Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000358.1 Kokia drynarioides strain JFW-HI SEQ_111143, 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: 229995
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Warning! 17 characters in sequence are not A, C, G, or T
Found at i:46066 original size:22 final size:23
Alignment explanation
Indices: 46034--46187 Score: 94
Period size: 22 Copynumber: 7.0 Consensus size: 23
46024 CCAATAATTA
*
46034 CCACAAAATTTGGAGATAAACTG
1 CCACATAATTTGGAGATAAACTG
*
46057 CCACAT-ATTTGTCA-AT-AA-TGG
1 CCACATAATTTG-GAGATAAACT-G
46078 CCACATAATTTGGAGATAAACTG
1 CCACATAATTTGGAGATAAACTG
** * ** *
46101 TGACATATTTTCCA-ATAATA-AG
1 CCACATAATTTGGAGATAA-ACTG
*
46123 -CACATAATTTGGAGAAAAACTG
1 CCACATAATTTGGAGATAAACTG
***
46145 CCACAT-ATTTTCCGAT-AA-TG
1 CCACATAATTTGGAGATAAACTG
46165 TCCACATAATTTGGAGATAAACT
1 -CCACATAATTTGGAGATAAACT
46188 ATCACATAGT
Statistics
Matches: 95, Mismatches: 22, Indels: 27
0.66 0.15 0.19
Matches are distributed among these distances:
20 3 0.03
21 28 0.29
22 36 0.38
23 26 0.27
24 2 0.02
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (23 bp):
CCACATAATTTGGAGATAAACTG
Found at i:46170 original size:88 final size:88
Alignment explanation
Indices: 46018--46207 Score: 274
Period size: 88 Copynumber: 2.2 Consensus size: 88
46008 AGCCACCACG
* *
46018 TATTTGCCAATAATTACCACAAAATTTGGAGATAAACTGCCACATATTTGTCAATAATGGCCACA
1 TATTTGCCAATAATAACCACAAAATTTGGAGAAAAACTGCCACATATTTGTCAATAATGGCCACA
* *
46083 TAATTTGGAGATAAACTGTGACA
66 TAATTTGGAGATAAACTATCACA
* * * * *
46106 TATTTTCCAATAATAAGCACATAATTTGGAGAAAAACTGCCACATATTT-TCCGATAATGTCCAC
1 TATTTGCCAATAATAACCACAAAATTTGGAGAAAAACTGCCACATATTTGT-CAATAATGGCCAC
46170 ATAATTTGGAGATAAACTATCACA
65 ATAATTTGGAGATAAACTATCACA
*
46194 TAGTTGCCAATAAT
1 TATTTGCCAATAAT
46208 GGTCACATAT
Statistics
Matches: 90, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
87 1 0.01
88 89 0.99
ACGTcount: A:0.39, C:0.17, G:0.13, T:0.31
Consensus pattern (88 bp):
TATTTGCCAATAATAACCACAAAATTTGGAGAAAAACTGCCACATATTTGTCAATAATGGCCACA
TAATTTGGAGATAAACTATCACA
Found at i:46208 original size:44 final size:44
Alignment explanation
Indices: 46013--46216 Score: 232
Period size: 44 Copynumber: 4.6 Consensus size: 44
46003 GGAAAAGCCA
* *
46013 CCACGTATTTGCCAATAAT-TACCACAAAATTTGGAGATAAACTG
1 CCACATATTTGCCAATAATGT-CCACATAATTTGGAGATAAACTG
* *
46057 CCACATATTTGTCAATAATGGCCACATAATTTGGAGATAAACTG
1 CCACATATTTGCCAATAATGTCCACATAATTTGGAGATAAACTG
** * *** *
46101 TGACATATTTTCCAATAATAAGCACATAATTTGGAGAAAAACTG
1 CCACATATTTGCCAATAATGTCCACATAATTTGGAGATAAACTG
* * *
46145 CCACATATTTTCCGATAATGTCCACATAATTTGGAGATAAACTA
1 CCACATATTTGCCAATAATGTCCACATAATTTGGAGATAAACTG
* *
46189 TCACATAGTTGCCAATAATGGT-CACATA
1 CCACATATTTGCCAATAAT-GTCCACATA
46217 TCTTCTACCT
Statistics
Matches: 134, Mismatches: 24, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
44 132 0.99
45 2 0.01
ACGTcount: A:0.38, C:0.19, G:0.14, T:0.29
Consensus pattern (44 bp):
CCACATATTTGCCAATAATGTCCACATAATTTGGAGATAAACTG
Found at i:51602 original size:219 final size:219
Alignment explanation
Indices: 51223--51623 Score: 563
Period size: 219 Copynumber: 1.8 Consensus size: 219
51213 CCATTTTGGT
* * *
51223 GTAGATTTAGGATTTTCATAGGTATACGGGTCAAGTTCTAAATATAGTGTGTTTCAACGGAACAC
1 GTAGATTTAGGATTTTCACAAGTATACGGGTCAAGTTCTAAATATAGTGTGTTACAACGGAACAC
* * * * * * * *
51288 TTGGTAGTTTTCTAAGGATCATACCCAAAGGAGACGTTAGGCGATAGTAAATCGAATCCATGCAG
66 TTGGTAGTATTCCAAGGATCATACCCAAAGGAGACGTAAGGCAATAATAAATCAAATCCATACAA
* * * * *
51353 AGAATAAAACTAATTAATAGTTATTTTAGGTATTATAGTACGAAGAAATAAATAGTAGATGATCG
131 AAAATAAAACTAATTAATACTCATTTTAGGTATTATAGCACAAAGAAATAAATAGTAGATGATCG
51418 CCCCCGAAAATACTCTTATTCGGC
196 CCCCCGAAAATACTCTTATTCGGC
* *
51442 GTAGATTTA-GACTTTTCACAAGTATACGGGTTAAGTTGTAAATATAGTGTGTTACAACGGAACA
1 GTAGATTTAGGA-TTTTCACAAGTATACGGGTCAAGTTCTAAATATAGTGTGTTACAACGGAACA
* * * *
51506 CTTGGTAGTATTCCGAGGATCATACCTAAAGGAGGCAG-AAGGCAATAATAAATCAAATCCCTAC
65 CTTGGTAGTATTCCAAGGATCATACCCAAAGGAGAC-GTAAGGCAATAATAAATCAAATCCATAC
*
51570 AAAAAATAAAATTAATTAATACTCATTTTAGGTATTATAGCACAAAGAAATAAA
129 AAAAAATAAAACTAATTAATACTCATTTTAGGTATTATAGCACAAAGAAATAAA
51624 GAGTGGATTT
Statistics
Matches: 157, Mismatches: 23, Indels: 4
0.85 0.12 0.02
Matches are distributed among these distances:
218 2 0.01
219 154 0.98
220 1 0.01
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (219 bp):
GTAGATTTAGGATTTTCACAAGTATACGGGTCAAGTTCTAAATATAGTGTGTTACAACGGAACAC
TTGGTAGTATTCCAAGGATCATACCCAAAGGAGACGTAAGGCAATAATAAATCAAATCCATACAA
AAAATAAAACTAATTAATACTCATTTTAGGTATTATAGCACAAAGAAATAAATAGTAGATGATCG
CCCCCGAAAATACTCTTATTCGGC
Found at i:53020 original size:26 final size:26
Alignment explanation
Indices: 52960--53016 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
52950 ATGCGGCGAA
*
52960 AATTCTGGGCACGTTCATACAGCGAC
1 AATTCTGGGCACGTTCATACAACGAC
* * *
52986 AATTCTGGGCATGTTCATGCAATGAC
1 AATTCTGGGCACGTTCATACAACGAC
53012 -ATTCT
1 AATTCT
53017 TGGGTGCAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
25 5 0.19
26 22 0.81
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30
Consensus pattern (26 bp):
AATTCTGGGCACGTTCATACAACGAC
Found at i:53612 original size:11 final size:11
Alignment explanation
Indices: 53596--53625 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
53586 TATATATAGA
53596 TTTTTTTTCTC
1 TTTTTTTTCTC
*
53607 TTTTTTTTTTC
1 TTTTTTTTCTC
53618 TTTTTTTT
1 TTTTTTTT
53626 ATATGTGACT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (11 bp):
TTTTTTTTCTC
Found at i:53614 original size:13 final size:12
Alignment explanation
Indices: 53596--53625 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
53586 TATATATAGA
53596 TTTTTTTTCTCTT
1 TTTTTTTTCT-TT
53609 TTTTTTTTCTTT
1 TTTTTTTTCTTT
53621 TTTTT
1 TTTTT
53626 ATATGTGACT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.41
13 10 0.59
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (12 bp):
TTTTTTTTCTTT
Found at i:57036 original size:26 final size:26
Alignment explanation
Indices: 57007--57077 Score: 90
Period size: 26 Copynumber: 2.7 Consensus size: 26
56997 CAGTTGTCAG
57007 ATGCAACGATAATTCTGGACACGTTC
1 ATGCAACGATAATTCTGGACACGTTC
* *
57033 ATGCAACGACAATTCTAGG-CATGTTC
1 ATGCAACGATAATTCT-GGACACGTTC
* *
57059 ATGCAGCGATAGTTCTGGA
1 ATGCAACGATAATTCTGGA
57078 TGCAATGTGA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
25 2 0.05
26 34 0.89
27 2 0.05
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.27
Consensus pattern (26 bp):
ATGCAACGATAATTCTGGACACGTTC
Found at i:57195 original size:37 final size:37
Alignment explanation
Indices: 57140--57211 Score: 108
Period size: 37 Copynumber: 1.9 Consensus size: 37
57130 ATTCTTACGA
* * * *
57140 CAATAGTTTTGGGTGCAATTTGGAAGTGCTTATGCGG
1 CAATAGTTTTGGGCGCAATCTAGAAGTGCTCATGCGG
57177 CAATAGTTTTGGGCGCAATCTAGAAGTGCTCATGC
1 CAATAGTTTTGGGCGCAATCTAGAAGTGCTCATGC
57212 AGCGACATTA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.24, C:0.15, G:0.29, T:0.32
Consensus pattern (37 bp):
CAATAGTTTTGGGCGCAATCTAGAAGTGCTCATGCGG
Found at i:58967 original size:21 final size:22
Alignment explanation
Indices: 58936--58977 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
58926 ATTCACATGT
58936 TTTCTTACTCATGATTCTTTTG
1 TTTCTTACTCATGATTCTTTTG
**
58958 TTTC-TACTCATTTTTCTTTT
1 TTTCTTACTCATGATTCTTTT
58978 CTTTTTGATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.12, C:0.19, G:0.05, T:0.64
Consensus pattern (22 bp):
TTTCTTACTCATGATTCTTTTG
Found at i:65134 original size:15 final size:14
Alignment explanation
Indices: 65109--65143 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
65099 TTTACATTTT
*
65109 ATTTTATTTGTTTC
1 ATTTTACTTGTTTC
65123 ACTTTTACTTGTTTC
1 A-TTTTACTTGTTTC
65138 ATTTTA
1 ATTTTA
65144 AATTTTACGC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.17, C:0.11, G:0.06, T:0.66
Consensus pattern (14 bp):
ATTTTACTTGTTTC
Found at i:77239 original size:30 final size:30
Alignment explanation
Indices: 77170--77240 Score: 124
Period size: 30 Copynumber: 2.4 Consensus size: 30
77160 GTGGTTCAAC
*
77170 AGTAGTGGTACTACACTCGGCTGTGGCTTA
1 AGTAGTGGTGCTACACTCGGCTGTGGCTTA
*
77200 AGTAGTGGTGCTACACTCGGTTGTGGCTTA
1 AGTAGTGGTGCTACACTCGGCTGTGGCTTA
77230 AGTAGTGGTGC
1 AGTAGTGGTGC
77241 AAGGGTTCAG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.18, C:0.17, G:0.34, T:0.31
Consensus pattern (30 bp):
AGTAGTGGTGCTACACTCGGCTGTGGCTTA
Found at i:82763 original size:160 final size:160
Alignment explanation
Indices: 82591--82907 Score: 616
Period size: 160 Copynumber: 2.0 Consensus size: 160
82581 ATTACATACT
**
82591 CTCTCTCTCTCCCACTTTCTCGTATATTTATAGTTAAATTAATATATGATTAGGCTTAATTAATC
1 CTCTCTCTCTCCCACTTTCTCACATATTTATAGTTAAATTAATATATGATTAGGCTTAATTAATC
82656 ATAATTAGTTAGTTAACAAAAGACCATTATACATAATAAATTATAATGATAATGATGAGTGGATT
66 ATAATTAGTTAGTTAACAAAAGACCATTATACATAATAAATTATAATGATAATGATGAGTGGATT
82721 TAATCATAACTTTCCAATAACTCATGGTTA
131 TAATCATAACTTTCCAATAACTCATGGTTA
82751 CTCTCTCTCTCCCACTTTCTCACATATTTATAGTTAAATTAATATATGATTAGGCTTAATTAATC
1 CTCTCTCTCTCCCACTTTCTCACATATTTATAGTTAAATTAATATATGATTAGGCTTAATTAATC
82816 ATAATTAGTTAGTTAACAAAAGACCATTATACATAATAAATTATAATGATAATGATGAGTGGATT
66 ATAATTAGTTAGTTAACAAAAGACCATTATACATAATAAATTATAATGATAATGATGAGTGGATT
82881 TAATCATAACTTTCCAATAACTCATGG
131 TAATCATAACTTTCCAATAACTCATGG
82908 AGTAGGGATT
Statistics
Matches: 155, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
160 155 1.00
ACGTcount: A:0.37, C:0.15, G:0.10, T:0.38
Consensus pattern (160 bp):
CTCTCTCTCTCCCACTTTCTCACATATTTATAGTTAAATTAATATATGATTAGGCTTAATTAATC
ATAATTAGTTAGTTAACAAAAGACCATTATACATAATAAATTATAATGATAATGATGAGTGGATT
TAATCATAACTTTCCAATAACTCATGGTTA
Found at i:83543 original size:84 final size:84
Alignment explanation
Indices: 83402--83571 Score: 322
Period size: 84 Copynumber: 2.0 Consensus size: 84
83392 CAAAACTTTG
* *
83402 GGTATATATGATGGACTTCGGGTGGCTTGGGATCCTAAATGGAATAAAGTTCTAGTTGAGACGGA
1 GGTATATATGATGGACTTCGAGTGGCTTGGGATCCTAAATGGAATAAAGTTCTAGTTGAGACGAA
83467 TTGTGCTCTTGCGATCAAA
66 TTGTGCTCTTGCGATCAAA
83486 GGTATATATGATGGACTTCGAGTGGCTTGGGATCCTAAATGGAATAAAGTTCTAGTTGAGACGAA
1 GGTATATATGATGGACTTCGAGTGGCTTGGGATCCTAAATGGAATAAAGTTCTAGTTGAGACGAA
83551 TTGTGCTCTTGCGATCAAA
66 TTGTGCTCTTGCGATCAAA
83570 GG
1 GG
83572 AATTAAGGAA
Statistics
Matches: 84, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
84 84 1.00
ACGTcount: A:0.27, C:0.13, G:0.29, T:0.31
Consensus pattern (84 bp):
GGTATATATGATGGACTTCGAGTGGCTTGGGATCCTAAATGGAATAAAGTTCTAGTTGAGACGAA
TTGTGCTCTTGCGATCAAA
Found at i:97717 original size:52 final size:52
Alignment explanation
Indices: 97660--97820 Score: 125
Period size: 52 Copynumber: 3.1 Consensus size: 52
97650 ATGGCCAAAG
97660 GAAAAAAACTTCAGAGTTTATCAAGAAAGATTCAATGACTCTGACACCATGT
1 GAAAAAAACTTCAGAGTTTATCAAGAAAGATTCAATGACTCTGACACCATGT
** * * ** * * * * * * * *
97712 GAAAAAGAAACGAC-GA-TTGA-GAAGATGGAGCTCAGTTAGGTATGGC-CAAAG-
1 G-AAAA-AAACTTCAGAGTTTATCAAGAAAGA-TTCAATGA-CTCTGACACCATGT
97763 GAAAAAAACTTCAGAGTTTATCAAGAAAGATTCAATGACTCTGACACCATGT
1 GAAAAAAACTTCAGAGTTTATCAAGAAAGATTCAATGACTCTGACACCATGT
97815 GAAAAA
1 GAAAAA
97821 GAAAACAATT
Statistics
Matches: 72, Mismatches: 28, Indels: 18
0.61 0.24 0.15
Matches are distributed among these distances:
49 5 0.07
50 10 0.14
51 18 0.25
52 24 0.33
53 10 0.14
54 5 0.07
ACGTcount: A:0.43, C:0.15, G:0.20, T:0.21
Consensus pattern (52 bp):
GAAAAAAACTTCAGAGTTTATCAAGAAAGATTCAATGACTCTGACACCATGT
Found at i:97796 original size:103 final size:103
Alignment explanation
Indices: 97617--97824 Score: 416
Period size: 103 Copynumber: 2.0 Consensus size: 103
97607 GAGAGAAGGC
97617 AACGACGATTGAGAAGATGGAGCTCAGTTAGGTATGGCCAAAGGAAAAAAACTTCAGAGTTTATC
1 AACGACGATTGAGAAGATGGAGCTCAGTTAGGTATGGCCAAAGGAAAAAAACTTCAGAGTTTATC
97682 AAGAAAGATTCAATGACTCTGACACCATGTGAAAAAGA
66 AAGAAAGATTCAATGACTCTGACACCATGTGAAAAAGA
97720 AACGACGATTGAGAAGATGGAGCTCAGTTAGGTATGGCCAAAGGAAAAAAACTTCAGAGTTTATC
1 AACGACGATTGAGAAGATGGAGCTCAGTTAGGTATGGCCAAAGGAAAAAAACTTCAGAGTTTATC
97785 AAGAAAGATTCAATGACTCTGACACCATGTGAAAAAGA
66 AAGAAAGATTCAATGACTCTGACACCATGTGAAAAAGA
97823 AA
1 AA
97825 ACAATTGTTG
Statistics
Matches: 105, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
103 105 1.00
ACGTcount: A:0.42, C:0.14, G:0.23, T:0.20
Consensus pattern (103 bp):
AACGACGATTGAGAAGATGGAGCTCAGTTAGGTATGGCCAAAGGAAAAAAACTTCAGAGTTTATC
AAGAAAGATTCAATGACTCTGACACCATGTGAAAAAGA
Found at i:99012 original size:426 final size:424
Alignment explanation
Indices: 98053--100171 Score: 3405
Period size: 426 Copynumber: 5.1 Consensus size: 424
98043 TGGTATAATT
*
98053 ACTAATCAGCTTCCTAAAGCTAATTAATCCTAGAATCATGATATAATTATGCAAGATATCACAGT
1 ACTAAACAGCTTCCTAAAGCTAATTAATCCTAGAATCATGATATAATTATGCAAGATATCACAGT
98118 TGTTCAAAACAATAAGCATCACAGTGCATCTACAAGACATTCTCTTGAAGCGTTGTTAGGTTTTA
66 TGTTCAAAACAATAAGCATCACAGTGCATCTACAAGACATTCTCTTGAAGCGTTGTTAGGTTTTA
* *
98183 ATATTAATTTTCGTATGGTGGAGGTTGCAAACATTTGCTTTTATGAACCTGATAGAGCTATTCTT
131 ATATTAATTTTGGTATGGTGGAGGTTGCAAACATTTGCTTTTATGAACCTAATAGAGCTATTCTT
* * *
98248 GTTTCCCTCATAGGCTGAGATGACGCTCTAAGCTTCTTGACAAAATTATAGTAAGCTTTCATGGG
196 GTTTCCCTCATAGGCTGAGATGACACTCTAAGCTCCTTGACAAAATTATAGTAAACTTTCATGGG
* *
98313 AATCTTATCAAGTTTTTTTTTATATTTCC-CTTACATGGTTTTATGCTAACCGTTAATCAACAGG
261 AATCTTATCAAG-TTTTTTTTATTTTTCCTC-TACATGGTTTTATGCTAACCGTTAATCAACAAG
98377 AAATATTTGATTGTGCTCCACCTAAGAAGAAAAAAATTGTTTTGGTAACAAATATTGTTGAAAGT
324 AAATATTTGATTGTGCTCCACCTAAGAAGAAAAAAATTGTTTTGGTAACAAATATTGTTGAAAGT
*
98442 AACATACCCATAATTGATCTTAAGAATTCAGATAAG
389 AACATACCCATAATTGATCTTGAGAATTCAGATAAG
98478 ACTAAACAGCTTCCTAAAGCTAATTAATCCTAGAATCATGATATAATTATGCAAGATATCACAGT
1 ACTAAACAGCTTCCTAAAGCTAATTAATCCTAGAATCATGATATAATTATGCAAGATATCACAGT
*
98543 TGTTCAAAACAATAAGCATCACAGTGCATCTACAAGACATTCTCTAGAAGCGTTGTTAGGTTTTA
66 TGTTCAAAACAATAAGCATCACAGTGCATCTACAAGACATTCTCTTGAAGCGTTGTTAGGTTTTA
* * * *
98608 ATATTAATTTTGGTACGGTGGAGGTTGCGAACATTTGCTTTTATGAACTTGATAGAGCTATTCTT
131 ATATTAATTTTGGTATGGTGGAGGTTGCAAACATTTGCTTTTATGAACCTAATAGAGCTATTCTT
* * *
98673 GTTTCCCTCATAGGCTGAGATGACACTCTAAGCTTCTTGATAAAATTATAGTAAGCTTTCATGGG
196 GTTTCCCTCATAGGCTGAGATGACACTCTAAGCTCCTTGACAAAATTATAGTAAACTTTCATGGG
* * *
98738 AATCTTATCAAGTTTGTTTTTTATTTTTCCCCTACATGGTTTTATGCTAACCGTTAATCAAGAGG
261 AATCTTATCAAG-TT-TTTTTTATTTTTCCTCTACATGGTTTTATGCTAACCGTTAATCAACAAG
* *
98803 AAATATTTGATTGTGCTCCACCTAAGCAGAAAAAAATTGTTTTTGTAACAAATATTGTTGAAAGT
324 AAATATTTGATTGTGCTCCACCTAAGAAGAAAAAAATTGTTTTGGTAACAAATATTGTTGAAAGT
*
98868 AACATACCCATAATTGATCTTAAGAATTCAGATAAG
389 AACATACCCATAATTGATCTTGAGAATTCAGATAAG
* * *
98904 ACTAAACAGCTTTCTAAAGCTAATTAATCCTAGAATCATGATATAACTATGCAAGATATCATAGT
1 ACTAAACAGCTTCCTAAAGCTAATTAATCCTAGAATCATGATATAATTATGCAAGATATCACAGT
*
98969 TGTTCAAAACAATAAGCATCACAGTGCATCTACAAGACATTCTCTAGAAGCGTTGTTAGGTTTTA
66 TGTTCAAAACAATAAGCATCACAGTGCATCTACAAGACATTCTCTTGAAGCGTTGTTAGGTTTTA
*
99034 ATATTAATTTTGGTATGGTGGAGGTTGCGAACATTTGCTTTTATGAACCTAATAGAGCTATTCTT
131 ATATTAATTTTGGTATGGTGGAGGTTGCAAACATTTGCTTTTATGAACCTAATAGAGCTATTCTT
* *
99099 GTTTCCCTCATAGGCTAAGATGACACTCTAAGCTCCTTGACAAAATTATAGCAAACTTTCATGGG
196 GTTTCCCTCATAGGCTGAGATGACACTCTAAGCTCCTTGACAAAATTATAGTAAACTTTCATGGG
* *
99164 AATCTTATTAAG---TTTTT-TTTTTCCTTTACATGGTTTTATGCTAACCGTTAATCAACAAGAA
261 AATCTTATCAAGTTTTTTTTATTTTTCCTCTACATGGTTTTATGCTAACCGTTAATCAACAAGAA
*
99225 ATATTTGATTGTGCTCCACCTAAGAAGAAAAAAATTGTTTTGGTAACAAATATTGTTGACAGTAA
326 ATATTTGATTGTGCTCCACCTAAGAAGAAAAAAATTGTTTTGGTAACAAATATTGTTGAAAGTAA
99290 CATACCCATAATTGATCTTGAGAATTCAGATAAG
391 CATACCCATAATTGATCTTGAGAATTCAGATAAG
* * *
99324 ACTCAACAGCTTCCTAAAGCTAATTAATCCTAGAATCATGATATAATTATGCATGTTATCACAGT
1 ACTAAACAGCTTCCTAAAGCTAATTAATCCTAGAATCATGATATAATTATGCAAGATATCACAGT
* *
99389 TGTTCACAACAATAAGCATCAAAGTGCATCTACAAGACATTCTCTTGAAGC------A-----T-
66 TGTTCAAAACAATAAGCATCACAGTGCATCTACAAGACATTCTCTTGAAGCGTTGTTAGGTTTTA
* *
99442 -TGTT-A-----G---GGTGGAGGTTGCAAACATTTGCTTTTATGAACCTAATTGAGCTATTCTT
131 ATATTAATTTTGGTATGGTGGAGGTTGCAAACATTTGCTTTTATGAACCTAATAGAGCTATTCTT
*
99497 GTTCCCCTC-TAAGGCTGAGATGACACTCTAAGCTCCTTGACAAAATTATAGTAAACTTTCATGG
196 GTTTCCCTCAT-AGGCTGAGATGACACTCTAAGCTCCTTGACAAAATTATAGTAAACTTTCATGG
* **
99561 GAATCTTATCAAGTTTTTTTTATTTTTCCTCTACAAGGTTTTATGCTAACAATTAATCAACAAGA
260 GAATCTTATCAAGTTTTTTTTATTTTTCCTCTACATGGTTTTATGCTAACCGTTAATCAACAAGA
99626 AATATTTGATTGTGCTCCACCTAAGAAGAAAAAAATTGTTTTGGTAACAAATATTGTTGAAAGTA
325 AATATTTGATTGTGCTCCACCTAAGAAGAAAAAAATTGTTTTGGTAACAAATATTGTTGAAAGTA
*
99691 ACATACCCATAATTGATCTTGAGAATTCATATAAG
390 ACATACCCATAATTGATCTTGAGAATTCAGATAAG
* * * * *
99726 ACTCAACAGCTTCCTAGAGCTAATTACTCCTAGAATCGTGATATAATTATGCAAGATATCACAAT
1 ACTAAACAGCTTCCTAAAGCTAATTAATCCTAGAATCATGATATAATTATGCAAGATATCACAGT
* *
99791 TGTTCATAACAATAAGCATCACAGTGCATCTACAAGACATTCTCTTGAAGCATTGTTAGGTTTTA
66 TGTTCAAAACAATAAGCATCACAGTGCATCTACAAGACATTCTCTTGAAGCGTTGTTAGGTTTTA
* * *
99856 ATACTAATTTTGGTATGGTGGAGGTTGCAAACATTAGCTTTTATGAACCTAATGGAGCTATTCTT
131 ATATTAATTTTGGTATGGTGGAGGTTGCAAACATTTGCTTTTATGAACCTAATAGAGCTATTCTT
* *
99921 GTTTCCCTCATAGGTTGAGATGACACTCTAAGCTCCGTGACAAAATTATAGTAAACTTTCATGGG
196 GTTTCCCTCATAGGCTGAGATGACACTCTAAGCTCCTTGACAAAATTATAGTAAACTTTCATGGG
* ** *
99986 AATCTTATCAAGTTTTTTCTATTTTTCCTCTACATAATTTTATGCTAACCGTTACTCAACAAGAA
261 AATCTTATCAAGTTTTTTTTATTTTTCCTCTACATGGTTTTATGCTAACCGTTAATCAACAAGAA
*
100051 ATATTTGATTGTGCTCCACCTACGAAG-AAAAAATTGTTTTGGTAACAAATATTGTTGAAAGTAA
326 ATATTTGATTGTGCTCCACCTAAGAAGAAAAAAATTGTTTTGGTAACAAATATTGTTGAAAGTAA
100115 CATACCCATAATTGATCTTGAGAATTCAGATAAG
391 CATACCCATAATTGATCTTGAGAATTCAGATAAG
* * *
100149 ACTCAACAACTTACTAAAGCTAA
1 ACTAAACAGCTTCCTAAAGCTAA
100172 AACAGATGTT
Statistics
Matches: 1583, Mismatches: 81, Indels: 62
0.92 0.05 0.04
Matches are distributed among these distances:
397 1 0.00
398 118 0.07
401 6 0.00
402 245 0.15
406 1 0.00
407 3 0.00
408 1 0.00
409 1 0.00
413 1 0.00
414 1 0.00
415 2 0.00
416 1 0.00
420 242 0.15
421 6 0.00
423 90 0.06
424 191 0.12
425 268 0.17
426 404 0.26
427 1 0.00
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (424 bp):
ACTAAACAGCTTCCTAAAGCTAATTAATCCTAGAATCATGATATAATTATGCAAGATATCACAGT
TGTTCAAAACAATAAGCATCACAGTGCATCTACAAGACATTCTCTTGAAGCGTTGTTAGGTTTTA
ATATTAATTTTGGTATGGTGGAGGTTGCAAACATTTGCTTTTATGAACCTAATAGAGCTATTCTT
GTTTCCCTCATAGGCTGAGATGACACTCTAAGCTCCTTGACAAAATTATAGTAAACTTTCATGGG
AATCTTATCAAGTTTTTTTTATTTTTCCTCTACATGGTTTTATGCTAACCGTTAATCAACAAGAA
ATATTTGATTGTGCTCCACCTAAGAAGAAAAAAATTGTTTTGGTAACAAATATTGTTGAAAGTAA
CATACCCATAATTGATCTTGAGAATTCAGATAAG
Found at i:103813 original size:21 final size:21
Alignment explanation
Indices: 103757--103813 Score: 55
Period size: 21 Copynumber: 2.7 Consensus size: 21
103747 CGATCAACGA
103757 TCAACAGTTGATCAATGTCGG
1 TCAACAGTTGATCAATGTCGG
* **
103778 TCAATAG-CAAGTCAATGATCGG
1 TCAACAGTTGA-TCAATG-TCGG
103800 TCAA-AGTTGATCAA
1 TCAACAGTTGATCAA
103814 CTAACGATCA
Statistics
Matches: 28, Mismatches: 5, Indels: 6
0.72 0.13 0.15
Matches are distributed among these distances:
20 1 0.04
21 18 0.64
22 9 0.32
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.26
Consensus pattern (21 bp):
TCAACAGTTGATCAATGTCGG
Found at i:112775 original size:26 final size:21
Alignment explanation
Indices: 112716--112770 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
112706 TAATTTATTG
*
112716 TATATTATATAATGTACAACAT
1 TATAATATA-AATGTACAACAT
112738 TATAATATAAATGTACAACAT
1 TATAATATAAATGTACAACAT
*
112759 TATAGTATAAAT
1 TATAATATAAAT
112771 TAAATATTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
21 23 0.74
22 8 0.26
ACGTcount: A:0.49, C:0.07, G:0.05, T:0.38
Consensus pattern (21 bp):
TATAATATAAATGTACAACAT
Found at i:112789 original size:16 final size:18
Alignment explanation
Indices: 112718--112801 Score: 59
Period size: 21 Copynumber: 4.5 Consensus size: 18
112708 ATTTATTGTA
112718 TATTATAT-AATGTACAACAT
1 TATTATATAAAT-TA-AA-AT
*
112738 TATAATATAAATGTACAACAT
1 TATTATATAAAT-TA-AA-AT
112759 TA-TAGTATAAATT-AAA-
1 TATTA-TATAAATTAAAAT
*
112775 TATTATATAATTTAAAAT
1 TATTATATAAATTAAAAT
112793 TATTATATA
1 TATTATATA
112802 CATGTATTTT
Statistics
Matches: 56, Mismatches: 3, Indels: 12
0.79 0.04 0.17
Matches are distributed among these distances:
16 9 0.16
17 6 0.11
18 11 0.20
20 9 0.16
21 21 0.38
ACGTcount: A:0.50, C:0.05, G:0.04, T:0.42
Consensus pattern (18 bp):
TATTATATAAATTAAAAT
Found at i:115557 original size:30 final size:30
Alignment explanation
Indices: 115492--115571 Score: 76
Period size: 30 Copynumber: 2.7 Consensus size: 30
115482 AAAATTTTAA
*
115492 TTTAATAAA-AATAAAATTATATTTTGATTT
1 TTTAA-AAATAATAAAATTATATTTTAATTT
* *
115522 CTTAAAAATAATAAAATT-TTTATTTAATTT
1 TTTAAAAATAATAAAATTATAT-TTTAATTT
* *
115552 TTT-AAAATTATAAAAATATA
1 TTTAAAAATAATAAAATTATA
115572 AACTATTAAA
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
29 17 0.43
30 23 0.57
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.47
Consensus pattern (30 bp):
TTTAAAAATAATAAAATTATATTTTAATTT
Found at i:131514 original size:10 final size:10
Alignment explanation
Indices: 131501--131543 Score: 63
Period size: 10 Copynumber: 4.5 Consensus size: 10
131491 AAAAAATCAC
131501 AAAAAGAAAG
1 AAAAAGAAAG
131511 AAAAAGAAAG
1 AAAAAGAAAG
*
131521 AAGAAGAAA-
1 AAAAAGAAAG
131530 AAAAA-AAAG
1 AAAAAGAAAG
131539 AAAAA
1 AAAAA
131544 AAATACATTG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
8 3 0.10
9 9 0.30
10 18 0.60
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (10 bp):
AAAAAGAAAG
Found at i:144105 original size:18 final size:18
Alignment explanation
Indices: 144060--144104 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 18
144050 CAAATGATAA
*
144060 ACAAATAAAATGTCAACG
1 ACAACTAAAATGTCAACG
*
144078 ACAACTAAAATG-CAATG
1 ACAACTAAAATGTCAACG
*
144095 ACAATTAAAA
1 ACAACTAAAA
144105 AAAATGCATG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
17 13 0.54
18 11 0.46
ACGTcount: A:0.58, C:0.16, G:0.09, T:0.18
Consensus pattern (18 bp):
ACAACTAAAATGTCAACG
Found at i:144209 original size:104 final size:104
Alignment explanation
Indices: 144095--144303 Score: 409
Period size: 104 Copynumber: 2.0 Consensus size: 104
144085 AAATGCAATG
144095 ACAATTAAAAAAAATGCATGCAACTAACTATCAAAAAGTAAACTAACTCAATGTGTCGCAGCTGA
1 ACAATTAAAAAAAATGCATGCAACTAACTATCAAAAAGTAAACTAACTCAATGTGTCGCAGCTGA
144160 GGAAGTGGCTGCCTTTTTATTTTTCTTCTTCTTTAGGGA
66 GGAAGTGGCTGCCTTTTTATTTTTCTTCTTCTTTAGGGA
144199 ACAATTAAAAAAAATGCATGCAACTAACTATCAAAAAGTAAACTAACTCAATGTGTCGCAGCTGA
1 ACAATTAAAAAAAATGCATGCAACTAACTATCAAAAAGTAAACTAACTCAATGTGTCGCAGCTGA
*
144264 GGAAGTGGCTGCCTTTTTCTTTTTCTTCTTCTTTAGGGA
66 GGAAGTGGCTGCCTTTTTATTTTTCTTCTTCTTTAGGGA
144303 A
1 A
144304 TCCTCTTTAG
Statistics
Matches: 104, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
104 104 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (104 bp):
ACAATTAAAAAAAATGCATGCAACTAACTATCAAAAAGTAAACTAACTCAATGTGTCGCAGCTGA
GGAAGTGGCTGCCTTTTTATTTTTCTTCTTCTTTAGGGA
Found at i:150384 original size:30 final size:30
Alignment explanation
Indices: 150348--150412 Score: 121
Period size: 30 Copynumber: 2.2 Consensus size: 30
150338 TTTCTCCCAC
150348 AATTTGTACAAACATGAACAACGCTATCCA
1 AATTTGTACAAACATGAACAACGCTATCCA
150378 AATTTGTACAAACATGAACAACGCTATCCA
1 AATTTGTACAAACATGAACAACGCTATCCA
*
150408 CATTT
1 AATTT
150413 CTAACACTAC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.42, C:0.23, G:0.09, T:0.26
Consensus pattern (30 bp):
AATTTGTACAAACATGAACAACGCTATCCA
Found at i:152672 original size:20 final size:20
Alignment explanation
Indices: 152624--152808 Score: 146
Period size: 20 Copynumber: 9.3 Consensus size: 20
152614 TTAGATTTTT
*
152624 CAAACA-GGGTATCGAAATG
1 CAAACAGGGGCATCGAAATG
* *
152643 CAACCTGGGGCATCGAAATG
1 CAAACAGGGGCATCGAAATG
* *
152663 CAAATAGGGGCA-CCAAAGTG
1 CAAACAGGGGCATCGAAA-TG
* *
152683 CAAGCAAGGGCATC-AAAGTG
1 CAAACAGGGGCATCGAAA-TG
*
152703 CAAACAGGGGC--CCAAAGTG
1 CAAACAGGGGCATCGAAA-TG
* * *
152722 CAAATAGGGCCATCGAAGTG
1 CAAACAGGGGCATCGAAATG
* * *
152742 CAAACAGGGGCACCGAACTA
1 CAAACAGGGGCATCGAAATG
* *
152762 CAAATAGGGGCATCGAAGTG
1 CAAACAGGGGCATCGAAATG
*
152782 CAAACAGGGGCATCGAAGTG
1 CAAACAGGGGCATCGAAATG
*
152802 AAAACAG
1 CAAACAG
152809 TAATCAACAT
Statistics
Matches: 133, Mismatches: 27, Indels: 11
0.78 0.16 0.06
Matches are distributed among these distances:
18 1 0.01
19 23 0.17
20 105 0.79
21 4 0.03
ACGTcount: A:0.38, C:0.21, G:0.30, T:0.11
Consensus pattern (20 bp):
CAAACAGGGGCATCGAAATG
Found at i:163800 original size:24 final size:24
Alignment explanation
Indices: 163768--163819 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
163758 CTGTGCTGCC
*
163768 ACATATGCAAGGATAGTATCATCA
1 ACATATGCAAGGATAGCATCATCA
*
163792 ACATGTGCAAGGATAGCATCATCA
1 ACATATGCAAGGATAGCATCATCA
163816 ACAT
1 ACAT
163820 CAACAGCAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.40, C:0.19, G:0.17, T:0.23
Consensus pattern (24 bp):
ACATATGCAAGGATAGCATCATCA
Found at i:165112 original size:50 final size:50
Alignment explanation
Indices: 165055--165155 Score: 184
Period size: 50 Copynumber: 2.0 Consensus size: 50
165045 CTGAGAAAGA
* *
165055 ATTGGCAATTGTAGTCTTTAGATTTGTCTAACAGGACAATCCCAATGTTT
1 ATTGGCAATTATAGTATTTAGATTTGTCTAACAGGACAATCCCAATGTTT
165105 ATTGGCAATTATAGTATTTAGATTTGTCTAACAGGACAATCCCAATGTTT
1 ATTGGCAATTATAGTATTTAGATTTGTCTAACAGGACAATCCCAATGTTT
165155 A
1 A
165156 AACCATCTGG
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.31, C:0.15, G:0.17, T:0.38
Consensus pattern (50 bp):
ATTGGCAATTATAGTATTTAGATTTGTCTAACAGGACAATCCCAATGTTT
Found at i:165474 original size:31 final size:31
Alignment explanation
Indices: 165436--165498 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
165426 GAAGTAGTGA
165436 AGAAGGAAATTATCAAATGGTCAGATGCGGG
1 AGAAGGAAATTATCAAATGGTCAGATGCGGG
*
165467 AGAAGGAAATTATCAATTGGTCAGATGCGGG
1 AGAAGGAAATTATCAAATGGTCAGATGCGGG
165498 A
1 A
165499 ATCATTTACC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.38, C:0.10, G:0.32, T:0.21
Consensus pattern (31 bp):
AGAAGGAAATTATCAAATGGTCAGATGCGGG
Found at i:167331 original size:20 final size:21
Alignment explanation
Indices: 167295--167333 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
167285 CATTTGTTTA
*
167295 TTTACTTTTATTTGTTTCACT
1 TTTACTTTTAGTTGTTTCACT
167316 TTTACTTTT-GTTGTTTCA
1 TTTACTTTTAGTTGTTTCA
167334 AATTCCTTGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.13, C:0.13, G:0.08, T:0.67
Consensus pattern (21 bp):
TTTACTTTTAGTTGTTTCACT
Found at i:183799 original size:33 final size:33
Alignment explanation
Indices: 183756--183823 Score: 118
Period size: 33 Copynumber: 2.1 Consensus size: 33
183746 AAACCGATTT
*
183756 AAGCTTAAAGTAAGCATCCACAGTAGGATACGC
1 AAGCTCAAAGTAAGCATCCACAGTAGGATACGC
*
183789 AAGCTCAAAGTTAGCATCCACAGTAGGATACGC
1 AAGCTCAAAGTAAGCATCCACAGTAGGATACGC
183822 AA
1 AA
183824 TGCACAATGG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.40, C:0.22, G:0.21, T:0.18
Consensus pattern (33 bp):
AAGCTCAAAGTAAGCATCCACAGTAGGATACGC
Found at i:185245 original size:19 final size:18
Alignment explanation
Indices: 185221--185262 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
185211 AAACATGAAT
185221 TAAATACAAAT-TTAAATAA
1 TAAATA-AAATCTTAAAT-A
*
185240 TAAATAATATCTTAAATA
1 TAAATAAAATCTTAAATA
185258 TAAAT
1 TAAAT
185263 CCTAATAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 9 0.43
19 12 0.57
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.36
Consensus pattern (18 bp):
TAAATAAAATCTTAAATA
Found at i:189641 original size:20 final size:20
Alignment explanation
Indices: 189624--189671 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
189614 TTAGTTGTTC
189624 CGGTAGAAGCTTACTTGTAT
1 CGGTAGAAGCTTACTTGTAT
*
189644 CGGTAGAA-CTGTAGTTGTAT
1 CGGTAGAAGCT-TACTTGTAT
*
189664 CAGTAGAA
1 CGGTAGAA
189672 AAGGAGTTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 2 0.08
20 23 0.92
ACGTcount: A:0.29, C:0.12, G:0.27, T:0.31
Consensus pattern (20 bp):
CGGTAGAAGCTTACTTGTAT
Found at i:189904 original size:20 final size:20
Alignment explanation
Indices: 189879--189932 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
189869 AGTCTTCAAG
*
189879 GTATCGGTAGAAGTGTAGTT
1 GTATCGGTAGAAGTGGAGTT
*
189899 GTATCGGTAGAAGTGGATTT
1 GTATCGGTAGAAGTGGAGTT
* *
189919 CTACCGGTAGAAGT
1 GTATCGGTAGAAGT
189933 CTCACAAGAG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.26, C:0.09, G:0.33, T:0.31
Consensus pattern (20 bp):
GTATCGGTAGAAGTGGAGTT
Found at i:196948 original size:46 final size:46
Alignment explanation
Indices: 196881--196972 Score: 157
Period size: 46 Copynumber: 2.0 Consensus size: 46
196871 TCTTGAGTTT
*
196881 GGTCACTTTCGCAATTTCCTCTGGATTTGCATTGAGGGAGGGATCC
1 GGTCACTTTCGCAATTTCCTCTGAATTTGCATTGAGGGAGGGATCC
* *
196927 GGTCACTTTCGTAATTTCCTCTGAATTTGCATTGGGGGAGGGATCC
1 GGTCACTTTCGCAATTTCCTCTGAATTTGCATTGAGGGAGGGATCC
196973 TCCACGGGTT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.17, C:0.21, G:0.28, T:0.34
Consensus pattern (46 bp):
GGTCACTTTCGCAATTTCCTCTGAATTTGCATTGAGGGAGGGATCC
Found at i:200676 original size:30 final size:30
Alignment explanation
Indices: 200616--200678 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
200606 TTTGACCACA
*
200616 AAACTTTAATTAATTCTCCAATTCATCCCT
1 AAACTTTAATTAATTCTCCAATTCAACCCT
*
200646 AAACTTTACTTAATT-TCCAAATT-AGACCCT
1 AAACTTTAATTAATTCTCC-AATTCA-ACCCT
200676 AAA
1 AAA
200679 ATTCACTAGG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 4 0.14
30 25 0.86
ACGTcount: A:0.38, C:0.24, G:0.02, T:0.37
Consensus pattern (30 bp):
AAACTTTAATTAATTCTCCAATTCAACCCT
Found at i:203763 original size:26 final size:26
Alignment explanation
Indices: 203734--203805 Score: 92
Period size: 26 Copynumber: 2.8 Consensus size: 26
203724 TAAAAAAATG
* * *
203734 TCAATAGTTAAAGTTAAAGTCAACGA
1 TCAAAAGTCAAAGTCAAAGTCAACGA
203760 TCAAAAGTCAAAGTCAAAGTCAACGA
1 TCAAAAGTCAAAGTCAAAGTCAACGA
*
203786 TC-AAAGTCAATGGTCAAAGT
1 TCAAAAGTCAA-AGTCAAAGT
203806 TAATGAGTCA
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
25 8 0.20
26 33 0.80
ACGTcount: A:0.46, C:0.15, G:0.17, T:0.22
Consensus pattern (26 bp):
TCAAAAGTCAAAGTCAAAGTCAACGA
Found at i:203772 original size:6 final size:6
Alignment explanation
Indices: 203733--203805 Score: 56
Period size: 6 Copynumber: 11.3 Consensus size: 6
203723 GTAAAAAAAT
* * * *
203733 GTCAATA GTTAAA GTTAAA GTCAAC GATCAAAA GTCAAA GTCAAA GTCAAC
1 GTCAA-A GTCAAA GTCAAA GTCAAA G-TC-AAA GTCAAA GTCAAA GTCAAA
*
203784 GATCAAA GTCAATG GTCAAA GT
1 G-TCAAA GTCAA-A GTCAAA GT
203806 TAATGAGTCA
Statistics
Matches: 54, Mismatches: 8, Indels: 9
0.76 0.11 0.13
Matches are distributed among these distances:
6 33 0.61
7 18 0.33
8 3 0.06
ACGTcount: A:0.45, C:0.15, G:0.18, T:0.22
Consensus pattern (6 bp):
GTCAAA
Found at i:203789 original size:13 final size:13
Alignment explanation
Indices: 203749--203823 Score: 73
Period size: 13 Copynumber: 5.8 Consensus size: 13
203739 AGTTAAAGTT
203749 AAAGTCAACGATC
1 AAAGTCAACGATC
*
203762 AAAAGTCAAAG-TC
1 -AAAGTCAACGATC
203775 AAAGTCAACGATC
1 AAAGTCAACGATC
* *
203788 AAAGTCAATGGTC
1 AAAGTCAACGATC
* *
203801 AAAGTTAATGAGTC
1 AAAGTCAACGA-TC
203815 -AAGTCAACG
1 AAAGTCAACG
203824 GGTCAACGGG
Statistics
Matches: 51, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
12 9 0.18
13 31 0.61
14 11 0.22
ACGTcount: A:0.45, C:0.17, G:0.19, T:0.19
Consensus pattern (13 bp):
AAAGTCAACGATC
Found at i:209056 original size:20 final size:22
Alignment explanation
Indices: 209016--209056 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 22
209006 AGTGCCTAAT
*
209016 GTCGCGATTTTGCATTCCTCAC
1 GTCGCGATTTTGCATTACTCAC
209038 GTCGCGA-TTT-CATTACTCA
1 GTCGCGATTTTGCATTACTCA
209057 GTTAGTCTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 8 0.44
21 3 0.17
22 7 0.39
ACGTcount: A:0.17, C:0.29, G:0.17, T:0.37
Consensus pattern (22 bp):
GTCGCGATTTTGCATTACTCAC
Found at i:212093 original size:2 final size:2
Alignment explanation
Indices: 212086--212118 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
212076 CTACTACCCC
*
212086 CT CT CT CT CT CT CT CT CT TT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
212119 ATATATATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
CT
Found at i:217823 original size:46 final size:45
Alignment explanation
Indices: 217766--217853 Score: 108
Period size: 46 Copynumber: 1.9 Consensus size: 45
217756 TACATAAAAC
*
217766 TTTTTGAAT-AAATTACCACTTAATTTGCCAATGAA-GGCCACACAG
1 TTTTTGAATAAAATTACCACAT-ATTTGCCAAT-AATGGCCACACAG
* *
217811 TTTTTGCAATAAAATTGCCACATATTTGCTAATAATGGCCACA
1 TTTTTG-AATAAAATTACCACATATTTGCCAATAATGGCCACA
217854 TCTTCCTCTT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
45 8 0.22
46 19 0.51
47 10 0.27
ACGTcount: A:0.35, C:0.19, G:0.12, T:0.33
Consensus pattern (45 bp):
TTTTTGAATAAAATTACCACATATTTGCCAATAATGGCCACACAG
Found at i:229851 original size:25 final size:25
Alignment explanation
Indices: 229823--229870 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
229813 TAAATATTTT
229823 TAATTATT-ACTTTCCATAATTTTAA
1 TAATT-TTAACTTTCCATAATTTTAA
**
229848 TAATTTTAACTTTCTTTAATTTT
1 TAATTTTAACTTTCCATAATTTT
229871 TTAATAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 2 0.10
25 18 0.90
ACGTcount: A:0.31, C:0.10, G:0.00, T:0.58
Consensus pattern (25 bp):
TAATTTTAACTTTCCATAATTTTAA
Done.