Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013484.1 Kokia drynarioides strain JFW-HI SEQ_128510, 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: 135263
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 136 characters in sequence are not A, C, G, or T
Found at i:1439 original size:37 final size:38
Alignment explanation
Indices: 1372--1450 Score: 97
Period size: 37 Copynumber: 2.1 Consensus size: 38
1362 GTGTCTTTAT
* **
1372 TTTACTTCGGATAGATTCGATGAGGTACTGGGTACCAC
1 TTTACTTCGGATAGATCCGATGAGACACTGGGTACCAC
* **
1410 TTTACTTCGGTTAGA-CCGATGAGACACTGGGTGTCAC
1 TTTACTTCGGATAGATCCGATGAGACACTGGGTACCAC
1447 TTTA
1 TTTA
1451 TTGCTTCGAA
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
37 21 0.60
38 14 0.40
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.33
Consensus pattern (38 bp):
TTTACTTCGGATAGATCCGATGAGACACTGGGTACCAC
Found at i:6715 original size:20 final size:19
Alignment explanation
Indices: 6692--6734 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
6682 AAAAAATAAA
6692 TTTTCATTAGTCTTTTTCTT
1 TTTTCATTAGTCTTTTT-TT
* **
6712 TTTTCTTTTTTCTTTTTTT
1 TTTTCATTAGTCTTTTTTT
6731 TTTT
1 TTTT
6735 TAATTTCAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.05, C:0.12, G:0.02, T:0.81
Consensus pattern (19 bp):
TTTTCATTAGTCTTTTTTT
Found at i:6716 original size:7 final size:7
Alignment explanation
Indices: 6704--6735 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
6694 TTCATTAGTC
6704 TTTTTCT
1 TTTTTCT
6711 TTTTTCT
1 TTTTTCT
6718 TTTTTCT
1 TTTTTCT
6725 TTTTT-T
1 TTTTTCT
6731 TTTTT
1 TTTTT
6736 AATTTCAAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 6 0.24
7 19 0.76
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (7 bp):
TTTTTCT
Found at i:11918 original size:3 final size:3
Alignment explanation
Indices: 11910--11935 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
11900 GGCTTCGTGG
11910 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
11936 TATGGAAATA
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:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:34065 original size:114 final size:114
Alignment explanation
Indices: 33865--34093 Score: 440
Period size: 114 Copynumber: 2.0 Consensus size: 114
33855 CAATAACTTG
33865 TTCACATCTCCCAAGGATGGAAAACTTTTAAATGAAAGGATTTGCTTATGACTAATAAAGGTTTT
1 TTCACATCTCCCAAGGATGGAAAACTTTTAAATGAAAGGATTTGCTTATGACTAATAAAGGTTTT
33930 GTCCATAAAAAAAGAATAACACCCAATACAAGTTTCAACGCCTCAACGT
66 GTCCATAAAAAAAGAATAACACCCAATACAAGTTTCAACGCCTCAACGT
33979 TTCACATCTCCCAAGGATGGAAAACTTTTAAATGAAAGGATTTGCTTATGACTAATAAAGGTTTT
1 TTCACATCTCCCAAGGATGGAAAACTTTTAAATGAAAGGATTTGCTTATGACTAATAAAGGTTTT
* *
34044 GTCCATAGAAAAAGAATAACACCCAATACAAGTTTTAACGCCTCAACGT
66 GTCCATAAAAAAAGAATAACACCCAATACAAGTTTCAACGCCTCAACGT
34093 T
1 T
34094 AAACTTCATG
Statistics
Matches: 113, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
114 113 1.00
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.28
Consensus pattern (114 bp):
TTCACATCTCCCAAGGATGGAAAACTTTTAAATGAAAGGATTTGCTTATGACTAATAAAGGTTTT
GTCCATAAAAAAAGAATAACACCCAATACAAGTTTCAACGCCTCAACGT
Found at i:36537 original size:2 final size:2
Alignment explanation
Indices: 36532--36559 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
36522 CATTGTCATA
36532 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
36560 ACACACACAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:45897 original size:51 final size:51
Alignment explanation
Indices: 45780--45965 Score: 239
Period size: 52 Copynumber: 3.6 Consensus size: 51
45770 TAATGGAAAA
* *
45780 AGGTCCGATGATTATGTGTTATCGTGAGTATATGAATCCTTTACGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATG-ATCCTTTACGGATTATG
*
45832 AGGTCCGATAACTATGTGTCATCGTGAGTATATGATCCTTTACGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGATCCTTTACGGATTATG
* * * * * *
45883 AGGTTCGATGACTATGTGTCATCGTGAGCATATGGATCATTTTATGAATT-TA
1 AGGTCCGATGACTATGTGTCATCGTGAGTATAT-GATC-CTTTACGGATTATG
* *
45935 AGGTCCGATGACTTTGTGTCATCATGAGTAT
1 AGGTCCGATGACTATGTGTCATCGTGAGTAT
45966 TAAATGGGAA
Statistics
Matches: 118, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
51 47 0.40
52 63 0.53
53 8 0.07
ACGTcount: A:0.25, C:0.13, G:0.24, T:0.37
Consensus pattern (51 bp):
AGGTCCGATGACTATGTGTCATCGTGAGTATATGATCCTTTACGGATTATG
Found at i:45964 original size:103 final size:103
Alignment explanation
Indices: 45780--45965 Score: 248
Period size: 103 Copynumber: 1.8 Consensus size: 103
45770 TAATGGAAAA
* * * * *
45780 AGGTCCGATGATTATGTGTTATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCCGATAACT
1 AGGTCCGATGACTATGTGTCATCGTGAGCATATGAATCCTTTACGAATTATAAGGTCCGATAACT
*
45845 ATGTGTCATCGTGAGTATATGATCCTTTACGGATTATG
66 ATGTGTCATCATGAGTATATGATCCTTTACGGATTATG
* * * * *
45883 AGGTTCGATGACTATGTGTCATCGTGAGCATATGGATCATTTTATGAATT-TAAGGTCCGATGAC
1 AGGTCCGATGACTATGTGTCATCGTGAGCATATGAATC-CTTTACGAATTATAAGGTCCGATAAC
*
45947 TTTGTGTCATCATGAGTAT
65 TATGTGTCATCATGAGTAT
45966 TAAATGGGAA
Statistics
Matches: 70, Mismatches: 12, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
103 62 0.89
104 8 0.11
ACGTcount: A:0.25, C:0.13, G:0.24, T:0.37
Consensus pattern (103 bp):
AGGTCCGATGACTATGTGTCATCGTGAGCATATGAATCCTTTACGAATTATAAGGTCCGATAACT
ATGTGTCATCATGAGTATATGATCCTTTACGGATTATG
Found at i:52927 original size:82 final size:82
Alignment explanation
Indices: 52790--52952 Score: 290
Period size: 82 Copynumber: 2.0 Consensus size: 82
52780 CTACTCCTTT
* * *
52790 GGAATTTTTCTTTGTTTATGTGTTAAGAGTGCTTGGATCCCAATGATGAGAGAACTTTTTCAAGG
1 GGAATTTTTCGTTGTTTATGTGTTAAGAATGATTGGATCCCAATGATGAGAGAACTTTTTCAAGG
52855 ATGAGTAGTGAATCTTC
66 ATGAGTAGTGAATCTTC
*
52872 GGAATTTTTCGTTGTTTATGTGTTAAGAATGATTGGATCCCACTGATGAGAGAACTTTTTCAAGG
1 GGAATTTTTCGTTGTTTATGTGTTAAGAATGATTGGATCCCAATGATGAGAGAACTTTTTCAAGG
52937 ATGAGTAGTGAATCTT
66 ATGAGTAGTGAATCTT
52953 AGAGTAGGTT
Statistics
Matches: 77, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
82 77 1.00
ACGTcount: A:0.26, C:0.10, G:0.25, T:0.39
Consensus pattern (82 bp):
GGAATTTTTCGTTGTTTATGTGTTAAGAATGATTGGATCCCAATGATGAGAGAACTTTTTCAAGG
ATGAGTAGTGAATCTTC
Found at i:72639 original size:18 final size:18
Alignment explanation
Indices: 72612--72662 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
72602 TATAAGAATA
72612 ATAATA-ATAATAAAATT
1 ATAATATATAATAAAATT
*
72629 A-AATATTATAATAATATT
1 ATAATA-TATAATAAAATT
*
72647 ATAATATAAAATAAAA
1 ATAATATATAATAAAA
72663 AAATTATATC
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
16 4 0.14
17 1 0.04
18 19 0.68
19 4 0.14
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
ATAATATATAATAAAATT
Found at i:72660 original size:21 final size:21
Alignment explanation
Indices: 72612--72670 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
72602 TATAAGAATA
72612 ATAATAATAATAAAATTA-AAT
1 ATAA-AATAATAAAATTATAAT
* *
72633 AT--TATAATAATATTATAAT
1 ATAAAATAATAAAATTATAAT
*
72652 ATAAAATAAAAAAATTATA
1 ATAAAATAATAAAATTATA
72671 TCTATCGTAT
Statistics
Matches: 30, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
18 11 0.37
19 5 0.17
21 14 0.47
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (21 bp):
ATAAAATAATAAAATTATAAT
Found at i:76700 original size:29 final size:30
Alignment explanation
Indices: 76668--76866 Score: 205
Period size: 30 Copynumber: 6.7 Consensus size: 30
76658 TTTGAGGTCG
*
76668 AAAATGGAGA-TTTTGG-AGGTTCGAGGGTA
1 AAAATGGA-ATTTTTGGAAGTTTCGAGGGTA
* *
76697 AAAATGAAACTTTTGGAAGTTTCG-GGGTCA
1 AAAATGGAATTTTTGGAAGTTTCGAGGGT-A
* * *
76727 AAAAGGGAATTTTTTGAAGTTTTGA-GGTCA
1 AAAATGGAATTTTTGGAAGTTTCGAGGGT-A
76757 AAAA-GGAAATTTTTGGAAG-TTCGAGGGTA
1 AAAATGG-AATTTTTGGAAGTTTCGAGGGTA
* *
76786 AAAATGGAATGTTTGGAAGTTTCG-GGGTT
1 AAAATGGAATTTTTGGAAGTTTCGAGGGTA
*
76815 AAAATGGAATTTTTGGAAGTTTCGAGGTTA
1 AAAATGGAATTTTTGGAAGTTTCGAGGGTA
* *
76845 AAAATGAAATTTTCGGACAGTT
1 AAAATGGAATTTTTGGA-AGTT
76867 CAGGGACCTT
Statistics
Matches: 144, Mismatches: 16, Indels: 18
0.81 0.09 0.10
Matches are distributed among these distances:
28 1 0.01
29 66 0.46
30 73 0.51
31 4 0.03
ACGTcount: A:0.34, C:0.05, G:0.29, T:0.32
Consensus pattern (30 bp):
AAAATGGAATTTTTGGAAGTTTCGAGGGTA
Found at i:76731 original size:89 final size:88
Alignment explanation
Indices: 76638--76871 Score: 271
Period size: 89 Copynumber: 2.6 Consensus size: 88
76628 ATTCGGGGGT
* * * *
76638 AAAAGGGTAA-TTTTGAGCGTTTTGAGGTCGAAAATGGAGA-TTTTGGAGGTTCGAGGGTAAAAA
1 AAAAGGG-AATTTTTGA-AGTTTTGAGGTC-AAAAAGGAAATTTTTGGAAGTTCGAGGGTAAAAA
76701 TGAAACT-TTTGGAAGTTTCGGGGTCA
63 TGAAA-TGTTTGGAAGTTTCGGGGTCA
76727 AAAAGGGAATTTTTTGAAGTTTTGAGGTCAAAAAGGAAATTTTTGGAAGTTCGAGGGTAAAAATG
1 AAAAGGGAA-TTTTTGAAGTTTTGAGGTCAAAAAGGAAATTTTTGGAAGTTCGAGGGTAAAAATG
* *
76792 GAATGTTTGGAAGTTTCGGGGT-T
65 AAATGTTTGGAAGTTTCGGGGTCA
* * * * *
76815 AAAATGGAATTTTTGGAAGTTTCGAGGTTAAAAATGAAATTTTCGGACAGTTC-AGGG
1 AAAAGGGAATTTTT-GAAGTTTTGAGGTCAAAAAGGAAATTTTTGGA-AGTTCGAGGG
76872 ACCTTTAGGG
Statistics
Matches: 128, Mismatches: 11, Indels: 13
0.84 0.07 0.09
Matches are distributed among these distances:
87 5 0.04
88 51 0.40
89 66 0.52
90 6 0.05
ACGTcount: A:0.32, C:0.06, G:0.30, T:0.32
Consensus pattern (88 bp):
AAAAGGGAATTTTTGAAGTTTTGAGGTCAAAAAGGAAATTTTTGGAAGTTCGAGGGTAAAAATGA
AATGTTTGGAAGTTTCGGGGTCA
Found at i:76806 original size:59 final size:60
Alignment explanation
Indices: 76668--76850 Score: 198
Period size: 59 Copynumber: 3.1 Consensus size: 60
76658 TTTGAGGTCG
* * *
76668 AAAATGGAGAT-TTTGG-AGGTTCGAGGGT-AAAAATGAAACTTTTGGAAGTTTCG-GGGTCA
1 AAAATGGA-ATGTTTGGAAGTTTCGA-GGTCAAAAAGGAAATTTTTGGAAGTTTCGAGGGT-A
* * * *
76727 AAAAGGGAATTTTTTGAAGTTTTGAGGTCAAAAAGGAAATTTTTGGAAG-TTCGAGGGTA
1 AAAATGGAATGTTTGGAAGTTTCGAGGTCAAAAAGGAAATTTTTGGAAGTTTCGAGGGTA
* * * *
76786 AAAATGGAATGTTTGGAAGTTTCGGGGTTAAAATGG-AATTTTTGGAAGTTTCGAGGTTA
1 AAAATGGAATGTTTGGAAGTTTCGAGGTCAAAAAGGAAATTTTTGGAAGTTTCGAGGGTA
76845 AAAATG
1 AAAATG
76851 AAATTTTCGG
Statistics
Matches: 105, Mismatches: 14, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
58 14 0.13
59 63 0.60
60 28 0.27
ACGTcount: A:0.34, C:0.04, G:0.30, T:0.32
Consensus pattern (60 bp):
AAAATGGAATGTTTGGAAGTTTCGAGGTCAAAAAGGAAATTTTTGGAAGTTTCGAGGGTA
Found at i:78005 original size:3 final size:3
Alignment explanation
Indices: 77997--78049 Score: 54
Period size: 3 Copynumber: 17.3 Consensus size: 3
77987 TTTCGGCTTT
* * *
77997 TTA TTA TTA TTA ATA TCTA TTA TTA TTA TTA -TA TTA TTA ATA ATA
1 TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA
78042 TTAA TTA T
1 TT-A TTA T
78050 AGTTACCATT
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
2 2 0.05
3 35 0.81
4 6 0.14
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:78784 original size:6 final size:6
Alignment explanation
Indices: 78769--78823 Score: 53
Period size: 6 Copynumber: 9.5 Consensus size: 6
78759 TTGGACATTG
* * *
78769 TTTAAT TTTAAA TTTATAA --TAAA TTTAAA TTTAAA -ATAAA CTTAAA
1 TTTAAA TTTAAA TTTA-AA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
78815 TTTAAA TTT
1 TTTAAA TTT
78824 TGTTGGGCCC
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
4 2 0.05
5 6 0.15
6 31 0.76
7 2 0.05
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (6 bp):
TTTAAA
Found at i:78797 original size:17 final size:17
Alignment explanation
Indices: 78775--78820 Score: 74
Period size: 17 Copynumber: 2.7 Consensus size: 17
78765 ATTGTTTAAT
*
78775 TTTAAATTTATAATAAA
1 TTTAAATTTAAAATAAA
78792 TTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
*
78809 CTTAAATTTAAA
1 TTTAAATTTAAA
78821 TTTTGTTGGG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.43
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:79529 original size:17 final size:18
Alignment explanation
Indices: 79498--79531 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
79488 AATTTAATTT
79498 TAATTAAATTATTTAAAA
1 TAATTAAATTATTTAAAA
*
79516 TAATT-AATTTTTTAAA
1 TAATTAAATTATTTAAA
79532 TTATAAATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TAATTAAATTATTTAAAA
Found at i:79641 original size:27 final size:26
Alignment explanation
Indices: 79603--79656 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 26
79593 CCCCAAACCC
*
79603 TAAGATTCAAGGTTTGTGTTTGAGATT
1 TAAGATTCAAGGTTTGAGTTTGA-ATT
*
79630 TAAGATTTAAGGTTTGAGTTTGAATT
1 TAAGATTCAAGGTTTGAGTTTGAATT
79656 T
1 T
79657 TGAATTTGGG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 4 0.16
27 21 0.84
ACGTcount: A:0.28, C:0.02, G:0.24, T:0.46
Consensus pattern (26 bp):
TAAGATTCAAGGTTTGAGTTTGAATT
Found at i:80614 original size:14 final size:14
Alignment explanation
Indices: 80595--80641 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
80585 CAATTTTTTT
80595 AAATTT-TTACATAA
1 AAATTTATTA-ATAA
80609 AAATTTATTAATAA
1 AAATTTATTAATAA
* *
80623 TATTTTATTAAATAA
1 AAATTTATT-AATAA
80638 AAAT
1 AAAT
80642 AACCTTTAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
14 17 0.63
15 10 0.37
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (14 bp):
AAATTTATTAATAA
Found at i:87877 original size:12 final size:12
Alignment explanation
Indices: 87856--87888 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
87846 TAACTTTAAA
87856 TTTCAATTTCAC
1 TTTCAATTTCAC
*
87868 TTTCACTTTCAC
1 TTTCAATTTCAC
87880 TTTCAATTT
1 TTTCAATTT
87889 TGATCACAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.21, C:0.24, G:0.00, T:0.55
Consensus pattern (12 bp):
TTTCAATTTCAC
Found at i:98590 original size:23 final size:23
Alignment explanation
Indices: 98538--98597 Score: 59
Period size: 23 Copynumber: 2.6 Consensus size: 23
98528 TTTAATGTTT
*
98538 ACGAACATGTTCATTTAACTTAA
1 ACGAACATGTTCATTGAACTTAA
* * *
98561 TCAAACATGTTTA-TGAACATTAA
1 ACGAACATGTTCATTGAAC-TTAA
*
98584 ACGAACATATTCAT
1 ACGAACATGTTCAT
98598 AAACATATAA
Statistics
Matches: 27, Mismatches: 8, Indels: 3
0.71 0.21 0.08
Matches are distributed among these distances:
22 4 0.15
23 23 0.85
ACGTcount: A:0.42, C:0.17, G:0.08, T:0.33
Consensus pattern (23 bp):
ACGAACATGTTCATTGAACTTAA
Found at i:100202 original size:31 final size:31
Alignment explanation
Indices: 100133--100204 Score: 85
Period size: 31 Copynumber: 2.3 Consensus size: 31
100123 AAGATTAAAC
* *
100133 ACTAACTTAAGAAAAAATGTTAAGTTTAGGT
1 ACTAAATTAAGAAAAAATGTCAAGTTTAGGT
*
100164 A-TCAAATTAGGAAAAAATGTCAAGTTT-GAGT
1 ACT-AAATTAAGAAAAAATGTCAAGTTTAG-GT
100195 ACTAAATTAA
1 ACTAAATTAA
100205 ATCAAAAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
30 2 0.06
31 31 0.91
32 1 0.03
ACGTcount: A:0.47, C:0.07, G:0.15, T:0.31
Consensus pattern (31 bp):
ACTAAATTAAGAAAAAATGTCAAGTTTAGGT
Found at i:100761 original size:167 final size:167
Alignment explanation
Indices: 100485--100986 Score: 968
Period size: 167 Copynumber: 3.0 Consensus size: 167
100475 AGTTTTGAAG
100485 AAAGTTTTGGAATAAGGAGATAGAATACTCTCTGGAGAAGAAGAAGATAAATTATGAATTCTTTA
1 AAAGTTTTGGAATAAGGAGATAGAATACTCTCTGGAGAAGAAGAAGATAAATTATGAATTCTTTA
100550 GCGTGTCTTTCTCTTCAAATGGAATGTCTCGGATTTATTTAAACTATGAGTCTTTTGGGTCAAAT
66 GCGTGTCTTTCTCTTCAAATGGAATGTCTCGGATTTATTTAAACTATGAGTCTTTTGGGTCAAAT
100615 TTCGAGTTAAACCTCGGGTCGGGTTATTTTTATTATA
131 TTCGAGTTAAACCTCGGGTCGGGTTATTTTTATTATA
*
100652 AAAGTTTTGGAATAAGGAGATAGAATACTCTCCGGAGAAGAAGAAGATAAATTATGAATTCTTTA
1 AAAGTTTTGGAATAAGGAGATAGAATACTCTCTGGAGAAGAAGAAGATAAATTATGAATTCTTTA
*
100717 GCGTGTCTTTCTCTTCAAATGGAATGTCTCGGATTTATTTAAACTATGAGTTTTTTGGGTCAAAT
66 GCGTGTCTTTCTCTTCAAATGGAATGTCTCGGATTTATTTAAACTATGAGTCTTTTGGGTCAAAT
100782 TTCGAGTTAAACCTCGGGTCGGGTTATTTTTATTATA
131 TTCGAGTTAAACCTCGGGTCGGGTTATTTTTATTATA
100819 AAAGTTTTGGAATAAGGAGATAGAATACTCTCTGGAGAAGAAGAAGATAAATTATGAATTCTTTA
1 AAAGTTTTGGAATAAGGAGATAGAATACTCTCTGGAGAAGAAGAAGATAAATTATGAATTCTTTA
* *
100884 ACGTGTCTTTCTCTTCAAATGGAATGTCTCGGATTTATTTAAACTATGAGTCTTTTGGGTTAAAT
66 GCGTGTCTTTCTCTTCAAATGGAATGTCTCGGATTTATTTAAACTATGAGTCTTTTGGGTCAAAT
100949 TTCGAGTTAAACCTCGGGTCGGGTTATTTTTATTATA
131 TTCGAGTTAAACCTCGGGTCGGGTTATTTTTATTATA
100986 A
1 A
100987 TTATATAACA
Statistics
Matches: 329, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
167 329 1.00
ACGTcount: A:0.31, C:0.11, G:0.21, T:0.37
Consensus pattern (167 bp):
AAAGTTTTGGAATAAGGAGATAGAATACTCTCTGGAGAAGAAGAAGATAAATTATGAATTCTTTA
GCGTGTCTTTCTCTTCAAATGGAATGTCTCGGATTTATTTAAACTATGAGTCTTTTGGGTCAAAT
TTCGAGTTAAACCTCGGGTCGGGTTATTTTTATTATA
Found at i:105897 original size:28 final size:28
Alignment explanation
Indices: 105865--105924 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 28
105855 ACAAATACAT
105865 ATTTT-GTAATTAATCTATATTTCATATA
1 ATTTTCGTAATTAAT-TATATTTCATATA
* * *
105893 ATTTTCGTAATTAATTATTTTTTATATT
1 ATTTTCGTAATTAATTATATTTCATATA
105921 ATTT
1 ATTT
105925 GAATAAAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 19 0.68
29 9 0.32
ACGTcount: A:0.32, C:0.05, G:0.03, T:0.60
Consensus pattern (28 bp):
ATTTTCGTAATTAATTATATTTCATATA
Found at i:106373 original size:21 final size:21
Alignment explanation
Indices: 106341--106382 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
106331 TTTTAAAATA
**
106341 TTAAAAATATTTTTATATTTT
1 TTAAAAATATTTAAATATTTT
106362 TTAAATAA-ATTTAAATATTTT
1 TTAAA-AATATTTAAATATTTT
106383 AAATTTTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TTAAAAATATTTAAATATTTT
Found at i:106399 original size:28 final size:27
Alignment explanation
Indices: 106345--106412 Score: 66
Period size: 27 Copynumber: 2.4 Consensus size: 27
106335 AAAATATTAA
* * * *
106345 AAATATTTTTATATTTTTTAAATAAATTT
1 AAATA-TTTTA-AATTTTAAAAAAAAATT
106374 AAATATTTTAAATTTTAAAAAAAAATT
1 AAATATTTTAAATTTTAAAAAAAAATT
106401 ATAAT-TTTTAAA
1 A-AATATTTTAAA
106413 AAATTTTAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
27 21 0.62
28 8 0.24
29 5 0.15
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (27 bp):
AAATATTTTAAATTTTAAAAAAAAATT
Found at i:120657 original size:34 final size:33
Alignment explanation
Indices: 120613--120697 Score: 82
Period size: 34 Copynumber: 2.5 Consensus size: 33
120603 AAAAAATCTA
*
120613 AAAAATTATAATTTTTTAAAAAATATAAATTTTG
1 AAAATTTATAATTTTTTAAAAAATA-AAATTTTG
* * ***
120647 AAAATTTATAAATATTTTGAATTTTAAAATTTTG
1 AAAATTTAT-AATTTTTTAAAAAATAAAATTTTG
120681 AAAATATTA-AATTTTTT
1 AAAAT-TTATAATTTTTT
120698 TTTTTTTGTA
Statistics
Matches: 42, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
33 7 0.17
34 21 0.50
35 14 0.33
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (33 bp):
AAAATTTATAATTTTTTAAAAAATAAAATTTTG
Found at i:120669 original size:17 final size:15
Alignment explanation
Indices: 120639--120682 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 15
120629 TAAAAAATAT
120639 AAATTTTGAAAATTTATA
1 AAATTTTG--AATTT-TA
120657 AATATTTTGAATTTTA
1 AA-ATTTTGAATTTTA
120673 AAATTTTGAA
1 AAATTTTGAA
120683 AATATTAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
15 8 0.32
16 4 0.16
17 5 0.20
18 2 0.08
19 6 0.24
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (15 bp):
AAATTTTGAATTTTA
Found at i:120690 original size:17 final size:17
Alignment explanation
Indices: 120639--120695 Score: 66
Period size: 16 Copynumber: 3.4 Consensus size: 17
120629 TAAAAAATAT
120639 AAATTTTGAAAATTTATA
1 AAATTTTGAAAATTT-TA
120657 AATATTTTG--AATTTTA
1 AA-ATTTTGAAAATTTTA
*
120673 AAATTTTGAAAATATT-
1 AAATTTTGAAAATTTTA
120689 AAATTTT
1 AAATTTT
120696 TTTTTTTTTG
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
15 6 0.17
16 11 0.31
17 10 0.29
18 2 0.06
19 6 0.17
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (17 bp):
AAATTTTGAAAATTTTA
Found at i:120696 original size:17 final size:17
Alignment explanation
Indices: 120612--120696 Score: 59
Period size: 17 Copynumber: 4.9 Consensus size: 17
120602 AAAAAAATCT
* *
120612 AAAAAATTATAATTTTTT
1 AAAATATTA-AATTTTTG
*
120630 AAAAAATATAAA-TTTTG
1 AAAATAT-TAAATTTTTG
*
120647 AAAATTTATAAATATTTTG
1 AAAATAT-TAAAT-TTTTG
* *
120666 --AATTTTAAAATTTTG
1 AAAATATTAAATTTTTG
120681 AAAATATTAAATTTTT
1 AAAATATTAAATTTTT
120697 TTTTTTTTGT
Statistics
Matches: 56, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
15 5 0.09
16 4 0.07
17 31 0.55
18 9 0.16
19 7 0.12
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (17 bp):
AAAATATTAAATTTTTG
Found at i:130782 original size:23 final size:23
Alignment explanation
Indices: 130756--130799 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
130746 TTTTGAACAA
* *
130756 TTTAATTTTTTTCTTTTATTTTT
1 TTTAACTTTTTTCTTTAATTTTT
*
130779 TTTAGCTTTTTTCTTTAATTT
1 TTTAACTTTTTTCTTTAATTT
130800 CCATTCTCTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.14, C:0.07, G:0.02, T:0.77
Consensus pattern (23 bp):
TTTAACTTTTTTCTTTAATTTTT
Found at i:133669 original size:29 final size:29
Alignment explanation
Indices: 133632--134054 Score: 308
Period size: 29 Copynumber: 14.3 Consensus size: 29
133622 AACATATTTT
* * *
133632 TTTTGGAAACTTTAAGGTTAAAAATAGAA
1 TTTTGGAAAGTTTAAGGGTAAAAATGGAA
*
133661 TTTTGGAAAATTT-AGCGGTAAAAA-GGTAA
1 TTTTGGAAAGTTTAAG-GGTAAAAATGG-AA
*
133690 TTTTGGGAAAGTTTGA-GGTCAAAAATGGAA
1 TTTT-GGAAAGTTTAAGGGT-AAAAATGGAA
* * *
133720 TTTTGGGAAGTTTAGGGGTAAAAAAATGAAA
1 TTTTGGAAAGTTTAAGGGT--AAAAATGGAA
* * ** *
133751 TTTTTGGAAAATTTGAGGCCAAAAAAGGAA
1 -TTTTGGAAAGTTTAAGGGTAAAAATGGAA
* * * *
133781 TTTTGGAAAATTTAGGGGTAAAATTGTAA
1 TTTTGGAAAGTTTAAGGGTAAAAATGGAA
* *
133810 TTTTTGGAAACTTT-AGGGTCAAAATGGAA
1 -TTTTGGAAAGTTTAAGGGTAAAAATGGAA
* *
133839 TTTTGGAAAGTTCAATGGGTAAAAATGTAA
1 TTTTGGAAAGTTTAA-GGGTAAAAATGGAA
* * *
133869 TTTTTGG-AAGATT-CGAGGTTAAAATGGAA
1 -TTTTGGAAAGTTTAAG-GGTAAAAATGGAA
*
133898 TTTTGGAAAGTTTAAGGGTAAAAAATGTAA
1 TTTTGGAAAGTTTAAGGGT-AAAAATGGAA
*
133928 TTTTTGGAAA-TTTTAGGGTTAAAAATGGAA
1 -TTTTGGAAAGTTTAAGGG-TAAAAATGGAA
* * *
133958 TTTTGGAAA-ATTCAGTGAGT-AAAATGTAA
1 TTTTGGAAAGTTTAAG-G-GTAAAAATGGAA
* ** *
133987 TTTTTGGAAA-CTTCGGGGTCAAAATGGAA
1 -TTTTGGAAAGTTTAAGGGTAAAAATGGAA
*
134016 TTTTGGAAAGTTTAAGGGTAAAAATGTAA
1 TTTTGGAAAGTTTAAGGGTAAAAATGGAA
134045 TTTTTGGAAA
1 -TTTTGGAAA
134055 ATTCGAGATT
Statistics
Matches: 314, Mismatches: 55, Indels: 49
0.75 0.13 0.12
Matches are distributed among these distances:
28 32 0.10
29 133 0.42
30 107 0.34
31 29 0.09
32 13 0.04
ACGTcount: A:0.39, C:0.03, G:0.24, T:0.34
Consensus pattern (29 bp):
TTTTGGAAAGTTTAAGGGTAAAAATGGAA
Found at i:133721 original size:59 final size:58
Alignment explanation
Indices: 133591--134144 Score: 487
Period size: 59 Copynumber: 9.4 Consensus size: 58
133581 GCTCGGGGGT
* * ** * *
133591 AAAATGGTAATTTT-GAAAGTTTCGAGGTTAAAACATATTTTTTTTGGAAACTTTAAGGTTA
1 AAAATGG-AATTTTGGAAAGTTT--AGGGTAAAA-ATGTAATTTTTGGAAACTTTGAGGTCA
* * * * *
133652 AAAATAGAATTTTGGAAAATTTAGCGGTAAAAAGGTAATTTTGGGAAAGTTTGAGGTCA
1 AAAATGGAATTTTGGAAAGTTTAG-GGTAAAAATGTAATTTTTGGAAACTTTGAGGTCA
* * * *
133711 AAAATGGAATTTTGGGAAGTTTAGGGGTAAAAAAATGAAATTTTTGGAAAATTTGAGGCCA
1 AAAATGGAATTTTGGAAAGTTTA-GGGT--AAAAATGTAATTTTTGGAAACTTTGAGGTCA
* * *
133772 AAAAAGGAATTTTGGAAAATTTAGGGGTAAAATTGTAATTTTTGGAAACTTT-AGGGTC-
1 AAAATGGAATTTTGGAAAGTTTA-GGGTAAAAATGTAATTTTTGGAAACTTTGA-GGTCA
* * *
133830 AAAATGGAATTTTGGAAAGTTCAATGGGTAAAAATGTAATTTTTGGAAGA-TTCGAGGT-T
1 AAAATGGAATTTTGGAAAGTT-TA-GGGTAAAAATGTAATTTTTGGAA-ACTTTGAGGTCA
* *
133889 AAAATGGAATTTTGGAAAGTTTAAGGGTAAAAAATGTAATTTTTGGAAA-TTTTAGGGTTA
1 AAAATGGAATTTTGGAAAGTTT-AGGGT-AAAAATGTAATTTTTGGAAACTTTGA-GGTCA
* * * *
133949 AAAATGGAATTTTGGAAAATTCAGTGAGT-AAAATGTAATTTTTGGAAACTTCGGGGTC-
1 AAAATGGAATTTTGGAAAGTTTAG-G-GTAAAAATGTAATTTTTGGAAACTTTGAGGTCA
* * * *
134007 AAAATGGAATTTTGGAAAGTTTAAGGGTAAAAATGTAATTTTTGGAAAATTCGAGAT-T
1 AAAATGGAATTTTGGAAAGTTT-AGGGTAAAAATGTAATTTTTGGAAACTTTGAGGTCA
* * * ** * * * * *
134065 AAAGTGGAACTTTAGAAAGTTCGGGGGTAAAAATGTAATTTTTAGAAAATTCGTGGTAA
1 AAAATGGAATTTTGGAAAGTT-TAGGGTAAAAATGTAATTTTTGGAAACTTTGAGGTCA
*
134124 AAAATGGAATTCTGGAAAGTT
1 AAAATGGAATTTTGGAAAGTT
134145 CGGGGACCTC
Statistics
Matches: 411, Mismatches: 60, Indels: 46
0.79 0.12 0.09
Matches are distributed among these distances:
57 2 0.00
58 122 0.30
59 183 0.45
60 38 0.09
61 66 0.16
ACGTcount: A:0.39, C:0.04, G:0.24, T:0.34
Consensus pattern (58 bp):
AAAATGGAATTTTGGAAAGTTTAGGGTAAAAATGTAATTTTTGGAAACTTTGAGGTCA
Found at i:134126 original size:29 final size:28
Alignment explanation
Indices: 133661--134148 Score: 218
Period size: 30 Copynumber: 16.6 Consensus size: 28
133651 AAAAATAGAA
* *
133661 TTTTGGAAAATTTAGCGGTAAAAAGGTAAT
1 TTTTGGAAAA-TTCG-GGTAAAAATGTAAT
* * * *
133691 TTTGGGAAAGTTTGAGGTCAAAAATGGAAT
1 TTTTGGAAAATTCG-GGT-AAAAATGTAAT
* ** * *
133721 TTTGGGAAGTTTAGGGGTAAAAAAATGAAAT
1 TTTTGGAAAATT-CGGGT--AAAAATGTAAT
* * * *
133752 TTTTGGAAAATTTGAGGCCAAAAAAGGAA-
1 TTTTGGAAAATTCG-GG-TAAAAATGTAAT
* *
133781 TTTTGGAAAATTTAGGGGTAAAATTGTAAT
1 TTTTGGAAAA-TT-CGGGTAAAAATGTAAT
* * * *
133811 TTTTGGAAACTTTAGGGTCAAAATGGAA-
1 TTTTGGAAA-ATTCGGGTAAAAATGTAAT
*
133839 TTTTGGAAAGTTCAATGGGTAAAAATGTAAT
1 TTTTGGAAAATTC---GGGTAAAAATGTAAT
* * *
133870 TTTTGGAAGATTCGAGGTTAAAATGGAA-
1 TTTTGGAAAATTCG-GGTAAAAATGTAAT
* *
133898 TTTTGGAAAGTTTAAGGGTAAAAAATGTAAT
1 TTTTGGAAA-ATT-CGGGT-AAAAATGTAAT
* * *
133929 TTTTGGAAATTTTAGGGTTAAAAATGGAA-
1 TTTTGGAAA-ATTCGGG-TAAAAATGTAAT
133958 TTTTGGAAAATTCAGTGAGT-AAAATGTAAT
1 TTTTGGAAAATTC-G-G-GTAAAAATGTAAT
* * *
133988 TTTTGGAAACTTCGGGGTCAAAATGGAA-
1 TTTTGGAAAATTC-GGGTAAAAATGTAAT
* *
134016 TTTTGGAAAGTTTAAGGGTAAAAATGTAAT
1 TTTTGGAAA-ATT-CGGGTAAAAATGTAAT
* * * *
134046 TTTTGGAAAATTCGAGATTAAAGTGGAA-
1 TTTTGGAAAATTCG-GGTAAAAATGTAAT
* * *
134074 CTTTAGAAAGTTCGGGGGTAAAAATGTAAT
1 TTTTGGAAAATTC--GGGTAAAAATGTAAT
* *
134104 TTTTAGAAAATTCGTGGTAAAAAATGGAA-
1 TTTTGGAAAATTCG-GGT-AAAAATGTAAT
* *
134133 TTCTGGAAAGTTCGGG
1 TTTTGGAAAATTCGGG
134149 GACCTCCTTG
Statistics
Matches: 353, Mismatches: 72, Indels: 68
0.72 0.15 0.14
Matches are distributed among these distances:
27 2 0.01
28 45 0.13
29 125 0.35
30 133 0.38
31 48 0.14
ACGTcount: A:0.38, C:0.04, G:0.25, T:0.33
Consensus pattern (28 bp):
TTTTGGAAAATTCGGGTAAAAATGTAAT
Found at i:135247 original size:3 final size:3
Alignment explanation
Indices: 135239--135263 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
135229 TTTTTACTCT
135239 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Done.