Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012672.1 Kokia drynarioides strain JFW-HI SEQ_127683, 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: 60833
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:10131 original size:205 final size:206
Alignment explanation
Indices: 9713--10473 Score: 969
Period size: 205 Copynumber: 3.7 Consensus size: 206
9703 ATAGCGATGT
* * * * * * *
9713 GGTCATCTTCCTGATGATATACTGAGAAGAAGACCAAATCAATGAAACGAGGCTCAAAGCGAGCA
1 GGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATC-A--AACCCACGCTCGATGTGAGCA
* * *
9778 AATCTTCGAACCCCAGTTTCTTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGC
63 AATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAACGGTTAGC
* * *
9843 TTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGTGGATT
128 TTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTAATGAGATACAGAGAAGCGGATT
* *
9908 GAAACAAGCGATAC
193 GAAACAAACGACAC
* * * *
9922 GGTCATCTCCCTGATAAGATACTGAAAAGAAGGCCAAATCAAACCCACGCTCGATGTGAGCAAAT
1 GGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAGCAAAT
*
9987 CTTCGAACCCCAACTTCCTGATGAGATACTGAGAAGCAGAG-CGAAGCAATAAAA-GGTTAGCTT
66 CTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAG-GTCGAAGCAATAAAACGGTTAGCTT
* * * * *
10050 CCTGACGAGATACTGAGAAGTGGACCAAATTCGTTTTCCTAACGAGGTACAAAGAAGCGGATTGA
130 CCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTAATGAGATACAGAGAAGCGGATTGA
*
10115 AACAAATGACAC
195 AACAAACGACAC
* * * *
10127 GGTCATCTTCCTGATGAGATATTGAGAAGAAGACCTAGTCAAATCCACGCTCGATGTGAGCAAAT
1 GGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAGCAAAT
* * * * *
10192 CTTCGAACCTCAGCTTCATGATGAGACAC-CAGAAGCAGGTCGAAGCAATAAAA-GGTTAGCTTA
66 CTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAACGGTTAGCTTC
* * * * *
10255 TTGATGAGATACGGAGAAGTGGACCAAATTCGTCTTCCTAATGAGATACAGAGAAACGAACTGAA
131 CTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTAATGAGATACAGAGAAGCGGATTGAA
*
10320 ACAAACGACGC
196 ACAAACGACAC
* *
10331 GGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCTC-TGCTCAAT-TCGAG-AG
1 GGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACC-CACGCTCGATGT-GAGCA-
* ** *
10393 AATCTTCGAACCCCAGCTTCCTGATGAGATATTGAGAAGCAGGTCGAAATAATAAAACGAATTAG
63 AATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAACG-GTTAG
*
10458 CTTCCTGATGAAATAC
127 CTTCCTGATGAGATAC
10474 GGGGAAGTAA
Statistics
Matches: 476, Mismatches: 68, Indels: 18
0.85 0.12 0.03
Matches are distributed among these distances:
203 3 0.01
204 172 0.36
205 179 0.38
206 68 0.14
207 18 0.04
208 1 0.00
209 35 0.07
ACGTcount: A:0.36, C:0.20, G:0.22, T:0.22
Consensus pattern (206 bp):
GGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAGCAAAT
CTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAACGGTTAGCTTC
CTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTAATGAGATACAGAGAAGCGGATTGAA
ACAAACGACAC
Found at i:10295 original size:204 final size:205
Alignment explanation
Indices: 9713--10579 Score: 965
Period size: 205 Copynumber: 4.2 Consensus size: 205
9703 ATAGCGATGT
* * * * *
9713 GGTCATCTTCCTGATGATATACTGAGAAGAAGACCAAATCAATGAAACGAGGCTCAAAGCGAGCA
1 GGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATC----AAACCACGCTCAATGTGAGCA
* * *
9778 AATCTTCGAACCCCAGTTTCTTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGC
62 AATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAACGGTTAGC
* * * *
9843 TTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGTGGATT
127 TTCCTGATGAGATACGGAGAAGTGAACCAAATTCGTCTTCCTAATGAGATACAAAGAAGCGGATT
* *
9908 GAAACAAGCGATAC
192 GAAACAAACGACAC
* * * * *
9922 GGTCATCTCCCTGATAAGATACTGAAAAGAAGGCCAAATCAAACCCACGCTCGATGTGAGCAAAT
1 GGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAA-CCACGCTCAATGTGAGCAAAT
*
9987 CTTCGAACCCCAACTTCCTGATGAGATACTGAGAAGCAGAG-CGAAGCAATAAAA-GGTTAGCTT
65 CTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAG-GTCGAAGCAATAAAACGGTTAGCTT
* * * * * *
10050 CCTGACGAGATACTGAGAAGTGGACCAAATTCGTTTTCCTAACGAGGTACAAAGAAGCGGATTGA
129 CCTGATGAGATACGGAGAAGTGAACCAAATTCGTCTTCCTAATGAGATACAAAGAAGCGGATTGA
*
10115 AACAAATGACAC
194 AACAAACGACAC
* * * *
10127 GGTCATCTTCCTGATGAGATATTGAGAAGAAGACCTAGTCAAATCCACGCTCGATGTGAGCAAAT
1 GGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAA-CCACGCTCAATGTGAGCAAAT
* * * * *
10192 CTTCGAACCTCAGCTTCATGATGAGACAC-CAGAAGCAGGTCGAAGCAATAAAA-GGTTAGCTTA
65 CTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAACGGTTAGCTTC
* * * * * *
10255 TTGATGAGATACGGAGAAGTGGACCAAATTCGTCTTCCTAATGAGATACAGAGAAACGAACTGAA
130 CTGATGAGATACGGAGAAGTGAACCAAATTCGTCTTCCTAATGAGATACAAAGAAGCGGATTGAA
*
10320 ACAAACGACGC
195 ACAAACGACAC
*
10331 GGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCTCTGCTCAAT-TCGAG-AGA
1 GGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCAC-GCTCAATGT-GAGCA-A
* ** *
10394 ATCTTCGAACCCCAGCTTCCTGATGAGATATTGAGAAGCAGGTCGAAATAATAAAACGAATTAGC
63 ATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAACG-GTTAGC
* * * * * * * * * *
10459 TTCCTGATGAAATACGGGGAAGTAAACCAAAATCATCTTCTTGATGA-AGCACAAAAAAGTGGAT
127 TTCCTGATGAGATACGGAGAAGTGAACCAAATTCGTCTTCCTAATGAGA-TACAAAGAAGCGGAT
** ** * *
10523 CAAAACAAGTGATAT
191 TGAAACAAACGACAC
* * * *
10538 GGTCGTCTTCTTGATGAGATACTGAGAAGAAGGCCAAGTCAA
1 GGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAA
10580 TGAAACCAAG
Statistics
Matches: 557, Mismatches: 91, Indels: 22
0.83 0.14 0.03
Matches are distributed among these distances:
203 6 0.01
204 171 0.31
205 181 0.32
206 67 0.12
207 97 0.17
209 35 0.06
ACGTcount: A:0.36, C:0.20, G:0.22, T:0.22
Consensus pattern (205 bp):
GGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCACGCTCAATGTGAGCAAATC
TTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAACGGTTAGCTTCC
TGATGAGATACGGAGAAGTGAACCAAATTCGTCTTCCTAATGAGATACAAAGAAGCGGATTGAAA
CAAACGACAC
Found at i:10921 original size:17 final size:17
Alignment explanation
Indices: 10899--10974 Score: 73
Period size: 17 Copynumber: 4.5 Consensus size: 17
10889 CAACAAAGAT
**
10899 TTAAATTTATTTTAAAA
1 TTAAATTTATCATAAAA
**
10916 TTAAATTTATCATAAGT
1 TTAAATTTATCATAAAA
*
10933 TTAAATTTA-CTTAAAA
1 TTAAATTTATCATAAAA
* *
10949 TTTAAATTTATTATAAAT
1 -TTAAATTTATCATAAAA
10967 TTAAATTT
1 TTAAATTT
10975 TAAATCTATT
Statistics
Matches: 47, Mismatches: 10, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
16 4 0.09
17 39 0.83
18 4 0.09
ACGTcount: A:0.45, C:0.03, G:0.01, T:0.51
Consensus pattern (17 bp):
TTAAATTTATCATAAAA
Found at i:10941 original size:34 final size:34
Alignment explanation
Indices: 10897--10974 Score: 113
Period size: 34 Copynumber: 2.3 Consensus size: 34
10887 CCCAACAAAG
*
10897 ATTTAAATTTATTTTAAAA-TTAAATTTATCATAA
1 ATTTAAATTTA-CTTAAAATTTAAATTTATCATAA
* *
10931 GTTTAAATTTACTTAAAATTTAAATTTATTATAA
1 ATTTAAATTTACTTAAAATTTAAATTTATCATAA
10965 ATTTAAATTT
1 ATTTAAATTT
10975 TAAATCTATT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
33 6 0.15
34 33 0.85
ACGTcount: A:0.45, C:0.03, G:0.01, T:0.51
Consensus pattern (34 bp):
ATTTAAATTTACTTAAAATTTAAATTTATCATAA
Found at i:10971 original size:24 final size:23
Alignment explanation
Indices: 10943--10989 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
10933 TTAAATTTAC
*
10943 TTAAAATTTAAATTTATTATAAAT
1 TTAAAATTTAAATCTATT-TAAAT
*
10967 TTAAATTTTAAATCTATTTAAAT
1 TTAAAATTTAAATCTATTTAAAT
10990 CAAGTCCAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 5 0.24
24 16 0.76
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (23 bp):
TTAAAATTTAAATCTATTTAAAT
Found at i:12843 original size:29 final size:30
Alignment explanation
Indices: 12800--12998 Score: 228
Period size: 30 Copynumber: 6.7 Consensus size: 30
12790 GGAGGTCCTG
*
12800 AAACTTTCAAAAATTCCATTTTT-ACCCCT
1 AAACTTCCAAAAATTCCATTTTTAACCCCT
* *
12829 TAACTTCTAAAAATTCCATTTTTAACCCCT
1 AAACTTCCAAAAATTCCATTTTTAACCCCT
* * *
12859 AAACTTCCAAAAATTCCATTTTTGACCTCG
1 AAACTTCCAAAAATTCCATTTTTAACCCCT
*
12889 AAACTTCC-AAAATTCCATTTTTGA-CCCT
1 AAACTTCCAAAAATTCCATTTTTAACCCCT
* * * *
12917 GTAACTTCCAAAAAATCTATTTTT-ACCCCC
1 -AAACTTCCAAAAATTCCATTTTTAACCCCT
* *
12947 GAACTTCCAAAAATTCCATTTTTAACCCCG
1 AAACTTCCAAAAATTCCATTTTTAACCCCT
12977 AAACTTCC-AAAATTACCATTTT
1 AAACTTCCAAAAATT-CCATTTT
12999 ACCCCCGGAT
Statistics
Matches: 145, Mismatches: 19, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
28 2 0.01
29 70 0.48
30 73 0.50
ACGTcount: A:0.34, C:0.28, G:0.03, T:0.35
Consensus pattern (30 bp):
AAACTTCCAAAAATTCCATTTTTAACCCCT
Found at i:12864 original size:30 final size:29
Alignment explanation
Indices: 12800--13003 Score: 227
Period size: 29 Copynumber: 7.0 Consensus size: 29
12790 GGAGGTCCTG
*
12800 AAACTTTCAAAAATTCCATTTTTACCCCT
1 AAACTTCCAAAAATTCCATTTTTACCCCT
* *
12829 TAACTTCTAAAAATTCCATTTTTAACCCCT
1 AAACTTCCAAAAATTCCATTTTT-ACCCCT
* *
12859 AAACTTCCAAAAATTCCATTTTTGACCTCG
1 AAACTTCCAAAAATTCCATTTTT-ACCCCT
12889 AAACTTCC-AAAATTCCATTTTTGA-CCCT
1 AAACTTCCAAAAATTCCATTTTT-ACCCCT
* * * *
12917 GTAACTTCCAAAAAATCTATTTTTACCCCC
1 -AAACTTCCAAAAATTCCATTTTTACCCCT
* *
12947 GAACTTCCAAAAATTCCATTTTTAACCCCG
1 AAACTTCCAAAAATTCCATTTTT-ACCCCT
12977 AAACTTCC-AAAATTACCA-TTTTACCCC
1 AAACTTCCAAAAATT-CCATTTTTACCCC
13004 CGGATGTCCA
Statistics
Matches: 150, Mismatches: 19, Indels: 13
0.82 0.10 0.07
Matches are distributed among these distances:
28 7 0.05
29 74 0.49
30 69 0.46
ACGTcount: A:0.34, C:0.29, G:0.03, T:0.34
Consensus pattern (29 bp):
AAACTTCCAAAAATTCCATTTTTACCCCT
Found at i:12999 original size:29 final size:29
Alignment explanation
Indices: 12799--13114 Score: 220
Period size: 29 Copynumber: 10.7 Consensus size: 29
12789 AGGAGGTCCT
*
12799 GAAACTTTCAAAAATTCCATTTTT-ACCCC
1 GAAAC-TTCCAAAATTCCATTTTTAACCCC
** *
12828 TTAACTTCTAAAAATTCCATTTTTAACCCC
1 GAAACTTC-CAAAATTCCATTTTTAACCCC
* * *
12858 TAAACTTCCAAAAATTCCATTTTTGACCTC
1 GAAACTTCC-AAAATTCCATTTTTAACCCC
* *
12888 GAAACTTCCAAAATTCCATTTTTGACCCT
1 GAAACTTCCAAAATTCCATTTTTAACCCC
* * * *
12917 GTAACTTCCAAAAAATCTATTTTTACCCCC
1 GAAACTTCC-AAAATTCCATTTTTAACCCC
12947 G-AACTTCCAAAAATTCCATTTTTAACCCC
1 GAAACTTCC-AAAATTCCATTTTTAACCCC
*
12976 GAAACTTCCAAAATTACCA-TTTTACCCCC
1 GAAACTTCCAAAATT-CCATTTTTAACCCC
* * * *
13005 G-GA-TGTCCAAAAACTCCATTTTCAACCTC
1 GAAACT-TCC-AAAATTCCATTTTTAACCCC
*
13034 GAAAC-TCTCAAAATTACC-CTTTT-ACTCCC
1 GAAACTTC-CAAAATT-CCATTTTTAAC-CCC
* *
13063 G-AA-TGTCTAAAAATTCCATTTTTAACTCC
1 GAAACT-TC-CAAAATTCCATTTTTAACCCC
**
13092 GAATTTTCCCAAAATTGCCATTT
1 GAAACTT-CCAAAATT-CCATTT
13115 CACCCTCGAG
Statistics
Matches: 231, Mismatches: 34, Indels: 42
0.75 0.11 0.14
Matches are distributed among these distances:
27 1 0.00
28 16 0.07
29 128 0.55
30 78 0.34
31 8 0.03
ACGTcount: A:0.33, C:0.28, G:0.05, T:0.34
Consensus pattern (29 bp):
GAAACTTCCAAAATTCCATTTTTAACCCC
Found at i:13001 original size:58 final size:59
Alignment explanation
Indices: 12799--13114 Score: 283
Period size: 58 Copynumber: 5.4 Consensus size: 59
12789 AGGAGGTCCT
* ** *
12799 GAAACTTTCAAAAATT-CCATTTTTACCCCTTAACTTCTAAAAATTCCATTTTTAACCCC
1 GAAAC-TTCCAAAATTACCATTTTTACCCCCGAACTTCCAAAAATTCCATTTTTAACCCC
* * * *
12858 TAAACTTCCAAAAATT-CCATTTTTGA-CCTCGAAACTTCC-AAAATTCCATTTTTGACCCT
1 GAAACTTCC-AAAATTACCATTTTT-ACCCCCG-AACTTCCAAAAATTCCATTTTTAACCCC
* * *
12917 GTAACTTCCAAAA-AATCTATTTTTACCCCCGAACTTCCAAAAATTCCATTTTTAACCCC
1 GAAACTTCCAAAATTA-CCATTTTTACCCCCGAACTTCCAAAAATTCCATTTTTAACCCC
* * * *
12976 GAAACTTCCAAAATTACCA-TTTTACCCCCGGA-TGTCCAAAAACTCCATTTTCAACCTC
1 GAAACTTCCAAAATTACCATTTTTACCCCCGAACT-TCCAAAAATTCCATTTTTAACCCC
* * * *
13034 GAAAC-TCTCAAAATTACC-CTTTTACTCCCGAA-TGTCTAAAAATTCCATTTTTAACTCC
1 GAAACTTC-CAAAATTACCATTTTTACCCCCGAACT-TCCAAAAATTCCATTTTTAACCCC
** *
13092 GAATTTTCCCAAAATTGCCATTT
1 GAAACTT-CCAAAATTACCATTT
13115 CACCCTCGAG
Statistics
Matches: 210, Mismatches: 33, Indels: 27
0.78 0.12 0.10
Matches are distributed among these distances:
57 3 0.01
58 98 0.47
59 98 0.47
60 11 0.05
ACGTcount: A:0.33, C:0.28, G:0.05, T:0.34
Consensus pattern (59 bp):
GAAACTTCCAAAATTACCATTTTTACCCCCGAACTTCCAAAAATTCCATTTTTAACCCC
Found at i:15863 original size:157 final size:157
Alignment explanation
Indices: 15645--15956 Score: 624
Period size: 157 Copynumber: 2.0 Consensus size: 157
15635 TCTCTGCTCA
15645 TTTTATCATATCGAGGCCTTTACGAACACTCGAGTGCTGCTACTCCAAGGCCAAAAAAGGCTTTT
1 TTTTATCATATCGAGGCCTTTACGAACACTCGAGTGCTGCTACTCCAAGGCCAAAAAAGGCTTTT
15710 TCTCAAGAGGAGAAATCGACAAACGAAGGGAAAGAAAATGAAAGAAAACAAAAGGGAATGAAAGA
66 TCTCAAGAGGAGAAATCGACAAACGAAGGGAAAGAAAATGAAAGAAAACAAAAGGGAATGAAAGA
15775 GTGAAAGTGAGTGAAAAAAAGAATGCT
131 GTGAAAGTGAGTGAAAAAAAGAATGCT
15802 TTTTATCATATCGAGGCCTTTACGAACACTCGAGTGCTGCTACTCCAAGGCCAAAAAAGGCTTTT
1 TTTTATCATATCGAGGCCTTTACGAACACTCGAGTGCTGCTACTCCAAGGCCAAAAAAGGCTTTT
15867 TCTCAAGAGGAGAAATCGACAAACGAAGGGAAAGAAAATGAAAGAAAACAAAAGGGAATGAAAGA
66 TCTCAAGAGGAGAAATCGACAAACGAAGGGAAAGAAAATGAAAGAAAACAAAAGGGAATGAAAGA
15932 GTGAAAGTGAGTGAAAAAAAGAATG
131 GTGAAAGTGAGTGAAAAAAAGAATG
15957 TGTTATGAAT
Statistics
Matches: 155, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
157 155 1.00
ACGTcount: A:0.44, C:0.14, G:0.24, T:0.18
Consensus pattern (157 bp):
TTTTATCATATCGAGGCCTTTACGAACACTCGAGTGCTGCTACTCCAAGGCCAAAAAAGGCTTTT
TCTCAAGAGGAGAAATCGACAAACGAAGGGAAAGAAAATGAAAGAAAACAAAAGGGAATGAAAGA
GTGAAAGTGAGTGAAAAAAAGAATGCT
Found at i:16465 original size:56 final size:56
Alignment explanation
Indices: 16403--16516 Score: 228
Period size: 56 Copynumber: 2.0 Consensus size: 56
16393 AAGATGACTT
16403 AAAAATTGAATTAATTTATTCAAGTTATTATTTAATTGATTGCAATTAAAAAATTA
1 AAAAATTGAATTAATTTATTCAAGTTATTATTTAATTGATTGCAATTAAAAAATTA
16459 AAAAATTGAATTAATTTATTCAAGTTATTATTTAATTGATTGCAATTAAAAAATTA
1 AAAAATTGAATTAATTTATTCAAGTTATTATTTAATTGATTGCAATTAAAAAATTA
16515 AA
1 AA
16517 GTTCGAAATA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 58 1.00
ACGTcount: A:0.47, C:0.04, G:0.07, T:0.42
Consensus pattern (56 bp):
AAAAATTGAATTAATTTATTCAAGTTATTATTTAATTGATTGCAATTAAAAAATTA
Found at i:16878 original size:161 final size:161
Alignment explanation
Indices: 16613--16937 Score: 632
Period size: 161 Copynumber: 2.0 Consensus size: 161
16603 GTTTAATGAA
* *
16613 ATTAGAATTGGATTGAGAAAATATTTTAATTAGATAAATTAACTAATTAAATAATATTTTGGGAA
1 ATTAGAATTGGATTAAGAAAATAATTTAATTAGATAAATTAACTAATTAAATAATATTTTGGGAA
16678 ATAGAAGTGTAGTTATTGTGTTGGTTACAAGTCCAAATAAGACATATAATTGTACCAAATACTCG
66 ATAGAAGTGTAGTTATTGTGTTGGTTACAAGTCCAAATAAGACATATAATTGTACCAAATACTCG
16743 AGACAGACTGATGGTATTTCAAATGACATAG
131 AGACAGACTGATGGTATTTCAAATGACATAG
16774 ATTAGAATTGGATTAAGAAAATAATTTAATTAGATAAATTAACTAATTAAATAATATTTTGGGAA
1 ATTAGAATTGGATTAAGAAAATAATTTAATTAGATAAATTAACTAATTAAATAATATTTTGGGAA
16839 ATAGAAGTGTAGTTATTGTGTTGGTTACAAGTCCAAATAAGACATATAATTGTACCAAATACTCG
66 ATAGAAGTGTAGTTATTGTGTTGGTTACAAGTCCAAATAAGACATATAATTGTACCAAATACTCG
16904 AGACAGACTGATGGTATTTCAAATGACATAG
131 AGACAGACTGATGGTATTTCAAATGACATAG
16935 ATT
1 ATT
16938 TTCTCCCCAA
Statistics
Matches: 162, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
161 162 1.00
ACGTcount: A:0.42, C:0.08, G:0.17, T:0.34
Consensus pattern (161 bp):
ATTAGAATTGGATTAAGAAAATAATTTAATTAGATAAATTAACTAATTAAATAATATTTTGGGAA
ATAGAAGTGTAGTTATTGTGTTGGTTACAAGTCCAAATAAGACATATAATTGTACCAAATACTCG
AGACAGACTGATGGTATTTCAAATGACATAG
Found at i:25023 original size:13 final size:13
Alignment explanation
Indices: 25005--25033 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
24995 TAAAAGTTTT
25005 TAGATTTTACAAG
1 TAGATTTTACAAG
25018 TAGATTTTACAAG
1 TAGATTTTACAAG
25031 TAG
1 TAG
25034 GATTAGGAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.38, C:0.07, G:0.17, T:0.38
Consensus pattern (13 bp):
TAGATTTTACAAG
Found at i:25473 original size:41 final size:41
Alignment explanation
Indices: 25428--25551 Score: 239
Period size: 41 Copynumber: 3.0 Consensus size: 41
25418 ACATATAAGA
25428 ATAAAATTAAGTATATTAACTTTTTATGAAAAAAAAACTAT
1 ATAAAATTAAGTATATTAACTTTTTATGAAAAAAAAACTAT
25469 ATAAAATTAAGTATATTAACTTTTTATGAAAAAAAAACTAT
1 ATAAAATTAAGTATATTAACTTTTTATGAAAAAAAAACTAT
25510 ATAAAATTAAGTATATTAACTTTTTATGAAAAAAAAAACTAT
1 ATAAAATTAAGTATATTAACTTTTTATG-AAAAAAAAACTAT
25552 GTTATTCTAA
Statistics
Matches: 82, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
41 69 0.84
42 13 0.16
ACGTcount: A:0.54, C:0.05, G:0.05, T:0.36
Consensus pattern (41 bp):
ATAAAATTAAGTATATTAACTTTTTATGAAAAAAAAACTAT
Found at i:32110 original size:13 final size:14
Alignment explanation
Indices: 32085--32113 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
32075 GAAGAGCATA
32085 GAGGGAGAAGAAGG
1 GAGGGAGAAGAAGG
32099 GAGGGA-AAGAAGG
1 GAGGGAGAAGAAGG
32112 GA
1 GA
32114 AGTAAAGGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.45, C:0.00, G:0.55, T:0.00
Consensus pattern (14 bp):
GAGGGAGAAGAAGG
Found at i:33142 original size:21 final size:21
Alignment explanation
Indices: 33118--33161 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
33108 TTTCTCACAT
*
33118 TCTCAAATCTCT-TTAAATTTC
1 TCTCAAATCCCTCTT-AATTTC
*
33139 TCTCAATTCCCTCTTAATTTC
1 TCTCAAATCCCTCTTAATTTC
33160 TC
1 TC
33162 ACTCAAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 18 0.90
22 2 0.10
ACGTcount: A:0.23, C:0.30, G:0.00, T:0.48
Consensus pattern (21 bp):
TCTCAAATCCCTCTTAATTTC
Found at i:33571 original size:13 final size:12
Alignment explanation
Indices: 33539--33563 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
33529 AATTGCATTC
33539 AAAAAATTCAAA
1 AAAAAATTCAAA
33551 AAAAAATTCAAA
1 AAAAAATTCAAA
33563 A
1 A
33564 CTAAAATTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.08, G:0.00, T:0.16
Consensus pattern (12 bp):
AAAAAATTCAAA
Found at i:33764 original size:20 final size:20
Alignment explanation
Indices: 33719--33765 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
33709 AAATTATATA
*
33719 AAAAGAATATATAAAAAACTT
1 AAAA-AATATATAAAAAACCT
33740 AAAAAATAT-TAAAAAACCT
1 AAAAAATATATAAAAAACCT
*
33759 ATAAAAT
1 AAAAAAT
33766 CCTAAACTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 15 0.62
20 5 0.21
21 4 0.17
ACGTcount: A:0.68, C:0.06, G:0.02, T:0.23
Consensus pattern (20 bp):
AAAAAATATATAAAAAACCT
Found at i:34339 original size:42 final size:43
Alignment explanation
Indices: 34293--34373 Score: 119
Period size: 42 Copynumber: 1.9 Consensus size: 43
34283 GTTAACATAA
* * * *
34293 AAATTGTGATAATTATACATT-TAAAATAATTCTAATTTTAAT
1 AAATTGTGATAATGACACATTAAAAAATAATTATAATTTTAAT
34335 AAATTGTGATAATGACACATTAAAAAATAATTATAATTT
1 AAATTGTGATAATGACACATTAAAAAATAATTATAATTT
34374 AATTTTCAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
42 19 0.56
43 15 0.44
ACGTcount: A:0.48, C:0.05, G:0.06, T:0.41
Consensus pattern (43 bp):
AAATTGTGATAATGACACATTAAAAAATAATTATAATTTTAAT
Found at i:34580 original size:24 final size:22
Alignment explanation
Indices: 34544--34589 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
34534 TGAAATTATT
*
34544 ATAAAAAAGTTATTTTAATTTTA
1 ATAAAAAAGTTA-TCTAATTTTA
*
34567 ATAAAAAGGTTTATCTAATTTTA
1 ATAAAAAAG-TTATCTAATTTTA
34590 TTTATGTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 17 0.85
24 3 0.15
ACGTcount: A:0.46, C:0.02, G:0.07, T:0.46
Consensus pattern (22 bp):
ATAAAAAAGTTATCTAATTTTA
Found at i:59779 original size:21 final size:20
Alignment explanation
Indices: 59753--59799 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 20
59743 ATTATTTAAG
59753 AAAATTTTTA-AACTTATTTTT
1 AAAATTTTTATAA-TT-TTTTT
59774 AAAATTTTTATAATTTTTTT
1 AAAATTTTTATAATTTTTTT
59794 AAAATT
1 AAAATT
59800 ATAATTTGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
20 11 0.44
21 12 0.48
22 2 0.08
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (20 bp):
AAAATTTTTATAATTTTTTT
Found at i:59851 original size:19 final size:19
Alignment explanation
Indices: 59768--59851 Score: 68
Period size: 18 Copynumber: 4.3 Consensus size: 19
59758 TTTTAAACTT
59768 ATTTTTAAAATT-TTTAT-A
1 ATTTTTAAAATTATTT-TGA
59786 ATTTTTTTAAAATTATAATTTGA
1 A--TTTTTAAAATTAT--TTTGA
* *
59809 ATTTTTATAGA-TATTTAGA
1 ATTTTTA-AAATTATTTTGA
59828 A-TTTTAAAATTATTTTGA
1 ATTTTTAAAATTATTTTGA
59846 ATTTTT
1 ATTTTT
59852 TCTTTTGTAA
Statistics
Matches: 53, Mismatches: 4, Indels: 17
0.72 0.05 0.23
Matches are distributed among these distances:
17 2 0.04
18 14 0.26
19 9 0.17
20 11 0.21
21 10 0.19
22 3 0.06
23 4 0.08
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (19 bp):
ATTTTTAAAATTATTTTGA
Done.