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 71 of 427
Found at i:17623198 original size:35 final size:34
Alignment explanation
Indices: 17623144--17623215 Score: 92
Period size: 35 Copynumber: 2.1 Consensus size: 34
17623134 AATTGAAAGA
*
17623144 GAAAAGAAAATAATTCAATTCC-AATGGAAATAG
1 GAAAAGAAAATAATCCAATTCCGAATGGAAATAG
* *
17623177 GAAAAGAGAGAATAATCCAATTCCGAATTGAAGTAG
1 GAAAAGA-A-AATAATCCAATTCCGAATGGAAATAG
17623213 GAA
1 GAA
17623216 TCCCAAAGTA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
33 7 0.21
34 1 0.03
35 13 0.39
36 12 0.36
ACGTcount: A:0.51, C:0.10, G:0.19, T:0.19
Consensus pattern (34 bp):
GAAAAGAAAATAATCCAATTCCGAATGGAAATAG
Found at i:17623673 original size:23 final size:23
Alignment explanation
Indices: 17623641--17623684 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
17623631 ATAATATAAA
* *
17623641 ATAATCTTATATTATCTATATCT
1 ATAATCTTATAATATATATATCT
*
17623664 ATAATTTTATAATATATATAT
1 ATAATCTTATAATATATATAT
17623685 AAAAACACAA
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:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (23 bp):
ATAATCTTATAATATATATATCT
Found at i:17624046 original size:16 final size:16
Alignment explanation
Indices: 17624027--17624057 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
17624017 GTCATTGGGA
17624027 TTTTATTTTATTTTTG
1 TTTTATTTTATTTTTG
17624043 TTTTATTTTATTTTT
1 TTTTATTTTATTTTT
17624058 AAAAAAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.13, C:0.00, G:0.03, T:0.84
Consensus pattern (16 bp):
TTTTATTTTATTTTTG
Found at i:17624275 original size:231 final size:230
Alignment explanation
Indices: 17624021--17624468 Score: 665
Period size: 231 Copynumber: 1.9 Consensus size: 230
17624011 GTTTATGTCA
17624021 TTGGGATTTTATTTTATTTTTGTTTTA-TTTTATTTTTAAAAAAATATTAATTAAATTAAAAGGT
1 TTGGGATTTTATTTTATTTTTGTTTTATTTTTATTTTT-AAAAAATATTAATTAAATTAAAAGG-
* *
17624085 TTTGTTTCCCACTTTTCACGTTTTCTT-TCTCACGTTCCATTGTCC-ATTCCCGTGATATTTTTG
64 TTTGTTTCCCACTTTTCACCTTTT-TTATCTCACGTTCAATTG-CCTATTCCCGTGATATTTTTG
* * * *
17624148 GCACTTCCAGTGAAGGAAAAAAAAAATC-AA-AAAAGGCTCCTTTCCTTTTTCTTGAATTTTGGC
127 GCACTTACAGTAAAGGAAAAAAAAAA-CAAAGAAAAGGCTCC-TTCCGTTTTCTTGAATTTTGAC
17624211 TTTTGTTTCAATAGGTCTTTACTTTTGAGAGTAGTGGATGG
190 TTTTGTTTCAATAGGTCTTTACTTTTGAGAGTAGTGGATGG
* *
17624252 TTGGGATTTTGTTTT-TGTTTTGTTTTATTTTTATTTTTAGAAAATATTAATTAAATTAAAAGGT
1 TTGGGATTTTATTTTAT-TTTTGTTTTATTTTTATTTTTAAAAAATATTAATTAAATTAAAAGGT
* * *
17624316 TTGTTTCCCACTTTTCACCTTTTTTATCTCATGTTCAATTGCCTATTCCTGTGATTTTTTTGGCA
65 TTGTTTCCCACTTTTCACCTTTTTTATCTCACGTTCAATTGCCTATTCCCGTGATATTTTTGGCA
17624381 CTTACAGTAAAGGAAAAAAAAAACAAAAGAAAAGGCTCCTTCCGTTTTCTTGAATTTTGACTTTT
130 CTTACAGTAAAGGAAAAAAAAAAC-AAAGAAAAGGCTCCTTCCGTTTTCTTGAATTTTGACTTTT
* *
17624446 GTTTCAATTGGTCTTTGCTTTTG
194 GTTTCAATAGGTCTTTACTTTTG
17624469 TTCCAATTGA
Statistics
Matches: 197, Mismatches: 13, Indels: 14
0.88 0.06 0.06
Matches are distributed among these distances:
229 5 0.03
230 77 0.39
231 95 0.48
232 20 0.10
ACGTcount: A:0.25, C:0.13, G:0.14, T:0.47
Consensus pattern (230 bp):
TTGGGATTTTATTTTATTTTTGTTTTATTTTTATTTTTAAAAAATATTAATTAAATTAAAAGGTT
TGTTTCCCACTTTTCACCTTTTTTATCTCACGTTCAATTGCCTATTCCCGTGATATTTTTGGCAC
TTACAGTAAAGGAAAAAAAAAACAAAGAAAAGGCTCCTTCCGTTTTCTTGAATTTTGACTTTTGT
TTCAATAGGTCTTTACTTTTGAGAGTAGTGGATGG
Found at i:17627092 original size:14 final size:16
Alignment explanation
Indices: 17627063--17627094 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
17627053 TTTATTTACT
17627063 CTTTTACACATATCAA
1 CTTTTACACATATCAA
17627079 CTTTTA-AC-TATCAA
1 CTTTTACACATATCAA
17627093 CT
1 CT
17627095 AAGTTTTACC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.50
15 2 0.12
16 6 0.38
ACGTcount: A:0.34, C:0.25, G:0.00, T:0.41
Consensus pattern (16 bp):
CTTTTACACATATCAA
Found at i:17628268 original size:2 final size:2
Alignment explanation
Indices: 17628261--17628298 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
17628251 CAAATTAACA
17628261 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
17628299 TTTAAAGTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17629535 original size:30 final size:30
Alignment explanation
Indices: 17629486--17629546 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 30
17629476 AAATATCTTT
* *
17629486 ACTTTCCCCTAATACTTTTACT-CCCTCCC
1 ACTTCCCCCTAAAACTTTTACTACCCTCCC
17629515 ACTTCCCCCTCAAAACTTTTACTACCCTCCC
1 ACTTCCCCCT-AAAACTTTTACTACCCTCCC
17629546 A
1 A
17629547 TCCCACTCCC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 9 0.32
30 11 0.39
31 8 0.29
ACGTcount: A:0.21, C:0.46, G:0.00, T:0.33
Consensus pattern (30 bp):
ACTTCCCCCTAAAACTTTTACTACCCTCCC
Found at i:17633967 original size:20 final size:21
Alignment explanation
Indices: 17633927--17633968 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
17633917 AAACTTGTAT
*
17633927 ATCTATCAACAAGCATTCAAA
1 ATCTATCAACAAACATTCAAA
*
17633948 ATCTATCAAGAAAC-TTCAAA
1 ATCTATCAACAAACATTCAAA
17633968 A
1 A
17633969 CTTGTACATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.50, C:0.21, G:0.05, T:0.24
Consensus pattern (21 bp):
ATCTATCAACAAACATTCAAA
Found at i:17643107 original size:45 final size:47
Alignment explanation
Indices: 17643023--17643151 Score: 183
Period size: 45 Copynumber: 2.8 Consensus size: 47
17643013 CACATTCGAT
* * *
17643023 AAGTACCTATACCATGGCCCGTAGCCAAGTCAAGATAACTTATTC-CA
1 AAGTACCTATACCATGGCCCGTAGCCAAATCAAGGTAACTT-CTCACA
*
17643070 AAGTACCTATACCAT-G-CCATAGCCAAATCAAGGTAACTTCTCACA
1 AAGTACCTATACCATGGCCCGTAGCCAAATCAAGGTAACTTCTCACA
*
17643115 AAATACCTATACCATGGCCCGTAGCCAAATCAAGGTA
1 AAGTACCTATACCATGGCCCGTAGCCAAATCAAGGTA
17643152 TTATTCACAC
Statistics
Matches: 73, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
44 2 0.03
45 36 0.49
46 2 0.03
47 33 0.45
ACGTcount: A:0.36, C:0.28, G:0.14, T:0.22
Consensus pattern (47 bp):
AAGTACCTATACCATGGCCCGTAGCCAAATCAAGGTAACTTCTCACA
Found at i:17644759 original size:3 final size:3
Alignment explanation
Indices: 17644751--17644827 Score: 145
Period size: 3 Copynumber: 25.7 Consensus size: 3
17644741 TATTAAAATG
17644751 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
17644799 ATA ATA ATA ATA ATA ATA ATA GTA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
17644828 GATGATGATT
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 72 1.00
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:17650354 original size:25 final size:25
Alignment explanation
Indices: 17650324--17650487 Score: 210
Period size: 25 Copynumber: 6.7 Consensus size: 25
17650314 GACCTCAGCA
17650324 TGCTCTCTGATTATTAGCACGTCAG
1 TGCTCTCTGATTATTAGCACGTCAG
* * *
17650349 TGCTCTCTGAATATTAGCACATTAG
1 TGCTCTCTGATTATTAGCACGTCAG
17650374 TGCTCTCTGATTATTAGCACGTCAG
1 TGCTCTCTGATTATTAGCACGTCAG
**
17650399 TGCTCTCTGAACATTAGCACGTCAG
1 TGCTCTCTGATTATTAGCACGTCAG
* *
17650424 TGCTCTCTGATTATTAGAACGCCAG
1 TGCTCTCTGATTATTAGCACGTCAG
*
17650449 TGCTCTCTG--TA-TAGCACTTCAG
1 TGCTCTCTGATTATTAGCACGTCAG
*
17650471 TGTTCTCTG-TTCATTAG
1 TGCTCTCTGATT-ATTAG
17650488 TGCATAATAA
Statistics
Matches: 120, Mismatches: 16, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
22 16 0.13
23 3 0.03
24 1 0.01
25 100 0.83
ACGTcount: A:0.21, C:0.24, G:0.19, T:0.36
Consensus pattern (25 bp):
TGCTCTCTGATTATTAGCACGTCAG
Found at i:17664905 original size:22 final size:23
Alignment explanation
Indices: 17664840--17664899 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 23
17664830 TTCAGGTAAA
* *
17664840 AATATAAAATATTTAAATTAAATAAT
1 AATAT-AAAT-TTAAAATTTAA-AAT
17664866 AATATAAATTTAAAATTTAAAAT
1 AATATAAATTTAAAATTTAAAAT
17664889 AATA-AAATTTA
1 AATATAAATTTA
17664900 GTATTTGATT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
22 7 0.22
23 7 0.22
24 9 0.28
25 4 0.12
26 5 0.16
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (23 bp):
AATATAAATTTAAAATTTAAAAT
Found at i:17664930 original size:14 final size:15
Alignment explanation
Indices: 17664913--17664949 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
17664903 TTTGATTTCT
17664913 TTAAATTAATTT-AA
1 TTAAATTAATTTGAA
*
17664927 TTAACTTAATTTGAA
1 TTAAATTAATTTGAA
17664942 -TAAATTAA
1 TTAAATTAA
17664950 AATTTAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 18 0.90
15 2 0.10
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (15 bp):
TTAAATTAATTTGAA
Found at i:17666474 original size:43 final size:43
Alignment explanation
Indices: 17666426--17666789 Score: 393
Period size: 43 Copynumber: 8.5 Consensus size: 43
17666416 GTAAAAAAAG
* *
17666426 GCCGCTATAGAACATGACCTTTAGTGGCGCTTTTTCCACAAAT
1 GCCGCTATAGAACATGACCTTTAGCGGCGCTTTTTCCACAAAC
17666469 GCCGCTATAGAACATGACCTTTAGCGGCGCTTTTTCCATC-AAC
1 GCCGCTATAGAACATGACCTTTAGCGGCGCTTTTTCCA-CAAAC
* * *
17666512 ACCGCTATAGAACATGACCTTTAGTGGCGC-TTTACCACAAAC
1 GCCGCTATAGAACATGACCTTTAGCGGCGCTTTTTCCACAAAC
* * *
17666554 GCCGCTAAAGAACATGACCTTTAGTC-GCGCTTTTCCCACAATC
1 GCCGCTATAGAACATGACCTTTAG-CGGCGCTTTTTCCACAAAC
* * * *
17666597 ACAGCTAAAGAACATGACCTTTAGCGGCAC-TTTTCCTACAAAC
1 GCCGCTATAGAACATGACCTTTAGCGGCGCTTTTTCC-ACAAAC
* * *
17666640 GCCGCTAAAGAACGTGACCTTTAGCGGCGCTTTTCCCACAAAC
1 GCCGCTATAGAACATGACCTTTAGCGGCGCTTTTTCCACAAAC
* * *
17666683 GCCTCTATAAAACA-GACCTTTAGTC-GCGCTTTTGCCACAAAC
1 GCCGCTATAGAACATGACCTTTAG-CGGCGCTTTTTCCACAAAC
* * * * *
17666725 ACCACTATAAAACA-AACCTTTAGCGGCGC-TATTCTCACAAAC
1 GCCGCTATAGAACATGACCTTTAGCGGCGCTTTTTC-CACAAAC
* * *
17666767 ACCGCTAAAGAAGATGACCTTTA
1 GCCGCTATAGAACATGACCTTTA
17666790 AAAAAATATT
Statistics
Matches: 275, Mismatches: 35, Indels: 22
0.83 0.11 0.07
Matches are distributed among these distances:
41 5 0.02
42 107 0.39
43 157 0.57
44 6 0.02
ACGTcount: A:0.30, C:0.29, G:0.16, T:0.25
Consensus pattern (43 bp):
GCCGCTATAGAACATGACCTTTAGCGGCGCTTTTTCCACAAAC
Found at i:17666570 original size:128 final size:128
Alignment explanation
Indices: 17666426--17666789 Score: 438
Period size: 128 Copynumber: 2.8 Consensus size: 128
17666416 GTAAAAAAAG
* * *
17666426 GCCGCTATAGAACATGACCTTTAGTGGCGCTTTTTCCACAAATGCCGCTATAGAACATGACCTTT
1 GCCGCTAAAGAACATGACCTTTAGTCGCGCTTTTCCCACAAAT-CCGCTATAGAACATGACCTTT
* *
17666491 AGCGGCGCTTTTTCCATC-AACACCGCTATAGAACATGACCTTTAGTGGCGC-TTTACCACAAAC
65 AGCGGCGC-TTTTCCATCAAACACCGCTAAAGAACATGACCTTTAGCGGCGCTTTTACCACAAAC
*
17666554 GCCGCTAAAGAACATGACCTTTAGTCGCGCTTTTCCCAC-AATCACAGCTAAAGAACATGACCTT
1 GCCGCTAAAGAACATGACCTTTAGTCGCGCTTTTCCCACAAATC-C-GCTATAGAACATGACCTT
* * * *
17666618 TAGCGGCACTTTTCC-TACAAACGCCGCTAAAGAACGTGACCTTTAGCGGCGCTTTTCCCACAAA
64 TAGCGGCGCTTTTCCAT-CAAACACCGCTAAAGAACATGACCTTTAGCGGCGCTTTTACCACAAA
17666682 C
128 C
* * * * * *
17666683 GCCTCTATAA-AACA-GACCTTTAGTCGCGCTTTTGCCACAAACACCACTATAAAACA-AACCTT
1 GCCGCTA-AAGAACATGACCTTTAGTCGCGCTTTTCCCACAAA-TCCGCTATAGAACATGACCTT
* *
17666745 TAGCGGCGCTATTCTCA-CAAACACCGCTAAAGAAGATGACCTTTA
64 TAGCGGCGCTTTTC-CATCAAACACCGCTAAAGAACATGACCTTTA
17666790 AAAAAATATT
Statistics
Matches: 204, Mismatches: 22, Indels: 21
0.83 0.09 0.09
Matches are distributed among these distances:
126 2 0.01
127 53 0.26
128 122 0.60
129 24 0.12
130 3 0.01
ACGTcount: A:0.30, C:0.29, G:0.16, T:0.25
Consensus pattern (128 bp):
GCCGCTAAAGAACATGACCTTTAGTCGCGCTTTTCCCACAAATCCGCTATAGAACATGACCTTTA
GCGGCGCTTTTCCATCAAACACCGCTAAAGAACATGACCTTTAGCGGCGCTTTTACCACAAAC
Found at i:17666584 original size:85 final size:86
Alignment explanation
Indices: 17666427--17666789 Score: 443
Period size: 85 Copynumber: 4.3 Consensus size: 86
17666417 TAAAAAAAGG
* *
17666427 CCGCTATAGAACATGACCTTTAGTGGCGCTTTTTCCACAAATGCCGCTATAGAACATGACCTTTA
1 CCGCTATAGAACATGACCTTTAGTGGCGCTTTTTCCACAAACGCCGCTAAAGAACATGACCTTTA
*
17666492 GCGGCGCTTTTTCCATC-AACA
66 GCGGCGCTTTTCCCA-CAAACA
*
17666513 CCGCTATAGAACATGACCTTTAGTGGCGC-TTTACCACAAACGCCGCTAAAGAACATGACCTTTA
1 CCGCTATAGAACATGACCTTTAGTGGCGCTTTTTCCACAAACGCCGCTAAAGAACATGACCTTTA
*
17666577 GTC-GCGCTTTTCCCACAATCA
66 G-CGGCGCTTTTCCCACAAACA
* * * * *
17666598 CAGCTAAAGAACATGACCTTTAGCGGCAC-TTTTCCTACAAACGCCGCTAAAGAACGTGACCTTT
1 CCGCTATAGAACATGACCTTTAGTGGCGCTTTTTCC-ACAAACGCCGCTAAAGAACATGACCTTT
*
17666662 AGCGGCGCTTTTCCCACAAACG
65 AGCGGCGCTTTTCCCACAAACA
* * * * * * *
17666684 CCTCTATAAAACA-GACCTTTAGTCGCGCTTTTGCCACAAACACCACTATAA-AACA-AACCTTT
1 CCGCTATAGAACATGACCTTTAGTGGCGCTTTTTCCACAAACGCCGCTA-AAGAACATGACCTTT
* *
17666746 AGCGGCGCTATTCTCACAAACA
65 AGCGGCGCTTTTCCCACAAACA
* *
17666768 CCGCTAAAGAAGATGACCTTTA
1 CCGCTATAGAACATGACCTTTA
17666790 AAAAAATATT
Statistics
Matches: 238, Mismatches: 32, Indels: 15
0.84 0.11 0.05
Matches are distributed among these distances:
84 35 0.15
85 112 0.47
86 91 0.38
ACGTcount: A:0.30, C:0.29, G:0.16, T:0.25
Consensus pattern (86 bp):
CCGCTATAGAACATGACCTTTAGTGGCGCTTTTTCCACAAACGCCGCTAAAGAACATGACCTTTA
GCGGCGCTTTTCCCACAAACA
Found at i:17670262 original size:17 final size:17
Alignment explanation
Indices: 17670212--17670262 Score: 66
Period size: 19 Copynumber: 2.9 Consensus size: 17
17670202 TGGAAACATG
*
17670212 ATCTTCGAAGATATGCA
1 ATCTTAGAAGATATGCA
*
17670229 ATCTTAGATATGATATGTA
1 ATCTTAGA-A-GATATGCA
17670248 ATCTTAGAAGATATG
1 ATCTTAGAAGATATG
17670263 ATTTTGTAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 13 0.43
18 2 0.07
19 15 0.50
ACGTcount: A:0.37, C:0.10, G:0.18, T:0.35
Consensus pattern (17 bp):
ATCTTAGAAGATATGCA
Found at i:17670262 original size:22 final size:21
Alignment explanation
Indices: 17670234--17670291 Score: 71
Period size: 22 Copynumber: 2.7 Consensus size: 21
17670224 ATGCAATCTT
* *
17670234 AGATATGATATGTAATCTTAG
1 AGATATGATTTGTAATCATAG
17670255 AAGATATGATTTTGTAATCATAG
1 -AGATATGA-TTTGTAATCATAG
*
17670278 AGATTTGATTTGTA
1 AGATATGATTTGTA
17670292 GATACCCTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 6 0.19
22 15 0.47
23 11 0.34
ACGTcount: A:0.36, C:0.03, G:0.19, T:0.41
Consensus pattern (21 bp):
AGATATGATTTGTAATCATAG
Found at i:17675396 original size:22 final size:23
Alignment explanation
Indices: 17675368--17675425 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 23
17675358 ATGCAATCTT
*
17675368 AGATATG-TTATGTAATCTTAGA
1 AGATATGATTATGTAATCATAGA
*
17675390 AGATATGATTTTGTAATCATAG-
1 AGATATGATTATGTAATCATAGA
*
17675412 AGATTTGATT-TGTA
1 AGATATGATTATGTA
17675426 GATACCCTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 4 0.12
22 16 0.50
23 12 0.38
ACGTcount: A:0.34, C:0.03, G:0.19, T:0.43
Consensus pattern (23 bp):
AGATATGATTATGTAATCATAGA
Found at i:17677587 original size:27 final size:26
Alignment explanation
Indices: 17677539--17677594 Score: 85
Period size: 26 Copynumber: 2.1 Consensus size: 26
17677529 GGATTTCGGG
* *
17677539 GGGAAAAAAAGTAAAAAGAAAATGTT
1 GGGAAAAAAAGTAAAAAAAAAAGGTT
17677565 GGGAAAAAAAGTAAAAGAAAAAAGGTT
1 GGGAAAAAAAGTAAAA-AAAAAAGGTT
17677592 GGG
1 GGG
17677595 TTACAAAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
26 16 0.59
27 11 0.41
ACGTcount: A:0.59, C:0.00, G:0.29, T:0.12
Consensus pattern (26 bp):
GGGAAAAAAAGTAAAAAAAAAAGGTT
Found at i:17678762 original size:15 final size:15
Alignment explanation
Indices: 17678742--17678794 Score: 65
Period size: 15 Copynumber: 3.7 Consensus size: 15
17678732 TCATAAAACC
17678742 AAACCCTTAAACCCT
1 AAACCCTTAAACCCT
* *
17678757 AAACCCCTAACCCCT
1 AAACCCTTAAACCCT
17678772 AAA-CCTTAAACCC-
1 AAACCCTTAAACCCT
*
17678785 CAACCCTTAA
1 AAACCCTTAA
17678795 TCCATCATCT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
13 2 0.06
14 14 0.44
15 16 0.50
ACGTcount: A:0.40, C:0.43, G:0.00, T:0.17
Consensus pattern (15 bp):
AAACCCTTAAACCCT
Found at i:17678764 original size:43 final size:43
Alignment explanation
Indices: 17678700--17678794 Score: 111
Period size: 43 Copynumber: 2.2 Consensus size: 43
17678690 TCTAAGCCCT
* * * * *
17678700 AAACCCCT-AACCCTTATCCCCTAACCTCTAAATCATAAAACC
1 AAACCCTTAAACCCTAAACCCCTAACCCCTAAACCATAAAACC
* *
17678742 AAACCCTTAAACCCTAAACCCCTAACCCCTAAACCTTAAACCC
1 AAACCCTTAAACCCTAAACCCCTAACCCCTAAACCATAAAACC
*
17678785 CAACCCTTAA
1 AAACCCTTAA
17678795 TCCATCATCT
Statistics
Matches: 44, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
42 7 0.16
43 37 0.84
ACGTcount: A:0.39, C:0.42, G:0.00, T:0.19
Consensus pattern (43 bp):
AAACCCTTAAACCCTAAACCCCTAACCCCTAAACCATAAAACC
Found at i:17678768 original size:14 final size:14
Alignment explanation
Indices: 17678691--17678776 Score: 59
Period size: 14 Copynumber: 5.9 Consensus size: 14
17678681 ACTAATTAAT
17678691 CTAAGCCCTAAACCC
1 CTAA-CCCTAAACCC
* *
17678706 CTAACCCTTATCCC
1 CTAACCCTAAACCC
*
17678720 CTAACCTCTAAA-TC
1 CTAACC-CTAAACCC
* *
17678734 ATAAAACC-AAACCC
1 CT-AACCCTAAACCC
*
17678748 TTAAACCCTAAACCC
1 CT-AACCCTAAACCC
17678763 CTAACCCCTAAACC
1 CTAA-CCCTAAACC
17678777 TTAAACCCCA
Statistics
Matches: 55, Mismatches: 11, Indels: 10
0.72 0.14 0.13
Matches are distributed among these distances:
13 3 0.05
14 26 0.47
15 26 0.47
ACGTcount: A:0.37, C:0.43, G:0.01, T:0.19
Consensus pattern (14 bp):
CTAACCCTAAACCC
Found at i:17678774 original size:22 final size:22
Alignment explanation
Indices: 17678708--17678790 Score: 71
Period size: 22 Copynumber: 3.9 Consensus size: 22
17678698 CTAAACCCCT
* * *
17678708 AACCCTTATCCCCTAACCTCTA
1 AACCCTAAACCCCTAACCCCTA
* * * * *
17678730 AATCATAAA-ACCAAACCCTTA
1 AACCCTAAACCCCTAACCCCTA
17678751 AACCCTAAACCCCTAACCCCTA
1 AACCCTAAACCCCTAACCCCTA
*
17678773 AACCTTAAACCCC-AACCC
1 AACCCTAAACCCCTAACCC
17678791 TTAATCCATC
Statistics
Matches: 46, Mismatches: 14, Indels: 3
0.73 0.22 0.05
Matches are distributed among these distances:
21 20 0.43
22 26 0.57
ACGTcount: A:0.39, C:0.43, G:0.00, T:0.18
Consensus pattern (22 bp):
AACCCTAAACCCCTAACCCCTA
Found at i:17678781 original size:7 final size:7
Alignment explanation
Indices: 17678742--17678784 Score: 50
Period size: 7 Copynumber: 5.9 Consensus size: 7
17678732 TCATAAAACC
17678742 AAACCCTT
1 AAACCC-T
17678750 AAACCCT
1 AAACCCT
17678757 AAACCCCT
1 AAA-CCCT
*
17678765 AACCCCT
1 AAACCCT
*
17678772 AAACCTT
1 AAACCCT
17678779 AAACCC
1 AAACCC
17678785 CAACCCTTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
7 18 0.60
8 12 0.40
ACGTcount: A:0.40, C:0.44, G:0.00, T:0.16
Consensus pattern (7 bp):
AAACCCT
Found at i:17678847 original size:14 final size:14
Alignment explanation
Indices: 17678828--17678874 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
17678818 TAGTAACTCC
*
17678828 TAAACCTTAAACCT
1 TAAACCATAAACCT
*
17678842 TAAACCATATA-CT
1 TAAACCATAAACCT
*
17678855 CTAAACCATAAACCC
1 -TAAACCATAAACCT
17678870 TAAAC
1 TAAAC
17678875 TATGTGATAA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
13 2 0.07
14 24 0.89
15 1 0.04
ACGTcount: A:0.47, C:0.30, G:0.00, T:0.23
Consensus pattern (14 bp):
TAAACCATAAACCT
Found at i:17679540 original size:40 final size:40
Alignment explanation
Indices: 17679410--17679540 Score: 145
Period size: 40 Copynumber: 3.3 Consensus size: 40
17679400 TACTTTTTTT
* * * *
17679410 GCGGCGTTTTTTAAAAAGCATCGCTAATGATCGACCTATA
1 GCGGCGTTTTTCAAAAAGCGTCGCTAATGCTCGATCTATA
* * * * *
17679450 GTGGTGTTTCTCAAAAAGCGTCACTAATTCTCGATCTATA
1 GCGGCGTTTTTCAAAAAGCGTCGCTAATGCTCGATCTATA
* * *
17679490 GTGGCATTTTTCAAAAAGCGCCGCTAATGCTCGATCTATA
1 GCGGCGTTTTTCAAAAAGCGTCGCTAATGCTCGATCTATA
*
17679530 GCGGTGTTTTT
1 GCGGCGTTTTT
17679541 TAATCCAAAC
Statistics
Matches: 73, Mismatches: 18, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
40 73 1.00
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.34
Consensus pattern (40 bp):
GCGGCGTTTTTCAAAAAGCGTCGCTAATGCTCGATCTATA
Found at i:17681596 original size:3 final size:3
Alignment explanation
Indices: 17681588--17681626 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
17681578 ATAGCCTCAA
17681588 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
17681627 TTTTGAGCAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:17683734 original size:17 final size:17
Alignment explanation
Indices: 17683712--17683760 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
17683702 AAATTAAAAT
17683712 ATCAATTTTAAGGATAA
1 ATCAATTTTAAGGATAA
*
17683729 ATCAA-TTTAA--A-AT
1 ATCAATTTTAAGGATAA
17683742 ATCAATTTTAAGGATAA
1 ATCAATTTTAAGGATAA
17683759 AT
1 AT
17683761 ATTTTTTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 8
0.72 0.06 0.22
Matches are distributed among these distances:
13 6 0.23
14 6 0.23
16 6 0.23
17 8 0.31
ACGTcount: A:0.49, C:0.06, G:0.08, T:0.37
Consensus pattern (17 bp):
ATCAATTTTAAGGATAA
Found at i:17688161 original size:90 final size:90
Alignment explanation
Indices: 17688023--17688328 Score: 323
Period size: 90 Copynumber: 3.4 Consensus size: 90
17688013 CACAACAAAT
* * * ** * * *
17688023 TTTTTTTTACATATACAAGAA-AATACGAACATACTACAAAACTAATATACGAAATTATATAATT
1 TTTTATTTACAGATACAAAAATAATACGAACATTTTACAAAACTGATATACGAAAATATAAAATT
** *
17688087 CAACCAACAAATAATACCGACTAAA
66 TGACCAACAAATAATACTGACTAAA
* * * ** *
17688112 TTTTATTTACATATAAAAAAATAATACGAACATTTTAGAAATTTGATATACAAAAATATAAAATT
1 TTTTATTTACAGATACAAAAATAATACGAACATTTTACAAAACTGATATACGAAAATATAAAATT
*
17688177 TGACCGACAAATAATA-TGAACTAAAA
66 TGACCAACAAATAATACTG-ACT-AAA
* * *
17688203 TATTT-TTT-CAGATCCAAAAATAATACAAACATTTTACAAAACTGATATGCGAAAATATAAAAT
1 T-TTTATTTACAGATACAAAAATAATACGAACATTTTACAAAACTGATATACGAAAATATAAAAT
*
17688266 TTGACCAATAAATAATACTGACTAAA
65 TTGACCAACAAATAATACTGACTAAA
* * * *
17688292 ATTGATTTACGGATACAAAAATAATACGAATATTTTA
1 TTTTATTTACAGATACAAAAATAATACGAACATTTTA
17688329 AATAGTAGTT
Statistics
Matches: 177, Mismatches: 33, Indels: 13
0.79 0.15 0.06
Matches are distributed among these distances:
88 2 0.01
89 25 0.14
90 138 0.78
91 9 0.05
92 3 0.02
ACGTcount: A:0.50, C:0.12, G:0.07, T:0.31
Consensus pattern (90 bp):
TTTTATTTACAGATACAAAAATAATACGAACATTTTACAAAACTGATATACGAAAATATAAAATT
TGACCAACAAATAATACTGACTAAA
Found at i:17690204 original size:16 final size:17
Alignment explanation
Indices: 17690183--17690217 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
17690173 TTATATAAGA
*
17690183 TAAATAAAACTAT-TTT
1 TAAATAAAAATATATTT
17690199 TAAATAAAAATATATTT
1 TAAATAAAAATATATTT
17690216 TA
1 TA
17690218 TTTGAATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (17 bp):
TAAATAAAAATATATTT
Found at i:17690983 original size:94 final size:96
Alignment explanation
Indices: 17690865--17691083 Score: 277
Period size: 94 Copynumber: 2.3 Consensus size: 96
17690855 TAAAATTTTT
* * * * * *
17690865 AAAAATTATATTTTA-TTTGATGGAGTCATTAATAATGGCGCCAACAGTGTATTGTACTTGTTTT
1 AAAAAATATATTTTATTTTG-TGGAGTCATTAAGAATGACACCAACAGTGTACTGTACCTGTTTT
17690929 TTT-AAATG-CATTTTTTTAATTTAAATATAA
65 TTTAAAATGTCATTTTTTTAATTTAAATATAA
* *
17690959 AAAAAATATATTTTATTTTGTGGAGTCATTAAGAATGATACCACCAGTGTACTGTACCTGTTTTT
1 AAAAAATATATTTTATTTTGTGGAGTCATTAAGAATGACACCAACAGTGTACTGTACCTGTTTTT
**
17691024 TTAAAATGTGTTTTTTTTAATTTAAATATAA
66 TTAAAATGTCATTTTTTTAATTTAAATATAA
* *
17691055 AAAATAA-A-ATTTTATTTGGTGGAGCCATT
1 AAAA-AATATATTTTATTTTGTGGAGTCATT
17691084 TCCTTTGGGG
Statistics
Matches: 109, Mismatches: 12, Indels: 7
0.85 0.09 0.05
Matches are distributed among these distances:
94 54 0.50
95 28 0.26
96 25 0.23
97 2 0.02
ACGTcount: A:0.35, C:0.08, G:0.13, T:0.44
Consensus pattern (96 bp):
AAAAAATATATTTTATTTTGTGGAGTCATTAAGAATGACACCAACAGTGTACTGTACCTGTTTTT
TTAAAATGTCATTTTTTTAATTTAAATATAA
Found at i:17692326 original size:17 final size:17
Alignment explanation
Indices: 17692300--17692339 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
17692290 TTAGAATTGG
* *
17692300 ATTAAAAAATTTATTTA
1 ATTAATAAATTAATTTA
17692317 ATTAATAAATTAATTTA
1 ATTAATAAATTAATTTA
*
17692334 GTTAAT
1 ATTAAT
17692340 TCAATCAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (17 bp):
ATTAATAAATTAATTTA
Found at i:17692352 original size:22 final size:21
Alignment explanation
Indices: 17692307--17692364 Score: 71
Period size: 22 Copynumber: 2.7 Consensus size: 21
17692297 TGGATTAAAA
*
17692307 AATTTATTTAATTAATAAATT
1 AATTTAGTTAATTAATAAATT
*
17692328 AATTTAGTTAATTCAATCAATT
1 AATTTAGTTAATT-AATAAATT
* *
17692350 AATTTAATTGATTAA
1 AATTTAGTTAATTAA
17692365 ATAGATAATA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 14 0.44
22 18 0.56
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.48
Consensus pattern (21 bp):
AATTTAGTTAATTAATAAATT
Found at i:17705545 original size:20 final size:20
Alignment explanation
Indices: 17705520--17705559 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
17705510 GAACATATAT
17705520 TTCATCTTCATATATGCTTA
1 TTCATCTTCATATATGCTTA
17705540 TTCATCTTCATATATGCTTA
1 TTCATCTTCATATATGCTTA
17705560 CCAACCCTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.20, G:0.05, T:0.50
Consensus pattern (20 bp):
TTCATCTTCATATATGCTTA
Found at i:17716678 original size:27 final size:27
Alignment explanation
Indices: 17716640--17716694 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
17716630 GCGAATAGAA
17716640 AACGTTGTAGACTGAGTACCATCATCT
1 AACGTTGTAGACTGAGTACCATCATCT
17716667 AACGTTGTAGACTGAGTACCATCATCT
1 AACGTTGTAGACTGAGTACCATCATCT
17716694 A
1 A
17716695 TGTTGTTTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.29
Consensus pattern (27 bp):
AACGTTGTAGACTGAGTACCATCATCT
Found at i:17717560 original size:12 final size:12
Alignment explanation
Indices: 17717543--17717567 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
17717533 GGAAATCAAA
17717543 GTTTGAAGCTTG
1 GTTTGAAGCTTG
17717555 GTTTGAAGCTTG
1 GTTTGAAGCTTG
17717567 G
1 G
17717568 CTGAAGCTCA
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:0.16, C:0.08, G:0.36, T:0.40
Consensus pattern (12 bp):
GTTTGAAGCTTG
Found at i:17725378 original size:23 final size:23
Alignment explanation
Indices: 17725352--17725396 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
17725342 GAGTTTAATA
*
17725352 TTAAGAGTTAAATCAACAATTAT
1 TTAAAAGTTAAATCAACAATTAT
* *
17725375 TTAAAATTTAAATCAACTATTA
1 TTAAAAGTTAAATCAACAATTA
17725397 AATTAAATAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.49, C:0.09, G:0.04, T:0.38
Consensus pattern (23 bp):
TTAAAAGTTAAATCAACAATTAT
Found at i:17725404 original size:23 final size:23
Alignment explanation
Indices: 17725359--17725403 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
17725349 ATATTAAGAG
*
17725359 TTAAATCAACAATTATTTAAAAT
1 TTAAATCAACAATTAATTAAAAT
*
17725382 TTAAATCAACTATTAAATTAAA
1 TTAAATCAACAATT-AATTAAA
17725404 TAGATTATTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (23 bp):
TTAAATCAACAATTAATTAAAAT
Found at i:17725472 original size:8 final size:8
Alignment explanation
Indices: 17725456--17725506 Score: 52
Period size: 8 Copynumber: 6.4 Consensus size: 8
17725446 TTAATTAACT
17725456 AATTA-AA
1 AATTATAA
17725463 AATTATAA
1 AATTATAA
*
17725471 AATATTTAA
1 AAT-TATAA
*
17725480 AA-TAAAA
1 AATTATAA
17725487 ACATTATAA
1 A-ATTATAA
17725496 AATTATAA
1 AATTATAA
17725504 AAT
1 AAT
17725507 ATTGATTTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
7 9 0.25
8 16 0.44
9 11 0.31
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (8 bp):
AATTATAA
Found at i:17725494 original size:25 final size:23
Alignment explanation
Indices: 17725460--17725507 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 23
17725450 TTAACTAATT
*
17725460 AAAAATTATAAAATATTTAAAATA
1 AAAAATTATAAAAT-TATAAAATA
17725484 AAAACATTATAAAATTATAAAATA
1 AAAA-ATTATAAAATTATAAAATA
17725508 TTGATTTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 12 0.55
25 10 0.45
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (23 bp):
AAAAATTATAAAATTATAAAATA
Found at i:17726701 original size:2 final size:2
Alignment explanation
Indices: 17726694--17726719 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
17726684 AGGTGTCTAA
17726694 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
17726720 CACCTTGAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17729945 original size:2 final size:2
Alignment explanation
Indices: 17729940--17729968 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
17729930 AAAAAAAAAA
17729940 AT 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 AT A
17729969 ACTGGTCGAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:17732662 original size:17 final size:17
Alignment explanation
Indices: 17732640--17732690 Score: 68
Period size: 16 Copynumber: 3.0 Consensus size: 17
17732630 TTTATTTTTT
*
17732640 ATATAAAAAAATTAAAA
1 ATATAAAAACATTAAAA
*
17732657 ATAT-AATACATTAAAA
1 ATATAAAAACATTAAAA
17732673 ATACTAAAAACATTAAAA
1 ATA-TAAAAACATTAAAA
17732691 TAAATGTTTC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
16 13 0.45
17 5 0.17
18 11 0.38
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.25
Consensus pattern (17 bp):
ATATAAAAACATTAAAA
Found at i:17732894 original size:21 final size:22
Alignment explanation
Indices: 17732860--17732915 Score: 78
Period size: 21 Copynumber: 2.6 Consensus size: 22
17732850 AGTAGCAAGG
*
17732860 ACAATAAAACAGTGAGAAAA-A
1 ACAACAAAACAGTGAGAAAACA
* *
17732881 ATAACAAAATAGTGAGAAAACA
1 ACAACAAAACAGTGAGAAAACA
17732903 ACAACAAAACAGT
1 ACAACAAAACAGT
17732916 AAATTTTTTC
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 17 0.59
22 12 0.41
ACGTcount: A:0.64, C:0.12, G:0.12, T:0.11
Consensus pattern (22 bp):
ACAACAAAACAGTGAGAAAACA
Found at i:17734576 original size:17 final size:17
Alignment explanation
Indices: 17734554--17734589 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
17734544 TAATATTGGA
17734554 GAATTTGATCA-ATACTT
1 GAATTTG-TCAGATACTT
17734571 GAATTTGTCAGATACTT
1 GAATTTGTCAGATACTT
17734588 GA
1 GA
17734590 TTCTCGATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 3 0.17
17 15 0.83
ACGTcount: A:0.33, C:0.11, G:0.17, T:0.39
Consensus pattern (17 bp):
GAATTTGTCAGATACTT
Found at i:17735476 original size:28 final size:30
Alignment explanation
Indices: 17735412--17735475 Score: 87
Period size: 29 Copynumber: 2.2 Consensus size: 30
17735402 TTCAATGCGG
*
17735412 ATTTTTAAAAGAATTAAATATATATTTTTT
1 ATTTTTAAAAGAATAAAATATATATTTTTT
*
17735442 ATTTTTAAAA-AATAAAATGTA-ATTTTATT
1 ATTTTTAAAAGAATAAAATATATATTTT-TT
17735471 ATTTT
1 ATTTT
17735476 ATAGAGAGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
28 5 0.16
29 16 0.52
30 10 0.32
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (30 bp):
ATTTTTAAAAGAATAAAATATATATTTTTT
Found at i:17735783 original size:31 final size:29
Alignment explanation
Indices: 17735743--17735817 Score: 87
Period size: 31 Copynumber: 2.5 Consensus size: 29
17735733 AAATTTTAAA
* *
17735743 TTAATAATGATAAAATTATACTTTAACCTT
1 TTAAAAATGATAAAATT-TAATTTAACCTT
*
17735773 CTTAAAAATGATATAAATTTAATTTAATCTT
1 -TTAAAAATGATA-AAATTTAATTTAACCTT
*
17735804 TTAAAAATTATAAA
1 TTAAAAATGATAAA
17735818 GATATAGACT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
29 2 0.05
30 11 0.28
31 21 0.54
32 5 0.13
ACGTcount: A:0.48, C:0.07, G:0.03, T:0.43
Consensus pattern (29 bp):
TTAAAAATGATAAAATTTAATTTAACCTT
Found at i:17742191 original size:75 final size:75
Alignment explanation
Indices: 17742110--17742256 Score: 222
Period size: 75 Copynumber: 2.0 Consensus size: 75
17742100 TAAGATCTAT
* * * *
17742110 TTTTCTTGAGTTTGAATTTTAGATTCAGAGTAATTATAATTGCAATAATCTAGCTATTATATTTC
1 TTTTCTTGAGTTTGAATTCTAGATTCAGAGTAACTATAATTGCAATAATATAGCTATTATAATTC
17742175 AAATCTAGAA
66 AAATCTAGAA
** * *
17742185 TTTTCTTGAGTTTGAATTCTAGATTTGGAGTAACTATAATTGCAATAATATAGTTGTTATAATTC
1 TTTTCTTGAGTTTGAATTCTAGATTCAGAGTAACTATAATTGCAATAATATAGCTATTATAATTC
17742250 AAATCTA
66 AAATCTA
17742257 AAAGTTGAAT
Statistics
Matches: 64, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
75 64 1.00
ACGTcount: A:0.34, C:0.09, G:0.13, T:0.44
Consensus pattern (75 bp):
TTTTCTTGAGTTTGAATTCTAGATTCAGAGTAACTATAATTGCAATAATATAGCTATTATAATTC
AAATCTAGAA
Found at i:17744187 original size:30 final size:31
Alignment explanation
Indices: 17744145--17744202 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
17744135 AATAGTTCAT
*
17744145 TTCTTTTATAATT-TGTCCCTTTTATTTTAG
1 TTCTTTTATAATTAAGTCCCTTTTATTTTAG
*
17744175 TTCTTTCT-TAATTAAGTCCTTTTTATTT
1 TTCTTT-TATAATTAAGTCCCTTTTATTT
17744203 ATTCATCTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 11 0.46
31 13 0.54
ACGTcount: A:0.17, C:0.14, G:0.05, T:0.64
Consensus pattern (31 bp):
TTCTTTTATAATTAAGTCCCTTTTATTTTAG
Found at i:17745639 original size:135 final size:136
Alignment explanation
Indices: 17745396--17745779 Score: 612
Period size: 135 Copynumber: 2.8 Consensus size: 136
17745386 CACAACTATA
*
17745396 AAAAAAAAATTCTTTAAAACGAAGGCGAGATTCGATATTTGGCAATTCACAGAATAGTGCCCTAA
1 AAAAAAAAATTCTTTAAAACGAAGGCGAGATTCGATATTTGGCAATTCACGGAATAGTGCCCTAA
* *
17745461 CGTGTTGGGTTGCAATTTCGCGTTTGCTCAAAATAATCAAATATCCTTTCACAATTTCACTCATG
66 CGTGTTGGGTTGCAATTTTGCGTTTGCTCAAAATAATCAAATATCCCTTCACAATTTCACTCATG
17745526 CCTTTT
131 CCTTTT
*
17745532 -AAAAAAAATTCTTTAAAACGAAGGCGAGATTCGATATTTTGCAATTCACGGAATAGTGCCCTAA
1 AAAAAAAAATTCTTTAAAACGAAGGCGAGATTCGATATTTGGCAATTCACGGAATAGTGCCCTAA
*
17745596 TGTGTTGGGTTGCAATTTTGCGTTTGCTCAAAATAATCAAATATCCCTTCACAATTTCACTCATG
66 CGTGTTGGGTTGCAATTTTGCGTTTGCTCAAAATAATCAAATATCCCTTCACAATTTCACTCATG
17745661 CCTTTT
131 CCTTTT
* * * *
17745667 AAAAAAAAATTCTTTAAAACGAAGGCGATG-TGCGATATTTGGCAATTCGCGGAATCGTGCACTA
1 AAAAAAAAATTCTTTAAAACGAAGGCGA-GATTCGATATTTGGCAATTCACGGAATAGTGCCCTA
* * * *
17745731 ACGTGCTGGGTTGCAACTTCT-CGTTTGTTTAAAATAATCAAATATCCCT
65 ACGTGTTGGGTTGCAA-TTTTGCGTTTGCTCAAAATAATCAAATATCCCT
17745780 CCATATTTTA
Statistics
Matches: 230, Mismatches: 15, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
135 130 0.57
136 96 0.42
137 4 0.02
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Consensus pattern (136 bp):
AAAAAAAAATTCTTTAAAACGAAGGCGAGATTCGATATTTGGCAATTCACGGAATAGTGCCCTAA
CGTGTTGGGTTGCAATTTTGCGTTTGCTCAAAATAATCAAATATCCCTTCACAATTTCACTCATG
CCTTTT
Found at i:17750099 original size:8 final size:8
Alignment explanation
Indices: 17750086--17750129 Score: 63
Period size: 8 Copynumber: 5.4 Consensus size: 8
17750076 GAGATCTTCG
17750086 AAAAATAA
1 AAAAATAA
17750094 AAAAATAA
1 AAAAATAA
17750102 AAAAATAA
1 AAAAATAA
17750110 ATAAAATAA
1 A-AAAATAA
17750119 ATAAAA-AA
1 A-AAAATAA
17750127 AAA
1 AAA
17750130 GAGAAAGAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
7 2 0.06
8 20 0.57
9 13 0.37
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (8 bp):
AAAAATAA
Found at i:17750104 original size:9 final size:9
Alignment explanation
Indices: 17750086--17750128 Score: 50
Period size: 9 Copynumber: 4.6 Consensus size: 9
17750076 GAGATCTTCG
17750086 AAAAATAAA
1 AAAAATAAA
*
17750095 AAAATAAAAA
1 AAAA-ATAAA
17750105 AATAAATAAA
1 AA-AAATAAA
*
17750115 ATAAATAAA
1 AAAAATAAA
17750124 AAAAA
1 AAAAA
17750129 AGAGAAAGAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
9 15 0.54
10 11 0.39
11 2 0.07
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (9 bp):
AAAAATAAA
Found at i:17751592 original size:131 final size:132
Alignment explanation
Indices: 17751357--17752292 Score: 1221
Period size: 131 Copynumber: 7.0 Consensus size: 132
17751347 TGGGCCTATG
* * * ** *
17751357 AGGCTAAAATTTTAGATCTTGTTTCCTTGAAATTAAAGTGAAGCAGATCGAAGACGGCAAATCTG
1 AGGCTAAAATTTCAGATCTTGTTTCCCTGAAGTTGCAGTGAAGCAGATCGAAGACGGCGAATCTG
*
17751422 AGCTTCCTGAAGTTGTAGTGAAGCAGATTTAAGCCACCAACCTAGCTCCCTAAAGTTGTAGTGGA
66 AGCTTCCTGAAGTTGCAGTGAAGCAGATTTAAGCCACCAACCTAGCTCCCTAAAGTTGTAGTGGA
17751487 GT
131 GT
*
17751489 AGGCTAAAATTTCAGATCTTGTTTCCCTGAAGTT-CAGTGAAGCAGATCAAAGACGGCGAATCTG
1 AGGCTAAAATTTCAGATCTTGTTTCCCTGAAGTTGCAGTGAAGCAGATCGAAGACGGCGAATCTG
*
17751553 AGCTTCTTGAAGTTGCAGTGAAGCAGATTTAAGCCACCAACCTAGCTCCCTAAAGTTGTAGTGGA
66 AGCTTCCTGAAGTTGCAGTGAAGCAGATTTAAGCCACCAACCTAGCTCCCTAAAGTTGTAGTGGA
17751618 GT
131 GT
*
17751620 AGGCTAAAATTTCAGATCTTATTTCCCTGAAGTTGCAGTGAAGCAGATCGAAGACGGCGAATCTG
1 AGGCTAAAATTTCAGATCTTGTTTCCCTGAAGTTGCAGTGAAGCAGATCGAAGACGGCGAATCTG
17751685 AGCTTCCTGAAGCTTCCTGAAGTTACAGTGAAGCAGATTTAAGCCACCAACCTAGCTCCCTAAAG
66 AGCTTCCTGAAG--T--T---G---CAGTGAAGCAGATTTAAGCCACCAACCTAGCTCCCTAAAG
17751750 TTGTAGTGGAGT
121 TTGTAGTGGAGT
* * *
17751762 AGGCTAAAATTTCAGATCTTATTTCCCTGAAGTTACAGTGAAGCAGATTGAAGACGGCGAATCTG
1 AGGCTAAAATTTCAGATCTTGTTTCCCTGAAGTTGCAGTGAAGCAGATCGAAGACGGCGAATCTG
17751827 AGCTTCCTGAAGTTGCAGTGAAGCAGATTTAAGCCACCAACCTAGCTCCCTAAAGTTGTAGTGGA
66 AGCTTCCTGAAGTTGCAGTGAAGCAGATTTAAGCCACCAACCTAGCTCCCTAAAGTTGTAGTGGA
17751892 GT
131 GT
* * *
17751894 AGGCTAAAATTTCAGATCTTGTTTCCCTGAAGTTGTAGTGAAACAGATCGAAGATGGCGAATCTG
1 AGGCTAAAATTTCAGATCTTGTTTCCCTGAAGTTGCAGTGAAGCAGATCGAAGACGGCGAATCTG
* * * *
17751959 AGTTTCCCGAAGTTGCAGTGAAGCAGATTTAAGCCACCATCCTAGCTCCCTAAGGTTGTAGTGGA
66 AGCTTCCTGAAGTTGCAGTGAAGCAGATTTAAGCCACCAACCTAGCTCCCTAAAGTTGTAGTGGA
17752024 GT
131 GT
* * **
17752026 AGGCTGAAGATTAT-AGATCTTGTTTCTCTG-AGATTGCAGTGGGGCAGATCGAAGACGGCGAAT
1 AGGCT-AAAATT-TCAGATCTTGTTTCCCTGAAG-TTGCAGTGAAGCAGATCGAAGACGGCGAAT
* * * *
17752089 CT-AGGCTTCCTGATGTTGCAGTAAAGCAGATTTAAG-CA--AGTCCTAGCTCTCTAAAGTTGTA
63 CTGA-GCTTCCTGAAGTTGCAGTGAAGCAGATTTAAGCCACCA-ACCTAGCTCCCTAAAGTTGTA
17752150 GTGGAGT
126 GTGGAGT
** * * * * * ***
17752157 AGGCTGAGGATTGT-AGATCTCGTCTCCCTGAAGTTGCAGTGAGGCAAATCAAAGACGATAAATC
1 AGGCT-AAAATT-TCAGATCTTGTTTCCCTGAAGTTGCAGTGAAGCAGATCGAAGACGGCGAATC
* * * *
17752221 TTG-GCTTCCTGAAGATGCAGCGAAGCAGATTTAAG-CA--AGTCCTAACTCCCTAAAGTTGTAG
64 -TGAGCTTCCTGAAGTTGCAGTGAAGCAGATTTAAGCCACCA-ACCTAGCTCCCTAAAGTTGTAG
*
17752282 TGAAGT
127 TGGAGT
*
17752288 GGGCT
1 AGGCT
17752293 GAAGATTGTA
Statistics
Matches: 730, Mismatches: 55, Indels: 39
0.89 0.07 0.05
Matches are distributed among these distances:
130 1 0.00
131 262 0.36
132 258 0.35
133 75 0.10
134 2 0.00
135 1 0.00
136 1 0.00
138 1 0.00
139 1 0.00
140 1 0.00
142 127 0.17
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.27
Consensus pattern (132 bp):
AGGCTAAAATTTCAGATCTTGTTTCCCTGAAGTTGCAGTGAAGCAGATCGAAGACGGCGAATCTG
AGCTTCCTGAAGTTGCAGTGAAGCAGATTTAAGCCACCAACCTAGCTCCCTAAAGTTGTAGTGGA
GT
Found at i:17751772 original size:142 final size:141
Alignment explanation
Indices: 17751560--17752213 Score: 773
Period size: 132 Copynumber: 4.8 Consensus size: 141
17751550 CTGAGCTTCT
17751560 TGAAGTTGCAGTGAAGCAGATTTAAGCCACCAACCTAGCTCCCTAAAGTTGTAGTGGAGTAGGCT
1 TGAAGTTGCAGTGAAGCAGATTTAAGCCACCAACCTAGCTCCCTAAAGTTGTAGTGGAGTAGGCT
17751625 AAAATTTCAGATCTTATTTCCCTGAAGTTGCAGTGAAGCAGATCGAAGACGGCGAATCTGAGCTT
66 AAAATTTCAGATCTTATTTCCCTGAAGTTGCAGTGAAGCAGATCGAAGACGGCGAATCTGAGCTT
17751690 CCTGAAGCTTCC
131 CCTGAAGC-TCC
*
17751702 TGAAGTTACAGTGAAGCAGATTTAAGCCACCAACCTAGCTCCCTAAAGTTGTAGTGGAGTAGGCT
1 TGAAGTTGCAGTGAAGCAGATTTAAGCCACCAACCTAGCTCCCTAAAGTTGTAGTGGAGTAGGCT
* *
17751767 AAAATTTCAGATCTTATTTCCCTGAAGTTACAGTGAAGCAGATTGAAGACGGCGAATCTGAG---
66 AAAATTTCAGATCTTATTTCCCTGAAGTTGCAGTGAAGCAGATCGAAGACGGCGAATCTGAGCTT
17751829 -CT-----TCC
131 CCTGAAGCTCC
17751834 TGAAGTTGCAGTGAAGCAGATTTAAGCCACCAACCTAGCTCCCTAAAGTTGTAGTGGAGTAGGCT
1 TGAAGTTGCAGTGAAGCAGATTTAAGCCACCAACCTAGCTCCCTAAAGTTGTAGTGGAGTAGGCT
* * * *
17751899 AAAATTTCAGATCTTGTTTCCCTGAAGTTGTAGTGAAACAGATCGAAGATGGCGAATCTGAG-TT
66 AAAATTTCAGATCTTATTTCCCTGAAGTTGCAGTGAAGCAGATCGAAGACGGCGAATCTGAGCTT
17751963 --T----C-CC
131 CCTGAAGCTCC
* *
17751967 -GAAGTTGCAGTGAAGCAGATTTAAGCCACCATCCTAGCTCCCTAAGGTTGTAGTGGAGTAGGCT
1 TGAAGTTGCAGTGAAGCAGATTTAAGCCACCAACCTAGCTCCCTAAAGTTGTAGTGGAGTAGGCT
* * * **
17752031 GAAGATTAT-AGATCTTGTTTCTCTG-AGATTGCAGTGGGGCAGATCGAAGACGGCGAATCT-AG
66 -AAAATT-TCAGATCTTATTTCCCTGAAG-TTGCAGTGAAGCAGATCGAAGACGGCGAATCTGA-
17752093 GCTTCCTG-A-----
127 GCTTCCTGAAGCTCC
* * *
17752102 T---GTTGCAGTAAAGCAGATTTAAG-CA--AGTCCTAGCTCTCTAAAGTTGTAGTGGAGTAGGC
1 TGAAGTTGCAGTGAAGCAGATTTAAGCCACCA-ACCTAGCTCCCTAAAGTTGTAGTGGAGTAGGC
** ** * * * *
17752161 TGAGGATTGT-AGATCTCGTCTCCCTGAAGTTGCAGTGAGGCAAATCAAAGACG
65 T-AAAATT-TCAGATCTTATTTCCCTGAAGTTGCAGTGAAGCAGATCGAAGACG
17752214 ATAAATCTTG
Statistics
Matches: 467, Mismatches: 30, Indels: 41
0.87 0.06 0.08
Matches are distributed among these distances:
130 1 0.00
131 72 0.15
132 192 0.41
133 72 0.15
134 3 0.01
136 1 0.00
138 2 0.00
142 124 0.27
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.27
Consensus pattern (141 bp):
TGAAGTTGCAGTGAAGCAGATTTAAGCCACCAACCTAGCTCCCTAAAGTTGTAGTGGAGTAGGCT
AAAATTTCAGATCTTATTTCCCTGAAGTTGCAGTGAAGCAGATCGAAGACGGCGAATCTGAGCTT
CCTGAAGCTCC
Found at i:17751897 original size:274 final size:271
Alignment explanation
Indices: 17751357--17752213 Score: 1159
Period size: 274 Copynumber: 3.2 Consensus size: 271
17751347 TGGGCCTATG
* * * ** *
17751357 AGGCTAAAATTTTAGATCTTGTTTCCTTGAAATTAAAGTGAAGCAGATCGAAGACGGCAAATCTG
1 AGGCTAAAATTTCAGATCTTGTTTCCCTGAAGTTGCAGTGAAGCAGATCGAAGACGGCGAATCTG
17751422 AGCTTCCTGAAG-T--T---G-T-AGTGAAGCAGATTTAAGCCACCAACCTAGCTCCCTAAAGTT
66 AGCTTCCTGAAGCTCCTGAAGTTCAGTGAAGCAGATTTAAGCCACCAACCTAGCTCCCTAAAGTT
*
17751479 GTAGTGGAGTAGGCTAAAATTTCAGATCTTGTTTCCCTGAAGTTCAGTGAAGCAGATCAAAGACG
131 GTAGTGGAGTAGGCTAAAATTTCAGATCTTGTTTCCCTGAAGTTCAGTGAAGCAGATCGAAGACG
*
17751544 GCGAATCTGAGCTTCTTGAAGTTGCAGTGAAGCAGATTTAAGCCACCAACCTAGCTCCCTAAAGT
196 GCGAATCTGAGCTTCCTGAAGTTGCAGTGAAGCAGATTTAAGCCACCAACCTAGCTCCCTAAAGT
17751609 TGTAGTGGAGT
261 TGTAGTGGAGT
*
17751620 AGGCTAAAATTTCAGATCTTATTTCCCTGAAGTTGCAGTGAAGCAGATCGAAGACGGCGAATCTG
1 AGGCTAAAATTTCAGATCTTGTTTCCCTGAAGTTGCAGTGAAGCAGATCGAAGACGGCGAATCTG
17751685 AGCTTCCTGAAGCTTCCTGAAGTTACAGTGAAGCAGATTTAAGCCACCAACCTAGCTCCCTAAAG
66 AGCTTCCTGAAGC-TCCTGAAGTT-CAGTGAAGCAGATTTAAGCCACCAACCTAGCTCCCTAAAG
* *
17751750 TTGTAGTGGAGTAGGCTAAAATTTCAGATCTTATTTCCCTGAAGTTACAGTGAAGCAGATTGAAG
129 TTGTAGTGGAGTAGGCTAAAATTTCAGATCTTGTTTCCCTGAAGTT-CAGTGAAGCAGATCGAAG
17751815 ACGGCGAATCTGAGCTTCCTGAAGTTGCAGTGAAGCAGATTTAAGCCACCAACCTAGCTCCCTAA
193 ACGGCGAATCTGAGCTTCCTGAAGTTGCAGTGAAGCAGATTTAAGCCACCAACCTAGCTCCCTAA
17751880 AGTTGTAGTGGAGT
258 AGTTGTAGTGGAGT
* * *
17751894 AGGCTAAAATTTCAGATCTTGTTTCCCTGAAGTTGTAGTGAAACAGATCGAAGATGGCGAATCTG
1 AGGCTAAAATTTCAGATCTTGTTTCCCTGAAGTTGCAGTGAAGCAGATCGAAGACGGCGAATCTG
* *
17751959 AG-TT--T----C-CC-GAAGTTGCAGTGAAGCAGATTTAAGCCACCATCCTAGCTCCCTAAGGT
66 AGCTTCCTGAAGCTCCTGAAGTT-CAGTGAAGCAGATTTAAGCCACCAACCTAGCTCCCTAAAGT
* * **
17752015 TGTAGTGGAGTAGGCTGAAGATTAT-AGATCTTGTTTCTCTG-AGATTGCAGTGGGGCAGATCGA
130 TGTAGTGGAGTAGGCT-AAAATT-TCAGATCTTGTTTCCCTGAAG-TT-CAGTGAAGCAGATCGA
* * * *
17752078 AGACGGCGAATCT-AGGCTTCCTGATGTTGCAGTAAAGCAGATTTAAG-CA--AGTCCTAGCTCT
191 AGACGGCGAATCTGA-GCTTCCTGAAGTTGCAGTGAAGCAGATTTAAGCCACCA-ACCTAGCTCC
17752139 CTAAAGTTGTAGTGGAGT
254 CTAAAGTTGTAGTGGAGT
** * * * * *
17752157 AGGCTGAGGATTGT-AGATCTCGTCTCCCTGAAGTTGCAGTGAGGCAAATCAAAGACG
1 AGGCT-AAAATT-TCAGATCTTGTTTCCCTGAAGTTGCAGTGAAGCAGATCGAAGACG
17752214 ATAAATCTTG
Statistics
Matches: 537, Mismatches: 39, Indels: 35
0.88 0.06 0.06
Matches are distributed among these distances:
262 1 0.00
263 101 0.19
264 105 0.20
265 81 0.15
266 1 0.00
267 2 0.00
270 1 0.00
271 2 0.00
273 86 0.16
274 157 0.29
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.27
Consensus pattern (271 bp):
AGGCTAAAATTTCAGATCTTGTTTCCCTGAAGTTGCAGTGAAGCAGATCGAAGACGGCGAATCTG
AGCTTCCTGAAGCTCCTGAAGTTCAGTGAAGCAGATTTAAGCCACCAACCTAGCTCCCTAAAGTT
GTAGTGGAGTAGGCTAAAATTTCAGATCTTGTTTCCCTGAAGTTCAGTGAAGCAGATCGAAGACG
GCGAATCTGAGCTTCCTGAAGTTGCAGTGAAGCAGATTTAAGCCACCAACCTAGCTCCCTAAAGT
TGTAGTGGAGT
Found at i:17752551 original size:44 final size:44
Alignment explanation
Indices: 17752488--17753153 Score: 973
Period size: 44 Copynumber: 15.1 Consensus size: 44
17752478 CAAGACCAGA
17752488 CAGATTTGGCGTCTCTGTATTGGCGGAGAGCAGATCGAAGATAG
1 CAGATTTGGCGTCTCTGTATTGGCGGAGAGCAGATCGAAGATAG
* *
17752532 CAGATTTGGCGTCTCTGTATTGGCGGAGAGCAGATCTAAGATAA
1 CAGATTTGGCGTCTCTGTATTGGCGGAGAGCAGATCGAAGATAG
*
17752576 CATATTTGGCGTCTCTGTATTGGCGGAGAGCAGATCGAAGATAG
1 CAGATTTGGCGTCTCTGTATTGGCGGAGAGCAGATCGAAGATAG
* *
17752620 CAGATTTGGTGTCTCTGTATTGACGGAGAGCAGATCGAAGATAG
1 CAGATTTGGCGTCTCTGTATTGGCGGAGAGCAGATCGAAGATAG
* *
17752664 CAGATTTGGCGTCTCTGTATTGGAGGAGAGCGGATCGAAGATAG
1 CAGATTTGGCGTCTCTGTATTGGCGGAGAGCAGATCGAAGATAG
* *
17752708 CAAATTTGGCGTCTCTGTATTGGAGGAGAGCAGATCGAAGATAG
1 CAGATTTGGCGTCTCTGTATTGGCGGAGAGCAGATCGAAGATAG
* *
17752752 CAGATTTGGCATCTCTGTATTGGCGGAAAGCAGATCGAAGATAG
1 CAGATTTGGCGTCTCTGTATTGGCGGAGAGCAGATCGAAGATAG
* * * *
17752796 TAGATTTGGCATCTCTGTAGTGGCGGAGAGCAGATCGAAGATAA
1 CAGATTTGGCGTCTCTGTATTGGCGGAGAGCAGATCGAAGATAG
* * * *
17752840 CAGATTTGGCATCTCTATAGTAGCGGAGAGCAGATCGAAGAT-G
1 CAGATTTGGCGTCTCTGTATTGGCGGAGAGCAGATCGAAGATAG
* * * * *
17752883 ACAGATTTGGCGTATCTGTGTTGACAGAGAGCAGATCAAAGAT-G
1 -CAGATTTGGCGTCTCTGTATTGGCGGAGAGCAGATCGAAGATAG
17752927 ACAGATTTGGCGTCTCTGTATTGGCGGAGAGCAGATCGAAGATAG
1 -CAGATTTGGCGTCTCTGTATTGGCGGAGAGCAGATCGAAGATAG
*
17752972 CAGATTTGGCGTTTCTGTATTGGCGGAGAGCAGATCGAAGATAG
1 CAGATTTGGCGTCTCTGTATTGGCGGAGAGCAGATCGAAGATAG
17753016 CAGATTTGGCGTCTCTGTATTGGCGGAGAGCAGATCGAAGAT-G
1 CAGATTTGGCGTCTCTGTATTGGCGGAGAGCAGATCGAAGATAG
* * * *
17753059 ACAAATTTGGCATCTCTGTATTGACAGAGAGCAGATCGAAGAT-G
1 -CAGATTTGGCGTCTCTGTATTGGCGGAGAGCAGATCGAAGATAG
* *
17753103 ACAGATTTGGCATCTCTGTATTGGCAGG-GAGCAGATCGAAGATAA
1 -CAGATTTGGCGTCTCTGTATTGGC-GGAGAGCAGATCGAAGATAG
17753148 CAGATT
1 CAGATT
17753154 GGTGTTCCCG
Statistics
Matches: 567, Mismatches: 50, Indels: 10
0.90 0.08 0.02
Matches are distributed among these distances:
43 1 0.00
44 564 0.99
45 2 0.00
ACGTcount: A:0.28, C:0.15, G:0.31, T:0.26
Consensus pattern (44 bp):
CAGATTTGGCGTCTCTGTATTGGCGGAGAGCAGATCGAAGATAG
Found at i:17754642 original size:30 final size:31
Alignment explanation
Indices: 17754600--17754657 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
17754590 AATAGTTCAT
*
17754600 TTCTTTTATAATT-TGTCCCTTTTATTTTAG
1 TTCTTTTATAATTAAGTCCCTTTTATTTTAG
*
17754630 TTCTTTCT-TAATTAAGTCCTTTTTATTT
1 TTCTTT-TATAATTAAGTCCCTTTTATTT
17754658 ATTCATCTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 11 0.46
31 13 0.54
ACGTcount: A:0.17, C:0.14, G:0.05, T:0.64
Consensus pattern (31 bp):
TTCTTTTATAATTAAGTCCCTTTTATTTTAG
Found at i:17756042 original size:136 final size:136
Alignment explanation
Indices: 17755853--17756101 Score: 410
Period size: 136 Copynumber: 1.8 Consensus size: 136
17755843 ACAACTATAA
*
17755853 AAAAAAAAATTCTTTAAAACGAAGGCGAGATTCGATATTTGGCAATTCACGGAATAGTGCCCTAA
1 AAAAAAAAATTCTTTAAAACGAAGGCGAGATGCGATATTTGGCAATTCACGGAATAGTGCCCTAA
* *
17755918 CGTGTTGGGTTGCAATTTCGCGTTTGCTCAAAATAATCAAATATCCCTTCACAATTTCACTCATG
66 CGTGCTGGGTTGCAACTTCGCGTTTGCTCAAAATAATCAAATATCCCTTCACAATTTCACTCATG
17755983 CCTTTT
131 CCTTTT
* *
17755989 AAAAAAAAATTCTTTAAAACGAAGGCGATG-TGCGATATTTGGCAATTCGCGGAATCGTGCCCTA
1 AAAAAAAAATTCTTTAAAACGAAGGCGA-GATGCGATATTTGGCAATTCACGGAATAGTGCCCTA
* * *
17756053 ACGTGCTGGGTTGCAACTTCTCGTTTGTTTAAAATAATCAAATATCCCT
65 ACGTGCTGGGTTGCAACTTCGCGTTTGCTCAAAATAATCAAATATCCCT
17756102 CCATATTTTC
Statistics
Matches: 104, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
136 103 0.99
137 1 0.01
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Consensus pattern (136 bp):
AAAAAAAAATTCTTTAAAACGAAGGCGAGATGCGATATTTGGCAATTCACGGAATAGTGCCCTAA
CGTGCTGGGTTGCAACTTCGCGTTTGCTCAAAATAATCAAATATCCCTTCACAATTTCACTCATG
CCTTTT
Found at i:17756128 original size:136 final size:136
Alignment explanation
Indices: 17755853--17756129 Score: 403
Period size: 136 Copynumber: 2.0 Consensus size: 136
17755843 ACAACTATAA
*
17755853 AAAAAAAAATTCTTTAAAACGAAGGCGAGATTCGATATTTGGCAATTCACGGAATAGTGCCCTAA
1 AAAAAAAAATTCTTTAAAACGAAGGCGAGATGCGATATTTGGCAATTCACGGAATAGTGCCCTAA
* * * * *
17755918 CGTGTTGGGTTGCAATTTCGCGTTTGCTCAAAATAATCAAATATCCCTTCACAATTTCACTCATG
66 CGTGCTGGGTTGCAACTTCGCGTTTGCTCAAAATAATCAAATATCCCTCCACAATTTCACGCAGG
*
17755983 CCTTTT
131 CCTTCT
* *
17755989 AAAAAAAAATTCTTTAAAACGAAGGCGATG-TGCGATATTTGGCAATTCGCGGAATCGTGCCCTA
1 AAAAAAAAATTCTTTAAAACGAAGGCGA-GATGCGATATTTGGCAATTCACGGAATAGTGCCCTA
* * * * *
17756053 ACGTGCTGGGTTGCAACTTCTCGTTTGTTTAAAATAATCAAATATCCCTCCATATTTTCACGCAG
65 ACGTGCTGGGTTGCAACTTCGCGTTTGCTCAAAATAATCAAATATCCCTCCACAATTTCACGCAG
*
17756118 GTCTTCT
130 GCCTTCT
17756125 AAAAA
1 AAAAA
17756130 TCCTTTCAAA
Statistics
Matches: 125, Mismatches: 15, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
136 124 0.99
137 1 0.01
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Consensus pattern (136 bp):
AAAAAAAAATTCTTTAAAACGAAGGCGAGATGCGATATTTGGCAATTCACGGAATAGTGCCCTAA
CGTGCTGGGTTGCAACTTCGCGTTTGCTCAAAATAATCAAATATCCCTCCACAATTTCACGCAGG
CCTTCT
Found at i:17756242 original size:131 final size:132
Alignment explanation
Indices: 17755902--17756277 Score: 287
Period size: 131 Copynumber: 2.8 Consensus size: 132
17755892 TGGCAATTCA
* * * * *
17755902 CGGAAT-AGTGCCCTAACGTGTTGGGTTGCAATTTCGCGTTTGCTCAAAATAATCAAATATCCCT
1 CGGAATCA-TGCCCTAACGTGCTGGGTTGCAACTTCTCGTTTGTTCAAAACAATCAAATATCCCT
* * * * * ** * ** * * *
17755966 TCACAATTTCACTCATGCCTTTTAAAAAAAAATTCTTT-AAAACGAAGGCGAT-GTGCGATATTT
65 CCAGATTTTCACGCA-G--GTTT-ACTAAAAA-CCTTTCAAAACGAAGGTAATACT-CGGTGTTT
* *
17756029 GGCAATTCG
124 GACAGTTCG
* * *
17756038 CGGAATCGTGCCCTAACGTGCTGGGTTGCAACTTCTCGTTTGTTTAAAATAATCAAATATCCCTC
1 CGGAATCATGCCCTAACGTGCTGGGTTGCAACTTCTCGTTTGTTCAAAACAATCAAATATCCCTC
*
17756103 CATATTTTCACGCAGGTCTT-CTAAAAATCCTTTC-AAACGAAGGTAATACTCGGTGTTTGACAG
66 CAGATTTTCACGCAGGT-TTACTAAAAA-CCTTTCAAAACGAAGGTAATACTCGGTGTTTGACAG
17756166 TTCG
129 TTCG
* * ** * * * *
17756170 -GGAATCATGCCGTATCGTGCTGGGTTGTGATTTCTCGTTTGTTCAAAACAATCGAATATTCCTT
1 CGGAATCATGCCCTAACGTGCTGGGTTGCAACTTCTCGTTTGTTCAAAACAATCAAATATCCCTC
* * ** * *
17756234 TAGGTTTTCATTCATGTTTATTAAAAACCTTTCAAAACGAAGGT
66 CAGATTTTCACGCAGGTTTACTAAAAACCTTTCAAAACGAAGGT
17756278 GATGTTTGAT
Statistics
Matches: 195, Mismatches: 39, Indels: 17
0.78 0.16 0.07
Matches are distributed among these distances:
130 8 0.04
131 80 0.41
132 34 0.17
133 2 0.01
134 2 0.01
135 1 0.01
136 68 0.35
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (132 bp):
CGGAATCATGCCCTAACGTGCTGGGTTGCAACTTCTCGTTTGTTCAAAACAATCAAATATCCCTC
CAGATTTTCACGCAGGTTTACTAAAAACCTTTCAAAACGAAGGTAATACTCGGTGTTTGACAGTT
CG
Found at i:17758082 original size:15 final size:15
Alignment explanation
Indices: 17758062--17758092 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
17758052 ATTCTGGATT
17758062 TTCGAGTATTTTAAA
1 TTCGAGTATTTTAAA
17758077 TTCGAGTATTTTAAA
1 TTCGAGTATTTTAAA
17758092 T
1 T
17758093 GAAAGTTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.06, G:0.13, T:0.48
Consensus pattern (15 bp):
TTCGAGTATTTTAAA
Found at i:17771446 original size:27 final size:27
Alignment explanation
Indices: 17771416--17771471 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
17771406 GAAATATCCT
17771416 CCCTAATAGAGTGCCCCAATAGACTCA
1 CCCTAATAGAGTGCCCCAATAGACTCA
*
17771443 CCCTAATAGAGTGCCCCCATAGACTCA
1 CCCTAATAGAGTGCCCCAATAGACTCA
17771470 CC
1 CC
17771472 ACTGAAATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.30, C:0.38, G:0.14, T:0.18
Consensus pattern (27 bp):
CCCTAATAGAGTGCCCCAATAGACTCA
Found at i:17778571 original size:25 final size:24
Alignment explanation
Indices: 17778505--17778571 Score: 62
Period size: 25 Copynumber: 2.7 Consensus size: 24
17778495 TATTATTTTG
* *
17778505 TTAATTATCTATTTAAAATATTATT
1 TTAATTAT-AATTTTAAATATTATT
* * * *
17778530 TTAAATAAAATTATAAATTTTATTT
1 TTAATTATAATTTTAAATATTA-TT
17778555 TTAATTATAATTTTAAA
1 TTAATTATAATTTTAAA
17778572 AATATTTGTT
Statistics
Matches: 32, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
24 10 0.31
25 22 0.69
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (24 bp):
TTAATTATAATTTTAAATATTATT
Found at i:17785761 original size:26 final size:26
Alignment explanation
Indices: 17785710--17785763 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
17785700 AATATGAAAT
* *
17785710 AAATAGATGATGTACTATATTGATCA
1 AAATAGATGATGTACAATATTCATCA
*
17785736 AAATGGATGAT-TACAATATTTCATCA
1 AAATAGATGATGTACAATA-TTCATCA
17785762 AA
1 AA
17785764 GTTTCTATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 6 0.25
26 18 0.75
ACGTcount: A:0.44, C:0.09, G:0.13, T:0.33
Consensus pattern (26 bp):
AAATAGATGATGTACAATATTCATCA
Found at i:17786829 original size:77 final size:78
Alignment explanation
Indices: 17786706--17786867 Score: 299
Period size: 77 Copynumber: 2.1 Consensus size: 78
17786696 TGATATAAAT
*
17786706 TGATAATAGGTTAGGTAAATGTTCCATGATAATAGGTTAGGTAAATGTTCCATGATAATGGGTTA
1 TGATAATAGGCTAGGTAAATGTTCCATGATAATAGGTTAGGTAAATGTTCCATGATAATGGGTTA
17786771 GGTAAATGTTTCA
66 GGTAAATGTTTCA
17786784 TGATAATAGGCTAGGTAAATGTT-CATGATAATAGGTTAGGTAAATGTTCCATGATAATGGGTTA
1 TGATAATAGGCTAGGTAAATGTTCCATGATAATAGGTTAGGTAAATGTTCCATGATAATGGGTTA
17786848 GGTAAATGTTTCA
66 GGTAAATGTTTCA
*
17786861 TAATAAT
1 TGATAAT
17786868 GGGATAATGT
Statistics
Matches: 82, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
77 60 0.73
78 22 0.27
ACGTcount: A:0.35, C:0.06, G:0.23, T:0.36
Consensus pattern (78 bp):
TGATAATAGGCTAGGTAAATGTTCCATGATAATAGGTTAGGTAAATGTTCCATGATAATGGGTTA
GGTAAATGTTTCA
Found at i:17786870 original size:26 final size:26
Alignment explanation
Indices: 17786706--17786867 Score: 263
Period size: 26 Copynumber: 6.3 Consensus size: 26
17786696 TGATATAAAT
17786706 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
17786732 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
17786758 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
*
17786784 TGATAATAGGCTAGGTAAATGTT-CA
1 TGATAATAGGTTAGGTAAATGTTCCA
17786809 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
17786835 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
*
17786861 TAATAAT
1 TGATAAT
17786868 GGGATAATGT
Statistics
Matches: 127, Mismatches: 8, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
25 24 0.19
26 103 0.81
ACGTcount: A:0.35, C:0.06, G:0.23, T:0.36
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:17788409 original size:25 final size:25
Alignment explanation
Indices: 17788370--17788420 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 25
17788360 TTTACAGTTT
17788370 TACCCCTAGGATAAATT-ACCGAAA
1 TACCCCTAGGATAAATTGACCGAAA
* *
17788394 TACCCCTAGGGTTAAATTGACCTAAA
1 TACCCCTA-GGATAAATTGACCGAAA
17788420 T
1 T
17788421 GCATGTTTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 8 0.35
25 8 0.35
26 7 0.30
ACGTcount: A:0.37, C:0.24, G:0.14, T:0.25
Consensus pattern (25 bp):
TACCCCTAGGATAAATTGACCGAAA
Found at i:17792613 original size:24 final size:24
Alignment explanation
Indices: 17792557--17792703 Score: 211
Period size: 25 Copynumber: 6.3 Consensus size: 24
17792547 TGATACAAAT
17792557 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAAT-GGTTAGGTAAATGTT-CA
17792583 TGATAATGGTTAGGTAAATGTTCA
1 TGATAATGGTTAGGTAAATGTTCA
17792607 TGATAATGGGTTAGGTAAATGTTCA
1 TGATAAT-GGTTAGGTAAATGTTCA
17792632 TGATAATGGTTAGGTAAATGTTCA
1 TGATAATGGTTAGGTAAATGTTCA
17792656 TGATAAT-GTTAGGT--ATGTTCA
1 TGATAATGGTTAGGTAAATGTTCA
17792677 TGATAAT--TTA-GT-AATG-TCA
1 TGATAATGGTTAGGTAAATGTTCA
17792696 TGATAATG
1 TGATAATG
17792704 CATGATAAGA
Statistics
Matches: 118, Mismatches: 0, Indels: 12
0.91 0.00 0.09
Matches are distributed among these distances:
19 12 0.10
20 6 0.05
21 14 0.12
23 7 0.06
24 33 0.28
25 39 0.33
26 7 0.06
ACGTcount: A:0.33, C:0.05, G:0.24, T:0.38
Consensus pattern (24 bp):
TGATAATGGTTAGGTAAATGTTCA
Found at i:17792652 original size:49 final size:49
Alignment explanation
Indices: 17792557--17792703 Score: 213
Period size: 49 Copynumber: 3.2 Consensus size: 49
17792547 TGATACAAAT
*
17792557 TGATAATAGGTTAGGTAAATGTTCCATGATAATGGTTAGGTAAATGTTCA
1 TGATAATGGGTTAGGTAAATGTT-CATGATAATGGTTAGGTAAATGTTCA
17792607 TGATAATGGGTTAGGTAAATGTTCATGATAATGGTTAGGTAAATGTTCA
1 TGATAATGGGTTAGGTAAATGTTCATGATAATGGTTAGGTAAATGTTCA
17792656 TGATAAT--GTTAGGT--ATGTTCATGATAAT--TTA-GT-AATG-TCA
1 TGATAATGGGTTAGGTAAATGTTCATGATAATGGTTAGGTAAATGTTCA
17792696 TGATAATG
1 TGATAATG
17792704 CATGATAAGA
Statistics
Matches: 95, Mismatches: 1, Indels: 11
0.89 0.01 0.10
Matches are distributed among these distances:
40 10 0.11
41 4 0.04
42 2 0.02
43 3 0.03
45 14 0.15
47 7 0.07
49 33 0.35
50 22 0.23
ACGTcount: A:0.33, C:0.05, G:0.24, T:0.38
Consensus pattern (49 bp):
TGATAATGGGTTAGGTAAATGTTCATGATAATGGTTAGGTAAATGTTCA
Found at i:17794212 original size:25 final size:26
Alignment explanation
Indices: 17794184--17794235 Score: 72
Period size: 25 Copynumber: 2.0 Consensus size: 26
17794174 TTTACAGTTT
17794184 TACCCCT-GGATTTAAATT-ACCGAAA
1 TACCCCTAGGA-TTAAATTGACCGAAA
*
17794209 TACCCCTAGGATTAAATTGACCTAAA
1 TACCCCTAGGATTAAATTGACCGAAA
17794235 T
1 T
17794236 GCATGTTTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 14 0.58
26 10 0.42
ACGTcount: A:0.37, C:0.23, G:0.12, T:0.29
Consensus pattern (26 bp):
TACCCCTAGGATTAAATTGACCGAAA
Found at i:17795713 original size:17 final size:17
Alignment explanation
Indices: 17795691--17795730 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
17795681 ATTCAAATTA
17795691 GAATTGAGAAAAAGATT
1 GAATTGAGAAAAAGATT
* *
17795708 GAATTGTGAAATAGATT
1 GAATTGAGAAAAAGATT
17795725 GCAATT
1 G-AATT
17795731 AGGAGTAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 16 0.80
18 4 0.20
ACGTcount: A:0.45, C:0.03, G:0.23, T:0.30
Consensus pattern (17 bp):
GAATTGAGAAAAAGATT
Found at i:17796597 original size:22 final size:22
Alignment explanation
Indices: 17796569--17796621 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
17796559 ACGTTAAGTT
17796569 CTCTCTGTTTAGCACATCT-GTG
1 CTCTCTGTTTAGCAC-TCTAGTG
* *
17796591 CTCTCTGTATAGCACTTTAGTG
1 CTCTCTGTTTAGCACTCTAGTG
17796613 CTCTCTGTT
1 CTCTCTGTT
17796622 CGTTTGTGCA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 2 0.07
22 25 0.93
ACGTcount: A:0.13, C:0.26, G:0.17, T:0.43
Consensus pattern (22 bp):
CTCTCTGTTTAGCACTCTAGTG
Found at i:17800611 original size:3 final size:3
Alignment explanation
Indices: 17800605--17800648 Score: 52
Period size: 3 Copynumber: 14.7 Consensus size: 3
17800595 CTATGATGAT
* * * *
17800605 GAG GAG GAG GAG GAG GAG GCG GAG GTG GAG GTG GAG GTG GAG GA
1 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GA
17800649 TTCTCAGCTT
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.25, C:0.02, G:0.66, T:0.07
Consensus pattern (3 bp):
GAG
Found at i:17801109 original size:5 final size:5
Alignment explanation
Indices: 17801092--17801122 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
17801082 TCTATCTATT
*
17801092 AGAAA AGAGA AGAAA AGAAA AGAAA AGAAA A
1 AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA A
17801123 CATGAAATGG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (5 bp):
AGAAA
Found at i:17801398 original size:3 final size:3
Alignment explanation
Indices: 17801392--17801416 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
17801382 AACAACTGAG
17801392 GCT GCT GCT GCT GCT GCT GCT GCT G
1 GCT GCT GCT GCT GCT GCT GCT GCT G
17801417 ATGATGATGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.36, T:0.32
Consensus pattern (3 bp):
GCT
Found at i:17801421 original size:3 final size:3
Alignment explanation
Indices: 17801415--17801446 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
17801405 CTGCTGCTGC
17801415 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TG
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TG
17801447 CAGCTGAGGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.34, T:0.34
Consensus pattern (3 bp):
TGA
Found at i:17802488 original size:2 final size:2
Alignment explanation
Indices: 17802483--17802507 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
17802473 TCCTTTTTTT
17802483 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
17802508 CTGCACTAAA
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:17812289 original size:2 final size:2
Alignment explanation
Indices: 17812284--17812309 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
17812274 ATATGCAGAC
17812284 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
17812310 TAACTGTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17813377 original size:21 final size:22
Alignment explanation
Indices: 17813343--17813383 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
17813333 TCGACTTTCG
17813343 TTCTTTTCC-CTTTTCTAATTT
1 TTCTTTTCCTCTTTTCTAATTT
* *
17813364 TTCTTTTTCTTTTTTCTAAT
1 TTCTTTTCCTCTTTTCTAAT
17813384 AAAATCTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.10, C:0.20, G:0.00, T:0.71
Consensus pattern (22 bp):
TTCTTTTCCTCTTTTCTAATTT
Found at i:17823705 original size:12 final size:12
Alignment explanation
Indices: 17823688--17823720 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
17823678 TGTGACACAC
17823688 GGCCGTGT-CGTA
1 GGCCGTGTAC-TA
17823700 GGCCGTGTACTA
1 GGCCGTGTACTA
17823712 GGCCGTGTA
1 GGCCGTGTA
17823721 ACACACTGGC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 19 0.95
13 1 0.05
ACGTcount: A:0.12, C:0.24, G:0.39, T:0.24
Consensus pattern (12 bp):
GGCCGTGTACTA
Found at i:17823707 original size:54 final size:54
Alignment explanation
Indices: 17823571--17823696 Score: 132
Period size: 54 Copynumber: 2.3 Consensus size: 54
17823561 ATCGAACAAA
* * *
17823571 GGGACACACGGGCA-TGTC-CTAGCC-TGTGTCTCAAACCGTGTAACTCACTGAGTT
1 GGGACACAC-GGCAGTGTCACAAGCCGTGTG-C-CAAACCCTGTAACTCACTGACTT
* * *
17823625 GGGTCACATGGTAGTGTCACAAGCCGTGTGCCAAACCCTGTAACTCACTGACTT
1 GGGACACACGGCAGTGTCACAAGCCGTGTGCCAAACCCTGTAACTCACTGACTT
* *
17823679 GTGACACACGGCCGTGTC
1 GGGACACACGGCAGTGTC
17823697 GTAGGCCGTG
Statistics
Matches: 58, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
53 3 0.05
54 45 0.78
55 6 0.10
56 4 0.07
ACGTcount: A:0.22, C:0.29, G:0.26, T:0.23
Consensus pattern (54 bp):
GGGACACACGGCAGTGTCACAAGCCGTGTGCCAAACCCTGTAACTCACTGACTT
Found at i:17830800 original size:4 final size:4
Alignment explanation
Indices: 17830791--17830815 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
17830781 GACAACCCAA
17830791 TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT T
17830816 TTATTTTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:17832409 original size:31 final size:31
Alignment explanation
Indices: 17832367--17832429 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
17832357 TGGGCCTATA
* *
17832367 GTGGCGTTTATAAATGCCACTAAAACTATTT
1 GTGGCGCTTATAAACGCCACTAAAACTATTT
*
17832398 GTGGCGCTTATAAACGCCATTAAAACTATTT
1 GTGGCGCTTATAAACGCCACTAAAACTATTT
17832429 G
1 G
17832430 CAGCGCTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Consensus pattern (31 bp):
GTGGCGCTTATAAACGCCACTAAAACTATTT
Found at i:17832436 original size:31 final size:31
Alignment explanation
Indices: 17832374--17832437 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
17832364 ATAGTGGCGT
* **
17832374 TTATAAATGCCACTAAAACTATTTGTGGCGC
1 TTATAAACGCCACTAAAACTATTTGCAGCGC
*
17832405 TTATAAACGCCATTAAAACTATTTGCAGCGC
1 TTATAAACGCCACTAAAACTATTTGCAGCGC
17832436 TT
1 TT
17832438 TTACAAGCGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.33, C:0.20, G:0.14, T:0.33
Consensus pattern (31 bp):
TTATAAACGCCACTAAAACTATTTGCAGCGC
Found at i:17832489 original size:34 final size:35
Alignment explanation
Indices: 17832451--17832535 Score: 127
Period size: 35 Copynumber: 2.5 Consensus size: 35
17832441 CAAGCGTCAC
17832451 AAAAACGCCGCTAAAATTTTAAGGCATTTATGTAA
1 AAAAACGCCGCTAAAATTTTAAGGCATTTATGTAA
* ** *
17832486 AAAAACGCCGCTAACATTTTGTGGCGTTTATGT-A
1 AAAAACGCCGCTAAAATTTTAAGGCATTTATGTAA
17832520 AAAAACGCCGCTAAAA
1 AAAAACGCCGCTAAAA
17832536 GTCATTACCT
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
34 16 0.36
35 29 0.64
ACGTcount: A:0.40, C:0.18, G:0.16, T:0.26
Consensus pattern (35 bp):
AAAAACGCCGCTAAAATTTTAAGGCATTTATGTAA
Found at i:17835634 original size:37 final size:37
Alignment explanation
Indices: 17835592--17835666 Score: 132
Period size: 37 Copynumber: 2.0 Consensus size: 37
17835582 AAAAAGTAGC
* *
17835592 ACGAACAACAAAAATAAGTGCAATAAGCATGATTGCA
1 ACGAACAAAAAAAATAAGGGCAATAAGCATGATTGCA
17835629 ACGAACAAAAAAAATAAGGGCAATAAGCATGATTGCA
1 ACGAACAAAAAAAATAAGGGCAATAAGCATGATTGCA
17835666 A
1 A
17835667 GTAAACAAAC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.53, C:0.15, G:0.17, T:0.15
Consensus pattern (37 bp):
ACGAACAAAAAAAATAAGGGCAATAAGCATGATTGCA
Found at i:17837232 original size:14 final size:14
Alignment explanation
Indices: 17837213--17837242 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
17837203 AAATCAAAGG
17837213 GATGGAGATTTAGA
1 GATGGAGATTTAGA
17837227 GATGGAGATTTAGA
1 GATGGAGATTTAGA
17837241 GA
1 GA
17837243 AACAGGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.37, C:0.00, G:0.37, T:0.27
Consensus pattern (14 bp):
GATGGAGATTTAGA
Found at i:17837327 original size:14 final size:14
Alignment explanation
Indices: 17837310--17837340 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
17837300 AATGATGGAA
17837310 GGATTTTGATTTGG
1 GGATTTTGATTTGG
17837324 GGATTTTGATTTGG
1 GGATTTTGATTTGG
17837338 GGA
1 GGA
17837341 AAAATTAGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.16, C:0.00, G:0.39, T:0.45
Consensus pattern (14 bp):
GGATTTTGATTTGG
Found at i:17838407 original size:22 final size:21
Alignment explanation
Indices: 17838377--17838440 Score: 74
Period size: 22 Copynumber: 3.0 Consensus size: 21
17838367 GATTTAGGCC
**
17838377 TAAATCCCTAACCCTTAGCCCT
1 TAAA-CCCTAACCCTTAAACCT
* *
17838399 TAGACCCCTAACCCCTAAACCT
1 TA-AACCCTAACCCTTAAACCT
17838421 TAAACCCTAACCCTTAAACC
1 TAAACCCTAACCCTTAAACC
17838441 ATAATCTAGA
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
21 16 0.46
22 18 0.51
23 1 0.03
ACGTcount: A:0.33, C:0.42, G:0.03, T:0.22
Consensus pattern (21 bp):
TAAACCCTAACCCTTAAACCT
Found at i:17838430 original size:14 final size:14
Alignment explanation
Indices: 17838411--17838440 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
17838401 GACCCCTAAC
17838411 CCCTAAACCTTAAA
1 CCCTAAACCTTAAA
*
17838425 CCCTAACCCTTAAA
1 CCCTAAACCTTAAA
17838439 CC
1 CC
17838441 ATAATCTAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.37, C:0.43, G:0.00, T:0.20
Consensus pattern (14 bp):
CCCTAAACCTTAAA
Found at i:17838459 original size:15 final size:15
Alignment explanation
Indices: 17838439--17838469 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
17838429 AACCCTTAAA
17838439 CCATAATCTAGAAAC
1 CCATAATCTAGAAAC
*
17838454 CCATAATCTATAAAC
1 CCATAATCTAGAAAC
17838469 C
1 C
17838470 TTAAAATAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.29, G:0.03, T:0.23
Consensus pattern (15 bp):
CCATAATCTAGAAAC
Found at i:17838900 original size:40 final size:40
Alignment explanation
Indices: 17838856--17838931 Score: 134
Period size: 40 Copynumber: 1.9 Consensus size: 40
17838846 AGTGGCTTTG
* *
17838856 TCTATAGTGGCGTTTTTCAAAAAGCGCCGCTAATGCTCCA
1 TCTATAGCGGCGTTTTTCAAAAAGCGCCGCAAATGCTCCA
17838896 TCTATAGCGGCGTTTTTCAAAAAGCGCCGCAAATGC
1 TCTATAGCGGCGTTTTTCAAAAAGCGCCGCAAATGC
17838932 AACTAAAGCT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.26, C:0.25, G:0.21, T:0.28
Consensus pattern (40 bp):
TCTATAGCGGCGTTTTTCAAAAAGCGCCGCAAATGCTCCA
Found at i:17839070 original size:41 final size:40
Alignment explanation
Indices: 17838963--17839136 Score: 197
Period size: 40 Copynumber: 4.3 Consensus size: 40
17838953 TAATTTTTTT
* *
17838963 GCGGCGTTTTTTATAAAGCGCCACTAATAG-TCGACCTATA
1 GCGGCGTTTTTTAAAAAGCGCCGCTAAT-GCTCGACCTATA
** * *
17839003 GCGGCGTTTTCCAAAAAGTGCCGCTAATGCTCGATCTATA
1 GCGGCGTTTTTTAAAAAGCGCCGCTAATGCTCGACCTATA
* *
17839043 GCGGCGTTATTTTAAAAAACGCCGCTAATGGTCGACCTATA
1 GCGGCGTT-TTTTAAAAAGCGCCGCTAATGCTCGACCTATA
* * * * *
17839084 GCAGCGTTTTTTAAGAAGCGCCGCTAATGCTCAATCTACA
1 GCGGCGTTTTTTAAAAAGCGCCGCTAATGCTCGACCTATA
*
17839124 GTGGCGTTTTTTA
1 GCGGCGTTTTTTA
17839137 TCCAAGTACC
Statistics
Matches: 111, Mismatches: 21, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
39 1 0.01
40 77 0.69
41 33 0.30
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.30
Consensus pattern (40 bp):
GCGGCGTTTTTTAAAAAGCGCCGCTAATGCTCGACCTATA
Found at i:17839107 original size:81 final size:80
Alignment explanation
Indices: 17838963--17839136 Score: 231
Period size: 81 Copynumber: 2.2 Consensus size: 80
17838953 TAATTTTTTT
* * * *
17838963 GCGGCGTTTTTTATAAAGCGCCACTAATAGTCGACCTATAGCGGCGTTTTCCAAAAAGTGCCGCT
1 GCGGCGTTTTTTAAAAAACGCCACTAATAGTCGACCTATAGCAGCGTTTTCCAAAAAGCGCCGCT
* *
17839028 AATGCTCGATCTATA
66 AATGCTCAATCTACA
* * ** *
17839043 GCGGCGTTATTTTAAAAAACGCCGCTAATGGTCGACCTATAGCAGCGTTTTTTAAGAAGCGCCGC
1 GCGGCGTT-TTTTAAAAAACGCCACTAATAGTCGACCTATAGCAGCGTTTTCCAAAAAGCGCCGC
17839108 TAATGCTCAATCTACA
65 TAATGCTCAATCTACA
*
17839124 GTGGCGTTTTTTA
1 GCGGCGTTTTTTA
17839137 TCCAAGTACC
Statistics
Matches: 81, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
80 13 0.16
81 68 0.84
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.30
Consensus pattern (80 bp):
GCGGCGTTTTTTAAAAAACGCCACTAATAGTCGACCTATAGCAGCGTTTTCCAAAAAGCGCCGCT
AATGCTCAATCTACA
Found at i:17840972 original size:22 final size:22
Alignment explanation
Indices: 17840942--17840983 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
17840932 AGATTATTAT
*
17840942 GATTTTATTTAGATTTATTTCA
1 GATTATATTTAGATTTATTTCA
**
17840964 GATTATATTTTTATTTATTT
1 GATTATATTTAGATTTATTT
17840984 TTTAGAGTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.26, C:0.02, G:0.07, T:0.64
Consensus pattern (22 bp):
GATTATATTTAGATTTATTTCA
Found at i:17842583 original size:31 final size:31
Alignment explanation
Indices: 17842545--17842608 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
17842535 CCTTTTCATA
*
17842545 TTTCATATTTCATAATACTGGGCCGAAGCCT
1 TTTCATATTTCATAATACTAGGCCGAAGCCT
*
17842576 TTTCATATTTCATATTACTAGGCCGAAGCCT
1 TTTCATATTTCATAATACTAGGCCGAAGCCT
17842607 TT
1 TT
17842609 ACTGTAAACG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.39
Consensus pattern (31 bp):
TTTCATATTTCATAATACTAGGCCGAAGCCT
Found at i:17842851 original size:24 final size:24
Alignment explanation
Indices: 17842800--17842895 Score: 131
Period size: 24 Copynumber: 4.0 Consensus size: 24
17842790 GCTTTATCAT
*
17842800 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
* *
17842825 ATAACTGGGGCAAAAGCCCTTTCA
1 ATAACTGGGGCATAAGCCCTTTTA
*
17842849 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
17842873 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
17842896 TCACTTCCTC
Statistics
Matches: 64, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
24 52 0.81
25 12 0.19
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.28
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:17842970 original size:20 final size:20
Alignment explanation
Indices: 17842945--17843005 Score: 104
Period size: 20 Copynumber: 3.0 Consensus size: 20
17842935 TTATGATTAC
17842945 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
17842965 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
* *
17842985 GTCATGTGCATCTCATACAT
1 ATCATGTGCATATCATACAT
17843005 A
1 A
17843006 CCATATTTAT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.33, C:0.21, G:0.11, T:0.34
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:17849802 original size:31 final size:31
Alignment explanation
Indices: 17849764--17849827 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
17849754 CCTTTTCATA
17849764 TTTCATATTTCATAATACTGGGCCGAAGCCT
1 TTTCATATTTCATAATACTGGGCCGAAGCCT
*
17849795 TTTCATATTTCATATTACTGGGCCGAAGCCT
1 TTTCATATTTCATAATACTGGGCCGAAGCCT
17849826 TT
1 TT
17849828 ACTGTAAACG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.23, C:0.22, G:0.16, T:0.39
Consensus pattern (31 bp):
TTTCATATTTCATAATACTGGGCCGAAGCCT
Found at i:17850069 original size:24 final size:24
Alignment explanation
Indices: 17850018--17850136 Score: 170
Period size: 24 Copynumber: 5.0 Consensus size: 24
17850008 GCTTTATCAT
*
17850018 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
* *
17850043 ATAACTGGGGCAAAAGCCCTTTCA
1 ATAACTGGGGCATAAGCCCTTTTA
17850067 ATAACTGGGGCATAAGCCCTTTT-
1 ATAACTGGGGCATAAGCCCTTTTA
*
17850090 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
17850114 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
17850137 TCACTTCCTC
Statistics
Matches: 87, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
23 23 0.26
24 52 0.60
25 12 0.14
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.29
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:17850097 original size:47 final size:48
Alignment explanation
Indices: 17850018--17850136 Score: 170
Period size: 47 Copynumber: 2.5 Consensus size: 48
17850008 GCTTTATCAT
*
17850018 ATAACTGGAGGCCT-AGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTCA
1 ATAACTGG-GGCATAAGCC-CTTTTAATAACTGGGGCAAAAGCCCTTTCA
* **
17850067 ATAACTGGGGCATAAGCCCTTTT-ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCAAAAGCCCTTTCA
17850114 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
17850137 TCACTTCCTC
Statistics
Matches: 65, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
47 44 0.68
48 9 0.14
49 12 0.18
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.29
Consensus pattern (48 bp):
ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCAAAAGCCCTTTCA
Found at i:17850216 original size:11 final size:11
Alignment explanation
Indices: 17850186--17850239 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 11
17850176 TTATGATTAC
17850186 TCATGTGCATA
1 TCATGTGCATA
*
17850197 TCA--TACATA
1 TCATGTGCATA
17850206 TCATGTGCATA
1 TCATGTGCATA
*
17850217 TCA--TACAT-
1 TCATGTGCATA
17850225 TCATGTGCATA
1 TCATGTGCATA
17850236 TCAT
1 TCAT
17850240 ACATACCATA
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
8 3 0.09
9 12 0.35
10 4 0.12
11 15 0.44
ACGTcount: A:0.31, C:0.20, G:0.11, T:0.37
Consensus pattern (11 bp):
TCATGTGCATA
Found at i:17850230 original size:19 final size:20
Alignment explanation
Indices: 17850186--17850244 Score: 111
Period size: 19 Copynumber: 3.0 Consensus size: 20
17850176 TTATGATTAC
17850186 TCATGTGCATATCATACATA
1 TCATGTGCATATCATACATA
17850206 TCATGTGCATATCATACAT-
1 TCATGTGCATATCATACATA
17850225 TCATGTGCATATCATACATA
1 TCATGTGCATATCATACATA
17850245 CCATATTTAT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
19 19 0.50
20 19 0.50
ACGTcount: A:0.34, C:0.20, G:0.10, T:0.36
Consensus pattern (20 bp):
TCATGTGCATATCATACATA
Found at i:17850319 original size:25 final size:25
Alignment explanation
Indices: 17850287--17850334 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
17850277 ATACATAAAC
* * *
17850287 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAACGGTCATTTTTA
17850312 CCTAGGGGCAAAACGGTCATTTT
1 CCTAGGGGCAAAACGGTCATTTT
17850335 CATTATAAGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (25 bp):
CCTAGGGGCAAAACGGTCATTTTTA
Found at i:17852773 original size:41 final size:41
Alignment explanation
Indices: 17852699--17852831 Score: 160
Period size: 41 Copynumber: 3.2 Consensus size: 41
17852689 TTTGAGATAA
* * * * *
17852699 TATATCAAGCTTTGTGCCTAGCAAGCTTTGTGCCGGTGATT
1 TATATCAGGCTTTGTACCTAGTAGGCTTCGTGCCGGTGATT
*
17852740 TATATCAGGCTTTGTAACTAGTAGGCTTCGTGCCGGTGATT
1 TATATCAGGCTTTGTACCTAGTAGGCTTCGTGCCGGTGATT
* * *
17852781 TATATCAGGCTTTGTACCTA-TCAGGTTTCATGTCGGTGATT
1 TATATCAGGCTTTGTACCTAGT-AGGCTTCGTGCCGGTGATT
*
17852822 TTTATCAGGC
1 TATATCAGGC
17852832 CTCGAGCCTA
Statistics
Matches: 80, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
40 1 0.01
41 79 0.99
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.38
Consensus pattern (41 bp):
TATATCAGGCTTTGTACCTAGTAGGCTTCGTGCCGGTGATT
Found at i:17853114 original size:2 final size:2
Alignment explanation
Indices: 17853107--17853151 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
17853097 TTAAATGACG
17853107 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
17853149 TA T
1 TA T
17853152 GTGTGTGTGT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:17853156 original size:2 final size:2
Alignment explanation
Indices: 17853151--17853186 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
17853141 TATATATATA
17853151 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
17853187 AAAATTCACT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:17856991 original size:45 final size:45
Alignment explanation
Indices: 17856941--17857027 Score: 165
Period size: 45 Copynumber: 1.9 Consensus size: 45
17856931 TCGATCTATG
17856941 GACTCCCTCATTAGGTTTCACCCTAATCCGGCAAAATCTTGTATA
1 GACTCCCTCATTAGGTTTCACCCTAATCCGGCAAAATCTTGTATA
*
17856986 GACTCCCTCATTAGGTTTCACCCTAATCCGGCAAAGTCTTGT
1 GACTCCCTCATTAGGTTTCACCCTAATCCGGCAAAATCTTGT
17857028 CACCCTATCT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.24, C:0.30, G:0.15, T:0.31
Consensus pattern (45 bp):
GACTCCCTCATTAGGTTTCACCCTAATCCGGCAAAATCTTGTATA
Found at i:17859592 original size:47 final size:47
Alignment explanation
Indices: 17859523--17859885 Score: 246
Period size: 47 Copynumber: 7.6 Consensus size: 47
17859513 GGTATAATGC
* *
17859523 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCCATCAAAT
1 CGATGCCATGTCCCAAACATGGTCTTACACTGGCTCATCCATCAAGT
** ** * *
17859570 CGATGCCATGTCCCAAACATGGTCTTACACTTACT-ATTGAAATCGAGGC
1 CGATGCCATGTCCCAAACATGGTCTTACACTGGCTCA-T-CCATC-AAGT
* * *
17859619 CAAAGCCATGTCCCGAACATGGTCTTACACTGGCTCATCCATCAAGT
1 CGATGCCATGTCCCAAACATGGTCTTACACTGGCTCATCCATCAAGT
* * * * * *
17859666 CGATGCCATGTTCTAAGCATGGTCTTACACTGACT-ATCGAAATCTAGGT
1 CGATGCCATGTCCCAAACATGGTCTTACACTGGCTCATC--CATC-AAGT
* * * *
17859715 CGACT-TCATGT-CCAGACATGGTCTTACACTAGCTC-TCACAT-ATCCGT
1 CGA-TGCCATGTCCCAAACATGGTCTTACACTGGCTCATC-CATCA--AGT
* * *
17859762 GCCGATGCCATGTCCCAGACATGGTCTTACACTGACACAT-C-TCATAGT
1 --CGATGCCATGTCCCAAACATGGTCTTACACTGGCTCATCCATCA-AGT
* * *
17859810 CGATG-CATGTCCTAAACAT-GTCTTACACTAGCTC-TCGTC-TCAATGC
1 CGATGCCATGTCCCAAACATGGTCTTACACTGGCTCATC--CATCAA-GT
*
17859856 CGATGCCATGTCCCAGACATGGTCTTACAC
1 CGATGCCATGTCCCAAACATGGTCTTACAC
17859886 AAGTTCTCAT
Statistics
Matches: 245, Mismatches: 48, Indels: 45
0.72 0.14 0.13
Matches are distributed among these distances:
43 1 0.00
44 12 0.05
45 14 0.06
46 19 0.08
47 80 0.33
48 42 0.17
49 53 0.22
50 23 0.09
51 1 0.00
ACGTcount: A:0.26, C:0.30, G:0.18, T:0.27
Consensus pattern (47 bp):
CGATGCCATGTCCCAAACATGGTCTTACACTGGCTCATCCATCAAGT
Found at i:17859691 original size:96 final size:96
Alignment explanation
Indices: 17859527--17859797 Score: 307
Period size: 96 Copynumber: 2.8 Consensus size: 96
17859517 TAATGCCGAT
17859527 GCCATGTCCC-AGACATGGTCTTACACTGGCTCATCCATCAAATCGATGCCATGTCCCAAACATG
1 GCCATGTCCCGA-ACATGGTCTTACACTGGCTCATCCATCAAATCGATGCCATGTCCCAAACATG
* *
17859591 GTCTTACACTTACTATTGAAATCGAGGCCAAA
65 GTCTTACACTGACTATCGAAATCGAGGCCAAA
* * * *
17859623 GCCATGTCCCGAACATGGTCTTACACTGGCTCATCCATCAAGTCGATGCCATGTTCTAAGCATGG
1 GCCATGTCCCGAACATGGTCTTACACTGGCTCATCCATCAAATCGATGCCATGTCCCAAACATGG
* * * *
17859688 TCTTACACTGACTATCGAAATCTAGGTCGAC
66 TCTTACACTGACTATCGAAATCGAGGCCAAA
** * * ** *
17859719 TTCATGTCCAG-ACATGGTCTTACACTAGCTC-TCACAT-ATCCGTGCCGATGCCATGTCCCAGA
1 GCCATGTCCCGAACATGGTCTTACACTGGCTCATC-CATCA--AAT--CGATGCCATGTCCCAAA
17859781 CATGGTCTTACACTGAC
61 CATGGTCTTACACTGAC
17859798 ACATCTCATA
Statistics
Matches: 150, Mismatches: 19, Indels: 10
0.84 0.11 0.06
Matches are distributed among these distances:
94 3 0.02
95 22 0.15
96 94 0.63
97 1 0.01
98 30 0.20
ACGTcount: A:0.26, C:0.30, G:0.18, T:0.27
Consensus pattern (96 bp):
GCCATGTCCCGAACATGGTCTTACACTGGCTCATCCATCAAATCGATGCCATGTCCCAAACATGG
TCTTACACTGACTATCGAAATCGAGGCCAAA
Found at i:17859912 original size:94 final size:92
Alignment explanation
Indices: 17859721--17859935 Score: 251
Period size: 94 Copynumber: 2.3 Consensus size: 92
17859711 AGGTCGACTT
**
17859721 CATGTCC-AGACATGGTCTTACACTAGCTCTCACATATCCGTGCCGATGCCATGTCCCAGACATG
1 CATGTCCTAGACAT-GTCTTACACTAGCTCT-ACATATCAATGCCGATGCCATGTCCCAGACATG
17859785 GTCTTACACTGACACATCTCATAGTCGATG
64 GTCTTACAC-GACACATCTCATAGTCGATG
* * *
17859815 CATGTCCTAAACATGTCTTACACTAGCTCT-CGTCTCAATGCCGATGCCATGTCCCAGACATGGT
1 CATGTCCTAGACATGTCTTACACTAGCTCTACATATCAATGCCGATGCCATGTCCCAGACATGGT
**
17859879 CTTACAC-A-AGTTCTCATAATGTGGCCGATG
66 CTTACACGACACATCTCAT-A-GT---CGATG
17859909 CATGT-CTCAGACATGTCTTACACTAGC
1 CATGTCCT-AGACATGTCTTACACTAGC
17859936 ACACAAACAA
Statistics
Matches: 106, Mismatches: 8, Indels: 14
0.83 0.06 0.11
Matches are distributed among these distances:
89 7 0.07
90 2 0.02
91 2 0.02
92 37 0.35
93 2 0.02
94 51 0.48
95 5 0.05
ACGTcount: A:0.25, C:0.30, G:0.18, T:0.28
Consensus pattern (92 bp):
CATGTCCTAGACATGTCTTACACTAGCTCTACATATCAATGCCGATGCCATGTCCCAGACATGGT
CTTACACGACACATCTCATAGTCGATG
Found at i:17862603 original size:13 final size:12
Alignment explanation
Indices: 17862571--17862620 Score: 52
Period size: 13 Copynumber: 4.2 Consensus size: 12
17862561 AACCATATAT
17862571 AAATAA-TAA-A
1 AAATAATTAATA
17862581 AAATAA-TAATA
1 AAATAATTAATA
*
17862592 ATAGTAATTAATA
1 A-AATAATTAATA
17862605 GAAATAATTAATA
1 -AAATAATTAATA
17862618 AAA
1 AAA
17862621 CAACAGTAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
10 9 0.26
11 2 0.06
12 7 0.21
13 15 0.44
14 1 0.03
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.28
Consensus pattern (12 bp):
AAATAATTAATA
Found at i:17862947 original size:14 final size:14
Alignment explanation
Indices: 17862928--17862958 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
17862918 ATATATTTAC
*
17862928 ATAATAAATATATA
1 ATAATAAATAAATA
17862942 ATAATAAATAAATA
1 ATAATAAATAAATA
17862956 ATA
1 ATA
17862959 TAATAATATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (14 bp):
ATAATAAATAAATA
Found at i:17862959 original size:19 final size:18
Alignment explanation
Indices: 17862930--17862966 Score: 65
Period size: 19 Copynumber: 2.0 Consensus size: 18
17862920 ATATTTACAT
17862930 AATAAATATATAATAATA
1 AATAAATATATAATAATA
17862948 AATAAATAATATAATAATA
1 AATAAAT-ATATAATAATA
17862967 TGAAACATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
AATAAATATATAATAATA
Found at i:17863018 original size:63 final size:63
Alignment explanation
Indices: 17862939--17863074 Score: 143
Period size: 62 Copynumber: 2.2 Consensus size: 63
17862929 TAATAAATAT
* * * * *
17862939 ATAATAATAAATAAATAATATAATAATATGAAACAT-AA-CTTAAATTAATTAAATTAATAG-AA
1 ATAATAAAAAACAAAT-ATAAAATAA-ATGAAA-ATAAAGCTCAAATTAATTAAATTAACAGTAA
17863001 A
63 A
* * *
17863002 ATAATAAAAAACAAATATAAAATTAATGAGAATAAAGCTCAAATTAATTAATTTAACAGTAAA
1 ATAATAAAAAACAAATATAAAATAAATGAAAATAAAGCTCAAATTAATTAAATTAACAGTAAA
*
17863065 ATAACAAAAA
1 ATAATAAAAA
17863075 TAAAAAAGGG
Statistics
Matches: 61, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
60 2 0.03
61 7 0.11
62 26 0.43
63 26 0.43
ACGTcount: A:0.62, C:0.05, G:0.04, T:0.28
Consensus pattern (63 bp):
ATAATAAAAAACAAATATAAAATAAATGAAAATAAAGCTCAAATTAATTAAATTAACAGTAAA
Found at i:17863371 original size:18 final size:18
Alignment explanation
Indices: 17863348--17863420 Score: 69
Period size: 18 Copynumber: 4.0 Consensus size: 18
17863338 ATAACAAGTA
*
17863348 GGGTGATGGAGTTAGTGG
1 GGGTGATGGAGGTAGTGG
17863366 GGGTGATGGAGGTAGTGG
1 GGGTGATGGAGGTAGTGG
* * *
17863384 ATGGT-TTAGTAGGGT-GTGG
1 -GGGTGAT-GGA-GGTAGTGG
17863403 GGGTGATGGAGGTAGTGG
1 GGGTGATGGAGGTAGTGG
17863421 ATAGTTTAGT
Statistics
Matches: 43, Mismatches: 7, Indels: 10
0.72 0.12 0.17
Matches are distributed among these distances:
17 3 0.07
18 27 0.63
19 10 0.23
20 3 0.07
ACGTcount: A:0.16, C:0.00, G:0.56, T:0.27
Consensus pattern (18 bp):
GGGTGATGGAGGTAGTGG
Found at i:17863399 original size:29 final size:30
Alignment explanation
Indices: 17863359--17863449 Score: 85
Period size: 37 Copynumber: 2.8 Consensus size: 30
17863349 GGTGATGGAG
* *
17863359 TTAGTGGGGGTGATGGAGGTAGTGGATGGT
1 TTAGTAGGGGTGATGGAGGTAGTGGATAGT
17863389 TTAGTAGGGTGTGGGGGTGATGGAGGTAGTGGATAGT
1 TTAGTA-------GGGGTGATGGAGGTAGTGGATAGT
*
17863426 TTAGTA-GGGTGATGGAGTTAGTGG
1 TTAGTAGGGGTGATGGAGGTAGTGG
17863450 GGGTGATGAA
Statistics
Matches: 51, Mismatches: 3, Indels: 15
0.74 0.04 0.22
Matches are distributed among these distances:
29 17 0.33
30 5 0.10
37 29 0.57
ACGTcount: A:0.19, C:0.00, G:0.51, T:0.31
Consensus pattern (30 bp):
TTAGTAGGGGTGATGGAGGTAGTGGATAGT
Found at i:17863412 original size:37 final size:37
Alignment explanation
Indices: 17863362--17863436 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
17863352 GATGGAGTTA
*
17863362 GTGGGGGTGATGGAGGTAGTGGATGGTTTAGTAGGGT
1 GTGGGGGTGATGGAGGTAGTGGATAGTTTAGTAGGGT
17863399 GTGGGGGTGATGGAGGTAGTGGATAGTTTAGTAGGGT
1 GTGGGGGTGATGGAGGTAGTGGATAGTTTAGTAGGGT
17863436 G
1 G
17863437 ATGGAGTTAG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.17, C:0.00, G:0.53, T:0.29
Consensus pattern (37 bp):
GTGGGGGTGATGGAGGTAGTGGATAGTTTAGTAGGGT
Found at i:17864936 original size:93 final size:93
Alignment explanation
Indices: 17864824--17864995 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
17864814 GCCCATAAGT
* *
17864824 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
17864889 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
*
17864917 GAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
17864982 CGAGTTCGGATGCC
66 CGAGTTCGGATGCC
17864996 CAAATATCCA
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
Done.