Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012007.1 Kokia drynarioides strain JFW-HI SEQ_127005, 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: 6690
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Found at i:1017 original size:43 final size:43
Alignment explanation
Indices: 854--1357 Score: 354
Period size: 43 Copynumber: 11.9 Consensus size: 43
844 CGTGACAATA
* * * *
854 GCATCTATACTGGCACAAACAGTGTATCATCGAGTAAACT-AA
1 GCATCTATTCTGGCACACACAGTGCATCATCGAGTAAACTGAG
* * * * *
896 GTATCTATACTAGTACACATAGTGCATCATCGAGTAAACTGAG
1 GCATCTATTCTGGCACACACAGTGCATCATCGAGTAAACTGAG
* **
939 GCATCTATAT-TGG--CACACAGTGCATCATCGGGTAAACCCAG
1 GCATCTAT-TCTGGCACACACAGTGCATCATCGAGTAAACTGAG
* * *
980 GCATCTATTCTGGCACACACAGTTCGTTATCGAGTAAACTGAG
1 GCATCTATTCTGGCACACACAGTGCATCATCGAGTAAACTGAG
* * * *
1023 GCATCTATACTAGCACACATAGTGCATCATCGAATAAACTGAG
1 GCATCTATTCTGGCACACACAGTGCATCATCGAGTAAACTGAG
* * *
1066 GCATCTATTATGG--CACACAGTTCGTCATCGAGTAAACTGAG
1 GCATCTATTCTGGCACACACAGTGCATCATCGAGTAAACTGAG
* * * *
1107 GCATCTATACTAGCACACATAGTGCATCAT-TAGGTAAA-TCGAG
1 GCATCTATTCTGGCACACACAGTGCATCATCGA-GTAAACT-GAG
* ** * *
1150 GCATCTATAT-TGGCACACACATTTTATCATCTAATAAA-TCGAG
1 GCATCTAT-TCTGGCACACACAGTGCATCATCGAGTAAACT-GAG
* * * * * * * * *
1193 ACATCTATACTAGTACACACAGTGCAACGTCAAATAAATTGAG
1 GCATCTATTCTGGCACACACAGTGCATCATCGAGTAAACTGAG
* * * *
1236 GCATCTATAT-TGGCACACATAATGCATAATCGAGTAAATTGAG
1 GCATCTAT-TCTGGCACACACAGTGCATCATCGAGTAAACTGAG
* * * * * *
1279 GCATCTATAT-TAGTATACATAATGCATCATCAAGTAAAC-GAG
1 GCATCTAT-TCTGGCACACACAGTGCATCATCGAGTAAACTGAG
* * * *
1321 GCATCCATACTAGCATACA-A-TGCATCATCGAGTAAAC
1 GCATCTATTCTGGCACACACAGTGCATCATCGAGTAAAC
1358 AGAAGTATCT
Statistics
Matches: 368, Mismatches: 79, Indels: 32
0.77 0.16 0.07
Matches are distributed among these distances:
40 17 0.05
41 70 0.19
42 54 0.15
43 224 0.61
44 3 0.01
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.26
Consensus pattern (43 bp):
GCATCTATTCTGGCACACACAGTGCATCATCGAGTAAACTGAG
Found at i:1073 original size:86 final size:85
Alignment explanation
Indices: 854--1380 Score: 412
Period size: 86 Copynumber: 6.2 Consensus size: 85
844 CGTGACAATA
* * * * * * * * * * *
854 GCATCTATACTGGCACAAACAGTGTATCATCGAGTAAACT-AAGTATCTATACTAGTACACATAG
1 GCATCTATACTAGCACACATAGTGCATCATCGAATAAACTGAGGCATCTAT-TTGGCACACACAG
*
918 TGCATCATCGAGTAAACTGAG
65 TTCATCATCGAGTAAACTGAG
* * ** **
939 GCATCTATATTGGCACAC--AGTGCATCATCGGGTAAACCCAGGCATCTATTCTGGCACACACAG
1 GCATCTATACTAGCACACATAGTGCATCATCGAATAAACTGAGGCATCTATT-TGGCACACACAG
* *
1002 TTCGTTATCGAGTAAACTGAG
65 TTCATCATCGAGTAAACTGAG
1023 GCATCTATACTAGCACACATAGTGCATCATCGAATAAACTGAGGCATCTATTATGG--CACACAG
1 GCATCTATACTAGCACACATAGTGCATCATCGAATAAACTGAGGCATCTATT-TGGCACACACAG
*
1086 TTCGTCATCGAGTAAACTGAG
65 TTCATCATCGAGTAAACTGAG
* *
1107 GCATCTATACTAGCACACATAGTGCATCAT-TAGGTAAA-TCGAGGCATCTATATTGGCACACAC
1 GCATCTATACTAGCACACATAGTGCATCATCGA-ATAAACT-GAGGCATCTAT-TTGGCACACAC
* * * *
1170 ATTTTATCATCTAATAAA-TCGAG
63 AGTTCATCATCGAGTAAACT-GAG
* * * * * * * * *
1193 ACATCTATACTAGTACACACAGTGCAACGTCAAATAAATTGAGGCATCTATATTGGCACACATAA
1 GCATCTATACTAGCACACATAGTGCATCATCGAATAAACTGAGGCATCTAT-TTGGCACACACAG
* * *
1258 TGCATAATCGAGTAAATTGAG
65 TTCATCATCGAGTAAACTGAG
* * * * * * * *
1279 GCATCTATATTAGTATACATAATGCATCATC-AAGTAAAC-GAGGCATCCATACTAGCATACA-A
1 GCATCTATACTAGCACACATAGTGCATCATCGAA-TAAACTGAGGCATCTAT-TTGGCACACACA
* * *
1341 -TGCATCATCGAGTAAACAGAA
64 GTTCATCATCGAGTAAACTGAG
* *
1362 GTATCTATAATAGCACACA
1 GCATCTATACTAGCACACA
1381 CAATGCATTA
Statistics
Matches: 365, Mismatches: 63, Indels: 30
0.80 0.14 0.07
Matches are distributed among these distances:
83 51 0.14
84 127 0.35
85 38 0.10
86 146 0.40
87 3 0.01
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.26
Consensus pattern (85 bp):
GCATCTATACTAGCACACATAGTGCATCATCGAATAAACTGAGGCATCTATTTGGCACACACAGT
TCATCATCGAGTAAACTGAG
Found at i:1080 original size:127 final size:126
Alignment explanation
Indices: 854--3634 Score: 582
Period size: 127 Copynumber: 22.2 Consensus size: 126
844 CGTGACAATA
* * *
854 GCATCTATACTGGCACAAACAGTGTATCATCGAGTAAACTAAGTATCTATACTAGTACACATAGT
1 GCATCTATACTGGCACACACAGTGTATCATCGAGTAAACTAAGCATCTATACTAGCACACATAGT
* *
919 GCATCATCGAGTAAACTGAGGCATCTATATTGGCACACAGTGCATCATCGGGTAAACCCAG
66 GCATCATCGAATAAACTGAGGCATCTATATTGGCACACAGTGCATCATCGAGTAAACCCAG
* *
980 GCATCTATTCTGGCACACACAGTTCGT-T-ATCGAGTAAACTGAGGCATCTATACTAGCACACAT
1 GCATCTATACTGGCACACACAG-T-GTATCATCGAGTAAACT-AAGCATCTATACTAGCACACAT
* * **
1043 AGTGCATCATCGAATAAACTGAGGCATCTAT-TATGGCACACAGTTCGTCATCGAGTAAACTGAG
63 AGTGCATCATCGAATAAACTGAGGCATCTATAT-TGGCACACAGTGCATCATCGAGTAAACCCAG
* * * * * * * * *
1107 GCATCTATACTAGCACACATAGTGCATCAT-TAGGTAAATCGAGGCATCTATATTGGCACACACA
1 GCATCTATACTGGCACACACAGTGTATCATCGA-GTAAA-CTAAGCATCTATACTAGCACACATA
* ** * * * * * * * * ***
1171 TTTTATCATCTAATAAA-TCGAGACATCTATACTAGTACACACAGTGCAACGTCAAATAAATTGA
64 GTGCATCATCGAATAAACT-GAGGCATCTATA-TTG-GCACACAGTGCATCATCGAGTAAACCCA
1235 G
126 G
* * * * * * * * * * *
1236 GCATCTATATTGGCACACATAATGCATAATCGAGTAAATTGAGGCATCTATATTAGTATACATAA
1 GCATCTATACTGGCACACACAGTGTATCATCGAGTAAACT-AAGCATCTATACTAGCACACATAG
* * * * * ** *
1301 TGCATCATC-AAGTAAAC-GAGGCATCCATACTAGCATACAATGCATCATCGAGTAAACAGAA
65 TGCATCATCGAA-TAAACTGAGGCATCTATATTGGCACACAGTGCATCATCGAGTAAACCCAG
* * * * * * * * * *
1362 GTATCTATAATAGCACACACAATGCATTATCTGA-TAAATCGT-GGCATCTATACTGGTACTCAT
1 GCATCTATACTGGCACACACAGTGTATCATC-GAGTAAA-C-TAAGCATCTATACTAGCACACAT
* * * * *
1425 AGTGCAAT-ATC-AAGTAAA-TCAAGGGC-TTTATACTGGCACACA-T-AATCCATCGAGTAAAT
63 AGTGC-ATCATCGAA-TAAACT-GA-GGCATCTATATTGGCACACAGTGCAT-CATCGAGTAAAC
*
1484 CGAG
123 CCAG
** * ** * * * * *
1488 AAATCTATACTGACACACACAGTACATCATC-AGGTAAGCCGAGGCATCTA-AATAAGCACACAG
1 GCATCTATACTGGCACACACAGTGTATCATCGA-GTAA-ACTAAGCATCTATACT-AGCACACAT
* * * * **
1551 AGTGCATCATC-AGGTAAGCCGATGCATCTATATT-------A--G--T-A-C-AGTAAACAGAG
63 AGTGCATCATCGA-ATAAACTGAGGCATCTATATTGGCACACAGTGCATCATCGAGTAAACCCAG
* ** * * * * * * * *
1601 AG-ATCTATGCT-G-ACACAATGTATCATCGAACAAACCG-AGAC--ATC-TGTAT--TGGCGCA
1 -GCATCTATACTGGCACACACAGTGT-ATC-ATC-GA--GTAAACTAAGCATCTATACTAGCACA
* * * * ** * * * * *
1657 TATAATGAATCAACGGGTAAACTGAGGTATCTGTATTGACACACACAATGCATCATCGAGAAAAC
60 CATAGTGCATCATCGAATAAACTGAGGCATCTATATTG--GCACACAGTGCATCATCGAGTAAAC
**
1722 TAAG
123 CCAG
* ** * * ** * * * * * *
1726 GCATCTATACTGACACACACAGTACATCATTGGGTAAACCGAGACATCTTTATTGGAACATACAG
1 GCATCTATACTGGCACACACAGTGTATCATCGAGTAAACTAAG-CATCTATACTAGCACACATAG
* * * * * *
1791 TGCATCATCTG-GTAAA-TCGAGAG-ATCTGTACTGGTACACAAAGTGTATCATCGAGTAAACCG
65 TGCATCATC-GAATAAACT-GAG-GCATCTATATTGG--CACACAGTGCATCATCGAGTAAACCC
1853 AG
125 AG
* * * * * *
1855 ACATCTTTACTGGCACACATGCA-T-TAT--TCG-GTAAACCGAGGCATCTATATTGGCACACAT
1 GCATCTATACTGGCACACA--CAGTGTATCATCGAGTAAA-CTAAGCATCTATACTAGCACACAT
* * ** * * *
1915 AGTGCAT--TAGTAAGTAAATTGAAACATCTATACTGGCACACACAATGCATCAT--A-TATA--
63 AGTGCATCATCG-AA-TAAACTGAGGCATCTATATTGG--CACACAGTGCATCATCGAGTAAACC
**
1973 CTT
124 CAG
* * * * * * * *
1976 GCA-C-ATAAT-GCATCA-TC-GGGTAT-ATC--G---AC---GCATCTATATTGGAACACACAC
1 GCATCTATACTGGCA-CACACAGTGTATCATCGAGTAAACTAAGCATCTATACTAGCACACATAG
* * ** * * * * *
2027 TGCATAATCTG-ATAAA-TCGAGGTATCTATACAAGTACACCCAGTACGAT-AACGAGTAAACCA
65 TGCATCATC-GAATAAACT-GAGGCATCTATA-TTG-GCACACAGTGC-ATCATCGAGTAAACCC
2089 AG
125 AG
* *** * * * * *
2091 GCATCTATACTGACACACACAGCACATCATCGAGTAAATCGAGGTATCTATATTGGCACAC--AG
1 GCATCTATACTGGCACACACAGTGTATCATCGAGTAAA-CTAAGCATCTATACTAGCACACATAG
* * * * * * *
2154 TGCATCATCTAGT-AAGTCGAGGCA---ATATTAGCACACACAGTTCATCATCGAGTAAATCGAG
65 TGCATCATCGAATAAACT-GAGGCATCTATATT-G-GCACACAGTGCATCATCGAGTAAACCCAG
* * * * * * *
2215 GCATCTATACTGG--TACACAGTATATCATCTAATAAATCAAAGCGTCTATACT-GACACACACA
1 GCATCTATACTGGCACACACAGTGTATCATCGAGTAAA-CTAAGCATCTATACTAG-CACACATA
* * * * * *
2277 GTGCAACATC-ATGTAAA-TCGAGGCATCTATATTGGCATACATAGTGCATAATCGAGTAAATCG
64 GTGCATCATCGA-ATAAACT-GAGGCATCTATATTGGC--ACACAGTGCATCATCGAGTAAACCC
*
2340 AC
125 AG
* * * * *
2342 GCATCTATACTAGTACACACAGTGCATCATC-AGGTAAACCAATGCATCTATACTGGCACACA-A
1 GCATCTATACTGGCACACACAGTGTATCATCGA-GTAAACTAA-GCATCTATACTAGCACACATA
* * * * * * ***
2405 -TGCCTCATCGAGTAAACTGAGGCATTTATACTGGCACACAGTGCATTATTTGA-TAAATTGAG
64 GTGCATCATCGAATAAACTGAGGCATCTATATTGGCACACAGTGCATCA-TCGAGTAAACCCAG
* * * * * * * * *
2467 GCATCTATATTGGTACACACAGGGCAAT-ATCAAGAAAATCGAGGCATCTATACTAGCATGCGCA
1 GCATCTATACTGGCACACACAGTG-TATCATCGAGTAAA-CTAAGCATCTATACTAGCA--CACA
* * * * *
2531 -A-TGCATCATTGAGTAAA-TCGAGGCATCTATATTGGCATGCGCAGTGCATCATTGAGTAAATC
62 TAGTGCATCATCGAATAAACT-GAGGCATCTATATTGGCA--CACAGTGCATCATCGAGTAAACC
* *
2593 GAA
124 CAG
* ** * * * * * *
2596 GCGTCTATACTGGCATGCGCAGTGCATCATTGAGTAAATTGAGGCATCTATACTA--ACACACAG
1 GCATCTATACTGGCACACACAGTGTATCATCGAGTAAACT-AAGCATCTATACTAGCACACATAG
* ** * * * * * * * *
2659 TGCATTATCGGGTAAACTGAGGCATCTAGACTGGCGCACAGTGTATTATCGGGTAAGCCGAG
65 TGCATCATCGAATAAACTGAGGCATCTATATTGGCACACAGTGCATCATCGAGTAAACCCAG
* * * *
2721 GCATCTATATTGGCACACACAGT-TCATCATCGAGAAAACCAAGGCATCTATACTAGCACACACA
1 GCATCTATACTGGCACACACAGTGT-ATCATCGAGTAAACTAA-GCATCTATACTAGCACACATA
* ** * * * ** * * ** *
2785 GTACATCATCGGGTAAACCGAGGCATCTATACTGGCACACACAATATATCATCTAATAATTCGAG
64 GTGCATCATCGAATAAACTGAGGCATCTATATTGG--CACACAGTGCATCATCGAGTAAACCCAG
* * * * * * * *
2850 GCATCTATACTGG--TACACAGTGCAACATCAAGTAAACTGAGGCAACTATATTGGCACAC--AG
1 GCATCTATACTGGCACACACAGTGTATCATCGAGTAAACT-AAGCATCTATACTAGCACACATAG
* * * * ** * * *
2911 TGCATAATC-AAGTAAA-TCAAGGCATTTGTATTGGCACACA-TAAATATTATCAAGTAAACCGA
65 TGCATCATCGAA-TAAACT-GAGGCATCTATATTGGCACACAGT--GCATCATCGAGTAAACCCA
2973 G
126 G
* * * * * * * *
2974 GCATCTATACT--AACACACAGTGCATCATCGAGTAAACTGAGACATTTATATTGGCACACACAA
1 GCATCTATACTGGCACACACAGTGTATCATCGAGTAAACTAAG-CATCTATACTAGCACACATAG
** * * * ***
3037 TGCATCATCTCATAAA-TCAAGGCATCTATACTGGTACACACAGTGCAAT-ATCGGGTAAATTGA
65 TGCATCATCGAATAAACT-GAGGCATCTATATTGG--CACACAGTGC-ATCATCGAGTAAACCCA
3100 G
126 G
* * * *** * * * * * * * * * *
3101 ACATTTATATTGGTGTACACAATGCATTATCGGGTAAGTCGAGGCATCTATATTGGCACACACAG
1 GCATCTATACTGGCACACACAGTGTATCATCGAGTAA-ACTAAGCATCTATACTAGCACACATAG
* * * * *
3166 TGCATCAT-AAAGTAAGCCGAAGG-ATCTATATTGGCACACATAATGCATCATCGAGTAAACTGC
65 TGCATCATCGAA-TAAACTG-AGGCATCTATATTGGCACAC--AGTGCATCATCGAGTAAAC-CC
3229 -G
125 AG
* * * * * * *
3230 GCATCTATATTGACACACACAATG---CATCGAGTAAA-TCGAGACATCTATACTGGCGCACACA
1 GCATCTATACTGGCACACACAGTGTATCATCGAGTAAACT-AAG-CATCTATACTAGCACACATA
* ** * * * *
3291 ATGCATCATCGGGTAAA-TCGAGGCATCTATACTTGCACACACAGTGCATCATTGAGTAAATCGA
64 GTGCATCATCGAATAAACT-GAGGCATCTATA-TTG-GCACACAGTGCATCATCGAGTAAACCCA
3355 G
126 G
* * * * * * * * *
3356 GCATTTATACTAGCATATACTGTGCATCATCAAGTAAA-TCAAGGGATCTATACT-G-GCACATA
1 GCATCTATACTGGCACACACAGTGTATCATCGAGTAAACT-AA-GCATCTATACTAGCACACATA
* * * * * *
3418 GTGCATTATCGAGTAAACCGAGGCATCTATACTTGCACACACAGTGCATTATCGAGTAAACCGAG
64 GTGCATCATCGAATAAACTGAGGCATCTATA-TTG-GCACACAGTGCATCATCGAGTAAACCCAG
* * * * * *
3483 GCATCTATACT-GCTACACACTA-TATATCATCGAGTAAATCGAGGCATCTGTACTGGCACACAC
1 GCATCTATACTGGC-ACACAC-AGTGTATCATCGAGTAAA-CTAAGCATCTATACTAGCACACAT
** * * * * *
3546 AGTGCATCATCGTGTAAA-TCGAGGCATCTATATTGGCACACACAATACATCATCAAGTAAATCG
63 AGTGCATCATCGAATAAACT-GAGGCATCTATATTGG--CACACAGTGCATCATCGAGTAAACCC
3610 AG
125 AG
*
3612 GCATCTATACTGACACACACAGT
1 GCATCTATACTGGCACACACAGT
3635 ACATCATCAG
Statistics
Matches: 1979, Mismatches: 472, Indels: 405
0.69 0.17 0.14
Matches are distributed among these distances:
109 30 0.02
110 46 0.02
111 15 0.01
112 6 0.00
113 24 0.01
114 3 0.00
115 6 0.00
116 3 0.00
117 11 0.01
118 9 0.00
119 9 0.00
120 5 0.00
121 3 0.00
122 38 0.02
123 18 0.01
124 126 0.06
125 182 0.09
126 372 0.19
127 524 0.26
128 59 0.03
129 476 0.24
130 12 0.01
131 2 0.00
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.25
Consensus pattern (126 bp):
GCATCTATACTGGCACACACAGTGTATCATCGAGTAAACTAAGCATCTATACTAGCACACATAGT
GCATCATCGAATAAACTGAGGCATCTATATTGGCACACAGTGCATCATCGAGTAAACCCAG
Found at i:1411 original size:43 final size:42
Alignment explanation
Indices: 854--1561 Score: 297
Period size: 43 Copynumber: 16.7 Consensus size: 42
844 CGTGACAATA
* * * * * *
854 GCATCTATACTGGCACAAACAGTGTATCATCGAGTAAA-CTAA
1 GCATCTATACTAGCACACACAATGCATCATCGA-TAAATCGAG
* * * *
896 GTATCTATACTAGTACACATAGTGCATCATCGAGTAAA-CTGAG
1 GCATCTATACTAGCACACACAATGCATCATCGA-TAAATC-GAG
* * * * * *
939 GCATCTATA-TTG-GCACACAGTGCATCATCGGGTAAACCCAG
1 GCATCTATACTAGCACACACAATGCATCATC-GATAAATCGAG
* * * * * *
980 GCATCTATTCTGGCACACACAGTTCGTTATCGAGTAAA-CTGAG
1 GCATCTATACTAGCACACACAATGCATCATCGA-TAAATC-GAG
* *
1023 GCATCTATACTAGCACACATAGTGCATCATCGAATAAA-CTGAG
1 GCATCTATACTAGCACACACAATGCATCATCG-ATAAATC-GAG
* * * *
1066 GCATCTAT--TATG-GCACACAGTTCGTCATCGAGTAAA-CTGAG
1 GCATCTATACTA-GCACACACAATGCATCATCGA-TAAATC-GAG
* * * *
1107 GCATCTATACTAGCACACATAGTGCATCATTAGGTAAATCGAG
1 GCATCTATACTAGCACACACAATGCATCA-TCGATAAATCGAG
* * * ** *
1150 GCATCTATATTGGCACACACATTTTATCATCTAATAAATCGAG
1 GCATCTATACTAGCACACACAATGCATCATC-GATAAATCGAG
* * * * * * *
1193 ACATCTATACTAGTACACACAGTGCAACGTCAAATAAATTGAG
1 GCATCTATACTAGCACACACAATGCATCATC-GATAAATCGAG
* * * * *
1236 GCATCTATATTGGCACACATAATGCATAATCGAGTAAATTGAG
1 GCATCTATACTAGCACACACAATGCATCATCGA-TAAATCGAG
* * * * *
1279 GCATCTATATTAGTATACATAATGCATCATCAAGTAAA-CGAG
1 GCATCTATACTAGCACACACAATGCATCATCGA-TAAATCGAG
* * *
1321 GCATCCATACTAG--CATACAATGCATCATCGAGTAAA-CAGAA
1 GCATCTATACTAGCACACACAATGCATCATCGA-TAAATC-GAG
* * * *
1362 GTATCTATAATAGCACACACAATGCATTATCTGATAAATCGTG
1 GCATCTATACTAGCACACACAATGCATCATC-GATAAATCGAG
* * * * * * *
1405 GCATCTATACTGGTACTCATAGTGCAAT-ATCAAGTAAATCAAGG
1 GCATCTATACTAGCACACACAATGC-ATCATCGA-TAAATCGA-G
* * *
1449 GC-TTTATACTGGCACACATAAT-C--CATCGAGTAAATCGAG
1 GCATCTATACTAGCACACACAATGCATCATCGA-TAAATCGAG
** * * * **
1488 AAATCTATACT-GACACACACAGTACATCATCAGGTAAGCCGAG
1 GCATCTATACTAG-CACACACAATGCATCATC-GATAAATCGAG
* * *
1531 GCATCTA-AATAAGCACACAGAGTGCATCATC
1 GCATCTATACT-AGCACACACAATGCATCATC
1562 AGGTAAGCCG
Statistics
Matches: 515, Mismatches: 117, Indels: 67
0.74 0.17 0.10
Matches are distributed among these distances:
39 2 0.00
40 48 0.09
41 75 0.15
42 63 0.12
43 313 0.61
44 14 0.03
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.25
Consensus pattern (42 bp):
GCATCTATACTAGCACACACAATGCATCATCGATAAATCGAG
Found at i:1722 original size:43 final size:43
Alignment explanation
Indices: 1613--1799 Score: 117
Period size: 43 Copynumber: 4.3 Consensus size: 43
1603 ATCTATGCTG
* * * * *
1613 ACACAATGTATCATCGA-ACAAACCGAGACATCTGTATTGGCGC
1 ACACAATGCATCATCGAGA-AAACTGAGGCATCTGTATTGACAC
* * * * * * *
1656 ATATAATGAATCAACGGGTAAACTGAGGTATCTGTATTGACAC
1 ACACAATGCATCATCGAGAAAACTGAGGCATCTGTATTGACAC
* * *
1699 ACACAATGCATCATCGAGAAAACTAAGGCATCTATACTGACAC
1 ACACAATGCATCATCGAGAAAACTGAGGCATCTGTATTGACAC
* * * * * * * *
1742 ACACAGTACATCATTGGGTAAACCGAGACATCTTTATTGGA-AC
1 ACACAATGCATCATCGAGAAAACTGAGGCATCTGTATT-GACAC
* *
1785 ATACAGTGCATCATC
1 ACACAATGCATCATC
1800 TGGTAAATCG
Statistics
Matches: 108, Mismatches: 34, Indels: 4
0.74 0.23 0.03
Matches are distributed among these distances:
43 106 0.98
44 2 0.02
ACGTcount: A:0.37, C:0.22, G:0.18, T:0.24
Consensus pattern (43 bp):
ACACAATGCATCATCGAGAAAACTGAGGCATCTGTATTGACAC
Found at i:1805 original size:43 final size:42
Alignment explanation
Indices: 1740--1967 Score: 167
Period size: 43 Copynumber: 5.4 Consensus size: 42
1730 CTATACTGAC
* * *
1740 ACACACAGTACATCATTGGGTAAACCGAGACATCTTTATTGG
1 ACACACAGTGCATCATTCGGTAAACCGAGACATCTTTACTGG
* * * *
1782 AACATACAGTGCATCA-TCTGGTAAATCGAGAGATCTGTACTGG
1 -ACACACAGTGCATCATTC-GGTAAACCGAGACATCTTTACTGG
* *
1825 TACACAAAGTGTATCA-TCGAGTAAACCGAGACATCTTTACTGG
1 -ACACACAGTGCATCATTCG-GTAAACCGAGACATCTTTACTGG
* * * *
1868 -CACACA-TGCATTATTCGGTAAACCGAGGCATCTATATTGG
1 ACACACAGTGCATCATTCGGTAAACCGAGACATCTTTACTGG
* * * ** ** * *
1908 CACACATAGTGCATTAGTAAGTAAATTGAAACATCTATACTGG
1 -ACACACAGTGCATCATTCGGTAAACCGAGACATCTTTACTGG
*
1951 CACACACAATGCATCAT
1 -ACACACAGTGCATCAT
1968 ATATACTTGC
Statistics
Matches: 146, Mismatches: 33, Indels: 12
0.76 0.17 0.06
Matches are distributed among these distances:
40 25 0.17
41 8 0.05
42 7 0.05
43 106 0.73
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (42 bp):
ACACACAGTGCATCATTCGGTAAACCGAGACATCTTTACTGG
Found at i:1967 original size:126 final size:128
Alignment explanation
Indices: 1696--1967 Score: 282
Period size: 126 Copynumber: 2.1 Consensus size: 128
1686 TCTGTATTGA
* * *
1696 CACACACAATGCATCATCGAGAAAACTAAGGCATCTATACTGACACACACAGTACATCATTGGGT
1 CACACACAATGCATCATCGAGAAAACCAAGACATCTATACTGA-ACACACAGTACATCATTCGGT
* * ** * * *
1761 AAACCGAGACATCTTTATTGGAACATACAGTGCATCATCTGGTAAATCGAGAGATCTGTACTGG
65 AAACCGAGACATCTATATTGGAACACACAGTGCATCATCAAGTAAATCGAAACATCTATACTGG
* * * * * * * *
1825 TACACA-AAGTGTATCATCGAGTAAACCGAGACATCTTTACTG-GCACACA-TGCATTATTCGGT
1 CACACACAA-TGCATCATCGAGAAAACCAAGACATCTATACTGAACACACAGTACATCATTCGGT
* * * * *
1887 AAACCGAGGCATCTATATTGGCACACATAGTGCATTAGT-AAGTAAATTGAAACATCTATACTGG
65 AAACCGAGACATCTATATTGGAACACACAGTGCATCA-TCAAGTAAATCGAAACATCTATACTGG
1951 CACACACAATGCATCAT
1 CACACACAATGCATCAT
1968 ATATACTTGC
Statistics
Matches: 115, Mismatches: 25, Indels: 9
0.77 0.17 0.06
Matches are distributed among these distances:
126 72 0.63
127 9 0.08
128 2 0.02
129 32 0.28
ACGTcount: A:0.36, C:0.22, G:0.18, T:0.25
Consensus pattern (128 bp):
CACACACAATGCATCATCGAGAAAACCAAGACATCTATACTGAACACACAGTACATCATTCGGTA
AACCGAGACATCTATATTGGAACACACAGTGCATCATCAAGTAAATCGAAACATCTATACTGG
Found at i:2125 original size:43 final size:43
Alignment explanation
Indices: 1984--3690 Score: 1299
Period size: 43 Copynumber: 40.3 Consensus size: 43
1974 TTGCACATAA
* * * * * *
1984 TGCATCATCGGGTATATCGACGCATCTATATTGGAACACACAC
1 TGCATCATCGAGTAAATCGAGGCATCTATACTGGCACACACAG
* * ** * *
2027 TGCATAATCTGA-TAAATCGAGGTATCTATACAAGTACACCCAG
1 TGCATCATC-GAGTAAATCGAGGCATCTATACTGGCACACACAG
* * * * *
2070 TACGAT-AACGAGTAAACCAAGGCATCTATACTGACACACACAG
1 TGC-ATCATCGAGTAAATCGAGGCATCTATACTGGCACACACAG
** * *
2113 CACATCATCGAGTAAATCGAGGTATCTATATTGG--CACACAG
1 TGCATCATCGAGTAAATCGAGGCATCTATACTGGCACACACAG
* * * *
2154 TGCATCATCTAGTAAGTCGAGGCA---ATATTAGCACACACAG
1 TGCATCATCGAGTAAATCGAGGCATCTATACTGGCACACACAG
* *
2194 TTCATCATCGAGTAAATCGAGGCATCTATACTGG--TACACAG
1 TGCATCATCGAGTAAATCGAGGCATCTATACTGGCACACACAG
** * * * * * *
2235 TATATCATCTAATAAATCAAAGCGTCTATACTGACACACACAG
1 TGCATCATCGAGTAAATCGAGGCATCTATACTGGCACACACAG
* * * *
2278 TGCAACATC-ATGTAAATCGAGGCATCTATATTGGCATACATAG
1 TGCATCATCGA-GTAAATCGAGGCATCTATACTGGCACACACAG
* * * *
2321 TGCATAATCGAGTAAATCGACGCATCTATACTAGTACACACAG
1 TGCATCATCGAGTAAATCGAGGCATCTATACTGGCACACACAG
* * *
2364 TGCATCATC-AGGTAAACCAATGCATCTATACTGGCACACA-A-
1 TGCATCATCGA-GTAAATCGAGGCATCTATACTGGCACACACAG
* *
2405 TGCCTCATCGAGTAAA-CTGAGGCATTTATACTGG--CACACAG
1 TGCATCATCGAGTAAATC-GAGGCATCTATACTGGCACACACAG
* * * * *
2446 TGCATTATTTGA-TAAATTGAGGCATCTATATTGGTACACACAG
1 TGCATCA-TCGAGTAAATCGAGGCATCTATACTGGCACACACAG
* * * * ** * *
2489 GGCAAT-ATCAAGAAAATCGAGGCATCTATACTAGCATGCGCAA
1 TGC-ATCATCGAGTAAATCGAGGCATCTATACTGGCACACACAG
* * ** *
2532 TGCATCATTGAGTAAATCGAGGCATCTATATTGGCATGCGCAG
1 TGCATCATCGAGTAAATCGAGGCATCTATACTGGCACACACAG
* * * ** *
2575 TGCATCATTGAGTAAATCGAAGCGTCTATACTGGCATGCGCAG
1 TGCATCATCGAGTAAATCGAGGCATCTATACTGGCACACACAG
* * *
2618 TGCATCATTGAGTAAATTGAGGCATCTATACT--AACACACAG
1 TGCATCATCGAGTAAATCGAGGCATCTATACTGGCACACACAG
* * * *
2659 TGCATTATCGGGTAAA-CTGAGGCATCTAGACTGG--CGCACAG
1 TGCATCATCGAGTAAATC-GAGGCATCTATACTGGCACACACAG
* * * ** *
2700 TGTATTATCGGGTAAGCCGAGGCATCTATATTGGCACACACAG
1 TGCATCATCGAGTAAATCGAGGCATCTATACTGGCACACACAG
* * * * *
2743 TTCATCATCGAGAAAACCAAGGCATCTATACTAGCACACACAG
1 TGCATCATCGAGTAAATCGAGGCATCTATACTGGCACACACAG
* * * *
2786 TACATCATCGGGTAAACCGAGGCATCTATACTGGCACACACAA
1 TGCATCATCGAGTAAATCGAGGCATCTATACTGGCACACACAG
** * * * *
2829 TATATCATCTAATAATTCGAGGCATCTATACTGG--TACACAG
1 TGCATCATCGAGTAAATCGAGGCATCTATACTGGCACACACAG
* * * *
2870 TGCAACATCAAGTAAA-CTGAGGCAACTATATTGG--CACACAG
1 TGCATCATCGAGTAAATC-GAGGCATCTATACTGGCACACACAG
* * * * * * * *
2911 TGCATAATCAAGTAAATCAAGGCATTTGTATTGGCACACATAAA
1 TGCATCATCGAGTAAATCGAGGCATCTATACTGGCACACA-CAG
* * * *
2955 T--ATTATCAAGTAAACCGAGGCATCTATACT--AACACACAG
1 TGCATCATCGAGTAAATCGAGGCATCTATACTGGCACACACAG
* * * *
2994 TGCATCATCGAGTAAA-CTGAGACATTTATATTGGCACACACAA
1 TGCATCATCGAGTAAATC-GAGGCATCTATACTGGCACACACAG
* * *
3037 TGCATCATCTCA-TAAATCAAGGCATCTATACTGGTACACACAG
1 TGCATCATC-GAGTAAATCGAGGCATCTATACTGGCACACACAG
* * * * * *** *
3080 TGCAAT-ATCGGGTAAATTGAGACATTTATATTGGTGTACACAA
1 TGC-ATCATCGAGTAAATCGAGGCATCTATACTGGCACACACAG
* * * *
3123 TGCATTATCGGGTAAGTCGAGGCATCTATATTGGCACACACAG
1 TGCATCATCGAGTAAATCGAGGCATCTATACTGGCACACACAG
** ** * * *
3166 TGCATCATAAAGTAAGCCGAAGG-ATCTATATTGGCACACATAA
1 TGCATCATCGAGTAAATCG-AGGCATCTATACTGGCACACACAG
* * * *
3209 TGCATCATCGAGTAAA-CTGCGGCATCTATATTGACACACACAA
1 TGCATCATCGAGTAAATC-GAGGCATCTATACTGGCACACACAG
* * *
3252 TG---CATCGAGTAAATCGAGACATCTATACTGGCGCACACAA
1 TGCATCATCGAGTAAATCGAGGCATCTATACTGGCACACACAG
* *
3292 TGCATCATCGGGTAAATCGAGGCATCTATACTTGCACACACAG
1 TGCATCATCGAGTAAATCGAGGCATCTATACTGGCACACACAG
* * * * * *
3335 TGCATCATTGAGTAAATCGAGGCATTTATACTAGCATATACTG
1 TGCATCATCGAGTAAATCGAGGCATCTATACTGGCACACACAG
* * * *
3378 TGCATCATCAAGTAAATCAAGGGATCTATACTGG--CACATAG
1 TGCATCATCGAGTAAATCGAGGCATCTATACTGGCACACACAG
* * *
3419 TGCATTATCGAGTAAACCGAGGCATCTATACTTGCACACACAG
1 TGCATCATCGAGTAAATCGAGGCATCTATACTGGCACACACAG
* *
3462 TGCATTATCGAGTAAACCGAGGCATCTATACT-GCTACACACTA-
1 TGCATCATCGAGTAAATCGAGGCATCTATACTGGC-ACACAC-AG
** *
3505 TATATCATCGAGTAAATCGAGGCATCTGTACTGGCACACACAG
1 TGCATCATCGAGTAAATCGAGGCATCTATACTGGCACACACAG
* * *
3548 TGCATCATCGTGTAAATCGAGGCATCTATATTGGCACACACAA
1 TGCATCATCGAGTAAATCGAGGCATCTATACTGGCACACACAG
* * *
3591 TACATCATCAAGTAAATCGAGGCATCTATACTGACACACACAG
1 TGCATCATCGAGTAAATCGAGGCATCTATACTGGCACACACAG
* * * * *
3634 TACATCATC-AGATAAATCGAGACATCTATATTGGCGCACACAA
1 TGCATCATCGAG-TAAATCGAGGCATCTATACTGGCACACACAG
*
3677 TGCATCATTGAGTA
1 TGCATCATCGAGTA
3691 CTAACGCACA
Statistics
Matches: 1327, Mismatches: 276, Indels: 122
0.77 0.16 0.07
Matches are distributed among these distances:
38 6 0.00
39 6 0.00
40 70 0.05
41 287 0.22
42 50 0.04
43 888 0.67
44 20 0.02
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.25
Consensus pattern (43 bp):
TGCATCATCGAGTAAATCGAGGCATCTATACTGGCACACACAG
Found at i:2982 original size:83 final size:83
Alignment explanation
Indices: 2876--3033 Score: 210
Period size: 83 Copynumber: 1.9 Consensus size: 83
2866 ACAGTGCAAC
* * ** * *
2876 ATCAAGTAAACTGAGGCAACTATATTGGCACACAGTGCATAATCAAGTAAA-TCAAGGCATTTGT
1 ATCAAGTAAACCGAGGCAACTATACTAACACACAGTGCATAATCAAGTAAACT-AAGACATTTAT
2940 ATTGGCACACATAAATATT
65 ATTGGCACACATAAATATT
* * * *
2959 ATCAAGTAAACCGAGGCATCTATACTAACACACAGTGCATCATCGAGTAAACTGAGACATTTATA
1 ATCAAGTAAACCGAGGCAACTATACTAACACACAGTGCATAATCAAGTAAACTAAGACATTTATA
3024 TTGGCACACA
66 TTGGCACACA
3034 CAATGCATCA
Statistics
Matches: 64, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
83 63 0.98
84 1 0.02
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.25
Consensus pattern (83 bp):
ATCAAGTAAACCGAGGCAACTATACTAACACACAGTGCATAATCAAGTAAACTAAGACATTTATA
TTGGCACACATAAATATT
Found at i:3782 original size:43 final size:43
Alignment explanation
Indices: 3730--3872 Score: 119
Period size: 43 Copynumber: 3.3 Consensus size: 43
3720 CCGAGACATC
* * * *
3730 TATACTGGCACACAAAGTGAAT-ATTTAAGTAAATCGAAG-TATA
1 TATATTGGCACACACAGTGAATCA-TCAAATAAATCGAAGCT-TA
* * *
3773 TATATTGGCACACACAGTGCATCATCAAATAAATTGAAGCTTC
1 TATATTGGCACACACAGTGAATCATCAAATAAATCGAAGCTTA
* * * * * * *
3816 TATATTGGCACACACAGTGCATTATCGAATAAACCGAATCCTC
1 TATATTGGCACACACAGTGAATCATCAAATAAATCGAAGCTTA
*
3859 TATACTGGCACACA
1 TATATTGGCACACA
3873 TAATGCATTG
Statistics
Matches: 84, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
43 82 0.98
44 2 0.02
ACGTcount: A:0.38, C:0.20, G:0.15, T:0.27
Consensus pattern (43 bp):
TATATTGGCACACACAGTGAATCATCAAATAAATCGAAGCTTA
Found at i:3880 original size:43 final size:43
Alignment explanation
Indices: 3773--3889 Score: 144
Period size: 43 Copynumber: 2.7 Consensus size: 43
3763 TCGAAGTATA
* ** *
3773 TATATTGGCACACACAGTGCATCATCAAATAAATTGAAGCTTC
1 TATATTGGCACACACAGTGCATTATCAAATAAACCGAAGCCTC
* *
3816 TATATTGGCACACACAGTGCATTATCGAATAAACCGAATCCTC
1 TATATTGGCACACACAGTGCATTATCAAATAAACCGAAGCCTC
* * * *
3859 TATACTGGCACACATAATGCATTGTCAAATA
1 TATATTGGCACACACAGTGCATTATCAAATA
3890 TATCGAAATA
Statistics
Matches: 63, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 63 1.00
ACGTcount: A:0.37, C:0.22, G:0.14, T:0.27
Consensus pattern (43 bp):
TATATTGGCACACACAGTGCATTATCAAATAAACCGAAGCCTC
Found at i:3880 original size:199 final size:199
Alignment explanation
Indices: 3516--3880 Score: 450
Period size: 199 Copynumber: 1.8 Consensus size: 199
3506 ATATCATCGA
* * * * * * *
3516 GTAAATCGAGGCATCTGTACTGGCACACACAGTGCATCATCGTGTAAATCGAGGCATCTATATTG
1 GTAAACCGAGACATCTATACTGGCACACAAAGTGAATCATCGTGTAAATCGAAGCATATATATTG
* *
3581 GCACACACAATACATCATCAAGTAAATCGAGGCATCTATACTGACACACACAGTACATCATCAGA
66 GCACACACAATACATCATCAAATAAATCGAAGCATCTATACTGACACACACAGTACATCATCAGA
* * *
3646 TAAATCGAGACATCTATATTGGCGCACACAATGCATCATTGAGTACTAACGCACACAATGAATCA
131 TAAACCGAGACATCTATACTGGCACACACAATGCATCATTGAGTACTAACGCACACAATGAATCA
3711 TTAC
196 TTAC
* *
3715 GTAAACCGAGACATCTATACTGGCACACAAAGTGAAT-AT-TTAAGTAAATCGAAGTATATATAT
1 GTAAACCGAGACATCTATACTGGCACACAAAGTGAATCATCGT--GTAAATCGAAGCATATATAT
* * * * * * * *
3778 TGGCACACACAGTGCATCATCAAATAAATTGAAGCTTCTATATTGGCACACACAGTGCATTATC-
64 TGGCACACACAATACATCATCAAATAAATCGAAGCATCTATACTGACACACACAGTACATCATCA
* *
3842 GAATAAACCGA-ATCCTCTATACTGGCACACATAATGCAT
129 G-ATAAACCGAGA-CATCTATACTGGCACACACAATGCAT
3881 TGTCAAATAT
Statistics
Matches: 138, Mismatches: 24, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
197 1 0.01
198 4 0.03
199 133 0.96
ACGTcount: A:0.37, C:0.22, G:0.16, T:0.24
Consensus pattern (199 bp):
GTAAACCGAGACATCTATACTGGCACACAAAGTGAATCATCGTGTAAATCGAAGCATATATATTG
GCACACACAATACATCATCAAATAAATCGAAGCATCTATACTGACACACACAGTACATCATCAGA
TAAACCGAGACATCTATACTGGCACACACAATGCATCATTGAGTACTAACGCACACAATGAATCA
TTAC
Done.