Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000700.1 Hibiscus syriacus cultivar Beakdansim tig00001362_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: 120924
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Found at i:55 original size:18 final size:19
Alignment explanation
Indices: 33--86 Score: 58
Period size: 18 Copynumber: 2.9 Consensus size: 19
23 CAGACTGGTT
33 AAACCAGTCAAAACGTTCG
1 AAACCAGTCAAAACGTTCG
*
52 -AACCA-TCAAAATCGGTCG
1 AAACCAGTCAAAA-CGTTCG
* *
70 AAACCGGTCAAACCGTT
1 AAACCAGTCAAAACGTT
87 TCCAGCAGCG
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
17 6 0.21
18 10 0.36
19 7 0.25
20 5 0.18
ACGTcount: A:0.39, C:0.28, G:0.17, T:0.17
Consensus pattern (19 bp):
AAACCAGTCAAAACGTTCG
Found at i:7229 original size:12 final size:12
Alignment explanation
Indices: 7212--7239 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
7202 GGAAGTAAAC
7212 GGTCAACGGTCG
1 GGTCAACGGTCG
7224 GGTCAACGGTCG
1 GGTCAACGGTCG
7236 GGTC
1 GGTC
7240 GGGTCGGTCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.14, C:0.25, G:0.43, T:0.18
Consensus pattern (12 bp):
GGTCAACGGTCG
Found at i:7249 original size:14 final size:14
Alignment explanation
Indices: 7230--7258 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
7220 GTCGGGTCAA
7230 CGGTCGGGTCGGGT
1 CGGTCGGGTCGGGT
7244 CGGTCGGGTCGGGT
1 CGGTCGGGTCGGGT
7258 C
1 C
7259 AGACCGGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.00, C:0.24, G:0.55, T:0.21
Consensus pattern (14 bp):
CGGTCGGGTCGGGT
Found at i:7321 original size:20 final size:18
Alignment explanation
Indices: 7255--7326 Score: 63
Period size: 20 Copynumber: 3.7 Consensus size: 18
7245 GGTCGGGTCG
*
7255 GGTCAGACCGGTTAAAAC
1 GGTCAAACCGGTTAAAAC
* *
7273 GGTTCGAACCGGTCAAAACC
1 GG-TCAAACCGGTTAAAA-C
*
7293 AGTCGAAACCGGTTGAAAAC
1 GGTC-AAACCGGTT-AAAAC
7313 TGGTCAAACCGGTT
1 -GGTCAAACCGGTT
7327 TCCAGCAGCG
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
18 2 0.05
19 14 0.33
20 19 0.45
21 7 0.17
ACGTcount: A:0.32, C:0.24, G:0.26, T:0.18
Consensus pattern (18 bp):
GGTCAAACCGGTTAAAAC
Found at i:8313 original size:20 final size:21
Alignment explanation
Indices: 8276--8315 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
8266 AAATTAAGTT
8276 AAATGAGTTTTAAGATTTTAC
1 AAATGAGTTTTAAGATTTTAC
8297 AAATGA-TTTTACA-ATTTTA
1 AAATGAGTTTTA-AGATTTTA
8316 TATTCGATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.40, C:0.05, G:0.10, T:0.45
Consensus pattern (21 bp):
AAATGAGTTTTAAGATTTTAC
Found at i:8701 original size:64 final size:65
Alignment explanation
Indices: 8524--8686 Score: 213
Period size: 65 Copynumber: 2.5 Consensus size: 65
8514 GAATTAATTG
* * ** *
8524 AACATCGAATGCATTCCATGCACCGATGCATTCTCCATGCATCGATGCACTCTGAATATTTTCAA
1 AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATATTTTCAA
* ** **
8589 AACATCGAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCAC-CAGGCTATTTTTC-
1 AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATA-TTTTCA
8652 A
65 A
8653 AACATCGAATGCATTTCATGCATCGATGCACACT
1 AACATCGAATGCATTTCATGCATCGATGCACACT
8687 TGGTGCACCG
Statistics
Matches: 84, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
64 36 0.43
65 48 0.57
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (65 bp):
AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATATTTTCAA
Found at i:15245 original size:21 final size:21
Alignment explanation
Indices: 15221--15281 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
15211 ACCGTCCTCT
15221 CGTTCCTCAACATCCTAATCC
1 CGTTCCTCAACATCCTAATCC
** *
15242 CGTTCCTCCTCAACCTAATCC
1 CGTTCCTCAACATCCTAATCC
* *
15263 TGATCCTCAAGC-TCCTAAT
1 CGTTCCTCAA-CATCCTAAT
15282 GGCTTATTGA
Statistics
Matches: 31, Mismatches: 8, Indels: 2
0.76 0.20 0.05
Matches are distributed among these distances:
21 30 0.97
22 1 0.03
ACGTcount: A:0.23, C:0.41, G:0.07, T:0.30
Consensus pattern (21 bp):
CGTTCCTCAACATCCTAATCC
Found at i:16103 original size:21 final size:21
Alignment explanation
Indices: 16077--16120 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
16067 ACTCCGGGAG
*
16077 CTAGTTCTTCTCGAGCTGCTC
1 CTAGTTCTTCTCGAGCTCCTC
*
16098 CTAGTTCTTCTCGTGCTCCTC
1 CTAGTTCTTCTCGAGCTCCTC
16119 CT
1 CT
16121 CCTCCTTCAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.07, C:0.36, G:0.16, T:0.41
Consensus pattern (21 bp):
CTAGTTCTTCTCGAGCTCCTC
Found at i:17191 original size:19 final size:19
Alignment explanation
Indices: 17167--17205 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
17157 TCGAATGCAT
17167 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
17186 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
17205 T
1 T
17206 GAATATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:17330 original size:64 final size:65
Alignment explanation
Indices: 17153--17315 Score: 220
Period size: 65 Copynumber: 2.5 Consensus size: 65
17143 GAATTAATTG
* * * *
17153 AACATCGAATGCATTCCATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTTAA
1 AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATATTTTTAA
* ** * ** *
17218 AACATCGAATGCATTTGATGCATCGATGCACAAGCCATGCATCAATGCAC-CAGGCTATTTTTCA
1 AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATATTTTTAA
17282 AACATCGAATGCATTTCATGCATCGATGCACACT
1 AACATCGAATGCATTTCATGCATCGATGCACACT
17316 TGGTGCACCG
Statistics
Matches: 84, Mismatches: 14, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
64 41 0.49
65 43 0.51
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.28
Consensus pattern (65 bp):
AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATATTTTTAA
Found at i:28639 original size:26 final size:26
Alignment explanation
Indices: 28608--28657 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
28598 GCATGGTCTT
*
28608 GTGCATCGATGCATCAAATGCATTAA
1 GTGCATCGATGCATAAAATGCATTAA
28634 GTGCATCGATGCATAAAATGCATT
1 GTGCATCGATGCATAAAATGCATT
28658 CGATGTTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28
Consensus pattern (26 bp):
GTGCATCGATGCATAAAATGCATTAA
Found at i:28645 original size:17 final size:18
Alignment explanation
Indices: 28625--28662 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
28615 GATGCATCAA
* *
28625 ATGCATTAAGTGCA-TCG
1 ATGCATAAAATGCATTCG
28642 ATGCATAAAATGCATTCG
1 ATGCATAAAATGCATTCG
28660 ATG
1 ATG
28663 TTAAATTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.34, C:0.16, G:0.21, T:0.29
Consensus pattern (18 bp):
ATGCATAAAATGCATTCG
Found at i:29909 original size:27 final size:27
Alignment explanation
Indices: 29879--30121 Score: 144
Period size: 27 Copynumber: 8.7 Consensus size: 27
29869 TTTATATCCA
* * *
29879 TAATTCAACTATTAATATCCATCATAT
1 TAATTCAACTATTGATATCAATCACAT
* *
29906 TAATTCAAATATTGATATTAATCACAT
1 TAATTCAACTATTGATATCAATCACAT
* *
29933 TAATTCAACTATTGATATTATTCACAT
1 TAATTCAACTATTGATATCAATCACAT
** *** * *
29960 TTCTTTTTCTATTGATATTAATCATAT
1 TAATTCAACTATTGATATCAATCACAT
* * * * *
29987 TCATTAAAATATATCGTCAACAAATATCCATCATAT
1 TAATTCAACTAT-T-G-------ATATCAATCACAT
* * *
30023 TAATTCAATTATTGATATTAATCGCAT
1 TAATTCAACTATTGATATCAATCACAT
* *
30050 TAATTCAACTATTGATATTATTCACAT
1 TAATTCAACTATTGATATCAATCACAT
* * *
30077 TCATTCAACTATTGATATTATTCACAT
1 TAATTCAACTATTGATATCAATCACAT
* *
30104 TCATTCAACTATTAATAT
1 TAATTCAACTATTGATAT
30122 TATCCATAAT
Statistics
Matches: 173, Mismatches: 34, Indels: 18
0.77 0.15 0.08
Matches are distributed among these distances:
27 149 0.86
28 1 0.01
29 1 0.01
34 1 0.01
35 1 0.01
36 20 0.12
ACGTcount: A:0.38, C:0.15, G:0.03, T:0.44
Consensus pattern (27 bp):
TAATTCAACTATTGATATCAATCACAT
Found at i:29942 original size:54 final size:54
Alignment explanation
Indices: 29879--30121 Score: 184
Period size: 54 Copynumber: 4.3 Consensus size: 54
29869 TTTATATCCA
* *
29879 TAATTCAACTATTAATATCCA-TCATATTAATTCAAATATTGATATTAATCACAT
1 TAATTCAACTATTAATAT-CATTCACATTAATTCAACTATTGATATTAATCACAT
* * ** *** *
29933 TAATTCAACTATTGATATTATTCACATTTCTTTTTCTATTGATATTAATCATAT
1 TAATTCAACTATTAATATCATTCACATTAATTCAACTATTGATATTAATCACAT
* * * * * *
29987 TCATTAAAATATATCGTCAACAAATATCCA-TCATATTAATTCAATTATTGATATTAATCGCAT
1 TAATT-CAA-CTAT--T-----AATAT-CATTCACATTAATTCAACTATTGATATTAATCACAT
* * * *
30050 TAATTCAACTATTGATATTATTCACATTCATTCAACTATTGATATTATTCACAT
1 TAATTCAACTATTAATATCATTCACATTAATTCAACTATTGATATTAATCACAT
*
30104 TCATTCAACTATTAATAT
1 TAATTCAACTATTAATAT
30122 TATCCATAAT
Statistics
Matches: 141, Mismatches: 36, Indels: 24
0.70 0.18 0.12
Matches are distributed among these distances:
53 2 0.01
54 94 0.67
55 2 0.01
56 3 0.02
58 1 0.01
59 1 0.01
61 3 0.02
62 2 0.01
63 32 0.23
64 1 0.01
ACGTcount: A:0.38, C:0.15, G:0.03, T:0.44
Consensus pattern (54 bp):
TAATTCAACTATTAATATCATTCACATTAATTCAACTATTGATATTAATCACAT
Found at i:30106 original size:117 final size:117
Alignment explanation
Indices: 29892--30108 Score: 355
Period size: 117 Copynumber: 1.9 Consensus size: 117
29882 TTCAACTATT
29892 AATATCCATCATATTAATTCAAATATTGATATTAATCACATTAATTCAACTATTGATATTATTCA
1 AATATCCATCATATTAATTCAAATATTGATATTAATCACATTAATTCAACTATTGATATTATTCA
*** *
29957 CATTTCTTTTTCTATTGATATTAATCATATTCATTAAAATATATCGTCAACA
66 CATTTCTTCAACTATTGATATTAATCACATTCATTAAAATATATCGTCAACA
* *
30009 AATATCCATCATATTAATTCAATTATTGATATTAATCGCATTAATTCAACTATTGATATTATTCA
1 AATATCCATCATATTAATTCAAATATTGATATTAATCACATTAATTCAACTATTGATATTATTCA
*
30074 CA-TTCATTCAACTATTGATATTATTCACATTCATT
66 CATTTC-TTCAACTATTGATATTAATCACATTCATT
30109 CAACTATTAA
Statistics
Matches: 92, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
116 3 0.03
117 89 0.97
ACGTcount: A:0.37, C:0.15, G:0.04, T:0.44
Consensus pattern (117 bp):
AATATCCATCATATTAATTCAAATATTGATATTAATCACATTAATTCAACTATTGATATTATTCA
CATTTCTTCAACTATTGATATTAATCACATTCATTAAAATATATCGTCAACA
Found at i:30122 original size:27 final size:27
Alignment explanation
Indices: 30025--30124 Score: 155
Period size: 27 Copynumber: 3.7 Consensus size: 27
30015 CATCATATTA
* * * *
30025 ATTCAATTATTGATATTAATCGCATTA
1 ATTCAACTATTGATATTATTCACATTC
30052 ATTCAACTATTGATATTATTCACATTC
1 ATTCAACTATTGATATTATTCACATTC
30079 ATTCAACTATTGATATTATTCACATTC
1 ATTCAACTATTGATATTATTCACATTC
*
30106 ATTCAACTATTAATATTAT
1 ATTCAACTATTGATATTAT
30125 CCATAATATG
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 68 1.00
ACGTcount: A:0.36, C:0.15, G:0.04, T:0.45
Consensus pattern (27 bp):
ATTCAACTATTGATATTATTCACATTC
Found at i:31615 original size:38 final size:38
Alignment explanation
Indices: 31553--31639 Score: 129
Period size: 38 Copynumber: 2.3 Consensus size: 38
31543 TGCAACCACC
*
31553 AACCACCAACCTACCCGGGATATTAATGGATAATTAAT
1 AACCACCAACCTACCCGAGATATTAATGGATAATTAAT
* * *
31591 AACCACCAACCTATCCGAGTTATTAATGGATAATTATT
1 AACCACCAACCTACCCGAGATATTAATGGATAATTAAT
*
31629 AACTACCAACC
1 AACCACCAACC
31640 ACCAACCTAT
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 44 1.00
ACGTcount: A:0.39, C:0.25, G:0.10, T:0.25
Consensus pattern (38 bp):
AACCACCAACCTACCCGAGATATTAATGGATAATTAAT
Found at i:33204 original size:19 final size:19
Alignment explanation
Indices: 33180--33265 Score: 91
Period size: 19 Copynumber: 4.2 Consensus size: 19
33170 GCGATTTTGA
*
33180 AAAATGTGTTGCGATAGTT
1 AAAATGTGTTGCGATAGTG
*
33199 AAAATGTGTTGCGAGAGTTTG
1 AAAATGTGTTGCGATAG--TG
33220 AAACACGTGTTGTTGCGATAGTG
1 AAA-A--TG-TGTTGCGATAGTG
*
33243 AAAAAGTGTTGCGATAGTG
1 AAAATGTGTTGCGATAGTG
33262 AAAA
1 AAAA
33266 ATCCAAAATA
Statistics
Matches: 57, Mismatches: 4, Indels: 12
0.78 0.05 0.16
Matches are distributed among these distances:
19 33 0.58
20 1 0.02
21 4 0.07
22 2 0.04
23 5 0.09
24 2 0.04
25 10 0.18
ACGTcount: A:0.34, C:0.07, G:0.29, T:0.30
Consensus pattern (19 bp):
AAAATGTGTTGCGATAGTG
Found at i:33727 original size:19 final size:19
Alignment explanation
Indices: 33705--33757 Score: 52
Period size: 21 Copynumber: 2.7 Consensus size: 19
33695 TAGTCTATCA
33705 CAACGAATTTGGAAAATCG
1 CAACGAATTTGGAAAATCG
* * **
33724 CAACGCGAACTTCGACTATCG
1 CAA--CGAATTTGGAAAATCG
33745 CAACGAATTTGGA
1 CAACGAATTTGGA
33758 CTAACGTAAA
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
19 11 0.42
21 15 0.58
ACGTcount: A:0.36, C:0.23, G:0.21, T:0.21
Consensus pattern (19 bp):
CAACGAATTTGGAAAATCG
Found at i:33732 original size:40 final size:40
Alignment explanation
Indices: 33677--33757 Score: 135
Period size: 40 Copynumber: 2.0 Consensus size: 40
33667 GCGATTTTCC
*
33677 AAAATCGCAACGCGAACTTAGTCTATCACAACGAATTTGG
1 AAAATCGCAACGCGAACTTAGACTATCACAACGAATTTGG
* *
33717 AAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGG
1 AAAATCGCAACGCGAACTTAGACTATCACAACGAATTTGG
33757 A
1 A
33758 CTAACGTAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.37, C:0.23, G:0.19, T:0.21
Consensus pattern (40 bp):
AAAATCGCAACGCGAACTTAGACTATCACAACGAATTTGG
Found at i:33744 original size:21 final size:21
Alignment explanation
Indices: 33680--33749 Score: 63
Period size: 21 Copynumber: 3.4 Consensus size: 21
33670 ATTTTCCAAA
*
33680 ATCGCAACGCGAACTTAGTCT
1 ATCGCAACGCGAACTTAGACT
* * * **
33701 ATCACAA--CGAATTTGGAAA
1 ATCGCAACGCGAACTTAGACT
*
33720 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTAGACT
33741 ATCGCAACG
1 ATCGCAACG
33750 AATTTGGACT
Statistics
Matches: 36, Mismatches: 11, Indels: 4
0.71 0.22 0.08
Matches are distributed among these distances:
19 13 0.36
21 23 0.64
ACGTcount: A:0.34, C:0.27, G:0.19, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGAACTTAGACT
Found at i:33759 original size:19 final size:19
Alignment explanation
Indices: 33699--33760 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 19
33689 CGAACTTAGT
*
33699 CTATCACAACGAATTTGGA
1 CTATCGCAACGAATTTGGA
** * *
33718 AAATCGCAACGCGAACTTCGA
1 CTATCGCAA--CGAATTTGGA
33739 CTATCGCAACGAATTTGGA
1 CTATCGCAACGAATTTGGA
33758 CTA
1 CTA
33761 ACGTAAATTT
Statistics
Matches: 32, Mismatches: 9, Indels: 4
0.71 0.20 0.09
Matches are distributed among these distances:
19 17 0.53
21 15 0.47
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (19 bp):
CTATCGCAACGAATTTGGA
Found at i:33877 original size:19 final size:19
Alignment explanation
Indices: 33853--33891 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
33843 TGCGATACTG
* *
33853 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTACGATTTA
33872 GAGATCGCATTACGATTTA
1 GAGATCGCATTACGATTTA
33891 G
1 G
33892 TTGGTTATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.31
Consensus pattern (19 bp):
GAGATCGCATTACGATTTA
Found at i:34322 original size:2 final size:2
Alignment explanation
Indices: 34315--34352 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
34305 TTGTTTGTTC
34315 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
34353 TTAAAGGAAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:36508 original size:7 final size:7
Alignment explanation
Indices: 36496--36530 Score: 70
Period size: 7 Copynumber: 5.0 Consensus size: 7
36486 ATGGGCGGTC
36496 CAGCCAT
1 CAGCCAT
36503 CAGCCAT
1 CAGCCAT
36510 CAGCCAT
1 CAGCCAT
36517 CAGCCAT
1 CAGCCAT
36524 CAGCCAT
1 CAGCCAT
36531 GCATGAATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.29, C:0.43, G:0.14, T:0.14
Consensus pattern (7 bp):
CAGCCAT
Found at i:44624 original size:23 final size:23
Alignment explanation
Indices: 44594--44674 Score: 144
Period size: 23 Copynumber: 3.5 Consensus size: 23
44584 CTCGTATAAA
*
44594 TGCACCGAAGTGCCATGAAGAAT
1 TGCACCGAAGTGCCATGTAGAAT
44617 TGCACCGAAGTGCCATGTAGAAT
1 TGCACCGAAGTGCCATGTAGAAT
*
44640 TGCACCGAAGTGCCGTGTAGAAT
1 TGCACCGAAGTGCCATGTAGAAT
44663 TGCACCGAAGTG
1 TGCACCGAAGTG
44675 TCATATAAAA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 56 1.00
ACGTcount: A:0.30, C:0.22, G:0.28, T:0.20
Consensus pattern (23 bp):
TGCACCGAAGTGCCATGTAGAAT
Found at i:49707 original size:23 final size:23
Alignment explanation
Indices: 49666--49721 Score: 85
Period size: 23 Copynumber: 2.4 Consensus size: 23
49656 CTCATATAAA
* *
49666 TGCACCAAAGTGCCATGTAGAAT
1 TGCACCGAAGAGCCATGTAGAAT
*
49689 TGCACCGAAGAGCCGTGTAGAAT
1 TGCACCGAAGAGCCATGTAGAAT
49712 TGCACCGAAG
1 TGCACCGAAG
49722 TGCTATATAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.32, C:0.23, G:0.27, T:0.18
Consensus pattern (23 bp):
TGCACCGAAGAGCCATGTAGAAT
Found at i:51929 original size:13 final size:13
Alignment explanation
Indices: 51911--51935 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
51901 GCTTCACGTG
51911 AAGAAGAAGAAGA
1 AAGAAGAAGAAGA
51924 AAGAAGAAGAAG
1 AAGAAGAAGAAG
51936 GGGAACTCTG
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:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (13 bp):
AAGAAGAAGAAGA
Found at i:54735 original size:23 final size:23
Alignment explanation
Indices: 54709--54769 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
54699 CTCGTATAAA
*
54709 TGCACCAAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
54732 TGCACCGAAGTGCCGCGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
54755 TCCACCGAAGTGCCA
1 TGCACCGAAGTGCCA
54770 TATAAAATGT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.30, C:0.30, G:0.25, T:0.16
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:63288 original size:180 final size:180
Alignment explanation
Indices: 62986--63326 Score: 556
Period size: 180 Copynumber: 1.9 Consensus size: 180
62976 AGAACTAAAG
* * *
62986 TTGTTGAAGATTTGAAGGCTGATCCAGAAATGAAGTCCGTGTCAATGGGAAAATTACTAGATATT
1 TTGTTGAAGATTTGAAGACTGATCCACAAATGAAGTCCGTGTCAATGGGAAAATCACTAGATATT
*
63051 GACTCAAATTTTAATTGGTAATCAATTTAGATTTTATTGTAATTCTAGTGATTAGAGATTTCTTG
66 AACTCAAATTTTAATTGGTAATCAATTTAGATTTTATTGTAATTCTAGTGATTAGAGATTTCTTG
63116 ATAATTAAATTTAAGTAAATGCTTATTTTAGGCTAGAAGTCTTTTGAATT
131 ATAATTAAATTTAAGTAAATGCTTATTTTAGGCTAGAAGTCTTTTGAATT
* * ** * * *
63166 TTGTTGAAGATTTGAAGACTGATGCACACATGAAGTTTGTGTCAATGGGGAGATCGCTAGATATT
1 TTGTTGAAGATTTGAAGACTGATCCACAAATGAAGTCCGTGTCAATGGGAAAATCACTAGATATT
* *
63231 AACTCCAATTTTAATTGGTAATTAATTTAGATTTTATTGTAATTCTAGTGATTAGAGATTTCTTG
66 AACTCAAATTTTAATTGGTAATCAATTTAGATTTTATTGTAATTCTAGTGATTAGAGATTTCTTG
*
63296 ATAATTAAGTTTAAGTAAATGCTTATTTTAG
131 ATAATTAAATTTAAGTAAATGCTTATTTTAG
63327 ACAAGAAATA
Statistics
Matches: 147, Mismatches: 14, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
180 147 1.00
ACGTcount: A:0.33, C:0.08, G:0.19, T:0.40
Consensus pattern (180 bp):
TTGTTGAAGATTTGAAGACTGATCCACAAATGAAGTCCGTGTCAATGGGAAAATCACTAGATATT
AACTCAAATTTTAATTGGTAATCAATTTAGATTTTATTGTAATTCTAGTGATTAGAGATTTCTTG
ATAATTAAATTTAAGTAAATGCTTATTTTAGGCTAGAAGTCTTTTGAATT
Found at i:65614 original size:2 final size:2
Alignment explanation
Indices: 65607--65640 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
65597 GTGAATCGTA
65607 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
65641 TAATTAGACC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:65724 original size:26 final size:27
Alignment explanation
Indices: 65695--65796 Score: 68
Period size: 27 Copynumber: 3.7 Consensus size: 27
65685 TTATTTTGGT
65695 CACC-AACTATTA-ATTTTTTTAAATCA
1 CACCTAAC-ATTATATTTTTTTAAATCA
* ** **
65721 CACCTAACATTATATTTTGATCATATTTTGGT
1 CACCTAACATTATATTTT--T-TTA-AAT-CA
65753 CACC-AACTATTA-ATTTTTTTAAATCA
1 CACCTAAC-ATTATATTTTTTTAAATCA
65779 CACCTAACATTATATTTT
1 CACCTAACATTATATTTT
65797 GATCATATTT
Statistics
Matches: 56, Mismatches: 10, Indels: 19
0.66 0.12 0.22
Matches are distributed among these distances:
26 16 0.29
27 17 0.30
28 2 0.04
29 2 0.04
30 2 0.04
31 9 0.16
32 8 0.14
ACGTcount: A:0.34, C:0.19, G:0.03, T:0.44
Consensus pattern (27 bp):
CACCTAACATTATATTTTTTTAAATCA
Found at i:65756 original size:58 final size:58
Alignment explanation
Indices: 65686--65813 Score: 256
Period size: 58 Copynumber: 2.2 Consensus size: 58
65676 CCCACCTTTT
65686 TATTTTGGTCACCAACTATTAATTTTTTTAAATCACACCTAACATTATATTTTGATCA
1 TATTTTGGTCACCAACTATTAATTTTTTTAAATCACACCTAACATTATATTTTGATCA
65744 TATTTTGGTCACCAACTATTAATTTTTTTAAATCACACCTAACATTATATTTTGATCA
1 TATTTTGGTCACCAACTATTAATTTTTTTAAATCACACCTAACATTATATTTTGATCA
65802 TATTTTGGTCAC
1 TATTTTGGTCAC
65814 TCATTGTTAA
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 70 1.00
ACGTcount: A:0.31, C:0.17, G:0.06, T:0.45
Consensus pattern (58 bp):
TATTTTGGTCACCAACTATTAATTTTTTTAAATCACACCTAACATTATATTTTGATCA
Found at i:70300 original size:42 final size:42
Alignment explanation
Indices: 70175--70300 Score: 119
Period size: 42 Copynumber: 3.0 Consensus size: 42
70165 TATTACCTTT
* **
70175 CCATTTTCCCAACACTTTGCCGTAATTAATCCGGATCTACTC
1 CCATTTTCCCAACACTTTACCCAAATTAATCCGGATCTACTC
* *** * * *
70217 CCATTTTTCCAATTTTTTA-TCATAATTAATCCAGATTTACTC
1 CCATTTTCCCAACACTTTACCCA-AATTAATCCGGATCTACTC
* * *
70259 CTATTTCCCCAACACTTTACCCAAATTAATTCGGATCTACTC
1 CCATTTTCCCAACACTTTACCCAAATTAATCCGGATCTACTC
70301 GTGACACACC
Statistics
Matches: 62, Mismatches: 20, Indels: 4
0.72 0.23 0.05
Matches are distributed among these distances:
42 60 0.97
43 2 0.03
ACGTcount: A:0.27, C:0.29, G:0.06, T:0.38
Consensus pattern (42 bp):
CCATTTTCCCAACACTTTACCCAAATTAATCCGGATCTACTC
Found at i:70848 original size:54 final size:54
Alignment explanation
Indices: 70778--70956 Score: 243
Period size: 54 Copynumber: 3.3 Consensus size: 54
70768 ATGGCCTCTT
* * * *
70778 GGATCAACATGCCTCTGTTGGTCCCTAGGATCAGCATGT-CTCTGTAGGTCCCTG
1 GGATCAACATGCCTCTGTTGGTCCCTGGGATCTGCAT-TCCTCTGTTGATCCCTG
** * * *
70832 GGATCGGCATGTCTCTGTGGGTCCCTGGGATCTGCATTCCTCTGTTGATCTCTG
1 GGATCAACATGCCTCTGTTGGTCCCTGGGATCTGCATTCCTCTGTTGATCCCTG
*
70886 GGATCAACATACCTCTGTTGGTCCCTGGGATCTGCATTCCTCTGTTGATCCCTG
1 GGATCAACATGCCTCTGTTGGTCCCTGGGATCTGCATTCCTCTGTTGATCCCTG
*
70940 GGATCAACATACCTCTG
1 GGATCAACATGCCTCTG
70957 GTGGCTTCCC
Statistics
Matches: 109, Mismatches: 15, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
53 1 0.01
54 108 0.99
ACGTcount: A:0.15, C:0.28, G:0.25, T:0.32
Consensus pattern (54 bp):
GGATCAACATGCCTCTGTTGGTCCCTGGGATCTGCATTCCTCTGTTGATCCCTG
Found at i:70954 original size:27 final size:27
Alignment explanation
Indices: 70778--70956 Score: 196
Period size: 27 Copynumber: 6.6 Consensus size: 27
70768 ATGGCCTCTT
* *
70778 GGATCAACATGCCTCTGTTGGTCCCTA
1 GGATCAGCATGCCTCTGTTGGTCCCTG
* *
70805 GGATCAGCATGTCTCTGTAGGTCCCTG
1 GGATCAGCATGCCTCTGTTGGTCCCTG
* * *
70832 GGATCGGCATGTCTCTGTGGGTCCCTG
1 GGATCAGCATGCCTCTGTTGGTCCCTG
* * * *
70859 GGATCTGCATTCCTCTGTTGATCTCTG
1 GGATCAGCATGCCTCTGTTGGTCCCTG
* *
70886 GGATCAACATACCTCTGTTGGTCCCTG
1 GGATCAGCATGCCTCTGTTGGTCCCTG
* * *
70913 GGATCTGCATTCCTCTGTTGATCCCTG
1 GGATCAGCATGCCTCTGTTGGTCCCTG
* *
70940 GGATCAACATACCTCTG
1 GGATCAGCATGCCTCTG
70957 GTGGCTTCCC
Statistics
Matches: 128, Mismatches: 24, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 128 1.00
ACGTcount: A:0.15, C:0.28, G:0.25, T:0.32
Consensus pattern (27 bp):
GGATCAGCATGCCTCTGTTGGTCCCTG
Found at i:70955 original size:81 final size:81
Alignment explanation
Indices: 70778--70956 Score: 216
Period size: 81 Copynumber: 2.2 Consensus size: 81
70768 ATGGCCTCTT
* * * **
70778 GGATCAACATGCCTCTGTTGGTCCCTAGGATCAGCATGTCTCTGTAGGTCCCTGGGATCGGCATG
1 GGATCAACATACCTCTGTTGATCCCTAGGATCAACATACCTCTGTAGGTCCCTGGGATCGGCATG
*
70843 TCTCTGTGGGTCCCTG
66 TCTCTGTGGATCCCTG
** * * * * *
70859 GGATCTGCATTCCTCTGTTGATCTCTGGGATCAACATACCTCTGTTGGTCCCTGGGATCTGCAT-
1 GGATCAACATACCTCTGTTGATCCCTAGGATCAACATACCTCTGTAGGTCCCTGGGATCGGCATG
*
70923 TCCTCTGTTGATCCCTG
66 T-CTCTGTGGATCCCTG
70940 GGATCAACATACCTCTG
1 GGATCAACATACCTCTG
70957 GTGGCTTCCC
Statistics
Matches: 81, Mismatches: 16, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
80 1 0.01
81 80 0.99
ACGTcount: A:0.15, C:0.28, G:0.25, T:0.32
Consensus pattern (81 bp):
GGATCAACATACCTCTGTTGATCCCTAGGATCAACATACCTCTGTAGGTCCCTGGGATCGGCATG
TCTCTGTGGATCCCTG
Found at i:85286 original size:23 final size:21
Alignment explanation
Indices: 85253--85356 Score: 95
Period size: 23 Copynumber: 4.8 Consensus size: 21
85243 CTGTGCGGTA
*
85253 GGTATCTATACCCCCTTTGAATG
1 GGTATCGATACCCCCTTTG-A-G
*
85276 GGTATCGATACCCTCTTTGAATG
1 GGTATCGATACCCCCTTTG-A-G
*
85299 GGTACCGATACCCCC--TGAG
1 GGTATCGATACCCCCTTTGAG
**
85318 GGTATCGATATCCCCCCCTGAG
1 GGTATCGATA-CCCCCTTTGAG
*
85340 GGTATCGATATCCCCTT
1 GGTATCGATACCCCCTT
85357 CGAGTTCTGG
Statistics
Matches: 70, Mismatches: 8, Indels: 8
0.81 0.09 0.09
Matches are distributed among these distances:
19 10 0.14
20 6 0.09
21 6 0.09
22 14 0.20
23 34 0.49
ACGTcount: A:0.20, C:0.30, G:0.21, T:0.29
Consensus pattern (21 bp):
GGTATCGATACCCCCTTTGAG
Found at i:85354 original size:21 final size:22
Alignment explanation
Indices: 85309--85354 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
85299 GGTACCGATA
85309 CCCCCTGAGGGTATCGATATCC
1 CCCCCTGAGGGTATCGATATCC
85331 CCCCCTGAGGGTATCGATATCC
1 CCCCCTGAGGGTATCGATATCC
85353 CC
1 CC
85355 TTCGAGTTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.17, C:0.39, G:0.22, T:0.22
Consensus pattern (22 bp):
CCCCCTGAGGGTATCGATATCC
Found at i:85595 original size:30 final size:30
Alignment explanation
Indices: 85561--85621 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 30
85551 TTCGATATAA
*
85561 CAAATTAAGTTAAA-TGGATTTTAAGATTTT
1 CAAATTAAGTTAAAGT-AATTTTAAGATTTT
85591 CAAATTAAGTTAAAGTAATTTTAAGATTTT
1 CAAATTAAGTTAAAGTAATTTTAAGATTTT
85621 C
1 C
85622 CAAACGATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 28 0.97
31 1 0.03
ACGTcount: A:0.41, C:0.05, G:0.11, T:0.43
Consensus pattern (30 bp):
CAAATTAAGTTAAAGTAATTTTAAGATTTT
Found at i:91733 original size:23 final size:21
Alignment explanation
Indices: 91679--91741 Score: 81
Period size: 21 Copynumber: 2.9 Consensus size: 21
91669 TTTTGGTGCA
*
91679 GAGGGAATCGATTCCCCCCCT
1 GAGGGAACCGATTCCCCCCCT
**
91700 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCCCCT
91721 GAAGAGGAACCGATTCCCCCC
1 G-AG-GGAACCGATTCCCCCC
91742 ACATGGGAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
21 19 0.53
22 2 0.06
23 15 0.42
ACGTcount: A:0.22, C:0.37, G:0.24, T:0.17
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCCCT
Found at i:94198 original size:30 final size:30
Alignment explanation
Indices: 94164--94224 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 30
94154 TTCGATATAA
*
94164 CAAATTAAGTTAAA-TGGATTTTAAGATTTT
1 CAAATTAAGTTAAAGT-AATTTTAAGATTTT
94194 CAAATTAAGTTAAAGTAATTTTAAGATTTT
1 CAAATTAAGTTAAAGTAATTTTAAGATTTT
94224 C
1 C
94225 CAAACGATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 28 0.97
31 1 0.03
ACGTcount: A:0.41, C:0.05, G:0.11, T:0.43
Consensus pattern (30 bp):
CAAATTAAGTTAAAGTAATTTTAAGATTTT
Found at i:95530 original size:13 final size:14
Alignment explanation
Indices: 95507--95546 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
95497 AAAACTATAT
95507 ATTGATTTTCAAAC
1 ATTGATTTTCAAAC
95521 ATTG-TTTTCAAAC
1 ATTGATTTTCAAAC
* *
95534 ATAGTTTTTCAAA
1 ATTGATTTTCAAA
95547 ATTTTCCCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 12 0.50
14 12 0.50
ACGTcount: A:0.35, C:0.12, G:0.07, T:0.45
Consensus pattern (14 bp):
ATTGATTTTCAAAC
Found at i:97579 original size:389 final size:389
Alignment explanation
Indices: 96862--97636 Score: 1478
Period size: 389 Copynumber: 2.0 Consensus size: 389
96852 TCGATCCTCA
*
96862 TATGGATTAAACCTTGTCTTGCTTTAGTTTTCTCTTGGTTTGATTTAGAACTTATTGTTAAACAT
1 TATGGATTAAACCTTGCCTTGCTTTAGTTTTCTCTTGGTTTGATTTAGAACTTATTGTTAAACAT
96927 TTTGATGTTTTTGGATTTGTTTGTTCTGGATGTTCTGGATGTTTGAACTTAATATGTATTTGGTT
66 TTTGATGTTTTTGGATTTGTTTGTTCTGGATGTTCTGGATGTTTGAACTTAATATGTATTTGGTT
*
96992 TGTTTGAATTTTTTAAATTTGATTTTAAGTTTTGCATCATATTAGAATATGACCAATTACCATTG
131 TGTTTGAATTTTTTAAATTTGATTTTAAGTTTTGCATCATATTAGAATATGACAAATTACCATTG
*
97057 CATATTATTAATGAATATTGATTTATGAAACTAATGGCTAACATTTCTCTTGATTGTGTTCTTAG
196 CATATTATTAATGAATATTGATTCATGAAACTAATGGCTAACATTTCTCTTGATTGTGTTCTTAG
97122 CAGCTTAAGCTTTAAATATCTAAATATCAATTGGCTAAGTTTTTCAAAACCCTTGTTTCAAAACG
261 CAGCTTAAGCTTTAAATATCTAAATATCAATTGGCTAAGTTTTTCAAAACCCTTGTTTCAAAACG
*
97187 TTTATAGAGTCTTTTTGATTTAACAAAAAGGGGGAAAAGTGTTATAGTAAGTGGGAGCAAGTCC
326 TTTATAGAGTCTTTTTGATTTAACAAAAAGGGGGAAAAGTGTTATAGTAAGGGGGAGCAAGTCC
97251 TATGGATTAAACCTTGCCTTGCTTTAGTTTTCTCTTGGTTTGATTTAGAACTTATTGTTAAACAT
1 TATGGATTAAACCTTGCCTTGCTTTAGTTTTCTCTTGGTTTGATTTAGAACTTATTGTTAAACAT
97316 TTTGATGTTTTTGGATTTGTTTGTTCTGGATGTTCTGGATGTTTGAACTTAATATGTATTTGGTT
66 TTTGATGTTTTTGGATTTGTTTGTTCTGGATGTTCTGGATGTTTGAACTTAATATGTATTTGGTT
97381 TGTTTGAATTTTTTAAATTTGATTTTAAGTTTTGCATCATATTAGAATATGACAAATTACCATTG
131 TGTTTGAATTTTTTAAATTTGATTTTAAGTTTTGCATCATATTAGAATATGACAAATTACCATTG
*
97446 CATATTATTAATGAATATTGATTCATGAAACTAATGGCTAACCTTTCTCTTGATTGTGTTCTTAG
196 CATATTATTAATGAATATTGATTCATGAAACTAATGGCTAACATTTCTCTTGATTGTGTTCTTAG
* * *
97511 TAGCTTAAGCTTTAAATTTCTAAATATCAATTGGCTAAGTTTTTCAAAACTCTTGTTTCAAAACG
261 CAGCTTAAGCTTTAAATATCTAAATATCAATTGGCTAAGTTTTTCAAAACCCTTGTTTCAAAACG
97576 TTTATAGAGTCTTTTTGATTTAACAAAAAGGGGGAAAAGTGTTATAGTAAGGGGGAGCAAG
326 TTTATAGAGTCTTTTTGATTTAACAAAAAGGGGGAAAAGTGTTATAGTAAGGGGGAGCAAG
97637 ACAAAATTAA
Statistics
Matches: 378, Mismatches: 8, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
389 378 1.00
ACGTcount: A:0.28, C:0.10, G:0.17, T:0.44
Consensus pattern (389 bp):
TATGGATTAAACCTTGCCTTGCTTTAGTTTTCTCTTGGTTTGATTTAGAACTTATTGTTAAACAT
TTTGATGTTTTTGGATTTGTTTGTTCTGGATGTTCTGGATGTTTGAACTTAATATGTATTTGGTT
TGTTTGAATTTTTTAAATTTGATTTTAAGTTTTGCATCATATTAGAATATGACAAATTACCATTG
CATATTATTAATGAATATTGATTCATGAAACTAATGGCTAACATTTCTCTTGATTGTGTTCTTAG
CAGCTTAAGCTTTAAATATCTAAATATCAATTGGCTAAGTTTTTCAAAACCCTTGTTTCAAAACG
TTTATAGAGTCTTTTTGATTTAACAAAAAGGGGGAAAAGTGTTATAGTAAGGGGGAGCAAGTCC
Found at i:102788 original size:53 final size:53
Alignment explanation
Indices: 102684--103424 Score: 949
Period size: 53 Copynumber: 13.9 Consensus size: 53
102674 TCTCCAAAAT
* * ** *
102684 CGGGTTCGCTCTCTATCGCTTCAGGGAGTAAGAACTCGAACAATCTTCTTCCTA
1 CGGGTCCGCTCTCTCTTTCTTCAGGGAGT-AGAACTCGAACAATCATCTTCCTA
* * *
102738 CGGGTCCACTCTCTCTTTCTTCAAGGAGTAGAACTCGAACAATCTTCTTCCTA
1 CGGGTCCGCTCTCTCTTTCTTCAGGGAGTAGAACTCGAACAATCATCTTCCTA
* * *
102791 CGGG-CTCGCTCTCTCTTTTTTCAGGGAGTAGAACTCGAACAATCTTCTTCTTA
1 CGGGTC-CGCTCTCTCTTTCTTCAGGGAGTAGAACTCGAACAATCATCTTCCTA
* * *
102844 CGGG-CTTGCTCTCTCTTTCTTCAGGGAGTAAGCACTCGAACAATAATCTTCCTA
1 CGGGTC-CGCTCTCTCTTTCTTCAGGGAGT-AGAACTCGAACAATCATCTTCCTA
* * *
102898 CGGGTCCACTCTCTCTTTTTTCAGGGAGTAGAACTCGAACAATCATCTGCCTA
1 CGGGTCCGCTCTCTCTTTCTTCAGGGAGTAGAACTCGAACAATCATCTTCCTA
* *
102951 CGGG-CTCGCTCTCTCTTTTTTCAGGGAGTAGAACTCGAACAATCATCTGCCTA
1 CGGGTC-CGCTCTCTCTTTCTTCAGGGAGTAGAACTCGAACAATCATCTTCCTA
* * *
103004 CGGG-CTCGCTCTCTCTTTCTTCAGGGAGTAGAACTCAAACGATAATCTTCCTA
1 CGGGTC-CGCTCTCTCTTTCTTCAGGGAGTAGAACTCGAACAATCATCTTCCTA
*
103057 CGGG-CTCGCTCTCTATTTCTTCAGGGAGTAGAACTCGAACAATCATCTTCCTA
1 CGGGTC-CGCTCTCTCTTTCTTCAGGGAGTAGAACTCGAACAATCATCTTCCTA
** *
103110 CGGGTCCTTTCTCT-TTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTA
1 CGGGTCCGCTCTCTCTTTCTTCAGGGAGTAGAACTCGAACAATCATCTTCCTA
* * *
103162 CGAGTCCGCTCTCTATTTCTTCAGGGAGTAAGAACTCGAACAATAATCTTCCTA
1 CGGGTCCGCTCTCTCTTTCTTCAGGGAGT-AGAACTCGAACAATCATCTTCCTA
* *
103216 CTGG-CTCGCTCTCTATTTCTTCAGGGAGTAGAACTCGAACAATCATCTTCCTA
1 CGGGTC-CGCTCTCTCTTTCTTCAGGGAGTAGAACTCGAACAATCATCTTCCTA
* * *
103269 CGGGTCCGCTCCCT-TTTCTTCAAGGAGTAGAACTCGAACAATAATCTTCCTA
1 CGGGTCCGCTCTCTCTTTCTTCAGGGAGTAGAACTCGAACAATCATCTTCCTA
* * * *
103321 CGGGTCCGCTCTCTATTTCTTCAGGCAGTAAGAACTCGAACAATAATCTTCTTA
1 CGGGTCCGCTCTCTCTTTCTTCAGGGAGT-AGAACTCGAACAATCATCTTCCTA
* * * * *
103375 CGGGTCCGCTCTTTTTTTTTTCAGGGTGTAGAACTCGAACAATCTTCTTC
1 CGGGTCCGCTCTCTCTTTCTTCAGGGAGTAGAACTCGAACAATCATCTTC
103425 TGCTTCACTA
Statistics
Matches: 620, Mismatches: 56, Indels: 23
0.89 0.08 0.03
Matches are distributed among these distances:
52 99 0.16
53 355 0.57
54 165 0.27
55 1 0.00
ACGTcount: A:0.23, C:0.27, G:0.18, T:0.32
Consensus pattern (53 bp):
CGGGTCCGCTCTCTCTTTCTTCAGGGAGTAGAACTCGAACAATCATCTTCCTA
Found at i:103475 original size:37 final size:37
Alignment explanation
Indices: 103425--103509 Score: 161
Period size: 37 Copynumber: 2.3 Consensus size: 37
103415 AATCTTCTTC
*
103425 TGCTTCACTACTTCCTTGTGAAGATTTTTAGATGATT
1 TGCTTCACTACTTCCTTGTGAAGATTTTCAGATGATT
103462 TGCTTCACTACTTCCTTGTGAAGATTTTCAGATGATT
1 TGCTTCACTACTTCCTTGTGAAGATTTTCAGATGATT
103499 TGCTTCACTAC
1 TGCTTCACTAC
103510 CCTTTCGTGA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 47 1.00
ACGTcount: A:0.21, C:0.20, G:0.15, T:0.44
Consensus pattern (37 bp):
TGCTTCACTACTTCCTTGTGAAGATTTTCAGATGATT
Found at i:104649 original size:5 final size:6
Alignment explanation
Indices: 104636--104672 Score: 58
Period size: 6 Copynumber: 6.3 Consensus size: 6
104626 CCCAATTTTA
*
104636 TTTGTT TTTGTT TTTGTT TTTG-T TTTGTT TTTCTT TT
1 TTTGTT TTTGTT TTTGTT TTTGTT TTTGTT TTTGTT TT
104673 CTCTTCTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
5 5 0.17
6 24 0.83
ACGTcount: A:0.00, C:0.03, G:0.14, T:0.84
Consensus pattern (6 bp):
TTTGTT
Found at i:104661 original size:11 final size:11
Alignment explanation
Indices: 104636--104672 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
104626 CCCAATTTTA
104636 TTTGTTTTTGTT
1 TTTGTTTTTG-T
104648 TTTGTTTTTGT
1 TTTGTTTTTGT
*
104659 TTTGTTTTTCT
1 TTTGTTTTTGT
104670 TTT
1 TTT
104673 CTCTTCTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 14 0.58
12 10 0.42
ACGTcount: A:0.00, C:0.03, G:0.14, T:0.84
Consensus pattern (11 bp):
TTTGTTTTTGT
Found at i:104687 original size:19 final size:18
Alignment explanation
Indices: 104652--104733 Score: 85
Period size: 19 Copynumber: 4.3 Consensus size: 18
104642 TTTGTTTTTG
* *
104652 TTTTTGTTTTGTTTTTCTT
1 TTTTTCTTTT-TTTTCCTT
104671 TTCTCTTCTTTTTTTTCCTT
1 TT-T-TTCTTTTTTTTCCTT
104691 TTTTTCCTTTTTTTTCCTT
1 TTTTT-CTTTTTTTTCCTT
*
104710 TTTTTCCTTTTTTT-CTT
1 TTTTTCTTTTTTTTCCTT
104727 CTTTTTC
1 -TTTTTC
104734 ATCATTTTCA
Statistics
Matches: 56, Mismatches: 3, Indels: 9
0.82 0.04 0.13
Matches are distributed among these distances:
17 3 0.05
18 16 0.29
19 21 0.38
20 10 0.18
21 6 0.11
ACGTcount: A:0.00, C:0.18, G:0.02, T:0.79
Consensus pattern (18 bp):
TTTTTCTTTTTTTTCCTT
Found at i:104694 original size:9 final size:9
Alignment explanation
Indices: 104680--104733 Score: 83
Period size: 9 Copynumber: 5.9 Consensus size: 9
104670 TTTCTCTTCT
104680 TTTTTTTCC
1 TTTTTTTCC
104689 TTTTTTTCC
1 TTTTTTTCC
104698 TTTTTTTTCC
1 -TTTTTTTCC
104708 TTTTTTTCC
1 TTTTTTTCC
104717 TTTTTTT-C
1 TTTTTTTCC
104725 TTCTTTTTC
1 TT-TTTTTC
104734 ATCATTTTCA
Statistics
Matches: 42, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
8 3 0.07
9 30 0.71
10 9 0.21
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (9 bp):
TTTTTTTCC
Found at i:104731 original size:10 final size:9
Alignment explanation
Indices: 104663--104733 Score: 79
Period size: 9 Copynumber: 7.7 Consensus size: 9
104653 TTTTGTTTTG
104663 TTTTTCTTT
1 TTTTTCTTT
*
104672 TCTCTTCTTT
1 T-TTTTCTTT
104682 TTTTTCCTTT
1 TTTTT-CTTT
*
104692 TTTTCCTTT
1 TTTTTCTTT
*
104701 TTTTTCCTT
1 TTTTTCTTT
*
104710 TTTTTCCTT
1 TTTTTCTTT
*
104719 TTTTTCTTC
1 TTTTTCTTT
104728 TTTTTC
1 TTTTTC
104734 ATCATTTTCA
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
9 37 0.70
10 16 0.30
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (9 bp):
TTTTTCTTT
Found at i:104731 original size:28 final size:27
Alignment explanation
Indices: 104663--104733 Score: 97
Period size: 28 Copynumber: 2.6 Consensus size: 27
104653 TTTTGTTTTG
* *
104663 TTTTTCTTTTCTCTTCTTTTTTTTCCTT
1 TTTTTCTTTT-TTTTCCTTTTTTTCCTT
104691 TTTTTCCTTTTTTTTCCTTTTTTTCCTT
1 TTTTT-CTTTTTTTTCCTTTTTTTCCTT
*
104719 TTTTTCTTCTTTTTC
1 TTTTTCTTTTTTTTC
104734 ATCATTTTCA
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
27 9 0.23
28 25 0.64
29 5 0.13
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (27 bp):
TTTTTCTTTTTTTTCCTTTTTTTCCTT
Found at i:113730 original size:15 final size:15
Alignment explanation
Indices: 113710--113740 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
113700 CGGACCAACA
113710 GGAAATTATAAATAG
1 GGAAATTATAAATAG
113725 GGAAATTATAAATAG
1 GGAAATTATAAATAG
113740 G
1 G
113741 CATACAAGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.23, T:0.26
Consensus pattern (15 bp):
GGAAATTATAAATAG
Found at i:116915 original size:23 final size:21
Alignment explanation
Indices: 116871--116911 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
116861 TCCTTGCCAT
116871 ATTTATATAGAATTTGAGTAC
1 ATTTATATAGAATTTGAGTAC
116892 ATTTATATAGAATTTGAGTA
1 ATTTATATAGAATTTGAGTA
116912 TACAACAACC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.39, C:0.02, G:0.15, T:0.44
Consensus pattern (21 bp):
ATTTATATAGAATTTGAGTAC
Done.