Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A01
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: 104050246
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 4660000 characters in sequence are not A, C, G, or T
File 68 of 316
Found at i:20239576 original size:20 final size:19
Alignment explanation
Indices: 20239532--20239577 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
20239522 ATAATAATGA
20239532 GAATAAAAAAAATAAAAAT
1 GAATAAAAAAAATAAAAAT
* *
20239551 GAAATAAATACAATAATAAAT
1 G-AATAAAAAAAATAA-AAAT
20239572 GAATAA
1 GAATAA
20239578 TAAATGAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 1 0.04
20 17 0.74
21 5 0.22
ACGTcount: A:0.72, C:0.02, G:0.07, T:0.20
Consensus pattern (19 bp):
GAATAAAAAAAATAAAAAT
Found at i:20239579 original size:23 final size:20
Alignment explanation
Indices: 20239521--20239597 Score: 70
Period size: 21 Copynumber: 3.7 Consensus size: 20
20239511 ATAATAAGAT
*
20239521 AATAAT-AATGAGAATAAAAAA
1 AATAATAAATGA-AAT-AAATA
20239542 AATAA-AAATGAAATAAATA
1 AATAATAAATGAAATAAATA
20239561 CAATAATAAATGAATAATAAATGA
1 -AATAATAAATG-A-AATAAAT-A
20239585 AATAATAAA-GAAA
1 AATAATAAATGAAA
20239598 ATTCTAGTGA
Statistics
Matches: 49, Mismatches: 1, Indels: 13
0.78 0.02 0.21
Matches are distributed among these distances:
19 4 0.08
20 10 0.20
21 16 0.33
22 2 0.04
23 16 0.33
24 1 0.02
ACGTcount: A:0.70, C:0.01, G:0.08, T:0.21
Consensus pattern (20 bp):
AATAATAAATGAAATAAATA
Found at i:20239597 original size:11 final size:11
Alignment explanation
Indices: 20239492--20239597 Score: 53
Period size: 11 Copynumber: 9.3 Consensus size: 11
20239482 ATAGAGACAT
20239492 AAATGAATAAACG
1 AAAT-AATAAA-G
20239505 AAATATATAATAAG
1 AAATA-AT-A-AAG
*
20239519 ATAATAATAATG
1 A-AATAATAAAG
20239531 AGAATAA-AAA-
1 A-AATAATAAAG
20239541 AAATAA-AAATG
1 AAATAATAAA-G
*
20239552 AAATAA-ATA-
1 AAATAATAAAG
*
20239561 CAATAATAAATG
1 AAATAATAAA-G
20239573 -AATAATAAATG
1 AAATAATAAA-G
20239584 AAATAATAAAG
1 AAATAATAAAG
20239595 AAA
1 AAA
20239598 ATTCTAGTGA
Statistics
Matches: 77, Mismatches: 6, Indels: 22
0.73 0.06 0.21
Matches are distributed among these distances:
9 13 0.17
10 3 0.04
11 25 0.32
12 18 0.23
13 7 0.09
14 5 0.06
15 6 0.08
ACGTcount: A:0.68, C:0.02, G:0.08, T:0.22
Consensus pattern (11 bp):
AAATAATAAAG
Found at i:20239599 original size:12 final size:12
Alignment explanation
Indices: 20239492--20239597 Score: 63
Period size: 12 Copynumber: 9.2 Consensus size: 12
20239482 ATAGAGACAT
*
20239492 AAATGAATAAACG
1 AAAT-AATAAATG
*
20239505 AAATATATAATAAG
1 AAATA-ATAA-ATG
20239519 ATAATAAT-AATG
1 A-AATAATAAATG
20239531 AGAATAA-AAA--
1 A-AATAATAAATG
20239541 AAATAA-AAATG
1 AAATAATAAATG
20239552 --A-AATAAAT-
1 AAATAATAAATG
20239560 ACAATAATAAATG
1 A-AATAATAAATG
20239573 -AATAATAAATG
1 AAATAATAAATG
20239584 AAATAATAAA-G
1 AAATAATAAATG
20239595 AAA
1 AAA
20239598 ATTCTAGTGA
Statistics
Matches: 77, Mismatches: 3, Indels: 28
0.71 0.03 0.26
Matches are distributed among these distances:
8 2 0.03
9 13 0.17
10 1 0.01
11 16 0.21
12 27 0.35
13 9 0.12
14 5 0.06
15 4 0.05
ACGTcount: A:0.68, C:0.02, G:0.08, T:0.22
Consensus pattern (12 bp):
AAATAATAAATG
Found at i:20239687 original size:3 final size:3
Alignment explanation
Indices: 20239679--20239860 Score: 132
Period size: 3 Copynumber: 62.7 Consensus size: 3
20239669 ATGGTTTAAA
* * * *
20239679 AAT AAT AAT GAT AAT AAT AAT AAT AGT AAT AAT AAT AAT CAT ACT -AT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * ** *
20239726 AAT GAT AGT AAT AAT GGT AA- AAT AAT AAT AAT GAT AAT AAT AAT AA-
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * *
20239772 AAT -AT AA- AA- AAT -TT AGCA- AAT GAT AAT AAT AAT ATT GAT AAT
1 AAT AAT AAT AAT AAT AAT A--AT AAT AAT AAT AAT AAT AAT AAT AAT
*
20239814 AAAT AAT AAT AGT AA- AAT AAT AAT AAT AAT AAT AAT AACT AA- AAT
1 -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT
20239859 AA
1 AA
20239861 CTAAAAAGGA
Statistics
Matches: 138, Mismatches: 28, Indels: 26
0.72 0.15 0.14
Matches are distributed among these distances:
2 17 0.12
3 114 0.83
4 7 0.05
ACGTcount: A:0.60, C:0.02, G:0.06, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:20241404 original size:14 final size:14
Alignment explanation
Indices: 20241387--20241413 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
20241377 CATAAAATAA
20241387 AGAAAATATTTTAT
1 AGAAAATATTTTAT
20241401 AGAAAATATTTTA
1 AGAAAATATTTTA
20241414 CTGGCAAACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (14 bp):
AGAAAATATTTTAT
Found at i:20246735 original size:21 final size:21
Alignment explanation
Indices: 20246711--20246751 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
20246701 ACGTGACAAG
* *
20246711 TTAACTGGCCACGTTAGCTAA
1 TTAACTAGCCACGTCAGCTAA
*
20246732 TTAACTAGCCATGTCAGCTA
1 TTAACTAGCCACGTCAGCTA
20246752 TTCCGTTAAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.29
Consensus pattern (21 bp):
TTAACTAGCCACGTCAGCTAA
Found at i:20247433 original size:12 final size:12
Alignment explanation
Indices: 20247416--20247448 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
20247406 CCGACCTTCC
20247416 ATATTAATTTTT
1 ATATTAATTTTT
20247428 ATATT-ATTTTT
1 ATATTAATTTTT
20247439 ATA-TAATTTT
1 ATATTAATTTT
20247449 AAAATATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 14 0.70
12 5 0.25
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
ATATTAATTTTT
Found at i:20247711 original size:22 final size:22
Alignment explanation
Indices: 20247663--20247711 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
20247653 ATATCCAAAC
*
20247663 AATAACAACAAAATAGTAGCAA
1 AATAACAACAAAATAGTAACAA
* * * *
20247685 CATAATAATAAAATGGTAACAA
1 AATAACAACAAAATAGTAACAA
20247707 AATAA
1 AATAA
20247712 GGAGAAAACA
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.63, C:0.10, G:0.08, T:0.18
Consensus pattern (22 bp):
AATAACAACAAAATAGTAACAA
Found at i:20254367 original size:29 final size:28
Alignment explanation
Indices: 20254330--20254384 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 28
20254320 AGTGGTATAC
20254330 TTTTTAAATAATTTGAATAATTTTTAAT
1 TTTTTAAATAATTTGAATAATTTTTAAT
* **
20254358 TTTTTAAAATATTTTTTATAATTTTTA
1 TTTTT-AAATAATTTGAATAATTTTTA
20254385 TTGAAATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 5 0.22
29 18 0.78
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (28 bp):
TTTTTAAATAATTTGAATAATTTTTAAT
Found at i:20265721 original size:4 final size:4
Alignment explanation
Indices: 20265712--20265738 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
20265702 CATTTGGTCC
20265712 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
20265739 TTACAATTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:20266088 original size:3 final size:3
Alignment explanation
Indices: 20266080--20266118 Score: 53
Period size: 3 Copynumber: 12.7 Consensus size: 3
20266070 ATTTAGGCCT
20266080 TTA TTA TTA TTA TTA TTA TT- TTCA TCTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TT-A T-TA TTA TTA TTA TT
20266119 TATTTATTCA
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
2 2 0.06
3 27 0.82
4 3 0.09
5 1 0.03
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:20266115 original size:25 final size:25
Alignment explanation
Indices: 20266081--20266134 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 25
20266071 TTTAGGCCTT
*
20266081 TATTATTATTA-TTATTATTTTCATC
1 TATTATTATTATTTATT-TATTCATC
20266106 TATTATTATTATTTATTTATTCATC
1 TATTATTATTATTTATTTATTCATC
20266131 TATT
1 TATT
20266135 TGTTTATCAC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 22 0.81
26 5 0.19
ACGTcount: A:0.28, C:0.07, G:0.00, T:0.65
Consensus pattern (25 bp):
TATTATTATTATTTATTTATTCATC
Found at i:20266454 original size:11 final size:11
Alignment explanation
Indices: 20266438--20266462 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
20266428 TATGACTATT
20266438 ATAGTACATTA
1 ATAGTACATTA
20266449 ATAGTACATTA
1 ATAGTACATTA
20266460 ATA
1 ATA
20266463 CTATCATAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.48, C:0.08, G:0.08, T:0.36
Consensus pattern (11 bp):
ATAGTACATTA
Found at i:20266937 original size:12 final size:12
Alignment explanation
Indices: 20266920--20266945 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
20266910 AGGGGTCGTA
20266920 TTTTAATTTTTT
1 TTTTAATTTTTT
20266932 TTTTAATTTTTT
1 TTTTAATTTTTT
20266944 TT
1 TT
20266946 AATTTTCGAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (12 bp):
TTTTAATTTTTT
Found at i:20269217 original size:26 final size:26
Alignment explanation
Indices: 20269159--20269211 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
20269149 TAAATAATGC
**
20269159 TTAATTAAAATTTAAGTTTTTATACA
1 TTAATTAAAATTTAAGTTTAAATACA
20269185 TTAATTAAAATTTAA-TTTAAATTACA
1 TTAATTAAAATTTAAGTTTAAA-TACA
20269211 T
1 T
20269212 ATATTACAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 4 0.17
26 20 0.83
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.49
Consensus pattern (26 bp):
TTAATTAAAATTTAAGTTTAAATACA
Found at i:20269704 original size:15 final size:15
Alignment explanation
Indices: 20269684--20269749 Score: 55
Period size: 14 Copynumber: 4.3 Consensus size: 15
20269674 ACTACAAAAC
20269684 ATTTATTATTAATAT
1 ATTTATTATTAATAT
*
20269699 ATTTATAATTGTAATAAAT
1 ATTTATTA-T-TAAT--AT
*
20269718 ATTTATTATTAAAAT
1 ATTTATTATTAATAT
*
20269733 A-TTAATATTAA-AT
1 ATTTATTATTAATAT
20269746 ATTT
1 ATTT
20269750 TCAACAATAT
Statistics
Matches: 42, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
13 3 0.07
14 11 0.26
15 10 0.24
16 1 0.02
17 7 0.17
18 1 0.02
19 9 0.21
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (15 bp):
ATTTATTATTAATAT
Found at i:20277732 original size:13 final size:13
Alignment explanation
Indices: 20277711--20277765 Score: 56
Period size: 13 Copynumber: 4.2 Consensus size: 13
20277701 AAATTTTTCC
20277711 AAAGCACTTCTCA
1 AAAGCACTTCTCA
*
20277724 AAAGTACTTCTCA
1 AAAGCACTTCTCA
* * *
20277737 AAAACACTTTTCC
1 AAAGCACTTCTCA
* *
20277750 ACAGCACTTTTCA
1 AAAGCACTTCTCA
20277763 AAA
1 AAA
20277766 ACAATAAAAA
Statistics
Matches: 33, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
13 33 1.00
ACGTcount: A:0.40, C:0.27, G:0.05, T:0.27
Consensus pattern (13 bp):
AAAGCACTTCTCA
Found at i:20277744 original size:26 final size:26
Alignment explanation
Indices: 20277715--20277768 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 26
20277705 TTTTCCAAAG
*
20277715 CACTTCTCAAAAGTACTTCTCAAAAA
1 CACTTCTCAAAAGCACTTCTCAAAAA
* * * *
20277741 CACTTTTCCACAGCACTTTTCAAAAA
1 CACTTCTCAAAAGCACTTCTCAAAAA
20277767 CA
1 CA
20277769 ATAAAAAACT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.39, C:0.30, G:0.04, T:0.28
Consensus pattern (26 bp):
CACTTCTCAAAAGCACTTCTCAAAAA
Found at i:20280921 original size:15 final size:15
Alignment explanation
Indices: 20280901--20280952 Score: 63
Period size: 15 Copynumber: 3.5 Consensus size: 15
20280891 TTCTAATACT
20280901 ATTATTATTTATCTA
1 ATTATTATTTATCTA
20280916 ATTATTATTTATCTA
1 ATTATTATTTATCTA
* *
20280931 TTTA-TATTTCTACT-
1 ATTATTATTTAT-CTA
20280945 ATTATTAT
1 ATTATTAT
20280953 ATTTCTATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
14 9 0.28
15 23 0.72
ACGTcount: A:0.31, C:0.08, G:0.00, T:0.62
Consensus pattern (15 bp):
ATTATTATTTATCTA
Found at i:20280931 original size:29 final size:29
Alignment explanation
Indices: 20280906--20280962 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
20280896 ATACTATTAT
20280906 TATTTAT-CTAATTATTAT-TTATCTATTTA
1 TATTTATACT-ATTATTATATT-TCTATTTA
*
20280935 TATTTCTACTATTATTATATTTCTATTT
1 TATTTATACTATTATTATATTTCTATTT
20280963 GTTATATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
29 21 0.84
30 4 0.16
ACGTcount: A:0.28, C:0.09, G:0.00, T:0.63
Consensus pattern (29 bp):
TATTTATACTATTATTATATTTCTATTTA
Found at i:20280969 original size:15 final size:15
Alignment explanation
Indices: 20280932--20280977 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 15
20280922 ATTTATCTAT
20280932 TTATATTTCTACTATTA
1 TTATATTTCTA-T-TTA
*
20280949 TTATATTTCTATTTG
1 TTATATTTCTATTTA
*
20280964 TTATATTTTTATTT
1 TTATATTTCTATTT
20280978 CTATTTATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
15 15 0.56
16 1 0.04
17 11 0.41
ACGTcount: A:0.24, C:0.07, G:0.02, T:0.67
Consensus pattern (15 bp):
TTATATTTCTATTTA
Found at i:20281217 original size:21 final size:22
Alignment explanation
Indices: 20281187--20281240 Score: 58
Period size: 23 Copynumber: 2.5 Consensus size: 22
20281177 TTTCAGACAT
**
20281187 TATA-TATTTTGAATTA-TTTA
1 TATATTATTTTGAAAGAGTTTA
*
20281207 TATATTATTTTTAAAGAGTTTTA
1 TATATTATTTTGAAAGAG-TTTA
20281230 TATATTATTTT
1 TATATTATTTT
20281241 ATCTTGAATG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 4 0.14
21 9 0.32
23 15 0.54
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (22 bp):
TATATTATTTTGAAAGAGTTTA
Found at i:20288114 original size:23 final size:23
Alignment explanation
Indices: 20288088--20288185 Score: 162
Period size: 23 Copynumber: 4.3 Consensus size: 23
20288078 ATAAGTGCCA
20288088 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
20288111 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
20288134 CACTG-GATGTAGCCAAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
20288156 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
20288179 CACTGAT
1 CACTGAT
20288186 CAATAACACT
Statistics
Matches: 69, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
22 20 0.29
23 49 0.71
ACGTcount: A:0.32, C:0.27, G:0.21, T:0.20
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:20288153 original size:45 final size:45
Alignment explanation
Indices: 20288095--20288183 Score: 160
Period size: 45 Copynumber: 2.0 Consensus size: 45
20288085 CCACACTGAT
* *
20288095 ATGTAGCCGAAGCTACCACTGATATGTAGCCGAAGCTACCACTGG
1 ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTGG
20288140 ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTG
1 ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTG
20288184 ATCAATAACA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.31, C:0.27, G:0.22, T:0.19
Consensus pattern (45 bp):
ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTGG
Found at i:20295482 original size:23 final size:23
Alignment explanation
Indices: 20295456--20295553 Score: 162
Period size: 23 Copynumber: 4.3 Consensus size: 23
20295446 ATAAGTGCCA
20295456 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
20295479 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
20295502 CACTG-GATGTAGCCAAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
20295524 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
20295547 CACTGAT
1 CACTGAT
20295554 CAATAACACT
Statistics
Matches: 69, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
22 20 0.29
23 49 0.71
ACGTcount: A:0.32, C:0.27, G:0.21, T:0.20
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:20295521 original size:45 final size:45
Alignment explanation
Indices: 20295463--20295551 Score: 160
Period size: 45 Copynumber: 2.0 Consensus size: 45
20295453 CCACACTGAT
* *
20295463 ATGTAGCCGAAGCTACCACTGATATGTAGCCGAAGCTACCACTGG
1 ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTGG
20295508 ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTG
1 ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTG
20295552 ATCAATAACA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.31, C:0.27, G:0.22, T:0.19
Consensus pattern (45 bp):
ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTGG
Found at i:20303200 original size:15 final size:15
Alignment explanation
Indices: 20303180--20303208 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
20303170 TTGCCAGACA
20303180 TGGATAATGAAAAAT
1 TGGATAATGAAAAAT
20303195 TGGATAATGAAAAA
1 TGGATAATGAAAAA
20303209 CAAGTCACTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.21, T:0.24
Consensus pattern (15 bp):
TGGATAATGAAAAAT
Found at i:20305980 original size:39 final size:39
Alignment explanation
Indices: 20305926--20306003 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
20305916 AGGTCATGAT
20305926 TGTCATGGTGTCATCTCAAGTCTTAAAGGCTCAGTATAC
1 TGTCATGGTGTCATCTCAAGTCTTAAAGGCTCAGTATAC
20305965 TGTCATGGTGTCATCTCAAGTCTTAAAGGCTCAGTATAC
1 TGTCATGGTGTCATCTCAAGTCTTAAAGGCTCAGTATAC
20306004 CCTCTGTGCA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.33
Consensus pattern (39 bp):
TGTCATGGTGTCATCTCAAGTCTTAAAGGCTCAGTATAC
Found at i:20307624 original size:17 final size:17
Alignment explanation
Indices: 20307602--20307636 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
20307592 CAAAGTAAAA
20307602 AACAGATATGAAGATAT
1 AACAGATATGAAGATAT
20307619 AACAGATATGAAGATAT
1 AACAGATATGAAGATAT
20307636 A
1 A
20307637 TGCACTTGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (17 bp):
AACAGATATGAAGATAT
Found at i:20312741 original size:50 final size:50
Alignment explanation
Indices: 20312682--20312796 Score: 151
Period size: 50 Copynumber: 2.3 Consensus size: 50
20312672 CTACTTATTT
* * *
20312682 GGCCGAATATGCAAGAT-CAAGAATAATATCACATATGTACATATCTATAA
1 GGCCGAATATGCAAGATCCAA-AATAACATCACATAAGTACATACCTATAA
* * **
20312732 GGCCGAATATGCAAGTTCCAATATAACATCACATAAGTACATACCTATGT
1 GGCCGAATATGCAAGATCCAAAATAACATCACATAAGTACATACCTATAA
20312782 GGCCGAATATGCAAG
1 GGCCGAATATGCAAG
20312797 GTCATTTAAC
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
50 54 0.95
51 3 0.05
ACGTcount: A:0.40, C:0.19, G:0.17, T:0.24
Consensus pattern (50 bp):
GGCCGAATATGCAAGATCCAAAATAACATCACATAAGTACATACCTATAA
Found at i:20314463 original size:19 final size:18
Alignment explanation
Indices: 20314432--20314476 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
20314422 CAAGCTTAAT
20314432 ATTAAATTAATTAAGATTTA
1 ATTAAA-TAATTAAG-TTTA
*
20314452 GTTAAATAATTAAGTTTA
1 ATTAAATAATTAAGTTTA
20314470 ATTAAAT
1 ATTAAAT
20314477 GTTAAACTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 10 0.43
19 8 0.35
20 5 0.22
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.44
Consensus pattern (18 bp):
ATTAAATAATTAAGTTTA
Found at i:20325405 original size:11 final size:11
Alignment explanation
Indices: 20325389--20325424 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
20325379 ACCAGTGGAG
20325389 AAAATTAAATT
1 AAAATTAAATT
20325400 AAAATTAAATT
1 AAAATTAAATT
*
20325411 AAAAATAAGATT
1 AAAATTAA-ATT
20325423 AA
1 AA
20325425 GAGTTGGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 18 0.78
12 5 0.22
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (11 bp):
AAAATTAAATT
Found at i:20330138 original size:17 final size:17
Alignment explanation
Indices: 20330066--20330160 Score: 57
Period size: 17 Copynumber: 5.5 Consensus size: 17
20330056 TTTAAGAATG
*
20330066 TTTTGAACTTAAAG-AAA
1 TTTTAAACTT-AAGTAAA
**
20330083 TTTTAGGCTTAAGTGAAA
1 TTTTAAACTTAAGT-AAA
* * * **
20330101 ATTTGAACTTAAGCATG
1 TTTTAAACTTAAGTAAA
20330118 TTTTAAACTTAAGTAAA
1 TTTTAAACTTAAGTAAA
* * *
20330135 TTTTGAATTTGAGTAAA
1 TTTTAAACTTAAGTAAA
*
20330152 TTTCAAACT
1 TTTTAAACT
20330161 GCTTTATCTA
Statistics
Matches: 55, Mismatches: 21, Indels: 4
0.69 0.26 0.05
Matches are distributed among these distances:
16 3 0.05
17 40 0.73
18 12 0.22
ACGTcount: A:0.39, C:0.07, G:0.14, T:0.40
Consensus pattern (17 bp):
TTTTAAACTTAAGTAAA
Found at i:20331872 original size:30 final size:30
Alignment explanation
Indices: 20331836--20331904 Score: 111
Period size: 30 Copynumber: 2.3 Consensus size: 30
20331826 TGCAGGACAC
20331836 AATAAATTGTTTTAATCTATCATGTAATTG
1 AATAAATTGTTTTAATCTATCATGTAATTG
* **
20331866 AATAAATTATTTTAATCTATTGTGTAATTG
1 AATAAATTGTTTTAATCTATCATGTAATTG
20331896 AATAAATTG
1 AATAAATTG
20331905 ACAAATATCT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.39, C:0.04, G:0.10, T:0.46
Consensus pattern (30 bp):
AATAAATTGTTTTAATCTATCATGTAATTG
Found at i:20335675 original size:50 final size:50
Alignment explanation
Indices: 20335600--20335776 Score: 264
Period size: 50 Copynumber: 3.5 Consensus size: 50
20335590 CCATGGCAAC
*
20335600 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATAAAGGACAAATGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
* *
20335650 AAGTGATAAGTAATAGCTTCGGCTACACTTATCTGATCAAGGACAAGTGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
* * *
20335700 AAGTGATAAGTGATAACTTCGGCTACATTTATCTGATCAAGGACAAATAA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
* * *
20335750 CAAGTGAAAAGTGGTAGCTTCTGCTAC
1 -AAGTGATAAGTGATAGCTTCGGCTAC
20335777 CTAATCAGTG
Statistics
Matches: 114, Mismatches: 12, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
50 92 0.81
51 22 0.19
ACGTcount: A:0.37, C:0.15, G:0.21, T:0.27
Consensus pattern (50 bp):
AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
Found at i:20335869 original size:31 final size:31
Alignment explanation
Indices: 20335752--20335861 Score: 175
Period size: 31 Copynumber: 3.5 Consensus size: 31
20335742 ACAAATAACA
* * *
20335752 AGTGAAAAGTGGTAGCTTCTGCTACCTAATC
1 AGTGAAAAGTGGTAGCTCCAGCTACCTGATC
20335783 AGTGAAAAGTGGTAGCTCCAGCTACCTGATC
1 AGTGAAAAGTGGTAGCTCCAGCTACCTGATC
*
20335814 AGTGAAAAATGGTAGCTCCAGCTACCTGATC
1 AGTGAAAAGTGGTAGCTCCAGCTACCTGATC
*
20335845 AGTGAATAGTGGTAGCT
1 AGTGAAAAGTGGTAGCT
20335862 TCGGCTACAA
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 73 1.00
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.25
Consensus pattern (31 bp):
AGTGAAAAGTGGTAGCTCCAGCTACCTGATC
Found at i:20335997 original size:49 final size:47
Alignment explanation
Indices: 20335891--20336062 Score: 205
Period size: 49 Copynumber: 3.7 Consensus size: 47
20335881 GATTTCCGTA
* * * * *
20335891 TAAGACCATATCTGGGATATGGCATCA-GTGAGATATGTGATTCATG
1 TAAGACCATAGCTGGGCTATGGCATCATATGTGATATGTGATTCGTG
20335937 TAAGACCATAGCTGGGCTATGGCATCGATATGTGATATGTGATTACGTG
1 TAAGACCATAGCTGGGCTATGGCATC-ATATGTGATATGTGATT-CGTG
*
20335986 TAAGACCATAGCTGGGCTATGGCATCGATATATGA-A--T-A-T-GTG
1 TAAGACCATAGCTGGGCTATGGCATC-ATATGTGATATGTGATTCGTG
20336028 TAAGACCATAGCTGGGCTATGGCATCATTATGTGA
1 TAAGACCATAGCTGGGCTATGGCATCA-TATGTGA
20336063 AGATGTGTAA
Statistics
Matches: 115, Mismatches: 7, Indels: 12
0.86 0.05 0.09
Matches are distributed among these distances:
41 1 0.01
42 35 0.30
44 1 0.01
45 1 0.01
46 25 0.22
47 1 0.01
48 14 0.12
49 37 0.32
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.30
Consensus pattern (47 bp):
TAAGACCATAGCTGGGCTATGGCATCATATGTGATATGTGATTCGTG
Found at i:20336029 original size:42 final size:43
Alignment explanation
Indices: 20335935--20336097 Score: 188
Period size: 42 Copynumber: 3.7 Consensus size: 43
20335925 ATGTGATTCA
*
20335935 TGTAAGACCATAGCTGGGCTATGGCATCGATATGTGATATG-TGATTACG
1 TGTAAGACCATAGCTGGGCTATGGCATCG--AT-T-ATATGAAGA-T--G
*
20335984 TGTAAGACCATAGCTGGGCTATGGCATCGA-TATATGAATATG
1 TGTAAGACCATAGCTGGGCTATGGCATCGATTATATGAAGATG
*
20336026 TGTAAGACCATAGCTGGGCTATGGCATC-ATTATGTGAAGATG
1 TGTAAGACCATAGCTGGGCTATGGCATCGATTATATGAAGATG
* **
20336068 TGTAAGACCATAGTTGAACTATGGCATCGA
1 TGTAAGACCATAGCTGGGCTATGGCATCGA
20336098 GAAAACGAAG
Statistics
Matches: 104, Mismatches: 7, Indels: 12
0.85 0.06 0.10
Matches are distributed among these distances:
41 1 0.01
42 64 0.62
43 1 0.01
44 6 0.06
45 2 0.02
47 1 0.01
49 29 0.28
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (43 bp):
TGTAAGACCATAGCTGGGCTATGGCATCGATTATATGAAGATG
Found at i:20337433 original size:17 final size:17
Alignment explanation
Indices: 20337411--20337444 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
20337401 TTACTGCTTC
20337411 CACCACCTGCGAAGCTA
1 CACCACCTGCGAAGCTA
20337428 CACCACCTGCGAAGCTA
1 CACCACCTGCGAAGCTA
20337445 ACTTCCTCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.41, G:0.18, T:0.12
Consensus pattern (17 bp):
CACCACCTGCGAAGCTA
Found at i:20358438 original size:39 final size:40
Alignment explanation
Indices: 20358393--20358564 Score: 222
Period size: 40 Copynumber: 4.3 Consensus size: 40
20358383 GCTCCTCGTT
* * *
20358393 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
*
20358433 C-AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * *
20358472 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * * *
20358512 CAAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGG-ATTTAGTAACTCGCA
20358552 CAAATGCCTTCGG
1 CAAATGCCTTCGG
20358565 ATCTTAGTCC
Statistics
Matches: 119, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
39 35 0.29
40 80 0.67
41 4 0.03
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
Found at i:20358493 original size:40 final size:39
Alignment explanation
Indices: 20358395--20358617 Score: 216
Period size: 40 Copynumber: 5.6 Consensus size: 39
20358385 TCCTCGTTCA
* * * *
20358395 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* *
20358434 AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
*
20358473 GAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* * *
20358513 AAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCAC
** * * * *
20358553 AAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC
1 -AATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCAC
* *
20358594 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
20358618 CAGCATTCAA
Statistics
Matches: 157, Mismatches: 21, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
39 40 0.25
40 105 0.67
41 12 0.08
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.26
Consensus pattern (39 bp):
AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
Found at i:20358577 original size:80 final size:79
Alignment explanation
Indices: 20358393--20358617 Score: 240
Period size: 80 Copynumber: 2.8 Consensus size: 79
20358383 GCTCCTCGTT
* * * * *
20358393 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACATAACCCGG-
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGT-ACTCGCACAAAGCCTTCGGGACTTAACCCGGA
20358457 ATTTAATAACTCGCA
65 ATTTAATAACTCGCA
* * *
20358472 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTCGGGGCTTAACCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTA-CTCGCACAAA-GCCTTCGGGACTTAACCCGG
* *
20358537 AATTT-GTATCTCGCA
64 AATTTAATAACTCGCA
* * * * *
20358552 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCACAAAGCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGT-AC-TCGCACAAAGCCTTCGGGACTTAACCCG
20358616 GA
63 GA
20358618 CAGCATTCAA
Statistics
Matches: 122, Mismatches: 18, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
78 1 0.01
79 39 0.32
80 69 0.57
81 13 0.11
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (79 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTACTCGCACAAAGCCTTCGGGACTTAACCCGGAA
TTTAATAACTCGCA
Found at i:20358626 original size:41 final size:41
Alignment explanation
Indices: 20358549--20358626 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
20358539 TTTGTATCTC
* * *
20358549 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
20358590 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
20358627 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:20364816 original size:39 final size:40
Alignment explanation
Indices: 20364771--20364942 Score: 222
Period size: 40 Copynumber: 4.3 Consensus size: 40
20364761 GCTCCTCGTT
* * *
20364771 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
*
20364811 C-AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * *
20364850 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * * *
20364890 CAAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGG-ATTTAGTAACTCGCA
20364930 CAAATGCCTTCGG
1 CAAATGCCTTCGG
20364943 ATCTTAGTCC
Statistics
Matches: 119, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
39 35 0.29
40 80 0.67
41 4 0.03
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
Found at i:20364871 original size:40 final size:39
Alignment explanation
Indices: 20364773--20364995 Score: 216
Period size: 40 Copynumber: 5.6 Consensus size: 39
20364763 TCCTCGTTCA
* * * *
20364773 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* *
20364812 AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
*
20364851 GAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* * *
20364891 AAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCAC
** * * * *
20364931 AAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC
1 -AATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCAC
* *
20364972 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
20364996 CAGCATTCAA
Statistics
Matches: 157, Mismatches: 21, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
39 40 0.25
40 105 0.67
41 12 0.08
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.26
Consensus pattern (39 bp):
AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
Found at i:20364955 original size:80 final size:79
Alignment explanation
Indices: 20364771--20364995 Score: 240
Period size: 80 Copynumber: 2.8 Consensus size: 79
20364761 GCTCCTCGTT
* * * * *
20364771 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACATAACCCGG-
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGT-ACTCGCACAAAGCCTTCGGGACTTAACCCGGA
20364835 ATTTAATAACTCGCA
65 ATTTAATAACTCGCA
* * *
20364850 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTCGGGGCTTAACCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTA-CTCGCACAAA-GCCTTCGGGACTTAACCCGG
* *
20364915 AATTT-GTATCTCGCA
64 AATTTAATAACTCGCA
* * * * *
20364930 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCACAAAGCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGT-AC-TCGCACAAAGCCTTCGGGACTTAACCCG
20364994 GA
63 GA
20364996 CAGCATTCAA
Statistics
Matches: 122, Mismatches: 18, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
78 1 0.01
79 39 0.32
80 69 0.57
81 13 0.11
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (79 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTACTCGCACAAAGCCTTCGGGACTTAACCCGGAA
TTTAATAACTCGCA
Found at i:20365004 original size:41 final size:41
Alignment explanation
Indices: 20364927--20365004 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
20364917 TTTGTATCTC
* * *
20364927 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
20364968 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
20365005 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:20367644 original size:196 final size:196
Alignment explanation
Indices: 20367309--20367690 Score: 523
Period size: 196 Copynumber: 1.9 Consensus size: 196
20367299 TTGGCTTTTT
* * *
20367309 CCACAAGCTCATTAAACAACTCTGTATTTTAGGCCGCTAAATAAACTCAAATCTCACGATTGAGC
1 CCACAAGCTCATCAAACAACTCTGTATTTTAGGCCACTAAATAAACCCAAATCTCACGATTGAGC
* * * * * ** *
20367374 CTAAAGCGAAACCTCTTATAGCGATACTTATCAGTCAAAACCATCTTAGGAGTATACTGACAAAG
66 CCAAAGCGAAACCTCTTACAACGATACTTATAAGTCAAAACCATCTCAAAAGCATACTGACAAAG
*
20367439 GCACACAAACTCTGCCTCATAGTCAGCCACAGACAAGCTACCTTGCACAAGATCCAAAAATTCCC
131 GCACACAAACTCTGCCTCATAGTCAGCCACAAACAAGCTACCTTGCACAAGATCCAAAAATTCCC
20367504 A
196 A
* * *
20367505 CCACAAGCTCATCAAACAACTTTGTATTTTGGGCCACTAAATAAACCCTAATCTCACGATTGAGC
1 CCACAAGCTCATCAAACAACTCTGTATTTTAGGCCACTAAATAAACCCAAATCTCACGATTGAGC
* * * * *
20367570 CCAAAGC-AGAACTTCTTACAACGATCCTTCTAAGTCAAAACTATCTCAAAAGCATACTGACTAA
66 CCAAAGCGA-AACCTCTTACAACGATACTTATAAGTCAAAACCATCTCAAAAGCATACTGACAAA
* * * * *
20367634 GGCGCACAAACTTTGTCTCATAGTCAGCCACAAACGAGCTACCTTGCGCAAGATCCA
130 GGCACACAAACTCTGCCTCATAGTCAGCCACAAACAAGCTACCTTGCACAAGATCCA
20367691 TAAACTTCTT
Statistics
Matches: 160, Mismatches: 25, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
195 1 0.01
196 159 0.99
ACGTcount: A:0.36, C:0.28, G:0.13, T:0.23
Consensus pattern (196 bp):
CCACAAGCTCATCAAACAACTCTGTATTTTAGGCCACTAAATAAACCCAAATCTCACGATTGAGC
CCAAAGCGAAACCTCTTACAACGATACTTATAAGTCAAAACCATCTCAAAAGCATACTGACAAAG
GCACACAAACTCTGCCTCATAGTCAGCCACAAACAAGCTACCTTGCACAAGATCCAAAAATTCCC
A
Found at i:20369520 original size:10 final size:10
Alignment explanation
Indices: 20369488--20369530 Score: 52
Period size: 10 Copynumber: 4.4 Consensus size: 10
20369478 ATTCTGACAC
20369488 ACAT-CAATT
1 ACATACAATT
**
20369497 ACATACAAGC
1 ACATACAATT
*
20369507 ACATATAATT
1 ACATACAATT
20369517 ACATACAATT
1 ACATACAATT
20369527 ACAT
1 ACAT
20369531 TTAATCAAAA
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
9 4 0.15
10 23 0.85
ACGTcount: A:0.49, C:0.21, G:0.02, T:0.28
Consensus pattern (10 bp):
ACATACAATT
Found at i:20377517 original size:18 final size:17
Alignment explanation
Indices: 20377464--20377513 Score: 73
Period size: 18 Copynumber: 2.8 Consensus size: 17
20377454 TGGATTATAA
20377464 TATTAATTAATAAAATAT
1 TATT-ATTAATAAAATAT
*
20377482 TATTACTTATTAAAATAT
1 TATTA-TTAATAAAATAT
20377500 TATTATTAATAAAA
1 TATTATTAATAAAA
20377514 ATATAATTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 9 0.31
18 20 0.69
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (17 bp):
TATTATTAATAAAATAT
Found at i:20378076 original size:20 final size:20
Alignment explanation
Indices: 20378053--20378090 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
20378043 ATGAAAATAA
20378053 TTAG-AATTAAATATTAAGGT
1 TTAGAAATTAAA-ATTAAGGT
20378073 TTAGAAATTAAAATTAAG
1 TTAGAAATTAAAATTAAG
20378091 TACCTGAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.50, C:0.00, G:0.13, T:0.37
Consensus pattern (20 bp):
TTAGAAATTAAAATTAAGGT
Found at i:20378657 original size:34 final size:34
Alignment explanation
Indices: 20378614--20378684 Score: 142
Period size: 34 Copynumber: 2.1 Consensus size: 34
20378604 ATCTTGTATT
20378614 ACTAAGCTAAACTTCTATTTTAAAGTGATTTCTA
1 ACTAAGCTAAACTTCTATTTTAAAGTGATTTCTA
20378648 ACTAAGCTAAACTTCTATTTTAAAGTGATTTCTA
1 ACTAAGCTAAACTTCTATTTTAAAGTGATTTCTA
20378682 ACT
1 ACT
20378685 CACTTTTATC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.35, C:0.15, G:0.08, T:0.41
Consensus pattern (34 bp):
ACTAAGCTAAACTTCTATTTTAAAGTGATTTCTA
Found at i:20381213 original size:27 final size:27
Alignment explanation
Indices: 20381165--20381323 Score: 184
Period size: 27 Copynumber: 5.9 Consensus size: 27
20381155 GCGAGGCTGC
* *
20381165 CAGATATTGTGAC-GAAGTCACCAGATA
1 CAGATATTGTGGCAG-AGCCACCAGATA
20381192 CAGATATTGTGGCAGAGCCACCAGA-A
1 CAGATATTGTGGCAGAGCCACCAGATA
20381218 CAGATATATGTGGCAGAGCCACCAGAT-
1 CAGATAT-TGTGGCAGAGCCACCAGATA
* *
20381245 CAGATAATTGTGGCATAGCCACCAG-GA
1 CAGAT-ATTGTGGCAGAGCCACCAGATA
*
20381272 CAGATATATGTGGCAGAGCCACCAAAT-
1 CAGATAT-TGTGGCAGAGCCACCAGATA
*
20381299 CAGATAATTGTGGCATAGCCACCAG
1 CAGAT-ATTGTGGCAGAGCCACCAG
20381324 GACGCTTCCT
Statistics
Matches: 115, Mismatches: 9, Indels: 16
0.82 0.06 0.11
Matches are distributed among these distances:
26 10 0.09
27 100 0.87
28 5 0.04
ACGTcount: A:0.35, C:0.22, G:0.25, T:0.19
Consensus pattern (27 bp):
CAGATATTGTGGCAGAGCCACCAGATA
Found at i:20381324 original size:54 final size:54
Alignment explanation
Indices: 20381183--20381326 Score: 245
Period size: 54 Copynumber: 2.7 Consensus size: 54
20381173 GTGACGAAGT
* *
20381183 CACCAGATACAGAT-ATTGTGGCAGAGCCACCAGAACAGATATATGTGGCAGAGC
1 CACCAGAT-CAGATAATTGTGGCATAGCCACCAGGACAGATATATGTGGCAGAGC
20381237 CACCAGATCAGATAATTGTGGCATAGCCACCAGGACAGATATATGTGGCAGAGC
1 CACCAGATCAGATAATTGTGGCATAGCCACCAGGACAGATATATGTGGCAGAGC
*
20381291 CACCAAATCAGATAATTGTGGCATAGCCACCAGGAC
1 CACCAGATCAGATAATTGTGGCATAGCCACCAGGAC
20381327 GCTTCCTCCA
Statistics
Matches: 86, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
53 5 0.06
54 81 0.94
ACGTcount: A:0.35, C:0.24, G:0.24, T:0.17
Consensus pattern (54 bp):
CACCAGATCAGATAATTGTGGCATAGCCACCAGGACAGATATATGTGGCAGAGC
Found at i:20382948 original size:26 final size:26
Alignment explanation
Indices: 20382918--20383025 Score: 198
Period size: 26 Copynumber: 4.2 Consensus size: 26
20382908 TGAAATTCCC
20382918 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
20382944 ATCATGGAACGTTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
20382970 ATCATGAAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
20382996 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
20383022 ATCA
1 ATCA
20383026 ATTTGTATCA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 78 1.00
ACGTcount: A:0.35, C:0.27, G:0.07, T:0.31
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:20386889 original size:47 final size:46
Alignment explanation
Indices: 20386769--20386946 Score: 209
Period size: 47 Copynumber: 3.8 Consensus size: 46
20386759 ATAATTTCAC
* *
20386769 CCATAATGAACTCGGAACGCAACTCAACGAGCTCGGGTGTTCACAT
1 CCATAATGAACTCGGAACGCAACTCAACGAGTTCGGATGTTCACAT
* *
20386815 CCATAATGAACTCGGAACACAACTCAACGAGTTCGGATGCTT-GCAT
1 CCATAATGAACTCGGAACGCAACTCAACGAGTTCGGATG-TTCACAT
*
20386861 CCATAAGTGAACTCGGAACGCAACTCAACGAGTTCGGAT-TCCTCATAAT
1 CCATAA-TGAACTCGGAACGCAACTCAACGAGTTCGGATGT--TCA-CAT
* * * *
20386910 TC-TCACGAACTCGGAACGCAACTCAATGAGTTCGGAT
1 CCATAATGAACTCGGAACGCAACTCAACGAGTTCGGAT
20386947 CTCAATTTCC
Statistics
Matches: 115, Mismatches: 11, Indels: 11
0.84 0.08 0.08
Matches are distributed among these distances:
45 1 0.01
46 45 0.39
47 64 0.56
48 2 0.02
49 3 0.03
ACGTcount: A:0.31, C:0.27, G:0.20, T:0.21
Consensus pattern (46 bp):
CCATAATGAACTCGGAACGCAACTCAACGAGTTCGGATGTTCACAT
Found at i:20386942 original size:94 final size:92
Alignment explanation
Indices: 20386769--20386946 Score: 234
Period size: 94 Copynumber: 1.9 Consensus size: 92
20386759 ATAATTTCAC
* * *
20386769 CCATAATGAACTCGGAACGCAACTCAACGAGCTCGGGTGTTCACATCCATAATGAACTCGGAACA
1 CCATAATGAACTCGGAACGCAACTCAACGAGCTCGGATGTTCAAATCCATAACGAACTCGGAACA
20386834 CAACTCAACGAGTTCGGATGCTTGCAT
66 CAACTCAACGAGTTCGGATGCTTGCAT
* * *
20386861 CCATAAGTGAACTCGGAACGCAACTCAACGAGTTCGGAT-TCCTCATAATTC-TCACGAACTCGG
1 CCATAA-TGAACTCGGAACGCAACTCAACGAGCTCGGATGT--TCA-AATCCATAACGAACTCGG
* *
20386924 AACGCAACTCAATGAGTTCGGAT
62 AACACAACTCAACGAGTTCGGAT
20386947 CTCAATTTCC
Statistics
Matches: 74, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
92 7 0.09
93 30 0.41
94 34 0.46
95 3 0.04
ACGTcount: A:0.31, C:0.27, G:0.20, T:0.21
Consensus pattern (92 bp):
CCATAATGAACTCGGAACGCAACTCAACGAGCTCGGATGTTCAAATCCATAACGAACTCGGAACA
CAACTCAACGAGTTCGGATGCTTGCAT
Found at i:20391321 original size:39 final size:39
Alignment explanation
Indices: 20391278--20391368 Score: 128
Period size: 39 Copynumber: 2.3 Consensus size: 39
20391268 TGCTTTTGAG
*
20391278 TATTGTGATATATGATTGAATGTTATGTGATTATATGAC
1 TATTGTGATATATGATTAAATGTTATGTGATTATATGAC
* * *
20391317 TATTGTGATATATGCTTAAATTTTATGTGATTATATGCC
1 TATTGTGATATATGATTAAATGTTATGTGATTATATGAC
* *
20391356 AAATGTGATATAT
1 TATTGTGATATAT
20391369 CCTTAAAAGT
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.32, C:0.04, G:0.18, T:0.46
Consensus pattern (39 bp):
TATTGTGATATATGATTAAATGTTATGTGATTATATGAC
Found at i:20395685 original size:28 final size:28
Alignment explanation
Indices: 20395653--20395779 Score: 155
Period size: 28 Copynumber: 4.5 Consensus size: 28
20395643 CCATGGCATA
* ** *
20395653 TTCAAGTAAGAGTTTGCATGGACTACCT
1 TTCAAGCAAGAGTCCGCATGGACTATCT
* *
20395681 TTCAAGTAAGAGTCTGCATGGACTATCT
1 TTCAAGCAAGAGTCCGCATGGACTATCT
* *
20395709 ATCAAGCAAGAGTCCGCATGGGCTATCT
1 TTCAAGCAAGAGTCCGCATGGACTATCT
* * *
20395737 TTCAAGAAAGAGTTCGCAAGGACTATCT
1 TTCAAGCAAGAGTCCGCATGGACTATCT
20395765 TTCAAGCAAGAGTCC
1 TTCAAGCAAGAGTCC
20395780 ACAAGGATTG
Statistics
Matches: 86, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 86 1.00
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (28 bp):
TTCAAGCAAGAGTCCGCATGGACTATCT
Found at i:20395797 original size:56 final size:57
Alignment explanation
Indices: 20395672--20395817 Score: 156
Period size: 56 Copynumber: 2.6 Consensus size: 57
20395662 GAGTTTGCAT
* * * * *
20395672 GGACTACCTTTCAAGTAAGAG-TCTGCATGGACTATCTATCAAGCAAGAGTCCGCAT
1 GGACTATCTTTCAAGAAAGAGTTCTGCAAGGACTATCTATCAAGCAAGAGTCCACAA
* *
20395728 GGGCTATCTTTCAAGAAAGAGTTC-GCAAGGACTATCTTTCAAGCAAGAGTCCACAA
1 GGACTATCTTTCAAGAAAGAGTTCTGCAAGGACTATCTATCAAGCAAGAGTCCACAA
* * * *
20395784 GGATTGT-TCTTCAAGAAGGAG-TCTGCAAAGACTA
1 GGACTATCT-TTCAAGAAAGAGTTCTGCAAGGACTA
20395818 ACTAATGGGT
Statistics
Matches: 75, Mismatches: 12, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
55 3 0.04
56 70 0.93
57 2 0.03
ACGTcount: A:0.32, C:0.21, G:0.23, T:0.25
Consensus pattern (57 bp):
GGACTATCTTTCAAGAAAGAGTTCTGCAAGGACTATCTATCAAGCAAGAGTCCACAA
Found at i:20395798 original size:84 final size:84
Alignment explanation
Indices: 20395653--20395806 Score: 186
Period size: 84 Copynumber: 1.8 Consensus size: 84
20395643 CCATGGCATA
* * * * ** *
20395653 TTCAAGTAAGAGTTTGCATGGACTACCTTTCAAGTAAGAGTCTGCATGGACTATCTATCAAGCAA
1 TTCAAGAAAGAGTTCGCAAGGACTACCTTTCAAGCAAGAGTCCACAAGGACTATCTATCAAG-AA
20395718 -GAGTCCGCATGGGCTATCT
65 GGAGTCCGCATGGGCTATCT
* * *
20395737 TTCAAGAAAGAGTTCGCAAGGACTATCTTTCAAGCAAGAGTCCACAAGGATTGTTCT-TCAAGAA
1 TTCAAGAAAGAGTTCGCAAGGACTACCTTTCAAGCAAGAGTCCACAAGGACT-ATCTATCAAGAA
20395801 GGAGTC
65 GGAGTC
20395807 TGCAAAGACT
Statistics
Matches: 58, Mismatches: 10, Indels: 4
0.81 0.14 0.06
Matches are distributed among these distances:
83 2 0.03
84 53 0.91
85 3 0.05
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (84 bp):
TTCAAGAAAGAGTTCGCAAGGACTACCTTTCAAGCAAGAGTCCACAAGGACTATCTATCAAGAAG
GAGTCCGCATGGGCTATCT
Found at i:20397949 original size:30 final size:30
Alignment explanation
Indices: 20397909--20397974 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
20397899 TATATTCAAA
*
20397909 TTATATTTTATTATATAACATTTATTATATT
1 TTATATTTTATTATATAACACTTATTAT-TT
* **
20397940 TTAT-TTTTATTTTATATTACTTATTATTT
1 TTATATTTTATTATATAACACTTATTATTT
20397969 TTATAT
1 TTATAT
20397975 ATGTTATGTA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
29 6 0.20
30 20 0.67
31 4 0.13
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (30 bp):
TTATATTTTATTATATAACACTTATTATTT
Found at i:20398123 original size:23 final size:23
Alignment explanation
Indices: 20398097--20398146 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
20398087 AAATTATTAA
*
20398097 TTATTTATT-TATTATGTATTGTT
1 TTATTT-TTATATTATGTATTATT
*
20398120 TTATTTTTATATTATGTGTTATT
1 TTATTTTTATATTATGTATTATT
20398143 TTAT
1 TTAT
20398147 AAATTCTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 2 0.08
23 22 0.92
ACGTcount: A:0.22, C:0.00, G:0.08, T:0.70
Consensus pattern (23 bp):
TTATTTTTATATTATGTATTATT
Found at i:20398476 original size:33 final size:33
Alignment explanation
Indices: 20398429--20398497 Score: 120
Period size: 33 Copynumber: 2.1 Consensus size: 33
20398419 TGTATTACTT
*
20398429 TTTTTTGTATATCATACATTATTTAATTATTAC
1 TTTTTTGTACATCATACATTATTTAATTATTAC
*
20398462 TTTTTTGTACATCATGCATTATTTAATTATTAC
1 TTTTTTGTACATCATACATTATTTAATTATTAC
20398495 TTT
1 TTT
20398498 GTATGTTTGT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.28, C:0.10, G:0.04, T:0.58
Consensus pattern (33 bp):
TTTTTTGTACATCATACATTATTTAATTATTAC
Found at i:20406325 original size:29 final size:30
Alignment explanation
Indices: 20406287--20406401 Score: 128
Period size: 30 Copynumber: 3.9 Consensus size: 30
20406277 TAAAAAATAA
* *
20406287 AAATTGCATTTTGACCCCTAAACTTTTC-CT
1 AAATTTCATTTTGACCCCTAAAC-TTTCATT
* *
20406317 -AATTTCATTTTGACCCTTAAACTTTCTTT
1 AAATTTCATTTTGACCCCTAAACTTTCATT
* *
20406346 AAATTTCACTTAGACCCCTAAACTTTCATT
1 AAATTTCATTTTGACCCCTAAACTTTCATT
* *
20406376 AAATTTCATTTT-AACCCTAAATTTTC
1 AAATTTCATTTTGACCCCTAAACTTTC
20406402 TAAAAATTAC
Statistics
Matches: 72, Mismatches: 11, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
28 4 0.06
29 33 0.46
30 35 0.49
ACGTcount: A:0.30, C:0.23, G:0.03, T:0.43
Consensus pattern (30 bp):
AAATTTCATTTTGACCCCTAAACTTTCATT
Found at i:20406353 original size:30 final size:30
Alignment explanation
Indices: 20406287--20406402 Score: 130
Period size: 29 Copynumber: 3.9 Consensus size: 30
20406277 TAAAAAATAA
* *
20406287 AAATTGCATTTTGACCCCTAAACTTT-TCCT
1 AAATTTCATTTTGACCCCTAAACTTTCT-TT
*
20406317 -AATTTCATTTTGACCCTTAAACTTTCTTT
1 AAATTTCATTTTGACCCCTAAACTTTCTTT
* * *
20406346 AAATTTCACTTAGACCCCTAAACTTTCATT
1 AAATTTCATTTTGACCCCTAAACTTTCTTT
* *
20406376 AAATTTCATTTT-AACCCTAAATTTTCT
1 AAATTTCATTTTGACCCCTAAACTTTCT
20406403 AAAAATTACA
Statistics
Matches: 72, Mismatches: 12, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
29 36 0.50
30 36 0.50
ACGTcount: A:0.29, C:0.23, G:0.03, T:0.44
Consensus pattern (30 bp):
AAATTTCATTTTGACCCCTAAACTTTCTTT
Found at i:20406408 original size:29 final size:29
Alignment explanation
Indices: 20406284--20406415 Score: 90
Period size: 29 Copynumber: 4.5 Consensus size: 29
20406274 ATTTAAAAAA
* *
20406284 TAAAAATTGCATTTTGACCCCTAAACTTT-
1 TAAAAATTTCATTTT-AACCCTAAACTTTC
*** *
20406313 TCCTAATTTCATTTTGACCCTTAAACTTTC
1 TAAAAATTTCATTTTAACCC-TAAACTTTC
** *
20406343 TTTAAATTTCA-CTTAGACCCCTAAACTTTC
1 TAAAAATTTCATTTTA-A-CCCTAAACTTTC
* *
20406373 -ATTAAATTTCATTTTAACCCTAAATTTTC
1 TA-AAAATTTCATTTTAACCCTAAACTTTC
*
20406402 TAAAAATTACATTT
1 TAAAAATTTCATTT
20406416 AGCCCCAGAA
Statistics
Matches: 80, Mismatches: 16, Indels: 14
0.73 0.15 0.13
Matches are distributed among these distances:
28 3 0.04
29 42 0.52
30 29 0.36
31 6 0.08
ACGTcount: A:0.33, C:0.21, G:0.03, T:0.43
Consensus pattern (29 bp):
TAAAAATTTCATTTTAACCCTAAACTTTC
Found at i:20406409 original size:59 final size:59
Alignment explanation
Indices: 20406284--20406409 Score: 148
Period size: 59 Copynumber: 2.1 Consensus size: 59
20406274 ATTTAAAAAA
* * *
20406284 TAAAAATTGCATTTTGACCCCTAAACTTTTCCTAATTTCATTTTGACCCTTAAACTTTC
1 TAAAAATTGCACTTAGACCCCTAAACTTTTCCTAATTTCATTTTAACCCTTAAACTTTC
** * * *
20406343 TTTAAATTTCACTTAGACCCCTAAAC-TTTCATTAAATTTCATTTTAACCC-TAAATTTTC
1 TAAAAATTGCACTTAGACCCCTAAACTTTTC-CT-AATTTCATTTTAACCCTTAAACTTTC
20406402 TAAAAATT
1 TAAAAATT
20406410 ACATTTAGCC
Statistics
Matches: 55, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
58 4 0.07
59 36 0.65
60 15 0.27
ACGTcount: A:0.33, C:0.21, G:0.03, T:0.43
Consensus pattern (59 bp):
TAAAAATTGCACTTAGACCCCTAAACTTTTCCTAATTTCATTTTAACCCTTAAACTTTC
Found at i:20406928 original size:10 final size:11
Alignment explanation
Indices: 20406910--20406979 Score: 61
Period size: 11 Copynumber: 6.0 Consensus size: 11
20406900 CAGCCCAAAA
20406910 AAAACAAAGCA-
1 AAAA-AAAGCAG
20406921 AAAAAAAGCAG
1 AAAAAAAGCAG
* *
20406932 CAAAAAAGAAG
1 AAAAAAAGCAG
20406943 AAGAAAGAAGCAG
1 AA-AAA-AAGCAG
*
20406956 AAAAAAAGAAG
1 AAAAAAAGCAG
20406967 AAGAAAGAAGCAG
1 AA-AAA-AAGCAG
20406980 CCCACTTTGT
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
10 6 0.12
11 21 0.44
12 9 0.19
13 12 0.25
ACGTcount: A:0.70, C:0.09, G:0.21, T:0.00
Consensus pattern (11 bp):
AAAAAAAGCAG
Found at i:20406953 original size:24 final size:24
Alignment explanation
Indices: 20406926--20406980 Score: 101
Period size: 24 Copynumber: 2.3 Consensus size: 24
20406916 AAGCAAAAAA
20406926 AAGCAGCAAAAAAGAAGAAGAAAG
1 AAGCAGCAAAAAAGAAGAAGAAAG
*
20406950 AAGCAGAAAAAAAGAAGAAGAAAG
1 AAGCAGCAAAAAAGAAGAAGAAAG
20406974 AAGCAGC
1 AAGCAGC
20406981 CCACTTTGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.65, C:0.09, G:0.25, T:0.00
Consensus pattern (24 bp):
AAGCAGCAAAAAAGAAGAAGAAAG
Found at i:20407609 original size:17 final size:17
Alignment explanation
Indices: 20407566--20407613 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
20407556 AGAAAAAAAT
20407566 CGTGTTTCAAAAATTTTCA
1 CGTGTTTC-AAAA-TTTCA
20407585 --TGTCTTCAAAATTTCA
1 CGTGT-TTCAAAATTTCA
20407601 CGTGTTTCAAAAT
1 CGTGTTTCAAAAT
20407614 AATAATAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
16 5 0.19
17 15 0.58
18 6 0.23
ACGTcount: A:0.31, C:0.17, G:0.10, T:0.42
Consensus pattern (17 bp):
CGTGTTTCAAAATTTCA
Found at i:20407716 original size:16 final size:16
Alignment explanation
Indices: 20407668--20407716 Score: 64
Period size: 16 Copynumber: 3.0 Consensus size: 16
20407658 TTTCTTTCTA
*
20407668 AAAAAATCGTGTTTTC
1 AAAAATTCGTGTTTTC
20407684 AAAAATTTCCGTG-TTTC
1 AAAAA-TT-CGTGTTTTC
20407701 AAAAATTCGTGTTTTC
1 AAAAATTCGTGTTTTC
20407717 GTGTTTTCAA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
15 4 0.14
16 11 0.38
17 10 0.34
18 4 0.14
ACGTcount: A:0.33, C:0.14, G:0.12, T:0.41
Consensus pattern (16 bp):
AAAAATTCGTGTTTTC
Found at i:20407746 original size:20 final size:21
Alignment explanation
Indices: 20407715--20407754 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
20407705 ATTCGTGTTT
20407715 TCGTGTTTTCAAAAAAAAATC
1 TCGTGTTTTCAAAAAAAAATC
20407736 TCGTG-TTTCAAAAAAAAAT
1 TCGTGTTTTCAAAAAAAAAT
20407755 AAAAAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.45, C:0.12, G:0.10, T:0.33
Consensus pattern (21 bp):
TCGTGTTTTCAAAAAAAAATC
Found at i:20407760 original size:9 final size:9
Alignment explanation
Indices: 20407746--20407774 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
20407736 TCGTGTTTCA
20407746 AAAAAAAAT
1 AAAAAAAAT
20407755 AAAAAAAAT
1 AAAAAAAAT
20407764 AAAAAAAAT
1 AAAAAAAAT
20407773 AA
1 AA
20407775 TTCTCGTGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (9 bp):
AAAAAAAAT
Found at i:20407929 original size:17 final size:17
Alignment explanation
Indices: 20407861--20408278 Score: 187
Period size: 17 Copynumber: 24.3 Consensus size: 17
20407851 GTGTTTTTTG
20407861 AAAAATTTTCGTGTTTTC
1 AAAAATTTTCGTG-TTTC
20407879 AAAAATCTTT-GTGTTTTC
1 AAAAAT-TTTCGTG-TTTC
* * *
20407897 AAAAATTCTGGCGTTTC
1 AAAAATTTTCGTGTTTC
*
20407914 AAAAATTTTCGTGTTTAAA
1 AAAAATTTTCGTGTTT--C
*
20407933 AAAAATTTACGTGTTTTC
1 AAAAATTTTCGTG-TTTC
* *
20407951 ACAAATTTTTGTGTTTC
1 AAAAATTTTCGTGTTTC
* *
20407968 ACAAATTCTCGTGTTTTC
1 AAAAATTTTCGTG-TTTC
* *
20407986 AAAAA-CTCCAGTGTTTC
1 AAAAATTTTC-GTGTTTC
* * *
20408003 -AAAGTTTCCATGTTTTC
1 AAAAATTTTCGTG-TTTC
* * *
20408020 AAAAATTCTCGCGTTTA
1 AAAAATTTTCGTGTTTC
**
20408037 AAAAAAATTCGTGTTTC
1 AAAAATTTTCGTGTTTC
* **
20408054 AAAATATTCTCGCATTTC
1 AAAA-ATTTTCGTGTTTC
*
20408072 ---AATTTT--TGTTTT
1 AAAAATTTTCGTGTTTC
**
20408084 TTAAA---TCGTGTTTC
1 AAAAATTTTCGTGTTTC
* * *
20408098 AAAAAATGTCGTGTTTT
1 AAAAATTTTCGTGTTTC
20408115 AAAAATTTTCGTGTTTC
1 AAAAATTTTCGTGTTTC
* * * *
20408132 TAAAATTTCCCTGTTTT
1 AAAAATTTTCGTGTTTC
*
20408149 AAAAA-TTCCTGTGTTTC
1 AAAAATTTTC-GTGTTTC
* * *
20408166 AAAAAAAAATGTCGTGTTTT
1 ---AAAAATTTTCGTGTTTC
* *
20408186 AAGAAAATTTCGTTTTTTC
1 AA-AAATTTTCG-TGTTTC
20408205 TAAAAATTTTCGTGTTTC
1 -AAAAATTTTCGTGTTTC
*
20408223 TAAAATTTTCGTGTTT-
1 AAAAATTTTCGTGTTTC
* *
20408239 ACAAATTCTCGTGTTTTC
1 AAAAATTTTCGTG-TTTC
* * *
20408257 AAAAATTCTCGTATTTT
1 AAAAATTTTCGTGTTTC
20408274 AAAAA
1 AAAAA
20408279 AAACTTTCGT
Statistics
Matches: 302, Mismatches: 69, Indels: 59
0.70 0.16 0.14
Matches are distributed among these distances:
12 4 0.01
14 12 0.04
15 3 0.01
16 19 0.06
17 137 0.45
18 82 0.27
19 27 0.09
20 16 0.05
21 2 0.01
ACGTcount: A:0.31, C:0.13, G:0.11, T:0.44
Consensus pattern (17 bp):
AAAAATTTTCGTGTTTC
Found at i:20407947 original size:54 final size:53
Alignment explanation
Indices: 20407861--20408265 Score: 147
Period size: 54 Copynumber: 7.8 Consensus size: 53
20407851 GTGTTTTTTG
** *
20407861 AAAAATTTTCGTGTTTTCAAAAATCTTTGTGTTTTCAAAAATTCTGGCGTTTC
1 AAAAATTTTCGTGTTTAAAAAAATCTTCGTGTTTTCAAAAATTCTGGCGTTTC
* * * *
20407914 AAAAATTTTCGTGTTTAAAAAAAAT-TTACGTGTTTTCACAAATTTTTGTGTTTC
1 AAAAATTTTCGTGTTT-AAAAAAATCTT-CGTGTTTTCAAAAATTCTGGCGTTTC
* * ** * ** *
20407968 ACAAATTCTCGTGTTTTCAAAAA-CTCCAGTG-TTTCAAAGTTTCCAT-G-TTTTC
1 AAAAATTTTCGTGTTTAAAAAAATCTTC-GTGTTTTCAAAAATT-C-TGGCGTTTC
* * * * *
20408020 AAAAATTCTCGCGTTTAAAAAAA-ATTCGTG-TTTCAAAATATTCTCGCATTTC
1 AAAAATTTTCGTGTTTAAAAAAATCTTCGTGTTTTCAAAA-ATTCTGGCGTTTC
*** * * * * *
20408072 ---AATTTT--TGTTT-TTTAAA---TCGTG-TTTCAAAAAATGTCGTGTTTT
1 AAAAATTTTCGTGTTTAAAAAAATCTTCGTGTTTTCAAAAATTCTGGCGTTTC
** * *
20408115 AAAAATTTTCGTGTTT-CTAAAAT-TTCCCTGTTTT-AAAAATTCCT-GTGTTTC
1 AAAAATTTTCGTGTTTAAAAAAATCTT-CGTGTTTTCAAAAATT-CTGGCGTTTC
* * * * * * *
20408166 AAAAAAAAATGTCGTGTTTTAAGAAAAT-TTCGTTTTTTCTAAAAATTTTCGTGTTTC
1 ---AAAAATTTTCGTG-TTTAAAAAAATCTTCGTGTTTTC-AAAAATTCTGGCGTTTC
* * *
20408223 TAAAATTTTCGTGTTT-ACAAATTC-TCGTGTTTTCAAAAATTCT
1 AAAAATTTTCGTGTTTAAAAAAATCTTCGTGTTTTCAAAAATTCT
20408266 CGTATTTTAA
Statistics
Matches: 268, Mismatches: 56, Indels: 58
0.70 0.15 0.15
Matches are distributed among these distances:
43 8 0.03
44 13 0.05
46 9 0.03
47 4 0.01
48 9 0.03
49 5 0.02
50 2 0.01
51 35 0.13
52 58 0.22
53 31 0.12
54 63 0.24
55 9 0.03
56 8 0.03
57 14 0.05
ACGTcount: A:0.31, C:0.13, G:0.11, T:0.45
Consensus pattern (53 bp):
AAAAATTTTCGTGTTTAAAAAAATCTTCGTGTTTTCAAAAATTCTGGCGTTTC
Found at i:20408000 original size:72 final size:72
Alignment explanation
Indices: 20407861--20408001 Score: 178
Period size: 72 Copynumber: 2.0 Consensus size: 72
20407851 GTGTTTTTTG
* * * *
20407861 AAAAATTTTCGTGTTTTCAAAAATCTTTGTGTTTTCAAAAATTCTGGCGTTTCAAAAATTTTCGT
1 AAAAATTTACGTGTTTTCAAAAATCTTTGTGTTTTCAAAAATTCTCGCGTTTCAAAAATCTCCGT
20407926 GTTTAAA
66 GTTTAAA
* * * *
20407933 AAAAATTTACGTGTTTTCACAAATTTTTGTG-TTTCACAAATTCTCGTGTTTTCAAAAA-CTCCA
1 AAAAATTTACGTGTTTTCAAAAATCTTTGTGTTTTCAAAAATTCTCGCG-TTTCAAAAATCTCC-
20407996 GTGTTT
64 GTGTTT
20408002 CAAAGTTTCC
Statistics
Matches: 59, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
71 16 0.27
72 43 0.73
ACGTcount: A:0.30, C:0.13, G:0.12, T:0.44
Consensus pattern (72 bp):
AAAAATTTACGTGTTTTCAAAAATCTTTGTGTTTTCAAAAATTCTCGCGTTTCAAAAATCTCCGT
GTTTAAA
Found at i:20408216 original size:91 final size:88
Alignment explanation
Indices: 20408089--20408261 Score: 233
Period size: 91 Copynumber: 1.9 Consensus size: 88
20408079 GTTTTTTAAA
20408089 TCGTGTTTCAAAAAATGTCGTGTTTTAAAAATTTTCGTGTTTCTAAAATTTCCCTGTTTTAAAAA
1 TCGTGTTTCAAAAAATGTCGTGTTTTAAAAATTTTCGTGTTTCTAAAATTTCCCTG-TTTAAAAA
20408154 TTC-C-TGTGTTTCAAAAAAAAATG
65 TTCTCGTGT-TTTCAAAAAAAAATG
* * * * * *
20408177 TCGTGTTTTAAGAAAATTTCGTTTTTTCTAAAAATTTTCGTGTTTCTAAAATTTTCGTGTTTACA
1 TCGTGTTTCAA-AAAATGTCG-TGTTT-TAAAAATTTTCGTGTTTCTAAAATTTCCCTGTTTAAA
20408242 AATTCTCGTGTTTTCAAAAA
63 AATTCTCGTGTTTTCAAAAA
20408262 TTCTCGTATT
Statistics
Matches: 74, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
88 10 0.14
89 8 0.11
90 14 0.19
91 39 0.53
92 3 0.04
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.45
Consensus pattern (88 bp):
TCGTGTTTCAAAAAATGTCGTGTTTTAAAAATTTTCGTGTTTCTAAAATTTCCCTGTTTAAAAAT
TCTCGTGTTTTCAAAAAAAAATG
Found at i:20408279 original size:18 final size:18
Alignment explanation
Indices: 20408241--20408279 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
20408231 TCGTGTTTAC
* *
20408241 AAATTCTCGTGTTTTCAA
1 AAATTCTCGTATTTTAAA
20408259 AAATTCTCGTATTTTAAA
1 AAATTCTCGTATTTTAAA
20408277 AAA
1 AAA
20408280 AACTTTCGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.38, C:0.13, G:0.08, T:0.41
Consensus pattern (18 bp):
AAATTCTCGTATTTTAAA
Found at i:20408758 original size:13 final size:14
Alignment explanation
Indices: 20408734--20408762 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
20408724 TTTAATTTTC
20408734 AAAATTTCAAAAAA
1 AAAATTTCAAAAAA
20408748 AAAATTT-AAAAAA
1 AAAATTTCAAAAAA
20408761 AA
1 AA
20408763 TTGCATTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (14 bp):
AAAATTTCAAAAAA
Found at i:20408803 original size:29 final size:30
Alignment explanation
Indices: 20408760--20408874 Score: 128
Period size: 30 Copynumber: 3.9 Consensus size: 30
20408750 AATTTAAAAA
* *
20408760 AAATTGCATTTTGACCCCTAAACTTTTC-CT
1 AAATTTCATTTTGACCCCTAAAC-TTTCATT
* *
20408790 -AATTTCATTTTGACCCTTAAACTTTCTTT
1 AAATTTCATTTTGACCCCTAAACTTTCATT
* *
20408819 AAATTTCACTTAGACCCCTAAACTTTCATT
1 AAATTTCATTTTGACCCCTAAACTTTCATT
* *
20408849 AAATTTCATTTT-AACCCTAAATTTTC
1 AAATTTCATTTTGACCCCTAAACTTTC
20408875 TAAAAATTAC
Statistics
Matches: 72, Mismatches: 11, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
28 4 0.06
29 33 0.46
30 35 0.49
ACGTcount: A:0.30, C:0.23, G:0.03, T:0.43
Consensus pattern (30 bp):
AAATTTCATTTTGACCCCTAAACTTTCATT
Found at i:20408826 original size:30 final size:30
Alignment explanation
Indices: 20408760--20408875 Score: 130
Period size: 29 Copynumber: 3.9 Consensus size: 30
20408750 AATTTAAAAA
* *
20408760 AAATTGCATTTTGACCCCTAAACTTT-TCCT
1 AAATTTCATTTTGACCCCTAAACTTTCT-TT
*
20408790 -AATTTCATTTTGACCCTTAAACTTTCTTT
1 AAATTTCATTTTGACCCCTAAACTTTCTTT
* * *
20408819 AAATTTCACTTAGACCCCTAAACTTTCATT
1 AAATTTCATTTTGACCCCTAAACTTTCTTT
* *
20408849 AAATTTCATTTT-AACCCTAAATTTTCT
1 AAATTTCATTTTGACCCCTAAACTTTCT
20408876 AAAAATTACA
Statistics
Matches: 72, Mismatches: 12, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
29 36 0.50
30 36 0.50
ACGTcount: A:0.29, C:0.23, G:0.03, T:0.44
Consensus pattern (30 bp):
AAATTTCATTTTGACCCCTAAACTTTCTTT
Found at i:20408881 original size:29 final size:29
Alignment explanation
Indices: 20408760--20408888 Score: 95
Period size: 29 Copynumber: 4.4 Consensus size: 29
20408750 AATTTAAAAA
* * *
20408760 AAATTGCATTTTGACCCCTAAACTTT-TCCT
1 AAATTTCATTTT-AACCCTAAACTTTCT-AT
* *
20408790 -AATTTCATTTTGACCCTTAAACTTTCTTT
1 AAATTTCATTTTAACCC-TAAACTTTCTAT
*
20408819 AAATTTCA-CTTAGACCCCTAAACTTTC-ATT
1 AAATTTCATTTTA-A-CCCTAAACTTTCTA-T
* *
20408849 AAATTTCATTTTAACCCTAAATTTTCTAA
1 AAATTTCATTTTAACCCTAAACTTTCTAT
*
20408878 AAATTACATTT
1 AAATTTCATTT
20408889 AGCCCCAGAA
Statistics
Matches: 80, Mismatches: 11, Indels: 17
0.74 0.10 0.16
Matches are distributed among these distances:
28 3 0.04
29 42 0.52
30 29 0.36
31 6 0.08
ACGTcount: A:0.32, C:0.22, G:0.03, T:0.43
Consensus pattern (29 bp):
AAATTTCATTTTAACCCTAAACTTTCTAT
Found at i:20408882 original size:59 final size:59
Alignment explanation
Indices: 20408758--20408882 Score: 146
Period size: 59 Copynumber: 2.1 Consensus size: 59
20408748 AAAATTTAAA
* * *
20408758 AAAAATTGCATTTTGACCCCTAAACTTTTCCTAATTTCATTTTGACCCTTAAACTTTCT
1 AAAAATTGCACTTAGACCCCTAAACTTTTCCTAATTTCATTTTAACCCTTAAACTTTCT
** * * *
20408817 TTAAATTTCACTTAGACCCCTAAAC-TTTCATTAAATTTCATTTTAACCC-TAAATTTTCT
1 AAAAATTGCACTTAGACCCCTAAACTTTTC-CT-AATTTCATTTTAACCCTTAAACTTTCT
20408876 AAAAATT
1 AAAAATT
20408883 ACATTTAGCC
Statistics
Matches: 54, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
58 4 0.07
59 35 0.65
60 15 0.28
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (59 bp):
AAAAATTGCACTTAGACCCCTAAACTTTTCCTAATTTCATTTTAACCCTTAAACTTTCT
Found at i:20409440 original size:23 final size:23
Alignment explanation
Indices: 20409401--20409455 Score: 94
Period size: 23 Copynumber: 2.4 Consensus size: 23
20409391 AAAGCAAAAA
*
20409401 AAAGCAGCA-AAAAAAGAAGAAG
1 AAAGAAGCAGAAAAAAGAAGAAG
20409423 AAAGAAGCAGAAAAAAGAAGAAG
1 AAAGAAGCAGAAAAAAGAAGAAG
20409446 AAAGAAGCAG
1 AAAGAAGCAG
20409456 CCCACTTTGT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 8 0.26
23 23 0.74
ACGTcount: A:0.67, C:0.07, G:0.25, T:0.00
Consensus pattern (23 bp):
AAAGAAGCAGAAAAAAGAAGAAG
Found at i:20409447 original size:13 final size:12
Alignment explanation
Indices: 20409382--20409448 Score: 53
Period size: 13 Copynumber: 5.2 Consensus size: 12
20409372 AGGCCAGCCC
*
20409382 AAAAAAAACAAAG
1 AAAAAAAA-GAAG
*
20409395 CAAAAAAAAGCAG
1 -AAAAAAAAGAAG
*
20409408 CAAAAAAAGAAG
1 AAAAAAAAGAAG
* *
20409420 AAGAAAGAAGCAG
1 AA-AAAAAAGAAG
20409433 AAAAAAGAAGAAG
1 AAAAAA-AAGAAG
20409446 AAA
1 AAA
20409449 GAAGCAGCCC
Statistics
Matches: 42, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
12 14 0.33
13 20 0.48
14 8 0.19
ACGTcount: A:0.75, C:0.07, G:0.18, T:0.00
Consensus pattern (12 bp):
AAAAAAAAGAAG
Found at i:20410120 original size:16 final size:17
Alignment explanation
Indices: 20410045--20410111 Score: 82
Period size: 17 Copynumber: 3.9 Consensus size: 17
20410035 AGAAAAAAAT
*
20410045 CGTGTTTCAAAAATTTT
1 CGTGTTTCAAAAATTTC
*
20410062 CATGTCTTC-AAAATTTC
1 CGTGT-TTCAAAAATTTC
*
20410079 ACGTGCTTCAAAAATTTC
1 -CGTGTTTCAAAAATTTC
20410097 CGTGTTTCAAAAATT
1 CGTGTTTCAAAAATT
20410112 CGTGTTTTCG
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
17 28 0.67
18 14 0.33
ACGTcount: A:0.31, C:0.18, G:0.10, T:0.40
Consensus pattern (17 bp):
CGTGTTTCAAAAATTTC
Found at i:20410164 original size:9 final size:9
Alignment explanation
Indices: 20410150--20410175 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
20410140 TTGTGTTTCA
20410150 AAAAAAAAT
1 AAAAAAAAT
20410159 AAAAAAAAT
1 AAAAAAAAT
20410168 AAAAAAAA
1 AAAAAAAA
20410176 ATTCTCGTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (9 bp):
AAAAAAAAT
Found at i:20410164 original size:10 final size:10
Alignment explanation
Indices: 20410149--20410177 Score: 51
Period size: 9 Copynumber: 3.0 Consensus size: 10
20410139 CTTGTGTTTC
20410149 AAAAAAAAAT
1 AAAAAAAAAT
20410159 -AAAAAAAAT
1 AAAAAAAAAT
20410168 AAAAAAAAAT
1 AAAAAAAAAT
20410178 TCTCGTGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.50
10 9 0.50
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (10 bp):
AAAAAAAAAT
Found at i:20410332 original size:17 final size:17
Alignment explanation
Indices: 20410264--20410681 Score: 194
Period size: 17 Copynumber: 24.3 Consensus size: 17
20410254 GTGTTTTTTG
20410264 AAAAATTTTCGTGTTTTC
1 AAAAATTTTCGTG-TTTC
20410282 AAAAATCTTT-GTGTTTTC
1 AAAAAT-TTTCGTG-TTTC
* * *
20410300 AAAAATTCTGGCGTTTC
1 AAAAATTTTCGTGTTTC
*
20410317 AAAAATTTTCGTGTTTAAA
1 AAAAATTTTCGTGTTT--C
*
20410336 AAAAATTTACGTGTTTTC
1 AAAAATTTTCGTG-TTTC
* *
20410354 ACAAATTTTTGTGTTTC
1 AAAAATTTTCGTGTTTC
* *
20410371 ACAAATTCTCGTGTTTTC
1 AAAAATTTTCGTG-TTTC
* *
20410389 AAAAA-CTCCAGTGTTTC
1 AAAAATTTTC-GTGTTTC
* * *
20410406 -AAAGTTTCCATGTTTTC
1 AAAAATTTTCGTG-TTTC
* * *
20410423 AAAAATTCTCGCGTTTA
1 AAAAATTTTCGTGTTTC
**
20410440 AAAAAAATTCGTGTTTC
1 AAAAATTTTCGTGTTTC
* **
20410457 AAAATATTCTCGCATTTC
1 AAAA-ATTTTCGTGTTTC
*
20410475 ---AATTTT--TGTTTT
1 AAAAATTTTCGTGTTTC
**
20410487 TTAAA---TCGTGTTTC
1 AAAAATTTTCGTGTTTC
* * *
20410501 AAAAAATGTCGTGTTTT
1 AAAAATTTTCGTGTTTC
20410518 AAAAATTTTCGTGTTTC
1 AAAAATTTTCGTGTTTC
* * * *
20410535 TAAAATTTCCCTGTTTT
1 AAAAATTTTCGTGTTTC
**
20410552 AAAAATTCCCGTGTTTC
1 AAAAATTTTCGTGTTTC
* * *
20410569 AAAAAAAAATGTCGTGTTTT
1 ---AAAAATTTTCGTGTTTC
* *
20410589 AAGAAAATTTCGTTTTTTC
1 AA-AAATTTTCG-TGTTTC
20410608 TAAAAATTTTCGTGTTTC
1 -AAAAATTTTCGTGTTTC
*
20410626 TAAAATTTTCGTGTTT-
1 AAAAATTTTCGTGTTTC
* *
20410642 ACAAATTCTCGTGTTTTC
1 AAAAATTTTCGTG-TTTC
* * *
20410660 AAAAATTCTCGTATTTT
1 AAAAATTTTCGTGTTTC
20410677 AAAAA
1 AAAAA
20410682 AAAACTTTCG
Statistics
Matches: 302, Mismatches: 71, Indels: 55
0.71 0.17 0.13
Matches are distributed among these distances:
12 4 0.01
14 12 0.04
15 3 0.01
16 15 0.05
17 141 0.47
18 82 0.27
19 27 0.09
20 18 0.06
ACGTcount: A:0.31, C:0.13, G:0.11, T:0.44
Consensus pattern (17 bp):
AAAAATTTTCGTGTTTC
Found at i:20410350 original size:54 final size:53
Alignment explanation
Indices: 20410264--20410668 Score: 145
Period size: 54 Copynumber: 7.8 Consensus size: 53
20410254 GTGTTTTTTG
** *
20410264 AAAAATTTTCGTGTTTTCAAAAATCTTTGTGTTTTCAAAAATTCTGGCGTTTC
1 AAAAATTTTCGTGTTTAAAAAAATCTTCGTGTTTTCAAAAATTCTGGCGTTTC
* * * *
20410317 AAAAATTTTCGTGTTTAAAAAAAAT-TTACGTGTTTTCACAAATTTTTGTGTTTC
1 AAAAATTTTCGTGTTT-AAAAAAATCTT-CGTGTTTTCAAAAATTCTGGCGTTTC
* * ** * ** *
20410371 ACAAATTCTCGTGTTTTCAAAAA-CTCCAGTG-TTTCAAAGTTTCCAT-G-TTTTC
1 AAAAATTTTCGTGTTTAAAAAAATCTTC-GTGTTTTCAAAAATT-C-TGGCGTTTC
* * * * *
20410423 AAAAATTCTCGCGTTTAAAAAAA-ATTCGTG-TTTCAAAATATTCTCGCATTTC
1 AAAAATTTTCGTGTTTAAAAAAATCTTCGTGTTTTCAAAA-ATTCTGGCGTTTC
*** * * * * *
20410475 ---AATTTT--TGTTT-TTTAAA---TCGTG-TTTCAAAAAATGTCGTGTTTT
1 AAAAATTTTCGTGTTTAAAAAAATCTTCGTGTTTTCAAAAATTCTGGCGTTTC
** * ** *
20410518 AAAAATTTTCGTGTTT-CTAAAAT-TTCCCTGTTTT-AAAAATTCCCGTGTTTC
1 AAAAATTTTCGTGTTTAAAAAAATCTT-CGTGTTTTCAAAAATTCTGGCGTTTC
* * * * * * *
20410569 AAAAAAAAATGTCGTGTTTTAAGAAAAT-TTCGTTTTTTCTAAAAATTTTCGTGTTTC
1 ---AAAAATTTTCGTG-TTTAAAAAAATCTTCGTGTTTTC-AAAAATTCTGGCGTTTC
* * *
20410626 TAAAATTTTCGTGTTT-ACAAATTC-TCGTGTTTTCAAAAATTCT
1 AAAAATTTTCGTGTTTAAAAAAATCTTCGTGTTTTCAAAAATTCT
20410669 CGTATTTTAA
Statistics
Matches: 268, Mismatches: 58, Indels: 54
0.71 0.15 0.14
Matches are distributed among these distances:
43 8 0.03
44 13 0.05
46 9 0.03
47 4 0.01
48 9 0.03
49 5 0.02
50 2 0.01
51 36 0.13
52 57 0.21
53 31 0.12
54 63 0.24
55 9 0.03
56 7 0.03
57 15 0.06
ACGTcount: A:0.31, C:0.14, G:0.11, T:0.44
Consensus pattern (53 bp):
AAAAATTTTCGTGTTTAAAAAAATCTTCGTGTTTTCAAAAATTCTGGCGTTTC
Found at i:20410403 original size:72 final size:72
Alignment explanation
Indices: 20410264--20410404 Score: 178
Period size: 72 Copynumber: 2.0 Consensus size: 72
20410254 GTGTTTTTTG
* * * *
20410264 AAAAATTTTCGTGTTTTCAAAAATCTTTGTGTTTTCAAAAATTCTGGCGTTTCAAAAATTTTCGT
1 AAAAATTTACGTGTTTTCAAAAATCTTTGTGTTTTCAAAAATTCTCGCGTTTCAAAAATCTCCGT
20410329 GTTTAAA
66 GTTTAAA
* * * *
20410336 AAAAATTTACGTGTTTTCACAAATTTTTGTG-TTTCACAAATTCTCGTGTTTTCAAAAA-CTCCA
1 AAAAATTTACGTGTTTTCAAAAATCTTTGTGTTTTCAAAAATTCTCGCG-TTTCAAAAATCTCC-
20410399 GTGTTT
64 GTGTTT
20410405 CAAAGTTTCC
Statistics
Matches: 59, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
71 16 0.27
72 43 0.73
ACGTcount: A:0.30, C:0.13, G:0.12, T:0.44
Consensus pattern (72 bp):
AAAAATTTACGTGTTTTCAAAAATCTTTGTGTTTTCAAAAATTCTCGCGTTTCAAAAATCTCCGT
GTTTAAA
Found at i:20410682 original size:18 final size:18
Alignment explanation
Indices: 20410644--20410682 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
20410634 TCGTGTTTAC
* *
20410644 AAATTCTCGTGTTTTCAA
1 AAATTCTCGTATTTTAAA
20410662 AAATTCTCGTATTTTAAA
1 AAATTCTCGTATTTTAAA
20410680 AAA
1 AAA
20410683 AAACTTTCGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.38, C:0.13, G:0.08, T:0.41
Consensus pattern (18 bp):
AAATTCTCGTATTTTAAA
Found at i:20410692 original size:21 final size:19
Alignment explanation
Indices: 20410660--20410706 Score: 51
Period size: 19 Copynumber: 2.3 Consensus size: 19
20410650 TCGTGTTTTC
20410660 AAAAATTCTCGTATTTTAAAA
1 AAAAATTCTCG--TTTTAAAA
20410681 AAAAACTT-TCGTTTTAAAA
1 AAAAA-TTCTCGTTTTAAAA
20410700 AAGAAAT
1 AA-AAAT
20410707 ACTGCGCTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
19 11 0.46
20 3 0.12
21 8 0.33
22 2 0.08
ACGTcount: A:0.51, C:0.09, G:0.06, T:0.34
Consensus pattern (19 bp):
AAAAATTCTCGTTTTAAAA
Found at i:20410695 original size:91 final size:89
Alignment explanation
Indices: 20410501--20410683 Score: 221
Period size: 91 Copynumber: 2.1 Consensus size: 89
20410491 ATCGTGTTTC
* *
20410501 AAAAAATGTCG-TGTTT-TAAAAATTTTCGTGTTTCTAAAATTTCCCTGTTTTAAAAATTCCCGT
1 AAAAAATTTCGTTTTTTCTAAAAATTTTCGTGTTTCTAAAATTTCCCTGTTTTAAAAATTCCCGT
* *
20410564 GTTTCAAAAAAAAATGTCGTGTTTTA
66 GTTTC--AAAAAAATCTCGTATTTTA
* * * * *
20410590 AGAAAATTTCGTTTTTTCTAAAAATTTTCGTGTTTCTAAAATTTTCGTG-TTTACAAATTCTCGT
1 AAAAAATTTCGTTTTTTCTAAAAATTTTCGTGTTTCTAAAATTTCCCTGTTTTAAAAATTCCCGT
*
20410654 GTTTTC-AAAAATTCTCGTATTTTA
66 G-TTTCAAAAAAATCTCGTATTTTA
20410678 AAAAAA
1 AAAAAA
20410684 AACTTTCGTT
Statistics
Matches: 80, Mismatches: 11, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
88 20 0.25
89 9 0.11
90 18 0.22
91 33 0.41
ACGTcount: A:0.33, C:0.12, G:0.11, T:0.44
Consensus pattern (89 bp):
AAAAAATTTCGTTTTTTCTAAAAATTTTCGTGTTTCTAAAATTTCCCTGTTTTAAAAATTCCCGT
GTTTCAAAAAAATCTCGTATTTTA
Found at i:20416161 original size:11 final size:11
Alignment explanation
Indices: 20416145--20416170 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
20416135 TACTTATCTT
20416145 TTTTCTTATCA
1 TTTTCTTATCA
20416156 TTTTCTTATCA
1 TTTTCTTATCA
20416167 TTTT
1 TTTT
20416171 AACTTTTGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.69
Consensus pattern (11 bp):
TTTTCTTATCA
Found at i:20437915 original size:37 final size:37
Alignment explanation
Indices: 20437874--20437950 Score: 84
Period size: 37 Copynumber: 2.1 Consensus size: 37
20437864 ATTCCCTGGA
* * *
20437874 AAAAGAAGATAG-GGATGAACATGAGTGATTCTCTGCC
1 AAAAGAA-ATAGAAGATGAACATGAGTGATTCCCCGCC
* * *
20437911 AAAAGCAATCGAAGATGAATATGAGTGATTCCCCGCC
1 AAAAGAAATAGAAGATGAACATGAGTGATTCCCCGCC
20437948 AAA
1 AAA
20437951 TGCGGACGAA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
36 3 0.09
37 30 0.91
ACGTcount: A:0.40, C:0.17, G:0.23, T:0.19
Consensus pattern (37 bp):
AAAAGAAATAGAAGATGAACATGAGTGATTCCCCGCC
Found at i:20438258 original size:21 final size:21
Alignment explanation
Indices: 20438219--20438258 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
20438209 AAATTTAATG
* *
20438219 TTAAAAAAATTTCTTAAATTA
1 TTAAAAAAATTTATAAAATTA
*
20438240 TTAAGAAAATTTATAAAAT
1 TTAAAAAAATTTATAAAAT
20438259 ATCAAAGTAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.40
Consensus pattern (21 bp):
TTAAAAAAATTTATAAAATTA
Found at i:20438496 original size:30 final size:32
Alignment explanation
Indices: 20438438--20438496 Score: 77
Period size: 30 Copynumber: 1.9 Consensus size: 32
20438428 TATTCTTGTT
*
20438438 TATATTCTTTACAAATTATTTTTGAATTTTGA
1 TATATTCTTTACAAATTATTTTTAAATTTTGA
* *
20438470 TATATTC-TTA-AATTTTTTTTTAAATTT
1 TATATTCTTTACAAATTATTTTTAAATTT
20438497 CAAGAATTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 14 0.58
31 3 0.12
32 7 0.29
ACGTcount: A:0.31, C:0.05, G:0.03, T:0.61
Consensus pattern (32 bp):
TATATTCTTTACAAATTATTTTTAAATTTTGA
Found at i:20440601 original size:18 final size:18
Alignment explanation
Indices: 20440580--20440689 Score: 96
Period size: 18 Copynumber: 6.1 Consensus size: 18
20440570 AGTCACTCTT
20440580 TAACAGTCAGTTATTCAG
1 TAACAGTCAGTTATTCAG
* * *
20440598 TAAC-GATAAATTATTTAG
1 TAACAG-TCAGTTATTCAG
* ** **
20440616 TAACAATCTTTTACACAG
1 TAACAGTCAGTTATTCAG
* *
20440634 TAGCAGTCAGTTATCCAG
1 TAACAGTCAGTTATTCAG
20440652 TAACAGTCAGTTATTCAG
1 TAACAGTCAGTTATTCAG
* *
20440670 TAGCAGTCAATTATTCAG
1 TAACAGTCAGTTATTCAG
20440688 TA
1 TA
20440690 CCTTTATTTA
Statistics
Matches: 70, Mismatches: 20, Indels: 4
0.74 0.21 0.04
Matches are distributed among these distances:
17 1 0.01
18 69 0.99
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (18 bp):
TAACAGTCAGTTATTCAG
Found at i:20440881 original size:51 final size:54
Alignment explanation
Indices: 20440777--20440891 Score: 148
Period size: 51 Copynumber: 2.2 Consensus size: 54
20440767 GTGTAACGGT
* * *
20440777 AACAGTAACAGTAACAATAGCGGTACATAGAGTACCTCATCGGAACAAATCCGG
1 AACAGTAACAATAACAATAGAGGTACATAGAGTACCTCATCGAAACAAATCCGG
* *
20440831 AACAGTAACAATAACAGTA-AGGTACA-A-AGTACCTC-TCCGAAACGAATCCGG
1 AACAGTAACAATAACAATAGAGGTACATAGAGTACCTCAT-CGAAACAAATCCGG
20440882 AACAGTAACA
1 AACAGTAACA
20440892 GTAAGGTGAC
Statistics
Matches: 55, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
50 1 0.02
51 30 0.55
52 1 0.02
53 6 0.11
54 17 0.31
ACGTcount: A:0.43, C:0.23, G:0.18, T:0.16
Consensus pattern (54 bp):
AACAGTAACAATAACAATAGAGGTACATAGAGTACCTCATCGAAACAAATCCGG
Found at i:20442182 original size:31 final size:32
Alignment explanation
Indices: 20442126--20442188 Score: 85
Period size: 31 Copynumber: 2.0 Consensus size: 32
20442116 TACATTTGTC
*
20442126 ATAATTTAATTTATTTATTACATAAAAATCTT
1 ATAATATAATTTATTTATTACATAAAAATCTT
*
20442158 ATAATATAA-TTATTTAATTA-ATAAATATCTT
1 ATAATATAATTTATTT-ATTACATAAAAATCTT
20442189 TTACTTAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 16 0.57
32 12 0.43
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (32 bp):
ATAATATAATTTATTTATTACATAAAAATCTT
Found at i:20442196 original size:18 final size:19
Alignment explanation
Indices: 20442168--20442221 Score: 67
Period size: 18 Copynumber: 2.9 Consensus size: 19
20442158 ATAATATAAT
20442168 TATTTAATTAATAAATATC
1 TATTTAATTAATAAATATC
* *
20442187 T-TTTACTTAATAATTATC
1 TATTTAATTAATAAATATC
20442205 TATTTAA-TAATTAAATA
1 TATTTAATTAA-TAAATA
20442222 CAAGTATTAC
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
18 19 0.66
19 10 0.34
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (19 bp):
TATTTAATTAATAAATATC
Found at i:20446647 original size:16 final size:18
Alignment explanation
Indices: 20446612--20446649 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
20446602 ATCCTTATTT
*
20446612 AAATCAAATACAATAGTA
1 AAATAAAATACAATAGTA
20446630 AAATAAAATA-AA-AGTA
1 AAATAAAATACAATAGTA
20446646 AAAT
1 AAAT
20446650 CCATATAGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 8 0.42
17 2 0.11
18 9 0.47
ACGTcount: A:0.68, C:0.05, G:0.05, T:0.21
Consensus pattern (18 bp):
AAATAAAATACAATAGTA
Found at i:20451051 original size:28 final size:28
Alignment explanation
Indices: 20451011--20451089 Score: 95
Period size: 28 Copynumber: 2.8 Consensus size: 28
20451001 GCAATCAAAT
*
20451011 ATGGCACTCAGTGTACGAAATATTGAGA
1 ATGGCACTTAGTGTACGAAATATTGAGA
* *
20451039 ATGGCACTTAGTGTTCGAGATATTGAGA
1 ATGGCACTTAGTGTACGAAATATTGAGA
* * **
20451067 ACGACACTTAGTGTGTGAAATAT
1 ATGGCACTTAGTGTACGAAATAT
20451090 CGAATGATTC
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 43 1.00
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.29
Consensus pattern (28 bp):
ATGGCACTTAGTGTACGAAATATTGAGA
Found at i:20451530 original size:21 final size:22
Alignment explanation
Indices: 20451499--20451539 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
20451489 GAATGTATTG
*
20451499 TGATGTATGTGGAAATGAAATA
1 TGATGTATGTGCAAATGAAATA
*
20451521 TGAT-TATGTGCTAATGAAA
1 TGATGTATGTGCAAATGAAA
20451540 CATAAATGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.39, C:0.02, G:0.24, T:0.34
Consensus pattern (22 bp):
TGATGTATGTGCAAATGAAATA
Found at i:20454028 original size:32 final size:32
Alignment explanation
Indices: 20453987--20454053 Score: 125
Period size: 32 Copynumber: 2.1 Consensus size: 32
20453977 AAAATAAAAC
20453987 AAAAAAAAAATCAAAGACTAACAGGGAAATTT
1 AAAAAAAAAATCAAAGACTAACAGGGAAATTT
*
20454019 AAAAAAAAAATGAAAGACTAACAGGGAAATTT
1 AAAAAAAAAATCAAAGACTAACAGGGAAATTT
20454051 AAA
1 AAA
20454054 GAAATTTGTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.64, C:0.07, G:0.13, T:0.15
Consensus pattern (32 bp):
AAAAAAAAAATCAAAGACTAACAGGGAAATTT
Found at i:20455030 original size:20 final size:20
Alignment explanation
Indices: 20454992--20455030 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
20454982 TTTAGAAATC
* *
20454992 ATACCAAAAATTACGAGTAA
1 ATACCAAAAAATACAAGTAA
*
20455012 ATACCAAAAAATATAAGTA
1 ATACCAAAAAATACAAGTA
20455031 TGTATAAAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.59, C:0.13, G:0.08, T:0.21
Consensus pattern (20 bp):
ATACCAAAAAATACAAGTAA
Found at i:20455135 original size:20 final size:24
Alignment explanation
Indices: 20455098--20455145 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 24
20455088 TATTCCCTAT
*
20455098 TTTTTTTTAGCATACCCTTAT-AA
1 TTTTTTTTAGCATACCCTAATAAA
20455121 TTTTTTTTA-C-T-CCCTAATAAA
1 TTTTTTTTAGCATACCCTAATAAA
20455142 TTTT
1 TTTT
20455146 GATTTTGGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
20 6 0.26
21 7 0.30
22 1 0.04
23 9 0.39
ACGTcount: A:0.25, C:0.17, G:0.02, T:0.56
Consensus pattern (24 bp):
TTTTTTTTAGCATACCCTAATAAA
Found at i:20455248 original size:21 final size:21
Alignment explanation
Indices: 20455203--20455249 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
20455193 GTATGCTTTT
* * * *
20455203 AAAATTAATTTTTTGTTTGAG
1 AAAATCAATTTTTTGTATAAA
20455224 AAAATCAATTTTTTGTATAAA
1 AAAATCAATTTTTTGTATAAA
20455245 AAAAT
1 AAAAT
20455250 TTGTACAATA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.45, C:0.02, G:0.09, T:0.45
Consensus pattern (21 bp):
AAAATCAATTTTTTGTATAAA
Found at i:20455877 original size:20 final size:21
Alignment explanation
Indices: 20455854--20455935 Score: 71
Period size: 20 Copynumber: 4.0 Consensus size: 21
20455844 TATATAAACA
20455854 AATACCAAAAATTATA-AGAG
1 AATACCAAAAATTATATAGAG
* * *
20455874 AATA-CAAAAAGTATATATAA
1 AATACCAAAAATTATATAGAG
* * * *
20455894 AATATCAAAAATCAT-GAGAT
1 AATACCAAAAATTATATAGAG
*
20455914 TATACCAAAAATTATATAGAG
1 AATACCAAAAATTATATAGAG
20455935 A
1 A
20455936 TGCAAAATAT
Statistics
Matches: 45, Mismatches: 14, Indels: 5
0.70 0.22 0.08
Matches are distributed among these distances:
19 10 0.22
20 24 0.53
21 11 0.24
ACGTcount: A:0.59, C:0.09, G:0.09, T:0.24
Consensus pattern (21 bp):
AATACCAAAAATTATATAGAG
Found at i:20464941 original size:7 final size:7
Alignment explanation
Indices: 20464911--20464958 Score: 60
Period size: 7 Copynumber: 6.3 Consensus size: 7
20464901 CCAAAAGTTA
20464911 TATTTAT
1 TATTTAT
20464918 TATCTTAT
1 TAT-TTAT
20464926 TATCTTTTAT
1 TA---TTTAT
20464936 TATTTAT
1 TATTTAT
20464943 TATTTAT
1 TATTTAT
20464950 TATTTAT
1 TATTTAT
20464957 TA
1 TA
20464959 GTCTATTGTA
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
7 24 0.65
8 6 0.16
10 6 0.16
11 1 0.03
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (7 bp):
TATTTAT
Found at i:20470725 original size:23 final size:23
Alignment explanation
Indices: 20470672--20470769 Score: 63
Period size: 23 Copynumber: 4.3 Consensus size: 23
20470662 AAAATCGATA
*
20470672 ATTTGCACCAGAGTGCCACTGTT
1 ATTTGCACCAGAGTGCCACTGTC
* * * * *
20470695 ATTCGCACGAGCGTGCTATTGTC
1 ATTTGCACCAGAGTGCCACTGTC
* *
20470718 ATTTGCA-CTGAAGTGCCACTATC
1 ATTTGCACCAG-AGTGCCACTGTC
* * * * *
20470741 ACTTGCATCATAGTGTCACTATC
1 ATTTGCACCAGAGTGCCACTGTC
20470764 ATTTGC
1 ATTTGC
20470770 GCACATAAAA
Statistics
Matches: 55, Mismatches: 18, Indels: 4
0.71 0.23 0.05
Matches are distributed among these distances:
22 1 0.02
23 53 0.96
24 1 0.02
ACGTcount: A:0.22, C:0.26, G:0.19, T:0.33
Consensus pattern (23 bp):
ATTTGCACCAGAGTGCCACTGTC
Found at i:20473698 original size:15 final size:15
Alignment explanation
Indices: 20473678--20473707 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
20473668 ATGCTAATAG
20473678 GTATAATGATTTTTT
1 GTATAATGATTTTTT
20473693 GTATAATGATTTTTT
1 GTATAATGATTTTTT
20473708 TGACCTTTCA
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:0.27, C:0.00, G:0.13, T:0.60
Consensus pattern (15 bp):
GTATAATGATTTTTT
Found at i:20473906 original size:9 final size:9
Alignment explanation
Indices: 20473894--20473970 Score: 52
Period size: 9 Copynumber: 8.4 Consensus size: 9
20473884 AGTAAAAACT
20473894 ATTTTTATA
1 ATTTTTATA
20473903 ATTTTTAAATA
1 ATTTTT--ATA
* *
20473914 ATTTTAATG
1 ATTTTTATA
20473923 ATTTTT-T-
1 ATTTTTATA
*
20473930 ATTTTTAAA
1 ATTTTTATA
20473939 ATATTTT-TA
1 AT-TTTTATA
*
20473948 TATTTTTTTA
1 -ATTTTTATA
*
20473958 ATTTTTAAA
1 ATTTTTATA
20473967 ATTT
1 ATTT
20473971 AATCGAATCC
Statistics
Matches: 54, Mismatches: 7, Indels: 14
0.72 0.09 0.19
Matches are distributed among these distances:
7 6 0.11
8 1 0.02
9 31 0.57
10 8 0.15
11 8 0.15
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.65
Consensus pattern (9 bp):
ATTTTTATA
Found at i:20473944 original size:27 final size:28
Alignment explanation
Indices: 20473893--20473968 Score: 95
Period size: 27 Copynumber: 2.7 Consensus size: 28
20473883 TAGTAAAAAC
20473893 TATTTTTATAATTTTT-AAATAATTTTAA
1 TATTTTT-TAATTTTTAAAATAATTTTAA
*
20473921 TGATTTTTT-ATTTTTAAAAT-ATTTTTA
1 T-ATTTTTTAATTTTTAAAATAATTTTAA
20473948 TATTTTTTTAATTTTTAAAAT
1 TA-TTTTTTAATTTTTAAAAT
20473969 TTAATCGAAT
Statistics
Matches: 43, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
26 1 0.02
27 19 0.44
28 17 0.40
29 6 0.14
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.64
Consensus pattern (28 bp):
TATTTTTTAATTTTTAAAATAATTTTAA
Found at i:20483511 original size:34 final size:34
Alignment explanation
Indices: 20483472--20483572 Score: 89
Period size: 34 Copynumber: 3.2 Consensus size: 34
20483462 CCATCCTATA
20483472 TTCTCAATCCTCAATTTTCAATTTATTTCTAATT
1 TTCTCAATCCTCAATTTTCAATTTATTTCTAATT
*
20483506 TTCTC-A-----AATTTT-ATACTTTGTTT-TACA--
1 TTCTCAATCCTCAATTTTCA-A-TTTATTTCTA-ATT
20483533 -TCTCAATCCTCAATTTTCAATTTATTTCTAATT
1 TTCTCAATCCTCAATTTTCAATTTATTTCTAATT
20483566 TTCTCAA
1 TTCTCAA
20483573 ATTGTATACT
Statistics
Matches: 51, Mismatches: 2, Indels: 28
0.63 0.02 0.35
Matches are distributed among these distances:
26 4 0.08
27 2 0.04
28 9 0.18
29 7 0.14
31 7 0.14
32 9 0.18
33 2 0.04
34 11 0.22
ACGTcount: A:0.27, C:0.20, G:0.01, T:0.52
Consensus pattern (34 bp):
TTCTCAATCCTCAATTTTCAATTTATTTCTAATT
Found at i:20483546 original size:60 final size:60
Alignment explanation
Indices: 20483473--20483598 Score: 243
Period size: 60 Copynumber: 2.1 Consensus size: 60
20483463 CATCCTATAT
*
20483473 TCTCAATCCTCAATTTTCAATTTATTTCTAATTTTCTCAAATTTTATACTTTGTTTTACA
1 TCTCAATCCTCAATTTTCAATTTATTTCTAATTTTCTCAAATTGTATACTTTGTTTTACA
20483533 TCTCAATCCTCAATTTTCAATTTATTTCTAATTTTCTCAAATTGTATACTTTGTTTTACA
1 TCTCAATCCTCAATTTTCAATTTATTTCTAATTTTCTCAAATTGTATACTTTGTTTTACA
20483593 TCTCAA
1 TCTCAA
20483599 ATGTACAATT
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 65 1.00
ACGTcount: A:0.27, C:0.19, G:0.02, T:0.52
Consensus pattern (60 bp):
TCTCAATCCTCAATTTTCAATTTATTTCTAATTTTCTCAAATTGTATACTTTGTTTTACA
Found at i:20489022 original size:3 final size:3
Alignment explanation
Indices: 20489014--20489041 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
20489004 ATATTACTAG
20489014 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
20489042 AATAAAATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Done.