Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000354.1 Hibiscus syriacus cultivar Beakdansim tig00000650_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: 117882
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:1047 original size:20 final size:20
Alignment explanation
Indices: 1022--1126 Score: 113
Period size: 20 Copynumber: 5.7 Consensus size: 20
1012 ATTTGAATTT
1022 TTTTATAATAATTAACTTGA
1 TTTTATAATAATTAACTTGA
1042 TTTTATAATAATT---TGTG-
1 TTTTATAATAATTAACT-TGA
*
1059 TATGTAT-AT-ATT----TGA
1 T-TTTATAATAATTAACTTGA
1074 TTTTATAATAATTAACTTGA
1 TTTTATAATAATTAACTTGA
1094 TTTTATAATAATTAACTTGA
1 TTTTATAATAATTAACTTGA
1114 TTTTATAATAATT
1 TTTTATAATAATT
1127 TATGTATATA
Statistics
Matches: 74, Mismatches: 2, Indels: 18
0.79 0.02 0.19
Matches are distributed among these distances:
14 6 0.08
15 3 0.04
16 6 0.08
17 4 0.05
18 6 0.08
20 49 0.66
ACGTcount: A:0.37, C:0.03, G:0.07, T:0.53
Consensus pattern (20 bp):
TTTTATAATAATTAACTTGA
Found at i:1172 original size:22 final size:22
Alignment explanation
Indices: 1147--1192 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
1137 ATTAACTTTA
*
1147 TTTTATAATATAA-TTATGTAT
1 TTTTTTAATATAATTTATGTAT
* *
1168 TTTTTTAGTATAATTTATGTGT
1 TTTTTTAATATAATTTATGTAT
1190 TTT
1 TTT
1193 AAGTTGAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.28, C:0.00, G:0.09, T:0.63
Consensus pattern (22 bp):
TTTTTTAATATAATTTATGTAT
Found at i:2446 original size:17 final size:17
Alignment explanation
Indices: 2415--2448 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
2405 ACCATTTGAT
2415 CATGATATTTCCATATG
1 CATGATATTTCCATATG
2432 CATGTATATTT-CATATG
1 CATG-ATATTTCCATATG
2449 ACATATATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.29, C:0.15, G:0.12, T:0.44
Consensus pattern (17 bp):
CATGATATTTCCATATG
Found at i:2457 original size:18 final size:18
Alignment explanation
Indices: 2419--2457 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
2409 TTTGATCATG
*
2419 ATATTTCCATATGCATGT
1 ATATTTCCATATGCATAT
2437 ATATTT-CATATGACATAT
1 ATATTTCCATATG-CATAT
2455 ATA
1 ATA
2458 ACCAAGTCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.36, C:0.13, G:0.08, T:0.44
Consensus pattern (18 bp):
ATATTTCCATATGCATAT
Found at i:3321 original size:18 final size:18
Alignment explanation
Indices: 3298--3332 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
3288 TTCATTTAGG
3298 GGGGAATCGATACCCCCA
1 GGGGAATCGATACCCCCA
3316 GGGGAATCGATACCCCC
1 GGGGAATCGATACCCCC
3333 TGAACATACT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.26, C:0.34, G:0.29, T:0.11
Consensus pattern (18 bp):
GGGGAATCGATACCCCCA
Found at i:12327 original size:21 final size:18
Alignment explanation
Indices: 12298--12351 Score: 63
Period size: 21 Copynumber: 2.8 Consensus size: 18
12288 AAACTTCTAC
*
12298 TATTTAATAATAATAGTT
1 TATTAAATAATAATAGTT
*
12316 TATTCTCAAATAATAATATTT
1 TA-T-T-AAATAATAATAGTT
12337 TATTAAATAATAATA
1 TATTAAATAATAATA
12352 ACATCATCTC
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
18 13 0.42
19 2 0.06
20 2 0.06
21 14 0.45
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (18 bp):
TATTAAATAATAATAGTT
Found at i:12574 original size:3 final size:3
Alignment explanation
Indices: 12566--12641 Score: 54
Period size: 3 Copynumber: 26.0 Consensus size: 3
12556 TATTTCTTTA
* *
12566 TTC TTC TTC TTC TTC TTT TTC TTCC TT- TAT- TTC TTC TCC TT- TTC
1 TTC TTC TTC TTC TTC TTC TTC TT-C TTC T-TC TTC TTC TTC TTC TTC
* *
12610 TTA TTC TT- TTC TTTC TTC -TC CTC TTC TTC TTC
1 TTC TTC TTC TTC -TTC TTC TTC TTC TTC TTC TTC
12642 GTTACTCCCG
Statistics
Matches: 59, Mismatches: 7, Indels: 14
0.74 0.09 0.17
Matches are distributed among these distances:
2 8 0.14
3 45 0.76
4 6 0.10
ACGTcount: A:0.03, C:0.30, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:13765 original size:17 final size:17
Alignment explanation
Indices: 13743--13778 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
13733 GATTTATATA
**
13743 AAAAAATATTTAAATTT
1 AAAAAATATAAAAATTT
13760 AAAAAATATAAAAATTT
1 AAAAAATATAAAAATTT
13777 AA
1 AA
13779 TTAAATAGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
AAAAAATATAAAAATTT
Found at i:14246 original size:42 final size:41
Alignment explanation
Indices: 14198--14345 Score: 144
Period size: 41 Copynumber: 3.6 Consensus size: 41
14188 TTAAACAATA
*
14198 CGGCGTTTATAGTAAAAACGCCGCAATATAGTAG-ACATTTAG
1 CGGCGTTTATAGTAAAAACGCCGCAATATAGT-GTA-ATATAG
14240 CGGCGTTT-TAGCT-AAAACGCCGCAATATAGTGTAATATAG
1 CGGCGTTTATAG-TAAAAACGCCGCAATATAGTGTAATATAG
* * * * * * *
14280 CGACGTTTATTGTATAAACGCCGCAAAAAACATGTGATATAG
1 CGGCGTTTATAGTAAAAACGCCGCAATATA-GTGTAATATAG
*
14322 TGGCGTTT-T-GTAAAAACGCCGCAA
1 CGGCGTTTATAGTAAAAACGCCGCAA
14346 AATGTTAAAT
Statistics
Matches: 90, Mismatches: 11, Indels: 12
0.80 0.10 0.11
Matches are distributed among these distances:
40 28 0.31
41 38 0.42
42 24 0.27
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.26
Consensus pattern (41 bp):
CGGCGTTTATAGTAAAAACGCCGCAATATAGTGTAATATAG
Found at i:15378 original size:57 final size:57
Alignment explanation
Indices: 15311--15498 Score: 367
Period size: 57 Copynumber: 3.3 Consensus size: 57
15301 GTGAAGACTG
*
15311 TTTATGCATAAGTACTTTAATGTTTCTAAATTATAATGTATTTTGTTTTTAAGTAGT
1 TTTATGCATAAGTACTTTAATGTTTCTAAATTATAATGTATTTTGTTGTTAAGTAGT
15368 TTTATGCATAAGTACTTTAATGTTTCTAAATTATAATGTATTTTGTTGTTAAGTAGT
1 TTTATGCATAAGTACTTTAATGTTTCTAAATTATAATGTATTTTGTTGTTAAGTAGT
15425 TTTATGCATAAGTACTTTAATGTTTCTAAATTATAATGTATTTTGTTGTTAAGTAGT
1 TTTATGCATAAGTACTTTAATGTTTCTAAATTATAATGTATTTTGTTGTTAAGTAGT
15482 TTTATGCATAAGTACTT
1 TTTATGCATAAGTACTT
15499 CTGTTTTAAT
Statistics
Matches: 130, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
57 130 1.00
ACGTcount: A:0.30, C:0.06, G:0.13, T:0.51
Consensus pattern (57 bp):
TTTATGCATAAGTACTTTAATGTTTCTAAATTATAATGTATTTTGTTGTTAAGTAGT
Found at i:15790 original size:41 final size:41
Alignment explanation
Indices: 15745--15839 Score: 136
Period size: 41 Copynumber: 2.3 Consensus size: 41
15735 ATATTTGTAT
* * * *
15745 TTTAGTGGTGTTTGTATGAACACGCCGCTATAGACTTATAC
1 TTTAGTGGCGTTTGTATAAAAACGCCGCTATAGACTCATAC
* *
15786 TTTAGTGGCGTTCGTATAAAAACGCCGCTATAGACTCGTAC
1 TTTAGTGGCGTTTGTATAAAAACGCCGCTATAGACTCATAC
15827 TTTAGTGGCGTTT
1 TTTAGTGGCGTTT
15840 TCGTAGAAAC
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 47 1.00
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.36
Consensus pattern (41 bp):
TTTAGTGGCGTTTGTATAAAAACGCCGCTATAGACTCATAC
Found at i:15850 original size:41 final size:40
Alignment explanation
Indices: 15745--15854 Score: 125
Period size: 41 Copynumber: 2.7 Consensus size: 40
15735 ATATTTGTAT
* *
15745 TTTAGTGGTGTTT-GTATGAACACGCCGCTATAGACTTATAC
1 TTTAGTGGCGTTTCGTA-GAA-ACGCCGCTATAGACTCATAC
* *
15786 TTTAGTGGCG-TTCGTATAAAAACGCCGCTATAGACTCGTAC
1 TTTAGTGGCGTTTCG--TAGAAACGCCGCTATAGACTCATAC
15827 TTTAGTGGCGTTTTCGTAGAAACGCCGC
1 TTTAGTGGCG-TTTCGTAGAAACGCCGC
15855 AAAGTATTAG
Statistics
Matches: 59, Mismatches: 5, Indels: 10
0.80 0.07 0.14
Matches are distributed among these distances:
40 2 0.03
41 49 0.83
42 2 0.03
43 6 0.10
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.33
Consensus pattern (40 bp):
TTTAGTGGCGTTTCGTAGAAACGCCGCTATAGACTCATAC
Found at i:15922 original size:42 final size:42
Alignment explanation
Indices: 15783--15939 Score: 114
Period size: 42 Copynumber: 3.8 Consensus size: 42
15773 TATAGACTTA
* *
15783 TACTTTAGTGGCG-TTCG-TATAAAAACGCCGCTATAG-ACT-CG
1 TACTTTAGTGGCGTTTTGCTA-AAAAACGCCGC-AAAGTA-TGCG
* **
15824 TACTTTAGTGGCGTTTT-CGT-AGAAACGCCGCAAAGTATTAG
1 TACTTTAGTGGCGTTTTGC-TAAAAAACGCCGCAAAGTATGCG
* *** *
15865 TAATTTAGCAACGTTTTGCTAACAAACGCCGCAAA-TGATGCG
1 TACTTTAGTGGCGTTTTGCTAAAAAACGCCGCAAAGT-ATGCG
15907 TACTTTAGTGGCGTTTTGAC-AAAAAACGCCGCA
1 TACTTTAGTGGCGTTTTG-CTAAAAAACGCCGCA
15940 TATGTTTTTA
Statistics
Matches: 91, Mismatches: 16, Indels: 17
0.73 0.13 0.14
Matches are distributed among these distances:
40 4 0.04
41 40 0.44
42 45 0.49
43 2 0.02
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Consensus pattern (42 bp):
TACTTTAGTGGCGTTTTGCTAAAAAACGCCGCAAAGTATGCG
Found at i:16818 original size:46 final size:46
Alignment explanation
Indices: 16765--16855 Score: 164
Period size: 46 Copynumber: 2.0 Consensus size: 46
16755 CTAAGGTACT
* *
16765 TACTTGCCTTCGTTCCTTTTTCTTGTTTGACCATGTAGTTATTTCG
1 TACTTGCCTTCGTTCCTCTGTCTTGTTTGACCATGTAGTTATTTCG
16811 TACTTGCCTTCGTTCCTCTGTCTTGTTTGACCATGTAGTTATTTC
1 TACTTGCCTTCGTTCCTCTGTCTTGTTTGACCATGTAGTTATTTC
16856 AGAATCGCTA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.11, C:0.23, G:0.15, T:0.51
Consensus pattern (46 bp):
TACTTGCCTTCGTTCCTCTGTCTTGTTTGACCATGTAGTTATTTCG
Found at i:20461 original size:21 final size:21
Alignment explanation
Indices: 20437--20492 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
20427 ATGAAACAAG
20437 GGAAGCAGAGAGAGCAGCAAC
1 GGAAGCAGAGAGAGCAGCAAC
** *
20458 GGAAGCAGCCAGAGCAGCAGC
1 GGAAGCAGAGAGAGCAGCAAC
20479 GGAAGCAGAGAGAG
1 GGAAGCAGAGAGAG
20493 AAACAGTGGC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.39, C:0.20, G:0.41, T:0.00
Consensus pattern (21 bp):
GGAAGCAGAGAGAGCAGCAAC
Found at i:20513 original size:21 final size:21
Alignment explanation
Indices: 20468--20560 Score: 114
Period size: 21 Copynumber: 4.4 Consensus size: 21
20458 GGAAGCAGCC
* * * *
20468 AGAGCAGCAGCGGAAGCAGAG
1 AGAGAAGCAGCGGCAGCACAA
* *
20489 AGAGAAACAGTGGCAGCACAA
1 AGAGAAGCAGCGGCAGCACAA
*
20510 AGAGAGGCAGCGGCAGCACAA
1 AGAGAAGCAGCGGCAGCACAA
*
20531 AGAGAGGCAGCGGCAGCACAA
1 AGAGAAGCAGCGGCAGCACAA
20552 AGAGAAGCA
1 AGAGAAGCA
20561 ACATATCAGC
Statistics
Matches: 62, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 62 1.00
ACGTcount: A:0.42, C:0.20, G:0.37, T:0.01
Consensus pattern (21 bp):
AGAGAAGCAGCGGCAGCACAA
Found at i:21027 original size:43 final size:43
Alignment explanation
Indices: 20925--21061 Score: 118
Period size: 43 Copynumber: 3.2 Consensus size: 43
20915 CCGATCTTTA
* * *
20925 GCGGCGTTTGTATTAAAGATGCCGCCAAATC-AAACACATATT
1 GCGGCGTTTGTAATAAAAATGCCGCCAAACCTAAACACATATT
* * *
20967 GCGGCG-TT-TAAGCTAAAAATGCCGCGAAACCTTAACACTTATT
1 GCGGCGTTTGTAA--TAAAAATGCCGCCAAACCTAAACACATATT
* * * * * * *
21010 GCGGCGTTTGTAATAAAAACGCCACTAAACATCAACACCTACT
1 GCGGCGTTTGTAATAAAAATGCCGCCAAACCTAAACACATATT
21053 GCGGCGTTT
1 GCGGCGTTT
21062 CTGGGAAAAA
Statistics
Matches: 77, Mismatches: 13, Indels: 9
0.78 0.13 0.09
Matches are distributed among these distances:
40 2 0.03
41 2 0.03
42 21 0.27
43 47 0.61
44 2 0.03
45 3 0.04
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.25
Consensus pattern (43 bp):
GCGGCGTTTGTAATAAAAATGCCGCCAAACCTAAACACATATT
Found at i:21236 original size:43 final size:43
Alignment explanation
Indices: 21000--21229 Score: 230
Period size: 43 Copynumber: 5.3 Consensus size: 43
20990 GCGAAACCTT
* ** ** * *
21000 AACACTTATTGCGGCGTTTGTAATAAAAACGCCACTAAACATC
1 AACACCTATTGCGGCGTTTGTCTTCCAAACGCCGCTAAATATC
* * ***** * *
21043 AACACCTACTGCGGCGTTTCTGGGAAAAACGCCGCTAAAAATTG
1 AACACCTATTGCGGCGTTTGTCTTCCAAACGCCGCTAAATA-TC
* *
21087 AA-ACCTACTGCGGCGTTTGTCTTCCAAATGCCGCTAAATATC
1 AACACCTATTGCGGCGTTTGTCTTCCAAACGCCGCTAAATATC
*
21129 AACATCTATTGCGGCGTTTGTCTTCCAAACGCCGCTAAATATC
1 AACACCTATTGCGGCGTTTGTCTTCCAAACGCCGCTAAATATC
* * *
21172 AACATCTATTGTGGCGTTTTTCTGT-CAAACGCCGCTAAATATC
1 AACACCTATTGCGGCGTTTGTCT-TCCAAACGCCGCTAAATATC
21215 AACACCTATTGCGGC
1 AACACCTATTGCGGC
21230 ATTTTTCATG
Statistics
Matches: 159, Mismatches: 25, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
42 3 0.02
43 152 0.96
44 4 0.03
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.27
Consensus pattern (43 bp):
AACACCTATTGCGGCGTTTGTCTTCCAAACGCCGCTAAATATC
Found at i:21995 original size:20 final size:20
Alignment explanation
Indices: 21956--21995 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
21946 TTGCTTATAA
*
21956 ATAAACTTACTAGTTTGTTT
1 ATAAACTTACTAGTTAGTTT
* *
21976 ATAAATTTACTTGTTAGTTT
1 ATAAACTTACTAGTTAGTTT
21996 GGTTAGTTGG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.30, C:0.07, G:0.10, T:0.53
Consensus pattern (20 bp):
ATAAACTTACTAGTTAGTTT
Found at i:23987 original size:2 final size:2
Alignment explanation
Indices: 23980--24010 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
23970 TGACATTAAC
23980 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
24011 AATTTAGTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:28637 original size:23 final size:23
Alignment explanation
Indices: 28581--28637 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
28571 TTAGTTAGAA
* *
28581 AATATGTTAATATAAGCTCTATCT
1 AATATGTT-ATATAAGCACTACCT
* **
28605 ATTACATTATATAAGCACTACCT
1 AATATGTTATATAAGCACTACCT
28628 AATATGTTAT
1 AATATGTTAT
28638 TGTACTTGAT
Statistics
Matches: 25, Mismatches: 8, Indels: 1
0.74 0.24 0.03
Matches are distributed among these distances:
23 20 0.80
24 5 0.20
ACGTcount: A:0.39, C:0.14, G:0.07, T:0.40
Consensus pattern (23 bp):
AATATGTTATATAAGCACTACCT
Found at i:28723 original size:23 final size:23
Alignment explanation
Indices: 28673--28724 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
28663 GTGCATATTT
* *
28673 TATTATATAAGCGTTACTTATTA
1 TATTATATAAGCGCTACTTAATA
*
28696 CATTATATAAGCGCTA-TCTAATA
1 TATTATATAAGCGCTACT-TAATA
28719 TATTAT
1 TATTAT
28725 TGATTCGAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
22 1 0.04
23 23 0.96
ACGTcount: A:0.37, C:0.12, G:0.08, T:0.44
Consensus pattern (23 bp):
TATTATATAAGCGCTACTTAATA
Found at i:31901 original size:22 final size:22
Alignment explanation
Indices: 31839--31909 Score: 72
Period size: 22 Copynumber: 3.3 Consensus size: 22
31829 TAACATTCGG
*
31839 TACTGTTCACGGTAATGTTCAC
1 TACTGTTCACGGTAATGTTCAT
* * * *
31861 TATTGTTCATGATATTGTTCAT
1 TACTGTTCACGGTAATGTTCAT
* *
31883 TACTATTCACGGTACTGTTCA-
1 TACTGTTCACGGTAATGTTCAT
31904 TACTGT
1 TACTGT
31910 ATTTGACTGT
Statistics
Matches: 38, Mismatches: 11, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
21 5 0.13
22 33 0.87
ACGTcount: A:0.23, C:0.18, G:0.15, T:0.44
Consensus pattern (22 bp):
TACTGTTCACGGTAATGTTCAT
Found at i:34924 original size:16 final size:16
Alignment explanation
Indices: 34903--34954 Score: 56
Period size: 16 Copynumber: 3.3 Consensus size: 16
34893 ATAAACTGTT
34903 CATATGTGCCTTTAAA
1 CATATGTGCCTTTAAA
*
34919 CATATGTAGACTATT---
1 CATATGT-GCCT-TTAAA
34934 CATATGTGCCTTTAAA
1 CATATGTGCCTTTAAA
34950 CATAT
1 CATAT
34955 ATAAACTGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
13 2 0.07
14 3 0.10
15 7 0.24
16 12 0.41
17 3 0.10
18 2 0.07
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.38
Consensus pattern (16 bp):
CATATGTGCCTTTAAA
Found at i:34936 original size:31 final size:31
Alignment explanation
Indices: 34894--35146 Score: 389
Period size: 31 Copynumber: 8.2 Consensus size: 31
34884 GGTCACAATA
34894 TAAACTGTTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
* * *
34925 TAGACTATTCATATGTGCCTTTAAACATATA
1 TAAACTGTTCATATGTGCCTTTAAACATATG
*
34956 TAAACTGTTTATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
* * *
34987 TAGACTGTTCATATGTGCCTTTAAATATATA
1 TAAACTGTTCATATGTGCCTTTAAACATATG
* * *
35018 TAAATTGTTTATATGTGCCTTTAAACATATA
1 TAAACTGTTCATATGTGCCTTTAAACATATG
* *
35049 TAGACTATTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
35080 TAAACTGTTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
*
35111 TAAACTGTTCATATGTGCCATTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
35142 TAAAC
1 TAAAC
35147 CCTCAACTCT
Statistics
Matches: 199, Mismatches: 23, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 199 1.00
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.40
Consensus pattern (31 bp):
TAAACTGTTCATATGTGCCTTTAAACATATG
Found at i:35079 original size:16 final size:16
Alignment explanation
Indices: 35028--35111 Score: 54
Period size: 16 Copynumber: 5.4 Consensus size: 16
35018 TAAATTGTTT
35028 ATATGTGCCTTTAAAC
1 ATATGTGCCTTTAAAC
* *
35044 ATATATAGACTATT---C
1 ATATGT-GCCT-TTAAAC
35059 ATATGTGCCTTTAAAC
1 ATATGTGCCTTTAAAC
**
35075 ATATGTAAACTGTT---C
1 ATATGT-GCCT-TTAAAC
35090 ATATGTGCCTTTAAAC
1 ATATGTGCCTTTAAAC
35106 ATATGT
1 ATATGT
35112 AAACTGTTCA
Statistics
Matches: 50, Mismatches: 8, Indels: 20
0.64 0.10 0.26
Matches are distributed among these distances:
13 4 0.08
14 5 0.10
15 13 0.26
16 19 0.38
17 5 0.10
18 4 0.08
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.39
Consensus pattern (16 bp):
ATATGTGCCTTTAAAC
Found at i:35764 original size:64 final size:64
Alignment explanation
Indices: 35656--35817 Score: 157
Period size: 64 Copynumber: 2.5 Consensus size: 64
35646 TAATGAAGGT
* * * *
35656 ATGCATCGATGCACTACTGATGCATTGGTGCATAAAATGTATTCGATGTTGT-ATTATTGCTGGG
1 ATGCATCGATGCACTACTGATGCATCGATGCACAAAATGCATTCGATGTT-TCATTATTGCTGGG
* * * * ****
35720 ATGCATCGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATGTTTCATTATT-AAAAG
1 ATGCATCGATGCACTACTGATGCATCGATGCACAAAATGCATTCGATGTTTCATTATTGCTGGG
** *
35783 AGTGCATCGATGCACTACCAATGCATCGGTGCACA
1 A-TGCATCGATGCACTACTGATGCATCGATGCACA
35818 TTCAAACAAT
Statistics
Matches: 79, Mismatches: 17, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
63 3 0.04
64 76 0.96
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.31
Consensus pattern (64 bp):
ATGCATCGATGCACTACTGATGCATCGATGCACAAAATGCATTCGATGTTTCATTATTGCTGGG
Found at i:38926 original size:31 final size:31
Alignment explanation
Indices: 38888--39047 Score: 293
Period size: 31 Copynumber: 5.2 Consensus size: 31
38878 GGTCACAATA
38888 TAAACTGTTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
* *
38919 TAGACTGTTCATATGTGCCTTTAAACATATA
1 TAAACTGTTCATATGTGCCTTTAAACATATG
38950 TAAACTGTTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
*
38981 TAGACTGTTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
39012 TAAACTGTTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
39043 TAAAC
1 TAAAC
39048 CCTCGACTCT
Statistics
Matches: 123, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 123 1.00
ACGTcount: A:0.33, C:0.16, G:0.13, T:0.38
Consensus pattern (31 bp):
TAAACTGTTCATATGTGCCTTTAAACATATG
Found at i:39665 original size:64 final size:64
Alignment explanation
Indices: 39557--39718 Score: 164
Period size: 64 Copynumber: 2.5 Consensus size: 64
39547 TAATGAAGGT
* * * *
39557 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAATGTATTCGATGTTGTATTATTGCTAGG
1 ATGCACCGATGCACTACTGATGCATCGATGCACAAAATGCATTCGATGTTGTATTATTGCTAGG
* * * * * ** *
39621 ATGCACCGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATGTTTTATTATT-AAAAG
1 ATGCACCGATGCACTACTGATGCATCGATGCACAAAATGCATTCGATGTTGTATTATTGCTAGG
* ** *
39684 AGTGCATCGATGCACTACCAATGCATCGGTGCACA
1 A-TGCACCGATGCACTACTGATGCATCGATGCACA
39719 TTCAAACAAT
Statistics
Matches: 79, Mismatches: 18, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
63 3 0.04
64 76 0.96
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.31
Consensus pattern (64 bp):
ATGCACCGATGCACTACTGATGCATCGATGCACAAAATGCATTCGATGTTGTATTATTGCTAGG
Found at i:50300 original size:16 final size:15
Alignment explanation
Indices: 50275--50304 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
50265 GCTTTGGAAA
50275 CTTCGCTTCATCATG
1 CTTCGCTTCATCATG
50290 CTTCTGCTTCATCAT
1 CTTC-GCTTCATCAT
50305 CGGAATCGTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.13, C:0.33, G:0.10, T:0.43
Consensus pattern (15 bp):
CTTCGCTTCATCATG
Found at i:52653 original size:8 final size:8
Alignment explanation
Indices: 52640--52674 Score: 61
Period size: 8 Copynumber: 4.2 Consensus size: 8
52630 TATAAAATAT
52640 AAAATTAA
1 AAAATTAA
52648 AAAATTAA
1 AAAATTAA
52656 AAAATTAA
1 AAAATTAA
52664 AAAATTGAA
1 AAAATT-AA
52673 AA
1 AA
52675 TAAAATTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 22 0.85
9 4 0.15
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (8 bp):
AAAATTAA
Found at i:53966 original size:23 final size:23
Alignment explanation
Indices: 53940--54040 Score: 104
Period size: 23 Copynumber: 4.5 Consensus size: 23
53930 TTTTGAACCA
53940 TTCTTCTTCTTCCATAAACTCAT
1 TTCTTCTTCTTCCATAAACTCAT
*
53963 TTCTTCGTCTTCCAT-AA-TACAT
1 TTCTTCTTCTTCCATAAACT-CAT
* *
53985 TT-TT-TTCTTCTACAAACTCAT
1 TTCTTCTTCTTCCATAAACTCAT
*
54006 TTCTAT-TTCTTCCATAAACCCAT
1 TTCT-TCTTCTTCCATAAACTCAT
*
54029 TTCTCCTTCTTC
1 TTCTTCTTCTTC
54041 AATTTTCTTG
Statistics
Matches: 64, Mismatches: 8, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
20 6 0.09
21 10 0.16
22 9 0.14
23 39 0.61
ACGTcount: A:0.21, C:0.30, G:0.01, T:0.49
Consensus pattern (23 bp):
TTCTTCTTCTTCCATAAACTCAT
Found at i:54080 original size:48 final size:48
Alignment explanation
Indices: 54027--54123 Score: 142
Period size: 48 Copynumber: 2.0 Consensus size: 48
54017 CCATAAACCC
* *
54027 ATTTCTCCTTCTTCAATT-TTCTTGTGAGAAAAAGTAGTGAGAAAAACG
1 ATTTCTCCTTCTTCAATTCGTCTT-AGAGAAAAAGTAGTGAGAAAAACG
* *
54075 ATTTCTTCTTCTTCCATTCGTCTTAGAGAAAAAGTAGTGAGAAAAACG
1 ATTTCTCCTTCTTCAATTCGTCTTAGAGAAAAAGTAGTGAGAAAAACG
54123 A
1 A
54124 GTGAATAAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
48 40 0.91
49 4 0.09
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.34
Consensus pattern (48 bp):
ATTTCTCCTTCTTCAATTCGTCTTAGAGAAAAAGTAGTGAGAAAAACG
Found at i:55687 original size:64 final size:65
Alignment explanation
Indices: 55575--55717 Score: 191
Period size: 64 Copynumber: 2.2 Consensus size: 65
55565 CCATTCAACA
* * * *
55575 GGTACCGATACCCTCTCAAACGAGAAAATTTCAGAATGTCATGGGGGTACTGATACCCCCAG-AT
1 GGTACCGATACCCCCTCAAACGAGAAAATTACAGAATGTCATGAGGGTACCGATACCCCCAGTA-
55639 G
65 G
** *
55640 GGTACCGATACCCCCTTGAACGA-AAAATTACAGAATGTTATGAGGGTACCGATACCCCCAGTAG
1 GGTACCGATACCCCCTCAAACGAGAAAATTACAGAATGTCATGAGGGTACCGATACCCCCAGTAG
*
55704 GGTATCGATACCCC
1 GGTACCGATACCCC
55718 ATAAAGTAAA
Statistics
Matches: 69, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
64 48 0.70
65 21 0.30
ACGTcount: A:0.31, C:0.26, G:0.22, T:0.21
Consensus pattern (65 bp):
GGTACCGATACCCCCTCAAACGAGAAAATTACAGAATGTCATGAGGGTACCGATACCCCCAGTAG
Found at i:61200 original size:20 final size:21
Alignment explanation
Indices: 61146--61208 Score: 65
Period size: 20 Copynumber: 2.9 Consensus size: 21
61136 GATTCCCCTG
61146 TGGGGGGAATCGGTTCCCCTTCAA
1 TGGGGGG-ATCGGTT-CCC-TCAA
* *
61170 AGGGGGAATCGGTTCCCTC-A
1 TGGGGGGATCGGTTCCCTCAA
*
61190 TGGGGGGATCGATTCCCTC
1 TGGGGGGATCGGTTCCCTC
61209 TGCACCAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 17 0.50
21 2 0.06
22 3 0.09
23 7 0.21
24 5 0.15
ACGTcount: A:0.16, C:0.25, G:0.35, T:0.24
Consensus pattern (21 bp):
TGGGGGGATCGGTTCCCTCAA
Found at i:65060 original size:22 final size:21
Alignment explanation
Indices: 65018--65057 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
65008 GAGTTTGTTT
*
65018 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
65039 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
65058 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:81051 original size:20 final size:20
Alignment explanation
Indices: 81026--81069 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
81016 TTTTTCCGAG
81026 TATGTAAATCGCAACGCGAA
1 TATGTAAATCGCAACGCGAA
* *
81046 TATGTAAATCGCAATGCGAT
1 TATGTAAATCGCAACGCGAA
81066 TATG
1 TATG
81070 ACTATCGCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.27
Consensus pattern (20 bp):
TATGTAAATCGCAACGCGAA
Found at i:81076 original size:20 final size:20
Alignment explanation
Indices: 81053--81119 Score: 107
Period size: 20 Copynumber: 3.4 Consensus size: 20
81043 GAATATGTAA
*
81053 ATCGCAATGCGATTATGACT
1 ATCGCAATGCGATTCTGACT
81073 ATCGCAATGCGATTCTGACT
1 ATCGCAATGCGATTCTGACT
* *
81093 ATCGCAACGCGATTCTGATT
1 ATCGCAATGCGATTCTGACT
81113 ATCGCAA
1 ATCGCAA
81120 CACTGAATTT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.28
Consensus pattern (20 bp):
ATCGCAATGCGATTCTGACT
Found at i:81968 original size:24 final size:24
Alignment explanation
Indices: 81941--81994 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
81931 GTATTCGAAA
81941 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
81965 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
81989 TTTGAT
1 TTTGAT
81995 GATGTTTCAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:84279 original size:18 final size:18
Alignment explanation
Indices: 84256--84290 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
84246 AGAAAAAGGC
*
84256 AATCAAAATCGCAATCAA
1 AATCAAAATCCCAATCAA
84274 AATCAAAATCCCAATCA
1 AATCAAAATCCCAATCA
84291 CAACCGGCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.26, G:0.03, T:0.17
Consensus pattern (18 bp):
AATCAAAATCCCAATCAA
Found at i:84711 original size:29 final size:28
Alignment explanation
Indices: 84677--84731 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 28
84667 ATAAGAATTA
*
84677 TTTACACATCAATATTAAACAAATCAACT
1 TTTACAAATCAAT-TTAAACAAATCAACT
**
84706 TTTACAAATCAATTTTTACAAATCAA
1 TTTACAAATCAATTTAAACAAATCAA
84732 TTAAACAAGC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 11 0.48
29 12 0.52
ACGTcount: A:0.47, C:0.18, G:0.00, T:0.35
Consensus pattern (28 bp):
TTTACAAATCAATTTAAACAAATCAACT
Found at i:84732 original size:14 final size:14
Alignment explanation
Indices: 84672--84733 Score: 70
Period size: 14 Copynumber: 4.3 Consensus size: 14
84662 CACAAATAAG
*
84672 AATTATTTACACATC
1 AATT-TTTACAAATC
**
84687 AATATTAAACAAATC
1 AAT-TTTTACAAATC
*
84702 AACTTTTACAAATC
1 AATTTTTACAAATC
84716 AATTTTTACAAATC
1 AATTTTTACAAATC
84730 AATT
1 AATT
84734 AAACAAGCAA
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
14 26 0.67
15 12 0.31
16 1 0.03
ACGTcount: A:0.47, C:0.16, G:0.00, T:0.37
Consensus pattern (14 bp):
AATTTTTACAAATC
Found at i:86228 original size:42 final size:42
Alignment explanation
Indices: 86149--86241 Score: 107
Period size: 42 Copynumber: 2.2 Consensus size: 42
86139 CCTCTTCAAC
* * *
86149 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGATGGGAGAGGACTCTTGAGG
* * **
86191 GATGATAGGGGCCTCTTGAACGATAGGG-GAGGCCTCTTGAAC
1 GATGACAGGGGCCTCTTGAACGAT-GGGAGAGGACTCTTGAGG
86233 GATGACAGG
1 GATGACAGG
86242 TGAGTCGGGC
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
42 39 0.93
43 3 0.07
ACGTcount: A:0.23, C:0.17, G:0.40, T:0.20
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGATGGGAGAGGACTCTTGAGG
Found at i:86821 original size:20 final size:20
Alignment explanation
Indices: 86796--86843 Score: 71
Period size: 20 Copynumber: 2.4 Consensus size: 20
86786 GCGATTCTTT
86796 CGTTGCGATAGTCAAATTT-G
1 CGTTGCGATAGTC-AATTTCG
*
86816 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAATTTCG
86836 CGTTGCGA
1 CGTTGCGA
86844 AAGTAAACTA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 4 0.15
20 22 0.85
ACGTcount: A:0.19, C:0.19, G:0.27, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCAATTTCG
Found at i:87015 original size:18 final size:18
Alignment explanation
Indices: 86992--87037 Score: 92
Period size: 18 Copynumber: 2.6 Consensus size: 18
86982 TTACTAAGCA
86992 TAAGTGAAATGGTTAATC
1 TAAGTGAAATGGTTAATC
87010 TAAGTGAAATGGTTAATC
1 TAAGTGAAATGGTTAATC
87028 TAAGTGAAAT
1 TAAGTGAAAT
87038 TACGAGTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.41, C:0.04, G:0.22, T:0.33
Consensus pattern (18 bp):
TAAGTGAAATGGTTAATC
Found at i:88758 original size:20 final size:20
Alignment explanation
Indices: 88735--88841 Score: 83
Period size: 20 Copynumber: 5.5 Consensus size: 20
88725 TCTGAAACTT
*
88735 AAAATCGCAACACGAAAATG
1 AAAATCGCAACGCGAAAATG
* *
88755 AAAATCGCAACACAAAAATG
1 AAAATCGCAACGCGAAAATG
** * * **
88775 ACTATCGTAACGTGAATTTG
1 AAAATCGCAACGCGAAAATG
**
88795 ACTATCGCAACGCG-AAATG
1 AAAATCGCAACGCGAAAATG
* *
88814 AAAATTGCAACGCGAAACT-
1 AAAATCGCAACGCGAAAATG
88833 AAAATCGCA
1 AAAATCGCA
88842 TTGCGATTCT
Statistics
Matches: 68, Mismatches: 18, Indels: 3
0.76 0.20 0.03
Matches are distributed among these distances:
19 22 0.32
20 46 0.68
ACGTcount: A:0.47, C:0.21, G:0.16, T:0.17
Consensus pattern (20 bp):
AAAATCGCAACGCGAAAATG
Found at i:89254 original size:22 final size:22
Alignment explanation
Indices: 89216--89279 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 22
89206 TCTGAGAGAT
89216 GGAGATA--GACGGATTTCGCC
1 GGAGATAGGGACGGATTTCGCC
* * **
89236 GGAGATGGGGACTGATTTCATC
1 GGAGATAGGGACGGATTTCGCC
*
89258 GGAGATAGGGACGGATATCGCC
1 GGAGATAGGGACGGATTTCGCC
89280 TTAGAGAGTG
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
20 6 0.18
22 27 0.82
ACGTcount: A:0.25, C:0.17, G:0.38, T:0.20
Consensus pattern (22 bp):
GGAGATAGGGACGGATTTCGCC
Found at i:89474 original size:20 final size:20
Alignment explanation
Indices: 89444--89577 Score: 205
Period size: 20 Copynumber: 6.7 Consensus size: 20
89434 GCGTTTTGAA
*
89444 AATCGCATTGCGATAGTCAG
1 AATCGCGTTGCGATAGTCAG
*
89464 CATCGCGTTGCGATAGTCAG
1 AATCGCGTTGCGATAGTCAG
89484 AATCGCGTTGCGATAGTCAG
1 AATCGCGTTGCGATAGTCAG
89504 AATCGCGTTGCGATAGTCAG
1 AATCGCGTTGCGATAGTCAG
* *
89524 AATCTCGTTGCGATAGTCAT
1 AATCGCGTTGCGATAGTCAG
* *
89544 AATCGCATTGCGATAGTCAT
1 AATCGCGTTGCGATAGTCAG
*
89564 ATTCGCGTTGCGAT
1 AATCGCGTTGCGAT
89578 TTACATATTC
Statistics
Matches: 105, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 105 1.00
ACGTcount: A:0.25, C:0.21, G:0.26, T:0.28
Consensus pattern (20 bp):
AATCGCGTTGCGATAGTCAG
Found at i:89584 original size:20 final size:20
Alignment explanation
Indices: 89561--89609 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
89551 TTGCGATAGT
89561 CATATTCGCGTTGCGATTTA
1 CATATTCGCGTTGCGATTTA
89581 CATATTCGCGTTGCGATTTA
1 CATATTCGCGTTGCGATTTA
*
89601 TATATTCGC
1 CATATTCGC
89610 ATTACGAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.20, C:0.20, G:0.18, T:0.41
Consensus pattern (20 bp):
CATATTCGCGTTGCGATTTA
Found at i:89595 original size:40 final size:40
Alignment explanation
Indices: 89444--89597 Score: 202
Period size: 40 Copynumber: 3.9 Consensus size: 40
89434 GCGTTTTGAA
* **
89444 AATCGCATTGCGATAGTCAGCATCGCGTTGCGATAGTCAG
1 AATCGCGTTGCGATAGTCATAATCGCGTTGCGATAGTCAG
*
89484 AATCGCGTTGCGATAGTCAGAATCGCGTTGCGATAGTCAG
1 AATCGCGTTGCGATAGTCATAATCGCGTTGCGATAGTCAG
* * *
89524 AATCTCGTTGCGATAGTCATAATCGCATTGCGATAGTCAT
1 AATCGCGTTGCGATAGTCATAATCGCGTTGCGATAGTCAG
* * *
89564 ATTCGCGTTGCGAT-TTACATATTCGCGTTGCGAT
1 AATCGCGTTGCGATAGT-CATAATCGCGTTGCGAT
89598 TTATATATTC
Statistics
Matches: 102, Mismatches: 11, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
39 1 0.01
40 101 0.99
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.30
Consensus pattern (40 bp):
AATCGCGTTGCGATAGTCATAATCGCGTTGCGATAGTCAG
Found at i:89610 original size:60 final size:60
Alignment explanation
Indices: 89444--89654 Score: 205
Period size: 60 Copynumber: 3.5 Consensus size: 60
89434 GCGTTTTGAA
* * * *
89444 AATCGCATTGCGATAGTCAGCATCGCGTTGCGATAGTCAGAATCGCGTTGCGATAGTCAG
1 AATCGCGTTGCGATAGTCAGAATCGCGTTGCGATAGTCATAATCGCATTGCGATAGTCAG
* *
89504 AATCGCGTTGCGATAGTCAGAATCTCGTTGCGATAGTCATAATCGCATTGCGATAGTCAT
1 AATCGCGTTGCGATAGTCAGAATCGCGTTGCGATAGTCATAATCGCATTGCGATAGTCAG
* * * * * * * *
89564 ATTCGCGTTGCGAT-TTACATATTCGCGTTGCGATTTA-T-ATATTCGCATTACGA-ATTCGGAA
1 AATCGCGTTGCGATAGT-CAGAATCGCGTTGCGA--TAGTCATAATCGCATTGCGATAGTC--AG
**
89625 AATCGCAATGCGATAGTCAGAATCGCGTTG
1 AATCGCGTTGCGATAGTCAGAATCGCGTTG
89655 TGAATCTGGA
Statistics
Matches: 124, Mismatches: 21, Indels: 11
0.79 0.13 0.07
Matches are distributed among these distances:
59 4 0.03
60 93 0.75
61 24 0.19
62 3 0.02
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.30
Consensus pattern (60 bp):
AATCGCGTTGCGATAGTCAGAATCGCGTTGCGATAGTCATAATCGCATTGCGATAGTCAG
Found at i:99692 original size:13 final size:13
Alignment explanation
Indices: 99674--99698 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
99664 CACATGGATT
99674 CCTCATCCCAACC
1 CCTCATCCCAACC
99687 CCTCATCCCAAC
1 CCTCATCCCAAC
99699 AATACCCACG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.60, G:0.00, T:0.16
Consensus pattern (13 bp):
CCTCATCCCAACC
Found at i:102926 original size:142 final size:137
Alignment explanation
Indices: 102674--102956 Score: 440
Period size: 142 Copynumber: 2.0 Consensus size: 137
102664 AATTTATTAG
102674 TTTATTAAATTTTATTGTACTAATTATTTTATTACTTTTTGCAGTTATAAAATGGAAGGCAAGCT
1 TTTATTAAATTTTATTGTACTAATTATTTTATTACTTTTTGCAGTTATAAAATGGAAGGCAAGCT
* *
102739 ACTACGTTTAGATGAGAATCATATCTCGAGGCATTTTGTCGATATGATAACAATTTTAAATTGTG
66 ACTACGTTTAGATGAGAATCATATCTAGAGGCATTTTGTCAATATGATAACAATTTTAAATTGTG
102804 TTGTTAT
131 TTGTTAT
*
102811 TTTATTAAATTTTATTGTACTAATTTTTTTTATTTATTACTTTTTGCAGTTATAAAATGGAAGGC
1 TTTATTAAATTTTATTGTACTAA----TTAT-TTTATTACTTTTTGCAGTTATAAAATGGAAGGC
* * * * * *
102876 ATGTTGCTACGTTTAGATGAGAATCATTTCTAGAGGCATTTTGTCAATATGGTAATAATTTTAAA
61 AAGCTACTACGTTTAGATGAGAATCATATCTAGAGGCATTTTGTCAATATGATAACAATTTTAAA
102941 TTGTGTTGTTAT
126 TTGTGTTGTTAT
102953 TTTA
1 TTTA
102957 ATTATTGTAA
Statistics
Matches: 132, Mismatches: 9, Indels: 5
0.90 0.06 0.03
Matches are distributed among these distances:
137 23 0.17
141 3 0.02
142 106 0.80
ACGTcount: A:0.30, C:0.08, G:0.15, T:0.47
Consensus pattern (137 bp):
TTTATTAAATTTTATTGTACTAATTATTTTATTACTTTTTGCAGTTATAAAATGGAAGGCAAGCT
ACTACGTTTAGATGAGAATCATATCTAGAGGCATTTTGTCAATATGATAACAATTTTAAATTGTG
TTGTTAT
Found at i:104873 original size:23 final size:23
Alignment explanation
Indices: 104843--104891 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
104833 TGGATGTGCT
*
104843 ACATCGTCATTTGTCCCTCATCA
1 ACATCGTCATTGGTCCCTCATCA
104866 ACATCGTCATTGGTCCCTCATCA
1 ACATCGTCATTGGTCCCTCATCA
104889 ACA
1 ACA
104892 AAATGTAGCT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.24, C:0.35, G:0.10, T:0.31
Consensus pattern (23 bp):
ACATCGTCATTGGTCCCTCATCA
Found at i:106341 original size:139 final size:137
Alignment explanation
Indices: 106019--106318 Score: 392
Period size: 139 Copynumber: 2.2 Consensus size: 137
106009 AATTTATTAG
*
106019 TTTATTAAATTTTATTGTACTAA--TTTTT-TTA-T--TTTTTGCCG-TATAAAATGGAAGGCAA
1 TTTATTAAA-TTTATTGTAC-AATTTTTTTATTATTACTTTTTGCAGTTATAAAATGGAAGGCAA
* *
106077 GCTACTACGTTTAGATGAGAATCATATCTCGAGGCATTTTGTCGATATGATAACAATTTTAAATT
64 GCTACTACGTTTAGATAAGAATCATATCTCGAGGCATTTTGTCAATATGATAACAATTTTAAATT
106142 GTGTTGTTA
129 GTGTTGTTA
*
106151 TTTTATTAAATTTATTGTACTAATTTTTTTATTATTACTTTTTGCAGTTATAAAATGGAAGGCAT
1 -TTTATTAAATTTATTGTAC-AATTTTTTTATTATTACTTTTTGCAGTTATAAAATGGAAGGCAA
* * * *
106216 GTTGCTACGTTTAGATAAGAATCATTTCTCGAGGCATTTTGTCAATATGGTAA-AATTTTAAATT
64 GCTACTACGTTTAGATAAGAATCATATCTCGAGGCATTTTGTCAATATGATAACAATTTTAAATT
106280 GTGTTGTTA
129 GTGTTGTTA
106289 -TT-TT-AA-TTATTGTA-AATGTTTTTTATTATT
1 TTTATTAAATTTATTGTACAAT-TTTTTTATTATT
106319 TAATTTTTTA
Statistics
Matches: 151, Mismatches: 8, Indels: 17
0.86 0.05 0.10
Matches are distributed among these distances:
131 3 0.02
132 25 0.17
133 17 0.11
134 7 0.05
135 5 0.03
136 3 0.02
138 28 0.19
139 63 0.42
ACGTcount: A:0.30, C:0.08, G:0.15, T:0.48
Consensus pattern (137 bp):
TTTATTAAATTTATTGTACAATTTTTTTATTATTACTTTTTGCAGTTATAAAATGGAAGGCAAGC
TACTACGTTTAGATAAGAATCATATCTCGAGGCATTTTGTCAATATGATAACAATTTTAAATTGT
GTTGTTA
Found at i:112146 original size:45 final size:46
Alignment explanation
Indices: 112051--112158 Score: 139
Period size: 45 Copynumber: 2.4 Consensus size: 46
112041 TGCACATACC
** * *
112051 ATGCATCGATGCACTAAGGATTTTATGAAAACATCGAATGCATTTG
1 ATGCATCGATGCACTCTGGATTTTATGAAAACATCGAATGCACTTA
* *
112097 ATGCATCGATGCACTCTGGCTATTT-TG-AAACATCGAATTCACTTA
1 ATGCATCGATGCACTCTGGAT-TTTATGAAAACATCGAATGCACTTA
112142 ATGCATCGATGCACTCT
1 ATGCATCGATGCACTCT
112159 TAGTGCACCG
Statistics
Matches: 55, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
45 32 0.58
46 20 0.36
47 3 0.05
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Consensus pattern (46 bp):
ATGCATCGATGCACTCTGGATTTTATGAAAACATCGAATGCACTTA
Found at i:112392 original size:10 final size:10
Alignment explanation
Indices: 112361--112395 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
112351 GAAGCCATTG
112361 ATCAACAACA
1 ATCAACAACA
**
112371 AGAAACAACA
1 ATCAACAACA
112381 ATCAACAACA
1 ATCAACAACA
112391 ATCAA
1 ATCAA
112396 GAGAGAATCA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.63, C:0.26, G:0.03, T:0.09
Consensus pattern (10 bp):
ATCAACAACA
Found at i:117872 original size:29 final size:30
Alignment explanation
Indices: 117783--117873 Score: 105
Period size: 29 Copynumber: 3.1 Consensus size: 30
117773 CCCGAAGGAC
**
117783 CTATCCAGAGGTCACAAAG-ACCCCGGTAA
1 CTATCCAGAGGTCACAAAGAACCTAGGTAA
* **
117812 CTATCCAGAGGTCACAAAGAACCTCGACAA
1 CTATCCAGAGGTCACAAAGAACCTAGGTAA
* *
117842 CTGTCCATAGGTCAC-AAGAACCTAGGTAA
1 CTATCCAGAGGTCACAAAGAACCTAGGTAA
117871 CTA
1 CTA
117874 ACCATATGT
Statistics
Matches: 52, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
29 32 0.62
30 20 0.38
ACGTcount: A:0.36, C:0.29, G:0.19, T:0.16
Consensus pattern (30 bp):
CTATCCAGAGGTCACAAAGAACCTAGGTAA
Done.