Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006647.1 Hibiscus syriacus cultivar Beakdansim tig00016386_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: 170885
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:1745 original size:20 final size:20
Alignment explanation
Indices: 1703--1748 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
1693 CTTGACTTTG
**
1703 CTCGAATTTTATAAACTTGA
1 CTCGAATTTTATAAACTAAA
*
1723 CTCGAGTTTTATAAACTAAA
1 CTCGAATTTTATAAACTAAA
1743 CTCGAA
1 CTCGAA
1749 AAAATTAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.37, C:0.17, G:0.11, T:0.35
Consensus pattern (20 bp):
CTCGAATTTTATAAACTAAA
Found at i:9151 original size:16 final size:16
Alignment explanation
Indices: 9130--9161 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
9120 ACTATTCACA
*
9130 TGAATAGTGAATTTCG
1 TGAATAGTGAAATTCG
9146 TGAATAGTGAAATTCG
1 TGAATAGTGAAATTCG
9162 GTCGGCGATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.06, G:0.25, T:0.34
Consensus pattern (16 bp):
TGAATAGTGAAATTCG
Found at i:13794 original size:16 final size:16
Alignment explanation
Indices: 13773--13805 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
13763 TCGAACTCGA
13773 ACCTGTCGTCGAGTTC
1 ACCTGTCGTCGAGTTC
13789 ACCTGTCGTCGAGTTC
1 ACCTGTCGTCGAGTTC
13805 A
1 A
13806 GCGTTTTCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.15, C:0.30, G:0.24, T:0.30
Consensus pattern (16 bp):
ACCTGTCGTCGAGTTC
Found at i:35114 original size:8 final size:8
Alignment explanation
Indices: 35101--35141 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
35091 CTCATTTTCA
35101 GAGAATTT
1 GAGAATTT
35109 GAGAATTT
1 GAGAATTT
*
35117 -AGAGTTT
1 GAGAATTT
*
35124 GGGAATTT
1 GAGAATTT
35132 GAGAATTT
1 GAGAATTT
35140 GA
1 GA
35142 AAGCTTGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (8 bp):
GAGAATTT
Found at i:35452 original size:128 final size:128
Alignment explanation
Indices: 35222--35581 Score: 650
Period size: 128 Copynumber: 2.8 Consensus size: 128
35212 ACTATTCACA
*
35222 TGAAGGCGCGTTCTCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
* *
35287 TTATGTCACTCATGTCCCTCGGGGACACTA-TTCATATCAGTACCTATTATTTCTCAGGGGACT
66 TTATGTCACTCATGTCCCTCGGGGACACTAGAT-ATATCAGTACCTATTATTTCTCAGAGGACT
*
35350 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCATAGAATATGTTATCATTGCCCTA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
35415 TTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCTCAGAGGACT
66 TTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCTCAGAGGACT
* *
35478 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTTTCAGAGAATATGTTATCATTGCCTTA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
35543 TTATGTCACTCATGTCCCTCGGGGACACTAGATATATCA
66 TTATGTCACTCATGTCCCTCGGGGACACTAGATATATCA
35582 TTGCCCTACT
Statistics
Matches: 224, Mismatches: 7, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
128 223 1.00
129 1 0.00
ACGTcount: A:0.21, C:0.24, G:0.22, T:0.33
Consensus pattern (128 bp):
TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
TTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCTCAGAGGACT
Found at i:36376 original size:33 final size:30
Alignment explanation
Indices: 36339--36424 Score: 91
Period size: 33 Copynumber: 2.7 Consensus size: 30
36329 AATAATTCTA
36339 AAAAAATAATAATTATATAAATATTATTTTAAT
1 AAAAAATAATAATTATATAAATA-TA--TTAAT
* *
36372 AAAAAATAATATTTACATAAATATATTAAT
1 AAAAAATAATAATTATATAAATATATTAAT
* *
36402 ATAAAATATAATAACTATTTAAA
1 A-AAAA-ATAATAATTATATAAA
36425 AAATACTAAC
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
30 6 0.13
31 4 0.09
32 14 0.31
33 21 0.47
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.38
Consensus pattern (30 bp):
AAAAAATAATAATTATATAAATATATTAAT
Found at i:36406 original size:32 final size:33
Alignment explanation
Indices: 36339--36415 Score: 95
Period size: 33 Copynumber: 2.4 Consensus size: 33
36329 AATAATTCTA
* *
36339 AAAAAATAATAATTATATAAATATTATTTTAAT
1 AAAAAATAATAATTACATAAATATTATTATAAT
*
36372 AAAAAATAATATTTACATAAATA-TATTA-ATAT
1 AAAAAATAATAATTACATAAATATTATTATA-AT
*
36404 AAAATATAATAA
1 AAAAAATAATAA
36416 CTATTTAAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
31 1 0.03
32 16 0.42
33 21 0.55
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (33 bp):
AAAAAATAATAATTACATAAATATTATTATAAT
Found at i:39186 original size:6 final size:7
Alignment explanation
Indices: 39172--39216 Score: 58
Period size: 7 Copynumber: 6.7 Consensus size: 7
39162 GTTGAGATTC
*
39172 AAAAGGA
1 AAAAGTA
39179 AAAAG-A
1 AAAAGTA
*
39185 AAATG-A
1 AAAAGTA
39191 AAAAGTA
1 AAAAGTA
39198 AAAAGTA
1 AAAAGTA
39205 AAAAGTA
1 AAAAGTA
39212 AAAAG
1 AAAAG
39217 GAAGAACAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
6 10 0.29
7 25 0.71
ACGTcount: A:0.73, C:0.00, G:0.18, T:0.09
Consensus pattern (7 bp):
AAAAGTA
Found at i:46314 original size:18 final size:17
Alignment explanation
Indices: 46291--46324 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
46281 TGATAACAAA
46291 AAAATTTATAGCATAAAT
1 AAAATTT-TAGCATAAAT
*
46309 AAAATTTTAGGATAAA
1 AAAATTTTAGCATAAA
46325 CACCATTAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.56, C:0.03, G:0.09, T:0.32
Consensus pattern (17 bp):
AAAATTTTAGCATAAAT
Found at i:54923 original size:19 final size:19
Alignment explanation
Indices: 54899--54935 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
54889 CGTCGTTTTG
54899 ATTTCTGAAATTTAAACTA
1 ATTTCTGAAATTTAAACTA
*
54918 ATTTCTTAAATTTAAACT
1 ATTTCTGAAATTTAAACT
54936 TGTGTAACGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.41, C:0.11, G:0.03, T:0.46
Consensus pattern (19 bp):
ATTTCTGAAATTTAAACTA
Found at i:60789 original size:21 final size:21
Alignment explanation
Indices: 60753--60949 Score: 120
Period size: 21 Copynumber: 9.2 Consensus size: 21
60743 GTTTCCAGAT
* *
60753 TCGCAACGCGAACTTCGACTA
1 TCGCAATGCAAACTTCGACTA
*
60774 TCGTAATGCAAACTTCG---A
1 TCGCAATGCAAACTTCGACTA
* *
60792 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCAAACTTCGACTA
* *
60813 TCGCAATGCGAA-TAT-GTA-AA
1 TCGCAATGCAAACT-TCG-ACTA
* *
60833 TCGCAATGCGATA-GTCGACTA
1 TCGCAATGC-AAACTTCGACTA
* *
60854 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCAAACTTCGACTA
*
60875 TCGCAATGCAAACTTGGACTA
1 TCGCAATGCAAACTTCGACTA
*
60896 TCGCATTGCGAAATGCGAACTTCGACTA
1 T--C---GC--AATGCAAACTTCGACTA
* *
60924 TCGCAACGCGAACTTCGACTA
1 TCGCAATGCAAACTTCGACTA
60945 TCGCA
1 TCGCA
60950 TTGCGATTTA
Statistics
Matches: 141, Mismatches: 19, Indels: 32
0.73 0.10 0.17
Matches are distributed among these distances:
18 15 0.11
20 15 0.11
21 89 0.63
23 3 0.02
26 3 0.02
28 16 0.11
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.23
Consensus pattern (21 bp):
TCGCAATGCAAACTTCGACTA
Found at i:60934 original size:28 final size:28
Alignment explanation
Indices: 60879--60935 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
60869 GGACTATCGC
* **
60879 AATGCAAACTTGGACTATCGCATTGCGA
1 AATGCAAACTTCGACTATCGCAACGCGA
*
60907 AATGCGAACTTCGACTATCGCAACGCGA
1 AATGCAAACTTCGACTATCGCAACGCGA
60935 A
1 A
60936 CTTCGACTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.33, C:0.25, G:0.21, T:0.21
Consensus pattern (28 bp):
AATGCAAACTTCGACTATCGCAACGCGA
Found at i:60938 original size:49 final size:49
Alignment explanation
Indices: 60858--60955 Score: 160
Period size: 49 Copynumber: 2.0 Consensus size: 49
60848 CGACTATCGC
* * *
60858 AATGCGAACTTGGACTATCGCAATGCAAACTTGGACTATCGCATTGCGA
1 AATGCGAACTTCGACTATCGCAACGCAAACTTCGACTATCGCATTGCGA
*
60907 AATGCGAACTTCGACTATCGCAACGCGAACTTCGACTATCGCATTGCGA
1 AATGCGAACTTCGACTATCGCAACGCAAACTTCGACTATCGCATTGCGA
60956 TTTACATATT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
49 45 1.00
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.23
Consensus pattern (49 bp):
AATGCGAACTTCGACTATCGCAACGCAAACTTCGACTATCGCATTGCGA
Found at i:60955 original size:21 final size:21
Alignment explanation
Indices: 60907--60955 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
60897 CGCATTGCGA
60907 AATGCGAACTTCGACTATCGC
1 AATGCGAACTTCGACTATCGC
*
60928 AACGCGAACTTCGACTATCGC
1 AATGCGAACTTCGACTATCGC
*
60949 ATTGCGA
1 AATGCGA
60956 TTTACATATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (21 bp):
AATGCGAACTTCGACTATCGC
Found at i:60989 original size:21 final size:21
Alignment explanation
Indices: 60945--61032 Score: 83
Period size: 21 Copynumber: 4.2 Consensus size: 21
60935 ACTTCGACTA
* * *
60945 TCGCATTGCGAT-TTACATAT
1 TCGCATTGCGATAGTCCAAAT
60965 TCGCATTGCGATAGTCCAAAT
1 TCGCATTGCGATAGTCCAAAT
* *
60986 TCGCGTTGCGATTTATTCCAAAT
1 TCGCATTGCGA--TAGTCCAAAT
*
61009 TCG--TTGCGATAGTCCAAAA
1 TCGCATTGCGATAGTCCAAAT
61028 TCGCA
1 TCGCA
61033 ACGACTGGTG
Statistics
Matches: 56, Mismatches: 7, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
19 11 0.20
20 12 0.21
21 21 0.38
23 12 0.21
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.33
Consensus pattern (21 bp):
TCGCATTGCGATAGTCCAAAT
Found at i:60995 original size:41 final size:40
Alignment explanation
Indices: 60944--61032 Score: 108
Period size: 42 Copynumber: 2.1 Consensus size: 40
60934 AACTTCGACT
*
60944 ATCGCATTGCGATTTA-CATATTCGCATTGCGATAGTCCAAA
1 ATCGCATTGCGATTTATCAAATTCG--TTGCGATAGTCCAAA
* *
60985 TTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAA
1 ATCGCATTGCGATTTA-T-CAAATTCGTTGCGATAGTCCAAA
61027 ATCGCA
1 ATCGCA
61033 ACGACTGGTG
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
41 14 0.35
42 19 0.47
44 7 0.17
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.33
Consensus pattern (40 bp):
ATCGCATTGCGATTTATCAAATTCGTTGCGATAGTCCAAA
Found at i:61211 original size:21 final size:21
Alignment explanation
Indices: 61181--61356 Score: 216
Period size: 21 Copynumber: 8.4 Consensus size: 21
61171 TTTAAAGATA
61181 GCATTGCGATAGTCCAAGTTC
1 GCATTGCGATAGTCCAAGTTC
* *
61202 GCATTACGATAGTCGAAGTTC
1 GCATTGCGATAGTCCAAGTTC
*
61223 GCGTTGCGATAGTCCAAGTTC
1 GCATTGCGATAGTCCAAGTTC
* *
61244 GCATTGCGATAGT-CGACTATC
1 GCATTGCGATAGTCCAAGT-TC
*
61265 GCATTGCGACT--TACATA-TTC
1 GCATTGCGA-TAGTCCA-AGTTC
61285 GCATTGCGATAGTCCAAGTTC
1 GCATTGCGATAGTCCAAGTTC
*
61306 GCATTGCGATAGTCGAAGTTC
1 GCATTGCGATAGTCCAAGTTC
*
61327 GCATTGCGATAGTCGAAGTTC
1 GCATTGCGATAGTCCAAGTTC
*
61348 GCGTTGCGA
1 GCATTGCGA
61357 ATCTGGAAAC
Statistics
Matches: 136, Mismatches: 12, Indels: 14
0.84 0.07 0.09
Matches are distributed among these distances:
19 1 0.01
20 16 0.12
21 117 0.86
22 2 0.01
ACGTcount: A:0.23, C:0.22, G:0.26, T:0.29
Consensus pattern (21 bp):
GCATTGCGATAGTCCAAGTTC
Found at i:65627 original size:12 final size:12
Alignment explanation
Indices: 65610--65635 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
65600 AAGGAGAATC
65610 CACTAATCACAT
1 CACTAATCACAT
65622 CACTAATCACAT
1 CACTAATCACAT
65634 CA
1 CA
65636 TATTAACTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.35, G:0.00, T:0.23
Consensus pattern (12 bp):
CACTAATCACAT
Found at i:68602 original size:35 final size:34
Alignment explanation
Indices: 68505--68602 Score: 92
Period size: 35 Copynumber: 2.8 Consensus size: 34
68495 TGCTGACATG
68505 AAAATTACACGTTAAGTATTATTTAAAATGATAT
1 AAAATTACACGTTAAGTATTATTTAAAATGATAT
* ** * * *
68539 AAAATGA-AAATTACA-AATGTGTACTAAAATGATAT
1 AAAATTACACGTTA-AGTAT-TAT-TTAAAATGATAT
68574 AAAAATTACACGTTAAGTATTATTTAAAA
1 -AAAATTACACGTTAAGTATTATTTAAAA
68603 AATTGAAAGT
Statistics
Matches: 46, Mismatches: 12, Indels: 11
0.67 0.17 0.16
Matches are distributed among these distances:
33 6 0.13
34 9 0.20
35 16 0.35
36 9 0.20
37 6 0.13
ACGTcount: A:0.51, C:0.06, G:0.09, T:0.34
Consensus pattern (34 bp):
AAAATTACACGTTAAGTATTATTTAAAATGATAT
Found at i:69194 original size:14 final size:16
Alignment explanation
Indices: 69175--69207 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
69165 TTTTCATTTC
69175 ATTTAAA-ATTT-TAT
1 ATTTAAATATTTGTAT
69189 ATTTAAATATTTGTAT
1 ATTTAAATATTTGTAT
69205 ATT
1 ATT
69208 CGAAATTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.41
15 4 0.24
16 6 0.35
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (16 bp):
ATTTAAATATTTGTAT
Found at i:73835 original size:24 final size:22
Alignment explanation
Indices: 73802--73848 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 22
73792 GTAAAATATT
*
73802 TTTATTTTGAAAAATAATTAAATA
1 TTTATATTGAAAAAT-A-TAAATA
*
73826 TTTATATTGATAAATATAAATA
1 TTTATATTGAAAAATATAAATA
73848 T
1 T
73849 GGCTTAATAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 7 0.33
23 1 0.05
24 13 0.62
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (22 bp):
TTTATATTGAAAAATATAAATA
Found at i:87930 original size:27 final size:27
Alignment explanation
Indices: 87899--87966 Score: 122
Period size: 27 Copynumber: 2.6 Consensus size: 27
87889 TCTATTTACA
87899 AAATCATATCTCTATAGGAATGGTAAC
1 AAATCATATCTCTATAGGAATGGTAAC
87926 AAATCATATCTCTATAGGAATGGTAAC
1 AAATCATATCTCTATAGGAATGGTAAC
87953 AAATC--ATCTCTATA
1 AAATCATATCTCTATA
87967 ATTCCTATAA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
25 9 0.22
27 32 0.78
ACGTcount: A:0.41, C:0.16, G:0.12, T:0.31
Consensus pattern (27 bp):
AAATCATATCTCTATAGGAATGGTAAC
Found at i:94476 original size:44 final size:43
Alignment explanation
Indices: 94408--94493 Score: 127
Period size: 44 Copynumber: 2.0 Consensus size: 43
94398 ATTCATCTGA
* *
94408 CATTTCTGCGAACCAAACATAATATGAAATTAGATTCCAATTT
1 CATTTCTGCCAACCAAACAGAATATGAAATTAGATTCCAATTT
* *
94451 CATTTCCTGCCAACCAAACAGAATATGAAATTTGATTCTAATT
1 CATTT-CTGCCAACCAAACAGAATATGAAATTAGATTCCAATT
94494 CCTGACAGAT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
43 5 0.13
44 33 0.87
ACGTcount: A:0.38, C:0.20, G:0.09, T:0.33
Consensus pattern (43 bp):
CATTTCTGCCAACCAAACAGAATATGAAATTAGATTCCAATTT
Found at i:96633 original size:125 final size:126
Alignment explanation
Indices: 96407--96672 Score: 320
Period size: 125 Copynumber: 2.1 Consensus size: 126
96397 TGCGCACAAA
* * * * * *
96407 ACTCGAGCCTTAATGGCATCCACTAAATGAAATTGTTTAGGTGCCGAAAGGGGCTAGGCCAAGGT
1 ACTCGAACCTTAATGGCATCCACTAAATGAAA-T-TTAAGATGACGAAAGGGGCCAGGCCAAGAT
* * * * * ** *
96472 CGGGGCTACCACCAGCCACATAGATGGTCGAGAGTGATACTTACAGGTCATCCACTAAATGAG
64 CAGGGCCACCACCAGCCACATAGATGGCCGAAAGTGATACTCACAAATCATCCACTAAACGAG
* * *
96535 ACTCGAACCTTAATGTCATCCACTAAATGAAA-TTAAGATGACGAAAGGTGCCAGTCCAAGAAT-
1 ACTCGAACCTTAATGGCATCCACTAAATGAAATTTAAGATGACGAAAGGGGCCAGGCCAAG-ATC
*
96598 AGGGCCACCACCAGCCACATAGATGGCCGAAAGTGATACTCACAAATCATTCACTAAACGAG
65 AGGGCCACCACCAGCCACATAGATGGCCGAAAGTGATACTCACAAATCATCCACTAAACGAG
*
96660 ATTCGAACCTTAA
1 ACTCGAACCTTAA
96673 ACGAGATTGT
Statistics
Matches: 118, Mismatches: 19, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
125 87 0.74
126 1 0.01
128 30 0.25
ACGTcount: A:0.34, C:0.24, G:0.22, T:0.20
Consensus pattern (126 bp):
ACTCGAACCTTAATGGCATCCACTAAATGAAATTTAAGATGACGAAAGGGGCCAGGCCAAGATCA
GGGCCACCACCAGCCACATAGATGGCCGAAAGTGATACTCACAAATCATCCACTAAACGAG
Found at i:98503 original size:25 final size:22
Alignment explanation
Indices: 98459--98503 Score: 54
Period size: 22 Copynumber: 1.9 Consensus size: 22
98449 TATTAAAATT
*
98459 TTGTTTTTTTAATATTTATATG
1 TTGTTTTTTTAATATATATATG
98481 TTGTTGTTTTTCAATATAATATA
1 TTGTT-TTTTT-AATAT-ATATA
98504 ATTTTTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 5 0.26
23 5 0.26
24 5 0.26
25 4 0.21
ACGTcount: A:0.27, C:0.02, G:0.09, T:0.62
Consensus pattern (22 bp):
TTGTTTTTTTAATATATATATG
Found at i:103390 original size:18 final size:18
Alignment explanation
Indices: 103363--103403 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
103353 ATTATTGCGA
103363 ATATTTTA-T-TTA-TTT
1 ATATTTTAGTATTAGTTT
*
103378 ATTTTTTAGTATTAGTTT
1 ATATTTTAGTATTAGTTT
103396 ATATTTTA
1 ATATTTTA
103404 ATTTGTATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 7 0.33
16 1 0.05
17 3 0.14
18 10 0.48
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (18 bp):
ATATTTTAGTATTAGTTT
Found at i:104997 original size:21 final size:21
Alignment explanation
Indices: 104955--104998 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
104945 GATGAGGATG
* * *
104955 CAACCATTTTAGATGGCTCCA
1 CAACCATTTCAGATGCCACCA
*
104976 CAACTATTTCAGATGCCACCA
1 CAACCATTTCAGATGCCACCA
104997 CA
1 CA
104999 GCAGCTTCTA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.32, C:0.32, G:0.11, T:0.25
Consensus pattern (21 bp):
CAACCATTTCAGATGCCACCA
Found at i:110444 original size:29 final size:24
Alignment explanation
Indices: 110358--110449 Score: 132
Period size: 24 Copynumber: 3.8 Consensus size: 24
110348 CATAAATCAT
* *
110358 GTCAAGTATCATATCA-AACTCCAG
1 GTCAAGTATCAGATCAGAA-TCCAA
110382 GTCAAGTATCAGATCAGAATCCAA
1 GTCAAGTATCAGATCAGAATCCAA
*
110406 GTCAAGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAA
*
110430 GTCAAGTATCATATCAGAAT
1 GTCAAGTATCAGATCAGAAT
110450 TCAAATAGAA
Statistics
Matches: 63, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
24 61 0.97
25 2 0.03
ACGTcount: A:0.39, C:0.21, G:0.15, T:0.25
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAA
Found at i:111452 original size:26 final size:26
Alignment explanation
Indices: 111423--111475 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
111413 TCAGTTTTAT
*
111423 TCCATTCATTTCAGAGCTCGAGGATA
1 TCCAATCATTTCAGAGCTCGAGGATA
* * *
111449 TCCAATCATTTCTGAGCTTGATGATA
1 TCCAATCATTTCAGAGCTCGAGGATA
111475 T
1 T
111476 TCTTGGGTCA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.36
Consensus pattern (26 bp):
TCCAATCATTTCAGAGCTCGAGGATA
Found at i:115050 original size:25 final size:23
Alignment explanation
Indices: 114998--115051 Score: 65
Period size: 25 Copynumber: 2.3 Consensus size: 23
114988 TAAAAAAAAA
*
114998 AATTA-TTAACTTTTATTGAATT
1 AATTATTTAACTTTTATTAAATT
*
115020 ATTTATTTAACTATTTAATTAAATT
1 AATTATTTAACT-TTT-ATTAAATT
115045 AATTATT
1 AATTATT
115052 ATTATTTAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
22 4 0.15
23 6 0.23
24 3 0.12
25 13 0.50
ACGTcount: A:0.39, C:0.04, G:0.02, T:0.56
Consensus pattern (23 bp):
AATTATTTAACTTTTATTAAATT
Found at i:115423 original size:23 final size:23
Alignment explanation
Indices: 115393--115439 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
115383 ATGATTTTTA
115393 AAAAAAATAACAATTTAAATATT
1 AAAAAAATAACAATTTAAATATT
115416 AAAAAAATAACAATTTAAATATT
1 AAAAAAATAACAATTTAAATATT
115439 A
1 A
115440 GATACTAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (23 bp):
AAAAAAATAACAATTTAAATATT
Found at i:121578 original size:21 final size:21
Alignment explanation
Indices: 121552--121626 Score: 82
Period size: 21 Copynumber: 3.6 Consensus size: 21
121542 GATTCTGACT
121552 ATCGTAACGCGATAATACAAA
1 ATCGTAACGCGATAATACAAA
** *
121573 ATCGTAACGCGATTCTGAC--T
1 ATCGTAACGCGATAAT-ACAAA
* *
121593 ATCGCAACGTGATAATACAAA
1 ATCGTAACGCGATAATACAAA
121614 ATCGTAACGCGAT
1 ATCGTAACGCGAT
121627 TCTCCAAATT
Statistics
Matches: 41, Mismatches: 10, Indels: 6
0.72 0.18 0.11
Matches are distributed among these distances:
19 2 0.05
20 12 0.29
21 25 0.61
22 2 0.05
ACGTcount: A:0.39, C:0.21, G:0.17, T:0.23
Consensus pattern (21 bp):
ATCGTAACGCGATAATACAAA
Found at i:121584 original size:41 final size:41
Alignment explanation
Indices: 121527--121629 Score: 179
Period size: 41 Copynumber: 2.5 Consensus size: 41
121517 AAAATGACCA
* *
121527 ACAAAATCGCAACGCGATTCTGACTATCGTAACGCGATAAT
1 ACAAAATCGTAACGCGATTCTGACTATCGCAACGCGATAAT
*
121568 ACAAAATCGTAACGCGATTCTGACTATCGCAACGTGATAAT
1 ACAAAATCGTAACGCGATTCTGACTATCGCAACGCGATAAT
121609 ACAAAATCGTAACGCGATTCT
1 ACAAAATCGTAACGCGATTCT
121630 CCAAATTTGT
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 59 1.00
ACGTcount: A:0.37, C:0.23, G:0.17, T:0.23
Consensus pattern (41 bp):
ACAAAATCGTAACGCGATTCTGACTATCGCAACGCGATAAT
Found at i:121634 original size:21 final size:20
Alignment explanation
Indices: 121528--121635 Score: 72
Period size: 20 Copynumber: 5.3 Consensus size: 20
121518 AAATGACCAA
*
121528 CAAAATCGCAACGCGATTCT
1 CAAAATCGTAACGCGATTCT
* ** **
121548 GACTATCGTAACGCGATAAT
1 CAAAATCGTAACGCGATTCT
121568 ACAAAATCGTAACGCGATTCT
1 -CAAAATCGTAACGCGATTCT
* ** * * **
121589 GACTATCGCAACGTGATAAT
1 CAAAATCGTAACGCGATTCT
121609 ACAAAATCGTAACGCGATTCT
1 -CAAAATCGTAACGCGATTCT
*
121630 CCAAAT
1 CAAAAT
121636 TTGTTGCGGT
Statistics
Matches: 60, Mismatches: 26, Indels: 4
0.67 0.29 0.04
Matches are distributed among these distances:
20 32 0.53
21 28 0.47
ACGTcount: A:0.37, C:0.24, G:0.16, T:0.23
Consensus pattern (20 bp):
CAAAATCGTAACGCGATTCT
Found at i:122004 original size:19 final size:20
Alignment explanation
Indices: 121979--122069 Score: 105
Period size: 19 Copynumber: 4.4 Consensus size: 20
121969 CTTATTTTGG
121979 ATTTTTCACTATCGCAACAC
1 ATTTTTCACTATCGCAACAC
121999 -TTTTTCACTATCGCAACAAC
1 ATTTTTCACTATCGCAAC-AC
*
122019 ACGTTTTTCAAACTCTCGCAACAC
1 A--TTTTTC--ACTATCGCAACAC
*
122043 A-TTTTAACTATCGCAACAC
1 ATTTTTCACTATCGCAACAC
122062 ATTTTTCA
1 ATTTTTCA
122070 AAATCGCGTT
Statistics
Matches: 60, Mismatches: 4, Indels: 14
0.77 0.05 0.18
Matches are distributed among these distances:
19 30 0.50
20 7 0.12
21 4 0.07
23 6 0.10
24 3 0.05
25 10 0.17
ACGTcount: A:0.31, C:0.29, G:0.05, T:0.35
Consensus pattern (20 bp):
ATTTTTCACTATCGCAACAC
Found at i:122041 original size:44 final size:41
Alignment explanation
Indices: 121990--122071 Score: 119
Period size: 44 Copynumber: 1.9 Consensus size: 41
121980 TTTTTCACTA
* *
121990 TCGCAACACTTTTTCACTATCGCAACAACACGTTTTTCAAACTC
1 TCGCAACACATTTTAACTATCGCAAC-ACA--TTTTTCAAACTC
122034 TCGCAACACATTTTAACTATCGCAACACATTTTTCAAA
1 TCGCAACACATTTTAACTATCGCAACACATTTTTCAAA
122072 ATCGCGTTGC
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
41 9 0.25
43 3 0.08
44 24 0.67
ACGTcount: A:0.33, C:0.29, G:0.06, T:0.32
Consensus pattern (41 bp):
TCGCAACACATTTTAACTATCGCAACACATTTTTCAAACTC
Found at i:122119 original size:21 final size:21
Alignment explanation
Indices: 122093--122152 Score: 111
Period size: 21 Copynumber: 2.9 Consensus size: 21
122083 AATCTTACAA
122093 TCGCGTTGCGAATATGGATAT
1 TCGCGTTGCGAATATGGATAT
122114 TCGCGTTGCGAATATGGATAT
1 TCGCGTTGCGAATATGGATAT
*
122135 TCGCGTTGCGAATTTGGA
1 TCGCGTTGCGAATATGGA
122153 AACTGAGTTG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.22, C:0.15, G:0.30, T:0.33
Consensus pattern (21 bp):
TCGCGTTGCGAATATGGATAT
Found at i:128310 original size:2 final size:2
Alignment explanation
Indices: 128303--128381 Score: 75
Period size: 2 Copynumber: 43.5 Consensus size: 2
128293 CCGCCCCGAT
*
128303 TA TA TA TA TA TA TA TA TA TA -A TA TA TA TA TA -A TA T- TT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
128342 TA T- TT TT TA TA T- TA -A T- TA TA TA TA TA TA TA TA TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
128379 TA T
1 TA T
128382 TTTATATTTT
Statistics
Matches: 67, Mismatches: 2, Indels: 16
0.79 0.02 0.19
Matches are distributed among these distances:
1 8 0.12
2 59 0.88
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:128392 original size:43 final size:45
Alignment explanation
Indices: 128313--128414 Score: 181
Period size: 44 Copynumber: 2.3 Consensus size: 45
128303 TATATATATA
128313 TATATATATAATATATATATAATATTTTATATTTTTTATATTAAT
1 TATATATATAATATATATATAATATTTTATATTTTTTATATTAAT
128358 TATATATAT-ATATATATATAATATTTTATA-TTTTTATATTAAT
1 TATATATATAATATATATATAATATTTTATATTTTTTATATTAAT
*
128401 TATATATAAAATAT
1 TATATATATAATAT
128415 TTTCGGGTTC
Statistics
Matches: 55, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
43 21 0.38
44 25 0.45
45 9 0.16
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (45 bp):
TATATATATAATATATATATAATATTTTATATTTTTTATATTAAT
Found at i:128414 original size:33 final size:35
Alignment explanation
Indices: 128315--128417 Score: 51
Period size: 35 Copynumber: 3.0 Consensus size: 35
128305 TATATATATA
* * * *
128315 TATATATAA-TATATATATA-ATATTTTATATTTTT
1 TATAT-TAATTATATATATATATATATAAAATATTT
*
128349 TATATTAA-T-TATATATATATATAT-ATATAATATTT
1 TATATTAATTATATATATATATATATAAAAT-AT-T-T
*
128384 TATATT-TTTATAT-TA-ATTATATATAAAATATTT
1 TATATTAATTATATATATA-TATATATAAAATATTT
128417 T
1 T
128418 CGGGTTCGGG
Statistics
Matches: 57, Mismatches: 4, Indels: 17
0.73 0.05 0.22
Matches are distributed among these distances:
32 12 0.21
33 12 0.21
34 8 0.14
35 19 0.33
36 6 0.11
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (35 bp):
TATATTAATTATATATATATATATATAAAATATTT
Found at i:131714 original size:13 final size:13
Alignment explanation
Indices: 131698--131728 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
131688 TATTTTTGAT
131698 TTTTTTTATTTTC
1 TTTTTTTATTTTC
*
131711 TTTTGTTATTTTC
1 TTTTTTTATTTTC
131724 TTTTT
1 TTTTT
131729 CTTTTCTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.06, C:0.06, G:0.03, T:0.84
Consensus pattern (13 bp):
TTTTTTTATTTTC
Found at i:131938 original size:17 final size:17
Alignment explanation
Indices: 131925--131961 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
131915 AGTAGAGTTG
131925 GTGGTAATGTAGAGATA
1 GTGGTAATGTAGAGATA
131942 GTGGTAATGTAGAGATA
1 GTGGTAATGTAGAGATA
131959 GTG
1 GTG
131962 CTGGAGATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.32, C:0.00, G:0.38, T:0.30
Consensus pattern (17 bp):
GTGGTAATGTAGAGATA
Found at i:148258 original size:33 final size:31
Alignment explanation
Indices: 148192--148258 Score: 89
Period size: 33 Copynumber: 2.1 Consensus size: 31
148182 CTAAAAATTA
* *
148192 ATATTGAATCATTAAACTATTGTTAAAGGTG
1 ATATTGAATCATTAAACTATTATCAAAGGTG
*
148223 ATATTGATATTCATTAAACTATTATCAAAGTTG
1 ATATTGA-A-TCATTAAACTATTATCAAAGGTG
148256 ATA
1 ATA
148259 GCTAGCTAGG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
31 7 0.23
32 1 0.03
33 23 0.74
ACGTcount: A:0.40, C:0.07, G:0.12, T:0.40
Consensus pattern (31 bp):
ATATTGAATCATTAAACTATTATCAAAGGTG
Found at i:148547 original size:22 final size:22
Alignment explanation
Indices: 148519--148572 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
148509 CGGGTTAAAA
*
148519 TTCGGTTTCGGTTCGAGTTACT
1 TTCGGTTTCGGTTCGAGATACT
*
148541 TTCGGTTTTGGTTCGAGATACT
1 TTCGGTTTCGGTTCGAGATACT
148563 TTCGGTTTCG
1 TTCGGTTTCG
148573 CTAAATTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.09, C:0.17, G:0.28, T:0.46
Consensus pattern (22 bp):
TTCGGTTTCGGTTCGAGATACT
Found at i:150468 original size:22 final size:22
Alignment explanation
Indices: 150436--150480 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
150426 TAAGTCAAAG
*
150436 AAAATGGTAAAATTTTACCATT
1 AAAATGATAAAATTTTACCATT
150458 AAAATGATAAAATTTTACCATT
1 AAAATGATAAAATTTTACCATT
150480 A
1 A
150481 GTCCTTAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.49, C:0.09, G:0.07, T:0.36
Consensus pattern (22 bp):
AAAATGATAAAATTTTACCATT
Found at i:150644 original size:24 final size:24
Alignment explanation
Indices: 150594--150647 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
150584 TTGAGAACTG
*
150594 AATAAACGAGCTCATAAACAAGTC
1 AATAAACGAGCTCATAAACAAGCC
* * **
150618 AATAAAGGAGCTTATAAATGAGCC
1 AATAAACGAGCTCATAAACAAGCC
150642 AATAAA
1 AATAAA
150648 TGAGTTTGTT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.52, C:0.15, G:0.15, T:0.19
Consensus pattern (24 bp):
AATAAACGAGCTCATAAACAAGCC
Found at i:152136 original size:37 final size:37
Alignment explanation
Indices: 152095--152168 Score: 139
Period size: 37 Copynumber: 2.0 Consensus size: 37
152085 CATGTTCGTG
152095 GTACGAACTCGTATTTCTTAATTCAAACTTTCAGTGT
1 GTACGAACTCGTATTTCTTAATTCAAACTTTCAGTGT
*
152132 GTACGAACTCGTATTTCTTAATTCGAACTTTCAGTGT
1 GTACGAACTCGTATTTCTTAATTCAAACTTTCAGTGT
152169 TTTTCAAGTT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.41
Consensus pattern (37 bp):
GTACGAACTCGTATTTCTTAATTCAAACTTTCAGTGT
Found at i:153767 original size:31 final size:31
Alignment explanation
Indices: 153693--153768 Score: 80
Period size: 31 Copynumber: 2.5 Consensus size: 31
153683 TTCAAATTTC
* *
153693 ATAAGATATGTTCACTTATATTTTTATTTAA
1 ATAAGATATGGTCACTTACATTTTTATTTAA
* * * *
153724 ACAATATTTGGTCACTTACGTTTTTATTTAA
1 ATAAGATATGGTCACTTACATTTTTATTTAA
* *
153755 TTAAGATGTGGTCA
1 ATAAGATATGGTCA
153769 TCCCGAGTTA
Statistics
Matches: 35, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.32, C:0.09, G:0.12, T:0.47
Consensus pattern (31 bp):
ATAAGATATGGTCACTTACATTTTTATTTAA
Found at i:154861 original size:17 final size:15
Alignment explanation
Indices: 154827--154862 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
154817 CCGTGACCCG
154827 AATTATATATAATAT
1 AATTATATATAATAT
154842 AATTATATATATATATT
1 AATTATATATA-ATA-T
154859 AATT
1 AATT
154863 TAAAATATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 11 0.58
16 3 0.16
17 5 0.26
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
AATTATATATAATAT
Found at i:154916 original size:27 final size:25
Alignment explanation
Indices: 154858--154928 Score: 74
Period size: 24 Copynumber: 2.8 Consensus size: 25
154848 ATATATATAT
154858 TAATTTAAAATATTTTTATATCAAC
1 TAATTTAAAATATTTTTATATCAAC
* *
154883 TTA-TT-AAATATATTTTATTATTAACC
1 TAATTTAAAATAT-TTTTA-TATCAA-C
154909 TAATTTAAAAATATTTTTAT
1 TAATTT-AAAATATTTTTAT
154929 TTTTATTTTC
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
23 6 0.16
24 7 0.19
25 7 0.19
26 3 0.08
27 3 0.08
28 5 0.14
29 6 0.16
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (25 bp):
TAATTTAAAATATTTTTATATCAAC
Found at i:154942 original size:28 final size:29
Alignment explanation
Indices: 154911--154967 Score: 82
Period size: 28 Copynumber: 2.0 Consensus size: 29
154901 TATTAACCTA
154911 ATTTAAAAATAT-T-TTTATTTTTATTTTC
1 ATTTAAAAATATATATTTA-TTTTATTTTC
154939 ATTTAAAAATATATAATTTATTTTATTTT
1 ATTTAAAAATATAT-ATTTATTTTATTTT
154968 ATTGAAAGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
28 12 0.46
29 1 0.04
30 9 0.35
31 4 0.15
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (29 bp):
ATTTAAAAATATATATTTATTTTATTTTC
Found at i:156201 original size:20 final size:20
Alignment explanation
Indices: 156176--156214 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
156166 TCGTAGAGTG
156176 AAATTATATTAGAGTTGACT
1 AAATTATATTAGAGTTGACT
156196 AAATTATATTAGAGTTGAC
1 AAATTATATTAGAGTTGAC
156215 AGAGATCACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.41, C:0.05, G:0.15, T:0.38
Consensus pattern (20 bp):
AAATTATATTAGAGTTGACT
Found at i:160670 original size:19 final size:19
Alignment explanation
Indices: 160629--160673 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
160619 TAAATGTCCT
* * *
160629 TGATTTTTATAATAAATTG
1 TGATATTTATAATAAACTC
*
160648 TGATATTTATAGTAAACTC
1 TGATATTTATAATAAACTC
160667 TGATATT
1 TGATATT
160674 AACTACTTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.36, C:0.04, G:0.11, T:0.49
Consensus pattern (19 bp):
TGATATTTATAATAAACTC
Found at i:161549 original size:54 final size:54
Alignment explanation
Indices: 161485--161588 Score: 199
Period size: 54 Copynumber: 1.9 Consensus size: 54
161475 TCAGCTTAGG
161485 TGTGGAATTATATTATTTCAGAGTGCAAAAGTAGATCATCAATTCAGGGTACGA
1 TGTGGAATTATATTATTTCAGAGTGCAAAAGTAGATCATCAATTCAGGGTACGA
*
161539 TGTGGAATTATATTATTTCAGAGTGCGAAAGTAGATCATCAATTCAGGGT
1 TGTGGAATTATATTATTTCAGAGTGCAAAAGTAGATCATCAATTCAGGGT
161589 GCGAAATTAT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 49 1.00
ACGTcount: A:0.34, C:0.11, G:0.23, T:0.33
Consensus pattern (54 bp):
TGTGGAATTATATTATTTCAGAGTGCAAAAGTAGATCATCAATTCAGGGTACGA
Found at i:161585 original size:26 final size:26
Alignment explanation
Indices: 161501--161594 Score: 75
Period size: 26 Copynumber: 3.5 Consensus size: 26
161491 ATTATATTAT
*
161501 TTCAGAGTGCAAAAGTAGATCATCAA
1 TTCAGAGTGCGAAAGTAGATCATCAA
* * * * *
161527 TTCAGGGTACG-ATGTGGAATTAT-ATTA
1 TTCAGAGTGCGAAAGTAG-ATCATCA--A
161554 TTTCAGAGTGCGAAAGTAGATCATCAA
1 -TTCAGAGTGCGAAAGTAGATCATCAA
*
161581 TTCAGGGTGCGAAA
1 TTCAGAGTGCGAAA
161595 TTATACGAGA
Statistics
Matches: 50, Mismatches: 12, Indels: 12
0.68 0.16 0.16
Matches are distributed among these distances:
25 5 0.10
26 25 0.50
27 2 0.04
28 13 0.26
29 5 0.10
ACGTcount: A:0.35, C:0.13, G:0.24, T:0.28
Consensus pattern (26 bp):
TTCAGAGTGCGAAAGTAGATCATCAA
Found at i:168183 original size:12 final size:12
Alignment explanation
Indices: 168166--168206 Score: 73
Period size: 12 Copynumber: 3.4 Consensus size: 12
168156 TTATTGTGCT
168166 TGCTCCTCGGGC
1 TGCTCCTCGGGC
168178 TGCTCCTCGGGC
1 TGCTCCTCGGGC
168190 TGCTCCTCGGGC
1 TGCTCCTCGGGC
*
168202 AGCTC
1 TGCTC
168207 AGGCTCATCT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.02, C:0.41, G:0.32, T:0.24
Consensus pattern (12 bp):
TGCTCCTCGGGC
Found at i:169832 original size:21 final size:20
Alignment explanation
Indices: 169807--169887 Score: 63
Period size: 20 Copynumber: 3.9 Consensus size: 20
169797 CAGAACCCCA
* *
169807 GGGGGTATCGATTCCCTTGT
1 GGGGGAATCGATTCCCTTAT
* *
169827 GGGGGGAATCGGTTCCCCTTCAAA
1 -GGGGGAATCGATT-CCCTT--AT
* *
169851 GGGGGAATCGGTTCCCTCAT
1 GGGGGAATCGATTCCCTTAT
*
169871 GGGGGTATCGATTCCCT
1 GGGGGAATCGATTCCCT
169888 CTGCACCAAA
Statistics
Matches: 49, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
20 16 0.33
21 11 0.22
22 9 0.18
23 13 0.27
ACGTcount: A:0.15, C:0.23, G:0.35, T:0.27
Consensus pattern (20 bp):
GGGGGAATCGATTCCCTTAT
Done.