Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009491.1 Kokia drynarioides strain JFW-HI SEQ_124200, 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: 129132
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Warning! 81 characters in sequence are not A, C, G, or T
Found at i:1891 original size:19 final size:21
Alignment explanation
Indices: 1869--1914 Score: 60
Period size: 19 Copynumber: 2.2 Consensus size: 21
1859 AATACAAAAA
1869 AAAAATCAAAA-TA-ATTTTT
1 AAAAATCAAAATTATATTTTT
*
1888 AAAATTCAAAATTTATATTTTT
1 AAAAATCAAAA-TTATATTTTT
1910 AAAAA
1 AAAAA
1915 ATTATAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
19 10 0.45
21 2 0.09
22 10 0.45
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (21 bp):
AAAAATCAAAATTATATTTTT
Found at i:15376 original size:20 final size:21
Alignment explanation
Indices: 15345--15386 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
15335 AGTGATACTA
15345 ATTTTTTATGAACTTTTATAT
1 ATTTTTTATGAACTTTTATAT
* *
15366 ATTTTTT-TGAATTTTTTTAT
1 ATTTTTTATGAACTTTTATAT
15386 A
1 A
15387 AATTTTAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.26, C:0.02, G:0.05, T:0.67
Consensus pattern (21 bp):
ATTTTTTATGAACTTTTATAT
Found at i:17873 original size:18 final size:18
Alignment explanation
Indices: 17859--17892 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
17849 GTAATTAATT
17859 TAAAATT-TTTAATTAAC
1 TAAAATTATTTAATTAAC
*
17876 TAAATTTATTTAATTAA
1 TAAAATTATTTAATTAA
17893 AAACTTGTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (18 bp):
TAAAATTATTTAATTAAC
Found at i:19521 original size:37 final size:37
Alignment explanation
Indices: 19466--19538 Score: 101
Period size: 37 Copynumber: 2.0 Consensus size: 37
19456 TTTTGAATTT
* *
19466 TTTAAAATTAAGATTAAATTGAAATAATTTGTAAAAA
1 TTTAAAATTAAGACTAAATTGAAATAATATGTAAAAA
* **
19503 TTTAAAATTATGACTAAATTGGTATAATATGTAAAA
1 TTTAAAATTAAGACTAAATTGAAATAATATGTAAAA
19539 GCTAAGGGAT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.51, C:0.01, G:0.10, T:0.38
Consensus pattern (37 bp):
TTTAAAATTAAGACTAAATTGAAATAATATGTAAAAA
Found at i:24197 original size:73 final size:74
Alignment explanation
Indices: 24078--24231 Score: 276
Period size: 73 Copynumber: 2.1 Consensus size: 74
24068 TAACATATTT
24078 TCCTT-AAGAAAGAAACAACCCGCTTGAGGTATGGCAGACTTCAATGCCAAGGAAAAAATGAAGA
1 TCCTTCAAGAAAGAAACAACCCGCTTGAGGTATGGCAGACTTCAATGCCAAGGAAAAAATGAAGA
24142 TCACCCAAA
66 TCACCCAAA
*
24151 TCCTTCAA-AAAGAAACAACCCGCTTGAGGTATGGCAGACTTCAATGCCATGGAAAAAATGAAGA
1 TCCTTCAAGAAAGAAACAACCCGCTTGAGGTATGGCAGACTTCAATGCCAAGGAAAAAATGAAGA
*
24215 TCACCCAGA
66 TCACCCAAA
24224 TCCTTCAA
1 TCCTTCAA
24232 CGAGAATATA
Statistics
Matches: 78, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
73 76 0.97
74 2 0.03
ACGTcount: A:0.40, C:0.23, G:0.18, T:0.18
Consensus pattern (74 bp):
TCCTTCAAGAAAGAAACAACCCGCTTGAGGTATGGCAGACTTCAATGCCAAGGAAAAAATGAAGA
TCACCCAAA
Found at i:26071 original size:18 final size:21
Alignment explanation
Indices: 26028--26070 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
26018 AATATCAGCT
26028 TCATTCTTTTGAAAAACAACA
1 TCATTCTTTTGAAAAACAACA
26049 TCATTCTTTTGAAAAACAACA
1 TCATTCTTTTGAAAAACAACA
26070 T
1 T
26071 TACAATGAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.42, C:0.19, G:0.05, T:0.35
Consensus pattern (21 bp):
TCATTCTTTTGAAAAACAACA
Found at i:31793 original size:34 final size:35
Alignment explanation
Indices: 31719--31799 Score: 96
Period size: 35 Copynumber: 2.3 Consensus size: 35
31709 TTTTTTAGCT
*
31719 TAAACCCAAAACCATGAATCTAAAATCTTGAACAC
1 TAAACCCAAAACCATGAATCCAAAATCTTGAACAC
*
31754 TAAACCCAAAA-TATAGAATCCAAAA-CTTGAAC-C
1 TAAACCCAAAACCAT-GAATCCAAAATCTTGAACAC
*
31787 TCAAACCCTAAAC
1 T-AAACCCAAAAC
31800 ACAAACACTT
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
33 2 0.05
34 18 0.45
35 20 0.50
ACGTcount: A:0.49, C:0.27, G:0.05, T:0.19
Consensus pattern (35 bp):
TAAACCCAAAACCATGAATCCAAAATCTTGAACAC
Found at i:33284 original size:31 final size:32
Alignment explanation
Indices: 33218--33277 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
33208 TAAAAATAAT
* * *
33218 AATTCAATTCTTTTTGAAAAATTTGATAATCA
1 AATTCAACTCTTTTTGAAAAAGTTGAGAATCA
33250 AATTCAACTCTTTTT-AAAAAGTTGAGAA
1 AATTCAACTCTTTTTGAAAAAGTTGAGAA
33278 CTAAATTGAC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
31 11 0.44
32 14 0.56
ACGTcount: A:0.42, C:0.10, G:0.08, T:0.40
Consensus pattern (32 bp):
AATTCAACTCTTTTTGAAAAAGTTGAGAATCA
Found at i:33584 original size:16 final size:16
Alignment explanation
Indices: 33563--33616 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
33553 AGTTGAAAAT
33563 AAAATTAGAAAGATAG
1 AAAATTAGAAAGATAG
* **
33579 AAAATTGGAGCGATAG
1 AAAATTAGAAAGATAG
* *
33595 AAAAAATAGAAAGATGG
1 -AAAATTAGAAAGATAG
33612 AAAAT
1 AAAAT
33617 ATAAATGTTC
Statistics
Matches: 28, Mismatches: 9, Indels: 2
0.72 0.23 0.05
Matches are distributed among these distances:
16 17 0.61
17 11 0.39
ACGTcount: A:0.59, C:0.02, G:0.22, T:0.17
Consensus pattern (16 bp):
AAAATTAGAAAGATAG
Found at i:38153 original size:21 final size:21
Alignment explanation
Indices: 38129--38205 Score: 61
Period size: 21 Copynumber: 3.7 Consensus size: 21
38119 TAGAGTTTTT
38129 AGTATCGGTAGAAGCATGTCA
1 AGTATCGGTAGAAGCATGTCA
*
38150 AGTATCGATAGAA--A-GTACA
1 AGTATCGGTAGAAGCATGT-CA
* * * *
38169 CTTGTATCGGTCGAACCATTTCA
1 --AGTATCGGTAGAAGCATGTCA
38192 AGTATCGGTAGAAG
1 AGTATCGGTAGAAG
38206 TTTGCTACTA
Statistics
Matches: 42, Mismatches: 8, Indels: 12
0.68 0.13 0.19
Matches are distributed among these distances:
18 2 0.05
19 3 0.07
21 33 0.79
23 3 0.07
24 1 0.02
ACGTcount: A:0.34, C:0.16, G:0.25, T:0.26
Consensus pattern (21 bp):
AGTATCGGTAGAAGCATGTCA
Found at i:41057 original size:23 final size:24
Alignment explanation
Indices: 41007--41058 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
40997 TCAATTGATC
*
41007 ATTAAAATTAATTTGATCAAAATTA
1 ATTAAAA-TAATTTGATAAAAATTA
41032 ATTAAAA-AATTT-ATAAAAATTCA
1 ATTAAAATAATTTGATAAAAATT-A
41055 ATTA
1 ATTA
41059 TCAATTAACT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
22 8 0.32
23 10 0.40
25 7 0.28
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.38
Consensus pattern (24 bp):
ATTAAAATAATTTGATAAAAATTA
Found at i:41976 original size:24 final size:23
Alignment explanation
Indices: 41938--41996 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 23
41928 AAAAACACAA
* *
41938 ATAAATA-TAATTATTGTTTAAT
1 ATAAATATTAATTATTATTTAAC
41960 ATAAATATTTAATTATTATTTAAC
1 ATAAATA-TTAATTATTATTTAAC
*
41984 ATATATAATTAAT
1 ATAAAT-ATTAAT
41997 ATAATTAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
22 7 0.23
24 23 0.74
25 1 0.03
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (23 bp):
ATAAATATTAATTATTATTTAAC
Found at i:47621 original size:18 final size:18
Alignment explanation
Indices: 47598--47633 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
47588 TTATTGAAGT
47598 GGAAATCCTAGGTGTTAA
1 GGAAATCCTAGGTGTTAA
47616 GGAAATCCTAGGTGTTAA
1 GGAAATCCTAGGTGTTAA
47634 TGGGATAGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.11, G:0.28, T:0.28
Consensus pattern (18 bp):
GGAAATCCTAGGTGTTAA
Found at i:64282 original size:19 final size:20
Alignment explanation
Indices: 64203--64287 Score: 68
Period size: 20 Copynumber: 4.2 Consensus size: 20
64193 ATATAGCATT
64203 AAAATATATAAA-ATAG-AAA
1 AAAATATA-AAATATAGAAAA
* *
64222 TAAATATAAAAATTTGAGAAAA
1 AAAATAT-AAAATAT-AGAAAA
* **
64244 TATGTATAAAATATAGAAAA
1 AAAATATAAAATATAGAAAA
*
64264 AAAATATAAATTATA-AAAA
1 AAAATATAAAATATAGAAAA
64283 AAAAT
1 AAAAT
64288 CTTACGGGGC
Statistics
Matches: 53, Mismatches: 9, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
19 18 0.34
20 19 0.36
21 8 0.15
22 8 0.15
ACGTcount: A:0.68, C:0.00, G:0.06, T:0.26
Consensus pattern (20 bp):
AAAATATAAAATATAGAAAA
Found at i:66633 original size:16 final size:17
Alignment explanation
Indices: 66601--66634 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
66591 AATTAGATGC
*
66601 TTTAATTAATCATAAAT
1 TTTAATTAATAATAAAT
66618 TTTAATTAA-AATAAAT
1 TTTAATTAATAATAAAT
66634 T
1 T
66635 ATTATAAGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (17 bp):
TTTAATTAATAATAAAT
Found at i:69263 original size:17 final size:17
Alignment explanation
Indices: 69241--69273 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
69231 CTTTCTTGAC
69241 CTTTAACCTTCCATATT
1 CTTTAACCTTCCATATT
*
69258 CTTTAACCTTTCATAT
1 CTTTAACCTTCCATAT
69274 CCCTGTAACT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.27, G:0.00, T:0.48
Consensus pattern (17 bp):
CTTTAACCTTCCATATT
Found at i:74577 original size:17 final size:17
Alignment explanation
Indices: 74557--74598 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
74547 CTCTCTTGAC
*
74557 CTTTAACCTTCCATCTT
1 CTTTAACCTTCCATATT
*
74574 CTTTAACCTTTCATATT
1 CTTTAACCTTCCATATT
74591 CTTGTAAC
1 CTT-TAAC
74599 TACTTTTTCC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 18 0.82
18 4 0.18
ACGTcount: A:0.21, C:0.29, G:0.02, T:0.48
Consensus pattern (17 bp):
CTTTAACCTTCCATATT
Found at i:74582 original size:24 final size:24
Alignment explanation
Indices: 74537--74584 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
74527 ATGGATGTTC
* *
74537 AACCTTTCATCTCTCTTGACCTTT
1 AACCTTCCATCTCTCTTAACCTTT
74561 AACCTTCCATCT-TCTTTAACCTTT
1 AACCTTCCATCTCTC-TTAACCTTT
74585 CATATTCTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 2 0.10
24 19 0.90
ACGTcount: A:0.19, C:0.33, G:0.02, T:0.46
Consensus pattern (24 bp):
AACCTTCCATCTCTCTTAACCTTT
Found at i:75087 original size:9 final size:9
Alignment explanation
Indices: 75005--75107 Score: 55
Period size: 9 Copynumber: 10.6 Consensus size: 9
74995 CCACGGACCA
75005 AAAAAATTT
1 AAAAAATTT
*
75014 AAAAATTGTT
1 AAAAAAT-TT
75024 AAAAAAATCATT
1 -AAAAAAT--TT
*
75036 AAAGAATATCT
1 AAA-AA-ATTT
75047 ATAAAAATTGT
1 A-AAAAATT-T
75058 AAAAATATTT
1 AAAAA-ATTT
* *
75068 -AAAAGTAT
1 AAAAAATTT
75076 AAAAAATTT
1 AAAAAATTT
* * *
75085 AAATAACTG
1 AAAAAATTT
75094 AAAAAATTT
1 AAAAAATTT
75103 AAAAA
1 AAAAA
75108 TGAAAACAAA
Statistics
Matches: 70, Mismatches: 15, Indels: 18
0.68 0.15 0.17
Matches are distributed among these distances:
8 2 0.03
9 33 0.47
10 9 0.13
11 18 0.26
12 6 0.09
13 2 0.03
ACGTcount: A:0.62, C:0.03, G:0.05, T:0.30
Consensus pattern (9 bp):
AAAAAATTT
Found at i:75099 original size:20 final size:16
Alignment explanation
Indices: 75048--75113 Score: 62
Period size: 18 Copynumber: 3.8 Consensus size: 16
75038 AGAATATCTA
75048 TAAAAATTGTAAAAATATT
1 TAAAAA-TG-AAAAA-ATT
75067 TAAAAGTAT-AAAAAATT
1 TAAAA--ATGAAAAAATT
75084 TAAATAACTGAAAAAATT
1 TAAA-AA-TGAAAAAATT
75102 TAAAAATGAAAA
1 TAAAAATGAAAA
75114 CAAATATTTA
Statistics
Matches: 42, Mismatches: 0, Indels: 13
0.76 0.00 0.24
Matches are distributed among these distances:
16 7 0.17
17 10 0.24
18 18 0.43
19 5 0.12
20 1 0.02
21 1 0.02
ACGTcount: A:0.64, C:0.02, G:0.06, T:0.29
Consensus pattern (16 bp):
TAAAAATGAAAAAATT
Found at i:75118 original size:18 final size:17
Alignment explanation
Indices: 75048--75128 Score: 58
Period size: 18 Copynumber: 4.4 Consensus size: 17
75038 AGAATATCTA
*
75048 TAAAAATTGTAAAAATATT
1 TAAAAA-TG-AAAAAAATT
*
75067 TAAAAGT-ATAAAAAATT
1 TAAAAATGA-AAAAAATT
75084 TAAATAACTG-AAAAAATT
1 TAAA-AA-TGAAAAAAATT
75102 TAAAAATGAAAACAAATATT
1 TAAAAATG-AAA-AAA-ATT
75122 TAAAAAT
1 TAAAAAT
75129 TATAAAAAAA
Statistics
Matches: 51, Mismatches: 3, Indels: 15
0.74 0.04 0.22
Matches are distributed among these distances:
16 3 0.06
17 13 0.25
18 16 0.31
19 9 0.18
20 10 0.20
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.30
Consensus pattern (17 bp):
TAAAAATGAAAAAAATT
Found at i:78395 original size:30 final size:30
Alignment explanation
Indices: 78350--78498 Score: 219
Period size: 30 Copynumber: 5.0 Consensus size: 30
78340 CCGAACTTCT
*
78350 AAAATTACCATTTTAACCCCTAAACTTTTCA
1 AAAATTA-TATTTTAACCCCTAAACTTTTCA
*
78381 AAAATTATATTTTAACCCCTAAACGTTTCA
1 AAAATTATATTTTAACCCCTAAACTTTTCA
* *
78411 AAAATTATATTTTGATCCCTAAACTTTTCA
1 AAAATTATATTTTAACCCCTAAACTTTTCA
* *
78441 AAAATTATATTTTAACCCTTAAACTTTCCA
1 AAAATTATATTTTAACCCCTAAACTTTTCA
*
78471 AAAATTATATTTTAACCCC-GAACTTTTC
1 AAAATTATATTTTAACCCCTAAACTTTTC
78499 TTTAATTTAA
Statistics
Matches: 106, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
29 7 0.07
30 92 0.87
31 7 0.07
ACGTcount: A:0.38, C:0.21, G:0.02, T:0.39
Consensus pattern (30 bp):
AAAATTATATTTTAACCCCTAAACTTTTCA
Found at i:89654 original size:18 final size:18
Alignment explanation
Indices: 89631--89667 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
89621 GCATCTAATA
*
89631 TTGTTCCTTGTAATTATT
1 TTGTTCCTTGTAAATATT
89649 TTGTTCCTTGTAAATATT
1 TTGTTCCTTGTAAATATT
89667 T
1 T
89668 GGCAATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.19, C:0.11, G:0.11, T:0.59
Consensus pattern (18 bp):
TTGTTCCTTGTAAATATT
Found at i:90223 original size:49 final size:51
Alignment explanation
Indices: 90102--90670 Score: 406
Period size: 49 Copynumber: 11.5 Consensus size: 51
90092 CATGAAGCAG
* * *
90102 GAAGGGAAAGATTTAAGCCGCAACGGCGAA-TCCAGTACCAC-GAAAATAA
1 GAAGGGAAAGATTTAAGCCGCAACGGCGAACTCTAGTACCTCAGAAGATAA
* * * *
90151 TGGAGGGAAAGGTTTAAGTCGCAACGGCGAACT-TTGTACCTCAGAAGA-AA
1 -GAAGGGAAAGATTTAAGCCGCAACGGCGAACTCTAGTACCTCAGAAGATAA
* * * * *
90201 GAAGGGAAAGATTTAACCCGCAATGGTGAA-TCCAGTACCAC-GAAGATAA
1 GAAGGGAAAGATTTAAGCCGCAACGGCGAACTCTAGTACCTCAGAAGATAA
* * * * * *
90250 TGGAA-GGAATGGTTTAAGTCGCAACGGCGAAC-CTTGTACCTCAGAAG-CAG
1 --GAAGGGAAAGATTTAAGCCGCAACGGCGAACTCTAGTACCTCAGAAGATAA
* * *
90300 GAAGGGAAAGATTTAACCCGCAATGGCGAA-TCCAGTA-CT-ATGAAGATAA
1 GAAGGGAAAGATTTAAGCCGCAACGGCGAACTCTAGTACCTCA-GAAGATAA
* * * *
90349 TTG-AGGGAAAGGTTTAAGTCGCAACGACGAAC-CTTGTACCTCAGAAGCAT--
1 --GAAGGGAAAGATTTAAGCCGCAACGGCGAACTCTAGTACCTCAGAAG-ATAA
* *
90399 GAAGGGAAAGATTTAAGCCGCAACGGCGAA-TCCAGTACCAC-GAAGATAA
1 GAAGGGAAAGATTTAAGCCGCAACGGCGAACTCTAGTACCTCAGAAGATAA
* * * * *
90448 TGAAGGGAAAGGTTTAAGTCGTAACGACGAAC-CTTGTACCTCAGAAGCAT--
1 -GAAGGGAAAGATTTAAGCCGCAACGGCGAACTCTAGTACCTCAGAAG-ATAA
* * * * *
90498 GAAGGGGAAGATTTAAGCCACAACGGC-AAATCTAATACCAC-GAAGATACA
1 GAAGGGAAAGATTTAAGCCGCAACGGCGAACTCTAGTACCTCAGAAGATA-A
* * * * *
90548 -AAGGGAAAGGTTTAAGTCACAACGGCGAAC-CTTGTACCCCAGAAGCAT--
1 GAAGGGAAAGATTTAAGCCGCAACGGCGAACTCTAGTACCTCAGAAG-ATAA
* * *
90596 GAAGGGAAAGATTTAAGCCGCAACGGCGAA-TCTAGTAACGC-GAAGACATA
1 GAAGGGAAAGATTTAAGCCGCAACGGCGAACTCTAGTACCTCAGAAGATA-A
*
90646 -AAGGGAAAGATTGAAGCCGCAACGG
1 GAAGGGAAAGATTTAAGCCGCAACGG
90671 TAAATCTTAT
Statistics
Matches: 400, Mismatches: 81, Indels: 77
0.72 0.15 0.14
Matches are distributed among these distances:
47 6 0.01
48 30 0.08
49 205 0.51
50 129 0.32
51 25 0.06
52 5 0.01
ACGTcount: A:0.38, C:0.19, G:0.27, T:0.17
Consensus pattern (51 bp):
GAAGGGAAAGATTTAAGCCGCAACGGCGAACTCTAGTACCTCAGAAGATAA
Found at i:90273 original size:99 final size:98
Alignment explanation
Indices: 90095--90641 Score: 765
Period size: 99 Copynumber: 5.5 Consensus size: 98
90085 TCATTACCAT
* * *
90095 GAAGCAGGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAAATAATGGAGGGAA
1 GAAGCATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGATAAT-GAAGGAA
*
90160 AGGTTTAAGTCGCAACGGCGAACTTTGTACCTCA
65 AGGTTTAAGTCGCAACGGCGAACCTTGTACCTCA
* * * * *
90194 GAAGAAAGAAGGGAAAGATTTAACCCGCAATGGTGAATCCAGTACCACGAAGATAATGGAAGGAA
1 GAAGCATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGATAAT-GAAGGAA
*
90259 TGGTTTAAGTCGCAACGGCGAACCTTGTACCTCA
65 AGGTTTAAGTCGCAACGGCGAACCTTGTACCTCA
* * * * * *
90293 GAAGCAGGAAGGGAAAGATTTAACCCGCAATGGCGAATCCAGTACTATGAAGATAATTGAGGGAA
1 GAAGCATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGATAA-TGAAGGAA
*
90358 AGGTTTAAGTCGCAACGACGAACCTTGTACCTCA
65 AGGTTTAAGTCGCAACGGCGAACCTTGTACCTCA
90392 GAAGCATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGATAATGAAGGGAA
1 GAAGCATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGATAATGAA-GGAA
* *
90457 AGGTTTAAGTCGTAACGACGAACCTTGTACCTCA
65 AGGTTTAAGTCGCAACGGCGAACCTTGTACCTCA
* * * * *
90491 GAAGCATGAAGGGGAAGATTTAAGCCACAACGGCAAATCTAATACCACGAAGATACA--AAGGGA
1 GAAGCATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGATA-ATGAA-GGA
* *
90554 AAGGTTTAAGTCACAACGGCGAACCTTGTACCCCA
64 AAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCA
* * *
90589 GAAGCATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTAACGCGAAGA
1 GAAGCATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGA
90642 CATAAAGGGA
Statistics
Matches: 406, Mismatches: 39, Indels: 7
0.90 0.09 0.02
Matches are distributed among these distances:
98 87 0.21
99 317 0.78
100 2 0.00
ACGTcount: A:0.38, C:0.19, G:0.27, T:0.17
Consensus pattern (98 bp):
GAAGCATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGATAATGAAGGAAA
GGTTTAAGTCGCAACGGCGAACCTTGTACCTCA
Found at i:91825 original size:18 final size:16
Alignment explanation
Indices: 91795--91838 Score: 54
Period size: 16 Copynumber: 2.7 Consensus size: 16
91785 TATATTCAAT
91795 ATTTATTTATTAGGTC
1 ATTTATTTATTAGGTC
91811 ATTTATATTATTTAGGT-
1 ATTTAT-TTA-TTAGGTC
*
91828 TTTTATTTATT
1 ATTTATTTATT
91839 GTTTGGAAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
15 2 0.08
16 9 0.36
17 8 0.32
18 6 0.24
ACGTcount: A:0.25, C:0.02, G:0.09, T:0.64
Consensus pattern (16 bp):
ATTTATTTATTAGGTC
Found at i:93060 original size:30 final size:30
Alignment explanation
Indices: 93011--93188 Score: 268
Period size: 30 Copynumber: 6.0 Consensus size: 30
93001 TTTTTGCCCC
*
93011 TAAACTTCT-AAAAATTATATTTTAACCCT
1 TAAACTTTTCAAAAATTATATTTTAACCCT
*
93040 TAAACTTTTCAAAAAATATATTTTAACCCT
1 TAAACTTTTCAAAAATTATATTTTAACCCT
* * *
93070 TAGACTTTTCAAAAATTATATTTTGACCAT
1 TAAACTTTTCAAAAATTATATTTTAACCCT
* * *
93100 TAAACTTTTCAAAAATTATGTTTTGACCCC
1 TAAACTTTTCAAAAATTATATTTTAACCCT
93130 TAAACTTTTCAAAAATTATATTTTAACCCT
1 TAAACTTTTCAAAAATTATATTTTAACCCT
*
93160 TAAACTTTCCAAAAATTATATTTTAACCC
1 TAAACTTTTCAAAAATTATATTTTAACCC
93189 CAAATTTTAC
Statistics
Matches: 134, Mismatches: 14, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
29 8 0.06
30 126 0.94
ACGTcount: A:0.39, C:0.17, G:0.02, T:0.41
Consensus pattern (30 bp):
TAAACTTTTCAAAAATTATATTTTAACCCT
Found at i:93303 original size:43 final size:44
Alignment explanation
Indices: 93222--93304 Score: 105
Period size: 43 Copynumber: 1.9 Consensus size: 44
93212 TCAAATCCTT
* *
93222 TTTAGCCTAGAAATTTCATTTTATTCTTCCATTAAATTTTCAAA
1 TTTAGCCTACAAATTTCATTTTATTCTTCCATCAAATTTTCAAA
* * * *
93266 TTTAGGCTACAAATTT-ATTTTGTTTTTCCCTCAAATTTT
1 TTTAGCCTACAAATTTCATTTTATTCTTCCATCAAATTTT
93305 ATTTTAAAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
43 19 0.58
44 14 0.42
ACGTcount: A:0.28, C:0.16, G:0.06, T:0.51
Consensus pattern (44 bp):
TTTAGCCTACAAATTTCATTTTATTCTTCCATCAAATTTTCAAA
Found at i:95366 original size:30 final size:30
Alignment explanation
Indices: 95332--95389 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
95322 TTTCAAAATC
* *
95332 ATATTTTTATCCTCAAATTTTTTAAAATTT
1 ATATTTTAATCATCAAATTTTTTAAAATTT
* *
95362 ATATTTTAATCATGAACTTTTTTAAAAT
1 ATATTTTAATCATCAAATTTTTTAAAAT
95390 CACATTTTGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.36, C:0.09, G:0.02, T:0.53
Consensus pattern (30 bp):
ATATTTTAATCATCAAATTTTTTAAAATTT
Found at i:95410 original size:30 final size:29
Alignment explanation
Indices: 95376--95613 Score: 241
Period size: 30 Copynumber: 8.1 Consensus size: 29
95366 TTTAATCATG
* *
95376 AACTTTTTTAAAATCACATTTTGACCTCTA
1 AACTTTTCTAAAATCACATTTTAACC-CTA
* *
95406 AACTTTT-TCAAAATCATATTTTGACACCTA
1 AACTTTTCT-AAAATCACATTTTAAC-CCTA
95436 AACTTTTCTAAAATCACATTTTAACCCCTA
1 AACTTTTCTAAAATCACATTTTAA-CCCTA
* *
95466 AACTTTTCCAAAATCACATTTTGACCCTTA
1 AACTTTTCTAAAATCACATTTTAACCC-TA
* **
95496 AATTTTTCTAAAATCATGTTTTAACCCTA
1 AACTTTTCTAAAATCACATTTTAACCCTA
* *
95525 AAC-TTTC-ATAATCACTTTTTAACCCCTA
1 AACTTTTCTAAAATCACATTTTAA-CCCTA
* * *
95553 AACTTTTCTAAAATTACATTTTGATCCTTA
1 AACTTTTCTAAAATCACATTTT-AACCCTA
*
95583 AA-TTTTCCTAAAATTACATTTTAACCCTA
1 AACTTTT-CTAAAATCACATTTTAACCCTA
95612 AA
1 AA
95614 TTCTCCGAAA
Statistics
Matches: 177, Mismatches: 21, Indels: 21
0.81 0.10 0.10
Matches are distributed among these distances:
27 12 0.07
28 12 0.07
29 23 0.13
30 126 0.71
31 4 0.02
ACGTcount: A:0.35, C:0.22, G:0.02, T:0.41
Consensus pattern (29 bp):
AACTTTTCTAAAATCACATTTTAACCCTA
Found at i:95566 original size:87 final size:88
Alignment explanation
Indices: 95376--95613 Score: 320
Period size: 87 Copynumber: 2.7 Consensus size: 88
95366 TTTAATCATG
* *
95376 AACTTTTTTAAAATCACATTTTGACCTCTAAACTTTTTC-AAAATCATATTTTGACACCTAAACT
1 AACTTTTCTAAAATCACATTTTGACCT-TAAA-TTTTTCTAAAATCATATTTTAAC-CCTAAACT
95440 TTTCTAAAATCACATTTTAACCCCTA
63 TTTCTAAAATCACATTTTAACCCCTA
* *
95466 AACTTTTCCAAAATCACATTTTGACCCTTAAATTTTTCTAAAATCATGTTTTAACCCTAAAC-TT
1 AACTTTTCTAAAATCACATTTTGA-CCTTAAATTTTTCTAAAATCATATTTTAACCCTAAACTTT
* *
95530 TC-ATAATCACTTTTTAACCCCTA
65 TCTAAAATCACATTTTAACCCCTA
* * * *
95553 AACTTTTCTAAAATTACATTTTGATCCTTAAATTTTCCTAAAATTACATTTTAACCCTAAA
1 AACTTTTCTAAAATCACATTTTGA-CCTTAAATTTTTCTAAAATCATATTTTAACCCTAAA
95614 TTCTCCGAAA
Statistics
Matches: 133, Mismatches: 13, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
87 73 0.55
88 4 0.03
89 13 0.10
90 40 0.30
91 3 0.02
ACGTcount: A:0.35, C:0.22, G:0.02, T:0.41
Consensus pattern (88 bp):
AACTTTTCTAAAATCACATTTTGACCTTAAATTTTTCTAAAATCATATTTTAACCCTAAACTTTT
CTAAAATCACATTTTAACCCCTA
Found at i:97870 original size:11 final size:11
Alignment explanation
Indices: 97827--97873 Score: 55
Period size: 11 Copynumber: 4.5 Consensus size: 11
97817 TTATAAAAAT
97827 TTAATTTAATAA
1 TTAATTTAAT-A
*
97839 TTATTTTAATA
1 TTAATTTAATA
97850 TT-ATTT--TA
1 TTAATTTAATA
97858 TTAATTTAATA
1 TTAATTTAATA
97869 TTAAT
1 TTAAT
97874 GTGATTATCT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
8 4 0.13
9 4 0.13
10 3 0.10
11 10 0.33
12 9 0.30
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
TTAATTTAATA
Found at i:97880 original size:20 final size:20
Alignment explanation
Indices: 97838--97892 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
97828 TAATTTAATA
* * *
97838 ATTATTTTAATATT-ATTTT
1 ATTAATTTAATATTAATGTG
97857 ATTAATTTAATATTAATGTG
1 ATTAATTTAATATTAATGTG
97877 ATT-ATCTTAATATTAA
1 ATTAAT-TTAATATTAA
97893 ATTTAATGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 15 0.48
20 16 0.52
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (20 bp):
ATTAATTTAATATTAATGTG
Found at i:97969 original size:62 final size:57
Alignment explanation
Indices: 97826--98019 Score: 133
Period size: 59 Copynumber: 3.2 Consensus size: 57
97816 TTTATAAAAA
* * * *
97826 TTTAATTTAATAATTAT-TTTA-ATATTATTTTATTAATTTAATATTAATGTGATTATCTTAAT
1 TTTAATTTAATATTTATCTTTATA-AATATTATATTAATTTAATATTAA----ATGA--TTAAT
* * *
97888 ATTAAATTTAATGTTTATCTTGTAGATAAATATTTTATTAATTTAATAAGATTAAAT-ATTAAT
1 -TTTAATTTAATATTTATCTT-T--ATAAATATTATATTAATTTAAT---ATTAAATGATTAAT
* * * *
97951 TTTAATTTACTATTTATCTTTATAAGTGTTATATTAATTTAATATTAAATGATTAAG
1 TTTAATTTAATATTTATCTTTATAAATATTATATTAATTTAATATTAAATGATTAAT
98008 TTTAATTATAAT
1 TTTAATT-TAAT
98020 TGATCTTTCT
Statistics
Matches: 109, Mismatches: 12, Indels: 25
0.75 0.08 0.17
Matches are distributed among these distances:
56 7 0.06
57 12 0.11
58 3 0.03
59 19 0.17
61 1 0.01
62 17 0.16
63 19 0.17
64 2 0.02
65 2 0.02
66 2 0.02
67 19 0.17
68 1 0.01
70 5 0.05
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.54
Consensus pattern (57 bp):
TTTAATTTAATATTTATCTTTATAAATATTATATTAATTTAATATTAAATGATTAAT
Found at i:101801 original size:13 final size:13
Alignment explanation
Indices: 101783--101820 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
101773 TCATTGCAAC
101783 ATATGTAAAATAT
1 ATATGTAAAATAT
*
101796 ATATGTAAAA-AC
1 ATATGTAAAATAT
101808 A-ATGTAAAATAT
1 ATATGTAAAATAT
101820 A
1 A
101821 AAATTATTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
11 8 0.36
12 4 0.18
13 10 0.45
ACGTcount: A:0.58, C:0.03, G:0.08, T:0.32
Consensus pattern (13 bp):
ATATGTAAAATAT
Found at i:102013 original size:20 final size:20
Alignment explanation
Indices: 101990--102040 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
101980 AAATATTATC
*
101990 TTTTTCAAAAAAGTAATTCA
1 TTTTACAAAAAAGTAATTCA
* *
102010 TTTTACAGAAAAGTAATTTA
1 TTTTACAAAAAAGTAATTCA
*
102030 TTTTCCAAAAA
1 TTTTACAAAAA
102041 TCATTTTTCA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.45, C:0.10, G:0.06, T:0.39
Consensus pattern (20 bp):
TTTTACAAAAAAGTAATTCA
Found at i:102446 original size:29 final size:30
Alignment explanation
Indices: 102404--102463 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 30
102394 GAATTTGATC
* *
102404 AAATCAAAATTTCATGTATAAAATTGCACA
1 AAATCAAAAGTTCATGTATAAAATTACACA
*
102434 AAATC-AAAGTTCATGTATATAATTACACA
1 AAATCAAAAGTTCATGTATAAAATTACACA
102463 A
1 A
102464 TTACACATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 22 0.81
30 5 0.19
ACGTcount: A:0.50, C:0.13, G:0.07, T:0.30
Consensus pattern (30 bp):
AAATCAAAAGTTCATGTATAAAATTACACA
Found at i:108346 original size:13 final size:14
Alignment explanation
Indices: 108329--108362 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
108319 CTTCTTTTTT
108329 TTGGGGGTGAGGGG
1 TTGGGGGTGAGGGG
108343 -TGGGGG-GAGGGG
1 TTGGGGGTGAGGGG
108355 TTGGGGGT
1 TTGGGGGT
108363 AATCTTATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
12 6 0.33
13 12 0.67
ACGTcount: A:0.06, C:0.00, G:0.74, T:0.21
Consensus pattern (14 bp):
TTGGGGGTGAGGGG
Found at i:111446 original size:17 final size:17
Alignment explanation
Indices: 111424--111461 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
111414 ATACGAAAAC
**
111424 GAAAATAAATTGAAGAA
1 GAAAATAAAAAGAAGAA
111441 GAAAATAAAAAGAAGAA
1 GAAAATAAAAAGAAGAA
111458 GAAA
1 GAAA
111462 CCTCCTCGGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.71, C:0.00, G:0.18, T:0.11
Consensus pattern (17 bp):
GAAAATAAAAAGAAGAA
Found at i:116080 original size:28 final size:27
Alignment explanation
Indices: 116040--116094 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 27
116030 AACTTGAAAT
116040 ATATAAAATTTATTATAAAAAGTCATAAAA
1 ATATAAAATTTATTA-AAAAA--CATAAAA
116070 ATAT-AAA-TTATTAAAAAACATAAAA
1 ATATAAAATTTATTAAAAAACATAAAA
116095 TTACATAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
25 7 0.28
27 5 0.20
28 6 0.24
29 3 0.12
30 4 0.16
ACGTcount: A:0.64, C:0.04, G:0.02, T:0.31
Consensus pattern (27 bp):
ATATAAAATTTATTAAAAAACATAAAA
Found at i:119726 original size:83 final size:82
Alignment explanation
Indices: 119457--120075 Score: 764
Period size: 82 Copynumber: 7.5 Consensus size: 82
119447 TAAAAATTAA
* **
119457 AATTGAATAATTTTGTTTTGGGATTTATTCCTG-CGATTCAAC-TGATTTTATTCTATTTTGATT
1 AATTGAATAATTCTGTTTCAGGATTTATTCCTGCCG-TTCAACAT-ATTTTATTCTATTTTGATT
* * *
119520 ATGTATCCTAACAAGAATT
64 TTGTTTCCAAACAAGAATT
* * * *
119539 AATTGAATAATTATGTTTCAGGATTTATTCCAGCTGTTCAACATATTTTATTCTATTTTGAATTT
1 AATTGAATAATTCTGTTTCAGGATTTATTCCTGCCGTTCAACATATTTTATTCTATTTTGATTTT
*
119604 GTTTCCAAA-AATAATT
66 GTTTCCAAACAAGAATT
* * * * * *
119620 AACTGAATAATTCTGTTTTAGGATTTATT-CTCGCCGTTCAATAGATTTTTTTTCGT-TTTTTAT
1 AATTGAATAATTCTGTTTCAGGATTTATTCCT-GCCGTTCAACATA-TTTTATTC-TATTTTGAT
119683 TTTGTTTCCAAACAAGAATT
63 TTTGTTTCCAAACAAGAATT
* * *
119703 AATTAAATAATTCTGTTTCAGGATTTATTCCTGTCGTTCAACATATTTTTATTCTATTTTGATTC
1 AATTGAATAATTCTGTTTCAGGATTTATTCCTGCCGTTCAACATA-TTTTATTCTATTTTGATTT
*
119768 TGTTTCCTAACAAGAATT
65 TGTTTCCAAACAAGAATT
* *
119786 AATTGAATAATTCTATTTCAGGATTTATTCCTCCCGTTCAACATATTTTATTCTATTTTGATTTT
1 AATTGAATAATTCTGTTTCAGGATTTATTCCTGCCGTTCAACATATTTTATTCTATTTTGATTTT
* *
119851 ATTTCCGAACAAGAATT
66 GTTTCCAAACAAGAATT
* * *
119868 AGTTGAATAATTCCGTTTCAGGATTTATTCTTGCCGTTCAACATATTTTATTCTATTTTGATTTT
1 AATTGAATAATTCTGTTTCAGGATTTATTCCTGCCGTTCAACATATTTTATTCTATTTTGATTTT
119933 GTTTCCAAACAAGAATT
66 GTTTCCAAACAAGAATT
* * * * * * * *
119950 AATTAAATAATTTTGTTTCGGGATTTATTCCTGCCATACAACAAAATTTTTTTC-ATTTTTTATT
1 AATTGAATAATTCTGTTTCAGGATTTATTCCTGCCGTTCAAC-ATATTTTATTCTA-TTTTGATT
120014 TTGTTTCCAAACAAGAATT
64 TTGTTTCCAAACAAGAATT
* ** *
120033 AATTAAATAATTCTGTTTCAGGATTTATTTTTGTCGTTCAACA
1 AATTGAATAATTCTGTTTCAGGATTTATTCCTGCCGTTCAACA
120076 GAATTGATTT
Statistics
Matches: 464, Mismatches: 63, Indels: 20
0.85 0.12 0.04
Matches are distributed among these distances:
80 1 0.00
81 42 0.09
82 231 0.50
83 188 0.41
84 2 0.00
ACGTcount: A:0.29, C:0.13, G:0.11, T:0.47
Consensus pattern (82 bp):
AATTGAATAATTCTGTTTCAGGATTTATTCCTGCCGTTCAACATATTTTATTCTATTTTGATTTT
GTTTCCAAACAAGAATT
Found at i:119938 original size:247 final size:246
Alignment explanation
Indices: 119457--120061 Score: 817
Period size: 247 Copynumber: 2.5 Consensus size: 246
119447 TAAAAATTAA
* *
119457 AATTGAATAATTTTGTTTTGGGATTTATTCCTGCGATTCAAC-TGA-TTTTATTCTATTTTGATT
1 AATTAAATAATTTTGTTTCGGGATTTATTCCTGCG-TTCAACAT-ATTTTTATTCTATTTTGATT
* * * *
119520 ATGTATCCTAACAAGAATTAATTGAATAATTATGTTTCAGGATTTATTCCAGCTGTTCAACATAT
64 ATGTTTCCTAACAAGAATTAATTGAATAATTCTGTTTCAGGATTTATTCCACCCGTTCAACATAT
* * * *
119585 TTTATTCTATTTTGAATTTGTTTCCAAAAATAATTAACTGAATAATTCTGTTTTAGGATTTATTC
129 TTTATTCTATTTTGAATTTATTTCCAAAAAGAATTAACTGAATAATTCCGTTTCAGGATTTATTC
* * *
119650 TCGCCGTTCAATAGATTTTTTTTCGTTTTTTATTTTGTTTCCAAACAAGAATT
194 TCGCCGTTCAACAGATTTTTATTCGTTTTTGATTTTGTTTCCAAACAAGAATT
* * *
119703 AATTAAATAATTCTGTTTCAGGATTTATTCCTGTCGTTCAACATATTTTTATTCTATTTTGATTC
1 AATTAAATAATTTTGTTTCGGGATTTATTCCTG-CGTTCAACATATTTTTATTCTATTTTGATTA
* *
119768 TGTTTCCTAACAAGAATTAATTGAATAATTCTATTTCAGGATTTATTCCTCCCGTTCAACATATT
65 TGTTTCCTAACAAGAATTAATTGAATAATTCTGTTTCAGGATTTATTCCACCCGTTCAACATATT
* * **
119833 TTATTCTATTTTGATTTTATTTCCGAACAAGAATTAGTTGAATAATTCCGTTTCAGGATTTATTC
130 TTATTCTATTTTGAATTTATTTCC-AAAAAGAATTAACTGAATAATTCCGTTTCAGGATTTATTC
* *
119898 TTGCCGTTCAACATA-TTTTATTC-TATTTTGATTTTGTTTCCAAACAAGAATT
194 TCGCCGTTCAACAGATTTTTATTCGT-TTTTGATTTTGTTTCCAAACAAGAATT
* * * *
119950 AATTAAATAATTTTGTTTCGGGATTTATTCCTGCCATACAACAAAATTTTT-TTC-ATTTTTTAT
1 AATTAAATAATTTTGTTTCGGGATTTATTCCTG-CGTTCAAC-ATATTTTTATTCTA-TTTTGAT
* * *
120013 TTTGTTTCCAAACAAGAATTAATTAAATAATTCTGTTTCAGGATTTATT
63 TATGTTTCCTAACAAGAATTAATTGAATAATTCTGTTTCAGGATTTATT
120062 TTTGTCGTTC
Statistics
Matches: 317, Mismatches: 35, Indels: 13
0.87 0.10 0.04
Matches are distributed among these distances:
246 38 0.12
247 226 0.71
248 53 0.17
ACGTcount: A:0.29, C:0.13, G:0.11, T:0.47
Consensus pattern (246 bp):
AATTAAATAATTTTGTTTCGGGATTTATTCCTGCGTTCAACATATTTTTATTCTATTTTGATTAT
GTTTCCTAACAAGAATTAATTGAATAATTCTGTTTCAGGATTTATTCCACCCGTTCAACATATTT
TATTCTATTTTGAATTTATTTCCAAAAAGAATTAACTGAATAATTCCGTTTCAGGATTTATTCTC
GCCGTTCAACAGATTTTTATTCGTTTTTGATTTTGTTTCCAAACAAGAATT
Found at i:120525 original size:17 final size:17
Alignment explanation
Indices: 120513--120548 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
120503 ATAAAAATTA
120513 TAAAAACTAAAAAATCAT
1 TAAAAA-TAAAAAATCAT
120531 TAAAAATAAAAAAT-AT
1 TAAAAATAAAAAATCAT
120547 TA
1 TA
120549 CATACCCCGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 4 0.22
17 8 0.44
18 6 0.33
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.25
Consensus pattern (17 bp):
TAAAAATAAAAAATCAT
Found at i:120548 original size:16 final size:16
Alignment explanation
Indices: 120503--120548 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 16
120493 ATTAGAATTT
*
120503 ATAAAAATTA-TAAAA
1 ATAAAAAATATTAAAA
120518 ACTAAAAAATCATTAAAA
1 A-TAAAAAAT-ATTAAAA
120536 ATAAAAAATATTA
1 ATAAAAAATATTA
120549 CATACCCCGA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
15 1 0.04
16 11 0.41
17 9 0.33
18 6 0.22
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.26
Consensus pattern (16 bp):
ATAAAAAATATTAAAA
Found at i:121289 original size:20 final size:20
Alignment explanation
Indices: 121240--121291 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
121230 CCACATTTTA
*
121240 TTTTCTATTATTTTTAATAT
1 TTTTATATTATTTTTAATAT
* *
121260 TTTTCTATTATTTTTCAT-T
1 TTTTATATTATTTTTAATAT
121279 TTTTATAATTATT
1 TTTTAT-ATTATT
121292 AAAAATTCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 6 0.21
20 23 0.79
ACGTcount: A:0.23, C:0.06, G:0.00, T:0.71
Consensus pattern (20 bp):
TTTTATATTATTTTTAATAT
Done.