Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009299.1 Hibiscus syriacus cultivar Beakdansim tig00113019_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: 148829
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:9399 original size:2 final size:2
Alignment explanation
Indices: 9392--9432 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
9382 AACAAATCAT
9392 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
9433 TTTCAAATGC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:18378 original size:29 final size:29
Alignment explanation
Indices: 18342--18440 Score: 110
Period size: 29 Copynumber: 3.4 Consensus size: 29
18332 CTAAGTTAAG
*
18342 GTTTAGGGTTTATATGTTATGGGGTTAGA
1 GTTTAGGGTTTAGATGTTATGGGGTTAGA
* *
18371 GTTTAGGGTTTAGATATTATGGTGTTATG-
1 GTTTAGGGTTTAGATGTTATGGGGTTA-GA
* * * *
18400 GTTTAGGGTTTAGAAGTTATAGGTTTATA
1 GTTTAGGGTTTAGATGTTATGGGGTTAGA
*
18429 ATTTAGGGTTTA
1 GTTTAGGGTTTA
18441 TAATTTAGGG
Statistics
Matches: 58, Mismatches: 10, Indels: 4
0.81 0.14 0.06
Matches are distributed among these distances:
29 57 0.98
30 1 0.02
ACGTcount: A:0.23, C:0.00, G:0.30, T:0.46
Consensus pattern (29 bp):
GTTTAGGGTTTAGATGTTATGGGGTTAGA
Found at i:18463 original size:14 final size:13
Alignment explanation
Indices: 18343--18470 Score: 78
Period size: 14 Copynumber: 9.0 Consensus size: 13
18333 TAAGTTAAGG
*
18343 TTTAGGGTTTATA
1 TTTAGGGTTTAGA
*
18356 TGTTATGGGGTTAGA
1 T-TTA-GGGTTTAGA
18371 GTTTAGGGTTTAGA
1 -TTTAGGGTTTAGA
* *
18385 TATTATGGTGTTATGG
1 T-TTAGGGT-TTA-GA
18401 TTTAGGGTTTAGAA
1 TTTAGGGTTTAG-A
*
18415 GTTATA-GGTTTATAA
1 -TT-TAGGGTTTA-GA
*
18430 TTTAGGGTTTATAA
1 TTTAGGGTTTA-GA
18444 TTTAGGGTTTAGA
1 TTTAGGGTTTAGA
*
18457 TTATAGGGTATAGA
1 TT-TAGGGTTTAGA
18471 ATGATGCAAT
Statistics
Matches: 93, Mismatches: 10, Indels: 23
0.74 0.08 0.18
Matches are distributed among these distances:
13 8 0.09
14 52 0.56
15 28 0.30
16 5 0.05
ACGTcount: A:0.26, C:0.00, G:0.29, T:0.45
Consensus pattern (13 bp):
TTTAGGGTTTAGA
Found at i:19662 original size:2 final size:2
Alignment explanation
Indices: 19655--19681 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
19645 TTTACCCTTT
19655 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
19682 GAATCATATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:25875 original size:39 final size:39
Alignment explanation
Indices: 25817--25902 Score: 136
Period size: 39 Copynumber: 2.2 Consensus size: 39
25807 CGGCGGCGGT
*
25817 TCCATGGTTAACGGGTTTGAACCCATAAAGAAGGGAGGC
1 TCCATGGTTAACGGCTTTGAACCCATAAAGAAGGGAGGC
* * *
25856 TCCATGGTTGACGGCTTTGAACCCGTAAAGAGGGGAGGC
1 TCCATGGTTAACGGCTTTGAACCCATAAAGAAGGGAGGC
25895 TCCATGGT
1 TCCATGGT
25903 AAATTACTCC
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 43 1.00
ACGTcount: A:0.26, C:0.20, G:0.33, T:0.22
Consensus pattern (39 bp):
TCCATGGTTAACGGCTTTGAACCCATAAAGAAGGGAGGC
Found at i:32826 original size:2 final size:2
Alignment explanation
Indices: 32821--32849 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
32811 TTTTTTTAAT
32821 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
32850 TGGGGTTGCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:44101 original size:6 final size:6
Alignment explanation
Indices: 44092--44182 Score: 62
Period size: 6 Copynumber: 14.5 Consensus size: 6
44082 TTTTCTGCTC
*
44092 TTTTCT TTTTCT CTTTGTCTTT TTTTCT TTTTCTT TCTTTTT TTTTCT
1 TTTTCT TTTTCT -TTT-TC--T TTTTCT TTTTC-T T-TTTCT TTTTCT
** *
44140 TTTTC- TTTT-T TTTTCT TTTT-T TCCCTCT TTTTCT TTTTAT TTT
1 TTTTCT TTTTCT TTTTCT TTTTCT T-TTTCT TTTTCT TTTTCT TTT
44183 CTCTGATGGA
Statistics
Matches: 68, Mismatches: 7, Indels: 20
0.72 0.07 0.21
Matches are distributed among these distances:
5 10 0.15
6 38 0.56
7 9 0.13
8 7 0.10
9 3 0.04
10 1 0.01
ACGTcount: A:0.01, C:0.16, G:0.01, T:0.81
Consensus pattern (6 bp):
TTTTCT
Found at i:44114 original size:14 final size:14
Alignment explanation
Indices: 44074--44150 Score: 77
Period size: 14 Copynumber: 5.4 Consensus size: 14
44064 TGATTCAATT
44074 TTTTTCTTTTTTCTGC
1 TTTTTC-TTTTTCT-C
44090 TCTTTTCTTTTTCTC
1 T-TTTTCTTTTTCTC
* *
44105 TTTGTCTTTTTTTC
1 TTTTTCTTTTTCTC
*
44119 TTTTTCTTTCTT-TT
1 TTTTTCTTT-TTCTC
44133 TTTTTCTTTTTCT-
1 TTTTTCTTTTTCTC
44146 TTTTT
1 TTTTT
44151 TTTCTTTTTT
Statistics
Matches: 54, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
13 7 0.13
14 30 0.56
15 4 0.07
16 8 0.15
17 5 0.09
ACGTcount: A:0.00, C:0.17, G:0.03, T:0.81
Consensus pattern (14 bp):
TTTTTCTTTTTCTC
Found at i:44126 original size:20 final size:20
Alignment explanation
Indices: 44072--44147 Score: 84
Period size: 20 Copynumber: 3.9 Consensus size: 20
44062 CTTGATTCAA
*
44072 TTTTTTTCTTTTT-TCTGCTC
1 TTTTTTTCTTTTTCTTTG-TC
* *
44092 TTTTCTT-TTTCTCTTTGTC
1 TTTTTTTCTTTTTCTTTGTC
* *
44111 TTTTTTTCTTTTTCTTTCTT
1 TTTTTTTCTTTTTCTTTGTC
44131 TTTTTTTCTTTTTCTTT
1 TTTTTTTCTTTTTCTTT
44148 TTTTTTCTTT
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
19 12 0.26
20 35 0.74
ACGTcount: A:0.00, C:0.17, G:0.03, T:0.80
Consensus pattern (20 bp):
TTTTTTTCTTTTTCTTTGTC
Found at i:44152 original size:20 final size:20
Alignment explanation
Indices: 44092--44158 Score: 89
Period size: 20 Copynumber: 3.2 Consensus size: 20
44082 TTTTCTGCTC
*
44092 TTTTCTTTTTCTCTTTGTCTTT
1 TTTTCTTTTTCT-TTT-TTTTT
*
44114 TTTTCTTTTTCTTTCTTTTT
1 TTTTCTTTTTCTTTTTTTTT
44134 TTTTCTTTTTCTTTTTTTTT
1 TTTTCTTTTTCTTTTTTTTT
44154 CTTTT
1 -TTTT
44159 TTTCCCTCTT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
20 23 0.56
21 6 0.15
22 12 0.29
ACGTcount: A:0.00, C:0.15, G:0.01, T:0.84
Consensus pattern (20 bp):
TTTTCTTTTTCTTTTTTTTT
Found at i:44170 original size:20 final size:18
Alignment explanation
Indices: 44072--44177 Score: 92
Period size: 18 Copynumber: 5.7 Consensus size: 18
44062 CTTGATTCAA
44072 TTTTTTTCTTTTTTCTGCTC
1 TTTTTTTCTTTTTT-T-CTC
* *
44092 TTTTCTTT-TTCTCTTTGTC
1 TTTT-TTTCTT-TTTTTCTC
44111 TTTTTTTCTTTTTCTT-TC
1 TTTTTTTCTTTTT-TTCTC
*
44129 TTTTTTT-TTCTTTTTCTT
1 TTTTTTTCTT-TTTTTCTC
*
44147 TTTTTTTCTTTTTTTCCC
1 TTTTTTTCTTTTTTTCTC
*
44165 TCTTTTTCTTTTT
1 TTTTTTTCTTTTT
44178 ATTTTCTCTG
Statistics
Matches: 72, Mismatches: 7, Indels: 16
0.76 0.07 0.17
Matches are distributed among these distances:
17 4 0.06
18 43 0.60
19 12 0.17
20 7 0.10
21 6 0.08
ACGTcount: A:0.00, C:0.18, G:0.02, T:0.80
Consensus pattern (18 bp):
TTTTTTTCTTTTTTTCTC
Found at i:44171 original size:34 final size:34
Alignment explanation
Indices: 44095--44182 Score: 97
Period size: 34 Copynumber: 2.5 Consensus size: 34
44085 TCTGCTCTTT
**
44095 TCTTTTTCTCTTTGTCTTTTTTTCTTTTTCTTTCTT
1 TCTTTTTCT-TTT-TCTTTTTTTCTTTTTCTTTCCC
* *
44131 TTTTTTTCTTTTTCTTTTTTT-TTCTTTTTTTCCC
1 TCTTTTTCTTTTTCTTTTTTTCTT-TTTCTTTCCC
*
44165 TCTTTTTCTTTTTATTTT
1 TCTTTTTCTTTTTCTTTT
44183 CTCTGATGGA
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
33 2 0.04
34 32 0.71
35 3 0.07
36 8 0.18
ACGTcount: A:0.01, C:0.17, G:0.01, T:0.81
Consensus pattern (34 bp):
TCTTTTTCTTTTTCTTTTTTTCTTTTTCTTTCCC
Found at i:46844 original size:22 final size:22
Alignment explanation
Indices: 46803--46870 Score: 127
Period size: 22 Copynumber: 3.0 Consensus size: 22
46793 CTCGTATAAA
46803 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTG-CCCGTAGAAT
46826 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
46848 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
46870 T
1 T
46871 ATGTCCATAA
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
22 33 0.73
23 12 0.27
ACGTcount: A:0.26, C:0.28, G:0.26, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:47129 original size:30 final size:30
Alignment explanation
Indices: 47084--47142 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
47074 ATCGCGTAGT
* *
47084 CATATTATTTCCATACCTTTATCACATAGA
1 CATATCATTTACATACCTTTATCACATAGA
47114 CATATCATTTACATACCTTTATCACATAG
1 CATATCATTTACATACCTTTATCACATAG
47143 CTCATATAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.34, C:0.24, G:0.03, T:0.39
Consensus pattern (30 bp):
CATATCATTTACATACCTTTATCACATAGA
Found at i:47684 original size:67 final size:67
Alignment explanation
Indices: 47526--47662 Score: 204
Period size: 67 Copynumber: 2.1 Consensus size: 67
47516 TCGGTTCCCC
* *
47526 CCCCCCTGGGGGTATCGATTCCCCTCAAGCAATCTGGAATTTCATATACGATGAGGGGGTATCGG
1 CCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATACGATGAGGGGGTATCGG
47591 TT
66 TT
* * ** *
47593 CCCCCCTGGGGGTACCGATTCCCCTCTAGCATTCTGGAAATTCAT-TTTGTTGAGGGGGTATCGG
1 CCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATACGATGAGGGGGTATCGG
47657 TT
66 TT
47659 CCCC
1 CCCC
47663 TTGAATTGGT
Statistics
Matches: 63, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
66 22 0.35
67 41 0.65
ACGTcount: A:0.18, C:0.28, G:0.26, T:0.28
Consensus pattern (67 bp):
CCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATACGATGAGGGGGTATCGG
TT
Found at i:53770 original size:22 final size:22
Alignment explanation
Indices: 53729--53796 Score: 127
Period size: 22 Copynumber: 3.0 Consensus size: 22
53719 CTCGTATAAA
53729 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTG-CCCGTAGAAT
53752 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
53774 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
53796 T
1 T
53797 ATGTCCATAA
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
22 33 0.73
23 12 0.27
ACGTcount: A:0.26, C:0.28, G:0.26, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:54055 original size:30 final size:30
Alignment explanation
Indices: 54010--54068 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
54000 ATCGCGTAGT
* *
54010 CATATTATTTCCATACCTTTATCACATAGA
1 CATATCATTTACATACCTTTATCACATAGA
54040 CATATCATTTACATACCTTTATCACATAG
1 CATATCATTTACATACCTTTATCACATAG
54069 CTCATATAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.34, C:0.24, G:0.03, T:0.39
Consensus pattern (30 bp):
CATATCATTTACATACCTTTATCACATAGA
Found at i:54568 original size:66 final size:67
Alignment explanation
Indices: 54434--54584 Score: 216
Period size: 66 Copynumber: 2.3 Consensus size: 67
54424 TTTTTCTCAT
* * *
54434 GGGGGAATCGGTTCCCCTCCTGGGGGTATCGATTCCCTCAAGCAATCTGGAATTTCATATACGAT
1 GGGGGTATCGGTTCCCCTCCTGGGGGTACCGATTCCCTCAAGCAATCTGGAAATTCATATACGAT
54499 GA
66 GA
* * * *
54501 GGGGGTATCGGTTCCCC-CCTGGGGGTACCGATTCCCCTCTAGCATTCTGGAAATTCAT-TTCGT
1 GGGGGTATCGGTTCCCCTCCTGGGGGTACCGATT-CCCTCAAGCAATCTGGAAATTCATATACGA
54564 TGA
65 TGA
54567 GGGGGTATCGGTTCCCCT
1 GGGGGTATCGGTTCCCCT
54585 TGAATGGGTA
Statistics
Matches: 75, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
66 38 0.51
67 37 0.49
ACGTcount: A:0.17, C:0.26, G:0.28, T:0.28
Consensus pattern (67 bp):
GGGGGTATCGGTTCCCCTCCTGGGGGTACCGATTCCCTCAAGCAATCTGGAAATTCATATACGAT
GA
Found at i:56163 original size:45 final size:45
Alignment explanation
Indices: 56112--56206 Score: 154
Period size: 45 Copynumber: 2.1 Consensus size: 45
56102 AAAAGCATAA
* *
56112 AAAGAAAAAAATAATATACAACACACAAATTTATTCTTTAACTCT
1 AAAGAAAAAAATAATATACAACACACAAATTTATTCTTTAAATAT
* *
56157 AAAGAAACAAATAATGTACAACACACAAATTTATTCTTTAAATAT
1 AAAGAAAAAAATAATATACAACACACAAATTTATTCTTTAAATAT
56202 AAAGA
1 AAAGA
56207 CATATAATTA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.55, C:0.14, G:0.04, T:0.27
Consensus pattern (45 bp):
AAAGAAAAAAATAATATACAACACACAAATTTATTCTTTAAATAT
Found at i:57322 original size:9 final size:9
Alignment explanation
Indices: 57308--57356 Score: 64
Period size: 9 Copynumber: 5.3 Consensus size: 9
57298 CTCATCCATC
57308 AGAGAAAAA
1 AGAGAAAAA
57317 AGAGAAAAA
1 AGAGAAAAA
*
57326 AGAAAAAAAAA
1 AG--AGAAAAA
57337 AGAGAAAAA
1 AGAGAAAAA
57346 A-AGAAAAA
1 AGAGAAAAA
57354 AGA
1 AGA
57357 AAGAAAATGA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
8 8 0.23
9 19 0.54
11 8 0.23
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (9 bp):
AGAGAAAAA
Found at i:57337 original size:20 final size:20
Alignment explanation
Indices: 57312--57401 Score: 94
Period size: 21 Copynumber: 4.3 Consensus size: 20
57302 TCCATCAGAG
57312 AAAAAAGAGAAAAAAGAAAA
1 AAAAAAGAGAAAAAAGAAAA
57332 AAAAAAGAGAAAAAAAGAAAA
1 AAAAAAGAG-AAAAAAGAAAA
*
57353 AAGAAAGA-AAATGAAAGGAAAGA
1 AAAAAAGAGAAA--AAA-GAAA-A
*
57376 AAAAAA-AGAAAAGAGAAAA
1 AAAAAAGAGAAAAAAGAAAA
57395 GAAAAAA
1 -AAAAAA
57402 AATTGAATCA
Statistics
Matches: 60, Mismatches: 3, Indels: 14
0.78 0.04 0.18
Matches are distributed among these distances:
19 4 0.07
20 19 0.32
21 23 0.38
22 5 0.08
23 9 0.15
ACGTcount: A:0.81, C:0.00, G:0.18, T:0.01
Consensus pattern (20 bp):
AAAAAAGAGAAAAAAGAAAA
Found at i:57363 original size:9 final size:9
Alignment explanation
Indices: 57315--57386 Score: 57
Period size: 9 Copynumber: 8.3 Consensus size: 9
57305 ATCAGAGAAA
57315 AAAGAGAAA-
1 AAAGA-AAAG
57324 AAAGAAAA-
1 AAAGAAAAG
57332 AAA-AAAGAG
1 AAAGAAA-AG
57341 AAA-AAAAG
1 AAAGAAAAG
57349 -AA-AAAAG
1 AAAGAAAAG
57356 AAAGAAAATG
1 AAAGAAAA-G
*
57366 AAAGGAAAG
1 AAAGAAAAG
*
57375 AAAAAAAAG
1 AAAGAAAAG
57384 AAA
1 AAA
57387 AGAGAAAAGA
Statistics
Matches: 55, Mismatches: 3, Indels: 10
0.81 0.04 0.15
Matches are distributed among these distances:
7 10 0.18
8 11 0.20
9 26 0.47
10 8 0.15
ACGTcount: A:0.81, C:0.00, G:0.18, T:0.01
Consensus pattern (9 bp):
AAAGAAAAG
Found at i:59348 original size:62 final size:62
Alignment explanation
Indices: 59238--59356 Score: 186
Period size: 62 Copynumber: 1.9 Consensus size: 62
59228 TCTTGTTTCC
*
59238 TAGAATCAATTTTTGACTTCCTCGTGAAGAGAAATCAACCTTTATTA-TTCATGACTCCCCAG
1 TAGAATCAATTTTTGACTTCCTCGTGAAGAGAAATCAACATTTATTATTTC-TGACTCCCCAG
* * *
59300 TAGAGTCAATTTTTGACTTCCTCGTGAAGAGAAGTCAACATTTGTTATTTCTGACTC
1 TAGAATCAATTTTTGACTTCCTCGTGAAGAGAAATCAACATTTATTATTTCTGACTC
59357 TCTAGCAGAG
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
62 49 0.94
63 3 0.06
ACGTcount: A:0.29, C:0.20, G:0.15, T:0.36
Consensus pattern (62 bp):
TAGAATCAATTTTTGACTTCCTCGTGAAGAGAAATCAACATTTATTATTTCTGACTCCCCAG
Found at i:79859 original size:14 final size:14
Alignment explanation
Indices: 79840--79876 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
79830 TGGGCTAAAT
*
79840 ATAAATGAACGGAC
1 ATAAATGAACGAAC
79854 ATAAATGAACGAAC
1 ATAAATGAACGAAC
79868 ATAAATGAA
1 ATAAATGAA
79877 TATAAACGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.57, C:0.11, G:0.16, T:0.16
Consensus pattern (14 bp):
ATAAATGAACGAAC
Found at i:81921 original size:57 final size:57
Alignment explanation
Indices: 81833--81955 Score: 246
Period size: 57 Copynumber: 2.2 Consensus size: 57
81823 TAAACTCAAA
81833 AGTTTGATAGAAAGCAGTACTTTTATCCAGACCTTCCAAAGGGTTACCAACTATCCC
1 AGTTTGATAGAAAGCAGTACTTTTATCCAGACCTTCCAAAGGGTTACCAACTATCCC
81890 AGTTTGATAGAAAGCAGTACTTTTATCCAGACCTTCCAAAGGGTTACCAACTATCCC
1 AGTTTGATAGAAAGCAGTACTTTTATCCAGACCTTCCAAAGGGTTACCAACTATCCC
81947 AGTTTGATA
1 AGTTTGATA
81956 TCCCAATAGA
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 66 1.00
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.29
Consensus pattern (57 bp):
AGTTTGATAGAAAGCAGTACTTTTATCCAGACCTTCCAAAGGGTTACCAACTATCCC
Found at i:89231 original size:17 final size:17
Alignment explanation
Indices: 89211--89289 Score: 88
Period size: 17 Copynumber: 4.6 Consensus size: 17
89201 TAGCAGCGCT
*
89211 GCTCTTCTCGCAGTGCC
1 GCTCTCCTCGCAGTGCC
*
89228 GCTCTCCTCGCAGTGCA
1 GCTCTCCTCGCAGTGCC
*
89245 GCTCTCCTTGCAGTGCC
1 GCTCTCCTCGCAGTGCC
* * *
89262 GCTC-CCGTTGCAGCGCT
1 GCTCTCC-TCGCAGTGCC
89279 GCTCTCCTCGC
1 GCTCTCCTCGC
89290 CGTACTGCTC
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
16 2 0.04
17 49 0.92
18 2 0.04
ACGTcount: A:0.06, C:0.43, G:0.24, T:0.27
Consensus pattern (17 bp):
GCTCTCCTCGCAGTGCC
Found at i:89283 original size:34 final size:34
Alignment explanation
Indices: 89203--89289 Score: 113
Period size: 34 Copynumber: 2.6 Consensus size: 34
89193 CACTTCCATA
*
89203 GCAGCGCTGCTCTTCTCGCAGTGCCGCTCTCCTC
1 GCAGCGCTGCTCTCCTCGCAGTGCCGCTCTCCTC
* * * *
89237 GCAGTGCAGCTCTCCTTGCAGTGCCGCTC-CCGTT
1 GCAGCGCTGCTCTCCTCGCAGTGCCGCTCTCC-TC
89271 GCAGCGCTGCTCTCCTCGC
1 GCAGCGCTGCTCTCCTCGC
89290 CGTACTGCTC
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
33 2 0.05
34 42 0.95
ACGTcount: A:0.07, C:0.43, G:0.25, T:0.25
Consensus pattern (34 bp):
GCAGCGCTGCTCTCCTCGCAGTGCCGCTCTCCTC
Found at i:92304 original size:26 final size:26
Alignment explanation
Indices: 92268--92321 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
92258 AGTAGAAGAA
92268 CTTTCAGCTCTTGAAAACAACAAAAC
1 CTTTCAGCTCTTGAAAACAACAAAAC
92294 CTTTCAGCTCTTGAAAACAACAAAAC
1 CTTTCAGCTCTTGAAAACAACAAAAC
92320 CT
1 CT
92322 GGACTATTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.41, C:0.28, G:0.07, T:0.24
Consensus pattern (26 bp):
CTTTCAGCTCTTGAAAACAACAAAAC
Found at i:102390 original size:17 final size:18
Alignment explanation
Indices: 102368--102402 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
102358 ATATATTAAT
*
102368 AATTTA-AAATTATGAAA
1 AATTTAGAAAATATGAAA
102385 AATTTAGAAAATATGAAA
1 AATTTAGAAAATATGAAA
102403 TTAGATAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.60, C:0.00, G:0.09, T:0.31
Consensus pattern (18 bp):
AATTTAGAAAATATGAAA
Found at i:102865 original size:15 final size:15
Alignment explanation
Indices: 102822--102866 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
102812 ATTCTTCCTT
102822 ATAAAAAGTCCTGAG
1 ATAAAAAGTCCTGAG
* *
102837 AT-AGAA--CTTGAG
1 ATAAAAAGTCCTGAG
102849 ATAAAAAGTCCTGAG
1 ATAAAAAGTCCTGAG
102864 ATA
1 ATA
102867 GAGAAATGAA
Statistics
Matches: 23, Mismatches: 4, Indels: 6
0.70 0.12 0.18
Matches are distributed among these distances:
12 7 0.30
13 3 0.13
14 3 0.13
15 10 0.43
ACGTcount: A:0.47, C:0.11, G:0.20, T:0.22
Consensus pattern (15 bp):
ATAAAAAGTCCTGAG
Found at i:104828 original size:57 final size:57
Alignment explanation
Indices: 104758--104871 Score: 192
Period size: 57 Copynumber: 2.0 Consensus size: 57
104748 TAGAAGATGA
* * *
104758 GCAACTACATGCATTGAGCACTGTTAAGTGTCAAATGTTCCATCCTCCGGCATATGG
1 GCAACTAAATGCATTGAGCACTGTTAAGTGCCAAATGTTCCATCCTCCCGCATATGG
*
104815 GCAACTAAATGCATTTAGCACTGTTAAGTGCCAAATGTTCCATCCTCCCGCATATGG
1 GCAACTAAATGCATTGAGCACTGTTAAGTGCCAAATGTTCCATCCTCCCGCATATGG
104872 CAGACCACTA
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
57 53 1.00
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.28
Consensus pattern (57 bp):
GCAACTAAATGCATTGAGCACTGTTAAGTGCCAAATGTTCCATCCTCCCGCATATGG
Found at i:107837 original size:39 final size:37
Alignment explanation
Indices: 107752--107825 Score: 96
Period size: 39 Copynumber: 1.9 Consensus size: 37
107742 GATTGAATTC
* *
107752 ATAAATAATATATTTGTATTTAATCGAATATAGATAT
1 ATAAATAATATATATGTATTTAATCGAATATAAATAT
107789 ATAAATAATATATCCATGT-TTTCAATCGAATATAAAT
1 ATAAATAATATAT--ATGTATTT-AATCGAATATAAAT
107826 CCTTAAATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
37 13 0.41
38 3 0.09
39 16 0.50
ACGTcount: A:0.46, C:0.07, G:0.07, T:0.41
Consensus pattern (37 bp):
ATAAATAATATATATGTATTTAATCGAATATAAATAT
Found at i:108646 original size:11 final size:11
Alignment explanation
Indices: 108630--108689 Score: 54
Period size: 11 Copynumber: 5.6 Consensus size: 11
108620 AATTACATTA
*
108630 TAAAAATTTAT
1 TAAAAATATAT
108641 TAAAAATATAT
1 TAAAAATATAT
***
108652 TATTGATA-AT
1 TAAAAATATAT
108662 TATAAAAT-T-T
1 TA-AAAATATAT
108672 TAAAAATATAT
1 TAAAAATATAT
108683 TAAAAAT
1 TAAAAAT
108690 TCTATAATAC
Statistics
Matches: 38, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
9 5 0.13
10 8 0.21
11 25 0.66
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.42
Consensus pattern (11 bp):
TAAAAATATAT
Found at i:108839 original size:14 final size:14
Alignment explanation
Indices: 108816--108906 Score: 94
Period size: 14 Copynumber: 6.6 Consensus size: 14
108806 GATTACACCT
108816 TAAACCCTAAACTC
1 TAAACCCTAAACTC
* *
108830 TAAACTCTAAACTA
1 TAAACCCTAAACTC
* *
108844 TAAACCTTAAACTA
1 TAAACCCTAAACTC
* *
108858 TAAATCCTAAACCC
1 TAAACCCTAAACTC
*
108872 TAAGCCCTAAA-TC
1 TAAACCCTAAACTC
* *
108885 TAAGCCCTAAACCC
1 TAAACCCTAAACTC
108899 TAAACCCT
1 TAAACCCT
108907 TAATCTAATT
Statistics
Matches: 63, Mismatches: 13, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
13 12 0.19
14 51 0.81
ACGTcount: A:0.43, C:0.32, G:0.02, T:0.23
Consensus pattern (14 bp):
TAAACCCTAAACTC
Found at i:108889 original size:13 final size:13
Alignment explanation
Indices: 108871--108914 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
108861 ATCCTAAACC
108871 CTAAGCCCTAAAT
1 CTAAGCCCTAAAT
*
108884 CTAAGCCCTAAACC
1 CTAAGCCCTAAA-T
* *
108898 CTAAACCCTTAAT
1 CTAAGCCCTAAAT
108911 CTAA
1 CTAA
108915 TTATGTGATA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
13 16 0.62
14 10 0.38
ACGTcount: A:0.39, C:0.34, G:0.05, T:0.23
Consensus pattern (13 bp):
CTAAGCCCTAAAT
Found at i:108904 original size:7 final size:7
Alignment explanation
Indices: 108816--108906 Score: 76
Period size: 7 Copynumber: 13.1 Consensus size: 7
108806 GATTACACCT
108816 TAAACCC
1 TAAACCC
*
108823 TAAACTC
1 TAAACCC
*
108830 TAAACTC
1 TAAACCC
**
108837 TAAACTA
1 TAAACCC
*
108844 TAAACCT
1 TAAACCC
**
108851 TAAACTA
1 TAAACCC
*
108858 TAAATCC
1 TAAACCC
108865 TAAACCC
1 TAAACCC
*
108872 TAAGCCC
1 TAAACCC
*
108879 TAAA-TC
1 TAAACCC
*
108885 TAAGCCC
1 TAAACCC
108892 TAAACCC
1 TAAACCC
108899 TAAACCC
1 TAAACCC
108906 T
1 T
108907 TAATCTAATT
Statistics
Matches: 67, Mismatches: 16, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
6 4 0.06
7 63 0.94
ACGTcount: A:0.43, C:0.32, G:0.02, T:0.23
Consensus pattern (7 bp):
TAAACCC
Found at i:109007 original size:14 final size:14
Alignment explanation
Indices: 108977--109020 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
108967 ATTAGAGTAT
*
108977 ACCATAAACCCTAA
1 ACCATAAACCTTAA
*
108991 ACCCT-AACCTATAA
1 ACCATAAACCT-TAA
109005 ACCATAAACCTTAA
1 ACCATAAACCTTAA
109019 AC
1 AC
109021 TCGATTATGT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
13 4 0.16
14 16 0.64
15 5 0.20
ACGTcount: A:0.48, C:0.34, G:0.00, T:0.18
Consensus pattern (14 bp):
ACCATAAACCTTAA
Found at i:112402 original size:20 final size:21
Alignment explanation
Indices: 112361--112424 Score: 67
Period size: 20 Copynumber: 3.0 Consensus size: 21
112351 TTCAATTTCC
* * *
112361 TCTTGAAGTGCATCGGTACAT
1 TCTTAAAGTGCATCGATGCAT
112382 TC-TAAAGTGCATCGATGCAT
1 TCTTAAAGTGCATCGATGCAT
112402 TCTTTAACATGTGCATCGATGCA
1 TC-TTAA-A-GTGCATCGATGCA
112425 CTAACCATGC
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
20 17 0.47
21 2 0.06
22 3 0.08
23 1 0.03
24 13 0.36
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (21 bp):
TCTTAAAGTGCATCGATGCAT
Found at i:112499 original size:64 final size:64
Alignment explanation
Indices: 112412--112572 Score: 154
Period size: 64 Copynumber: 2.5 Consensus size: 64
112402 TCTTTAACAT
* *
112412 GTGCATCGATGCA-CTAACC-ATGCATCGATACACCAA-T-CACCTTCGATGTTTTCA-TTTTAA
1 GTGCATCGATGCATCT--CCTATGCATCGATACACCAACTGCA--TTCAATGTTTCCATTTTTAA
112472 GGAG
62 GG-G
* * * *
112476 GTGCATCGATGTA-CTCCTTATGCATCGATGCACTAACTGCATTCAATGTTTCCATTTTTAATGG
1 GTGCATCGATGCATCTCC-TATGCATCGATACACCAACTGCATTCAATGTTTCCATTTTTAAGGG
* *
112540 GTGCATCGATGCATTTCCTGTGCATCGATACAC
1 GTGCATCGATGCATCTCCTATGCATCGATACAC
112573 ACTAGCAATT
Statistics
Matches: 81, Mismatches: 10, Indels: 12
0.79 0.10 0.12
Matches are distributed among these distances:
62 2 0.02
64 66 0.81
65 11 0.14
66 2 0.02
ACGTcount: A:0.25, C:0.24, G:0.18, T:0.33
Consensus pattern (64 bp):
GTGCATCGATGCATCTCCTATGCATCGATACACCAACTGCATTCAATGTTTCCATTTTTAAGGG
Found at i:113547 original size:22 final size:22
Alignment explanation
Indices: 113522--113565 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
113512 CGGCCCGACC
113522 GGTCGGAAGAACCGGACGACAT
1 GGTCGGAAGAACCGGACGACAT
113544 GGTCGGAAGAACCGGACGACAT
1 GGTCGGAAGAACCGGACGACAT
113566 AATAATTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.32, C:0.23, G:0.36, T:0.09
Consensus pattern (22 bp):
GGTCGGAAGAACCGGACGACAT
Found at i:116770 original size:26 final size:27
Alignment explanation
Indices: 116719--116770 Score: 63
Period size: 26 Copynumber: 1.9 Consensus size: 27
116709 TAACATGTGC
*
116719 ATTTTCACTTATCTCATTTCACTATACA
1 ATTTTCAC-TATCACATTTCACTATACA
116747 ATTTTCA-TATCACATGTTCA-TATA
1 ATTTTCACTATCACAT-TTCACTATA
116771 AGCTCATAGC
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
26 11 0.50
27 4 0.18
28 7 0.32
ACGTcount: A:0.31, C:0.21, G:0.02, T:0.46
Consensus pattern (27 bp):
ATTTTCACTATCACATTTCACTATACA
Found at i:117505 original size:24 final size:20
Alignment explanation
Indices: 117449--117506 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 20
117439 TTCTTCTTGA
*
117449 AGTGCATCGATACATTCTAC
1 AGTGCATCGATGCATTCTAC
*
117469 AGTACATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC--T-AC
117492 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
117507 CTACCCATGC
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 15 0.48
22 1 0.03
23 3 0.10
24 12 0.39
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.31
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:120528 original size:20 final size:20
Alignment explanation
Indices: 120434--120822 Score: 473
Period size: 20 Copynumber: 19.4 Consensus size: 20
120424 GATTTTCCAT
* ** *
120434 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
120454 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
120474 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
120494 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
120514 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
120534 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
120554 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
120574 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
120594 AA-CTGCAACGTGTATCCGTA
1 AATC-GCAACGCGTATCCGTA
120614 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
120634 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
120654 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
120674 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
120694 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
120714 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* *
120734 AATCGCAACGAGAATCCGTA
1 AATCGCAACGCGTATCCGTA
* * *
120754 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
120774 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
120794 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
120814 AATCACAAC
1 AATCGCAAC
120823 ACTTAAATTT
Statistics
Matches: 325, Mismatches: 34, Indels: 20
0.86 0.09 0.05
Matches are distributed among these distances:
19 4 0.01
20 317 0.98
21 4 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:121543 original size:24 final size:24
Alignment explanation
Indices: 121504--121550 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
121494 AAATTTGGTC
121504 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
121528 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
121551 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:121742 original size:12 final size:12
Alignment explanation
Indices: 121725--121749 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
121715 ATATAATCCT
121725 GAAGAAGAAAAA
1 GAAGAAGAAAAA
121737 GAAGAAGAAAAA
1 GAAGAAGAAAAA
121749 G
1 G
121750 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:124053 original size:19 final size:19
Alignment explanation
Indices: 124031--124304 Score: 345
Period size: 19 Copynumber: 15.4 Consensus size: 19
124021 CGGAAAATAC
*
124031 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
124050 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
124064 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
124084 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
124098 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
124117 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
124136 AATCGCAA--CGACA-G--
1 AATCGCAATGCGAAATGAA
*
124150 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
*
124169 AATCGCAATGCGGAATGAA
1 AATCGCAATGCGAAATGAA
124188 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
124207 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
124226 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
124245 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
124259 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
124278 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
124297 AATCGCAA
1 AATCGCAA
124305 CGAGATAATC
Statistics
Matches: 224, Mismatches: 10, Indels: 42
0.81 0.04 0.15
Matches are distributed among these distances:
14 38 0.17
15 1 0.00
16 14 0.06
17 12 0.05
18 2 0.01
19 144 0.64
20 13 0.06
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:124186 original size:71 final size:74
Alignment explanation
Indices: 124059--124304 Score: 293
Period size: 71 Copynumber: 3.4 Consensus size: 74
124049 AAATCCCAAC
* *
124059 ATGAAAATCGCAATGCGGAAATGAAAATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAAAA
1 ATGAAAATCGCAA-GC-GAAATG-AAATCGCAATGCGAAATGAAAATCGCAATGCGGAATGAAAA
124119 TCGCAATGCGAA
63 TCGCAATGCGAA
* *
124131 ATGAAAATCGCAA-CGACA-G-AATCGCAATGCGAAATTAAAATCGCAATGCGGAATGAAAATCG
1 ATGAAAATCGCAAGCGAAATGAAATCGCAATGCGAAATGAAAATCGCAATGCGGAATGAAAATCG
124193 CAATGCGAA
66 CAATGCGAA
*
124202 ATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA--C-GAA--AGAAT
1 ATGAAAATCGCAA-GCGAAATG-AAATCGCAATGCGAAATGAAAATCGCAATGCGGAATGAAAAT
124262 CGCAATGCGAA
64 CGCAATGCGAA
124273 ATGAAAATCGCAATGCGAAATGAAAATCGCAA
1 ATGAAAATCGCAA-GCGAAATG-AAATCGCAA
124305 CGAGATAATC
Statistics
Matches: 157, Mismatches: 7, Indels: 21
0.85 0.04 0.11
Matches are distributed among these distances:
66 8 0.05
68 3 0.02
69 3 0.02
70 2 0.01
71 93 0.59
72 13 0.08
73 7 0.04
74 2 0.01
76 26 0.17
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.15
Consensus pattern (74 bp):
ATGAAAATCGCAAGCGAAATGAAATCGCAATGCGAAATGAAAATCGCAATGCGGAATGAAAATCG
CAATGCGAA
Found at i:124233 original size:109 final size:104
Alignment explanation
Indices: 124059--124326 Score: 437
Period size: 109 Copynumber: 2.5 Consensus size: 104
124049 AAATCCCAAC
*
124059 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCA
1 ATGAAAATCGCAATGCGG-AATGAAAATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCA
*
124124 ATGCGAAATGAAAATCGCAACGACAGAATCGCAATGCGAA
65 ATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
*
124164 ATTAAAATCGCAATGCGGAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAAT
1 ATGAAAATCGCAATGCGGAATGAAAATCGCAA--CG--A-GAAAATCGCAATGCGAAATGAAAAT
124229 CGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
61 CGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
* *
124273 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAAAT
1 ATGAAAATCGCAATGCGGAATGAAAATCGCAACGAGAAAATCGCAATGCGAAAT
124327 TATAAACGCA
Statistics
Matches: 152, Mismatches: 6, Indels: 11
0.90 0.04 0.07
Matches are distributed among these distances:
104 32 0.21
105 18 0.12
106 2 0.01
107 2 0.01
108 1 0.01
109 97 0.64
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.15
Consensus pattern (104 bp):
ATGAAAATCGCAATGCGGAATGAAAATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCAA
TGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
Found at i:124274 original size:161 final size:157
Alignment explanation
Indices: 124031--124341 Score: 500
Period size: 161 Copynumber: 2.0 Consensus size: 157
124021 CGGAAAATAC
*
124031 AATCGCAACGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAG
1 AATCGCAACGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAA
124096 AGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGCAATGC
66 AGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGCAATGC
124161 GAAATTA-AAATCGCAATGCGGAATGAA
131 GAAATTATAAA-CGCAATGCGGAATGAA
* *
124188 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCA
1 AATCGCAACGCGAAATGAAAATCCCAA--C---ATGAAAATCGCAATGCGGAAATGAAAATCGCA
* *
124252 ACGAAAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGC
61 ACGAAAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGC
*
124317 AATGCGAAATTATAAACGCATTGCG
126 AATGCGAAATTATAAACGCAATGCG
124342 ATTTTCATTT
Statistics
Matches: 142, Mismatches: 6, Indels: 8
0.91 0.04 0.05
Matches are distributed among these distances:
157 25 0.18
159 1 0.01
161 97 0.68
162 19 0.13
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.15
Consensus pattern (157 bp):
AATCGCAACGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAA
AGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGCAATGC
GAAATTATAAACGCAATGCGGAATGAA
Found at i:124342 original size:52 final size:52
Alignment explanation
Indices: 124059--124326 Score: 428
Period size: 52 Copynumber: 5.0 Consensus size: 52
124049 AAATCCCAAC
124059 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
124112 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
* * *
124164 ATTAAAATCGCAATGCGGAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAGAATCGCAATGCGAA
*
124221 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
124273 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
124325 AT
1 AT
124327 TATAAACGCA
Statistics
Matches: 199, Mismatches: 11, Indels: 11
0.90 0.05 0.05
Matches are distributed among these distances:
52 132 0.66
53 17 0.09
54 2 0.01
55 2 0.01
56 1 0.01
57 45 0.23
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.15
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:124442 original size:19 final size:19
Alignment explanation
Indices: 124333--124434 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
124323 AAATTATAAA
124333 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
124352 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
124372 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
124388 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
124405 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
124424 CGCATTGCGAT
1 CGCATTGCGAT
124435 AGTCATTTTT
Statistics
Matches: 75, Mismatches: 2, Indels: 11
0.85 0.02 0.12
Matches are distributed among these distances:
14 6 0.08
16 7 0.09
17 7 0.09
19 36 0.48
20 19 0.25
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:124560 original size:14 final size:14
Alignment explanation
Indices: 124541--124577 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
124531 CATCAATTAC
124541 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
124555 ACAAATCATCTTTT
1 ACAAATCAACTTTT
124569 ACAAATCAA
1 ACAAATCAA
124578 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:126551 original size:14 final size:14
Alignment explanation
Indices: 126532--126588 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
126522 GCGAAATGAA
*
126532 AATCGCAACGACAG
1 AATCGCAACGAAAG
126546 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
126563 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
126579 AATCGCAACG
1 AATCGCAACG
126589 CGAATGAAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:126559 original size:33 final size:33
Alignment explanation
Indices: 126513--126604 Score: 159
Period size: 33 Copynumber: 2.8 Consensus size: 33
126503 GCGAAACCAA
*
126513 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
126546 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
126579 AATCGCAACGCG-AATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
126605 TGCGATTTTG
Statistics
Matches: 56, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
32 14 0.25
33 42 0.75
ACGTcount: A:0.47, C:0.22, G:0.21, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:126570 original size:19 final size:19
Alignment explanation
Indices: 126476--126609 Score: 119
Period size: 19 Copynumber: 7.6 Consensus size: 19
126466 TAGTTTACTT
* *
126476 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
126496 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
126515 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
126534 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
126548 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
126567 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
126581 TCGCAACGCG-AATGAAAA
1 TCGCAACGCGAAATGAAAA
*
126599 TCGCAATGCGA
1 TCGCAACGCGA
126610 TTTTGGTTTC
Statistics
Matches: 95, Mismatches: 8, Indels: 23
0.75 0.06 0.18
Matches are distributed among these distances:
14 16 0.17
15 2 0.02
16 9 0.09
17 10 0.11
18 11 0.12
19 35 0.37
20 12 0.13
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:126627 original size:19 final size:19
Alignment explanation
Indices: 126605--126733 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
126595 AAAATCGCAA
126605 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
126624 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
126638 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
126657 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
126671 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
126690 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
126709 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
126729 TGCGA
1 TGCGA
126734 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:126647 original size:33 final size:33
Alignment explanation
Indices: 126605--126696 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
126595 AAAATCGCAA
126605 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
126638 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
126671 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
126697 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:127067 original size:93 final size:93
Alignment explanation
Indices: 126777--127246 Score: 894
Period size: 93 Copynumber: 5.1 Consensus size: 93
126767 TTGAATGGAT
126777 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
126842 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
126870 AAATTTACTTTCAACCAAAAGAC-AAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
126933 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
126961 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
127026 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
*
127054 AAATTTACTTTCAACCAAAAGAC-AAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATATAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
127117 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
127145 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
127210 AGTTTAGCAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
127238 AAATTTACT
1 AAATTTACT
127247 AAGCAATCTA
Statistics
Matches: 370, Mismatches: 3, Indels: 8
0.97 0.01 0.02
Matches are distributed among these distances:
91 151 0.41
92 60 0.16
93 159 0.43
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.23
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:127086 original size:184 final size:184
Alignment explanation
Indices: 126777--127246 Score: 922
Period size: 184 Copynumber: 2.6 Consensus size: 184
126767 TTGAATGGAT
126777 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
126842 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAACAAAGACAAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAACAAAGACAAAT
126907 ATATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 ATATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
126961 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
127026 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAACAAAGACAAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAACAAAGACAAAT
*
127091 ATATTTCACAGTGTTAAAGAATATACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 ATATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
127145 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
127210 AGTTTAGCAGAATTGGCAGCAACCGAATAAATTTACT
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
127247 AAGCAATCTA
Statistics
Matches: 284, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
184 284 1.00
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.23
Consensus pattern (184 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAACAAAGACAAAT
ATATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:128986 original size:33 final size:33
Alignment explanation
Indices: 128941--129054 Score: 203
Period size: 33 Copynumber: 3.5 Consensus size: 33
128931 TCTTTTGGTT
128941 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
128974 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
129007 GAAATG-AAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
129039 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
129055 TGCGATTTTG
Statistics
Matches: 76, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
32 31 0.41
33 45 0.59
ACGTcount: A:0.45, C:0.21, G:0.25, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:128987 original size:19 final size:18
Alignment explanation
Indices: 128948--129059 Score: 95
Period size: 14 Copynumber: 6.8 Consensus size: 18
128938 GTTGAAATGA
128948 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
128963 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
128980 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
128996 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
129013 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
*
129028 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
129045 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
129060 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 24
0.74 0.04 0.22
Matches are distributed among these distances:
14 24 0.30
15 1 0.01
16 18 0.23
17 8 0.10
18 8 0.10
19 20 0.25
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:129090 original size:14 final size:14
Alignment explanation
Indices: 129071--129125 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
129061 TTTGGTTTCG
129071 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
129085 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
129104 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
129118 CGTTGCGA
1 CGTTGCGA
129126 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.25, G:0.24, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:129103 original size:33 final size:33
Alignment explanation
Indices: 129055--129125 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
129045 AAAATCGCAA
**
129055 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
129088 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
129121 TGCGA
1 TGCGA
129126 CAGTCATTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.08, C:0.23, G:0.25, T:0.44
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:129133 original size:33 final size:33
Alignment explanation
Indices: 129066--129147 Score: 119
Period size: 33 Copynumber: 2.5 Consensus size: 33
129056 GCGATTTTGG
***
129066 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
129099 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
*
129132 TTCTCTCGTTGCGATT
1 TT-TCGCGTTGCGATT
129148 TTCATTTATC
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 32 0.73
34 12 0.27
ACGTcount: A:0.10, C:0.26, G:0.22, T:0.43
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
Found at i:129152 original size:20 final size:20
Alignment explanation
Indices: 129078--129166 Score: 75
Period size: 20 Copynumber: 4.8 Consensus size: 20
129068 TCGCGTTGCG
129078 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
129098 ATT-TCGCGTTGCG------
1 ATTCTCTCGTTGCGATTTTC
***
129111 ATTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTC
129131 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
129151 ATTTATCTCGTTGCGA
1 A-TTCTCTCGTTGCGA
129167 CTCTTCTGCA
Statistics
Matches: 55, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
13 3 0.05
14 9 0.16
19 9 0.16
20 21 0.38
21 13 0.24
ACGTcount: A:0.12, C:0.25, G:0.19, T:0.44
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:129288 original size:33 final size:33
Alignment explanation
Indices: 129246--129316 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
129236 AATACTAACT
*
129246 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
129279 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
129312 TGAAA
1 TGAAA
129317 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:129550 original size:22 final size:22
Alignment explanation
Indices: 129498--129552 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
129488 TGGTTGTGAG
**
129498 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
129520 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
129542 GGATTTCTTCG
1 GGATTTCTTCG
129553 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:129723 original size:20 final size:20
Alignment explanation
Indices: 129698--129871 Score: 217
Period size: 20 Copynumber: 8.7 Consensus size: 20
129688 CTTTAAATAT
129698 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
129718 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
129740 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
129759 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
129779 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
129799 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
129819 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
129839 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
129859 CGCGTTGCGATTT
1 CGCGTTGCGATTT
129872 TCATATTCGC
Statistics
Matches: 132, Mismatches: 18, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
19 2 0.02
20 113 0.86
21 15 0.11
22 2 0.02
ACGTcount: A:0.20, C:0.20, G:0.26, T:0.34
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:129880 original size:20 final size:20
Alignment explanation
Indices: 129697--129890 Score: 66
Period size: 20 Copynumber: 9.7 Consensus size: 20
129687 GCTTTAAATA
***
129697 TCGCGTTGCGATTTACGGAT
1 TCGCGTTGCGATTTATATAT
* *
129717 ACGCGTTGCGATTTTATGTAT
1 TCGCGTTGCGA-TTTATATAT
** ***
129738 TATCGTTGCGATTTACGGAT
1 TCGCGTTGCGATTTATATAT
* * ***
129758 ACGCGTTGCGATATACGGAT
1 TCGCGTTGCGATTTATATAT
* * ***
129778 ACGCATTGCGATTTACCCAT
1 TCGCGTTGCGATTTATATAT
* ***
129798 ACGCGTTGCGATTTACGGAT
1 TCGCGTTGCGATTTATATAT
* * ***
129818 ACACGTTGCGATTTACGGAT
1 TCGCGTTGCGATTTATATAT
* * *
129838 ACGCGTTGCGATTTATGTGT
1 TCGCGTTGCGATTTATATAT
129858 TCGCGTTGCGATTT-TCATAT
1 TCGCGTTGCGATTTAT-ATAT
*
129878 TCGCATTGCGATT
1 TCGCGTTGCGATT
129891 ATGGAAAATC
Statistics
Matches: 144, Mismatches: 28, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
19 1 0.01
20 128 0.89
21 15 0.10
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.36
Consensus pattern (20 bp):
TCGCGTTGCGATTTATATAT
Found at i:129890 original size:60 final size:60
Alignment explanation
Indices: 129698--129871 Score: 249
Period size: 60 Copynumber: 2.9 Consensus size: 60
129688 CTTTAAATAT
**
129698 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
129759 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* *
129819 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTT
129872 TCATATTCGC
Statistics
Matches: 97, Mismatches: 16, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
60 69 0.71
61 28 0.29
ACGTcount: A:0.20, C:0.20, G:0.26, T:0.34
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:129971 original size:20 final size:20
Alignment explanation
Indices: 129946--129993 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
129936 AAGAATCGCG
129946 TTGCGATTTTGGAAACTGAT
1 TTGCGATTTTGGAAACTGAT
129966 TTGCGATTTTGGAAACTGAT
1 TTGCGATTTTGGAAACTGAT
129986 TTGCGATT
1 TTGCGATT
129994 CTGGGGATCG
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:0.23, C:0.10, G:0.25, T:0.42
Consensus pattern (20 bp):
TTGCGATTTTGGAAACTGAT
Found at i:133891 original size:9 final size:9
Alignment explanation
Indices: 133873--133905 Score: 59
Period size: 9 Copynumber: 3.8 Consensus size: 9
133863 GCTTTACCTA
133873 TATT-TTGT
1 TATTATTGT
133881 TATTATTGT
1 TATTATTGT
133890 TATTATTGT
1 TATTATTGT
133899 TATTATT
1 TATTATT
133906 AATTTTCTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 4 0.17
9 20 0.83
ACGTcount: A:0.21, C:0.00, G:0.09, T:0.70
Consensus pattern (9 bp):
TATTATTGT
Found at i:139604 original size:20 final size:20
Alignment explanation
Indices: 139579--139619 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
139569 AAGTAAGTAT
139579 TTCATTTGAATATCTTATGA
1 TTCATTTGAATATCTTATGA
139599 TTCATTTGAATATCTTATGA
1 TTCATTTGAATATCTTATGA
139619 T
1 T
139620 GCATATGAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.29, C:0.10, G:0.10, T:0.51
Consensus pattern (20 bp):
TTCATTTGAATATCTTATGA
Found at i:139628 original size:20 final size:20
Alignment explanation
Indices: 139585--139628 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
139575 GTATTTCATT
* *
139585 TGAATATCTTATGATTCATT
1 TGAATATCTTATGATGCATA
139605 TGAATATCTTATGATGCATA
1 TGAATATCTTATGATGCATA
139625 TGAA
1 TGAA
139629 CTCGATATAT
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:0.34, C:0.09, G:0.14, T:0.43
Consensus pattern (20 bp):
TGAATATCTTATGATGCATA
Found at i:147849 original size:17 final size:17
Alignment explanation
Indices: 147822--147860 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
147812 AATTTACAAT
*
147822 TAATT-TAAATAGTATC
1 TAATTATAAATAATATC
147838 TAATTATAAATAATATC
1 TAATTATAAATAATATC
147855 TAATTA
1 TAATTA
147861 ATTTGATTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 5 0.24
17 16 0.76
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.44
Consensus pattern (17 bp):
TAATTATAAATAATATC
Done.