Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004853.1 Hibiscus syriacus cultivar Beakdansim tig00010943_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: 89524
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:11736 original size:38 final size:37
Alignment explanation
Indices: 11655--11894 Score: 133
Period size: 36 Copynumber: 6.5 Consensus size: 37
11645 TATATACACA
* * * * *
11655 TATATATTATATAGTTTGCAAATTGTTTTTGAAAATACA
1 TATATAATATATAGTTT-AAAAATATTTTTGAAAATA-T
11694 TATATAATATATAGTTTAAAACAT-TTTTTGAAAATAT
1 TATATAATATATAGTTTAAAA-ATATTTTTGAAAATAT
*
11731 GTATAT--TATATAGTTTTTAAAATATTTTTG-AAA-AT
1 -TATATAATATATAG-TTTAAAAATATTTTTGAAAATAT
* **
11766 TATATAATATATAGTTTTTGAAAA-CGTTTT-AAAATA-
1 TATATAATATATAG--TTTAAAAATATTTTTGAAAATAT
* ** ** * *
11802 TATATAATATATACTTTTGGAAA-CGTTATGAAAACATT
1 TATATAATATATA-GTTTAAAAATATTTTTGAAAATA-T
* *
11840 TATATAATATATAATTTTTAAAAACCA-TTTTGAAAATA-
1 TATATAATATAT-A-GTTTAAAAA-TATTTTTGAAAATAT
11878 TATATAATATATAGTTT
1 TATATAATATATAGTTT
11895 TTTTTAAAAC
Statistics
Matches: 166, Mismatches: 19, Indels: 35
0.75 0.09 0.16
Matches are distributed among these distances:
34 5 0.03
35 14 0.08
36 47 0.28
37 22 0.13
38 44 0.27
39 25 0.15
40 9 0.05
ACGTcount: A:0.43, C:0.04, G:0.07, T:0.45
Consensus pattern (37 bp):
TATATAATATATAGTTTAAAAATATTTTTGAAAATAT
Found at i:11777 original size:36 final size:36
Alignment explanation
Indices: 11680--11896 Score: 199
Period size: 38 Copynumber: 5.9 Consensus size: 36
11670 TTGCAAATTG
11680 TTTTTGAAAATACATATATAATATATAG--TTTAAAACA
1 TTTTTGAAAAT--ATATATAATATATAGTTTTTAAAA-A
* *
11717 TTTTTTGAAAATATGTATATTATATAGTTTTTAAAATA
1 -TTTTTGAAAATATATATAATATATAGTTTTTAAAA-A
*
11755 TTTTTGAAAAT-TATATAATATATAGTTTTTGAAAAC
1 TTTTTGAAAATATATATAATATATAGTTTTT-AAAAA
* * ** *
11791 GTTTT-AAAATATATATAATATATACTTTTGGAAAC
1 TTTTTGAAAATATATATAATATATAGTTTTTAAAAA
* * * *
11826 GTTATGAAAACATTTATATAATATATAATTTTTAAAAA
1 TTTTTG-AAA-ATATATATAATATATAGTTTTTAAAAA
*
11864 CCATTTTGAAAATATATATAATATATAGTTTTT
1 --TTTTTGAAAATATATATAATATATAGTTTTT
11897 TTTAAAACAT
Statistics
Matches: 150, Mismatches: 20, Indels: 18
0.80 0.11 0.10
Matches are distributed among these distances:
35 13 0.09
36 51 0.34
37 18 0.12
38 61 0.41
39 3 0.02
40 4 0.03
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.46
Consensus pattern (36 bp):
TTTTTGAAAATATATATAATATATAGTTTTTAAAAA
Found at i:11896 original size:38 final size:37
Alignment explanation
Indices: 11681--11922 Score: 210
Period size: 36 Copynumber: 6.5 Consensus size: 37
11671 TGCAAATTGT
11681 TTTTGAAAATACATATATAATATATAG--TTT-AAAACA
1 TTTTGAAAAT--ATATATAATATATAGTTTTTAAAAACA
* * *
11717 TTTTTTGAAAATATGTATATTATATAGTTTTTAAAATA-T
1 --TTTTGAAAATATATATAATATATAGTTTTTAAAA-ACA
* *
11756 TTTTGAAAAT-TATATAATATATAGTTTTTGAAAACG
1 TTTTGAAAATATATATAATATATAGTTTTTAAAAACA
* ** *
11792 TTTT-AAAATATATATAATATATA-CTTTTGGAAACG
1 TTTTGAAAATATATATAATATATAGTTTTTAAAAACA
* * *
11827 TTATGAAAACATTTATATAATATATAATTTTTAAAAACCA
1 TTTTG-AAA-ATATATATAATATATAGTTTTTAAAAA-CA
*
11867 TTTTGAAAATATATATAATATATAGTTTTTTTTAAAACA
1 TTTTGAAAATATATATAATATATAG--TTTTTAAAAACA
* *
11906 TTTTAAAAATTTATATA
1 TTTTGAAAATATATATA
11923 TTTTTGAAAA
Statistics
Matches: 170, Mismatches: 21, Indels: 25
0.79 0.10 0.12
Matches are distributed among these distances:
35 19 0.11
36 50 0.29
37 13 0.08
38 43 0.25
39 30 0.18
40 15 0.09
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (37 bp):
TTTTGAAAATATATATAATATATAGTTTTTAAAAACA
Found at i:13281 original size:26 final size:24
Alignment explanation
Indices: 13243--13303 Score: 61
Period size: 26 Copynumber: 2.5 Consensus size: 24
13233 GTTTTATCTT
* *
13243 TATTTTTTTATTTTACTTTTTAAA
1 TATTTTTTTATTTAACCTTTTAAA
*
13267 TATTTTTTTAAATTTAACCTTTT-AT
1 TATTTTTTT--ATTTAACCTTTTAAA
*
13292 TATTATTTTATT
1 TATTTTTTTATT
13304 ATTTCTTTCT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
23 3 0.10
24 9 0.29
25 9 0.29
26 10 0.32
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.69
Consensus pattern (24 bp):
TATTTTTTTATTTAACCTTTTAAA
Found at i:13295 original size:25 final size:25
Alignment explanation
Indices: 13242--13301 Score: 61
Period size: 24 Copynumber: 2.4 Consensus size: 25
13232 AGTTTTATCT
* *
13242 TTATTTTTTT-ATTTTACTTTTTAA
1 TTATTTTTTTAATTTAACCTTTTAA
*
13266 ATATTTTTTTAAATTTAACCTTTT-A
1 TTATTTTTTT-AATTTAACCTTTTAA
*
13291 TTATTATTTTA
1 TTATTTTTTTA
13302 TTATTTCTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
24 10 0.34
25 9 0.31
26 10 0.34
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.68
Consensus pattern (25 bp):
TTATTTTTTTAATTTAACCTTTTAA
Found at i:15089 original size:18 final size:19
Alignment explanation
Indices: 15068--15112 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
15058 ATTTAGACAT
15068 TTTGCATTTT-TTATTTTC
1 TTTGCATTTTATTATTTTC
15086 TTTGCATTTTATTATTTTC
1 TTTGCATTTTATTATTTTC
*
15105 TCTGCATT
1 TTTGCATT
15113 CACATTAACT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 10 0.40
19 15 0.60
ACGTcount: A:0.13, C:0.13, G:0.07, T:0.67
Consensus pattern (19 bp):
TTTGCATTTTATTATTTTC
Found at i:18743 original size:164 final size:164
Alignment explanation
Indices: 18501--19804 Score: 2241
Period size: 164 Copynumber: 7.9 Consensus size: 164
18491 ACCTGCCACC
*
18501 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGAG
1 AAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGAG
* *
18566 AAGGGCTATCTGCCAAAGACCCTCAAGTTCGATTACACTCATCTTCAAGGGCATAACATTTACAA
66 AAGGGCTATCTGCCAAAGACCCTCAAGTTCGATTACACTCAGCTTCAAGGGCATAACATTTACAG
18631 CATAACTCAAGGCTAGAAGGGTTATCTGTTAGCA
131 CATAACTCAAGGCTAGAAGGGTTATCTGTTAGCA
* *
18665 AAGACCTTTGAGTTCGACTACGCTTAGCTCCTAGGCACATCATTTGCAGAATAGCTTAAGTCGAG
1 AAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGAG
*
18730 AAGGGCTATCTGCCAAAGACCCTTAAGTTCGATTACACTCAGCTTCAAGGGCATAACATTTACAG
66 AAGGGCTATCTGCCAAAGACCCTCAAGTTCGATTACACTCAGCTTCAAGGGCATAACATTTACAG
18795 CATAACTCAAGGCTAGAAGGGTTATCTGTTAGCA
131 CATAACTCAAGGCTAGAAGGGTTATCTGTTAGCA
*
18829 AAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCAAG
1 AAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGAG
* * *
18894 AAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCAAGGGAATAACATTTACAG
66 AAGGGCTATCTGCCAAAGACCCTCAAGTTCGATTACACTCAGCTTCAAGGGCATAACATTTACAG
18959 CATAACTCAAGGCTAGAAGGGTTATCTGTTAGCA
131 CATAACTCAAGGCTAGAAGGGTTATCTGTTAGCA
*
18993 AAGACCTTTGAGTTCGACTACGCTCAGCTCCTAGGCACATCATTTGCAGAATAGCTTAAGTCGAG
1 AAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGAG
*
19058 AAGGGCTATCTGCCAAAGACCCTTAAGTTCGATTACACTCAGCTTCAAGGGCATAACATTTACAG
66 AAGGGCTATCTGCCAAAGACCCTCAAGTTCGATTACACTCAGCTTCAAGGGCATAACATTTACAG
19123 CATAACTCAAGGCTAGAAGGGTTATCTGTTAGCA
131 CATAACTCAAGGCTAGAAGGGTTATCTGTTAGCA
*
19157 AAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCAAG
1 AAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGAG
* *
19222 AAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCAAGGGCATAACATTTACAG
66 AAGGGCTATCTGCCAAAGACCCTCAAGTTCGATTACACTCAGCTTCAAGGGCATAACATTTACAG
19287 CATAACTCAAGGCTAGAAGGGTTATCTGTTAGCA
131 CATAACTCAAGGCTAGAAGGGTTATCTGTTAGCA
*
19321 AAGACCTTTGAGTTCGACTACGCTCAGCTCCTAGGCACATCATTTGCAGAATAGCTTAAGTCGAG
1 AAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGAG
*
19386 AAGGGCTATCTGCCAAAGACCCTTAAGTTCGATTACACTCAGCTTCAAGGGCATAACATTTACAG
66 AAGGGCTATCTGCCAAAGACCCTCAAGTTCGATTACACTCAGCTTCAAGGGCATAACATTTACAG
19451 CATAACTCAAGGCTAGAAGGGTTATCTGTTAGCA
131 CATAACTCAAGGCTAGAAGGGTTATCTGTTAGCA
*
19485 AAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCAAG
1 AAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGAG
* * * * * *
19550 AAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGAGCACATCATTTACAG
66 AAGGGCTATCTGCCAAAGACCCTCAAGTTCGATTACACTCAGCTTCAAGGGCATAACATTTACAG
* *
19615 CATAACTCAAGGCTAGAAGGGTTATCTGTGACCAA
131 CATAACTCAAGGCTAGAAGGGTTATCTGTTAGC-A
* * *
19650 AATACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATATGCAGCATAGCTTAAGTCGAG
1 AAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGAG
* * * * *
19715 AAGGGCTATCTGCCAAAGACTCC-CGAGTTCGATTACACTCAACTTCGAGGTCATATCATTTACA
66 AAGGGCTATCTGCCAAAGAC-CCTCAAGTTCGATTACACTCAGCTTCAAGGGCATAACATTTACA
* * * *
19779 ACATAACTCATGGCAAGAAAGGTTAT
130 GCATAACTCAAGGCTAGAAGGGTTAT
19805 TTGTCAATAA
Statistics
Matches: 1086, Mismatches: 52, Indels: 3
0.95 0.05 0.00
Matches are distributed among these distances:
164 943 0.87
165 141 0.13
166 2 0.00
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (164 bp):
AAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGAG
AAGGGCTATCTGCCAAAGACCCTCAAGTTCGATTACACTCAGCTTCAAGGGCATAACATTTACAG
CATAACTCAAGGCTAGAAGGGTTATCTGTTAGCA
Found at i:20447 original size:38 final size:37
Alignment explanation
Indices: 20391--20605 Score: 132
Period size: 36 Copynumber: 5.8 Consensus size: 37
20381 TTGCAAATTG
*
20391 TTTTTGAAAATACATATATAATATATAGTTTAAAACAT
1 TTTTTGAAAATA-TTATATAATATATAGTTTAAAACAT
*
20429 TTTTTGAAAATATGTATAT--TATATAGTTTTTAAA-AT
1 TTTTTGAAAATAT-TATATAATATATAG-TTTAAAACAT
*
20465 ATTTTTG-AAA-ATTATATAATATATAGTTTTTGAAA-AT
1 -TTTTTGAAAATATTATATAATATATAG--TTTAAAACAT
* * *
20502 GTTTT-AAAATA-TATATAATATATACTTTTGGAAAC--
1 TTTTTGAAAATATTATATAATATATA-GTTT-AAAACAT
* * * *
20537 GTTATGAAAACATTTATATAATATATAATTTTTAAAAACCA-
1 TTTTTGAAAATA-TTATATAATATAT-A-GTTT-AAAA-CAT
20578 -TTTTGAAAATA-TATATAATATATAGTTT
1 TTTTTGAAAATATTATATAATATATAGTTT
20606 TTTTAAAACA
Statistics
Matches: 147, Mismatches: 13, Indels: 36
0.75 0.07 0.18
Matches are distributed among these distances:
34 5 0.03
35 9 0.06
36 51 0.35
37 23 0.16
38 41 0.28
39 8 0.05
40 10 0.07
ACGTcount: A:0.44, C:0.03, G:0.07, T:0.46
Consensus pattern (37 bp):
TTTTTGAAAATATTATATAATATATAGTTTAAAACAT
Found at i:20488 original size:36 final size:37
Alignment explanation
Indices: 20365--20607 Score: 203
Period size: 38 Copynumber: 6.5 Consensus size: 37
20355 ATATATACAC
* ** * *
20365 ATATATATTATATAGTTTGCAAATTGTTTTTGAAAAT
1 ATATATAATATATAGTTTTTAAAATATTTTTGAAAAT
*
20402 ACATATATAATATATAG--TTTAAAACATTTTTTGAAAAT
1 --ATATATAATATATAGTTTTTAAAATA-TTTTTGAAAAT
* *
20440 ATGTATATTATATAGTTTTTAAAATATTTTTGAAAAT
1 ATATATAATATATAGTTTTTAAAATATTTTTGAAAAT
*
20477 -TATATAATATATAGTTTTTGAAAAT-GTTTT-AAAAT
1 ATATATAATATATAGTTTTT-AAAATATTTTTGAAAAT
* ** ** *
20512 ATATATAATATATACTTTTGGAAA-CGTTATGAAAACAT
1 ATATATAATATATAGTTTTTAAAATATTTTTG-AAA-AT
* * *
20550 TTATATAATATATAATTTTTAAAA-ACCATTTTGAAAAT
1 ATATATAATATATAGTTTTTAAAATA--TTTTTGAAAAT
20588 ATATATAATATATAGTTTTT
1 ATATATAATATATAGTTTTT
20608 TTAAAACATT
Statistics
Matches: 168, Mismatches: 25, Indels: 23
0.78 0.12 0.11
Matches are distributed among these distances:
35 12 0.07
36 51 0.30
37 23 0.14
38 61 0.36
39 17 0.10
40 4 0.02
ACGTcount: A:0.43, C:0.03, G:0.07, T:0.46
Consensus pattern (37 bp):
ATATATAATATATAGTTTTTAAAATATTTTTGAAAAT
Found at i:20513 original size:25 final size:24
Alignment explanation
Indices: 20454--20515 Score: 65
Period size: 25 Copynumber: 2.6 Consensus size: 24
20444 ATATTATATA
*
20454 GTTTTTAAA-ATATTTTTGAAAAT
1 GTTTTAAAATATATTTTTGAAAAT
* *
20477 -TATATAATATATAGTTTTTGAAAAT
1 GT-TTTAAAATATA-TTTTTGAAAAT
20502 GTTTTAAAATATAT
1 GTTTTAAAATATAT
20516 ATAATATATA
Statistics
Matches: 30, Mismatches: 5, Indels: 7
0.71 0.12 0.17
Matches are distributed among these distances:
22 1 0.03
23 4 0.13
24 4 0.13
25 20 0.67
26 1 0.03
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (24 bp):
GTTTTAAAATATATTTTTGAAAAT
Found at i:20607 original size:38 final size:37
Alignment explanation
Indices: 20392--20632 Score: 208
Period size: 38 Copynumber: 6.5 Consensus size: 37
20382 TGCAAATTGT
20392 TTTTGAAAATACATATATAATATATAG--TTT-AAAACA
1 TTTTGAAAAT--ATATATAATATATAGTTTTTAAAAACA
* * *
20428 TTTTTTGAAAATATGTATATTATATAGTTTTTAAAATA-T
1 --TTTTGAAAATATATATAATATATAGTTTTTAAAA-ACA
* **
20467 TTTTGAAAAT-TATATAATATATAGTTTTTGAAAATG
1 TTTTGAAAATATATATAATATATAGTTTTTAAAAACA
* ** *
20503 TTTT-AAAATATATATAATATATA-CTTTTGGAAACG
1 TTTTGAAAATATATATAATATATAGTTTTTAAAAACA
* * *
20538 TTATGAAAACATTTATATAATATATAATTTTTAAAAACCA
1 TTTTG-AAA-ATATATATAATATATAGTTTTTAAAAA-CA
*
20578 TTTTGAAAATATATATAATATATAGTTTTTTTAAAACA
1 TTTTGAAAATATATATAATATATAG-TTTTTAAAAACA
* *
20616 TTTTAAAAATTTATATA
1 TTTTGAAAATATATATA
20633 TTTTTGAAAA
Statistics
Matches: 169, Mismatches: 22, Indels: 24
0.79 0.10 0.11
Matches are distributed among these distances:
35 18 0.11
36 50 0.30
37 13 0.08
38 60 0.36
39 22 0.13
40 6 0.04
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.46
Consensus pattern (37 bp):
TTTTGAAAATATATATAATATATAGTTTTTAAAAACA
Found at i:22152 original size:6 final size:6
Alignment explanation
Indices: 22141--22177 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
22131 TCGGATCGAA
* *
22141 TAATTT TAATTT TAATTT TAATTT AAATTC TAATTT T
1 TAATTT TAATTT TAATTT TAATTT TAATTT TAATTT T
22178 CGCAATTAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (6 bp):
TAATTT
Found at i:22512 original size:17 final size:18
Alignment explanation
Indices: 22492--22525 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
22482 TTTAATTTAA
22492 TATTA-ATTAATATTTTT
1 TATTATATTAATATTTTT
*
22509 TATTATATTACTATTTT
1 TATTATATTAATATTTT
22526 ATTTCTCGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (18 bp):
TATTATATTAATATTTTT
Found at i:24354 original size:19 final size:18
Alignment explanation
Indices: 24315--24354 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
24305 AAATTTTAAA
* *
24315 TATTTTATATTAATAATT
1 TATTTTATATTAAAAAGT
24333 TATTTTATATTTAAAAAGT
1 TATTTTATA-TTAAAAAGT
24352 TAT
1 TAT
24355 AATTTTATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (18 bp):
TATTTTATATTAAAAAGT
Found at i:41354 original size:23 final size:25
Alignment explanation
Indices: 41314--41363 Score: 68
Period size: 23 Copynumber: 2.1 Consensus size: 25
41304 ATCGATGATT
*
41314 TAATTTTACGTTCTCTAATATTTTA
1 TAATTTTACGATCTCTAATATTTTA
*
41339 TAATTTTAC-ATC-CTAATTTTTTA
1 TAATTTTACGATCTCTAATATTTTA
41362 TA
1 TA
41364 TAATTTATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 12 0.52
24 2 0.09
25 9 0.39
ACGTcount: A:0.30, C:0.12, G:0.02, T:0.56
Consensus pattern (25 bp):
TAATTTTACGATCTCTAATATTTTA
Found at i:42494 original size:2 final size:2
Alignment explanation
Indices: 42482--42519 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
42472 TTAATTCTAG
42482 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
42520 CAAAACCTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:46339 original size:22 final size:22
Alignment explanation
Indices: 46297--46339 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
46287 TTTACTTTAT
* *
46297 TATATTTTAGTCATTTTAATTC
1 TATATTTTAATCATTTGAATTC
46319 TATATTTTAAT-ATTCTGAATT
1 TATATTTTAATCATT-TGAATT
46340 ATTTTATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 3 0.17
22 15 0.83
ACGTcount: A:0.30, C:0.07, G:0.05, T:0.58
Consensus pattern (22 bp):
TATATTTTAATCATTTGAATTC
Found at i:50076 original size:21 final size:21
Alignment explanation
Indices: 50039--50079 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
50029 ATTATCCAAT
*
50039 AAACTTGACATCTATAACAAC
1 AAACTTGAAATCTATAACAAC
50060 AAACTTGAAATGC-ATAACAA
1 AAACTTGAAAT-CTATAACAA
50080 TAAATCAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.51, C:0.20, G:0.07, T:0.22
Consensus pattern (21 bp):
AAACTTGAAATCTATAACAAC
Found at i:52672 original size:30 final size:30
Alignment explanation
Indices: 52637--52721 Score: 93
Period size: 30 Copynumber: 2.8 Consensus size: 30
52627 TTAAAATGAC
52637 AAAAATAGAAACTTAAAAGG-CTAAAATAGT
1 AAAAATAGAAA-TTAAAAGGACTAAAATAGT
* * *
52667 GAAAATATAAATTTAAAGGACTAAAATAGT
1 AAAAATAGAAATTAAAAGGACTAAAATAGT
* *
52697 AAAAACA-AAATTTTAAAGGACTAAA
1 AAAAATAGAAA-TTAAAAGGACTAAA
52722 CAATACATAA
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
29 10 0.21
30 38 0.79
ACGTcount: A:0.60, C:0.06, G:0.12, T:0.22
Consensus pattern (30 bp):
AAAAATAGAAATTAAAAGGACTAAAATAGT
Found at i:54008 original size:131 final size:129
Alignment explanation
Indices: 53729--54027 Score: 431
Period size: 131 Copynumber: 2.3 Consensus size: 129
53719 TGGTCGTCTA
*
53729 AGGGTTGACACGGCTCCTACGTGATGAGGAAATCAGGTCGGGTGATGACACGATTCCTACGCGAT
1 AGGGTTGACACGGCTCCTACGTGATGAGGAGATCAGGTCGGGTGATGACACGATTCCTACGCGAT
** *
53794 GAGGACGACAGGTCATCTAAGGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCT
66 GAGGACGACAGACCATCTAAGGGTGATAACACGATTCCTACGTGATGAGGACGGCTGGTTATCT
* * ** *
53858 GGGGTTGACACGGCGCCTACGTGATGAGGAGATTTGGTCGAGG-GATGACAC-AGTTCCTACGTG
1 AGGGTTGACACGGCTCCTACGTGATGAGGAGATCAGGTCG-GGTGATGACACGA-TTCCTACGCG
*
53921 ATGAGGACGACAGACCATCATTAGGGATGATAACACGATTCCTACGTGATGAGGACGGCTGGTTA
64 ATGAGGACGACAGACCATC-TAAGGG-TGATAACACGATTCCTACGTGATGAGGACGGCTGGTTA
53986 TCT
127 TCT
* **
53989 ATGGTTGACACAACTCCTACGTGATGAGGAGATCAGGTC
1 AGGGTTGACACGGCTCCTACGTGATGAGGAGATCAGGTC
54028 AGGTTGGATA
Statistics
Matches: 149, Mismatches: 17, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
128 1 0.01
129 69 0.46
130 7 0.05
131 72 0.48
ACGTcount: A:0.25, C:0.20, G:0.32, T:0.23
Consensus pattern (129 bp):
AGGGTTGACACGGCTCCTACGTGATGAGGAGATCAGGTCGGGTGATGACACGATTCCTACGCGAT
GAGGACGACAGACCATCTAAGGGTGATAACACGATTCCTACGTGATGAGGACGGCTGGTTATCT
Found at i:54141 original size:66 final size:66
Alignment explanation
Indices: 54035--54192 Score: 174
Period size: 66 Copynumber: 2.4 Consensus size: 66
54025 GTCAGGTTGG
* *** * * *
54035 ATATCCTTCATCGTGAAGTTGAAATCGCAGATGGTTCCTTCATTC-TGAAGTTGAACTTTAAATT
1 ATATCCTTCGTCGTGAAGTTGAAATCGCAGATGACCCCTTC-GTCGTGAAGTTGAACATCAAATT
54099 GA
65 GA
** * * *
54101 ATATCCTTCGTCGTGAAGTTGAAATCGTGGATGACCCCTTCGTCGTGAATTTGAGCATCGAATTG
1 ATATCCTTCGTCGTGAAGTTGAAATCGCAGATGACCCCTTCGTCGTGAAGTTGAACATCAAATTG
*
54166 G
66 A
*
54167 ATATCCTTTGTCGTGAAGTTGAAATC
1 ATATCCTTCGTCGTGAAGTTGAAATC
54193 CAATCTAAAG
Statistics
Matches: 77, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
65 2 0.03
66 75 0.97
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.35
Consensus pattern (66 bp):
ATATCCTTCGTCGTGAAGTTGAAATCGCAGATGACCCCTTCGTCGTGAAGTTGAACATCAAATTG
A
Found at i:54259 original size:124 final size:123
Alignment explanation
Indices: 54101--54694 Score: 474
Period size: 121 Copynumber: 4.8 Consensus size: 123
54091 TTTAAATTGA
* * * *
54101 ATATCCTTCGTCGTGAAGTTGAAATCGTGGATGACCCCTTCGTCGTGAATTTGAGCATCGAATTG
1 ATATCCTTCGTCGTGAAGTTGAAATCGTGGATGACCCCTTTGTCGTGAAGTTGAGCCTTGAATTG
*
54166 GATATCCTTTGTCGTGAAGTTGAAATCCAATCTAAAGATG-AATGTTGCTGGTG-GACACG
66 GATATCCTTTGTCGTGAAGTTGAAATCCAATCT--AGATGCAATGCTGCTGGTGAG-CACG
* *
54225 ATATCCTTCGTCGTGAAGTTGAAATCGTGGATGACCCCTTTGTTGTCAAGTTGAGCCTTGAATTG
1 ATATCCTTCGTCGTGAAGTTGAAATCGTGGATGACCCCTTTGTCGTGAAGTTGAGCCTTGAATTG
* * * * *
54290 GATATCCTTTGTCGTGAAGTTGAAGTCCAA--TGGTTGCATTGCTGCTTGTGAGCACG
66 GATATCCTTTGTCGTGAAGTTGAAATCCAATCTAGATGCAATGCTGCTGGTGAGCACG
* * * *
54346 ATATTCATCGTCGTGAAGTTAAAATCGTGGATGACCCATTTGTCGTGAAGTTGAGCCTTGAATTG
1 ATATCCTTCGTCGTGAAGTTGAAATCGTGGATGACCCCTTTGTCGTGAAGTTGAGCCTTGAATTG
* * * ** * * *
54411 AATATCCTTCT-TTGTGAAGTTGAAATCCAATCTTG-TGCAAGTTG-TATTGTTTCAAGTC-CA
66 GATATCCTT-TGTCGTGAAGTTGAAATCCAATCTAGATGCAA--TGCTGCTG-GT-GAG-CACG
* * *
54471 ATATCCTTCGCCGTGAAGTTGAAATTAGCTCTGAATGAAACTGGGAAGCCCTTTCG-CTGTGAAG
1 ATATCCTTCGTCGTGAAGTTG-AA--A--TC-G--TG-GA-T--G-ACCCCTTT-GTC-GTGAAG
* * *
54535 TTGAGCTTTGAATTGGATATCCTTCGTTGTGAAGTTGAAAT-C---C-A-ATGC--TGCT--T-G
51 TTGAGCCTTGAATTGGATATCCTTTGTCGTGAAGTTGAAATCCAATCTAGATGCAATGCTGCTGG
54589 TGAGCACG
116 TGAGCACG
* * * * *
54597 ATACCCTTCATCGTGAAGTTAAAATCGTGGATGACCCATTCG-CTGTGAAGTTGAGCCTTGAATT
1 ATATCCTTCGTCGTGAAGTTGAAATCGTGGATGACCCCTTTGTC-GTGAAGTTGAGCCTTGAATT
* * *
54661 GGATATCATTCGTCGTGAAGTTAAAATCCAATCT
65 GGATATCCTTTGTCGTGAAGTTGAAATCCAATCT
54695 TGAGTAAATT
Statistics
Matches: 381, Mismatches: 55, Indels: 75
0.75 0.11 0.15
Matches are distributed among these distances:
112 46 0.12
113 6 0.02
114 1 0.00
116 2 0.01
117 1 0.00
118 2 0.01
120 4 0.01
121 100 0.26
122 7 0.02
123 5 0.01
124 91 0.24
125 23 0.06
126 23 0.06
127 1 0.00
128 1 0.00
129 1 0.00
130 4 0.01
131 2 0.01
133 2 0.01
134 4 0.01
135 2 0.01
137 1 0.00
138 8 0.02
139 44 0.12
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.33
Consensus pattern (123 bp):
ATATCCTTCGTCGTGAAGTTGAAATCGTGGATGACCCCTTTGTCGTGAAGTTGAGCCTTGAATTG
GATATCCTTTGTCGTGAAGTTGAAATCCAATCTAGATGCAATGCTGCTGGTGAGCACG
Found at i:54805 original size:34 final size:34
Alignment explanation
Indices: 54767--54863 Score: 82
Period size: 28 Copynumber: 3.1 Consensus size: 34
54757 TGAAACTGAA
54767 AAGTTGTTTGTTGAGTCCAATATCCTTCGTTGTG
1 AAGTTGTTTGTTGAGTCCAATATCCTTCGTTGTG
*** * * * *
54801 AAGTTG-AAATTGACTCTAA-ATGC-T-G--G-A
1 AAGTTGTTTGTTGAGTCCAATATCCTTCGTTGTG
54828 AAGTTGTTTGTTGAGTCCAATATCCTTCGTTGTG
1 AAGTTGTTTGTTGAGTCCAATATCCTTCGTTGTG
54862 AA
1 AA
54864 ATCGAAATTG
Statistics
Matches: 42, Mismatches: 14, Indels: 14
0.60 0.20 0.20
Matches are distributed among these distances:
27 6 0.14
28 9 0.21
29 3 0.07
30 2 0.05
31 2 0.05
32 3 0.07
33 9 0.21
34 8 0.19
ACGTcount: A:0.25, C:0.13, G:0.23, T:0.39
Consensus pattern (34 bp):
AAGTTGTTTGTTGAGTCCAATATCCTTCGTTGTG
Found at i:54851 original size:61 final size:61
Alignment explanation
Indices: 54715--54891 Score: 228
Period size: 61 Copynumber: 2.8 Consensus size: 61
54705 GCGTGGCTTC
* * ** * *
54715 GAGTCCAATTTCTTTCACTGTGAAGTTGAAATTGACTCTGATTGAAACTGAAAAGTTGTTTGTT
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTAAATG---CTGAAAAGTTGTTTGTT
*
54779 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTAAATGCTGGAAAGTTGTTTGTT
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTAAATGCTGAAAAGTTGTTTGTT
* * *
54840 GAGTCCAATATCCTTCGTTGTGAAATCGAAATTGACTCTAAAAGCTGCAAAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTAAATGCTG-AAAA
54892 TATTATGTAT
Statistics
Matches: 101, Mismatches: 11, Indels: 4
0.87 0.09 0.03
Matches are distributed among these distances:
61 60 0.59
62 3 0.03
64 38 0.38
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.35
Consensus pattern (61 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTAAATGCTGAAAAGTTGTTTGTT
Found at i:57862 original size:103 final size:102
Alignment explanation
Indices: 57638--57854 Score: 425
Period size: 103 Copynumber: 2.1 Consensus size: 102
57628 GTCGAGGGTC
57638 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTTGGTGAGACACATACT
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTTGGTGAGACACATACT
57703 TGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
57740 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGT-TGGTGAGACACATAC
57805 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
65 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
57843 TATGTGGTCCTT
1 TATGTGGTCCTT
57855 ATGGACATTA
Statistics
Matches: 114, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
102 49 0.43
103 65 0.57
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.37
Consensus pattern (102 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTTGGTGAGACACATACT
TGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
Found at i:57920 original size:23 final size:23
Alignment explanation
Indices: 57866--57938 Score: 87
Period size: 23 Copynumber: 3.3 Consensus size: 23
57856 TGGACATTAT
*
57866 TATATGGCACTACGGTGCAACTC
1 TATATGGCACTACGGTGCAATTC
***
57889 TACGCGGCACTACGGTGCAATTC
1 TATATGGCACTACGGTGCAATTC
*
57912 TATATGGCACTTCGGTGC-ATT-
1 TATATGGCACTACGGTGCAATTC
57933 TATATG
1 TATATG
57939 AGCTGTGGTG
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
21 6 0.14
22 3 0.07
23 33 0.79
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.30
Consensus pattern (23 bp):
TATATGGCACTACGGTGCAATTC
Found at i:62147 original size:17 final size:16
Alignment explanation
Indices: 62125--62158 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
62115 ATAGTAATCC
*
62125 TACCCACACATGCTTTT
1 TACCCACA-ATGATTTT
62142 TACCCACAATGATTTT
1 TACCCACAATGATTTT
62158 T
1 T
62159 CAAGAAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.26, C:0.29, G:0.06, T:0.38
Consensus pattern (16 bp):
TACCCACAATGATTTT
Found at i:63370 original size:30 final size:30
Alignment explanation
Indices: 63314--63370 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
63304 AGAGATCTAG
*
63314 CAAAAACATGAACTTAAAGTATTAAAATGA
1 CAAAAACATGAACTTAAAGTACTAAAATGA
63344 CAAAAACA-GAAACTTAAAAG-ACTAAAA
1 CAAAAACATG-AACTT-AAAGTACTAAAA
63371 CAGTGAAAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
29 1 0.04
30 19 0.79
31 4 0.17
ACGTcount: A:0.61, C:0.12, G:0.09, T:0.18
Consensus pattern (30 bp):
CAAAAACATGAACTTAAAGTACTAAAATGA
Found at i:63415 original size:29 final size:30
Alignment explanation
Indices: 63345--63429 Score: 109
Period size: 30 Copynumber: 2.8 Consensus size: 30
63335 TTAAAATGAC
* *
63345 AAAAACAGAAACTTAAAAGACTAAAACAGT
1 AAAAACAGAAATTTAAAGGACTAAAACAGT
* * *
63375 GAAAACATAAATTTAAAGGACTAAAATAGT
1 AAAAACAGAAATTTAAAGGACTAAAACAGT
63405 AAAAACA-AAATTTTAAAGGACTAAA
1 AAAAACAGAAA-TTTAAAGGACTAAA
63430 CAATACATAA
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
29 3 0.06
30 45 0.94
ACGTcount: A:0.61, C:0.09, G:0.11, T:0.19
Consensus pattern (30 bp):
AAAAACAGAAATTTAAAGGACTAAAACAGT
Found at i:66031 original size:41 final size:42
Alignment explanation
Indices: 65986--66081 Score: 124
Period size: 41 Copynumber: 2.3 Consensus size: 42
65976 GTTTTCAAAC
*
65986 AAAACGCCACTAACGGTTC-AACATATTGCGGCATTT-TTTTA
1 AAAACGCCACTAACGGTTCGAAC-TATTGCGGCATTTGTTTCA
* * * *
66027 AAAACACCACAAATGTTTCGAACTATTGCGGCATTTGTTTCA
1 AAAACGCCACTAACGGTTCGAACTATTGCGGCATTTGTTTCA
66069 AAAACGCCACTAA
1 AAAACGCCACTAA
66082 AGAATGATTC
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
41 28 0.61
42 18 0.39
ACGTcount: A:0.35, C:0.23, G:0.14, T:0.28
Consensus pattern (42 bp):
AAAACGCCACTAACGGTTCGAACTATTGCGGCATTTGTTTCA
Found at i:66183 original size:41 final size:41
Alignment explanation
Indices: 66138--66280 Score: 114
Period size: 41 Copynumber: 3.5 Consensus size: 41
66128 TAGGTTTTAG
66138 CAGCGTTTGTCTAAAAACGCTACAATATATGTACCCTATTA
1 CAGCGTTTGTCTAAAAACGCTACAATATATGTACCCTATTA
* * * * ** *
66179 CAGCGTTTGTTTAAAAACAC--CACTA-AAGTACTAGATTTTA
1 CAGCGTTTGTCTAAAAACGCTACAATATATGTAC--CCTATTA
* * *
66219 GCGGCGTTTGTCTAAAAATG-TCACAATATATGTACCCTATTT
1 -CAGCGTTTGTCTAAAAACGCT-ACAATATATGTACCCTATTA
* *
66261 CGGCGTTTGTTTAAAAACGC
1 CAGCGTTTGTCTAAAAACGC
66281 CACTAAAGAA
Statistics
Matches: 75, Mismatches: 19, Indels: 15
0.69 0.17 0.14
Matches are distributed among these distances:
38 5 0.07
39 4 0.05
40 4 0.05
41 50 0.67
42 3 0.04
43 4 0.05
44 5 0.07
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.33
Consensus pattern (41 bp):
CAGCGTTTGTCTAAAAACGCTACAATATATGTACCCTATTA
Found at i:66206 original size:82 final size:82
Alignment explanation
Indices: 66102--66288 Score: 286
Period size: 82 Copynumber: 2.3 Consensus size: 82
66092 TTTTGCGGCA
* * *
66102 TTTGTTTAGAAATGCCACTAAAGTACTAGGTTTTAGCAGCGTTTGTCTAAAAACG-CTACAATAT
1 TTTGTTTAAAAACGCCACTAAAGTACTAGATTTTAGCAGCGTTTGTCTAAAAACGTC-ACAATAT
66166 ATGTACCCTATTACAGCG
65 ATGTACCCTATTACAGCG
* * *
66184 TTTGTTTAAAAACACCACTAAAGTACTAGATTTTAGCGGCGTTTGTCTAAAAATGTCACAATATA
1 TTTGTTTAAAAACGCCACTAAAGTACTAGATTTTAGCAGCGTTTGTCTAAAAACGTCACAATATA
* *
66249 TGTACCCTATTTCGGCG
66 TGTACCCTATTACAGCG
66266 TTTGTTTAAAAACGCCACTAAAG
1 TTTGTTTAAAAACGCCACTAAAG
66289 AATCATTCTT
Statistics
Matches: 95, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
82 94 0.99
83 1 0.01
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (82 bp):
TTTGTTTAAAAACGCCACTAAAGTACTAGATTTTAGCAGCGTTTGTCTAAAAACGTCACAATATA
TGTACCCTATTACAGCG
Found at i:66267 original size:123 final size:123
Alignment explanation
Indices: 66140--66411 Score: 296
Period size: 123 Copynumber: 2.2 Consensus size: 123
66130 GGTTTTAGCA
* * *
66140 GCGTTTGTCTAAAAACGCTAC-AATA-TATGTACCCTATTACAGCGTTTGTTTAAAAACACCACT
1 GCGTTTGTCTAAAAACGCCACTAA-AGAAT-CACCCTATTACAGCGTTTGTTTAAAAACACCACT
* ** * *
66203 AAAGTACTAGATTTTAGCGGCGTTTGTCTAAAAATGTCACAATATATGTACCCTATTTCG
64 AAAGTACTAGATTTTAGCGACACTTGTCTAAAAATGCCACAATATATATACCCTATTTCG
* ** * ** * *
66263 GCGTTTGTTTAAAAACGCCACTAAAGAATCATTCTTTTGTAGCGTTTGTTTAGAAACGCCACTAA
1 GCGTTTGTCTAAAAACGCCACTAAAGAATCACCCTATTACAGCGTTTGTTTAAAAACACCACTAA
* * * *
66328 AGTACTGGGTTTTAGCGACACTTGTCTAAAAATGCCACAATATATATACCCTATTGCA
66 AGTACTAGATTTTAGCGACACTTGTCTAAAAATGCCACAATATATATACCCTATTTCG
** * *
66386 GTATTTATTTAAAAACGCCACTAAAG
1 GCGTTTGTCTAAAAACGCCACTAAAG
66412 TACTTATATG
Statistics
Matches: 124, Mismatches: 23, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
123 120 0.97
124 4 0.03
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.33
Consensus pattern (123 bp):
GCGTTTGTCTAAAAACGCCACTAAAGAATCACCCTATTACAGCGTTTGTTTAAAAACACCACTAA
AGTACTAGATTTTAGCGACACTTGTCTAAAAATGCCACAATATATATACCCTATTTCG
Found at i:68920 original size:43 final size:43
Alignment explanation
Indices: 68852--68959 Score: 155
Period size: 43 Copynumber: 2.5 Consensus size: 43
68842 GCAAAAATGA
* * *
68852 TAAGGTCTTATCCTTGCACATAGCAAA-AGAGTCTGGGGAAACTG
1 TAAGG-CTTACCCTTGCACACAGCAAAGAGA-CCTGGGGAAACTG
*
68896 TAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGAAACTG
1 TAAGGCTTACCCTTGCACACAGCAAAGAGACCTGGGGAAACTG
68939 TAAGGCTTACCCTTGCACACA
1 TAAGGCTTACCCTTGCACACA
68960 AGTAAGGCTT
Statistics
Matches: 59, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
43 52 0.88
44 7 0.12
ACGTcount: A:0.31, C:0.24, G:0.24, T:0.21
Consensus pattern (43 bp):
TAAGGCTTACCCTTGCACACAGCAAAGAGACCTGGGGAAACTG
Found at i:68968 original size:23 final size:23
Alignment explanation
Indices: 68938--68983 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
68928 TGGGGAAACT
68938 GTAAGGCTTACCCTTGCACACAA
1 GTAAGGCTTACCCTTGCACACAA
68961 GTAAGGCTTACCCTTGCACACAA
1 GTAAGGCTTACCCTTGCACACAA
68984 CAAAGGGACC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.30, C:0.30, G:0.17, T:0.22
Consensus pattern (23 bp):
GTAAGGCTTACCCTTGCACACAA
Found at i:68989 original size:23 final size:23
Alignment explanation
Indices: 68940--68989 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
68930 GGGAAACTGT
**
68940 AAGGCTTACCCTTGCACACAAGT
1 AAGGCTTACCCTTGCACACAACA
68963 AAGGCTTACCCTTGCACACAACA
1 AAGGCTTACCCTTGCACACAACA
68986 AAGG
1 AAGG
68990 GACCTGGGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.34, C:0.30, G:0.18, T:0.18
Consensus pattern (23 bp):
AAGGCTTACCCTTGCACACAACA
Found at i:69020 original size:42 final size:42
Alignment explanation
Indices: 68961--69163 Score: 354
Period size: 42 Copynumber: 4.8 Consensus size: 42
68951 TTGCACACAA
68961 GTAAGGCTTACCCTTGCACACAACAAAGGGACCTGGGAAACT
1 GTAAGGCTTACCCTTGCACACAACAAAGGGACCTGGGAAACT
*
69003 GTAAGGCTTACCCTTGCACA-AAGCAAAGGGACCTGGGGAACT
1 GTAAGGCTTACCCTTGCACACAA-CAAAGGGACCTGGGAAACT
69045 GTAAGGCTTACCCTTGCACACAACAAAGGGACCTGGGAAACT
1 GTAAGGCTTACCCTTGCACACAACAAAGGGACCTGGGAAACT
*
69087 GTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGAAACT
1 GTAAGGCTTACCCTTGCACACAACAAAGGGACCTGGGAAACT
* *
69129 GTAAGGCTTACCCTTGCACACAGCAAAGGAACCTG
1 GTAAGGCTTACCCTTGCACACAACAAAGGGACCTG
69164 CTGTAACGGT
Statistics
Matches: 155, Mismatches: 4, Indels: 4
0.95 0.02 0.02
Matches are distributed among these distances:
41 2 0.01
42 151 0.97
43 2 0.01
ACGTcount: A:0.32, C:0.26, G:0.25, T:0.17
Consensus pattern (42 bp):
GTAAGGCTTACCCTTGCACACAACAAAGGGACCTGGGAAACT
Found at i:78210 original size:19 final size:19
Alignment explanation
Indices: 78181--78233 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
78171 AATATTAGAA
*
78181 AATTATAAATATTACATTACT
1 AATT-TAAATATTACAATA-T
*
78202 -ATTTAAATATACACAATAT
1 AATTTAAATAT-TACAATAT
78221 AATTTAAATATTA
1 AATTTAAATATTA
78234 AACTAATATA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
19 9 0.33
20 18 0.67
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.42
Consensus pattern (19 bp):
AATTTAAATATTACAATAT
Found at i:78244 original size:22 final size:20
Alignment explanation
Indices: 78202--78244 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 20
78192 TTACATTACT
*
78202 ATTTAAATATACACAATATA
1 ATTTAAATATAAACAATATA
78222 ATTTAAATATTAAACTAATATA
1 ATTTAAATA-TAAAC-AATATA
78244 A
1 A
78245 AATAAAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 9 0.45
21 4 0.20
22 7 0.35
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (20 bp):
ATTTAAATATAAACAATATA
Found at i:78519 original size:18 final size:18
Alignment explanation
Indices: 78477--78520 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
78467 TAAAATATAA
*
78477 AAATAATTTTTTTTGCTC
1 AAATAATATTTTTTGCTC
*
78495 TAATAATATTTTTT-CTC
1 AAATAATATTTTTTGCTC
78512 AAACTAATA
1 AAA-TAATA
78521 ATAAAATGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 5 0.23
18 17 0.77
ACGTcount: A:0.36, C:0.11, G:0.02, T:0.50
Consensus pattern (18 bp):
AAATAATATTTTTTGCTC
Done.