Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010122.1 Kokia drynarioides strain JFW-HI SEQ_124915, 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: 13309
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.38
Warning! 234 characters in sequence are not A, C, G, or T
Found at i:1017 original size:192 final size:192
Alignment explanation
Indices: 685--1038 Score: 566
Period size: 192 Copynumber: 1.8 Consensus size: 192
675 ATAACTTCGG
* * * * *
685 TTCCTGATAGTAGTCAAGACGATCCATTCCTTCGACCAATTTTTTGAACATTCCATGCTTGGGAA
1 TTCCAGATAGTAGTCAGGATGATCCATTCCTTCGACCAATTTTTTGAACATTCCATGCTCGAGAA
*
750 ATCGCATCATTTGGTCTAAAAAGTTTGTCATTTTATAAACAACATTTAGTCTTTGAATTAAAAAC
66 ATCGCATCATTTGGTCTAAAACGTTTGTCATTTTATAAACAACATTTAGTCTTTGAATTAAAAAC
*
815 TTTATTACGTGAGAATTATTTCTCTCTCGGTTGTTGGATAAAGTGCCAAACTTGTCAAACGT
131 TTTATTACGTGAGAATTATTTCTCTCTCGGTTGTTGGATAAAGTGCCGAACTTGTCAAACGT
*
877 TTCCAGATAGTAGTCAGGATGATCCATTCCTTTGACCAATTTTTTGAACATTCCATGCTCGAGAA
1 TTCCAGATAGTAGTCAGGATGATCCATTCCTTCGACCAATTTTTTGAACATTCCATGCTCGAGAA
* * *
942 ATCGCATCATTTGGTCTAAAACGTTTGTCATTTTGTAAA-AAGCTTTTGGTCTTTGAATTAAAAA
66 ATCGCATCATTTGGTCTAAAACGTTTGTCATTTTATAAACAA-CATTTAGTCTTTGAATTAAAAA
* * *
1006 CTTTTTTACGTGAGAATTGTTTCTCTCTTGGTT
130 CTTTATTACGTGAGAATTATTTCTCTCTCGGTT
1039 CTTAGATGAA
Statistics
Matches: 148, Mismatches: 13, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
191 2 0.01
192 146 0.99
ACGTcount: A:0.28, C:0.17, G:0.16, T:0.39
Consensus pattern (192 bp):
TTCCAGATAGTAGTCAGGATGATCCATTCCTTCGACCAATTTTTTGAACATTCCATGCTCGAGAA
ATCGCATCATTTGGTCTAAAACGTTTGTCATTTTATAAACAACATTTAGTCTTTGAATTAAAAAC
TTTATTACGTGAGAATTATTTCTCTCTCGGTTGTTGGATAAAGTGCCGAACTTGTCAAACGT
Found at i:1275 original size:216 final size:216
Alignment explanation
Indices: 882--1280 Score: 620
Period size: 216 Copynumber: 1.8 Consensus size: 216
872 AACGTTTCCA
* *
882 GATAGTAGTCAGGATGATCCATTCCTTTGACCAATTTTTTGAACATTCCATGCTCGAGAAATCGC
1 GATAGTAGTCAAGACGATCCATTCCTTTGACCAATTTTTTGAACATTCCATGCTCGAGAAATCGC
* * * * *
947 ATCATTTGGTCTAAAACGTTTGTCATTTTGTAAAAAGCTTTTGGTCTTTGAATTAAAAACTTTTT
66 ATCATTTGGTCTAAAAAGTTTGTCATTTTATAAAAAGCATTTAGTCTTTGAATTAAAAACTTTAT
* * * **
1012 TACGTGAGAATTGTTTCTCTCTTGGTTCTTAGATGAAGTTTCGAACTTATCAAGCATTTACTAAA
131 TACGTGAGAATTATTTCTCTCTCGGTTCTTAGATAAAGTGCCGAACTTATCAAGCATTTACTAAA
1077 TCTTTTATAACTTCGGTTCTT
196 TCTTTTATAACTTCGGTTCTT
* *
1098 GATAGTAGTCAAGACGATCCATTCCTTTGACCAATTTTTTGAACATTCCATGCTTGGGAAATCGC
1 GATAGTAGTCAAGACGATCCATTCCTTTGACCAATTTTTTGAACATTCCATGCTCGAGAAATCGC
*
1163 ATCATTTGGTCTAAAAAGTTTGTCATTTTATAAACAA-CATTTATTCTTTGAATTAAAAACTTTA
66 ATCATTTGGTCTAAAAAGTTTGTCATTTTATAAA-AAGCATTTAGTCTTTGAATTAAAAACTTTA
* * *
1227 TTACGTGAGAATTATTTCTCTCTCGGTTGTTGGATAAAGTGCCGAACTTGTCAA
130 TTACGTGAGAATTATTTCTCTCTCGGTTCTTAGATAAAGTGCCGAACTTATCAA
1281 ACGTTTCCAG
Statistics
Matches: 164, Mismatches: 18, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
216 162 0.99
217 2 0.01
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.40
Consensus pattern (216 bp):
GATAGTAGTCAAGACGATCCATTCCTTTGACCAATTTTTTGAACATTCCATGCTCGAGAAATCGC
ATCATTTGGTCTAAAAAGTTTGTCATTTTATAAAAAGCATTTAGTCTTTGAATTAAAAACTTTAT
TACGTGAGAATTATTTCTCTCTCGGTTCTTAGATAAAGTGCCGAACTTATCAAGCATTTACTAAA
TCTTTTATAACTTCGGTTCTT
Found at i:1294 original size:408 final size:408
Alignment explanation
Indices: 539--2085 Score: 2515
Period size: 407 Copynumber: 3.7 Consensus size: 408
529 NNNNNNNNNN
539 ATCATTTGGTCTAAAACGTTTGTCATTTTGTAAAAAGCTTTTGGTCTTTGAATTAAAAACTTTTT
1 ATCATTTGGTCTAAAACGTTTGTCATTTTGTAAAAAGCTTTTGGTCTTTGAATTAAAAACTTTTT
* * * * *
604 TACGTGAGAATTGTTTCTCTCTAGGTTCTTGGATGAAGTTCCGAACTTGTCAAGCATTTACTGAA
66 TACGTGAGAATTGTTTCTCTCTTGGTTCTTAGATGAAGTTTCGAACTTATCAAGCATTTACTAAA
* *
669 TCATTTATAACTTCGGTTCCTGATAGTAGTCAAGACGATCCATTCCTTCGACCAATTTTTTGAAC
131 TCTTTTATAACTTCGGTTCCTGATAGTAGTCAAGACGATCCATTCCTTCAACCAATTTTTTGAAC
734 ATTCCATGCTTGGGAAATCGCATCATTTGGTCTAAAAAGTTTGTCATTTTATAAACAACATTTAG
196 ATTCCATGCTTGGGAAATCGCATCATTTGGTCTAAAAAGTTTGTCATTTTATAAACAACATTTAG
*
799 TCTTTGAATTAAAAACTTTATTACGTGAGAATTATTTCTCTCTCGGTTGTTGGATAAAGTGCCAA
261 TCTTTGAATTAAAAACTTTATTACGTGAGAATTATTTCTCTCTCGGTTGTTGGATAAAGTGCCGA
864 ACTTGTCAAACGTTTCCAGATAGTAGTCAGGATGATCCATTCCTTTGACCAATTTTTTGAACATT
326 ACTTGTCAAACGTTTCCAGATAGTAGTCAGGATGATCCATTCCTTTGACCAATTTTTTGAACATT
929 CCATGCTCGAGAAATCGC
391 CCATGCTCGAGAAATCGC
947 ATCATTTGGTCTAAAACGTTTGTCATTTTGTAAAAAGCTTTTGGTCTTTGAATTAAAAACTTTTT
1 ATCATTTGGTCTAAAACGTTTGTCATTTTGTAAAAAGCTTTTGGTCTTTGAATTAAAAACTTTTT
1012 TACGTGAGAATTGTTTCTCTCTTGGTTCTTAGATGAAGTTTCGAACTTATCAAGCATTTACTAAA
66 TACGTGAGAATTGTTTCTCTCTTGGTTCTTAGATGAAGTTTCGAACTTATCAAGCATTTACTAAA
* **
1077 TCTTTTATAACTTCGGTTCTTGATAGTAGTCAAGACGATCCATTCCTTTGACCAATTTTTTGAAC
131 TCTTTTATAACTTCGGTTCCTGATAGTAGTCAAGACGATCCATTCCTTCAACCAATTTTTTGAAC
*
1142 ATTCCATGCTTGGGAAATCGCATCATTTGGTCTAAAAAGTTTGTCATTTTATAAACAACATTTAT
196 ATTCCATGCTTGGGAAATCGCATCATTTGGTCTAAAAAGTTTGTCATTTTATAAACAACATTTAG
1207 TCTTTGAATTAAAAACTTTATTACGTGAGAATTATTTCTCTCTCGGTTGTTGGATAAAGTGCCGA
261 TCTTTGAATTAAAAACTTTATTACGTGAGAATTATTTCTCTCTCGGTTGTTGGATAAAGTGCCGA
*
1272 ACTTGTCAAACGTTTCCAGATAGTAGTCAGGATGATCC-TTCCTTTGACAAATTTTTTGAACATT
326 ACTTGTCAAACGTTTCCAGATAGTAGTCAGGATGATCCATTCCTTTGACCAATTTTTTGAACATT
1336 CCATGCTC-AGGAAATCGC
391 CCATGCTCGA-GAAATCGC
1354 ATCATTTGGTCTAAAACGTTTGTCATTTTGTAAAAAGCTTTTGGTCTTTGAATTAAAAACTTTTT
1 ATCATTTGGTCTAAAACGTTTGTCATTTTGTAAAAAGCTTTTGGTCTTTGAATTAAAAACTTTTT
1419 TACGTGAGAATTGTTTCTCTCTTGGTTCTTAGATGAAGTTTCGAACTTATCAAGCATTTACTAAA
66 TACGTGAGAATTGTTTCTCTCTTGGTTCTTAGATGAAGTTTCGAACTTATCAAGCATTTACTAAA
* *
1484 TCTTTTATAACTTCGATTCTTGATAGTAGTCAAGACGATCCATTCCTTCAACCAATTTTTTGAAC
131 TCTTTTATAACTTCGGTTCCTGATAGTAGTCAAGACGATCCATTCCTTCAACCAATTTTTTGAAC
*
1549 ATTCCATGCTTGGGAAATCGCATTATTTGGTCTAAAAAGTTTGTCATTTTATAAACAACATTTAG
196 ATTCCATGCTTGGGAAATCGCATCATTTGGTCTAAAAAGTTTGTCATTTTATAAACAACATTTAG
1614 TCTTTGAATTAAAAACTTTATTACGTGAGAATTATTTCTCTCTCGGTTGTTGGATAAAGTGCCGA
261 TCTTTGAATTAAAAACTTTATTACGTGAGAATTATTTCTCTCTCGGTTGTTGGATAAAGTGCCGA
*
1679 ACTTGTCAAACGTTTCCTAGTTCTTTTATAACTTACGTTCCAGATAGTAGTCAAGATGATCCATT
326 ACTTGTCAAA------C--G-------------T---TTCCAGATAGTAGTCAGGATGATCCATT
*
1744 CCTTTGACCAATTTTTTGAACATTCCATGCTCGGGAAATCGC
367 CCTTTGACCAATTTTTTGAACATTCCATGCTCGAGAAATCGC
*
1786 ATCATTTGGTCTAAAACGTTTGTCATTTTGTAAAAAGCTTTTAGTCTTTGAATTAAAAACTTTTT
1 ATCATTTGGTCTAAAACGTTTGTCATTTTGTAAAAAGCTTTTGGTCTTTGAATTAAAAACTTTTT
* *
1851 TACGTGAGAATTGTTTCTCTCTTGGTTCTTGGATGAAG-TTCTGAACTTGTCAAGCATTTACTAA
66 TACGTGAGAATTGTTTCTCTCTTGGTTCTTAGATGAAGTTTC-GAACTTATCAAGCATTTACTAA
* *
1915 ATCTTTTATAACTTCGGTTCCTGATAGTAGTCAAGACGATCCATTTCTTCAACCAATTTTTCGAA
130 ATCTTTTATAACTTCGGTTCCTGATAGTAGTCAAGACGATCCATTCCTTCAACCAATTTTTTGAA
* * * * * * * *
1980 CATTCCATGATCGGGATATAGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTG
195 CATTCCATGCTTGGGAAATCGCATCATTTGGTCTAAAAAGTTTGTCATTTTATAAACAACATTTA
* * * * *
2045 GTCTTTGAATTAGAAATTTTTTTACGAGAGAATTGTTTCTC
260 GTCTTTGAATTAAAAACTTTATTACGTGAGAATTATTTCTC
2086 AATTGGTTCT
Statistics
Matches: 1071, Mismatches: 40, Indels: 32
0.94 0.03 0.03
Matches are distributed among these distances:
406 1 0.00
407 371 0.35
408 353 0.33
413 1 0.00
415 1 0.00
428 1 0.00
431 27 0.03
432 316 0.30
ACGTcount: A:0.28, C:0.17, G:0.16, T:0.40
Consensus pattern (408 bp):
ATCATTTGGTCTAAAACGTTTGTCATTTTGTAAAAAGCTTTTGGTCTTTGAATTAAAAACTTTTT
TACGTGAGAATTGTTTCTCTCTTGGTTCTTAGATGAAGTTTCGAACTTATCAAGCATTTACTAAA
TCTTTTATAACTTCGGTTCCTGATAGTAGTCAAGACGATCCATTCCTTCAACCAATTTTTTGAAC
ATTCCATGCTTGGGAAATCGCATCATTTGGTCTAAAAAGTTTGTCATTTTATAAACAACATTTAG
TCTTTGAATTAAAAACTTTATTACGTGAGAATTATTTCTCTCTCGGTTGTTGGATAAAGTGCCGA
ACTTGTCAAACGTTTCCAGATAGTAGTCAGGATGATCCATTCCTTTGACCAATTTTTTGAACATT
CCATGCTCGAGAAATCGC
Found at i:1466 original size:191 final size:192
Alignment explanation
Indices: 1098--1471 Score: 554
Period size: 191 Copynumber: 2.0 Consensus size: 192
1088 TTCGGTTCTT
* **
1098 GATAGTAGTCAAGACGATCCATTCCTTTGACCAATTTTTTGAACATTCCATGCTTGGGAAATCGC
1 GATAGTAGTCAAGACGATCCATTCCTTTGACAAATTTTTTGAACATTCCATGCTCAGGAAATCGC
*
1163 ATCATTTGGTCTAAAAAGTTTGTCATTTTATAAACAACATTTATTCTTTGAATTAAAAACTTTAT
66 ATCATTTGGTCTAAAAAGTTTGTCATTTTATAAACAACATTTAGTCTTTGAATTAAAAACTTTAT
* * *
1228 TACGTGAGAATTATTTCTCTCTCGGTTGTTGGATAAAGTGCCGAACTTGTCAAACGTTTCCA
131 TACGTGAGAATTATTTCTCTCTCGGTTCTTAGATAAAGTGCCGAACTTATCAAACGTTTCCA
* *
1290 GATAGTAGTCAGGATGATCC-TTCCTTTGACAAATTTTTTGAACATTCCATGCTCAGGAAATCGC
1 GATAGTAGTCAAGACGATCCATTCCTTTGACAAATTTTTTGAACATTCCATGCTCAGGAAATCGC
* * * * *
1354 ATCATTTGGTCTAAAACGTTTGTCATTTTGTAAA-AAGCTTTTGGTCTTTGAATTAAAAACTTTT
66 ATCATTTGGTCTAAAAAGTTTGTCATTTTATAAACAA-CATTTAGTCTTTGAATTAAAAACTTTA
* * * **
1418 TTACGTGAGAATTGTTTCTCTCTTGGTTCTTAGATGAAGTTTCGAACTTATCAA
130 TTACGTGAGAATTATTTCTCTCTCGGTTCTTAGATAAAGTGCCGAACTTATCAA
1472 GCATTTACTA
Statistics
Matches: 162, Mismatches: 19, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
190 2 0.01
191 142 0.88
192 18 0.11
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.39
Consensus pattern (192 bp):
GATAGTAGTCAAGACGATCCATTCCTTTGACAAATTTTTTGAACATTCCATGCTCAGGAAATCGC
ATCATTTGGTCTAAAAAGTTTGTCATTTTATAAACAACATTTAGTCTTTGAATTAAAAACTTTAT
TACGTGAGAATTATTTCTCTCTCGGTTCTTAGATAAAGTGCCGAACTTATCAAACGTTTCCA
Found at i:1523 original size:407 final size:406
Alignment explanation
Indices: 539--3793 Score: 2664
Period size: 432 Copynumber: 7.8 Consensus size: 406
529 NNNNNNNNNN
539 ATCATTTGGTCTAAAACGTTTGTCATTTTGTAAAAAGCTTTTGGTCTTTGAATTAAAAACTTTTT
1 ATCATTTGGTCTAAAACGTTTGTCATTTTGTAAAAAGCTTTTGGTCTTTGAATTAAAAACTTTTT
* * * * *
604 TACGTGAGAATTGTTTCTCTCTAGGTTCTTGGATGAAGTTCCGAACTTGTCAAGCATTTACTGAA
66 TACGTGAGAATTGTTTCTCTCTTGGTTCTTAGATGAAGTTTCGAACTTATCAAGCATTTACTAAA
* *
669 TCATTTATAACTTCGGTTCCTGATAGTAGTCAAGACGATCCATTCCTTCGACCAATTTTTTGAAC
131 TCTTTTATAACTTCGGTTCCTGATAGTAGTCAAGACGATCCATTCCTTCAACCAATTTTTTGAAC
734 ATTCCATGCTTGGGAAATCGCATCATTTGGTCTAAAAAGTTTGTCATTTTATAAACAACATTTAG
196 ATTCCATGCTTGGGAAATCGCATCATTTGGTCTAAAAAGTTTGTCATTTTATAAACAACATTTAG
*
799 TCTTTGAATTAAAAACTTTATTACGTGAGAATTATTTCTCTCTCGGTTGTTGGATAAAGTGCCAA
261 TCTTTGAATTAAAAACTTTATTACGTGAGAATTATTTCTCTCTCGGTTGTTGGATAAAGTGCCGA
864 ACTTGTCAAACGTTTCCAGATAGTAGTCAGGATGATCCATTCCTTTGACCAATTTTTTGAACATT
326 ACTTGTCAAACGTTTCCAGATAGTAGTCAGGATGATCC-TTCCTTTGA-CAATTTTTTGAACATT
929 CCATGCTC-GAGAAATCGC
389 CCATGCTCAG-GAAATCGC
947 ATCATTTGGTCTAAAACGTTTGTCATTTTGTAAAAAGCTTTTGGTCTTTGAATTAAAAACTTTTT
1 ATCATTTGGTCTAAAACGTTTGTCATTTTGTAAAAAGCTTTTGGTCTTTGAATTAAAAACTTTTT
1012 TACGTGAGAATTGTTTCTCTCTTGGTTCTTAGATGAAGTTTCGAACTTATCAAGCATTTACTAAA
66 TACGTGAGAATTGTTTCTCTCTTGGTTCTTAGATGAAGTTTCGAACTTATCAAGCATTTACTAAA
* **
1077 TCTTTTATAACTTCGGTTCTTGATAGTAGTCAAGACGATCCATTCCTTTGACCAATTTTTTGAAC
131 TCTTTTATAACTTCGGTTCCTGATAGTAGTCAAGACGATCCATTCCTTCAACCAATTTTTTGAAC
*
1142 ATTCCATGCTTGGGAAATCGCATCATTTGGTCTAAAAAGTTTGTCATTTTATAAACAACATTTAT
196 ATTCCATGCTTGGGAAATCGCATCATTTGGTCTAAAAAGTTTGTCATTTTATAAACAACATTTAG
1207 TCTTTGAATTAAAAACTTTATTACGTGAGAATTATTTCTCTCTCGGTTGTTGGATAAAGTGCCGA
261 TCTTTGAATTAAAAACTTTATTACGTGAGAATTATTTCTCTCTCGGTTGTTGGATAAAGTGCCGA
1272 ACTTGTCAAACGTTTCCAGATAGTAGTCAGGATGATCCTTCCTTTGACAAATTTTTTGAACATTC
326 ACTTGTCAAACGTTTCCAGATAGTAGTCAGGATGATCCTTCCTTTGAC-AATTTTTTGAACATTC
1337 CATGCTCAGGAAATCGC
390 CATGCTCAGGAAATCGC
1354 ATCATTTGGTCTAAAACGTTTGTCATTTTGTAAAAAGCTTTTGGTCTTTGAATTAAAAACTTTTT
1 ATCATTTGGTCTAAAACGTTTGTCATTTTGTAAAAAGCTTTTGGTCTTTGAATTAAAAACTTTTT
1419 TACGTGAGAATTGTTTCTCTCTTGGTTCTTAGATGAAGTTTCGAACTTATCAAGCATTTACTAAA
66 TACGTGAGAATTGTTTCTCTCTTGGTTCTTAGATGAAGTTTCGAACTTATCAAGCATTTACTAAA
* *
1484 TCTTTTATAACTTCGATTCTTGATAGTAGTCAAGACGATCCATTCCTTCAACCAATTTTTTGAAC
131 TCTTTTATAACTTCGGTTCCTGATAGTAGTCAAGACGATCCATTCCTTCAACCAATTTTTTGAAC
*
1549 ATTCCATGCTTGGGAAATCGCATTATTTGGTCTAAAAAGTTTGTCATTTTATAAACAACATTTAG
196 ATTCCATGCTTGGGAAATCGCATCATTTGGTCTAAAAAGTTTGTCATTTTATAAACAACATTTAG
1614 TCTTTGAATTAAAAACTTTATTACGTGAGAATTATTTCTCTCTCGGTTGTTGGATAAAGTGCCGA
261 TCTTTGAATTAAAAACTTTATTACGTGAGAATTATTTCTCTCTCGGTTGTTGGATAAAGTGCCGA
*
1679 ACTTGTCAAACGTTTCCTAGTTCTTTTATAACTTACGTTCCAGATAGTAGTCAAGATGATCCATT
326 ACTTGTCAAA------C--G-------------T---TTCCAGATAGTAGTCAGGATGATCC-TT
*
1744 CCTTTGACCAATTTTTTGAACATTCCATGCTCGGGAAATCGC
366 CCTTTGA-CAATTTTTTGAACATTCCATGCTCAGGAAATCGC
*
1786 ATCATTTGGTCTAAAACGTTTGTCATTTTGTAAAAAGCTTTTAGTCTTTGAATTAAAAACTTTTT
1 ATCATTTGGTCTAAAACGTTTGTCATTTTGTAAAAAGCTTTTGGTCTTTGAATTAAAAACTTTTT
* *
1851 TACGTGAGAATTGTTTCTCTCTTGGTTCTTGGATGAAG-TTCTGAACTTGTCAAGCATTTACTAA
66 TACGTGAGAATTGTTTCTCTCTTGGTTCTTAGATGAAGTTTC-GAACTTATCAAGCATTTACTAA
* *
1915 ATCTTTTATAACTTCGGTTCCTGATAGTAGTCAAGACGATCCATTTCTTCAACCAATTTTTCGAA
130 ATCTTTTATAACTTCGGTTCCTGATAGTAGTCAAGACGATCCATTCCTTCAACCAATTTTTTGAA
* * * * * * * *
1980 CATTCCATGATCGGGATATAGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTG
195 CATTCCATGCTTGGGAAATCGCATCATTTGGTCTAAAAAGTTTGTCATTTTATAAACAACATTTA
* * * * * ** * * ** * **
2045 GTCTTTGAATTAGAAATTTTTTTACGAGAGAATTGTTTCTCAATTGGTTCTTGGACGAACTTTCG
260 GTCTTTGAATTAAAAACTTTATTACGTGAGAATTATTTCTCTCTCGGTTGTTGGATAAAGTGCCG
* * * *** * * ** ***
2110 AACTTGTTAAACATTT--ACA-AGT--TCTTTTATAACTCCGGTTCCTGTGAGTA-TTCAAG-AC
325 AACTTGTCAAACGTTTCCAGATAGTAGTC-AGGATGA-TCC--TTCCTTTGACAATTTTTTGAAC
* **
2168 GA-TCCATTC-CTTTG--A-C-C
386 -ATTCCATGCTC-AGGAAATCGC
* * *
2185 A--ATTTTGTCTAAATA-GATTGTCATTTTGTAAACAA-CTTTTGGTCTTTAAATTAAAAACTTT
1 ATCATTTGGTCTAAA-ACGTTTGTCATTTTGTAAA-AAGCTTTTGGTCTTTGAATTAAAAAC-TT
* * * * * * * *** * * *
2246 TTTTATGTGAGAATTGTTTCTCTATTAGTTCTTGGACGAACTTCCGAACACGTCAAACATTTTCG
63 TTTTACGTGAGAATTGTTTCTCTCTTGGTTCTTAGATGAAGTTTCGAACTTATCAAGCATTTACT
** * * * * * *
2311 AGTTCTTTTATAACTTCGATTCCTGAGAGTATTAAAGACGATCCATTCCTTCAGCCAATTTTTCG
128 AAATCTTTTATAACTTCGGTTCCTGATAGTAGTCAAGACGATCCATTCCTTCAACCAATTTTTTG
* *** *
2376 AACATTCAATGCCCAGGAAATCG---C---T--TC-----A-TTTG--A--TT-TAAA-TA-ATT
193 AACATTCCATGCTTGGGAAATCGCATCATTTGGTCTAAAAAGTTTGTCATTTTATAAACAACATT
* * * * *
2420 TAGTCTTTGAATTAAATAC-TTATTTATGTGAGAATTATTTCCCTCTTGGTTCTTGGACGAACAT
258 TAGTCTTTGAATTAAAAACTTTA-TTACGTGAGAATTATTTCTCTCTCGGTTGTT-G--G---AT
* * * * * * * * * *
2484 ATGAACTAGTCAAACTTTTAGAAGTTCTTTTATAACTTCGGTTCCTGAGACTATTCAAGACGATC
316 A--AAGT-GCCGAAC--TT----G-TC----A-AA---CGTTTCCAGATAGTAGTCAGGATGATC
* * **
2549 CATTCCTTTGACAAATTTTTTGAAGATTCCGTTTTC-GAGAAATCGC
363 C-TTCCTTTGACAA-TTTTTTGAACATTCCATGCTCAG-GAAATCGC
* * * * *
2595 AGCATTTGGTC-AAAATAGTTTGCCA-TTTGTAAATAA-ATTTTGGTTTTTGAATTAAAAACTTT
1 ATCATTTGGTCTAAAA-CGTTTGTCATTTTGTAAA-AAGCTTTTGGTCTTTGAATTAAAAACTTT
* * * * * * * * *
2657 TTTACATTAGAATTCTTTCTCTCTTGGTTCTTGGACGAAGTATCAAACTTGTCAAACATTTACTA
64 TTTACGTGAGAATTGTTTCTCTCTTGGTTCTTAGATGAAGTTTCGAACTTATCAAGCATTTACTA
** * * * * *
2722 GTTCTTTTACAACTTCGGTTCTTGATAGTAGTCAAGATGATCCATTCCTTCGACCAATTTTTCGA
129 AATCTTTTATAACTTCGGTTCCTGATAGTAGTCAAGACGATCCATTCCTTCAACCAATTTTTTGA
* * ** * * * *
2787 GCATTCCATGATCAGGAAATCGTATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTT
194 ACATTCCATGCTTGGGAAATCGCATCATTTGGTCTAAAAAGTTTGTCATTTTATAAACAACATTT
* * * * * * * * **
2852 GGTCATTGAATTAAAAACTTTATTATGAGAGAATGATTTCTCTCTTGGTTCTTGGACGAACTTCT
259 AGTCTTTGAATTAAAAACTTTATTACGTGAGAATTATTTCTCTCTCGGTTGTTGGA-TAA--AGT
* ** * ** *
2917 GAACCGGTTAAACATTTACGAGTTCTTTTATAACTTCGGTTCTTGAGAGTTTTCAAGATGATCCA
321 G--CC-G---AAC--TT----G-TC----A-AA---CGTTTCCAGATAGTAGTCAGGATGATCC-
* *
2982 TTCCTTTGACCAATTTTTTGAAGATTCCATGACT-GGGAAATCGC
364 TTCCTTTGAC-AATTTTTTGAACATTCCATG-CTCAGGAAATCGC
* * ****
3026 ATTATTTGGTC-AAAATAGTTTGTCATTTTGTAAATAA-CTTTTGGTCTTTGAATTAATTTTTTT
1 ATCATTTGGTCTAAAA-CGTTTGTCATTTTGTAAA-AAGCTTTTGGTCTTTGAATTAAAAACTTT
* * * * * * * * * * *
3089 TTTACATTAGAATTCTTTCTCTCTTGGTTCTTGGACGAA-CTTCTAAACGT-GCTAAACATTAAC
64 TTTACGTGAGAATTGTTTCTCTCTTGGTTCTTAGATGAAGTTTC-GAACTTATC-AAGCATTTAC
** * * * * *
3152 TAGTTCTTCTATACCTTCGGTTCCTGATAGTAGTCAAGACGATACATTCCTTCGACCAATTTTTC
127 TAAATCTTTTATAACTTCGGTTCCTGATAGTAGTCAAGACGATCCATTCCTTCAACCAATTTTTT
* * * * * * * * *
3217 GAACATTCCATGATCGGGAAATCACATCATTTGGTTTAAATAGCTAGTCAATTTGTAAACAAC-T
192 GAACATTCCATGCTTGGGAAATCGCATCATTTGGTCTAAAAAGTTTGTCATTTTATAAACAACAT
* * * * * * * * *
3281 TTTGTGCTTTGAACTAAATACTTTTTTATGTGAGAATTGTTTCCCTCTTGGTTCTTGGACGAACT
257 TTAGT-CTTTGAATTAAAAACTTTATTACGTGAGAATTATTTCTCTCTCGGTTGTT-G--G-A--
* * * * * * *
3346 TTTGAACTTGTTAAACATTTACGAATTCTTTTATAACATCGGTTCCTACG--AGTATTCAAGATG
315 --T-AA--AG-T--GC-----CGAA--CTTGT-CAA-A-CGTTTCC-A-GATAGTAGTCAGGATG
* *
3409 ATCCATTCCTTTGACCAATTTTTTGAAGATTCCATGGC-CGGGAAATCGC
360 ATCC-TTCCTTTGA-CAATTTTTTGAACATTCCAT-GCTCAGGAAATCGC
* *
3458 ATCATTTGGTC-AAAATAGTTTGTCATTTTGTAAATAA-CTTTTGGTCTTTGAATTAAAAGCTTT
1 ATCATTTGGTCTAAAA-CGTTTGTCATTTTGTAAA-AAGCTTTTGGTCTTTGAATTAAAAACTTT
* * * * * * * * *
3521 TTTACGTTAGAATTCTTTCTCTCTTGGTTCTTGGACGAA-CTTCTGAACTTGTGAAACATTTACG
64 TTTACGTGAGAATTGTTTCTCTCTTGGTTCTTAGATGAAGTTTC-GAACTTATCAAGCATTTACT
** * * * * * * * ** *
3585 AGTTCTTTTATAACTTCAGTTCTTGAGAGTATTTAATACGATCCATTCCTTCGACTTATTTTTCG
128 AAATCTTTTATAACTTCGGTTCCTGATAGTAGTCAAGACGATCCATTCCTTCAACCAATTTTTTG
* * * * * * * *
3650 AACATTTCATTCTCGGGAAATCGCATCACTTGGTCTAAAAAGTTTGGCATGTTGTAAAAAACATT
193 AACATTCCATGCTTGGGAAATCGCATCATTTGGTCTAAAAAGTTTGTCATTTTATAAACAACATT
* * * * ** * * * * *
3715 TGGTCTTTGATTTGAAAACTTTTTTACGTGAGAATTGGTTCTCTCTTGGTTCTTGGACAAACTTC
258 TAGTCTTTGAATTAAAAACTTTATTACGTGAGAATTATTTCTCTCTCGGTTGTTGGATAAAGTGC
3780 CGAACTTGTCAAAC
323 CGAACTTGTCAAAC
3794 ATTTATGAGT
Statistics
Matches: 2416, Mismatches: 284, Indels: 294
0.81 0.09 0.10
Matches are distributed among these distances:
376 2 0.00
377 42 0.02
378 2 0.00
379 4 0.00
380 3 0.00
382 1 0.00
383 1 0.00
384 4 0.00
385 5 0.00
386 5 0.00
388 2 0.00
390 2 0.00
392 2 0.00
393 1 0.00
395 1 0.00
397 49 0.02
398 132 0.05
399 4 0.00
400 1 0.00
401 4 0.00
402 1 0.00
403 21 0.01
404 12 0.00
405 13 0.01
406 20 0.01
407 371 0.15
408 358 0.15
409 2 0.00
410 133 0.06
411 38 0.02
412 13 0.01
413 6 0.00
415 1 0.00
416 1 0.00
418 3 0.00
420 1 0.00
423 3 0.00
424 5 0.00
425 2 0.00
426 5 0.00
427 1 0.00
428 5 0.00
429 5 0.00
430 2 0.00
431 186 0.08
432 911 0.38
433 10 0.00
434 3 0.00
435 1 0.00
436 1 0.00
437 1 0.00
440 5 0.00
441 2 0.00
442 4 0.00
444 1 0.00
445 1 0.00
446 1 0.00
ACGTcount: A:0.28, C:0.17, G:0.16, T:0.40
Consensus pattern (406 bp):
ATCATTTGGTCTAAAACGTTTGTCATTTTGTAAAAAGCTTTTGGTCTTTGAATTAAAAACTTTTT
TACGTGAGAATTGTTTCTCTCTTGGTTCTTAGATGAAGTTTCGAACTTATCAAGCATTTACTAAA
TCTTTTATAACTTCGGTTCCTGATAGTAGTCAAGACGATCCATTCCTTCAACCAATTTTTTGAAC
ATTCCATGCTTGGGAAATCGCATCATTTGGTCTAAAAAGTTTGTCATTTTATAAACAACATTTAG
TCTTTGAATTAAAAACTTTATTACGTGAGAATTATTTCTCTCTCGGTTGTTGGATAAAGTGCCGA
ACTTGTCAAACGTTTCCAGATAGTAGTCAGGATGATCCTTCCTTTGACAATTTTTTGAACATTCC
ATGCTCAGGAAATCGC
Found at i:1706 original size:216 final size:216
Alignment explanation
Indices: 1285--2190 Score: 1230
Period size: 216 Copynumber: 4.2 Consensus size: 216
1275 TGTCAAACGT
* * * * *
1285 TTCCAGATAGTAGTCAGGATGATCC-TTCCTTTGACAAATTTTTTGAACATTCCATGCTCAGGAA
1 TTCCTGATAGTAGTCAAGACGATCCATTCCTTTGACCAATTTTTTGAACATTCCATGCTCGGGAA
* *
1349 ATCGCATCATTTGGTCTAAAACGTTTGTCATTTTGTAAAAAGCTTTTGGTCTTTGAATTAAAAAC
66 ATCGCATCATTTGGTCTAAAAAGTTTGTCATTTTGTAAAAAGCTTTTAGTCTTTGAATTAAAAAC
* * * *
1414 TTTTTTACGTGAGAATTGTTTCTCTCTTGGTTCTTAGATGAAGTTTCGAACTTATCAAGCATTTA
131 TTTTTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGATGAAGTTCCGAACTTGTCAAACATTTA
*
1479 CTAAATCTTTTATAACTTCGA
196 CTAAATCTTTTATAACTTCGG
* ** *
1500 TTCTTGATAGTAGTCAAGACGATCCATTCCTTCAACCAATTTTTTGAACATTCCATGCTTGGGAA
1 TTCCTGATAGTAGTCAAGACGATCCATTCCTTTGACCAATTTTTTGAACATTCCATGCTCGGGAA
* * *
1565 ATCGCATTATTTGGTCTAAAAAGTTTGTCATTTTATAAACAA-CATTTAGTCTTTGAATTAAAAA
66 ATCGCATCATTTGGTCTAAAAAGTTTGTCATTTTGTAAA-AAGCTTTTAGTCTTTGAATTAAAAA
* * * * * * *
1629 CTTTATTACGTGAGAATTATTTCTCTCTCGGTTGTTGGATAAAGTGCCGAACTTGTCAAACGTTT
130 CTTTTTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGATGAAGTTCCGAACTTGTCAAACATTT
* **
1694 CCTAGTTCTTTTATAACTTAC-G
195 ACTAAATCTTTTATAACTT-CGG
* *
1716 TTCCAGATAGTAGTCAAGATGATCCATTCCTTTGACCAATTTTTTGAACATTCCATGCTCGGGAA
1 TTCCTGATAGTAGTCAAGACGATCCATTCCTTTGACCAATTTTTTGAACATTCCATGCTCGGGAA
*
1781 ATCGCATCATTTGGTCTAAAACGTTTGTCATTTTGTAAAAAGCTTTTAGTCTTTGAATTAAAAAC
66 ATCGCATCATTTGGTCTAAAAAGTTTGTCATTTTGTAAAAAGCTTTTAGTCTTTGAATTAAAAAC
* *
1846 TTTTTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGATGAAGTTCTGAACTTGTCAAGCATTTA
131 TTTTTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGATGAAGTTCCGAACTTGTCAAACATTTA
1911 CTAAATCTTTTATAACTTCGG
196 CTAAATCTTTTATAACTTCGG
* ** * * *
1932 TTCCTGATAGTAGTCAAGACGATCCATTTCTTCAACCAATTTTTCGAACATTCCATGATCGGGAT
1 TTCCTGATAGTAGTCAAGACGATCCATTCCTTTGACCAATTTTTTGAACATTCCATGCTCGGGAA
* * * *
1997 ATAGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAA-CTTTTGGTCTTTGAATTAGAAA
66 ATCGCATCATTTGGTCTAAAAAGTTTGTCATTTTGTAAA-AAGCTTTTAGTCTTTGAATTAAAAA
* * ** * * * *
2061 TTTTTTTACGAGAGAATTGTTTCTCAATTGGTTCTTGGACGAACTTTCGAACTTGTTAAACATTT
130 CTTTTTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGATGAAGTTCCGAACTTGTCAAACATTT
* *
2126 AC-AAGTTCTTTTATAACTCCGG
195 ACTAA-ATCTTTTATAACTTCGG
*
2148 TTCCTG-TGAGTATTCAAGACGATCCATTCCTTTGACCAATTTT
1 TTCCTGAT-AGTAGTCAAGACGATCCATTCCTTTGACCAATTTT
2191 GTCTAAATAG
Statistics
Matches: 603, Mismatches: 80, Indels: 15
0.86 0.11 0.02
Matches are distributed among these distances:
215 27 0.04
216 571 0.95
217 5 0.01
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (216 bp):
TTCCTGATAGTAGTCAAGACGATCCATTCCTTTGACCAATTTTTTGAACATTCCATGCTCGGGAA
ATCGCATCATTTGGTCTAAAAAGTTTGTCATTTTGTAAAAAGCTTTTAGTCTTTGAATTAAAAAC
TTTTTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGATGAAGTTCCGAACTTGTCAAACATTTA
CTAAATCTTTTATAACTTCGG
Found at i:2317 original size:182 final size:181
Alignment explanation
Indices: 2005--2567 Score: 580
Period size: 182 Copynumber: 3.0 Consensus size: 181
1995 ATATAGCATC
* * *
2005 ATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAGAAA-TTTTTTTA
1 ATTTTGTCTAAATAGATTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTTTTTTA
* * * * * * * *
2069 CGAGAGAATTGTTTCTCAATTGGTTCTTGGACGAACTTTCGAACTTGTTAAACATTTACAAGTTC
66 TGTGAGAATTGTTTCTCTATTGGTTCTTGGACGAACTTACGAAC-AGTCAAACATTTTCGAGTTC
* *
2134 TTTTATAACTCCGGTTCCTGTGAGTATTCAAGACGATCCATTCCTTTGACCA
130 TTTTATAACTTCGGTTCCTGAGAGTATTCAAGACGATCCATTCCTTTGACCA
*
2186 ATTTTGTCTAAATAGATTGTCATTTTGTAAACAACTTTTGGTCTTTAAATTAAAAACTTTTTTTA
1 ATTTTGTCTAAATAGATTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTTTTTTA
* *
2251 TGTGAGAATTGTTTCTCTATTAGTTCTTGGACGAACTTCCGAACACGTCAAACATTTTCGAGTTC
66 TGTGAGAATTGTTTCTCTATTGGTTCTTGGACGAACTTACGAACA-GTCAAACATTTTCGAGTTC
* * *
2316 TTTTATAACTTCGATTCCTGAGAGTATTAAAGACGATCCATTCC-TTCAGCCA
130 TTTTATAACTTCGGTTCCTGAGAGTATTCAAGACGATCCATTCCTTTGA-CCA
* * * * * *
2368 ATTTTTCGAACATTCAATGCCCAGGAAATCGCTTCATTTGATTTAAATAA--TTTAGTCTTTGAA
1 A-TTTT-G-TC--TAAAT----A-G--ATTG--TCATTT--TGTAAACAACTTTTGGTCTTTGAA
* * * * * * *
2431 TTAAATAC-TTATTTATGTGAGAATTATTTCCCTCTTGGTTCTTGGACGAACATATGAACTAGTC
50 TTAAAAACTTTTTTTATGTGAGAATTGTTTCTCTATTGGTTCTTGGACGAACTTACGAAC-AGTC
* *
2495 AAAC-TTTTAGAAGTTCTTTTATAACTTCGGTTCCTGAGACTATTCAAGACGATCCATTCCTTTG
114 AAACATTTTCG-AGTTCTTTTATAACTTCGGTTCCTGAGAGTATTCAAGACGATCCATTCCTTTG
*
2559 ACAA
178 ACCA
2563 ATTTT
1 ATTTT
2568 TTGAAGATTC
Statistics
Matches: 320, Mismatches: 40, Indels: 31
0.82 0.10 0.08
Matches are distributed among these distances:
181 55 0.17
182 107 0.33
183 4 0.01
184 1 0.00
185 1 0.00
187 4 0.01
191 1 0.00
192 1 0.00
194 12 0.04
195 99 0.31
196 28 0.09
198 7 0.02
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.41
Consensus pattern (181 bp):
ATTTTGTCTAAATAGATTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTTTTTTA
TGTGAGAATTGTTTCTCTATTGGTTCTTGGACGAACTTACGAACAGTCAAACATTTTCGAGTTCT
TTTATAACTTCGGTTCCTGAGAGTATTCAAGACGATCCATTCCTTTGACCA
Found at i:2943 original size:216 final size:216
Alignment explanation
Indices: 2422--3816 Score: 1638
Period size: 216 Copynumber: 6.5 Consensus size: 216
2412 AAATAATTTA
* * * * * *
2422 GTCTTTGAATTAAATACTTATTTATGTGAGAATTATTTCCCTCTTGGTTCTTGGACGAACATATG
1 GTCTTTGAATTAAAAACTTTTTTATGTGAGAATTCTTTCTCTCTTGGTTCTTGGACGAACTTCTG
* * *
2487 AACTAGTCAAACTTTTA-GAAGTTCTTTTATAACTTCGGTTCCTGAGACTATTCAAGACGATCCA
66 AACTTGTCAAACATTTACG-AGTTCTTTTATAACTTCGGTTCCTGAGAGTATTCAAGACGATCCA
* * * * ** * *
2551 TTCCTTTGACAAATTTTTTGAAGATTCCGTTTTCGAGAAATCGCAGCATTTGGTCAAAATAGTTT
130 TTCCTTCGACCAATTTTTCGAAGATTCCATGATCGGGAAATCGCATCATTTGGTCAAAATAGTTT
* *
2616 GCCA-TTTGTAAATAAATTTTG
195 GTCATTTTGTAAATAACTTTTG
* ** * *
2637 GTTTTTGAATTAAAAACTTTTTTACATTAGAATTCTTTCTCTCTTGGTTCTTGGACGAAGTATC-
1 GTCTTTGAATTAAAAACTTTTTTATGTGAGAATTCTTTCTCTCTTGGTTCTTGGACGAACT-TCT
* * * * * * *
2701 AAACTTGTCAAACATTTACTAGTTCTTTTACAACTTCGGTTCTTGATAGTAGTCAAGATGATCCA
65 GAACTTGTCAAACATTTACGAGTTCTTTTATAACTTCGGTTCCTGAGAGTATTCAAGACGATCCA
* * *
2766 TTCCTTCGACCAATTTTTCG-AGCATTCCATGATCAGGAAATCGTATCATTTGGTCTAAATAGTT
130 TTCCTTCGACCAATTTTTCGAAG-ATTCCATGATCGGGAAATCGCATCATTTGGTCAAAATAGTT
*
2830 TGTCATTTTGTAAACAACTTTTG
194 TGTCATTTTGTAAATAACTTTTG
* * * **
2853 GTCATTGAATTAAAAACTTTATTATGAGAGAATGATTTCTCTCTTGGTTCTTGGACGAACTTCTG
1 GTCTTTGAATTAAAAACTTTTTTATGTGAGAATTCTTTCTCTCTTGGTTCTTGGACGAACTTCTG
** * * * *
2918 AACCGGTTAAACATTTACGAGTTCTTTTATAACTTCGGTTCTTGAGAGTTTTCAAGATGATCCAT
66 AACTTGTCAAACATTTACGAGTTCTTTTATAACTTCGGTTCCTGAGAGTATTCAAGACGATCCAT
* * *
2983 TCCTTTGACCAATTTTTTGAAGATTCCATGA-CTGGGAAATCGCATTATTTGGTCAAAATAGTTT
131 TCCTTCGACCAATTTTTCGAAGATTCCATGATC-GGGAAATCGCATCATTTGGTCAAAATAGTTT
3047 GTCATTTTGTAAATAACTTTTG
195 GTCATTTTGTAAATAACTTTTG
**** ** * *
3069 GTCTTTGAATTAATTTTTTTTTTACATTAGAATTCTTTCTCTCTTGGTTCTTGGACGAACTTCTA
1 GTCTTTGAATTAAAAACTTTTTTATGTGAGAATTCTTTCTCTCTTGGTTCTTGGACGAACTTCTG
* * * * * * * *
3134 AACGTG-CTAAACATTAACTAGTTCTTCTATACCTTCGGTTCCTGATAGTAGTCAAGACGATACA
66 AACTTGTC-AAACATTTACGAGTTCTTTTATAACTTCGGTTCCTGAGAGTATTCAAGACGATCCA
* * ** * *
3198 TTCCTTCGACCAATTTTTCGAACATTCCATGATCGGGAAATCACATCATTTGGTTTAAATAGCTA
130 TTCCTTCGACCAATTTTTCGAAGATTCCATGATCGGGAAATCGCATCATTTGGTCAAAATAGTTT
* *
3263 GTCAATTTGTAAACAACTTTT-
195 GTCATTTTGTAAATAACTTTTG
* * * * *
3284 GTGCTTTGAACTAAATACTTTTTTATGTGAGAATTGTTTCCCTCTTGGTTCTTGGACGAACTTTT
1 GT-CTTTGAATTAAAAACTTTTTTATGTGAGAATTCTTTCTCTCTTGGTTCTTGGACGAACTTCT
* * * *
3349 GAACTTGTTAAACATTTACGAATTCTTTTATAACATCGGTTCCT-ACGAGTATTCAAGATGATCC
65 GAACTTGTCAAACATTTACGAGTTCTTTTATAACTTCGGTTCCTGA-GAGTATTCAAGACGATCC
* * **
3413 ATTCCTTTGACCAATTTTTTGAAGATTCCATGGCCGGGAAATCGCATCATTTGGTCAAAATAGTT
129 ATTCCTTCGACCAATTTTTCGAAGATTCCATGATCGGGAAATCGCATCATTTGGTCAAAATAGTT
3478 TGTCATTTTGTAAATAACTTTTG
194 TGTCATTTTGTAAATAACTTTTG
* * *
3501 GTCTTTGAATTAAAAGCTTTTTTACGTTAGAATTCTTTCTCTCTTGGTTCTTGGACGAACTTCTG
1 GTCTTTGAATTAAAAACTTTTTTATGTGAGAATTCTTTCTCTCTTGGTTCTTGGACGAACTTCTG
* * * * *
3566 AACTTGTGAAACATTTACGAGTTCTTTTATAACTTCAGTTCTTGAGAGTATTTAATACGATCCAT
66 AACTTGTCAAACATTTACGAGTTCTTTTATAACTTCGGTTCCTGAGAGTATTCAAGACGATCCAT
** * * ** *
3631 TCCTTCGACTTATTTTTCGAACATTTCATTCTCGGGAAATCGCATCACTTGGTCTAAAA-AGTTT
131 TCCTTCGACCAATTTTTCGAAGATTCCATGATCGGGAAATCGCATCATTTGGTC-AAAATAGTTT
* * * *
3695 GGCATGTTGTAAAAAACATTTG
195 GTCATTTTGTAAATAACTTTTG
* * * ** * *
3717 GTCTTTGATTTGAAAACTTTTTTACGTGAGAATTGGTTCTCTCTTGGTTCTTGGACAAACTTCCG
1 GTCTTTGAATTAAAAACTTTTTTATGTGAGAATTCTTTCTCTCTTGGTTCTTGGACGAACTTCTG
*
3782 AACTTGTCAAACATTTATGAGTTCTTTTATAACTT
66 AACTTGTCAAACATTTACGAGTTCTTTTATAACTT
3817 TGNNNNNNNN
Statistics
Matches: 992, Mismatches: 173, Indels: 29
0.83 0.14 0.02
Matches are distributed among these distances:
214 2 0.00
215 165 0.17
216 815 0.82
217 10 0.01
ACGTcount: A:0.27, C:0.17, G:0.16, T:0.41
Consensus pattern (216 bp):
GTCTTTGAATTAAAAACTTTTTTATGTGAGAATTCTTTCTCTCTTGGTTCTTGGACGAACTTCTG
AACTTGTCAAACATTTACGAGTTCTTTTATAACTTCGGTTCCTGAGAGTATTCAAGACGATCCAT
TCCTTCGACCAATTTTTCGAAGATTCCATGATCGGGAAATCGCATCATTTGGTCAAAATAGTTTG
TCATTTTGTAAATAACTTTTG
Found at i:4545 original size:216 final size:216
Alignment explanation
Indices: 3927--7390 Score: 3581
Period size: 216 Copynumber: 16.2 Consensus size: 216
3917 NNNNNNTTTA
* * * ** *
3927 TTACGTGAGAATTGTTTCTCTCTCGGTTCTTGGATGAAGTGCCGAACTTGTCAAACATTT-CCTA
1 TTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTTCGAACTTGTCAAACATTTACAT-
* * * * * * *
3991 GTTCTTTTATAACTTCTGTTCCAGATAGTAGTCAAGATGATCCATTCCTTTGACAAATTTTTTGA
65 GTTCTTTTATAACTTCGGTTCCTGAGAGTATTCAAGACGATCCATTCCTTTGACCAATTTTTCGA
* *
4056 ACATTCCATGCTCGAGAAATCGCATCATTTGGTCTAAA-ACGTTTGTCATTTTGTAAA-AAGCTT
130 ACATTCCATGATCGGGAAATCGCATCATTTGGTCTAAATA-GTTTGTCATTTTGTAAACAA-CTT
4119 TTGGTCTTTGAATTAAAAACTTTT
193 TTGGTCTTTGAATTAAAAACTTTT
* * * **
4143 TTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGATGAAGTTTCAAACTT-T-TTAC---TA-A--
1 TTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTTCGAACTTGTCAAACATTTACATG
* * * * *
4200 ATCTTTTATAACTTCGGTTCCTGATAGT-GTCAAGACGATCCATTTCTTCGACCAATTTTTCGAA
66 TTCTTTTATAACTTCGGTTCCTGAGAGTATTCAAGACGATCCATTCCTTTGACCAATTTTTCGAA
* *
4264 CATTCCATGATCGGGATATCACATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTG
131 CATTCCATGATCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTG
*
4329 GTCTTTGAATTAAAAACATTT
196 GTCTTTGAATTAAAAACTTTT
** * ** * *
4350 TTACAAGAGAATTGTTTATCAATTGGTTCTTGGACGAACTTTCTAACTTGTTAAACATTTACATG
1 TTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTTCGAACTTGTCAAACATTTACATG
* *
4415 TTCTTTTATAACTCCGGTTCCTGAGAGTATTCAAGATGATCCATTCCTTTGACCAA-TTTTCTGA
66 TTCTTTTATAACTTCGGTTCCTGAGAGTATTCAAGACGATCCATTCCTTTGACCAATTTTTC-GA
* * * * * * * *
4479 AGATTTCATTATTGGGAAATCGCATCATTTGGTCAAAATAATTTGTCATTTTGTAAATAGCTTTT
130 ACATTCCATGATCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTT
*
4544 GGTTTTTGAATT-AAAACTTTT
195 GGTCTTTGAATTAAAAACTTTT
* * * *
4565 TTGCGTTAGAATTCTTTCTCTCTTGGTTCTTGGACGAACTTCCGAACTTGTCAAACATTTAC-TA
1 TTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTTCGAACTTGTCAAACATTTACAT-
* * * * * * *
4629 GTTC-TTTATAACTTTGGTTCCTGATAGTAGTCAAGATGATCAATTCCCTAGACCAATTTTTCGA
65 GTTCTTTTATAACTTCGGTTCCTGAGAGTATTCAAGACGATCCATTCCTTTGACCAATTTTTCGA
* * **
4693 ACATTCCATGATCGGGAAATCACATCATTTGGTTTAAATAGTTTGTCATTTCATAAACAACTTTT
130 ACATTCCATGATCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTT
*
4758 GGTCTTTGAATTAAAAACTTTA
195 GGTCTTTGAATTAAAAACTTTT
*** * * * *
4780 TTACAAAAGAATTGTTTCTCTCTTGGCTCTTGGACAAACTTTCGAA-TTGGTTAAACGTTTACGA
1 TTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTTCGAACTT-GTCAAACATTTAC-A
* * * * * *
4844 -GTTCTTTCATAAATTCGGTTCCTGAGAGTATTCGAGACAATCTATTCCTTTGACCAATTTTCCG
64 TGTTCTTTTATAACTTCGGTTCCTGAGAGTATTCAAGACGATCCATTCCTTTGACCAATTTTTCG
* * * * * * * * *
4908 CAGATTCTATTATCGAGAAATAGCATTATTTGGTCAAAATAGTTTGTCACTTTGTAAACAACTTT
129 AACATTCCATGATCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTT
* *
4973 TGGTCTTTGAATTAAATACTTAT
194 TGGTCTTTGAATTAAAAACTTTT
* * * * * * *
4996 TTACGTGAGAATT-ATT-TC-C----TTCTTGGACGGACATACGAACTAGTCAAACTTTTACAAG
1 TTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTTCGAACTTGTCAAACATTTACATG
* * * *
5054 TTCTATTATAACTTCGGTTCCTGAGAGTATTCAAGACGATTCATTCCGTTGACCATTTTTTCGAA
66 TTCTTTTATAACTTCGGTTCCTGAGAGTATTCAAGACGATCCATTCCTTTGACCAATTTTTCGAA
* * **
5119 GATTCCATGATCGGGAAATCGCATCATTTGGT-TAAAATAGTTTATCATTTTGTAATTAACTTTT
131 CATTCCATGATCGGGAAATCGCATCATTTGGTCT-AAATAGTTTGTCATTTTGTAAACAACTTTT
*
5183 GGTCTTTGGATT-AAAAC-TTT
195 GGTCTTTGAATTAAAAACTTTT
* * * *
5203 TTACGTTAGAATTCTTTCTCTCTTGGTTCTTAGACAAAC-TTCTGAACTTGTCAAACATTTAC-T
1 TTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTTC-GAACTTGTCAAACATTTACAT
** *
5266 AGTTCTTTTATAACTTCGGTTCCTG-GTAGTAGCCAAGACGATCCATTCCTTCGACCAATTTTTC
65 -GTTCTTTTATAACTTCGGTTCCTGAG-AGTATTCAAGACGATCCATTCCTTTGACCAATTTTTC
* * *
5330 AAACATTCCATGATCGAGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTGGTAAACAAC-T
128 GAACATTCCATGATCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTT
* * * *
5394 TTCGTGCTCTGAACTAAATACTTTT
193 TTGGT-CTTTGAATTAAAAACTTTT
* * * * * * * *
5419 TTAAGTGAGAATTGTTTCCCTCTTGGTTCTAGGACGAACATACAAACTGGTCAAA-ATTTTACAA
1 TTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTTCGAACTTGTCAAACA-TTTACAT
* * * ** *
5483 GTTCTTTTATAACTTCGGTTCCTTAAAGTATTTAAGACGATCCATTGATTTGAGCAATTTTTCGA
65 GTTCTTTTATAACTTCGGTTCCTGAGAGTATTCAAGACGATCCATTCCTTTGACCAATTTTTCGA
* * * * * * * *
5548 ATATTTCA-CA-CTGAGAATTCACATTATTTTGTCTAAATAGTTTGTCATTTTGTAAACAACTTT
130 ACATTCCATGATC-GGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTT
*
5611 TGGTCTTTAAATTAAAAACTTTT
194 TGGTCTTTGAATTAAAAACTTTT
* * * * * **
5634 TTACGTGAGAATTGTTTCTC-CATTAGTTCTTAGACGAACTTCCTAACATGTCAAACATTT-TTT
1 TTACGTGAGAATTGTTTCTCTC-TTGGTTCTTGGACGAACTTTCGAACTTGTCAAACATTTACAT
* * * *
5697 AGTTCTTTTATAACTTCGATTCCTGAGAGTATTAAAGATGATCCATTCC-TTCAGCCAATTTTTC
65 -GTTCTTTTATAACTTCGGTTCCTGAGAGTATTCAAGACGATCCATTCCTTTGA-CCAATTTTTC
* * * * * * *
5761 GAACATTCCATG-CCTGGGAAATCGCTTCATTTGATTTAAATAGTTTATCATTTTGTATACAAGT
128 GAACATTCCATGATC-GGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACT
* * * *
5825 TTTAGTATTTGAATTAAATACTTAT
192 TTTGGTCTTTGAATTAAAAACTTTT
* * * * * * * *
5850 TTACGTGAGAATTATTTCCCTATTGGTTCTTGGATGAACATAT-GAACTAGTCAAACTTTTACAA
1 TTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAAC-TTTCGAACTTGTCAAACATTTACAT
* * *
5914 GTTCTTTTATAAATTCGATTCCTGAGAGTATTCAAGACGATCCATTCCTTTGAACAA-TTTTCTG
65 GTTCTTTTATAACTTCGGTTCCTGAGAGTATTCAAGACGATCCATTCCTTTGACCAATTTTTC-G
* * * * * * * *
5978 AAGATTCCTTTATCGAGAAATCGCATCATTTGGTCAAAATAGTTTGCCATTTTGTAAATAAATTT
129 AACATTCCATGATCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTT
6043 TGGTCTTTGAATTAAAAACTTTT
194 TGGTCTTTGAATTAAAAACTTTT
* * * * *
6066 TTACATTAGAATTCTTTCTCTCTTGGTTCTTGGACGAAGTATCGAACTTGTCAAACATTTAC-TA
1 TTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTTCGAACTTGTCAAACATTTACAT-
* * * * * * *
6130 GTTCTTTTACAACTTCGGTTCCTAATAGTAGTCTAGATGATCCATTCCTTTGACCAATCTTTCGA
65 GTTCTTTTATAACTTCGGTTCCTGAGAGTATTCAAGACGATCCATTCCTTTGACCAATTTTTCGA
* * * *
6195 GCATTCCATGATCAGGAAATCGTATCATTTGGTCTAAATAATTTGTCATTTTGTAAACAACTTTT
130 ACATTCCATGATCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTT
*
6260 GGTCTTTGAATGAAAAACTTTT
195 GGTCTTTGAATTAAAAACTTTT
* * * * *
6282 TTACGAGAGAATTATTTCTCTCTTGGTTCTTGGACGAAC-TTCTAAACTGGTTAAACATTTACGA
1 TTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTTC-GAACTTGTCAAACATTTAC-A
* * * *
6346 -GTTATTTTATAACTTCGGTTCTTGAGAGTATTCAAGAAGATCCATTCCTTTGACCAATTTTTTG
64 TGTTCTTTTATAACTTCGGTTCCTGAGAGTATTCAAGACGATCCATTCCTTTGACCAATTTTTCG
* * * *
6410 AAGATTCCATGA-CTGGGAAATCGCATTATTTGGTCAAAATAGTTTGTCATTTTGTAAATAACTT
129 AACATTCCATGATC-GGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTT
6474 TTGGTCTTTGAATTAAAAACTTTT
193 TTGGTCTTTGAATTAAAAACTTTT
* * * * *
6498 TTACGTTAGAATTCTTTCTCTCCTGGTTCTTGGACGAAC-TTCTGAACGTG-CTAAACATTAAC-
1 TTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTTC-GAACTTGTC-AAACATTTACA
* * *
6560 TAGTTCTTCTATAACTTCGGTTCCTGATAGTAGTT-AAGACGATCCATTCCTTCGACCAATTTTT
64 T-GTTCTTTTATAACTTCGGTTCCTGAGAGTA-TTCAAGACGATCCATTCCTTTGACCAATTTTT
* * *
6624 CAAACATTCCATGATCGGGAAATCGCATCATTTGGTCTAAATAGCTTGTCAATTTGTAAACAACT
127 CGAACATTCCATGATCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACT
* *
6689 TTT-GTGCTTTGAACTAAATACTTTT
192 TTTGGT-CTTTGAATTAAAAACTTTT
* * * * * * * * *
6714 TTATGTGAGAACTGTTTCCCTCTTGGTTCTTGAACGAACATACAAACTGGTCAAA-ATTTTACAA
1 TTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTTCGAACTTGTCAAACA-TTTACAT
* * * ** * *
6778 GTTCATTTATAAC-TCTGGTTCCTTAAAGTATTCAAGAC-ATTCCATTGATTTGAGCAATTTTTT
65 GTTCTTTTATAACTTC-GGTTCCTGAGAGTATTCAAGACGA-TCCATTCCTTTGACCAATTTTTC
* * ** * *
6841 GAATATTCCATGCT-AAGAAATCGCATCATTTGGTCTAAAGAGTTAGTCATTTTGTAAACAACTT
128 GAACATTCCATGATCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTT
* *
6905 TTGGTCTTTGAATTAAATACTTAT
193 TTGGTCTTTGAATTAAAAACTTTT
* * * * * *
6929 TTACGTGAGAATTG-TT-TC-C----TTCTTGGACGGACATACGAACTAGTCAAACTTTTACAAG
1 TTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTTCGAACTTGTCAAACATTTACATG
* * *
6987 TTCTATTATAACTTCGGTTCCTGAGAGTATTCAAGACGATCCATTCCGTTGACCATTTTTTC-AA
66 TTCTTTTATAACTTCGGTTCCTGAGAGTATTCAAGACGATCCATTCCTTTGACCAATTTTTCGAA
* * *
7051 CGATTCCATGATCGAGAAATCGCATCATTTGGTCAAAATAGTTTGTCATTTTGTAAATAACTTTT
131 C-ATTCCATGATCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTT
*
7116 GGTCTTTGGATT-AAAAC-TTT
195 GGTCTTTGAATTAAAAACTTTT
* * * * * *
7136 TTATGTTATAATTCTTTATCTCTTGGTTCTTAGACGAAC-TTCTGAACTTGTCAAACATTTAC-T
1 TTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTTC-GAACTTGTCAAACATTTACAT
* * * * *
7199 AGTTCTTTTATAACTTCGGTTCCTG-GTAGTAGTCAGGACGATCCATCCCTTCGACAAATTTTTC
65 -GTTCTTTTATAACTTCGGTTCCTGAG-AGTATTCAAGACGATCCATTCCTTTGACCAATTTTTC
* *
7263 AAACATTCCATGATCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAAATT
128 GAACATTCCATGATCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTT
* * * * *
7328 TT-CTGCTCTAAACTAAATACTTTT
193 TTGGT-CTTTGAATTAAAAACTTTT
* * * *
7352 TTACGTGAGAATTATTTCCCTCTTGGTTCTAGCACGAAC
1 TTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAAC
7391 ATACAAACTG
Statistics
Matches: 2673, Mismatches: 480, Indels: 190
0.80 0.14 0.06
Matches are distributed among these distances:
207 176 0.07
208 131 0.05
209 212 0.08
210 3 0.00
211 1 0.00
212 3 0.00
213 15 0.01
214 411 0.15
215 432 0.16
216 1272 0.48
217 17 0.01
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (216 bp):
TTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTTCGAACTTGTCAAACATTTACATG
TTCTTTTATAACTTCGGTTCCTGAGAGTATTCAAGACGATCCATTCCTTTGACCAATTTTTCGAA
CATTCCATGATCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTG
GTCTTTGAATTAAAAACTTTT
Found at i:12689 original size:21 final size:19
Alignment explanation
Indices: 12664--12711 Score: 53
Period size: 19 Copynumber: 2.4 Consensus size: 19
12654 CAAAAAAGTG
12664 ATAAAAAAGTCGAGAAAAA-A
1 ATAAAAAAG--GAGAAAAATA
*
12684 AGTAAAATAGGAGAAAAATA
1 A-TAAAAAAGGAGAAAAATA
12704 ATAAAAAA
1 ATAAAAAA
12712 ATATTCTGTG
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
19 14 0.58
20 3 0.12
21 7 0.29
ACGTcount: A:0.71, C:0.02, G:0.15, T:0.12
Consensus pattern (19 bp):
ATAAAAAAGGAGAAAAATA
Done.