Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002111.1 Hibiscus syriacus cultivar Beakdansim tig00004320_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: 58136
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Found at i:6012 original size:29 final size:26
Alignment explanation
Indices: 5958--6012 Score: 65
Period size: 29 Copynumber: 2.0 Consensus size: 26
5948 TGCATGGTGT
*
5958 GAATAAGAGAGATCCCAAAACAAAAG
1 GAATAAGAGAGATCACAAAACAAAAG
*
5984 GAATAAGAGATGCCATCACAAACCAAAAG
1 GAATAAGAGA-G--ATCACAAAACAAAAG
6013 CAAAAATTAG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 10 0.42
27 1 0.04
29 13 0.54
ACGTcount: A:0.55, C:0.18, G:0.18, T:0.09
Consensus pattern (26 bp):
GAATAAGAGAGATCACAAAACAAAAG
Found at i:15879 original size:21 final size:22
Alignment explanation
Indices: 15839--15883 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
15829 TTATATTATT
*
15839 TTATAAAATTTATATTAAATTA
1 TTATAAAATATATATTAAATTA
*
15861 TTATAAAA-ATATTTTAAATTA
1 TTATAAAATATATATTAAATTA
15882 TT
1 TT
15884 TATTTATTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 13 0.62
22 8 0.38
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
TTATAAAATATATATTAAATTA
Found at i:26993 original size:78 final size:78
Alignment explanation
Indices: 26864--27112 Score: 291
Period size: 78 Copynumber: 3.0 Consensus size: 78
26854 AATATTCCCA
* * * *
26864 GTTGTATTTTAGGAGTGTAAAAGAGTCGAGCTTGAACTAACAAGGTTATGTTCGTATTCGTTGTT
1 GTTGTATTTTAGGAGTGTAAATGAATCGAGCTTGAACGAATAAGGTTATGTTCGTATTCGTTGTT
26929 TATTTTTAAAGGT
66 TATTTTTAAAGGT
** * * *
26942 GTTGTATTTTAGGAGTGTAAATGAATTAAGTTTGAACGAATAAGGTTATGTTCATATTCATTGTT
1 GTTGTATTTTAGGAGTGTAAATGAATCGAGCTTGAACGAATAAGGTTATGTTCGTATTCGTTGTT
27007 TATTTTTAAAGGTGTTCAAAT
66 TATTTTTAAA-G-G------T
* *
27028 CCCAGTTGTATTTTAGGAGTGTAAATGAATCGGGCTTGAACGAATAAGGTTATGTTTGTATTCGT
1 ----GTTGTATTTTAGGAGTGTAAATGAATCGAGCTTGAACGAATAAGGTTATGTTCGTATTCGT
27093 TGTTTATTTTTAAAGGT
62 TGTTTATTTTTAAAGGT
27110 GTT
1 GTT
27113 CATGTTTGGT
Statistics
Matches: 143, Mismatches: 16, Indels: 24
0.78 0.09 0.13
Matches are distributed among these distances:
78 69 0.48
79 1 0.01
80 1 0.01
82 1 0.01
86 1 0.01
88 1 0.01
89 1 0.01
90 68 0.48
ACGTcount: A:0.28, C:0.07, G:0.23, T:0.43
Consensus pattern (78 bp):
GTTGTATTTTAGGAGTGTAAATGAATCGAGCTTGAACGAATAAGGTTATGTTCGTATTCGTTGTT
TATTTTTAAAGGT
Found at i:27096 original size:90 final size:90
Alignment explanation
Indices: 26942--27114 Score: 283
Period size: 90 Copynumber: 1.9 Consensus size: 90
26932 TTTTAAAGGT
* *
26942 GTTGTATTTTAGGAGTGTAAATGAATTAAGTTTGAACGAATAAGGTTATGTTCATATTCATTGTT
1 GTTGTATTTTAGGAGTGTAAATGAATCAAGCTTGAACGAATAAGGTTATGTTCATATTCATTGTT
27007 TATTTTTAAAGGTGTTCAAATCCCA
66 TATTTTTAAAGGTGTTCAAATCCCA
** ** *
27032 GTTGTATTTTAGGAGTGTAAATGAATCGGGCTTGAACGAATAAGGTTATGTTTGTATTCGTTGTT
1 GTTGTATTTTAGGAGTGTAAATGAATCAAGCTTGAACGAATAAGGTTATGTTCATATTCATTGTT
27097 TATTTTTAAAGGTGTTCA
66 TATTTTTAAAGGTGTTCA
27115 TGTTTGGTTC
Statistics
Matches: 76, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
90 76 1.00
ACGTcount: A:0.28, C:0.07, G:0.22, T:0.43
Consensus pattern (90 bp):
GTTGTATTTTAGGAGTGTAAATGAATCAAGCTTGAACGAATAAGGTTATGTTCATATTCATTGTT
TATTTTTAAAGGTGTTCAAATCCCA
Found at i:28652 original size:37 final size:37
Alignment explanation
Indices: 28494--28935 Score: 256
Period size: 37 Copynumber: 12.6 Consensus size: 37
28484 CTACATATAT
*
28494 ATATATATACAGTATATAG-TTTGAAAACATTTTT-AAT
1 ATATATATA-A-TATATAGTTTTGAAAACATTTTTGAAA
* *
28531 ATATATATAATATATAATTTTGAAAAGCATGTTTGAAAA
1 ATATATATAATATATAGTTTTGAAAA-CATTTTTG-AAA
* * *
28570 CATTTATATATTATATAGTTCTT-AAGACA-TTTTGAAA
1 -ATATATATAATATATAGTT-TTGAAAACATTTTTGAAA
* *
28607 AT-TAATATAATATATGGTTTTCAAAACATTTTTGAAA
1 ATAT-ATATAATATATAGTTTTGAAAACATTTTTGAAA
* *
28644 ATATATATATTATATAGTTTTTAAAAACA-TTTTGAAA
1 ATATATATAATATATAG-TTTTGAAAACATTTTTGAAA
* *
28681 AT-TAATATAATATATAGTTTTTAAAATATTTTTGAAA
1 ATAT-ATATAATATATAGTTTTGAAAACATTTTTGAAA
* * *
28718 ATACATGT--TATATAGTTTTTAAAACA-TTTT-AAA
1 ATATATATAATATATAGTTTTGAAAACATTTTTGAAA
* ***
28751 A-ATATAT-A-GT-T--TTAAAAAAACA-TTTTGAAA
1 ATATATATAATATATAGTTTTGAAAACATTTTTGAAA
* * * *
28781 ACATAAATATTATATAGTTTTTGAAATCA-TTTTG-AA
1 ATATATATAATATATAG-TTTTGAAAACATTTTTGAAA
* *
28817 A-ACATATAATATATAGTTTTAAAAAACATTTTT-AAA
1 ATATATATAATATATAGTTTT-GAAAACATTTTTGAAA
*
28853 A-A-A-CT-ATATA-A-TTTTGAAAACATTTTT-AGAA
1 ATATATATAATATATAGTTTTGAAAACATTTTTGA-AA
* *
28884 A-GTATATAATATA-A-TTTT-AAAATATTTTT-AAA
1 ATATATATAATATATAGTTTTGAAAACATTTTTGAAA
28916 AGTATAT-T-ATATA-AGTTTTG
1 A-TATATATAATATATAGTTTTG
28936 GGAAAATATT
Statistics
Matches: 327, Mismatches: 44, Indels: 71
0.74 0.10 0.16
Matches are distributed among these distances:
29 12 0.04
30 16 0.05
31 13 0.04
32 16 0.05
33 27 0.08
34 23 0.07
35 44 0.13
36 50 0.15
37 86 0.26
38 15 0.05
39 4 0.01
40 19 0.06
41 2 0.01
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.43
Consensus pattern (37 bp):
ATATATATAATATATAGTTTTGAAAACATTTTTGAAA
Found at i:28795 original size:100 final size:103
Alignment explanation
Indices: 28654--28916 Score: 280
Period size: 100 Copynumber: 2.6 Consensus size: 103
28644 ATATATATAT
* *
28654 TATATAGTTTTTAAAAACATTTTGAAAATTAATATAATATATAGTTTTTAAAAT-ATTTTTGAAA
1 TATATAGTTTTAAAAAACATTTTGAAAAATAATATAATATATAGTTTTTAAAATCA-TTTTGAAA
* ** *
28718 ATACATGTTATATAGTTTT-TAAAACA-TTTT-AAAAA-
65 ACACATAATATATAGTTTTAAAAAACATTTTTAAAAAAC
* *
28753 TATATAGTTTTAAAAAAACATTTTGAAAACATAA-ATATTATATAGTTTTTGAAATCATTTTGAA
1 TATATAGTTTT-AAAAAACATTTTGAAAA-ATAATATAATATATAGTTTTTAAAATCATTTTGAA
*
28817 AACATATAATATATAGTTTTAAAAAACATTTTTAAAAAAC
64 AACACATAATATATAGTTTTAAAAAACATTTTTAAAAAAC
* * * * *
28857 TATATAATTTT-GAAAACATTTTTAGAAAGT-ATATAATATA-A--TTTTAAAAT-ATTTTTAAA
1 TATATAGTTTTAAAAAACATTTTGA-AAAATAATATAATATATAGTTTTTAAAATCATTTTGAAA
28916 A
65 A
28917 GTATATTATA
Statistics
Matches: 139, Mismatches: 16, Indels: 19
0.80 0.09 0.11
Matches are distributed among these distances:
98 9 0.06
99 19 0.14
100 58 0.42
101 12 0.09
102 23 0.17
103 8 0.06
104 10 0.07
ACGTcount: A:0.48, C:0.04, G:0.06, T:0.43
Consensus pattern (103 bp):
TATATAGTTTTAAAAAACATTTTGAAAAATAATATAATATATAGTTTTTAAAATCATTTTGAAAA
CACATAATATATAGTTTTAAAAAACATTTTTAAAAAAC
Found at i:28847 original size:35 final size:36
Alignment explanation
Indices: 28751--28853 Score: 136
Period size: 35 Copynumber: 2.8 Consensus size: 36
28741 ACATTTTAAA
28751 AATATATAGTTTTAAAAAAACATTTTGAAAACATAAAT
1 AATATATAGTTTT-AAAAAACATTTTGAAAACAT-AAT
* ** *
28789 ATTATATAGTTTTTGAAATCATTTTGAAAACAT-AT
1 AATATATAGTTTTAAAAAACATTTTGAAAACATAAT
*
28824 AATATATAGTTTTAAAAAACATTTTTAAAA
1 AATATATAGTTTTAAAAAACATTTTGAAAA
28854 AACTATATAA
Statistics
Matches: 56, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
35 27 0.48
37 17 0.30
38 12 0.21
ACGTcount: A:0.50, C:0.05, G:0.06, T:0.40
Consensus pattern (36 bp):
AATATATAGTTTTAAAAAACATTTTGAAAACATAAT
Found at i:28901 original size:34 final size:33
Alignment explanation
Indices: 28799--28935 Score: 124
Period size: 33 Copynumber: 4.2 Consensus size: 33
28789 ATTATATAGT
* * *
28799 TTTTGAAATCATTTTGAAAA-CATATAATATATA
1 TTTTGAAAACATTTTTAAAAGTATATAATATA-A
*
28832 GTTTTAAAAAACATTTTTAAAA--A-ACT-ATATAA
1 -TTTT-GAAAACATTTTTAAAAGTATA-TAATATAA
28864 TTTTGAAAACATTTTTAGAAAGTATATAATATAA
1 TTTTGAAAACATTTTTA-AAAGTATATAATATAA
* *
28898 TTTT-AAAATATTTTTAAAAGTATATTATATAA
1 TTTTGAAAACATTTTTAAAAGTATATAATATAA
28930 GTTTTG
1 -TTTTG
28936 GGAAAATATT
Statistics
Matches: 88, Mismatches: 6, Indels: 18
0.79 0.05 0.16
Matches are distributed among these distances:
30 12 0.14
31 7 0.08
32 16 0.18
33 23 0.26
34 17 0.19
35 13 0.15
ACGTcount: A:0.46, C:0.04, G:0.07, T:0.44
Consensus pattern (33 bp):
TTTTGAAAACATTTTTAAAAGTATATAATATAA
Found at i:31565 original size:17 final size:17
Alignment explanation
Indices: 31545--31577 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
31535 CTCACTAACC
*
31545 CTTTTATTTTTTGTTCT
1 CTTTTATTTTGTGTTCT
31562 CTTTTATTTTGTGTTC
1 CTTTTATTTTGTGTTC
31578 ATCGTTTGCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.06, C:0.12, G:0.09, T:0.73
Consensus pattern (17 bp):
CTTTTATTTTGTGTTCT
Found at i:35843 original size:84 final size:84
Alignment explanation
Indices: 35627--36520 Score: 1076
Period size: 84 Copynumber: 10.7 Consensus size: 84
35617 TAAACAAACT
* ** *
35627 ATTTGCAGCATAATTTAAGTCGAGAAGGGTTATCTG-TGACCAAAAGACCTTTGAGTTCGATTAC
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACC-AAAGACCTTTGAGTTCGACTAC
* * *
35691 ACTCAGCTTCGAGGGCACATC
65 GCTCAGC-TCCAAGGCACATC
* * * * * **
35712 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATATG-TGACCAAAAGACCTTTGAGTTCGACTAC
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACC-AAAGACCTTTGAGTTCGACTAC
35776 GCTCAGCTCCAAGGCACATC
65 GCTCAGCTCCAAGGCACATC
*
35796 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTACG
*
35861 CTCAGCTCCAAGGCATATC
66 CTCAGCTCCAAGGCACATC
* * * * *
35880 ATTTGCAACACAACTTAAGTCTAGAAGGGTTGTCTGCCAACAAAAGACCTTTGAGTTCGACTACG
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTACG
35945 CTCAGCTCCAAGGCACATC
66 CTCAGCTCCAAGGCACATC
* *
35964 ATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTACG
*
36029 CTCAGCTCCAAGGCATATC
66 CTCAGCTCCAAGGCACATC
* * * * * *
36048 ATTTGCAGTACAACTTAAGTCTACAAGGGTTGTCTGCCAACAAAAGACCTTTGAGTTCGACTACG
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTACG
*
36113 ATCAGCT-CAACGGCACATC
66 CTCAGCTCCAA-GGCACATC
* * *** * *
36132 ATTTGCAGTATAACTTAAGTCGAGAAGGGCTATCTG----CCAAAGACCCCCGAGTTCGATTACA
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTACG
* *
36193 CTCAGCTTCGAGGGCACATC
66 CTCAGC-TCCAAGGCACATC
* * *
36213 ATTTTCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAGAGACCTTCGAGTTCGACTACG
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTACG
*
36278 CTCAGCTCCAAGGCATATC
66 CTCAGCTCCAAGGCACATC
* * * * * *
36297 ATTTGCAACACAGCTTAAGTCTAGAAGGGTTGTCTGCCAACAAAAGACCTTTGAGTTCGACTACG
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTACG
36362 CTCAGCT-CAACGGCACATC
66 CTCAGCTCCAA-GGCACATC
* * * * ** * *
36381 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTG-TGACCAAAAGACCTTCGAGTTCGACTCC
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACC-AAAGACCTTTGAGTTCGACTAC
*
36445 GCTCAGCTCCAAGGCATATC
65 GCTCAGCTCCAAGGCACATC
* * *
36465 ATTTGCAGCATAGCTTAAGTCAAGAAGGGTTATCTG-CTA--AAA-ACCTTTGAGTTCGA
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGA
36521 TTATATTCAA
Statistics
Matches: 698, Mismatches: 100, Indels: 27
0.85 0.12 0.03
Matches are distributed among these distances:
80 37 0.05
81 45 0.06
82 1 0.00
83 8 0.01
84 512 0.73
85 95 0.14
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.25
Consensus pattern (84 bp):
ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTACG
CTCAGCTCCAAGGCACATC
Found at i:36602 original size:417 final size:414
Alignment explanation
Indices: 35627--36606 Score: 1281
Period size: 417 Copynumber: 2.3 Consensus size: 414
35617 TAAACAAACT
* *
35627 ATTTGCAGCATAATTTAAGTCGAGAAGGGTTATCTGTGACCAAAAGACCTTTGAGTTCGATTACA
1 ATTTGCAGCATAACTTAAGTCAAGAAGGGTTATC--TGACCAAAAGACCTTTGAGTTCGATTACA
* * * * *
35692 CTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATATGTGACCAAAA
64 -TCAGCTTAGACGGCACATCATTTACAGAATAACTCAAGGCAAGAAGGGTTATCTGT---CAAAA
* * *
35757 GACCTTT-GAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGA
125 -A-ATTTCGAGTTCGATTACACTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGA
35821 AGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGC
188 AGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGC
35886 AACACAACTTAAGTCTAGAAGGGTTGTCTGCCAACAAAAGACCTTTGAGTTCGACTACGCTCAGC
253 AACACAACTTAAGTCTAGAAGGGTTGTCTGCCAACAAAAGACCTTTGAGTTCGACTACGCTCAGC
* * * *
35951 TCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTC
318 TCCAAGGCACATCATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTGCCAACCAAAGACCTTC
36016 GAGTTCGACTACGCTCAGCTCCAAGGCATATC
383 GAGTTCGACTACGCTCAGCTCCAAGGCATATC
* * * * * * *
36048 ATTTGCAGTACAACTTAAGTCTACAAGGGTTGTCTGCCAACAAAAGACCTTTGAGTTCGACTACG
1 ATTTGCAGCATAACTTAAGTCAAGAAGGGTTATCTG--ACCAAAAGACCTTTGAGTTCGATTAC-
* * * * * * * * * **
36113 ATCAGCTCA-ACGGCACATCATTTGCAGTATAACTTAAGTCGAGAAGGGCTATCTGCCAAAGACC
63 ATCAGCTTAGACGGCACATCATTTACAGAATAACTCAAGGCAAGAAGGGTTATCTGTCAAAAAAT
** * * *
36177 CCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTTCAGCATAACTTAAGTCGAGAAGGG
128 TTCGAGTTCGATTACACTCAGC-TCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGG
*
36242 TTATCTGCCAACCAGAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAACA
192 TTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAACA
*
36307 CAGCTTAAGTCTAGAAGGGTTGTCTGCCAACAAAAGACCTTTGAGTTCGACTACGCTCAGCT-CA
257 CAACTTAAGTCTAGAAGGGTTGTCTGCCAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCCA
* **
36371 ACGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTG-TGACCAAAAGACCTTCGA
322 A-GGCACATCATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTGCCAACC-AAAGACCTTCGA
*
36435 GTTCGACTCCGCTCAGCTCCAAGGCATATC
385 GTTCGACTACGCTCAGCTCCAAGGCATATC
* * *
36465 ATTTGCAGCATAGCTTAAGTCAAGAAGGGTTATCTG-CTAAAA-ACCTTTGAGTTCGATTATATT
1 ATTTGCAGCATAACTTAAGTCAAGAAGGGTTATCTGACCAAAAGACCTTTGAGTTCGATTACA-T
* * * * *
36528 CAACTTAGA-GGCAAATCAAGCTTACAGAATAGCTCAAGGCAATAAGGGTTATCTGTCAATAAAA
65 CAGCTTAGACGGCACATC-A-TTTACAGAATAACTCAAGGCAAGAAGGGTTATCTGTCAA-AAAA
36592 TTGTCGAGTTCGATT
127 TT-TCGAGTTCGATT
36607 CCAATTAGCT
Statistics
Matches: 480, Mismatches: 66, Indels: 30
0.83 0.11 0.05
Matches are distributed among these distances:
412 1 0.00
413 29 0.06
414 6 0.01
415 30 0.06
416 26 0.05
417 289 0.60
419 2 0.00
420 38 0.08
421 58 0.12
422 1 0.00
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (414 bp):
ATTTGCAGCATAACTTAAGTCAAGAAGGGTTATCTGACCAAAAGACCTTTGAGTTCGATTACATC
AGCTTAGACGGCACATCATTTACAGAATAACTCAAGGCAAGAAGGGTTATCTGTCAAAAAATTTC
GAGTTCGATTACACTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTAT
CTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAACACAAC
TTAAGTCTAGAAGGGTTGTCTGCCAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGC
ACATCATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGA
CTACGCTCAGCTCCAAGGCATATC
Found at i:37181 original size:35 final size:35
Alignment explanation
Indices: 37130--37578 Score: 214
Period size: 36 Copynumber: 12.6 Consensus size: 35
37120 TTTTCTATAT
*
37130 ATATATATACAGTATATAGTTTGAAAACATTTTTAAT
1 ATATATATA-A-TATATAGTTTGAAAACATTTTTAAA
* *
37167 ATATATATAATATATAATTTTGAAAAGCATGTTTGAAAA
1 ATATATATAATATAT-AGTTTGAAAA-CAT-TTT-TAAA
* * * * *
37206 CATTTATATATTATATAGTTCTTAAGACATTTTGAAA
1 -ATATATATAATATATAGTT-TGAAAACATTTTTAAA
* *
37243 AT-TAATATAATATATGGTTTTCAAAACATTTTTGAAA
1 ATAT-ATATAATATATAG-TTTGAAAACATTTTT-AAA
* * * *
37280 ATATATATATTATATAATTTTTAAAAACATTTTGAAA
1 ATATATATAATATAT-A-GTTTGAAAACATTTTTAAA
* *
37317 AT-TAATATAATATATAGTTTTTAAAATATTTTTGAAA
1 ATAT-ATATAATATATAG-TTTGAAAACATTTTT-AAA
* * * *
37354 ATACATGT--TATATAGTTTTTAAAACATTTTAAAA
1 ATATATATAATATATAG-TTTGAAAACATTTTTAAA
* ** *
37388 ATATATATAGT-T-T--TTAAAAAAACATTTTGAAAA
1 ATATATATAATATATAGTT-TGAAAACATTTT-TAAA
* * * *
37421 CATAAATATATTATATAGTTTTTGAAATCA-TTTTGAA
1 -ATATATATAATATATAG--TTTGAAAACATTTTTAAA
* *
37458 A-ACATATAATATATAGTTTTAAAAAACATTTTTAAA
1 ATATATATAATATATAG-TTT-GAAAACATTTTTAAA
37494 A-A-ACTAT-ATA-AT--TTTGAAAACATTTTTAGAA
1 ATATA-TATAATATATAGTTTGAAAACATTTTTA-AA
* * * *
37525 A-GTATATAATATATAATTTTAAAATATTTTTAAA
1 ATATATATAATATATAGTTTGAAAACATTTTTAAA
*
37559 AGTATATATTATATA-AGTTT
1 A-TATATATAATATATAGTTT
37579 TGGGAAAATA
Statistics
Matches: 323, Mismatches: 51, Indels: 78
0.71 0.11 0.17
Matches are distributed among these distances:
30 12 0.04
31 11 0.03
32 14 0.04
33 6 0.02
34 28 0.09
35 69 0.21
36 71 0.22
37 57 0.18
38 23 0.07
39 13 0.04
40 19 0.06
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.44
Consensus pattern (35 bp):
ATATATATAATATATAGTTTGAAAACATTTTTAAA
Found at i:37288 original size:37 final size:37
Alignment explanation
Indices: 37130--37580 Score: 278
Period size: 37 Copynumber: 12.6 Consensus size: 37
37120 TTTTCTATAT
*
37130 ATATATATACAGTATATAG-TTTGAAAACATTTTT-AAT
1 ATATATATA-A-TATATAGTTTTGAAAACATTTTTGAAA
* *
37167 ATATATATAATATATAATTTTGAAAAGCATGTTTGAAAA
1 ATATATATAATATATAGTTTTGAAAA-CATTTTTG-AAA
* * *
37206 CATTTATATATTATATAGTTCTT-AAGACA-TTTTGAAA
1 -ATATATATAATATATAGTT-TTGAAAACATTTTTGAAA
* *
37243 AT-TAATATAATATATGGTTTTCAAAACATTTTTGAAA
1 ATAT-ATATAATATATAGTTTTGAAAACATTTTTGAAA
* * *
37280 ATATATATATTATATAATTTTTAAAAACA-TTTTGAAA
1 ATATATATAATATAT-AGTTTTGAAAACATTTTTGAAA
* *
37317 AT-TAATATAATATATAGTTTTTAAAATATTTTTGAAA
1 ATAT-ATATAATATATAGTTTTGAAAACATTTTTGAAA
* * * *
37354 ATACATGT--TATATAGTTTTTAAAACA-TTTTAAAA
1 ATATATATAATATATAGTTTTGAAAACATTTTTGAAA
* ***
37388 ATATATATAGT-T-T--TTAAAAAAACA-TTTTGAAAA
1 ATATATATAATATATAGTTTTGAAAACATTTTTG-AAA
* * *
37421 CATAAATATATTATATAGTTTTTGAAATCA-TTTTG-AA
1 -ATATATATAATATATAG-TTTTGAAAACATTTTTGAAA
* *
37458 A-ACATATAATATATAGTTTTAAAAAACATTTTT-AAA
1 ATATATATAATATATAGTTTT-GAAAACATTTTTGAAA
*
37494 A-A-A-CT-ATATA-A-TTTTGAAAACATTTTT-AGAA
1 ATATATATAATATATAGTTTTGAAAACATTTTTGA-AA
* * *
37525 A-GTATATAATATATAATTTT-AAAATATTTTT-AAA
1 ATATATATAATATATAGTTTTGAAAACATTTTTGAAA
*
37559 AGTATATATTATATA-AGTTTTG
1 A-TATATATAATATATAGTTTTG
37581 GGAAAATATT
Statistics
Matches: 332, Mismatches: 47, Indels: 71
0.74 0.10 0.16
Matches are distributed among these distances:
30 12 0.04
31 7 0.02
32 14 0.04
33 9 0.03
34 36 0.11
35 64 0.19
36 65 0.20
37 73 0.22
38 15 0.05
39 16 0.05
40 19 0.06
41 2 0.01
ACGTcount: A:0.46, C:0.04, G:0.07, T:0.44
Consensus pattern (37 bp):
ATATATATAATATATAGTTTTGAAAACATTTTTGAAA
Found at i:37314 original size:74 final size:71
Alignment explanation
Indices: 37153--37579 Score: 332
Period size: 74 Copynumber: 6.0 Consensus size: 71
37143 ATATAGTTTG
* * * * *
37153 AAAACATTTTTAATATATATATAATATATAATTTTGAAAAGCATGTTTGAAAACATTTATATATT
1 AAAACATTTTGAAAATA-ATATAATATATAGTTTT-AAAAACATTTTTGAAAA-A--TATATATT
* *
37218 ATATAGTTCTT
61 ATATAATTTTT
* * *
37229 AAGACATTTTGAAAATTAATATAATATATGGTTTTCAAAACATTTTTGAAAATATATATATTATA
1 AAAACATTTTGAAAA-TAATATAATATATAGTTTTAAAAACATTTTTGAAAA-ATATATATTATA
37294 TAATTTTT
64 TAATTTTT
* * * *
37302 AAAAACATTTTGAAAATTAATATAATATATAGTTTTTAAAATATTTTTG-AAAATACATGTTATA
1 -AAAACATTTTGAAAA-TAATATAATATATAGTTTTAAAAACATTTTTGAAAAATATATATTATA
*
37366 TAGTTTTT
64 TAATTTTT
37374 AAAACATTTT---AA-AA-AT-ATATATAGTTTTTAAAAAAACA-TTTTGAAAACATAAATATAT
1 AAAACATTTTGAAAATAATATAATATATAG-TTTT--AAAAACATTTTTGAAAA-AT--ATATAT
*
37432 TATATAGTTTTT
60 TATATAATTTTT
* * *
37444 GAAATCATTTTGAAAA-CATATAATATATAGTTTTAAAAAACATTTTT---AAA-A-A-ACTATA
1 -AAAACATTTTGAAAATAATATAATATATAGTTTT-AAAAACATTTTTGAAAAATATATATTATA
*
37502 TAATTTTG
64 TAATTTTT
* * * *
37510 AAAACATTTTTAGAAAGT-ATATAATATATAATTTT-AAAATATTTTT-AAAAGTATATATTATA
1 AAAACA-TTTT-GAAAATAATATAATATATAGTTTTAAAAACATTTTTGAAAAATATATATTATA
*
37572 TAAGTTTT
64 TAATTTTT
37580 GGGAAAATAT
Statistics
Matches: 292, Mismatches: 35, Indels: 54
0.77 0.09 0.14
Matches are distributed among these distances:
64 8 0.03
65 21 0.07
66 22 0.08
67 31 0.11
68 6 0.02
69 1 0.00
70 27 0.09
71 20 0.07
72 19 0.07
73 20 0.07
74 55 0.19
75 25 0.09
76 35 0.12
77 2 0.01
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.44
Consensus pattern (71 bp):
AAAACATTTTGAAAATAATATAATATATAGTTTTAAAAACATTTTTGAAAAATATATATTATATA
ATTTTT
Found at i:37540 original size:36 final size:35
Alignment explanation
Indices: 37149--37580 Score: 214
Period size: 35 Copynumber: 12.1 Consensus size: 35
37139 CAGTATATAG
37149 TTTGAAAACATTTTTAATATA-TATATAATATATAAT
1 TTTGAAAACATTTTTAA-A-AGTATATAATATATAAT
* * * *
37185 TTTGAAAAGCATGTTTGAAAACATTTATATATTATATAGT
1 TTTGAAAA-CAT-TTT-TAAA-A-GTATATAATATATAAT
* * * **
37225 TCTT-AAGACATTTTGAAAATTAATATAATATATGGT
1 T-TTGAAAACATTTTTAAAAGT-ATATAATATATAAT
*
37261 TTTCAAAACATTTTTGAAAA-TATATATATTATATAATT
1 TTTGAAAACATTTTT-AAAAGTATATA-A-TATATAA-T
* * * *
37299 TTTAAAAACATTTTGAAAATTAATATAATATATAGT
1 TTTGAAAACATTTTTAAAAGT-ATATAATATATAAT
* * * ** *
37335 TTTTAAAATATTTTTGAAAA-TACATGTTATATAGT
1 TTTGAAAACATTTTT-AAAAGTATATAATATATAAT
*
37370 TTTTAAAACA-TTTTAAAA--ATAT-ATATAGT--T
1 TTTGAAAACATTTTTAAAAGTATATAATATA-TAAT
* * * * *
37400 TTTAAAAAAACATTTTGAAAACATAAATATATTATATAGTT
1 TTT--GAAAACATTTTTAAAA-GT--ATATAATATATA-AT
* * * *
37441 TTTGAAATCATTTTGAAAA-CATATAATATATAGT
1 TTTGAAAACATTTTTAAAAGTATATAATATATAAT
* *
37475 TTTAAAAAACATTTTT-AAA--A-A-ACTATATAAT
1 TTT-GAAAACATTTTTAAAAGTATATAATATATAAT
37506 TTTGAAAACATTTTTAGAAAGTATATAATATATAAT
1 TTTGAAAACATTTTTA-AAAGTATATAATATATAAT
* *
37542 TTT-AAAATATTTTTAAAAGTATATATTATATAAGT
1 TTTGAAAACATTTTTAAAAGTATATAATATATAA-T
37577 TTTG
1 TTTG
37581 GGAAAATATT
Statistics
Matches: 318, Mismatches: 41, Indels: 74
0.73 0.09 0.17
Matches are distributed among these distances:
30 15 0.05
31 15 0.05
32 14 0.04
33 12 0.04
34 29 0.09
35 65 0.20
36 59 0.19
37 29 0.09
38 29 0.09
39 28 0.09
40 17 0.05
41 6 0.02
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.44
Consensus pattern (35 bp):
TTTGAAAACATTTTTAAAAGTATATAATATATAAT
Found at i:42472 original size:17 final size:17
Alignment explanation
Indices: 42450--42489 Score: 80
Period size: 17 Copynumber: 2.4 Consensus size: 17
42440 TTGTTCCGAA
42450 ACTCCCTGTTCCCTTAC
1 ACTCCCTGTTCCCTTAC
42467 ACTCCCTGTTCCCTTAC
1 ACTCCCTGTTCCCTTAC
42484 ACTCCC
1 ACTCCC
42490 ACTCTCATCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.12, C:0.50, G:0.05, T:0.33
Consensus pattern (17 bp):
ACTCCCTGTTCCCTTAC
Found at i:42836 original size:3 final size:3
Alignment explanation
Indices: 42828--42910 Score: 166
Period size: 3 Copynumber: 27.7 Consensus size: 3
42818 AAATAAAAGC
42828 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
42876 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
42911 AGTGAAAGCT
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 80 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:49582 original size:2 final size:2
Alignment explanation
Indices: 49575--49606 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
49565 TATGTTATTA
49575 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
49607 TTATCCTCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:54474 original size:22 final size:22
Alignment explanation
Indices: 54443--54532 Score: 119
Period size: 22 Copynumber: 4.1 Consensus size: 22
54433 CATATATAGT
*
54443 ATACAGAGGTCCTTCGAGACAA
1 ATACATAGGTCCTTCGAGACAA
*
54465 ATACATAGGTCTTTC-ATGACAA
1 ATACATAGGTCCTTCGA-GACAA
* *
54487 ATACATAGGTCATTCGGGACAA
1 ATACATAGGTCCTTCGAGACAA
*
54509 ATACATAGGTCCTTCGGGACAA
1 ATACATAGGTCCTTCGAGACAA
54531 AT
1 AT
54533 TTCACATGCC
Statistics
Matches: 61, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
21 1 0.02
22 60 0.98
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.24
Consensus pattern (22 bp):
ATACATAGGTCCTTCGAGACAA
Found at i:55361 original size:21 final size:21
Alignment explanation
Indices: 55335--55376 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
55325 GATGTTTTTT
55335 GTGCATCGGTACACTGTAGCA
1 GTGCATCGGTACACTGTAGCA
55356 GTGCATCGGTACACTGTAGCA
1 GTGCATCGGTACACTGTAGCA
55377 CTGTTCATGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.24, G:0.29, T:0.24
Consensus pattern (21 bp):
GTGCATCGGTACACTGTAGCA
Found at i:55395 original size:12 final size:12
Alignment explanation
Indices: 55378--55418 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
55368 ACTGTAGCAC
55378 TGTTCATGGTAT
1 TGTTCATGGTAT
*
55390 TGTTCAT--TAC
1 TGTTCATGGTAT
*
55400 TGTTCACGGTAT
1 TGTTCATGGTAT
55412 TGTTCAT
1 TGTTCAT
55419 ACCGTATAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
10 8 0.35
12 15 0.65
ACGTcount: A:0.17, C:0.15, G:0.20, T:0.49
Consensus pattern (12 bp):
TGTTCATGGTAT
Found at i:55401 original size:22 final size:22
Alignment explanation
Indices: 55376--55418 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
55366 ACACTGTAGC
*
55376 ACTGTTCATGGTATTGTTCATT
1 ACTGTTCACGGTATTGTTCATT
55398 ACTGTTCACGGTATTGTTCAT
1 ACTGTTCACGGTATTGTTCAT
55419 ACCGTATAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.19, C:0.16, G:0.19, T:0.47
Consensus pattern (22 bp):
ACTGTTCACGGTATTGTTCATT
Found at i:56737 original size:2 final size:2
Alignment explanation
Indices: 56730--56760 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
56720 CTTCAATTCT
56730 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
56761 GTTTCGTTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Done.