Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012200.1 Kokia drynarioides strain JFW-HI SEQ_127201, 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: 111160
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Warning! 5 characters in sequence are not A, C, G, or T
Found at i:1579 original size:6 final size:6
Alignment explanation
Indices: 1568--1593 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
1558 TTAATTCCAG
1568 TTTCAC TTTCAC TTTCAC TTTCAC TT
1 TTTCAC TTTCAC TTTCAC TTTCAC TT
1594 GCAATTTTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.31, G:0.00, T:0.54
Consensus pattern (6 bp):
TTTCAC
Found at i:8604 original size:24 final size:22
Alignment explanation
Indices: 8573--8617 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
8563 TTAAAGGTTA
*
8573 AAGAAGATCAAAGGTGGAAAGTC
1 AAGAAGATCAAAGAT-GAAAGTC
*
8596 AAGAGAGATGAAAGATGAAAGT
1 AAGA-AGATCAAAGATGAAAGT
8618 TTGAACATTC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.51, C:0.04, G:0.31, T:0.13
Consensus pattern (22 bp):
AAGAAGATCAAAGATGAAAGTC
Found at i:14109 original size:39 final size:40
Alignment explanation
Indices: 14065--14224 Score: 270
Period size: 40 Copynumber: 4.0 Consensus size: 40
14055 AAAAATTAAT
*
14065 ATGGAAATAATTTTTTAATATCTAG-TTTTTTTTATGACA
1 ATGGAAATAATTTTTTAATATCTAGTTTTTTTTTATGAAA
*
14104 ATGGAAATAATTTTTTAATATCTAGTTTTTTTTTATTAAA
1 ATGGAAATAATTTTTTAATATCTAGTTTTTTTTTATGAAA
* *
14144 ATGGAAATAATTTTTTAATATTTAGTTTTTTTTTATTAAA
1 ATGGAAATAATTTTTTAATATCTAGTTTTTTTTTATGAAA
14184 ATGGAAATAATTTTTTAATATCTAG-TTTTTTTTATGAAA
1 ATGGAAATAATTTTTTAATATCTAGTTTTTTTTTATGAAA
14223 AT
1 AT
14225 TTATTTGATA
Statistics
Matches: 115, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
39 40 0.35
40 75 0.65
ACGTcount: A:0.35, C:0.03, G:0.09, T:0.54
Consensus pattern (40 bp):
ATGGAAATAATTTTTTAATATCTAGTTTTTTTTTATGAAA
Found at i:14170 original size:79 final size:79
Alignment explanation
Indices: 14059--14224 Score: 271
Period size: 79 Copynumber: 2.1 Consensus size: 79
14049 CATAACAAAA
* *
14059 ATTAATATGGAAATAATTTTTTAATATCTAG-TTTTTTTTATGACAATGGAAATAATTTTTTAAT
1 ATTAAAATGGAAATAATTTTTTAATATCTAGTTTTTTTTTATGAAAATGGAAATAATTTTTTAAT
14123 ATCTAGTTTTTTTTT
66 ATCTAG-TTTTTTTT
* *
14138 ATTAAAATGGAAATAATTTTTTAATATTTAGTTTTTTTTTATTAAAATGGAAATAATTTTTTAAT
1 ATTAAAATGGAAATAATTTTTTAATATCTAGTTTTTTTTTATGAAAATGGAAATAATTTTTTAAT
14203 ATCTAGTTTTTTTT
66 ATCTAGTTTTTTTT
*
14217 ATGAAAAT
1 ATTAAAAT
14225 TTATTTGATA
Statistics
Matches: 81, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
79 44 0.54
80 37 0.46
ACGTcount: A:0.36, C:0.02, G:0.08, T:0.54
Consensus pattern (79 bp):
ATTAAAATGGAAATAATTTTTTAATATCTAGTTTTTTTTTATGAAAATGGAAATAATTTTTTAAT
ATCTAGTTTTTTTT
Found at i:16371 original size:47 final size:47
Alignment explanation
Indices: 16302--16396 Score: 172
Period size: 47 Copynumber: 2.0 Consensus size: 47
16292 GATTGTCGCC
*
16302 GCATCTCTAGTCGTGATATGTAATCTTTGATTGCAACGACAATATGT
1 GCATCTCTACTCGTGATATGTAATCTTTGATTGCAACGACAATATGT
*
16349 GCATCTCTACTCGTGATATGTAATCTTTGATTGCAGCGACAATATGT
1 GCATCTCTACTCGTGATATGTAATCTTTGATTGCAACGACAATATGT
16396 G
1 G
16397 AAATCCATGC
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.36
Consensus pattern (47 bp):
GCATCTCTACTCGTGATATGTAATCTTTGATTGCAACGACAATATGT
Found at i:17669 original size:17 final size:18
Alignment explanation
Indices: 17649--17682 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
17639 GTAGATGTAC
17649 TAACAAATG-AAATGCAG
1 TAACAAATGAAAATGCAG
17666 TAACAAATGAAAATGCA
1 TAACAAATGAAAATGCA
17683 ATGAGAACTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.56, C:0.12, G:0.15, T:0.18
Consensus pattern (18 bp):
TAACAAATGAAAATGCAG
Found at i:17701 original size:21 final size:23
Alignment explanation
Indices: 17653--17707 Score: 64
Period size: 21 Copynumber: 2.5 Consensus size: 23
17643 ATGTACTAAC
*
17653 AAATGAAATGCAGTAACAAATGA
1 AAATGCAATGCAGTAACAAATGA
17676 AAATGCAATG-AG-AACTAAAT-A
1 AAATGCAATGCAGTAAC-AAATGA
17697 AAATGC-ATGCA
1 AAATGCAATGCA
17708 ATTAACTACT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
20 3 0.10
21 11 0.38
22 6 0.21
23 9 0.31
ACGTcount: A:0.55, C:0.11, G:0.16, T:0.18
Consensus pattern (23 bp):
AAATGCAATGCAGTAACAAATGA
Found at i:17797 original size:16 final size:15
Alignment explanation
Indices: 17776--17805 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
17766 TGGTTTTCTT
17776 TTTCTTCTTCCTTGTG
1 TTTCTTCTT-CTTGTG
17792 TTTCTTCTTCTTGT
1 TTTCTTCTTCTTGT
17806 CCATGCACTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.00, C:0.23, G:0.10, T:0.67
Consensus pattern (15 bp):
TTTCTTCTTCTTGTG
Found at i:33823 original size:36 final size:36
Alignment explanation
Indices: 33776--33903 Score: 164
Period size: 36 Copynumber: 3.8 Consensus size: 36
33766 TGGTAACATG
33776 CATGACCTTTGGGTCAACAGGGAGTAAAATGAGCAT
1 CATGACCTTTGGGTCAACAGGGAGTAAAATGAGCAT
** *
33812 CATGACCTTTGGGTCAATGGGGAGTGAAATGAGCAT
1 CATGACCTTTGGGTCAACAGGGAGTAAAATGAGCAT
*
33848 CATGACCTTTGGGTCAACAGAGAGT---A--AG---
1 CATGACCTTTGGGTCAACAGGGAGTAAAATGAGCAT
33876 CATGACCTTTGGGTCAACAGGGAGTAAA
1 CATGACCTTTGGGTCAACAGGGAGTAAA
33904 TCGGATATCG
Statistics
Matches: 82, Mismatches: 7, Indels: 11
0.82 0.07 0.11
Matches are distributed among these distances:
28 24 0.29
31 2 0.02
33 1 0.01
36 55 0.67
ACGTcount: A:0.31, C:0.16, G:0.30, T:0.23
Consensus pattern (36 bp):
CATGACCTTTGGGTCAACAGGGAGTAAAATGAGCAT
Found at i:33879 original size:28 final size:28
Alignment explanation
Indices: 33848--33902 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
33838 AAATGAGCAT
33848 CATGACCTTTGGGTCAACAGAGAGTAAG
1 CATGACCTTTGGGTCAACAGAGAGTAAG
*
33876 CATGACCTTTGGGTCAACAGGGAGTAA
1 CATGACCTTTGGGTCAACAGAGAGTAA
33903 ATCGGATATC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.31, C:0.18, G:0.29, T:0.22
Consensus pattern (28 bp):
CATGACCTTTGGGTCAACAGAGAGTAAG
Found at i:35862 original size:13 final size:12
Alignment explanation
Indices: 35831--35870 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
35821 TATTATTTAG
*
35831 AAATAGAAAAAA
1 AAATTGAAAAAA
*
35843 AAGTTGAAAAGAA
1 AAATTGAAAA-AA
35856 AAATTGAAAAAA
1 AAATTGAAAAAA
35868 AAA
1 AAA
35871 AGGAAAATTG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
12 13 0.54
13 11 0.46
ACGTcount: A:0.75, C:0.00, G:0.12, T:0.12
Consensus pattern (12 bp):
AAATTGAAAAAA
Found at i:35871 original size:13 final size:13
Alignment explanation
Indices: 35837--35871 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
35827 TTAGAAATAG
*
35837 AAAAAAAAGTTGA
1 AAAAAAAAATTGA
*
35850 AAAGAAAAATTGA
1 AAAAAAAAATTGA
35863 AAAAAAAAA
1 AAAAAAAAA
35872 GGAAAATTGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.77, C:0.00, G:0.11, T:0.11
Consensus pattern (13 bp):
AAAAAAAAATTGA
Found at i:35877 original size:19 final size:20
Alignment explanation
Indices: 35849--35894 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 20
35839 AAAAAAGTTG
35849 AAAAGAAAAATTGA-AAAAA
1 AAAAGAAAAATTGAGAAAAA
*
35868 AAAAGGAAAATTGAGAAAAA
1 AAAAGAAAAATTGAGAAAAA
*
35888 AAGAGAA
1 AAAAGAA
35895 GAAAAAGACA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 13 0.57
20 10 0.43
ACGTcount: A:0.74, C:0.00, G:0.17, T:0.09
Consensus pattern (20 bp):
AAAAGAAAAATTGAGAAAAA
Found at i:42853 original size:19 final size:20
Alignment explanation
Indices: 42811--42853 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
42801 ACTGCATGTT
*
42811 AATTTTTTAAAATTTTTATG
1 AATTTTTTAAAAATTTTATG
42831 -ATTTTTTAAAAATTTT-TG
1 AATTTTTTAAAAATTTTATG
42849 AATTT
1 AATTT
42854 GAATTTTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 2 0.10
19 19 0.90
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (20 bp):
AATTTTTTAAAAATTTTATG
Found at i:54042 original size:26 final size:26
Alignment explanation
Indices: 54006--54056 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
53996 AATCAGATTG
*
54006 TATTTTATTTTTTCTATTAAAAAATA
1 TATTTTATTTTCTCTATTAAAAAATA
54032 TATTTTATTTTCTCTATTAAAAAAT
1 TATTTTATTTTCTCTATTAAAAAAT
54057 GGGCAAGTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.57
Consensus pattern (26 bp):
TATTTTATTTTCTCTATTAAAAAATA
Found at i:59540 original size:23 final size:22
Alignment explanation
Indices: 59509--59552 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
59499 TGATTTCCTA
*
59509 TAAGAAGAAATAAGGACGGTGAC
1 TAAGAAGAAATAAAG-CGGTGAC
*
59532 TAAGGAGAAATAAAGCGGTGA
1 TAAGAAGAAATAAAGCGGTGA
59553 GTGAGAAAGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.48, C:0.07, G:0.32, T:0.14
Consensus pattern (22 bp):
TAAGAAGAAATAAAGCGGTGAC
Found at i:64849 original size:20 final size:20
Alignment explanation
Indices: 64813--64862 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
64803 TCATAAGGCT
*
64813 TTAATTAATCACTTTTAATC
1 TTAATTAAACACTTTTAATC
*
64833 TTAATTAAAC-CTATTTACTC
1 TTAATTAAACACT-TTTAATC
64853 TTAATATAAA
1 TTAAT-TAAA
64863 TCAAGCTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 2 0.08
20 20 0.77
21 4 0.15
ACGTcount: A:0.40, C:0.14, G:0.00, T:0.46
Consensus pattern (20 bp):
TTAATTAAACACTTTTAATC
Found at i:65514 original size:20 final size:20
Alignment explanation
Indices: 65478--65527 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
65468 TCATTAGGCT
*
65478 TTAATTAATCACTTTTAATC
1 TTAATTAAACACTTTTAATC
*
65498 TTAATTAAAC-CTATTTACTC
1 TTAATTAAACACT-TTTAATC
65518 TTAATATAAA
1 TTAAT-TAAA
65528 TCATGCTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 2 0.08
20 20 0.77
21 4 0.15
ACGTcount: A:0.40, C:0.14, G:0.00, T:0.46
Consensus pattern (20 bp):
TTAATTAAACACTTTTAATC
Found at i:74965 original size:30 final size:31
Alignment explanation
Indices: 74909--74970 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
74899 AAATTTAAAG
*
74909 TCTAAAATTTCAAAACTAACATATCTAAATT
1 TCTAAAAATTCAAAACTAACATATCTAAATT
*
74940 TCTAAAAATTCAAAAC-AATATATCTAAATT
1 TCTAAAAATTCAAAACTAACATATCTAAATT
74970 T
1 T
74971 TGCTATTTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 14 0.48
31 15 0.52
ACGTcount: A:0.50, C:0.15, G:0.00, T:0.35
Consensus pattern (31 bp):
TCTAAAAATTCAAAACTAACATATCTAAATT
Found at i:75054 original size:21 final size:22
Alignment explanation
Indices: 75028--75105 Score: 70
Period size: 21 Copynumber: 3.5 Consensus size: 22
75018 TTTTAAGGTT
*
75028 TTTTAAATTATAGTTTTGG-TA
1 TTTTAAATTATAGTTTAGGATA
* **
75049 TTTTAAATAAGGGTTTAGGATA
1 TTTTAAATTATAGTTTAGGATA
*
75071 TTTTAAATTAATAGTTATAGAATA
1 TTTTAAATT-ATAGTT-TAGGATA
75095 TATTT-AATTAT
1 T-TTTAAATTAT
75106 TTTATTTTTA
Statistics
Matches: 45, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
21 15 0.33
22 10 0.22
23 6 0.13
24 11 0.24
25 3 0.07
ACGTcount: A:0.37, C:0.00, G:0.13, T:0.50
Consensus pattern (22 bp):
TTTTAAATTATAGTTTAGGATA
Found at i:86759 original size:18 final size:18
Alignment explanation
Indices: 86736--86783 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
86726 ACAATTCATA
86736 TCACTTTCAATTCCAATT
1 TCACTTTCAATTCCAATT
* * * *
86754 TCACTTCCACTTTCACTT
1 TCACTTTCAATTCCAATT
86772 TCACTTTCAATT
1 TCACTTTCAATT
86784 TTGATCACAA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.23, C:0.31, G:0.00, T:0.46
Consensus pattern (18 bp):
TCACTTTCAATTCCAATT
Found at i:86764 original size:6 final size:6
Alignment explanation
Indices: 86736--86780 Score: 54
Period size: 6 Copynumber: 7.5 Consensus size: 6
86726 ACAATTCATA
* * * *
86736 TCACTT TCAATT CCAATT TCACTT CCACTT TCACTT TCACTT TCA
1 TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCA
86781 ATTTTGATCA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.22, C:0.33, G:0.00, T:0.44
Consensus pattern (6 bp):
TCACTT
Found at i:86776 original size:12 final size:12
Alignment explanation
Indices: 86737--86780 Score: 61
Period size: 12 Copynumber: 3.7 Consensus size: 12
86727 CAATTCATAT
*
86737 CACTTTCAATTC
1 CACTTTCACTTC
*
86749 CAATTTCACTTC
1 CACTTTCACTTC
*
86761 CACTTTCACTTT
1 CACTTTCACTTC
86773 CACTTTCA
1 CACTTTCA
86781 ATTTTGATCA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.23, C:0.34, G:0.00, T:0.43
Consensus pattern (12 bp):
CACTTTCACTTC
Found at i:90567 original size:17 final size:17
Alignment explanation
Indices: 90535--90581 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 17
90525 CCAATTTTAG
* *
90535 ATTTTAAATTTTAATTC
1 ATTTTAAGTTTAAATTC
*
90552 ATTTTAAGTTTAAATTT
1 ATTTTAAGTTTAAATTC
*
90569 ATTGTAAGTTTAA
1 ATTTTAAGTTTAA
90582 GCTTATTTGG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.36, C:0.02, G:0.06, T:0.55
Consensus pattern (17 bp):
ATTTTAAGTTTAAATTC
Found at i:90604 original size:17 final size:18
Alignment explanation
Indices: 90547--90606 Score: 63
Period size: 17 Copynumber: 3.5 Consensus size: 18
90537 TTTAAATTTT
*
90547 AATTCATTT-TAAGTTTA
1 AATTTATTTGTAAGTTTA
90564 AATTTA-TTGTAAGTTTA
1 AATTTATTTGTAAGTTTA
** *
90581 AGCTTATTTG-GAGTTTA
1 AATTTATTTGTAAGTTTA
90598 AATTTATTT
1 AATTTATTT
90607 TGAAATAAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
16 2 0.06
17 30 0.86
18 3 0.09
ACGTcount: A:0.32, C:0.03, G:0.12, T:0.53
Consensus pattern (18 bp):
AATTTATTTGTAAGTTTA
Found at i:91569 original size:18 final size:18
Alignment explanation
Indices: 91536--91580 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
91526 GAAGGTATTA
** *
91536 AAAAATGAAATGGATTTG
1 AAAAATGAAACAGATTCG
91554 AAAAATGAAACAGATTCG
1 AAAAATGAAACAGATTCG
91572 -AAAATGAAA
1 AAAAATGAAA
91581 GGCAGATATG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
17 9 0.38
18 15 0.62
ACGTcount: A:0.58, C:0.04, G:0.18, T:0.20
Consensus pattern (18 bp):
AAAAATGAAACAGATTCG
Found at i:92346 original size:30 final size:30
Alignment explanation
Indices: 92320--92596 Score: 131
Period size: 29 Copynumber: 9.5 Consensus size: 30
92310 CAAACTTTTT
92320 AAAAATTACATTTTAACTCTCGAACTTTCC
1 AAAAATTACATTTTAACTCTCGAACTTTCC
* *
92350 AAAAATTACCATTTT-GCTC-CCAGAC-TTCAC
1 AAAAATTA-CATTTTAACTCTCGA-ACTTTC-C
92380 AAAAATTACATTTTTAAC-CTCGAAC-TTCC
1 AAAAATTACA-TTTTAACTCTCGAACTTTCC
* * *
92409 AAAAAATACATTTT-ACCCCCGAA-TTTCC
1 AAAAATTACATTTTAACTCTCGAACTTTCC
* * * *
92437 AAAAAATCCTATTTT-AC-CCCAAAAC-TTCC
1 AAAAATTAC-ATTTTAACTCTC-GAACTTTCC
* *
92466 AAAAATAACCA-TTT-ACCCTCGAA-TTTCC
1 AAAAATTA-CATTTTAACTCTCGAACTTTCC
* * * * **
92494 AAAAATTCCATTTTTGACACT-AAACTTTTT
1 AAAAATTACA-TTTTAACTCTCGAACTTTCC
* *
92524 GAAAATTACCATTTT-AC-CCCGAA-TTTCC
1 AAAAATTA-CATTTTAACTCTCGAACTTTCC
* * * *
92552 AAAAATTCCATTTTGAC-CCCAAACTTTCC
1 AAAAATTACATTTTAACTCTCGAACTTTCC
92581 AAAAATTACAATTTTA
1 AAAAATTAC-ATTTTA
92597 CCCCGGACAT
Statistics
Matches: 194, Mismatches: 30, Indels: 46
0.72 0.11 0.17
Matches are distributed among these distances:
27 10 0.05
28 58 0.30
29 60 0.31
30 55 0.28
31 11 0.06
ACGTcount: A:0.38, C:0.26, G:0.04, T:0.33
Consensus pattern (30 bp):
AAAAATTACATTTTAACTCTCGAACTTTCC
Found at i:92411 original size:29 final size:28
Alignment explanation
Indices: 92320--92614 Score: 172
Period size: 28 Copynumber: 10.2 Consensus size: 28
92310 CAAACTTTTT
*
92320 AAAAATTACATTTTAACTCTCGAACTTTCC
1 AAAAATTACATTTTAAC-CCCGAAC-TTCC
*
92350 AAAAATTACCATTTT-GCTCCC-AGACTTCAC
1 AAAAATTA-CATTTTAAC-CCCGA-ACTTC-C
*
92380 AAAAATTACATTTTTAACCTCGAACTTCC
1 AAAAATTACA-TTTTAACCCCGAACTTCC
* * *
92409 AAAAAATACATTTTACCCCCGAATTTCC
1 AAAAATTACATTTTAACCCCGAACTTCC
* * *
92437 AAAAAATCCTATTTT-ACCCCAAAACTTCC
1 AAAAATTAC-ATTTTAACCCC-GAACTTCC
* *
92466 AAAAATAACCA-TTT-ACCCTCGAATTTCC
1 AAAAATTA-CATTTTAACCC-CGAACTTCC
* * * ** **
92494 AAAAATTCCATTTTTGACACTAAACTTTTT
1 AAAAATTACA-TTTTAACCCCGAAC-TTCC
* *
92524 GAAAATTACCATTTT-ACCCCGAATTTCC
1 AAAAATTA-CATTTTAACCCCGAACTTCC
* * *
92552 AAAAATTCCATTTTGACCCCAAACTTTCC
1 AAAAATTACATTTTAACCCCGAAC-TTCC
* *
92581 AAAAATTACAATTTT-ACCCCGGACATCC
1 AAAAATTAC-ATTTTAACCCCGAACTTCC
92609 AAAAAT
1 AAAAAT
92615 CGCATTTTTT
Statistics
Matches: 206, Mismatches: 41, Indels: 38
0.72 0.14 0.13
Matches are distributed among these distances:
27 8 0.04
28 70 0.34
29 63 0.31
30 55 0.27
31 10 0.05
ACGTcount: A:0.38, C:0.26, G:0.04, T:0.32
Consensus pattern (28 bp):
AAAAATTACATTTTAACCCCGAACTTCC
Found at i:92601 original size:57 final size:58
Alignment explanation
Indices: 92342--92623 Score: 267
Period size: 57 Copynumber: 4.9 Consensus size: 58
92332 TTAACTCTCG
* * * * * *
92342 AACTTTCCAAAAATTACCATTTTGCTCCC-AGACTTCACAAAAATTACATTTTTAACCTCG
1 AACTTTCCAAAAATTACCATTTTAC-CCCGA-ATTTC-CAAAAATTCCATTTTTGACCCCA
* *
92402 AAC-TTCCAAAAAATA-CATTTTACCCCCGAATTTCCAAAAAATCC-TATTTT-ACCCCAA
1 AACTTTCCAAAAATTACCATTTTA-CCCCGAATTTCCAAAAATTCCAT-TTTTGACCCC-A
* * *
92459 AAC-TTCCAAAAATAACCA-TTTACCCTCGAATTTCCAAAAATTCCATTTTTGACACTA
1 AACTTTCCAAAAATTACCATTTTACCC-CGAATTTCCAAAAATTCCATTTTTGACCCCA
***
92516 AACTTTTTGAAAATTACCATTTTACCCCGAATTTCCAAAAATTCCA-TTTTGACCCCA
1 AACTTTCCAAAAATTACCATTTTACCCCGAATTTCCAAAAATTCCATTTTTGACCCCA
* * **
92573 AACTTTCCAAAAATTACAATTTTACCCCGGACATCCAAAAA-TCGCATTTTT
1 AACTTTCCAAAAATTACCATTTTACCCCGAATTTCCAAAAATTC-CATTTTT
92624 TTACTCTGTT
Statistics
Matches: 185, Mismatches: 25, Indels: 26
0.78 0.11 0.11
Matches are distributed among these distances:
56 10 0.05
57 99 0.54
58 53 0.29
59 20 0.11
60 3 0.02
ACGTcount: A:0.37, C:0.27, G:0.04, T:0.32
Consensus pattern (58 bp):
AACTTTCCAAAAATTACCATTTTACCCCGAATTTCCAAAAATTCCATTTTTGACCCCA
Found at i:95542 original size:16 final size:17
Alignment explanation
Indices: 95505--95548 Score: 56
Period size: 16 Copynumber: 2.7 Consensus size: 17
95495 TATGAAAATT
*
95505 ATTTATATAATATATAA
1 ATTTATATAAAATATAA
95522 A-TTATATAAAATA-AA
1 ATTTATATAAAATATAA
*
95537 ATTTATTTAAAA
1 ATTTATATAAAA
95549 AAGGAAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 3 0.12
16 20 0.83
17 1 0.04
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
ATTTATATAAAATATAA
Found at i:95589 original size:17 final size:19
Alignment explanation
Indices: 95559--95597 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
95549 AAGGAAAAAT
*
95559 AAAAATTTTAAAATA-ATA
1 AAAAATTCTAAAATATATA
95577 AAAAATTCT-AAATATATA
1 AAAAATTCTAAAATATATA
95595 AAA
1 AAA
95598 GTATAGAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (19 bp):
AAAAATTCTAAAATATATA
Found at i:98894 original size:57 final size:57
Alignment explanation
Indices: 98801--98996 Score: 180
Period size: 57 Copynumber: 3.2 Consensus size: 57
98791 ATCACTTTAA
* *
98801 TATTAAATTAATATAATACTTATCAAGATAAATATTAGATTAAATTTAATATTAATTCT
1 TATTAAATTAATAAAATAC-TAT-AAGATAAATATTAAATTAAATTTAATATTAATTCT
*
98860 TATTAAATTAATAAAA-ATCTATAAGATAAATATTAAATTATATTTAATATTAAGATAATCACTT
1 TATTAAATTAATAAAATA-CTATAAGATAAATATTAAATTAAATTTAATATT-A-AT--T--C-T
* * * *
98924 TAATATAAAATTAATAAAATGCTATTAAGATAAGTATTAAATTTAATTTAATATTAAATC-
1 T-AT-T-AAATTAATAAAATACTA-TAAGATAAATATTAAATTAAATTTAATATTAATTCT
*
98984 TATTAAAATAATA
1 TATTAAATTAATA
98997 TTATTTTTGA
Statistics
Matches: 115, Mismatches: 9, Indels: 28
0.76 0.06 0.18
Matches are distributed among these distances:
57 35 0.30
58 6 0.05
59 20 0.17
60 1 0.01
61 1 0.01
62 1 0.01
63 1 0.01
64 3 0.03
65 2 0.02
66 2 0.02
67 16 0.14
68 27 0.23
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.41
Consensus pattern (57 bp):
TATTAAATTAATAAAATACTATAAGATAAATATTAAATTAAATTTAATATTAATTCT
Found at i:98996 original size:68 final size:67
Alignment explanation
Indices: 98864--98997 Score: 157
Period size: 68 Copynumber: 2.0 Consensus size: 67
98854 AATTCTTATT
***
98864 AAATTAATAAAAATCTATAAGATAAATATTAAATTATATTTAATATTAAGATAATCACTTTAATA
1 AAATTAATAAAAATCTATAAGATAAATATTAAATTATATTTAATATTAAGATAATCAAAATAATA
98929 TA
66 TA
* * *
98931 AAATTAAT-AAAATGCTATTAAGATAAGTATTAAATT-TAATTTAATATTAA-ATCTATTAAAAT
1 AAATTAATAAAAAT-CTA-TAAGATAAATATTAAATTAT-ATTTAATATTAAGAT-AATCAAAAT
98993 AATAT
62 AATAT
98998 TATTTTTGAA
Statistics
Matches: 57, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
66 5 0.09
67 14 0.25
68 38 0.67
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.40
Consensus pattern (67 bp):
AAATTAATAAAAATCTATAAGATAAATATTAAATTATATTTAATATTAAGATAATCAAAATAATA
TA
Found at i:99436 original size:18 final size:19
Alignment explanation
Indices: 99407--99448 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
99397 AAAATATCAT
*
99407 ATTAATTTTAATTAATTTG
1 ATTAATTTTAATTAACTTG
*
99426 ATTAA-TTTAATTTACTTG
1 ATTAATTTTAATTAACTTG
99444 ATTAA
1 ATTAA
99449 AATTAATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 16 0.76
19 5 0.24
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.55
Consensus pattern (19 bp):
ATTAATTTTAATTAACTTG
Found at i:105434 original size:41 final size:41
Alignment explanation
Indices: 105377--105459 Score: 148
Period size: 41 Copynumber: 2.0 Consensus size: 41
105367 TTGTGATAAG
*
105377 ATGTTGAGGCTAACAATGGACAAAAGCCATGAGACAAGGGC
1 ATGTTGAGGCTAACAATGGACAAAAGCCATGAGACAAAGGC
*
105418 ATGTTGAGGCTAACAATGGACAAAAGCCATGAGGCAAAGGC
1 ATGTTGAGGCTAACAATGGACAAAAGCCATGAGACAAAGGC
105459 A
1 A
105460 CAATCTTGTT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.40, C:0.17, G:0.29, T:0.14
Consensus pattern (41 bp):
ATGTTGAGGCTAACAATGGACAAAAGCCATGAGACAAAGGC
Found at i:106158 original size:33 final size:33
Alignment explanation
Indices: 106121--106187 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
106111 GGTGAAGTAT
106121 AATAATTCTCTAATTTGAGAATTATGACTACAG
1 AATAATTCTCTAATTTGAGAATTATGACTACAG
106154 AATAATTCTCTAATTTGAGAATTATGACTACAG
1 AATAATTCTCTAATTTGAGAATTATGACTACAG
106187 A
1 A
106188 TGAAGACAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.36
Consensus pattern (33 bp):
AATAATTCTCTAATTTGAGAATTATGACTACAG
Found at i:106402 original size:20 final size:20
Alignment explanation
Indices: 106361--106402 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
106351 AAATTCCTCT
*
106361 TTTTCTCTTGTTTGAGAGTA
1 TTTTCTCTTGTTTGAGACTA
106381 TTTTCTCTTGTATT-AGACTA
1 TTTTCTCTTGT-TTGAGACTA
106401 TT
1 TT
106403 AGGTAGGTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 18 0.90
21 2 0.10
ACGTcount: A:0.17, C:0.12, G:0.14, T:0.57
Consensus pattern (20 bp):
TTTTCTCTTGTTTGAGACTA
Found at i:107005 original size:14 final size:14
Alignment explanation
Indices: 106969--107014 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
106959 AAATAATTTT
106969 AATT-TAAATTAAA
1 AATTATAAATTAAA
*
106982 AA-AATAAATTAAA
1 AATTATAAATTAAA
*
106995 AATTATCAATTAAA
1 AATTATAAATTAAA
*
107009 ATTTAT
1 AATTAT
107015 TATTAAATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
13 13 0.48
14 14 0.52
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (14 bp):
AATTATAAATTAAA
Found at i:107223 original size:23 final size:24
Alignment explanation
Indices: 107197--107247 Score: 77
Period size: 23 Copynumber: 2.2 Consensus size: 24
107187 CGTGGTAAAA
* *
107197 TAATTTTTTTAACAATTACATT-T
1 TAATTTTCTTAACAATCACATTCT
107220 TAATTTTCTTAACAATCACATTCT
1 TAATTTTCTTAACAATCACATTCT
107244 TAAT
1 TAAT
107248 AATCACATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 20 0.80
24 5 0.20
ACGTcount: A:0.35, C:0.14, G:0.00, T:0.51
Consensus pattern (24 bp):
TAATTTTCTTAACAATCACATTCT
Found at i:107245 original size:15 final size:15
Alignment explanation
Indices: 107225--107256 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
107215 CATTTTAATT
107225 TTCTTAACAATCACA
1 TTCTTAACAATCACA
*
107240 TTCTTAATAATCACA
1 TTCTTAACAATCACA
107255 TT
1 TT
107257 TCATTAGAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.38, C:0.22, G:0.00, T:0.41
Consensus pattern (15 bp):
TTCTTAACAATCACA
Done.