Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011645.1 Kokia drynarioides strain JFW-HI SEQ_126637, 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: 100296
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:142 original size:30 final size:30
Alignment explanation
Indices: 115--311 Score: 208
Period size: 30 Copynumber: 6.6 Consensus size: 30
105 TTAAAAATCC
*
115 CATTTTGACCCTTAAACTTCTCTAAAATTA
1 CATTTTAACCCTTAAACTTCTCTAAAATTA
* * * *
145 CTTTTTTTACTC-TAAACTTCTCCAAAATTA
1 C-ATTTTAACCCTTAAACTTCTCTAAAATTA
* *
175 CA-TTTAACCCCTAAACTTCTCTAAAAATA
1 CATTTTAACCCTTAAACTTCTCTAAAATTA
204 CATTTTAACCCTTAAACTTCT-TCAAAATTA
1 CATTTTAACCCTTAAACTTCTCT-AAAATTA
*
234 CATTTTAA-CCTCTAAACTTCTC-CAAATTA
1 CATTTTAACCCT-TAAACTTCTCTAAAATTA
* * *
263 CATTTTAACCATCAAACTTCTCCAAAATTA
1 CATTTTAACCCTTAAACTTCTCTAAAATTA
*
293 CATTTTGATCCC-TAAACTT
1 CATTTT-AACCCTTAAACTT
312 TCAAAAAAAA
Statistics
Matches: 140, Mismatches: 18, Indels: 18
0.80 0.10 0.10
Matches are distributed among these distances:
28 6 0.04
29 45 0.32
30 79 0.56
31 10 0.07
ACGTcount: A:0.35, C:0.25, G:0.01, T:0.39
Consensus pattern (30 bp):
CATTTTAACCCTTAAACTTCTCTAAAATTA
Found at i:220 original size:59 final size:60
Alignment explanation
Indices: 115--319 Score: 238
Period size: 59 Copynumber: 3.5 Consensus size: 60
105 TTAAAAATCC
* * * * * *
115 CATTTTGACCCTTAAACTTCTCTAAAATTACTTTTTTTACTC-TAAACTTCTCCAAAATTA
1 CATTTTAACCCCTAAACTTCTCTAAAAATAC-ATTTTAACCCTTAAACTTCTCCAAAATTA
*
175 CA-TTTAACCCCTAAACTTCTCTAAAAATACATTTTAACCCTTAAACTTCTTCAAAATTA
1 CATTTTAACCCCTAAACTTCTCTAAAAATACATTTTAACCCTTAAACTTCTCCAAAATTA
* * * * *
234 CATTTTAACCTCTAAACTTCTC-CAAATTACATTTTAACCATCAAACTTCTCCAAAATTA
1 CATTTTAACCCCTAAACTTCTCTAAAAATACATTTTAACCCTTAAACTTCTCCAAAATTA
* * *
293 CATTTTGATCCCTAAACTT-TCAAAAAA
1 CATTTTAACCCCTAAACTTCTCTAAAAA
320 AAATCACATT
Statistics
Matches: 124, Mismatches: 18, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
58 9 0.07
59 95 0.77
60 20 0.16
ACGTcount: A:0.37, C:0.25, G:0.01, T:0.38
Consensus pattern (60 bp):
CATTTTAACCCCTAAACTTCTCTAAAAATACATTTTAACCCTTAAACTTCTCCAAAATTA
Found at i:247 original size:89 final size:89
Alignment explanation
Indices: 101--311 Score: 252
Period size: 89 Copynumber: 2.4 Consensus size: 89
91 AGCCCCTATT
* * * * *
101 TTCTTTAAAAATCCCATTTTGACCCTTAAACTTCTCTAAAATTACTTTTTTTACTCTAAACTTCT
1 TTCTCTAAAAAT-ACATTTTAACCCTTAAACTTCTCTAAAATTACTATTTTAACTCTAAACTTCT
*
166 CCAAAATTACA-TTTAACC-CCTAAAC
65 CC-AAATTACATTTTAACCATC-AAAC
191 TTCTCTAAAAATACATTTTAACCCTTAAACTTCT-TCAAAATTAC-ATTTTAACCTCTAAACTTC
1 TTCTCTAAAAATACATTTTAACCCTTAAACTTCTCT-AAAATTACTATTTTAA-CTCTAAACTTC
254 TCCAAATTACATTTTAACCATCAAAC
64 TCCAAATTACATTTTAACCATCAAAC
* * *
280 TTCTCCAAAATTACATTTTGATCCC-TAAACTT
1 TTCTCTAAAAATACATTTT-AACCCTTAAACTT
312 TCAAAAAAAA
Statistics
Matches: 107, Mismatches: 9, Indels: 11
0.84 0.07 0.09
Matches are distributed among these distances:
88 14 0.13
89 77 0.72
90 16 0.15
ACGTcount: A:0.35, C:0.25, G:0.01, T:0.39
Consensus pattern (89 bp):
TTCTCTAAAAATACATTTTAACCCTTAAACTTCTCTAAAATTACTATTTTAACTCTAAACTTCTC
CAAATTACATTTTAACCATCAAAC
Found at i:2740 original size:16 final size:16
Alignment explanation
Indices: 2715--2746 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2705 TACCACTACC
*
2715 CCAATGATAATTCTTG
1 CCAATAATAATTCTTG
2731 CCAATAATAATTCTTG
1 CCAATAATAATTCTTG
2747 AATTAATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.19, G:0.09, T:0.38
Consensus pattern (16 bp):
CCAATAATAATTCTTG
Found at i:4038 original size:91 final size:90
Alignment explanation
Indices: 3873--4076 Score: 241
Period size: 91 Copynumber: 2.2 Consensus size: 90
3863 TTGGGATAAT
* * *
3873 ATATTTGTACTTTTAAAATGTCTAATGTGATATTTGAACTGTTAATTTGTATATTATTTGGTACA
1 ATATTTGTAC-TTTAAAATGTCTAATGTGATATTTGAACTATCAATTTGTATATTATTTAGTACA
* * *
3938 TATATTTTCATAAAATGTTTGATGTG
65 TATACTTTCATAAAATATCTGATGTG
* *
3964 ATATTTGTACTTTAATAATAT-TCAATGTGATATTTGAATTATCAATTTGTATATTATTTAGT-C
1 ATATTTGTACTTTAA-AATGTCT-AATGTGATATTTGAACTATCAATTTGTATATTATTTAGTAC
* *
4027 TTTGTACTTTCATAAAATATCTGATGTG
64 -ATATACTTTCATAAAATATCTGATGTG
* *
4055 ATACTTATACTTTAAAAATGTC
1 ATATTTGTACTTT-AAAATGTC
4077 CAATATAATA
Statistics
Matches: 95, Mismatches: 13, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
90 7 0.07
91 86 0.91
92 2 0.02
ACGTcount: A:0.32, C:0.07, G:0.12, T:0.49
Consensus pattern (90 bp):
ATATTTGTACTTTAAAATGTCTAATGTGATATTTGAACTATCAATTTGTATATTATTTAGTACAT
ATACTTTCATAAAATATCTGATGTG
Found at i:9706 original size:82 final size:82
Alignment explanation
Indices: 9597--9993 Score: 360
Period size: 82 Copynumber: 4.9 Consensus size: 82
9587 ATGTCAGGAT
* * * * * *
9597 TAAATCCTGAAACAGAATTATTTAATTATTTATTGTTTTGAAACAAAATAAAAATAGAATAAAAT
1 TAAATCCCGAAACAAAATTATTCAATTAATTATTATTTGGAAACAAAATAAAAATAGAATAAAAT
* * * *
9662 TTGTTTATCGACAAGAA
66 CTGTTGAACGACGAGAA
* * * *
9679 TAAATCCCGAAACAAAAGTT-TTCAATTAATTCTTGTTTGGAAACAAAATCAAAATCA-AATTAA
1 TAAATCCCGAAACAAAA-TTATTCAATTAATTATTATTTGGAAACAAAATAAAAAT-AGAATAAA
** *
9742 ATCTGTTGAACGGTGGGAA
64 ATCTGTTGAACGACGAGAA
* * * **
9761 TGAATCTCGAAACAAAATTATTCAATTAATTCTTATTTGGAAACAAAATCCAAATA-AAT----T
1 TAAATCCCGAAACAAAATTATTCAATTAATTATTATTTGGAAACAAAATAAAAATAGAATAAAAT
*
9821 CTGTTGAACAAC-AGAAA
66 CTGTTGAACGACGAG-AA
* *
9838 TAAATCCCGAAACATAATTATTCAATTAATTATTATTTGGAAACAAAATCCAAATATAGAATAAA
1 TAAATCCCGAAACAAAATTATTCAATTAATTATTATTTGGAAACAAAAT--AAAAATAGAATAAA
* * * *
9903 ATCTATTGAATGACGGGAG
64 ATCTGTTGAACGACGAGAA
* * * * *
9922 TAAATCTCGAAATAGAATTATTCAATTAATTATTATTTAGAAACAAAATCCAAATATAGAATAAA
1 TAAATCCCGAAACAAAATTATTCAATTAATTATTATTTGGAAACAAAAT--AAAAATAGAATAAA
*
9987 ATTTGTT
64 ATCTGTT
9994 AAATGAAGGA
Statistics
Matches: 262, Mismatches: 41, Indels: 22
0.81 0.13 0.07
Matches are distributed among these distances:
76 1 0.00
77 57 0.22
79 4 0.02
80 3 0.01
81 6 0.02
82 110 0.42
83 3 0.01
84 77 0.29
85 1 0.00
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (82 bp):
TAAATCCCGAAACAAAATTATTCAATTAATTATTATTTGGAAACAAAATAAAAATAGAATAAAAT
CTGTTGAACGACGAGAA
Found at i:9732 original size:159 final size:160
Alignment explanation
Indices: 9559--9993 Score: 422
Period size: 159 Copynumber: 2.7 Consensus size: 160
9549 TTAAAATTCT
* * *
9559 GAAACAAAATCAAAATCAAT-TCTGTTGAATGTCAGGATTAAATC-CTGAAACAGAATTATTTAA
1 GAAACAAAATCAAAATCAATATCTGTTGAATGTCGGGAATAAATCTC-GAAACAGAATTATTCAA
* * * * * *
9622 TTATTTATTGTTTTGAAACAAAATAAAAATAGAATAAAATTTGTTTATCGACA-AGAATAAATCC
65 TTAATTATTATTTAGAAACAAAATAAAAATAGAATAAAATTTGTTGAACAACAGA-AATAAATCC
* *
9686 CGAAACAAAAGTT-TTCAATTAATTCTTGTTTG
129 CGAAACAAAA-TTATTCAATTAATTATTATTTG
* * *
9718 GAAACAAAATCAAAATCAAATTAAATCTGTTGAACGGT-GGGAATGAATCTCGAAACAAAATTAT
1 GAAACAAAATCAAAATC-AA-T--ATCTGTTGAA-TGTCGGGAATAAATCTCGAAACAGAATTAT
* * ** *
9782 TCAATTAATTCTTATTTGGAAACAAAATCCAAATA-AAT----TCTGTTGAACAACAGAAATAAA
61 TCAATTAATTATTATTTAGAAACAAAATAAAAATAGAATAAAATTTGTTGAACAACAGAAATAAA
*
9842 TCCCGAAACATAATTATTCAATTAATTATTATTTG
126 TCCCGAAACAAAATTATTCAATTAATTATTATTTG
* * * * *
9877 GAAACAAAATCCAAATATAGAATAAAATCTATTGAATGACGGGAGTAAATCTCGAAATAGAATTA
1 GAAACAAAAT-CAAA-AT-CAAT---ATCTGTTGAATGTCGGGAATAAATCTCGAAACAGAATTA
*
9942 TTCAATTAATTATTATTTAGAAACAAAATCCAAATATAGAATAAAATTTGTT
60 TTCAATTAATTATTATTTAGAAACAAAAT--AAAAATAGAATAAAATTTGTT
9994 AAATGAAGGA
Statistics
Matches: 222, Mismatches: 33, Indels: 33
0.77 0.11 0.11
Matches are distributed among these distances:
158 2 0.01
159 72 0.32
160 9 0.04
161 64 0.29
163 7 0.03
164 60 0.27
165 3 0.01
168 5 0.02
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.31
Consensus pattern (160 bp):
GAAACAAAATCAAAATCAATATCTGTTGAATGTCGGGAATAAATCTCGAAACAGAATTATTCAAT
TAATTATTATTTAGAAACAAAATAAAAATAGAATAAAATTTGTTGAACAACAGAAATAAATCCCG
AAACAAAATTATTCAATTAATTATTATTTG
Found at i:9933 original size:84 final size:84
Alignment explanation
Indices: 9834--10028 Score: 282
Period size: 84 Copynumber: 2.3 Consensus size: 84
9824 TTGAACAACA
* * *
9834 GAAATAAATCCCGAAACATAATTATTCAATTAATTATTATTTGGAAACAAAATCCAAATATAGAA
1 GAAATAAATCTCGAAACAGAATTATTCAATTAATTATTATTTAGAAACAAAATCCAAATATAGAA
* *
9899 TAAAATCTATTGAATGACG
66 TAAAATCTATTAAATGAAG
* * *
9918 GGAGTAAATCTCGAAATAGAATTATTCAATTAATTATTATTTAGAAACAAAATCCAAATATAGAA
1 GAAATAAATCTCGAAACAGAATTATTCAATTAATTATTATTTAGAAACAAAATCCAAATATAGAA
* *
9983 TAAAATTTGTTAAATGAAG
66 TAAAATCTATTAAATGAAG
* *
10002 GAAATAAATCTCGAAATAGATTTATTC
1 GAAATAAATCTCGAAACAGAATTATTC
10029 GATTTTAATT
Statistics
Matches: 98, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
84 98 1.00
ACGTcount: A:0.48, C:0.10, G:0.11, T:0.31
Consensus pattern (84 bp):
GAAATAAATCTCGAAACAGAATTATTCAATTAATTATTATTTAGAAACAAAATCCAAATATAGAA
TAAAATCTATTAAATGAAG
Found at i:9977 original size:161 final size:159
Alignment explanation
Indices: 9677--9977 Score: 426
Period size: 161 Copynumber: 1.9 Consensus size: 159
9667 TATCGACAAG
* * *
9677 AATAAATCCCGAAACAAAAGTTTTCAATTAATTCTTGTTTGGAAACAAAATCAAAATCAAATTAA
1 AATAAATCCCGAAACAAAAGTTTTCAATTAATTATTATTTGGAAACAAAATCAAAATCAAATAAA
* ** * * *
9742 ATCTGTTGAACGGTGGGAATGAATCTCGAAACAAAATTATTCAATTAATTCTTATTTGGAAACAA
66 ATCTATTGAACGACGGGAATAAATCTCGAAACAAAATTATTCAATTAATTATTATTTAGAAACAA
9807 AATCCAAATAAATTCTGTTGAACAACAGA
131 AATCCAAATAAATTCTGTTGAACAACAGA
*
9836 AATAAATCCCGAAACATAA-TTATTCAATTAATTATTATTTGGAAACAAAATCCAAATAT-AGAA
1 AATAAATCCCGAAACAAAAGTT-TTCAATTAATTATTATTTGGAAACAAAAT-CAAA-ATCA-AA
* * * *
9899 TAAAATCTATTGAATGACGGGAGTAAATCTCGAAATAGAATTATTCAATTAATTATTATTTAGAA
62 TAAAATCTATTGAACGACGGGAATAAATCTCGAAACAAAATTATTCAATTAATTATTATTTAGAA
9964 ACAAAATCCAAATA
127 ACAAAATCCAAATA
9978 TAGAATAAAA
Statistics
Matches: 124, Mismatches: 14, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
158 2 0.02
159 45 0.36
160 5 0.04
161 72 0.58
ACGTcount: A:0.47, C:0.13, G:0.11, T:0.30
Consensus pattern (159 bp):
AATAAATCCCGAAACAAAAGTTTTCAATTAATTATTATTTGGAAACAAAATCAAAATCAAATAAA
ATCTATTGAACGACGGGAATAAATCTCGAAACAAAATTATTCAATTAATTATTATTTAGAAACAA
AATCCAAATAAATTCTGTTGAACAACAGA
Found at i:10268 original size:53 final size:51
Alignment explanation
Indices: 10177--10280 Score: 138
Period size: 53 Copynumber: 2.0 Consensus size: 51
10167 ATTTATATAC
*
10177 ATACAAGATCTCAACAAAATAATATAAATAAATATTTATATTTATGTAAAA
1 ATACAAGATCTCAACAAAAAAATATAAATAAATATTTATATTTATGTAAAA
* * *
10228 ATACCAGATCTCAAACAAAAACAA-ATTAAATACATATTTATATTTATTTAAAA
1 ATACAAGATCTC-AACAAAAA-AATA-TAAATAAATATTTATATTTATGTAAAA
10281 CATCAGATTC
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
51 11 0.24
52 8 0.17
53 27 0.59
ACGTcount: A:0.54, C:0.11, G:0.03, T:0.33
Consensus pattern (51 bp):
ATACAAGATCTCAACAAAAAAATATAAATAAATATTTATATTTATGTAAAA
Found at i:10771 original size:17 final size:17
Alignment explanation
Indices: 10751--10783 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
10741 TTTGATTTCC
10751 AATCAAATTGAGATATA
1 AATCAAATTGAGATATA
10768 AATCAAATTGAGATAT
1 AATCAAATTGAGATAT
10784 TTGTCCTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.30
Consensus pattern (17 bp):
AATCAAATTGAGATATA
Found at i:11407 original size:29 final size:29
Alignment explanation
Indices: 11374--11433 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 29
11364 TTAAAACTAA
* *
11374 AAAAAATCATA-ATTTATGTTTAAAAATTAT
1 AAAAAAT-ATATATATAT-TTTAAAAAATAT
11404 AAAAAATATATATATATTTTAAAAAATAT
1 AAAAAATATATATATATTTTAAAAAATAT
11433 A
1 A
11434 TTTATGTGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
29 15 0.56
30 12 0.44
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (29 bp):
AAAAAATATATATATATTTTAAAAAATAT
Found at i:15016 original size:16 final size:16
Alignment explanation
Indices: 14995--15025 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
14985 GCTTAAAAAA
14995 CTTACTTGTGATTTAG
1 CTTACTTGTGATTTAG
15011 CTTACTTGTGATTTA
1 CTTACTTGTGATTTA
15026 TTATTGTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.19, C:0.13, G:0.16, T:0.52
Consensus pattern (16 bp):
CTTACTTGTGATTTAG
Found at i:23521 original size:36 final size:35
Alignment explanation
Indices: 23449--23521 Score: 85
Period size: 36 Copynumber: 2.1 Consensus size: 35
23439 TAATCAGTCT
* **
23449 CATGGCATGAAAACATACCCATATATTTTTTGTCA
1 CATGGCATGAAAACATACCCACATATTACTTGTCA
*
23484 CATGGCATGAATAGCATACCCACATATTCACTT-TCA
1 CATGGCATGAA-AACATACCCACATATT-ACTTGTCA
23520 CA
1 CA
23522 ACAATTATCA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
35 11 0.34
36 19 0.59
37 2 0.06
ACGTcount: A:0.34, C:0.25, G:0.11, T:0.30
Consensus pattern (35 bp):
CATGGCATGAAAACATACCCACATATTACTTGTCA
Found at i:24437 original size:39 final size:40
Alignment explanation
Indices: 24353--24438 Score: 111
Period size: 40 Copynumber: 2.2 Consensus size: 40
24343 ATAGAGTCAA
* * *
24353 TTCATTATTGTATTGTAGTATTTACAATGCCACTGGCCAG
1 TTCAGTATTGTATTGCAGTATTTACAATGCCACTGACCAG
* * *
24393 TTCAGTATTGTATTGCAGTGTTTATAATGTCACT-ACCAG
1 TTCAGTATTGTATTGCAGTATTTACAATGCCACTGACCAG
24432 TTCAGTA
1 TTCAGTA
24439 ATTTGATAAC
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
39 11 0.28
40 29 0.73
ACGTcount: A:0.26, C:0.16, G:0.17, T:0.41
Consensus pattern (40 bp):
TTCAGTATTGTATTGCAGTATTTACAATGCCACTGACCAG
Found at i:27747 original size:5 final size:5
Alignment explanation
Indices: 27737--27765 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
27727 GGACTGTCCT
27737 TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
27766 TTTAATAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTC
Found at i:28037 original size:20 final size:21
Alignment explanation
Indices: 27999--28041 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
27989 GTGTTTTTTA
*
27999 ATAAATTTTTTATTGATATTT
1 ATAAATTTTTTATTAATATTT
28020 ATAAATTTTTTA-TAATATTT
1 ATAAATTTTTTATTAATATTT
28040 AT
1 AT
28042 TTAAGTACGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (21 bp):
ATAAATTTTTTATTAATATTT
Found at i:31069 original size:13 final size:13
Alignment explanation
Indices: 31046--31087 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 13
31036 AGTTGAGAAA
31046 ATAATTTAATTAAGT
1 ATAA-TTAATTAA-T
31061 -TAATTAATTAAT
1 ATAATTAATTAAT
31073 ATAATTAATTGAAT
1 ATAATTAATT-AAT
31087 A
1 A
31088 AATGATATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
12 1 0.04
13 17 0.68
14 7 0.28
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (13 bp):
ATAATTAATTAAT
Found at i:33529 original size:21 final size:21
Alignment explanation
Indices: 33503--33546 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
33493 ATGAAATATA
33503 GACTTAAAAATGTAATGTAAT
1 GACTTAAAAATGTAATGTAAT
33524 GACTTAAAAATGTAATGTAAT
1 GACTTAAAAATGTAATGTAAT
33545 GA
1 GA
33547 TTTGGAACTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.48, C:0.05, G:0.16, T:0.32
Consensus pattern (21 bp):
GACTTAAAAATGTAATGTAAT
Found at i:55886 original size:51 final size:51
Alignment explanation
Indices: 55811--55951 Score: 219
Period size: 51 Copynumber: 2.8 Consensus size: 51
55801 AATGCAAAAT
**
55811 AATATTTTCAGAATATTTTCAGTTGACAAAAATCCTCTGACTATTGCAGAA
1 AATATTTTCAGAATATTTTCAGTTGAGGAAAATCCTCTGACTATTGCAGAA
* * *
55862 AATATTTTCAGAATATTTTTAGTTGAGGAAAATCCTCTAACTGTTGCAGAA
1 AATATTTTCAGAATATTTTCAGTTGAGGAAAATCCTCTGACTATTGCAGAA
* *
55913 AATATTTTTAGAATATTTTCAGTTTAGGAAAATCCTCTG
1 AATATTTTCAGAATATTTTCAGTTGAGGAAAATCCTCTG
55952 TTATTTTTGG
Statistics
Matches: 81, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 81 1.00
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.38
Consensus pattern (51 bp):
AATATTTTCAGAATATTTTCAGTTGAGGAAAATCCTCTGACTATTGCAGAA
Found at i:56728 original size:22 final size:22
Alignment explanation
Indices: 56703--56749 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
56693 TCCATGATAA
56703 TGATAAAATGGGATCCCCAACG
1 TGATAAAATGGGATCCCCAACG
56725 TGATAAAATGGGATCCCCAACG
1 TGATAAAATGGGATCCCCAACG
56747 TGA
1 TGA
56750 ATATTCAACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.36, C:0.21, G:0.23, T:0.19
Consensus pattern (22 bp):
TGATAAAATGGGATCCCCAACG
Found at i:57497 original size:30 final size:30
Alignment explanation
Indices: 57461--57521 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
57451 AAGTTGGTTA
57461 TACCAGACTGGATAGCTCACACATTTTTGT
1 TACCAGACTGGATAGCTCACACATTTTTGT
57491 TACCAGACTGGATAGCTCACACATTTTTGT
1 TACCAGACTGGATAGCTCACACATTTTTGT
57521 T
1 T
57522 CTTATTCAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.26, C:0.23, G:0.16, T:0.34
Consensus pattern (30 bp):
TACCAGACTGGATAGCTCACACATTTTTGT
Found at i:59713 original size:6 final size:7
Alignment explanation
Indices: 59698--59722 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
59688 TTTGTTTTTC
59698 TTTCCTT
1 TTTCCTT
59705 TTTCCTT
1 TTTCCTT
59712 TTTCCTT
1 TTTCCTT
59719 TTTC
1 TTTC
59723 ACTAATATCA
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:0.28, G:0.00, T:0.72
Consensus pattern (7 bp):
TTTCCTT
Found at i:61289 original size:20 final size:20
Alignment explanation
Indices: 61264--61301 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
61254 CTCCAATGAG
*
61264 ACTTCTACCGATAGAACTCC
1 ACTTCTACCGATACAACTCC
61284 ACTTCTACCGATACAACT
1 ACTTCTACCGATACAACT
61302 AAAGTCCTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.34, G:0.08, T:0.26
Consensus pattern (20 bp):
ACTTCTACCGATACAACTCC
Found at i:64172 original size:33 final size:33
Alignment explanation
Indices: 64107--64169 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
64097 ACTTTTATGT
* * *
64107 CTTAAATTGAAAATGATTTTTATATAAGGGGAG
1 CTTAAATTCAAAATGACTTCTATATAAGGGGAG
*
64140 CTTAATTTCAAAATGACTTCTAT-TAAGGGG
1 CTTAAATTCAAAATGACTTCTATATAAGGGG
64170 GAGAAATTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
32 7 0.27
33 19 0.73
ACGTcount: A:0.37, C:0.08, G:0.19, T:0.37
Consensus pattern (33 bp):
CTTAAATTCAAAATGACTTCTATATAAGGGGAG
Found at i:65030 original size:45 final size:45
Alignment explanation
Indices: 64966--65057 Score: 184
Period size: 45 Copynumber: 2.0 Consensus size: 45
64956 GTTTAGGTAG
64966 AAACCTTAAGGAGTTATCTCTTAGGACTTTGGGGTATAAGTCTTA
1 AAACCTTAAGGAGTTATCTCTTAGGACTTTGGGGTATAAGTCTTA
65011 AAACCTTAAGGAGTTATCTCTTAGGACTTTGGGGTATAAGTCTTA
1 AAACCTTAAGGAGTTATCTCTTAGGACTTTGGGGTATAAGTCTTA
65056 AA
1 AA
65058 TGATTGTAAG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.30, C:0.13, G:0.22, T:0.35
Consensus pattern (45 bp):
AAACCTTAAGGAGTTATCTCTTAGGACTTTGGGGTATAAGTCTTA
Found at i:65055 original size:22 final size:22
Alignment explanation
Indices: 64984--65055 Score: 65
Period size: 22 Copynumber: 3.2 Consensus size: 22
64974 AGGAGTTATC
64984 TCTTAGGACTTTGGGGTATAAG
1 TCTTAGGACTTTGGGGTATAAG
** * * **
65006 TCTTAAAACCTTAAGGAGT-TATC
1 TCTTAGGA-CTT-TGGGGTATAAG
65029 TCTTAGGACTTTGGGGTATAAG
1 TCTTAGGACTTTGGGGTATAAG
65051 TCTTA
1 TCTTA
65056 AATGATTGTA
Statistics
Matches: 35, Mismatches: 12, Indels: 6
0.66 0.23 0.11
Matches are distributed among these distances:
21 4 0.11
22 16 0.46
23 11 0.31
24 4 0.11
ACGTcount: A:0.26, C:0.12, G:0.24, T:0.38
Consensus pattern (22 bp):
TCTTAGGACTTTGGGGTATAAG
Found at i:73099 original size:2 final size:2
Alignment explanation
Indices: 73092--73143 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
73082 TGTTGCTCTC
73092 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
73134 AT AT AT AT AT
1 AT AT AT AT AT
73144 TTATTTATTT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:81881 original size:34 final size:34
Alignment explanation
Indices: 81843--81908 Score: 89
Period size: 34 Copynumber: 1.9 Consensus size: 34
81833 CTATAGTATA
*
81843 ATTGTCCCTGCAT-TATTAATGTCATTGCATTTTT
1 ATTGTCCCTGCATCTA-CAATGTCATTGCATTTTT
* *
81877 ATTGTCGCTGCATCTACATTGTCATTGCATTT
1 ATTGTCCCTGCATCTACAATGTCATTGCATTT
81909 CCATATATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 26 0.93
35 2 0.07
ACGTcount: A:0.20, C:0.20, G:0.14, T:0.47
Consensus pattern (34 bp):
ATTGTCCCTGCATCTACAATGTCATTGCATTTTT
Found at i:81882 original size:17 final size:17
Alignment explanation
Indices: 81851--81908 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 17
81841 TAATTGTCCC
* *
81851 TGCATTATTAATGTCAT
1 TGCATTTTTATTGTCAT
**
81868 TGCATTTTTATTGTCGC
1 TGCATTTTTATTGTCAT
* **
81885 TGCATCTACATTGTCAT
1 TGCATTTTTATTGTCAT
81902 TGCATTT
1 TGCATTT
81909 CCATATATAT
Statistics
Matches: 31, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.21, C:0.17, G:0.14, T:0.48
Consensus pattern (17 bp):
TGCATTTTTATTGTCAT
Found at i:82478 original size:13 final size:12
Alignment explanation
Indices: 82456--82485 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
82446 TCAGTCACAT
82456 AAAAAGAAAAGA
1 AAAAAGAAAAGA
82468 AAAAGAGAAAAGA
1 AAAA-AGAAAAGA
82481 AAAAA
1 AAAAA
82486 ATATTTATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (12 bp):
AAAAAGAAAAGA
Found at i:83683 original size:17 final size:17
Alignment explanation
Indices: 83661--83694 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
83651 CTAGAGATAG
*
83661 TAAGCTTCGATTGTATT
1 TAAGCTTCAATTGTATT
83678 TAAGCTTCAATTGTATT
1 TAAGCTTCAATTGTATT
83695 CAATAATCCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.26, C:0.12, G:0.15, T:0.47
Consensus pattern (17 bp):
TAAGCTTCAATTGTATT
Found at i:85326 original size:53 final size:53
Alignment explanation
Indices: 85269--85374 Score: 212
Period size: 53 Copynumber: 2.0 Consensus size: 53
85259 AGGAAGATAT
85269 GCCTAAGGAAGAAAATAGTGTCTTACTTCCATTCCCGAAAAGGTTAGAAGAAA
1 GCCTAAGGAAGAAAATAGTGTCTTACTTCCATTCCCGAAAAGGTTAGAAGAAA
85322 GCCTAAGGAAGAAAATAGTGTCTTACTTCCATTCCCGAAAAGGTTAGAAGAAA
1 GCCTAAGGAAGAAAATAGTGTCTTACTTCCATTCCCGAAAAGGTTAGAAGAAA
85375 AGAAGTATCA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.40, C:0.17, G:0.21, T:0.23
Consensus pattern (53 bp):
GCCTAAGGAAGAAAATAGTGTCTTACTTCCATTCCCGAAAAGGTTAGAAGAAA
Found at i:88694 original size:148 final size:137
Alignment explanation
Indices: 88480--88779 Score: 377
Period size: 138 Copynumber: 2.1 Consensus size: 137
88470 TTTCTTTTCT
* * * * *
88480 TTTTTTTTTAAAAAGAAAGTTTCGATTTTTAAAAATAAAAATATTTTTTTAGTTATTTTAAAGAA
1 TTTTATTTTAAAAAAAAAGTTTAGATTTATAAAAATAAAAATATGTTTTTAGTTATTTTAAAGAA
88545 AAAGTTTAAATTTTTAAACAAAGTTTTG-ATTTTTTTAAAACTATTTCAAAATAAAAGTTTTAAA
66 AAAGTTTAAA----T----AAAG-TTTGAATTTTTTT--AACTATTTCAAAATAAAAGTTTTAAA
88609 TTTTAAGAAAAATAGTGA
120 TTTTAAGAAAAATAGTGA
* * *
88627 TTTTCTTTAAAAAAAAAATTTTAGATTTATAAAAATAAAAATATGGTTTTTAGTTATTTTAAAGA
1 TTTTATTTTAAAAAAAAAGTTTAGATTTATAAAAATAAAAATAT-GTTTTTAGTTATTTTAAAGA
* * *
88692 AAAAGTTTAAATAAAGTTTGAATTTTTTTAACTATTTCGAAATAAAAGTTTTGATTTTTAAGAAA
65 AAAAGTTTAAATAAAGTTTGAATTTTTTTAACTATTTCAAAATAAAAGTTTTAAATTTTAAGAAA
*
88757 AGTAGTGA
130 AATAGTGA
88765 TTTTATTTTAAAAAA
1 TTTTATTTTAAAAAA
88780 GAGAAAACTT
Statistics
Matches: 138, Mismatches: 13, Indels: 13
0.84 0.08 0.08
Matches are distributed among these distances:
138 53 0.38
139 4 0.03
140 12 0.09
144 1 0.01
147 38 0.28
148 30 0.22
ACGTcount: A:0.44, C:0.02, G:0.09, T:0.44
Consensus pattern (137 bp):
TTTTATTTTAAAAAAAAAGTTTAGATTTATAAAAATAAAAATATGTTTTTAGTTATTTTAAAGAA
AAAGTTTAAATAAAGTTTGAATTTTTTTAACTATTTCAAAATAAAAGTTTTAAATTTTAAGAAAA
ATAGTGA
Found at i:90115 original size:3 final size:3
Alignment explanation
Indices: 90107--90132 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
90097 AAATCTTTTA
90107 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
90133 AAGAACGAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Done.