Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007305.1 Hibiscus syriacus cultivar Beakdansim tig00019458_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: 59631
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.35
Found at i:702 original size:30 final size:30
Alignment explanation
Indices: 658--753 Score: 111
Period size: 30 Copynumber: 3.2 Consensus size: 30
648 GCGGTGACCA
* *
658 GAGCGTCGATAGGAGACGGATTAGCAACCG
1 GAGCGGCGATAGGAGACGGATTGGCAACCG
* *
688 GAGCGGCGACAGGAGACGGATTGGCAACCA
1 GAGCGGCGATAGGAGACGGATTGGCAACCG
* * * *
718 GAGGGGTGATAGGCGACGAATTGGCAACCG
1 GAGCGGCGATAGGAGACGGATTGGCAACCG
*
748 TAGCGG
1 GAGCGG
754 TGGCCGACCA
Statistics
Matches: 54, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 54 1.00
ACGTcount: A:0.28, C:0.20, G:0.41, T:0.11
Consensus pattern (30 bp):
GAGCGGCGATAGGAGACGGATTGGCAACCG
Found at i:1109 original size:15 final size:15
Alignment explanation
Indices: 1089--1126 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
1079 ATCCCTAACT
1089 TTTAATTCTTTCTAA
1 TTTAATTCTTTCTAA
*
1104 TTTAATCCTTTCTAA
1 TTTAATTCTTTCTAA
1119 TTTGAATT
1 TTT-AATT
1127 TTCTTTATTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 17 0.85
16 3 0.15
ACGTcount: A:0.26, C:0.13, G:0.03, T:0.58
Consensus pattern (15 bp):
TTTAATTCTTTCTAA
Found at i:4173 original size:65 final size:65
Alignment explanation
Indices: 4102--4258 Score: 210
Period size: 65 Copynumber: 2.4 Consensus size: 65
4092 CACACCCATT
* *
4102 TCGAATGCATTTTGTGTACCAATGCACA-ATCCATGCATCGATGCACTCTTGAATATTTTGAAAC
1 TCGAATGCATTTTGTGTACCAATGCACAGA-CCATGCATCAATGCACTCCTGAATATTTTGAAAC
4166 A
65 A
* *
4167 TCGAATGCATTTTGTGTA-CAGATGCACAGACCATGCATCAATGCACTCCTGACTTTTTTGAAAC
1 TCGAATGCATTTTGTGTACCA-ATGCACAGACCATGCATCAATGCACTCCTGAATATTTTGAAAC
4231 A
65 A
* * * *
4232 TCGAATGTAATTAGTGTACCGATGCAC
1 TCGAATGCATTTTGTGTACCAATGCAC
4259 CCCTAGTGTA
Statistics
Matches: 81, Mismatches: 8, Indels: 6
0.85 0.08 0.06
Matches are distributed among these distances:
64 2 0.02
65 77 0.95
66 2 0.02
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.31
Consensus pattern (65 bp):
TCGAATGCATTTTGTGTACCAATGCACAGACCATGCATCAATGCACTCCTGAATATTTTGAAACA
Found at i:8748 original size:44 final size:43
Alignment explanation
Indices: 8666--8761 Score: 131
Period size: 44 Copynumber: 2.2 Consensus size: 43
8656 TTATGCACTA
* * *
8666 TGCATCGATACACTAGACAGTGTATCGATGCATCCCTTGAATG
1 TGCATCGATACACCAGACAGTGCACCGATGCATCCCTTGAATG
*
8709 TGCATCGATACACCATGA-AGGTGCACCGATGCATTCCTTGAATG
1 TGCATCGATACACCA-GACA-GTGCACCGATGCATCCCTTGAATG
8753 TGCATCGAT
1 TGCATCGAT
8762 GCACTCTGTT
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
43 15 0.32
44 32 0.68
ACGTcount: A:0.27, C:0.24, G:0.22, T:0.27
Consensus pattern (43 bp):
TGCATCGATACACCAGACAGTGCACCGATGCATCCCTTGAATG
Found at i:8755 original size:23 final size:22
Alignment explanation
Indices: 8689--8764 Score: 91
Period size: 23 Copynumber: 3.4 Consensus size: 22
8679 TAGACAGTGT
8689 ATCGATGCATCCCTTGAATGTGC
1 ATCGATGCAT-CCTTGAATGTGC
* * *
8712 ATCGATACA-CCATGAAGGTGC
1 ATCGATGCATCCTTGAATGTGC
*
8733 ACCGATGCATTCCTTGAATGTGC
1 ATCGATGCA-TCCTTGAATGTGC
8756 ATCGATGCA
1 ATCGATGCA
8765 CTCTGTTGTA
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
21 17 0.40
23 26 0.60
ACGTcount: A:0.26, C:0.25, G:0.22, T:0.26
Consensus pattern (22 bp):
ATCGATGCATCCTTGAATGTGC
Found at i:10696 original size:8 final size:8
Alignment explanation
Indices: 10683--10730 Score: 53
Period size: 8 Copynumber: 5.8 Consensus size: 8
10673 TTGGATTGAT
10683 ATGTTTGG
1 ATGTTTGG
10691 ATGTTTGG
1 ATGTTTGG
*
10699 ATGTTTGA
1 ATGTTTGG
10707 ATTTGTTTTGG
1 A--TG-TTTGG
10718 ATG-TTGG
1 ATGTTTGG
10725 ATGTTT
1 ATGTTT
10731 AACTTGAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
7 7 0.21
8 18 0.53
9 2 0.06
10 2 0.06
11 5 0.15
ACGTcount: A:0.15, C:0.00, G:0.31, T:0.54
Consensus pattern (8 bp):
ATGTTTGG
Found at i:11392 original size:65 final size:65
Alignment explanation
Indices: 11318--11454 Score: 222
Period size: 65 Copynumber: 2.1 Consensus size: 65
11308 CACACCCATT
*
11318 TCGAATGCATTTTGTGTACCGATGCACA-ATCCATGCATCGATGCACTCTTGAATATTTTGAAAC
1 TCGAATGCATTTTGTGTACCGATGCACATA-CCATGCATCGATGCACTCCTGAATATTTTGAAAC
11382 A
65 A
** *
11383 TCGAATGCATTTTGTGTACCGATGCACATACCATGCATCGATGCACTCCTGGCTTTTTTGAAACA
1 TCGAATGCATTTTGTGTACCGATGCACATACCATGCATCGATGCACTCCTGAATATTTTGAAACA
11448 TCGAATG
1 TCGAATG
11455 TAATTAGTAG
Statistics
Matches: 67, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
65 66 0.99
66 1 0.01
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.32
Consensus pattern (65 bp):
TCGAATGCATTTTGTGTACCGATGCACATACCATGCATCGATGCACTCCTGAATATTTTGAAACA
Found at i:11635 original size:16 final size:16
Alignment explanation
Indices: 11614--11644 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
11604 TCTAGTTTTT
*
11614 CCGAGTACCTGGTTAC
1 CCGAGTACCCGGTTAC
11630 CCGAGTACCCGGTTA
1 CCGAGTACCCGGTTA
11645 GTCTTTATTT
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:0.19, C:0.32, G:0.26, T:0.23
Consensus pattern (16 bp):
CCGAGTACCCGGTTAC
Found at i:11867 original size:15 final size:15
Alignment explanation
Indices: 11847--11903 Score: 69
Period size: 15 Copynumber: 3.7 Consensus size: 15
11837 AATCGGGTAT
11847 CGGGTACCCGATTAC
1 CGGGTACCCGATTAC
**
11862 CGGGTACCCGCAAAATC
1 CGGGTACCCG-ATTA-C
*
11879 TGGGTACCCGATTAC
1 CGGGTACCCGATTAC
11894 CGGGTACCCG
1 CGGGTACCCG
11904 TAACATCCAG
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
15 20 0.59
16 4 0.12
17 10 0.29
ACGTcount: A:0.21, C:0.33, G:0.28, T:0.18
Consensus pattern (15 bp):
CGGGTACCCGATTAC
Found at i:14347 original size:85 final size:85
Alignment explanation
Indices: 14182--14668 Score: 591
Period size: 85 Copynumber: 5.7 Consensus size: 85
14172 TTATAGAATT
* * * ** * *
14182 ATTTGCAACATAGCTCAAGGCGAGAAGAGCTATTTGCCAACAAAAAACCTTCGAGTTCAATTCCA
1 ATTTACAACATAGCTCAAGGCGAGAAGGGCTATCTATCAAC-AAAAACCTTCGAGTTCGATTACA
*
14247 TTAAGCTCAAGGGCATATCAA
65 TTCAGCTCAAGGGCATATCAA
* * * * *
14268 ATTTACAACATAGCTCAAGGCGAGAAGTGTTATCTTTCAACCAAAACCTTTGAGTTCGATTACAT
1 ATTTACAACATAGCTCAAGGCGAGAAGGGCTATCTATCAACAAAAACCTTCGAGTTCGATTACAT
*
14333 TCAGCTTAAGGGCATATCAA
66 TCAGCTCAAGGGCATATCAA
** * *
14353 ATTTACAACATAGCTCAATACGAAAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACAT
1 ATTTACAACATAGCTCAAGGCGAGAAGGGCTATCTATCAACAAAAACCTTCGAGTTCGATTACAT
*
14418 TTAGCTCAAGGGCATATCAA
66 TCAGCTCAAGGGCATATCAA
* * * * * *
14438 ATTTACAGCATAGCTCAAGACGAGAAGGTCTATCCGAT-AACAAAAACCTTTGAGTTTGATTACA
1 ATTTACAACATAGCTCAAGGCGAGAAGGGCTAT-CTATCAACAAAAACCTTCGAGTTCGATTACA
* **
14502 TTCAGCTGAAAAGCATATCAA
65 TTCAGCTCAAGGGCATATCAA
* ** *
14523 ATTTACAGA-ATAGCTTAAGGCGAGAAGGGCTATCCGTCAACAAAAAACTTCGAGTTCGATTACA
1 ATTTACA-ACATAGCTCAAGGCGAGAAGGGCTATCTATCAACAAAAACCTTCGAGTTCGATTACA
14587 TTCAGCTCAAGGGCATATCAA
65 TTCAGCTCAAGGGCATATCAA
* * * * * *
14608 ATTTATAGCATAGCTCAAGGCGAGTAGGGTTATCTATCACCAAAAACCTTTGAGTTCGATT
1 ATTTACAACATAGCTCAAGGCGAGAAGGGCTATCTATCAACAAAAACCTTCGAGTTCGATT
14669 CCACTCAGTT
Statistics
Matches: 341, Mismatches: 56, Indels: 9
0.84 0.14 0.02
Matches are distributed among these distances:
84 2 0.01
85 302 0.89
86 37 0.11
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.26
Consensus pattern (85 bp):
ATTTACAACATAGCTCAAGGCGAGAAGGGCTATCTATCAACAAAAACCTTCGAGTTCGATTACAT
TCAGCTCAAGGGCATATCAA
Found at i:14486 original size:170 final size:169
Alignment explanation
Indices: 14182--14668 Score: 672
Period size: 170 Copynumber: 2.9 Consensus size: 169
14172 TTATAGAATT
* * * * * *
14182 ATTTGCAACATAGCTCAAGGCGAGAAGAGCTATTTGCCAACAAAAAACCTTCGAGTTCAATTCCA
1 ATTTACAACATAGCTCAAGGCGAGAAGGGCTATCTGTCAAC-AAAAACCTTCGAGTTCGATTACA
* * *
14247 TTAAGCTCAAGGGCATATCAAATTTACAACATAGCTCAAGGCGAGAAGTGTTATCTTTCAACCAA
65 TTAAGCTCAAGGGCATATCAAATTTACAGCATAGCTCAAGGCGAGAAG-GTTATCTATCAACAAA
* **
14312 AACCTTTGAGTTCGATTACATTCAGCTTAAGGGCATATCAA
129 AACCTTTGAGTTCGATTACATTCAGCTGAAAAGCATATCAA
** *
14353 ATTTACAACATAGCTCAATACGAAAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACAT
1 ATTTACAACATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACAT
* * *
14418 TTAGCTCAAGGGCATATCAAATTTACAGCATAGCTCAAGACGAGAAGGTCTATCCGAT-AACAAA
66 TAAGCTCAAGGGCATATCAAATTTACAGCATAGCTCAAGGCGAGAAGGT-TAT-CTATCAACAAA
*
14482 AACCTTTGAGTTTGATTACATTCAGCTGAAAAGCATATCAA
129 AACCTTTGAGTTCGATTACATTCAGCTGAAAAGCATATCAA
* * *
14523 ATTTACAGA-ATAGCTTAAGGCGAGAAGGGCTATCCGTCAACAAAAAACTTCGAGTTCGATTACA
1 ATTTACA-ACATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACA
* * * *
14587 TTCAGCTCAAGGGCATATCAAATTTATAGCATAGCTCAAGGCGAGTAGGGTTATCTATCACCAAA
65 TTAAGCTCAAGGGCATATCAAATTTACAGCATAGCTCAAGGCGAG-AAGGTTATCTATCAACAAA
14652 AACCTTTGAGTTCGATT
129 AACCTTTGAGTTCGATT
14669 CCACTCAGTT
Statistics
Matches: 279, Mismatches: 32, Indels: 11
0.87 0.10 0.03
Matches are distributed among these distances:
169 5 0.02
170 233 0.84
171 41 0.15
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.26
Consensus pattern (169 bp):
ATTTACAACATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACAT
TAAGCTCAAGGGCATATCAAATTTACAGCATAGCTCAAGGCGAGAAGGTTATCTATCAACAAAAA
CCTTTGAGTTCGATTACATTCAGCTGAAAAGCATATCAA
Found at i:15397 original size:38 final size:38
Alignment explanation
Indices: 15340--15628 Score: 376
Period size: 38 Copynumber: 7.6 Consensus size: 38
15330 TATTTTGAAA
*
15340 ATATAT-ATATATAGTTTTTGTAAACATTTTAAAAACAT
1 ATATATAATATATAG-TTTTGAAAACATTTTAAAAACAT
* * *
15378 ATATATAATATAAAGTTTTGAAAACATTTTGAAATCAT
1 ATATATAATATATAGTTTTGAAAACATTTTAAAAACAT
15416 ATATATAATATATAGTTTTGAAAACATTTTAAAAACAT
1 ATATATAATATATAGTTTTGAAAACATTTTAAAAACAT
15454 ATATATAATATATAGTTTTGAAAACATTTTAAAAACAT
1 ATATATAATATATAGTTTTGAAAACATTTTAAAAACAT
*
15492 ATATATAATATATAGTTTTGGAAACATTTTAAAAACAT
1 ATATATAATATATAGTTTTGAAAACATTTTAAAAACAT
* *
15530 ATATAT--TATATAGTTTTTGAAAACATTTTGAAAATAT
1 ATATATAATATATAG-TTTTGAAAACATTTTAAAAACAT
** **
15567 ATATATATATAATATAGTTTTTTTTAAACATTTT--TTA-A-
1 ATATATA-AT-ATATAG--TTTTGAAAACATTTTAAAAACAT
15605 ATATATAATATATAGTTTTGAAAA
1 ATATATAATATATAGTTTTGAAAA
15629 TGTTTTTTAA
Statistics
Matches: 227, Mismatches: 17, Indels: 18
0.87 0.06 0.07
Matches are distributed among these distances:
34 7 0.03
36 13 0.06
37 28 0.12
38 149 0.66
39 8 0.04
40 2 0.01
41 6 0.03
42 14 0.06
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.43
Consensus pattern (38 bp):
ATATATAATATATAGTTTTGAAAACATTTTAAAAACAT
Found at i:17851 original size:23 final size:23
Alignment explanation
Indices: 17814--17874 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
17804 CACCTCATAT
17814 AAATGCACCGAAGTGCCACGTAG
1 AAATGCACCGAAGTGCCACGTAG
* * *
17837 AATTGCACCGTAGTGCCGCGTAG
1 AAATGCACCGAAGTGCCACGTAG
17860 AAATGCACCGAAGTG
1 AAATGCACCGAAGTG
17875 TCATATAAGG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.31, C:0.25, G:0.28, T:0.16
Consensus pattern (23 bp):
AAATGCACCGAAGTGCCACGTAG
Found at i:18375 original size:2 final size:2
Alignment explanation
Indices: 18370--18449 Score: 160
Period size: 2 Copynumber: 40.0 Consensus size: 2
18360 TACCTTATTC
18370 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
18412 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
18450 CCGCAAATAC
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 78 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:22525 original size:13 final size:13
Alignment explanation
Indices: 22503--22535 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
22493 CCCTTATTCA
*
22503 TGTAAAAAATCCC
1 TGTAACAAATCCC
22516 TGTAACAAATCCC
1 TGTAACAAATCCC
22529 TGTAACA
1 TGTAACA
22536 CATATGCAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.42, C:0.24, G:0.09, T:0.24
Consensus pattern (13 bp):
TGTAACAAATCCC
Found at i:22909 original size:23 final size:23
Alignment explanation
Indices: 22883--22948 Score: 96
Period size: 23 Copynumber: 2.9 Consensus size: 23
22873 CACCACAGCT
*
22883 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* * *
22906 CGTAGAATTGCACCGTAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
22929 CGTAGAAATGCACCGAAGTG
1 CGTAGAAATGCACCGAAGTG
22949 TCATATAAGG
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.30, C:0.24, G:0.27, T:0.18
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:26299 original size:2 final size:2
Alignment explanation
Indices: 26292--26323 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
26282 TTATCAAATG
26292 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
26324 ATACGATTCA
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):
TA
Found at i:28472 original size:18 final size:19
Alignment explanation
Indices: 28449--28496 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
28439 TTCACAATAA
*
28449 TTTTATTCT-TTGATAATC
1 TTTTATTCTACTGATAATC
28467 TTTTATTCCTACTGATAATC
1 TTTTATT-CTACTGATAATC
*
28487 TTATATTCTA
1 TTTTATTCTA
28497 TAAACCAAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 7 0.27
19 5 0.19
20 14 0.54
ACGTcount: A:0.25, C:0.15, G:0.04, T:0.56
Consensus pattern (19 bp):
TTTTATTCTACTGATAATC
Found at i:31130 original size:19 final size:19
Alignment explanation
Indices: 31106--31143 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
31096 TTATTGGGCG
31106 TTTTACCAATTTTGTTATT
1 TTTTACCAATTTTGTTATT
*
31125 TTTTACCTATTTTGTTATT
1 TTTTACCAATTTTGTTATT
31144 GTTGGACATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.18, C:0.11, G:0.05, T:0.66
Consensus pattern (19 bp):
TTTTACCAATTTTGTTATT
Found at i:32442 original size:3 final size:3
Alignment explanation
Indices: 32431--32467 Score: 58
Period size: 3 Copynumber: 12.3 Consensus size: 3
32421 TTTTTTATCG
32431 TTA TT- TTA TTA TTA TTA TTA TTA TTTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA T
32468 GTTTATTAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.06
3 27 0.84
4 3 0.09
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:32479 original size:13 final size:13
Alignment explanation
Indices: 32432--32475 Score: 58
Period size: 12 Copynumber: 3.6 Consensus size: 13
32422 TTTTTATCGT
32432 TATT-TTATTAT-
1 TATTATTATTATG
*
32443 TATTATTATTATT
1 TATTATTATTATG
32456 TATTATTATTATG
1 TATTATTATTATG
32469 T-TTATTA
1 TATTATTA
32476 ATTACATATT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
11 4 0.13
12 13 0.43
13 13 0.43
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (13 bp):
TATTATTATTATG
Found at i:32479 original size:19 final size:19
Alignment explanation
Indices: 32438--32479 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
32428 TCGTTATTTT
*
32438 ATTATTATTATTATTATTT
1 ATTATTATTATTATTATTA
32457 ATTATTATTATGT-TTATTA
1 ATTATTATTAT-TATTATTA
32476 ATTA
1 ATTA
32480 CATATTACAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 20 0.95
20 1 0.05
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (19 bp):
ATTATTATTATTATTATTA
Found at i:32564 original size:25 final size:25
Alignment explanation
Indices: 32535--32659 Score: 250
Period size: 25 Copynumber: 5.0 Consensus size: 25
32525 CAATCAACCC
32535 ATCAGATTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
32560 ATCAGATTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
32585 ATCAGATTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
32610 ATCAGATTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
32635 ATCAGATTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
32660 TCCCCTAAAT
Statistics
Matches: 100, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 100 1.00
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.28
Consensus pattern (25 bp):
ATCAGATTAGGGTTTCAAACCCTAA
Found at i:34888 original size:29 final size:29
Alignment explanation
Indices: 34842--34901 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 29
34832 AGTCCCTACG
* * *
34842 TTTCTGTTTTGCTATTTTAGTCTTTTAAT
1 TTTCTATTTTGCTATTTTAGCCCTTTAAT
* *
34871 TTTCTATTTTTCTGTTTTAGCCCTTTAAT
1 TTTCTATTTTGCTATTTTAGCCCTTTAAT
34900 TT
1 TT
34902 ATTATTACCA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.13, C:0.13, G:0.08, T:0.65
Consensus pattern (29 bp):
TTTCTATTTTGCTATTTTAGCCCTTTAAT
Found at i:40725 original size:105 final size:102
Alignment explanation
Indices: 40584--40822 Score: 277
Period size: 105 Copynumber: 2.3 Consensus size: 102
40574 TGAGAATTTT
** * *
40584 AAAACAAATTGCGTCTCGCTTGAGACATTTTTCCTTTGAGATACAAATTTTAAATTTGATTCAC-
1 AAAACAAATTTTGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCAAATTTGATTCACA
*
40648 TAAAAACAAAATTAATCTCACCTT-AGATTGTTGTTTCTTTC-
66 T-AAAACAAAATTAATCTCA-CTTGAGATCG-T-TTTC--TCA
* * * *
40689 AAAACAAATTTTGTCTCGCTTGAGACCTTTTCCCTTTGAGATCCAAATTTCGAATTTGTTTCACA
1 AAAACAAATTTTGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCAAATTTGATTCACA
* * *
40754 TTAAACAAAGTTGATCTCACTTGAGATCGTTTTCTCA
66 TAAAACAAAATTAATCTCACTTGAGATCGTTTTCTCA
* *
40791 AAAACAAACTTTGTCTCGCTTGAGACAATTTC
1 AAAACAAATTTTGTCTCGCTTGAGACATTTTC
40823 TCTAAAAACA
Statistics
Matches: 116, Mismatches: 15, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
101 2 0.02
102 29 0.25
103 4 0.03
104 4 0.03
105 76 0.66
106 1 0.01
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.38
Consensus pattern (102 bp):
AAAACAAATTTTGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCAAATTTGATTCACA
TAAAACAAAATTAATCTCACTTGAGATCGTTTTCTCA
Found at i:40813 original size:36 final size:36
Alignment explanation
Indices: 40768--40887 Score: 113
Period size: 36 Copynumber: 3.4 Consensus size: 36
40758 ACAAAGTTGA
**
40768 TCTCACTTGAGATCGTTTTCTC-AAAAACAAACTTTG
1 TCTCACTTGAGA-CAATTTCTCTAAAAACAAACTTTG
* *
40804 TCTCGCTTGAGACAATTTCTCTAAAAACAAATTTTG
1 TCTCACTTGAGACAATTTCTCTAAAAACAAACTTTG
* * * *
40840 TCTCATTTGAGACTATATCT-T-AAAGCAAA-TTTCG
1 TCTCACTTGAGACAATTTCTCTAAAAACAAACTTT-G
*
40874 TCTCGCTTGAGACA
1 TCTCACTTGAGACA
40888 TCATTTTCTC
Statistics
Matches: 70, Mismatches: 12, Indels: 6
0.80 0.14 0.07
Matches are distributed among these distances:
33 3 0.04
34 19 0.27
35 8 0.11
36 40 0.57
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.36
Consensus pattern (36 bp):
TCTCACTTGAGACAATTTCTCTAAAAACAAACTTTG
Found at i:41177 original size:29 final size:29
Alignment explanation
Indices: 41135--41219 Score: 118
Period size: 29 Copynumber: 3.0 Consensus size: 29
41125 TTTCTCTTGA
*
41135 AAAAATCTTTGAGTTTGTTCCTTTTGAAT
1 AAAAATCTTTGAGTTCGTTCCTTTTGAAT
* *
41164 AAAAATCTTGGAGTTGGTTCCTTTTGAAT
1 AAAAATCTTTGAGTTCGTTCCTTTTGAAT
* *
41193 AAATATCTTTGAG-TCGTTTCTTTTGAA
1 AAAAATCTTTGAGTTCGTTCCTTTTGAA
41220 AAACTTTGAG
Statistics
Matches: 50, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
28 12 0.24
29 38 0.76
ACGTcount: A:0.27, C:0.11, G:0.16, T:0.46
Consensus pattern (29 bp):
AAAAATCTTTGAGTTCGTTCCTTTTGAAT
Found at i:41395 original size:37 final size:36
Alignment explanation
Indices: 41345--41465 Score: 130
Period size: 37 Copynumber: 3.5 Consensus size: 36
41335 TCTTGAGTTT
*
41345 GTTTCTTTGGAAACAAAATTCTTTCTCTCTTAAGATA
1 GTTTCTTTTGAAACAAAATT-TTTCTCTCTTAAGATA
* * *
41382 GTTTCTTTTGAAACAAAA------TCT-TTGAGTTT
1 GTTTCTTTTGAAACAAAATTTTTCTCTCTTAAGATA
41411 GTTTCTTTTGAAACAAAATTTTGTCTCTCTTAAGATA
1 GTTTCTTTTGAAACAAAATTTT-TCTCTCTTAAGATA
*
41448 ATTTCTTTTGAAACAAAA
1 GTTTCTTTTGAAACAAAA
41466 ATCTTTGAAT
Statistics
Matches: 68, Mismatches: 8, Indels: 16
0.74 0.09 0.17
Matches are distributed among these distances:
29 23 0.34
30 3 0.04
36 3 0.04
37 39 0.57
ACGTcount: A:0.31, C:0.13, G:0.11, T:0.45
Consensus pattern (36 bp):
GTTTCTTTTGAAACAAAATTTTTCTCTCTTAAGATA
Found at i:41411 original size:66 final size:66
Alignment explanation
Indices: 41292--41483 Score: 250
Period size: 66 Copynumber: 3.0 Consensus size: 66
41282 CTTTGAGTCT
* * * * *
41292 GAAACAAAGTTTTGTATCTCTTGAGACAA-TT-TTGTGAAA-AAAATC-TTGAGTTTGTTTCTTT
1 GAAACAAAATTTTGTCTCTCTTAAGATAATTTCTTTTGAAACAAAATCTTTGAGTTTGTTTCTTT
41353 G
66 G
*
41354 GAAACAAAATTCTT-TCTCTCTTAAGATAGTTTCTTTTGAAACAAAATCTTTGAGTTTGTTTCTT
1 GAAACAAAATT-TTGTCTCTCTTAAGATAATTTCTTTTGAAACAAAATCTTTGAGTTTGTTTCTT
*
41418 TT
65 TG
* *
41420 GAAACAAAATTTTGTCTCTCTTAAGATAATTTCTTTTGAAACAAAAATCTTTGAATCTGTTTCT
1 GAAACAAAATTTTGTCTCTCTTAAGATAATTTCTTTTGAAAC-AAAATCTTTGAGTTTGTTTCT
41484 CTTAAATTGA
Statistics
Matches: 113, Mismatches: 10, Indels: 9
0.86 0.08 0.07
Matches are distributed among these distances:
62 21 0.19
63 4 0.04
64 7 0.06
65 8 0.07
66 54 0.48
67 19 0.17
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.44
Consensus pattern (66 bp):
GAAACAAAATTTTGTCTCTCTTAAGATAATTTCTTTTGAAACAAAATCTTTGAGTTTGTTTCTTT
G
Found at i:42004 original size:15 final size:15
Alignment explanation
Indices: 41981--42024 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
41971 TTTTGAGTCG
*
41981 TTTCACTTGAAACAT
1 TTTCTCTTGAAACAT
*
41996 TTTCTCTTGAAACGT
1 TTTCTCTTGAAACAT
*
42011 TTTCTCTTAAAACA
1 TTTCTCTTGAAACA
42025 AGATCATCTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.30, C:0.20, G:0.07, T:0.43
Consensus pattern (15 bp):
TTTCTCTTGAAACAT
Found at i:42792 original size:129 final size:129
Alignment explanation
Indices: 42557--42809 Score: 461
Period size: 129 Copynumber: 2.0 Consensus size: 129
42547 ATTATCCTAG
42557 AGATAACCAGCCGTCCCCGTCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCA
1 AGATAACCAGCCGTCCCCGTCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCA
42622 TCACGTATGAGCCGTGTCATTCCCCGACCAGATCTCCTCATCACGTAGGAGCCATGTCAACCAT
66 TCACGTATGAGCCGTGTCATTCCCCGACCAGATCTCCTCATCACGTAGGAGCCATGTCAACCAT
* *
42686 AGATAACCAGCCGTCCTCGTCACGTAGGAACCGTGTTATTACCTTTAGATGGCCAGAACTCTTCA
1 AGATAACCAGCCGTCCCCGTCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCA
* * *
42751 TCACGTATGAGCCGTGTCATTCCCCGACCAGATCTCTTCATCACGTATGAGCCGTGTCA
66 TCACGTATGAGCCGTGTCATTCCCCGACCAGATCTCCTCATCACGTAGGAGCCATGTCA
42810 TTCCCCGACC
Statistics
Matches: 119, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
129 119 1.00
ACGTcount: A:0.24, C:0.31, G:0.20, T:0.25
Consensus pattern (129 bp):
AGATAACCAGCCGTCCCCGTCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCA
TCACGTATGAGCCGTGTCATTCCCCGACCAGATCTCCTCATCACGTAGGAGCCATGTCAACCAT
Found at i:42975 original size:209 final size:210
Alignment explanation
Indices: 42609--43060 Score: 762
Period size: 209 Copynumber: 2.1 Consensus size: 210
42599 CTTTAGATGG
42609 CCAGAACTCTTCATCACGTATGAGCCGTGTCATTCCCCGACCAGATCTCCTCATCACGTAGGAGC
1 CCAGAACTCTTCATCACGTATGAGCCGTGTCATTCCCCGACCAGATCTCCTCATCACGTAGGAGC
* *
42674 CATGTCAACCATAGATAACCAGCCGTCCTCGTCACGTAGGAACCGTGTTATTACCTTTAGATGGC
66 CATGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGC
* * *
42739 CAGAACTCTTCATCACGTATGAGCCGTGTCATTCCCCGACCAGATCTCTTCATCACGTATGAGCC
131 CAGAACTCTTCATCACGTATGAGCCGTGTCATTCCCCGACCAGATCTCCTCATCACGTAGGAACC
* * *
42804 GTGTCA-TTCCCCGA
196 ATGTCACTTACACGA
*
42818 CCAGATCTCTTCATCACGTATGAGCCGTGTCATTCCCCGACCAGATCTCCTCATCACGTAGGAGC
1 CCAGAACTCTTCATCACGTATGAGCCGTGTCATTCCCCGACCAGATCTCCTCATCACGTAGGAGC
42883 CATGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGC
66 CATGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGC
*
42948 CAGAACTCTTCATCACGTATGAGCCGTGTCATTCCCCGACCAGATGTCCTCATCACGTAGGAACC
131 CAGAACTCTTCATCACGTATGAGCCGTGTCATTCCCCGACCAGATCTCCTCATCACGTAGGAACC
*
43013 ATGTCACCCTTAGACGA
196 ATGTCA--CTTACACGA
* *
43030 CAAGAACTCTTCATCACGTATGAGCAGTGTC
1 CCAGAACTCTTCATCACGTATGAGCCGTGTC
43061 GTCCCCAACA
Statistics
Matches: 226, Mismatches: 14, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
209 193 0.85
212 33 0.15
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.25
Consensus pattern (210 bp):
CCAGAACTCTTCATCACGTATGAGCCGTGTCATTCCCCGACCAGATCTCCTCATCACGTAGGAGC
CATGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGC
CAGAACTCTTCATCACGTATGAGCCGTGTCATTCCCCGACCAGATCTCCTCATCACGTAGGAACC
ATGTCACTTACACGA
Found at i:43018 original size:40 final size:40
Alignment explanation
Indices: 42609--43006 Score: 275
Period size: 40 Copynumber: 9.5 Consensus size: 40
42599 CTTTAGATGG
* *
42609 CCAGAACTCTTCATCACGTATGAGCCGTGTCATTCCCCGA
1 CCAGATCTCCTCATCACGTATGAGCCGTGTCATTCCCCGA
* * * **
42649 CCAGATCTCCTCATCACGTAGGAGCCATGTCA-ACCATAGATAA
1 CCAGATCTCCTCATCACGTATGAGCCGTGTCATTCC-CCG---A
* * * * * **
42692 CCAG-CCGTCCTCGTCACGTAGGAACCGTGTTATTACCTTTAGA
1 CCAGATC-TCCTCATCACGTATGAGCCGTGTCATT-CC--CCGA
* *
42735 TGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATTCCCCGA
1 ---CCAGATCTCCTCATCACGTATGAGCCGTGTCATTCCCCGA
*
42778 CCAGATCTCTTCATCACGTATGAGCCGTGTCATTCCCCGA
1 CCAGATCTCCTCATCACGTATGAGCCGTGTCATTCCCCGA
*
42818 CCAGATCTCTTCATCACGTATGAGCCGTGTCATTCCCCGA
1 CCAGATCTCCTCATCACGTATGAGCCGTGTCATTCCCCGA
* * * **
42858 CCAGATCTCCTCATCACGTAGGAGCCATGTCA-ACCATAGATAA
1 CCAGATCTCCTCATCACGTATGAGCCGTGTCATTCC-CCG---A
* * * * *
42901 CCAG-CCGTCCTCATCACGTAGGAACCGTGTTA-TCACCTTTAGA
1 CCAGATC-TCCTCATCACGTATGAGCCGTGTCATTC-CC---CGA
* *
42944 TGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATTCCCCGA
1 ---CCAGATCTCCTCATCACGTATGAGCCGTGTCATTCCCCGA
*
42987 CCAGATGTCCTCATCACGTA
1 CCAGATCTCCTCATCACGTA
43007 GGAACCATGT
Statistics
Matches: 288, Mismatches: 44, Indels: 52
0.75 0.11 0.14
Matches are distributed among these distances:
39 4 0.01
40 155 0.54
42 2 0.01
43 60 0.21
44 1 0.00
45 4 0.01
46 58 0.20
47 4 0.01
ACGTcount: A:0.24, C:0.33, G:0.18, T:0.25
Consensus pattern (40 bp):
CCAGATCTCCTCATCACGTATGAGCCGTGTCATTCCCCGA
Found at i:43229 original size:3 final size:3
Alignment explanation
Indices: 43218--43254 Score: 58
Period size: 3 Copynumber: 12.3 Consensus size: 3
43208 TTTTTTATCG
43218 TTA TT- TTA TTA TTA TTA TTA TTA TTTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA T
43255 GTTTATTAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.06
3 27 0.84
4 3 0.09
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:43266 original size:13 final size:13
Alignment explanation
Indices: 43219--43262 Score: 58
Period size: 12 Copynumber: 3.6 Consensus size: 13
43209 TTTTTATCGT
43219 TATT-TTATTAT-
1 TATTATTATTATG
*
43230 TATTATTATTATT
1 TATTATTATTATG
43243 TATTATTATTATG
1 TATTATTATTATG
43256 T-TTATTA
1 TATTATTA
43263 ATTACATATT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
11 4 0.13
12 13 0.43
13 13 0.43
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (13 bp):
TATTATTATTATG
Found at i:43266 original size:19 final size:19
Alignment explanation
Indices: 43225--43266 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
43215 TCGTTATTTT
*
43225 ATTATTATTATTATTATTT
1 ATTATTATTATTATTATTA
43244 ATTATTATTATGT-TTATTA
1 ATTATTATTAT-TATTATTA
43263 ATTA
1 ATTA
43267 CATATTACAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 20 0.95
20 1 0.05
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (19 bp):
ATTATTATTATTATTATTA
Found at i:43351 original size:25 final size:25
Alignment explanation
Indices: 43322--43421 Score: 200
Period size: 25 Copynumber: 4.0 Consensus size: 25
43312 CAATCAACCC
43322 ATCAGATTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
43347 ATCAGATTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
43372 ATCAGATTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
43397 ATCAGATTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
43422 TCCCCTAAAT
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 75 1.00
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.28
Consensus pattern (25 bp):
ATCAGATTAGGGTTTCAAACCCTAA
Found at i:45642 original size:29 final size:29
Alignment explanation
Indices: 45596--45655 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 29
45586 AGTCCCTACG
* * *
45596 TTTCTGTTTTGCTATTTTAGTCTTTTAAT
1 TTTCTATTTTGCTATTTTAGCCCTTTAAT
* *
45625 TTTCTATTTTTCTGTTTTAGCCCTTTAAT
1 TTTCTATTTTGCTATTTTAGCCCTTTAAT
45654 TT
1 TT
45656 ATTATTACCA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.13, C:0.13, G:0.08, T:0.65
Consensus pattern (29 bp):
TTTCTATTTTGCTATTTTAGCCCTTTAAT
Found at i:47581 original size:36 final size:35
Alignment explanation
Indices: 47501--47601 Score: 114
Period size: 36 Copynumber: 2.9 Consensus size: 35
47491 TGAACAATTG
* * * * *
47501 AATCGAAAGTGCTGACGATTCCTTCCTTTCACTTA
1 AATCGAAAGTGCTGATGCTTCATTTCGTTCACTTA
*
47536 AATCGAAAGTG-TCGATGCTTCATTTCGTTCACTTTG
1 AATCGAAAGTGCT-GATGCTTCATTTCGTTCAC-TTA
*
47572 AATCGAAAGTGCTGATGCTTCCTTTCGTTC
1 AATCGAAAGTGCTGATGCTTCATTTCGTTC
47602 TTCTTATTCA
Statistics
Matches: 56, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
34 1 0.02
35 25 0.45
36 29 0.52
37 1 0.02
ACGTcount: A:0.23, C:0.23, G:0.18, T:0.37
Consensus pattern (35 bp):
AATCGAAAGTGCTGATGCTTCATTTCGTTCACTTA
Found at i:56535 original size:31 final size:31
Alignment explanation
Indices: 56479--56544 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
56469 GGTGGAGATC
* * *
56479 ATATCTTAATTAAATAAAAATGAAAGTGATA
1 ATATCTTAACTAAACAAAAACGAAAGTGATA
* *
56510 ATATTTTAACTAAACAAAAACGAAAGTGATC
1 ATATCTTAACTAAACAAAAACGAAAGTGATA
56541 ATAT
1 ATAT
56545 ATTATGATTT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.53, C:0.08, G:0.09, T:0.30
Consensus pattern (31 bp):
ATATCTTAACTAAACAAAAACGAAAGTGATA
Found at i:56950 original size:15 final size:17
Alignment explanation
Indices: 56932--56965 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
56922 AAAATTTCAG
56932 AAAATAT-AAT-TTTTA
1 AAAATATGAATCTTTTA
56947 AAAATATGAATCTTTTA
1 AAAATATGAATCTTTTA
56964 AA
1 AA
56966 TATTTATTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
16 3 0.18
17 7 0.41
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.41
Consensus pattern (17 bp):
AAAATATGAATCTTTTA
Found at i:58338 original size:33 final size:33
Alignment explanation
Indices: 58296--58367 Score: 117
Period size: 33 Copynumber: 2.2 Consensus size: 33
58286 ATTTTGTAGG
* * *
58296 TGATGAAGGTGGGCTAGTTGAAGATGGGTCAAA
1 TGATGAAGGTGGGCCAGTTGAAGATAGGCCAAA
58329 TGATGAAGGTGGGCCAGTTGAAGATAGGCCAAA
1 TGATGAAGGTGGGCCAGTTGAAGATAGGCCAAA
58362 TGATGA
1 TGATGA
58368 TAATTGGTGG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.32, C:0.08, G:0.38, T:0.22
Consensus pattern (33 bp):
TGATGAAGGTGGGCCAGTTGAAGATAGGCCAAA
Done.