Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006111.1 Kokia drynarioides strain JFW-HI SEQ_120621, 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: 46617
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:1381 original size:31 final size:30
Alignment explanation
Indices: 1254--1455 Score: 210
Period size: 30 Copynumber: 6.7 Consensus size: 30
1244 CGAAGAATAC
* * **
1254 GAGGTCAAAATGTGATTTTGGGGAAGTTT-
1 GAGGTTAAAATGTAATTTTGGAAAAGTTTA
*
1283 GAAGGTTAAAATGCAATTTTGGAACAA-TTTA
1 G-AGGTTAAAATGTAATTTTGGAA-AAGTTTA
* * * *
1314 GGGGTAAAAATATAATTTTAGAAAAGTTTA
1 GAGGTTAAAATGTAATTTTGGAAAAGTTTA
*
1344 GGGGTTAAAATGTAATTTTGGAAAAGTTTAA
1 GAGGTTAAAATGTAATTTTGGAAAAGTTT-A
*
1375 GAGGTTAAAATGTAGTTTTGGAAAAGTTTGA
1 GAGGTTAAAATGTAATTTTGGAAAAGTTT-A
* * *
1406 GGGGTCAAAATGCAATTTTGGAAAAGTTTA
1 GAGGTTAAAATGTAATTTTGGAAAAGTTTA
* *
1436 AAGGTTAAAATGCAATTTTG
1 GAGGTTAAAATGTAATTTTG
1456 AGAAGCTTAG
Statistics
Matches: 145, Mismatches: 23, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
29 3 0.02
30 85 0.59
31 57 0.39
ACGTcount: A:0.38, C:0.03, G:0.25, T:0.34
Consensus pattern (30 bp):
GAGGTTAAAATGTAATTTTGGAAAAGTTTA
Found at i:1442 original size:61 final size:61
Alignment explanation
Indices: 1255--1478 Score: 231
Period size: 61 Copynumber: 3.7 Consensus size: 61
1245 GAAGAATACG
* * ** * * *
1255 AGGTCAAAATGTGATTTTGGGGAAGTTTGA-AGGTTAAAATGCAATTTTGGAACAA-TTTAG
1 AGGTTAAAATGTAATTTTGGAAAAGTTTGAGGGGTCAAAATGCAATTTTGGAA-AAGTTTAA
* * * * * *
1315 GGGTAAAAATATAATTTTAGAAAAGTTT-AGGGGTTAAAATGTAATTTTGGAAAAGTTTAA
1 AGGTTAAAATGTAATTTTGGAAAAGTTTGAGGGGTCAAAATGCAATTTTGGAAAAGTTTAA
*
1375 GAGGTTAAAATGTAGTTTTGGAAAAGTTTGAGGGGTCAAAATGCAATTTTGGAAAAGTTTAA
1 -AGGTTAAAATGTAATTTTGGAAAAGTTTGAGGGGTCAAAATGCAATTTTGGAAAAGTTTAA
* * * *
1437 AGGTTAAAATGCAATTTT-GAGAAGCTTAGGGGGGTCAAAATG
1 AGGTTAAAATGTAATTTTGGAAAAG-TTTGAGGGGTCAAAATG
1479 TGATTTTAAA
Statistics
Matches: 137, Mismatches: 22, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
59 3 0.02
60 50 0.36
61 54 0.39
62 30 0.22
ACGTcount: A:0.38, C:0.04, G:0.26, T:0.32
Consensus pattern (61 bp):
AGGTTAAAATGTAATTTTGGAAAAGTTTGAGGGGTCAAAATGCAATTTTGGAAAAGTTTAA
Found at i:4021 original size:14 final size:14
Alignment explanation
Indices: 4002--4039 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
3992 CCGGTGTCTT
4002 ATTGTTCATCTATC
1 ATTGTTCATCTATC
* *
4016 ATTGTTCATCTTTT
1 ATTGTTCATCTATC
4030 ATT-TTCATCT
1 ATTGTTCATCT
4040 CATTCAATCA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 7 0.32
14 15 0.68
ACGTcount: A:0.18, C:0.18, G:0.05, T:0.58
Consensus pattern (14 bp):
ATTGTTCATCTATC
Found at i:5226 original size:52 final size:52
Alignment explanation
Indices: 5161--5451 Score: 431
Period size: 52 Copynumber: 5.6 Consensus size: 52
5151 TTCCCATTTA
* * * * *
5161 ATACTCACGATGACACAAAGTCATTGGACCTTA-AATCCATAAAAGGATCCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGT-AAAGGATTCAT
* * * *
5213 ATGCTCACGATGACACATAATCATCAGACCTCATAATCCGTAAATGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* * *
5265 ATACTCATGATGACACATAGTCATCGAACCTCATAATCTGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
*
5317 ATACTCACGATGACACACAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
*
5369 ATACTCACGATGACACATAGTCATCGGACCTCATAATTCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
*
5421 ATACTCACGATGACACATAGTCATTGGACCT
1 ATACTCACGATGACACATAGTCATCGGACCT
5452 TTTTGCATTT
Statistics
Matches: 215, Mismatches: 23, Indels: 2
0.90 0.10 0.01
Matches are distributed among these distances:
52 209 0.97
53 6 0.03
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.26
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
Found at i:7068 original size:15 final size:15
Alignment explanation
Indices: 7050--7078 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
7040 AATCCTCATT
7050 TAATTAGGACTAAAC
1 TAATTAGGACTAAAC
7065 TAATTAGGACTAAA
1 TAATTAGGACTAAA
7079 TGAATAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.10, G:0.14, T:0.28
Consensus pattern (15 bp):
TAATTAGGACTAAAC
Found at i:21188 original size:16 final size:16
Alignment explanation
Indices: 21168--21211 Score: 63
Period size: 16 Copynumber: 2.7 Consensus size: 16
21158 AAAAGAACAT
21168 AAAAAGAGAGAAAA-AAG
1 AAAAAGA-A-AAAAGAAG
21185 AAAAAGAAAAAAGAAG
1 AAAAAGAAAAAAGAAG
21201 AAAAAGAAAAA
1 AAAAAGAAAAA
21212 GGGGCCAAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
15 4 0.15
16 15 0.58
17 7 0.27
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (16 bp):
AAAAAGAAAAAAGAAG
Found at i:21202 original size:23 final size:23
Alignment explanation
Indices: 21168--21212 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
21158 AAAAGAACAT
21168 AAAAAGAGAGAAAAAAGAAAAAGA
1 AAAAAGAGAG-AAAAAGAAAAAGA
21192 AAAAAGA-AGAAAAAGAAAAAG
1 AAAAAGAGAGAAAAAGAAAAAG
21213 GGGCCAAGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 12 0.57
23 2 0.10
24 7 0.33
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (23 bp):
AAAAAGAGAGAAAAAGAAAAAGA
Found at i:22353 original size:49 final size:49
Alignment explanation
Indices: 22277--23290 Score: 428
Period size: 49 Copynumber: 20.7 Consensus size: 49
22267 TTTAATGCCT
* * * * * *
22277 TAAAATCGAAAAGGGATATATTGAAGCCGTAACGGTAGATCTAACACCC
1 TAAAACCGAAGAGGGAAAGATTGAAGCCGCAACGATAGATCTAACACCC
* * * * * * *
22326 TAAAACCAAAGAGAGAAAGATTAAAGCCGCAATGATAGATCTTACAGCT
1 TAAAACCGAAGAGGGAAAGATTGAAGCCGCAACGATAGATCTAACACCC
* ** * * * ** * *
22375 TAAAACTGAAGAGGGATTGGTTGAATCCACAACG-GCGAACCTAGCA-CC
1 TAAAACCGAAGAGGGAAAGATTGAAGCCGCAACGATAG-ATCTAACACCC
* * * *
22423 TAAAAACCGAAGAGGGAAAGATTGAAGTCGTAACGAT-GAATCTTACACCT
1 T-AAAACCGAAGAGGGAAAGATTGAAGCCGCAACGATAG-ATCTAACACCC
* * * * * * * *
22473 TAAAATCGAAGAGGGATAGGTTTAAGTCGTAACGATTGACCTAACACCC
1 TAAAACCGAAGAGGGAAAGATTGAAGCCGCAACGATAGATCTAACACCC
* * * * *
22522 TAAAACTGAAGAGGGATAGATTGAAACCGCAACGACAGATCTAACACCT
1 TAAAACCGAAGAGGGAAAGATTGAAGCCGCAACGATAGATCTAACACCC
* * * * * * *
22571 TAAAACCAAAGAGGGAAAGGTTGAAGCCGCAACGACATACCTTACACCT
1 TAAAACCGAAGAGGGAAAGATTGAAGCCGCAACGATAGATCTAACACCC
** * * * * * * * **
22620 TAAAATTGAAGAGGGATAGGTTGAAGCCGTAATGGTGGACCTAATGCCC
1 TAAAACCGAAGAGGGAAAGATTGAAGCCGCAACGATAGATCTAACACCC
* * * * ** * * * * *
22669 TAAAACCAAATAAGGAAAGGTTGAAGCCATAACGGTGGACCTTACACCT
1 TAAAACCGAAGAGGGAAAGATTGAAGCCGCAACGATAGATCTAACACCC
** * * ** * * * * *
22718 TAAAATTGAAGAGGGATAGGTTGAAGCCATAATGGTGGACCTAACACCT
1 TAAAACCGAAGAGGGAAAGATTGAAGCCGCAACGATAGATCTAACACCC
* * * * *
22767 TAAAATCGAAGAGGGAAAGATTAAAGTCGCAACGAT-GAATCTTACACCT
1 TAAAACCGAAGAGGGAAAGATTGAAGCCGCAACGATAG-ATCTAACACCC
* ** * * * * *
22816 TAAAACTGAAGAGGGTTAGGTTGAAGCTGCAACGGT-GAACCTAACATCC
1 TAAAACCGAAGAGGGAAAGATTGAAGCCGCAACGATAG-ATCTAACACCC
* * * *
22865 AAAAACCGAAGAGGGAAAGATTGAAGTCGCAACGAT-GAATCTTACACCT
1 TAAAACCGAAGAGGGAAAGATTGAAGCCGCAACGATAG-ATCTAACACCC
*** * * * * * * * * *
22914 TAAAATAAAAAATGGATAGGTTGAAGTCGTAATGATGGACCTAACACCC
1 TAAAACCGAAGAGGGAAAGATTGAAGCCGCAACGATAGATCTAACACCC
*** * * * *
22963 TAAAAATAAAGAGGGATAGACTGAAGCCGTAACTATA-AGTCTAACACCC
1 TAAAACCGAAGAGGGAAAGATTGAAGCCGCAACGATAGA-TCTAACACCC
* * * * *** * * * * *
23012 TAAAATCAAAGTGGGAAAGGTTGAAGCTATAACGGTGGACCTTACACCT
1 TAAAACCGAAGAGGGAAAGATTGAAGCCGCAACGATAGATCTAACACCC
* * * * * ** *
23061 TAAAACTGAAGAGGAATAAG-TTGAAGTCGTAATGACGGACCTAACACCC
1 TAAAACCGAAGAGGGA-AAGATTGAAGCCGCAACGATAGATCTAACACCC
* * * * *
23110 TAAAATCGAA-AGGGAAAGATTGAAGTCGCAACGGTAGATCTTACACCT
1 TAAAACCGAAGAGGGAAAGATTGAAGCCGCAACGATAGATCTAACACCC
* * * * * *** *
23158 TAAAATCGAAGAGGGATAGGTTGAAGCTGCGACGGCGGA-CATAATACCC
1 TAAAACCGAAGAGGGAAAGATTGAAGCCGCAACGATAGATC-TAACACCC
* * * * * * *
23207 TAAAACCAAAGAGGGATAGATTGAAGCCACGACGATGGATCTAACAACA
1 TAAAACCGAAGAGGGAAAGATTGAAGCCGCAACGATAGATCTAACACCC
* * *
23256 TAAAACCAAAGAGGGAACATATTGAAGCTGCAACG
1 TAAAACCGAAGAGGGAA-AGATTGAAGCCGCAACG
23291 GTGAACTTAC
Statistics
Matches: 725, Mismatches: 225, Indels: 29
0.74 0.23 0.03
Matches are distributed among these distances:
47 3 0.00
48 41 0.06
49 659 0.91
50 22 0.03
ACGTcount: A:0.40, C:0.18, G:0.23, T:0.19
Consensus pattern (49 bp):
TAAAACCGAAGAGGGAAAGATTGAAGCCGCAACGATAGATCTAACACCC
Found at i:22526 original size:147 final size:147
Alignment explanation
Indices: 22375--23184 Score: 621
Period size: 147 Copynumber: 5.5 Consensus size: 147
22365 TCTTACAGCT
* * *
22375 TAAAACTGAAGAGGGATTGGTTGAATCCACAACGGCGAACCTAGCACCTAAAAACCGAAGAGGGA
1 TAAAACTGAAGAGGGATAGGTTGAAGCCACAACGGCGAACCTAACACCTAAAAACCGAAGAGGGA
* * * *
22440 AAGATTGAAGTCGTAACGATGAATCTTACACCTTAAAATCGAAGAGGGATAGGTTTAAGTCGTAA
66 AAGATTGAAGCCGCAACGATGAACCTTACACCTTAAAATCGAAGAGGGATAGGTTGAAGTCGTAA
*
22505 CGATTGACCTAACACCC
131 CGATGGACCTAACACCC
* * * * * * *
22522 TAAAACTGAAGAGGGATAGATTGAAACCGCAACGAC-AGATCTAACACCTTAAAACCAAAGAGGG
1 TAAAACTGAAGAGGGATAGGTTGAAGCCACAACGGCGA-ACCTAACACCTAAAAACCGAAGAGGG
* * * *
22586 AAAGGTTGAAGCCGCAACGA-CATACCTTACACCTTAAAATTGAAGAGGGATAGGTTGAAGCCGT
65 AAAGATTGAAGCCGCAACGATGA-ACCTTACACCTTAAAATCGAAGAGGGATAGGTTGAAGTCGT
* * **
22650 AATGGTGGACCTAATGCCC
129 AACGATGGACCTAACACCC
** * * * * * * * * **
22669 TAAAACCAAATAAGGAAAGGTTGAAGCCATAACGGTGGACCTTACACCTTAAAATTGAAGAGGGA
1 TAAAACTGAAGAGGGATAGGTTGAAGCCACAACGGCGAACCTAACACCTAAAAACCGAAGAGGGA
* * ** * * * * * * * *
22734 TAGGTTGAAGCCATAATGGTGGACCTAACACCTTAAAATCGAAGAGGGAAAGATTAAAGTCGCAA
66 AAGATTGAAGCCGCAACGATGAACCTTACACCTTAAAATCGAAGAGGGATAGGTTGAAGTCGTAA
* * * *
22799 CGATGAATCTTACACCT
131 CGATGGACCTAACACCC
* ** *
22816 TAAAACTGAAGAGGGTTAGGTTGAAGCTGCAACGGTGAACCTAACATCC-AAAAACCGAAGAGGG
1 TAAAACTGAAGAGGGATAGGTTGAAGCCACAACGGCGAACCTAACA-CCTAAAAACCGAAGAGGG
* * ** * *
22880 AAAGATTGAAGTCGCAACGATGAATCTTACACCTTAAAATAAAAAATGGATAGGTTGAAGTCGTA
65 AAAGATTGAAGCCGCAACGATGAACCTTACACCTTAAAATCGAAGAGGGATAGGTTGAAGTCGTA
*
22945 ATGATGGACCTAACACCC
130 ACGATGGACCTAACACCC
* * ** ** *** * * * *
22963 TAAAAATAAAGAGGGATAGACTGAAGCCGTAAC-TATAAGTCTAACACCCT-AAAATCAAAGTGG
1 TAAAACTGAAGAGGGATAGGTTGAAGCCACAACGGCGAA-CCTAACA-CCTAAAAACCGAAGAGG
* *** * * * *
23026 GAAAGGTTGAAGCTATAACGGTGGACCTTACACCTTAAAA-CTGAAGAGGAATAAGTTGAAGTCG
64 GAAAGATTGAAGCCGCAACGATGAACCTTACACCTTAAAATC-GAAGAGGGATAGGTTGAAGTCG
* *
23090 TAATGACGGACCTAACACCC
128 TAACGATGGACCTAACACCC
* * * * * * * * *
23110 TAAAA-TCGAA-AGGGAAAGATTGAAGTCGCAACGG-TAGATCTTACACCTTAAAATCGAAGAGG
1 TAAAACT-GAAGAGGGATAGGTTGAAGCCACAACGGCGA-ACCTAACACCTAAAAACCGAAGAGG
* *
23172 GATAGGTTGAAGC
64 GAAAGATTGAAGC
23185 TGCGACGGCG
Statistics
Matches: 513, Mismatches: 138, Indels: 25
0.76 0.20 0.04
Matches are distributed among these distances:
145 3 0.01
146 54 0.11
147 454 0.88
148 2 0.00
ACGTcount: A:0.40, C:0.18, G:0.23, T:0.20
Consensus pattern (147 bp):
TAAAACTGAAGAGGGATAGGTTGAAGCCACAACGGCGAACCTAACACCTAAAAACCGAAGAGGGA
AAGATTGAAGCCGCAACGATGAACCTTACACCTTAAAATCGAAGAGGGATAGGTTGAAGTCGTAA
CGATGGACCTAACACCC
Found at i:22605 original size:98 final size:97
Alignment explanation
Indices: 22187--23290 Score: 547
Period size: 98 Copynumber: 11.3 Consensus size: 97
22177 CATAGAGTTT
* * * * * *
22187 GAAGA-GGAATAGGTTGAAGCCGCAACAACGGACCTAACATCTTAAAACTAAAGAGGGACA-AGT
1 GAAGAGGGAA-AGGTTGAAGCCGCAACGA-TGACCTAACACCCTAAAACTGAAGAGGGATAGA-T
* ** * ** *
22250 TGAAGTCGTAAC-ACAGATTTAATGCCTTAAAATC
63 TGAAGCCGTAACGATGGATCTAACACCTTAAAACC
* * ** * * * ** * * *
22284 GAAAAGGGATATATTGAAGCCGTAACGGTAGATCTAACACCCTAAAACCAAAGAGAGAAAGATTA
1 GAAGAGGGAAAGGTTGAAGCCGCAACGAT-GACCTAACACCCTAAAACTGAAGAGGGATAGATTG
* * * * * *
22349 AAGCCGCAATGATAGATCTTACAGCTTAAAACT
65 AAGCCGTAACGATGGATCTAACACCTTAAAACC
** * * ** * * *
22382 GAAGAGGGATTGGTTGAATCCACAACGGCGAACCTAGCA-CCTAAAAACCGAAGAGGGAAAGATT
1 GAAGAGGGAAAGGTTGAAGCCGCAACGATG-ACCTAACACCCT-AAAACTGAAGAGGGATAGATT
* * * *
22446 GAAGTCGTAACGATGAATCTTACACCTTAAAATC
64 GAAGCCGTAACGATGGATCTAACACCTTAAAACC
* * * *
22480 GAAGAGGGATAGGTTTAAGTCGTAACGATTGACCTAACACCCTAAAACTGAAGAGGGATAGATTG
1 GAAGAGGGAAAGGTTGAAGCCGCAACGA-TGACCTAACACCCTAAAACTGAAGAGGGATAGATTG
* * **
22545 AAACCGCAACGACAGATCTAACACCTTAAAACC
65 AAGCCGTAACGATGGATCTAACACCTTAAAACC
* * * * *
22578 AAAGAGGGAAAGGTTGAAGCCGCAACGACAT-ACCTTACACCTTAAAATTGAAGAGGGATAGGTT
1 GAAGAGGGAAAGGTTGAAGCCGCAACG--ATGACCTAACACCCTAAAACTGAAGAGGGATAGATT
* * * ** *
22642 GAAGCCGTAATGGTGGACCTAATGCCCTAAAACC
64 GAAGCCGTAACGATGGATCTAACACCTTAAAACC
* * * ** * * * * *
22676 AAATAAGGAAAGGTTGAAGCCATAACGGTGGACCTTACACCTTAAAATTGAAGAGGGATAGGTTG
1 GAAGAGGGAAAGGTTGAAGCCGCAACGAT-GACCTAACACCCTAAAACTGAAGAGGGATAGATTG
* * * * *
22741 AAGCCATAATGGTGGACCTAACACCTTAAAATC
65 AAGCCGTAACGATGGATCTAACACCTTAAAACC
* * * * * * * *
22774 GAAGAGGGAAAGATTAAAGTCGCAACGATGAATCTTACACCTTAAAACTGAAGAGGGTTAGGTTG
1 GAAGAGGGAAAGGTTGAAGCCGCAACGATG-ACCTAACACCCTAAAACTGAAGAGGGATAGATTG
* * * * * *
22839 AAGCTGCAACGGTGAACCTAACATCC-AAAAACC
65 AAGCCGTAACGATGGATCTAACA-CCTTAAAACC
* * * * * * * * *
22872 GAAGAGGGAAAGATTGAAGTCGCAACGATGAATCTTACACCTTAAAA-TAAAAAATGGATAGGTT
1 GAAGAGGGAAAGGTTGAAGCCGCAACGATG-ACCTAACACCCTAAAACT-GAAGAGGGATAGATT
* * * * **
22936 GAAGTCGTAATGATGGACCTAACACCCTAAAAAT
64 GAAGCCGTAACGATGGATCTAACACCTTAAAACC
* * ** * * * * * * * *
22970 AAAGAGGGATAGACTGAAGCCGTAACTATAAGTCTAACACCCTAAAA-TCAAAGTGGGAAAGGTT
1 GAAGAGGGAAAGGTTGAAGCCGCAACGATGA-CCTAACACCCTAAAACT-GAAGAGGGATAGATT
** * * * *
23034 GAAGCTATAACGGTGGACCTTACACCTTAAAACT
64 GAAGCCGTAACGATGGATCTAACACCTTAAAACC
* * * * * *
23068 GAAGA-GGAATAAGTTGAAGTCGTAATGACGGACCTAACACCCTAAAA-TCGAA-AGGGAAAGAT
1 GAAGAGGGAA-AGGTTGAAGCCGCAACGA-TGACCTAACACCCTAAAACT-GAAGAGGGATAGAT
* * * * * *
23130 TGAAGTCGCAACGGTAGATCTTACACCTTAAAATC
63 TGAAGCCGTAACGATGGATCTAACACCTTAAAACC
* * * ** * * **
23165 GAAGAGGGATAGGTTGAAGCTGCGACGGCGGACATAATACCCTAAAACCAAAGAGGGATAGATTG
1 GAAGAGGGAAAGGTTGAAGCCGCAAC-GATGACCTAACACCCTAAAACTGAAGAGGGATAGATTG
*** * *
23230 AAGCCACGACGATGGATCTAACAACATAAAACC
65 AAGCCGTAACGATGGATCTAACACCTTAAAACC
* ** *
23263 AAAGAGGGAACATATTGAAGCTGCAACG
1 GAAGAGGGAA-AGGTTGAAGCCGCAACG
23291 GTGAACTTAC
Statistics
Matches: 784, Mismatches: 199, Indels: 47
0.76 0.19 0.05
Matches are distributed among these distances:
96 1 0.00
97 130 0.17
98 631 0.80
99 21 0.03
100 1 0.00
ACGTcount: A:0.40, C:0.18, G:0.23, T:0.19
Consensus pattern (97 bp):
GAAGAGGGAAAGGTTGAAGCCGCAACGATGACCTAACACCCTAAAACTGAAGAGGGATAGATTGA
AGCCGTAACGATGGATCTAACACCTTAAAACC
Found at i:23169 original size:97 final size:97
Alignment explanation
Indices: 23003--23233 Score: 247
Period size: 97 Copynumber: 2.4 Consensus size: 97
22993 AACTATAAGT
* * *
23003 CTAACACCCTAAAATCAAAGTGGGAAAGGTTGAAGCTATAACGGTGGACCTTACACCTTAAAACT
1 CTAACACCCTAAAATCAAAG-GGGAAAGATTGAAGCTACAACGGTAGACCTTACACCTTAAAACT
23068 GAAGAGGAATAAGTTGAAGTCGTAATGACGGAC
65 GAAGAGGAATAAGTTGAAGTCGTAATGACGGAC
* *
23101 CTAACACCCTAAAATCGAAA-GGGAAAGATTGAAG-TCGCAACGGTAGATCTTACACCTTAAAA-
1 CTAACACCCTAAAATC-AAAGGGGAAAGATTGAAGCT-ACAACGGTAGACCTTACACCTTAAAAC
* * * *
23163 TCGAAGAGGGATAGGTTGAAGCTGCG--ACGGCGGAC
64 T-GAAGAGGAATAAGTTGAAG-T-CGTAATGACGGAC
* * * *
23198 ATAATACCCTAAAACCAAAGAGGGATAGATTGAAGC
1 CTAACACCCTAAAATCAAAG-GGGAAAGATTGAAGC
23234 CACGACGATG
Statistics
Matches: 112, Mismatches: 13, Indels: 15
0.80 0.09 0.11
Matches are distributed among these distances:
96 5 0.04
97 72 0.64
98 30 0.27
99 5 0.04
ACGTcount: A:0.39, C:0.18, G:0.24, T:0.19
Consensus pattern (97 bp):
CTAACACCCTAAAATCAAAGGGGAAAGATTGAAGCTACAACGGTAGACCTTACACCTTAAAACTG
AAGAGGAATAAGTTGAAGTCGTAATGACGGAC
Found at i:23219 original size:146 final size:147
Alignment explanation
Indices: 22933--23220 Score: 330
Period size: 146 Copynumber: 2.0 Consensus size: 147
22923 AAATGGATAG
* * * *
22933 GTTGAAGTCGTAATGATGGACCTAACACCCTAAAAATAAAGAGGGATAGACTGAAGCCGTAACTA
1 GTTGAAGTCGTAATGACGGACCTAACACCCTAAAAATAAAGAGGGAAAGACTGAAGCCGCAACGA
* * * * * *
22998 TAAGTCTAACACCCTAAAATCAAAGTGGGAAAGGTTGAAGCTATAACGGTGGACCTTACACCTTA
66 TAAGTCTAACACCCTAAAATCAAAGAGGGAAAGGTTGAAGCTACAACGGCGGACATAACACCCTA
**
23063 AAACTGAAGAGGAATAA
131 AAACCAAAGAGGAATAA
* * *
23080 GTTGAAGTCGTAATGACGGACCTAACACCCT-AAAATCGAA-AGGGAAAGATTGAAGTCGCAACG
1 GTTGAAGTCGTAATGACGGACCTAACACCCTAAAAAT-AAAGAGGGAAAGACTGAAGCCGCAACG
* * * * * * * *
23143 GT-AGATCTTACACCTTAAAATCGAAGAGGGATAGGTTGAAGCTGCGACGGCGGACATAATACCC
65 ATAAG-TCTAACACCCTAAAATCAAAGAGGGAAAGGTTGAAGCTACAACGGCGGACATAACACCC
23207 TAAAACCAAAGAGG
129 TAAAACCAAAGAGG
23221 GATAGATTGA
Statistics
Matches: 116, Mismatches: 23, Indels: 5
0.81 0.16 0.03
Matches are distributed among these distances:
145 2 0.02
146 82 0.71
147 32 0.28
ACGTcount: A:0.39, C:0.18, G:0.24, T:0.19
Consensus pattern (147 bp):
GTTGAAGTCGTAATGACGGACCTAACACCCTAAAAATAAAGAGGGAAAGACTGAAGCCGCAACGA
TAAGTCTAACACCCTAAAATCAAAGAGGGAAAGGTTGAAGCTACAACGGCGGACATAACACCCTA
AAACCAAAGAGGAATAA
Found at i:24639 original size:22 final size:25
Alignment explanation
Indices: 24595--24640 Score: 62
Period size: 22 Copynumber: 2.0 Consensus size: 25
24585 TTTCCCATAT
*
24595 TTGTGTTATATATATATATTTATTG
1 TTGTGTTATATATATATAATTATTG
24620 TTGT-TTATAT-TAT-TAATTATT
1 TTGTGTTATATATATATAATTATT
24641 TAATATTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 7 0.35
23 3 0.15
24 6 0.30
25 4 0.20
ACGTcount: A:0.28, C:0.00, G:0.09, T:0.63
Consensus pattern (25 bp):
TTGTGTTATATATATATAATTATTG
Found at i:29208 original size:22 final size:22
Alignment explanation
Indices: 29181--29246 Score: 64
Period size: 22 Copynumber: 3.0 Consensus size: 22
29171 TCTCTGATTT
29181 ATTAGCACTTTAGTGCTCTCT-
1 ATTAGCACTTTAGTGCTCTCTG
*
29202 ATTTAGCA-TATTAGTGTTCTCTG
1 A-TTAGCACT-TTAGTGCTCTCTG
* * *
29225 ATCACCTCTTTAGTGCTCTCTG
1 ATTAGCACTTTAGTGCTCTCTG
29247 TTCTGTTAGT
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
21 2 0.06
22 32 0.89
23 2 0.06
ACGTcount: A:0.18, C:0.23, G:0.15, T:0.44
Consensus pattern (22 bp):
ATTAGCACTTTAGTGCTCTCTG
Found at i:37551 original size:21 final size:20
Alignment explanation
Indices: 37526--37565 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
37516 AAATTAAAAC
*
37526 AAAACAAGTAAAAGTAAAAGT
1 AAAACAAATAAAAG-AAAAGT
37547 AAAACAAATAAAAGAAAAG
1 AAAACAAATAAAAGAAAAG
37566 GTGAAAATGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.72, C:0.05, G:0.12, T:0.10
Consensus pattern (20 bp):
AAAACAAATAAAAGAAAAGT
Found at i:43041 original size:3 final size:3
Alignment explanation
Indices: 43035--43061 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
43025 ATGGTGGTAA
43035 GTT GTT GTT GTT GTT GTT GTT GTT GTT
1 GTT GTT GTT GTT GTT GTT GTT GTT GTT
43062 ACCAGCTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.33, T:0.67
Consensus pattern (3 bp):
GTT
Done.