Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012259.1 Kokia drynarioides strain JFW-HI SEQ_127260, 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: 65094
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 24 characters in sequence are not A, C, G, or T
Found at i:2195 original size:199 final size:199
Alignment explanation
Indices: 1846--2439 Score: 879
Period size: 199 Copynumber: 3.0 Consensus size: 199
1836 AACGACGCGG
* **
1846 TCATCTTCCTAGA-GAGATACTGAGAAGAAGA-CCAAATTAGGCCTACGCTCAAAGCGAGCGAAA
1 TCATCTTCCTA-ATGAGACACTGAGAAGAAGACCCAAACGAGG-CT-CG---AAA-CGAGC-AAA
* * * *
1909 TCTTC-GAACCCTAGCTTCCTGATGAGACACTGAGAAGTAAGTGGAAGAAATAAATGGATAGCTT
58 TCTTCAAAACCC-AGCTTCCTGATGAGACACTGAGAAGCAGGTGGAAGAAATAAATGGTTAGCTT
*
1973 CCAGATGAGGTACTGATAAGTGAACCGAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGA
122 CCAGATGAGGTACTGAGAAGTGAACCGAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGA
2038 AACAGTGATGGGA
187 AACAGTGATGGGA
* *
2051 TCATCTTCCTGATGAGGCACTGAGAAGAAGACCCAAACGAGGCTCGAAACGAGCAAATCTTCAAA
1 TCATCTTCCTAATGAGACACTGAGAAGAAGACCCAAACGAGGCTCGAAACGAGCAAATCTTCAAA
* *
2116 ACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTGGAAGAAATAAATGGTTAGCTTCTAGAGGAG
66 ACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTGGAAGAAATAAATGGTTAGCTTCCAGATGAG
* * *
2181 GTACTGAGAAGTGAACCAAATTCGTCTTCCTTATGAGATACAGAGAAGCGAATTGAAACAGTGAT
131 GTACTGAGAAGTGAACCGAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAACAGTGAT
2246 GGGA
196 GGGA
* * *
2250 TCATCTTCCTAATGAGACACTGAGAAGAAGACCTAAACGAGGCTTGAAACGAGAAAATCTTCAAA
1 TCATCTTCCTAATGAGACACTGAGAAGAAGACCCAAACGAGGCTCGAAACGAGCAAATCTTCAAA
* *
2315 ACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTGGAAGCAATAAATGGTTAGCTTCCAGATAAG
66 ACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTGGAAGAAATAAATGGTTAGCTTCCAGATGAG
* * *
2380 GTACTGAGAAGTGAGCCGAATTCGCCTTCTTGATGAGATACAGAGAAGCGGATTGAAACA
131 GTACTGAGAAGTGAACCGAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAACA
2440 AACGACGCGG
Statistics
Matches: 356, Mismatches: 30, Indels: 12
0.89 0.08 0.03
Matches are distributed among these distances:
199 304 0.85
200 10 0.03
201 3 0.01
204 3 0.01
205 28 0.08
206 8 0.02
ACGTcount: A:0.36, C:0.19, G:0.25, T:0.21
Consensus pattern (199 bp):
TCATCTTCCTAATGAGACACTGAGAAGAAGACCCAAACGAGGCTCGAAACGAGCAAATCTTCAAA
ACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTGGAAGAAATAAATGGTTAGCTTCCAGATGAG
GTACTGAGAAGTGAACCGAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAACAGTGAT
GGGA
Found at i:2816 original size:6 final size:6
Alignment explanation
Indices: 2805--2882 Score: 74
Period size: 6 Copynumber: 13.5 Consensus size: 6
2795 ATTTGTTTAA
* * *
2805 AAATTT AAATTT -ATTTT AAATTT AAATTT -ATTTT GAATTT AAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT
* *
2851 -AATTT AAGTTT AAATTT -ATTTT CAAATTT AAA
1 AAATTT AAATTT AAATTT AAATTT -AAATTT AAA
2883 ATTACTATAA
Statistics
Matches: 58, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
5 17 0.29
6 37 0.64
7 4 0.07
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (6 bp):
AAATTT
Found at i:2824 original size:11 final size:11
Alignment explanation
Indices: 2825--2880 Score: 51
Period size: 11 Copynumber: 4.9 Consensus size: 11
2815 TTATTTTAAA
2825 TTTAAATTTAT
1 TTTAAATTTAT
* *
2836 TTTGAATTTAAA
1 TTTAAATTT-AT
*
2848 TTT-AATTTAAG
1 TTTAAATTT-AT
2859 TTTAAATTTAT
1 TTTAAATTTAT
2870 TTTCAAATTTA
1 TTT-AAATTTA
2881 AAATTACTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
11 22 0.58
12 16 0.42
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.57
Consensus pattern (11 bp):
TTTAAATTTAT
Found at i:2827 original size:17 final size:17
Alignment explanation
Indices: 2790--2882 Score: 123
Period size: 17 Copynumber: 5.4 Consensus size: 17
2780 CTAAACTCCC
* *
2790 TTTAAATTTGTTTAAAAA
1 TTTAAATTTATTT-TAAA
2808 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
*
2825 TTTAAATTTATTTTGAA
1 TTTAAATTTATTTTAAA
* *
2842 TTTAAATTTAATTTAAG
1 TTTAAATTTATTTTAAA
2859 TTTAAATTTATTTTCAAA
1 TTTAAATTTATTTT-AAA
2877 TTTAAA
1 TTTAAA
2883 ATTACTATAA
Statistics
Matches: 66, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
17 46 0.70
18 20 0.30
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:2833 original size:23 final size:23
Alignment explanation
Indices: 2805--2882 Score: 54
Period size: 23 Copynumber: 3.4 Consensus size: 23
2795 ATTTGTTTAA
* *
2805 AAATTTAAATTTATTTTAAATTT
1 AAATTTAAATTTAATTTAAGTTT
* *
2828 AAATTT-ATTTTGAATTTAAATTT
1 AAATTTAAATTT-AATTTAAGTTT
* *
2851 -AATTTAAGTTTAAATTT-ATTTT
1 AAATTTAAATTT-AATTTAAGTTT
2873 CAAATTTAAA
1 -AAATTTAAA
2883 ATTACTATAA
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
22 13 0.29
23 25 0.56
24 7 0.16
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (23 bp):
AAATTTAAATTTAATTTAAGTTT
Found at i:4859 original size:30 final size:29
Alignment explanation
Indices: 4815--5010 Score: 137
Period size: 30 Copynumber: 6.6 Consensus size: 29
4805 TAGATTGTCC
** **
4815 AAAAATCATGTTTTAACCCCAAAACTTTT
1 AAAAATCACATTTTAACCCCAAAACTTCA
* * *
4844 GAAAATTACTATTTT-ACCCCCAAACTTCCA
1 AAAAATCAC-ATTTTAACCCCAAAACTT-CA
*
4874 AAAAATCACATTTCTAACCCCGAAACTTCA
1 AAAAATCACATTT-TAACCCCAAAACTTCA
* *
4904 AAAAATCACCATTTTAACCCCAAAA-TACC
1 AAAAATCA-CATTTTAACCCCAAAACTTCA
* * * ** *
4933 AAAAATCCCATTTTGACCTCGAACCCTT-T
1 AAAAATCACATTTTAACC-CCAAAACTTCA
* *
4962 AAAAATCCCAATTTTAACCCCAAAACTTCC
1 AAAAATCAC-ATTTTAACCCCAAAACTTCA
*
4992 AAAAATCCCATTTTTAACC
1 AAAAATCACA-TTTTAACC
5011 TTGAACCTTC
Statistics
Matches: 132, Mismatches: 25, Indels: 19
0.75 0.14 0.11
Matches are distributed among these distances:
28 9 0.07
29 49 0.37
30 58 0.44
31 16 0.12
ACGTcount: A:0.41, C:0.29, G:0.03, T:0.28
Consensus pattern (29 bp):
AAAAATCACATTTTAACCCCAAAACTTCA
Found at i:4900 original size:60 final size:58
Alignment explanation
Indices: 4812--5075 Score: 201
Period size: 60 Copynumber: 4.4 Consensus size: 58
4802 CCTTAGATTG
** * * * * *
4812 TCCAAAAATCATGTTTTAACCCCAAAACTTTTGAAAATTACTATTTTACCCCCAAACT
1 TCCAAAAATCACATTTTAACCCCGAAACTTCTAAAAATCACCATTTTACCCCCAAACT
* * *
4870 TCCAAAAAATCACATTTCTAACCCCGAAACTTCAAAAAATCACCATTTTAACCCCAAAAT
1 TCC-AAAAATCACATTT-TAACCCCGAAACTTCTAAAAATCACCATTTTACCCCCAAACT
* * * * * *
4930 ACCAAAAATCCCATTTTGACCTCGAACCCTT-TAAAAATC-CCAATTTTAACCCCAAAACT
1 TCCAAAAATCACATTTTAACCCCGAA-ACTTCTAAAAATCACC-ATTTT-ACCCCCAAACT
* ** * * * *
4989 TCCAAAAATCCCATTTTTAACCTTGAACCTTCTAAAAATTACCATTTTGCCCCCGAA-T
1 TCCAAAAATCACA-TTTTAACCCCGAAACTTCTAAAAATCACCATTTTACCCCCAAACT
* *
5047 TCTCAAAAATCCCAATTTTTAACCTCGAA
1 TC-CAAAAATCAC-A-TTTTAACCCCGAA
5076 TGTCCAAACT
Statistics
Matches: 169, Mismatches: 27, Indels: 18
0.79 0.13 0.08
Matches are distributed among these distances:
57 2 0.01
58 26 0.15
59 66 0.39
60 73 0.43
61 2 0.01
ACGTcount: A:0.39, C:0.29, G:0.03, T:0.29
Consensus pattern (58 bp):
TCCAAAAATCACATTTTAACCCCGAAACTTCTAAAAATCACCATTTTACCCCCAAACT
Found at i:4965 original size:29 final size:29
Alignment explanation
Indices: 4874--5075 Score: 124
Period size: 30 Copynumber: 6.8 Consensus size: 29
4864 CAAACTTCCA
* * * *
4874 AAAAATCACATTTCTAACCCCGAAACTTCA
1 AAAAATCCCATTT-TAACCTCGAACCTTCT
* ** * *
4904 AAAAATCACCATTTTAACC-CCAAAATACC
1 AAAAATC-CCATTTTAACCTCGAACCTTCT
*
4933 AAAAATCCCATTTTGACCTCGAACCCTT-T
1 AAAAATCCCATTTTAACCTCGAA-CCTTCT
* * * *
4962 AAAAATCCCAATTTTAACCCCAAAACTTCC
1 AAAAATCCC-ATTTTAACCTCGAACCTTCT
*
4992 AAAAATCCCATTTTTAACCTTGAACCTTCT
1 AAAAATCCCA-TTTTAACCTCGAACCTTCT
* ** *
5022 AAAAATTACCATTTTGCCCCCGAA--TTCT
1 AAAAA-TCCCATTTTAACCTCGAACCTTCT
5050 CAAAAATCCCAATTTTTAACCTCGAA
1 -AAAAATCCC-A-TTTTAACCTCGAA
5076 TGTCCAAACT
Statistics
Matches: 132, Mismatches: 30, Indels: 20
0.73 0.16 0.11
Matches are distributed among these distances:
28 17 0.13
29 35 0.27
30 71 0.54
31 9 0.07
ACGTcount: A:0.39, C:0.30, G:0.03, T:0.28
Consensus pattern (29 bp):
AAAAATCCCATTTTAACCTCGAACCTTCT
Found at i:4994 original size:59 final size:59
Alignment explanation
Indices: 4845--5075 Score: 222
Period size: 60 Copynumber: 3.9 Consensus size: 59
4835 AAAACTTTTG
* * * * * * *
4845 AAAATTACTATTTT-ACCCCCAAACTTCCAAAAAATCACATTTCTAACCCCGAAACTTCAA
1 AAAATCACCATTTTAACCCCAAAACTTCC-AAAAATCCCATTT-TAACCTCGAACCTTCTA
* *
4905 AAAATCACCATTTTAACCCCAAAA-TACCAAAAATCCCATTTTGACCTCGAACCCTT-TA
1 AAAATCACCATTTTAACCCCAAAACTTCCAAAAATCCCATTTTAACCTCGAA-CCTTCTA
*
4963 AAAATC-CCAATTTTAACCCCAAAACTTCCAAAAATCCCATTTTTAACCTTGAACCTTCTA
1 AAAATCACC-ATTTTAACCCCAAAACTTCCAAAAATCCCA-TTTTAACCTCGAACCTTCTA
* * **
5023 AAAATTACCATTTT-GCCCCCGAA-TTCTCAAAAATCCCAATTTTTAACCTCGAA
1 AAAATCACCATTTTAACCCCAAAACTTC-CAAAAATCCC-A-TTTTAACCTCGAA
5076 TGTCCAAACT
Statistics
Matches: 145, Mismatches: 17, Indels: 18
0.81 0.09 0.10
Matches are distributed among these distances:
57 2 0.01
58 33 0.23
59 48 0.33
60 52 0.36
61 10 0.07
ACGTcount: A:0.39, C:0.30, G:0.03, T:0.28
Consensus pattern (59 bp):
AAAATCACCATTTTAACCCCAAAACTTCCAAAAATCCCATTTTAACCTCGAACCTTCTA
Found at i:14905 original size:24 final size:26
Alignment explanation
Indices: 14878--14925 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
14868 TTTACCATTT
14878 AGGTTTA-AAAAT-ATTGTGAAAAAG
1 AGGTTTATAAAATAATTGTGAAAAAG
*
14902 AGGTTTATAAAATAATTTTGAAAA
1 AGGTTTATAAAATAATTGTGAAAA
14926 GTTTGATAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.33
25 5 0.24
26 9 0.43
ACGTcount: A:0.50, C:0.00, G:0.17, T:0.33
Consensus pattern (26 bp):
AGGTTTATAAAATAATTGTGAAAAAG
Found at i:15509 original size:16 final size:18
Alignment explanation
Indices: 15488--15522 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
15478 AACATATGAA
15488 TAATA-TTTT-ATAAATT
1 TAATATTTTTCATAAATT
15504 TAATATTTTTCATAAATT
1 TAATATTTTTCATAAATT
15522 T
1 T
15523 TTAAAGTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.29
17 4 0.24
18 8 0.47
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (18 bp):
TAATATTTTTCATAAATT
Found at i:15532 original size:27 final size:26
Alignment explanation
Indices: 15487--15579 Score: 75
Period size: 28 Copynumber: 3.4 Consensus size: 26
15477 TAACATATGA
15487 ATAATATTTTATAAATTTAATATTTTT
1 ATAATATTTT-TAAATTTAATATTTTT
*
15514 CATAA-ATTTTTAAAGTTT-ATGATATTTA
1 -ATAATATTTTTAAA-TTTAAT-AT-TTTT
*
15542 ATAA-ACTTTTTAGAATTTCAAAATTTTT
1 ATAATA-TTTTTA-AATTT-AATATTTTT
15570 ATAATATTTT
1 ATAATATTTT
15580 AATAATTTCA
Statistics
Matches: 54, Mismatches: 3, Indels: 16
0.74 0.04 0.22
Matches are distributed among these distances:
26 6 0.11
27 15 0.28
28 27 0.50
29 5 0.09
30 1 0.02
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.54
Consensus pattern (26 bp):
ATAATATTTTTAAATTTAATATTTTT
Found at i:16906 original size:17 final size:18
Alignment explanation
Indices: 16881--16914 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
16871 TGTTTTACTT
*
16881 ATTTTCATT-TTTATTTA
1 ATTTCCATTATTTATTTA
16898 ATTTCCATTATTTATTT
1 ATTTCCATTATTTATTT
16915 CAAATTTAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.24, C:0.09, G:0.00, T:0.68
Consensus pattern (18 bp):
ATTTCCATTATTTATTTA
Found at i:18964 original size:6 final size:6
Alignment explanation
Indices: 18953--19002 Score: 57
Period size: 6 Copynumber: 8.5 Consensus size: 6
18943 GTTTAAGTCG
* * **
18953 ATTTAA ATTTAA ATTTAA ATTTAT CTTTAA ATTT-A ATCAAA ATTTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
19000 ATT
1 ATT
19003 GATATTAAAT
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
5 3 0.09
6 32 0.91
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (6 bp):
ATTTAA
Found at i:20823 original size:30 final size:31
Alignment explanation
Indices: 20781--20884 Score: 117
Period size: 30 Copynumber: 3.5 Consensus size: 31
20771 TAAATTGTCT
*
20781 AAAAATT-CCATTTTTTACCTCAAAACTTTC
1 AAAAATTACTATTTTTTACCTCAAAACTTTC
* * * *
20811 GAAAATTAC-A-TTTTTACCCCCAAACTTCC
1 AAAAATTACTATTTTTTACCTCAAAACTTTC
* *
20840 AAAAATT-CTATTTTTGACCTCGAAACTTTC
1 AAAAATTACTATTTTTTACCTCAAAACTTTC
20870 AAAAATTACTATTTT
1 AAAAATTACTATTTT
20885 ACCCTAGAAT
Statistics
Matches: 61, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
28 1 0.02
29 23 0.38
30 29 0.48
31 8 0.13
ACGTcount: A:0.37, C:0.22, G:0.03, T:0.38
Consensus pattern (31 bp):
AAAAATTACTATTTTTTACCTCAAAACTTTC
Found at i:20835 original size:29 final size:29
Alignment explanation
Indices: 20781--20888 Score: 103
Period size: 29 Copynumber: 3.7 Consensus size: 29
20771 TAAATTGTCT
* *
20781 AAAAATTCCATTTTTTACCTCAAAACTTTC
1 AAAAATTACA-TTTTTACCCCAAAACTTTC
* * *
20811 GAAAATTACATTTTTACCCCCAAACTTCC
1 AAAAATTACATTTTTACCCCAAAACTTTC
* *
20840 AAAAATT-CTATTTTTGACCTCGAAACTTTC
1 AAAAATTAC-ATTTTT-ACCCCAAAACTTTC
20870 AAAAATTAC-TATTTTACCC
1 AAAAATTACAT-TTTTACCC
20889 TAGAATATCC
Statistics
Matches: 64, Mismatches: 10, Indels: 9
0.77 0.12 0.11
Matches are distributed among these distances:
28 1 0.02
29 32 0.50
30 30 0.47
31 1 0.02
ACGTcount: A:0.36, C:0.24, G:0.03, T:0.37
Consensus pattern (29 bp):
AAAAATTACATTTTTACCCCAAAACTTTC
Found at i:20875 original size:59 final size:59
Alignment explanation
Indices: 20781--20913 Score: 173
Period size: 59 Copynumber: 2.3 Consensus size: 59
20771 TAAATTGTCT
* *
20781 AAAAATTCCATTTTTTACCTCAAAACTTTCGAAAATTAC-ATTTTTACCCCCA-AACT-TCC
1 AAAAATTCCATTTTTGACCTCAAAACTTTCAAAAATTACTA-TTTTA-CCCCAGAA-TATCC
* * *
20840 AAAAATTCTATTTTTGACCTCGAAACTTTCAAAAATTACTATTTTACCCTAGAATATCC
1 AAAAATTCCATTTTTGACCTCAAAACTTTCAAAAATTACTATTTTACCCCAGAATATCC
20899 AAAAATTCCATTTTT
1 AAAAATTCCATTTTT
20914 TTTATCCTGA
Statistics
Matches: 65, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
58 5 0.08
59 59 0.91
60 1 0.02
ACGTcount: A:0.37, C:0.23, G:0.03, T:0.38
Consensus pattern (59 bp):
AAAAATTCCATTTTTGACCTCAAAACTTTCAAAAATTACTATTTTACCCCAGAATATCC
Found at i:21348 original size:96 final size:96
Alignment explanation
Indices: 21242--21425 Score: 257
Period size: 96 Copynumber: 1.9 Consensus size: 96
21232 AAAACTTTAA
*
21242 AATCGAGGCAATA-TTCTTTTAT-TTCGAGTT-TCGAAAATTTCCGCCTTAACTTACTAGGTGCA
1 AATCGAGGCAATATTTC-CTTATCTTCGA-TTCT-GAAAATTTCCGCCTTAACTTACTAGGTGCA
**
21304 ATTTTTCTTCAAATCGAAATAATCGAGTACCTTT
63 ACCTTTCTTCAAATCGAAATAATCGAGTACCTTT
* *
21338 AATCGAGGCAATGTTTCCTTATCTTCGATTCTGAAAATTTGCGCCTTAACTTACTAGGTGCAACC
1 AATCGAGGCAATATTTCCTTATCTTCGATTCTGAAAATTTCCGCCTTAACTTACTAGGTGCAACC
* *
21403 TTTCTTCAAATTGAGATAATCGA
66 TTTCTTCAAATCGAAATAATCGA
21426 ACATCCTTTT
Statistics
Matches: 78, Mismatches: 7, Indels: 6
0.86 0.08 0.07
Matches are distributed among these distances:
96 69 0.88
97 9 0.12
ACGTcount: A:0.29, C:0.20, G:0.15, T:0.37
Consensus pattern (96 bp):
AATCGAGGCAATATTTCCTTATCTTCGATTCTGAAAATTTCCGCCTTAACTTACTAGGTGCAACC
TTTCTTCAAATCGAAATAATCGAGTACCTTT
Found at i:21579 original size:16 final size:16
Alignment explanation
Indices: 21558--21594 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
21548 ACTTCCAAAC
21558 AAACTCGATTTCTCTT
1 AAACTCGATTTCTCTT
21574 AAACTCGATTTCTCTT
1 AAACTCGATTTCTCTT
21590 AAACT
1 AAACT
21595 TAACTCATGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.30, C:0.24, G:0.05, T:0.41
Consensus pattern (16 bp):
AAACTCGATTTCTCTT
Found at i:24900 original size:2 final size:2
Alignment explanation
Indices: 24893--24919 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
24883 AATCTGTGGC
24893 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
24920 TACCAATAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:28183 original size:19 final size:18
Alignment explanation
Indices: 28129--28184 Score: 55
Period size: 19 Copynumber: 3.1 Consensus size: 18
28119 TTTGTATGTT
28129 ATTATTAT-TTTAGTTTTA
1 ATTATTATATTTA-TTTTA
*
28147 A--ATTATATTTTTTATTA
1 ATTATTATATTTATT-TTA
28164 ATTATTATATGTTATTTTA
1 ATTATTATAT-TTATTTTA
28183 AT
1 AT
28185 AATAATAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
16 7 0.23
17 7 0.23
18 1 0.03
19 12 0.39
20 4 0.13
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (18 bp):
ATTATTATATTTATTTTA
Found at i:31420 original size:18 final size:18
Alignment explanation
Indices: 31380--31422 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
31370 TTTTCAGTTG
31380 TAATTAACTTAAAATTTT
1 TAATTAACTTAAAATTTT
* *
31398 CAATTAA-TTAAATTTATT
1 TAATTAACTTAAAATT-TT
31416 TAATTAA
1 TAATTAA
31423 AAATTTCCTC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.49
Consensus pattern (18 bp):
TAATTAACTTAAAATTTT
Found at i:31904 original size:7 final size:8
Alignment explanation
Indices: 31872--31901 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
31862 TAAACCACCA
31872 TAAAAATT
1 TAAAAATT
31880 ATAAAAATT
1 -TAAAAATT
31889 TAAAAATT
1 TAAAAATT
31897 TAAAA
1 TAAAA
31902 TTTTTATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 13 0.62
9 8 0.38
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (8 bp):
TAAAAATT
Found at i:39211 original size:19 final size:20
Alignment explanation
Indices: 39187--39224 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
39177 TTTACTCCTG
39187 AATTTGATC-ATTTTATTTT
1 AATTTGATCAATTTTATTTT
39206 AATTTGATCAATTTTATTT
1 AATTTGATCAATTTTATTT
39225 AGTGTATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.29, C:0.05, G:0.05, T:0.61
Consensus pattern (20 bp):
AATTTGATCAATTTTATTTT
Found at i:41296 original size:7 final size:7
Alignment explanation
Indices: 41284--41324 Score: 75
Period size: 7 Copynumber: 6.0 Consensus size: 7
41274 CAGGATGGAC
41284 TCTTTTT
1 TCTTTTT
41291 TCTTTTT
1 TCTTTTT
41298 TCTTTTT
1 TCTTTTT
41305 TCTTTTT
1 TCTTTTT
41312 T-TTTTT
1 TCTTTTT
41318 TCTTTTT
1 TCTTTTT
41325 CCTTGCGGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 6 0.18
7 27 0.82
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (7 bp):
TCTTTTT
Found at i:46261 original size:27 final size:27
Alignment explanation
Indices: 46196--46268 Score: 83
Period size: 27 Copynumber: 2.7 Consensus size: 27
46186 GATTTGGTGC
* * *
46196 TTAAGATTTTGAGTTCAGAGTTAAAGAT
1 TTAA-ATTTTGGGTTTAGGGTTAAAGAT
* *
46224 TTAAGTTTTGGGTTTAGGGTTAGAGAT
1 TTAAATTTTGGGTTTAGGGTTAAAGAT
*
46251 TTAAATTTTGGATTTAGG
1 TTAAATTTTGGGTTTAGG
46269 ATTATTCTAG
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
27 34 0.89
28 4 0.11
ACGTcount: A:0.29, C:0.01, G:0.26, T:0.44
Consensus pattern (27 bp):
TTAAATTTTGGGTTTAGGGTTAAAGAT
Found at i:56365 original size:23 final size:24
Alignment explanation
Indices: 56339--56383 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
56329 AGACAGAAGT
56339 GTGCCAC-AAGGCAGAGAAAAAGC
1 GTGCCACAAAGGCAGAGAAAAAGC
*
56362 GTGCCACAAAGGCAGATAAAAA
1 GTGCCACAAAGGCAGAGAAAAA
56384 CTAGAAGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.47, C:0.20, G:0.27, T:0.07
Consensus pattern (24 bp):
GTGCCACAAAGGCAGAGAAAAAGC
Done.