Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 124536837
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: 124536837
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 312 characters in sequence are not A, C, G, or T
File 340 of 427
Found at i:99135019 original size:12 final size:12
Alignment explanation
Indices: 99135004--99135032 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
99134994 AGGATCATCC
99135004 TCATCATCAGAT
1 TCATCATCAGAT
99135016 TCATCATCAGAT
1 TCATCATCAGAT
99135028 TCATC
1 TCATC
99135033 CCTCGATCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.31, C:0.28, G:0.07, T:0.34
Consensus pattern (12 bp):
TCATCATCAGAT
Found at i:99136719 original size:9 final size:9
Alignment explanation
Indices: 99136705--99136872 Score: 121
Period size: 9 Copynumber: 18.9 Consensus size: 9
99136695 TTACAGTTAC
99136705 TTATGTAAG
1 TTATGTAAG
99136714 TTATGTAAG
1 TTATGTAAG
99136723 TTATG-ATA-
1 TTATGTA-AG
* * *
99136731 TAATAT-AT
1 TTATGTAAG
*
99136739 TTATGTACG
1 TTATGTAAG
*
99136748 TTATGTAAA
1 TTATGTAAG
99136757 TTATGTAAG
1 TTATGTAAG
99136766 TTATGTAAG
1 TTATGTAAG
99136775 TTATGTAAG
1 TTATGTAAG
*
99136784 TTATGATATG
1 TTATG-TAAG
* * *
99136794 ATATAT-AT
1 TTATGTAAG
*
99136802 TTATGTATG
1 TTATGTAAG
*
99136811 TTATGTAAA
1 TTATGTAAG
99136820 TTATGTAAG
1 TTATGTAAG
*
99136829 TTATGGTATG
1 TTAT-GTAAG
* * *
99136839 ATATAT-AT
1 TTATGTAAG
*
99136847 TTATGTACG
1 TTATGTAAG
*
99136856 TTATGTAAC
1 TTATGTAAG
99136865 TTATGTAA
1 TTATGTAA
99136873 ATTTTAACAC
Statistics
Matches: 119, Mismatches: 32, Indels: 16
0.71 0.19 0.10
Matches are distributed among these distances:
7 1 0.01
8 16 0.13
9 89 0.75
10 13 0.11
ACGTcount: A:0.35, C:0.02, G:0.17, T:0.47
Consensus pattern (9 bp):
TTATGTAAG
Found at i:99136808 original size:45 final size:45
Alignment explanation
Indices: 99136757--99136872 Score: 187
Period size: 45 Copynumber: 2.6 Consensus size: 45
99136747 GTTATGTAAA
*
99136757 TTATGTAAGTTATGTAAGTTATGTAAGTTATGATATGATATATAT
1 TTATGTAAGTTATGTAAATTATGTAAGTTATGATATGATATATAT
* *
99136802 TTATGTATGTTATGTAAATTATGTAAGTTATGGTATGATATATAT
1 TTATGTAAGTTATGTAAATTATGTAAGTTATGATATGATATATAT
* *
99136847 TTATGTACGTTATGTAACTTATGTAA
1 TTATGTAAGTTATGTAAATTATGTAA
99136873 ATTTTAACAC
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 66 1.00
ACGTcount: A:0.34, C:0.02, G:0.17, T:0.47
Consensus pattern (45 bp):
TTATGTAAGTTATGTAAATTATGTAAGTTATGATATGATATATAT
Found at i:99136829 original size:63 final size:61
Alignment explanation
Indices: 99136705--99136833 Score: 231
Period size: 63 Copynumber: 2.1 Consensus size: 61
99136695 TTACAGTTAC
99136705 TTATGTAAGTTATGTAAGTTATGATATAATATATTTATGTACGTTATGTAAATTATGTAAG
1 TTATGTAAGTTATGTAAGTTATGATATAATATATTTATGTACGTTATGTAAATTATGTAAG
*
99136766 TTATGTAAGTTATGTAAGTTATGATATGATATATATTTATGTATGTTATGTAAATTATGTAAG
1 TTATGTAAGTTATGTAAGTTATGATAT-A-ATATATTTATGTACGTTATGTAAATTATGTAAG
99136829 TTATG
1 TTATG
99136834 GTATGATATA
Statistics
Matches: 65, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
61 27 0.42
62 1 0.02
63 37 0.57
ACGTcount: A:0.35, C:0.01, G:0.17, T:0.47
Consensus pattern (61 bp):
TTATGTAAGTTATGTAAGTTATGATATAATATATTTATGTACGTTATGTAAATTATGTAAG
Found at i:99139621 original size:88 final size:89
Alignment explanation
Indices: 99139497--99139660 Score: 276
Period size: 88 Copynumber: 1.9 Consensus size: 89
99139487 CTATTGCAGC
* *
99139497 GTTTTACCCTAAAACGCCACTAAAAATCAAACAAAACGACGCCGTTTTGTTATAAACAGAATAAC
1 GTTTTACCCTAAAACACCACTAAAAATCAAACAAAACGACGCCGTTTTGATATAAACAGAATAAC
99139562 CTTTAGTGGCACTAGGCTAAAGGT
66 CTTTAGTGGCACTAGGCTAAAGGT
* *
99139586 GTTTTACCCTAAAACACCAC-AAAAATCCAACAAAACGACGTCGTTTTGATATAAACAGAATAAC
1 GTTTTACCCTAAAACACCACTAAAAATCAAACAAAACGACGCCGTTTTGATATAAACAGAATAAC
*
99139650 TTTTAGTGGCA
66 CTTTAGTGGCA
99139661 TTTATCCCCT
Statistics
Matches: 70, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
88 51 0.73
89 19 0.27
ACGTcount: A:0.40, C:0.21, G:0.14, T:0.25
Consensus pattern (89 bp):
GTTTTACCCTAAAACACCACTAAAAATCAAACAAAACGACGCCGTTTTGATATAAACAGAATAAC
CTTTAGTGGCACTAGGCTAAAGGT
Found at i:99139918 original size:112 final size:114
Alignment explanation
Indices: 99139583--99139923 Score: 485
Period size: 114 Copynumber: 3.0 Consensus size: 114
99139573 CTAGGCTAAA
* *
99139583 GGTGTTTTACCCTAAAACACCAC-AAAAATCCAACAAAACGACGTCGTTTTGATATAAACAGAAT
1 GGTGTTTTACCCTAAAACGCCACTAAAAATCCAACAAAACGACTTCGTTTTGATATAAACAGAAT
*
99139647 AA-CTTTTAGTGGCATTTATCCCCTAGCGCCGCTAAATCCAACCTATTGC
66 AACCTTTT-GTGGCGTTTATCCCCTAGCGCCGCTAAATCCAACCTATTGC
* *
99139696 GGTGTTTTACCCTAAAATGCCATTAAAAATCCAACAAAACGA-TGTCGTTTTGATATAAACAGAA
1 GGTGTTTTACCCTAAAACGCCACTAAAAATCCAACAAAACGACT-TCGTTTTGATATAAACAGAA
* ** *
99139760 TAACCGTTAATGGCGTTTATCCCCTAGCGCCGCTAAATCCAGCCTATTGC
65 TAACCTTTTGTGGCGTTTATCCCCTAGCGCCGCTAAATCCAACCTATTGC
* * * * *
99139810 TGTGTTTTACCTTAAAACGCCACTAAAAATCCAACAAAATGACTTCG-TTTGGTGT-AACAGAAT
1 GGTGTTTTACCCTAAAACGCCACTAAAAATCCAACAAAACGACTTCGTTTTGATATAAACAGAAT
* *
99139873 AACCTTTTGTGGCGTTTATACCCTAGCACCGCTAAATCCAACCTATTGC
66 AACCTTTTGTGGCGTTTATCCCCTAGCGCCGCTAAATCCAACCTATTGC
99139922 GG
1 GG
99139924 CGTTCAACTA
Statistics
Matches: 201, Mismatches: 23, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
112 52 0.26
113 26 0.13
114 119 0.59
115 4 0.02
ACGTcount: A:0.33, C:0.24, G:0.15, T:0.28
Consensus pattern (114 bp):
GGTGTTTTACCCTAAAACGCCACTAAAAATCCAACAAAACGACTTCGTTTTGATATAAACAGAAT
AACCTTTTGTGGCGTTTATCCCCTAGCGCCGCTAAATCCAACCTATTGC
Found at i:99140508 original size:21 final size:21
Alignment explanation
Indices: 99140487--99140533 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
99140477 CCTAAAACTT
99140487 AACCCCTAACCATTAAGCCTTA
1 AACCCC-AACCATTAAGCCTTA
* * *
99140509 AACCCCAACCCTTAAACCATA
1 AACCCCAACCATTAAGCCTTA
99140530 AACC
1 AACC
99140534 ATAATCCCTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 16 0.73
22 6 0.27
ACGTcount: A:0.40, C:0.40, G:0.02, T:0.17
Consensus pattern (21 bp):
AACCCCAACCATTAAGCCTTA
Found at i:99140550 original size:15 final size:15
Alignment explanation
Indices: 99140515--99140562 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
99140505 CTTAAACCCC
* *
99140515 AACCCTTAAACCATA
1 AACCCATAATCCATA
*
99140530 AA-CCATAATCCCTA
1 AACCCATAATCCATA
99140544 AACCCATAATCCATA
1 AACCCATAATCCATA
99140559 AACC
1 AACC
99140563 TTAAAATAGT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
14 11 0.39
15 17 0.61
ACGTcount: A:0.46, C:0.35, G:0.00, T:0.19
Consensus pattern (15 bp):
AACCCATAATCCATA
Found at i:99140567 original size:22 final size:22
Alignment explanation
Indices: 99140518--99140611 Score: 90
Period size: 22 Copynumber: 4.4 Consensus size: 22
99140508 AAACCCCAAC
*
99140518 CCTTAAA-CCATAAACCATAAT
1 CCTTAAACCCATAAACCATAAA
* *
99140539 CCCTAAACCCATAATCCATAAA
1 CCTTAAACCCATAAACCATAAA
99140561 CCTTAAA---ATAGTAACTCATAAA
1 CCTTAAACCCATA--AAC-CATAAA
*
99140583 CTTTAAACCC-TAAACCATAAA
1 CCTTAAACCCATAAACCATAAA
99140604 CCTTAAAC
1 CCTTAAAC
99140612 TATAAGATAA
Statistics
Matches: 59, Mismatches: 7, Indels: 14
0.74 0.09 0.17
Matches are distributed among these distances:
19 3 0.05
21 21 0.36
22 33 0.56
24 2 0.03
ACGTcount: A:0.47, C:0.29, G:0.01, T:0.23
Consensus pattern (22 bp):
CCTTAAACCCATAAACCATAAA
Found at i:99140603 original size:14 final size:14
Alignment explanation
Indices: 99140515--99140616 Score: 55
Period size: 14 Copynumber: 7.1 Consensus size: 14
99140505 CTTAAACCCC
99140515 AACCCTTAAACCATA
1 AACCC-TAAACCATA
* * *
99140530 AACCATAATCCCTA
1 AACCCTAAACCATA
*
99140544 AACCCATAATCCATA
1 AACCC-TAAACCATA
*
99140559 AACCTTAAA--ATA
1 AACCCTAAACCATA
* **
99140571 GTAACTCATAAACTTTA
1 --AAC-CCTAAACCATA
99140588 AACCCTAAACCATA
1 AACCCTAAACCATA
* *
99140602 AACCTTAAACTATA
1 AACCCTAAACCATA
99140616 A
1 A
99140617 GATAATTAAT
Statistics
Matches: 67, Mismatches: 14, Indels: 13
0.71 0.15 0.14
Matches are distributed among these distances:
12 3 0.04
14 38 0.57
15 24 0.36
17 2 0.03
ACGTcount: A:0.48, C:0.27, G:0.01, T:0.24
Consensus pattern (14 bp):
AACCCTAAACCATA
Found at i:99141154 original size:14 final size:14
Alignment explanation
Indices: 99141054--99141154 Score: 91
Period size: 14 Copynumber: 7.3 Consensus size: 14
99141044 ATATTTACCC
*
99141054 CTAAACCCTAAACT
1 CTAAACCATAAACT
*
99141068 -TAAACCTTAAA-T
1 CTAAACCATAAACT
*
99141080 CTCAAACCATAAACC
1 CT-AAACCATAAACT
*
99141095 CCAAACCATAAACT
1 CTAAACCATAAACT
* *
99141109 CT-AAGCACTAAATT
1 CTAAACCA-TAAACT
* *
99141123 ATAAACCATAAACC
1 CTAAACCATAAACT
99141137 CTAAACCATAAACT
1 CTAAACCATAAACT
99141151 CTAA
1 CTAA
99141155 TGACACTAAT
Statistics
Matches: 68, Mismatches: 14, Indels: 10
0.74 0.15 0.11
Matches are distributed among these distances:
12 1 0.01
13 15 0.22
14 47 0.69
15 5 0.07
ACGTcount: A:0.49, C:0.30, G:0.01, T:0.21
Consensus pattern (14 bp):
CTAAACCATAAACT
Found at i:99141377 original size:40 final size:38
Alignment explanation
Indices: 99141321--99141459 Score: 146
Period size: 40 Copynumber: 3.7 Consensus size: 38
99141311 TTTTTTTGCC
* *
99141321 GCGTTTTTCAGAAAGCGCCGCTAATGGTCGACCTATAGCG
1 GCGTTTTT-AG-AAGCGCCGCTAATGCTCGATCTATAGCG
*
99141361 GCGTTTTTCAAGAAGCGCC-CTAATGCTCGATCTATAGCA
1 GCGTTTTT--AGAAGCGCCGCTAATGCTCGATCTATAGCG
*
99141400 GCG--TTT--AA-CGCCGCTAATGCTTGATCTATAGCG
1 GCGTTTTTAGAAGCGCCGCTAATGCTCGATCTATAGCG
99141433 GCGTTTTTAGGAATGCGCCGCTAATGC
1 GCGTTTTTA-GAA-GCGCCGCTAATGC
99141460 CAGTAAAGCT
Statistics
Matches: 84, Mismatches: 6, Indels: 18
0.78 0.06 0.17
Matches are distributed among these distances:
32 4 0.05
33 23 0.27
35 3 0.04
37 3 0.04
38 2 0.02
39 20 0.24
40 27 0.32
41 2 0.02
ACGTcount: A:0.22, C:0.24, G:0.25, T:0.28
Consensus pattern (38 bp):
GCGTTTTTAGAAGCGCCGCTAATGCTCGATCTATAGCG
Found at i:99141426 original size:33 final size:32
Alignment explanation
Indices: 99141376--99141438 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 32
99141366 TTTCAAGAAG
99141376 CGCCCTAATGCTCGATCTATAGCAGCGTTTAA
1 CGCCCTAATGCTCGATCTATAGCAGCGTTTAA
* *
99141408 CGCCGCTAATGCTTGATCTATAGCGGCGTTT
1 CGCC-CTAATGCTCGATCTATAGCAGCGTTT
99141439 TTAGGAATGC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
32 4 0.14
33 24 0.86
ACGTcount: A:0.21, C:0.27, G:0.22, T:0.30
Consensus pattern (32 bp):
CGCCCTAATGCTCGATCTATAGCAGCGTTTAA
Found at i:99141573 original size:187 final size:187
Alignment explanation
Indices: 99141223--99141637 Score: 560
Period size: 187 Copynumber: 2.3 Consensus size: 187
99141213 TCGAAAAGCT
* *
99141223 CCGCTAATGCTCGATCTATGGCAGCGATTTTAAAAAAGCGCCGCTAATGCCATTAAAGCTCAACA
1 CCGCTAATGCTCGATCTATAGCAGCGATTTTAAAAAAGCGCCGCTAATGCCAGTAAAGCTCAACA
*
99141288 TAAAACGACGACATTGTGCTTAATTTTTTTGCCGCGTTTTTCAGAAAGCGCCGCTAATGGTCGAC
66 TAAAACGACGACATTGTGCTTAATTTTTTTGCAGCGTTTTTCAGAAAGCGCCGCTAATGGTCGAC
99141353 CTATAGCGGCGTTTTTCAAGAAGCGCCCTAATGCTCGATCTATAGCAGCGTTTAACG
131 CTATAGCGGCGTTTTTCAAGAAGCGCCCTAATGCTCGATCTATAGCAGCGTTTAACG
* * * ** *
99141410 CCGCTAATGCTTGATCTATAGCGGCGTTTTTAGGAATGCGCCGCTAATGCCAGTAAAGCTCAACA
1 CCGCTAATGCTCGATCTATAGCAGCGATTTTAAAAAAGCGCCGCTAATGCCAGTAAAGCTCAACA
* * *
99141475 TAAAACGGCGACGTTGTGCTTAATTTTTTT-CAGCGTTTTTCAGAAAGCGTCGCTAATGGTCGAC
66 TAAAACGACGACATTGTGCTTAATTTTTTTGCAGCGTTTTTCAGAAAGCGCCGCTAATGGTCGAC
* ** * * *
99141539 CTATAGCGGCATTTTT-TGGAAAGCGTCGCTAATGCTCGATCTATAGCGGCGATT----
131 CTATAGCGGCGTTTTTCAAG-AAGCG-CCCTAATGCTCGATCTATAGCAGCGTTTAACG
* * *
99141593 ---CTAATGCTCGATCTATAGCGGCGATTTTCAAAAAGCGCCACTAAT
1 CCGCTAATGCTCGATCTATAGCAGCGATTTTAAAAAAGCGCCGCTAAT
99141638 TCTCGATCTA
Statistics
Matches: 201, Mismatches: 25, Indels: 11
0.85 0.11 0.05
Matches are distributed among these distances:
180 38 0.19
185 1 0.00
186 52 0.26
187 110 0.55
ACGTcount: A:0.26, C:0.23, G:0.22, T:0.29
Consensus pattern (187 bp):
CCGCTAATGCTCGATCTATAGCAGCGATTTTAAAAAAGCGCCGCTAATGCCAGTAAAGCTCAACA
TAAAACGACGACATTGTGCTTAATTTTTTTGCAGCGTTTTTCAGAAAGCGCCGCTAATGGTCGAC
CTATAGCGGCGTTTTTCAAGAAGCGCCCTAATGCTCGATCTATAGCAGCGTTTAACG
Found at i:99141596 original size:26 final size:26
Alignment explanation
Indices: 99141567--99141618 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
99141557 GAAAGCGTCG
99141567 CTAATGCTCGATCTATAGCGGCGATT
1 CTAATGCTCGATCTATAGCGGCGATT
99141593 CTAATGCTCGATCTATAGCGGCGATT
1 CTAATGCTCGATCTATAGCGGCGATT
99141619 TTCAAAAAGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.31
Consensus pattern (26 bp):
CTAATGCTCGATCTATAGCGGCGATT
Found at i:99141637 original size:66 final size:66
Alignment explanation
Indices: 99141527--99141654 Score: 168
Period size: 66 Copynumber: 1.9 Consensus size: 66
99141517 GAAAGCGTCG
* *** * *
99141527 CTAATGGTCGACCTATAGCGGCATTTTTTGGAAAGCGTCGCTAATGCTCGATCTATAGCGGCGAT
1 CTAATGCTCGACCTATAGCGGCATTTTTCAAAAAGCGCCACTAATGCTCGATCTATAGCGGCGAT
99141592 T
66 T
* *
99141593 CTAATGCTCGATCTATAGCGGCGA-TTTTCAAAAAGCGCCACTAATTCTCGATCTATAGCGGC
1 CTAATGCTCGACCTATAGCGGC-ATTTTTCAAAAAGCGCCACTAATGCTCGATCTATAGCGGC
99141655 ATTTTTGGTC
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
66 52 0.98
67 1 0.02
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.29
Consensus pattern (66 bp):
CTAATGCTCGACCTATAGCGGCATTTTTCAAAAAGCGCCACTAATGCTCGATCTATAGCGGCGAT
T
Found at i:99145572 original size:34 final size:32
Alignment explanation
Indices: 99145534--99145599 Score: 80
Period size: 32 Copynumber: 2.0 Consensus size: 32
99145524 GATAATTTAA
99145534 ACATAAATTATTCAATTTATTT-TATTATATATAT
1 ACATAAA-TATT-AATTTATTTATATT-TATATAT
**
99145568 ACATAAATATTTTTTTATTTATATTTATATAT
1 ACATAAATATTAATTTATTTATATTTATATAT
99145600 TTTTGTTTGT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
32 14 0.48
33 8 0.28
34 7 0.24
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.56
Consensus pattern (32 bp):
ACATAAATATTAATTTATTTATATTTATATAT
Found at i:99148662 original size:18 final size:21
Alignment explanation
Indices: 99148622--99148663 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
99148612 TTTTATCCAT
99148622 AATTAACAATAAATTAATGTA
1 AATTAACAATAAATTAATGTA
*
99148643 AATTAATAA-AAA-TAAT-TA
1 AATTAACAATAAATTAATGTA
99148661 AAT
1 AAT
99148664 AAAAATCCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
18 5 0.25
19 4 0.20
20 3 0.15
21 8 0.40
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.33
Consensus pattern (21 bp):
AATTAACAATAAATTAATGTA
Found at i:99148680 original size:21 final size:23
Alignment explanation
Indices: 99148650--99148691 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
99148640 GTAAATTAAT
99148650 AAAAATAATTAA-ATAAAAATCC
1 AAAAATAATTAATATAAAAATCC
99148672 AAAAA-AATTAATATAAAAAT
1 AAAAATAATTAATATAAAAAT
99148692 GTACATTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (23 bp):
AAAAATAATTAATATAAAAATCC
Found at i:99154909 original size:2 final size:2
Alignment explanation
Indices: 99154902--99154938 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
99154892 AGTGATGGTT
99154902 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
99154939 TCCCAGACTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:99156968 original size:21 final size:22
Alignment explanation
Indices: 99156928--99156968 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
99156918 TTATGTTTCT
99156928 TGCTTTAGATTTCTATGTTAAA
1 TGCTTTAGATTTCTATGTTAAA
* *
99156950 TGCTTTTGGTTTC-ATGTTA
1 TGCTTTAGATTTCTATGTTA
99156969 TTTAAGTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.20, C:0.10, G:0.17, T:0.54
Consensus pattern (22 bp):
TGCTTTAGATTTCTATGTTAAA
Found at i:99157888 original size:38 final size:39
Alignment explanation
Indices: 99157837--99157913 Score: 129
Period size: 38 Copynumber: 2.0 Consensus size: 39
99157827 AGGATTTATA
*
99157837 GATATGACATTTTTTGTTGTTTTTATTTA-TTTTTAGAT
1 GATATGACATTTTTTGTTGTTTTTATTAAGTTTTTAGAT
*
99157875 GATATGACCTTTTTTGTTGTTTTTATTAAGTTTTTAGAT
1 GATATGACATTTTTTGTTGTTTTTATTAAGTTTTTAGAT
99157914 TTAATTAACT
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
38 27 0.75
39 9 0.25
ACGTcount: A:0.21, C:0.04, G:0.14, T:0.61
Consensus pattern (39 bp):
GATATGACATTTTTTGTTGTTTTTATTAAGTTTTTAGAT
Found at i:99158233 original size:45 final size:45
Alignment explanation
Indices: 99158179--99158284 Score: 140
Period size: 45 Copynumber: 2.4 Consensus size: 45
99158169 AATGATCCAG
* *
99158179 ATGAATGAGGATCCAAATCAACACATTAAACAATTTTAAGGGTTT
1 ATGAATGAGGATCCAAATCAACACATTAAACAATTTCAAGGGTCT
* * * ** *
99158224 ATGAGTGAGGATCTAAATCAACACCTTAAGTAATTTCGAGGGTCT
1 ATGAATGAGGATCCAAATCAACACATTAAACAATTTCAAGGGTCT
99158269 ATGAATGAGGATCCAA
1 ATGAATGAGGATCCAA
99158285 GTCGAGGGTT
Statistics
Matches: 51, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
45 51 1.00
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.27
Consensus pattern (45 bp):
ATGAATGAGGATCCAAATCAACACATTAAACAATTTCAAGGGTCT
Found at i:99162791 original size:16 final size:18
Alignment explanation
Indices: 99162770--99162802 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
99162760 TTTTATTTCT
99162770 AATATA-AATTT-TCCCA
1 AATATATAATTTATCCCA
99162786 AATATATAATTTATCCC
1 AATATATAATTTATCCC
99162803 TTAATTTCCA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 5 0.33
18 4 0.27
ACGTcount: A:0.42, C:0.18, G:0.00, T:0.39
Consensus pattern (18 bp):
AATATATAATTTATCCCA
Found at i:99165271 original size:15 final size:15
Alignment explanation
Indices: 99165251--99165319 Score: 84
Period size: 15 Copynumber: 4.6 Consensus size: 15
99165241 GTATCTTGGG
99165251 TTTCTTTATCCTGGA
1 TTTCTTTATCCTGGA
* *
99165266 TCTCTTTATTCTGGA
1 TTTCTTTATCCTGGA
* *
99165281 TTTCTTTATTCTGGG
1 TTTCTTTATCCTGGA
* *
99165296 TTTCTCTATCTTGGA
1 TTTCTTTATCCTGGA
99165311 TTTCTTTAT
1 TTTCTTTAT
99165320 TCGGTTTTCT
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 45 1.00
ACGTcount: A:0.12, C:0.17, G:0.13, T:0.58
Consensus pattern (15 bp):
TTTCTTTATCCTGGA
Found at i:99165320 original size:30 final size:30
Alignment explanation
Indices: 99165242--99165329 Score: 99
Period size: 30 Copynumber: 3.0 Consensus size: 30
99165232 CATAGTATCG
* * * *
99165242 TATCTTGGGTTTCTTTATCCTGGATCTCTT
1 TATCTTGGATTTCTTTATTCTGGATTTCTC
*
99165272 TAT-TCTGGATTTCTTTATTCTGGGTTTCTC
1 TATCT-TGGATTTCTTTATTCTGGATTTCTC
*
99165302 TATCTTGGATTTCTTTATTC-GGTTTTCT
1 TATCTTGGATTTCTTTATTCTGGATTTCT
99165330 TGTTATCTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
29 8 0.16
30 41 0.82
31 1 0.02
ACGTcount: A:0.10, C:0.17, G:0.16, T:0.57
Consensus pattern (30 bp):
TATCTTGGATTTCTTTATTCTGGATTTCTC
Found at i:99166318 original size:19 final size:19
Alignment explanation
Indices: 99166294--99166331 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
99166284 CTCCTCCAAC
99166294 TTCTATTTTCATGAATCTA
1 TTCTATTTTCATGAATCTA
99166313 TTCTATTTTCATGAATCTA
1 TTCTATTTTCATGAATCTA
99166332 ACTTGATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.05, T:0.53
Consensus pattern (19 bp):
TTCTATTTTCATGAATCTA
Found at i:99166816 original size:24 final size:22
Alignment explanation
Indices: 99166789--99166832 Score: 61
Period size: 24 Copynumber: 1.9 Consensus size: 22
99166779 GATCCTTCCA
*
99166789 CCCTTTAAATATTTTCACTATTAG
1 CCCTTCAAAT-TTTTCA-TATTAG
99166813 CCCTTCAAATTTTTCATATT
1 CCCTTCAAATTTTTCATATT
99166833 TATACTTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 4 0.21
23 6 0.32
24 9 0.47
ACGTcount: A:0.27, C:0.23, G:0.02, T:0.48
Consensus pattern (22 bp):
CCCTTCAAATTTTTCATATTAG
Found at i:99167320 original size:25 final size:24
Alignment explanation
Indices: 99167288--99167345 Score: 57
Period size: 27 Copynumber: 2.4 Consensus size: 24
99167278 GTTATTTTTA
99167288 TTTC-TTAAGAAATCAAAGCCAAAT
1 TTTCATTAAGAAATCAAA-CCAAAT
* *
99167312 TTTCATTAAAATAAATCAAACCAAGT
1 TTTCATT--AAGAAATCAAACCAAAT
99167338 TTT-ATTAA
1 TTTCATTAA
99167346 AGCCAAAACT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
23 2 0.07
24 4 0.14
25 5 0.17
26 8 0.28
27 10 0.34
ACGTcount: A:0.47, C:0.14, G:0.05, T:0.34
Consensus pattern (24 bp):
TTTCATTAAGAAATCAAACCAAAT
Found at i:99167340 original size:26 final size:26
Alignment explanation
Indices: 99167297--99167346 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
99167287 ATTTCTTAAG
99167297 AAATCAAAGCCAAATTTTCATTAAAAT
1 AAATCAAAGCCAAATTTT-ATTAAAAT
*
99167324 AAATCAAA-CCAAGTTTTATTAAA
1 AAATCAAAGCCAAATTTTATTAAA
99167347 GCCAAAACTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 6 0.27
26 8 0.36
27 8 0.36
ACGTcount: A:0.52, C:0.14, G:0.04, T:0.30
Consensus pattern (26 bp):
AAATCAAAGCCAAATTTTATTAAAAT
Found at i:99168552 original size:14 final size:15
Alignment explanation
Indices: 99168520--99168562 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 15
99168510 TTTTTTTTAG
99168520 AATTATTGTTAAGAAA
1 AATTATT-TTAAGAAA
99168536 AATTATTTTAA-AAA
1 AATTATTTTAAGAAA
99168550 AATGATATTTTAA
1 AAT--TATTTTAA
99168563 CTATAATTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
14 6 0.24
15 4 0.16
16 15 0.60
ACGTcount: A:0.51, C:0.00, G:0.07, T:0.42
Consensus pattern (15 bp):
AATTATTTTAAGAAA
Found at i:99188621 original size:16 final size:16
Alignment explanation
Indices: 99188572--99188633 Score: 74
Period size: 16 Copynumber: 3.9 Consensus size: 16
99188562 TATAAATAGC
*
99188572 AAAATAAAAAT-TAAA
1 AAAATTAAAATATAAA
* *
99188587 ATAA-TAAAAGTATATA
1 AAAATTAAAA-TATAAA
99188603 AAAATTAAAATATAAA
1 AAAATTAAAATATAAA
99188619 AAAATTAAAATATAA
1 AAAATTAAAATATAA
99188634 GTATAAGAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
14 4 0.10
15 4 0.10
16 26 0.67
17 5 0.13
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.26
Consensus pattern (16 bp):
AAAATTAAAATATAAA
Found at i:99195457 original size:6 final size:6
Alignment explanation
Indices: 99195450--99195486 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
99195440 CCTTCTTCTG
* *
99195450 CCTCTG CCTCTG CCTCTA CCTCTA CCTCTA CCTCTA C
1 CCTCTA CCTCTA CCTCTA CCTCTA CCTCTA CCTCTA C
99195487 TATAACCATG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.11, C:0.51, G:0.05, T:0.32
Consensus pattern (6 bp):
CCTCTA
Found at i:99195463 original size:12 final size:12
Alignment explanation
Indices: 99195446--99195484 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
99195436 CATTCCTTCT
*
99195446 TCTGCCTCTGCC
1 TCTGCCTCTACC
99195458 TCTGCCTCTACC
1 TCTGCCTCTACC
*
99195470 TCTACCTCTACC
1 TCTGCCTCTACC
99195482 TCT
1 TCT
99195485 ACTATAACCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.08, C:0.49, G:0.08, T:0.36
Consensus pattern (12 bp):
TCTGCCTCTACC
Found at i:99196754 original size:38 final size:38
Alignment explanation
Indices: 99196703--99196777 Score: 141
Period size: 38 Copynumber: 2.0 Consensus size: 38
99196693 TGACTTGATT
99196703 TTATTGATCAATCTTTTGTCACTTTATATTATCTGCCA
1 TTATTGATCAATCTTTTGTCACTTTATATTATCTGCCA
*
99196741 TTATTGATCAATCTTTTGTCGCTTTATATTATCTGCC
1 TTATTGATCAATCTTTTGTCACTTTATATTATCTGCC
99196778 TTTAGTATTT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.21, C:0.19, G:0.09, T:0.51
Consensus pattern (38 bp):
TTATTGATCAATCTTTTGTCACTTTATATTATCTGCCA
Found at i:99206248 original size:21 final size:21
Alignment explanation
Indices: 99206222--99206262 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
99206212 AGACAAGCGA
* *
99206222 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
99206243 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
99206263 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:99209490 original size:22 final size:22
Alignment explanation
Indices: 99209465--99209507 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
99209455 TCTCCATATT
99209465 TTGCTACCATTTTACTATTATG
1 TTGCTACCATTTTACTATTATG
* *
99209487 TTGCTACTATTTTATTATTAT
1 TTGCTACCATTTTACTATTAT
99209508 TATTTGGATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.23, C:0.14, G:0.07, T:0.56
Consensus pattern (22 bp):
TTGCTACCATTTTACTATTATG
Found at i:99209680 original size:11 final size:11
Alignment explanation
Indices: 99209664--99209694 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
99209654 TATATATATT
99209664 TAAAAATTATA
1 TAAAAATTATA
*
99209675 TAAAAATAATA
1 TAAAAATTATA
99209686 TAAAAATTA
1 TAAAAATTA
99209695 ATACGGGCTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
TAAAAATTATA
Found at i:99213104 original size:26 final size:23
Alignment explanation
Indices: 99213075--99213125 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 23
99213065 AATTGTCAAA
99213075 AAATAATTTTTGAAATAAAATATAAT
1 AAATAA-TTTT-AAATAAAAT-TAAT
* *
99213101 AAATTATTTTAAATATAATTAAT
1 AAATAATTTTAAATAAAATTAAT
99213124 AA
1 AA
99213126 CCTATATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 6 0.26
24 8 0.35
25 4 0.17
26 5 0.22
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (23 bp):
AAATAATTTTAAATAAAATTAAT
Found at i:99218650 original size:31 final size:31
Alignment explanation
Indices: 99218615--99218675 Score: 122
Period size: 31 Copynumber: 2.0 Consensus size: 31
99218605 ATGATTGTTA
99218615 AATAATTGATTACATTTGATGTAGTCCAAAC
1 AATAATTGATTACATTTGATGTAGTCCAAAC
99218646 AATAATTGATTACATTTGATGTAGTCCAAA
1 AATAATTGATTACATTTGATGTAGTCCAAA
99218676 TATCAATTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.36
Consensus pattern (31 bp):
AATAATTGATTACATTTGATGTAGTCCAAAC
Found at i:99221898 original size:53 final size:53
Alignment explanation
Indices: 99221817--99221967 Score: 214
Period size: 53 Copynumber: 2.8 Consensus size: 53
99221807 CTTACACGGT
* *
99221817 TCACATATCATACCGAAGCCATATCCCAGAC-ATGGTCTTATACGGAATCACATTA
1 TCACAT-T-ATACCGATGCCATAGCCCAG-CTATGGTCTTATACGGAATCACATTA
*
99221872 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAGTCACATTA
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
** *
99221925 TCACATTGCACCGATGCCATAGCCCAGCTATGGTCTTAAACGG
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGG
99221968 GCGCACTTAT
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
52 1 0.01
53 81 0.91
54 1 0.01
55 6 0.07
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.26
Consensus pattern (53 bp):
TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
Found at i:99223501 original size:18 final size:18
Alignment explanation
Indices: 99223478--99223514 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
99223468 GCCAGGTGCA
*
99223478 TATCCTAGCCCTTATATG
1 TATCCTAACCCTTATATG
99223496 TATCCTAACCCTTATATG
1 TATCCTAACCCTTATATG
99223514 T
1 T
99223515 TTCATTTTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.24, C:0.27, G:0.08, T:0.41
Consensus pattern (18 bp):
TATCCTAACCCTTATATG
Found at i:99223806 original size:21 final size:21
Alignment explanation
Indices: 99223760--99223824 Score: 60
Period size: 21 Copynumber: 3.0 Consensus size: 21
99223750 CCAACACCCA
* *
99223760 CAACCA-AATCCCCTGTCGGAG
1 CAACCACAATCCCCT-CCGAAG
*
99223781 GAACCACAATCCCCTCCGAAG
1 CAACCACAATCCCCTCCGAAG
* *
99223802 CAACCACAACCCCCACCGGAAG
1 CAACCACAATCCCCTCC-GAAG
99223824 C
1 C
99223825 TGAACCAAGG
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
21 23 0.64
22 13 0.36
ACGTcount: A:0.32, C:0.45, G:0.15, T:0.08
Consensus pattern (21 bp):
CAACCACAATCCCCTCCGAAG
Found at i:99223941 original size:8 final size:9
Alignment explanation
Indices: 99223897--99223959 Score: 69
Period size: 8 Copynumber: 7.2 Consensus size: 9
99223887 GGCACCAACA
99223897 TTAAT-TTT
1 TTAATATTT
99223905 TTAATATTTT
1 TTAATA-TTT
**
99223915 TTAATA-AG
1 TTAATATTT
*
99223923 GTAATATTT
1 TTAATATTT
99223932 TTAATATTT
1 TTAATATTT
99223941 TT-ATATTT
1 TTAATATTT
99223949 TTAATATTT
1 TTAATATTT
99223958 TT
1 TT
99223960 GTACAAACTT
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
8 18 0.40
9 18 0.40
10 9 0.20
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (9 bp):
TTAATATTT
Found at i:99223946 original size:17 final size:17
Alignment explanation
Indices: 99223926--99223959 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
99223916 TAATAAGGTA
99223926 ATATTTTTAATATTTTT
1 ATATTTTTAATATTTTT
99223943 ATATTTTTAATATTTTT
1 ATATTTTTAATATTTTT
99223960 GTACAAACTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
ATATTTTTAATATTTTT
Found at i:99224089 original size:8 final size:9
Alignment explanation
Indices: 99224072--99224102 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
99224062 TTAAATAAGG
99224072 TAATATTTT
1 TAATATTTT
99224081 TAATATTTT
1 TAATATTTT
99224090 T-ATATTTT
1 TAATATTTT
99224098 TAATA
1 TAATA
99224103 AAATATAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.38
9 13 0.62
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (9 bp):
TAATATTTT
Found at i:99224096 original size:55 final size:55
Alignment explanation
Indices: 99223987--99224107 Score: 156
Period size: 56 Copynumber: 2.2 Consensus size: 55
99223977 TTGTTTCATC
* ** *
99223987 TAATAAAATAAAAGTTATTTTTAATAATTTAATTGTAATTTACTTTTTTATATTTT
1 TAATAAAATAAAAGTTATTTTAAATAAGGTAATTGT-ATTTAATTTTTTATATTTT
*
99224043 TAATAAAATAAAAGTTCTTTTAAATAAGGTAATAT-T-TTTAATATTTTTATATTTT
1 TAATAAAATAAAAGTTATTTTAAATAAGGTAAT-TGTATTTAAT-TTTTTATATTTT
99224098 TAATAAAATA
1 TAATAAAATA
99224108 TAAATAATGC
Statistics
Matches: 58, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
54 5 0.09
55 22 0.38
56 30 0.52
57 1 0.02
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (55 bp):
TAATAAAATAAAAGTTATTTTAAATAAGGTAATTGTATTTAATTTTTTATATTTT
Found at i:99225371 original size:43 final size:43
Alignment explanation
Indices: 99225307--99225431 Score: 133
Period size: 43 Copynumber: 2.9 Consensus size: 43
99225297 TTCTTTGGCG
* * * **
99225307 TTAGCGGCATATGTGGGAGAAGCACCGCTAAAAGTTTTGTTCT
1 TTAGCGGCGTTTGTGGTAGAAGCACCGCTAAAAGTCATGTTCT
*
99225350 TTAGCGGCGTTTGTGGTAGAAGCACCGCTAAATGTCATGTTCT
1 TTAGCGGCGTTTGTGGTAGAAGCACCGCTAAAAGTCATGTTCT
* * ** * * *
99225393 ATAGTGGCGTTTGAAGTAAAAGCGCCGCTAAAGGTCATG
1 TTAGCGGCGTTTGTGGTAGAAGCACCGCTAAAAGTCATG
99225432 CTCTATATCG
Statistics
Matches: 69, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
43 69 1.00
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.29
Consensus pattern (43 bp):
TTAGCGGCGTTTGTGGTAGAAGCACCGCTAAAAGTCATGTTCT
Found at i:99225437 original size:43 final size:43
Alignment explanation
Indices: 99225354--99225473 Score: 125
Period size: 43 Copynumber: 2.8 Consensus size: 43
99225344 TGTTCTTTAG
** * * *
99225354 CGGCGTTTGTGGTAGAAGCACCGCTAAATGTCATGTTCTATAGT
1 CGGCGTTTGAAGTAGAAGCGCCGCTAAAGGTCATGCTCTATA-T
*
99225398 -GGCGTTTGAAGTAAAAGCGCCGCTAAAGGTCATGCTCTATAT
1 CGGCGTTTGAAGTAGAAGCGCCGCTAAAGGTCATGCTCTATAT
* * * * *
99225440 CGGTGTTTGCAGGAGAAGCGCTGTTAAAGGTCAT
1 CGGCGTTTGAAGTAGAAGCGCCGCTAAAGGTCAT
99225474 TTTCTATAAG
Statistics
Matches: 63, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
42 1 0.02
43 62 0.98
ACGTcount: A:0.25, C:0.17, G:0.29, T:0.28
Consensus pattern (43 bp):
CGGCGTTTGAAGTAGAAGCGCCGCTAAAGGTCATGCTCTATAT
Found at i:99232190 original size:3 final size:3
Alignment explanation
Indices: 99232182--99232208 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
99232172 TACTTTTACG
99232182 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
99232209 CGATATAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:99236199 original size:291 final size:291
Alignment explanation
Indices: 99235675--99236261 Score: 1174
Period size: 291 Copynumber: 2.0 Consensus size: 291
99235665 AATTTTAGAG
99235675 ATAAATTTAATAGGAAATCTAAACCCCTAACTTATAATTAATTCAAGGCATTAAAGCCCCATTCC
1 ATAAATTTAATAGGAAATCTAAACCCCTAACTTATAATTAATTCAAGGCATTAAAGCCCCATTCC
99235740 CATAACTTATCTTCACATTCGAAAGTGCTATTTGTGGATGTTGTTTGGTATTGTTTATTGGGATA
66 CATAACTTATCTTCACATTCGAAAGTGCTATTTGTGGATGTTGTTTGGTATTGTTTATTGGGATA
99235805 AATATTAAAGTTATATATAAATTATAGTTTAATGTGTAATTATATACATGCAATTTTGATTTAAT
131 AATATTAAAGTTATATATAAATTATAGTTTAATGTGTAATTATATACATGCAATTTTGATTTAAT
99235870 TTAATTCTTGTAAATTATTAGTATAATTATTGATATAATATTATTTTATGTTTAGATATTGCATA
196 TTAATTCTTGTAAATTATTAGTATAATTATTGATATAATATTATTTTATGTTTAGATATTGCATA
99235935 ATGTATACATAAATAATTATATTTATCCAAT
261 ATGTATACATAAATAATTATATTTATCCAAT
99235966 ATAAATTTAATAGGAAATCTAAACCCCTAACTTATAATTAATTCAAGGCATTAAAGCCCCATTCC
1 ATAAATTTAATAGGAAATCTAAACCCCTAACTTATAATTAATTCAAGGCATTAAAGCCCCATTCC
99236031 CATAACTTATCTTCACATTCGAAAGTGCTATTTGTGGATGTTGTTTGGTATTGTTTATTGGGATA
66 CATAACTTATCTTCACATTCGAAAGTGCTATTTGTGGATGTTGTTTGGTATTGTTTATTGGGATA
99236096 AATATTAAAGTTATATATAAATTATAGTTTAATGTGTAATTATATACATGCAATTTTGATTTAAT
131 AATATTAAAGTTATATATAAATTATAGTTTAATGTGTAATTATATACATGCAATTTTGATTTAAT
99236161 TTAATTCTTGTAAATTATTAGTATAATTATTGATATAATATTATTTTATGTTTAGATATTGCATA
196 TTAATTCTTGTAAATTATTAGTATAATTATTGATATAATATTATTTTATGTTTAGATATTGCATA
99236226 ATGTATACATAAATAATTATATTTATCCAAT
261 ATGTATACATAAATAATTATATTTATCCAAT
99236257 ATAAA
1 ATAAA
99236262 AATAAATTGA
Statistics
Matches: 296, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
291 296 1.00
ACGTcount: A:0.37, C:0.10, G:0.11, T:0.43
Consensus pattern (291 bp):
ATAAATTTAATAGGAAATCTAAACCCCTAACTTATAATTAATTCAAGGCATTAAAGCCCCATTCC
CATAACTTATCTTCACATTCGAAAGTGCTATTTGTGGATGTTGTTTGGTATTGTTTATTGGGATA
AATATTAAAGTTATATATAAATTATAGTTTAATGTGTAATTATATACATGCAATTTTGATTTAAT
TTAATTCTTGTAAATTATTAGTATAATTATTGATATAATATTATTTTATGTTTAGATATTGCATA
ATGTATACATAAATAATTATATTTATCCAAT
Found at i:99240683 original size:27 final size:26
Alignment explanation
Indices: 99240618--99240684 Score: 62
Period size: 28 Copynumber: 2.5 Consensus size: 26
99240608 GAGTTTTTAA
* * *
99240618 AAATATTTTATTTTTTAATTATATTT
1 AAATATCTCATTTTTAAATTATATTT
*
99240644 AAAGTAATCTCATTTTTAAATTAATTTTT
1 AAA-T-ATCTCATTTTTAAATT-ATATTT
*
99240673 AAATATGTCATT
1 AAATATCTCATT
99240685 AATAATAATA
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
26 3 0.09
27 8 0.24
28 14 0.42
29 8 0.24
ACGTcount: A:0.37, C:0.04, G:0.03, T:0.55
Consensus pattern (26 bp):
AAATATCTCATTTTTAAATTATATTT
Found at i:99241188 original size:31 final size:31
Alignment explanation
Indices: 99241125--99241190 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
99241115 TACTCTTAAC
* * *
99241125 TTAATTTAATTACATTATATAACATTTTAAT
1 TTAATTTAATCACATTATATAACAGTTCAAT
*
99241156 TTAATTTAATCACATTATATAATAGTTCAAT
1 TTAATTTAATCACATTATATAACAGTTCAAT
99241187 TTAA
1 TTAA
99241191 ATTGATTTAG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.42, C:0.08, G:0.02, T:0.48
Consensus pattern (31 bp):
TTAATTTAATCACATTATATAACAGTTCAAT
Found at i:99242588 original size:26 final size:26
Alignment explanation
Indices: 99242551--99242634 Score: 150
Period size: 26 Copynumber: 3.2 Consensus size: 26
99242541 TGATACAAAT
* *
99242551 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTTCA
99242577 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
99242603 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
99242629 TGATAA
1 TGATAA
99242635 GAATTTCATG
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 56 1.00
ACGTcount: A:0.33, C:0.05, G:0.25, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTTCA
Found at i:99247651 original size:25 final size:26
Alignment explanation
Indices: 99247611--99247660 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 26
99247601 TATGTATATG
*
99247611 TATATTTCCTTAAATAATAAGTAAAA
1 TATATTTCATTAAATAATAAGTAAAA
* *
99247637 TATATTT-ATTAAATATTAATTAAA
1 TATATTTCATTAAATAATAAGTAAA
99247661 TTATTAAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 14 0.67
26 7 0.33
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (26 bp):
TATATTTCATTAAATAATAAGTAAAA
Found at i:99247907 original size:23 final size:23
Alignment explanation
Indices: 99247867--99247911 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
99247857 ACAAATTGAA
99247867 TAATGACAATTGTAATAAGAATAT
1 TAATGACAATTGTAATAA-AATAT
* *
99247891 TAAT-ACATTTGTTATAAAATA
1 TAATGACAATTGTAATAAAATA
99247912 ATTTGTTTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 4 0.21
23 11 0.58
24 4 0.21
ACGTcount: A:0.49, C:0.04, G:0.09, T:0.38
Consensus pattern (23 bp):
TAATGACAATTGTAATAAAATAT
Found at i:99247977 original size:9 final size:9
Alignment explanation
Indices: 99247963--99248009 Score: 51
Period size: 9 Copynumber: 5.1 Consensus size: 9
99247953 AATTATTAAT
*
99247963 ATAAAACAA
1 ATAAAATAA
99247972 ATAAAATTAA
1 ATAAAA-TAA
99247982 AT-AAATAA
1 ATAAAATAA
99247990 ATAAAATTAA
1 ATAAAA-TAA
*
99248000 ATAGAATAA
1 ATAAAATAA
99248009 A
1 A
99248010 ACGAAATAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
8 5 0.15
9 16 0.48
10 12 0.36
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.23
Consensus pattern (9 bp):
ATAAAATAA
Found at i:99247991 original size:18 final size:19
Alignment explanation
Indices: 99247970--99248009 Score: 73
Period size: 18 Copynumber: 2.2 Consensus size: 19
99247960 AATATAAAAC
99247970 AAATAAAATTAAATA-AAT
1 AAATAAAATTAAATAGAAT
99247988 AAATAAAATTAAATAGAAT
1 AAATAAAATTAAATAGAAT
99248007 AAA
1 AAA
99248010 ACGAAATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 15 0.71
19 6 0.29
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (19 bp):
AAATAAAATTAAATAGAAT
Found at i:99252509 original size:35 final size:35
Alignment explanation
Indices: 99252418--99252584 Score: 192
Period size: 35 Copynumber: 4.6 Consensus size: 35
99252408 CATGGCAAAG
*
99252418 TGTGAAATGTAGGTATGGTATCATCCATACTGAGT
1 TGTGAAATGTAGGTATGGTATTATCCATACTGAGT
*
99252453 TGTGAAATGTAGGTATGGTATTATCCATACTGAGC
1 TGTGAAATGTAGGTATGGTATTATCCATACTGAGT
99252488 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGT
1 TGTGAAATGTAGGTATGGTA-T-T---ATCCATACTGAGT
** * * *
99252528 TAAGAAATATAGGTATGGCATT-TCCCATACCGAGT
1 TGTGAAATGTAGGTATGGTATTAT-CCATACTGAGT
**
99252563 TGAAAAATGTAGGTATGGTATT
1 TGTGAAATGTAGGTATGGTATT
99252585 TCAATGAGGA
Statistics
Matches: 114, Mismatches: 12, Indels: 12
0.83 0.09 0.09
Matches are distributed among these distances:
34 1 0.01
35 81 0.71
36 1 0.01
37 1 0.01
38 1 0.01
39 1 0.01
40 28 0.25
ACGTcount: A:0.32, C:0.11, G:0.24, T:0.34
Consensus pattern (35 bp):
TGTGAAATGTAGGTATGGTATTATCCATACTGAGT
Found at i:99252541 original size:75 final size:75
Alignment explanation
Indices: 99252418--99252588 Score: 212
Period size: 75 Copynumber: 2.4 Consensus size: 75
99252408 CATGGCAAAG
** * *
99252418 TGTGAAATGTAGGTATGG---TATC--ATCCATACTGAGTTGTGAAATGTAGGTATGGTATTAT-
1 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATATAGGTATGGCATT-TC
*
99252477 CCATACTGAGC
65 CCATACCGAGC
99252488 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATATAGGTATGGCATTTCC
1 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATATAGGTATGGCATTTCC
*
99252553 CATACCGAGT
66 CATACCGAGC
**
99252563 TGAAAAATGTAGGTATGGTATT-TCAA
1 TGTGAAATGTAGGTATGGTATTATCAA
99252589 TGAGGAAAAC
Statistics
Matches: 87, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
70 18 0.21
73 4 0.05
74 5 0.06
75 60 0.69
ACGTcount: A:0.32, C:0.11, G:0.23, T:0.33
Consensus pattern (75 bp):
TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATATAGGTATGGCATTTCC
CATACCGAGC
Found at i:99256763 original size:25 final size:25
Alignment explanation
Indices: 99256722--99256771 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
99256712 TATATGTTTA
*
99256722 TTTTTAAATTTAATAAATAATATAT
1 TTTTTAAATTTAATAAAAAATATAT
*
99256747 TTTTTATAATTT-TTAAAAAATATAT
1 TTTTTA-AATTTAATAAAAAATATAT
99256772 ATTTGCTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 17 0.77
26 5 0.23
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (25 bp):
TTTTTAAATTTAATAAAAAATATAT
Found at i:99259036 original size:21 final size:21
Alignment explanation
Indices: 99258986--99259026 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
99258976 ATGTATATGT
99258986 TGAAAATTAGAAATTTATGGC
1 TGAAAATTAGAAATTTATGGC
99259007 TGAAAATTAGAAATTTATGG
1 TGAAAATTAGAAATTTATGG
99259027 TATAAAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.44, C:0.02, G:0.20, T:0.34
Consensus pattern (21 bp):
TGAAAATTAGAAATTTATGGC
Found at i:99264191 original size:48 final size:48
Alignment explanation
Indices: 99264120--99264216 Score: 149
Period size: 48 Copynumber: 2.0 Consensus size: 48
99264110 AAGTACCAAA
* * *
99264120 GCCATGTCCCAGACATGGTCTTACACTAGCACACATATCATCGTCGAT
1 GCCATGTCCCAAACATGGTCTTACACTAGCACACATATCAACATCGAT
* *
99264168 GCCATGTCCCAAATATGGTCTTACACTGGCACACATATCAACATCGAT
1 GCCATGTCCCAAACATGGTCTTACACTAGCACACATATCAACATCGAT
99264216 G
1 G
99264217 AAGACTGGCA
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
48 44 1.00
ACGTcount: A:0.29, C:0.30, G:0.16, T:0.25
Consensus pattern (48 bp):
GCCATGTCCCAAACATGGTCTTACACTAGCACACATATCAACATCGAT
Found at i:99264293 original size:48 final size:48
Alignment explanation
Indices: 99264220--99264413 Score: 298
Period size: 48 Copynumber: 4.0 Consensus size: 48
99264210 ATCGATGAAG
*
99264220 ACTGGCACACATATCAACGCCGATGCCATGTCCCAGACATGGTTTTAC
1 ACTGGCACACATATCAACGCCGATGCCATGTCCCAGACATGGTCTTAC
* *
99264268 ACTGGCACACATATCAACGCTGATGCCATGTACCAGACATGGTCTTAC
1 ACTGGCACACATATCAACGCCGATGCCATGTCCCAGACATGGTCTTAC
*
99264316 ACTGGCACACATATCAACGCCGATGCCATGTCCTAGACATGGTCTTAC
1 ACTGGCACACATATCAACGCCGATGCCATGTCCCAGACATGGTCTTAC
* * * * *
99264364 ACTGACTCTCATATCAGATGCCGATGTCATGTCCCAGACATGGTCTTAC
1 ACTGGCACACATATCA-ACGCCGATGCCATGTCCCAGACATGGTCTTAC
99264413 A
1 A
99264414 TGGGATCTCA
Statistics
Matches: 133, Mismatches: 12, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
48 103 0.77
49 30 0.23
ACGTcount: A:0.27, C:0.30, G:0.19, T:0.24
Consensus pattern (48 bp):
ACTGGCACACATATCAACGCCGATGCCATGTCCCAGACATGGTCTTAC
Found at i:99268887 original size:18 final size:20
Alignment explanation
Indices: 99268854--99268890 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
99268844 GATTGATATC
99268854 TCCCCATTATCAACCAATTG
1 TCCCCATTATCAACCAATTG
99268874 TCCCCA-TA-CAACCAATT
1 TCCCCATTATCAACCAATT
99268891 TCGTCTCAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.53
19 2 0.12
20 6 0.35
ACGTcount: A:0.32, C:0.38, G:0.03, T:0.27
Consensus pattern (20 bp):
TCCCCATTATCAACCAATTG
Found at i:99270128 original size:24 final size:22
Alignment explanation
Indices: 99270076--99270130 Score: 85
Period size: 22 Copynumber: 2.5 Consensus size: 22
99270066 TGCACAAACG
99270076 AACAGAGAGCACTAAAGTGCTA
1 AACAGAGAGCACTAAAGTGCTA
*
99270098 AACAGAGAGCAC-AGATGTGCTA
1 AACAGAGAGCACTA-AAGTGCTA
99270120 AACAGAGAGCA
1 AACAGAGAGCA
99270131 TTTAACGTGC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
21 1 0.03
22 30 0.97
ACGTcount: A:0.45, C:0.18, G:0.25, T:0.11
Consensus pattern (22 bp):
AACAGAGAGCACTAAAGTGCTA
Found at i:99271329 original size:5 final size:5
Alignment explanation
Indices: 99271321--99271365 Score: 60
Period size: 5 Copynumber: 9.6 Consensus size: 5
99271311 TATGTTTTAT
*
99271321 ATATA ATAT- A-ATA ATATA ATATA TTAT- ATATA ATATA ATATA ATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATA
99271366 ATATATTATA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
3 2 0.06
4 5 0.14
5 28 0.80
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (5 bp):
ATATA
Found at i:99271355 original size:27 final size:27
Alignment explanation
Indices: 99271317--99271405 Score: 105
Period size: 27 Copynumber: 3.3 Consensus size: 27
99271307 ACTTTATGTT
99271317 TTATATATAATATAATAATATAATATA
1 TTATATATAATATAATAATATAATATA
99271344 TTATATATAATATAAT-ATAATAATATA
1 TTATATATAATATAATAAT-ATAATATA
*
99271371 TTATAT-T-ATATATTAATACTTAA-ATA
1 TTATATATAATATAATAATA--TAATATA
99271397 TTAATATAT
1 TT-ATATAT
99271406 TTTATATAAA
Statistics
Matches: 55, Mismatches: 1, Indels: 11
0.82 0.01 0.16
Matches are distributed among these distances:
25 7 0.13
26 10 0.18
27 37 0.67
28 1 0.02
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (27 bp):
TTATATATAATATAATAATATAATATA
Found at i:99271358 original size:32 final size:33
Alignment explanation
Indices: 99271321--99271388 Score: 120
Period size: 32 Copynumber: 2.1 Consensus size: 33
99271311 TATGTTTTAT
99271321 ATATAATATAATAATATAATATATTATATA-TA
1 ATATAATATAATAATATAATATATTATATATTA
*
99271353 ATATAATATAATAATATATTATATTATATATTA
1 ATATAATATAATAATATAATATATTATATATTA
99271386 ATA
1 ATA
99271389 CTTAAATATT
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 29 0.85
33 5 0.15
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (33 bp):
ATATAATATAATAATATAATATATTATATATTA
Found at i:99272387 original size:25 final size:25
Alignment explanation
Indices: 99272325--99272392 Score: 100
Period size: 25 Copynumber: 2.7 Consensus size: 25
99272315 TTTCGATACT
* * *
99272325 ACGTGCTATTCAACAAACAGAGAAA
1 ACGTGTTATTCAGCAGACAGAGAAA
*
99272350 ACGTGTTATTCAGCAGATAGAGAAA
1 ACGTGTTATTCAGCAGACAGAGAAA
99272375 ACGTGTTATTCAGCAGAC
1 ACGTGTTATTCAGCAGAC
99272393 TCTTTCTTTC
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 38 1.00
ACGTcount: A:0.40, C:0.18, G:0.21, T:0.22
Consensus pattern (25 bp):
ACGTGTTATTCAGCAGACAGAGAAA
Found at i:99276012 original size:25 final size:23
Alignment explanation
Indices: 99275962--99276014 Score: 61
Period size: 25 Copynumber: 2.2 Consensus size: 23
99275952 TTCATATGTT
* *
99275962 TATTTTTAATTTATTAAATAATA
1 TATTTTTAATTTATTAAAAAAAA
*
99275985 TATTTTATAACTTTTTTAAAAAAAA
1 TATTTT-TAA-TTTATTAAAAAAAA
99276010 TATTT
1 TATTT
99276015 ATTTTAATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 6 0.24
24 3 0.12
25 16 0.64
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (23 bp):
TATTTTTAATTTATTAAAAAAAA
Found at i:99276838 original size:16 final size:16
Alignment explanation
Indices: 99276811--99276850 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
99276801 CTAATTATAT
* *
99276811 TTAATGATTTTATTGA
1 TTAATAATTTTATTAA
*
99276827 TTTATAATTTTATTAA
1 TTAATAATTTTATTAA
99276843 TTAATAAT
1 TTAATAAT
99276851 ATATTATGTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (16 bp):
TTAATAATTTTATTAA
Found at i:99282341 original size:93 final size:93
Alignment explanation
Indices: 99282229--99282400 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
99282219 GCCCATAAGT
* *
99282229 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
99282294 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
*
99282322 GAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
99282387 CGAGTTCGGATGCC
66 CGAGTTCGGATGCC
99282401 CAAATATCCC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.27, C:0.30, G:0.22, T:0.20
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:99282396 original size:46 final size:46
Alignment explanation
Indices: 99282221--99282396 Score: 232
Period size: 46 Copynumber: 3.8 Consensus size: 46
99282211 TGTAACCCGC
* * *
99282221 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
* *
99282267 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACG-CTCG---CAT
* *
99282317 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
99282360 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
99282397 TGCCCAAATA
Statistics
Matches: 112, Mismatches: 11, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
43 3 0.03
44 1 0.01
45 2 0.02
46 68 0.61
47 32 0.29
48 2 0.02
49 1 0.01
50 3 0.03
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.20
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
Found at i:99284825 original size:30 final size:30
Alignment explanation
Indices: 99284781--99284869 Score: 101
Period size: 30 Copynumber: 3.0 Consensus size: 30
99284771 CAAAGATAAC
99284781 AAGAAAACC-GAATAAAGAAATCCAAGATA
1 AAGAAAACCAGAATAAAGAAATCCAAGATA
* *
99284810 GAGAAACCCAGAATAAAGAAATCC-AGAATA
1 AAGAAAACCAGAATAAAGAAATCCAAG-ATA
* * * *
99284840 AAGAGATCCAGGATAAAGAAACCCAAGATA
1 AAGAAAACCAGAATAAAGAAATCCAAGATA
99284870 CGATACTATG
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
29 9 0.18
30 39 0.78
31 2 0.04
ACGTcount: A:0.57, C:0.16, G:0.17, T:0.10
Consensus pattern (30 bp):
AAGAAAACCAGAATAAAGAAATCCAAGATA
Found at i:99284829 original size:15 final size:15
Alignment explanation
Indices: 99284781--99284860 Score: 92
Period size: 15 Copynumber: 5.4 Consensus size: 15
99284771 CAAAGATAAC
*
99284781 AAGAAAACC-GAATA
1 AAGAAATCCAGAATA
99284795 AAGAAATCCA-AGATA
1 AAGAAATCCAGA-ATA
* *
99284810 GAGAAACCCAGAATA
1 AAGAAATCCAGAATA
99284825 AAGAAATCCAGAATA
1 AAGAAATCCAGAATA
* *
99284840 AAGAGATCCAGGATA
1 AAGAAATCCAGAATA
99284855 AAGAAA
1 AAGAAA
99284861 CCCAAGATAC
Statistics
Matches: 55, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
14 9 0.16
15 45 0.82
16 1 0.02
ACGTcount: A:0.59, C:0.14, G:0.17, T:0.10
Consensus pattern (15 bp):
AAGAAATCCAGAATA
Found at i:99284869 original size:15 final size:15
Alignment explanation
Indices: 99284792--99284869 Score: 79
Period size: 15 Copynumber: 5.2 Consensus size: 15
99284782 AGAAAACCGA
99284792 ATAAAGAAATCCAAG
1 ATAAAGAAATCCAAG
* *
99284807 ATAGAGAAA-CCCAG
1 ATAAAGAAATCCAAG
99284821 AATAAAGAAATCC-AG
1 -ATAAAGAAATCCAAG
* *
99284836 AATAAAGAGATCCAGG
1 -ATAAAGAAATCCAAG
*
99284852 ATAAAGAAACCCAAG
1 ATAAAGAAATCCAAG
99284867 ATA
1 ATA
99284870 CGATACTATG
Statistics
Matches: 52, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
14 4 0.08
15 45 0.87
16 3 0.06
ACGTcount: A:0.56, C:0.15, G:0.17, T:0.12
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:99287933 original size:93 final size:93
Alignment explanation
Indices: 99287821--99287992 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
99287811 GCCCATAAGT
* *
99287821 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
99287886 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
*
99287914 GAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
99287979 CGAGTTCGGATGCC
66 CGAGTTCGGATGCC
99287993 CAAATATCCC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.27, C:0.30, G:0.22, T:0.20
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:99287988 original size:46 final size:46
Alignment explanation
Indices: 99287813--99287988 Score: 232
Period size: 46 Copynumber: 3.8 Consensus size: 46
99287803 TGTAACCCGC
* * *
99287813 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
* *
99287859 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACG-CTCG---CAT
* *
99287909 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
99287952 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
99287989 TGCCCAAATA
Statistics
Matches: 112, Mismatches: 11, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
43 3 0.03
44 1 0.01
45 2 0.02
46 68 0.61
47 32 0.29
48 2 0.02
49 1 0.01
50 3 0.03
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.20
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
Found at i:99293522 original size:19 final size:18
Alignment explanation
Indices: 99293498--99293545 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 18
99293488 CATCTATTAA
99293498 TTAATTTTTTAATTCATTT
1 TTAATTTTTTAA-TCATTT
*
99293517 TTAATTTTTTTAATGATTT
1 TTAA-TTTTTTAATCATTT
99293536 TTATATTTTT
1 TTA-ATTTTT
99293546 ATTAAAATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
19 17 0.65
20 9 0.35
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.71
Consensus pattern (18 bp):
TTAATTTTTTAATCATTT
Found at i:99293527 original size:20 final size:19
Alignment explanation
Indices: 99293498--99293550 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
99293488 CATCTATTAA
99293498 TTAA-TTTTTTAATTCATTT
1 TTAATTTTTTTAA-TCATTT
*
99293517 TTAATTTTTTTAATGATTT
1 TTAATTTTTTTAATCATTT
99293536 TTATATTTTTATTAA
1 TTA-ATTTTT-TTAA
99293551 AATTTTAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 12 0.40
20 14 0.47
21 4 0.13
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.68
Consensus pattern (19 bp):
TTAATTTTTTTAATCATTT
Found at i:99296058 original size:24 final size:24
Alignment explanation
Indices: 99296027--99296111 Score: 91
Period size: 24 Copynumber: 3.6 Consensus size: 24
99296017 TCAGCTCGTA
99296027 AGAGCTTACTGTTTTCAACTTGTT
1 AGAGCTTACTGTTTTCAACTTGTT
* * * *
99296051 GGAGCTTACT-ATTTCAACTTATA
1 AGAGCTTACTGTTTTCAACTTGTT
* * * *
99296074 AAAGCTTACTGTTTTTAGCTCGTT
1 AGAGCTTACTGTTTTCAACTTGTT
99296098 AGAGCTTACTGTTT
1 AGAGCTTACTGTTT
99296112 CAGCTCAATA
Statistics
Matches: 47, Mismatches: 13, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
23 18 0.38
24 29 0.62
ACGTcount: A:0.24, C:0.16, G:0.16, T:0.44
Consensus pattern (24 bp):
AGAGCTTACTGTTTTCAACTTGTT
Found at i:99296123 original size:23 final size:23
Alignment explanation
Indices: 99296076--99296132 Score: 78
Period size: 23 Copynumber: 2.4 Consensus size: 23
99296066 AACTTATAAA
* **
99296076 AGCTTACTGTTTTTAGCTCGTTAG
1 AGCTTACTG-TTTCAGCTCAATAG
99296100 AGCTTACTGTTTCAGCTCAATAG
1 AGCTTACTGTTTCAGCTCAATAG
99296123 AGCTTACTGT
1 AGCTTACTGT
99296133 CCATAAGCTC
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
23 21 0.70
24 9 0.30
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.40
Consensus pattern (23 bp):
AGCTTACTGTTTCAGCTCAATAG
Found at i:99296127 original size:47 final size:47
Alignment explanation
Indices: 99296025--99296132 Score: 128
Period size: 47 Copynumber: 2.3 Consensus size: 47
99296015 TATCAGCTCG
* * *
99296025 TAAGAGCTTACTGTTTTCAACTTGTTGGAGCTTACTATTTCAACTTA
1 TAAGAGCTTACTGTTTTCAACTCGTTAGAGCTTACTATTTCAACTAA
* * * * *
99296072 TAAAAGCTTACTGTTTTTAGCTCGTTAGAGCTTACTGTTTCAGCTCAA
1 TAAGAGCTTACTGTTTTCAACTCGTTAGAGCTTACTATTTCAACT-AA
99296120 T-AGAGCTTACTGT
1 TAAGAGCTTACTGT
99296133 CCATAAGCTC
Statistics
Matches: 51, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
47 49 0.96
48 2 0.04
ACGTcount: A:0.25, C:0.18, G:0.17, T:0.41
Consensus pattern (47 bp):
TAAGAGCTTACTGTTTTCAACTCGTTAGAGCTTACTATTTCAACTAA
Found at i:99296313 original size:20 final size:20
Alignment explanation
Indices: 99296267--99296307 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
99296257 CAATGAGCAT
*
99296267 AAATACTGTTTATTTGGATG
1 AAATACTGTTTATATGGATG
99296287 AAATACTGTTTATATGGATG
1 AAATACTGTTTATATGGATG
99296307 A
1 A
99296308 GCTACTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.34, C:0.05, G:0.20, T:0.41
Consensus pattern (20 bp):
AAATACTGTTTATATGGATG
Found at i:99300897 original size:5 final size:5
Alignment explanation
Indices: 99300887--99300915 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
99300877 TTCTTTATTT
99300887 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
99300916 TCATAAATTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTA
Found at i:99311240 original size:25 final size:25
Alignment explanation
Indices: 99311184--99311240 Score: 60
Period size: 25 Copynumber: 2.3 Consensus size: 25
99311174 AAAAGTTAAA
* * * *
99311184 TAATTAAATTGAATAAAATTAATAG
1 TAATTAAAATAAAAAAAATTAAAAG
* *
99311209 TATTTAAAATAAAAAAAATTAAAAT
1 TAATTAAAATAAAAAAAATTAAAAG
99311234 TAATTAA
1 TAATTAA
99311241 TTCAAAAATT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (25 bp):
TAATTAAAATAAAAAAAATTAAAAG
Found at i:99314233 original size:9 final size:9
Alignment explanation
Indices: 99314220--99314287 Score: 73
Period size: 9 Copynumber: 7.6 Consensus size: 9
99314210 ATAATTATAA
*
99314220 AATTAACCA
1 AATTAACCG
**
99314229 AATTAATTG
1 AATTAACCG
99314238 AATTAACCG
1 AATTAACCG
*
99314247 AATTACCCG
1 AATTAACCG
* *
99314256 AATTATCCA
1 AATTAACCG
*
99314265 AATTAATCG
1 AATTAACCG
99314274 AATTAACCG
1 AATTAACCG
99314283 AATTA
1 AATTA
99314288 TTTGTATAAA
Statistics
Matches: 47, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
9 47 1.00
ACGTcount: A:0.46, C:0.18, G:0.07, T:0.29
Consensus pattern (9 bp):
AATTAACCG
Found at i:99314243 original size:18 final size:18
Alignment explanation
Indices: 99314220--99314287 Score: 82
Period size: 18 Copynumber: 3.8 Consensus size: 18
99314210 ATAATTATAA
*
99314220 AATTAACCAAATTAATTG
1 AATTAACCAAATTAATCG
* **
99314238 AATTAACCGAATTACCCG
1 AATTAACCAAATTAATCG
*
99314256 AATTATCCAAATTAATCG
1 AATTAACCAAATTAATCG
*
99314274 AATTAACCGAATTA
1 AATTAACCAAATTA
99314288 TTTGTATAAA
Statistics
Matches: 40, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 40 1.00
ACGTcount: A:0.46, C:0.18, G:0.07, T:0.29
Consensus pattern (18 bp):
AATTAACCAAATTAATCG
Found at i:99314322 original size:5 final size:6
Alignment explanation
Indices: 99314307--99314347 Score: 55
Period size: 6 Copynumber: 6.5 Consensus size: 6
99314297 AATTATATGT
*
99314307 TTTTTA TTTTTA TTTTTA GTTTTAGA TTTTTA TTTTTA TTT
1 TTTTTA TTTTTA TTTTTA -TTTT-TA TTTTTA TTTTTA TTT
99314348 ATTAAATTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
6 22 0.71
7 8 0.26
8 1 0.03
ACGTcount: A:0.17, C:0.00, G:0.05, T:0.78
Consensus pattern (6 bp):
TTTTTA
Found at i:99317406 original size:2 final size:2
Alignment explanation
Indices: 99317401--99317450 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
99317391 ACACACACAC
99317401 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
99317443 AT AT AT AT
1 AT AT AT AT
99317451 TTGGTCTCAT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:99326901 original size:55 final size:55
Alignment explanation
Indices: 99326840--99326944 Score: 149
Period size: 55 Copynumber: 1.9 Consensus size: 55
99326830 CATAGGCATG
* *
99326840 CGACACGCCTGTGTGGAAGAACCGTGGGT-GAACCTGTTAAAACAACACGGTCGTT
1 CGACACGCCTGTGTGGAACAACCGT-GATCGAACCTGTTAAAACAACACGGTCGTT
* **
99326895 CGACACGCCTGTGTGGAACACCCGTGATCGAACCTGTTAAATTAACACGG
1 CGACACGCCTGTGTGGAACAACCGTGATCGAACCTGTTAAAACAACACGG
99326945 GCATGGGGCT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
54 2 0.05
55 42 0.95
ACGTcount: A:0.28, C:0.26, G:0.27, T:0.20
Consensus pattern (55 bp):
CGACACGCCTGTGTGGAACAACCGTGATCGAACCTGTTAAAACAACACGGTCGTT
Found at i:99327338 original size:19 final size:20
Alignment explanation
Indices: 99327310--99327352 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
99327300 CTTATAATGC
99327310 TATTTATCATATTA-ATCTA
1 TATTTATCATATTATATCTA
* * *
99327329 TATTTTTCATGTTATTTCTA
1 TATTTATCATATTATATCTA
99327349 TATT
1 TATT
99327353 GATAATCACA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.28, C:0.09, G:0.02, T:0.60
Consensus pattern (20 bp):
TATTTATCATATTATATCTA
Found at i:99330955 original size:13 final size:13
Alignment explanation
Indices: 99330937--99330961 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
99330927 AAGTAATCGA
99330937 ACACGGGCGTGTT
1 ACACGGGCGTGTT
99330950 ACACGGGCGTGT
1 ACACGGGCGTGT
99330962 CCCTACCGAG
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:0.24, G:0.40, T:0.20
Consensus pattern (13 bp):
ACACGGGCGTGTT
Found at i:99349879 original size:35 final size:35
Alignment explanation
Indices: 99349833--99349903 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
99349823 GGTAAGCTAC
99349833 CTTATGGTCATTCGGAGATTAGTTTGGATAGCTGG
1 CTTATGGTCATTCGGAGATTAGTTTGGATAGCTGG
99349868 CTTATGGTCATTCGGAGATTAGTTTGGATAGCTGG
1 CTTATGGTCATTCGGAGATTAGTTTGGATAGCTGG
99349903 C
1 C
99349904 CTATCTGAGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.20, C:0.13, G:0.31, T:0.37
Consensus pattern (35 bp):
CTTATGGTCATTCGGAGATTAGTTTGGATAGCTGG
Found at i:99355533 original size:13 final size:13
Alignment explanation
Indices: 99355515--99355539 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
99355505 ACTTCTATTT
99355515 TACTTATTACTAA
1 TACTTATTACTAA
99355528 TACTTATTACTA
1 TACTTATTACTA
99355540 GCATAATCTT
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:0.36, C:0.16, G:0.00, T:0.48
Consensus pattern (13 bp):
TACTTATTACTAA
Found at i:99359203 original size:13 final size:13
Alignment explanation
Indices: 99359185--99359211 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
99359175 GGAGTAATCG
99359185 CACACGGGCGTGT
1 CACACGGGCGTGT
99359198 CACACGGGCGTGT
1 CACACGGGCGTGT
99359211 C
1 C
99359212 CTTGCCGAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.33, G:0.37, T:0.15
Consensus pattern (13 bp):
CACACGGGCGTGT
Found at i:99367289 original size:696 final size:696
Alignment explanation
Indices: 99365958--99367305 Score: 2283
Period size: 696 Copynumber: 1.9 Consensus size: 696
99365948 GGGCTGTTAC
* * * *
99365958 ACTGTCAATCCAGTCGATCACATCTATGTCTCTATCTTCTAGGAGTCATCTGCACTGATGCCTAA
1 ACTGTCAATCCAGTCGATCACATCTATGTCTCTATATTCTAAGAGTCATCTACACCGATGCCTAA
*
99366023 AACAAAACATCTTTCCAATTGGACTTGATAGACAACATATTAGTCATTCAATTGGTTTGCTCATT
66 AACAAAACATCTCTCCAATTGGACTTGATAGACAACATATTAGTCATTCAATTGGTTTGCTCATT
* * *
99366088 TTCGATTAAACTAATTACATGTTTAGGCCCATCTACTAATATAAACTGTCTTTTAGCATTATGAT
131 TTCGATTAAACTAATGACATGTTTAGCCCCATCTACTAATATAAACTGTCTTTTAGCATTACGAT
* **
99366153 CCAACCACATAATACCTCTCACTATTAGTTAAATATTAGACAACCAATGAGCTAATATTTTTTTC
196 CCAACCACATAATACCTCTCACTATTAGTTAAACATTAGACAACCAATGAGCTAATATTTGCTTC
*
99366218 TATTTTGCTTTACATGAAAAAATCACATGAGGACATTATACAAATAATATTAGTGTAATTCATGA
261 TATTTTGCTTTACATGAAAAAATCACATGAGGACATTATACAAAGAATATTAGTGTAATTCATGA
* *
99366283 ATAATTTTATTAATAAATTTGTTCAAAAAAATTACAAATGTACAAATGAATATACTACACTTAGA
326 ATAATTTTATTAATAAATTTGTTCAAAAAAATTAAAAATGTACAAATGAATAGACTACACTTAGA
* *
99366348 GCATCGGATTCAACACTATAATGAACAGATGCTTAGCAGAAAAAAATACTCTTCCATATAAACGA
391 GCATCAGATCCAACACTATAATGAACAGATGCTTAGCAGAAAAAAATACTCTTCCATATAAACGA
*
99366413 AGGGTTATTACCCTTTGTGGCTTTAAAAAAGCCACAACACAGAAAATATCTAGCTTTGAAAATTC
456 AGGGTTATTACCCTTTGTGACTTTAAAAAAGCCACAACACAGAAAATATCTAGCTTTGAAAATTC
*
99366478 TACTAGGAAGAGATCGAGATTGAAATAAAACTCCAACCTTGCTTACAAAGCATATCTAAATTAAA
521 TACTAGGAAGAGATCGAGATTGAAATAAAACTCCAACCTTGCTTACAAAGCATAGCTAAATTAAA
*
99366543 ATAGTGAAGATTATGAAATTCCATTCTGCCAGACTTCTTCACCATGCATAATTTATCCCACGAAG
586 ATAGTGAAGATTATGAAATTCCATTCTGCCAAACTTCTTCACCATGCATAATTTATCCCACGAAG
99366608 CCTAAAACATATTTACGGTATATTCTACTTGGGCCCAATTCAATGT
651 CCTAAAACATATTTACGGTATATTCTACTTGGGCCCAATTCAATGT
**
99366654 ACTGTCAATCCAGTC-AGTCACATCTATGTCTCTATATTCTAAGAGTCATCTATTCCGATGCCTA
1 ACTGTCAATCCAGTCGA-TCACATCTATGTCTCTATATTCTAAGAGTCATCTACACCGATGCCTA
* *
99366718 AAACAAAGCATCTCTCTAATTGGACTTGATAGACAACATATTAGTCATTCAATTGGTTTGCT-AT
65 AAACAAAACATCTCTCCAATTGGACTTGATAGACAACATATTAGTCATTCAATTGGTTTGCTCAT
* *
99366782 TTTCTGATTAGACTAATGACATGTTTACGCCCCGTCTACTAATATAAACTGTCTTTTAGCATTAC
130 TTTC-GATTAAACTAATGACATGTTTA-GCCCCATCTACTAATATAAACTGTCTTTTAGCATTAC
* *
99366847 GATCCAACCACGTAATA-CTGCTCAGTATTAGTTAAACATTAGACAACCAATGAGCTAATATTTG
193 GATCCAACCACATAATACCT-CTCACTATTAGTTAAACATTAGACAACCAATGAGCTAATATTTG
99366911 CTTCTATTTTGCTTTACATGAAAAAATCACATGAGGACATTATACAAAGAATATTAGTGTAATTC
257 CTTCTATTTTGCTTTACATGAAAAAATCACATGAGGACATTATACAAAGAATATTAGTGTAATTC
*
99366976 ATGAATAATTTTATTCATAAATTTGTTCAAAAAAATTAAAAATGTACAAATGAATAGACTACACT
322 ATGAATAATTTTATTAATAAATTTGTTCAAAAAAATTAAAAATGTACAAATGAATAGACTACACT
** *
99367041 TAGAGCATCAGATCCAACACTATAATGAGGAGATGCTTAGCAG-AAAAAATGCTCTTCCATATAA
387 TAGAGCATCAGATCCAACACTATAATGAACAGATGCTTAGCAGAAAAAAATACTCTTCCATATAA
* * *
99367105 ATGAAGGGTTATTGCCCTTTGTGACTTTAAAAAAGCCACAAGACAGAAAATATCTAGC-TTGAAA
452 ACGAAGGGTTATTACCCTTTGTGACTTTAAAAAAGCCACAACACAGAAAATATCTAGCTTTGAAA
* *
99367169 ATTCTACTAGGAAGAGATTGGAGATTGAAATAAAACTCTAACCTTGCTTACAAAGCATAGCTAAA
517 ATTCTACTAGGAAGAGA-TCGAGATTGAAATAAAACTCCAACCTTGCTTACAAAGCATAGCTAAA
*
99367234 TTAAAATAGTGAAGATTATGAAATTCCATTCTGCCAAACTTCTTCGCCATGCATAATTTATCCCA
581 TTAAAATAGTGAAGATTATGAAATTCCATTCTGCCAAACTTCTTCACCATGCATAATTTATCCCA
99367299 CGAAGCC
646 CGAAGCC
99367306 CACCAAATGC
Statistics
Matches: 610, Mismatches: 37, Indels: 10
0.93 0.06 0.02
Matches are distributed among these distances:
695 30 0.05
696 325 0.53
697 255 0.42
ACGTcount: A:0.37, C:0.18, G:0.13, T:0.32
Consensus pattern (696 bp):
ACTGTCAATCCAGTCGATCACATCTATGTCTCTATATTCTAAGAGTCATCTACACCGATGCCTAA
AACAAAACATCTCTCCAATTGGACTTGATAGACAACATATTAGTCATTCAATTGGTTTGCTCATT
TTCGATTAAACTAATGACATGTTTAGCCCCATCTACTAATATAAACTGTCTTTTAGCATTACGAT
CCAACCACATAATACCTCTCACTATTAGTTAAACATTAGACAACCAATGAGCTAATATTTGCTTC
TATTTTGCTTTACATGAAAAAATCACATGAGGACATTATACAAAGAATATTAGTGTAATTCATGA
ATAATTTTATTAATAAATTTGTTCAAAAAAATTAAAAATGTACAAATGAATAGACTACACTTAGA
GCATCAGATCCAACACTATAATGAACAGATGCTTAGCAGAAAAAAATACTCTTCCATATAAACGA
AGGGTTATTACCCTTTGTGACTTTAAAAAAGCCACAACACAGAAAATATCTAGCTTTGAAAATTC
TACTAGGAAGAGATCGAGATTGAAATAAAACTCCAACCTTGCTTACAAAGCATAGCTAAATTAAA
ATAGTGAAGATTATGAAATTCCATTCTGCCAAACTTCTTCACCATGCATAATTTATCCCACGAAG
CCTAAAACATATTTACGGTATATTCTACTTGGGCCCAATTCAATGT
Found at i:99371816 original size:44 final size:44
Alignment explanation
Indices: 99371753--99371846 Score: 188
Period size: 44 Copynumber: 2.1 Consensus size: 44
99371743 GATTCGAGGA
99371753 AGAGATCGATGAATAAATCTTATCATTCCTCATCAAAGAAACCT
1 AGAGATCGATGAATAAATCTTATCATTCCTCATCAAAGAAACCT
99371797 AGAGATCGATGAATAAATCTTATCATTCCTCATCAAAGAAACCT
1 AGAGATCGATGAATAAATCTTATCATTCCTCATCAAAGAAACCT
99371841 AGAGAT
1 AGAGAT
99371847 TATTTTAATC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 50 1.00
ACGTcount: A:0.41, C:0.19, G:0.13, T:0.27
Consensus pattern (44 bp):
AGAGATCGATGAATAAATCTTATCATTCCTCATCAAAGAAACCT
Found at i:99381862 original size:55 final size:55
Alignment explanation
Indices: 99381764--99381901 Score: 159
Period size: 55 Copynumber: 2.5 Consensus size: 55
99381754 TATATAGGCC
* * * * * *
99381764 CACGCCCGTGTTAATCTGACAGGTTCACCCATGGTTGCTAGGCACGGACGTGTCG
1 CACGCCCATGTTAATTTGACAGGTTCGCCCACGGTTGCCAGGCACGGACATGTCG
* * *
99381819 CACGCCCATGTTAATTTGACAGGTTCGGCCACGGTTTCCAGGCACGGGCATGTCG
1 CACGCCCATGTTAATTTGACAGGTTCGCCCACGGTTGCCAGGCACGGACATGTCG
* ** *
99381874 CATGCCCATGTTGTTTTGGCAGGTTCGC
1 CACGCCCATGTTAATTTGACAGGTTCGC
99381902 ACAGCCGTGG
Statistics
Matches: 69, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
55 69 1.00
ACGTcount: A:0.17, C:0.28, G:0.29, T:0.26
Consensus pattern (55 bp):
CACGCCCATGTTAATTTGACAGGTTCGCCCACGGTTGCCAGGCACGGACATGTCG
Found at i:99388018 original size:22 final size:22
Alignment explanation
Indices: 99387968--99388037 Score: 81
Period size: 22 Copynumber: 3.2 Consensus size: 22
99387958 AGATTACCAA
99387968 TTTAGCTCGTATA-AGCTTACTG
1 TTTAGCTCG-ATAGAGCTTACTG
*
99387990 TTCAGCTCGATAGAGCTTAC-G
1 TTTAGCTCGATAGAGCTTACTG
* *
99388011 TTTTAGCTCAATAGAGCTTACTA
1 -TTTAGCTCGATAGAGCTTACTG
99388034 TTTA
1 TTTA
99388038 TCAGATCAGG
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
21 4 0.10
22 37 0.90
ACGTcount: A:0.26, C:0.19, G:0.17, T:0.39
Consensus pattern (22 bp):
TTTAGCTCGATAGAGCTTACTG
Found at i:99388235 original size:20 final size:19
Alignment explanation
Indices: 99388212--99388320 Score: 65
Period size: 20 Copynumber: 5.5 Consensus size: 19
99388202 GTTGAAATGA
99388212 ATGAATTACTATTGATACGG
1 ATGAATTACTATT-ATACGG
* * ***
99388232 ATGAATTATTGTTGATATAA
1 ATGAATTACTATT-ATACGG
* *
99388252 ATAAATTATTATTATTACGG
1 ATGAATTACTATTA-TACGG
* *
99388272 ATGAATTACTGGTTATACAG
1 ATGAATTACT-ATTATACGG
* * *
99388292 ATGAACTACTAGTTATATGA
1 ATGAATTACTA-TTATACGG
99388312 ATGAATTAC
1 ATGAATTAC
99388321 AGTTTATACG
Statistics
Matches: 66, Mismatches: 20, Indels: 6
0.72 0.22 0.07
Matches are distributed among these distances:
19 1 0.02
20 62 0.94
21 3 0.05
ACGTcount: A:0.39, C:0.07, G:0.16, T:0.39
Consensus pattern (19 bp):
ATGAATTACTATTATACGG
Found at i:99388259 original size:40 final size:40
Alignment explanation
Indices: 99388201--99388279 Score: 106
Period size: 40 Copynumber: 2.0 Consensus size: 40
99388191 GAATAAGCTA
* *
99388201 TGTTGAAATGAATGAATTACTATTGA-TACGGATGAATTAT
1 TGTTGAAATAAATAAATTACTATT-ATTACGGATGAATTAT
* *
99388241 TGTTGATATAAATAAATTATTATTATTACGGATGAATTA
1 TGTTGAAATAAATAAATTACTATTATTACGGATGAATTA
99388280 CTGGTTATAC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
39 1 0.03
40 33 0.97
ACGTcount: A:0.39, C:0.04, G:0.16, T:0.41
Consensus pattern (40 bp):
TGTTGAAATAAATAAATTACTATTATTACGGATGAATTAT
Found at i:99404296 original size:101 final size:102
Alignment explanation
Indices: 99404120--99404320 Score: 377
Period size: 101 Copynumber: 2.0 Consensus size: 102
99404110 TGTGATTATT
99404120 TTGTAGATACATCTACCAAAATCATATAATATCAAAATCATCTACATGGTGGATGAATGAGCCCA
1 TTGTAGATACATCTACCAAAATCATATAATATCAAAATCATCTACATGGTGGATGAATGAGCCCA
**
99404185 TATTCATTTCAGAAATGCAAGACATTGTATCTCAATC
66 TATTCATTTCAGAAATGCAAGACATTAAATCTCAATC
99404222 TTGTAGATACATCTACC-AAATCATATAATATCAAAATCATCTACATGGTGGATGAATGAGCCCA
1 TTGTAGATACATCTACCAAAATCATATAATATCAAAATCATCTACATGGTGGATGAATGAGCCCA
99404286 TATTCATTTCAGAAATGCAAGACATTAAATCTCAA
66 TATTCATTTCAGAAATGCAAGACATTAAATCTCAA
99404321 CTTTAGCTAG
Statistics
Matches: 97, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
101 80 0.82
102 17 0.18
ACGTcount: A:0.39, C:0.18, G:0.12, T:0.30
Consensus pattern (102 bp):
TTGTAGATACATCTACCAAAATCATATAATATCAAAATCATCTACATGGTGGATGAATGAGCCCA
TATTCATTTCAGAAATGCAAGACATTAAATCTCAATC
Found at i:99410142 original size:72 final size:72
Alignment explanation
Indices: 99409780--99410116 Score: 419
Period size: 72 Copynumber: 4.7 Consensus size: 72
99409770 TCACCTGTGA
* * * * * * ****
99409780 ATAAATTTTATATCC-AAAATCATATATAAACAACAATTGTTAAAACTA-ATTTTGTATAAATAA
1 ATAAATTTAATATCCAAAAACCAAACATAAACAACTATTGATAAAACTAGATTACACATAAATAA
*
99409843 GTAAAAC
66 GTAGAAC
* * **
99409850 ATAAATTTAATATCCAAAAATCAAACATAAACAATTATTGATAAAACTAGCCCTA-AGCATAAAT
1 ATAAATTTAATATCCAAAAACCAAACATAAACAACTATTGATAAAACTAG-ATTACA-CATAAAT
*
99409914 AAGTAGACC
64 AAGTAGAAC
* * * * *
99409923 ATAAATTCAATATCCAAAGACCAAACATAAACAACTATTAATAGAACAAGATTACACATAAATAA
1 ATAAATTTAATATCCAAAAACCAAACATAAACAACTATTGATAAAACTAGATTACACATAAATAA
99409988 GTAGAAC
66 GTAGAAC
* *
99409995 ATAAATTTAATATCCAAAAACCAAACATAAACAACCATTGACAAAACTAGATTACACATAAATAA
1 ATAAATTTAATATCCAAAAACCAAACATAAACAACTATTGATAAAACTAGATTACACATAAATAA
99410060 GTAGAAC
66 GTAGAAC
*
99410067 ATAAATTTAATATCCAAAAACCAAACATAAATAACTATTGATAAAACTAG
1 ATAAATTTAATATCCAAAAACCAAACATAAACAACTATTGATAAAACTAG
99410117 TTTAGCATTG
Statistics
Matches: 229, Mismatches: 33, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
70 14 0.06
71 28 0.12
72 129 0.56
73 58 0.25
ACGTcount: A:0.54, C:0.15, G:0.06, T:0.25
Consensus pattern (72 bp):
ATAAATTTAATATCCAAAAACCAAACATAAACAACTATTGATAAAACTAGATTACACATAAATAA
GTAGAAC
Found at i:99410142 original size:144 final size:145
Alignment explanation
Indices: 99409835--99410113 Score: 418
Period size: 145 Copynumber: 1.9 Consensus size: 145
99409825 CTAATTTTGT
* * ** *
99409835 ATAAATAAGTAAAACATAAATTTAATATCCAAAAATCAAACATAAACAATTATTGATAAAACTAG
1 ATAAATAAGTAGAACATAAATTTAATATCCAAAAACCAAACATAAACAACCATTGACAAAACTAG
* * *
99409900 CCCTAAGCATAAATAAGTAGACCATAAATTCAATATCCAAAGACCAAACATAAACAACTATTAAT
66 CACTAAGCATAAATAAGTAGAACATAAATTCAATATCCAAAAACCAAACATAAACAACTATTAAT
*
99409965 AGAACAAGATTACAC
131 AAAACAAGATTACAC
99409980 ATAAATAAGTAGAACATAAATTTAATATCCAAAAACCAAACATAAACAACCATTGACAAAACTAG
1 ATAAATAAGTAGAACATAAATTTAATATCCAAAAACCAAACATAAACAACCATTGACAAAACTAG
* * * *
99410045 -ATTACA-CATAAATAAGTAGAACATAAATTTAATATCCAAAAACCAAACATAAATAACTATTGA
66 CACTA-AGCATAAATAAGTAGAACATAAATTCAATATCCAAAAACCAAACATAAACAACTATTAA
99410108 TAAAAC
130 TAAAAC
99410114 TAGTTTAGCA
Statistics
Matches: 120, Mismatches: 13, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
144 59 0.49
145 61 0.51
ACGTcount: A:0.56, C:0.16, G:0.06, T:0.23
Consensus pattern (145 bp):
ATAAATAAGTAGAACATAAATTTAATATCCAAAAACCAAACATAAACAACCATTGACAAAACTAG
CACTAAGCATAAATAAGTAGAACATAAATTCAATATCCAAAAACCAAACATAAACAACTATTAAT
AAAACAAGATTACAC
Found at i:99410567 original size:18 final size:18
Alignment explanation
Indices: 99410544--99410609 Score: 114
Period size: 18 Copynumber: 3.7 Consensus size: 18
99410534 TTCCATCAAT
99410544 TGAACATCATTTGAAATG
1 TGAACATCATTTGAAATG
99410562 TGAACATCATTTGAAATG
1 TGAACATCATTTGAAATG
* *
99410580 TAAACATCATTTAAAATG
1 TGAACATCATTTGAAATG
99410598 TGAACATCATTT
1 TGAACATCATTT
99410610 CTCACATTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 45 1.00
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.35
Consensus pattern (18 bp):
TGAACATCATTTGAAATG
Found at i:99415188 original size:93 final size:93
Alignment explanation
Indices: 99415076--99415247 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
99415066 CGCCCATAAG
* *
99415076 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
99415141 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
*
99415169 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
99415234 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
99415248 TCAACCATCC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:99415244 original size:46 final size:46
Alignment explanation
Indices: 99415069--99415244 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
99415059 TGTAACCCGC
* * *
99415069 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
99415115 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
99415165 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
99415208 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
99415245 TGCTCAACCA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 63 0.57
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:99421007 original size:8 final size:8
Alignment explanation
Indices: 99420994--99421018 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
99420984 GTTGAGGAAT
99420994 TGGGGAGG
1 TGGGGAGG
99421002 TGGGGAGG
1 TGGGGAGG
99421010 TGGGGAGG
1 TGGGGAGG
99421018 T
1 T
99421019 CGTACATTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.12, C:0.00, G:0.72, T:0.16
Consensus pattern (8 bp):
TGGGGAGG
Found at i:99422766 original size:93 final size:93
Alignment explanation
Indices: 99422654--99422825 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
99422644 CGCCCATAAG
* *
99422654 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
99422719 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
*
99422747 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
99422812 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
99422826 TCAACCATCC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:99422822 original size:46 final size:46
Alignment explanation
Indices: 99422647--99422822 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
99422637 TGTAACCCGC
* * *
99422647 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
99422693 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
99422743 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
99422786 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
99422823 TGCTCAACCA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 63 0.57
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:99427433 original size:39 final size:39
Alignment explanation
Indices: 99427371--99427569 Score: 353
Period size: 39 Copynumber: 5.1 Consensus size: 39
99427361 AATTATATTA
* * *
99427371 CCAGCACAAAGCCTACGGAACTTTAGCCCGGATACATTT
1 CCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT
*
99427410 CCAACACGAAGCCTGCGGGACTTTAGCCCGGATACATTT
1 CCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT
99427449 CCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT
1 CCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT
*
99427488 CCAGCACGAAGCCTGCGGGACTTTAGCCCAGATACATTT
1 CCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT
99427527 CCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT
1 CCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT
99427566 CCAG
1 CCAG
99427570 TGTCTTGAAT
Statistics
Matches: 153, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 153 1.00
ACGTcount: A:0.26, C:0.31, G:0.23, T:0.20
Consensus pattern (39 bp):
CCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT
Found at i:99434569 original size:3 final size:3
Alignment explanation
Indices: 99434561--99434603 Score: 77
Period size: 3 Copynumber: 14.3 Consensus size: 3
99434551 TTTGTGCCTA
*
99434561 TAT TAT TAT TAT TAT TAC TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
99434604 TATTCATTAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:99438337 original size:19 final size:19
Alignment explanation
Indices: 99438313--99438350 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
99438303 ACAAGAACAG
99438313 CTTCACTGATCTCAAGATC
1 CTTCACTGATCTCAAGATC
99438332 CTTCACTGATCTCAAGATC
1 CTTCACTGATCTCAAGATC
99438351 GGGTCAGGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.32, G:0.11, T:0.32
Consensus pattern (19 bp):
CTTCACTGATCTCAAGATC
Found at i:99446683 original size:190 final size:190
Alignment explanation
Indices: 99446402--99446823 Score: 582
Period size: 190 Copynumber: 2.2 Consensus size: 190
99446392 GATTATAGTC
* * *
99446402 ATCATGGCAAATCTTATCTCCCTGAAATTGCAGTGGAGA-AGATTGAGGCCACTAATCTTATCTC
1 ATCATGGCAAATCTTATCTCCCTGAAGTTGCAGTGGA-ACAGATGGAAGCCACTAATCTTATCTC
* * * *
99446466 CTTGATGTTACGATGGAGCAGATTGAAGATAGTGAATTTTATTTCCCTGAAGTTGTAGTGAAATA
65 CCTGAAGTTACGATGGAGCAGATTGAAGATAGAGAATCTTATTTCCCTGAAGTTGTAGTGAAATA
* * * *
99446531 GATTAAAGCTACAAGTTACAAATCCTAGACCTCTGAAGTTACCGTAGGTCGGATCAAATCT
130 GATTAAAGCTACAAGTCACAAATCCTAGACCTCTAAAGTTACAGTAGATCGGATCAAATCT
* *
99446592 ATCATGGCAAATTTTATCTCCCTGAAGTTGCAGTGGATCAGATGGAAGCCACTAATCTTATCTCC
1 ATCATGGCAAATCTTATCTCCCTGAAGTTGCAGTGGAACAGATGGAAGCCACTAATCTTATCTCC
* *
99446657 CTGAAGTTAC-AGTGGAGCAGATTGAAGATAGAGAATCTTATTTTCCTGAAGTTGTAGTGGAATA
66 CTGAAGTTACGA-TGGAGCAGATTGAAGATAGAGAATCTTATTTCCCTGAAGTTGTAGTGAAATA
* * * *
99446721 GATTAAAGCTACAAGTCACAAATCTTATACCTCTAAAGTTGCAGTAGATTGGATCAAATCT
130 GATTAAAGCTACAAGTCACAAATCCTAGACCTCTAAAGTTACAGTAGATCGGATCAAATCT
* * * *
99446782 ACCATAGG--AATCTTATTTCTCTAAAGTTGCAGTGGAACAGAT
1 ATCAT-GGCAAATCTTATCTCCCTGAAGTTGCAGTGGAACAGAT
99446824 TAAAGCTGCA
Statistics
Matches: 204, Mismatches: 25, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
189 30 0.15
190 172 0.84
191 2 0.01
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Consensus pattern (190 bp):
ATCATGGCAAATCTTATCTCCCTGAAGTTGCAGTGGAACAGATGGAAGCCACTAATCTTATCTCC
CTGAAGTTACGATGGAGCAGATTGAAGATAGAGAATCTTATTTCCCTGAAGTTGTAGTGAAATAG
ATTAAAGCTACAAGTCACAAATCCTAGACCTCTAAAGTTACAGTAGATCGGATCAAATCT
Found at i:99446824 original size:100 final size:101
Alignment explanation
Indices: 99446684--99446875 Score: 262
Period size: 100 Copynumber: 1.9 Consensus size: 101
99446674 CAGATTGAAG
* * * *
99446684 ATAGAGAATCTTATTTTCCTGAAGTTGTAGTGGAATAGATTAAAGCTACAAGTCACAAATCTTAT
1 ATAGAGAATCTTATTTTCCTAAAGTTGCAGTGGAACAGATTAAAGCTACAAATCACAAATCTTAT
* * *
99446749 ACCTCTAAAGTTGCAGTAGATTGGATCAAATCTACC
66 ACCTCTAAAATTGCAATAGAGTGGATCAAATCTACC
* * *
99446785 ATAG-GAATCTTA-TTTCTCTAAAGTTGCAGTGGAACAGATTAAAGCTGCAAATTACAAGTCTTA
1 ATAGAGAATCTTATTTTC-CTAAAGTTGCAGTGGAACAGATTAAAGCTACAAATCACAAATCTTA
*
99446848 TATCTCTAAAATTGCAATAGAGTGGATC
65 TACCTCTAAAATTGCAATAGAGTGGATC
99446876 GAAGCAACAG
Statistics
Matches: 79, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
99 4 0.05
100 71 0.90
101 4 0.05
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.32
Consensus pattern (101 bp):
ATAGAGAATCTTATTTTCCTAAAGTTGCAGTGGAACAGATTAAAGCTACAAATCACAAATCTTAT
ACCTCTAAAATTGCAATAGAGTGGATCAAATCTACC
Found at i:99448733 original size:3 final size:3
Alignment explanation
Indices: 99448725--99448782 Score: 116
Period size: 3 Copynumber: 19.3 Consensus size: 3
99448715 TTTGTGCCTA
99448725 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
99448773 TAT TAT TAT T
1 TAT TAT TAT T
99448783 TATTCATCAA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:99449054 original size:3 final size:3
Alignment explanation
Indices: 99449046--99449115 Score: 131
Period size: 3 Copynumber: 23.3 Consensus size: 3
99449036 CTCACACACT
99449046 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
99449094 TTA TTA TTA TTA TTG TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA T
99449116 CATCTTGTCT
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 65 1.00
ACGTcount: A:0.31, C:0.00, G:0.01, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:99451250 original size:11 final size:10
Alignment explanation
Indices: 99451180--99451251 Score: 62
Period size: 9 Copynumber: 7.4 Consensus size: 10
99451170 ACAAATTGAA
99451180 AAAAATATATT
1 AAAAAT-TATT
**
99451191 AAAAATTACA
1 AAAAATTATT
*
99451201 AAAAAATA-T
1 AAAAATTATT
*
99451210 AAAAAATA-T
1 AAAAATTATT
99451219 AAAAATTA-T
1 AAAAATTATT
99451228 -AAAATTATT
1 AAAAATTATT
99451237 AAAAATTATGT
1 AAAAATTAT-T
99451248 AAAA
1 AAAA
99451252 GAGTTTGCAT
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
8 7 0.13
9 18 0.34
10 17 0.32
11 11 0.21
ACGTcount: A:0.68, C:0.01, G:0.01, T:0.29
Consensus pattern (10 bp):
AAAAATTATT
Done.