Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001927.1 Hibiscus syriacus cultivar Beakdansim tig00003898_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: 124260
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1063 original size:224 final size:224
Alignment explanation
Indices: 668--1109 Score: 755
Period size: 224 Copynumber: 2.0 Consensus size: 224
658 TTAAAACTGC
668 TTTTAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATA
1 TTTTAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATA
**
733 TTAATTTAATAATTTAATTTACACAAAATTTTATTTGATTGTTTTGATATTTTATAAAATATTAT
66 TTAATTTAATAATTTAATTTACACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTAT
* * *
798 TTAGAATTTAAATTTAACAATATTAACAAATATAATAATAATA-GTTTTCAATAGTGAAATAAGT
131 TTAGAATTTAAATTTAACAATATTAACAAAGATAATAATAATATATTTTC-ACAGTGAAATAAGT
*
862 ATGGACACTTTTATAAAAATGATATTACTT
195 ATGGACACTTTTATAAAAAGGATATTACTT
*
892 TTTTGAAAGTTATGTAATTTATGTTTCAATTTTTTTAATAGTGTTTCATG-TTTCCACCTACAAT
1 TTTT-AAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAAT
*
956 ATTAATTTAATAATTTCATTTACACAAAAAATTATTTGATTGTTTTGATATTTT-TAAAATATTA
65 ATTAATTTAATAATTTAATTTACACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTA
*
1020 TTTAGATTTTAAATTTAACAATATTAACTAAAGATAATAATAATATATTTTCACAGTGAAATAAG
130 TTTAGAATTTAAATTTAACAATATTAAC-AAAGATAATAATAATATATTTTCACAGTGAAATAAG
1085 TATGGACACTTTTATAAAAAGGATA
194 TATGGACACTTTTATAAAAAGGATA
1110 GATAATTTAC
Statistics
Matches: 206, Mismatches: 9, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
223 37 0.18
224 120 0.58
225 49 0.24
ACGTcount: A:0.39, C:0.07, G:0.08, T:0.46
Consensus pattern (224 bp):
TTTTAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATA
TTAATTTAATAATTTAATTTACACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTAT
TTAGAATTTAAATTTAACAATATTAACAAAGATAATAATAATATATTTTCACAGTGAAATAAGTA
TGGACACTTTTATAAAAAGGATATTACTT
Found at i:3293 original size:31 final size:31
Alignment explanation
Indices: 3250--3315 Score: 75
Period size: 31 Copynumber: 2.1 Consensus size: 31
3240 TAACCTTACA
*
3250 ACTCTATATTTTC-AATGGCTAAGA-TAGAATC
1 ACTCTATATTTTCTAA-GGCTAA-ACTAGAACC
3281 ACTCTAGT-TTTTCTAAGGCTAAACTAGAACC
1 ACTCTA-TATTTTCTAAGGCTAAACTAGAACC
3312 ACTC
1 ACTC
3316 CCCTTTTTCG
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
30 1 0.03
31 27 0.87
32 3 0.10
ACGTcount: A:0.33, C:0.21, G:0.12, T:0.33
Consensus pattern (31 bp):
ACTCTATATTTTCTAAGGCTAAACTAGAACC
Found at i:4660 original size:17 final size:17
Alignment explanation
Indices: 4635--4672 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
4625 TGGGATACTA
4635 ATATGTAAATAAAAT-TG
1 ATATGTAAA-AAAATATG
*
4652 ATATTTAAAAAAATATG
1 ATATGTAAAAAAATATG
4669 ATAT
1 ATAT
4673 CAATTGTAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 5 0.26
17 14 0.74
ACGTcount: A:0.55, C:0.00, G:0.08, T:0.37
Consensus pattern (17 bp):
ATATGTAAAAAAATATG
Found at i:6480 original size:31 final size:30
Alignment explanation
Indices: 6432--6507 Score: 93
Period size: 31 Copynumber: 2.4 Consensus size: 30
6422 TCTTACAAAT
6432 CTATCTTTTCAATGGCTAAGA-TAGAACCACT-
1 CTAT-TTTTCAA-GGCTAA-ACTAGAACCACTC
6463 CTAGTTTTTCTAAGGCTAAACTAGAACCACTC
1 CTA-TTTTTC-AAGGCTAAACTAGAACCACTC
6495 CTATTTTTCAAGG
1 CTATTTTTCAAGG
6508 TTTGATTTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
30 5 0.12
31 30 0.73
32 6 0.15
ACGTcount: A:0.30, C:0.22, G:0.13, T:0.34
Consensus pattern (30 bp):
CTATTTTTCAAGGCTAAACTAGAACCACTC
Found at i:6888 original size:21 final size:21
Alignment explanation
Indices: 6863--6918 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
6853 GGAACATGGA
6863 GGGTTTCGAAACCTATGAGGG
1 GGGTTTCGAAACCTATGAGGG
*
6884 GGGTTTTGAAACCTATGAGGG
1 GGGTTTCGAAACCTATGAGGG
6905 GGGTTTCGAAACCT
1 GGGTTTCGAAACCT
6919 TTAGGCCAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.23, C:0.14, G:0.36, T:0.27
Consensus pattern (21 bp):
GGGTTTCGAAACCTATGAGGG
Found at i:7633 original size:83 final size:83
Alignment explanation
Indices: 7544--7718 Score: 208
Period size: 83 Copynumber: 2.1 Consensus size: 83
7534 ATATCCTAAT
* ** * ** * *
7544 ATATAGTGTCATTTTTG-GGAAAACGCCGCTACAAACGCGTATTTTAGTGGTGTTTATGTAAAAA
1 ATATAGTGGCATTTTTGTCAAAAACACCGCTA-AAAAACGTACTTTAGTGGCGTTTATGTAAAAA
** * * *
7608 CGTGCTGCGATATCTAGAC
65 AATGCCGCGATAGCCAGAC
7627 ATATAGTGGCATTTTTGTCAAAAACACCGCTAAAAAACGTACTTTAGTGGCGTTTATGTAAAAAA
1 ATATAGTGGCATTTTTGTCAAAAACACCGCTAAAAAACGTACTTTAGTGGCGTTTATGTAAAAAA
*
7692 ATGCCGCGATAGCCAGAT
66 ATGCCGCGATAGCCAGAC
7710 ATATAGTGG
1 ATATAGTGG
7719 TGTTTTGTTA
Statistics
Matches: 77, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
83 66 0.86
84 11 0.14
ACGTcount: A:0.33, C:0.15, G:0.22, T:0.30
Consensus pattern (83 bp):
ATATAGTGGCATTTTTGTCAAAAACACCGCTAAAAAACGTACTTTAGTGGCGTTTATGTAAAAAA
ATGCCGCGATAGCCAGAC
Found at i:7895 original size:42 final size:41
Alignment explanation
Indices: 7839--7957 Score: 125
Period size: 41 Copynumber: 2.9 Consensus size: 41
7829 TTGTTAATGG
* *
7839 AACGCCGCAATAGACTTGTACAATAGTGGCGTTTTTCATACA
1 AACGCCACAATAGACGTGTACAATAGTGGCGTTTTT-ATACA
** *
7881 CGCGCCACAATAGACGCGTA-AATAGTGGCGTTTGTTATACA
1 AACGCCACAATAGACGTGTACAATAGTGGCGTTT-TTATACA
* * *
7922 AACGTCGA-AATAAACGTGTACATTAGTGGCGTTTTT
1 AACG-CCACAATAGACGTGTACAATAGTGGCGTTTTT
7958 TGTGAAAATG
Statistics
Matches: 63, Mismatches: 11, Indels: 7
0.78 0.14 0.09
Matches are distributed among these distances:
41 32 0.51
42 31 0.49
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (41 bp):
AACGCCACAATAGACGTGTACAATAGTGGCGTTTTTATACA
Found at i:8128 original size:21 final size:21
Alignment explanation
Indices: 8102--8161 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 21
8092 CAATCATCAT
*
8102 CATCGCACCGCCAGTCACCAT
1 CATCGCACCGCCAGTCACCAC
** * *
8123 TGTCGCACCTCCAGTGACCAC
1 CATCGCACCGCCAGTCACCAC
*
8144 CATCGCACCGTCAGTCAC
1 CATCGCACCGCCAGTCAC
8162 TCCTCAAGGC
Statistics
Matches: 29, Mismatches: 10, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.22, C:0.45, G:0.17, T:0.17
Consensus pattern (21 bp):
CATCGCACCGCCAGTCACCAC
Found at i:20923 original size:12 final size:12
Alignment explanation
Indices: 20900--20930 Score: 53
Period size: 12 Copynumber: 2.5 Consensus size: 12
20890 ATAAACTTTG
20900 TTGTTGTTGTTTT
1 TTGTT-TTGTTTT
20913 TTGTTTTGTTTT
1 TTGTTTTGTTTT
20925 TTGTTT
1 TTGTTT
20931 ATCTATGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 13 0.72
13 5 0.28
ACGTcount: A:0.00, C:0.00, G:0.19, T:0.81
Consensus pattern (12 bp):
TTGTTTTGTTTT
Found at i:22302 original size:24 final size:24
Alignment explanation
Indices: 22256--22302 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
22246 ATTTTTTTAA
* *
22256 AAAAATATAAAAAAACTATTTTTT
1 AAAAATATAAAAAAAATAATTTTT
22280 AAAAATA-AAATAAAAATAATTTT
1 AAAAATATAAA-AAAAATAATTTT
22303 GAGAACCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 3 0.15
24 17 0.85
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (24 bp):
AAAAATATAAAAAAAATAATTTTT
Found at i:26585 original size:8 final size:8
Alignment explanation
Indices: 26572--26750 Score: 241
Period size: 8 Copynumber: 22.4 Consensus size: 8
26562 TTATCTAAAC
26572 CATCCATG
1 CATCCATG
26580 CATCCATG
1 CATCCATG
*
26588 CATACATG
1 CATCCATG
26596 CATCCATG
1 CATCCATG
26604 CATCCATG
1 CATCCATG
26612 CATCCATG
1 CATCCATG
26620 CATCCATG
1 CATCCATG
*
26628 CATCCATT
1 CATCCATG
26636 CATCCATG
1 CATCCATG
26644 CATCCATG
1 CATCCATG
*
26652 CATACATG
1 CATCCATG
26660 CATCCATG
1 CATCCATG
*
26668 CATACATG
1 CATCCATG
26676 CATCCATG
1 CATCCATG
26684 CATCCATG
1 CATCCATG
* *
26692 CATGCATA
1 CATCCATG
26700 CATCCATG
1 CATCCATG
* *
26708 CATACATC
1 CATCCATG
* *
26716 CATGCATA
1 CATCCATG
*
26724 CATGCATG
1 CATCCATG
* *
26732 CATACATC
1 CATCCATG
26740 CATCCATG
1 CATCCATG
26748 CAT
1 CAT
26751 GCATACATAC
Statistics
Matches: 150, Mismatches: 21, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
8 150 1.00
ACGTcount: A:0.29, C:0.34, G:0.11, T:0.26
Consensus pattern (8 bp):
CATCCATG
Found at i:31051 original size:23 final size:23
Alignment explanation
Indices: 30996--31054 Score: 109
Period size: 23 Copynumber: 2.6 Consensus size: 23
30986 GCTGTCCCTT
*
30996 TTTTCTCTCACTACCAACTTTTG
1 TTTTCTCTCTCTACCAACTTTTG
31019 TTTTCTCTCTCTACCAACTTTTG
1 TTTTCTCTCTCTACCAACTTTTG
31042 TTTTCTCTCTCTA
1 TTTTCTCTCTCTA
31055 AATCCTTCAG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.14, C:0.31, G:0.03, T:0.53
Consensus pattern (23 bp):
TTTTCTCTCTCTACCAACTTTTG
Found at i:31467 original size:15 final size:15
Alignment explanation
Indices: 31447--31490 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 15
31437 AATATAATTG
*
31447 ATTTTTTTATATCTTT
1 ATTTTCTTAT-TCTTT
31463 ATTTTCTTATTCTTTT
1 ATTTTCTTATTC-TTT
31479 AATTTTCTTATT
1 -ATTTTCTTATT
31491 ATTTCCTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
15 2 0.08
16 12 0.48
17 11 0.44
ACGTcount: A:0.18, C:0.09, G:0.00, T:0.73
Consensus pattern (15 bp):
ATTTTCTTATTCTTT
Found at i:31985 original size:17 final size:18
Alignment explanation
Indices: 31948--31991 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
31938 ATGTATTTAA
* *
31948 AGTTCAAACTTGAACTTG
1 AGTTCGAACTTGAAATTG
31966 AGTTCGAACTT-AAATTG
1 AGTTCGAACTTGAAATTG
*
31983 AGTTTGAAC
1 AGTTCGAAC
31992 CTGATTTATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
17 13 0.57
18 10 0.43
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.34
Consensus pattern (18 bp):
AGTTCGAACTTGAAATTG
Found at i:33369 original size:31 final size:31
Alignment explanation
Indices: 33334--33404 Score: 106
Period size: 31 Copynumber: 2.3 Consensus size: 31
33324 ATTTGTACAC
* * * *
33334 TTTTGGTCATTTATGTTATCGTTTTATTAAG
1 TTTTGGTCACTTACGTTACCATTTTATTAAG
33365 TTTTGGTCACTTACGTTACCATTTTATTAAG
1 TTTTGGTCACTTACGTTACCATTTTATTAAG
33396 TTTTGGTCA
1 TTTTGGTCA
33405 GATGAATGTA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.20, C:0.11, G:0.15, T:0.54
Consensus pattern (31 bp):
TTTTGGTCACTTACGTTACCATTTTATTAAG
Found at i:34404 original size:31 final size:31
Alignment explanation
Indices: 34361--34428 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
34351 CACTGACCAC
34361 ATCTTAAGTAAAATGAAACGAAAA-CAACTAA
1 ATCTTAAGTAAAATGAAAC-AAAAGCAACTAA
* **
34392 ATCTTAATTAAAATGAAACAAAAGTGACTAA
1 ATCTTAAGTAAAATGAAACAAAAGCAACTAA
34423 ATCTTA
1 ATCTTA
34429 TATTTTTTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
30 4 0.12
31 29 0.88
ACGTcount: A:0.54, C:0.12, G:0.09, T:0.25
Consensus pattern (31 bp):
ATCTTAAGTAAAATGAAACAAAAGCAACTAA
Found at i:38522 original size:60 final size:60
Alignment explanation
Indices: 38438--38551 Score: 151
Period size: 60 Copynumber: 1.9 Consensus size: 60
38428 CATATGTCTC
* * *
38438 TAAATTATAACTCTTATTTTAAATTGGTCTTTAAACTTTTAAATAATTC-AATTTCATTCT
1 TAAATTATAACTCTTATTCTAAATTAGTCCTTAAACTTTTAAAT-ATTCTAATTTCATTCT
* *
38498 TAAATTATGAA-TCTTGTTCTAAATTAGTCCTTAAACTTTTGAATATTCTAATTT
1 TAAATTAT-AACTCTTATTCTAAATTAGTCCTTAAACTTTTAAATATTCTAATTT
38552 TATCCCTAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
59 4 0.09
60 41 0.87
61 2 0.04
ACGTcount: A:0.34, C:0.11, G:0.05, T:0.49
Consensus pattern (60 bp):
TAAATTATAACTCTTATTCTAAATTAGTCCTTAAACTTTTAAATATTCTAATTTCATTCT
Found at i:38652 original size:60 final size:61
Alignment explanation
Indices: 38530--38682 Score: 202
Period size: 60 Copynumber: 2.5 Consensus size: 61
38520 ATTAGTCCTT
* * *
38530 AAACTTTTGAATATTCTAATTTTATCCCTAAACTATGACCTATATTTTTAATATGGTCCCC
1 AAACTTTTGAATATTCCAATTTCATCCCTAAACTATGACCTATATTCTTAATATGGTCCCC
* * * *
38591 AAATTTTTGAATCTTCCAATTTCATCCCTATAAC-ATG-CCTATCTTCTTAATTTGGTCCCC
1 AAACTTTTGAATATTCCAATTTCATCCCTA-AACTATGACCTATATTCTTAATATGGTCCCC
* *
38651 AAACTCTTGAATATTTCAATTTCATCCCTAAA
1 AAACTTTTGAATATTCCAATTTCATCCCTAAA
38683 TTCATCCAAA
Statistics
Matches: 80, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
59 2 0.03
60 46 0.57
61 29 0.36
62 3 0.04
ACGTcount: A:0.30, C:0.23, G:0.06, T:0.41
Consensus pattern (61 bp):
AAACTTTTGAATATTCCAATTTCATCCCTAAACTATGACCTATATTCTTAATATGGTCCCC
Found at i:38976 original size:60 final size:58
Alignment explanation
Indices: 38807--38976 Score: 171
Period size: 59 Copynumber: 2.8 Consensus size: 58
38797 ATATGTATAG
* * *
38807 TTTGGGATGAAATTAAGAATGTTCAAAAAGTTT-AGAGACCAATTTAGAATGAAAGTCATAA
1 TTTGGGATGAAATTAA-AAT-TT-TAAAAGTTTAAG-GACCAATTTAAAATGAAAGTCACAA
* * * * * * * *
38868 TTTGGGAATGAAATTGAAATGTTCAACGTTCAAGGACTAATTTAAAATGATAGTCACGA
1 TTTGGG-ATGAAATTAAAATTTTAAAAGTTTAAGGACCAATTTAAAATGAAAGTCACAA
38927 TTTAGGGATGAAATTAAAATATTTAAAAGTTTAAGGACCAATTTAAAATG
1 TTT-GGGATGAAATTAAAAT-TTTAAAAGTTTAAGGACCAATTTAAAATG
38977 GGAATCATAC
Statistics
Matches: 88, Mismatches: 17, Indels: 9
0.77 0.15 0.08
Matches are distributed among these distances:
59 40 0.45
60 30 0.34
61 9 0.10
62 9 0.10
ACGTcount: A:0.43, C:0.07, G:0.19, T:0.31
Consensus pattern (58 bp):
TTTGGGATGAAATTAAAATTTTAAAAGTTTAAGGACCAATTTAAAATGAAAGTCACAA
Found at i:45319 original size:80 final size:81
Alignment explanation
Indices: 44989--45465 Score: 742
Period size: 81 Copynumber: 5.9 Consensus size: 81
44979 AACCTTTCGT
** * * * * *
44989 TTTTACTCAAAAGTGTTTAACCTTTCATCTAACTGGCATAAATGGTACCTTTTTACCAATTGCAC
1 TTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGGCACCTTTCTACCAATTGCAC
45054 AGTTAGGCCATTATTC
66 AGTTAGGCCATTATTC
* **
45070 TTTTACTCAACGGTATTTAACCGTTCATCTAACTGTCATAATTGGCATATTTCTACCAATTGCAC
1 TTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGGCACCTTTCTACCAATTGCAC
45135 AGTTAGGCCATTATTC
66 AGTTAGGCCATTATTC
*
45151 TTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGGCACATTTCTACCAATTGCAC
1 TTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGGCACCTTTCTACCAATTGCAC
45216 AGTTAGGCCATTATTC
66 AGTTAGGCCATTATTC
* * * *
45232 TTTTACTCAACGGTATTTAACCGTTCATCTAACT-GCATAATTGACACCTTTTTACCGATTGTAC
1 TTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGGCACCTTTCTACCAATTGCAC
45296 AGTTAGGCCATTATTC
66 AGTTAGGCCATTATTC
* * * *
45312 TTTTACTCAAAGGTATTTAACCGTTCACCTAACTGGCATAATTGACACCTTTCTACCAATTGTAC
1 TTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGGCACCTTTCTACCAATTGCAC
*
45377 AATTAGGCCATTATTC
66 AGTTAGGCCATTATTC
* *
45393 -TTTACTCAACGGTATTTAATCGTTCATCTAATTGGCATAATTGGCACCTTTCTACCAATTGCAC
1 TTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGGCACCTTTCTACCAATTGCAC
45457 AGTTAGGCC
66 AGTTAGGCC
45466 TCAAAGGCAG
Statistics
Matches: 366, Mismatches: 29, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
80 139 0.38
81 227 0.62
ACGTcount: A:0.27, C:0.23, G:0.13, T:0.37
Consensus pattern (81 bp):
TTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGGCACCTTTCTACCAATTGCAC
AGTTAGGCCATTATTC
Found at i:45353 original size:161 final size:161
Alignment explanation
Indices: 44989--45465 Score: 749
Period size: 161 Copynumber: 3.0 Consensus size: 161
44979 AACCTTTCGT
* * * * * *
44989 TTTTACTCAAAAGTGTTTAACCTTTCATCTAACTGGCATAAATGGTACCTTTTTACCAATTGCAC
1 TTTTACTCAAAGGTATTTAACCGTTCATCTAACTGGCATAATTGGCACCTTTCTACCAATTGCAC
**
45054 AGTTAGGCCATTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGTCATAATTGGCATA
66 AGTTAGGCCATTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTG-CATAATTGGCACC
45119 TTTCTACCAATTGCACAGTTAGGCCATTATTC
130 TTTCTACCAATTGCACAGTTAGGCCATTATTC
* *
45151 TTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGGCACATTTCTACCAATTGCAC
1 TTTTACTCAAAGGTATTTAACCGTTCATCTAACTGGCATAATTGGCACCTTTCTACCAATTGCAC
*
45216 AGTTAGGCCATTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGCATAATTGACACCT
66 AGTTAGGCCATTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGCATAATTGGCACCT
* * *
45281 TTTTACCGATTGTACAGTTAGGCCATTATTC
131 TTCTACCAATTGCACAGTTAGGCCATTATTC
* * *
45312 TTTTACTCAAAGGTATTTAACCGTTCACCTAACTGGCATAATTGACACCTTTCTACCAATTGTAC
1 TTTTACTCAAAGGTATTTAACCGTTCATCTAACTGGCATAATTGGCACCTTTCTACCAATTGCAC
* * *
45377 AATTAGGCCATTATTC-TTTACTCAACGGTATTTAATCGTTCATCTAATTGGCATAATTGGCACC
66 AGTTAGGCCATTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACT-GCATAATTGGCACC
45441 TTTCTACCAATTGCACAGTTAGGCC
130 TTTCTACCAATTGCACAGTTAGGCC
45466 TCAAAGGCAG
Statistics
Matches: 288, Mismatches: 26, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
160 31 0.11
161 149 0.52
162 108 0.38
ACGTcount: A:0.27, C:0.23, G:0.13, T:0.37
Consensus pattern (161 bp):
TTTTACTCAAAGGTATTTAACCGTTCATCTAACTGGCATAATTGGCACCTTTCTACCAATTGCAC
AGTTAGGCCATTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGCATAATTGGCACCT
TTCTACCAATTGCACAGTTAGGCCATTATTC
Found at i:45524 original size:28 final size:27
Alignment explanation
Indices: 45480--45540 Score: 77
Period size: 28 Copynumber: 2.2 Consensus size: 27
45470 AGGCAGTTAG
*
45480 CCTTTCATCTAACTGGCTTAAATTGACA
1 CCTTTCATCTAACTGGCATAAA-TGACA
* *
45508 CCTTTCGTCTAATTGGCATAAATGACA
1 CCTTTCATCTAACTGGCATAAATGACA
*
45535 CATTTC
1 CCTTTC
45541 TGATAAATGC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
27 10 0.34
28 19 0.66
ACGTcount: A:0.28, C:0.25, G:0.11, T:0.36
Consensus pattern (27 bp):
CCTTTCATCTAACTGGCATAAATGACA
Found at i:45843 original size:54 final size:56
Alignment explanation
Indices: 45774--45915 Score: 173
Period size: 56 Copynumber: 2.6 Consensus size: 56
45764 CATATATTTT
* * *
45774 CCCATACGAACATTCATACACTTGGTATGAATTT-ATTA-GTTAGCACACATAGTG
1 CCCATACGAAAATTCATACACTTAGTATGAATTTCATTATGTTAGCACACAAAGTG
* * *
45828 CCCATACGAAAATTCATACACTTAGTATGAATTTCCTTATTTTTGCACACAAAGTG
1 CCCATACGAAAATTCATACACTTAGTATGAATTTCATTATGTTAGCACACAAAGTG
* * *
45884 TCCATA-TAGAAATTTATACACTTAGTATGAAT
1 CCCATACGA-AAATTCATACACTTAGTATGAAT
45916 ATCTTACATT
Statistics
Matches: 76, Mismatches: 9, Indels: 4
0.85 0.10 0.04
Matches are distributed among these distances:
54 32 0.42
55 4 0.05
56 40 0.53
ACGTcount: A:0.35, C:0.19, G:0.12, T:0.34
Consensus pattern (56 bp):
CCCATACGAAAATTCATACACTTAGTATGAATTTCATTATGTTAGCACACAAAGTG
Found at i:48428 original size:45 final size:46
Alignment explanation
Indices: 48364--48462 Score: 166
Period size: 46 Copynumber: 2.2 Consensus size: 46
48354 TATCTGTAAA
*
48364 CGATGCATAAAATGCATTCGATG-TTTTA-AAATAGCCTGAGTGCAT
1 CGATGCATAAAATGCATTCGATGTTTTTATAAA-AACCTGAGTGCAT
48409 CGATGCATAAAATGCATTCGATGTTTTTATAAAAACCTGAGTGCAT
1 CGATGCATAAAATGCATTCGATGTTTTTATAAAAACCTGAGTGCAT
48455 CGATGCAT
1 CGATGCAT
48463 GGTATATGCA
Statistics
Matches: 51, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
45 23 0.45
46 25 0.49
47 3 0.06
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.31
Consensus pattern (46 bp):
CGATGCATAAAATGCATTCGATGTTTTTATAAAAACCTGAGTGCAT
Found at i:49196 original size:10 final size:10
Alignment explanation
Indices: 49183--49213 Score: 62
Period size: 10 Copynumber: 3.1 Consensus size: 10
49173 ACCAAAATAT
49183 AAATTCAAAC
1 AAATTCAAAC
49193 AAATTCAAAC
1 AAATTCAAAC
49203 AAATTCAAAC
1 AAATTCAAAC
49213 A
1 A
49214 TCCAACAATC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.61, C:0.19, G:0.00, T:0.19
Consensus pattern (10 bp):
AAATTCAAAC
Found at i:51061 original size:20 final size:20
Alignment explanation
Indices: 51036--51083 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
51026 GTGGAATATG
51036 ATGATGTTTTGCATGATTTA
1 ATGATGTTTTGCATGATTTA
51056 ATGATGTTTTGCATGATTTA
1 ATGATGTTTTGCATGATTTA
51076 ATGATGTT
1 ATGATGTT
51084 AGCAGAATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.25, C:0.04, G:0.21, T:0.50
Consensus pattern (20 bp):
ATGATGTTTTGCATGATTTA
Found at i:51273 original size:20 final size:20
Alignment explanation
Indices: 51248--51300 Score: 106
Period size: 20 Copynumber: 2.6 Consensus size: 20
51238 AACCCGACGG
51248 GTGCATCGATGCATGGCAGT
1 GTGCATCGATGCATGGCAGT
51268 GTGCATCGATGCATGGCAGT
1 GTGCATCGATGCATGGCAGT
51288 GTGCATCGATGCA
1 GTGCATCGATGCA
51301 CATTAAAGGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.21, C:0.21, G:0.34, T:0.25
Consensus pattern (20 bp):
GTGCATCGATGCATGGCAGT
Found at i:51394 original size:12 final size:12
Alignment explanation
Indices: 51377--51401 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
51367 CACTATTCGG
51377 TGTATCGATGCA
1 TGTATCGATGCA
51389 TGTATCGATGCA
1 TGTATCGATGCA
51401 T
1 T
51402 TATGCACAAA
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:0.16, G:0.24, T:0.36
Consensus pattern (12 bp):
TGTATCGATGCA
Found at i:60430 original size:118 final size:117
Alignment explanation
Indices: 60160--60661 Score: 455
Period size: 120 Copynumber: 4.3 Consensus size: 117
60150 AAAAAAGGGA
* * * * * * * * * *
60160 TCAAATTCATCATAGAAGGAGTTAGATCAACATTTCCATTGGAGAGTTCATAATGAGAAGAACCC
1 TCAAATCCATCACAGAATGAGGTGGATTAACATTTCAAATGGTGAGTTCATAATGAGAAGAACTC
* * * * * *
60225 ATCCAAGAGGGAGAAGAAGATCATAATGAGAAGAACTTGTTCGACCTTTCGC
66 ATTCACGAGGGAGAAGAAGTTCATAATGAGAAGAACATATTCGACCTTTTGC
* * *
60277 TCAAATCCATCATAGAATAAGGTGGATTAACATTTC-AATGAG-GAGTTCATAATGAGAATAACT
1 TCAAATCCATCACAGAATGAGGTGGATTAACATTTCAAATG-GTGAGTTCATAATGAGAAGAACT
* * * *
60340 CATTCACGAAGTGAGAAGAAGTTCATAATGAAAAGAATC-TATTCGATCTTTTTAC
65 CATTCACG-AGGGAGAAGAAGTTCATAATGAGAAGAA-CATATTCGA-CCTTTTGC
* *
60395 TCAAATCCATCACAGAATGAGATGGATTAATATTTCCAAATGGTGAGTTCATAATGAGAAGAACT
1 TCAAATCCATCACAGAATGAGGTGGATTAACATTT-CAAATGGTGAGTTCATAATGAGAAGAACT
* *
60460 CA-TCTACGGAGGGA-AAAACAGGTTCATAATGAGAAGAACATATTCAACCTTTTGC
65 CATTC-AC-GAGGGAGAAGA-A-GTTCATAATGAGAAGAACATATTCGACCTTTTGC
* * * *
60515 TCAAATCCATCACAGAAAGAGGTGGATCAACATTTCTAAACGGTGAATTCATAATGAGAAGAACT
1 TCAAATCCATCACAGAATGAGGTGGATTAACATTTC-AAATGGTGAGTTCATAATGAGAAGAACT
* * * * ** * **
60580 C-GTCGACAGAGGGATAAAAAGTTCACAATGAGAAGAATTTGTTCGA-CTTTTAT
65 CATTC-AC-GAGGGAGAAGAAGTTCATAATGAGAAGAACATATTCGACCTTTTGC
*
60633 TTAAA-CCATCACAGAA-GAAGGTGGATTAA
1 TCAAATCCATCACAGAATG-AGGTGGATTAA
60662 TAGGGAGTTC
Statistics
Matches: 323, Mismatches: 46, Indels: 32
0.81 0.11 0.08
Matches are distributed among these distances:
116 29 0.09
117 83 0.26
118 46 0.14
119 29 0.09
120 109 0.34
121 27 0.08
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.26
Consensus pattern (117 bp):
TCAAATCCATCACAGAATGAGGTGGATTAACATTTCAAATGGTGAGTTCATAATGAGAAGAACTC
ATTCACGAGGGAGAAGAAGTTCATAATGAGAAGAACATATTCGACCTTTTGC
Found at i:61452 original size:2 final size:2
Alignment explanation
Indices: 61445--61503 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
61435 TTATTTGTGT
61445 TA TA TA TA TA 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 TA TA TA TA TA
61487 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
61504 TTCTAGACAT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:65931 original size:29 final size:29
Alignment explanation
Indices: 65881--65957 Score: 100
Period size: 29 Copynumber: 2.6 Consensus size: 29
65871 AAAAATTCGG
* *
65881 TTAATCGAACCAAAATTTATTTGAAAATTA
1 TTAACCGAACC-AAATTAATTTGAAAATTA
* *
65911 TTAACCTAACCAAATTAATTTTAAAATTA
1 TTAACCGAACCAAATTAATTTGAAAATTA
*
65940 TTAACCGAACCGAATTAA
1 TTAACCGAACCAAATTAA
65958 CCAATTTTGT
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
29 32 0.78
30 9 0.22
ACGTcount: A:0.47, C:0.14, G:0.05, T:0.34
Consensus pattern (29 bp):
TTAACCGAACCAAATTAATTTGAAAATTA
Found at i:66071 original size:29 final size:29
Alignment explanation
Indices: 66034--66161 Score: 121
Period size: 29 Copynumber: 4.2 Consensus size: 29
66024 ATCGAACCAA
* *
66034 AATTTATTTGAAAATTATTAACCGAACTG
1 AATTAATTTGAAAATTATTAACCGAACCG
*
66063 AATTAATTTGAAAATTATTAACCAAACCG
1 AATTAATTTGAAAATTATTAACCGAACCG
*** * *
66092 AATTAACTTATTTTTTTAATTATTAATCGAACCAA
1 AATT-A---A-TTTGAAAATTATTAACCGAACC-G
*
66127 AATTTATTTGAAAATTATTAACCGAACCG
1 AATTAATTTGAAAATTATTAACCGAACCG
66156 AATTAA
1 AATTAA
66162 CCGATTTTTT
Statistics
Matches: 77, Mismatches: 16, Indels: 12
0.73 0.15 0.11
Matches are distributed among these distances:
29 35 0.45
30 19 0.25
31 1 0.01
33 1 0.01
34 17 0.22
35 4 0.05
ACGTcount: A:0.44, C:0.12, G:0.07, T:0.38
Consensus pattern (29 bp):
AATTAATTTGAAAATTATTAACCGAACCG
Found at i:66091 original size:34 final size:32
Alignment explanation
Indices: 66021--66158 Score: 119
Period size: 30 Copynumber: 4.5 Consensus size: 32
66011 TTCGATTTAG
* *
66021 TTAATCGAACC-AA-AATTTATTTGAAAATTA
1 TTAACCGAACCGAATAATTAATTTGAAAATTA
*
66051 TTAACCGAACTG---AATTAATTTGAAAATTA
1 TTAACCGAACCGAATAATTAATTTGAAAATTA
* * ***
66080 TTAACCAAACCGAATTAACTTATTTTTTTAATTA
1 TTAACCGAACCGAA-TAA-TTAATTTGAAAATTA
* *
66114 TTAATCGAACC-AA-AATTTATTTGAAAATTA
1 TTAACCGAACCGAATAATTAATTTGAAAATTA
66144 TTAACCGAACCGAAT
1 TTAACCGAACCGAAT
66159 TAACCGATTT
Statistics
Matches: 83, Mismatches: 17, Indels: 14
0.73 0.15 0.12
Matches are distributed among these distances:
29 26 0.31
30 29 0.35
31 4 0.05
33 4 0.05
34 20 0.24
ACGTcount: A:0.43, C:0.13, G:0.07, T:0.36
Consensus pattern (32 bp):
TTAACCGAACCGAATAATTAATTTGAAAATTA
Found at i:66145 original size:64 final size:63
Alignment explanation
Indices: 66046--66189 Score: 189
Period size: 64 Copynumber: 2.2 Consensus size: 63
66036 TTTATTTGAA
** **
66046 AATTATTAACCGAACTGAATTAATTTGAAAATTATTAACCAAACCGAATTAACTTATTTTTTT
1 AATTATTAACCGAACAAAATTAATTTGAAAATTATTAACCAAACCGAATTAACCGATTTTTTT
* * *
66109 AATTATTAATCGAACCAAAATTTATTTGAAAATTATTAACCGAACCGAATTAACCGATTTTTTTT
1 AATTATTAACCGAA-CAAAATTAATTTGAAAATTATTAACCAAACCGAATTAACCGA-TTTTTTT
66174 AAAATTATTAACCGAA
1 --AATTATTAACCGAA
66190 TTAATCGAAG
Statistics
Matches: 69, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
63 13 0.19
64 36 0.52
65 7 0.10
67 13 0.19
ACGTcount: A:0.42, C:0.13, G:0.07, T:0.38
Consensus pattern (63 bp):
AATTATTAACCGAACAAAATTAATTTGAAAATTATTAACCAAACCGAATTAACCGATTTTTTT
Found at i:66282 original size:29 final size:29
Alignment explanation
Indices: 66236--66299 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 29
66226 TAATCGAACA
* * * *
66236 AATTTATTAGAAATTTATTAACCGAACTG
1 AATTAATTAGAAAATTATTAACCAAACCG
*
66265 AATTAATTTGAAAATTATTAACCAAACCG
1 AATTAATTAGAAAATTATTAACCAAACCG
66294 AATTAA
1 AATTAA
66300 CCGATTTTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.47, C:0.11, G:0.08, T:0.34
Consensus pattern (29 bp):
AATTAATTAGAAAATTATTAACCAAACCG
Found at i:66286 original size:138 final size:137
Alignment explanation
Indices: 66109--66564 Score: 483
Period size: 122 Copynumber: 3.5 Consensus size: 137
66099 TTATTTTTTT
* *
66109 AATTATTAATCGAACCAAAATTTATTTGAAAATTATTAACCGAACCGAATTAACCGATTTTTTTT
1 AATTATTAACCGAACC-AAATTAATTTGAAAATTATTAACCGAACCGAATTAACCGA-TTTTTTT
* * *
66174 AAAATTATTAACCGAATTAATCGAAGCAAAAATTCGGTTAATTC-AGTTTGGTTAATCGAA-C-A
64 --AATTATTAACCGAATTAATCGAAGAAAAAATTCGGTTAATTCGACTCT-GTTAATCGAACCAA
66236 AATTTATTAGAA
126 AATTTATTAGAA
* ** *
66248 ATTTATTAACCGAACTGAATTAATTTGAAAATTATTAACCAAACCGAATTAACCGATTTTTTTAA
1 AATTATTAACCGAACCAAATTAATTTGAAAATTATTAACCGAACCGAATTAACCGATTTTTTTAA
* *
66313 TTATTAATCGAATTAATCGAAGAAAAAATTGGGTTAATTCGACTCTGTTAATCGAACCAAAATTT
66 TTATTAACCGAATTAATCGAAGAAAAAATTCGGTTAATTCGACTCTGTTAATCGAACCAAAATTT
*
66378 ATTTGAA
131 ATTAGAA
66385 AATTATTAACCGAACCAAATTAATTTG-AAA--ATT-----------ATTAACCGA-TTTTTTAA
1 AATTATTAACCGAACCAAATTAATTTGAAAATTATTAACCGAACCGAATTAACCGATTTTTTTAA
** * ** * *
66435 TTATTAATTGAATTAATCGAAGCAAAAAA-TCGGCTAATTCGGTTCGGTTAATGGAACCAAAATT
66 TTATTAACCGAATTAATCGAAG-AAAAAATTCGGTTAATTCGACTCTGTTAATCGAACCAAAATT
* *
66499 TATTTGTA
130 TATTAGAA
* *
66507 AATTATTAACCG-----AATTAATTTGAAAATTATTCACCGAACCGAATTAACCGTTTTTTTT
1 AATTATTAACCGAACCAAATTAATTTGAAAATTATTAACCGAACCGAATTAACCGATTTTTTT
66565 TCTTTAACCA
Statistics
Matches: 274, Mismatches: 24, Indels: 45
0.80 0.07 0.13
Matches are distributed among these distances:
117 10 0.04
118 3 0.01
120 3 0.01
122 77 0.28
123 15 0.05
131 8 0.03
132 6 0.02
134 3 0.01
135 49 0.18
136 7 0.03
137 43 0.16
138 37 0.14
139 13 0.05
ACGTcount: A:0.40, C:0.12, G:0.11, T:0.36
Consensus pattern (137 bp):
AATTATTAACCGAACCAAATTAATTTGAAAATTATTAACCGAACCGAATTAACCGATTTTTTTAA
TTATTAACCGAATTAATCGAAGAAAAAATTCGGTTAATTCGACTCTGTTAATCGAACCAAAATTT
ATTAGAA
Found at i:66322 original size:202 final size:203
Alignment explanation
Indices: 65906--66324 Score: 684
Period size: 204 Copynumber: 2.1 Consensus size: 203
65896 TTTATTTGAA
* * *
65906 AATTATTAACCTAACCAAATTAATTTTAAAATTATTAACCGAACCGAATTAACCAATTTTGTTTT
1 AATTATTAATCGAACCAAATTAATTTGAAAATTATTAACCGAACCGAATTAACCAATTTTGTTTT
65971 AAATTATTAACCGAATTAATCGAAGAAAAAATTCGGTTAATTCGATTTAGTTAATCGAACCAAAA
66 AAATTATTAACCGAATTAATCGAAGAAAAAATTCGGTTAATTCGATTTAGTTAATCGAACCAAAA
* **
66036 TTTATTTGAAAATTATTAACCGAACTGAATTAATTTGAAAATTATTAACCAAACCGAATTAACTT
131 TTTATTAGAAAATTATTAACCGAACTGAATTAATTTGAAAATTATTAACCAAACCGAATTAACCG
66101 ATTTTTTT
196 ATTTTTTT
* *
66109 AATTATTAATCGAACCAAAATTTATTTGAAAATTATTAACCGAACCGAATTAACCGATTTT-TTT
1 AATTATTAATCGAACC-AAATTAATTTGAAAATTATTAACCGAACCGAATTAACCAATTTTGTTT
* *
66173 TAAAATTATTAACCGAATTAATCGAAGCAAAAATTCGGTTAATTC-AGTTTGGTTAATCGAA-C-
65 T-AAATTATTAACCGAATTAATCGAAGAAAAAATTCGGTTAATTCGA-TTTAGTTAATCGAACCA
*
66235 AAATTTATTAGAAATTTATTAACCGAACTGAATTAATTTGAAAATTATTAACCAAACCGAATTAA
128 AAATTTATTAGAAAATTATTAACCGAACTGAATTAATTTGAAAATTATTAACCAAACCGAATTAA
66300 CCGATTTTTTT
193 CCGATTTTTTT
66311 AATTATTAATCGAA
1 AATTATTAATCGAA
66325 TTAATCGAAG
Statistics
Matches: 202, Mismatches: 11, Indels: 7
0.92 0.05 0.03
Matches are distributed among these distances:
202 86 0.43
203 20 0.10
204 96 0.48
ACGTcount: A:0.42, C:0.13, G:0.09, T:0.37
Consensus pattern (203 bp):
AATTATTAATCGAACCAAATTAATTTGAAAATTATTAACCGAACCGAATTAACCAATTTTGTTTT
AAATTATTAACCGAATTAATCGAAGAAAAAATTCGGTTAATTCGATTTAGTTAATCGAACCAAAA
TTTATTAGAAAATTATTAACCGAACTGAATTAATTTGAAAATTATTAACCAAACCGAATTAACCG
ATTTTTTT
Found at i:66410 original size:29 final size:30
Alignment explanation
Indices: 66360--66426 Score: 109
Period size: 29 Copynumber: 2.3 Consensus size: 30
66350 TTCGACTCTG
* *
66360 TTAATCGAACCAAAATTTATTTGAAAATTA
1 TTAACCGAACCAAAATTAATTTGAAAATTA
66390 TTAACCGAACC-AAATTAATTTGAAAATTA
1 TTAACCGAACCAAAATTAATTTGAAAATTA
66419 TTAACCGA
1 TTAACCGA
66427 TTTTTTAATT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
29 25 0.71
30 10 0.29
ACGTcount: A:0.46, C:0.13, G:0.07, T:0.33
Consensus pattern (30 bp):
TTAACCGAACCAAAATTAATTTGAAAATTA
Found at i:66527 original size:24 final size:24
Alignment explanation
Indices: 66495--66544 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
66485 ATGGAACCAA
* *
66495 AATTTATTTGTAAATTATTAACCG
1 AATTAATTTGAAAATTATTAACCG
*
66519 AATTAATTTGAAAATTATTCACCG
1 AATTAATTTGAAAATTATTAACCG
66543 AA
1 AA
66545 CCGAATTAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.42, C:0.10, G:0.08, T:0.40
Consensus pattern (24 bp):
AATTAATTTGAAAATTATTAACCG
Found at i:67375 original size:183 final size:184
Alignment explanation
Indices: 67067--67453 Score: 629
Period size: 183 Copynumber: 2.1 Consensus size: 184
67057 TTTTCTAATT
* * * *
67067 TATATAA-AAATTAAATATTTTTTAATTCAAAAAAAGTTTATAATTAATTTAAATAATATATAAC
1 TATATAATATATTTAATATTTTTTAATTCAAAAAAAGTTTACAAATAATTTAAATAATATATAAC
*
67131 TATAAAATAAAAATTTTAGATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATT
66 TATAAAATAAAAAATTTAGATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATT
* *
67196 GGATCTTAAATTATTAATTGGATTTTAAATGGTTTGGGCTT-AGTCCATATGTTA
131 GGATCTTAAATTATTAATTGGATTTTAAATGATTTGGG-TTGAGCCCATATGTTA
67250 TATATAATATATTTAATATTTTTTAATT-AAAAAACAGTTTACAAATAATTTAAATAATATATAA
1 TATATAATATATTTAATATTTTTTAATTCAAAAAA-AGTTTACAAATAATTTAAATAATATATAA
* *
67314 TTATAAAATAAAAAATTTATAT-AATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTAT
65 CTATAAAATAAAAAATTTAGATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTAT
*
67378 TGGATCTTAAATTATTAATTGGGTTTTAAATGATTTGGGTTGAGCCCATATGTTA
130 TGGATCTTAAATTATTAATTGGATTTTAAATGATTTGGGTTGAGCCCATATGTTA
*
67433 TATATAATATATTTAAAATTT
1 TATATAATATATTTAATATTT
67454 AAAATTTAAT
Statistics
Matches: 190, Mismatches: 11, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
182 2 0.01
183 124 0.65
184 64 0.34
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.45
Consensus pattern (184 bp):
TATATAATATATTTAATATTTTTTAATTCAAAAAAAGTTTACAAATAATTTAAATAATATATAAC
TATAAAATAAAAAATTTAGATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATT
GGATCTTAAATTATTAATTGGATTTTAAATGATTTGGGTTGAGCCCATATGTTA
Found at i:67867 original size:30 final size:30
Alignment explanation
Indices: 67831--67897 Score: 93
Period size: 30 Copynumber: 2.3 Consensus size: 30
67821 AGAATATGTA
*
67831 AATATTA-AGGACTAAATATATAATTATGCC
1 AATATTATA-GACCAAATATATAATTATGCC
*
67861 AATATTATAGACCAAATATATAATTATGCA
1 AATATTATAGACCAAATATATAATTATGCC
67891 AAT-TTAT
1 AATATTAT
67898 TAACGGACAC
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
29 4 0.12
30 29 0.85
31 1 0.03
ACGTcount: A:0.48, C:0.09, G:0.07, T:0.36
Consensus pattern (30 bp):
AATATTATAGACCAAATATATAATTATGCC
Found at i:68377 original size:12 final size:12
Alignment explanation
Indices: 68344--68385 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
68334 CTTGATCTGT
68344 TCTT-TTGTTAC
1 TCTTCTTGTTAC
*
68355 TGTTACTTGTTAC
1 TCTT-CTTGTTAC
68368 TCTTCTTGTTAC
1 TCTTCTTGTTAC
*
68380 TATTCT
1 TCTTCT
68386 CTTTTATTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
11 3 0.12
12 13 0.50
13 10 0.38
ACGTcount: A:0.12, C:0.19, G:0.10, T:0.60
Consensus pattern (12 bp):
TCTTCTTGTTAC
Found at i:70052 original size:18 final size:19
Alignment explanation
Indices: 70029--70071 Score: 70
Period size: 20 Copynumber: 2.3 Consensus size: 19
70019 CAGTAATCCT
70029 ATTCC-CTGGTAATCTTAC
1 ATTCCACTGGTAATCTTAC
70047 ATTCCCACTGGTAATCTTAC
1 ATT-CCACTGGTAATCTTAC
70067 ATTCC
1 ATTCC
70072 GTGAACCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 3 0.13
19 4 0.17
20 16 0.70
ACGTcount: A:0.23, C:0.30, G:0.09, T:0.37
Consensus pattern (19 bp):
ATTCCACTGGTAATCTTAC
Found at i:70059 original size:20 final size:20
Alignment explanation
Indices: 70034--70071 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
70024 ATCCTATTCC
70034 CTGGTAATCTTACATTCCCA
1 CTGGTAATCTTACATTCCCA
70054 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
70072 GTGAACCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.24, C:0.29, G:0.11, T:0.37
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:76753 original size:21 final size:22
Alignment explanation
Indices: 76715--76757 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
76705 TATGAGAAAT
*
76715 TGTTTTTAAAGTATAAAAATGA
1 TGTTTTGAAAGTATAAAAATGA
*
76737 TGTTTTGAAATTA-AAAAATGA
1 TGTTTTGAAAGTATAAAAATGA
76758 AAATAAACTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.47, C:0.00, G:0.14, T:0.40
Consensus pattern (22 bp):
TGTTTTGAAAGTATAAAAATGA
Found at i:80604 original size:20 final size:21
Alignment explanation
Indices: 80569--80628 Score: 59
Period size: 20 Copynumber: 2.8 Consensus size: 21
80559 TATTTGGCAG
* *
80569 AGGGAATCGATACCCCTAT-A
1 AGGGAATTGATTCCCCTATGA
*
80589 AGGGAATTGATTCCCCATTTGA
1 AGGGAATTGATTCCCC-TATGA
*
80611 ATAGGAATTGATTCCCCT
1 A-GGGAATTGATTCCCCT
80629 TGTAGGGGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
20 14 0.42
21 2 0.06
22 3 0.09
23 14 0.42
ACGTcount: A:0.30, C:0.22, G:0.20, T:0.28
Consensus pattern (21 bp):
AGGGAATTGATTCCCCTATGA
Found at i:82610 original size:22 final size:23
Alignment explanation
Indices: 82585--82628 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
82575 AATTAAGTTT
82585 TAATCTT--AAAATAATTTCAAAA
1 TAATCTTACAAAAT-ATTTCAAAA
*
82607 TAATTTTACAAAATATTTCAAA
1 TAATCTTACAAAATATTTCAAA
82629 CCATTTCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 6 0.32
23 8 0.42
24 5 0.26
ACGTcount: A:0.52, C:0.09, G:0.00, T:0.39
Consensus pattern (23 bp):
TAATCTTACAAAATATTTCAAAA
Found at i:88496 original size:15 final size:15
Alignment explanation
Indices: 88478--88533 Score: 67
Period size: 15 Copynumber: 3.6 Consensus size: 15
88468 TAACCGGTTT
88478 CGGTTTTAAAAAAAC
1 CGGTTTTAAAAAAAC
*
88493 CGGTTTTTTTAAAAAAC
1 CGG--TTTTAAAAAAAC
*
88510 CGGTTATAAAAAAAC
1 CGGTTTTAAAAAAAC
*
88525 CGATTTTAA
1 CGGTTTTAA
88534 TATTCCAGAT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
15 20 0.59
17 14 0.41
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.32
Consensus pattern (15 bp):
CGGTTTTAAAAAAAC
Found at i:88506 original size:17 final size:17
Alignment explanation
Indices: 88481--88531 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
88471 CCGGTTTCGG
88481 TTTTAAAAAAACCGGTT
1 TTTTAAAAAAACCGGTT
*
88498 TTTTTAAAAAACCGG--
1 TTTTAAAAAAACCGGTT
* *
88513 TTATAAAAAAACCGATT
1 TTTTAAAAAAACCGGTT
88530 TT
1 TT
88532 AATATTCCAG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 12 0.43
17 16 0.57
ACGTcount: A:0.43, C:0.12, G:0.10, T:0.35
Consensus pattern (17 bp):
TTTTAAAAAAACCGGTT
Found at i:88950 original size:13 final size:13
Alignment explanation
Indices: 88929--88983 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
88919 AAGTTCGATA
*
88929 AATTCAAATACTT
1 AATTGAAATACTT
88942 AATTGAAATACTT
1 AATTGAAATACTT
* *
88955 AATT-AACTCAACAT
1 AATTGAAAT--ACTT
88969 AATTGAAATACTT
1 AATTGAAATACTT
88982 AA
1 AA
88984 ATACTTCCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.35
Consensus pattern (13 bp):
AATTGAAATACTT
Found at i:89065 original size:32 final size:33
Alignment explanation
Indices: 88969--89067 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
88959 AACTCAACAT
* * *
88969 AATTGAAATACTTAAATACTTCCAAGTTTGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
89002 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
89035 AATTCAAATACTTAAAAACTT-CAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
89067 A
1 A
89068 TTGAAACAAA
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 12 0.19
33 51 0.81
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.32
Consensus pattern (33 bp):
AATTCAAATACTTAAAAACTTCCAAGTTCGATA
Found at i:89087 original size:20 final size:20
Alignment explanation
Indices: 89057--89101 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
89047 TAAAAACTTC
89057 AAGTT-CGATAATTGAAACA
1 AAGTTACGATAATTGAAACA
*
89076 AAGTTACGATAATTGAAATA
1 AAGTTACGATAATTGAAACA
89096 AAGTTA
1 AAGTTA
89102 TAAAATAAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 5 0.21
20 19 0.79
ACGTcount: A:0.49, C:0.07, G:0.16, T:0.29
Consensus pattern (20 bp):
AAGTTACGATAATTGAAACA
Found at i:91407 original size:12 final size:12
Alignment explanation
Indices: 91390--91435 Score: 56
Period size: 12 Copynumber: 3.6 Consensus size: 12
91380 TTCGGATAAA
91390 AACCGGTTTTTT
1 AACCGGTTTTTT
91402 AACCGGTTTTTTT
1 AACCGG-TTTTTT
91415 CAAACCGGTTTTTT
1 --AACCGGTTTTTT
*
91429 ATCCGGT
1 AACCGGT
91436 AAAAAAACCG
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
12 12 0.40
13 6 0.20
14 6 0.20
15 6 0.20
ACGTcount: A:0.17, C:0.20, G:0.17, T:0.46
Consensus pattern (12 bp):
AACCGGTTTTTT
Found at i:91420 original size:15 final size:14
Alignment explanation
Indices: 91389--91428 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
91379 TTTCGGATAA
91389 AAACCGG-TTTTTT
1 AAACCGGTTTTTTT
91402 -AACCGGTTTTTTT
1 AAACCGGTTTTTTT
91415 CAAACCGGTTTTTT
1 -AAACCGGTTTTTT
91429 ATCCGGTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 6 0.25
13 6 0.25
15 12 0.50
ACGTcount: A:0.20, C:0.17, G:0.15, T:0.47
Consensus pattern (14 bp):
AAACCGGTTTTTTT
Found at i:95603 original size:24 final size:24
Alignment explanation
Indices: 95575--95620 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
95565 TTACATTATC
* *
95575 TAAGCGGATCTTACCTCTTAATCT
1 TAAGCGGATCCTACCTCCTAATCT
95599 TAAGCGGATCCTACCTCCTAAT
1 TAAGCGGATCCTACCTCCTAAT
95621 AAAATATGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.26, C:0.28, G:0.13, T:0.33
Consensus pattern (24 bp):
TAAGCGGATCCTACCTCCTAATCT
Found at i:102530 original size:17 final size:18
Alignment explanation
Indices: 102488--102530 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
102478 AATGATTATG
*
102488 TTATAATATTTTGATAAA
1 TTATAATATTATGATAAA
*
102506 TTAT-ATATTATGAT-AT
1 TTATAATATTATGATAAA
102522 TTATAATAT
1 TTATAATAT
102531 GTTATAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 5 0.23
17 13 0.59
18 4 0.18
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (18 bp):
TTATAATATTATGATAAA
Found at i:106057 original size:6 final size:6
Alignment explanation
Indices: 106046--106161 Score: 90
Period size: 6 Copynumber: 19.3 Consensus size: 6
106036 TTGAGTTGGG
* * **
106046 GGTGGT GGTGGT GATGGT GAT-GT GGATGGT GGTGGT GGTGAA GGTGGT
1 GGTGGT GGTGGT GGTGGT GGTGGT GG-TGGT GGTGGT GGTGGT GGTGGT
* * * ** * *
106094 GGTGAT GATGGT GGTGGT GGTGAT GGTGAC GGTGGT GGTGGA GTTGGT
1 GGTGGT GGTGGT GGTGGT GGTGGT GGTGGT GGTGGT GGTGGT GGTGGT
* * *
106142 TGTGGT GGCGGT GGCGGT GG
1 GGTGGT GGTGGT GGTGGT GG
106162 AGGAGTTGAG
Statistics
Matches: 87, Mismatches: 21, Indels: 4
0.78 0.19 0.04
Matches are distributed among these distances:
5 3 0.03
6 80 0.92
7 4 0.05
ACGTcount: A:0.09, C:0.03, G:0.59, T:0.30
Consensus pattern (6 bp):
GGTGGT
Found at i:106130 original size:15 final size:15
Alignment explanation
Indices: 106046--106121 Score: 104
Period size: 15 Copynumber: 5.3 Consensus size: 15
106036 TTGAGTTGGG
106046 GGTGGTGGTGGTGAT
1 GGTGGTGGTGGTGAT
*
106061 GGTGAT-GT-G-GAT
1 GGTGGTGGTGGTGAT
*
106073 GGTGGTGGTGGTGAA
1 GGTGGTGGTGGTGAT
*
106088 GGTGGTGGTGATGAT
1 GGTGGTGGTGGTGAT
106103 GGTGGTGGTGGTGAT
1 GGTGGTGGTGGTGAT
106118 GGTG
1 GGTG
106122 ACGGTGGTGG
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
12 8 0.15
13 3 0.06
14 3 0.06
15 38 0.73
ACGTcount: A:0.11, C:0.00, G:0.58, T:0.32
Consensus pattern (15 bp):
GGTGGTGGTGGTGAT
Found at i:106132 original size:27 final size:28
Alignment explanation
Indices: 106046--106134 Score: 110
Period size: 30 Copynumber: 3.2 Consensus size: 28
106036 TTGAGTTGGG
*
106046 GGTGGTGGTGGTGATGGTGA-TGTGGAT
1 GGTGGTGGTGGTGATGGTGACGGTGGAT
* **
106073 GGTGGTGGTGGTGAAGGTGGTGGTGATGAT
1 GGTGGTGGTGGTGATGGTGACGGTG--GAT
106103 GGTGGTGGTGGTGATGGTGACGGTGG-T
1 GGTGGTGGTGGTGATGGTGACGGTGGAT
106130 GGTGG
1 GGTGG
106135 AGTTGGTTGT
Statistics
Matches: 53, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
27 24 0.45
28 4 0.08
30 25 0.47
ACGTcount: A:0.10, C:0.01, G:0.58, T:0.30
Consensus pattern (28 bp):
GGTGGTGGTGGTGATGGTGACGGTGGAT
Found at i:106141 original size:27 final size:27
Alignment explanation
Indices: 106046--106163 Score: 93
Period size: 27 Copynumber: 4.5 Consensus size: 27
106036 TTGAGTTGGG
* *
106046 GGTGGTGGTGGTGATGGTGAT-GTGGAT
1 GGTGGTGGTGGAGATGGTGATGGT-GAC
* * * *
106073 GGTGGTGGTGGTGAAGGTGGTGGTGAT
1 GGTGGTGGTGGAGATGGTGATGGTGAC
*
106100 GATGGTGGT-G-G-TGGTGATGGTGAC
1 GGTGGTGGTGGAGATGGTGATGGTGAC
* *
106124 GGTGGTGGTGGAGTTGGTTG-TGGTGGC
1 GGTGGTGGTGGAGATGG-TGATGGTGAC
*
106151 GGTGGCGGTGGAG
1 GGTGGTGGTGGAG
106164 GAGTTGAGTC
Statistics
Matches: 77, Mismatches: 9, Indels: 10
0.80 0.09 0.10
Matches are distributed among these distances:
24 18 0.23
25 2 0.03
26 2 0.03
27 51 0.66
28 4 0.05
ACGTcount: A:0.09, C:0.03, G:0.58, T:0.30
Consensus pattern (27 bp):
GGTGGTGGTGGAGATGGTGATGGTGAC
Found at i:106547 original size:12 final size:12
Alignment explanation
Indices: 106530--106568 Score: 69
Period size: 12 Copynumber: 3.2 Consensus size: 12
106520 ATGAAGAGGG
106530 AAAAGAAAAGAA
1 AAAAGAAAAGAA
106542 AAAAGAAAAGAA
1 AAAAGAAAAGAA
106554 AAAAGAAATAGAA
1 AAAAGAAA-AGAA
106567 AA
1 AA
106569 TGAAAATGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 20 0.77
13 6 0.23
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (12 bp):
AAAAGAAAAGAA
Found at i:106573 original size:24 final size:25
Alignment explanation
Indices: 106530--106579 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 25
106520 ATGAAGAGGG
106530 AAAAGAAAAGAAAAAAGAAAA-GAA
1 AAAAGAAAAGAAAAAAGAAAATGAA
*
106554 AAAAGAAATAG-AAAATGAAAATGAA
1 AAAAGAAA-AGAAAAAAGAAAATGAA
106579 A
1 A
106580 GTACCTTGAG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 17 0.74
25 6 0.26
ACGTcount: A:0.78, C:0.00, G:0.16, T:0.06
Consensus pattern (25 bp):
AAAAGAAAAGAAAAAAGAAAATGAA
Done.