Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013712.1 Kokia drynarioides strain JFW-HI SEQ_128740, 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: 240913
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 144 characters in sequence are not A, C, G, or T
Found at i:2193 original size:16 final size:16
Alignment explanation
Indices: 2168--2200 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
2158 TTATCCACCC
2168 AAACCCAATCCAATAT
1 AAACCCAATCCAATAT
*
2184 AAACCTAATCCAATAT
1 AAACCCAATCCAATAT
2200 A
1 A
2201 TACAAACTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.52, C:0.27, G:0.00, T:0.21
Consensus pattern (16 bp):
AAACCCAATCCAATAT
Found at i:2264 original size:18 final size:18
Alignment explanation
Indices: 2232--2266 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
2222 CAACCCAATC
2232 TTAAAAATTACAAATAAT
1 TTAAAAATTACAAATAAT
2250 TTAATAAATTA-AAATAA
1 TTAA-AAATTACAAATAA
2267 AAATCCTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (18 bp):
TTAAAAATTACAAATAAT
Found at i:3460 original size:6 final size:7
Alignment explanation
Indices: 3439--3463 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
3429 NNNCCTTTTA
3439 TTTCTTT
1 TTTCTTT
3446 TTTCTTT
1 TTTCTTT
3453 TTTCTTT
1 TTTCTTT
3460 TTTC
1 TTTC
3464 ATTATTTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (7 bp):
TTTCTTT
Found at i:6531 original size:138 final size:134
Alignment explanation
Indices: 6298--6562 Score: 300
Period size: 138 Copynumber: 1.9 Consensus size: 134
6288 TTAGAAATTT
* ** * *
6298 TCCTTCACCATTCATGGTTTGATCTCTAAAAACTGTTCAGTAATTGTTTCTTGCAATTTTGAATT
1 TCCTTAACCATTCATGGTTCAATCTCTAAAAACTGTTCAGAAATAGTTTCTTGCAATTTTGAATT
* * * * *
6363 TTCTTGCAAATTCCAACAAGCTGTATTTTTTGTAATTTACTGCAAATGTCAGGAAAATGAGAGGT
66 TTCTTGCAAATTCCAACAAGCTGTAGTTTTTGGAACTTACTGCAAATATCAGGAAAACGAGAGGT
6428 ATTG
131 ATTG
* *
6432 TCCTTAACCATTCATGGTTCAATCTCTGAAAAACTGTTGTTAGAAGATAGTTTCTTGCTATTTTG
1 TCCTTAACCATTCATGGTTCAATCTCT-AAAAACTG-T-TCAGAA-ATAGTTTCTTGCAATTTTG
** * * * *
6497 TGTTTTCTTTC-AATTCCCTAA-AATCTTTAGTTTTTGGAACTTACTGCAGATATCAGGAAAACG
62 AATTTTCTTGCAAATT-CC-AACAAGCTGTAGTTTTTGGAACTTACTGCAAATATCAGGAAAACG
6560 AGA
125 AGA
6563 TGTCACAAAG
Statistics
Matches: 107, Mismatches: 18, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
134 24 0.22
135 8 0.07
136 1 0.01
137 8 0.07
138 64 0.60
139 2 0.02
ACGTcount: A:0.28, C:0.16, G:0.15, T:0.40
Consensus pattern (134 bp):
TCCTTAACCATTCATGGTTCAATCTCTAAAAACTGTTCAGAAATAGTTTCTTGCAATTTTGAATT
TTCTTGCAAATTCCAACAAGCTGTAGTTTTTGGAACTTACTGCAAATATCAGGAAAACGAGAGGT
ATTG
Found at i:8504 original size:19 final size:19
Alignment explanation
Indices: 8463--8513 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 19
8453 AATTACAAAC
* *
8463 AAAATTCACAATAATTTTT
1 AAAATTCAAAATAATTTTG
8482 AAAATTCAAAAT-ATTTATG
1 AAAATTCAAAATAATTT-TG
8501 AAAATTTCAAAAT
1 AAAA-TTCAAAAT
8514 TTATATTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 4 0.14
19 16 0.57
20 8 0.29
ACGTcount: A:0.53, C:0.08, G:0.02, T:0.37
Consensus pattern (19 bp):
AAAATTCAAAATAATTTTG
Found at i:8544 original size:19 final size:18
Alignment explanation
Indices: 8520--8586 Score: 64
Period size: 19 Copynumber: 3.6 Consensus size: 18
8510 AAATTTATAT
*
8520 TTTAAAAAAATTCTAAAAA
1 TTTAAAAAAATT-AAAAAA
8539 TTTAAAAAACATTAAAAAA
1 TTTAAAAAA-ATTAAAAAA
* *
8558 TCTAAAGAACATATAAAAAA
1 TTTAAA-AAAAT-TAAAAAA
8578 -TTAAAAAAA
1 TTTAAAAAAA
8587 AATTCTAAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
18 3 0.08
19 25 0.62
20 12 0.30
ACGTcount: A:0.67, C:0.06, G:0.01, T:0.25
Consensus pattern (18 bp):
TTTAAAAAAATTAAAAAA
Found at i:8546 original size:20 final size:19
Alignment explanation
Indices: 8518--8590 Score: 65
Period size: 20 Copynumber: 3.7 Consensus size: 19
8508 CAAAATTTAT
* *
8518 ATTTTAAAAAAATTCTAAAA
1 ATTTAAAAAAAATT-AAAAA
*
8538 ATTTAAAAAACATTAAAAA
1 ATTTAAAAAAAATTAAAAA
* * *
8557 ATCTAAAGAACATATAAAAA
1 ATTTAAAAAAAAT-TAAAAA
*
8577 ATTAAAAAAAAATT
1 ATTTAAAAAAAATT
8591 CTAAAATAAT
Statistics
Matches: 43, Mismatches: 9, Indels: 3
0.78 0.16 0.05
Matches are distributed among these distances:
19 16 0.37
20 27 0.63
ACGTcount: A:0.66, C:0.05, G:0.01, T:0.27
Consensus pattern (19 bp):
ATTTAAAAAAAATTAAAAA
Found at i:19142 original size:51 final size:51
Alignment explanation
Indices: 19025--19259 Score: 283
Period size: 51 Copynumber: 4.6 Consensus size: 51
19015 TTTCATTTAA
* * ** * * *
19025 TACTCACGATGATA-TATAGTCATCGGACCTCTTGTTCCATATAGGAATCCATA
1 TACTCACGATGACACT-TAGTCATCGGACC-ATTAATCCATAAAGG-ATTCATT
* *
19078 AACTCACGATGACACTTAGTCATTGGACCATTAATCCATAAAGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCATTAATCCATAAAGGATTCATT
*
19129 TACTCACAATGACACTTAGTCATCGGACCATTAATCCATAAAGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCATTAATCCATAAAGGATTCATT
* * * *
19180 CACTCATGATGACACTTAGTCATCGAACCTTTAATCCATAAAGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCATTAATCCATAAAGGATTCATT
* * *
19231 TGCTCACGACGACACTTAGTCATCAGACC
1 TACTCACGATGACACTTAGTCATCGGACC
19260 CTTTCGTTTA
Statistics
Matches: 158, Mismatches: 23, Indels: 4
0.85 0.12 0.02
Matches are distributed among these distances:
51 122 0.77
52 11 0.07
53 24 0.15
54 1 0.01
ACGTcount: A:0.33, C:0.24, G:0.14, T:0.29
Consensus pattern (51 bp):
TACTCACGATGACACTTAGTCATCGGACCATTAATCCATAAAGGATTCATT
Found at i:23360 original size:6 final size:6
Alignment explanation
Indices: 23349--23374 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
23339 GATATTTGTG
23349 AAGAAC AAGAAC AAGAAC AAGAAC AA
1 AAGAAC AAGAAC AAGAAC AAGAAC AA
23375 TAAAAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.69, C:0.15, G:0.15, T:0.00
Consensus pattern (6 bp):
AAGAAC
Found at i:23886 original size:17 final size:18
Alignment explanation
Indices: 23847--23886 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
23837 AGCATTTATC
23847 ATTTTAAATGTAATTTAA
1 ATTTTAAATGTAATTTAA
23865 A-TTTAAATTGT-A-TTAA
1 ATTTTAAA-TGTAATTTAA
23881 ATTTTA
1 ATTTTA
23887 TTTTCTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
16 5 0.25
17 11 0.55
18 4 0.20
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (18 bp):
ATTTTAAATGTAATTTAA
Found at i:25970 original size:32 final size:32
Alignment explanation
Indices: 25925--25990 Score: 98
Period size: 32 Copynumber: 2.1 Consensus size: 32
25915 CGGATTTAGG
25925 GAAAATAAAAGAAAAGATGGATTGAGATTAAA
1 GAAAATAAAAGAAAAGATGGATTGAGATTAAA
* *
25957 GAAAA-AAAGAGAAAGGATTGATTGAGATTAAA
1 GAAAATAAA-AGAAAAGATGGATTGAGATTAAA
25989 GA
1 GA
25991 GAAGAAAATG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
31 3 0.10
32 28 0.90
ACGTcount: A:0.58, C:0.00, G:0.24, T:0.18
Consensus pattern (32 bp):
GAAAATAAAAGAAAAGATGGATTGAGATTAAA
Found at i:35070 original size:21 final size:22
Alignment explanation
Indices: 35046--35087 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
35036 TAATTAATTT
*
35046 TAAAT-TTTTATGATATAAAAA
1 TAAATGTTTTATAATATAAAAA
*
35067 TAAATGTTTTATAATTTAAAA
1 TAAATGTTTTATAATATAAAA
35088 GTTCTTGAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (22 bp):
TAAATGTTTTATAATATAAAAA
Found at i:35711 original size:18 final size:18
Alignment explanation
Indices: 35657--35733 Score: 59
Period size: 18 Copynumber: 4.2 Consensus size: 18
35647 ATTATTTGAA
35657 ATAATTATTTTTAATTTTT
1 ATAA-TATTTTTAATTTTT
** *
35676 ATTTTATTTTTAAATTTT
1 ATAATATTTTTAATTTTT
35694 A-AATAGTTTTTAATTTTT
1 ATAATA-TTTTTAATTTTT
* *
35712 CACAA-ATTTTATAATTGTT
1 -ATAATATTTT-TAATTTTT
35731 ATA
1 ATA
35734 CTTTTTATTG
Statistics
Matches: 46, Mismatches: 8, Indels: 9
0.73 0.13 0.14
Matches are distributed among these distances:
17 2 0.04
18 31 0.67
19 11 0.24
20 2 0.04
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.61
Consensus pattern (18 bp):
ATAATATTTTTAATTTTT
Found at i:40587 original size:18 final size:19
Alignment explanation
Indices: 40564--40603 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
40554 GATTTTATTT
* *
40564 TTATATTATT-TATTTATG
1 TTATATGATTCTATTTAGG
40582 TTATATGATTCTATTTAGG
1 TTATATGATTCTATTTAGG
40601 TTA
1 TTA
40604 ATTTTTACTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.28, C:0.03, G:0.10, T:0.60
Consensus pattern (19 bp):
TTATATGATTCTATTTAGG
Found at i:41668 original size:21 final size:21
Alignment explanation
Indices: 41639--41744 Score: 90
Period size: 21 Copynumber: 4.9 Consensus size: 21
41629 AATTAACACG
*
41639 AAAACAACAACCAAAACAATA
1 AAAAAAACAACCAAAACAATA
* *
41660 AAAAAAAC-ACCAAAATAGTAAA
1 AAAAAAACAACCAAAACA--ATA
*
41682 AAAAAAACAACACGAAAACAACA
1 AAAAAAACAAC-C-AAAACAATA
* * *
41705 AAAAAAGCAATCAAAACAGTA
1 AAAAAAACAACCAAAACAATA
41726 AAAAAAAGC-ACCAAAACAA
1 AAAAAAA-CAACCAAAACAA
41745 CAATATAATT
Statistics
Matches: 67, Mismatches: 12, Indels: 12
0.74 0.13 0.13
Matches are distributed among these distances:
20 8 0.12
21 28 0.42
22 12 0.18
23 13 0.19
24 1 0.01
25 5 0.07
ACGTcount: A:0.72, C:0.19, G:0.05, T:0.05
Consensus pattern (21 bp):
AAAAAAACAACCAAAACAATA
Found at i:41708 original size:45 final size:47
Alignment explanation
Indices: 41639--41732 Score: 129
Period size: 46 Copynumber: 2.0 Consensus size: 47
41629 AATTAACACG
* *
41639 AAAACAACAACCAAAACAATAAAAAAAAC-ACCAAAATAGTAAAAAA
1 AAAACAACAACCAAAACAACAAAAAAAACAACCAAAACAGTAAAAAA
* * *
41685 AAAACAAC-ACGAAAACAACAAAAAAAGCAATCAAAACAGTAAAAAA
1 AAAACAACAACCAAAACAACAAAAAAAACAACCAAAACAGTAAAAAA
41731 AA
1 AA
41733 GCACCAAAAC
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
45 17 0.40
46 25 0.60
ACGTcount: A:0.73, C:0.17, G:0.04, T:0.05
Consensus pattern (47 bp):
AAAACAACAACCAAAACAACAAAAAAAACAACCAAAACAGTAAAAAA
Found at i:46850 original size:29 final size:28
Alignment explanation
Indices: 46795--47034 Score: 184
Period size: 29 Copynumber: 8.3 Consensus size: 28
46785 CCTTGGAGGT
*
46795 CCCT-AAACTATCCAAAAATTCCATTTTGA
1 CCCTCAAACT-TCCAAAAATT-CATTTTTA
* *
46824 CCC-AAAACTTCAAAAAATTACATTTTTA
1 CCCTCAAACTTCCAAAAATT-CATTTTTA
46852 CCC-CTAAACTTCCAAAAATTCTATTTTTA
1 CCCTC-AAACTTCCAAAAATTC-ATTTTTA
46881 CCCTCAAACTTCCAAAATATTCATTTTTGA
1 CCCTCAAACTTCCAAAA-ATTCATTTTT-A
** *** *
46911 CCCAAAAACTTTTGAGAATTACATTTTTA
1 CCCTCAAACTTCCAAAAATT-CATTTTTA
* *
46940 CCCTCGAACTTCTAAAAATTCTATTTTTGA
1 CCCTCAAACTTCCAAAAATTC-ATTTTT-A
*** *
46970 -CCTCGAAACTTTTGAAATTTACATTTTTA
1 CCCTC-AAACTTCCAAAAATT-CATTTTTA
*
46999 CCCTCAAACTTCCAAAAATTCCATTTTAA
1 CCCTCAAACTTCCAAAAATT-CATTTTTA
47028 CCC-CAAA
1 CCCTCAAA
47035 TTTTCCCAAA
Statistics
Matches: 172, Mismatches: 27, Indels: 25
0.77 0.12 0.11
Matches are distributed among these distances:
28 25 0.15
29 100 0.58
30 46 0.27
31 1 0.01
ACGTcount: A:0.36, C:0.25, G:0.03, T:0.35
Consensus pattern (28 bp):
CCCTCAAACTTCCAAAAATTCATTTTTA
Found at i:46937 original size:59 final size:58
Alignment explanation
Indices: 46874--47025 Score: 218
Period size: 59 Copynumber: 2.6 Consensus size: 58
46864 CAAAAATTCT
46874 ATTTTTACCCTCAAACTTCCAAAATATTCATTTTTGACC-CAAAAACTTTTGAGAA-TTAC
1 ATTTTTACCCTCAAACTTCCAAAA-ATTCATTTTTGACCTC-AAAACTTTTGA-AATTTAC
* * *
46933 ATTTTTACCCTCGAACTTCTAAAAATTCTATTTTTGACCTCGAAACTTTTGAAATTTAC
1 ATTTTTACCCTCAAACTTCCAAAAATTC-ATTTTTGACCTCAAAACTTTTGAAATTTAC
46992 ATTTTTACCCTCAAACTTCCAAAAATTCCATTTT
1 ATTTTTACCCTCAAACTTCCAAAAATT-CATTTT
47026 AACCCCAAAT
Statistics
Matches: 84, Mismatches: 5, Indels: 8
0.87 0.05 0.08
Matches are distributed among these distances:
58 6 0.07
59 76 0.90
60 2 0.02
ACGTcount: A:0.33, C:0.22, G:0.05, T:0.40
Consensus pattern (58 bp):
ATTTTTACCCTCAAACTTCCAAAAATTCATTTTTGACCTCAAAACTTTTGAAATTTAC
Found at i:46950 original size:88 final size:87
Alignment explanation
Indices: 46795--47031 Score: 232
Period size: 88 Copynumber: 2.7 Consensus size: 87
46785 CCTTGGAGGT
46795 CCCT-AAACTATCCAAAAATTCCATTTTGACCCAAAACTTCAAAAAATTACATTTTTACCCCTAA
1 CCCTCAAACT-TCCAAAAATTCCATTTTGACCCAAAACTTCAAAAAATTACATTTTTACCCCTAA
46859 ACTTCCAAAAATTCTATTTTT-A
65 ACTTCCAAAAATTCTATTTTTGA
*** *
46881 CCCTCAAACTTCCAAAATATT-CATTTTTGACCCAAAAACTTTTGAGAATTACATTTTTA-CCCT
1 CCCTCAAACTTCCAAAA-ATTCCA-TTTTGACCC-AAAACTTCAAAAAATTACATTTTTACCCCT
* *
46944 CGAACTTCTAAAAATTCTATTTTTGA
63 -AAACTTCCAAAAATTCTATTTTTGA
*** * * * * * * *
46970 -CCTCGAAACTTTTGAAATTTACATTTTTACCCTCAAACTTCCAAAAATTCCATTTTAACCCC
1 CCCTC-AAACTTCCAAAAATTCCATTTTGACCC-AAAACTTCAAAAAATTACATTTTTACCCC
47032 AAATTTTCCC
Statistics
Matches: 123, Mismatches: 19, Indels: 15
0.78 0.12 0.10
Matches are distributed among these distances:
86 13 0.11
87 21 0.17
88 74 0.60
89 15 0.12
ACGTcount: A:0.35, C:0.25, G:0.03, T:0.36
Consensus pattern (87 bp):
CCCTCAAACTTCCAAAAATTCCATTTTGACCCAAAACTTCAAAAAATTACATTTTTACCCCTAAA
CTTCCAAAAATTCTATTTTTGA
Found at i:47040 original size:29 final size:28
Alignment explanation
Indices: 46994--47060 Score: 73
Period size: 30 Copynumber: 2.3 Consensus size: 28
46984 AAATTTACAT
*
46994 TTTTACCCTCAAACTT-CCAAAAATTCCA
1 TTTTACCC-CAAACTTCCCAAAAATACCA
* *
47022 TTTTAACCCCAAATTTTCCCAAAAGTACCA
1 TTTT-ACCCCAAA-CTTCCCAAAAATACCA
47052 TTTTACCCC
1 TTTTACCCC
47061 TCGAGAGTCC
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
28 8 0.24
29 11 0.33
30 14 0.42
ACGTcount: A:0.33, C:0.33, G:0.01, T:0.33
Consensus pattern (28 bp):
TTTTACCCCAAACTTCCCAAAAATACCA
Found at i:47054 original size:59 final size:60
Alignment explanation
Indices: 46805--47059 Score: 201
Period size: 59 Copynumber: 4.4 Consensus size: 60
46795 CCCTAAACTA
* * * * *
46805 TCCAAAAATTCCATTTTGACCC-AAAACTTCAAAAAATTACATTTTT-ACCCCTAAAC--T
1 TCCAAAAATACCATTTTTACCCTCAAACTTCCAAAAATTCCATTTTTGACCCC-AAACTTT
* * *
46862 TCCAAAAATTCTATTTTTACCCTCAAACTTCCAAAATATT-CATTTTTGACCCAAAAACTTT
1 TCCAAAAATACCATTTTTACCCTCAAACTTCCAAAA-ATTCCATTTTTGACCC-CAAACTTT
* * * * * * *
46923 T-GAGAATTA-CATTTTTACCCTCGAACTTCTAAAAATTCTATTTTTGACCTCGAAACTTT
1 TCCAAAAATACCATTTTTACCCTCAAACTTCCAAAAATTCCATTTTTGACC-CCAAACTTT
* ** *
46982 T-GAAATTTA-CATTTTTACCCTCAAACTTCCAAAAATTCCA-TTTTAACCCCAAA-TTT
1 TCCAAAAATACCATTTTTACCCTCAAACTTCCAAAAATTCCATTTTTGACCCCAAACTTT
*
47038 TCCCAAAAGTACCA-TTTTACCC
1 T-CCAAAAATACCATTTTTACCC
47060 CTCGAGAGTC
Statistics
Matches: 163, Mismatches: 24, Indels: 21
0.78 0.12 0.10
Matches are distributed among these distances:
56 4 0.02
57 24 0.15
58 41 0.25
59 87 0.53
60 5 0.03
61 2 0.01
ACGTcount: A:0.35, C:0.25, G:0.04, T:0.36
Consensus pattern (60 bp):
TCCAAAAATACCATTTTTACCCTCAAACTTCCAAAAATTCCATTTTTGACCCCAAACTTT
Found at i:47918 original size:9 final size:10
Alignment explanation
Indices: 47894--47918 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
47884 TAGAGCACAA
47894 ATTTTTTAAG
1 ATTTTTTAAG
47904 ATTTTTTAAG
1 ATTTTTTAAG
47914 ATTTT
1 ATTTT
47919 AGAGAGAGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.28, C:0.00, G:0.08, T:0.64
Consensus pattern (10 bp):
ATTTTTTAAG
Found at i:57173 original size:2 final size:2
Alignment explanation
Indices: 57166--57190 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
57156 AATTTTAGAA
57166 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 A
57191 GTATTTCATA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:64695 original size:19 final size:21
Alignment explanation
Indices: 64656--64697 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
64646 TTGTAAAAAT
64656 TATAATATGTTGGTGTTTTTAA
1 TATAATATGTT-GTGTTTTTAA
64678 TATAATATGTT-T-TTTTTAA
1 TATAATATGTTGTGTTTTTAA
64697 T
1 T
64698 TATATTTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 8 0.40
20 1 0.05
22 11 0.55
ACGTcount: A:0.29, C:0.00, G:0.12, T:0.60
Consensus pattern (21 bp):
TATAATATGTTGTGTTTTTAA
Found at i:67304 original size:22 final size:23
Alignment explanation
Indices: 67278--67321 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
67268 TTTCTTAGAA
67278 AGAAAGA-AAAGAAGGA-AAAAAG
1 AGAAAGATAAA-AAGGACAAAAAG
67300 AGAAAGATAAAAAGGACAAAAA
1 AGAAAGATAAAAAGGACAAAAA
67322 CCATAGTCAC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.73, C:0.02, G:0.23, T:0.02
Consensus pattern (23 bp):
AGAAAGATAAAAAGGACAAAAAG
Found at i:93165 original size:16 final size:17
Alignment explanation
Indices: 93144--93177 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
93134 AAGGTCATAA
93144 ATAAAAG-CAAAATTAC
1 ATAAAAGACAAAATTAC
*
93160 ATAAAAGACCAAATTAC
1 ATAAAAGACAAAATTAC
93177 A
1 A
93178 CAATATGTAA
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:0.62, C:0.15, G:0.06, T:0.18
Consensus pattern (17 bp):
ATAAAAGACAAAATTAC
Found at i:93961 original size:9 final size:9
Alignment explanation
Indices: 93944--94025 Score: 65
Period size: 9 Copynumber: 8.3 Consensus size: 9
93934 TTACATATTC
*
93944 TTTAGATTT
1 TTTAAATTT
93953 TTTAAATTT
1 TTTAAATTT
*
93962 TTTAATTTT
1 TTTAAATTT
93971 TTTAAATATAAAT
1 TTTAAAT-T---T
93984 TTTGAAATTT
1 TTT-AAATTT
93994 TTATAAATTT
1 TT-TAAATTT
*
94004 TTTGAATTT
1 TTTAAATTT
*
94013 TTAAAATTGT
1 TTTAAATT-T
94023 TTT
1 TTT
94026 GATATTTTTA
Statistics
Matches: 59, Mismatches: 7, Indels: 13
0.75 0.09 0.16
Matches are distributed among these distances:
9 34 0.58
10 15 0.25
11 1 0.02
13 5 0.08
14 4 0.07
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (9 bp):
TTTAAATTT
Found at i:93971 original size:18 final size:19
Alignment explanation
Indices: 93950--94034 Score: 75
Period size: 18 Copynumber: 4.2 Consensus size: 19
93940 ATTCTTTAGA
93950 TTTTTTAAATTTTTT-AAT
1 TTTTTTAAATTTTTTGAAT
93968 TTTTTTAAATATAAATTTTGAAAT
1 TTTTTTAAAT-T---TTTTG-AAT
*
93992 TTTTATAAATTTTTTGAA-
1 TTTTTTAAATTTTTTGAAT
*
94010 TTTTTAAAATTGTTTTGATAT
1 TTTTTTAAATT-TTTTGA-AT
94031 TTTT
1 TTTT
94035 AATTTTTGTT
Statistics
Matches: 55, Mismatches: 3, Indels: 15
0.75 0.04 0.21
Matches are distributed among these distances:
18 19 0.35
19 9 0.16
20 6 0.11
21 4 0.07
22 4 0.07
23 1 0.02
24 12 0.22
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.64
Consensus pattern (19 bp):
TTTTTTAAATTTTTTGAAT
Found at i:93982 original size:24 final size:24
Alignment explanation
Indices: 93955--94001 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
93945 TTAGATTTTT
** *
93955 TAAATTTTTTAATTTTTTTAAATA
1 TAAATTTTGAAATTTTTATAAATA
93979 TAAATTTTGAAATTTTTATAAAT
1 TAAATTTTGAAATTTTTATAAAT
94002 TTTTTGAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (24 bp):
TAAATTTTGAAATTTTTATAAATA
Found at i:94036 original size:20 final size:18
Alignment explanation
Indices: 93983--94036 Score: 72
Period size: 19 Copynumber: 2.8 Consensus size: 18
93973 TAAATATAAA
93983 TTTTGAAATTTTTATAAATT
1 TTTTG-AATTTTTA-AAATT
94003 TTTTGAATTTTTAAAATT
1 TTTTGAATTTTTAAAATT
94021 GTTTTGATATTTTTAA
1 -TTTTGA-ATTTTTAA
94037 TTTTTGTTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.16
19 14 0.44
20 13 0.41
ACGTcount: A:0.31, C:0.00, G:0.07, T:0.61
Consensus pattern (18 bp):
TTTTGAATTTTTAAAATT
Found at i:111808 original size:35 final size:35
Alignment explanation
Indices: 111764--111834 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
111754 TGTGTTTAAG
111764 TAAAATTAGAAATTTAATTTGAAAATTAAAAAATT
1 TAAAATTAGAAATTTAATTTGAAAATTAAAAAATT
111799 TAAAATTAGAAATTTAATTTGAAAATTAAAAAATT
1 TAAAATTAGAAATTTAATTTGAAAATTAAAAAATT
111834 T
1 T
111835 TAATGTACTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (35 bp):
TAAAATTAGAAATTTAATTTGAAAATTAAAAAATT
Found at i:112429 original size:12 final size:12
Alignment explanation
Indices: 112408--112441 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
112398 CGATCAAATC
*
112408 AAAACTAAAAAG
1 AAAAATAAAAAG
112420 -AAAATAAAAAG
1 AAAAATAAAAAG
112431 AAAAATAAAAA
1 AAAAATAAAAA
112442 AACTATGAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.82, C:0.03, G:0.06, T:0.09
Consensus pattern (12 bp):
AAAAATAAAAAG
Found at i:116182 original size:6 final size:6
Alignment explanation
Indices: 116171--116200 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
116161 AGCGGTGCCT
*
116171 TCGTCA TCGTCA TCGTCA TCATCA TCGTCA
1 TCGTCA TCGTCA TCGTCA TCGTCA TCGTCA
116201 AGGTTAGTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.20, C:0.33, G:0.13, T:0.33
Consensus pattern (6 bp):
TCGTCA
Found at i:128350 original size:24 final size:23
Alignment explanation
Indices: 128322--128367 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
128312 AACTTGTGCT
128322 TTATCACT-TTTCTTATTTGCTTCC
1 TTATCACTCTTTC-TATTT-CTTCC
*
128346 TTATCATTCTTTCTATTTCTTC
1 TTATCACTCTTTCTATTTCTTC
128368 TTTAAAGGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 4 0.20
24 12 0.60
25 4 0.20
ACGTcount: A:0.13, C:0.24, G:0.02, T:0.61
Consensus pattern (23 bp):
TTATCACTCTTTCTATTTCTTCC
Found at i:135963 original size:41 final size:42
Alignment explanation
Indices: 135882--135975 Score: 118
Period size: 41 Copynumber: 2.3 Consensus size: 42
135872 TTTTCAACAT
* * *
135882 AACCCAGTGCAAGGTTAAAGCTTTGTTGGCCGACTCGGACCC
1 AACCCAGTGCAAGGTTAAAGCTTGGTTAGCAGACTCGGACCC
** *
135924 AACCCAGTGCCGGGTT-AAGCTTGGTTAGCAGACTTGGACCC
1 AACCCAGTGCAAGGTTAAAGCTTGGTTAGCAGACTCGGACCC
*
135965 GACCCAGTGCA
1 AACCCAGTGCA
135976 CAGACCATAC
Statistics
Matches: 44, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
41 30 0.68
42 14 0.32
ACGTcount: A:0.23, C:0.29, G:0.28, T:0.20
Consensus pattern (42 bp):
AACCCAGTGCAAGGTTAAAGCTTGGTTAGCAGACTCGGACCC
Found at i:137692 original size:21 final size:21
Alignment explanation
Indices: 137651--137698 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
137641 CTAGTTCTCT
**
137651 CGATACAAGTATGATTTCTAC
1 CGATACAAGTATGATAACTAC
137672 CGATACAAGTCATG-TAACTAC
1 CGATACAAGT-ATGATAACTAC
137693 CGATAC
1 CGATAC
137699 CAAAAACTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 21 0.88
22 3 0.12
ACGTcount: A:0.35, C:0.23, G:0.15, T:0.27
Consensus pattern (21 bp):
CGATACAAGTATGATAACTAC
Found at i:139544 original size:20 final size:21
Alignment explanation
Indices: 139508--139563 Score: 55
Period size: 20 Copynumber: 2.7 Consensus size: 21
139498 TCATTAAGCT
*
139508 TTAATT-AATCATTTTTA-ATC
1 TTAATTAAATCATATTTATA-C
139528 TTAATTAAATC-TATTTATAC
1 TTAATTAAATCATATTTATAC
*
139548 TTAATATAAACCATAT
1 TTAAT-TAAATCATAT
139564 CAATCCACTA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
20 17 0.57
21 10 0.33
22 3 0.10
ACGTcount: A:0.41, C:0.11, G:0.00, T:0.48
Consensus pattern (21 bp):
TTAATTAAATCATATTTATAC
Found at i:141022 original size:26 final size:26
Alignment explanation
Indices: 140986--141038 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
140976 GCTCAATGAT
*
140986 TAAAATATTACAACATAATAACATAA
1 TAAAATATTACAACACAATAACATAA
*
141012 TAAAATATTACAATACAATAACATAA
1 TAAAATATTACAACACAATAACATAA
141038 T
1 T
141039 TAATTAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.60, C:0.11, G:0.00, T:0.28
Consensus pattern (26 bp):
TAAAATATTACAACACAATAACATAA
Found at i:144373 original size:23 final size:23
Alignment explanation
Indices: 144347--144410 Score: 83
Period size: 23 Copynumber: 2.7 Consensus size: 23
144337 TTCATTTAAT
144347 TTAATCGAACATGTTCATGAACA
1 TTAATCGAACATGTTCATGAACA
* *
144370 TTAAACAAACATGTTCATGAACA
1 TTAATCGAACATGTTCATGAACA
* *
144393 TATAATTGAACTTGTTCA
1 T-TAATCGAACATGTTCA
144411 CGAATAATGT
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
23 22 0.65
24 12 0.35
ACGTcount: A:0.41, C:0.16, G:0.11, T:0.33
Consensus pattern (23 bp):
TTAATCGAACATGTTCATGAACA
Found at i:144516 original size:12 final size:12
Alignment explanation
Indices: 144494--144542 Score: 64
Period size: 12 Copynumber: 4.2 Consensus size: 12
144484 ATAAATATAT
144494 GAGTC-ATAAAC
1 GAGTCAATAAAC
144505 GAGTCAATAAAC
1 GAGTCAATAAAC
** *
144517 GAGTTTATAAAT
1 GAGTCAATAAAC
144529 GAGTCAATAAAC
1 GAGTCAATAAAC
144541 GA
1 GA
144543 ACTTGTTCGT
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
11 5 0.16
12 26 0.84
ACGTcount: A:0.47, C:0.12, G:0.18, T:0.22
Consensus pattern (12 bp):
GAGTCAATAAAC
Found at i:146246 original size:30 final size:31
Alignment explanation
Indices: 146212--146274 Score: 94
Period size: 30 Copynumber: 2.1 Consensus size: 31
146202 AATTTATATG
*
146212 TTTATAATTTATAAAGA-ATTAAATTA-AATT
1 TTTATAATTT-TAAAGAGATTAAAATATAATT
146242 TTTATAATTTTAAAGAGATTAAAATATAATT
1 TTTATAATTTTAAAGAGATTAAAATATAATT
146273 TT
1 TT
146275 ATTATTATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
29 6 0.20
30 18 0.60
31 6 0.20
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (31 bp):
TTTATAATTTTAAAGAGATTAAAATATAATT
Found at i:146627 original size:16 final size:16
Alignment explanation
Indices: 146608--146652 Score: 56
Period size: 16 Copynumber: 2.7 Consensus size: 16
146598 TTTTTTTTGA
146608 ATTTTATAAATTTTT-T
1 ATTTT-TAAATTTTTAT
146624 ATTTTTGAATATTTTTAT
1 ATTTTT-AA-ATTTTTAT
146642 ATTTTTAAATT
1 ATTTTTAAATT
146653 ATTTGTCCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
15 1 0.04
16 10 0.38
17 8 0.31
18 7 0.27
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (16 bp):
ATTTTTAAATTTTTAT
Found at i:146648 original size:24 final size:24
Alignment explanation
Indices: 146601--146647 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
146591 TACTTCATTT
146601 TTTTTGAATTTTATAAATTTTTTA
1 TTTTTGAATTTTATAAATTTTTTA
* *
146625 TTTTTGAATATTTTTATATTTTT
1 TTTTTGAAT-TTTATAAATTTTT
146648 AAATTATTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 9 0.45
25 11 0.55
ACGTcount: A:0.26, C:0.00, G:0.04, T:0.70
Consensus pattern (24 bp):
TTTTTGAATTTTATAAATTTTTTA
Found at i:147885 original size:30 final size:30
Alignment explanation
Indices: 147851--147915 Score: 130
Period size: 30 Copynumber: 2.2 Consensus size: 30
147841 AAATTTTATT
147851 AACTTGAATTATTAAACTCAAAATAATTCA
1 AACTTGAATTATTAAACTCAAAATAATTCA
147881 AACTTGAATTATTAAACTCAAAATAATTCA
1 AACTTGAATTATTAAACTCAAAATAATTCA
147911 AACTT
1 AACTT
147916 TAAATAGTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.49, C:0.14, G:0.03, T:0.34
Consensus pattern (30 bp):
AACTTGAATTATTAAACTCAAAATAATTCA
Found at i:147920 original size:16 final size:16
Alignment explanation
Indices: 147871--147921 Score: 52
Period size: 15 Copynumber: 3.3 Consensus size: 16
147861 ATTAAACTCA
147871 AAATAATTCAAAC-TT
1 AAATAATTCAAACTTT
* * **
147886 GAATTATT-AAACTCA
1 AAATAATTCAAACTTT
147901 AAATAATTCAAACTTT
1 AAATAATTCAAACTTT
147917 AAATA
1 AAATA
147922 GTTAATATCT
Statistics
Matches: 26, Mismatches: 8, Indels: 3
0.70 0.22 0.08
Matches are distributed among these distances:
14 4 0.15
15 12 0.46
16 10 0.38
ACGTcount: A:0.53, C:0.12, G:0.02, T:0.33
Consensus pattern (16 bp):
AAATAATTCAAACTTT
Found at i:151115 original size:23 final size:24
Alignment explanation
Indices: 151060--151115 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 24
151050 AATTAATGAG
*
151060 TATTTTATATTTGAAATTTATTTAA
1 TATTTT-TATTTGAAATTTATTAAA
* *
151085 T-TTATTATTTGATATTTA-TAAA
1 TATTTTTATTTGAAATTTATTAAA
151107 TATTTTTAT
1 TATTTTTAT
151116 ATACATGTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
22 4 0.15
23 18 0.69
24 3 0.12
25 1 0.04
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (24 bp):
TATTTTTATTTGAAATTTATTAAA
Found at i:154164 original size:20 final size:20
Alignment explanation
Indices: 154131--154169 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
154121 CAGCTGCTCC
154131 ATTGTATAAAATTC-TCTAG
1 ATTGTATAAAATTCATCTAG
*
154150 ATTGTTATAATATTCATCTA
1 ATTG-TATAAAATTCATCTA
154170 TGAGGGGGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 9 0.53
21 4 0.24
ACGTcount: A:0.36, C:0.10, G:0.08, T:0.46
Consensus pattern (20 bp):
ATTGTATAAAATTCATCTAG
Found at i:168920 original size:21 final size:20
Alignment explanation
Indices: 168892--168933 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 20
168882 GTTTTTTTTT
*
168892 TTTAAGA-TCGAGGCTCGATC
1 TTTAAGATTCGA-GCCCGATC
168912 TTTATAGATTCGAGCCCGATC
1 TTTA-AGATTCGAGCCCGATC
168933 T
1 T
168934 ATGCTTTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 4 0.21
21 11 0.58
22 4 0.21
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.33
Consensus pattern (20 bp):
TTTAAGATTCGAGCCCGATC
Found at i:170616 original size:324 final size:324
Alignment explanation
Indices: 170002--170598 Score: 806
Period size: 324 Copynumber: 1.8 Consensus size: 324
169992 AAATAATTTC
* * *
170002 AAAACCGAGGCAACATCCTTTCGTGTGAAAATTTCAGAAAATTATGCCCTAACGTGCTGGGTGTG
1 AAAAACGAGGCAACATCCTTCCGTGTGAAAATTTCAGAAAATTATGCCCTAACGTGCTGGGTATG
*
170067 ATTTTTCGTATAATTTACGCGATCGAATATCCTCTTTAAAACCTTTCAAAATGTCCTTCAATTTC
66 ATTTTTCGTATAATTTACGCGATCGAATATCCTCTTTAAAACCTTTCAAAACGTCCTTCAATTTC
** *
170132 AAAATTTCGAGAACGTCGTGCCCTAACGTGTTTGACACGACTTCAATTCTCCAATAAATTCGAAA
131 AAAATTTCGAGAAAATCGTGCCCTAACGTGTTTGACACGACTTCAATTCTCCAAGAAATTCGAAA
* * * *** *
170197 CACGCGGGCATTTTTCTTCAAATTCAATTTTTTTGAAAATCACGTGAAATAAGTTGTGTCTGAGG
196 CACACGGGCATTTTTCTTCAAATTCAA-TTTTTTGAAAATCACGAGAAACAAGTTGTGTAAAAAG
*
170262 ATTGTATGTTAAACTTCAATCGAAATTTCAAGTTCTCAAAAAATATATATCAGTAATTTTAAACA
260 ATCGTATGTTAAACTTCAATCGAAATTTCAAGTTCTCAAAAAATATATATCAGTAATTTTAAACA
* **
170327 AAAAACGAGGCAATATCCTTCCGTGTGAAGGTTTC-GAAAATTTATGCCCTAACGTGCTGGGTAT
1 AAAAACGAGGCAACATCCTTCCGTGTGAAAATTTCAGAAAA-TTATGCCCTAACGTGCTGGGTAT
* * **
170391 GATTTTTCGTATAA-TT-CGTGCATTGAATATCCTCTTTAAAATTTTTCAAAACGTCCTTCAATT
65 GATTTTTCGTATAATTTACGCG-ATCGAATATCCTCTTTAAAACCTTTCAAAACGTCCTTCAATT
* * * ** *
170454 TCCAAATTTTGAGAAAATCTTGCCCTAACGTGTTTGACACGACTTCAATTCTCTGAGGAATTCGA
129 TCAAAATTTCGAGAAAATCGTGCCCTAACGTGTTTGACACGACTTCAATTCTCCAAGAAATTCGA
* ** * * *
170519 AACACATGGGCATTTTTCTTCAAATTTGA-TTTTTGAAAATTATGAGAAACGAGTTATGTGTAAA
194 AACACACGGGCATTTTTCTTCAAATTCAATTTTTTGAAAATCACGAGAAACAAG-T-TGTGTAAA
*
170583 AAGATCGTATTTTAAA
257 AAGATCGTATGTTAAA
170599 TTTCGCTTGA
Statistics
Matches: 233, Mismatches: 35, Indels: 9
0.84 0.13 0.03
Matches are distributed among these distances:
322 19 0.08
323 4 0.02
324 144 0.62
325 66 0.28
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35
Consensus pattern (324 bp):
AAAAACGAGGCAACATCCTTCCGTGTGAAAATTTCAGAAAATTATGCCCTAACGTGCTGGGTATG
ATTTTTCGTATAATTTACGCGATCGAATATCCTCTTTAAAACCTTTCAAAACGTCCTTCAATTTC
AAAATTTCGAGAAAATCGTGCCCTAACGTGTTTGACACGACTTCAATTCTCCAAGAAATTCGAAA
CACACGGGCATTTTTCTTCAAATTCAATTTTTTGAAAATCACGAGAAACAAGTTGTGTAAAAAGA
TCGTATGTTAAACTTCAATCGAAATTTCAAGTTCTCAAAAAATATATATCAGTAATTTTAAACA
Found at i:180690 original size:39 final size:39
Alignment explanation
Indices: 180640--180719 Score: 160
Period size: 39 Copynumber: 2.1 Consensus size: 39
180630 TGATCAGTTG
180640 AATGATTGCCTAATAGGACGGAGAAACTTTACAGCTTGA
1 AATGATTGCCTAATAGGACGGAGAAACTTTACAGCTTGA
180679 AATGATTGCCTAATAGGACGGAGAAACTTTACAGCTTGA
1 AATGATTGCCTAATAGGACGGAGAAACTTTACAGCTTGA
180718 AA
1 AA
180720 CATCAACAAG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.38, C:0.15, G:0.23, T:0.25
Consensus pattern (39 bp):
AATGATTGCCTAATAGGACGGAGAAACTTTACAGCTTGA
Found at i:181890 original size:212 final size:208
Alignment explanation
Indices: 181489--181904 Score: 501
Period size: 212 Copynumber: 2.0 Consensus size: 208
181479 ACTCCAAACC
* * * * *
181489 TCGTCTTCCTGATGAGATACAGAGAAGTGGATTGAAATAGTGATGCGATCATCTTCTTGATAAGA
1 TCGTCTTCCTGATGAGATACAGAGAAGTGGATTAAAAAAATGAGGCGATCATCTTCCTGATAAGA
* * * * *
181554 TACAGAGAAGTAGATCAAATCAATGAAGCGAAGCTCAATACGAACGAAACTTCGAATCCCAGCTT
66 TACAAAGAAGTAGACCAAATCAATGAAGCAAAGCTCAATACGAACGAAACTTCAAACCCCAGCTT
* * * * * *
181619 CCTGATGAGATAATGAGAAGCAGGTCGAAGCAATAAAGTGGTCGTCTTCTTAATGAGATATAGAG
131 CCTGATGAGATAATGAGAAGCAGGTCAAAACAATAAAGCGATCATCTTCTTAATGAGATACAGAG
*
181684 AAGTGGACCAAAT
196 AAGTAGACCAAAT
* * * *
181697 TCGTCTTCTTGATGAGATACAGCGAAGTGGATTAAAACAAATGAGGCGGTCATCTTCCTGATGAG
1 TCGTCTTCCTGATGAGATACAGAGAAGTGGATTAAAA-AAATGAGGCGATCATCTTCCTGATAAG
* * ** *
181762 ATACAAAGAAGTAGACCAAATCAAGTGAAGCAAAGTTCAGATGCGAGTGAAGCTTCAAACCCCTA
65 ATACAAAGAAGTAGACCAAATCAA-TGAAGCAAAGCTCA-ATACGAACGAAACTTCAAACCCC-A
* * * * *
181827 TCTTCTTGATGAGATACA-GAGAAGTAGGTCAAAATAATAAAGCGATCATCTTCTTGATGAGATA
127 GCTTCCTGATGAGATA-ATGAGAAGCAGGTCAAAACAATAAAGCGATCATCTTCTTAATGAGATA
181891 CAGAGAAGTAGACC
191 CAGAGAAGTAGACC
181905 GAGAGATGAA
Statistics
Matches: 172, Mismatches: 31, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
208 34 0.20
209 43 0.25
210 12 0.07
211 17 0.10
212 65 0.38
213 1 0.01
ACGTcount: A:0.37, C:0.16, G:0.23, T:0.24
Consensus pattern (208 bp):
TCGTCTTCCTGATGAGATACAGAGAAGTGGATTAAAAAAATGAGGCGATCATCTTCCTGATAAGA
TACAAAGAAGTAGACCAAATCAATGAAGCAAAGCTCAATACGAACGAAACTTCAAACCCCAGCTT
CCTGATGAGATAATGAGAAGCAGGTCAAAACAATAAAGCGATCATCTTCTTAATGAGATACAGAG
AAGTAGACCAAAT
Found at i:184041 original size:29 final size:28
Alignment explanation
Indices: 184009--184107 Score: 83
Period size: 29 Copynumber: 3.4 Consensus size: 28
183999 TTAAAAATCT
184009 CATTTTGACCCCGAACTTCTTCAAAATTA
1 CATTTTGACCCCGAA-TTCTTCAAAATTA
*
184038 CATTTTGATCCCCAAATT-TCTCAAAAATTA
1 CATTTTGA-CCCCGAATTCT-TC-AAAATTA
** * ** *
184068 TGTTTTGACCTCGAATTCTTTTAAATTT
1 CATTTTGACCCCGAATTCTTCAAAATTA
184096 CATTTTCGACCC
1 CATTTT-GACCC
184108 TGTTTTTCGT
Statistics
Matches: 54, Mismatches: 11, Indels: 10
0.72 0.15 0.13
Matches are distributed among these distances:
28 10 0.19
29 24 0.44
30 20 0.37
ACGTcount: A:0.28, C:0.24, G:0.07, T:0.40
Consensus pattern (28 bp):
CATTTTGACCCCGAATTCTTCAAAATTA
Found at i:184067 original size:30 final size:30
Alignment explanation
Indices: 183995--184077 Score: 82
Period size: 30 Copynumber: 2.8 Consensus size: 30
183985 AGCCCATGTT
* *
183995 TTCTTTAAAAATCT-CATTTTGACCCCGAAC
1 TTCTTCAAAAAT-TACATTTTGACCCCAAAC
*
184025 TTCTTC-AAAATTACATTTTGATCCCCAAAT
1 TTCTTCAAAAATTACATTTTGA-CCCCAAAC
**
184055 TTC-TCAAAAATTATGTTTTGACC
1 TTCTTCAAAAATTACATTTTGACC
184078 TCGAATTCTT
Statistics
Matches: 45, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
28 1 0.02
29 17 0.38
30 27 0.60
ACGTcount: A:0.31, C:0.23, G:0.06, T:0.40
Consensus pattern (30 bp):
TTCTTCAAAAATTACATTTTGACCCCAAAC
Found at i:185417 original size:26 final size:29
Alignment explanation
Indices: 185379--185435 Score: 68
Period size: 26 Copynumber: 2.1 Consensus size: 29
185369 TGATTAGACT
*
185379 TTTTTATTTGTGAATAA-AATA-AAT-ATA
1 TTTTTATTGGTG-ATAAGAATAGAATAATA
185406 TTTTT-TTGGTGATAAGAATAGAATAATA
1 TTTTTATTGGTGATAAGAATAGAATAATA
185434 TT
1 TT
185436 ATACTTATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
25 4 0.15
26 9 0.35
27 8 0.31
28 5 0.19
ACGTcount: A:0.40, C:0.00, G:0.12, T:0.47
Consensus pattern (29 bp):
TTTTTATTGGTGATAAGAATAGAATAATA
Found at i:187523 original size:31 final size:32
Alignment explanation
Indices: 187486--187554 Score: 97
Period size: 31 Copynumber: 2.2 Consensus size: 32
187476 AAATTGGCTC
*
187486 TCAACCTTTTTAAAA-GAGTTAAATTTAACTA
1 TCAACCTTTTTAAAACGAGTTAAATTTAACCA
* *
187517 TCAACC-TTTTAAAACGAGTTGAATTTGACCA
1 TCAACCTTTTTAAAACGAGTTAAATTTAACCA
187548 TCAACCT
1 TCAACCT
187555 AGCAACAAGG
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
30 8 0.24
31 25 0.76
ACGTcount: A:0.38, C:0.19, G:0.09, T:0.35
Consensus pattern (32 bp):
TCAACCTTTTTAAAACGAGTTAAATTTAACCA
Found at i:188233 original size:17 final size:19
Alignment explanation
Indices: 188194--188233 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
188184 TGGTGAGGTG
188194 GAAAAAAATTAGAGAGATA
1 GAAAAAAATTAGAGAGATA
188213 -AAAAAAATTA-AGA-ATA
1 GAAAAAAATTAGAGAGATA
188229 GAAAA
1 GAAAA
188234 GAAAAAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
16 3 0.15
17 7 0.35
18 10 0.50
ACGTcount: A:0.70, C:0.00, G:0.15, T:0.15
Consensus pattern (19 bp):
GAAAAAAATTAGAGAGATA
Found at i:189842 original size:20 final size:20
Alignment explanation
Indices: 189804--189846 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
189794 AAGAAAAAAA
189804 TTTAGAAATTTATGGAATTAT
1 TTTAGAAATTTATGGAATT-T
* *
189825 TTTAG-AATTTTTGTAATTT
1 TTTAGAAATTTATGGAATTT
189844 TTT
1 TTT
189847 TTGGAACATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 4 0.20
20 11 0.55
21 5 0.25
ACGTcount: A:0.30, C:0.00, G:0.12, T:0.58
Consensus pattern (20 bp):
TTTAGAAATTTATGGAATTT
Found at i:194990 original size:19 final size:19
Alignment explanation
Indices: 194953--194990 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
194943 TTATGCGGTG
**
194953 AAATTTTATTTTACTTTAA
1 AAATTTTATTTTAAATTAA
194972 AAATTTTATTTTAAATTAA
1 AAATTTTATTTTAAATTAA
194991 GTCACATAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (19 bp):
AAATTTTATTTTAAATTAA
Found at i:195846 original size:20 final size:20
Alignment explanation
Indices: 195821--195874 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
195811 CTCCTATGAG
* *
195821 ACTTCTACCGGTAGAACTCC
1 ACTTCTACCGATACAACTCC
195841 ACTTCTACCGATACAACTCC
1 ACTTCTACCGATACAACTCC
*
195861 ACTTCTACCAATAC
1 ACTTCTACCGATAC
195875 CTTGAAGACT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.30, C:0.37, G:0.07, T:0.26
Consensus pattern (20 bp):
ACTTCTACCGATACAACTCC
Found at i:197408 original size:96 final size:96
Alignment explanation
Indices: 197224--197415 Score: 212
Period size: 96 Copynumber: 2.0 Consensus size: 96
197214 CTTTTGCGAA
* ** *
197224 AAGGATATTTGATTATCTCGATTTGAAGAAAGGTTGCACCTAGTGAGTTAAGGCGTAATATTTCA
1 AAGGATATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTGAGTTAAGGCGCAATATTTCA
** * *
197289 GAATCGGGGATAAGGAAACATTGCCTTGATT
66 GAATCGGAAATAAAGAAACATTGCCTCGATT
* * *
197320 AAGGGTATTCGATTATTTTGATTTGAAGAAAAATTGCACCTAGTGAGTTAAGGCGCAA-AGTTTC
1 AAGGATATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTGAGTTAAGGCGCAATA-TTTC
*
197384 -GAAACTC-GAAATAAA-AGAATATTGCCTCGATT
65 AG-AA-TCGGAAATAAAGA-AACATTGCCTCGATT
197416 TTAAAGTTTT
Statistics
Matches: 80, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
95 3 0.04
96 75 0.94
97 2 0.03
ACGTcount: A:0.34, C:0.12, G:0.23, T:0.31
Consensus pattern (96 bp):
AAGGATATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTGAGTTAAGGCGCAATATTTCA
GAATCGGAAATAAAGAAACATTGCCTCGATT
Found at i:197692 original size:29 final size:28
Alignment explanation
Indices: 197660--197964 Score: 195
Period size: 29 Copynumber: 10.7 Consensus size: 28
197650 GTTCGGAACC
*
197660 AAAAATGGGATTTTTGGAAGTTCGAGGGT
1 AAAAATGGAATTTTTGGAAGTTCG-GGGT
* * *
197689 AAAATTGTAATTTTTAGAAGGTTCGGGGT
1 AAAAATGGAATTTTTGGAA-GTTCGGGGT
* *
197718 CAAAAAT-GAGATTTTTGGAAGTTTGAGG-
1 -AAAAATGGA-ATTTTTGGAAGTTCGGGGT
* *
197746 ATAAAATGATAATTTTTAGAAGGTTCGGGGT
1 A-AAAATG-GAATTTTTGGAA-GTTCGGGGT
* * *
197777 CAAAAATGGGATTTTTGGAAGTTC-GAGA
1 -AAAAATGGAATTTTTGGAAGTTCGGGGT
*
197805 ATAAAATGGTAATTTTTAGAAGGTTCGGGG-
1 A-AAAATGG-AATTTTTGGAA-GTTCGGGGT
* *
197835 -----T--AATTTTTAGAAGGTTTGGGGT
1 AAAAATGGAATTTTTGGAA-GTTCGGGGT
* *
197857 CAAAAATGGGATTTTTGGGAGTTCGGGGGT
1 -AAAAATGGAATTTTTGGAAGTTC-GGGGT
197887 -AAAATGGTAATTTTTGGAAAGTTCGGGGT
1 AAAAATGG-AATTTTTGG-AAGTTCGGGGT
*
197916 CAAAAATGGGATTTTTGGAAGTTCGAGGGT
1 -AAAAATGGAATTTTTGGAAGTTCG-GGGT
197946 -AAAATGGTAATTTTTGGAA
1 AAAAATGG-AATTTTTGGAA
197965 TGTTTAAGGA
Statistics
Matches: 217, Mismatches: 30, Indels: 58
0.71 0.10 0.19
Matches are distributed among these distances:
21 19 0.09
24 1 0.00
27 2 0.01
28 29 0.13
29 81 0.37
30 69 0.32
31 15 0.07
32 1 0.00
ACGTcount: A:0.32, C:0.04, G:0.30, T:0.34
Consensus pattern (28 bp):
AAAAATGGAATTTTTGGAAGTTCGGGGT
Found at i:197712 original size:59 final size:59
Alignment explanation
Indices: 197641--197835 Score: 293
Period size: 59 Copynumber: 3.3 Consensus size: 59
197631 AAAATGGTAG
* *** *
197641 TTTTGGAAGGTTCGGAACCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATTGTAAT
1 TTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGATAAAATTGTAAT
* *
197700 TTTTAGAAGGTTCGGGGTCAAAAATGAGATTTTTGGAAGTTTGAGGATAAAA-TGATAAT
1 TTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGATAAAATTG-TAAT
* *
197759 TTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGAATAAAATGGTAAT
1 TTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGATAAAATTGTAAT
197818 TTTTAGAAGGTTCGGGGT
1 TTTTAGAAGGTTCGGGGT
197836 AATTTTTAGA
Statistics
Matches: 123, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
58 2 0.02
59 120 0.98
60 1 0.01
ACGTcount: A:0.32, C:0.05, G:0.29, T:0.33
Consensus pattern (59 bp):
TTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGATAAAATTGTAAT
Found at i:197836 original size:21 final size:21
Alignment explanation
Indices: 197812--197856 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
197802 AGAATAAAAT
197812 GGTAATTTTTAGAAGGTTCGG
1 GGTAATTTTTAGAAGGTTCGG
*
197833 GGTAATTTTTAGAAGGTTTGG
1 GGTAATTTTTAGAAGGTTCGG
197854 GGT
1 GGT
197857 CAAAAATGGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.22, C:0.02, G:0.36, T:0.40
Consensus pattern (21 bp):
GGTAATTTTTAGAAGGTTCGG
Found at i:197890 original size:80 final size:80
Alignment explanation
Indices: 197755--197915 Score: 259
Period size: 80 Copynumber: 2.0 Consensus size: 80
197745 GATAAAATGA
197755 TAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGAATAAAATGGTAATTT
1 TAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGAATAAAATGGTAATTT
*
197820 TTAGAAGGTTCGGGG
66 TTAGAAAGTTCGGGG
* * * **
197835 TAATTTTTAGAAGGTTTGGGGTCAAAAATGGGATTTTTGGGAGTTCGGGGGTAAAATGGTAATTT
1 TAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGAATAAAATGGTAATTT
*
197900 TTGGAAAGTTCGGGG
66 TTAGAAAGTTCGGGG
197915 T
1 T
197916 CAAAAATGGG
Statistics
Matches: 74, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
80 74 1.00
ACGTcount: A:0.29, C:0.04, G:0.32, T:0.35
Consensus pattern (80 bp):
TAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGAATAAAATGGTAATTT
TTAGAAAGTTCGGGG
Found at i:197890 original size:139 final size:139
Alignment explanation
Indices: 197695--197960 Score: 433
Period size: 139 Copynumber: 1.9 Consensus size: 139
197685 GGGTAAAATT
*
197695 GTAATTTTTAGAAGGTTCGGGGTCAAAAATGAGATTTTTGGAAGTTTGAGGATAAAATGATAATT
1 GTAATTTTTAGAAGGTTCGGGGTCAAAAATGAGATTTTTGGAAGTTCGAGGATAAAATGATAATT
*
197760 TTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGAATAAAATGGTAATTTTTAGA
66 TTTAGAAAGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGAATAAAATGGTAATTTTTAGA
197825 AGGTTCGGG
131 AGGTTCGGG
* * * * * *
197834 GTAATTTTTAGAAGGTTTGGGGTCAAAAATGGGATTTTTGGGAGTTCGGGGGTAAAATGGTAATT
1 GTAATTTTTAGAAGGTTCGGGGTCAAAAATGAGATTTTTGGAAGTTCGAGGATAAAATGATAATT
* **
197899 TTTGGAAAGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTT
66 TTTAGAAAGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGAATAAAATGGTAATTTTT
197961 GGAATGTTTA
Statistics
Matches: 116, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
139 116 1.00
ACGTcount: A:0.31, C:0.04, G:0.30, T:0.35
Consensus pattern (139 bp):
GTAATTTTTAGAAGGTTCGGGGTCAAAAATGAGATTTTTGGAAGTTCGAGGATAAAATGATAATT
TTTAGAAAGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGAATAAAATGGTAATTTTTAGA
AGGTTCGGG
Found at i:197925 original size:59 final size:59
Alignment explanation
Indices: 197833--197964 Score: 219
Period size: 59 Copynumber: 2.2 Consensus size: 59
197823 GAAGGTTCGG
* * * * *
197833 GGTAATTTTTAGAAGGTTTGGGGTCAAAAATGGGATTTTTGGGAGTTCGGGGGTAAAAT
1 GGTAATTTTTGGAAAGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAT
197892 GGTAATTTTTGGAAAGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAT
1 GGTAATTTTTGGAAAGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAT
197951 GGTAATTTTTGGAA
1 GGTAATTTTTGGAA
197965 TGTTTAAGGA
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
59 68 1.00
ACGTcount: A:0.29, C:0.04, G:0.33, T:0.34
Consensus pattern (59 bp):
GGTAATTTTTGGAAAGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAT
Found at i:199126 original size:7 final size:7
Alignment explanation
Indices: 199116--199140 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
199106 TTTTTTTTAT
199116 TAATTAA
1 TAATTAA
199123 TAATTAA
1 TAATTAA
199130 TAATTAA
1 TAATTAA
199137 TAAT
1 TAAT
199141 ATTATTAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (7 bp):
TAATTAA
Found at i:199777 original size:15 final size:15
Alignment explanation
Indices: 199759--199813 Score: 69
Period size: 15 Copynumber: 3.7 Consensus size: 15
199749 TTTGGGTAGT
199759 TTGTAATTGGGCCAA
1 TTGTAATTGGGCCAA
199774 TTGT-ATTCGGGCC-A
1 TTGTAATT-GGGCCAA
*
199788 TCTGTAATTGGGCCAT
1 T-TGTAATTGGGCCAA
199804 TTGTAATTGG
1 TTGTAATTGG
199814 ACTTTGTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
14 5 0.14
15 26 0.74
16 4 0.11
ACGTcount: A:0.20, C:0.15, G:0.27, T:0.38
Consensus pattern (15 bp):
TTGTAATTGGGCCAA
Found at i:199867 original size:17 final size:16
Alignment explanation
Indices: 199845--199923 Score: 95
Period size: 17 Copynumber: 4.8 Consensus size: 16
199835 TTGAACTTTC
199845 TAAATTTAATTTTATAA
1 TAAATTTAATTTTA-AA
199862 TAAATTTAAATTTTAAA
1 TAAATTT-AATTTTAAA
*
199879 TAAATTTAAATTTAAAA
1 TAAATTT-AATTTTAAA
* *
199896 TAAACTTAAATTTAAA
1 TAAATTTAATTTTAAA
*
199912 TAAATTCAATTT
1 TAAATTTAATTT
199924 CCAATAAGTC
Statistics
Matches: 54, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
16 16 0.30
17 31 0.57
18 7 0.13
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.46
Consensus pattern (16 bp):
TAAATTTAATTTTAAA
Found at i:199883 original size:34 final size:33
Alignment explanation
Indices: 199845--199923 Score: 113
Period size: 34 Copynumber: 2.4 Consensus size: 33
199835 TTGAACTTTC
* *
199845 TAAATTTAATTTTATAATAAATTTAAATTTTAAA
1 TAAATTTAATTTTAAAATAAACTTAAA-TTTAAA
*
199879 TAAATTTAAATTTAAAATAAACTTAAATTTAAA
1 TAAATTTAATTTTAAAATAAACTTAAATTTAAA
*
199912 TAAATTCAATTT
1 TAAATTTAATTT
199924 CCAATAAGTC
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
33 16 0.40
34 24 0.60
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.46
Consensus pattern (33 bp):
TAAATTTAATTTTAAAATAAACTTAAATTTAAA
Found at i:199896 original size:7 final size:6
Alignment explanation
Indices: 199845--199912 Score: 56
Period size: 6 Copynumber: 11.8 Consensus size: 6
199835 TTGAACTTTC
*
199845 TAAATT TAATTT TATAA-- TAAATT TAAATTT TAAA-- TAAATT TAAATT
1 TAAATT TAAATT TA-AATT TAAATT TAAA-TT TAAATT TAAATT TAAATT
* *
199891 TAAA-A TAAACT TAAATT TAAAT
1 TAAATT TAAATT TAAATT TAAAT
199913 AAATTCAATT
Statistics
Matches: 50, Mismatches: 5, Indels: 14
0.72 0.07 0.20
Matches are distributed among these distances:
4 6 0.12
5 6 0.12
6 31 0.62
7 7 0.14
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (6 bp):
TAAATT
Found at i:202093 original size:20 final size:20
Alignment explanation
Indices: 202068--202120 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
202058 TTCCTGTGAG
* *
202068 ACTTCTATCGGTAGAACTCC
1 ACTTCTACCGATAGAACTCC
*
202088 ACTTCTACCGATATAACTCC
1 ACTTCTACCGATAGAACTCC
202108 ACTTCTACCGATA
1 ACTTCTACCGATA
202121 CCTTGAAGAC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.28, C:0.32, G:0.09, T:0.30
Consensus pattern (20 bp):
ACTTCTACCGATAGAACTCC
Found at i:203774 original size:27 final size:28
Alignment explanation
Indices: 203690--203852 Score: 96
Period size: 29 Copynumber: 5.6 Consensus size: 28
203680 ATTTTCGAGG
* *
203690 AATTTGGGGGTCAAAATTGAAATTTTTGGAA
1 AATTTGGGGGT-AAAATGGTAA-TTTTGG-A
* *
203721 AAGTTTAGGGGTCAAAAT-GTGATTTTTGGA
1 AA-TTTGGGGGT-AAAATGGT-AATTTTGGA
*
203751 AATTTGGGGG-GAAATGGTAATTTTGGA
1 AATTTGGGGGTAAAATGGTAATTTTGGA
**
203778 TGTTTGGGGGTAAAATGGTAATTTTTGGA
1 AATTTGGGGGTAAAATGGTAA-TTTTGGA
* * * ** **
203807 TATTCGAGGACAAAATCATAATTTTGAAGA
1 AATTTGGGGGTAAAATGGTAATTTTG--GA
*
203837 AATTTGGGGTTAAAAT
1 AATTTGGGGGTAAAAT
203853 AAGATTTTAG
Statistics
Matches: 104, Mismatches: 21, Indels: 15
0.74 0.15 0.11
Matches are distributed among these distances:
27 20 0.19
28 16 0.15
29 28 0.27
30 16 0.15
31 9 0.09
32 15 0.14
ACGTcount: A:0.33, C:0.03, G:0.28, T:0.36
Consensus pattern (28 bp):
AATTTGGGGGTAAAATGGTAATTTTGGA
Found at i:203774 original size:28 final size:29
Alignment explanation
Indices: 203690--203806 Score: 114
Period size: 27 Copynumber: 4.0 Consensus size: 29
203680 ATTTTCGAGG
* *
203690 AATTTGGGGGTCAAAATTGAAATTTTTGGAA
1 AATTTGGGGGT-AAAATGGTAATTTTTGG-A
* *
203721 AAGTTTAGGGGTCAAAAT-GTGATTTTTGGA
1 AA-TTTGGGGGT-AAAATGGTAATTTTTGGA
*
203751 AATTTGGGGG-GAAATGGTAA-TTTTGGA
1 AATTTGGGGGTAAAATGGTAATTTTTGGA
**
203778 TGTTTGGGGGTAAAATGGTAATTTTTGGA
1 AATTTGGGGGTAAAATGGTAATTTTTGGA
203807 TATTCGAGGA
Statistics
Matches: 73, Mismatches: 9, Indels: 10
0.79 0.10 0.11
Matches are distributed among these distances:
27 19 0.26
28 12 0.16
29 14 0.19
30 3 0.04
31 11 0.15
32 14 0.19
ACGTcount: A:0.30, C:0.02, G:0.32, T:0.37
Consensus pattern (29 bp):
AATTTGGGGGTAAAATGGTAATTTTTGGA
Found at i:204029 original size:90 final size:88
Alignment explanation
Indices: 203837--204093 Score: 279
Period size: 90 Copynumber: 2.9 Consensus size: 88
203827 ATTTTGAAGA
* * * *
203837 AATTTGGGGTTAAAATAAGATTTTAGAGAAGTTTTGGGGTCAAAATGTAGTTTTAAAGAAGTTTG
1 AATTTGGGGTTAAAATATGATTTTAGAGAAGTTTAGGGTTCAAAATGTAATTTTAAAGAAGTTTG
**
203902 -GGAGTCAAAATGTAATTTTGGA-
66 AGG-GTCAAAATGTAATCATGGAG
* * * * *
203924 AATGTTCGAGAGTTAAAATATGCTTTTGGAAAAGTTTAGGGTTCAAAATGTAATTTTATAGAAGT
1 AAT-TT-G-GGGTTAAAATATGATTTTAGAGAAGTTTAGGGTTCAAAATGTAATTTTAAAGAAGT
203989 TTGAGGGTCAAAATGTAATCATGGAG
63 TTGAGGGTCAAAATGTAATCATGGAG
* * * *
204015 AAGTTTAGGGGTTAAAATGTAATTTTAGAGAAGTTTAGGGGTT-AAAATATAATTTTAAAGAAAT
1 AA-TTT-GGGGTTAAAATATGATTTTAGAGAAGTTTA-GGGTTCAAAATGTAATTTTAAAGAAGT
204079 TT-AGGGGTCAAAATG
63 TTGA-GGGTCAAAATG
204094 AGATTTTTTT
Statistics
Matches: 141, Mismatches: 21, Indels: 13
0.81 0.12 0.07
Matches are distributed among these distances:
87 3 0.02
88 2 0.01
89 2 0.01
90 121 0.86
91 12 0.09
92 1 0.01
ACGTcount: A:0.37, C:0.03, G:0.25, T:0.35
Consensus pattern (88 bp):
AATTTGGGGTTAAAATATGATTTTAGAGAAGTTTAGGGTTCAAAATGTAATTTTAAAGAAGTTTG
AGGGTCAAAATGTAATCATGGAG
Found at i:204100 original size:30 final size:30
Alignment explanation
Indices: 203825--204093 Score: 192
Period size: 30 Copynumber: 9.0 Consensus size: 30
203815 GACAAAATCA
* * *
203825 TAATTTTGAAGAAATTT-GGGGTTAAAAT-
1 TAATTTTAAAGAAGTTTAGGGGTCAAAATG
* * *
203853 AAGATTTTAGAGAAGTTTTGGGGTCAAAATG
1 TA-ATTTTAAAGAAGTTTAGGGGTCAAAATG
*
203884 TAGTTTTAAAGAAGTTT-GGGAGTCAAAATG
1 TAATTTTAAAGAAGTTTAGGG-GTCAAAATG
* * * * * *
203914 TAATTTT--GGAAATGTTCGAGAGTTAAAATA
1 TAATTTTAAAGAAGT-TTAG-GGGTCAAAATG
** * *
203944 TGCTTTTGGAA-AAGTTTAGGGTTCAAAATG
1 TAATTTT-AAAGAAGTTTAGGGGTCAAAATG
*
203974 TAATTTTATAGAAGTTT-GAGGGTCAAAATG
1 TAATTTTAAAGAAGTTTAG-GGGTCAAAATG
** ** *
204004 TAATCATGGAGAAGTTTAGGGGTTAAAATG
1 TAATTTTAAAGAAGTTTAGGGGTCAAAATG
* * *
204034 TAATTTTAGAGAAGTTTAGGGGTTAAAATA
1 TAATTTTAAAGAAGTTTAGGGGTCAAAATG
*
204064 TAATTTTAAAGAAATTTAGGGGTCAAAATG
1 TAATTTTAAAGAAGTTTAGGGGTCAAAATG
204094 AGATTTTTTT
Statistics
Matches: 187, Mismatches: 41, Indels: 24
0.74 0.16 0.10
Matches are distributed among these distances:
28 5 0.03
29 19 0.10
30 154 0.82
31 6 0.03
32 3 0.02
ACGTcount: A:0.38, C:0.03, G:0.25, T:0.35
Consensus pattern (30 bp):
TAATTTTAAAGAAGTTTAGGGGTCAAAATG
Found at i:204100 original size:60 final size:60
Alignment explanation
Indices: 203672--204093 Score: 252
Period size: 60 Copynumber: 7.1 Consensus size: 60
203662 ATTCGGGATG
* * *
203672 AAAACGTAATTTTCGAGGAA-TTTGGGGGTCAAAAT-TGAAATTTTTGGAA-AAGTTTAGGGGTC
1 AAAATGTAATTTTAGA-GAAGTTTGAGGGTCAAAATAT--AA-TTTT-GAAGAAGTTTAGGGGTC
* * * ** * * *
203734 AAAATGTGATTTTTG-GAAATTTG-GGG-GGAAATGGTAATTTTG--GATGTTTGGGGGT-
1 AAAATGTAATTTTAGAGAAGTTTGAGGGTCAAAAT-ATAATTTTGAAGAAGTTTAGGGGTC
* * * * *
203789 AAAATGGTAATTTTTG-GATA-TTCGA-GGACAAAATCATAATTTTGAAGAAATTT-GGGGTT
1 AAAAT-GTAATTTTAGAGA-AGTTTGAGGGTCAAAAT-ATAATTTTGAAGAAGTTTAGGGGTC
* * * *
203848 AAAAT-AAGATTTTAGAGAAGTTTTG-GGGTCAAAATGTAGTTTTAAAGAAGTTT-GGGAGTC
1 AAAATGTA-ATTTTAGAGAAG-TTTGAGGGTCAAAATATAATTTTGAAGAAGTTTAGGG-GTC
* * * * ** *
203908 AAAATGTAATTTTGGA-AATGTTCGAGAGTTAAAATATGCTTTTGGAA-AAGTTTAGGGTTC
1 AAAATGTAATTTTAGAGAA-GTTTGAGGGTCAAAATATAATTTT-GAAGAAGTTTAGGGGTC
* * ** * *
203968 AAAATGTAATTTTATAGAAGTTTGAGGGTCAAAATGTAATCATGGAGAAGTTTAGGGGTT
1 AAAATGTAATTTTAGAGAAGTTTGAGGGTCAAAATATAATTTTGAAGAAGTTTAGGGGTC
* * *
204028 AAAATGTAATTTTAGAGAAGTTT-AGGGGTTAAAATATAATTTTAAAGAAATTTAGGGGTC
1 AAAATGTAATTTTAGAGAAGTTTGA-GGGTCAAAATATAATTTTGAAGAAGTTTAGGGGTC
204088 AAAATG
1 AAAATG
204094 AGATTTTTTT
Statistics
Matches: 279, Mismatches: 56, Indels: 52
0.72 0.14 0.13
Matches are distributed among these distances:
55 5 0.02
56 26 0.09
57 15 0.05
58 16 0.06
59 43 0.15
60 149 0.53
61 13 0.05
62 12 0.04
ACGTcount: A:0.36, C:0.04, G:0.26, T:0.35
Consensus pattern (60 bp):
AAAATGTAATTTTAGAGAAGTTTGAGGGTCAAAATATAATTTTGAAGAAGTTTAGGGGTC
Found at i:205759 original size:7 final size:7
Alignment explanation
Indices: 205749--205774 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
205739 ATTTAAAATG
205749 AATTTTA
1 AATTTTA
205756 AATTTTA
1 AATTTTA
205763 AATTTTA
1 AATTTTA
205770 AATTT
1 AATTT
205775 GGGTTTTGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (7 bp):
AATTTTA
Found at i:208250 original size:28 final size:26
Alignment explanation
Indices: 208213--208278 Score: 71
Period size: 27 Copynumber: 2.5 Consensus size: 26
208203 TTTTCATATA
* *
208213 TTTAAAATTTAGTTCCATAC-TTTTATT
1 TTTAAAATTTA-ATCC-TACTTTTTAAT
208240 TTTAGAAATTTAATCCTACTTTTTAAT
1 TTTA-AAATTTAATCCTACTTTTTAAT
*
208267 TTTAAAAATTAA
1 TTTAAAATTTAA
208279 AGTTCAATTA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
26 10 0.29
27 17 0.50
28 7 0.21
ACGTcount: A:0.36, C:0.09, G:0.03, T:0.52
Consensus pattern (26 bp):
TTTAAAATTTAATCCTACTTTTTAAT
Found at i:208417 original size:17 final size:18
Alignment explanation
Indices: 208395--208430 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
208385 ATAATAATAA
208395 TAAGAG-AAATTAATTTT
1 TAAGAGAAAATTAATTTT
208412 TAAGAGAAAATTAATTTT
1 TAAGAGAAAATTAATTTT
208430 T
1 T
208431 TGATTAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.47, C:0.00, G:0.11, T:0.42
Consensus pattern (18 bp):
TAAGAGAAAATTAATTTT
Found at i:208699 original size:11 final size:10
Alignment explanation
Indices: 208673--208722 Score: 55
Period size: 10 Copynumber: 4.9 Consensus size: 10
208663 TCATAAAATG
*
208673 TTAAAAAATA
1 TTAAAAATTA
*
208683 TAAAAAATTA
1 TTAAAAATTA
208693 TTTAAAAATTA
1 -TTAAAAATTA
*
208704 TTGAAAATTA
1 TTAAAAATTA
*
208714 CTAAAAATT
1 TTAAAAATT
208723 TAAATTTAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
10 24 0.73
11 9 0.27
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (10 bp):
TTAAAAATTA
Found at i:229791 original size:29 final size:29
Alignment explanation
Indices: 229736--229791 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 29
229726 ACTTGTCCAC
* ** *
229736 TTCTCCCAAATTGGTACTTAAAGTTTTAT
1 TTCTCCCAAATTGATACCCAAACTTTTAT
*
229765 TTCTCCCAGATTGATACCCAAACTTTT
1 TTCTCCCAAATTGATACCCAAACTTTT
229792 TCTCCATCAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 22 1.00
ACGTcount: A:0.27, C:0.23, G:0.09, T:0.41
Consensus pattern (29 bp):
TTCTCCCAAATTGATACCCAAACTTTTAT
Found at i:230846 original size:27 final size:28
Alignment explanation
Indices: 230804--230856 Score: 90
Period size: 27 Copynumber: 1.9 Consensus size: 28
230794 GCTATGGTGC
*
230804 ATGTTGGTGGCGGCTAGGGTT-GGGAAA
1 ATGTTGGTGGCAGCTAGGGTTAGGGAAA
230831 ATGTTGGTGGCAGCTAGGGTTAGGGA
1 ATGTTGGTGGCAGCTAGGGTTAGGGA
230857 GGGGATGAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
27 20 0.83
28 4 0.17
ACGTcount: A:0.19, C:0.08, G:0.47, T:0.26
Consensus pattern (28 bp):
ATGTTGGTGGCAGCTAGGGTTAGGGAAA
Found at i:231669 original size:22 final size:22
Alignment explanation
Indices: 231641--231682 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
231631 CAACTCTTGC
**
231641 TTAATAATTAATTGATATAATT
1 TTAATAATTAAGAGATATAATT
231663 TTAATAATTAAGAGATATAA
1 TTAATAATTAAGAGATATAA
231683 CTGAACACTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (22 bp):
TTAATAATTAAGAGATATAATT
Done.