Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002723.1 Hibiscus syriacus cultivar Beakdansim tig00005617_pilon, 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: 204016
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
File 2 of 2
Found at i:167491 original size:41 final size:41
Alignment explanation
Indices: 167379--167508 Score: 163
Period size: 41 Copynumber: 3.2 Consensus size: 41
167369 AAGTATCGAG
* ** * *
167379 TTGCGAAAGTCAGTATCGCGTTGCGATTTT-GTATTATCGCG
1 TTGCGATAGTCAGTATCGCGTTGCGATTTTCCAAAT-TCGCA
* *
167420 TTGCGATAGTCAGTACCGCGTTGTGATTTTCCAAATTCGCA
1 TTGCGATAGTCAGTATCGCGTTGCGATTTTCCAAATTCGCA
* *
167461 TTGCGATAGTCAGTATCGCATTGCGATTTTCCAAATTTGCA
1 TTGCGATAGTCAGTATCGCGTTGCGATTTTCCAAATTCGCA
167502 TTGCGAT
1 TTGCGAT
167509 TTACTTATTC
Statistics
Matches: 77, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
41 75 0.97
42 2 0.03
ACGTcount: A:0.22, C:0.19, G:0.23, T:0.36
Consensus pattern (41 bp):
TTGCGATAGTCAGTATCGCGTTGCGATTTTCCAAATTCGCA
Found at i:167504 original size:21 final size:21
Alignment explanation
Indices: 167444--167527 Score: 75
Period size: 20 Copynumber: 4.1 Consensus size: 21
167434 ACCGCGTTGT
167444 GATTTTCCAAATTCGCATTGC
1 GATTTTCCAAATTCGCATTGC
** *
167465 GATAGT-C-AGTATCGCATTGC
1 GATTTTCCAAAT-TCGCATTGC
*
167485 GATTTTCCAAATTTGCATTGC
1 GATTTTCCAAATTCGCATTGC
* **
167506 GA-TTTACTTATTCGCATTGC
1 GATTTTCCAAATTCGCATTGC
167526 GA
1 GA
167528 ATTGGGAAAA
Statistics
Matches: 49, Mismatches: 11, Indels: 7
0.73 0.16 0.10
Matches are distributed among these distances:
19 2 0.04
20 30 0.61
21 15 0.31
22 2 0.04
ACGTcount: A:0.24, C:0.20, G:0.18, T:0.38
Consensus pattern (21 bp):
GATTTTCCAAATTCGCATTGC
Found at i:167569 original size:21 final size:22
Alignment explanation
Indices: 167517--167569 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
167507 ATTTACTTAT
167517 TCGCATTGCG-AATTGGGAAAA
1 TCGCATTGCGAAATTGGGAAAA
**
167538 TCGCAACGCGAAATT-GGAAAA
1 TCGCATTGCGAAATTGGGAAAA
167559 TCGCATTGCGA
1 TCGCATTGCGA
167570 TAGTCATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (22 bp):
TCGCATTGCGAAATTGGGAAAA
Found at i:167627 original size:20 final size:20
Alignment explanation
Indices: 167604--167649 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
167594 GGAAACTGAT
*
167604 TTGCGATAATAGAGATCGCG
1 TTGCGATAATAGAGATCGCA
* *
167624 TTGCGA-ATTAGCGATCGCA
1 TTGCGATAATAGAGATCGCA
167643 TTGCGAT
1 TTGCGAT
167650 TTTATTGGTC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.28
Consensus pattern (20 bp):
TTGCGATAATAGAGATCGCA
Found at i:170012 original size:23 final size:23
Alignment explanation
Indices: 169986--170030 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
169976 CACCACAGCT
*
169986 CGTATAAATGCACCGAAGTGCCC
1 CGTAGAAATGCACCGAAGTGCCC
* *
170009 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
170031 ATATAATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.29, G:0.24, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCC
Found at i:170279 original size:149 final size:149
Alignment explanation
Indices: 170009--170312 Score: 572
Period size: 149 Copynumber: 2.0 Consensus size: 149
169999 CGAAGTGCCC
* *
170009 CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCATATAGAATTCTTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
170074 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
66 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
170139 CATATGTCCCAAAGAACCG
131 CATATGTCCCAAAGAACCG
*
170158 CGTAGAATTGTACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
170223 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
66 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
*
170288 CATATGTCCCGAAGAACCG
131 CATATGTCCCAAAGAACCG
170307 CGTAGA
1 CGTAGA
170313 CCCTCGACTC
Statistics
Matches: 151, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
149 151 1.00
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (149 bp):
CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
CATATGTCCCAAAGAACCG
Found at i:170856 original size:2 final size:2
Alignment explanation
Indices: 170849--170876 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
170839 TCTCTTAGAC
170849 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
170877 TCACATGTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:171156 original size:23 final size:22
Alignment explanation
Indices: 171104--171157 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 22
171094 TAATTCAATT
171104 TCATATAACTCCTATAATCTTC
1 TCATATAACTCCTATAATCTTC
* *
171126 TCATATAACTTC-ATAATTTTC
1 TCATATAACTCCTATAATCTTC
171147 TATCATATAAC
1 --TCATATAAC
171158 CCATGTGTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 8 0.29
22 11 0.39
23 9 0.32
ACGTcount: A:0.35, C:0.22, G:0.00, T:0.43
Consensus pattern (22 bp):
TCATATAACTCCTATAATCTTC
Found at i:171228 original size:18 final size:18
Alignment explanation
Indices: 171205--171239 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
171195 TCCCATCTAG
171205 CTTATC-TTATATGTTCAT
1 CTTATCATT-TATGTTCAT
171223 CTTATCATTTATGTTCA
1 CTTATCATTTATGTTCA
171240 AATCTCCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.54
Consensus pattern (18 bp):
CTTATCATTTATGTTCAT
Found at i:171851 original size:21 final size:21
Alignment explanation
Indices: 171821--171865 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
171811 ATTTTGTCGT
* *
171821 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
171842 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
171863 TTG
1 TTG
171866 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:186456 original size:16 final size:16
Alignment explanation
Indices: 186435--186466 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
186425 CATATAGCAG
186435 GTAAAAATATGATAAA
1 GTAAAAATATGATAAA
186451 GTAAAAATATGATAAA
1 GTAAAAATATGATAAA
186467 ACCGGTGTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.62, C:0.00, G:0.12, T:0.25
Consensus pattern (16 bp):
GTAAAAATATGATAAA
Found at i:186758 original size:182 final size:181
Alignment explanation
Indices: 186451--187068 Score: 812
Period size: 182 Copynumber: 3.4 Consensus size: 181
186441 ATATGATAAA
* * ** * *
186451 GTAAAAATATGATAAAACCGGTGTC-ATTATGATAAAATAGGTAAACCGCTACCGGTTATATTAA
1 GTAAAAATATGACAAAACCGGTGTCGA-AATGATAAAACCGGTAAAACGCTACCGGATATATTAA
*
186515 AAGTGTCGATAAATTAATATAAGTATCGACACTTTTGTAATTTAAAAGAGAAGAAGTTATAGCGC
65 AAGTGTCGATAAATTAATATAAGTATCGACACTTTT-TAATTTAAAAGAGAAAAAGTTATAGCGC
* *
186580 CTATAAAGTGTCGATACTTTATACAAATGTATCGATCCATAGAAATATAACAG
129 CTAAAAAGTATCGATACTTTATACAAATGTATCGATCCATAGAAATATAACAG
* * *
186633 GTAAAAATATGATAAAACCGGTGTC-ATTATGATAAAACCGGTAAACCGCTACCGGATATATTAA
1 GTAAAAATATGACAAAACCGGTGTCGA-AATGATAAAACCGGTAAAACGCTACCGGATATATTAA
* *
186697 AAGTGTCGATAAATTAATATAAGTATCGACACTTTTTATATTTAAAAGAGAAAAAGTTATAGTGT
65 AAGTGTCGATAAATTAATATAAGTATCGACACTTTTTA-ATTTAAAAGAGAAAAAGTTATAGCGC
* *
186762 CTAAAAAGTATCGATACTTTATACAAATGTATCGATCCATAGCAATATAACAT
129 CTAAAAAGTATCGATACTTTATACAAATGTATCGATCCATAGAAATATAACAG
* * * * ** ** * *
186815 GTAATAATATGACAAAACAGGTCTCGAAATGAAAAAAAGGGTAAAAAACTACCAGATATATTGAA
1 GTAAAAATATGACAAAACCGGTGTCGAAATGATAAAACCGGTAAAACGCTACCGGATATATTAAA
* *
186880 AGTGTCGATAAATTAATGTAAGTATCGACACTTTCGTAATTTAAAAGAGAAGAAA-TTATAGCGC
66 AGTGTCGATAAATTAATATAAGTATCGACACTTT-TTAATTTAAAAGAGAA-AAAGTTATAGCGC
* * *
186944 CTAAAAAGTATCGATACTTTATAAAAATGTATCTATCCATA-ACAATATAATAG
129 CTAAAAAGTATCGATACTTTATACAAATGTATCGATCCATAGA-AATATAACAG
* * * * * *
186997 GTAAAAATATGACAAAATCGGTATCGAAATGACAAAACCGGTAAAACGCTACCGGTTATGTTGAA
1 GTAAAAATATGACAAAACCGGTGTCGAAATGATAAAACCGGTAAAACGCTACCGGATATATTAAA
187062 AGTGTCG
66 AGTGTCG
187069 GTACTTTAAT
Statistics
Matches: 387, Mismatches: 44, Indels: 10
0.88 0.10 0.02
Matches are distributed among these distances:
181 2 0.01
182 379 0.98
183 6 0.02
ACGTcount: A:0.43, C:0.12, G:0.16, T:0.28
Consensus pattern (181 bp):
GTAAAAATATGACAAAACCGGTGTCGAAATGATAAAACCGGTAAAACGCTACCGGATATATTAAA
AGTGTCGATAAATTAATATAAGTATCGACACTTTTTAATTTAAAAGAGAAAAAGTTATAGCGCCT
AAAAAGTATCGATACTTTATACAAATGTATCGATCCATAGAAATATAACAG
Found at i:188972 original size:22 final size:22
Alignment explanation
Indices: 188921--188976 Score: 60
Period size: 24 Copynumber: 2.5 Consensus size: 22
188911 AATGTTTTTG
*
188921 TTTTTTTATATAAAATGATGGTA
1 TTTTATTATATAAAATGAT-GTA
*
188944 TAGTTATTATATAAAATGAT-TAA
1 T-TTTATTATATAAAATGATGT-A
188967 TTTTATTATA
1 TTTTATTATA
188977 AATGCAGGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
22 9 0.32
23 3 0.11
24 16 0.57
ACGTcount: A:0.39, C:0.00, G:0.09, T:0.52
Consensus pattern (22 bp):
TTTTATTATATAAAATGATGTA
Found at i:189279 original size:15 final size:15
Alignment explanation
Indices: 189256--189285 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
189246 TTGGAGGGGT
189256 GGATGACGGTCAGGG
1 GGATGACGGTCAGGG
*
189271 GGATTACGGTCAGGG
1 GGATGACGGTCAGGG
189286 AAAACAGAGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.13, G:0.50, T:0.17
Consensus pattern (15 bp):
GGATGACGGTCAGGG
Found at i:189663 original size:18 final size:18
Alignment explanation
Indices: 189640--189678 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
189630 GAGAAAATTT
* *
189640 GAAGAAGAAAAGATGGAG
1 GAAGAAAAAAAAATGGAG
189658 GAAGAAAAAAAAATGGAG
1 GAAGAAAAAAAAATGGAG
189676 GAA
1 GAA
189679 ATGAGGAGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.33, T:0.05
Consensus pattern (18 bp):
GAAGAAAAAAAAATGGAG
Found at i:191172 original size:19 final size:19
Alignment explanation
Indices: 191148--191197 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
191138 AAATGTAGGG
191148 TTAATTTTGTATAAG-TTT
1 TTAATTTTGTATAAGATTT
*
191166 CTTAATTTTGTATACGATTT
1 -TTAATTTTGTATAAGATTT
*
191186 ATAATTTTGTAT
1 TTAATTTTGTAT
191198 GTGAATGTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 25 0.89
20 3 0.11
ACGTcount: A:0.28, C:0.04, G:0.10, T:0.58
Consensus pattern (19 bp):
TTAATTTTGTATAAGATTT
Found at i:192084 original size:397 final size:396
Alignment explanation
Indices: 191339--192274 Score: 1495
Period size: 397 Copynumber: 2.4 Consensus size: 396
191329 TATTCCAAGT
**
191339 ATACTTTGTGTCCAGAATGATTTCCTTACCAA-GTGCATGGA-AATGTGTCGATACATTTATAAA
1 ATACTTTGTGTCCAGAATGATTTCCTTACCAAGGT-CA-CCACAATGTGTCGATACATTTATAAA
* *
191402 AAGTATCGATCCAAAAAATATCGAGACCCATAATTATAATATAATAGGTAAATTATCAATCTAAC
64 AAGTATCGATCCAAAAAACATCGAGACCCATAATTATAATGTAATAGGTAAATTATCAATCTAAC
* * *
191467 CGGTCTAAATATACCGGTTTATGAGAAAACAGGTGTACATAAAGTATCGACACTTGTTTAATTTG
129 CGGTCTAAATACACCGGTTTATGAGAAAACAGGAGTACATAAAGTATCGACACTTGTTCAATTTG
* *
191532 TGTCGATCCCGTACTTTGTGTCAGAATGATTTCCTTACCAAGGTCACCATAATGTGTCGATACCT
194 TGTCGA---C-TACTTTGTGTCAGAATGATTTCCTTACCAAGGTCACCACAATGTGTCGATACAT
*
191597 TTATAAAAAGTATCGATCCCAAAAACATCGAGACCCATAATTATAATGTAATAGGTAAATTATCA
255 TTATAAAAAGTATCGATCCAAAAAACATCGAGACCCATAATTATAATGTAATAGGTAAATTATCA
*
191662 ATCTAACCGCTCTAAACACACCGGTTTATAAGAAAACAAGTGTACATGAAGTATCGACACGTTTT
320 ATCTAACCGCTCTAAACAAACCGGTTTATAAGAAAACAAGTGTACATGAAGTATCGACACGTTTT
191727 GAATTTGTGTCG
385 GAATTTGTGTCG
*
191739 ATACTTTGTGTCCAGAATGATTTCCTTACCAAGGTTACCACAATGTGTCGATACATTTATAAAAA
1 ATACTTTGTGTCCAGAATGATTTCCTTACCAAGGTCACCACAATGTGTCGATACATTTAT-AAAA
* *
191804 AATATCGATCCAAAAAACATCGAGACTCATAATTATAATGTAATAGGTAAATTATCAATCTAACC
65 AGTATCGATCCAAAAAACATCGAGACCCATAATTATAATGTAATAGGTAAATTATCAATCTAACC
* *
191869 GGTCTAAATACACCGGTTTTTGAGAAAACAGGAGTACATGAAGTATCGACACTCT-TTCAATTTG
130 GGTCTAAATACACCGGTTTATGAGAAAACAGGAGTACATAAAGTATCGACACT-TGTTCAATTTG
191933 TGTCGA-TACTTTGTGTCCAGAATGATTTCCTTACCAAGGTCACCACAATGTGTCGATACATTTA
194 TGTCGACTACTTTGTGT-CAGAATGATTTCCTTACCAAGGTCACCACAATGTGTCGATACATTTA
*
191997 TAAAAAGTATCGATCCAAAAAATATCGAGACCCATAATTATAATGTAATAGGTAAATTATCAATC
258 TAAAAAGTATCGATCCAAAAAACATCGAGACCCATAATTATAATGTAATAGGTAAATTATCAATC
* * * * * *
192062 TAACCGGTCTAAATAAACCGGTTTATGAGAAAACAGGTGTACATGAAGTATCGACACTTTTTTAA
323 TAACCGCTCTAAACAAACCGGTTTATAAGAAAACAAGTGTACATGAAGTATCGACACGTTTTGAA
192127 TTTGTGTCG
388 TTTGTGTCG
* *
192136 ATACTTTGTATCCAGAATGATTTCCTTACCAAGGTCACCACAATGTGTCGCTACATTTATAAAAA
1 ATACTTTGTGTCCAGAATGATTTCCTTACCAAGGTCACCACAATGTGTCGATACATTTATAAAAA
* *
192201 GTATCGATCCAAAAAACATCGAGACCCATAAATATAATGTAATAGGTAAATT-TGCAATGTAACC
66 GTATCGATCCAAAAAACATCGAGACCCATAATTATAATGTAATAGGTAAATTAT-CAATCTAACC
*
192265 GGTATAAATA
130 GGTCTAAATA
192275 TACCTATTTA
Statistics
Matches: 499, Mismatches: 31, Indels: 16
0.91 0.06 0.03
Matches are distributed among these distances:
395 1 0.00
396 82 0.16
397 232 0.46
399 1 0.00
400 52 0.10
401 130 0.26
402 1 0.00
ACGTcount: A:0.37, C:0.17, G:0.15, T:0.31
Consensus pattern (396 bp):
ATACTTTGTGTCCAGAATGATTTCCTTACCAAGGTCACCACAATGTGTCGATACATTTATAAAAA
GTATCGATCCAAAAAACATCGAGACCCATAATTATAATGTAATAGGTAAATTATCAATCTAACCG
GTCTAAATACACCGGTTTATGAGAAAACAGGAGTACATAAAGTATCGACACTTGTTCAATTTGTG
TCGACTACTTTGTGTCAGAATGATTTCCTTACCAAGGTCACCACAATGTGTCGATACATTTATAA
AAAGTATCGATCCAAAAAACATCGAGACCCATAATTATAATGTAATAGGTAAATTATCAATCTAA
CCGCTCTAAACAAACCGGTTTATAAGAAAACAAGTGTACATGAAGTATCGACACGTTTTGAATTT
GTGTCG
Found at i:192106 original size:198 final size:197
Alignment explanation
Indices: 191339--192274 Score: 1484
Period size: 198 Copynumber: 4.7 Consensus size: 197
191329 TATTCCAAGT
**
191339 ATACTTTGTGTCCAGAATGATTTCCTTACCAA-GTGCATGGA-AATGTGTCGATACATTTATAAA
1 ATACTTTGTGTCCAGAATGATTTCCTTACCAAGGT-CA-CCACAATGTGTCGATACATTTATAAA
* *
191402 AAGTATCGATCCAAAAAATATCGAGACCCATAATTATAATATAATAGGTAAATTATCAATCTAAC
64 AAGTATCGATCCAAAAAACATCGAGACCCATAATTATAATGTAATAGGTAAATTATCAATCTAAC
* *
191467 CGGTCTAAATATACCGGTTTATGAGAAAACAGGTGTACATAAAGTATCGACACTTGTTTAATTTG
129 CGGTCTAAATACACCGGTTTATGAGAAAACAGGTGTACATGAAGTATCGACACTT-TTTAATTTG
191532 TGTCG
193 TGTCG
* *
191537 ATCCCGTACTTTGTGT-CAGAATGATTTCCTTACCAAGGTCACCATAATGTGTCGATACCTTTAT
1 A-----TACTTTGTGTCCAGAATGATTTCCTTACCAAGGTCACCACAATGTGTCGATACATTTAT
*
191601 AAAAAGTATCGATCCCAAAAACATCGAGACCCATAATTATAATGTAATAGGTAAATTATCAATCT
61 AAAAAGTATCGATCCAAAAAACATCGAGACCCATAATTATAATGTAATAGGTAAATTATCAATCT
* * * * *
191666 AACCGCTCTAAACACACCGGTTTATAAGAAAACAAGTGTACATGAAGTATCGACACGTTTTGAAT
126 AACCGGTCTAAATACACCGGTTTATGAGAAAACAGGTGTACATGAAGTATCGACAC-TTTTTAAT
191731 TTGTGTCG
190 TTGTGTCG
*
191739 ATACTTTGTGTCCAGAATGATTTCCTTACCAAGGTTACCACAATGTGTCGATACATTTATAAAAA
1 ATACTTTGTGTCCAGAATGATTTCCTTACCAAGGTCACCACAATGTGTCGATACATTTAT-AAAA
* *
191804 AATATCGATCCAAAAAACATCGAGACTCATAATTATAATGTAATAGGTAAATTATCAATCTAACC
65 AGTATCGATCCAAAAAACATCGAGACCCATAATTATAATGTAATAGGTAAATTATCAATCTAACC
* * *
191869 GGTCTAAATACACCGGTTTTTGAGAAAACAGGAGTACATGAAGTATCGACACTCTTTCAATTTGT
130 GGTCTAAATACACCGGTTTATGAGAAAACAGGTGTACATGAAGTATCGACACT-TTTTAATTTGT
191934 GTCG
194 GTCG
191938 ATACTTTGTGTCCAGAATGATTTCCTTACCAAGGTCACCACAATGTGTCGATACATTTATAAAAA
1 ATACTTTGTGTCCAGAATGATTTCCTTACCAAGGTCACCACAATGTGTCGATACATTTATAAAAA
*
192003 GTATCGATCCAAAAAATATCGAGACCCATAATTATAATGTAATAGGTAAATTATCAATCTAACCG
66 GTATCGATCCAAAAAACATCGAGACCCATAATTATAATGTAATAGGTAAATTATCAATCTAACCG
*
192068 GTCTAAATAAACCGGTTTATGAGAAAACAGGTGTACATGAAGTATCGACACTTTTTTAATTTGTG
131 GTCTAAATACACCGGTTTATGAGAAAACAGGTGTACATGAAGTATCGACAC-TTTTTAATTTGTG
192133 TCG
195 TCG
* *
192136 ATACTTTGTATCCAGAATGATTTCCTTACCAAGGTCACCACAATGTGTCGCTACATTTATAAAAA
1 ATACTTTGTGTCCAGAATGATTTCCTTACCAAGGTCACCACAATGTGTCGATACATTTATAAAAA
* *
192201 GTATCGATCCAAAAAACATCGAGACCCATAAATATAATGTAATAGGTAAATT-TGCAATGTAACC
66 GTATCGATCCAAAAAACATCGAGACCCATAATTATAATGTAATAGGTAAATTAT-CAATCTAACC
*
192265 GGTATAAATA
130 GGTCTAAATA
192275 TACCTATTTA
Statistics
Matches: 685, Mismatches: 40, Indels: 26
0.91 0.05 0.03
Matches are distributed among these distances:
197 11 0.02
198 307 0.45
199 186 0.27
201 1 0.00
202 166 0.24
203 14 0.02
ACGTcount: A:0.37, C:0.17, G:0.15, T:0.31
Consensus pattern (197 bp):
ATACTTTGTGTCCAGAATGATTTCCTTACCAAGGTCACCACAATGTGTCGATACATTTATAAAAA
GTATCGATCCAAAAAACATCGAGACCCATAATTATAATGTAATAGGTAAATTATCAATCTAACCG
GTCTAAATACACCGGTTTATGAGAAAACAGGTGTACATGAAGTATCGACACTTTTTAATTTGTGT
CG
Found at i:192659 original size:15 final size:15
Alignment explanation
Indices: 192638--192675 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
192628 CATAGTCGGG
192638 GCTCTTCTCAACCCA
1 GCTCTTCTCAACCCA
*
192653 TCTCTTCTCAACCCA
1 GCTCTTCTCAACCCA
192668 GCTCTTCT
1 GCTCTTCT
192676 GAGGAAATCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.16, C:0.45, G:0.05, T:0.34
Consensus pattern (15 bp):
GCTCTTCTCAACCCA
Found at i:193845 original size:12 final size:12
Alignment explanation
Indices: 193811--193848 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
193801 TAAGCGGTCA
*
193811 ATGAAGATGACG
1 ATGAAGATGATG
193823 ATGAAGATGATG
1 ATGAAGATGATG
*
193835 ATGATGATGATG
1 ATGAAGATGATG
193847 AT
1 AT
193849 CCAAACAAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.39, C:0.03, G:0.32, T:0.26
Consensus pattern (12 bp):
ATGAAGATGATG
Found at i:195190 original size:12 final size:12
Alignment explanation
Indices: 195175--195213 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
195165 TTATAATTAG
195175 AATTTGAATTTA
1 AATTTGAATTTA
* *
195187 AATTTCAATTTG
1 AATTTGAATTTA
*
195199 AGTTTGAATTTA
1 AATTTGAATTTA
195211 AAT
1 AAT
195214 GTAAATTTCG
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.38, C:0.03, G:0.10, T:0.49
Consensus pattern (12 bp):
AATTTGAATTTA
Found at i:195196 original size:18 final size:18
Alignment explanation
Indices: 195175--195209 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
195165 TTATAATTAG
195175 AATTTGAATTTAAATTTC
1 AATTTGAATTTAAATTTC
* *
195193 AATTTGAGTTTGAATTT
1 AATTTGAATTTAAATTT
195210 AAATGTAAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.34, C:0.03, G:0.11, T:0.51
Consensus pattern (18 bp):
AATTTGAATTTAAATTTC
Found at i:196024 original size:201 final size:198
Alignment explanation
Indices: 195667--196700 Score: 1290
Period size: 198 Copynumber: 5.2 Consensus size: 198
195657 AATTCAAAAA
* **
195667 TATCGACACTTTATACATTTGTGTCGATACTTTGTGTCCATAATGTATTTTCCAACCAAAACAAG
1 TATCGACACTTTATACATTTGTGTCGATACTTTATGTCCATAATAAATTTT----CC-AAACAAG
* * * * *
195732 TTCAC-AAATAAGTGTCGACACATTTATATCAAGTGTCGATCCCAAAAACATCGAAACTCGTAAC
61 TTCACGAAA-AAGTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAACACATAAT
* * * * * * * * *
195796 TATAACGTAATAGGTCACTTTACAATGTAACCGGTTTAAATTTATCAGTT-TTATGAGAAAATAG
125 TATAATGTAATAGGTAACATAACAATGTAACCGGTCTAAATATACCGGTTATTA--A-AAAAAAG
*
195860 GTCTACA-ATATG
187 GTATACATA-ATG
* * * ** *
195872 TATCGACACTTTATTCATTTGTGTCGATACATGT-TGTCCAGAATGTA-TTTCCAAACCAAGTGC
1 TATCGACACTTTATACATTTGTGTCGATAC-TTTATGTCCATAATAAATTTTCCAAA-CAAGTTC
195935 ACGAAAAAAGTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAACACATAATTAT
64 ACG-AAAAAGTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAACACATAATTAT
196000 AATGTAATAGGTAACATAACAATGTAACCGGTCTAAATATACCGGTTATTAAAAAAGAAAGGTAT
128 AATGTAATAGGTAACATAACAATGTAACCGGTCTAAATATACCGGTTATT-AAAAA-AAAGGTAT
196065 ACATAATG
191 ACATAATG
* *
196073 TATCGATACTTTATACATTTGTGTCTG-CACTTTATGTCCATAATAAATTTTCCAAACAAGTTCA
1 TATCGACACTTTATACATTTGTGTC-GATACTTTATGTCCATAATAAATTTTCCAAACAAGTTCA
*
196137 CGTAAAAGTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAACACATAATTATAA
65 CGAAAAAGTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAACACATAATTATAA
* * * * *
196202 TGTAAAAGGTAATATAACAATGTAACCGGTCTAAACATACCAGTTATTAAAAAAAAGGTATACGT
130 TGTAATAGGTAACATAACAATGTAACCGGTCTAAATATACCGGTTATTAAAAAAAAGGTATACAT
196267 AATG
195 AATG
* *
196271 TATCGATACTTTATACATTTGTGTCGACACTTTATGTCCATAATAAATTTTCCAAACAAGTTCAC
1 TATCGACACTTTATACATTTGTGTCGATACTTTATGTCCATAATAAATTTTCCAAACAAGTTCAC
*
196336 GAAAAAGTGTCGATATATTTATAACAAGTGTCGATCCCAAAAACATCGAAACACATAATTATAAT
66 GAAAAAGTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAACACATAATTATAAT
* * *
196401 GTAATAGGTAATATAACAATGTAACCGGTCTAAACATACCGGTTATTAAAAAAAAGGTATACGTA
131 GTAATAGGTAACATAACAATGTAACCGGTCTAAATATACCGGTTATTAAAAAAAAGGTATACATA
196466 ATG
196 ATG
* * * *
196469 TATCGATAATTTATACATTTGTGTCGACACTTTATGTCCATAATAAATTTTCAAAACAAGTTCAC
1 TATCGACACTTTATACATTTGTGTCGATACTTTATGTCCATAATAAATTTTCCAAACAAGTTCAC
* * * * *
196534 GAAAAAGTGTCAATACATTTATAAAAAGTGTCGATCCTAAAAACATCGAAACCCGTAATTATAAT
66 GAAAAAGTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAACACATAATTATAAT
* * * * * * * * * * * * *
196599 GTAATAGATCACTTTACAATGTAACCAGT-TTAATTTTCTGGTTTCATGAGAAAATAGGTCTACA
131 GTAATAGGTAACATAACAATGTAACCGGTCTAAATATACCGG-TT-ATTAAAAAAAAGGTATACA
196663 TAATG
194 TAATG
* * *
196668 CATCGACACTTTTTAAATTTGTGTCGATACTTT
1 TATCGACACTTTATACATTTGTGTCGATACTTT
196701 TTAAAATTAC
Statistics
Matches: 748, Mismatches: 67, Indels: 34
0.88 0.08 0.04
Matches are distributed among these distances:
197 8 0.01
198 354 0.47
199 54 0.07
200 121 0.16
201 149 0.20
202 15 0.02
203 1 0.00
204 3 0.00
205 41 0.05
206 2 0.00
ACGTcount: A:0.39, C:0.16, G:0.13, T:0.32
Consensus pattern (198 bp):
TATCGACACTTTATACATTTGTGTCGATACTTTATGTCCATAATAAATTTTCCAAACAAGTTCAC
GAAAAAGTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAACACATAATTATAAT
GTAATAGGTAACATAACAATGTAACCGGTCTAAATATACCGGTTATTAAAAAAAAGGTATACATA
ATG
Found at i:200253 original size:198 final size:197
Alignment explanation
Indices: 199847--200364 Score: 550
Period size: 198 Copynumber: 2.6 Consensus size: 197
199837 ATTAAATTTT
*
199847 GTGTCGATACATTTATAACAA-GTATCGATCAC--AAA-ATCAAAGAGACCGATAATTATAATGT
1 GTGTCGATACATTTA-AA-AATGTATCGATCCCGAAAACATC-AA-A-ACCGATAATTATAATGT
* *
199908 AATAGGTAAATTTTCAATGTAACCGG-TAGAAATATACCGGGTTCATGAGAGAATAGGTCAACAA
61 AATAGGTAAATTTACAATGTAACCGGTTA-AAATATACC-GGTTAATGAGAGAATAGGTCAACAA
* * * * *** *
199972 TATGTATCAACACTTTTTTAATTTGTGTCGATACATTTTTCCAAAATGAATGGCAAACGAGATGT
124 TATGTATCAACACTCTTTAAATATGTGTCGATACATTTTTCCAAAATAAAACACAAACGAGATGC
200037 ACGCATAAA
189 ACGCATAAA
* *
200046 GTGTCGATACATTTGTAAAAAT-TATCGATCCTCG-AAACATCAAAATCGATAATTATTATGTAA
1 GTGTCGATACA-TT-TAAAAATGTATCGATCC-CGAAAACATCAAAACCGATAATTATAATGTAA
* * * *
200109 CAGGTAAATTTACAATGTAACCGGTTAAAATATACCGGTTAATTAGCA-AATAGGTCTACATTAT
63 TAGGTAAATTTACAATGTAACCGGTTAAAATATACCGGTTAATGAG-AGAATAGGTCAACAATAT
*** * *
200173 GTATCGGTACTCTTTAAATATGTGTCGATACTTTTTTCCAAAATAAAACACAAACGAGTTGCACG
127 GTATCAACACTCTTTAAATATGTGTCGATACATTTTTCCAAAATAAAACACAAACGAGATGCACG
200238 CATAAA
192 CATAAA
* * *
200244 GTGTCGATACATTTAAAATTGTATCGATCCCGAAAACATCGAAACCGAT-ATACATAATGTAATA
1 GTGTCGATACATTTAAAAATGTATCGATCCCGAAAACATCAAAACCGATAAT-TATAATGTAATA
* * * * * * * * *
200308 GGTCAATTTATAATGTAACTGGTTTAAATTTACTGGTTTTATGAGAAAATATGTCAA
65 GGTAAATTTACAATGTAACCGGTTAAAATATACCGG-TTAATGAGAGAATAGGTCAA
200365 TATAAGCGCT
Statistics
Matches: 268, Mismatches: 38, Indels: 27
0.80 0.11 0.08
Matches are distributed among these distances:
196 10 0.04
197 65 0.24
198 105 0.39
199 70 0.26
200 8 0.03
201 7 0.03
202 3 0.01
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.31
Consensus pattern (197 bp):
GTGTCGATACATTTAAAAATGTATCGATCCCGAAAACATCAAAACCGATAATTATAATGTAATAG
GTAAATTTACAATGTAACCGGTTAAAATATACCGGTTAATGAGAGAATAGGTCAACAATATGTAT
CAACACTCTTTAAATATGTGTCGATACATTTTTCCAAAATAAAACACAAACGAGATGCACGCATA
AA
Found at i:201078 original size:36 final size:38
Alignment explanation
Indices: 201029--201105 Score: 113
Period size: 37 Copynumber: 2.1 Consensus size: 38
201019 ATAATATTAC
201029 AAATTGTAAAATATTTATAT-ATTTTCTTTAAAAAATT
1 AAATTGTAAAATATTTATATAATTTTCTTTAAAAAATT
* * *
201066 AAATT-TATAATATTTATATAATTTTTTTTACAAAATT
1 AAATTGTAAAATATTTATATAATTTTCTTTAAAAAATT
201103 AAA
1 AAA
201106 ATATAAAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
36 13 0.36
37 23 0.64
ACGTcount: A:0.47, C:0.03, G:0.01, T:0.49
Consensus pattern (38 bp):
AAATTGTAAAATATTTATATAATTTTCTTTAAAAAATT
Done.