Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002207.1 Hibiscus syriacus cultivar Beakdansim tig00004498_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: 90338
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:1256 original size:31 final size:30
Alignment explanation
Indices: 1220--1366 Score: 188
Period size: 31 Copynumber: 4.8 Consensus size: 30
1210 GTTGATAACG
1220 ATAATGCTCAATCAACTAGTATTGAATGTTA
1 ATAATGCTCAATC-ACTAGTATTGAATGTTA
* * *
1251 ATAATGCTCAATCAACTAGTATTGATTATTG
1 ATAATGCTCAATC-ACTAGTATTGAATGTTA
1282 ATAATGCTCAATTCACTAGTATTGAATGTTA
1 ATAATGCTCAA-TCACTAGTATTGAATGTTA
* *
1313 ATAATGCTCAGTTCACTAGTATTAAATG-TA
1 ATAATGCTCA-ATCACTAGTATTGAATGTTA
*
1343 ATAATGCTCAAACCACTAGTATTG
1 ATAATGCTC-AATCACTAGTATTG
1367 GAAATGACAA
Statistics
Matches: 102, Mismatches: 11, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
30 21 0.21
31 79 0.77
32 2 0.02
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.36
Consensus pattern (30 bp):
ATAATGCTCAATCACTAGTATTGAATGTTA
Found at i:4179 original size:31 final size:31
Alignment explanation
Indices: 4144--4204 Score: 122
Period size: 31 Copynumber: 2.0 Consensus size: 31
4134 GTTCCTTCTA
4144 TACCAGAGTTACAAGGAATCTTCACCATCCG
1 TACCAGAGTTACAAGGAATCTTCACCATCCG
4175 TACCAGAGTTACAAGGAATCTTCACCATCC
1 TACCAGAGTTACAAGGAATCTTCACCATCC
4205 ACACTGTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.33, C:0.30, G:0.15, T:0.23
Consensus pattern (31 bp):
TACCAGAGTTACAAGGAATCTTCACCATCCG
Found at i:4498 original size:14 final size:14
Alignment explanation
Indices: 4479--4508 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
4469 TTGCATCCCC
4479 TTCTTCCCCTCTAT
1 TTCTTCCCCTCTAT
4493 TTCTTCCCCTCTAT
1 TTCTTCCCCTCTAT
4507 TT
1 TT
4509 TTGAATATGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.07, C:0.40, G:0.00, T:0.53
Consensus pattern (14 bp):
TTCTTCCCCTCTAT
Found at i:7414 original size:115 final size:115
Alignment explanation
Indices: 7216--7434 Score: 300
Period size: 115 Copynumber: 1.9 Consensus size: 115
7206 TTAATTTAAG
* *
7216 TTGCCTTTGTTCGGCTAGATGAAGGAATCTATCCATAAAGTCAGGATTTTTAACCAATTGCTTTA
1 TTGCCTTTATTCGGCTAGATGAAGGAATCTATCCATAAAGTCAGGATTTATAACCAATTGCTTTA
* *
7281 AAGGAATAACTCAGCTTTATTGTATATATACATATATATTTTAATTATAT
66 AAGGAATAACTCAACTTTATTATATATATACATATATATTTTAATTATAT
* * *
7331 TTGCCTTTATTTGGCTAG-TGAAGGAATCTAT-TAGTAAAGTCAGAGCTTTATAACCAATTGCTT
1 TTGCCTTTATTCGGCTAGATGAAGGAATCTATCCA-TAAAGTCAG-GATTTATAACCAATTGCTT
* * *
7394 TAGAA-TAATAGCTCAACTTTATTATATATATATATATATAT
64 TA-AAGGAATAACTCAACTTTATTATATATATACATATATAT
7435 AATTATATTA
Statistics
Matches: 91, Mismatches: 10, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
113 1 0.01
114 22 0.24
115 66 0.73
116 2 0.02
ACGTcount: A:0.34, C:0.12, G:0.14, T:0.40
Consensus pattern (115 bp):
TTGCCTTTATTCGGCTAGATGAAGGAATCTATCCATAAAGTCAGGATTTATAACCAATTGCTTTA
AAGGAATAACTCAACTTTATTATATATATACATATATATTTTAATTATAT
Found at i:18218 original size:21 final size:21
Alignment explanation
Indices: 18194--18250 Score: 55
Period size: 21 Copynumber: 2.7 Consensus size: 21
18184 TTAGTAAAAC
*
18194 ATTTATCTAAAAATAGATA-TA
1 ATTTAT-TAAAAATAAATATTA
*
18215 ATTTA-TAAAAATAAAATATTT
1 ATTTATTAAAAAT-AAATATTA
18236 ATTTATTTAAAAATA
1 ATTTA-TTAAAAATA
18251 TCAGAAAATG
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
19 7 0.23
20 4 0.13
21 11 0.37
22 1 0.03
23 7 0.23
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (21 bp):
ATTTATTAAAAATAAATATTA
Found at i:18237 original size:17 final size:19
Alignment explanation
Indices: 18201--18237 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
18191 AACATTTATC
*
18201 TAAAAATAGATATAATTTA
1 TAAAAATAGAAATAATTTA
18220 TAAAAATA-AAAT-ATTTA
1 TAAAAATAGAAATAATTTA
18237 T
1 T
18238 TTATTTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 6 0.35
18 3 0.18
19 8 0.47
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (19 bp):
TAAAAATAGAAATAATTTA
Found at i:19294 original size:19 final size:19
Alignment explanation
Indices: 19251--19295 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 19
19241 TTCTTTTTTT
19251 GTTGTTTGTGGATTGTTCTG
1 GTTG-TTGTGGATTGTTCTG
*
19271 TTTGTTGTGG-TTGTTCTCG
1 GTTGTTGTGGATTGTTCT-G
19290 GTTGTT
1 GTTGTT
19296 CTGTCTGCTC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 7 0.32
19 12 0.55
20 3 0.14
ACGTcount: A:0.02, C:0.07, G:0.33, T:0.58
Consensus pattern (19 bp):
GTTGTTGTGGATTGTTCTG
Found at i:19821 original size:3 final size:3
Alignment explanation
Indices: 19813--19876 Score: 78
Period size: 3 Copynumber: 22.0 Consensus size: 3
19803 AAAAATTATT
* * * *
19813 TAA TAA TAA TAA TAA TAA TAA -AA TAA TAA TTA TGA TAA TAA TTA TTA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
19860 TAA TAA TAA -AA TAA TAA
1 TAA TAA TAA TAA TAA TAA
19877 AATCGGGATA
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
2 4 0.07
3 50 0.93
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:20507 original size:112 final size:114
Alignment explanation
Indices: 20231--20527 Score: 426
Period size: 112 Copynumber: 2.6 Consensus size: 114
20221 TCATGCAAAG
* *
20231 GTTGAACAAGTTCTTCTCATTATGAACTTTTTCTTCC-TCTTTAGATGAGTTCTTCTCATTATGA
1 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
* * * * *
20295 ACT-TCCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAAGCAAAAG
66 ACTCTACTCTGGAAAAGCTGATCCATCAAGTGATGAATTCAAGAAAAAA
* * * *
20343 GTTGAACAAATTCTTCTCATTATCAATTTCTTATTCCTTCTTCAGATGAGTTCTTCTCATTATGA
1 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
*
20408 ACTCTAC-CT-GATAATA-CTGATCCATCAAGTGATG-ATTCGAGAAAAAA
66 ACTCTACTCTGGA-AA-AGCTGATCCATCAAGTGATGAATTCAAGAAAAAA
20455 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
1 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
20520 ACTCTACT
66 ACTCTACT
20528 GGAAATGCTG
Statistics
Matches: 164, Mismatches: 16, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
112 112 0.68
113 49 0.30
114 3 0.02
ACGTcount: A:0.28, C:0.20, G:0.13, T:0.39
Consensus pattern (114 bp):
GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
ACTCTACTCTGGAAAAGCTGATCCATCAAGTGATGAATTCAAGAAAAAA
Found at i:21385 original size:22 final size:22
Alignment explanation
Indices: 21357--21404 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
21347 AATAAAGCGT
*
21357 TCATCTTTGAAAAGTGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
21379 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
21401 TCAT
1 TCAT
21405 TTTTAAAGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:26048 original size:1 final size:1
Alignment explanation
Indices: 26044--26095 Score: 50
Period size: 1 Copynumber: 52.0 Consensus size: 1
26034 AATTTTTTCC
* * * * **
26044 TTTTTTTTCTTTTTTTCTTTTTTTTTCTTTTTTTTCTTTTTTCCTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
26096 CAAGCATTTC
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
1 41 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (1 bp):
T
Found at i:26050 original size:9 final size:9
Alignment explanation
Indices: 26036--26094 Score: 75
Period size: 9 Copynumber: 6.7 Consensus size: 9
26026 CTTGGTTCAA
26036 TTTTTTCCT
1 TTTTTTCCT
*
26045 TTTTTTTCT
1 TTTTTTCCT
*
26054 TTTTTTCTT
1 TTTTTTCCT
*
26063 TTTTTTTCT
1 TTTTTTCCT
*
26072 TTTTTTTC-
1 TTTTTTCCT
26080 TTTTTTCCT
1 TTTTTTCCT
26089 TTTTTT
1 TTTTTT
26095 TCAAGCATTT
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
8 7 0.16
9 36 0.84
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (9 bp):
TTTTTTCCT
Found at i:26059 original size:18 final size:18
Alignment explanation
Indices: 26036--26094 Score: 84
Period size: 18 Copynumber: 3.3 Consensus size: 18
26026 CTTGGTTCAA
26036 TTTTTTCCTTTTTTTTCT
1 TTTTTTCCTTTTTTTTCT
*
26054 TTTTTTCTTTTTTTTTCT
1 TTTTTTCCTTTTTTTTCT
* *
26072 TTTTTTTC-TTTTTTCCT
1 TTTTTTCCTTTTTTTTCT
26089 TTTTTT
1 TTTTTT
26095 TCAAGCATTT
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
17 14 0.38
18 23 0.62
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (18 bp):
TTTTTTCCTTTTTTTTCT
Found at i:26073 original size:27 final size:27
Alignment explanation
Indices: 26036--26096 Score: 104
Period size: 27 Copynumber: 2.3 Consensus size: 27
26026 CTTGGTTCAA
*
26036 TTTTTTCCTTTTTTTTCTTTTTTTCTT
1 TTTTTTCCTTTTTTTTCTTTTTTCCTT
*
26063 TTTTTTTCTTTTTTTTCTTTTTTCCTT
1 TTTTTTCCTTTTTTTTCTTTTTTCCTT
26090 TTTTTTC
1 TTTTTTC
26097 AAGCATTTCT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (27 bp):
TTTTTTCCTTTTTTTTCTTTTTTCCTT
Found at i:29116 original size:43 final size:43
Alignment explanation
Indices: 29036--29118 Score: 121
Period size: 43 Copynumber: 1.9 Consensus size: 43
29026 TGCATCAAAA
* * *
29036 AAAACTTTACATATAGGGGACAGCTTTCAGTCCTAACTTCAAC
1 AAAACTTTACATATAGGGGACAACTTTCACTCATAACTTCAAC
* *
29079 AAAACTTTACATATAGGGGATAACTTTCCCTCATAACTTC
1 AAAACTTTACATATAGGGGACAACTTTCACTCATAACTTC
29119 TCTAACACCA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 35 1.00
ACGTcount: A:0.35, C:0.23, G:0.12, T:0.30
Consensus pattern (43 bp):
AAAACTTTACATATAGGGGACAACTTTCACTCATAACTTCAAC
Found at i:30538 original size:24 final size:23
Alignment explanation
Indices: 30511--30563 Score: 54
Period size: 24 Copynumber: 2.2 Consensus size: 23
30501 ATACTTGAAA
30511 AATAAAATAAAGCATTAAT-AAAAT
1 AATAAAATAAA-CATT-ATGAAAAT
* *
30535 AATATATATAAATATTATGAAAAT
1 AATA-AAATAAACATTATGAAAAT
30559 AATAA
1 AATAA
30564 GTATATATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
23 3 0.12
24 16 0.64
25 6 0.24
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (23 bp):
AATAAAATAAACATTATGAAAAT
Found at i:30583 original size:28 final size:27
Alignment explanation
Indices: 30532--30585 Score: 81
Period size: 28 Copynumber: 2.0 Consensus size: 27
30522 GCATTAATAA
*
30532 AATAATATATATAAATATTATGAAAAT
1 AATAATATATATAAAAATTATGAAAAT
*
30559 AATAAGTATATATAAAAATTTTGAAAA
1 AATAA-TATATATAAAAATTATGAAAA
30586 AAAAAATTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 5 0.21
28 19 0.79
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.35
Consensus pattern (27 bp):
AATAATATATATAAAAATTATGAAAAT
Found at i:30596 original size:28 final size:28
Alignment explanation
Indices: 30537--30596 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
30527 AATAAAATAA
* * *
30537 TATATATAAATATTATGAAAATAATAAG
1 TATATATAAAAATTATGAAAAAAAAAAG
* *
30565 TATATATAAAAATTTTGAAAAAAAAAAT
1 TATATATAAAAATTATGAAAAAAAAAAG
30593 TATA
1 TATA
30597 AATTAAATAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (28 bp):
TATATATAAAAATTATGAAAAAAAAAAG
Found at i:32863 original size:3 final size:3
Alignment explanation
Indices: 32855--32906 Score: 54
Period size: 3 Copynumber: 18.0 Consensus size: 3
32845 AATTATTTAT
* * * *
32855 TAA TAA TAA TAA -AA TAA TTA TAA TAA TTA TTA TTA TAA TAA TAA -AA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
32901 TAA TAA
1 TAA TAA
32907 AACCGGGATA
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
2 4 0.09
3 39 0.91
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:37517 original size:17 final size:17
Alignment explanation
Indices: 37482--37544 Score: 58
Period size: 17 Copynumber: 3.6 Consensus size: 17
37472 ATGACGAAAA
*
37482 CATATTTATTTGTAAAAAT
1 CATATTTA-TT-TATAAAT
*
37501 CTTATTTATTTATAAAT
1 CATATTTATTTATAAAT
37518 GCAT-TTTATTTTATAAAT
1 -CATATTTA-TTTATAAAT
37536 -ATATTTATT
1 CATATTTATT
37545 ACAAGGTATA
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
16 4 0.11
17 14 0.37
18 13 0.34
19 7 0.18
ACGTcount: A:0.37, C:0.05, G:0.03, T:0.56
Consensus pattern (17 bp):
CATATTTATTTATAAAT
Found at i:46947 original size:21 final size:21
Alignment explanation
Indices: 46921--46965 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
46911 GATTTTTGGG
* *
46921 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
46942 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
46963 CAA
1 CAA
46966 ACGACAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:47673 original size:32 final size:32
Alignment explanation
Indices: 47632--47727 Score: 126
Period size: 32 Copynumber: 3.0 Consensus size: 32
47622 GAGTCGAGGG
47632 TTTACCTATGTTCTACGGAACATATGGACAGT
1 TTTACCTATGTTCTACGGAACATATGGACAGT
*
47664 TTTACCTATG-TCTTTC-GAGACATATGGACAG-
1 TTTACCTATGTTC-TACGGA-ACATATGGACAGT
* *
47695 TATACCTATGTTCTAAGGAACATATGGACAGT
1 TTTACCTATGTTCTACGGAACATATGGACAGT
47727 T
1 T
47728 ACCGAGGATC
Statistics
Matches: 55, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
31 26 0.47
32 29 0.53
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (32 bp):
TTTACCTATGTTCTACGGAACATATGGACAGT
Found at i:47755 original size:30 final size:30
Alignment explanation
Indices: 47719--47901 Score: 332
Period size: 30 Copynumber: 6.1 Consensus size: 30
47709 AAGGAACATA
47719 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
47749 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
47779 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
47809 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
47839 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
* * *
47869 TGGATAGTTACCG-GGGTCTTTGTGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
47898 TGGA
1 TGGA
47902 TAGGTCCTTC
Statistics
Matches: 150, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
29 18 0.12
30 132 0.88
ACGTcount: A:0.22, C:0.22, G:0.25, T:0.31
Consensus pattern (30 bp):
TGGACAGTTACCGAGGATCTTTATGACCTC
Found at i:52344 original size:21 final size:21
Alignment explanation
Indices: 52315--52393 Score: 64
Period size: 17 Copynumber: 4.0 Consensus size: 21
52305 ATCTGCAAAA
*
52315 AAATTAATTAAATAAAATATT
1 AAATAAATTAAATAAAATATT
*
52336 AAATAAATTAAAT---A-CTT
1 AAATAAATTAAATAAAATATT
52353 AAATAAATTAAATACAAAATATT
1 AAATAAATTAAAT--AAAATATT
52376 AAA-AATATT--ATAAAATAT
1 AAATAA-ATTAAATAAAATAT
52394 ACCTTAGACA
Statistics
Matches: 48, Mismatches: 3, Indels: 16
0.72 0.04 0.24
Matches are distributed among these distances:
17 15 0.31
18 1 0.02
19 7 0.15
21 14 0.29
22 3 0.06
23 8 0.17
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (21 bp):
AAATAAATTAAATAAAATATT
Found at i:52345 original size:9 final size:9
Alignment explanation
Indices: 52315--52366 Score: 56
Period size: 9 Copynumber: 6.1 Consensus size: 9
52305 ATCTGCAAAA
*
52315 AAATTAATT
1 AAATTAAAT
52324 AAA-TAAA-
1 AAATTAAAT
*
52331 ATATTAAAT
1 AAATTAAAT
52340 AAATTAAAT
1 AAATTAAAT
*
52349 -ACTTAAAT
1 AAATTAAAT
52357 AAATTAAAT
1 AAATTAAAT
52366 A
1 A
52367 CAAAATATTA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
7 2 0.06
8 14 0.40
9 19 0.54
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (9 bp):
AAATTAAAT
Found at i:52347 original size:17 final size:17
Alignment explanation
Indices: 52312--52364 Score: 65
Period size: 16 Copynumber: 3.2 Consensus size: 17
52302 TATATCTGCA
* *
52312 AAAAAATTAATTAAA-T
1 AAAATATTAAATAAATT
52328 AAAATATTAAATAAATT
1 AAAATATTAAATAAATT
52345 -AAATACTTAAATAAATT
1 AAAATA-TTAAATAAATT
52362 AAA
1 AAA
52365 TACAAAATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
16 18 0.56
17 12 0.38
18 2 0.06
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (17 bp):
AAAATATTAAATAAATT
Found at i:52365 original size:17 final size:17
Alignment explanation
Indices: 52318--52367 Score: 75
Period size: 17 Copynumber: 3.0 Consensus size: 17
52308 TGCAAAAAAA
* *
52318 TTAATTAAATAAAATA-
1 TTAAATAAATTAAATAC
52334 TTAAATAAATTAAATAC
1 TTAAATAAATTAAATAC
52351 TTAAATAAATTAAATAC
1 TTAAATAAATTAAATAC
52368 AAAATATTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
16 14 0.45
17 17 0.55
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (17 bp):
TTAAATAAATTAAATAC
Found at i:52426 original size:10 final size:10
Alignment explanation
Indices: 52420--52448 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
52410 ATAAGAGTAT
52420 TTGAGAGAAG
1 TTGAGAGAAG
52430 TTGAGAGAAG
1 TTGAGAGAAG
52440 TTGAGAGAA
1 TTGAGAGAA
52449 TTTGGTGTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.41, C:0.00, G:0.38, T:0.21
Consensus pattern (10 bp):
TTGAGAGAAG
Found at i:53964 original size:2 final size:2
Alignment explanation
Indices: 53957--53992 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
53947 CAATACATAA
53957 AT 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 AT
53993 CCATTTCATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:55149 original size:24 final size:24
Alignment explanation
Indices: 55117--55225 Score: 209
Period size: 24 Copynumber: 4.5 Consensus size: 24
55107 ACACACTATA
*
55117 GTGTATCGATACATTCCTTAACAT
1 GTGTATCGATACATTCCTCAACAT
55141 GTGTATCGATACATTCCTCAACAT
1 GTGTATCGATACATTCCTCAACAT
55165 GTGTATCGATACATTCCTCAACAT
1 GTGTATCGATACATTCCTCAACAT
55189 GTGTATCGATACATTCCTCAACAT
1 GTGTATCGATACATTCCTCAACAT
55213 GTGTATCGATACA
1 GTGTATCGATACA
55226 CTACCTATGT
Statistics
Matches: 84, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
24 84 1.00
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.34
Consensus pattern (24 bp):
GTGTATCGATACATTCCTCAACAT
Found at i:59075 original size:16 final size:16
Alignment explanation
Indices: 59054--59086 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
59044 AAATTAAAAA
59054 ATCAAGTA-AAAGAATT
1 ATCAAGTACAAA-AATT
59070 ATCAAGTACAAAAATT
1 ATCAAGTACAAAAATT
59086 A
1 A
59087 ATGTAAACCC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.81
17 3 0.19
ACGTcount: A:0.58, C:0.09, G:0.09, T:0.24
Consensus pattern (16 bp):
ATCAAGTACAAAAATT
Found at i:65879 original size:31 final size:31
Alignment explanation
Indices: 65830--65894 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
65820 ATATATTATG
*
65830 ATAAGTTTAAGGATTATTTCATAATAGTTTA
1 ATAAGTTTAAGGATTATTTCATAATAATTTA
* **
65861 ATAAGTTTAATG-TCTATTTTGTAATAATTTA
1 ATAAGTTTAAGGAT-TATTTCATAATAATTTA
65892 ATA
1 ATA
65895 CTGCTTATTG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 1 0.03
31 28 0.97
ACGTcount: A:0.38, C:0.03, G:0.11, T:0.48
Consensus pattern (31 bp):
ATAAGTTTAAGGATTATTTCATAATAATTTA
Found at i:68036 original size:19 final size:19
Alignment explanation
Indices: 68012--68048 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
68002 TTTAGATATT
*
68012 CGAAACTCGTACTTGAATC
1 CGAAACTCATACTTGAATC
*
68031 CGAAACTCATAGTTGAAT
1 CGAAACTCATACTTGAAT
68049 TTGAATAACT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.35, C:0.22, G:0.16, T:0.27
Consensus pattern (19 bp):
CGAAACTCATACTTGAATC
Found at i:70390 original size:22 final size:22
Alignment explanation
Indices: 70365--70432 Score: 65
Period size: 22 Copynumber: 3.3 Consensus size: 22
70355 TTAGTTTTTA
70365 TAATTAAATTTGTTATTCATCC
1 TAATTAAATTTGTTATTCATCC
* *
70387 TAATT-AATTAGTT-TT--T-G
1 TAATTAAATTTGTTATTCATCC
* *
70404 TACTTAAATTTGCTATTCATCC
1 TAATTAAATTTGTTATTCATCC
70426 TAATTAA
1 TAATTAA
70433 TTAGCGTGCT
Statistics
Matches: 34, Mismatches: 7, Indels: 10
0.67 0.14 0.20
Matches are distributed among these distances:
17 4 0.12
18 7 0.21
19 2 0.06
20 2 0.06
21 8 0.24
22 11 0.32
ACGTcount: A:0.32, C:0.12, G:0.06, T:0.50
Consensus pattern (22 bp):
TAATTAAATTTGTTATTCATCC
Found at i:70398 original size:39 final size:39
Alignment explanation
Indices: 70355--70436 Score: 137
Period size: 39 Copynumber: 2.1 Consensus size: 39
70345 TAATAATTCC
*
70355 TTAGTTTTTATAATTAAATTTGTTATTCATCCTAATTAA
1 TTAGTTTTTATAATTAAATTTGCTATTCATCCTAATTAA
* *
70394 TTAGTTTTTGTACTTAAATTTGCTATTCATCCTAATTAA
1 TTAGTTTTTATAATTAAATTTGCTATTCATCCTAATTAA
70433 TTAG
1 TTAG
70437 CGTGCTATTT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.30, C:0.10, G:0.07, T:0.52
Consensus pattern (39 bp):
TTAGTTTTTATAATTAAATTTGCTATTCATCCTAATTAA
Found at i:73613 original size:17 final size:17
Alignment explanation
Indices: 73592--73639 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
73582 TTTGAAACTA
73592 ATATCTAAAAGAAATGAT
1 ATATCTAAAAGAAAT-AT
*
73610 -TATC-AAGAAGAAATTT
1 ATATCTAA-AAGAAATAT
73626 ATATCTAAAAGAAA
1 ATATCTAAAAGAAA
73640 CTGTTTTATC
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
16 3 0.12
17 21 0.81
18 2 0.08
ACGTcount: A:0.56, C:0.06, G:0.10, T:0.27
Consensus pattern (17 bp):
ATATCTAAAAGAAATAT
Found at i:76708 original size:18 final size:18
Alignment explanation
Indices: 76685--76721 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
76675 TGATCCCAAC
*
76685 TTTATACCTAACAGTTAA
1 TTTATAACTAACAGTTAA
*
76703 TTTATAACTAACATTTAA
1 TTTATAACTAACAGTTAA
76721 T
1 T
76722 GGGTTAATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.41, C:0.14, G:0.03, T:0.43
Consensus pattern (18 bp):
TTTATAACTAACAGTTAA
Found at i:79871 original size:18 final size:18
Alignment explanation
Indices: 79848--79886 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
79838 ACCATAAACA
*
79848 GAATAAA-TGAAATTAAAT
1 GAATAAAGTG-AATAAAAT
79866 GAATAAAGTGAATAAAAT
1 GAATAAAGTGAATAAAAT
79884 GAA
1 GAA
79887 AAGAAATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 17 0.89
19 2 0.11
ACGTcount: A:0.62, C:0.00, G:0.15, T:0.23
Consensus pattern (18 bp):
GAATAAAGTGAATAAAAT
Found at i:80034 original size:33 final size:31
Alignment explanation
Indices: 79991--80058 Score: 84
Period size: 33 Copynumber: 2.1 Consensus size: 31
79981 ACTATATACC
79991 ATATAGTTTTCAAAAATGA-TTTTAAAAATATT
1 ATATAGTTTTCAAAAAT-ATTTTTAAAAATA-T
* *
80023 ATATGAGTTTTCCAAAATATTTTTAAAACTAT
1 ATAT-AGTTTTCAAAAATATTTTTAAAAATAT
80055 ATAT
1 ATAT
80059 TATATAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
32 10 0.31
33 22 0.69
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44
Consensus pattern (31 bp):
ATATAGTTTTCAAAAATATTTTTAAAAATAT
Found at i:80655 original size:106 final size:106
Alignment explanation
Indices: 80470--82632 Score: 3979
Period size: 106 Copynumber: 20.4 Consensus size: 106
80460 TGCAGATGGC
* * * *
80470 TCCTTCGTCGTGAAGTCGAGATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCC
1 TCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAACCAGCGGTCC
80535 CTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATA
66 CTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATA
*
80576 TCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCC
1 TCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAACCAGCGGTCC
80641 CTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATA
66 CTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATA
80682 TCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAACCAGCGGTCC
1 TCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAACCAGCGGTCC
* * *
80747 CTTCGTCGTGAAGTTGAACGTGCGTTGTCTCGAGTCCAATA
66 CTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATA
* * *
80788 TCATTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGCTGACAACTAGC-GTCC
1 TCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAACCAGCGGTCC
80852 CTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATA
66 CTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATA
* * *
80893 TCCTTCGTTGTGAAGTTGAAATTGGCTCTAAAATTGAGAAATTGTTTATTGACAACCAGCGATCC
1 TCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAACCAGCGGTCC
80958 CTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATA
66 CTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATA
80999 TCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAACCAGCGGTCC
1 TCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAACCAGCGGTCC
81064 CTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATA
66 CTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATA
* *
81105 TCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAACCAGCGGTCC
1 TCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAACCAGCGGTCC
81170 CTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATA
66 CTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATA
81211 TCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAACCAGCGGTCC
1 TCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAACCAGCGGTCC
81276 CTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATA
66 CTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATA
* *
81317 TCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAACCAGCGGTAC
1 TCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAACCAGCGGTCC
81382 CTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATA
66 CTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATA
* *
81423 TCCTTCGTTGTGAAGTCGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCC
1 TCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAACCAGCGGTCC
81488 CTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATA
66 CTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATA
*
81529 TCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCC
1 TCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAACCAGCGGTCC
81594 CTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATA
66 CTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATA
* *
81635 TCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAACCAGCGGTCC
1 TCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAACCAGCGGTCC
81700 CTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATA
66 CTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATA
* *
81741 TCCTTCGTTGTGAAGTCGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCC
1 TCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAACCAGCGGTCC
81806 CTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATA
66 CTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATA
*
81847 TCCTTCGTTGTGAAGTTGAAATTGGCTCTG-AATTGAGAAGTTGTTTGTTGACAACCAGCGGTCC
1 TCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAACCAGCGGTCC
81911 CTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATA
66 CTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATA
81952 TCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAACCAGCGGTCC
1 TCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAACCAGCGGTCC
* *
82017 CTTCGTCGTGAAGTTGAACTTGCGTTGTCTCGAGTCCAATA
66 CTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATA
**
82058 TCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTACTGACAACCAGCGGTCC
1 TCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAACCAGCGGTCC
82123 CTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATA
66 CTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATA
* * *
82164 TCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAACCAGCGATCC
1 TCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAACCAGCGGTCC
82229 CTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATA
66 CTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATA
82270 TCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAACCAGCGGTCC
1 TCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAACCAGCGGTCC
82335 CTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATA
66 CTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATA
*
82376 TCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAACCAGCGGTCC
1 TCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAACCAGCGGTCC
82441 CTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATA
66 CTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATA
* *
82482 TCCTTCGTTGTGAAGTCGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCC
1 TCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAACCAGCGGTCC
82547 CTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATA
66 CTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATA
*
82588 TCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAATTTGT
1 TCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGT
82633 AATTTACTCT
Statistics
Matches: 1999, Mismatches: 56, Indels: 4
0.97 0.03 0.00
Matches are distributed among these distances:
105 202 0.10
106 1797 0.90
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
TCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAACCAGCGGTCC
CTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATA
Found at i:87823 original size:18 final size:18
Alignment explanation
Indices: 87800--87838 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
87790 ACCATAAACA
*
87800 GAATAAA-TGAAATTAAAT
1 GAATAAAGTG-AATAAAAT
87818 GAATAAAGTGAATAAAAT
1 GAATAAAGTGAATAAAAT
87836 GAA
1 GAA
87839 AAGAAATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 17 0.89
19 2 0.11
ACGTcount: A:0.62, C:0.00, G:0.15, T:0.23
Consensus pattern (18 bp):
GAATAAAGTGAATAAAAT
Found at i:88086 original size:35 final size:35
Alignment explanation
Indices: 88047--88124 Score: 95
Period size: 35 Copynumber: 2.1 Consensus size: 35
88037 TATACATTAT
88047 ATTTTCAAAATGATTTCAAAA-ATATATGTTATATA
1 ATTTTCAAAATGATTTCAAAATATATATG-TATATA
* *
88082 ATTTTCAAAATGTTTTTAAAACTTATATATGTATATA
1 ATTTTCAAAATGATTTCAAAA--TATATATGTATATA
88119 AGTTTT
1 A-TTTT
88125 TAGAAACGTT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
35 19 0.51
37 7 0.19
38 11 0.30
ACGTcount: A:0.41, C:0.05, G:0.06, T:0.47
Consensus pattern (35 bp):
ATTTTCAAAATGATTTCAAAATATATATGTATATA
Found at i:88141 original size:40 final size:38
Alignment explanation
Indices: 88068--88142 Score: 98
Period size: 38 Copynumber: 1.9 Consensus size: 38
88058 GATTTCAAAA
*
88068 ATATATGTTATATAATTTTCAAAATGTTTTTAAAACTT
1 ATATATGTTATATAATTTTCAAAACGTTTTTAAAACTT
*
88106 ATATATG-TATATAAGTTTTTAGAAACGTTTTTTAAAA
1 ATATATGTTATATAA-TTTTCA-AAACG-TTTTTAAAA
88143 AAACTATATT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
37 7 0.22
38 12 0.38
39 4 0.12
40 9 0.28
ACGTcount: A:0.40, C:0.04, G:0.08, T:0.48
Consensus pattern (38 bp):
ATATATGTTATATAATTTTCAAAACGTTTTTAAAACTT
Found at i:88156 original size:108 final size:105
Alignment explanation
Indices: 87937--88156 Score: 227
Period size: 108 Copynumber: 2.0 Consensus size: 105
87927 CTATATACCA
*
87937 TATAGTTTTCAAAAATGATTTAAAAATATTATATGAGTTTTCCAAAATATTTTTAAAACTATATA
1 TATA-TTTTCAAAAATGATTTAAAAATATTATATGAATTTTCCAAAATATTTTTAAAACTATATA
* **
88002 TTATATAAAATTTTCAAAAATGTTTTATTTTAAACTATACAT
65 TTATATAAAATTTTCAAAAACGTTTTATTAAAAACTATA-AT
*
88044 TATATTTTC-AAAATGATTTCAAAAATATATGTTATAT-AATTTT-CAAAATGTTTTTAAAACTT
1 TATATTTTCAAAAATGATTT--AAAA-ATA--TTATATGAATTTTCCAAAATATTTTTAAAAC-T
* * *
88106 ATATATGTATAT-AAGTTTTTAGAAACGTTTT-TTAAAAAAACTAT-AT
60 ATATAT-TATATAAAATTTTCAAAAACGTTTTATT--AAAAACTATAAT
88152 TATAT
1 TATAT
88157 ATATATTTTC
Statistics
Matches: 96, Mismatches: 8, Indels: 17
0.79 0.07 0.14
Matches are distributed among these distances:
105 10 0.10
106 5 0.05
107 8 0.08
108 28 0.29
109 27 0.28
110 18 0.19
ACGTcount: A:0.43, C:0.06, G:0.05, T:0.45
Consensus pattern (105 bp):
TATATTTTCAAAAATGATTTAAAAATATTATATGAATTTTCCAAAATATTTTTAAAACTATATAT
TATATAAAATTTTCAAAAACGTTTTATTAAAAACTATAAT
Found at i:88179 original size:41 final size:43
Alignment explanation
Indices: 88099--88179 Score: 96
Period size: 41 Copynumber: 1.9 Consensus size: 43
88089 AAATGTTTTT
* * **
88099 AAAACTTATATATGTATATAAGTTTTTAGAAACGTTTTTTAAA
1 AAAACTTATATATATATATAAGTTTTCAGAAACCATTTTTAAA
88142 AAAAC-TATAT-TATATATATA-TTTTCAGAAACCATTTTT
1 AAAACTTATATATATATATA-AGTTTTCAGAAACCATTTTT
88180 GTAAACTATA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
41 22 0.67
42 6 0.18
43 5 0.15
ACGTcount: A:0.42, C:0.07, G:0.06, T:0.44
Consensus pattern (43 bp):
AAAACTTATATATATATATAAGTTTTCAGAAACCATTTTTAAA
Found at i:89574 original size:14 final size:14
Alignment explanation
Indices: 89555--89592 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
89545 AACGTTCATA
*
89555 AACGAACACGAACG
1 AACGAACACAAACG
*
89569 AACGAACATAAACG
1 AACGAACACAAACG
89583 AAC-AACACAA
1 AACGAACACAA
89593 CACAAAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
13 6 0.29
14 15 0.71
ACGTcount: A:0.58, C:0.26, G:0.13, T:0.03
Consensus pattern (14 bp):
AACGAACACAAACG
Done.