Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012775.1 Kokia drynarioides strain JFW-HI SEQ_127787, 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: 89748
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:503 original size:30 final size:30
Alignment explanation
Indices: 481--779 Score: 310
Period size: 30 Copynumber: 10.1 Consensus size: 30
471 TTTGGGAAAA
*
481 TTCGGGGTTAAAAATGGGATTTTTGAAAGT
1 TTCGGGGTTAAAAATGGGATTTTTGGAAGT
511 TT-GAGGG-T-AAAATGGGATTTTTGGAAGT
1 TTCG-GGGTTAAAAATGGGATTTTTGGAAGT
*
539 TTTGGGGTTAAAAATGGGATTTTTGGAAGT
1 TTCGGGGTTAAAAATGGGATTTTTGGAAGT
** *
569 TT-GAGGG-TAAAAATGAAATTTTTTTGAAGT
1 TTCG-GGGTTAAAAATGGGA-TTTTTGGAAGT
* *
599 TTCGAGGTTAAAAATGGGGTTTTTGGAAGT
1 TTCGGGGTTAAAAATGGGATTTTTGGAAGT
*
629 TTAGGGG-TAAAAATGGGATTTTTGGAAGT
1 TTCGGGGTTAAAAATGGGATTTTTGGAAGT
* ***
658 TTCGGGGTCAAAAATGGGATTTTTTTTA-T
1 TTCGGGGTTAAAAATGGGATTTTTGGAAGT
* * *
687 GTTCGAGGG-TAAAATTAGAATTTTTGGAAGT
1 -TTCG-GGGTTAAAAATGGGATTTTTGGAAGT
* *
718 TTTGGGGTCAAAAATGGGATTTTTGGAAG-
1 TTCGGGGTTAAAAATGGGATTTTTGGAAGT
* *
747 TTCGGGGGTAAAAATGGAATTTTTGGATAGT
1 TTCGGGGTTAAAAATGGGATTTTTGGA-AGT
778 TT
1 TT
780 AAGGACCTTC
Statistics
Matches: 221, Mismatches: 33, Indels: 29
0.78 0.12 0.10
Matches are distributed among these distances:
28 24 0.11
29 68 0.31
30 114 0.52
31 15 0.07
ACGTcount: A:0.29, C:0.02, G:0.31, T:0.38
Consensus pattern (30 bp):
TTCGGGGTTAAAAATGGGATTTTTGGAAGT
Found at i:622 original size:60 final size:59
Alignment explanation
Indices: 481--779 Score: 377
Period size: 60 Copynumber: 5.0 Consensus size: 59
471 TTTGGGAAAA
* *
481 TTCGGGGTTAAAAATGGGATTTTTGAAAGTTTGAGGGT-AAAATGGGATTTTTGGAAGT
1 TTCGGGGTTAAAAATGGGATTTTTGGAAGTTTGAGGGTAAAAATGGAATTTTTGGAAGT
* * *
539 TTTGGGGTTAAAAATGGGATTTTTGGAAGTTTGAGGGTAAAAATGAAATTTTTTTGAAGT
1 TTCGGGGTTAAAAATGGGATTTTTGGAAGTTTGAGGGTAAAAATGGAA-TTTTTGGAAGT
* * *
599 TTCGAGGTTAAAAATGGGGTTTTTGGAAGTTT-AGGGGTAAAAATGGGATTTTTGGAAGT
1 TTCGGGGTTAAAAATGGGATTTTTGGAAGTTTGA-GGGTAAAAATGGAATTTTTGGAAGT
* ** * * * *
658 TTCGGGGTCAAAAATGGGATTTTTTTTATGTTCGAGGGTAAAATTAGAATTTTTGGAAGT
1 TTCGGGGTTAAAAATGGGA-TTTTTGGAAGTTTGAGGGTAAAAATGGAATTTTTGGAAGT
* * * *
718 TTTGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAAATGGAATTTTTGGATAGT
1 TTCGGGGTTAAAAATGGGATTTTTGGAAGTTTGAGGGTAAAAATGGAATTTTTGGA-AGT
778 TT
1 TT
780 AAGGACCTTC
Statistics
Matches: 207, Mismatches: 28, Indels: 10
0.84 0.11 0.04
Matches are distributed among these distances:
58 36 0.17
59 65 0.31
60 105 0.51
61 1 0.00
ACGTcount: A:0.29, C:0.02, G:0.31, T:0.38
Consensus pattern (59 bp):
TTCGGGGTTAAAAATGGGATTTTTGGAAGTTTGAGGGTAAAAATGGAATTTTTGGAAGT
Found at i:642 original size:89 final size:88
Alignment explanation
Indices: 484--770 Score: 359
Period size: 89 Copynumber: 3.2 Consensus size: 88
474 GGGAAAATTC
*
484 GGGGTTAAAAATGGGA--TTTTTGAAAGTTT-GAGGGT-AAAATGGGATTTTTGGAAGTTTTGGG
1 GGGG-TAAAAATGGAATTTTTTTG-AAGTTTCGAGGGTAAAAATGGGATTTTTGGAAGTTTTGGG
545 GTTAAAAATGGGATTTTTGGAAGTTT
64 G-TAAAAATGGGATTTTTGGAAGTTT
* * * *
571 GAGGGTAAAAATGAAATTTTTTTGAAGTTTCGAGGTTAAAAATGGGGTTTTTGGAAGTTTAGGGG
1 G-GGGTAAAAATGGAATTTTTTTGAAGTTTCGAGGGTAAAAATGGGATTTTTGGAAGTTTTGGGG
636 TAAAAATGGGATTTTTGGAAGTTT
65 TAAAAATGGGATTTTTGGAAGTTT
* * * * * *
660 CGGGGTCAAAAATGGGATTTTTTTTATG-TTCGAGGGTAAAATTAGAATTTTTGGAAGTTTTGGG
1 -GGGGT-AAAAATGGAATTTTTTTGAAGTTTCGAGGGTAAAAATGGGATTTTTGGAAGTTTTGGG
*
724 GTCAAAAATGGGATTTTTGGAAGTTCG
64 GT-AAAAATGGGATTTTTGGAAGTT-T
751 GGGGTAAAAATGGAATTTTT
1 GGGGTAAAAATGGAATTTTT
771 GGATAGTTTA
Statistics
Matches: 174, Mismatches: 17, Indels: 16
0.84 0.08 0.08
Matches are distributed among these distances:
87 10 0.06
88 9 0.05
89 85 0.49
90 70 0.40
ACGTcount: A:0.30, C:0.02, G:0.31, T:0.37
Consensus pattern (88 bp):
GGGGTAAAAATGGAATTTTTTTGAAGTTTCGAGGGTAAAAATGGGATTTTTGGAAGTTTTGGGGT
AAAAATGGGATTTTTGGAAGTTT
Found at i:2732 original size:6 final size:6
Alignment explanation
Indices: 2718--2781 Score: 64
Period size: 6 Copynumber: 11.2 Consensus size: 6
2708 ATTTGGAAAA
* *
2718 TAAATT TAAACT TAAA-T TAAATT TAAATT CGAAA-- TAAATT TAAATT
1 TAAATT TAAATT TAAATT TAAATT TAAATT -TAAATT TAAATT TAAATT
*
2764 T-AATA TAAATT TAAATT T
1 TAAATT TAAATT TAAATT T
2782 CTAAACAAAT
Statistics
Matches: 48, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
4 3 0.06
5 9 0.19
6 33 0.69
7 3 0.06
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.44
Consensus pattern (6 bp):
TAAATT
Found at i:2758 original size:34 final size:35
Alignment explanation
Indices: 2704--2813 Score: 125
Period size: 35 Copynumber: 3.1 Consensus size: 35
2694 TATAATAATC
*
2704 TTAAATTTGGAAAATAAATTTAAACTTAAATTAAAT
1 TTAAATTTCG-AAATAAATTTAAACTTAAATTAAAT
*
2740 TTAAA-TTCGAAATAAATTTAAA-TTTAATATAAAT
1 TTAAATTTCGAAATAAATTTAAACTTAAAT-TAAAT
* * ** *
2774 TTAAATTTCTAAACAAATTTATTCTTAAAATAAAT
1 TTAAATTTCGAAATAAATTTAAACTTAAATTAAAT
2809 TTAAA
1 TTAAA
2814 GGTAGTTTGG
Statistics
Matches: 63, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
33 5 0.08
34 23 0.37
35 26 0.41
36 9 0.14
ACGTcount: A:0.52, C:0.05, G:0.03, T:0.41
Consensus pattern (35 bp):
TTAAATTTCGAAATAAATTTAAACTTAAATTAAAT
Found at i:2781 original size:17 final size:16
Alignment explanation
Indices: 2686--2813 Score: 98
Period size: 17 Copynumber: 7.4 Consensus size: 16
2676 CCTTATTTAT
2686 TTTAAATTTATAAT-AA
1 TTTAAATTTA-AATAAA
2702 TCTTAAATTTGGAAAATAAA
1 T-TTAAATTT---AAATAAA
*
2722 TTTAAACTTAAATTAAA
1 TTTAAATTTAAA-TAAA
*
2739 TTTAAATTCGAAATAAA
1 TTTAAATT-TAAATAAA
2756 TTTAAATTTAATATAAA
1 TTTAAATTTAA-ATAAA
*
2773 TTTAAATTTCTAAACAAA
1 TTTAAA-TT-TAAATAAA
*
2791 TTT-ATTCTTAAAATAAA
1 TTTAAAT-TT-AAATAAA
2808 TTTAAA
1 TTTAAA
2814 GGTAGTTTGG
Statistics
Matches: 91, Mismatches: 8, Indels: 24
0.74 0.07 0.20
Matches are distributed among these distances:
16 8 0.09
17 53 0.58
18 13 0.14
19 13 0.14
20 4 0.04
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.42
Consensus pattern (16 bp):
TTTAAATTTAAATAAA
Found at i:3623 original size:35 final size:34
Alignment explanation
Indices: 3577--3646 Score: 104
Period size: 35 Copynumber: 2.0 Consensus size: 34
3567 TTAAAAAAAG
* * *
3577 TCTTTATACTTGAATAATACTAAGATGGTTGCAAC
1 TCTTTATACTTGAATAACACT-AGATAGTTACAAC
3612 TCTTTATACTTGAATAACACTAGATAGTTACAAC
1 TCTTTATACTTGAATAACACTAGATAGTTACAAC
3646 T
1 T
3647 TAGCAAGCAA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
34 12 0.38
35 20 0.62
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.37
Consensus pattern (34 bp):
TCTTTATACTTGAATAACACTAGATAGTTACAAC
Found at i:3994 original size:21 final size:21
Alignment explanation
Indices: 3963--4003 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
3953 TGAGTTACTA
3963 TTTAATTATTA-AAAAATATT
1 TTTAATTATTATAAAAATATT
*
3983 TTTAATTTATTATGAAAATAT
1 TTTAA-TTATTATAAAAATAT
4004 AGAATTATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 6 0.33
22 7 0.39
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (21 bp):
TTTAATTATTATAAAAATATT
Found at i:5272 original size:27 final size:28
Alignment explanation
Indices: 5216--5272 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 28
5206 CGTACCGATC
5216 TTTGCCACAAAGGCATTTCCTTTCACCA
1 TTTGCCACAAAGGCATTTCCTTTCACCA
* *
5244 TTTGCCATAAAGGC-TTTCCTTTCATCA
1 TTTGCCACAAAGGCATTTCCTTTCACCA
5271 TT
1 TT
5273 AACAAGCTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
27 14 0.52
28 13 0.48
ACGTcount: A:0.23, C:0.28, G:0.11, T:0.39
Consensus pattern (28 bp):
TTTGCCACAAAGGCATTTCCTTTCACCA
Found at i:16706 original size:73 final size:73
Alignment explanation
Indices: 16587--16734 Score: 296
Period size: 73 Copynumber: 2.0 Consensus size: 73
16577 ATGAGGCGCC
16587 ATTCAAGTCTTTCAATTTCCTAGATGCCCTATAATTCTTGAGAGTCATCATGAGTTTTTGCCTCT
1 ATTCAAGTCTTTCAATTTCCTAGATGCCCTATAATTCTTGAGAGTCATCATGAGTTTTTGCCTCT
16652 AGCCTTCA
66 AGCCTTCA
16660 ATTCAAGTCTTTCAATTTCCTAGATGCCCTATAATTCTTGAGAGTCATCATGAGTTTTTGCCTCT
1 ATTCAAGTCTTTCAATTTCCTAGATGCCCTATAATTCTTGAGAGTCATCATGAGTTTTTGCCTCT
16725 AGCCTTCA
66 AGCCTTCA
16733 AT
1 AT
16735 CCCTGCAAAT
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
73 75 1.00
ACGTcount: A:0.24, C:0.23, G:0.14, T:0.40
Consensus pattern (73 bp):
ATTCAAGTCTTTCAATTTCCTAGATGCCCTATAATTCTTGAGAGTCATCATGAGTTTTTGCCTCT
AGCCTTCA
Found at i:28782 original size:23 final size:20
Alignment explanation
Indices: 28759--28809 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
28749 CATTAGATTA
28759 AATTAATTAAAAATTAAAGCTT
1 AATTAATTAAAAATT-AAG-TT
* *
28781 AATTAAAT-ATAATTAAGTT
1 AATTAATTAAAAATTAAGTT
28800 AATTAATTAA
1 AATTAATTAA
28810 GTTTACTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
19 9 0.36
20 4 0.16
21 5 0.20
22 7 0.28
ACGTcount: A:0.55, C:0.02, G:0.04, T:0.39
Consensus pattern (20 bp):
AATTAATTAAAAATTAAGTT
Found at i:29671 original size:37 final size:37
Alignment explanation
Indices: 29621--29744 Score: 116
Period size: 37 Copynumber: 3.4 Consensus size: 37
29611 TATGAAAATG
29621 ATTGAGAAATGGTATATGTATTAAATTGTAAAATGGA
1 ATTGAGAAATGGTATATGTATTAAATTGTAAAATGGA
* * ** *
29658 ATTGA-AAATTGGTACCA--TATT-AGTTGT-TCATGCTA
1 ATTGAGAAA-TGGTA-TATGTATTAAATTGTAAAATG-GA
29693 TATTGAGAAATGGTATATGTATTAAATTGTAAAATGGA
1 -ATTGAGAAATGGTATATGTATTAAATTGTAAAATGGA
29731 ATTGA-AAATTGGTA
1 ATTGAGAAA-TGGTA
29745 CCATATTAGT
Statistics
Matches: 67, Mismatches: 10, Indels: 20
0.69 0.10 0.21
Matches are distributed among these distances:
34 3 0.04
35 7 0.10
36 20 0.30
37 27 0.40
38 7 0.10
39 3 0.04
ACGTcount: A:0.40, C:0.03, G:0.20, T:0.37
Consensus pattern (37 bp):
ATTGAGAAATGGTATATGTATTAAATTGTAAAATGGA
Found at i:29698 original size:36 final size:36
Alignment explanation
Indices: 29658--29770 Score: 108
Period size: 36 Copynumber: 3.1 Consensus size: 36
29648 GTAAAATGGA
29658 ATTGAAAATTGGTACCATATTAGTTGTTCATGCTAT
1 ATTGAAAATTGGTACCATATTAGTTGTTCATGCTAT
* * ** *
29694 ATTGAGAAA-TGGTA-TATGTATTAAATTGTAAAATG-GA-
1 ATTGA-AAATTGGTACCA--TATT-AGTTGT-TCATGCTAT
29731 ATTGAAAATTGGTACCATATTAGTTGTTCATGCTAT
1 ATTGAAAATTGGTACCATATTAGTTGTTCATGCTAT
29767 ATTG
1 ATTG
29771 GATATAGTTG
Statistics
Matches: 58, Mismatches: 10, Indels: 18
0.67 0.12 0.21
Matches are distributed among these distances:
34 3 0.05
35 7 0.12
36 21 0.36
37 17 0.29
38 7 0.12
39 3 0.05
ACGTcount: A:0.35, C:0.07, G:0.19, T:0.40
Consensus pattern (36 bp):
ATTGAAAATTGGTACCATATTAGTTGTTCATGCTAT
Found at i:29740 original size:73 final size:73
Alignment explanation
Indices: 29621--29770 Score: 300
Period size: 73 Copynumber: 2.1 Consensus size: 73
29611 TATGAAAATG
29621 ATTGAGAAATGGTATATGTATTAAATTGTAAAATGGAATTGAAAATTGGTACCATATTAGTTGTT
1 ATTGAGAAATGGTATATGTATTAAATTGTAAAATGGAATTGAAAATTGGTACCATATTAGTTGTT
29686 CATGCTAT
66 CATGCTAT
29694 ATTGAGAAATGGTATATGTATTAAATTGTAAAATGGAATTGAAAATTGGTACCATATTAGTTGTT
1 ATTGAGAAATGGTATATGTATTAAATTGTAAAATGGAATTGAAAATTGGTACCATATTAGTTGTT
29759 CATGCTAT
66 CATGCTAT
29767 ATTG
1 ATTG
29771 GATATAGTTG
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
73 77 1.00
ACGTcount: A:0.37, C:0.05, G:0.19, T:0.39
Consensus pattern (73 bp):
ATTGAGAAATGGTATATGTATTAAATTGTAAAATGGAATTGAAAATTGGTACCATATTAGTTGTT
CATGCTAT
Found at i:30405 original size:2 final size:2
Alignment explanation
Indices: 30398--30429 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
30388 TAAGCTCATA
30398 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
30430 ATGGAATTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:33624 original size:17 final size:17
Alignment explanation
Indices: 33602--33640 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
33592 AGGTGGAGAA
* *
33602 CTTGTTCGTTGAGAGTT
1 CTTGTTCGTAGAGAATT
*
33619 CTTGTTTGTAGAGAATT
1 CTTGTTCGTAGAGAATT
33636 CTTGT
1 CTTGT
33641 CAAGCTGGAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.15, C:0.10, G:0.26, T:0.49
Consensus pattern (17 bp):
CTTGTTCGTAGAGAATT
Found at i:34897 original size:16 final size:15
Alignment explanation
Indices: 34876--34916 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 15
34866 TTGTTTTGAA
*
34876 TATTTTATTATTATTT
1 TATTTTAATA-TATTT
34892 TATTTTAATATATTT
1 TATTTTAATATATTT
34907 TATTATTAAT
1 TATT-TTAAT
34917 TAATAGTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 9 0.39
16 14 0.61
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (15 bp):
TATTTTAATATATTT
Found at i:37762 original size:20 final size:20
Alignment explanation
Indices: 37725--37778 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
37715 CTCCAGTGAA
* * *
37725 ACTTCTACCGGTAAAACTCC
1 ACTTCTACCGATACAACTAC
*
37745 ACTTTTACCGATACAACTAC
1 ACTTCTACCGATACAACTAC
*
37765 AGTTCTACCGATAC
1 ACTTCTACCGATAC
37779 CTTGAAGACT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.31, C:0.31, G:0.09, T:0.28
Consensus pattern (20 bp):
ACTTCTACCGATACAACTAC
Found at i:41491 original size:48 final size:45
Alignment explanation
Indices: 41431--41580 Score: 151
Period size: 48 Copynumber: 3.2 Consensus size: 45
41421 CCGAAGTACT
* *
41431 TAATAGAGGGCACATAAGTGTTGGGTAACAGAGGGCACACAAAGTGC
1 TAATAGAGGGCACACAAGTGCT--GTAACAGAGGGCACACAAAGTGC
* *
41478 TAATCAGAGGGCACACGAAGTGCTAATAACAGAGGGCACGA-AACGTGC
1 TAAT-AGAGGGCACAC-AAGTGCT-GTAACAGAGGGCAC-ACAAAGTGC
* *
41526 TAAATAGAGGGCACACACAGTGCTG-AACAGAGAGCACACACAGTGC
1 T-AATAGAGGGCACACA-AGTGCTGTAACAGAGGGCACACAAAGTGC
41572 TAATCAGAG
1 TAAT-AGAG
41581 AGCGCGCTAG
Statistics
Matches: 87, Mismatches: 9, Indels: 15
0.78 0.08 0.14
Matches are distributed among these distances:
45 4 0.05
46 21 0.24
47 5 0.06
48 47 0.54
49 10 0.11
ACGTcount: A:0.38, C:0.19, G:0.29, T:0.14
Consensus pattern (45 bp):
TAATAGAGGGCACACAAGTGCTGTAACAGAGGGCACACAAAGTGC
Found at i:41583 original size:23 final size:23
Alignment explanation
Indices: 41459--41580 Score: 135
Period size: 23 Copynumber: 5.2 Consensus size: 23
41449 TGTTGGGTAA
*
41459 CAGAGGGCACACAAAGTGCTAAT
1 CAGAGGGCACACACAGTGCTAAT
41482 CAGAGGGCACACGA-AGTGCTAAT
1 CAGAGGGCACAC-ACAGTGCTAAT
*
41505 AACAGAGGGCACGAAAC-GTGCTAAAT
1 --CAGAGGGCAC-ACACAGTGCT-AAT
41531 -AGAGGGCACACACAGTGCTGAA-
1 CAGAGGGCACACACAGTGCT-AAT
*
41553 CAGAGAGCACACACAGTGCTAAT
1 CAGAGGGCACACACAGTGCTAAT
41576 CAGAG
1 CAGAG
41581 AGCGCGCTAG
Statistics
Matches: 86, Mismatches: 4, Indels: 18
0.80 0.04 0.17
Matches are distributed among these distances:
22 5 0.06
23 60 0.70
24 1 0.01
25 16 0.19
26 4 0.05
ACGTcount: A:0.39, C:0.22, G:0.28, T:0.11
Consensus pattern (23 bp):
CAGAGGGCACACACAGTGCTAAT
Found at i:44028 original size:41 final size:41
Alignment explanation
Indices: 43933--44148 Score: 276
Period size: 41 Copynumber: 5.2 Consensus size: 41
43923 GAGTCGTAGA
* * *
43933 TCTTCCTTTTAA-ACAATCTTATGCTC-TACT-GAGTCATAAG
1 TCTTCC-TTTAATATAATCTCATGCTCAT-CTCGAGTCATGAG
*
43973 TCTTCCTTTAAATATAATCTCATGCTCATCTCGAGTCACGAG
1 TCTTCCTTT-AATATAATCTCATGCTCATCTCGAGTCATGAG
* * *
44015 TCTTCCTTTAATATAATCTCATGCTCACCCCGAGACATGAG
1 TCTTCCTTTAATATAATCTCATGCTCATCTCGAGTCATGAG
*
44056 TCTTCCTTTAATATAATCTCATGCTCATTTCGAGTCATGAG
1 TCTTCCTTTAATATAATCTCATGCTCATCTCGAGTCATGAG
* * *
44097 TCTTTCTTTAATATAATCTCATGCTCATTTCGAGACATGAG
1 TCTTCCTTTAATATAATCTCATGCTCATCTCGAGTCATGAG
44138 TCTTCCATTTA
1 TCTTCC-TTTA
44149 TACATCAAGT
Statistics
Matches: 156, Mismatches: 15, Indels: 8
0.87 0.08 0.04
Matches are distributed among these distances:
39 3 0.02
40 8 0.05
41 123 0.79
42 22 0.14
ACGTcount: A:0.26, C:0.24, G:0.11, T:0.39
Consensus pattern (41 bp):
TCTTCCTTTAATATAATCTCATGCTCATCTCGAGTCATGAG
Found at i:54769 original size:2 final size:2
Alignment explanation
Indices: 54762--54797 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
54752 ATGATGTGTT
*
54762 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
54798 AAAATGTTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:55183 original size:3 final size:3
Alignment explanation
Indices: 55175--55216 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
55165 TAGTATTAGT
*
55175 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG TTG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
55217 CTGTTGTTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.31, C:0.00, G:0.33, T:0.36
Consensus pattern (3 bp):
ATG
Found at i:55221 original size:9 final size:9
Alignment explanation
Indices: 55176--55222 Score: 58
Period size: 9 Copynumber: 5.2 Consensus size: 9
55166 AGTATTAGTA
*
55176 TGATGATGA
1 TGATGATGT
*
55185 TGATGATGA
1 TGATGATGT
*
55194 TGATGATGA
1 TGATGATGT
55203 TGATGATGT
1 TGATGATGT
*
55212 TGATGCTGT
1 TGATGATGT
55221 TG
1 TG
55223 TTTTCGTGGT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 36 1.00
ACGTcount: A:0.26, C:0.02, G:0.34, T:0.38
Consensus pattern (9 bp):
TGATGATGT
Found at i:57326 original size:2 final size:2
Alignment explanation
Indices: 57319--57348 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
57309 TATTATCAAC
57319 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
57349 AGTTAAAAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:76677 original size:16 final size:16
Alignment explanation
Indices: 76656--76688 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
76646 AACACTAGTC
76656 ACATAA-TTAAATCTTA
1 ACATAATTTAAAT-TTA
76672 ACATAATTTAAATTTA
1 ACATAATTTAAATTTA
76688 A
1 A
76689 GGATCAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.52, C:0.09, G:0.00, T:0.39
Consensus pattern (16 bp):
ACATAATTTAAATTTA
Found at i:77698 original size:13 final size:15
Alignment explanation
Indices: 77677--77716 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 15
77667 TATTGTTTTT
77677 AAACAAAATGTATA-
1 AAACAAAATGTATAC
*
77691 AAAC-AAAT-AATAC
1 AAACAAAATGTATAC
77704 AAACAAAATGTAT
1 AAACAAAATGTAT
77717 TTAAATGAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 5
0.75 0.07 0.18
Matches are distributed among these distances:
12 3 0.14
13 8 0.38
14 8 0.38
15 2 0.10
ACGTcount: A:0.65, C:0.10, G:0.05, T:0.20
Consensus pattern (15 bp):
AAACAAAATGTATAC
Found at i:79437 original size:25 final size:26
Alignment explanation
Indices: 79384--79437 Score: 67
Period size: 25 Copynumber: 2.1 Consensus size: 26
79374 GATTTAAACA
* *
79384 AAAGAAAATGTAAAGATAAAAAATCG
1 AAAGAAAATGTAAAAATAAAAAATAG
79410 AAAG-AAATG-AAAAATAAAAAGATAG
1 AAAGAAAATGTAAAAATAAAAA-ATAG
79435 AAA
1 AAA
79438 ATAAATTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 10 0.40
25 11 0.44
26 4 0.16
ACGTcount: A:0.70, C:0.02, G:0.15, T:0.13
Consensus pattern (26 bp):
AAAGAAAATGTAAAAATAAAAAATAG
Found at i:85508 original size:16 final size:16
Alignment explanation
Indices: 85487--85535 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 16
85477 ATTTGAATCC
85487 AATCCAAGCTCGAGAA
1 AATCCAAGCTCGAGAA
* * *
85503 AATCCAAACTTGAAAA
1 AATCCAAGCTCGAGAA
* *
85519 AATCTAAGTTCGAGAA
1 AATCCAAGCTCGAGAA
85535 A
1 A
85536 GCCTAAACCC
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.49, C:0.18, G:0.14, T:0.18
Consensus pattern (16 bp):
AATCCAAGCTCGAGAA
Found at i:85901 original size:31 final size:31
Alignment explanation
Indices: 85829--85904 Score: 82
Period size: 31 Copynumber: 2.4 Consensus size: 31
85819 TTAATGTGTA
* *
85829 TAATAAATATTCAAAATTAATAATTATTTGAAT
1 TAATAAAT-TT-AAAATTAATAATTATATAAAT
* *
85862 TAAAAAATTTAAATTTAATAATTATATAAA-
1 TAATAAATTTAAAATTAATAATTATATAAAT
85892 TATATAAATTTAA
1 TA-ATAAATTTAA
85905 TGATATGAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
30 2 0.05
31 26 0.70
32 2 0.05
33 7 0.19
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (31 bp):
TAATAAATTTAAAATTAATAATTATATAAAT
Done.