Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012664.1 Kokia drynarioides strain JFW-HI SEQ_127675, 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: 25446
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Found at i:670 original size:57 final size:56
Alignment explanation
Indices: 568--687 Score: 147
Period size: 57 Copynumber: 2.1 Consensus size: 56
558 ACGAGAATTT
* *
568 GAAAAAAAAATTGGTGTTGGCCATGCAATGGATGACACCTCCTTTTTTATTTGATA
1 GAAAAAAAAATTGGTATTGGCCATGCAATGGATGACACCTCCTTTTTAATTTGATA
* * *
624 GGAAAAAAAAATTTGGTATTGGTCATTGC-ATGGCTGACATC-CCTTTTTAATTTGATA
1 -GAAAAAAAAA-TTGGTATTGGCCA-TGCAATGGATGACACCTCCTTTTTAATTTGATA
681 -AAAAAAA
1 GAAAAAAA
688 TTTAAATTTT
Statistics
Matches: 56, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
55 7 0.12
57 25 0.45
58 21 0.38
59 3 0.05
ACGTcount: A:0.36, C:0.12, G:0.18, T:0.33
Consensus pattern (56 bp):
GAAAAAAAAATTGGTATTGGCCATGCAATGGATGACACCTCCTTTTTAATTTGATA
Found at i:730 original size:62 final size:59
Alignment explanation
Indices: 578--1147 Score: 337
Period size: 60 Copynumber: 9.5 Consensus size: 59
568 GAAAAAAAAA
** *
578 TTGGTGTTGGCCATGCAATGGATGACACCTCCTTTTTTATTTGATAGGAAAAAA--AAA--T
1 TTGGTGTTGGCCATGCAATGGCCGACACC-CC-TTTTTATTTGATA-AAAAAAATTAAATTT
* * * *
636 TTGGTATTGGTCATTGC-ATGGCTGACATCCCTTTTTAATTTGATAAAAAAAATTTAAATTT
1 TTGGTGTTGGCCA-TGCAATGGCCGACACCCCTTTTT-ATTTGATAAAAAAAA-TTAAATTT
* * * * * *
697 TTGAGTGTTGGTCATGCAATGGCCGACACCCCTTTTT-TGTCAGATAAAAAATTCAATTTT
1 TTG-GTGTTGGCCATGCAATGGCCGACACCCCTTTTTATTTGATAAAAAAAATT-AAATTT
* * * * * * *
757 TTTGTGTTGGCCATGCAATGGTCAACACCTCTATTTATCTGAT--AAAAAATCAAATTT
1 TTGGTGTTGGCCATGCAATGGCCGACACCCCTTTTTATTTGATAAAAAAAATTAAATTT
** * *
814 TTGGTGTTGGCCATGCAATGATCTACACCCCTTTTT-TTTAGATAAAAAAATTTCAAAATTTT
1 TTGGTGTTGGCCATGCAATGGCCGACACCCCTTTTTATTT-GATAAAAAAAATT--AAA-TTT
* * * * * * * * *
876 TTGGTGTTGGCCAGGCCATTGTCGACACCCCTTTTT-TGTCAGATAAAAAATTCGAATTTTTT
1 TTGGTGTTGGCCATGCAATGGCCGACACCCCTTTTTATTTGATAAAAAAAATT--AA--ATTT
* * * * * *
938 TTTGTGTTGGCCATGCCATGGCCGACACCCTTTTTTTATCT-AGT-AAAAAAATCAATTTTTT
1 TTGGTGTTGGCCATGCAATGGCCGACACCC-CTTTTTATTTGA-TAAAAAAAATTAA--ATTT
* * *
999 TTTGTGTTGGCCTTGCAATGGCCGACACTCCCTTTTTA--TGA-AATAAAAAATTCAATTTTT
1 TTGGTGTTGGCCATGCAATGGCCGACAC-CCCTTTTTATTTGATAA-AAAAAATT-AA-ATTT
* * * * *
1059 TTTGTGTTGGCCATGCCATAGCCGACATCCCTTTTTTATTTGGT--AAAAAATTAAATTTTT
1 TTGGTGTTGGCCATGCAATGGCCGACA-CCCCTTTTTATTTGATAAAAAAAATTAAA--TTT
* *
1119 TTGGTGTTGGCCATGTAATGACCGACACC
1 TTGGTGTTGGCCATGCAATGGCCGACACC
1148 AACTTTCCCT
Statistics
Matches: 411, Mismatches: 68, Indels: 65
0.76 0.12 0.12
Matches are distributed among these distances:
56 13 0.03
57 49 0.12
58 28 0.07
59 48 0.12
60 98 0.24
61 65 0.16
62 95 0.23
63 13 0.03
64 2 0.00
ACGTcount: A:0.27, C:0.17, G:0.17, T:0.39
Consensus pattern (59 bp):
TTGGTGTTGGCCATGCAATGGCCGACACCCCTTTTTATTTGATAAAAAAAATTAAATTT
Found at i:911 original size:61 final size:58
Alignment explanation
Indices: 682--1147 Score: 370
Period size: 60 Copynumber: 7.8 Consensus size: 58
672 AATTTGATAA
* * *
682 AAAAAATTTAAA-TTTTTGAGTGTTGGTCATGCAATGGCCGACACCCCTTTTTTGTCAGAT
1 AAAAAATTCAAATTTTTTG-GTGTTGGCCATGCCATGGCCGACACCCCTTTTTT-T-AGAT
* * * * * *
742 AAAAAATTC-AATTTTTTTGTGTTGGCCATGCAATGGTCAACACCTCTATTTATCT-GAT
1 AAAAAATTCAAATTTTTTGGTGTTGGCCATGCCATGGCCGACACCCCT-TTT-TTTAGAT
* ** *
800 AAAAAA-TCAAA-TTTTTGGTGTTGGCCATGCAATGATCTACACCCCTTTTTTTTAGAT
1 AAAAAATTCAAATTTTTTGGTGTTGGCCATGCCATGGCCGACACCCC-TTTTTTTAGAT
* * *
857 AAAAAAATTTCAAAATTTTTTGGTGTTGGCCAGGCCATTGTCGACACCCCTTTTTTGTCAGAT
1 -AAAAAA-TTC-AAATTTTTTGGTGTTGGCCATGCCATGGCCGACACCCCTTTTTT-T-AGAT
* * *
920 AAAAAATTCGAATTTTTTTTTGTGTTGGCCATGCCATGGCCGACA-CCCTTTTTTTATCTAGT
1 AAAAAATTC-AA-ATTTTTTGGTGTTGGCCATGCCATGGCCGACACCCCTTTTTTTA--GA-T
* * * * * * *
982 AAAAAAATCAATTTTTTTTTGTGTTGGCCTTGCAATGGCCGACACTCCCTTTTTATGAAAT
1 AAAAAATTCAA-ATTTTTTGGTGTTGGCCATGCCATGGCCGACAC-CCCTTTTT-TTAGAT
* * * * * *
1043 AAAAAATTCAATTTTTTTTGTGTTGGCCATGCCATAGCCGACATCCCTTTTTTATTTGGT
1 AAAAAATTCAAATTTTTTGGTGTTGGCCATGCCATGGCCGACA-CCCCTTTTT-TTAGAT
** *
1103 AAAAAATT-AAATTTTTTTGGTGTTGGCCATGTAATGACCGACACC
1 AAAAAATTCAAA-TTTTTTGGTGTTGGCCATGCCATGGCCGACACC
1148 AACTTTCCCT
Statistics
Matches: 340, Mismatches: 44, Indels: 45
0.79 0.10 0.10
Matches are distributed among these distances:
56 2 0.01
57 38 0.11
58 18 0.05
59 32 0.09
60 93 0.27
61 70 0.21
62 73 0.21
63 12 0.04
64 2 0.01
ACGTcount: A:0.27, C:0.18, G:0.16, T:0.39
Consensus pattern (58 bp):
AAAAAATTCAAATTTTTTGGTGTTGGCCATGCCATGGCCGACACCCCTTTTTTTAGAT
Found at i:2411 original size:24 final size:24
Alignment explanation
Indices: 2384--2461 Score: 63
Period size: 24 Copynumber: 3.2 Consensus size: 24
2374 CAAAACATTA
*
2384 AATAAAGGTATTAATAATATTAAT
1 AATAAAGGTATTAATAATAATAAT
** *
2408 AATAATTGTTTTAATAATAATAAT
1 AATAAAGGTATTAATAATAATAAT
*
2432 ATTTAGTAA--TATTAATAATAATAA-
1 A-ATA--AAGGTATTAATAATAATAAT
2456 AATAAA
1 AATAAA
2462 AGTCGAAAGG
Statistics
Matches: 43, Mismatches: 8, Indels: 9
0.72 0.13 0.15
Matches are distributed among these distances:
21 2 0.05
23 2 0.05
24 22 0.51
25 16 0.37
27 1 0.02
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (24 bp):
AATAAAGGTATTAATAATAATAAT
Found at i:3685 original size:29 final size:29
Alignment explanation
Indices: 3522--3787 Score: 175
Period size: 30 Copynumber: 8.9 Consensus size: 29
3512 CCTTAGGGGT
* * * *
3522 CCCTAAACTATCAAAAAATCATATTTTAAC
1 CCCTAAACT-TCCAAAAATTACATTTTTAC
* *
3552 CCCTAAACTTTTCC-AAAATTATATTTTAAC
1 CCCTAAAC--TTCCAAAAATTACATTTTTAC
*
3582 CCCTGAATA-TTCAAAAAATTACATTTTTACC
1 CCCT-AA-ACTTCCAAAAATTACATTTTTA-C
* *
3613 CCCCAAACTTCCCAAAATT-CTATTTTTGAC
1 CCCTAAACTTCCAAAAATTAC-ATTTTT-AC
* * **
3643 CTC-GATTTTCCCAAAAATTACATTTTTAC
1 CCCTAAACTT-CCAAAAATTACATTTTTAC
* *
3672 CCCTAAACTTCCAAAAATTCCAATTTTAAC
1 CCCTAAACTTCCAAAAATTAC-ATTTTTAC
* *
3702 CTCAAAACTTCCAAAAATTACCA-TTTTAC
1 CCCTAAACTTCCAAAAATTA-CATTTTTAC
** *
3731 CCCCGAACTTCCAAAAATT-CTATTTTAAC
1 CCCTAAACTTCCAAAAATTAC-ATTTTTAC
* *
3760 CCCGAAACTTTCAAAAATTACAATTTTT
1 CCCTAAACTTCCAAAAATTAC-ATTTTT
3788 CCCTCGAAAG
Statistics
Matches: 187, Mismatches: 32, Indels: 34
0.74 0.13 0.13
Matches are distributed among these distances:
27 1 0.01
28 1 0.01
29 64 0.34
30 108 0.58
31 11 0.06
32 2 0.01
ACGTcount: A:0.38, C:0.26, G:0.02, T:0.34
Consensus pattern (29 bp):
CCCTAAACTTCCAAAAATTACATTTTTAC
Found at i:3837 original size:117 final size:117
Alignment explanation
Indices: 3654--3967 Score: 314
Period size: 117 Copynumber: 2.7 Consensus size: 117
3644 TCGATTTTCC
* * * * * * *
3654 CAAAAATTACATTTTTA-CCCCTAAACTTCCAAAAATTCCAATTTTAACCTCAAAAC-TTCCAAA
1 CAAAAATTACAATTTTACCCCCGAAA-GT-CGAAAATTCCATTTTTAACCTC-GAACTTTTCAAA
*
3717 AATTACCATTTTACCCCCGAACT-TCCAAAAATTCT-ATTTTAACCCCGAAACTTT
63 AATTACCATTTTGCCCCCGAA-TGTCCAAAAATTCTAATTTTAACCCCGAAACTTT
* * * * * *
3771 CAAAAATTACAATTTTTCCCTCGAAAGTTCGAAAATTCTATTTTTGATCTCG-ATTTTTCTAAAA
1 CAAAAATTACAATTTTACCCCCGAAAG-TCGAAAATTCCATTTTTAACCTCGAACTTTTC-AAAA
* * ***
3835 ATTACCATTTTGCCCCCGAATGTCCAAAAATTCTAATTTTTATCCCGATTTTTT
64 ATTACCATTTTGCCCCCGAATGTCCAAAAATTCTAATTTTAACCCCGAAACTTT
* * * * * *
3889 TAAAAATTACCATTTTACCCCCGAATGTCTAAAATTCCCTTTTTAACCTCGAACTTTTCCAAAAT
1 CAAAAATTACAATTTTACCCCCGAAAGTCGAAAATTCCATTTTTAACCTCGAACTTTTCAAAAAT
3954 TACCATTTTGCCCC
66 TACCATTTTGCCCC
3968 TCAAGAGTCC
Statistics
Matches: 159, Mismatches: 31, Indels: 14
0.78 0.15 0.07
Matches are distributed among these distances:
115 1 0.01
116 4 0.03
117 105 0.66
118 49 0.31
ACGTcount: A:0.33, C:0.25, G:0.05, T:0.36
Consensus pattern (117 bp):
CAAAAATTACAATTTTACCCCCGAAAGTCGAAAATTCCATTTTTAACCTCGAACTTTTCAAAAAT
TACCATTTTGCCCCCGAATGTCCAAAAATTCTAATTTTAACCCCGAAACTTT
Found at i:3845 original size:59 final size:59
Alignment explanation
Indices: 3595--3967 Score: 291
Period size: 59 Copynumber: 6.3 Consensus size: 59
3585 TGAATATTCA
* * * *
3595 AAAAATTA-CATTTTTACCCCCCAAACTTCCCAAAATTCTATTTTTGACCTCGATTTTCCC
1 AAAAATTACCATTTTT-CCCCCGAAACTTCCAAAAATTCTATTTTTAACCTCGATTTT-TC
* * * * * ** *
3655 AAAAATTA-CATTTTTACCCCTAAACTTCCAAAAATTCCAATTTTAACCTCAAAACTTCC
1 AAAAATTACCATTTTTCCCCCGAAACTTCCAAAAATTCTATTTTTAACCTC-GATTTTTC
* * **
3714 AAAAATTACCATTTTACCCCCG-AACTTCCAAAAATTCTA-TTTTAACCCCGAAACTTTC
1 AAAAATTACCATTTTTCCCCCGAAACTTCCAAAAATTCTATTTTTAACCTCG-ATTTTTC
* * * * * *
3772 AAAAATTACAATTTTTCCCTCGAAAGTT-CGAAAATTCTATTTTTGATCTCGATTTTTC
1 AAAAATTACCATTTTTCCCCCGAAACTTCCAAAAATTCTATTTTTAACCTCGATTTTTC
* * *
3830 TAAAAATTACCATTTTGCCCCCG-AA-TGTCCAAAAATTCTAATTTTTATCC-CGATTTTTTT
1 -AAAAATTACCATTTTTCCCCCGAAACT-TCCAAAAATTCT-ATTTTTAACCTCGA-TTTTTC
* * ** *
3890 AAAAATTACCATTTTACCCCCG-AA-TGT-CTAAAATTCCCTTTTTAACCTCGAACTTTTC
1 AAAAATTACCATTTTTCCCCCGAAACT-TCCAAAAATTCTATTTTTAACCTCG-ATTTTTC
* *
3948 CAAAATTACCATTTTGCCCC
1 AAAAATTACCATTTTTCCCC
3968 TCAAGAGTCC
Statistics
Matches: 258, Mismatches: 43, Indels: 26
0.79 0.13 0.08
Matches are distributed among these distances:
57 9 0.03
58 84 0.33
59 125 0.48
60 40 0.16
ACGTcount: A:0.33, C:0.26, G:0.05, T:0.36
Consensus pattern (59 bp):
AAAAATTACCATTTTTCCCCCGAAACTTCCAAAAATTCTATTTTTAACCTCGATTTTTC
Found at i:3912 original size:30 final size:30
Alignment explanation
Indices: 3821--3912 Score: 82
Period size: 30 Copynumber: 3.1 Consensus size: 30
3811 TTTTTGATCT
*
3821 CGATTTTTCTAAAAATTACCATTTTGCCCC
1 CGATTTTTCTAAAAATTACCATTTTACCCC
* * * * *
3851 CGA-ATGTCCAAAAATT-CTAATTTTTA-TCC
1 CGATTTTTCTAAAAATTAC-CA-TTTTACCCC
*
3880 CGATTTTTTTAAAAATTACCATTTTACCCC
1 CGATTTTTCTAAAAATTACCATTTTACCCC
3910 CGA
1 CGA
3913 ATGTCTAAAA
Statistics
Matches: 45, Mismatches: 12, Indels: 10
0.67 0.18 0.15
Matches are distributed among these distances:
28 1 0.02
29 21 0.47
30 22 0.49
31 1 0.02
ACGTcount: A:0.30, C:0.24, G:0.07, T:0.39
Consensus pattern (30 bp):
CGATTTTTCTAAAAATTACCATTTTACCCC
Found at i:3921 original size:29 final size:29
Alignment explanation
Indices: 3828--3922 Score: 86
Period size: 29 Copynumber: 3.2 Consensus size: 29
3818 TCTCGATTTT
*
3828 TCTAAAAATTACCATTTTGCCCCCGAATG
1 TCTAAAAATTACCATTTTACCCCCGAATG
* * * * *
3857 TCCAAAAATT-CTAATTTTTA-TCCCGATTTT
1 TCTAAAAATTAC-CA-TTTTACCCCCGA-ATG
*
3887 TTTAAAAATTACCATTTTACCCCCGAATG
1 TCTAAAAATTACCATTTTACCCCCGAATG
3916 TCTAAAA
1 TCTAAAA
3923 TTCCCTTTTT
Statistics
Matches: 48, Mismatches: 13, Indels: 10
0.68 0.18 0.14
Matches are distributed among these distances:
28 1 0.02
29 27 0.56
30 19 0.40
31 1 0.02
ACGTcount: A:0.34, C:0.23, G:0.06, T:0.37
Consensus pattern (29 bp):
TCTAAAAATTACCATTTTACCCCCGAATG
Found at i:5730 original size:18 final size:18
Alignment explanation
Indices: 5707--5743 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
5697 TTGAACACTA
5707 AGGCGCAATCATATGCGT
1 AGGCGCAATCATATGCGT
5725 AGGCGCAATCATATGCGT
1 AGGCGCAATCATATGCGT
5743 A
1 A
5744 TCTGTATTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.30, C:0.22, G:0.27, T:0.22
Consensus pattern (18 bp):
AGGCGCAATCATATGCGT
Found at i:9543 original size:13 final size:12
Alignment explanation
Indices: 9518--9550 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
9508 TTCAATGAAT
9518 AAAAGAAAAGAA
1 AAAAGAAAAGAA
9530 AAAAGAAGAAGAA
1 AAAAGAA-AAGAA
9543 AAAA-AAAA
1 AAAAGAAAA
9551 ATGAGAGGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 2 0.10
12 9 0.45
13 9 0.45
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (12 bp):
AAAAGAAAAGAA
Found at i:10978 original size:47 final size:49
Alignment explanation
Indices: 10850--10962 Score: 149
Period size: 49 Copynumber: 2.3 Consensus size: 49
10840 TTGTACCTCA
* * * * * *
10850 AAGACATGACGGGAAAGATCTAAGCCGCAACGGCGGATCCAATGCCGCG
1 AAGACATCAAGGGAAAGATCTAAGTCGCAATGGCGGATCCAATGACACG
*
10899 AAGACATGAAGGGAAAGATCTAAGTCGCAATGGCGGATCCAAT-ACACG
1 AAGACATCAAGGGAAAGATCTAAGTCGCAATGGCGGATCCAATGACACG
10947 AAGACA-CAAGGGAAAG
1 AAGACATCAAGGGAAAG
10963 GTTTAAGTTG
Statistics
Matches: 58, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
47 9 0.16
48 9 0.16
49 40 0.69
ACGTcount: A:0.39, C:0.21, G:0.29, T:0.11
Consensus pattern (49 bp):
AAGACATCAAGGGAAAGATCTAAGTCGCAATGGCGGATCCAATGACACG
Found at i:11076 original size:50 final size:50
Alignment explanation
Indices: 11022--11174 Score: 143
Period size: 50 Copynumber: 3.1 Consensus size: 50
11012 ATCTAAACCA
11022 CAACGACGGATCCAGTACCACAAAGATACAAAAGGGAAAGGTTTAAGTTG
1 CAACGACGGATCCAGTACCACAAAGATACAAAAGGGAAAGGTTTAAGTTG
* * * *
11072 CAACGGCGGA-CC-GTGAACCTCAGAAG--ACAAGAAGGGAAAGATTTAAGCTG
1 CAACGACGGATCCAGT--ACCACA-AAGATACAA-AAGGGAAAGGTTTAAGTTG
* * * ** * *
11122 CAACGATGAATCCAGTACCACGAAGATTTAAAGGGGAAAGGTTTAAGTCG
1 CAACGACGGATCCAGTACCACAAAGATACAAAAGGGAAAGGTTTAAGTTG
11172 CAA
1 CAA
11175 TGGCGAACCC
Statistics
Matches: 80, Mismatches: 15, Indels: 16
0.72 0.14 0.14
Matches are distributed among these distances:
48 2 0.03
49 9 0.11
50 60 0.75
51 7 0.09
52 2 0.03
ACGTcount: A:0.40, C:0.18, G:0.26, T:0.16
Consensus pattern (50 bp):
CAACGACGGATCCAGTACCACAAAGATACAAAAGGGAAAGGTTTAAGTTG
Found at i:11126 original size:100 final size:100
Alignment explanation
Indices: 10898--11183 Score: 298
Period size: 100 Copynumber: 2.9 Consensus size: 100
10888 CCAATGCCGC
* * * * *
10898 GAAGACATGAAGGGAAAGATCTAAG-TCGCAATGGCGGATCCAATA-CACGAAG--ACACAAGGG
1 GAAGACAAGAAGGGAAAGATCTAAGCT-GCAACGACGGATCCAGTACCACGAAGATACAAAAGGG
* * * *
10959 AAAGGTTTAAGTTGTAATGGTGAACCTGGTACCTTA
65 AAAGGTTTAAGTTGCAATGGCGAACCTGGAACCTCA
* ** *
10995 G-AGACATA-AAGGGAAAGATCTAAACCACAACGACGGATCCAGTACCACAAAGATACAAAAGGG
1 GAAGACA-AGAAGGGAAAGATCTAAGCTGCAACGACGGATCCAGTACCACGAAGATACAAAAGGG
* *
11058 AAAGGTTTAAGTTGCAACGGCGGACC-GTGAACCTCA
65 AAAGGTTTAAGTTGCAATGGCGAACCTG-GAACCTCA
* * * ** *
11094 GAAGACAAGAAGGGAAAGATTTAAGCTGCAACGATGAATCCAGTACCACGAAGATTTAAAGGGGA
1 GAAGACAAGAAGGGAAAGATCTAAGCTGCAACGACGGATCCAGTACCACGAAGATACAAAAGGGA
*
11159 AAGGTTTAAGTCGCAATGGCGAACC
66 AAGGTTTAAGTTGCAATGGCGAACC
11184 CGATACCTTA
Statistics
Matches: 153, Mismatches: 28, Indels: 13
0.79 0.14 0.07
Matches are distributed among these distances:
96 34 0.22
97 7 0.05
98 1 0.01
99 38 0.25
100 73 0.48
ACGTcount: A:0.40, C:0.17, G:0.27, T:0.16
Consensus pattern (100 bp):
GAAGACAAGAAGGGAAAGATCTAAGCTGCAACGACGGATCCAGTACCACGAAGATACAAAAGGGA
AAGGTTTAAGTTGCAATGGCGAACCTGGAACCTCA
Found at i:11625 original size:39 final size:40
Alignment explanation
Indices: 11538--11682 Score: 138
Period size: 39 Copynumber: 3.7 Consensus size: 40
11528 TCGTTAACTA
* * * ** *
11538 ATCTCTTACCCCGAGCCTGGGGCAGATC-ATCA-TCAACCA
1 ATCTCTTACCACGAGCCTGAGGCAGATCGA-CAGCCATTCG
* *
11577 ATCTCTTACCAAGAGCCTGAGGCAGATCGA-AGCCATTTG
1 ATCTCTTACCACGAGCCTGAGGCAGATCGACAGCCATTCG
* *
11616 ATCTTTTACCACGAGCCTGAGGCAGAT-TACAGCCATTCG
1 ATCTCTTACCACGAGCCTGAGGCAGATCGACAGCCATTCG
*
11655 ATCTCTTATCC-CGAGCTTGAGGCAGATC
1 ATCTCTTA-CCACGAGCCTGAGGCAGATC
11683 ATCGTCAACC
Statistics
Matches: 87, Mismatches: 14, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
38 2 0.02
39 82 0.94
40 3 0.03
ACGTcount: A:0.26, C:0.30, G:0.21, T:0.24
Consensus pattern (40 bp):
ATCTCTTACCACGAGCCTGAGGCAGATCGACAGCCATTCG
Found at i:12294 original size:206 final size:205
Alignment explanation
Indices: 11790--12567 Score: 1066
Period size: 206 Copynumber: 3.8 Consensus size: 205
11780 CAACTCAAAG
* * * *
11790 GTGAGCAAATCTTCAAATCCCAGCTTCTTAATGAGATACTGAGAAGCAGGTCGAAGCAATAAAAT
1 GTGAGCAAATCTTCAAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCAAAGCAATAAAAT
*
11855 GGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACTGAGAA
66 GGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAA
* * * * * *
11920 GCGAATTGAAACAAGTGAGGCGGTCATCTTCCTGATGAGATAC-AG-AGATG--TATA-CCAACT
131 GCGAATTGAAACAAATGATGCGGTCATCTTCCTGATGAGATACTAGAAGAAGACCAAATCAAACT
*
11980 CGACGCTCAAT
196 C-ACGCTCGAT
* *
11991 GTGAGCAAATCTTCAAACCCCAGCTT-CTGATGAGATACTGAGAAGCAGGACAAAGTAATAAAAT
1 GTGAGCAAATCTTCAAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCAAAGCAATAAAAT
* * *
12055 GGTTAGCTTACTGATGAGATACCGAGAAGTGGACCAAATTTGTCTTCCTGATGAGATACAGAGAA
66 GGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAA
*
12120 GCGGATTGAAACAAATGATGCGGTCATCTTCCTGATGAGATACTAAGAAGAAGACCAAATCAAAC
131 GCGAATTGAAACAAATGATGCGGTCATCTTCCTGATGAGATACT-AGAAGAAGACCAAATCAAAC
12185 TCACGCTCGAT
195 TCACGCTCGAT
* ** * * *
12196 ATGAGCAAATCTTTGAACCCCAGCTTCCTGATGAGATACTGAGAAGTAGGTCGAAGTAATAAAAT
1 GTGAGCAAATCTTCAAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCAAAGCAATAAAAT
12261 GGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAA
66 GGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAA
*
12326 GCGAATTGAAACAAACGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAAC
131 GCGAATTGAAACAAATGATGCGGTCATCTTCCTGATGAGATACT-AGAAGAAGACCAAATCAAAC
*
12391 CCACGCTCGAT
195 TCACGCTCGAT
* ** * * * *
12402 GTGAACAAATCTTTGAACCCCAACTTCTTGATGAGATACTGAGAAGCAGGTCAAAACAATAAAGT
1 GTGAGCAAATCTTCAAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCAAAGCAATAAAAT
* * * * *
12467 GGTTAGCTTCCTGATGAGATA-TGGAGAAGTGAACCTAATCCGTCTTCCTGATGAAACACAGAGA
66 GGTTAGCTTCCTGATGAGATACT-GAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGA
* * ** * * *
12531 AGTGGATCAAAACAAGTGATACGATCATCTTCCTGAT
130 AGCGAATTGAAACAAATGATGCGGTCATCTTCCTGAT
12568 AAGAAGGCCA
Statistics
Matches: 516, Mismatches: 53, Indels: 11
0.89 0.09 0.02
Matches are distributed among these distances:
200 134 0.26
201 25 0.05
202 2 0.00
203 4 0.01
205 34 0.07
206 317 0.61
ACGTcount: A:0.35, C:0.19, G:0.22, T:0.24
Consensus pattern (205 bp):
GTGAGCAAATCTTCAAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCAAAGCAATAAAAT
GGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAA
GCGAATTGAAACAAATGATGCGGTCATCTTCCTGATGAGATACTAGAAGAAGACCAAATCAAACT
CACGCTCGAT
Found at i:12957 original size:34 final size:34
Alignment explanation
Indices: 12919--13014 Score: 88
Period size: 34 Copynumber: 2.9 Consensus size: 34
12909 TCTAATTTTT
* * *
12919 AATTTTAATTTACTTTAAGTTTGAATTT-GTTCTA
1 AATTTAAATTTACTTTAAGTTTAAATTTACTT-TA
* * *
12953 AATTTAAATTCATTTTTAGTTTAAATTTACTTTA
1 AATTTAAATTTACTTTAAGTTTAAATTTACTTTA
* * *
12987 AATTTAAATTTCCTGTAA-ATTAAATTTA
1 AATTTAAATTTACTTTAAGTTTAAATTTA
13015 ATTAAAAAGT
Statistics
Matches: 49, Mismatches: 12, Indels: 3
0.77 0.19 0.05
Matches are distributed among these distances:
33 9 0.18
34 38 0.78
35 2 0.04
ACGTcount: A:0.35, C:0.06, G:0.05, T:0.53
Consensus pattern (34 bp):
AATTTAAATTTACTTTAAGTTTAAATTTACTTTA
Found at i:12992 original size:17 final size:17
Alignment explanation
Indices: 12919--13014 Score: 79
Period size: 17 Copynumber: 5.7 Consensus size: 17
12909 TCTAATTTTT
*
12919 AATTTTAATTTACTTTA
1 AATTTAAATTTACTTTA
* * *
12936 AGTTTGAATTT-GTTCTA
1 AATTTAAATTTACTT-TA
* * *
12953 AATTTAAATTCATTTTT
1 AATTTAAATTTACTTTA
*
12970 AGTTTAAATTTACTTTA
1 AATTTAAATTTACTTTA
* *
12987 AATTTAAATTTCCTGTA
1 AATTTAAATTTACTTTA
13004 AA-TTAAATTTA
1 AATTTAAATTTA
13015 ATTAAAAAGT
Statistics
Matches: 61, Mismatches: 16, Indels: 5
0.74 0.20 0.06
Matches are distributed among these distances:
16 10 0.16
17 49 0.80
18 2 0.03
ACGTcount: A:0.35, C:0.06, G:0.05, T:0.53
Consensus pattern (17 bp):
AATTTAAATTTACTTTA
Found at i:13006 original size:51 final size:50
Alignment explanation
Indices: 12913--13012 Score: 128
Period size: 51 Copynumber: 2.0 Consensus size: 50
12903 ACTGAGTCTA
* * * **
12913 ATTTTTAATTTTAATTTACTTTAAGTTTGAATTTGTTCTAAATTTAAATTC
1 ATTTTTAATTTAAATTTACTTTAAATTTAAATTTCCTCTAAA-TTAAATTC
* *
12964 ATTTTTAGTTTAAATTTACTTTAAATTTAAATTTCCTGTAAATTAAATT
1 ATTTTTAATTTAAATTTACTTTAAATTTAAATTTCCTCTAAATTAAATT
13013 TAATTAAAAA
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
50 7 0.17
51 35 0.83
ACGTcount: A:0.34, C:0.06, G:0.05, T:0.55
Consensus pattern (50 bp):
ATTTTTAATTTAAATTTACTTTAAATTTAAATTTCCTCTAAATTAAATTC
Found at i:13772 original size:16 final size:17
Alignment explanation
Indices: 13735--13782 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 17
13725 TTAATAATAT
13735 TAATAATAACTATTTTAA
1 TAATAATAA-TATTTTAA
13753 TAATAATAATATTTAGTAA
1 TAATAATAATATTT--TAA
*
13772 TATTAATAATA
1 TAATAATAATA
13783 ATAAAATAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 5 0.19
18 9 0.33
19 13 0.48
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (17 bp):
TAATAATAATATTTTAA
Found at i:14904 original size:30 final size:29
Alignment explanation
Indices: 14870--15108 Score: 90
Period size: 30 Copynumber: 8.1 Consensus size: 29
14860 AACTATCTAG
*
14870 AATTCATATTTTAACCCCTAACTTTTCCAA
1 AATTCATATTTTAACCCCAAAC-TTTCCAA
* *
14900 AATTC-TATTTTGACCCCCAAACATTCCAAA
1 AATTCATATTTT-AACCCCAAACTTTCC-AA
*
14930 AATTACAT-TTTT-ACCCACGAACTTTCCAA
1 AATT-CATATTTTAACCC-CAAACTTTCCAA
* * * ***
14959 AATTCTTTTTTTGA-CCTTGA-TTTCCCAA
1 AATTCATATTTTAACCCCAAACTTT-CCAA
**
14987 AATTACAT-TTTT-ACCCCTAAACTTTGAAA
1 AATT-CATATTTTAACCCC-AAACTTTCCAA
*
15016 AATTCCA-ATTTTAACCTCGAAAC-TTCCAAA
1 AATT-CATATTTTAACC-CCAAACTTTCC-AA
* * *
15046 AATT-ACCATTTT-ACCCTCGAAC-TTCAAAA
1 AATTCA-TATTTTAACCC-CAAACTTTC-CAA
*
15075 AATTCCAT-TTTTAACCCCAAAACTTTCAAA
1 AATT-CATATTTTAACCCC-AAACTTTCCAA
15105 AATT
1 AATT
15109 ACCATTTTGC
Statistics
Matches: 159, Mismatches: 25, Indels: 50
0.68 0.11 0.21
Matches are distributed among these distances:
27 4 0.03
28 19 0.12
29 62 0.39
30 63 0.40
31 10 0.06
32 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.03, T:0.36
Consensus pattern (29 bp):
AATTCATATTTTAACCCCAAACTTTCCAA
Found at i:14957 original size:59 final size:58
Alignment explanation
Indices: 14877--15116 Score: 168
Period size: 59 Copynumber: 4.1 Consensus size: 58
14867 TAGAATTCAT
* * *
14877 ATTTTAACCCCTAACTTTTCCAAAATTCTATTTTGACCCCCAAACATTCCAAAAATTA-C
1 ATTTTTACCCCGAAC-TTTCAAAAATTCTATTTTGACCCCCAAA-ATTCCAAAAATTACC
* * *** * *
14936 ATTTTTACCCACGAACTTTCCAAAATTCTTTTTTTGA--CCTTGATTTCCCAAAATTA-C
1 ATTTTTACCC-CGAACTTTCAAAAATTC-TATTTTGACCCCCAAAATTCCAAAAATTACC
* * * * * * *
14993 ATTTTTACCCCTAAACTTTGAAAAATTCCAATTTTAACCTCGAAACTTCCAAAAATTACC
1 ATTTTTACCCC-GAACTTTCAAAAATT-CTATTTTGACCCCCAAAATTCCAAAAATTACC
* * * *
15053 A-TTTTACCCTCGAAC-TTCAAAAAATTCCATTTTTAACCCCAAAACTTTCAAAAATTACC
1 ATTTTTACCC-CGAACTTTC-AAAAATTCTATTTTGACCCCCAAAA-TTCCAAAAATTACC
15112 ATTTT
1 ATTTT
15117 GCCCTCAGAT
Statistics
Matches: 141, Mismatches: 29, Indels: 21
0.74 0.15 0.11
Matches are distributed among these distances:
56 1 0.01
57 39 0.28
58 18 0.13
59 66 0.47
60 17 0.12
ACGTcount: A:0.35, C:0.26, G:0.03, T:0.36
Consensus pattern (58 bp):
ATTTTTACCCCGAACTTTCAAAAATTCTATTTTGACCCCCAAAATTCCAAAAATTACC
Found at i:15281 original size:59 final size:58
Alignment explanation
Indices: 15013--15292 Score: 218
Period size: 59 Copynumber: 4.8 Consensus size: 58
15003 CTAAACTTTG
*
15013 AAAAATTCCAATTTTAACCTCGAAAC-TTCC-AAAAATTACCATTTTACCCTCGAACTTC
1 AAAAATTCCATTTTTAACCTCG-AACTTTCCTAAAAATTACCATTTTACCCTCGAA-TTC
* * *
15071 AAAAAATTCCATTTTTAACCCCAAAACTTT-C-AAAAATTACCATTTTGCCCTCAGATATT-
1 -AAAAATTCCATTTTTAACCTC-GAACTTTCCTAAAAATTACCATTTTACCCTC-GA-ATTC
* * * * *
15130 AGAAAATTCCATTTTTAATCCT-G-ATTTTTCTAAAAATTACCATTTTGCCCCCAAATGTTC
1 A-AAAATTCCATTTTTAA-CCTCGAACTTTCCTAAAAATTACCATTTTACCCTCGAA--TTC
* * * * * * *
15190 AAAAATTCTACTTTTGATCTTG-ATTTTTCTAAAAATTACCATTTTACCCTCGAATGTC
1 AAAAATTCCATTTTTAACCTCGAACTTTCCTAAAAATTACCATTTTACCCTCGAAT-TC
* * * *
15248 TAAAATTCCCTTTTTAAACTCGAACTTTCCT-AAAATTATCATTTT
1 AAAAATTCCATTTTTAACCTCGAACTTTCCTAAAAATTACCATTTT
15293 GCCCCCCTGA
Statistics
Matches: 181, Mismatches: 26, Indels: 29
0.77 0.11 0.12
Matches are distributed among these distances:
57 6 0.03
58 35 0.19
59 130 0.72
60 9 0.05
61 1 0.01
ACGTcount: A:0.35, C:0.23, G:0.05, T:0.38
Consensus pattern (58 bp):
AAAAATTCCATTTTTAACCTCGAACTTTCCTAAAAATTACCATTTTACCCTCGAATTC
Found at i:19192 original size:83 final size:84
Alignment explanation
Indices: 18718--21500 Score: 3938
Period size: 84 Copynumber: 33.1 Consensus size: 84
18708 AATTTAACAT
* * * * *
18718 TATTTAAATAAAAAGATTATTATTATATTACAATTTATATAAAATATTGTGTTCATTTGATAATA
1 TATTTAAATAAAAA-ATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAATA
* *
18783 TATTATTTATCAAATTTTCA
65 CATTATTTATCAAATTTTAA
* * *
18803 TATTTAAATTACAAATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAATAT
1 TATTTAAATAAAAAATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAATAC
*
18868 ATTATTTA-CTAAATTTAAA
66 ATTATTTATC-AAATTTTAA
*
18887 TATTTAAATAAAAAATTATTATTATATTACAATTTTTATCAAATAATATGTTGATTTGACAATAC
1 TATTTAAATAAAAAATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAATAC
*
18952 ATTATTT-TCTAAATTTAAA
66 ATTATTTATC-AAATTTTAA
* *
18971 TATTTAAATAAAAAATTATTATTATATTATAATTTTTATCAAATAATGTGTTGATTTAACAATAC
1 TATTTAAATAAAAAATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAATAC
*
19036 ATTATTTA-CTAATTTTAAA
66 ATTATTTATCAAATTTT-AA
*
19055 TATTTAAATAAAAAATTATTATTATATTACAATTTTTATCAAATAATGTATTGATTTGACAATAC
1 TATTTAAATAAAAAATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAATAC
* *
19120 ATTATGTATCAAATTTTCA
66 ATTATTTATCAAATTTTAA
* * * *
19139 TATTTAAAT-AAAAATTATTATTATATTATAGTTTTTATCAAATAATATGTTGATTTGAAAATAC
1 TATTTAAATAAAAAATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAATAC
* *
19203 ATTATTCA-CTAATTTTAAA
66 ATTATTTATCAAATTTT-AA
* *
19222 TATTTAAATAAAAAAATTATTATTATATTACATTTTTTATCAAATAACGTGTTGATTTGACAATA
1 TATTTAAAT-AAAAAATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAATA
*
19287 CATTATTTATCAAATTTTCA
65 CATTATTTATCAAATTTTAA
* * * *
19307 TATTTAAATAAAAAATTATTATTATATTACATTTTTTATCAAATAATTTGTTGATTTAATAATAC
1 TATTTAAATAAAAAATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAATAC
*
19372 ATTATTTATCAAATTTTTA
66 ATTATTTATCAAATTTTAA
*
19391 TATTTAAATAAAAAATTATTATTATATTACAATTTTTATCAAATAATATGTTGATTTGACAATAC
1 TATTTAAATAAAAAATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAATAC
* *
19456 ATTATATATCAAATTTTTA
66 ATTATTTATCAAATTTTAA
* * * *
19475 TATTTAAATAAAAAATTATTATTATATTACATTTTTTATAAAATAATGTGTTGATTTGATAATAT
1 TATTTAAATAAAAAATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAATAC
* *
19540 ATTACTTA-CTAATTTTAAA
66 ATTATTTATCAAATTTT-AA
* ** * *
19559 TATTTAAATAAAAAATTATTATTATATTATAATTTTTATCAAATAATGTACTGATTTGACAACAT
1 TATTTAAATAAAAAATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAATAC
*
19624 ATTATTTATCAAATTTTCA
66 ATTATTTATCAAATTTTAA
* * * *
19643 TATTTAAAT-AAAAATTATTATTATATTAAAATTCTTATCAAATAAAGTGTTGATTTGATAATAC
1 TATTTAAATAAAAAATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAATAC
*
19707 ATTATTTA-CTAATTTTAAA
66 ATTATTTATCAAATTTT-AA
* *
19726 TAATTAAATAAAAAATTATTATTATATTACAATTTTTATCAAATAAAT-TGTTTATTTGACAATA
1 TATTTAAATAAAAAATTATTATTATATTACAATTTTTATCAAAT-AATGTGTTGATTTGACAATA
* *
19790 CTTTATTTATCAAATTTTCA
65 CATTATTTATCAAATTTTAA
* * * *
19810 TATCTAAAT-AAAAATTATTATTATATTACAATTTTTATCAAATAATATATTAATTTGACAATAC
1 TATTTAAATAAAAAATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAATAC
* *
19874 ATTATTTAT-TAATTTTGGA
66 ATTATTTATCAAATTTT-AA
* * * * *
19893 TATTTAAATAAAAAATTACTATTATATTATAATTTTTATCAAATGATGTGTTGATTTTACAATAT
1 TATTTAAATAAAAAATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAATAC
* *
19958 ACTATTTATCAAATTTTCA
66 ATTATTTATCAAATTTTAA
* **
19977 TATTTAAATAAAAAATTATTATTATATTACAATTTTTATCAAATAATGTGTTAATTTGACAATTT
1 TATTTAAATAAAAAATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAATAC
*
20042 ATTATTTATCAAATTTTCA
66 ATTATTTATCAAATTTTAA
*
20061 TATTTAAATAAAAAATTATTATTATATTACAATTTTTATAAAATAATGTGTTGATTTGACAATAC
1 TATTTAAATAAAAAATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAATAC
*
20126 ATTATTTATCAAATTTTCA
66 ATTATTTATCAAATTTTAA
* *
20145 TATTTAAATAAAAAATTATTATTATATT-CAATTTTTATCAAATAATGTGTTGATTTGATAATAT
1 TATTTAAATAAAAAATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAATAC
*
20209 ATTATTTATCAAATTTTCA
66 ATTATTTATCAAATTTTAA
*
20228 TATTTAAAT-AAAAATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGATAATAC
1 TATTTAAATAAAAAATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAATAC
* *
20292 ATTATTTA-CTAGTTTTAAA
66 ATTATTTATCAAATTTT-AA
*
20311 TATTTAAATAAAAAATTATTATTATTATATTACAATTTTTATCAAATAATATGTTGATTTGACAA
1 TATTTAAAT-AAAAA--ATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAA
20376 TACATTATTTA--ATAATTTTAAA
63 TACATTATTTATCA-AATTTT-AA
* * *
20398 TATTTAAAT-AAAAATTATTATTATATTACAATTTTTATAAAATAATGTATTGATTTAACAATAC
1 TATTTAAATAAAAAATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAATAC
*
20462 ATTATTTATCAAATTTTCA
66 ATTATTTATCAAATTTTAA
** *
20481 TATTTAAATAAAAAATTATTATTATATT-CAATTTTTATCAAATAATACGTTGATTTGACAACAC
1 TATTTAAATAAAAAATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAATAC
* *
20545 ATTATTTATTAAATTTTCA
66 ATTATTTATCAAATTTTAA
*
20564 TATTTAAAT-AAAAATTATTATTATATTACAATTTTTATCAAATAATATGTTGATTTGACAATAC
1 TATTTAAATAAAAAATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAATAC
*
20628 ATTATTTAT-TAATTTTAAA
66 ATTATTTATCAAATTTT-AA
* *
20647 TATTTAAAT-AAAAATTATTATTATATTACAATTTTTATCAAATAATGTGTTGACTTGAAAATAC
1 TATTTAAATAAAAAATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAATAC
* * *
20711 AATAGTTATCAAATTTTCA
66 ATTATTTATCAAATTTTAA
* *
20730 TATTTAAAT-AAAAATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGATAATAT
1 TATTTAAATAAAAAATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAATAC
**
20794 ATTATTT-TTTAATTTTAAA
66 ATTATTTATCAAATTTT-AA
20813 TATTTAAATAAAAAATTATTATTATATTACAA-TTTTATCAAATAATGTGTTGATTTGACAATAC
1 TATTTAAATAAAAAATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAATAC
* *
20877 ATTATTTATAAAATTTTCA
66 ATTATTTATCAAATTTTAA
*
20896 TATTTAAATAAAAAATTATTATTATTATATTACAATTTTTATCAAGTAATGTGTTGATTTGACAA
1 TATTTAAAT-AAAAA--ATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAA
*
20961 TACATTATTTA-CTAATTTTAAA
63 TACATTATTTATCAAATTTT-AA
* * *
20983 TATTTAAATAAAAAATTATTATTATATTATAATTTTTATCAAATAAT-TATTGATTTGACAATAT
1 TATTTAAATAAAAAATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAATAC
*
21047 ATTATTTA-CTAATTTTAAA
66 ATTATTTATCAAATTTT-AA
21066 TATTTAAATAAAAAATTATTATTATATTACAA-TTTTATCAAATAATGTGTTGATTTGACAATAC
1 TATTTAAATAAAAAATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAATAC
* *
21130 ATTATTTATCGAATTTTCA
66 ATTATTTATCAAATTTTAA
*
21149 TATTTAAATAAAAAATTATTATTATTATATTACAATTTTTATCAAATAATGTATTGATTTGACAA
1 TATTTAAAT-AAAAA--ATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAA
*
21214 TACATTATTTATCAAATTTTCA
63 TACATTATTTATCAAATTTTAA
21236 TATTTAAATAAAAAAATATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAA
1 TATTTAAAT--AAAAA-ATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAA
*
21301 TACATTATTTA-CTAATTTTAA
63 TACATTATTTATCAAATTTTAA
* * *
21322 AATTTTAAATAAAATATTATTATTATATTACAATTTTTATCAAATAATATGTTGATTT-ACAATA
1 TA-TTTAAATAAAAAATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAATA
*
21386 CATTATTTAT-TAATTTTAAA
65 CATTATTTATCAAATTTT-AA
* *
21406 TATTTAAATAAAAAATTATTATTATATTATAATTTTTATCAAATAATATGTTGATTTGACAATAC
1 TATTTAAATAAAAAATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAATAC
* *
21471 ATTATATA-CTAATTTTAAA
66 ATTATTTATCAAATTTT-AA
21490 TATTTAAATAA
1 TATTTAAATAA
21501 CCAAAATAAC
Statistics
Matches: 2455, Mismatches: 191, Indels: 105
0.89 0.07 0.04
Matches are distributed among these distances:
82 92 0.04
83 854 0.35
84 1072 0.44
85 121 0.05
86 63 0.03
87 247 0.10
88 6 0.00
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.47
Consensus pattern (84 bp):
TATTTAAATAAAAAATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAATAC
ATTATTTATCAAATTTTAA
Found at i:21016 original size:39 final size:39
Alignment explanation
Indices: 20964--21102 Score: 124
Period size: 39 Copynumber: 3.4 Consensus size: 39
20954 TTGACAATAC
20964 ATTATTTACTAATTTTAAATATTTAAATAAAAAATTATT
1 ATTATTTACTAATTTTAAATATTTAAATAAAAAATTATT
* * ** *
21003 ATTATATTA-TAATTTTTATCAAATAATTATTGATTTGACAA-TA-T
1 ATTAT-TTACTAA--TTT-T-AAAT-A-T-TTAAATAAAAAATTATT
21047 ATTATTTACTAATTTTAAATATTTAAATAAAAAATTATT
1 ATTATTTACTAATTTTAAATATTTAAATAAAAAATTATT
21086 ATTATATTAC-AATTTTA
1 ATTAT-TTACTAATTTTA
21103 TCAAATAATG
Statistics
Matches: 78, Mismatches: 10, Indels: 24
0.70 0.09 0.21
Matches are distributed among these distances:
37 7 0.09
38 3 0.04
39 22 0.28
40 11 0.14
41 4 0.05
42 4 0.05
43 7 0.09
44 10 0.13
45 3 0.04
46 7 0.09
ACGTcount: A:0.45, C:0.04, G:0.01, T:0.50
Consensus pattern (39 bp):
ATTATTTACTAATTTTAAATATTTAAATAAAAAATTATT
Found at i:22849 original size:22 final size:22
Alignment explanation
Indices: 22790--22849 Score: 57
Period size: 22 Copynumber: 2.7 Consensus size: 22
22780 TATTTTTTAC
*
22790 AAATAAATTTTTTACATTTTCA
1 AAATATATTTTTTACATTTTCA
*****
22812 AAATATAAAAAATACATTTTCA
1 AAATATATTTTTTACATTTTCA
*
22834 AAATATTTTTTTTACA
1 AAATATATTTTTTACA
22850 AAAAAAAATT
Statistics
Matches: 26, Mismatches: 12, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.45
Consensus pattern (22 bp):
AAATATATTTTTTACATTTTCA
Found at i:24700 original size:84 final size:84
Alignment explanation
Indices: 24604--25446 Score: 1133
Period size: 84 Copynumber: 10.1 Consensus size: 84
24594 TAAATTGAAA
* * *
24604 ATTTGATAAAAATTGTAATATAATAATAATTTTTGATTTAAATATTTAAAATTAGTAAACAATTT
1 ATTTGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTTAAAATTAGTAAATAATGT
* *
24669 ATTGCCAAATCAACACAGT
66 ATTGTCAAATCAACACATT
* *
24688 ATTTGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTTAAATTTAGTAAATAAAGT
1 ATTTGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTTAAAATTAGTAAATAATGT
*
24753 ATTGTCAAATCAATACATT
66 ATTGTCAAATCAACACATT
* * * *
24772 ATTTGATAAAAATTGTAATATAATAATAATTTTTTATTTAAAT-GTGAAAATTCGATAAATAAAG
1 ATTTGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTTAAAATTAG-TAAATAATG
* *
24836 TATTATAAAATCAACACATT
65 TATTGTCAAATCAACACATT
* * * *
24856 ATTTGATAAAAATTATAGTATAATAATAATTTTTTATTGAAATATTTAAATTTAGTAAATAATGT
1 ATTTGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTTAAAATTAGTAAATAATGT
*
24921 ATTATCAAATCAACACATT
66 ATTGTCAAATCAACACATT
* * *
24940 ATTTGATAAAAATTGTAAAATAATAATAATTTTTTATTTAAATA-TGAAAATTTGATAAATAATG
1 ATTTGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTTAAAATTAG-TAAATAATG
25004 TATTGTCAAATCAACACATT
65 TATTGTCAAATCAACACATT
** * * *
25024 ATTTGAT-AAAATTACAATATAATAATAATTTTTTATTTAAATA-TGAAAATTTGATAAGTAATG
1 ATTTGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTTAAAATTAG-TAAATAATG
*
25087 TATTGTCAAATCAACACACT
65 TATTGTCAAATCAACACATT
* * * * * *
25107 ATTTAATAGAAACTGTAATATAATAATAATTTTTTACTTAAATATTTAAAATTAATAAATAACGT
1 ATTTGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTTAAAATTAGTAAATAATGT
* * *
25172 ATCGTCAAATCATCATATT
66 ATTGTCAAATCAACACATT
* * * *
25191 ATTTGATAAAAATTGTAATATAAAAATAATTTTTTATTTAAATA-TGAAAATTTGATATATAATG
1 ATTTGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTTAAAATTAG-TAAATAATG
*
25255 TATTGTCAAATCAATACATT
65 TATTGTCAAATCAACACATT
* ** *
25275 ATTTGATAAAAATTATAATATAATAAT-ATTTTTTATTTAAATATTT-AAATTAAAAAAATAATA
1 ATTTGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTTAAAATT-AGTAAATAATG
* *
25338 TATTGTCAAATTAACACAAT
65 TATTGTCAAATCAACACATT
* *
25358 ATTTAATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTTAAAATTAGTAAATAATTT
1 ATTTGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTTAAAATTAGTAAATAATGT
*
25423 ATTATCAAATCAACACATT
66 ATTGTCAAATCAACACATT
25442 ATTTG
1 ATTTG
Statistics
Matches: 663, Mismatches: 86, Indels: 20
0.86 0.11 0.03
Matches are distributed among these distances:
83 167 0.25
84 477 0.72
85 19 0.03
ACGTcount: A:0.47, C:0.05, G:0.06, T:0.42
Consensus pattern (84 bp):
ATTTGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTTAAAATTAGTAAATAATGT
ATTGTCAAATCAACACATT
Found at i:25194 original size:251 final size:252
Alignment explanation
Indices: 24604--25446 Score: 1242
Period size: 251 Copynumber: 3.4 Consensus size: 252
24594 TAAATTGAAA
* * * *
24604 ATTTGATAAAAATTGTAATATAATAATAATTTTTGATTTAAATATTTAAAATTAGTAAACAATTT
1 ATTTAATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTTAAAATTAGTAAATAATGT
** * *
24669 ATTGCCAAATCAACACAGTATTTGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATT
66 ATTATCAAATCAACACATTATTTGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATG
* * *
24734 TAAATTT-AGTAAATAAAGTATTGTCAAATCAATACATTATTTGATAAAAATTGTAATATAATAA
131 AAAATTTGA-TAAATAATGTATTGTCAAATCAATACATTATTTGATAAAAATTATAATATAATAA
* * * * * *
24798 TAATTTTTTATTTAAATGTGAAAATTCGATAAATAAAGTATTATAAAATCAACACATT
195 TAATTTTTTATTTAAATATGAAAATTAGATAAATAATGTATTGTCAAATCAACACAAT
* * * * *
24856 ATTTGATAAAAATTATAGTATAATAATAATTTTTTATTGAAATATTTAAATTTAGTAAATAATGT
1 ATTTAATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTTAAAATTAGTAAATAATGT
*
24921 ATTATCAAATCAACACATTATTTGATAAAAATTGTAAAATAATAATAATTTTTTATTTAAATATG
66 ATTATCAAATCAACACATTATTTGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATG
* *
24986 AAAATTTGATAAATAATGTATTGTCAAATCAACACATTATTTGAT-AAAATTACAATATAATAAT
131 AAAATTTGATAAATAATGTATTGTCAAATCAATACATTATTTGATAAAAATTATAATATAATAAT
* * *
25050 AATTTTTTATTTAAATATGAAAATTTGATAAGTAATGTATTGTCAAATCAACACACT
196 AATTTTTTATTTAAATATGAAAATTAGATAAATAATGTATTGTCAAATCAACACAAT
* * * * *
25107 ATTTAATAGAAACTGTAATATAATAATAATTTTTTACTTAAATATTTAAAATTAATAAATAACGT
1 ATTTAATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTTAAAATTAGTAAATAATGT
** * * *
25172 ATCGTCAAATCATCATATTATTTGATAAAAATTGTAATATAAAAATAATTTTTTATTTAAATATG
66 ATTATCAAATCAACACATTATTTGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATG
*
25237 AAAATTTGATATATAATGTATTGTCAAATCAATACATTATTTGATAAAAATTATAATATAATAAT
131 AAAATTTGATAAATAATGTATTGTCAAATCAATACATTATTTGATAAAAATTATAATATAATAAT
** * * * *
25302 -ATTTTTTATTTAAATATTTAAATTAAAAAAATAATATATTGTCAAATTAACACAAT
196 AATTTTTTATTTAAATATGAAAATTAGATAAATAATGTATTGTCAAATCAACACAAT
*
25358 ATTTAATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTTAAAATTAGTAAATAATTT
1 ATTTAATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTTAAAATTAGTAAATAATGT
25423 ATTATCAAATCAACACATTATTTG
66 ATTATCAAATCAACACATTATTTG
Statistics
Matches: 527, Mismatches: 62, Indels: 5
0.89 0.10 0.01
Matches are distributed among these distances:
251 350 0.66
252 176 0.33
253 1 0.00
ACGTcount: A:0.47, C:0.05, G:0.06, T:0.42
Consensus pattern (252 bp):
ATTTAATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTTAAAATTAGTAAATAATGT
ATTATCAAATCAACACATTATTTGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATG
AAAATTTGATAAATAATGTATTGTCAAATCAATACATTATTTGATAAAAATTATAATATAATAAT
AATTTTTTATTTAAATATGAAAATTAGATAAATAATGTATTGTCAAATCAACACAAT
Done.