Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_229 ID=scaffold_229-JGI_221_v2.0
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: 9169
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Found at i:5981 original size:50 final size:50
Alignment explanation
Indices: 5927--6530 Score: 434
Period size: 50 Copynumber: 12.2 Consensus size: 50
5917 GCAATGGAAC
* * ** *
5927 AGATTGAAGCTACGACAGCGAATCCTGTTTCCCCGACATTGCAGTTAAAT
1 AGATTGAAGCTACAACAGCGAATCTTACTTCCCCGACAGTGCAGTTAAAT
* * * * **
5977 AGATTGAAGCTACAACAGCAAATCTTACTTCCCTGGCGGTGCAGTGGAAT
1 AGATTGAAGCTACAACAGCGAATCTTACTTCCCCGACAGTGCAGTTAAAT
** ** *
6027 AGATTGAAGCTACAATGGCGAATCTTGTTTCCCCGACATTGCAGTTAAAT
1 AGATTGAAGCTACAACAGCGAATCTTACTTCCCCGACAGTGCAGTTAAAT
* * ** *
6077 AGATT---G--ACAACAGCGAATCTTACTTCCCCGGCGGTGCAGTGGAAC
1 AGATTGAAGCTACAACAGCGAATCTTACTTCCCCGACAGTGCAGTTAAAT
* * ** * * *
6122 AGATTGAAGCTACGACGGCGAATCTTGTTTCCTCGACATTGCAATTAAAT
1 AGATTGAAGCTACAACAGCGAATCTTACTTCCCCGACAGTGCAGTTAAAT
* ** * * ** *
6172 AGATTGAAGCTACAACAGCGAATCTTGCTTCCTTGGCGGTGCAGTGGAAC
1 AGATTGAAGCTACAACAGCGAATCTTACTTCCCCGACAGTGCAGTTAAAT
* ** ** * *
6222 AGATTGAAGCTACGACAGTAAATCTTGTTTCCCCAACATTGCAGTTAAAT
1 AGATTGAAGCTACAACAGCGAATCTTACTTCCCCGACAGTGCAGTTAAAT
* * * * * * *
6272 AGATTGAAGCTACAACAGTGAATCTCACTACCCTGGCGGTGCAG-TAGAAC
1 AGATTGAAGCTACAACAGCGAATCTTACTTCCCCGACAGTGCAGTTA-AAT
* * * * *
6322 ATATTGAAGCTACGA-TGTCGAATCTTGA-TTCCCCGACATTGCAGTTAGAT
1 AGATTGAAGCTACAACAG-CGAATCTT-ACTTCCCCGACAGTGCAGTTAAAT
* * * * * * * *
6372 AGATTTAAGCTACAACAGTGAATCTCACTACCCTGGCGGTGCAG-TAGAAC
1 AGATTGAAGCTACAACAGCGAATCTTACTTCCCCGACAGTGCAGTTA-AAT
* * * * * * **
6422 AGATTGAAGCTACAACAACAAATCTTACTTCCCTGGCGGTGTAGTGGAAT
1 AGATTGAAGCTACAACAGCGAATCTTACTTCCCCGACAGTGCAGTTAAAT
* * * *
6472 AGATTGAAGCTACGACAGCGAATTTTACTTCCCCGACATTACAGTTAAAT
1 AGATTGAAGCTACAACAGCGAATCTTACTTCCCCGACAGTGCAGTTAAAT
6522 AGATTGAAG
1 AGATTGAAG
6531 ATGGCGAACC
Statistics
Matches: 414, Mismatches: 127, Indels: 26
0.73 0.22 0.05
Matches are distributed among these distances:
45 34 0.08
47 1 0.00
48 1 0.00
49 6 0.01
50 368 0.89
51 4 0.01
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.26
Consensus pattern (50 bp):
AGATTGAAGCTACAACAGCGAATCTTACTTCCCCGACAGTGCAGTTAAAT
Found at i:6078 original size:100 final size:100
Alignment explanation
Indices: 5905--6504 Score: 742
Period size: 100 Copynumber: 6.0 Consensus size: 100
5895 CAGATCCTAT
** * * *
5905 TTCCCTGGCTTTGCAATGGAACAGATTGAAGCTACGACAGCGAATCCTGTTTCCCCGACATTGCA
1 TTCCCTGGCGGTGCAGTGGAACAGATTGAAGCTACGACGGCGAATCTTGTTTCCCCGACATTGCA
*
5970 GTTAAATAGATTGAAGCTACAACAGCAAATCTTAC
66 GTTAAATAGATTGAAGCTACAACAGCGAATCTTAC
* * *
6005 TTCCCTGGCGGTGCAGTGGAATAGATTGAAGCTACAATGGCGAATCTTGTTTCCCCGACATTGCA
1 TTCCCTGGCGGTGCAGTGGAACAGATTGAAGCTACGACGGCGAATCTTGTTTCCCCGACATTGCA
6070 GTTAAATAGATT---G--ACAACAGCGAATCTTAC
66 GTTAAATAGATTGAAGCTACAACAGCGAATCTTAC
* *
6100 TTCCCCGGCGGTGCAGTGGAACAGATTGAAGCTACGACGGCGAATCTTGTTTCCTCGACATTGCA
1 TTCCCTGGCGGTGCAGTGGAACAGATTGAAGCTACGACGGCGAATCTTGTTTCCCCGACATTGCA
* *
6165 ATTAAATAGATTGAAGCTACAACAGCGAATCTTGC
66 GTTAAATAGATTGAAGCTACAACAGCGAATCTTAC
* * ** *
6200 TTCCTTGGCGGTGCAGTGGAACAGATTGAAGCTACGACAGTAAATCTTGTTTCCCCAACATTGCA
1 TTCCCTGGCGGTGCAGTGGAACAGATTGAAGCTACGACGGCGAATCTTGTTTCCCCGACATTGCA
* *
6265 GTTAAATAGATTGAAGCTACAACAGTGAATCTCAC
66 GTTAAATAGATTGAAGCTACAACAGCGAATCTTAC
* * * * * *
6300 TACCCTGGCGGTGCAGTAGAACATATTGAAGCTACGATGTCGAATCTTGATTCCCCGACATTGCA
1 TTCCCTGGCGGTGCAGTGGAACAGATTGAAGCTACGACGGCGAATCTTGTTTCCCCGACATTGCA
* * * *
6365 GTTAGATAGATTTAAGCTACAACAGTGAATCTCAC
66 GTTAAATAGATTGAAGCTACAACAGCGAATCTTAC
* * * ** * ** * * ** *
6400 TACCCTGGCGGTGCAGTAGAACAGATTGAAGCTACAACAACAAATCTTACTTCCCTGGCGGTGTA
1 TTCCCTGGCGGTGCAGTGGAACAGATTGAAGCTACGACGGCGAATCTTGTTTCCCCGACATTGCA
** * *
6465 GTGGAATAGATTGAAGCTACGACAGCGAATTTTAC
66 GTTAAATAGATTGAAGCTACAACAGCGAATCTTAC
6500 TTCCC
1 TTCCC
6505 CGACATTACA
Statistics
Matches: 433, Mismatches: 62, Indels: 10
0.86 0.12 0.02
Matches are distributed among these distances:
95 87 0.20
97 1 0.00
98 1 0.00
100 344 0.79
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.26
Consensus pattern (100 bp):
TTCCCTGGCGGTGCAGTGGAACAGATTGAAGCTACGACGGCGAATCTTGTTTCCCCGACATTGCA
GTTAAATAGATTGAAGCTACAACAGCGAATCTTAC
Found at i:6253 original size:195 final size:197
Alignment explanation
Indices: 5916--6447 Score: 744
Period size: 195 Copynumber: 2.7 Consensus size: 197
5906 TCCCTGGCTT
* * *
5916 TGCAATGGAACAGATTGAAGCTACGACAGCGAATCCTGTTTCCCCGACATTGCAGTTAAATAGAT
1 TGCAGTGGAACAGATTGAAGCTACGACGGCGAATCTTGTTTCCCCGACATTGCAGTTAAATAGAT
* * **
5981 TGAAGCTACAACAGCAAATCTTACTTCCCTGGCGGTGCAGTGGAATAGATTGAAGCTACAATGGC
66 TGAAGCTACAACAGCGAATCTTACTTCCCTGGCGGTGCAGTGGAACAGATTGAAGCTACAACAGC
* * * *
6046 GAATCTTGTTTCCCCGACATTGCAGTTAAATAGATT-G-ACAACAGCGAATCTTACTTCCCCGGC
131 AAATCTTGTTTCCCCAACATTGCAGTTAAATAGATTAGCACAACAGCGAATCTCACTACCCCGGC
6109 GG
196 GG
* *
6111 TGCAGTGGAACAGATTGAAGCTACGACGGCGAATCTTGTTTCCTCGACATTGCAATTAAATAGAT
1 TGCAGTGGAACAGATTGAAGCTACGACGGCGAATCTTGTTTCCCCGACATTGCAGTTAAATAGAT
* * * *
6176 TGAAGCTACAACAGCGAATCTTGCTTCCTTGGCGGTGCAGTGGAACAGATTGAAGCTACGACAGT
66 TGAAGCTACAACAGCGAATCTTACTTCCCTGGCGGTGCAGTGGAACAGATTGAAGCTACAACAGC
* *
6241 AAATCTTGTTTCCCCAACATTGCAGTTAAATAGATTGAAGCTACAACAGTGAATCTCACTACCCT
131 AAATCTTGTTTCCCCAACATTGCAGTTAAATAGATT--AGC-ACAACAGCGAATCTCACTACCCC
6306 GGCGG
193 GGCGG
* * * * * *
6311 TGCAGTAGAACATATTGAAGCTACGATGTCGAATCTTGATTCCCCGACATTGCAGTTAGATAGAT
1 TGCAGTGGAACAGATTGAAGCTACGACGGCGAATCTTGTTTCCCCGACATTGCAGTTAAATAGAT
* * * * * *
6376 TTAAGCTACAACAGTGAATCTCACTACCCTGGCGGTGCAGTAGAACAGATTGAAGCTACAACAAC
66 TGAAGCTACAACAGCGAATCTTACTTCCCTGGCGGTGCAGTGGAACAGATTGAAGCTACAACAGC
6441 AAATCTT
131 AAATCTT
6448 ACTTCCCTGG
Statistics
Matches: 295, Mismatches: 37, Indels: 5
0.88 0.11 0.01
Matches are distributed among these distances:
195 151 0.51
198 1 0.00
200 143 0.48
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.26
Consensus pattern (197 bp):
TGCAGTGGAACAGATTGAAGCTACGACGGCGAATCTTGTTTCCCCGACATTGCAGTTAAATAGAT
TGAAGCTACAACAGCGAATCTTACTTCCCTGGCGGTGCAGTGGAACAGATTGAAGCTACAACAGC
AAATCTTGTTTCCCCAACATTGCAGTTAAATAGATTAGCACAACAGCGAATCTCACTACCCCGGC
GG
Found at i:6376 original size:150 final size:150
Alignment explanation
Indices: 5927--6530 Score: 544
Period size: 150 Copynumber: 4.1 Consensus size: 150
5917 GCAATGGAAC
* ** * *
5927 AGATTGAAGCTACGACAGCGAATCCTGTTTCCCCGACATTGCAGTTAAATAGATTGAAGCTACAA
1 AGATTGAAGCTACGACAGCGAATCTTACTTCCCCGACAGTGCAGTTAAACAGATTGAAGCTACAA
* ** *
5992 CAGCAAATCTTACTTCCCTGGCGGTGCAGTGGAATAGATTGAAGCTACAATGGCGAATCTTGTTT
66 CAGCAAATCTTACTTCCCTGGCGGTGCAGTAGAATAGATTGAAGCTACAACAGCGAATCTTGATT
6057 CCCCGACATTGCAGTTAAAT
131 CCCCGACATTGCAGTTAAAT
* * ** *
6077 AGATTG-A-C-A--ACAGCGAATCTTACTTCCCCGGCGGTGCAGTGGAACAGATTGAAGCTACGA
1 AGATTGAAGCTACGACAGCGAATCTTACTTCCCCGACAGTGCAGTTAAACAGATTGAAGCTACAA
* * * * * ** * *
6137 CGGCGAATCTT-GTTTCCTCGACATTGCAATTA-AATAGATTGAAGCTACAACAGCGAATCTTGC
66 CAGCAAATCTTACTTCCCT-GGCGGTGC-AGTAGAATAGATTGAAGCTACAACAGCGAATCTTGA
** * ** ** *
6200 TTCCTTGGCGGTGCAGTGGAAC
129 TTCCCCGACATTGCAGTTAAAT
** ** * * *
6222 AGATTGAAGCTACGACAGTAAATCTTGTTTCCCCAACATTGCAGTTAAATAGATTGAAGCTACAA
1 AGATTGAAGCTACGACAGCGAATCTTACTTCCCCGACAGTGCAGTTAAACAGATTGAAGCTACAA
** * * * * * *
6287 CAGTGAATCTCACTACCCTGGCGGTGCAGTAGAACATATTGAAGCTACGA-TGTCGAATCTTGAT
66 CAGCAAATCTTACTTCCCTGGCGGTGCAGTAGAATAGATTGAAGCTACAACAG-CGAATCTTGAT
*
6351 TCCCCGACATTGCAGTTAGAT
130 TCCCCGACATTGCAGTTAAAT
* * * * * * * *
6372 AGATTTAAGCTACAACAGTGAATCTCACTACCCTGGCGGTGCAG-TAGAACAGATTGAAGCTACA
1 AGATTGAAGCTACGACAGCGAATCTTACTTCCCCGACAGTGCAGTTA-AACAGATTGAAGCTACA
* * * * *
6436 ACAACAAATCTTACTTCCCTGGCGGTGTAGTGGAATAGATTGAAGCTACGACAGCGAAT-TTTAC
65 ACAGCAAATCTTACTTCCCTGGCGGTGCAGTAGAATAGATTGAAGCTACAACAGCGAATCTTGA-
*
6500 TTCCCCGACATTACAGTTAAAT
129 TTCCCCGACATTGCAGTTAAAT
6522 AGATTGAAG
1 AGATTGAAG
6531 ATGGCGAACC
Statistics
Matches: 348, Mismatches: 93, Indels: 26
0.75 0.20 0.06
Matches are distributed among these distances:
144 5 0.01
145 103 0.30
146 3 0.01
147 2 0.01
148 2 0.01
149 10 0.03
150 218 0.63
151 5 0.01
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.26
Consensus pattern (150 bp):
AGATTGAAGCTACGACAGCGAATCTTACTTCCCCGACAGTGCAGTTAAACAGATTGAAGCTACAA
CAGCAAATCTTACTTCCCTGGCGGTGCAGTAGAATAGATTGAAGCTACAACAGCGAATCTTGATT
CCCCGACATTGCAGTTAAAT
Found at i:6683 original size:45 final size:45
Alignment explanation
Indices: 6522--6876 Score: 197
Period size: 44 Copynumber: 7.9 Consensus size: 45
6512 ACAGTTAAAT
** * * * * * *
6522 AGATTGAAGATGGCGAACCTTATCTCTCTAAAGATGCAGCGGAGC
1 AGATTGAAGATAACGAATCTTATCTCCCTGAAGTTACAGTGGAGC
* * * *
6567 AGATTGAAGCTAA-TAATCCTATCTCCCTGAAGTTACAGTGGGGC
1 AGATTGAAGATAACGAATCTTATCTCCCTGAAGTTACAGTGGAGC
* * * * *
6611 AGGTTGAA-ATTACGAGTCTTATCTCCCTAAAGTTATAGTGGAGC
1 AGATTGAAGATAACGAATCTTATCTCCCTGAAGTTACAGTGGAGC
* * * * *
6655 AGACTGAAGATAACGAATCTTATTTCCCTGAAGTTGCACTGGAAC
1 AGATTGAAGATAACGAATCTTATCTCCCTGAAGTTACAGTGGAGC
* * *
6700 AGATTGAAGCTATAAATTATCG-ATCTTATCTCTCTGAAGTTATAGTGGAGT
1 AGATTGAAG--AT--A--A-CGAATCTTATCTCCCTGAAGTTACAGTGGAGC
* * * * * * *
6751 AGA-T---CATATCAAACCTTATCTCTCTGAAGTTGCAGTGGGGC
1 AGATTGAAGATAACGAATCTTATCTCCCTGAAGTTACAGTGGAGC
* * * * *
6792 AGGTTGAA-ATTACGAGTCTTATCTCCTTGAAGTTGCAGTGGAGC
1 AGATTGAAGATAACGAATCTTATCTCCCTGAAGTTACAGTGGAGC
* * * * *
6836 AGACTGAAGATAGC-AAGTCTTATTTTCCTGAAGTTGCAGTG
1 AGATTGAAGATAACGAA-TCTTATCTCCCTGAAGTTACAGTG
6877 AGATAGATGG
Statistics
Matches: 230, Mismatches: 64, Indels: 32
0.71 0.20 0.10
Matches are distributed among these distances:
40 1 0.00
41 26 0.11
42 1 0.00
43 3 0.01
44 95 0.41
45 72 0.31
47 2 0.01
49 1 0.00
50 1 0.00
51 26 0.11
52 2 0.01
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.30
Consensus pattern (45 bp):
AGATTGAAGATAACGAATCTTATCTCCCTGAAGTTACAGTGGAGC
Found at i:6747 original size:96 final size:95
Alignment explanation
Indices: 6617--6926 Score: 297
Period size: 96 Copynumber: 3.3 Consensus size: 95
6607 GGGCAGGTTG
* *
6617 AAATTACGAGTCTTATCTCCCTAAAGTTATAGTGGAGCAGACTGAAGATAACGAATCTTATTTCC
1 AAATTACGAGTCTTATCTCTCTGAAGTTATAGTGGAGCAGACTGAAGATAAC-AATCTTATTTCC
*
6682 CTGAAGTTGCACTGGAACAGATTGAAGCTAT
65 CTGAAGTTGCAGTGGAACAGATTGAAGCTAT
* * * * * * *
6713 AAATTATCGA-TCTTATCTCTCTGAAGTTATAGTGGAGTAGA-T-CATATCA-AACCTTATCTCT
1 AAATTA-CGAGTCTTATCTCTCTGAAGTTATAGTGGAGCAGACTGAAGATAACAATCTTATTTCC
** *
6774 CTGAAGTTGCAGTGGGGCAGGTT---G----
65 CTGAAGTTGCAGTGGAACAGATTGAAGCTAT
** * *
6798 AAATTACGAGTCTTATCTC-CTTGAAGTTGCAGTGGAGCAGACTGAAGATAGCAAGTCTTATTTT
1 AAATTACGAGTCTTATCTCTC-TGAAGTTATAGTGGAGCAGACTGAAGATAACAA-TCTTATTTC
* *
6862 CCTGAAGTTGCAGT-GAGATAGATGGAAGCTAT
64 CCTGAAGTTGCAGTGGA-ACAGATTGAAGCTAT
6894 AAATTATCGA-TCTTATCTCTCTGAAGTTATAGT
1 AAATTA-CGAGTCTTATCTCTCTGAAGTTATAGT
6927 AGAGTAGATC
Statistics
Matches: 166, Mismatches: 31, Indels: 34
0.72 0.13 0.15
Matches are distributed among these distances:
84 4 0.02
85 32 0.19
86 1 0.01
87 3 0.02
88 3 0.02
89 23 0.14
92 29 0.17
94 4 0.02
95 1 0.01
96 59 0.36
97 7 0.04
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.32
Consensus pattern (95 bp):
AAATTACGAGTCTTATCTCTCTGAAGTTATAGTGGAGCAGACTGAAGATAACAATCTTATTTCCC
TGAAGTTGCAGTGGAACAGATTGAAGCTAT
Found at i:7008 original size:181 final size:181
Alignment explanation
Indices: 6586--7013 Score: 644
Period size: 181 Copynumber: 2.4 Consensus size: 181
6576 CTAATAATCC
* * **
6586 TATCTCCCTGAAGTTACAGTGGGGCAGGTTGAAATTACGAGTCTTATCTCCCTAAAGTTATAGTG
1 TATCTCTCTGAAGTTGCAGTGGGGCAGGTTGAAATTACGAGTCTTATCTCCCTAAAGTTGCAGTG
*
6651 GAGCAGACTGAAGATAACGAATCTTATTTCCCTGAAGTTGCACTGGAACAGATTGAAGCTATAAA
66 GAGCAGACTGAAGATAACGAATCTTATTTCCCTGAAGTTGCACTGGAACAGATGGAAGCTATAAA
*
6716 TTATCGATCTTATCTCTCTGAAGTTATAGTGGAGTAGATCATATCAAACCT
131 TTATCGATCTTATCTCTCTGAAGTTATAGTAGAGTAGATCATATCAAACCT
* *
6767 TATCTCTCTGAAGTTGCAGTGGGGCAGGTTGAAATTACGAGTCTTATCTCCTTGAAGTTGCAGTG
1 TATCTCTCTGAAGTTGCAGTGGGGCAGGTTGAAATTACGAGTCTTATCTCCCTAAAGTTGCAGTG
* * * *
6832 GAGCAGACTGAAGATAGC-AAGTCTTATTTTCCTGAAGTTGCAGT-GAGATAGATGGAAGCTATA
66 GAGCAGACTGAAGATAACGAA-TCTTATTTCCCTGAAGTTGCACTGGA-ACAGATGGAAGCTATA
6895 AATTATCGATCTTATCTCTCTGAAGTTATAGTAGAGTAGATCATATCAAACCT
129 AATTATCGATCTTATCTCTCTGAAGTTATAGTAGAGTAGATCATATCAAACCT
* * * * ** * *
6948 TATCTCTCTGAAGTTGCAGTAGAGCAGGTTGAAATCACTAACCTTGTCACCCTAAAGTTGCAGTG
1 TATCTCTCTGAAGTTGCAGTGGGGCAGGTTGAAATTACGAGTCTTATCTCCCTAAAGTTGCAGTG
7013 G
66 G
7014 GGTAAGTTGA
Statistics
Matches: 223, Mismatches: 22, Indels: 4
0.90 0.09 0.02
Matches are distributed among these distances:
180 4 0.02
181 219 0.98
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.31
Consensus pattern (181 bp):
TATCTCTCTGAAGTTGCAGTGGGGCAGGTTGAAATTACGAGTCTTATCTCCCTAAAGTTGCAGTG
GAGCAGACTGAAGATAACGAATCTTATTTCCCTGAAGTTGCACTGGAACAGATGGAAGCTATAAA
TTATCGATCTTATCTCTCTGAAGTTATAGTAGAGTAGATCATATCAAACCT
Found at i:7242 original size:44 final size:44
Alignment explanation
Indices: 7152--7285 Score: 133
Period size: 44 Copynumber: 3.0 Consensus size: 44
7142 CTCATTGAGG
* * * * * *
7152 TTGCAGTAGAGCAGACTAAAGATAGCAATCCTTATCTCCCTGAAA
1 TTGCAGTAGAACAGATTAAA-ACAACAAACCTTATCTCCCTAAAA
* * *
7197 TTGCAGTGGAACAGATTAAAACCACAAACCTTATCTCTCTAAAA
1 TTGCAGTAGAACAGATTAAAACAACAAACCTTATCTCCCTAAAA
* * * * *
7241 TTGCAGTAGAGCAGGTTAAAATAACAAACCTTATCCCCCTGAAA
1 TTGCAGTAGAACAGATTAAAACAACAAACCTTATCTCCCTAAAA
7285 T
1 T
7286 AGCAACGGGG
Statistics
Matches: 72, Mismatches: 17, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
44 55 0.76
45 17 0.24
ACGTcount: A:0.38, C:0.22, G:0.15, T:0.25
Consensus pattern (44 bp):
TTGCAGTAGAACAGATTAAAACAACAAACCTTATCTCCCTAAAA
Found at i:7422 original size:44 final size:44
Alignment explanation
Indices: 7322--7406 Score: 118
Period size: 44 Copynumber: 1.9 Consensus size: 44
7312 GTCTTATTTT
* * * *
7322 CCTGAAGTTGCAGTGGAATAGATTGAAGCTACTAATCCTATCTC
1 CCTGAAGTTGCAGTGGAACAGATTAAAACGACTAATCCTATCTC
7366 CCTGAAGTTGCAGTGGAACAGATTAAAACGA-TGAATCCTAT
1 CCTGAAGTTGCAGTGGAACAGATTAAAACGACT-AATCCTAT
7407 ACCTTTGAAG
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
43 1 0.03
44 35 0.97
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (44 bp):
CCTGAAGTTGCAGTGGAACAGATTAAAACGACTAATCCTATCTC
Found at i:7563 original size:44 final size:43
Alignment explanation
Indices: 7451--7608 Score: 167
Period size: 44 Copynumber: 3.6 Consensus size: 43
7441 ATCATATCAG
* * *
7451 ACCTTATCT-CTCTGAAGTTGCAGTAGAGTAGGTTGAAGTAACAA
1 ACCTTATCTCCT-TGAAGTTGCAGTGGGGCAGGTTGAAG-AACAA
* *
7495 ACCTTATCCCCTTAAAGTTGCAGTGGGGCAGGTTGAAGACACAA
1 ACCTTATCTCCTTGAAGTTGCAGTGGGGCAGGTTGAAGA-ACAA
* *
7539 ACCTTATCTCCTTGAAGTTGCAGTGGGGCAGATTGAA-AATATA
1 ACCTTATCTCCTTGAAGTTGCAGTGGGGCAGGTTGAAGAACA-A
* * *
7582 AGTCTTATCTCCCTGAAGTTGTAGTGG
1 A-CCTTATCTCCTTGAAGTTGCAGTGG
7609 AGCGAATTAA
Statistics
Matches: 98, Mismatches: 12, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 90 0.92
45 2 0.02
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.29
Consensus pattern (43 bp):
ACCTTATCTCCTTGAAGTTGCAGTGGGGCAGGTTGAAGAACAA
Done.