Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 ID=Chr03-JGI_221_v2.0
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: 45765648
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 655849 characters in sequence are not A, C, G, or T
File 23 of 150
Found at i:6018246 original size:25 final size:25
Alignment explanation
Indices: 6018212--6018261 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
6018202 AAAGCAATTC
6018212 CTTAGCTTCTCAATTTCACAAATCT
1 CTTAGCTTCTCAATTTCACAAATCT
6018237 CTTAGCTTCTCAATTTCACAAATCT
1 CTTAGCTTCTCAATTTCACAAATCT
6018262 TCTTTCTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.28, C:0.28, G:0.04, T:0.40
Consensus pattern (25 bp):
CTTAGCTTCTCAATTTCACAAATCT
Found at i:6025990 original size:31 final size:31
Alignment explanation
Indices: 6025955--6026022 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
6025945 AAAAAAACAT
*
6025955 AATAGCCCAATGACTTAAATAAAAACTTTCA
1 AATAGCCCAATAACTTAAATAAAAACTTTCA
** * *
6025986 AATAGTTCAATAACTTAAATGAAAACTTTCG
1 AATAGCCCAATAACTTAAATAAAAACTTTCA
6026017 AATAGC
1 AATAGC
6026023 TCTGTGACCA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.47, C:0.16, G:0.09, T:0.28
Consensus pattern (31 bp):
AATAGCCCAATAACTTAAATAAAAACTTTCA
Found at i:6027547 original size:7 final size:7
Alignment explanation
Indices: 6027535--6027560 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
6027525 TCAGGCTATG
6027535 TTTAAAT
1 TTTAAAT
6027542 TTTAAAT
1 TTTAAAT
6027549 TTTAAAT
1 TTTAAAT
6027556 TTTAA
1 TTTAA
6027561 GAATTTTCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (7 bp):
TTTAAAT
Found at i:6035878 original size:29 final size:30
Alignment explanation
Indices: 6035829--6035888 Score: 70
Period size: 29 Copynumber: 2.0 Consensus size: 30
6035819 CCAAAAATAT
* *
6035829 TATGTTATAAAAATATTATAT-TAATTATA
1 TATGTTATAAAAAAATGATATATAATTATA
*
6035858 TATGTTA-AATAAAAATGATATATATTTATA
1 TATGTTATAA-AAAAATGATATATAATTATA
6035888 T
1 T
6035889 TAAATCACTA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
28 2 0.08
29 16 0.62
30 8 0.31
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.47
Consensus pattern (30 bp):
TATGTTATAAAAAAATGATATATAATTATA
Found at i:6039960 original size:13 final size:13
Alignment explanation
Indices: 6039942--6039966 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6039932 AGATGACAGG
6039942 TGTTTTTTTTTTT
1 TGTTTTTTTTTTT
6039955 TGTTTTTTTTTT
1 TGTTTTTTTTTT
6039967 GTGTGTGTGT
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:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (13 bp):
TGTTTTTTTTTTT
Found at i:6042540 original size:19 final size:20
Alignment explanation
Indices: 6042518--6042561 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
6042508 TAATAAAACC
*
6042518 AAAAATTTATTTTAAAA-TA
1 AAAAATGTATTTTAAAATTA
6042537 AAAAA-GTATTTTAAAATTA
1 AAAAATGTATTTTAAAATTA
6042556 AAAAAT
1 AAAAAT
6042562 AAAAAATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 10 0.45
19 12 0.55
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.36
Consensus pattern (20 bp):
AAAAATGTATTTTAAAATTA
Found at i:6042546 original size:18 final size:19
Alignment explanation
Indices: 6042525--6042560 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
6042515 ACCAAAAATT
6042525 TATTTTAAAA-TAAAAAAG
1 TATTTTAAAATTAAAAAAG
6042543 TATTTTAAAATTAAAAAA
1 TATTTTAAAATTAAAAAA
6042561 TAAAAAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (19 bp):
TATTTTAAAATTAAAAAAG
Found at i:6043576 original size:3 final size:3
Alignment explanation
Indices: 6043568--6043608 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
6043558 AAATTAGTTA
6043568 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
6043609 AAGGATAGAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:6049766 original size:3 final size:3
Alignment explanation
Indices: 6049758--6049819 Score: 124
Period size: 3 Copynumber: 20.7 Consensus size: 3
6049748 AAATTAGTTA
6049758 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
6049806 AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AA
6049820 AAGGATAGAT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:6052520 original size:27 final size:27
Alignment explanation
Indices: 6052465--6052521 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
6052455 AACTGCAGGG
* * *
6052465 TTCAAATCCTCAGCTGGAGAGTGATGA
1 TTCAAAGCCTCAGCTGGACAGTGAAGA
*
6052492 TTCAAAGCCTCAGCTGGACATTGAAGA
1 TTCAAAGCCTCAGCTGGACAGTGAAGA
6052519 TTC
1 TTC
6052522 GAAGGTGCAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (27 bp):
TTCAAAGCCTCAGCTGGACAGTGAAGA
Found at i:6053781 original size:15 final size:15
Alignment explanation
Indices: 6053761--6053793 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
6053751 CAAAACGGCG
6053761 CAAATGGAATTCTGA
1 CAAATGGAATTCTGA
6053776 CAAATGGAATTCTGA
1 CAAATGGAATTCTGA
6053791 CAA
1 CAA
6053794 TATAGAAGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.42, C:0.15, G:0.18, T:0.24
Consensus pattern (15 bp):
CAAATGGAATTCTGA
Found at i:6056259 original size:12 final size:12
Alignment explanation
Indices: 6056242--6056269 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
6056232 TATTATATTG
6056242 ATAAAAAAATAT
1 ATAAAAAAATAT
6056254 ATAAAAAAATAT
1 ATAAAAAAATAT
6056266 ATAA
1 ATAA
6056270 TATATAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (12 bp):
ATAAAAAAATAT
Found at i:6056461 original size:24 final size:26
Alignment explanation
Indices: 6056434--6056489 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 26
6056424 TATTTCAGAT
6056434 TTTTTATAAAA-A-AATTATTTT-TAA
1 TTTTTATAAAATATAATT-TTTTATAA
*
6056458 TTTTTTTAAAATATAATTTTTTATAA
1 TTTTTATAAAATATAATTTTTTATAA
6056484 TTTTTA
1 TTTTTA
6056490 CAATTTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
24 10 0.37
25 5 0.19
26 12 0.44
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (26 bp):
TTTTTATAAAATATAATTTTTTATAA
Found at i:6056468 original size:23 final size:25
Alignment explanation
Indices: 6056432--6056478 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 25
6056422 TATATTTCAG
*
6056432 ATTTTTTATAAAAAAATTATTTTTA
1 ATTTTTTATAAAAAAATAATTTTTA
*
6056457 ATTTTTT-T-AAAATATAATTTTT
1 ATTTTTTATAAAAAAATAATTTTT
6056479 TATAATTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 12 0.60
24 1 0.05
25 7 0.35
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (25 bp):
ATTTTTTATAAAAAAATAATTTTTA
Found at i:6056475 original size:26 final size:25
Alignment explanation
Indices: 6056432--6056488 Score: 73
Period size: 25 Copynumber: 2.2 Consensus size: 25
6056422 TATATTTCAG
6056432 ATTTTTTATAAAAAAATTATTTT-TA
1 ATTTTTTATAAAAAAATT-TTTTATA
6056457 ATTTTTT-TAAAATATAATTTTTTATA
1 ATTTTTTATAAAA-A-AATTTTTTATA
6056483 ATTTTT
1 ATTTTT
6056489 ACAATTTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
24 5 0.17
25 12 0.41
26 12 0.41
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (25 bp):
ATTTTTTATAAAAAAATTTTTTATA
Found at i:6057827 original size:20 final size:20
Alignment explanation
Indices: 6057804--6057847 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
6057794 AAAATTATAG
6057804 AAAATT-CTAAAAAAACTATT
1 AAAATTACTAAAAAAA-TATT
* *
6057824 AAAATTATTTAAAAAATATT
1 AAAATTACTAAAAAAATATT
6057844 AAAA
1 AAAA
6057848 ATAACATTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 14 0.67
21 7 0.33
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.32
Consensus pattern (20 bp):
AAAATTACTAAAAAAATATT
Found at i:6059173 original size:2 final size:2
Alignment explanation
Indices: 6059166--6059200 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
6059156 TGTTACAGGA
6059166 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6059201 CGTGAATGAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:6065974 original size:138 final size:138
Alignment explanation
Indices: 6065721--6066127 Score: 627
Period size: 138 Copynumber: 2.9 Consensus size: 138
6065711 ACATTAAGCG
*
6065721 TGTTGTGTCACGACACCAAGCCTCCAAGGTCGCGATACCACTGCTGATTGTTGAAGTGAAGAAGC
1 TGTTTTGTCACGACACCAAGCCTCCAAGGTCGCGATACCACTGCTGATTGTTGAAGTGAAGAAGC
* * * *
6065786 CAGGACTACTGCTGAGGATATCGCAACACCAACCAGTTAGTGTTGCAACATTGAGAACCCCTAAA
66 CAGGACTACTGTTGAGAATGTCGCAACACCAACCAGTTAGTGTTGCAACATTGAGAACCCCCAAA
6065851 GCTAAGAA
131 GCTAAGAA
* * * *
6065859 TGTTTTGTCACAACACCAAGCCTCCAAGGTCGCGATACCATTGCTGACTGTTGAAGTGAGGAAGC
1 TGTTTTGTCACGACACCAAGCCTCCAAGGTCGCGATACCACTGCTGATTGTTGAAGTGAAGAAGC
* * *
6065924 CAGGAGTACTGTTGAGAATGTCGCAACACCAATCAGTTGGTGTTGCAACATTGAGAACCCCCAAA
66 CAGGACTACTGTTGAGAATGTCGCAACACCAACCAGTTAGTGTTGCAACATTGAGAACCCCCAAA
* *
6065989 GCTAATAG
131 GCTAAGAA
*
6065997 TGTTTTGTCACGACACCAAGCCTCCAAGGTCGCGGTACCACTGCTGATTGTTGAAGTGAAGAAGC
1 TGTTTTGTCACGACACCAAGCCTCCAAGGTCGCGATACCACTGCTGATTGTTGAAGTGAAGAAGC
* ** *
6066062 CAGGACTACTGTTGA-AGATGTCGGAACACCAACCAGTTAAAGTTGCAACATTGAGAACCTCCAA
66 CAGGACTACTGTTGAGA-ATGTCGCAACACCAACCAGTTAGTGTTGCAACATTGAGAACCCCCAA
6066126 AG
130 AG
6066128 TCAAGAGTGT
Statistics
Matches: 242, Mismatches: 26, Indels: 2
0.90 0.10 0.01
Matches are distributed among these distances:
137 1 0.00
138 241 1.00
ACGTcount: A:0.30, C:0.24, G:0.24, T:0.22
Consensus pattern (138 bp):
TGTTTTGTCACGACACCAAGCCTCCAAGGTCGCGATACCACTGCTGATTGTTGAAGTGAAGAAGC
CAGGACTACTGTTGAGAATGTCGCAACACCAACCAGTTAGTGTTGCAACATTGAGAACCCCCAAA
GCTAAGAA
Found at i:6068850 original size:12 final size:12
Alignment explanation
Indices: 6068823--6068856 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
6068813 CTACATCTAC
*
6068823 GAAAATAAAAAA
1 GAAAAGAAAAAA
6068835 -AAAAGAAAAAA
1 GAAAAGAAAAAA
6068846 GAAAAGAAAAA
1 GAAAAGAAAAA
6068857 GACTTTGATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.85, C:0.00, G:0.12, T:0.03
Consensus pattern (12 bp):
GAAAAGAAAAAA
Found at i:6068850 original size:18 final size:18
Alignment explanation
Indices: 6068824--6068858 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
6068814 TACATCTACG
*
6068824 AAAATAAAAAAAAAAGAA
1 AAAAGAAAAAAAAAAGAA
*
6068842 AAAAGAAAAGAAAAAGA
1 AAAAGAAAAAAAAAAGA
6068859 CTTTGATTTC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.86, C:0.00, G:0.11, T:0.03
Consensus pattern (18 bp):
AAAAGAAAAAAAAAAGAA
Found at i:6069728 original size:14 final size:14
Alignment explanation
Indices: 6069692--6069729 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
6069682 TATGATTCCC
6069692 TTTTTA-TATTTTA
1 TTTTTATTATTTTA
6069705 TTTATT-TTATTTTA
1 TTT-TTATTATTTTA
6069719 TTTTTATTATT
1 TTTTTATTATT
6069730 CATATTAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
13 5 0.23
14 17 0.77
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (14 bp):
TTTTTATTATTTTA
Found at i:6073315 original size:2 final size:2
Alignment explanation
Indices: 6073308--6073390 Score: 157
Period size: 2 Copynumber: 41.5 Consensus size: 2
6073298 TCTTTCCATT
*
6073308 TC TC TC TC TT TC TC 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 TC TC TC TC TC TC TC
6073350 TC TC TC TC TC TC TC TC 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 TC TC TC TC TC TC TC TC T
6073391 TATTATCAAT
Statistics
Matches: 79, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
2 79 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:6074903 original size:2 final size:2
Alignment explanation
Indices: 6074896--6074933 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
6074886 TTTCTTAGTT
*
6074896 TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6074934 CATTTACATT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:6074941 original size:18 final size:18
Alignment explanation
Indices: 6074899--6074961 Score: 74
Period size: 18 Copynumber: 3.5 Consensus size: 18
6074889 CTTAGTTTAT
* *
6074899 ATATATATATATATATAT
1 ATATACATATATATATAC
6074917 ATATACATATATATATAC
1 ATATACATATATATATAC
* *
6074935 ATTTACAT-TTTATAATAC
1 ATATACATATATAT-ATAC
6074953 ATATACATA
1 ATATACATA
6074962 CTTTTATATT
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
17 4 0.11
18 34 0.89
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (18 bp):
ATATACATATATATATAC
Found at i:6079030 original size:19 final size:19
Alignment explanation
Indices: 6079006--6079078 Score: 62
Period size: 19 Copynumber: 3.9 Consensus size: 19
6078996 GATTCAATGC
6079006 AAAAAAAAACACAAAAACA
1 AAAAAAAAACACAAAAACA
** *
6079025 AAAAAAAAATGCAAAAAGA
1 AAAAAAAAACACAAAAACA
* *
6079044 AGAACAAAAA-ATAAAAAC-
1 A-AAAAAAAACACAAAAACA
*
6079062 AAAAAGAAACA-AAAAAC
1 AAAAAAAAACACAAAAAC
6079079 CTCCACCGGG
Statistics
Matches: 43, Mismatches: 9, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
17 12 0.28
18 2 0.05
19 22 0.51
20 7 0.16
ACGTcount: A:0.81, C:0.11, G:0.05, T:0.03
Consensus pattern (19 bp):
AAAAAAAAACACAAAAACA
Found at i:6079039 original size:31 final size:31
Alignment explanation
Indices: 6079001--6079078 Score: 90
Period size: 31 Copynumber: 2.5 Consensus size: 31
6078991 GTGCAGATTC
6079001 AATGCAAAAAAAAACACAAAAACAAAAA-AAA
1 AATGCAAAAAAAAACA-AAAAACAAAAACAAA
*
6079032 AATGCAAAAAGAAGAACAAAAAATAAAAACAAA
1 AATGCAAAAA-AA-AACAAAAAACAAAAACAAA
6079065 AA-G-AAACAAAAAAC
1 AATGCAAA-AAAAAAC
6079079 CTCCACCGGG
Statistics
Matches: 42, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
30 3 0.07
31 15 0.36
32 15 0.36
33 9 0.21
ACGTcount: A:0.78, C:0.12, G:0.06, T:0.04
Consensus pattern (31 bp):
AATGCAAAAAAAAACAAAAAACAAAAACAAA
Found at i:6079051 original size:25 final size:23
Alignment explanation
Indices: 6079020--6079077 Score: 73
Period size: 25 Copynumber: 2.4 Consensus size: 23
6079010 AAAAACACAA
*
6079020 AAACAAAAAA-AAAATGCAAAAAG
1 AAACAAAAAATAAAA-ACAAAAAG
6079043 AAGAACAAAAAATAAAAACAAAAAG
1 -A-AACAAAAAATAAAAACAAAAAG
6079068 AAACAAAAAA
1 AAACAAAAAA
6079078 CCTCCACCGG
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
23 9 0.29
24 2 0.06
25 16 0.52
26 4 0.13
ACGTcount: A:0.81, C:0.09, G:0.07, T:0.03
Consensus pattern (23 bp):
AAACAAAAAATAAAAACAAAAAG
Found at i:6079066 original size:13 final size:12
Alignment explanation
Indices: 6079018--6079066 Score: 53
Period size: 13 Copynumber: 3.9 Consensus size: 12
6079008 AAAAAAACAC
6079018 AAAAACAAAAAA
1 AAAAACAAAAAA
* *
6079030 AAAATGCAAAAAG
1 AAAA-ACAAAAAA
*
6079043 AAGAACAAAAAA
1 AAAAACAAAAAA
6079055 TAAAAACAAAAA
1 -AAAAACAAAAA
6079067 GAAACAAAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
12 10 0.34
13 19 0.66
ACGTcount: A:0.82, C:0.08, G:0.06, T:0.04
Consensus pattern (12 bp):
AAAAACAAAAAA
Found at i:6079623 original size:15 final size:14
Alignment explanation
Indices: 6079591--6079628 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
6079581 AAAAAGATGT
*
6079591 GAAAAAT-GAAAAT
1 GAAAAATGGAAAAA
6079604 GAAAAATGGAAAAA
1 GAAAAATGGAAAAA
6079618 GTAAAAATGGA
1 G-AAAAATGGA
6079629 GAGGCTAAGG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 7 0.32
14 6 0.27
15 9 0.41
ACGTcount: A:0.66, C:0.00, G:0.21, T:0.13
Consensus pattern (14 bp):
GAAAAATGGAAAAA
Found at i:6079624 original size:22 final size:23
Alignment explanation
Indices: 6079582--6079626 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
6079572 AAGAGAGGGA
*
6079582 AAAAGATGTGAAAAATGAAAATG
1 AAAAGATGTGAAAAATAAAAATG
6079605 AAAA-ATG-GAAAAAGTAAAAATG
1 AAAAGATGTGAAAAA-TAAAAATG
6079627 GAGAGGCTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 6 0.30
22 10 0.50
23 4 0.20
ACGTcount: A:0.64, C:0.00, G:0.20, T:0.16
Consensus pattern (23 bp):
AAAAGATGTGAAAAATAAAAATG
Found at i:6080966 original size:45 final size:45
Alignment explanation
Indices: 6080915--6081054 Score: 122
Period size: 45 Copynumber: 3.2 Consensus size: 45
6080905 GGAGCGGGTT
*
6080915 GAAGATAGCAGATCTTGTCTTCCTGTATTGACAGAGAAGCAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTACTGACAGAGAAGCAGATC
* * * * ** * * * * * *
6080960 GAAGATACCAG-CCTTTTCTCCCTGGGCAG-TAGTGGAGCAGGTT
1 GAAGATAGCAGATCTTGTCTTCCTGTACTGACAGAGAAGCAGATC
* * *
6081003 GAAAATAGCAAATCTTGCCTTCCTGTACTGACAGAGAAGCAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTACTGACAGAGAAGCAGATC
6081048 GAAGATA
1 GAAGATA
6081055 CCTGCCTTAT
Statistics
Matches: 64, Mismatches: 29, Indels: 4
0.66 0.30 0.04
Matches are distributed among these distances:
43 17 0.27
44 22 0.34
45 25 0.39
ACGTcount: A:0.31, C:0.20, G:0.25, T:0.24
Consensus pattern (45 bp):
GAAGATAGCAGATCTTGTCTTCCTGTACTGACAGAGAAGCAGATC
Found at i:6081093 original size:88 final size:88
Alignment explanation
Indices: 6080883--6081086 Score: 336
Period size: 88 Copynumber: 2.3 Consensus size: 88
6080873 GAAACTTTAA
* * * * * *
6080883 CCTTGTCTCCCTGGGCAGTAGTGGAGCGGGTTGAAGATAGCAGATCTTGTCTTCCTGTATTGACA
1 CCTTATCTCCCTGGGCAGTAGTGGAGCAGGTTGAAAATAGCAAATCTTGCCTTCCTGTACTGACA
6080948 GAGAAGCAGATCGAAGATACCAG
66 GAGAAGCAGATCGAAGATACCAG
*
6080971 CCTTTTCTCCCTGGGCAGTAGTGGAGCAGGTTGAAAATAGCAAATCTTGCCTTCCTGTACTGACA
1 CCTTATCTCCCTGGGCAGTAGTGGAGCAGGTTGAAAATAGCAAATCTTGCCTTCCTGTACTGACA
*
6081036 GAGAAGCAGATCGAAGATACCTG
66 GAGAAGCAGATCGAAGATACCAG
6081059 CCTTATCTCCCTGGGCAGTAGTGGAGCA
1 CCTTATCTCCCTGGGCAGTAGTGGAGCA
6081087 AATTGAAGTC
Statistics
Matches: 108, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
88 108 1.00
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (88 bp):
CCTTATCTCCCTGGGCAGTAGTGGAGCAGGTTGAAAATAGCAAATCTTGCCTTCCTGTACTGACA
GAGAAGCAGATCGAAGATACCAG
Found at i:6081214 original size:100 final size:100
Alignment explanation
Indices: 6081078--6081794 Score: 1096
Period size: 100 Copynumber: 7.2 Consensus size: 100
6081068 CCTGGGCAGT
* * *
6081078 AGTGGAGCAAATTGAAGTCACAACGGTAGATCTGGTTTTCCCGACAGCGCAATTAAAAAGATTGA
1 AGTGGAGCAGATTGAAGTCACAACGGCAGATCTGGTTTCCCCGACAGCGCAATTAAAAAGATTGA
*
6081143 AGCCACGACGGCAGATCTTACTTCCCTGGCGGTGC
66 AGCCACAACGGCAGATCTTACTTCCCTGGCGGTGC
* * * *
6081178 AGTAGAGCAGATTGAAGCCACAACGGCAGATCTGGTTTCCCCGATAGCGCAATTAAAAATATTGA
1 AGTGGAGCAGATTGAAGTCACAACGGCAGATCTGGTTTCCCCGACAGCGCAATTAAAAAGATTGA
* *
6081243 AGCCACAACGGCAGATCTTACTTCTCTGGCGGTGT
66 AGCCACAACGGCAGATCTTACTTCCCTGGCGGTGC
* *
6081278 AGTGGAGCAGATTGAAGTCACAACGGCAGATCTGGTTTCCCCGATAGCTCAATTAAAAAGATTGA
1 AGTGGAGCAGATTGAAGTCACAACGGCAGATCTGGTTTCCCCGACAGCGCAATTAAAAAGATTGA
** * *
6081343 AGCCACAACGAAAGATCTTACTTCTCTGGCAGTGC
66 AGCCACAACGGCAGATCTTACTTCCCTGGCGGTGC
* * *
6081378 AGTGGAGCAGATTGAAGTCACAACGGCAGGTCTGGTATCCCCGACAGCGCATTTAAAAAGATTGA
1 AGTGGAGCAGATTGAAGTCACAACGGCAGATCTGGTTTCCCCGACAGCGCAATTAAAAAGATTGA
6081443 AGCCACAACGGCAGATCTTACTTCCCTGGCGGTGC
66 AGCCACAACGGCAGATCTTACTTCCCTGGCGGTGC
6081478 AGTGGAGCAGATTGAAGTCACAACGGCAGATCTGGTTTCCCCGACAGCGCAATTAAAAAGATTGA
1 AGTGGAGCAGATTGAAGTCACAACGGCAGATCTGGTTTCCCCGACAGCGCAATTAAAAAGATTGA
* * *
6081543 AGCCACAACGACA-AACATTACTTCCTTGGCGGTGC
66 AGCCACAACGGCAGATC-TTACTTCCCTGGCGGTGC
* *
6081578 AGTGGAGCAAATTGAAGTCACAACTGCAGATCTGGTTTCCCCGACAGCGCAATTAAAAAGATTGA
1 AGTGGAGCAGATTGAAGTCACAACGGCAGATCTGGTTTCCCCGACAGCGCAATTAAAAAGATTGA
* * * *
6081643 AGCTATAACGGCAGATCTTACTTCTCTGGCGGTGT
66 AGCCACAACGGCAGATCTTACTTCCCTGGCGGTGC
* *
6081678 AGTGGAGCAGATTGAAGTCACAACGGCAGGTCTGGTTTCCCCGACAGTGCAATTAAAAAGATTGA
1 AGTGGAGCAGATTGAAGTCACAACGGCAGATCTGGTTTCCCCGACAGCGCAATTAAAAAGATTGA
* * *
6081743 AGCCACAACGGCAAATCTTACTTCCCTAGTGGTGC
66 AGCCACAACGGCAGATCTTACTTCCCTGGCGGTGC
*
6081778 AGCT-GAACAGATTGAAG
1 AG-TGGAGCAGATTGAAG
6081795 CTACGACAGC
Statistics
Matches: 560, Mismatches: 54, Indels: 6
0.90 0.09 0.01
Matches are distributed among these distances:
99 2 0.00
100 555 0.99
101 3 0.01
ACGTcount: A:0.30, C:0.23, G:0.25, T:0.22
Consensus pattern (100 bp):
AGTGGAGCAGATTGAAGTCACAACGGCAGATCTGGTTTCCCCGACAGCGCAATTAAAAAGATTGA
AGCCACAACGGCAGATCTTACTTCCCTGGCGGTGC
Found at i:6083620 original size:2 final size:2
Alignment explanation
Indices: 6083613--6083646 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
6083603 TTTCTTAGTT
6083613 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6083647 CATTTACATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6083669 original size:28 final size:29
Alignment explanation
Indices: 6083629--6083686 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 29
6083619 TATATATATA
* *
6083629 TATATATATATATATATACATTTACATTT
1 TATATATACATATACATACATTTACATTT
* *
6083658 TATA-ATACATATACATACTTTTATATTT
1 TATATATACATATACATACATTTACATTT
6083686 T
1 T
6083687 TATCTTATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
28 21 0.84
29 4 0.16
ACGTcount: A:0.40, C:0.09, G:0.00, T:0.52
Consensus pattern (29 bp):
TATATATACATATACATACATTTACATTT
Found at i:6086743 original size:20 final size:20
Alignment explanation
Indices: 6086702--6086755 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
6086692 AATTAGATTT
* **
6086702 ATTTAAAATAAAAATATTAA
1 ATTTAAATTAAAAATAGAAA
6086722 ATTTAAATTAAAAATAGAAA
1 ATTTAAATTAAAAATAGAAA
6086742 ATTATAATATTAAA
1 ATT-TAA-ATTAAA
6086756 TATTTAAATC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 20 0.69
21 3 0.10
22 6 0.21
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (20 bp):
ATTTAAATTAAAAATAGAAA
Found at i:6086827 original size:20 final size:20
Alignment explanation
Indices: 6086804--6086842 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
6086794 CATTGATCGG
* *
6086804 TGTTTATCAGCGTTGACCAA
1 TGTTTATAAGCATTGACCAA
6086824 TGTTTATAAGCATTGACCA
1 TGTTTATAAGCATTGACCA
6086843 GACGTTGACC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (20 bp):
TGTTTATAAGCATTGACCAA
Found at i:6087070 original size:28 final size:27
Alignment explanation
Indices: 6086993--6087076 Score: 78
Period size: 28 Copynumber: 2.9 Consensus size: 27
6086983 TTAAATTTTT
* *
6086993 TATAAAATTATAAAAAATATAATCATAAAT
1 TATAAAATTTTAAAAAATAT-AT-A-AAAA
* *
6087023 TTTAAAATTTCAAAATAATATATAAAAA
1 TATAAAATTTTAAAA-AATATATAAAAA
*
6087051 TATAAAATTTTTAAAAAATATTTAAA
1 TATAAAA-TTTTAAAAAATATATAAA
6087077 TTTCAAGTAA
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
28 18 0.40
29 8 0.18
30 14 0.31
31 5 0.11
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (27 bp):
TATAAAATTTTAAAAAATATATAAAAA
Found at i:6087239 original size:26 final size:26
Alignment explanation
Indices: 6087208--6087272 Score: 96
Period size: 26 Copynumber: 2.5 Consensus size: 26
6087198 ACAATTATTG
6087208 TATTTTTTGTAAATTTTATTTTAATA
1 TATTTTTTGTAAATTTTATTTTAATA
* *
6087234 TGTTTTTT-TATAATTTTATTTTAATT
1 TATTTTTTGTA-AATTTTATTTTAATA
6087260 TATTTTTTGTAAA
1 TATTTTTTGTAAA
6087273 AAAAAATCAG
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
25 2 0.06
26 30 0.88
27 2 0.06
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.68
Consensus pattern (26 bp):
TATTTTTTGTAAATTTTATTTTAATA
Found at i:6087255 original size:13 final size:12
Alignment explanation
Indices: 6087217--6087265 Score: 50
Period size: 13 Copynumber: 4.1 Consensus size: 12
6087207 GTATTTTTTG
6087217 TAAATTTTATTT
1 TAAATTTTATTT
6087229 TAATATGTTT-TTT
1 TAA-AT-TTTATTT
6087242 TATAATTTTATTT
1 TA-AATTTTATTT
6087255 T-AA-TTTATTT
1 TAAATTTTATTT
6087265 T
1 T
6087266 TTGTAAAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
10 8 0.24
11 2 0.06
12 6 0.18
13 13 0.39
14 4 0.12
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (12 bp):
TAAATTTTATTT
Found at i:6089071 original size:18 final size:18
Alignment explanation
Indices: 6088994--6089071 Score: 52
Period size: 18 Copynumber: 4.2 Consensus size: 18
6088984 GCAACTAGTT
*
6088994 AATTTTTTAAA-ATTAAA
1 AATTTTTTAAATTTTAAA
6089011 AATATTTTTAAATTTTTAAA
1 AAT-TTTTTAAA-TTTTAAA
* * ***
6089031 TAA-TTTATATATTTGTTTG
1 -AATTTTTTAAATTT-TAAA
6089050 AATTTTTTAAATTTTAAA
1 AATTTTTTAAATTTTAAA
6089068 AATT
1 AATT
6089072 AATTAATTAT
Statistics
Matches: 44, Mismatches: 11, Indels: 11
0.67 0.17 0.17
Matches are distributed among these distances:
17 3 0.07
18 18 0.41
19 16 0.36
20 5 0.11
21 2 0.05
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (18 bp):
AATTTTTTAAATTTTAAA
Found at i:6093896 original size:17 final size:18
Alignment explanation
Indices: 6093864--6093898 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
6093854 GATTTTAAAT
*
6093864 TAATTTTTATTATTAATA
1 TAATTTCTATTATTAATA
6093882 TAATTTCTA-TATTAATA
1 TAATTTCTATTATTAATA
6093899 GAAAGAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (18 bp):
TAATTTCTATTATTAATA
Found at i:6095433 original size:28 final size:29
Alignment explanation
Indices: 6095377--6095435 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
6095367 TTTCTTGTTA
*
6095377 ATTTTGGATTTATTAAATGGTGTACTTTT
1 ATTTTGGATTTATTAAATGGAGTACTTTT
6095406 ATTTGTGGACTTTATT-AAT-GAGTA-TTTT
1 ATTT-TGGA-TTTATTAAATGGAGTACTTTT
6095434 AT
1 AT
6095436 ATAATTATGA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
28 6 0.22
29 8 0.30
30 7 0.26
31 6 0.22
ACGTcount: A:0.25, C:0.03, G:0.17, T:0.54
Consensus pattern (29 bp):
ATTTTGGATTTATTAAATGGAGTACTTTT
Found at i:6097508 original size:2 final size:2
Alignment explanation
Indices: 6097503--6097527 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
6097493 ATAATAGTTG
6097503 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
6097528 AAATGCATCT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6099472 original size:126 final size:125
Alignment explanation
Indices: 6099248--6099626 Score: 564
Period size: 125 Copynumber: 3.0 Consensus size: 125
6099238 TAAGGGTTTT
*** * **
6099248 TAGGTC-CTGGAAGAAATAATTTTGAGTTGACGATTCTGATAAAATAGTATAAAATCGCTTCTAG
1 TAGGTCAC-GGAAGAAATAATTTTTTTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAG
*
6099312 CAGGATGCTATTTGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTTCTACAG
65 CAGGATGCTATTTGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAG
6099373 TAGGTCACGGAAGAAATAATTATTTTTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAG
1 TAGGTCACGGAAGAAATAATT-TTTTTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAG
* * *
6099438 CAGGATGCTATTTGAGAAGAATTTATGAAATCGCGGCCTCGT-TAGCGCGCTTTTGCTACAG
65 CAGGATGCTATTTGAGAAGAATTTGTGAAATCGCGCCCTCGTGGA-CGCGCTTTTGCTACAG
* * * * *
6099499 TAGGTCATGTAAGAAATAAATTTTTTTTGACGTTTCTAAGCAAATAATATAAAATCGCTTCTAGC
1 TAGGTCACGGAAGAAATAATTTTTTTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGC
* *
6099564 AAGATGCTATTTCAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAG
66 AGGATGCTATTTGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAG
6099624 TAG
1 TAG
6099627 CATGTTTGGG
Statistics
Matches: 230, Mismatches: 20, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
125 118 0.51
126 112 0.49
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.32
Consensus pattern (125 bp):
TAGGTCACGGAAGAAATAATTTTTTTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGC
AGGATGCTATTTGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAG
Found at i:6102994 original size:116 final size:116
Alignment explanation
Indices: 6102790--6103007 Score: 400
Period size: 116 Copynumber: 1.9 Consensus size: 116
6102780 TGATAAATTG
*
6102790 TATTAAGTCAAAAAATTGTTTTAATGGTTAGTAAAATTATCAAATTATATAAAATTATTAATTGT
1 TATTAAGTCAAAAAATTGTATTAATGGTTAGTAAAATTATCAAATTATATAAAATTATTAATTGT
6102855 TAGTACCAGTCAAAACATTTTTCCAAATCTAACATTATGTGAACGTAAAAT
66 TAGTACCAGTCAAAACATTTTTCCAAATCTAACATTATGTGAACGTAAAAT
* * *
6102906 TATTAAGTCAAAAAATTGTATTAATGGTTAGTAAAATTTTCAAATTATGTAAAATTATTATTTGT
1 TATTAAGTCAAAAAATTGTATTAATGGTTAGTAAAATTATCAAATTATATAAAATTATTAATTGT
6102971 TAGTACCAGTCAAAACATTTTTCCAAATCTAACATTA
66 TAGTACCAGTCAAAACATTTTTCCAAATCTAACATTA
6103008 CGTTAAGGTT
Statistics
Matches: 98, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
116 98 1.00
ACGTcount: A:0.42, C:0.10, G:0.09, T:0.39
Consensus pattern (116 bp):
TATTAAGTCAAAAAATTGTATTAATGGTTAGTAAAATTATCAAATTATATAAAATTATTAATTGT
TAGTACCAGTCAAAACATTTTTCCAAATCTAACATTATGTGAACGTAAAAT
Found at i:6103037 original size:21 final size:21
Alignment explanation
Indices: 6103012--6103055 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
6103002 ACATTACGTT
*
6103012 AAGG-TTAGTGTTTTTAAGTTA
1 AAGGTTTAGGGTTTTTAA-TTA
6103033 AAGGTTTAGGGTTTTTAATTA
1 AAGGTTTAGGGTTTTTAATTA
6103054 AA
1 AA
6103056 TTAGATTAGG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.32, C:0.00, G:0.23, T:0.45
Consensus pattern (21 bp):
AAGGTTTAGGGTTTTTAATTA
Found at i:6103070 original size:29 final size:29
Alignment explanation
Indices: 6103038--6103390 Score: 556
Period size: 29 Copynumber: 12.3 Consensus size: 29
6103028 AGTTAAAGGT
*
6103038 TTAGGGTTTTTAATTAAATTAGATTAGGG
1 TTAGGGTTTTTAATTAAATTAGGTTAGGG
6103067 TTAGGGTTTTTAATT-AA--A--TTA-GG
1 TTAGGGTTTTTAATTAAATTAGGTTAGGG
6103090 TTAGGGTTTTTAATTAAATTAGGTTAGGG
1 TTAGGGTTTTTAATTAAATTAGGTTAGGG
6103119 TTAGGGTTTTTAATTAAATTAGGTTAGGG
1 TTAGGGTTTTTAATTAAATTAGGTTAGGG
*
6103148 TTAGGGTTTGTAATTAAATTAGGTTAGGGG
1 TTAGGGTTTTTAATTAAATTAGGTTA-GGG
*
6103178 TTAGGGTTTTTAATTAAATTAGGTTAGTG
1 TTAGGGTTTTTAATTAAATTAGGTTAGGG
6103207 TTAGGGTTTTTAATTAAATTAGGTTAGGG
1 TTAGGGTTTTTAATTAAATTAGGTTAGGG
* *
6103236 TTAGGGTTTGTAATTAATTTAGGTTAGGGG
1 TTAGGGTTTTTAATTAAATTAGGTTA-GGG
*
6103266 TTAGGGTTTTTAATTAAATCAGGTTAGGG
1 TTAGGGTTTTTAATTAAATTAGGTTAGGG
6103295 TTAGGGTTTTTAATTAAATTAGGTTAGGG
1 TTAGGGTTTTTAATTAAATTAGGTTAGGG
6103324 TTAGGGTTTTTAATTAAATTAGGTTAGGG
1 TTAGGGTTTTTAATTAAATTAGGTTAGGG
* * *
6103353 TTAGGATTTTTAATTCATTTAGGTTAGGG
1 TTAGGGTTTTTAATTAAATTAGGTTAGGG
6103382 TTTAGGGTT
1 -TTAGGGTT
6103391 AAATTAGGTT
Statistics
Matches: 301, Mismatches: 14, Indels: 17
0.91 0.04 0.05
Matches are distributed among these distances:
23 17 0.06
24 5 0.02
26 2 0.01
28 5 0.02
29 211 0.70
30 61 0.20
ACGTcount: A:0.27, C:0.01, G:0.27, T:0.45
Consensus pattern (29 bp):
TTAGGGTTTTTAATTAAATTAGGTTAGGG
Found at i:6103111 original size:18 final size:21
Alignment explanation
Indices: 6103066--6103120 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 21
6103056 TTAGATTAGG
6103066 GTTAGGGTTTTTAATTAAATTA
1 GTTAGGGTTTTTAATTAAA-TA
6103088 GGTTAGGGTTTTTAATTAAATTA
1 -GTTAGGGTTTTTAATTAAA-TA
6103111 GGTTAGGGTT
1 -GTTAGGGTT
6103121 AGGGTTTTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.27, C:0.00, G:0.25, T:0.47
Consensus pattern (21 bp):
GTTAGGGTTTTTAATTAAATA
Found at i:6103185 original size:88 final size:87
Alignment explanation
Indices: 6103038--6103390 Score: 556
Period size: 88 Copynumber: 4.1 Consensus size: 87
6103028 AGTTAAAGGT
* *
6103038 TTAGGGTTTTTAATTAAATTAGATTAGGGTTAGGGTTTTTAATT-AA--A--TTA-GGTTAGGGT
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTGTAATTAAATTAGGTTAGGGTTAGGGT
6103097 TTTTAATTAAATTAGGTTAGGG
66 TTTTAATTAAATTAGGTTAGGG
6103119 TTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTGTAATTAAATTAGGTTAGGGGTTAGGG
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTGTAATTAAATTAGGTTA-GGGTTAGGG
*
6103184 TTTTTAATTAAATTAGGTTAGTG
65 TTTTTAATTAAATTAGGTTAGGG
*
6103207 TTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTGTAATTAATTTAGGTTAGGGGTTAGGG
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTGTAATTAAATTAGGTTA-GGGTTAGGG
*
6103272 TTTTTAATTAAATCAGGTTAGGG
65 TTTTTAATTAAATTAGGTTAGGG
* *
6103295 TTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGAT
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTGTAATTAAATTAGGTTAGGGTTAGGGT
* *
6103360 TTTTAATTCATTTAGGTTAGGG
66 TTTTAATTAAATTAGGTTAGGG
6103382 TTTAGGGTT
1 -TTAGGGTT
6103391 AAATTAGGTT
Statistics
Matches: 252, Mismatches: 12, Indels: 9
0.92 0.04 0.03
Matches are distributed among these distances:
81 42 0.17
82 2 0.01
84 1 0.00
86 3 0.01
87 28 0.11
88 176 0.70
ACGTcount: A:0.27, C:0.01, G:0.27, T:0.45
Consensus pattern (87 bp):
TTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTGTAATTAAATTAGGTTAGGGTTAGGGT
TTTTAATTAAATTAGGTTAGGG
Found at i:6103237 original size:117 final size:115
Alignment explanation
Indices: 6103038--6103390 Score: 563
Period size: 117 Copynumber: 3.1 Consensus size: 115
6103028 AGTTAAAGGT
*
6103038 TTAGGGTTTTTAATTAAATTAGATTAGGGTTAGGGTTTTTAATT-AA--A--TTAGGTTAGGGTT
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGTTAGGGTT
*
6103098 TTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGG
66 TTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAATTTAGGTTAGGG
*
6103148 TTAGGGTTTGTAATTAAATTAGGTTAGGGGTTAGGGTTTTTAATTAAATTAGGTTAGTGTTAGGG
1 TTAGGGTTTTTAATTAAATTAGGTTA-GGGTTAGGGTTTTTAATTAAATTAGGTTAG-GTTAGGG
*
6103213 TTTTTAATTAAATTAGGTTAGGGTTAGGGTTTGTAATTAATTTAGGTTAGGGG
64 TTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAATTTAGGTTA-GGG
*
6103266 TTAGGGTTTTTAATTAAATCAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGT
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTA-GGTTAGGGT
* *
6103331 TTTTAATTAAATTAGGTTAGGGTTAGGATTTTTAATTCATTTAGGTTAGGG
65 TTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAATTTAGGTTAGGG
6103382 TTTAGGGTT
1 -TTAGGGTT
6103391 AAATTAGGTT
Statistics
Matches: 224, Mismatches: 9, Indels: 13
0.91 0.04 0.05
Matches are distributed among these distances:
110 24 0.11
111 18 0.08
112 2 0.01
114 1 0.00
116 7 0.03
117 144 0.64
118 28 0.12
ACGTcount: A:0.27, C:0.01, G:0.27, T:0.45
Consensus pattern (115 bp):
TTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGTTAGGGTT
TTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAATTTAGGTTAGGG
Found at i:6103494 original size:43 final size:45
Alignment explanation
Indices: 6103416--6103501 Score: 131
Period size: 43 Copynumber: 2.0 Consensus size: 45
6103406 TTTTATTACA
*
6103416 TCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAAC
1 TCAAATAAACTTCTATTTTATTACATAAAATAATATCAAAATAAC
* *
6103461 TCAAA-AAATTTCTATTTT-TTATATAAAATAATATCAAAATA
1 TCAAATAAACTTCTATTTTATTACATAAAATAATATCAAAATA
6103502 TTAAAAATAT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
43 21 0.55
44 12 0.32
45 5 0.13
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (45 bp):
TCAAATAAACTTCTATTTTATTACATAAAATAATATCAAAATAAC
Found at i:6105675 original size:94 final size:94
Alignment explanation
Indices: 6105514--6105700 Score: 329
Period size: 94 Copynumber: 2.0 Consensus size: 94
6105504 AGGAGCATGC
* *
6105514 ATATTCCGGATATTGCATTCCAATACCCGATCTTCTGACTTTTATAACAAATAATAAATTAATAA
1 ATATTCCAGATATTGCATTCCAATACCCGATCTTCAGACTTTTATAACAAATAATAAATTAATAA
* *
6105579 TTATCTAAAAATGCATAACTAATAAATTA
66 TTATCTAAAAATGCATAAATAAAAAATTA
*
6105608 ATATTCCAGATATTGCATTCCAATCCCCGATCTTCAGACTTTTATAACAAATAATAAATTAATAA
1 ATATTCCAGATATTGCATTCCAATACCCGATCTTCAGACTTTTATAACAAATAATAAATTAATAA
6105673 TTATCTAAAAATGCATAAATAAAAAATT
66 TTATCTAAAAATGCATAAATAAAAAATT
6105701 CTTAAATAAT
Statistics
Matches: 88, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
94 88 1.00
ACGTcount: A:0.44, C:0.16, G:0.06, T:0.34
Consensus pattern (94 bp):
ATATTCCAGATATTGCATTCCAATACCCGATCTTCAGACTTTTATAACAAATAATAAATTAATAA
TTATCTAAAAATGCATAAATAAAAAATTA
Found at i:6105928 original size:11 final size:11
Alignment explanation
Indices: 6105914--6105946 Score: 50
Period size: 10 Copynumber: 3.0 Consensus size: 11
6105904 GAATTTTGGA
6105914 AGGAAATTGAG
1 AGGAAATTGAG
6105925 AGG-AATTGAG
1 AGGAAATTGAG
6105935 AGGAAATATGAG
1 AGGAAAT-TGAG
6105947 TGAGGATTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 10 0.50
11 6 0.30
12 4 0.20
ACGTcount: A:0.45, C:0.00, G:0.36, T:0.18
Consensus pattern (11 bp):
AGGAAATTGAG
Found at i:6109767 original size:13 final size:14
Alignment explanation
Indices: 6109726--6109791 Score: 64
Period size: 13 Copynumber: 4.6 Consensus size: 14
6109716 ATATATAATC
6109726 AAATAATAAATTATT
1 AAATAATAAATT-TT
**
6109741 AACATAATTTATTTT
1 AA-ATAATAAATTTT
6109756 -AATAATAAATTTT
1 AAATAATAAATTTT
6109769 AAAAATAATAAA-TTT
1 --AAATAATAAATTTT
6109784 AAATAATA
1 AAATAATA
6109792 TTCTTCATAT
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
13 18 0.42
14 1 0.02
15 7 0.16
16 17 0.40
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.41
Consensus pattern (14 bp):
AAATAATAAATTTT
Found at i:6109776 original size:29 final size:29
Alignment explanation
Indices: 6109726--6109791 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 29
6109716 ATATATAATC
* **
6109726 AAATAATAAATTATTAACATAATTTATTT
1 AAATAATAAATTATTAAAATAATAAATTT
*
6109755 TAATAATAAATT-TTAAAAATAATAAATTT
1 AAATAATAAATTATT-AAAATAATAAATTT
6109784 AAATAATA
1 AAATAATA
6109792 TTCTTCATAT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
28 2 0.06
29 29 0.94
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.41
Consensus pattern (29 bp):
AAATAATAAATTATTAAAATAATAAATTT
Found at i:6109791 original size:16 final size:17
Alignment explanation
Indices: 6109755--6109791 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
6109745 TAATTTATTT
6109755 TAATAATAAATTTTAAA
1 TAATAATAAATTTTAAA
6109772 -AATAATAAA-TTTAAA
1 TAATAATAAATTTTAAA
6109787 TAATA
1 TAATA
6109792 TTCTTCATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 6 0.32
16 13 0.68
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TAATAATAAATTTTAAA
Found at i:6110905 original size:107 final size:107
Alignment explanation
Indices: 6110719--6111020 Score: 550
Period size: 107 Copynumber: 2.8 Consensus size: 107
6110709 AAGCTAAGAA
*
6110719 GATATTTAGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTCTCTCGAAT
1 GATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTCTCTCGAAT
6110784 TTCCAAACGCAAAACATTGCCTCGTTTTGAAAGTTTAAAAAG
66 TTCCAAACGCAAAACATTGCCTCGTTTTGAAAGTTTAAAAAG
6110826 GATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTCTCTCGAAT
1 GATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTCTCTCGAAT
6110891 TTCCAAACGCAAAACATTGCCTCGTTTTGAAAGTTTAAAAAG
66 TTCCAAACGCAAAACATTGCCTCGTTTTGAAAGTTTAAAAAG
* *
6110933 GATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGTACGTTAGGGCACGTTTTCTCGAAT
1 GATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTCTCTCGAA-
* *
6110998 TTTCCAAACGCGAAATATTGCCT
65 TTTCCAAACGCAAAACATTGCCT
6111021 TATTTAGGAA
Statistics
Matches: 189, Mismatches: 5, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
107 168 0.89
108 21 0.11
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.28
Consensus pattern (107 bp):
GATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTCTCTCGAAT
TTCCAAACGCAAAACATTGCCTCGTTTTGAAAGTTTAAAAAG
Found at i:6112010 original size:3 final size:3
Alignment explanation
Indices: 6112002--6112044 Score: 70
Period size: 3 Copynumber: 14.7 Consensus size: 3
6111992 TGTACATAGC
*
6112002 AAT AAT AAT AAT AAT AAT AAT AAT AAC AAT AAT AAT AA- AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
6112045 CGGGACTAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:6112641 original size:2 final size:2
Alignment explanation
Indices: 6112636--6112669 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
6112626 TATATATTCT
* *
6112636 TA TA TA CA TA TA TA TA TA TA TA AA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6112670 CATAATAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (2 bp):
TA
Found at i:6115930 original size:22 final size:22
Alignment explanation
Indices: 6115905--6115947 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
6115895 TACTCAAACA
6115905 ATAACAACAAAAT-AGTAGCAAT
1 ATAACAACAAAATGA-TAGCAAT
*
6115927 ATAATAACAAAATGATAGCAA
1 ATAACAACAAAATGATAGCAA
6115948 AACAATGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 18 0.95
23 1 0.05
ACGTcount: A:0.60, C:0.12, G:0.09, T:0.19
Consensus pattern (22 bp):
ATAACAACAAAATGATAGCAAT
Found at i:6115960 original size:22 final size:22
Alignment explanation
Indices: 6115913--6115991 Score: 77
Period size: 22 Copynumber: 3.6 Consensus size: 22
6115903 CAATAACAAC
* * * *
6115913 AAAATAGTAGCAATATAATAAC
1 AAAATAATAGCAAAACAATAAA
* *
6115935 AAAATGATAGCAAAACAATGAA
1 AAAATAATAGCAAAACAATAAA
* *
6115957 AAAACAATGGCAAAACAATAAA
1 AAAATAATAGCAAAACAATAAA
*
6115979 AAAATAACAGCAA
1 AAAATAATAGCAA
6115992 TTTTTTTTTC
Statistics
Matches: 44, Mismatches: 13, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
22 44 1.00
ACGTcount: A:0.65, C:0.11, G:0.10, T:0.14
Consensus pattern (22 bp):
AAAATAATAGCAAAACAATAAA
Found at i:6126424 original size:35 final size:35
Alignment explanation
Indices: 6126384--6126452 Score: 129
Period size: 35 Copynumber: 2.0 Consensus size: 35
6126374 CCGTCCACTG
6126384 ATACATATTTTAGCATGGTATAATTTCTGTTTTGA
1 ATACATATTTTAGCATGGTATAATTTCTGTTTTGA
*
6126419 ATACATATTTTAGCATGGTATAATTTTTGTTTTG
1 ATACATATTTTAGCATGGTATAATTTCTGTTTTG
6126453 TATTTTTGTC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.28, C:0.07, G:0.14, T:0.51
Consensus pattern (35 bp):
ATACATATTTTAGCATGGTATAATTTCTGTTTTGA
Found at i:6128571 original size:12 final size:12
Alignment explanation
Indices: 6128554--6128586 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
6128544 AATTTTTAAA
6128554 TTTTAAAATAAT
1 TTTTAAAATAAT
*
6128566 TTTTAAAATACT
1 TTTTAAAATAAT
6128578 TTTTAAAAT
1 TTTTAAAAT
6128587 TTTATTAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (12 bp):
TTTTAAAATAAT
Found at i:6128617 original size:18 final size:19
Alignment explanation
Indices: 6128566--6128623 Score: 66
Period size: 18 Copynumber: 3.1 Consensus size: 19
6128556 TTAAAATAAT
6128566 TTTTAAAATACTTTTTAAAA
1 TTTTAAAATA-TTTTTAAAA
* *
6128586 TTTTATTAAT-TTTTT-TAA
1 TTTTA-AAATATTTTTAAAA
6128604 TTTTAAAATATTTTTAAAA
1 TTTTAAAATATTTTTAAAA
6128623 T
1 T
6128624 ACTTTTTTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
17 3 0.10
18 12 0.39
19 8 0.26
20 5 0.16
21 3 0.10
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.59
Consensus pattern (19 bp):
TTTTAAAATATTTTTAAAA
Found at i:6128651 original size:21 final size:21
Alignment explanation
Indices: 6128613--6128652 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
6128603 ATTTTAAAAT
**
6128613 ATTTTTAAAATACTTTTTTTA
1 ATTTTTAAAATAAATTTTTTA
6128634 ATTTTTAAAATAAATTTTT
1 ATTTTTAAAATAAATTTTT
6128653 GGTATTTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (21 bp):
ATTTTTAAAATAAATTTTTTA
Found at i:6128659 original size:22 final size:20
Alignment explanation
Indices: 6128612--6128659 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 20
6128602 AATTTTAAAA
* *
6128612 TATTTTTAAAATACTTTTTT
1 TATTTTTAAAATAATTTTTG
6128632 TAATTTTTAAAATAAATTTTTGG
1 T-ATTTTTAAAAT-AATTTTT-G
6128655 TATTT
1 TATTT
6128660 ATTTAAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 1 0.04
21 11 0.48
22 10 0.43
23 1 0.04
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.60
Consensus pattern (20 bp):
TATTTTTAAAATAATTTTTG
Found at i:6129529 original size:11 final size:11
Alignment explanation
Indices: 6129494--6129530 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
6129484 TGTTTATGAT
6129494 TATGATATGTA
1 TATGATATGTA
**
6129505 TAAAATATGTA
1 TATGATATGTA
6129516 TATGATATGTA
1 TATGATATGTA
6129527 TATG
1 TATG
6129531 TGTGGGGTGG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.41, C:0.00, G:0.16, T:0.43
Consensus pattern (11 bp):
TATGATATGTA
Found at i:6133541 original size:21 final size:20
Alignment explanation
Indices: 6133508--6133549 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 20
6133498 CCCGAAGAAC
*
6133508 TTTATTTAAAAATTGAATACT
1 TTTATTTAAAAA-TAAATACT
6133529 TTTATTGT-AAAATAAATACT
1 TTTATT-TAAAAATAAATACT
6133549 T
1 T
6133550 GGCTATCTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 8 0.42
21 10 0.53
22 1 0.05
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.48
Consensus pattern (20 bp):
TTTATTTAAAAATAAATACT
Found at i:6134014 original size:3 final size:3
Alignment explanation
Indices: 6134008--6134052 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
6133998 AAAAAAGCTT
6134008 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
6134053 GTATACAACT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:6134345 original size:25 final size:24
Alignment explanation
Indices: 6134305--6134351 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
6134295 ATAGAAATAT
* *
6134305 ATAAAAAGAATTTTAAATTATAAC
1 ATAAAAAAAATTTTAAAATATAAC
6134329 ATAAAATAAAATTTTAAAATATA
1 ATAAAA-AAAATTTTAAAATATA
6134352 TACAAATTAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 6 0.30
25 14 0.70
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (24 bp):
ATAAAAAAAATTTTAAAATATAAC
Found at i:6137378 original size:12 final size:12
Alignment explanation
Indices: 6137350--6137382 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
6137340 AGCTCATCAA
6137350 ATATACA-ATAG
1 ATATACATATAG
*
6137361 ATATACATATAT
1 ATATACATATAG
6137373 ATATACATAT
1 ATATACATAT
6137383 TCGAACTTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 7 0.35
12 13 0.65
ACGTcount: A:0.52, C:0.09, G:0.03, T:0.36
Consensus pattern (12 bp):
ATATACATATAG
Found at i:6137483 original size:112 final size:110
Alignment explanation
Indices: 6137287--6137488 Score: 359
Period size: 112 Copynumber: 1.8 Consensus size: 110
6137277 NTCACACATG
6137287 TGCATATATATACATTCATACTTAACTAATTCAATTCATATACTTTTAATTATAGCTCATCAAAT
1 TGCATATATATACATTCATACTTAACTAATTCAATTCATATACTTTTAATTATAGCTCATCAAAT
6137352 ATACAATAGATATACATATATATATACATATTCGAACTTCATTTA
66 ATACAATAGATATACATATATATATACATATTCGAACTTCATTTA
*
6137397 TGCATATATATATCATTCATACTTAACTAATTTCAATTCGTATACTTTTAATTATAGCTCATCAA
1 TGCATATATATA-CATTCATACTTAACTAA-TTCAATTCATATACTTTTAATTATAGCTCATCAA
* *
6137462 ATGTACAATAGTTATACATATATATAT
64 ATATACAATAGATATACATATATATAT
6137489 GCTGATTTAA
Statistics
Matches: 87, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
110 12 0.14
111 17 0.20
112 58 0.67
ACGTcount: A:0.40, C:0.15, G:0.04, T:0.41
Consensus pattern (110 bp):
TGCATATATATACATTCATACTTAACTAATTCAATTCATATACTTTTAATTATAGCTCATCAAAT
ATACAATAGATATACATATATATATACATATTCGAACTTCATTTA
Found at i:6138009 original size:13 final size:13
Alignment explanation
Indices: 6137991--6138015 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6137981 CAATCAAATG
6137991 CACACAAAATAAA
1 CACACAAAATAAA
6138004 CACACAAAATAA
1 CACACAAAATAA
6138016 TATTAAATTA
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:0.68, C:0.24, G:0.00, T:0.08
Consensus pattern (13 bp):
CACACAAAATAAA
Found at i:6143762 original size:41 final size:41
Alignment explanation
Indices: 6143707--6143856 Score: 219
Period size: 41 Copynumber: 3.7 Consensus size: 41
6143697 TTTAACATAT
* * * *
6143707 TCACCGGCATTTAGCTTGCTAAGCTTATAGCCTGATTTAGA
1 TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGA
* * *
6143748 TCACTGACACTTAGCCTGCTAGGTTTATAGCCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGA
*
6143789 TCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGA
*
6143830 TCACCGGCACTTAGCCTGCTAGACTTA
1 TCACCGGCACTTAGCCTGCTAGGCTTA
6143857 AAGTCTGAAA
Statistics
Matches: 97, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 97 1.00
ACGTcount: A:0.24, C:0.27, G:0.19, T:0.30
Consensus pattern (41 bp):
TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGA
Found at i:6144356 original size:12 final size:12
Alignment explanation
Indices: 6144328--6144360 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
6144318 AGCTCATCAA
6144328 ATATACA-ATAG
1 ATATACATATAG
*
6144339 ATATACATATAT
1 ATATACATATAG
6144351 ATATACATAT
1 ATATACATAT
6144361 TCGAACTTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 7 0.35
12 13 0.65
ACGTcount: A:0.52, C:0.09, G:0.03, T:0.36
Consensus pattern (12 bp):
ATATACATATAG
Found at i:6144577 original size:112 final size:114
Alignment explanation
Indices: 6144316--6144584 Score: 456
Period size: 110 Copynumber: 2.4 Consensus size: 114
6144306 NNNNNNNNNN
*
6144316 ATAGCTCATCAAATATACAATAGATATACATATATATATACATATTCGAACTTCATTTATGTGTA
1 ATAGCTCATCAAATATACAATAGATATACATATATATATACATATTCGAACTTCATTTATGTGCA
*
6144381 TATATATAACATTCATACTTAACTAATTTCAATTCATATACTTTTAATT
66 TATATATAACATTCATACTTAACTAATTTCAATTCATATACTTTTAAAT
6144430 ATAGCTCATCAAATATACAATAGATATAC--ATATATATACATATTCGAACTTCATTTAT-T-CA
1 ATAGCTCATCAAATATACAATAGATATACATATATATATACATATTCGAACTTCATTTATGTGCA
*
6144491 TATATATATCATTCATACTTAACTAATTTCAATTCATATACTTTTAAAT
66 TATATATAACATTCATACTTAACTAATTTCAATTCATATACTTTTAAAT
* * *
6144540 ATAGCTCATCAAATGTACAATAGTTATACATATATATATATATAT
1 ATAGCTCATCAAATATACAATAGATATACATATATATATACATAT
6144585 GCTGATTTAA
Statistics
Matches: 147, Mismatches: 6, Indels: 6
0.92 0.04 0.04
Matches are distributed among these distances:
110 75 0.51
111 1 0.01
112 42 0.29
114 29 0.20
ACGTcount: A:0.41, C:0.14, G:0.04, T:0.41
Consensus pattern (114 bp):
ATAGCTCATCAAATATACAATAGATATACATATATATATACATATTCGAACTTCATTTATGTGCA
TATATATAACATTCATACTTAACTAATTTCAATTCATATACTTTTAAAT
Found at i:6145105 original size:13 final size:13
Alignment explanation
Indices: 6145087--6145111 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6145077 CAATCAAATG
6145087 CACACAAAATAAA
1 CACACAAAATAAA
6145100 CACACAAAATAA
1 CACACAAAATAA
6145112 TATTAAATTA
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:0.68, C:0.24, G:0.00, T:0.08
Consensus pattern (13 bp):
CACACAAAATAAA
Found at i:6147833 original size:22 final size:22
Alignment explanation
Indices: 6147803--6147845 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
6147793 ACACCAAAAC
* *
6147803 AGGCTTTTAGCGGCGCTTTTTT
1 AGGCCTTTAGCGGCACTTTTTT
6147825 AGGCCTTTAGCGGCACTTTTT
1 AGGCCTTTAGCGGCACTTTTT
6147846 AGCGCCGCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.12, C:0.21, G:0.26, T:0.42
Consensus pattern (22 bp):
AGGCCTTTAGCGGCACTTTTTT
Found at i:6148051 original size:43 final size:42
Alignment explanation
Indices: 6148004--6148128 Score: 135
Period size: 43 Copynumber: 2.9 Consensus size: 42
6147994 AGACTAAGAG
* *
6148004 CTTTAGCGGCGTTTTTAATAGAACCGCCGCTATAGAT-TGGTGT
1 CTTTAGCGGCGTTTTT-ATAGAAGCGCCGCTATAGATCAGG-GT
* * *
6148047 CTTTAGCGGCATTTTTGTTGAAAGCGCCGCTATAGATCAGGGT
1 CTTTAGCGGCGTTTTTATAG-AAGCGCCGCTATAGATCAGGGT
* * *
6148090 CTGTAACGGCGTTTTTTATATAAGCGCCGCTATAGATCA
1 CTTTAGCGGCG-TTTTTATAGAAGCGCCGCTATAGATCA
6148129 TGACCTTTAA
Statistics
Matches: 68, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
42 2 0.03
43 58 0.85
44 8 0.12
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.34
Consensus pattern (42 bp):
CTTTAGCGGCGTTTTTATAGAAGCGCCGCTATAGATCAGGGT
Found at i:6148295 original size:43 final size:44
Alignment explanation
Indices: 6148139--6148294 Score: 156
Period size: 43 Copynumber: 3.6 Consensus size: 44
6148129 TGACCTTTAA
6148139 CGGCGCTTTTCCCAAAAACGCCGC-AATAGACCCTGATCTATAG
1 CGGCGCTTTTCCCAAAAACGCCGCTAATAGACCCTGATCTATAG
*** * *
6148182 CGGTATTTTTCCCACAAACGCCG-TAATAGACCCTGATCTCTAG
1 CGGCGCTTTTCCCAAAAACGCCGCTAATAGACCCTGATCTATAG
* * *** * * *
6148225 CGGCGCTTCTGCTGCAAGCGCCACTAA-AGACCCGGATCTATAG
1 CGGCGCTTTTCCCAAAAACGCCGCTAATAGACCCTGATCTATAG
* *
6148268 CGGCGCTTTTACCAAAAACACCGCTAA
1 CGGCGCTTTTCCCAAAAACGCCGCTAA
6148295 ATTTGGCAGA
Statistics
Matches: 87, Mismatches: 24, Indels: 4
0.76 0.21 0.03
Matches are distributed among these distances:
43 84 0.97
44 3 0.03
ACGTcount: A:0.27, C:0.32, G:0.19, T:0.22
Consensus pattern (44 bp):
CGGCGCTTTTCCCAAAAACGCCGCTAATAGACCCTGATCTATAG
Found at i:6148629 original size:21 final size:21
Alignment explanation
Indices: 6148600--6148711 Score: 116
Period size: 21 Copynumber: 5.3 Consensus size: 21
6148590 TTTGACGCTA
6148600 CTCTGCTTCCCTCGCTGCAGC
1 CTCTGCTTCCCTCGCTGCAGC
* **
6148621 CTCTACTTCCCTCGCTTTAGC
1 CTCTGCTTCCCTCGCTGCAGC
*
6148642 CTCTGCTTCCCTTGCTGCAGC
1 CTCTGCTTCCCTCGCTGCAGC
* * * *
6148663 CTGTTCTTCTCTCGCTGCCGC
1 CTCTGCTTCCCTCGCTGCAGC
* * *
6148684 CTCTGCTTCTCTTGCTGCCGC
1 CTCTGCTTCCCTCGCTGCAGC
*
6148705 ATCTGCT
1 CTCTGCT
6148712 CTAAGCTGCT
Statistics
Matches: 75, Mismatches: 16, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 75 1.00
ACGTcount: A:0.04, C:0.43, G:0.17, T:0.36
Consensus pattern (21 bp):
CTCTGCTTCCCTCGCTGCAGC
Found at i:6148647 original size:42 final size:42
Alignment explanation
Indices: 6148600--6148701 Score: 132
Period size: 42 Copynumber: 2.4 Consensus size: 42
6148590 TTTGACGCTA
* **
6148600 CTCTGCTTCCCTCGCTGCAGCCTCTACTTCCCTCGCTTTAGC
1 CTCTGCTTCCCTTGCTGCAGCCTCTACTTCCCTCGCTGCAGC
* * * *
6148642 CTCTGCTTCCCTTGCTGCAGCCTGTTCTTCTCTCGCTGCCGC
1 CTCTGCTTCCCTTGCTGCAGCCTCTACTTCCCTCGCTGCAGC
*
6148684 CTCTGCTTCTCTTGCTGC
1 CTCTGCTTCCCTTGCTGC
6148702 CGCATCTGCT
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 52 1.00
ACGTcount: A:0.04, C:0.43, G:0.17, T:0.36
Consensus pattern (42 bp):
CTCTGCTTCCCTTGCTGCAGCCTCTACTTCCCTCGCTGCAGC
Found at i:6148767 original size:66 final size:66
Alignment explanation
Indices: 6148683--6148829 Score: 199
Period size: 66 Copynumber: 2.2 Consensus size: 66
6148673 CTCGCTGCCG
* *
6148683 CCTCTGCTTCTCTTGCTGCCGCATCTGCTCTAAGCTGCT-GCTGGAGTTCTTCATA-CTTTCGTT
1 CCTCAGCTTCTCTCGCTGCCGCATCTGCTCTAAGCTG-TAGCTGGAGTTCTTCATATCTTT-GTT
6148746 GAA
64 GAA
* * * *
6148749 CCTCAGCTTCTCTCGCTGCTGCATCTGCTTTAAGTTGTAGCTGGAGTTCTTCATATCTTTTTTGA
1 CCTCAGCTTCTCTCGCTGCCGCATCTGCTCTAAGCTGTAGCTGGAGTTCTTCATATCTTTGTTGA
6148814 A
66 A
*
6148815 CATCAGCTTCTCTCG
1 CCTCAGCTTCTCTCG
6148830 ATGTTGCCTC
Statistics
Matches: 72, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
65 1 0.01
66 67 0.93
67 4 0.06
ACGTcount: A:0.14, C:0.29, G:0.18, T:0.39
Consensus pattern (66 bp):
CCTCAGCTTCTCTCGCTGCCGCATCTGCTCTAAGCTGTAGCTGGAGTTCTTCATATCTTTGTTGA
A
Found at i:6148845 original size:66 final size:66
Alignment explanation
Indices: 6148722--6148852 Score: 192
Period size: 66 Copynumber: 2.0 Consensus size: 66
6148712 CTAAGCTGCT
* * *
6148722 GCTGGAGTTCTTCATACTTTCGTTGAACCTCAGCTTCTCTCGCTGCTGCATCTGCTTTAAGTTGT
1 GCTGGAGTTCTTCATACTTTCGTTGAACATCAGCTTCTCTCGATGCTGCATCCGCTTTAAGTTGT
6148787 A
66 A
* * *
6148788 GCTGGAGTTCTTCATATCTTT-TTTGAACATCAGCTTCTCTCGATGTTGCCTCCGCTTTAAGTTG
1 GCTGGAGTTCTTCATA-CTTTCGTTGAACATCAGCTTCTCTCGATGCTGCATCCGCTTTAAGTTG
6148852 T
65 T
6148853 GTAATTTGCT
Statistics
Matches: 58, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
66 54 0.93
67 4 0.07
ACGTcount: A:0.15, C:0.24, G:0.19, T:0.41
Consensus pattern (66 bp):
GCTGGAGTTCTTCATACTTTCGTTGAACATCAGCTTCTCTCGATGCTGCATCCGCTTTAAGTTGT
A
Found at i:6154566 original size:31 final size:31
Alignment explanation
Indices: 6154529--6154874 Score: 351
Period size: 31 Copynumber: 11.4 Consensus size: 31
6154519 ATTAATTAAC
* **
6154529 TAAGTTATGTCATTTATGTATCGTATTAATG
1 TAAGTTATGTAATTTATGTATAATATTAATG
* *
6154560 TAAGTTATGTAATTTATGTATATTAACTAAT-
1 TAAGTTATGTAATTTATGTATAAT-ATTAATG
* * *
6154591 TAATTTATGTAAGTTATGTATAATATTAATTAAT
1 TAAGTTATGTAATTTATGTATAATATTAA-T--G
*
6154625 TAAGTTATGTCATTTATGTATAATATTAATG
1 TAAGTTATGTAATTTATGTATAATATTAATG
* *
6154656 TAAGTTATGT-A--TA-ATATTA-ATTAAT-
1 TAAGTTATGTAATTTATGTATAATATTAATG
*
6154681 TAAGTTATGTCATTTATGTATAATATTAATG
1 TAAGTTATGTAATTTATGTATAATATTAATG
* *
6154712 TAAGTTATGT-A--TA-ATATTA-ATTAAT-
1 TAAGTTATGTAATTTATGTATAATATTAATG
* *
6154737 TAAGTTATGTCATTTATGTATAATATTAATTAAC
1 TAAGTTATGTAATTTATGTATAATATTAA-T--G
6154771 TAAGTTATGTAATTTATGTATAATATTAATG
1 TAAGTTATGTAATTTATGTATAATATTAATG
* * *
6154802 TAAGTAATGTAATTTATGTATATTAACTAAT-
1 TAAGTTATGTAATTTATGTATAAT-ATTAATG
6154833 TAAGTTATGTAATTTATGTATAATATTAATG
1 TAAGTTATGTAATTTATGTATAATATTAATG
6154864 TAAGTTATGTA
1 TAAGTTATGTA
6154875 TAATATTTAA
Statistics
Matches: 265, Mismatches: 28, Indels: 44
0.79 0.08 0.13
Matches are distributed among these distances:
25 20 0.08
26 14 0.05
27 8 0.03
28 8 0.03
29 8 0.03
30 22 0.08
31 119 0.45
32 10 0.04
33 2 0.01
34 54 0.20
ACGTcount: A:0.38, C:0.02, G:0.11, T:0.48
Consensus pattern (31 bp):
TAAGTTATGTAATTTATGTATAATATTAATG
Found at i:6154658 original size:56 final size:56
Alignment explanation
Indices: 6154597--6154766 Score: 340
Period size: 56 Copynumber: 3.0 Consensus size: 56
6154587 TAATTAATTT
6154597 ATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTCATTTATGTATAATATTA
1 ATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTCATTTATGTATAATATTA
6154653 ATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTCATTTATGTATAATATTA
1 ATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTCATTTATGTATAATATTA
6154709 ATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTCATTTATGTATAATATTA
1 ATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTCATTTATGTATAATATTA
6154765 AT
1 AT
6154767 TAACTAAGTT
Statistics
Matches: 114, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 114 1.00
ACGTcount: A:0.39, C:0.02, G:0.11, T:0.48
Consensus pattern (56 bp):
ATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTCATTTATGTATAATATTA
Found at i:6154712 original size:22 final size:22
Alignment explanation
Indices: 6154694--6154881 Score: 94
Period size: 22 Copynumber: 8.6 Consensus size: 22
6154684 GTTATGTCAT
6154694 TTATGTATAATATTAATGTAAG
1 TTATGTATAATATTAATGTAAG
6154716 TTATGTATAATATTAAT-TAA-
1 TTATGTATAATATTAATGTAAG
* * *
6154736 TTAAGT-TATGTCATTTATGTATA-
1 TTATGTATA-AT-ATTAATGTA-AG
* ** *
6154759 ATATTAATTAACTAAGTT-ATGTAAT
1 TTATGTA-TAA-T-A-TTAATGTAAG
6154784 TTATGTATAATATTAATGTAAG
1 TTATGTATAATATTAATGTAAG
*
6154806 TAATG--TAAT-TT-ATGTATA-
1 TTATGTATAATATTAATGTA-AG
** * *
6154824 TTAACTAATTAA-GTT-ATGTAAT
1 TTATGT-A-TAATATTAATGTAAG
6154846 TTATGTATAATATTAATGTAAG
1 TTATGTATAATATTAATGTAAG
6154868 TTATGTATAATATT
1 TTATGTATAATATT
6154882 TAAATCGATC
Statistics
Matches: 126, Mismatches: 21, Indels: 38
0.68 0.11 0.21
Matches are distributed among these distances:
18 7 0.06
19 5 0.04
20 13 0.10
21 14 0.11
22 64 0.51
23 4 0.03
24 4 0.03
25 13 0.10
26 2 0.02
ACGTcount: A:0.40, C:0.02, G:0.11, T:0.48
Consensus pattern (22 bp):
TTATGTATAATATTAATGTAAG
Found at i:6154754 original size:34 final size:34
Alignment explanation
Indices: 6154709--6154862 Score: 212
Period size: 34 Copynumber: 4.7 Consensus size: 34
6154699 TATAATATTA
*
6154709 ATGTAAGTTATGTATAATATTAATTAATTAAGTT
1 ATGTAATTTATGTATAATATTAATTAATTAAGTT
* *
6154743 ATGTCATTTATGTATAATATTAATTAACTAAGTT
1 ATGTAATTTATGTATAATATTAATTAATTAAGTT
* *
6154777 ATGTAATTTATGTATAATATTAA-T--GTAAGTA
1 ATGTAATTTATGTATAATATTAATTAATTAAGTT
*
6154808 ATGTAATTTATG--T-ATATTAACTAATTAAGTT
1 ATGTAATTTATGTATAATATTAATTAATTAAGTT
6154839 ATGTAATTTATGTATAATATTAAT
1 ATGTAATTTATGTATAATATTAAT
6154863 GTAAGTTATG
Statistics
Matches: 105, Mismatches: 9, Indels: 12
0.83 0.07 0.10
Matches are distributed among these distances:
28 7 0.07
29 2 0.02
31 34 0.32
33 2 0.02
34 60 0.57
ACGTcount: A:0.40, C:0.02, G:0.10, T:0.47
Consensus pattern (34 bp):
ATGTAATTTATGTATAATATTAATTAATTAAGTT
Found at i:6154754 original size:90 final size:91
Alignment explanation
Indices: 6154553--6154862 Score: 343
Period size: 90 Copynumber: 3.4 Consensus size: 91
6154543 TATGTATCGT
* * *
6154553 ATTAATGTAAGTTATGTAATTTATG--T-ATATTAACTAATTAATTTATGTAAGTTATGTATAAT
1 ATTAAT-TAAGTTATGTAATTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATAAT
* * *
6154615 ATTAATTAATTAAGTTATGTCAT-TTATGT-
65 ATTAA-T--GTAAGTTATGTAATAATAT-TA
* *
6154644 A-TAA-T-A-TTAATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTCATTTATGTATAAT
1 ATTAATTAAGTT-ATGTAATTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATAAT
6154705 ATTAATGTAAGTTATGT-ATAATATTA
65 ATTAATGTAAGTTATGTAATAATATTA
* *
6154731 ATTAATTAAGTTATGTCATTTATGTATAATATTAATTAACTAAGTTATGTAATTTATGTATAATA
1 ATTAATTAAGTTATGTAATTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATAATA
*
6154796 TTAATGTAAGTAATGTAATTTATGTATATTA
66 TTAATGTAAGTTATGTAA--TA---ATATTA
*
6154827 ACTAATTAAGTTATGTAATTTATGTATAATATTAAT
1 ATTAATTAAGTTATGTAATTTATGTATAATATTAAT
6154863 GTAAGTTATG
Statistics
Matches: 189, Mismatches: 14, Indels: 27
0.82 0.06 0.12
Matches are distributed among these distances:
86 5 0.03
87 26 0.14
88 4 0.02
89 3 0.02
90 105 0.56
91 4 0.02
93 2 0.01
96 40 0.21
ACGTcount: A:0.40, C:0.02, G:0.10, T:0.48
Consensus pattern (91 bp):
ATTAATTAAGTTATGTAATTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATAATA
TTAATGTAAGTTATGTAATAATATTA
Found at i:6155260 original size:2 final size:2
Alignment explanation
Indices: 6155253--6155299 Score: 51
Period size: 2 Copynumber: 23.5 Consensus size: 2
6155243 AAGCATAAGA
* * *
6155253 AT AT AT AT AT AT AT AT AT AT AT AC AT AT AC AGT GT -T AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT
6155295 AT AT A
1 AT AT A
6155300 ACACTGTTCA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (2 bp):
AT
Found at i:6155506 original size:24 final size:24
Alignment explanation
Indices: 6155474--6155526 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 24
6155464 AGTATTTTAT
6155474 AATATAATATTAATTTTAGATACA
1 AATATAATATTAATTTTAGATACA
* *
6155498 AATATAATATTAATTTTAGTTAGA
1 AATATAATATTAATTTTAGATACA
6155522 AATAT
1 AATAT
6155527 TATACAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.49, C:0.02, G:0.06, T:0.43
Consensus pattern (24 bp):
AATATAATATTAATTTTAGATACA
Found at i:6156177 original size:33 final size:33
Alignment explanation
Indices: 6156130--6156197 Score: 118
Period size: 33 Copynumber: 2.1 Consensus size: 33
6156120 ATATACATAT
*
6156130 ATTCATACCTAACACTAATCTCATTTAACTCGA
1 ATTCATACCCAACACTAATCTCATTTAACTCGA
*
6156163 ATTCATACCCAACACTCATCTCATTTAACTCGA
1 ATTCATACCCAACACTAATCTCATTTAACTCGA
6156196 AT
1 AT
6156198 AACATAGATG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.35, C:0.29, G:0.03, T:0.32
Consensus pattern (33 bp):
ATTCATACCCAACACTAATCTCATTTAACTCGA
Found at i:6156451 original size:15 final size:14
Alignment explanation
Indices: 6156419--6156458 Score: 53
Period size: 15 Copynumber: 2.8 Consensus size: 14
6156409 AATTGGGAAA
*
6156419 TTGGGGAAAATAAT
1 TTGGGGAAAATAAC
6156433 TTGGGGAAGAATAAC
1 TTGGGGAA-AATAAC
*
6156448 TTGGGGGAAAT
1 TTGGGGAAAAT
6156459 TGGGGGAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
14 11 0.48
15 12 0.52
ACGTcount: A:0.38, C:0.03, G:0.35, T:0.25
Consensus pattern (14 bp):
TTGGGGAAAATAAC
Found at i:6156462 original size:25 final size:22
Alignment explanation
Indices: 6156433--6156489 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 22
6156423 GGAAAATAAT
*
6156433 TTGGGGAAGAATAACTTGGGGGAAA
1 TTGGGGAA-AAGAACTT--GGGAAA
*
6156458 TTGGGGGAAAAGAAGTTGGGAAA
1 TT-GGGGAAAAGAACTTGGGAAA
6156481 TTGGGGAAA
1 TTGGGGAAA
6156490 TGAAATCGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
22 7 0.24
23 8 0.28
25 8 0.28
26 6 0.21
ACGTcount: A:0.37, C:0.02, G:0.42, T:0.19
Consensus pattern (22 bp):
TTGGGGAAAAGAACTTGGGAAA
Found at i:6156502 original size:23 final size:23
Alignment explanation
Indices: 6156452--6156505 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
6156442 AATAACTTGG
* *
6156452 GGGAAATTGGGGGAAAAGAAGTT
1 GGGAAATTGGGGGAAAAGAAATC
*
6156475 GGGAAATT-GGGGAAATGAAATC
1 GGGAAATTGGGGGAAAAGAAATC
6156497 GTGGAAATT
1 G-GGAAATT
6156506 TGACTTGGGG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
22 12 0.44
23 15 0.56
ACGTcount: A:0.39, C:0.02, G:0.39, T:0.20
Consensus pattern (23 bp):
GGGAAATTGGGGGAAAAGAAATC
Found at i:6157928 original size:41 final size:41
Alignment explanation
Indices: 6157843--6157986 Score: 243
Period size: 41 Copynumber: 3.5 Consensus size: 41
6157833 NNNNNNNNNN
* * *
6157843 CTTAGACGAAAACGCCGCTAAAGACTCGGAGCATTAGCGGCG
1 CTTAGACAAAAACGCCGCTATAGAC-CCGAGCATTAGCGGCG
*
6157885 CTTAGACGAAAACGCCGCTATAGACCCGAGCATTAGCGGCG
1 CTTAGACAAAAACGCCGCTATAGACCCGAGCATTAGCGGCG
6157926 CTTAGACAAAAACGCCGCTATAGACCCGAGCATTAGCGGCG
1 CTTAGACAAAAACGCCGCTATAGACCCGAGCATTAGCGGCG
6157967 CTTAGACAAAAACGCCGCTA
1 CTTAGACAAAAACGCCGCTA
6157987 AATGTTTAAA
Statistics
Matches: 99, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
41 75 0.76
42 24 0.24
ACGTcount: A:0.32, C:0.28, G:0.25, T:0.15
Consensus pattern (41 bp):
CTTAGACAAAAACGCCGCTATAGACCCGAGCATTAGCGGCG
Found at i:6157931 original size:23 final size:24
Alignment explanation
Indices: 6157900--6157973 Score: 65
Period size: 24 Copynumber: 3.4 Consensus size: 24
6157890 ACGAAAACGC
6157900 CGCTATAGACCCGAGCATTAGCGG
1 CGCTATAGACCCGAGCATTAGCGG
* * *
6157924 CGCT-TAGA--C-A--A-AAACGC
1 CGCTATAGACCCGAGCATTAGCGG
6157941 CGCTATAGACCCGAGCATTAGCGG
1 CGCTATAGACCCGAGCATTAGCGG
6157965 CGCT-TAGAC
1 CGCTATAGAC
6157974 AAAAACGCCG
Statistics
Matches: 37, Mismatches: 6, Indels: 15
0.64 0.10 0.26
Matches are distributed among these distances:
17 7 0.19
18 5 0.14
20 2 0.05
21 2 0.05
23 10 0.27
24 11 0.30
ACGTcount: A:0.28, C:0.30, G:0.26, T:0.16
Consensus pattern (24 bp):
CGCTATAGACCCGAGCATTAGCGG
Found at i:6159817 original size:27 final size:27
Alignment explanation
Indices: 6159787--6159845 Score: 100
Period size: 27 Copynumber: 2.2 Consensus size: 27
6159777 TGAAAAAGGT
6159787 GGCACCAATGGTGCCTTTCCCATAGGC
1 GGCACCAATGGTGCCTTTCCCATAGGC
* *
6159814 GGCACCAATGGTGCCTTTCTCATAGTC
1 GGCACCAATGGTGCCTTTCCCATAGGC
6159841 GGCAC
1 GGCAC
6159846 AGGACTAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.19, C:0.32, G:0.25, T:0.24
Consensus pattern (27 bp):
GGCACCAATGGTGCCTTTCCCATAGGC
Found at i:6160591 original size:27 final size:27
Alignment explanation
Indices: 6160553--6160615 Score: 108
Period size: 27 Copynumber: 2.3 Consensus size: 27
6160543 TTTTAGTCCT
*
6160553 GTGCCGCCTATGAGAAAGGCACTATTG
1 GTGCCGCCTATGAGAAAGGCACCATTG
*
6160580 GTGCCGCCTATGGGAAAGGCACCATTG
1 GTGCCGCCTATGAGAAAGGCACCATTG
6160607 GTGCCGCCT
1 GTGCCGCCT
6160616 TTTTCATGCC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.21, C:0.27, G:0.32, T:0.21
Consensus pattern (27 bp):
GTGCCGCCTATGAGAAAGGCACCATTG
Found at i:6171681 original size:26 final size:26
Alignment explanation
Indices: 6171649--6171717 Score: 122
Period size: 26 Copynumber: 2.7 Consensus size: 26
6171639 AAATAAAAAA
6171649 TTACCAAAATAT-TAAATTTTTTTTAT
1 TTACCAAAATATATAAA-TTTTTTTAT
6171675 TTACCAAAATATATAAATTTTTTTAT
1 TTACCAAAATATATAAATTTTTTTAT
6171701 TTACCAAAATATATAAA
1 TTACCAAAATATATAAA
6171718 AAACCAAAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
26 38 0.90
27 4 0.10
ACGTcount: A:0.45, C:0.09, G:0.00, T:0.46
Consensus pattern (26 bp):
TTACCAAAATATATAAATTTTTTTAT
Found at i:6171814 original size:27 final size:27
Alignment explanation
Indices: 6171784--6171877 Score: 136
Period size: 27 Copynumber: 3.5 Consensus size: 27
6171774 CGCCAATGGA
* *
6171784 ATTGGCGGCACCAAAGGTGCCAAAACC
1 ATTGGCGGCACCAATGGTGCCAATACC
*
6171811 ATTGGCGGCACCAATGGTGCCAATGCC
1 ATTGGCGGCACCAATGGTGCCAATACC
*
6171838 ATTGGCGGCACCAATGGTGCC-ATACTA
1 ATTGGCGGCACCAATGGTGCCAATAC-C
6171865 ATTGGCGGCACCA
1 ATTGGCGGCACCA
6171878 CTCGTATTAT
Statistics
Matches: 61, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
26 3 0.05
27 58 0.95
ACGTcount: A:0.27, C:0.29, G:0.28, T:0.17
Consensus pattern (27 bp):
ATTGGCGGCACCAATGGTGCCAATACC
Found at i:6171993 original size:12 final size:12
Alignment explanation
Indices: 6171966--6172000 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
6171956 CGGAAAAGAA
6171966 GAGAAAAA-GA-
1 GAGAAAAATGAG
6171976 GAGAAAAATGAG
1 GAGAAAAATGAG
6171988 GAGAAAAATGAG
1 GAGAAAAATGAG
6172000 G
1 G
6172001 TTTTTTTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 8 0.35
11 2 0.09
12 13 0.57
ACGTcount: A:0.60, C:0.00, G:0.34, T:0.06
Consensus pattern (12 bp):
GAGAAAAATGAG
Found at i:6172060 original size:19 final size:21
Alignment explanation
Indices: 6172022--6172060 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
6172012 AATAATTAAT
*
6172022 TATATTGTTGTTATTATTTTG
1 TATATTGTTGTTAATATTTTG
6172043 TATATT-TTG-TAATATTTT
1 TATATTGTTGTTAATATTTT
6172061 TTTTGTTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 3 0.18
21 6 0.35
ACGTcount: A:0.23, C:0.00, G:0.10, T:0.67
Consensus pattern (21 bp):
TATATTGTTGTTAATATTTTG
Found at i:6172422 original size:12 final size:12
Alignment explanation
Indices: 6172405--6172435 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
6172395 ATAATTTTAG
6172405 TGTGTATTATTT
1 TGTGTATTATTT
6172417 TGTGTATTATTT
1 TGTGTATTATTT
*
6172429 TGAGTAT
1 TGTGTAT
6172436 AAAATTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.19, C:0.00, G:0.19, T:0.61
Consensus pattern (12 bp):
TGTGTATTATTT
Found at i:6173013 original size:21 final size:18
Alignment explanation
Indices: 6172982--6173035 Score: 90
Period size: 18 Copynumber: 3.0 Consensus size: 18
6172972 AATATTACAC
* *
6172982 CCGATGAAGAAGAATGTG
1 CCGACGAAGAAGAAGGTG
6173000 CCGACGAAGAAGAAGGTG
1 CCGACGAAGAAGAAGGTG
6173018 CCGACGAAGAAGAAGGTG
1 CCGACGAAGAAGAAGGTG
6173036 GTGGCGATCA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.39, C:0.15, G:0.37, T:0.09
Consensus pattern (18 bp):
CCGACGAAGAAGAAGGTG
Found at i:6178115 original size:22 final size:21
Alignment explanation
Indices: 6178061--6178112 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
6178051 ATTTGTGCCG
* *
6178061 CCTTTTTTTCCCCTCCATCAC
1 CCTTTTTTTTCCCTACATCAC
6178082 CCTTTTTTTTCCCTACATCAC
1 CCTTTTTTTTCCCTACATCAC
6178103 CCTTTTTTTT
1 CCTTTTTTTT
6178113 TCCTCTATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.10, C:0.38, G:0.00, T:0.52
Consensus pattern (21 bp):
CCTTTTTTTTCCCTACATCAC
Found at i:6178861 original size:21 final size:21
Alignment explanation
Indices: 6178823--6179024 Score: 98
Period size: 21 Copynumber: 9.5 Consensus size: 21
6178813 TTACCTTTTT
*
6178823 TTCTTTTTTTTTCCTTTCCTCTTC
1 TTCTTTCTTTTT--TTT-CTCTTC
6178847 TTC-TTCTTTTTTTTCTCTTC
1 TTCTTTCTTTTTTTTCTCTTC
* *
6178867 TCCTTTCCTTTTCTTTC-CTTC
1 TTCTTT-CTTTTTTTTCTCTTC
6178888 TTTCTTTCTTTTTTCTTCTCTT-
1 -TTCTTTCTTTTTT-TTCTCTTC
* * *
6178910 TTCCTTC--TCTTCT-TCTTC
1 TTCTTTCTTTTTTTTCTCTTC
6178928 TTTCTTTC-TTTTTTTCTCTTC
1 -TTCTTTCTTTTTTTTCTCTTC
* * *
6178949 TCCTTTCCCTTTCTTTC-CTTC
1 TTCTTT-CTTTTTTTTCTCTTC
* ** *
6178970 TT-TTTCTTTCTTCCCTCTCC
1 TTCTTTCTTTTTTTTCTCTTC
* *
6178990 TTTCTTCCTTTCTTTCTCTCTTTC
1 -TTCTTTCTTT-TTTTTCTC-TTC
6179014 TTCCTTTCTTT
1 TT-CTTTCTTT
6179025 CCCTCCCCTT
Statistics
Matches: 136, Mismatches: 25, Indels: 34
0.70 0.13 0.17
Matches are distributed among these distances:
17 4 0.03
18 1 0.01
19 14 0.10
20 23 0.17
21 34 0.25
22 30 0.22
23 18 0.13
24 12 0.09
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (21 bp):
TTCTTTCTTTTTTTTCTCTTC
Found at i:6178871 original size:33 final size:33
Alignment explanation
Indices: 6178834--6178936 Score: 93
Period size: 39 Copynumber: 2.9 Consensus size: 33
6178824 TCTTTTTTTT
6178834 TCCTTTCCTCTTCTTCTTCTTTTTTTTCTCTTC
1 TCCTTTCCTCTTCTTCTTCTTTTTTTTCTCTTC
6178867 TCCTTTCCTTTTCTTTCCTTCTTTCTTTCTTTTT-TCTTC
1 TCCTTTCC---TC-TT-CTTC-TTCTTT-TTTTTCTCTTC
*
6178906 TCTTTTCCT-TCTCTTCTTCTTCTTTCTTTCT
1 TCCTTTCCTCT-TCTTCTTCTT-TTT-TTTCT
6178937 TTTTTTCTCT
Statistics
Matches: 58, Mismatches: 1, Indels: 20
0.73 0.01 0.25
Matches are distributed among these distances:
33 15 0.26
34 9 0.16
35 2 0.03
36 3 0.05
37 2 0.03
38 4 0.07
39 18 0.31
40 5 0.09
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (33 bp):
TCCTTTCCTCTTCTTCTTCTTTTTTTTCTCTTC
Found at i:6178874 original size:38 final size:37
Alignment explanation
Indices: 6178818--6179006 Score: 154
Period size: 38 Copynumber: 5.0 Consensus size: 37
6178808 TAAAATTACC
* **
6178818 TTTTTTTCTTTTTTTTTCCTTTCCTCTTCTTC-TTCTT
1 TTTTTTTCTTCTCCTTTCCTTTCCT-TTCTTCTTTCTT
*
6178855 TTTTTTCTCTTCTCCTTTCCTTTTCTTTCCTTCTTTCTT
1 TTTTTT-TCTTCTCCTTTCCTTTCCTTT-CTTCTTTCTT
* *
6178894 TCTTTTTTCTTCTCTTTTCCTTCTCTTCTTCTTCTTTCTT
1 T-TTTTTTCTTCTCCTTTCCTT-TCCT-TTCTTCTTTCTT
* *
6178934 TCTTTTT-TTCT-CTTCTCCTTTCCCTTTCTTTCCTTCTT
1 TTTTTTTCTTCTCCTT-TCCTTT-CCTTTC-TTCTTTCTT
* * *
6178972 TTTCTTTCTTC-CCTCTCCTTT-CTTCCTTTCTTTCT
1 TTTTTTTCTTCTCCTTTCCTTTCCTTTC-TTCTTTCT
6179007 CTCTTTCTTC
Statistics
Matches: 125, Mismatches: 16, Indels: 23
0.76 0.10 0.14
Matches are distributed among these distances:
36 12 0.10
37 14 0.11
38 49 0.39
39 30 0.24
40 18 0.14
41 2 0.02
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (37 bp):
TTTTTTTCTTCTCCTTTCCTTTCCTTTCTTCTTTCTT
Found at i:6178892 original size:4 final size:4
Alignment explanation
Indices: 6178876--6179025 Score: 96
Period size: 4 Copynumber: 37.0 Consensus size: 4
6178866 CTCCTTTCCT
* *
6178876 TTTC TTTC CTTC TTTC TTTC TTT- TTTC TTCTC TTTTC CTTC TCTTC -TTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TT-TC -TTTC TTTC T-TTC TTTC
* * *
6178925 -TTC TTTC TTTC TTTT TTTC TCTTC -TCC TTTCCC TTTC TTTC CTTC -TT-
1 TTTC TTTC TTTC TTTC TTTC T-TTC TTTC TTT--C TTTC TTTC TTTC TTTC
* * * * *
6178972 TTTC TTTC TTCCC TCTCC TTTC TTCC TTTC TTTC TCTC TTTC TTCC TTTC
1 TTTC TTTC TT-TC T-TTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC
6179022 TTTC
1 TTTC
6179026 CCTCCCCTTC
Statistics
Matches: 116, Mismatches: 17, Indels: 26
0.73 0.11 0.16
Matches are distributed among these distances:
3 15 0.13
4 79 0.68
5 15 0.13
6 7 0.06
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (4 bp):
TTTC
Found at i:6178907 original size:44 final size:43
Alignment explanation
Indices: 6178843--6178981 Score: 175
Period size: 44 Copynumber: 3.3 Consensus size: 43
6178833 TTCCTTTCCT
6178843 CTTC-TTC-TTCTTTTTTTTCTCTTCTCCTTTCCTTTTCTTTC
1 CTTCTTTCTTTCTTTTTTTTCTCTTCTCCTTTCCTTTTCTTTC
* *
6178884 CTTCTTTCTTTCTTTTTTCTTCTCTTTTCC-TT-CTCTTC-TT-
1 CTTCTTTCTTTCTTTTTT-TTCTCTTCTCCTTTCCTTTTCTTTC
*
6178924 CTTCTTTCTTTC-TTTTTTTCTCTTCTCCTTTCCCTTTCTTTC
1 CTTCTTTCTTTCTTTTTTTTCTCTTCTCCTTTCCTTTTCTTTC
6178966 CTTCTTTTTCTTTCTT
1 CTTC--TTTCTTTCTT
6178982 CCCTCTCCTT
Statistics
Matches: 83, Mismatches: 5, Indels: 16
0.80 0.05 0.15
Matches are distributed among these distances:
38 10 0.12
39 7 0.08
40 16 0.19
41 8 0.10
42 12 0.14
43 11 0.13
44 18 0.22
45 1 0.01
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (43 bp):
CTTCTTTCTTTCTTTTTTTTCTCTTCTCCTTTCCTTTTCTTTC
Found at i:6178912 original size:29 final size:28
Alignment explanation
Indices: 6178862--6178977 Score: 93
Period size: 29 Copynumber: 4.2 Consensus size: 28
6178852 CTTTTTTTTC
*
6178862 TCTTCTCCTTTCCTTT-TCTTTCCTTCT-T
1 TCTTCTTCTTT-CTTTCT-TTTCCTTCTCT
*
6178890 TCTTTCTTTTTTCTTCTCTTTTCCTTCTCT
1 TC-TTCTTCTTTCTT-TCTTTTCCTTCTCT
*
6178920 TCTTCTTCTTTCTTTCTTTT-TTTCTCT
1 TCTTCTTCTTTCTTTCTTTTCCTTCTCT
* **
6178947 TCTCCTT-TCCCTTTC-TTTCCTTCT-T
1 TCTTCTTCTTTCTTTCTTTTCCTTCTCT
6178972 T-TTCTT
1 TCTTCTT
6178978 TCTTCCCTCT
Statistics
Matches: 74, Mismatches: 9, Indels: 14
0.76 0.09 0.14
Matches are distributed among these distances:
24 4 0.05
25 5 0.07
26 10 0.14
27 12 0.16
28 11 0.15
29 28 0.38
30 4 0.05
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (28 bp):
TCTTCTTCTTTCTTTCTTTTCCTTCTCT
Found at i:6178950 original size:82 final size:78
Alignment explanation
Indices: 6178819--6178981 Score: 229
Period size: 82 Copynumber: 2.0 Consensus size: 78
6178809 AAAATTACCT
* * *
6178819 TTTTTTCTTTTTTTTTCCTTTCCTCTTCTTCTTCTTTTTTTTCTCTTCTCCTTTCCTTTTCTTTC
1 TTTTTTCTTCTCTTTTCCTTTCCTCTTCTTCTTCTTTTTTTTCTCTTCTCCTTTCCCTTTCTTTC
6178884 CTTC-TTTCTTTC
66 CTTCTTTTCTTTC
*
6178896 TTTTTTCTTCTCTTTTCCTTCTCTTCTTCTTCTTTCTTTCTTTTTTTCTCTTCTCCTTTCCCTTT
1 TTTTTTCTTCTCTTTTCCTT-TCCTCTTCTTC-TTC--T-TTTTTTTCTCTTCTCCTTTCCCTTT
6178961 CTTTCCTTCTTTTTCTTTC
61 CTTTCCTTC-TTTTCTTTC
6178980 TT
1 TT
6178982 CCCTCTCCTT
Statistics
Matches: 75, Mismatches: 4, Indels: 7
0.87 0.05 0.08
Matches are distributed among these distances:
77 18 0.24
78 10 0.13
79 3 0.04
81 1 0.01
82 33 0.44
84 10 0.13
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (78 bp):
TTTTTTCTTCTCTTTTCCTTTCCTCTTCTTCTTCTTTTTTTTCTCTTCTCCTTTCCCTTTCTTTC
CTTCTTTTCTTTC
Found at i:6178961 original size:70 final size:72
Alignment explanation
Indices: 6178819--6179026 Score: 182
Period size: 70 Copynumber: 2.8 Consensus size: 72
6178809 AAAATTACCT
* * *
6178819 TTTTTTCTTTTTTTTTCCTTTCCTCTTCTTCTTCTTTTTTTTCTCTTCTCCTTTCCTTTTCTTTC
1 TTTTTTC-TTCTTTTTCC-TT-CTCTTCTTCTTC-TTTCTTTCTCTTCT-CTTTCCTTTCCTTTC
6178884 CTTCTTTCTTT-C
61 C-TCTTTCTTTCC
6178896 TTTTTTCTTCTCTTTTCCTTCTCTTCTTCTTCTTTCTTTCT-TT-T-TTTCTCTTCTCCTTTCC-
1 TTTTTTCTTCT-TTTTCCTTCTCTTCTTCTTCTTTCTTTCTCTTCTCTTTC-CTT-TCCTTTCCT
6178957 CTTTCTTTCC
63 CTTTCTTTCC
* * * *
6178967 TTCTTT-TTCTTTCTTCCCTCTCCT-TTCTTCCTTTCTTTCTC-TCTTTCTTCCTTT-CTTTCC
1 TTTTTTCTTCTTT-TTCCTTCTCTTCTTCTT-CTTTCTTTCTCTTCTCT-TTCCTTTCCTTTCC
6179027 CTCCCCTTCT
Statistics
Matches: 115, Mismatches: 6, Indels: 27
0.78 0.04 0.18
Matches are distributed among these distances:
69 7 0.06
70 42 0.37
71 11 0.10
72 12 0.10
73 5 0.04
74 8 0.07
75 12 0.10
76 5 0.04
77 13 0.11
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (72 bp):
TTTTTTCTTCTTTTTCCTTCTCTTCTTCTTCTTTCTTTCTCTTCTCTTTCCTTTCCTTTCCTCTT
TCTTTCC
Found at i:6178992 original size:20 final size:22
Alignment explanation
Indices: 6178947--6179034 Score: 84
Period size: 20 Copynumber: 4.3 Consensus size: 22
6178937 TTTTTTCTCT
*
6178947 TCTCCTTTC--CCTTTCTTTCC
1 TCTCCTTTCTTCCTTTCTTCCC
6178967 T-T-CTTT-TT-CTTTCTTCCC
1 TCTCCTTTCTTCCTTTCTTCCC
*
6178985 TCTCCTTTCTTCCTTTCTT-TC
1 TCTCCTTTCTTCCTTTCTTCCC
6179006 TCT-CTTTCTTCCTTTCTTTCCC
1 TCTCCTTTCTTCCTTTC-TTCCC
*
6179028 TCCCCTT
1 TCTCCTT
6179035 CTGTTAATTG
Statistics
Matches: 55, Mismatches: 4, Indels: 15
0.74 0.05 0.20
Matches are distributed among these distances:
18 14 0.25
19 2 0.04
20 18 0.33
21 8 0.15
22 10 0.18
23 3 0.05
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (22 bp):
TCTCCTTTCTTCCTTTCTTCCC
Found at i:6179012 original size:82 final size:82
Alignment explanation
Indices: 6178842--6179025 Score: 234
Period size: 82 Copynumber: 2.3 Consensus size: 82
6178832 TTTCCTTTCC
* * * *
6178842 TCTTC-TTCTTCTTTTTTTTCTCTTCTCCTTTCCTTTTCTTTCCTTCTTTCTTTCTTTTTTCTTC
1 TCTTCTTTCTTCCTTTTTTTCTCTTCTCCTTTCCCTTTCTTTCCTTCTTTCTTTCTTTTTCCCTC
*
6178906 TCTTTTCCTTCTCTTCT
66 TCCTTTCCTTCTCTTCT
*
6178923 TCTTCTTTCTTTCTTTTTTTCTCTTCTCCTTTCCCTTTCTTTCCTTC-TT-TTTCTTTCTTCCCT
1 TCTTCTTTCTTCCTTTTTTTCTCTTCTCCTTTCCCTTTCTTTCCTTCTTTCTTTCTTT-TTCCCT
6178986 CTCCTTT-CTTC-CTTTCTT
65 CTCCTTTCCTTCTC-TTC-T
*
6179004 TCTCTCTTTCTTCCTTTCTTTC
1 TCT-TCTTTCTTCCTTTTTTTC
6179026 CCTCCCCTTC
Statistics
Matches: 90, Mismatches: 8, Indels: 9
0.84 0.07 0.08
Matches are distributed among these distances:
79 1 0.01
80 14 0.16
81 21 0.23
82 54 0.60
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (82 bp):
TCTTCTTTCTTCCTTTTTTTCTCTTCTCCTTTCCCTTTCTTTCCTTCTTTCTTTCTTTTTCCCTC
TCCTTTCCTTCTCTTCT
Found at i:6179027 original size:70 final size:71
Alignment explanation
Indices: 6178823--6179028 Score: 183
Period size: 77 Copynumber: 2.9 Consensus size: 71
6178813 TTACCTTTTT
* * * *
6178823 TTCTTTTTTTTTCCTTTCCTCTTC-TTCTT-CTTT-TTTTTCTC-TTC-TCCTTTCCTTT-TCTT
1 TTCTTTTTTTTT-CTTCCCTCTCCTTTCTTCCTTTCTTTCTCTCTTTCTTCCTTTCCTTTCCCTT
*
6178882 TCCTTCT
65 TCCTTCC
* * * * *
6178889 TTCTTTCTTTTTTCTTCTCTTTTCCTTCTCTTCTTCTTCTTTCTTTCTTTTTTTCTCTTCTCCTT
1 TTCTTT-TTTTTTCTTC-CCTCTCCTT-TCTTCCT-TTCTTTCTCTC-TTTCTTC-CTT-TCCTT
*
6178954 TCCCTTTCTTTCC
59 TCCCTTTCCTTCC
*
6178967 TTCTTTTTCTTTCTTCCCTCTCCTTTCTTCCTTTCTTTCTCTCTTTCTTCCTTT-CTTTCCCT
1 TTCTTTTTTTTTCTTCCCTCTCCTTTCTTCCTTTCTTTCTCTCTTTCTTCCTTTCCTTTCCCT
6179029 CCCCTTCTGT
Statistics
Matches: 110, Mismatches: 17, Indels: 22
0.74 0.11 0.15
Matches are distributed among these distances:
66 9 0.08
67 10 0.09
68 1 0.01
69 4 0.04
70 9 0.08
71 3 0.03
72 9 0.08
73 6 0.05
74 12 0.11
75 8 0.07
76 10 0.09
77 15 0.14
78 14 0.13
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (71 bp):
TTCTTTTTTTTTCTTCCCTCTCCTTTCTTCCTTTCTTTCTCTCTTTCTTCCTTTCCTTTCCCTTT
CCTTCC
Found at i:6201122 original size:23 final size:24
Alignment explanation
Indices: 6201086--6201143 Score: 75
Period size: 23 Copynumber: 2.5 Consensus size: 24
6201076 AATATGATTT
6201086 ATATATTTAAATTAAATA-TTACAA
1 ATATATTTAAATTAAATATTTA-AA
* *
6201110 ATA-ATTTATATTAATTATTTAAA
1 ATATATTTAAATTAAATATTTAAA
6201133 ATATATTTAAA
1 ATATATTTAAA
6201144 ATTTATATGT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
23 17 0.59
24 12 0.41
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (24 bp):
ATATATTTAAATTAAATATTTAAA
Found at i:6204339 original size:72 final size:72
Alignment explanation
Indices: 6204221--6204361 Score: 230
Period size: 72 Copynumber: 2.0 Consensus size: 72
6204211 AGGAACTAAG
* *
6204221 GGAGGCAACAGAGTAAATATATTGAATGTTAAGTAAGTCCACATGAAATTTACTTAACTTACCTT
1 GGAGGCAACAGAGTAAACATATTAAATGTTAAGTAAGTCCACATGAAATTTACTTAACTTACCTT
6204286 AACAAAA
66 AACAAAA
* *
6204293 GGAGGCAACGGAGTAAACATATTAAATGCTT-AGTAAGTCCATATGAAATTTACTTAACTTACCT
1 GGAGGCAACAGAGTAAACATATTAAATG-TTAAGTAAGTCCACATGAAATTTACTTAACTTACCT
6204357 TAACA
65 TAACA
6204362 TTACAACAAA
Statistics
Matches: 64, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
72 62 0.97
73 2 0.03
ACGTcount: A:0.41, C:0.15, G:0.16, T:0.28
Consensus pattern (72 bp):
GGAGGCAACAGAGTAAACATATTAAATGTTAAGTAAGTCCACATGAAATTTACTTAACTTACCTT
AACAAAA
Done.