Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002893.1 Hibiscus syriacus cultivar Beakdansim tig00005978_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: 52666
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:8693 original size:21 final size:21
Alignment explanation
Indices: 8677--8764 Score: 133
Period size: 21 Copynumber: 4.2 Consensus size: 21
8667 AGTGCATTTG
8677 TGCACCCCTGCAGTGCATCCA
1 TGCACCCCTGCAGTGCATCCA
*
8698 TGCACCCATGCAGTGCATCCA
1 TGCACCCCTGCAGTGCATCCA
*
8719 TGCACCCCTGCAGTGCATCGA
1 TGCACCCCTGCAGTGCATCCA
* *
8740 TGCA-CCATGTAGTGCATCCA
1 TGCACCCCTGCAGTGCATCCA
8760 TGCAC
1 TGCAC
8765 TCCATTTCGA
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
20 17 0.28
21 43 0.72
ACGTcount: A:0.22, C:0.38, G:0.20, T:0.20
Consensus pattern (21 bp):
TGCACCCCTGCAGTGCATCCA
Found at i:8726 original size:42 final size:41
Alignment explanation
Indices: 8677--8764 Score: 149
Period size: 42 Copynumber: 2.1 Consensus size: 41
8667 AGTGCATTTG
8677 TGCACCCCTGCAGTGCATCCATGCACCCATGCAGTGCATCCA
1 TGCACCCCTGCAGTGCATCCATGCA-CCATGCAGTGCATCCA
* *
8719 TGCACCCCTGCAGTGCATCGATGCACCATGTAGTGCATCCA
1 TGCACCCCTGCAGTGCATCCATGCACCATGCAGTGCATCCA
8760 TGCAC
1 TGCAC
8765 TCCATTTCGA
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
41 20 0.45
42 24 0.55
ACGTcount: A:0.22, C:0.38, G:0.20, T:0.20
Consensus pattern (41 bp):
TGCACCCCTGCAGTGCATCCATGCACCATGCAGTGCATCCA
Found at i:8956 original size:20 final size:22
Alignment explanation
Indices: 8918--8957 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
8908 TTTGAGTAGA
8918 AAAATCATCCCCTAATGGTTTC
1 AAAATCATCCCCTAATGGTTTC
8940 AAAA-CATCCCC-AATGGTT
1 AAAATCATCCCCTAATGGTT
8958 ATATACGACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.35, C:0.28, G:0.10, T:0.28
Consensus pattern (22 bp):
AAAATCATCCCCTAATGGTTTC
Found at i:9177 original size:28 final size:28
Alignment explanation
Indices: 9145--9200 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
9135 GGTTTTCTTG
9145 TACATTTTCCTTTCATTGTAAAGGGGAA
1 TACATTTTCCTTTCATTGTAAAGGGGAA
9173 TACATTTTCCTTTCATTGTAAAGGGGAA
1 TACATTTTCCTTTCATTGTAAAGGGGAA
9201 AGGTTATAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (28 bp):
TACATTTTCCTTTCATTGTAAAGGGGAA
Found at i:10591 original size:2 final size:2
Alignment explanation
Indices: 10584--10617 Score: 52
Period size: 2 Copynumber: 17.0 Consensus size: 2
10574 ATGGATTGCT
10584 TA TA TA TA -A TA TGA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA
10618 GTATTATGAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 1 0.03
2 27 0.90
3 2 0.07
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:10675 original size:2 final size:2
Alignment explanation
Indices: 10668--10694 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
10658 TCAATCTACA
10668 AT 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 AT A
10695 ATTTACGACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12921 original size:21 final size:21
Alignment explanation
Indices: 12895--12944 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
12885 AGGGTGTCAA
12895 AGTGCATCCATGCACCCCTAC
1 AGTGCATCCATGCACCCCTAC
*
12916 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCACCCCTAC
*
12937 AGTACATC
1 AGTGCATC
12945 TGCCACCAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.24, C:0.40, G:0.16, T:0.20
Consensus pattern (21 bp):
AGTGCATCCATGCACCCCTAC
Found at i:14340 original size:19 final size:18
Alignment explanation
Indices: 14289--14340 Score: 50
Period size: 19 Copynumber: 2.7 Consensus size: 18
14279 ACGATTTTCC
*
14289 TTTGAAAATAAAAATAGAT
1 TTTGAAAA-AAAAATAAAT
**
14308 TTTGAAAGCCAAAATGAAAT
1 TTTGAAA-AAAAAAT-AAAT
14328 TTTGAAAAAAAAA
1 TTTGAAAAAAAAA
14341 ACGATTTAGA
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
19 16 0.62
20 10 0.38
ACGTcount: A:0.58, C:0.04, G:0.12, T:0.27
Consensus pattern (18 bp):
TTTGAAAAAAAAATAAAT
Found at i:14341 original size:20 final size:19
Alignment explanation
Indices: 14289--14341 Score: 52
Period size: 20 Copynumber: 2.7 Consensus size: 19
14279 ACGATTTTCC
* *
14289 TTTGAAAATAAAAATAGAT
1 TTTGAAAAAAAAAATAAAT
***
14308 TTTGAAAGCCAAAATGAAAT
1 TTTGAAAAAAAAAAT-AAAT
14328 TTTGAAAAAAAAAA
1 TTTGAAAAAAAAAA
14342 CGATTTAGAG
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
19 12 0.46
20 14 0.54
ACGTcount: A:0.58, C:0.04, G:0.11, T:0.26
Consensus pattern (19 bp):
TTTGAAAAAAAAAATAAAT
Found at i:15479 original size:21 final size:22
Alignment explanation
Indices: 15453--15498 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
15443 AAACAATTGG
15453 TAACAATTGATATCATTTT-AT
1 TAACAATTGATATCATTTTCAT
* *
15474 TAACAATTGGTATCTTTTTCAT
1 TAACAATTGATATCATTTTCAT
15496 TAA
1 TAA
15499 ACATTTTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.35, C:0.11, G:0.07, T:0.48
Consensus pattern (22 bp):
TAACAATTGATATCATTTTCAT
Found at i:33575 original size:51 final size:50
Alignment explanation
Indices: 33448--33584 Score: 125
Period size: 51 Copynumber: 2.7 Consensus size: 50
33438 CTGTACCGCG
* ** * * *
33448 CTATACCCCACGTGTCAGATAAA-CAGCTATAGCGCGGAACAGGGGGCGCG
1 CTATA-CCCACGTGTAAGCCAAATCAGCTATAGCGCAGAACAGGAGGCGCA
** *
33498 CTATACCCACGTGTAAGCCATGTCAGCGTATAGCGCAGTACAGGAGGCGCA
1 CTATACCCACGTGTAAGCCAAATCAGC-TATAGCGCAGAACAGGAGGCGCA
* *
33549 CTATACCC-CATGTGACGCCAAATCAGCATATAGCGC
1 CTATACCCACGTGT-AAGCCAAATCAGC-TATAGCGC
33585 GGGGCAAGGA
Statistics
Matches: 70, Mismatches: 14, Indels: 5
0.79 0.16 0.06
Matches are distributed among these distances:
49 12 0.17
50 13 0.19
51 45 0.64
ACGTcount: A:0.28, C:0.29, G:0.26, T:0.17
Consensus pattern (50 bp):
CTATACCCACGTGTAAGCCAAATCAGCTATAGCGCAGAACAGGAGGCGCA
Found at i:35215 original size:43 final size:43
Alignment explanation
Indices: 35132--35472 Score: 280
Period size: 43 Copynumber: 8.0 Consensus size: 43
35122 AATAAAAACG
* * * *
35132 CCGCAAAAAGTCAAGATCTATAGCGGCGGTTTT-GAAACAAAGA
1 CCGCAAAAGGTC-AGATCTATAGCGACGTTTTTGGATACAAAGA
* * * * *
35175 CCACAAAAGATTAGATTTATACCGACGTTTTTGGATACAAACG-
1 CCGCAAAAGGTCAGATCTATAGCGACGTTTTTGGATACAAA-GA
* * *
35218 CCGCTAAAGGTCAAGATCTATAGCGACGTTTTTTG-TACATACG-
1 CCGCAAAAGGTC-AGATCTATAGCGACGTTTTTGGATACA-AAGA
* * *
35261 CCGCAAAAGGTCAAATCTATAGCGATGTTTTTGGATACAAACA
1 CCGCAAAAGGTCAGATCTATAGCGACGTTTTTGGATACAAAGA
* * *
35304 CCGCAAAAGGTCAGACCTATAGCGATGTTTTTGGA-ACAAACA
1 CCGCAAAAGGTCAGATCTATAGCGACGTTTTTGGATACAAAGA
* ** *
35346 CCGCAAAAGATCAGATCTATAGCGACGTTTTTAAATACAAAAA
1 CCGCAAAAGGTCAGATCTATAGCGACGTTTTTGGATACAAAGA
* * * * **
35389 CCACAAAAGGTCAAATCTATAGCGGCATTTTTTTATACAAACG-
1 CCGCAAAAGGTCAGATCTATAGCGACGTTTTTGGATACAAA-GA
* * * * * * *
35432 CCGCAAAAAGTTATATCTATAACGGCATTTTTTGATACAAA
1 CCGCAAAAGGTCAGATCTATAGCGACGTTTTTGGATACAAA
35473 CGCCGCTAAT
Statistics
Matches: 245, Mismatches: 45, Indels: 16
0.80 0.15 0.05
Matches are distributed among these distances:
42 73 0.30
43 151 0.62
44 21 0.09
ACGTcount: A:0.37, C:0.19, G:0.18, T:0.26
Consensus pattern (43 bp):
CCGCAAAAGGTCAGATCTATAGCGACGTTTTTGGATACAAAGA
Found at i:35268 original size:86 final size:86
Alignment explanation
Indices: 35127--35478 Score: 345
Period size: 86 Copynumber: 4.1 Consensus size: 86
35117 TCTAAAATAA
* * * * *
35127 AAACGCCGCAAAAAGTCAAGATCTATAGCGGCG-GTTTTGAAACAAA-GACCACAAAAGATTAGA
1 AAACGCCGCAAAAGGTCAAGATCTATAGCGACGTTTTTTG-AACAAACG-CCGCAAAAGATCAGA
* *
35190 TTTATACCGACGTTTTTGGATAC
64 TCTATAGCGACGTTTTTGGATAC
* * * * *
35213 AAACGCCGCTAAAGGTCAAGATCTATAGCGACGTTTTTTGTACATACGCCGCAAAAGGTCAAATC
1 AAACGCCGCAAAAGGTCAAGATCTATAGCGACGTTTTTTGAACAAACGCCGCAAAAGATCAGATC
*
35278 TATAGCGATGTTTTTGGATAC
66 TATAGCGACGTTTTTGGATAC
* * * * *
35299 AAACACCGCAAAAGGTC-AGACCTATAGCGATGTTTTTGGAACAAACACCGCAAAAGATCAGATC
1 AAACGCCGCAAAAGGTCAAGATCTATAGCGACGTTTTTTGAACAAACGCCGCAAAAGATCAGATC
**
35363 TATAGCGACGTTTTTAAATAC
66 TATAGCGACGTTTTTGGATAC
** * * * * * *
35384 AAAAACCACAAAAGGTCAA-ATCTATAGCGGCATTTTTTTATACAAACGCCGCAAAA-AGTTATA
1 AAACGCCGCAAAAGGTCAAGATCTATAGCGACGTTTTTTGA-ACAAACGCCGCAAAAGA-TCAGA
* * * *
35447 TCTATAACGGCATTTTTTGATAC
64 TCTATAGCGACGTTTTTGGATAC
35470 AAACGCCGC
1 AAACGCCGC
35479 TAATTAGCAT
Statistics
Matches: 216, Mismatches: 45, Indels: 10
0.80 0.17 0.04
Matches are distributed among these distances:
85 88 0.41
86 122 0.56
87 6 0.03
ACGTcount: A:0.37, C:0.20, G:0.18, T:0.25
Consensus pattern (86 bp):
AAACGCCGCAAAAGGTCAAGATCTATAGCGACGTTTTTTGAACAAACGCCGCAAAAGATCAGATC
TATAGCGACGTTTTTGGATAC
Found at i:35397 original size:128 final size:129
Alignment explanation
Indices: 35135--35439 Score: 332
Period size: 128 Copynumber: 2.4 Consensus size: 129
35125 AAAAACGCCG
* ** * * * * * **
35135 CAAAAAGTCAAGATCTATAGCGGC-GGTTTTGAAACAAAGACCACAAAAGATTAGATTTATACCG
1 CAAAAGGTCAA-ATCTATAGCGGCATTTTTTGATACAAACACCGCAAAAGGTCAGACCTATACCG
* * * ** * ** *
35199 ACGTTTTTGGATACAAACGCCGCTAAAGGTCAAGATCTATAGCGACGTTTTTTGTACATACGCCG
65 ACGTTTTTGGATACAAACACCGCAAAAGATCAAGATCTATAGCGACGTTTTTAATACAAAAACCA
*
35264 CAAAAGGTCAAATCTATAGC-G-ATGTTTTTGGATACAAACACCGCAAAAGGTCAGACCTATAGC
1 CAAAAGGTCAAATCTATAGCGGCAT-TTTTT-GATACAAACACCGCAAAAGGTCAGACCTATACC
*
35327 GATGTTTTTGGA-ACAAACACCGCAAAAGATC-AGATCTATAGCGACGTTTTTAAATACAAAAAC
64 GACGTTTTTGGATACAAACACCGCAAAAGATCAAGATCTATAGCGACGTTTTT-AATACAAAAAC
35390 CA
128 CA
* *
35392 CAAAAGGTCAAATCTATAGCGGCATTTTTTTATACAAACGCCGCAAAA
1 CAAAAGGTCAAATCTATAGCGGCATTTTTTGATACAAACACCGCAAAA
35440 AGTTATATCT
Statistics
Matches: 147, Mismatches: 23, Indels: 13
0.80 0.13 0.07
Matches are distributed among these distances:
127 21 0.14
128 72 0.49
129 52 0.35
130 2 0.01
ACGTcount: A:0.38, C:0.20, G:0.18, T:0.25
Consensus pattern (129 bp):
CAAAAGGTCAAATCTATAGCGGCATTTTTTGATACAAACACCGCAAAAGGTCAGACCTATACCGA
CGTTTTTGGATACAAACACCGCAAAAGATCAAGATCTATAGCGACGTTTTTAATACAAAAACCA
Found at i:35435 original size:171 final size:172
Alignment explanation
Indices: 35127--35478 Score: 415
Period size: 171 Copynumber: 2.1 Consensus size: 172
35117 TCTAAAATAA
* * * * *
35127 AAACGCCGCAAAAAGTCAAGATCTATAGCGGCGGTTTTGAAACAAAGACCACAAAAGATTAGATT
1 AAACGCCGCAAAAAGTCAAGACCTATAGCGACGGTTTTGAAACAAACACCACAAAAGATCAGATC
** ** * * *
35192 TATACCGACGTTTTTGGATACAAACGCCGCTAAAGGTCAAGATCTATAGCGACGTTTTTTGTACA
66 TATACCGACGTTTTTAAATACAAAAACCACAAAAGGTCAAGATCTATAGCGACGTTTTTTATACA
* * *
35257 TACGCCGCAAAAGGTCAAATCTATAGC-G-ATGTTTTTGGATAC
131 AACGCCGCAAAAAGTCAAATCTATAACGGCAT-TTTTT-GATAC
* * * * * *
35299 AAACACCGCAAAAGGTC-AGACCTATAGCGATGTTTTTGGAACAAACACCGCAAAAGATCAGATC
1 AAACGCCGCAAAAAGTCAAGACCTATAGCGACGGTTTTGAAACAAACACCACAAAAGATCAGATC
* * *
35363 TATAGCGACGTTTTTAAATACAAAAACCACAAAAGGTCAA-ATCTATAGCGGCATTTTTTTATAC
66 TATACCGACGTTTTTAAATACAAAAACCACAAAAGGTCAAGATCTATAGCGAC-GTTTTTTATAC
* *
35427 AAACGCCGCAAAAAGTTATATCTATAACGGCATTTTTTGATAC
130 AAACGCCGCAAAAAGTCAAATCTATAACGGCATTTTTTGATAC
35470 AAACGCCGC
1 AAACGCCGC
35479 TAATTAGCAT
Statistics
Matches: 150, Mismatches: 27, Indels: 7
0.82 0.15 0.04
Matches are distributed among these distances:
170 11 0.07
171 116 0.77
172 21 0.14
173 2 0.01
ACGTcount: A:0.37, C:0.20, G:0.18, T:0.25
Consensus pattern (172 bp):
AAACGCCGCAAAAAGTCAAGACCTATAGCGACGGTTTTGAAACAAACACCACAAAAGATCAGATC
TATACCGACGTTTTTAAATACAAAAACCACAAAAGGTCAAGATCTATAGCGACGTTTTTTATACA
AACGCCGCAAAAAGTCAAATCTATAACGGCATTTTTTGATAC
Found at i:35452 original size:128 final size:129
Alignment explanation
Indices: 35192--35478 Score: 321
Period size: 128 Copynumber: 2.2 Consensus size: 129
35182 AGATTAGATT
* * * **
35192 TATACCGACGTTTTTGGATACAAACGCCGCTAAAGGTCAAGATCTATAGCGACGTTTTTTGTACA
1 TATACCGACGTTTTTGGATACAAACACCGCAAAAGATCAAGATCTATAGCGACGTTTTTAATACA
* ** * *
35257 TACGCCGCAAAAGGTCAAATCTATAGCGATGTTTTTGGATACAAACACCGCAAAAGGTCAGACC
66 AAAACCACAAAAGGTCAAATCTATAGCGATGTTTTTGGATACAAACACCGCAAAAAGTCAGACC
* *
35321 TATAGCGATGTTTTTGGA-ACAAACACCGCAAAAGATC-AGATCTATAGCGACGTTTTTAAATAC
1 TATACCGACGTTTTTGGATACAAACACCGCAAAAGATCAAGATCTATAGCGACGTTTTT-AATAC
* * * *
35384 AAAAACCACAAAAGGTCAAATCTATAGCGGCAT-TTTTT-TATACAAACGCCGCAAAAAGTTATA
65 AAAAACCACAAAAGGTCAAATCTATAGC-G-ATGTTTTTGGATACAAACACCGCAAAAAGTCAGA
*
35447 TC
128 CC
* * * * *
35449 TATAACGGCATTTTTTGATACAAACGCCGC
1 TATACCGACGTTTTTGGATACAAACACCGC
35479 TAATTAGCAT
Statistics
Matches: 131, Mismatches: 23, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
127 20 0.15
128 77 0.59
129 32 0.24
130 2 0.02
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.26
Consensus pattern (129 bp):
TATACCGACGTTTTTGGATACAAACACCGCAAAAGATCAAGATCTATAGCGACGTTTTTAATACA
AAAACCACAAAAGGTCAAATCTATAGCGATGTTTTTGGATACAAACACCGCAAAAAGTCAGACC
Found at i:36509 original size:3 final size:3
Alignment explanation
Indices: 36501--36538 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
36491 GACATCAGAA
36501 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
36539 ATCACCATTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:39304 original size:81 final size:82
Alignment explanation
Indices: 39169--39324 Score: 217
Period size: 81 Copynumber: 1.9 Consensus size: 82
39159 AATTCAAACA
* *
39169 ATTGCGGCGTTTATTGAAAAAAACCACTATAGGTAAACACTATTACGGCGTTTGTAT-AAAACGC
1 ATTGCGGCGTTTATTGAAAAAAACCACTATAAGTAAACACTATTACAGCGTTTGTATAAAAACGC
39233 CGCTAAAGTTCTATTTT
66 CGCTAAAGTTCTATTTT
* * * * * *
39250 ATTGCGGTGTTTATTGAAAAACA-CATGTATAAGTTAACCCTATTGCAGCGTTTGTATAAAAACG
1 ATTGCGGCGTTTATTGAAAAAAACCA-CTATAAGTAAACACTATTACAGCGTTTGTATAAAAACG
39314 CCGCTAAAGTT
65 CCGCTAAAGTT
39325 GCCATTTTGT
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
80 2 0.03
81 46 0.71
82 17 0.26
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Consensus pattern (82 bp):
ATTGCGGCGTTTATTGAAAAAAACCACTATAAGTAAACACTATTACAGCGTTTGTATAAAAACGC
CGCTAAAGTTCTATTTT
Found at i:42888 original size:156 final size:154
Alignment explanation
Indices: 42728--43051 Score: 503
Period size: 156 Copynumber: 2.1 Consensus size: 154
42718 TTCCATATTA
*
42728 TATTATATATAT-ATTTTTCTTCTCACC-TTTTTTCTTCATAGGTCCCCTCCCTTTTTTTTGTCT
1 TATTATATATATAATTTTTC-TCTCACCTTTTTTTCTTCATAGG-CCCCTCCCCTTTTTTTGTCT
* * *
42791 CCACCCAAATTTAATCATTCTTTCGGTGCATTAATTATAGTAG-GCTAAGTTTTATTTTTTTATT
64 CCACCCAAATTTAATCATT-TTT-AGTGCATTAATAATAGTAGAG-TAAGTTTT-GTTTTTTATT
42855 A-TTTTTTTCTTCTTTATTATTATTATAGT
125 ACTTTTTTTCTTCTTTATTATTATTATAGT
*
42884 TATTATATATATAATTTTTCTCTCACCTTTTTTTCTTCCTAGGCCCCTCCCCTTTTTTTGTCTCC
1 TATTATATATATAATTTTTCTCTCACCTTTTTTTCTTCATAGGCCCCTCCCCTTTTTTTGTCTCC
42949 ACCCAAATTTAATCATTTTTAGTGCATTAATAATAGTAGAGTAAGTTTTGTTTTTTATTACTCTT
66 ACCCAAATTTAATCATTTTTAGTGCATTAATAATAGTAGAGTAAGTTTTGTTTTTTATTA--CTT
43014 TTTTTCTTCTTTATTATTATTATAGT
129 TTTTTCTTCTTTATTATTATTATAGT
43040 TATTATATATAT
1 TATTATATATAT
43052 TTTATTATTA
Statistics
Matches: 157, Mismatches: 5, Indels: 12
0.90 0.03 0.07
Matches are distributed among these distances:
153 10 0.06
154 25 0.16
155 4 0.03
156 97 0.62
157 21 0.13
ACGTcount: A:0.22, C:0.17, G:0.07, T:0.54
Consensus pattern (154 bp):
TATTATATATATAATTTTTCTCTCACCTTTTTTTCTTCATAGGCCCCTCCCCTTTTTTTGTCTCC
ACCCAAATTTAATCATTTTTAGTGCATTAATAATAGTAGAGTAAGTTTTGTTTTTTATTACTTTT
TTTCTTCTTTATTATTATTATAGT
Found at i:42905 original size:154 final size:154
Alignment explanation
Indices: 42689--43051 Score: 494
Period size: 156 Copynumber: 2.3 Consensus size: 154
42679 TATATGTATA
*
42689 TATTTTCTT-TTATTTTTTTACTTACTTTATTCCA-TATTATA-TTA-TATATATAT-TTTTCT-
1 TATTTTTTTATTATTTTTTT-CTT-CTTTATT--ATTATTATAGTTATTATATATATATTTTCTC
*
42748 TCTCACC-TTTTTTCTTCATAGGTCCCCTCCCTTTTTTTTGTCTCCACCCAAATTTAATCATTCT
62 TCTCACCTTTTTTTCTTCATAGG-CCCCTCCCCTTTTTTTGTCTCCACCCAAATTTAATCATT-T
* *
42812 TTCGGTGCATTAATTATAGTAG-GCTAAGTTT
125 TT-AGTGCATTAATAATAGTAGAG-TAAGTTT
42843 TATTTTTTTATTATTTTTTTCTTCTTTATTATTATTATAGTTATTATATATATAATTTT-TCTCT
1 TATTTTTTTATTATTTTTTTCTTCTTTATTATTATTATAGTTATTATATATAT-ATTTTCTCTCT
*
42907 CACCTTTTTTTCTTCCTAGGCCCCTCCCCTTTTTTTGTCTCCACCCAAATTTAATCATTTTTAGT
65 CACCTTTTTTTCTTCATAGGCCCCTCCCCTTTTTTTGTCTCCACCCAAATTTAATCATTTTTAGT
42972 GCATTAATAATAGTAGAGTAAGTTT
130 GCATTAATAATAGTAGAGTAAGTTT
*
42997 T-GTTTTTTATTACTCTTTTTTTCTTCTTTATTATTATTATAGTTATTATATATAT
1 TATTTTTTTATTA---TTTTTTTCTTCTTTATTATTATTATAGTTATTATATATAT
43052 TTTATTATTA
Statistics
Matches: 191, Mismatches: 6, Indels: 22
0.87 0.03 0.10
Matches are distributed among these distances:
151 1 0.01
152 7 0.04
153 20 0.10
154 45 0.24
155 15 0.08
156 89 0.47
157 14 0.07
ACGTcount: A:0.22, C:0.17, G:0.06, T:0.56
Consensus pattern (154 bp):
TATTTTTTTATTATTTTTTTCTTCTTTATTATTATTATAGTTATTATATATATATTTTCTCTCTC
ACCTTTTTTTCTTCATAGGCCCCTCCCCTTTTTTTGTCTCCACCCAAATTTAATCATTTTTAGTG
CATTAATAATAGTAGAGTAAGTTT
Found at i:43030 original size:3 final size:3
Alignment explanation
Indices: 43024--43079 Score: 64
Period size: 3 Copynumber: 18.7 Consensus size: 3
43014 TTTTTCTTCT
43024 TTA TTA TTA TTA -TA GTTA TTA -TA TATA TT- TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA -TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA
43068 TTA TTA TATA TT
1 TTA TTA T-TA TT
43080 CTTTATACTT
Statistics
Matches: 47, Mismatches: 0, Indels: 12
0.80 0.00 0.20
Matches are distributed among these distances:
2 6 0.13
3 33 0.70
4 8 0.17
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:43084 original size:29 final size:29
Alignment explanation
Indices: 43020--43085 Score: 100
Period size: 29 Copynumber: 2.3 Consensus size: 29
43010 TCTTTTTTTC
43020 TTCTTTATTATTATTATAGTTATTATATA
1 TTCTTTATTATTATTATAGTTATTATATA
43049 TAT-TTTATTATTATTATTA-TTATTATATA
1 T-TCTTTATTATTATTA-TAGTTATTATATA
43078 TTCTTTAT
1 TTCTTTAT
43086 ACTTTTTCCT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
28 1 0.03
29 30 0.88
30 3 0.09
ACGTcount: A:0.30, C:0.03, G:0.02, T:0.65
Consensus pattern (29 bp):
TTCTTTATTATTATTATAGTTATTATATA
Found at i:43199 original size:33 final size:31
Alignment explanation
Indices: 43141--43202 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 31
43131 ATTCACTTAC
* * *
43141 TTATTTTTTTTATTTTGTTTTTTATATATTT
1 TTATTTTTTTTATCTTGATTATTATATATTT
43172 TTATTTATTTTTATCTTGCATTATTATATAT
1 TTATTT-TTTTTATCTTG-ATTATTATATAT
43203 GCGTCATTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 6 0.23
32 10 0.38
33 10 0.38
ACGTcount: A:0.21, C:0.03, G:0.03, T:0.73
Consensus pattern (31 bp):
TTATTTTTTTTATCTTGATTATTATATATTT
Found at i:43288 original size:29 final size:29
Alignment explanation
Indices: 43217--43344 Score: 118
Period size: 29 Copynumber: 4.4 Consensus size: 29
43207 CATTATTGTC
* *
43217 TTTATTTTATTTATTTATTTATTA-TTAT
1 TTTATTTTATTTTTTTATTTTTTATTTAT
*
43245 TTT-TTTTACCCTTTTTTATTTTTTATTTAT
1 TTTATTTTA--TTTTTTTATTTTTTATTTAT
* * *
43275 TTTATTTTATTTTTTTATTCTTTGTTTCT
1 TTTATTTTATTTTTTTATTTTTTATTTAT
** *
43304 TTTGCTTTATTTTATTTGTTTTTTATTT-T
1 TTTATTTTATTTT-TTTATTTTTTATTTAT
43333 CTTTATTTTATT
1 -TTTATTTTATT
43345 CATTTTCACT
Statistics
Matches: 80, Mismatches: 14, Indels: 10
0.77 0.13 0.10
Matches are distributed among these distances:
27 5 0.06
28 3 0.04
29 40 0.50
30 27 0.34
31 5 0.06
ACGTcount: A:0.15, C:0.05, G:0.02, T:0.77
Consensus pattern (29 bp):
TTTATTTTATTTTTTTATTTTTTATTTAT
Found at i:43342 original size:25 final size:25
Alignment explanation
Indices: 43259--43350 Score: 91
Period size: 25 Copynumber: 3.7 Consensus size: 25
43249 TTTACCCTTT
* *
43259 TTTATTTT-TTATTTATTTTATTTTA
1 TTTATTTTATTCTTT-TTTTATTTTC
* *
43284 TTT-TTTTATTCTTTGTTTCTTTTGC
1 TTTATTTTATTCTTTTTTTATTTT-C
43309 TTTATTTTATT-TGTTTTTTATTTTC
1 TTTATTTTATTCT-TTTTTTATTTTC
*
43334 TTTATTTTATTCATTTT
1 TTTATTTTATTCTTTTT
43351 CACTTTTTTC
Statistics
Matches: 55, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
24 11 0.20
25 28 0.51
26 16 0.29
ACGTcount: A:0.13, C:0.05, G:0.03, T:0.78
Consensus pattern (25 bp):
TTTATTTTATTCTTTTTTTATTTTC
Found at i:44360 original size:15 final size:16
Alignment explanation
Indices: 44340--44381 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
44330 GGATTCTAAG
44340 CATGT-GGGTAGATAT
1 CATGTAGGGTAGATAT
*
44355 CATGTGGGGTAGATAT
1 CATGTAGGGTAGATAT
44371 CATGTAGGGTA
1 CATGTAGGGTA
44382 AGACTTTTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 5 0.20
16 20 0.80
ACGTcount: A:0.26, C:0.07, G:0.36, T:0.31
Consensus pattern (16 bp):
CATGTAGGGTAGATAT
Found at i:46118 original size:95 final size:95
Alignment explanation
Indices: 45992--46192 Score: 303
Period size: 95 Copynumber: 2.1 Consensus size: 95
45982 AGATTATGAT
* * *
45992 ATTATATATATACAATAAAGCTTGAACTGTCCCTCTAAAGCAATTGGTTAAACATCCAAACTTTA
1 ATTATA-ATATACAATAAAACTTGAACTGTCCCCCTAAAGCAATTGGTTAAACACCCAAACTTTA
46057 TGGATAATATTCAGCTAGCCTGATAAAGGTG
65 TGGATAATATTCAGCTAGCCTGATAAAGGTG
** * * ***
46088 ATTATAATATACAATAAAACTTGAGTTGTCCCCCTAGAGCAATTGGTTAAACGCCCCGGCTTTAT
1 ATTATAATATACAATAAAACTTGAACTGTCCCCCTAAAGCAATTGGTTAAACACCCAAACTTTAT
46153 GGATAATATTCAGCTAGCCTGATAAAGGTG
66 GGATAATATTCAGCTAGCCTGATAAAGGTG
46183 ATTATAATAT
1 ATTATAATAT
46193 CTATACAATG
Statistics
Matches: 95, Mismatches: 10, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
95 89 0.94
96 6 0.06
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31
Consensus pattern (95 bp):
ATTATAATATACAATAAAACTTGAACTGTCCCCCTAAAGCAATTGGTTAAACACCCAAACTTTAT
GGATAATATTCAGCTAGCCTGATAAAGGTG
Found at i:47244 original size:64 final size:64
Alignment explanation
Indices: 47104--47397 Score: 328
Period size: 64 Copynumber: 4.7 Consensus size: 64
47094 TTTTTGCAGC
* * ** * * **
47104 TTCAGAGCCAATTTCAATTTCACAGTGAAGGATACT-AGACTCAA-AAATAACTTTCCAACTT--
1 TTCAGAGTCAATTTCAACTTCACAACGAAGGATATTGA-ACTCAACAAACAACTTTCCAGTTTCA
* * *
47165 TT-AGAGTCAATTTCAACTTCATAACAAAGGATATTGGACTCAACAAACAACTTTCCAGTTTCA
1 TTCAGAGTCAATTTCAACTTCACAACGAAGGATATTGAACTCAACAAACAACTTTCCAGTTTCA
* * * * *
47228 GTCAGAGTCAATTTCAACTTCATATCGAAGGATATTGAACTCAACAAATAACTTTTCAGTTTCA
1 TTCAGAGTCAATTTCAACTTCACAACGAAGGATATTGAACTCAACAAACAACTTTCCAGTTTCA
* * * ** * *
47292 TTCAGAGTCAATTTGAACCTCACAACGAAGGATATTGGACTCAACAAACATTTTTCTAATTTCA
1 TTCAGAGTCAATTTCAACTTCACAACGAAGGATATTGAACTCAACAAACAACTTTCCAGTTTCA
*
47356 TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGAACTC
1 TTCAGAGTCAATTTCAACTTCACAACGAAGGATATTGAACTC
47398 GAAGCGACAC
Statistics
Matches: 195, Mismatches: 33, Indels: 7
0.83 0.14 0.03
Matches are distributed among these distances:
60 32 0.16
61 16 0.08
63 1 0.01
64 146 0.75
ACGTcount: A:0.36, C:0.20, G:0.13, T:0.31
Consensus pattern (64 bp):
TTCAGAGTCAATTTCAACTTCACAACGAAGGATATTGAACTCAACAAACAACTTTCCAGTTTCA
Found at i:47336 original size:128 final size:124
Alignment explanation
Indices: 47105--47397 Score: 365
Period size: 128 Copynumber: 2.3 Consensus size: 124
47095 TTTTGCAGCT
* * *
47105 TCAGAGCCAATTTCAATTTCACAGT-GAAGGATACT-AGACTCAAAAATAACTTTCCAACTTTTA
1 TCAGAGTCAATTTCAACTTCACA-TCGAAGGATATTGA-ACTCAAAAATAACTTTCCAACTTTTA
* * *
47168 GAGTCAATTTCAACTTCATAACAAAGGATATTGGACTCAACAAACAACTTTCCAGTTTCAG
64 GAGTCAATTTCAACCTCACAACAAAGGATATTGGACTCAACAAACAACTTTCCAATTTCAG
* * **
47229 TCAGAGTCAATTTCAACTTCATATCGAAGGATATTGAACTCAACAAATAACTTTTCAGTTTCATT
1 TCAGAGTCAATTTCAACTTCACATCGAAGGATATTGAACTCAA-AAATAACTTTCCAACTT--TT
* * ** * *
47294 CAGAGTCAATTTGAACCTCACAACGAAGGATATTGGACTCAACAAACATTTTTCTAATTTCAT
63 -AGAGTCAATTTCAACCTCACAACAAAGGATATTGGACTCAACAAACAACTTTCCAATTTCAG
*
47357 TCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGAACTC
1 TCAGAGTCAATTTCAACTTCACATCGAAGGATATTGAACTC
47398 GAAGCGACAC
Statistics
Matches: 145, Mismatches: 18, Indels: 8
0.85 0.11 0.05
Matches are distributed among these distances:
123 1 0.01
124 35 0.24
125 15 0.10
127 2 0.01
128 92 0.63
ACGTcount: A:0.37, C:0.20, G:0.13, T:0.30
Consensus pattern (124 bp):
TCAGAGTCAATTTCAACTTCACATCGAAGGATATTGAACTCAAAAATAACTTTCCAACTTTTAGA
GTCAATTTCAACCTCACAACAAAGGATATTGGACTCAACAAACAACTTTCCAATTTCAG
Found at i:47643 original size:121 final size:121
Alignment explanation
Indices: 47474--48112 Score: 714
Period size: 120 Copynumber: 5.3 Consensus size: 121
47464 ATTTGGTAAA
* * *
47474 ACAACCATTGGATTTCAACTTTACGACGAATGATATCCAATTCCAGGCTCAACTTCACAACGAAG
1 ACAACCCTTGGATTTCAACTTCACGACGAAGGATATCCAATTCCAGGCTCAACTTCACAACGAAG
* *
47539 GGGCCATCCACGATTTCAACTTCATGACGAAGGATATCGTGCTCACAATCAGCAAT
66 GGGCCATCCACGATTTCAACTTCACGACGAAGGATATCGTGCTCACAAGCAGCAAT
* * ** * *
47595 GCAACCCTTGGATTTCAACTTCACGACGAAGGATATCTAATTTAAGGCTCAACTTCACGATGAAG
1 ACAACCCTTGGATTTCAACTTCACGACGAAGGATATCCAATTCCAGGCTCAACTTCACAACGAAG
* * * * * * * *
47660 GGACCATCAATGATTTCAACTTCACGA-TAATGGATATTGTGTTCACAACCA-CCAT
66 GGGCCATCCACGATTTCAACTTCACGACGAA-GGATATCGTGCTCACAAGCAGCAAT
** * * * *
47715 ACAATACTTGGATTTAAACTTAACAACGAAGGATATCCAATTCCAGGCTCAACTTCACAACGAAA
1 ACAACCCTTGGATTTCAACTTCACGACGAAGGATATCCAATTCCAGGCTCAACTTCACAACGAAG
* ** * * *
47780 GAGTAATCCCCGATTTTAACTTCACGACGAAGGATATCGTGCCCACAAGCAGCAAT
66 GGGCCATCCACGATTTCAACTTCACGACGAAGGATATCGTGCTCACAAGCAGCAAT
* * ** ** * * *
47836 ACAACCCTTGCATGTCAACTTCACGATAAAGGATATCCAATTTAAGGTTCAACTTCACGACGAAT
1 ACAACCCTTGGATTTCAACTTCACGACGAAGGATATCCAATTCCAGGCTCAACTTCACAACGAAG
* * *
47901 GGGCCATCCACGATTTCAACTTCACGACGAAGGATATCGTGTTCACCAGCA-CCAT
66 GGGCCATCCACGATTTCAACTTCACGACGAAGGATATCGTGCTCACAAGCAGCAAT
** * *
47956 ACAATACTTGGATTTCAACTTCACGACGAAGGATATCCAATTCCAGGCTCAATTTCACAACGAAT
1 ACAACCCTTGGATTTCAACTTCACGACGAAGGATATCCAATTCCAGGCTCAACTTCACAACGAAG
* * *
48021 GGGTCATCCACGATTTCAACTTCACGACGAAGGGA-ATCGTGCCCACAAGAAGCAAT
66 GGGCCATCCACGATTTCAACTTCACGACGAA-GGATATCGTGCTCACAAGCAGCAAT
* * * * *
48077 GTC-ATCCAT-GATTTCAACTTCAAGACGAATGATATC
1 -ACAACCCTTGGATTTCAACTTCACGACGAAGGATATC
48113 GTGTTCATTT
Statistics
Matches: 423, Mismatches: 89, Indels: 13
0.81 0.17 0.02
Matches are distributed among these distances:
120 217 0.51
121 205 0.48
122 1 0.00
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.24
Consensus pattern (121 bp):
ACAACCCTTGGATTTCAACTTCACGACGAAGGATATCCAATTCCAGGCTCAACTTCACAACGAAG
GGGCCATCCACGATTTCAACTTCACGACGAAGGATATCGTGCTCACAAGCAGCAAT
Found at i:47760 original size:241 final size:241
Alignment explanation
Indices: 47481--48112 Score: 878
Period size: 241 Copynumber: 2.6 Consensus size: 241
47471 AAAACAACCA
* * * *
47481 TTGGATTTCAACTTTACGACGAATGATATCCAATTCCAGGCTCAACTTCACAACGAAGGGGCCAT
1 TTGGATTTCAACTTAACGACGAAGGATATCCAATTCCAGGCTCAACTTCACAACGAAAGGGTCAT
* * *
47546 CCACGATTTCAACTTCATGACGAAGGATATCGTGCTCACAATCAGCAATGCAACCCTTGGATTTC
66 CCACGATTTCAACTTCACGACGAAGGATATCGTGCCCACAAGCAGCAATGCAACCCTTGGATTTC
* * *
47611 AACTTCACGACGAAGGATATCTAATTTAAGGCTCAACTTCACGATGAA-GGGACCATCAATGATT
131 AACTTCACGACGAAGGATATCCAATTTAAGGCTCAACTTCACGACGAATGGG-CCATCAACGATT
* *
47675 TCAACTTCACGA-TAATGGATATTGTGTTCACAACCACCATACAATAC
195 TCAACTTCACGACGAA-GGATATCGTGTTCACAACCACCATACAATAC
* * * *
47722 TTGGATTTAAACTTAACAACGAAGGATATCCAATTCCAGGCTCAACTTCACAACGAAAGAGTAAT
1 TTGGATTTCAACTTAACGACGAAGGATATCCAATTCCAGGCTCAACTTCACAACGAAAGGGTCAT
* * * * *
47787 CCCCGATTTTAACTTCACGACGAAGGATATCGTGCCCACAAGCAGCAATACAACCCTTGCATGTC
66 CCACGATTTCAACTTCACGACGAAGGATATCGTGCCCACAAGCAGCAATGCAACCCTTGGATTTC
** * *
47852 AACTTCACGATAAAGGATATCCAATTTAAGGTTCAACTTCACGACGAATGGGCCATCCACGATTT
131 AACTTCACGACGAAGGATATCCAATTTAAGGCTCAACTTCACGACGAATGGGCCATCAACGATTT
* *
47917 CAACTTCACGACGAAGGATATCGTGTTCACCAGCACCATACAATAC
196 CAACTTCACGACGAAGGATATCGTGTTCACAACCACCATACAATAC
* * *
47963 TTGGATTTCAACTTCACGACGAAGGATATCCAATTCCAGGCTCAATTTCACAACGAATGGGTCAT
1 TTGGATTTCAACTTAACGACGAAGGATATCCAATTCCAGGCTCAACTTCACAACGAAAGGGTCAT
* * *
48028 CCACGATTTCAACTTCACGACGAAGGGA-ATCGTGCCCACAAGAAGCAATGTC-ATCCAT-GATT
66 CCACGATTTCAACTTCACGACGAA-GGATATCGTGCCCACAAGCAGCAATG-CAACCCTTGGATT
* *
48090 TCAACTTCAAGACGAATGATATC
129 TCAACTTCACGACGAAGGATATC
48113 GTGTTCATTT
Statistics
Matches: 341, Mismatches: 46, Indels: 9
0.86 0.12 0.02
Matches are distributed among these distances:
240 21 0.06
241 311 0.91
242 9 0.03
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (241 bp):
TTGGATTTCAACTTAACGACGAAGGATATCCAATTCCAGGCTCAACTTCACAACGAAAGGGTCAT
CCACGATTTCAACTTCACGACGAAGGATATCGTGCCCACAAGCAGCAATGCAACCCTTGGATTTC
AACTTCACGACGAAGGATATCCAATTTAAGGCTCAACTTCACGACGAATGGGCCATCAACGATTT
CAACTTCACGACGAAGGATATCGTGTTCACAACCACCATACAATAC
Found at i:48258 original size:84 final size:84
Alignment explanation
Indices: 48117--49378 Score: 1184
Period size: 84 Copynumber: 15.0 Consensus size: 84
48107 GATATCGTGT
* * * *
48117 TCATTTACAACATAACTCAAGGCT-AGAAGGGTTATTTGCCAACAAAAGAACTTCGAGTTCAACT
1 TCATTTGCAACATAGCTCAAGG-TAAGAAGGGTTATTTGCCAACAAAAGACCTTCGAGTTCGACT
48181 ACACTCAGCTCAAAGG-AGCA
65 ACACTCAGCTCAAAGGCA-CA
* * * * *
48201 TCATTTTCAACATAGCTCAAGGTAACAAGGGCTATTTTCCAACAAAAGACCATCGAGTTCGACTA
1 TCATTTGCAACATAGCTCAAGGTAAGAAGGGTTATTTGCCAACAAAAGACCTTCGAGTTCGACTA
* *
48266 CACTTAGTTTC-AAGGCACA
66 CACTCAG-CTCAAAGGCACA
* * * *
48285 TCATTTGCAACATAGCTCAAGGCAAGAAGGGCTATTTGCCAAAAAAAGACCTTCGCGTTCGACTA
1 TCATTTGCAACATAGCTCAAGGTAAGAAGGGTTATTTGCCAACAAAAGACCTTCGAGTTCGACTA
** * *
48350 TGCTCAGCTCTAAGGAACA
66 CACTCAGCTCAAAGGCACA
* * * * * * *
48369 TCATTTACAACATAACTCAA-GTCTAGAAAGGTTATCTGCCAACAAAATACCTTCGAGTTTGACT
1 TCATTTGCAACATAGCTCAAGGT-AAGAAGGGTTATTTGCCAACAAAAGACCTTCGAGTTCGACT
* * *
48433 GCGCTCAGCTCTAAGGCACA
65 ACACTCAGCTCAAAGGCACA
* * * * *
48453 TTATTTGCAACATAGCTCAAGGCAAGAAGGGATATTTGCCAAAAAAATACCTTCGAGTTCGACTA
1 TCATTTGCAACATAGCTCAAGGTAAGAAGGGTTATTTGCCAACAAAAGACCTTCGAGTTCGACTA
* * *
48518 CTCTCAGCTCCAAGACACA
66 CACTCAGCTCAAAGGCACA
* * * * * *
48537 TCATTTGCAGCTTAGCTCAAGGTAAGAAGGGCTATATGCCAA-TAATGACCTTCGAGTTCGACTA
1 TCATTTGCAACATAGCTCAAGGTAAGAAGGGTTATTTGCCAACAAAAGACCTTCGAGTTCGACTA
*
48601 CACTCAGCTCTAA-GCACA
66 CACTCAGCTCAAAGGCACA
* * * * *
48619 TCATTTGTAGCATAACTCAAGGCT-AGAAGGGTTATCTACCAACAAAAGACCTTCGAGTTCGACT
1 TCATTTGCAACATAGCTCAAGG-TAAGAAGGGTTATTTGCCAACAAAAGACCTTCGAGTTCGACT
* * * *
48683 ACGCTTAGCTCCAATGCACA
65 ACACTCAGCTCAAAGGCACA
* ** * *
48703 TCATTTGCAACATAACTCAAGACAAGAA-GGTCTATTTGCTAACAAAAGACCTTCGAGTTCAACT
1 TCATTTGCAACATAGCTCAAGGTAAGAAGGGT-TATTTGCCAACAAAAGACCTTCGAGTTCGACT
** *
48767 ATGCTCAGCTCCAAGGCACA
65 ACACTCAGCTCAAAGGCACA
* * * ** * *
48787 TTATTTGCAACATAGCTCAAGGCACGGCGGGTTATTTGCCAACAAAATATCTTCGAGTTCGACTA
1 TCATTTGCAACATAGCTCAAGGTAAGAAGGGTTATTTGCCAACAAAAGACCTTCGAGTTCGACTA
* *
48852 CACTCAGCTCCAAGGCATA
66 CACTCAGCTCAAAGGCACA
* * * * * * * *
48871 TCATTTGCAGCATAACTCAAGGCT-AGAAGGGTTATCTGCCAATAATATACCTTTGAGTTCGATT
1 TCATTTGCAACATAGCTCAAGG-TAAGAAGGGTTATTTGCCAACAAAAGACCTTCGAGTTCGACT
*
48935 ACACTCAGCTCAAAGGTACAA
65 ACACTCAGCTCAAAGGCAC-A
** * * * * *
48956 T-ATTTG-AAGCATAGCTCAAGGCGAGAAGGGCTATCTGACAACAAAAGACCTTCGATTTTGACT
1 TCATTTGCAA-CATAGCTCAAGGTAAGAAGGGTTATTTGCCAACAAAAGACCTTCGAGTTCGACT
** * *
49019 ATGCTCAGTTCCAAGGCACA
65 ACACTCAGCTCAAAGGCACA
* * * * * * *
49039 TCATTTGTAGCATAACTCAAGGCT-AGAAGGGTTATCTACCAACAAAAGACCTTCGAGTTTGATT
1 TCATTTGCAACATAGCTCAAGG-TAAGAAGGGTTATTTGCCAACAAAAGACCTTCGAGTTCGACT
49103 ACACTCAGCTCAAAGGCACA
65 ACACTCAGCTCAAAGGCACA
* * ** * * *
49123 ACATTTGTAGTATAACTCAAGGCT-AGAAGGGTTATATGCCAACAAAAGACCTTCGAGTTCGATT
1 TCATTTGCAACATAGCTCAAGG-TAAGAAGGGTTATTTGCCAACAAAAGACCTTCGAGTTCGACT
*
49187 ACACTCAACTCAAAGGCACA
65 ACACTCAGCTCAAAGGCACA
* * * * * *
49207 TCATTTACAACATAGCTCAAGGTGAGAAGGGTTATATGCCAACAAAAGACCTTTGCGTTCGATTA
1 TCATTTGCAACATAGCTCAAGGTAAGAAGGGTTATTTGCCAACAAAAGACCTTCGAGTTCGACTA
* *
49272 GACTCAGCTCAAAGGCGCA
66 CACTCAGCTCAAAGGCACA
* * ** * * * * * *
49291 TCAAATTTGCAGCATAGCTCAAGGTGAGAAAAGCTATATGTCATC-AAAGACCTTAGAGTTCGAT
1 TC--ATTTGCAACATAGCTCAAGGTAAGAAGGGTTATTTGCCAACAAAAGACCTTCGAGTTCGAC
* *
49355 TACATTCAGCTCAAAGGCATA
64 TACACTCAGCTCAAAGGCACA
49376 TCA
1 TCA
49379 AATTTATAGC
Statistics
Matches: 984, Mismatches: 172, Indels: 45
0.82 0.14 0.04
Matches are distributed among these distances:
82 38 0.04
83 73 0.07
84 793 0.81
85 46 0.05
86 34 0.03
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.25
Consensus pattern (84 bp):
TCATTTGCAACATAGCTCAAGGTAAGAAGGGTTATTTGCCAACAAAAGACCTTCGAGTTCGACTA
CACTCAGCTCAAAGGCACA
Found at i:48566 original size:252 final size:251
Alignment explanation
Indices: 48117--49436 Score: 1396
Period size: 252 Copynumber: 5.2 Consensus size: 251
48107 GATATCGTGT
* * * * *
48117 TCATTTACAACATAACTCAAGGCTAGAAGGGTTATTTGCCAACAAAAGAACTTCGAGTTCAACTA
1 TCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTA
* * * *
48182 CACTCAGCTCAAAGG-AGCATCATTTTCAACATAGCTCAAGGTAACAAGGGCTATTTTCCAACAA
66 CACTCAGCTCAAAGGCA-CATCATTTGCAACATAGCTCAAGGCAAGAAGGGCTATTTGCCAACAA
* * * * * * *
48246 AAGACCATCGAGTTCGACTACACTTAGTTTCAAGGCACATCATTTGCAACATAGCTCAAGGCAAG
130 AAGACCTTCGAGTTCGACTA-TCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTCAAGGTAAG
* ** *
48311 AAGGGCTATTTGCCAAAAAAAGACCTTCGCGTTCGACTATGCTCAGCTCTAAGGAACA
194 AAGGGCTATTTGCCAAAAAAAGACCTTCGAGTTCGACTACACTCAGCTCTAAGGCACA
* * * * * * *
48369 TCATTTACAACATAACTCAAGTCTAGAAAGGTTATCTGCCAACAAAATACCTTCGAGTTTGACTG
1 TCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTA
* * * * *
48434 CGCTCAGCTCTAAGGCACATTATTTGCAACATAGCTCAAGGCAAGAAGGGATATTTGCCAAAAAA
66 CACTCAGCTCAAAGGCACATCATTTGCAACATAGCTCAAGGCAAGAAGGGCTATTTGCCAACAAA
* * *
48499 ATACCTTCGAGTTCGACTACTCTCAGCTCCAAGACACATCATTTGCAGCTTAGCTCAAGGTAAGA
131 AGACCTTCGAGTTCGACTA-TCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTCAAGGTAAGA
* * *
48564 AGGGCTATATGCC-AATAATGACCTTCGAGTTCGACTACACTCAGCTCTAA-GCACA
195 AGGGCTATTTGCCAAAAAAAGACCTTCGAGTTCGACTACACTCAGCTCTAAGGCACA
* *
48619 TCATTTGTAGCATAACTCAAGGCTAGAAGGGTTATCTACCAACAAAAGACCTTCGAGTTCGACTA
1 TCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTA
* * * * * * * *
48684 CGCTTAGCTCCAATGCACATCATTTGCAACATAACTCAAGACAAGAAGGTCTATTTGCTAACAAA
66 CACTCAGCTCAAAGGCACATCATTTGCAACATAGCTCAAGGCAAGAAGGGCTATTTGCCAACAAA
* * * * * *
48749 AGACCTTCGAGTTCAACTATGCTCAGCTCCAAGGCACATTATTTGCAACATAGCTCAAGGCACGG
131 AGACCTTCGAGTTCGACTAT-CTCAGCTCCAAGGCACATCATTTGCAGCATAGCTCAAGGTAAGA
* * * * * * *
48814 CGGGTTATTTGCCAACAAAATATCTTCGAGTTCGACTACACTCAGCTCCAAGGCATA
195 AGGGCTATTTGCCAAAAAAAGACCTTCGAGTTCGACTACACTCAGCTCTAAGGCACA
* * * * *
48871 TCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAATAATATACCTTTGAGTTCGATTA
1 TCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTA
* * * *
48936 CACTCAGCTCAAAGGTACAAT-ATTTG-AAGCATAGCTCAAGGCGAGAAGGGCTATCTGACAACA
66 CACTCAGCTCAAAGGCAC-ATCATTTGCAA-CATAGCTCAAGGCAAGAAGGGCTATTTGCCAACA
* * * * *
48999 AAAGACCTTCGATTTTGACTATGCTCAGTTCCAAGGCACATCATTTGTAGCATAACTCAAGGCT-
129 AAAGACCTTCGAGTTCGACTAT-CTCAGCTCCAAGGCACATCATTTGCAGCATAGCTCAAGG-TA
* * * * * * *
49063 AGAAGGGTTATCTACCAACAAAAGACCTTCGAGTTTGATTACACTCAGCTCAAAGGCACA
192 AGAAGGGCTATTTGCCAAAAAAAGACCTTCGAGTTCGACTACACTCAGCTCTAAGGCACA
* * * * *
49123 ACATTTGTAGTATAACTCAAGGCTAGAAGGGTTATATGCCAACAAAAGACCTTCGAGTTCGATTA
1 TCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTA
* * ** * *
49188 CACTCAACTCAAAGGCACATCATTTACAACATAGCTCAAGGTGAGAAGGGTTATATGCCAACAAA
66 CACTCAGCTCAAAGGCACATCATTTGCAACATAGCTCAAGGCAAGAAGGGCTATTTGCCAACAAA
* * * * * * *
49253 AGACCTTTGCGTTCGATTAGACTCAGCTCAAAGGCGCATCAAATTTGCAGCATAGCTCAAGGTGA
131 AGACCTTCGAGTTCGACTA-TCTCAGCTCCAAGGCACATC--ATTTGCAGCATAGCTCAAGGTAA
** * * ** * * * * *
49318 GAAAAGCTATATGTC-ATCAAAGACCTTAGAGTTCGATTACATTCAGCTCAAAGGCATA
193 GAAGGGCTATTTGCCAAAAAAAGACCTTCGAGTTCGACTACACTCAGCTCTAAGGCACA
** * * * ** *
49376 TCAAATTTATAGCATAACTCTAGGCGATAAGGGTTATCTATCATC-AAAGACCTTCGAGTTC
1 TC--ATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTC
49437 CATTGACACA
Statistics
Matches: 894, Mismatches: 159, Indels: 28
0.83 0.15 0.03
Matches are distributed among these distances:
249 1 0.00
250 179 0.20
251 67 0.07
252 527 0.59
253 44 0.05
254 44 0.05
255 32 0.04
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.25
Consensus pattern (251 bp):
TCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTA
CACTCAGCTCAAAGGCACATCATTTGCAACATAGCTCAAGGCAAGAAGGGCTATTTGCCAACAAA
AGACCTTCGAGTTCGACTATCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTCAAGGTAAGAA
GGGCTATTTGCCAAAAAAAGACCTTCGAGTTCGACTACACTCAGCTCTAAGGCACA
Found at i:51067 original size:8 final size:8
Alignment explanation
Indices: 51052--51084 Score: 59
Period size: 8 Copynumber: 4.2 Consensus size: 8
51042 TCTTACTTTC
51052 TATT-TTT
1 TATTATTT
51059 TATTATTT
1 TATTATTT
51067 TATTATTT
1 TATTATTT
51075 TATTATTT
1 TATTATTT
51083 TA
1 TA
51085 CTCTATTACC
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 4 0.16
8 21 0.84
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
TATTATTT
Found at i:51075 original size:16 final size:15
Alignment explanation
Indices: 51034--51084 Score: 59
Period size: 16 Copynumber: 3.3 Consensus size: 15
51024 TTGTTATTTA
*
51034 TTTA-TTTTTCTTACT
1 TTTATTTTTTATTA-T
51049 TTCTATTTTTTATTAT
1 TT-TATTTTTTATTAT
51065 TTTATTATTTTATTAT
1 TTTATT-TTTTATTAT
51081 TTTA
1 TTTA
51085 CTCTATTACC
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
15 6 0.19
16 18 0.56
17 8 0.25
ACGTcount: A:0.20, C:0.06, G:0.00, T:0.75
Consensus pattern (15 bp):
TTTATTTTTTATTAT
Found at i:51304 original size:148 final size:146
Alignment explanation
Indices: 51129--51472 Score: 432
Period size: 146 Copynumber: 2.3 Consensus size: 146
51119 TATATGTATA
* *
51129 TATTTTTTTTGTTTTTTTACTTACTTTATTCCATATTATATTATATATATAT-ATTTTCCTCTCA
1 TATTTTTTTTATTTTTTTTCTT-CTTTATT---TATTATATTATATATATATAATTTTCCTCTCA
* * *
51193 CC-TTTTTCTTCCTAGGCCCCT-CCCTTTTTTG-GTCCACCCAAATTTAATCATTCTTTCGGCGC
62 CCTTTTTTCTTCCTAGGCCCCTCCCCCTTTTTGTCTCCACCCAAATTTAATCATT-TTT-AGCGC
*
51255 ATTAATTATAGTAGGGTAAGTT
125 ATTAATTATAGTAGAGTAAGTT
* *
51277 TTTTTTTTTTATTATTTTTTCTTCTTTATTT-TATATATTAT-TATATATAATTTTTCTCTCACC
1 TATTTTTTTTATT-TTTTTTCTTCTTTATTTAT-TATATTATATATATATAATTTTCCTCTCACC
* **
51340 TTTTTTCTTCCTAGGCCCCTCCCCCTTTTTGTCTCCATCCAAATTTAATCATTTTTAGTTCATTA
64 TTTTTTCTTCCTAGGCCCCTCCCCCTTTTTGTCTCCACCCAAATTTAATCATTTTTAGCGCATTA
51405 ATTATAGTAGAGTAAGTT
129 ATTATAGTAGAGTAAGTT
*
51423 TATTTTTATTATTCTTTTTTTCTTCTTTA-TTATTATAGTTATATATATAT
1 TATTTTTTTTA-T-TTTTTTTCTTCTTTATTTATTATA-TTATATATATAT
51473 TTTATTATCT
Statistics
Matches: 172, Mismatches: 13, Indels: 22
0.83 0.06 0.11
Matches are distributed among these distances:
144 8 0.05
145 22 0.13
146 57 0.33
147 32 0.19
148 45 0.26
149 8 0.05
ACGTcount: A:0.22, C:0.17, G:0.06, T:0.55
Consensus pattern (146 bp):
TATTTTTTTTATTTTTTTTCTTCTTTATTTATTATATTATATATATATAATTTTCCTCTCACCTT
TTTTCTTCCTAGGCCCCTCCCCCTTTTTGTCTCCACCCAAATTTAATCATTTTTAGCGCATTAAT
TATAGTAGAGTAAGTT
Found at i:51485 original size:8 final size:8
Alignment explanation
Indices: 51450--51506 Score: 50
Period size: 8 Copynumber: 7.4 Consensus size: 8
51440 TTTTCTTCTT
51450 TATTATTA
1 TATTATTA
51458 TAGTTA-TA
1 TA-TTATTA
51466 TA-TA-TA
1 TATTATTA
*
51472 TTTTATTA
1 TATTATTA
*
51480 TCTTATTA
1 TATTATTA
51488 TATTATTA
1 TATTATTA
51496 T-TATATTA
1 TAT-TATTA
51504 TAT
1 TAT
51507 ATACTTTTTC
Statistics
Matches: 41, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
6 5 0.12
7 3 0.07
8 29 0.71
9 4 0.10
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (8 bp):
TATTATTA
Found at i:51573 original size:11 final size:11
Alignment explanation
Indices: 51543--51595 Score: 54
Period size: 11 Copynumber: 4.7 Consensus size: 11
51533 TGCATATACA
51543 TTTTATTTATT
1 TTTTATTTATT
**
51554 CACTTATTTATT
1 -TTTTATTTATT
51566 TTTTATTT-TGT
1 TTTTATTTAT-T
51577 TTTTATTTATT
1 TTTTATTTATT
*
51588 ATTTATTT
1 TTTTATTT
51596 TTATCTTGCA
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
10 1 0.03
11 23 0.68
12 10 0.29
ACGTcount: A:0.19, C:0.04, G:0.02, T:0.75
Consensus pattern (11 bp):
TTTTATTTATT
Found at i:51668 original size:13 final size:13
Alignment explanation
Indices: 51632--51707 Score: 66
Period size: 14 Copynumber: 5.8 Consensus size: 13
51622 ATCATTATTG
*
51632 TCTTTATTTTTAT
1 TCTTTATTTTTTT
51645 T-TTTACCTTTTTTT
1 TCTTTA--TTTTTTT
*
51659 T-TTTATTTTTAT
1 TCTTTATTTTTTT
*
51671 TCTTTGTTTCTTTT
1 TCTTTATTT-TTTT
* *
51685 GCTTTATTTTATT
1 TCTTTATTTTTTT
51698 TCTTTATTTT
1 TCTTTATTTT
51708 ATTCTTTTAA
Statistics
Matches: 51, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
12 11 0.22
13 19 0.37
14 21 0.41
ACGTcount: A:0.11, C:0.09, G:0.03, T:0.78
Consensus pattern (13 bp):
TCTTTATTTTTTT
Found at i:51708 original size:13 final size:12
Alignment explanation
Indices: 51632--51714 Score: 69
Period size: 13 Copynumber: 6.4 Consensus size: 12
51622 ATCATTATTG
51632 TCTTTATTTTTAT
1 TCTTTATTTTT-T
51645 T-TTTACCTTTTTT
1 TCTTTA--TTTTTT
*
51658 TTTTTATTTTTAT
1 TCTTTATTTTT-T
*
51671 TCTTTGTTTCTTT
1 TCTTTATTT-TTT
51684 TGCTTTATTTTATT
1 T-CTTTATTTT-TT
*
51698 TCTTTATTTTAT
1 TCTTTATTTTTT
51710 TCTTT
1 TCTTT
51715 TAACTTTTTT
Statistics
Matches: 59, Mismatches: 4, Indels: 15
0.76 0.05 0.19
Matches are distributed among these distances:
12 15 0.25
13 23 0.39
14 21 0.36
ACGTcount: A:0.11, C:0.10, G:0.02, T:0.77
Consensus pattern (12 bp):
TCTTTATTTTTT
Done.