Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003326.1 Hibiscus syriacus cultivar Beakdansim tig00007007_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: 139053
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:2501 original size:3 final size:3
Alignment explanation
Indices: 2488--2522 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
2478 TAATGAATTG
*
2488 ATT ACT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
2523 CAAGGATAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:5167 original size:944 final size:934
Alignment explanation
Indices: 3307--5194 Score: 3087
Period size: 944 Copynumber: 2.0 Consensus size: 934
3297 CAATATGATT
3307 TAATTCAATTAATTTGACATATTATAAAATTGTCGATTCCGTTTTTTTCGCCATGGCAGAGAAAG
1 TAATTCAATTAATTTGACATATTATAAAATTGTCGATTCCG--TTTTTCGCCATGGCAGAGAAAG
3372 ATCAGTACCGACTTGGGGTTTTTCTTTGAAAAGAATTTTAAAATGTGAGGAGTTCACCACCAATC
64 ATCAGTACCGACTTGGGGTTTTTCTTTGAAAAGAATTTTAAAATGTGAGGAGTTCACCACCAATC
3437 ATTTAGTGTGATTATGACACTATAAAAACGGGTGATTTTAATAAAAACATTTTATTTTTATCAAA
129 ATTTAGTGTGATTATGACACTATAAAAACGGGTGATTTTAATAAAAACATTTTATTTTTATCAAA
* **
3502 ATATCAAATTTTAAGGTTTGCGAAAATCCAAAAATCAGGTTCGAGAGTCGGTTACGCGTGGGAAG
194 ATACCAAATTTTAAGGTTTGCGAAAATCCAAAAATCAAATTCGAGAGTCGGTTACGCGTGGGAAG
3567 GATTACACCCCCACAAGTGCCCAAAATTGGTACCTAGTTGATTACCCTATATTAGAATCGAAAAT
259 GATTACACCCCCACAAGTGCCCAAAATTGGTACCTAGTTGATTACCCTATATTAGAATCGAAAAT
3632 TTTGAGTTCGAACTTTACTTAATTTAAAAATTATTACGGATGCAAAGTTGAAAAGAGTATTCGTT
324 TTTGAGTTCGAACTTTACTTAATTTAAAAATTATTACGGATGCAAAGTTGAAAAGAGTATTCGTT
* **
3697 TATTAGGCCGATAGCATTCGCCCCTAGCATAAATGCGGAGATCAACTATTGTGCCTATAATCGAA
389 TATTAGGCCGATAACATAAGCCCCTAGCATAAATGCGGAGATCAACTATTGTGCCTATAATCGAA
*
3762 CATTGCCTTAATTTTAGAAATCATGATGTGGTCTTGAAAATGATGTCTACCTATTTCGGGAATCT
454 CATTGCCTTAATTTTAG-AA-CATGATGTGGTCTTGAAAATGATGTCAACCTATTTCGGGAATCT
3827 CCAGTAGTCACCCCTGGGCATACTTGCGGGAGATATATCATTAATTCCCTAATAAGTGAACATTG
517 -CAGTAGTCACCCCTGGGCATACTTGCGGGAGA-ATATCATTAATTCCCTAATAAGTGAACATTG
*
3892 CCTTAGGTTTAAAAATAAAATGCAATCAAACAAATTTTTATTCATCATAATTAAGCTGGGTAAAT
580 CCTTAGGTTTAAAAATAAAATGCAATCAAACAAATTTTTATTCATCATAATTAAACTGGGTAAAT
* *
3957 TAAGGCTTTTTCTAACTTAAAGTGTCAAATTATGAATAATTAAAAAACCTAGAGGCATAAACCTA
645 TAAGGCTTTTTCTAACTTAAAATATCAAATTATGAATAATTAAAAAACCTAGAGGCA-AAACCTA
*
4022 AAAGGTGTAGGCTCTAATATTAATCTTAATCATTTTTGGTAAATTATTGAATTGAACAACCAAAA
709 AAAGGTGTAGGCTCTAATATTAATCTTAATAATTTTTGGTAAATTATTGAATTGAACAACCAAAA
*
4087 TGGAGCCTCGAGCATAAGTGAAGACCAAATCGAAAATTCTTAGATTAAAGGACAAAGTTAAAAGG
774 TGGAGCCTCGAGCATAAGTGAAGACCAAATCAAAAATTCTTAGATTAAAGGACAAAGTTAAAAGG
4152 AATTTAAAATTGAAGGCAAAATTAGAAAAAATTAATGAATACAAAAGGACTAAATTAAAGAGAAT
839 AATTTAAAATTGAAGGCAAAATTAGAAAAAATTAATGAATACAAAAGGACTAAATTAAAGAGAAT
4217 AAAAAATGGAAGGCTAAATTGAAATATTGAG
904 AAAAAATGGAAGGCTAAATTGAAATATTGAG
** *
4248 TAATTCAATTTAATTTTGACATAATATTATAAAATTGTCGATT-CG-TTTTCGCCATGGTGGGGA
1 TAATTCAA-TTAA-TTTGAC---ATATTATAAAATTGTCGATTCCGTTTTTCGCCATGGCAGAGA
*
4311 AAGATCAGTACCGACTTGGGGGTTTTTCTTTGAAAAGAATTTTGAAATGTGAGGAG-TCACCACC
61 AAGATCAGTACCGACTT-GGGGTTTTTCTTTGAAAAGAATTTTAAAATGTGAGGAGTTCACCACC
4375 AATCATTTAAGGTGTGATTATGACACTATAAAAACCGGGTGATTTTAAT-AAAACATTTTATTTT
125 AATCATTT-A-GTGTGATTATGACACTATAAAAA-CGGGTGATTTTAATAAAAACATTTTATTTT
* * *
4439 TATCAAAATACCAAATTTTAAGGTTTGCGAAAATCCAGAAATCAAATTCGGGAGTCGGTTACGTG
187 TATCAAAATACCAAATTTTAAGGTTTGCGAAAATCCAAAAATCAAATTCGAGAGTCGGTTACGCG
4504 -GGGAAGGATTA-ACACCCCACAAGTGCCCAAATATTGGTACCTAGTTGATTACCCTAT-TTAGA
252 TGGGAAGGATTACAC-CCCCACAAGTGCCCAAA-ATTGGTACCTAGTTGATTACCCTATATTAGA
* *
4566 ATCGAAAATTTTGAGTTCGAACTTTACTTAATTTAAAAATTATTATGGATGCAAATTTGAAAAGA
315 ATCGAAAATTTTGAGTTCGAACTTTACTTAATTTAAAAATTATTACGGATGCAAAGTTGAAAAGA
* *
4631 GTATTCGTTTATTAAGGCCGATAACATAATCCCCTAGCATAAATGGGGAGATCAACTATTGTGCC
380 GTATTCGTTTATT-AGGCCGATAACATAAGCCCCTAGCATAAATGCGGAGATCAACTATTGTGCC
4696 TAATAATCGAACATTGCCTTAATTTTAG-A-AT-ATGTGGTCTTGAAAATGATGTCAACCTA-TT
444 T-ATAATCGAACATTGCCTTAATTTTAGAACATGATGTGGTCTTGAAAATGATGTCAACCTATTT
4757 CGGGAATCT-AGTAGTCACCCCTGGGCATACTTGCGGGAG-ATATCATTAATTCCCTAATAAGTG
508 CGGGAATCTCAGTAGTCACCCCTGGGCATACTTGCGGGAGAATATCATTAATTCCCTAATAAGTG
4820 AACATTGCCTTAGGTTTAAAAATAAAATGCAATCAAACAAA-TTTTATTCATCATAATTAAACTA
573 AACATTGCCTTAGGTTTAAAAATAAAATGCAATCAAACAAATTTTTATTCATCATAATTAAACT-
4884 AGGGTAAATTAAGGCTTTTTCTAACTTAAATTTTATTCATCATAATCAAATTATGAATAATTAAA
637 -GGGTAAATTAAGGCTTTTTCTAACTT--A----A---A--AT-ATCAAATTATGAATAATTAAA
*
4949 GAACCTAGAGGC-AAACCTAAAAGGTGTAGGCTCTAATATTAATCTTAATAATTTTTGGTAAATT
689 AAACCTAGAGGCAAAACCTAAAAGGTGTAGGCTCTAATATTAATCTTAATAATTTTTGGTAAATT
5013 ATTGAATTGAAC-ACCAAAATGGAGCCTCGAGCATAAGTGAAGACCAAATCAAAAATTCTCTTAG
754 ATTGAATTGAACAACCAAAATGGAGCCTCGAGCATAAGTGAAGACCAAATCAAAAA-T-TCTTAG
5077 ATTAAAGGACAAAGTTAAAAGGAATTTAAAATTGAAGGC-AAATTAGAAAACAATTAATGAATAC
817 ATTAAAGGACAAAGTTAAAAGGAATTTAAAATTGAAGGCAAAATTAGAAAA-AATTAATGAATAC
5141 AAAAGGACT-AATTAAAGAG-A-AAAAAATGGAAGGCTAAATTGAAATATTGAG
881 AAAAGGACTAAATTAAAGAGAATAAAAAATGGAAGGCTAAATTGAAATATTGAG
5192 TAA
1 TAA
5195 AGGACTAAAA
Statistics
Matches: 893, Mismatches: 24, Indels: 57
0.92 0.02 0.06
Matches are distributed among these distances:
934 21 0.02
935 65 0.07
936 26 0.03
937 30 0.03
938 1 0.00
939 11 0.01
940 27 0.03
941 10 0.01
942 55 0.06
943 154 0.17
944 203 0.23
945 86 0.10
946 105 0.12
947 68 0.08
948 31 0.03
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.31
Consensus pattern (934 bp):
TAATTCAATTAATTTGACATATTATAAAATTGTCGATTCCGTTTTTCGCCATGGCAGAGAAAGAT
CAGTACCGACTTGGGGTTTTTCTTTGAAAAGAATTTTAAAATGTGAGGAGTTCACCACCAATCAT
TTAGTGTGATTATGACACTATAAAAACGGGTGATTTTAATAAAAACATTTTATTTTTATCAAAAT
ACCAAATTTTAAGGTTTGCGAAAATCCAAAAATCAAATTCGAGAGTCGGTTACGCGTGGGAAGGA
TTACACCCCCACAAGTGCCCAAAATTGGTACCTAGTTGATTACCCTATATTAGAATCGAAAATTT
TGAGTTCGAACTTTACTTAATTTAAAAATTATTACGGATGCAAAGTTGAAAAGAGTATTCGTTTA
TTAGGCCGATAACATAAGCCCCTAGCATAAATGCGGAGATCAACTATTGTGCCTATAATCGAACA
TTGCCTTAATTTTAGAACATGATGTGGTCTTGAAAATGATGTCAACCTATTTCGGGAATCTCAGT
AGTCACCCCTGGGCATACTTGCGGGAGAATATCATTAATTCCCTAATAAGTGAACATTGCCTTAG
GTTTAAAAATAAAATGCAATCAAACAAATTTTTATTCATCATAATTAAACTGGGTAAATTAAGGC
TTTTTCTAACTTAAAATATCAAATTATGAATAATTAAAAAACCTAGAGGCAAAACCTAAAAGGTG
TAGGCTCTAATATTAATCTTAATAATTTTTGGTAAATTATTGAATTGAACAACCAAAATGGAGCC
TCGAGCATAAGTGAAGACCAAATCAAAAATTCTTAGATTAAAGGACAAAGTTAAAAGGAATTTAA
AATTGAAGGCAAAATTAGAAAAAATTAATGAATACAAAAGGACTAAATTAAAGAGAATAAAAAAT
GGAAGGCTAAATTGAAATATTGAG
Found at i:7511 original size:20 final size:20
Alignment explanation
Indices: 7486--7524 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
7476 TCTTTTACAT
7486 ACAAGAGTGGAGTCAAGAAA
1 ACAAGAGTGGAGTCAAGAAA
7506 ACAAGAGTGGAGTCAAGAA
1 ACAAGAGTGGAGTCAAGAA
7525 TTTGATGTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.49, C:0.10, G:0.31, T:0.10
Consensus pattern (20 bp):
ACAAGAGTGGAGTCAAGAAA
Found at i:9086 original size:22 final size:22
Alignment explanation
Indices: 9061--9111 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
9051 ACGTGAGAAT
*
9061 CACGGGTTCTGCAAGGAGAGAG
1 CACGGGTTCTGCAAGGAGAAAG
*
9083 CACGGGTTCTGCAAGGAGAAAT
1 CACGGGTTCTGCAAGGAGAAAG
9105 CACGGGT
1 CACGGGT
9112 CCTGGGTCCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.27, C:0.20, G:0.37, T:0.16
Consensus pattern (22 bp):
CACGGGTTCTGCAAGGAGAAAG
Found at i:9154 original size:23 final size:23
Alignment explanation
Indices: 9128--9171 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
9118 TCCTGCAAGG
9128 CTGCACGTCTGCATGTGGGGGTC
1 CTGCACGTCTGCATGTGGGGGTC
*
9151 CTGCACTTCTGCATGTGGGGG
1 CTGCACGTCTGCATGTGGGGG
9172 GCATGCAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.09, C:0.25, G:0.39, T:0.27
Consensus pattern (23 bp):
CTGCACGTCTGCATGTGGGGGTC
Found at i:9178 original size:23 final size:23
Alignment explanation
Indices: 9129--9178 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
9119 CCTGCAAGGC
* *
9129 TGCACGTCTGCATGTGGGGGTCC
1 TGCACGTCTGCATGTGGGGGGCA
*
9152 TGCACTTCTGCATGTGGGGGGCA
1 TGCACGTCTGCATGTGGGGGGCA
9175 TGCA
1 TGCA
9179 ACTGTTGGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.12, C:0.24, G:0.38, T:0.26
Consensus pattern (23 bp):
TGCACGTCTGCATGTGGGGGGCA
Found at i:9915 original size:170 final size:173
Alignment explanation
Indices: 9630--9986 Score: 551
Period size: 171 Copynumber: 2.1 Consensus size: 173
9620 TTGTAAAGTT
* * *
9630 TTAGGGACCGTTTTGTAAAATTTAAGGAATTTAAGGAATAAGAGTAAATTATTAAAAGTTGCTAT
1 TTAGGGATCGTTTTGCAAAATTTAAGGAATTTAAGAAATAAGAGTAAATTATTAAAAGTTGCTAT
*
9695 ACTATGCTGGAATTTAGTATTAGTATGCTTAATTGGTTAAATTAGAAAGAATTTA-AAATTTA-T
66 ACTATGCTGGAATTTAGTATTAATATGCTTAATTGGTTAAATTAGAAAGAATTTATAAATTTAGT
*
9758 GGATTAAATTGCTAACTCTG-AAATGTTGAGAACCAAATAGTAA
131 -GATTAAATTGCAAACTCTGAAAATGTTGAGAACCAAATAGTAA
* * *
9801 TTAGGGATCGTTTTGCAAAATTTGAGGAATTTAAGAAATTAGAGTAAATTA-TAAAAGTTGGTAT
1 TTAGGGATCGTTTTGCAAAATTTAAGGAATTTAAGAAATAAGAGTAAATTATTAAAAGTTGCTAT
* *
9865 ACTATGCTTGAATTTAGTATTAATATGCTTAATTGGTTAAATTTGAAAGAATTTATAAATTTAGT
66 ACTATGCTGGAATTTAGTATTAATATGCTTAATTGGTTAAATTAGAAAGAATTTATAAATTTAGT
* * *
9930 GATTAAATTGCAAAGTTTGAAAATGTTGAGAAGCAAATAGTAA
131 GATTAAATTGCAAACTCTGAAAATGTTGAGAACCAAATAGTAA
*
9973 TTAGGGATCATTTT
1 TTAGGGATCGTTTT
9987 ATATTTTATG
Statistics
Matches: 169, Mismatches: 14, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
170 64 0.38
171 69 0.41
172 36 0.21
ACGTcount: A:0.39, C:0.05, G:0.18, T:0.37
Consensus pattern (173 bp):
TTAGGGATCGTTTTGCAAAATTTAAGGAATTTAAGAAATAAGAGTAAATTATTAAAAGTTGCTAT
ACTATGCTGGAATTTAGTATTAATATGCTTAATTGGTTAAATTAGAAAGAATTTATAAATTTAGT
GATTAAATTGCAAACTCTGAAAATGTTGAGAACCAAATAGTAA
Found at i:13161 original size:18 final size:18
Alignment explanation
Indices: 13138--13178 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
13128 TATATATTAG
13138 TCTCACGCTTCAGACGAA
1 TCTCACGCTTCAGACGAA
13156 TCTCACGCTTCAGACGAA
1 TCTCACGCTTCAGACGAA
13174 TCTCA
1 TCTCA
13179 ACAGACGCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.27, C:0.34, G:0.15, T:0.24
Consensus pattern (18 bp):
TCTCACGCTTCAGACGAA
Found at i:13631 original size:109 final size:109
Alignment explanation
Indices: 13432--13691 Score: 454
Period size: 109 Copynumber: 2.4 Consensus size: 109
13422 GAGATTCCCG
* *
13432 CCAGACGACAGGTGAAGACGCCGAGAGATCCACATTGGCAT-TCCTTGTAGCATGCAGAAGATGC
1 CCAGACGACAGGTGAAGACGCCGAGAGATCCACCTTGGCATGTCCTTGTAGCATGCAGAAGACGC
13496 CGAGAGATCCCGCAGTCCAATTGCTTGAAGACGCCGAGCATTCC
66 CGAGAGATCCCGCAGTCCAATTGCTTGAAGACGCCGAGCATTCC
13540 CATCAGACG-CAGGTGAAGACGCCGAGAGATCCACCTTGGCATGT-CTTGTAGCATGCAGAAGAC
1 C--CAGACGACAGGTGAAGACGCCGAGAGATCCACCTTGGCATGTCCTTGTAGCATGCAGAAGAC
13603 GCCGAGAGATCCCGCAGTCCAATTGCTTGAAGACGCCGAGCATTCC
64 GCCGAGAGATCCCGCAGTCCAATTGCTTGAAGACGCCGAGCATTCC
*
13649 CCAGACGACAGGTGAAGACGCTGAGAGATCCACCTTGGCATGT
1 CCAGACGACAGGTGAAGACGCCGAGAGATCCACCTTGGCATGT
13692 AAAAATTAAC
Statistics
Matches: 145, Mismatches: 3, Indels: 8
0.93 0.02 0.05
Matches are distributed among these distances:
107 6 0.04
108 35 0.24
109 97 0.67
110 7 0.05
ACGTcount: A:0.27, C:0.28, G:0.28, T:0.17
Consensus pattern (109 bp):
CCAGACGACAGGTGAAGACGCCGAGAGATCCACCTTGGCATGTCCTTGTAGCATGCAGAAGACGC
CGAGAGATCCCGCAGTCCAATTGCTTGAAGACGCCGAGCATTCC
Found at i:20921 original size:26 final size:28
Alignment explanation
Indices: 20870--20936 Score: 86
Period size: 26 Copynumber: 2.5 Consensus size: 28
20860 TGATCCGTTT
*
20870 GTTTTTAGAAAATATTTTCTA-TTTTTA
1 GTTTTTAGAAAATATTTTCTAGTTTTCA
20897 -TTTTTAGAAAATATTTT-TCAGTTTTCA
1 GTTTTTAGAAAATATTTTCT-AGTTTTCA
*
20924 GTTTTTTGAAAAT
1 GTTTTTAGAAAAT
20937 TAGAAAATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
25 1 0.03
26 18 0.51
27 5 0.14
28 11 0.31
ACGTcount: A:0.30, C:0.04, G:0.09, T:0.57
Consensus pattern (28 bp):
GTTTTTAGAAAATATTTTCTAGTTTTCA
Found at i:34102 original size:160 final size:160
Alignment explanation
Indices: 33672--34468 Score: 1252
Period size: 157 Copynumber: 5.0 Consensus size: 160
33662 GTATTCTTCA
* *
33672 GTTCCTACAGCCACAACGACATGCACTACTTCATATCTGCATCCCTATGGTAGATAATACAAAAC
1 GTTCCTACAGCCACAACGACATGCACTACTTCATATCTGCATCCCTATGGTAGATGATACAAAAT
33737 TTATAACTAGAACTGGTGATTACTGCAAATTACCAGAATATA-T-TT-TTGTTGTTGTTCAACCA
66 TTATAACTAGAACTGGTGATTACTGCAAATTACCAGAATATATTGTTGTTGTTGTTGTTCAACCA
* *
33799 TTGTCATCTGTTTCAAAAGATGCCTTTGTT
131 TTGTCTTCTGTTCCAAAAGATGCCTTTGTT
* *
33829 GTTCCTGCAGCCACAACGACATGCACTACTTCATATCTGCATCCCTAGGGTAGATGATACAAAAT
1 GTTCCTACAGCCACAACGACATGCACTACTTCATATCTGCATCCCTATGGTAGATGATACAAAAT
*
33894 TTATACCTAGAACTGGTGATTACTGCAAATTACCAGAATATATTGTTGTTGTTGTTGTTCAACCA
66 TTATAACTAGAACTGGTGATTACTGCAAATTACCAGAATATATTGTTGTTGTTGTTGTTCAACCA
*
33959 TTGCCTTCTGTTCCAAAAGATGCCTTTGTT
131 TTGTCTTCTGTTCCAAAAGATGCCTTTGTT
*
33989 GTTCCTACAG-C-C-ACGACATGCACTACTTCATATCTGCATCCCTATGGCAGATGATACAAAAT
1 GTTCCTACAGCCACAACGACATGCACTACTTCATATCTGCATCCCTATGGTAGATGATACAAAAT
* * * *
34051 TTACAACTAGAAATGATGATTACTGCAAATTACCAAAATATATTGTTGTTGTTGTTGTTCAACCA
66 TTATAACTAGAACTGGTGATTACTGCAAATTACCAGAATATATTGTTGTTGTTGTTGTTCAACCA
*
34116 TTGTCTTCTGTTCCAAAAGATGCTTTTGTT
131 TTGTCTTCTGTTCCAAAAGATGCCTTTGTT
*
34146 GTTCCTACAGCCACAACAACATGCACTACTTCATATCTGCATCCCTATGGTAGATGATACAAAAT
1 GTTCCTACAGCCACAACGACATGCACTACTTCATATCTGCATCCCTATGGTAGATGATACAAAAT
* * *
34211 TTATAACTGGAACTGATGATTACTGCAAATTACCAGAAGATATTGTTGTTGTTGTTGTTCAACCA
66 TTATAACTAGAACTGGTGATTACTGCAAATTACCAGAATATATTGTTGTTGTTGTTGTTCAACCA
* *
34276 TTTTCTTCTGTTCCGAAAGATGCCTTTGTT
131 TTGTCTTCTGTTCCAAAAGATGCCTTTGTT
* * * * * *
34306 GTTCCTACAGCCACAATGACATGCATTATTTCATATCTGCATCCATATGGCAGATGATAGAAAAT
1 GTTCCTACAGCCACAACGACATGCACTACTTCATATCTGCATCCCTATGGTAGATGATACAAAAT
* * *
34371 TTATAACTAGAACTGGTGATTACTGCGAAGTACCAGAATATA---CTGTTGTTGTTGTTCAACCA
66 TTATAACTAGAACTGGTGATTACTGCAAATTACCAGAATATATTGTTGTTGTTGTTGTTCAACCA
* *
34433 TTGTCTTCTGTTTCAAAAGAAGCCTTTGTT
131 TTGTCTTCTGTTCCAAAAGATGCCTTTGTT
34463 GTTCCT
1 GTTCCT
34469 CATCGGTATT
Statistics
Matches: 589, Mismatches: 45, Indels: 12
0.91 0.07 0.02
Matches are distributed among these distances:
157 299 0.51
158 3 0.01
159 4 0.01
160 283 0.48
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.35
Consensus pattern (160 bp):
GTTCCTACAGCCACAACGACATGCACTACTTCATATCTGCATCCCTATGGTAGATGATACAAAAT
TTATAACTAGAACTGGTGATTACTGCAAATTACCAGAATATATTGTTGTTGTTGTTGTTCAACCA
TTGTCTTCTGTTCCAAAAGATGCCTTTGTT
Found at i:34247 original size:317 final size:315
Alignment explanation
Indices: 33672--34468 Score: 1256
Period size: 317 Copynumber: 2.5 Consensus size: 315
33662 GTATTCTTCA
* * *
33672 GTTCCTACAGCCACAACGACATGCACTACTTCATATCTGCATCCCTATGGTAGATAATACAAAAC
1 GTTCCTACAG-C-C-ACGACATGCACTACTTCATATCTGCATCCCTATGGCAGATGATACAAAAT
33737 TTATAACTAGAACTGGTGATTACTGCAAATTACCAGAATATATTT-TTGTTGTTGTTCAACCATT
63 TTATAACTAGAACTGGTGATTACTGCAAATTACCAGAATATATTTGTTGTTGTTGTTCAACCATT
* * *
33801 GTCATCTGTTTCAAAAGATGCCTTTGTTGTTCCTGCAGCCACAACGACATGCACTACTTCATATC
128 GTCTTCTGTTTCAAAAGATGCCTTTGTTGTTCCTACAGCCACAACAACATGCACTACTTCATATC
* *
33866 TGCATCCCTAGGGTAGATGATACAAAATTTATACCTAGAACTGGTGATTACTGCAAATTACCAGA
193 TGCATCCCTAGGGTAGATGATACAAAATTTATAACTAGAACTGATGATTACTGCAAATTACCAGA
*
33931 ATATATTGTTGTTGTTGTTGTTCAACCATTGCCTTCTGTTCCAAAAGATGCCTTTGTT
258 AGATATTGTTGTTGTTGTTGTTCAACCATTGCCTTCTGTTCCAAAAGATGCCTTTGTT
33989 GTTCCTACAGCCACGACATGCACTACTTCATATCTGCATCCCTATGGCAGATGATACAAAATTTA
1 GTTCCTACAGCCACGACATGCACTACTTCATATCTGCATCCCTATGGCAGATGATACAAAATTTA
* * * *
34054 CAACTAGAAATGATGATTACTGCAAATTACCAAAATATATTGTTGTTGTTGTTGTTCAACCATTG
66 TAACTAGAACTGGTGATTACTGCAAATTACCAGAATATA-T-TTGTTGTTGTTGTTCAACCATTG
* *
34119 TCTTCTGTTCCAAAAGATGCTTTTGTTGTTCCTACAGCCACAACAACATGCACTACTTCATATCT
129 TCTTCTGTTTCAAAAGATGCCTTTGTTGTTCCTACAGCCACAACAACATGCACTACTTCATATCT
* *
34184 GCATCCCTATGGTAGATGATACAAAATTTATAACTGGAACTGATGATTACTGCAAATTACCAGAA
194 GCATCCCTAGGGTAGATGATACAAAATTTATAACTAGAACTGATGATTACTGCAAATTACCAGAA
** *
34249 GATATTGTTGTTGTTGTTGTTCAACCATTTTCTTCTGTTCCGAAAGATGCCTTTGTT
259 GATATTGTTGTTGTTGTTGTTCAACCATTGCCTTCTGTTCCAAAAGATGCCTTTGTT
* * * *
34306 GTTCCTACAGCCACAATGACATGCATTATTTCATATCTGCATCCATATGGCAGATGATAGAAAAT
1 GTTCCTACAGCCAC---GACATGCACTACTTCATATCTGCATCCCTATGGCAGATGATACAAAAT
* * *
34371 TTATAACTAGAACTGGTGATTACTGCGAAGTACCAGAATATA-CTGTTGTTGTTGTTCAACCATT
63 TTATAACTAGAACTGGTGATTACTGCAAATTACCAGAATATATTTGTTGTTGTTGTTCAACCATT
*
34435 GTCTTCTGTTTCAAAAGAAGCCTTTGTTGTTCCT
128 GTCTTCTGTTTCAAAAGATGCCTTTGTTGTTCCT
34469 CATCGGTATT
Statistics
Matches: 440, Mismatches: 34, Indels: 12
0.91 0.07 0.02
Matches are distributed among these distances:
314 85 0.19
315 2 0.00
316 3 0.01
317 270 0.61
320 80 0.18
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.35
Consensus pattern (315 bp):
GTTCCTACAGCCACGACATGCACTACTTCATATCTGCATCCCTATGGCAGATGATACAAAATTTA
TAACTAGAACTGGTGATTACTGCAAATTACCAGAATATATTTGTTGTTGTTGTTCAACCATTGTC
TTCTGTTTCAAAAGATGCCTTTGTTGTTCCTACAGCCACAACAACATGCACTACTTCATATCTGC
ATCCCTAGGGTAGATGATACAAAATTTATAACTAGAACTGATGATTACTGCAAATTACCAGAAGA
TATTGTTGTTGTTGTTGTTCAACCATTGCCTTCTGTTCCAAAAGATGCCTTTGTT
Found at i:34568 original size:18 final size:18
Alignment explanation
Indices: 34544--34595 Score: 68
Period size: 18 Copynumber: 2.9 Consensus size: 18
34534 ACAGTTTCCT
34544 CTGCTGGTGCCTCTACCA
1 CTGCTGGTGCCTCTACCA
* * *
34562 GTGCTGGCGCCTCTACCT
1 CTGCTGGTGCCTCTACCA
*
34580 CCGCTGGTGCCTCTAC
1 CTGCTGGTGCCTCTAC
34596 TTCTACCTCA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.08, C:0.40, G:0.25, T:0.27
Consensus pattern (18 bp):
CTGCTGGTGCCTCTACCA
Found at i:39525 original size:30 final size:29
Alignment explanation
Indices: 39445--39549 Score: 117
Period size: 30 Copynumber: 3.6 Consensus size: 29
39435 GAAAAAACTT
39445 AAATACTTTAGATA-TATATTTTGACC-AA
1 AAATACTTTAGATACT-TATTTTGACCAAA
* *
39473 AAATATTTTA-AGTACCTATTTTGACCAAA
1 AAATACTTTAGA-TACTTATTTTGACCAAA
**
39502 AAATAACTTTAGATACTTATTTTGATTAAA
1 AAAT-ACTTTAGATACTTATTTTGACCAAA
*
39532 AAATACTTTAAATACTTA
1 AAATACTTTAGATACTTA
39550 GATGAAAAAA
Statistics
Matches: 65, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
27 1 0.02
28 21 0.32
29 19 0.29
30 23 0.35
31 1 0.02
ACGTcount: A:0.44, C:0.10, G:0.06, T:0.40
Consensus pattern (29 bp):
AAATACTTTAGATACTTATTTTGACCAAA
Found at i:43612 original size:24 final size:23
Alignment explanation
Indices: 43562--43639 Score: 95
Period size: 23 Copynumber: 3.3 Consensus size: 23
43552 TTTGGTTACA
* *
43562 TTCGTTTATGTTCATTTATTGTG
1 TTCGTTTACGTTCCTTTATTGTG
*
43585 TTCGTTTACGTTCGTTCGT-TTGTG
1 TTCGTTTACGTTCCTT--TATTGTG
*
43609 TTCGCTTACGTTCCTTTATTGTG
1 TTCGTTTACGTTCCTTTATTGTG
43632 TTCGTTTA
1 TTCGTTTA
43640 TATTCGTTTA
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
22 1 0.02
23 26 0.55
24 19 0.40
25 1 0.02
ACGTcount: A:0.09, C:0.15, G:0.19, T:0.56
Consensus pattern (23 bp):
TTCGTTTACGTTCCTTTATTGTG
Found at i:43682 original size:24 final size:23
Alignment explanation
Indices: 43562--43688 Score: 112
Period size: 24 Copynumber: 5.4 Consensus size: 23
43552 TTTGGTTACA
*
43562 TTCGTTTATGTTCATTTATTGTG
1 TTCGTTTATGTTCGTTTATTGTG
*
43585 TTCGTTTACGTTCGTTCGT-TTGTG
1 TTCGTTTATGTTCGTT--TATTGTG
* * *
43609 TTCGCTTACGTTCCTTTATTGTG
1 TTCGTTTATGTTCGTTTATTGTG
* * **
43632 TTCGTTTATATTCGTTTACATCCG
1 TTCGTTTATGTTCGTTTA-TTGTG
* *
43656 TTCGTTTATGTTTGTTCATTTGTG
1 TTCGTTTATGTTCGTTTA-TTGTG
43680 TTCGTTTAT
1 TTCGTTTAT
43689 CATTTAAATG
Statistics
Matches: 82, Mismatches: 18, Indels: 7
0.77 0.17 0.07
Matches are distributed among these distances:
22 1 0.01
23 33 0.40
24 47 0.57
25 1 0.01
ACGTcount: A:0.10, C:0.15, G:0.18, T:0.57
Consensus pattern (23 bp):
TTCGTTTATGTTCGTTTATTGTG
Found at i:44448 original size:22 final size:22
Alignment explanation
Indices: 44423--44467 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
44413 GGCCCTGTGC
44423 AAATTCTTAAAAAGAGACCCTT
1 AAATTCTTAAAAAGAGACCCTT
*
44445 AAATTCTTATAAAGAGACCCTT
1 AAATTCTTAAAAAGAGACCCTT
44467 A
1 A
44468 GTAAAAATTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.44, C:0.18, G:0.09, T:0.29
Consensus pattern (22 bp):
AAATTCTTAAAAAGAGACCCTT
Found at i:55714 original size:16 final size:16
Alignment explanation
Indices: 55683--55715 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
55673 TGTACTTACT
55683 TATTTTTAAAATAATA
1 TATTTTTAAAATAATA
55699 TATTATTTAAAA-AATA
1 TATT-TTTAAAATAATA
55715 T
1 T
55716 TTTAAAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TATTTTTAAAATAATA
Found at i:56296 original size:2 final size:2
Alignment explanation
Indices: 56289--56322 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
56279 ACATACATAC
56289 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
56323 TCAAATGCTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:59933 original size:2 final size:2
Alignment explanation
Indices: 59926--59955 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
59916 AGTGGGACCA
59926 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
59956 TGAAAGTTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:60528 original size:16 final size:16
Alignment explanation
Indices: 60507--60537 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
60497 TACAAAATCT
60507 AATAATTCATAATATA
1 AATAATTCATAATATA
*
60523 AATAATTCATTATAT
1 AATAATTCATAATAT
60538 TTTATATATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (16 bp):
AATAATTCATAATATA
Found at i:73893 original size:13 final size:14
Alignment explanation
Indices: 73865--73898 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
73855 TTCTTTTTAA
73865 TTTA-TTTTCAATT
1 TTTAGTTTTCAATT
73878 TTTAGTTTTCAATT
1 TTTAGTTTTCAATT
73892 TTT-GTTT
1 TTTAGTTT
73899 GTTATTTTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.18, C:0.06, G:0.06, T:0.71
Consensus pattern (14 bp):
TTTAGTTTTCAATT
Found at i:74960 original size:14 final size:14
Alignment explanation
Indices: 74941--74975 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
74931 ATTACTAATG
*
74941 TGGCATCCTATTTT
1 TGGCATCCTATTCT
74955 TGGCATCCTATTCT
1 TGGCATCCTATTCT
74969 TGGCATC
1 TGGCATC
74976 GGTAATCGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.14, C:0.26, G:0.17, T:0.43
Consensus pattern (14 bp):
TGGCATCCTATTCT
Found at i:83082 original size:22 final size:23
Alignment explanation
Indices: 83027--83082 Score: 78
Period size: 22 Copynumber: 2.4 Consensus size: 23
83017 GATACCCTGT
83027 TCACTATTTCACGGGTACTGTTCA
1 TCACTA-TTCACGGGTACTGTTCA
* *
83051 TCAATGTTCAC-GGTACTGTTCA
1 TCACTATTCACGGGTACTGTTCA
83073 TCACTATTCA
1 TCACTATTCA
83083 TAAACAATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 19 0.68
23 5 0.18
24 4 0.14
ACGTcount: A:0.23, C:0.25, G:0.14, T:0.38
Consensus pattern (23 bp):
TCACTATTCACGGGTACTGTTCA
Found at i:88917 original size:63 final size:63
Alignment explanation
Indices: 88738--88888 Score: 189
Period size: 63 Copynumber: 2.4 Consensus size: 63
88728 GTGCACTAAG
* * * * * *
88738 TATGCATCGATGCATAAAATGCATTCGCT-GTTTGA-AAAATAGCCTGGTGCATCGATGCATGGA
1 TATGCATCGGTGCATCAAATGCATTCGATATTTTCATAAAAT--CCAGGTGCATCGATGCATGGA
* *
88801 TGTGCATCGGTGCATCAAATGCATTCGATATTTTCATAAAATCCAAGTGCATCGATGCATGGA
1 TATGCATCGGTGCATCAAATGCATTCGATATTTTCATAAAATCCAGGTGCATCGATGCATGGA
*
88864 TATGCATCGGTGCATGAAATGCATT
1 TATGCATCGGTGCATCAAATGCATT
88889 TGATGTTCAA
Statistics
Matches: 76, Mismatches: 10, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
63 67 0.88
64 4 0.05
65 5 0.07
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.30
Consensus pattern (63 bp):
TATGCATCGGTGCATCAAATGCATTCGATATTTTCATAAAATCCAGGTGCATCGATGCATGGA
Found at i:94045 original size:22 final size:21
Alignment explanation
Indices: 94003--94042 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
93993 GAGTTTATTT
94003 TCATTTTTCAATTTTAAAACA
1 TCATTTTTCAATTTTAAAACA
94024 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
94043 ACAGTTTCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:94509 original size:6 final size:6
Alignment explanation
Indices: 94495--94526 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
94485 TCCAATGTTT
*
94495 TTCTTC TTCTCC TTCTCC TTCTCC TTCTCC TT
1 TTCTCC TTCTCC TTCTCC TTCTCC TTCTCC TT
94527 TGGCGTCTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.00, C:0.44, G:0.00, T:0.56
Consensus pattern (6 bp):
TTCTCC
Found at i:96167 original size:63 final size:63
Alignment explanation
Indices: 95981--96138 Score: 203
Period size: 63 Copynumber: 2.5 Consensus size: 63
95971 GTGCACTAAG
** * * *
95981 TATGCATCGAAGCATAAAATGCATTCGATG-TTTGA-AAAATAGCCTGGTGCATCGATGCATGGA
1 TATGCATCGGTGCATCAAATGCATTCGATGTTTTCATAAAAT--CCAGGTGCATCGATGCATGGA
* *
96044 TGTGCATCGGTGCATCAAATGCATTCGATGTTTTCATAAAATCCAAGTGCATCGATGCATGGA
1 TATGCATCGGTGCATCAAATGCATTCGATGTTTTCATAAAATCCAGGTGCATCGATGCATGGA
* *
96107 TATGCATCGGTGCATGAAATGCATTTGATGTT
1 TATGCATCGGTGCATCAAATGCATTCGATGTT
96139 CAATTTATTC
Statistics
Matches: 83, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
63 74 0.89
64 4 0.05
65 5 0.06
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.30
Consensus pattern (63 bp):
TATGCATCGGTGCATCAAATGCATTCGATGTTTTCATAAAATCCAGGTGCATCGATGCATGGA
Found at i:96245 original size:16 final size:16
Alignment explanation
Indices: 96224--96255 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
96214 GTGAAAATTG
96224 TTTCAAAAATAGTTTA
1 TTTCAAAAATAGTTTA
96240 TTTCAAAAATAGTTTA
1 TTTCAAAAATAGTTTA
96256 AGTATAAATC
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:0.44, C:0.06, G:0.06, T:0.44
Consensus pattern (16 bp):
TTTCAAAAATAGTTTA
Found at i:98221 original size:40 final size:40
Alignment explanation
Indices: 98161--98322 Score: 290
Period size: 40 Copynumber: 4.0 Consensus size: 40
98151 TGCAGGTTTA
*
98161 TAATACACTTCGGTATATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
*
98201 TAATGCACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
98241 TAATACAC-TCTGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTC-GGTGTATATGGTGGGCACGACCTTATGTG
98281 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
98321 TA
1 TA
98323 GCACTACGGT
Statistics
Matches: 117, Mismatches: 3, Indels: 4
0.94 0.02 0.03
Matches are distributed among these distances:
39 2 0.02
40 113 0.97
41 2 0.02
ACGTcount: A:0.23, C:0.17, G:0.27, T:0.33
Consensus pattern (40 bp):
TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
Found at i:98884 original size:30 final size:30
Alignment explanation
Indices: 98848--98908 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
98838 TGCTGAAATT
98848 ACTGTAGCAGTCACTGTAGCGTACCGATGC
1 ACTGTAGCAGTCACTGTAGCGTACCGATGC
* *
98878 ACTGTAGCAGTTACTGTAGCGTATCGATGC
1 ACTGTAGCAGTCACTGTAGCGTACCGATGC
98908 A
1 A
98909 TAATATTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.25, C:0.23, G:0.26, T:0.26
Consensus pattern (30 bp):
ACTGTAGCAGTCACTGTAGCGTACCGATGC
Found at i:107063 original size:20 final size:20
Alignment explanation
Indices: 107005--107063 Score: 84
Period size: 20 Copynumber: 2.9 Consensus size: 20
106995 TATTGCCCAA
*
107005 GGGGTACAGATTTCCCCCCAG
1 GGGGTACAGA-TTCCCCCTAG
107026 GGGGTACAGATTCCCCCTAG
1 GGGGTACAGATTCCCCCTAG
107046 GGGGTATCA-ATTCCCCCT
1 GGGGTA-CAGATTCCCCCT
107064 GTCTAACGGT
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
20 24 0.67
21 12 0.33
ACGTcount: A:0.19, C:0.32, G:0.27, T:0.22
Consensus pattern (20 bp):
GGGGTACAGATTCCCCCTAG
Found at i:107608 original size:24 final size:24
Alignment explanation
Indices: 107578--107640 Score: 126
Period size: 24 Copynumber: 2.6 Consensus size: 24
107568 TAACAAAAAG
107578 GGGGAGAAGTGTTAAGGTGTTAAA
1 GGGGAGAAGTGTTAAGGTGTTAAA
107602 GGGGAGAAGTGTTAAGGTGTTAAA
1 GGGGAGAAGTGTTAAGGTGTTAAA
107626 GGGGAGAAGTGTTAA
1 GGGGAGAAGTGTTAA
107641 AGTAAGGGGG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.43, T:0.24
Consensus pattern (24 bp):
GGGGAGAAGTGTTAAGGTGTTAAA
Found at i:108006 original size:20 final size:20
Alignment explanation
Indices: 107981--108092 Score: 134
Period size: 20 Copynumber: 5.5 Consensus size: 20
107971 AAGAAAAATT
* *
107981 AGATTCTCCCTAGGGGGTAC
1 AGATTCCCCCCAGGGGGTAC
* *
108001 AGATTCCCCCCAGGGGGAAT
1 AGATTCCCCCCAGGGGGTAC
*
108021 AGATTCCCCTCCCAAGGGGTAC
1 AGATT-CCC-CCCAGGGGGTAC
* *
108043 CGATTCCCCCCAGGGGGAAC
1 AGATTCCCCCCAGGGGGTAC
108063 AGATTCCCCCCAGGGGGTAC
1 AGATTCCCCCCAGGGGGTAC
*
108083 CGATTCCCCC
1 AGATTCCCCC
108093 TGTCTAACGG
Statistics
Matches: 77, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
20 58 0.75
21 6 0.08
22 13 0.17
ACGTcount: A:0.21, C:0.36, G:0.27, T:0.17
Consensus pattern (20 bp):
AGATTCCCCCCAGGGGGTAC
Found at i:108048 original size:42 final size:40
Alignment explanation
Indices: 107994--108092 Score: 153
Period size: 42 Copynumber: 2.4 Consensus size: 40
107984 TTCTCCCTAG
* *
107994 GGGGTACAGATTCCCCCCAGGGGGAATAGATTCCCCTCCCAA
1 GGGGTACCGATTCCCCCCAGGGGGAACAGATT-CCC-CCCAA
*
108036 GGGGTACCGATTCCCCCCAGGGGGAACAGATTCCCCCCAG
1 GGGGTACCGATTCCCCCCAGGGGGAACAGATTCCCCCCAA
108076 GGGGTACCGATTCCCCC
1 GGGGTACCGATTCCCCC
108093 TGTCTAACGG
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
40 21 0.39
41 3 0.06
42 30 0.56
ACGTcount: A:0.20, C:0.36, G:0.28, T:0.15
Consensus pattern (40 bp):
GGGGTACCGATTCCCCCCAGGGGGAACAGATTCCCCCCAA
Found at i:109192 original size:14 final size:14
Alignment explanation
Indices: 109173--109199 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
109163 TTGACTTTCC
109173 GGTCAAAGTCAACG
1 GGTCAAAGTCAACG
109187 GGTCAAAGTCAAC
1 GGTCAAAGTCAAC
109200 ATATTGACTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.22, G:0.26, T:0.15
Consensus pattern (14 bp):
GGTCAAAGTCAACG
Found at i:109641 original size:22 final size:22
Alignment explanation
Indices: 109615--109670 Score: 112
Period size: 22 Copynumber: 2.5 Consensus size: 22
109605 CTCAGAGGGA
109615 ACCGATTCCCCCCTAAGGGGGT
1 ACCGATTCCCCCCTAAGGGGGT
109637 ACCGATTCCCCCCTAAGGGGGT
1 ACCGATTCCCCCCTAAGGGGGT
109659 ACCGATTCCCCC
1 ACCGATTCCCCC
109671 TGAATGGTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.18, C:0.41, G:0.23, T:0.18
Consensus pattern (22 bp):
ACCGATTCCCCCCTAAGGGGGT
Found at i:115199 original size:23 final size:21
Alignment explanation
Indices: 115147--115208 Score: 81
Period size: 23 Copynumber: 2.9 Consensus size: 21
115137 TTTTGGTGCA
*
115147 GAGGGAATCGA-TCCCCCCTT
1 GAGGGAACCGATTCCCCCCTT
*
115167 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCCCTT
115188 GAAGGGGAACCGATTCCCCCC
1 G-A-GGGAACCGATTCCCCCC
115209 CCACAGGGGA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
20 10 0.28
21 9 0.25
22 1 0.03
23 16 0.44
ACGTcount: A:0.21, C:0.35, G:0.26, T:0.18
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCCTT
Found at i:124144 original size:42 final size:42
Alignment explanation
Indices: 124081--124161 Score: 135
Period size: 42 Copynumber: 1.9 Consensus size: 42
124071 TTGGTGGATC
* *
124081 TTTCTTCCTTGTCTTCTTCAAATCCTCATTTTCTTGTTGATT
1 TTTCTTCCTTGTCTTCGTCAAAGCCTCATTTTCTTGTTGATT
*
124123 TTTCTTCTTTGTCTTCGTCAAAGCCTCATTTTCTTGTTG
1 TTTCTTCCTTGTCTTCGTCAAAGCCTCATTTTCTTGTTG
124162 TAACAATGAT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.11, C:0.23, G:0.10, T:0.56
Consensus pattern (42 bp):
TTTCTTCCTTGTCTTCGTCAAAGCCTCATTTTCTTGTTGATT
Found at i:124824 original size:2 final size:2
Alignment explanation
Indices: 124817--124843 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
124807 CGATTTTAGC
124817 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
124844 GCAATATGGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:132242 original size:28 final size:28
Alignment explanation
Indices: 132204--132260 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
132194 TTTATGTTAA
*
132204 GGGCAAACTTGAAATTATAAAATTTTAG
1 GGGCAAACTTGAAATTATAAAATTGTAG
*
132232 GGGCAAACTTGAACTTATAAAATTGTAG
1 GGGCAAACTTGAAATTATAAAATTGTAG
132260 G
1 G
132261 AGGGTTGAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.40, C:0.09, G:0.21, T:0.30
Consensus pattern (28 bp):
GGGCAAACTTGAAATTATAAAATTGTAG
Found at i:138414 original size:2 final size:2
Alignment explanation
Indices: 138409--138452 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
138399 TAAAAAATTG
138409 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
138451 AT
1 AT
138453 GGACTAACAA
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
Done.