Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009087.1 Kokia drynarioides strain JFW-HI SEQ_123787, 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: 83219
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 30 characters in sequence are not A, C, G, or T
Found at i:29136 original size:23 final size:23
Alignment explanation
Indices: 29110--29171 Score: 88
Period size: 23 Copynumber: 2.7 Consensus size: 23
29100 CGCGCTATAG
*
29110 AAGCAGACATAATCGTGCCATAA
1 AAGCAGACATAATCATGCCATAA
29133 AAGCAGACATAATCATGCCATAA
1 AAGCAGACATAATCATGCCATAA
* * *
29156 AAACATACAAAATCAT
1 AAGCAGACATAATCAT
29172 TGTAAGAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.50, C:0.21, G:0.11, T:0.18
Consensus pattern (23 bp):
AAGCAGACATAATCATGCCATAA
Found at i:29599 original size:18 final size:19
Alignment explanation
Indices: 29576--29614 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
29566 TTAATTTTTT
29576 AATATTAAAAT-ATTAAAA
1 AATATTAAAATAATTAAAA
* *
29594 AATATTTAATTAATTAAAA
1 AATATTAAAATAATTAAAA
29613 AA
1 AA
29615 GGGTATGGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
AATATTAAAATAATTAAAA
Found at i:29730 original size:10 final size:10
Alignment explanation
Indices: 29717--29741 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
29707 CGCCTGCTGC
29717 TGCTGCTTGT
1 TGCTGCTTGT
29727 TGCTGCTTGT
1 TGCTGCTTGT
29737 TGCTG
1 TGCTG
29742 GCTACTGACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.00, C:0.20, G:0.32, T:0.48
Consensus pattern (10 bp):
TGCTGCTTGT
Found at i:29919 original size:21 final size:21
Alignment explanation
Indices: 29894--29949 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
29884 AAAAAACACA
29894 AAGAAAGAAAGAAG-AGAAGGG
1 AAGAAAGAAAGAAGCAGAA-GG
* * *
29915 TAGAACGACAGAAGCAGAAGG
1 AAGAAAGAAAGAAGCAGAAGG
*
29936 AAGAAGGAAAGAAG
1 AAGAAAGAAAGAAG
29950 GGTAGGAAGG
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
21 24 0.86
22 4 0.14
ACGTcount: A:0.57, C:0.05, G:0.36, T:0.02
Consensus pattern (21 bp):
AAGAAAGAAAGAAGCAGAAGG
Found at i:30421 original size:207 final size:207
Alignment explanation
Indices: 30006--30571 Score: 916
Period size: 207 Copynumber: 2.8 Consensus size: 207
29996 TTGTTTGTGT
*
30006 TTGATTTTTATTTAAATGTTATTTAAATTTAAATTTTATCTA-TATAATTTGATCTTAGTTAGTC
1 TTGATTTTTATTTAAATGTTATTTAAATTTAAATTTTATCTATTA-AATTTGATCTTAGTTAGTG
* *
30070 TAAA-CATTTGAAATTTAACATTAATTTAATTGAAATAAAAAAAACTATGATTCATAAAATTACA
65 TAAACCA-TTGAAATTTAACATTAATTTATTTGAAATAAAAAAAATTATGATTCATAAAATTACA
* * *
30134 ATAATGTTAAAATGGTCCCC------AAAAAAATTATTAAATAAAAATTAAAACTTTATTTTGAT
129 ATAGTGCTAAAATGGTCCCCAAAATTAAAAAAAATATTAAATAAAAATTAAAACTTTATTTTGAT
30193 ACAAAGTTTTAGGG
194 ACAAAGTTTTAGGG
* * *
30207 CTGATTTTTATTTAAATGTTATTTAAATATAAATTTTATCTATTAAATTTAATCTTCA-TTAGTG
1 TTGATTTTTATTTAAATGTTATTTAAATTTAAATTTTATCTATTAAATTTGATCTT-AGTTAGTG
* *
30271 TAAACCATTGAAATTTAACATTAATTTATTTGAAATAAAAAAATTTGTGATTCATAAAATTACAA
65 TAAACCATTGAAATTTAACATTAATTTATTTGAAATAAAAAAAATTATGATTCATAAAATTACAA
30336 TAGTGCTAAAATGGTCCCCAAAATTAAAAAAAATATTAAATAAAAATTAAAACTTTATTTTGATA
130 TAGTGCTAAAATGGTCCCCAAAATTAAAAAAAATATTAAATAAAAATTAAAACTTTATTTTGATA
30401 CAAAGTTTTAGGG
195 CAAAGTTTTAGGG
*
30414 TTGATTTTTATTTAAATGTTATTTAAATTTAAATTTTATCTATTTAATTTGATCTTAGTTAGTGT
1 TTGATTTTTATTTAAATGTTATTTAAATTTAAATTTTATCTATTAAATTTGATCTTAGTTAGTGT
*
30479 AAACCCTTGAAATTTAACATTAATTTATTTGAAATAAAAAAAATTATGATTCATAAAATTACAAT
66 AAACCATTGAAATTTAACATTAATTTATTTGAAATAAAAAAAATTATGATTCATAAAATTACAAT
*
30544 AGTGCTAAAATGATCCCCAAAATTAAAA
131 AGTGCTAAAATGGTCCCCAAAATTAAAA
30572 CTTTATTTTG
Statistics
Matches: 336, Mismatches: 19, Indels: 14
0.91 0.05 0.04
Matches are distributed among these distances:
201 130 0.39
202 5 0.01
206 1 0.00
207 200 0.60
ACGTcount: A:0.43, C:0.08, G:0.08, T:0.41
Consensus pattern (207 bp):
TTGATTTTTATTTAAATGTTATTTAAATTTAAATTTTATCTATTAAATTTGATCTTAGTTAGTGT
AAACCATTGAAATTTAACATTAATTTATTTGAAATAAAAAAAATTATGATTCATAAAATTACAAT
AGTGCTAAAATGGTCCCCAAAATTAAAAAAAATATTAAATAAAAATTAAAACTTTATTTTGATAC
AAAGTTTTAGGG
Found at i:30581 original size:184 final size:183
Alignment explanation
Indices: 30378--30750 Score: 694
Period size: 184 Copynumber: 2.0 Consensus size: 183
30368 ATATTAAATA
*
30378 AAAATTAAAACTTTATTTTGATACAAAGTTTTAGGGTTGATTTTTATTTAAATGTTATTTAAATT
1 AAAATTAAAACTTTATTTTGATACAAAGTTTTAGAGTTGATTTTTATTTAAATGTTATTTAAATT
*
30443 TAAATTTTATCTATTTAATTTGATCTTAGTTAGTGTAAACCCTTGAAATTTAACATTAATTTATT
66 TAAATTTTATCTATTTAATTTGATCTTAATTAGTGTAAACCCTTGAAATTTAACATTAATTTATT
30508 TGAAATAAAAAAAATTATGATTCATAAAATTACAATAGTGCTAAAAT-GATCCCC
131 TGAAAT-AAAAAAATTATGATTCATAAAATTACAATAGTGCTAAAATAG-TCCCC
30562 AAAATTAAAACTTTATTTTGATACAAAGTTTTAGAGTTGATTTTTATTTAAATGTTATTTAAATT
1 AAAATTAAAACTTTATTTTGATACAAAGTTTTAGAGTTGATTTTTATTTAAATGTTATTTAAATT
30627 TAAATTTTATCTATTTAATTTGATCTTAATTAGTGTAAACCCTTGAAATTTAACATTAATTTATT
66 TAAATTTTATCTATTTAATTTGATCTTAATTAGTGTAAACCCTTGAAATTTAACATTAATTTATT
*
30692 TGAAATAAAAAAATTATGATTCATAAAATTACAATAGTGTTAAAATAGTCCCC
131 TGAAATAAAAAAATTATGATTCATAAAATTACAATAGTGCTAAAATAGTCCCC
30745 AAAATT
1 AAAATT
30751 TATTTGTATT
Statistics
Matches: 185, Mismatches: 3, Indels: 3
0.97 0.02 0.02
Matches are distributed among these distances:
183 50 0.27
184 135 0.73
ACGTcount: A:0.40, C:0.08, G:0.09, T:0.43
Consensus pattern (183 bp):
AAAATTAAAACTTTATTTTGATACAAAGTTTTAGAGTTGATTTTTATTTAAATGTTATTTAAATT
TAAATTTTATCTATTTAATTTGATCTTAATTAGTGTAAACCCTTGAAATTTAACATTAATTTATT
TGAAATAAAAAAATTATGATTCATAAAATTACAATAGTGCTAAAATAGTCCCC
Found at i:33102 original size:21 final size:20
Alignment explanation
Indices: 33049--33105 Score: 57
Period size: 20 Copynumber: 2.9 Consensus size: 20
33039 GAGATGGGCC
33049 TTTGAA-AT-ATATTTTTCA
1 TTTGAATATAATATTTTTCA
* *
33067 TTTGTATATATTATTTTTCA
1 TTTGAATATAATATTTTTCA
33087 TTTGGAAT-TAAATATTTTT
1 TTT-GAATAT-AATATTTTT
33106 ATGTTCTTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
18 5 0.16
19 2 0.06
20 13 0.42
21 11 0.35
ACGTcount: A:0.30, C:0.04, G:0.07, T:0.60
Consensus pattern (20 bp):
TTTGAATATAATATTTTTCA
Found at i:36295 original size:25 final size:26
Alignment explanation
Indices: 36251--36302 Score: 79
Period size: 25 Copynumber: 2.0 Consensus size: 26
36241 ACTCTTCTAT
*
36251 TTCCTTTCATTCTTTAAAAATTTTGC
1 TTCCTTTCATTCTTTAAAAAATTTGC
*
36277 TTCCTTTC-TTTTTTAAAAAATTTGC
1 TTCCTTTCATTCTTTAAAAAATTTGC
36302 T
1 T
36303 GTTAAAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 16 0.67
26 8 0.33
ACGTcount: A:0.23, C:0.17, G:0.04, T:0.56
Consensus pattern (26 bp):
TTCCTTTCATTCTTTAAAAAATTTGC
Found at i:36804 original size:27 final size:27
Alignment explanation
Indices: 36766--36836 Score: 142
Period size: 27 Copynumber: 2.6 Consensus size: 27
36756 AAATTGGAGC
36766 TTGGTGTCGCCTGTCAGGATGGCACTT
1 TTGGTGTCGCCTGTCAGGATGGCACTT
36793 TTGGTGTCGCCTGTCAGGATGGCACTT
1 TTGGTGTCGCCTGTCAGGATGGCACTT
36820 TTGGTGTCGCCTGTCAG
1 TTGGTGTCGCCTGTCAG
36837 ATAAACACCA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 44 1.00
ACGTcount: A:0.10, C:0.23, G:0.34, T:0.34
Consensus pattern (27 bp):
TTGGTGTCGCCTGTCAGGATGGCACTT
Found at i:37379 original size:7 final size:7
Alignment explanation
Indices: 37367--37394 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
37357 ACGAATCCGT
37367 GGAGAAG
1 GGAGAAG
37374 GGAGAAG
1 GGAGAAG
37381 GGAGAAG
1 GGAGAAG
37388 GGAGAAG
1 GGAGAAG
37395 AAAGAAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.57, T:0.00
Consensus pattern (7 bp):
GGAGAAG
Found at i:39208 original size:39 final size:39
Alignment explanation
Indices: 39149--39226 Score: 147
Period size: 39 Copynumber: 2.0 Consensus size: 39
39139 TGCAATGCTC
39149 GTATCATGTTTTAGAAGTAAAATCAAACTACATTGTGAA
1 GTATCATGTTTTAGAAGTAAAATCAAACTACATTGTGAA
*
39188 GTATGATGTTTTAGAAGTAAAATCAAACTACATTGTGAA
1 GTATCATGTTTTAGAAGTAAAATCAAACTACATTGTGAA
39227 AAACCAAAAT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.41, C:0.09, G:0.17, T:0.33
Consensus pattern (39 bp):
GTATCATGTTTTAGAAGTAAAATCAAACTACATTGTGAA
Found at i:58927 original size:30 final size:30
Alignment explanation
Indices: 58893--59147 Score: 173
Period size: 29 Copynumber: 8.8 Consensus size: 30
58883 AATTTTTTCC
*
58893 AAAATTACATTTTAACCCCTAAACTTTCTA
1 AAAATTACATTTTTACCCCTAAACTTTCTA
** *
58923 AAAA-T-CATATTCGACCCCCAAACTTTTCT-
1 AAAATTACAT-TTTTACCCCTAAAC-TTTCTA
* * * *
58952 AAAATCACA-TTTTGCCACTGAAC--T-TA
1 AAAATTACATTTTTACCCCTAAACTTTCTA
* *
58978 AAAATTACATTTTTGCCCATAAAC-TTCTCA
1 AAAATTACATTTTTACCCCTAAACTTTCT-A
* * *
59008 AAAATTACA-TTTTGCCCTTAAAC-TTCCA
1 AAAATTACATTTTTACCCCTAAACTTTCTA
59036 AAAATTACATTTTTA-CCCTCAAAC-TTCTA
1 AAAATTACATTTTTACCCCT-AAACTTTCTA
* *
59065 AAAATCACATTTTTACCCC-AAATTTTCCT-
1 AAAATTACATTTTTACCCCTAAACTTT-CTA
** *
59094 AAAATGGCATTTTTACCCCTAAAACTTTC-C
1 AAAATTACATTTTTACCCCT-AAACTTTCTA
*
59124 AAAATTACA-TTTTAACCCTAAACT
1 AAAATTACATTTTTACCCCTAAACT
59148 CTCCGAAACT
Statistics
Matches: 181, Mismatches: 27, Indels: 36
0.74 0.11 0.15
Matches are distributed among these distances:
25 1 0.01
26 9 0.05
27 11 0.06
28 25 0.14
29 95 0.52
30 32 0.18
31 8 0.04
ACGTcount: A:0.37, C:0.25, G:0.03, T:0.35
Consensus pattern (30 bp):
AAAATTACATTTTTACCCCTAAACTTTCTA
Found at i:59018 original size:56 final size:57
Alignment explanation
Indices: 58936--59077 Score: 175
Period size: 56 Copynumber: 2.5 Consensus size: 57
58926 ATCATATTCG
* * * *
58936 ACCCCCAAACTTTTCTAAAATCACATTTTGCCAC-TGAACTT-AAAAATTACATTTTT
1 ACCCTCAAACTTCTCAAAAATCACATTTTGCC-CTTAAACTTCAAAAATTACATTTTT
* *
58992 GCCCAT-AAACTTCTCAAAAATTACATTTTGCCCTTAAACTTCCAAAAATTACATTTTT
1 ACCC-TCAAACTTCTCAAAAATCACATTTTGCCCTTAAACTT-CAAAAATTACATTTTT
59050 ACCCTCAAACTTCT-AAAAATCACATTTT
1 ACCCTCAAACTTCTCAAAAATCACATTTT
59078 TACCCCAAAT
Statistics
Matches: 73, Mismatches: 8, Indels: 9
0.81 0.09 0.10
Matches are distributed among these distances:
55 1 0.01
56 32 0.44
57 14 0.19
58 26 0.36
ACGTcount: A:0.37, C:0.25, G:0.03, T:0.35
Consensus pattern (57 bp):
ACCCTCAAACTTCTCAAAAATCACATTTTGCCCTTAAACTTCAAAAATTACATTTTT
Found at i:59060 original size:58 final size:57
Alignment explanation
Indices: 58893--59164 Score: 191
Period size: 58 Copynumber: 4.7 Consensus size: 57
58883 AATTTTTTCC
* ** * * *
58893 AAAATTACATTTTAACCCCTAAACTTTCTAAAAA-T-CATATTCGACCCCCAAACTTTTCT
1 AAAATTACATTTT-A-CCCTAAAC-TTCCAAAAATTACAT-TTTTACCCTCAAACTTCTCA
* * * *
58952 AAAATCACATTTTGCCACTGAACTT--AAAAATTACATTTTTGCCCAT-AAACTTCTCA
1 AAAATTACATTTTACC-CTAAACTTCCAAAAATTACATTTTTACCC-TCAAACTTCTCA
*
59008 AAAATTACATTTTGCCCTTAAACTTCCAAAAATTACATTTTTACCCTCAAACTTCT-A
1 AAAATTACATTTTACCC-TAAACTTCCAAAAATTACATTTTTACCCTCAAACTTCTCA
* * * * ** * *
59065 AAAATCACATTTTTACCCCAAATTTTCCTAAAATGGCATTTTTACCCCTAAAACTT-TCC
1 AAAATTACA-TTTTACCCTAAA-CTTCCAAAAATTACATTTTTA-CCCTCAAACTTCTCA
* *
59124 AAAATTACATTTTAACCCTAAACTCTCCGAAACTT-CATTTT
1 AAAATTACATTTT-ACCCTAAACT-TCCAAAAATTACATTTT
59165 CGACCCCTTT
Statistics
Matches: 172, Mismatches: 27, Indels: 29
0.75 0.12 0.13
Matches are distributed among these distances:
55 6 0.03
56 35 0.20
57 20 0.12
58 67 0.39
59 44 0.26
ACGTcount: A:0.36, C:0.25, G:0.03, T:0.35
Consensus pattern (57 bp):
AAAATTACATTTTACCCTAAACTTCCAAAAATTACATTTTTACCCTCAAACTTCTCA
Found at i:59303 original size:15 final size:15
Alignment explanation
Indices: 59276--59317 Score: 54
Period size: 14 Copynumber: 2.9 Consensus size: 15
59266 TGAATCATAA
59276 TTCGTAT-TTTATTT
1 TTCGTATATTTATTT
59290 TTC-TCATATTTA-TT
1 TTCGT-ATATTTATTT
59304 TTCGTATATTTATT
1 TTCGTATATTTATT
59318 CATTCTTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
13 1 0.04
14 17 0.71
15 6 0.25
ACGTcount: A:0.19, C:0.10, G:0.05, T:0.67
Consensus pattern (15 bp):
TTCGTATATTTATTT
Found at i:59606 original size:97 final size:97
Alignment explanation
Indices: 59440--59630 Score: 301
Period size: 97 Copynumber: 2.0 Consensus size: 97
59430 ATAATTAAAA
* * * *
59440 TCGAGGCAATATTCCTTTATTTCAGGTTTTGAAATTTTGTGCCTTAACTTACTAGGCGCGATTTT
1 TCGAGGCAATATTCCTTTATCTCAGGTTTCGAAAATTTGTGCCTTAACTCACTAGGCGCGATTTT
* * *
59505 TCTTCAAACTGGGATGATTGAATACCCTTAAG
66 TCTTCAAACCGGGATAATCGAATACCCTTAAG
* *
59537 TCGAGGCAATATTGCTTTATCTCGGGTTTCGAAAATTTGTGCCTTAACTCACTAGGCGCGATTTT
1 TCGAGGCAATATTCCTTTATCTCAGGTTTCGAAAATTTGTGCCTTAACTCACTAGGCGCGATTTT
59602 TCTTCAAACCGGGATAATCGAATACCCTT
66 TCTTCAAACCGGGATAATCGAATACCCTT
59631 TTTCAAGGTT
Statistics
Matches: 85, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
97 85 1.00
ACGTcount: A:0.25, C:0.20, G:0.19, T:0.37
Consensus pattern (97 bp):
TCGAGGCAATATTCCTTTATCTCAGGTTTCGAAAATTTGTGCCTTAACTCACTAGGCGCGATTTT
TCTTCAAACCGGGATAATCGAATACCCTTAAG
Found at i:71092 original size:39 final size:39
Alignment explanation
Indices: 71043--71721 Score: 344
Period size: 39 Copynumber: 17.4 Consensus size: 39
71033 TCTCTGATCT
* * *
71043 CGAGCCTGGGGCAGATTTCAACCATTCGATCTTTTACCC
1 CGAGCTTGGGGCAGATTTCAACCATTCAATCTCTTACCC
* * ** * ** *
71082 CAAGCTTGGGGCAAATCACCACCAGCCAATCTCTTATCC
1 CGAGCTTGGGGCAGATTTCAACCATTCAATCTCTTACCC
* * * * *
71121 CTAACCTAGGGCAGATTACAACCATTCAATCTCTTACCC
1 CGAGCTTGGGGCAGATTTCAACCATTCAATCTCTTACCC
* * * *
71160 CGAGCCTGAGGCAGA--TC-ACCATAAACAAATCTCTTACCT
1 CGAGCTTGGGGCAGATTTCAACCAT--TC-AATCTCTTACCC
* * *
71199 CGAGCCTGGGGCAAATTGT-AACCATTCGATCTCTTACCC
1 CGAGCTTGGGGCAGATT-TCAACCATTCAATCTCTTACCC
* * *
71238 CGAGCTTGGGCCA-A-ATC-ACCATCAGCAAATCTCTTACCC
1 CGAGCTTGGGGCAGATTTCAACCAT--TC-AATCTCTTACCC
* * * * *
71277 CGAGCCTGAGGTAGATTACAACCATTCAATCTCTTACCG
1 CGAGCTTGGGGCAGATTTCAACCATTCAATCTCTTACCC
* * ** * ** * *
71316 CGAGCTTGAGGTAGATCACCACCAGCCAATCTTTTACCT
1 CGAGCTTGGGGCAGATTTCAACCATTCAATCTCTTACCC
* *
71355 CGAGCCTGGGGCAGATTGT-AACCATTCGATCTCTTACCC
1 CGAGCTTGGGGCAGATT-TCAACCATTCAATCTCTTACCC
* * * ** * **
71394 TGAGCCTAGGGCAGATCACCACCAGCCAATCTCTTACCC
1 CGAGCTTGGGGCAGATTTCAACCATTCAATCTCTTACCC
* * * * ** *
71433 CGAACTTAGGGCAAATTGT-AACTATTTGATCTCTTACAC
1 CGAGCTTGGGGCAGATT-TCAACCATTCAATCTCTTACCC
* * * *
71472 CGAGCCTT-AGGCAGATTACCACCAGTCAATCTCTTACCC
1 CGAG-CTTGGGGCAGATTTCAACCATTCAATCTCTTACCC
* * * *
71511 CGAGCTTGGGCCAGATTGCAACCATTCAATCTTTTACCT
1 CGAGCTTGGGGCAGATTTCAACCATTCAATCTCTTACCC
* * *
71550 CGAACTTGGGGCA-A-ATC-ACCATCAACAAATCTCTTACCC
1 CGAGCTTGGGGCAGATTTCAACCAT--TC-AATCTCTTACCC
* * * * *
71589 CGAGCTTGGGGCAAATTGCAACCATTCGATCTTTTACCT
1 CGAGCTTGGGGCAGATTTCAACCATTCAATCTCTTACCC
* * * * * *
71628 TGAGCATGGGGCAAATCATC-ATCA-ACAAATCTCTTACCC
1 CGAGCTTGGGGCAGAT-TTCAACCATTC-AATCTCTTACCC
* * * ** *
71667 CGATCATGGGGCAGATTGCAACCATTTGATCTTTTACCC
1 CGAGCTTGGGGCAGATTTCAACCATTCAATCTCTTACCC
*
71706 CGAGCTTGAGGCAGAT
1 CGAGCTTGGGGCAGAT
71722 CACCATCAGC
Statistics
Matches: 472, Mismatches: 138, Indels: 60
0.70 0.21 0.09
Matches are distributed among these distances:
36 16 0.03
37 2 0.00
38 10 0.02
39 417 0.88
40 9 0.02
41 2 0.00
42 16 0.03
ACGTcount: A:0.27, C:0.30, G:0.18, T:0.25
Consensus pattern (39 bp):
CGAGCTTGGGGCAGATTTCAACCATTCAATCTCTTACCC
Found at i:71743 original size:39 final size:38
Alignment explanation
Indices: 70993--71747 Score: 306
Period size: 39 Copynumber: 19.4 Consensus size: 38
70983 TGAAGATTTG
* * *
70993 ATCTTTTACCCCGAGCCTGGGGCAGATCACCATCAACAA
1 ATCTCTTACCCCGAGCTTGGGGCAGATCACCATCAGC-A
* * * *
71032 ATCTCTGATCTCGAGCCTGGGGCAGATTTCAACCATTC-G--
1 ATCTCTTACCCCGAGCTTGGGGCAGA--TC-ACCA-TCAGCA
* * * *
71071 ATCTTTTACCCCAAGCTTGGGGCAAATCACCACCAGCCA
1 ATCTCTTACCCCGAGCTTGGGGCAGATCACCATCAG-CA
* * * * * * * * *
71110 ATCTCTTATCCCTAACCTAGGGCAGATTACAACCATTCA
1 ATCTCTTACCCCGAGCTTGGGGCAGATCACCATCA-GCA
* * * *
71149 ATCTCTTACCCCGAGCCTGAGGCAGATCACCATAAACAA
1 ATCTCTTACCCCGAGCTTGGGGCAGATCACCATCAGC-A
* * * *
71188 ATCTCTTACCTCGAGCCTGGGGCAAATTGTAACCATTC-G--
1 ATCTCTTACCCCGAGCTTGGGGCAGA---TCACCA-TCAGCA
* *
71227 ATCTCTTACCCCGAGCTTGGGCCAAATCACCATCAGCAA
1 ATCTCTTACCCCGAGCTTGGGGCAGATCACCATCAGC-A
* * * * * * *
71266 ATCTCTTACCCCGAGCCTGAGGTAGATTACAACCATTCA
1 ATCTCTTACCCCGAGCTTGGGGCAGATCACCATCA-GCA
* * * *
71305 ATCTCTTACCGCGAGCTTGAGGTAGATCACCACCAGCCA
1 ATCTCTTACCCCGAGCTTGGGGCAGATCACCATCAG-CA
* * * *
71344 ATCTTTTACCTCGAGCCTGGGGCAGATTGTAACCATTC-G--
1 ATCTCTTACCCCGAGCTTGGGGCAGA---TCACCA-TCAGCA
* * * *
71383 ATCTCTTACCCTGAGCCTAGGGCAGATCACCACCAGCCA
1 ATCTCTTACCCCGAGCTTGGGGCAGATCACCATCAG-CA
* * * * * **
71422 ATCTCTTACCCCGAACTTAGGGCAAATTGTAACTATTTG--
1 ATCTCTTACCCCGAGCTTGGGGCAGA---TCACCATCAGCA
* * * *
71461 ATCTCTTACACCGAGCCTT-AGGCAGATTACCACCAGTCA
1 ATCTCTTACCCCGAG-CTTGGGGCAGATCACCATCAG-CA
* *
71500 ATCTCTTACCCCGAGCTTGGGCCAGATTGCAACCAT--TCA
1 ATCTCTTACCCCGAGCTTGGGGCAGA-T-C-ACCATCAGCA
* * * * *
71539 ATCTTTTACCTCGAACTTGGGGCAAATCACCATCAACAA
1 ATCTCTTACCCCGAGCTTGGGGCAGATCACCATCAGC-A
*
71578 ATCTCTTACCCCGAGCTTGGGGCAAATTGCAACCATTC-G--
1 ATCTCTTACCCCGAGCTTGGGGCAGA-T-C-ACCA-TCAGCA
* ** * * * *
71617 ATCTTTTACCTTGAGCATGGGGCAAATCATCATCAACAA
1 ATCTCTTACCCCGAGCTTGGGGCAGATCACCATCAGC-A
* * **
71656 ATCTCTTACCCCGATCATGGGGCAGATTGCAACCATTTG--
1 ATCTCTTACCCCGAGCTTGGGGCAGA-T-C-ACCATCAGCA
* *
71695 ATCTTTTACCCCGAGCTTGAGGCAGATCACCATCAGCAA
1 ATCTCTTACCCCGAGCTTGGGGCAGATCACCATCAGC-A
71734 ATCTCTTACCCCGA
1 ATCTCTTACCCCGA
71748 TCATGAGGAA
Statistics
Matches: 534, Mismatches: 126, Indels: 112
0.69 0.16 0.15
Matches are distributed among these distances:
35 6 0.01
36 36 0.07
37 5 0.01
38 8 0.01
39 430 0.81
40 7 0.01
41 4 0.01
42 32 0.06
43 6 0.01
ACGTcount: A:0.27, C:0.31, G:0.17, T:0.25
Consensus pattern (38 bp):
ATCTCTTACCCCGAGCTTGGGGCAGATCACCATCAGCA
Found at i:71748 original size:78 final size:78
Alignment explanation
Indices: 70992--71773 Score: 780
Period size: 78 Copynumber: 10.0 Consensus size: 78
70982 TTGAAGATTT
* * * * * * *
70992 GATCTTTTACCCCGAGCCTGGGGCAGATCACCATCAACAAATCTCTGATCTCGAGCCTGGGGCAG
1 GATCTCTTACCCCGAGCTTGAGGCAGATCACCATCAGCAAATCTCTTACCCCGAGCCTGGGGCAG
*
71057 ATTTCAACCATTC
66 ATTGCAACCATTC
* * * * * * * * * *
71070 GATCTTTTACCCCAAGCTTGGGGCAAATCACCACCAGCCAATCTCTTATCCCTAACCTAGGGCAG
1 GATCTCTTACCCCGAGCTTGAGGCAGATCACCATCAGCAAATCTCTTACCCCGAGCCTGGGGCAG
*
71135 ATTACAACCATTC
66 ATTGCAACCATTC
* * * * * *
71148 AATCTCTTACCCCGAGCCTGAGGCAGATCACCATAAACAAATCTCTTACCTCGAGCCTGGGGCAA
1 GATCTCTTACCCCGAGCTTGAGGCAGATCACCATCAGCAAATCTCTTACCCCGAGCCTGGGGCAG
*
71213 ATTGTAACCATTC
66 ATTGCAACCATTC
* * *
71226 GATCTCTTACCCCGAGCTTG-GGCCAAATCACCATCAGCAAATCTCTTACCCCGAGCCTGAGGTA
1 GATCTCTTACCCCGAGCTTGAGG-CAGATCACCATCAGCAAATCTCTTACCCCGAGCCTGGGGCA
*
71290 GATTACAACCATTC
65 GATTGCAACCATTC
* * * * * * *
71304 AATCTCTTACCGCGAGCTTGAGGTAGATCACCACCAGCCAATCTTTTACCTCGAGCCTGGGGCAG
1 GATCTCTTACCCCGAGCTTGAGGCAGATCACCATCAGCAAATCTCTTACCCCGAGCCTGGGGCAG
*
71369 ATTGTAACCATTC
66 ATTGCAACCATTC
* * * * * * *
71382 GATCTCTTACCCTGAGCCT-AGGGCAGATCACCACCAGCCAATCTCTTACCCCGAACTTAGGGCA
1 GATCTCTTACCCCGAGCTTGA-GGCAGATCACCATCAGCAAATCTCTTACCCCGAGCCTGGGGCA
* * * *
71446 AATTGTAACTATTT
65 GATTGCAACCATTC
* * * * *
71460 GATCTCTTACACCGAGCCTT-AGGCAGATTACCACCAGTC-AATCTCTTACCCCGAGCTTGGGCC
1 GATCTCTTACCCCGAG-CTTGAGGCAGATCACCATCAG-CAAATCTCTTACCCCGAGCCTGGGGC
71523 AGATTGCAACCATTC
64 AGATTGCAACCATTC
* * * * * * * * *
71538 AATCTTTTACCTCGAACTTGGGGCAAATCACCATCAACAAATCTCTTACCCCGAGCTTGGGGCAA
1 GATCTCTTACCCCGAGCTTGAGGCAGATCACCATCAGCAAATCTCTTACCCCGAGCCTGGGGCAG
71603 ATTGCAACCATTC
66 ATTGCAACCATTC
* ** * * * * * * *
71616 GATCTTTTACCTTGAGCATGGGGCAAATCATCATCAACAAATCTCTTACCCCGATCATGGGGCAG
1 GATCTCTTACCCCGAGCTTGAGGCAGATCACCATCAGCAAATCTCTTACCCCGAGCCTGGGGCAG
*
71681 ATTGCAACCATTT
66 ATTGCAACCATTC
* * * * *
71694 GATCTTTTACCCCGAGCTTGAGGCAGATCACCATCAGCAAATCTCTTACCCCGATCATGAGGAAG
1 GATCTCTTACCCCGAGCTTGAGGCAGATCACCATCAGCAAATCTCTTACCCCGAGCCTGGGGCAG
*
71759 ATTGCAATCATTC
66 ATTGCAACCATTC
71772 GA
1 GA
71774 AGCAATAAAG
Statistics
Matches: 588, Mismatches: 109, Indels: 14
0.83 0.15 0.02
Matches are distributed among these distances:
77 7 0.01
78 575 0.98
79 6 0.01
ACGTcount: A:0.27, C:0.30, G:0.18, T:0.25
Consensus pattern (78 bp):
GATCTCTTACCCCGAGCTTGAGGCAGATCACCATCAGCAAATCTCTTACCCCGAGCCTGGGGCAG
ATTGCAACCATTC
Found at i:71755 original size:39 final size:39
Alignment explanation
Indices: 71632--71760 Score: 111
Period size: 39 Copynumber: 3.3 Consensus size: 39
71622 TTACCTTGAG
* * * *
71632 CATGGGGCAAATCATCATCAACAAATCTCTTACCCCGAT
1 CATGAGGCAGATCACCATCAGCAAATCTCTTACCCCGAT
* ** * *
71671 CATGGGGCAGATTGCAACCATTTG---ATCTTTTACCCCGAG
1 CATGAGGCAGA-T-C-ACCATCAGCAAATCTCTTACCCCGAT
*
71710 CTTGAGGCAGATCACCATCAGCAAATCTCTTACCCCGAT
1 CATGAGGCAGATCACCATCAGCAAATCTCTTACCCCGAT
*
71749 CATGAGGAAGAT
1 CATGAGGCAGAT
71761 TGCAATCATT
Statistics
Matches: 69, Mismatches: 15, Indels: 12
0.72 0.16 0.12
Matches are distributed among these distances:
36 6 0.09
37 1 0.01
38 1 0.01
39 55 0.80
40 1 0.01
41 1 0.01
42 4 0.06
ACGTcount: A:0.29, C:0.28, G:0.19, T:0.24
Consensus pattern (39 bp):
CATGAGGCAGATCACCATCAGCAAATCTCTTACCCCGAT
Found at i:72201 original size:6 final size:6
Alignment explanation
Indices: 72190--72258 Score: 58
Period size: 6 Copynumber: 12.2 Consensus size: 6
72180 GACCCAAACA
* *
72190 AAATTT AAATTT AAATTT -ATTTT AAGTTT AAATTT --ATTGT AAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATT-T AAATTT
* *
72236 AAGTTT AAAATT --ATTT AAATTT A
1 AAATTT AAATTT AAATTT AAATTT A
72259 CTAATGTCCA
Statistics
Matches: 50, Mismatches: 7, Indels: 12
0.72 0.10 0.17
Matches are distributed among these distances:
4 6 0.12
5 5 0.10
6 36 0.72
7 3 0.06
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.52
Consensus pattern (6 bp):
AAATTT
Found at i:72219 original size:17 final size:17
Alignment explanation
Indices: 72193--72242 Score: 73
Period size: 17 Copynumber: 2.9 Consensus size: 17
72183 CCAAACAAAA
72193 TTTAAATTTAAATTTAT
1 TTTAAATTTAAATTTAT
*
72210 TTTAAGTTTAAATTTAT
1 TTTAAATTTAAATTTAT
* *
72227 TGTAAATTTAAGTTTA
1 TTTAAATTTAAATTTA
72243 AAATTATTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (17 bp):
TTTAAATTTAAATTTAT
Found at i:72236 original size:23 final size:22
Alignment explanation
Indices: 72210--72258 Score: 80
Period size: 23 Copynumber: 2.2 Consensus size: 22
72200 TTAAATTTAT
*
72210 TTTAAGTTTAAATTTATTGTAAA
1 TTTAAGTTTAAAATTATT-TAAA
72233 TTTAAGTTTAAAATTATTTAAA
1 TTTAAGTTTAAAATTATTTAAA
72255 TTTA
1 TTTA
72259 CTAATGTCCA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
22 8 0.32
23 17 0.68
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (22 bp):
TTTAAGTTTAAAATTATTTAAA
Found at i:73907 original size:30 final size:30
Alignment explanation
Indices: 73795--74111 Score: 159
Period size: 30 Copynumber: 10.7 Consensus size: 30
73785 CTGAATTGTC
* * * *
73795 CAAAAATCATATTTTGACCCCTAAACTTTTT
1 CAAAAATTACATTTTTACCCTTAAAC-TTTT
*
73826 CCAAAATTGA-ATTTTAATA-CC-TAAACTTTT
1 CAAAAATT-ACATTTT--TACCCTTAAACTTTT
* * * *
73856 TAAAAATCATATTTTAACCCTTAAACTTTT
1 CAAAAATTACATTTTTACCCTTAAACTTTT
* * * *
73886 CCAAAATCACATTTTTACCCTTGAACTTCT
1 CAAAAATTACATTTTTACCCTTAAACTTTT
** *
73916 CAAAAATTACA-TTTTA-CCTCGAACTTCT
1 CAAAAATTACATTTTTACCCTTAAACTTTT
* ** *
73944 CAAAAATTATATTTTTACCCTCGAAC-TTC
1 CAAAAATTACATTTTTACCCTTAAACTTTT
* * **
73973 CAAAAATTATATTTTTGCCCCCCAAACTTTT
1 CAAAAATTACATTTTT-ACCCTTAAACTTTT
* * **
74004 -AAAAATTACATTTTTTCCCTTGAACTCCT
1 CAAAAATTACATTTTTACCCTTAAACTTTT
* * * **
74033 -AAAAATCACGTTTTT-GCCTCGAA-TTTT
1 CAAAAATTACATTTTTACCCTTAAACTTTT
* * *
74060 CCTAAAATGACATTTTTACCCCTTAAAATTTT
1 -CAAAAATTACATTTTTA-CCCTTAAACTTTT
* *
74092 CCAAAATTACATTTTAACCC
1 CAAAAATTACATTTTTACCC
74112 CAAACTCTCC
Statistics
Matches: 226, Mismatches: 45, Indels: 31
0.75 0.15 0.10
Matches are distributed among these distances:
27 2 0.01
28 28 0.12
29 63 0.28
30 88 0.39
31 37 0.16
32 7 0.03
33 1 0.00
ACGTcount: A:0.35, C:0.23, G:0.03, T:0.39
Consensus pattern (30 bp):
CAAAAATTACATTTTTACCCTTAAACTTTT
Found at i:73947 original size:28 final size:30
Alignment explanation
Indices: 73879--74080 Score: 166
Period size: 29 Copynumber: 6.9 Consensus size: 30
73869 TTAACCCTTA
* * * *
73879 AACTTTTCCAAAATCACATTTTTACCCTTG
1 AACTTCTCAAAAATTACATTTTTACCCTCG
73909 AACTTCTCAAAAATTACA-TTTTA-CCTCG
1 AACTTCTCAAAAATTACATTTTTACCCTCG
*
73937 AACTTCTCAAAAATTATATTTTTACCCTCG
1 AACTTCTCAAAAATTACATTTTTACCCTCG
* * * *
73967 AACTTC-CAAAAATTATATTTTTGCCCCCCA
1 AACTTCTCAAAAATTACATTTTT-ACCCTCG
* * *
73997 AACTT-TTAAAAATTACATTTTTTCCCTTG
1 AACTTCTCAAAAATTACATTTTTACCCTCG
* * * *
74026 AACTCCT-AAAAATCACGTTTTT-GCCTCG
1 AACTTCTCAAAAATTACATTTTTACCCTCG
* * *
74054 AA-TTTTCCTAAAATGACATTTTTACCC
1 AACTTCT-CAAAAATTACATTTTTACCC
74081 CTTAAAATTT
Statistics
Matches: 139, Mismatches: 25, Indels: 16
0.77 0.14 0.09
Matches are distributed among these distances:
27 2 0.01
28 27 0.19
29 58 0.42
30 52 0.37
ACGTcount: A:0.32, C:0.25, G:0.04, T:0.39
Consensus pattern (30 bp):
AACTTCTCAAAAATTACATTTTTACCCTCG
Found at i:73971 original size:88 final size:87
Alignment explanation
Indices: 73856--74107 Score: 217
Period size: 88 Copynumber: 2.9 Consensus size: 87
73846 CTAAACTTTT
* ** *
73856 TAAAAATCATATTTTAACCCTTAAACTTTTCC-AAAATCACATTTTTACCCTTGAACTTCTCAAA
1 TAAAAATCATATTTTTACCCTCGAACTTTTCCAAAAATCACATTTTTACCCTTAAACTT-TCAAA
*
73920 AATTACATTTTACCTCGAACTTC
65 AATTACATTTTACCTCGAACTCC
* * * * ** *
73943 TCAAAAATTATATTTTTACCCTCGAAC--TTCCAAAAATTATATTTTTGCCCCCCAAACTTTTAA
1 T-AAAAATCATATTTTTACCCTCGAACTTTTCCAAAAATCACATTTTT-ACCCTTAAACTTTCAA
* *
74006 AAATTACATTTTTTCCCTTGAACTCC
64 AAATTACA--TTTTACCTCGAACTCC
** * * * * *
74032 TAAAAATCACGTTTTT-GCCTCGAA-TTTTCCTAAAATGACATTTTTACCCCTTAAAATTTTCCA
1 TAAAAATCATATTTTTACCCTCGAACTTTTCCAAAAATCACATTTTTA-CCCTT-AAACTTTCAA
74095 AAATTACATTTTA
64 AAATTACATTTTA
74108 ACCCCAAACT
Statistics
Matches: 128, Mismatches: 28, Indels: 18
0.74 0.16 0.10
Matches are distributed among these distances:
86 4 0.03
87 35 0.27
88 60 0.47
89 29 0.23
ACGTcount: A:0.34, C:0.23, G:0.04, T:0.39
Consensus pattern (87 bp):
TAAAAATCATATTTTTACCCTCGAACTTTTCCAAAAATCACATTTTTACCCTTAAACTTTCAAAA
ATTACATTTTACCTCGAACTCC
Found at i:74513 original size:21 final size:21
Alignment explanation
Indices: 74489--74533 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
74479 TCGAATACCC
74489 TTAAGTCGAGGCAATATTCCT
1 TTAAGTCGAGGCAATATTCCT
74510 TTAAGTCGAGGCAATATTCCT
1 TTAAGTCGAGGCAATATTCCT
74531 TTA
1 TTA
74534 TCTCGAGTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.36
Consensus pattern (21 bp):
TTAAGTCGAGGCAATATTCCT
Found at i:74539 original size:21 final size:21
Alignment explanation
Indices: 74489--74540 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
74479 TCGAATACCC
*
74489 TTAAGTCGAGGCAATATTCCT
1 TTAACTCGAGGCAATATTCCT
*
74510 TTAAGTCGAGGCAATATTCCT
1 TTAACTCGAGGCAATATTCCT
*
74531 TTATCTCGAG
1 TTAACTCGAG
74541 TTTCAAAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (21 bp):
TTAACTCGAGGCAATATTCCT
Found at i:77705 original size:74 final size:74
Alignment explanation
Indices: 77569--77715 Score: 231
Period size: 74 Copynumber: 2.0 Consensus size: 74
77559 GATACTCTTT
* *
77569 TTACCAATGTATGAATCCTATGTATAATATAGGATTGCAATAGAAGAGAAAACAAACCTTAGTAA
1 TTACCAATGTATGAATCCTATGTATAATATAGGATTGCAATAGAAAACAAAACAAACCTTAGTAA
77634 CATTTATTC
66 CATTTATTC
* * ** *
77643 TTACCAATGTATGAATCCTATTTATAGTATAGGATTGCAATAGAAAACAAAATTAACTTTAGTAA
1 TTACCAATGTATGAATCCTATGTATAATATAGGATTGCAATAGAAAACAAAACAAACCTTAGTAA
77708 CATTTATT
66 CATTTATT
77716 AGTAGTAATG
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
74 66 1.00
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.34
Consensus pattern (74 bp):
TTACCAATGTATGAATCCTATGTATAATATAGGATTGCAATAGAAAACAAAACAAACCTTAGTAA
CATTTATTC
Found at i:83064 original size:6 final size:6
Alignment explanation
Indices: 83053--83078 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
83043 CAAACAAGAT
83053 TGAGTG TGAGTG TGAGTG TGAGTG TG
1 TGAGTG TGAGTG TGAGTG TGAGTG TG
83079 TGGGAGCCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.50, T:0.35
Consensus pattern (6 bp):
TGAGTG
Done.