Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007060.1 Kokia drynarioides strain JFW-HI SEQ_121669, 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: 71911
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Warning! 22 characters in sequence are not A, C, G, or T
Found at i:1730 original size:158 final size:158
Alignment explanation
Indices: 1416--1710 Score: 459
Period size: 158 Copynumber: 1.9 Consensus size: 158
1406 TTTCGAGATT
* * * * * *
1416 TACAGGTTATATGGGTGTTGGTCTTAGATGTCTTACACATGGTTGAGATCCTGCATTTATTGCGG
1 TACAAGTTATATGGGTGCTAGTCTTAGATGTCTTACACATGGCTGAGATACTGCATTTATTGCGA
* *
1481 ATTCTCCACAGCTCGTGTGAGTAGCATCGTGTAGCCCAACATCTCGACCCACAGCTCATGTGAGC
66 ATTCTCCACAGCTCATGTGAGCAGCATCGTGTAGCCCAACATCTCGACCCACAGCTCATGTGAGC
1546 AGGCCCACTTTACAACTCATGTGAGCAC
131 AGGCCCACTTTACAACTCATGTGAGCAC
*
1574 TACAAGTTATATGGGTGCTAGTCTTAGATGTCTTAC-CGATGGCTGAGATATTGCATTTATTGCG
1 TACAAGTTATATGGGTGCTAGTCTTAGATGTCTTACAC-ATGGCTGAGATACTGCATTTATTGCG
*
1638 AATTCTCCACAGCTCATGTGAGCAGCATCGTGTAGCCCAACATCTCGACCTACAGCT-ATTGTGA
65 AATTCTCCACAGCTCATGTGAGCAGCATCGTGTAGCCCAACATCTCGACCCACAGCTCA-TGTGA
*
1702 GCATGCCCA
129 GCAGGCCCA
1711 TTTCATAGCT
Statistics
Matches: 124, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
157 2 0.02
158 122 0.98
ACGTcount: A:0.24, C:0.24, G:0.23, T:0.29
Consensus pattern (158 bp):
TACAAGTTATATGGGTGCTAGTCTTAGATGTCTTACACATGGCTGAGATACTGCATTTATTGCGA
ATTCTCCACAGCTCATGTGAGCAGCATCGTGTAGCCCAACATCTCGACCCACAGCTCATGTGAGC
AGGCCCACTTTACAACTCATGTGAGCAC
Found at i:5109 original size:25 final size:26
Alignment explanation
Indices: 5064--5113 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
5054 AATTTTAAAT
*
5064 CATCAAAATTTTACTGGGAGTAAAAG
1 CATCAAAATTTTACTGAGAGTAAAAG
5090 CATCAAAATTTTACT-AGAGTAAAA
1 CATCAAAATTTTACTGAGAGTAAAA
5114 TTGGGATGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 8 0.35
26 15 0.65
ACGTcount: A:0.46, C:0.12, G:0.14, T:0.28
Consensus pattern (26 bp):
CATCAAAATTTTACTGAGAGTAAAAG
Found at i:13194 original size:44 final size:44
Alignment explanation
Indices: 13126--13210 Score: 152
Period size: 44 Copynumber: 1.9 Consensus size: 44
13116 GATAAATTGA
*
13126 CCATCTTGGAAGGAAGCCATATGGACACTTGACCTTCTAAGTTC
1 CCATCTTGGAAGGAAGCCACATGGACACTTGACCTTCTAAGTTC
*
13170 CCATCTTGGAATGAAGCCACATGGACACTTGACCTTCTAAG
1 CCATCTTGGAAGGAAGCCACATGGACACTTGACCTTCTAAG
13211 CTCTAAATTA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.28, C:0.26, G:0.20, T:0.26
Consensus pattern (44 bp):
CCATCTTGGAAGGAAGCCACATGGACACTTGACCTTCTAAGTTC
Found at i:15536 original size:57 final size:58
Alignment explanation
Indices: 15422--15557 Score: 132
Period size: 57 Copynumber: 2.3 Consensus size: 58
15412 AATTAAACAC
* * ** *
15422 TAAAGTCACACTCGAGTACTTAAATGGGACAAAGAAAAACTCAGGTACCAAAGTGAACTT
1 TAAAGTCAAACTCAAGTA--TAAATGGGACAAAGAAAAACTCAGACACCAAAGTGAACGT
** *
15482 TAAAGTCAAACTCAAGTATAAATTGGGAC-AA-AAAAACTCAGACACGGAATTGAACGT
1 TAAAGTCAAACTCAAGTATAAA-TGGGACAAAGAAAAACTCAGACACCAAAGTGAACGT
* * *
15539 TGAAGCCAAATTCAAGTAT
1 TAAAGTCAAACTCAAGTAT
15558 CAAACAGTAT
Statistics
Matches: 64, Mismatches: 11, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
57 36 0.56
58 6 0.09
59 6 0.09
60 16 0.25
ACGTcount: A:0.45, C:0.17, G:0.18, T:0.21
Consensus pattern (58 bp):
TAAAGTCAAACTCAAGTATAAATGGGACAAAGAAAAACTCAGACACCAAAGTGAACGT
Found at i:23636 original size:28 final size:30
Alignment explanation
Indices: 23574--23639 Score: 79
Period size: 28 Copynumber: 2.3 Consensus size: 30
23564 CCCTAGTAAG
23574 ATTTTTAAAAAAATTAGGAGTTTAATGAGA
1 ATTTTTAAAAAAATTAGGAGTTTAATGAGA
*
23604 A--TTTAAAAAAATT--GAGGTTTAATTA-A
1 ATTTTTAAAAAAATTAGGA-GTTTAATGAGA
23630 ATTTTTAAAA
1 ATTTTTAAAA
23640 TTTTTTGTGA
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
26 4 0.12
27 8 0.25
28 19 0.59
30 1 0.03
ACGTcount: A:0.48, C:0.00, G:0.12, T:0.39
Consensus pattern (30 bp):
ATTTTTAAAAAAATTAGGAGTTTAATGAGA
Found at i:23639 original size:27 final size:29
Alignment explanation
Indices: 23574--23639 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 29
23564 CCCTAGTAAG
23574 ATTTTTAAAAAAATTAGGAGTTTAATGAGA
1 ATTTTT-AAAAAATTAGGAGTTTAATGAGA
* *
23604 A-TTTAAAAAAATT--GAGGTTTAATTA-A
1 ATTTTTAAAAAATTAGGA-GTTTAATGAGA
23630 ATTTTTAAAA
1 ATTTTTAAAA
23640 TTTTTTGTGA
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
26 4 0.13
27 15 0.48
28 8 0.26
29 3 0.10
30 1 0.03
ACGTcount: A:0.48, C:0.00, G:0.12, T:0.39
Consensus pattern (29 bp):
ATTTTTAAAAAATTAGGAGTTTAATGAGA
Found at i:33911 original size:28 final size:24
Alignment explanation
Indices: 33830--33900 Score: 88
Period size: 24 Copynumber: 3.0 Consensus size: 24
33820 AGAAATAATC
* * * *
33830 TTTCAGTTAAACTCTGTTTAATTG
1 TTTCAATTAAACTCTATTTATTTT
*
33854 TTACAATTAAACTCTATTTATTTT
1 TTTCAATTAAACTCTATTTATTTT
*
33878 TTTCAATTAAACTGTATTTATTT
1 TTTCAATTAAACTCTATTTATTT
33901 GTTTGAGTCA
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.30, C:0.11, G:0.06, T:0.54
Consensus pattern (24 bp):
TTTCAATTAAACTCTATTTATTTT
Found at i:33913 original size:24 final size:24
Alignment explanation
Indices: 33838--33916 Score: 77
Period size: 24 Copynumber: 3.3 Consensus size: 24
33828 TCTTTCAGTT
* * * *
33838 AAACTCTGTTTAATTGTTACAATT
1 AAACTCTATTTATTTGTTTCAATC
* *
33862 AAACTCTATTTATTTTTTTCAATT
1 AAACTCTATTTATTTGTTTCAATC
* * *
33886 AAACTGTATTTATTTGTTTGAGTC
1 AAACTCTATTTATTTGTTTCAATC
33910 AAACTCT
1 AAACTCT
33917 TATTAGTCTA
Statistics
Matches: 45, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 45 1.00
ACGTcount: A:0.30, C:0.13, G:0.08, T:0.49
Consensus pattern (24 bp):
AAACTCTATTTATTTGTTTCAATC
Found at i:37637 original size:24 final size:24
Alignment explanation
Indices: 37560--37625 Score: 114
Period size: 24 Copynumber: 2.8 Consensus size: 24
37550 CTTTTAGTTG
*
37560 AACTCTGTTTAATTGTTTCAATTA
1 AACTCTGTTTATTTGTTTCAATTA
37584 AACTCTGTTTATTTGTTTCAATTA
1 AACTCTGTTTATTTGTTTCAATTA
*
37608 AACTCTATTTATTTGTTT
1 AACTCTGTTTATTTGTTT
37626 GAGTCAAACT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.26, C:0.12, G:0.08, T:0.55
Consensus pattern (24 bp):
AACTCTGTTTATTTGTTTCAATTA
Found at i:39509 original size:24 final size:24
Alignment explanation
Indices: 39423--39497 Score: 114
Period size: 24 Copynumber: 3.1 Consensus size: 24
39413 AGAAATACTC
* * *
39423 TTTCAGTTGAACTCTGTTTAATTG
1 TTTCAATTAAACTCTGTTTATTTG
39447 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAATTAAACTCTGTTTATTTG
*
39471 TTTCAATTAAACTCTATTTATTTG
1 TTTCAATTAAACTCTGTTTATTTG
39495 TTT
1 TTT
39498 AAGTCAAACT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 47 1.00
ACGTcount: A:0.24, C:0.12, G:0.09, T:0.55
Consensus pattern (24 bp):
TTTCAATTAAACTCTGTTTATTTG
Found at i:48389 original size:28 final size:25
Alignment explanation
Indices: 48331--48385 Score: 94
Period size: 24 Copynumber: 2.2 Consensus size: 25
48321 GAGAAATAAT
48331 TTTCAAGTTAAACTCTATTTATTTG
1 TTTCAAGTTAAACTCTATTTATTTG
*
48356 TTTCAA-TTAAACTCTGTTTATTTG
1 TTTCAAGTTAAACTCTATTTATTTG
48380 TTTCAA
1 TTTCAA
48386 TCAAATTCTT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
24 23 0.79
25 6 0.21
ACGTcount: A:0.27, C:0.13, G:0.07, T:0.53
Consensus pattern (25 bp):
TTTCAAGTTAAACTCTATTTATTTG
Found at i:48877 original size:27 final size:27
Alignment explanation
Indices: 48835--48891 Score: 105
Period size: 27 Copynumber: 2.1 Consensus size: 27
48825 TGAGATTATT
*
48835 AATTGCATTGTTAGCATTCCACCTCCA
1 AATTGCATTGTCAGCATTCCACCTCCA
48862 AATTGCATTGTCAGCATTCCACCTCCA
1 AATTGCATTGTCAGCATTCCACCTCCA
48889 AAT
1 AAT
48892 CCTTCTGCGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.28, C:0.30, G:0.11, T:0.32
Consensus pattern (27 bp):
AATTGCATTGTCAGCATTCCACCTCCA
Found at i:50030 original size:26 final size:25
Alignment explanation
Indices: 49986--50035 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
49976 AGCTGCTAAA
** *
49986 ATTTAAAATTATTAGTTAAGTTTAAT
1 ATTTAAAATTAAAAATTAA-TTTAAT
50012 ATTTAAAATTAAAAATTAATTTAA
1 ATTTAAAATTAAAAATTAATTTAA
50036 AATATCAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 5 0.24
26 16 0.76
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (25 bp):
ATTTAAAATTAAAAATTAATTTAAT
Found at i:55928 original size:19 final size:19
Alignment explanation
Indices: 55895--55947 Score: 58
Period size: 18 Copynumber: 2.9 Consensus size: 19
55885 GTATTATATT
55895 TTTAAATAAAAAAATAA-A
1 TTTAAATAAAAAAATAATA
*
55913 TTTAAATATTAAAAATAATA
1 TTTAAATA-AAAAAATAATA
*
55933 TTT--TTAAAAAAATAA
1 TTTAAATAAAAAAATAA
55948 CCACGAATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
17 8 0.27
18 10 0.33
19 8 0.27
20 4 0.13
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
TTTAAATAAAAAAATAATA
Found at i:56317 original size:3 final size:3
Alignment explanation
Indices: 56226--56306 Score: 56
Period size: 3 Copynumber: 27.0 Consensus size: 3
56216 AATAAGACTT
** * * *
56226 TAA TAA TAA TAA TGG TAA TAA TAA TAA TAA TAA TAT TAC TAA T-A TCAT
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA
* * ** *
56274 TAA TAA TAT TAA TGA CGA CAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
56307 ACATTAATAA
Statistics
Matches: 61, Mismatches: 15, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
2 2 0.03
3 58 0.95
4 1 0.02
ACGTcount: A:0.56, C:0.05, G:0.05, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:57447 original size:29 final size:29
Alignment explanation
Indices: 57393--57788 Score: 250
Period size: 29 Copynumber: 13.7 Consensus size: 29
57383 TAAACTATTA
* *
57393 AAAAATTCCATTTTTTCCCCTG-AACTTCC
1 AAAAATTCCATTTTTACCTC-GAAACTTCC
57422 -AAAATTCCATTTTTGACCTCGAAACTTCC
1 AAAAATTCCATTTTT-ACCTCGAAACTTCC
* *
57451 AAAAATTCTATTTTTACCCCCG-AACTTCC
1 AAAAATTCCATTTTTA-CCTCGAAACTTCC
*
57480 AAAAATTCTATTTTTAACC-CGAAACTTCC
1 AAAAATTCCATTTTT-ACCTCGAAACTTCC
* * *
57509 AAAAATTCCA-TTTTACCCCCAAACATCC
1 AAAAATTCCATTTTTACCTCGAAACTTCC
*
57537 AAAAATTCCATTTTGACC-CGGAAACTTCC
1 AAAAATTCCATTTTTACCTC-GAAACTTCC
*
57566 AAAAATT-CATTTTTTTCCCTCG-AACTTCC
1 AAAAATTCCA--TTTTTACCTCGAAACTTCC
** *
57595 AAAAATTATATTTTTTACCTCGAAAATTCC
1 AAAAATTCCA-TTTTTACCTCGAAACTTCC
** * *
57625 AAAAATAACATGTTTACCCTCG-AACCTCC
1 AAAAATTCCATTTTTA-CCTCGAAACTTCC
* * *
57654 AAAATTTCCATTTTTGATCC-CAAAACTTTC
1 AAAAATTCCATTTTT-A-CCTCGAAACTTCC
* * * *
57684 AAAAATTATCA-TTTTCCCCCG-GA-TGTCC
1 AAAAATT-CCATTTTTACCTCGAAACT-TCC
* * *
57712 AAAAACTCCATTTTCGACCTTGAAAC-TCTC
1 AAAAATTCCATTTT-TACCTCGAAACTTC-C
* *
57742 -AAAATTACACTTTTACCCTCG-AA-TGTCC
1 AAAAATTCCATTTTTA-CCTCGAAACT-TCC
*
57770 AAAAATTCCATTTTGACCT
1 AAAAATTCCATTTTTACCT
57789 TGAGAATCCA
Statistics
Matches: 289, Mismatches: 49, Indels: 59
0.73 0.12 0.15
Matches are distributed among these distances:
27 6 0.02
28 63 0.22
29 152 0.53
30 65 0.22
31 3 0.01
ACGTcount: A:0.34, C:0.28, G:0.05, T:0.34
Consensus pattern (29 bp):
AAAAATTCCATTTTTACCTCGAAACTTCC
Found at i:57476 original size:58 final size:58
Alignment explanation
Indices: 57393--57788 Score: 359
Period size: 58 Copynumber: 6.8 Consensus size: 58
57383 TAAACTATTA
* *
57393 AAAAATTCCATTTTTTCCCCTGAACTTCC-AAAATTCCATTTTTGACCTCGAAACTTCC
1 AAAAATT-CATTTTTACCCCCGAACTTCCAAAAATTCCATTTTTGACCTCGAAACTTCC
* *
57451 AAAAATTCTATTTTTACCCCCGAACTTCCAAAAATTCTATTTTTAACC-CGAAACTTCC
1 AAAAATTC-ATTTTTACCCCCGAACTTCCAAAAATTCCATTTTTGACCTCGAAACTTCC
* *
57509 AAAAATTCCA-TTTTACCCCCAAACATCCAAAAATTCCA-TTTTGACC-CGGAAACTTCC
1 AAAAATT-CATTTTTACCCCCGAACTTCCAAAAATTCCATTTTTGACCTC-GAAACTTCC
* * ** * *
57566 AAAAATTCATTTTTTTCCCTCGAACTTCCAAAAATTATATTTTTTACCTCGAAAATTCC
1 AAAAATTCA-TTTTTACCCCCGAACTTCCAAAAATTCCATTTTTGACCTCGAAACTTCC
* * * * * * *
57625 AAAAATAACATGTTTACCCTCGAACCTCCAAAATTTCCATTTTTGATCC-CAAAACTTTC
1 AAAAAT-TCATTTTTACCCCCGAACTTCCAAAAATTCCATTTTTGA-CCTCGAAACTTCC
* * * *
57684 AAAAATT-ATCATTTT-CCCCCGGA-TGTCCAAAAACTCCATTTTCGACCTTGAAAC-TCTC
1 AAAAATTCAT--TTTTACCCCCGAACT-TCCAAAAATTCCATTTTTGACCTCGAAACTTC-C
* *
57742 -AAAATTACACTTTTACCCTCGAA-TGTCCAAAAATTCCA-TTTTGACCT
1 AAAAATT-CATTTTTACCCCCGAACT-TCCAAAAATTCCATTTTTGACCT
57789 TGAGAATCCA
Statistics
Matches: 277, Mismatches: 43, Indels: 37
0.78 0.12 0.10
Matches are distributed among these distances:
56 10 0.04
57 65 0.23
58 113 0.41
59 84 0.30
60 5 0.02
ACGTcount: A:0.34, C:0.28, G:0.05, T:0.34
Consensus pattern (58 bp):
AAAAATTCATTTTTACCCCCGAACTTCCAAAAATTCCATTTTTGACCTCGAAACTTCC
Found at i:57563 original size:86 final size:86
Alignment explanation
Indices: 57393--57668 Score: 258
Period size: 86 Copynumber: 3.2 Consensus size: 86
57383 TAAACTATTA
* * *
57393 AAAAATTCCATTTTTTCCCCTGAACTTCC-AAAATTCCATTTTTGACCTCGAAACTTCCAAAAAT
1 AAAAATT-CATTTTTTCCCC-GAACTTCCAAAAATTCCATTTTTGACCCCCAAACATCCAAAAAT
* *
57457 TCTATTTTTACCCCCGAACTTCC
64 TCCATTTTGACCCCCGAACTTCC
**
57480 AAAAATTCTATTTTTAACCCGAAACTTCCAAAAATTCCA-TTTT-ACCCCCAAACATCCAAAAAT
1 AAAAATTC-ATTTTTTCCCCG-AACTTCCAAAAATTCCATTTTTGACCCCCAAACATCCAAAAAT
*
57543 TCCATTTTGA-CCCGGAAACTTCC
64 TCCATTTTGACCCCCG-AACTTCC
** * * *
57566 AAAAATTCATTTTTTTCCCTCGAACTTCCAAAAATTATATTTTTTACCTCGAAA-ATTCCAAAAA
1 AAAAATTCA-TTTTTTCCC-CGAACTTCCAAAAATTCCATTTTTGACCCCCAAACA-TCCAAAAA
** * *
57630 TAACATGTTT-ACCCTCGAACCTCC
63 TTCCAT-TTTGACCCCCGAACTTCC
*
57654 AAAATTTCCATTTTT
1 AAAAATT-CATTTTT
57669 GATCCCAAAA
Statistics
Matches: 157, Mismatches: 20, Indels: 23
0.79 0.10 0.12
Matches are distributed among these distances:
85 5 0.03
86 64 0.41
87 34 0.22
88 46 0.29
89 8 0.05
ACGTcount: A:0.34, C:0.27, G:0.04, T:0.34
Consensus pattern (86 bp):
AAAAATTCATTTTTTCCCCGAACTTCCAAAAATTCCATTTTTGACCCCCAAACATCCAAAAATTC
CATTTTGACCCCCGAACTTCC
Found at i:69908 original size:204 final size:205
Alignment explanation
Indices: 69548--70359 Score: 1067
Period size: 206 Copynumber: 4.0 Consensus size: 205
69538 GTGATTATCC
69548 ACAAACGACGCGGTCATCTTCCTGATGAGATATTGAGAAGAAGACCAAATCAAACCCACGCTTC-
1 ACAAACGACGCGGTCATCTTCCTGATGAGATATTGAGAAGAAGACCAAATCAAACCCACGC-TCG
* * * *
69612 ATGTGAGCAAATCTTCAAACCCTAGCTTCCTGATAAGACACTGAGAAGCAGGTCGAAGCAATAAA
65 ATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGTAATAAA
* * * *
69677 AAGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTTGTCTTCTTAATGAGATACAAAAA
130 AGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTAATGAGATACAAAGA
*
69742 AGCAAATTGAA
195 AGCGAATTGAA
** * * *
69753 ACAAATAATGCGGTCATCTTCCTGATTAGATATTGAGAAGAAGACCAAATCAAACCCATGCTCGA
1 ACAAACGACGCGGTCATCTTCCTGATGAGATATTGAGAAGAAGACCAAATCAAACCCACGCTCGA
69818 TGTGAGCAAATCTTCGAA-CCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAA-TCAATAAA
66 TGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGT-AATAAA
* * * *
69881 AGGTTAGCTTCCTGATGAGATACTGAGAAGTAGACCAAATTCATCTTCCTGATGAGATACAGAGA
130 AGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTAATGAGATACAAAGA
69946 AGCGAATTGAA
195 AGCGAATTGAA
* * * *
69957 ACAAACGGCGCGGTCATCTTCTTGATGAGATATTAAGAAGAAGACCAAATCAAACCCCCGCTCGA
1 ACAAACGACGCGGTCATCTTCCTGATGAGATATTGAGAAGAAGACCAAATCAAACCCACGCTCGA
* * * * *
70022 TGTGAGCAAATCCTCGAATCTCAGCTTCCTGATGAGATACTGAGAAGCAGGTTGAAGTAATAAAA
66 TGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGTAATAAAA
* *
70087 TGGTTAGCTTCCTGATGAGATACTGAGAAGTGTACCAAATTCGTCTTCCTATTGAGATACAAAGA
131 -GGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTAATGAGATACAAAGA
*
70152 AGCGGATTGAA
195 AGCGAATTGAA
* * * ** * *
70163 ACAAACGACGCGATCAGCTTCCTGATGAGACACAGA-AGAGAAGACCAAATCAAACTCATGCTCG
1 ACAAACGACGCGGTCATCTTCCTGATGAGATATTGAGA-AGAAGACCAAATCAAACCCACGCTCG
* * * *
70227 ATGTGAGCAAATCTTCGAACCCCAACTTCCTGATGAGATACTGAGAAGTAAGTCGAAGTAATAAA
65 ATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGTAAT-AA
* * * * * ** * * * *
70292 AAGGTTAAG-TTCCTGATAAAATACGGGGAAGTGAACCAAAACCATCTTCCTGATGAAACACAAA
129 AAGGTT-AGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTAATGAGATACAAA
70356 GAAG
193 GAAG
70360 TGGATCAAAA
Statistics
Matches: 531, Mismatches: 68, Indels: 15
0.86 0.11 0.02
Matches are distributed among these distances:
204 183 0.34
205 116 0.22
206 226 0.43
207 6 0.01
ACGTcount: A:0.37, C:0.20, G:0.21, T:0.22
Consensus pattern (205 bp):
ACAAACGACGCGGTCATCTTCCTGATGAGATATTGAGAAGAAGACCAAATCAAACCCACGCTCGA
TGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGTAATAAAA
GGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTAATGAGATACAAAGAA
GCGAATTGAA
Found at i:70794 original size:6 final size:6
Alignment explanation
Indices: 70772--70843 Score: 60
Period size: 6 Copynumber: 12.0 Consensus size: 6
70762 GTTTAAATTG
* * *
70772 ATTTAA ATTTAT TTTTAA ATTTAA ATTT-- ATCTTAA ATTTAA ATTTATCT
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA AT-TTAA ATTTAA ATTTA--A
*
70821 TTTTAA ATTTAA ATTT-A ATTTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA
70844 TTTGACTTAA
Statistics
Matches: 52, Mismatches: 8, Indels: 12
0.72 0.11 0.17
Matches are distributed among these distances:
4 2 0.04
5 7 0.13
6 37 0.71
7 2 0.04
8 4 0.08
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (6 bp):
ATTTAA
Found at i:70808 original size:17 final size:17
Alignment explanation
Indices: 70772--70837 Score: 87
Period size: 17 Copynumber: 3.6 Consensus size: 17
70762 GTTTAAATTG
*
70772 ATTTAAATTTATTTTTAA
1 ATTTAAATTTA-TCTTAA
70790 ATTTAAATTTATCTTAA
1 ATTTAAATTTATCTTAA
70807 ATTTAAATTTATCTTTTTAA
1 ATTTAAATTTATC---TTAA
70827 ATTTAAATTTA
1 ATTTAAATTTA
70838 ATTTAATTTG
Statistics
Matches: 44, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
17 18 0.41
18 11 0.25
20 15 0.34
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (17 bp):
ATTTAAATTTATCTTAA
Found at i:70817 original size:29 final size:28
Alignment explanation
Indices: 70763--70817 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 28
70753 TTAAGTTTGG
**
70763 TTTAAATTGATTTAAATTTATTTTTAAA
1 TTTAAATTGATTTAAATTTAAATTTAAA
*
70791 TTTAAATTTATCTTAAATTTAAATTTA
1 TTTAAATTGAT-TTAAATTTAAATTTA
70818 TCTTTTTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 10 0.43
29 13 0.57
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (28 bp):
TTTAAATTGATTTAAATTTAAATTTAAA
Done.