Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001273.1 Hibiscus syriacus cultivar Beakdansim tig00002499_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: 84912
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:15371 original size:13 final size:14
Alignment explanation
Indices: 15355--15385 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
15345 ATATACATCG
15355 TTAATATAT-AAAA
1 TTAATATATAAAAA
15368 TTAATATATAAAAA
1 TTAATATATAAAAA
15382 TTAA
1 TTAA
15386 ATTTTAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.53
14 8 0.47
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
TTAATATATAAAAA
Found at i:15394 original size:13 final size:14
Alignment explanation
Indices: 15355--15396 Score: 52
Period size: 13 Copynumber: 3.1 Consensus size: 14
15345 ATATACATCG
15355 TTAATATA-TAAAA
1 TTAATATATTAAAA
*
15368 TTAATATATAAAAA
1 TTAATATATTAAAA
*
15382 TTAA-ATTTTAAAA
1 TTAATATATTAAAA
15395 TT
1 TT
15397 CAAAATAGTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
13 17 0.68
14 8 0.32
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
TTAATATATTAAAA
Found at i:31474 original size:18 final size:18
Alignment explanation
Indices: 31451--31489 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
31441 TTTTTTCCCC
* *
31451 TTTATATGTACCTACATA
1 TTTATATATACATACATA
*
31469 TTTATATATATATACATA
1 TTTATATATACATACATA
31487 TTT
1 TTT
31490 TGAAACTACG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.36, C:0.10, G:0.03, T:0.51
Consensus pattern (18 bp):
TTTATATATACATACATA
Found at i:31603 original size:38 final size:36
Alignment explanation
Indices: 31500--31821 Score: 234
Period size: 38 Copynumber: 8.8 Consensus size: 36
31490 TGAAACTACG
* * *
31500 TATATAATATATAGTTTTT-AATA-GTTTTTAAAAT
1 TATATAATATATAGTTTTTAAAAACATTTTGAAAAT
31534 TATATAATATATAGTTTTTAAAAAAAACATTTTAGAAAAT
1 TATATAATATATAGTTTTT---AAAAACATTTT-GAAAAT
** *
31574 ATATATAATATATAAATTTTAAAATCATTTTGAAAACT
1 -TATATAATATATAGTTTTTAAAAACATTTTGAAAA-T
*
31612 TATAT-ATATATAGTTTTTGAAAACATTTTTGAAAA-
1 TATATAATATATAGTTTTTAAAAACA-TTTTGAAAAT
* *
31647 CATAT-ATATTATAG-TTTTGAAAACATTTTGAAAACATT
1 TATATAATA-TATAGTTTTTAAAAACATTTTG-AAA-A-T
* *
31685 TATATATTATATAGTTTTT-AAAACGTTTTTGGAAAATT
1 TATATAATATATAGTTTTTAAAAAC-ATTTT-GAAAA-T
* ** * *
31723 TATATAATCT-TTTTTTTTGAAAACATGTTGAAAAAT
1 TATATAATATATAGTTTTTAAAAACATTTTG-AAAAT
* *
31759 TCATATATTATATAG--TTTAAAAACATTTTGAAATT
1 T-ATATAATATATAGTTTTTAAAAACATTTTGAAAAT
* * *
31794 TATATATTATAT-GTTTTTGAAAATATTT
1 TATATAATATATAGTTTTTAAAAACATTT
31822 ATGTATATAT
Statistics
Matches: 235, Mismatches: 29, Indels: 47
0.76 0.09 0.15
Matches are distributed among these distances:
33 1 0.00
34 35 0.15
35 37 0.16
36 38 0.16
37 39 0.17
38 45 0.19
39 17 0.07
40 6 0.03
41 17 0.07
ACGTcount: A:0.43, C:0.04, G:0.07, T:0.47
Consensus pattern (36 bp):
TATATAATATATAGTTTTTAAAAACATTTTGAAAAT
Found at i:31639 original size:36 final size:36
Alignment explanation
Indices: 31486--31821 Score: 221
Period size: 37 Copynumber: 9.1 Consensus size: 36
31476 ATATATACAT
* *
31486 ATTTTGAAACTACGTATATAATATATAGTTTTT-AATA-
1 ATTTTGAAA--ACTTATAT-ATATATAGTTTTTGAAAAC
* * * *
31523 GTTTTTAAAAT-TATATAATATATAGTTTTTAAAAAAAAC
1 ATTTTGAAAACTTATAT-ATATATAGTTTTT---GAAAAC
**
31562 ATTTTAGAAAA-TATATATAATATATAAATTTT-AAAATC
1 ATTTT-GAAAACT-TATAT-ATATATAGTTTTTGAAAA-C
31600 ATTTTGAAAACTTATATATATATAGTTTTTGAAAAC
1 ATTTTGAAAACTTATATATATATAGTTTTTGAAAAC
*
31636 ATTTTTGAAAACATATATAT-TATAG-TTTTGAAAAC
1 A-TTTTGAAAACTTATATATATATAGTTTTTGAAAAC
31671 ATTTTGAAAACATTTATATATTATATAGTTTTT-AAAAC
1 ATTTTGAAAAC--TTATATA-TATATAGTTTTTGAAAAC
* * * **
31709 GTTTTTGGAAAATTTATATA-ATCTTTTTTTTTGAAAAC
1 -ATTTT-GAAAACTTATATATAT-ATAGTTTTTGAAAAC
* * *
31747 ATGTTGAAAAATTCATATATTATATAG--TTTAAAAAC
1 ATTTTGAAAACTT-ATATA-TATATAGTTTTTGAAAAC
* *
31783 ATTTTG-AAATTTATATAT-TATATGTTTTTGAAAAT
1 ATTTTGAAAACTTATATATATATA-GTTTTTGAAAAC
31818 ATTT
1 ATTT
31822 ATGTATATAT
Statistics
Matches: 244, Mismatches: 28, Indels: 56
0.74 0.09 0.17
Matches are distributed among these distances:
32 4 0.02
33 2 0.01
34 34 0.14
35 28 0.11
36 46 0.19
37 57 0.23
38 33 0.14
39 14 0.06
40 9 0.04
41 17 0.07
ACGTcount: A:0.43, C:0.04, G:0.07, T:0.46
Consensus pattern (36 bp):
ATTTTGAAAACTTATATATATATAGTTTTTGAAAAC
Found at i:31677 original size:11 final size:11
Alignment explanation
Indices: 31661--31685 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
31651 TATATTATAG
31661 TTTTGAAAACA
1 TTTTGAAAACA
31672 TTTTGAAAACA
1 TTTTGAAAACA
31683 TTT
1 TTT
31686 ATATATTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (11 bp):
TTTTGAAAACA
Found at i:31828 original size:24 final size:24
Alignment explanation
Indices: 31784--31829 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
31774 TTTAAAAACA
*
31784 TTTTGAAATTTATATATTATATGT
1 TTTTGAAATATATATATTATATGT
*
31808 TTTTGAAA-ATATTTATGTATAT
1 TTTTGAAATATATATAT-TATAT
31830 ATATATTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 6 0.32
24 13 0.68
ACGTcount: A:0.35, C:0.00, G:0.09, T:0.57
Consensus pattern (24 bp):
TTTTGAAATATATATATTATATGT
Found at i:34918 original size:19 final size:19
Alignment explanation
Indices: 34884--34928 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
34874 ATTTAGACAT
34884 TTTGCA-TTTCTTATTTTC
1 TTTGCATTTTCTTATTTTC
*
34902 TTTGCATTTTGTTATTTTC
1 TTTGCATTTTCTTATTTTC
34921 TTTGCATT
1 TTTGCATT
34929 CACATTAACT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 6 0.24
19 19 0.76
ACGTcount: A:0.11, C:0.13, G:0.09, T:0.67
Consensus pattern (19 bp):
TTTGCATTTTCTTATTTTC
Found at i:38492 original size:84 final size:81
Alignment explanation
Indices: 38261--38879 Score: 618
Period size: 81 Copynumber: 7.6 Consensus size: 81
38251 TAAACAAACT
* * * *
38261 ATTTGCAGCTTAGCTCAAGGCCAGAAGGGCTATCTG-CCACCAAGACCTTTGAGTTCGACTACGC
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGACCA--AAGACCTTTGAGTTCGACTACGC
*
38325 TCAACTCCAAGGCACATC
64 TCAGCTCCAAGGCACATC
* * * * * * *
38343 ATTTGCAGTATAGCTTAAGTCGAGAAGAGCTATCTG-CCAAAGACCCTTAAGTTCAATTACACTC
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGACCAAAGACCTTTGAGTTCGACTACGCTC
* * *
38407 AGCTTCAAGGGCATAAC
66 AGCTCCAA-GGCACATC
* * * * * * *
38424 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTTAGCAAAGACCTTTGAGTTCGACTACGC
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG--ACCAAAGACCTTTGAGTTCGACTACGC
38489 TCAGCTCCAAGGCACATC
64 TCAGCTCCAAGGCACATC
* * * * * *
38507 ATTTGCAGTATAGCTTAAGTCGAGAAGAGCTATCTG-CCAAAGACCCTTAAGTTCGATTACACTC
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGACCAAAGACCTTTGAGTTCGACTACGCTC
* * *
38571 AGCTTCAAGGGCATAAC
66 AGCTCCAA-GGCACATC
* * * * * * *
38588 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTTAGCAAAGACCTTTGAGTTCGACTACGC
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG--ACCAAAGACCTTTGAGTTCGACTACGC
38653 TCAGCTCCAAGGCACATC
64 TCAGCTCCAAGGCACATC
* *** *
38671 ATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTG-CCAAAGACCCCCGAGTTCGATTACGCTC
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGACCAAAGACCTTTGAGTTCGACTACGCTC
** * *
38735 AGCTTTGAGGGCGCATC
66 AGC-TCCAAGGCACATC
* * * *
38752 ATTTGCAGCATAACTTAAGTCAAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG---ACCAAAGACCTTTGAGTTCGACTACG
*
38817 CTCAGCTCCAAGGCATATC
63 CTCAGCTCCAAGGCACATC
*
38836 ATTTGCAGCATAGCTTAAGTCAAGAAGGGCTATCTG-CCAAAGAC
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGACCAAAGAC
38880 TCCCGAGTTC
Statistics
Matches: 430, Mismatches: 94, Indels: 28
0.78 0.17 0.05
Matches are distributed among these distances:
80 90 0.21
81 109 0.25
82 33 0.08
83 69 0.16
84 101 0.23
85 28 0.07
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.24
Consensus pattern (81 bp):
ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGACCAAAGACCTTTGAGTTCGACTACGCTC
AGCTCCAAGGCACATC
Found at i:38544 original size:164 final size:164
Alignment explanation
Indices: 38274--38945 Score: 952
Period size: 164 Copynumber: 4.1 Consensus size: 164
38264 TGCAGCTTAG
* * * * *
38274 CTCAAGGCCAGAAGGGCTATCTGCCA-CCAAGACCTTTGAGTTCGACTACGCTCAACTCCAAGGC
1 CTCAAGGCAAGAAGGGTTATCTGCTAGCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGC
* *
38338 ACATCATTTGCAGTATAGCTTAAGTCGAGAAGAGCTATCTGCCAAAGACCCTTAAGTTCAATTAC
66 ACATCATTTGCAGTATAGCTTAAGTCGAGAAGAGCTATCTGCCAAAGACCCTCAAGTTCGATTAC
38403 ACTCAGCTTCAAGGGCATAACATTTACAGCATAA
131 ACTCAGCTTCAAGGGCATAACATTTACAGCATAA
* *
38437 CTCAAGGCTAGAAGGGTTATCTGTTAGCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGC
1 CTCAAGGCAAGAAGGGTTATCTGCTAGCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGC
*
38502 ACATCATTTGCAGTATAGCTTAAGTCGAGAAGAGCTATCTGCCAAAGACCCTTAAGTTCGATTAC
66 ACATCATTTGCAGTATAGCTTAAGTCGAGAAGAGCTATCTGCCAAAGACCCTCAAGTTCGATTAC
38567 ACTCAGCTTCAAGGGCATAACATTTACAGCATAA
131 ACTCAGCTTCAAGGGCATAACATTTACAGCATAA
* *
38601 CTCAAGGCTAGAAGGGTTATCTGTTAGCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGC
1 CTCAAGGCAAGAAGGGTTATCTGCTAGCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGC
* * * *
38666 ACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTAC
66 ACATCATTTGCAGTATAGCTTAAGTCGAGAAGAGCTATCTGCCAAAGACCCTCAAGTTCGATTAC
* ** ** * *
38731 GCTCAGCTTTGAGGGCGCATCATTTGCAGCATAA
131 ACTCAGCTTCAAGGGCATAACATTTACAGCATAA
* * * * *
38765 CTTAAGTCAAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGG
1 CTCAAGGCAAGAAGGGTTATCTG-CTAGCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGG
* * * * *
38830 CATATCATTTGCAGCATAGCTTAAGTCAAGAAGGGCTATCTGCCAAAGACTCC-CGAGTTCGATT
65 CACATCATTTGCAGTATAGCTTAAGTCGAGAAGAGCTATCTGCCAAAGAC-CCTCAAGTTCGATT
* * * * * *
38894 ACACTCAACTTCGAGGTCATATCATTTACAACATAG
129 ACACTCAGCTTCAAGGGCATAACATTTACAGCATAA
*
38930 CTCATGGCAAGAAGGG
1 CTCAAGGCAAGAAGGG
38946 CTATTTGTCA
Statistics
Matches: 465, Mismatches: 41, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
163 22 0.05
164 306 0.66
165 135 0.29
166 2 0.00
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.24
Consensus pattern (164 bp):
CTCAAGGCAAGAAGGGTTATCTGCTAGCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGC
ACATCATTTGCAGTATAGCTTAAGTCGAGAAGAGCTATCTGCCAAAGACCCTCAAGTTCGATTAC
ACTCAGCTTCAAGGGCATAACATTTACAGCATAA
Found at i:38976 original size:328 final size:327
Alignment explanation
Indices: 38274--38956 Score: 938
Period size: 329 Copynumber: 2.1 Consensus size: 327
38264 TGCAGCTTAG
* * *
38274 CTCAAGGCCAGAAGGGCTATCTG-CCACCAAGACCTTTGAGTTCGACTACGCTCAACTCCAAGGC
1 CTCAAGGCAAGAAGGGCTATCTGTCAACAAAGA-CTTTGAGTTCGACTACGCTCAACTCCAAGGC
* **
38338 ACATCATTTGCAGTATAGCTTAAGTCGAGAAGAGCTATCTGCCAAAGACCCTTAAGTTCAATTAC
65 ACATCATTTGCAGAATAGCTTAAGTCGAGAAGAGCTATCTGCCAAAGACCCCCAAGTTCAATTAC
* * ** *
38403 ACTCAGCTTCAAGGGCATAACATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTTAGCAAA
130 ACTCAGCTTCAAGGGCACAACATTTACAGCATAACTCAAGGCAAGAAGGGTTATCTGCAACCAAA
* * *
38468 GACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGTATAGCTTAAGTCGAGAA
195 GACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCAAGAA
* * *
38533 GAGCTATCTGCCAAAGACCCTTAAGTTCGATTACACTCAGCTTCAAGGGCATAACATTTACAGCA
260 GAGCTATCTGCCAAAGACCCTCAAGTTCGATTACACTCAACTTCAAGGGCATAACATTTACAACA
38598 TAA
325 TAA
* * * * *
38601 CTCAAGGCTAGAAGGGTTATCTGTTAGCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGC
1 CTCAAGGCAAGAAGGGCTATCTGTCAACAAAGA-CTTTGAGTTCGACTACGCTCAACTCCAAGGC
* * *
38666 ACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTAC
65 ACATCATTTGCAGAATAGCTTAAGTCGAGAAGAGCTATCTGCCAAAGACCCCCAAGTTCAATTAC
* ** * * * * *
38731 GCTCAGCTTTGAGGGCGCATCATTTGCAGCATAACTTAAGTCAAGAAGGGTTATCTGCCAACCAA
130 ACTCAGCTTCAAGGGCACAACATTTACAGCATAACTCAAGGCAAGAAGGGTTATCTG-CAACCAA
*
38796 AGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAGCTTAAGTCAAGA
194 AGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCAAGA
* * * * *
38861 AGGGCTATCTGCCAAAGACTCC-CGAGTTCGATTACACTCAACTTCGAGGTCATATCATTTACAA
259 AGAGCTATCTGCCAAAGAC-CCTCAAGTTCGATTACACTCAACTTCAAGGGCATAACATTTACAA
*
38925 CATAG
323 CATAA
* *
38930 CTCATGGCAAGAAGGGCTATTTGTCAA
1 CTCAAGGCAAGAAGGGCTATCTGTCAA
38957 TAAAATTGTC
Statistics
Matches: 308, Mismatches: 45, Indels: 4
0.86 0.13 0.01
Matches are distributed among these distances:
327 21 0.07
328 142 0.46
329 143 0.46
330 2 0.01
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (327 bp):
CTCAAGGCAAGAAGGGCTATCTGTCAACAAAGACTTTGAGTTCGACTACGCTCAACTCCAAGGCA
CATCATTTGCAGAATAGCTTAAGTCGAGAAGAGCTATCTGCCAAAGACCCCCAAGTTCAATTACA
CTCAGCTTCAAGGGCACAACATTTACAGCATAACTCAAGGCAAGAAGGGTTATCTGCAACCAAAG
ACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCAAGAAG
AGCTATCTGCCAAAGACCCTCAAGTTCGATTACACTCAACTTCAAGGGCATAACATTTACAACAT
AA
Found at i:39621 original size:39 final size:36
Alignment explanation
Indices: 39544--39855 Score: 199
Period size: 38 Copynumber: 8.8 Consensus size: 36
39534 TGAAACTACG
* * *
39544 TATATAATATATAGTTTTT-AATA-GTTTTTAAAAT
1 TATATAATATATAGTTTTTAAAAACATTTTGAAAAT
**
39578 TATATAATATATAGTTTAAAAAAAACATTTTAGAAAAT
1 TATATAATATATAGTTT-TTAAAAACATTTT-GAAAAT
* *
39616 ATATATAATATATAATTTTTAAAATCATTTTGAAAACT
1 -TATATAATATATAGTTTTTAAAAACATTTTGAAAA-T
*
39654 TATATATATATATAGTTTTTGAAAACATTTTTGAAAA-
1 TATATA-ATATATAGTTTTTAAAAACA-TTTTGAAAAT
* *
39691 CATAT-ATATTATAG-TTTTGAAAACA-TTT----A-
1 TATATAATA-TATAGTTTTTAAAAACATTTTGAAAAT
*
39720 TATAT--TATATAGTTTTT-AAAACGTTTTTGGAAAATT
1 TATATAATATATAGTTTTTAAAAAC-ATTTT-GAAAA-T
* * ** * *
39756 TATATAATCTTTTTTTTTTGAAAACATGTTGAAAAAT
1 TATATAATATATAGTTTTTAAAAACATTTTG-AAAAT
* *
39793 TCATATATTATATAG--TTTAAAAACATTTTGAAATT
1 T-ATATAATATATAGTTTTTAAAAACATTTTGAAAAT
* * *
39828 TATATATTATAT-GTTTTTGAAAATATTT
1 TATATAATATATAGTTTTTAAAAACATTT
39856 ATGTATATAT
Statistics
Matches: 221, Mismatches: 31, Indels: 51
0.73 0.10 0.17
Matches are distributed among these distances:
27 10 0.05
28 6 0.03
29 8 0.04
33 4 0.02
34 29 0.13
35 30 0.14
36 26 0.12
37 22 0.10
38 56 0.25
39 30 0.14
ACGTcount: A:0.43, C:0.04, G:0.07, T:0.47
Consensus pattern (36 bp):
TATATAATATATAGTTTTTAAAAACATTTTGAAAAT
Found at i:39651 original size:37 final size:36
Alignment explanation
Indices: 39530--39869 Score: 194
Period size: 37 Copynumber: 9.5 Consensus size: 36
39520 ATATATACAT
* *
39530 ATTTTGAAACTACGTATATAATATATAGTTTTTAATA-
1 ATTTTGAAAATA--TATATAATATATAGTTTTTAAAAC
* * **
39567 GTTTTTAAAAT-TATATAATATATAGTTTAAAAAAAAC
1 ATTTTGAAAATATATATAATATATAGTTT--TTAAAAC
*
39604 ATTTTAGAAAATATATATAATATATAATTTTTAAAATC
1 ATTTT-GAAAATATATATAATATATAGTTTTTAAAA-C
39642 ATTTTGAAAACT-TATATATATATATAGTTTTTGAAAAC
1 ATTTTGAAAA-TATATATA-ATATATAGTTTTT-AAAAC
* *
39680 ATTTTTGAAAACATATAT-AT-TATAGTTTTGAAAAC
1 A-TTTTGAAAATATATATAATATATAGTTTTTAAAAC
39715 A--TT-----TATATAT--TATATAGTTTTTAAAAC
1 ATTTTGAAAATATATATAATATATAGTTTTTAAAAC
* * * * **
39742 GTTTTTGGAAAATTTATATAATCTTTTTTTTTTGAAAAC
1 -ATTTT-GAAAATATATATAATATATAGTTTTT-AAAAC
* * *
39781 ATGTTGAAAA-ATTCATATATTATATAG-TTTAAAAAC
1 ATTTTGAAAATA-T-ATATAATATATAGTTTTTAAAAC
* * *
39817 ATTTTG-AAATTTATATATTATAT-GTTTTTGAAAAT
1 ATTTTGAAAATATATATAATATATAGTTTTT-AAAAC
* *
39852 ATTTATGTATATATATAT
1 ATTT-TGAAAATATATAT
39870 TATTTATTAT
Statistics
Matches: 235, Mismatches: 37, Indels: 62
0.70 0.11 0.19
Matches are distributed among these distances:
26 1 0.00
27 20 0.09
30 2 0.01
32 2 0.01
33 1 0.00
34 31 0.13
35 18 0.08
36 30 0.13
37 46 0.20
38 45 0.19
39 39 0.17
ACGTcount: A:0.42, C:0.04, G:0.07, T:0.47
Consensus pattern (36 bp):
ATTTTGAAAATATATATAATATATAGTTTTTAAAAC
Found at i:39686 original size:12 final size:12
Alignment explanation
Indices: 39669--39693 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
39659 ATATATATAG
39669 TTTTTGAAAACA
1 TTTTTGAAAACA
39681 TTTTTGAAAACA
1 TTTTTGAAAACA
39693 T
1 T
39694 ATATATTATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (12 bp):
TTTTTGAAAACA
Found at i:39712 original size:23 final size:24
Alignment explanation
Indices: 39682--39728 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
39672 TTGAAAACAT
39682 TTTTGAAAACA-TATATATTATAG
1 TTTTGAAAACATTATATATTATAG
39705 TTTTGAAAACATTTATATATTATA
1 TTTTGAAAACA-TTATATATTATA
39729 TAGTTTTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 11 0.50
25 11 0.50
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.47
Consensus pattern (24 bp):
TTTTGAAAACATTATATATTATAG
Found at i:39722 original size:101 final size:101
Alignment explanation
Indices: 39617--39804 Score: 231
Period size: 101 Copynumber: 1.9 Consensus size: 101
39607 TTAGAAAATA
39617 TATATAATATATAATTTTTAAAATC-ATTTT-GAAAACTTATATATATATATAGTTTTTGAAAAC
1 TATATAATATATAATTTTTAAAA-CGATTTTGGAAAACTTATATA-ATATATAGTTTTTGAAAAC
*
39680 ATTTTTGAAAACA-T-ATATATTATAGTTTTGAAAACATT
64 A-TGTTGAAAA-ATTCATATATTATAGTTTTGAAAACATT
* * * * * * **
39718 TATATATTATATAGTTTTTAAAACGTTTTTGGAAAATTTATATAATCTTTTTTTTTTGAAAACAT
1 TATATAATATATAATTTTTAAAACGATTTTGGAAAACTTATATAATATATAGTTTTTGAAAACAT
39783 GTTGAAAAATTCATATATTATA
66 GTTGAAAAATTCATATATTATA
39805 TAGTTTAAAA
Statistics
Matches: 74, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
99 1 0.01
100 10 0.14
101 51 0.69
102 12 0.16
ACGTcount: A:0.41, C:0.05, G:0.07, T:0.47
Consensus pattern (101 bp):
TATATAATATATAATTTTTAAAACGATTTTGGAAAACTTATATAATATATAGTTTTTGAAAACAT
GTTGAAAAATTCATATATTATAGTTTTGAAAACATT
Found at i:39740 original size:27 final size:23
Alignment explanation
Indices: 39681--39741 Score: 68
Period size: 27 Copynumber: 2.4 Consensus size: 23
39671 TTTGAAAACA
39681 TTTTTGAAAACATATATATTATAG
1 TTTTT-AAAACATATATATTATAG
*
39705 TTTTGAAAACATTTATATATTATATAG
1 TTTTTAAAACA--TATATA-T-TATAG
39732 TTTTTAAAAC
1 TTTTTAAAAC
39742 GTTTTTGGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
23 6 0.19
24 4 0.13
25 6 0.19
26 1 0.03
27 14 0.45
ACGTcount: A:0.41, C:0.05, G:0.07, T:0.48
Consensus pattern (23 bp):
TTTTTAAAACATATATATTATAG
Found at i:39862 original size:24 final size:24
Alignment explanation
Indices: 39818--39863 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
39808 TTTAAAAACA
*
39818 TTTTGAAATTTATATATTATATGT
1 TTTTGAAATATATATATTATATGT
*
39842 TTTTGAAA-ATATTTATGTATAT
1 TTTTGAAATATATATAT-TATAT
39864 ATATATTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 6 0.32
24 13 0.68
ACGTcount: A:0.35, C:0.00, G:0.09, T:0.57
Consensus pattern (24 bp):
TTTTGAAATATATATATTATATGT
Found at i:41636 original size:3 final size:3
Alignment explanation
Indices: 41630--41659 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
41620 TTCTCTTTCA
41630 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
41660 TCAAAATAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:42557 original size:25 final size:25
Alignment explanation
Indices: 42529--42613 Score: 98
Period size: 25 Copynumber: 3.3 Consensus size: 25
42519 GTAGCTAAAC
42529 TTTATTTTATTTATAATATTATTTA
1 TTTATTTTATTTATAATATTATTTA
* * * *
42554 TTTATTTTGTTAATGAATATATTCTTTT
1 TTTATTTTATTTAT--A-ATATTATTTA
*
42582 TTTATTTTTTTTATAATATTATTTA
1 TTTATTTTATTTATAATATTATTTA
42607 TTTATTT
1 TTTATTT
42614 ATTCTTTATA
Statistics
Matches: 49, Mismatches: 8, Indels: 6
0.78 0.13 0.10
Matches are distributed among these distances:
25 27 0.55
26 1 0.02
27 1 0.02
28 20 0.41
ACGTcount: A:0.27, C:0.01, G:0.02, T:0.69
Consensus pattern (25 bp):
TTTATTTTATTTATAATATTATTTA
Found at i:42604 original size:28 final size:27
Alignment explanation
Indices: 42529--42633 Score: 83
Period size: 28 Copynumber: 3.8 Consensus size: 27
42519 GTAGCTAAAC
42529 TTTATTTTATTTATAATATTA--TTTA
1 TTTATTTTATTTATAATATTATTTTTA
* * *
42554 TTTATTTTGTTAATGAATA-TATTCTTTT
1 TTTATTTTATTTAT-AATATTATT-TTTA
*
42582 TTTATTTTTTTTATAATATTATTTATTTA
1 TTTATTTTATTTATAATATTA-TT-TTTA
42611 TTTATTCTTTATATTAT-ATATTA
1 TTTA-T-TTTAT-TTATAATATTA
42634 AATAAAATTT
Statistics
Matches: 63, Mismatches: 8, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
25 14 0.22
26 4 0.06
27 4 0.06
28 17 0.27
29 9 0.14
30 1 0.02
31 10 0.16
32 4 0.06
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.68
Consensus pattern (27 bp):
TTTATTTTATTTATAATATTATTTTTA
Found at i:42780 original size:24 final size:24
Alignment explanation
Indices: 42759--42808 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 24
42749 ATACTTAATG
42759 TTAAT-ATAAAAATTTAATTTAAAA
1 TTAATCAT-AAAATTTAATTTAAAA
*
42783 TTAATCATGAAATTTAATTTTAAAA
1 TTAATCATAAAATTTAA-TTTAAAA
42808 T
1 T
42809 AACTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 13 0.57
25 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (24 bp):
TTAATCATAAAATTTAATTTAAAA
Found at i:50208 original size:16 final size:17
Alignment explanation
Indices: 50187--50221 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
50177 TTACTATTCA
50187 CGTGAATAGTG-AATTT
1 CGTGAATAGTGAAATTT
50203 CGTGAATAGTGAAATTT
1 CGTGAATAGTGAAATTT
50220 CG
1 CG
50222 GTCAGCGATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.31, C:0.09, G:0.26, T:0.34
Consensus pattern (17 bp):
CGTGAATAGTGAAATTT
Found at i:50989 original size:15 final size:16
Alignment explanation
Indices: 50971--51003 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
50961 GTGGCAGATC
50971 AAAATCCAG-ACGGGA
1 AAAATCCAGAACGGGA
*
50986 AAAATCTAGAACGGGA
1 AAAATCCAGAACGGGA
51002 AA
1 AA
51004 GAAAGATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.52, C:0.15, G:0.24, T:0.09
Consensus pattern (16 bp):
AAAATCCAGAACGGGA
Found at i:55979 original size:2 final size:2
Alignment explanation
Indices: 55972--56004 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
55962 CTGCCTTTTA
55972 AT AT AT 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 AT AT AT A
56005 AACTTAATTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:56622 original size:2 final size:2
Alignment explanation
Indices: 56615--56639 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
56605 TTCTGTATAT
56615 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 T
56640 TATATTTTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:59889 original size:2 final size:2
Alignment explanation
Indices: 59882--59953 Score: 144
Period size: 2 Copynumber: 36.0 Consensus size: 2
59872 TTCGATTCGA
59882 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
59924 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
59954 GTCATTGTGA
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 70 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:60267 original size:2 final size:2
Alignment explanation
Indices: 60260--60293 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
60250 AAGCTTTCTG
60260 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
60294 GGATCGTTTT
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:60465 original size:15 final size:15
Alignment explanation
Indices: 60445--60474 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
60435 AATGATTTTT
60445 AATATAATTACAAAA
1 AATATAATTACAAAA
*
60460 AATATATTTACAAAA
1 AATATAATTACAAAA
60475 TGACAAAAGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (15 bp):
AATATAATTACAAAA
Found at i:64745 original size:21 final size:21
Alignment explanation
Indices: 64719--64763 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
64709 GATTTCTGGG
* *
64719 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
64740 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
64761 CAA
1 CAA
64764 ACGAACAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:65141 original size:16 final size:16
Alignment explanation
Indices: 65116--65146 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
65106 CATGGACATG
*
65116 ATTATGTGTGGTTATA
1 ATTATATGTGGTTATA
65132 ATTATATGTGGTTAT
1 ATTATATGTGGTTAT
65147 CTGTATTACA
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:0.26, C:0.00, G:0.23, T:0.52
Consensus pattern (16 bp):
ATTATATGTGGTTATA
Found at i:66464 original size:25 final size:25
Alignment explanation
Indices: 66430--66498 Score: 138
Period size: 25 Copynumber: 2.8 Consensus size: 25
66420 GAGTAGAGGG
66430 TCTACGCGGTCCTTCGGGACAATAT
1 TCTACGCGGTCCTTCGGGACAATAT
66455 TCTACGCGGTCCTTCGGGACAATAT
1 TCTACGCGGTCCTTCGGGACAATAT
66480 TCTACGCGGTCCTTCGGGA
1 TCTACGCGGTCCTTCGGGA
66499 TATATATATA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 44 1.00
ACGTcount: A:0.17, C:0.29, G:0.26, T:0.28
Consensus pattern (25 bp):
TCTACGCGGTCCTTCGGGACAATAT
Found at i:66657 original size:23 final size:23
Alignment explanation
Indices: 66613--66657 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
66603 ATCATTATAT
* *
66613 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTACAATTATACGC
* *
66636 GGCACTTCGGTACATTTATACG
1 GGCACTACGGTACAATTATACG
66658 AGCTGTGGTG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.22, C:0.27, G:0.24, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTACAATTATACGC
Found at i:68653 original size:7 final size:7
Alignment explanation
Indices: 68643--68667 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
68633 TGATTTATGT
68643 ATAAGGA
1 ATAAGGA
68650 ATAAGGA
1 ATAAGGA
68657 ATAAGGA
1 ATAAGGA
68664 ATAA
1 ATAA
68668 AGAAATGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.00, G:0.24, T:0.16
Consensus pattern (7 bp):
ATAAGGA
Found at i:69821 original size:21 final size:21
Alignment explanation
Indices: 69795--69839 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
69785 GATTTCTGGG
* *
69795 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
69816 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
69837 CAA
1 CAA
69840 ACGAACAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:70217 original size:16 final size:16
Alignment explanation
Indices: 70192--70222 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
70182 CATGGACATG
*
70192 ATTATGTGTGGTTATA
1 ATTATATGTGGTTATA
70208 ATTATATGTGGTTAT
1 ATTATATGTGGTTAT
70223 CTGTATTACA
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:0.26, C:0.00, G:0.23, T:0.52
Consensus pattern (16 bp):
ATTATATGTGGTTATA
Found at i:71531 original size:25 final size:25
Alignment explanation
Indices: 71497--71590 Score: 161
Period size: 25 Copynumber: 3.8 Consensus size: 25
71487 GAGTAGAGGG
*
71497 TCTACGCGGTCCTTCAGGACAATAT
1 TCTACGCGGTCCTTCGGGACAATAT
*
71522 TCTACGCGGTCCTTCGGGATAATAT
1 TCTACGCGGTCCTTCGGGACAATAT
71547 TCTACGCGGTCCTTCGGGACAATAT
1 TCTACGCGGTCCTTCGGGACAATAT
*
71572 TCTACGCGGTCTTTCGGGA
1 TCTACGCGGTCCTTCGGGA
71591 TATATATATA
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 65 1.00
ACGTcount: A:0.19, C:0.27, G:0.24, T:0.30
Consensus pattern (25 bp):
TCTACGCGGTCCTTCGGGACAATAT
Found at i:71749 original size:23 final size:23
Alignment explanation
Indices: 71705--71749 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
71695 ATCATTATAT
*
71705 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
* *
71728 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
71750 AGCTATGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:74309 original size:5 final size:5
Alignment explanation
Indices: 74299--74323 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
74289 GCAATCATAT
74299 ATTCC ATTCC ATTCC ATTCC ATTCC
1 ATTCC ATTCC ATTCC ATTCC ATTCC
74324 GATGGCTACA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.40, G:0.00, T:0.40
Consensus pattern (5 bp):
ATTCC
Found at i:76163 original size:21 final size:21
Alignment explanation
Indices: 76139--76179 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
76129 CAATGATTAA
76139 TTATTAATAATATACACACCT
1 TTATTAATAATATACACACCT
76160 TTATTAATAATATACACACC
1 TTATTAATAATATACACACC
76180 ATCTAAAGAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.44, C:0.20, G:0.00, T:0.37
Consensus pattern (21 bp):
TTATTAATAATATACACACCT
Found at i:76579 original size:2 final size:2
Alignment explanation
Indices: 76572--76604 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
76562 TAAAAATAAT
76572 TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
76605 ATAAATTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:76608 original size:10 final size:11
Alignment explanation
Indices: 76572--76608 Score: 53
Period size: 10 Copynumber: 3.6 Consensus size: 11
76562 TAAAAATAAT
76572 TATAT-ATATA
1 TATATAATATA
76582 TATAT-ATATA
1 TATATAATATA
76592 TATATAATATA
1 TATATAATATA
76603 TA-ATAA
1 TATATAA
76609 ATTTAAATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 19 0.73
11 7 0.27
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (11 bp):
TATATAATATA
Found at i:77136 original size:26 final size:27
Alignment explanation
Indices: 77107--77180 Score: 114
Period size: 27 Copynumber: 2.8 Consensus size: 27
77097 TTACACTATG
* *
77107 TCGTCGAGTCAGTGCTTGAAATA-TTT
1 TCGTCGAGACAATGCTTGAAATATTTT
77133 TCGTCGAGACAATGCTTGAAATATTTT
1 TCGTCGAGACAATGCTTGAAATATTTT
*
77160 TCGTCGAGACAATACTTGAAA
1 TCGTCGAGACAATGCTTGAAA
77181 GTAACGGTGG
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
26 21 0.48
27 23 0.52
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.34
Consensus pattern (27 bp):
TCGTCGAGACAATGCTTGAAATATTTT
Found at i:78145 original size:21 final size:20
Alignment explanation
Indices: 78108--78146 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
78098 AAAAATTTAA
**
78108 AATTAAATTATGTATAAATT
1 AATTAAATTATCAATAAATT
78128 AATTAAATTTATCAATAAA
1 AATTAAA-TTATCAATAAA
78147 AATATCTTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (20 bp):
AATTAAATTATCAATAAATT
Found at i:79025 original size:12 final size:12
Alignment explanation
Indices: 79008--79032 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
78998 CATCTTAAAT
79008 TCTATTTTTTAA
1 TCTATTTTTTAA
79020 TCTATTTTTTAA
1 TCTATTTTTTAA
79032 T
1 T
79033 GAATTAAAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.68
Consensus pattern (12 bp):
TCTATTTTTTAA
Found at i:79118 original size:24 final size:22
Alignment explanation
Indices: 79060--79118 Score: 64
Period size: 24 Copynumber: 2.5 Consensus size: 22
79050 AGACGTTAAG
79060 TATAATTTTAAAATAAAATAAAA
1 TATAA-TTTAAAATAAAATAAAA
*
79083 TTTAAATATTAAAATAAAATAATAA
1 TAT-AAT-TTAAAATAAAATAA-AA
79108 TAATAATTTAA
1 T-ATAATTTAA
79119 TATTAAATGG
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
23 3 0.10
24 20 0.67
25 6 0.20
26 1 0.03
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (22 bp):
TATAATTTAAAATAAAATAAAA
Found at i:79121 original size:30 final size:29
Alignment explanation
Indices: 79068--79125 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 29
79058 AGTATAATTT
79068 TAAAATAAAATAAAATTTAAATATTAAAA
1 TAAAATAAAATAAAATTTAAATATTAAAA
79097 TAAAATAATAATAATAATTT-AATATTAAA
1 TAAAATAA-AATAA-AATTTAAATATTAAA
79126 TGGGTAATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 8 0.30
30 14 0.52
31 5 0.19
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (29 bp):
TAAAATAAAATAAAATTTAAATATTAAAA
Found at i:82868 original size:14 final size:15
Alignment explanation
Indices: 82846--82882 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
82836 AAAATTCTTG
82846 TATTA-AAAAATAA-
1 TATTATAAAAATAAC
82859 TATTATAAAAATAAC
1 TATTATAAAAATAAC
*
82874 TTTTATAAA
1 TATTATAAA
82883 TTTTATTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 5 0.24
14 8 0.38
15 8 0.38
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (15 bp):
TATTATAAAAATAAC
Found at i:83746 original size:20 final size:20
Alignment explanation
Indices: 83723--83760 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
83713 GCAACACAGA
83723 AGTCAAATTCACAACGCGAT
1 AGTCAAATTCACAACGCGAT
*
83743 AGTCAAATTCGCAACGCG
1 AGTCAAATTCACAACGCG
83761 GAATTTCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.37, C:0.26, G:0.18, T:0.18
Consensus pattern (20 bp):
AGTCAAATTCACAACGCGAT
Found at i:83785 original size:19 final size:19
Alignment explanation
Indices: 83745--83814 Score: 113
Period size: 19 Copynumber: 3.6 Consensus size: 19
83735 AACGCGATAG
*
83745 TCAAATTCGCAACGCGGAATT
1 TCAAATTCGCAA--CTGAATT
83766 TCAAATTCGCAACTGAATT
1 TCAAATTCGCAACTGAATT
83785 TCAAATTCGCAACTGAATT
1 TCAAATTCGCAACTGAATT
83804 TCAAATTCGCA
1 TCAAATTCGCA
83815 CAGATTTTAG
Statistics
Matches: 48, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
19 36 0.75
21 12 0.25
ACGTcount: A:0.36, C:0.23, G:0.13, T:0.29
Consensus pattern (19 bp):
TCAAATTCGCAACTGAATT
Done.