Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000540.1 Hibiscus syriacus cultivar Beakdansim tig00001046_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: 50209
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:3190 original size:37 final size:36
Alignment explanation
Indices: 2993--3289 Score: 236
Period size: 37 Copynumber: 8.1 Consensus size: 36
2983 TTTTAAAAAC
*
2993 ATATAATATAT-TTTTT-AAAATCGGTTTTCAAAAATAT
1 ATATAATATATATTTTTAAAAAT--ATTTT-AAAAATAT
* * *
3030 ATATAATATATAGTTTTGAAAATATTTGAAATATATAT
1 ATATAATATATATTTTTAAAAATATTTTAAA-A-ATAT
* *
3068 ATATAATATATAGTTTTTTAAAATGATTTTTGAAAATAT
1 ATATAATATATA-TTTTTAAAAAT-A-TTTTAAAAATAT
* * * * * *
3107 GTATATTATATAGTTTTTGAAAACATTTTGAAACT-T
1 ATATAATATATA-TTTTTAAAAATATTTTAAAAATAT
*
3143 ATAT-ATAT-GATTTTTAAAAATATTTTAAAAATAT
1 ATATAATATATATTTTTAAAAATATTTTAAAAATAT
* *
3177 ATATAATATATGATTTTTAAAAAACATTTT-GAAATAT
1 ATATAATATAT-ATTTTT-AAAAATATTTTAAAAATAT
* *
3214 ATATAATATATAGTTTTT-AAAACATTTTGAAAAT-T
1 ATATAATATATA-TTTTTAAAAATATTTTAAAAATAT
*
3249 ATATAATATATAATTTTGAAAACAT-TTTTAAAAA-AT
1 ATATAATATAT-ATTTTTAAAA-ATATTTTAAAAATAT
3285 ATATA
1 ATATA
3290 GAGAGAGTTT
Statistics
Matches: 216, Mismatches: 26, Indels: 37
0.77 0.09 0.13
Matches are distributed among these distances:
33 18 0.08
34 6 0.03
35 33 0.15
36 30 0.14
37 53 0.25
38 31 0.14
39 38 0.18
40 2 0.01
41 5 0.02
ACGTcount: A:0.46, C:0.02, G:0.06, T:0.45
Consensus pattern (36 bp):
ATATAATATATATTTTTAAAAATATTTTAAAAATAT
Found at i:3236 original size:35 final size:35
Alignment explanation
Indices: 3024--3333 Score: 224
Period size: 35 Copynumber: 8.5 Consensus size: 35
3014 CGGTTTTCAA
* *
3024 AAATATATATAATATATAGTTTTGAAAATA-TTTG
1 AAATATATATAATATATAGTTTTTAAAACATTTTG
*
3058 AAATATATATATATAATATATAGTTTTTTAAAATGATTTTTG
1 --A-A-ATATATATAATATATAG-TTTTTAAAA-CA-TTTTG
* *
3100 AAAATATGTATATTATATAGTTTTTGAAAACATTTTG
1 -AAATATATATAATATATAGTTTTT-AAAACATTTTG
* * *
3137 AAACT-TATAT-ATATGAT--TTTTAAAAATATTTTAA
1 AAA-TATATATAATAT-ATAGTTTTTAAAACATTTT-G
3171 AAATATATATAATATAT-GATTTTTAAAAAACATTTTG
1 AAATATATATAATATATAG-TTTTT--AAAACATTTTG
3208 AAATATATATAATATATAGTTTTTAAAACATTTTG
1 AAATATATATAATATATAGTTTTTAAAACATTTTG
* * *
3243 AAA-ATTATATAATATATAATTTTGAAAACATTTTT
1 AAATA-TATATAATATATAGTTTTTAAAACATTTTG
* * * * *
3278 AAA-AAATAT-ATAGAGAGAGTTTTAAAATATTATTTG
1 AAATATATATAATATATAG-TTTTTAAAACA-T-TTTG
3314 AATATATATATATATATATA
1 AA-ATATATATA-ATATATA
3334 TTATATGGTT
Statistics
Matches: 222, Mismatches: 27, Indels: 46
0.75 0.09 0.16
Matches are distributed among these distances:
33 15 0.07
34 27 0.12
35 53 0.24
36 19 0.09
37 30 0.14
38 38 0.17
39 27 0.12
40 7 0.03
41 2 0.01
42 4 0.02
ACGTcount: A:0.47, C:0.02, G:0.07, T:0.45
Consensus pattern (35 bp):
AAATATATATAATATATAGTTTTTAAAACATTTTG
Found at i:3375 original size:3 final size:3
Alignment explanation
Indices: 3367--3416 Score: 63
Period size: 3 Copynumber: 18.0 Consensus size: 3
3357 TTGAAAATAT
*
3367 TTA TTA TTA TTA TTA TTA TTA TTT TTA TTA -TA TT- TTA TT- TTA TT-
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3411 TTA TTA
1 TTA TTA
3417 ATCCTATTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
2 8 0.20
3 33 0.80
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (3 bp):
TTA
Found at i:3758 original size:19 final size:19
Alignment explanation
Indices: 3736--3779 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
3726 AGTCGGAAAA
3736 ACAACAAGTAACCGGAACC
1 ACAACAAGTAACCGGAACC
* * *
3755 ACAATAAGTAACTGGTACC
1 ACAACAAGTAACCGGAACC
3774 ACAACA
1 ACAACA
3780 TCCAAATACC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.48, C:0.27, G:0.14, T:0.11
Consensus pattern (19 bp):
ACAACAAGTAACCGGAACC
Found at i:4356 original size:48 final size:47
Alignment explanation
Indices: 4304--4427 Score: 130
Period size: 48 Copynumber: 2.6 Consensus size: 47
4294 TCCTTTAAAG
4304 TTTTAGTTATTCATTTTTTTCTTTTCTTCTTAATTTAAGCATTCTTCA
1 TTTTAGTTATTCATTTTTTTCTTTTCTT-TTAATTTAAGCATTCTTCA
* * * * *
4352 TTTTAGTAATTCATTTCCTTTTC-TTTCTTTTAATTTTAGTATTTTTTA
1 TTTTAGTTATTCATTT--TTTTCTTTTCTTTTAATTTAAGCATTCTTCA
*
4400 TTTT--TTATTTATTTTTTAT-TTTTCTTTT
1 TTTTAGTTATTCATTTTTT-TCTTTTCTTTT
4428 TTTTGTCTCA
Statistics
Matches: 65, Mismatches: 7, Indels: 11
0.78 0.08 0.13
Matches are distributed among these distances:
44 3 0.05
45 9 0.14
46 8 0.12
48 34 0.52
49 6 0.09
50 5 0.08
ACGTcount: A:0.17, C:0.10, G:0.03, T:0.69
Consensus pattern (47 bp):
TTTTAGTTATTCATTTTTTTCTTTTCTTTTAATTTAAGCATTCTTCA
Found at i:4412 original size:11 final size:11
Alignment explanation
Indices: 4396--4420 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
4386 TTTAGTATTT
4396 TTTATTTTTTA
1 TTTATTTTTTA
4407 TTTATTTTTTA
1 TTTATTTTTTA
4418 TTT
1 TTT
4421 TTCTTTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTATTTTTTA
Found at i:5735 original size:11 final size:11
Alignment explanation
Indices: 5678--5763 Score: 60
Period size: 10 Copynumber: 8.3 Consensus size: 11
5668 TTCGATAATA
5678 TAATAATTATTT
1 TAATAA-TATTT
*
5690 T-ATAGTATTT
1 TAATAATATTT
*
5700 AAATAA-A-TT
1 TAATAATATTT
*
5709 TATTAATATTT
1 TAATAATATTT
*
5720 T-ATAATCTTT
1 TAATAATATTT
5730 TAATAA-A-TT
1 TAATAATATTT
5739 TAATAAGTATTT
1 TAATAA-TATTT
*
5751 T-ATAATTTTT
1 TAATAATATTT
5761 TAA
1 TAA
5764 ACTTTATTGA
Statistics
Matches: 57, Mismatches: 9, Indels: 17
0.69 0.11 0.20
Matches are distributed among these distances:
9 14 0.25
10 20 0.35
11 19 0.33
12 4 0.07
ACGTcount: A:0.42, C:0.01, G:0.02, T:0.55
Consensus pattern (11 bp):
TAATAATATTT
Found at i:5750 original size:31 final size:30
Alignment explanation
Indices: 5678--5763 Score: 109
Period size: 30 Copynumber: 2.8 Consensus size: 30
5668 TTCGATAATA
* *
5678 TAATAATTATTTTATAGTATTTAAATAAATT
1 TAATAA-TATTTTATAATATTTTAATAAATT
* *
5709 TATTAATATTTTATAATCTTTTAATAAATT
1 TAATAATATTTTATAATATTTTAATAAATT
*
5739 TAATAAGTATTTTATAATTTTTTAA
1 TAATAA-TATTTTATAATATTTTAA
5764 ACTTTATTGA
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
30 26 0.54
31 22 0.46
ACGTcount: A:0.42, C:0.01, G:0.02, T:0.55
Consensus pattern (30 bp):
TAATAATATTTTATAATATTTTAATAAATT
Found at i:6515 original size:31 final size:30
Alignment explanation
Indices: 6473--6559 Score: 95
Period size: 31 Copynumber: 2.8 Consensus size: 30
6463 TCAATAAAAT
6473 TTAAAAAATTATAAAATACTTATTAAATTTA
1 TTAAAAAATTATAAAATA-TTATTAAATTTA
* *
6504 TTAAAAGATTATAAAATTATTAATAAATTTA
1 TTAAAAAATTATAAAA-TATTATTAAATTTA
* *
6535 TCT-AAATACTATAAAATAATTATTA
1 T-TAAAAAATTATAAAAT-ATTATTA
6560 TATTATCGAA
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
30 1 0.02
31 44 0.92
32 3 0.06
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.41
Consensus pattern (30 bp):
TTAAAAAATTATAAAATATTATTAAATTTA
Found at i:12296 original size:35 final size:33
Alignment explanation
Indices: 12212--12297 Score: 86
Period size: 35 Copynumber: 2.5 Consensus size: 33
12202 AAAATATTTT
12212 TAATACAA-AAAACTTACAATAAGTATTAAATGG
1 TAATACAACAAAA-TTACAATAAGTATTAAATGG
* *
12245 TAAATGATAACCAAATTACAATAACTGATATTAAATGG
1 T-AAT-ACAACAAAATTACAATAA--G-TATTAAATGG
12283 TAATA-AACAAAATTA
1 TAATACAACAAAATTA
12298 ACTGAAATAC
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
33 1 0.02
34 3 0.07
35 21 0.48
36 4 0.09
37 4 0.09
38 11 0.25
ACGTcount: A:0.55, C:0.09, G:0.08, T:0.28
Consensus pattern (33 bp):
TAATACAACAAAATTACAATAAGTATTAAATGG
Found at i:16057 original size:23 final size:23
Alignment explanation
Indices: 16031--16088 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
16021 TTACATTTAT
*
16031 ATTTA-AATTTAAAATTTTAATTA
1 ATTTATAATTTAAAAGTTTAA-TA
*
16054 ATTTATAA-TTATAAGTTTAATA
1 ATTTATAATTTAAAAGTTTAATA
*
16076 CTTTATAATTTAA
1 ATTTATAATTTAA
16089 CGTTTTATAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
22 9 0.31
23 18 0.62
24 2 0.07
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (23 bp):
ATTTATAATTTAAAAGTTTAATA
Found at i:16058 original size:17 final size:17
Alignment explanation
Indices: 16009--16063 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
15999 TAAATATTAT
*
16009 ATTTTAATTAATTT-AC
1 ATTTTAATTAATTTAAA
*
16025 ATTTATATTTAAATTTAAA
1 ATTT-TAATT-AATTTAAA
*
16044 ATTTTAATTAATTTATA
1 ATTTTAATTAATTTAAA
16061 ATT
1 ATT
16064 ATAAGTTTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
16 4 0.12
17 14 0.44
18 9 0.28
19 5 0.16
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (17 bp):
ATTTTAATTAATTTAAA
Found at i:16082 original size:22 final size:23
Alignment explanation
Indices: 16046--16093 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 23
16036 AATTTAAAAT
16046 TTTAATTAATTTATAATTATAA-G
1 TTTAATTAATTTATAATT-TAACG
*
16069 TTTAA-TACTTTATAATTTAACG
1 TTTAATTAATTTATAATTTAACG
16091 TTT
1 TTT
16094 TATAAATCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 3 0.13
22 15 0.65
23 5 0.22
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.54
Consensus pattern (23 bp):
TTTAATTAATTTATAATTTAACG
Found at i:16095 original size:23 final size:23
Alignment explanation
Indices: 16031--16095 Score: 64
Period size: 23 Copynumber: 2.8 Consensus size: 23
16021 TTACATTTAT
*
16031 ATTTA-AATTTAAAATTTTAATTA
1 ATTTATAATTT-AAGTTTTAATTA
16054 ATTTATAATTATAAG-TTTAA-TA
1 ATTTATAATT-TAAGTTTTAATTA
*
16076 CTTTATAATTTAACGTTTTA
1 ATTTATAATTTAA-GTTTTA
16096 TAAATCAATT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
21 3 0.08
22 12 0.33
23 14 0.39
24 6 0.17
25 1 0.03
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.52
Consensus pattern (23 bp):
ATTTATAATTTAAGTTTTAATTA
Found at i:23335 original size:16 final size:16
Alignment explanation
Indices: 23314--23400 Score: 111
Period size: 16 Copynumber: 5.4 Consensus size: 16
23304 GGTATTACCC
23314 GACCTGTTTTCAACCT
1 GACCTGTTTTCAACCT
*
23330 GACCTGTTTTCAACAT
1 GACCTGTTTTCAACCT
* *
23346 GACTTGTTTTTAACCT
1 GACCTGTTTTCAACCT
* *
23362 GACTTGTTTTCAATCT
1 GACCTGTTTTCAACCT
* *
23378 GACATGTTTTTAACCT
1 GACCTGTTTTCAACCT
23394 GACCTGT
1 GACCTGT
23401 AAATGATCCA
Statistics
Matches: 61, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 61 1.00
ACGTcount: A:0.21, C:0.23, G:0.14, T:0.43
Consensus pattern (16 bp):
GACCTGTTTTCAACCT
Found at i:23361 original size:32 final size:32
Alignment explanation
Indices: 23318--23400 Score: 123
Period size: 32 Copynumber: 2.6 Consensus size: 32
23308 TTACCCGACC
* *
23318 TGTTTTCAACCTGACCTGTTTTCAA-CATGACT
1 TGTTTTTAACCTGACCTGTTTTCAATC-TGACA
*
23350 TGTTTTTAACCTGACTTGTTTTCAATCTGACA
1 TGTTTTTAACCTGACCTGTTTTCAATCTGACA
23382 TGTTTTTAACCTGACCTGT
1 TGTTTTTAACCTGACCTGT
23401 AAATGATCCA
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
32 45 0.98
33 1 0.02
ACGTcount: A:0.20, C:0.22, G:0.13, T:0.45
Consensus pattern (32 bp):
TGTTTTTAACCTGACCTGTTTTCAATCTGACA
Found at i:23691 original size:14 final size:14
Alignment explanation
Indices: 23669--23715 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
23659 TGCAAAGGAA
*
23669 AATTAATATAGTTT
1 AATTTATATAGTTT
23683 AATTTATATA----
1 AATTTATATAGTTT
23693 AA-TTATATAGTTT
1 AATTTATATAGTTT
23706 AATTTATATA
1 AATTTATATA
23716 ATGACAAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 10
0.71 0.03 0.26
Matches are distributed among these distances:
9 7 0.26
10 2 0.07
13 2 0.07
14 16 0.59
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (14 bp):
AATTTATATAGTTT
Found at i:23702 original size:23 final size:24
Alignment explanation
Indices: 23668--23716 Score: 91
Period size: 23 Copynumber: 2.1 Consensus size: 24
23658 ATGCAAAGGA
23668 AAATTAATATAGTTTAATTTATAT
1 AAATTAATATAGTTTAATTTATAT
23692 AAATT-ATATAGTTTAATTTATAT
1 AAATTAATATAGTTTAATTTATAT
23715 AA
1 AA
23717 TGACAAATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 20 0.80
24 5 0.20
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (24 bp):
AAATTAATATAGTTTAATTTATAT
Found at i:24027 original size:15 final size:15
Alignment explanation
Indices: 24007--24043 Score: 65
Period size: 15 Copynumber: 2.4 Consensus size: 15
23997 TAATTTACTT
24007 TATATAGTTTATATA
1 TATATAGTTTATATA
24022 TATATAGTTTATATA
1 TATATAGTTTATATA
24037 TACTATA
1 TA-TATA
24044 CATGGTACAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 17 0.81
16 4 0.19
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (15 bp):
TATATAGTTTATATA
Found at i:24513 original size:49 final size:49
Alignment explanation
Indices: 24469--24562 Score: 136
Period size: 48 Copynumber: 1.9 Consensus size: 49
24459 ATTTATGATT
* ** *
24469 TAGGGTTTTTATAAACTATATATTTTA-TTACTTTATATAGTTTATGCA
1 TAGGGTTTCTATAAACTATATAAGTAATTTACTTTATATAGTTTATGCA
*
24517 TAGTGTTTCTATAAACTATATAAGTAATTTACTTTATATAGTTTAT
1 TAGGGTTTCTATAAACTATATAAGTAATTTACTTTATATAGTTTAT
24563 ATATATATAG
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
48 22 0.55
49 18 0.45
ACGTcount: A:0.33, C:0.06, G:0.10, T:0.51
Consensus pattern (49 bp):
TAGGGTTTCTATAAACTATATAAGTAATTTACTTTATATAGTTTATGCA
Found at i:24571 original size:15 final size:15
Alignment explanation
Indices: 24551--24587 Score: 65
Period size: 15 Copynumber: 2.4 Consensus size: 15
24541 TAATTTACTT
24551 TATATAGTTTATATA
1 TATATAGTTTATATA
24566 TATATAGTTTATATA
1 TATATAGTTTATATA
24581 TACTATA
1 TA-TATA
24588 CATGGTTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 17 0.81
16 4 0.19
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (15 bp):
TATATAGTTTATATA
Found at i:24628 original size:14 final size:13
Alignment explanation
Indices: 24612--24636 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
24602 ACATATTATA
24612 AAAATTATTTAAT
1 AAAATTATTTAAT
24625 AAAATTATTTAA
1 AAAATTATTTAA
24637 ATGTAAATTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
AAAATTATTTAAT
Found at i:25009 original size:21 final size:20
Alignment explanation
Indices: 24944--25017 Score: 76
Period size: 21 Copynumber: 3.5 Consensus size: 20
24934 TCCATTTACA
*
24944 TTAGGGTTTATGATTTAGTAT
1 TTAGGGTTTATGGTTTAG-AT
* * *
24965 TTAGTGTTTGTGGTTTAAAGT
1 TTAGGGTTTATGGTTTAGA-T
24986 TTAGGGTTTATGGTTTATGAT
1 TTAGGGTTTATGGTTTA-GAT
*
25007 TTAAGGTTTAT
1 TTAGGGTTTAT
25018 ATAAACTATA
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
20 1 0.02
21 41 0.95
22 1 0.02
ACGTcount: A:0.22, C:0.00, G:0.26, T:0.53
Consensus pattern (20 bp):
TTAGGGTTTATGGTTTAGAT
Found at i:25051 original size:49 final size:50
Alignment explanation
Indices: 24998--25126 Score: 124
Period size: 49 Copynumber: 2.6 Consensus size: 50
24988 AGGGTTTATG
** *
24998 GTTTATGATTTAAGGTTTATATAAACTATATATTTTA-CTACTTTATATA
1 GTTTATGATTTAAGGTTTATATAAACTATATAAGTAATCTACTTTATATA
* * *
25047 GTTTATG-TAT-AGTGTTTCTATAAACTATATAAGTAATTTACTTTATATA
1 GTTTATGATTTAAG-GTTTATATAAACTATATAAGTAATCTACTTTATATA
*
25096 GTTTAT-ATATATATA-GTTTATATATACTATA
1 GTTTATGAT-T-TA-AGGTTTATATAAACTATA
25127 CATGGTTTAT
Statistics
Matches: 64, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
47 2 0.03
48 21 0.33
49 25 0.39
51 15 0.23
53 1 0.02
ACGTcount: A:0.36, C:0.05, G:0.09, T:0.50
Consensus pattern (50 bp):
GTTTATGATTTAAGGTTTATATAAACTATATAAGTAATCTACTTTATATA
Found at i:25110 original size:15 final size:15
Alignment explanation
Indices: 25090--25126 Score: 65
Period size: 15 Copynumber: 2.4 Consensus size: 15
25080 TAATTTACTT
25090 TATATAGTTTATATA
1 TATATAGTTTATATA
25105 TATATAGTTTATATA
1 TATATAGTTTATATA
25120 TACTATA
1 TA-TATA
25127 CATGGTTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 17 0.81
16 4 0.19
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (15 bp):
TATATAGTTTATATA
Found at i:25326 original size:549 final size:544
Alignment explanation
Indices: 23798--26578 Score: 4458
Period size: 558 Copynumber: 5.1 Consensus size: 544
23788 TTTTGGCAAT
* * *
23798 ACATTAGTTTACAAAGG-CTAATACATAAGCCCACTCTTTTATTACAAATATATATGCATTAGTG
1 ACATTAGTTTACATAGGCCCAATGC--AAGCCCACTCTTTTATTACAAATATATATGCATTAGTG
* *
23862 CTAGTCCATTTAAATTAGGATTTATGGTTTA-A---A-G-TTTA----AAATTGGGGTTTATGAT
64 CTAGTCCATTTAAATTAGGGTTTATGGTTTATATTTATGTTTTAGTTTAAATTAGGGTTTATGAT
* *
23917 TTAGGGTTTAGGGTTTCTATAAACTATATATTTTATTACTTTATATAGTTTATGCATAGTGTTTC
129 TTATGATTTAGGGTTTCTATAAACTATATATTTTATTACTTTATATAGTTTATGCATAGTGTTTC
23982 TATAAACTATATAAGTAATTTACTTTATATAGTTTATATATATATAGTTTATATATACTATACAT
194 TATAAACTATATAAGTAATTTACTTTATATAGTTTATATATATATAGTTTATATATACTATACAT
24047 GG----TACATACATATTATATAAAATTATTTAATAAAATTAATAAAATTATTTAAATGTAAATT
259 GGTTTATACATACATATTATATAAAATTATTTAATAAAATTAATAAAATTATTTAAATGTAAATT
*
24108 ATATAAAACATGATTAATGAGGTGTTAAATAATTAGTATGTCACATTGCATATTATATGGTTCAT
324 ATATAAAACATGATTAATTAGGTGTTAAATAATTAGTATGTCACATTGCATATTATATGGTTCAT
24173 AAATAGTAGTACATGTCATATTAATTTAAATTGCATAATTTGTATTTTAGTTGCATGTTAGGTTA
389 AAATAGTAGTACATGTCATATTAATTTAAATTGCATAATTTGTATTTTAGTTGCATGTTAGGTTA
24238 ATTCACATTAATGGCTCATTTATTTTGTTGTTATGAATAAGTAATAATAAAACCCAAAAATAAGT
454 ATTCACATTAATGGCTCATTTATTTTGTTGTTATGAATAAGTAATAATAAAACCCAAAAATAAGT
24303 CCATTTGCAATAGTGCTAGTCCATTA
519 CCATTTGCAATAGTGCTAGTCCATTA
24329 ACATTAGTTTACATAGGCCCAATGCAAGCCCACTCTTTTATTACAAATATATATGCATTAGTGCT
1 ACATTAGTTTACATAGGCCCAATGCAAGCCCACTCTTTTATTACAAATATATATGCATTAGTGCT
* * * * *
24394 AGTCCATTCAAATTAGGGTTTATAGTTTAGTGTTTATGGTTTAAAGTTTAGAATTAAGGTTTATG
66 AGTCCATTTAAATTAGGGTTTATGGTTTA-TATTTAT-GTTT-TAGTTTA-AATTAGGGTTTATG
*
24459 ATTTATGATTTAGGGTTTTTATAAACTATATATTTTATTACTTTATATAGTTTATGCATAGTGTT
127 ATTTATGATTTAGGGTTTCTATAAACTATATATTTTATTACTTTATATAGTTTATGCATAGTGTT
24524 TCTATAAACTATATAAGTAATTTACTTTATATAGTTTATATATATATAGTTTATATATACTATAC
192 TCTATAAACTATATAAGTAATTTACTTTATATAGTTTATATATATATAGTTTATATATACTATAC
24589 ATGGTTTATACATACATA-T-TATAAAA--A-TT-AT----TTAATAAAATTATTTAAATGTAAA
257 ATGGTTTATACATACATATTATATAAAATTATTTAATAAAATTAATAAAATTATTTAAATGTAAA
24644 TTATATAAAACATGATTAATTAGGTGTTAAATAATTAGTATGTCACATTGCATATTATATGGTTC
322 TTATATAAAACATGATTAATTAGGTGTTAAATAATTAGTATGTCACATTGCATATTATATGGTTC
*
24709 ATAAATAGTAGTTCATGTCATATTAATTTAAATTGCATAATTTGTATTTTAGTTGCATGTTAGGT
387 ATAAATAGTAGTACATGTCATATTAATTTAAATTGCATAATTTGTATTTTAGTTGCATGTTAGGT
* *
24774 TAATTCACATTAATGTCTCATTTATTTTGTTGTTATGAATAAGTAATAATAAAACCAAAAAATAA
452 TAATTCACATTAATGGCTCATTTATTTTGTTGTTATGAATAAGTAATAATAAAACCCAAAAATAA
24839 GTCCATTTGCAATAGTGCTAGTCCATTA
517 GTCCATTTGCAATAGTGCTAGTCCATTA
* * *
24867 ACATTAGTTTACATAGGCCTAGTGCAAGCCCACTCTTTTATTACAAATATATATGCAATAGTGCT
1 ACATTAGTTTACATAGGCCCAATGCAAGCCCACTCTTTTATTACAAATATATATGCATTAGTGCT
* * *
24932 AGTCCATTTACATTAGGGTTTATGATTTAGTATTTAGTGTTTGTGGTTTAAAGTTTAGGGTTTAT
66 AGTCCATTTAAATTAGGGTTTATGGTTTA-TATTTA-TGTTT-TAGTTTAAA--TTAGGGTTTAT
* * * * *
24997 GGTTTATGATTTAAGGTTTATATAAACTATATATTTTACTACTTTATATAGTTTATGTATAGTGT
126 GATTTATGATTTAGGGTTTCTATAAACTATATATTTTATTACTTTATATAGTTTATGCATAGTGT
25062 TTCTATAAACTATATAAGTAATTTACTTTATATAGTTTATATATATATAGTTTATATATACTATA
191 TTCTATAAACTATATAAGTAATTTACTTTATATAGTTTATATATATATAGTTTATATATACTATA
25127 CATGGTTTATACATACATATTATATAAAATTATTTAATAAAATTAATAAAATTATTTAAATGTAA
256 CATGGTTTATACATACATATTATATAAAATTATTTAATAAAATTAATAAAATTATTTAAATGTAA
25192 ATTATATAAAACATGATTAATTAGGTGTTAAATAATTAGTATGTCACATTGCATATTATATGGTT
321 ATTATATAAAACATGATTAATTAGGTGTTAAATAATTAGTATGTCACATTGCATATTATATGGTT
25257 CATAAATAGTAGTACATGTCATATTAATTTAAATTGCATAATTTGTATTTTAGTTGCATGTTAGG
386 CATAAATAGTAGTACATGTCATATTAATTTAAATTGCATAATTTGTATTTTAGTTGCATGTTAGG
25322 TTAATTCACATTAATGGCTCATTTATTTTGTTGTTATGAATAAGTAATAATAAAACCCAAAAATA
451 TTAATTCACATTAATGGCTCATTTATTTTGTTGTTATGAATAAGTAATAATAAAACCCAAAAATA
25387 AGTCCATTTGCAATAGTGCTAGTCCATTA
516 AGTCCATTTGCAATAGTGCTAGTCCATTA
25416 ACATTAGTTTACATAGGCCCAATGCAAGCCCACTCTTTTATTACAAATATATATGCATTAGTGCT
1 ACATTAGTTTACATAGGCCCAATGCAAGCCCACTCTTTTATTACAAATATATATGCATTAGTGCT
*
25481 AGTCCATTTAAATTAGGGTTTATGGTTTATGGTTTATGGTTTATGGTTTAAAGTTTAGAATTAGG
66 AGTCCATTTAAATTAGGGTTTATGGTTTA-----TA---TTTAT-GTTT-TAGTTTA-AATTAGG
* *
25546 GTTTATGATTTAGGATTTAGGGTTTTTATAAACTATATATTTTATTACTTTATATAGTTTATGCA
120 GTTTATGATTTATGATTTAGGGTTTCTATAAACTATATATTTTATTACTTTATATAGTTTATGCA
*
25611 TAGTATTTCTATAAACTATATAAGTAATTTACTTTATATAGTTTATATATATATGTTAGTTTATA
185 TAGTGTTTCTATAAACTATATAAGTAATTTACTTTATATAGTTTATATATATA---TAGTTTATA
25676 TATACTATACATGGTTTATACATACATATTATATAAAATTATTTAATAAAATTAATAAAATTATT
247 TATACTATACATGGTTTATACATACATATTATATAAAATTATTTAATAAAATTAATAAAATTATT
*
25741 TAAATGTAAATGATATAAAACATGATTAATTAGGTGTTAAATAATTAGTATGTCACATTGCATAT
312 TAAATGTAAATTATATAAAACATGATTAATTAGGTGTTAAATAATTAGTATGTCACATTGCATAT
25806 TATATGGTTCATAAATAGTAGTACATGTCATATTAATTTAAATTGCATAATTTGTATTTTAGTTG
377 TATATGGTTCATAAATAGTAGTACATGTCATATTAATTTAAATTGCATAATTTGTATTTTAGTTG
*
25871 CATGTTAGGTTAATTCACATTAATGGCTCATTTATTTTGTTGTTACGAATAAGTAATAATAAAAC
442 CATGTTAGGTTAATTCACATTAATGGCTCATTTATTTTGTTGTTATGAATAAGTAATAATAAAAC
*
25936 CAAAAAATAAGTCCATTTGCAATAGTGCTAGTCCATTA
507 CCAAAAATAAGTCCATTTGCAATAGTGCTAGTCCATTA
25974 ACATTAGTTTACATAGGCCCAATGCAAGCCCACTCTTTTATTACAAATATATATGCATTAGTGCT
1 ACATTAGTTTACATAGGCCCAATGCAAGCCCACTCTTTTATTACAAATATATATGCATTAGTGCT
26039 AGTCCATTTAAATTAGGGTTTATGGTTTA-A---A-G-TTTAG----AATTAGGGTTTATGA-TT
66 AGTCCATTTAAATTAGGGTTTATGGTTTATATTTATGTTTTAGTTTAAATTAGGGTTTATGATTT
* *
26093 -T-A---A-GGTTTCTATAAACTATATATTTTACTACTTTATATAGTTTATGTATAGTGTTTCTA
131 ATGATTTAGGGTTTCTATAAACTATATATTTTATTACTTTATATAGTTTATGCATAGTGTTTCTA
*
26152 TAAACTATATAAGTAATTTACTTTATATAGTTTATATATATATATATATATATATTTATATATAC
196 TAAACTATATAAGTAATTTACTTTATATAG------T-T-TATATATATATA-GTTTATATATAC
*
26217 TATGCATGGTTTATACATACATATTATATAAAATTATTTAATAAAATTAATAAAATTATTTAAAT
252 TATACATGGTTTATACATACATATTATATAAAATTATTTAATAAAATTAATAAAATTATTTAAAT
* *
26282 GTAAATTATATAAAACATGATTAATTAGGTGTTAAATAATTAGTATGTCACATTCCTTATTATAT
317 GTAAATTATATAAAACATGATTAATTAGGTGTTAAATAATTAGTATGTCACATTGCATATTATAT
* * * * *
26347 GGTTCATAAATAGTAGTACGTGTCATATTAATTTCATTTGCATAATTAGTATTTTAGTTACATGT
382 GGTTCATAAATAGTAGTACATGTCATATTAATTTAAATTGCATAATTTGTATTTTAGTTGCATGT
* * *
26412 TAGGTTAATTCACATTAATAGCCCATTTATTTTATTGTTATGAATAAGTAATAATAAAACCCAAA
447 TAGGTTAATTCACATTAATGGCTCATTTATTTTGTTGTTATGAATAAGTAATAATAAAACCCAAA
**
26477 AATAAGTCCATTTGCAATTTTGCTAGTCCATTA
512 AATAAGTCCATTTGCAATAGTGCTAGTCCATTA
* * * * *
26510 ACATTAATTTAGATAGACCCAATGTAAGCCCACTCTTTTATTACAAATATATATGCATTAGTGAT
1 ACATTAGTTTACATAGGCCCAATGCAAGCCCACTCTTTTATTACAAATATATATGCATTAGTGCT
26575 AGTC
66 AGTC
26579 TTTTTACATT
Statistics
Matches: 2113, Mismatches: 84, Indels: 101
0.92 0.04 0.04
Matches are distributed among these distances:
530 148 0.07
531 17 0.01
532 5 0.00
534 1 0.00
535 3 0.00
536 355 0.17
537 19 0.01
538 357 0.17
539 156 0.07
540 1 0.00
541 7 0.00
542 4 0.00
543 6 0.00
544 147 0.07
545 2 0.00
546 8 0.00
547 1 0.00
548 10 0.00
549 333 0.16
552 1 0.00
553 2 0.00
555 117 0.06
556 13 0.01
557 2 0.00
558 398 0.19
ACGTcount: A:0.36, C:0.09, G:0.12, T:0.42
Consensus pattern (544 bp):
ACATTAGTTTACATAGGCCCAATGCAAGCCCACTCTTTTATTACAAATATATATGCATTAGTGCT
AGTCCATTTAAATTAGGGTTTATGGTTTATATTTATGTTTTAGTTTAAATTAGGGTTTATGATTT
ATGATTTAGGGTTTCTATAAACTATATATTTTATTACTTTATATAGTTTATGCATAGTGTTTCTA
TAAACTATATAAGTAATTTACTTTATATAGTTTATATATATATAGTTTATATATACTATACATGG
TTTATACATACATATTATATAAAATTATTTAATAAAATTAATAAAATTATTTAAATGTAAATTAT
ATAAAACATGATTAATTAGGTGTTAAATAATTAGTATGTCACATTGCATATTATATGGTTCATAA
ATAGTAGTACATGTCATATTAATTTAAATTGCATAATTTGTATTTTAGTTGCATGTTAGGTTAAT
TCACATTAATGGCTCATTTATTTTGTTGTTATGAATAAGTAATAATAAAACCCAAAAATAAGTCC
ATTTGCAATAGTGCTAGTCCATTA
Found at i:25509 original size:7 final size:7
Alignment explanation
Indices: 25497--25530 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
25487 TTTAAATTAG
25497 GGTTTAT
1 GGTTTAT
25504 GGTTTAT
1 GGTTTAT
25511 GGTTTAT
1 GGTTTAT
25518 GGTTTAT
1 GGTTTAT
25525 GGTTTA
1 GGTTTA
25531 AAGTTTAGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (7 bp):
GGTTTAT
Found at i:25536 original size:21 final size:21
Alignment explanation
Indices: 25497--25537 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
25487 TTTAAATTAG
**
25497 GGTTTATGGTTTATGGTTTAT
1 GGTTTATGGTTTAAAGTTTAT
25518 GGTTTATGGTTTAAAGTTTA
1 GGTTTATGGTTTAAAGTTTA
25538 GAATTAGGGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.00, G:0.27, T:0.54
Consensus pattern (21 bp):
GGTTTATGGTTTAAAGTTTAT
Found at i:25567 original size:21 final size:21
Alignment explanation
Indices: 25493--25570 Score: 63
Period size: 21 Copynumber: 3.8 Consensus size: 21
25483 TCCATTTAAA
* * *
25493 TTAGGGTTTATGGTTTATGGT
1 TTAGGATTTAGGGTTTATGAT
* *
25514 TTATGG-TTTATGGTTTA-AAGT
1 TTA-GGATTTAGGGTTTATGA-T
*
25535 TTA-GAATTAGGGTTTATGAT
1 TTAGGATTTAGGGTTTATGAT
25555 TTAGGATTTAGGGTTT
1 TTAGGATTTAGGGTTT
25571 TTATAAACTA
Statistics
Matches: 46, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
19 1 0.02
20 13 0.28
21 30 0.65
22 2 0.04
ACGTcount: A:0.22, C:0.00, G:0.28, T:0.50
Consensus pattern (21 bp):
TTAGGATTTAGGGTTTATGAT
Found at i:26082 original size:27 final size:26
Alignment explanation
Indices: 26045--26100 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 26
26035 TGCTAGTCCA
*
26045 TTTAAATTAGGGTTTATGGTTTAAAG
1 TTTAAATTAGGGTTTATGATTTAAAG
*
26071 TTTAGAATTAGGGTTTATGATTTAAGG
1 TTTA-AATTAGGGTTTATGATTTAAAG
26098 TTT
1 TTT
26101 CTATAAACTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
26 4 0.15
27 23 0.85
ACGTcount: A:0.29, C:0.00, G:0.23, T:0.48
Consensus pattern (26 bp):
TTTAAATTAGGGTTTATGATTTAAAG
Found at i:26155 original size:48 final size:49
Alignment explanation
Indices: 26097--26191 Score: 138
Period size: 49 Copynumber: 2.0 Consensus size: 49
26087 ATGATTTAAG
** * *
26097 GTTTCTATAAACTATATATTTTA-CTACTTTATATAGTTTATGTATAGT
1 GTTTCTATAAACTATATAAGTAATCTACTTTATATAGTTTATATATAGT
*
26145 GTTTCTATAAACTATATAAGTAATTTACTTTATATAGTTTATATATA
1 GTTTCTATAAACTATATAAGTAATCTACTTTATATAGTTTATATATA
26192 TATATATATA
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
48 20 0.49
49 21 0.51
ACGTcount: A:0.35, C:0.07, G:0.07, T:0.51
Consensus pattern (49 bp):
GTTTCTATAAACTATATAAGTAATCTACTTTATATAGTTTATATATAGT
Found at i:26189 original size:2 final size:2
Alignment explanation
Indices: 26184--26215 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
26174 TTATATAGTT
*
26184 TA TA TA TA TA TA TA TA TA TA TA TT TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
26216 CTATGCATGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:27129 original size:64 final size:64
Alignment explanation
Indices: 27001--27140 Score: 192
Period size: 64 Copynumber: 2.2 Consensus size: 64
26991 GAACTGAAAA
* *
27001 TGACCCGACCTGAACCCGATCTGGATCTGGTGTCAAATCAACCTGAAAATAACCCGAACTGATT
1 TGACCCGACCTGAACCCGATCTGGATCTGATGTCAAATCAACCTGAAAATAACCCGAACCGATT
* * * * *
27065 TGACCTGACCTGAACCCGATCTGGATCTGATGTCAAATCAACCT-AAATTGACCTGTATCCGATT
1 TGACCCGACCTGAACCCGATCTGGATCTGATGTCAAATCAACCTGAAAATAACCCG-AACCGATT
*
27129 TTACCCGACCTG
1 TGACCCGACCTG
27141 TCAAGATCCG
Statistics
Matches: 66, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
63 8 0.12
64 58 0.88
ACGTcount: A:0.29, C:0.29, G:0.18, T:0.25
Consensus pattern (64 bp):
TGACCCGACCTGAACCCGATCTGGATCTGATGTCAAATCAACCTGAAAATAACCCGAACCGATT
Found at i:29830 original size:17 final size:17
Alignment explanation
Indices: 29810--29842 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
29800 CTCACTAACC
*
29810 CTTTTATTTTTTGTTCT
1 CTTTTATTTTGTGTTCT
29827 CTTTTATTTTGTGTTC
1 CTTTTATTTTGTGTTC
29843 ATCGTTTGCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.06, C:0.12, G:0.09, T:0.73
Consensus pattern (17 bp):
CTTTTATTTTGTGTTCT
Found at i:30475 original size:18 final size:19
Alignment explanation
Indices: 30454--30498 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
30444 ATTTAGACAT
30454 TTTGCATTTT-TTATTTTC
1 TTTGCATTTTGTTATTTTC
30472 TTTGCATTTTGTTATTTTC
1 TTTGCATTTTGTTATTTTC
*
30491 ATTGCATT
1 TTTGCATT
30499 CACATTAACT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 10 0.40
19 15 0.60
ACGTcount: A:0.13, C:0.11, G:0.09, T:0.67
Consensus pattern (19 bp):
TTTGCATTTTGTTATTTTC
Found at i:34068 original size:84 final size:82
Alignment explanation
Indices: 33902--34760 Score: 809
Period size: 84 Copynumber: 10.4 Consensus size: 82
33892 TAAAAGATAG
* * * * ** *
33902 CATTTGCAGCATAACTCAAGGCTATAAGGGTTATCTGCCAGTAAAGACCTTCGAGTTCGACCACG
1 CATTTGCAGCATAGCTCAAGGCGAGAAGGGCTATCTG-CAACAAAGACCTTCGAGTTCGACTACG
33967 CTCAGCTCCAAGGCACAT
65 CTCAGCTCCAAGGCACAT
** * * * *
33985 CATTTGCAATATAGCTCAAGGCAAGAAGGGCTATTTGCCAACAAAAGACCTTTGAGTTCGACTAT
1 CATTTGCAGCATAGCTCAAGGCGAGAAGGGCTATCTG-CAAC-AAAGACCTTCGAGTTCGACTAC
* *
34050 GCTCAACT-CAACGACACAT
64 GCTCAGCTCCAA-GGCACAT
* * * ** * *
34069 CATTTGTAGCATAGCTTAAGTCGAGAAGGGCTATCTGC--CAAAGACCCCCGAGTTCGATTACAC
1 CATTTGCAGCATAGCTCAAGGCGAGAAGGGCTATCTGCAACAAAGACCTTCGAGTTCGACTACGC
*
34132 TCAGCTTCAAGGGCACAT
66 TCAGCTCCAA-GGCACAT
* * * * *
34150 CATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTAACCAAAGACCTTCGAGTTCGACTACG
1 CATTTGCAGCATAGCTCAAGGCGAGAAGGGCTATCTGCAA-CAAAGACCTTCGAGTTCGACTACG
34215 CTCAGCTCCAAGGCACAT
65 CTCAGCTCCAAGGCACAT
* * * * * *
34233 CATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATATGC--CAAAGACCCTCGAGTTCGACTATGC
1 CATTTGCAGCATAGCTCAAGGCGAGAAGGGCTATCTGCAACAAAGACCTTCGAGTTCGACTACGC
* *
34296 TCAGCTTCGAGGGCACAT
66 TCAGC-TCCAAGGCACAT
* * * * * *
34314 CATTTACAGTATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACTAC
1 CATTTGCAGCATAGCTCAAGGCGAGAAGGGCTATCTG-CAAC-AAAGACCTTCGAGTTCGACTAC
34379 GCTCAGCTCCAAGGCACAT
64 GCTCAGCTCCAAGGCACAT
* * ** * *
34398 CATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGC--CAAAGACCCCCGAGTTCGATTACAC
1 CATTTGCAGCATAGCTCAAGGCGAGAAGGGCTATCTGCAACAAAGACCTTCGAGTTCGACTACGC
* * * *
34461 TTAGCTTCGAGGGCATAT
66 TCAGC-TCCAAGGCACAT
* * * * * * *
34479 CATTTACAGCATAACTCAAGGCTATAAGGGTTATATGTCACCAAAGACCTTCGAGTTCGACTACG
1 CATTTGCAGCATAGCTCAAGGCGAGAAGGGCTATCTG-CAACAAAGACCTTCGAGTTCGACTACG
* *
34544 CTCAGCTCCAAGGTATAT
65 CTCAGCTCCAAGGCACAT
* * * * * * * * *
34562 CATTTGCGGCACAACTTAAGTCTAGAAGGGTTGTCTACCAACCAAAGACCTTCGAGTTCGACTAC
1 CATTTGCAGCATAGCTCAAGGCGAGAAGGGCTATCT-GCAA-CAAAGACCTTCGAGTTCGACTAC
34627 GCTCAGCTCCAAGGCACAT
64 GCTCAGCTCCAAGGCACAT
* * * * *
34646 CATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG--TCAAAGACCTTCGAGTTCGATTACAC
1 CATTTGCAGCATAGCTCAAGGCGAGAAGGGCTATCTGCAACAAAGACCTTCGAGTTCGACTACGC
* *
34709 TCAACTCAAAGGCACCAT
66 TCAGCTCCAAGGCA-CAT
* * *
34727 CATTTACAACATAGCTCAAGGCAAGAAGGGCTAT
1 CATTTGCAGCATAGCTCAAGGCGAGAAGGGCTAT
34761 TTGTCAATAA
Statistics
Matches: 631, Mismatches: 127, Indels: 38
0.79 0.16 0.05
Matches are distributed among these distances:
80 110 0.17
81 151 0.24
82 2 0.00
83 113 0.18
84 228 0.36
85 27 0.04
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.24
Consensus pattern (82 bp):
CATTTGCAGCATAGCTCAAGGCGAGAAGGGCTATCTGCAACAAAGACCTTCGAGTTCGACTACGC
TCAGCTCCAAGGCACAT
Found at i:34234 original size:164 final size:164
Alignment explanation
Indices: 33902--34760 Score: 974
Period size: 164 Copynumber: 5.2 Consensus size: 164
33892 TAAAAGATAG
* * * * * * * *
33902 CATTTGCAGCATAACTCAAGGCTATAAGGGTTATCTGCCAGTAAAGACCTTCGAGTTCGACCACG
1 CATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCC---AAAGACCCTCGAGTTCGACTACG
* * ** * * * * * *
33967 CTCAGCTCCAA-GGCACATCATTTGCAATATAGCTCAAGGCAAGAAGGGCTATTTGCCAACAAAA
63 CTCAGCTTCAAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTG-TAACCAAA
* * * *
34031 GACCTTTGAGTTCGACTATGCTCAACT-CAACGACACAT
127 GACCTTCGAGTTCGACTACGCTCAGCTCCAA-GGCACAT
* * * *
34069 CATTTGTAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTC
1 CATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGACTACGCTC
34134 AGCTTCAAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTAACCAAAGACC
66 AGCTTCAAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTAACCAAAGACC
34199 TTCGAGTTCGACTACGCTCAGCTCCAAGGCACAT
131 TTCGAGTTCGACTACGCTCAGCTCCAAGGCACAT
* * *
34233 CATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATATGCCAAAGACCCTCGAGTTCGACTATGCTC
1 CATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGACTACGCTC
* * *
34298 AGCTTCGAGGGCACATCATTTACAGTATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGAC
66 AGCTTCAAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTAACC-AAAGAC
34363 CTTCGAGTTCGACTACGCTCAGCTCCAAGGCACAT
130 CTTCGAGTTCGACTACGCTCAGCTCCAAGGCACAT
* * * *
34398 CATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTT
1 CATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGACTACGCTC
* * * * *
34463 AGCTTCGAGGGCATATCATTTACAGCATAACTCAAGGCTATAAGGGTTATATGTCACCAAAGACC
66 AGCTTCAAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTAACCAAAGACC
* *
34528 TTCGAGTTCGACTACGCTCAGCTCCAAGGTATAT
131 TTCGAGTTCGACTACGCTCAGCTCCAAGGCACAT
* * * * * ** *
34562 CATTTGCGGCACAACTTAAGTCTAGAAGGGTTGTCTACCAACCAAAGACCTTCGAGTTCGACTAC
1 CATTTGCAGCATAGCTTAAGTCGAGAA-GG--G-CTATCTGCCAAAGACCCTCGAGTTCGACTAC
* * * * * * *
34627 GCTCAGCTCCAA-GGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGT---CAAA
62 GCTCAGCTTCAAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTAACCAAA
* * * *
34688 GACCTTCGAGTTCGATTACACTCAACTCAAAGGCACCAT
127 GACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCA-CAT
* * * * *
34727 CATTTACAACATAGCTCAAGGCAAGAAGGGCTAT
1 CATTTGCAGCATAGCTTAAGTCGAGAAGGGCTAT
34761 TTGTCAATAA
Statistics
Matches: 597, Mismatches: 87, Indels: 22
0.85 0.12 0.03
Matches are distributed among these distances:
161 3 0.01
162 1 0.00
164 275 0.46
165 216 0.36
167 69 0.12
168 33 0.06
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.24
Consensus pattern (164 bp):
CATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGACTACGCTC
AGCTTCAAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTAACCAAAGACC
TTCGAGTTCGACTACGCTCAGCTCCAAGGCACAT
Found at i:34397 original size:248 final size:244
Alignment explanation
Indices: 33902--34760 Score: 911
Period size: 248 Copynumber: 3.5 Consensus size: 244
33892 TAAAAGATAG
* * * *
33902 CATTTGCAGCATAACTCAAGGCTATAAGGGTTATCTG-CCAGTAAAGACCTTCGAGTTCGACCAC
1 CATTTGCAGCATAACTCAAGGCGAGAAGGGCTATCTGTCC---AAAGACCTTCGAGTTCGACTAC
* * * *
33966 GCTCAGCTCCAAGGCACATCATTTGCAATATAGCTCAAGGCAAGAAGGGCTATTTGCCAACAAAA
63 ACTCAGCTCCAAGGCACATCATTTACAACATAGCTCAAGGCAAGAAGGGCTATATGCC--C-AAA
* * * * * * *
34031 GACCTTTGAGTTCGACTATGCTCAACTCAACGACACATCATTTGTAGCATAGCTTAAGTCGAGAA
125 GACCTTCGAGTTCGACTATGCTCAGCTCAAAGGCACATCATTTGCAGCATAACTTAAGTCTAGAA
* ** * * *
34096 GGGCTATCTG--CCAAAGACCCCCGAGTTCGATTACACTCAGCTTCAAGGGCACAT
190 GGGTTATCTGCACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAA-GGCACAT
* * * *
34150 CATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTAACCAAAGACCTTCGAGTTCGACTACG
1 CATTTGCAGCATAACTCAAGGCGAGAAGGGCTATCTGT--CCAAAGACCTTCGAGTTCGACTACA
* ** * * *
34215 CTCAGCTCCAAGGCACATCATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATATG-CCAAAGACC
64 CTCAGCTCCAAGGCACATCATTTACAACATAGCTCAAGGCAAGAAGGGCTATATGCCCAAAGACC
* * * * * * *
34279 CTCGAGTTCGACTATGCTCAGCTTCGAGGGCACATCATTTACAGTATAACTCAAGGCTAGAAGGG
129 TTCGAGTTCGACTATGCTCAGC-TCAAAGGCACATCATTTGCAGCATAACTTAAGTCTAGAAGGG
34344 TTATCTGTCACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACAT
193 TTATCTG-CACC-AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACAT
* * * ** *
34398 CATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG-CCAAAGACCCCCGAGTTCGATTACACT
1 CATTTGCAGCATAACTCAAGGCGAGAAGGGCTATCTGTCCAAAGACCTTCGAGTTCGACTACACT
* * * * * * * * *
34462 TAGCTTCGAGGGCATATCATTTACAGCATAACTCAAGGCTATAAGGGTTATATGTCACCAAAGAC
66 CAGC-TCCAAGGCACATCATTTACAACATAGCTCAAGGCAAGAAGGGCTATATG-C-CCAAAGAC
* * * * * *
34527 CTTCGAGTTCGACTACGCTCAGCTCCAAGGTATATCATTTGCGGCACAACTTAAGTCTAGAAGGG
128 CTTCGAGTTCGACTATGCTCAGCTCAAAGGCACATCATTTGCAGCATAACTTAAGTCTAGAAGGG
* *
34592 TTGTCTACCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACAT
193 TTATCT-GC-ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACAT
* * * *
34646 CATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGT-CAAAGACCTTCGAGTTCGATTACACT
1 CATTTGCAGCATAACTCAAGGCGAGAAGGGCTATCTGTCCAAAGACCTTCGAGTTCGACTACACT
* *
34710 CAACTCAAAGGCACCATCATTTACAACATAGCTCAAGGCAAGAAGGGCTAT
66 CAGCTCCAAGGCA-CATCATTTACAACATAGCTCAAGGCAAGAAGGGCTAT
34761 TTGTCAATAA
Statistics
Matches: 520, Mismatches: 75, Indels: 32
0.83 0.12 0.05
Matches are distributed among these distances:
244 26 0.05
245 65 0.12
246 38 0.07
247 8 0.02
248 320 0.62
249 61 0.12
251 2 0.00
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.24
Consensus pattern (244 bp):
CATTTGCAGCATAACTCAAGGCGAGAAGGGCTATCTGTCCAAAGACCTTCGAGTTCGACTACACT
CAGCTCCAAGGCACATCATTTACAACATAGCTCAAGGCAAGAAGGGCTATATGCCCAAAGACCTT
CGAGTTCGACTATGCTCAGCTCAAAGGCACATCATTTGCAGCATAACTTAAGTCTAGAAGGGTTA
TCTGCACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACAT
Found at i:34582 original size:329 final size:330
Alignment explanation
Indices: 33944--34760 Score: 1119
Period size: 329 Copynumber: 2.5 Consensus size: 330
33934 ATCTGCCAGT
* *
33944 AAAGACCTTCGAGTTCGACCACGCTCAGCTCCAAGGCACATCATTTGCAATATAGCTCAAGGCAA
1 AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGTATAGCTCAAGGCAA
* * * * *
34009 GAAGGGCTATTTGCCAACAAAAGACCTTTGAGTTCGACTATGCTCAACT-CAACGACACATCATT
66 GAAGGGCTATCTGTC-ACAAAAGACCTTCGAGTTCGACTACGCTCAACTCCAA-GGCACATCATT
*
34073 TGTAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCT
129 TGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCT
*
34138 TCAAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTAACCAAAGACCTTCG
194 TCAAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATATGTAACCAAAGACCTTCG
* * *
34203 AGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGTATAGCTTAAGTCGAGAA-GG-G-CT
259 AGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCACAACTTAAGTCGAGAAGGGTGTCT
* *
34265 A-TATGCC
324 ACCA-ACC
* * * * * * *
34272 AAAGACCCTCGAGTTCGACTATGCTCAGCTTCGAGGGCACATCATTTACAGTATAACTCAAGGCT
1 AAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTGCAGTATAGCTCAAGGCA
* *
34337 AGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
65 AGAAGGGCTATCTGTCA-CAAAAGACCTTCGAGTTCGACTACGCTCAACTCCAAGGCACATCATT
*
34402 TGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTTAGCT
129 TGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCT
* * * *
34467 TCGAGGGCATATCATTTACAGCATAACTCAAGGCTATAAGGGTTATATGTCACCAAAGACCTTCG
194 TCAAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATATGTAACCAAAGACCTTCG
* * * *
34532 AGTTCGACTACGCTCAGCTCCAAGGTATATCATTTGCGGCACAACTTAAGTCTAGAAGGGTTGTC
259 AGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCACAACTTAAGTCGAGAAGGG-TGTC
34597 TACCAACC
323 TACCAACC
* * * *
34605 AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGA
1 AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGTATAGCTCAAGGCAA
* * *
34670 GAAGGGCTATCTGT--C-AAAGACCTTCGAGTTCGATTACACTCAACTCAAAGGCACCATCATTT
66 GAAGGGCTATCTGTCACAAAAGACCTTCGAGTTCGACTACGCTCAACTCCAAGGCA-CATCATTT
* * * * *
34732 ACAACATAGCTCAAGGCAAGAAGGGCTAT
130 GCAGCATAGCTTAAGTCGAGAAGGGCTAT
34761 TTGTCAATAA
Statistics
Matches: 428, Mismatches: 52, Indels: 17
0.86 0.10 0.03
Matches are distributed among these distances:
328 61 0.14
329 287 0.67
330 5 0.01
332 42 0.10
333 32 0.07
334 1 0.00
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (330 bp):
AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGTATAGCTCAAGGCAA
GAAGGGCTATCTGTCACAAAAGACCTTCGAGTTCGACTACGCTCAACTCCAAGGCACATCATTTG
CAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTC
AAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATATGTAACCAAAGACCTTCGAG
TTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCACAACTTAAGTCGAGAAGGGTGTCTAC
CAACC
Found at i:42012 original size:42 final size:42
Alignment explanation
Indices: 41966--42056 Score: 164
Period size: 42 Copynumber: 2.2 Consensus size: 42
41956 TTGGTTAATT
*
41966 ACTTATTAGTTATACTCTGTTTTTTGGAGTGAATTTTGGTGA
1 ACTTATTAGTTATACTCTGTTTCTTGGAGTGAATTTTGGTGA
*
42008 ACTTATTAGTTGTACTCTGTTTCTTGGAGTGAATTTTGGTGA
1 ACTTATTAGTTATACTCTGTTTCTTGGAGTGAATTTTGGTGA
42050 ACTTATT
1 ACTTATT
42057 CGTTCTACAC
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.21, C:0.09, G:0.21, T:0.49
Consensus pattern (42 bp):
ACTTATTAGTTATACTCTGTTTCTTGGAGTGAATTTTGGTGA
Found at i:47696 original size:17 final size:18
Alignment explanation
Indices: 47661--47697 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
47651 GGATTAATAA
47661 ATCTGAAAAGACATATTG
1 ATCTGAAAAGACATATTG
47679 ATCTGATAAA-AC-TATTG
1 ATCTGA-AAAGACATATTG
47696 AT
1 AT
47698 GTGCATAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.39
18 8 0.44
19 3 0.17
ACGTcount: A:0.43, C:0.11, G:0.14, T:0.32
Consensus pattern (18 bp):
ATCTGAAAAGACATATTG
Done.