Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001611.1 Hibiscus syriacus cultivar Beakdansim tig00003200_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: 81657
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:1295 original size:40 final size:40
Alignment explanation
Indices: 1240--1328 Score: 169
Period size: 40 Copynumber: 2.2 Consensus size: 40
1230 AAAATAATGG
*
1240 AATAGCAGTCCGCTATTGCCGCGATTGGCCGCTACCCATT
1 AATAGCAGCCCGCTATTGCCGCGATTGGCCGCTACCCATT
1280 AATAGCAGCCCGCTATTGCCGCGATTGGCCGCTACCCATT
1 AATAGCAGCCCGCTATTGCCGCGATTGGCCGCTACCCATT
1320 AATAGCAGC
1 AATAGCAGC
1329 TGTAACTCAC
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 48 1.00
ACGTcount: A:0.22, C:0.33, G:0.22, T:0.22
Consensus pattern (40 bp):
AATAGCAGCCCGCTATTGCCGCGATTGGCCGCTACCCATT
Found at i:12188 original size:20 final size:20
Alignment explanation
Indices: 12158--12197 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
12148 GCTTCCAGCT
12158 TAATCAAATATGAATAAAAAA
1 TAATCAAATAT-AATAAAAAA
*
12179 TAAT-AAATATATTAAAAAA
1 TAATCAAATATAATAAAAAA
12198 GGGAAAATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 8 0.44
20 6 0.33
21 4 0.22
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.28
Consensus pattern (20 bp):
TAATCAAATATAATAAAAAA
Found at i:13676 original size:18 final size:18
Alignment explanation
Indices: 13650--13684 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
13640 TACCTATTAT
13650 TAAAATATAAAAAAATTC
1 TAAAATATAAAAAAATTC
* *
13668 TAAATTATATAAAAATT
1 TAAAATATAAAAAAATT
13685 TAGTAGAACA
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:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (18 bp):
TAAAATATAAAAAAATTC
Found at i:21228 original size:2 final size:2
Alignment explanation
Indices: 21221--21251 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
21211 TCTGTCCGAC
*
21221 TA TA TA TA TA TA CA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
21252 GTATGTGTGC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:29081 original size:57 final size:57
Alignment explanation
Indices: 28991--29102 Score: 206
Period size: 57 Copynumber: 2.0 Consensus size: 57
28981 TATCTCTAGA
* *
28991 TTGAGAGTTAGGAGGAAGAAGGAAAAGCTCATTTTCTATTTCTCATAGGAGTTTAGT
1 TTGAGAGATAGGAGGAAGAAGGAAAAGCCCATTTTCTATTTCTCATAGGAGTTTAGT
29048 TTGAGAGATAGGAGGAAGAAGGAAAAGCCCATTTTCTATTTCTCATAGGAGTTTA
1 TTGAGAGATAGGAGGAAGAAGGAAAAGCCCATTTTCTATTTCTCATAGGAGTTTA
29103 TATTGTTGGT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
57 53 1.00
ACGTcount: A:0.33, C:0.10, G:0.26, T:0.31
Consensus pattern (57 bp):
TTGAGAGATAGGAGGAAGAAGGAAAAGCCCATTTTCTATTTCTCATAGGAGTTTAGT
Found at i:29702 original size:2 final size:2
Alignment explanation
Indices: 29695--29731 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
29685 GATGTATAAG
29695 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29732 TTGGCCATCT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:44752 original size:29 final size:28
Alignment explanation
Indices: 44710--44776 Score: 89
Period size: 29 Copynumber: 2.3 Consensus size: 28
44700 CAAATCTGTC
* *
44710 CCCGTTTAGCATAAACAGTTTTTTCCCCT
1 CCCGTTTAACATAAACA-ATTTTTCCCCT
*
44739 CCCGTTTAACATAAACAATTTTTCCCGT
1 CCCGTTTAACATAAACAATTTTTCCCCT
44767 CTCCGTTTAA
1 C-CCGTTTAA
44777 TTCGGTTTTC
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
28 10 0.29
29 24 0.71
ACGTcount: A:0.24, C:0.30, G:0.09, T:0.37
Consensus pattern (28 bp):
CCCGTTTAACATAAACAATTTTTCCCCT
Found at i:52497 original size:77 final size:76
Alignment explanation
Indices: 52396--52619 Score: 254
Period size: 77 Copynumber: 2.9 Consensus size: 76
52386 ATATGATTGC
* * *
52396 GCCTAAAAATATCATGATTTACTAAGGAATATGTTACAATCTGGAATGTTAATATTTTTATTAAT
1 GCCTAAAAATATCATGATTCACTAAGAAATAAGTTACAATCTGGAATGTTAATATTTTTATTAAT
52461 AAAATGAGTT-
66 AAAATGAGTTA
* * * *** *
52471 GTTCTCAAAAATATCATGATTCACTAAAAAAATAGGTTTTGATCTGGAACG-TAATATTTTTATT
1 G-CCT-AAAAATATCATGATTCACT-AAGAAATAAGTTACAATCTGGAATGTTAATATTTTTATT
52535 AATAAAATGAGTTA
63 AATAAAATGAGTTA
* * * * * *
52549 CGCCTAAGAATGTCATAATTCACTAAGAAATAAGTTGCAATCTGAAATGTTAATAATTTTATTAA
1 -GCCTAAAAATATCATGATTCACTAAGAAATAAGTTACAATCTGGAATGTTAATATTTTTATTAA
52614 TAAAAT
65 TAAAAT
52620 AGATTGCACA
Statistics
Matches: 122, Mismatches: 21, Indels: 10
0.80 0.14 0.07
Matches are distributed among these distances:
75 1 0.01
76 20 0.16
77 80 0.66
78 20 0.16
79 1 0.01
ACGTcount: A:0.42, C:0.09, G:0.12, T:0.37
Consensus pattern (76 bp):
GCCTAAAAATATCATGATTCACTAAGAAATAAGTTACAATCTGGAATGTTAATATTTTTATTAAT
AAAATGAGTTA
Found at i:52638 original size:77 final size:76
Alignment explanation
Indices: 52380--52655 Score: 243
Period size: 77 Copynumber: 3.6 Consensus size: 76
52370 TGAATATACA
* * * * *
52380 TAATAAATATGA-TTGCGCCTAAAAATATCATGATTTACTAAGGAATATGTTACAATCTGGAATG
1 TAATAAA-ATGAGTTGCACC-AAAAATGTCATGATTCACTAAGAAATAAGTTACAATCTGGAATG
52444 TTAATATTTTTAT
64 TTAATATTTTTAT
** * * * *** *
52457 TAATAAAATGAGTTGTTCTCAAAAATATCATGATTCACTAAAAAAATAGGTTTTGATCTGGAACG
1 TAATAAAATGAGTTGCAC-CAAAAATGTCATGATTCACT-AAGAAATAAGTTACAATCTGGAATG
52522 -TAATATTTTTAT
64 TTAATATTTTTAT
* * * * * *
52534 TAATAAAATGAGTTACGCCTAAGAATGTCATAATTCACTAAGAAATAAGTTGCAATCTGAAATGT
1 TAATAAAATGAGTTGCACC-AAAAATGTCATGATTCACTAAGAAATAAGTTACAATCTGGAATGT
*
52599 TAATAATTTTAT
65 TAATATTTTTAT
* * * *
52611 TAATAAAAT-AGATTGCACACAATAATGTTATGGTCCACTAAGAAA
1 TAATAAAATGAG-TTGCAC-CAAAAATGTCATGATTCACTAAGAAA
52656 GTACTATGTG
Statistics
Matches: 161, Mismatches: 31, Indels: 14
0.78 0.15 0.07
Matches are distributed among these distances:
76 25 0.16
77 116 0.72
78 20 0.12
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.35
Consensus pattern (76 bp):
TAATAAAATGAGTTGCACCAAAAATGTCATGATTCACTAAGAAATAAGTTACAATCTGGAATGTT
AATATTTTTAT
Found at i:52668 original size:154 final size:153
Alignment explanation
Indices: 52380--52694 Score: 332
Period size: 154 Copynumber: 2.1 Consensus size: 153
52370 TGAATATACA
* * * * * *
52380 TAATAAATATGATTGCGCCTAAAAATATCATGATTTACTAAGGAATATGTTACAATCTGGAATGT
1 TAATAAA-ATGATTACGCCTAAAAATATCATAATTCACTAAGAAATAAGTTACAATCTGAAATGT
* ** * * * *
52445 TAATATTTTTATTAATAAAATGAGTTGTTCTCAAAAATATCATGATTCACTAAAAAAATAGGTTT
65 TAATAATTTTATTAATAAAATGAGTTGCACACAAAAATATCATGATCCACTAAAAAAATAGCTTG
*
52510 TGATCTGGAACGTAATATTTT-TAT
130 TGATCTAGAACGTAAT-TTTTCTAT
* * *
52534 TAATAAAATGAGTTACGCCTAAGAATGTCATAATTCACTAAGAAATAAGTTGCAATCTGAAATGT
1 TAATAAAATGA-TTACGCCTAAAAATATCATAATTCACTAAGAAATAAGTTACAATCTGAAATGT
* * * * * *
52599 TAATAATTTTATTAATAAAAT-AGATTGCACACAATAATGTTATGGTCCACTAAGAAAGTA-CTA
65 TAATAATTTTATTAATAAAATGAG-TTGCACACAAAAATATCATGATCCACTAAAAAAATAGCT-
* *
52662 TGTGATCTAGAATGTTATTTTTCTAT
128 TGTGATCTAGAACGTAATTTTTCTAT
52688 T-ATAAAA
1 TAATAAAA
52695 AATTTAAAAG
Statistics
Matches: 132, Mismatches: 25, Indels: 9
0.80 0.15 0.05
Matches are distributed among these distances:
153 17 0.13
154 115 0.87
ACGTcount: A:0.41, C:0.10, G:0.13, T:0.37
Consensus pattern (153 bp):
TAATAAAATGATTACGCCTAAAAATATCATAATTCACTAAGAAATAAGTTACAATCTGAAATGTT
AATAATTTTATTAATAAAATGAGTTGCACACAAAAATATCATGATCCACTAAAAAAATAGCTTGT
GATCTAGAACGTAATTTTTCTAT
Found at i:52737 original size:20 final size:20
Alignment explanation
Indices: 52697--52737 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
52687 TTATAAAAAA
**
52697 TTTAAAAGTATGGATACTTT
1 TTTAAAAGTATCAATACTTT
52717 TTTAAAAGTATCAATA-TTT
1 TTTAAAAGTATCAATACTTT
52736 TT
1 TT
52738 GAATTTAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.37, C:0.05, G:0.10, T:0.49
Consensus pattern (20 bp):
TTTAAAAGTATCAATACTTT
Found at i:53133 original size:77 final size:77
Alignment explanation
Indices: 53019--53479 Score: 519
Period size: 76 Copynumber: 6.1 Consensus size: 77
53009 TAATGGACAA
* * * * * * *
53019 ATTAACATTCCAGATCACAACTTGATTTCTTAGTGAACCATAACATTCTTGTGTGCAATTCATTT
1 ATTAACATTCCATATCGCAACCT-ATTTATTAGTGAACCATGACATTCTTGTGCGCAACTCATTT
53084 TATTAATAAAAAT
65 TATTAATAAAAAT
* * *
53097 ATTAACACTCCATATCGCAACCTATTTATTAGTGAACAATGACATTC-T-T--G-AATTCATTTT
1 ATTAACATTCCATATCGCAACCTATTTATTAGTGAACCATGACATTCTTGTGCGCAACTCA-TTT
53157 TATTAAT-AAAAT
65 TATTAATAAAAAT
* * * * *
53169 ATTAACATTCCAAATCGCAACCTATTTATTAGTGATCTATGACATTCTTGTTCGCAACCCATTTT
1 ATTAACATTCCATATCGCAACCTATTTATTAGTGAACCATGACATTCTTGTGCGCAACTCATTTT
53234 ATTAATAAAAAT
66 ATTAATAAAAAT
* * * * *
53246 ATTAACATTTCATATCG-TACCTATTTATTTGTGAACCATGATATTCTTGGGCGCAACTCATTTT
1 ATTAACATTCCATATCGCAACCTATTTATTAGTGAACCATGACATTCTTGTGCGCAACTCATTTT
53310 ATTAATAAAAAT
66 ATTAATAAAAAT
* * * *
53322 ATTAACATTCCATATCGTAA-CTCATTTATTAGTGAACCATGATATTCTTGTGCACAACCCATTT
1 ATTAACATTCCATATCGCAACCT-ATTTATTAGTGAACCATGACATTCTTGTGCGCAACTCATTT
*
53386 TATTATTAAAAAT
65 TATTAATAAAAAT
* * * * ** *
53399 ATTAACATTTCATATCACAACATGTTT-TTAGTGAAGAATGACATTCTTG-GACGCAACTTATTT
1 ATTAACATTCCATATCGCAACCTATTTATTAGTGAACCATGACATTCTTGTG-CGCAACTCATTT
*
53462 TGTTAATAAAAAT
65 TATTAATAAAAAT
53475 ATTAA
1 ATTAA
53480 TAAAAATATT
Statistics
Matches: 329, Mismatches: 43, Indels: 24
0.83 0.11 0.06
Matches are distributed among these distances:
72 54 0.16
73 12 0.04
74 1 0.00
75 2 0.01
76 125 0.38
77 115 0.35
78 20 0.06
ACGTcount: A:0.36, C:0.16, G:0.09, T:0.39
Consensus pattern (77 bp):
ATTAACATTCCATATCGCAACCTATTTATTAGTGAACCATGACATTCTTGTGCGCAACTCATTTT
ATTAATAAAAAT
Found at i:53198 original size:38 final size:38
Alignment explanation
Indices: 53155--53274 Score: 91
Period size: 38 Copynumber: 3.2 Consensus size: 38
53145 TGAATTCATT
53155 TTTATTAATAAAATATTAACATTCCAAATCGCAACCTA
1 TTTATTAATAAAATATTAACATTCCAAATCGCAACCTA
* * ** * **** *
53193 TTTATTAGTGATCTA-TGACATTCTTGTTCGCAACCCA
1 TTTATTAATAAAATATTAACATTCCAAATCGCAACCTA
* * *
53230 TTTTATTAATAAAAATATTAACATTTCATATCG-TACCTA
1 -TTTATTAAT-AAAATATTAACATTCCAAATCGCAACCTA
53269 TTTATT
1 TTTATT
53275 TGTGAACCAT
Statistics
Matches: 57, Mismatches: 22, Indels: 6
0.67 0.26 0.07
Matches are distributed among these distances:
37 16 0.28
38 25 0.44
39 7 0.12
40 9 0.16
ACGTcount: A:0.36, C:0.17, G:0.06, T:0.42
Consensus pattern (38 bp):
TTTATTAATAAAATATTAACATTCCAAATCGCAACCTA
Found at i:53369 original size:153 final size:152
Alignment explanation
Indices: 53019--53479 Score: 533
Period size: 153 Copynumber: 3.0 Consensus size: 152
53009 TAATGGACAA
* * * * * **
53019 ATTAACATTCCAGATCACAACTTGATTTCTTAGTGAACCATAACATTCTTGTGT-GCAATTCATT
1 ATTAACATTCCAAATCGCAAC-TCATTTATTAGTGAACCATGACATTCTTGT-TCGCAACCCATT
* * *
53083 TTATTAATAAAAATATTAACACTCCATATCGCAACCTATTTATTAGTGAACAATGACATTCTT--
64 TTATTAATAAAAATATTAACATTTCATATCG-AACCTATTTATTTGTGAACAATGACATTCTTGG
*
53146 -G-AATTCATTTTTATTAAT-AAAAT
128 CGCAACTCA-TTTTATTAATAAAAAT
* *
53169 ATTAACATTCCAAATCGCAAC-CTATTTATTAGTGATCTATGACATTCTTGTTCGCAACCCATTT
1 ATTAACATTCCAAATCGCAACTC-ATTTATTAGTGAACCATGACATTCTTGTTCGCAACCCATTT
* * *
53233 TATTAATAAAAATATTAACATTTCATATCGTACCTATTTATTTGTGAACCATGATATTCTTGGGC
65 TATTAATAAAAATATTAACATTTCATATCGAACCTATTTATTTGTGAACAATGACATTCTT-GGC
53298 GCAACTCATTTTATTAATAAAAAT
129 GCAACTCATTTTATTAATAAAAAT
* * * * *
53322 ATTAACATTCCATATCGTAACTCATTTATTAGTGAACCATGATATTCTTGTGCACAACCCATTTT
1 ATTAACATTCCAAATCGCAACTCATTTATTAGTGAACCATGACATTCTTGTTCGCAACCCATTTT
* * * * * *
53387 ATTATTAAAAATATTAACATTTCATATCACAACATGTTT-TTAGTGAAGAATGACATTCTTGGAC
66 ATTAATAAAAATATTAACATTTCATATC-GAACCTATTTATTTGTGAACAATGACATTCTTGG-C
* *
53451 GCAACTTATTTTGTTAATAAAAAT
129 GCAACTCATTTTATTAATAAAAAT
53475 ATTAA
1 ATTAA
53480 TAAAAATATT
Statistics
Matches: 266, Mismatches: 34, Indels: 19
0.83 0.11 0.06
Matches are distributed among these distances:
148 28 0.11
149 61 0.23
150 19 0.07
152 13 0.05
153 138 0.52
154 7 0.03
ACGTcount: A:0.36, C:0.16, G:0.09, T:0.39
Consensus pattern (152 bp):
ATTAACATTCCAAATCGCAACTCATTTATTAGTGAACCATGACATTCTTGTTCGCAACCCATTTT
ATTAATAAAAATATTAACATTTCATATCGAACCTATTTATTTGTGAACAATGACATTCTTGGCGC
AACTCATTTTATTAATAAAAAT
Found at i:53481 original size:12 final size:12
Alignment explanation
Indices: 53464--53491 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
53454 ACTTATTTTG
53464 TTAATAAAAATA
1 TTAATAAAAATA
53476 TTAATAAAAATA
1 TTAATAAAAATA
53488 TTAA
1 TTAA
53492 CATTCTAGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (12 bp):
TTAATAAAAATA
Found at i:53776 original size:77 final size:77
Alignment explanation
Indices: 53656--53798 Score: 198
Period size: 77 Copynumber: 1.9 Consensus size: 77
53646 GGTGTAACCC
* * * * *
53656 ATTTTATTATTAAAAATATTAAGATTACAGATAACAACATATTTAC-TAGTGAACCATGACATTA
1 ATTTTATTAATAAAAATATTAACACTACAGATAACAACATATTT-CTTAATGAACCATAACATTA
53720 TTGGGCGTAACAT
65 TTGGGCGTAACAT
* * *
53733 ATTTTATTAATAAAAATATTAACACTACAGATCATAACATATTTCTTAATGAACCATAATATTAT
1 ATTTTATTAATAAAAATATTAACACTACAGATAACAACATATTTCTTAATGAACCATAACATTAT
53798 T
66 T
53799 TGGTGCAATC
Statistics
Matches: 57, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
76 1 0.02
77 56 0.98
ACGTcount: A:0.43, C:0.12, G:0.08, T:0.37
Consensus pattern (77 bp):
ATTTTATTAATAAAAATATTAACACTACAGATAACAACATATTTCTTAATGAACCATAACATTAT
TGGGCGTAACAT
Found at i:57209 original size:21 final size:21
Alignment explanation
Indices: 57185--57224 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
57175 GATTTTATGT
*
57185 TGGGGACGAACTTAAATTTAA
1 TGGGGACGAACTAAAATTTAA
*
57206 TGGGGATGAACTAAAATTT
1 TGGGGACGAACTAAAATTT
57225 TAAAGAGGTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.07, G:0.25, T:0.30
Consensus pattern (21 bp):
TGGGGACGAACTAAAATTTAA
Found at i:62407 original size:2 final size:2
Alignment explanation
Indices: 62400--62443 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
62390 ATAAACTTTA
62400 AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT
62442 AT
1 AT
62444 CCAAATATTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:65352 original size:24 final size:24
Alignment explanation
Indices: 65320--65366 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
65310 AACGGTCCAT
65320 GACTAAAATAGAAAAATATAACAC
1 GACTAAAATAGAAAAATATAACAC
65344 GACTAAAATAGAAAAATATAACA
1 GACTAAAATAGAAAAATATAACA
65367 TTGCTGATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.64, C:0.11, G:0.09, T:0.17
Consensus pattern (24 bp):
GACTAAAATAGAAAAATATAACAC
Found at i:67578 original size:114 final size:111
Alignment explanation
Indices: 67378--67683 Score: 313
Period size: 111 Copynumber: 2.7 Consensus size: 111
67368 CAAAGAACAT
*
67378 ATTGAAGATCCCATAGCTGGGCAGCAAAAAAAGTAAACCCCTTAGGAGTAGAAGCAGAGAAATAA
1 ATTGAAGATCCCATAGCTAGGCAGCAAAAAAAGTAAACCCCTTAGGAGTAGAAGCAGAGAAATAA
*
67443 TGAGGCAGACCCAGAACATGCCGAATGGGACTCACAAAGATCAAAG
66 TGAGGCAGACCCAGAACATGCCAAATGGGACTCACAAAGATCAAAG
* * * *
67489 ATTGATGATCCCATAG-TCAGGCAGCAAGCAAAGAAGTAAATCCCTTGGGTGTAGAAGCAGAGAA
1 ATTGAAGATCCCATAGCT-AGGCAGCAA--AAA-AAGTAAACCCCTTAGGAGTAGAAGCAGAGAA
* * * * *
67553 GTAATGAGGCATACGCAGAAGATGCCAAATGGGACCTGACCCACAAATATC-AAG
62 ATAATGAGGCAGACCCAGAACATGCCAAATGGGA-CT----CACAAAGATCAAAG
* ** * *
67607 CATTGAAGAT----GAGCCGGGCAGC-AAAGAAGTAAACCCCTTAGGTGTAGAAGCAGA-AAAGT
1 -ATTGAAGATCCCATAGCTAGGCAGCAAAAAAAGTAAACCCCTTAGGAGTAGAAGCAGAGAAA-T
67666 AATGAGGCAGACCCAGAA
64 AATGAGGCAGACCCAGAA
67684 GACACCTCAA
Statistics
Matches: 162, Mismatches: 21, Indels: 24
0.78 0.10 0.12
Matches are distributed among these distances:
110 3 0.02
111 66 0.41
112 2 0.01
113 3 0.02
114 58 0.36
115 10 0.06
118 3 0.02
119 17 0.10
ACGTcount: A:0.40, C:0.19, G:0.26, T:0.15
Consensus pattern (111 bp):
ATTGAAGATCCCATAGCTAGGCAGCAAAAAAAGTAAACCCCTTAGGAGTAGAAGCAGAGAAATAA
TGAGGCAGACCCAGAACATGCCAAATGGGACTCACAAAGATCAAAG
Found at i:73042 original size:20 final size:20
Alignment explanation
Indices: 73019--73066 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
73009 TAAAGAAGTG
73019 GGTGAAAGCTCAAAGGCCAA
1 GGTGAAAGCTCAAAGGCCAA
*
73039 GGTGAAAGCTCAAAGGCGAA
1 GGTGAAAGCTCAAAGGCCAA
*
73059 GGGGAAAG
1 GGTGAAAG
73067 AGAAAGCTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.40, C:0.15, G:0.38, T:0.08
Consensus pattern (20 bp):
GGTGAAAGCTCAAAGGCCAA
Found at i:75390 original size:16 final size:19
Alignment explanation
Indices: 75358--75397 Score: 59
Period size: 17 Copynumber: 2.3 Consensus size: 19
75348 ATGAAAATTG
75358 ATTTATCTTTGATTAATA-
1 ATTTATCTTTGATTAATAT
75376 ATTTAT-TTT-ATTAATAT
1 ATTTATCTTTGATTAATAT
75393 ATTTA
1 ATTTA
75398 CCTTGAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.33
17 8 0.38
18 6 0.29
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.60
Consensus pattern (19 bp):
ATTTATCTTTGATTAATAT
Found at i:75580 original size:2 final size:2
Alignment explanation
Indices: 75567--75608 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
75557 TCCGTCACTA
*
75567 AT AT AA AT AT AT AT 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 AT AT AT AT AT AT AT
75609 TAAGCTTTGG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:76809 original size:30 final size:29
Alignment explanation
Indices: 76745--76815 Score: 72
Period size: 30 Copynumber: 2.4 Consensus size: 29
76735 ATATTAAGAA
* * *
76745 AATAAATTTAAATTTATGAGTTTTAATAG
1 AATAAAATTAAATTTATAAATTTTAATAG
*
76774 GATAAAATTAAATTTATAAAATTTTAA-ATG
1 AATAAAATTAAATTTAT-AAATTTTAATA-G
*
76804 AATAAAAATAAA
1 AATAAAATTAAA
76816 AAAATTAATA
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
29 16 0.47
30 18 0.53
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.38
Consensus pattern (29 bp):
AATAAAATTAAATTTATAAATTTTAATAG
Found at i:76938 original size:35 final size:35
Alignment explanation
Indices: 76887--76955 Score: 122
Period size: 35 Copynumber: 2.0 Consensus size: 35
76877 GACGTTGTTG
76887 TTATTTATTTCACTAGTTCCATCCATGATTATAGC
1 TTATTTATTTCACTAGTTCCATCCATGATTATAGC
76922 TTATTTATTT-AGCTAGTTCCATCCATGATTATAG
1 TTATTTATTTCA-CTAGTTCCATCCATGATTATAG
76956 AGACGTGATG
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
34 1 0.03
35 32 0.97
ACGTcount: A:0.26, C:0.17, G:0.10, T:0.46
Consensus pattern (35 bp):
TTATTTATTTCACTAGTTCCATCCATGATTATAGC
Found at i:78147 original size:2 final size:2
Alignment explanation
Indices: 78140--78175 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
78130 ATTCTAACCC
78140 AT AT AT AT AT AT AT AT -T AT A- AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
78176 CATCACATCT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 30 0.94
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:78188 original size:20 final size:20
Alignment explanation
Indices: 78142--78188 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
78132 TCTAACCCAT
* *
78142 ATATATATATATATTATAAT
1 ATATATATATATATCATAAC
*
78162 ATATATATATATATCATCAC
1 ATATATATATATATCATAAC
*
78182 ATCTATA
1 ATATATA
78189 ATAATGAGCA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.45
Consensus pattern (20 bp):
ATATATATATATATCATAAC
Done.