Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr8
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: 78745976
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 2640508 characters in sequence are not A, C, G, or T
File 8 of 235
Found at i:2132829 original size:44 final size:45
Alignment explanation
Indices: 2132781--2133178 Score: 180
Period size: 45 Copynumber: 8.6 Consensus size: 45
2132771 CTTACCTACT
* *
2132781 TGAAGTTGCAGTAGAGCAGATTGAAGCCA-CAAGTCTTATCCCCC
1 TGAAGTTGCAGTGGAGCAGATTGAAGCCAGCAAGTCTTATCTCCC
* * * * * * *
2132825 TGAAGTTACAGCGAAGCAGACTAAAGACAGCGAA-TCTTATTTCCC
1 TGAAGTTGCAGTGGAGCAGATTGAAGCCAGC-AAGTCTTATCTCCC
* * *
2132870 TGAAGTTGCAGTGGAACAGATTAAAGCTACAAATTATGGCGAA-TCTTATCTTCC
1 TGAAGTTGCAGTGGAGCAGATTGAAGC--C-----A--GC-AAGTCTTATCTCCC
* * * *
2132924 TGAAGTTG-AGTGAAGCAGATTGAAGCCA-CCAGCCTTATCTTCC
1 TGAAGTTGCAGTGGAGCAGATTGAAGCCAGCAAGTCTTATCTCCC
* * * * ** * * * *
2132967 TGAAATTGCAGCGGAGTAGACTGAAGATACCAAATCTCATGTCCC
1 TGAAGTTGCAGTGGAGCAGATTGAAGCCAGCAAGTCTTATCTCCC
* * * *
2133012 TGAAGTTGCAGTTGAACAGATTGAAGCTACAAGTCACAATCATTGTCTCCC
1 TGAAGTTGCAGTGGAGCAGATTGAAGC--C-AG-CA-AGTC-TTATCTCCC
* * * * *
2133063 TGAAGTTGCAGTAGAGCAAATTGAAGCCATC-AGCCTTATCTCTC
1 TGAAGTTGCAGTGGAGCAGATTGAAGCCAGCAAGTCTTATCTCCC
* * *** * * *
2133107 TGAAGTTGCAGTGGAGCAGGTTAAAATTACCAATTTTTATCT-CC
1 TGAAGTTGCAGTGGAGCAGATTGAAGCCAGCAAGTCTTATCTCCC
* *
2133151 TCGAAGTTCCAGTGGAGTAGATTGAAGC
1 T-GAAGTTGCAGTGGAGCAGATTGAAGC
2133179 TACAAATCTC
Statistics
Matches: 259, Mismatches: 73, Indels: 43
0.69 0.19 0.11
Matches are distributed among these distances:
42 1 0.00
43 18 0.07
44 68 0.26
45 89 0.34
46 3 0.01
47 2 0.01
48 2 0.01
49 3 0.01
50 4 0.02
51 31 0.12
52 1 0.00
53 15 0.06
54 22 0.08
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (45 bp):
TGAAGTTGCAGTGGAGCAGATTGAAGCCAGCAAGTCTTATCTCCC
Found at i:2132988 original size:142 final size:142
Alignment explanation
Indices: 2132759--2133125 Score: 413
Period size: 142 Copynumber: 2.6 Consensus size: 142
2132749 GAATTAAATC
* * * * * *
2132759 ATCATGGTGAATCTTACCTACTTGAAGTTGCAGTAGAGCAGATTGAAGCCACAAGTCTTATCCCC
1 ATCATGGCGAATCTTATCTACCTGAAGTTGCAGTAGAGCAGATTGAAGCCACCAGCCTTAT-CTC
* * * * * *
2132824 CTGAAGTTACAGCGAAGCAGACTAAAGACAGCGAATCTTATTTCCCTGAAGTTGCAGTGGAACAG
65 CTGAAGTTGCAGCGGAGCAGACTAAAGACACCAAATCTCATGTCCCTGAAGTTGCAGTGGAACAG
2132889 ATTAAAGCTACAA
130 ATTAAAGCTACAA
* *
2132902 ATTATGGCGAATCTTATCTTCCTGAAGTTG-AGT-GAAGCAGATTGAAGCCACCAGCCTTATCTT
1 ATCATGGCGAATCTTATCTACCTGAAGTTGCAGTAG-AGCAGATTGAAGCCACCAGCCTTATC-T
* * * * *
2132965 CCTGAAATTGCAGCGGAGTAGACTGAAGATACCAAATCTCATGTCCCTGAAGTTGCAGTTGAACA
64 CCTGAAGTTGCAGCGGAGCAGACTAAAGACACCAAATCTCATGTCCCTGAAGTTGCAGTGGAACA
*
2133030 GATTGAAGCTACAA
129 GATTAAAGCTACAA
* * * * *
2133044 GTCA---C-AATCATTGTCTCCCTGAAGTTGCAGTAGAGCAAATTGAAGCCATCAGCCTTATCTC
1 ATCATGGCGAATC-TTATCTACCTGAAGTTGCAGTAGAGCAGATTGAAGCCACCAGCCTTATCTC
*
2133105 TCTGAAGTTGCAGTGGAGCAG
65 -CTGAAGTTGCAGCGGAGCAG
2133126 GTTAAAATTA
Statistics
Matches: 189, Mismatches: 29, Indels: 15
0.81 0.12 0.06
Matches are distributed among these distances:
138 4 0.02
139 18 0.10
140 44 0.23
141 3 0.02
142 95 0.50
143 25 0.13
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (142 bp):
ATCATGGCGAATCTTATCTACCTGAAGTTGCAGTAGAGCAGATTGAAGCCACCAGCCTTATCTCC
TGAAGTTGCAGCGGAGCAGACTAAAGACACCAAATCTCATGTCCCTGAAGTTGCAGTGGAACAGA
TTAAAGCTACAA
Found at i:2134745 original size:26 final size:28
Alignment explanation
Indices: 2134716--2134776 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
2134706 ATTTATTATT
*
2134716 TTTAAAC-T-GTTTTGTATATTATTTAG
1 TTTAAACTTCGTTTTATATATTATTTAG
* * *
2134742 TTTAGACTTCTTTTTATATATTATTTAT
1 TTTAAACTTCGTTTTATATATTATTTAG
2134770 TTTAAAC
1 TTTAAAC
2134777 ATTTTTCATA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
26 6 0.21
27 1 0.04
28 21 0.75
ACGTcount: A:0.28, C:0.07, G:0.07, T:0.59
Consensus pattern (28 bp):
TTTAAACTTCGTTTTATATATTATTTAG
Found at i:2134892 original size:24 final size:23
Alignment explanation
Indices: 2134863--2134913 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 23
2134853 TTTTACATAT
2134863 TATTTATCTT-AAACCGTTTTATA
1 TATTTA-CTTCAAACCGTTTTATA
*
2134886 CTATTTACTTCAAACTGTTTTATA
1 -TATTTACTTCAAACCGTTTTATA
2134910 TATT
1 TATT
2134914 ATGTTGTTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
23 7 0.28
24 18 0.72
ACGTcount: A:0.29, C:0.14, G:0.04, T:0.53
Consensus pattern (23 bp):
TATTTACTTCAAACCGTTTTATA
Found at i:2136231 original size:28 final size:28
Alignment explanation
Indices: 2136188--2136243 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
2136178 CAATCACTCA
*
2136188 ACTTTCGAAAACTGACAAAACAGTCATT
1 ACTTTCGAAAACTGACAAAACAATCATT
*
2136216 ACTTTCGAAAAGTGACAAAACAATCATT
1 ACTTTCGAAAACTGACAAAACAATCATT
2136244 TTTATCGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.45, C:0.20, G:0.11, T:0.25
Consensus pattern (28 bp):
ACTTTCGAAAACTGACAAAACAATCATT
Found at i:2137508 original size:21 final size:21
Alignment explanation
Indices: 2137484--2137528 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2137474 TCTTGGGGCA
* * *
2137484 GCAACTTTTTGGTGAGTTGGG
1 GCAACTTGTTGATAAGTTGGG
2137505 GCAACTTGTTGATAAGTTGGG
1 GCAACTTGTTGATAAGTTGGG
2137526 GCA
1 GCA
2137529 GTTTGTTACT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.20, C:0.11, G:0.36, T:0.33
Consensus pattern (21 bp):
GCAACTTGTTGATAAGTTGGG
Found at i:2137534 original size:21 final size:21
Alignment explanation
Indices: 2137498--2137557 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
2137488 CTTTTTGGTG
*
2137498 AGTTGGGGCAACTTGTTGA-TA
1 AGTTGGGGCAGCTTGTT-ACTA
* *
2137519 AGTTGGGGCAGTTTGTTACTG
1 AGTTGGGGCAGCTTGTTACTA
*
2137540 AGTTGGGGCAGCCTGTTA
1 AGTTGGGGCAGCTTGTTA
2137558 AGTTGGGGTA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
20 1 0.03
21 32 0.97
ACGTcount: A:0.18, C:0.12, G:0.37, T:0.33
Consensus pattern (21 bp):
AGTTGGGGCAGCTTGTTACTA
Found at i:2137563 original size:18 final size:18
Alignment explanation
Indices: 2137517--2137565 Score: 53
Period size: 21 Copynumber: 2.6 Consensus size: 18
2137507 AACTTGTTGA
**
2137517 TAAGTTGGGGCAGTTTGT
1 TAAGTTGGGGCAGCCTGT
2137535 TACTGAGTTGGGGCAGCCTGT
1 TA---AGTTGGGGCAGCCTGT
2137556 TAAGTTGGGG
1 TAAGTTGGGG
2137566 TATTTTCTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
18 10 0.38
21 16 0.62
ACGTcount: A:0.16, C:0.10, G:0.41, T:0.33
Consensus pattern (18 bp):
TAAGTTGGGGCAGCCTGT
Found at i:2138534 original size:85 final size:85
Alignment explanation
Indices: 2138386--2138541 Score: 208
Period size: 85 Copynumber: 1.8 Consensus size: 85
2138376 ACAATCACTG
* * * *
2138386 CATGCATATTAAAAAAAACAGTCATACACATACACACACATCTAAAAAATAGCCACTGCATGCAT
1 CATGCATATTAAAAAAAACAGTCATACACATACACACACACCTAAAAAACAGCCAATGAATGCAT
2138451 ATTAAAAAAATAGACAACAA
66 ATTAAAAAAATAGACAACAA
* * * *
2138471 CATGTATATT-AAAAAAA-AGTTATACACATACATACACACACCTAAAAAGCAGTCAATGAATGC
1 CATGCATATTAAAAAAAACAGTCATACACATAC--ACACACACCTAAAAAACAGCCAATGAATGC
2138534 ATATTAAA
64 ATATTAAA
2138542 TAGTCATACA
Statistics
Matches: 61, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
83 13 0.21
84 7 0.11
85 41 0.67
ACGTcount: A:0.52, C:0.19, G:0.08, T:0.21
Consensus pattern (85 bp):
CATGCATATTAAAAAAAACAGTCATACACATACACACACACCTAAAAAACAGCCAATGAATGCAT
ATTAAAAAAATAGACAACAA
Found at i:2138578 original size:63 final size:66
Alignment explanation
Indices: 2138500--2138671 Score: 235
Period size: 63 Copynumber: 2.6 Consensus size: 66
2138490 TTATACACAT
* * *
2138500 ACATACACACACCTAAAAAGCAGTCAATGAATGCATATTAAATAGTCATACACACCAA-AA-AT-
1 ACATACACACCCCTAAAAAACAGTCACTGAATGCATATTAAATAGTCATACACACCAACAACATA
2138562 C
66 C
* * *
2138563 ATATACACACCCCTAAAAAATAGTCACT-AGATGCATATTAAATAGTCATACACACTAACAATCA
1 ACATACACACCCCTAAAAAACAGTCACTGA-ATGCATATTAAATAGTCATACACACCAACAA-CA
2138627 TAC
64 TAC
*
2138630 ACATACACACCCCTAAAAAACAGTCACTGTATGCATATTAAA
1 ACATACACACCCCTAAAAAACAGTCACTGAATGCATATTAAA
2138672 AAGTAGTCAA
Statistics
Matches: 94, Mismatches: 9, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
62 1 0.01
63 50 0.53
64 2 0.02
66 2 0.02
67 39 0.41
ACGTcount: A:0.47, C:0.24, G:0.07, T:0.22
Consensus pattern (66 bp):
ACATACACACCCCTAAAAAACAGTCACTGAATGCATATTAAATAGTCATACACACCAACAACATA
C
Found at i:2141360 original size:39 final size:39
Alignment explanation
Indices: 2141306--2141436 Score: 217
Period size: 39 Copynumber: 3.4 Consensus size: 39
2141296 GCATCGGTCC
*
2141306 TGTCCAGATATATTTCCAGCATATAGCCTGCGGACCTCA
1 TGTCCGGATATATTTCCAGCATATAGCCTGCGGACCTCA
* *
2141345 TGTCCGGATATATTTCCAGCATATAGCTTGCGAACCTCA
1 TGTCCGGATATATTTCCAGCATATAGCCTGCGGACCTCA
* *
2141384 TGTCCGGGTATATTCCCAGCATATAGCCTGCGGACCTCA
1 TGTCCGGATATATTTCCAGCATATAGCCTGCGGACCTCA
2141423 TGTCCGGATATATT
1 TGTCCGGATATATT
2141437 CCCAATATCA
Statistics
Matches: 84, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 84 1.00
ACGTcount: A:0.24, C:0.27, G:0.20, T:0.30
Consensus pattern (39 bp):
TGTCCGGATATATTTCCAGCATATAGCCTGCGGACCTCA
Found at i:2143728 original size:9 final size:9
Alignment explanation
Indices: 2143707--2143750 Score: 61
Period size: 10 Copynumber: 4.6 Consensus size: 9
2143697 TTGTTTTTAA
2143707 TATTTATTTT
1 TATTTA-TTT
2143717 TATTTATTT
1 TATTTATTT
2143726 TATTTATTT
1 TATTTATTT
2143735 TATTTTATTT
1 TA-TTTATTT
2143745 CTATTT
1 -TATTT
2143751 TTGGAAACGG
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
9 14 0.44
10 16 0.50
11 2 0.06
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.77
Consensus pattern (9 bp):
TATTTATTT
Found at i:2143729 original size:5 final size:5
Alignment explanation
Indices: 2143709--2143751 Score: 54
Period size: 5 Copynumber: 8.6 Consensus size: 5
2143699 GTTTTTAATA
2143709 TTTAT TTT-T ATTTAT TTTA- TTTAT TTTAT TTTAT TTCTAT TTT
1 TTTAT TTTAT -TTTAT TTTAT TTTAT TTTAT TTTAT TT-TAT TTT
2143752 TGGAAACGGG
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
4 5 0.15
5 23 0.68
6 6 0.18
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTAT
Found at i:2145571 original size:25 final size:25
Alignment explanation
Indices: 2145542--2145593 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 25
2145532 AAAAATAATT
**
2145542 TGAATATTTGATATTGCCTAATAAA
1 TGAATATCCGATATTGCCTAATAAA
* *
2145567 TGAATATCCGATATTGCTTAGTAAA
1 TGAATATCCGATATTGCCTAATAAA
2145592 TG
1 TG
2145594 TTAAGCCCAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.37, C:0.10, G:0.15, T:0.38
Consensus pattern (25 bp):
TGAATATCCGATATTGCCTAATAAA
Found at i:2148158 original size:61 final size:62
Alignment explanation
Indices: 2148082--2148219 Score: 206
Period size: 63 Copynumber: 2.2 Consensus size: 62
2148072 CCATTTTTGT
* *
2148082 CAGACAATAACCAATAC-AAAATAATTTAATATAAACACAATCATTTCTGTCATGCACATAG
1 CAGACAATAACCAATACAAAAATAATTTAATACAAACACAACCATTTCTGTCATGCACATAG
* * * *
2148143 CAGACAATAATCAATACAAAAAATAATTTAGTACAAGCACAACCATTTCTGTCATGCACATGG
1 CAGACAATAACCAATAC-AAAAATAATTTAATACAAACACAACCATTTCTGTCATGCACATAG
2148206 CAGACAATAACCAA
1 CAGACAATAACCAA
2148220 ACATTTTAAC
Statistics
Matches: 68, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
61 16 0.24
63 52 0.76
ACGTcount: A:0.47, C:0.21, G:0.09, T:0.23
Consensus pattern (62 bp):
CAGACAATAACCAATACAAAAATAATTTAATACAAACACAACCATTTCTGTCATGCACATAG
Found at i:2148585 original size:6 final size:6
Alignment explanation
Indices: 2148534--2148567 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
2148524 CCCTAAATTG
2148534 AAATCA AAATCA AAATCA AAATCA AAATCA AAAT
1 AAATCA AAATCA AAATCA AAATCA AAATCA AAAT
2148568 TAGCATCGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.68, C:0.15, G:0.00, T:0.18
Consensus pattern (6 bp):
AAATCA
Found at i:2148597 original size:18 final size:18
Alignment explanation
Indices: 2148528--2148589 Score: 72
Period size: 18 Copynumber: 3.4 Consensus size: 18
2148518 AAATAACCCT
2148528 AAATTGAAATCAAAATCA
1 AAATTGAAATCAAAATCA
**
2148546 AAATCAAAATCAAAATCA
1 AAATTGAAATCAAAATCA
* *
2148564 AAATT-AGCATCGAAATCA
1 AAATTGA-AATCAAAATCA
2148582 AAATTGAA
1 AAATTGAA
2148590 GTCGAAATAA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
17 1 0.03
18 34 0.94
19 1 0.03
ACGTcount: A:0.60, C:0.13, G:0.06, T:0.21
Consensus pattern (18 bp):
AAATTGAAATCAAAATCA
Found at i:2148614 original size:16 final size:16
Alignment explanation
Indices: 2148593--2148623 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2148583 AATTGAAGTC
*
2148593 GAAATAATCCTAAATT
1 GAAATAACCCTAAATT
2148609 GAAATAACCCTAAAT
1 GAAATAACCCTAAAT
2148624 CCAAAAAATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.16, G:0.06, T:0.26
Consensus pattern (16 bp):
GAAATAACCCTAAATT
Found at i:2154690 original size:44 final size:44
Alignment explanation
Indices: 2154640--2154727 Score: 176
Period size: 44 Copynumber: 2.0 Consensus size: 44
2154630 TCATCAATAA
2154640 AAGTTAGCATATAATTAACTTCACCTCTCGAAGGCACTTTGGAT
1 AAGTTAGCATATAATTAACTTCACCTCTCGAAGGCACTTTGGAT
2154684 AAGTTAGCATATAATTAACTTCACCTCTCGAAGGCACTTTGGAT
1 AAGTTAGCATATAATTAACTTCACCTCTCGAAGGCACTTTGGAT
2154728 GGCCCCCACA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (44 bp):
AAGTTAGCATATAATTAACTTCACCTCTCGAAGGCACTTTGGAT
Found at i:2159876 original size:22 final size:23
Alignment explanation
Indices: 2159834--2159878 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
2159824 ATTGATTTGG
* *
2159834 ATTTTATATTTTTTTATAATTTT
1 ATTTTATATTTCTTTAAAATTTT
2159857 ATTTTAT-TTTCTTTAAAATTTT
1 ATTTTATATTTCTTTAAAATTTT
2159879 TAATATTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (23 bp):
ATTTTATATTTCTTTAAAATTTT
Found at i:2160094 original size:18 final size:18
Alignment explanation
Indices: 2160054--2160095 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
2160044 ATTAAAATTT
2160054 AATTAATTAATTTTATAA
1 AATTAATTAATTTTATAA
*
2160072 TATTAATTAATTTTA-AA
1 AATTAATTAATTTTATAA
2160089 CAATTAA
1 -AATTAA
2160096 CATCAATAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 2 0.10
18 19 0.90
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (18 bp):
AATTAATTAATTTTATAA
Found at i:2162701 original size:43 final size:43
Alignment explanation
Indices: 2162654--2162759 Score: 194
Period size: 43 Copynumber: 2.5 Consensus size: 43
2162644 TTACGCCTGG
*
2162654 TAGGCACGAAGGCCCGAATGCACATCACCGGCACGAAGCCTAC
1 TAGGCACGAAGGCCCGAATACACATCACCGGCACGAAGCCTAC
*
2162697 TAGGCACGAAGGCCCGAATACACATCACCGGCACGAAGCCTGC
1 TAGGCACGAAGGCCCGAATACACATCACCGGCACGAAGCCTAC
2162740 TAGGCACGAAGGCCCGAATA
1 TAGGCACGAAGGCCCGAATA
2162760 TAATACCAGC
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
43 61 1.00
ACGTcount: A:0.31, C:0.33, G:0.26, T:0.09
Consensus pattern (43 bp):
TAGGCACGAAGGCCCGAATACACATCACCGGCACGAAGCCTAC
Found at i:2162800 original size:38 final size:38
Alignment explanation
Indices: 2162757--2162859 Score: 152
Period size: 38 Copynumber: 2.7 Consensus size: 38
2162747 GAAGGCCCGA
* * * *
2162757 ATATAATACCAGCACTAGGCCTGCGGGATTTATCCCTG
1 ATATAATACCAGCACGAAGCCTGCGGGATTTAACCCAG
2162795 ATATAATACCAGCACGAAGCCTGCGGGATTTAACCCAG
1 ATATAATACCAGCACGAAGCCTGCGGGATTTAACCCAG
**
2162833 ATATTTTACCAGCACGAAGCCTGCGGG
1 ATATAATACCAGCACGAAGCCTGCGGG
2162860 TCTTTAAGCC
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
38 59 1.00
ACGTcount: A:0.29, C:0.26, G:0.22, T:0.22
Consensus pattern (38 bp):
ATATAATACCAGCACGAAGCCTGCGGGATTTAACCCAG
Found at i:2164209 original size:23 final size:23
Alignment explanation
Indices: 2164183--2164249 Score: 125
Period size: 23 Copynumber: 2.9 Consensus size: 23
2164173 ACGGATTTCC
2164183 ACCCAAACACACCAGAATATCCA
1 ACCCAAACACACCAGAATATCCA
2164206 ACCCAAACACACCAGAATATCCA
1 ACCCAAACACACCAGAATATCCA
2164229 ACCCAAACACACCCAGAATAT
1 ACCCAAACACA-CCAGAATAT
2164250 TGTAAATCCT
Statistics
Matches: 43, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
23 34 0.79
24 9 0.21
ACGTcount: A:0.48, C:0.39, G:0.04, T:0.09
Consensus pattern (23 bp):
ACCCAAACACACCAGAATATCCA
Found at i:2165706 original size:21 final size:23
Alignment explanation
Indices: 2165682--2165725 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
2165672 AAACCCTATT
*
2165682 TCCCCT-TTTCTT-TCTTTTTTC
1 TCCCCTGTTTCTTCTCTGTTTTC
2165703 TCCCCTGTTTCTTCTCTGTTTTC
1 TCCCCTGTTTCTTCTCTGTTTTC
2165726 GTTTTCATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 6 0.30
22 6 0.30
23 8 0.40
ACGTcount: A:0.00, C:0.34, G:0.05, T:0.61
Consensus pattern (23 bp):
TCCCCTGTTTCTTCTCTGTTTTC
Found at i:2169408 original size:48 final size:48
Alignment explanation
Indices: 2169348--2169450 Score: 118
Period size: 48 Copynumber: 2.1 Consensus size: 48
2169338 GTCCAACTAT
* * * * * *
2169348 GGTCTTATACTAGCTCTGCTCT-GCCCGTGCTGATGCCTATTCCTGATA
1 GGTCTTACACTAGCACT-CACTGGCCCGTGCCGATGCCTATCCCAGATA
* *
2169396 GGTCTTACACTAGCACTCACTGGGCTGTGCCGATGCCTATCCCAGATA
1 GGTCTTACACTAGCACTCACTGGCCCGTGCCGATGCCTATCCCAGATA
2169444 GGTCTTA
1 GGTCTTA
2169451 AGCTTAGCAC
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
47 3 0.07
48 43 0.93
ACGTcount: A:0.17, C:0.29, G:0.22, T:0.31
Consensus pattern (48 bp):
GGTCTTACACTAGCACTCACTGGCCCGTGCCGATGCCTATCCCAGATA
Found at i:2171101 original size:38 final size:38
Alignment explanation
Indices: 2171045--2171145 Score: 121
Period size: 38 Copynumber: 2.7 Consensus size: 38
2171035 GGCACGAAGG
* * *
2171045 CCCAAATATAATACCAGCACTAGGCCTACGGGATTTAA
1 CCCAGATATAATACCAGCACGAAGCCTACGGGATTTAA
**
2171083 CCCAGATATAATACCAGCACGAAGCCTGTGGGATTTAA
1 CCCAGATATAATACCAGCACGAAGCCTACGGGATTTAA
* * **
2171121 CTCGGATATTTTACCAGCACGAAGC
1 CCCAGATATAATACCAGCACGAAGC
2171146 TTGCGGGTCT
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 54 1.00
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.22
Consensus pattern (38 bp):
CCCAGATATAATACCAGCACGAAGCCTACGGGATTTAA
Found at i:2176473 original size:33 final size:33
Alignment explanation
Indices: 2176431--2176496 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
2176421 ATGGATATTG
2176431 AGTTAAATTACAAAATCATTTTGATTTTTTATC
1 AGTTAAATTACAAAATCATTTTGATTTTTTATC
*
2176464 AGTTAAATTACATAATCATTTTGATTTTTTATC
1 AGTTAAATTACAAAATCATTTTGATTTTTTATC
2176497 TCATTTTATG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.35, C:0.09, G:0.06, T:0.50
Consensus pattern (33 bp):
AGTTAAATTACAAAATCATTTTGATTTTTTATC
Found at i:2177018 original size:22 final size:22
Alignment explanation
Indices: 2176990--2177045 Score: 103
Period size: 22 Copynumber: 2.5 Consensus size: 22
2176980 GACTATTAAA
2176990 ATCGTAAAAATACATTTTTATC
1 ATCGTAAAAATACATTTTTATC
2177012 ATCGTAAAAATACATTTTTATC
1 ATCGTAAAAATACATTTTTATC
*
2177034 ATCATAAAAATA
1 ATCGTAAAAATA
2177046 TACAATTTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.46, C:0.12, G:0.04, T:0.38
Consensus pattern (22 bp):
ATCGTAAAAATACATTTTTATC
Found at i:2177470 original size:18 final size:18
Alignment explanation
Indices: 2177427--2177461 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
2177417 GAGAGTAGTT
2177427 GGAAGAGCTTGGATGCAC
1 GGAAGAGCTTGGATGCAC
2177445 GGAAGAGCTTGGATGCA
1 GGAAGAGCTTGGATGCA
2177462 ACGACGAGCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.29, C:0.14, G:0.40, T:0.17
Consensus pattern (18 bp):
GGAAGAGCTTGGATGCAC
Found at i:2178446 original size:19 final size:18
Alignment explanation
Indices: 2178424--2178464 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
2178414 GATTTTATAT
* *
2178424 TTTTTAAATATTTTTTTTA
1 TTTTT-AATAATTTATTTA
2178443 TTTTTAATAATTTATTTA
1 TTTTTAATAATTTATTTA
2178461 TTTT
1 TTTT
2178465 GAACAAACAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (18 bp):
TTTTTAATAATTTATTTA
Found at i:2180950 original size:34 final size:34
Alignment explanation
Indices: 2180911--2180981 Score: 142
Period size: 34 Copynumber: 2.1 Consensus size: 34
2180901 GAAAAGTATC
2180911 TTTAGAAATTTTCTAAAATAATTTCTTCAGAGAA
1 TTTAGAAATTTTCTAAAATAATTTCTTCAGAGAA
2180945 TTTAGAAATTTTCTAAAATAATTTCTTCAGAGAA
1 TTTAGAAATTTTCTAAAATAATTTCTTCAGAGAA
2180979 TTT
1 TTT
2180982 TCTCTGTACA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.39, C:0.08, G:0.08, T:0.44
Consensus pattern (34 bp):
TTTAGAAATTTTCTAAAATAATTTCTTCAGAGAA
Found at i:2187568 original size:34 final size:34
Alignment explanation
Indices: 2187529--2187599 Score: 142
Period size: 34 Copynumber: 2.1 Consensus size: 34
2187519 GAAAAGTATC
2187529 TTTAGAAATTTTCTAAAATAATTTCTTCAGAGAA
1 TTTAGAAATTTTCTAAAATAATTTCTTCAGAGAA
2187563 TTTAGAAATTTTCTAAAATAATTTCTTCAGAGAA
1 TTTAGAAATTTTCTAAAATAATTTCTTCAGAGAA
2187597 TTT
1 TTT
2187600 TCTCTGTACA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.39, C:0.08, G:0.08, T:0.44
Consensus pattern (34 bp):
TTTAGAAATTTTCTAAAATAATTTCTTCAGAGAA
Found at i:2193305 original size:42 final size:42
Alignment explanation
Indices: 2193259--2193346 Score: 167
Period size: 42 Copynumber: 2.1 Consensus size: 42
2193249 AATAATTTAT
2193259 TTTACTTTGTGGTTGATTTGACATGTATTTGTATTTTTATAC
1 TTTACTTTGTGGTTGATTTGACATGTATTTGTATTTTTATAC
*
2193301 TTTACTTTGTGGTTGTTTTGACATGTATTTGTATTTTTATAC
1 TTTACTTTGTGGTTGATTTGACATGTATTTGTATTTTTATAC
2193343 TTTA
1 TTTA
2193347 ATTTTATCGT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.18, C:0.07, G:0.16, T:0.59
Consensus pattern (42 bp):
TTTACTTTGTGGTTGATTTGACATGTATTTGTATTTTTATAC
Found at i:2205816 original size:36 final size:37
Alignment explanation
Indices: 2205776--2205856 Score: 119
Period size: 37 Copynumber: 2.2 Consensus size: 37
2205766 GTGATATGAT
* **
2205776 GAGTACATCTGTGTTGAAAT-CCTCCAAATGATTAAA
1 GAGTACATCTATAATGAAATACCTCCAAATGATTAAA
*
2205812 GAGTACATCTATAATGAAATACCTTCAAATGATTAAA
1 GAGTACATCTATAATGAAATACCTCCAAATGATTAAA
2205849 GAGTACAT
1 GAGTACAT
2205857 ATATGCTTAT
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
36 17 0.43
37 23 0.57
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (37 bp):
GAGTACATCTATAATGAAATACCTCCAAATGATTAAA
Found at i:2208502 original size:35 final size:35
Alignment explanation
Indices: 2208456--2208526 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
2208446 CTTATTTCTT
2208456 ACAAAATTACTAAACACCAATCCCATTTGGTTAAA
1 ACAAAATTACTAAACACCAATCCCATTTGGTTAAA
2208491 ACAAAATTACTAAACACCAATCCCATTTGGTTAAA
1 ACAAAATTACTAAACACCAATCCCATTTGGTTAAA
2208526 A
1 A
2208527 ATGATCCCAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.46, C:0.23, G:0.06, T:0.25
Consensus pattern (35 bp):
ACAAAATTACTAAACACCAATCCCATTTGGTTAAA
Found at i:2216039 original size:15 final size:15
Alignment explanation
Indices: 2216019--2216051 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
2216009 GTTTATGATT
2216019 TGACTCCATTACTCA
1 TGACTCCATTACTCA
*
2216034 TGACTCCATTGCTCA
1 TGACTCCATTACTCA
2216049 TGA
1 TGA
2216052 ATTAACCTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.24, C:0.30, G:0.12, T:0.33
Consensus pattern (15 bp):
TGACTCCATTACTCA
Found at i:2221514 original size:15 final size:16
Alignment explanation
Indices: 2221494--2221531 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
2221484 TATACGAATG
*
2221494 AATTTAACTCA-ATTT
1 AATTTAACTCATATTC
*
2221509 AATTTAATTCATATTC
1 AATTTAACTCATATTC
2221525 AATTTAA
1 AATTTAA
2221532 TCGAACACAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.42, C:0.11, G:0.00, T:0.47
Consensus pattern (16 bp):
AATTTAACTCATATTC
Found at i:2221530 original size:16 final size:15
Alignment explanation
Indices: 2221494--2221532 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
2221484 TATACGAATG
* *
2221494 AATTTAACTCAATTT
1 AATTTAATTCAATTC
2221509 AATTTAATTCATATTC
1 AATTTAATTCA-ATTC
2221525 AATTTAAT
1 AATTTAAT
2221533 CGAACACACA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 10 0.48
16 11 0.52
ACGTcount: A:0.41, C:0.10, G:0.00, T:0.49
Consensus pattern (15 bp):
AATTTAATTCAATTC
Found at i:2228731 original size:25 final size:25
Alignment explanation
Indices: 2228702--2228763 Score: 81
Period size: 25 Copynumber: 2.5 Consensus size: 25
2228692 TACGAGCTTT
* *
2228702 GTATCGGGAAGCTCTTGCA-AGCCAA
1 GTATCAGGAAGCTCATG-AGAGCCAA
*
2228727 TTATCAGGAAGCTCATGAGAGCCAA
1 GTATCAGGAAGCTCATGAGAGCCAA
2228752 GTATCAGGAAGC
1 GTATCAGGAAGC
2228764 GCAAGAGAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
24 1 0.03
25 31 0.97
ACGTcount: A:0.32, C:0.21, G:0.27, T:0.19
Consensus pattern (25 bp):
GTATCAGGAAGCTCATGAGAGCCAA
Found at i:2228771 original size:25 final size:25
Alignment explanation
Indices: 2228721--2228771 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
2228711 AGCTCTTGCA
* * *
2228721 AGCCAATTATCAGGAAGCTCATGAG
1 AGCCAAGTATCAGGAAGCGCAAGAG
2228746 AGCCAAGTATCAGGAAGCGCAAGAG
1 AGCCAAGTATCAGGAAGCGCAAGAG
2228771 A
1 A
2228772 ACTGTGGTCT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.39, C:0.20, G:0.27, T:0.14
Consensus pattern (25 bp):
AGCCAAGTATCAGGAAGCGCAAGAG
Found at i:2231688 original size:61 final size:60
Alignment explanation
Indices: 2231612--2231764 Score: 181
Period size: 60 Copynumber: 2.5 Consensus size: 60
2231602 CCTATTCAGA
* * *
2231612 AATCAGAGT-TAACTGGGCCTTAGCCCATATCAATATTAATCTGGGCCATAGCCC-CTTAC
1 AATCAGAGTAT-ACTGGGCCTTAGCCCATATCAATATCAATCTGGGCAATAGCCCTATTAC
*
2231671 AGTATCAGAGTATACTGGGCC-TAGCCCATATCAATATCAATCTTGGCAATAGCCCTATTAC
1 A--ATCAGAGTATACTGGGCCTTAGCCCATATCAATATCAATCTGGGCAATAGCCCTATTAC
*
2231732 AAGTC-GAGATATATTGGGCCTT-GCCCATATCAA
1 AA-TCAGAG-TATACTGGGCCTTAGCCCATATCAA
2231765 CACAGTTGGG
Statistics
Matches: 82, Mismatches: 5, Indels: 13
0.82 0.05 0.13
Matches are distributed among these distances:
59 5 0.06
60 54 0.66
61 22 0.27
62 1 0.01
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.27
Consensus pattern (60 bp):
AATCAGAGTATACTGGGCCTTAGCCCATATCAATATCAATCTGGGCAATAGCCCTATTAC
Found at i:2233934 original size:21 final size:18
Alignment explanation
Indices: 2233907--2233956 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 18
2233897 AACTTATCTC
*
2233907 TTTCTTTCTTCTCTCATTTT
1 TTTCTTTCTTCTC-C-TTCT
2233927 TTCTCTTTCTTCTCCTTCT
1 TT-TCTTTCTTCTCCTTCT
2233946 TTTCTTTCTTC
1 TTTCTTTCTTC
2233957 CTTTCCTTCT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 9 0.32
19 5 0.18
20 3 0.11
21 11 0.39
ACGTcount: A:0.02, C:0.30, G:0.00, T:0.68
Consensus pattern (18 bp):
TTTCTTTCTTCTCCTTCT
Found at i:2233945 original size:9 final size:9
Alignment explanation
Indices: 2233903--2233966 Score: 55
Period size: 9 Copynumber: 7.3 Consensus size: 9
2233893 CCGGAACTTA
2233903 TCTCTTTCT
1 TCTCTTTCT
2233912 T-TC-TTC-
1 TCTCTTTCT
*
2233918 TCTCATTTTT
1 TCTC-TTTCT
2233928 TCTCTTTCT
1 TCTCTTTCT
*
2233937 TCTCCTTCT
1 TCTCTTTCT
*
2233946 TTTCTTTCT
1 TCTCTTTCT
2233955 TC-CTTTCCT
1 TCTCTTT-CT
2233964 TCT
1 TCT
2233967 TGGCCTTCTC
Statistics
Matches: 43, Mismatches: 6, Indels: 11
0.72 0.10 0.18
Matches are distributed among these distances:
6 1 0.02
7 5 0.12
8 6 0.14
9 27 0.63
10 4 0.09
ACGTcount: A:0.02, C:0.33, G:0.00, T:0.66
Consensus pattern (9 bp):
TCTCTTTCT
Found at i:2233963 original size:21 final size:20
Alignment explanation
Indices: 2233907--2233967 Score: 63
Period size: 19 Copynumber: 3.0 Consensus size: 20
2233897 AACTTATCTC
* *
2233907 TTTCTTTCTTCTCTCATT-T
1 TTTCTTTCTTCTTTCCTTCT
*
2233926 TTTCTCT-TTCTTCTCCTTCT
1 TTTCTTTCTTCTT-TCCTTCT
2233946 TTTCTTTCTTCCTTTCCTTCT
1 TTTCTTTCTT-CTTTCCTTCT
2233967 T
1 T
2233968 GGCCTTCTCT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
18 4 0.12
19 10 0.29
20 7 0.21
21 10 0.29
22 3 0.09
ACGTcount: A:0.02, C:0.31, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTCTTTCTTCTTTCCTTCT
Found at i:2236283 original size:46 final size:46
Alignment explanation
Indices: 2236233--2236332 Score: 130
Period size: 46 Copynumber: 2.2 Consensus size: 46
2236223 CGAGGGCTAT
* * *
2236233 TGTAAGACATGTTTGGGATAT-GCATCGACCTCGAGATGTAAGCCAG
1 TGTAAGACATGTCTGGGACATGGCATCGA-CTCGAGATATAAGCCAG
* *
2236279 TGTAAGACATGTCTGGGACATGGCATCGACTTGAGATATGAGCCAG
1 TGTAAGACATGTCTGGGACATGGCATCGACTCGAGATATAAGCCAG
*
2236325 TTTAAGAC
1 TGTAAGAC
2236333 CGTATCTAAG
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
46 40 0.85
47 7 0.15
ACGTcount: A:0.29, C:0.17, G:0.28, T:0.26
Consensus pattern (46 bp):
TGTAAGACATGTCTGGGACATGGCATCGACTCGAGATATAAGCCAG
Found at i:2241846 original size:24 final size:24
Alignment explanation
Indices: 2241814--2241860 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
2241804 TCCTTTTATA
2241814 CTTAAT-AAATAAATAATAAAATAT
1 CTTAATAAAAT-AATAATAAAATAT
* *
2241838 CTTATTAAAATATTAATAAAATA
1 CTTAATAAAATAATAATAAAATA
2241861 ATATTTATCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (24 bp):
CTTAATAAAATAATAATAAAATAT
Found at i:2241859 original size:11 final size:12
Alignment explanation
Indices: 2241811--2241860 Score: 50
Period size: 11 Copynumber: 4.2 Consensus size: 12
2241801 CCTTCCTTTT
2241811 ATACTTAAT-AA
1 ATACTTAATAAA
**
2241822 ATAAATAATAAA
1 ATACTTAATAAA
*
2241834 ATATCTTATTAAA
1 ATA-CTTAATAAA
2241847 ATA-TTAATAAA
1 ATACTTAATAAA
2241858 ATA
1 ATA
2241861 ATATTTATCT
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
11 17 0.55
12 5 0.16
13 9 0.29
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (12 bp):
ATACTTAATAAA
Found at i:2242702 original size:29 final size:30
Alignment explanation
Indices: 2242646--2242702 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 30
2242636 TTGGGCCTTC
* * **
2242646 CCACACGGGCTGGGCACATGGCTGTGTGAG
1 CCACACAGGCTGGCCACATGGCCATGTGAG
2242676 CCACACAGGCT-GCCACATGGCCATGTG
1 CCACACAGGCTGGCCACATGGCCATGTG
2242703 CTACATCGTG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
29 13 0.57
30 10 0.43
ACGTcount: A:0.19, C:0.32, G:0.33, T:0.16
Consensus pattern (30 bp):
CCACACAGGCTGGCCACATGGCCATGTGAG
Found at i:2244719 original size:15 final size:15
Alignment explanation
Indices: 2244695--2244725 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2244685 ATGGCAAATT
2244695 TCACTGTACTAAGGA
1 TCACTGTACTAAGGA
*
2244710 TCACTTTACTAAGGA
1 TCACTGTACTAAGGA
2244725 T
1 T
2244726 TTTCATGGAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.32
Consensus pattern (15 bp):
TCACTGTACTAAGGA
Found at i:2245053 original size:21 final size:21
Alignment explanation
Indices: 2245027--2245073 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
2245017 CCATAAGTGA
*
2245027 ACTCGGAGTCAACTCAACGAG
1 ACTCGGACTCAACTCAACGAG
2245048 ACTCGGACTCAACTCAACGAG
1 ACTCGGACTCAACTCAACGAG
2245069 -CTCGG
1 ACTCGG
2245074 GCGTTCGCAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
20 5 0.20
21 20 0.80
ACGTcount: A:0.30, C:0.32, G:0.23, T:0.15
Consensus pattern (21 bp):
ACTCGGACTCAACTCAACGAG
Found at i:2245094 original size:67 final size:67
Alignment explanation
Indices: 2244981--2245114 Score: 241
Period size: 67 Copynumber: 2.0 Consensus size: 67
2244971 CCATAAGTGA
*
2244981 ACTCAGACTCAAATCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGAGTCAACTCAACG
1 ACTCAGACTCAAATCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAACG
2245046 AG
66 AG
* *
2245048 ACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAACG
1 ACTCAGACTCAAATCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAACG
2245113 AG
66 AG
2245115 TTCGGATGCT
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
67 64 1.00
ACGTcount: A:0.30, C:0.30, G:0.22, T:0.18
Consensus pattern (67 bp):
ACTCAGACTCAAATCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAACG
AG
Found at i:2245588 original size:30 final size:30
Alignment explanation
Indices: 2245552--2245612 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
2245542 CATTTAATAC
* *
2245552 AAACTTTGGCAAAATTATATTTTTGCCCCT
1 AAACTTTGGCAAAATTACACTTTTGCCCCT
* *
2245582 AAACTTTTGCATAATTACACTTTTGCCCCT
1 AAACTTTGGCAAAATTACACTTTTGCCCCT
2245612 A
1 A
2245613 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.23, G:0.08, T:0.39
Consensus pattern (30 bp):
AAACTTTGGCAAAATTACACTTTTGCCCCT
Found at i:2251651 original size:17 final size:17
Alignment explanation
Indices: 2251626--2251667 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
2251616 ATATTTTCAA
*
2251626 AATATTTATAACAT-TCC
1 AATAGTTATAA-ATGTCC
2251643 AATAGTTATAAATGTCC
1 AATAGTTATAAATGTCC
*
2251660 AAAAGTTA
1 AATAGTTA
2251668 CTCATTTAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 2 0.09
17 20 0.91
ACGTcount: A:0.45, C:0.12, G:0.07, T:0.36
Consensus pattern (17 bp):
AATAGTTATAAATGTCC
Found at i:2254486 original size:21 final size:21
Alignment explanation
Indices: 2254447--2254487 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 21
2254437 TCAAGTTATC
2254447 AATTAAAAACTAAAATGAACTA
1 AATTAAAAACT-AAATGAACTA
2254469 AATTAAATAACT-AATGAAC
1 AATTAAA-AACTAAATGAAC
2254488 ACGACAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 7 0.39
22 7 0.39
23 4 0.22
ACGTcount: A:0.61, C:0.10, G:0.05, T:0.24
Consensus pattern (21 bp):
AATTAAAAACTAAATGAACTA
Found at i:2255719 original size:4 final size:4
Alignment explanation
Indices: 2255710--2255735 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
2255700 ATGGATTAAT
2255710 ATAA ATAA ATAA ATAA ATAA ATAA AT
1 ATAA ATAA ATAA ATAA ATAA ATAA AT
2255736 TAAGCCCTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (4 bp):
ATAA
Found at i:2259434 original size:21 final size:22
Alignment explanation
Indices: 2259408--2259448 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
2259398 GACTAAACCA
*
2259408 AAAAATTG-AAAAAGATTTATT
1 AAAAATAGTAAAAAGATTTATT
*
2259429 AAAAATAGTAAAAATATTTA
1 AAAAATAGTAAAAAGATTTA
2259449 AATTATTTAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.61, C:0.00, G:0.07, T:0.32
Consensus pattern (22 bp):
AAAAATAGTAAAAAGATTTATT
Found at i:2259471 original size:9 final size:9
Alignment explanation
Indices: 2259425--2259589 Score: 50
Period size: 9 Copynumber: 17.1 Consensus size: 9
2259415 GAAAAAGATT
2259425 TATTAAAAA
1 TATTAAAAA
*
2259434 TAGTAAAAA
1 TATTAAAAA
* *
2259443 TATTTAAAT
1 TATTAAAAA
*
2259452 TATTTAGAAA
1 TA-TTAAAAA
2259462 TATTAAAAA
1 TATTAAAAA
2259471 T-TGTAAAAAAA
1 TAT-T--AAAAA
2259482 TATTGTAAAAAA
1 TA-T-T-AAAAA
*
2259494 TTATTAAATA
1 -TATTAAAAA
* * *
2259504 TTTTTAAAT
1 TATTAAAAA
* *
2259513 TGTAAAAAAA
1 TAT-TAAAAA
*
2259523 TTATTAAAAT
1 -TATTAAAAA
*
2259533 TATAAAAAA
1 TATTAAAAA
*
2259542 T-TTAAAAG
1 TATTAAAAA
2259550 T-TGTAAAAA
1 TAT-TAAAAA
2259559 TTATTAAAAA
1 -TATTAAAAA
2259569 T-TGTAAAAA
1 TAT-TAAAAA
2259578 TTATTTAAAAA
1 -TA-TTAAAAA
2259589 T
1 T
2259590 TGAAAATAAA
Statistics
Matches: 115, Mismatches: 25, Indels: 31
0.67 0.15 0.18
Matches are distributed among these distances:
8 9 0.08
9 51 0.44
10 26 0.23
11 16 0.14
12 8 0.07
13 5 0.04
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (9 bp):
TATTAAAAA
Found at i:2259482 original size:20 final size:19
Alignment explanation
Indices: 2259425--2259623 Score: 133
Period size: 20 Copynumber: 10.3 Consensus size: 19
2259415 GAAAAAGATT
*
2259425 TATTAAAAATAGT-AAAAA
1 TATTAAAAATTGTAAAAAA
* *
2259443 TATTTAAATTATT-T-AGAAA
1 TA-TTAAA-AATTGTAAAAAA
2259462 TATTAAAAATTGTAAAAAAA
1 TATTAAAAATTGT-AAAAAA
* **
2259482 TATTGTAAAAAAT-TATTAAA
1 TA-T-TAAAAATTGTAAAAAA
**
2259502 TATTTTTAAATTGTAAAAAA
1 TA-TTAAAAATTGTAAAAAA
*
2259522 -ATTATTAAAATTATAAAAAA
1 TATTA--AAAATTGTAAAAAA
* *
2259542 T-TTAAAAGTTGTAAAAAT
1 TATTAAAAATTGTAAAAAA
*
2259560 TATTAAAAATTGTAAAAAT
1 TATTAAAAATTGTAAAAAA
*
2259579 TATTTAAAAATTGAAAATAAA
1 TA-TTAAAAATTGTAAA-AAA
2259600 TATTAAAAAATTGTAAAAAA
1 TATT-AAAAATTGTAAAAAA
2259620 -ATTA
1 TATTA
2259624 TTTAATCAGA
Statistics
Matches: 143, Mismatches: 23, Indels: 30
0.73 0.12 0.15
Matches are distributed among these distances:
17 3 0.02
18 23 0.16
19 39 0.27
20 54 0.38
21 17 0.12
22 7 0.05
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.37
Consensus pattern (19 bp):
TATTAAAAATTGTAAAAAA
Found at i:2259491 original size:12 final size:13
Alignment explanation
Indices: 2259466--2259498 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
2259456 TAGAAATATT
2259466 AAAA-ATTGTAAA
1 AAAATATTGTAAA
2259478 AAAATATTGTAAA
1 AAAATATTGTAAA
*
2259491 AAATTATT
1 AAAATATT
2259499 AAATATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (13 bp):
AAAATATTGTAAA
Found at i:2259547 original size:29 final size:29
Alignment explanation
Indices: 2259478--2259548 Score: 76
Period size: 29 Copynumber: 2.4 Consensus size: 29
2259468 AAATTGTAAA
2259478 AAAATATTGT-AAAAAATTATTAAATATTT
1 AAAA-ATTGTAAAAAAATTATTAAATATTT
**
2259507 TTAAATTGTAAAAAAATTATTAAA-ATTAT
1 AAAAATTGTAAAAAAATTATTAAATATT-T
2259536 AAAAAATT-TAAAA
1 -AAAAATTGTAAAA
2259549 GTTGTAAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
28 8 0.23
29 22 0.63
30 5 0.14
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (29 bp):
AAAAATTGTAAAAAAATTATTAAATATTT
Found at i:2259600 original size:98 final size:98
Alignment explanation
Indices: 2259407--2259625 Score: 245
Period size: 98 Copynumber: 2.2 Consensus size: 98
2259397 TGACTAAACC
* *
2259407 AAAAAATTG-AAAAAGATTTATTAAAAATAGTAAAAATATTTAAATTATTTAGAAATATTAAAAA
1 AAAAAATTGTAAAAA-AATTATTAAAAATAGTAAAAATATTTAAA-TATTTAAAAATATTAAAAA
*
2259471 TTGTAAAAAAATATTGTAAAAAATTATTAAATATT
64 TTGTAAAAAAATATTGTAAAAAATTAATAAATATT
*** *
2259506 TTTAAATTGTAAAAAAATTATTAAAATTA-TAAAAA-ATTTAAA-AGTTGTAAAAATTATTAAAA
1 AAAAAATTGTAAAAAAATTATTAAAAATAGTAAAAATATTTAAATA-TT-TAAAAA-TATTAAAA
*
2259568 ATTGT-AAAAATTATT-T-AAAAATTGAAAATAAATATT
63 ATTGTAAAAAAATATTGTAAAAAATT---AATAAATATT
2259604 AAAAAATTGTAAAAAAATTATT
1 AAAAAATTGTAAAAAAATTATT
2259626 TAATCAGAAA
Statistics
Matches: 102, Mismatches: 11, Indels: 15
0.80 0.09 0.12
Matches are distributed among these distances:
95 8 0.08
96 3 0.03
97 21 0.21
98 47 0.46
99 18 0.18
100 5 0.05
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.36
Consensus pattern (98 bp):
AAAAAATTGTAAAAAAATTATTAAAAATAGTAAAAATATTTAAATATTTAAAAATATTAAAAATT
GTAAAAAAATATTGTAAAAAATTAATAAATATT
Found at i:2259623 original size:19 final size:19
Alignment explanation
Indices: 2259509--2259623 Score: 99
Period size: 19 Copynumber: 5.9 Consensus size: 19
2259499 AAATATTTTT
*
2259509 AAATTGTAAAAAAATTATTA
1 AAATTGTAAAAAAATTA-AA
* *
2259529 AAATTAT-AAAAAATTTAA
1 AAATTGTAAAAAAATTAAA
* *
2259547 AAGTTGTAAAAATTATT-AA
1 AAATTGTAAAAA-AATTAAA
* *
2259566 AAATTGTAAAAATTATTTAA
1 AAATTGTAAAAA-AATTAAA
*
2259586 AAATTGAAAATAAATATTAAA
1 AAATTGTAAA-AAA-ATTAAA
2259607 AAATTGTAAAAAAATTA
1 AAATTGTAAAAAAATTA
2259624 TTTAATCAGA
Statistics
Matches: 79, Mismatches: 11, Indels: 11
0.78 0.11 0.11
Matches are distributed among these distances:
18 6 0.08
19 34 0.43
20 23 0.29
21 16 0.20
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (19 bp):
AAATTGTAAAAAAATTAAA
Found at i:2259695 original size:20 final size:19
Alignment explanation
Indices: 2259672--2259741 Score: 61
Period size: 21 Copynumber: 3.5 Consensus size: 19
2259662 CTGTTGTTAC
2259672 TAATTTTTAACAAATTTAA
1 TAATTTTTAACAAATTTAA
*
2259691 GTAATTTTTTTACAAATTTAA
1 -TAA-TTTTTAACAAATTTAA
* *
2259712 -ATTTTTTTGACAATATTTAA
1 TA-ATTTTTAACAA-ATTTAA
2259732 TAATTATTTA
1 TAATT-TTTA
2259742 CAATTTTTAA
Statistics
Matches: 40, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
19 10 0.25
20 11 0.28
21 19 0.47
ACGTcount: A:0.40, C:0.04, G:0.03, T:0.53
Consensus pattern (19 bp):
TAATTTTTAACAAATTTAA
Found at i:2259705 original size:21 final size:20
Alignment explanation
Indices: 2259675--2259736 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 20
2259665 TTGTTACTAA
*
2259675 TTTTTAACAAATTTAAGTAAT
1 TTTTTTACAAATTTAA-TAAT
2259696 TTTTTTACAAATTT-A-AAT
1 TTTTTTACAAATTTAATAAT
2259714 TTTTTTGACAATATTTAATAAT
1 TTTTTT-ACAA-ATTTAATAAT
2259736 T
1 T
2259737 ATTTACAATT
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
18 9 0.25
19 4 0.11
20 5 0.14
21 14 0.39
22 4 0.11
ACGTcount: A:0.39, C:0.05, G:0.03, T:0.53
Consensus pattern (20 bp):
TTTTTTACAAATTTAATAAT
Found at i:2259716 original size:18 final size:20
Alignment explanation
Indices: 2259693--2259731 Score: 64
Period size: 18 Copynumber: 2.0 Consensus size: 20
2259683 AAATTTAAGT
2259693 AATTTTTTT-ACAA-ATTTA
1 AATTTTTTTGACAATATTTA
2259711 AATTTTTTTGACAATATTTA
1 AATTTTTTTGACAATATTTA
2259731 A
1 A
2259732 TAATTATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 9 0.47
19 4 0.21
20 6 0.32
ACGTcount: A:0.38, C:0.05, G:0.03, T:0.54
Consensus pattern (20 bp):
AATTTTTTTGACAATATTTA
Found at i:2259744 original size:20 final size:20
Alignment explanation
Indices: 2259647--2259753 Score: 71
Period size: 20 Copynumber: 5.3 Consensus size: 20
2259637 TTCACAAATT
**
2259647 TTTAATAATTATTTACTGT-
1 TTTAATAATTATTTACAATA
*
2259666 TGTTACTAATT-TTTAACAA-A
1 T-TTAATAATTATTT-ACAATA
*
2259686 TTTAAGTAATTTTTTTACAA-A
1 TTTAA-TAA-TTATTTACAATA
* *
2259707 TTTAA-ATTTTTTTGACAATA
1 TTTAATAATTATTT-ACAATA
*
2259727 TTTAATAATTATTTACAATT
1 TTTAATAATTATTTACAATA
2259747 TTTAATA
1 TTTAATA
2259754 CTTTCAATTT
Statistics
Matches: 71, Mismatches: 8, Indels: 17
0.74 0.08 0.18
Matches are distributed among these distances:
18 6 0.08
19 12 0.17
20 32 0.45
21 18 0.25
22 3 0.04
ACGTcount: A:0.37, C:0.06, G:0.04, T:0.53
Consensus pattern (20 bp):
TTTAATAATTATTTACAATA
Found at i:2259795 original size:19 final size:19
Alignment explanation
Indices: 2259744--2259795 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 19
2259734 ATTATTTACA
* *
2259744 ATTTTTAAT-ACTTTCAAT
1 ATTTTTTATAACTTTTAAT
* *
2259762 -TTTTTTACAATTTTTAAT
1 ATTTTTTATAACTTTTAAT
2259780 ATTTTTTATAACTTTT
1 ATTTTTTATAACTTTT
2259796 TTACAAATTT
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
17 6 0.23
18 7 0.27
19 13 0.50
ACGTcount: A:0.29, C:0.08, G:0.00, T:0.63
Consensus pattern (19 bp):
ATTTTTTATAACTTTTAAT
Found at i:2261312 original size:51 final size:52
Alignment explanation
Indices: 2261217--2261314 Score: 137
Period size: 51 Copynumber: 1.9 Consensus size: 52
2261207 GATAGAAATG
** *
2261217 ATGAAAATGGAGAAAAGAGAAATATTTGGAAATGATTATGGTTTTCTTTAAA
1 ATGAAAATGGAGAAAAGAGAAATATTTAAAAATGAATATGGTTTTCTTTAAA
*
2261269 ATGAAAATGGAG-AAATAG-AATCATTTAAAAATGAATATGGTTTTCT
1 ATGAAAATGGAGAAAAGAGAAAT-ATTTAAAAATGAATATGGTTTTCT
2261315 GCTGAAAATG
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
50 3 0.07
51 26 0.63
52 12 0.29
ACGTcount: A:0.45, C:0.03, G:0.19, T:0.33
Consensus pattern (52 bp):
ATGAAAATGGAGAAAAGAGAAATATTTAAAAATGAATATGGTTTTCTTTAAA
Found at i:2266836 original size:47 final size:47
Alignment explanation
Indices: 2266767--2266862 Score: 183
Period size: 47 Copynumber: 2.0 Consensus size: 47
2266757 AAGAGTATTC
*
2266767 CGTATTTAGGTTAAATGAGAAAAATCGAAACTCAGTAAGTTAGGGCA
1 CGTATTTAGGTTAAATAAGAAAAATCGAAACTCAGTAAGTTAGGGCA
2266814 CGTATTTAGGTTAAATAAGAAAAATCGAAACTCAGTAAGTTAGGGCA
1 CGTATTTAGGTTAAATAAGAAAAATCGAAACTCAGTAAGTTAGGGCA
2266861 CG
1 CG
2266863 ATTGTCTCGA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.41, C:0.11, G:0.23, T:0.25
Consensus pattern (47 bp):
CGTATTTAGGTTAAATAAGAAAAATCGAAACTCAGTAAGTTAGGGCA
Found at i:2267629 original size:3 final size:3
Alignment explanation
Indices: 2267621--2268408 Score: 185
Period size: 3 Copynumber: 259.0 Consensus size: 3
2267611 GTAAATATTG
2267621 ATA 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 ATA
* * * * * *
2267669 AAA AGTA GAGCA ACAA ATA ATA ATA ATA CGTTA ATA AAA ATA ATA AGA
1 ATA A-TA -A-TA A-TA ATA ATA ATA ATA --ATA ATA ATA ATA ATA ATA
* * * * *
2267717 AT- ATG TTA GTA ATA ATA A-A TTA ATGGA CTA ATA ATA A-A ATGA ATAA
1 ATA ATA ATA ATA ATA ATA ATA ATA AT--A ATA ATA ATA ATA AT-A AT-A
* * * * ** *
2267763 ATAA ATA A-A CACA AAA ATA A-A GT- ATA ATT ATA ATA GCA ATA TTA
1 AT-A ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * * * *
2267807 ACA A-A A-A AGA GTC ATA ATA ATA ATA ACA ATA ATA ATA ATG ATA ACA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2267853 ATA 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 ATA
* * ** * * * * * * * *
2267901 ATA GTA GTA GCA ATA ATT TTGA AAA ACA GTA AGGTA ATA A-G ATG GTA
1 ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA A--TA ATA ATA ATA ATA
* * * * *
2267948 ATA ATA A-A A-A AGGA ATA ACA AT- ATG TTA GATA GTA AGTA ATA A-A
1 ATA ATA ATA ATA A-TA ATA ATA ATA ATA ATA -ATA ATA A-TA ATA ATA
* * * * *
2267992 A-A ATA ATA ACA ATA ATA A-A A-A ATG ATA ATA GTG A-A ATA CCT-
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA
* * ** *
2268033 ATA ACA ATA TATA CTA ATA ATA GCA ATA AT- ATGA AGA ATGA GA-A ATA
1 ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA AT-A ATA AT-A -ATA ATA
* * * * * * * * * * * * * *
2268080 ACA GTA CACGA ACA GTA AGGGA TTG CT- ATG ATA ATG GTAA ATA TTG
1 ATA ATA -A-TA ATA ATA A--TA ATA ATA ATA ATA ATA AT-A ATA ATA
2268126 ATA 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 ATA
* * * * * *
2268174 AAA AGTA GAGCA ACAA ATA ATA ATA ATA CGTTA ATA AAA ATA ATA AGA
1 ATA A-TA -A-TA A-TA ATA ATA ATA ATA --ATA ATA ATA ATA ATA ATA
* * * * *
2268222 AT- ATG TTA GTA ATA ATA A-A TTA ATGGA CTA ATA ATA A-A ATGA ATAA
1 ATA ATA ATA ATA ATA ATA ATA ATA AT--A ATA ATA ATA ATA AT-A AT-A
* * * * ** *
2268268 ATAA ATA A-A CACA AAA ATA A-A GT- ATA ATT ATA ATA GCA ATA TTA
1 AT-A ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * * * * *
2268312 ACA A-A A-A AGA GTC ATA ATA ATA ATA ACA ATA ACA ATA ATG ATA ACA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2268358 ATA 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 ATA
2268406 ATA
1 ATA
2268409 GTGATAACAA
Statistics
Matches: 568, Mismatches: 161, Indels: 112
0.68 0.19 0.13
Matches are distributed among these distances:
2 45 0.08
3 458 0.81
4 45 0.08
5 20 0.04
ACGTcount: A:0.60, C:0.05, G:0.08, T:0.27
Consensus pattern (3 bp):
ATA
Found at i:2267713 original size:23 final size:23
Alignment explanation
Indices: 2267683--2267734 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
2267673 GTAGAGCAAC
*
2267683 AAATAATAATAATACGTTAATAA
1 AAATAATAAGAATACGTTAATAA
* *
2267706 AAATAATAAGAATATGTTAGTAA
1 AAATAATAAGAATACGTTAATAA
*
2267729 TAATAA
1 AAATAA
2267735 ATTAATGGAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.60, C:0.02, G:0.08, T:0.31
Consensus pattern (23 bp):
AAATAATAAGAATACGTTAATAA
Found at i:2267811 original size:34 final size:34
Alignment explanation
Indices: 2267773--2267837 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 34
2267763 ATAAATAAAC
* *
2267773 ACAAAAATAAAGT-ATAATTATAATAGCAATATTA
1 ACAAAAA-AAAGTCATAATAATAATAACAATATTA
*
2267807 ACAAAAAAGAGTCATAATAATAATAACAATA
1 ACAAAAAAAAGTCATAATAATAATAACAATA
2267838 ATAATAATGA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
33 4 0.15
34 23 0.85
ACGTcount: A:0.62, C:0.08, G:0.06, T:0.25
Consensus pattern (34 bp):
ACAAAAAAAAGTCATAATAATAATAACAATATTA
Found at i:2267916 original size:505 final size:505
Alignment explanation
Indices: 2267370--2268410 Score: 2046
Period size: 505 Copynumber: 2.1 Consensus size: 505
2267360 TAATATGTCA
* *
2267370 AATAATAAAAATTAATAATAATAATAATAATAGTAGCAATAATTTTGAAAAACAGTAAGGTAATA
1 AATAATAATAA-TAATAATAATAATAATAGTAGTAGCAATAATTTTGAAAAACAGTAAGGTAATA
2267435 AGATGGTAATAATAAAAAAGGAATAACAATATGTTAGATAGTAAGTAATAAAAAATAATAACAAT
65 AGATGGTAATAATAAAAAAGGAATAACAATATGTTAGATAGTAAGTAATAAAAAATAATAACAAT
2267500 AATAAAAAATGATAATAGTGAAATACCTATAACAATATATACTAATAATAGCAATAATATGAAGA
130 AATAAAAAATGATAATAGTGAAATACCTATAACAATATATACTAATAATAGCAATAATATGAAGA
2267565 ATGAGAAATAACAGTACACGAACAGTAAGGGATTGCTATGATAATGGTAAATATTGATAATAATA
195 ATGAGAAATAACAGTACACGAACAGTAAGGGATTGCTATGATAATGGTAAATATTGATAATAATA
2267630 ATAATAATAATAATAATAATAATAATAATAATAATAATAAAAAGTAGAGCAACAAATAATAATAA
260 ATAATAATAATAATAATAATAATAATAATAATAATAATAAAAAGTAGAGCAACAAATAATAATAA
2267695 TACGTTAATAAAAATAATAAGAATATGTTAGTAATAATAAATTAATGGACTAATAATAAAATGAA
325 TACGTTAATAAAAATAATAAGAATATGTTAGTAATAATAAATTAATGGACTAATAATAAAATGAA
2267760 TAAATAAATAAACACAAAAATAAAGTATAATTATAATAGCAATATTAACAAAAAAGAGTCATAAT
390 TAAATAAATAAACACAAAAATAAAGTATAATTATAATAGCAATATTAACAAAAAAGAGTCATAAT
*
2267825 AATAATAACAATAATAATAATGATAACAATAATAATAATAATAATAATAAT
455 AATAATAACAATAACAATAATGATAACAATAATAATAATAATAATAATAAT
2267876 AATAATAATAATAATAATAATAATAATAGTAGTAGCAATAATTTTGAAAAACAGTAAGGTAATAA
1 AATAATAATAATAATAATAATAATAATAGTAGTAGCAATAATTTTGAAAAACAGTAAGGTAATAA
2267941 GATGGTAATAATAAAAAAGGAATAACAATATGTTAGATAGTAAGTAATAAAAAATAATAACAATA
66 GATGGTAATAATAAAAAAGGAATAACAATATGTTAGATAGTAAGTAATAAAAAATAATAACAATA
2268006 ATAAAAAATGATAATAGTGAAATACCTATAACAATATATACTAATAATAGCAATAATATGAAGAA
131 ATAAAAAATGATAATAGTGAAATACCTATAACAATATATACTAATAATAGCAATAATATGAAGAA
2268071 TGAGAAATAACAGTACACGAACAGTAAGGGATTGCTATGATAATGGTAAATATTGATAATAATAA
196 TGAGAAATAACAGTACACGAACAGTAAGGGATTGCTATGATAATGGTAAATATTGATAATAATAA
2268136 TAATAATAATAATAATAATAATAATAATAATAATAATAAAAAGTAGAGCAACAAATAATAATAAT
261 TAATAATAATAATAATAATAATAATAATAATAATAATAAAAAGTAGAGCAACAAATAATAATAAT
2268201 ACGTTAATAAAAATAATAAGAATATGTTAGTAATAATAAATTAATGGACTAATAATAAAATGAAT
326 ACGTTAATAAAAATAATAAGAATATGTTAGTAATAATAAATTAATGGACTAATAATAAAATGAAT
2268266 AAATAAATAAACACAAAAATAAAGTATAATTATAATAGCAATATTAACAAAAAAGAGTCATAATA
391 AAATAAATAAACACAAAAATAAAGTATAATTATAATAGCAATATTAACAAAAAAGAGTCATAATA
2268331 ATAATAACAATAACAATAATGATAACAATAATAATAATAATAATAATAAT
456 ATAATAACAATAACAATAATGATAACAATAATAATAATAATAATAATAAT
2268381 AATAATAATAATAATAATAATAATAATAGT
1 AATAATAATAATAATAATAATAATAATAGT
2268411 GATAACAACC
Statistics
Matches: 532, Mismatches: 3, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
505 522 0.98
506 10 0.02
ACGTcount: A:0.58, C:0.05, G:0.10, T:0.27
Consensus pattern (505 bp):
AATAATAATAATAATAATAATAATAATAGTAGTAGCAATAATTTTGAAAAACAGTAAGGTAATAA
GATGGTAATAATAAAAAAGGAATAACAATATGTTAGATAGTAAGTAATAAAAAATAATAACAATA
ATAAAAAATGATAATAGTGAAATACCTATAACAATATATACTAATAATAGCAATAATATGAAGAA
TGAGAAATAACAGTACACGAACAGTAAGGGATTGCTATGATAATGGTAAATATTGATAATAATAA
TAATAATAATAATAATAATAATAATAATAATAATAATAAAAAGTAGAGCAACAAATAATAATAAT
ACGTTAATAAAAATAATAAGAATATGTTAGTAATAATAAATTAATGGACTAATAATAAAATGAAT
AAATAAATAAACACAAAAATAAAGTATAATTATAATAGCAATATTAACAAAAAAGAGTCATAATA
ATAATAACAATAACAATAATGATAACAATAATAATAATAATAATAATAAT
Found at i:2268218 original size:23 final size:23
Alignment explanation
Indices: 2268188--2268239 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
2268178 GTAGAGCAAC
*
2268188 AAATAATAATAATACGTTAATAA
1 AAATAATAAGAATACGTTAATAA
* *
2268211 AAATAATAAGAATATGTTAGTAA
1 AAATAATAAGAATACGTTAATAA
*
2268234 TAATAA
1 AAATAA
2268240 ATTAATGGAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.60, C:0.02, G:0.08, T:0.31
Consensus pattern (23 bp):
AAATAATAAGAATACGTTAATAA
Found at i:2268316 original size:34 final size:34
Alignment explanation
Indices: 2268278--2268342 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 34
2268268 ATAAATAAAC
* *
2268278 ACAAAAATAAAGT-ATAATTATAATAGCAATATTA
1 ACAAAAA-AAAGTCATAATAATAATAACAATATTA
*
2268312 ACAAAAAAGAGTCATAATAATAATAACAATA
1 ACAAAAAAAAGTCATAATAATAATAACAATA
2268343 ACAATAATGA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
33 4 0.15
34 23 0.85
ACGTcount: A:0.62, C:0.08, G:0.06, T:0.25
Consensus pattern (34 bp):
ACAAAAAAAAGTCATAATAATAATAACAATATTA
Found at i:2273763 original size:17 final size:14
Alignment explanation
Indices: 2273725--2273751 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2273715 AGTTTCTCCC
2273725 TTTCTTTTTCTTTA
1 TTTCTTTTTCTTTA
2273739 TTTCTTTTTCTTT
1 TTTCTTTTTCTTT
2273752 CCTATTTCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.04, C:0.15, G:0.00, T:0.81
Consensus pattern (14 bp):
TTTCTTTTTCTTTA
Found at i:2273801 original size:9 final size:9
Alignment explanation
Indices: 2273773--2273811 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
2273763 TGCTTATCTG
*
2273773 TTTCTTTTC
1 TTTCTTTTA
*
2273782 TATTGTTTTA
1 T-TTCTTTTA
2273792 TTTCTTTTA
1 TTTCTTTTA
2273801 TTTCTTTTA
1 TTTCTTTTA
2273810 TT
1 TT
2273812 ATTAAACTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
9 19 0.73
10 7 0.27
ACGTcount: A:0.10, C:0.10, G:0.03, T:0.77
Consensus pattern (9 bp):
TTTCTTTTA
Found at i:2276732 original size:24 final size:26
Alignment explanation
Indices: 2276699--2276757 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 26
2276689 CTATATAACG
*
2276699 GGAAGCTCAT-AAG-AGTTATAATCA
1 GGAAGCTCATAAAGAAATTATAATCA
* *
2276723 GGAAGTTCATAAAGAAATTTTAATCA
1 GGAAGCTCATAAAGAAATTATAATCA
2276749 GGAAGCTCA
1 GGAAGCTCA
2276758 CGAAGCTCAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
24 9 0.31
25 3 0.10
26 17 0.59
ACGTcount: A:0.42, C:0.12, G:0.20, T:0.25
Consensus pattern (26 bp):
GGAAGCTCATAAAGAAATTATAATCA
Found at i:2276939 original size:65 final size:65
Alignment explanation
Indices: 2276835--2276958 Score: 203
Period size: 65 Copynumber: 1.9 Consensus size: 65
2276825 ATATTAGGAC
** * *
2276835 TTTGTGTCTGTAATATATGCAGGATCACAACCAATCATATAACAGGACGCTTACAAAGAGCTACG
1 TTTGTGTCTACAATATATGCAGGATCACAACCAATCATATAACAGGACACTCACAAAGAGCTACG
*
2276900 TTTGTGTCTACAATATATGCAGGATCACAACCGATCATATAACAGGACACTCACAAAGA
1 TTTGTGTCTACAATATATGCAGGATCACAACCAATCATATAACAGGACACTCACAAAGA
2276959 ACTATGATAG
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
65 54 1.00
ACGTcount: A:0.37, C:0.21, G:0.17, T:0.25
Consensus pattern (65 bp):
TTTGTGTCTACAATATATGCAGGATCACAACCAATCATATAACAGGACACTCACAAAGAGCTACG
Found at i:2277519 original size:30 final size:30
Alignment explanation
Indices: 2277460--2277520 Score: 72
Period size: 30 Copynumber: 2.0 Consensus size: 30
2277450 TTATTTAATT
2277460 AATTATCATCTTTTATTTTTTTCACTTTCC
1 AATTATCATCTTTTATTTTTTTCACTTTCC
* *
2277490 AATT-TCATCCTTTTCTTTATTTT-ATTTTCC
1 AATTATCAT-CTTTTATTT-TTTTCACTTTCC
2277520 A
1 A
2277521 TGGATGAATC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
29 4 0.15
30 19 0.70
31 4 0.15
ACGTcount: A:0.20, C:0.20, G:0.00, T:0.61
Consensus pattern (30 bp):
AATTATCATCTTTTATTTTTTTCACTTTCC
Found at i:2285200 original size:30 final size:30
Alignment explanation
Indices: 2285156--2285215 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
2285146 ATTATTTAAT
*
2285156 TAATTATCATCTTTTATTTTTTTTACTTTC
1 TAATTATCATCTTTTATTTATTTTACTTTC
* *
2285186 TAATT-TCATCCTTTTCTTTATTTTATTTTC
1 TAATTATCAT-CTTTTATTTATTTTACTTTC
2285216 CATGGATGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 4 0.15
30 22 0.85
ACGTcount: A:0.18, C:0.15, G:0.00, T:0.67
Consensus pattern (30 bp):
TAATTATCATCTTTTATTTATTTTACTTTC
Found at i:2298458 original size:18 final size:18
Alignment explanation
Indices: 2298435--2298480 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
2298425 TGGGCCATGA
*
2298435 TCATGGTCATGGTCACGG
1 TCATGGTCATGATCACGG
*
2298453 TCATGGCCATGATCACGG
1 TCATGGTCATGATCACGG
*
2298471 TCATGCTCAT
1 TCATGGTCAT
2298481 AGCCATAGCC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.20, C:0.26, G:0.26, T:0.28
Consensus pattern (18 bp):
TCATGGTCATGATCACGG
Found at i:2305616 original size:43 final size:43
Alignment explanation
Indices: 2305555--2305638 Score: 132
Period size: 43 Copynumber: 2.0 Consensus size: 43
2305545 CACACACCCA
* * * *
2305555 TGTGGTCAGACCGTGTGGCTTACATGGTCAAGAGACACGCTCT
1 TGTGGTCAAACCATGTGGCTCACACGGTCAAGAGACACGCTCT
2305598 TGTGGTCAAACCATGTGGCTCACACGGTCAAGAGACACGCT
1 TGTGGTCAAACCATGTGGCTCACACGGTCAAGAGACACGCT
2305639 TGTGTTTCAG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.24, C:0.25, G:0.29, T:0.23
Consensus pattern (43 bp):
TGTGGTCAAACCATGTGGCTCACACGGTCAAGAGACACGCTCT
Found at i:2313247 original size:87 final size:87
Alignment explanation
Indices: 2313147--2313320 Score: 321
Period size: 87 Copynumber: 2.0 Consensus size: 87
2313137 TAAACAGAGA
*
2313147 AACAGAAATAATGCCTCTTCAAATGAGCATATATGAAGTCCCTGCACATTGTTTCAGCATTGAAA
1 AACAGAAATAATGCCTCTTCAAATGAGCATATATGAAGTCCCTGCACATTATTTCAGCATTGAAA
*
2313212 AAGAGCCAGATGGACGGCCATG
66 AAGAGCCAGATAGACGGCCATG
*
2313234 AACAGAAATAATGCCTCTTCAAATGAGCATATATGAAGTCCCTGCACATTATTTCAGGATTGAAA
1 AACAGAAATAATGCCTCTTCAAATGAGCATATATGAAGTCCCTGCACATTATTTCAGCATTGAAA
2313299 AAGAGCCAGATAGACGGCCATG
66 AAGAGCCAGATAGACGGCCATG
2313321 GTTCTATGAT
Statistics
Matches: 84, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
87 84 1.00
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.23
Consensus pattern (87 bp):
AACAGAAATAATGCCTCTTCAAATGAGCATATATGAAGTCCCTGCACATTATTTCAGCATTGAAA
AAGAGCCAGATAGACGGCCATG
Found at i:2322550 original size:2 final size:2
Alignment explanation
Indices: 2322545--2322581 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
2322535 GCGTGGAAAA
*
2322545 AC AC AC AC AC AC AC AC AC AC AG AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
2322582 TCCATCACAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.46, G:0.03, T:0.00
Consensus pattern (2 bp):
AC
Found at i:2323954 original size:22 final size:22
Alignment explanation
Indices: 2323929--2323995 Score: 65
Period size: 22 Copynumber: 3.3 Consensus size: 22
2323919 GTGAGATAAA
2323929 GAAATATGAATTGATGGTACAT
1 GAAATATGAATTGATGGTACAT
* *
2323951 G-AA-AT--ATTGA-GATA-AA
1 GAAATATGAATTGATGGTACAT
*
2323967 GAAATATGAGTTGATGGTACAT
1 GAAATATGAATTGATGGTACAT
2323989 GAAATAT
1 GAAATAT
2323996 TGATATAATG
Statistics
Matches: 34, Mismatches: 5, Indels: 12
0.67 0.10 0.24
Matches are distributed among these distances:
16 2 0.06
17 5 0.15
18 7 0.21
20 6 0.18
21 5 0.15
22 9 0.26
ACGTcount: A:0.45, C:0.03, G:0.22, T:0.30
Consensus pattern (22 bp):
GAAATATGAATTGATGGTACAT
Found at i:2323971 original size:38 final size:38
Alignment explanation
Indices: 2323920--2324003 Score: 150
Period size: 38 Copynumber: 2.2 Consensus size: 38
2323910 CCTAATTATG
2323920 TGAGATAAAGAAATATGAATTGATGGTACATGAAATAT
1 TGAGATAAAGAAATATGAATTGATGGTACATGAAATAT
*
2323958 TGAGATAAAGAAATATGAGTTGATGGTACATGAAATAT
1 TGAGATAAAGAAATATGAATTGATGGTACATGAAATAT
*
2323996 TGATATAA
1 TGAGATAA
2324004 TGAATTAACT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
38 44 1.00
ACGTcount: A:0.46, C:0.02, G:0.21, T:0.30
Consensus pattern (38 bp):
TGAGATAAAGAAATATGAATTGATGGTACATGAAATAT
Found at i:2328620 original size:16 final size:15
Alignment explanation
Indices: 2328586--2328630 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 15
2328576 TGTATTTACT
* *
2328586 TATTATTTAAATAAA
1 TATTATTTATATTAA
2328601 TATTATTATATATTAA
1 TATTATT-TATATTAA
2328617 TATTATTTTATATT
1 TATTA-TTTATATT
2328631 GGTTAAATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
15 7 0.27
16 17 0.65
17 2 0.08
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TATTATTTATATTAA
Found at i:2330120 original size:51 final size:53
Alignment explanation
Indices: 2330043--2330161 Score: 179
Period size: 51 Copynumber: 2.3 Consensus size: 53
2330033 AAGTGTCGCT
* *
2330043 TTACTGTTACTGTTCCGGATTAGTTCCGAAGAGGTACTC-TGTACC-TTACTG
1 TTACTGTTACTGTTCCAGATTAGTTCCGAAGAGGTACTCGTGTACCGCTACTG
* *
2330094 TTACTGTTACTGTTCCAGATTTGTTCCGATGAGGTACTCTGTGTACCGCTACTG
1 TTACTGTTACTGTTCCAGATTAGTTCCGAAGAGGTACTC-GTGTACCGCTACTG
2330148 TTACTGTTACTGTT
1 TTACTGTTACTGTT
2330162 ACCATTATGG
Statistics
Matches: 61, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
51 36 0.59
53 6 0.10
54 19 0.31
ACGTcount: A:0.18, C:0.21, G:0.21, T:0.40
Consensus pattern (53 bp):
TTACTGTTACTGTTCCAGATTAGTTCCGAAGAGGTACTCGTGTACCGCTACTG
Found at i:2338104 original size:51 final size:50
Alignment explanation
Indices: 2337962--2338105 Score: 211
Period size: 50 Copynumber: 2.9 Consensus size: 50
2337952 ATACACGGTG
2337962 GCCTTCACATAGTACCATC-CTTGTAG-CCAAAGCTATTTTATTCACAAAGT
1 GCCTTCACATAGTACCA-CACTTGT-GTCCAAAGCTATTTTATTCACAAAGT
* *
2338012 GGCTTCACATAGTACCACACTTGTGTCCAAAGCAATTTTATTCACAAAGT
1 GCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTTTATTCACAAAGT
* *
2338062 AGCCTTCACATAGTACCACACTTGTGTCCAAAGTTATGTTATTC
1 -GCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTTTATTC
2338106 CTAAGGTTCA
Statistics
Matches: 85, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
49 2 0.02
50 44 0.52
51 39 0.46
ACGTcount: A:0.30, C:0.25, G:0.13, T:0.32
Consensus pattern (50 bp):
GCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTTTATTCACAAAGT
Found at i:2338186 original size:52 final size:52
Alignment explanation
Indices: 2338129--2338320 Score: 241
Period size: 52 Copynumber: 3.7 Consensus size: 52
2338119 AAGAAATTTC
*
2338129 TCACTTAGCACCA-TGCCATGGACTTATTTCACTTAGATGCCGTGGACTTATT
1 TCACTTAGCA-CATTGCCATGGACTTATTTCACTTAGATGCCATGGACTTATT
*
2338181 TCACTTAGCACATTGCCATGGACTTATTTCACTTAGATGCCATGGTCTTATT
1 TCACTTAGCACATTGCCATGGACTTATTTCACTTAGATGCCATGGACTTATT
* * *
2338233 TCACTTAGCACATTGCCACGGTCTTATTTTACTTAGCACATTGCCATGGACTTATT
1 TCACTTAGCACATTGCCATGGACTTATTTCACTTAG---A-TGCCATGGACTTATT
* *
2338289 TCACTTAG---A-TGTCATGGTCTTATTTCACTTAG
1 TCACTTAGCACATTGCCATGGACTTATTTCACTTAG
2338321 CCCATTGCTA
Statistics
Matches: 126, Mismatches: 9, Indels: 10
0.87 0.06 0.07
Matches are distributed among these distances:
51 2 0.02
52 100 0.79
53 1 0.01
55 1 0.01
56 22 0.17
ACGTcount: A:0.23, C:0.23, G:0.16, T:0.38
Consensus pattern (52 bp):
TCACTTAGCACATTGCCATGGACTTATTTCACTTAGATGCCATGGACTTATT
Found at i:2338206 original size:28 final size:27
Alignment explanation
Indices: 2338129--2338321 Score: 224
Period size: 28 Copynumber: 7.3 Consensus size: 27
2338119 AAGAAATTTC
2338129 TCACTTAGCACCATGCCATGGACTTATT
1 TCACTTAGCA-CATGCCATGGACTTATT
*
2338157 TCACTTAG---ATGCCGTGGACTTATT
1 TCACTTAGCACATGCCATGGACTTATT
2338181 TCACTTAGCACATTGCCATGGACTTATT
1 TCACTTAGCACA-TGCCATGGACTTATT
*
2338209 TCACTTAG---ATGCCATGGTCTTATT
1 TCACTTAGCACATGCCATGGACTTATT
* *
2338233 TCACTTAGCACATTGCCACGGTCTTATT
1 TCACTTAGCACA-TGCCATGGACTTATT
*
2338261 TTACTTAGCACATTGCCATGGACTTATT
1 TCACTTAGCACA-TGCCATGGACTTATT
* *
2338289 TCACTTAG---ATGTCATGGTCTTATT
1 TCACTTAGCACATGCCATGGACTTATT
2338313 TCACTTAGC
1 TCACTTAGC
2338322 CCATTGCTAT
Statistics
Matches: 146, Mismatches: 10, Indels: 21
0.82 0.06 0.12
Matches are distributed among these distances:
24 66 0.45
25 2 0.01
27 2 0.01
28 76 0.52
ACGTcount: A:0.23, C:0.24, G:0.16, T:0.38
Consensus pattern (27 bp):
TCACTTAGCACATGCCATGGACTTATT
Found at i:2338336 original size:80 final size:80
Alignment explanation
Indices: 2338141--2338328 Score: 285
Period size: 80 Copynumber: 2.4 Consensus size: 80
2338131 ACTTAGCACC
* ** *
2338141 ATGCCATGGACTTATTTCACTTAG---A-TGCCGTGGACTTATTTCACTTAGCACATTGCCATGG
1 ATGCCATGGTCTTATTTCACTTAGCACATTGCCACGGTCTTATTTCACTTAGCACATTGCCATGG
2338202 ACTTATTTCACTTAG
66 ACTTATTTCACTTAG
*
2338217 ATGCCATGGTCTTATTTCACTTAGCACATTGCCACGGTCTTATTTTACTTAGCACATTGCCATGG
1 ATGCCATGGTCTTATTTCACTTAGCACATTGCCACGGTCTTATTTCACTTAGCACATTGCCATGG
2338282 ACTTATTTCACTTAG
66 ACTTATTTCACTTAG
* *
2338297 ATGTCATGGTCTTATTTCACTTAGCCCATTGC
1 ATGCCATGGTCTTATTTCACTTAGCACATTGC
2338329 TATGGTCTAA
Statistics
Matches: 101, Mismatches: 7, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
76 23 0.23
79 1 0.01
80 77 0.76
ACGTcount: A:0.22, C:0.23, G:0.16, T:0.38
Consensus pattern (80 bp):
ATGCCATGGTCTTATTTCACTTAGCACATTGCCACGGTCTTATTTCACTTAGCACATTGCCATGG
ACTTATTTCACTTAG
Found at i:2340715 original size:11 final size:12
Alignment explanation
Indices: 2340701--2340733 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
2340691 ATCTTTTTGC
2340701 TTAGTTTTC-CT
1 TTAGTTTTCTCT
2340712 TTAGTTTTCTCT
1 TTAGTTTTCTCT
*
2340724 TAAGTTTTCT
1 TTAGTTTTCT
2340734 TTCCCATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 9 0.45
12 11 0.55
ACGTcount: A:0.12, C:0.15, G:0.09, T:0.64
Consensus pattern (12 bp):
TTAGTTTTCTCT
Found at i:2346880 original size:60 final size:60
Alignment explanation
Indices: 2346808--2346924 Score: 175
Period size: 60 Copynumber: 1.9 Consensus size: 60
2346798 TAGTCACCTA
* *
2346808 AACTATTAGTAAATTT-TTTATCTGGTCA-TCTAACTATGAAAAGTTACAAAATGGTCATCT
1 AACTATTAGTAAATTTCTTT-TCTGGTAACT-TAACTATGAAAAGTTACAAAATCGTCATCT
*
2346868 AACTATTAGTAAATTTCTTTTTTGGTAACTTAACTATGAAAAGTTACAAAATCGTCA
1 AACTATTAGTAAATTTCTTTTCTGGTAACTTAACTATGAAAAGTTACAAAATCGTCA
2346925 CCCAATTATT
Statistics
Matches: 52, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
60 48 0.92
61 4 0.08
ACGTcount: A:0.38, C:0.13, G:0.11, T:0.38
Consensus pattern (60 bp):
AACTATTAGTAAATTTCTTTTCTGGTAACTTAACTATGAAAAGTTACAAAATCGTCATCT
Found at i:2347200 original size:62 final size:60
Alignment explanation
Indices: 2347126--2347252 Score: 193
Period size: 62 Copynumber: 2.1 Consensus size: 60
2347116 GAATAGTTTA
2347126 GTGACCATTTTGTAACTTTTCATG-GTTGGGTAACCAAAAAAAAGAAATTTACTAATAATTAG
1 GTGACCATTTTGTAACTTTTCA-GAGTTGGGTAACC--AAAAAAGAAATTTACTAATAATTAG
* * *
2347188 GTGACCATTTTGTAGCTTTTCAGAGTTGGGTGACCAAAAAAGAAATTTACTAATATTTAG
1 GTGACCATTTTGTAACTTTTCAGAGTTGGGTAACCAAAAAAGAAATTTACTAATAATTAG
2347248 GTGAC
1 GTGAC
2347253 TACTAGTGTG
Statistics
Matches: 61, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
60 29 0.48
61 1 0.02
62 31 0.51
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.34
Consensus pattern (60 bp):
GTGACCATTTTGTAACTTTTCAGAGTTGGGTAACCAAAAAAGAAATTTACTAATAATTAG
Found at i:2358813 original size:14 final size:14
Alignment explanation
Indices: 2358794--2358826 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
2358784 TGAGGTTGAC
2358794 TCTTTCAAAAGAAG
1 TCTTTCAAAAGAAG
*
2358808 TCTTTCGAAAGAAG
1 TCTTTCAAAAGAAG
2358822 TCTTT
1 TCTTT
2358827 GAAGTGTAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.36
Consensus pattern (14 bp):
TCTTTCAAAAGAAG
Found at i:2363585 original size:17 final size:17
Alignment explanation
Indices: 2363560--2363594 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
2363550 TAATGTTATT
2363560 GACAAAATAACCAAATG
1 GACAAAATAACCAAATG
* *
2363577 GACAGAATAACGAAATG
1 GACAAAATAACCAAATG
2363594 G
1 G
2363595 TTACAAGTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.54, C:0.14, G:0.20, T:0.11
Consensus pattern (17 bp):
GACAAAATAACCAAATG
Found at i:2364537 original size:6 final size:7
Alignment explanation
Indices: 2364518--2364543 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
2364508 GTTTTTGTGT
2364518 TTAAAAA
1 TTAAAAA
2364525 TTAAAAA
1 TTAAAAA
2364532 TTAAAAA
1 TTAAAAA
2364539 TTAAA
1 TTAAA
2364544 TTCGCTTAAT
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (7 bp):
TTAAAAA
Found at i:2372312 original size:15 final size:15
Alignment explanation
Indices: 2372292--2372325 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
2372282 AAAATAAAAT
2372292 AATTTATTATATTTA
1 AATTTATTATATTTA
* *
2372307 AATTTATTTTATTTG
1 AATTTATTATATTTA
2372322 AATT
1 AATT
2372326 AAAAAGAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (15 bp):
AATTTATTATATTTA
Found at i:2379146 original size:30 final size:30
Alignment explanation
Indices: 2379099--2379312 Score: 356
Period size: 30 Copynumber: 7.1 Consensus size: 30
2379089 TTCATATTTA
* * *
2379099 TGGAAAATCAAAGATATGAGTATCAAATAA
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
* * *
2379129 TAGAAAGTCAAAAATATGGGTATCAAGTAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
2379159 TGGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
2379189 TGGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
2379219 TGGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
2379249 TGGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
*
2379279 TGGAAAGTCAAAGATATGGGTATCGAGATAT
1 TGGAAAGTCAAAGATATGGGTATC-AAATAT
2379310 TGG
1 TGG
2379313 CATAATAAAA
Statistics
Matches: 173, Mismatches: 10, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
30 165 0.95
31 8 0.05
ACGTcount: A:0.44, C:0.07, G:0.23, T:0.26
Consensus pattern (30 bp):
TGGAAAGTCAAAGATATGGGTATCAAATAT
Found at i:2383926 original size:30 final size:30
Alignment explanation
Indices: 2383883--2384786 Score: 1763
Period size: 30 Copynumber: 30.1 Consensus size: 30
2383873 TCCATATTTA
* *
2383883 TGGAAAATCAAAGATATGGGTATCAAATAA
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
*
2383913 TAGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
2383943 TGGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
2383973 TGGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
2384003 TGGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
2384033 TGGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
2384063 TGGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
2384093 TGGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
2384123 TGGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
2384153 TGGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
2384183 TGGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
2384213 TGGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
2384243 TGGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
2384273 TGGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
2384303 TGGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
2384333 TGGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
2384363 TGGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
2384393 TGGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
2384423 TGGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
2384453 TGGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
2384483 TGGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
2384513 TGGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
2384543 TGGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
2384573 TGGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
2384603 TGGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
2384633 TGGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
2384663 TGGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
2384693 TGGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
2384723 TGGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
*
2384753 TGGAAAGTCAAAGATATGGGTATCGAGATAT
1 TGGAAAGTCAAAGATATGGGTATC-AAATAT
2384784 TGG
1 TGG
2384787 CATAATAAAA
Statistics
Matches: 868, Mismatches: 5, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
30 860 0.99
31 8 0.01
ACGTcount: A:0.43, C:0.07, G:0.23, T:0.27
Consensus pattern (30 bp):
TGGAAAGTCAAAGATATGGGTATCAAATAT
Found at i:2385375 original size:42 final size:42
Alignment explanation
Indices: 2385329--2385444 Score: 144
Period size: 42 Copynumber: 2.8 Consensus size: 42
2385319 ACTGAAGCAC
*
2385329 ATAAGTGCTAAACGGAAACCTGAAAGGGTTAAACGGAAGCTT
1 ATAAGAGCTAAACGGAAACCTGAAAGGGTTAAACGGAAGCTT
* * *
2385371 ATAAGAGCTAAATGGAAA-CTCATAAGGGTTAAATGGAAGCTT
1 ATAAGAGCTAAACGGAAACCTGA-AAGGGTTAAACGGAAGCTT
* * * *
2385413 ATAAGAGCTGAACTGAAACCCGTAAGGGTTAA
1 ATAAGAGCTAAACGGAAACCTGAAAGGGTTAA
2385445 CTGAAACTCA
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
41 3 0.05
42 58 0.94
43 1 0.02
ACGTcount: A:0.41, C:0.13, G:0.25, T:0.21
Consensus pattern (42 bp):
ATAAGAGCTAAACGGAAACCTGAAAGGGTTAAACGGAAGCTT
Found at i:2385382 original size:21 final size:21
Alignment explanation
Indices: 2385358--2385421 Score: 83
Period size: 21 Copynumber: 3.0 Consensus size: 21
2385348 CTGAAAGGGT
*
2385358 TAAACGGAAGCTTATAAGAGC
1 TAAATGGAAGCTTATAAGAGC
* * * *
2385379 TAAATGGAAACTCATAAGGGT
1 TAAATGGAAGCTTATAAGAGC
2385400 TAAATGGAAGCTTATAAGAGC
1 TAAATGGAAGCTTATAAGAGC
2385421 T
1 T
2385422 GAACTGAAAC
Statistics
Matches: 34, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.42, C:0.11, G:0.23, T:0.23
Consensus pattern (21 bp):
TAAATGGAAGCTTATAAGAGC
Found at i:2388328 original size:20 final size:20
Alignment explanation
Indices: 2388305--2388349 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
2388295 AAATCTAAAT
2388305 TAAAATATTAAAATTCAGAA
1 TAAAATATTAAAATTCAGAA
*
2388325 TAAAATCTTAAAATTCAGAA
1 TAAAATATTAAAATTCAGAA
2388345 TAAAA
1 TAAAA
2388350 ATACTAATGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.60, C:0.07, G:0.04, T:0.29
Consensus pattern (20 bp):
TAAAATATTAAAATTCAGAA
Found at i:2398053 original size:10 final size:10
Alignment explanation
Indices: 2398039--2398076 Score: 67
Period size: 10 Copynumber: 3.8 Consensus size: 10
2398029 ATTTTAGCTT
*
2398039 TTATCTTTAT
1 TTATCTTTAA
2398049 TTATCTTTAA
1 TTATCTTTAA
2398059 TTATCTTTAA
1 TTATCTTTAA
2398069 TTATCTTT
1 TTATCTTT
2398077 TATAATTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.24, C:0.11, G:0.00, T:0.66
Consensus pattern (10 bp):
TTATCTTTAA
Found at i:2398056 original size:17 final size:17
Alignment explanation
Indices: 2398031--2398079 Score: 53
Period size: 20 Copynumber: 2.7 Consensus size: 17
2398021 TAGATTTAAT
*
2398031 TTTAGCTTTTATCTTTA
1 TTTATCTTTTATCTTTA
2398048 TTTATCTTTAATTATCTTTA
1 TTTATC-TT--TTATCTTTA
*
2398068 ATTATCTTTTAT
1 TTTATCTTTTAT
2398080 AATTTAATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
17 9 0.33
18 2 0.07
19 2 0.07
20 14 0.52
ACGTcount: A:0.22, C:0.10, G:0.02, T:0.65
Consensus pattern (17 bp):
TTTATCTTTTATCTTTA
Found at i:2404837 original size:23 final size:23
Alignment explanation
Indices: 2404794--2404838 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
2404784 GTACTTTAAT
* *
2404794 TTTATTTTTTTGAACTTTTTATA
1 TTTATATTTTTGAAATTTTTATA
2404817 TTTATATTTTT-AAATTATTTAT
1 TTTATATTTTTGAAATT-TTTAT
2404839 TGATGTGACA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (23 bp):
TTTATATTTTTGAAATTTTTATA
Found at i:2407434 original size:29 final size:29
Alignment explanation
Indices: 2407372--2407434 Score: 67
Period size: 28 Copynumber: 2.2 Consensus size: 29
2407362 TATAGTTTTT
* *
2407372 ATTAATTTTTTTATATTTTTATAATTAAT
1 ATTAATTTTTTTATATTTTTATAAATAAA
*
2407401 TTTAA-TTTTTTATATTTTT-TAAATAGAGA
1 ATTAATTTTTTTATATTTTTATAAATA-A-A
2407430 ATTAA
1 ATTAA
2407435 GCTATTCTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
27 5 0.18
28 15 0.54
29 8 0.29
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (29 bp):
ATTAATTTTTTTATATTTTTATAAATAAA
Found at i:2414129 original size:31 final size:31
Alignment explanation
Indices: 2414091--2414150 Score: 120
Period size: 31 Copynumber: 1.9 Consensus size: 31
2414081 AAAAAAACTC
2414091 CATATGGCTGCTAATGATGAAATTATATACT
1 CATATGGCTGCTAATGATGAAATTATATACT
2414122 CATATGGCTGCTAATGATGAAATTATATA
1 CATATGGCTGCTAATGATGAAATTATATA
2414151 ATTTCATAGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.35
Consensus pattern (31 bp):
CATATGGCTGCTAATGATGAAATTATATACT
Found at i:2418781 original size:21 final size:21
Alignment explanation
Indices: 2418740--2418781 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
2418730 ATGATTTTCT
*
2418740 AATGCTAACTATTTCGATTAA
1 AATGCTAACTATTTAGATTAA
2418761 AATGCTAACATATTTAG-TTAA
1 AATGCTAAC-TATTTAGATTAA
2418782 TCATTTAACG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.40, C:0.12, G:0.10, T:0.38
Consensus pattern (21 bp):
AATGCTAACTATTTAGATTAA
Found at i:2419181 original size:29 final size:29
Alignment explanation
Indices: 2419134--2419189 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
2419124 TTTAATTCTT
* *
2419134 TTTAATAGTACAGGTACT-ATATTGATCTA
1 TTTAACAGTACAGGGACTAAT-TTGATCTA
*
2419163 TTTAACAGTAGAGGGACTAATTTGATC
1 TTTAACAGTACAGGGACTAATTTGATC
2419190 AAATCCCTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 21 0.91
30 2 0.09
ACGTcount: A:0.34, C:0.11, G:0.18, T:0.38
Consensus pattern (29 bp):
TTTAACAGTACAGGGACTAATTTGATCTA
Found at i:2420313 original size:83 final size:81
Alignment explanation
Indices: 2420156--2420306 Score: 221
Period size: 81 Copynumber: 1.8 Consensus size: 81
2420146 ACATCTTCTG
* * **
2420156 TTATAACACATAACAATGCCATATATATAGACACGTAAGTATTTGCAATTCATCTTTGCTTATCC
1 TTATAACACATAACAATGCCATATATATAGACACATAAGTATTTGCAATTCATCTTTACTTAAAC
2420221 TACCTTGCAACCTCCA
66 TACCTTGCAACCTCCA
* * *
2420237 TTATAACACGTAACAATGCCATATATATATACACTCATAAGTATTTGCAATTCATTTTTACTTAA
1 TTATAACACATAACAATGCCATATATATAGACA--CATAAGTATTTGCAATTCATCTTTACTTAA
2420302 ACTAC
64 ACTAC
2420307 TATGCAATCT
Statistics
Matches: 61, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
81 31 0.51
83 30 0.49
ACGTcount: A:0.36, C:0.22, G:0.07, T:0.35
Consensus pattern (81 bp):
TTATAACACATAACAATGCCATATATATAGACACATAAGTATTTGCAATTCATCTTTACTTAAAC
TACCTTGCAACCTCCA
Found at i:2421755 original size:29 final size:28
Alignment explanation
Indices: 2421691--2421762 Score: 99
Period size: 29 Copynumber: 2.5 Consensus size: 28
2421681 GTTTTTTTTT
*
2421691 TATCACCAAACTATGAAAAGTTACAAAA
1 TATCACCCAACTATGAAAAGTTACAAAA
* *
2421719 TAGCCACCCAACTGTGAAAAGTTACAAAA
1 TA-TCACCCAACTATGAAAAGTTACAAAA
2421748 TGATCACCCAACTAT
1 T-ATCACCCAACTAT
2421763 TTAATTTTAT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
28 2 0.05
29 34 0.92
30 1 0.03
ACGTcount: A:0.46, C:0.24, G:0.10, T:0.21
Consensus pattern (28 bp):
TATCACCCAACTATGAAAAGTTACAAAA
Found at i:2439000 original size:13 final size:15
Alignment explanation
Indices: 2438976--2439012 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
2438966 AAAATATAAT
*
2438976 AATAACATTAAT-TA
1 AATAATATTAATATA
2438990 AAT-ATATTAATATA
1 AATAATATTAATATA
2439004 AATAATATT
1 AATAATATT
2439013 GAAATTAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
13 7 0.35
14 8 0.40
15 5 0.25
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.41
Consensus pattern (15 bp):
AATAATATTAATATA
Found at i:2439009 original size:22 final size:22
Alignment explanation
Indices: 2438967--2439009 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
2438957 AGAATACCAA
*
2438967 AAATATAATAATAACATTAATT
1 AAATATAATAATAACAATAATT
*
2438989 AAATATATTAATATA-AATAAT
1 AAATATAATAATA-ACAATAAT
2439010 ATTGAAATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 17 0.94
23 1 0.06
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.37
Consensus pattern (22 bp):
AAATATAATAATAACAATAATT
Found at i:2439604 original size:14 final size:15
Alignment explanation
Indices: 2439585--2439614 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2439575 GGTAAGTTTT
2439585 TTTATTT-TTTTATA
1 TTTATTTGTTTTATA
2439599 TTTATTTGTTTTATA
1 TTTATTTGTTTTATA
2439614 T
1 T
2439615 CTTTCTATGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.20, C:0.00, G:0.03, T:0.77
Consensus pattern (15 bp):
TTTATTTGTTTTATA
Found at i:2447123 original size:16 final size:16
Alignment explanation
Indices: 2447102--2447132 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
2447092 TTTTTTTTTT
2447102 TGGGGGGGGGGGGTTC
1 TGGGGGGGGGGGGTTC
2447118 TGGGGGGGGGGGGTT
1 TGGGGGGGGGGGGTT
2447133 GCAATCTGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.00, C:0.03, G:0.77, T:0.19
Consensus pattern (16 bp):
TGGGGGGGGGGGGTTC
Found at i:2448881 original size:29 final size:29
Alignment explanation
Indices: 2448848--2448906 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
2448838 ACAAAATTGA
* *
2448848 ATAGTTGAGTG-CCAATATTATAACTTTTC
1 ATAGTTGAATGACCAAT-TTATAACGTTTC
*
2448877 ATAGTTGAATGACCACTTTATAACGTTTC
1 ATAGTTGAATGACCAATTTATAACGTTTC
2448906 A
1 A
2448907 CAACTGAATG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 22 0.85
30 4 0.15
ACGTcount: A:0.32, C:0.15, G:0.14, T:0.39
Consensus pattern (29 bp):
ATAGTTGAATGACCAATTTATAACGTTTC
Done.