Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007859.1 Corchorus capsularis cultivar CVL-1 contig07880, 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: 53415
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:207 original size:21 final size:21
Alignment explanation
Indices: 183--237 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
173 ATTTAATGCT
*
183 AATTAATACTAAATT-GTAGTA
1 AATTAAAAC-AAATTAGTAGTA
*
204 AATTAAAACAAATTAAGTATTA
1 AATTAAAACAAATT-AGTAGTA
226 AATT-AAACAAAT
1 AATTAAAACAAAT
238 CATCAAAATG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 5 0.17
21 16 0.53
22 9 0.30
ACGTcount: A:0.56, C:0.05, G:0.05, T:0.33
Consensus pattern (21 bp):
AATTAAAACAAATTAGTAGTA
Found at i:948 original size:33 final size:33
Alignment explanation
Indices: 910--1054 Score: 136
Period size: 33 Copynumber: 4.5 Consensus size: 33
900 TTAGCCACGT
*
910 GGAGCCTCCCCACTAAGACGGCTCTGCCACGGC
1 GGAGCCTCCCCACTAAGACGACTCTGCCACGGC
* * * **
943 GGAGCCTCCCCACTAGGATGGCTCTGCCACGAT
1 GGAGCCTCCCCACTAAGACGACTCTGCCACGGC
* *
976 GGAG-CTGCCCCACTAGGACGATTCTGCCACGGC
1 GGAGCCT-CCCCACTAAGACGACTCTGCCACGGC
* *
1009 -TAGCCGCCCCACT-AGAACGACTCTGCCACGGC
1 GGAGCCTCCCCACTAAG-ACGACTCTGCCACGGC
* *
1041 -TAGCCGCCCCACTA
1 GGAGCCTCCCCACTA
1055 GGGCGACAAG
Statistics
Matches: 95, Mismatches: 13, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
31 1 0.01
32 39 0.41
33 55 0.58
ACGTcount: A:0.19, C:0.41, G:0.26, T:0.14
Consensus pattern (33 bp):
GGAGCCTCCCCACTAAGACGACTCTGCCACGGC
Found at i:1023 original size:32 final size:32
Alignment explanation
Indices: 903--1061 Score: 160
Period size: 32 Copynumber: 4.9 Consensus size: 32
893 TTTGCCATTA
* * *
903 GCCACGTG-GAGCCTCCCCACTAAGACGGCTCT
1 GCCACG-GCGAGCCGCCCCACTAGGACGACTCT
* * *
935 GCCACGGCGGAGCCTCCCCACTAGGATGGCTCT
1 GCCACGGC-GAGCCGCCCCACTAGGACGACTCT
* *
968 GCCACGATG-GAGCTGCCCCACTAGGACGATTCT
1 GCCACG--GCGAGCCGCCCCACTAGGACGACTCT
* *
1001 GCCACGGCTAGCCGCCCCACTAGAACGACTCT
1 GCCACGGCGAGCCGCCCCACTAGGACGACTCT
* *
1033 GCCACGGCTAGCCGCCCCACTAGGGCGAC
1 GCCACGGCGAGCCGCCCCACTAGGACGAC
1062 AAGGCTTTTT
Statistics
Matches: 109, Mismatches: 13, Indels: 10
0.83 0.10 0.08
Matches are distributed among these distances:
31 2 0.02
32 53 0.49
33 53 0.49
35 1 0.01
ACGTcount: A:0.19, C:0.40, G:0.27, T:0.14
Consensus pattern (32 bp):
GCCACGGCGAGCCGCCCCACTAGGACGACTCT
Found at i:1035 original size:65 final size:65
Alignment explanation
Indices: 903--1038 Score: 168
Period size: 65 Copynumber: 2.1 Consensus size: 65
893 TTTGCCATTA
* * * * *
903 GCCACGTGGAGCCTCCCCACTAAGACGGCTCTGCCACGGCGGAGCCTCCCCACTAGGATGGCTCT
1 GCCACGTGGAGCCTCCCCACTAAGACGACTCTGCCACGGCGGAGCCGCCCCACTAGAACGACTCT
* * *
968 GCCACGATGGAG-CTGCCCCACTAGGACGATTCTGCCACGGC-TAGCCGCCCCACTAGAACGACT
1 GCCACG-TGGAGCCT-CCCCACTAAGACGACTCTGCCACGGCGGAGCCGCCCCACTAGAACGACT
1031 CT
64 CT
1033 GCCACG
1 GCCACG
1039 GCTAGCCGCC
Statistics
Matches: 61, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
65 33 0.54
66 28 0.46
ACGTcount: A:0.19, C:0.40, G:0.26, T:0.15
Consensus pattern (65 bp):
GCCACGTGGAGCCTCCCCACTAAGACGACTCTGCCACGGCGGAGCCGCCCCACTAGAACGACTCT
Found at i:1177 original size:33 final size:33
Alignment explanation
Indices: 1127--1221 Score: 93
Period size: 33 Copynumber: 2.9 Consensus size: 33
1117 TAGTACCGGT
* * *
1127 GCCGCCCTAGGGGGGCGGTCTATCCATGGTAGA
1 GCCGCCCTAGGGAGGCGGCCTAGCCATGGTAGA
* * *
1160 GCCGGCCTAGGGAGGCGGCCTGGCCATGGTAGT
1 GCCGCCCTAGGGAGGCGGCCTAGCCATGGTAGA
* * *
1193 GCCGCCCCAGGG-GAGCGGCTTGGCCATGG
1 GCCGCCCTAGGGAG-GCGGCCTAGCCATGG
1222 CTCAGCCGCC
Statistics
Matches: 52, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
32 1 0.02
33 51 0.98
ACGTcount: A:0.13, C:0.29, G:0.43, T:0.15
Consensus pattern (33 bp):
GCCGCCCTAGGGAGGCGGCCTAGCCATGGTAGA
Found at i:6979 original size:22 final size:24
Alignment explanation
Indices: 6954--7050 Score: 84
Period size: 22 Copynumber: 4.3 Consensus size: 24
6944 TAAAGGTAAA
6954 CAAAATTTTTCA-AGGAA-G-TTAT
1 CAAAATTTTT-ATAGGAAGGTTTAT
*
6976 CAAAA-ATTTATAGGAAGGTTTAT
1 CAAAATTTTTATAGGAAGGTTTAT
* *
6999 CAAAA-TTTCATAGTAAGGTTT-T
1 CAAAATTTTTATAGGAAGGTTTAT
* *
7021 CAAAA-TTTTATACGAAGG-TTAA
1 CAAAATTTTTATAGGAAGGTTTAT
7043 CAAAATTT
1 CAAAATTT
7051 CATGGGAATG
Statistics
Matches: 62, Mismatches: 8, Indels: 9
0.78 0.10 0.11
Matches are distributed among these distances:
20 1 0.02
21 10 0.16
22 27 0.44
23 24 0.39
ACGTcount: A:0.42, C:0.08, G:0.13, T:0.36
Consensus pattern (24 bp):
CAAAATTTTTATAGGAAGGTTTAT
Found at i:6998 original size:23 final size:23
Alignment explanation
Indices: 6972--7040 Score: 88
Period size: 23 Copynumber: 3.0 Consensus size: 23
6962 TTCAAGGAAG
6972 TTATCAAAAATTTATAGGAAGGT
1 TTATCAAAAATTTATAGGAAGGT
*
6995 TTATC-AAAATTTCATAGTAAGGT
1 TTATCAAAAATTT-ATAGGAAGGT
* *
7018 TT-TCAAAATTTTATACGAAGGT
1 TTATCAAAAATTTATAGGAAGGT
7040 T
1 T
7041 AACAAAATTT
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
22 18 0.45
23 22 0.55
ACGTcount: A:0.39, C:0.07, G:0.14, T:0.39
Consensus pattern (23 bp):
TTATCAAAAATTTATAGGAAGGT
Found at i:7003 original size:45 final size:46
Alignment explanation
Indices: 6946--7050 Score: 119
Period size: 45 Copynumber: 2.3 Consensus size: 46
6936 AAACATATTA
* *
6946 AAGGTAAACAAAATTTTTCA-AGGAA-GTTATCAAAAATTTATAGG
1 AAGGTTAACAAAATTTTTCATAGGAAGGTTATCAAAAATTTATACG
* * * *
6990 AAGGTTTATCAAAA--TTTCATAGTAAGGTTTTCAAAATTTTATACG
1 AAGG-TTAACAAAATTTTTCATAGGAAGGTTATCAAAAATTTATACG
7035 AAGGTTAACAAAATTT
1 AAGGTTAACAAAATTT
7051 CATGGGAATG
Statistics
Matches: 49, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
43 5 0.10
44 16 0.33
45 27 0.55
46 1 0.02
ACGTcount: A:0.44, C:0.08, G:0.14, T:0.34
Consensus pattern (46 bp):
AAGGTTAACAAAATTTTTCATAGGAAGGTTATCAAAAATTTATACG
Found at i:7116 original size:22 final size:22
Alignment explanation
Indices: 7091--7163 Score: 92
Period size: 22 Copynumber: 3.3 Consensus size: 22
7081 GGTTTTGGAC
* *
7091 ATTTCATAGGGAGAATCTCAAA
1 ATTTCATAGGGAGATTATCAAA
* **
7113 ATTTCATAGTGTCATTATCAAA
1 ATTTCATAGGGAGATTATCAAA
*
7135 ATTTCAGAGGGAGATTATCAAA
1 ATTTCATAGGGAGATTATCAAA
7157 ATTTCAT
1 ATTTCAT
7164 TGTGTAATTA
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.34
Consensus pattern (22 bp):
ATTTCATAGGGAGATTATCAAA
Found at i:7139 original size:44 final size:44
Alignment explanation
Indices: 7091--7187 Score: 131
Period size: 44 Copynumber: 2.2 Consensus size: 44
7081 GGTTTTGGAC
* *
7091 ATTTCATAGGGAGAATCTCAAAATTTCATAGTGTCATTATCAAA
1 ATTTCATAGGGAGAATATCAAAATTTCATAGTGTAATTATCAAA
* * * *
7135 ATTTCAGAGGGAGATTATCAAAATTTCATTGTGTAATTATCACA
1 ATTTCATAGGGAGAATATCAAAATTTCATAGTGTAATTATCAAA
*
7179 ATTCCATAG
1 ATTTCATAG
7188 TGTGGTAGGA
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.35
Consensus pattern (44 bp):
ATTTCATAGGGAGAATATCAAAATTTCATAGTGTAATTATCAAA
Found at i:7173 original size:22 final size:22
Alignment explanation
Indices: 7108--7190 Score: 96
Period size: 22 Copynumber: 3.8 Consensus size: 22
7098 AGGGAGAATC
*
7108 TCAAAATTTCATAGTGTCATTA
1 TCAAAATTTCATAGTGTAATTA
* *
7130 TCAAAATTTCAGAG-GGAGATTA
1 TCAAAATTTCATAGTGTA-ATTA
*
7152 TCAAAATTTCATTGTGTAATTA
1 TCAAAATTTCATAGTGTAATTA
* *
7174 TCACAATTCCATAGTGT
1 TCAAAATTTCATAGTGT
7191 GGTAGGATGT
Statistics
Matches: 50, Mismatches: 9, Indels: 4
0.79 0.14 0.06
Matches are distributed among these distances:
21 1 0.02
22 47 0.94
23 2 0.04
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.37
Consensus pattern (22 bp):
TCAAAATTTCATAGTGTAATTA
Found at i:16378 original size:29 final size:30
Alignment explanation
Indices: 16325--16385 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 30
16315 GTTCTAATTA
* * *
16325 ATGTATACATATGAATTGTTCAATTTTATT
1 ATGTATAAATATGAATTATTCAATTATATT
*
16355 ATGTATAAATAT-AATTATTTAATTATATT
1 ATGTATAAATATGAATTATTCAATTATATT
16384 AT
1 AT
16386 ATTATATTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
29 16 0.59
30 11 0.41
ACGTcount: A:0.39, C:0.03, G:0.07, T:0.51
Consensus pattern (30 bp):
ATGTATAAATATGAATTATTCAATTATATT
Found at i:18144 original size:31 final size:31
Alignment explanation
Indices: 18109--18170 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
18099 AAAGTCATTA
*
18109 ATGAATATTGTGATTATTCATGAATCAAGAG
1 ATGAATATTGTAATTATTCATGAATCAAGAG
*
18140 ATGAATATTGTAATTATTTATGAATCAAGAG
1 ATGAATATTGTAATTATTCATGAATCAAGAG
18171 TTCTCTTGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.40, C:0.05, G:0.18, T:0.37
Consensus pattern (31 bp):
ATGAATATTGTAATTATTCATGAATCAAGAG
Found at i:19224 original size:21 final size:21
Alignment explanation
Indices: 19198--19237 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
19188 GGGGGAGGAG
19198 GAATTTCACAATAATACCAGC
1 GAATTTCACAATAATACCAGC
*
19219 GAATTTCAGAATAATACCA
1 GAATTTCACAATAATACCA
19238 TTACAACTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.45, C:0.20, G:0.10, T:0.25
Consensus pattern (21 bp):
GAATTTCACAATAATACCAGC
Found at i:19644 original size:11 final size:11
Alignment explanation
Indices: 19601--19638 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
19591 TTCCTATATA
*
19601 AAATAAATTAT
1 AAATTAATTAT
19612 CAAA-TAATTAT
1 -AAATTAATTAT
19623 AAATTAATTAT
1 AAATTAATTAT
19634 AAATT
1 AAATT
19639 TGTTATGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATTAATTAT
Found at i:19666 original size:19 final size:19
Alignment explanation
Indices: 19639--19677 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
19629 ATTATAAATT
19639 TGTTATGAATATACATGTA
1 TGTTATGAATATACATGTA
* * *
19658 TGTTGTGAATGTCCATGTA
1 TGTTATGAATATACATGTA
19677 T
1 T
19678 CTAATTAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.28, C:0.08, G:0.21, T:0.44
Consensus pattern (19 bp):
TGTTATGAATATACATGTA
Found at i:20326 original size:18 final size:17
Alignment explanation
Indices: 20305--20343 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
20295 TTGATTTTTT
20305 ATATAATTTTTATTTTGA
1 ATAT-ATTTTTATTTTGA
* *
20323 ATATTTTTTTGTTTTGA
1 ATATATTTTTATTTTGA
20340 ATAT
1 ATAT
20344 TTAATTCTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.28, C:0.00, G:0.08, T:0.64
Consensus pattern (17 bp):
ATATATTTTTATTTTGA
Found at i:20331 original size:17 final size:17
Alignment explanation
Indices: 20311--20345 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
20301 TTTTATATAA
20311 TTTTTATTTTGAATATT
1 TTTTTATTTTGAATATT
*
20328 TTTTTGTTTTGAATATT
1 TTTTTATTTTGAATATT
20345 T
1 T
20346 AATTCTACAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.20, C:0.00, G:0.09, T:0.71
Consensus pattern (17 bp):
TTTTTATTTTGAATATT
Found at i:20399 original size:2 final size:2
Alignment explanation
Indices: 20392--20416 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
20382 AAGAGCGCGA
20392 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
20417 ATTTTTAGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:23184 original size:2 final size:2
Alignment explanation
Indices: 23177--23204 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
23167 TTTTAATCGC
23177 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
23205 TTGTGGTGTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:27576 original size:156 final size:155
Alignment explanation
Indices: 27399--27932 Score: 584
Period size: 155 Copynumber: 3.4 Consensus size: 155
27389 TTCGAGCCCT
* * * * *
27399 CCTTCATGGTGAACTAGGTTTCACACCCCAAATTGTCCTTAAATGAAAAACTAACATAATTTTTT
1 CCTTCATGGTGAACTTGGTTTCTCACCCCAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTT
* * *
27464 CATTCTATGTCTGTTTGAGCTGAAACTTTTCCACGAGACTTAGACTATCTCCATAAGACTATGAA
66 CATTCTAAGTCTGTTTGAGCTGAAACTTTTCCACGAGACTTAGATTATCTCCATAA-ACTATGGA
* *
27529 AAAAATTCCAAGTAAAACCGACCTCC
130 AAAAATTCTAAGTAAAACCGAACTCC
* * *
27555 CCTTGATGGTGAACTTGGTTTCTCTCCCTAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTT
1 CCTTCATGGTGAACTTGGTTTCTCACCCCAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTT
*** * *
27620 CATTCTAAGTC-CAATAAGGCTG--A-TTTTCCACAAGTAGGCTTAGATTATCTCCATAATACTA
66 CATTCTAAGTCTGTTTGA-GCTGAAACTTTTCCAC--G-AGACTTAGATTATCTCCATAA-ACTA
* * *
27681 TGGAAAAAATTCTAAGTAAAACTGAGCTCT
126 TGGAAAAAATTCTAAGTAAAACCGAACTCC
* ** * *
27711 CCTTGGCA--GTGAAC-CGACTTCTCACCTCAAACTGTCCTTAAATGAAAAACTAGCATAGGTTT
1 CCTT--CATGGTGAACTTGGTTTCTCACCCCAAACTGTCCTTAAATGAAAAACTAGCATAAGTTT
* * * * * * *
27773 TTCATTCGAAGTCTGTTTGAGATGAAACTTGGT-CAAGAGACTTATATTATCTGCACAAACTTAT
64 TTCATTCTAAGTCTGTTTGAGCTGAAACTT-TTCCACGAGACTTAGATTATCTCCATAAAC-TAT
27837 GGAAAAAATTCTAAGTAAAACCGAACT-C
127 GGAAAAAATTCTAAGTAAAACCGAACTCC
* *
27865 CCTATCATGGTGAA-GTGGTTTCTCACCCCAAACTATCCTTAAATGAAAAACTAGCATAAGTTTT
1 CCT-TCATGGTGAACTTGGTTTCTCACCCCAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTT
27929 TCAT
65 TCAT
27933 CTTAAGTTCG
Statistics
Matches: 312, Mismatches: 50, Indels: 33
0.79 0.13 0.08
Matches are distributed among these distances:
153 10 0.03
154 6 0.02
155 157 0.50
156 132 0.42
157 1 0.00
158 5 0.02
159 1 0.00
ACGTcount: A:0.34, C:0.21, G:0.14, T:0.31
Consensus pattern (155 bp):
CCTTCATGGTGAACTTGGTTTCTCACCCCAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTT
CATTCTAAGTCTGTTTGAGCTGAAACTTTTCCACGAGACTTAGATTATCTCCATAAACTATGGAA
AAAATTCTAAGTAAAACCGAACTCC
Found at i:29137 original size:16 final size:16
Alignment explanation
Indices: 29100--29144 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
29090 GGACAACTTA
*
29100 TATCATCGAGACG-CT
1 TATCATCAAGACGACT
*
29115 TACCATCAAGACGACT
1 TATCATCAAGACGACT
*
29131 TATCATCAGGACGA
1 TATCATCAAGACGA
29145 GTTGATGGTG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
15 11 0.44
16 14 0.56
ACGTcount: A:0.33, C:0.27, G:0.18, T:0.22
Consensus pattern (16 bp):
TATCATCAAGACGACT
Found at i:30164 original size:15 final size:15
Alignment explanation
Indices: 30144--30180 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
30134 AATTCTCCTA
30144 GGAGAGTGATTCTTG
1 GGAGAGTGATTCTTG
30159 GGAGAGTGATTCTTG
1 GGAGAGTGATTCTTG
30174 GGAGAGT
1 GGAGAGT
30181 AACTCTAGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.22, C:0.05, G:0.43, T:0.30
Consensus pattern (15 bp):
GGAGAGTGATTCTTG
Found at i:37080 original size:29 final size:29
Alignment explanation
Indices: 36984--37072 Score: 178
Period size: 29 Copynumber: 3.1 Consensus size: 29
36974 AGTCCATATC
36984 TACCCATAAAATAAATAAAAAAATTTATT
1 TACCCATAAAATAAATAAAAAAATTTATT
37013 TACCCATAAAATAAATAAAAAAATTTATT
1 TACCCATAAAATAAATAAAAAAATTTATT
37042 TACCCATAAAATAAATAAAAAAATTTATT
1 TACCCATAAAATAAATAAAAAAATTTATT
37071 TA
1 TA
37073 GACCTAAACT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 60 1.00
ACGTcount: A:0.58, C:0.10, G:0.00, T:0.31
Consensus pattern (29 bp):
TACCCATAAAATAAATAAAAAAATTTATT
Found at i:40104 original size:15 final size:13
Alignment explanation
Indices: 40084--40121 Score: 58
Period size: 14 Copynumber: 2.8 Consensus size: 13
40074 GCCTAGAACC
40084 AAAAAAAAACAAA
1 AAAAAAAAACAAA
40097 GAAAAAAAAACAAA
1 -AAAAAAAAACAAA
40111 AACAAAAAAAC
1 AA-AAAAAAAC
40122 CCTAAGAACC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 2 0.09
14 21 0.91
ACGTcount: A:0.87, C:0.11, G:0.03, T:0.00
Consensus pattern (13 bp):
AAAAAAAAACAAA
Found at i:40389 original size:80 final size:82
Alignment explanation
Indices: 40298--40459 Score: 256
Period size: 80 Copynumber: 2.0 Consensus size: 82
40288 TTTCCATTTC
* *
40298 TCCTCCTAATCCATAGACTGCCCAAAAAATTCCTTACAAAAA-AATT-AACTTGAAGAATAACAC
1 TCCTCCTAATCCATAGACTGCCCAAAAAATTCCTAACAAAAATAATTAAACTTAAAGAATAACAC
*
40361 ATTAAAAATGAAAAGAT
66 ATGAAAAATGAAAAGAT
* * *
40378 TCCTTCTAATCCATAGACTGCCCAAAACATTCCTAACAAAAATTATTAAACTTAAAGAATAACAC
1 TCCTCCTAATCCATAGACTGCCCAAAAAATTCCTAACAAAAATAATTAAACTTAAAGAATAACAC
40443 ATGAAAAATGAAAAGAT
66 ATGAAAAATGAAAAGAT
40460 GCAAAACCAT
Statistics
Matches: 74, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
80 39 0.53
81 3 0.04
82 32 0.43
ACGTcount: A:0.49, C:0.20, G:0.07, T:0.24
Consensus pattern (82 bp):
TCCTCCTAATCCATAGACTGCCCAAAAAATTCCTAACAAAAATAATTAAACTTAAAGAATAACAC
ATGAAAAATGAAAAGAT
Found at i:41200 original size:107 final size:107
Alignment explanation
Indices: 41028--41396 Score: 616
Period size: 107 Copynumber: 3.5 Consensus size: 107
41018 AGTTTAGTCT
* * *
41028 TAATTTCACTAAGTTTAGCCTCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTTCAAAATT
1 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCATAATT
41093 AATAATTCATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
66 AATAATTCATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
41135 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCATAATT
1 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCATAATT
41200 AATAATTCATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
66 AATAATTCATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
41242 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCATAATT
1 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCATAATT
* * * *
41307 AATAATTTATTGTTATAAGGTTTTAGAAATAAAATATATAAC
66 AATAATTCATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
* * ** *
41349 TAA-TTCACTAAGTTTA-ACTCAAATTAAAATTAAAATTTTATTTTAAGG
1 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGG
41397 ATTAGAAAAA
Statistics
Matches: 250, Mismatches: 12, Indels: 2
0.95 0.05 0.01
Matches are distributed among these distances:
105 27 0.11
106 13 0.05
107 210 0.84
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.41
Consensus pattern (107 bp):
TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCATAATT
AATAATTCATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
Found at i:45133 original size:23 final size:23
Alignment explanation
Indices: 45103--45148 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
45093 ATTAGACATG
45103 CAGCTAACATATCAGCACTTCCA
1 CAGCTAACATATCAGCACTTCCA
*
45126 CAGCTAACATATCAGCATTTCCA
1 CAGCTAACATATCAGCACTTCCA
45149 GGTAGCACTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.33, G:0.09, T:0.24
Consensus pattern (23 bp):
CAGCTAACATATCAGCACTTCCA
Found at i:50802 original size:44 final size:44
Alignment explanation
Indices: 50754--50852 Score: 137
Period size: 44 Copynumber: 2.2 Consensus size: 44
50744 TCCATGAGGA
* *
50754 GGTTATCAAAACTCCATAGTGTGGTTACCAAAATTTCATAGTAT
1 GGTTACCAAAACTCCATAGTGTAGTTACCAAAATTTCATAGTAT
* *
50798 GGTTACCAAAATTTCATAGTGTAGTTACCAAAATTTCATAG-AGT
1 GGTTACCAAAACTCCATAGTGTAGTTACCAAAATTTCATAGTA-T
*
50842 GGCTACCAAAA
1 GGTTACCAAAA
50853 TTTCATAGGA
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
43 1 0.02
44 48 0.98
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.31
Consensus pattern (44 bp):
GGTTACCAAAACTCCATAGTGTAGTTACCAAAATTTCATAGTAT
Found at i:50830 original size:66 final size:65
Alignment explanation
Indices: 50707--50860 Score: 168
Period size: 66 Copynumber: 2.3 Consensus size: 65
50697 CTTGTCTCTA
* ** * *
50707 TGTGGTTATCAAAATTTCATAAGATGGTTATTATAATTCCATGAGGAGGTTATCAAAACTCCATA
1 TGTGGTTACCAAAATTTCAT-AGATGGTTACCAAAATTCCATGAGGAGGTTACCAAAACTCCATA
50772 G
65 G
* * *
50773 TGTGGTTACCAAAATTTCATAGTATGGTTACCAAAATTTCAT-AGTGTA-GTTACCAAAATTTCA
1 TGTGGTTACCAAAATTTCATAG-ATGGTTACCAAAATTCCATGAG-G-AGGTTACCAAAACTCCA
50836 TAG
63 TAG
* *
50839 AGTGGCTACCAAAATTTCATAG
1 TGTGGTTACCAAAATTTCATAG
50861 GATCAGGTTA
Statistics
Matches: 75, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
65 4 0.05
66 70 0.93
67 1 0.01
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.34
Consensus pattern (65 bp):
TGTGGTTACCAAAATTTCATAGATGGTTACCAAAATTCCATGAGGAGGTTACCAAAACTCCATAG
Found at i:50853 original size:44 final size:44
Alignment explanation
Indices: 50768--50860 Score: 152
Period size: 44 Copynumber: 2.1 Consensus size: 44
50758 ATCAAAACTC
* *
50768 CATAGTGTGGTTACCAAAATTTCATAGTATGGTTACCAAAATTT
1 CATAGTGTAGTTACCAAAATTTCATAGTATGGCTACCAAAATTT
50812 CATAGTGTAGTTACCAAAATTTCATAG-AGTGGCTACCAAAATTT
1 CATAGTGTAGTTACCAAAATTTCATAGTA-TGGCTACCAAAATTT
50856 CATAG
1 CATAG
50861 GATCAGGTTA
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
43 1 0.02
44 45 0.98
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.33
Consensus pattern (44 bp):
CATAGTGTAGTTACCAAAATTTCATAGTATGGCTACCAAAATTT
Found at i:50885 original size:24 final size:22
Alignment explanation
Indices: 50710--50907 Score: 111
Period size: 22 Copynumber: 8.9 Consensus size: 22
50700 GTCTCTATGT
* *
50710 GGTTATCAAAATTTCATAAG-A
1 GGTTATTAAAATTTCATAGGTA
* *
50731 TGGTTATTATAATTCCATGAGG-A
1 -GGTTATTAAAATTTCAT-AGGTA
* * *
50754 GGTTATCAAAACTCCATAGTGT-
1 GGTTATTAAAATTTCATAG-GTA
**
50776 GGTTACCAAAATTTCATA-GTA
1 GGTTATTAAAATTTCATAGGTA
**
50797 TGGTTACCAAAATTTCATAGTGTA
1 -GGTTATTAAAATTTCATAG-GTA
**
50821 -GTTACCAAAATTTCATAGAGT-
1 GGTTATTAAAATTTCATAG-GTA
* **
50842 GGCTACCAAAATTTCATAGGATCA
1 GGTTATTAAAATTTCATAGG-T-A
* *
50866 GGTTATTAAAATTTCTTAGGTT
1 GGTTATTAAAATTTCATAGGTA
*
50888 GGTTATTGAAATTTCATAGG
1 GGTTATTAAAATTTCATAGG
50908 GTGGTTAATT
Statistics
Matches: 146, Mismatches: 19, Indels: 22
0.78 0.10 0.12
Matches are distributed among these distances:
20 2 0.01
21 3 0.02
22 118 0.81
23 4 0.03
24 19 0.13
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.36
Consensus pattern (22 bp):
GGTTATTAAAATTTCATAGGTA
Found at i:50987 original size:24 final size:22
Alignment explanation
Indices: 50953--51009 Score: 69
Period size: 24 Copynumber: 2.5 Consensus size: 22
50943 AAAAAGATTT
*
50953 CAAAATGTCATAGCGAGGTTATA
1 CAAAATTTCATAGCGAGGTTA-A
* *
50976 CGAAAATTTCATAGTGTGGTTAA
1 C-AAAATTTCATAGCGAGGTTAA
50999 CAAAATTTCAT
1 CAAAATTTCAT
51010 TAGAAGGTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
22 10 0.33
23 3 0.10
24 17 0.57
ACGTcount: A:0.39, C:0.12, G:0.18, T:0.32
Consensus pattern (22 bp):
CAAAATTTCATAGCGAGGTTAA
Found at i:51006 original size:22 final size:23
Alignment explanation
Indices: 50953--51076 Score: 73
Period size: 22 Copynumber: 5.5 Consensus size: 23
50943 AAAAAGATTT
*
50953 CAAAATGTCATAGCGAGGTTATA
1 CAAAATTTCATAGCGAGGTTATA
* *
50976 CGAAAATTTCATAGTGTGGTTA-A
1 C-AAAATTTCATAGCGAGGTTATA
*
50999 CAAAATTTCATTAG-AAGGTTACTA
1 CAAAATTTCA-TAGCGAGGTTA-TA
* * * *
51023 -ATACTTT-ATCGGGAGGTTAT-
1 CAAAATTTCATAGCGAGGTTATA
* *
51043 CAAAATTTGATAGTGTA-GTTAT-
1 CAAAATTTCATAGCG-AGGTTATA
51065 CAAAATTTCATA
1 CAAAATTTCATA
51077 TGAAGGTTAT
Statistics
Matches: 79, Mismatches: 14, Indels: 17
0.72 0.13 0.15
Matches are distributed among these distances:
21 8 0.10
22 41 0.52
23 12 0.15
24 18 0.23
ACGTcount: A:0.37, C:0.10, G:0.18, T:0.35
Consensus pattern (23 bp):
CAAAATTTCATAGCGAGGTTATA
Found at i:51085 original size:22 final size:22
Alignment explanation
Indices: 50968--51210 Score: 78
Period size: 22 Copynumber: 10.8 Consensus size: 22
50958 TGTCATAGCG
50968 AGGTTATACGAAAATTTCATAGTG-
1 AGGTTAT-C-AAAATTTCATA-TGA
* *
50992 TGGTTAACAAAATTTCAT-TAGA
1 AGGTTATCAAAATTTCATAT-GA
* ** *
51014 AGGTTA-CTAATACTTT-ATCGGG
1 AGGTTATC-AA-AATTTCATATGA
* *
51036 AGGTTATCAAAATTTGATAGTGT
1 AGGTTATCAAAATTTCATA-TGA
51059 A-GTTATCAAAATTTCATATGA
1 AGGTTATCAAAATTTCATATGA
* *
51080 AGGTTAT-AAAAGTCTAATTTCAT-A
1 AGGTTATCAAAA-TTTCA--T-ATGA
* * *
51104 AGGAGTACCAAAATTTGATA-GA
1 AGG-TTATCAAAATTTCATATGA
*
51126 AGGTTATC-AAATCTCATA--A
1 AGGTTATCAAAATTTCATATGA
* *
51145 AGTGATTATCGAAATTTCATAAAGA
1 AG-G-TTATCAAAATTTCAT-ATGA
*
51170 TAGGATTAACAAAATTT-ATATGA
1 -AGG-TTATCAAAATTTCATATGA
**
51193 ATATTATCAAAATTTCAT
1 AGGTTATCAAAATTTCAT
51211 GGTGTTGTTA
Statistics
Matches: 166, Mismatches: 29, Indels: 50
0.68 0.12 0.20
Matches are distributed among these distances:
19 3 0.02
20 10 0.06
21 32 0.19
22 70 0.42
23 13 0.08
24 12 0.07
25 20 0.12
26 6 0.04
ACGTcount: A:0.41, C:0.09, G:0.15, T:0.35
Consensus pattern (22 bp):
AGGTTATCAAAATTTCATATGA
Found at i:51330 original size:22 final size:22
Alignment explanation
Indices: 51095--51340 Score: 66
Period size: 22 Copynumber: 11.3 Consensus size: 22
51085 ATAAAAGTCT
* *
51095 AATTTCAT-AAGGAG-TACCAA
1 AATTTCATAAAGAAGTTATCAA
*
51115 AATTTGAT--AGAAGGTTATC-A
1 AATTTCATAAAGAA-GTTATCAA
* * *
51135 AATCTCATAAAG-TGATTATCGA
1 AATTTCATAAAGAAG-TTATCAA
*
51157 AATTTCATAAAGATAGGATTAACAA
1 AATTTCATAAAGA-A-G-TTATCAA
* *
51182 AATTT-AT-ATGAATATTATCAA
1 AATTTCATAAAGAA-GTTATCAA
*** **
51203 AATTTCATGGTGTTGTTATCAA
1 AATTTCATAAAGAAGTTATCAA
* * *
51225 AATTTCA-AAGCGAGGTTATTAA
1 AATTTCATAA-AGAAGTTATCAA
* * * *
51247 AA-TTAATAATG-TGATTTTCAA
1 AATTTCATAAAGAAG-TTATCAA
* ** * *
51268 AATTTCATAGAGGGGTCAACAA
1 AATTTCATAAAGAAGTTATCAA
*
51290 AATTTTATAAAGATA-TTATCAA
1 AATTTCATAAAGA-AGTTATCAA
*
51312 AATTTCATAAAGAAGTTATCGA
1 AATTTCATAAAGAAGTTATCAA
*
51334 ATTTTCA
1 AATTTCA
51341 AAATGTGATT
Statistics
Matches: 163, Mismatches: 45, Indels: 34
0.67 0.19 0.14
Matches are distributed among these distances:
19 3 0.02
20 17 0.10
21 31 0.19
22 92 0.56
23 6 0.04
24 2 0.01
25 12 0.07
ACGTcount: A:0.43, C:0.09, G:0.13, T:0.35
Consensus pattern (22 bp):
AATTTCATAAAGAAGTTATCAA
Found at i:51478 original size:19 final size:19
Alignment explanation
Indices: 51446--51512 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
51436 TGATGTAGTA
51446 ATCAAAATTTCAGGGAGGAT
1 ATCAAAA-TTCAGGGAGGAT
*
51466 ACCAAAATTCAGGGAGGAT
1 ATCAAAATTCAGGGAGGAT
* * *
51485 ATCGAAATTCAGTGAGTAT
1 ATCAAAATTCAGGGAGGAT
51504 ATCAAAATT
1 ATCAAAATT
51513 TCATATGAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
19 35 0.85
20 6 0.15
ACGTcount: A:0.42, C:0.12, G:0.21, T:0.25
Consensus pattern (19 bp):
ATCAAAATTCAGGGAGGAT
Found at i:51529 original size:22 final size:21
Alignment explanation
Indices: 51503--51584 Score: 92
Period size: 22 Copynumber: 3.8 Consensus size: 21
51493 TCAGTGAGTA
51503 TATCAAAATTTCATATGAATGT
1 TATCAAAATTTCATA-GAATGT
* **
51525 TATCAAATTTTCATAAGAGGGT
1 TATCAAAATTTCAT-AGAATGT
*
51547 TATCAAAATTTCATAGTATGT
1 TATCAAAATTTCATAGAATGT
*
51568 AGATCAAAATTTCATAG
1 -TATCAAAATTTCATAG
51585 GGAGATAACA
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
21 4 0.08
22 45 0.90
23 1 0.02
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.38
Consensus pattern (21 bp):
TATCAAAATTTCATAGAATGT
Found at i:51553 original size:44 final size:43
Alignment explanation
Indices: 51502--51644 Score: 123
Period size: 44 Copynumber: 3.3 Consensus size: 43
51492 TTCAGTGAGT
* *
51502 ATATCAAAATTTCATATGAATGT-TATCAAATTTTCATAAGAGG-G
1 ATATCAAAATTTCATA-GAATGTAGATCAAAATTTCAT-AG-GGAG
* *
51546 TTATCAAAATTTCATAGTATGTAGATCAAAATTTCATAGGGAG
1 ATATCAAAATTTCATAGAATGTAGATCAAAATTTCATAGGGAG
* * **
51589 ATAACAAAATTTCATA-ATGAGGTA-ATCAAAAAATCATAGGGAG
1 ATATCAAAATTTCATAGA--ATGTAGATCAAAATTTCATAGGGAG
*
51632 CTTATCAAAATTT
1 -ATATCAAAATTT
51645 GTAGTTATCA
Statistics
Matches: 82, Mismatches: 12, Indels: 10
0.79 0.12 0.10
Matches are distributed among these distances:
42 2 0.02
43 39 0.48
44 41 0.50
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (43 bp):
ATATCAAAATTTCATAGAATGTAGATCAAAATTTCATAGGGAG
Found at i:51598 original size:21 final size:22
Alignment explanation
Indices: 51548--51644 Score: 83
Period size: 22 Copynumber: 4.5 Consensus size: 22
51538 TAAGAGGGTT
*
51548 ATCAAAATTTCATA-GTATG-TA
1 ATCAAAATTTCATAGGGA-GATA
51569 GATCAAAATTTCATAGGGAGATA
1 -ATCAAAATTTCATAGGGAGATA
** *
51592 A-CAAAATTTCATAATGAGGTA
1 ATCAAAATTTCATAGGGAGATA
** * *
51613 ATCAAAAAATCATAGGGAGCTT
1 ATCAAAATTTCATAGGGAGATA
51635 ATCAAAATTT
1 ATCAAAATTT
51645 GTAGTTATCA
Statistics
Matches: 60, Mismatches: 12, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
21 18 0.30
22 38 0.63
23 4 0.07
ACGTcount: A:0.45, C:0.10, G:0.14, T:0.30
Consensus pattern (22 bp):
ATCAAAATTTCATAGGGAGATA
Found at i:51617 original size:43 final size:43
Alignment explanation
Indices: 51506--51631 Score: 123
Period size: 43 Copynumber: 2.9 Consensus size: 43
51496 GTGAGTATAT
* * * *
51506 CAAAATTTCAT-ATGAATGTTATCAAATTTTCATAAGAGG-GTTAT
1 CAAAATTTCATAATG-ATGTAATCAAAATTTCAT-AG-GGAGATAA
*
51550 CAAAATTTCATAGT-ATGTAGATCAAAATTTCATAGGGAGATAA
1 CAAAATTTCATAATGATGTA-ATCAAAATTTCATAGGGAGATAA
* **
51593 CAAAATTTCATAATGAGGTAATCAAAAAATCATAGGGAG
1 CAAAATTTCATAATGATGTAATCAAAATTTCATAGGGAG
51632 CTTATCAAAA
Statistics
Matches: 69, Mismatches: 9, Indels: 9
0.79 0.10 0.10
Matches are distributed among these distances:
42 2 0.03
43 39 0.57
44 27 0.39
45 1 0.01
ACGTcount: A:0.44, C:0.10, G:0.16, T:0.31
Consensus pattern (43 bp):
CAAAATTTCATAATGATGTAATCAAAATTTCATAGGGAGATAA
Found at i:51702 original size:23 final size:23
Alignment explanation
Indices: 51649--51728 Score: 81
Period size: 23 Copynumber: 3.5 Consensus size: 23
51639 AAATTTGTAG
* * * *
51649 TTATCAAGATTTCATAAGAA-AG
1 TTATCAAAATTTTATAGGAAGAT
* * *
51671 TTATCAAAATTTTATTGGGAGGT
1 TTATCAAAATTTTATAGGAAGAT
*
51694 TTATTAAAATTTTATAGGAAGAT
1 TTATCAAAATTTTATAGGAAGAT
51717 TTATCAAAATTT
1 TTATCAAAATTT
51729 CATAACGAGG
Statistics
Matches: 45, Mismatches: 12, Indels: 1
0.78 0.21 0.02
Matches are distributed among these distances:
22 15 0.33
23 30 0.67
ACGTcount: A:0.40, C:0.05, G:0.14, T:0.41
Consensus pattern (23 bp):
TTATCAAAATTTTATAGGAAGAT
Found at i:51886 original size:23 final size:22
Alignment explanation
Indices: 51846--52039 Score: 74
Period size: 22 Copynumber: 8.9 Consensus size: 22
51836 TATCACATGG
* * *
51846 AGGTTATCAACATCTCATAGTGT
1 AGGTTATCAAAATTTCATAG-GA
* *
51869 TGGTTATCAAAATTTCATTGGA
1 AGGTTATCAAAATTTCATAGGA
* *
51891 AAGTTATCAAAATTTCATATTG-
1 AGGTTATCAAAATTTCATA-GGA
* *
51913 AGGTCT-TCAAAA-TTCGTTAGGG
1 AGGT-TATCAAAATTTC-ATAGGA
* *
51935 AGGTTAACAAAATTTCATAAGA
1 AGGTTATCAAAATTTCATAGGA
* * ** **
51957 AAGTTA-AAAAAAAT-ATAAAA
1 AGGTTATCAAAATTTCATAGGA
* * ** * *
51977 AGATTCTTGAAATTCCATAGTA
1 AGGTTATCAAAATTTCATAGGA
** *
51999 TCGTTATTAAAATTTCATAGGA
1 AGGTTATCAAAATTTCATAGGA
*
52021 AGATTATCAAAATTTCATA
1 AGGTTATCAAAATTTCATA
52040 ATGGGATCAT
Statistics
Matches: 121, Mismatches: 42, Indels: 17
0.67 0.23 0.09
Matches are distributed among these distances:
20 8 0.07
21 13 0.11
22 79 0.65
23 21 0.17
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.35
Consensus pattern (22 bp):
AGGTTATCAAAATTTCATAGGA
Found at i:52298 original size:22 final size:22
Alignment explanation
Indices: 52242--52298 Score: 105
Period size: 22 Copynumber: 2.6 Consensus size: 22
52232 CCCTAGTGTA
*
52242 ATTATCATAATTCAGTAGAGAT
1 ATTATCATAATTTAGTAGAGAT
52264 ATTATCATAATTTAGTAGAGAT
1 ATTATCATAATTTAGTAGAGAT
52286 ATTATCATAATTT
1 ATTATCATAATTT
52299 CATATGAATA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.40, C:0.07, G:0.11, T:0.42
Consensus pattern (22 bp):
ATTATCATAATTTAGTAGAGAT
Done.