Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009739.1 Kokia drynarioides strain JFW-HI SEQ_124458, 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: 4240
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.23
Found at i:395 original size:114 final size:114
Alignment explanation
Indices: 247--461 Score: 324
Period size: 114 Copynumber: 1.9 Consensus size: 114
237 TCAAACCCAC
* *
247 GCTCGATGTGAGCAAATCCTCGAACCCCAACTTCCTGATGATACACTGAAAAGCAGGGCGAAGCA
1 GCTCGATGTGAGCAAATCCTCGAACCCCAACTTCCTAATGAGACACTGAAAAGCAGGGCGAAGCA
*
312 ATAAAAGGTTAGCTTCCTGATGAGATAC-AGAGAAGTATACCAACTCAAT
66 ATAAAAGGTTAACTTCCTGATGAGATACTA-AGAAGTATACCAACTCAAT
* * * * * *
361 GCTCGATGTGAGCAAATCTTCGAATCCCAGCTTCCTAATGAGATACTGAGAAGCAGGGTGAAGCA
1 GCTCGATGTGAGCAAATCCTCGAACCCCAACTTCCTAATGAGACACTGAAAAGCAGGGCGAAGCA
*
426 ATAAAAGGTTAACTTCTTGATGAGATACTAAGAAGT
66 ATAAAAGGTTAACTTCCTGATGAGATACTAAGAAGT
462 GGACCAAATT
Statistics
Matches: 90, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
114 89 0.99
115 1 0.01
ACGTcount: A:0.35, C:0.20, G:0.22, T:0.22
Consensus pattern (114 bp):
GCTCGATGTGAGCAAATCCTCGAACCCCAACTTCCTAATGAGACACTGAAAAGCAGGGCGAAGCA
ATAAAAGGTTAACTTCCTGATGAGATACTAAGAAGTATACCAACTCAAT
Found at i:621 original size:319 final size:322
Alignment explanation
Indices: 1--675 Score: 1095
Period size: 319 Copynumber: 2.1 Consensus size: 322
*
1 TTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACTCACGCTCGATGTGAGCAAATCTTCGAA
1 TTCCTGATGAGATACTGAGAAGTAGACCAAATCAAACT--CGCTCGATGTGAGCAAATCTTCGAA
* *
66 CCCCAGCTTCCTGATGAGACACTGAAAAGCAGGGCGAAGCAATAAAAGGTTAGCTTCTTGATGAG
64 CCCCAGCTTCCTAATGAGACACTGAAAAGCAGGGCGAAGCAATAAAAGGTTAACTTCTTGATGAG
* *
131 ATACTGAGAAGTAGACCAAATTCATCTTCCTGATGAGATACAGAGAAGCGAATTGAAACAAACGA
129 ATACTAAGAAGTAGACCAAATTCATCTTCCTGATGAGATACAGAGAAGCGAATTAAAACAAACGA
*
196 CGCAGTCATCTTCTTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAGCA
194 CGCAGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAGCA
*
261 AATCCTCGAACCCCAACTTCCTGATGATACACTGAAAAGCAGGGCGAAGCAATAAAAGGTTAGC
259 AATCCTCGAACCCCAACTTCCTGATGAGACACTGAAAAGCAGGGCGAAGCAATAAAAGGTTAGC
* * * *
325 TTCCTGATGAGATACAGAGAAGTATACCAACTC-AA-T-GCTCGATGTGAGCAAATCTTCGAATC
1 TTCCTGATGAGATACTGAGAAGTAGACCAAATCAAACTCGCTCGATGTGAGCAAATCTTCGAACC
* * *
387 CCAGCTTCCTAATGAGATACTGAGAAGCAGGGTGAAGCAATAAAAGGTTAACTTCTTGATGAGAT
66 CCAGCTTCCTAATGAGACACTGAAAAGCAGGGCGAAGCAATAAAAGGTTAACTTCTTGATGAGAT
* * **
452 ACTAAGAAGTGGACCAAATTCGTCTTCCTGATGAGATATTGAGAAGCGAATTAAAACAAACGACG
131 ACTAAGAAGTAGACCAAATTCATCTTCCTGATGAGATACAGAGAAGCGAATTAAAACAAACGACG
*
517 CAGTCATCTTCCTGATGAGATACTGAGAAGAAGGCCAAATCAAACCCACGCTCGATGTGAGCAAA
196 CAGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAGCAAA
* * *
582 TCTTCGAACCCCAGCTTCCTGATGAGACACTGAAAAGCAGGGTGAAGCAATAAAAGGTTAGC
261 TCCTCGAACCCCAACTTCCTGATGAGACACTGAAAAGCAGGGCGAAGCAATAAAAGGTTAGC
* *
644 TTACTGATGAGATACTGAGAAGTAGAACAAAT
1 TTCCTGATGAGATACTGAGAAGTAGACCAAAT
676 TCGTCTTCCT
Statistics
Matches: 324, Mismatches: 27, Indels: 5
0.91 0.08 0.01
Matches are distributed among these distances:
319 292 0.90
322 1 0.00
323 2 0.01
324 29 0.09
ACGTcount: A:0.37, C:0.20, G:0.22, T:0.21
Consensus pattern (322 bp):
TTCCTGATGAGATACTGAGAAGTAGACCAAATCAAACTCGCTCGATGTGAGCAAATCTTCGAACC
CCAGCTTCCTAATGAGACACTGAAAAGCAGGGCGAAGCAATAAAAGGTTAACTTCTTGATGAGAT
ACTAAGAAGTAGACCAAATTCATCTTCCTGATGAGATACAGAGAAGCGAATTAAAACAAACGACG
CAGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAGCAAA
TCCTCGAACCCCAACTTCCTGATGAGACACTGAAAAGCAGGGCGAAGCAATAAAAGGTTAGC
Found at i:716 original size:205 final size:205
Alignment explanation
Indices: 361--3149 Score: 4153
Period size: 205 Copynumber: 13.7 Consensus size: 205
351 CCAACTCAAT
* * * *
361 GCTCGATGTGAGCAAATCTTCGAATCCCAGCTTCCTAATGAGATACTGAGAAGCAGGGTGAAGCA
1 GCTCGATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAAAAGCAGGGTGAAGCA
* * * *
426 ATAAAAGGTTAACTTCTTGATGAGATACTAAGAAGTGGACCAAATTCGTCTTCCTGATGAGATAT
66 ATAAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATAC
* * *
491 TGAGAAGCGAATTAAAACAAACGACGCAGTCATCTTCCTGATGAGATACTGAGAAGAAGGCCAAA
131 AGAGAAGCGAATTGAAACAAACGACGCAGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAA
556 TCAAACCCAC
196 TCAAACCCAC
566 GCTCGATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAAAAGCAGGGTGAAGCA
1 GCTCGATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAAAAGCAGGGTGAAGCA
* * *
631 ATAAAAGGTTAGCTTACTGATGAGATACTGAGAAGTAGAACAAATTCGTCTTCCTGATGAGATAC
66 ATAAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATAC
* * * *
696 AGAGAAACAAATTGAAACAAACGACGCAGTTATCTTCCTGATGAGATACTAAGAAGAAGACCAAA
131 AGAGAAGCGAATTGAAACAAACGACGCAGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAA
761 TCAAACCCAC
196 TCAAACCCAC
* * * * * *
771 GCTCGATGTGAGTAAATCTTCGAACCCCAGCTTCCTAATGAGACATTGAAAAGCAAGGCGAAACA
1 GCTCGATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAAAAGCAGGGTGAAGCA
* *
836 ATAAAAGGTTAGCTTCCTGATGAGATATTGAGAAGTTGACCAAATTCGTCTTCCTGATGAGATAC
66 ATAAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATAC
* * *
901 AGAAAAGCGAATTGAAACAAACGACACAGTCATCTTCCTGATGAGATACTAAGAAGAAGACCAAA
131 AGAGAAGCGAATTGAAACAAACGACGCAGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAA
*
966 TCAAACTCAC
196 TCAAACCCAC
* * *
976 GCTCGATGTGAGCAAATCTTCGAACCTCAGCTTCCTGATGAGACACTGAGAAGTA-GGTCGAAGC
1 GCTCGATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAAAAGCAGGGT-GAAGC
* * *
1040 AATAAAAGGTCAGCTTCCTGATAAGATATTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATA
65 AATAAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATA
* *
1105 CAGAGAAGCGAATTGAAACAAATGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAA
130 CAGAGAAGCGAATTGAAACAAACGACGCAGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAA
1170 ATCAAACCCAC
195 ATCAAACCCAC
* * * *
1181 GCTCGATGTGAGTAAATCTTCGAACCCCAGCTTCTTGATGAGACACTGAAAAGCAGGGCGAAACA
1 GCTCGATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAAAAGCAGGGTGAAGCA
* * *
1246 ATAAAATGTTAGCTTCCTGATGAGATACTGAGAAGTTGACCAAATTCGTCTTCCTGATGAGAT-T
66 ATAAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATAC
* * * * *
1310 AGAAAAGCGAATTGAAACAAACAACACAGTCATCTTCCTAATGAGATACT-ACGAAGAAGACTAA
131 AGAGAAGCGAATTGAAACAAACGACGCAGTCATCTTCCTGATGAGATACTGA-GAAGAAGACCAA
1374 ATCAAACCCAC
195 ATCAAACCCAC
* *
1385 GCTCGATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAAAAGTA-GGTCGAAGT
1 GCTCGATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAAAAGCAGGGT-GAAGC
* * *
1449 AATAAAAGGTCAGCTTCCTTATGAGATATTGAGAAGTGGACCAAATTCGTCTTCCT--TGAGATA
65 AATAAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATA
* *
1512 CAGAGAAGCGAATTGAAACAAATGACGCAGTCATCTTCCTAATGAGATACTGAGAAGAAGACCAA
130 CAGAGAAGCGAATTGAAACAAACGACGCAGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAA
*
1577 ATCAAACTCAC
195 ATCAAACCCAC
* * * *
1588 GCTC-----GAGCAAATCTTCGAACCTCAGCTTTCTAATGAGACACTGAAAAGCA-AGTCGAAGC
1 GCTCGATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAAAAGCAGGGT-GAAGC
* * *
1647 AATAAAAGGTCAACTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTAATGAGATA
65 AATAAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATA
*
1712 CAGAGAAGCGAATTGAAACAAACGACGCAGTCATCTTCCTGATGAGATACAGAGAAGAAGACCAA
130 CAGAGAAGCGAATTGAAACAAACGACGCAGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAA
* *
1777 ATCAATCTCAC
195 ATCAAACCCAC
* *
1788 GTTCGATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAAAAGCAGGGCGAAGCA
1 GCTCGATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAAAAGCAGGGTGAAGCA
*
1853 ATAAAAGTTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATAC
66 ATAAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATAC
*
1918 AGAGAAGCGAATTGAAACAAACGACGCAGTCATCTTCTTGATGAGATACTGAGAAGAAGACCAAA
131 AGAGAAGCGAATTGAAACAAACGACGCAGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAA
*
1983 TCAAACTCAC
196 TCAAACCCAC
* * * *
1993 GCTCGATGTGAGCAAATCCTCGAACCCCAGCTTCCTGATGAGACACTAAAAAGCAGGGCGAAGTA
1 GCTCGATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAAAAGCAGGGTGAAGCA
* * *
2058 ATAAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCATCTTCTTGATGAGATAT
66 ATAAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATAC
* *
2123 AGAGAAGCGAATTGAAACAAACGACGCGGTCATCTTCTTGATGAGATACTGAGAAGAAGACCAAA
131 AGAGAAGCGAATTGAAACAAACGACGCAGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAA
2188 TCAAACCCAC
196 TCAAACCCAC
* * *
2198 GCTCGATGTGAGCAAATCTTCGAACCCTAGCTTCCTGATGAGACTCTGAGAAGCA-GGTCGAAGC
1 GCTCGATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAAAAGCAGGGT-GAAGC
* * *
2262 AATAAAAGGTCAGCTTCTTGATGAGATATTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATA
65 AATAAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATA
* * * *
2327 TAGAGAAGCGAATTGAAACAAATGACGC-GATTATCTTCCTGATGAGATACTGAGAAGAAGGCCA
130 CAGAGAAGCGAATTGAAACAAACGACGCAG-TCATCTTCCTGATGAGATACTGAGAAGAAGACCA
2391 AATCAAACCCAC
194 AATCAAACCCAC
* **
2403 GCTC-----GAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACATTGAAAAGCA-AATCGAAGC
1 GCTCGATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAAAAGCAGGGT-GAAGC
* * * *
2462 AATAAAAGGTCAACTTCCTGATGAGATACTAAGAAGTGGACCAAATTCGTCTTACTGATGAGATA
65 AATAAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATA
* * *
2527 CAGAGAAGCGAATTGAAACAAACGACGCAGTCATCTTCTTGATGAGACACTAAGAAGAAGACCAA
130 CAGAGAAGCGAATTGAAACAAACGACGCAGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAA
* *
2592 ATCAAACTCAT
195 ATCAAACCCAC
* * * *
2603 GCTGGATGTGAGCAAATCTTCGAACCCCAGCTTCCTAATGGGACACTGAAAAGCAGGGAGAAGCA
1 GCTCGATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAAAAGCAGGGTGAAGCA
* *
2668 ATAAAAGGTTAGCTTCTTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCTTGATGAGATAC
66 ATAAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATAC
* *
2733 AGAGAAGCGAATTTAAACAAACGACGCAATCATCTTCCTGATGAGATACTGAGAAGAAGACCAAA
131 AGAGAAGCGAATTGAAACAAACGACGCAGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAA
* *
2798 TCAAATCCAT
196 TCAAACCCAC
* * * *
2808 GCTCGATGTGAGCAAATCATCGAACCCCAGCTTCCTAATGAGACACTGAAAAGTAGGGCGAAGCA
1 GCTCGATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAAAAGCAGGGTGAAGCA
*
2873 ATAAAATGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATAC
66 ATAAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATAC
* *
2938 AGAGAAGCGAATTGAAACAAACGACGTAGTCATCTTCCTGATGAGATACTGAGAAAAAGACCAAA
131 AGAGAAGCGAATTGAAACAAACGACGCAGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAA
3003 TCAAACCCAC
196 TCAAACCCAC
* * *
3013 GCTCGATGTGAGCAAATCTTCGAACCCCAGCTTCTTGATGAGACACTGAGAAGTA-GGTCGAAGC
1 GCTCGATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAAAAGCAGGGT-GAAGC
* * * * ** ** *
3077 AATAAAAGGTTAACTTCCTGATGAAATACGGGGAAGTAAACCAAAACCATCTTCCTGATGAGATA
65 AATAAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATA
*
3142 CTGAGAAG
130 CAGAGAAG
3150 AAGGCCAAAT
Statistics
Matches: 2349, Mismatches: 211, Indels: 48
0.90 0.08 0.02
Matches are distributed among these distances:
198 102 0.04
200 259 0.11
201 1 0.00
202 6 0.00
203 74 0.03
204 180 0.08
205 1724 0.73
206 3 0.00
ACGTcount: A:0.37, C:0.20, G:0.21, T:0.22
Consensus pattern (205 bp):
GCTCGATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAAAAGCAGGGTGAAGCA
ATAAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATAC
AGAGAAGCGAATTGAAACAAACGACGCAGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAA
TCAAACCCAC
Found at i:2626 original size:815 final size:816
Alignment explanation
Indices: 324--3149 Score: 4390
Period size: 815 Copynumber: 3.5 Consensus size: 816
314 AAAAGGTTAG
* * * *
324 CTTCCTGATGAGATACAGAGAAGTATACCAACTC-AA-T---GCTCGATGTGAGCAAATCTTCGA
1 CTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACTCACGCTCGATGTGAGCAAATCTTCGA
* * * * * *
384 ATCCCAGCTTCCTAATGAGATACTGAGAAGCAGGGTGAAGCAATAAAAGGTTAACTTCTTGATGA
66 ACCCCAGCTTCCTAATGAGACACTGAAAAGCAGGGCGAAGCAATAAAAGGTTAGCTTCCTGATGA
* * *
449 GATACTAAGAAGTGGACCAAATTCGTCTTCCTGATGAGATATTGAGAAGCGAATTAAAACAAACG
131 GATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATATAGAGAAGCGAATTGAAACAAACG
*
514 ACGCAGTCATCTTCCTGATGAGATACTGAGAAGAAGGCCAAATCAAACCCACGCTCGATGTGAGC
196 ACGCAGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAGC
*
579 AAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAAAAGCAGGGT-GAAGCAATAAAAGGTTAG
261 AAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAAAAGCA-GGTCGAAGCAATAAAAGGTCAG
* * *
643 CTTAC-TGATGAGATACTGAGAAGTAGAACAAATTCGTCTTCCTGATGAGATACAGAGAAACAAA
325 CTTACTTGATGAGATACTGAGAAGTAGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAA
* *
707 TTGAAACAAACGACGCAGTTATCTTCCTGATGAGATACTAAGAAGAAGACCAAATCAAACCCACG
390 TTGAAACAAATGACGCAGTTATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACG
* * *
772 CTCGATGTGAGTAAATCTTCGAACCCCAGCTTCCTAATGAGACATTGAAAAGCAAGGCGAAACAA
455 CTC-----GAGCAAATCTTCGAACCCCAGCTTCCTAATGAGACATTGAAAAGCAAGTCGAAGCAA
* * * *
837 TAAAAGGTTAGCTTCCTGATGAGATATTGAGAAGTTGACCAAATTCGTCTTCCTGATGAGATACA
515 TAAAAGGTCAACTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACA
* *
902 GAAAAGCGAATTGAAACAAACGACACAGTCATCTTCCTGATGAGATACTAAGAAGAAGACCAAAT
580 GAGAAGCGAATTGAAACAAACGACGCAGTCATCTTCCTGATGAGATACTAAGAAGAAGACCAAAT
* * *
967 CAAACTCACGCTCGATGTGAGCAAATCTTCGAACCTCAGCTTCCTGATGAGACACTGAGAAGTAG
645 CAAACTCACGCTCGATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAAAAGCAG
* * * *
1032 GTCGAAGCAATAAAAGGTCAGCTTCCTGATAAGATATTGAGAAGTGGACCAAATTCGTCTTCCTG
710 GGCGAAGCAATAAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTG
* *
1097 ATGAGATACAGAGAAGCGAATTGAAACAAATGACGCGGTCAT
775 ATGAGATACAGAGAAGCGAATTGAAACAAACGACGCAGTCAT
* *
1139 CTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAGTAAATCTTCGA
1 CTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACTCACGCTCGATGTGAGCAAATCTTCGA
* * * *
1204 ACCCCAGCTTCTTGATGAGACACTGAAAAGCAGGGCGAAACAATAAAATGTTAGCTTCCTGATGA
66 ACCCCAGCTTCCTAATGAGACACTGAAAAGCAGGGCGAAGCAATAAAAGGTTAGCTTCCTGATGA
* * *
1269 GATACTGAGAAGTTGACCAAATTCGTCTTCCTGATGAGAT-TAGAAAAGCGAATTGAAACAAACA
131 GATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATATAGAGAAGCGAATTGAAACAAACG
* * *
1333 ACACAGTCATCTTCCTAATGAGATACT-ACGAAGAAGACTAAATCAAACCCACGCTCGATGTGAG
196 ACGCAGTCATCTTCCTGATGAGATACTGA-GAAGAAGACCAAATCAAACCCACGCTCGATGTGAG
* *
1397 CAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAAAAGTAGGTCGAAGTAATAAAAGGTCAG
260 CAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAAAAGCAGGTCGAAGCAATAAAAGGTCAG
* * *
1462 CTTCCTT-ATGAGATATTGAGAAGTGGACCAAATTCGTCTTCCT--TGAGATACAGAGAAGCGAA
325 CTTACTTGATGAGATACTGAGAAGTAGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAA
* * *
1524 TTGAAACAAATGACGCAGTCATCTTCCTAATGAGATACTGAGAAGAAGACCAAATCAAACTCACG
390 TTGAAACAAATGACGCAGTTATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACG
* * *
1589 CTCGAGCAAATCTTCGAACCTCAGCTTTCTAATGAGACACTGAAAAGCAAGTCGAAGCAATAAAA
455 CTCGAGCAAATCTTCGAACCCCAGCTTCCTAATGAGACATTGAAAAGCAAGTCGAAGCAATAAAA
*
1654 GGTCAACTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTAATGAGATACAGAGAA
520 GGTCAACTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAA
*
1719 GCGAATTGAAACAAACGACGCAGTCATCTTCCTGATGAGATAC-AGAGAAGAAGACCAAATCAAT
585 GCGAATTGAAACAAACGACGCAGTCATCTTCCTGATGAGATACTA-AGAAGAAGACCAAATCAAA
*
1783 CTCACGTTCGATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAAAAGCAGGGCG
649 CTCACGCTCGATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAAAAGCAGGGCG
*
1848 AAGCAATAAAAGTTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGA
714 AAGCAATAAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGA
1913 GATACAGAGAAGCGAATTGAAACAAACGACGCAGTCAT
779 GATACAGAGAAGCGAATTGAAACAAACGACGCAGTCAT
* *
1951 CTTCTTGATGAGATACTGAGAAGAAGACCAAATCAAACTCACGCTCGATGTGAGCAAATCCTCGA
1 CTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACTCACGCTCGATGTGAGCAAATCTTCGA
* * *
2016 ACCCCAGCTTCCTGATGAGACACTAAAAAGCAGGGCGAAGTAATAAAAGGTTAGCTTCCTGATGA
66 ACCCCAGCTTCCTAATGAGACACTGAAAAGCAGGGCGAAGCAATAAAAGGTTAGCTTCCTGATGA
* *
2081 GATACTGAGAAGTGGACCAAATTCATCTTCTTGATGAGATATAGAGAAGCGAATTGAAACAAACG
131 GATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATATAGAGAAGCGAATTGAAACAAACG
* *
2146 ACGCGGTCATCTTCTTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAGC
196 ACGCAGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAGC
* * *
2211 AAATCTTCGAACCCTAGCTTCCTGATGAGACTCTGAGAAGCAGGTCGAAGCAATAAAAGGTCAGC
261 AAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAAAAGCAGGTCGAAGCAATAAAAGGTCAGC
* * *
2276 TT-CTTGATGAGATATTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATATAGAGAAGCGAAT
326 TTACTTGATGAGATACTGAGAAGTAGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAAT
*
2340 TGAAACAAATGACGC-GATTATCTTCCTGATGAGATACTGAGAAGAAGGCCAAATCAAACCCACG
391 TGAAACAAATGACGCAG-TTATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACG
* *
2404 CTCGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACATTGAAAAGCAAATCGAAGCAATAAAA
455 CTCGAGCAAATCTTCGAACCCCAGCTTCCTAATGAGACATTGAAAAGCAAGTCGAAGCAATAAAA
* *
2469 GGTCAACTTCCTGATGAGATACTAAGAAGTGGACCAAATTCGTCTTACTGATGAGATACAGAGAA
520 GGTCAACTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAA
* *
2534 GCGAATTGAAACAAACGACGCAGTCATCTTCTTGATGAGACACTAAGAAGAAGACCAAATCAAAC
585 GCGAATTGAAACAAACGACGCAGTCATCTTCCTGATGAGATACTAAGAAGAAGACCAAATCAAAC
* * * * *
2599 TCATGCTGGATGTGAGCAAATCTTCGAACCCCAGCTTCCTAATGGGACACTGAAAAGCAGGGAGA
650 TCACGCTCGATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAAAAGCAGGGCGA
* *
2664 AGCAATAAAAGGTTAGCTTCTTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCTTGATGAG
715 AGCAATAAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAG
* *
2729 ATACAGAGAAGCGAATTTAAACAAACGACGCAATCAT
780 ATACAGAGAAGCGAATTGAAACAAACGACGCAGTCAT
* *
2766 CTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAA-TCCATGCTCGATGTGAGCAAATCATCG
1 CTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACT-CACGCTCGATGTGAGCAAATCTTCG
* *
2830 AACCCCAGCTTCCTAATGAGACACTGAAAAGTAGGGCGAAGCAATAAAATGTTAGCTTCCTGATG
65 AACCCCAGCTTCCTAATGAGACACTGAAAAGCAGGGCGAAGCAATAAAAGGTTAGCTTCCTGATG
*
2895 AGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAATTGAAACAAAC
130 AGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATATAGAGAAGCGAATTGAAACAAAC
* *
2960 GACGTAGTCATCTTCCTGATGAGATACTGAGAAAAAGACCAAATCAAACCCACGCTCGATGTGAG
195 GACGCAGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAG
* * * * *
3025 CAAATCTTCGAACCCCAGCTTCTTGATGAGACACTGAGAAGTAGGTCGAAGCAATAAAAGGTTAA
260 CAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAAAAGCAGGTCGAAGCAATAAAAGGTCAG
* * * * * ** * *
3090 CTT-CCTGATGAAATACGGGGAAGTAAACCAAAACCATCTTCCTGATGAGATACTGAGAAG
325 CTTACTTGATGAGATACTGAGAAGTAGACCAAATTCGTCTTCCTGATGAGATACAGAGAAG
3150 AAGGCCAAAT
Statistics
Matches: 1845, Mismatches: 149, Indels: 34
0.91 0.07 0.02
Matches are distributed among these distances:
811 1 0.00
812 493 0.27
813 178 0.10
814 3 0.00
815 794 0.43
816 3 0.00
817 80 0.04
818 4 0.00
819 173 0.09
820 116 0.06
ACGTcount: A:0.37, C:0.20, G:0.21, T:0.22
Consensus pattern (816 bp):
CTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACTCACGCTCGATGTGAGCAAATCTTCGA
ACCCCAGCTTCCTAATGAGACACTGAAAAGCAGGGCGAAGCAATAAAAGGTTAGCTTCCTGATGA
GATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATATAGAGAAGCGAATTGAAACAAACG
ACGCAGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAGC
AAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAAAAGCAGGTCGAAGCAATAAAAGGTCAGC
TTACTTGATGAGATACTGAGAAGTAGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAAT
TGAAACAAATGACGCAGTTATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGC
TCGAGCAAATCTTCGAACCCCAGCTTCCTAATGAGACATTGAAAAGCAAGTCGAAGCAATAAAAG
GTCAACTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAG
CGAATTGAAACAAACGACGCAGTCATCTTCCTGATGAGATACTAAGAAGAAGACCAAATCAAACT
CACGCTCGATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAAAAGCAGGGCGAA
GCAATAAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGA
TACAGAGAAGCGAATTGAAACAAACGACGCAGTCAT
Found at i:3522 original size:16 final size:18
Alignment explanation
Indices: 3486--3529 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 18
3476 TAAAATCTTT
3486 TTTAAATTTATTATAAGA
1 TTTAAATTTATTATAAGA
*
3504 TTT-AATTTATT-TCAGA
1 TTTAAATTTATTATAAGA
3520 TTTAAATTTA
1 TTTAAATTTA
3530 AATTTACTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 7 0.29
17 14 0.58
18 3 0.12
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.55
Consensus pattern (18 bp):
TTTAAATTTATTATAAGA
Found at i:3564 original size:41 final size:40
Alignment explanation
Indices: 3486--3566 Score: 99
Period size: 41 Copynumber: 2.0 Consensus size: 40
3476 TAAAATCTTT
* * * *
3486 TTTAAATTTATTATAAGATTTAATTTATTTCAGATTTAAA
1 TTTAAATTTATTATAAAATTAAAATTATTTCAAATTTAAA
* *
3526 TTTAAATTTACTTTTAAAATTAAAATTATTTTAAATTTAAA
1 TTTAAATTTA-TTATAAAATTAAAATTATTTCAAATTTAAA
3567 AAGTCTCATT
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
40 10 0.29
41 24 0.71
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (40 bp):
TTTAAATTTATTATAAAATTAAAATTATTTCAAATTTAAA
Found at i:3568 original size:18 final size:18
Alignment explanation
Indices: 3520--3567 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
3510 TTATTTCAGA
*
3520 TTTAAATTTAAATTTACT
1 TTTAAATTTAAAATTACT
*
3538 TTTAAAATTAAAATTA-T
1 TTTAAATTTAAAATTACT
3555 TTTAAATTTAAAA
1 TTTAAATTTAAAA
3568 AGTCTCATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 13 0.48
18 14 0.52
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (18 bp):
TTTAAATTTAAAATTACT
Done.