA
53496206 TCGGTAAAGC
Statistics
Matches: 52, Mismatches: 10, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
21 34 0.65
22 3 0.06
23 15 0.29
ACGTcount: A:0.39, C:0.26, G:0.21, T:0.14
Consensus pattern (21 bp):
ACGACACACAAAGTGCCTAAA
Found at i:53496171 original size:23 final size:22
Alignment explanation
Indices: 53496119--53496193 Score: 91
Period size: 21 Copynumber: 3.5 Consensus size: 22
53496109 CCTGATCAGT
** *
53496119 ATACGACACATAAAGTGCCT-A
1 ATACGACACACGAGGTGCCTGA
*
53496140 AAACGACACACGAGGTGCCTG-
1 ATACGACACACGAGGTGCCTGA
53496161 ATACGACACACGAGGTGCCTGAA
1 ATACGACACACGAGGTGCCTG-A
53496184 ATACGACACA
1 ATACGACACA
53496194 TAAAGTGCCT
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
21 36 0.78
23 10 0.22
ACGTcount: A:0.39, C:0.27, G:0.21, T:0.13
Consensus pattern (22 bp):
ATACGACACACGAGGTGCCTGA
Found at i:53496436 original size:17 final size:17
Alignment explanation
Indices: 53496393--53496439 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 17
53496383 TTCAATTCAA
* *
53496393 CAATATATTTCAATTATT
1 CAATATAATTC-ATAATT
53496411 CACAT-TAATTCATAATT
1 CA-ATATAATTCATAATT
53496428 CAATATAATTCA
1 CAATATAATTCA
53496440 ATTCATTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
16 2 0.08
17 14 0.56
18 7 0.28
19 2 0.08
ACGTcount: A:0.43, C:0.15, G:0.00, T:0.43
Consensus pattern (17 bp):
CAATATAATTCATAATT
Found at i:53496599 original size:15 final size:15
Alignment explanation
Indices: 53496574--53496631 Score: 89
Period size: 15 Copynumber: 3.8 Consensus size: 15
53496564 TCATATATAT
53496574 TATATAATTCAATCAA
1 TATA-AATTCAATCAA
53496590 TATAAATTCAATCAA
1 TATAAATTCAATCAA
* *
53496605 AATAATTTCAATCAA
1 TATAAATTCAATCAA
53496620 TATAAATTCAAT
1 TATAAATTCAAT
53496632 AAAACAGATA
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
15 34 0.89
16 4 0.11
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (15 bp):
TATAAATTCAATCAA
Found at i:53496616 original size:30 final size:28
Alignment explanation
Indices: 53496577--53496635 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 28
53496567 TATATATTAT
53496577 ATAATTCAATCAATATAAATTCAATCAAA
1 ATAATTCAATCAATATAAATTCAAT-AAA
53496606 ATAATTTCAATCAATATAAATTCAATAAA
1 ATAA-TTCAATCAATATAAATTCAATAAA
53496635 A
1 A
53496636 CAGATATTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 8 0.28
30 21 0.72
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.32
Consensus pattern (28 bp):
ATAATTCAATCAATATAAATTCAATAAA
Found at i:53496793 original size:2 final size:2
Alignment explanation
Indices: 53496786--53496815 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
53496776 ATATCTCATT
53496786 CA CA CA CA 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
53496816 TATATATATA
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:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:53496820 original size:2 final size:2
Alignment explanation
Indices: 53496815--53496858 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
53496805 ACACACACAC
*
53496815 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
53496856 AT A
1 AT A
53496859 ATTCAATTTA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:53497659 original size:13 final size:13
Alignment explanation
Indices: 53497641--53497668 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
53497631 CCTCTTTTTA
53497641 TTCTTTTGTTTCT
1 TTCTTTTGTTTCT
53497654 TTCTTTTGTTTCT
1 TTCTTTTGTTTCT
53497667 TT
1 TT
53497669 TATATATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.00, C:0.14, G:0.07, T:0.79
Consensus pattern (13 bp):
TTCTTTTGTTTCT
Found at i:53499251 original size:29 final size:29
Alignment explanation
Indices: 53499215--53499348 Score: 162
Period size: 29 Copynumber: 4.6 Consensus size: 29
53499205 AATAAACGAT
* *
53499215 CTCGCACACTTAGTGCCATGCGATTTAAG
1 CTCGCACACTTAGTGCCATACAATTTAAG
* *
53499244 CTCGCACACATAGTGCCATATAATTTAAG
1 CTCGCACACTTAGTGCCATACAATTTAAG
* * *
53499273 TTTGCACACTTAGTGCCATATAATTTAAG
1 CTCGCACACTTAGTGCCATACAATTTAAG
* * *
53499302 TTCGCACACTTAGTGCCATAC-CTTCCAAG
1 CTCGCACACTTAGTGCCATACAATT-TAAG
53499331 CTCGCACACTTAGTGCCA
1 CTCGCACACTTAGTGCCA
53499349 ATCTTGTCAC
Statistics
Matches: 92, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
28 2 0.02
29 90 0.98
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.29
Consensus pattern (29 bp):
CTCGCACACTTAGTGCCATACAATTTAAG
Found at i:53502617 original size:40 final size:40
Alignment explanation
Indices: 53502543--53502766 Score: 337
Period size: 40 Copynumber: 5.6 Consensus size: 40
53502533 AACCCAAGTA
* *
53502543 CCTTCGGGAT-TTAG-CCGGATATA-ACAACTCGCACAAATG
1 CCTTCGGG-TCTTAGCCCGGATATAGTC-ACTAGCACAAATG
*
53502582 CCTTCGGGTCTTAGCCCGAATATAGTCACTAGCACAAATG
1 CCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATG
*
53502622 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATG
* *
53502662 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCATAAAATG
1 CCTTCGGGTCTTAGCCCGGATATAGTCACTAGCA-CAAATG
53502703 CCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAAATG
1 CCTTCGGGTCTTAGCCCGGATATAGTCACTAGCAC-AAATG
53502744 CCTTCGGGTCTTAGCCCGGATAT
1 CCTTCGGGTCTTAGCCCGGATAT
53502767 CATCCGAATA
Statistics
Matches: 172, Mismatches: 8, Indels: 8
0.91 0.04 0.04
Matches are distributed among these distances:
38 1 0.01
39 12 0.07
40 92 0.53
41 67 0.39
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATG
Found at i:53516729 original size:40 final size:40
Alignment explanation
Indices: 53516670--53516811 Score: 124
Period size: 40 Copynumber: 3.5 Consensus size: 40
53516660 AAATTGAATG
* * *
53516670 ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
* * * ***
53516710 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
* * * ** *
53516750 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTTATT
1 ATATCCGGGCTAAGACCCGAAGACAATT-ATGCTAGAAACT
*
53516790 CTATCCGGGCTAAGACCCGAAG
1 ATATCCGGGCTAAGACCCGAAG
53516812 GCATTTGTGC
Statistics
Matches: 86, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
39 3 0.03
40 83 0.97
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
Found at i:53516812 original size:40 final size:39
Alignment explanation
Indices: 53516709--53516837 Score: 152
Period size: 40 Copynumber: 3.2 Consensus size: 39
53516699 TGCTGGAAAT
* * *
53516709 TATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGC
1 TATATCCGGGCTAAGACCCGAAGGC-ATTGTGCGAGTGAC
* *
53516749 TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTAT
1 TATATCCGGGCTAAGACCCGAAGGCATT-GTGCGAGTGAC
* *
53516789 TCTATCCGGGCTAAGACCCGAAGGCATTTGTGC-ACGTGAT
1 TATATCCGGGCTAAGACCCGAAGGCA-TTGTGCGA-GTGAC
53516829 TATATCCGG
1 TATATCCGG
53516838 TTATATTCCG
Statistics
Matches: 78, Mismatches: 8, Indels: 6
0.85 0.09 0.07
Matches are distributed among these distances:
39 4 0.05
40 72 0.92
41 2 0.03
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (39 bp):
TATATCCGGGCTAAGACCCGAAGGCATTGTGCGAGTGAC
Found at i:53519158 original size:33 final size:34
Alignment explanation
Indices: 53519086--53519158 Score: 94
Period size: 34 Copynumber: 2.2 Consensus size: 34
53519076 TCAGTCGCAA
*
53519086 TATCAGTGTGGGCCTTAGCCCAATACAGTAACAG
1 TATCAGTGTGGGACTTAGCCCAATACAGTAACAG
* * * *
53519120 TATCAGTGTTGGACTTAGTCCATTTCAGT-ACAG
1 TATCAGTGTGGGACTTAGCCCAATACAGTAACAG
53519153 TATCAG
1 TATCAG
53519159 AAATGCATAT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
33 10 0.29
34 24 0.71
ACGTcount: A:0.27, C:0.21, G:0.22, T:0.30
Consensus pattern (34 bp):
TATCAGTGTGGGACTTAGCCCAATACAGTAACAG
Found at i:53526708 original size:40 final size:40
Alignment explanation
Indices: 53526664--53526776 Score: 138
Period size: 40 Copynumber: 2.8 Consensus size: 40
53526654 TGCTGGAAAT
* * *
53526664 TATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGC
1 TATATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGTGAC
* * *
53526704 TATATCCGGGCTAAGGCCCGAAGGC-ATTCGTGCGAGTTAT
1 TATATCCGGGCTAAGACCCGAAGGCAATT-GTGCGAGTGAC
* *
53526744 TCTATCCGGGCTAAGACCCGAAGGCATTTGTGC
1 TATATCCGGGCTAAGACCCGAAGGCAATTGTGC
53526777 ACGTGATTAA
Statistics
Matches: 62, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
39 3 0.05
40 57 0.92
41 2 0.03
ACGTcount: A:0.23, C:0.23, G:0.29, T:0.25
Consensus pattern (40 bp):
TATATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGTGAC
Found at i:53528493 original size:13 final size:14
Alignment explanation
Indices: 53528477--53528512 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
53528467 CAATCTCATA
53528477 TCTCAATTTCAA-T
1 TCTCAATTTCAATT
53528490 TCTCAA-TTCAATT
1 TCTCAATTTCAATT
53528503 TCTC-ATTTCA
1 TCTCAATTTCA
53528513 TTCCAATAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 6 0.29
13 15 0.71
ACGTcount: A:0.28, C:0.25, G:0.00, T:0.47
Consensus pattern (14 bp):
TCTCAATTTCAATT
Found at i:53528502 original size:18 final size:19
Alignment explanation
Indices: 53528464--53528504 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
53528454 TGGTTCATGT
53528464 TTTCAATCTCATATCTCAA
1 TTTCAATCTCATATCTCAA
53528483 TTTCAATTCTCA-AT-TCAA
1 TTTCAA-TCTCATATCTCAA
53528501 TTTC
1 TTTC
53528505 TCATTTCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 8 0.38
20 5 0.24
ACGTcount: A:0.29, C:0.24, G:0.00, T:0.46
Consensus pattern (19 bp):
TTTCAATCTCATATCTCAA
Found at i:53528694 original size:21 final size:21
Alignment explanation
Indices: 53528668--53528752 Score: 80
Period size: 21 Copynumber: 4.0 Consensus size: 21
53528658 TGATTAGTAT
*
53528668 ACGACACATAAAGTGCCTAAA
1 ACGACACACAAAGTGCCTAAA
* * * *
53528689 ACGACACACGAGGTGCCTGAT
1 ACGACACACAAAGTGCCTAAA
* *
53528710 ACGACACACGAGGTGCCTGAAA
1 ACGACACACAAAGTGCCT-AAA
*
53528732 TACGACACATAAAGTGCCTAA
1 -ACGACACACAAAGTGCCTAA
53528753 TCGGTAAAGC
Statistics
Matches: 52, Mismatches: 10, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
21 34 0.65
22 3 0.06
23 15 0.29
ACGTcount: A:0.39, C:0.26, G:0.21, T:0.14
Consensus pattern (21 bp):
ACGACACACAAAGTGCCTAAA
Found at i:53528718 original size:23 final size:22
Alignment explanation
Indices: 53528666--53528740 Score: 91
Period size: 21 Copynumber: 3.5 Consensus size: 22
53528656 CCTGATTAGT
** *
53528666 ATACGACACATAAAGTGCCT-A
1 ATACGACACACGAGGTGCCTGA
*
53528687 AAACGACACACGAGGTGCCTG-
1 ATACGACACACGAGGTGCCTGA
53528708 ATACGACACACGAGGTGCCTGAA
1 ATACGACACACGAGGTGCCTG-A
53528731 ATACGACACA
1 ATACGACACA
53528741 TAAAGTGCCT
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
21 36 0.78
23 10 0.22
ACGTcount: A:0.39, C:0.27, G:0.21, T:0.13
Consensus pattern (22 bp):
ATACGACACACGAGGTGCCTGA
Found at i:53529141 original size:15 final size:15
Alignment explanation
Indices: 53529116--53529173 Score: 89
Period size: 15 Copynumber: 3.8 Consensus size: 15
53529106 TCATATATAT
53529116 TATATAATTCAATCAA
1 TATA-AATTCAATCAA
53529132 TATAAATTCAATCAA
1 TATAAATTCAATCAA
* *
53529147 AATAATTTCAATCAA
1 TATAAATTCAATCAA
53529162 TATAAATTCAAT
1 TATAAATTCAAT
53529174 AAAACAGATA
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
15 34 0.89
16 4 0.11
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (15 bp):
TATAAATTCAATCAA
Found at i:53529158 original size:30 final size:28
Alignment explanation
Indices: 53529119--53529177 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 28
53529109 TATATATTAT
53529119 ATAATTCAATCAATATAAATTCAATCAAA
1 ATAATTCAATCAATATAAATTCAAT-AAA
53529148 ATAATTTCAATCAATATAAATTCAATAAA
1 ATAA-TTCAATCAATATAAATTCAATAAA
53529177 A
1 A
53529178 CAGATATTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 8 0.28
30 21 0.72
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.32
Consensus pattern (28 bp):
ATAATTCAATCAATATAAATTCAATAAA
Found at i:53529981 original size:13 final size:13
Alignment explanation
Indices: 53529963--53529990 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
53529953 CCTCTTTTTA
53529963 TTCTTTTGTTTCT
1 TTCTTTTGTTTCT
53529976 TTCTTTTGTTTCT
1 TTCTTTTGTTTCT
53529989 TT
1 TT
53529991 ATATATATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.00, C:0.14, G:0.07, T:0.79
Consensus pattern (13 bp):
TTCTTTTGTTTCT
Found at i:53532979 original size:49 final size:49
Alignment explanation
Indices: 53532858--53533155 Score: 537
Period size: 49 Copynumber: 6.1 Consensus size: 49
53532848 TTTACCACAT
* *
53532858 ATATATATACACTTTCACATTCATCACGTCGGCCATTAGGCCTTATCAC
1 ATATATATACATTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
*
53532907 --ATATATACATTTTCACATTCATCACATCGGCCATTAGGCCTCATCAC
1 ATATATATACATTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
*
53532954 ATATATATACATTTTCACATTCATCACGTCGGCCATTAGGCCTTATCAC
1 ATATATATACATTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
*
53533003 ATATATATATATTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
1 ATATATATACATTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
53533052 ATATATATACATTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
1 ATATATATACATTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
53533101 ATATATATACATTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
1 ATATATATACATTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
53533150 ATATAT
1 ATATAT
53533156 TATTATGTAC
Statistics
Matches: 239, Mismatches: 8, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
47 44 0.18
49 195 0.82
ACGTcount: A:0.30, C:0.27, G:0.09, T:0.35
Consensus pattern (49 bp):
ATATATATACATTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
Found at i:53537319 original size:40 final size:40
Alignment explanation
Indices: 53537253--53537402 Score: 259
Period size: 40 Copynumber: 3.8 Consensus size: 40
53537243 CCAGCATGAT
* *
53537253 TGCTCTTCGGGACCTAG-CCGGATACATCACTAGCACGAA
1 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
53537292 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
53537332 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
*
53537372 TGCTCTTCGGAACTTAGTCC-GATATATCACT
1 TGCTCTTCGGAACTTAGTCCGGATACATCACT
53537403 CTCAATTCTC
Statistics
Matches: 107, Mismatches: 3, Indels: 2
0.96 0.03 0.02
Matches are distributed among these distances:
39 25 0.23
40 82 0.77
ACGTcount: A:0.26, C:0.28, G:0.20, T:0.26
Consensus pattern (40 bp):
TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
Found at i:53539257 original size:37 final size:36
Alignment explanation
Indices: 53539207--53539293 Score: 147
Period size: 37 Copynumber: 2.3 Consensus size: 36
53539197 TACGAAGTCT
53539207 TACCCGGACATAATCTCCACACGTAGTCATCGGGTC
1 TACCCGGACATAATCTCCACACGTAGTCATCGGGTC
53539243 GTACCCGGACATAATCTCCACACGTAGTCATCGGGTC
1 -TACCCGGACATAATCTCCACACGTAGTCATCGGGTC
53539280 TCACCCGGAACATA
1 T-ACCCGG-ACATA
53539294 TTTCCAAGTT
Statistics
Matches: 48, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
36 1 0.02
37 42 0.88
38 5 0.10
ACGTcount: A:0.26, C:0.33, G:0.20, T:0.21
Consensus pattern (36 bp):
TACCCGGACATAATCTCCACACGTAGTCATCGGGTC
Found at i:53539429 original size:49 final size:49
Alignment explanation
Indices: 53539362--53539670 Score: 467
Period size: 49 Copynumber: 6.1 Consensus size: 49
53539352 TTTACCACAT
* *
53539362 ATATATATACACTTTCACATTCATCACGTCGGCCATTAGGCCTTATCAC
1 ATATATATACATTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
*
53539411 ATATATATACATTTTCACATTCATCACATCGGCCATTAGGCCTCATCAC
1 ATATATATACATTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
*
53539460 ATATATATACA-TTTCACATTCATCACGTCGGCCATTAGGCCTTATCAC
1 ATATATATACATTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
*
53539508 ATATATATATATTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATCTTATCAC
1 ATATATATACATTTTCACATTCATCACATCGGCCATTAGG--------C--CTTATCAC
53539567 ATATATATACATTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
1 ATATATATACATTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
*
53539616 ATATATATACATTTTCACATTCATCACATCGGGCATTAGGCCTTATCAC
1 ATATATATACATTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
53539665 ATATAT
1 ATATAT
53539671 TATTATGTAC
Statistics
Matches: 240, Mismatches: 9, Indels: 22
0.89 0.03 0.08
Matches are distributed among these distances:
48 45 0.19
49 146 0.61
51 1 0.00
57 1 0.00
59 47 0.20
ACGTcount: A:0.30, C:0.26, G:0.09, T:0.35
Consensus pattern (49 bp):
ATATATATACATTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
Found at i:53539496 original size:97 final size:98
Alignment explanation
Indices: 53539362--53539670 Score: 476
Period size: 97 Copynumber: 3.1 Consensus size: 98
53539352 TTTACCACAT
53539362 ATATATATACACTTTCACATTCATCACGTCGGCCATTAGGCCTTATCACATATATATACATTTTC
1 ATATATATACACTTTCACATTCATCACGTCGGCCATTAGGCCTTATCACATATATATACATTTTC
53539427 ACATTCATCACATCGGCCATTAGGCCTCATCAC
66 ACATTCATCACATCGGCCATTAGGCCTCATCAC
*
53539460 ATATATATACA-TTTCACATTCATCACGTCGGCCATTAGGCCTTATCACATATATATATATTTTC
1 ATATATATACACTTTCACATTCATCACGTCGGCCATTAGGCCTTATCACATATATATACATTTTC
53539524 ACATTCATCACATCGGCCATTAGGCCTTATCACATCTTATCAC
66 ACATTCATCACATCGGCCATTAGG------C-C-TC--ATCAC
* *
53539567 ATATATATACATTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACATTTTC
1 ATATATATACACTTTCACATTCATCACGTCGGCCATTAGGCCTTATCACATATATATACATTTTC
* *
53539632 ACATTCATCACATCGGGCATTAGGCCTTATCAC
66 ACATTCATCACATCGGCCATTAGGCCTCATCAC
53539665 ATATAT
1 ATATAT
53539671 TATTATGTAC
Statistics
Matches: 195, Mismatches: 5, Indels: 22
0.88 0.02 0.10
Matches are distributed among these distances:
97 76 0.39
98 22 0.11
100 1 0.01
101 1 0.01
102 1 0.01
103 1 0.01
104 1 0.01
105 2 0.01
107 16 0.08
108 74 0.38
ACGTcount: A:0.30, C:0.26, G:0.09, T:0.35
Consensus pattern (98 bp):
ATATATATACACTTTCACATTCATCACGTCGGCCATTAGGCCTTATCACATATATATACATTTTC
ACATTCATCACATCGGCCATTAGGCCTCATCAC
Found at i:53539594 original size:27 final size:27
Alignment explanation
Indices: 53539503--53539595 Score: 71
Period size: 27 Copynumber: 3.3 Consensus size: 27
53539493 ATTAGGCCTT
*
53539503 ATCACATATATATATATTTTCACATTC
1 ATCACATATATATACATTTTCACATTC
** * * *
53539530 ATCACATCGGCCAT-TAGGCCTTATCACATCTT
1 ATCACAT-----ATATATACATTTTCACAT-TC
53539562 ATCACATATATATACATTTTCACATTC
1 ATCACATATATATACATTTTCACATTC
53539589 ATCACAT
1 ATCACAT
53539596 CGGCCATTAG
Statistics
Matches: 48, Mismatches: 11, Indels: 14
0.66 0.15 0.19
Matches are distributed among these distances:
27 17 0.35
28 11 0.23
31 10 0.21
32 10 0.21
ACGTcount: A:0.33, C:0.25, G:0.04, T:0.38
Consensus pattern (27 bp):
ATCACATATATATACATTTTCACATTC
Found at i:53539599 original size:108 final size:107
Alignment explanation
Indices: 53539455--53539666 Score: 388
Period size: 108 Copynumber: 2.0 Consensus size: 107
53539445 ATTAGGCCTC
* *
53539455 ATCACATATATATACATTTCACATTCATCACGTCGGCCATTAGGCCTTATCACATATATATATAT
1 ATCACATATATATACATTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACAT
53539520 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATCTT
66 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATCTT
53539562 ATCACATATATATACATTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACA
1 ATCACATATATATACA-TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACA
*
53539627 TTTTCACATTCATCACATCGGGCATTAGGCCTTATCACAT
65 TTTTCACATTCATCACATCGGCCATTAGGCCTTATCACAT
53539667 ATATTATTAT
Statistics
Matches: 101, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
107 16 0.16
108 85 0.84
ACGTcount: A:0.31, C:0.26, G:0.08, T:0.35
Consensus pattern (107 bp):
ATCACATATATATACATTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACAT
TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATCTT
Found at i:53542819 original size:41 final size:40
Alignment explanation
Indices: 53542646--53542869 Score: 346
Period size: 40 Copynumber: 5.6 Consensus size: 40
53542636 AACCCAAGTA
* *
53542646 CCTTCGGGAT-TTAG-CCGGATATA-ACAACTCGCACAAATG
1 CCTTCGGG-TCTTAGCCCGGATATAGTC-ACTAGCACAAATG
53542685 CCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATG
*
53542725 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATG
* *
53542765 CCTTTGGGACTTAGCCCGGATATAGTCACTAGCACAAAATG
1 CCTTCGGGTCTTAGCCCGGATATAGTCACTAGCAC-AAATG
53542806 CCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAAATG
1 CCTTCGGGTCTTAGCCCGGATATAGTCACTAGCAC-AAATG
53542847 CCTTCGGGTCTTAGCCCGGATAT
1 CCTTCGGGTCTTAGCCCGGATAT
53542870 CATCCGAATA
Statistics
Matches: 175, Mismatches: 6, Indels: 6
0.94 0.03 0.03
Matches are distributed among these distances:
38 1 0.01
39 12 0.07
40 94 0.54
41 68 0.39
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATG
Found at i:53550463 original size:11 final size:12
Alignment explanation
Indices: 53550433--53550466 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
53550423 GTATATTTAC
53550433 TTATTATATAAG
1 TTATTATATAAG
53550445 TATATTAT-TAAG
1 T-TATTATATAAG
53550457 TTATTATATA
1 TTATTATATA
53550467 TATATATAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
11 6 0.30
12 8 0.40
13 6 0.30
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (12 bp):
TTATTATATAAG
Found at i:53552564 original size:40 final size:40
Alignment explanation
Indices: 53552506--53552612 Score: 112
Period size: 40 Copynumber: 2.7 Consensus size: 40
53552496 TTCGAATGAT
* *
53552506 ATCCGGGCTAAGTCCCGAAGGCTTT-GTGCTAAG-TGACTAA
1 ATCCGGACTAAGTCCCGAAGGCTTTCGAGC-AAGCT-ACTAA
53552546 ATCCGGACTAAGAT-CCGAAGGCTTTCGAGCAAGCTACTAA
1 ATCCGGACTAAG-TCCCGAAGGCTTTCGAGCAAGCTACTAA
** * *
53552586 ATCCGGGTTGAGTCCCGAAGGCATTCG
1 ATCCGGACTAAGTCCCGAAGGCTTTCG
53552613 TGCGAGTTAT
Statistics
Matches: 57, Mismatches: 6, Indels: 8
0.80 0.08 0.11
Matches are distributed among these distances:
39 1 0.02
40 51 0.89
41 5 0.09
ACGTcount: A:0.26, C:0.24, G:0.27, T:0.22
Consensus pattern (40 bp):
ATCCGGACTAAGTCCCGAAGGCTTTCGAGCAAGCTACTAA
Found at i:53564475 original size:31 final size:29
Alignment explanation
Indices: 53564372--53564454 Score: 166
Period size: 29 Copynumber: 2.9 Consensus size: 29
53564362 GTGACGAGAT
53564372 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
53564401 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
53564430 TGGCACTAAGTGTGCATGCTGGAAA
1 TGGCACTAAGTGTGCATGCTGGAAA
53564455 AAAATACGGC
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 54 1.00
ACGTcount: A:0.30, C:0.14, G:0.29, T:0.27
Consensus pattern (29 bp):
TGGCACTAAGTGTGCATGCTGGAAATATA
Found at i:53564495 original size:60 final size:58
Alignment explanation
Indices: 53564368--53564504 Score: 152
Period size: 60 Copynumber: 2.3 Consensus size: 58
53564358 TACGGTGACG
* * *
53564368 AGAT-TGGCACTAAGTGTGCATGCTGGAAATATATGGCACTAAGTGTGCATGCTGGAA
1 AGATATGGCACTAAGTGTGCATGCTGGAAAAATACGGCACTAAGTGTGCATGCTCGAA
* **
53564425 ATATATGGCACTAAGTGTGCATGCTGGAAAAAAATACGGCACTGGGTGTGCGA-GCTCGAA
1 AGATATGGCACTAAGTGTGCATGCTGG--AAAAATACGGCACTAAGTGTGC-ATGCTCGAA
* * *
53564485 GGGTATGGCACTATGTGTGC
1 AGATATGGCACTAAGTGTGC
53564505 GGGCTTAAAT
Statistics
Matches: 66, Mismatches: 10, Indels: 5
0.81 0.12 0.06
Matches are distributed among these distances:
57 3 0.05
58 22 0.33
60 40 0.61
61 1 0.02
ACGTcount: A:0.28, C:0.15, G:0.31, T:0.25
Consensus pattern (58 bp):
AGATATGGCACTAAGTGTGCATGCTGGAAAAATACGGCACTAAGTGTGCATGCTCGAA
Found at i:53572501 original size:29 final size:29
Alignment explanation
Indices: 53572468--53572550 Score: 166
Period size: 29 Copynumber: 2.9 Consensus size: 29
53572458 GTGACGAGAT
53572468 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
53572497 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
53572526 TGGCACTAAGTGTGCATGCTGGAAA
1 TGGCACTAAGTGTGCATGCTGGAAA
53572551 AAATACGGCA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 54 1.00
ACGTcount: A:0.30, C:0.14, G:0.29, T:0.27
Consensus pattern (29 bp):
TGGCACTAAGTGTGCATGCTGGAAATATA
Found at i:53572590 original size:59 final size:58
Alignment explanation
Indices: 53572464--53572599 Score: 159
Period size: 59 Copynumber: 2.3 Consensus size: 58
53572454 TACGGTGACG
* * *
53572464 AGAT-TGGCACTAAGTGTGCATGCTGGAAATATATGGCACTAAGTGTGCATGCTGGAA
1 AGATATGGCACTAAGTGTGCATGCTGGAAAAATACGGCACTAAGTGTGCATGCTCGAA
* **
53572521 ATATATGGCACTAAGTGTGCATGCTGGAAAAAATACGGCACTGGGTGTGCGA-GCTCGAA
1 AGATATGGCACTAAGTGTGCATGCTGG-AAAAATACGGCACTAAGTGTGC-ATGCTCGAA
* * *
53572580 GGGTATGGCACTATGTGTGC
1 AGATATGGCACTAAGTGTGC
53572600 GGGCTTAAAT
Statistics
Matches: 66, Mismatches: 10, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
57 3 0.05
58 22 0.33
59 40 0.61
60 1 0.02
ACGTcount: A:0.28, C:0.15, G:0.32, T:0.25
Consensus pattern (58 bp):
AGATATGGCACTAAGTGTGCATGCTGGAAAAATACGGCACTAAGTGTGCATGCTCGAA
Found at i:53575140 original size:68 final size:67
Alignment explanation
Indices: 53575068--53575217 Score: 171
Period size: 67 Copynumber: 2.2 Consensus size: 67
53575058 CATCATGTGT
* * * *
53575068 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACC
1 ACAAGAGAGCTAC--GACA-TAT-ATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACC
53575130 ATGTAG
62 ATGTAG
** * *
53575136 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGT
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
53575201 AG
66 AG
53575203 ACAAGAGAGCTACGA
1 ACAAGAGAGCTACGA
53575218 GATAAACTGG
Statistics
Matches: 70, Mismatches: 9, Indels: 7
0.81 0.10 0.08
Matches are distributed among these distances:
64 20 0.29
65 7 0.10
66 4 0.06
67 26 0.37
68 13 0.19
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.21
Consensus pattern (67 bp):
ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
AG
Found at i:53575173 original size:64 final size:64
Alignment explanation
Indices: 53575092--53575275 Score: 194
Period size: 67 Copynumber: 2.8 Consensus size: 64
53575082 AGACATTATG
* *
53575092 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * * *
53575156 ATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
53575221 AA
63 AA
* * * *
53575223 ACTG--GCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-GTACAAGAGAGC
1 A-TGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAG-ACAAGAGAGC
53575276 CGAACTATAT
Statistics
Matches: 98, Mismatches: 17, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
62 1 0.01
63 19 0.19
64 21 0.21
65 8 0.08
66 16 0.16
67 31 0.32
68 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:53579161 original size:48 final size:48
Alignment explanation
Indices: 53579034--53579161 Score: 122
Period size: 48 Copynumber: 2.7 Consensus size: 48
53579024 GACGAGAGCT
* *
53579034 AGTGTAAGACATGTCTGGGACAT-GCATCGACCTCTATATATGAAAGTC
1 AGTGTAAGACATGTCTGGGACATGGCGTCGA-CTCTATATATGAAAGCC
* * * *
53579082 AGTGTAAGACCTGTCTAGGACACGG-GATCGACT-T-TA-ATGCACTAGCC
1 AGTGTAAGACATGTCTGGGACATGGCG-TCGACTCTATATATG-A-AAGCC
53579129 AGTGTAAGACGATGTCTGGGACATGGCGTCGAC
1 AGTGTAAGAC-ATGTCTGGGACATGGCGTCGAC
53579162 ATCTTATCCC
Statistics
Matches: 65, Mismatches: 9, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
45 3 0.05
46 3 0.05
47 14 0.22
48 39 0.60
49 6 0.09
ACGTcount: A:0.28, C:0.20, G:0.27, T:0.24
Consensus pattern (48 bp):
AGTGTAAGACATGTCTGGGACATGGCGTCGACTCTATATATGAAAGCC
Found at i:53580361 original size:21 final size:20
Alignment explanation
Indices: 53580336--53580374 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
53580326 TCAACAGGGT
53580336 CACACGGGCGTGTTGCCCTTC
1 CACACGGGCGTG-TGCCCTTC
*
53580357 CACACGGGGGTGTGCCCT
1 CACACGGGCGTGTGCCCT
53580375 GTTTTAAGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.10, C:0.36, G:0.33, T:0.21
Consensus pattern (20 bp):
CACACGGGCGTGTGCCCTTC
Done.