Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D03
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: 50986338
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 218898 characters in sequence are not A, C, G, or T
File 8 of 170
Found at i:2430867 original size:105 final size:107
Alignment explanation
Indices: 2430748--2430989 Score: 328
Period size: 109 Copynumber: 2.3 Consensus size: 107
2430738 CATTTAATTT
*
2430748 TTTTTTTCATATACTGATATTTAATTCTAACACGAAAAAAAA-AA-AATTTAAATTGTACTGGGT
1 TTTTTTTCATATACTGATATTTGATTCTAACACGAAAAAAAAGAATAATTTAAATTGTACTGGGT
*** * *
2430811 GTCGGCCATTGACAGGCCAGAATCC-AAATTTTTTTATTTTTA
66 GAAAGCCATTGACAGGCCAGAACCCAAAATTTTCTT-TTTTTA
* **
2430853 TTTTTTTCATATACTGATATCTGATTCTAACACGAAAAAAAAGAATTTTTTTTAAATTGTACTGG
1 TTTTTTTCATATACTGATATTTGATTCTAACACGAAAAAAAAGAA--TAATTTAAATTGTACTGG
* *
2430918 GTGAAAGCCATTGACAGGCCTGCACCCAAAATTTTCTTTTTTTA
64 GTGAAAGCCATTGACAGGCCAGAACCCAAAATTTTCTTTTTTTA
*
2430962 TTTTTTTCGTATACTGATATTTGATTCT
1 TTTTTTTCATATACTGATATTTGATTCT
2430990 TAGACAATTT
Statistics
Matches: 119, Mismatches: 13, Indels: 6
0.86 0.09 0.04
Matches are distributed among these distances:
105 40 0.34
106 2 0.02
109 68 0.57
110 9 0.08
ACGTcount: A:0.32, C:0.14, G:0.12, T:0.42
Consensus pattern (107 bp):
TTTTTTTCATATACTGATATTTGATTCTAACACGAAAAAAAAGAATAATTTAAATTGTACTGGGT
GAAAGCCATTGACAGGCCAGAACCCAAAATTTTCTTTTTTTA
Found at i:2431757 original size:25 final size:25
Alignment explanation
Indices: 2431719--2431768 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
2431709 TGAATGTTGG
* *
2431719 TACTTAAACCAACATTAAATTTAAA
1 TACTTAAACCAACATGAAAATTAAA
**
2431744 TACTTAAATTAACATGAAAATTAAA
1 TACTTAAACCAACATGAAAATTAAA
2431769 CTCAAGTACC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.54, C:0.12, G:0.02, T:0.32
Consensus pattern (25 bp):
TACTTAAACCAACATGAAAATTAAA
Found at i:2436058 original size:25 final size:26
Alignment explanation
Indices: 2436004--2436058 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 26
2435994 CGGCCCGTTT
* * *
2436004 TTAATTAAAATTAAAATTAGTTTTTT
1 TTAATTAAAATTAAAATTAATTGTTA
2436030 TTAA-TAAAATTAAAATTAATTGTTA
1 TTAATTAAAATTAAAATTAATTGTTA
2436055 TTAA
1 TTAA
2436059 AATTAATTGT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
25 22 0.85
26 4 0.15
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (26 bp):
TTAATTAAAATTAAAATTAATTGTTA
Found at i:2436059 original size:16 final size:16
Alignment explanation
Indices: 2436038--2436079 Score: 75
Period size: 16 Copynumber: 2.6 Consensus size: 16
2436028 TTTTAATAAA
2436038 ATTAAAATTAATTGTT
1 ATTAAAATTAATTGTT
2436054 ATTAAAATTAATTGTT
1 ATTAAAATTAATTGTT
*
2436070 AATAAAATTA
1 ATTAAAATTA
2436080 TCAAATTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (16 bp):
ATTAAAATTAATTGTT
Found at i:2436164 original size:9 final size:9
Alignment explanation
Indices: 2436152--2436179 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
2436142 TTTATCAAAT
2436152 TATTAATTG
1 TATTAATTG
2436161 TATTAATTG
1 TATTAATTG
2436170 TATTAATTG
1 TATTAATTG
2436179 T
1 T
2436180 TGTAACAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:2436184 original size:68 final size:66
Alignment explanation
Indices: 2436072--2436211 Score: 244
Period size: 68 Copynumber: 2.1 Consensus size: 66
2436062 TAATTGTTAA
*
2436072 TAAAATTATCAAATTATTAATTGTTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTA
1 TAAAATTATCAAATTATTAATTGTTAATTGTATTAATTGTTGTAACAAAATCTAACATTTGATTA
2436137 G
66 G
*
2436138 TAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAACAAAATCTAACATTTGAT
1 TAAAATTATCAAATTATTAATTG--TTAATTGTATTAATTGTTGTAACAAAATCTAACATTTGAT
2436203 TAG
64 TAG
2436206 TAAAAT
1 TAAAAT
2436212 AAACTTGATG
Statistics
Matches: 69, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
66 22 0.32
68 47 0.68
ACGTcount: A:0.41, C:0.05, G:0.09, T:0.45
Consensus pattern (66 bp):
TAAAATTATCAAATTATTAATTGTTAATTGTATTAATTGTTGTAACAAAATCTAACATTTGATTA
G
Found at i:2436316 original size:22 final size:24
Alignment explanation
Indices: 2436276--2436319 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
2436266 AAATAAACTT
2436276 AAAATAAAAAACTATTATATTTTA
1 AAAATAAAAAACTATTATATTTTA
2436300 AAAATAAAAAA-TA-TATATTT
1 AAAATAAAAAACTATTATATTT
2436320 ATTATTTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 7 0.35
23 2 0.10
24 11 0.55
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.36
Consensus pattern (24 bp):
AAAATAAAAAACTATTATATTTTA
Found at i:2436428 original size:31 final size:33
Alignment explanation
Indices: 2436393--2436463 Score: 83
Period size: 31 Copynumber: 2.2 Consensus size: 33
2436383 ATTTTTTAAA
*
2436393 CGGGCCTAAAATTTTGCCC-AA-TCCCATATTT
1 CGGGCCTAAAATTTTACCCAAACTCCCATATTT
* *
2436424 CGGGCCTATATTTTTACCCAAACCCTCCCATATTT
1 CGGGCCTAAAATTTTACCCAAA--CTCCCATATTT
2436459 CGGGC
1 CGGGC
2436464 GGGCCGTCGG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
31 16 0.48
32 2 0.06
35 15 0.45
ACGTcount: A:0.23, C:0.32, G:0.14, T:0.31
Consensus pattern (33 bp):
CGGGCCTAAAATTTTACCCAAACTCCCATATTT
Found at i:2437395 original size:14 final size:16
Alignment explanation
Indices: 2437371--2437404 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
2437361 TTTGAAACAA
2437371 AAAAAAGTT-AAAAAG
1 AAAAAAGTTAAAAAAG
2437386 AAAAAA-TTAAAAAAG
1 AAAAAAGTTAAAAAAG
2437401 AAAA
1 AAAA
2437405 CCCTATAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 2 0.11
15 16 0.89
ACGTcount: A:0.79, C:0.00, G:0.09, T:0.12
Consensus pattern (16 bp):
AAAAAAGTTAAAAAAG
Found at i:2444711 original size:60 final size:57
Alignment explanation
Indices: 2444610--2444720 Score: 141
Period size: 60 Copynumber: 1.9 Consensus size: 57
2444600 TTAATTTAAC
* * *
2444610 ATTTGGTACTTAAATTTAATTTTTTTTCTAATTTAGTACCTAAACTTTTTTGGCCTT
1 ATTTGGTACTTAAATTGAATTTTTTTCCTAATTTAGCACCTAAACTTTTTTGGCCTT
* * *
2444667 ATTTGGTACTTGAACTTGACATTTTTTTCCCTAATTTGGCACCTAAGCTTTTTT
1 ATTTGGTACTT-AAATTGA-ATTTTTTT-CCTAATTTAGCACCTAAACTTTTTT
2444721 AAGTTCAATT
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
57 11 0.24
58 5 0.11
59 8 0.18
60 21 0.47
ACGTcount: A:0.23, C:0.15, G:0.11, T:0.51
Consensus pattern (57 bp):
ATTTGGTACTTAAATTGAATTTTTTTCCTAATTTAGCACCTAAACTTTTTTGGCCTT
Found at i:2445240 original size:31 final size:30
Alignment explanation
Indices: 2445187--2445245 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 30
2445177 AACTTAAGAA
*
2445187 GAAAAATGTTAAGTTTAAGTATCAAATTAG
1 GAAAAATGTCAAGTTTAAGTATCAAATTAG
**
2445217 GAAAAAGTGTCAAGTTTGGGTATCAAATT
1 GAAAAA-TGTCAAGTTTAAGTATCAAATT
2445246 GGACCAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 6 0.24
31 19 0.76
ACGTcount: A:0.42, C:0.05, G:0.20, T:0.32
Consensus pattern (30 bp):
GAAAAATGTCAAGTTTAAGTATCAAATTAG
Found at i:2446004 original size:17 final size:17
Alignment explanation
Indices: 2445974--2446008 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
2445964 CATTTAACTT
2445974 TTGTAAAAAATATTTAA
1 TTGTAAAAAATATTTAA
* *
2445991 TTGTATAAATTATTTAA
1 TTGTAAAAAATATTTAA
2446008 T
1 T
2446009 ATGTCAGGAC
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:0.46, C:0.00, G:0.06, T:0.49
Consensus pattern (17 bp):
TTGTAAAAAATATTTAA
Found at i:2447655 original size:39 final size:37
Alignment explanation
Indices: 2447588--2447680 Score: 98
Period size: 39 Copynumber: 2.5 Consensus size: 37
2447578 ACCAGAATGG
* *
2447588 CACCCAGTGCCTCATCGGATAGTTCGAAGCAATAGTTGA
1 CACCCAGTGCCTCATCGGAAAGTCCGAAG-AA-AGTTGA
* *
2447627 CACCCAGTGTCTCATCGGCAAAG-CCGAAGAAAGTTGG
1 CACCCAGTGCCTCATCGG-AAAGTCCGAAGAAAGTTGA
* *
2447664 TACCCAGTACCTCATCG
1 CACCCAGTGCCTCATCG
2447681 AATCTATCCG
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
37 19 0.41
38 2 0.04
39 22 0.48
40 3 0.07
ACGTcount: A:0.28, C:0.29, G:0.23, T:0.20
Consensus pattern (37 bp):
CACCCAGTGCCTCATCGGAAAGTCCGAAGAAAGTTGA
Found at i:2449147 original size:45 final size:44
Alignment explanation
Indices: 2449072--2449175 Score: 138
Period size: 45 Copynumber: 2.3 Consensus size: 44
2449062 TTTTCTTTTC
*
2449072 TTTCTTTCTTTCCTTCCTTCCTTCTCTGTTTCGTTTTGCTCTCTG
1 TTTCTTTCTTT-CTCCCTTCCTTCTCTGTTTCGTTTTGCTCTCTG
* *
2449117 TTTCTTTCTTTCTCCCTTCTCTGT-TTTGTTTTGTTTTGCTCTCTG
1 TTTCTTTCTTTCTCCCTTC-CT-TCTCTGTTTCGTTTTGCTCTCTG
2449162 TTTCTTTTCTTTCT
1 TTTC-TTTCTTTCT
2449176 TTCTTTGTCA
Statistics
Matches: 53, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
44 7 0.13
45 36 0.68
46 10 0.19
ACGTcount: A:0.00, C:0.27, G:0.09, T:0.64
Consensus pattern (44 bp):
TTTCTTTCTTTCTCCCTTCCTTCTCTGTTTCGTTTTGCTCTCTG
Found at i:2455314 original size:33 final size:30
Alignment explanation
Indices: 2455277--2455343 Score: 82
Period size: 31 Copynumber: 2.1 Consensus size: 30
2455267 TTAAAGTTTC
2455277 ATGTGTATATATTTGA-ACCATAATCAAAATTT
1 ATGTGTATA-ATTT-ACACCA-AATCAAAATTT
*
2455309 GATGTGTATAATTTACACCAAATCAATATTT
1 -ATGTGTATAATTTACACCAAATCAAAATTT
2455340 ATGT
1 ATGT
2455344 ATCAAATTGT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
30 4 0.12
31 11 0.34
32 8 0.25
33 9 0.28
ACGTcount: A:0.39, C:0.10, G:0.10, T:0.40
Consensus pattern (30 bp):
ATGTGTATAATTTACACCAAATCAAAATTT
Found at i:2456153 original size:5 final size:5
Alignment explanation
Indices: 2456145--2456171 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
2456135 GTAAACTAAA
2456145 CGCAC CGCAC CGCAC CGCAC CGCAC CG
1 CGCAC CGCAC CGCAC CGCAC CGCAC CG
2456172 AATCGCCCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.59, G:0.22, T:0.00
Consensus pattern (5 bp):
CGCAC
Found at i:2459482 original size:88 final size:90
Alignment explanation
Indices: 2459343--2459549 Score: 215
Period size: 94 Copynumber: 2.3 Consensus size: 90
2459333 GTTTTTTTAT
* * ** *
2459343 TTAATTGGGTATTTGAATTTTCAAAATACATTAAAAAAGTCTTTAAA-TTTTTTTAAAAAAAGTA
1 TTAATTGGGTACTTGAACTTTCAAAATACATTAAAAAAGTCTACAAATTTTTTTTAAAAAAAGCA
*
2459407 ATTAAATCCCTG-TTTTTTTTCCAC
66 ATTAAATCACTGTTTTTTTTTCCAC
* * *
2459431 TTAATTGGGTACTTGAACTTTCAAAATATA-TCAAAAAG-CTCACAAACTTTTTTTTTTAAAAAG
1 TTAATTGGGTACTTGAACTTTCAAAATACATTAAAAAAGTCT-ACAAA---TTTTTTTTAAAAAA
*
2459494 AGCAATTAAATCACTGATTTTTTTTTTGCAC
62 AGCAATTAAATCACTG--TTTTTTTTTCCAC
* * *
2459525 TCAATTGGTTACTTGAACTATCAAA
1 TTAATTGGGTACTTGAACTTTCAAA
2459550 TGCTTCAAAA
Statistics
Matches: 98, Mismatches: 13, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
86 2 0.02
87 10 0.10
88 27 0.28
91 26 0.27
94 33 0.34
ACGTcount: A:0.37, C:0.13, G:0.09, T:0.42
Consensus pattern (90 bp):
TTAATTGGGTACTTGAACTTTCAAAATACATTAAAAAAGTCTACAAATTTTTTTTAAAAAAAGCA
ATTAAATCACTGTTTTTTTTTCCAC
Found at i:2459592 original size:20 final size:20
Alignment explanation
Indices: 2459567--2459604 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2459557 AAAAGGCCCT
*
2459567 TTGACCATTAACGTTAACAG
1 TTGACCATTAAAGTTAACAG
2459587 TTGACCATTAAAGTTAAC
1 TTGACCATTAAAGTTAAC
2459605 TGCCCCTAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.37, C:0.18, G:0.13, T:0.32
Consensus pattern (20 bp):
TTGACCATTAAAGTTAACAG
Found at i:2459679 original size:10 final size:10
Alignment explanation
Indices: 2459666--2459764 Score: 52
Period size: 10 Copynumber: 10.4 Consensus size: 10
2459656 ACATGTGACA
2459666 AAAAAATTAT
1 AAAAAATTAT
2459676 AAAAAA--AT
1 AAAAAATTAT
*
2459684 -AAAAATCA-
1 AAAAAATTAT
*
2459692 ATAAAAGTTAT
1 A-AAAAATTAT
*
2459703 -AACAATTAT
1 AAAAAATTAT
*
2459712 -TA-AATTAT
1 AAAAAATTAT
* *
2459720 ATTAAAAAATAG
1 A--AAAAATTAT
2459732 AAAAAATTAT
1 AAAAAATTAT
*
2459742 -AAAAATCAT
1 AAAAAATTAT
2459751 AAAAAATTAT
1 AAAAAATTAT
2459761 AAAA
1 AAAA
2459765 TGCATAAAAA
Statistics
Matches: 67, Mismatches: 12, Indels: 20
0.68 0.12 0.20
Matches are distributed among these distances:
7 5 0.07
8 8 0.12
9 17 0.25
10 31 0.46
11 1 0.01
12 5 0.07
ACGTcount: A:0.68, C:0.03, G:0.02, T:0.27
Consensus pattern (10 bp):
AAAAAATTAT
Found at i:2459745 original size:9 final size:9
Alignment explanation
Indices: 2459667--2459764 Score: 63
Period size: 9 Copynumber: 10.4 Consensus size: 9
2459657 CATGTGACAA
2459667 AAAAATTAT
1 AAAAATTAT
*
2459676 AAAAA-AAT
1 AAAAATTAT
*
2459684 AAAAATCAAT
1 AAAAAT-TAT
*
2459694 AAAAGTTAT
1 AAAAATTAT
*
2459703 AACAATTAT
1 AAAAATTAT
* *
2459712 TAAATTATATT
1 AAAAAT-TA-T
* *
2459723 AAAAAATAGA
1 AAAAATTA-T
2459733 AAAAATTAT
1 AAAAATTAT
*
2459742 AAAAATCAT
1 AAAAATTAT
2459751 AAAAAATTAT
1 -AAAAATTAT
2459761 AAAA
1 AAAA
2459765 TGCATAAAAA
Statistics
Matches: 67, Mismatches: 17, Indels: 10
0.71 0.18 0.11
Matches are distributed among these distances:
8 7 0.10
9 29 0.43
10 27 0.40
11 4 0.06
ACGTcount: A:0.67, C:0.03, G:0.02, T:0.28
Consensus pattern (9 bp):
AAAAATTAT
Found at i:2459770 original size:19 final size:19
Alignment explanation
Indices: 2459667--2459776 Score: 79
Period size: 19 Copynumber: 5.8 Consensus size: 19
2459657 CATGTGACAA
*
2459667 AAAAATTATAAAAAA--AT
1 AAAAATCATAAAAAATTAT
*
2459684 AAAAATCA-ATAAAAGTTAT
1 AAAAATCATA-AAAAATTAT
* * *
2459703 AACAATTATTAAATTATATTA-
1 AAAAATCA-TAAA--AAATTAT
*
2459724 AAAAAT-AGAAAAAATTAT
1 AAAAATCATAAAAAATTAT
2459742 AAAAATCATAAAAAATTAT
1 AAAAATCATAAAAAATTAT
2459761 -AAAATGCATAAAAAAT
1 AAAAAT-CATAAAAAAT
2459777 GTCATTTAAT
Statistics
Matches: 73, Mismatches: 10, Indels: 18
0.72 0.10 0.18
Matches are distributed among these distances:
16 1 0.01
17 16 0.22
18 11 0.15
19 32 0.44
20 3 0.04
21 6 0.08
22 4 0.05
ACGTcount: A:0.66, C:0.04, G:0.03, T:0.27
Consensus pattern (19 bp):
AAAAATCATAAAAAATTAT
Found at i:2460019 original size:19 final size:20
Alignment explanation
Indices: 2459997--2460044 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
2459987 TTTTATAATT
2459997 TTTTTACGA-CTTTATAAAA
1 TTTTTACGATCTTTATAAAA
*
2460016 TTTTATA--ATTTTTATAAAA
1 TTTT-TACGATCTTTATAAAA
2460035 TTTTTACGAT
1 TTTTTACGAT
2460045 ATTTGTAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 7
0.75 0.03 0.22
Matches are distributed among these distances:
18 3 0.12
19 17 0.71
20 4 0.17
ACGTcount: A:0.35, C:0.06, G:0.04, T:0.54
Consensus pattern (20 bp):
TTTTTACGATCTTTATAAAA
Found at i:2460093 original size:20 final size:21
Alignment explanation
Indices: 2460064--2460104 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
2460054 TTTTTTCTAA
2460064 TTTTAATAAAATTTAA-ATAT
1 TTTTAATAAAATTTAATATAT
*
2460084 TTTTATTAAAATTTAATATAT
1 TTTTAATAAAATTTAATATAT
2460105 ATATATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
TTTTAATAAAATTTAATATAT
Found at i:2460384 original size:89 final size:87
Alignment explanation
Indices: 2460204--2460454 Score: 253
Period size: 89 Copynumber: 2.8 Consensus size: 87
2460194 TAAGGGCGGT
* * * ** ** *
2460204 TCAAGTACCCAATTAAGTGCAAAAAAAGGCAGGGGCTTAATTG-TTTTTTTT--TTAATTTTGAG
1 TCAAGTGCCCAATTGAGTGCAAAAAAA--AAATGGCTTAATTGATTTTTTTTGAAAAAATTTGAG
* *
2460266 GGTCTTTTTATACATTTTGAAAGT
64 GGTCTTTTTATACATTGTGAAAGC
2460290 TCAAGTGCCCAATTGAGTGCAAAAAAAATAATGGCTTAATTGATTTTTTTTGAAAAAATTTGAGG
1 TCAAGTGCCCAATTGAGTGCAAAAAAAA-AATGGCTTAATTGATTTTTTTTGAAAAAATTTGAGG
*
2460355 GT-TATTTTGATGCATTGTGAAAGC
65 GTCT-TTTT-ATACATTGTGAAAGC
* *
2460379 TCAAGTGCCCAAGTGAGTGCAAAAAAAAAATGCAGGGGCTTAATT-ACTTTTTTTGAAAAAATTT
1 TCAAGTGCCCAATTGAGTGCAAAAAAAAAAT-----GGCTTAATTGATTTTTTTTGAAAAAATTT
2460443 GAGGG-CTTTTTA
61 GAGGGTCTTTTTA
2460455 CACGAAAAAT
Statistics
Matches: 140, Mismatches: 13, Indels: 20
0.81 0.08 0.12
Matches are distributed among these distances:
85 11 0.08
86 33 0.24
87 1 0.01
88 18 0.13
89 39 0.28
90 1 0.01
91 4 0.03
92 24 0.17
93 9 0.06
ACGTcount: A:0.33, C:0.10, G:0.20, T:0.36
Consensus pattern (87 bp):
TCAAGTGCCCAATTGAGTGCAAAAAAAAAATGGCTTAATTGATTTTTTTTGAAAAAATTTGAGGG
TCTTTTTATACATTGTGAAAGC
Found at i:2461408 original size:32 final size:30
Alignment explanation
Indices: 2461324--2461408 Score: 93
Period size: 32 Copynumber: 2.8 Consensus size: 30
2461314 CTAGGCTCCC
*
2461324 AAAATTTTT-AAAATTCACATTATAGCTTTT
1 AAAATTTTTGAAAATTCTCATTA-AGCTTTT
* * *
2461354 -ATATTTTTGAAAATTTTGATTAAGCTTTCTT
1 AAAATTTTTGAAAATTCTCATTAAGC-TT-TT
2461385 AAAATTTTTGAAAATTCTCATTAA
1 AAAATTTTTGAAAATTCTCATTAA
2461409 TCTCACACAA
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
29 10 0.23
30 12 0.27
31 2 0.05
32 20 0.45
ACGTcount: A:0.38, C:0.08, G:0.06, T:0.48
Consensus pattern (30 bp):
AAAATTTTTGAAAATTCTCATTAAGCTTTT
Found at i:2462205 original size:21 final size:21
Alignment explanation
Indices: 2462179--2462284 Score: 69
Period size: 21 Copynumber: 5.0 Consensus size: 21
2462169 TATATATTAC
* *
2462179 AATAAAACAAAATAAATAAAG
1 AATAAAACAAAAGAAAGAAAG
*
2462200 AATAAATCAAAAGAAAGAAAG
1 AATAAAACAAAAGAAAGAAAG
*
2462221 -ATAGAAACGAAACGGAAAGAAA-
1 AATA-AAAC-AAA-AGAAAGAAAG
*
2462243 AAGAAAA-AGAAAGAAAGAAAAG
1 AATAAAACA-AAAGAAAG-AAAG
*
2462265 AA-AAGAA-AAAGGAAAGAAAG
1 AATAA-AACAAAAGAAAGAAAG
2462285 GAAGGAGAAA
Statistics
Matches: 69, Mismatches: 8, Indels: 17
0.73 0.09 0.18
Matches are distributed among these distances:
20 13 0.19
21 35 0.51
22 11 0.16
23 10 0.14
ACGTcount: A:0.73, C:0.04, G:0.18, T:0.06
Consensus pattern (21 bp):
AATAAAACAAAAGAAAGAAAG
Found at i:2462216 original size:4 final size:4
Alignment explanation
Indices: 2462209--2462284 Score: 57
Period size: 4 Copynumber: 18.0 Consensus size: 4
2462199 GAATAAATCA
* *
2462209 AAAG AAAG AAAG ATAG AAACG AAACGG AAAG AAA- AAGAA AAAG AAAG
1 AAAG AAAG AAAG AAAG AAA-G AAA--G AAAG AAAG AA-AG AAAG AAAG
*
2462256 AAAG AAAAG AAAAG AAA- AAGG AAAG AAAG
1 AAAG -AAAG -AAAG AAAG AAAG AAAG AAAG
2462285 GAAGGAGAAA
Statistics
Matches: 60, Mismatches: 6, Indels: 12
0.77 0.08 0.15
Matches are distributed among these distances:
3 4 0.07
4 37 0.62
5 15 0.25
6 4 0.07
ACGTcount: A:0.72, C:0.03, G:0.24, T:0.01
Consensus pattern (4 bp):
AAAG
Found at i:2463205 original size:41 final size:40
Alignment explanation
Indices: 2463160--2463291 Score: 130
Period size: 40 Copynumber: 3.4 Consensus size: 40
2463150 ACTTCGAGTT
2463160 GATGAGACACTGGGTGTCAATTTACTACTTCGGATTAATTC
1 GATGAGACACTGGGTGTCAATTTA-TACTTCGGATTAATTC
* * * * *
2463201 GATGAGGCACTGGATG-CGAA-TT-TACTTCTGTTTAA-CC
1 GATGAGACACTGGGTGTC-AATTTATACTTCGGATTAATTC
* *
2463238 GATGAGACACTGGGTGTCAATTTATTATTTCGAATT-ATTC
1 GATGAGACACTGGGTGTCAATTTA-TACTTCGGATTAATTC
*
2463278 GATGAGGCACTGGG
1 GATGAGACACTGGG
2463292 AGCCAAACTG
Statistics
Matches: 72, Mismatches: 13, Indels: 13
0.73 0.13 0.13
Matches are distributed among these distances:
37 17 0.24
38 14 0.19
39 1 0.01
40 24 0.33
41 16 0.22
ACGTcount: A:0.26, C:0.16, G:0.25, T:0.33
Consensus pattern (40 bp):
GATGAGACACTGGGTGTCAATTTATACTTCGGATTAATTC
Found at i:2463260 original size:37 final size:38
Alignment explanation
Indices: 2463160--2463261 Score: 109
Period size: 37 Copynumber: 2.6 Consensus size: 38
2463150 ACTTCGAGTT
*
2463160 GATGAGACACTGGGTGTCAATTTACTACTTCGGATTAATTC
1 GATGAGACACTGGGTGTCAA-TT--TACTTCGGATTAATCC
* * * *
2463201 GATGAGGCACTGGATG-CGAATTTACTTCTGTTTAA-CC
1 GATGAGACACTGGGTGTC-AATTTACTTCGGATTAATCC
2463238 GATGAGACACTGGGTGTCAATTTA
1 GATGAGACACTGGGTGTCAATTTA
2463262 TTATTTCGAA
Statistics
Matches: 52, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
37 21 0.40
38 12 0.23
40 3 0.06
41 16 0.31
ACGTcount: A:0.26, C:0.17, G:0.25, T:0.32
Consensus pattern (38 bp):
GATGAGACACTGGGTGTCAATTTACTTCGGATTAATCC
Found at i:2470895 original size:75 final size:73
Alignment explanation
Indices: 2470779--2470934 Score: 215
Period size: 75 Copynumber: 2.1 Consensus size: 73
2470769 TGGGTTTAGA
* ** *
2470779 GGAAGGAAAAGAAAGGTTTGAAAGGAAACTAGTTTCATTTTTGCTTTTTTTTTTTTGGTAGAAGG
1 GGAAGGAAAAGAAAGATTTGAAAGGAAACTAGTTTCATTTTT--TCCTTTTTCTTTGGTAGAA-G
2470844 AAA-ATAAGAG
63 AAAGATAAGAG
*
2470854 GGAAGGAAAAGAAAGATTTGAAAGGAAACTAGTTTCCTTTTTTCCTTTTTCTTTGGTAGAAGAAA
1 GGAAGGAAAAGAAAGATTTGAAAGGAAACTAGTTTCATTTTTTCCTTTTTCTTTGGTAGAAGAAA
*
2470919 GATAGGAG
66 GATAAGAG
*
2470927 GGAGGGAA
1 GGAAGGAA
2470935 GGAAGGAAAA
Statistics
Matches: 73, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
72 4 0.05
73 29 0.40
75 40 0.55
ACGTcount: A:0.36, C:0.06, G:0.27, T:0.31
Consensus pattern (73 bp):
GGAAGGAAAAGAAAGATTTGAAAGGAAACTAGTTTCATTTTTTCCTTTTTCTTTGGTAGAAGAAA
GATAAGAG
Found at i:2471827 original size:17 final size:18
Alignment explanation
Indices: 2471802--2471877 Score: 63
Period size: 18 Copynumber: 4.3 Consensus size: 18
2471792 TAAGAGAGAA
*
2471802 AGAAAGAAC-TGAAAAGG
1 AGAAGGAACGTGAAAAGG
2471819 AGAAGGAACGTGAAAAGG
1 AGAAGGAACGTGAAAAGG
* *
2471837 A-AAGGGAGAAG-G-AACGCG
1 AGAA-GGA-ACGTGAAAAG-G
2471855 AGAAGGAACGTGAAAAGG
1 AGAAGGAACGTGAAAAGG
2471873 A-AAGG
1 AGAAGG
2471878 GAGAAGGCTG
Statistics
Matches: 47, Mismatches: 5, Indels: 14
0.71 0.08 0.21
Matches are distributed among these distances:
17 19 0.40
18 21 0.45
19 7 0.15
ACGTcount: A:0.51, C:0.07, G:0.38, T:0.04
Consensus pattern (18 bp):
AGAAGGAACGTGAAAAGG
Found at i:2471844 original size:24 final size:24
Alignment explanation
Indices: 2471812--2471862 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
2471802 AGAAAGAACT
*
2471812 GAAAAGGAGAAGGAACGTGAAAAG
1 GAAAAGGAGAAGGAACGCGAAAAG
* *
2471836 GAAAGGGAGAAGGAACGCGAGAAG
1 GAAAAGGAGAAGGAACGCGAAAAG
2471860 GAA
1 GAA
2471863 CGTGAAAAGG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.51, C:0.06, G:0.41, T:0.02
Consensus pattern (24 bp):
GAAAAGGAGAAGGAACGCGAAAAG
Found at i:2471884 original size:12 final size:12
Alignment explanation
Indices: 2471812--2471884 Score: 65
Period size: 12 Copynumber: 6.1 Consensus size: 12
2471802 AGAAAGAACT
*
2471812 GAAAAGGAGAAG
1 GAAAGGGAGAAG
* * *
2471824 GAACGTGAAAAG
1 GAAAGGGAGAAG
2471836 GAAAGGGAGAAG
1 GAAAGGGAGAAG
* *
2471848 GAACGCGAGAAG
1 GAAAGGGAGAAG
* * *
2471860 GAACGTGAAAAG
1 GAAAGGGAGAAG
2471872 GAAAGGGAGAAG
1 GAAAGGGAGAAG
2471884 G
1 G
2471885 CTGAAAGCAA
Statistics
Matches: 47, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
12 47 1.00
ACGTcount: A:0.49, C:0.05, G:0.42, T:0.03
Consensus pattern (12 bp):
GAAAGGGAGAAG
Found at i:2473646 original size:25 final size:25
Alignment explanation
Indices: 2473612--2473662 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
2473602 TTTTCTTGAG
2473612 ATCATATAATGAACCTGATTAGTTT
1 ATCATATAATGAACCTGATTAGTTT
2473637 ATCATATAATGAACCTGATTAGTTT
1 ATCATATAATGAACCTGATTAGTTT
2473662 A
1 A
2473663 GTTGTTATGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.39
Consensus pattern (25 bp):
ATCATATAATGAACCTGATTAGTTT
Found at i:2480859 original size:4 final size:4
Alignment explanation
Indices: 2480852--2480888 Score: 56
Period size: 4 Copynumber: 9.2 Consensus size: 4
2480842 TGCATGCATC
* *
2480852 TATG TATG TATA TATG TATG TCTG TATG TATG TATG T
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG T
2480889 TTTGCAGGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.24, C:0.03, G:0.22, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:2480867 original size:12 final size:12
Alignment explanation
Indices: 2480836--2480886 Score: 57
Period size: 12 Copynumber: 4.2 Consensus size: 12
2480826 ACATCATATA
*
2480836 TATATATGCATG
1 TATATATGTATG
* *
2480848 CATCTATGTATG
1 TATATATGTATG
2480860 TATATATGTATG
1 TATATATGTATG
* *
2480872 TCTGTATGTATG
1 TATATATGTATG
2480884 TAT
1 TAT
2480887 GTTTTGCAGG
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.27, C:0.08, G:0.18, T:0.47
Consensus pattern (12 bp):
TATATATGTATG
Found at i:2483613 original size:21 final size:24
Alignment explanation
Indices: 2483580--2483627 Score: 57
Period size: 21 Copynumber: 2.1 Consensus size: 24
2483570 ATTGGTAGGT
2483580 ATTTAATTATT-AA-TA-AAAAAA
1 ATTTAATTATTAAATTATAAAAAA
* *
2483601 ATTTAGTTGTTAAATTATAAAAAA
1 ATTTAATTATTAAATTATAAAAAA
2483625 ATT
1 ATT
2483628 ATAAAATTAG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
21 9 0.41
22 2 0.09
23 2 0.09
24 9 0.41
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (24 bp):
ATTTAATTATTAAATTATAAAAAA
Found at i:2488274 original size:3 final size:3
Alignment explanation
Indices: 2488266--2488291 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2488256 GAAGTTCTGA
2488266 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
2488292 ATGCCATCAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:2495714 original size:27 final size:27
Alignment explanation
Indices: 2495684--2495750 Score: 89
Period size: 27 Copynumber: 2.5 Consensus size: 27
2495674 TAAGTTTCGT
*
2495684 GGGACAGTCCACCATATAGGTGTTTGC
1 GGGACAGTCCACCAAATAGGTGTTTGC
* ** *
2495711 GGGACATTCCATAAAATAGGTGTTTGT
1 GGGACAGTCCACCAAATAGGTGTTTGC
2495738 GGGACAGTCCACC
1 GGGACAGTCCACC
2495751 GTTTAGCCTG
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.25
Consensus pattern (27 bp):
GGGACAGTCCACCAAATAGGTGTTTGC
Found at i:2498564 original size:27 final size:27
Alignment explanation
Indices: 2498498--2498572 Score: 71
Period size: 27 Copynumber: 2.7 Consensus size: 27
2498488 CTTTCTTTAG
* *
2498498 AATATGCCACGAAGGCGTTTCTTTTCATA
1 AATAT-CCACAAAGGC-TTCCTTTTCATA
*
2498527 AATCAT-TACAAAGGCTTCCTTTTCATA
1 AAT-ATCCACAAAGGCTTCCTTTTCATA
* *
2498554 GATATCCACAAAGACTTCC
1 AATATCCACAAAGGCTTCC
2498573 CTTCTTTAGA
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
26 2 0.05
27 24 0.63
28 7 0.18
29 3 0.08
30 2 0.05
ACGTcount: A:0.32, C:0.24, G:0.12, T:0.32
Consensus pattern (27 bp):
AATATCCACAAAGGCTTCCTTTTCATA
Found at i:2498759 original size:50 final size:50
Alignment explanation
Indices: 2498676--2498775 Score: 137
Period size: 50 Copynumber: 2.0 Consensus size: 50
2498666 TCTTTTAGTC
* * * * * *
2498676 CTTTCTATATTATGTCATAACCCACCAGTTATGGTCTTATATAATATGGT
1 CTTTCCATATGATGCCATAACCCACCAGCTATGGTCTTACACAATATGGT
*
2498726 CTTTCCATATGATGCCATAGCCCACCAGCTATGGTCTTACACAATATGGT
1 CTTTCCATATGATGCCATAACCCACCAGCTATGGTCTTACACAATATGGT
2498776 GCCATGGTCA
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
50 43 1.00
ACGTcount: A:0.27, C:0.23, G:0.14, T:0.36
Consensus pattern (50 bp):
CTTTCCATATGATGCCATAACCCACCAGCTATGGTCTTACACAATATGGT
Found at i:2500273 original size:14 final size:14
Alignment explanation
Indices: 2500254--2500282 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
2500244 AAGATACCCC
2500254 ATTGGAAATGCTAA
1 ATTGGAAATGCTAA
2500268 ATTGGAAATGCTAA
1 ATTGGAAATGCTAA
2500282 A
1 A
2500283 GGTACATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.45, C:0.07, G:0.21, T:0.28
Consensus pattern (14 bp):
ATTGGAAATGCTAA
Found at i:2509653 original size:105 final size:105
Alignment explanation
Indices: 2509471--2509789 Score: 620
Period size: 105 Copynumber: 3.0 Consensus size: 105
2509461 CTGGTGCGAG
2509471 TCAAACAATGTGAAGTTGCCTGATCTCGTGGAGTCCACTTTAAATCAGGTCTATCCGCCTTGTGC
1 TCAAACAATGTGAAGTTGCCTGATCTCGTGGAGTCCACTTTAAATCAGGTCTATCCGCCTTGTGC
2509536 AACTAAGGTTAAGAAGTTGGTTGAGGACTTGAAGAGTACA
66 AACTAAGGTTAAGAAGTTGGTTGAGGACTTGAAGAGTACA
* *
2509576 TCAAACAATGTGAAGTTGCCTGATCTTGTGGAGTCCACTTTAAATCAGGTCTATCCGCCTCGTGC
1 TCAAACAATGTGAAGTTGCCTGATCTCGTGGAGTCCACTTTAAATCAGGTCTATCCGCCTTGTGC
2509641 AACTAAGGTTAAGAAGTTGGTTGAGGACTTGAAGAGTACA
66 AACTAAGGTTAAGAAGTTGGTTGAGGACTTGAAGAGTACA
2509681 TCAAACAATGTGAAGTTGCCTGATCTCGTGGAGTCCACTTTAAATCAGGTCTATCCGCCTTGTGC
1 TCAAACAATGTGAAGTTGCCTGATCTCGTGGAGTCCACTTTAAATCAGGTCTATCCGCCTTGTGC
2509746 AACTAAGGTTAAGAAGTTGGTTGAGGACTTGAAGAGTACA
66 AACTAAGGTTAAGAAGTTGGTTGAGGACTTGAAGAGTACA
2509786 TCAA
1 TCAA
2509790 CTTATACTCA
Statistics
Matches: 210, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
105 210 1.00
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (105 bp):
TCAAACAATGTGAAGTTGCCTGATCTCGTGGAGTCCACTTTAAATCAGGTCTATCCGCCTTGTGC
AACTAAGGTTAAGAAGTTGGTTGAGGACTTGAAGAGTACA
Found at i:2515128 original size:15 final size:15
Alignment explanation
Indices: 2515101--2515187 Score: 81
Period size: 15 Copynumber: 6.0 Consensus size: 15
2515091 AATGAATACA
* *
2515101 AATAA-AAACATAAC
1 AATAATAAAAATAAT
2515115 AATAATAAAAATAAT
1 AATAATAAAAATAAT
*
2515130 ATTAAT--AAATAAT
1 AATAATAAAAATAAT
**
2515143 AATAATAGTAATAAT
1 AATAATAAAAATAAT
* *
2515158 AATATTATAAATAAT
1 AATAATAAAAATAAT
*
2515173 AATGATAAAAATAAT
1 AATAATAAAAATAAT
2515188 TAGCTAAATA
Statistics
Matches: 59, Mismatches: 11, Indels: 5
0.79 0.15 0.07
Matches are distributed among these distances:
13 12 0.20
14 5 0.08
15 42 0.71
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (15 bp):
AATAATAAAAATAAT
Found at i:2515130 original size:3 final size:3
Alignment explanation
Indices: 2515110--2515187 Score: 68
Period size: 3 Copynumber: 25.7 Consensus size: 3
2515100 AAATAAAAAC
* * * *
2515110 ATA ACA ATA ATA AAA ATA ATA TTA ATAA ATA ATA ATA ATA GTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA
* * *
2515156 ATA AT- ATT ATAA ATA ATA ATG ATA AAA ATA AT
1 ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA AT
2515188 TAGCTAAATA
Statistics
Matches: 59, Mismatches: 13, Indels: 6
0.76 0.17 0.08
Matches are distributed among these distances:
2 2 0.03
3 52 0.88
4 5 0.08
ACGTcount: A:0.64, C:0.01, G:0.03, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:2515200 original size:15 final size:13
Alignment explanation
Indices: 2515123--2515201 Score: 52
Period size: 13 Copynumber: 5.7 Consensus size: 13
2515113 ACAATAATAA
* *
2515123 AAATAATATTAAT
1 AAATAATAATGAT
*
2515136 AAATAATAATAAT
1 AAATAATAATGAT
*
2515149 AGTAATAATAATATTAT
1 A--AATAAT-A-ATGAT
2515166 AAATAATAATGAT
1 AAATAATAATGAT
*
2515179 AAA-AATAATTAGCT
1 AAATAATAA-T-GAT
2515193 AAATAATAA
1 AAATAATAA
2515202 AGAAAGCAAA
Statistics
Matches: 55, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
12 5 0.09
13 21 0.38
14 6 0.11
15 17 0.31
16 1 0.02
17 5 0.09
ACGTcount: A:0.62, C:0.01, G:0.04, T:0.33
Consensus pattern (13 bp):
AAATAATAATGAT
Found at i:2516431 original size:45 final size:46
Alignment explanation
Indices: 2516354--2516448 Score: 156
Period size: 45 Copynumber: 2.1 Consensus size: 46
2516344 TATTTTGAGT
*
2516354 TTGGTTCTGTAATGGGCTAGGCTAGTTGGGTCTGAGTTATTTGGGC
1 TTGGTTCTGTAATGGGCTAGGCTAGTTAGGTCTGAGTTATTTGGGC
* *
2516400 TTGGTTCTGTAAT-GGCTAGGTTAGTTAGGTCTGGGTTATTTGGGC
1 TTGGTTCTGTAATGGGCTAGGCTAGTTAGGTCTGAGTTATTTGGGC
2516445 TTGG
1 TTGG
2516449 GCAATAATTG
Statistics
Matches: 46, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
45 33 0.72
46 13 0.28
ACGTcount: A:0.13, C:0.09, G:0.37, T:0.41
Consensus pattern (46 bp):
TTGGTTCTGTAATGGGCTAGGCTAGTTAGGTCTGAGTTATTTGGGC
Found at i:2523008 original size:104 final size:106
Alignment explanation
Indices: 2522898--2523094 Score: 294
Period size: 104 Copynumber: 1.9 Consensus size: 106
2522888 AATATATATA
* * *
2522898 TTTTTTACTTTTGGTT-TGTCAATGTCCGGCACCAGTATACGAAAAAAGT-AAAAAAAAA-A-TT
1 TTTTTTACTTTT--TTCTGTCAATGGCAGGCACCAGTATACAAAAAAAGTAAAAAAAAAAGATTT
2522959 GGTGGTGGCCTGCCAATGGCCGGCACCACCTTTATTGGAATTT
64 GGTGGTGGCCTGCCAATGGCCGGCACCACCTTTATTGGAATTT
2523002 TTTTTTACTTTTTTCGTGTCAATGGCAGGCACCAGTATACAAAAAAAGTAAAAAAAAAAGATTTT
1 TTTTTTACTTTTTTC-TGTCAATGGCAGGCACCAGTATACAAAAAAAGTAAAAAAAAAAGA-TTT
*
2523067 GGTGGTGGCCTGCCAATGGTCGGCACCA
64 GGTGGTGGCCTGCCAATGGCCGGCACCA
2523095 GTAAAATTTT
Statistics
Matches: 83, Mismatches: 4, Indels: 8
0.87 0.04 0.08
Matches are distributed among these distances:
102 2 0.02
104 42 0.51
105 9 0.11
106 1 0.01
108 29 0.35
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.30
Consensus pattern (106 bp):
TTTTTTACTTTTTTCTGTCAATGGCAGGCACCAGTATACAAAAAAAGTAAAAAAAAAAGATTTGG
TGGTGGCCTGCCAATGGCCGGCACCACCTTTATTGGAATTT
Found at i:2523107 original size:104 final size:100
Alignment explanation
Indices: 2522898--2523127 Score: 261
Period size: 104 Copynumber: 2.2 Consensus size: 100
2522888 AATATATATA
* * *
2522898 TTTTTTACTTTTGGTT--TGTCAATGTCCGGCACCAGTATACGAAAAAAGTAAAAAAAAAATTGG
1 TTTTTTACTTTT--TTCGTGTCAATGGCAGGCACCAGTATACAAAAAAAGTAAAAAAAAAATTGG
* *
2522961 TGGTGGCCTGCCAATGGCCGGCACCACCTTTATTGGAATTT
64 TGGTGGCCTGCCAATGGCCGGCACCACC-TAAAT---ATTT
2523002 TTTTTTACTTTTTTCGTGTCAATGGCAGGCACCAGTATACAAAAAAAGTAAAAAAAAAAGATTTT
1 TTTTTTACTTTTTTCGTGTCAATGGCAGGCACCAGTATACAAAAAAAGT-AAAAAAAAA-A--TT
* *
2523067 GGTGGTGGCCTGCCAATGGTCGGCACCA-GTAAA-ATTTT
62 GGTGGTGGCCTGCCAATGGCCGGCACCACCTAAATA-TTT
*
2523105 TTTTTTACTTTTTTCGTATCAAT
1 TTTTTTACTTTTTTCGTGTCAAT
2523128 AGCCGGCCCA
Statistics
Matches: 111, Mismatches: 8, Indels: 15
0.83 0.06 0.11
Matches are distributed among these distances:
102 3 0.03
103 25 0.23
104 42 0.38
105 9 0.08
106 3 0.03
108 29 0.26
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.35
Consensus pattern (100 bp):
TTTTTTACTTTTTTCGTGTCAATGGCAGGCACCAGTATACAAAAAAAGTAAAAAAAAAATTGGTG
GTGGCCTGCCAATGGCCGGCACCACCTAAATATTT
Found at i:2524920 original size:104 final size:106
Alignment explanation
Indices: 2524720--2524922 Score: 293
Period size: 104 Copynumber: 1.9 Consensus size: 106
2524710 TTTTTCCAAT
*
2524720 AAAGGTGGTGCTGGCCATTGGCAGGCCATCACCAAAATTTTTTTTATTACTTTTTTCGTATACTG
1 AAAGGTGGTGCTGGCCATTGGCAGGCCACCACCAAAATTTTTTTTATTACTTTTTTCGTATACTG
* * **
2524785 GTGCCGTCCATTGACAGACCAAAAGTAAAAAAAAATTGAAA
66 GTACCGACCATTGACAGACCAAAACCAAAAAAAAATTGAAA
* *
2524826 AAAGGTGGTGCTGGCCATTGGCAGGCCACCA-CTAAATTTTTTTT-TTACTTTTTTCGTATTCTG
1 AAAGGTGGTGCTGGCCATTGGCAGGCCACCACCAAAATTTTTTTTATTACTTTTTTCGTATACTG
* * * *
2524889 GTATCGACCATTGACAGACTAATACCCAAAAAAA
66 GTACCGACCATTGACAGACCAAAACCAAAAAAAA
2524923 TATTTTTTTC
Statistics
Matches: 86, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
104 44 0.51
105 12 0.14
106 30 0.35
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Consensus pattern (106 bp):
AAAGGTGGTGCTGGCCATTGGCAGGCCACCACCAAAATTTTTTTTATTACTTTTTTCGTATACTG
GTACCGACCATTGACAGACCAAAACCAAAAAAAAATTGAAA
Found at i:2527479 original size:17 final size:17
Alignment explanation
Indices: 2527459--2527508 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 17
2527449 CTTTTTTATA
2527459 TAATATATTTGTTTAAT
1 TAATATATTTGTTTAAT
2527476 TAATACTAGTTT-TTT-AT
1 TAATA-TA-TTTGTTTAAT
*
2527493 AAATATATTTGTTTAA
1 TAATATATTTGTTTAA
2527509 GTTACTTATC
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
15 3 0.11
16 5 0.18
17 12 0.43
18 5 0.18
19 3 0.11
ACGTcount: A:0.36, C:0.02, G:0.06, T:0.56
Consensus pattern (17 bp):
TAATATATTTGTTTAAT
Found at i:2533902 original size:23 final size:22
Alignment explanation
Indices: 2533863--2533910 Score: 53
Period size: 23 Copynumber: 2.1 Consensus size: 22
2533853 TATTTAATTC
*
2533863 TTTTCTTTTATGTTCTTTTAACT
1 TTTTCTTTTATGTTCTTCT-ACT
*
2533886 TTTTTTTTTAT-TCTCTTCTACT
1 TTTTCTTTTATGT-TCTTCTACT
2533908 TTT
1 TTT
2533911 CCCTCTATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 7 0.32
23 15 0.68
ACGTcount: A:0.10, C:0.15, G:0.02, T:0.73
Consensus pattern (22 bp):
TTTTCTTTTATGTTCTTCTACT
Found at i:2536115 original size:13 final size:13
Alignment explanation
Indices: 2536097--2536127 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
2536087 CAGGAGAGTG
2536097 AGCTCGACCTGCA
1 AGCTCGACCTGCA
*
2536110 AGCTCGGCCTGCA
1 AGCTCGACCTGCA
2536123 AGCTC
1 AGCTC
2536128 ATCCAACGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.19, C:0.39, G:0.26, T:0.16
Consensus pattern (13 bp):
AGCTCGACCTGCA
Found at i:2541767 original size:27 final size:27
Alignment explanation
Indices: 2541729--2541784 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
2541719 TCATCGCCTT
2541729 CCACACCGCTTTTGAAAACCCACAATC
1 CCACACCGCTTTTGAAAACCCACAATC
2541756 CCACACCGCTTTTGAAAACCCACAATC
1 CCACACCGCTTTTGAAAACCCACAATC
2541783 CC
1 CC
2541785 GTAAAGCATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.32, C:0.43, G:0.07, T:0.18
Consensus pattern (27 bp):
CCACACCGCTTTTGAAAACCCACAATC
Found at i:2542641 original size:5 final size:5
Alignment explanation
Indices: 2542631--2542658 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
2542621 AAAGGTGATA
2542631 TCGGT TCGGT TCGGT TCGGT TCGGT TCG
1 TCGGT TCGGT TCGGT TCGGT TCGGT TCG
2542659 ATTCAATCGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.00, C:0.21, G:0.39, T:0.39
Consensus pattern (5 bp):
TCGGT
Found at i:2543735 original size:18 final size:19
Alignment explanation
Indices: 2543664--2543737 Score: 57
Period size: 18 Copynumber: 4.0 Consensus size: 19
2543654 TTTTGTCACT
2543664 ATATATTTTGAAAT-T-AAA
1 ATATATTTT-AAATATAAAA
* *
2543682 ATATATATTAAATGTAAAA
1 ATATATTTTAAATATAAAA
* **
2543701 ATGTGATTTTTTA-ATAAAA
1 ATAT-ATTTTAAATATAAAA
2543720 AT-TATTTTAAATATAAAA
1 ATATATTTTAAATATAAAA
2543738 TGTGAAATTG
Statistics
Matches: 44, Mismatches: 8, Indels: 8
0.73 0.13 0.13
Matches are distributed among these distances:
17 10 0.23
18 16 0.36
19 13 0.30
20 5 0.11
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.43
Consensus pattern (19 bp):
ATATATTTTAAATATAAAA
Found at i:2553679 original size:10 final size:11
Alignment explanation
Indices: 2553655--2553691 Score: 67
Period size: 11 Copynumber: 3.5 Consensus size: 11
2553645 ATTTTTTAAA
2553655 TTTTAAAATAT
1 TTTTAAAATAT
2553666 TTTTAAAATAT
1 TTTTAAAATAT
2553677 TTTTAAAAT-T
1 TTTTAAAATAT
2553687 TTTTA
1 TTTTA
2553692 TTTTAAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 6 0.23
11 20 0.77
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:2553689 original size:9 final size:10
Alignment explanation
Indices: 2553644--2553689 Score: 51
Period size: 9 Copynumber: 4.7 Consensus size: 10
2553634 TAAATATATT
*
2553644 TATTTTTTAA
1 TATTTTTAAA
*
2553654 -ATTTTAAAA
1 TATTTTTAAA
2553663 TATTTTTAAAA
1 TATTTTT-AAA
2553674 TATTTTTAAA
1 TATTTTTAAA
2553684 -ATTTTT
1 TATTTTT
2553690 TATTTTAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
9 13 0.42
10 8 0.26
11 10 0.32
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (10 bp):
TATTTTTAAA
Found at i:2554554 original size:61 final size:61
Alignment explanation
Indices: 2554478--2554658 Score: 299
Period size: 61 Copynumber: 3.0 Consensus size: 61
2554468 CTTTGTCTAC
* * **
2554478 CCCTTGGCTAGGCTATATTCTATCCACGTGTTTTTGAGCGAATCTAATTCGATTTTTTTGT
1 CCCTTGGCTAGGCTATAATCTATCCACGTGTTTCTGATTGAATCTAATTCGATTTTTTTGT
* *
2554539 CCCTTAGCTAGGCTATAATCTATCCACGTGTTTCTGATTGAATCTAATTCAATTTTTTTGT
1 CCCTTGGCTAGGCTATAATCTATCCACGTGTTTCTGATTGAATCTAATTCGATTTTTTTGT
*
2554600 CCCTTGGCTAGGCTATAATCTATCCACGTGTTTCTGATTTAATCTAATTCGATTTTTTT
1 CCCTTGGCTAGGCTATAATCTATCCACGTGTTTCTGATTGAATCTAATTCGATTTTTTT
2554659 TGTTTGTATA
Statistics
Matches: 111, Mismatches: 9, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
61 111 1.00
ACGTcount: A:0.20, C:0.20, G:0.15, T:0.45
Consensus pattern (61 bp):
CCCTTGGCTAGGCTATAATCTATCCACGTGTTTCTGATTGAATCTAATTCGATTTTTTTGT
Found at i:2562641 original size:13 final size:13
Alignment explanation
Indices: 2562623--2562652 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
2562613 TTTGTCTCAG
2562623 AAACTGACTACCC
1 AAACTGACTACCC
*
2562636 AAACTGAGTACCC
1 AAACTGACTACCC
2562649 AAAC
1 AAAC
2562653 ATTACCCAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.43, C:0.33, G:0.10, T:0.13
Consensus pattern (13 bp):
AAACTGACTACCC
Found at i:2566677 original size:17 final size:16
Alignment explanation
Indices: 2566655--2566688 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2566645 AAATCCAGGG
2566655 ATTAAAGTGAAAAGAAT
1 ATTAAA-TGAAAAGAAT
*
2566672 ATTAAATTAAAAGAAT
1 ATTAAATGAAAAGAAT
2566688 A
1 A
2566689 AATGTTATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.62, C:0.00, G:0.12, T:0.26
Consensus pattern (16 bp):
ATTAAATGAAAAGAAT
Found at i:2574453 original size:19 final size:20
Alignment explanation
Indices: 2574420--2574467 Score: 53
Period size: 22 Copynumber: 2.4 Consensus size: 20
2574410 AAAATTAGTA
* *
2574420 TTTATTTGTG-TTTTTATTT
1 TTTATTTCTGATTTTCATTT
2574439 TTTATTTCTGATTTTCCAATTT
1 TTTATTTCTGATTTT-C-ATTT
2574461 TTTATTT
1 TTTATTT
2574468 TTACTTTTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 9 0.38
20 4 0.17
22 11 0.46
ACGTcount: A:0.15, C:0.06, G:0.06, T:0.73
Consensus pattern (20 bp):
TTTATTTCTGATTTTCATTT
Found at i:2584227 original size:3 final size:3
Alignment explanation
Indices: 2584219--2584256 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
2584209 ATAAACTCTG
* *
2584219 CAT CAT CAT CAT CAT CAT CAT CAT CAG CAT CAG CAT CA
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CA
2584257 GCTGGATGTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.34, C:0.34, G:0.05, T:0.26
Consensus pattern (3 bp):
CAT
Found at i:2586065 original size:14 final size:15
Alignment explanation
Indices: 2586031--2586059 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
2586021 TAACTTTCTG
2586031 AATATATATTTATTT
1 AATATATATTTATTT
2586046 AATATA-ATTTATTT
1 AATATATATTTATTT
2586060 TTTATAGGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
AATATATATTTATTT
Found at i:2587957 original size:21 final size:22
Alignment explanation
Indices: 2587916--2587964 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
2587906 GGTTTTCAGG
2587916 AATAATTCAGATTTTTAAAAAA
1 AATAATTCAGATTTTTAAAAAA
2587938 AATAATTCAGATTTTTAAAAAA
1 AATAATTCAGATTTTTAAAAAA
2587960 AATAA
1 AATAA
2587965 AATATGCTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.57, C:0.04, G:0.04, T:0.35
Consensus pattern (22 bp):
AATAATTCAGATTTTTAAAAAA
Found at i:2591211 original size:15 final size:16
Alignment explanation
Indices: 2591181--2591213 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
2591171 TGGTTAATTG
2591181 ATTTTATAATTATTTT
1 ATTTTATAATTATTTT
*
2591197 ATTTT-TAATTTTTTT
1 ATTTTATAATTATTTT
2591212 AT
1 AT
2591214 ATCCATATGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (16 bp):
ATTTTATAATTATTTT
Found at i:2593074 original size:24 final size:24
Alignment explanation
Indices: 2593047--2593098 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
2593037 TTAGTAAGTC
*
2593047 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
2593071 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
2593095 AAAT
1 AAAT
2593099 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:2595041 original size:24 final size:24
Alignment explanation
Indices: 2595014--2595065 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
2595004 TTAGTAAGTC
*
2595014 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
2595038 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
2595062 AAAT
1 AAAT
2595066 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:2596678 original size:16 final size:16
Alignment explanation
Indices: 2596657--2596693 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
2596647 CTACAATAAC
* *
2596657 AATTAATTAATTTTTA
1 AATTAATTAATATTAA
2596673 AATTAATTAATATTAA
1 AATTAATTAATATTAA
2596689 AATTA
1 AATTA
2596694 CTCTTTATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
AATTAATTAATATTAA
Found at i:2599784 original size:50 final size:50
Alignment explanation
Indices: 2599660--2599909 Score: 277
Period size: 50 Copynumber: 4.9 Consensus size: 50
2599650 GATAATAACA
* * ** * *
2599660 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGAT-GG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCAT-CTCGG
* *
2599711 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
2599761 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
2599811 TGCCCATACCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTC---ATC-T-CGG
* *
2599866 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCTC
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTC
2599910 GGTACCAATT
Statistics
Matches: 169, Mismatches: 23, Indels: 9
0.84 0.11 0.04
Matches are distributed among these distances:
49 1 0.01
50 91 0.54
51 33 0.20
53 2 0.01
54 1 0.01
55 2 0.01
56 39 0.23
ACGTcount: A:0.21, C:0.30, G:0.24, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:2599839 original size:100 final size:104
Alignment explanation
Indices: 2599659--2599910 Score: 352
Period size: 100 Copynumber: 2.4 Consensus size: 104
2599649 TGATAATAAC
** *
2599659 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGATGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCGTGATGGTGCCCATACCATG
* *
2599724 TCCCAGACATGGTCTTATAGGGGACCTCTC-ATC-T-CGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
* *
2599761 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGT-CTCGGTGCCCATACCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGAT-GGTGCCCATACCATG
2599824 TCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCA--ATCTTAAGG
* *
2599866 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCTCG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCG
2599911 GTACCAATTA
Statistics
Matches: 134, Mismatches: 9, Indels: 10
0.88 0.06 0.07
Matches are distributed among these distances:
99 1 0.01
100 49 0.37
101 36 0.27
103 3 0.02
104 1 0.01
105 2 0.01
106 42 0.31
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26
Consensus pattern (104 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGATGGTGCCCATACCATGT
CCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
Found at i:2603464 original size:31 final size:30
Alignment explanation
Indices: 2603428--2603506 Score: 81
Period size: 31 Copynumber: 2.6 Consensus size: 30
2603418 TCTATTGGTA
2603428 GTAAAATTTTAAATTAATCCCTTCTTAAAA-TT
1 GTAAAATTTTAAATTAAT-CC-T-TTAAAAGTT
* *
2603460 -TAAAATTCATAACTTAATCCTTTAAAAGTT
1 GTAAAATT-TTAAATTAATCCTTTAAAAGTT
*
2603490 GTAAAATTTTACATTAA
1 GTAAAATTTTAAATTAA
2603507 AATAATAAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
29 6 0.15
30 9 0.23
31 16 0.41
32 8 0.21
ACGTcount: A:0.43, C:0.11, G:0.04, T:0.42
Consensus pattern (30 bp):
GTAAAATTTTAAATTAATCCTTTAAAAGTT
Found at i:2611174 original size:31 final size:31
Alignment explanation
Indices: 2611134--2611199 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
2611124 AAAATCTCAA
* *
2611134 AATTTGAAAAGTACAATGG-CTAAAATTGACC
1 AATTCGAAAAGCACAA-GGACTAAAATTGACC
* *
2611165 AATTCGAAAAGCATAAGGACTAAAATTGATC
1 AATTCGAAAAGCACAAGGACTAAAATTGACC
2611196 AATT
1 AATT
2611200 AATGTATAGG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 2 0.07
31 28 0.93
ACGTcount: A:0.47, C:0.12, G:0.15, T:0.26
Consensus pattern (31 bp):
AATTCGAAAAGCACAAGGACTAAAATTGACC
Found at i:2611497 original size:51 final size:51
Alignment explanation
Indices: 2611416--2611532 Score: 148
Period size: 51 Copynumber: 2.3 Consensus size: 51
2611406 TTAGGTATAA
* * *
2611416 TAACAAATTTAGCTCTCAAAATTTACACATTTTGTCAA-TTTGATCTTGATT
1 TAACAAATTTAGCTCACAAAATTTACACATTCTATCAATTTTG-TCTTGATT
* * *
2611467 TAACAAATTTAGC-CAACAATATTTATACATTCTATTAATTTTGTCTTGATT
1 TAACAAATTTAGCTC-ACAAAATTTACACATTCTATCAATTTTGTCTTGATT
2611518 TAACAAATTTAGCTC
1 TAACAAATTTAGCTC
2611533 GTGATATTTA
Statistics
Matches: 57, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
50 1 0.02
51 51 0.89
52 5 0.09
ACGTcount: A:0.35, C:0.15, G:0.07, T:0.43
Consensus pattern (51 bp):
TAACAAATTTAGCTCACAAAATTTACACATTCTATCAATTTTGTCTTGATT
Found at i:2618345 original size:118 final size:114
Alignment explanation
Indices: 2618100--2618456 Score: 319
Period size: 118 Copynumber: 3.1 Consensus size: 114
2618090 TGATGTCTTG
* * * * *
2618100 TCCCCTTATTACCTTGAAGGCTAAG-ATGAGAGGTCTCATCCCCTTTGATAGAATCAACCGAAGG
1 TCCCCTTATGACCTTGAAGGCCAAGCA--AGAGGTCTTATCCCC-TTGGTAGAATCAACCAAAGG
* * * * **
2618164 CCAATGTGTGAGGTCTCATCCCTTTGAGGGATTGGCAAAGTTGTTAGGTCTTG
63 CCAA-GTGTGAGGTCTCATCCCATTGAGGAATTGGCAAAGATGTAAGGTCTCA
* *
2618217 TCCCTTTTATGACCTTGAAGGCCAATGCAAGAGGACTTATCCTCCTTGGTAGAATCAACCAAAGG
1 TCCC-CTTATGACCTTGAAGGCCAA-GCAAGAGGTCTTATCC-CCTTGGTAGAATCAACCAAAGG
* *
2618282 CCAAGGTGTGAGGTATCATCTTCATTGAGGAATTGGCTAAA-ATGTAAGGTCTCA
63 CCAA-GTGTGAGGTCTCATC-CCATTGAGGAATTGGC-AAAGATGTAAGGTCTCA
* * * *
2618336 TCCCCTTATGCCCTTGAAGACCAAGGCGAGAGGTCTTATCCCCTTAGGTAGAATCAAACGAAA-G
1 TCCCCTTATGACCTTGAAGGCCAA-GCAAGAGGTCTTATCCCCTT-GGTAGAATC-AACCAAAGG
* * * * * * *
2618400 TCAAGTGTGAGGTCTCATTCCCTTTTAGGAAATGACTAAG-GGTAAGGTCTCA
63 CCAAGTGTGAGGTCTCA-TCCCATTGAGGAATTGGCAAAGATGTAAGGTCTCA
2618452 -CCCCT
1 TCCCCT
2618457 ATTGGTAGGA
Statistics
Matches: 198, Mismatches: 32, Indels: 22
0.79 0.13 0.09
Matches are distributed among these distances:
115 5 0.03
116 13 0.07
117 31 0.16
118 110 0.56
119 35 0.18
120 4 0.02
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.28
Consensus pattern (114 bp):
TCCCCTTATGACCTTGAAGGCCAAGCAAGAGGTCTTATCCCCTTGGTAGAATCAACCAAAGGCCA
AGTGTGAGGTCTCATCCCATTGAGGAATTGGCAAAGATGTAAGGTCTCA
Found at i:2618772 original size:19 final size:19
Alignment explanation
Indices: 2618748--2618790 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
2618738 GTTGCTCACC
2618748 CTCTTCATAACAAAATTAT
1 CTCTTCATAACAAAATTAT
2618767 CTCTTCATAACAAAATTAT
1 CTCTTCATAACAAAATTAT
2618786 CTCTT
1 CTCTT
2618791 TAGGCTTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.37, C:0.23, G:0.00, T:0.40
Consensus pattern (19 bp):
CTCTTCATAACAAAATTAT
Found at i:2623253 original size:122 final size:122
Alignment explanation
Indices: 2623035--2623335 Score: 417
Period size: 122 Copynumber: 2.5 Consensus size: 122
2623025 TACAACAACG
* * *
2623035 ACCTAATGACTTAAATAAAAACTTTTGAATAGTTTAGTGACCATTTTGTAACTTTTTGAGGTTAC
1 ACCTAATGAATTAAATAAAAACTTTTGAATAGTTTAGTGACCATTTTGTAACTTTTTGAAGCTAC
2623100 AAATAACAATTTTAACTTTCTGCGAGGAGAGAAGGCTATACAACAATAATTTTAACA
66 AAATAACAATTTTAACTTTCTGCGAGGAGAGAAGGCTATACAACAATAATTTTAACA
** * * *
2623157 ACCTAATGAATTAAATAAAAACTTTAAAATAGTTTAATGATCATTTTGTAACTTTTTGAAGCTGC
1 ACCTAATGAATTAAATAAAAACTTTTGAATAGTTTAGTGACCATTTTGTAACTTTTTGAAGCTAC
* * * * *
2623222 AAATAATAATTTTAACTTTTTGC-AGATAGAGAAGGCTATACAATAATGATTTTAACA
66 AAATAACAATTTTAACTTTCTGCGAG-GAGAGAAGGCTATACAACAATAATTTTAACA
* * **
2623279 GCTTAAT-AATTTAAATAAAATTTTTTGAATAGTTTAGTGACCATTTTGTAACTTTTT
1 ACCTAATGAA-TTAAATAAAAACTTTTGAATAGTTTAGTGACCATTTTGTAACTTTTT
2623336 AAAGTTGAAT
Statistics
Matches: 156, Mismatches: 21, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
121 4 0.03
122 152 0.97
ACGTcount: A:0.39, C:0.11, G:0.12, T:0.38
Consensus pattern (122 bp):
ACCTAATGAATTAAATAAAAACTTTTGAATAGTTTAGTGACCATTTTGTAACTTTTTGAAGCTAC
AAATAACAATTTTAACTTTCTGCGAGGAGAGAAGGCTATACAACAATAATTTTAACA
Found at i:2629727 original size:49 final size:49
Alignment explanation
Indices: 2629655--2629753 Score: 198
Period size: 49 Copynumber: 2.0 Consensus size: 49
2629645 TCAAAAACTC
2629655 ACTATTTGATTTAGCCAAAACCATCCACTTGATACAAATACATAGTACA
1 ACTATTTGATTTAGCCAAAACCATCCACTTGATACAAATACATAGTACA
2629704 ACTATTTGATTTAGCCAAAACCATCCACTTGATACAAATACATAGTACA
1 ACTATTTGATTTAGCCAAAACCATCCACTTGATACAAATACATAGTACA
2629753 A
1 A
2629754 TGGCCGCTGA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.41, C:0.22, G:0.08, T:0.28
Consensus pattern (49 bp):
ACTATTTGATTTAGCCAAAACCATCCACTTGATACAAATACATAGTACA
Found at i:2630158 original size:30 final size:30
Alignment explanation
Indices: 2630119--2630193 Score: 71
Period size: 30 Copynumber: 2.5 Consensus size: 30
2630109 TTAAATTAAT
* *
2630119 AATAGTAAAATTATACTTTAACCTCTCAAA
1 AATAATAAAATTATAATTTAACCTCTCAAA
* * * *
2630149 AATGATAAAAATT-TAATTTAATCTTTTAAA
1 AATAAT-AAAATTATAATTTAACCTCTCAAA
*
2630179 AATAATAAAAATATA
1 AATAATAAAATTATA
2630194 GACGATTAAA
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
29 5 0.14
30 24 0.69
31 6 0.17
ACGTcount: A:0.53, C:0.08, G:0.03, T:0.36
Consensus pattern (30 bp):
AATAATAAAATTATAATTTAACCTCTCAAA
Found at i:2631594 original size:23 final size:23
Alignment explanation
Indices: 2631567--2631620 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 23
2631557 TTTGTAACCG
2631567 AAAAA-CAA-ATTACCTATGTTAAA
1 AAAAATCAACATTA-CTAT-TTAAA
*
2631590 AAAAATTAACATTACTATTTAAA
1 AAAAATCAACATTACTATTTAAA
*
2631613 AAACATCA
1 AAAAATCA
2631621 TTAATTTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
23 16 0.62
24 6 0.23
25 4 0.15
ACGTcount: A:0.57, C:0.13, G:0.02, T:0.28
Consensus pattern (23 bp):
AAAAATCAACATTACTATTTAAA
Found at i:2635912 original size:23 final size:23
Alignment explanation
Indices: 2635881--2635931 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
2635871 ACCTACTTCC
* *
2635881 TTACTGTAGTAATTTTCGGGGTA
1 TTACAGTAGTAATTTTCGGGATA
2635904 TTACAGTAGTAATTTTCGGGATA
1 TTACAGTAGTAATTTTCGGGATA
2635927 TTACA
1 TTACA
2635932 TTTCTCCCCC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.27, C:0.10, G:0.22, T:0.41
Consensus pattern (23 bp):
TTACAGTAGTAATTTTCGGGATA
Found at i:2651839 original size:13 final size:14
Alignment explanation
Indices: 2651811--2651839 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2651801 AAATAATTTT
2651811 AATATTTATCCTAA
1 AATATTTATCCTAA
2651825 AATATTTAT-CTAA
1 AATATTTATCCTAA
2651838 AA
1 AA
2651840 CGAATTTTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.48, C:0.10, G:0.00, T:0.41
Consensus pattern (14 bp):
AATATTTATCCTAA
Found at i:2657985 original size:40 final size:40
Alignment explanation
Indices: 2657915--2657990 Score: 100
Period size: 40 Copynumber: 1.9 Consensus size: 40
2657905 ATTTCAACAC
* * *
2657915 TTATATGCACGAAATTAACAAAATTGAATAATCCAACAAT
1 TTATATGCACGAAATTAACAAAAATAAATAACCCAACAAT
*
2657955 TTATATGCAAC-AAATTAATAAAAATAAATAACCCAA
1 TTATATGC-ACGAAATTAACAAAAATAAATAACCCAA
2657991 AGGCAAAGAG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
40 29 0.94
41 2 0.06
ACGTcount: A:0.54, C:0.14, G:0.05, T:0.26
Consensus pattern (40 bp):
TTATATGCACGAAATTAACAAAAATAAATAACCCAACAAT
Found at i:2662063 original size:18 final size:18
Alignment explanation
Indices: 2662037--2662071 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2662027 TTGTCAGGCT
*
2662037 ATCTACCCAAGTTTGAAA
1 ATCTACCCAAATTTGAAA
*
2662055 ATCTGCCCAAATTTGAA
1 ATCTACCCAAATTTGAA
2662072 GGGTTCCAAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.37, C:0.23, G:0.11, T:0.29
Consensus pattern (18 bp):
ATCTACCCAAATTTGAAA
Found at i:2662587 original size:14 final size:14
Alignment explanation
Indices: 2662556--2662595 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
2662546 TATGAAATTT
*
2662556 AATTAAATATTTAAA
1 AATTAAA-ATTAAAA
2662571 AATTAAAATTAAAA
1 AATTAAAATTAAAA
*
2662585 AATAAAAATTA
1 AATTAAAATTA
2662596 CCTCCTTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 16 0.70
15 7 0.30
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
AATTAAAATTAAAA
Found at i:2674352 original size:29 final size:31
Alignment explanation
Indices: 2674319--2674381 Score: 85
Period size: 29 Copynumber: 2.1 Consensus size: 31
2674309 TCTAACTTTC
*
2674319 TTTATATATATTTTTAGATT-TTTTTA-AAT
1 TTTATAAATATTTTTAGATTATTTTTATAAT
**
2674348 TTTATAAATATTTTTATTTTATTTTTATAAT
1 TTTATAAATATTTTTAGATTATTTTTATAAT
2674379 TTT
1 TTT
2674382 TGTTAAGAGA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 17 0.59
30 6 0.21
31 6 0.21
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (31 bp):
TTTATAAATATTTTTAGATTATTTTTATAAT
Found at i:2676528 original size:29 final size:28
Alignment explanation
Indices: 2676481--2676559 Score: 86
Period size: 30 Copynumber: 2.7 Consensus size: 28
2676471 GTGAATGTTT
* * *
2676481 TCAATTTAGTCTTTATATTTTAATTTGA
1 TCAATTTAGTTTTTGTATTTTAAATTGA
*
2676509 TCATATTTAGTTTTTGTATTTTTAAATTGG
1 TCA-ATTTAGTTTTTGTA-TTTTAAATTGA
*
2676539 TCAATTTTAGTTTATGTATTT
1 TCAA-TTTAGTTTTTGTATTT
2676560 AAAAAAAATT
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
28 3 0.07
29 16 0.37
30 24 0.56
ACGTcount: A:0.25, C:0.05, G:0.10, T:0.59
Consensus pattern (28 bp):
TCAATTTAGTTTTTGTATTTTAAATTGA
Found at i:2683108 original size:27 final size:29
Alignment explanation
Indices: 2683052--2683109 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 29
2683042 TTAAATAAAA
* * *
2683052 AATATAAAATTTTAAAAATTATAATTTTT
1 AATATAAAATTATAAAAATGATAATCTTT
2683081 AATA-AAAATTATAAAAATGA-AATCTTT
1 AATATAAAATTATAAAAATGATAATCTTT
2683108 AA
1 AA
2683110 AATTCAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 8 0.31
28 14 0.54
29 4 0.15
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (29 bp):
AATATAAAATTATAAAAATGATAATCTTT
Found at i:2683400 original size:16 final size:17
Alignment explanation
Indices: 2683379--2683416 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
2683369 TAAACATTAA
2683379 TATTTATATA-AT-TTTT
1 TATTTA-ATACATATTTT
2683395 TATTTAATACATATTTT
1 TATTTAATACATATTTT
2683412 TATTT
1 TATTT
2683417 TCGTAATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 3 0.15
16 8 0.40
17 9 0.45
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.66
Consensus pattern (17 bp):
TATTTAATACATATTTT
Found at i:2686168 original size:16 final size:18
Alignment explanation
Indices: 2686137--2686174 Score: 53
Period size: 16 Copynumber: 2.2 Consensus size: 18
2686127 AAAATTCACG
2686137 AAATTGAAACATTAAAAA
1 AAATTGAAACATTAAAAA
*
2686155 AAATT-AAA-ATTAAAAC
1 AAATTGAAACATTAAAAA
2686171 AAAT
1 AAAT
2686175 CTTCACATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 11 0.58
17 3 0.16
18 5 0.26
ACGTcount: A:0.68, C:0.05, G:0.03, T:0.24
Consensus pattern (18 bp):
AAATTGAAACATTAAAAA
Found at i:2696123 original size:17 final size:18
Alignment explanation
Indices: 2696098--2696132 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
2696088 CCAATTCAAT
*
2696098 TAAACAAAT-TATTAAAA
1 TAAAAAAATATATTAAAA
2696115 TAAAAAAATATATTAAAA
1 TAAAAAAATATATTAAAA
2696133 ATTCTATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.29
Consensus pattern (18 bp):
TAAAAAAATATATTAAAA
Found at i:2702057 original size:2 final size:2
Alignment explanation
Indices: 2702052--2702097 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
2702042 TTGTTGTGCA
2702052 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2702094 AG AG
1 AG AG
2702098 TCCTTGTTTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2706421 original size:47 final size:47
Alignment explanation
Indices: 2706353--2706493 Score: 185
Period size: 47 Copynumber: 3.0 Consensus size: 47
2706343 TTCGTTTTCT
**
2706353 CGATGCCATAGACCA-ACTATGGTCTTACACAGAATCACATATCACAC
1 CGATGCCATATCCCAGA-TATGGTCTTACACAGAATCACATATCACAC
* * * *
2706400 CGATGTCATATCCCAGATATGGTCTTACACAGTAGCGCATATCACAC
1 CGATGCCATATCCCAGATATGGTCTTACACAGAATCACATATCACAC
* *
2706447 TGATGCCATATCCCAGATATGGTCTTACACGGAAATCACATATCACA
1 CGATGCCATATCCCAGATATGGTCTTACACAG-AATCACATATCACA
2706494 TATTGCCATG
Statistics
Matches: 80, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
47 68 0.85
48 12 0.15
ACGTcount: A:0.33, C:0.28, G:0.15, T:0.24
Consensus pattern (47 bp):
CGATGCCATATCCCAGATATGGTCTTACACAGAATCACATATCACAC
Found at i:2719526 original size:20 final size:20
Alignment explanation
Indices: 2719484--2719526 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
2719474 AAGTATCATC
* *
2719484 AAATAATTTAAATTTTATAA
1 AAATAATTTAAAATTTAAAA
*
2719504 AAATATTTTAAAATTTAAAA
1 AAATAATTTAAAATTTAAAA
2719524 AAA
1 AAA
2719527 AAACACACAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
AAATAATTTAAAATTTAAAA
Found at i:2719526 original size:21 final size:20
Alignment explanation
Indices: 2719484--2719527 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
2719474 AAGTATCATC
* *
2719484 AAATAATTTAAATTTTATAA
1 AAATAATTTAAATTTAAAAA
*
2719504 AAATATTTTAAAATTTAAAAA
1 AAATAATTT-AAATTTAAAAA
2719525 AAA
1 AAA
2719528 AACACACAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
AAATAATTTAAATTTAAAAA
Found at i:2721717 original size:20 final size:20
Alignment explanation
Indices: 2721679--2721717 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
2721669 TGAACCAAAA
*
2721679 TTTTAATATTTTTTATAATT
1 TTTTAATATTTATTATAATT
2721699 TTTTAATGATTTATT-TAAT
1 TTTTAAT-ATTTATTATAAT
2721718 CAAATCAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (20 bp):
TTTTAATATTTATTATAATT
Found at i:2727726 original size:31 final size:31
Alignment explanation
Indices: 2727691--2727749 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
2727681 CAATCCAATA
*
2727691 ACTTAAATAAAAACTTTCGAATAATTTAATG
1 ACTTAAATAAAAACTTTCAAATAATTTAATG
* * *
2727722 ACTTAAATGAGAACTTTTAAATAATTTA
1 ACTTAAATAAAAACTTTCAAATAATTTA
2727750 CTGATCATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.47, C:0.08, G:0.07, T:0.37
Consensus pattern (31 bp):
ACTTAAATAAAAACTTTCAAATAATTTAATG
Found at i:2728416 original size:14 final size:14
Alignment explanation
Indices: 2728372--2728413 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
2728362 AGAGAAAAAA
2728372 AAAAG-AGAGAAAGG
1 AAAAGAAGAG-AAGG
*
2728386 AGAAGAAGAGAAGG
1 AAAAGAAGAGAAGG
2728400 AAAAGAAGAAGAAG
1 AAAAGAAG-AGAAG
2728414 AAAGAAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 15 0.62
15 9 0.38
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (14 bp):
AAAAGAAGAGAAGG
Found at i:2728423 original size:20 final size:20
Alignment explanation
Indices: 2728381--2728422 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
2728371 AAAAAGAGAG
* *
2728381 AAAGGAGAAGAAGAGAAGGA
1 AAAGAAGAAGAAGAGAAGAA
2728401 AAAGAAGAAGAAGA-AAGAA
1 AAAGAAGAAGAAGAGAAGAA
2728420 AAA
1 AAA
2728423 AAAAAGGTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (20 bp):
AAAGAAGAAGAAGAGAAGAA
Found at i:2728612 original size:22 final size:21
Alignment explanation
Indices: 2728585--2728918 Score: 191
Period size: 22 Copynumber: 15.1 Consensus size: 21
2728575 TAGATTAGAA
*
2728585 TTTTGTATGAATATTTTAAATT
1 TTTTGTATGAATATTGT-AATT
*
2728607 TTTTGTATGAATATTATAA-T
1 TTTTGTATGAATATTGTAATT
2728627 TTTT-TATGAATATTGTAA--
1 TTTTGTATGAATATTGTAATT
*
2728645 TGTTGTATGAATATTGTAATT
1 TTTTGTATGAATATTGTAATT
* *
2728666 ATTTTATAATTAA-ATTTGT-ATT
1 -TTTTGT-ATGAATA-TTGTAATT
* * * * *
2728688 TATAGTTTTGGAT-TAGTAATT
1 TTTTG-TATGAATATTGTAATT
*
2728709 TTTTGTAAGAATATTGTAA--
1 TTTTGTATGAATATTGTAATT
*
2728728 TTTTGTATGAATATTATAAATT
1 TTTTGTATGAATATTGT-AATT
*
2728750 TTTTGTATGAATATTATAATATTAT
1 TTTTGTATGAATATTGT-A-A-T-T
*
2728775 AGTTTTGTATGAATATTGCAATTT
1 --TTTTGTATGAATATTGTAA-TT
* *
2728799 TTTTGCATGAATATTATAATTTTGT
1 TTTTGTATGAATATTGTAA---T-T
* *
2728824 AATTTTGTATGAATATTATATTT
1 --TTTTGTATGAATATTGTAATT
*
2728847 TTTTGTATGAATGTTGTAATATTAT
1 TTTTGTATGAATATTGT-A-A-T-T
*
2728872 AATTTTGTATGAATATTGCAATTT
1 --TTTTGTATGAATATTGTAA-TT
2728896 TTTTGTATGAATATTGTAATT
1 TTTTGTATGAATATTGTAATT
2728917 TT
1 TT
2728919 GTAATTTTGT
Statistics
Matches: 249, Mismatches: 34, Indels: 59
0.73 0.10 0.17
Matches are distributed among these distances:
18 3 0.01
19 42 0.17
20 14 0.06
21 36 0.14
22 79 0.32
23 10 0.04
24 7 0.03
25 9 0.04
26 2 0.01
27 47 0.19
ACGTcount: A:0.32, C:0.01, G:0.12, T:0.55
Consensus pattern (21 bp):
TTTTGTATGAATATTGTAATT
Found at i:2728634 original size:19 final size:19
Alignment explanation
Indices: 2728578--2728769 Score: 95
Period size: 19 Copynumber: 9.4 Consensus size: 19
2728568 TATAGTTTAG
* *
2728578 ATTAGAATTTTGTATGAAT
1 ATTATAATTTTTTATGAAT
*
2728597 ATTTTAAATTTTTTGTATGAAT
1 ATTAT-AA-TTTTT-TATGAAT
2728619 ATTATAATTTTTTATGAAT
1 ATTATAATTTTTTATGAAT
* * *
2728638 ATTGTAATGTTGTATGAAT
1 ATTATAATTTTTTATGAAT
*
2728657 ATTGTAATTATTTTAT--A-
1 ATTATAATT-TTTTATGAAT
**
2728674 ATTA-AATTTGTATTTATAGTTTT
1 ATTATAA-TT-T-TTTAT-G-AAT
*
2728697 GGATTAGTAATTTTTTGTAAGAAT
1 --ATTA-TAA-TTTTT-TATGAAT
* *
2728721 ATTGTAATTTTGTATGAAT
1 ATTATAATTTTTTATGAAT
2728740 ATTATAAATTTTTTGTATGAAT
1 ATTAT-AA-TTTTT-TATGAAT
2728762 ATTATAAT
1 ATTATAAT
2728770 ATTATAGTTT
Statistics
Matches: 134, Mismatches: 20, Indels: 37
0.70 0.10 0.19
Matches are distributed among these distances:
16 2 0.01
17 6 0.04
18 6 0.04
19 44 0.33
20 19 0.14
21 15 0.11
22 26 0.19
24 1 0.01
25 7 0.05
26 3 0.02
27 5 0.04
ACGTcount: A:0.34, C:0.00, G:0.12, T:0.54
Consensus pattern (19 bp):
ATTATAATTTTTTATGAAT
Found at i:2728670 original size:41 final size:40
Alignment explanation
Indices: 2728585--2728769 Score: 130
Period size: 41 Copynumber: 4.5 Consensus size: 40
2728575 TAGATTAGAA
* * *
2728585 TTTTGTATGAATATTTTAAATTTTTTGTATGAATATTATAA-T
1 TTTTGTATGAATATTGT-AA--TGTTGTATGAATATTGTAATT
2728627 TTTT-TATGAATATTGTAATGTTGTATGAATATTGTAATT
1 TTTTGTATGAATATTGTAATGTTGTATGAATATTGTAATT
* * * *
2728666 ATTTTATAATTAA-ATTTGTATTTATAGTT-T-TGGAT-TAGTAATT
1 -TTTTGT-ATGAATA-TTGTA---AT-GTTGTATGAATATTGTAATT
* * *
2728709 TTTTGTAAGAATATTGTAATTTTGTATGAATATTATAAATT
1 TTTTGTATGAATATTGTAATGTTGTATGAATATTGT-AATT
*
2728750 TTTTGTATGAATATTATAAT
1 TTTTGTATGAATATTGTAAT
2728770 ATTATAGTTT
Statistics
Matches: 114, Mismatches: 15, Indels: 29
0.72 0.09 0.18
Matches are distributed among these distances:
37 2 0.02
38 20 0.18
39 5 0.04
40 8 0.07
41 43 0.38
42 19 0.17
43 7 0.06
44 4 0.04
45 3 0.03
46 3 0.03
ACGTcount: A:0.34, C:0.00, G:0.12, T:0.55
Consensus pattern (40 bp):
TTTTGTATGAATATTGTAATGTTGTATGAATATTGTAATT
Found at i:2728771 original size:49 final size:49
Alignment explanation
Indices: 2728718--2728935 Score: 303
Period size: 49 Copynumber: 4.5 Consensus size: 49
2728708 TTTTTGTAAG
* *
2728718 AATATTGTAATTTTGTATGAATATTATAAATTTTTTGTATGAATATTAT
1 AATATTGTAATTTTGTATGAATATTACAATTTTTTTGTATGAATATTAT
* * * *
2728767 AATATTATAGTTTTGTATGAATATTGCAATTTTTTTGCATGAATATTAT
1 AATATTGTAATTTTGTATGAATATTACAATTTTTTTGTATGAATATTAT
* * * *
2728816 AATTTTGTAATTTTGTATGAATATTA-TATTTTTTTGTATGAATGTTGT
1 AATATTGTAATTTTGTATGAATATTACAATTTTTTTGTATGAATATTAT
* * *
2728864 AATATTATAATTTTGTATGAATATTGCAATTTTTTTGTATGAATATTGT
1 AATATTGTAATTTTGTATGAATATTACAATTTTTTTGTATGAATATTAT
*
2728913 AATTTTGTAATTTTGTATGAATA
1 AATATTGTAATTTTGTATGAATA
2728936 ATGTAATGTG
Statistics
Matches: 147, Mismatches: 21, Indels: 2
0.86 0.12 0.01
Matches are distributed among these distances:
48 41 0.28
49 106 0.72
ACGTcount: A:0.33, C:0.01, G:0.12, T:0.54
Consensus pattern (49 bp):
AATATTGTAATTTTGTATGAATATTACAATTTTTTTGTATGAATATTAT
Found at i:2728882 original size:97 final size:98
Alignment explanation
Indices: 2728722--2728935 Score: 367
Period size: 97 Copynumber: 2.2 Consensus size: 98
2728712 TGTAAGAATA
*
2728722 TTGTAATTTTGTATGAATATTATAAATTTTTTGTATGAATATTATAATATTATAGTTTTGTATGA
1 TTGTAATTTTGTATGAATATTATAAATTTTTTGTATGAATATTATAATATTATAATTTTGTATGA
2728787 ATATTGCAATTTTTTTGCATGAATATTATAATT
66 ATATTGCAATTTTTTTGCATGAATATTATAATT
* * *
2728820 TTGTAATTTTGTATGAATATTAT-ATTTTTTTGTATGAATGTTGTAATATTATAATTTTGTATGA
1 TTGTAATTTTGTATGAATATTATAAATTTTTTGTATGAATATTATAATATTATAATTTTGTATGA
* *
2728884 ATATTGCAATTTTTTTGTATGAATATTGTAATT
66 ATATTGCAATTTTTTTGCATGAATATTATAATT
2728917 TTGTAATTTTGTATGAATA
1 TTGTAATTTTGTATGAATA
2728936 ATGTAATGTG
Statistics
Matches: 110, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
97 87 0.79
98 23 0.21
ACGTcount: A:0.32, C:0.01, G:0.13, T:0.54
Consensus pattern (98 bp):
TTGTAATTTTGTATGAATATTATAAATTTTTTGTATGAATATTATAATATTATAATTTTGTATGA
ATATTGCAATTTTTTTGCATGAATATTATAATT
Found at i:2728940 original size:27 final size:25
Alignment explanation
Indices: 2728718--2728942 Score: 179
Period size: 27 Copynumber: 9.1 Consensus size: 25
2728708 TTTTTGTAAG
*
2728718 AATATTGTAATTTTGTATGAATATTAT
1 AATATT-T-ATTTTGTATGAATATTGT
*
2728745 AA-A-TT-TTTTGTATGAATATTAT
1 AATATTTATTTTGTATGAATATTGT
2728767 AATATTATAGTTTTGTATGAATATTG-
1 AATATT-TA-TTTTGTATGAATATTGT
* * *
2728793 CA-ATTT-TTTTGCATGAATATTAT
1 AATATTTATTTTGTATGAATATTGT
*
2728816 AATTTTGTAATTTTGTATGAATA-T-T
1 AATATT-T-ATTTTGTATGAATATTGT
*
2728841 -ATATTT-TTTTGTATGAATGTTGT
1 AATATTTATTTTGTATGAATATTGT
2728864 AATATTATAATTTTGTATGAATATTG-
1 AATATT-T-ATTTTGTATGAATATTGT
*
2728890 CA-ATTT-TTTTGTATGAATATTGT
1 AATATTTATTTTGTATGAATATTGT
* *
2728913 AATTTTGTAATTTTGTATGAATAATGT
1 AATATT-T-ATTTTGTATGAATATTGT
2728940 AAT
1 AAT
2728943 GTGAGGATAT
Statistics
Matches: 163, Mismatches: 14, Indels: 42
0.74 0.06 0.19
Matches are distributed among these distances:
21 12 0.07
22 50 0.31
23 5 0.03
24 17 0.10
25 12 0.07
26 4 0.02
27 63 0.39
ACGTcount: A:0.33, C:0.01, G:0.12, T:0.53
Consensus pattern (25 bp):
AATATTTATTTTGTATGAATATTGT
Found at i:2729325 original size:15 final size:15
Alignment explanation
Indices: 2729284--2729325 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
2729274 GTTAACTTAT
*
2729284 TTAATTTTTATATAA
1 TTAAATTTTATATAA
*
2729299 TGTAACTTTTATATAA
1 T-TAAATTTTATATAA
2729315 TTAAATTTTAT
1 TTAAATTTTAT
2729326 TTGATTTTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (15 bp):
TTAAATTTTATATAA
Found at i:2731152 original size:16 final size:18
Alignment explanation
Indices: 2731131--2731167 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
2731121 CTAATTTTTT
2731131 TTCTTTT-TT-TCCTTCC
1 TTCTTTTCTTCTCCTTCC
*
2731147 TTCTTTTCTTCTGCTTCC
1 TTCTTTTCTTCTCCTTCC
2731165 TTC
1 TTC
2731168 CTTCTTCTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 7 0.39
17 2 0.11
18 9 0.50
ACGTcount: A:0.00, C:0.32, G:0.03, T:0.65
Consensus pattern (18 bp):
TTCTTTTCTTCTCCTTCC
Found at i:2731181 original size:18 final size:18
Alignment explanation
Indices: 2731131--2731182 Score: 54
Period size: 22 Copynumber: 2.8 Consensus size: 18
2731121 CTAATTTTTT
2731131 TTCTT-TTT-TTCCTTCC
1 TTCTTCTTTCTTCCTTCC
2731147 TTCTTTTCTTCTGCTTCCTTCC
1 TTC--TTCTT-T-CTTCCTTCC
2731169 TTCTTCTTTCTTCC
1 TTCTTCTTTCTTCC
2731183 GTTTTTGTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
16 3 0.10
18 7 0.23
19 3 0.10
20 6 0.20
22 11 0.37
ACGTcount: A:0.00, C:0.35, G:0.02, T:0.63
Consensus pattern (18 bp):
TTCTTCTTTCTTCCTTCC
Found at i:2731339 original size:27 final size:27
Alignment explanation
Indices: 2731239--2731341 Score: 147
Period size: 27 Copynumber: 3.8 Consensus size: 27
2731229 AAAATCACAG
2731239 CATTGGCGCCTCCTA-ATATGGCACCAC
1 CATTGGCGCCTCCTAGATA-GGCACCAC
*
2731266 CATTGGCGACTCCTAGATAGGCACCAC
1 CATTGGCGCCTCCTAGATAGGCACCAC
* *
2731293 CATTGGCGCCTCCCAAATAGGCACCAC
1 CATTGGCGCCTCCTAGATAGGCACCAC
2731320 CATTGGCGCCTTCC-AGATAGGC
1 CATTGGCGCC-TCCTAGATAGGC
2731342 GCCAATACTA
Statistics
Matches: 69, Mismatches: 5, Indels: 4
0.88 0.06 0.05
Matches are distributed among these distances:
27 63 0.91
28 6 0.09
ACGTcount: A:0.23, C:0.36, G:0.21, T:0.19
Consensus pattern (27 bp):
CATTGGCGCCTCCTAGATAGGCACCAC
Found at i:2731895 original size:20 final size:20
Alignment explanation
Indices: 2731852--2731895 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
2731842 TTAAAATACT
* *
2731852 TTTAAAATAATTTTTTTATT
1 TTTAAAATAATTTTTTAATG
2731872 TTTAAAATAATTTTTTAATG
1 TTTAAAATAATTTTTTAATG
2731892 TTTA
1 TTTA
2731896 TTTTAAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.61
Consensus pattern (20 bp):
TTTAAAATAATTTTTTAATG
Found at i:2733018 original size:9 final size:9
Alignment explanation
Indices: 2733004--2733037 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
2732994 ATAATTTTTG
2733004 AAAATTTAA
1 AAAATTTAA
2733013 AAAATTTAA
1 AAAATTTAA
*
2733022 AAAAATTATA
1 AAAATTTA-A
2733032 AAAATT
1 AAAATT
2733038 ATTTTTAAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 16 0.73
10 6 0.27
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (9 bp):
AAAATTTAA
Found at i:2737312 original size:30 final size:29
Alignment explanation
Indices: 2737255--2737317 Score: 83
Period size: 29 Copynumber: 2.1 Consensus size: 29
2737245 CGCGGAAAAT
2737255 GGCCCATTCCGGTAAATAATTAAAAAACC
1 GGCCCATTCCGGTAAATAATTAAAAAACC
* *
2737284 GGCCCATTTCGGTAAAT-TTTGAAAAAAACC
1 GGCCCATTCCGGTAAATAATT--AAAAAACC
2737314 GGCC
1 GGCC
2737318 TTTTTTGGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
28 2 0.07
29 16 0.53
30 12 0.40
ACGTcount: A:0.37, C:0.24, G:0.17, T:0.22
Consensus pattern (29 bp):
GGCCCATTCCGGTAAATAATTAAAAAACC
Found at i:2737439 original size:25 final size:26
Alignment explanation
Indices: 2737385--2737454 Score: 124
Period size: 25 Copynumber: 2.7 Consensus size: 26
2737375 AAAAATAAAA
2737385 ATTTACCAAAATATTATAACTTTTTTT
1 ATTTACCAAAATA-TATAACTTTTTTT
2737412 ATTTACCAAAATATATAA-TTTTTTT
1 ATTTACCAAAATATATAACTTTTTTT
2737437 ATTTACCAAAATATATAA
1 ATTTACCAAAATATATAA
2737455 AAAAACTAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
25 25 0.58
26 5 0.12
27 13 0.30
ACGTcount: A:0.43, C:0.10, G:0.00, T:0.47
Consensus pattern (26 bp):
ATTTACCAAAATATATAACTTTTTTT
Found at i:2737614 original size:4 final size:4
Alignment explanation
Indices: 2737605--2737751 Score: 97
Period size: 4 Copynumber: 36.0 Consensus size: 4
2737595 GAAGGAGAGG
* * * * *
2737605 GAAA GAAA GAAA GAAA GAGA GAAA GAAA GGAAG GAAG GAGAG GGAA GAAA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA -GAAA GAAA GA-AA GAAA GAAA
* * *
2737655 G-AA -AAA GAAG GAAA GAAA GGGAAA G-GA GAAGA GAAA AAAA GAAA GAAA
1 GAAA GAAA GAAA GAAA GAAA --GAAA GAAA GAA-A GAAA GAAA GAAA GAAA
* *
2737703 G-AA GAAGA GAAG GAAAA GAGAA GAAA -AAA GAAA GAAA GAAG GAAA GAAA
1 GAAA GAA-A GAAA G-AAA GA-AA GAAA GAAA GAAA GAAA GAAA GAAA GAAA
2737752 AGGAAAGGAG
Statistics
Matches: 114, Mismatches: 16, Indels: 26
0.73 0.10 0.17
Matches are distributed among these distances:
3 12 0.11
4 77 0.68
5 21 0.18
6 4 0.04
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:2737654 original size:38 final size:37
Alignment explanation
Indices: 2737611--2737746 Score: 122
Period size: 38 Copynumber: 3.7 Consensus size: 37
2737601 GAGGGAAAGA
* *
2737611 AAGAAAGAAAGAGAGAAAGAAAGGAAGGAAGGAGAGGG
1 AAGAAAGAAAGAAAGAAAG-AAGGAAGGAAGGAGAGAG
* *
2737649 AAGAAAGAAAAAGAAGGAAAGAAAGG--GAAAGGAGA-AG
1 AAGAAAG--AAAGAAAGAAAG-AAGGAAGGAAGGAGAGAG
* *
2737686 -AGAAAAAAAGAAAGAAAGAA-GAAGAGAAGGAAAAGAG
1 AAGAAAGAAAGAAAGAAAGAAGGAAG-GAAGG-AGAGAG
2737723 AAGAAA-AAAGAAAGAAAGAAGGAA
1 AAGAAAGAAAGAAAGAAAGAAGGAA
2737747 AGAAAAGGAA
Statistics
Matches: 81, Mismatches: 8, Indels: 18
0.76 0.07 0.17
Matches are distributed among these distances:
32 1 0.01
33 2 0.02
34 12 0.15
35 4 0.05
36 7 0.09
37 17 0.21
38 23 0.28
40 15 0.19
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (37 bp):
AAGAAAGAAAGAAAGAAAGAAGGAAGGAAGGAGAGAG
Found at i:2737696 original size:26 final size:27
Alignment explanation
Indices: 2737666--2737776 Score: 99
Period size: 26 Copynumber: 4.2 Consensus size: 27
2737656 AAAAAGAAGG
2737666 AAAGAAAGGGAAAGGAGAAGAGAA-AA
1 AAAGAAAGGGAAAGGAGAAGAGAAGAA
* *
2737692 AAAGAAA--GAAAGAAGAAGAGAAGGA
1 AAAGAAAGGGAAAGGAGAAGAGAAGAA
** *
2737717 AAAGAGAAGAAAAAAGA-AAGA-AAGAA
1 AAAGA-AAGGGAAAGGAGAAGAGAAGAA
*
2737743 GGAAAGAAAAGGAAAGGAGAAGAGAA-AA
1 --AAAGAAAGGGAAAGGAGAAGAGAAGAA
2737771 AAAGAA
1 AAAGAA
2737777 GAAGAAGAAG
Statistics
Matches: 67, Mismatches: 10, Indels: 16
0.72 0.11 0.17
Matches are distributed among these distances:
24 14 0.21
25 6 0.09
26 19 0.28
27 11 0.16
28 15 0.22
29 2 0.03
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (27 bp):
AAAGAAAGGGAAAGGAGAAGAGAAGAA
Found at i:2737701 original size:30 final size:33
Alignment explanation
Indices: 2737650--2737741 Score: 93
Period size: 37 Copynumber: 2.7 Consensus size: 33
2737640 AGGAGAGGGA
2737650 AGAA-AGAAAAAGAAGGAAAGAAAG-G-GA-AAGG
1 AGAAGAGAAAAA-AA-GAAAGAAAGAGAGAGAAGG
2737681 AGAAGAGAAAAAAAGAAAGAAAGAAGAAGAGAAGG
1 AGAAGAGAAAAAAAGAAAGAAAG-AG-AGAGAAGG
*
2737716 AAAAGAGAAGAAAAAAGAAAGAAAGA
1 AGAAGAG-A-AAAAAAGAAAGAAAGA
2737742 AGGAAAGAAA
Statistics
Matches: 52, Mismatches: 1, Indels: 11
0.81 0.02 0.17
Matches are distributed among these distances:
30 9 0.17
31 6 0.12
32 8 0.15
34 2 0.04
35 10 0.19
36 2 0.04
37 15 0.29
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (33 bp):
AGAAGAGAAAAAAAGAAAGAAAGAGAGAGAAGG
Found at i:2737707 original size:3 final size:3
Alignment explanation
Indices: 2737701--2737793 Score: 53
Period size: 3 Copynumber: 33.3 Consensus size: 3
2737691 AAAAGAAAGA
2737701 AAG AAG AAG -AG AAGG AA- AAG -AG AAG AA- AA- AAG AAAG AAAG AAG
1 AAG AAG AAG AAG AA-G AAG AAG AAG AAG AAG AAG AAG -AAG -AAG AAG
* * * *
2737744 GA- AAG AA- AAG GA- AAG GAG AAG -AG AA- AAA AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
2737787 AAG AAG A
1 AAG AAG A
2737794 GGGAAGGAAG
Statistics
Matches: 72, Mismatches: 7, Indels: 22
0.71 0.07 0.22
Matches are distributed among these distances:
2 18 0.25
3 44 0.61
4 10 0.14
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:2737765 original size:16 final size:15
Alignment explanation
Indices: 2737657--2737788 Score: 58
Period size: 16 Copynumber: 8.5 Consensus size: 15
2737647 GGAAGAAAGA
2737657 AAAAG-AAGGA-AAG
1 AAAAGAAAGGAGAAG
*
2737670 AAAGGGAAAGGAGAAG
1 AAA-AGAAAGGAGAAG
* *
2737686 AGAAAAAAAGAAAGAAAG
1 A-AAAGAAAG-GAG-AAG
*
2737704 AAGAAGAGAAGGAAAAG
1 AA-AAGA-AAGGAGAAG
* **
2737721 AGAAGAAAAAAGAA-
1 AAAAGAAAGGAGAAG
2737735 AGAAAG-AAGGA-AAG
1 A-AAAGAAAGGAGAAG
2737749 AAAAGGAAAGGAGAAG
1 AAAA-GAAAGGAGAAG
* *
2737765 AGAAAAAAAGAAGAAG
1 A-AAAGAAAGGAGAAG
2737781 AAGAAGAA
1 AA-AAGAA
2737789 GAAGAGGGAA
Statistics
Matches: 87, Mismatches: 17, Indels: 27
0.66 0.13 0.21
Matches are distributed among these distances:
13 8 0.09
14 7 0.08
15 19 0.22
16 30 0.34
17 12 0.14
18 8 0.09
19 3 0.03
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (15 bp):
AAAAGAAAGGAGAAG
Found at i:2737769 original size:34 final size:33
Alignment explanation
Indices: 2737605--2737794 Score: 98
Period size: 34 Copynumber: 5.8 Consensus size: 33
2737595 GAAGGAGAGG
*
2737605 GAAAGAA-AGAAAGAAAGAGAGAA-AGAAAGGAA
1 GAAAGAAGAGAAAGAAA-AGAGAAGAGAAAGAAA
* * * * *
2737637 GGAAGGAGAGGGAAG-AAAGA-AAAAGAAGGAAA
1 GAAAGAAGA-GAAAGAAAAGAGAAGAGAAAGAAA
* *
2737669 GAAAG--G-GAAAGGAGAAGAGAA-AAAAAGAAA
1 GAAAGAAGAGAAA-GAAAAGAGAAGAGAAAGAAA
*
2737699 GAAAGAAGAAGAGAAGGAAAAGAGAAGAAAAAAGAAA
1 GAAAGAAG-AGA-AA-GAAAAGAGAAG-AGAAAGAAA
2737736 GAAAGAAG-GAAAGAAAAG-GAAAGGAGAAGAGAAA
1 GAAAGAAGAGAAAGAAAAGAG-AA-GAGAA-AGAAA
* *
2737770 AAAAGAAGA-AGAAGAAGA-AGAAGAG
1 GAAAGAAGAGA-AAGAAAAGAGAAGAG
2737795 GGAAGGAAGG
Statistics
Matches: 125, Mismatches: 14, Indels: 37
0.71 0.08 0.21
Matches are distributed among these distances:
28 3 0.02
29 1 0.01
30 17 0.14
31 4 0.03
32 21 0.17
33 17 0.14
34 24 0.19
35 21 0.17
37 17 0.14
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (33 bp):
GAAAGAAGAGAAAGAAAAGAGAAGAGAAAGAAA
Done.