Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002017.1 Hibiscus syriacus cultivar Beakdansim tig00004121_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: 58488
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:6409 original size:60 final size:60
Alignment explanation
Indices: 6304--6496 Score: 280
Period size: 60 Copynumber: 3.2 Consensus size: 60
6294 TAATGTGATA
** * * *
6304 CTTTGTTGAGTGAATCGATTATTAAATGTTATAAAATA-ACACTTCGACTATAGGGTGTTG
1 CTTTGTTGAGTCCATCGACTATTAAAAGTTACAAAATAGAC-CTTCGACTATAGGGTGTTG
* *
6364 CTTTGTTGAGTCCCTCGACTATTAAAAGTTACAAAACAGACCTTCGACTATAGGGTGTTG
1 CTTTGTTGAGTCCATCGACTATTAAAAGTTACAAAATAGACCTTCGACTATAGGGTGTTG
* * *
6424 CTTTGTTGAGTCCATCAACTATTAAAAGTTACATAATAGTCCTTCGACTATAGGGTGTTG
1 CTTTGTTGAGTCCATCGACTATTAAAAGTTACAAAATAGACCTTCGACTATAGGGTGTTG
6484 CTTTGTTGAGTCC
1 CTTTGTTGAGTCC
6497 CCCGATTATT
Statistics
Matches: 120, Mismatches: 12, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
60 118 0.98
61 2 0.02
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.36
Consensus pattern (60 bp):
CTTTGTTGAGTCCATCGACTATTAAAAGTTACAAAATAGACCTTCGACTATAGGGTGTTG
Found at i:6496 original size:31 final size:31
Alignment explanation
Indices: 6404--6496 Score: 75
Period size: 31 Copynumber: 3.1 Consensus size: 31
6394 ACAAAACAGA
6404 CCTTCGACTATAGGGTGTTGCTTTGTTGAGT
1 CCTTCGACTATAGGGTGTTGCTTTGTTGAGT
* * *** * * **
6435 CCATCAACTATTA-AAAGTTAC-ATAAT-AGT
1 CCTTCGACTA-TAGGGTGTTGCTTTGTTGAGT
6464 CCTTCGACTATAGGGTGTTGCTTTGTTGAGT
1 CCTTCGACTATAGGGTGTTGCTTTGTTGAGT
6495 CC
1 CC
6497 CCCGATTATT
Statistics
Matches: 40, Mismatches: 18, Indels: 8
0.61 0.27 0.12
Matches are distributed among these distances:
28 2 0.05
29 15 0.38
30 4 0.10
31 17 0.43
32 2 0.05
ACGTcount: A:0.23, C:0.18, G:0.22, T:0.38
Consensus pattern (31 bp):
CCTTCGACTATAGGGTGTTGCTTTGTTGAGT
Found at i:6707 original size:58 final size:58
Alignment explanation
Indices: 6616--6746 Score: 167
Period size: 58 Copynumber: 2.2 Consensus size: 58
6606 TCGAGTGACC
** *
6616 ATTTTGTAACTTTTAGTAGTCGAGAGACTCAAC-AAGTAACACCGTATAGTTAAAGGACT
1 ATTTTGTAAC-TTTAACAGTCGAGAGACTCAACAAAGTAACACCCTATAG-TAAAGGACT
* **
6675 ATTTTGTAACTTTAACAGTCGAGAGACTCAACAAAGTATCACCCTATAGTCGAGGACT
1 ATTTTGTAACTTTAACAGTCGAGAGACTCAACAAAGTAACACCCTATAGTAAAGGACT
6733 ATTTGTGT-ACTTTA
1 ATTT-TGTAACTTTA
6747 CCCAATAAAT
Statistics
Matches: 64, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
58 37 0.58
59 27 0.42
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.32
Consensus pattern (58 bp):
ATTTTGTAACTTTAACAGTCGAGAGACTCAACAAAGTAACACCCTATAGTAAAGGACT
Found at i:8189 original size:25 final size:25
Alignment explanation
Indices: 8152--8211 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 25
8142 AAGTTTAAAG
* *
8152 TTAAACTCAACTCGAAATAAAAAAT
1 TTAAGCTCAACTCGAAATAAAAAAA
* **
8177 TTAAGCTCGACTCGAGCTAAAAAAA
1 TTAAGCTCAACTCGAAATAAAAAAA
*
8202 TAAAGCTCAA
1 TTAAGCTCAA
8212 AACATTCACA
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.50, C:0.18, G:0.10, T:0.22
Consensus pattern (25 bp):
TTAAGCTCAACTCGAAATAAAAAAA
Found at i:12352 original size:27 final size:27
Alignment explanation
Indices: 12290--12353 Score: 74
Period size: 27 Copynumber: 2.4 Consensus size: 27
12280 ATGGAAATGC
* *
12290 GAGATAAGATGGACAGGGATAGAGAAA
1 GAGATAGGAGGGACAGGGATAGAGAAA
** * *
12317 GAGGCAGGAGGGATAGGGATGGAGAAA
1 GAGATAGGAGGGACAGGGATAGAGAAA
12344 GAGATAGGAG
1 GAGATAGGAG
12354 TAGGCATAAA
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.42, C:0.03, G:0.45, T:0.09
Consensus pattern (27 bp):
GAGATAGGAGGGACAGGGATAGAGAAA
Found at i:20559 original size:15 final size:16
Alignment explanation
Indices: 20523--20557 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
20513 TTAAAAAGTA
20523 AATTTAATATTGATTG
1 AATTTAATATTGATTG
20539 AATTTAAT-TTGATT-
1 AATTTAATATTGATTG
20553 AATTT
1 AATTT
20558 TATTATAGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 5 0.26
15 6 0.32
16 8 0.42
ACGTcount: A:0.37, C:0.00, G:0.09, T:0.54
Consensus pattern (16 bp):
AATTTAATATTGATTG
Found at i:23381 original size:15 final size:14
Alignment explanation
Indices: 23344--23379 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
23334 AATATTTAAA
23344 ATATAAATTTTATG
1 ATATAAATTTTATG
*
23358 ATTTCAAATTTTATG
1 ATAT-AAATTTTATG
23373 ATATAAA
1 ATATAAA
23380 ATCAAAATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (14 bp):
ATATAAATTTTATG
Found at i:25642 original size:42 final size:42
Alignment explanation
Indices: 25583--25702 Score: 213
Period size: 42 Copynumber: 2.9 Consensus size: 42
25573 TTTCCCCGAA
* *
25583 TTCCCGTGTTTATTTCACGTAATTCGTTTTCCGGAAAATGTT
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTT
25625 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTT
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTT
*
25667 TTCCCGTGTTTGTTTTACGTAATTCGTTTTCCGGAA
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAA
25703 TGTAATTCAT
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 75 1.00
ACGTcount: A:0.17, C:0.20, G:0.18, T:0.45
Consensus pattern (42 bp):
TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTT
Found at i:25938 original size:22 final size:23
Alignment explanation
Indices: 25891--25951 Score: 65
Period size: 22 Copynumber: 2.8 Consensus size: 23
25881 TAATTATTAA
* *
25891 AATATTTAAAAT-ATAT-TTATT
1 AATATTTATAATAATATAATATT
25912 AATATTTATAATAATATAATATT
1 AATATTTATAATAATATAATATT
* *
25935 -ATATTTTTAATATTATA
1 AATATTTATAATAATATA
25952 TAAAATAATC
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
21 11 0.32
22 19 0.56
23 4 0.12
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
AATATTTATAATAATATAATATT
Found at i:26004 original size:29 final size:28
Alignment explanation
Indices: 25967--26065 Score: 89
Period size: 29 Copynumber: 3.5 Consensus size: 28
25957 TAATCAATTA
*
25967 TATTATAATAATATA-AGAT-ATTATATTTT
1 TATTTTAATAATATATA-ATAATT-T-TTTT
25996 TATTTTAATAATATATAATAATTTTTTT
1 TATTTTAATAATATATAATAATTTTTTT
* *
26024 TATATTTAATAATGA-ATAAT-ATTATTTA
1 TAT-TTTAATAAT-ATATAATAATTTTTTT
*
26052 TATTTCAATAATAT
1 TATTTTAATAATAT
26066 TTTAGTAAAG
Statistics
Matches: 61, Mismatches: 4, Indels: 12
0.79 0.05 0.16
Matches are distributed among these distances:
26 1 0.02
27 8 0.13
28 16 0.26
29 31 0.51
30 5 0.08
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.54
Consensus pattern (28 bp):
TATTTTAATAATATATAATAATTTTTTT
Found at i:26011 original size:24 final size:23
Alignment explanation
Indices: 25979--26025 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
25969 TTATAATAAT
* *
25979 ATAAGATATTATATTTTTATTTTA
1 ATAAGATATAATAATTTT-TTTTA
*
26003 ATAATATATAATAATTTTTTTTA
1 ATAAGATATAATAATTTTTTTTA
26026 TATTTAATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (23 bp):
ATAAGATATAATAATTTTTTTTA
Found at i:26021 original size:26 final size:26
Alignment explanation
Indices: 25992--26065 Score: 78
Period size: 28 Copynumber: 2.7 Consensus size: 26
25982 AGATATTATA
25992 TTTTTATTTTAATAATATATAATAATTT
1 TTTTTATTTTAATAATATATAAT-A-TT
26020 TTTTTATATTTAATAATGA-ATAATATT
1 TTTTTAT-TTTAATAAT-ATATAATATT
* *
26047 ATTTATATTTCAATAATAT
1 -TTTTTATTTTAATAATAT
26066 TTTAGTAAAG
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
26 1 0.03
27 10 0.25
28 14 0.35
29 14 0.35
30 1 0.03
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (26 bp):
TTTTTATTTTAATAATATATAATATT
Found at i:26307 original size:20 final size:20
Alignment explanation
Indices: 26229--26298 Score: 122
Period size: 20 Copynumber: 3.5 Consensus size: 20
26219 TTTCCAGATG
26229 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
26249 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
* *
26269 TTTTACAAAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
26289 TTTTCCAGAA
1 TTTTCCAGAA
26299 TTCAAATTCC
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.37, C:0.14, G:0.09, T:0.40
Consensus pattern (20 bp):
TTTTCCAGAAATGTAATTCA
Found at i:26317 original size:15 final size:15
Alignment explanation
Indices: 26281--26362 Score: 112
Period size: 15 Copynumber: 5.5 Consensus size: 15
26271 TTACAAAAAT
**
26281 GTAATTCATTTTCCA
1 GTAATTCAAATTCCA
26296 G-AATTCAAATTCCA
1 GTAATTCAAATTCCA
**
26310 GTAATTCATTTTCCA
1 GTAATTCAAATTCCA
26325 GTAATTCAAATTCCA
1 GTAATTCAAATTCCA
*
26340 GTAATTCAAATTACA
1 GTAATTCAAATTCCA
26355 GTAATTCA
1 GTAATTCA
26363 TTTTCTGGAA
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
14 12 0.20
15 47 0.80
ACGTcount: A:0.37, C:0.18, G:0.07, T:0.38
Consensus pattern (15 bp):
GTAATTCAAATTCCA
Found at i:26333 original size:30 final size:30
Alignment explanation
Indices: 26281--26362 Score: 130
Period size: 30 Copynumber: 2.8 Consensus size: 30
26271 TTACAAAAAT
26281 GTAATTCATTTTCCAG-AATTCAAATTCCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
26310 GTAATTCATTTTCCAGTAATTCAAATTCCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
** *
26340 GTAATTCAAATTACAGTAATTCA
1 GTAATTCATTTTCCAGTAATTCA
26363 TTTTCTGGAA
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
29 16 0.33
30 33 0.67
ACGTcount: A:0.37, C:0.18, G:0.07, T:0.38
Consensus pattern (30 bp):
GTAATTCATTTTCCAGTAATTCAAATTCCA
Found at i:26357 original size:45 final size:44
Alignment explanation
Indices: 26281--26367 Score: 138
Period size: 45 Copynumber: 2.0 Consensus size: 44
26271 TTACAAAAAT
** *
26281 GTAATTCATTTTCCAGAATTCAAATTCCAGTAATTCATTTTCCA
1 GTAATTCAAATTCCAGAATTCAAATTACAGTAATTCATTTTCCA
26325 GTAATTCAAATTCCAGTAATTCAAATTACAGTAATTCATTTTC
1 GTAATTCAAATTCCAG-AATTCAAATTACAGTAATTCATTTTC
26368 TGGAAAACCA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
44 14 0.36
45 25 0.64
ACGTcount: A:0.34, C:0.18, G:0.07, T:0.40
Consensus pattern (44 bp):
GTAATTCAAATTCCAGAATTCAAATTACAGTAATTCATTTTCCA
Found at i:27199 original size:12 final size:10
Alignment explanation
Indices: 27176--27211 Score: 54
Period size: 10 Copynumber: 3.4 Consensus size: 10
27166 ATTTTATCAT
27176 TAAAATAATC
1 TAAAATAATC
27186 TAAAATTGAATC
1 TAAAA-T-AATC
27198 TAAAATAATC
1 TAAAATAATC
27208 TAAA
1 TAAA
27212 GAGTTCAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 13 0.54
11 2 0.08
12 9 0.38
ACGTcount: A:0.58, C:0.08, G:0.03, T:0.31
Consensus pattern (10 bp):
TAAAATAATC
Found at i:28508 original size:20 final size:20
Alignment explanation
Indices: 28485--28536 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
28475 AACGCGATCC
28485 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
28505 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
28525 CCAAAATCGCAA
1 CCAGAATCGCAA
28537 CGCGATTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:28553 original size:21 final size:20
Alignment explanation
Indices: 28526--28624 Score: 72
Period size: 21 Copynumber: 4.8 Consensus size: 20
28516 AATCAGTTTC
28526 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * * *
28547 GAAAATCGCGATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
28568 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
28588 CAATAATCGCAACGCGAATAT
1 CAA-AATCGCAACGCGATTTT
*
28609 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
28625 ACACATAAAT
Statistics
Matches: 59, Mismatches: 17, Indels: 5
0.73 0.21 0.06
Matches are distributed among these distances:
20 17 0.29
21 42 0.71
ACGTcount: A:0.36, C:0.22, G:0.19, T:0.22
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:28617 original size:20 final size:20
Alignment explanation
Indices: 28592--28785 Score: 76
Period size: 20 Copynumber: 9.7 Consensus size: 20
28582 GATTTTCAAT
* *
28592 AATCGCAACGCGAATATGA-A
1 AATCGCAACGCGAACA-CATA
28612 AATCGCAACGCGAACACATA
1 AATCGCAACGCGAACACATA
* *
28632 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
28652 AATCGCAACGTGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* ****
28672 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGAACACATA
* * *
28692 AATCGCAATGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
28712 TATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
** *
28732 AATCGCAACGATAATACATAA
1 AATCGCAACGCGAACACAT-A
* *
28753 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
28773 AATCGCAACGCGA
1 AATCGCAACGCGA
28786 TATTTAAAGC
Statistics
Matches: 139, Mismatches: 28, Indels: 15
0.76 0.15 0.08
Matches are distributed among these distances:
19 3 0.02
20 120 0.86
21 15 0.11
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAACACATA
Found at i:28637 original size:40 final size:39
Alignment explanation
Indices: 28592--28785 Score: 199
Period size: 40 Copynumber: 4.8 Consensus size: 39
28582 GATTTTCAAT
* ** *
28592 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAAC-CATA
* * *
28632 AATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCG-AACCATA
** * * *
28672 AATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCG-AACCATA
* ** *
28712 TATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAA-CCAT-A
28753 AATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGA
28786 TATTTAAAGC
Statistics
Matches: 128, Mismatches: 23, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
39 1 0.01
40 94 0.73
41 33 0.26
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (39 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAACCATA
Found at i:28675 original size:60 final size:60
Alignment explanation
Indices: 28592--28784 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
28582 GATTTTCAAT
* ** * *
28592 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* * *** *
28652 AATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* **
28712 TATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGTA
28773 AATCGCAACGCG
1 AATCGCAACGCG
28785 ATATTTAAAG
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 80 0.72
61 31 0.28
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
Found at i:29202 original size:33 final size:33
Alignment explanation
Indices: 29163--29233 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
29153 TTCACTTAGA
*
29163 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
29196 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
29229 TTTCA
1 TTTCA
29234 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:29373 original size:14 final size:14
Alignment explanation
Indices: 29354--29408 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
29344 AGAATGACTG
29354 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
29368 TCGCAACGCGAAATGAAAA
1 TCGCAA--CG--A-GAGAA
29387 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
29401 TCGCAACG
1 TCGCAACG
29409 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.42, C:0.24, G:0.25, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:29391 original size:33 final size:33
Alignment explanation
Indices: 29354--29424 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
29344 AGAATGACTG
**
29354 TCGCAACGAGAGAATCGCAACGCGAAATGAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
29387 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
29420 TCGCA
1 TCGCA
29425 TTGCGATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.44, C:0.25, G:0.23, T:0.08
Consensus pattern (33 bp):
TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
Found at i:29442 original size:19 final size:19
Alignment explanation
Indices: 29420--29517 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
29410 GAAACCAAAA
*
29420 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
29439 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
29453 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
29472 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
29486 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
29505 TCGCGTTGCGATT
1 TCGCGTTGCGATT
29518 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:29461 original size:14 final size:14
Alignment explanation
Indices: 29442--29531 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
29432 TTTCATTTCG
29442 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
29456 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
29475 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
29489 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
29506 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
29522 CGTTGCGATT
1 CGTTGCGATT
29532 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:29467 original size:33 final size:33
Alignment explanation
Indices: 29425--29539 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
29415 CAAAATCGCA
29425 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
29458 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
29491 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
29524 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
29540 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:31467 original size:185 final size:186
Alignment explanation
Indices: 31237--31801 Score: 1098
Period size: 185 Copynumber: 3.0 Consensus size: 186
31227 TAGATTGCTT
*
31237 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
31302 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
*
31367 GTATATTCTTTAACACTGTGAAATA-TATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
31422 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
31487 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
31552 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
31608 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
31672 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
31737 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
31793 AGTAAATTT
1 AGTAAATTT
31802 ATCCATTCAA
Statistics
Matches: 377, Mismatches: 2, Indels: 2
0.99 0.01 0.01
Matches are distributed among these distances:
185 285 0.76
186 92 0.24
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (186 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:31551 original size:93 final size:93
Alignment explanation
Indices: 31237--31801 Score: 1098
Period size: 93 Copynumber: 6.1 Consensus size: 93
31227 TAGATTGCTT
*
31237 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
31302 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
31330 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTATATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
31394 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
31422 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
31487 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
31515 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
31580 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
31608 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
31672 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
31700 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
31765 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
31793 AGTAAATTT
1 AGTAAATTT
31802 ATCCATTCAA
Statistics
Matches: 467, Mismatches: 3, Indels: 4
0.99 0.01 0.01
Matches are distributed among these distances:
92 183 0.39
93 284 0.61
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:31734 original size:278 final size:278
Alignment explanation
Indices: 31237--31803 Score: 1116
Period size: 278 Copynumber: 2.0 Consensus size: 278
31227 TAGATTGCTT
31237 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
31302 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
31367 GTATATTCTTTAACACTGTGAAATATATTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTG
131 GTATATTCTTTAACACTGTGAAATATATTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTG
31432 TTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTG
196 TTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTG
31497 TTTTGTCTTTTGGTTGAA
261 TTTTGTCTTTTGGTTGAA
*
31515 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
31580 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
*
31645 GTGTATTCTTTAACACTGTGAAATATATTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTG
131 GTATATTCTTTAACACTGTGAAATATATTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTG
31710 TTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTG
196 TTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTG
31775 TTTTGTCTTTTGGTTGAA
261 TTTTGTCTTTTGGTTGAA
31793 AGTAAATTTAT
1 AGTAAATTTAT
31804 CCATTCAAGT
Statistics
Matches: 286, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
278 286 1.00
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (278 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
GTATATTCTTTAACACTGTGAAATATATTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTG
TTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTG
TTTTGTCTTTTGGTTGAA
Found at i:31885 original size:19 final size:19
Alignment explanation
Indices: 31845--31973 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
31835 TAGTTTACTT
* *
31845 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
31865 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
31884 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
31903 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
31917 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
31936 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
31950 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
31969 TCGCA
1 TCGCA
31974 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:31924 original size:33 final size:32
Alignment explanation
Indices: 31881--31973 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
31871 CGCGAAACCA
**
31881 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
31913 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
31946 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
31974 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:31971 original size:52 final size:52
Alignment explanation
Indices: 31845--31973 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
31835 TAGTTTACTT
**
31845 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
31897 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
31950 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
31974 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:31991 original size:19 final size:18
Alignment explanation
Indices: 31969--32068 Score: 99
Period size: 19 Copynumber: 5.8 Consensus size: 18
31959 GAAACCAAAA
31969 TCGCATTGCGATTTTCATT
1 TCGC-TTGCGATTTTCATT
31988 TCGCGTTGCGA--TTC-TT
1 TCGC-TTGCGATTTTCATT
32004 TCG-TTGCGATTTTCATT
1 TCGCTTGCGATTTTCATT
*
32021 TCGCATTGCGA--TTC-TG
1 TCGC-TTGCGATTTTCATT
32037 TCG-TTGCGATTTTCATT
1 TCGCTTGCGATTTTCATT
32054 TCGCGTTGCGATTTT
1 TCGC-TTGCGATTTT
32069 AAGTTTCGTG
Statistics
Matches: 68, Mismatches: 3, Indels: 20
0.75 0.03 0.22
Matches are distributed among these distances:
14 12 0.18
16 15 0.22
17 15 0.22
19 26 0.38
ACGTcount: A:0.11, C:0.21, G:0.21, T:0.47
Consensus pattern (18 bp):
TCGCTTGCGATTTTCATT
Found at i:32010 original size:14 final size:14
Alignment explanation
Indices: 31991--32047 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
31981 TTTCATTTCG
31991 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
32005 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
32022 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
32038 CGTTGCGATT
1 CGTTGCGATT
32048 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:32016 original size:33 final size:33
Alignment explanation
Indices: 31974--32066 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
31964 CAAAATCGCA
*
31974 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
32007 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
32040 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
32067 TTAAGTTTCG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:32081 original size:20 final size:19
Alignment explanation
Indices: 31969--32084 Score: 72
Period size: 19 Copynumber: 6.6 Consensus size: 19
31959 GAAACCAAAA
* *
31969 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTAATT
*
31988 TCGCGTTGCGA--TT-CTT
1 TCGCGTTGCGATTTTAATT
*
32004 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTAATT
* * *
32021 TCGCATTGCGA--TT-CTG
1 TCGCGTTGCGATTTTAATT
*
32037 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTAATT
32054 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTAA-TT
*
32074 TCGTGTTGCGA
1 TCGCGTTGCGA
32085 AAGTAAACTA
Statistics
Matches: 75, Mismatches: 11, Indels: 21
0.70 0.10 0.20
Matches are distributed among these distances:
14 15 0.20
16 9 0.12
17 9 0.12
19 30 0.40
20 12 0.16
ACGTcount: A:0.12, C:0.20, G:0.22, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTAATT
Found at i:34006 original size:14 final size:14
Alignment explanation
Indices: 33987--34022 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
33977 ATTGTTTAAT
33987 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
34001 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
34015 TGATTTGT
1 TGATTTGT
34023 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:34145 original size:19 final size:19
Alignment explanation
Indices: 34129--34230 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
34119 AAAAATGACT
34129 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
34148 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
34167 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
34181 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
34200 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
34220 ATCGCAATGCG
1 ATCGCAATGCG
34231 TTTATAATTT
Statistics
Matches: 75, Mismatches: 2, Indels: 12
0.84 0.02 0.13
Matches are distributed among these distances:
14 10 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 40 0.53
20 19 0.25
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:34283 original size:19 final size:19
Alignment explanation
Indices: 34259--34551 Score: 392
Period size: 19 Copynumber: 16.4 Consensus size: 19
34249 GATTATCTCG
34259 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
34278 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
34297 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
34311 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
34330 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
34349 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
34368 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
34387 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
34406 TTGCGATTTTAATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
34425 TTGCGA--TTC-TGTCG--
1 TTGCGATTTTCATTTCGCA
34439 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
34458 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
34477 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
34491 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
34511 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
34525 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
34544 TTGCGATT
1 TTGCGATT
34552 GTATTTTCCG
Statistics
Matches: 245, Mismatches: 8, Indels: 42
0.83 0.03 0.14
Matches are distributed among these distances:
14 29 0.12
16 24 0.10
17 20 0.08
18 3 0.01
19 157 0.64
20 12 0.05
ACGTcount: A:0.14, C:0.20, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:34299 original size:52 final size:52
Alignment explanation
Indices: 34237--34551 Score: 330
Period size: 52 Copynumber: 5.9 Consensus size: 52
34227 TGCGTTTATA
*
34237 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTATTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
34289 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTATTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
34341 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA--TT-ATTTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
*
34398 ATTTCGCATTGCGATTTTAATTTCGCATTGCGA--TTC-TGTCG--TTGCGATTTTC
1 ATTTCGCATTGCGA--TT-ATTTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
*
34450 ATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTC
1 ATTTCGCATTGCGA--TT-ATTTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
* *
34502 ATTTCCGCATTGCGA-T-TTTCATGTTGGGATTTTCATTTCGCGTTGCGATT
1 ATTT-CGCATTGCGATTATTTC--GTTGCGATTTTCATTTCGCATTGCGATT
34552 GTATTTTCCG
Statistics
Matches: 241, Mismatches: 9, Indels: 25
0.88 0.03 0.09
Matches are distributed among these distances:
48 9 0.04
50 5 0.02
51 4 0.02
52 129 0.54
53 18 0.07
54 6 0.02
55 8 0.03
57 62 0.26
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.47
Consensus pattern (52 bp):
ATTTCGCATTGCGATTATTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:34407 original size:128 final size:122
Alignment explanation
Indices: 34259--34523 Score: 194
Period size: 128 Copynumber: 2.1 Consensus size: 122
34249 GATTATCTCG
*
34259 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA-TTC-TTTCG-TTGCGATTTT
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TGTCG--TTGCGATTTCATTTCGATTGCGATTTT
*
34321 CATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTT-CGCATTGCGATTTTCATTTCG
61 CATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCCGCATTGCGATTTTCATTTCG
34385 CA
121 CA
* * *
34387 TTGCGATTTTCATTTCGCATTGCGATTTTAATTTCGCATTGCGA-TTC-TGTCG-TTGCGATTTT
1 TTGCGATTTTCATTTCGCATTGCGA--TT-CTGTCG--TTGCGATTTCATTTCGATTGCGATTTT
* * *
34449 CATTTCGCATTGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCG--TTGCGATTTTCATTTCCG
61 CATTTCGCATTGCGATTCTCTCGTTGCG-ATTTTC-ATT-TC-CGCATTGCGATTTTCATTT-CG
34509 CA
121 CA
34511 TTGCGATTTTCAT
1 TTGCGATTTTCAT
34524 GTTGGGATTT
Statistics
Matches: 125, Mismatches: 5, Indels: 18
0.84 0.03 0.12
Matches are distributed among these distances:
121 7 0.06
122 4 0.03
123 18 0.14
124 18 0.14
125 2 0.02
126 2 0.02
128 74 0.59
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.47
Consensus pattern (122 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTGTCGTTGCGATTTCATTTCGATTGCGATTTTCATTT
CGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATTTCGCA
Found at i:36849 original size:12 final size:12
Alignment explanation
Indices: 36832--36856 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
36822 TCTTCGGGGA
36832 CTTTTTCTTCTT
1 CTTTTTCTTCTT
36844 CTTTTTCTTCTT
1 CTTTTTCTTCTT
36856 C
1 C
36857 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:37065 original size:24 final size:24
Alignment explanation
Indices: 37031--37077 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
37021 CTGAAACATC
37031 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
37055 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
37078 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:37788 original size:20 final size:20
Alignment explanation
Indices: 37760--38128 Score: 451
Period size: 20 Copynumber: 18.4 Consensus size: 20
37750 AAATTTAAGT
* * * *
37760 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
37780 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
37800 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
37820 GTTGCGATTTACGGAGTA-TC
1 GTTGCGATTTACGGA-TACGC
37840 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
37860 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
37880 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
37900 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
37920 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
37940 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
37960 GTTGC-AGTTTACGGATACGC
1 GTTGCGA-TTTACGGATACGC
37980 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
38000 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
38020 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
38040 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
38060 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
38080 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
38100 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
38120 GTTGCGATT
1 GTTGCGATT
38129 ATGGAAAATC
Statistics
Matches: 309, Mismatches: 30, Indels: 20
0.86 0.08 0.06
Matches are distributed among these distances:
19 6 0.02
20 297 0.96
21 6 0.02
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.34
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:41864 original size:13 final size:13
Alignment explanation
Indices: 41846--41872 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
41836 CATAGTTGAA
41846 CAGTCTTCATATG
1 CAGTCTTCATATG
41859 CAGTCTTCATATG
1 CAGTCTTCATATG
41872 C
1 C
41873 GTGTCTGTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.26, G:0.15, T:0.37
Consensus pattern (13 bp):
CAGTCTTCATATG
Found at i:44258 original size:23 final size:23
Alignment explanation
Indices: 44225--44268 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
44215 AAGTCGAGGG
44225 TCTACGCGGTCCTTCGGGACAAT
1 TCTACGCGGTCCTTCGGGACAAT
*
44248 TCTACGTGGTCCTTCGGGACA
1 TCTACGCGGTCCTTCGGGACA
44269 TATATGTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.16, C:0.30, G:0.27, T:0.27
Consensus pattern (23 bp):
TCTACGCGGTCCTTCGGGACAAT
Found at i:44408 original size:18 final size:18
Alignment explanation
Indices: 44387--44429 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
44377 GTGGTCTTTC
44387 GGGACATAATGGTCCTCA
1 GGGACATAATGGTCCTCA
*
44405 GGGACATAGTGGTCCTCA
1 GGGACATAATGGTCCTCA
44423 GGGACAT
1 GGGACAT
44430 TTCTACGCGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.26, C:0.21, G:0.33, T:0.21
Consensus pattern (18 bp):
GGGACATAATGGTCCTCA
Found at i:45132 original size:21 final size:21
Alignment explanation
Indices: 45103--45143 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
45093 GAAATTTTGG
*
45103 TGCATCGATGCACTGTAGCAA
1 TGCACCGATGCACTGTAGCAA
45124 TGCACCGATGCACTGTAGCA
1 TGCACCGATGCACTGTAGCA
45144 CTGTTCATGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.27, C:0.27, G:0.24, T:0.22
Consensus pattern (21 bp):
TGCACCGATGCACTGTAGCAA
Found at i:53476 original size:36 final size:36
Alignment explanation
Indices: 53436--53504 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
53426 GATTTCTATT
*
53436 TTGGTTTGTAATGGCT-AAGTGTTTATTTTGAGTTTA
1 TTGGTTTGTAATAGCTGAA-TGTTTATTTTGAGTTTA
53472 TTGGTTTGTAATAGCTGAATGTTTATTTTGAGT
1 TTGGTTTGTAATAGCTGAATGTTTATTTTGAGT
53505 CTACCCTTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
36 29 0.94
37 2 0.06
ACGTcount: A:0.20, C:0.03, G:0.25, T:0.52
Consensus pattern (36 bp):
TTGGTTTGTAATAGCTGAATGTTTATTTTGAGTTTA
Found at i:55938 original size:21 final size:19
Alignment explanation
Indices: 55911--55979 Score: 66
Period size: 20 Copynumber: 3.4 Consensus size: 19
55901 TTAAAATAAT
*
55911 AATAATTTTAATATTTTAA
1 AATAAATTTAATATTTTAA
* * *
55930 AGTAAAATTCAATATGTATAA
1 AAT-AAATTTAATAT-TTTAA
55951 AATAAATTTAATATTTTTAA
1 AATAAATTTAATA-TTTTAA
55971 AATGAAATT
1 AAT-AAATT
55980 GAAATTAGAA
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
19 2 0.05
20 25 0.64
21 12 0.31
ACGTcount: A:0.51, C:0.01, G:0.04, T:0.43
Consensus pattern (19 bp):
AATAAATTTAATATTTTAA
Done.