Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 124041150
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: 124041150
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 335 characters in sequence are not A, C, G, or T
File 11 of 410
Found at i:2742963 original size:15 final size:15
Alignment explanation
Indices: 2742914--2742965 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
2742904 ACATGTATGT
* *
2742914 GCGAACCTTACGTGA
1 GCGAACCCTAAGTGA
*
2742929 GCGAACCCCT-A-TGG
1 GCGAA-CCCTAAGTGA
2742943 GCGAACCCTAAGTGA
1 GCGAACCCTAAGTGA
2742958 GCGAACCC
1 GCGAACCC
2742966 CTATGTGTGA
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
13 4 0.13
14 8 0.27
15 15 0.50
16 3 0.10
ACGTcount: A:0.27, C:0.33, G:0.27, T:0.13
Consensus pattern (15 bp):
GCGAACCCTAAGTGA
Found at i:2742977 original size:29 final size:29
Alignment explanation
Indices: 2742909--2742992 Score: 105
Period size: 29 Copynumber: 2.9 Consensus size: 29
2742899 AGCGAACATG
* *
2742909 TATGTGCGAACCTTACGTGAGCGAACCCC
1 TATGTGCGAACCATAAGTGAGCGAACCCC
* *
2742938 TATGGGCGAACCCTAAGTGAGCGAACCCC
1 TATGTGCGAACCATAAGTGAGCGAACCCC
* * *
2742967 TATGTGTGAACCATAGGTGTGCGAAC
1 TATGTGCGAACCATAAGTGAGCGAAC
2742993 TCTTAGGTGC
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 47 1.00
ACGTcount: A:0.26, C:0.26, G:0.27, T:0.20
Consensus pattern (29 bp):
TATGTGCGAACCATAAGTGAGCGAACCCC
Found at i:2743285 original size:22 final size:21
Alignment explanation
Indices: 2743246--2743290 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
2743236 ACATGTGAAT
*
2743246 CCTGAAAAAATATGATGCGAA
1 CCTGAAAAAATATGATGCAAA
* *
2743267 CCTGAGAAAAATTTTATGCAAA
1 CCTGA-AAAAATATGATGCAAA
2743289 CC
1 CC
2743291 ATATATGTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.44, C:0.18, G:0.16, T:0.22
Consensus pattern (21 bp):
CCTGAAAAAATATGATGCAAA
Found at i:2744726 original size:31 final size:31
Alignment explanation
Indices: 2744691--2744758 Score: 129
Period size: 31 Copynumber: 2.2 Consensus size: 31
2744681 CACTCTCAAA
2744691 ACAATTACCAAATCATAGATAAACCATAAAT
1 ACAATTACCAAATCATAGATAAACCATAAAT
2744722 ACAATTACCAAATCATAGATAAACCATAAAT
1 ACAATTACCAAATCATAGATAAACCATAAAT
2744753 A-AATTA
1 ACAATTA
2744759 TCTTAAACAG
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 5 0.14
31 32 0.86
ACGTcount: A:0.56, C:0.18, G:0.03, T:0.24
Consensus pattern (31 bp):
ACAATTACCAAATCATAGATAAACCATAAAT
Found at i:2744972 original size:13 final size:13
Alignment explanation
Indices: 2744947--2744983 Score: 58
Period size: 13 Copynumber: 2.8 Consensus size: 13
2744937 TACAGATCCG
2744947 GATTCAGATATCA
1 GATTCAGATATCA
2744960 GATTACAGA-ATCA
1 GATT-CAGATATCA
2744973 GATTCAGATAT
1 GATTCAGATAT
2744984 ACAAAATCCT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 4 0.18
13 14 0.64
14 4 0.18
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.30
Consensus pattern (13 bp):
GATTCAGATATCA
Found at i:2744975 original size:20 final size:20
Alignment explanation
Indices: 2744950--2744991 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
2744940 AGATCCGGAT
*
2744950 TCAGATATCAGAT-TACAGAA
1 TCAGAT-TCAGATATACAAAA
2744970 TCAGATTCAGATATACAAAA
1 TCAGATTCAGATATACAAAA
2744990 TC
1 TC
2744992 CTACCCTCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.45, C:0.17, G:0.12, T:0.26
Consensus pattern (20 bp):
TCAGATTCAGATATACAAAA
Found at i:2747091 original size:13 final size:13
Alignment explanation
Indices: 2747073--2747100 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
2747063 TCCTTACTGT
2747073 TGAATTTAACATA
1 TGAATTTAACATA
2747086 TGAATTTAACATA
1 TGAATTTAACATA
2747099 TG
1 TG
2747101 CAATCGTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.43, C:0.07, G:0.11, T:0.39
Consensus pattern (13 bp):
TGAATTTAACATA
Found at i:2748622 original size:20 final size:20
Alignment explanation
Indices: 2748599--2748637 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
2748589 CTTAAATGGC
*
2748599 TTTTTTTAATATTTTTTATG
1 TTTTTATAATATTTTTTATG
2748619 TTTTTATAATATTTTTTAT
1 TTTTTATAATATTTTTTAT
2748638 AATTCATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (20 bp):
TTTTTATAATATTTTTTATG
Found at i:2748752 original size:18 final size:17
Alignment explanation
Indices: 2748728--2748791 Score: 74
Period size: 18 Copynumber: 3.5 Consensus size: 17
2748718 AATTAATTAA
*
2748728 AATTTTATAAATTTTAT
1 AATTTTATAATTTTTAT
2748745 AATATTTATAAGTTTTTTATT
1 AAT-TTTATAA--TTTTTA-T
*
2748766 ATTTTTATAATTTTTAT
1 AATTTTATAATTTTTAT
2748783 AATTTTATA
1 AATTTTATA
2748792 TCAATTTCAA
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
17 12 0.30
18 13 0.32
20 12 0.30
21 3 0.08
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (17 bp):
AATTTTATAATTTTTAT
Found at i:2748770 original size:10 final size:10
Alignment explanation
Indices: 2748730--2748798 Score: 56
Period size: 9 Copynumber: 7.1 Consensus size: 10
2748720 TTAATTAAAA
*
2748730 TTTTATAA-A
1 TTTTATAATT
2748739 TTTTATAA-T
1 TTTTATAATT
*
2748748 ATTTATAAGTT
1 TTTTATAA-TT
*
2748759 TTTTATTA-T
1 TTTTATAATT
2748768 TTTTATAA-T
1 TTTTATAATT
2748777 TTTTATAATT
1 TTTTATAATT
*
2748787 TTATATCAATT
1 TTTTAT-AATT
2748798 T
1 T
2748799 CAATATTTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
9 32 0.64
10 6 0.12
11 12 0.24
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.64
Consensus pattern (10 bp):
TTTTATAATT
Found at i:2748771 original size:29 final size:28
Alignment explanation
Indices: 2748730--2748798 Score: 84
Period size: 29 Copynumber: 2.4 Consensus size: 28
2748720 TTAATTAAAA
2748730 TTTTATAAATTTTATAATATTTATAAGTT
1 TTTTATAAATTTTATAATATTTATAA-TT
* * *
2748759 TTTTATTATTTTTATAATTTTTATAATT
1 TTTTATAAATTTTATAATATTTATAATT
* *
2748787 TTATATCAATTT
1 TTTTATAAATTT
2748799 CAATATTTTT
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
28 11 0.32
29 23 0.68
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.64
Consensus pattern (28 bp):
TTTTATAAATTTTATAATATTTATAATT
Found at i:2748825 original size:19 final size:17
Alignment explanation
Indices: 2748794--2748829 Score: 54
Period size: 19 Copynumber: 2.0 Consensus size: 17
2748784 ATTTTATATC
2748794 AATTTCAATATTTTTTT
1 AATTTCAATATTTTTTT
2748811 AATTGTCAATGATTTTTTT
1 AATT-TCAAT-ATTTTTTT
2748830 CTTATTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.24
18 5 0.29
19 8 0.47
ACGTcount: A:0.28, C:0.06, G:0.06, T:0.61
Consensus pattern (17 bp):
AATTTCAATATTTTTTT
Found at i:2748871 original size:20 final size:21
Alignment explanation
Indices: 2748846--2748890 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
2748836 TTTAATGCTT
2748846 TTTTTATA-AGTTTTAAAGAA
1 TTTTTATATAGTTTTAAAGAA
* *
2748866 TTTTTATATGGTTTTATAGAA
1 TTTTTATATAGTTTTAAAGAA
2748887 TTTT
1 TTTT
2748891 AAATATTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 8 0.36
21 14 0.64
ACGTcount: A:0.31, C:0.00, G:0.11, T:0.58
Consensus pattern (21 bp):
TTTTTATATAGTTTTAAAGAA
Found at i:2748978 original size:37 final size:36
Alignment explanation
Indices: 2748927--2749030 Score: 88
Period size: 39 Copynumber: 2.8 Consensus size: 36
2748917 ATTTGTTCTA
*
2748927 ATTTATTATATATTTTAAATTTTTTATAATA-TTTAAGTT
1 ATTT-TTAT-TATTTTAAAATTTTTATAATATTTTAA--T
* * *
2748966 ATTTTTTTTATTTTTATAAGTTTCTATAA-ATTTTAAT
1 ATTTTTATTA-TTTTA-AAATTTTTATAATATTTTAAT
2749003 ATTTTTATTA-TTTAATAATTTTTATAAT
1 ATTTTTATTATTTTAA-AATTTTTATAAT
2749031 TTCTTCTGAT
Statistics
Matches: 54, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
34 1 0.02
35 13 0.24
37 12 0.22
38 9 0.17
39 19 0.35
ACGTcount: A:0.34, C:0.01, G:0.02, T:0.63
Consensus pattern (36 bp):
ATTTTTATTATTTTAAAATTTTTATAATATTTTAAT
Found at i:2749018 original size:16 final size:17
Alignment explanation
Indices: 2748997--2749032 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
2748987 TTCTATAAAT
*
2748997 TTTAAT-ATTTTTATTA
1 TTTAATAATTTTTATAA
2749013 TTTAATAATTTTTATAA
1 TTTAATAATTTTTATAA
2749030 TTT
1 TTT
2749033 CTTCTGATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 6 0.33
17 12 0.67
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTAATAATTTTTATAA
Found at i:2749029 original size:9 final size:9
Alignment explanation
Indices: 2748914--2749032 Score: 57
Period size: 9 Copynumber: 12.8 Consensus size: 9
2748904 CATTTTAAAA
2748914 ATAATTTGTT
1 ATAATTT-TT
*
2748924 CTAATTTATT
1 ATAATTT-TT
2748934 AT-ATATTTT
1 ATAAT-TTTT
2748943 A-AATTTTTT
1 ATAA-TTTTT
*
2748952 ATAATATTTA
1 ATAAT-TTTT
*
2748962 AGTTATTTTT
1 A-TAATTTTT
* *
2748972 TTTATTTTT
1 ATAATTTTT
*
2748981 ATAAGTTTCT
1 ATAA-TTTTT
*
2748991 ATAAATTTT
1 ATAATTTTT
2749000 A-ATATTTTT
1 ATA-ATTTTT
* *
2749009 ATTA-TTTA
1 ATAATTTTT
2749017 ATAATTTTT
1 ATAATTTTT
2749026 ATAATTT
1 ATAATTT
2749033 CTTCTGATTT
Statistics
Matches: 82, Mismatches: 17, Indels: 21
0.68 0.14 0.17
Matches are distributed among these distances:
8 7 0.09
9 43 0.52
10 29 0.35
11 3 0.04
ACGTcount: A:0.33, C:0.02, G:0.03, T:0.63
Consensus pattern (9 bp):
ATAATTTTT
Found at i:2749100 original size:19 final size:18
Alignment explanation
Indices: 2749069--2749105 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
2749059 TGATATATTT
*
2749069 TTTTTATATTTTTTATGA
1 TTTTTATAATTTTTATGA
2749087 TTTTTAGTAATTTTTATGA
1 TTTTTA-TAATTTTTATGA
2749106 GAAGATATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (18 bp):
TTTTTATAATTTTTATGA
Found at i:2749654 original size:135 final size:133
Alignment explanation
Indices: 2749352--2750143 Score: 789
Period size: 135 Copynumber: 5.9 Consensus size: 133
2749342 TCAAAAAAAG
* * * *
2749352 TCCAATTTCGAAGCTTGAGTGTCGCAGTATCCAACTTAAAAAAT-ATTTTTAAAACAAAAAAAAT
1 TCCAATTTCAAAGCTTGAGTGTCGCAGTATCCAACTTAAAAATTGTTTTTTAAAA-GAAAAAAAT
* * *
2749416 GTAGTAT-TGAAAAAAGCCCTTAAGAAAATGTAAAAAATGTTTTTGTATTAAATTCACA-CCAAT
65 GTAAT-TGTGAAAAAAGCCCTTAAGAAAATGTAAAAAAAGTCTTTGTATTAAATTCACACCCAAT
2749479 TGAGC
129 TGAGC
* * * *
2749484 TCCAATTTCAAAGCTTAAGTGTCGAAGTATTCAACTTAAAAATTGTTCTTTAAAAAGAAAAAAAT
1 TCCAATTTCAAAGCTTGAGTGTCGCAGTATCCAACTTAAAAATTGTT-TTTTAAAAGAAAAAAA-
* * * *
2749549 TTTAATTATGAAAAAAGCCTTTAAGAAAATGTAAAAAAAGTCTTTATATTAAATTCACACCCAAT
64 TGTAATTGTGAAAAAAGCCCTTAAGAAAATGTAAAAAAAGTCTTTGTATTAAATTCACACCCAAT
2749614 TGAGC
129 TGAGC
* * *
2749619 TCCAATTTTAAAGCTTGAGTGACGCAGTATCCAACTTAAAAAATGTTATTTTAAAAGAAAAAAAT
1 TCCAATTTCAAAGCTTGAGTGTCGCAGTATCCAACTTAAAAATTGTT-TTTTAAAAGAAAAAAAT
* * * * **
2749684 GTAATT-TAAAACAAAAACCCTTAAGAAAATGTCAAAAAAGTCTTTATATTAAATTCACACAAAA
65 GTAATTGT-GAA-AAAAGCCCTTAAGAAAATGTAAAAAAAGTCTTTGTATTAAATTCACACCCAA
*
2749748 TTTAGC
128 TTGAGC
* * * * * * * * * * *
2749754 TCCAATTCCTAA-CTTAAATATAGTAGTATCCAACTTAAAAAATATCTTTTTAAAAGAATAATAT
1 TCCAATTTCAAAGCTTGAGTGTCGCAGTATCCAACTTAAAAATTGT-TTTTTAAAAGAAAAAAAT
* * * * * *
2749818 TTAATTGTTAAAAAA-TCCTTACA-AAAATGTAAAAAAATATATATTTTGTATTAAATTCACACT
65 GTAATTGTGAAAAAAGCCCTTA-AGAAAATGT-AAAAAA-A-GT-CTTTGTATTAAATTCACACC
*
2749881 CACTTGAGC
125 CAATTGAGC
* * *
2749890 TCTAATTTCAAAACTTGAGTGTCGCAGTATCCAACTTAAAAGA-TGTTTTTTAAAAGAAAATAAT
1 TCCAATTTCAAAGCTTGAGTGTCGCAGTATCCAACTTAAAA-ATTGTTTTTTAAAAGAAAAAAAT
* * * * *
2749954 GCAATTGTGAAAAAAGCCCTTAA-AAATATGT-CAAAAAGTCTTTGTAATAAATTCACACCTATT
65 GTAATTGTGAAAAAAGCCCTTAAGAAA-ATGTAAAAAAAGTCTTTGTATTAAATTCACACCCAAT
2750017 TGAGC
129 TGAGC
** * *
2750022 TCCAATTTCAAAAG-TTGAGTGTCATAATATCCAACTTAGAAAATAT-TTTTTTTAAAGAAAAAA
1 TCCAATTTC-AAAGCTTGAGTGTCGCAGTATCCAACTTA-AAAAT-TGTTTTTTAAAAGAAAAAA
* * *
2750085 ATTTAATTGTGAAAAAAGCCTTTAAGAAAATGTCAAAAAAAAAATCTTTGTATTAAATT
63 ATGTAATTGTGAAAAAAGCCCTTAAGAAAATGT---AAAAAAAGTCTTTGTATTAAATT
2750144 TTTACCTAAT
Statistics
Matches: 544, Mismatches: 89, Indels: 49
0.80 0.13 0.07
Matches are distributed among these distances:
132 105 0.19
133 68 0.12
134 120 0.22
135 134 0.25
136 63 0.12
137 53 0.10
138 1 0.00
ACGTcount: A:0.45, C:0.13, G:0.10, T:0.32
Consensus pattern (133 bp):
TCCAATTTCAAAGCTTGAGTGTCGCAGTATCCAACTTAAAAATTGTTTTTTAAAAGAAAAAAATG
TAATTGTGAAAAAAGCCCTTAAGAAAATGTAAAAAAAGTCTTTGTATTAAATTCACACCCAATTG
AGC
Found at i:2749682 original size:21 final size:20
Alignment explanation
Indices: 2749656--2749700 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
2749646 TATCCAACTT
* *
2749656 AAAAAATGTTATTTTAAAAGA
1 AAAAAATG-TAATTTAAAACA
2749677 AAAAAATGTAATTTAAAACA
1 AAAAAATGTAATTTAAAACA
2749697 AAAA
1 AAAA
2749701 CCCTTAAGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 14 0.64
21 8 0.36
ACGTcount: A:0.64, C:0.02, G:0.07, T:0.27
Consensus pattern (20 bp):
AAAAAATGTAATTTAAAACA
Found at i:2749743 original size:269 final size:264
Alignment explanation
Indices: 2749352--2750143 Score: 922
Period size: 269 Copynumber: 2.9 Consensus size: 264
2749342 TCAAAAAAAG
* * *
2749352 TCCAATTTCGAAGCTTGAGTGTCGCAGTATCCAACTTAAAAAAT-ATTTTTAAAACAAAAAAAAT
1 TCCAATTTCAAAGCTTGAGTGTCGCAGTATCCAACTTAAAAAATGTTTTTTAAAA-GAAAAAAAT
* *
2749416 GTAGTATTGAAAAAAGCCCTTAAGAAAATGT-AAAAAATGTTTTTGTATTAAATTCACACCAATT
65 GTAAT-TTGAAAAAAGCCCTTAAGAAAATGTCAAAAAA-GTCTTTGTATTAAATTCACACCAATT
*
2749480 GAGCTCCAATTTCAAAGCTTAAGTGTCGAAGTATTCAACTTAAAAAT-TGTTCTTTAAAAAGAAA
128 GAGCTCCAATTTCAAAGCTTAAGTGTCGAAGTATCCAACTTAAAAATAT-TT-TTT-AAAAGAAA
* * *
2749544 AAAATTTTAATTATGAAAAAAGCCTTTAAGAAAATGT-AAAAAAAGTCTTTATATTAAATTCACA
190 AAAA-TTTAATTGTGAAAAAAGCCTTTAAGAAAATGTAAAAAAAAATCTTTGTATTAAATTCACA
2749608 CCCAATTGAGC
254 CCCAATTGAGC
* *
2749619 TCCAATTTTAAAGCTTGAGTGACGCAGTATCCAACTTAAAAAATGTTATTTTAAAAGAAAAAAAT
1 TCCAATTTCAAAGCTTGAGTGTCGCAGTATCCAACTTAAAAAATGTT-TTTTAAAAGAAAAAAAT
* * * *
2749684 GTAATTTAAAACAAAAACCCTTAAGAAAATGTCAAAAAAGTCTTTATATTAAATTCACACAAAAT
65 GTAATTT-GAA-AAAAGCCCTTAAGAAAATGTCAAAAAAGTCTTTGTATTAAATTCACAC-CAAT
* * * * * * * *
2749749 TTAGCTCCAATTCCTAA-CTTAAATATAGTAGTATCCAACTTAAAAAATATCTTTTTAAAAGAAT
127 TGAGCTCCAATTTCAAAGCTTAAGTGTCGAAGTATCCAACTT-AAAAATAT-TTTTTAAAAGAAA
* * * *
2749813 AATATTTAATTGTTAAAAAATCC-TTACA-AAAATGTAAAAAAATATATATTTTGTATTAAATTC
190 AAAATTTAATTGTGAAAAAAGCCTTTA-AGAAAATGTAAAAAAA-A-AT-CTTTGTATTAAATTC
* *
2749876 ACACTCACTTGAGC
251 ACACCCAATTGAGC
* * * *
2749890 TCTAATTTCAAAACTTGAGTGTCGCAGTATCCAACTTAAAAGATGTTTTTTAAAAGAAAATAATG
1 TCCAATTTCAAAGCTTGAGTGTCGCAGTATCCAACTTAAAAAATGTTTTTTAAAAGAAAAAAATG
* * *
2749955 CAATTGTGAAAAAAGCCCTTAA-AAATATGTC-AAAAAGTCTTTGTAATAAATTCACACCTATTT
66 TAATT-TGAAAAAAGCCCTTAAGAAA-ATGTCAAAAAAGTCTTTGTATTAAATTCACACC-AATT
* * *
2750018 GAGCTCCAATTTCAAAAG-TTGAGTGTC-ATAATATCCAACTTAGAAAATATTTTTTTTAAAGAA
128 GAGCTCCAATTTC-AAAGCTTAAGTGTCGA-AGTATCCAACTTA-AAAATA-TTTTTTAAAAGAA
2750081 AAAAATTTAATTGTGAAAAAAGCCTTTAAGAAAATGTCAAAAAAAAAATCTTTGTATTAAATT
189 AAAAATTTAATTGTGAAAAAAGCCTTTAAGAAAATGT--AAAAAAAAATCTTTGTATTAAATT
2750144 TTTACCTAAT
Statistics
Matches: 442, Mismatches: 58, Indels: 48
0.81 0.11 0.09
Matches are distributed among these distances:
267 53 0.12
268 80 0.18
269 161 0.36
270 69 0.16
271 72 0.16
272 7 0.02
ACGTcount: A:0.45, C:0.13, G:0.10, T:0.32
Consensus pattern (264 bp):
TCCAATTTCAAAGCTTGAGTGTCGCAGTATCCAACTTAAAAAATGTTTTTTAAAAGAAAAAAATG
TAATTTGAAAAAAGCCCTTAAGAAAATGTCAAAAAAGTCTTTGTATTAAATTCACACCAATTGAG
CTCCAATTTCAAAGCTTAAGTGTCGAAGTATCCAACTTAAAAATATTTTTTAAAAGAAAAAAATT
TAATTGTGAAAAAAGCCTTTAAGAAAATGTAAAAAAAAATCTTTGTATTAAATTCACACCCAATT
GAGC
Found at i:2750335 original size:23 final size:23
Alignment explanation
Indices: 2750309--2750353 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
2750299 TAAAAATAAA
2750309 TAAAA-ATAAAAATATATATTTAT
1 TAAAATATAAAAA-ATATATTTAT
2750332 TAAAATATAAAAAATATATTTA
1 TAAAATATAAAAAATATATTTA
2750354 AATTGATAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 14 0.67
24 7 0.33
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (23 bp):
TAAAATATAAAAAATATATTTAT
Found at i:2750423 original size:10 final size:9
Alignment explanation
Indices: 2750410--2750527 Score: 60
Period size: 10 Copynumber: 12.4 Consensus size: 9
2750400 CAAATTATAG
2750410 AAAATTTTAT
1 AAAA-TTTAT
*
2750420 AAAATTAAT
1 AAAATTTAT
*
2750429 AAAACATTTTT
1 -AAA-ATTTAT
2750440 AAAAATTTAT
1 -AAAATTTAT
*
2750450 AAAATGTAT
1 AAAATTTAT
*
2750459 AAAAATTAT
1 AAAATTTAT
*
2750468 AAAAAATTAT
1 -AAAATTTAT
*
2750478 AAAAATTCAT
1 -AAAATTTAT
*
2750488 AAAA-ATATT
1 AAAATTTA-T
**
2750497 AAAATTGGT
1 AAAATTTAT
*
2750506 AGAAACTTAT
1 A-AAATTTAT
2750516 AAAA-TTAT
1 AAAATTTAT
2750524 AAAA
1 AAAA
2750528 AAAATCATAA
Statistics
Matches: 85, Mismatches: 17, Indels: 14
0.73 0.15 0.12
Matches are distributed among these distances:
8 9 0.11
9 33 0.39
10 35 0.41
11 8 0.09
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.35
Consensus pattern (9 bp):
AAAATTTAT
Found at i:2750459 original size:9 final size:8
Alignment explanation
Indices: 2750441--2750527 Score: 57
Period size: 9 Copynumber: 9.5 Consensus size: 8
2750431 AACATTTTTA
2750441 AAAATTTAT
1 AAAA-TTAT
2750450 AAAATGTAT
1 AAAAT-TAT
2750459 AAAAATTAT
1 -AAAATTAT
2750468 AAAAAATTAT
1 --AAAATTAT
2750478 AAAAATTCAT
1 -AAAATT-AT
*
2750488 AAAAATATT
1 AAAATTA-T
*
2750497 AAAATTGGT
1 AAAATT-AT
2750506 AGAAACTTAT
1 A-AAA-TTAT
2750516 AAAATTAT
1 AAAATTAT
2750524 AAAA
1 AAAA
2750528 AAAATCATAA
Statistics
Matches: 66, Mismatches: 4, Indels: 17
0.76 0.05 0.20
Matches are distributed among these distances:
8 10 0.15
9 33 0.50
10 21 0.32
11 2 0.03
ACGTcount: A:0.61, C:0.02, G:0.05, T:0.32
Consensus pattern (8 bp):
AAAATTAT
Found at i:2750463 original size:19 final size:18
Alignment explanation
Indices: 2750401--2750528 Score: 89
Period size: 19 Copynumber: 6.7 Consensus size: 18
2750391 TAACTCTAAC
2750401 AAATTATAGAAAATTTTATA
1 AAATTATA-AAAA-TTTATA
*
2750421 AAATTAATAAAACATTTTTAA
1 AAATT-ATAAAA-ATTTAT-A
*
2750442 AAATT-TATAAAATGTATAA
1 AAATTATA-AAAATTTAT-A
*
2750461 AAATTATAAAAAATTATAA
1 AAATTATAAAAATTTAT-A
*
2750480 AAATTCATAAAAATAT-TA
1 AAATT-ATAAAAATTTATA
* * *
2750498 AAATTGGTAGAAACTTATA
1 AAATT-ATAAAAATTTATA
2750517 AAATTATAAAAA
1 AAATTATAAAAA
2750529 AAATCATAAA
Statistics
Matches: 87, Mismatches: 14, Indels: 16
0.74 0.12 0.14
Matches are distributed among these distances:
18 17 0.20
19 35 0.40
20 25 0.29
21 10 0.11
ACGTcount: A:0.59, C:0.02, G:0.04, T:0.34
Consensus pattern (18 bp):
AAATTATAAAAATTTATA
Found at i:2754826 original size:2 final size:2
Alignment explanation
Indices: 2754819--2754848 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2754809 AATACTTATC
2754819 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2754849 CCAAAATATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2757981 original size:26 final size:26
Alignment explanation
Indices: 2757952--2758033 Score: 146
Period size: 26 Copynumber: 3.2 Consensus size: 26
2757942 TGGTACAAAT
2757952 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
2757978 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
2758004 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
2758030 TGAT
1 TGAT
2758034 GGGCATTTCA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 52 1.00
ACGTcount: A:0.33, C:0.07, G:0.24, T:0.35
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:2759545 original size:26 final size:26
Alignment explanation
Indices: 2759516--2759568 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
2759506 TTTACAGTTT
*
2759516 TACCCCTAGGAGATAAATT-ACCGAAA
1 TACCCATAGG-GATAAATTGACCGAAA
* *
2759542 TACCCATAGGGTTAAATTGACCTAAA
1 TACCCATAGGGATAAATTGACCGAAA
2759568 T
1 T
2759569 GCATGTTTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 7 0.30
26 16 0.70
ACGTcount: A:0.40, C:0.21, G:0.15, T:0.25
Consensus pattern (26 bp):
TACCCATAGGGATAAATTGACCGAAA
Found at i:2766126 original size:26 final size:26
Alignment explanation
Indices: 2766097--2766178 Score: 146
Period size: 26 Copynumber: 3.2 Consensus size: 26
2766087 TGGTACAAAT
2766097 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
2766123 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
2766149 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
2766175 TGAT
1 TGAT
2766179 GGGCATTTCA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 52 1.00
ACGTcount: A:0.33, C:0.07, G:0.24, T:0.35
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:2770005 original size:2 final size:2
Alignment explanation
Indices: 2769998--2770024 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2769988 ATGGTTTCTT
2769998 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
2770025 TAAACTGAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2780836 original size:21 final size:21
Alignment explanation
Indices: 2780807--2780860 Score: 56
Period size: 22 Copynumber: 2.4 Consensus size: 21
2780797 CTTTTACGTA
2780807 TTATATATTTTAAACTT-CTTAT
1 TTAT-TATTTTAAA-TTACTTAT
2780829 TTATTATTTTTAAATTAACTTAT
1 TTATTA-TTTTAAATT-ACTTAT
*
2780852 ATATTATTT
1 TTATTATTT
2780861 ATTTTGAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
21 4 0.14
22 14 0.50
23 10 0.36
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (21 bp):
TTATTATTTTAAATTACTTAT
Found at i:2783388 original size:12 final size:12
Alignment explanation
Indices: 2783371--2783413 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
2783361 AAGCAATAGG
2783371 TAATAATAAATA
1 TAATAATAAATA
2783383 TAATAATAGAAATA
1 TAATAAT--AAATA
* *
2783397 TAATATTAAAGA
1 TAATAATAAATA
2783409 TAATA
1 TAATA
2783414 TTGAGTATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
12 16 0.59
14 11 0.41
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.33
Consensus pattern (12 bp):
TAATAATAAATA
Found at i:2783443 original size:14 final size:14
Alignment explanation
Indices: 2783371--2783474 Score: 52
Period size: 14 Copynumber: 7.0 Consensus size: 14
2783361 AAGCAATAGG
2783371 TAATAATAAATATAA
1 TAATAAT-AATATAA
2783386 TAATAGA-AATATAA
1 TAATA-ATAATATAA
* *
2783400 T-ATTA-AAGATAA
1 TAATAATAATATAA
*
2783412 TATTGAGTATAATATAA
1 TAAT-A--ATAATATAA
*
2783429 TAATAATAATGTAA
1 TAATAATAATATAA
*
2783443 TAATGATAGTAATGATGA
1 TAAT-A-A-TAAT-ATAA
*
2783461 CAATAATAATATAA
1 TAATAATAATATAA
2783475 AAGGAATAGA
Statistics
Matches: 68, Mismatches: 11, Indels: 21
0.68 0.11 0.21
Matches are distributed among these distances:
12 8 0.12
13 3 0.04
14 23 0.34
15 10 0.15
16 5 0.07
17 14 0.21
18 5 0.07
ACGTcount: A:0.57, C:0.01, G:0.09, T:0.34
Consensus pattern (14 bp):
TAATAATAATATAA
Found at i:2785007 original size:53 final size:53
Alignment explanation
Indices: 2784927--2785032 Score: 212
Period size: 53 Copynumber: 2.0 Consensus size: 53
2784917 TTAATTATTG
2784927 TTATTTACATTATTTTCAATATATAAGACAATGCTTAGAATTATTTATAACTC
1 TTATTTACATTATTTTCAATATATAAGACAATGCTTAGAATTATTTATAACTC
2784980 TTATTTACATTATTTTCAATATATAAGACAATGCTTAGAATTATTTATAACTC
1 TTATTTACATTATTTTCAATATATAAGACAATGCTTAGAATTATTTATAACTC
2785033 CTCTCCAACC
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.38, C:0.11, G:0.06, T:0.45
Consensus pattern (53 bp):
TTATTTACATTATTTTCAATATATAAGACAATGCTTAGAATTATTTATAACTC
Found at i:2785592 original size:2 final size:2
Alignment explanation
Indices: 2785585--2785622 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2785575 CAAAATTGAC
2785585 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2785623 GTCGTTAGTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2788097 original size:22 final size:21
Alignment explanation
Indices: 2788067--2788132 Score: 64
Period size: 19 Copynumber: 3.2 Consensus size: 21
2788057 TACAAATTAA
2788067 ATCTCCAAGATTACAAGATCAT
1 ATCTCCAAGATTAC-AGATCAT
* * *
2788089 ATCTTCAAGATTGCATATCAT
1 ATCTCCAAGATTACAGATCAT
* *
2788110 ATCT--AAGATTGCATATCAT
1 ATCTCCAAGATTACAGATCAT
2788129 ATCT
1 ATCT
2788133 AAGATTGTAT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
19 19 0.46
21 10 0.24
22 12 0.29
ACGTcount: A:0.36, C:0.20, G:0.09, T:0.35
Consensus pattern (21 bp):
ATCTCCAAGATTACAGATCAT
Found at i:2788119 original size:19 final size:19
Alignment explanation
Indices: 2788084--2788162 Score: 126
Period size: 19 Copynumber: 4.2 Consensus size: 19
2788074 AGATTACAAG
2788084 ATCATATCTTCAAGATTGCAT
1 ATCATATC-T-AAGATTGCAT
2788105 ATCATATCTAAGATTGCAT
1 ATCATATCTAAGATTGCAT
2788124 ATCATATCTAAGATTG--T
1 ATCATATCTAAGATTGCAT
2788141 ATCATATCTAAGATTGCAT
1 ATCATATCTAAGATTGCAT
2788160 ATC
1 ATC
2788163 CTTAAAGATT
Statistics
Matches: 56, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
17 17 0.30
19 30 0.54
20 1 0.02
21 8 0.14
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.38
Consensus pattern (19 bp):
ATCATATCTAAGATTGCAT
Found at i:2788126 original size:14 final size:15
Alignment explanation
Indices: 2788106--2788162 Score: 53
Period size: 17 Copynumber: 3.5 Consensus size: 15
2788096 AGATTGCATA
2788106 TCATATCTAAGATTG
1 TCATATCTAAGATTG
2788121 CATATCATATCTAAGATTG
1 ----TCATATCTAAGATTG
2788140 TATCATATCTAAGATTG
1 --TCATATCTAAGATTG
2788157 -CATATC
1 TCATATC
2788163 CTTAAAGATT
Statistics
Matches: 38, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
14 6 0.16
17 17 0.45
19 15 0.39
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.39
Consensus pattern (15 bp):
TCATATCTAAGATTG
Found at i:2788148 original size:36 final size:39
Alignment explanation
Indices: 2788084--2788162 Score: 128
Period size: 36 Copynumber: 2.1 Consensus size: 39
2788074 AGATTACAAG
2788084 ATCATATCTTCAAGATTGCATATCATATCTAAGATTGCAT
1 ATCATATCTTCAAGATTG-ATATCATATCTAAGATTGCAT
2788124 ATCATATC-T-AAGATTG-TATCATATCTAAGATTGCAT
1 ATCATATCTTCAAGATTGATATCATATCTAAGATTGCAT
2788160 ATC
1 ATC
2788163 CTTAAAGATT
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
36 23 0.59
38 7 0.18
39 1 0.03
40 8 0.21
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.38
Consensus pattern (39 bp):
ATCATATCTTCAAGATTGATATCATATCTAAGATTGCAT
Found at i:2794880 original size:14 final size:14
Alignment explanation
Indices: 2794861--2794888 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2794851 CTTTGTACAC
2794861 TAGTCACAGGCTTT
1 TAGTCACAGGCTTT
2794875 TAGTCACAGGCTTT
1 TAGTCACAGGCTTT
2794889 GATTTGCGGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.36
Consensus pattern (14 bp):
TAGTCACAGGCTTT
Found at i:2797541 original size:16 final size:16
Alignment explanation
Indices: 2797517--2797547 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2797507 TGGTTTACAA
2797517 AGGAAGAGGAAGAAGG
1 AGGAAGAGGAAGAAGG
*
2797533 AGGAGGAGGAAGAAG
1 AGGAAGAGGAAGAAG
2797548 AGGGTGAATT
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:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (16 bp):
AGGAAGAGGAAGAAGG
Found at i:2802921 original size:49 final size:49
Alignment explanation
Indices: 2802861--2802961 Score: 193
Period size: 49 Copynumber: 2.1 Consensus size: 49
2802851 ACGTCACTAA
*
2802861 AATTAATAGGCATTAACTTTTCTATCTATTTTAGGACGATTGGACAAAC
1 AATTAACAGGCATTAACTTTTCTATCTATTTTAGGACGATTGGACAAAC
2802910 AATTAACAGGCATTAACTTTTCTATCTATTTTAGGACGATTGGACAAAC
1 AATTAACAGGCATTAACTTTTCTATCTATTTTAGGACGATTGGACAAAC
2802959 AAT
1 AAT
2802962 GTAAGTGTAA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 51 1.00
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.36
Consensus pattern (49 bp):
AATTAACAGGCATTAACTTTTCTATCTATTTTAGGACGATTGGACAAAC
Found at i:2804305 original size:16 final size:16
Alignment explanation
Indices: 2804266--2804304 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
2804256 AAAACTATGG
2804266 TGTCTTTTGGGTTTCT
1 TGTCTTTTGGGTTTCT
2804282 TGTCTTTTGGGTTTCT
1 TGTCTTTTGGGTTTCT
2804298 TGT-TTTT
1 TGTCTTTT
2804305 TAAGGCAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 4 0.17
16 19 0.83
ACGTcount: A:0.00, C:0.10, G:0.23, T:0.67
Consensus pattern (16 bp):
TGTCTTTTGGGTTTCT
Found at i:2806481 original size:47 final size:47
Alignment explanation
Indices: 2806427--2806522 Score: 183
Period size: 47 Copynumber: 2.0 Consensus size: 47
2806417 AACTCACTTA
*
2806427 ACTGTTAAAATCTTTGTTATATGATCTTCTTTGTTTGCATCACATGT
1 ACTGTTAAAATCCTTGTTATATGATCTTCTTTGTTTGCATCACATGT
2806474 ACTGTTAAAATCCTTGTTATATGATCTTCTTTGTTTGCATCACATGT
1 ACTGTTAAAATCCTTGTTATATGATCTTCTTTGTTTGCATCACATGT
2806521 AC
1 AC
2806523 CAACTGAAAA
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:0.24, C:0.17, G:0.12, T:0.47
Consensus pattern (47 bp):
ACTGTTAAAATCCTTGTTATATGATCTTCTTTGTTTGCATCACATGT
Found at i:2812880 original size:33 final size:33
Alignment explanation
Indices: 2812841--2812907 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
2812831 TCTAATCATA
*
2812841 ATAACTTATTAATACAAGAGTGTGACATGCATC
1 ATAACTTATTAATACAAGAGTGTGACACGCATC
2812874 ATAACTTATTAATACAAGAGTGTGACACGCATC
1 ATAACTTATTAATACAAGAGTGTGACACGCATC
2812907 A
1 A
2812908 AACCTTTTAG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.40, C:0.16, G:0.15, T:0.28
Consensus pattern (33 bp):
ATAACTTATTAATACAAGAGTGTGACACGCATC
Found at i:2813944 original size:18 final size:18
Alignment explanation
Indices: 2813919--2813977 Score: 68
Period size: 19 Copynumber: 3.2 Consensus size: 18
2813909 TAAAAAAATA
2813919 TTTATAATTTTTATACTTT
1 TTTATAATTTTTA-ACTTT
*
2813938 TTT-TAATTATTCTAATTTT
1 TTTATAATT-TT-TAACTTT
2813957 TTTATAATTTTTAA-TTT
1 TTTATAATTTTTAACTTT
2813974 TTTA
1 TTTA
2813978 AAAAAATAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
17 7 0.19
18 8 0.22
19 14 0.39
20 7 0.19
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.69
Consensus pattern (18 bp):
TTTATAATTTTTAACTTT
Found at i:2813958 original size:17 final size:18
Alignment explanation
Indices: 2813936--2813978 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
2813926 TTTTTATACT
*
2813936 TTTTTTAATTA-TTCTAA
1 TTTTTTAATAATTTCTAA
* *
2813953 TTTTTTTATAATTTTTAA
1 TTTTTTAATAATTTCTAA
2813971 TTTTTTAA
1 TTTTTTAA
2813979 AAAAATAATT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 9 0.43
18 12 0.57
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (18 bp):
TTTTTTAATAATTTCTAA
Found at i:2814865 original size:17 final size:18
Alignment explanation
Indices: 2814834--2814867 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
2814824 AATTTAAATT
2814834 TAATTAAATTATTTAAAA
1 TAATTAAATTATTTAAAA
*
2814852 TAATT-AATTTTTTAAA
1 TAATTAAATTATTTAAA
2814868 TTATAAACAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TAATTAAATTATTTAAAA
Found at i:2824445 original size:26 final size:26
Alignment explanation
Indices: 2824411--2824462 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
2824401 AGTTATATCC
2824411 AATAACATCACTGTAAAATCGAACAT
1 AATAACATCACTGTAAAATCGAACAT
2824437 AATAACATCACTGTAAAATCGAACAT
1 AATAACATCACTGTAAAATCGAACAT
2824463 CTTTGTAAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.50, C:0.19, G:0.08, T:0.23
Consensus pattern (26 bp):
AATAACATCACTGTAAAATCGAACAT
Found at i:2828784 original size:16 final size:17
Alignment explanation
Indices: 2828750--2828789 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
2828740 ATAGAATTAG
2828750 AATTAGATTGAGAAAATT
1 AATTA-ATTGAGAAAATT
*
2828768 ATTTAATTGAG-AAATT
1 AATTAATTGAGAAAATT
2828784 AATTAA
1 AATTAA
2828790 ATTATTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 10 0.50
17 6 0.30
18 4 0.20
ACGTcount: A:0.50, C:0.00, G:0.12, T:0.38
Consensus pattern (17 bp):
AATTAATTGAGAAAATT
Found at i:2828792 original size:17 final size:18
Alignment explanation
Indices: 2828750--2828792 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
2828740 ATAGAATTAG
*
2828750 AATTAGATTGAGAAAATT
1 AATTAAATTGAGAAAATT
*
2828768 -ATTTAATTGAG-AAATT
1 AATTAAATTGAGAAAATT
2828784 AATTAAATT
1 AATTAAATT
2828793 ATTTAAATTA
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
16 5 0.24
17 16 0.76
ACGTcount: A:0.49, C:0.00, G:0.12, T:0.40
Consensus pattern (18 bp):
AATTAAATTGAGAAAATT
Found at i:2831184 original size:20 final size:20
Alignment explanation
Indices: 2831153--2831259 Score: 83
Period size: 20 Copynumber: 5.3 Consensus size: 20
2831143 TTGTATAGGA
* *
2831153 TAGAAATATTGGTAAATTTT
1 TAGAAATTTTGGTAAATCTT
* *
2831173 TAGAATTTTTGGTAAATCGT
1 TAGAAATTTTGGTAAATCTT
* * **
2831193 TA-AATATTTTGATATAGGTT
1 TAGAA-ATTTTGGTAAATCTT
*
2831213 TAGAAATTTTGGTAAATCAT
1 TAGAAATTTTGGTAAATCTT
* *
2831233 TAGAAATATTAGTAAAAT-TT
1 TAGAAATTTTGGT-AAATCTT
2831253 TAGAAAT
1 TAGAAAT
2831260 ATAGTAAATC
Statistics
Matches: 66, Mismatches: 18, Indels: 6
0.73 0.20 0.07
Matches are distributed among these distances:
19 2 0.03
20 58 0.88
21 6 0.09
ACGTcount: A:0.40, C:0.02, G:0.15, T:0.43
Consensus pattern (20 bp):
TAGAAATTTTGGTAAATCTT
Found at i:2831255 original size:40 final size:40
Alignment explanation
Indices: 2831153--2831259 Score: 110
Period size: 40 Copynumber: 2.7 Consensus size: 40
2831143 TTGTATAGGA
* * * *
2831153 TAGAAATATTGGTAAATTTTTAGAATTTTTGGTAAATCGT
1 TAGAAATATTAGTAAAATTTTAGAAATTTTGGTAAATCAT
* * **
2831193 T--AAATATTTTGATATAGGTTTAGAAATTTTGGTAAATCAT
1 TAGAAATA-TTAG-TAAAATTTTAGAAATTTTGGTAAATCAT
2831233 TAGAAATATTAGTAAAATTTTAGAAAT
1 TAGAAATATTAGTAAAATTTTAGAAAT
2831260 ATAGTAAATC
Statistics
Matches: 53, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
38 5 0.09
39 3 0.06
40 37 0.70
41 3 0.06
42 5 0.09
ACGTcount: A:0.40, C:0.02, G:0.15, T:0.43
Consensus pattern (40 bp):
TAGAAATATTAGTAAAATTTTAGAAATTTTGGTAAATCAT
Found at i:2831277 original size:19 final size:21
Alignment explanation
Indices: 2831212--2831278 Score: 72
Period size: 20 Copynumber: 3.4 Consensus size: 21
2831202 TGATATAGGT
* *
2831212 TTAGAAATTTTGGTAAATC-A
1 TTAGAAATATTAGTAAATCTA
2831232 TTAGAAATATTAGTAAAAT-T-
1 TTAGAAATATTAGT-AAATCTA
2831252 TTAGAAATA-TAGTAAATCTA
1 TTAGAAATATTAGTAAATCTA
2831272 TT-GAAAT
1 TTAGAAAT
2831279 TATGATAAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
18 4 0.10
19 10 0.24
20 23 0.56
21 4 0.10
ACGTcount: A:0.46, C:0.03, G:0.12, T:0.39
Consensus pattern (21 bp):
TTAGAAATATTAGTAAATCTA
Found at i:2835742 original size:12 final size:12
Alignment explanation
Indices: 2835722--2835759 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
2835712 CTATCTCTTA
*
2835722 ACTTCGAAACAC
1 ACTTTGAAACAC
2835734 ACTTTGAAACAC
1 ACTTTGAAACAC
2835746 ACTTT-AAATCAC
1 ACTTTGAAA-CAC
2835758 AC
1 AC
2835760 GATTTCGAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 3 0.12
12 21 0.88
ACGTcount: A:0.42, C:0.29, G:0.05, T:0.24
Consensus pattern (12 bp):
ACTTTGAAACAC
Found at i:2837392 original size:13 final size:13
Alignment explanation
Indices: 2837374--2837399 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2837364 TTCCCAAAAT
2837374 ATTAATTAATTTA
1 ATTAATTAATTTA
2837387 ATTAATTAATTTA
1 ATTAATTAATTTA
2837400 CCTAATTAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
ATTAATTAATTTA
Found at i:2838401 original size:26 final size:25
Alignment explanation
Indices: 2838372--2838441 Score: 77
Period size: 26 Copynumber: 2.7 Consensus size: 25
2838362 TTAGCAGATA
**
2838372 TTGAGCCAGTGATTATTTAGTAGACC
1 TTGAGCC-GTGATTATTTAACAGACC
* *
2838398 TTGAGCCGGTGTTTATTTAACAGACT
1 TTGAGCC-GTGATTATTTAACAGACC
2838424 TTGAGCCGATGATTATTT
1 TTGAGCCG-TGATTATTT
2838442 GTGATTATTT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
25 1 0.03
26 36 0.97
ACGTcount: A:0.24, C:0.14, G:0.23, T:0.39
Consensus pattern (25 bp):
TTGAGCCGTGATTATTTAACAGACC
Found at i:2846409 original size:28 final size:28
Alignment explanation
Indices: 2846369--2846424 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
2846359 ATCCTTGTGC
2846369 TTTTTTTTACTGTTCTCTTCATTTACCA
1 TTTTTTTTACTGTTCTCTTCATTTACCA
2846397 TTTTTTTTACTGTTCTCTTCATTTACCA
1 TTTTTTTTACTGTTCTCTTCATTTACCA
2846425 GCTTTAGTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.14, C:0.21, G:0.04, T:0.61
Consensus pattern (28 bp):
TTTTTTTTACTGTTCTCTTCATTTACCA
Found at i:2857324 original size:31 final size:30
Alignment explanation
Indices: 2857267--2857324 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 30
2857257 TTTAAAAAAT
*
2857267 TTGTTATTTTAGTAACTCTTGTTAGATAAA
1 TTGTTATTTTAGTAACTCCTGTTAGATAAA
*
2857297 TTGTTAATTTTAGTCACTCCCTG-TAGAT
1 TTGTT-ATTTTAGTAACT-CCTGTTAGAT
2857325 GAGTTGTCAG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 5 0.21
31 16 0.67
32 3 0.12
ACGTcount: A:0.26, C:0.12, G:0.14, T:0.48
Consensus pattern (30 bp):
TTGTTATTTTAGTAACTCCTGTTAGATAAA
Found at i:2868067 original size:31 final size:31
Alignment explanation
Indices: 2868006--2868082 Score: 77
Period size: 31 Copynumber: 2.5 Consensus size: 31
2867996 ATTTTCATCC
* * *
2868006 AATTAAGTCTTTGAATTTAGTTTTAAGATTT
1 AATTTAGTATTTGAATTTAGATTTAAGATTT
*
2868037 AATTTAGTATTTGAATTT-GATTTATTGATTT
1 AATTTAGTATTTGAATTTAGATTTA-AGATTT
*
2868068 AAATT-GATATTTGAA
1 AATTTAG-TATTTGAA
2868083 CTCAATTTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
30 6 0.15
31 33 0.85
ACGTcount: A:0.34, C:0.01, G:0.13, T:0.52
Consensus pattern (31 bp):
AATTTAGTATTTGAATTTAGATTTAAGATTT
Found at i:2868072 original size:19 final size:18
Alignment explanation
Indices: 2868019--2868072 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 18
2868009 TAAGTCTTTG
2868019 AATTTAGT-TTTAAGATTT
1 AATTTAGTATTTAA-ATTT
*
2868037 AATTTAGTATTTGAATTT
1 AATTTAGTATTTAAATTT
* *
2868055 GATTTATTGATTTAAATT
1 AATTTAGT-ATTTAAATT
2868073 GATATTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
18 18 0.60
19 12 0.40
ACGTcount: A:0.33, C:0.00, G:0.11, T:0.56
Consensus pattern (18 bp):
AATTTAGTATTTAAATTT
Found at i:2868179 original size:32 final size:31
Alignment explanation
Indices: 2868120--2868179 Score: 84
Period size: 32 Copynumber: 1.9 Consensus size: 31
2868110 TAGGTAACTT
* *
2868120 ATTTAAATTATAAAGTTAAGTTCAAATACTA
1 ATTTAAATTAAAAAATTAAGTTCAAATACTA
*
2868151 ATTTAAATTAAAAAAATTAAGTTTAAATA
1 ATTTAAATT-AAAAAATTAAGTTCAAATA
2868180 TTAAATTGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
31 9 0.36
32 16 0.64
ACGTcount: A:0.53, C:0.03, G:0.05, T:0.38
Consensus pattern (31 bp):
ATTTAAATTAAAAAATTAAGTTCAAATACTA
Found at i:2877636 original size:11 final size:11
Alignment explanation
Indices: 2877622--2877663 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
2877612 GTTGTTTTTC
2877622 ACTATTTTGCT
1 ACTATTTTGCT
**
2877633 ACTATTTCACT
1 ACTATTTTGCT
*
2877644 ACTATGTTGCT
1 ACTATTTTGCT
2877655 ACTATTTTG
1 ACTATTTTG
2877664 TTGCTATTGT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.21, C:0.19, G:0.10, T:0.50
Consensus pattern (11 bp):
ACTATTTTGCT
Found at i:2877712 original size:17 final size:19
Alignment explanation
Indices: 2877679--2877713 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
2877669 ATTGTTTGTA
2877679 TATTGTATAACTTTTGTTT
1 TATTGTATAACTTTTGTTT
2877698 TATTGT-TAA-TTTTGTT
1 TATTGTATAACTTTTGTT
2877714 ACTATTTTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 3 0.19
19 6 0.38
ACGTcount: A:0.20, C:0.03, G:0.11, T:0.66
Consensus pattern (19 bp):
TATTGTATAACTTTTGTTT
Found at i:2883145 original size:15 final size:14
Alignment explanation
Indices: 2883125--2883181 Score: 69
Period size: 15 Copynumber: 3.9 Consensus size: 14
2883115 CGATGAATTT
2883125 ATTGAACTTATATTG
1 ATTGAA-TTATATTG
*
2883140 ATTGAAATTATTTTG
1 ATTG-AATTATATTG
*
2883155 ATTGAATTTTTATTG
1 ATTGAA-TTATATTG
2883170 ATTGAATTATAT
1 ATTGAATTATAT
2883182 AATATATATG
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
14 7 0.19
15 27 0.75
16 2 0.06
ACGTcount: A:0.33, C:0.02, G:0.12, T:0.53
Consensus pattern (14 bp):
ATTGAATTATATTG
Found at i:2883399 original size:18 final size:18
Alignment explanation
Indices: 2883376--2883410 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
2883366 TTGAATTAAA
2883376 TGAAAATGTATGAAATTG
1 TGAAAATGTATGAAATTG
2883394 TGAAAATGTATGAAATT
1 TGAAAATGTATGAAATT
2883411 CTTTCATCAA
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:0.46, C:0.00, G:0.20, T:0.34
Consensus pattern (18 bp):
TGAAAATGTATGAAATTG
Found at i:2884873 original size:19 final size:22
Alignment explanation
Indices: 2884834--2884873 Score: 59
Period size: 19 Copynumber: 2.0 Consensus size: 22
2884824 AGAAACCCAA
2884834 CCATATCCAACCGTATACACCC
1 CCATATCCAACCGTATACACCC
2884856 CCATA-CCAACC-T-TACACC
1 CCATATCCAACCGTATACACC
2884874 GTGTGGGGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.33
20 1 0.06
21 6 0.33
22 5 0.28
ACGTcount: A:0.33, C:0.47, G:0.03, T:0.17
Consensus pattern (22 bp):
CCATATCCAACCGTATACACCC
Found at i:2884972 original size:27 final size:26
Alignment explanation
Indices: 2884935--2885045 Score: 132
Period size: 27 Copynumber: 4.1 Consensus size: 26
2884925 AGCATGGCTG
* *
2884935 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
*
2884961 CCAGATACAGATAATCGTGGTAGAGCCA
1 CCAGA-ACAGATAAT-GTGGCAGAGCCA
2884989 CCAGAACAGATATATGTGGCAGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
* * *
2885016 CCAGATCAGATATTTGTGGCATAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
2885043 CCA
1 CCA
2885046 AAACGCTTCC
Statistics
Matches: 75, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
26 5 0.07
27 54 0.72
28 16 0.21
ACGTcount: A:0.36, C:0.23, G:0.23, T:0.18
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:2884994 original size:54 final size:54
Alignment explanation
Indices: 2884935--2885045 Score: 152
Period size: 54 Copynumber: 2.1 Consensus size: 54
2884925 AGCATGGCTG
* *
2884935 CCAGAACAGATA-ATGTGACAGAGTCACCAGATACAGATAATCGTGGTAGAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGAT-CAGATAATCGTGGCAGAGCCA
* * * *
2884989 CCAGAACAGATATATGTGGCAGAGCCACCAGATCAGATATTTGTGGCATAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
2885043 CCA
1 CCA
2885046 AAACGCTTCC
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
54 32 0.64
55 18 0.36
ACGTcount: A:0.36, C:0.23, G:0.23, T:0.18
Consensus pattern (54 bp):
CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
Found at i:2885223 original size:28 final size:28
Alignment explanation
Indices: 2885180--2885255 Score: 134
Period size: 28 Copynumber: 2.7 Consensus size: 28
2885170 ATTTTGCACC
* *
2885180 TAGGGGTATAACAGTAATTTTCCATACA
1 TAGGGGTATTATAGTAATTTTCCATACA
2885208 TAGGGGTATTATAGTAATTTTCCATACA
1 TAGGGGTATTATAGTAATTTTCCATACA
2885236 TAGGGGTATTATAGTAATTT
1 TAGGGGTATTATAGTAATTT
2885256 AGCTACTTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 46 1.00
ACGTcount: A:0.33, C:0.09, G:0.20, T:0.38
Consensus pattern (28 bp):
TAGGGGTATTATAGTAATTTTCCATACA
Found at i:2886713 original size:26 final size:26
Alignment explanation
Indices: 2886677--2886786 Score: 175
Period size: 26 Copynumber: 4.2 Consensus size: 26
2886667 CATGAAATTC
2886677 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
*
2886703 TTATCATGAAACATTTACCTAACTCA
1 TTATCATGAAACATTTACCTAACCCA
* *
2886729 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
* *
2886755 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
2886781 TTATCA
1 TTATCA
2886787 ATTTGTATCA
Statistics
Matches: 80, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 80 1.00
ACGTcount: A:0.36, C:0.24, G:0.05, T:0.35
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:2887137 original size:15 final size:15
Alignment explanation
Indices: 2887119--2887172 Score: 65
Period size: 15 Copynumber: 3.6 Consensus size: 15
2887109 GGGGCGTTAC
2887119 AAATTCAATCAATAA
1 AAATTCAATCAATAA
*
2887134 AAATTCAATTAA-AA
1 AAATTCAATCAATAA
* *
2887148 TAATTTCAATCAATAT
1 -AAATTCAATCAATAA
2887164 AAATTCAAT
1 AAATTCAAT
2887173 AAATTCATCG
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
14 2 0.06
15 29 0.91
16 1 0.03
ACGTcount: A:0.56, C:0.11, G:0.00, T:0.33
Consensus pattern (15 bp):
AAATTCAATCAATAA
Found at i:2887971 original size:2 final size:2
Alignment explanation
Indices: 2887964--2887992 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2887954 CATTAAACGA
2887964 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 A
2887993 ATAATAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2888162 original size:15 final size:16
Alignment explanation
Indices: 2888128--2888164 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
2888118 CTTTTACTTA
2888128 ATAATAATATATAATT
1 ATAATAATATATAATT
*
2888144 -TAATAATATAT-TTT
1 ATAATAATATATAATT
2888158 ATAATAA
1 ATAATAA
2888165 GTAAATATAC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
14 2 0.11
15 17 0.89
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
ATAATAATATATAATT
Found at i:2888326 original size:17 final size:18
Alignment explanation
Indices: 2888282--2888326 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 18
2888272 AATATAATTA
2888282 TTTAATTAATAAATATCTT
1 TTTAA-TAATAAATATCTT
2888301 TTGTAAATAATAAATATC-T
1 TT-T-AATAATAAATATCTT
2888320 TTTAATA
1 TTTAATA
2888327 CTTAAATACA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
17 4 0.17
18 1 0.04
19 5 0.21
20 12 0.50
21 2 0.08
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.49
Consensus pattern (18 bp):
TTTAATAATAAATATCTT
Found at i:2893708 original size:19 final size:18
Alignment explanation
Indices: 2893673--2893713 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
2893663 TTGTTAATTC
2893673 ACTTTTGTCCATTTTTTT
1 ACTTTTGTCCATTTTTTT
*
2893691 ACTTTT-TCTCATTATTTT
1 ACTTTTGTC-CATTTTTTT
2893709 A-TTTT
1 ACTTTT
2893714 AGTCTTAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 6 0.29
18 15 0.71
ACGTcount: A:0.15, C:0.15, G:0.02, T:0.68
Consensus pattern (18 bp):
ACTTTTGTCCATTTTTTT
Found at i:2893787 original size:25 final size:24
Alignment explanation
Indices: 2893759--2893816 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 24
2893749 CTGCTATCAT
*
2893759 TATTATATT-TTATTTATTAGCATGG
1 TATTATATTATTA-TTATTA-CATAG
*
2893784 TATTATTATTATTATTATTACTTAG
1 TATTA-TATTATTATTATTACATAG
2893809 TATTATAT
1 TATTATAT
2893817 ACATATATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
24 3 0.10
25 13 0.45
26 10 0.34
27 3 0.10
ACGTcount: A:0.31, C:0.03, G:0.07, T:0.59
Consensus pattern (24 bp):
TATTATATTATTATTATTACATAG
Found at i:2893870 original size:18 final size:19
Alignment explanation
Indices: 2893834--2893871 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
2893824 TATCATATAG
*
2893834 TATTATTAATTTGTTTTAA
1 TATTATTAATTTGTGTTAA
*
2893853 TATTATTATTTTG-GTTAA
1 TATTATTAATTTGTGTTAA
2893871 T
1 T
2893872 GTATTTGACA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.29, C:0.00, G:0.08, T:0.63
Consensus pattern (19 bp):
TATTATTAATTTGTGTTAA
Found at i:2896279 original size:23 final size:23
Alignment explanation
Indices: 2896249--2896295 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
2896239 GCTTTTTCTA
* *
2896249 TATCTTACGGTCATTTCGGTACT
1 TATCTTACCGTCATTTCGGAACT
2896272 TATCTTACCGTCATTTCGGAACT
1 TATCTTACCGTCATTTCGGAACT
2896295 T
1 T
2896296 TAGACTTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.19, C:0.23, G:0.15, T:0.43
Consensus pattern (23 bp):
TATCTTACCGTCATTTCGGAACT
Found at i:2897630 original size:22 final size:22
Alignment explanation
Indices: 2897602--2897660 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 22
2897592 CTCAAAACCC
2897602 AGGTACCAAACCCTT-ACTCAAG
1 AGGTACCAAACCCTTGAC-CAAG
* *
2897624 AGGTACCAAACCCTTGACGATG
1 AGGTACCAAACCCTTGACCAAG
*
2897646 AGGTACAAAACCCTT
1 AGGTACCAAACCCTT
2897661 CCTAATTGTG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
22 31 0.94
23 2 0.06
ACGTcount: A:0.36, C:0.29, G:0.17, T:0.19
Consensus pattern (22 bp):
AGGTACCAAACCCTTGACCAAG
Found at i:2901252 original size:5 final size:5
Alignment explanation
Indices: 2901242--2901285 Score: 63
Period size: 5 Copynumber: 8.8 Consensus size: 5
2901232 GTTATTATTA
*
2901242 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCA TTTCAT TTT-T TTTC
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTC-T TTTCT TTTC
2901286 CCTCTAGAAC
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
4 4 0.11
5 28 0.80
6 3 0.09
ACGTcount: A:0.05, C:0.18, G:0.00, T:0.77
Consensus pattern (5 bp):
TTTCT
Found at i:2904109 original size:36 final size:36
Alignment explanation
Indices: 2904069--2904137 Score: 120
Period size: 36 Copynumber: 1.9 Consensus size: 36
2904059 TGCGTCGATG
*
2904069 CCCTCCTGGTGGATCTCCCACTTACAGCTCTGGATA
1 CCCTCCTGGTGGATCTCCCACTTACAGCACTGGATA
*
2904105 CCCTCCTGGTGGATCTCCCACTTTCAGCACTGG
1 CCCTCCTGGTGGATCTCCCACTTACAGCACTGG
2904138 GAGCCAGTCT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.14, C:0.38, G:0.20, T:0.28
Consensus pattern (36 bp):
CCCTCCTGGTGGATCTCCCACTTACAGCACTGGATA
Found at i:2905525 original size:24 final size:21
Alignment explanation
Indices: 2905497--2905550 Score: 54
Period size: 24 Copynumber: 2.4 Consensus size: 21
2905487 GCAAAAAAAA
2905497 TTTAAAATATATATTTATATTATT
1 TTTAAAATA-ATATTT-T-TTATT
**
2905521 TTTAATTTAATATTTTTTATT
1 TTTAAAATAATATTTTTTATT
2905542 TATTAAAAT
1 T-TTAAAAT
2905551 TTTATATAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
21 6 0.24
22 6 0.24
23 6 0.24
24 7 0.28
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
TTTAAAATAATATTTTTTATT
Found at i:2916410 original size:22 final size:23
Alignment explanation
Indices: 2916378--2916430 Score: 81
Period size: 22 Copynumber: 2.3 Consensus size: 23
2916368 AAAACTCCTG
2916378 GTTTTCTTTACTATTTTCTTGCT
1 GTTTTCTTTACTATTTTCTTGCT
*
2916401 GTTTT-TTTACTATTTTGTTGCT
1 GTTTTCTTTACTATTTTCTTGCT
*
2916423 ATTTTCTT
1 GTTTTCTT
2916431 GTTCTTTTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
22 20 0.74
23 7 0.26
ACGTcount: A:0.09, C:0.13, G:0.09, T:0.68
Consensus pattern (23 bp):
GTTTTCTTTACTATTTTCTTGCT
Found at i:2916449 original size:11 final size:11
Alignment explanation
Indices: 2916379--2916449 Score: 61
Period size: 11 Copynumber: 6.4 Consensus size: 11
2916369 AAACTCCTGG
2916379 TTTTCTTTACTA
1 TTTTC-TTACTA
* *
2916391 TTTTCTTGCTG
1 TTTTCTTACTA
*
2916402 TTTTTTTACTA
1 TTTTCTTACTA
* *
2916413 TTTTGTTGCTA
1 TTTTCTTACTA
** *
2916424 TTTTCTTGTTC
1 TTTTCTTACTA
2916435 TTTTCTTACTA
1 TTTTCTTACTA
2916446 TTTT
1 TTTT
2916450 ACTATAATTT
Statistics
Matches: 46, Mismatches: 13, Indels: 1
0.77 0.22 0.02
Matches are distributed among these distances:
11 41 0.89
12 5 0.11
ACGTcount: A:0.10, C:0.14, G:0.07, T:0.69
Consensus pattern (11 bp):
TTTTCTTACTA
Found at i:2916871 original size:47 final size:47
Alignment explanation
Indices: 2916816--2916912 Score: 194
Period size: 47 Copynumber: 2.1 Consensus size: 47
2916806 GGTCCCAACC
2916816 CGATTCATAGATACTTCTAAACACTTATCAACCTTTTAACTTACCTA
1 CGATTCATAGATACTTCTAAACACTTATCAACCTTTTAACTTACCTA
2916863 CGATTCATAGATACTTCTAAACACTTATCAACCTTTTAACTTACCTA
1 CGATTCATAGATACTTCTAAACACTTATCAACCTTTTAACTTACCTA
2916910 CGA
1 CGA
2916913 AGTCTAAATA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 50 1.00
ACGTcount: A:0.34, C:0.26, G:0.05, T:0.35
Consensus pattern (47 bp):
CGATTCATAGATACTTCTAAACACTTATCAACCTTTTAACTTACCTA
Found at i:2916924 original size:47 final size:47
Alignment explanation
Indices: 2916820--2916924 Score: 167
Period size: 47 Copynumber: 2.2 Consensus size: 47
2916810 CCAACCCGAT
* *
2916820 TCATAGATACTTCTAAACACTTATCAACCTTTTAACTTACCTACGAT
1 TCATAAATACTTCTAAACACTTATCAACCTTTTAACTTACCTACGAG
*
2916867 TCATAGATACTTCTAAACACTTATCAACCTTTTAACTTACCTACGAAG
1 TCATAAATACTTCTAAACACTTATCAACCTTTTAACTTACCTACG-AG
2916915 TC-TAAATACT
1 TCATAAATACT
2916925 ATAATGGTAC
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
47 52 0.95
48 3 0.05
ACGTcount: A:0.35, C:0.25, G:0.05, T:0.35
Consensus pattern (47 bp):
TCATAAATACTTCTAAACACTTATCAACCTTTTAACTTACCTACGAG
Found at i:2928765 original size:3 final size:3
Alignment explanation
Indices: 2928757--2928799 Score: 63
Period size: 3 Copynumber: 15.0 Consensus size: 3
2928747 TACTGCATTA
*
2928757 ATG ATG ATG ATG ATG ATG AT- ATT ATG ATG ATG ATG ATG -TG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
2928800 GCTTCAGTGA
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
2 4 0.11
3 33 0.89
ACGTcount: A:0.33, C:0.00, G:0.30, T:0.37
Consensus pattern (3 bp):
ATG
Found at i:2929662 original size:25 final size:25
Alignment explanation
Indices: 2929610--2929660 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 25
2929600 TCATATTATT
*
2929610 AATATATATATAAATTTTTATAATA
1 AATATATATATAAAGTTTTATAATA
* *
2929635 AATATATTTATTAAGTTTTAT-ATA
1 AATATATATATAAAGTTTTATAATA
2929659 AA
1 AA
2929661 ATTTAAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 5 0.22
25 18 0.78
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (25 bp):
AATATATATATAAAGTTTTATAATA
Found at i:2934420 original size:15 final size:15
Alignment explanation
Indices: 2934400--2934450 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 15
2934390 TTGCCTTAAA
2934400 TTATATTTTAATCAT
1 TTATATTTTAATCAT
*
2934415 TTATA-TTTAA-AATT
1 TTATATTTTAATCA-T
*
2934429 TTACATTTTAATCAT
1 TTATATTTTAATCAT
2934444 TTATATT
1 TTATATT
2934451 ATTATTTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
13 1 0.03
14 10 0.34
15 17 0.59
16 1 0.03
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.59
Consensus pattern (15 bp):
TTATATTTTAATCAT
Found at i:2934653 original size:31 final size:29
Alignment explanation
Indices: 2934590--2934653 Score: 76
Period size: 29 Copynumber: 2.1 Consensus size: 29
2934580 CTATAACGTG
*
2934590 AGTAACTAAAATGTAACATTTTAAACATA
1 AGTAACTAAAATGTAACATTTTAAACAAA
*
2934619 AGTAATTAAAATGTAA-ATTTAAGTAAACAAA
1 AGTAACTAAAATGTAACATTT---TAAACAAA
2934650 AGTA
1 AGTA
2934654 CTATTTTTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 4 0.13
29 15 0.50
31 11 0.37
ACGTcount: A:0.55, C:0.06, G:0.09, T:0.30
Consensus pattern (29 bp):
AGTAACTAAAATGTAACATTTTAAACAAA
Found at i:2935379 original size:19 final size:18
Alignment explanation
Indices: 2935355--2935398 Score: 56
Period size: 17 Copynumber: 2.4 Consensus size: 18
2935345 GGAAACAAAT
2935355 TATAAAAATCAT-TGAGAAA
1 TATAAAAAT-ATAT-AGAAA
2935374 TAT-AAAATATATAGAAA
1 TATAAAAATATATAGAAA
2935391 TATAAAAA
1 TATAAAAA
2935399 AAACTATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
17 10 0.43
18 10 0.43
19 3 0.13
ACGTcount: A:0.64, C:0.02, G:0.07, T:0.27
Consensus pattern (18 bp):
TATAAAAATATATAGAAA
Found at i:2935513 original size:9 final size:9
Alignment explanation
Indices: 2935499--2935551 Score: 54
Period size: 10 Copynumber: 5.7 Consensus size: 9
2935489 AAAAGAAGTA
2935499 TTTTATAATT
1 TTTTATAA-T
2935509 TTTATATAAT
1 TTT-TATAAT
2935519 TTTTATTAAT
1 TTTTA-TAAT
*
2935529 TTTT-TATT
1 TTTTATAAT
*
2935537 TTTTATCAT
1 TTTTATAAT
2935546 TTTTAT
1 TTTTAT
2935552 CACATTTCAC
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
8 7 0.19
9 10 0.27
10 15 0.41
11 5 0.14
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (9 bp):
TTTTATAAT
Found at i:2935518 original size:11 final size:11
Alignment explanation
Indices: 2935502--2935532 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
2935492 AGAAGTATTT
2935502 TATAATTTTTA
1 TATAATTTTTA
2935513 TATAATTTTTA
1 TATAATTTTTA
2935524 T-TAATTTTT
1 TATAATTTTT
2935533 TATTTTTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 8 0.40
11 12 0.60
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
TATAATTTTTA
Found at i:2938710 original size:15 final size:15
Alignment explanation
Indices: 2938690--2938719 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2938680 TTCCCCTCCG
2938690 TAACACAGGTTTTTA
1 TAACACAGGTTTTTA
2938705 TAACACAGGTTTTTA
1 TAACACAGGTTTTTA
2938720 ATATGTCAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.40
Consensus pattern (15 bp):
TAACACAGGTTTTTA
Found at i:2941879 original size:29 final size:29
Alignment explanation
Indices: 2941847--2941902 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 29
2941837 GTAATACATG
* * *
2941847 TATTATTCAAGTATAAGATATTTATTATT
1 TATTATTCAAATAAAAGATAATTATTATT
* *
2941876 TATTTTTTAAATAAAAGATAATTATTA
1 TATTATTCAAATAAAAGATAATTATTA
2941903 GATAATTAAT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 22 1.00
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (29 bp):
TATTATTCAAATAAAAGATAATTATTATT
Found at i:2942175 original size:14 final size:15
Alignment explanation
Indices: 2942156--2942186 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
2942146 TAATTAAAAC
2942156 AATAAAGT-AAATAA
1 AATAAAGTAAAATAA
2942170 AATAAAGTAAAATAA
1 AATAAAGTAAAATAA
2942185 AA
1 AA
2942187 GAAACTAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.50
15 8 0.50
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.19
Consensus pattern (15 bp):
AATAAAGTAAAATAA
Found at i:2942198 original size:9 final size:9
Alignment explanation
Indices: 2942179--2942231 Score: 56
Period size: 9 Copynumber: 5.9 Consensus size: 9
2942169 AAATAAAGTA
2942179 AAATAAAAG
1 AAATAAAAG
2942188 AAACT-AAAG
1 AAA-TAAAAG
2942197 AAATAAAAG
1 AAATAAAAG
*
2942206 AAAAAAAAAG
1 -AAATAAAAG
*
2942216 AAGTAAAAG
1 AAATAAAAG
2942225 AAA-AAAA
1 AAATAAAA
2942232 AAGAACAGCG
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
8 5 0.14
9 23 0.62
10 9 0.24
ACGTcount: A:0.79, C:0.02, G:0.11, T:0.08
Consensus pattern (9 bp):
AAATAAAAG
Found at i:2942202 original size:18 final size:18
Alignment explanation
Indices: 2942179--2942232 Score: 72
Period size: 18 Copynumber: 2.9 Consensus size: 18
2942169 AAATAAAGTA
**
2942179 AAATAAAAGAAACTAAAG
1 AAATAAAAGAAAAAAAAG
2942197 AAATAAAAGAAAAAAAAAG
1 AAATAAAAG-AAAAAAAAG
*
2942216 AAGTAAAAGAAAAAAAA
1 AAATAAAAGAAAAAAAA
2942233 AGAACAGCGG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
18 17 0.53
19 15 0.47
ACGTcount: A:0.80, C:0.02, G:0.11, T:0.07
Consensus pattern (18 bp):
AAATAAAAGAAAAAAAAG
Found at i:2942217 original size:19 final size:19
Alignment explanation
Indices: 2942179--2942236 Score: 82
Period size: 19 Copynumber: 3.1 Consensus size: 19
2942169 AAATAAAGTA
**
2942179 AAATAAAAG-AAACTAAAG
1 AAATAAAAGAAAAAAAAAG
2942197 AAATAAAAGAAAAAAAAAG
1 AAATAAAAGAAAAAAAAAG
*
2942216 AAGTAAAAGAAAAAAAAAG
1 AAATAAAAGAAAAAAAAAG
2942235 AA
1 AA
2942237 CAGCGGAAGC
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
18 9 0.25
19 27 0.75
ACGTcount: A:0.79, C:0.02, G:0.12, T:0.07
Consensus pattern (19 bp):
AAATAAAAGAAAAAAAAAG
Found at i:2942224 original size:28 final size:30
Alignment explanation
Indices: 2942159--2942232 Score: 77
Period size: 28 Copynumber: 2.6 Consensus size: 30
2942149 TTAAAACAAT
*
2942159 AAAGTAAATA-AAAT-AAAGTAAAATAAAAG
1 AAAGTAAA-AGAAATAAAAGTAAAAAAAAAG
*
2942188 AAACT-AAAGAAATAAAAG-AAAAAAAAAG
1 AAAGTAAAAGAAATAAAAGTAAAAAAAAAG
*
2942216 -AAGTAAAAGAAAAAAAA
1 AAAGTAAAAGAAATAAAA
2942233 AGAACAGCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
27 4 0.11
28 26 0.68
29 8 0.21
ACGTcount: A:0.77, C:0.01, G:0.11, T:0.11
Consensus pattern (30 bp):
AAAGTAAAAGAAATAAAAGTAAAAAAAAAG
Found at i:2943143 original size:44 final size:44
Alignment explanation
Indices: 2943093--2943184 Score: 116
Period size: 44 Copynumber: 2.1 Consensus size: 44
2943083 TGCTCAGGGA
*
2943093 TACTTCGACCTT-GAGTTGATAAGGCA-CTATAAGTGTCGTACTGT
1 TACTTCGA-CTTCGAGTCGATAAGGCACCT-TAAGTGTCGTACTGT
* **
2943137 TACTTCGACTTCGAGTCGATGAGGCACCTTGTGTGTCGTACTGT
1 TACTTCGACTTCGAGTCGATAAGGCACCTTAAGTGTCGTACTGT
2943181 TACT
1 TACT
2943185 ATTATTTCGG
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
43 3 0.07
44 37 0.88
45 2 0.05
ACGTcount: A:0.21, C:0.21, G:0.24, T:0.35
Consensus pattern (44 bp):
TACTTCGACTTCGAGTCGATAAGGCACCTTAAGTGTCGTACTGT
Found at i:2943392 original size:18 final size:18
Alignment explanation
Indices: 2943369--2943412 Score: 88
Period size: 18 Copynumber: 2.4 Consensus size: 18
2943359 ATTACCGGAC
2943369 TGAATAACTGATTGTTAT
1 TGAATAACTGATTGTTAT
2943387 TGAATAACTGATTGTTAT
1 TGAATAACTGATTGTTAT
2943405 TGAATAAC
1 TGAATAAC
2943413 AATAATCAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.36, C:0.07, G:0.16, T:0.41
Consensus pattern (18 bp):
TGAATAACTGATTGTTAT
Found at i:2945433 original size:29 final size:29
Alignment explanation
Indices: 2945377--2945433 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
2945367 TTATTTAATT
*
2945377 TTATTTAATAGCAAAGAGATTAAATTGAC
1 TTATTTAATAGCAAAGAGAATAAATTGAC
* *
2945406 TTATTTAATAGTACAAGA-AATAATTTGA
1 TTATTTAATAGCA-AAGAGAATAAATTGA
2945434 TACGTATAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 20 0.83
30 4 0.17
ACGTcount: A:0.46, C:0.05, G:0.12, T:0.37
Consensus pattern (29 bp):
TTATTTAATAGCAAAGAGAATAAATTGAC
Found at i:2949080 original size:53 final size:53
Alignment explanation
Indices: 2948939--2949089 Score: 214
Period size: 53 Copynumber: 2.8 Consensus size: 53
2948929 ACAAGTGTGC
* **
2948939 CCGTTTAAGACCATAGCTGGGCTATGGCATCGGTGCAATGTGATAATGTGACT
1 CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGACT
*
2948992 CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGATT
1 CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGACT
* *
2949045 CCGTATAAGACCAT-GTCTGGGATATGGCTTCGGTATGATATGTGA
1 CCGTATAAGACCATAG-CTGGGCTATGGCATCGGTAT-A-ATGTGA
2949090 ACCGTGTAAG
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
52 1 0.01
53 81 0.91
54 1 0.01
55 6 0.07
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.30
Consensus pattern (53 bp):
CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGACT
Found at i:2961618 original size:48 final size:46
Alignment explanation
Indices: 2961508--2961720 Score: 209
Period size: 46 Copynumber: 4.6 Consensus size: 46
2961498 TCATTTGTGT
* * * * *
2961508 GCTAATGTAAGACATGTCTGGGACATGTATCAGCCAC-A-ATATGAAA
1 GCTAGTGTAAGACATGTCTAGGACATGCATCGGCCTCGAGATAT--AA
*
2961554 GATAGTGTAAGACATGTCTAGGACATGCATCGGCCTCGAGATATTTAA
1 GCTAGTGTAAGACATGTCTAGGACATGCATCGGCCTCGAGATA--TAA
* * * *
2961602 GCTAGTGTAAGACATGTCTAGGACATGCATCGGCATTGAGGTGA-GA
1 GCTAGTGTAAGACATGTCTAGGACATGCATCGGCCTCGAGAT-ATAA
* * *
2961648 GCTAGTGTAAGACATGTCTCGGACATGCATCGGCCTCGCGAGATACA
1 GCTAGTGTAAGACATGTCTAGGACATGCATCGGCCTCGAGATATA-A
* *
2961695 GCTAGTGTAA-ACCTGTCTGGGACATG
1 GCTAGTGTAAGACATGTCTAGGACATG
2961721 GCGTCAACTT
Statistics
Matches: 140, Mismatches: 20, Indels: 14
0.80 0.11 0.08
Matches are distributed among these distances:
45 1 0.01
46 82 0.59
47 12 0.09
48 43 0.31
49 1 0.01
50 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.27, T:0.24
Consensus pattern (46 bp):
GCTAGTGTAAGACATGTCTAGGACATGCATCGGCCTCGAGATATAA
Found at i:2966178 original size:17 final size:19
Alignment explanation
Indices: 2966158--2966201 Score: 51
Period size: 17 Copynumber: 2.5 Consensus size: 19
2966148 AACTTTAAAA
2966158 ATAATTTTA-ATTT-AATT
1 ATAATTTTATATTTAAATT
*
2966175 ATAA-TATATATTTAAATT
1 ATAATTTTATATTTAAATT
2966193 -TAATTTTAT
1 ATAATTTTAT
2966202 TAAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
16 3 0.14
17 11 0.50
18 8 0.36
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
ATAATTTTATATTTAAATT
Found at i:2968183 original size:39 final size:39
Alignment explanation
Indices: 2968118--2968216 Score: 162
Period size: 39 Copynumber: 2.5 Consensus size: 39
2968108 ATCGTGATCT
* * *
2968118 GAAGCCCGAAGTCTACCTGAAGCACATAAGTGCTAAACG
1 GAAGCCCGAAGGCTAACTGAAACACATAAGTGCTAAACG
*
2968157 GAAGCCCGAAGGCTAATTGAAACACATAAGTGCTAAACG
1 GAAGCCCGAAGGCTAACTGAAACACATAAGTGCTAAACG
2968196 GAAGCCCGAAGGCTAACTGAA
1 GAAGCCCGAAGGCTAACTGAA
2968217 GCTGATCAGA
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 55 1.00
ACGTcount: A:0.38, C:0.23, G:0.24, T:0.14
Consensus pattern (39 bp):
GAAGCCCGAAGGCTAACTGAAACACATAAGTGCTAAACG
Found at i:2969457 original size:16 final size:18
Alignment explanation
Indices: 2969426--2969460 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
2969416 TAATTAACCC
2969426 CTCAATTAAGATAATTTT
1 CTCAATTAAGATAATTTT
2969444 CTCAATT-A-ATAATTTT
1 CTCAATTAAGATAATTTT
2969460 C
1 C
2969461 ATAAACATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.53
17 1 0.06
18 7 0.41
ACGTcount: A:0.37, C:0.14, G:0.03, T:0.46
Consensus pattern (18 bp):
CTCAATTAAGATAATTTT
Found at i:2971526 original size:74 final size:75
Alignment explanation
Indices: 2971423--2971572 Score: 284
Period size: 74 Copynumber: 2.0 Consensus size: 75
2971413 AAAAGAGCAA
2971423 GAAACGGGACAAAAACAGACAAAATATGCTAATTTTAGTGTTCCACACGGACTAGGTACTTTCAC
1 GAAACGGGACAAAAACAGACAAAATATGCTAATTTTAGTGTTCCACACGGACTAGGTACTTTCAC
2971488 ACGCCCGTGT
66 ACGCCCGTGT
*
2971498 GAAACGGGAC-AAAATAGACAAAATATGCTAATTTTAGTGTTCCACACGGACTAGGTACTTTCAC
1 GAAACGGGACAAAAACAGACAAAATATGCTAATTTTAGTGTTCCACACGGACTAGGTACTTTCAC
2971562 ACGCCCGTGT
66 ACGCCCGTGT
2971572 G
1 G
2971573 TGGCACACGG
Statistics
Matches: 74, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
74 64 0.86
75 10 0.14
ACGTcount: A:0.34, C:0.22, G:0.21, T:0.23
Consensus pattern (75 bp):
GAAACGGGACAAAAACAGACAAAATATGCTAATTTTAGTGTTCCACACGGACTAGGTACTTTCAC
ACGCCCGTGT
Found at i:2975437 original size:76 final size:76
Alignment explanation
Indices: 2975356--2975504 Score: 244
Period size: 76 Copynumber: 2.0 Consensus size: 76
2975346 ACCCTTTATA
** * **
2975356 TTGGGCACAATGACATTGCTTTAATGAAGACATGGTCCATTTTATGAGAAATAGGAATCCATTTA
1 TTGGGCACAAACACATTGCTTTAATGAAGACATGATCCATTTTATGAGAAATAGGAATCCATCAA
2975421 TTTACTTTAGG
66 TTTACTTTAGG
*
2975432 TTGGGCACAAACACATTGCTTTAATGAAGACATGATCCATTTTTTGAGAAATAGGAATCCATCAA
1 TTGGGCACAAACACATTGCTTTAATGAAGACATGATCCATTTTATGAGAAATAGGAATCCATCAA
2975497 TTTACTTT
66 TTTACTTT
2975505 CTATGTAGAT
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
76 67 1.00
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (76 bp):
TTGGGCACAAACACATTGCTTTAATGAAGACATGATCCATTTTATGAGAAATAGGAATCCATCAA
TTTACTTTAGG
Found at i:2976303 original size:17 final size:19
Alignment explanation
Indices: 2976280--2976323 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
2976270 AAGAAGATTT
2976280 AAATGAAAA-TTGT-TAAA
1 AAATGAAAAGTTGTATAAA
*
2976297 TAATGAAAAGTTGTATAAA
1 AAATGAAAAGTTGTATAAA
2976316 AAATGAAA
1 AAATGAAA
2976324 TGACAGGGTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 8 0.35
18 4 0.17
19 11 0.48
ACGTcount: A:0.59, C:0.00, G:0.14, T:0.27
Consensus pattern (19 bp):
AAATGAAAAGTTGTATAAA
Found at i:2976423 original size:38 final size:38
Alignment explanation
Indices: 2976379--2976455 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
2976369 ATCCTGAAGT
2976379 ACCTATTCAAGAAAAACTAAAACTTTTCCTAAGTACCA
1 ACCTATTCAAGAAAAACTAAAACTTTTCCTAAGTACCA
2976417 ACCTATTCAAGAAAAACTAAAACTTTTCCTAAGTACCA
1 ACCTATTCAAGAAAAACTAAAACTTTTCCTAAGTACCA
2976455 A
1 A
2976456 AAGTCAAGGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.45, C:0.23, G:0.05, T:0.26
Consensus pattern (38 bp):
ACCTATTCAAGAAAAACTAAAACTTTTCCTAAGTACCA
Found at i:2983689 original size:16 final size:16
Alignment explanation
Indices: 2983668--2983699 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
2983658 CCCAATTTGT
2983668 TACCATGTTGCTTTCA
1 TACCATGTTGCTTTCA
2983684 TACCATGTTGCTTTCA
1 TACCATGTTGCTTTCA
2983700 AAGTCTATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.25, G:0.12, T:0.44
Consensus pattern (16 bp):
TACCATGTTGCTTTCA
Found at i:2989544 original size:25 final size:26
Alignment explanation
Indices: 2989509--2989557 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
2989499 TTTATTTAAA
*
2989509 AAATAGTTTG-TAAAATCTATAATTAT
1 AAATAGTTTGTTAAAA-ATATAATTAT
2989535 AAAT-GTTTGTTAAAAATATAATT
1 AAATAGTTTGTTAAAAATATAATT
2989558 TAACCTTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 12 0.57
26 9 0.43
ACGTcount: A:0.47, C:0.02, G:0.08, T:0.43
Consensus pattern (26 bp):
AAATAGTTTGTTAAAAATATAATTAT
Found at i:2995000 original size:24 final size:25
Alignment explanation
Indices: 2994955--2995001 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
2994945 TATTATGGAT
* * *
2994955 AATAATTATAAGATAATCCCAAACA
1 AATAATTATAAAAAAATACCAAACA
2994980 AATAA-TATAAAAAAATACCAAA
1 AATAATTATAAAAAAATACCAAA
2995002 ACATAAATAG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 14 0.74
25 5 0.26
ACGTcount: A:0.64, C:0.13, G:0.02, T:0.21
Consensus pattern (25 bp):
AATAATTATAAAAAAATACCAAACA
Found at i:2995445 original size:91 final size:91
Alignment explanation
Indices: 2995290--2995471 Score: 364
Period size: 91 Copynumber: 2.0 Consensus size: 91
2995280 CATATTATAA
2995290 ATACAAATAATAAGACCAAATTAACATATTGATAGATTCCACTTGCTCTAGTCAATGCCAATGGT
1 ATACAAATAATAAGACCAAATTAACATATTGATAGATTCCACTTGCTCTAGTCAATGCCAATGGT
2995355 AAATTATGTTTCTTGACAGCATAGTC
66 AAATTATGTTTCTTGACAGCATAGTC
2995381 ATACAAATAATAAGACCAAATTAACATATTGATAGATTCCACTTGCTCTAGTCAATGCCAATGGT
1 ATACAAATAATAAGACCAAATTAACATATTGATAGATTCCACTTGCTCTAGTCAATGCCAATGGT
2995446 AAATTATGTTTCTTGACAGCATAGTC
66 AAATTATGTTTCTTGACAGCATAGTC
2995472 TAACCAGGCC
Statistics
Matches: 91, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
91 91 1.00
ACGTcount: A:0.37, C:0.18, G:0.13, T:0.32
Consensus pattern (91 bp):
ATACAAATAATAAGACCAAATTAACATATTGATAGATTCCACTTGCTCTAGTCAATGCCAATGGT
AAATTATGTTTCTTGACAGCATAGTC
Found at i:2999761 original size:28 final size:29
Alignment explanation
Indices: 2999706--2999774 Score: 77
Period size: 28 Copynumber: 2.4 Consensus size: 29
2999696 AAAATCAATA
*
2999706 TTGAGAGGTAAAATTTAAAAAAAAAAAAG
1 TTGAGTGGTAAAATTTAAAAAAAAAAAAG
** * *
2999735 TTGA-TGGTAAAATTTAATCACATAAAAG
1 TTGAGTGGTAAAATTTAAAAAAAAAAAAG
*
2999763 TTTAGTGGTAAA
1 TTGAGTGGTAAA
2999775 TATACAGAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
28 22 0.67
29 11 0.33
ACGTcount: A:0.51, C:0.03, G:0.17, T:0.29
Consensus pattern (29 bp):
TTGAGTGGTAAAATTTAAAAAAAAAAAAG
Found at i:3002097 original size:2 final size:2
Alignment explanation
Indices: 3002092--3002119 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3002082 TTCAATTCCT
3002092 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
3002120 AAGTCAAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3009924 original size:57 final size:58
Alignment explanation
Indices: 3009860--3009979 Score: 156
Period size: 58 Copynumber: 2.1 Consensus size: 58
3009850 TCTTTTTCAC
* *
3009860 TTTTCA-TTTTCATTTTGGAGAAAACCA-CATCCATTTCCAAATGATTT-CATTTCTCCA
1 TTTTCATTTTTCATTTTGGAGAAAACCATAAT-CATTTCAAAATG-TTTCCATTTCTCCA
* *
3009917 TTTTCATTTTTCATTTTGGAGAAACCCATAATCGTTTCAAAATGTTTCCCATTTCTCCA
1 TTTTCATTTTTCATTTTGGAGAAAACCATAATCATTTCAAAATGTTT-CCATTTCTCCA
3009976 TTTT
1 TTTT
3009980 TCACCATTTC
Statistics
Matches: 55, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
57 9 0.16
58 30 0.55
59 16 0.29
ACGTcount: A:0.26, C:0.22, G:0.07, T:0.45
Consensus pattern (58 bp):
TTTTCATTTTTCATTTTGGAGAAAACCATAATCATTTCAAAATGTTTCCATTTCTCCA
Found at i:3012476 original size:43 final size:44
Alignment explanation
Indices: 3012415--3012528 Score: 135
Period size: 43 Copynumber: 2.6 Consensus size: 44
3012405 TAAAGATAGA
*
3012415 ATTTAGCCTGGACTGGTAATTCTGATCT-TACGTT-GAAATCGGG
1 ATTTAGCCTGGACTGGTAATTCTGATCTATACGTTAGAAAT-GAG
* * * *
3012458 ATTTAGCCTGGATTGGTAATCCTGAT-TATATGTTAGAGATGAG
1 ATTTAGCCTGGACTGGTAATTCTGATCTATACGTTAGAAATGAG
* *
3012501 ATTTAGCCTGAACTGGTAATTCTTATCT
1 ATTTAGCCTGGACTGGTAATTCTGATCT
3012529 CACTGATTAT
Statistics
Matches: 59, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
42 1 0.02
43 53 0.90
44 5 0.08
ACGTcount: A:0.25, C:0.14, G:0.23, T:0.38
Consensus pattern (44 bp):
ATTTAGCCTGGACTGGTAATTCTGATCTATACGTTAGAAATGAG
Done.