Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032253.1 Gossypioides kirkii chromosome KI_11
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: 55708359
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 61 of 182
Found at i:19759109 original size:21 final size:21
Alignment explanation
Indices: 19759070--19759109 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
19759060 GCAATCTATA
*
19759070 GATTTTCAAAAGCAAACTGTG
1 GATTTTCAAAAGAAAACTGTG
19759091 GATTTTCAAAAGAAAACTG
1 GATTTTCAAAAGAAAACTG
19759110 AGGCATCTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.28
Consensus pattern (21 bp):
GATTTTCAAAAGAAAACTGTG
Found at i:19760298 original size:5 final size:5
Alignment explanation
Indices: 19760281--19760340 Score: 51
Period size: 5 Copynumber: 13.0 Consensus size: 5
19760271 GGCAACCCAA
* *
19760281 TTATT TT-TT TTATT TTATT TT-TAT TT-TT CTATC TTATT TTA-T TTA-T
1 TTATT TTATT TTATT TTATT TTAT-T TTATT TTATT TTATT TTATT TTATT
19760327 TTA-T TTATT TTATT
1 TTATT TTATT TTATT
19760341 CCAGGAAACT
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
4 19 0.40
5 28 0.60
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.78
Consensus pattern (5 bp):
TTATT
Found at i:19768096 original size:17 final size:18
Alignment explanation
Indices: 19768057--19768098 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
19768047 ATGCATCTCA
*
19768057 TTTAGTTGTCAATGCATT
1 TTTATTTGTCAATGCATT
*
19768075 TTTATTTGTCACTGCA-T
1 TTTATTTGTCAATGCATT
19768092 TTTATTT
1 TTTATTT
19768099 ATTAGTACAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.19, C:0.12, G:0.12, T:0.57
Consensus pattern (18 bp):
TTTATTTGTCAATGCATT
Found at i:19776309 original size:17 final size:17
Alignment explanation
Indices: 19776287--19776319 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
19776277 AATGATTTTT
19776287 TAATTTT-TTGAAAATAA
1 TAATTTTATT-AAAATAA
19776304 TAATTTTATTAAAATA
1 TAATTTTATTAAAATA
19776320 TTTTTAAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 13 0.87
18 2 0.13
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (17 bp):
TAATTTTATTAAAATAA
Found at i:19782179 original size:28 final size:28
Alignment explanation
Indices: 19782119--19782179 Score: 72
Period size: 27 Copynumber: 2.2 Consensus size: 28
19782109 GTGTTCGTGT
*
19782119 TTTTATGGTTTGGGGTTATGAGTTTGGG
1 TTTTATGGTTTGGGGTTATGAATTTGGG
*
19782147 ATTTAT-GTTTGGGGTCTA-GAATTTGTGG
1 TTTTATGGTTTGGGGT-TATGAATTTG-GG
19782175 TTTTA
1 TTTTA
19782180 GATTTAAGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
27 15 0.54
28 13 0.46
ACGTcount: A:0.15, C:0.02, G:0.33, T:0.51
Consensus pattern (28 bp):
TTTTATGGTTTGGGGTTATGAATTTGGG
Found at i:19782711 original size:14 final size:14
Alignment explanation
Indices: 19782688--19782726 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
19782678 AACACTTAGG
19782688 AAAGTGTCGGCCCA
1 AAAGTGTCGGCCCA
* *
19782702 AAAGTATCGGTCCA
1 AAAGTGTCGGCCCA
19782716 AAAGTGTCGGC
1 AAAGTGTCGGC
19782727 ATAGTGTTGG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.23, G:0.28, T:0.18
Consensus pattern (14 bp):
AAAGTGTCGGCCCA
Found at i:19788732 original size:27 final size:27
Alignment explanation
Indices: 19788683--19788734 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
19788673 ACCAATTTGA
* *
19788683 CAAAAAAAGATTAAGTGTGAAAGTGTT
1 CAAAAAAACATTAAGGGTGAAAGTGTT
19788710 CAAAAAAACATTAAGGGCT-AAAGTG
1 CAAAAAAACATTAAGGG-TGAAAGTG
19788735 ACCCAACATC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 21 0.95
28 1 0.05
ACGTcount: A:0.50, C:0.08, G:0.21, T:0.21
Consensus pattern (27 bp):
CAAAAAAACATTAAGGGTGAAAGTGTT
Found at i:19789661 original size:27 final size:27
Alignment explanation
Indices: 19789631--19789717 Score: 75
Period size: 27 Copynumber: 3.2 Consensus size: 27
19789621 GACTTCTCTG
* *
19789631 TGTTTAACGTCCCGTCGGATTATCCCA
1 TGTTTAACGTCCCATCGGACTATCCCA
* * * *
19789658 TGTTTAATGTCTCATTGGACTATCCCG
1 TGTTTAACGTCCCATCGGACTATCCCA
** * * *
19789685 TGTTTAATATCCTATCAGACTATCCCG
1 TGTTTAACGTCCCATCGGACTATCCCA
19789712 TGTTTA
1 TGTTTA
19789718 TCATCCTGTC
Statistics
Matches: 49, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 49 1.00
ACGTcount: A:0.21, C:0.24, G:0.16, T:0.39
Consensus pattern (27 bp):
TGTTTAACGTCCCATCGGACTATCCCA
Found at i:19789938 original size:45 final size:45
Alignment explanation
Indices: 19789874--19789979 Score: 131
Period size: 45 Copynumber: 2.4 Consensus size: 45
19789864 CGTGCTTTCA
* * **
19789874 CATGATGCCATAGCGTCTTTCAATTAAGGTCTTACTCATTATTAC
1 CATGATGTCATAGCATCTTTCAACCAAGGTCTTACTCATTATTAC
* * * *
19789919 CATGATGTCATAGCATCTTTCAACCATGGTCTTACTTATTTTTAT
1 CATGATGTCATAGCATCTTTCAACCAAGGTCTTACTCATTATTAC
*
19789964 AATGATGTCATAGCAT
1 CATGATGTCATAGCAT
19789980 AGTTCATCTA
Statistics
Matches: 52, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
45 52 1.00
ACGTcount: A:0.27, C:0.20, G:0.13, T:0.40
Consensus pattern (45 bp):
CATGATGTCATAGCATCTTTCAACCAAGGTCTTACTCATTATTAC
Found at i:19789993 original size:45 final size:45
Alignment explanation
Indices: 19789901--19789998 Score: 124
Period size: 45 Copynumber: 2.2 Consensus size: 45
19789891 TTTCAATTAA
* **
19789901 GGTCTTACTCATTATTACCATGATGTCATAGCATCTTTCAACCAT
1 GGTCTTACTCATTATTACAATGATGTCATAGCATAGTTCAACCAT
* * * * *
19789946 GGTCTTACTTATTTTTATAATGATGTCATAGCATAGTTCATCTAT
1 GGTCTTACTCATTATTACAATGATGTCATAGCATAGTTCAACCAT
19789991 GGTCTTAC
1 GGTCTTAC
19789999 ACATCAGTTT
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.26, C:0.19, G:0.13, T:0.42
Consensus pattern (45 bp):
GGTCTTACTCATTATTACAATGATGTCATAGCATAGTTCAACCAT
Found at i:19798458 original size:29 final size:29
Alignment explanation
Indices: 19798425--19798487 Score: 126
Period size: 29 Copynumber: 2.2 Consensus size: 29
19798415 TCATGCTGAC
19798425 GTAGCCATTAAAGGACTAATAGCGTTGAT
1 GTAGCCATTAAAGGACTAATAGCGTTGAT
19798454 GTAGCCATTAAAGGACTAATAGCGTTGAT
1 GTAGCCATTAAAGGACTAATAGCGTTGAT
19798483 GTAGC
1 GTAGC
19798488 AAGTTTTATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.33, C:0.14, G:0.25, T:0.27
Consensus pattern (29 bp):
GTAGCCATTAAAGGACTAATAGCGTTGAT
Found at i:19800252 original size:16 final size:16
Alignment explanation
Indices: 19800231--19800269 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
19800221 TGTCAATACG
19800231 CTAAAAGTGCTTCCAA
1 CTAAAAGTGCTTCCAA
*
19800247 CTAAAAATGCTTCCAA
1 CTAAAAGTGCTTCCAA
*
19800263 CTGAAAG
1 CTAAAAG
19800270 CCTTTTTTTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.41, C:0.23, G:0.13, T:0.23
Consensus pattern (16 bp):
CTAAAAGTGCTTCCAA
Found at i:19805944 original size:16 final size:17
Alignment explanation
Indices: 19805923--19805969 Score: 62
Period size: 16 Copynumber: 2.8 Consensus size: 17
19805913 TTATCAAAAA
19805923 TTTCTTTCTTTTTCT-T
1 TTTCTTTCTTTTTCTAT
*
19805939 TTTCTTCCTTTTTCTCAT
1 TTTCTTTCTTTTTCT-AT
19805957 TTT-TTTCTTTTTC
1 TTTCTTTCTTTTTC
19805970 AAATGACTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
16 14 0.52
17 9 0.33
18 4 0.15
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (17 bp):
TTTCTTTCTTTTTCTAT
Found at i:19806573 original size:17 final size:18
Alignment explanation
Indices: 19806532--19806573 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
19806522 TTAACAAAAG
*
19806532 GAATGTAGTGACAAAACA
1 GAATGCAGTGACAAAACA
* *
19806550 AAATGCAGTGACAATA-A
1 GAATGCAGTGACAAAACA
19806567 GAATGCA
1 GAATGCA
19806574 TGAAAACTAT
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.50, C:0.12, G:0.21, T:0.17
Consensus pattern (18 bp):
GAATGCAGTGACAAAACA
Found at i:19808866 original size:20 final size:21
Alignment explanation
Indices: 19808841--19808879 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
19808831 GCAAGGAATT
19808841 TGAAAC-AACAAAAGTAAAAG
1 TGAAACAAACAAAAGTAAAAG
*
19808861 TGAAACAAATAAAAGTAAA
1 TGAAACAAACAAAAGTAAA
19808880 TAGAAAAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.67, C:0.08, G:0.13, T:0.13
Consensus pattern (21 bp):
TGAAACAAACAAAAGTAAAAG
Found at i:19816536 original size:20 final size:22
Alignment explanation
Indices: 19816513--19816562 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
19816503 CAAATCATTC
19816513 GAAAAGG-A-ACAAAATCAAGA
1 GAAAAGGTACACAAAATCAAGA
19816533 G-AAAGGTATCACAAAATCAAGA
1 GAAAAGGTA-CACAAAATCAAGA
19816555 G-AAAGGTA
1 GAAAAGGTA
19816563 TCTCTAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
19 5 0.19
20 2 0.07
22 20 0.74
ACGTcount: A:0.58, C:0.10, G:0.22, T:0.10
Consensus pattern (22 bp):
GAAAAGGTACACAAAATCAAGA
Found at i:19816549 original size:22 final size:22
Alignment explanation
Indices: 19816521--19816564 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
19816511 TCGAAAAGGA
19816521 ACAAAATCAAGAGAAAGGTATC
1 ACAAAATCAAGAGAAAGGTATC
19816543 ACAAAATCAAGAGAAAGGTATC
1 ACAAAATCAAGAGAAAGGTATC
19816565 TCTAAAATTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.55, C:0.14, G:0.18, T:0.14
Consensus pattern (22 bp):
ACAAAATCAAGAGAAAGGTATC
Found at i:19817876 original size:80 final size:80
Alignment explanation
Indices: 19817743--19817893 Score: 212
Period size: 80 Copynumber: 1.9 Consensus size: 80
19817733 GGGCACAAAC
* * * * * *
19817743 CGTTGGTTAATCCAACTATAGCTGAGCTAATTTATCGCGGTTTGTTCGTTAGGCACTGGGTGCCA
1 CGTTGGTTAATCCAACTAGAGCTGAGCTAACTTATCGCGGTCTATTCGCTAGGCACTAGGTGCCA
*
19817808 TGAATTGACGAAATT
66 GGAATTGACGAAATT
* * *
19817823 CGTTGGTTAATCCAACTAGAGCTGGGCTTACTTATTGCGGTCTATTCGCTAGGCACTAGGTGCCA
1 CGTTGGTTAATCCAACTAGAGCTGAGCTAACTTATCGCGGTCTATTCGCTAGGCACTAGGTGCCA
19817888 GGAATT
66 GGAATT
19817894 TACGGTTTTG
Statistics
Matches: 61, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
80 61 1.00
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.32
Consensus pattern (80 bp):
CGTTGGTTAATCCAACTAGAGCTGAGCTAACTTATCGCGGTCTATTCGCTAGGCACTAGGTGCCA
GGAATTGACGAAATT
Found at i:19825013 original size:80 final size:80
Alignment explanation
Indices: 19824880--19825033 Score: 202
Period size: 80 Copynumber: 1.9 Consensus size: 80
19824870 GGGCGCAAAC
* * * * *
19824880 CGTTGGTTAATCCAACTAGAGTTGAGCTCATTTATTGCGGTTTGTCCGCTAGGCACTAGGTGCAA
1 CGTTGGTTAATCCAAATAGAGTAGAGCTCACTTATTGCGGTCTATCCGCTAGGCACTAGGTGCAA
*
19824945 TGAATTGACAGAATT
66 GGAATTGACAGAATT
* * * *
19824960 CGTTGGTTAATCCAAATAGAGCTAG-GCTTACTTATTGCGGTCTATCCGTTAGGCACTGGGTGCC
1 CGTTGGTTAATCCAAATAGAG-TAGAGCTCACTTATTGCGGTCTATCCGCTAGGCACTAGGTGCA
19825024 AGGAATTGAC
65 AGGAATTGAC
19825034 GGATTTGGTT
Statistics
Matches: 63, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
80 61 0.97
81 2 0.03
ACGTcount: A:0.24, C:0.19, G:0.26, T:0.31
Consensus pattern (80 bp):
CGTTGGTTAATCCAAATAGAGTAGAGCTCACTTATTGCGGTCTATCCGCTAGGCACTAGGTGCAA
GGAATTGACAGAATT
Found at i:19854423 original size:248 final size:248
Alignment explanation
Indices: 19853985--19854481 Score: 827
Period size: 248 Copynumber: 2.0 Consensus size: 248
19853975 CTATTCGTAC
*
19853985 TATAATCCCTAAAGCAAGTACTAATTACTTTTTTTCTTTGCAGGAATCTAATTTACTATCGCGTT
1 TATAATCCCTAAAGCAAGTACTAATTACTTTTATTCTTTGCAGGAATCTAATTTACTATCGCGTT
* * * *
19854050 ACGCCTCCTTTGGGTACGATCCTCAGAATAGTACCAAGTGTTTCGTTATACATACTATATTTACA
66 ACGCCTCCTTTGGGTACGATCCTCAGAATACTACCAAGTGTTTCATTATACACAATATATTTACA
*
19854115 ACCTGACCCGTATACTTGCGAAAAGCCTAAAATCTACACCAAACAGGAGTACATTCGGGGGTGGT
131 ACCTGACCCGTATACTTGCGAAAAGCCTAAAATCTACACCAAACAGGAGTACATTCGGGGGCGGT
* *
19854180 CAAGTTGTTGGCA-CCGTTGTCGGGGAAGCAATGCTTTTTTAAATTTTATTCTT
196 CAAGTTATTGG-AGCCGTTGTCGGGGAAGCAATGCTTTATTAAATTTTATTCTT
*
19854233 TATAATCCCTAAAGCAAGTACTAATTACTTTTATTCTTTGCAGGAATCTAATTTACTATCGTGTT
1 TATAATCCCTAAAGCAAGTACTAATTACTTTTATTCTTTGCAGGAATCTAATTTACTATCGCGTT
** *
19854298 ACGCCTCCTTTGGGTAC-AGTCCTTGGAATACTACCAAGTGTTTCATTGTACACAATATATTTAC
66 ACGCCTCCTTTGGGTACGA-TCCTCAGAATACTACCAAGTGTTTCATTATACACAATATATTTAC
* *
19854362 AACTTGACCCGTATACTTGCGAAAAGCCTAAAATCTACACCGAACAGGAGTACATTCGGGGGCGG
130 AACCTGACCCGTATACTTGCGAAAAGCCTAAAATCTACACCAAACAGGAGTACATTCGGGGGCGG
*
19854427 TCAAGTTATTGGAGCTGTTGTCGGGGAAGCAATGCTTTATTAAATTTTATTCTT
195 TCAAGTTATTGGAGCCGTTGTCGGGGAAGCAATGCTTTATTAAATTTTATTCTT
19854481 T
1 T
19854482 CTTTATTAAT
Statistics
Matches: 232, Mismatches: 15, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
247 2 0.01
248 230 0.99
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (248 bp):
TATAATCCCTAAAGCAAGTACTAATTACTTTTATTCTTTGCAGGAATCTAATTTACTATCGCGTT
ACGCCTCCTTTGGGTACGATCCTCAGAATACTACCAAGTGTTTCATTATACACAATATATTTACA
ACCTGACCCGTATACTTGCGAAAAGCCTAAAATCTACACCAAACAGGAGTACATTCGGGGGCGGT
CAAGTTATTGGAGCCGTTGTCGGGGAAGCAATGCTTTATTAAATTTTATTCTT
Found at i:19860511 original size:13 final size:14
Alignment explanation
Indices: 19860482--19860511 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
19860472 TTCAGTACAT
19860482 TGACATTTAACCTC
1 TGACATTTAACCTC
19860496 TGACATTTAA-CTC
1 TGACATTTAACCTC
19860509 TGA
1 TGA
19860512 TTGCGTTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.30, C:0.23, G:0.10, T:0.37
Consensus pattern (14 bp):
TGACATTTAACCTC
Found at i:19861956 original size:21 final size:20
Alignment explanation
Indices: 19861916--19861958 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
19861906 GAGCTTGGAA
19861916 TTAATCGTTATTTTTAAGTT
1 TTAATCGTTATTTTTAAGTT
19861936 TTAATC-TTATTTTAGTAAGTT
1 TTAATCGTTATTTT--TAAGTT
19861957 TT
1 TT
19861959 GATAAAACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 7 0.33
20 6 0.29
21 8 0.38
ACGTcount: A:0.26, C:0.05, G:0.09, T:0.60
Consensus pattern (20 bp):
TTAATCGTTATTTTTAAGTT
Found at i:19865095 original size:28 final size:28
Alignment explanation
Indices: 19865054--19865118 Score: 85
Period size: 28 Copynumber: 2.3 Consensus size: 28
19865044 ATTACCGTAA
* *
19865054 ATGTGGAAGTCCGTTAGGACTGTATTAT
1 ATGTGGAAGCCCGTCAGGACTGTATTAT
* * *
19865082 ATGTGGAAGCCCGTCAGTATTGTCTTAT
1 ATGTGGAAGCCCGTCAGGACTGTATTAT
19865110 ATGTGGAAG
1 ATGTGGAAG
19865119 TTGTAAACTC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.25, C:0.12, G:0.29, T:0.34
Consensus pattern (28 bp):
ATGTGGAAGCCCGTCAGGACTGTATTAT
Found at i:19866774 original size:15 final size:15
Alignment explanation
Indices: 19866730--19866780 Score: 59
Period size: 15 Copynumber: 3.3 Consensus size: 15
19866720 ATTTGCATAC
19866730 TTAGATTAATTTGCA-
1 TTAGATTAA-TTGCAT
*
19866745 TTAGGGATCAATTGCAT
1 TTA--GATTAATTGCAT
19866762 TTAGATTAATTGCAT
1 TTAGATTAATTGCAT
19866777 TTAG
1 TTAG
19866781 TTTTAATCAT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
15 18 0.58
16 5 0.16
17 8 0.26
ACGTcount: A:0.31, C:0.08, G:0.18, T:0.43
Consensus pattern (15 bp):
TTAGATTAATTGCAT
Found at i:19871214 original size:17 final size:17
Alignment explanation
Indices: 19871159--19871218 Score: 66
Period size: 17 Copynumber: 3.5 Consensus size: 17
19871149 ACTAAACTCT
*
19871159 AATGACAAATAAAAATGC
1 AATGACAATTAAAAA-GC
** *
19871177 AATGACAATGCAAATGC
1 AATGACAATTAAAAAGC
*
19871194 AATGACAATTAAAAAGT
1 AATGACAATTAAAAAGC
19871211 AATGACAA
1 AATGACAA
19871219 CGAGAATGTG
Statistics
Matches: 34, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
17 23 0.68
18 11 0.32
ACGTcount: A:0.57, C:0.12, G:0.13, T:0.18
Consensus pattern (17 bp):
AATGACAATTAAAAAGC
Found at i:19885289 original size:21 final size:21
Alignment explanation
Indices: 19885263--19885310 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
19885253 ATGACCACCT
*
19885263 GAAGGAAAAGGAAAAAGAAGA
1 GAAGGAAAAAGAAAAAGAAGA
* *
19885284 GAAGGAAAAAGAGAATGAAGA
1 GAAGGAAAAAGAAAAAGAAGA
19885305 GAAGGA
1 GAAGGA
19885311 CCCTACCGAG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.62, C:0.00, G:0.35, T:0.02
Consensus pattern (21 bp):
GAAGGAAAAAGAAAAAGAAGA
Found at i:19886313 original size:16 final size:16
Alignment explanation
Indices: 19886292--19886322 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
19886282 AAAAAAATTG
*
19886292 AGAAAAAGGAAGAAAA
1 AGAAAAAGAAAGAAAA
19886308 AGAAAAAGAAAGAAA
1 AGAAAAAGAAAGAAA
19886323 TTTTTGATAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (16 bp):
AGAAAAAGAAAGAAAA
Found at i:19893434 original size:25 final size:25
Alignment explanation
Indices: 19893406--19893453 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
19893396 ACAGGTTATC
19893406 GCTCTTTCGAGCCAGACAGAATATT
1 GCTCTTTCGAGCCAGACAGAATATT
*
19893431 GCTCTTTTGAGCCAGACAGAATA
1 GCTCTTTCGAGCCAGACAGAATA
19893454 ACACTCTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.27
Consensus pattern (25 bp):
GCTCTTTCGAGCCAGACAGAATATT
Found at i:19893460 original size:25 final size:25
Alignment explanation
Indices: 19893407--19893471 Score: 76
Period size: 25 Copynumber: 2.6 Consensus size: 25
19893397 CAGGTTATCG
* ***
19893407 CTCTTTCGAGCCAGACAGAATATTG
1 CTCTTTTGAGCCAGACAGAATAACA
19893432 CTCTTTTGAGCCAGACAGAATAACA
1 CTCTTTTGAGCCAGACAGAATAACA
* *
19893457 CTCTTATGAACCAGA
1 CTCTTTTGAGCCAGA
19893472 ATCTAGAGTA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.26
Consensus pattern (25 bp):
CTCTTTTGAGCCAGACAGAATAACA
Found at i:19894885 original size:20 final size:20
Alignment explanation
Indices: 19894860--19894897 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
19894850 TCTTGTTAGT
*
19894860 CGGTAAGAGGTCATGGCCGA
1 CGGTAAGAGGTCACGGCCGA
19894880 CGGTAAGAGGTCACGGCC
1 CGGTAAGAGGTCACGGCC
19894898 TTCCAATAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.24, C:0.24, G:0.39, T:0.13
Consensus pattern (20 bp):
CGGTAAGAGGTCACGGCCGA
Found at i:19901920 original size:9 final size:9
Alignment explanation
Indices: 19901906--19901948 Score: 52
Period size: 9 Copynumber: 4.8 Consensus size: 9
19901896 CTTTCAGACC
19901906 CCTCTTCGT
1 CCTCTTCGT
*
19901915 CCTCTTTGT
1 CCTCTTCGT
19901924 CCTCTTCGT
1 CCTCTTCGT
*
19901933 TCTCTT-GT
1 CCTCTTCGT
19901941 CCTTCTTC
1 CC-TCTTC
19901949 ATTATCAATG
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
8 3 0.11
9 25 0.89
ACGTcount: A:0.00, C:0.40, G:0.09, T:0.51
Consensus pattern (9 bp):
CCTCTTCGT
Found at i:19901929 original size:18 final size:17
Alignment explanation
Indices: 19901906--19901948 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 17
19901896 CTTTCAGACC
19901906 CCTCTTCGTCCTCTTTGT
1 CCTCTTCGTCCTC-TTGT
*
19901924 CCTCTTCGTTCTCTTGT
1 CCTCTTCGTCCTCTTGT
19901941 CCTTCTTC
1 CC-TCTTC
19901949 ATTATCAATG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 6 0.26
18 17 0.74
ACGTcount: A:0.00, C:0.40, G:0.09, T:0.51
Consensus pattern (17 bp):
CCTCTTCGTCCTCTTGT
Found at i:19909564 original size:20 final size:20
Alignment explanation
Indices: 19909515--19909564 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
19909505 TTCAAGGTAT
* *
19909515 CGGTAGAAGTGGAGTTGTAT
1 CGGTAGAAGTGGAGTTCTAC
* *
19909535 CAGTACAAGTGGAGTTCTAC
1 CGGTAGAAGTGGAGTTCTAC
19909555 CGGTAGAAGT
1 CGGTAGAAGT
19909565 CTCACTGGAG
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.28, C:0.12, G:0.34, T:0.26
Consensus pattern (20 bp):
CGGTAGAAGTGGAGTTCTAC
Found at i:19910170 original size:15 final size:17
Alignment explanation
Indices: 19910150--19910185 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
19910140 GAATAAAGTG
19910150 TTTTT-GAGACTT-TAA
1 TTTTTGGAGACTTGTAA
19910165 TTTTTGGAGACTTGTAA
1 TTTTTGGAGACTTGTAA
19910182 TTTT
1 TTTT
19910186 GAATTATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 5 0.26
16 7 0.37
17 7 0.37
ACGTcount: A:0.22, C:0.06, G:0.17, T:0.56
Consensus pattern (17 bp):
TTTTTGGAGACTTGTAA
Found at i:19919108 original size:24 final size:24
Alignment explanation
Indices: 19919081--19919133 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
19919071 TCGACAAGGG
*
19919081 AATTTCAATCAGCAGCAGCAGTAA
1 AATTTCAATCAGCAGCAGCAATAA
19919105 AATTTCAATCAGCAGCAGCAATAA
1 AATTTCAATCAGCAGCAGCAATAA
19919129 AATTT
1 AATTT
19919134 TAACCAGAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.43, C:0.19, G:0.13, T:0.25
Consensus pattern (24 bp):
AATTTCAATCAGCAGCAGCAATAA
Found at i:19925850 original size:12 final size:12
Alignment explanation
Indices: 19925833--19925857 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
19925823 TAAGCTTGGA
19925833 GGGAATGGAAAT
1 GGGAATGGAAAT
19925845 GGGAATGGAAAT
1 GGGAATGGAAAT
19925857 G
1 G
19925858 CAATTGCACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.00, G:0.44, T:0.16
Consensus pattern (12 bp):
GGGAATGGAAAT
Found at i:19933357 original size:21 final size:21
Alignment explanation
Indices: 19933331--19933380 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
19933321 ACAAAATATT
* * *
19933331 ATGTTTGTAGCTCTCCTCATA
1 ATGTTTATAACTCTCCCCATA
*
19933352 ATGTTTATAACTCTCCCCATT
1 ATGTTTATAACTCTCCCCATA
19933373 ATGTTTAT
1 ATGTTTAT
19933381 TTTAAATTTC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.22, C:0.22, G:0.10, T:0.46
Consensus pattern (21 bp):
ATGTTTATAACTCTCCCCATA
Found at i:19934744 original size:21 final size:22
Alignment explanation
Indices: 19934718--19934775 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 22
19934708 ACGGGTATTG
* *
19934718 AGAAAGAAAGAATGAATGAA-A
1 AGAAAGAAAGAAAGAAGGAAGA
*
19934739 AGAAAGAAAAAAAGAAGGAAGA
1 AGAAAGAAAGAAAGAAGGAAGA
19934761 AGGAGAAGAAAGAAA
1 A-GA-AAGAAAGAAA
19934776 AGAGAATGAG
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
21 17 0.57
22 2 0.07
23 2 0.07
24 9 0.30
ACGTcount: A:0.69, C:0.00, G:0.28, T:0.03
Consensus pattern (22 bp):
AGAAAGAAAGAAAGAAGGAAGA
Found at i:19934746 original size:25 final size:24
Alignment explanation
Indices: 19934718--19934775 Score: 64
Period size: 25 Copynumber: 2.4 Consensus size: 24
19934708 ACGGGTATTG
*
19934718 AGAAAGAAAGAATGAATGAAA-AGAA
1 AGAAAGAAAGAAGGAA-GAAAGAG-A
* *
19934743 AGAAAAAAAGAAGGAAGAAGGAGA
1 AGAAAGAAAGAAGGAAGAAAGAGA
19934767 AGAAAGAAA
1 AGAAAGAAA
19934776 AGAGAATGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
24 12 0.43
25 16 0.57
ACGTcount: A:0.69, C:0.00, G:0.28, T:0.03
Consensus pattern (24 bp):
AGAAAGAAAGAAGGAAGAAAGAGA
Found at i:19934754 original size:8 final size:9
Alignment explanation
Indices: 19934720--19934778 Score: 50
Period size: 9 Copynumber: 6.6 Consensus size: 9
19934710 GGGTATTGAG
19934720 AAAGAAAG-
1 AAAGAAAGA
* *
19934728 AATGAATGA
1 AAAGAAAGA
19934737 AAAGAAAGA
1 AAAGAAAGA
19934746 AAA-AAAGA
1 AAAGAAAGA
*
19934754 AGGAAGAAGGA
1 A--AAGAAAGA
*
19934765 GAAGAAAGA
1 AAAGAAAGA
19934774 AAAGA
1 AAAGA
19934779 GAATGAGAAT
Statistics
Matches: 39, Mismatches: 8, Indels: 7
0.72 0.15 0.13
Matches are distributed among these distances:
8 12 0.31
9 21 0.54
10 2 0.05
11 4 0.10
ACGTcount: A:0.69, C:0.00, G:0.27, T:0.03
Consensus pattern (9 bp):
AAAGAAAGA
Found at i:19934775 original size:28 final size:29
Alignment explanation
Indices: 19934720--19934776 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 29
19934710 GGGTATTGAG
*
19934720 AAAGAAAGAATGAATGAAAAGAAAGAAAA
1 AAAGAAAGAATGAAGGAAAAGAAAGAAAA
* *
19934749 AAAGAAGGAA-GAAGGAGAAGAAAGAAAA
1 AAAGAAAGAATGAAGGAAAAGAAAGAAAA
19934777 GAGAATGAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
28 16 0.64
29 9 0.36
ACGTcount: A:0.70, C:0.00, G:0.26, T:0.04
Consensus pattern (29 bp):
AAAGAAAGAATGAAGGAAAAGAAAGAAAA
Found at i:19935513 original size:16 final size:16
Alignment explanation
Indices: 19935466--19935514 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
19935456 AAATACTCTA
*
19935466 AATTAATTACCAAAAT
1 AATTAATTACAAAAAT
*
19935482 -A-TAATATA-AAAGAT
1 AATTAAT-TACAAAAAT
19935496 AATTAATTACAAAAAT
1 AATTAATTACAAAAAT
19935512 AAT
1 AAT
19935515 ATCCTCATCC
Statistics
Matches: 26, Mismatches: 3, Indels: 8
0.70 0.08 0.22
Matches are distributed among these distances:
14 8 0.31
15 6 0.23
16 12 0.46
ACGTcount: A:0.61, C:0.06, G:0.02, T:0.31
Consensus pattern (16 bp):
AATTAATTACAAAAAT
Found at i:19936912 original size:43 final size:43
Alignment explanation
Indices: 19936830--19936914 Score: 109
Period size: 43 Copynumber: 2.0 Consensus size: 43
19936820 ATTAACATGT
* *
19936830 TAAATTATACTACTTGACTCGTGTTAATATGGTTGCATGTTAC
1 TAAATTATACTACTTGACTCGTATTAATATGCTTGCATGTTAC
* * *
19936873 TAAATTATATTACTTTACTCTTATTAATAT-CTTGACATGTTA
1 TAAATTATACTACTTGACTCGTATTAATATGCTTG-CATGTTA
19936915 TGAATTGTGT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
42 3 0.08
43 33 0.92
ACGTcount: A:0.31, C:0.13, G:0.11, T:0.46
Consensus pattern (43 bp):
TAAATTATACTACTTGACTCGTATTAATATGCTTGCATGTTAC
Found at i:19937534 original size:45 final size:45
Alignment explanation
Indices: 19937470--19937561 Score: 150
Period size: 45 Copynumber: 2.0 Consensus size: 45
19937460 GCCTAGCTCA
*
19937470 TCAAGCCAAAGATATCAGCCTCAGTTTGACGAGCCACCGCAATAC
1 TCAAGCCAAAGATATCAGCCTCAATTTGACGAGCCACCGCAATAC
*
19937515 TCAAGCC-AAGAATATCAGCCTCAATTTGACGAGCCACCGTAATAC
1 TCAAGCCAAAG-ATATCAGCCTCAATTTGACGAGCCACCGCAATAC
19937560 TC
1 TC
19937562 TACTCCTCTC
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
44 3 0.07
45 41 0.93
ACGTcount: A:0.34, C:0.30, G:0.16, T:0.20
Consensus pattern (45 bp):
TCAAGCCAAAGATATCAGCCTCAATTTGACGAGCCACCGCAATAC
Found at i:19937855 original size:21 final size:21
Alignment explanation
Indices: 19937831--19937871 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
19937821 CCCTAAATCA
* *
19937831 TAAATCATAAGCCCTTAACCC
1 TAAATCAAAAGCCATTAACCC
*
19937852 TAAATTAAAAGCCATTAACC
1 TAAATCAAAAGCCATTAACC
19937872 TCAATTTCAC
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:0.44, C:0.27, G:0.05, T:0.24
Consensus pattern (21 bp):
TAAATCAAAAGCCATTAACCC
Found at i:19937915 original size:14 final size:14
Alignment explanation
Indices: 19937896--19937938 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
19937886 TTAACCTTTT
*
19937896 TTTAAAACCTTAAA
1 TTTAAAACCCTAAA
19937910 TTTAAAACCCTAAAA
1 TTTAAAACCCT-AAA
* *
19937925 TTCAAAACTCTAAA
1 TTTAAAACCCTAAA
19937939 CCCTTAAACC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 13 0.52
15 12 0.48
ACGTcount: A:0.51, C:0.19, G:0.00, T:0.30
Consensus pattern (14 bp):
TTTAAAACCCTAAA
Found at i:19940744 original size:15 final size:15
Alignment explanation
Indices: 19940724--19940752 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
19940714 AATTTGTTAA
19940724 TAAATAAATAAAATT
1 TAAATAAATAAAATT
19940739 TAAATAAATAAAAT
1 TAAATAAATAAAAT
19940753 ACAAATTTAA
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
TAAATAAATAAAATT
Found at i:19940758 original size:15 final size:15
Alignment explanation
Indices: 19940725--19940758 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
19940715 ATTTGTTAAT
**
19940725 AAATAAATAAAATTT
1 AAATAAATAAAATAC
19940740 AAATAAATAAAATAC
1 AAATAAATAAAATAC
19940755 AAAT
1 AAAT
19940759 TTAAAAATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (15 bp):
AAATAAATAAAATAC
Found at i:19940766 original size:19 final size:19
Alignment explanation
Indices: 19940720--19940767 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 19
19940710 AATAAATTTG
19940720 TTAATAAAT-AAATAAAAT
1 TTAATAAATAAAATAAAAT
19940738 TTAAATAAATAAAATACAAAT
1 TT-AATAAATAAAATA-AAAT
19940759 TTAA-AAATA
1 TTAATAAATA
19940768 TATCATACTA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
18 2 0.07
19 12 0.44
20 7 0.26
21 6 0.22
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (19 bp):
TTAATAAATAAAATAAAAT
Found at i:19940775 original size:21 final size:21
Alignment explanation
Indices: 19940722--19940763 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
19940712 TAAATTTGTT
19940722 AATAAAT-AAATA-AAATTTA
1 AATAAATAAAATACAAATTTA
19940741 AATAAATAAAATACAAATTTA
1 AATAAATAAAATACAAATTTA
19940762 AA
1 AA
19940764 AATATATCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 7 0.33
20 5 0.24
21 9 0.43
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (21 bp):
AATAAATAAAATACAAATTTA
Found at i:19940887 original size:19 final size:23
Alignment explanation
Indices: 19940863--19940909 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 23
19940853 ACCTTTTTAA
19940863 TTCTCCTCT-TT-TTC-TCTT-T
1 TTCTCCTCTGTTCTTCTTCTTGT
19940882 TTCTCCTCTGTTCTTCTTCTTGT
1 TTCTCCTCTGTTCTTCTTCTTGT
19940905 TTCTC
1 TTCTC
19940910 TTTATTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 9 0.38
20 2 0.08
21 3 0.12
22 4 0.17
23 6 0.25
ACGTcount: A:0.00, C:0.32, G:0.04, T:0.64
Consensus pattern (23 bp):
TTCTCCTCTGTTCTTCTTCTTGT
Found at i:19941229 original size:35 final size:35
Alignment explanation
Indices: 19941158--19941231 Score: 91
Period size: 35 Copynumber: 2.1 Consensus size: 35
19941148 TTATTTTTAT
*
19941158 TAAATTAATAATTTTTTAATATTACTTTAGTCAAA
1 TAAAATAATAATTTTTTAATATTACTTTAGTCAAA
19941193 TAAAATAATTAATTTTTGT-ATATTA-TTTGAGT-AAA
1 TAAAATAA-TAATTTTT-TAATATTACTTT-AGTCAAA
19941228 TAAA
1 TAAA
19941232 TATTTTTTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
35 17 0.49
36 17 0.49
37 1 0.03
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (35 bp):
TAAAATAATAATTTTTTAATATTACTTTAGTCAAA
Found at i:19943046 original size:21 final size:21
Alignment explanation
Indices: 19943017--19943056 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
19943007 TTATACATGT
*
19943017 TACTATTCATGGAATTGACTC
1 TACTATTCATGAAATTGACTC
*
19943038 TACTGTTCATGAAATTGAC
1 TACTATTCATGAAATTGAC
19943057 GTTCTGAACG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.38
Consensus pattern (21 bp):
TACTATTCATGAAATTGACTC
Found at i:19943868 original size:14 final size:14
Alignment explanation
Indices: 19943851--19943887 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
19943841 TTGGGATATA
19943851 AAATATATGATACG
1 AAATATATGATACG
*
19943865 AAATATGTGATACG
1 AAATATATGATACG
19943879 AATATATAT
1 AA-ATATAT
19943888 AAACCTAAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
14 15 0.75
15 5 0.25
ACGTcount: A:0.49, C:0.05, G:0.14, T:0.32
Consensus pattern (14 bp):
AAATATATGATACG
Found at i:19953788 original size:15 final size:16
Alignment explanation
Indices: 19953768--19953797 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
19953758 AGCAATATAT
19953768 AAAAAATAAA-AATTC
1 AAAAAATAAATAATTC
19953783 AAAAAATAAATAATT
1 AAAAAATAAATAATT
19953798 TTTCTATAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.23
Consensus pattern (16 bp):
AAAAAATAAATAATTC
Found at i:19960406 original size:22 final size:22
Alignment explanation
Indices: 19960376--19960427 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
19960366 TATGATATTA
* * *
19960376 AAGTGAAAGAAGTGTATTAATT
1 AAGTTAAAGAAATGGATTAATT
19960398 AAGTTAAAGAAATGGATTAATT
1 AAGTTAAAGAAATGGATTAATT
19960420 AAGCTTAA
1 AAG-TTAA
19960428 TGATGAAAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 22 0.85
23 4 0.15
ACGTcount: A:0.48, C:0.02, G:0.19, T:0.31
Consensus pattern (22 bp):
AAGTTAAAGAAATGGATTAATT
Found at i:19961361 original size:51 final size:51
Alignment explanation
Indices: 19961287--19961466 Score: 209
Period size: 51 Copynumber: 3.5 Consensus size: 51
19961277 CGAAAGGGTT
* *
19961287 CGATGACTGAGTGTCATCATGAGTAAATGAATCCTTTACGGATTAAAGGTC
1 CGATGACTAAGTGTCATCATGAGTAAATGAATCCTTTACGAATTAAAGGTC
* * *
19961338 CGATGACTAAGTGTCATCGTGAGTAAATGAATCCATAACGAATTAAAGGTC
1 CGATGACTAAGTGTCATCATGAGTAAATGAATCCTTTACGAATTAAAGGTC
* * * * * ** *
19961389 CGATGACTCAGTGTCATCGTAAGTATATGAATTCCTATACGAAACAAGGGGTC
1 CGATGACTAAGTGTCATCATGAGTAAATGAA-TCCTTTACGAATTAA-AGGTC
19961442 CGATGACTATA-TGTCATCATGAGTA
1 CGATGACTA-AGTGTCATCATGAGTA
19961467 TTAAATGAAA
Statistics
Matches: 109, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
51 74 0.68
52 10 0.09
53 24 0.22
54 1 0.01
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.28
Consensus pattern (51 bp):
CGATGACTAAGTGTCATCATGAGTAAATGAATCCTTTACGAATTAAAGGTC
Found at i:19962245 original size:21 final size:22
Alignment explanation
Indices: 19962221--19962280 Score: 70
Period size: 21 Copynumber: 2.8 Consensus size: 22
19962211 TAGTTGCATG
19962221 ACTTGTATCGGTAGAAATTA-T
1 ACTTGTATCGGTAGAAATTATT
*
19962242 ACTTGTATCGATAG-AATTATT
1 ACTTGTATCGGTAGAAATTATT
***
19962263 AAAAGTATCGGTAGAAAT
1 ACTTGTATCGGTAGAAAT
19962281 CTACACAGTT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
20 5 0.16
21 24 0.75
22 3 0.09
ACGTcount: A:0.38, C:0.08, G:0.18, T:0.35
Consensus pattern (22 bp):
ACTTGTATCGGTAGAAATTATT
Found at i:19968619 original size:36 final size:36
Alignment explanation
Indices: 19968573--19968642 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
19968563 AAGAGAAAAA
* * *
19968573 AAAGGAAGAAAAAATTACGTATAAAATGGTGCTAAG
1 AAAGAAAGAAAAAATTACATATAAAATGGAGCTAAG
19968609 AAAGAAAGAAAAAATTACATATAAAATGGAGCTA
1 AAAGAAAGAAAAAATTACATATAAAATGGAGCTA
19968643 GTCATGCAGT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.57, C:0.06, G:0.19, T:0.19
Consensus pattern (36 bp):
AAAGAAAGAAAAAATTACATATAAAATGGAGCTAAG
Found at i:19969986 original size:3 final size:3
Alignment explanation
Indices: 19969978--19970015 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
19969968 TTTGTATTCA
19969978 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
19970016 GTGTCTTAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:19971292 original size:37 final size:37
Alignment explanation
Indices: 19971251--19971327 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 37
19971241 ATTTTTATAA
* *
19971251 ATTAAAAAGAGTAAAATA-TCTTCGAATAAAATAATTT
1 ATTAAAAAAAGTAAAATACTC-TCGAATAAAATAACTT
* *
19971288 ATTAAAAAAATTAAAATACTCTCGAATAATATAACTT
1 ATTAAAAAAAGTAAAATACTCTCGAATAAAATAACTT
19971325 ATT
1 ATT
19971328 TTAATTATAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
37 33 0.94
38 2 0.06
ACGTcount: A:0.53, C:0.08, G:0.05, T:0.34
Consensus pattern (37 bp):
ATTAAAAAAAGTAAAATACTCTCGAATAAAATAACTT
Found at i:19975704 original size:32 final size:30
Alignment explanation
Indices: 19975668--19975728 Score: 86
Period size: 32 Copynumber: 2.0 Consensus size: 30
19975658 TGGGAGGTTT
*
19975668 GAGGGTCAAATCTGAATTTTTTTGGAAAGTTC
1 GAGGGTCAAAACTGAA--TTTTTGGAAAGTTC
*
19975700 GAGGGTCAAAACTTAATTTTTGGAAAGTT
1 GAGGGTCAAAACTGAATTTTTGGAAAGTT
19975729 TGGGGCTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 13 0.48
32 14 0.52
ACGTcount: A:0.31, C:0.08, G:0.25, T:0.36
Consensus pattern (30 bp):
GAGGGTCAAAACTGAATTTTTGGAAAGTTC
Found at i:19975722 original size:30 final size:30
Alignment explanation
Indices: 19975668--19975755 Score: 90
Period size: 30 Copynumber: 2.9 Consensus size: 30
19975658 TGGGAGGTTT
* *
19975668 GAGGGTCAAATCTGAATTTTTTTGGAAAGTTC
1 GAGGGTCAAAACTTAA--TTTTTGGAAAGTTC
*
19975700 GAGGGTCAAAACTTAATTTTTGGAAAGTTT
1 GAGGGTCAAAACTTAATTTTTGGAAAGTTC
*
19975730 G-GGG-CTAAAAATATAATTTTTGGAAA
1 GAGGGTC-AAAACT-TAATTTTTGGAAA
19975756 TTTTAGGGGT
Statistics
Matches: 50, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
28 1 0.02
29 8 0.16
30 27 0.54
32 14 0.28
ACGTcount: A:0.34, C:0.07, G:0.24, T:0.35
Consensus pattern (30 bp):
GAGGGTCAAAACTTAATTTTTGGAAAGTTC
Found at i:19975776 original size:29 final size:29
Alignment explanation
Indices: 19975713--19975808 Score: 117
Period size: 29 Copynumber: 3.3 Consensus size: 29
19975703 GGTCAAAACT
* *
19975713 TAATTTTTGGAAAGTTT-GGGGCTAAAAATA
1 TAATTTTTGGAAATTTTAGGGG-T-CAAATA
19975743 TAATTTTTGGAAATTTTAGGGGTCAAAT-
1 TAATTTTTGGAAATTTTAGGGGTCAAATA
19975771 TCAATTTTTGG-AATTTTAGGGGTCAAAATA
1 T-AATTTTTGGAAATTTTAGGGGTC-AAATA
19975801 TAATTTTT
1 TAATTTTT
19975809 AAATAATTTA
Statistics
Matches: 60, Mismatches: 2, Indels: 9
0.85 0.03 0.13
Matches are distributed among these distances:
28 14 0.23
29 24 0.40
30 18 0.30
31 4 0.07
ACGTcount: A:0.33, C:0.04, G:0.20, T:0.43
Consensus pattern (29 bp):
TAATTTTTGGAAATTTTAGGGGTCAAATA
Found at i:19975807 original size:28 final size:29
Alignment explanation
Indices: 19975702--19975829 Score: 131
Period size: 30 Copynumber: 4.3 Consensus size: 29
19975692 GAAAGTTCGA
*
19975702 GGGTCAAAACTTAATTTTTGGAAAGTTT-G
1 GGGTCAAAA-TTAATTTTTGGAAATTTTAG
*
19975731 GGGCTAAAAATATAATTTTTGGAAATTTTAG
1 GGG-TCAAAAT-TAATTTTTGGAAATTTTAG
19975762 GGGTC-AAATTCAATTTTTGG-AATTTTAG
1 GGGTCAAAATT-AATTTTTGGAAATTTTAG
19975790 GGGTCAAAATATAATTTTT--AAATAATTTAG
1 GGGTCAAAAT-TAATTTTTGGAAAT--TTTAG
*
19975820 GGGTTAAAAT
1 GGGTCAAAAT
19975830 GCAATTTCTA
Statistics
Matches: 86, Mismatches: 4, Indels: 17
0.80 0.04 0.16
Matches are distributed among these distances:
28 17 0.20
29 28 0.33
30 37 0.43
31 4 0.05
ACGTcount: A:0.36, C:0.05, G:0.20, T:0.39
Consensus pattern (29 bp):
GGGTCAAAATTAATTTTTGGAAATTTTAG
Found at i:19975835 original size:59 final size:58
Alignment explanation
Indices: 19975714--19975836 Score: 144
Period size: 58 Copynumber: 2.1 Consensus size: 58
19975704 GTCAAAACTT
* *
19975714 AATTTTTGGAAAGTTTGGGGCTAAAAATATAATTTTTGGAAATTTTAGGGGTCAAATTC
1 AATTTTTGGAAAGTTTGGGGCTAAAAATATAATTTTT-GAAATTTTAGGGGTAAAATGC
* *
19975773 AATTTTTGG-AATTTTAGGGG-TCAAAATATAATTTTT-AAATAATTTAGGGGTTAAAATGC
1 AATTTTTGGAAAGTTT-GGGGCTAAAAATATAATTTTTGAAAT--TTTAGGGG-TAAAATGC
19975832 AATTT
1 AATTT
19975837 CTAAATAAAA
Statistics
Matches: 56, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
56 4 0.07
58 28 0.50
59 24 0.43
ACGTcount: A:0.36, C:0.04, G:0.20, T:0.41
Consensus pattern (58 bp):
AATTTTTGGAAAGTTTGGGGCTAAAAATATAATTTTTGAAATTTTAGGGGTAAAATGC
Found at i:19975836 original size:30 final size:30
Alignment explanation
Indices: 19975785--19975844 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
19975775 TTTTTGGAAT
* *
19975785 TTTAGGGGTCAAAATATAATTTTTAAATAA
1 TTTAGGGGTCAAAATACAATTTCTAAATAA
* *
19975815 TTTAGGGGTTAAAATGCAATTTCTAAATAA
1 TTTAGGGGTCAAAATACAATTTCTAAATAA
19975845 AATATGGGCT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.42, C:0.05, G:0.15, T:0.38
Consensus pattern (30 bp):
TTTAGGGGTCAAAATACAATTTCTAAATAA
Found at i:19976611 original size:15 final size:16
Alignment explanation
Indices: 19976573--19976619 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
19976563 TGATTTTCTT
*
19976573 TTATTTGTTGTTTTTTG
1 TTATTTCTT-TTTTTTG
19976590 TTATTTCTCTTTTTTTG
1 TTATTTCT-TTTTTTTG
19976607 -T-TTTCTTTTTTTT
1 TTATTTCTTTTTTTT
19976620 TCATATATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
14 7 0.25
15 5 0.18
16 1 0.04
17 14 0.50
18 1 0.04
ACGTcount: A:0.04, C:0.06, G:0.09, T:0.81
Consensus pattern (16 bp):
TTATTTCTTTTTTTTG
Found at i:19976620 original size:15 final size:17
Alignment explanation
Indices: 19976583--19976619 Score: 53
Period size: 14 Copynumber: 2.4 Consensus size: 17
19976573 TTATTTGTTG
19976583 TTTTTTGTTATTTCTCT
1 TTTTTTGTTATTTCTCT
19976600 TTTTTTG-T-TTTCT-T
1 TTTTTTGTTATTTCTCT
19976614 TTTTTT
1 TTTTTT
19976620 TCATATATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 7 0.35
15 5 0.25
16 1 0.05
17 7 0.35
ACGTcount: A:0.03, C:0.08, G:0.05, T:0.84
Consensus pattern (17 bp):
TTTTTTGTTATTTCTCT
Found at i:19977686 original size:124 final size:124
Alignment explanation
Indices: 19977466--19977703 Score: 377
Period size: 124 Copynumber: 1.9 Consensus size: 124
19977456 GTAGCTTCAC
*
19977466 GTTCACTTCTTTGTATCTCATCAGGAAGATGACCGCTTCATCATTTTGATCCACTTCTCTATATC
1 GTTCACTTCTCTGTATCTCATCAGGAAGATGACCGCTTCATCATTTTGATCCACTTCTCTATATC
* * *
19977531 TCATCAGGGAGTTAAGGGTTTGAAGTTTCACTCACATTGAGCTGCGCTTAATTGTTTTG
66 TCATCAAGAAGATAAGGGTTTGAAGTTTCACTCACATTGAGCTGCGCTTAATTGTTTTG
* * *
19977590 GTTCAGTTCTCTGTATCTCATCAGGAAGATGTCCGCTTCATCATTTTGATCCACTTCTCTGTATC
1 GTTCACTTCTCTGTATCTCATCAGGAAGATGACCGCTTCATCATTTTGATCCACTTCTCTATATC
** * *
19977655 TCATCAAGAAGATGGGGGTTTGAGGTTTCACTCACATTGAGCTTCGCTT
66 TCATCAAGAAGATAAGGGTTTGAAGTTTCACTCACATTGAGCTGCGCTT
19977704 CCTGTAAAGC
Statistics
Matches: 103, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
124 103 1.00
ACGTcount: A:0.21, C:0.22, G:0.19, T:0.38
Consensus pattern (124 bp):
GTTCACTTCTCTGTATCTCATCAGGAAGATGACCGCTTCATCATTTTGATCCACTTCTCTATATC
TCATCAAGAAGATAAGGGTTTGAAGTTTCACTCACATTGAGCTGCGCTTAATTGTTTTG
Found at i:19979670 original size:186 final size:183
Alignment explanation
Indices: 19979353--19979717 Score: 658
Period size: 186 Copynumber: 2.0 Consensus size: 183
19979343 ATAGATCTGG
*
19979353 CATTTATGGCACCTCTTAGCATAAATGATGCAATCACCTTCTAGGGTAGACCAGTAATACCCAAA
1 CATTTATGGCACCTCTTAGCATAAATGATGCAATCACCTTCCAGGGTAGACCAGTAATACCCAAA
*
19979418 TCTCATTATCTACCTAGCCATTGTGAAACCATTGACGTGTGTCCCACAAATGCCTTCGTAAACTT
66 TCTCATTATCTACCTAGCCATTGTGAAACCATTGACGTGTGTCCCACAAATACCTTCGTAAACTT
19979483 CTTCTAAGATCTTTTTAGCTTCTATTGCATCGACACATCTTAGCAACACATGA
131 CTTCTAAGATCTTTTTAGCTTCTATTGCATCGACACATCTTAGCAACACATGA
*
19979536 CATTTATGGCACCTCTTAGCATAAATGATGATGCAATCACCTTCCAGGGTGGACCAGTAATACCC
1 CATTTATGGCACCTCTTAGCAT-AA--ATGATGCAATCACCTTCCAGGGTAGACCAGTAATACCC
* *
19979601 AAATCTCATTATCTACCTAGCCATTGTGAAACCATTGGCGTGTGTCCCACAAATACCTTCGTGAA
63 AAATCTCATTATCTACCTAGCCATTGTGAAACCATTGACGTGTGTCCCACAAATACCTTCGTAAA
19979666 CTTCTTCTAAGATCTTTTTAGCTTCTATTGCATCGACACATCTTAGCAACAC
128 CTTCTTCTAAGATCTTTTTAGCTTCTATTGCATCGACACATCTTAGCAACAC
19979718 CTGATCCTTT
Statistics
Matches: 174, Mismatches: 5, Indels: 3
0.96 0.03 0.02
Matches are distributed among these distances:
183 22 0.13
184 2 0.01
186 150 0.86
ACGTcount: A:0.29, C:0.26, G:0.14, T:0.31
Consensus pattern (183 bp):
CATTTATGGCACCTCTTAGCATAAATGATGCAATCACCTTCCAGGGTAGACCAGTAATACCCAAA
TCTCATTATCTACCTAGCCATTGTGAAACCATTGACGTGTGTCCCACAAATACCTTCGTAAACTT
CTTCTAAGATCTTTTTAGCTTCTATTGCATCGACACATCTTAGCAACACATGA
Found at i:19982860 original size:89 final size:90
Alignment explanation
Indices: 19982627--19982972 Score: 362
Period size: 89 Copynumber: 3.9 Consensus size: 90
19982617 GGAAAAATAG
** * * * * *
19982627 GGTCAAAAATAAATTTTTAGAAAGTTCGAGGGT-GAAATTTAAATTTTTGGGAAGTTTGAGGGT-
1 GGTCAAATCTAAATTTTTGGAAAGTTCGAGGGTCAAAACTT-AATTTTTGGAAAGTTCGAGGGTA
* * * *
19982690 TAAATATGAATTTTTGGGAA-GTTTAA
65 AAAATAT-AATTTTTGGAAATTTTTGA
* * *
19982716 GGGTTAAATCTAAATTTTTGGAAAGTTCAAGGGTCAAAACTAAATTTTTGGAAAGTTCGAGGGTA
1 -GGTCAAATCTAAATTTTTGGAAAGTTCGAGGGTCAAAACTTAATTTTTGGAAAGTTCGAGGGTA
19982781 AAAATATAATTTTTGGAAATTTTTGA
65 AAAATATAATTTTTGGAAATTTTTGA
*
19982807 GGTCAAATCTAAA-TTTTGGAAAGTTCGAGGGTCAAAACTTAATTTTTGAAAAGTTCGAGGGTAA
1 GGTCAAATCTAAATTTTTGGAAAGTTCGAGGGTCAAAACTTAATTTTTGGAAAGTTCGAGGGTAA
** *
19982871 AAATATAATTTTTGGAAATTTAAGT
66 AAATATAATTTTTGGAAATTTTTGA
* * * * * * * * * *
19982896 GGTCAAATTTAAA-TTTTGAAAAGTT-TAGGGGTCAAAACATATTTTTTTGATAGTTTGGGGGTT
1 GGTCAAATCTAAATTTTTGGAAAGTTCGA-GGGTCAAAACTTAATTTTTGGAAAGTTCGAGGGTA
19982959 AAAATATAATTTTT
65 AAAATATAATTTTT
19982973 AAATAAAATA
Statistics
Matches: 220, Mismatches: 32, Indels: 9
0.84 0.12 0.03
Matches are distributed among these distances:
88 1 0.00
89 134 0.61
90 71 0.32
91 14 0.06
ACGTcount: A:0.36, C:0.05, G:0.21, T:0.38
Consensus pattern (90 bp):
GGTCAAATCTAAATTTTTGGAAAGTTCGAGGGTCAAAACTTAATTTTTGGAAAGTTCGAGGGTAA
AAATATAATTTTTGGAAATTTTTGA
Found at i:19982911 original size:30 final size:30
Alignment explanation
Indices: 19982625--19982920 Score: 257
Period size: 30 Copynumber: 9.9 Consensus size: 30
19982615 AAGGAAAAAT
* *
19982625 AGGGTCAAAAATAAATTTTTAGAAAGTTCG
1 AGGGTCAAATATAAATTTTTGGAAAGTTCG
* * * *
19982655 AGGGTGAAATTTAAATTTTTGGGAAGTTTG
1 AGGGTCAAATATAAATTTTTGGAAAGTTCG
* * * **
19982685 AGGGTTAAATATGAATTTTTGGGAAGTTTA
1 AGGGTCAAATATAAATTTTTGGAAAGTTCG
* * *
19982715 AGGGTTAAATCTAAATTTTTGGAAAGTTCA
1 AGGGTCAAATATAAATTTTTGGAAAGTTCG
19982745 AGGGTCAAA-ACTAAATTTTTGGAAAGTTCG
1 AGGGTCAAATA-TAAATTTTTGGAAAGTTCG
* * *
19982775 AGGGT-AAAAATATAATTTTTGGAAATTTTTG
1 AGGGTCAAATATA-AATTTTTGGAAA-GTTCG
*
19982806 A-GGTCAAATCTAAA-TTTTGGAAAGTTCG
1 AGGGTCAAATATAAATTTTTGGAAAGTTCG
* *
19982834 AGGGTCAAA-ACTTAATTTTTGAAAAGTTCG
1 AGGGTCAAATA-TAAATTTTTGGAAAGTTCG
* **
19982864 AGGGT-AAAAATATAATTTTTGGAAA-TTTA
1 AGGGTCAAATATA-AATTTTTGGAAAGTTCG
* *
19982893 AGTGGTCAAATTTAAA-TTTTGAAAAGTT
1 AG-GGTCAAATATAAATTTTTGGAAAGTT
19982921 TAGGGGTCAA
Statistics
Matches: 220, Mismatches: 33, Indels: 26
0.79 0.12 0.09
Matches are distributed among these distances:
28 4 0.02
29 40 0.18
30 162 0.74
31 14 0.06
ACGTcount: A:0.38, C:0.05, G:0.22, T:0.36
Consensus pattern (30 bp):
AGGGTCAAATATAAATTTTTGGAAAGTTCG
Found at i:19983850 original size:12 final size:12
Alignment explanation
Indices: 19983835--19983873 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
19983825 ATAAATGGTA
*
19983835 AAATAAATATAT
1 AAATATATATAT
19983847 AAATATATATAT
1 AAATATATATAT
* *
19983859 ATATATATATGT
1 AAATATATATAT
19983871 AAA
1 AAA
19983874 CGAATGTACC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (12 bp):
AAATATATATAT
Found at i:19984315 original size:3 final size:3
Alignment explanation
Indices: 19984307--19984336 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
19984297 ATAAATTTTA
19984307 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
19984337 TTAGGTTGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:19994519 original size:17 final size:16
Alignment explanation
Indices: 19994481--19994519 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
19994471 AAACAAATAT
19994481 GAAG-AAGGAAAAGAA
1 GAAGAAAGGAAAAGAA
19994496 GAGAGAAAGGAAAAGAA
1 GA-AGAAAGGAAAAGAA
19994513 GGAAGAA
1 -GAAGAA
19994520 GAAGAAGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 2 0.10
16 2 0.10
17 15 0.71
18 2 0.10
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (16 bp):
GAAGAAAGGAAAAGAA
Found at i:19995959 original size:20 final size:21
Alignment explanation
Indices: 19995934--19995973 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
19995924 ATCATATTTA
19995934 GCATTTTAT-ACTTAGTGTTT
1 GCATTTTATAACTTAGTGTTT
19995954 GCATTTTATAACTTAGTGTT
1 GCATTTTATAACTTAGTGTT
19995974 GTTTGATCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.23, C:0.10, G:0.15, T:0.53
Consensus pattern (21 bp):
GCATTTTATAACTTAGTGTTT
Found at i:20003674 original size:15 final size:16
Alignment explanation
Indices: 20003654--20003689 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
20003644 GTAATTTTAG
20003654 ATATA-TATTTTATAC
1 ATATATTATTTTATAC
*
20003669 ATATATTTTTTTATAC
1 ATATATTATTTTATAC
20003685 ATATA
1 ATATA
20003690 AACTGTTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.26
16 14 0.74
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.56
Consensus pattern (16 bp):
ATATATTATTTTATAC
Found at i:20014457 original size:15 final size:17
Alignment explanation
Indices: 20014436--20014476 Score: 59
Period size: 15 Copynumber: 2.5 Consensus size: 17
20014426 TAACTTTTTA
20014436 AAAATTATAAAAAT-AT
1 AAAATTATAAAAATAAT
*
20014452 -AAATTATTAAAATAAT
1 AAAATTATAAAAATAAT
20014468 AAAATTATA
1 AAAATTATA
20014477 TTTTTACTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 12 0.57
16 2 0.10
17 7 0.33
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
AAAATTATAAAAATAAT
Found at i:20017438 original size:95 final size:95
Alignment explanation
Indices: 20017272--20017456 Score: 334
Period size: 95 Copynumber: 1.9 Consensus size: 95
20017262 GTGCCTAGAG
*
20017272 ATGAAAGACATATGACAGCTTTTAGAGAAGTACTAGGGGATTGCTAATTGTTTGATCTTGGATAT
1 ATGAAAGACATATGACAGCTTTTAGAGAAGTACTAAGGGATTGCTAATTGTTTGATCTTGGATAT
20017337 TCAGGATCTTGGTTCACTTGGGAAAAAGGT
66 TCAGGATCTTGGTTCACTTGGGAAAAAGGT
*
20017367 ATGAAAGACATATGGCAGCTTTTAGAGAAGTACTAAGGGATTGCTAATTGTTTGATCTTGGATAT
1 ATGAAAGACATATGACAGCTTTTAGAGAAGTACTAAGGGATTGCTAATTGTTTGATCTTGGATAT
* *
20017432 TTAGGATCTTGGTTTACTTGGGAAA
66 TCAGGATCTTGGTTCACTTGGGAAA
20017457 GGGGTAATTT
Statistics
Matches: 86, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
95 86 1.00
ACGTcount: A:0.30, C:0.10, G:0.26, T:0.34
Consensus pattern (95 bp):
ATGAAAGACATATGACAGCTTTTAGAGAAGTACTAAGGGATTGCTAATTGTTTGATCTTGGATAT
TCAGGATCTTGGTTCACTTGGGAAAAAGGT
Found at i:20019012 original size:13 final size:13
Alignment explanation
Indices: 20018994--20019029 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
20018984 GTTGGTGTCT
20018994 CATTCATTATCCA
1 CATTCATTATCCA
20019007 CATTCATTATCCA
1 CATTCATTATCCA
*
20019020 GATTCATTAT
1 CATTCATTAT
20019030 TAGCGCGTGC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.31, C:0.25, G:0.03, T:0.42
Consensus pattern (13 bp):
CATTCATTATCCA
Found at i:20021205 original size:20 final size:21
Alignment explanation
Indices: 20021162--20021205 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
20021152 ATTTTTAGAA
*
20021162 TTTTTTATATTTTTAGAATTAT
1 TTTTTTATATTTTTA-AATAAT
20021184 TTTTTTATATTTTT-AATAAT
1 TTTTTTATATTTTTAAATAAT
20021204 TT
1 TT
20021206 ATAAATTTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 7 0.33
22 14 0.67
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.70
Consensus pattern (21 bp):
TTTTTTATATTTTTAAATAAT
Found at i:20027390 original size:17 final size:19
Alignment explanation
Indices: 20027346--20027388 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
20027336 TTTATATTTT
* *
20027346 TAAAAAATATTAATTATTA
1 TAAAAAATATTAAGTATGA
20027365 TAAAAAATATT-AGTATGA
1 TAAAAAATATTAAGTATGA
20027383 TAAAAA
1 TAAAAA
20027389 TAACTTCTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 11 0.50
19 11 0.50
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (19 bp):
TAAAAAATATTAAGTATGA
Found at i:20030224 original size:378 final size:378
Alignment explanation
Indices: 20029529--20030288 Score: 1423
Period size: 378 Copynumber: 2.0 Consensus size: 378
20029519 ATTACAATTG
20029529 TTACCTAAACGTGTCACCAATGTATAATTACAAGTAATTACACCCAAATTCAATTACTAGGTGGC
1 TTACCTAAACGTGTCACCAATGTATAATTACAAGTAATTACACCCAAATTCAATTACTAGGTGGC
20029594 TTTCTTTCTTTTTTTGAAGAAATGTTTAGTTTGGAATTAATAAACAGGGCATGAAAAGCTTCCAA
66 TTTCTTTCTTTTTTTGAAGAAATGTTTAGTTTGGAATTAATAAACAGGGCATGAAAAGCTTCCAA
*
20029659 ATACAAAACATAAATAACAAACCCAAAGAACCAACCCATAACTAGGTCTGGCCCAACTAGCACCC
131 ATACAAAACATAAATAAAAAACCCAAAGAACCAACCCATAACTAGGTCTGGCCCAACTAGCACCC
20029724 GACCATAAGAAAACCAAAGAAAGAAAAAGGAAACACTTGAAAATATCTAGGAAAAATAAAACACA
196 GACCATAAGAAAACCAAAGAAAGAAAAAGGAAACACTTGAAAATATCTAGGAAAAATAAAACACA
*
20029789 CAAAAAAAAAAGATCCAAAAGCTTCTCTGAAACCCTTTTCAGTTACCAAAATACAACCAAGACAA
261 CAAAAAAAAAAGATCCAAAAGCTTCTCTGAAACCCTCTTCAGTTACCAAAATACAACCAAGACAA
*
20029854 CAAATGACCTTCCCAATTGGAGAAACCACTTGGGAAGGAAGATTGAGGTTTGC
326 CAAATGACCTTCCCAATTGGAGAAACCACTTGGGAAGCAAGATTGAGGTTTGC
20029907 TTACCTAAACGTGTCACCAATGTATAATTACAAGTAATTACACCCAAATTCAATTACTAGGTGGC
1 TTACCTAAACGTGTCACCAATGTATAATTACAAGTAATTACACCCAAATTCAATTACTAGGTGGC
* * *
20029972 TTTCTTTCTTTTTTTGAAGAAATGTTTCGTTTGGTATTCATAAACAGGGCATGAAAAGCTTCCAA
66 TTTCTTTCTTTTTTTGAAGAAATGTTTAGTTTGGAATTAATAAACAGGGCATGAAAAGCTTCCAA
20030037 ATACAAAACATAAATAAAAAACCCAAAGAACCAACCCATAACTAGGTCTGGCCCAACTAGCACCC
131 ATACAAAACATAAATAAAAAACCCAAAGAACCAACCCATAACTAGGTCTGGCCCAACTAGCACCC
*
20030102 GACCATAAGAATACCAAAGAAAGAAAAAGGAAACACTTGAAAATATCTAGGAAAAATAAAACACA
196 GACCATAAGAAAACCAAAGAAAGAAAAAGGAAACACTTGAAAATATCTAGGAAAAATAAAACACA
*
20030167 CAAAAAAAAACA-ATCCAGAAGCTTCTCTGAAACCCTCTTCAGTTACCAAAATACAACCAAGACA
261 CAAAAAAAAA-AGATCCAAAAGCTTCTCTGAAACCCTCTTCAGTTACCAAAATACAACCAAGACA
*
20030231 ACAAATGACCTTTCCAATTGGAGAAACCACTTGGGAAGCAAGATTGAGGTTTGC
325 ACAAATGACCTTCCCAATTGGAGAAACCACTTGGGAAGCAAGATTGAGGTTTGC
20030285 TTAC
1 TTAC
20030289 ACAACAAAAT
Statistics
Matches: 372, Mismatches: 9, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
378 371 1.00
379 1 0.00
ACGTcount: A:0.43, C:0.21, G:0.14, T:0.23
Consensus pattern (378 bp):
TTACCTAAACGTGTCACCAATGTATAATTACAAGTAATTACACCCAAATTCAATTACTAGGTGGC
TTTCTTTCTTTTTTTGAAGAAATGTTTAGTTTGGAATTAATAAACAGGGCATGAAAAGCTTCCAA
ATACAAAACATAAATAAAAAACCCAAAGAACCAACCCATAACTAGGTCTGGCCCAACTAGCACCC
GACCATAAGAAAACCAAAGAAAGAAAAAGGAAACACTTGAAAATATCTAGGAAAAATAAAACACA
CAAAAAAAAAAGATCCAAAAGCTTCTCTGAAACCCTCTTCAGTTACCAAAATACAACCAAGACAA
CAAATGACCTTCCCAATTGGAGAAACCACTTGGGAAGCAAGATTGAGGTTTGC
Found at i:20033025 original size:14 final size:13
Alignment explanation
Indices: 20033004--20033078 Score: 60
Period size: 14 Copynumber: 5.3 Consensus size: 13
20032994 TTATTTTTAG
20033004 TTTTTTTATAATT
1 TTTTTTTATAATT
*
20033017 TTTTATTTATATTT
1 TTTT-TTTATAATT
* *
20033031 TTCATTTATTTTTATT
1 TT--TTT-TTATAATT
20033047 CTTTTTTTATAATT
1 -TTTTTTTATAATT
*
20033061 TTTTTCTTATTATT
1 TTTTT-TTATAATT
20033075 TTTT
1 TTTT
20033079 ATTTTTTATT
Statistics
Matches: 49, Mismatches: 7, Indels: 11
0.73 0.10 0.16
Matches are distributed among these distances:
13 9 0.18
14 27 0.55
15 4 0.08
16 7 0.14
17 2 0.04
ACGTcount: A:0.19, C:0.04, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTTTTTATAATT
Found at i:20033055 original size:17 final size:16
Alignment explanation
Indices: 20033015--20033087 Score: 50
Period size: 17 Copynumber: 4.8 Consensus size: 16
20033005 TTTTTTATAA
20033015 TTTTTTATTTATATTT
1 TTTTTTATTTATATTT
* *
20033031 TTCATTTATTTTTATTCT
1 TT-TTTTATTTATATT-T
20033049 TTTTTTA--TA-ATTT
1 TTTTTTATTTATATTT
20033062 TTTTCTTA-TTAT-TTT
1 TTTT-TTATTTATATTT
*
20033077 TTATTT-TTTAT
1 TTTTTTATTTAT
20033088 TTCCTATTAT
Statistics
Matches: 46, Mismatches: 5, Indels: 14
0.71 0.08 0.22
Matches are distributed among these distances:
13 5 0.11
14 12 0.26
15 9 0.20
16 2 0.04
17 15 0.33
18 3 0.07
ACGTcount: A:0.18, C:0.04, G:0.00, T:0.78
Consensus pattern (16 bp):
TTTTTTATTTATATTT
Found at i:20033079 original size:24 final size:23
Alignment explanation
Indices: 20032992--20033080 Score: 71
Period size: 24 Copynumber: 3.9 Consensus size: 23
20032982 ATATGTCGTT
*
20032992 TTTTATTTTTAGT-TTTTTTATAA
1 TTTT-TTTTTATTATTTTTTATAA
*
20033015 TTTTTTATTTA-TA--TTTT-TCA
1 TTTTTT-TTTATTATTTTTTATAA
* *
20033035 TTTATTTTTATTCTTTTTTTATAA
1 TTTTTTTTTATT-ATTTTTTATAA
20033059 TTTTTTTCTTATTATTTTTTAT
1 TTTTTTT-TTATTATTTTTTAT
20033081 TTTTTATTTC
Statistics
Matches: 52, Mismatches: 6, Indels: 15
0.71 0.08 0.21
Matches are distributed among these distances:
19 4 0.08
20 8 0.15
21 4 0.08
22 3 0.06
23 12 0.23
24 16 0.31
25 5 0.10
ACGTcount: A:0.19, C:0.03, G:0.01, T:0.76
Consensus pattern (23 bp):
TTTTTTTTTATTATTTTTTATAA
Found at i:20033090 original size:24 final size:24
Alignment explanation
Indices: 20033035--20033112 Score: 72
Period size: 24 Copynumber: 3.2 Consensus size: 24
20033025 ATATTTTTCA
* *
20033035 TTTATTT-TTATTCTTTTTTTATAAT
1 TTTATTTCTTATT-ATTTTTTAT-TT
20033060 TTT-TTTCTTATTATTTTTTATTT
1 TTTATTTCTTATTATTTTTTATTT
* *
20033083 TTTATTTCCTATTATCTTTGT-TTT
1 TTTATTTCTTATTAT-TTTTTATTT
20033107 TTTATT
1 TTTATT
20033113 CTTTTTCTTT
Statistics
Matches: 46, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
23 4 0.09
24 30 0.65
25 12 0.26
ACGTcount: A:0.15, C:0.06, G:0.01, T:0.77
Consensus pattern (24 bp):
TTTATTTCTTATTATTTTTTATTT
Found at i:20052066 original size:19 final size:18
Alignment explanation
Indices: 20052023--20052076 Score: 74
Period size: 19 Copynumber: 3.0 Consensus size: 18
20052013 GAATGATGAA
*
20052023 CATACTGGATCGT-TGAG
1 CATACTGGATCGTAAGAG
*
20052040 CATACTGGCTCGTAAGAG
1 CATACTGGATCGTAAGAG
20052058 CATTACTGGATCGTAAGAG
1 CA-TACTGGATCGTAAGAG
20052077 TTAATTTCTT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
17 12 0.38
18 5 0.16
19 15 0.47
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.26
Consensus pattern (18 bp):
CATACTGGATCGTAAGAG
Found at i:20056841 original size:18 final size:18
Alignment explanation
Indices: 20056801--20056844 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 18
20056791 CCACTTCCAC
20056801 GTTCTCCTCCCTTTTTATA
1 GTTC-CCTCCCTTTTTATA
20056820 -TTCCCTCCCTCTTTT-TA
1 GTTCCCTCCCT-TTTTATA
20056837 GTTCCCTC
1 GTTCCCTC
20056845 ACTACCAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
17 9 0.39
18 14 0.61
ACGTcount: A:0.07, C:0.39, G:0.05, T:0.50
Consensus pattern (18 bp):
GTTCCCTCCCTTTTTATA
Found at i:20057095 original size:30 final size:30
Alignment explanation
Indices: 20057059--20057153 Score: 181
Period size: 30 Copynumber: 3.2 Consensus size: 30
20057049 CCGACCCCAT
20057059 CCCCAACCCCATCTGCATCTCCAGCTCCAA
1 CCCCAACCCCATCTGCATCTCCAGCTCCAA
20057089 CCCCAACCCCATCTGCATCTCCAGCTCCAA
1 CCCCAACCCCATCTGCATCTCCAGCTCCAA
*
20057119 CCCCAACCCCATCTGCATCTCCAGCTCAAA
1 CCCCAACCCCATCTGCATCTCCAGCTCCAA
20057149 CCCCA
1 CCCCA
20057154 TCACCCACCA
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 64 1.00
ACGTcount: A:0.24, C:0.54, G:0.06, T:0.16
Consensus pattern (30 bp):
CCCCAACCCCATCTGCATCTCCAGCTCCAA
Found at i:20059147 original size:22 final size:21
Alignment explanation
Indices: 20059122--20059174 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 21
20059112 GAAATACATG
20059122 GGAAAAAATCGACTAACAAGAA
1 GGAAAAAATCGACTAACAAG-A
* *
20059144 GGAAAAAATTCGATTTACAAGA
1 GGAAAAAA-TCGACTAACAAGA
*
20059166 GCAAAAAAT
1 GGAAAAAAT
20059175 TTCGACAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 1 0.04
22 16 0.59
23 10 0.37
ACGTcount: A:0.57, C:0.11, G:0.17, T:0.15
Consensus pattern (21 bp):
GGAAAAAATCGACTAACAAGA
Found at i:20059175 original size:22 final size:23
Alignment explanation
Indices: 20059124--20059180 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 23
20059114 AATACATGGG
*
20059124 AAAAAA-TCGACTAACAAGAAGG
1 AAAAAATTCGACTAACAAGAAGC
* *
20059146 AAAAAATTCGATTTACAAG-AGC
1 AAAAAATTCGACTAACAAGAAGC
20059168 AAAAAATTTCGAC
1 AAAAAA-TTCGAC
20059181 AAATAAAGGG
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
22 14 0.48
23 15 0.52
ACGTcount: A:0.54, C:0.14, G:0.14, T:0.18
Consensus pattern (23 bp):
AAAAAATTCGACTAACAAGAAGC
Found at i:20059739 original size:22 final size:22
Alignment explanation
Indices: 20059710--20059757 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
20059700 ACAGTGTACC
*
20059710 AAAT-ATTTTCCTTAATTATAT
1 AAATAATTTTCATTAATTATAT
*
20059731 TAATAATTTTCATTAATTATAT
1 AAATAATTTTCATTAATTATAT
20059753 AAATA
1 AAATA
20059758 CTAAATTGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 3 0.13
22 20 0.87
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (22 bp):
AAATAATTTTCATTAATTATAT
Found at i:20065301 original size:23 final size:24
Alignment explanation
Indices: 20065269--20065328 Score: 72
Period size: 23 Copynumber: 2.5 Consensus size: 24
20065259 CCTAGTTGCT
*
20065269 GAAAGAAGAA-ATAGAAGAGAAGAA
1 GAAAGAAGAAGA-AGAAGAAAAGAA
20065293 GAAA-AAGAAGAAGAAGAAAAGAA
1 GAAAGAAGAAGAAGAAGAAAAGAA
20065316 GATAAG-AGAAGAA
1 GA-AAGAAGAAGAA
20065329 ATGGAGATAC
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
23 18 0.56
24 14 0.44
ACGTcount: A:0.68, C:0.00, G:0.28, T:0.03
Consensus pattern (24 bp):
GAAAGAAGAAGAAGAAGAAAAGAA
Found at i:20065325 original size:18 final size:16
Alignment explanation
Indices: 20065271--20065329 Score: 55
Period size: 18 Copynumber: 3.4 Consensus size: 16
20065261 TAGTTGCTGA
*
20065271 AAGAAGAAATAGAAGAG
1 AAGAA-AAAAAGAAGAG
20065288 AAGAAGAAAAAGAAGAAG
1 AAGAA-AAAAAGAAG-AG
*
20065306 AAGAAAAGAAGATAAGAG
1 AAGAAAA-AA-AGAAGAG
20065324 AAGAAA
1 AAGAAA
20065330 TGGAGATACC
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
17 16 0.43
18 17 0.46
19 4 0.11
ACGTcount: A:0.69, C:0.00, G:0.27, T:0.03
Consensus pattern (16 bp):
AAGAAAAAAAGAAGAG
Found at i:20065328 original size:3 final size:3
Alignment explanation
Indices: 20065271--20065317 Score: 55
Period size: 3 Copynumber: 16.3 Consensus size: 3
20065261 TAGTTGCTGA
*
20065271 AAG AAG AA- ATAG AAG -AG AAG AAG AAA AAG AAG AAG AAG AA- AAG
1 AAG AAG AAG A-AG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
20065314 AAG A
1 AAG A
20065318 TAAGAGAAGA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
2 5 0.13
3 32 0.84
4 1 0.03
ACGTcount: A:0.70, C:0.00, G:0.28, T:0.02
Consensus pattern (3 bp):
AAG
Found at i:20090066 original size:9 final size:9
Alignment explanation
Indices: 20090054--20090086 Score: 66
Period size: 9 Copynumber: 3.7 Consensus size: 9
20090044 CTTTTGTTGT
20090054 TTTTTAATA
1 TTTTTAATA
20090063 TTTTTAATA
1 TTTTTAATA
20090072 TTTTTAATA
1 TTTTTAATA
20090081 TTTTTA
1 TTTTTA
20090087 TCACAAAACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (9 bp):
TTTTTAATA
Found at i:20090952 original size:15 final size:15
Alignment explanation
Indices: 20090932--20090978 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
20090922 TTTTATAGGC
20090932 TAATTAACTTTTAAT
1 TAATTAACTTTTAAT
**
20090947 TAATT-ACAATTAACT
1 TAATTAACTTTTAA-T
20090962 TAATTAA-TTTTAAT
1 TAATTAACTTTTAAT
20090976 TAA
1 TAA
20090979 AGAGTGGAGC
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
14 10 0.38
15 15 0.58
16 1 0.04
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.49
Consensus pattern (15 bp):
TAATTAACTTTTAAT
Found at i:20090976 original size:19 final size:20
Alignment explanation
Indices: 20090932--20090978 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
20090922 TTTTATAGGC
20090932 TAATTAACTTTTAATTAATTA
1 TAATTAAC-TTTAATTAATTA
* *
20090953 CAATTAAC-TTAATTAATTT
1 TAATTAACTTTAATTAATTA
20090972 TAATTAA
1 TAATTAA
20090979 AGAGTGGAGC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 16 0.70
21 7 0.30
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.49
Consensus pattern (20 bp):
TAATTAACTTTAATTAATTA
Found at i:20092839 original size:3 final size:3
Alignment explanation
Indices: 20092831--20092855 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
20092821 GCGCTCAACA
20092831 TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT T
20092856 GAGGATGTAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:20093717 original size:25 final size:25
Alignment explanation
Indices: 20093657--20093710 Score: 90
Period size: 25 Copynumber: 2.2 Consensus size: 25
20093647 TCCTAAGGGA
* *
20093657 TTTAAACTCTATACAATCTTATCCC
1 TTTAAACTTTATACAATCTTACCCC
20093682 TTTAAACTTTATACAATCTTACCCC
1 TTTAAACTTTATACAATCTTACCCC
20093707 TTTA
1 TTTA
20093711 GGATTTACAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.31, C:0.26, G:0.00, T:0.43
Consensus pattern (25 bp):
TTTAAACTTTATACAATCTTACCCC
Found at i:20095150 original size:22 final size:23
Alignment explanation
Indices: 20095125--20095202 Score: 79
Period size: 25 Copynumber: 3.3 Consensus size: 23
20095115 GAGCACCGAA
20095125 GTGCTAAATGAAGAGCACA-AAC
1 GTGCTAAATGAAGAGCACATAAC
*
20095147 GTGCT-AATCGGAGAGCACATAAC
1 GTGCTAAAT-GAAGAGCACATAAC
* * *
20095170 GTTCTAATATCAGAGAGCACATAAA
1 GTGCTAA-ATGA-AGAGCACATAAC
20095195 GTGCTAAA
1 GTGCTAAA
20095203 CGGAAAGCGC
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
21 3 0.07
22 14 0.31
23 7 0.16
24 2 0.04
25 19 0.42
ACGTcount: A:0.41, C:0.18, G:0.22, T:0.19
Consensus pattern (23 bp):
GTGCTAAATGAAGAGCACATAAC
Found at i:20095176 original size:23 final size:25
Alignment explanation
Indices: 20095136--20095201 Score: 84
Period size: 25 Copynumber: 2.8 Consensus size: 25
20095126 TGCTAAATGA
*
20095136 AGAGCACA-AACGTGCT-A-ATCGG
1 AGAGCACATAACGTGCTAATATCAG
*
20095158 AGAGCACATAACGTTCTAATATCAG
1 AGAGCACATAACGTGCTAATATCAG
*
20095183 AGAGCACATAAAGTGCTAA
1 AGAGCACATAACGTGCTAA
20095202 ACGGAAAGCG
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
22 8 0.22
23 7 0.19
24 1 0.03
25 21 0.57
ACGTcount: A:0.41, C:0.20, G:0.21, T:0.18
Consensus pattern (25 bp):
AGAGCACATAACGTGCTAATATCAG
Found at i:20095415 original size:27 final size:27
Alignment explanation
Indices: 20095381--20095450 Score: 133
Period size: 27 Copynumber: 2.6 Consensus size: 27
20095371 ATTAATTCCA
20095381 CAAT-TTCATCATTAAATTCACATAAT
1 CAATATTCATCATTAAATTCACATAAT
20095407 CAATATTCATCATTAAATTCACATAAT
1 CAATATTCATCATTAAATTCACATAAT
20095434 CAATATTCATCATTAAA
1 CAATATTCATCATTAAA
20095451 CACATTAAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
26 4 0.09
27 39 0.91
ACGTcount: A:0.44, C:0.19, G:0.00, T:0.37
Consensus pattern (27 bp):
CAATATTCATCATTAAATTCACATAAT
Found at i:20107641 original size:14 final size:12
Alignment explanation
Indices: 20107617--20107691 Score: 50
Period size: 13 Copynumber: 6.2 Consensus size: 12
20107607 TCCCAATTAT
20107617 TTTTATTGTTTA
1 TTTTATTGTTTA
20107629 TATTTATTTGTTTA
1 T-TTTA-TTGTTTA
***
20107643 TTTTAGCATTTAA
1 TTTTATTGTTT-A
20107656 TTTTAATT-TTTA
1 TTTT-ATTGTTTA
*
20107668 -TTT-TTATTTA
1 TTTTATTGTTTA
20107678 TTTT-TTGTTTA
1 TTTTATTGTTTA
20107689 TTT
1 TTT
20107692 ATGTAGTTGT
Statistics
Matches: 51, Mismatches: 6, Indels: 13
0.73 0.09 0.19
Matches are distributed among these distances:
9 2 0.04
10 4 0.08
11 15 0.29
12 5 0.10
13 16 0.31
14 9 0.18
ACGTcount: A:0.20, C:0.01, G:0.05, T:0.73
Consensus pattern (12 bp):
TTTTATTGTTTA
Found at i:20107790 original size:4 final size:4
Alignment explanation
Indices: 20107735--20107797 Score: 51
Period size: 4 Copynumber: 15.2 Consensus size: 4
20107725 TATTATCTCT
*
20107735 TTTA -TTA TTT- TTTA TTTAA TTTGAA TTTA TGTTA -TTA TCTTA TTTG
1 TTTA TTTA TTTA TTTA TTT-A TTT--A TTTA T-TTA TTTA T-TTA TTTA
20107781 TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA T
20107798 CATTAATTTT
Statistics
Matches: 50, Mismatches: 2, Indels: 14
0.76 0.03 0.21
Matches are distributed among these distances:
3 9 0.18
4 25 0.50
5 11 0.22
6 5 0.10
ACGTcount: A:0.24, C:0.02, G:0.05, T:0.70
Consensus pattern (4 bp):
TTTA
Found at i:20107922 original size:17 final size:16
Alignment explanation
Indices: 20107889--20107985 Score: 74
Period size: 17 Copynumber: 5.8 Consensus size: 16
20107879 GTATTTCATA
*
20107889 TATTTA-TTGTTTTAT
1 TATTTATTTATTTTAT
20107904 TATTTATTTATTATTAT
1 TATTTATTTATT-TTAT
*
20107921 TATTT-GTTATTTATAT
1 TATTTATTTATTT-TAT
* *
20107937 TATTGTTTTTATTTAATTT
1 TATT-TATTTATTT--TAT
20107956 TATTTA-TTATTTTAT
1 TATTTATTTATTTTAT
20107971 GTATTTTATTTATTT
1 -TA-TTTATTTATTT
20107986 GTTATTTTTA
Statistics
Matches: 67, Mismatches: 6, Indels: 15
0.76 0.07 0.17
Matches are distributed among these distances:
15 9 0.13
16 18 0.27
17 20 0.30
18 13 0.19
19 7 0.10
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.72
Consensus pattern (16 bp):
TATTTATTTATTTTAT
Found at i:20107936 original size:45 final size:46
Alignment explanation
Indices: 20107887--20108078 Score: 165
Period size: 44 Copynumber: 4.2 Consensus size: 46
20107877 TTGTATTTCA
20107887 TATATTTATTGTTTTATTATTTATTTA-TTATTATTATT-TGTTATT
1 TATATTTATTGTTTTATTATTTATTTATTTATTATT-TTATGTTATT
20107932 TATA-TTATTG-TTT-TTATTTAATTTTATTTATTATTTTATG-TATT
1 TATATTTATTGTTTTATTATTT-A-TTTATTTATTATTTTATGTTATT
* *
20107976 T-TATTTATT-TGTTATT-TTTATGCTATTTA-TATTTT-TGCCTTCATT
1 TATATTTATTGTTTTATTATTTAT-TTATTTATTATTTTATG--TT-ATT
20108021 TAATTTAATTTATTGTTTTATGTATTTTATTTATTTATT-TTTTATGTTATT
1 T-A--T-ATTTATTGTTTTAT-TA-TTTATTTATTTATTATTTTATGTTATT
20108072 TATATTT
1 TATATTT
20108079 TTGCCTTCAT
Statistics
Matches: 120, Mismatches: 4, Indels: 44
0.71 0.02 0.26
Matches are distributed among these distances:
41 2 0.02
42 13 0.11
43 13 0.11
44 28 0.23
45 20 0.17
47 4 0.03
48 1 0.01
49 1 0.01
50 8 0.07
51 9 0.08
52 3 0.03
53 10 0.08
54 8 0.07
ACGTcount: A:0.23, C:0.02, G:0.05, T:0.70
Consensus pattern (46 bp):
TATATTTATTGTTTTATTATTTATTTATTTATTATTTTATGTTATT
Found at i:20107949 original size:31 final size:32
Alignment explanation
Indices: 20107899--20107996 Score: 111
Period size: 31 Copynumber: 3.2 Consensus size: 32
20107889 TATTTATTGT
*
20107899 TTTATTATT-TATTTATTATTA-TTATTTGTTA
1 TTTATTATTATATGTATT-TTATTTATTTGTTA
*
20107930 TTTA-TATTAT-TGT-TTTTATTTAATT-TTA
1 TTTATTATTATATGTATTTTATTTATTTGTTA
*
20107958 TTTATTATTTTATGTATTTTATTTATTTGTTA
1 TTTATTATTATATGTATTTTATTTATTTGTTA
20107990 TTT-TTAT
1 TTTATTAT
20107997 GCTATTTATA
Statistics
Matches: 57, Mismatches: 4, Indels: 12
0.78 0.05 0.16
Matches are distributed among these distances:
28 10 0.18
29 12 0.21
30 9 0.16
31 20 0.35
32 6 0.11
ACGTcount: A:0.23, C:0.00, G:0.04, T:0.72
Consensus pattern (32 bp):
TTTATTATTATATGTATTTTATTTATTTGTTA
Found at i:20107959 original size:22 final size:21
Alignment explanation
Indices: 20107892--20107980 Score: 67
Period size: 22 Copynumber: 4.1 Consensus size: 21
20107882 TTTCATATAT
20107892 TTATTGTTTTATTATTTA-TTTA
1 TTATTG-TTT-TTATTTATTTTA
* *
20107914 TTATTATTATTT-GTTATTTATA
1 TTATTGTT-TTTATTTATTT-TA
20107936 TTATTGTTTTTATTTAATTTTA
1 TTATTGTTTTTATTT-ATTTTA
* *
20107958 TTTATT-ATTTTATGTATTTTA
1 -TTATTGTTTTTATTTATTTTA
20107979 TT
1 TT
20107981 TATTTGTTAT
Statistics
Matches: 55, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
20 5 0.09
21 15 0.27
22 26 0.47
23 9 0.16
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.72
Consensus pattern (21 bp):
TTATTGTTTTTATTTATTTTA
Found at i:20107992 original size:25 final size:28
Alignment explanation
Indices: 20107946--20108009 Score: 82
Period size: 26 Copynumber: 2.4 Consensus size: 28
20107936 TTATTGTTTT
20107946 TATTTA-ATTTTATTTATTA-TTTTATG-
1 TATTTATA-TTTATTTATTATTTTTATGC
*
20107972 TATTT-TATTTATTTGTTATTTTTATGC
1 TATTTATATTTATTTATTATTTTTATGC
20107999 TATTTATATTT
1 TATTTATATTT
20108010 TTGCCTTCAT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
25 10 0.30
26 13 0.39
27 5 0.15
28 5 0.15
ACGTcount: A:0.23, C:0.02, G:0.05, T:0.70
Consensus pattern (28 bp):
TATTTATATTTATTTATTATTTTTATGC
Found at i:20108034 original size:71 final size:70
Alignment explanation
Indices: 20107889--20108103 Score: 303
Period size: 71 Copynumber: 3.1 Consensus size: 70
20107879 GTATTTCATA
* * * ** *
20107889 TATTTATTGTTTTAT-TA-TTTATTTATTATTATTATT-TGTTATTTATATTATTGTTTTTATTT
1 TATTTATTGTTTTATGTATTTTATTTATTTTTATTTTTATGTTATTTATATTTTTGCCTTCATTT
20107951 AATTT
66 AATTT
* *
20107956 TATTTATTATTTTATGTATTTTATTTATTTGTTATTTTTATGCTATTTATATTTTTGCCTTCATT
1 TATTTATTGTTTTATGTATTTTATTTATTT-TTATTTTTATGTTATTTATATTTTTGCCTTCATT
20108021 TAATTT
65 TAATTT
* *
20108027 AATTTATTGTTTTATGTATTTTATTTATTTAT-TTTTTATGTTATTTATATTTTTGCCTTCATTT
1 TATTTATTGTTTTATGTATTTTATTTATTTTTATTTTTATGTTATTTATATTTTTGCCTTCATTT
20108091 AATTT
66 AATTT
20108096 TATTTATT
1 TATTTATT
20108104 CATGGATTTG
Statistics
Matches: 131, Mismatches: 13, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
67 14 0.11
68 2 0.02
69 53 0.40
70 8 0.06
71 54 0.41
ACGTcount: A:0.22, C:0.03, G:0.05, T:0.69
Consensus pattern (70 bp):
TATTTATTGTTTTATGTATTTTATTTATTTTTATTTTTATGTTATTTATATTTTTGCCTTCATTT
AATTT
Found at i:20108057 original size:17 final size:17
Alignment explanation
Indices: 20107878--20108074 Score: 66
Period size: 17 Copynumber: 11.1 Consensus size: 17
20107868 TTTTTATGAT
* *
20107878 TGTATTTCATATATTTA
1 TGTATTTTATTTATTTA
*
20107895 TTGTTTTATTATTTATTTA
1 -TGTATT-TTATTTATTTA
*
20107914 T-TATTATTATTT-GTTA
1 TGTATT-TTATTTATTTA
* * *
20107930 TTTATATTATTGTTTTTA
1 TGTATTTTATT-TATTTA
*
20107948 TTTAATTTTATTTATTATTTTA
1 TGT-ATTTTA--T-TTA-TTTA
*
20107970 TGTATTTTATTTATTTG
1 TGTATTTTATTTATTTA
*
20107987 T-TATTTTTATGCTATTTA
1 TGTA-TTTTAT-TTATTTA
* * *
20108005 TAT-TTTTGCCTTCATTTAA
1 TGTATTTT--ATTTATTT-A
* *
20108024 TTTAATTTATTGT-TTTA
1 TGTATTTTATT-TATTTA
20108041 TGTATTTTATTTATTTA
1 TGTATTTTATTTATTTA
20108058 T-T-TTTTATGTTATTTA
1 TGTATTTTAT-TTATTTA
20108074 T
1 T
20108075 ATTTTTGCCT
Statistics
Matches: 138, Mismatches: 22, Indels: 40
0.69 0.11 0.20
Matches are distributed among these distances:
15 6 0.04
16 21 0.15
17 43 0.31
18 30 0.22
19 20 0.14
20 3 0.02
21 8 0.06
22 7 0.05
ACGTcount: A:0.23, C:0.03, G:0.06, T:0.69
Consensus pattern (17 bp):
TGTATTTTATTTATTTA
Found at i:20108073 original size:9 final size:8
Alignment explanation
Indices: 20107889--20108074 Score: 68
Period size: 9 Copynumber: 22.4 Consensus size: 8
20107879 GTATTTCATA
20107889 TATTTATT
1 TATTTATT
20107897 GT-TTTA-T
1 -TATTTATT
20107904 TATTTATT
1 TATTTATT
20107912 TA-TTA-T
1 TATTTATT
20107918 TA-TTATT
1 TATTTATT
*
20107925 T-GTTATT
1 TATTTATT
20107932 TATATTATT
1 TAT-TTATT
*
20107941 GTTTTTATT
1 -TATTTATT
20107950 TAATTTTATT
1 T-A-TTTATT
20107960 TA-TTATTT
1 TATTTA-TT
*
20107968 TATGTATTT
1 TATTTA-TT
20107977 TATTTATT
1 TATTTATT
* *
20107985 TGTTATTTT
1 TATT-TATT
*
20107994 TATGCTATT
1 TAT-TTATT
20108003 TATATT-TT
1 TAT-TTATT
* *
20108011 TGCCTTCATT
1 T--ATTTATT
20108021 TAATTTAATT
1 T-ATTT-ATT
20108031 TATTGT-TT
1 TATT-TATT
*
20108039 TATGTATTT
1 TATTTA-TT
20108048 TATTTATT
1 TATTTATT
20108056 TATTT-TT
1 TATTTATT
20108063 TATGTTATT
1 TAT-TTATT
20108072 TAT
1 TAT
20108075 ATTTTTGCCT
Statistics
Matches: 136, Mismatches: 19, Indels: 44
0.68 0.10 0.22
Matches are distributed among these distances:
6 7 0.05
7 25 0.18
8 34 0.25
9 52 0.38
10 18 0.13
ACGTcount: A:0.23, C:0.02, G:0.05, T:0.70
Consensus pattern (8 bp):
TATTTATT
Found at i:20108318 original size:29 final size:29
Alignment explanation
Indices: 20108208--20108319 Score: 91
Period size: 29 Copynumber: 3.7 Consensus size: 29
20108198 TTATGTTTTA
* * *
20108208 TATATATTTATTGTTGTTTATATTATTAAT
1 TATATTTTTATTGTTATTAATATTA-TAAT
* * * *
20108238 TAATATTTATTTATTGTCATTATTACTATGAT
1 T-ATA-TT-TTTATTGTTATTAATATTATAAT
**
20108270 TATATTGCTATT-TTATTTAATATTATAAT
1 TATATTTTTATTGTTA-TTAATATTATAAT
20108299 TATATTTTTATTGTTATTAAT
1 TATATTTTTATTGTTATTAAT
20108320 TGTATTTGAA
Statistics
Matches: 62, Mismatches: 15, Indels: 11
0.70 0.17 0.12
Matches are distributed among these distances:
28 2 0.03
29 29 0.47
30 6 0.10
31 6 0.10
32 5 0.08
33 14 0.23
ACGTcount: A:0.31, C:0.03, G:0.05, T:0.61
Consensus pattern (29 bp):
TATATTTTTATTGTTATTAATATTATAAT
Found at i:20109683 original size:4 final size:4
Alignment explanation
Indices: 20109669--20109720 Score: 63
Period size: 4 Copynumber: 12.8 Consensus size: 4
20109659 GAAGAAGGAG
20109669 GAAA GGAAA GAAA GAAA GAAA GAAA G-AA GAAGGA GAAA -AAA GAAA GAAA
1 GAAA -GAAA GAAA GAAA GAAA GAAA GAAA GAA--A GAAA GAAA GAAA GAAA
20109718 GAA
1 GAA
20109721 TACGGAGAAG
Statistics
Matches: 43, Mismatches: 0, Indels: 9
0.83 0.00 0.17
Matches are distributed among these distances:
3 6 0.14
4 29 0.67
5 4 0.09
6 4 0.09
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:20109697 original size:32 final size:32
Alignment explanation
Indices: 20109657--20109720 Score: 101
Period size: 32 Copynumber: 1.9 Consensus size: 32
20109647 GCTACGGGAG
20109657 AAGAAGAAGGAGGAAAGGAAAGAAAGAAAGAAAGA
1 AAGAAGAAGGA-GAAA--AAAGAAAGAAAGAAAGA
20109692 AAGAAGAAGGAGAAAAAAGAAAGAAAGAA
1 AAGAAGAAGGAGAAAAAAGAAAGAAAGAA
20109721 TACGGAGAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
32 14 0.48
34 4 0.14
35 11 0.38
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (32 bp):
AAGAAGAAGGAGAAAAAAGAAAGAAAGAAAGA
Found at i:20109710 original size:24 final size:25
Alignment explanation
Indices: 20109677--20109729 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 25
20109667 AGGAAAGGAA
20109677 AGAAAGAAAGAAAGAAAGAAGAAGG
1 AGAAAGAAAGAAAGAAAGAAGAAGG
* *
20109702 AGAAA-AAAGAAAGAAAGAATACGG
1 AGAAAGAAAGAAAGAAAGAAGAAGG
20109726 AGAA
1 AGAA
20109730 GATTTTATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
24 21 0.81
25 5 0.19
ACGTcount: A:0.68, C:0.02, G:0.28, T:0.02
Consensus pattern (25 bp):
AGAAAGAAAGAAAGAAAGAAGAAGG
Found at i:20111485 original size:43 final size:43
Alignment explanation
Indices: 20111434--20111533 Score: 157
Period size: 43 Copynumber: 2.3 Consensus size: 43
20111424 TGTTATTCCT
*
20111434 TGACATGTTATTAAATTATATTACTTGAC-CTGTGTTAATATCG
1 TGACATGTTATTAAATTATATTACTTGACTCT-TATTAATATCG
* *
20111477 TGGCATGTTATTAAATTATATTATTTGACTCTTATTAATATCG
1 TGACATGTTATTAAATTATATTACTTGACTCTTATTAATATCG
20111520 TGACATGTTATTAA
1 TGACATGTTATTAA
20111534 TTGTGCAGTT
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
43 50 0.96
44 2 0.04
ACGTcount: A:0.31, C:0.10, G:0.13, T:0.46
Consensus pattern (43 bp):
TGACATGTTATTAAATTATATTACTTGACTCTTATTAATATCG
Done.