Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013332.1 Kokia drynarioides strain JFW-HI SEQ_128354, 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: 100904
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Warning! 32 characters in sequence are not A, C, G, or T
Found at i:906 original size:6 final size:6
Alignment explanation
Indices: 895--929 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
885 TGATCAAAAT
895 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAA
1 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAA
930 TTGGAATTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.51, C:0.00, G:0.31, T:0.17
Consensus pattern (6 bp):
TGAAAG
Found at i:3267 original size:7 final size:7
Alignment explanation
Indices: 3255--3287 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
3245 ATTTTATATG
3255 GAATTTT
1 GAATTTT
3262 GAATTTT
1 GAATTTT
3269 GAATTTT
1 GAATTTT
3276 -AATTATT
1 GAATT-TT
3283 GAATT
1 GAATT
3288 AAAACTTAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
6 4 0.17
7 16 0.67
8 4 0.17
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.55
Consensus pattern (7 bp):
GAATTTT
Found at i:4553 original size:52 final size:52
Alignment explanation
Indices: 4473--4867 Score: 574
Period size: 52 Copynumber: 7.6 Consensus size: 52
4463 TAAATGAAAA
* * * *
4473 AGGTCCGATAACTATGTGTCATTGTGAGTATAAGAATCCTTTACGAATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* *
4525 AGGTCCGATGACTATGTGTCATCATGAGTATATGAATCCTTTAAGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* * *
4577 AGGTCCGATAACTATGTGTCATCATGAGTATATGAATCCTTTATGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* **
4629 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAACCCTTTATTGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* * * **
4681 AGGTTCGATGACTATGTGTCATCATGAGTATATGAACCCTTTAATGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
*
4733 AGGTCCGATGACTATGTGTCATCGTGAATATATGAATCCTTTACGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* * * * *
4785 AGGTTCGATGACTATGTTTCATCGGGAGTATATGATTCCTTTACGGATTAAG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
*
4837 AGGTCCGATGATTATGTGTCATCGTGAGTAT
1 AGGTCCGATGACTATGTGTCATCGTGAGTAT
4868 TAAATGAAAT
Statistics
Matches: 312, Mismatches: 31, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 312 1.00
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.36
Consensus pattern (52 bp):
AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
Found at i:18901 original size:16 final size:16
Alignment explanation
Indices: 18873--18905 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
18863 CTTTTGCTCC
18873 TATTTCTTATTTTATT
1 TATTTCTTATTTTATT
18889 TATTT-TTATTTTTATT
1 TATTTCTTA-TTTTATT
18905 T
1 T
18906 TTATTCTCTC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 3 0.19
16 13 0.81
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (16 bp):
TATTTCTTATTTTATT
Found at i:23517 original size:40 final size:40
Alignment explanation
Indices: 23473--23551 Score: 106
Period size: 40 Copynumber: 2.0 Consensus size: 40
23463 GTGTTGCAAC
* *
23473 ATAGGGCGTTTGTCGCGACGTAGACAT-TCTATGTCACGAA
1 ATAGGGCGTTTGTCACGACATAGACATGT-TATGTCACGAA
* *
23513 ATAGGGGGTTTGTTACGACATAGACATGTTATGTCACGA
1 ATAGGGCGTTTGTCACGACATAGACATGTTATGTCACGA
23552 CGAAGAAGGC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
40 33 0.97
41 1 0.03
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.29
Consensus pattern (40 bp):
ATAGGGCGTTTGTCACGACATAGACATGTTATGTCACGAA
Found at i:37868 original size:8 final size:8
Alignment explanation
Indices: 37824--37850 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
37814 ATATTTCCAT
37824 ATTTTTTA
1 ATTTTTTA
37832 ATTTTTTA
1 ATTTTTTA
37840 ATTTTTTA
1 ATTTTTTA
37848 ATT
1 ATT
37851 ATATATTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (8 bp):
ATTTTTTA
Found at i:42075 original size:20 final size:20
Alignment explanation
Indices: 42050--42089 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
42040 ATGACAAATG
42050 TCTTATAGGGTTAAAATATT
1 TCTTATAGGGTTAAAATATT
42070 TCTTATAGGGTTAAAATATT
1 TCTTATAGGGTTAAAATATT
42090 AAGGATAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.05, G:0.15, T:0.45
Consensus pattern (20 bp):
TCTTATAGGGTTAAAATATT
Found at i:42306 original size:14 final size:15
Alignment explanation
Indices: 42289--42324 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
42279 AATTTAAAGA
42289 AAAAATA-ATGTTGT
1 AAAAATAGATGTTGT
42303 AAAAATAGATGTTGT
1 AAAAATAGATGTTGT
*
42318 AGAAATA
1 AAAAATA
42325 TTTTTTCTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (15 bp):
AAAAATAGATGTTGT
Found at i:42922 original size:21 final size:21
Alignment explanation
Indices: 42896--42935 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
42886 TTACATTTTA
42896 TCTTATTTT-TAATATAATTAT
1 TCTTATTTTATAAT-TAATTAT
42917 TCTTATTTTATAATTAATT
1 TCTTATTTTATAATTAATT
42936 TTTAACTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (21 bp):
TCTTATTTTATAATTAATTAT
Found at i:45587 original size:13 final size:13
Alignment explanation
Indices: 45569--45595 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
45559 AGAAACTCGT
45569 ATTTAAAATTTAA
1 ATTTAAAATTTAA
45582 ATTTAAAATTTAA
1 ATTTAAAATTTAA
45595 A
1 A
45596 AGGATATTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
ATTTAAAATTTAA
Found at i:46326 original size:11 final size:12
Alignment explanation
Indices: 46310--46339 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
46300 TTTATTTATT
46310 TAATAAAT-AAA
1 TAATAAATAAAA
46321 TAATAAATAAAA
1 TAATAAATAAAA
46333 TAATAAA
1 TAATAAA
46340 ATTTGAATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 8 0.44
12 10 0.56
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (12 bp):
TAATAAATAAAA
Found at i:50691 original size:20 final size:20
Alignment explanation
Indices: 50666--50714 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
50656 CTGCGATCTT
*
50666 ATATTTGGTAATTGTAAT-TC
1 ATATTTGGAAATTG-AATATC
*
50686 ATATTTAGAAATTGAATATC
1 ATATTTGGAAATTGAATATC
*
50706 ATTTTTGGA
1 ATATTTGGA
50715 TTCTTTATCT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
19 3 0.12
20 21 0.88
ACGTcount: A:0.35, C:0.04, G:0.14, T:0.47
Consensus pattern (20 bp):
ATATTTGGAAATTGAATATC
Found at i:50812 original size:6 final size:6
Alignment explanation
Indices: 50803--50866 Score: 69
Period size: 6 Copynumber: 11.0 Consensus size: 6
50793 TTAAATTTGT
* **
50803 TTTAAA TTTAAA TTTAAA -TTAAG TTTAAA TTTACT TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* *
50850 ATT-AT TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA
50867 ATTCATTAGA
Statistics
Matches: 46, Mismatches: 10, Indels: 4
0.77 0.17 0.07
Matches are distributed among these distances:
5 7 0.15
6 39 0.85
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (6 bp):
TTTAAA
Found at i:50835 original size:29 final size:29
Alignment explanation
Indices: 50803--50866 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
50793 TTAAATTTGT
50803 TTTAAATTTAAATTT-AAATTAAGTTTAAA
1 TTTAAATTTAAATTTAAAATT-AGTTTAAA
** *
50832 TTTACTTTTAAATTTAAAATTATTTTAAA
1 TTTAAATTTAAATTTAAAATTAGTTTAAA
50861 TTTAAA
1 TTTAAA
50867 ATTCATTAGA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
29 24 0.83
30 5 0.17
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (29 bp):
TTTAAATTTAAATTTAAAATTAGTTTAAA
Found at i:50869 original size:17 final size:17
Alignment explanation
Indices: 50775--50866 Score: 114
Period size: 17 Copynumber: 5.4 Consensus size: 17
50765 CTAAACTCTT
50775 TTTAAATTTATTTTAAGA
1 TTTAAATTTATTTTAA-A
*
50793 -TTAAATTTGTTTTAAA
1 TTTAAATTTATTTTAAA
** *
50809 TTTAAATTTAAATTAAG
1 TTTAAATTTATTTTAAA
50826 TTTAAATTTACTTTTAAA
1 TTTAAATTTA-TTTTAAA
*
50844 TTTAAAATTATTTTAAA
1 TTTAAATTTATTTTAAA
50861 TTTAAA
1 TTTAAA
50867 ATTCATTAGA
Statistics
Matches: 63, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
16 1 0.02
17 49 0.78
18 13 0.21
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.53
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:52684 original size:30 final size:30
Alignment explanation
Indices: 52620--52861 Score: 142
Period size: 30 Copynumber: 8.1 Consensus size: 30
52610 TAAACTGTAA
* * * ***
52620 AAAAATTATATTTTGACCCCCGAACTTTTT
1 AAAAATTACATTTTAACCCTCGAACTTCAC
*
52650 AAAAATTATATTTTAACCCTCGAACTTCAC
1 AAAAATTACATTTTAACCCTCGAACTTCAC
**
52680 AAAAATTACATTTTTGCCCTCGAACTTCAC
1 AAAAATTACATTTTAACCCTCGAACTTCAC
* ** *
52710 AAAATTTACATTTT-TGCCTCTAAACTTTC-C
1 AAAAATTACATTTTAACCCTC-GAAC-TTCAC
* ** ***
52740 AAAAACTACATTTGT-ACCCTTTAACTTTTT
1 AAAAATTACATTT-TAACCCTCGAACTTCAC
*
52770 AAAAATTACCATTTT-ACCCCCGAACTTC-C
1 AAAAATTA-CATTTTAACCCTCGAACTTCAC
*
52799 AAAAA-TATCATTTTGACTCCT-GAACTTTCA-
1 AAAAATTA-CATTTTAAC-CCTCGAAC-TTCAC
* **
52829 AAAAATCACATTTTTGCCCTCGAACTTC-C
1 AAAAATTACATTTTAACCCTCGAACTTCAC
52858 AAAA
1 AAAA
52862 TATAATTTTT
Statistics
Matches: 169, Mismatches: 31, Indels: 25
0.75 0.14 0.11
Matches are distributed among these distances:
28 8 0.05
29 27 0.16
30 121 0.72
31 13 0.08
ACGTcount: A:0.35, C:0.24, G:0.05, T:0.36
Consensus pattern (30 bp):
AAAAATTACATTTTAACCCTCGAACTTCAC
Found at i:52685 original size:60 final size:58
Alignment explanation
Indices: 52620--52875 Score: 187
Period size: 60 Copynumber: 4.3 Consensus size: 58
52610 TAAACTGTAA
*
52620 AAAAATTATATTTTGACCCCCGAACTTTTTAAAAATTATATTTTAACCCTCGAACTTCAC
1 AAAAATTATATTTTGACCCCCGAACTTTTTAAAAATTACATTTT-ACCCTCGAACTTC-C
* * *** * ** *
52680 AAAAATTACATTTTTG-CCCTCGAACTTCACAAAATTTACATTTTTGCCTCTAAACTTTCC
1 AAAAATTATA-TTTTGACCCCCGAACTTTTTAAAAATTACATTTTACCCTC-GAAC-TTCC
* * *** *
52740 AAAAACTACA-TTTGTACCCTTTAACTTTTTAAAAATTACCATTTTACCCCCGAACTTCC
1 AAAAATTATATTTTG-ACCCCCGAACTTTTTAAAAATTA-CATTTTACCCTCGAACTTCC
* * ** * *
52799 AAAAA-TATCATTTTGACTCCTGAACTTTCAAAAAATCACATTTTTGCCCTCGAACTTCC
1 AAAAATTAT-ATTTTGACCCCCGAACTTTTTAAAAATTACA-TTTTACCCTCGAACTTCC
*
52858 AAAATATAAT-TTTTGACC
1 AAAA-ATTATATTTTGACC
52876 TCGAGTTTTC
Statistics
Matches: 153, Mismatches: 32, Indels: 23
0.74 0.15 0.11
Matches are distributed among these distances:
58 8 0.05
59 58 0.38
60 68 0.44
61 19 0.12
ACGTcount: A:0.35, C:0.24, G:0.05, T:0.36
Consensus pattern (58 bp):
AAAAATTATATTTTGACCCCCGAACTTTTTAAAAATTACATTTTACCCTCGAACTTCC
Found at i:65302 original size:209 final size:209
Alignment explanation
Indices: 64930--66048 Score: 1425
Period size: 209 Copynumber: 5.4 Consensus size: 209
64920 AGGCGGTCAT
* * * * *
64930 CTTCCTAATGAGATACAGAGAAGTGAACCAGATCTGTTTTCCAGATGAGACACAGAGAAGTGGAT
1 CTTCCTGATGAGATACAGAGAAGTGAACCAGATCCGTCTTCCTGATGAGACACAGAGAAGCGGAT
* * **
64995 CAAAACAAGTGATGCGGTCATCTTCTTGATGAGATATAGAGAAGTATACCAACTCAACAAAACCA
66 CAAAACAAGTGATGCGGTCATCTTCCTGATGAGATACAGAGAAGTATACCAACTCAATGAAACCA
* * *
65060 GGCTCAATGTGAGAAAATCTTCGAACTCCAGCTTCCTGACGAGATACTGAGAAGCAGGTCGAAGC
131 GGCTCAATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGC
*
65125 AATAAAGCGGTTAC
196 AATAAAACGGTTAC
* **
65139 CTTCTTGATGAGATACAGAGAAGTGAACCAGATCCGTCTTCCTGATGAGACACAGAGAAGTTGAT
1 CTTCCTGATGAGATACAGAGAAGTGAACCAGATCCGTCTTCCTGATGAGACACAGAGAAGCGGAT
* * * *
65204 CAAAACAGGTGATACGGTCATCTTCTTGATGAGATACAGAGAAGTATACCAACTCAATAAAACCA
66 CAAAACAAGTGATGCGGTCATCTTCCTGATGAGATACAGAGAAGTATACCAACTCAATGAAACCA
** * *
65269 CACTCAATGTGAGCAAATCTTCGAACCCCAGCTTCCTAATAAGATACTGAGAAGCAGGTCGAAGC
131 GGCTCAATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGC
*
65334 AATAAAGCGGTTAC
196 AATAAAACGGTTAC
* * * * *
65348 CTTTCTGATGAGATATAGAGAAGTGAACCAGATCCGTCTTCATGATGAGACACAGAGAAGTGAAT
1 CTTCCTGATGAGATACAGAGAAGTGAACCAGATCCGTCTTCCTGATGAGACACAGAGAAGCGGAT
* * * *
65413 CAAAACAAGTGATGCAGTCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACCA
66 CAAAACAAGTGATGCGGTCATCTTCCTGATGAGATACAGAGAAGTATACCAACTCAATGAAACCA
* * * * *
65478 GGCTCAAAGTGAGCAAATCTTGGAACCCTAGCTTCCTGATGAGATACTGAGAAGTATGTCGAAGC
131 GGCTCAATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGC
*
65543 AATAAAATGGTTAGC
196 AATAAAACGGTTA-C
* * * * * *
65558 C-TCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACTGAGAAGCGGAT
1 CTTCCTGATGAGATACAGAGAAGTGAACCAGATCCGTCTTCCTGATGAGACACAGAGAAGCGGAT
** * * * * * *
65622 TGAAACAA-TCGAGGCGATCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATTAATGAAACC
66 CAAAACAAGT-GATGCGGTCATCTTCCTGATGAGATACAGAGAAGTATACCAACTCAATGAAACC
* * *
65686 AGGCTCAAAGTGAGCAAATCTTGGAACCCTAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAG
130 AGGCTCAATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAG
* *
65751 CAATAAAATGGTTAG
195 CAATAAAACGGTTAC
* * * * * * * * *
65766 CTTCCTGATGAGGTACTGAGAAGTGGACCAAATCCGTCTTCTTGATAAGATACTGAGAAGCAGAT
1 CTTCCTGATGAGATACAGAGAAGTGAACCAGATCCGTCTTCCTGATGAGACACAGAGAAGCGGAT
** * * * * * *
65831 TGAAACAAGCGAGGCGATCATCTTCCTGATGAGATATAGAGAAGTATGCCAACTCAATGAAATCA
66 CAAAACAAGTGATGCGGTCATCTTCCTGATGAGATACAGAGAAGTATACCAACTCAATGAAACCA
* * * *
65896 GGCTCAATGAGAGCAAATCTTCGAATCCCAGCTTCCTGATGAGAT-GTCGAGAAGCAGGTCGAAC
131 GGCTCAATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACT-GAGAAGCAGGTCGAAG
65960 CAATAAAACGGTTAC
195 CAATAAAACGGTTAC
* ** * *
65975 CTTCCTGATGAGATACTGAGAAGTGAACCAGATCCGTCTTCCTGATGAGTTACAGAGAAGAGGCT
1 CTTCCTGATGAGATACAGAGAAGTGAACCAGATCCGTCTTCCTGATGAGACACAGAGAAGCGGAT
66040 CAAAACAAG
66 CAAAACAAG
66049 CGAAATGGTC
Statistics
Matches: 809, Mismatches: 96, Indels: 10
0.88 0.10 0.01
Matches are distributed among these distances:
208 3 0.00
209 804 0.99
210 2 0.00
ACGTcount: A:0.35, C:0.19, G:0.23, T:0.22
Consensus pattern (209 bp):
CTTCCTGATGAGATACAGAGAAGTGAACCAGATCCGTCTTCCTGATGAGACACAGAGAAGCGGAT
CAAAACAAGTGATGCGGTCATCTTCCTGATGAGATACAGAGAAGTATACCAACTCAATGAAACCA
GGCTCAATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGC
AATAAAACGGTTAC
Found at i:66497 original size:11 final size:11
Alignment explanation
Indices: 66481--66554 Score: 50
Period size: 11 Copynumber: 7.0 Consensus size: 11
66471 CTAAACCTCT
66481 TTTTAAATTTA
1 TTTTAAATTTA
66492 TTTT-AA---A
1 TTTTAAATTTA
*
66499 -TTTAAATTTG
1 TTTTAAATTTA
*
66509 CTTTAAATTTAA
1 TTTTAAATTT-A
* *
66521 ATTTAAATTAA
1 TTTTAAATTTA
*
66532 GTTTAAATTTA
1 TTTTAAATTTA
66543 CTTTTAAATTTA
1 -TTTTAAATTTA
66555 AAATTCATTA
Statistics
Matches: 49, Mismatches: 7, Indels: 13
0.71 0.10 0.19
Matches are distributed among these distances:
6 3 0.06
7 3 0.06
10 2 0.04
11 23 0.47
12 18 0.37
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (11 bp):
TTTTAAATTTA
Found at i:66502 original size:6 final size:6
Alignment explanation
Indices: 66482--66556 Score: 75
Period size: 6 Copynumber: 13.0 Consensus size: 6
66472 TAAACCTCTT
* **
66482 TTTAAA TTT-AT TTTAAA TTTAAA TTT-GC TTTAAA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* **
66528 -TTAAG TTTAAA TTTACT TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
66557 ATTCATTAGA
Statistics
Matches: 54, Mismatches: 12, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
5 11 0.20
6 43 0.80
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.53
Consensus pattern (6 bp):
TTTAAA
Found at i:66502 original size:17 final size:17
Alignment explanation
Indices: 66482--66556 Score: 96
Period size: 17 Copynumber: 4.4 Consensus size: 17
66472 TAAACCTCTT
66482 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
**
66499 TTTAAATTTGCTTTAAA
1 TTTAAATTTATTTTAAA
** *
66516 TTTAAATTTAAATTAAG
1 TTTAAATTTATTTTAAA
66533 TTTAAATTTACTTTTAAA
1 TTTAAATTTA-TTTTAAA
66551 TTTAAA
1 TTTAAA
66557 ATTCATTAGA
Statistics
Matches: 48, Mismatches: 9, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
17 38 0.79
18 10 0.21
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.53
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:66519 original size:23 final size:22
Alignment explanation
Indices: 66493--66553 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 22
66483 TTAAATTTAT
66493 TTTAAATTTAAATTTGCTTTAAA
1 TTTAAATTTAAATTTG-TTTAAA
*
66516 TTTAAATTTAAATTAAGTTTAAA
1 TTTAAATTTAAATT-TGTTTAAA
**
66539 TTTACTTTTAAATTT
1 TTTAAATTTAAATTT
66554 AAAATTCATT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
23 32 0.97
24 1 0.03
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.54
Consensus pattern (22 bp):
TTTAAATTTAAATTTGTTTAAA
Found at i:67182 original size:3 final size:3
Alignment explanation
Indices: 67174--67250 Score: 136
Period size: 3 Copynumber: 25.7 Consensus size: 3
67164 AAAGATATTA
67174 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
67222 AAC AAT AAT AAC AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
67251 GGAGATATGA
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 70 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:68224 original size:58 final size:58
Alignment explanation
Indices: 68103--68270 Score: 189
Period size: 59 Copynumber: 2.8 Consensus size: 58
68093 CTGAACTTTT
* * * *
68103 CAAAAATTACATTTTGACCCTCGAACTTCATAAAAATTACAGTTTTCCCTTGAACTTCA
1 CAAAAATTACATTTT-ACCCCCAAACTTTATAAAAATTACAGTTTTCCCTTAAACTTCA
*
68162 CAAAAATTACATTTTACCCCCAAACTTTATAAAAATTACATTTTTACCC-TAAACCTTC-
1 CAAAAATTACATTTTACCCCCAAACTTTATAAAAATTACAGTTTT-CCCTTAAA-CTTCA
** *
68220 CAAAAATTACATTTTTACCCCTTAACTTT-TAAAAAATTACCAGTTTGCCCT
1 CAAAAATTACA-TTTTACCCCCAAACTTTAT-AAAAATTA-CAGTTTTCCCT
68271 CGAACTTTCG
Statistics
Matches: 94, Mismatches: 9, Indels: 11
0.82 0.08 0.10
Matches are distributed among these distances:
58 41 0.44
59 48 0.51
60 5 0.05
ACGTcount: A:0.37, C:0.24, G:0.04, T:0.35
Consensus pattern (58 bp):
CAAAAATTACATTTTACCCCCAAACTTTATAAAAATTACAGTTTTCCCTTAAACTTCA
Found at i:68247 original size:88 final size:87
Alignment explanation
Indices: 68090--68399 Score: 267
Period size: 88 Copynumber: 3.5 Consensus size: 87
68080 CATATTTTGT
* * * * *
68090 CCCCTGAACTTTTCAAAAATTACATTTTGACCCTCGAACTTCATAAAAATTACAGTTTT--CCCT
1 CCCCCGAACTTTT-AAAAATCACATTTTTACCCTCAAACTTC-CAAAAATTACA-TTTTACCCCT
68153 TGAACTTCACAAAAATTA-CATTTTA
63 T-AACTTCACAAAAATTACCATTTTA
* *
68178 CCCCCAAACTTTATAAAAATTACATTTTTACCCT-AAACCTTCCAAAAATTACATTTTTACCCCT
1 CCCCCGAACTTT-TAAAAATCACATTTTTACCCTCAAA-CTTCCAAAAATTACA-TTTTACCCCT
* * *
68242 TAACTTTTA-AAAAATTACCAGTTTG
63 TAAC-TTCACAAAAATTACCATTTTA
* ** * * * *
68267 CCCTCGAACTTTCGAAAATCATATTTTTGCCCTTAAACTTCCAAAAATTATCATTTTACCCCTGA
1 CCCCCGAACTTTTAAAAATCACATTTTTACCCTCAAACTTCCAAAAATTA-CATTTTACCCCTTA
*
68332 ACTTC-CAAAAA-TATCATTTTTGA
65 ACTTCACAAAAATTACCA-TTTT-A
** * *
68355 -CCCCGAACTTCAAAAAATCACATTTTTGCCCTCGAACTTCCAAAA
1 CCCCCGAACTTTTAAAAATCACATTTTTACCCTCAAACTTCCAAAA
68400 TATCATTTTT
Statistics
Matches: 183, Mismatches: 28, Indels: 23
0.78 0.12 0.10
Matches are distributed among these distances:
86 4 0.02
87 64 0.35
88 86 0.47
89 29 0.16
ACGTcount: A:0.35, C:0.26, G:0.05, T:0.34
Consensus pattern (87 bp):
CCCCCGAACTTTTAAAAATCACATTTTTACCCTCAAACTTCCAAAAATTACATTTTACCCCTTAA
CTTCACAAAAATTACCATTTTA
Found at i:68364 original size:58 final size:56
Alignment explanation
Indices: 68089--68399 Score: 238
Period size: 58 Copynumber: 5.3 Consensus size: 56
68079 TCATATTTTG
* *
68089 TCCCCTGAACTTTTCAAAAATTACA-TTTTGACCCTCGAACTTCATAAAAATTACAGTTT
1 TCCCCTGAAC-TTCCAAAAATTACATTTTTGACCC-CAAACTTCA-AAAAATTACA-TTT
* *
68148 TCCCTTGAACTTCACAAAAATTACA-TTTT-ACCCCCAAACTTTATAAAAATTACATTTT
1 TCCCCTGAACTTC-CAAAAATTACATTTTTGA-CCCCAAACTTCA-AAAAATTACA-TTT
* * * * *
68206 TACCCTAAACCTTCCAAAAATTACATTTTT-ACCCCTTAACTTTTAAAAAATTACCAGTT
1 TCCCCTGAA-CTTCCAAAAATTACATTTTTGACCCC-AAAC-TTCAAAAAATTA-CATTT
* * * * * * *
68265 TGCCCTCGAACTTTCGAAAATCATATTTTTG-CCCTTAAACTTCCAAAAATTATCATTT
1 TCCCCT-GAACTTCCAAAAATTACATTTTTGACCC-CAAACTTCAAAAAATTA-CATTT
* *
68323 TACCCCTGAACTTCCAAAAA-TATCATTTTTGACCCCGAACTTCAAAAAATCACATTTT
1 T-CCCCTGAACTTCCAAAAATTA-CATTTTTGACCCCAAACTTCAAAAAATTACA-TTT
*
68381 TGCCCTCGAACTTCCAAAA
1 TCCCCT-GAACTTCCAAAA
68400 TATCATTTTT
Statistics
Matches: 205, Mismatches: 32, Indels: 31
0.76 0.12 0.12
Matches are distributed among these distances:
57 7 0.03
58 107 0.52
59 83 0.40
60 8 0.04
ACGTcount: A:0.35, C:0.26, G:0.05, T:0.34
Consensus pattern (56 bp):
TCCCCTGAACTTCCAAAAATTACATTTTTGACCCCAAACTTCAAAAAATTACATTT
Found at i:68399 original size:29 final size:29
Alignment explanation
Indices: 68103--68399 Score: 207
Period size: 29 Copynumber: 10.2 Consensus size: 29
68093 CTGAACTTTT
68103 CAAAAATTACA-TTTTGACCCTCGAACTTC
1 CAAAAATTACATTTTTG-CCCTCGAACTTC
* * *
68132 ATAAAAATTACAGTTTT-CCCTTGAACTTC
1 -CAAAAATTACATTTTTGCCCTCGAACTTC
* * * *
68161 ACAAAAATTACA-TTTTACCCCCAAACTTTA
1 -CAAAAATTACATTTTTGCCCTCGAAC-TTC
* * *
68191 TAAAAATTACATTTTTACCCT-AAACCTTC
1 CAAAAATTACATTTTTGCCCTCGAA-CTTC
* * *
68220 CAAAAATTACATTTTTACCC-CTTAACTTTT
1 CAAAAATTACATTTTTGCCCTC-GAAC-TTC
* * *
68250 AAAAAATTACCA-GTTTGCCCTCGAACTTT
1 CAAAAATTA-CATTTTTGCCCTCGAACTTC
* * * **
68279 CGAAAATCATATTTTTGCCCTTAAACTTC
1 CAAAAATTACATTTTTGCCCTCGAACTTC
**
68308 CAAAAATTATCATTTTACCCCT-GAACTTC
1 CAAAAATTA-CATTTTTGCCCTCGAACTTC
68337 CAAAAA-TATCATTTTTGACCC-CGAACTTC
1 CAAAAATTA-CATTTTTG-CCCTCGAACTTC
* *
68366 AAAAAATCACATTTTTGCCCTCGAACTTC
1 CAAAAATTACATTTTTGCCCTCGAACTTC
68395 CAAAA
1 CAAAA
68400 TATCATTTTT
Statistics
Matches: 215, Mismatches: 36, Indels: 33
0.76 0.13 0.12
Matches are distributed among these distances:
28 17 0.08
29 139 0.65
30 52 0.24
31 7 0.03
ACGTcount: A:0.36, C:0.25, G:0.05, T:0.34
Consensus pattern (29 bp):
CAAAAATTACATTTTTGCCCTCGAACTTC
Found at i:83227 original size:94 final size:93
Alignment explanation
Indices: 83056--83542 Score: 590
Period size: 93 Copynumber: 5.3 Consensus size: 93
83046 GCCGATCAAC
* * * * * *
83056 AACTCAGGGGTATAGGATCTGGTGCTTCAATCTACTCCACTGTAACCTCAGGGATGTTGAGATCT
1 AACTTAGGGGTATAGGATTTGGTGCTTCACTCCACTCCACTGTAACCTCAAGGACGTTGAGATCT
* *
83121 GCTTCTTTGTTTTAATCCGACCCACTAT
66 GCTTCATTGTTTTAATCTGACCCACTAT
* * * * * *
83149 AACTTGGGGGTTATAGGGTTTGGTGCTTCACTCCACTCTATTATAACCTCAAGGACGTTAAGATC
1 AACTTAGGGG-TATAGGATTTGGTGCTTCACTCCACTCCACTGTAACCTCAAGGACGTTGAGATC
* * **
83214 TACGTCATTGTTTTAATCTGACCCACTGC
65 TGCTTCATTGTTTTAATCTGACCCACTAT
* * * * * *
83243 AACTCAAGGGTATAAGATTTAGTGCTTCACTCCACTTCACTGTAACCTCAAGAACGTTGAGATCT
1 AACTTAGGGGTATAGGATTTGGTGCTTCACTCCACTCCACTGTAACCTCAAGGACGTTGAGATCT
* *
83308 G-TCTCATTGTTTTAATTTGACCCACTGT
66 GCT-TCATTGTTTTAATCTGACCCACTAT
*
83336 AACTTAGGGGTATATGATTTGGTGCTTCACTCCACTCCACTGTAACCTCAAGGACGTTGAGATCT
1 AACTTAGGGGTATAGGATTTGGTGCTTCACTCCACTCCACTGTAACCTCAAGGACGTTGAGATCT
* * *
83401 GCTTCATTTATTTTTATCTGACCCACTAC
66 GCTTCA-TTGTTTTAATCTGACCCACTAT
* *
83430 AACTTAGAGGTATAGGATTTGGTGCTTCACTCCACTCCAC-----CCTCAAGGACGTTAAGATCT
1 AACTTAGGGGTATAGGATTTGGTGCTTCACTCCACTCCACTGTAACCTCAAGGACGTTGAGATCT
* *
83490 GCCTCATTATTTTAATCTGACCCCACTAT
66 GCTTCATTGTTTTAATCTGA-CCCACTAT
83519 AACTTAGGGGTATAGGATTTGGTG
1 AACTTAGGGGTATAGGATTTGGTG
83543 TTTACTTGGC
Statistics
Matches: 337, Mismatches: 52, Indels: 14
0.84 0.13 0.03
Matches are distributed among these distances:
88 13 0.04
89 54 0.16
93 140 0.42
94 130 0.39
ACGTcount: A:0.24, C:0.23, G:0.19, T:0.34
Consensus pattern (93 bp):
AACTTAGGGGTATAGGATTTGGTGCTTCACTCCACTCCACTGTAACCTCAAGGACGTTGAGATCT
GCTTCATTGTTTTAATCTGACCCACTAT
Found at i:83422 original size:187 final size:185
Alignment explanation
Indices: 83054--83542 Score: 603
Period size: 187 Copynumber: 2.6 Consensus size: 185
83044 AGGCCGATCA
* * * * * * *
83054 ACAACTCAGGGGTATAGGATCTGGTGCTTCAATCTACTCCACTGTAACCTCAGGGATGTTGAGAT
1 ACAACTCAAGGGTATAGGATTTGGTGCTTCACTCCACTTCACTGTAACCTCAAGGACGTTGAGAT
* * * *
83119 CTGCTTCTTTGTTTTAATCCGACCCACTATAACTTGGGGGTTATAGGGTTTGGTGCTTCACTCCA
66 CTGC-TCATTGTTTTAATCTGACCCACTATAACTTAGGGG-TATAGGATTTGGTGCTTCACTCCA
* * *
83184 CTCTATTATAACCTCAAGGACGTTAAGATCTACGTCATTGTTTTAATCTGACCCACT
129 CTCCACTATAACCTCAAGGACGTTAAGATCTACGTCATTATTTTAATCTGACCCACT
* * * *
83241 GCAACTCAAGGGTATAAGATTTAGTGCTTCACTCCACTTCACTGTAACCTCAAGAACGTTGAGAT
1 ACAACTCAAGGGTATAGGATTTGGTGCTTCACTCCACTTCACTGTAACCTCAAGGACGTTGAGAT
* * *
83306 CTGTCTCATTGTTTTAATTTGACCCACTGTAACTTAGGGGTATATGATTTGGTGCTTCACTCCAC
66 CTG-CTCATTGTTTTAATCTGACCCACTATAACTTAGGGGTATAGGATTTGGTGCTTCACTCCAC
* * * * *
83371 TCCACTGTAACCTCAAGGACGTTGAGATCTGCTTCATTTATTTTTATCTGACCCACT
130 TCCACTATAACCTCAAGGACGTTAAGATCTACGTCA-TTATTTTAATCTGACCCACT
* * *
83428 ACAACT-TAGAGGTATAGGATTTGGTGCTTCACTCCAC-TC-C---ACCCTCAAGGACGTTAAGA
1 ACAACTCAAG-GGTATAGGATTTGGTGCTTCACTCCACTTCACTGTAACCTCAAGGACGTTGAGA
*
83487 TCTGCCTCATTATTTTAATCTGACCCCACTATAACTTAGGGGTATAGGATTTGGTG
65 TCTG-CTCATTGTTTTAATCTGA-CCCACTATAACTTAGGGGTATAGGATTTGGTG
83543 TTTACTTGGC
Statistics
Matches: 260, Mismatches: 38, Indels: 12
0.84 0.12 0.04
Matches are distributed among these distances:
182 36 0.14
183 30 0.12
185 1 0.00
186 57 0.22
187 135 0.52
188 1 0.00
ACGTcount: A:0.25, C:0.23, G:0.19, T:0.34
Consensus pattern (185 bp):
ACAACTCAAGGGTATAGGATTTGGTGCTTCACTCCACTTCACTGTAACCTCAAGGACGTTGAGAT
CTGCTCATTGTTTTAATCTGACCCACTATAACTTAGGGGTATAGGATTTGGTGCTTCACTCCACT
CCACTATAACCTCAAGGACGTTAAGATCTACGTCATTATTTTAATCTGACCCACT
Found at i:86435 original size:14 final size:14
Alignment explanation
Indices: 86416--86444 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
86406 TTAGGCTAAT
86416 TATCATGAGATATA
1 TATCATGAGATATA
86430 TATCATGAGATATA
1 TATCATGAGATATA
86444 T
1 T
86445 TAGAAGTCTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.07, G:0.14, T:0.38
Consensus pattern (14 bp):
TATCATGAGATATA
Found at i:93769 original size:21 final size:21
Alignment explanation
Indices: 93721--93772 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
93711 GGAGTTTTTA
93721 GTATCGGTAGAGGCATGACAT
1 GTATCGGTAGAGGCATGACAT
* * *
93742 GTTTCGGTAGAAGTCAT-ACTT
1 GTATCGGTAG-AGGCATGACAT
93763 GTATCGGTAG
1 GTATCGGTAG
93773 TATTGTCTCA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 21 0.81
22 5 0.19
ACGTcount: A:0.25, C:0.13, G:0.31, T:0.31
Consensus pattern (21 bp):
GTATCGGTAGAGGCATGACAT
Found at i:95911 original size:52 final size:52
Alignment explanation
Indices: 95841--96037 Score: 245
Period size: 52 Copynumber: 3.8 Consensus size: 52
95831 TAAGTCGTAA
* * *
95841 ATTAAGAGGTCCGTTGACTTTGTGTCATCGTGAGTATATGAGTCCTTTACGG
1 ATTAAGAGGTCCGATGACTCTATGTCATCGTGAGTATATGAGTCCTTTACGG
* * * *
95893 ATTAAGGGGACCGATGACTCTATTTCATCGTAAGTATATGAGTCCTTTACGG
1 ATTAAGAGGTCCGATGACTCTATGTCATCGTGAGTATATGAGTCCTTTACGG
*
95945 ATTAAGAGGTCCGATGACTCTATGTCATCGTGAGTATATGAATTCC-TTACGG
1 ATTAAGAGGTCCGATGACTCTATGTCATCGTGAGTATATG-AGTCCTTTACGG
* * * * *
95997 ATTATGAGGTTC-AGTGGCTATGTGTCATCGTGAGTATATGA
1 ATTAAGAGGTCCGA-TGACTCTATGTCATCGTGAGTATATGA
96038 ATAAAGAGAA
Statistics
Matches: 126, Mismatches: 17, Indels: 5
0.85 0.11 0.03
Matches are distributed among these distances:
51 2 0.02
52 120 0.95
53 4 0.03
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.35
Consensus pattern (52 bp):
ATTAAGAGGTCCGATGACTCTATGTCATCGTGAGTATATGAGTCCTTTACGG
Done.