Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012614.1 Kokia drynarioides strain JFW-HI SEQ_127623, 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: 6129
ACGTcount: A:0.27, C:0.18, G:0.13, T:0.39
Warning! 150 characters in sequence are not A, C, G, or T
Found at i:659 original size:216 final size:215
Alignment explanation
Indices: 2--870 Score: 930
Period size: 216 Copynumber: 4.0 Consensus size: 215
1 G
* * * *
2 TTCCTTAAAGTATTCAAGAGGATCGATTCCTTCGAGCAATTTTCTGAACATTCCA-TGCTCGGGA
1 TTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTCTAAACATTCCAGT-CTCGAGA
* * * * *
66 AATTC-CATCATTTGGACCAAATAGTTTGTCCTTTTGAAAAAAACTTTCAATCTTTGAATTAAAA
65 AA-TCACATCATTTGGTCCAAATAATTTGTCATTTTGTAAAAAACTTT-GATCTTTGAATTAAAA
* * *** *
130 ACTTATTTACGTGAGAA-TGATTTCTCTCTTGGTTCTTGGCCGAATTTTTTAACTTTTCAAACTT
128 ACTTATTTATGTGAGAATTG-TTTCTCTCTTGGTTCTTGGCCGAACTTCCGAACTTTTCAAAATT
* *
194 TTTCGAGTTCCTTTATAACTTCGA
192 TTTTGAGTTCTTTTATAACTTCGA
* * ** *
218 TTTCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTTTAAACATTCCCTTCTCGGGAA
1 TTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTCTAAACATTCCAGTCTCGAGAA
* * * *
283 ATCACATC-TTATGGTCCAAATAATATGTCATTTTGTAAAGAACTGTTGGTCTTTGGATTAAAAA
66 ATCACATCATT-TGGTCCAAATAATTTGTCATTTTGTAAAAAACT-TTGATCTTTGAATTAAAAA
* * * * *
347 CTTATTTATTTGAGAATT-TTT-TCTCTTCGTTCTTGGCCAAACTTCCGAACTTGTGAAAATTTT
129 CTTATTTATGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTTCCGAACTTTTCAAAATTTT
410 TCT-AGTTCTTTTATAACTTCGA
194 T-TGAGTTCTTTTATAACTTCGA
* * * * * *
432 TTCCTTAAAGTAATCAAGATGATCGATTCCTCCCGA-CAATTTTCCAAACATTCCAGCCTCGAGA
1 TTCCTTAAAGTATTCAAGACGATCCATTCCT-TCGAGCAATTTTCTAAACATTCCAGTCTCGAGA
* * * * * * * *
496 TATGACACCATTTGGTCCAAACAGTTTGTCCTTTTTTAAAAAACATTTGATCTTTGAATTAAAAG
65 AATCACATCATTTGGTCCAAATAATTTGTCATTTTGTAAAAAAC-TTTGATCTTTGAATTAAAAA
* * * * *
561 CTTATTTATGTAAGAATTGTTTCTCTCTTTGTTCTTGGCCGAACTTTCGAACTTTTTAAACTTTT
129 CTTATTTATGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTTCCGAACTTTTCAAAATTTT
626 TTGAGTTCTTTTATAACTTCGA
194 TTGAGTTCTTTTATAACTTCGA
* ** ** * * * *
648 TTCCTTAAAGTATTTAAGACGATCCATTATTTCGAATAATTTTTCGAAA-ATTCCATTATCGAAA
1 TTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAA-TTTTCTAAACATTCCAGTCTCGAGA
* * * * * *
712 AATCACATCATTTGGTCTAAAATAATCTGTCATTTTCTAAACAACTTTTGGTCATT-AGATTAAA
65 AATCACATCATTTGGTC-CAAATAATTTGTCATTTTGTAAAAAAC-TTTGATCTTTGA-ATTAAA
*
776 AACTTATTTATGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTTCCGAAATTTTCAAAATT
127 AACTTATTTATGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTTCCGAACTTTTCAAAATT
* * *
841 TTTTGAGTTCTTTCACAACTTCGG
192 TTTTGAGTTCTTTTATAACTTCGA
865 TTCCTT
1 TTCCTT
871 TCCTTCAAGC
Statistics
Matches: 542, Mismatches: 95, Indels: 31
0.81 0.14 0.05
Matches are distributed among these distances:
214 165 0.30
215 20 0.04
216 226 0.42
217 131 0.24
ACGTcount: A:0.28, C:0.18, G:0.13, T:0.41
Consensus pattern (215 bp):
TTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTCTAAACATTCCAGTCTCGAGAA
ATCACATCATTTGGTCCAAATAATTTGTCATTTTGTAAAAAACTTTGATCTTTGAATTAAAAACT
TATTTATGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTTCCGAACTTTTCAAAATTTTTT
GAGTTCTTTTATAACTTCGA
Found at i:1018 original size:195 final size:196
Alignment explanation
Indices: 685--1065 Score: 534
Period size: 195 Copynumber: 1.9 Consensus size: 196
675 TATTTCGAAT
*
685 AATTTTTCGAAAATTCCATTATCGAAAAATCACATCATTTGGTCTAAAATAATCTGTCATTTTCT
1 AATTTTTCGAAAATTCCATTATCGAAAAATCACATCATTTGGTCCAAAATAATCTGTCATTTTCT
* * *
750 AAACAACTTTTGGTCATTAGATTAAAAACTTATTTATGTGAGAATTGTTTCTCTCTTGGTTCTTG
66 AAACAACTTTTAGTCATTAGATTAAAAACTAAATTATGTGAGAATTGTTTCTCTCTTGGTTCTTG
* * * * *
815 GCCGAACTTCCGAAATTTTCAAAATTTTTTGAGTTCTTTCACAACTTCGGTTCCTTTCCTTCAAG
131 GACGAACTTCCGAAATTATCAAAATTTTTCGAGTTCTTTCAAAACTTCGATTCCTTTCCTTCAAG
880 C
196 C
* * * * *
881 AATTTTTTGAACATTCCATTATCGAGAAAT-AGCATCATTTGGTCC-AAATAAAT-TTTCCTTTT
1 AATTTTTCGAAAATTCCATTATCGAAAAATCA-CATCATTTGGTCCAAAAT-AATCTGTCATTTT
* * *
943 GTAAACAACTTTTAGTCTTTGGATTAAAAACTAAATTATGTGAGAATTGTTTCTCTCTTGGTTCT
64 CTAAACAACTTTTAGTCATTAGATTAAAAACTAAATTATGTGAGAATTGTTTCTCTCTTGGTTCT
* ** *
1008 TGGACGAACTTCCGAACTTATCAAGCTTTTTCGAGTTCTTTTAAAACTTCGATTCCTT
129 TGGACGAACTTCCGAAATTATCAAAATTTTTCGAGTTCTTTCAAAACTTCGATTCCTT
1066 AAAGTATTCA
Statistics
Matches: 162, Mismatches: 21, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
195 120 0.74
196 42 0.26
ACGTcount: A:0.29, C:0.18, G:0.12, T:0.41
Consensus pattern (196 bp):
AATTTTTCGAAAATTCCATTATCGAAAAATCACATCATTTGGTCCAAAATAATCTGTCATTTTCT
AAACAACTTTTAGTCATTAGATTAAAAACTAAATTATGTGAGAATTGTTTCTCTCTTGGTTCTTG
GACGAACTTCCGAAATTATCAAAATTTTTCGAGTTCTTTCAAAACTTCGATTCCTTTCCTTCAAG
C
Found at i:1376 original size:215 final size:214
Alignment explanation
Indices: 871--1394 Score: 665
Period size: 216 Copynumber: 2.4 Consensus size: 214
861 TCGGTTCCTT
* * * * * *
871 TCCTTCAAGCAATTTTTTGAACATTCCATTATCGAGAAATAGCATCATTTGGTCCAAATAAATTT
1 TCCTTCGAGCAATTTTTCGAACATT-CATTCTCGAGAAATCGCATCATTTGGTCAAAAT-AATTG
* * * * *
936 TCCTTTTGTAAACAACTTTTAGTCTTTGGATTAAAAACTAAATTATGTGAGAATTGTTTCTCTCT
64 TCCTTTTGTAAACAACTTTTGGTCTTTGAATTAAAAAATAAATTACGTGAGAATGGTTTCTCTCT
*
1001 TGGTTCTTGGACGAACTTCCGAACTTATCAAGCTTTTTCGAGTTCTTTTAAAACTTCGATTCCTT
129 TGGTTCTTGGACGAACTTCCGAACTTATCAAACTTTTTCGAGTTCTTTTAAAACTTCGATTCCTT
* * * *
1066 AAAGTATTCAAGAGGATCGAT
194 AAAGTAATAAAGAGGATCCAC
* * * * *
1087 TCCTTCGAGCAATTTTCCTAACATTCGATGCTCGAAAAATCGCATCATTTGGTCAAAATAGTTTG
1 TCCTTCGAGCAATTTTTCGAACATTC-ATTCTCGAGAAATCGCATCATTTGGTCAAAATA-ATTG
* * *
1152 TCCTTTTGT-AACAAACTTTTGGTCTTTGAATTAAAAAATTATTTACGTGAGAATGGTTTTTCTC
64 TCCTTTTGTAAAC-AACTTTTGGTCTTTGAATTAAAAAATAAATTACGTGAGAATGGTTTCTCTC
* * * *
1216 TTGGTTCTTGGCCGAACTTCCGAACTTTTCAAAC-TTTTCGAGTTCTTTTATAACTTCGTTTCCT
128 TTGGTTCTTGGACGAACTTCCGAACTTATCAAACTTTTTCGAGTTCTTTTAAAACTTCGATTCCT
*
1280 TAAAGTAATAAAGATGATCCAC
193 TAAAGTAATAAAGAGGATCCAC
* *
1302 TCCTTCGAGCAATTTTTCGAACATTACATTCTCGAGAAATCGCATCTTTTGGTCTAAATAATCTG
1 TCCTTCGAGCAATTTTTCGAACATT-CATTCTCGAGAAATCGCATCATTTGGTCAAAATAAT-TG
* * *
1367 TCATTTTGTAAAGAAGTTTTGGTCTTTG
64 TCCTTTTGTAAACAACTTTTGGTCTTTG
1395 NNNNNNNNNN
Statistics
Matches: 263, Mismatches: 39, Indels: 13
0.83 0.12 0.04
Matches are distributed among these distances:
214 1 0.00
215 126 0.48
216 136 0.52
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.40
Consensus pattern (214 bp):
TCCTTCGAGCAATTTTTCGAACATTCATTCTCGAGAAATCGCATCATTTGGTCAAAATAATTGTC
CTTTTGTAAACAACTTTTGGTCTTTGAATTAAAAAATAAATTACGTGAGAATGGTTTCTCTCTTG
GTTCTTGGACGAACTTCCGAACTTATCAAACTTTTTCGAGTTCTTTTAAAACTTCGATTCCTTAA
AGTAATAAAGAGGATCCAC
Found at i:3354 original size:215 final size:215
Alignment explanation
Indices: 1992--6129 Score: 3506
Period size: 216 Copynumber: 19.4 Consensus size: 215
1982 TTTCTCTCCT
* * *
1992 GGTTCCTTAAAGTATTCAAGATGATCCATTCCTTCGAGCAATTTTTTGAGCATTCCATGCTCGAG
1 GGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTTCGAACATTCCATGCTCGAG
** * * * * * *
2057 AAATCGCATCATTTCAAT-GAAGTAGTTTGTTATTTTGTAAGCAAATTTTAGTCTTTGAATTAAA
66 AAATCGCATCATTT-GGTCCAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAA
* * * * * * * *
2121 AACTTATTAACATTAGAATTGTTTTTCTCTTGGTTCCTAGTCGAACTTTCGAACTTTTCAAACTT
130 AACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTTTCGAACTTGTCAAACTT
* *
2186 TTTCGAGTTCTATTATAGCTTC
195 TTTCGAGTTCT-TTTTAACTTC
* * * * * * *
2208 GATTCCTTATAGGATTCAAGGCGATCCATTCCTTCGAGAAATTTTTCGAACATTCCAAGCTCGGG
1 GGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTTCGAACATTCCATGCTCGAG
* *
2273 AAATCGCATCATTTGGTCCAAATAGTTTGTCATTTTGTAAAAAACTTTTGGTCTTAGAATTAAAA
66 AAATCGCATCATTTGGTCCAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAA
* * * *
2338 ACTTATTTACGTGAGAATGGTTTCTCCCTTGGTTCTTGACTGAACTTTCGAACTTGTCAAAC-TT
131 ACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTTTCGAACTTGTCAAACTTT
2402 TTCGAGTTC-TTTT-A--T-
196 TTCGAGTTCTTTTTAACTTC
* * * * *
2417 --TTGCTTAAAGTATTCAAGACGATCGATTCCTTCGAGCAATTTTCCAAACATTCTA-GCCTCGA
1 GGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTTCGAACATTCCATG-CTCGA
* * * * * *
2479 GAAATCACACCATTTGGTCCAAATAGTTTGTCCTTTTGTAAAAAACTTTCGATCTTTGAATTAAA
65 GAAATCGCATCATTTGGTCCAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAA
** * * * *
2544 AACTTATTTATATGAGAATTATTTCTCTCTTGGTTCTTGACCGAACTTCCGAACTTTTCAAACTT
130 AACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTTTCGAACTTGTCAAACTT
* *
2609 TTTCGAGTTCTTTTACAACATC
195 TTTCGAGTTCTTTT-TAACTTC
* * * * *
2631 GGTTCCTTAAAGTATTCAAGACGATCCATTTCTT-GAAACAATTTTTTGAACATTCCATTCTCGG
1 GGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCG-AGCAATTTTTCGAACATTCCATGCTCGA
* * * * * *
2695 GATATCACATCATTTGGTCCAAGTAATCTGTCATTTTGTAAACAACTTTTGGTATTTTG-ATTAA
65 GAAATCGCATCATTTGGTCCAAATAGTTTGTCATTTTGTAAACAACTTTTGGT-CTTTGAATTAA
* * * * *
2759 AAACTTATTTACGTGAGAATGGTTTCTCTCTTGGTTCATGGCCGAACTTCCAAACTAGTCAAACT
129 AAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTTTCGAACTTGTCAAACT
* *
2824 TTTTTGAGTTCATTTATAACTTC
194 TTTTCGAGTTC-TTTTTAACTTC
* * * * *
2847 GGTTGCTTAAAGTATTCAAGACGATCGATTCCTTCGAGCAATTTTCCAAACATTCTA-GCCTCGA
1 GGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTTCGAACATTCCATG-CTCGA
* * * * *** * *
2911 -AAATCGCACCATTTGGTCAAAATAGTTTGTTC-TTTTGTAAAAAAACATTCAATCTTTAAAATA
65 GAAATCGCATCATTTGGTCCAAATAGTTTG-TCATTTTGT-AAACAACTTTTGGTCTTTGAATTA
* * *
2974 AAAACTTATTTATGTGAGAATTGTTTCTCACTTGGTTCTTGGCCGAACTTTCGAACTTTTCAAAC
128 AAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTTTCGAACTTGTCAAAC
* *
3039 TATTTCGAGTTCTCTTATAACTTC
193 TTTTTCGAGTTCT-TTTTAACTTC
* * *
3063 GGTTCCTTAAAGTATTCAAGATGATCCATTCCTTCGAGCAATTTTTCGAACATTCGATTCTC-AG
1 GGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTTCGAACATTCCATGCTCGA-
* * * * * * *
3127 GAAATTGCATCATTTGGTCCAAATAATCTGTTATTCTGTAAACAACTTTTGTTCTTTGGATTAAA
65 GAAATCGCATCATTTGGTCCAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAA
* * * * * *
3192 AACTTATTTACATGAGAATTATTTCTCGCTTGGTTCTTAGTCGAACTTTTGAACTTGTCAAACTT
130 AACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTTTCGAACTTGTCAAACTT
* *
3257 TTACGAGTTCTTTTTAACTTT
195 TTTCGAGTTCTTTTTAACTTC
* * * * * **
3278 GGTTCCTTAAAGTATTCAAGATGATTCATTCCTTCTAACAATTTTCCGAACATTCCATGCTTTAG
1 GGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTTCGAACATTCCATGCTCGAG
* * ** * *
3343 AAATCGCATCATTTGGTCCAAATAGTTTATCAGTTCATAAACAACTTTTGGTCTTTGAATTGAAG
66 AAATCGCATCATTTGGTCCAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAA
* *
3408 ACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCATGGCCGAAC-ATCTGAA-TATGTCAAACT
131 ACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTTTC-GAACT-TGTCAAACT
* * *
3471 TTTACAAGTTCTTTTATAACTTT
194 TTTTCGAGTTCTTTT-TAACTTC
* * * * * ** *
3494 GG-T-CTT--TGAATTAAAGATGATCAATTCCTTCGAATAA-TTTTCTAAGCATTCCATGCTCGA
1 GGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTTCGAA-CATTCCATGCTCGA
* * * *
3554 GAAA-CTACATCATTTTGACCAAGA-AGTTTGTCATTTTGTAAACAACTTTTGCTCTTTGAATTA
65 GAAATC-GCATCATTTGGTCCAA-ATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTA
* * * * * * * *
3617 AAAACTTATTAACATTAAAATT-TTTCTCTCTTGGTCCTTGGTCGAACTTTCAAACTTTTCAAAC
128 AAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTTTCGAACTTGTCAAAC
** * **
3681 TTTTTCTTGTTCTATTATAGGTTC
193 TTTTTCGAGTTCT-TTTTAACTTC
* *
3705 GATTCCTTATAGTATTCAAGACGATCCATTCCTTCGAGCAA----T------TTCCATGCTCGAG
1 GGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTTCGAACATTCCATGCTCGAG
* * * *
3760 AAATCGCATCAATTGGTCCAAATAGTTTTTCATTTTGTAAATAACTTTTGGTCTTAGAATTAAAA
66 AAATCGCATCATTTGGTCCAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAA
** * * * * *
3825 A-TTATTTACGTGAGAACGGCTTCTCCCTTGGTTCTTGACTGAACTTTCGAACATGTC-AACTTT
131 ACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTTTCGAACTTGTCAAACTTT
* * *
3888 TTACGTGTTATTTTATAATTTC
196 TT-CGAGTTCTTTT-TAACTTC
* *
3910 GGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCAAGCAATTTTTCAAACATTCCATGCTC-AG
1 GGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTTCGAACATTCCATGCTCGA-
* * * * * * *****
3974 GAAATCGAATCATTTGGTTCAAATATTTTATCCTTTTGTAAACAACTTTCGGTCTCNNNNNNNNN
65 GAAATCGCATCATTTGGTCCAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCT-----TTGAA
****************************************** *
4039 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNATGGCCGAAC-ATCTGAA-TATGT
125 TTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTTTC-GAACT-TGT
* * *
4102 CAAACTTTTACAAGTTCTTTTATAACTTT
188 CAAACTTTTTCGAGTTCTTTT-TAACTTC
* * * * * * *
4131 GG-T-CTT--TGAATTAAAGATGATCAATTCCTTCGAGTAA-TTTTCTAAGCATTCCATGCTCGA
1 GGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTTCGAA-CATTCCATGCTCGA
* * * **
4191 GAAA-CTACATCATTTTGACCAAGA-AGTTTGTCATTTTGTAAACAACTTTTTCTCTTTGAATTA
65 GAAATC-GCATCATTTGGTCCAA-ATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTA
* * * * *
4254 AAAACTTATTAACATTAAAATT-TTTCTCTCTTGGTCCTT-G--G-----TCGAACTT-TCAAAC
128 AAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTTTCGAACTTGTCAAAC
** * **
4309 TTTTTCTTGTTCTATTATAGGTTC
193 TTTTTCGAGTTCT-TTTTAACTTC
* *
4333 GATTCCTTACAGTATTCAAGACGATCCATTCCTTCGAGCAA----T------TTCCATGCTCGAG
1 GGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTTCGAACATTCCATGCTCGAG
* * * *
4388 AAATCGCATCAATTCGTCCAAATAGTTTTTCATTTTGTAAACAACTTTTGGTCTTAGAATTAAAA
66 AAATCGCATCATTTGGTCCAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAA
* * * * * * *
4453 A-TTATTTACGTGAGAATGGCTTCTCCCTTGGTTCTTGACTGAACTTTCGAACATGTCAACCTTT
131 ACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTTTCGAACTTGTCAAACTTT
* ** * *
4517 TACGTCTTATTTATAACTTC
196 TTCGAGTTCTTTTTAACTTC
* *
4537 GGTTCCCTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTTCAAACATTCCATGCTC-AG
1 GGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTTCGAACATTCCATGCTCGA-
* * * * * * *
4601 GAAATCGAATCATTTGGTTCAAATATTTTATCCTTTTGTAAACAACTTTCGGTCTCTGAATTAAA
65 GAAATCGCATCATTTGGTCCAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAA
* *
4666 ATCTTATTTATGTGAGAATT-TTGTCTCTCTTGGTTCTTGGCCGAACTTTCGAACTTGTCAAACT
130 AACTTATTTACGTGAGAATTGTT-TCTCTCTTGGTTCTTGGCCGAACTTTCGAACTTGTCAAACT
4730 TTTTCGAGTTCTTTTATAACTTC
194 TTTTCGAGTTCTTTT-TAACTTC
* * * * * *
4753 AGTTCCTTAAAGTATTCAAGATGATCGATTCCTTCGA-AAATTTTTTTGAACATTCCATTCTCCG
1 GGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAA-TTTTTCGAACATTCCATGCT-CG
** * * ***
4817 -GAAATCGCATCATTTGGTCCAAATAGTTAATCCTTTTGTAAAAAACTTTCAATCTTTGAATTAA
64 AGAAATCGCATCATTTGGTCCAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAA
* * * * *
4881 AAACTTATTTA-ATCGATAA-TGATTTCTCTCCTAGTTCTAGGCCGAACTTTCCGAACTAT-TCA
129 AAACTTATTTACGT-GAGAATTG-TTTCTCTCTTGGTTCTTGGCCGAACTTT-CGAACT-TGTCA
*
4943 AACTTTTTCGAGTTCTTTTATAACTTT
190 AACTTTTTCGAGTTCTTTT-TAACTTC
* * * * *
4970 AGTTCCTTAAAGTATTCAAGACGATCCATTTCTTCGAACAATTTTTCGAACATTCCATTCTCGGG
1 GGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTTCGAACATTCCATGCTCGAG
* * * * * *
5035 AAATTGCATCATTTGGTCCAAATAATCTATCATTTTGTAAACAACTCTTGGTCTTTGGA-TAAAA
66 AAATCGCATCATTTGGTCCAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAA
* * * * * *
5099 ATTTATTTATGTGAGAATT-ATT-TCTCTTGCTTCTTGGCCAAAC-TTCTGAACTTGTCAAAATT
131 ACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTTTC-GAACTTGTCAAACTT
* * *
5161 TTTTGGGTTCTCTTATAACTTC
195 TTTCGAGTTCT-TTTTAACTTC
* * * * * * * * **
5183 GATT-CTTAAAGTATTTATGACAATCGATTCCTTCGAGCAATTATCCAAACATTTAATGCTCGAG
1 GGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTTCGAACATTCCATGCTCGAG
* * *
5247 AAATCGCATCATTTGGTCCAAATAGTTTGTCCTTTTGTAAAAAACTTTTAGTCTTTGAATTAAAA
66 AAATCGCATCATTTGGTCCAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAA
* * * * * ** * *
5312 ACTTATTTACATGAGAATTATTTATGTCTTGGTTCTTAGCTAAACTTCCGAACTTTTCAAACTTT
131 ACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTTTCGAACTTGTCAAACTTT
*
5377 TTTGAGTTCTTTTATAACTTC
196 TTCGAGTTCTTTT-TAACTTC
* * * * * * * * *
5398 GGTTCCTTAAAGCATCCAAGATGAT-C-TT-CTTCGAACAATTTCTAGAACATTTCATTCTCGGG
1 GGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTTCGAACATTCCATGCTCGAG
* * * * *
5460 AAATCGCATCATTTGATCTAAATAATCTGTCATTTTGTAAACAACTTTTGGTCTTTGGATTAAAA
66 AAATCGCATCATTTGGTCCAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAA
** * * * * * *
5525 ACTTATTTATATGAGAAATCTTTCTCTCTTGGTTATTGGCCGAA-TTTCTGAAATTTTCAAAAAA
131 ACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTTTC-GAACTTGTC--AAAC
*
5589 TTTTT-GAGTTCTTTTACAACTTC
193 TTTTTCGAGTTCTTTT-TAACTTC
* * * * *
5612 GGTTCCTTAAAGTATTCAAGACGATCCATTCCTGCAAGCAATTTTTCAAACATTCAATTCTC-AG
1 GGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTTCGAACATTCCATGCTCGA-
* * * * * * * *
5676 GATATCGTATCATTTGGTCCAAATAATCTT-TCATTTTGTAAACAACTTTTAGTATTTGGACTAG
65 GAAATCGCATCATTTGGTCCAAATAGT-TTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAA
* * * *
5740 AAACTTATTTATGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTTTGAACTTGTGAAACT
129 AAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTTTCGAACTTGTCAAACT
*
5805 TTTTCGAGTTCTTTTGAAACTTC
194 TTTTCGAGTTCTTTT-TAACTTC
* * * * * * *
5828 GATTCCTTAAAGCATTCAAGAGGATCGAATCCTTCGATCAATTTTTCGAACATTCCATGCTCAAG
1 GGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTTCGAACATTCCATGCTCGAG
* * *
5893 AAATCGCATCATTTGGTCCAAATAGTTTGTCCTTTTGTAAAAAACTTTCGGTCTTTGAATTAAAA
66 AAATCGCATCATTTGGTCCAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAA
* * * * * *
5958 ACTTATTTACGTGAGAATGGTTTCCCTCTTGGTTCTTGGCCAAACTTCCGAAGTT-TTAAAGCTT
131 ACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTTTCGAACTTGTCAAA-CTT
* *
6022 TTTCGAGTCCCTTTATAACTTC
195 TTTCGAGT-TCTTTTTAACTTC
* * * *
6044 GATTCCTTACAA-TATTCAAGACGATCCATTCCTTCGAGCAATTTTTCGAACATTACATTCTCGG
1 GGTTCCTTA-AAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTTCGAACATTCCATGCTCGA
*
6108 GAAATCGCATCTTTTGGTCCAA
65 GAAATCGCATCATTTGGTCCAA
Statistics
Matches: 3119, Mismatches: 667, Indels: 272
0.77 0.16 0.07
Matches are distributed among these distances:
195 13 0.00
196 81 0.03
197 1 0.00
199 1 0.00
202 21 0.01
203 8 0.00
204 81 0.03
205 159 0.05
206 27 0.01
207 164 0.05
208 13 0.00
209 4 0.00
210 2 0.00
211 55 0.02
212 212 0.07
213 186 0.06
214 136 0.04
215 449 0.14
216 1069 0.34
217 385 0.12
218 9 0.00
219 3 0.00
220 3 0.00
221 30 0.01
222 7 0.00
ACGTcount: A:0.28, C:0.18, G:0.13, T:0.39
Consensus pattern (215 bp):
GGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTTCGAACATTCCATGCTCGAG
AAATCGCATCATTTGGTCCAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAA
ACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTTTCGAACTTGTCAAACTTT
TTCGAGTTCTTTTTAACTTC
Found at i:3808 original size:205 final size:205
Alignment explanation
Indices: 3542--3953 Score: 483
Period size: 205 Copynumber: 2.0 Consensus size: 205
3532 TTTCTAAGCA
* *
3542 TTCCATGCTCGAGAAACTACATCATTTTGACCAAGAAGTTTGTCATTTTGTAAACAACTTTTGCT
1 TTCCATGCTCGAGAAACTACATCAATTGGACCAAGAAGTTTGTCATTTTGTAAACAACTTTTGCT
* * *** * *
3607 CTTTGAATTAAAAACTTATTAACATTA-AAATTTTTCTCTCTTGGTCCTTG-GTCGAACTTTCAA
66 CTTAGAATTAAAAA-TTATTAACATGAGAAAGGCTTCTCCCTTGGTCCTTGACT-GAACTTTCAA
* * * * * *
3670 ACTTTTCAAACTTTTT-CTTGTTCTATTATAGGTTCGATTCCTTATAGTATTCAAGACGATCCAT
129 ACATGTC-AACTTTTTACGTGTTATATTATAAGTTCGATTCCTTAAAGTATTCAAGACGATCCAT
*
3734 TCCTTCGAGCAAT
193 TCCTTCAAGCAAT
* * * *
3747 TTCCATGCTCGAGAAA-TCGCATCAATTGGTCCAA-ATAGTTTTTCATTTTGTAAATAACTTTTG
1 TTCCATGCTCGAGAAACT-ACATCAATTGGACCAAGA-AGTTTGTCATTTTGTAAACAACTTTTG
* * * * * *
3810 GTCTTAGAATTAAAAATTATTTACGTGAGAACGGCTTCTCCCTTGGTTCTTGACTGAACTTTCGA
64 CTCTTAGAATTAAAAATTATTAACATGAGAAAGGCTTCTCCCTTGGTCCTTGACTGAACTTTCAA
* * *
3875 ACATGTCAACTTTTTACGTGTTATTTTATAATTTCGGTTCCTTAAAGTATTCAAGACGATCCATT
129 ACATGTCAACTTTTTACGTGTTATATTATAAGTTCGATTCCTTAAAGTATTCAAGACGATCCATT
3940 CCTTCAAGCAAT
194 CCTTCAAGCAAT
3952 TT
1 TT
3954 TTCAAACATT
Statistics
Matches: 173, Mismatches: 29, Indels: 10
0.82 0.14 0.05
Matches are distributed among these distances:
204 19 0.11
205 153 0.88
206 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.13, T:0.40
Consensus pattern (205 bp):
TTCCATGCTCGAGAAACTACATCAATTGGACCAAGAAGTTTGTCATTTTGTAAACAACTTTTGCT
CTTAGAATTAAAAATTATTAACATGAGAAAGGCTTCTCCCTTGGTCCTTGACTGAACTTTCAAAC
ATGTCAACTTTTTACGTGTTATATTATAAGTTCGATTCCTTAAAGTATTCAAGACGATCCATTCC
TTCAAGCAAT
Done.