Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000482.1 Hibiscus syriacus cultivar Beakdansim tig00000916_pilon, whole genome shotgun sequence
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: 2886609
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 16
Found at i:1803260 original size:21 final size:21
Alignment explanation
Indices: 1803234--1803280 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 21
1803224 TTACTTTTTC
*
1803234 TTTTTTTCTTTTGTTTTTTTTAA
1 TTTTTTTC-TTT-TTTTTTTCAA
1803257 TTTTTTTCTTTTTTTTTTCAA
1 TTTTTTTCTTTTTTTTTTCAA
1803278 TTT
1 TTT
1803281 AGGGCGTCCT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 12 0.52
22 3 0.13
23 8 0.35
ACGTcount: A:0.09, C:0.06, G:0.02, T:0.83
Consensus pattern (21 bp):
TTTTTTTCTTTTTTTTTTCAA
Found at i:1803337 original size:23 final size:23
Alignment explanation
Indices: 1803311--1803354 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
1803301 CACCCTAAAC
* *
1803311 TTTTTTCTCTTTTTTGTTTTTTA
1 TTTTTTCTCTTGTTTCTTTTTTA
*
1803334 TTTTTTTTCTTGTTTCTTTTT
1 TTTTTTCTCTTGTTTCTTTTT
1803355 CTTCTTCGAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.02, C:0.09, G:0.05, T:0.84
Consensus pattern (23 bp):
TTTTTTCTCTTGTTTCTTTTTTA
Found at i:1804453 original size:25 final size:25
Alignment explanation
Indices: 1804425--1804482 Score: 98
Period size: 25 Copynumber: 2.3 Consensus size: 25
1804415 CATTTATATG
**
1804425 TCTTCCACAAACTCTGTCGTGTACT
1 TCTTCCACAAACTCCATCGTGTACT
1804450 TCTTCCACAAACTCCATCGTGTACT
1 TCTTCCACAAACTCCATCGTGTACT
1804475 TCTTCCAC
1 TCTTCCAC
1804483 TATCATCTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.21, C:0.36, G:0.09, T:0.34
Consensus pattern (25 bp):
TCTTCCACAAACTCCATCGTGTACT
Found at i:1813920 original size:23 final size:22
Alignment explanation
Indices: 1813865--1813934 Score: 72
Period size: 23 Copynumber: 3.1 Consensus size: 22
1813855 TAACAAAATG
*
1813865 ATAAGAAT-AAAA-ATAAAAAAC
1 ATAAGAATGAAAACA-AAAAAAA
* *
1813886 ATAAAAAAGAAAACAAAAATAAA
1 ATAAGAATGAAAACAAAAA-AAA
1813909 ATAAGAATGAAAACAAAGAAAAA
1 ATAAGAATGAAAACAAA-AAAAA
1813932 ATA
1 ATA
1813935 TGGAAATGAA
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
21 6 0.15
22 8 0.20
23 24 0.60
24 2 0.05
ACGTcount: A:0.77, C:0.04, G:0.07, T:0.11
Consensus pattern (22 bp):
ATAAGAATGAAAACAAAAAAAA
Found at i:1815531 original size:25 final size:25
Alignment explanation
Indices: 1815497--1815577 Score: 82
Period size: 25 Copynumber: 3.4 Consensus size: 25
1815487 CAAACTCTTG
1815497 TTGAATAAATAGCTTGTTTTATCTA
1 TTGAATAAATAGCTTGTTTTATCTA
* *
1815522 TTGAATAAAT-G--TG--TGATCTTG
1 TTGAATAAATAGCTTGTTTTATC-TA
* *
1815543 TTGTATAAATAGCTTGTTTTAGCTA
1 TTGAATAAATAGCTTGTTTTATCTA
1815568 TTGAATAAAT
1 TTGAATAAAT
1815578 GTGTGATTTC
Statistics
Matches: 43, Mismatches: 7, Indels: 12
0.69 0.11 0.19
Matches are distributed among these distances:
20 4 0.09
21 10 0.23
22 3 0.07
24 3 0.07
25 20 0.47
26 3 0.07
ACGTcount: A:0.32, C:0.06, G:0.16, T:0.46
Consensus pattern (25 bp):
TTGAATAAATAGCTTGTTTTATCTA
Found at i:1815559 original size:46 final size:46
Alignment explanation
Indices: 1815492--1815584 Score: 168
Period size: 46 Copynumber: 2.0 Consensus size: 46
1815482 TATCTCAAAC
*
1815492 TCTTGTTGAATAAATAGCTTGTTTTATCTATTGAATAAATGTGTGA
1 TCTTGTTGAATAAATAGCTTGTTTTAGCTATTGAATAAATGTGTGA
*
1815538 TCTTGTTGTATAAATAGCTTGTTTTAGCTATTGAATAAATGTGTGA
1 TCTTGTTGAATAAATAGCTTGTTTTAGCTATTGAATAAATGTGTGA
1815584 T
1 T
1815585 TTCAGCAGGT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.29, C:0.06, G:0.18, T:0.46
Consensus pattern (46 bp):
TCTTGTTGAATAAATAGCTTGTTTTAGCTATTGAATAAATGTGTGA
Found at i:1818720 original size:2 final size:2
Alignment explanation
Indices: 1818713--1818745 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1818703 AATATGAAGA
1818713 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1818746 TGTAGAGGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:1819719 original size:22 final size:21
Alignment explanation
Indices: 1819694--1819745 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 21
1819684 ACGTAAAATC
1819694 ATATTTTCAATA-AAAAAATTAT
1 ATATTTT-AATATAAAAAATT-T
*
1819716 ATATATATAATATAAAAAATTT
1 ATAT-TTTAATATAAAAAATTT
1819738 AT-TTTTAA
1 ATATTTTAA
1819746 GAGAACGACC
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
20 4 0.15
21 1 0.04
22 11 0.42
23 10 0.38
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (21 bp):
ATATTTTAATATAAAAAATTT
Found at i:1833842 original size:22 final size:21
Alignment explanation
Indices: 1833814--1833879 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 21
1833804 GGGCATGTGA
1833814 AATTTGTCCCGAAGGACCTATG
1 AATTTGTCCCGAA-GACCTATG
*
1833836 AATTTGTCCCGATAGACCTCTG
1 AATTTGTCCCGA-AGACCTATG
* *
1833858 TATATGTCCCGAATGACCTATG
1 AATTTGTCCCGAA-GACCTATG
1833880 TAACCCTTGA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
21 1 0.03
22 36 0.95
23 1 0.03
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.30
Consensus pattern (21 bp):
AATTTGTCCCGAAGACCTATG
Found at i:1834731 original size:19 final size:19
Alignment explanation
Indices: 1834707--1834745 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
1834697 TCGAATGCAT
1834707 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
1834726 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
1834745 T
1 T
1834746 GAATATTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:1834762 original size:65 final size:64
Alignment explanation
Indices: 1834693--1834853 Score: 198
Period size: 65 Copynumber: 2.5 Consensus size: 64
1834683 GAATTAATTG
* * *** *
1834693 AACATCGAATGCATTCCATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATA-TTTTCA
1 AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCAC-CAGAATATTTTTC-
1834757 A
64 A
* * **
1834758 AACATCGAATGCATTTGATGTATCGATGCACAAGCCATGCATCGATGCACCAGGCTATTTTTCA
1 AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACCAGAATATTTTTCA
*
1834822 AACATCGAATGCATTTCGTGCATCGATGCACA
1 AACATCGAATGCATTTCATGCATCGATGCACA
1834854 CTTGGTGCAC
Statistics
Matches: 82, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
64 34 0.41
65 48 0.59
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27
Consensus pattern (64 bp):
AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACCAGAATATTTTTCA
Found at i:1840674 original size:20 final size:21
Alignment explanation
Indices: 1840645--1840700 Score: 62
Period size: 22 Copynumber: 2.7 Consensus size: 21
1840635 TTTGTGCTTC
*
1840645 ATGCACCGATGCAT-TT-AACA
1 ATGCATCGATGCATCTTGAA-A
*
1840665 ATGCATCGATGCATCCTTGAAT
1 ATGCATCGATGCAT-CTTGAAA
1840687 ATGCATCGATGCAT
1 ATGCATCGATGCAT
1840701 AAGACCATGC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 13 0.42
22 16 0.52
23 2 0.06
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.29
Consensus pattern (21 bp):
ATGCATCGATGCATCTTGAAA
Found at i:1842262 original size:21 final size:21
Alignment explanation
Indices: 1842220--1842263 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1842210 ACCCCGGGAG
*
1842220 CTAGTTCTTCACGAGCTGCTC
1 CTAGTTCTTCACGAGCTCCTC
* *
1842241 CTAGTTCTTCTCGTGCTCCTC
1 CTAGTTCTTCACGAGCTCCTC
1842262 CT
1 CT
1842264 CCTCCTCCAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.09, C:0.36, G:0.16, T:0.39
Consensus pattern (21 bp):
CTAGTTCTTCACGAGCTCCTC
Found at i:1843309 original size:19 final size:19
Alignment explanation
Indices: 1843285--1843323 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
1843275 TCGAATGCAT
1843285 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
1843304 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
1843323 T
1 T
1843324 GAATATTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:1843391 original size:45 final size:46
Alignment explanation
Indices: 1843306--1843411 Score: 144
Period size: 45 Copynumber: 2.3 Consensus size: 46
1843296 ATGCACTCTC
* *
1843306 CATGCATCGATGCACTCTGAATATTTTCAAAACATTGAATGCATTT
1 CATGCATCGATGCACTCAGAATATTTTCAAAACATCGAATGCATTT
* **
1843352 GATGCATCGATGCAC-CAGGCTATTTTTC-AAACATCGAATGCATTT
1 CATGCATCGATGCACTCAGAATA-TTTTCAAAACATCGAATGCATTT
1843397 CATGCATCGATGCAC
1 CATGCATCGATGCAC
1843412 ACTTGGTGCA
Statistics
Matches: 53, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
45 34 0.64
46 19 0.36
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.31
Consensus pattern (46 bp):
CATGCATCGATGCACTCAGAATATTTTCAAAACATCGAATGCATTT
Found at i:1851740 original size:22 final size:22
Alignment explanation
Indices: 1851708--1851778 Score: 81
Period size: 22 Copynumber: 3.2 Consensus size: 22
1851698 ACTAGGGGCA
1851708 TATGAAATTTGTCCCGAATGACC
1 TATG-AATTTGTCCCGAATGACC
1851731 TATGAATTTGTCCCG-ATAGACC
1 TATGAATTTGTCCCGAAT-GACC
* * * *
1851753 TCTGTATATGTCCCGAAGGACC
1 TATGAATTTGTCCCGAATGACC
1851775 TATG
1 TATG
1851779 TAACCCTCGA
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
21 2 0.05
22 34 0.83
23 5 0.12
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.31
Consensus pattern (22 bp):
TATGAATTTGTCCCGAATGACC
Found at i:1854701 original size:251 final size:250
Alignment explanation
Indices: 1854252--1854753 Score: 761
Period size: 251 Copynumber: 2.0 Consensus size: 250
1854242 GACGAGTCTT
* *
1854252 AGACAAATAGAAACGCAACACTGAATGATCATTCTGGTGATGCTCGAGCTGTTGGACCACGTTCA
1 AGACAAACAGAAACGCAACACTGAATGATCATTCTGCTGATGCTCGAGCTGTTGGACCACGTTCA
* * *
1854317 TAGCATCACTTTTGACAAAGCGCACGGAAACCCATCTCGACCGCCAGACGAACACCTTGACAGAT
66 TAACATCACTTTCGACAAAGCGCACGGAAACCCATCTCGACCACCAGACGAACACCTTGACAGAT
* * * *
1854382 GGCATGGGCTTCAACTATGCAACAAATAACGTACAAGTGAAATGAAAAGCTCGCCCAGCCATGAC
131 GGCACGGGCTTCAACTATGCAACAAATAACGCACAAGTGAAATGAAAAGCACGCCCAGCCAGGAC
*
1854447 AGAACCATCGCAGTCGCGCACCACAACACCTACCGCCGGGGAGCCAAGACGCCTC
196 AGAACCATCGCAGTAGCGCACCACAACACCTACCGCCGGGGAGCCAAGACGCCTC
* * * *
1854502 AGACAAACAGAAATGCAGCACTGAATGATCATTTTGCTGGTGCTCGAGCTGTTGGACCACGTTCA
1 AGACAAACAGAAACGCAACACTGAATGATCATTCTGCTGATGCTCGAGCTGTTGGACCACGTTCA
* * * * **
1854567 TAACATTACTTTCGACAATAGCGCATGGAAACCCATCTCGACCACTAGATGAACACCTTGGTAGA
66 TAACATCACTTTCGACAA-AGCGCACGGAAACCCATCTCGACCACCAGACGAACACCTTGACAGA
* *
1854632 TGGCACGGGCTTCAACTATGCAACAGATAACGCACCAGTGAAATGAAAAGCACGCCCAGCCAGGA
130 TGGCACGGGCTTCAACTATGCAACAAATAACGCACAAGTGAAATGAAAAGCACGCCCAGCCAGGA
* * * *
1854697 CAGAACCATCGCAGTAGCGCGCCACAACACTTACCGCTGGGGAGCCAAGACGTCTC
195 CAGAACCATCGCAGTAGCGCACCACAACACCTACCGCCGGGGAGCCAAGACGCCTC
1854753 A
1 A
1854754 AACAGACGCC
Statistics
Matches: 225, Mismatches: 26, Indels: 1
0.89 0.10 0.00
Matches are distributed among these distances:
250 74 0.33
251 151 0.67
ACGTcount: A:0.32, C:0.28, G:0.22, T:0.17
Consensus pattern (250 bp):
AGACAAACAGAAACGCAACACTGAATGATCATTCTGCTGATGCTCGAGCTGTTGGACCACGTTCA
TAACATCACTTTCGACAAAGCGCACGGAAACCCATCTCGACCACCAGACGAACACCTTGACAGAT
GGCACGGGCTTCAACTATGCAACAAATAACGCACAAGTGAAATGAAAAGCACGCCCAGCCAGGAC
AGAACCATCGCAGTAGCGCACCACAACACCTACCGCCGGGGAGCCAAGACGCCTC
Found at i:1855582 original size:6 final size:7
Alignment explanation
Indices: 1855563--1855593 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
1855553 TTTAATTGTG
1855563 AAAATTT
1 AAAATTT
1855570 AAAATTT
1 AAAATTT
1855577 -AAATTT
1 AAAATTT
1855583 AAAATTT
1 AAAATTT
1855590 AAAA
1 AAAA
1855594 ACCTTATTCG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.26
7 17 0.74
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (7 bp):
AAAATTT
Found at i:1855582 original size:13 final size:13
Alignment explanation
Indices: 1855564--1855592 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
1855554 TTAATTGTGA
1855564 AAATTTAAAATTT
1 AAATTTAAAATTT
1855577 AAATTTAAAATTT
1 AAATTTAAAATTT
1855590 AAA
1 AAA
1855593 AACCTTATTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
AAATTTAAAATTT
Found at i:1857694 original size:21 final size:21
Alignment explanation
Indices: 1857668--1857707 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1857658 GGAAACTGTC
1857668 TCAAGAGAGACAAAATTTGTT
1 TCAAGAGAGACAAAATTTGTT
*
1857689 TCAAGAGAGACAAGATTTG
1 TCAAGAGAGACAAAATTTG
1857708 CTCCAAGGGA
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:0.10, G:0.23, T:0.25
Consensus pattern (21 bp):
TCAAGAGAGACAAAATTTGTT
Found at i:1857714 original size:21 final size:21
Alignment explanation
Indices: 1857669--1857714 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
1857659 GAAACTGTCT
* *
1857669 CAAGAGAGACAAAATTTGTTT
1 CAAGAGAGACAAAATTTGCTC
*
1857690 CAAGAGAGACAAGATTTGCTC
1 CAAGAGAGACAAAATTTGCTC
1857711 CAAG
1 CAAG
1857715 GGAAACTATC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.41, C:0.15, G:0.22, T:0.22
Consensus pattern (21 bp):
CAAGAGAGACAAAATTTGCTC
Found at i:1857829 original size:65 final size:65
Alignment explanation
Indices: 1857711--1857886 Score: 307
Period size: 65 Copynumber: 2.7 Consensus size: 65
1857701 AGATTTGCTC
* * *
1857711 CAAGGGAAACTATCTCAAGAGAGACAAAATTTCATTTCAAGGGAAATGTTTTCAATGTTTATGTT
1 CAAGAGAAACTGTCTCAAGGGAGACAAAA-TTCATTTCAAGGGAAATGTTTTCAATGTTTATGTT
1857776 T
65 T
1857777 CAAGAGAAACTGTCTCAAGGGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTATGTTT
1 CAAGAGAAACTGTCTCAAGGGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTATGTTT
*
1857842 CAAGAGAAACTGTCTCAAGGGAGACAAAATTTATTTCAAGGGAAA
1 CAAGAGAAACTGTCTCAAGGGAGACAAAATTCATTTCAAGGGAAA
1857887 CTGTCTCAAG
Statistics
Matches: 106, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
65 80 0.75
66 26 0.25
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (65 bp):
CAAGAGAAACTGTCTCAAGGGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTATGTTT
Found at i:1866041 original size:20 final size:19
Alignment explanation
Indices: 1866014--1866074 Score: 68
Period size: 20 Copynumber: 3.1 Consensus size: 19
1866004 CATTTTGGTG
1866014 CAGAGGGAATCGATACCCC
1 CAGAGGGAATCGATACCCC
* *
1866033 CATGAGGGAACCGATTCCCCC
1 CA-GAGGGAATCGA-TACCCC
*
1866054 CACAGGGGAATCGATACCCC
1 CAGA-GGGAATCGATACCCC
1866074 C
1 C
1866075 CTGGGGTTCT
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
19 2 0.06
20 17 0.50
21 15 0.44
ACGTcount: A:0.28, C:0.36, G:0.25, T:0.11
Consensus pattern (19 bp):
CAGAGGGAATCGATACCCC
Found at i:1868090 original size:17 final size:17
Alignment explanation
Indices: 1868057--1868090 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1868047 TTGAATATTT
* *
1868057 TGGATTGTTTGATTTTG
1 TGGATTGTTAGACTTTG
1868074 TGGATTGTTAGACTTTG
1 TGGATTGTTAGACTTTG
1868091 GATTTGTTTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.03, G:0.29, T:0.53
Consensus pattern (17 bp):
TGGATTGTTAGACTTTG
Found at i:1868883 original size:20 final size:20
Alignment explanation
Indices: 1868858--1868908 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
1868848 CACTTAGGGA
1868858 ACCGATTCCCCTTAAGGGGT
1 ACCGATTCCCCTTAAGGGGT
1868878 ACCGATTCCCCTTAAGGGGT
1 ACCGATTCCCCTTAAGGGGT
1868898 ACCGATTCCCC
1 ACCGATTCCCC
1868909 CCACGCTCCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.20, C:0.35, G:0.22, T:0.24
Consensus pattern (20 bp):
ACCGATTCCCCTTAAGGGGT
Found at i:1869667 original size:27 final size:25
Alignment explanation
Indices: 1869620--1869669 Score: 82
Period size: 27 Copynumber: 1.9 Consensus size: 25
1869610 TTTTTCTTCA
1869620 ATTTTCCTTTGTTTTTTCTCTTTTT
1 ATTTTCCTTTGTTTTTTCTCTTTTT
1869645 ATTTTCTCTTTGCTTTTTTCTCTTT
1 ATTTTC-CTTTG-TTTTTTCTCTTT
1869670 GCTTCTCTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 6 0.26
26 5 0.22
27 12 0.52
ACGTcount: A:0.04, C:0.18, G:0.04, T:0.74
Consensus pattern (25 bp):
ATTTTCCTTTGTTTTTTCTCTTTTT
Found at i:1869673 original size:14 final size:13
Alignment explanation
Indices: 1869621--1869670 Score: 68
Period size: 13 Copynumber: 3.8 Consensus size: 13
1869611 TTTTCTTCAA
1869621 TTTTC-CTTTGTT
1 TTTTCTCTTTGTT
1869633 TTTTCTCTTT-TT
1 TTTTCTCTTTGTT
1869645 ATTTTCTCTTTGCTT
1 -TTTTCTCTTTG-TT
1869660 TTTTCTCTTTG
1 TTTTCTCTTTG
1869671 CTTCTCTTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
12 7 0.21
13 14 0.41
14 11 0.32
15 2 0.06
ACGTcount: A:0.02, C:0.18, G:0.06, T:0.74
Consensus pattern (13 bp):
TTTTCTCTTTGTT
Found at i:1869682 original size:26 final size:26
Alignment explanation
Indices: 1869626--1869684 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 26
1869616 TTCAATTTTC
* *
1869626 CTTTGTTTTTTCTCTTTTTATTTTCT
1 CTTTGTTTTTTCTCTTTTGATTCTCT
*
1869652 CTTTGCTTTTTTCTC-TTTGCTTCTCT
1 CTTTG-TTTTTTCTCTTTTGATTCTCT
*
1869678 TTTTGTT
1 CTTTGTT
1869685 CTGATTGAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
25 2 0.07
26 17 0.61
27 9 0.32
ACGTcount: A:0.02, C:0.19, G:0.07, T:0.73
Consensus pattern (26 bp):
CTTTGTTTTTTCTCTTTTGATTCTCT
Found at i:1876589 original size:42 final size:42
Alignment explanation
Indices: 1876543--1876641 Score: 137
Period size: 42 Copynumber: 2.4 Consensus size: 42
1876533 TTACATCAAT
** *
1876543 TTATTTATTTTGATATTACACAGTATATCACAATAGCCTTTA
1 TTATTTATTTAAATATTACACAGTATATCACAATAACCTTTA
* *
1876585 TTATTTATATAAATTTTACACAGTATATCACAATAACCTTTA
1 TTATTTATTTAAATATTACACAGTATATCACAATAACCTTTA
1876627 TTA-TTATTTAGAATA
1 TTATTTATTTA-AATA
1876642 CCATATTCTT
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
41 6 0.12
42 43 0.88
ACGTcount: A:0.37, C:0.12, G:0.05, T:0.45
Consensus pattern (42 bp):
TTATTTATTTAAATATTACACAGTATATCACAATAACCTTTA
Found at i:1881448 original size:2 final size:2
Alignment explanation
Indices: 1881443--1881469 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1881433 ATATTCAGAG
1881443 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1881470 GGTACGAGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1883507 original size:30 final size:30
Alignment explanation
Indices: 1883446--1883530 Score: 82
Period size: 30 Copynumber: 2.8 Consensus size: 30
1883436 GAATGTCGTT
* *
1883446 ATAATCAATAATACTTATCATAA-TATTATAAA
1 ATAATCATTAA-ATTTATCA-AATTA-TATAAA
* *
1883478 ATGATCATTAAATTTATTAAATTATATAAA
1 ATAATCATTAAATTTATCAAATTATATAAA
* *
1883508 ATAATTATTATATTTATCAAATT
1 ATAATCATTAAATTTATCAAATT
1883531 TTATTATTAT
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
30 27 0.61
31 8 0.18
32 9 0.20
ACGTcount: A:0.49, C:0.06, G:0.01, T:0.44
Consensus pattern (30 bp):
ATAATCATTAAATTTATCAAATTATATAAA
Found at i:1916403 original size:26 final size:26
Alignment explanation
Indices: 1916352--1916404 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
1916342 AGGTTGATAT
*
1916352 TATCGTCAATACATTAGAAAGTAAGA
1 TATCGTCAATACATTAGAAAGGAAGA
* **
1916378 TATCTTCAATACATTAGATCGGAAGA
1 TATCGTCAATACATTAGAAAGGAAGA
1916404 T
1 T
1916405 CTGAGATTGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.42, C:0.13, G:0.15, T:0.30
Consensus pattern (26 bp):
TATCGTCAATACATTAGAAAGGAAGA
Found at i:1924943 original size:21 final size:21
Alignment explanation
Indices: 1924919--1924969 Score: 102
Period size: 21 Copynumber: 2.4 Consensus size: 21
1924909 GCAAGTGTGT
1924919 CGATGCACATTCAATGTGTAC
1 CGATGCACATTCAATGTGTAC
1924940 CGATGCACATTCAATGTGTAC
1 CGATGCACATTCAATGTGTAC
1924961 CGATGCACA
1 CGATGCACA
1924970 AGTAGTGCAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.29, C:0.25, G:0.20, T:0.25
Consensus pattern (21 bp):
CGATGCACATTCAATGTGTAC
Found at i:1925846 original size:2 final size:2
Alignment explanation
Indices: 1925839--1925885 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
1925829 TGGAGTTATG
1925839 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
1925881 AT AT A
1 AT AT A
1925886 GACTATATGA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1926712 original size:23 final size:23
Alignment explanation
Indices: 1926680--1926741 Score: 97
Period size: 23 Copynumber: 2.7 Consensus size: 23
1926670 ACTTTATATA
1926680 GCACTTCGGTGCATTTCTACGTG
1 GCACTTCGGTGCATTTCTACGTG
* *
1926703 GCACTACGGTGCAATTCTACGTG
1 GCACTTCGGTGCATTTCTACGTG
*
1926726 GCACTTCAGTGCATTT
1 GCACTTCGGTGCATTT
1926742 ATATGAGCTG
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.18, C:0.26, G:0.24, T:0.32
Consensus pattern (23 bp):
GCACTTCGGTGCATTTCTACGTG
Found at i:1930690 original size:19 final size:19
Alignment explanation
Indices: 1930668--1930706 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
1930658 GAAATTTCGT
1930668 GCTTAAAATGAGATTTCTG
1 GCTTAAAATGAGATTTCTG
1930687 GCTTAAAATGAGATTTCTG
1 GCTTAAAATGAGATTTCTG
1930706 G
1 G
1930707 GCAAAGTGCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.31, C:0.10, G:0.23, T:0.36
Consensus pattern (19 bp):
GCTTAAAATGAGATTTCTG
Found at i:1931217 original size:59 final size:59
Alignment explanation
Indices: 1931154--1931653 Score: 443
Period size: 59 Copynumber: 8.4 Consensus size: 59
1931144 TGGCACTATA
*
1931154 TGTGCTAAAATGATAAGGAAATCATACTGAATGTATGAATTTTCATAT-GGAGCACTGAG
1 TGTGCTAAAATGATAAGGAAATCATACTGAATGTATGGATTTTCATATAGG-GCACTGAG
* *
1931213 TGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTTCATAT-GGAGCAATGAG
1 TGTGCTAAAATGATAAGGAAATCATACTGAATGTATGGATTTTCATATAGG-GCACTGAG
* * * *
1931272 TGTGATAAAATGATAAGCAAATCATACTGAGTGTATGGATTTCCATAT-GGAGCACTGAG
1 TGTGCTAAAATGATAAGGAAATCATACTGAATGTATGGATTTTCATATAGG-GCACTGAG
* * * * *
1931331 TGTGCTAAAATGATAAGGAAATCATATTGAATATATGGA-TTTCTAGATAGGGCA-TTATA
1 TGTGCTAAAATGATAAGGAAATCATACTGAATGTATGGATTTTC-ATATAGGGCACTGA-G
* * * * * * ** *
1931390 TGTGCTAAAATGGTAA-GAGAATCATATTGAGTGTATGGATTTCCAAAAAAAGCACTAAG
1 TGTGCTAAAATGATAAGGA-AATCATACTGAATGTATGGATTTTCATATAGGGCACTGAG
* * * *
1931449 GGTGCTACAAGGATAAGGAAATCATACT-AATAGTATGGATTTTCATATAGGGCACTTCA-
1 TGTGCTAAAATGATAAGGAAATCATACTGAAT-GTATGGATTTTCATATAGGGCAC-TGAG
* * * *
1931508 TGTGCTAAAAATGGTAAAGG-GATCATACT-AATGGTATGGATTCTCGA-ATAGGGCACTTCA-
1 TGTGCT-AAAATGAT-AAGGAAATCATACTGAAT-GTATGGATTTTC-ATATAGGGCAC-TGAG
* * * **
1931568 TGTGCTAAAAATGGTAAAGG-AATCATAC-GAATGGTATGGATTCTCAAATAGGGCACTTCG
1 TGTGCT-AAAATGAT-AAGGAAATCATACTGAAT-GTATGGATTTTCATATAGGGCACTGAG
*
1931628 TGTGCTAAAATGAGAAGGAAATCATA
1 TGTGCTAAAATGATAAGGAAATCATA
1931654 TTAAGTATAT
Statistics
Matches: 375, Mismatches: 50, Indels: 32
0.82 0.11 0.07
Matches are distributed among these distances:
58 13 0.03
59 248 0.66
60 109 0.29
61 5 0.01
ACGTcount: A:0.37, C:0.11, G:0.23, T:0.29
Consensus pattern (59 bp):
TGTGCTAAAATGATAAGGAAATCATACTGAATGTATGGATTTTCATATAGGGCACTGAG
Found at i:1931368 original size:118 final size:116
Alignment explanation
Indices: 1931145--1931713 Score: 462
Period size: 118 Copynumber: 4.8 Consensus size: 116
1931135 ATTACCAAAT
* * *
1931145 GGCACTATATGTGCTAAAATGATAAGGAAATCATACTGAATGTATGAATTTTCATATGGAGCACT
1 GGCA-TATATGTGCTAAAATGATAA-GAAATCATACTGAGTGTATGGATTTCCATATGGAGCACT
* *
1931210 GAGTGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTTCATAT-G
64 GAGTGTGCTAAAATGATAAGGAAATCATACTGAATATATGGATTTTCATATAG
*
1931262 GAGCA-ATGAGTGTGATAAAATGATAAGCAAATCATACTGAGTGTATGGATTTCCATATGGAGCA
1 G-GCATAT-A-TGTGCTAAAATGATAAG-AAATCATACTGAGTGTATGGATTTCCATATGGAGCA
* *
1931326 CTGAGTGTGCTAAAATGATAAGGAAATCATATTGAATATATGGA-TTTCTAGATAG
62 CTGAGTGTGCTAAAATGATAAGGAAATCATACTGAATATATGGATTTTC-ATATAG
* * * ***
1931381 GGCATTATATGTGCTAAAATGGTAAGAGAATCATATTGAGTGTATGGATTTCCAAAAAAAGCACT
1 GGCA-TATATGTGCTAAAATGATAAGA-AATCATACTGAGTGTATGGATTTCCATATGGAGCACT
* * * *
1931446 AAGGGTGCTACAAGGATAAGGAAATCATACT-AATAGTATGGATTTTCATATAG
64 GAGTGTGCTAAAATGATAAGGAAATCATACTGAATA-TATGGATTTTCATATAG
* ** * *
1931499 GGCACT-TCATGTGCTAAAAATGGTAAAGGGATCATACT-AATGGTATGGATTCTCGA-ATAGG-
1 GGCA-TAT-ATGTGCT-AAAATGAT-AAGAAATCATACTGAGT-GTATGGATT-TCCATAT-GGA
* * * * *
1931560 GCACTTCA-TGTGCTAAAAATGGTAAAGG-AATCATAC-GAATGGTATGGATTCTCAAATAG
59 GCAC-TGAGTGTGCT-AAAATGAT-AAGGAAATCATACTGAAT-ATATGGATTTTCATATAG
* * * * * * *
1931619 GGCACT-TCGTGTGCTAAAATGAGAAGGAAATCATATTAAGTATAT-GATATTCCAGATAGAGCA
1 GGCA-TAT-ATGTGCTAAAATGATAA-GAAATCATACTGAGTGTATGGAT-TTCCATATGGAGCA
* * * * *
1931682 CCGAGAGTGCTAATATTATAAGGAAATTATAC
62 CTGAGTGTGCTAAAATGATAAGGAAATCATAC
1931714 AAATTGTATA
Statistics
Matches: 368, Mismatches: 55, Indels: 57
0.77 0.11 0.12
Matches are distributed among these distances:
116 2 0.01
117 17 0.05
118 218 0.59
119 70 0.19
120 57 0.15
121 4 0.01
ACGTcount: A:0.37, C:0.11, G:0.23, T:0.29
Consensus pattern (116 bp):
GGCATATATGTGCTAAAATGATAAGAAATCATACTGAGTGTATGGATTTCCATATGGAGCACTGA
GTGTGCTAAAATGATAAGGAAATCATACTGAATATATGGATTTTCATATAG
Found at i:1931473 original size:177 final size:174
Alignment explanation
Indices: 1931154--1931713 Score: 485
Period size: 177 Copynumber: 3.2 Consensus size: 174
1931144 TGGCACTATA
* * * *
1931154 TGTGCTAAAATGATAAGGAAATCATACTGAATGTATGAATTT-TCATATGGAGCACTGAGTGTGC
1 TGTGCTAAAATGATAAGGAAATCATACTGAATGTATGGATTTCTGATA-GG-GCACTTAATGTGC
* * * * * * *
1931218 TAAAATGATAAG-GAAATCATACTGAGTGTATGGATTTTCATATGGAGCAATGAGTGTGATAAAA
64 TAAAATGGTAAGAG-AATCATA-TGAGTGTATGGATTTCCAAATAGAGCACTAAGTGTGCTAAAA
*
1931282 TGATAAGCAAATCATACTGAGTGTATGGATTTCCATATGGAGCACTGAG
127 TGATAAGGAAATCATACT-AGTGTATGGATTTCCATATGGAGCACTGAG
* *
1931331 TGTGCTAAAATGATAAGGAAATCATATTGAATATATGGATTTCTAGATAGGGCA-TTATATGTGC
1 TGTGCTAAAATGATAAGGAAATCATACTGAATGTATGGATTTCT-GATAGGGCACTTA-ATGTGC
* * * * *
1931395 TAAAATGGTAAGAGAATCATATTGAGTGTATGGATTTCCAAAAAAAGCACTAAGGGTGCTACAAG
64 TAAAATGGTAAGAGAATCATA-TGAGTGTATGGATTTCCAAATAGAGCACTAAGTGTGCTAAAAT
* * *
1931460 GATAAGGAAATCATACTAATAGTATGGATTTTCATATAGG-GCACTTCA-
128 GATAAGGAAATCATACTAGT-GTATGGATTTCCATAT-GGAGCAC-TGAG
* * *
1931508 TGTGCTAAAAATGGTAAAGG-GATCATACT-AATGGTATGGA-TTCTCGAATAGGGCACTTCATG
1 TGTGCT-AAAATGAT-AAGGAAATCATACTGAAT-GTATGGATTTCT-G-ATAGGGCACTTAATG
* * * **
1931570 TGCTAAAAATGGTAA-AGGAATCATACGAATGGTATGGA-TTCTCAAATAGGGCACTTCGTGTGC
61 TGCT-AAAATGGTAAGA-GAATCATATGAGT-GTATGGATTTC-CAAATAGAGCACTAAGTGTGC
* * * * * *
1931633 TAAAATGAGAAGGAAATCATATTAAGTATAT-GATATTCCAGATAGAGCACCGAG
122 TAAAATGATAAGGAAATCATACT-AGTGTATGGAT-TTCCATATGGAGCACTGAG
* * * *
1931687 AGTGCTAATATTATAAGGAAATTATAC
1 TGTGCTAAAATGATAAGGAAATCATAC
1931714 AAATTGTATA
Statistics
Matches: 308, Mismatches: 54, Indels: 41
0.76 0.13 0.10
Matches are distributed among these distances:
176 4 0.01
177 150 0.49
178 66 0.21
179 86 0.28
180 2 0.01
ACGTcount: A:0.37, C:0.11, G:0.23, T:0.29
Consensus pattern (174 bp):
TGTGCTAAAATGATAAGGAAATCATACTGAATGTATGGATTTCTGATAGGGCACTTAATGTGCTA
AAATGGTAAGAGAATCATATGAGTGTATGGATTTCCAAATAGAGCACTAAGTGTGCTAAAATGAT
AAGGAAATCATACTAGTGTATGGATTTCCATATGGAGCACTGAG
Found at i:1931549 original size:60 final size:59
Alignment explanation
Indices: 1931463--1931637 Score: 269
Period size: 60 Copynumber: 2.9 Consensus size: 59
1931453 CTACAAGGAT
* *
1931463 AAGGAAATCATACTAATAGTATGGATTTTCATATAGGGCACTTCATGTGCTAAAAATGGTA
1 AAGG-AATCATACTAATGGTATGGATTCTCA-ATAGGGCACTTCATGTGCTAAAAATGGTA
*
1931524 AAGGGATCATACTAATGGTATGGATTCTCGAATAGGGCACTTCATGTGCTAAAAATGGTA
1 AAGGAATCATACTAATGGTATGGATTCTC-AATAGGGCACTTCATGTGCTAAAAATGGTA
* *
1931584 AAGGAATCATACGAATGGTATGGATTCTCAAATAGGGCACTTCGTGTGCTAAAA
1 AAGGAATCATACTAATGGTATGGATTCTC-AATAGGGCACTTCATGTGCTAAAA
1931638 TGAGAAGGAA
Statistics
Matches: 106, Mismatches: 7, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
60 101 0.95
61 5 0.05
ACGTcount: A:0.35, C:0.13, G:0.23, T:0.29
Consensus pattern (59 bp):
AAGGAATCATACTAATGGTATGGATTCTCAATAGGGCACTTCATGTGCTAAAAATGGTA
Found at i:1931858 original size:44 final size:44
Alignment explanation
Indices: 1931790--1932232 Score: 618
Period size: 44 Copynumber: 10.0 Consensus size: 44
1931780 TCAGTGATGC
* *
1931790 AAATAATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTAAG
1 AAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATG
1931834 AAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATG
1 AAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATG
* *
1931878 AAATTATAATAAGTACTTATTGGTAAAATAAGCTTACGAGGTTATG
1 AAATTATAGTAAGTA--TATTGGTAAAATAAGCTTACGAGCTTATG
* *
1931924 AAATTATAGTAAGTATATTGATAAAATAAGCTTATGAGCTTATG
1 AAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATG
*
1931968 AAATTATAGTAAGTATATTGGTAAAATAAGCTTATGAGCTTATG
1 AAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATG
* *
1932012 AAATTATAGTAAGAATATTGGTAAAATAAGTTTACGAGCTTATG
1 AAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATG
* * *
1932056 GAATAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATG
1 AAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATG
* * * * *
1932100 GAATAATGGTAAGTATATTGGTAAAATAAACTTATGAGCTTATG
1 AAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATG
* * * *
1932144 GAATAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTAGG
1 AAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATG
* * * *
1932188 GATTTA-ACGGTAAGTATATTGGTAAAATAAGCTTACAAGGTTATG
1 AAATTATA--GTAAGTATATTGGTAAAATAAGCTTACGAGCTTATG
1932233 GATTAAATGG
Statistics
Matches: 367, Mismatches: 28, Indels: 7
0.91 0.07 0.02
Matches are distributed among these distances:
44 292 0.80
45 33 0.09
46 42 0.11
ACGTcount: A:0.41, C:0.06, G:0.20, T:0.33
Consensus pattern (44 bp):
AAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATG
Found at i:1932744 original size:7 final size:7
Alignment explanation
Indices: 1932732--1932761 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
1932722 TGTATCGGTA
1932732 CATTGTT
1 CATTGTT
1932739 CATTGTT
1 CATTGTT
1932746 CATTGTT
1 CATTGTT
1932753 CATTGTT
1 CATTGTT
1932760 CA
1 CA
1932762 CGGGTATTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.17, C:0.17, G:0.13, T:0.53
Consensus pattern (7 bp):
CATTGTT
Found at i:1932772 original size:20 final size:20
Alignment explanation
Indices: 1932747--1932799 Score: 70
Period size: 23 Copynumber: 2.5 Consensus size: 20
1932737 TTCATTGTTC
*
1932747 ATTGTTCATTGTTCACGGGT
1 ATTGTTCATTGTTCACGAGT
1932767 ATTGTTCATCATTGTTCACGAGT
1 ATTG-T--TCATTGTTCACGAGT
1932790 ATTGTTCATT
1 ATTGTTCATT
1932800 CGTATAATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
20 9 0.31
21 1 0.03
22 1 0.03
23 18 0.62
ACGTcount: A:0.19, C:0.15, G:0.19, T:0.47
Consensus pattern (20 bp):
ATTGTTCATTGTTCACGAGT
Found at i:1932782 original size:23 final size:23
Alignment explanation
Indices: 1932752--1932798 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
1932742 TGTTCATTGT
*
1932752 TCATTGTTCACGGGTATTGTTCA
1 TCATTGTTCACGAGTATTGTTCA
1932775 TCATTGTTCACGAGTATTGTTCA
1 TCATTGTTCACGAGTATTGTTCA
1932798 T
1 T
1932799 TCGTATAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.19, C:0.17, G:0.19, T:0.45
Consensus pattern (23 bp):
TCATTGTTCACGAGTATTGTTCA
Found at i:1937952 original size:20 final size:21
Alignment explanation
Indices: 1937927--1937978 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
1937917 TTTTCCCAAT
*
1937927 TCGCAATGCGAATAAG-TAAA
1 TCGCAATGCGAATAAGAAAAA
* **
1937947 TCGCAACGCGAATTGGAAAAA
1 TCGCAATGCGAATAAGAAAAA
1937968 TCGCAATGCGA
1 TCGCAATGCGA
1937979 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 13 0.50
21 13 0.50
ACGTcount: A:0.40, C:0.19, G:0.23, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATAAGAAAAA
Found at i:1937992 original size:20 final size:20
Alignment explanation
Indices: 1937967--1938080 Score: 113
Period size: 20 Copynumber: 5.7 Consensus size: 20
1937957 AATTGGAAAA
*
1937967 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
1937987 ATCGCAATGCGATACTTACT
1 ATCGCAACGCGATACTGACT
* * *
1938007 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
*
1938028 ATCGCAACGAGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
1938048 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
1938068 TTCGCAACGCGAT
1 ATCGCAACGCGAT
1938081 TTACATAGCG
Statistics
Matches: 81, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
19 2 0.02
20 64 0.79
21 13 0.16
22 2 0.02
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:1938011 original size:61 final size:61
Alignment explanation
Indices: 1937964--1938080 Score: 162
Period size: 61 Copynumber: 1.9 Consensus size: 61
1937954 GCGAATTGGA
* * * * *
1937964 AAAATCGCAATGCGATACTGACTATCGCAATGCGATACTTACTATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* * *
1938025 AAAATCGCAACGAGATACTGACTTTCGCAACGCGATTCTGACTTTCGCAACGCGAT
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGAT
1938081 TTACATAGCG
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 48 1.00
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.24
Consensus pattern (61 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:1938671 original size:19 final size:19
Alignment explanation
Indices: 1938635--1938676 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
1938625 ACGAGAGAAT
*
1938635 CGCAACGCGAAATAAAAAA
1 CGCAACGCGAAACAAAAAA
* *
1938654 CGCAACGCGAAACCAAAAT
1 CGCAACGCGAAACAAAAAA
1938673 CGCA
1 CGCA
1938677 TTGCGATTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.50, C:0.29, G:0.17, T:0.05
Consensus pattern (19 bp):
CGCAACGCGAAACAAAAAA
Found at i:1938694 original size:19 final size:19
Alignment explanation
Indices: 1938672--1938750 Score: 122
Period size: 19 Copynumber: 4.1 Consensus size: 19
1938662 GAAACCAAAA
*
1938672 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1938691 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
1938710 TCGCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATT
*
1938729 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
1938749 TC
1 TC
1938751 AACCAAAAGA
Statistics
Matches: 55, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
19 38 0.69
20 17 0.31
ACGTcount: A:0.13, C:0.23, G:0.18, T:0.47
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1938745 original size:39 final size:38
Alignment explanation
Indices: 1938672--1938750 Score: 122
Period size: 39 Copynumber: 2.1 Consensus size: 38
1938662 GAAACCAAAA
*
1938672 TCGCATTGCGATTTTCATTTCGCGTTGCGATTTTCATT
1 TCGCATTGCGATTCTCATTTCGCGTTGCGATTTTCATT
* *
1938710 TCGCGTTGCGATTCTCATTATCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTCTCATT-TCGCGTTGCGATTTTCATT
1938749 TC
1 TC
1938751 AACCAAAAGA
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
38 17 0.46
39 20 0.54
ACGTcount: A:0.13, C:0.23, G:0.18, T:0.47
Consensus pattern (38 bp):
TCGCATTGCGATTCTCATTTCGCGTTGCGATTTTCATT
Found at i:1940302 original size:63 final size:63
Alignment explanation
Indices: 1940203--1940333 Score: 244
Period size: 63 Copynumber: 2.1 Consensus size: 63
1940193 GTTACATGAT
* *
1940203 GAGGTCAATGCCTTGCGTGAGGAGATCGGTACTCTACGCGATAACGATGGTGCATGGCGTGTG
1 GAGGTCAATGACTTGCGTGAGGAGATCGGTACTCTACGCGATAACGATGGTGCATGGCATGTG
1940266 GAGGTCAATGACTTGCGTGAGGAGATCGGTACTCTACGCGATAACGATGGTGCATGGCATGTG
1 GAGGTCAATGACTTGCGTGAGGAGATCGGTACTCTACGCGATAACGATGGTGCATGGCATGTG
1940329 GAGGT
1 GAGGT
1940334 GTCTACTTTA
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 66 1.00
ACGTcount: A:0.22, C:0.18, G:0.37, T:0.24
Consensus pattern (63 bp):
GAGGTCAATGACTTGCGTGAGGAGATCGGTACTCTACGCGATAACGATGGTGCATGGCATGTG
Found at i:1940637 original size:17 final size:17
Alignment explanation
Indices: 1940615--1940647 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1940605 GTTGCTGCCA
1940615 ATTCTTCTAA-ACTGTGT
1 ATTCTT-TAACACTGTGT
1940632 ATTCTTTAACACTGTG
1 ATTCTTTAACACTGTG
1940648 AAGTTAGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.24, C:0.18, G:0.12, T:0.45
Consensus pattern (17 bp):
ATTCTTTAACACTGTGT
Found at i:1942213 original size:14 final size:14
Alignment explanation
Indices: 1942194--1942229 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1942184 ATTGTTTAAT
1942194 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
1942208 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
1942222 TGATTTGT
1 TGATTTGT
1942230 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:1942373 original size:14 final size:14
Alignment explanation
Indices: 1942354--1942410 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
1942344 GCGAAATGAA
1942354 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
1942368 AATCGCAACGTGAAATGAA
1 AATCGCAAC--G--A-GAG
1942387 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
1942401 AAACGCAACG
1 AATCGCAACG
1942411 CGAAATTAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 20 0.57
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
19 11 0.31
ACGTcount: A:0.46, C:0.21, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1942383 original size:33 final size:33
Alignment explanation
Indices: 1942336--1942425 Score: 135
Period size: 33 Copynumber: 2.7 Consensus size: 33
1942326 AAAAAGTACT
*
1942336 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
*
1942369 ATCGCAACGTGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
* * *
1942402 AACGCAACGCGAAATTAAATTCGC
1 ATCGCAACGCGAAATGAAAATCGC
1942426 GTTGCGATTT
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 51 1.00
ACGTcount: A:0.44, C:0.20, G:0.22, T:0.13
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
Found at i:1942395 original size:19 final size:18
Alignment explanation
Indices: 1942336--1942396 Score: 58
Period size: 19 Copynumber: 3.5 Consensus size: 18
1942326 AAAAAGTACT
*
1942336 ATCGCAATGCGAAATGAAA
1 ATCGCAACG-GAAATGAAA
*
1942355 ATCGCAAC-G--A-GAGA
1 ATCGCAACGGAAATGAAA
1942369 ATCGCAACGTGAAATGAAA
1 ATCGCAACG-GAAATGAAA
1942388 ATCGCAACG
1 ATCGCAACG
1942397 AGAGAAACGC
Statistics
Matches: 34, Mismatches: 3, Indels: 10
0.72 0.06 0.21
Matches are distributed among these distances:
14 11 0.32
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
19 19 0.56
ACGTcount: A:0.44, C:0.20, G:0.23, T:0.13
Consensus pattern (18 bp):
ATCGCAACGGAAATGAAA
Found at i:1942443 original size:19 final size:19
Alignment explanation
Indices: 1942421--1942571 Score: 53
Period size: 19 Copynumber: 8.7 Consensus size: 19
1942411 CGAAATTAAA
1942421 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* *
1942440 TTCGCATTGTGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
1942455 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* *
1942473 TTCGCATTGCGA-----AA
1 TTCGCGTTGCGATTTTCAT
* *
1942487 TTAGCGTTGCGATTTTTAT
1 TTCGCGTTGCGATTTTCAT
*
1942506 TTCGCATTGCGA--TTC-T
1 TTCGCGTTGCGATTTTCAT
* *
1942522 AT--CGTTGTGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
1942539 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
1942558 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
1942572 AGACATTAAG
Statistics
Matches: 90, Mismatches: 26, Indels: 31
0.61 0.18 0.21
Matches are distributed among these distances:
14 24 0.27
16 8 0.09
17 7 0.08
19 41 0.46
20 10 0.11
ACGTcount: A:0.16, C:0.20, G:0.21, T:0.44
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:1942467 original size:33 final size:32
Alignment explanation
Indices: 1942425--1942551 Score: 166
Period size: 33 Copynumber: 3.9 Consensus size: 32
1942415 ATTAAATTCG
* *
1942425 CGTTGCGATTTTCATTTCGCATTGTGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CAT
*
1942458 CGTTGCGATTTTCATTTCGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCAT
*
1942491 CGTTGCGATTTTTATTTCGCATTGCGATTCTAT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-AT
*
1942524 CGTTGTGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
1942552 AGTAATTTCC
Statistics
Matches: 83, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
31 3 0.04
33 77 0.93
35 3 0.04
ACGTcount: A:0.16, C:0.20, G:0.20, T:0.45
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCAT
Found at i:1942498 original size:66 final size:66
Alignment explanation
Indices: 1942418--1942550 Score: 212
Period size: 66 Copynumber: 2.0 Consensus size: 66
1942408 ACGCGAAATT
* * *
1942418 AAATTCGCGTTGCGATTTTCATTTCGCATTGTGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCATCGTTGCGATTTTCATTTCGCATTGC
1942483 G
66 G
* * *
1942484 AAATTAGCGTTGCGATTTTTATTTCGCATTGCGATTCTATCGTTGTGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCATCGTTGCGATTTTCATTTCGCATTGC
1942549 G
66 G
1942550 A
1 A
1942551 TAGTAATTTC
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
66 61 1.00
ACGTcount: A:0.17, C:0.20, G:0.20, T:0.44
Consensus pattern (66 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCATCGTTGCGATTTTCATTTCGCATTGC
G
Found at i:1944860 original size:12 final size:12
Alignment explanation
Indices: 1944843--1944867 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1944833 TCTTCGGGGA
1944843 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1944855 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1944867 C
1 C
1944868 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:1945076 original size:24 final size:24
Alignment explanation
Indices: 1945042--1945095 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1945032 CTGAAACATC
* *
1945042 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAG
*
1945066 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGGGTATTGACCAAG
1945090 ATCAAA
1 ATCAAA
1945096 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGACCAAG
Found at i:1946181 original size:20 final size:20
Alignment explanation
Indices: 1946156--1946213 Score: 107
Period size: 20 Copynumber: 2.9 Consensus size: 20
1946146 ATTCATTTGA
1946156 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
1946176 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
*
1946196 CTATCGCAACGAGAAAAT
1 CTATCGCAACGCGAAAAT
1946214 CGCAATGCGA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.38, C:0.24, G:0.22, T:0.16
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:1946269 original size:33 final size:33
Alignment explanation
Indices: 1946232--1946347 Score: 142
Period size: 33 Copynumber: 3.4 Consensus size: 33
1946222 GAAATGAAAA
1946232 TCGCATTGCGATTTTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCTCGTTGCGATTTTCATT
*
1946265 TCGCATTGCGATTTTCATTTTGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTC----T-CGTTGCGATTTTCATT
***
1946303 TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
1 TCGCATTGCGATTTTCTCGTTGCGATTTTCATT
*
1946336 TCGCGTTGCGAT
1 TCGCATTGCGAT
1946348 AGTCTGTTTT
Statistics
Matches: 72, Mismatches: 6, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
33 39 0.54
34 1 0.01
37 1 0.01
38 31 0.43
ACGTcount: A:0.14, C:0.22, G:0.20, T:0.45
Consensus pattern (33 bp):
TCGCATTGCGATTTTCTCGTTGCGATTTTCATT
Found at i:1946273 original size:19 final size:19
Alignment explanation
Indices: 1946232--1946318 Score: 130
Period size: 19 Copynumber: 4.8 Consensus size: 19
1946222 GAAATGAAAA
1946232 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
1946248 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1946265 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
1946284 TTGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1946303 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
1946319 TCGTTGCGAT
Statistics
Matches: 64, Mismatches: 2, Indels: 7
0.88 0.03 0.10
Matches are distributed among these distances:
14 11 0.17
16 3 0.05
17 3 0.05
19 47 0.73
ACGTcount: A:0.14, C:0.21, G:0.17, T:0.48
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:1946454 original size:14 final size:14
Alignment explanation
Indices: 1946435--1946471 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1946425 CATCAATTAA
1946435 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
1946449 ACAAATCATCTTTT
1 ACAAATCAACATTT
1946463 ACAAATCAA
1 ACAAATCAA
1946472 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:1947942 original size:42 final size:42
Alignment explanation
Indices: 1947891--1947972 Score: 119
Period size: 42 Copynumber: 2.0 Consensus size: 42
1947881 TTCAACGATG
* * *
1947891 ATAGTGGCCTCTTGAACGGTGGGGGGGGAATCTTGAGGGAGA
1 ATAGGGGCCTCTTGAACGATGGGAGGGGAATCTTGAGGGAGA
* *
1947933 ATAGGGGCCTCTTGAACGATTGGAGGGGACTCTTGAGGGA
1 ATAGGGGCCTCTTGAACGATGGGAGGGGAATCTTGAGGGA
1947973 TGACCGGTGA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.22, C:0.13, G:0.43, T:0.22
Consensus pattern (42 bp):
ATAGGGGCCTCTTGAACGATGGGAGGGGAATCTTGAGGGAGA
Found at i:1948365 original size:19 final size:18
Alignment explanation
Indices: 1948339--1948477 Score: 123
Period size: 19 Copynumber: 7.9 Consensus size: 18
1948329 ACGAAACTTA
1948339 AAATCGCAACGCGAAATG
1 AAATCGCAACGCGAAATG
*
1948357 ACTATCGCAACGCGAAAATGG
1 A-AATCGCAACGCG-AAAT-G
** *
1948378 CTATCGCAATGCGAAATG
1 AAATCGCAACGCGAAATG
*
1948396 AAAATCGCAA--CGACA--
1 -AAATCGCAACGCGAAATG
1948411 AAATCGCAACGCGAAATG
1 AAATCGCAACGCGAAATG
1948429 AAATCGCAA--CGAAA--
1 AAATCGCAACGCGAAATG
1948443 AAATCGCAACGCGAAATG
1 AAATCGCAACGCGAAATG
*
1948461 AAAATCGCAATGCGAAA
1 -AAATCGCAACGCGAAA
1948478 CACAAATCGC
Statistics
Matches: 100, Mismatches: 8, Indels: 25
0.75 0.06 0.19
Matches are distributed among these distances:
14 18 0.18
16 14 0.14
17 4 0.04
18 11 0.11
19 37 0.37
20 15 0.15
21 1 0.01
ACGTcount: A:0.45, C:0.22, G:0.20, T:0.12
Consensus pattern (18 bp):
AAATCGCAACGCGAAATG
Found at i:1948415 original size:14 final size:14
Alignment explanation
Indices: 1948396--1948453 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
1948386 ATGCGAAATG
*
1948396 AAAATCGCAACGAC
1 AAAATCGCAACGAA
1948410 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAA
1948426 ATGAAATCGCAACGAA
1 A--AAATCGCAACGAA
1948442 AAAATCGCAACG
1 AAAATCGCAACG
1948454 CGAAATGAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
14 21 0.54
16 9 0.23
18 9 0.23
ACGTcount: A:0.50, C:0.24, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAA
Found at i:1948438 original size:32 final size:33
Alignment explanation
Indices: 1948338--1948470 Score: 160
Period size: 32 Copynumber: 3.9 Consensus size: 33
1948328 CACGAAACTT
**
1948338 AAAATCGCAACGCGAAATGACTATCGCAACGCGAA
1 AAAATCGCAACGCGAAATGAAAATCGCAA--CGAA
* * *
1948373 AATGGCTATCGCAATGCGAAATGAAAATCGCAACGAC
1 AA----AATCGCAACGCGAAATGAAAATCGCAACGAA
1948410 AAAATCGCAACGCGAAATG-AAATCGCAACGAA
1 AAAATCGCAACGCGAAATGAAAATCGCAACGAA
1948442 AAAATCGCAACGCGAAATGAAAATCGCAA
1 AAAATCGCAACGCGAAATGAAAATCGCAA
1948471 TGCGAAACAC
Statistics
Matches: 85, Mismatches: 8, Indels: 12
0.81 0.08 0.11
Matches are distributed among these distances:
32 31 0.36
33 24 0.28
35 2 0.02
37 5 0.06
39 23 0.27
ACGTcount: A:0.46, C:0.23, G:0.20, T:0.12
Consensus pattern (33 bp):
AAAATCGCAACGCGAAATGAAAATCGCAACGAA
Found at i:1948484 original size:19 final size:19
Alignment explanation
Indices: 1948380--1948494 Score: 83
Period size: 19 Copynumber: 6.6 Consensus size: 19
1948370 GAAAATGGCT
*
1948380 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATCAAA
1948399 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATCAAA
* *
1948413 ATCGCAACGCGAAAT-GAA
1 ATCGCAATGCGAAATCAAA
1948431 ATCGCAA--CG-AA--AAA
1 ATCGCAATGCGAAATCAAA
* *
1948445 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATCAAA
1948464 ATCGCAATGCGAAA-CACAA
1 ATCGCAATGCGAAATCA-AA
*
1948483 ATCGCATTGCGA
1 ATCGCAATGCGA
1948495 TTTTCATTTC
Statistics
Matches: 79, Mismatches: 6, Indels: 22
0.74 0.06 0.21
Matches are distributed among these distances:
14 19 0.24
15 3 0.04
16 6 0.08
17 4 0.05
18 11 0.14
19 36 0.46
ACGTcount: A:0.46, C:0.23, G:0.19, T:0.12
Consensus pattern (19 bp):
ATCGCAATGCGAAATCAAA
Found at i:1948506 original size:19 final size:16
Alignment explanation
Indices: 1948484--1948561 Score: 56
Period size: 14 Copynumber: 4.7 Consensus size: 16
1948474 GAAACACAAA
1948484 TCGCATTGCGATTTTCATT
1 TCGC-TTGCGATTTT--TT
1948503 TCGCGTTGCGA-TTTTT
1 TCGC-TTGCGATTTTTT
*
1948519 TCG-TTGCGA-TTTTG
1 TCGCTTGCGATTTTTT
1948533 TCG-TTGCGATTTTCATT
1 TCGCTTGCGATTTT--TT
1948550 TCGCATTGCGAT
1 TCGC-TTGCGAT
1948562 AGCCATTTCC
Statistics
Matches: 51, Mismatches: 3, Indels: 10
0.80 0.05 0.16
Matches are distributed among these distances:
14 19 0.37
15 3 0.06
16 5 0.10
17 4 0.08
18 3 0.06
19 17 0.33
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.47
Consensus pattern (16 bp):
TCGCTTGCGATTTTTT
Found at i:1948525 original size:14 final size:14
Alignment explanation
Indices: 1948506--1948545 Score: 71
Period size: 14 Copynumber: 2.9 Consensus size: 14
1948496 TTTCATTTCG
*
1948506 CGTTGCGATTTTTT
1 CGTTGCGATTTTGT
1948520 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
1948534 CGTTGCGATTTT
1 CGTTGCGATTTT
1948546 CATTTCGCAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.07, C:0.15, G:0.25, T:0.53
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:1948580 original size:20 final size:19
Alignment explanation
Indices: 1948546--1948600 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
1948536 TTGCGATTTT
*
1948546 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
1948565 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
1948585 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
1948601 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:1949108 original size:18 final size:18
Alignment explanation
Indices: 1949082--1949126 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
1949072 GTCGATCAGA
*
1949082 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
1949100 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
1949118 TGATGGCTC
1 TGATGGCTC
1949127 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:1950494 original size:20 final size:20
Alignment explanation
Indices: 1950446--1950504 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
1950436 AATAGTTTCT
** *
1950446 GAAAATGAAAATCGCAACAC
1 GAAAATGACTATCGCAACGC
1950466 GAAAATGACTATCGCAACGC
1 GAAAATGACTATCGCAACGC
**
1950486 GAATTTGACTATCGCAACG
1 GAAAATGACTATCGCAACG
1950505 AGAGAATCGC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.42, C:0.22, G:0.19, T:0.17
Consensus pattern (20 bp):
GAAAATGACTATCGCAACGC
Found at i:1950809 original size:21 final size:21
Alignment explanation
Indices: 1950759--1950797 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1950749 CTCTGAGAGA
*
1950759 TGGAGAT-AGACGGATTTCAC
1 TGGAGATGGGACGGATTTCAC
1950779 TGGAGATGGGACGGATTTC
1 TGGAGATGGGACGGATTTC
1950798 GTCGGAGATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.26, C:0.13, G:0.36, T:0.26
Consensus pattern (21 bp):
TGGAGATGGGACGGATTTCAC
Found at i:1951026 original size:20 final size:20
Alignment explanation
Indices: 1950998--1951069 Score: 90
Period size: 20 Copynumber: 3.6 Consensus size: 20
1950988 ATTATGTATT
* *
1950998 ATCGAGTTGCGAAATTCAGA
1 ATCGCGTTGCGAAAGTCAGA
*
1951018 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGAAAGTCAGA
* *
1951038 ATCGCGTTGCGAAAGTAAGT
1 ATCGCGTTGCGAAAGTCAGA
*
1951058 ATCTCGTTGCGA
1 ATCGCGTTGCGA
1951070 TTTTGTATTA
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.28, C:0.18, G:0.28, T:0.26
Consensus pattern (20 bp):
ATCGCGTTGCGAAAGTCAGA
Found at i:1951124 original size:20 final size:20
Alignment explanation
Indices: 1951080--1951172 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
1951070 TTTTGTATTA
* **
1951080 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTTAT
*
1951101 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
* **
1951121 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTTAT
*
1951142 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
1951162 TCGCATTGCGA
1 TCGCATTGCGA
1951173 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (20 bp):
TCGCATTGCGATTTACTTAT
Found at i:1951125 original size:41 final size:41
Alignment explanation
Indices: 1951080--1951172 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
1951070 TTTTGTATTA
1951080 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1951121 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1951162 TCGCATTGCGA
1 TCGCATTGCGA
1951173 ATTGGGAAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:1953484 original size:2 final size:2
Alignment explanation
Indices: 1953477--1953501 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1953467 ATTTAAGCTT
1953477 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 T
1953502 GTATGCAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1959402 original size:15 final size:15
Alignment explanation
Indices: 1959384--1959416 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
1959374 ATTATAAATA
1959384 TATTTATATTTATAT
1 TATTTATATTTATAT
1959399 TATTTATATTTATAT
1 TATTTATATTTATAT
1959414 TAT
1 TAT
1959417 AATTTAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
TATTTATATTTATAT
Found at i:1967328 original size:3 final size:3
Alignment explanation
Indices: 1967320--1967377 Score: 116
Period size: 3 Copynumber: 19.3 Consensus size: 3
1967310 AAGTTAATAG
1967320 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
1967368 TAT TAT TAT T
1 TAT TAT TAT T
1967378 CTGGTCATAT
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:1967546 original size:29 final size:29
Alignment explanation
Indices: 1967513--1967577 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
1967503 CATTTTATCC
*
1967513 TTATATTAT-ACTAATTATAAAATTAATCT
1 TTATATTATAACTAATT-TAAAATCAATCT
* * *
1967542 TTATATTCTAATTTATTTAAAATCAATCT
1 TTATATTATAACTAATTTAAAATCAATCT
1967571 TTATATT
1 TTATATT
1967578 TTTCAAATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 26 0.84
30 5 0.16
ACGTcount: A:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (29 bp):
TTATATTATAACTAATTTAAAATCAATCT
Found at i:1977517 original size:12 final size:12
Alignment explanation
Indices: 1977500--1977524 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1977490 ATCTCAAAAT
1977500 ACAAACAGAAAC
1 ACAAACAGAAAC
1977512 ACAAACAGAAAC
1 ACAAACAGAAAC
1977524 A
1 A
1977525 GGTTGATTAC
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:0.68, C:0.24, G:0.08, T:0.00
Consensus pattern (12 bp):
ACAAACAGAAAC
Found at i:1978319 original size:14 final size:14
Alignment explanation
Indices: 1978300--1978339 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
1978290 TTAATAAATA
1978300 AACGAACACAAACG
1 AACGAACACAAACG
*
1978314 AACGAACATAAACG
1 AACGAACACAAACG
1978328 AAC-AACACAAAC
1 AACGAACACAAAC
1978340 ACAAAAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 8 0.33
14 16 0.67
ACGTcount: A:0.60, C:0.28, G:0.10, T:0.03
Consensus pattern (14 bp):
AACGAACACAAACG
Found at i:1978614 original size:14 final size:14
Alignment explanation
Indices: 1978595--1978640 Score: 74
Period size: 14 Copynumber: 3.1 Consensus size: 14
1978585 GCCCTCTGTT
1978595 CGAACATAAATGAA
1 CGAACATAAATGAA
1978609 CGAACATAAATGAA
1 CGAACATAAATGAA
1978623 CGAACATATAATCGAA
1 CGAACATA-AAT-GAA
1978639 CG
1 CG
1978641 TTCACGAACG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
14 22 0.73
15 3 0.10
16 5 0.17
ACGTcount: A:0.52, C:0.17, G:0.15, T:0.15
Consensus pattern (14 bp):
CGAACATAAATGAA
Found at i:1979431 original size:3 final size:3
Alignment explanation
Indices: 1979414--1979481 Score: 68
Period size: 3 Copynumber: 22.7 Consensus size: 3
1979404 CTATAAAAAA
* *
1979414 TAT TAT TAG TA- TAT TAT TAT TAT TAT TAT TAAT TA- TAT TAC TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT
* *
1979458 TAT TAT TCT TTT TAAT TAT TAT TA
1 TAT TAT TAT TAT T-AT TAT TAT TA
1979482 CATGTTACAG
Statistics
Matches: 55, Mismatches: 6, Indels: 8
0.80 0.09 0.12
Matches are distributed among these distances:
2 4 0.07
3 46 0.84
4 5 0.09
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:1979458 original size:27 final size:28
Alignment explanation
Indices: 1979428--1979482 Score: 85
Period size: 27 Copynumber: 2.0 Consensus size: 28
1979418 ATTAGTATAT
1979428 TATTATTATTATTATTAATTA-TATTAC
1 TATTATTATTATTATTAATTATTATTAC
* *
1979455 TATTATTATTCTTTTTAATTATTATTAC
1 TATTATTATTATTATTAATTATTATTAC
1979483 ATGTTACAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 19 0.76
28 6 0.24
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (28 bp):
TATTATTATTATTATTAATTATTATTAC
Found at i:1990132 original size:21 final size:21
Alignment explanation
Indices: 1990098--1990137 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1990088 TGTTATATAT
*
1990098 AGCCGTTGGGGATG-TTTTGG
1 AGCCGTTGGAGATGATTTTGG
1990118 AGCCGTTTGGAGATGATTTT
1 AGCCG-TTGGAGATGATTTT
1990138 TCTACTCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 8 0.47
22 4 0.24
ACGTcount: A:0.15, C:0.10, G:0.38, T:0.38
Consensus pattern (21 bp):
AGCCGTTGGAGATGATTTTGG
Found at i:1990279 original size:20 final size:20
Alignment explanation
Indices: 1990250--1990364 Score: 104
Period size: 20 Copynumber: 5.7 Consensus size: 20
1990240 GCAACCTTCG
* *
1990250 TGCATGGATGCACAGCAGGA
1 TGCATCGATGCACACCAGGA
**
1990270 TGCATCGATGCACAACCTTGA
1 TGCATCGATGCAC-ACCAGGA
* **
1990291 TGCATCGATGGACAAAAGGA
1 TGCATCGATGCACACCAGGA
* **
1990311 TGCATCGATGTACAACCTTGA
1 TGCATCGATGCAC-ACCAGGA
**
1990332 TGCATCGATGCACAGAAGGA
1 TGCATCGATGCACACCAGGA
1990352 TGCATCGATGCAC
1 TGCATCGATGCAC
1990365 TAATTGCATT
Statistics
Matches: 74, Mismatches: 19, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
20 43 0.58
21 31 0.42
ACGTcount: A:0.31, C:0.23, G:0.26, T:0.20
Consensus pattern (20 bp):
TGCATCGATGCACACCAGGA
Found at i:1990286 original size:41 final size:41
Alignment explanation
Indices: 1990241--1990364 Score: 187
Period size: 41 Copynumber: 3.0 Consensus size: 41
1990231 CTAGCCATTG
* *
1990241 CAACCTTCG-TGCATGGATGCACAGCAGGATGCATCGATGCA
1 CAACCTT-GATGCATCGATGCACAGAAGGATGCATCGATGCA
* * *
1990282 CAACCTTGATGCATCGATGGACAAAAGGATGCATCGATGTA
1 CAACCTTGATGCATCGATGCACAGAAGGATGCATCGATGCA
1990323 CAACCTTGATGCATCGATGCACAGAAGGATGCATCGATGCA
1 CAACCTTGATGCATCGATGCACAGAAGGATGCATCGATGCA
1990364 C
1 C
1990365 TAATTGCATT
Statistics
Matches: 74, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
40 1 0.01
41 73 0.99
ACGTcount: A:0.31, C:0.24, G:0.25, T:0.20
Consensus pattern (41 bp):
CAACCTTGATGCATCGATGCACAGAAGGATGCATCGATGCA
Found at i:1990294 original size:21 final size:21
Alignment explanation
Indices: 1990268--1990345 Score: 104
Period size: 21 Copynumber: 3.8 Consensus size: 21
1990258 TGCACAGCAG
1990268 GATGCATCGATGCACAACCTT
1 GATGCATCGATGCACAACCTT
* ***
1990289 GATGCATCGATGGACAA-AAG
1 GATGCATCGATGCACAACCTT
*
1990309 GATGCATCGATGTACAACCTT
1 GATGCATCGATGCACAACCTT
1990330 GATGCATCGATGCACA
1 GATGCATCGATGCACA
1990346 GAAGGATGCA
Statistics
Matches: 47, Mismatches: 9, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
20 16 0.34
21 31 0.66
ACGTcount: A:0.32, C:0.23, G:0.23, T:0.22
Consensus pattern (21 bp):
GATGCATCGATGCACAACCTT
Found at i:1990602 original size:30 final size:30
Alignment explanation
Indices: 1990555--1990614 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
1990545 AAACTTTGAA
1990555 TAAATTCAATTAAGTCCAAAAAC-ATTTTG
1 TAAATTCAATTAAGTCCAAAAACAATTTTG
1990584 TAAATTCAATTCAAGTCCAAAAACAATTTTG
1 TAAATTCAATT-AAGTCCAAAAACAATTTTG
1990615 CCTTAAATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 12 0.41
31 6 0.21
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.33
Consensus pattern (30 bp):
TAAATTCAATTAAGTCCAAAAACAATTTTG
Found at i:1993898 original size:21 final size:20
Alignment explanation
Indices: 1993829--1993948 Score: 152
Period size: 21 Copynumber: 5.8 Consensus size: 20
1993819 CGGTGTTTGA
* *
1993829 GTGCATCGATGCACTGCATG
1 GTGCATGGATGCACTGCAGG
*
1993849 GTGCATCGATGCACTAGTGCA-G
1 GTGCATGGATGCAC---TGCAGG
1993871 GTGCATGGATGCACTGCAGG
1 GTGCATGGATGCACTGCAGG
1993891 GATGCATGGATGCACTGCAGAG
1 G-TGCATGGATGCACTGCAG-G
1993913 GTGCATGGATGCACTGCAGGG
1 GTGCATGGATGCACTGCA-GG
1993934 GTGCATGGATGCACT
1 GTGCATGGATGCACT
1993949 TTGACACCCT
Statistics
Matches: 92, Mismatches: 1, Indels: 13
0.87 0.01 0.12
Matches are distributed among these distances:
19 4 0.04
20 16 0.17
21 51 0.55
22 17 0.18
23 4 0.04
ACGTcount: A:0.22, C:0.21, G:0.36, T:0.22
Consensus pattern (20 bp):
GTGCATGGATGCACTGCAGG
Found at i:1994049 original size:29 final size:29
Alignment explanation
Indices: 1994028--1994085 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 29
1994018 AAACTTTGAA
1994028 TAAATTCAATT-AAGTCCAAAAACATTTTG
1 TAAATTCAATTCAAGTCCAAAAACA-TTTG
1994057 TAAATTCAATTCAAGTCCAAAAACCATTT
1 TAAATTCAATTCAAGTCCAAAAA-CATTT
1994086 TGCCTTAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 11 0.41
30 14 0.52
31 2 0.07
ACGTcount: A:0.45, C:0.17, G:0.05, T:0.33
Consensus pattern (29 bp):
TAAATTCAATTCAAGTCCAAAAACATTTG
Found at i:1994075 original size:30 final size:30
Alignment explanation
Indices: 1994028--1994087 Score: 104
Period size: 29 Copynumber: 2.0 Consensus size: 30
1994018 AAACTTTGAA
1994028 TAAATTCAATTAAGTCCAAAAA-CATTTTG
1 TAAATTCAATTAAGTCCAAAAACCATTTTG
1994057 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATT-AAGTCCAAAAACCATTTTG
1994088 CCTTAAATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 11 0.38
31 7 0.24
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (30 bp):
TAAATTCAATTAAGTCCAAAAACCATTTTG
Found at i:1994164 original size:34 final size:36
Alignment explanation
Indices: 1994126--1994199 Score: 89
Period size: 36 Copynumber: 2.1 Consensus size: 36
1994116 CAACAATTTC
**
1994126 TTTTA-AAA-ACAAAATTTTGTCTCGCATGAGACAG
1 TTTTATAAATACAAAATTTCATCTCGCATGAGACAG
* * *
1994160 TTTTATAAATAGAAAATTTCATCTCGCTTGAGACAT
1 TTTTATAAATACAAAATTTCATCTCGCATGAGACAG
1994196 TTTT
1 TTTT
1994200 TTCTCTGAGA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
34 5 0.15
35 3 0.09
36 25 0.76
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.39
Consensus pattern (36 bp):
TTTTATAAATACAAAATTTCATCTCGCATGAGACAG
Found at i:1994438 original size:31 final size:32
Alignment explanation
Indices: 1994385--1994503 Score: 82
Period size: 31 Copynumber: 3.7 Consensus size: 32
1994375 TTTGTCACTC
* * * *
1994385 TTGAGACATTTTCTCTTAAAACAAAATCATCT
1 TTGAGTCAGTTTCCCTTGAAACAAAATCATCT
*
1994417 TTGAGTC-GTTTCCCTTGAAACAGATTTTATC-TCT
1 TTGAGTCAGTTTCCCTTGAAACA-A---AATCATCT
* ** *
1994451 CTTGAGACAGTTTCTATTGAAA-TAAATCATCT
1 -TTGAGTCAGTTTCCCTTGAAACAAAATCATCT
*
1994483 TTGAGTCTGTTTCCCTTGAAA
1 TTGAGTCAGTTTCCCTTGAAA
1994504 TAAATCCCTA
Statistics
Matches: 66, Mismatches: 14, Indels: 15
0.69 0.15 0.16
Matches are distributed among these distances:
31 32 0.48
32 10 0.15
34 4 0.06
35 9 0.14
36 11 0.17
ACGTcount: A:0.29, C:0.18, G:0.13, T:0.40
Consensus pattern (32 bp):
TTGAGTCAGTTTCCCTTGAAACAAAATCATCT
Found at i:1994454 original size:67 final size:68
Alignment explanation
Indices: 1994344--1994503 Score: 207
Period size: 67 Copynumber: 2.4 Consensus size: 68
1994334 AAAATTGACA
* * * * * *
1994344 ATCTTTGAGTCTTTTTCTCTTAAAACATAATTTTGTCACTCTTGAGACATTTTCTCTTAAAACAA
1 ATCTTTGAGTCTGTTTCCCTTGAAACATAATTTTATCACTCTTGAGACAGTTTCTATTAAAA-AA
1994409 AATC
65 AATC
* * * *
1994413 ATCTTTGAGTC-GTTTCCCTTGAAACA-GATTTTATCTCTCTTGAGACAGTTTCTATTGAAATAA
1 ATCTTTGAGTCTGTTTCCCTTGAAACATAATTTTATCACTCTTGAGACAGTTTCTATTAAAAAAA
1994476 ATC
66 ATC
1994479 ATCTTTGAGTCTGTTTCCCTTGAAA
1 ATCTTTGAGTCTGTTTCCCTTGAAA
1994504 TAAATCCCTA
Statistics
Matches: 80, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
66 16 0.20
67 41 0.51
68 12 0.15
69 11 0.14
ACGTcount: A:0.28, C:0.19, G:0.11, T:0.42
Consensus pattern (68 bp):
ATCTTTGAGTCTGTTTCCCTTGAAACATAATTTTATCACTCTTGAGACAGTTTCTATTAAAAAAA
ATC
Found at i:1994504 original size:31 final size:30
Alignment explanation
Indices: 1994408--1994509 Score: 89
Period size: 31 Copynumber: 3.2 Consensus size: 30
1994398 TCTTAAAACA
*
1994408 AAATCATCTTTGAGTCGTTTCCCTTGAAAC
1 AAATCATCTTTGAGTCGTTTCCCTTGAAAT
* **
1994438 AGATTTTATC-TCTCTTGAGACAGTTTCTATTGAAAT
1 A-A----ATCATCT-TTGAGTC-GTTTCCCTTGAAAT
1994474 AAATCATCTTTGAGTCTGTTTCCCTTGAAAT
1 AAATCATCTTTGAGTC-GTTTCCCTTGAAAT
1994505 AAATC
1 AAATC
1994510 CCTAAAGATG
Statistics
Matches: 56, Mismatches: 8, Indels: 15
0.71 0.10 0.19
Matches are distributed among these distances:
30 1 0.02
31 27 0.48
32 3 0.05
34 3 0.05
35 10 0.18
36 12 0.21
ACGTcount: A:0.28, C:0.19, G:0.13, T:0.40
Consensus pattern (30 bp):
AAATCATCTTTGAGTCGTTTCCCTTGAAAT
Found at i:1994741 original size:131 final size:131
Alignment explanation
Indices: 1994507--1995111 Score: 575
Period size: 131 Copynumber: 4.6 Consensus size: 131
1994497 CTTGAAATAA
** * * * *
1994507 ATCCCTAAAGATGGTCTGTCGTTCTCATCACGTAGGAATCGTGTCATCCCCCGCCCAGACCTCCT
1 ATCCCTAAAGATGGTCTACCATCCTCATCACGTAGGAATCGTGTCATCCACCGACCAGACCTCCT
* * * * * * * * *
1994572 TATCGCTTATGAGCCATATCAACCTCAGATAACCAGTCGTCCTCATCACGTAGGAACTATACTAT
66 CATCACGTAGGAGCCATGTCAACATTAGATAACCAGTCGTCCTCATCACGTAGGAACCATATTAT
1994637 C
131 C
* * * * *
1994638 ATCCCTAAAGATAGTCTGA-CGTCCTTATCACGTAGGAACCGTGTCATCCACCGACCAGACCTTC
1 ATCCCTAAAGATGGTCT-ACCATCCTCATCACGTAGGAATCGTGTCATCCACCGACCAGACCTCC
* * * * * *
1994702 TCATCACGTAGGAGTCGTGTCAACATTAGATAATCAGTCGTCCTCATTACGTAGGAACCGTGTTA
65 TCATCACGTAGGAGCCATGTCAACATTAGATAACCAGTCGTCCTCATCACGTAGGAACCATATTA
1994767 TC
130 TC
* * * *
1994769 ATCCCTAAAGATGGTATATCATTCTCATCGCGTAGGAATCGTGTCATCCACCGACCAGACCTCCT
1 ATCCCTAAAGATGGTCTACCATCCTCATCACGTAGGAATCGTGTCATCCACCGACCAGACCTCCT
** * * * * *
1994834 CATCACGTAGGAGCCGCGTCACCATTAGATAACCAGTCGTCCTTATCATGTAAGAACCAGATTAT
66 CATCACGTAGGAGCCATGTCAACATTAGATAACCAGTCGTCCTCATCACGTAGGAACCATATTAT
1994899 C
131 C
* * * *
1994900 ATCCCTAAAGATGGTCTACCATCCTCATCACTTCGGAATCGTGTCATCCATCGACCAGACCTCTT
1 ATCCCTAAAGATGGTCTACCATCCTCATCACGTAGGAATCGTGTCATCCACCGACCAGACCTCCT
* * ** * * * *** *** *
1994965 CATCACGTAGGAGTCATGTCATCCCTATATAACCAGCCATCCTCATTTTGTAGGAATTGTGTTAT
66 CATCACGTAGGAGCCATGTCAACATTAGATAACCAGTCGTCCTCATCACGTAGGAACCATATTAT
1995030 C
131 C
* * * ** * * *
1995031 ACCCTTCCTAAAGAGGGTC-AGTCATCCTCATCGTGTAGGAACCGTGTCATCCACCAACCAGATC
1 A---TCCCTAAAGATGGTCTA-CCATCCTCATCACGTAGGAATCGTGTCATCCACCGACCAGACC
*
1995095 TCCTCACCACGTAGGAG
62 TCCTCATCACGTAGGAG
1995112 TCGTGCCACC
Statistics
Matches: 387, Mismatches: 81, Indels: 9
0.81 0.17 0.02
Matches are distributed among these distances:
130 1 0.00
131 323 0.83
133 1 0.00
134 62 0.16
ACGTcount: A:0.26, C:0.30, G:0.17, T:0.26
Consensus pattern (131 bp):
ATCCCTAAAGATGGTCTACCATCCTCATCACGTAGGAATCGTGTCATCCACCGACCAGACCTCCT
CATCACGTAGGAGCCATGTCAACATTAGATAACCAGTCGTCCTCATCACGTAGGAACCATATTAT
C
Found at i:1994972 original size:262 final size:262
Alignment explanation
Indices: 1994507--1995111 Score: 696
Period size: 262 Copynumber: 2.3 Consensus size: 262
1994497 CTTGAAATAA
* * * * *
1994507 ATCCCTAAAGATGGTCTGTCGTTCTCATCACGTAGGAATCGTGTCATCCCCCGCCCAGACCTCCT
1 ATCCCTAAAGATGGTATGTCATTCTCATCGCGTAGGAATCGTGTCATCCACCGACCAGACCTCCT
* * * * * * * *
1994572 TATCGCTTATGAGCCATATCAACCTCAGATAACCAGTCGTCCTCATCACGTAGGAACTATACTAT
66 CATCACGTAGGAGCCACATCAACCTCAGATAACCAGTCGTCCTCATCACGTAAGAACCAGACTAT
* *
1994637 CATCCCTAAAGATAGTCTGACGTCCTTATCACGTAGGAACCGTGTCATCCACCGACCAGACCTTC
131 CATCCCTAAAGATAGTCTGACATCCTCATCACGTAGGAACCGTGTCATCCACCGACCAGACCTTC
* * * * *
1994702 TCATCACGTAGGAGTCGTGTCAACATTAGATAATCAGTCGTCCTCATTACGTAGGAACCGTGTTA
196 TCATCACGTAGGAGTCATGTCAACACTAGATAACCAGCCATCCTCATTACGTAGGAACCGTGTTA
1994767 TC
261 TC
*
1994769 ATCCCTAAAGATGGTATATCATTCTCATCGCGTAGGAATCGTGTCATCCACCGACCAGACCTCCT
1 ATCCCTAAAGATGGTATGTCATTCTCATCGCGTAGGAATCGTGTCATCCACCGACCAGACCTCCT
* * * * * *
1994834 CATCACGTAGGAGCCGCGTC-ACCATTAGATAACCAGTCGTCCTTATCATGTAAGAACCAGATTA
66 CATCACGTAGGAGCCACATCAACC-TCAGATAACCAGTCGTCCTCATCACGTAAGAACCAGACTA
* * * * *
1994898 TCATCCCTAAAGATGGTCT-ACCATCCTCATCACTTCGGAATCGTGTCATCCATCGACCAGACC-
130 TCATCCCTAAAGATAGTCTGA-CATCCTCATCACGTAGGAACCGTGTCATCCACCGACCAGACCT
* * * ** **
1994961 TCTTCATCACGTAGGAGTCATGTCATCCCTATATAACCAGCCATCCTCATTTTGTAGGAATTGTG
194 TC-TCATCACGTAGGAGTCATGTCAACACTAGATAACCAGCCATCCTCATTACGTAGGAACCGTG
1995026 TTATC
258 TTATC
* * * * * * *
1995031 ACCCTTCCTAAAGAGGGTCA-GTCATCCTCATCGTGTAGGAACCGTGTCATCCACCAACCAGATC
1 A---TCCCTAAAGATGGT-ATGTCATTCTCATCGCGTAGGAATCGTGTCATCCACCGACCAGACC
*
1995095 TCCTCACCACGTAGGAG
62 TCCTCATCACGTAGGAG
1995112 TCGTGCCACC
Statistics
Matches: 288, Mismatches: 48, Indels: 11
0.83 0.14 0.03
Matches are distributed among these distances:
261 6 0.02
262 215 0.75
265 66 0.23
266 1 0.00
ACGTcount: A:0.26, C:0.30, G:0.17, T:0.26
Consensus pattern (262 bp):
ATCCCTAAAGATGGTATGTCATTCTCATCGCGTAGGAATCGTGTCATCCACCGACCAGACCTCCT
CATCACGTAGGAGCCACATCAACCTCAGATAACCAGTCGTCCTCATCACGTAAGAACCAGACTAT
CATCCCTAAAGATAGTCTGACATCCTCATCACGTAGGAACCGTGTCATCCACCGACCAGACCTTC
TCATCACGTAGGAGTCATGTCAACACTAGATAACCAGCCATCCTCATTACGTAGGAACCGTGTTA
TC
Found at i:1995323 original size:3 final size:3
Alignment explanation
Indices: 1995317--1995381 Score: 71
Period size: 3 Copynumber: 21.7 Consensus size: 3
1995307 ACAAAAATAA
* *
1995317 TAT TAT TAG TA- TAT TAT TAT TAT TAAT TA- TAT TAC TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT
*
1995361 TCT TAT TAAT TAT TAT TAT TA
1 TAT TAT T-AT TAT TAT TAT TA
1995382 CATGTTACAA
Statistics
Matches: 53, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
2 4 0.08
3 43 0.81
4 6 0.11
ACGTcount: A:0.35, C:0.03, G:0.02, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:1995366 original size:27 final size:27
Alignment explanation
Indices: 1995317--1995378 Score: 90
Period size: 27 Copynumber: 2.3 Consensus size: 27
1995307 ACAAAAATAA
*
1995317 TATTATTAGTATATTATTATTATTAAT
1 TATTATTACTATATTATTATTATTAAT
*
1995344 TA-TATTACTATTATTATTCTTATTAAT
1 TATTATTACTA-TATTATTATTATTAAT
1995371 TATTATTA
1 TATTATTA
1995379 TTACATGTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
26 7 0.23
27 19 0.61
28 5 0.16
ACGTcount: A:0.35, C:0.03, G:0.02, T:0.60
Consensus pattern (27 bp):
TATTATTACTATATTATTATTATTAAT
Found at i:1997721 original size:32 final size:29
Alignment explanation
Indices: 1997661--1997745 Score: 80
Period size: 32 Copynumber: 2.7 Consensus size: 29
1997651 AAGTTTTGAT
* *
1997661 AAATTTAATAATCATTTTGTAATAGTTTATTA
1 AAATTTAATAAT-ATTTTATAACAGTTTA--A
* *
1997693 AAATTTAATGATAATTTTATAACCGTTTAA
1 AAATTTAATAAT-ATTTTATAACAGTTTAA
1997723 AAATTATAATAACTATTTTATAA
1 AAATT-TAATAA-TATTTTATAA
1997746 TATTTGAATG
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
30 6 0.13
31 14 0.31
32 25 0.56
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.46
Consensus pattern (29 bp):
AAATTTAATAATATTTTATAACAGTTTAA
Found at i:1999230 original size:31 final size:31
Alignment explanation
Indices: 1999173--1999249 Score: 102
Period size: 31 Copynumber: 2.5 Consensus size: 31
1999163 CTTTTAAAAC
* *
1999173 TTGTAATACAGT-CCCTAACATTTAGTCTAT
1 TTGTAATATAGTCCCCCAACATTTAGTCTAT
*
1999203 TTGTAATATAGTCCCCCAATATTTAGTCTAT
1 TTGTAATATAGTCCCCCAACATTTAGTCTAT
* *
1999234 TTGCAATATGGTCCCC
1 TTGTAATATAGTCCCC
1999250 AATGTAACCG
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
30 11 0.27
31 30 0.73
ACGTcount: A:0.27, C:0.22, G:0.12, T:0.39
Consensus pattern (31 bp):
TTGTAATATAGTCCCCCAACATTTAGTCTAT
Found at i:2003687 original size:18 final size:18
Alignment explanation
Indices: 2003664--2003698 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
2003654 GAATGGATGG
2003664 GCTCTTCTGCTTCAGCGA
1 GCTCTTCTGCTTCAGCGA
2003682 GCTCTTCTGCTTCAGCG
1 GCTCTTCTGCTTCAGCG
2003699 GGCTGGTGGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.09, C:0.34, G:0.23, T:0.34
Consensus pattern (18 bp):
GCTCTTCTGCTTCAGCGA
Found at i:2013478 original size:20 final size:17
Alignment explanation
Indices: 2013453--2013501 Score: 55
Period size: 20 Copynumber: 2.8 Consensus size: 17
2013443 CGTTTCAAAG
2013453 ATGGTATCGATACCATCCTT
1 ATGGTATCGATACC--CC-T
*
2013473 ATGGTATCGGTACCCCT
1 ATGGTATCGATACCCCT
2013490 -TGGTATCGATAC
1 ATGGTATCGATAC
2013502 TGTTCTTCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 11 0.41
17 1 0.04
18 2 0.07
20 13 0.48
ACGTcount: A:0.22, C:0.24, G:0.20, T:0.33
Consensus pattern (17 bp):
ATGGTATCGATACCCCT
Found at i:2016868 original size:32 final size:32
Alignment explanation
Indices: 2016831--2016957 Score: 218
Period size: 32 Copynumber: 4.0 Consensus size: 32
2016821 GAAGAACCTA
2016831 TCCATATGTCCCGAAGGACATAGATAATCCTG
1 TCCATATGTCCCGAAGGACATAGATAATCCTG
2016863 TCCATATGTCCCGAAGGACATAGATAATCCTG
1 TCCATATGTCCCGAAGGACATAGATAATCCTG
* *
2016895 TCCATATGTCCCGAAAGACATAGGTAATCCTG
1 TCCATATGTCCCGAAGGACATAGATAATCCTG
* *
2016927 TCCATATATCCCGAAGGACATAGGTAATCCT
1 TCCATATGTCCCGAAGGACATAGATAATCCT
2016958 CAACTCTTGG
Statistics
Matches: 91, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 91 1.00
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.25
Consensus pattern (32 bp):
TCCATATGTCCCGAAGGACATAGATAATCCTG
Found at i:2020502 original size:31 final size:31
Alignment explanation
Indices: 2020464--2020541 Score: 122
Period size: 31 Copynumber: 2.5 Consensus size: 31
2020454 CGATTACGTC
2020464 GGGGACCATATTGCAAA-TAGACTAAATGTTG
1 GGGGACCATATTGCAAACT-GACTAAATGTTG
2020495 GGGGACCATATTGCAAACTGACTAAATGTTG
1 GGGGACCATATTGCAAACTGACTAAATGTTG
**
2020526 GGGGACTGTATTGCAA
1 GGGGACCATATTGCAA
2020542 GTTTTAAAAG
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
31 43 0.98
32 1 0.02
ACGTcount: A:0.32, C:0.14, G:0.28, T:0.26
Consensus pattern (31 bp):
GGGGACCATATTGCAAACTGACTAAATGTTG
Found at i:2022538 original size:16 final size:16
Alignment explanation
Indices: 2022509--2022546 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
2022499 TTCACTATCG
2022509 AAATG-TTAGATTTAA
1 AAATGTTTAGATTTAA
* *
2022524 ATATGTTTAGGTTTAA
1 AAATGTTTAGATTTAA
2022540 AAATGTT
1 AAATGTT
2022547 GGGTTAAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 4 0.21
16 15 0.79
ACGTcount: A:0.39, C:0.00, G:0.16, T:0.45
Consensus pattern (16 bp):
AAATGTTTAGATTTAA
Found at i:2025173 original size:38 final size:38
Alignment explanation
Indices: 2025119--2025203 Score: 107
Period size: 38 Copynumber: 2.2 Consensus size: 38
2025109 TTTTGTCTCA
* **
2025119 ACCCGAAAATTATATACTTTCCACCAGAATTCGACCCG
1 ACCCGAAAATCATATACTTTCCACCAGAACCCGACCCG
* * * *
2025157 ACTCGAAAATCATATACTTTTCACTAGTACCCGACCCG
1 ACCCGAAAATCATATACTTTCCACCAGAACCCGACCCG
2025195 ACCCGAAAA
1 ACCCGAAAA
2025204 GTACACACCC
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.35, C:0.32, G:0.11, T:0.22
Consensus pattern (38 bp):
ACCCGAAAATCATATACTTTCCACCAGAACCCGACCCG
Found at i:2025459 original size:4 final size:4
Alignment explanation
Indices: 2025450--2027035 Score: 2887
Period size: 4 Copynumber: 398.0 Consensus size: 4
2025440 GTTTGCAATA
2025450 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
2025498 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
2025546 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
2025594 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
2025642 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
2025690 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
2025738 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
2025786 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
2025834 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
2025882 TATG TATG TATG TATG TATG TATG TATG TATG TA-- TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
2025928 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
2025976 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TA-G TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
2026023 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
2026071 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
2026119 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
2026167 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
2026215 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* * * * * * * * *
2026263 TATG TATG TATG CATG CATG CATG CATG CATG CATG CATG CATG CATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* * * * * * * * * * * *
2026311 CATG CATG CATG CATG CATG CATG CATG CATG CATG CATG CATG CATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* * *
2026359 CATG CATG CATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
2026407 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
2026455 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
2026503 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
2026551 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
2026599 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
2026647 TATG TATG TATG TATG TATG TATG TATG TATG TATG TA-- TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
*
2026693 TATG TATA TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
2026741 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
2026789 TA-G TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
2026836 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
2026884 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
2026932 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
*
2026980 TATG TATG TATG TATG TATG TATG TATG TATG CATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
*
2027028 CATG TATG
1 TATG TATG
2027036 CACACTCATA
Statistics
Matches: 1568, Mismatches: 8, Indels: 12
0.99 0.01 0.01
Matches are distributed among these distances:
2 4 0.00
3 6 0.00
4 1558 0.99
ACGTcount: A:0.25, C:0.02, G:0.25, T:0.48
Consensus pattern (4 bp):
TATG
Found at i:2032361 original size:42 final size:41
Alignment explanation
Indices: 2032285--2032430 Score: 127
Period size: 41 Copynumber: 3.6 Consensus size: 41
2032275 AGAGATAAAA
* * ** *
2032285 TTAACGGCGTTTTTGAACAAACATTACTAAAGACTCATATT
1 TTAATGGCGTTTTTGAATAAACGCTGCTAAAGACTCATATT
* * * *
2032326 TTAATGGCGTTTTTTAGTTAAACGAC-GCTATAGACTCACATT
1 TTAATGGCGTTTTTGA-ATAAACG-CTGCTAAAGACTCATATT
* * *
2032368 TTAGTGGTGTTTTTGAATAAACGCTGCTAAAGACTCATA-C
1 TTAATGGCGTTTTTGAATAAACGCTGCTAAAGACTCATATT
* *
2032408 TT-GTGGCGTTTCTGAATAAACGC
1 TTAATGGCGTTTTTGAATAAACGC
2032431 CGTAATAAGA
Statistics
Matches: 84, Mismatches: 18, Indels: 8
0.76 0.16 0.07
Matches are distributed among these distances:
39 19 0.23
40 3 0.04
41 32 0.38
42 30 0.36
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.36
Consensus pattern (41 bp):
TTAATGGCGTTTTTGAATAAACGCTGCTAAAGACTCATATT
Found at i:2032402 original size:41 final size:41
Alignment explanation
Indices: 2032290--2032430 Score: 135
Period size: 42 Copynumber: 3.5 Consensus size: 41
2032280 TAAAATTAAC
* ** * *
2032290 GGCGTTTTTGAACAAACATTACTAAAGACTCATATTTTAAT
1 GGCGTTTTTGAATAAACGCTGCTAAAGACTCATATTTTAGT
* * * *
2032331 GGCGTTTTTTAGTTAAACGAC-GCTATAGACTCACATTTTAGT
1 GGCGTTTTTGA-ATAAACG-CTGCTAAAGACTCATATTTTAGT
* *
2032373 GGTGTTTTTGAATAAACGCTGCTAAAGACTCATA-CTT-GT
1 GGCGTTTTTGAATAAACGCTGCTAAAGACTCATATTTTAGT
*
2032412 GGCGTTTCTGAATAAACGC
1 GGCGTTTTTGAATAAACGC
2032431 CGTAATAAGA
Statistics
Matches: 80, Mismatches: 17, Indels: 8
0.76 0.16 0.08
Matches are distributed among these distances:
39 19 0.24
40 3 0.04
41 28 0.35
42 30 0.38
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.35
Consensus pattern (41 bp):
GGCGTTTTTGAATAAACGCTGCTAAAGACTCATATTTTAGT
Found at i:2033178 original size:36 final size:36
Alignment explanation
Indices: 2033131--2033202 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
2033121 AGTATTGATT
2033131 AATATTGAATGCTTTTTTGTTTTAAATAAAACGACA
1 AATATTGAATGCTTTTTTGTTTTAAATAAAACGACA
2033167 AATATTGAATGCTTTTTTGTTTTAAATAAAACGACA
1 AATATTGAATGCTTTTTTGTTTTAAATAAAACGACA
2033203 GATGGTGTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.39, C:0.08, G:0.11, T:0.42
Consensus pattern (36 bp):
AATATTGAATGCTTTTTTGTTTTAAATAAAACGACA
Found at i:2035795 original size:31 final size:32
Alignment explanation
Indices: 2035752--2035818 Score: 111
Period size: 31 Copynumber: 2.2 Consensus size: 32
2035742 ATTATAAAGA
2035752 TATTAGATACAATGAGTTCTTAA-GGAAATTT
1 TATTAGATACAATGAGTTCTTAAGGGAAATTT
*
2035783 TATTTGATACAATGAGTTCTTAAGGGAAA-TT
1 TATTAGATACAATGAGTTCTTAAGGGAAATTT
2035814 TATTA
1 TATTA
2035819 TTAAATATGT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
31 28 0.85
32 5 0.15
ACGTcount: A:0.37, C:0.06, G:0.16, T:0.40
Consensus pattern (32 bp):
TATTAGATACAATGAGTTCTTAAGGGAAATTT
Found at i:2037528 original size:15 final size:15
Alignment explanation
Indices: 2037508--2037537 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2037498 AAAGAATGTT
2037508 GCACATGCAACAACA
1 GCACATGCAACAACA
2037523 GCACATGCAACAACA
1 GCACATGCAACAACA
2037538 ACTTTCTCTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.33, G:0.13, T:0.07
Consensus pattern (15 bp):
GCACATGCAACAACA
Found at i:2038298 original size:60 final size:61
Alignment explanation
Indices: 2038196--2038347 Score: 179
Period size: 60 Copynumber: 2.5 Consensus size: 61
2038186 TATAACCCTA
*
2038196 ATTTTAAATT-GATTCTTAAACTTTTGAAT-TTTTCAAACTCATCCCTAAACTATGA-CTCTC
1 ATTTTAAATTAG-TCCTTAAACTTTTGAATATTTTCAAACTCATCCCTAAACTATGATC-CTC
* **
2038256 ATTTTAAATTAGTCCTTAAACTTCTGAATATTTT-AATTTCATCCCTAAACTATGATCCTC
1 ATTTTAAATTAGTCCTTAAACTTTTGAATATTTTCAAACTCATCCCTAAACTATGATCCTC
* **
2038316 -TTTCTAAAGTAGTCCCCAAACTTTTGAATATT
1 ATTT-TAAATTAGTCCTTAAACTTTTGAATATT
2038348 CCAATTCCAT
Statistics
Matches: 80, Mismatches: 8, Indels: 8
0.83 0.08 0.08
Matches are distributed among these distances:
59 3 0.04
60 71 0.89
61 6 0.08
ACGTcount: A:0.32, C:0.20, G:0.06, T:0.43
Consensus pattern (61 bp):
ATTTTAAATTAGTCCTTAAACTTTTGAATATTTTCAAACTCATCCCTAAACTATGATCCTC
Found at i:2038359 original size:60 final size:60
Alignment explanation
Indices: 2038213--2038368 Score: 167
Period size: 60 Copynumber: 2.6 Consensus size: 60
2038203 ATTGATTCTT
* * * **
2038213 AAACTTTTGAATTTTTCAA-ACTCATCCCTAAACTATGACTCTCATTTTAAATTAGTCCTT
1 AAACTTTTGAATATTTCAATTC-CATCCCTAAACTATGACTCTCATTTTAAAGTAGTCCCC
* * *
2038273 AAACTTCTGAATATTTTAATTTCATCCCTAAACTATGA-TCCTC-TTTCTAAAGTAGTCCCC
1 AAACTTTTGAATATTTCAATTCCATCCCTAAACTATGACT-CTCATTT-TAAAGTAGTCCCC
* *
2038333 AAACTTTTGAATATTCCAATTCCATCCCCAAA-TATG
1 AAACTTTTGAATATTTCAATTCCATCCCTAAACTATG
2038369 TAATTAGTTT
Statistics
Matches: 80, Mismatches: 13, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
59 8 0.10
60 72 0.90
ACGTcount: A:0.32, C:0.24, G:0.06, T:0.38
Consensus pattern (60 bp):
AAACTTTTGAATATTTCAATTCCATCCCTAAACTATGACTCTCATTTTAAAGTAGTCCCC
Done.