Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005523.1 Hibiscus syriacus cultivar Beakdansim tig00012758_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: 54423
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Found at i:808 original size:29 final size:29
Alignment explanation
Indices: 766--826 Score: 122
Period size: 29 Copynumber: 2.1 Consensus size: 29
756 AATGATTCAT
766 TGAAAAGTTCTACTGTGACTTTCATACTA
1 TGAAAAGTTCTACTGTGACTTTCATACTA
795 TGAAAAGTTCTACTGTGACTTTCATACTA
1 TGAAAAGTTCTACTGTGACTTTCATACTA
824 TGA
1 TGA
827 TTTTAAATCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.38
Consensus pattern (29 bp):
TGAAAAGTTCTACTGTGACTTTCATACTA
Found at i:2550 original size:3 final size:3
Alignment explanation
Indices: 2542--2577 Score: 63
Period size: 3 Copynumber: 11.7 Consensus size: 3
2532 ATTGAAAAAT
2542 TTA TTA TTA TTA TTA TTA TTA TTTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TT
2578 TTGAAAAATG
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:3610 original size:2 final size:2
Alignment explanation
Indices: 3603--3636 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3593 ACTAAAGTAA
3603 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3637 TTAGGGTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5280 original size:3 final size:3
Alignment explanation
Indices: 5272--5306 Score: 52
Period size: 3 Copynumber: 11.0 Consensus size: 3
5262 ACAATTTATT
5272 TAA TAA TAA TAA TAA TATA TAA TAAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TA-A TAA T-AA TAA TAA TAA
5307 AAAATAAGTG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
3 24 0.80
4 6 0.20
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:5312 original size:17 final size:17
Alignment explanation
Indices: 5279--5313 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
5269 ATTTAATAAT
* *
5279 AATAATAATATATAATA
1 AATAATAATAAAAAATA
5296 AATAATAATAAAAAATA
1 AATAATAATAAAAAATA
5313 A
1 A
5314 GTGAAAAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
AATAATAATAAAAAATA
Found at i:5762 original size:140 final size:136
Alignment explanation
Indices: 5451--5808 Score: 441
Period size: 140 Copynumber: 2.6 Consensus size: 136
5441 TGGAAATATT
* * * *
5451 GAACAAATTCTTCTTATTATGAACTT-TTCTTCCTTTTCAAATGAGTTCTTCTCATTATGAACTC
1 GAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTC
* * * * * * *
5515 CTTCTGAAAATATCGATCCTCAAAAGAGGTGTCGTTGATTCAACTTCATATGTGATGAATTAAGG
66 C-TCTGAAAATGTTGATCCTCAAAAGAGGTGTCGTTAATTCAACTCCATAGGTGACGAATCAAGG
**
5580 CAAGGTT
130 CAAGGCC
* *
5587 GAACAAGTTCTTCTCATTATGAATTTCTTCTTCCTCTTCAGATGAGTTATTCTCATTATGAACTT
1 GAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAAC-T
* * *
5652 CCTCTGAAAATGTTGATCCCTCGAATGAGGT-TCTTTTCTAATTCAACTCCATAGGTGACGAATC
65 CCTCTGAAAATGTTGAT-CCTCAAAAGAGGTGTC--GT-TAATTCAACTCCATAGGTGACGAATC
**
5716 AAGTTAAGGCC
126 AAGGCAAGGCC
5727 GAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTC
1 GAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTC
* *
5792 TATCTGGAAATGTTGAT
66 -CTCTGAAAATGTTGAT
5809 GTTGATCTAT
Statistics
Matches: 191, Mismatches: 24, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
136 23 0.12
137 48 0.25
138 14 0.07
139 3 0.02
140 103 0.54
ACGTcount: A:0.27, C:0.20, G:0.15, T:0.39
Consensus pattern (136 bp):
GAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTC
CTCTGAAAATGTTGATCCTCAAAAGAGGTGTCGTTAATTCAACTCCATAGGTGACGAATCAAGGC
AAGGCC
Found at i:5946 original size:123 final size:123
Alignment explanation
Indices: 5727--6051 Score: 553
Period size: 123 Copynumber: 2.6 Consensus size: 123
5717 AGTTAAGGCC
5727 GAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTC
1 GAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTC
* *
5792 TATCTGGAAATGTTGATGTTGATCTATCTCCTTCTGTGATAGAGTCGAGAAAAAGGTT
66 TCTCTGGAAATGTTGATGTTGATATATCTCCTTCTGTGATAGAGTCGAGAAAAAGGTT
*
5850 GAACAATTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTC
1 GAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTC
* *
5915 TCTCTGGAAATGTTGGTGTTGATATATCTCCTTCTGTGATAGAGTCGAGCAAAAGGTT
66 TCTCTGGAAATGTTGATGTTGATATATCTCCTTCTGTGATAGAGTCGAGAAAAAGGTT
* * *
5973 GCACAAGTTCTTCTCATTATGAACTTATTCTTCCTCTTCAAATGAGTTCTTCTCATTATGAACTC
1 GAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTC
*
6038 TAC-CTGGCAATGTT
66 T-CTCTGGAAATGTT
6052 AATCCATCGA
Statistics
Matches: 191, Mismatches: 10, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
123 190 0.99
124 1 0.01
ACGTcount: A:0.24, C:0.20, G:0.16, T:0.40
Consensus pattern (123 bp):
GAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTC
TCTCTGGAAATGTTGATGTTGATATATCTCCTTCTGTGATAGAGTCGAGAAAAAGGTT
Found at i:6973 original size:15 final size:15
Alignment explanation
Indices: 6953--6987 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
6943 CTTGACCCTC
6953 TTTTTTTATTTTATT
1 TTTTTTTATTTTATT
*
6968 TTTTTTTATTTTCTT
1 TTTTTTTATTTTATT
6983 TTTTT
1 TTTTT
6988 ATTCAAGCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.09, C:0.03, G:0.00, T:0.89
Consensus pattern (15 bp):
TTTTTTTATTTTATT
Found at i:6988 original size:13 final size:14
Alignment explanation
Indices: 6951--6990 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
6941 ATCTTGACCC
6951 TCTTTTTTTATTTTA
1 TCTTTTTTTA-TTTA
*
6966 TTTTTTTTTATTT-
1 TCTTTTTTTATTTA
6979 TCTTTTTTTATT
1 TCTTTTTTTATT
6991 CAAGCATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
13 11 0.48
14 3 0.13
15 9 0.39
ACGTcount: A:0.10, C:0.05, G:0.00, T:0.85
Consensus pattern (14 bp):
TCTTTTTTTATTTA
Found at i:10531 original size:13 final size:13
Alignment explanation
Indices: 10513--10545 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
10503 AAAGAATGAA
10513 AAATAATAAATGT
1 AAATAATAAATGT
10526 AAATAATAAATGT
1 AAATAATAAATGT
10539 AAATAAT
1 AAATAAT
10546 GTAAAATGTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.30
Consensus pattern (13 bp):
AAATAATAAATGT
Found at i:14290 original size:14 final size:16
Alignment explanation
Indices: 14273--14304 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
14263 ATTATTTTTT
14273 TGAAT-TTTA-CTTAA
1 TGAATGTTTATCTTAA
14287 TGAATGTTTATCTTAA
1 TGAATGTTTATCTTAA
14303 TG
1 TG
14305 TGAAATATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.31
15 4 0.25
16 7 0.44
ACGTcount: A:0.31, C:0.06, G:0.12, T:0.50
Consensus pattern (16 bp):
TGAATGTTTATCTTAA
Found at i:14357 original size:15 final size:15
Alignment explanation
Indices: 14333--14364 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
14323 ATACATATAT
14333 AAAATAAATGTATGC
1 AAAATAAATGTATGC
*
14348 AAAATGAATGTATGC
1 AAAATAAATGTATGC
14363 AA
1 AA
14365 GAGGTATTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.53, C:0.06, G:0.16, T:0.25
Consensus pattern (15 bp):
AAAATAAATGTATGC
Found at i:17163 original size:16 final size:17
Alignment explanation
Indices: 17144--17177 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
17134 TTATAATCCC
*
17144 TAATTCTCAT-AATTTA
1 TAATTCACATGAATTTA
17160 TAATTCACATGAATTTA
1 TAATTCACATGAATTTA
17177 T
1 T
17178 TTAAAAGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.38, C:0.12, G:0.03, T:0.47
Consensus pattern (17 bp):
TAATTCACATGAATTTA
Found at i:18385 original size:18 final size:21
Alignment explanation
Indices: 18362--18401 Score: 59
Period size: 18 Copynumber: 2.0 Consensus size: 21
18352 CCTTTTCTTC
18362 AATATTAA-AA-AATA-AATA
1 AATATTAATAAGAATATAATA
18380 AATATTAATAAGAATATAATA
1 AATATTAATAAGAATATAATA
18401 A
1 A
18402 TTTTTTATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 8 0.42
19 2 0.11
20 4 0.21
21 5 0.26
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (21 bp):
AATATTAATAAGAATATAATA
Found at i:18600 original size:22 final size:21
Alignment explanation
Indices: 18554--18601 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
18544 CCTTAAAATT
* * *
18554 ATTAAATATATCACATTATAG
1 ATTAAAAATATAAAATTATAG
18575 -TTAAAAATATAAAATTATAGG
1 ATTAAAAATATAAAATTATA-G
18596 ATTAAA
1 ATTAAA
18602 TTAAAAAGTA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
20 16 0.73
21 1 0.05
22 5 0.23
ACGTcount: A:0.54, C:0.04, G:0.06, T:0.35
Consensus pattern (21 bp):
ATTAAAAATATAAAATTATAG
Found at i:20045 original size:21 final size:21
Alignment explanation
Indices: 20020--20059 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
20010 TAATGCATAC
20020 ATTATAAATA-AGTATATAATT
1 ATTATAAATATA-TATATAATT
*
20041 ATTATATATATATATATAA
1 ATTATAAATATATATATAA
20060 AGTATGTATG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 16 0.94
22 1 0.06
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (21 bp):
ATTATAAATATATATATAATT
Found at i:20200 original size:15 final size:15
Alignment explanation
Indices: 20182--20302 Score: 56
Period size: 15 Copynumber: 7.9 Consensus size: 15
20172 ATACATGCAT
20182 CATACATACATTATA
1 CATACATACATTATA
* *
20197 CATATATACACTT-CA
1 CATACATACA-TTATA
20212 CATACATATCATTATA
1 CATACATA-CATTATA
* *
20228 CAT-TATACA-TAGA
1 CATACATACATTATA
* *
20241 -ATATCAATTTATAATATA
1 CATA-C-A--TACATTATA
20259 TCATACATACATTATA
1 -CATACATACATTATA
20275 CATTA-ATTA-ATTATA
1 CA-TACA-TACATTATA
*
20290 AATACATACATTA
1 CATACATACATTA
20303 ATCATTAATG
Statistics
Matches: 79, Mismatches: 12, Indels: 30
0.65 0.10 0.25
Matches are distributed among these distances:
12 2 0.03
13 3 0.04
14 6 0.08
15 38 0.48
16 19 0.24
17 3 0.04
18 4 0.05
19 1 0.01
20 3 0.04
ACGTcount: A:0.46, C:0.16, G:0.01, T:0.37
Consensus pattern (15 bp):
CATACATACATTATA
Found at i:20205 original size:30 final size:30
Alignment explanation
Indices: 20169--20237 Score: 97
Period size: 30 Copynumber: 2.3 Consensus size: 30
20159 CTATCTTATG
20169 TATATACATGCATCATACATA-CATTATACA
1 TATATACATGCA-CATACATATCATTATACA
*
20199 TATATACACTTCACATACATATCATTATACA
1 TATATACA-TGCACATACATATCATTATACA
20230 T-TATACAT
1 TATATACAT
20238 AGAATATCAA
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
29 1 0.03
30 22 0.61
31 13 0.36
ACGTcount: A:0.42, C:0.20, G:0.01, T:0.36
Consensus pattern (30 bp):
TATATACATGCACATACATATCATTATACA
Found at i:20325 original size:30 final size:30
Alignment explanation
Indices: 20255--20365 Score: 81
Period size: 30 Copynumber: 3.7 Consensus size: 30
20245 CAATTTATAA
*
20255 TATATCATACATACATTATACATTAATTAAT
1 TATA-CATACATACATTATACATTAATGAAT
*
20286 TATAAATACATACATTA-ATCATTAATGAAT
1 TATACATACATACATTATA-CATTAATGAAT
* * *
20316 T-T---TGCATACAATATACATATATATCAAT
1 TATACATACATACATTATACAT-TA-ATGAAT
*
20344 TCATACCT-CATACATTATACAT
1 T-ATACATACATACATTATACAT
20366 ACATTAATAA
Statistics
Matches: 65, Mismatches: 6, Indels: 17
0.74 0.07 0.19
Matches are distributed among these distances:
26 12 0.18
27 3 0.05
28 6 0.09
29 2 0.03
30 24 0.37
31 4 0.06
32 13 0.20
33 1 0.02
ACGTcount: A:0.44, C:0.15, G:0.02, T:0.39
Consensus pattern (30 bp):
TATACATACATACATTATACATTAATGAAT
Found at i:26129 original size:28 final size:27
Alignment explanation
Indices: 26097--26156 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 27
26087 AACAATTTAT
26097 TTTAAATT-TCAAAAATTAATCATATTAA
1 TTTAAATTATCAAAAATTAATCATA--AA
* *
26125 TTT-AATTATCATAAGTTAATCATAAA
1 TTTAAATTATCAAAAATTAATCATAAA
26151 TTTAAA
1 TTTAAA
26157 AATCTCATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
26 5 0.18
27 6 0.21
28 17 0.61
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.43
Consensus pattern (27 bp):
TTTAAATTATCAAAAATTAATCATAAA
Found at i:27478 original size:30 final size:30
Alignment explanation
Indices: 27443--27535 Score: 132
Period size: 30 Copynumber: 3.1 Consensus size: 30
27433 TTTATTTTAT
* * *
27443 TTTGGGGACTAAATTAAAATTTTGGTGAAA
1 TTTGGGGATTAAAATAAAATTTTGGTAAAA
27473 TTTGGGGATTAAAATAAAATTTTGGTAAAA
1 TTTGGGGATTAAAATAAAATTTTGGTAAAA
* * *
27503 TTTGGGGATTAAAATGAAATTTTGATTAAA
1 TTTGGGGATTAAAATAAAATTTTGGTAAAA
27533 TTT
1 TTT
27536 AGATCCAAAT
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 57 1.00
ACGTcount: A:0.39, C:0.01, G:0.20, T:0.40
Consensus pattern (30 bp):
TTTGGGGATTAAAATAAAATTTTGGTAAAA
Found at i:29531 original size:20 final size:22
Alignment explanation
Indices: 29486--29543 Score: 75
Period size: 20 Copynumber: 2.6 Consensus size: 22
29476 GCATGGGTAG
29486 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TGTT-AAGAA
29510 TGCATCGATGCACTG-T-AGAA
1 TGCATCGATGCACTGTTAAGAA
*
29530 TGTATCGATGCACT
1 TGCATCGATGCACT
29544 TCAAAGGGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 17 0.52
22 1 0.03
23 2 0.06
24 13 0.39
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (22 bp):
TGCATCGATGCACTGTTAAGAA
Found at i:31113 original size:21 final size:20
Alignment explanation
Indices: 31069--31113 Score: 63
Period size: 21 Copynumber: 2.2 Consensus size: 20
31059 CAAGAGTCGA
* *
31069 GGGATTATCAGTGGTCCTTT
1 GGGATTATCAGTGGTCATTC
31089 GGGATATATCAGTGGTCATTC
1 GGGAT-TATCAGTGGTCATTC
31110 GGGA
1 GGGA
31114 CATAGTGGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 5 0.23
21 17 0.77
ACGTcount: A:0.20, C:0.13, G:0.33, T:0.33
Consensus pattern (20 bp):
GGGATTATCAGTGGTCATTC
Found at i:31122 original size:18 final size:18
Alignment explanation
Indices: 31099--31151 Score: 70
Period size: 18 Copynumber: 2.9 Consensus size: 18
31089 GGGATATATC
31099 AGTGGTCATTCGGGACAT
1 AGTGGTCATTCGGGACAT
* *
31117 AGTGGTCTTTCGAGACAT
1 AGTGGTCATTCGGGACAT
* *
31135 AGTGGTCCTTTGGGACA
1 AGTGGTCATTCGGGACA
31152 AATATTCAGT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.21, C:0.17, G:0.32, T:0.30
Consensus pattern (18 bp):
AGTGGTCATTCGGGACAT
Found at i:34574 original size:19 final size:19
Alignment explanation
Indices: 34550--34601 Score: 104
Period size: 19 Copynumber: 2.7 Consensus size: 19
34540 GAATGCAATT
34550 AGTGCATCGATGCATAAGG
1 AGTGCATCGATGCATAAGG
34569 AGTGCATCGATGCATAAGG
1 AGTGCATCGATGCATAAGG
34588 AGTGCATCGATGCA
1 AGTGCATCGATGCA
34602 CCCCCTTAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.31, C:0.17, G:0.31, T:0.21
Consensus pattern (19 bp):
AGTGCATCGATGCATAAGG
Found at i:34699 original size:20 final size:20
Alignment explanation
Indices: 34674--34711 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
34664 CACATGTTAA
34674 AGAATGCATCGATGCACTGT
1 AGAATGCATCGATGCACTGT
*
34694 AGAATGTATCGATGCACT
1 AGAATGCATCGATGCACT
34712 TCAAAGGGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (20 bp):
AGAATGCATCGATGCACTGT
Found at i:36270 original size:21 final size:21
Alignment explanation
Indices: 36246--36305 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
36236 GTCGAGGGAT
36246 TATCAGTGGTCCTTCGGGACA
1 TATCAGTGGTCCTTCGGGACA
*
36267 TATCAGTGGTTCTTCGGGAC-
1 TATCAGTGGTCCTTCGGGACA
*
36287 -AT-AGTGGTCCTTCAGGACA
1 TATCAGTGGTCCTTCGGGACA
36306 AATATTCAGT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
18 14 0.40
19 2 0.06
21 19 0.54
ACGTcount: A:0.20, C:0.22, G:0.28, T:0.30
Consensus pattern (21 bp):
TATCAGTGGTCCTTCGGGACA
Found at i:38341 original size:2 final size:2
Alignment explanation
Indices: 38334--38369 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
38324 AAAAACATTA
38334 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
38370 TAGCCATGCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40412 original size:111 final size:111
Alignment explanation
Indices: 40218--40640 Score: 550
Period size: 111 Copynumber: 3.8 Consensus size: 111
40208 ATTAAATCGA
* ** * * * ** *
40218 GGTAGACTTCTTCCATTGTCACTTATGGAATATCAAATCTTGAAAGAGAGGGATTTATTTTGTTT
1 GGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATTTGTTCCGCTT
* **
40283 CTTCTAAGGGAATATCAGATATGGGAAAA-TTGATCTATTGAATTGG
66 CTTCTAAGGGAATATCAGATCT-GGAAAAGTTGATCTATTGAATCAG
*
40329 GGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTT-AGAAGAGAGGGATTTGTTTCGCT
1 GGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGA-AAGAGAGGGATTTGTTCCGCT
* ** *
40393 TCTTCTAAGGGAATATCAGATCTGTAAAAGTTGATCCGTTAAATCAG
65 TCTTCTAAGGGAATATCAGATCTGGAAAAGTTGATCTATTGAATCAG
* *
40440 GGTAGACTTGTTCTGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATCTGTTCCGCTT
1 GGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATTTGTTCCGCTT
40505 CTTCTAAGGGAATATCAGATCTGGAAAAGTTGAT-TCATTGAATCAG
66 CTTCTAAGGGAATATCAGATCTGGAAAAGTTGATCT-ATTGAATCAG
* * * *
40551 AGTAAACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGGAAGAGAGGGATATT-TTCCACT
1 GGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGGGAT-TTGTTCCGCT
*
40615 TCTT-TGAAAGGAATATCAGATCTGGA
65 TCTTCT-AAGGGAATATCAGATCTGGA
40641 TCAATTAATC
Statistics
Matches: 277, Mismatches: 29, Indels: 12
0.87 0.09 0.04
Matches are distributed among these distances:
110 7 0.03
111 268 0.97
112 2 0.01
ACGTcount: A:0.30, C:0.15, G:0.23, T:0.32
Consensus pattern (111 bp):
GGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATTTGTTCCGCTT
CTTCTAAGGGAATATCAGATCTGGAAAAGTTGATCTATTGAATCAG
Found at i:47696 original size:2 final size:2
Alignment explanation
Indices: 47691--47717 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
47681 TTTATTTTAT
47691 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
47718 TACCAACATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:52866 original size:4 final size:4
Alignment explanation
Indices: 52857--52882 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
52847 GGTTTTTCCC
52857 TTTA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TT
52883 ATTATTATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:52886 original size:3 final size:3
Alignment explanation
Indices: 52878--52904 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
52868 ATTTATTTAT
52878 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
52905 ATGTGTTTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Done.