Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010331.1 Kokia drynarioides strain JFW-HI SEQ_125196, 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: 31438
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.34
Warning! 52 characters in sequence are not A, C, G, or T
Found at i:377 original size:4 final size:4
Alignment explanation
Indices: 368--442 Score: 50
Period size: 4 Copynumber: 19.0 Consensus size: 4
358 NNNNNNNNNN
* * * *
368 TTTC TTTC TTCCC TTTC TTCTC CTTC -TTC CTTC -TTC -TTC TTTT TTTC
1 TTTC TTTC TT-TC TTTC TT-TC TTTC TTTC TTTC TTTC TTTC TTTC TTTC
*
415 TTTC TTTC TTTTT TTTC TTTC TTT- TTTC
1 TTTC TTTC -TTTC TTTC TTTC TTTC TTTC
443 CTTCAATTTT
Statistics
Matches: 58, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
3 12 0.21
4 37 0.64
5 9 0.16
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (4 bp):
TTTC
Found at i:426 original size:13 final size:13
Alignment explanation
Indices: 380--439 Score: 61
Period size: 13 Copynumber: 4.7 Consensus size: 13
370 TCTTTCTTCC
* *
380 CTTTCTTCTCCTT
1 CTTTCTTTTCTTT
*
393 CTTCCTTCTTC-TT
1 CTTTCTT-TTCTTT
406 CTTT-TTTTCTTT
1 CTTTCTTTTCTTT
*
418 CTTTCTTTTTTTT
1 CTTTCTTTTCTTT
431 CTTTCTTTT
1 CTTTCTTTT
440 TTCCTTCAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
11 3 0.08
12 8 0.20
13 27 0.68
14 2 0.05
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (13 bp):
CTTTCTTTTCTTT
Found at i:1707 original size:16 final size:17
Alignment explanation
Indices: 1677--1717 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
1667 TACTTGTGGA
*
1677 AAATAATAAAATAAA-T
1 AAATAATACAATAAATT
*
1693 AAATAATACATTAAATT
1 AAATAATACAATAAATT
1710 AAA-AATAC
1 AAATAATAC
1718 TCTTAATTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 18 0.82
17 4 0.18
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (17 bp):
AAATAATACAATAAATT
Found at i:5908 original size:12 final size:12
Alignment explanation
Indices: 5891--5915 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5881 AGCTGCCTCT
5891 ACTGCCCCGTTC
1 ACTGCCCCGTTC
5903 ACTGCCCCGTTC
1 ACTGCCCCGTTC
5915 A
1 A
5916 TTTTTAGGCG
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:0.12, C:0.48, G:0.16, T:0.24
Consensus pattern (12 bp):
ACTGCCCCGTTC
Found at i:14979 original size:29 final size:29
Alignment explanation
Indices: 14937--15284 Score: 135
Period size: 29 Copynumber: 11.8 Consensus size: 29
14927 TCTTTAGATA
14937 TTCGAGGAT-AAAAATGGAATTTTTGGAGT
1 TTCGAGG-TCAAAAATGGAATTTTTGGAGT
* * * *
14966 TTCGAGGTCGAAAATAGAGTTTTTGGA-C
1 TTCGAGGTCAAAAATGGAATTTTTGGAGT
* * * *
14994 ATCTGGGGGC-AAAATGGTAATTTTTGAAAGT
1 TTC-GAGGTCAAAAATGG-AATTTTTG-GAGT
* * *
15025 TTCG-GTTTAAAAATGGAAATTTTGGAGGT
1 TTCGAGGTCAAAAATGGAATTTTTGGA-GT
* *
15054 TT-GAGGGT-AAAAATGTAATTTATGGAAGT
1 TTCGA-GGTCAAAAATGGAATTTTTGG-AGT
* * *
15083 TTCGGGGGTTAAAAATAGAATTTTTGGAAG-
1 TTC-GAGGTCAAAAATGGAATTTTTGG-AGT
* * * *
15113 TTCAAGGGCCAAAATGGAATTTTTGGAAAT
1 TTCGAGGTCAAAAATGGAATTTTTGG-AGT
* * **
15143 TT-TAGGGTCGAAAATGGAATTCTTTGGAAA
1 TTCGA-GGTCAAAAATGGAATT-TTTGGAGT
* *
15173 TTCAAGGGT-AAAAATGGAA-TTTTGGAAAT
1 TTCGA-GGTCAAAAATGGAATTTTTGG-AGT
* * * * *
15202 TTTGGGGTAAAAAATAGAATTTTTAGAAG-
1 TTCGAGGTCAAAAATGGAATTTTT-GGAGT
* * *
15231 TTCAAGGGT-AAAAATGGAATTTTTGAAAAT
1 TTCGA-GGTCAAAAATGGAATTTTTG-GAGT
* *
15261 TTCGGGGTCGAAAATGGAATTTTT
1 TTCGAGGTCAAAAATGGAATTTTT
15285 AGAAGTTCGA
Statistics
Matches: 241, Mismatches: 53, Indels: 49
0.70 0.15 0.14
Matches are distributed among these distances:
28 20 0.08
29 118 0.49
30 72 0.30
31 31 0.13
ACGTcount: A:0.35, C:0.05, G:0.26, T:0.34
Consensus pattern (29 bp):
TTCGAGGTCAAAAATGGAATTTTTGGAGT
Found at i:15107 original size:118 final size:115
Alignment explanation
Indices: 14937--15304 Score: 389
Period size: 118 Copynumber: 3.1 Consensus size: 115
14927 TCTTTAGATA
* * ** * **
14937 TTCGAGGATAAAAATGGAATTTTTGG-AGTTTCGAGGTCGAAAATAGAGTTTTTGGACA-TCTGG
1 TTCGAGGGTAAAAATGGAA-TTTTGGAAGTTTCGGGGTAAAAAATAGAATTTTTGGA-AGTCAAG
* * * ** * *
15000 GGGCAAAATGGTAATTTTTGAAAGTTTCGGTTTAAAAATGGAAATTTTGGAGG
64 GGCCAAAATGG-AATTTTTGAAAATTTCGGGTCGAAAATGGAATTTTTGGAAG
* * *
15053 TTTGAGGGTAAAAATGTAATTTATGGAAGTTTCGGGGGTTAAAAATAGAATTTTTGGAAGTTCAA
1 TTCGAGGGTAAAAATGGAATTT-TGGAAGTTTC-GGGGTAAAAAATAGAATTTTTGGAAG-TCAA
* * *
15118 GGGCCAAAATGGAATTTTTGGAAATTTTAGGGTCGAAAATGGAATTCTTTGGAAA
63 GGGCCAAAATGGAATTTTT-GAAAATTTCGGGTCGAAAATGGAATT-TTTGGAAG
* * * *
15173 TTCAAGGGTAAAAATGGAATTTTGGAAATTTTGGGGTAAAAAATAGAATTTTTAGAAGTTCAAGG
1 TTCGAGGGTAAAAATGGAATTTTGGAAGTTTCGGGGTAAAAAATAGAATTTTTGGAAG-TCAAGG
** *
15238 GTAAAAATGGAATTTTTGAAAATTTCGGGGTCGAAAATGGAATTTTTAGAAG
65 GCCAAAATGGAATTTTTGAAAATTTC-GGGTCGAAAATGGAATTTTTGGAAG
15290 TTCGAGGGTAAAAAT
1 TTCGAGGGTAAAAAT
15305 ATAATTTTTA
Statistics
Matches: 212, Mismatches: 32, Indels: 15
0.82 0.12 0.06
Matches are distributed among these distances:
115 3 0.01
116 19 0.09
117 34 0.16
118 90 0.42
119 41 0.19
120 25 0.12
ACGTcount: A:0.36, C:0.05, G:0.27, T:0.33
Consensus pattern (115 bp):
TTCGAGGGTAAAAATGGAATTTTGGAAGTTTCGGGGTAAAAAATAGAATTTTTGGAAGTCAAGGG
CCAAAATGGAATTTTTGAAAATTTCGGGTCGAAAATGGAATTTTTGGAAG
Found at i:15200 original size:59 final size:59
Alignment explanation
Indices: 15004--15313 Score: 300
Period size: 59 Copynumber: 5.2 Consensus size: 59
14994 ATCTGGGGGC
* * * * * * * * **
15004 AAAATGGTAATTTTT-GAAAGTTTCGGTTTAAAAATGGAAATTTTGGAGGTTTGAGGGTA
1 AAAATGG-AATTTTTGGAAATTTTGGGGTCAAAAATAGAATTTTTAGAAGTTCAAGGGTA
* * * * * * **
15063 AAAATGTAATTTATGGAAGTTTCGGGGGTTAAAAATAGAATTTTTGGAAGTTCAAGGGCC
1 AAAATGGAATTTTTGGAAATTT-TGGGGTCAAAAATAGAATTTTTAGAAGTTCAAGGGTA
* * * * *
15123 AAAATGGAATTTTTGGAAATTTTAGGGTCGAAAATGGAATTCTTTGGAAATTCAAGGGTA
1 AAAATGGAATTTTTGGAAATTTTGGGGTCAAAAATAGAATT-TTTAGAAGTTCAAGGGTA
*
15183 AAAATGGAA-TTTTGGAAATTTTGGGGTAAAAAATAGAATTTTTAGAAGTTCAAGGGTA
1 AAAATGGAATTTTTGGAAATTTTGGGGTCAAAAATAGAATTTTTAGAAGTTCAAGGGTA
* * * * *
15241 AAAATGGAATTTTTGAAAATTTCGGGGTCGAAAATGGAATTTTTAGAAGTTCGAGGGTA
1 AAAATGGAATTTTTGGAAATTTTGGGGTCAAAAATAGAATTTTTAGAAGTTCAAGGGTA
**
15300 AAAATATAATTTTT
1 AAAATGGAATTTTT
15314 AGATAGTTTA
Statistics
Matches: 208, Mismatches: 39, Indels: 8
0.82 0.15 0.03
Matches are distributed among these distances:
58 31 0.15
59 107 0.51
60 70 0.34
ACGTcount: A:0.37, C:0.04, G:0.25, T:0.34
Consensus pattern (59 bp):
AAAATGGAATTTTTGGAAATTTTGGGGTCAAAAATAGAATTTTTAGAAGTTCAAGGGTA
Found at i:15293 original size:29 final size:28
Alignment explanation
Indices: 15032--15326 Score: 169
Period size: 29 Copynumber: 10.0 Consensus size: 28
15022 AGTTTCGGTT
* * * *
15032 TAAAAATGGAAATTTTGGAGGTTTGAGGG
1 TAAAAATGGAATTTTTAGAAG-TTCAGGG
* * * *
15061 TAAAAATGTAATTTATGGAAGTTTCGGGGG
1 TAAAAATGGAATTTTTAGAAG-TTC-AGGG
* *
15091 TTAAAAATAGAATTTTTGGAAGTTCAAGGG
1 -TAAAAATGGAATTTTTAGAAGTTC-AGGG
** * * *
15121 CCAAAATGGAATTTTTGGAAATTTTAGGG
1 TAAAAATGGAATTTTTAG-AAGTTCAGGG
* * *
15150 TCGAAAATGGAATTCTTTGGAAATTCAAGGG
1 T-AAAAATGGAATT-TTTAGAAGTTC-AGGG
* * **
15181 TAAAAATGGAA-TTTTGGAAATTTTGGGG
1 TAAAAATGGAATTTTTAG-AAGTTCAGGG
*
15209 TAAAAAATAGAATTTTTAGAAGTTCAAGGG
1 T-AAAAATGGAATTTTTAGAAGTTC-AGGG
* * *
15239 TAAAAATGGAATTTTTGAAAATTTCGGGG
1 TAAAAATGGAATTTTT-AGAAGTTCAGGG
*
15268 TCGAAAATGGAATTTTTAGAAGTTCGAGGG
1 T-AAAAATGGAATTTTTAGAAGTTC-AGGG
** *
15298 TAAAAATATAATTTTTAGATAGTTTAGGG
1 TAAAAATGGAATTTTTAGA-AGTTCAGGG
15327 ACCTCCAAGG
Statistics
Matches: 211, Mismatches: 41, Indels: 28
0.75 0.15 0.10
Matches are distributed among these distances:
28 9 0.04
29 100 0.47
30 74 0.35
31 28 0.13
ACGTcount: A:0.37, C:0.04, G:0.26, T:0.33
Consensus pattern (28 bp):
TAAAAATGGAATTTTTAGAAGTTCAGGG
Found at i:16176 original size:44 final size:43
Alignment explanation
Indices: 16113--16196 Score: 150
Period size: 44 Copynumber: 1.9 Consensus size: 43
16103 TTTATTCCCG
16113 ATCATTTCGGTTCTTTGTTTCTTCGCAGATCCACGGATGAGGA
1 ATCATTTCGGTTCTTTGTTTCTTCGCAGATCCACGGATGAGGA
*
16156 NATCATTTCGGTTCTTTGTTTCTTCGCAGATTCACGGATGA
1 -ATCATTTCGGTTCTTTGTTTCTTCGCAGATCCACGGATGA
16197 CGAAGCATCG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.18, C:0.20, G:0.21, T:0.39
Consensus pattern (43 bp):
ATCATTTCGGTTCTTTGTTTCTTCGCAGATCCACGGATGAGGA
Found at i:16311 original size:3 final size:3
Alignment explanation
Indices: 16305--16399 Score: 75
Period size: 3 Copynumber: 31.0 Consensus size: 3
16295 GTTTCTTTTT
* * * * **
16305 TTA TTA TTAA TTA ATA TTA TTT TTA TTT TTA TTA -AA ACA GTTA TTA
1 TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA
* * *
16351 TTA TTA TTA TTTA TTA TTA TTA TTA TTA TTA TTA ATG CTA TTA TTA
1 TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
16397 TTA
1 TTA
16400 AAACGTTTGA
Statistics
Matches: 73, Mismatches: 15, Indels: 8
0.76 0.16 0.08
Matches are distributed among these distances:
2 1 0.01
3 65 0.89
4 7 0.10
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:16559 original size:19 final size:19
Alignment explanation
Indices: 16508--16553 Score: 92
Period size: 19 Copynumber: 2.4 Consensus size: 19
16498 CAAAAATTCA
16508 TTGAATGTACCTGAATGCC
1 TTGAATGTACCTGAATGCC
16527 TTGAATGTACCTGAATGCC
1 TTGAATGTACCTGAATGCC
16546 TTGAATGT
1 TTGAATGT
16554 TTCTGACTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.35
Consensus pattern (19 bp):
TTGAATGTACCTGAATGCC
Found at i:16993 original size:6 final size:6
Alignment explanation
Indices: 16982--17065 Score: 65
Period size: 6 Copynumber: 14.7 Consensus size: 6
16972 TTAAATAGAT
16982 TTTAAA TTTAAA TTTATAA --TAAA TTTAAA TTTCAAA --TAAA TTTAAA
1 TTTAAA TTTAAA TTTA-AA TTTAAA TTTAAA TTT-AAA TTTAAA TTTAAA
* * *
17028 TTTAGAA --TAAA CTTAAT TTTAAA -ATAAA TTTAAA TTTA
1 TTTA-AA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTA
17066 TTGGGCCCAG
Statistics
Matches: 63, Mismatches: 5, Indels: 20
0.72 0.06 0.23
Matches are distributed among these distances:
4 7 0.11
5 9 0.14
6 40 0.63
7 7 0.11
ACGTcount: A:0.51, C:0.02, G:0.01, T:0.45
Consensus pattern (6 bp):
TTTAAA
Found at i:17004 original size:17 final size:17
Alignment explanation
Indices: 16984--17066 Score: 114
Period size: 17 Copynumber: 4.9 Consensus size: 17
16974 AAATAGATTT
16984 TAAATTTAAATTTATAA
1 TAAATTTAAATTTATAA
17001 TAAATTTAAATTTCA-AA
1 TAAATTTAAATTT-ATAA
*
17018 TAAATTTAAATTTAGAA
1 TAAATTTAAATTTATAA
* * *
17035 TAAACTTAATTTTAAAA
1 TAAATTTAAATTTATAA
17052 TAAATTTAAATTTAT
1 TAAATTTAAATTTAT
17067 TGGGCCCAGA
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
16 1 0.02
17 56 0.97
18 1 0.02
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.45
Consensus pattern (17 bp):
TAAATTTAAATTTATAA
Found at i:17022 original size:34 final size:34
Alignment explanation
Indices: 16984--17066 Score: 130
Period size: 34 Copynumber: 2.4 Consensus size: 34
16974 AAATAGATTT
* *
16984 TAAATTTAAATTTATAATAAATTTAAATTTCAAA
1 TAAATTTAAATTTATAATAAACTTAAATTTAAAA
* *
17018 TAAATTTAAATTTAGAATAAACTTAATTTTAAAA
1 TAAATTTAAATTTATAATAAACTTAAATTTAAAA
17052 TAAATTTAAATTTAT
1 TAAATTTAAATTTAT
17067 TGGGCCCAGA
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 44 1.00
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.45
Consensus pattern (34 bp):
TAAATTTAAATTTATAATAAACTTAAATTTAAAA
Found at i:17688 original size:37 final size:37
Alignment explanation
Indices: 17638--17735 Score: 142
Period size: 37 Copynumber: 2.6 Consensus size: 37
17628 GTTTCAGTCT
* * *
17638 GCTTCTTTGTATCTCATCAGGAAGATGAATTTGGTTC
1 GCTTCTCTGTATCTCATCAGGAAGACGAATTTGGTCC
17675 GCTTCTCTGTATCTCATCAGGAAGACGAATTTGGTCC
1 GCTTCTCTGTATCTCATCAGGAAGACGAATTTGGTCC
* * *
17712 ACTTCTCAGTATCTTATCAGGAAG
1 GCTTCTCTGTATCTCATCAGGAAG
17736 CTAATTGTTT
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 55 1.00
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.36
Consensus pattern (37 bp):
GCTTCTCTGTATCTCATCAGGAAGACGAATTTGGTCC
Found at i:17842 original size:119 final size:119
Alignment explanation
Indices: 17703--18096 Score: 352
Period size: 119 Copynumber: 3.3 Consensus size: 119
17693 AGGAAGACGA
* **
17703 ATTTGGTCCACTTCTCAGTATCTTATCAGGAAGCTAATTGTTTATTGCTTTGACCTGCTTCTCAG
1 ATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACAGTTTATTGCTTTGACCTGCTTCTCAG
*
17768 TGTCTCATTAAGAAGCTGGGATTCGAAGATTTGCTCACATCGAGCATGGGTTTG
66 TGTCTCATCAAGAAGCTGGGATTCGAAGATTTGCTCACATCGAGCATGGGTTTG
** * ** * * **
17822 ATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATAACCACATCATTTG-TTTCAATTTGCTTCT
1 ATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAA-CAGTTTA-TTGCTTT-GACCTGCTTCT
* * * * * **** * ****
17886 CTGTATCTCATCAGGAAAATGAATTTGG-TTCGCTTCTTTG-T-ATC-TC-ATCA-GGAAAACG
63 CAGTGTCTCATCA--AGAA-G--CTGGGATTCGAAGATTTGCTCA-CATCGAGCATGG-GTTTG
* * *
17944 AATTTGGTCCACTTCTCAGTATCTTATCAGGAAGCTAACCGTTTATTGCTTCGACCTGCTTCTCA
1 -ATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACAGTTTATTGCTTTGACCTGCTTCTCA
18009 GTGTCTCATCAAGAAGCTGGGATTCGAAGATTTGCTCACATCGAGCATGGGTTTG
65 GTGTCTCATCAAGAAGCTGGGATTCGAAGATTTGCTCACATCGAGCATGGGTTTG
**
18064 ATTTGGTCTTCTTCTCAGTATCTCATCAGGAAG
1 ATTTGGTCCACTTCTCAGTATCTCATCAGGAAG
18097 ATGACCACGT
Statistics
Matches: 201, Mismatches: 56, Indels: 36
0.69 0.19 0.12
Matches are distributed among these distances:
116 3 0.01
117 8 0.04
118 3 0.01
119 69 0.34
120 9 0.04
121 47 0.23
122 9 0.04
123 39 0.19
124 3 0.01
125 8 0.04
126 3 0.01
ACGTcount: A:0.23, C:0.21, G:0.20, T:0.37
Consensus pattern (119 bp):
ATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACAGTTTATTGCTTTGACCTGCTTCTCAG
TGTCTCATCAAGAAGCTGGGATTCGAAGATTTGCTCACATCGAGCATGGGTTTG
Found at i:17873 original size:242 final size:242
Alignment explanation
Indices: 17426--18182 Score: 1083
Period size: 242 Copynumber: 3.1 Consensus size: 242
17416 TATCACTTGT
* * * * * * * ** * *
17426 TTTGATTCACTTCTCTGTGTTTCATCAAGAAGATGATTTTGGTTTACTTCCCCGTAT-TTCATCA
1 TTTGGTTCGCTTCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTT-ATCA
* * * * *
17490 GGAAGCTAACTGTTTTATT-ATTTCGACCCGCTTCTCAGTGTCTCAACAAGAAACTAGGG-TTTG
65 GGAAGCTAACTG-TTTATTGCTTT-GACCTGCTTCTCAGTGTCTCATCAAGAAGCT-GGGATTCG
* * * *
17553 AAGATTTG-T-TCATCGAGCGTGGGTTTGATTTGGTATTCTTCTCAGTACCTCATCAGGAAGATG
127 AAGATTTGCTCACATCGAGCATGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATG
* * * * * *
17616 ATCGCGTCGTTTGTTTCAGTCTGCTTCTTTGTATCTCATCAGGAAGATGAA
192 ACCACGTCATTTGTTTCAATTTGCTTCTCTGTATCTCATCAGGAAGATGAA
17667 TTTGGTTCGCTTCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTTATCAG
1 TTTGGTTCGCTTCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTTATCAG
* *
17732 GAAGCTAATTGTTTATTGCTTTGACCTGCTTCTCAGTGTCTCATTAAGAAGCTGGGATTCGAAGA
66 GAAGCTAACTGTTTATTGCTTTGACCTGCTTCTCAGTGTCTCATCAAGAAGCTGGGATTCGAAGA
*
17797 TTTGCTCACATCGAGCATGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATAACCA
131 TTTGCTCACATCGAGCATGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCA
* *
17862 CATCATTTGTTTCAATTTGCTTCTCTGTATCTCATCAGGAAAATGAA
196 CGTCATTTGTTTCAATTTGCTTCTCTGTATCTCATCAGGAAGATGAA
* *
17909 TTTGGTTCGCTTCTTTGTATCTCATCAGGAAAACGAATTTGGTCCACTTCTCAGTATCTTATCAG
1 TTTGGTTCGCTTCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTTATCAG
* *
17974 GAAGCTAACCGTTTATTGCTTCGACCTGCTTCTCAGTGTCTCATCAAGAAGCTGGGATTCGAAGA
66 GAAGCTAACTGTTTATTGCTTTGACCTGCTTCTCAGTGTCTCATCAAGAAGCTGGGATTCGAAGA
18039 TTTGCTCACATCGAGCATGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCA
131 TTTGCTCACATCGAGCATGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCA
* * *
18104 CGTCATTTGTTTCAATTTACTTCTCTGTATCTCATCAAGAAGACGAA
196 CGTCATTTGTTTCAATTTGCTTCTCTGTATCTCATCAGGAAGATGAA
* *
18151 TTTGGTTAGCTTCTCAGTATCTCATCAGGAAG
1 TTTGGTTCGCTTCTCTGTATCTCATCAGGAAG
18183 CTCACCGTTT
Statistics
Matches: 464, Mismatches: 47, Indels: 9
0.89 0.09 0.02
Matches are distributed among these distances:
239 3 0.01
240 44 0.09
241 65 0.14
242 352 0.76
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.37
Consensus pattern (242 bp):
TTTGGTTCGCTTCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTTATCAG
GAAGCTAACTGTTTATTGCTTTGACCTGCTTCTCAGTGTCTCATCAAGAAGCTGGGATTCGAAGA
TTTGCTCACATCGAGCATGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCA
CGTCATTTGTTTCAATTTGCTTCTCTGTATCTCATCAGGAAGATGAA
Found at i:17930 original size:37 final size:37
Alignment explanation
Indices: 17880--17976 Score: 140
Period size: 37 Copynumber: 2.6 Consensus size: 37
17870 GTTTCAATTT
* *
17880 GCTTCTCTGTATCTCATCAGGAAAATGAATTTGGTTC
1 GCTTCTCTGTATCTCATCAGGAAAACGAATTTGGTCC
*
17917 GCTTCTTTGTATCTCATCAGGAAAACGAATTTGGTCC
1 GCTTCTCTGTATCTCATCAGGAAAACGAATTTGGTCC
* * *
17954 ACTTCTCAGTATCTTATCAGGAA
1 GCTTCTCTGTATCTCATCAGGAA
17977 GCTAACCGTT
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 53 1.00
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.36
Consensus pattern (37 bp):
GCTTCTCTGTATCTCATCAGGAAAACGAATTTGGTCC
Found at i:18276 original size:205 final size:205
Alignment explanation
Indices: 17917--18620 Score: 1153
Period size: 205 Copynumber: 3.4 Consensus size: 205
17907 AATTTGGTTC
* * * * *
17917 GCTTCTTTGTATCTCATCAGGAAAACGAATTTGGTCCACTTCTCAGTATCTTATCAGGAAGCTAA
1 GCTTCTCTGTATCTCATCAAGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAA
17982 CCGTTTATTGCTTCGACCTGCTTCTCAGTGTCTCATCA-AGAAGCTGGGATTCGAAGATTTGCTC
66 CCGTTTATTGCTTCGACCTGCTTCTCAGTGTCTCATCAGA-AAGCTGGGATTCGAAGATTTGCTC
*
18046 ACATCGAGCATGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCACGTCATT
130 ACATCGAGCATGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCATT
18111 TGTTTCAATTT
195 TGTTTCAATTT
* *
18122 ACTTCTCTGTATCTCATCAAGAAGACGAATTTGGTT-AGCTTCTCAGTATCTCATCAGGAAGCTC
1 GCTTCTCTGTATCTCATCAAGAAGACGAATTTGGTTCA-CTTCTCAGTATCTCATCAGGAAGCTA
* *
18186 ACCGTTTTTTGCTTCGACCTGCTTCTCAGTGTCTCATCAGAAAGCTGGGGTTCGAAGATTTGCTC
65 ACCGTTTATTGCTTCGACCTGCTTCTCAGTGTCTCATCAGAAAGCTGGGATTCGAAGATTTGCTC
* * *
18251 ACATCGAGCGTGGGTTTGATTTGGTCTTCTTTTCAGTATCTCATCAGAAAGATGACCGCGTCATT
130 ACATCGAGCATGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCATT
*
18316 TGTTTCGATTT
195 TGTTTCAATTT
*
18327 GCTTCTCTGTATCTCATCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAA
1 GCTTCTCTGTATCTCATCAAGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAA
* * * * *
18392 CCGTTTATTGCTTTGACTTGCTTCTCGGTGTCTCATCAGGAAGCTGAGATTCGAAGATTTGCTCA
66 CCGTTTATTGCTTCGACCTGCTTCTCAGTGTCTCATCAGAAAGCTGGGATTCGAAGATTTGCTCA
18457 CATCGAGCATGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCATTT
131 CATCGAGCATGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCATTT
18522 GTTTCAATTT
196 GTTTCAATTT
* *
18532 GCTTCTCTGTATCTCATC-AGAAAGACGAATTTGATTCACTTCTCAGTATCTCATTAGGAAGCTA
1 GCTTCTCTGTATCTCATCAAG-AAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTA
*
18596 ACCGTTTATTGCTTCGACTTGCTTC
65 ACCGTTTATTGCTTCGACCTGCTTC
18621 GACTTGCTTC
Statistics
Matches: 463, Mismatches: 32, Indels: 8
0.92 0.06 0.02
Matches are distributed among these distances:
204 2 0.00
205 459 0.99
206 2 0.00
ACGTcount: A:0.22, C:0.22, G:0.20, T:0.36
Consensus pattern (205 bp):
GCTTCTCTGTATCTCATCAAGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAA
CCGTTTATTGCTTCGACCTGCTTCTCAGTGTCTCATCAGAAAGCTGGGATTCGAAGATTTGCTCA
CATCGAGCATGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCATTT
GTTTCAATTT
Found at i:18619 original size:10 final size:10
Alignment explanation
Indices: 18604--18630 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
18594 TAACCGTTTA
18604 TTGCTTCGAC
1 TTGCTTCGAC
18614 TTGCTTCGAC
1 TTGCTTCGAC
18624 TTGCTTC
1 TTGCTTC
18631 TCGGTGGTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.07, C:0.30, G:0.19, T:0.44
Consensus pattern (10 bp):
TTGCTTCGAC
Found at i:30459 original size:117 final size:117
Alignment explanation
Indices: 30318--30771 Score: 315
Period size: 117 Copynumber: 3.8 Consensus size: 117
30308 AAAATGGTAA
* * * *
30318 TTTTGGACCTTCGGGGTAAGATGGTAATTTTGGGGAAG-TTCGAGGTTAAAAGAT-GAAATTTTT
1 TTTTGGACATTCGGGGCAAAATGGTAATTTT-GGAAAGTTTCGAGGTTAAAA-ATGGAAA-TTTT
* *
30381 AGATATTT-AGGGGTAAAAATGGAATTTTTGG-AGTTTCGGGGTCGAAAATAGAGT
63 AGAGATTTGA-GGGTAAAAATGGAATTTTTGGAAGTTTCGAGGTCGAAAATAGAGT
* * * *
30435 TTTTGGACATTTGGGGCAAAATGGTAATTTTTGAAAGTTTTGGGGTTAAAAATGGAAATTTTAGA
1 TTTTGGACATTCGGGGCAAAATGGTAATTTTGGAAAGTTTCGAGGTTAAAAATGGAAATTTTAGA
* * * * * *
30500 GGTTTGAGGGTAAAATTGTAATTTTTGGAAGTTTCGAGGTTGAAAATGGTATT
66 GATTTGAGGGTAAAAATGGAATTTTTGGAAGTTTCGAGGTCGAAAATAG-AGT
* * * ** *
30553 TTTTGGA-AGTTCAAGGGTCAAAATGG-AATTTTTGGAAATTTTAG-GGTCGAAAATGGAATTCT
1 TTTTGGACA-TTC--GGGGCAAAATGGTAA-TTTTGGAAAGTTTCGAGGTTAAAAATGGAAAT-T
* * * * * *
30615 TTAGA-AGTTCGAGTGTAAAAATGGAA-TTTTGGAAATTT-TAGGGTCGAAAATGGAAT
61 TTAGAGA-TTTGAGGGTAAAAATGGAATTTTTGGAAGTTTCGA-GGTCGAAAATAGAGT
* * * * ** *
30671 TTTTGGA-AGTTCGGGGGTAAAAATGG-AATTTTTAGAAATTTTAG-GGTCGAAAATGGAATTTT
1 TTTTGGACA-TTC-GGGG-CAAAATGGTAA-TTTTGGAAAGTTTCGAGGTTAAAAATGGAAATTT
* *
30733 TAGA-AGTTCGGGGGTAAAAATGGAATTTTTGGATAGTTT
62 TAGAGA-TTTGAGGGTAAAAATGGAATTTTTGGA-AGTTT
30772 AGGGACCTTT
Statistics
Matches: 282, Mismatches: 40, Indels: 28
0.81 0.11 0.08
Matches are distributed among these distances:
116 35 0.12
117 89 0.32
118 73 0.26
119 41 0.15
120 44 0.16
ACGTcount: A:0.32, C:0.04, G:0.28, T:0.36
Consensus pattern (117 bp):
TTTTGGACATTCGGGGCAAAATGGTAATTTTGGAAAGTTTCGAGGTTAAAAATGGAAATTTTAGA
GATTTGAGGGTAAAAATGGAATTTTTGGAAGTTTCGAGGTCGAAAATAGAGT
Found at i:30576 original size:30 final size:29
Alignment explanation
Indices: 30303--30770 Score: 278
Period size: 29 Copynumber: 15.9 Consensus size: 29
30293 TGGATACCCA
**
30303 AGGG-CAAAATGGTAA-TTTTGGACCTTCG
1 AGGGTCAAAATGG-AATTTTTGGAAGTTCG
* *
30331 -GGGT-AAGATGGTAATTTTGGGGAAGTTCG
1 AGGGTCAAAATGG-AATTTT-TGGAAGTTCG
* * * * * *
30360 AGGTTAAAAGATGAAATTTTTAGATATTTAG
1 AGGGTCAAA-ATGGAATTTTTGGA-AGTTCG
*
30391 -GGGTAAAAATGGAATTTTTGG-AGTTTCG
1 AGGGTCAAAATGGAATTTTTGGAAG-TTCG
* * *
30419 -GGGTCGAAAATAGAGTTTTTGGACA-TTTG
1 AGGGTC-AAAATGGAATTTTTGGA-AGTTCG
* *
30448 -GGG-CAAAATGGTAATTTTTGAAAGTTTTG
1 AGGGTCAAAATGG-AATTTTTGGAAG-TTCG
* * * * *
30477 -GGGTTAAAAATGGAAATTTTAGAGGTTTG
1 AGGG-TCAAAATGGAATTTTTGGAAGTTCG
*
30506 AGGGT-AAAATTGTAATTTTTGGAAGTTTCG
1 AGGGTCAAAA-TGGAATTTTTGGAAG-TTCG
* * * *
30536 AGGTTGAAAATGGTATTTTTTGGAAGTTCA
1 AGGGTCAAAATGG-AATTTTTGGAAGTTCG
* **
30566 AGGGTCAAAATGGAATTTTTGGAAATTTT
1 AGGGTCAAAATGGAATTTTTGGAAGTTCG
*
30595 AGGGTCGAAAATGGAATTCTTTAGAAGTTCG
1 AGGGTC-AAAATGGAATT-TTTGGAAGTTCG
* * * **
30626 AGTGTAAAAATGGAA-TTTTGGAAATTTT
1 AGGGTCAAAATGGAATTTTTGGAAGTTCG
30654 AGGGTCGAAAATGGAATTTTTGGAAGTTCG
1 AGGGTC-AAAATGGAATTTTTGGAAGTTCG
* * * * **
30684 GGGGTAAAAATGGAATTTTTAGAAATTTT
1 AGGGTCAAAATGGAATTTTTGGAAGTTCG
*
30713 AGGGTCGAAAATGGAATTTTTAGAAGTTCG
1 AGGGTC-AAAATGGAATTTTTGGAAGTTCG
* *
30743 GGGGTAAAAATGGAATTTTTGGATAGTT
1 AGGGTCAAAATGGAATTTTTGGA-AGTT
30771 TAGGGACCTT
Statistics
Matches: 341, Mismatches: 72, Indels: 52
0.73 0.15 0.11
Matches are distributed among these distances:
27 20 0.06
28 35 0.10
29 128 0.38
30 108 0.32
31 47 0.14
32 3 0.01
ACGTcount: A:0.32, C:0.04, G:0.29, T:0.35
Consensus pattern (29 bp):
AGGGTCAAAATGGAATTTTTGGAAGTTCG
Found at i:30773 original size:59 final size:59
Alignment explanation
Indices: 30390--30775 Score: 383
Period size: 59 Copynumber: 6.6 Consensus size: 59
30380 TAGATATTTA
* * * * *
30390 GGGGTAAAAATGGAATTTTTGG--AGTTTCGGGGTCGAAAATAGAGTTTTTGGACA-TT-T
1 GGGGTAAAAATGGAATTTTTGGAAAGTTT-AGGGTCGAAAATGGAATTTTTAGA-AGTTCG
* * ** * * *
30447 GGGG-CAAAATGGTAATTTTT-GAAAGTTTTGGGGTTAAAAATGGAAATTTTAGAGGTTTG
1 GGGGTAAAAATGG-AATTTTTGGAAAG-TTTAGGGTCGAAAATGGAATTTTTAGAAGTTCG
* * * * * * * *
30506 AGGGTAAAATTGTAATTTTTGG-AAGTTTCGAGGTTGAAAATGGTATTTTTTGGAAGTTCA
1 GGGGTAAAAATGGAATTTTTGGAAAGTTTAG-GGTCGAAAATGG-AATTTTTAGAAGTTCG
* * *
30566 AGGGTCAAAATGGAATTTTTGGAAATTTTAGGGTCGAAAATGGAATTCTTTAGAAGTTCG
1 GGGGTAAAAATGGAATTTTTGGAAAGTTTAGGGTCGAAAATGGAATT-TTTAGAAGTTCG
* * * *
30626 AGTGTAAAAATGGAA-TTTTGGAAATTTTAGGGTCGAAAATGGAATTTTTGGAAGTTCG
1 GGGGTAAAAATGGAATTTTTGGAAAGTTTAGGGTCGAAAATGGAATTTTTAGAAGTTCG
* *
30684 GGGGTAAAAATGGAATTTTTAGAAATTTTAGGGTCGAAAATGGAATTTTTAGAAGTTCG
1 GGGGTAAAAATGGAATTTTTGGAAAGTTTAGGGTCGAAAATGGAATTTTTAGAAGTTCG
*
30743 GGGGTAAAAATGGAATTTTTGGATAGTTTAGGG
1 GGGGTAAAAATGGAATTTTTGGAAAGTTTAGGG
30776 ACCTTTAGGG
Statistics
Matches: 276, Mismatches: 40, Indels: 24
0.81 0.12 0.07
Matches are distributed among these distances:
56 8 0.03
57 11 0.04
58 50 0.18
59 132 0.48
60 69 0.25
61 6 0.02
ACGTcount: A:0.32, C:0.04, G:0.29, T:0.35
Consensus pattern (59 bp):
GGGGTAAAAATGGAATTTTTGGAAAGTTTAGGGTCGAAAATGGAATTTTTAGAAGTTCG
Done.