Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D12
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: 63843421
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1690000 characters in sequence are not A, C, G, or T
File 74 of 214
Found at i:21130963 original size:10 final size:11
Alignment explanation
Indices: 21130939--21130992 Score: 56
Period size: 12 Copynumber: 4.8 Consensus size: 11
21130929 TTAACTCGAT
21130939 TTTTTTTGTCAC
1 TTTTTTT-TCAC
21130951 TTTTTTTTC-C
1 TTTTTTTTCAC
*
21130961 TTTTTTTTCGAT
1 TTTTTTTTC-AC
* *
21130973 TTTTTTTTGAA
1 TTTTTTTTCAC
21130984 TTTTTTTTC
1 TTTTTTTTC
21130993 TGAATTTCTT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
10 10 0.28
11 11 0.31
12 15 0.42
ACGTcount: A:0.07, C:0.11, G:0.06, T:0.76
Consensus pattern (11 bp):
TTTTTTTTCAC
Found at i:21130975 original size:11 final size:11
Alignment explanation
Indices: 21130951--21130992 Score: 50
Period size: 10 Copynumber: 3.8 Consensus size: 11
21130941 TTTTTGTCAC
*
21130951 TTTTTTTTC-C
1 TTTTTTTTCGA
21130961 TTTTTTTTCGA
1 TTTTTTTTCGA
*
21130972 TTTTTTTTTGAA
1 TTTTTTTTCG-A
21130984 TTTTTTTTC
1 TTTTTTTTC
21130993 TGAATTTCTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
10 9 0.33
11 9 0.33
12 9 0.33
ACGTcount: A:0.07, C:0.10, G:0.05, T:0.79
Consensus pattern (11 bp):
TTTTTTTTCGA
Found at i:21130988 original size:13 final size:13
Alignment explanation
Indices: 21130961--21130999 Score: 57
Period size: 11 Copynumber: 3.2 Consensus size: 13
21130951 TTTTTTTTCC
21130961 TTTTTTTTC-G-A
1 TTTTTTTTCTGAA
21130972 TTTTTTTT-TGAA
1 TTTTTTTTCTGAA
21130984 TTTTTTTTCTGAA
1 TTTTTTTTCTGAA
21130997 TTT
1 TTT
21131000 CTTCTCTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 9 0.36
12 9 0.36
13 7 0.28
ACGTcount: A:0.13, C:0.05, G:0.08, T:0.74
Consensus pattern (13 bp):
TTTTTTTTCTGAA
Found at i:21132386 original size:11 final size:10
Alignment explanation
Indices: 21132361--21132421 Score: 54
Period size: 10 Copynumber: 6.1 Consensus size: 10
21132351 ACCAATAAAA
21132361 TAAA-TGAGC
1 TAAATTGAGC
*
21132370 TGAATTGTAGC
1 TAAATTG-AGC
21132381 TAAATTGAGC
1 TAAATTGAGC
**
21132391 TCGATTGAGC
1 TAAATTGAGC
21132401 TGAAA-TGAGC
1 T-AAATTGAGC
*
21132411 TCAATTGAGC
1 TAAATTGAGC
21132421 T
1 T
21132422 GGTCGGAGTT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
9 5 0.12
10 26 0.63
11 10 0.24
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.30
Consensus pattern (10 bp):
TAAATTGAGC
Found at i:21132422 original size:20 final size:20
Alignment explanation
Indices: 21132362--21132422 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
21132352 CCAATAAAAT
*
21132362 AAATGAGCTGAATTGTAGCT-
1 AAATGAGCTCAATTG-AGCTG
*
21132382 AAATTGAGCTCGATTGAGCTG
1 AAA-TGAGCTCAATTGAGCTG
21132403 AAATGAGCTCAATTGAGCTG
1 AAATGAGCTCAATTGAGCTG
21132423 GTCGGAGTTG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (20 bp):
AAATGAGCTCAATTGAGCTG
Found at i:21133747 original size:23 final size:22
Alignment explanation
Indices: 21133696--21133747 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
21133686 CCTCGTCTTT
*
21133696 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
21133718 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
21133741 TTCTTTT
1 TTCTTTT
21133748 TCAATTTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:21143784 original size:4 final size:4
Alignment explanation
Indices: 21143775--21143801 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
21143765 TTAAACTAAG
21143775 TAAA TAAA TAAA TAAA TAAA TAAA TAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAA
21143802 CTTTACAACT
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:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
TAAA
Found at i:21150017 original size:13 final size:12
Alignment explanation
Indices: 21149976--21150010 Score: 70
Period size: 12 Copynumber: 2.9 Consensus size: 12
21149966 TTTATACTTC
21149976 AATTTTTTTTTG
1 AATTTTTTTTTG
21149988 AATTTTTTTTTG
1 AATTTTTTTTTG
21150000 AATTTTTTTTT
1 AATTTTTTTTT
21150011 CAAATTTCCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.17, C:0.00, G:0.06, T:0.77
Consensus pattern (12 bp):
AATTTTTTTTTG
Found at i:21153318 original size:23 final size:22
Alignment explanation
Indices: 21153267--21153319 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
21153257 CCTCGTCTTT
*
21153267 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
21153289 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
21153312 TTCTTTTC
1 TTCTTTTC
21153320 AAATTTCTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.19
23 14 0.54
24 5 0.19
ACGTcount: A:0.09, C:0.25, G:0.02, T:0.64
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:21156083 original size:24 final size:23
Alignment explanation
Indices: 21156029--21156106 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 23
21156019 GGATAATTAA
**
21156029 GAAATGGTATTTGGTTTTGGTAC
1 GAAATGGTATTTGGAATTGGTAC
***
21156052 GTTTTGGTATTTGGGAATTGGTAC
1 GAAATGGTATTT-GGAATTGGTAC
*
21156076 GAAATGGTA--TGGAATTGGTAT
1 GAAATGGTATTTGGAATTGGTAC
*
21156097 GAAATAGTAT
1 GAAATGGTAT
21156107 GGTATTTGGT
Statistics
Matches: 43, Mismatches: 10, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
21 18 0.42
22 1 0.02
23 9 0.21
24 15 0.35
ACGTcount: A:0.27, C:0.03, G:0.31, T:0.40
Consensus pattern (23 bp):
GAAATGGTATTTGGAATTGGTAC
Found at i:21156091 original size:21 final size:21
Alignment explanation
Indices: 21156065--21156131 Score: 80
Period size: 21 Copynumber: 3.1 Consensus size: 21
21156055 TTGGTATTTG
21156065 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
21156086 GGAATTGGTATGAAATAGTAT
1 GGAATTGGTACGAAATGGTAT
* *
21156107 GGTATTTGGTACGAATTGGTTAT
1 GG-AATTGGTACGAAATGG-TAT
21156130 GG
1 GG
21156132 TTCAAAGAGG
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
21 21 0.55
22 12 0.32
23 5 0.13
ACGTcount: A:0.30, C:0.03, G:0.33, T:0.34
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:21162657 original size:12 final size:12
Alignment explanation
Indices: 21162640--21162685 Score: 67
Period size: 11 Copynumber: 3.8 Consensus size: 12
21162630 CGTATGCAAT
21162640 TTTTTTTTTCAA
1 TTTTTTTTTCAA
21162652 -TTTTTTTTCAA
1 TTTTTTTTTCAA
21162663 TTTTTTTTTCGAA
1 TTTTTTTTTC-AA
21162676 CTTTTTTTTT
1 -TTTTTTTTT
21162686 ACGCACCTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.35
12 9 0.29
13 2 0.06
14 9 0.29
ACGTcount: A:0.13, C:0.09, G:0.02, T:0.76
Consensus pattern (12 bp):
TTTTTTTTTCAA
Found at i:21163002 original size:24 final size:23
Alignment explanation
Indices: 21162948--21163025 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 23
21162938 GGATAATTAA
**
21162948 GAAATGGTATTTGGTTTTGGTAC
1 GAAATGGTATTTGGAATTGGTAC
***
21162971 GTTTTGGTATTTGGGAATTGGTAC
1 GAAATGGTATTT-GGAATTGGTAC
*
21162995 GAAATGGTA--TGGAATTGGTAT
1 GAAATGGTATTTGGAATTGGTAC
*
21163016 GAAATAGTAT
1 GAAATGGTAT
21163026 GGTATTTGGT
Statistics
Matches: 43, Mismatches: 10, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
21 18 0.42
22 1 0.02
23 9 0.21
24 15 0.35
ACGTcount: A:0.27, C:0.03, G:0.31, T:0.40
Consensus pattern (23 bp):
GAAATGGTATTTGGAATTGGTAC
Found at i:21163010 original size:21 final size:21
Alignment explanation
Indices: 21162984--21163050 Score: 80
Period size: 21 Copynumber: 3.1 Consensus size: 21
21162974 TTGGTATTTG
21162984 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
21163005 GGAATTGGTATGAAATAGTAT
1 GGAATTGGTACGAAATGGTAT
* *
21163026 GGTATTTGGTACGAATTGGTTAT
1 GG-AATTGGTACGAAATGG-TAT
21163049 GG
1 GG
21163051 TTCAAAGAGG
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
21 21 0.55
22 12 0.32
23 5 0.13
ACGTcount: A:0.30, C:0.03, G:0.33, T:0.34
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:21164895 original size:30 final size:30
Alignment explanation
Indices: 21164861--21164957 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
21164851 TAAAGTAAAA
*
21164861 TGAGCTAAGTTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
* * * * * * *
21164891 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
21164921 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
21164950 ATGAGCTA
1 -TGAGCTA
21164958 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
Found at i:21167153 original size:12 final size:12
Alignment explanation
Indices: 21167138--21167168 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
21167128 TTCTTTTTGC
21167138 TTTTCAAAGGCT
1 TTTTCAAAGGCT
21167150 TTTTCAAAGGCT
1 TTTTCAAAGGCT
21167162 TTTTCAA
1 TTTTCAA
21167169 GTTCTCTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (12 bp):
TTTTCAAAGGCT
Found at i:21167245 original size:6 final size:6
Alignment explanation
Indices: 21167229--21167278 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
21167219 TTTCTTTTTA
*
21167229 TTTCAT TTTCTT TTTCTT CTCTTGCTT TTTCTT TTTC-T TTTC-T TTTCTT
1 TTTCTT TTTCTT TTTCTT -T-TT-CTT TTTCTT TTTCTT TTTCTT TTTCTT
21167278 T
1 T
21167279 GTTTTCTCTT
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
5 10 0.26
6 20 0.51
7 3 0.08
8 3 0.08
9 3 0.08
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.76
Consensus pattern (6 bp):
TTTCTT
Found at i:21167261 original size:37 final size:37
Alignment explanation
Indices: 21167218--21167288 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
21167208 CTTGCCTCTC
21167218 TTTTCTTTTT-ATTTCATTTTCTTT-TTCTTCTCTTGCT
1 TTTTCTTTTTCATTTC-TTTTCTTTGTT-TTCTCTTGCT
*
21167255 TTTTCTTTTTCTTTTCTTTTCTTTGTTTTCTCTT
1 TTTTCTTTTTCATTTCTTTTCTTTGTTTTCTCTT
21167289 TACAAGAATG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 25 0.81
38 6 0.19
ACGTcount: A:0.03, C:0.18, G:0.03, T:0.76
Consensus pattern (37 bp):
TTTTCTTTTTCATTTCTTTTCTTTGTTTTCTCTTGCT
Found at i:21167289 original size:16 final size:16
Alignment explanation
Indices: 21167214--21167274 Score: 63
Period size: 16 Copynumber: 3.8 Consensus size: 16
21167204 GCCTCTTGCC
*
21167214 TCTCTTTTCTTTTTAT
1 TCTCTTTTCTTTTTCT
21167230 T-TCATTTTCTTTTTCT
1 TCTC-TTTTCTTTTTCT
*
21167246 TCTC-TTGCTTTTTCTT
1 TCTCTTTTCTTTTTC-T
*
21167262 TTTCTTTTCTTTT
1 TCTCTTTTCTTTT
21167275 CTTTGTTTTC
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
15 11 0.30
16 17 0.46
17 9 0.24
ACGTcount: A:0.03, C:0.20, G:0.02, T:0.75
Consensus pattern (16 bp):
TCTCTTTTCTTTTTCT
Found at i:21168228 original size:12 final size:12
Alignment explanation
Indices: 21168213--21168264 Score: 59
Period size: 12 Copynumber: 4.2 Consensus size: 12
21168203 GATTTTTCGA
21168213 TTTTTTTTAAATT
1 TTTTTTTTAAA-T
**
21168226 TTTTTTTTCGAT
1 TTTTTTTTAAAT
*
21168238 TTTTTTTTCAAT
1 TTTTTTTTAAAT
21168250 TTTTTTTTCAAAT
1 TTTTTTTT-AAAT
21168263 TT
1 TT
21168265 CCTCTTCTCT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
12 20 0.59
13 14 0.41
ACGTcount: A:0.17, C:0.06, G:0.02, T:0.75
Consensus pattern (12 bp):
TTTTTTTTAAAT
Found at i:21168231 original size:13 final size:13
Alignment explanation
Indices: 21168213--21168264 Score: 61
Period size: 13 Copynumber: 4.1 Consensus size: 13
21168203 GATTTTTCGA
21168213 TTTTTTTTAAATT
1 TTTTTTTTAAATT
**
21168226 TTTTTTTTCGA-T
1 TTTTTTTTAAATT
*
21168238 TTTTTTTTCAATT
1 TTTTTTTTAAATT
*
21168251 TTTTTTTCAAATT
1 TTTTTTTTAAATT
21168264 T
1 T
21168265 CCTCTTCTCT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
12 11 0.33
13 22 0.67
ACGTcount: A:0.17, C:0.06, G:0.02, T:0.75
Consensus pattern (13 bp):
TTTTTTTTAAATT
Found at i:21168232 original size:24 final size:25
Alignment explanation
Indices: 21168187--21168257 Score: 90
Period size: 25 Copynumber: 2.8 Consensus size: 25
21168177 CTTTTCACTC
* **
21168187 TTTTTTTTTATACTTTGATTTTTCGA
1 TTTTTTTTTA-AATTTTTTTTTTCGA
21168213 -TTTTTTTTAAATTTTTTTTTTCGA
1 TTTTTTTTTAAATTTTTTTTTTCGA
*
21168237 TTTTTTTTTCAATTTTTTTTT
1 TTTTTTTTTAAATTTTTTTTT
21168258 CAAATTTCCT
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
24 12 0.30
25 28 0.70
ACGTcount: A:0.14, C:0.06, G:0.04, T:0.76
Consensus pattern (25 bp):
TTTTTTTTTAAATTTTTTTTTTCGA
Found at i:21169981 original size:30 final size:30
Alignment explanation
Indices: 21169947--21170043 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
21169937 TAAAGTAAAA
*
21169947 TGAGCTAAGTTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
* * * * * * *
21169977 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
21170007 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
21170036 ATGAGCTA
1 -TGAGCTA
21170044 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
Found at i:21181016 original size:22 final size:22
Alignment explanation
Indices: 21180986--21181032 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
21180976 TTTGGTATTT
21180986 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
21181008 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
21181030 GGG
1 GGG
21181033 TTCAAAAAGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.32, C:0.04, G:0.40, T:0.23
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:21186322 original size:13 final size:12
Alignment explanation
Indices: 21186281--21186357 Score: 57
Period size: 13 Copynumber: 6.0 Consensus size: 12
21186271 GTAGCTTCGA
21186281 AAAAAAAAAGTT-
1 AAAAAAAAA-TTG
*
21186293 AAAAAAAAGTTTCG
1 AAAAAAAA-ATT-G
21186307 AAAAAAAAATCTG
1 AAAAAAAAAT-TG
**
21186320 AAAAAAAAAGAAG
1 AAAAAAAAA-TTG
*
21186333 GAAAAAAAATTG
1 AAAAAAAAATTG
21186345 CAAAAAAAAATTG
1 -AAAAAAAAATTG
21186358 CATACGGTCT
Statistics
Matches: 51, Mismatches: 8, Indels: 11
0.73 0.11 0.16
Matches are distributed among these distances:
12 11 0.22
13 31 0.61
14 9 0.18
ACGTcount: A:0.70, C:0.04, G:0.12, T:0.14
Consensus pattern (12 bp):
AAAAAAAAATTG
Found at i:21186323 original size:27 final size:27
Alignment explanation
Indices: 21186276--21186327 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
21186266 AAATCGTAGC
* *
21186276 TTCGAAAAAAAAAAGTTAAAAAAAAGT
1 TTCGAAAAAAAAAACTGAAAAAAAAGT
*
21186303 TTCGAAAAAAAAATCTGAAAAAAAA
1 TTCGAAAAAAAAAACTGAAAAAAAA
21186328 AGAAGGAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.67, C:0.06, G:0.10, T:0.17
Consensus pattern (27 bp):
TTCGAAAAAAAAAACTGAAAAAAAAGT
Found at i:21188634 original size:24 final size:25
Alignment explanation
Indices: 21188607--21188660 Score: 60
Period size: 23 Copynumber: 2.2 Consensus size: 25
21188597 ATGAGTGATA
*
21188607 AAAAAAGAGA-GAGTGATTCAAAA-G
1 AAAAAAGAAACGAGTGA-TCAAAATG
*
21188631 -AAAAAGAAACGAGTGATGAAAATG
1 AAAAAAGAAACGAGTGATCAAAATG
21188655 AAAAAA
1 AAAAAA
21188661 AGAATTTGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
23 13 0.52
24 7 0.28
25 5 0.20
ACGTcount: A:0.63, C:0.04, G:0.22, T:0.11
Consensus pattern (25 bp):
AAAAAAGAAACGAGTGATCAAAATG
Found at i:21197734 original size:23 final size:22
Alignment explanation
Indices: 21197682--21197734 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
21197672 TCCACGTCTT
*
21197682 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
21197704 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
21197727 TTTCTTTT
1 TTTCTTTT
21197735 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:21201318 original size:10 final size:10
Alignment explanation
Indices: 21201303--21201350 Score: 53
Period size: 10 Copynumber: 4.8 Consensus size: 10
21201293 TTGGGTTAAG
21201303 ATTGAGCTGA
1 ATTGAGCTGA
21201313 ATTGAGCTCGA
1 ATTGAGCT-GA
21201324 A-TGAGCTGA
1 ATTGAGCTGA
* *
21201333 CTTGAGCTCA
1 ATTGAGCTGA
*
21201343 AGTGAGCT
1 ATTGAGCT
21201351 AGAAACGAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
9 2 0.06
10 27 0.84
11 3 0.09
ACGTcount: A:0.27, C:0.17, G:0.29, T:0.27
Consensus pattern (10 bp):
ATTGAGCTGA
Found at i:21201328 original size:20 final size:20
Alignment explanation
Indices: 21201305--21201350 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
21201295 GGGTTAAGAT
21201305 TGAGCTGAATTGAGCTCGAA-
1 TGAGCTGAATTGAGCTC-AAG
*
21201325 TGAGCTGACTTGAGCTCAAG
1 TGAGCTGAATTGAGCTCAAG
21201345 TGAGCT
1 TGAGCT
21201351 AGAAACGAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 2 0.08
20 22 0.92
ACGTcount: A:0.26, C:0.17, G:0.30, T:0.26
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCAAG
Found at i:21201701 original size:18 final size:17
Alignment explanation
Indices: 21201678--21201716 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
21201668 CTCTTTTTGC
21201678 TCTTTTTCATTCTCTTTT
1 TCTTTTTCATT-TCTTTT
*
21201696 TCTTTTTTGATTTCTTTT
1 TC-TTTTTCATTTCTTTT
21201714 TCT
1 TCT
21201717 GTCTTTCTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
17 1 0.05
18 10 0.53
19 8 0.42
ACGTcount: A:0.05, C:0.18, G:0.03, T:0.74
Consensus pattern (17 bp):
TCTTTTTCATTTCTTTT
Found at i:21202895 original size:13 final size:13
Alignment explanation
Indices: 21202877--21202901 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
21202867 GTATTGATCA
21202877 TGTGTTCACACCT
1 TGTGTTCACACCT
21202890 TGTGTTCACACC
1 TGTGTTCACACC
21202902 ATGATGACCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.32, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTGTTCACACCT
Found at i:21203853 original size:29 final size:29
Alignment explanation
Indices: 21203818--21203876 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
21203808 AAAATTGGGC
21203818 CAAGATTTGAAATCATGATTTTCTTGATT
1 CAAGATTTGAAATCATGATTTTCTTGATT
21203847 CAAGATTTGAAATCATGATTTTCTTGATT
1 CAAGATTTGAAATCATGATTTTCTTGATT
21203876 C
1 C
21203877 TTGAAATAGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.31, C:0.12, G:0.14, T:0.44
Consensus pattern (29 bp):
CAAGATTTGAAATCATGATTTTCTTGATT
Found at i:21204786 original size:22 final size:23
Alignment explanation
Indices: 21204755--21204797 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
21204745 ACCTTTTTGA
*
21204755 ACCATTACCAATTCGTACCAAAT
1 ACCATTACCAATTCATACCAAAT
*
21204778 ACCA-TACCATTTCATACCAA
1 ACCATTACCAATTCATACCAA
21204798 CTTTGATGTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.40, C:0.33, G:0.02, T:0.26
Consensus pattern (23 bp):
ACCATTACCAATTCATACCAAAT
Found at i:21206376 original size:15 final size:14
Alignment explanation
Indices: 21206341--21206408 Score: 56
Period size: 13 Copynumber: 4.9 Consensus size: 14
21206331 AAATCGTAGC
21206341 TTCGAAAAAAAAAAG
1 TTCG-AAAAAAAAAG
21206356 TT--AAAAAAAAAG
1 TTCGAAAAAAAAAG
21206368 TTTCGAAAAAAAAA-
1 -TTCGAAAAAAAAAG
*
21206382 TCCGAAAAAAGAAA-
1 TTCGAAAAAA-AAAG
21206396 TT-GCAAAAAAAAA
1 TTCG-AAAAAAAAA
21206409 ATTGCATACG
Statistics
Matches: 46, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
12 10 0.22
13 15 0.33
14 10 0.22
15 11 0.24
ACGTcount: A:0.68, C:0.07, G:0.10, T:0.15
Consensus pattern (14 bp):
TTCGAAAAAAAAAG
Found at i:21206411 original size:14 final size:14
Alignment explanation
Indices: 21206345--21206414 Score: 56
Period size: 14 Copynumber: 5.1 Consensus size: 14
21206335 CGTAGCTTCG
21206345 AAAAAAAAAAGTT--
1 AAAAAAAAAA-TTGC
* *
21206358 AAAAAAAAAGTTTC
1 AAAAAAAAAATTGC
* *
21206372 GAAAAAAAAA-TCC
1 AAAAAAAAAATTGC
*
21206385 GAAAAAAGAAATTGC
1 -AAAAAAAAAATTGC
21206400 AAAAAAAAAATTGC
1 AAAAAAAAAATTGC
21206414 A
1 A
21206415 TACGGTCTAG
Statistics
Matches: 45, Mismatches: 8, Indels: 7
0.75 0.13 0.12
Matches are distributed among these distances:
12 2 0.04
13 11 0.24
14 30 0.67
15 2 0.04
ACGTcount: A:0.69, C:0.07, G:0.10, T:0.14
Consensus pattern (14 bp):
AAAAAAAAAATTGC
Found at i:21208693 original size:24 final size:25
Alignment explanation
Indices: 21208666--21208719 Score: 60
Period size: 23 Copynumber: 2.2 Consensus size: 25
21208656 ATGAGTGATA
*
21208666 AAAAAAGAGA-GAGTGATTCAAAA-G
1 AAAAAAGAAACGAGTGA-TCAAAATG
*
21208690 -AAAAAGAAACGAGTGATGAAAATG
1 AAAAAAGAAACGAGTGATCAAAATG
21208714 AAAAAA
1 AAAAAA
21208720 AGAATTTGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
23 13 0.52
24 7 0.28
25 5 0.20
ACGTcount: A:0.63, C:0.04, G:0.22, T:0.11
Consensus pattern (25 bp):
AAAAAAGAAACGAGTGATCAAAATG
Found at i:21222059 original size:20 final size:20
Alignment explanation
Indices: 21222012--21222059 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
21222002 AGTAAGCTCG
21222012 GTTGAGCTCAAACGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
**** *
21222032 AACAAGCTCAAATGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
21222052 GTTGAGCT
1 GTTGAGCT
21222060 GGACGGTGCT
Statistics
Matches: 19, Mismatches: 9, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.19, G:0.27, T:0.21
Consensus pattern (20 bp):
GTTGAGCTCAAACGAGCTGA
Found at i:21223464 original size:17 final size:18
Alignment explanation
Indices: 21223442--21223475 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
21223432 ACAACACTCC
*
21223442 TTTCTT-CTTCACTCTCG
1 TTTCTTCCTTCAATCTCG
21223459 TTTCTTCCTTCAATCTC
1 TTTCTTCCTTCAATCTC
21223476 ACTCTCTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.09, C:0.35, G:0.03, T:0.53
Consensus pattern (18 bp):
TTTCTTCCTTCAATCTCG
Found at i:21224552 original size:16 final size:17
Alignment explanation
Indices: 21224518--21224556 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
21224508 TTTAACTTGA
* *
21224518 TTTTTTTTGGTCACCTT
1 TTTTTTTTGCTCACATT
21224535 TTTTTTTTGCTCA-ATT
1 TTTTTTTTGCTCACATT
21224551 TTTTTT
1 TTTTTT
21224557 CACTTTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 8 0.40
17 12 0.60
ACGTcount: A:0.08, C:0.13, G:0.08, T:0.72
Consensus pattern (17 bp):
TTTTTTTTGCTCACATT
Found at i:21224578 original size:14 final size:13
Alignment explanation
Indices: 21224534--21224624 Score: 53
Period size: 14 Copynumber: 6.6 Consensus size: 13
21224524 TTGGTCACCT
*
21224534 TTTTTTTTTGCTCA
1 TTTTTTTTTGAT-A
* *
21224548 ATTTTTTTTCACT-
1 TTTTTTTTTGA-TA
21224561 TTTTTTTTTGAATA
1 TTTTTTTTTG-ATA
*
21224575 TTTTTTTTTCAATCAA
1 TTTTTTTTT-GAT--A
21224591 TTTTTTTTTTCGA-A
1 -TTTTTTTTT-GATA
21224605 TTTTTTTTTGAT-
1 TTTTTTTTTGATA
21224617 TTTTTTTT
1 TTTTTTTT
21224625 GTTACTCCAA
Statistics
Matches: 62, Mismatches: 7, Indels: 18
0.71 0.08 0.21
Matches are distributed among these distances:
12 10 0.16
13 18 0.29
14 21 0.34
15 1 0.02
16 1 0.02
17 11 0.18
ACGTcount: A:0.14, C:0.08, G:0.04, T:0.74
Consensus pattern (13 bp):
TTTTTTTTTGATA
Found at i:21224618 original size:11 final size:12
Alignment explanation
Indices: 21224592--21224625 Score: 52
Period size: 11 Copynumber: 2.8 Consensus size: 12
21224582 TTCAATCAAT
21224592 TTTTTTTTTCGAA
1 TTTTTTTTT-GAA
21224605 TTTTTTTTTG-A
1 TTTTTTTTTGAA
21224616 TTTTTTTTTG
1 TTTTTTTTTG
21224626 TTACTCCAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 11 0.52
12 1 0.05
13 9 0.43
ACGTcount: A:0.09, C:0.03, G:0.09, T:0.79
Consensus pattern (12 bp):
TTTTTTTTTGAA
Found at i:21224624 original size:12 final size:13
Alignment explanation
Indices: 21224590--21224624 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
21224580 TTTTCAATCA
21224590 ATTTTTTTTTTCG
1 ATTTTTTTTTTCG
*
21224603 AATTTTTTTTT-G
1 ATTTTTTTTTTCG
21224615 ATTTTTTTTT
1 ATTTTTTTTT
21224625 GTTACTCCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
12 10 0.50
13 10 0.50
ACGTcount: A:0.11, C:0.03, G:0.06, T:0.80
Consensus pattern (13 bp):
ATTTTTTTTTTCG
Found at i:21226050 original size:20 final size:20
Alignment explanation
Indices: 21226003--21226050 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
21225993 AGTAAGCTCG
21226003 GTTGAGCTCAAACGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
**** *
21226023 AACAAGCTCAAATGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
21226043 GTTGAGCT
1 GTTGAGCT
21226051 GGACGGTGCT
Statistics
Matches: 19, Mismatches: 9, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.19, G:0.27, T:0.21
Consensus pattern (20 bp):
GTTGAGCTCAAACGAGCTGA
Found at i:21226466 original size:21 final size:21
Alignment explanation
Indices: 21226441--21226484 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
21226431 TTGGTACTTG
*
21226441 GGAATTGGTTCGAAATAGTAT
1 GGAATTGGTACGAAATAGTAT
*
21226462 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATAGTAT
21226483 GG
1 GG
21226485 TTTTTGGTAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.32, C:0.05, G:0.34, T:0.30
Consensus pattern (21 bp):
GGAATTGGTACGAAATAGTAT
Found at i:21226494 original size:22 final size:23
Alignment explanation
Indices: 21226466--21226509 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
21226456 TAGTATGGAA
21226466 TTGGTACGAAATGGT-ATGGTTT
1 TTGGTACGAAATGGTAATGGTTT
*
21226488 TTGGTACGAATTGGTAATGGTT
1 TTGGTACGAAATGGTAATGGTT
21226510 CAAAGAGGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.23, C:0.05, G:0.32, T:0.41
Consensus pattern (23 bp):
TTGGTACGAAATGGTAATGGTTT
Found at i:21228433 original size:10 final size:11
Alignment explanation
Indices: 21228420--21228465 Score: 69
Period size: 10 Copynumber: 4.4 Consensus size: 11
21228410 TTTTTTCTTC
21228420 TTTTCAATTTT
1 TTTTCAATTTT
*
21228431 TTTT-GATTTT
1 TTTTCAATTTT
21228441 TTTTCAATTTT
1 TTTTCAATTTT
21228452 TTTTC-ATTTT
1 TTTTCAATTTT
21228462 TTTT
1 TTTT
21228466 AAATATCTAC
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
10 18 0.56
11 14 0.44
ACGTcount: A:0.13, C:0.07, G:0.02, T:0.78
Consensus pattern (11 bp):
TTTTCAATTTT
Found at i:21228444 original size:21 final size:21
Alignment explanation
Indices: 21228420--21228465 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
21228410 TTTTTTCTTC
*
21228420 TTTTCAATTTTTTTTGATTTT
1 TTTTCAATTTTTTTTCATTTT
21228441 TTTTCAATTTTTTTTCATTTT
1 TTTTCAATTTTTTTTCATTTT
21228462 TTTT
1 TTTT
21228466 AAATATCTAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.13, C:0.07, G:0.02, T:0.78
Consensus pattern (21 bp):
TTTTCAATTTTTTTTCATTTT
Found at i:21231167 original size:20 final size:20
Alignment explanation
Indices: 21231121--21231169 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
21231111 TTTTTCATTG
*
21231121 CTCTTGTTTTCTCACAATCT
1 CTCTTCTTTTCTCACAATCT
** *
21231141 CGATTCTTTTCTCTCAATCT
1 CTCTTCTTTTCTCACAATCT
21231161 CTCTTCTTT
1 CTCTTCTTT
21231170 CTTTTCTTTT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.12, C:0.31, G:0.04, T:0.53
Consensus pattern (20 bp):
CTCTTCTTTTCTCACAATCT
Found at i:21239522 original size:12 final size:12
Alignment explanation
Indices: 21239505--21239576 Score: 54
Period size: 12 Copynumber: 5.6 Consensus size: 12
21239495 TTGGAGTAAC
21239505 AAAAAAAATCAA
1 AAAAAAAATCAA
*
21239517 AAAAAAATTCGAA
1 AAAAAAAATC-AA
*
21239530 AAAAAAATTGATTGAA
1 AAAAAAA---A-TCAA
*
21239546 AAAAAAATTCAA
1 AAAAAAAATCAA
* *
21239558 AAAAAAAGTGAA
1 AAAAAAAATCAA
21239570 AAAAAAA
1 AAAAAAA
21239577 TCGAGCAAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
12 29 0.60
13 9 0.19
16 9 0.19
17 1 0.02
ACGTcount: A:0.75, C:0.04, G:0.07, T:0.14
Consensus pattern (12 bp):
AAAAAAAATCAA
Found at i:21239587 original size:28 final size:27
Alignment explanation
Indices: 21239556--21239627 Score: 81
Period size: 28 Copynumber: 2.6 Consensus size: 27
21239546 AAAAAAATTC
*
21239556 AAAAAAAAAGTGAAAAAAAAATCGAGCA
1 AAAAAAAAAGTGAAAAAAAAATCAAG-A
* * *
21239584 AAAAAAAAGGTGACCAAAAAAATCAAGT
1 AAAAAAAAAGTGA-AAAAAAAATCAAGA
*
21239612 TAAAAAAAAGTGAAAA
1 AAAAAAAAAGTGAAAA
21239628 GTCTTGCGAG
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
27 2 0.06
28 23 0.64
29 11 0.31
ACGTcount: A:0.69, C:0.07, G:0.14, T:0.10
Consensus pattern (27 bp):
AAAAAAAAAGTGAAAAAAAAATCAAGA
Found at i:21239588 original size:40 final size:40
Alignment explanation
Indices: 21239505--21239591 Score: 115
Period size: 41 Copynumber: 2.2 Consensus size: 40
21239495 TTGGAGTAAC
* *
21239505 AAAAAAAATCAAAAAAAAATTCGAAAAAAAAATTGATTG-AA
1 AAAAAAAATCAAAAAAAAAGTCGAAAAAAAAATCGA--GCAA
*
21239546 AAAAAAATTCAAAAAAAAAGT-GAAAAAAAAATCGAGCAA
1 AAAAAAAATCAAAAAAAAAGTCGAAAAAAAAATCGAGCAA
21239585 AAAAAAA
1 AAAAAAA
21239592 GGTGACCAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
38 1 0.02
39 9 0.21
40 13 0.31
41 19 0.45
ACGTcount: A:0.74, C:0.06, G:0.08, T:0.13
Consensus pattern (40 bp):
AAAAAAAATCAAAAAAAAAGTCGAAAAAAAAATCGAGCAA
Found at i:21239602 original size:29 final size:28
Alignment explanation
Indices: 21239555--21239627 Score: 87
Period size: 29 Copynumber: 2.6 Consensus size: 28
21239545 AAAAAAAATT
*
21239555 CAAAAAAAAA-GTGAAAAAAAAATCGAG
1 CAAAAAAAAAGGTGAAAAAAAAATCAAG
*
21239582 CAAAAAAAAAGGTGACCAAAAAAATCAAG
1 CAAAAAAAAAGGTGA-AAAAAAAATCAAG
**
21239611 TTAAAAAAAA-GTGAAAA
1 CAAAAAAAAAGGTGAAAA
21239628 GTCTTGCGAG
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
27 12 0.31
28 8 0.21
29 19 0.49
ACGTcount: A:0.68, C:0.08, G:0.14, T:0.10
Consensus pattern (28 bp):
CAAAAAAAAAGGTGAAAAAAAAATCAAG
Found at i:21240517 original size:18 final size:18
Alignment explanation
Indices: 21240496--21240530 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
21240486 AGAAAAGAAA
21240496 ATTGA-AAAAGAAATTGAG
1 ATTGAGAAAA-AAATTGAG
21240514 ATTGAGAAAAAAATTGA
1 ATTGAGAAAAAAATTGA
21240531 AAAAGAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.57, C:0.00, G:0.20, T:0.23
Consensus pattern (18 bp):
ATTGAGAAAAAAATTGAG
Found at i:21247219 original size:22 final size:22
Alignment explanation
Indices: 21247189--21247232 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
21247179 TTTGGTATTT
21247189 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
21247211 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
21247233 TGGTTCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.05, G:0.36, T:0.25
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:21249244 original size:30 final size:30
Alignment explanation
Indices: 21249210--21249306 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 30
21249200 TAAACTAAAA
*
21249210 TGAGCTAAGTTTTAGCTCATGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCATGAGCTAAAGT
* * * * * * *
21249240 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCATGAGCTAAAGT
*
21249270 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGGTTTAGCTCATGAGCTAAAGT
21249299 ATGAGCTA
1 -TGAGCTA
21249307 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCATGAGCTAAAGT
Found at i:21250485 original size:30 final size:30
Alignment explanation
Indices: 21250451--21250543 Score: 98
Period size: 30 Copynumber: 3.1 Consensus size: 30
21250441 AGCTCACTCC
21250451 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
21250481 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
21250511 CAGCTCAACTTTAGCTCACGAGCTAAAACT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
21250541 TAG
1 TAG
21250544 GTCATTTTAC
Statistics
Matches: 47, Mismatches: 15, Indels: 2
0.73 0.23 0.03
Matches are distributed among these distances:
29 1 0.02
30 46 0.98
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:21251319 original size:20 final size:20
Alignment explanation
Indices: 21251296--21251349 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
21251286 AGTTTTTCCC
*
21251296 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
21251316 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
21251336 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
21251350 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:21251331 original size:30 final size:30
Alignment explanation
Indices: 21251296--21251369 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
21251286 AGTTTTTCCC
21251296 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
21251326 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
21251356 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
21251370 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:21251359 original size:20 final size:20
Alignment explanation
Indices: 21251296--21251360 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
21251286 AGTTTTTCCC
* * * *
21251296 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
21251316 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
21251335 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
21251356 AGCTC
1 AGCTC
21251361 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:21253009 original size:14 final size:15
Alignment explanation
Indices: 21252990--21253039 Score: 59
Period size: 15 Copynumber: 3.4 Consensus size: 15
21252980 AAAAAAAATC
21252990 AAAAAAAT-TTGAAA
1 AAAAAAATATTGAAA
*
21253004 AAAAAATTGATTG-AA
1 AAAAAAAT-ATTGAAA
*
21253019 AAAAAAATATTCAAA
1 AAAAAAATATTGAAA
21253034 AAAAAA
1 AAAAAA
21253040 GTGAAAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
14 10 0.33
15 17 0.57
16 3 0.10
ACGTcount: A:0.72, C:0.02, G:0.06, T:0.20
Consensus pattern (15 bp):
AAAAAAATATTGAAA
Found at i:21253063 original size:17 final size:17
Alignment explanation
Indices: 21253043--21253082 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
21253033 AAAAAAAGTG
*
21253043 AAAAAAAAA-TTGAGCAA
1 AAAAAAAAAGGTGA-CAA
21253060 AAAAAAAAAGGTGACAA
1 AAAAAAAAAGGTGACAA
21253077 AAAAAA
1 AAAAAA
21253083 TCAAGTTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 18 0.86
18 3 0.14
ACGTcount: A:0.75, C:0.05, G:0.12, T:0.07
Consensus pattern (17 bp):
AAAAAAAAAGGTGACAA
Found at i:21253066 original size:18 final size:17
Alignment explanation
Indices: 21253043--21253082 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
21253033 AAAAAAAGTG
*
21253043 AAAAAAAAATTGAGCAAA
1 AAAAAAAAAGTGA-CAAA
*
21253061 AAAAAAAAGGTGACAAA
1 AAAAAAAAAGTGACAAA
21253078 AAAAA
1 AAAAA
21253083 TCAAGTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.75, C:0.05, G:0.12, T:0.07
Consensus pattern (17 bp):
AAAAAAAAAGTGACAAA
Found at i:21253079 original size:42 final size:42
Alignment explanation
Indices: 21252989--21253081 Score: 100
Period size: 42 Copynumber: 2.2 Consensus size: 42
21252979 CAAAAAAAAT
* * *
21252989 CAAAAAAATTTGAAAAAAAAATTGATTGAAAAAAAAATATTCA
1 CAAAAAAATGTGAAAAAAAAATTGA-TGAAAAAAAAAAAGTCA
* *
21253032 -AAAAAAAAGTGAAAAAAAAATTGA-GCAAAAAAAAAAAGGTGA
1 CAAAAAAATGTGAAAAAAAAATTGATG-AAAAAAAAAAA-GTCA
21253074 CAAAAAAA
1 CAAAAAAA
21253082 ATCAAGTTAA
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
40 1 0.02
41 10 0.24
42 24 0.57
43 7 0.17
ACGTcount: A:0.70, C:0.04, G:0.11, T:0.15
Consensus pattern (42 bp):
CAAAAAAATGTGAAAAAAAAATTGATGAAAAAAAAAAAGTCA
Found at i:21253094 original size:31 final size:29
Alignment explanation
Indices: 21253031--21253105 Score: 89
Period size: 29 Copynumber: 2.6 Consensus size: 29
21253021 AAAAATATTC
**
21253031 AAAAAAAAAGTGAAAAAAAAATTGAGCAA
1 AAAAAAAAAGTGAAAAAAAAATCAAGCAA
**
21253060 AAAAAAAAAGGTGACAAAAAAAATCAAG-TT
1 AAAAAAAAA-GTGA-AAAAAAAATCAAGCAA
21253090 AAAAAAAAAGTGAAAA
1 AAAAAAAAAGTGAAAA
21253106 GTCTTGTGAG
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
28 3 0.08
29 13 0.32
30 13 0.32
31 11 0.28
ACGTcount: A:0.72, C:0.04, G:0.13, T:0.11
Consensus pattern (29 bp):
AAAAAAAAAGTGAAAAAAAAATCAAGCAA
Found at i:21254157 original size:17 final size:18
Alignment explanation
Indices: 21254125--21254158 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
21254115 AAAAGAGAGT
*
21254125 GAGATTGAAGGAAGAAAC
1 GAGAGTGAAGGAAGAAAC
21254143 GAGAGTGAA-GAAGAAA
1 GAGAGTGAAGGAAGAAA
21254159 GGAGTATTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.53, C:0.03, G:0.35, T:0.09
Consensus pattern (18 bp):
GAGAGTGAAGGAAGAAAC
Found at i:21255447 original size:20 final size:20
Alignment explanation
Indices: 21255424--21255477 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
21255414 AGTTTTTCCC
*
21255424 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
21255444 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
21255464 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
21255478 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:21255459 original size:30 final size:30
Alignment explanation
Indices: 21255424--21255497 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
21255414 AGTTTTTCCC
21255424 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
21255454 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
21255484 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
21255498 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:21255487 original size:20 final size:20
Alignment explanation
Indices: 21255424--21255488 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
21255414 AGTTTTTCCC
* * * *
21255424 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
21255444 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
21255463 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
21255484 AGCTC
1 AGCTC
21255489 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:21257981 original size:11 final size:12
Alignment explanation
Indices: 21257955--21257980 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
21257945 AAAAAAAAGG
21257955 AAATCAAAAAAA
1 AAATCAAAAAAA
21257967 AAATCAAAAAAA
1 AAATCAAAAAAA
21257979 AA
1 AA
21257981 TTTTTGAGTT
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:0.85, C:0.08, G:0.00, T:0.08
Consensus pattern (12 bp):
AAATCAAAAAAA
Found at i:21258078 original size:11 final size:11
Alignment explanation
Indices: 21258064--21258114 Score: 59
Period size: 11 Copynumber: 4.6 Consensus size: 11
21258054 GAAGAAATTC
21258064 AAAAAAAATCA
1 AAAAAAAATCA
21258075 AAAAAAAATC-
1 AAAAAAAATCA
**
21258085 AAAAAAAAGGA
1 AAAAAAAATCA
*
21258096 AAAAAAAAGTGA
1 AAAAAAAA-TCA
21258108 AAAAAAA
1 AAAAAAA
21258115 TCGAGTTAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
10 8 0.23
11 18 0.51
12 9 0.26
ACGTcount: A:0.82, C:0.04, G:0.08, T:0.06
Consensus pattern (11 bp):
AAAAAAAATCA
Found at i:21258086 original size:21 final size:22
Alignment explanation
Indices: 21258062--21258116 Score: 76
Period size: 21 Copynumber: 2.5 Consensus size: 22
21258052 GAGAAGAAAT
21258062 TCAAAAAAAATCAAAAAAAAA-
1 TCAAAAAAAATCAAAAAAAAAG
**
21258083 TCAAAAAAAAGGAAAAAAAAAG
1 TCAAAAAAAATCAAAAAAAAAG
*
21258105 TGAAAAAAAATC
1 TCAAAAAAAATC
21258117 GAGTTAAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
21 19 0.68
22 9 0.32
ACGTcount: A:0.76, C:0.07, G:0.07, T:0.09
Consensus pattern (22 bp):
TCAAAAAAAATCAAAAAAAAAG
Found at i:21259066 original size:21 final size:21
Alignment explanation
Indices: 21259036--21259096 Score: 77
Period size: 21 Copynumber: 2.8 Consensus size: 21
21259026 AAGAGAAAAC
21259036 AAAGAAAAGAAAAGAAAAAGAA
1 AAAG-AAAGAAAAGAAAAAGAA
* *
21259058 AAAGTAAGAGAAGAAAAAGAA
1 AAAGAAAGAAAAGAAAAAGAA
*
21259079 AAAGAAATAAAAAGAAAA
1 AAAGAAA-GAAAAGAAAA
21259097 GAGAGGCAAG
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
21 21 0.64
22 12 0.36
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (21 bp):
AAAGAAAGAAAAGAAAAAGAA
Found at i:21259077 original size:37 final size:37
Alignment explanation
Indices: 21259026--21259096 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
21259016 CATTCTTGTA
21259026 AAGAGAAAACAAAG-AAAAGAAAAGAAAAAGAAAAAGT
1 AAGAGAAAACAAAGAAAAAG-AAAGAAAAAGAAAAAGT
*
21259063 AAGAGAAGAA-AAAGAAAAAGAAATAAAAAGAAAA
1 AAGAGAA-AACAAAGAAAAAGAAAGAAAAAGAAAA
21259097 GAGAGGCAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 24 0.77
38 7 0.23
ACGTcount: A:0.77, C:0.01, G:0.18, T:0.03
Consensus pattern (37 bp):
AAGAGAAAACAAAGAAAAAGAAAGAAAAAGAAAAAGT
Found at i:21259084 original size:15 final size:16
Alignment explanation
Indices: 21259025--21259096 Score: 67
Period size: 16 Copynumber: 4.5 Consensus size: 16
21259015 ACATTCTTGT
*
21259025 AAAGAGAAAACAAAG-A
1 AAAGA-AAAAGAAAGAA
*
21259041 AAAGAAAAGAAAAAGAA
1 AAAGAAAA-AGAAAGAA
* *
21259058 AAAGTAAGAG-AAGAA
1 AAAGAAAAAGAAAGAA
*
21259073 AAAGAAAAAGAAATAA
1 AAAGAAAAAGAAAGAA
21259089 AAAGAAAA
1 AAAGAAAA
21259097 GAGAGGCAAG
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
15 16 0.35
16 23 0.50
17 7 0.15
ACGTcount: A:0.78, C:0.01, G:0.18, T:0.03
Consensus pattern (16 bp):
AAAGAAAAAGAAAGAA
Found at i:21259096 original size:6 final size:6
Alignment explanation
Indices: 21259036--21259085 Score: 59
Period size: 6 Copynumber: 8.2 Consensus size: 6
21259026 AAGAGAAAAC
21259036 AAAG-A AAAG-A AAAGAA AAAGAA AAAGTAA GAGAAGAA AAAGAA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAG-AA -A-AAGAA AAAGAA AAAGAA
21259085 A
1 A
21259086 TAAAAAGAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
5 9 0.22
6 23 0.56
7 3 0.07
8 3 0.07
9 3 0.07
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (6 bp):
AAAGAA
Found at i:21259097 original size:21 final size:23
Alignment explanation
Indices: 21259040--21259098 Score: 68
Period size: 27 Copynumber: 2.5 Consensus size: 23
21259030 GAAAACAAAG
21259040 AAAAGAAAAGAAAAAGAAAAAGTA
1 AAAAGAAAAGAAAAAG-AAAAGTA
21259064 AGAGAAGAAAAAGAAAAAG-AAA-TA
1 A-A-AAG-AAAAGAAAAAGAAAAGTA
21259088 AAAAGAAAAGA
1 AAAAGAAAAGA
21259099 GAGGCAAGAG
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
21 6 0.19
22 3 0.09
23 1 0.03
24 4 0.12
25 4 0.12
26 3 0.09
27 11 0.34
ACGTcount: A:0.78, C:0.00, G:0.19, T:0.03
Consensus pattern (23 bp):
AAAAGAAAAGAAAAAGAAAAGTA
Found at i:21259178 original size:11 final size:12
Alignment explanation
Indices: 21259146--21259176 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
21259136 TTGAGAGAAC
21259146 TTGAAAAAGCCT
1 TTGAAAAAGCCT
21259158 TTGAAAAAGCCT
1 TTGAAAAAGCCT
21259170 TTGAAAA
1 TTGAAAA
21259177 GCAAAAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:21261389 original size:30 final size:30
Alignment explanation
Indices: 21261355--21261447 Score: 98
Period size: 30 Copynumber: 3.1 Consensus size: 30
21261345 AGCTCACTCC
21261355 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
21261385 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
21261415 CAGCTCAACTTTAGCTCACGAGCTAAAACT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
21261445 TAG
1 TAG
21261448 GTCATTTTAC
Statistics
Matches: 47, Mismatches: 15, Indels: 2
0.73 0.23 0.03
Matches are distributed among these distances:
29 1 0.02
30 46 0.98
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:21264189 original size:12 final size:12
Alignment explanation
Indices: 21264174--21264204 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
21264164 TTCTTTTTGC
21264174 TTTTCAAAGGCT
1 TTTTCAAAGGCT
21264186 TTTTCAAAGGCT
1 TTTTCAAAGGCT
21264198 TTTTCAA
1 TTTTCAA
21264205 GTTCTCTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (12 bp):
TTTTCAAAGGCT
Found at i:21264281 original size:6 final size:6
Alignment explanation
Indices: 21264265--21264314 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
21264255 TTTCTTTTTA
*
21264265 TTTCAT TTTCTT TTTCTT CTCTTGCTT TTTCTT TTTC-T TTTC-T TTTCTT
1 TTTCTT TTTCTT TTTCTT -T-TT-CTT TTTCTT TTTCTT TTTCTT TTTCTT
21264314 T
1 T
21264315 GTTTTCTCTT
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
5 10 0.26
6 20 0.51
7 3 0.08
8 3 0.08
9 3 0.08
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.76
Consensus pattern (6 bp):
TTTCTT
Found at i:21264297 original size:37 final size:37
Alignment explanation
Indices: 21264254--21264324 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
21264244 CTTGCCTCTC
21264254 TTTTCTTTTT-ATTTCATTTTCTTT-TTCTTCTCTTGCT
1 TTTTCTTTTTCATTTC-TTTTCTTTGTT-TTCTCTTGCT
*
21264291 TTTTCTTTTTCTTTTCTTTTCTTTGTTTTCTCTT
1 TTTTCTTTTTCATTTCTTTTCTTTGTTTTCTCTT
21264325 TACAAGAATG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 25 0.81
38 6 0.19
ACGTcount: A:0.03, C:0.18, G:0.03, T:0.76
Consensus pattern (37 bp):
TTTTCTTTTTCATTTCTTTTCTTTGTTTTCTCTTGCT
Found at i:21264325 original size:16 final size:16
Alignment explanation
Indices: 21264250--21264310 Score: 63
Period size: 16 Copynumber: 3.8 Consensus size: 16
21264240 GCCTCTTGCC
*
21264250 TCTCTTTTCTTTTTAT
1 TCTCTTTTCTTTTTCT
21264266 T-TCATTTTCTTTTTCT
1 TCTC-TTTTCTTTTTCT
*
21264282 TCTC-TTGCTTTTTCTT
1 TCTCTTTTCTTTTTC-T
*
21264298 TTTCTTTTCTTTT
1 TCTCTTTTCTTTT
21264311 CTTTGTTTTC
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
15 11 0.30
16 17 0.46
17 9 0.24
ACGTcount: A:0.03, C:0.20, G:0.02, T:0.75
Consensus pattern (16 bp):
TCTCTTTTCTTTTTCT
Found at i:21267015 original size:30 final size:30
Alignment explanation
Indices: 21266981--21267077 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 30
21266971 TAAACTAAAA
*
21266981 TGAGCTAAGTTTTAGCTCATGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCATGAGCTAAAGT
* * * * * * *
21267011 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCATGAGCTAAAGT
*
21267041 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGGTTTAGCTCATGAGCTAAAGT
21267070 ATGAGCTA
1 -TGAGCTA
21267078 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCATGAGCTAAAGT
Found at i:21283672 original size:29 final size:29
Alignment explanation
Indices: 21283630--21283701 Score: 117
Period size: 29 Copynumber: 2.5 Consensus size: 29
21283620 TTTAATCATG
* *
21283630 TAGGACATATTTAAAACACTTGAACTAAT
1 TAGGACATATTTAAAACACCTAAACTAAT
*
21283659 TAGGACATATTTAAAATACCTAAACTAAT
1 TAGGACATATTTAAAACACCTAAACTAAT
21283688 TAGGACATATTTAA
1 TAGGACATATTTAA
21283702 TAATATCTAA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.46, C:0.12, G:0.10, T:0.32
Consensus pattern (29 bp):
TAGGACATATTTAAAACACCTAAACTAAT
Found at i:21284779 original size:15 final size:15
Alignment explanation
Indices: 21284739--21284780 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
21284729 CGTATACAAT
* *
21284739 TTTTTTTTCAATTTT
1 TTTTTTTTCGATTTC
21284754 TTTTCTTTTCGATTTC
1 TTTT-TTTTCGATTTC
21284770 TTTTTTTTCGA
1 TTTTTTTTCGA
21284781 AACTACAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 11 0.46
16 13 0.54
ACGTcount: A:0.10, C:0.12, G:0.05, T:0.74
Consensus pattern (15 bp):
TTTTTTTTCGATTTC
Found at i:21288526 original size:11 final size:10
Alignment explanation
Indices: 21288479--21288540 Score: 52
Period size: 10 Copynumber: 5.9 Consensus size: 10
21288469 TTTGAACCAT
*
21288479 TACCAATTCG
1 TACCAATTCA
*
21288489 TACCAAATACCA
1 TACC-AAT-TCA
*
21288501 TACCATTTCA
1 TACCAATTCA
21288511 TACCAATTCTA
1 TACCAATTC-A
* *
21288522 TACCATTTCG
1 TACCAATTCA
21288532 TACCAATTC
1 TACCAATTC
21288541 CCAAATACCA
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
10 22 0.54
11 14 0.34
12 5 0.12
ACGTcount: A:0.34, C:0.31, G:0.03, T:0.32
Consensus pattern (10 bp):
TACCAATTCA
Found at i:21288526 original size:21 final size:21
Alignment explanation
Indices: 21288500--21288540 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
21288490 ACCAAATACC
21288500 ATACCATTTCATACCAATTCT
1 ATACCATTTCATACCAATTCT
*
21288521 ATACCATTTCGTACCAATTC
1 ATACCATTTCATACCAATTC
21288541 CCAAATACCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.32, C:0.29, G:0.02, T:0.37
Consensus pattern (21 bp):
ATACCATTTCATACCAATTCT
Found at i:21289311 original size:26 final size:27
Alignment explanation
Indices: 21289257--21289322 Score: 75
Period size: 26 Copynumber: 2.6 Consensus size: 27
21289247 TATTATTTGT
* * *
21289257 TTTAAATTG-GTCT-TAGTTTAGACAC
1 TTTAAATTGAGTCTATTGTTTAGAAAA
*
21289282 TTT-AATTGTGTCTATTGTTTAGAAAA
1 TTTAAATTGAGTCTATTGTTTAGAAAA
21289308 TTTAAATTGAGTCTA
1 TTTAAATTGAGTCTA
21289323 AATTAAGTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
24 5 0.15
25 7 0.21
26 12 0.35
27 10 0.29
ACGTcount: A:0.30, C:0.08, G:0.15, T:0.47
Consensus pattern (27 bp):
TTTAAATTGAGTCTATTGTTTAGAAAA
Found at i:21292945 original size:12 final size:12
Alignment explanation
Indices: 21292924--21292968 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
21292914 TTACTTAGTT
*
21292924 TAAATTTTTATG
1 TAAATATTTATG
*
21292936 TAAATATTTAGTT
1 TAAATATTTA-TG
*
21292949 TAAATTTTTATG
1 TAAATATTTATG
21292961 TAAATATT
1 TAAATATT
21292969 CAGTCCAAGA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
12 17 0.63
13 10 0.37
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.56
Consensus pattern (12 bp):
TAAATATTTATG
Found at i:21292958 original size:13 final size:13
Alignment explanation
Indices: 21292918--21292958 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
21292908 ATTTATTTAC
21292918 TTAGTTTAAATTT
1 TTAGTTTAAATTT
* *
21292931 TTA-TGTAAATAT
1 TTAGTTTAAATTT
21292943 TTAGTTTAAATTT
1 TTAGTTTAAATTT
21292956 TTA
1 TTA
21292959 TGTAAATATT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
12 10 0.43
13 13 0.57
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (13 bp):
TTAGTTTAAATTT
Found at i:21292967 original size:25 final size:25
Alignment explanation
Indices: 21292918--21292968 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
21292908 ATTTATTTAC
21292918 TTAGTTTAAATTTTTATGTAAATAT
1 TTAGTTTAAATTTTTATGTAAATAT
21292943 TTAGTTTAAATTTTTATGTAAATAT
1 TTAGTTTAAATTTTTATGTAAATAT
21292968 T
1 T
21292969 CAGTCCAAGA
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:0.35, C:0.00, G:0.08, T:0.57
Consensus pattern (25 bp):
TTAGTTTAAATTTTTATGTAAATAT
Found at i:21293815 original size:15 final size:16
Alignment explanation
Indices: 21293795--21293827 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
21293785 AACGGTGAGA
21293795 TTTGTTAAT-TTTGTT
1 TTTGTTAATGTTTGTT
*
21293810 TTTGTTAGTGTTTGTT
1 TTTGTTAATGTTTGTT
21293826 TT
1 TT
21293828 GCAGGTATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.09, C:0.00, G:0.18, T:0.73
Consensus pattern (16 bp):
TTTGTTAATGTTTGTT
Found at i:21298481 original size:11 final size:11
Alignment explanation
Indices: 21298465--21298498 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
21298455 ATTGGAGTAA
21298465 CAAAAAAAAAT
1 CAAAAAAAAAT
21298476 CAAAAAAAAATT
1 CAAAAAAAAA-T
*
21298488 CGAAAAAAAAT
1 CAAAAAAAAAT
21298499 TGATTGAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.76, C:0.09, G:0.03, T:0.12
Consensus pattern (11 bp):
CAAAAAAAAAT
Found at i:21298520 original size:11 final size:12
Alignment explanation
Indices: 21298465--21298525 Score: 70
Period size: 12 Copynumber: 4.8 Consensus size: 12
21298455 ATTGGAGTAA
21298465 CAAAAAAAAA-T
1 CAAAAAAAAATT
21298476 CAAAAAAAAATT
1 CAAAAAAAAATT
21298488 CGAAAAAAAATTGATT
1 C-AAAAAAAA---ATT
*
21298504 GAAAAAAAAATT
1 CAAAAAAAAATT
21298516 CAAAAAAAAA
1 CAAAAAAAAA
21298526 AGTGAAAAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 9
0.80 0.04 0.17
Matches are distributed among these distances:
11 10 0.23
12 14 0.33
13 8 0.19
15 8 0.19
16 3 0.07
ACGTcount: A:0.74, C:0.07, G:0.05, T:0.15
Consensus pattern (12 bp):
CAAAAAAAAATT
Found at i:21298533 original size:12 final size:12
Alignment explanation
Indices: 21298466--21298537 Score: 65
Period size: 13 Copynumber: 5.7 Consensus size: 12
21298456 TTGGAGTAAC
*
21298466 AAAAAAAAA-TC
1 AAAAAAAAATTG
21298477 AAAAAAAAATTCG
1 AAAAAAAAATT-G
21298490 AAAAAAAATTGATTG
1 AAAAAAAA---ATTG
*
21298505 AAAAAAAAATTCA
1 AAAAAAAAATT-G
*
21298518 AAAAAAAAAGTG
1 AAAAAAAAATTG
21298530 AAAAAAAA
1 AAAAAAAA
21298538 TCGAGCAAAA
Statistics
Matches: 51, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
11 9 0.18
12 12 0.24
13 18 0.35
15 9 0.18
16 3 0.06
ACGTcount: A:0.75, C:0.04, G:0.07, T:0.14
Consensus pattern (12 bp):
AAAAAAAAATTG
Found at i:21298536 original size:28 final size:28
Alignment explanation
Indices: 21298477--21298537 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 28
21298467 AAAAAAAATC
* * **
21298477 AAAAAAAAATTCGAAAAAAAATTGATTG
1 AAAAAAAAATTCAAAAAAAAAGTGATAA
21298505 AAAAAAAAATTCAAAAAAAAAAGTGA-AA
1 AAAAAAAAATTC-AAAAAAAAAGTGATAA
21298533 AAAAA
1 AAAAA
21298538 TCGAGCAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 17 0.61
29 11 0.39
ACGTcount: A:0.74, C:0.03, G:0.08, T:0.15
Consensus pattern (28 bp):
AAAAAAAAATTCAAAAAAAAAGTGATAA
Found at i:21298547 original size:14 final size:14
Alignment explanation
Indices: 21298530--21298568 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 14
21298520 AAAAAAAGTG
21298530 AAAAAAAATCGAGC
1 AAAAAAAATCGAGC
21298544 AAAAAAAAGGT-GAGC
1 AAAAAAAA--TCGAGC
21298559 AAAAAAAATC
1 AAAAAAAATC
21298569 AAGTTAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
13 1 0.05
14 8 0.36
15 12 0.55
16 1 0.05
ACGTcount: A:0.67, C:0.10, G:0.15, T:0.08
Consensus pattern (14 bp):
AAAAAAAATCGAGC
Found at i:21298549 original size:40 final size:39
Alignment explanation
Indices: 21298466--21298551 Score: 104
Period size: 40 Copynumber: 2.2 Consensus size: 39
21298456 TTGGAGTAAC
* *
21298466 AAAAAAAAATCAAAAAAAAATTCGAAAAAAAATTGATTG-A
1 AAAAAAAAATCAAAAAAAAAGTCGAAAAAAAATCGA--GCA
*
21298506 AAAAAAAATTCAAAAAAAAAAGT-GAAAAAAAATCGAGCA
1 AAAAAAAAATC-AAAAAAAAAGTCGAAAAAAAATCGAGCA
21298545 AAAAAAA
1 AAAAAAA
21298552 GGTGAGCAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
38 1 0.02
39 8 0.20
40 22 0.54
41 10 0.24
ACGTcount: A:0.73, C:0.06, G:0.08, T:0.13
Consensus pattern (39 bp):
AAAAAAAAATCAAAAAAAAAGTCGAAAAAAAATCGAGCA
Found at i:21298578 original size:30 final size:29
Alignment explanation
Indices: 21298518--21298586 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 29
21298508 AAAAAATTCA
*
21298518 AAAAAAAAAGT--G-AAAAAAAATCGAGC
1 AAAAAAAAAGTGAGCAAAAAAAATCAAGC
* *
21298544 AAAAAAAAGGTGAGCAAAAAAAATCAAGTT
1 AAAAAAAAAGTGAGCAAAAAAAATCAAG-C
21298574 AAAAAAAAAGTGA
1 AAAAAAAAAGTGA
21298587 AAAGTCTTGC
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
26 10 0.29
28 1 0.03
29 12 0.34
30 12 0.34
ACGTcount: A:0.68, C:0.06, G:0.16, T:0.10
Consensus pattern (29 bp):
AAAAAAAAAGTGAGCAAAAAAAATCAAGC
Found at i:21299482 original size:18 final size:18
Alignment explanation
Indices: 21299461--21299495 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
21299451 AGAAAAGAAA
21299461 ATTGA-AAAAGAAATTGAG
1 ATTGAGAAAA-AAATTGAG
21299479 ATTGAGAAAAAAATTGA
1 ATTGAGAAAAAAATTGA
21299496 AAAAGAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.57, C:0.00, G:0.20, T:0.23
Consensus pattern (18 bp):
ATTGAGAAAAAAATTGAG
Found at i:21304609 original size:13 final size:13
Alignment explanation
Indices: 21304566--21304614 Score: 57
Period size: 13 Copynumber: 3.7 Consensus size: 13
21304556 GTAGCTTCGA
21304566 AAAAAAAAAGTT-
1 AAAAAAAAAGTTC
21304578 AAAAAAAAAGTTTC
1 AAAAAAAAAG-TTC
21304592 GAAAAAAAAA-TTGC
1 -AAAAAAAAAGTT-C
21304606 AAAAAAAAA
1 AAAAAAAAA
21304615 AAATTGCATA
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
12 10 0.30
13 13 0.39
14 1 0.03
15 9 0.27
ACGTcount: A:0.73, C:0.04, G:0.08, T:0.14
Consensus pattern (13 bp):
AAAAAAAAAGTTC
Found at i:21304614 original size:14 final size:13
Alignment explanation
Indices: 21304565--21304615 Score: 50
Period size: 14 Copynumber: 3.8 Consensus size: 13
21304555 CGTAGCTTCG
21304565 AAAAAAAAAAGTT-
1 AAAAAAAAAA-TTC
*
21304578 AAAAAAAAAGTTTC
1 AAAAAAAAA-ATTC
*
21304592 GAAAAAAAAATTGC
1 AAAAAAAAAATT-C
21304606 AAAAAAAAAA
1 AAAAAAAAAA
21304616 AATTGCATAC
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
13 13 0.42
14 18 0.58
ACGTcount: A:0.75, C:0.04, G:0.08, T:0.14
Consensus pattern (13 bp):
AAAAAAAAAATTC
Found at i:21306898 original size:24 final size:25
Alignment explanation
Indices: 21306871--21306924 Score: 60
Period size: 23 Copynumber: 2.2 Consensus size: 25
21306861 ATGAGTGATA
*
21306871 AAAAAAGAGA-GAGTGATTCAAAA-G
1 AAAAAAGAAACGAGTGA-TCAAAATG
*
21306895 -AAAAAGAAACGAGTGATGAAAATG
1 AAAAAAGAAACGAGTGATCAAAATG
21306919 AAAAAA
1 AAAAAA
21306925 AGAATTTGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
23 13 0.52
24 7 0.28
25 5 0.20
ACGTcount: A:0.63, C:0.04, G:0.22, T:0.11
Consensus pattern (25 bp):
AAAAAAGAAACGAGTGATCAAAATG
Found at i:21315109 original size:6 final size:6
Alignment explanation
Indices: 21315098--21315155 Score: 62
Period size: 6 Copynumber: 9.7 Consensus size: 6
21315088 TTGTAGTGAA
* ** ** *
21315098 AAAAAG AAAAAG AAAACG AAAAAG AAAAAG AAATCG AAAAAG TGAGAG
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG
21315146 AAAAAG AAAA
1 AAAAAG AAAA
21315156 TGAAGAAAAG
Statistics
Matches: 40, Mismatches: 12, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.74, C:0.03, G:0.19, T:0.03
Consensus pattern (6 bp):
AAAAAG
Found at i:21315121 original size:18 final size:18
Alignment explanation
Indices: 21315098--21315139 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
21315088 TTGTAGTGAA
21315098 AAAAAGAAAAAGAAAACG
1 AAAAAGAAAAAGAAAACG
*
21315116 AAAAAGAAAAAGAAATCG
1 AAAAAGAAAAAGAAAACG
21315134 AAAAAG
1 AAAAAG
21315140 TGAGAGAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.76, C:0.05, G:0.17, T:0.02
Consensus pattern (18 bp):
AAAAAGAAAAAGAAAACG
Found at i:21315184 original size:12 final size:12
Alignment explanation
Indices: 21315098--21315200 Score: 63
Period size: 12 Copynumber: 8.6 Consensus size: 12
21315088 TTGTAGTGAA
*
21315098 AAAAAGAAAAAG
1 AAAAAGAAAATG
* *
21315110 AAAACGAAAAAG
1 AAAAAGAAAATG
21315122 AAAAAG-AAATCG
1 AAAAAGAAAAT-G
* *
21315134 AAAAAGTGAGA-G
1 AAAAAG-AAAATG
21315146 AAAAAGAAAATG
1 AAAAAGAAAATG
*
21315158 AAGAAAAGAACATTG
1 -A-AAAAGAA-AATG
*
21315173 AAAAAGAAATTG
1 AAAAAGAAAATG
21315185 --AAAG-AAATG
1 AAAAAGAAAATG
21315194 AAAAAGA
1 AAAAAGA
21315201 TGAAGATGAA
Statistics
Matches: 73, Mismatches: 8, Indels: 20
0.72 0.08 0.20
Matches are distributed among these distances:
9 4 0.05
10 4 0.05
11 9 0.12
12 35 0.48
13 8 0.11
14 10 0.14
15 3 0.04
ACGTcount: A:0.70, C:0.03, G:0.19, T:0.08
Consensus pattern (12 bp):
AAAAAGAAAATG
Found at i:21322029 original size:17 final size:17
Alignment explanation
Indices: 21322003--21322035 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
21321993 TTTAGAATTG
21322003 TAATTGCAATTTTTTTT
1 TAATTGCAATTTTTTTT
*
21322020 TAATTTCAATTTTTTT
1 TAATTGCAATTTTTTT
21322036 AATTTTAGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.06, G:0.03, T:0.67
Consensus pattern (17 bp):
TAATTGCAATTTTTTTT
Found at i:21323791 original size:21 final size:21
Alignment explanation
Indices: 21323746--21323808 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
21323736 TTTGAACCAT
* *
21323746 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
21323768 TACCATTTCGTACCAATTCCA
1 TACCATTTCGTACCAATTCCA
* *
21323789 TACTATTTCGAACCAATTCC
1 TACCATTTCGTACCAATTCC
21323809 CAAATACCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 24 0.65
22 13 0.35
ACGTcount: A:0.33, C:0.32, G:0.05, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:21324128 original size:14 final size:14
Alignment explanation
Indices: 21324106--21324144 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
21324096 AAGTCAAAAT
*
21324106 AAAAAAAAAAATTG
1 AAAAGAAAAAATTG
*
21324120 AAAGGAAAAAATTG
1 AAAAGAAAAAATTG
21324134 AAAAGAAAAAA
1 AAAAGAAAAAA
21324145 AATTGCATAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.13, T:0.10
Consensus pattern (14 bp):
AAAAGAAAAAATTG
Found at i:21324128 original size:15 final size:15
Alignment explanation
Indices: 21324106--21324145 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
21324096 AAGTCAAAAT
21324106 AAAA-AAAAAAATTG
1 AAAAGAAAAAAATTG
*
21324120 -AAAGGAAAAAATTG
1 AAAAGAAAAAAATTG
21324134 AAAAGAAAAAAA
1 AAAAGAAAAAAA
21324146 ATTGCATACG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
13 3 0.14
14 9 0.41
15 10 0.45
ACGTcount: A:0.78, C:0.00, G:0.12, T:0.10
Consensus pattern (15 bp):
AAAAGAAAAAAATTG
Found at i:21324607 original size:14 final size:14
Alignment explanation
Indices: 21324588--21324614 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
21324578 TGAGAGATTT
21324588 TGTGAGGTTTTTAC
1 TGTGAGGTTTTTAC
21324602 TGTGAGGTTTTTA
1 TGTGAGGTTTTTA
21324615 TTTACATGTC
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:0.15, C:0.04, G:0.30, T:0.52
Consensus pattern (14 bp):
TGTGAGGTTTTTAC
Found at i:21327877 original size:20 final size:20
Alignment explanation
Indices: 21327852--21327896 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
21327842 GCGAAAATAC
*
21327852 AAAAGAAAAGAAAAATGAAA
1 AAAAGAAAAGAAAAATCAAA
*
21327872 AAAAG-AAAGAAAATTCAAA
1 AAAAGAAAAGAAAAATCAAA
21327891 AAAAGA
1 AAAAGA
21327897 GAATGAAAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 17 0.77
20 5 0.23
ACGTcount: A:0.78, C:0.02, G:0.13, T:0.07
Consensus pattern (20 bp):
AAAAGAAAAGAAAAATCAAA
Found at i:21333807 original size:22 final size:22
Alignment explanation
Indices: 21333779--21333822 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
21333769 TTTTGAACCA
21333779 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
21333801 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
21333823 AAATACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.25, C:0.36, G:0.05, T:0.34
Consensus pattern (22 bp):
TTACCATTTCGTACCAAATCCC
Found at i:21336442 original size:12 final size:11
Alignment explanation
Indices: 21336422--21336452 Score: 53
Period size: 12 Copynumber: 2.7 Consensus size: 11
21336412 TAGTAGTTTC
21336422 TTCAAAAAAAA
1 TTCAAAAAAAA
21336433 TTCGAAAAAAAA
1 TTC-AAAAAAAA
21336445 TTCAAAAA
1 TTCAAAAA
21336453 TTTTTTTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 8 0.42
12 11 0.58
ACGTcount: A:0.68, C:0.10, G:0.03, T:0.19
Consensus pattern (11 bp):
TTCAAAAAAAA
Found at i:21337919 original size:46 final size:46
Alignment explanation
Indices: 21337866--21337959 Score: 163
Period size: 46 Copynumber: 2.0 Consensus size: 46
21337856 CAAAGAAAAG
*
21337866 ACCTCGACCCACTATCAA-GAATGATAGGAACCTTGGTATATGATGA
1 ACCTCGACCCACTATCAATG-ATGATAAGAACCTTGGTATATGATGA
21337912 ACCTCGACCCACTATCAATGATGATAAGAACCTTGGTATATGATGA
1 ACCTCGACCCACTATCAATGATGATAAGAACCTTGGTATATGATGA
21337958 AC
1 AC
21337960 GCCACACTAT
Statistics
Matches: 46, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
46 45 0.98
47 1 0.02
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.24
Consensus pattern (46 bp):
ACCTCGACCCACTATCAATGATGATAAGAACCTTGGTATATGATGA
Found at i:21343435 original size:30 final size:30
Alignment explanation
Indices: 21343401--21343497 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
21343391 AGCTCACTCC
21343401 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
21343431 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
21343461 CAGCTCAACTTTAGCTCACGAGCTAAAACT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
21343491 TAGCTCA
1 TAGCTCA
21343498 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:21346204 original size:37 final size:37
Alignment explanation
Indices: 21346153--21346223 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
21346143 CATTGTTGTA
21346153 AAGAGAAAACAAAGAAAA-GAAAAGAAAAAGAAAAAGC
1 AAGAGAAAACAAAGAAAATG-AAAGAAAAAGAAAAAGC
*
21346190 AAGAGAAGAA-AAAGAAAATGAAATAAAAAGAAAA
1 AAGAGAA-AACAAAGAAAATGAAAGAAAAAGAAAA
21346224 GAGAGGCAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 28 0.90
38 3 0.10
ACGTcount: A:0.76, C:0.03, G:0.18, T:0.03
Consensus pattern (37 bp):
AAGAGAAAACAAAGAAAATGAAAGAAAAAGAAAAAGC
Found at i:21346223 original size:6 final size:6
Alignment explanation
Indices: 21346163--21346212 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
21346153 AAGAGAAAAC
*
21346163 AAAG-A AAAG-A AAAGAA AAAGAA AAAGCAA GAGAAGAA AAAGAA AATGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAG-AA -A-AAGAA AAAGAA AAAGAA
21346212 A
1 A
21346213 TAAAAAGAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
5 9 0.22
6 22 0.55
7 3 0.08
8 3 0.08
9 3 0.08
ACGTcount: A:0.76, C:0.02, G:0.20, T:0.02
Consensus pattern (6 bp):
AAAGAA
Found at i:21346305 original size:11 final size:12
Alignment explanation
Indices: 21346273--21346303 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
21346263 TTGAGAGAAC
21346273 TTGAAAAAGCCT
1 TTGAAAAAGCCT
21346285 TTGAAAAAGCCT
1 TTGAAAAAGCCT
21346297 TTGAAAA
1 TTGAAAA
21346304 GCAAAAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (12 bp):
TTGAAAAAGCCT
Done.