Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007318.1 Corchorus capsularis cultivar CVL-1 contig07339, 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: 21829
ACGTcount: A:0.30, C:0.15, G:0.21, T:0.34
Found at i:2605 original size:929 final size:928
Alignment explanation
Indices: 1--2810 Score: 4877
Period size: 928 Copynumber: 3.0 Consensus size: 928
1 TTGTCTACAAGCTGAAGAAGTCCAAGTAGATTCTTGGCAGGTCTCAAGGATAGATTTTATCATGG
1 TTGTCTACAAGCTGAAGAAGTCCAAGTAGATTCTTGGCAGGTCTCAAGGATAGATTTTATCATGG
* *
66 AGGTCCAAGGACTTCTCCTGGTCTTGGAGACAAGCATGGAGACCATAGAAAGGATGTGCATGGAC
66 AGGTCCAAGGACTTCTCATGGTCTTGGAGACAAGCATGGAGACCATAGAAAGGATGTGCATGGGC
131 TGCAAGGAAGCATGGAGATGCATGAAGATTATCGAGATATTGATAAGCATGTTCCAAGCACCAAA
131 TGCAAGGAAGCATGGAGATGCATGAAGATTATCGAGATATTGATAAGCATGTTCCAAGCACCAAA
196 AAGATG-TTATTCGATTCATTGAAGATGCCTATTAGCCCGATGACAAGAGCAAGAGCTAAGAGAT
196 AAGATGCTTATTCGATTCATTGAAGATGCCTATTAGCCCGATGACAAGAGCAAGAGCTAAGAGAT
260 TCAGGGATGCACTCATGAGCCTTGTTCGAACTCATCTTGAAGACTTGAAGACCATTCAAGTTCAA
261 TCAGGGATGCACTCATGAGCCTTGTTCGAACTCATCTTGAAGACTTGAAGACCATTCAAGTTCAA
325 TTGAAGAGCTTTGATGATGATTTGAGCAAGAAAACACCAATGAATTACAAGTTCATCACTTTGCT
326 TTGAAGAGCTTTGATGATGATTTGAGCAAGAAAACACCAATGAATTACAAGTTCATCACTTTGCT
390 TGCTATTGATTCTAAATGGCCGGATTGACATAGTGGCATGAGCCCAATATGC-TCAGTTATCTTT
391 TGCTATTGATTCTAAATGGCCGGATTGACATAGTGGCATGAGCCCAATAT-CATCAGTTATCTTT
*
454 GTTTGGGCTTAATTCTATCTTAGATTAGCTTATTTTTAAGTTTGGATGTTATTTGGATTTGGCCT
455 GTTTGGGCTTAATTCTATCTTAGATTAGCTTATTTTTAAGTTTGGATGTTATTTGGATTGGGCCT
519 TGTTTGACTAAGTCCAATCCTTGTTTAATTATACTTTTATTTCCTTTTCCTAGTTGGGCTTGGAC
520 TGTTTGACTAAGTCCAATCCTTGTTTAATTATAC-TTTATTTCCTTTTCCTAGTTGGGCTTGGAC
584 TAGTTTTTCCCTAGCCCTTATATTTGGACGAAAATTAGGATTTATTTTAGGATTTTGGTTGACCC
584 TAGTTTTTCCCTAGCCCTTATATTTGGACGAAAATTAGGATTTATTTTAGGATTTTGGTTGACCC
*
649 TATCACTATATAAGGCCACCAATATCTCTTGTAAAAGTGGAAGTTGAGTTGATTAATAAAATTGA
649 TATCACTATATAAGGCCACAAATATCTCTTGTAAAAGTGGAAGTTGAGTTGATTAATAAAATTGA
714 GGTTGATTCTCCCAAATTGATTATCTTGGCTTCATTGTTCTAGTTCGAGGAAACTTAGGGTTCTT
714 GGTTGATTCTCCCAAATTGATTATCTTGGCTTCATTGTTCTAGTTCGAGGAAACTTAGGGTTCTT
779 CGATCTTGTAGAGTCCTAGCAAACAATTAGGTTGTGTGATGCTTAATTGTTTGTGAATCTTGTGA
779 CGATCTTGTAGAGTCCTAGCAAACAATTAGGTTGTGTGATGCTTAATTGTTTGTGAATCTTGTGA
844 TCTTAGGTTATTCAATTGCAGGTCTAATTGAAGACTTAAGGCCGACGAACGAAGAGAGATTGCTT
844 TCTTAGGTTATTCAATTGCAGGTCTAATTGAAGACTTAAGGCCGACGAACGAAGAGAGATTGCTT
909 TGTGAAGGTTGTCGACATAC
909 TGTGAAGGTTGTCGACATAC
*
929 TTGTCTAGAAGCTGAAGAAGTCCAAGTAGATTCTTGGCAGGTCTCAAGGATAGATTTTATCATGG
1 TTGTCTACAAGCTGAAGAAGTCCAAGTAGATTCTTGGCAGGTCTCAAGGATAGATTTTATCATGG
994 AGGTCCAAGGACTTCTCATGGTCTTGGAGACAAGCATGGAGACCATAGAAAGGATGTGCATGGGC
66 AGGTCCAAGGACTTCTCATGGTCTTGGAGACAAGCATGGAGACCATAGAAAGGATGTGCATGGGC
* * *
1059 TGCAAGGAAGTATGCAGATGCAAGAAGATTATCGAGATATTGATAAGCATGTTCCAAGCACCAAA
131 TGCAAGGAAGCATGGAGATGCATGAAGATTATCGAGATATTGATAAGCATGTTCCAAGCACCAAA
*
1124 AAGATGC-TATTCGATTCATTGAAGATTCCTATTAGCCCGATGACAAGAGCAAGAGCTAAGAGAT
196 AAGATGCTTATTCGATTCATTGAAGATGCCTATTAGCCCGATGACAAGAGCAAGAGCTAAGAGAT
**
1188 TCAGGGATGCACTCATGAGCCTTAATCGAACTCATCTTGAAGACTTGAAGACCATTCAAGTTCAA
261 TCAGGGATGCACTCATGAGCCTTGTTCGAACTCATCTTGAAGACTTGAAGACCATTCAAGTTCAA
1253 TTGAAGAGCTTTGATGATGATTTGAGCAAGAAAACACCAATGAATTACAAGTTCATCACTTTGCT
326 TTGAAGAGCTTTGATGATGATTTGAGCAAGAAAACACCAATGAATTACAAGTTCATCACTTTGCT
*
1318 TGCTATTGATTCTAAATGGCCGGATTGACATAGTGGCATGATCCCAATATCATCAGTTATCTTTG
391 TGCTATTGATTCTAAATGGCCGGATTGACATAGTGGCATGAGCCCAATATCATCAGTTATCTTTG
* *
1383 TTTGGGCTTAATTCAATCTTAGATTAGCTTATTTTTAAGTTTGGATGTTATTTCGATTGGGCCTT
456 TTTGGGCTTAATTCTATCTTAGATTAGCTTATTTTTAAGTTTGGATGTTATTTGGATTGGGCCTT
* *
1448 GTTTGACAAAGTCCAATCCTTGTTTAATTATACTCTTATTTCCTTTTCCTAGTTTGGCTTGGACT
521 GTTTGACTAAGTCCAATCCTTGTTTAATTATACT-TTATTTCCTTTTCCTAGTTGGGCTTGGACT
*
1513 AGTTTTTCCCTAGCCCTTATATTTGGACGAAAATTAGGATTTATTTTAGGATTTTCGTTGACCCT
585 AGTTTTTCCCTAGCCCTTATATTTGGACGAAAATTAGGATTTATTTTAGGATTTTGGTTGACCCT
*
1578 ATCACTATATAAGGCCACGAATATCTCTTGTAAAAGTGGAAGTTGAGTTGATTAATAAAATTGAG
650 ATCACTATATAAGGCCACAAATATCTCTTGTAAAAGTGGAAGTTGAGTTGATTAATAAAATTGAG
1643 GTTGATTCTCCCAAATTGATTATCTTGGCTTCATTGTTCTAGTTCGAGGAAACTTAGGGTTCTTC
715 GTTGATTCTCCCAAATTGATTATCTTGGCTTCATTGTTCTAGTTCGAGGAAACTTAGGGTTCTTC
*
1708 GATCTTGTAAAGTCCTAGCAAACAATTAGGTTGTGTGATGCTTAATTGTTTGTGAATCTTGTGAT
780 GATCTTGTAGAGTCCTAGCAAACAATTAGGTTGTGTGATGCTTAATTGTTTGTGAATCTTGTGAT
1773 CTTAGGTTATTCAATTGCAGGTCTAATTGAAGACTTAAGGCCGACGAACGAAGAGAGATTGCTTT
845 CTTAGGTTATTCAATTGCAGGTCTAATTGAAGACTTAAGGCCGACGAACGAAGAGAGATTGCTTT
1838 GTGAAGGTTGTCGACATAC
910 GTGAAGGTTGTCGACATAC
1857 TTGTCTACAAGCTGAAGAAGTCCAAGTAGATTCTTGGCAGGTCTCAAGGATAGATTTTATCATGG
1 TTGTCTACAAGCTGAAGAAGTCCAAGTAGATTCTTGGCAGGTCTCAAGGATAGATTTTATCATGG
1922 AGGTCCAAGGACTTCTCATGGTCTTGGAGACAAGCATGGAGACCATAGAAAGGATGTGCATGGGC
66 AGGTCCAAGGACTTCTCATGGTCTTGGAGACAAGCATGGAGACCATAGAAAGGATGTGCATGGGC
*
1987 TGCAAGGGAGCATGGAGATGCATGAAGATTATCGAGATATTGATAAGCATGTTCCAAGCACCAAA
131 TGCAAGGAAGCATGGAGATGCATGAAGATTATCGAGATATTGATAAGCATGTTCCAAGCACCAAA
2052 AAGATGCTTATTCGATTCATTGAAGATGCCTATTAGCCCGATGACAAGAGCAAGAGCTAAGAGAT
196 AAGATGCTTATTCGATTCATTGAAGATGCCTATTAGCCCGATGACAAGAGCAAGAGCTAAGAGAT
*
2117 TCAGGGATGCACTCATGAGCCTTGTTCGAACTCATCTTGAAGACTTGAAGACCATTGAAGTTCAA
261 TCAGGGATGCACTCATGAGCCTTGTTCGAACTCATCTTGAAGACTTGAAGACCATTCAAGTTCAA
* * ** * * * *
2182 TTGAAGAGCTTTGGTGATGATTTGGGCAAGAAATTACAAATCAATTACAAGTTCATCGCATTGCT
326 TTGAAGAGCTTTGATGATGATTTGAGCAAGAAAACACCAATGAATTACAAGTTCATCACTTTGCT
* * * *
2247 TGCTATTGATTCTAGATGGCCGGATTGACGTCA-TGGCATGAGCCCATTATCATTAGTTATCTTT
391 TGCTATTGATTCTAAATGGCCGGATTGACAT-AGTGGCATGAGCCCAATATCATCAGTTATCTTT
**
2311 GTTTGGGCTTAATTCTATCTTAGATTAGCTTATTTTTAAGTTTGGACCTTATTTGGATTGGGCCT
455 GTTTGGGCTTAATTCTATCTTAGATTAGCTTATTTTTAAGTTTGGATGTTATTTGGATTGGGCCT
* * * *
2376 TGGTTGACTAAGTCCAATCCTTGTTTAATTATGTCTTTATTTCCTTTTCCTAGTTGGGTTTTGAC
520 TGTTTGACTAAGTCCAATCCTTGTTTAATTAT-ACTTTATTTCCTTTTCCTAGTTGGGCTTGGAC
*
2441 TTGTTTTTCCCTAGCCCTTATATTTGGACGAAAATTAGGATTTATTTTAGGATTTTGGTTGACCC
584 TAGTTTTTCCCTAGCCCTTATATTTGGACGAAAATTAGGATTTATTTTAGGATTTTGGTTGACCC
** * *
2506 TATCACTATATAAGGCCACAAATATCTCTTGTAAAAGTTTAAGTTTAGTTGATTAATAAAGTTGA
649 TATCACTATATAAGGCCACAAATATCTCTTGTAAAAGTGGAAGTTGAGTTGATTAATAAAATTGA
* * * *
2571 GGATT-ATTTTCCCAAATTGATTATCTTAGCTTCATTGTTCTAGTTTGAGCAAACTTAGGGTTCT
714 GG-TTGATTCTCCCAAATTGATTATCTTGGCTTCATTGTTCTAGTTCGAGGAAACTTAGGGTTCT
* *
2635 TCAATCTTGTAGAGTCCTAGCAAGCAATTAGG-T-TGTGATTGCTTAATTGTTTGTGAATCTTGT
778 TCGATCTTGTAGAGTCCTAGCAAACAATTAGGTTGTGTGA-TGCTTAATTGTTTGTGAATCTTGT
* * * * *
2698 GATCTT-GAG-AATTAAATTGCAGGTCTAATTG-AGTGCTTAAGGCCGACGAAAGAGGAG-GAAT
842 GATCTTAG-GTTATTCAATTGCAGGTCTAATTGAAG-ACTTAAGGCCGACGAACGAAGAGAG-AT
* * **
2759 AGCCTTGTGAAGGTCATCGACATAC
904 TGCTTTGTGAAGGTTGTCGACATAC
** * * *
2784 AAGTCTAGAAGTTGAAGAAGTTCAAGT
1 TTGTCTACAAGCTGAAGAAGTCCAAGT
2811 CGACTTTGGT
Statistics
Matches: 1793, Mismatches: 78, Indels: 23
0.95 0.04 0.01
Matches are distributed among these distances:
926 3 0.00
927 93 0.05
928 1134 0.63
929 558 0.31
930 5 0.00
ACGTcount: A:0.29, C:0.16, G:0.22, T:0.34
Consensus pattern (928 bp):
TTGTCTACAAGCTGAAGAAGTCCAAGTAGATTCTTGGCAGGTCTCAAGGATAGATTTTATCATGG
AGGTCCAAGGACTTCTCATGGTCTTGGAGACAAGCATGGAGACCATAGAAAGGATGTGCATGGGC
TGCAAGGAAGCATGGAGATGCATGAAGATTATCGAGATATTGATAAGCATGTTCCAAGCACCAAA
AAGATGCTTATTCGATTCATTGAAGATGCCTATTAGCCCGATGACAAGAGCAAGAGCTAAGAGAT
TCAGGGATGCACTCATGAGCCTTGTTCGAACTCATCTTGAAGACTTGAAGACCATTCAAGTTCAA
TTGAAGAGCTTTGATGATGATTTGAGCAAGAAAACACCAATGAATTACAAGTTCATCACTTTGCT
TGCTATTGATTCTAAATGGCCGGATTGACATAGTGGCATGAGCCCAATATCATCAGTTATCTTTG
TTTGGGCTTAATTCTATCTTAGATTAGCTTATTTTTAAGTTTGGATGTTATTTGGATTGGGCCTT
GTTTGACTAAGTCCAATCCTTGTTTAATTATACTTTATTTCCTTTTCCTAGTTGGGCTTGGACTA
GTTTTTCCCTAGCCCTTATATTTGGACGAAAATTAGGATTTATTTTAGGATTTTGGTTGACCCTA
TCACTATATAAGGCCACAAATATCTCTTGTAAAAGTGGAAGTTGAGTTGATTAATAAAATTGAGG
TTGATTCTCCCAAATTGATTATCTTGGCTTCATTGTTCTAGTTCGAGGAAACTTAGGGTTCTTCG
ATCTTGTAGAGTCCTAGCAAACAATTAGGTTGTGTGATGCTTAATTGTTTGTGAATCTTGTGATC
TTAGGTTATTCAATTGCAGGTCTAATTGAAGACTTAAGGCCGACGAACGAAGAGAGATTGCTTTG
TGAAGGTTGTCGACATAC
Found at i:3102 original size:9 final size:9
Alignment explanation
Indices: 3082--3116 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
3072 AGTTATATCG
*
3082 AAAAATATA
1 AAAAAAATA
*
3091 AAACAAATA
1 AAAAAAATA
3100 AAAAAAATA
1 AAAAAAATA
3109 AAAAAAAT
1 AAAAAAAT
3117 TTCGACCAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.83, C:0.03, G:0.00, T:0.14
Consensus pattern (9 bp):
AAAAAAATA
Found at i:4653 original size:33 final size:33
Alignment explanation
Indices: 4602--4674 Score: 92
Period size: 33 Copynumber: 2.2 Consensus size: 33
4592 GTGTTTTAGA
*
4602 TGTTGTTTGCAATGATACTAAACCTAATTTAAG
1 TGTTATTTGCAATGATACTAAACCTAATTTAAG
* * ** *
4635 TGTTATTTGCAATTATACTAAATCTGTTTTAGG
1 TGTTATTTGCAATGATACTAAACCTAATTTAAG
4668 TGTTATT
1 TGTTATT
4675 GGTGATGACA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.29, C:0.10, G:0.15, T:0.47
Consensus pattern (33 bp):
TGTTATTTGCAATGATACTAAACCTAATTTAAG
Found at i:4688 original size:33 final size:34
Alignment explanation
Indices: 4651--4732 Score: 100
Period size: 33 Copynumber: 2.5 Consensus size: 34
4641 TTGCAATTAT
* *
4651 ACTAAATCTGTTTTAGG-TG-TTATTGGTGATG-AC
1 ACTAAATCTGTTTT-GGATGCTAATT-GTGATGAAA
4684 ACTAAATCTGTTTTGGATGCTAATTGTGATGAAA
1 ACTAAATCTGTTTTGGATGCTAATTGTGATGAAA
4718 AC-AAATCTGTTTTGG
1 ACTAAATCTGTTTTGG
4733 TTGATCATAG
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
32 2 0.05
33 35 0.80
34 7 0.16
ACGTcount: A:0.28, C:0.10, G:0.22, T:0.40
Consensus pattern (34 bp):
ACTAAATCTGTTTTGGATGCTAATTGTGATGAAA
Found at i:4762 original size:33 final size:33
Alignment explanation
Indices: 4725--4831 Score: 169
Period size: 33 Copynumber: 3.2 Consensus size: 33
4715 AAAACAAATC
4725 TGTTTTGGTTGATCATAGCATTGCAAATAATTA
1 TGTTTTGGTTGATCATAGCATTGCAAATAATTA
* * *
4758 TGTTTTAGTTGATCATAGCATTTCAAATAATTT
1 TGTTTTGGTTGATCATAGCATTGCAAATAATTA
* *
4791 TGTTTTGTTTGATCATAGCATTGCAAATAATTC
1 TGTTTTGGTTGATCATAGCATTGCAAATAATTA
4824 TGTTTTGG
1 TGTTTTGG
4832 GTGAAAAGAA
Statistics
Matches: 66, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 66 1.00
ACGTcount: A:0.27, C:0.09, G:0.17, T:0.47
Consensus pattern (33 bp):
TGTTTTGGTTGATCATAGCATTGCAAATAATTA
Found at i:5214 original size:30 final size:30
Alignment explanation
Indices: 5174--5232 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
5164 CAAGGGGGAG
5174 GGAATGATGCGCCCAAGG-CTTATCATGGAA
1 GGAATGATGCG-CCAAGGACTTATCATGGAA
* *
5204 GGAATTATGCGCCAAGGACTTATTATGGA
1 GGAATGATGCGCCAAGGACTTATCATGGA
5233 CTTGAAGACA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 6 0.23
30 20 0.77
ACGTcount: A:0.31, C:0.17, G:0.29, T:0.24
Consensus pattern (30 bp):
GGAATGATGCGCCAAGGACTTATCATGGAA
Found at i:5755 original size:29 final size:29
Alignment explanation
Indices: 5722--5781 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
5712 CCTAGTTGGG
* *
5722 TTTGGACTAGTTTTCCCCTAGCCCTTATA
1 TTTGGACGAATTTTCCCCTAGCCCTTATA
5751 TTTGGACGAATTTTCCCCTAGCCCTTATA
1 TTTGGACGAATTTTCCCCTAGCCCTTATA
5780 TT
1 TT
5782 AGGATTTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.18, C:0.27, G:0.13, T:0.42
Consensus pattern (29 bp):
TTTGGACGAATTTTCCCCTAGCCCTTATA
Found at i:7907 original size:33 final size:33
Alignment explanation
Indices: 7870--7946 Score: 82
Period size: 33 Copynumber: 2.3 Consensus size: 33
7860 TTGCAAAGAG
* * * *
7870 TGTTTTTGATGTTGTTTGCAATGATACTAAATC
1 TGTTTTAGATGTTATTGGCAATGACACTAAATC
* **
7903 TGTTTTAGGTGTTATTGGTGATGACACTAAATC
1 TGTTTTAGATGTTATTGGCAATGACACTAAATC
*
7936 TGTTTTGGATG
1 TGTTTTAGATG
7947 CTAATTTTGA
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.22, C:0.08, G:0.23, T:0.47
Consensus pattern (33 bp):
TGTTTTAGATGTTATTGGCAATGACACTAAATC
Found at i:7958 original size:33 final size:32
Alignment explanation
Indices: 7890--7977 Score: 90
Period size: 33 Copynumber: 2.7 Consensus size: 32
7880 GTTGTTTGCA
* *
7890 ATGATACTAAATCTGTTTTAGGTGTTATTGGTG
1 ATGAAACTAAATCTGTTTT-GGTGTAATTGGTG
* *
7923 ATGACACTAAATCTGTTTTGGATGCTAATT-TTG
1 ATGAAACTAAATCTGTTTTGG-TG-TAATTGGTG
7956 ATGAAAAC-AAATCTGTTTTGGT
1 ATG-AAACTAAATCTGTTTTGGT
7978 TGATCATAGC
Statistics
Matches: 48, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
32 3 0.06
33 38 0.79
34 7 0.15
ACGTcount: A:0.28, C:0.09, G:0.20, T:0.42
Consensus pattern (32 bp):
ATGAAACTAAATCTGTTTTGGTGTAATTGGTG
Found at i:9466 original size:10 final size:10
Alignment explanation
Indices: 9451--9479 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
9441 ATCGAAAAAT
9451 AAAAAAATTA
1 AAAAAAATTA
9461 AAAAAAATTA
1 AAAAAAATTA
9471 AAAAAAATT
1 AAAAAAATT
9480 TCGACCAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (10 bp):
AAAAAAATTA
Found at i:11034 original size:33 final size:33
Alignment explanation
Indices: 10937--11041 Score: 120
Period size: 33 Copynumber: 3.2 Consensus size: 33
10927 TTGAAAAGAG
* * * *
10937 TGTTTTAGATGTTGTTTGCGATGATACTGAACC
1 TGTTTTAGGTGTTGTTTGCGATGAAACTAAATC
** * * *
10970 TAATTTGGGTGTTGTTTGCAATGACACTAAATC
1 TGTTTTAGGTGTTGTTTGCGATGAAACTAAATC
*
11003 TGTTTTAGGTGTTGTTTGTGATGAAACTAAATC
1 TGTTTTAGGTGTTGTTTGCGATGAAACTAAATC
11036 TGTTTT
1 TGTTTT
11042 GGATGCTAAT
Statistics
Matches: 58, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
33 58 1.00
ACGTcount: A:0.23, C:0.10, G:0.23, T:0.45
Consensus pattern (33 bp):
TGTTTTAGGTGTTGTTTGCGATGAAACTAAATC
Found at i:11055 original size:33 final size:33
Alignment explanation
Indices: 10990--11061 Score: 92
Period size: 33 Copynumber: 2.2 Consensus size: 33
10980 GTTGTTTGCA
* * **
10990 ATGACACTAAATCTGTTTTAGGTGTTGTTTGTG
1 ATGAAACTAAATCTGTTTTAGGTGCTAATTGTG
11023 ATGAAACTAAATCTGTTTT-GGATGCTAATTGTG
1 ATGAAACTAAATCTGTTTTAGG-TGCTAATTGTG
11056 ATGAAA
1 ATGAAA
11062 ACAATTCTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
32 2 0.06
33 32 0.94
ACGTcount: A:0.29, C:0.08, G:0.22, T:0.40
Consensus pattern (33 bp):
ATGAAACTAAATCTGTTTTAGGTGCTAATTGTG
Found at i:11106 original size:33 final size:32
Alignment explanation
Indices: 11057--11172 Score: 128
Period size: 33 Copynumber: 3.6 Consensus size: 32
11047 CTAATTGTGA
*
11057 TGAAAACAATTCTATTTTGGTTGAACATAGCAT
1 TGAAAATAATTCTATTTTGGTTG-ACATAGCAT
* *
11090 TAAAAATAATTTTATTTTGGTTGATCATAGCAT
1 TGAAAATAATTCTATTTTGGTTGA-CATAGCAT
* * *
11123 TGCAAATAATCCTGTTTTGGTTG--ATAGCAT
1 TGAAAATAATTCTATTTTGGTTGACATAGCAT
* *
11153 TGAAAATAAATCTGTTTTGG
1 TGAAAATAATTCTATTTTGG
11173 GTGAAAAGAA
Statistics
Matches: 71, Mismatches: 11, Indels: 5
0.82 0.13 0.06
Matches are distributed among these distances:
30 24 0.34
32 1 0.01
33 46 0.65
ACGTcount: A:0.34, C:0.09, G:0.16, T:0.41
Consensus pattern (32 bp):
TGAAAATAATTCTATTTTGGTTGACATAGCAT
Found at i:11152 original size:30 final size:30
Alignment explanation
Indices: 11083--11172 Score: 92
Period size: 30 Copynumber: 2.9 Consensus size: 30
11073 TTGGTTGAAC
* * * *
11083 ATAGCATTAAAAATAATTTTATTTTGGTTG
1 ATAGCATTGAAAATAAATCTGTTTTGGTTG
*
11113 ATCATAGCATTGCAAAT-AATCCTGTTTTGGTTG
1 ---ATAGCATTGAAAATAAAT-CTGTTTTGGTTG
11146 ATAGCATTGAAAATAAATCTGTTTTGG
1 ATAGCATTGAAAATAAATCTGTTTTGG
11173 GTGAAAAGAA
Statistics
Matches: 49, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
30 22 0.45
31 3 0.06
32 2 0.04
33 22 0.45
ACGTcount: A:0.33, C:0.09, G:0.17, T:0.41
Consensus pattern (30 bp):
ATAGCATTGAAAATAAATCTGTTTTGGTTG
Found at i:11591 original size:30 final size:30
Alignment explanation
Indices: 11551--11609 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
11541 CAAGGCGGAG
11551 GGAATGATGCGCCCAAGG-CTTATCATGGAA
1 GGAATGATGCG-CCAAGGACTTATCATGGAA
* *
11581 GGAATTATGCGCCAAGGACTTATTATGGA
1 GGAATGATGCGCCAAGGACTTATCATGGA
11610 CTTGAAGACA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 6 0.23
30 20 0.77
ACGTcount: A:0.31, C:0.17, G:0.29, T:0.24
Consensus pattern (30 bp):
GGAATGATGCGCCAAGGACTTATCATGGAA
Found at i:14651 original size:32 final size:33
Alignment explanation
Indices: 14576--14677 Score: 120
Period size: 31 Copynumber: 3.2 Consensus size: 33
14566 TTGCAAAGAG
*
14576 TGTTTTAGATGTTGTTTGCAATGATACTAAA-C
1 TGTTTTAGGTGTTGTTTGCAATGATACTAAATC
* *
14608 -CTTTTAAGTGTTGTTTGCAATGATA-TAAATC
1 TGTTTTAGGTGTTGTTTGCAATGATACTAAATC
* ** *
14639 TGTTTTAGGTGTTGTTGGTGATGACACTAAATC
1 TGTTTTAGGTGTTGTTTGCAATGATACTAAATC
14672 TGTTTT
1 TGTTTT
14678 GGATGCTAAT
Statistics
Matches: 58, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
30 4 0.07
31 23 0.40
32 19 0.33
33 12 0.21
ACGTcount: A:0.25, C:0.09, G:0.21, T:0.46
Consensus pattern (33 bp):
TGTTTTAGGTGTTGTTTGCAATGATACTAAATC
Found at i:14740 original size:33 final size:33
Alignment explanation
Indices: 14703--14811 Score: 184
Period size: 33 Copynumber: 3.3 Consensus size: 33
14693 TGAAAACAAA
14703 TCTGTTTTGGTTTATCATAGCATTGCAAATAAT
1 TCTGTTTTGGTTTATCATAGCATTGCAAATAAT
*
14736 TCTGTTTTAG-TTATTCATAGCATTGCAAATAAT
1 TCTGTTTTGGTTTA-TCATAGCATTGCAAATAAT
*
14769 TCTGTTTTGGTTGATCATAGCATTGCAAATAAT
1 TCTGTTTTGGTTTATCATAGCATTGCAAATAAT
14802 TCTGTTTTGG
1 TCTGTTTTGG
14812 GTGAAAAGAA
Statistics
Matches: 71, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
32 3 0.04
33 66 0.93
34 2 0.03
ACGTcount: A:0.26, C:0.12, G:0.17, T:0.46
Consensus pattern (33 bp):
TCTGTTTTGGTTTATCATAGCATTGCAAATAAT
Found at i:15194 original size:30 final size:30
Alignment explanation
Indices: 15154--15212 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
15144 CAAGGGGGAG
*
15154 GGAATGATGCGCCCAA-GACTTATCATGGAA
1 GGAATAATGCG-CCAAGGACTTATCATGGAA
*
15184 GGAATAATGCGCCAAGGACTTATTATGGA
1 GGAATAATGCGCCAAGGACTTATCATGGA
15213 CTTGAAGACA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 4 0.15
30 22 0.85
ACGTcount: A:0.34, C:0.17, G:0.27, T:0.22
Consensus pattern (30 bp):
GGAATAATGCGCCAAGGACTTATCATGGAA
Found at i:18039 original size:927 final size:924
Alignment explanation
Indices: 16246--18722 Score: 4222
Period size: 927 Copynumber: 2.7 Consensus size: 924
16236 GGGCGCATCA
*
16246 CTCTTTCTTTGAGCTTAATTCTATCTTAGATCAGCTTATTTTTAAGTTTAAATGTTATTTGGGTT
1 CTCTTTCTTTGGGCTTAATTCTATCTTAGATCAGCTTATTTTTAAGTTTAAATGTTATTTGGGTT
*
16311 GGGCCTTGTTTGACTAAGTCCAATCCTTGTTTAATTATGCTTTTATTTCCCTTTCCTAGTTGGGC
66 GGGCCTTGTTTGACTAAGTCCAATCCTTGTTTAATTATGCTTTTATTTCCC-TTCCTAGTTGGAC
*
16376 TTGGACTAGTTTTTCCCTAGCCCTTATATTTGGACGCAAATTAGGATTTATTTTAGGATTTTGGT
130 TTGGACTAGTTTTTCCCTAGCCCTTATATTTGGACGAAAATTAGGATTTATTTTAGGATTTTGGT
16441 TGACCCTATCACTATATAAGGCCACCAATATCTCTTGTAAAAGTGGAAGTTGAGTTGATTAATAA
195 TGACCCTATCACTATATAAGGCCACCAATATCTCTTGTAAAAGTGGAAGTTGAGTTGATTAATAA
* * *
16506 AATTGAGATTTATTCTACCAAATTGATTATCTTAGCTTCATTGTTCTAGTTTGAGCAAACTAAGG
260 AATTGAGATTTATTCTCCCAAATTGATTATCTTGGCTTCATTGTTCTAGTTTGAGCAAACTTAGG
*
16571 GTTCTTCAATCTTGTAGAGTCCTAGCAAACAATTAGGTTGTGTGATGGTTAATTGTTTGTTAATC
325 GTTCTTCAATCTTGTAGAGTCCTAGCAAACAATTAGGTTGTGTGATGGTTAATTGTTTGTGAATC
*
16636 TTGTGATCCTAGGTATTCAATTGCAGGTCTAATTGAAGACTTAAGGCTGACGAACGAAGAGAGAT
390 TTGTGATCTTAGGTATTCAATTGCAGGTCTAATTGAAGACTTAAGGCTGACGAACGAAGAGAGAT
* * *
16701 TGCTATGTGAAGCTTGGCGACATACTTGTATAGAAGTTGAAGAAGTTCAAGTAGATTCGTGGCAG
455 TGCT-TGTGAAGGTTGTCGACATACTTGTATAGAAGTTCAAGAAGTTCAAGTAGATTCGTGGCAG
* *
16766 ATCTCAAGGATAGATTTTATCATGGAGGGCGAAGGACTTATCATAGTCTTGAAGACAAGCATGGA
519 -TCTCAAGGATAGATTTTATCATGGAGGGCCAAGGACTTATCATGGTCTTGAAGACAAGCATGGA
* *
16831 GAGCATGGAAAGGATGTGCATGTGCTACAAGGAAGCATGGAGATGAATGAAGATTATCGAGATAT
583 GAGCATGGAAAGGATGTGCATGGGCTGCAAGGAAGCATGGAGATGAATGAAGATTATCGAGATAT
* *
16896 TGATAAGCATGCTCCAAGCACCAAATAGATGCTAATCGATTCATTGAAGAGGCCTATTTGTCCGA
648 TGATAAGCATGCTCCAAGCACCAAAAAGATGCTAATCGATTCATTGAAGAGGCCTATTAGTCCGA
* *
16961 TGACAAGAGCAAGAGCTAAGAGATTCAAGGATGCACTCATGGGCCTTGTTCGAACTAATCTTGAA
713 TGACAAGAGCAAGAGCTAAGAGATTCAAGGATGCAATCATGGGCCTTGTCCGAACTAATCTTGAA
*
17026 GACTTGAAGACCATTCAAGTTCAATTGAAGAGCTTTGATGGTGATTTGAGCAAGAAAACCCCAAT
778 GACTTGAAGACCATTCAAGTTCAATTGAAGAGCTTTGATGATGATTTGAGCAAGAAAACCCCAAT
* * * * *
17091 CAATTACAAGTTCATCACTTTGCTTGCTGTTGATTCTAAATGGCC-TGATTTACATAGTGGCATG
843 AAATTACAAGTTCATCACTTTGCTTGCTATTGATTCTAAATGGCCGT-ATTGACATAGTCGCATA
*
17155 AGCCCAATATCATTAGTT
907 AGCCCAATATCACTAGTT
*
17173 CTCTTTCTTTGGGCTTAATTCTATCTTAGATCAGCTTATTTTTAAGTTTAAATGTAATTTGGGTT
1 CTCTTTCTTTGGGCTTAATTCTATCTTAGATCAGCTTATTTTTAAGTTTAAATGTTATTTGGGTT
17238 GGGCCTTGTTTGACTAAGTCCAATCCTTGTTTAATTATGCTTTTATTTCCCTATCCTAGTTGGAC
66 GGGCCTTGTTTGACTAAGTCCAATCCTTGTTTAATTATGCTTTTATTTCCCT-TCCTAGTTGGAC
* *
17303 TTGGACTTGTTTTTCCCTATCCCTTATATTTGGACGAAAATTAGGATTTATTTTAGGATTTTGGT
130 TTGGACTAGTTTTTCCCTAGCCCTTATATTTGGACGAAAATTAGGATTTATTTTAGGATTTTGGT
*
17368 TGACCCTATCACTATATAAGGCCACCAATATCTCTTGTAAAAGTGGAAGTTGTGTTGATTAATAA
195 TGACCCTATCACTATATAAGGCCACCAATATCTCTTGTAAAAGTGGAAGTTGAGTTGATTAATAA
17433 AATTGAGATTTATTCTCCCAAATTGATTATCTTGGCTTCATTGTTCTAGTTTGAGCAAACTTAGG
260 AATTGAGATTTATTCTCCCAAATTGATTATCTTGGCTTCATTGTTCTAGTTTGAGCAAACTTAGG
* *
17498 GTTCTTCAATCTTGTTGAGTCCTAGCAAACAATTAGGTTGTGTGATGGTTAATTGGTTGTGAATC
325 GTTCTTCAATCTTGTAGAGTCCTAGCAAACAATTAGGTTGTGTGATGGTTAATTGTTTGTGAATC
* * *
17563 TTGTGATCTTAGGTATTCAATTGTAGGTCTAATTGAAGACTTATGGCTGAGGAACGAAGAGAGAT
390 TTGTGATCTTAGGTATTCAATTGCAGGTCTAATTGAAGACTTAAGGCTGACGAACGAAGAGAGAT
*
17628 TGCTTGGTGAAGGTTGTCGACATACTTTTATAGAAGTTCAAGAAGTTCAAGTAGATTCGTGGCAC
455 TGCTT-GTGAAGGTTGTCGACATACTTGTATAGAAGTTCAAGAAGTTCAAGTAGATTCGTGGCA-
* * *
17693 GTCTCAAGAATAGATTTTATCATGGAGCGCCAAAGACTTATCATGGTCTTGAAGACAAGCATGGA
518 GTCTCAAGGATAGATTTTATCATGGAGGGCCAAGGACTTATCATGGTCTTGAAGACAAGCATGGA
17758 GAGCATGGAAAGGATGTGCATGGGCTGCAAGGAAGCATGGAGATGAATGAAGATTATCGAGATAT
583 GAGCATGGAAAGGATGTGCATGGGCTGCAAGGAAGCATGGAGATGAATGAAGATTATCGAGATAT
* * * *
17823 TGATAAGCATGTTCCAAGCACCAAAAAGGTGCTATTCGATTCATTGAAGATGCCTATTAGTCCGA
648 TGATAAGCATGCTCCAAGCACCAAAAAGATGCTAATCGATTCATTGAAGAGGCCTATTAGTCCGA
* *
17888 TGACAAGAGCAATAGCTAAGAGATTCAAGGATGCAATCATGGGCCTTGTCCGAACTCATCTTGAA
713 TGACAAGAGCAAGAGCTAAGAGATTCAAGGATGCAATCATGGGCCTTGTCCGAACTAATCTTGAA
*
17953 GACTTGAAGACCATTCAAGTTCAATTGAAGAGCTTTGATGATGATTTGAGCAAG-AAACCATCAA
778 GACTTGAAGACCATTCAAGTTCAATTGAAGAGCTTTGATGATGATTTGAGCAAGAAAACC-CCAA
18017 TAAATTACAAGTTCATCACTTTGCTTGCTATTGATTCTAAATGGCCGTATTGACATAGTCGCATA
842 TAAATTACAAGTTCATCACTTTGCTTGCTATTGATTCTAAATGGCCGTATTGACATAGTCGCATA
18082 AGCCCAATATCACTAGTT
907 AGCCCAATATCACTAGTT
* * * * * ** * *
18100 ATCTTTGTATGGGCTTAATTCTATCTTAAATTAGCTTATTTTTAAGTTTGGATTTTATTTAGGTT
1 CTCTTTCTTTGGGCTTAATTCTATCTTAGATCAGCTTATTTTTAAGTTTAAATGTTATTTGGGTT
* * * *
18165 GGGCATAGTTTGACTAAGTCCAATCCTTGTTTAATTATTCTTTTAATTCCCTTCCCTAGTTGGAC
66 GGGCCTTGTTTGACTAAGTCCAATCCTTGTTTAATTATGCTTTTATTTCCCTT-CCTAGTTGGAC
18230 TTGGACTAGTTTTTCCCTAGCCCTTATATTTGGACGAAAATTAGGATTTATTTTAGGATTTTGGT
130 TTGGACTAGTTTTTCCCTAGCCCTTATATTTGGACGAAAATTAGGATTTATTTTAGGATTTTGGT
18295 TGACCCTATCACTATATAAGGCCACCAATATCTCTTGTAAAAGTGGAAGTTGAGTTGATTAATAA
195 TGACCCTATCACTATATAAGGCCACCAATATCTCTTGTAAAAGTGGAAGTTGAGTTGATTAATAA
* *
18360 AATTGAGATTTATTCTCCCAAATTGATTATCTTGGCTTCATTGGTCTAGTTTGAGCAAACTTAGT
260 AATTGAGATTTATTCTCCCAAATTGATTATCTTGGCTTCATTGTTCTAGTTTGAGCAAACTTAGG
** * *
18425 GTTCTTCAATCTTGCCGAGTCCTAGTAAACAATTAGGTTGTGTGATGCTTAATTGTTTGTGAATC
325 GTTCTTCAATCTTGTAGAGTCCTAGCAAACAATTAGGTTGTGTGATGGTTAATTGTTTGTGAATC
* *
18490 TTGTGATCTTAGGTATTCAATTGCAGGTCTAATTAAAGACTTACA-GCTGACGAACGAAGAAAGA
390 TTGTGATCTTAGGTATTCAATTGCAGGTCTAATTGAAGACTTA-AGGCTGACGAACGAAGAGAGA
18554 TTGCTTTGTGAAGGTTGTCGACATACTTGTATAGAAGTTCAAGAAGTTCAAGTAGATTCGTGGCA
454 TTGC-TTGTGAAGGTTGTCGACATACTTGTATAGAAGTTCAAGAAGTTCAAGTAGATTCGTGGC-
18619 AGTCTCAAGGATAGATTTTATCATGGAGGGCCAAGGACTTATCATGGTCTTGAAGACAAGCATGG
517 AGTCTCAAGGATAGATTTTATCATGGAGGGCCAAGGACTTATCATGGTCTTGAAGACAAGCATGG
18684 AGAGCATGGAAAGGATGTGCATGGGCTGCAAGGAAGCAT
582 AGAGCATGGAAAGGATGTGCATGGGCTGCAAGGAAGCAT
18723 CCGATGACAA
Statistics
Matches: 1462, Mismatches: 79, Indels: 18
0.94 0.05 0.01
Matches are distributed among these distances:
926 8 0.01
927 1449 0.99
928 5 0.00
ACGTcount: A:0.29, C:0.15, G:0.21, T:0.35
Consensus pattern (924 bp):
CTCTTTCTTTGGGCTTAATTCTATCTTAGATCAGCTTATTTTTAAGTTTAAATGTTATTTGGGTT
GGGCCTTGTTTGACTAAGTCCAATCCTTGTTTAATTATGCTTTTATTTCCCTTCCTAGTTGGACT
TGGACTAGTTTTTCCCTAGCCCTTATATTTGGACGAAAATTAGGATTTATTTTAGGATTTTGGTT
GACCCTATCACTATATAAGGCCACCAATATCTCTTGTAAAAGTGGAAGTTGAGTTGATTAATAAA
ATTGAGATTTATTCTCCCAAATTGATTATCTTGGCTTCATTGTTCTAGTTTGAGCAAACTTAGGG
TTCTTCAATCTTGTAGAGTCCTAGCAAACAATTAGGTTGTGTGATGGTTAATTGTTTGTGAATCT
TGTGATCTTAGGTATTCAATTGCAGGTCTAATTGAAGACTTAAGGCTGACGAACGAAGAGAGATT
GCTTGTGAAGGTTGTCGACATACTTGTATAGAAGTTCAAGAAGTTCAAGTAGATTCGTGGCAGTC
TCAAGGATAGATTTTATCATGGAGGGCCAAGGACTTATCATGGTCTTGAAGACAAGCATGGAGAG
CATGGAAAGGATGTGCATGGGCTGCAAGGAAGCATGGAGATGAATGAAGATTATCGAGATATTGA
TAAGCATGCTCCAAGCACCAAAAAGATGCTAATCGATTCATTGAAGAGGCCTATTAGTCCGATGA
CAAGAGCAAGAGCTAAGAGATTCAAGGATGCAATCATGGGCCTTGTCCGAACTAATCTTGAAGAC
TTGAAGACCATTCAAGTTCAATTGAAGAGCTTTGATGATGATTTGAGCAAGAAAACCCCAATAAA
TTACAAGTTCATCACTTTGCTTGCTATTGATTCTAAATGGCCGTATTGACATAGTCGCATAAGCC
CAATATCACTAGTT
Found at i:19501 original size:839 final size:839
Alignment explanation
Indices: 17883--19561 Score: 3056
Period size: 839 Copynumber: 2.0 Consensus size: 839
17873 TGCCTATTAG
*
17883 TCCGATGACAAGAGCAATAGCTAAGAGATTCAAGGATGCAATCATGGGCCTTGTCCGAACTCATC
1 TCCGATGACAAGAGCAAGAGCTAAGAGATTCAAGGATGCAATCATGGGCCTTGTCCGAACTCATC
*
17948 TTGAAGACTTGAAGACCATTCAAGTTCAATTGAAGAGCTTTGATGATGATTTGAGCAAGAAACCA
66 TTGAAGACTTGAAGACCATTCAAGTTCAATTGAAGAGCTTTGATGATGATTTGAGCAAGAAAACA
*
18013 TCAATAAATTACAAGTTCATCACTTTGCTTGCTATTGATTCTAAATGGCCGTATTGACATAGTCG
131 TCAATAAATTACAAGTTCATCACTTTGCTTGCTATTGATTCTAAATGGCCGGATTGACATAGTCG
18078 CATAAGCCCAATATCACTAGTTATCTTTGTATGGGCTTAATTCTATCTTAAATTAGCTTATTTTT
196 CATAAGCCCAATATCACTAGTTATCTTTGTATGGGCTTAATTCTATCTTAAATTAGCTTATTTTT
* * *
18143 AAGTTTGGATTTTATTTAGGTTGGGCATAGTTTGACTAAGTCCAATCCTTGTTTAATTATTCTTT
261 AAGTTTGGATGTTATTTAGGTTGGGCATAGTTTGACTAAGTCCAATCCTTGTTTAACTATGCTTT
18208 TAATTCCCTTCCCTAGTTGGACTTGGACTAGTTTTTCCCTAGCCCTTATATTTGGACGAAAATTA
326 TAATTCCCTTCCCTAGTTGGACTTGGACTAGTTTTTCCCTAGCCCTTATATTTGGACGAAAATTA
18273 GGATTTATTTTAGGATTTTGGTTGACCCTATCACTATATAAGGCCACCAATATCTCTTGTAAAAG
391 GGATTTATTTTAGGATTTTGGTTGACCCTATCACTATATAAGGCCACCAATATCTCTTGTAAAAG
* *
18338 TGGAAGTTGAGTTGATTAATAAAATTGAGATTTATTCTCCCAAATTGATTATCTTGGCTTCATTG
456 TGGAAATTGAATTGATTAATAAAATTGAGATTTATTCTCCCAAATTGATTATCTTGGCTTCATTG
18403 GTCTAGTTTGAGCAAACTTAGTGTTCTTCAATCTTGCCGAGTCCTAGTAAACAATTAGGTTGTGT
521 GTCTAGTTTGAGCAAACTTAGTGTTCTTCAATCTTGCCGAGTCCTAGTAAACAATTAGGTTGTGT
18468 GATGCTTAATTGTTTGTGAATCTTGTGATCTTAGGTATTCAATTGCAGGTCTAATTAAAGACTTA
586 GATGCTTAATTGTTTGTGAATCTTGTGATCTTAGGTATTCAATTGCAGGTCTAATTAAAGACTTA
18533 CAGCTGACGAACGAAGAAAGATTGCTTTGTGAAGGTTGTCGACATACTTGTATAGAAGTTCAAGA
651 CAGCTGACGAACGAAGAAAGATTGCTTTGTGAAGGTTGTCGACATACTTGTATAGAAGTTCAAGA
*
18598 AGTTCAAGTAGATTCGTGGCAAGTCTCAAGGATAGATTTTATCATGGAGGGCCAAGGACTTATCA
716 AGTTCAAGTAGATTCATGGCAAGTCTCAAGGATAGATTTTATCATGGAGGGCCAAGGACTTATCA
18663 TGGTCTTGAAGACAAGCATGGAGAGCATGGAAAGGATGTGCATGGGCTGCAAGGAAGCA
781 TGGTCTTGAAGACAAGCATGGAGAGCATGGAAAGGATGTGCATGGGCTGCAAGGAAGCA
*
18722 TCCGATGACAAGAGCAAGAGCTAAGAGATTCAAGGATGCACTCATGGGCCTTGTCCGAACTCATC
1 TCCGATGACAAGAGCAAGAGCTAAGAGATTCAAGGATGCAATCATGGGCCTTGTCCGAACTCATC
18787 TTGAAGACTTGAAGACCATTCAAGTTCAATTGAAGAGCTTTGATGATGATTTGAGCAAGAAAACA
66 TTGAAGACTTGAAGACCATTCAAGTTCAATTGAAGAGCTTTGATGATGATTTGAGCAAGAAAACA
* *
18852 TCAATCAATTACAAGTTCATCACTTTGCTTGCTATTGATTCTAAATGGCCGGATTGACATAGTGG
131 TCAATAAATTACAAGTTCATCACTTTGCTTGCTATTGATTCTAAATGGCCGGATTGACATAGTCG
* * * **
18917 CATAAGCCCAATATCATTAGTTATTTTTGTATTGGCTTAATTCTATCTTTGATTAGCTTATTTTT
196 CATAAGCCCAATATCACTAGTTATCTTTGTATGGGCTTAATTCTATCTTAAATTAGCTTATTTTT
* * * *
18982 AAGTTTGGATGTTATTTGGGTTGGTCCTTGTTTGACTAAGTCCAATCCTTGTTTAACTATGCTTT
261 AAGTTTGGATGTTATTTAGGTTGGGCATAGTTTGACTAAGTCCAATCCTTGTTTAACTATGCTTT
* *
19047 TATTTCCCTTTCCTAGTTGGACTTGGACTAGTTTTTCCCTAGCCCTTATATTTGGACGAAAATTA
326 TAATTCCCTTCCCTAGTTGGACTTGGACTAGTTTTTCCCTAGCCCTTATATTTGGACGAAAATTA
19112 GGATTTATTTTAGGATTTTGGTTGACCCTATCACTATATAAGGCCACCAATATCTCTTGTAAAAG
391 GGATTTATTTTAGGATTTTGGTTGACCCTATCACTATATAAGGCCACCAATATCTCTTGTAAAAG
* *
19177 TGGAAATTGAATTGATTAATAAAATTGAGGTTTATTCTCCCAAATTGATTATCTTGGCTTCGTTG
456 TGGAAATTGAATTGATTAATAAAATTGAGATTTATTCTCCCAAATTGATTATCTTGGCTTCATTG
* *
19242 TTTTAGTTTGAGCAAACTTAAG-GTTCTTCAATCTTGCCGAGTCCTAGTAAACAATTAGGTTGTG
521 GTCTAGTTTGAGCAAACTT-AGTGTTCTTCAATCTTGCCGAGTCCTAGTAAACAATTAGGTTGTG
19306 TGATGCTTAATTGTTTGTGAATCTTGTGATCTTAGGTATTCAATTGCAGGTCTAATTAAAGACTT
585 TGATGCTTAATTGTTTGTGAATCTTGTGATCTTAGGTATTCAATTGCAGGTCTAATTAAAGACTT
*
19371 A-AGGCTGACGAACGAAGAGAGATTGCTTTGTGAAGGTTGTCGACATACTTGTATAGAAGTTCAA
650 ACA-GCTGACGAACGAAGAAAGATTGCTTTGTGAAGGTTGTCGACATACTTGTATAGAAGTTCAA
* *
19435 TAAGTTCAAGTAGATTTATGGCAAGTCTCAAGGATAGATTTTATCATGGAGGGCCAAGGACTTAT
714 GAAGTTCAAGTAGATTCATGGCAAGTCTCAAGGATAGATTTTATCATGGAGGGCCAAGGACTTAT
19500 CATGGTCTTGAAGACAAGCATGGAGAGCATGGAAAGGATGTGCATGGGCTGCAAGGAAGCA
779 CATGGTCTTGAAGACAAGCATGGAGAGCATGGAAAGGATGTGCATGGGCTGCAAGGAAGCA
19561 T
1 T
19562 GGAGATGAAT
Statistics
Matches: 808, Mismatches: 30, Indels: 4
0.96 0.04 0.00
Matches are distributed among these distances:
838 1 0.00
839 805 1.00
840 2 0.00
ACGTcount: A:0.29, C:0.15, G:0.21, T:0.35
Consensus pattern (839 bp):
TCCGATGACAAGAGCAAGAGCTAAGAGATTCAAGGATGCAATCATGGGCCTTGTCCGAACTCATC
TTGAAGACTTGAAGACCATTCAAGTTCAATTGAAGAGCTTTGATGATGATTTGAGCAAGAAAACA
TCAATAAATTACAAGTTCATCACTTTGCTTGCTATTGATTCTAAATGGCCGGATTGACATAGTCG
CATAAGCCCAATATCACTAGTTATCTTTGTATGGGCTTAATTCTATCTTAAATTAGCTTATTTTT
AAGTTTGGATGTTATTTAGGTTGGGCATAGTTTGACTAAGTCCAATCCTTGTTTAACTATGCTTT
TAATTCCCTTCCCTAGTTGGACTTGGACTAGTTTTTCCCTAGCCCTTATATTTGGACGAAAATTA
GGATTTATTTTAGGATTTTGGTTGACCCTATCACTATATAAGGCCACCAATATCTCTTGTAAAAG
TGGAAATTGAATTGATTAATAAAATTGAGATTTATTCTCCCAAATTGATTATCTTGGCTTCATTG
GTCTAGTTTGAGCAAACTTAGTGTTCTTCAATCTTGCCGAGTCCTAGTAAACAATTAGGTTGTGT
GATGCTTAATTGTTTGTGAATCTTGTGATCTTAGGTATTCAATTGCAGGTCTAATTAAAGACTTA
CAGCTGACGAACGAAGAAAGATTGCTTTGTGAAGGTTGTCGACATACTTGTATAGAAGTTCAAGA
AGTTCAAGTAGATTCATGGCAAGTCTCAAGGATAGATTTTATCATGGAGGGCCAAGGACTTATCA
TGGTCTTGAAGACAAGCATGGAGAGCATGGAAAGGATGTGCATGGGCTGCAAGGAAGCA
Found at i:21233 original size:926 final size:927
Alignment explanation
Indices: 18722--21829 Score: 5382
Period size: 927 Copynumber: 3.4 Consensus size: 927
18712 CAAGGAAGCA
*
18722 TCCGATGACAAGAGCAAGAGCTAAGAGATTCAAGGATGCACTCATGGGCCTTGTCCGAACTCATC
1 TCCGATGACAAGAGCAAGAGCTAAGAGATTCAAGGATGCACTCATGGGCCATGTCCGAACTCATC
18787 TTGAAGACTTGAAGACCATTCAAGTTCAATTGAAGAGCTTTGATGATGATTTGAGCAAGAAAACA
66 TTGAAGACTTGAAGACCATTCAAGTTCAATTGAAGAGCTTTGATGATGATTTGAGCAAGAAAACA
18852 TCAATCAATTACAAGTTCATCACTTTGCTTGCTATTGATTCTAAATGGCCGGATTGACATAGTGG
131 TCAATCAATTACAAGTTCATCACTTTGCTTGCTATTGATTCTAAATGGCCGGATTGACATAGTGG
* * * *
18917 CATAAGCCCAATATCATTAGTTATTTTTGTATT-GGCTTAATTCTATCTTTGATTAGCTTATTTT
196 CATAAGCCCAATATCATTAGTTATCTTTCT-TTGGGCTTAATTCTATCTTAGATCAGCTTATTTT
** * *
18981 TAAGTTTGGATGTTATTTGGGTTGGTCCTTGTTTGACTAAGTCCAATCCTTGTTTAACTATGCTT
260 TAAGTTTAAATGTTATTTGGGTTGGGCCTTGTTTGACTAAGTCCAATCCTTGTTTAATTATGCTT
* *
19046 TTATTTCCCTTTCCTAGTTGGACTTGGACTAGTTTTTCCCTAGCCCTTATATTTGGACGAAAATT
325 TTATTTCCTTTTCCTAGTTGGGCTTGGACTAGTTTTTCCCTAGCCCTTATATTTGGACGAAAATT
19111 AGGATTTATTTTAGGATTTTGGTTGACCCTATCACTATATAAGGCCACCAATATCTCTTGTAAAA
390 AGGATTTATTTTAGGATTTTGGTTGACCCTATCACTATATAAGGCCACCAATATCTCTTGTAAAA
* * *
19176 GTGGAAATTGAATTGATTAATAAAATTGAGGTTTATTCTCCCAAATTGATTATCTTGGCTTCGTT
455 GTGGAAGTTGAGTTGATTAATAAAATTGAGGTTTATTCTCCCAAATTGATTATCTTGGCTTCATT
* * ** *
19241 GTTTTAGTTTGAGCAAACTTAAGGTTCTTCAATCTTGCCGAGTCCTAGTAAACAATTAGGTTGTG
520 GTTCTAGTTTGAGCAAACTTAGGGTTCTTCAATCTTGTAGAGTCCTAGCAAACAATTAGGTTGTG
*
19306 TGATGCTTAATTGTTTGTGAATCTTGTGATCTTAGGTATTCAATTGCAGGTCTAATTAAAGACTT
585 TGATGGTTAATTGTTTGTGAATCTTGTGATCTTAGGTATTCAATTGCAGGTCTAATTAAAGACTT
* * *
19371 AAGGCTGACGAACGAAGAGAGATTGCTTTGTGAAGGTTGTCGACATACTTGTATAGAAGTTCAAT
650 AAGGCTGACGAACGAAGAGAGATTGCTTTGTGAAGGTTGTCGACATACTTGTCTAGAAGTTGAAG
*
19436 AAGTTCAAGTAGATT-TATGGCAAGTCTCAAGGATAGATTTTATCATGGAGGGCCAAGGACTTAT
715 AAGTTCAAGTAGATTCT-TGGCAGGTCTCAAGGATAGATTTTATCATGGAGGGCCAAGGACTTAT
19500 CATGGTCTTGAAGACAAGCATGGAGAGCATGGAAAGGATGTGCATGGGCTGCAAGGAAGCATGGA
779 CATGGTCTTGAAGACAAGCATGGAGAGCATGGAAAGGATGTGCATGGGCTGCAAGGAAGCATGGA
*
19565 GATGAATGAAGATTATCGAGATATTGATAAACATGCTCCAAGCACCAAAAAGATGCTATTCGATT
844 GATGAATGAAGATTATCGAGATATTGATAAGCATGCTCCAAGCACCAAAAAGATGCTATTCGATT
19630 CATTGAAGATGCCTATTAG
909 CATTGAAGATGCCTATTAG
* *
19649 TCCGATGACAAGAGCAAGAGCTAAGAGATTCAAGGATGCAATCATGGGCCTTGTCCGAACTCATC
1 TCCGATGACAAGAGCAAGAGCTAAGAGATTCAAGGATGCACTCATGGGCCATGTCCGAACTCATC
*
19714 TTGAAGACTTGAAGACCATTCAAGTTCAATTGAAGAGCTTTGATGATGATTTGAGCAAGACAACA
66 TTGAAGACTTGAAGACCATTCAAGTTCAATTGAAGAGCTTTGATGATGATTTGAGCAAGAAAACA
* * *
19779 TCAATCAATTACAAGTTCATCACTTTGCTTGCTATTGATTCTAAATGGCCGTACTGACATAGTCG
131 TCAATCAATTACAAGTTCATCACTTTGCTTGCTATTGATTCTAAATGGCCGGATTGACATAGTGG
* * *
19844 CATAAGCCCAATGTCATTAGTTCTCTTTCTTTGGGCTTAATTCTATCTTATATCAGCTTATTTTT
196 CATAAGCCCAATATCATTAGTTATCTTTCTTTGGGCTTAATTCTATCTTAGATCAGCTTATTTTT
*
19909 AAGTTTAAATGTTATTTGGGTTGGGCCTTGTTTGACTAAGTCCAATGCTTGTTTAATTATGCTTT
261 AAGTTTAAATGTTATTTGGGTTGGGCCTTGTTTGACTAAGTCCAATCCTTGTTTAATTATGCTTT
*
19974 TATTTCCTTTTCCTAGTTGGGCTTGGACTAGTTTTTCCCTAGCCCTTATATTGGGACGAAAATTA
326 TATTTCCTTTTCCTAGTTGGGCTTGGACTAGTTTTTCCCTAGCCCTTATATTTGGACGAAAATTA
20039 GGATTTATTTTAGGATTTTGGTTGACCCTATCACTATATAAGGCCACCAATATCTCTTGTAAAAG
391 GGATTTATTTTAGGATTTTGGTTGACCCTATCACTATATAAGGCCACCAATATCTCTTGTAAAAG
*
20104 TGGAAGTTGAGTTGATTAATAAAATTGAGATTTATTCTCCCAAATTGATTATCTTGGCTTCATTG
456 TGGAAGTTGAGTTGATTAATAAAATTGAGGTTTATTCTCCCAAATTGATTATCTTGGCTTCATTG
* * * *
20169 TTCTAGTTCT-AACAAACATAGGGTTCTTCAATCTTGTAGAGTTCTAGCAAGCAATTAGGTTGTG
521 TTCTAGTT-TGAGCAAACTTAGGGTTCTTCAATCTTGTAGAGTCCTAGCAAACAATTAGGTTGTG
* *
20233 TGATGGTTAATTGTTTGTGAATCTTGTGAACTTAGGTATTCAATTGCAGGTCTAATTGAAGACTT
585 TGATGGTTAATTGTTTGTGAATCTTGTGATCTTAGGTATTCAATTGCAGGTCTAATTAAAGACTT
* *
20298 AAGGCTGACGAACGAAGAGAGATTGATTTGTGAAGCTTGTCGACATACTTGTCTAGAAGTTGAAG
650 AAGGCTGACGAACGAAGAGAGATTGCTTTGTGAAGGTTGTCGACATACTTGTCTAGAAGTTGAAG
*
20363 AATTTCAAGTAGATTCTTGGCAGGTCTCAAGGATAGATTTTATCATGGAGGGCCAAGGACTTATC
715 AAGTTCAAGTAGATTCTTGGCAGGTCTCAAGGATAGATTTTATCATGGAGGGCCAAGGACTTATC
*
20428 ATGGTCTTGAAGACAAGCATGGAGAGCATGGAAAGGATGTGCATGGGCTGCAAGGAAGAATGGAG
780 ATGGTCTTGAAGACAAGCATGGAGAGCATGGAAAGGATGTGCATGGGCTGCAAGGAAGCATGGAG
* * *
20493 ATGAATGAAGATTATCGAGATATTGGTAAGCATGCTCCAAGCAACAAAAAGATGCTAATCGATTC
845 ATGAATGAAGATTATCGAGATATTGATAAGCATGCTCCAAGCACCAAAAAGATGCTATTCGATTC
* *
20558 ATTGAAAATGCCTATTTG
910 ATTGAAGATGCCTATTAG
* *
20576 TCCGATGACAAGAAG-AAGAGCTAAGAGATTCAAGGATGCACTCATGGGCCATGTTCAAACTCAT
1 TCCGATGACAAG-AGCAAGAGCTAAGAGATTCAAGGATGCACTCATGGGCCATGTCCGAACTCAT
*
20640 CTTGAAGACTTGAAGACCATTCAAGTTCAATTGAAGAGCTTTGATGGTGATTTGAGCAAGAAAAC
65 CTTGAAGACTTGAAGACCATTCAAGTTCAATTGAAGAGCTTTGATGATGATTTGAGCAAGAAAAC
* *
20705 ACCAATCAATTACAAGTTCATCACTTTGCTTGCTGTTGATTCTAAATGGCCGGATTGACATAGTG
130 ATCAATCAATTACAAGTTCATCACTTTGCTTGCTATTGATTCTAAATGGCCGGATTGACATAGTG
* * * *
20770 GCATGAGCCCTATAT-ATTAGTTCTCTTTCTTTGGGCTTAATTCTATCTTAGCTCAGCTTATTTT
195 GCATAAGCCCAATATCATTAGTTATCTTTCTTTGGGCTTAATTCTATCTTAGATCAGCTTATTTT
20834 TAAGTTTAAATGTTATTTGGGTTGGGCCTTGTTTGACTAAGTCCAATCCTTGTTTAATTATGCTT
260 TAAGTTTAAATGTTATTTGGGTTGGGCCTTGTTTGACTAAGTCCAATCCTTGTTTAATTATGCTT
*
20899 TTATTTCCTTTTCCTAGTTGGGCTTGGACTAGTTTTTCGCTAGCCCTTATATTTGGACGAAAATT
325 TTATTTCCTTTTCCTAGTTGGGCTTGGACTAGTTTTTCCCTAGCCCTTATATTTGGACGAAAATT
20964 AGGATTTATTTTAGGATTTTGGTTGACCCTATCACTATATAAGGCCACCAATATCTCTTGTAAAA
390 AGGATTTATTTTAGGATTTTGGTTGACCCTATCACTATATAAGGCCACCAATATCTCTTGTAAAA
21029 GTGGAAGTTGAGTTGATTAATAAAATTGAGGTTTATTCTCCCAAATTGATTATCTTGGCTTCATT
455 GTGGAAGTTGAGTTGATTAATAAAATTGAGGTTTATTCTCCCAAATTGATTATCTTGGCTTCATT
21094 GTTCTAGTTTGAGCAAACTTAGGGTTCTTCAATCTTGTAGAGTCCTAGCAAACAATTAGGTTGTG
520 GTTCTAGTTTGAGCAAACTTAGGGTTCTTCAATCTTGTAGAGTCCTAGCAAACAATTAGGTTGTG
*
21159 TGATGGTTAATTGTTTGTGAATCTTGTGATCTTAGGTATTCAATTGCAGGTCTAATTTAAGACTT
585 TGATGGTTAATTGTTTGTGAATCTTGTGATCTTAGGTATTCAATTGCAGGTCTAATTAAAGACTT
* *
21224 AAGGCTGACGAACGAAGAGAGATTGCTTTGTGAAGGTTCTCGACAAACTTGTCTAGAAGTTGAAG
650 AAGGCTGACGAACGAAGAGAGATTGCTTTGTGAAGGTTGTCGACATACTTGTCTAGAAGTTGAAG
*
21289 AAGTTCAAGTAGATTCTTGGCAGGTCTCAAGGATAGGTTTTATCATGGAGGGCCAAGGACTTATC
715 AAGTTCAAGTAGATTCTTGGCAGGTCTCAAGGATAGATTTTATCATGGAGGGCCAAGGACTTATC
21354 ATGGTCTTGAAGACAAGCATGGAGAGCATGGAAAGGATGTGCATGGGCTGCAAGGAAGCATGGAG
780 ATGGTCTTGAAGACAAGCATGGAGAGCATGGAAAGGATGTGCATGGGCTGCAAGGAAGCATGGAG
* *
21419 ATGCATGAAGATTATCGAGATATTGATAAGCATGTTCCAAGCACCAAAAAGATGCTATTCGATTC
845 ATGAATGAAGATTATCGAGATATTGATAAGCATGCTCCAAGCACCAAAAAGATGCTATTCGATTC
21484 ATTGAAGATGCCTATTAG
910 ATTGAAGATGCCTATTAG
*
21502 TCCGATGACAAGAGCAAGAGCTAAGAGATTCAAGGATGCACTCATGGGCCATGTTCGAACTCATC
1 TCCGATGACAAGAGCAAGAGCTAAGAGATTCAAGGATGCACTCATGGGCCATGTCCGAACTCATC
*
21567 TTGAAGACTTGAAGACCATTCAAGTTCAATTGAAGAGCTTTGATGATGATTTGACCAAGAAAACA
66 TTGAAGACTTGAAGACCATTCAAGTTCAATTGAAGAGCTTTGATGATGATTTGAGCAAGAAAACA
* *
21632 TCAATCAATTACAAGTTCATCACTTTGCTTGCTATTGATTCTAAATGGCCGTATTGACATAGTTG
131 TCAATCAATTACAAGTTCATCACTTTGCTTGCTATTGATTCTAAATGGCCGGATTGACATAGTGG
* * * * * * * *
21697 CATAAGCCCAATATTATAAGTTATCTTTGTATGGGCTTAATTCTTTCTTAAATTAGCTTATTTAT
196 CATAAGCCCAATATCATTAGTTATCTTTCTTTGGGCTTAATTCTATCTTAGATCAGCTTATTTTT
* **
21762 ATGTTTGGATGTTATTTGGGTTGGGCCTTGTTT-ATCTAAGTCCAATCCTTGTTTAATTATGCTT
261 AAGTTTAAATGTTATTTGGGTTGGGCCTTGTTTGA-CTAAGTCCAATCCTTGTTTAATTATGCTT
21826 TTAT
325 TTAT
Statistics
Matches: 2062, Mismatches: 111, Indels: 16
0.94 0.05 0.01
Matches are distributed among these distances:
925 3 0.00
926 889 0.43
927 1166 0.57
928 4 0.00
ACGTcount: A:0.29, C:0.15, G:0.21, T:0.34
Consensus pattern (927 bp):
TCCGATGACAAGAGCAAGAGCTAAGAGATTCAAGGATGCACTCATGGGCCATGTCCGAACTCATC
TTGAAGACTTGAAGACCATTCAAGTTCAATTGAAGAGCTTTGATGATGATTTGAGCAAGAAAACA
TCAATCAATTACAAGTTCATCACTTTGCTTGCTATTGATTCTAAATGGCCGGATTGACATAGTGG
CATAAGCCCAATATCATTAGTTATCTTTCTTTGGGCTTAATTCTATCTTAGATCAGCTTATTTTT
AAGTTTAAATGTTATTTGGGTTGGGCCTTGTTTGACTAAGTCCAATCCTTGTTTAATTATGCTTT
TATTTCCTTTTCCTAGTTGGGCTTGGACTAGTTTTTCCCTAGCCCTTATATTTGGACGAAAATTA
GGATTTATTTTAGGATTTTGGTTGACCCTATCACTATATAAGGCCACCAATATCTCTTGTAAAAG
TGGAAGTTGAGTTGATTAATAAAATTGAGGTTTATTCTCCCAAATTGATTATCTTGGCTTCATTG
TTCTAGTTTGAGCAAACTTAGGGTTCTTCAATCTTGTAGAGTCCTAGCAAACAATTAGGTTGTGT
GATGGTTAATTGTTTGTGAATCTTGTGATCTTAGGTATTCAATTGCAGGTCTAATTAAAGACTTA
AGGCTGACGAACGAAGAGAGATTGCTTTGTGAAGGTTGTCGACATACTTGTCTAGAAGTTGAAGA
AGTTCAAGTAGATTCTTGGCAGGTCTCAAGGATAGATTTTATCATGGAGGGCCAAGGACTTATCA
TGGTCTTGAAGACAAGCATGGAGAGCATGGAAAGGATGTGCATGGGCTGCAAGGAAGCATGGAGA
TGAATGAAGATTATCGAGATATTGATAAGCATGCTCCAAGCACCAAAAAGATGCTATTCGATTCA
TTGAAGATGCCTATTAG
Done.