Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007061.1 Kokia drynarioides strain JFW-HI SEQ_121670, 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: 52868
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:3438 original size:64 final size:64
Alignment explanation
Indices: 3360--3492 Score: 248
Period size: 64 Copynumber: 2.1 Consensus size: 64
3350 ATGTACTAGT
*
3360 AATTATTGTACTTCTATTATTTAACTGATAAATTCGAGTGATTGATTATAACTAAAATTAACTA
1 AATTATTGTACTTCTATTATTTAACTGATAAATCCGAGTGATTGATTATAACTAAAATTAACTA
*
3424 AATTATTGTCCTTCTATTATTTAACTGATAAATCCGAGTGATTGATTATAACTAAAATTAACTA
1 AATTATTGTACTTCTATTATTTAACTGATAAATCCGAGTGATTGATTATAACTAAAATTAACTA
3488 AATTA
1 AATTA
3493 ATTAACTACG
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
64 67 1.00
ACGTcount: A:0.39, C:0.11, G:0.09, T:0.41
Consensus pattern (64 bp):
AATTATTGTACTTCTATTATTTAACTGATAAATCCGAGTGATTGATTATAACTAAAATTAACTA
Found at i:4387 original size:60 final size:60
Alignment explanation
Indices: 4311--4439 Score: 222
Period size: 60 Copynumber: 2.1 Consensus size: 60
4301 TGCAATCGAT
* * *
4311 AAAAAAGATAGTAAATATCTTAAGAAAAACAACAATCCAAAATCATAATGTAATCCAACC
1 AAAAAACATAATAAATATCCTAAGAAAAACAACAATCCAAAATCATAATGTAATCCAACC
*
4371 AAAAAACATAATAAATATCCTAAGAAAAACTACAATCCAAAATCATAATGTAATCCAACC
1 AAAAAACATAATAAATATCCTAAGAAAAACAACAATCCAAAATCATAATGTAATCCAACC
4431 AAAAAACAT
1 AAAAAACAT
4440 GTAGAACTCA
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
60 65 1.00
ACGTcount: A:0.58, C:0.18, G:0.05, T:0.19
Consensus pattern (60 bp):
AAAAAACATAATAAATATCCTAAGAAAAACAACAATCCAAAATCATAATGTAATCCAACC
Found at i:5647 original size:17 final size:17
Alignment explanation
Indices: 5625--5726 Score: 82
Period size: 17 Copynumber: 5.8 Consensus size: 17
5615 CGTATATATA
*
5625 TATATATATATAAACAG
1 TATATATATATAAAAAG
*
5642 TATATATGTATAAAAA-
1 TATATATATATAAAAAG
*
5658 -ATATGTATATAAAATAG
1 TATATATATATAAAA-AG
*
5675 ATAAGTATATATATAATACAG
1 -T-A-TATATATATAA-AAAG
* *
5696 TATATATTTATAAAAAA
1 TATATATATATAAAAAG
*
5713 TATATATGTATAAA
1 TATATATATATAAA
5727 TATATAATTT
Statistics
Matches: 68, Mismatches: 10, Indels: 14
0.74 0.11 0.15
Matches are distributed among these distances:
15 12 0.18
16 1 0.01
17 29 0.43
18 10 0.15
19 1 0.01
20 2 0.03
21 12 0.18
22 1 0.01
ACGTcount: A:0.54, C:0.02, G:0.07, T:0.37
Consensus pattern (17 bp):
TATATATATATAAAAAG
Found at i:5661 original size:15 final size:15
Alignment explanation
Indices: 5626--5758 Score: 59
Period size: 17 Copynumber: 7.9 Consensus size: 15
5616 GTATATATAT
*
5626 ATATATATATAAACAGT
1 ATATATATATAAA-A-A
*
5643 ATATATGTATAAAAA
1 ATATATATATAAAAA
*
5658 ATATGTATATAAAATA
1 ATATATATATAAAA-A
5674 GATAAGTATATATATAATACA
1 -AT-A-TATATATA-AA-A-A
*
5695 GTATATATTTATAAAAA
1 --ATATATATATAAAAA
* *
5712 ATATATATGTATAAAT
1 ATATATATATA-AAAA
* *
5728 ATATAATTTGTAAAAAA
1 ATAT-ATATAT-AAAAA
*
5745 ATATGTATATAAAA
1 ATATATATATAAAA
5759 TTACTAATCT
Statistics
Matches: 90, Mismatches: 16, Indels: 22
0.70 0.12 0.17
Matches are distributed among these distances:
15 25 0.28
16 12 0.13
17 27 0.30
18 3 0.03
19 9 0.10
20 9 0.10
21 3 0.03
22 2 0.02
ACGTcount: A:0.55, C:0.02, G:0.07, T:0.37
Consensus pattern (15 bp):
ATATATATATAAAAA
Found at i:5717 original size:33 final size:34
Alignment explanation
Indices: 5680--5756 Score: 88
Period size: 33 Copynumber: 2.3 Consensus size: 34
5670 AATAGATAAG
*
5680 TATATATATAATACAGTATAT-ATTTAT-AAAAAA
1 TATATATATAATA-AATATATAATTTATAAAAAAA
* *
5713 TATATATGT-ATAAATATATAATTTGTAAAAAAA
1 TATATATATAATAAATATATAATTTATAAAAAAA
*
5746 TATGTATATAA
1 TATATATATAA
5757 AATTACTAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
31 6 0.17
32 8 0.22
33 21 0.58
34 1 0.03
ACGTcount: A:0.53, C:0.01, G:0.05, T:0.40
Consensus pattern (34 bp):
TATATATATAATAAATATATAATTTATAAAAAAA
Found at i:5731 original size:31 final size:31
Alignment explanation
Indices: 5680--5757 Score: 84
Period size: 31 Copynumber: 2.4 Consensus size: 31
5670 AATAGATAAG
*
5680 TATATATATAATACAGTATATATTTATAAAAAATA
1 TATATATATAA-ATA-TATA-ATTTATAAAAAA-A
* *
5715 TATATGTATAAATATATAATTTGTAAAAAAA
1 TATATATATAAATATATAATTTATAAAAAAA
*
5746 TATGTATATAAA
1 TATATATATAAA
5758 ATTACTAATC
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
31 11 0.29
32 11 0.29
33 4 0.11
34 2 0.05
35 10 0.26
ACGTcount: A:0.54, C:0.01, G:0.05, T:0.40
Consensus pattern (31 bp):
TATATATATAAATATATAATTTATAAAAAAA
Found at i:6203 original size:76 final size:76
Alignment explanation
Indices: 6077--6225 Score: 271
Period size: 76 Copynumber: 2.0 Consensus size: 76
6067 AACGCTATTG
6077 GGGGTATATAAATGCTCGCAACTACCAATACTTGTCCACTTCTACTGATAGAAGTGTACAGGTTT
1 GGGGTATATAAATGCTCGCAACTACCAATACTTGTCCACTTCTACTGATAGAAGTGTACAGGTTT
6142 CGGTAGATACT
66 CGGTAGATACT
* * *
6153 GGGGTATATAAATGCTCGCAACTATCGATACTTGTCCACTTCTACTGATAGAAGTGTACATGTTT
1 GGGGTATATAAATGCTCGCAACTACCAATACTTGTCCACTTCTACTGATAGAAGTGTACAGGTTT
6218 CGGTAGAT
66 CGGTAGAT
6226 GTTCGCTTCT
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
76 70 1.00
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.32
Consensus pattern (76 bp):
GGGGTATATAAATGCTCGCAACTACCAATACTTGTCCACTTCTACTGATAGAAGTGTACAGGTTT
CGGTAGATACT
Found at i:13763 original size:17 final size:17
Alignment explanation
Indices: 13738--13848 Score: 143
Period size: 17 Copynumber: 6.5 Consensus size: 17
13728 ACCCATTCTT
13738 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
* *
13755 GTGAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
* *
13772 TTTAAATTTGTTTAAAAA
1 TTTAAATTTATTT-TAAA
13790 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
13807 TTTAAA-TTATTTTTAAA
1 TTTAAATTTA-TTTTAAA
* *
13824 TTTAAAATTATTCTAAA
1 TTTAAATTTATTTTAAA
13841 TTTAAATT
1 TTTAAATT
13849 AATAATATCC
Statistics
Matches: 81, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
16 3 0.04
17 60 0.74
18 18 0.22
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:14488 original size:20 final size:19
Alignment explanation
Indices: 14463--14508 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
14453 CATTTATTGT
14463 ATATTAAGT-ATAATAAATAA
1 ATATTAAGTAATAAT-AAT-A
*
14483 ATATTAATTAATAATAATA
1 ATATTAAGTAATAATAATA
14502 ATATTAA
1 ATATTAA
14509 TAAAAAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 8 0.33
20 11 0.46
21 5 0.21
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (19 bp):
ATATTAAGTAATAATAATA
Found at i:15160 original size:10 final size:10
Alignment explanation
Indices: 15145--15172 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
15135 TGACCCGAAT
15145 TCGACCCGAC
1 TCGACCCGAC
15155 TCGACCCGAC
1 TCGACCCGAC
15165 TCGACCCG
1 TCGACCCG
15173 CTCTAGAGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.18, C:0.50, G:0.21, T:0.11
Consensus pattern (10 bp):
TCGACCCGAC
Found at i:15626 original size:28 final size:28
Alignment explanation
Indices: 15567--16032 Score: 203
Period size: 30 Copynumber: 16.2 Consensus size: 28
15557 TAAAAATCAT
* * *
15567 ATTTTGACCCTTAAACTTTTCTAAAATCAC
1 ATTTTTACCCTCAAAC--TTCTAAAATTAC
* * *
15597 ATTTTTACCCTAAAATTTCTCAAATTAC
1 ATTTTTACCCTCAAACTTCTAAAATTAC
* ** * * *
15625 ATTTTTA-CCACGTATTTCCAAAAATTAT
1 ATTTTTACCCTCAAACTT-CTAAAATTAC
* **
15653 ATTTTTGCCCTTGAACTTCTCAAAAATTAC
1 ATTTTTACCCTCAAACTTCT--AAAATTAC
* * *
15683 ATTTTTGCCCTCGAACTTCAAAAAATTAC
1 ATTTTTACCCTCAAACTTC-TAAAATTAC
*
15712 ATTTTT-CCCTC-AACTTTCAAAAATTAC
1 ATTTTTACCCTCAAAC-TTCTAAAATTAC
* * *
15739 CTTTTTACCCTCGAACTTCTAAAAATCAC
1 ATTTTTACCCTCAAACTTCT-AAAATTAC
15768 ATTTTTACCCTCAAACTTCTCAAAAATTAC
1 ATTTTTACCCTCAAACTTCT--AAAATTAC
* ** * *
15798 ATTTTTATCC-CGTATTTCAAAAAATTAC
1 ATTTTTACCCTCAAACTTC-TAAAATTAC
* **
15826 ATTTTTGCCCTTGAACTTCTCAAAAATTAC
1 ATTTTTACCCTCAAACTTCT--AAAATTAC
* ** *
15856 ATTTTTGCCCTTGAACTTCCAAAAATTAC
1 ATTTTTACCCTCAAACTT-CTAAAATTAC
** *
15885 A-TTTTGGCCTC-GACTT-TCAAAATTATC
1 ATTTTTACCCTCAAACTTCT-AAAATTA-C
* * *
15912 -TTTTTACCCCCGAACTTCCAAAAATTAC
1 ATTTTTACCCTCAAACTT-CTAAAATTAC
* **
15940 AATTTTTCCCCT-AAACTTCTCAAAAACCAC
1 -ATTTTTACCCTCAAACTTCT--AAAATTAC
* * ** * * *
15970 ATTTTTGCTCTTGAACTTCAAAAATCAT
1 ATTTTTACCCTCAAACTTCTAAAATTAC
* *
15998 ATTTTTACCCCTCAAATTTCCAAAATTACC
1 ATTTTTA-CCCTCAAACTTCTAAAATTA-C
16028 ATTTT
1 ATTTT
16033 ACACCATTTT
Statistics
Matches: 340, Mismatches: 68, Indels: 56
0.73 0.15 0.12
Matches are distributed among these distances:
26 7 0.02
27 35 0.10
28 89 0.26
29 102 0.30
30 106 0.31
31 1 0.00
ACGTcount: A:0.33, C:0.24, G:0.04, T:0.39
Consensus pattern (28 bp):
ATTTTTACCCTCAAACTTCTAAAATTAC
Found at i:15679 original size:30 final size:30
Alignment explanation
Indices: 15643--15988 Score: 330
Period size: 30 Copynumber: 12.0 Consensus size: 30
15633 CACGTATTTC
*
15643 CAAAAATTATATTTTTGCCCTTGAACTTCT
1 CAAAAATTACATTTTTGCCCTTGAACTTCT
*
15673 CAAAAATTACATTTTTGCCCTCGAACTTC-
1 CAAAAATTACATTTTTGCCCTTGAACTTCT
* *
15702 AAAAAATTACATTTTT-CCC-TCAACTT-T
1 CAAAAATTACATTTTTGCCCTTGAACTTCT
* * *
15729 CAAAAATTACCTTTTTACCCTCGAACTTCT
1 CAAAAATTACATTTTTGCCCTTGAACTTCT
* * **
15759 -AAAAATCACATTTTTACCCTCAAACTTCT
1 CAAAAATTACATTTTTGCCCTTGAACTTCT
* *
15788 CAAAAATTACATTTTTATCCC--GTA-TT-T
1 CAAAAATTACATTTTT-GCCCTTGAACTTCT
15815 CAAAAAATTACATTTTTGCCCTTGAACTTCT
1 C-AAAAATTACATTTTTGCCCTTGAACTTCT
15846 CAAAAATTACATTTTTGCCCTTGAACTTC-
1 CAAAAATTACATTTTTGCCCTTGAACTTCT
* *
15875 CAAAAATTACA-TTTTGGCCTCG-ACTT-T
1 CAAAAATTACATTTTTGCCCTTGAACTTCT
* **
15902 C-AAAATTATC-TTTTTACCCCCGAACTTC-
1 CAAAAATTA-CATTTTTGCCCTTGAACTTCT
* *
15930 CAAAAATTACAATTTTT-CCCCTAAACTTCT
1 CAAAAATTAC-ATTTTTGCCCTTGAACTTCT
** *
15960 CAAAAACCACATTTTTGCTCTTGAACTTC
1 CAAAAATTACATTTTTGCCCTTGAACTTC
15989 AAAAATCATA
Statistics
Matches: 265, Mismatches: 30, Indels: 42
0.79 0.09 0.12
Matches are distributed among these distances:
26 7 0.03
27 38 0.14
28 38 0.14
29 83 0.31
30 94 0.35
31 5 0.02
ACGTcount: A:0.32, C:0.25, G:0.05, T:0.38
Consensus pattern (30 bp):
CAAAAATTACATTTTTGCCCTTGAACTTCT
Found at i:15707 original size:29 final size:29
Alignment explanation
Indices: 15618--16032 Score: 357
Period size: 29 Copynumber: 14.4 Consensus size: 29
15608 AAAATTTCTC
* * * *
15618 AAATTACATTTTT-ACCACGTATTTCCAA
1 AAATTACATTTTTGCCCTCGAACTTCCAA
* *
15646 AAATTATATTTTTGCCCTTGAACTTCTCAA
1 AAATTACATTTTTGCCCTCGAACTTC-CAA
*
15676 AAATTACATTTTTGCCCTCGAACTTCAAA
1 AAATTACATTTTTGCCCTCGAACTTCCAA
*
15705 AAATTACATTTTT-CCCTC-AACTTTCAA
1 AAATTACATTTTTGCCCTCGAACTTCCAA
* * *
15732 AAATTACCTTTTTACCCTCGAACTTCTAA
1 AAATTACATTTTTGCCCTCGAACTTCCAA
* * *
15761 AAATCACATTTTTACCCTCAAACTTCTCAA
1 AAATTACATTTTTGCCCTCGAACTTC-CAA
** * * *
15791 AAATTACATTTTTATCC-CGTATTTCAAA
1 AAATTACATTTTTGCCCTCGAACTTCCAA
*
15819 AAATTACATTTTTGCCCTTGAACTTCTCAA
1 AAATTACATTTTTGCCCTCGAACTTC-CAA
*
15849 AAATTACATTTTTGCCCTTGAACTTCCAA
1 AAATTACATTTTTGCCCTCGAACTTCCAA
* *
15878 AAATTACA-TTTTGGCCTCG-ACTTTC-A
1 AAATTACATTTTTGCCCTCGAACTTCCAA
* *
15904 AAATTATC-TTTTTACCCCCGAACTTCCAA
1 AAATTA-CATTTTTGCCCTCGAACTTCCAA
* *
15933 AAATTACAATTTTTCCCCT-AAACTTCTCAA
1 AAATTAC-ATTTTTGCCCTCGAACTTC-CAA
** * *
15963 AAACCACATTTTTGCTCTTGAACTT-CAA
1 AAATTACATTTTTGCCCTCGAACTTCCAA
* * * * *
15991 AAATCATATTTTTACCCCTCAAATTTCC-A
1 AAATTACATTTTT-GCCCTCGAACTTCCAA
16020 AAATTACCATTTT
1 AAATTA-CATTTT
16033 ACACCATTTT
Statistics
Matches: 315, Mismatches: 54, Indels: 34
0.78 0.13 0.08
Matches are distributed among these distances:
26 7 0.02
27 33 0.10
28 68 0.22
29 108 0.34
30 99 0.31
ACGTcount: A:0.33, C:0.25, G:0.04, T:0.38
Consensus pattern (29 bp):
AAATTACATTTTTGCCCTCGAACTTCCAA
Found at i:15882 original size:173 final size:171
Alignment explanation
Indices: 15585--15975 Score: 574
Period size: 173 Copynumber: 2.3 Consensus size: 171
15575 CCTTAAACTT
* *
15585 TTCT-AAAATCACATTTTTACCCTAAAATTTCTC--AAATTACATTTTTACCACGTATTTCCAAA
1 TTCTAAAAATCACATTTTTACCCT-AAACTTCTCAAAAATTACATTTTTACCACGTATTTCAAAA
*
15647 AATTATATTTTTGCCCTTGAACTTCTCAAAAATTACATTTTTGCCCTCGAACTTCAAAAAATTAC
65 AATTACATTTTTGCCCTTGAACTTCTCAAAAATTACATTTTTGCCCTCGAACTTCAAAAAATTAC
* *
15712 ATTTTTCCCTCAACTTTCAAAAATTACCTTTTTACCCTCGAAC
130 ATTTTGCCCTCAACTTTC-AAAATTACCTTTTTACCCCCGAAC
15755 TTCTAAAAATCACATTTTTACCCTCAAACTTCTCAAAAATTACATTTTTATCC-CGTATTTCAAA
1 TTCTAAAAATCACATTTTTACCCT-AAACTTCTCAAAAATTACATTTTTA-CCACGTATTTCAAA
* *
15819 AAATTACATTTTTGCCCTTGAACTTCTCAAAAATTACATTTTTGCCCTTGAACTTCCAAAAATTA
64 AAATTACATTTTTGCCCTTGAACTTCTCAAAAATTACATTTTTGCCCTCGAACTTCAAAAAATTA
* * *
15884 CATTTTGGCCTCGACTTTCAAAATTATCTTTTTACCCCCGAAC
129 CATTTTGCCCTCAACTTTCAAAATTACCTTTTTACCCCCGAAC
* * * **
15927 TTCCAAAAATTACAATTTTTCCCCTAAACTTCTCAAAAACCACATTTTT
1 TTCTAAAAATCAC-ATTTTTACCCTAAACTTCTCAAAAATTACATTTTT
15976 GCTCTTGAAC
Statistics
Matches: 200, Mismatches: 16, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
170 4 0.02
171 27 0.14
172 55 0.28
173 112 0.56
174 2 0.01
ACGTcount: A:0.33, C:0.25, G:0.04, T:0.39
Consensus pattern (171 bp):
TTCTAAAAATCACATTTTTACCCTAAACTTCTCAAAAATTACATTTTTACCACGTATTTCAAAAA
ATTACATTTTTGCCCTTGAACTTCTCAAAAATTACATTTTTGCCCTCGAACTTCAAAAAATTACA
TTTTGCCCTCAACTTTCAAAATTACCTTTTTACCCCCGAAC
Found at i:32524 original size:13 final size:14
Alignment explanation
Indices: 32497--32527 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
32487 ATGAAATTTC
32497 TCAAGATTCTTCAA
1 TCAAGATTCTTCAA
32511 TCAAGATT-TTCAA
1 TCAAGATTCTTCAA
32524 TCAA
1 TCAA
32528 AGGATTTAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.53
14 8 0.47
ACGTcount: A:0.39, C:0.19, G:0.06, T:0.35
Consensus pattern (14 bp):
TCAAGATTCTTCAA
Found at i:33749 original size:59 final size:57
Alignment explanation
Indices: 33686--34059 Score: 298
Period size: 58 Copynumber: 6.4 Consensus size: 57
33676 CCTTGGGAAC
* * * *
33686 AAAATGGTAATTTTTGGAAGGTTTGGGGTCAAAAATGGAATTTTTAGACATTCGGGGGT-
1 AAAATGG-AA-TTTTGGAAAGTTTGGGG-CAAAAATGTAATTTTTAGAAATTCAGGGGTA
* * *
33745 AAAATGGTAATTTTGCAAAGTTTGAGGCTAAAAATGTAATTTTTGGAAAATT-AGGGGTCAA
1 AAAATGG-AATTTTGGAAAGTTTGGGGC-AAAAATGTAATTTTTAG-AAATTCAGGGGT--A
* * * *
33806 AAAATGGAATTTTGGAAAGTTTAGGGG--AAAATGTATTTTTTGGAAATTC-GAGGTC
1 AAAATGGAATTTTGGAAAGTTT-GGGGCAAAAATGTAATTTTTAGAAATTCAGGGGTA
* * * **
33861 AAAATGGAATTTTGGAAAGTTCGAGGGGAAAAATGTAATTTTTACAAAATTC-GAGGACA
1 AAAATGGAATTTTGGAAAGTTTG-GGGCAAAAATGTAATTTTTA-GAAATTCAG-GGGTA
* * *
33920 AAAATAGAATTTTAGG-AAGTTTGGGGGCAAAAATGTAATTTTTAGAAATTTAGGGTTA
1 AAAATGGAATTTT-GGAAAGTTT-GGGGCAAAAATGTAATTTTTAGAAATTCAGGGGTA
* * *
33978 AAAATGGAATTTTAGG-AAGTTCGAGGGGCAAAAATGTAATTTTTAGAAA-ACACGAGGTCA
1 AAAATGGAATTTT-GGAAAGTT--TGGGGCAAAAATGTAATTTTTAGAAATTCA-GGGGT-A
* *
34038 AAAATGAAATTTTGGGAAGTTT
1 AAAATGGAATTTTGGAAAGTTT
34060 AGGGACGTCC
Statistics
Matches: 260, Mismatches: 35, Indels: 41
0.77 0.10 0.12
Matches are distributed among these distances:
54 1 0.00
55 24 0.09
57 23 0.09
58 85 0.33
59 82 0.32
60 35 0.13
61 10 0.04
ACGTcount: A:0.38, C:0.05, G:0.25, T:0.32
Consensus pattern (57 bp):
AAAATGGAATTTTGGAAAGTTTGGGGCAAAAATGTAATTTTTAGAAATTCAGGGGTA
Found at i:33789 original size:30 final size:29
Alignment explanation
Indices: 33686--34055 Score: 177
Period size: 30 Copynumber: 12.6 Consensus size: 29
33676 CCTTGGGAAC
* * *
33686 AAAATGGTAATTTTTGGAAGGTTTGGGGTCA
1 AAAAT-GTAATTTTTGGAAAGTTCGAGG-CA
* * * * **
33717 AAAATGGAATTTTTAGACA-TTCGGGGGT
1 AAAATGTAATTTTTGGAAAGTTCGAGGCA
* *
33745 AAAATGGTAA-TTTTGCAAAGTTTGAGGCTA
1 AAAAT-GTAATTTTTGGAAAGTTCGAGGC-A
* * *
33775 AAAATGTAATTTTTGGAAAATTAGGGGTCAA
1 AAAATGTAATTTTTGGAAAGTTCGAGG-C-A
* * **
33806 AAAATGGAA-TTTTGGAAAGTT-TAGGGG
1 AAAATGTAATTTTTGGAAAGTTCGAGGCA
*
33833 AAAATGTATTTTTTGGAAA-TTCGAGGTC-
1 AAAATGTAATTTTTGGAAAGTTCGAGG-CA
* *
33861 AAAATGGAA-TTTTGGAAAGTTCGAGGGGA
1 AAAATGTAATTTTTGGAAAGTTCGA-GGCA
** *
33890 AAAATGTAATTTTTACAAAATTCGAGGACA
1 AAAATGTAATTTTTGGAAAGTTCGAGG-CA
* * *
33920 AAAATAG-AATTTTAGG-AAGTTTGGGGGCA
1 AAAAT-GTAATTTTTGGAAAG-TTCGAGGCA
* * * *
33949 AAAATGTAATTTTTAGAAATTTAG-GGTTA
1 AAAATGTAATTTTTGGAAAGTTCGAGG-CA
* *
33978 AAAATGGAATTTTAGG-AAGTTCGAGGGGCA
1 AAAATGTAATTTTTGGAAAGTTCGA--GGCA
* ***
34008 AAAATGTAATTTTTAGAAAACACGAGGTCA
1 AAAATGTAATTTTTGGAAAGTTCGAGG-CA
* *
34038 AAAATGAAATTTTGGGAA
1 AAAATGTAATTTTTGGAA
34056 GTTTAGGGAC
Statistics
Matches: 252, Mismatches: 64, Indels: 47
0.69 0.18 0.13
Matches are distributed among these distances:
27 18 0.07
28 43 0.17
29 67 0.27
30 101 0.40
31 23 0.09
ACGTcount: A:0.39, C:0.05, G:0.25, T:0.31
Consensus pattern (29 bp):
AAAATGTAATTTTTGGAAAGTTCGAGGCA
Found at i:33847 original size:28 final size:28
Alignment explanation
Indices: 33806--33903 Score: 92
Period size: 28 Copynumber: 3.5 Consensus size: 28
33796 TAGGGGTCAA
* * *
33806 AAAATGGAATTTTGGAAAGTT-TAGGGG
1 AAAATGTATTTTTGGAAAGTTCGAGGGG
**
33833 AAAATGTATTTTTTGGAAA-TTCGAGGTC
1 AAAATGTA-TTTTTGGAAAGTTCGAGGGG
* *
33861 AAAATGGAATTTTGGAAAGTTCGAGGGG
1 AAAATGTATTTTTGGAAAGTTCGAGGGG
33889 AAAAATGTAATTTTT
1 -AAAATGT-ATTTTT
33904 ACAAAATTCG
Statistics
Matches: 55, Mismatches: 11, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
27 18 0.33
28 26 0.47
29 6 0.11
30 5 0.09
ACGTcount: A:0.37, C:0.03, G:0.27, T:0.34
Consensus pattern (28 bp):
AAAATGTATTTTTGGAAAGTTCGAGGGG
Found at i:36043 original size:17 final size:17
Alignment explanation
Indices: 35993--36070 Score: 93
Period size: 17 Copynumber: 4.5 Consensus size: 17
35983 TTTAATTTTT
35993 AATTTAAAATAAATTTA
1 AATTTAAAATAAATTTA
* * * *
36010 AACTCAAAGTAAGTTTA
1 AATTTAAAATAAATTTA
36027 AATTTAAAATAAATTTA
1 AATTTAAAATAAATTTA
* *
36044 AAATTAAAATAAATTAA
1 AATTTAAAATAAATTTA
36061 AATTTTAAAA
1 AA-TTTAAAA
36071 ACAATCCAAA
Statistics
Matches: 49, Mismatches: 11, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
17 43 0.88
18 6 0.12
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.36
Consensus pattern (17 bp):
AATTTAAAATAAATTTA
Found at i:40108 original size:21 final size:21
Alignment explanation
Indices: 40084--40136 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
40074 TATCAACAAA
40084 GGCTTCCGAAATATCGATGGT
1 GGCTTCCGAAATATCGATGGT
* * * **
40105 GGCTTCAGCAATTTCTTTGGT
1 GGCTTCCGAAATATCGATGGT
40126 GGCTTCCGAAA
1 GGCTTCCGAAA
40137 CGTCATCTGC
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.32
Consensus pattern (21 bp):
GGCTTCCGAAATATCGATGGT
Found at i:44063 original size:12 final size:12
Alignment explanation
Indices: 44046--44070 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
44036 CTTAATTTAT
44046 ACATATCATTTC
1 ACATATCATTTC
44058 ACATATCATTTC
1 ACATATCATTTC
44070 A
1 A
44071 TGTAATAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.24, G:0.00, T:0.40
Consensus pattern (12 bp):
ACATATCATTTC
Found at i:44511 original size:24 final size:24
Alignment explanation
Indices: 44479--44579 Score: 157
Period size: 24 Copynumber: 4.2 Consensus size: 24
44469 AAGTTCAGTA
*
44479 CATTTATGCTCGTCAGCTAATATG
1 CATTTATGCTCGCCAGCTAATATG
*
44503 CATTTATGCTCGCCAACTAATATG
1 CATTTATGCTCGCCAGCTAATATG
* *
44527 CGTTTATGCTCGCCAGCTAGTATG
1 CATTTATGCTCGCCAGCTAATATG
*
44551 CATTTACGCTCGCCAGCTAATATG
1 CATTTATGCTCGCCAGCTAATATG
44575 CATTT
1 CATTT
44580 TGTTGAACAC
Statistics
Matches: 69, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 69 1.00
ACGTcount: A:0.24, C:0.25, G:0.17, T:0.35
Consensus pattern (24 bp):
CATTTATGCTCGCCAGCTAATATG
Found at i:48873 original size:27 final size:27
Alignment explanation
Indices: 48843--48921 Score: 140
Period size: 27 Copynumber: 2.9 Consensus size: 27
48833 GTTGTCGTTA
*
48843 TGTAAGTCAGTCATTGCGCCGACAATG
1 TGTAAGTCAGTCATTGTGCCGACAATG
48870 TGTAAGTCAGTCATTGTGCCGACAATG
1 TGTAAGTCAGTCATTGTGCCGACAATG
*
48897 TGTAAGTCAATCATTGTGCCGACAA
1 TGTAAGTCAGTCATTGTGCCGACAA
48922 ACGATCCTTA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 50 1.00
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.28
Consensus pattern (27 bp):
TGTAAGTCAGTCATTGTGCCGACAATG
Found at i:49492 original size:24 final size:24
Alignment explanation
Indices: 49465--49651 Score: 169
Period size: 24 Copynumber: 7.8 Consensus size: 24
49455 TATTTCAACA
*
49465 CGTTTACGCTCGTCAGCTAACATG
1 CGTTTACGCTCGCCAGCTAACATG
*
49489 CGTTTATGCTCGCCAGCTAACATG
1 CGTTTACGCTCGCCAGCTAACATG
*
49513 AGTTTACGCTCGCCAGCTAACATG
1 CGTTTACGCTCGCCAGCTAACATG
* * *
49537 CATTTACGCTTGCCAACT-ACTATG
1 CGTTTACGCTCGCCAGCTAAC-ATG
* * * * *
49561 CGTTTATGCTCACCAACTAATATA
1 CGTTTACGCTCGCCAGCTAACATG
** *
49585 CGTTTACGCTCGTTAGCTAATATG
1 CGTTTACGCTCGCCAGCTAACATG
* * ** *
49609 TGTTTCCGCTCGTTAGCTAATATG
1 CGTTTACGCTCGCCAGCTAACATG
* *
49633 TGCTTACGCTCGCCAGCTA
1 CGTTTACGCTCGCCAGCTA
49652 TTCGGATAAA
Statistics
Matches: 135, Mismatches: 26, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
23 2 0.01
24 132 0.98
25 1 0.01
ACGTcount: A:0.22, C:0.27, G:0.18, T:0.32
Consensus pattern (24 bp):
CGTTTACGCTCGCCAGCTAACATG
Done.