Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010796.1 Kokia drynarioides strain JFW-HI SEQ_125763, 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: 4461
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.40
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:583 original size:219 final size:216
Alignment explanation
Indices: 9--1016 Score: 838
Period size: 216 Copynumber: 4.7 Consensus size: 216
1 AAGTACTC
* * * *
9 AAGACTATCCATTCATTTGAGCCATTTTCCAAACATTCCATGCTC-GATAAATCGCATCATTTGG
1 AAGACGATCCATTCCTTTGAGCAATTTTTCAAACATTCCATGCTCGGA-AAATCGCATCATTTGG
* * *
73 TCTAAATAGTTTTTCATTTTGTAAACAACTTTTTGTCTTTGAATTAAAAACTTATTTACGTGAGA
65 TCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACATGAGA
**** *
138 ATTGTTTCTCTCCCAATTCTTGGATGAACATCCGAACTTTTCAAAAATTTACAAGTTCTTTTATA
130 ATTGTTTCTCTCTTGGTTCTTGGATGAACATCCAAACTTTTCAAAAATTTACAAGTTCTTTTATA
* *
203 ACTTTGGTTCCTAATAGTATTT
195 ACTTTGGTTCCTAAGAGTATTA
* * * ** * * * * **
225 AAGAAGATGCATACCTTCAACCAATTTTTCGAACATTCGATTCTCGGAAAATTTCATCATTTGGT
1 AAGACGATCCATTCCTTTGAGCAATTTTTCAAACATTCCATGCTCGGAAAATCGCATCATTTGGT
* * * * * * * * *
290 CAAAATATTTTGTAATATGGTAAACAACTTTTGGTGTTTGAATTTAAAATTTATTTGCATGAGAA
66 CTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACATGAGAA
* * *
355 TAT-TTTCTCTCTTGGTTCTTGGATTAACTTTCAAACTTTT-ATAAAATTTACAAGTTCTTTTAT
131 T-TGTTTCTCTCTTGGTTCTTGGATGAACATCCAAACTTTTCA-AAAATTTACAAGTTC--TT-T
* *
418 TATAACTTTGGTTCTTGAGAGTATTA
191 TATAACTTTGGTTCCTAAGAGTATTA
* *
444 AAGACGATCCATTCCTTTGTGCAATTTTTCAAACATTCCATGCTCGGGAAATCGCATCATATT-G
1 AAGACGATCCATTCCTTTGAGCAATTTTTCAAACATTCCATGCTCGGAAAATCGCATCAT-TTGG
*
508 TCTAAATAGTTTGTCATTTTGTAAA-AACCTTTTGGTCTTTGAATTAAAAACTTCTTTACATGAG
65 TCTAAATAGTTTGTCATTTTGTAAACAA-CTTTTGGTCTTTGAATTAAAAACTTATTTACATGAG
* * ** * ** * *
572 GATTGTTTCTCTCTTGGTTCTTGGACGAAC-TTTAGAACTTGTCAAGTATTTACCATTTCTTTTA
129 AATTGTTTCTCTCTTGGTTCTTGGATGAACATCCA-AACTTTTCAAAAATTTACAAGTTCTTTTA
* * *
636 TAACTTCGGTTTCTAAGAGCATTA
193 TAACTTTGGTTCCTAAGAGTATTA
* * * * * * * * * ***
660 AAGATGACCCATTCCTTCGA-CTAACTTTTCGAGCATTCCAGGCTCGGGAAATCGCATCAATCAT
1 AAGACGATCCATTCCTTTGAGC-AATTTTTCAAACATTCCATGCTCGGAAAATCGCATCATTTGG
* * * * * *
724 TCTAAAT-GTTTTTTTAATTTTCT--A-AA------GTCTTTGAATTGAAAACTAATTTACGTGA
65 TCTAAATAG--TTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACATGA
* * * ** * ** *
779 GAATTGTTTCTCTCTTAGTTTTTGGATGAACTTCTGAACTTGTCAAACTTTTACGAGTTCTTTTA
128 GAATTGTTTCTCTCTTGGTTCTTGGATGAACATCCAAACTTTTCAAAAATTTACAAGTTCTTTTA
* *
844 TAACTTCT-GTTCCTTAA-ATTATTC
193 TAACTT-TGGTTCC-TAAGAGTATTA
* * * * * *
868 AAGCCGATCC-TATCCTTCGA-CTAGTTTTTCGAAA-ATTCAATGCTCGAAAAATCGCATTATTT
1 AAGACGATCCAT-TCCTTTGAGC-AATTTTTC-AAACATTCCATGCTCGGAAAATCGCATCATTT
* * * * *
930 GGTCTAAATAGTTTGTCATTTCGTAAACAACTTTTGCTCTTTG-ATTTAAAACTTATTTACGTGC
63 GGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACATGA
* *
994 GAACTGTTTCTCTCTTTGTTCTT
128 GAATTGTTTCTCTCTTGGTTCTT
1017 CGCTGAACTT
Statistics
Matches: 625, Mismatches: 137, Indels: 61
0.76 0.17 0.07
Matches are distributed among these distances:
207 10 0.02
208 141 0.23
209 8 0.01
210 2 0.00
215 45 0.07
216 229 0.37
217 15 0.02
218 8 0.01
219 164 0.26
220 3 0.00
ACGTcount: A:0.28, C:0.17, G:0.13, T:0.42
Consensus pattern (216 bp):
AAGACGATCCATTCCTTTGAGCAATTTTTCAAACATTCCATGCTCGGAAAATCGCATCATTTGGT
CTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACATGAGAA
TTGTTTCTCTCTTGGTTCTTGGATGAACATCCAAACTTTTCAAAAATTTACAAGTTCTTTTATAA
CTTTGGTTCCTAAGAGTATTA
Found at i:922 original size:208 final size:208
Alignment explanation
Indices: 542--924 Score: 459
Period size: 208 Copynumber: 1.8 Consensus size: 208
532 AAACCTTTTG
** * *
542 GTCTTTGAATTAAAAACTTCTTTACATGAGGATTGTTTCTCTCTTGGTTCTTGGACGAACTTTAG
1 GTCTTTGAATTAAAAACTAATTTACATGAGAATTGTTTCTCTCTTAGTTCTTGGACGAACTTTAG
* * * *
607 AACTTGTCAAGTATTTACCATTTCTTTTATAACTTCGGTTTCTAAGAGCATTAAAGATGACCCAT
66 AACTTGTCAACTATTTACCAGTTCTTTTATAACTTCGGTTCCTAAGAGCATTAAAGACGACCCAT
** * **
672 TCCTTCGACTAACTTTTCGAGCATTCCAGGCTCGGGAAATCGCATCAATCATTCTAAATGTTTTT
131 TCCTTCGACTAACTTTTCGAAAATTCAAGGCTCGAAAAATCGCATCAATCATTCTAAATGTTTTT
737 TTAATTTTCTAAA
196 TTAATTTTCTAAA
* * * *
750 GTCTTTGAATTGAAAACTAATTTACGTGAGAATTGTTTCTCTCTTAGTTTTTGGATGAACTTCT-
1 GTCTTTGAATTAAAAACTAATTTACATGAGAATTGTTTCTCTCTTAGTTCTTGGACGAACTT-TA
* * ** * * *
814 GAACTTGTCAAACT-TTTACGAGTTCTTTTATAACTTCTGTTCCTTAA-ATTATTCAAGCCGATC
65 GAACTTGTC-AACTATTTACCAGTTCTTTTATAACTTCGGTTCC-TAAGAGCATTAAAGACGACC
** *
877 C-TATCCTTCGACTAGTTTTTCGAAAATTCAATGCTCGAAAAATCGCAT
128 CAT-TCCTTCGACTAACTTTTCGAAAATTCAAGGCTCGAAAAATCGCAT
925 TATTTGGTCT
Statistics
Matches: 144, Mismatches: 27, Indels: 8
0.80 0.15 0.04
Matches are distributed among these distances:
207 1 0.01
208 136 0.94
209 7 0.05
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.40
Consensus pattern (208 bp):
GTCTTTGAATTAAAAACTAATTTACATGAGAATTGTTTCTCTCTTAGTTCTTGGACGAACTTTAG
AACTTGTCAACTATTTACCAGTTCTTTTATAACTTCGGTTCCTAAGAGCATTAAAGACGACCCAT
TCCTTCGACTAACTTTTCGAAAATTCAAGGCTCGAAAAATCGCATCAATCATTCTAAATGTTTTT
TTAATTTTCTAAA
Found at i:1238 original size:177 final size:177
Alignment explanation
Indices: 916--1255 Score: 440
Period size: 177 Copynumber: 1.9 Consensus size: 177
906 AATGCTCGAA
* *
916 AAATCGCATTATTTGGTCTAAATAGTTTGTCATTTCGTAAACAACTTTTGCTCTTTGATTTAAAA
1 AAATCGCATCATTTGGTCTAAATAGTTTGTCATTTCGTAAACAACTTTTGCTCTTTGAATTAAAA
* * * * *
981 CTTATTTACGTGCGAACTGTTTCTCTCTTTGTTCTTCGCTGAACTTTCGAACTTGTCAAGCTTTT
66 CATATTTACATGCGAACTGTTTCTCTCTTGGTTCTTCGCTGAACTTTCAAACTTGTCAAACTTTT
* *
1046 ATGAGTTCTTTTATAACCTCAGTTCCTTAAACTTATTTACGCTTGGG
131 ATCAGTTCCTTTATAACCTCAGTTCCTTAAACTTATTTACGCTTGGG
* * *
1093 AAATCGCATCGTTTGGTCTAAATAGTTTTTCATTTTGTAATA-AACTTTT-CATCTTTGAATTAA
1 AAATCGCATCATTTGGTCTAAATAGTTTGTCATTTCGTAA-ACAACTTTTGC-TCTTTGAATTAA
* *
1156 AA-ATATTTACATGAC-AATTGTTTCTCTCTTGGTTCTTGGAC-GAAC-TTCTAAACTTGTCAAA
64 AACATATTTACATG-CGAACTGTTTCTCTCTTGGTTCTTCG-CTGAACTTTC-AAACTTGTCAAA
* *
1217 CTTTTTATCAGTTCCTTTATAACTTCGGTTCCTTAAACT
126 C-TTTTATCAGTTCCTTTATAACCTCAGTTCCTTAAACT
1256 ATTAAAGGTG
Statistics
Matches: 141, Mismatches: 16, Indels: 12
0.83 0.09 0.07
Matches are distributed among these distances:
175 3 0.02
176 46 0.33
177 91 0.65
178 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.13, T:0.44
Consensus pattern (177 bp):
AAATCGCATCATTTGGTCTAAATAGTTTGTCATTTCGTAAACAACTTTTGCTCTTTGAATTAAAA
CATATTTACATGCGAACTGTTTCTCTCTTGGTTCTTCGCTGAACTTTCAAACTTGTCAAACTTTT
ATCAGTTCCTTTATAACCTCAGTTCCTTAAACTTATTTACGCTTGGG
Found at i:1662 original size:608 final size:599
Alignment explanation
Indices: 489--1670 Score: 1310
Period size: 608 Copynumber: 2.0 Consensus size: 599
479 TTCCATGCTC
**
489 GGGAAATCGCATCATATTGTCTAAATAGTTTGTCATTTTGTAAAAACCTTTTGGTCTTTGAATTA
1 GGGAAATCGCATCATATTGTCTAAATAGTTTGTCATTTTGTAAAAACCTTTTCATCTTTGAATTA
* ** *
554 AAAACTTCTTTACATGAGGATTGTTTCTCTCTTGGTTCTTGGACGAACTTTAGAACTTGTCAAGT
66 AAAAC-TATTTACATGACAATTGTTTCTCTCTTGGTTCTTGGACGAACTTTAGAACTTGTCAACT
* * *
619 ATTTACCATTTCTTTTATAACTTCGGTTTCTAAGAGCATTAAAGATGACCCATTCCTTCGACTAA
130 ATTTACCAGTTCCTTTATAACTTCGGTTCCTAAGAGCATTAAAGATGACCCATTCCTTCGACTAA
* * *
684 CTTTTCGAGCATTCCAGGCTCGGGAAATCGCATCAATCATTCTAAATGTTTTTTTAATTTTCTAA
195 CTTTTCAAGCATTCCAGGCTCGAGAAATCGCATCAATCAGTCTAAATGTTTTTTTAATTTTCT-A
* *
749 AGTCTTTGAATTGAAAACTAATTTACGTGAGAATTGTTTCTCTCTTAGTTTTTGGATGAACTTCT
259 AGTCTTTGAATTAAAAACTAATTTACGTGAGAATTGTTTCTCTCATAGTTTTTGGATGAACTTCT
* * * * ** * * *
814 GAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCTGTTCCTTAAATTATTCAAGCCGATCCT
324 GAACTAGTCAAACATTTAAGAGCTCTTTTATAACTTAAGTTCCTGAAAGTATTCAAGACGATCCT
* * * * * *
879 ATCCTTCGACTAGTTTTTCGAAAATTCAATGCTCGAAAAATCGCATTATTTGGTCTAAATAGTTT
389 ATCCTTCGACCAATTTTTCGAAAATTCAATGCTCGAAAAATCGCATCATTCGGTCTAAAAACTTT
* * * *
944 GTCATTTCGTAAACAACTTTTGCTCTTTGATTTAAAACTTATTTACGTGCGAACTGTTTCTCTCT
454 GTCATTTCGTAAACAACTTTTGCTCTTCGATTAAAAACCTATTTACGTGAGAACTGTTTCTCTCT
* * * *
1009 TTGTTCTTCGCTGAACTTTCGAACTTGTCAAGCTTTTATGAGTTCTTTTATAACCTCAGTTCCTT
519 TGGTTCTACGCTGAACTTACGAACTTGTCAAGCTTTTACGAGTTCTTTTATAACCTCAGTTCCTT
1074 AAACTTATTTACGCTT
584 AAACTTATTTACGCTT
* *
1090 GGGAAATCGCATCGT-TTGGTCTAAATAGTTTTTCATTTTGTAATAAA-CTTTTCATCTTTGAAT
1 GGGAAATCGCATCATATT-GTCTAAATAGTTTGTCATTTTGTAA-AAACCTTTTCATCTTTGAAT
1153 TAAAAA-TATTTACATGACAATTGTTTCTCTCTTGGTTCTTGGACGAACTTCTA-AACTTGTCAA
64 TAAAAACTATTTACATGACAATTGTTTCTCTCTTGGTTCTTGGACGAACTT-TAGAACTTGTC-A
* * * * *
1216 ACTTTTTATCAGTTCCTTTATAACTTCGGTTCCTTAA-A-CTATTAAAGGTGATCCATTCCTTTG
127 ACTATTTACCAGTTCCTTTATAACTTCGGTTCC-TAAGAGC-ATTAAAGATGACCCATTCCTTCG
* * * **
1279 TGC-AA-TTTCTCAAGCATTCCATGCTCGAGAAAT-GACATCATTTGGTCTAAATAGGTTATCAT
190 -ACTAACTTT-TCAAGCATTCCAGGCTCGAGAAATCG-CATCAATCAGTCTAAAT--G-T-T--T
* * *
1341 TTTCTAAACAATTTT-T-GGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCATG
246 TTT-T----AATTTTCTAAGTCTTTGAATTAAAAACTAATTTACGTGAGAATTGTTTCTCTCATA
* * * * *
1404 GTTTTT-GTTCGAACTTCTGTACTAG-CGGAACATTTAATAGCTCTTTTGTAACTTAAGTTCCTG
306 GTTTTTGGAT-GAACTTCTGAACTAGTC-AAACATTTAAGAGCTCTTTTATAACTTAAGTTCCTG
* * * * **
1467 AGAGTATTCAAGACGATCC-ATTCCTTTGACCAATTTTTC-AAACTTTCCATGCTCG-GGAATCG
369 AAAGTATTCAAGACGATCCTA-TCCTTCGACCAATTTTTCGAAA-ATTCAATGCTCGAAAAATCG
* *
1529 TATCATTCGGTCTAAAAACTTTGTCATTAT-GTAAGCAACTTTTAG-TCTTCGAATTAAAAACCT
432 CATCATTCGGTCTAAAAACTTTGTCATT-TCGTAAACAACTTTT-GCTCTTCG-ATTAAAAACCT
* *
1592 ATTTACGTGAGAATTGTTTCTCT-TGTGGTTCTAGGAC-GAACTTACGAAC-TGATCGAA-CTTT
494 ATTTACGTGAGAACTGTTTCTCTCT-TGGTTCTACG-CTGAACTTACGAACTTG-TC-AAGCTTT
1653 TACGAGTTCTTTTATAAC
555 TACGAGTTCTTTTATAAC
1671 TTTGGTTCCT
Statistics
Matches: 483, Mismatches: 67, Indels: 55
0.80 0.11 0.09
Matches are distributed among these distances:
599 54 0.11
600 89 0.18
601 62 0.13
602 4 0.01
603 1 0.00
604 1 0.00
606 4 0.01
607 56 0.12
608 202 0.42
609 3 0.01
610 1 0.00
611 6 0.01
ACGTcount: A:0.27, C:0.18, G:0.14, T:0.41
Consensus pattern (599 bp):
GGGAAATCGCATCATATTGTCTAAATAGTTTGTCATTTTGTAAAAACCTTTTCATCTTTGAATTA
AAAACTATTTACATGACAATTGTTTCTCTCTTGGTTCTTGGACGAACTTTAGAACTTGTCAACTA
TTTACCAGTTCCTTTATAACTTCGGTTCCTAAGAGCATTAAAGATGACCCATTCCTTCGACTAAC
TTTTCAAGCATTCCAGGCTCGAGAAATCGCATCAATCAGTCTAAATGTTTTTTTAATTTTCTAAG
TCTTTGAATTAAAAACTAATTTACGTGAGAATTGTTTCTCTCATAGTTTTTGGATGAACTTCTGA
ACTAGTCAAACATTTAAGAGCTCTTTTATAACTTAAGTTCCTGAAAGTATTCAAGACGATCCTAT
CCTTCGACCAATTTTTCGAAAATTCAATGCTCGAAAAATCGCATCATTCGGTCTAAAAACTTTGT
CATTTCGTAAACAACTTTTGCTCTTCGATTAAAAACCTATTTACGTGAGAACTGTTTCTCTCTTG
GTTCTACGCTGAACTTACGAACTTGTCAAGCTTTTACGAGTTCTTTTATAACCTCAGTTCCTTAA
ACTTATTTACGCTT
Found at i:2110 original size:216 final size:213
Alignment explanation
Indices: 1093--3834 Score: 2194
Period size: 216 Copynumber: 12.7 Consensus size: 213
1083 TACGCTTGGG
* * **
1093 AAATCGCATCGTTTGGTCTAAATAGTTTTTCATTTTGTAATA-AACTTTTCATCTTTGAATTAAA
1 AAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAA-ACAACTTTTGGTCTTTGAATTAAA
* * *
1157 AA--TATTTACATGACAATTGTTTCTCTCTTGGTTCTTGGACGAACTT-CTAAACTTGTCAAACT
65 AACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTAC-GAACTTGTCAAAC-
* * * * * * *
1219 TTTTATC-AGTTCCTTTATAACTTCGGTTCCTTAAACTATTAAAG-GTGATCCATTCCTTTGTGC
128 TTTTA-CGAGTTCTTTTATAACTTTGGTTCCTCAAAGTATTCAAGACT-ATCCATTCCTTTG-AC
* * *
1282 AATTTCTCAAGCATTCCATGCTCGA
190 CATTTTTGAA-CATTCCATGCTCGA
* * * *
1307 GAAAT-GACATCATTTGGTCTAAATAGGTTATCATTTTCTAAACAATTTTTGGTCTTTGAATTAA
1 -AAATCG-CATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAA
* * ** * * *
1371 AAACTTATTTACGTGAGAATTGTTTCTCTCATGGTTTTTGTTCGAACTT-CTGTACTAG-CGGAA
64 AAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTAC-GAACTTGTC-AAA
* ** * * ** * * *
1434 CATTTAATAGCTCTTTTGTAACTTAAGTTCCTGAGAGTATTCAAGACGATCCATTCCTTTGACCA
127 CTTTTACGAGTTCTTTTATAACTTTGGTTCCTCAAAGTATTCAAGACTATCCATTCCTTTGACC-
* * *
1499 ATTTTTCAAACTTTCCATGCTCGG
191 ATTTTT-GAACATTCCATGCTCGA
* * * * * * * * *
1523 GAATCGTATCATTCGGTCTAAAAACTTTGTCATTATGTAAGCAACTTTTAGTCTTCGAATTAAAA
1 AAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAA
* * *
1588 ACCTATTTACGTGAGAATTGTTTCTCT-TGTGGTTCTAGGACGAACTTACGAAC-TGATCGAACT
66 ACTTATTTACGTGAGAATTGTTTCTCTCT-TGGTTCTTGGACGAACTTACGAACTTG-TCAAACT
* * *
1651 TTTACGAGTTCTTTTATAACTTTGGTTCCTGAAAGTATTCAAGACTATCCATTCCTTCGACAAAT
129 TTTACGAGTTCTTTTATAACTTTGGTTCCTCAAAGTATTCAAGACTATCCATTCCTTTGAC-CA-
* *
1716 TTTTTGAACTTTTCATGCTCCGA
192 TTTTTGAACATTCCATGCT-CGA
* * * ** * * * *
1739 AAATCGCATCATTCGATCTAAAAACATTGTCATTATGTAAACAACATTTAGTCTTCGAATTCAAA
1 AAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATT-AAA
* * * * * *
1804 AACCTATTTACGTGAGAATTGCTTCTCT-TGTGGTTATCGGACGAACTTACGAACTAGTCGAACT
65 AACTTATTTACGTGAGAATTGTTTCTCTCT-TGGTTCTTGGACGAACTTACGAACTTGTCAAACT
*
1868 TTTACGAGTTCTTTTATAATTTTGGTTCCTCAAAGTATTCAAGACTATCCATTCCTTTGAGCCAT
129 TTTACGAGTTCTTTTATAACTTTGGTTCCTCAAAGTATTCAAGACTATCCATTCCTTTGA-CCAT
*
1933 TTCTTGAATATTCCATGCTCCGA
193 TT-TTGAACATTCCATGCT-CGA
* * * * *
1956 AAATCGTATCTTTTGGTCTAAATAGTTTGTGATTTTGTAAACAAATTTTGGTCTTTAAATTAAAA
1 AAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAA
** *
2021 ACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTCAGACGAACTTACGAACTAGTCAAACTTT
66 ACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTACGAACTTGTCAAACTTT
* * * *
2086 TACGAGTTCTTTTACAACTTTGGTTCCTTAAAGTATTAAAGACTATCCATTCATTTGAGCCATTT
131 TACGAGTTCTTTTATAACTTTGGTTCCTCAAAGTATTCAAGACTATCCATTCCTTTGA-CCATTT
**
2151 TCCAAACATTCCATGCTCGA
195 T-TGAACATTCCATGCTCGA
* * * * * * * * *
2171 GAAATCGCATCATTCGGTCTAAAAACTTTGTCATTATGTTACCAACATTTAGTCTTCGAATTAAA
1 -AAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAA
* * * * *
2236 AACCTATTTACGTGAGAATTATTTCTCT-TGTGGTTCTAGGATGAACTTACGAACTGGTCGAAA-
65 AACTTATTTACGTGAGAATTGTTTCTCTCT-TGGTTCTTGGACGAACTTACGAACTTGTC-AAAC
* *
2299 TTTTATGAGTTCTTTTATAACTTTGGTTCCTCAAAGTATTCAAGACTATCCATTCCTTCGACCAA
128 TTTTACGAGTTCTTTTATAACTTTGGTTCCTCAAAGTATTCAAGACTATCCATTCCTTTGACC-A
* * **
2364 TTTTTCGAACTTTTCATG--CNN
192 TTTTT-GAACATTCCATGCTCGA
************************************************ * *
2385 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTAGTCTTCGAATTAAAA
1 AAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAA
* * * * * *
2450 ACCTATTTACGTGAGAATTATTTCTCT-TGTGGTTCTAGGACGAACTTACTAACTGGTCGAACTT
66 ACTTATTTACGTGAGAATTGTTTCTCTCT-TGGTTCTTGGACGAACTTACGAACTTGTCAAACTT
** *
2514 TTATTAGTTCTTTTATAACTTTGGTTCCTCAAAGTATTCAAGACTATCCATTCCTTCGACCAATT
130 TTACGAGTTCTTTTATAACTTTGGTTCCTCAAAGTATTCAAGACTATCCATTCCTTTGACC-ATT
*
2579 TTTCGAACATTTCATGCTCCGA
194 TTT-GAACATTCCATGCT-CGA
* * * * * *
2601 AAATCGCATCATTTGGTCTAAAAACTTTGTCATTATGTAAACAACATTTAGTCTTCGAATTCAAA
1 AAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATT-AAA
* * * * * *
2666 AACCTATTTACGTGATAATTGTTTCTCT-TGTGGTTCTCGGATGAACTTACGAACTAGTCGAACT
65 AACTTATTTACGTGAGAATTGTTTCTCTCT-TGGTTCTTGGACGAACTTACGAACTTGTCAAACT
* *
2730 TTTACGAGTTCTTTTATAACTTTGGTTCCTCAAAGTACTCAAGACTATCCATTCATTTGAGCCAT
129 TTTACGAGTTCTTTTATAACTTTGGTTCCTCAAAGTATTCAAGACTATCCATTCCTTTGA-CCAT
2795 TTTTCGAACATTCCATGCTCGA
193 TTTT-GAACATTCCATGCTCGA
*
2817 TAAATCACATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAA
1 -AAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAA
* *** * * **
2882 AATTTATTTACGTGAGAATTGTTTCTCTCCCAGTTCTTGGATGAACTT-CAGAACTTTTCAAAAA
65 AACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTAC-GAACTTGTCAAACT
* * ** * **
2946 TTTACAAGTTCTTTTATAACTTTGGTTCCT-AATAGTATTTAAGAAGATGCATTCCTTCAACCAA
129 TTTACGAGTTCTTTTATAACTTTGGTTCCTCAA-AGTATTCAAGACTATCCATTCCTTTGACC-A
* *
3010 TTTTTATAACATTCCATTCTCGAA
192 TTTTT-GAACATTCCATGCTCG-A
* * * * * * * *
3034 AAATTGCATCATTTGGCCAAAATAGTTTGTAATATAGTAAACAACTTTTGGTGTTTGAATTTAAA
1 AAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAA
* * * ** * * * * **
3099 ATTTATTTGCATGAGAATAT-TTTCTCTCTTGGTTCTTGGATTAACTTTCAAACTTTTAAAAAAT
66 ACTTATTTACGTGAGAAT-TGTTTCTCTCTTGGTTCTTGGACGAACTTACGAACTTGTCAAACTT
* * * * * * * *
3163 TTACAAGTTCTTTTATTATAACTTTGGTTCTTGAGAGTATTAAAGACGATCCATTCCTTTGTGCA
130 TTACGAGTTC--TT-TTATAACTTTGGTTCCTCAAAGTATTCAAGACTATCCATTCCTTTG-ACC
** *
3228 ATTTTCAAACATTCCATGCTCGGG
191 ATTTTTGAACATTCCATGCTC-GA
*
3252 AAATCGTATCATTTGGTCTAAATAGTTTGTCATTTTGTAAA-AACCTTTTGGTCTTTGAATTAAA
1 AAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAA-CTTTTGGTCTTTGAATTAAA
*
3316 AACTTATTTACGTGAGGATTGTTTCTCTCTTGGTTCTTGGACGAACTTTA-GAACTTGTCAAA-T
65 AACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAAC-TTACGAACTTGTCAAACT
* * * * * * * * * *
3379 ATTTACCAGTTCTTTTATAACTTCGGTTTCTGAGAGCATTAAAGA-TGACCCATTCCTTCGACTA
129 -TTTACGAGTTCTTTTATAACTTTGGTTCCTCAAAGTATTCAAGACT-ATCCATTCCTTTGAC-C
* * * *
3443 ACTTTTCGAGCATTCCAGGCTCGGG
191 A-TTTTTGAACATTCCATGCTC-GA
* *** * * *
3468 AAATCGCATAATTCATTCTAAAT-GTTTTTTTAATTTTCTAAACAACTTTTGGTCTTTGAATTAA
1 AAATCGCATCATTTGGTCTAAATAG--TTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAA
* * * * ** *
3532 AAACTAATTTACGTGAGAATAGTATCTCTCTTGGTTTTTGGATTAACTT-CTGAACTTGTGAAAC
64 AAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTAC-GAACTTGTCAAAC
* * * * * * *
3596 TTTTACGAGTTCTTTTAAAACTTCGGTTCCTTAAATTATTCAAGCCGATCC-TATCCTTCGACCA
128 TTTTACGAGTTCTTTTATAACTTTGGTTCCTCAAAGTATTCAAGACTATCCAT-TCCTTTGACC-
*
3660 ATTTTTCGAACATTCAATGCTCGAA
191 ATTTTT-GAACATTCCATGCTCG-A
* * * *
3685 AAATCGCATTATTTGGTCTAAATAGTTTGTCATTTCGTAAACAGCTTTTGCTCTTTGAATTAAAA
1 AAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAA
** * *
3750 ACTTATTTACGTGAGAATTGTTTCTCTCTTTATTCTTGG-CTGAACTTTCGAACTTGTCAAGCTT
66 ACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGAC-GAACTTACGAACTTGTCAAACTT
*
3814 TTATGAGTTCTTTTATAACTT
130 TTACGAGTTCTTTTATAACTT
3835 CAGTTCCTTA
Statistics
Matches: 2048, Mismatches: 410, Indels: 137
0.79 0.16 0.05
Matches are distributed among these distances:
212 2 0.00
213 154 0.08
214 5 0.00
215 271 0.13
216 842 0.41
217 595 0.29
218 132 0.06
219 45 0.02
220 2 0.00
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.39
Consensus pattern (213 bp):
AAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAA
ACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTACGAACTTGTCAAACTTT
TACGAGTTCTTTTATAACTTTGGTTCCTCAAAGTATTCAAGACTATCCATTCCTTTGACCATTTT
TGAACATTCCATGCTCGA
Found at i:4460 original size:215 final size:211
Alignment explanation
Indices: 3877--4461 Score: 518
Period size: 215 Copynumber: 2.7 Consensus size: 211
3867 CGCATCGTTT
* * * * * *
3877 GGTCTAAATAGTTTTTCATTTTGTAATCAACTTTTCGTCTTTGAATTAAAAA-TATTTACATGAC
1 GGTCTAAATAGATTATCATTTTGTAAACAACTTTTAGTCTTTGAATTAAAAACTATTTACGTGAG
* * * *
3941 AATTGTTTCTCTCTTGGTTCTTGGACGAACTTCTAAACTTTTCAAACTTTTTATCAGTTCCTTTA
66 AATTGTTTCTCT-TTGGTTCTTGGACGAACTTC-GAAC-TATCGAAC-TTTTA-CAGTTCTTTTA
* * * * *** *** *
4006 TAACTTCGGTTCCTTAAACTATTAAAGGTTATCATTTCCTTTGTGTAATTTTTCAAGCTTTCCAT
126 TAACTTAGGTTCCTCAAAGTATTCAAGACGATCATTTCCTTTGACCAATTTTTCAAACTTTCCAT
*
4071 GCTCGAGAAATGACATCATTT
191 GCTCGAGAAATGACATCATTC
* * * *
4092 GGTCTAAATAGGTTATCATTTTCTAAACAATTTTTGGTCTTTGAATTAAAAACTTATTTACGTGA
1 GGTCTAAATAGATTATCATTTTGTAAACAACTTTTAGTCTTTGAATTAAAAAC-TATTTACGTGA
* * * ** * * * *
4157 GAATTGTTTCACTCATGGTTTTTGTTCGAACTTCCGTACTAGCGGAA-TATTTAATAGCTCTTTT
65 GAATTGTTTCTCT-TTGGTTCTTGGACGAACTT-CGAACTATC-GAACT-TTT-ACAGTTCTTTT
* * * *
4221 GTAACTTAAGTTCCTGAGAGTATTCAAGACGATCCA-TTCCTTTGACCAATTTTTCAAACTTTCC
125 ATAACTTAGGTTCCTCAAAGTATTCAAGACGAT-CATTTCCTTTGACCAATTTTTCAAACTTTCC
* *
4285 ATGCTCG-GGAATCG-TATCATTC
189 ATGCTCGAGAAAT-GACATCATTC
* * *
4307 GGTCTAAA-A-ATTATGTCATTATGTAAACAACATTTAGTCTTCGAATTAAAAACCTATTTACGT
1 GGTCTAAATAGATTA--TCATTTTGTAAACAACTTTTAGTCTTTGAATTAAAAA-CTATTTACGT
* *
4370 GAGAATTATTTCTCTTGTGGTTCTAGGACGAACTTACGAACTGATCGAACTTTTACGAGTTCTTT
63 GAGAATTGTTTCTCTT-TGGTTCTTGGACGAACTT-CGAACT-ATCGAACTTTTAC-AGTTCTTT
*
4435 TATAACTTTGGTTCCTCAAAGTATTCA
124 TATAACTTAGGTTCCTCAAAGTATTCA
Statistics
Matches: 293, Mismatches: 62, Indels: 30
0.76 0.16 0.08
Matches are distributed among these distances:
213 3 0.01
214 2 0.01
215 172 0.59
216 71 0.24
217 44 0.15
218 1 0.00
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.41
Consensus pattern (211 bp):
GGTCTAAATAGATTATCATTTTGTAAACAACTTTTAGTCTTTGAATTAAAAACTATTTACGTGAG
AATTGTTTCTCTTTGGTTCTTGGACGAACTTCGAACTATCGAACTTTTACAGTTCTTTTATAACT
TAGGTTCCTCAAAGTATTCAAGACGATCATTTCCTTTGACCAATTTTTCAAACTTTCCATGCTCG
AGAAATGACATCATTC
Done.