Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012019.1 Kokia drynarioides strain JFW-HI SEQ_127017, 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: 4447
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.39
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:540 original size:209 final size:209
Alignment explanation
Indices: 208--590 Score: 513
Period size: 209 Copynumber: 1.8 Consensus size: 209
198 CATTTGGTAT
*
208 ACAACTTTTGGTCATTGAATTAAAAACTTATTTACGTGAGAATTTATTATCTCTTGGATCATGGA
1 ACAACTTTTGGTCATTAAATTAAAAACTTATTTACGTGAGAATTTATTATCTCTTGGATCATGGA
* * * **
273 CAAACTTCCGAACTTTACAAACTTTAGCCAGTTGTTCTATAACTTTGGTTCATTTAAGTATTCAT
66 CAAACTTCCGAACTTGACAAACTTTAGCCAGTTCTTCTAAAACTTCAGTTCATTTAAGTATTCAT
* *
338 GACGATCCTTTCCTTCGAGCAATGTTCCGAACATTCCAAGCACGGGGAATCGTATCATTCTGCCT
131 GACGATCCGTTCCTTCGAGAAATGTTCCGAACATTCCAAGCACGGGGAATCGTATCATTCTGCCT
403 TTTTCATTTTCTAA
196 TTTTCATTTTCTAA
* * * * *
417 ACAACTTTTGGTC-TATAAATTAAAAAGTTATTTACGTGAGAGTTGT-TTCTCTCATT-GTTCTT
1 ACAACTTTTGGTCAT-TAAATTAAAAACTTATTTACGTGAGAATT-TATTATCTC-TTGGATCAT
* ** * *
479 GGACGAACTTCCGAACTTGACGAAGTTTTA-CGAGTTCTTCTAAAACTTCAGTTCCTTTAAGTAT
63 GGACAAACTTCCGAACTTGAC-AAACTTTAGCCAGTTCTTCTAAAACTTCAGTTCATTTAAGTAT
* * *
543 TCATGACGATCCGTTCCTTCTAGAAATTTTCCGAACATTCCATGCACG
127 TCATGACGATCCGTTCCTTCGAGAAATGTTCCGAACATTCCAAGCACG
591 AGAAATCGCA
Statistics
Matches: 149, Mismatches: 21, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
208 1 0.01
209 139 0.93
210 9 0.06
ACGTcount: A:0.27, C:0.20, G:0.15, T:0.38
Consensus pattern (209 bp):
ACAACTTTTGGTCATTAAATTAAAAACTTATTTACGTGAGAATTTATTATCTCTTGGATCATGGA
CAAACTTCCGAACTTGACAAACTTTAGCCAGTTCTTCTAAAACTTCAGTTCATTTAAGTATTCAT
GACGATCCGTTCCTTCGAGAAATGTTCCGAACATTCCAAGCACGGGGAATCGTATCATTCTGCCT
TTTTCATTTTCTAA
Found at i:1217 original size:216 final size:215
Alignment explanation
Indices: 742--1763 Score: 1011
Period size: 216 Copynumber: 4.7 Consensus size: 215
732 NNNNNNATTA
* * * * * * * * * ***
742 TCTCTTGGATCATGGACAAACTTCCGAACTTTACAAACTTTAACCAGTTGTTCTATAACTTTGGT
1 TCTCTTGGTTCTTAGACGAACTTCC-AACTTGACAAACTTTTACGAGTTCTTCTAAAACTTCACT
* * * * * * * ** *
807 TCATTAAAGTATTCACGACGATCCTTTCCTTCAAGTAATTTTCCGAACATTCCAAGCACGGGGAA
65 TCCTTAAAGTATTCATGACGATCCATTCCTTCGAGCAATTTTTCGAACATTCCATGCTTGGGAAA
* * ** * * * *
872 CCGCATCATTCTGCCTAAATAGTTT-TCATTTTCTAAACAACTTTTGGTCTATAAATTAAAAAGT
130 TCGCATCATTTTTTCTAAATAGTTTGTCATTTTCTAAACAACTTTTGGTCTTTGAATGAAAAACT
936 TATTTACGTGAGAGTTGTTTC
195 TATTTACGTGAGAGTTGTTTC
* * * *
957 TCTAATT-GTTCTTGGACGAACTTCCGAACTTGACGAAGTTTTACGAGTTCTTCTAAAACTTCAC
1 TCT-CTTGGTTCTTAGACGAACTTCC-AACTTGACAAACTTTTACGAGTTCTTCTAAAACTTCAC
* * * **
1021 TTCCTCT-AAGTATTCATGACGATCCGTTCCTTCTAGAAATTTTTCGAACATTCCATGCACGGGA
64 TTCCT-TAAAGTATTCATGACGATCCATTCCTTCGAGCAATTTTTCGAACATTCCATGCTTGGGA
* * ** *
1085 AATCGCATCGTTTTTTCTAAATTGTTTGTCATTTTCTAAACAACTTTTTATCTTTGAATTAAAAA
128 AATCGCATCATTTTTTCTAAATAGTTTGTCATTTTCTAAACAACTTTTGGTCTTTGAATGAAAAA
* *
1150 CCTATTTACGCGAGAGTTGTCTT-
193 CTTATTTACGTGAGAGTTGT-TTC
* * ***
1173 TCTCTTGCTTCTTAGATGAACTTCCAAGCTTGACAAACTTTTACGAGTTCTTC-AATAACTTTGG
1 TCTCTTGGTTCTTAGACGAACTTCCAA-CTTGACAAACTTTTACGAGTTCTTCTAA-AACTTCAC
* * * *
1237 TTTCTTAAAGTATTCAGGACAATCCATTCCTTTGAGCAATTTGTT-GAACATTCCATGCTTGGGA
64 TTCCTTAAAGTATTCATGACGATCCATTCCTTCGAGCAATTT-TTCGAACATTCCATGCTTGGGA
* ** * * *
1301 AATCACATCATTTGATCTAAATACTTTGTCATTTTCTAAACTACTTTTGGTCTTTCAATGAAAAA
128 AATCGCATCATTTTTTCTAAATAGTTTGTCATTTTCTAAACAACTTTTGGTCTTTGAATGAAAAA
*
1366 CTTATTCACGTGAGAGTTGTTTC
193 CTTATTTACGTGAGAGTTGTTTC
* * * * * *
1389 TATCTTGGTTCTTAGACGAACTTTCGAACTTGGCAAACTTTTACGAGTTCTTTTATAACTTCAGT
1 TCTCTTGGTTCTTAGACGAAC-TTCCAACTTGACAAACTTTTACGAGTTCTTCTAAAACTTCACT
* * * ** * * *
1454 TCCATAAAGTATCCATGACCATCCATTATTTCGAGCAATTTTCCGAACATTTCAAGCTTGGGAAA
65 TCCTTAAAGTATTCATGACGATCCATTCCTTCGAGCAATTTTTCGAACATTCCATGCTTGGGAAA
* **
1519 ACGCATCATTTTTTCTAAACTA-TTTGTCATTTGGTAAACAACTTTTGGTCTTTGAATGAAAAAC
130 TCGCATCATTTTTTCTAAA-TAGTTTGTCATTTTCTAAACAACTTTTGGTCTTTGAATGAAAAAC
* *
1583 TTATTTACGTGAGAATTGTTCC
194 TTATTTACGTGAGAGTTGTTTC
* * * * * * * * *
1605 TCTCTTGGATATTGGATGAACTTCTAAACTTGACAAACTTTGACGAGTTCTTCTATAGCTTCGGC
1 TCTCTTGGTTCTTAGACGAACTTC-CAACTTGACAAACTTTTACGAGTTCTTCTAAAACTTC-AC
*
1670 --CCTTTAAAGTATTCATGATGATCCATTCCTTCGAGCAA-TTTTCTGAACATTCCATGCTTGGG
64 TTCC-TTAAAGTATTCATGACGATCCATTCCTTCGAGCAATTTTTC-GAACATTCCATGCTTGGG
* *
1732 AAATCACATCATTTTCTCTAAATAGTTTGTCA
127 AAATCGCATCATTTTTTCTAAATAGTTTGTCA
1764 GGACAATCCA
Statistics
Matches: 666, Mismatches: 122, Indels: 37
0.81 0.15 0.04
Matches are distributed among these distances:
215 143 0.21
216 511 0.77
217 12 0.02
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.38
Consensus pattern (215 bp):
TCTCTTGGTTCTTAGACGAACTTCCAACTTGACAAACTTTTACGAGTTCTTCTAAAACTTCACTT
CCTTAAAGTATTCATGACGATCCATTCCTTCGAGCAATTTTTCGAACATTCCATGCTTGGGAAAT
CGCATCATTTTTTCTAAATAGTTTGTCATTTTCTAAACAACTTTTGGTCTTTGAATGAAAAACTT
ATTTACGTGAGAGTTGTTTC
Found at i:1547 original size:432 final size:430
Alignment explanation
Indices: 760--1763 Score: 1183
Period size: 432 Copynumber: 2.3 Consensus size: 430
750 ATCATGGACA
* * *
760 AACTTCCGAACTTTACAAACTTTAACCAGTTGTTCTATAACTTTGGTTCATTAAAGTATTCACGA
1 AACTTCC-AACTTGACAAACTTTAACGAGTTCTTCTATAACTTTGGTTCATTAAAGTATTCACGA
* * * * * ** * * * *
825 CGATCCTTTCCTTCAAGTAATTTTCCGAACATTCCAAGCACGGGGAACCGCATCATTCTGCCTAA
65 CGATCCATTCCTTCGAGCAATTTTCTGAACATTCCATGCTTGGGAAATCACATCATT-TGTCTAA
* * *
890 ATAGTTT-TCATTTTCTAAACAACTTTTGGTCTATAAATTAAAAAGTTATTTACGTGAGAGTTGT
129 ATAGTTTGTCATTTTCTAAACAACTTTTGGTCTATAAATGAAAAACTTATTCACGTGAGAGTTGT
* * * *
954 TTCTCTAATTGTTCTTGGACGAACTTCCGAACTTGACGAAGTTTTACGAGTTCTTCTAAAACTTC
194 TTCTATAATTGTTCTTAGACGAACTTCCGAACTTGACAAACTTTTACGAGTTCTTCTAAAACTTC
* * * * * * * *
1019 ACTTCCTCTAAGTATTCATGACGATCCGTTCCTTCTAGAAATTTTTCGAACATTCCATGCACGGG
259 ACTTCCTCAAAGTATCCATGACCATCCATTACTTCGAGAAATTTTCCGAACATTCCAAGCACGGG
* * * * * * *
1084 AAATCGCATCGTTTTTTCTAAATTGTTTGTCATTTTCTAAACAACTTTTTATCTTTGAATTAAAA
324 AAAACGCATCATTTTTTCTAAACTATTTGTCATTTGCTAAACAACTTTTGATCTTTGAATGAAAA
* * * *
1149 ACCTATTTACGCGAGAGTTG-TCTTTCTCTTGCTTCTTAGATG
389 ACCTATTTACGCGAGAATTGTTC-CTCTCTTGCATATTAGATG
* * *
1191 AACTTCCAAGCTTGACAAACTTTTACGAGTTCTTCAATAACTTTGGTTTC-TTAAAGTATTCAGG
1 AACTTCCAA-CTTGACAAACTTTAACGAGTTCTTCTATAACTTTGG-TTCATTAAAGTATTCACG
* *
1255 ACAATCCATTCCTTTGAGCAATTTGT-TGAACATTCCATGCTTGGGAAATCACATCATTTGATCT
64 ACGATCCATTCCTTCGAGCAATTT-TCTGAACATTCCATGCTTGGGAAATCACATCATTTG-TCT
* * * *
1319 AAATACTTTGTCATTTTCTAAACTACTTTTGGTCTTTCAATGAAAAACTTATTCACGTGAGAGTT
127 AAATAGTTTGTCATTTTCTAAACAACTTTTGGTCTATAAATGAAAAACTTATTCACGTGAGAGTT
* * * * *
1384 GTTTCTAT-CTTGGTTCTTAGACGAACTTTCGAACTTGGCAAACTTTTACGAGTTCTTTTATAAC
192 GTTTCTATAATT-GTTCTTAGACGAACTTCCGAACTTGACAAACTTTTACGAGTTCTTCTAAAAC
* * * * *
1448 TTCAGTTCCAT-AAAGTATCCATGACCATCCATTATTTCGAGCAATTTTCCGAACATTTCAAGCT
256 TTCACTTCC-TCAAAGTATCCATGACCATCCATTACTTCGAGAAATTTTCCGAACATTCCAAGCA
* * *
1512 TGGGAAAACGCATCATTTTTTCTAAACTATTTGTCATTTGGTAAACAACTTTTGGTCTTTGAATG
320 CGGGAAAACGCATCATTTTTTCTAAACTATTTGTCATTTGCTAAACAACTTTTGATCTTTGAATG
* * * *
1577 AAAAACTTATTTACGTGAGAATTGTTCCTCTCTTGGATATTGGATG
385 AAAAACCTATTTACGCGAGAATTGTTCCTCTCTTGCATATTAGATG
* * * * ** * *
1623 AACTTCTAAACTTGACAAACTTTGACGAGTTCTTCTATAGCTTCGGCCCTTTAAAGTATTCATGA
1 AACTTC-CAACTTGACAAACTTTAACGAGTTCTTCTATAACTTTGGTTCATTAAAGTATTCACGA
* *
1688 TGATCCATTCCTTCGAGCAATTTTCTGAACATTCCATGCTTGGGAAATCACATCATTTTCTCTAA
65 CGATCCATTCCTTCGAGCAATTTTCTGAACATTCCATGCTTGGGAAATCACATCA-TTTGTCTAA
1753 ATAGTTTGTCA
129 ATAGTTTGTCA
1764 GGACAATCCA
Statistics
Matches: 482, Mismatches: 79, Indels: 23
0.83 0.14 0.04
Matches are distributed among these distances:
430 4 0.01
431 109 0.23
432 361 0.75
433 8 0.02
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.38
Consensus pattern (430 bp):
AACTTCCAACTTGACAAACTTTAACGAGTTCTTCTATAACTTTGGTTCATTAAAGTATTCACGAC
GATCCATTCCTTCGAGCAATTTTCTGAACATTCCATGCTTGGGAAATCACATCATTTGTCTAAAT
AGTTTGTCATTTTCTAAACAACTTTTGGTCTATAAATGAAAAACTTATTCACGTGAGAGTTGTTT
CTATAATTGTTCTTAGACGAACTTCCGAACTTGACAAACTTTTACGAGTTCTTCTAAAACTTCAC
TTCCTCAAAGTATCCATGACCATCCATTACTTCGAGAAATTTTCCGAACATTCCAAGCACGGGAA
AACGCATCATTTTTTCTAAACTATTTGTCATTTGCTAAACAACTTTTGATCTTTGAATGAAAAAC
CTATTTACGCGAGAATTGTTCCTCTCTTGCATATTAGATG
Found at i:1821 original size:79 final size:79
Alignment explanation
Indices: 1690--1842 Score: 254
Period size: 79 Copynumber: 1.9 Consensus size: 79
1680 ATTCATGATG
* *
1690 ATCCATTCCTTCGAGCAATTTTCTGAACATTCCATGCTTGGGAAATCACATCATTTTCTCTAAAT
1 ATCCATTCCTTCGAGCAATTTTCTGAACATTCCATGCTTGAGAAATCACATCATTTGCTCTAAAT
1755 AGTTTGTCAGGACA
66 AGTTTGTCAGGACA
* *
1769 ATCCATTCCTTCGAGCAATTTTTTGAACATTCCATGCTCT-AGAAATCACATCATTTGGTCTAAA
1 ATCCATTCCTTCGAGCAATTTTCTGAACATTCCATGCT-TGAGAAATCACATCATTTGCTCTAAA
1833 TAGTTTGTCA
65 TAGTTTGTCA
1843 TTTTCTAAAC
Statistics
Matches: 69, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
79 68 0.99
80 1 0.01
ACGTcount: A:0.28, C:0.22, G:0.13, T:0.37
Consensus pattern (79 bp):
ATCCATTCCTTCGAGCAATTTTCTGAACATTCCATGCTTGAGAAATCACATCATTTGCTCTAAAT
AGTTTGTCAGGACA
Found at i:2211 original size:511 final size:511
Alignment explanation
Indices: 1250--2222 Score: 1369
Period size: 511 Copynumber: 1.9 Consensus size: 511
1240 CTTAAAGTAT
* *
1250 TCAGGACAATCCATTCCTTTGAGCAATTTGTTGAACATTCCATGCTTGGGAAATCACATCATTTG
1 TCAGGACAATCCATTCCTTCGAGCAATTTGTTGAACATTCCATGCTTGAGAAATCACATCATTTG
*
1315 ATCTAAATACTTTGTCATTTTCTAAACTACTTTTGGTCTTTCAATGAAAAACTTATTCACGTGAG
66 ATCTAAATACTTTGTCATTTTCTAAACAACTTTTGGTCTTTCAATGAAAAACTTATTCACGTGAG
*
1380 AGTTGTTTCTATCTTGGTTCTTAGACGAACTTTCGAACTTGGCAAACTTTTACGAGTTCTTTTAT
131 AGTTGTTTCTATCTTGGTTCTTAGACGAACTTCCGAACTTGGCAAACTTTTACGAGTTCTTTTAT
** * * *
1445 AACTTCAGTTCCATAAAGTATCCATGACCATCCATTATTTCGAGCAATTTTCCGAACATTTCAAG
196 AACTTCAGTTCCATAAAGTATAAATGACCATCCATTACTTCGAGCAATTTTCCAAACATTCCAAG
* * ** *
1510 CTTGGGAAAACGCATCATTTTTTCTAAACTATTTGTCATTTGGTAAACAACTTTTGGTCTTTGAA
261 CTCGGCAAAACGCATCATTTGGTCTAAACTACTTGTCATTTGGTAAACAACTTTTGGTCTTTGAA
* * * * *
1575 TGAAAAACTTATTTACGTGAGAATTGTTCCTCTCTTGGATATTGGATGAACTTCTAAACTTGACA
326 TGAAAAACATATTTACGTGAGAATTGTTCCTCTCTAGGATATCGGACGAACTTCCAAACTTGACA
* * * *
1640 AACTTTGACGAGTTCTTCTATAGCTTCGGCCCTTTAAAGTATTCATGATGATCCATTCCTTCGAG
391 AACTTTGACGAGTTCTTCTAAAACTTCGGCCCTTTAAAGTATTCATGACGATCCATTCCTTCAAG
1705 CAATTTTCTGAACATTCCATGCTTGGGAAATCACATCATTTTCTCTAAATAGTTTG
456 CAATTTTCTGAACATTCCATGCTTGGGAAATCACATCATTTTCTCTAAATAGTTTG
*
1761 TCAGGACAATCCATTCCTTCGAGCAATTTTTTGAACATTCCATGCTCT-AGAAATCACATCATTT
1 TCAGGACAATCCATTCCTTCGAGCAATTTGTTGAACATTCCATGCT-TGAGAAATCACATCATTT
* * * * *
1825 GGTCTAAATAGTTTGTCATTTTCTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGA
65 GATCTAAATACTTTGTCATTTTCTAAACAACTTTTGGTCTTTCAATGAAAAACTTATTCACGTGA
* * *
1890 GAGTTGTTTCTCTCTTGGTTCTTGGACGAACTTCCGAACTTGGTAAACTTTTACGAGTTCTTTTA
130 GAGTTGTTTCTATCTTGGTTCTTAGACGAACTTCCGAACTTGGCAAACTTTTACGAGTTCTTTTA
* * * * * *
1955 TAACTTCAGTTCCTTAAAGTATAAATGACGATCCATTCCTTCGAGTAATTTTCTAAACATTCCAT
195 TAACTTCAGTTCCATAAAGTATAAATGACCATCCATTACTTCGAGCAATTTTCCAAACATTCCAA
* * * * *
2020 GCTCGTCAAATCGCATCATTTGGTCTAAA-TGGCTTGTTATTTTGTAAACAACTTTTGGTCTTTG
260 GCTCGGCAAAACGCATCATTTGGTCTAAACT-ACTTGTCATTTGGTAAACAACTTTTGGTCTTTG
* * * * *
2084 AATTAAAAACATATTTATGTGAGAATTGTTTCTCTCTAGGATCTCGGACGAACTTCCGAACTTGA
324 AATGAAAAACATATTTACGTGAGAATTGTTCCTCTCTAGGATATCGGACGAACTTCCAAACTTGA
* * * * * ** *
2149 CAAACTTTTATGATTTGTTTTAAAACTTCAGTTCC-TTATAGTATT-ATTGACGATCCATTCCTT
389 CAAACTTTGACGAGTTCTTCTAAAACTTC-GGCCCTTTAAAGTATTCA-TGACGATCCATTCCTT
*
2212 CAAGTAATTTT
452 CAAGCAATTTT
2223 TTGACTTGGG
Statistics
Matches: 401, Mismatches: 57, Indels: 8
0.86 0.12 0.02
Matches are distributed among these distances:
510 2 0.00
511 395 0.99
512 4 0.01
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.39
Consensus pattern (511 bp):
TCAGGACAATCCATTCCTTCGAGCAATTTGTTGAACATTCCATGCTTGAGAAATCACATCATTTG
ATCTAAATACTTTGTCATTTTCTAAACAACTTTTGGTCTTTCAATGAAAAACTTATTCACGTGAG
AGTTGTTTCTATCTTGGTTCTTAGACGAACTTCCGAACTTGGCAAACTTTTACGAGTTCTTTTAT
AACTTCAGTTCCATAAAGTATAAATGACCATCCATTACTTCGAGCAATTTTCCAAACATTCCAAG
CTCGGCAAAACGCATCATTTGGTCTAAACTACTTGTCATTTGGTAAACAACTTTTGGTCTTTGAA
TGAAAAACATATTTACGTGAGAATTGTTCCTCTCTAGGATATCGGACGAACTTCCAAACTTGACA
AACTTTGACGAGTTCTTCTAAAACTTCGGCCCTTTAAAGTATTCATGACGATCCATTCCTTCAAG
CAATTTTCTGAACATTCCATGCTTGGGAAATCACATCATTTTCTCTAAATAGTTTG
Found at i:3586 original size:215 final size:215
Alignment explanation
Indices: 1765--4447 Score: 2849
Period size: 216 Copynumber: 12.5 Consensus size: 215
1755 AGTTTGTCAG
* ** ** *
1765 GACAATCCATTCCTTCGAGCAATTTTTTGAACATTCCATGCTCTAGAAATCACATCATTTGGTCT
1 GACAATCCATTCCTTCGAGTAA-TTTTCAAACATTCCATGCTCGGGAAATCGCATCATTTGGTCT
* *
1830 AAATAGTTTGTCATTTTCTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAGTT
65 AAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATT
* **
1895 GTTTCTCTCTTGGTTCTTGGACGAACTTCCGAACTTGGTAAACTTTTACGAGTTCTTTTATAACT
130 GTTTCTCTCTTGGTTCTTGGACGAACTTTCGAACTTGACAAACTTTTACGAGTTCTTTTATAACT
**
1960 TCAGTTCCTTAAAGTATAAAT
195 TCAGTTCCTTAAAGTATTCAT
* **
1981 GACGATCCATTCCTTCGAGTAATTTTCTAAACATTCCATGCTCGTCAAATCGCATCATTTGGTCT
1 GACAATCCATTCCTTCGAGTAATTTTC-AAACATTCCATGCTCGGGAAATCGCATCATTTGGTCT
* * * * *
2046 AAATGGCTTGTTATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACATATTTATGTGAGAATT
65 AAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATT
* * * * * * * *
2111 GTTTCTCTCTAGGATCTCGGACGAACTTCCGAACTTGACAAACTTTTATGATTTGTTTTAAAACT
130 GTTTCTCTCTTGGTTCTTGGACGAACTTTCGAACTTGACAAACTTTTACGAGTTCTTTTATAACT
*
2176 TCAGTTCCTTATAGTATT-ATT
195 TCAGTTCCTTAAAGTATTCA-T
* * * * * *
2197 GACGATCCATTCCTTCAAGTAATTTT------TT-GA--CTTGGGAAATCACATTATTTGGTCTA
1 GACAATCCATTCCTTCGAGTAATTTTCAAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTA
*
2253 AAT-GTTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACATGAGAATT
66 AATAG-TTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATT
* * * * *
2317 GTTTCTTTCTTGGATCTTGGACAAACTTTCGAACTTGGCAAACTTCTACGAGTTCTTTTATAACT
130 GTTTCTCTCTTGGTTCTTGGACGAACTTTCGAACTTGACAAACTTTTACGAGTTCTTTTATAACT
2382 TCAGTTCCTTAAAGTATTCAT
195 TCAGTTCCTTAAAGTATTCAT
* * * *
2403 AACAATCCATTCCTTCGAGCT-A--CT-AAACATTCCATGCTTGGGAAATCACATCATTTGGTCT
1 GACAATCCATTCCTTCGAG-TAATTTTCAAACATTCCATGCTCGGGAAATCGCATCATTTGGTCT
* ** * * *
2464 AAAATAGTTTGTTATTTTGTAAACAACAATTAGTGTTTGAATTAAAAACTTATTTACGCGAGAAT
65 -AAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAAT
* * *
2529 TGTTCCTCTCTTTGTTCTTGGACGAACTTTCGAACTTGACAAACTTTTACGAGTTCTTCTATAAC
129 TGTTTCTCTCTTGGTTCTTGGACGAACTTTCGAACTTGACAAACTTTTACGAGTTCTTTTATAAC
* * *
2594 TT-TGATTCTTTAAAGTATTCAG
194 TTCAG-TTCCTTAAAGTATTCAT
* * * * * *
2616 GATAATTCATTCCTTTGCGTAATTTTCGGAACATTCCATGCTCGAGAAATCGCATCATTTGGTCT
1 GACAATCCATTCCTTCGAGTAATTTTC-AAACATTCCATGCTCGGGAAATCGCATCATTTGGTCT
* * * * **
2681 AAAATAGTTTTTCATTTTGTAAACAACTATTCGTCTTTGAAATAAAAACTTATTTACACGAGAAT
65 -AAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAAT
* * * * *
2746 TATTTCTCTCTTTGTTCTTGGACAAACTTTCAAACTTGACAAACTTTTACGAGTTCTTCTATAAC
129 TGTTTCTCTCTTGGTTCTTGGACGAACTTTCGAACTTGACAAACTTTTACGAGTTCTTTTATAAC
** * * * *
2811 TTTGGTCCCTTAAAATATTAAA
194 TTCAGTTCCTTAAAGTATTCAT
*** * * * * *
2833 GGTGATACATTCCTTCAAG-ATATATTTCAAAAATTTCATGCTCGGGAAATCTCATCATTTGGTC
1 GACAATCCATTCCTTCGAGTA-AT-TTTCAAACATTCCATGCTCGGGAAATCGCATCATTTGGTC
* * * * * *
2897 TAAATGGTTTATCATTATGTAAACAACTTTTGGTCTTTGAACTAAAAACTTATTTATGTGAGAAC
64 TAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAAT
* * * * * * *
2962 TATTTTTTTCTTGGTTCTTTGACAAAC-TTCTAAACTTGACAAAC---T--G-TTTCTTTTATAA
129 TGTTTCTCTCTTGGTTCTTGGACGAACTTTC-GAACTTGACAAACTTTTACGAGTTCTTTTATAA
* *
3020 CTGT-AGTTCCTGAAAGTATTCGT
193 CT-TCAGTTCCTTAAAGTATTCAT
* * * * *
3043 AACAATCCATTCCTTCGAGCT-ATTTCCCAAACATTCCATGCTCGGGAAATTGAATCATTT-TTC
1 GACAATCCATTCCTTCGAG-TAATTT-TCAAACATTCCATGCTCGGGAAATCGCATCATTTGGTC
* *
3106 TAAATAGTTTGTCATTTTCTAAACAACTTTTGGTCTTTGAATTAAAAAACTT-TTCTACGTCAGA
64 TAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATT-AAAAACTTATT-TACGTGAGA
* * * * * *
3170 GTTGTTTCTCTCTTGGATCTTGGACAAACTTTCGAACATGACAAACTTTTACAAGTTCTTCTATA
127 ATTGTTTCTCTCTTGGTTCTTGGACGAACTTTCGAACTTGACAAACTTTTACGAGTTCTTTTATA
* * *
3235 ACTTC-GATTCCTTAAAGCATTTAG
192 ACTTCAG-TTCCTTAAAGTATTCAT
** * *
3259 GACAATTAATAT-CTTCGAGCAATTTT-ATGAACATTCCATGCTCGAGAAATCGCATCATTTGGT
1 GACAATCCAT-TCCTTCGAGTAATTTTCA--AACATTCCATGCTCGGGAAATCGCATCATTTGGT
* *
3322 TTAAATAGTTTGTCATTTTCTAAACAA-TTGTTGGTCTTTGAATTAAAAACTTATTTACGTGAGA
63 CTAAATAGTTTGTCATTTTGTAAACAACTT-TTGGTCTTTGAATTAAAAACTTATTTACGTGAGA
* *
3386 GTTGTTTCTCTCTTGGTTCTTGGACGAAC-TTCTGAACTTGGC-AACTTTTACGAGTTCTTTTAT
127 ATTGTTTCTCTCTTGGTTCTTGGACGAACTTTC-GAACTTGACAAACTTTTACGAGTTCTTTTAT
*
3449 AACTTCAGTTCCTTAAAGTATTCAC
191 AACTTCAGTTCCTTAAAGTATTCAT
** * *
3474 GATGATCCATTCCTTCGATTAATTTTCAGAACATTCCATGCTCGGGAAATTGCATCATTTGGTCT
1 GACAATCCATTCCTTCGAGTAATTTTCA-AACATTCCATGCTCGGGAAATCGCATCATTTGGTCT
* * * *
3539 AAATGGTTTGTTATTTTGTAAACAACTTTTGGTCTTTGAAGTAAAAACTTAGTTACGTGAGAATT
65 AAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATT
* * * * *
3604 -TTTCTCTCTTGGATCTTGGACGAACTTTCGAACTTGGCAAACTTTTATG-GATTCTTTAAAAAC
130 GTTTCTCTCTTGGTTCTTGGACGAACTTTCGAACTTGACAAACTTTTACGAG-TTCTTTTATAAC
*
3667 TTCAGTTCCTTAAAGTATTCTT
194 TTCAGTTCCTTAAAGTATTCAT
** * * * * *
3689 GATGATCCATTCCTTCGAGCAATTTTCCAAACATTCCATGCTTGTGAAAAT-GTATTATTTGGTC
1 GACAATCCATTCCTTCGAGTAATTTT-CAAACATTCCATGCTCG-GGAAATCGCATCATTTGGTC
** * * *
3753 TAAACGGTTTATCATTTTGTAAACAACTTTTAGTCTTTGAATTAAAAACTTATTTATGTGAGAAT
64 TAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAAT
* * ** * * * * ** *
3818 TGTTTATGTCTTGGGCCTCGGACGAACTTCCGAGGCTGGA-AAACTTACACAAGTTCTTTTATAA
129 TGTTTCTCTCTTGGTTCTTGGACGAACTTTCGA-ACTTGACAAACTTTTACGAGTTCTTTTATAA
* *
3882 CTTCAGTTCCGTAAAATATTCAT
193 CTTCAGTTCCTTAAAGTATTCAT
* ** * * * * **
3905 AACAATCCATTGTTTTGAGCAATTTTCGAACATTCCATGCTCGAGAAATTACATCATTTGGTCTA
1 GACAATCCATTCCTTCGAGTAATTTTCAAACATTCCATGCTCGGGAAATCGCATCATTTGGTCT-
*
3970 AAATAGTTTGTCATTTTGTAAACAACATTTT-GTCTTTGAATTAAAAACTTATTTACGCGAGAAT
65 AAATAGTTTGTCATTTTGTAAACAAC-TTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAAT
* * * ** * *
4034 TGTTCCGCTCTTTGTTCTTGGACGAAC-TTCTGAACTTGATGAACTTTTACGACTTCTTTTAAAA
129 TGTTTCTCTCTTGGTTCTTGGACGAACTTTC-GAACTTGACAAACTTTTACGAGTTCTTTTATAA
* * *
4098 CTTCAATTCCTAAAAGAATTCAT
193 CTTCAGTTCCTTAAAGTATTCAT
* ** * **
4121 GACGATCCATTCCACCGAGAAATTTTCCAAACATTCCATGCTCGAAAAATCGCATCATTTGGTCT
1 GACAATCCATTCCTTCGAGTAATTTT-CAAACATTCCATGCTCGGGAAATCGCATCATTTGGTCT
* * ** *
4186 AAACAGTTTGTCATTTTGTAAACAACTTTTGGTTTTTGAATTAAAAACTTATTTATATGAGAGTT
65 AAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATT
** *
4251 GTTTCTCTCTTGGTTCTTGGATAAACTTTCGAACTTGACAAACTTTTATGAGTTCTTATT-TAAC
130 GTTTCTCTCTTGGTTCTTGGACGAACTTTCGAACTTGACAAACTTTTACGAGTTCTT-TTATAAC
** * *
4315 TTTGGTTCCATAAAGTATTCAA
194 TTCAGTTCCTTAAAGTATTCAT
** ** *
4337 GACAATCCATTCCATT-GAACAATTATTTGAACATTCCATGCTCGGGAAATCGCACCATTTGGTC
1 GACAATCCATTCC-TTCGAGTAATT-TTCAAACATTCCATGCTCGGGAAATCGCATCATTTGGTC
*
4401 TAAATAGTTTGTCATTTTCTAAACAACTTTTGGTCTTTGAATTAAAA
64 TAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAA
Statistics
Matches: 2064, Mismatches: 332, Indels: 142
0.81 0.13 0.06
Matches are distributed among these distances:
204 1 0.00
205 1 0.00
206 167 0.08
207 2 0.00
208 1 0.00
209 48 0.02
210 116 0.06
211 5 0.00
212 26 0.01
213 146 0.07
214 41 0.02
215 347 0.17
216 852 0.41
217 306 0.15
218 5 0.00
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.40
Consensus pattern (215 bp):
GACAATCCATTCCTTCGAGTAATTTTCAAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTA
AATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTG
TTTCTCTCTTGGTTCTTGGACGAACTTTCGAACTTGACAAACTTTTACGAGTTCTTTTATAACTT
CAGTTCCTTAAAGTATTCAT
Done.