Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000605.1 Hibiscus syriacus cultivar Beakdansim tig00001175_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: 52342
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:2173 original size:32 final size:32
Alignment explanation
Indices: 2132--2193 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
2122 TGGTTAAATA
*
2132 CATAGAGTTAATTATTGATGGACTCGAATTTT
1 CATAGAGTTAATTATTGATAGACTCGAATTTT
2164 CATAGAGTTAATTATTGATAGACTCGAATT
1 CATAGAGTTAATTATTGATAGACTCGAATT
2194 GAATATGGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.34, C:0.10, G:0.18, T:0.39
Consensus pattern (32 bp):
CATAGAGTTAATTATTGATAGACTCGAATTTT
Found at i:16636 original size:11 final size:11
Alignment explanation
Indices: 16622--16654 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
16612 TTTTGAATTA
16622 ATTAATATTTT
1 ATTAATATTTT
16633 ATTAATATTATT
1 ATTAATATT-TT
16645 -TTAATATTTT
1 ATTAATATTTT
16655 TATTCAAGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 2 0.10
11 17 0.81
12 2 0.10
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (11 bp):
ATTAATATTTT
Found at i:16979 original size:36 final size:37
Alignment explanation
Indices: 16939--17045 Score: 116
Period size: 36 Copynumber: 2.9 Consensus size: 37
16929 GGTTCAGTTA
16939 TGATCAAGC-ATGTAATTCCTTATATAGGTTTAGCAT-
1 TGATCAAGCTA-GTAATTCCTTATATAGGTTTAGCATC
* * *
16975 TGATCAA-TTGGTAATTCCTTAT-TGCAGGTTTAG-TTC
1 TGATCAAGCTAGTAATTCCTTATAT--AGGTTTAGCATC
*
17011 TGATCAAGCTAGTAATTCCTTATATAGGTTCAGCA
1 TGATCAAGCTAGTAATTCCTTATATAGGTTTAGCA
17046 CCGATTAGTT
Statistics
Matches: 57, Mismatches: 7, Indels: 13
0.74 0.09 0.17
Matches are distributed among these distances:
34 1 0.02
35 13 0.23
36 29 0.51
37 13 0.23
38 1 0.02
ACGTcount: A:0.28, C:0.15, G:0.18, T:0.39
Consensus pattern (37 bp):
TGATCAAGCTAGTAATTCCTTATATAGGTTTAGCATC
Found at i:16996 original size:35 final size:35
Alignment explanation
Indices: 16950--17065 Score: 110
Period size: 36 Copynumber: 3.3 Consensus size: 35
16940 GATCAAGCAT
16950 GTAATTCCTTATATAGGTTTAGCATTGATCAATTG
1 GTAATTCCTTATATAGGTTTAGCATTGATCAATTG
* * *
16985 GTAATTCCTTAT-TGCAGGTTTAG-TTCTGATCAAGCTA
1 GTAATTCCTTATAT--AGGTTTAGCAT-TGATCAA-TTG
* ** * *
17022 GTAATTCCTTATATAGGTTCAGCACCGATTAGTTG
1 GTAATTCCTTATATAGGTTTAGCATTGATCAATTG
17057 GTAATTCCT
1 GTAATTCCT
17066 AATGGACCTA
Statistics
Matches: 64, Mismatches: 11, Indels: 12
0.74 0.13 0.14
Matches are distributed among these distances:
34 1 0.02
35 23 0.36
36 26 0.41
37 13 0.20
38 1 0.02
ACGTcount: A:0.26, C:0.16, G:0.18, T:0.41
Consensus pattern (35 bp):
GTAATTCCTTATATAGGTTTAGCATTGATCAATTG
Found at i:17058 original size:72 final size:72
Alignment explanation
Indices: 16925--17065 Score: 203
Period size: 72 Copynumber: 2.0 Consensus size: 72
16915 GTGAAGTCTC
* **
16925 TGCAGGTTCAGTTATGATCAAGCATGTAATTCCTTATATAGGTTTAGCATTGATCAATTGGTAAT
1 TGCAGGTTCAGTTATGATCAAGCATGTAATTCCTTATATAGGTTCAGCACCGATCAATTGGTAAT
16990 TCCTTAT
66 TCCTTAT
* * * *
16997 TGCAGGTTTAGTTCTGATCAAGC-TAGTAATTCCTTATATAGGTTCAGCACCGATTAGTTGGTAA
1 TGCAGGTTCAGTTATGATCAAGCAT-GTAATTCCTTATATAGGTTCAGCACCGATCAATTGGTAA
17061 TTCCT
65 TTCCT
17066 AATGGACCTA
Statistics
Matches: 61, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
71 1 0.02
72 60 0.98
ACGTcount: A:0.26, C:0.16, G:0.19, T:0.39
Consensus pattern (72 bp):
TGCAGGTTCAGTTATGATCAAGCATGTAATTCCTTATATAGGTTCAGCACCGATCAATTGGTAAT
TCCTTAT
Found at i:18536 original size:34 final size:34
Alignment explanation
Indices: 18477--18543 Score: 84
Period size: 34 Copynumber: 1.9 Consensus size: 34
18467 TTCTATTAAG
*
18477 TTGTTTTCTCCTTTTTATCAAGAGAGAA-TTGTTT
1 TTGTTTTCTCCTTTTAATC-AGAGAGAAGTTGTTT
18511 TTGTTTTCTCCTTGTTAAATC-GAGAGAAGTTGT
1 TTGTTTTCTCCTT-TT-AATCAGAGAGAAGTTGT
18544 AACTCATATT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
34 20 0.69
35 6 0.21
36 3 0.10
ACGTcount: A:0.21, C:0.12, G:0.18, T:0.49
Consensus pattern (34 bp):
TTGTTTTCTCCTTTTAATCAGAGAGAAGTTGTTT
Found at i:20145 original size:17 final size:17
Alignment explanation
Indices: 20123--20169 Score: 85
Period size: 17 Copynumber: 2.8 Consensus size: 17
20113 AAACATTGTC
20123 ATTTTAAATAAAAATTA
1 ATTTTAAATAAAAATTA
20140 ATTTTAAATAAAAATTA
1 ATTTTAAATAAAAATTA
*
20157 ATTTTAATTAAAA
1 ATTTTAAATAAAA
20170 TAACAAATTG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
ATTTTAAATAAAAATTA
Found at i:21383 original size:45 final size:45
Alignment explanation
Indices: 21323--21412 Score: 153
Period size: 45 Copynumber: 2.0 Consensus size: 45
21313 TGATGTACCA
*
21323 ACTAAAGACTAATATTTAAACTTAAAAACAAAACCACGTGAAACC
1 ACTAAAGACTAATATTTAAACTTAAAAACAAAACCACGCGAAACC
* *
21368 ACTAAAGACTAATATTTTAACTTAAAAACTAAACCACGCGAAACC
1 ACTAAAGACTAATATTTAAACTTAAAAACAAAACCACGCGAAACC
21413 TAAACTTTTC
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.51, C:0.21, G:0.07, T:0.21
Consensus pattern (45 bp):
ACTAAAGACTAATATTTAAACTTAAAAACAAAACCACGCGAAACC
Found at i:23045 original size:42 final size:41
Alignment explanation
Indices: 22964--23064 Score: 130
Period size: 42 Copynumber: 2.4 Consensus size: 41
22954 AGGTCTTATG
* * * *
22964 GATGGCCCGAAGGACTTATCATCTTGCTCTAAAGGCTTACA
1 GATGGCCCGAAGGACTTAGCATCATGCTCGAAAGACTTACA
* * *
23005 GATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACT
1 GATGGCCCGAAGGACTT-AGCATCATGCTCGAAAGACTTACA
23047 GATGGCCCGAAGGACTTA
1 GATGGCCCGAAGGACTTA
23065 TAAATTGTGA
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
41 16 0.32
42 34 0.68
ACGTcount: A:0.30, C:0.23, G:0.24, T:0.24
Consensus pattern (41 bp):
GATGGCCCGAAGGACTTAGCATCATGCTCGAAAGACTTACA
Found at i:23244 original size:214 final size:216
Alignment explanation
Indices: 22717--23695 Score: 1441
Period size: 214 Copynumber: 4.5 Consensus size: 216
22707 ATCTTGGTGA
* * * * * * * * *
22717 AAAACATCCTGCCCGAAGATCTTATGGATGACCCGAAGGATTTATCATCTTTCTCGAGAGACTCA
1 AAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCTAAAGGCTTA
* * * * * * *
22782 CAAATGGCCCGAAGGATTTAAACATCATGCTCGAAAGACATATTGATGGCTCAAAGGACTTACT-
66 CAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTA-TA
* * * *
22846 AAGTGTGAAATTTTGAAAATCGA-ATTCTTAGTTTCCAAAAATTTCATCATCTTCAAACATCATT
130 AATTGTGAAATTTTGAAAATC-ACATTCTTAGTTTTCAAAAATTTCATCTTCTTAAAACATCA--
22910 TTCTCATTTTCATTTTCAAATTCATGTG
192 TT-T--TTTTCATTTTCAAATTCATGTG
22938 AAAACATCCTACCC-AGAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCTAAAGGCTT
1 AAAACATCCTACCCGA-AGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCTAAAGGCTT
23002 ACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATA
65 ACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATA
*
23067 AATTGTGAAATTTTGAAAATCACATTCTTAGTTTTTAAAAATTTCATCTTCTTAAAACATCA-TT
130 AATTGTGAAATTTTGAAAATCACATTCTTAGTTTTCAAAAATTTCATCTTCTTAAAACATCATTT
23131 TTTT-ATTTTCAAATTCATGTG
195 TTTTCATTTTCAAATTCATGTG
* * * *
23152 AAAACATCTTACCCGAAGGTTTTATGGATGGCTCGAAGGACTTATCATCTTGCCCTAAAGGCTTA
1 AAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCTAAAGGCTTA
* *
23217 CAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTATTGATGGCCCGAATGACTTATAA
66 CAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAA
*
23282 ATTGTGAAATTTTGAAAATCGCATTCTTAGTTTTCAAAAATTTCATCTTCTTAAAACATCA--TT
131 ATTGTGAAATTTTGAAAATCACATTCTTAGTTTTCAAAAATTTCATCTTCTTAAAACATCATTTT
23345 TTTCATTTTCAAATTCATGTG
196 TTTCATTTTCAAATTCATGTG
*
23366 AAAACATCCTACCCGAAGGTCTTATGGATGGCCCAAAGGACTTATCATCTTGCTCTAAAGGCTTA
1 AAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCTAAAGGCTTA
* * * *
23431 CAGATGACCTGAAGGTTTTAAGCATCATGCTCAAAAGACTTACTGATGGCCCGAATGACTTATAA
66 CAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAA
** * * *
23496 ATTGTGAAATTTTGAAAATCGTATTCTTCGTTTTAAAAAATTCCATCTTCTTAAAACATCATTTT
131 ATTGTGAAATTTTGAAAATCACATTCTTAGTTTTCAAAAATTTCATCTTCTTAAAACATCATTTT
23561 TTTCATTTTCAAATTCATGTG
196 TTTCATTTTCAAATTCATGTG
* * * * *
23582 AAAACATCCAACTCGAAGGTTTTATGGATGGCCTGAAGGACTTATCATCTTTCTCTAAAGGCTTA
1 AAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCTAAAGGCTTA
*
23647 CAGATGTCCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGG
66 CAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGG
23696 GTTTGCTTCA
Statistics
Matches: 699, Mismatches: 52, Indels: 19
0.91 0.07 0.02
Matches are distributed among these distances:
213 5 0.01
214 393 0.56
215 5 0.01
216 127 0.18
217 1 0.00
218 1 0.00
220 3 0.00
221 164 0.23
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Consensus pattern (216 bp):
AAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCTAAAGGCTTA
CAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAA
ATTGTGAAATTTTGAAAATCACATTCTTAGTTTTCAAAAATTTCATCTTCTTAAAACATCATTTT
TTTCATTTTCAAATTCATGTG
Found at i:23900 original size:37 final size:37
Alignment explanation
Indices: 23733--23921 Score: 231
Period size: 36 Copynumber: 5.1 Consensus size: 37
23723 CTCAAGGTGG
* * * *
23733 TGCTTCACTACTCTTCGATGAAGGCTTACAAATTGATT
1 TGCTTCACTCCTTTTCGGTGAAGGCTTA-AGATTGATT
* * *
23771 TGCTTCCCTCCTTTTTGGTGAAGGCTTAAGA-TGGTT
1 TGCTTCACTCCTTTTCGGTGAAGGCTTAAGATTGATT
* * *
23807 TTCTTCACTCCTTTTTGGTGAAGGCTTAAGA-TGGTT
1 TGCTTCACTCCTTTTCGGTGAAGGCTTAAGATTGATT
*
23843 TTCTTCACTCCTCTTT-GGTGAAGGCTTAAGATTGATT
1 TGCTTCACTCCT-TTTCGGTGAAGGCTTAAGATTGATT
23880 TGCTTCACTCCTTTTCGGTGAAGGCTTAAGATTGACTT
1 TGCTTCACTCCTTTTCGGTGAAGGCTTAAGATTGA-TT
23918 TGCT
1 TGCT
23922 CCAATCTCAT
Statistics
Matches: 136, Mismatches: 11, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
36 68 0.50
37 39 0.29
38 29 0.21
ACGTcount: A:0.19, C:0.20, G:0.21, T:0.41
Consensus pattern (37 bp):
TGCTTCACTCCTTTTCGGTGAAGGCTTAAGATTGATT
Found at i:23906 original size:73 final size:72
Alignment explanation
Indices: 23733--23921 Score: 234
Period size: 73 Copynumber: 2.6 Consensus size: 72
23723 CTCAAGGTGG
* * * * * *
23733 TGCTTCACTACTCTTCGATGAAGGCTTACAAATTGATTTGCTTCCCTCCTTTTTGGTGAAGGCTT
1 TGCTTCACTCCTTTTCGGTGAAGGCTTA-AGA-TGATTTGCTTCACTCCTCTTTGGTGAAGGCTT
*
23798 AAGATGGTT
64 AAGATGATT
* * * *
23807 TTCTTCACTCCTTTTTGGTGAAGGCTTAAGATGGTTTTCTTCACTCCTCTTTGGTGAAGGCTTAA
1 TGCTTCACTCCTTTTCGGTGAAGGCTTAAGATGATTTGCTTCACTCCTCTTTGGTGAAGGCTTAA
23872 GATTGATT
66 GA-TGATT
23880 TGCTTCACTCCTTTTCGGTGAAGGCTTAAGATTGACTTTGCT
1 TGCTTCACTCCTTTTCGGTGAAGGCTTAAGA-TGA-TTTGCT
23922 CCAATCTCAT
Statistics
Matches: 97, Mismatches: 15, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
72 32 0.33
73 35 0.36
74 25 0.26
75 5 0.05
ACGTcount: A:0.19, C:0.20, G:0.21, T:0.41
Consensus pattern (72 bp):
TGCTTCACTCCTTTTCGGTGAAGGCTTAAGATGATTTGCTTCACTCCTCTTTGGTGAAGGCTTAA
GATGATT
Found at i:31551 original size:17 final size:17
Alignment explanation
Indices: 31529--31570 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
31519 AAACATTGTC
*
31529 ATTTTAAATAAAAATTA
1 ATTTTAAATAAAAAGTA
31546 ATTTTAAATAAAAAGTA
1 ATTTTAAATAAAAAGTA
*
31563 AATTTAAA
1 ATTTTAAA
31571 ATTAATTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (17 bp):
ATTTTAAATAAAAAGTA
Found at i:32801 original size:45 final size:45
Alignment explanation
Indices: 32750--32839 Score: 180
Period size: 45 Copynumber: 2.0 Consensus size: 45
32740 TGATATACCA
32750 ACTAAAGACTAATATTTTAACTTAAAAACAAAACCACGTGAAACC
1 ACTAAAGACTAATATTTTAACTTAAAAACAAAACCACGTGAAACC
32795 ACTAAAGACTAATATTTTAACTTAAAAACAAAACCACGTGAAACC
1 ACTAAAGACTAATATTTTAACTTAAAAACAAAACCACGTGAAACC
32840 TAAACTTTTC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.51, C:0.20, G:0.07, T:0.22
Consensus pattern (45 bp):
ACTAAAGACTAATATTTTAACTTAAAAACAAAACCACGTGAAACC
Found at i:35094 original size:3 final size:3
Alignment explanation
Indices: 35086--35200 Score: 230
Period size: 3 Copynumber: 38.3 Consensus size: 3
35076 TCTATAAAAT
35086 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
35134 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
35182 ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA A
35201 AATGGTTTCA
Statistics
Matches: 112, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 112 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:35729 original size:131 final size:129
Alignment explanation
Indices: 35411--35753 Score: 397
Period size: 129 Copynumber: 2.6 Consensus size: 129
35401 AGCTCTGATG
* * ** *
35411 CTTTTCAGGGTAGATC-AGATTTGGAAACTTTGATTCACTTCACTGCTCTTTAGATAAGATTAAA
1 CTTTTTAGGGTAGATCTA-ATTTGGAAACTTTGATTCACTTCACTGCTCTTCAGGGAAGATTGAA
* * * * * * * *
35475 TC-AGGGTTGATTTGCTTCTCTGCTCTTTAGGGAAGATCAAATCTACAAAAGGTATATGATCCTC
65 TCGA-GGTTGATTTGCTTCACTGCTCTTCAGGGAAGAGCAAATATAAAAAAGGGACA-GATCCAC
35539 TA
128 TA
* *
35541 CTTTTTAGGGTAGAT-TAATCTGGAAACTTTGATTCACTTCACTGTTCTTCAGGGAAGATTGAAT
1 CTTTTTAGGGTAGATCTAATTTGGAAACTTTGATTCACTTCACTGCTCTTCAGGGAAGATTGAAT
* *
35605 CGAGGTAGATTTGCTTCACTGCTCTTCAGGGAAGAGCATATATGAAAAAAGGGACCA-ACTCCAC
66 CGAGGTTGATTTGCTTCACTGCTCTTCAGGGAAGAGCAAATAT-AAAAAAGGGA-CAGA-TCCAC
35669 TA
128 TA
* * ** * *
35671 CTTTTTAGGTTAGATCTTATTTGGAAACGATGATTCACTTCGCTGCTCTTCAGGGAAGATTGGAT
1 CTTTTTAGGGTAGATCTAATTTGGAAACTTTGATTCACTTCACTGCTCTTCAGGGAAGATTGAAT
35736 CGAGGTTGATTTGCTTCA
66 CGAGGTTGATTTGCTTCA
35754 TTGTTTTTCA
Statistics
Matches: 181, Mismatches: 26, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
129 77 0.43
130 44 0.24
131 60 0.33
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.35
Consensus pattern (129 bp):
CTTTTTAGGGTAGATCTAATTTGGAAACTTTGATTCACTTCACTGCTCTTCAGGGAAGATTGAAT
CGAGGTTGATTTGCTTCACTGCTCTTCAGGGAAGAGCAAATATAAAAAAGGGACAGATCCACTA
Found at i:35770 original size:131 final size:130
Alignment explanation
Indices: 35411--35779 Score: 341
Period size: 131 Copynumber: 2.8 Consensus size: 130
35401 AGCTCTGATG
* * * ** * ** *
35411 CTTTTCAGGGTAGATCAGATTTGGAAACTTTGATTCACTTCACTGCTCTTTAGATAAGATTAAAT
1 CTTTTTAGGGTAGATTA-ATCTGGAAACGATGATTCACTTCACTGCTCTTCAGGGAAGATTGAAT
* * * ** * * * * *
35476 C-AGGGTTGATTTGCTTCTCTGCTCTTTAGGGAAGATCAAATCT-ACAAAAGGTA-TATGA-TCC
65 CGA-GGTAGATTTGCTTCACTGCTCTTCAAAGAAGAGCAAATATGAAAAAAGGGACCA--ACTCC
*
35537 TCTA
127 ACTA
** *
35541 CTTTTTAGGGTAGATTAATCTGGAAACTTTGATTCACTTCACTGTTCTTCAGGGAAGATTGAATC
1 CTTTTTAGGGTAGATTAATCTGGAAACGATGATTCACTTCACTGCTCTTCAGGGAAGATTGAATC
** *
35606 GAGGTAGATTTGCTTCACTGCTCTTCAGGGAAGAGCATATATGAAAAAAGGGACCAACTCCACTA
66 GAGGTAGATTTGCTTCACTGCTCTTCAAAGAAGAGCAAATATGAAAAAAGGGACCAACTCCACTA
* * * * *
35671 CTTTTTAGGTTAGATCTTATTTGGAAACGATGATTCACTTCGCTGCTCTTCAGGGAAGATTGGAT
1 CTTTTTAGGGTAGAT-TAATCTGGAAACGATGATTCACTTCACTGCTCTTCAGGGAAGATTGAAT
* * * * *
35736 CGAGGTTGATTTGCTTCATTGTTTTTCAAAGAAGATCAAATATG
65 CGAGGTAGATTTGCTTCACTGCTCTTCAAAGAAGAGCAAATATG
35780 GAGAAAGATG
Statistics
Matches: 200, Mismatches: 34, Indels: 9
0.82 0.14 0.04
Matches are distributed among these distances:
129 77 0.38
130 44 0.22
131 79 0.40
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.35
Consensus pattern (130 bp):
CTTTTTAGGGTAGATTAATCTGGAAACGATGATTCACTTCACTGCTCTTCAGGGAAGATTGAATC
GAGGTAGATTTGCTTCACTGCTCTTCAAAGAAGAGCAAATATGAAAAAAGGGACCAACTCCACTA
Found at i:36967 original size:45 final size:45
Alignment explanation
Indices: 36907--37441 Score: 624
Period size: 45 Copynumber: 11.9 Consensus size: 45
36897 AGTCAAGTTG
* * *
36907 AGAATGACATCACTAAAAGGTTTACTCATCTTCCCGAGAAAGTCA
1 AGAATGACATCACTAAAAGGTTGACTCCTCTTCGCGAGAAAGTCA
* * * * *
36952 AGAATCATATAACTAAAAGGTTGACTCATCTTCGCGAGGAAGTCA
1 AGAATGACATCACTAAAAGGTTGACTCCTCTTCGCGAGAAAGTCA
* *
36997 AGAATGACATCACTAAAAGGTTGACTCATCTTCGTGAGAAAGTCA
1 AGAATGACATCACTAAAAGGTTGACTCCTCTTCGCGAGAAAGTCA
* *
37042 AGAATGACATTACTAAAAGGTTGACTCCTCTTCACGAGAAAGTCA
1 AGAATGACATCACTAAAAGGTTGACTCCTCTTCGCGAGAAAGTCA
*
37087 AGAATGACATCACTAAAAGGTTGACTCCTCTTCGCGATAAAGTCA
1 AGAATGACATCACTAAAAGGTTGACTCCTCTTCGCGAGAAAGTCA
*
37132 AGAATGACATCACTAAAAGGTTGACTCCTCTTTGCGAGAAAGTCA
1 AGAATGACATCACTAAAAGGTTGACTCCTCTTCGCGAGAAAGTCA
* * *
37177 AGAATGACATCA-TTAAAGGTTTACTCCTTTTCGCGAGAAAGTCA
1 AGAATGACATCACTAAAAGGTTGACTCCTCTTCGCGAGAAAGTCA
* * * ** * * * *
37221 AGAAGGAAAACACCGAAAGATTGACTCCTCTTCACAAGAAAGTTA
1 AGAATGACATCACTAAAAGGTTGACTCCTCTTCGCGAGAAAGTCA
* * * * *
37266 AGAATGACAACGCTAAAAGATTAACTCCTCTTCACGAGAAAGTCA
1 AGAATGACATCACTAAAAGGTTGACTCCTCTTCGCGAGAAAGTCA
* * * * * *
37311 AGAATGATAACACTGAAAGATTGACTCCTCTTCACGAGAAATTCA
1 AGAATGACATCACTAAAAGGTTGACTCCTCTTCGCGAGAAAGTCA
* * * ** * *
37356 AGATTGA-AACACTGAAATATTGATTCCTCTTCACGAGAAAGTCA
1 AGAATGACATCACTAAAAGGTTGACTCCTCTTCGCGAGAAAGTCA
* * * *
37400 AGAATGACATCACTAAAAGATTGACCCCTATTCACGAGAAAG
1 AGAATGACATCACTAAAAGGTTGACTCCTCTTCGCGAGAAAG
37442 GTAAGTTGAG
Statistics
Matches: 429, Mismatches: 59, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
44 77 0.18
45 352 0.82
ACGTcount: A:0.39, C:0.20, G:0.18, T:0.24
Consensus pattern (45 bp):
AGAATGACATCACTAAAAGGTTGACTCCTCTTCGCGAGAAAGTCA
Found at i:37395 original size:179 final size:180
Alignment explanation
Indices: 36901--37446 Score: 666
Period size: 179 Copynumber: 3.0 Consensus size: 180
36891 CGAGAAAGTC
* * * * *
36901 AAGTTGAGAATGACATCACTAAAAGGTTTACTCATCTTCCCGAGAAAGTCAAGAATCATATA-AC
1 AAGTTAAGAATGACATCACTAAAAGGTTAACTCCTCTTCACGAGAAAGTCAAGAATGATA-ACAC
* * *
36965 TAAAAGGTTGACTCATCTTCGCGAGGAAGTCAAGAATGACATCACTAAAAGGTTGACTCATCTTC
65 TAAAAGGTTGACTCCTCTTCGCGAGAAAGTCAAGAATGACATCACTAAAAGGTTGACTCCTCTTC
* * *
37030 GTGAGAAAGTCAAGAATGACATTACTAAAAGGTTGACTCCTCTTCACGAGA
130 GCGAGAAAGTCAAGAATGACATCACTAAAAGATTGACTCCTCTTCACGAGA
* * * * * *
37081 AAGTCAAGAATGACATCACTAAAAGGTTGACTCCTCTTCGCGATAAAGTCAAGAATGACATCACT
1 AAGTTAAGAATGACATCACTAAAAGGTTAACTCCTCTTCACGAGAAAGTCAAGAATGATAACACT
* * * *
37146 AAAAGGTTGACTCCTCTTTGCGAGAAAGTCAAGAATGACATCA-TTAAAGGTTTACTCCTTTTCG
66 AAAAGGTTGACTCCTCTTCGCGAGAAAGTCAAGAATGACATCACTAAAAGGTTGACTCCTCTTCG
* * * ** *
37210 CGAGAAAGTCAAGAAGGAAAACACCGAAAGATTGACTCCTCTTCACAAGA
131 CGAGAAAGTCAAGAATGACATCACTAAAAGATTGACTCCTCTTCACGAGA
* * *
37260 AAGTTAAGAATGACAACGCTAAAAGATTAACTCCTCTTCACGAGAAAGTCAAGAATGATAACACT
1 AAGTTAAGAATGACATCACTAAAAGGTTAACTCCTCTTCACGAGAAAGTCAAGAATGATAACACT
* * * * * * * ** * *
37325 GAAAGATTGACTCCTCTTCACGAGAAATTCAAGATTGA-AACACTGAAATATTGATTCCTCTTCA
66 AAAAGGTTGACTCCTCTTCGCGAGAAAGTCAAGAATGACATCACTAAAAGGTTGACTCCTCTTCG
* *
37389 CGAGAAAGTCAAGAATGACATCACTAAAAGATTGACCCCTATTCACGAGA
131 CGAGAAAGTCAAGAATGACATCACTAAAAGATTGACTCCTCTTCACGAGA
*
37439 AAGGTAAG
1 AAGTTAAG
37447 TTGAGGTTTA
Statistics
Matches: 307, Mismatches: 57, Indels: 5
0.83 0.15 0.01
Matches are distributed among these distances:
178 3 0.01
179 209 0.68
180 95 0.31
ACGTcount: A:0.39, C:0.20, G:0.18, T:0.24
Consensus pattern (180 bp):
AAGTTAAGAATGACATCACTAAAAGGTTAACTCCTCTTCACGAGAAAGTCAAGAATGATAACACT
AAAAGGTTGACTCCTCTTCGCGAGAAAGTCAAGAATGACATCACTAAAAGGTTGACTCCTCTTCG
CGAGAAAGTCAAGAATGACATCACTAAAAGATTGACTCCTCTTCACGAGA
Found at i:38958 original size:9 final size:9
Alignment explanation
Indices: 38946--39085 Score: 54
Period size: 8 Copynumber: 16.2 Consensus size: 9
38936 TATGTTCTAT
38946 TTCTTCTTC
1 TTCTTCTTC
*
38955 TTCTTATTC
1 TTCTTCTTC
*
38964 TTCTTCTTT
1 TTCTTCTTC
*
38973 TTC-TCTTT
1 TTCTTCTTC
*
38981 TTC-TCTTT
1 TTCTTCTTC
38989 TTC-TCTT-
1 TTCTTCTTC
38996 TTCATT-TT-
1 TTC-TTCTTC
*
39004 TTCTTCTCTA
1 TTCTTCT-TC
*
39014 TTTTTCTTC
1 TTCTTCTTC
*
39023 TT-TTTTTC
1 TTCTTCTTC
39031 TT-TTCATTC
1 TTCTTC-TTC
39040 TTTCTT-TTC
1 -TTCTTCTTC
39049 ATTCTTTCTT-
1 -TTC-TTCTTC
*
39059 TTCTTTTTC
1 TTCTTCTTC
39068 TATCTT-TTC
1 T-TCTTCTTC
39077 -TCTT-TTC
1 TTCTTCTTC
39084 TT
1 TT
39086 TCTTGGTCTT
Statistics
Matches: 109, Mismatches: 9, Indels: 27
0.75 0.06 0.19
Matches are distributed among these distances:
7 12 0.11
8 40 0.37
9 39 0.36
10 14 0.13
11 4 0.04
ACGTcount: A:0.04, C:0.23, G:0.00, T:0.73
Consensus pattern (9 bp):
TTCTTCTTC
Found at i:38981 original size:8 final size:8
Alignment explanation
Indices: 38968--39034 Score: 61
Period size: 8 Copynumber: 8.8 Consensus size: 8
38958 TTATTCTTCT
38968 TCTTTTTC
1 TCTTTTTC
38976 TCTTTTTC
1 TCTTTTTC
38984 TCTTTTTC
1 TCTTTTTC
38992 TC-TTTTC
1 TCTTTTTC
*
38999 -ATTTTT-
1 TCTTTTTC
*
39005 TC-TTCTC
1 TCTTTTTC
*
39012 TATTTTTC
1 TCTTTTTC
*
39020 TTCTTTTTT
1 -TCTTTTTC
39029 TCTTTT
1 TCTTTT
39035 CATTCTTTCT
Statistics
Matches: 47, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
6 3 0.06
7 10 0.21
8 28 0.60
9 6 0.13
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.76
Consensus pattern (8 bp):
TCTTTTTC
Found at i:39008 original size:13 final size:13
Alignment explanation
Indices: 38986--39086 Score: 84
Period size: 13 Copynumber: 7.8 Consensus size: 13
38976 TCTTTTTCTC
38986 TTTTTCTCTTTTCA
1 TTTTT-TCTTTTCA
*
39000 TTTTTTCTTCTC-
1 TTTTTTCTTTTCA
*
39012 TATTTTTC--TTCT
1 T-TTTTTCTTTTCA
39024 TTTTTTCTTTTCA
1 TTTTTTCTTTTCA
*
39037 TTCTTTCTTTTCA
1 TTTTTTCTTTTCA
* *
39050 TTCTTTCTTTTCT
1 TTTTTTCTTTTCA
39063 TTTTCTATCTTTTC-
1 TTTT-T-TCTTTTCA
*
39077 TCTTTTCTTT
1 TTTTTTCTTT
39087 CTTGGTCTTG
Statistics
Matches: 74, Mismatches: 7, Indels: 14
0.78 0.07 0.15
Matches are distributed among these distances:
11 8 0.11
12 7 0.09
13 43 0.58
14 9 0.12
15 7 0.09
ACGTcount: A:0.05, C:0.21, G:0.00, T:0.74
Consensus pattern (13 bp):
TTTTTTCTTTTCA
Found at i:39008 original size:37 final size:36
Alignment explanation
Indices: 38971--39086 Score: 117
Period size: 37 Copynumber: 3.1 Consensus size: 36
38961 TTCTTCTTCT
38971 TTTTCTCTTTTTCTCTTTTTCTCTTTTCATTTTTTC
1 TTTTCTCTTTTTCTCTTTTTCTCTTTTCATTTTTTC
* * * *
39007 TTCTCTATTTTTCTTCTTTTTTTCTTTTCATTCTTTC
1 TTTTCTCTTTTTC-TCTTTTTCTCTTTTCATTTTTTC
* *
39044 TTTTCATTCTTTCTTTTCTTTTTCTATCTTTTC-TCTTTTC
1 TTTTC--TCTTT-TTCTCTTTTTC--TCTTTTCATTTTTTC
39084 TTT
1 TTT
39087 CTTGGTCTTG
Statistics
Matches: 64, Mismatches: 10, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
36 11 0.17
37 25 0.39
39 11 0.17
40 10 0.16
41 7 0.11
ACGTcount: A:0.04, C:0.22, G:0.00, T:0.74
Consensus pattern (36 bp):
TTTTCTCTTTTTCTCTTTTTCTCTTTTCATTTTTTC
Found at i:39089 original size:9 final size:9
Alignment explanation
Indices: 38945--39089 Score: 57
Period size: 9 Copynumber: 16.7 Consensus size: 9
38935 ATATGTTCTA
38945 TTTCTTCTTC
1 TTTCTT-TTC
38955 -TTCTTATTC
1 TTTCTT-TTC
38964 -TTCTTCTT-
1 TTTCTT-TTC
38972 TTTCTCTTT-
1 TTTCT-TTTC
38981 TTCTCTTTT-
1 TT-TCTTTTC
*
38990 TCTCTTTTC
1 TTTCTTTTC
*
38999 ATT-TTTTC
1 TTTCTTTTC
*
39007 TTCTCTATT-
1 TT-TCTTTTC
39016 TTTC--TTC
1 TTTCTTTTC
39023 TTT-TTTTC
1 TTTCTTTTC
*
39031 TTT-TCATTC
1 TTTCT-TTTC
39040 TTTCTTTTC
1 TTTCTTTTC
*
39049 ATTC-TTTC
1 TTTCTTTTC
39057 TTTTCTTTTTC
1 -TTTC-TTTTC
*
39068 TATCTTTTC
1 TTTCTTTTC
39077 --TCTTTTC
1 TTTCTTTTC
39084 TTTCTT
1 TTTCTT
39090 GGTCTTGAAT
Statistics
Matches: 107, Mismatches: 12, Indels: 33
0.70 0.08 0.22
Matches are distributed among these distances:
6 2 0.02
7 10 0.09
8 25 0.23
9 55 0.51
10 11 0.10
11 4 0.04
ACGTcount: A:0.04, C:0.23, G:0.00, T:0.73
Consensus pattern (9 bp):
TTTCTTTTC
Done.