Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005028.1 Hibiscus syriacus cultivar Beakdansim tig00011282_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: 112525
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:7256 original size:20 final size:20
Alignment explanation
Indices: 7164--7301 Score: 79
Period size: 20 Copynumber: 6.6 Consensus size: 20
7154 AAATATATAT
*
7164 ATAATATATAATTTTGATAA
1 ATAATATATAATTTTGAAAA
*
7184 ATATATAATATAGTATTTG-AAA
1 ATA-AT-ATATAAT-TTTGAAAA
* *
7206 AT-ATGTTATACTTTTTGAAATATA
1 ATAAT-ATATA-ATTTTG-AA-A-A
7230 TATAATATATAATTTTGAAAA
1 -ATAATATATAATTTTGAAAA
*
7251 ATAATA-ATAGTTTTTGAAAA
1 ATAATATATA-ATTTTGAAAA
* *
7271 TATATTATATATTTTTG-AAA
1 -ATAATATATAATTTTGAAAA
7291 AT-ATATATAAT
1 ATAATATATAAT
7302 GTATAATTTT
Statistics
Matches: 94, Mismatches: 11, Indels: 28
0.71 0.08 0.21
Matches are distributed among these distances:
18 7 0.07
19 5 0.05
20 31 0.33
21 15 0.16
22 15 0.16
23 7 0.07
24 6 0.06
25 6 0.06
26 2 0.02
ACGTcount: A:0.47, C:0.01, G:0.07, T:0.46
Consensus pattern (20 bp):
ATAATATATAATTTTGAAAA
Found at i:7373 original size:22 final size:22
Alignment explanation
Indices: 7160--7373 Score: 179
Period size: 22 Copynumber: 9.6 Consensus size: 22
7150 TTTGAAATAT
*
7160 ATATATAATATATAATTTTGATAA
1 ATATATAATATAT-TTTTTGA-AA
* *
7184 ATATATAATATAGTATTTGAAA
1 ATATATAATATATTTTTTGAAA
* *
7206 ATATGT--TATACTTTTTGAAA
1 ATATATAATATATTTTTTGAAA
*
7226 TATATATAATATATAATTTTG-AA
1 -ATATATAATATAT-TTTTTGAAA
*
7249 A-A-ATAATAATAGTTTTTGAAA
1 ATATATAAT-ATATTTTTTGAAA
*
7270 ATATATTATATA-TTTTTGAAAA
1 ATATATAATATATTTTTTG-AAA
* *
7292 TATATATAATGTATAATTTTGGAAA
1 -ATATATAA--TATATTTTTTGAAA
**
7317 ATATATAATATAGGTTTTGAAA
1 ATATATAATATATTTTTTGAAA
* *
7339 ATATGTTATATATTTTTTGAAA
1 ATATATAATATATTTTTTGAAA
7361 ATATATAATATAT
1 ATATATAATATAT
7374 ATAATTTTTG
Statistics
Matches: 154, Mismatches: 23, Indels: 28
0.75 0.11 0.14
Matches are distributed among these distances:
20 22 0.14
21 18 0.12
22 55 0.36
23 22 0.14
24 25 0.16
25 7 0.05
26 5 0.03
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (22 bp):
ATATATAATATATTTTTTGAAA
Found at i:7419 original size:16 final size:16
Alignment explanation
Indices: 7398--7445 Score: 55
Period size: 15 Copynumber: 3.0 Consensus size: 16
7388 CATAATAGAA
7398 TTTTGAAAATAAATAT
1 TTTTGAAAATAAATAT
7414 TTTTGAAAAT--ATAGT
1 TTTTGAAAATAAATA-T
*
7429 GTTTGAAAATATAATAT
1 TTTTGAAAATA-AATAT
7446 ATATTTTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
14 3 0.11
15 10 0.37
16 10 0.37
17 1 0.04
18 3 0.11
ACGTcount: A:0.46, C:0.00, G:0.10, T:0.44
Consensus pattern (16 bp):
TTTTGAAAATAAATAT
Found at i:7461 original size:22 final size:20
Alignment explanation
Indices: 7436--7489 Score: 58
Period size: 20 Copynumber: 2.7 Consensus size: 20
7426 AGTGTTTGAA
*
7436 AATATAATATATATTTTTTTT
1 AATATAATATATA-TGTTTTT
*
7457 GA-ATAATATATA-GTTTTT
1 AATATAATATATATGTTTTT
7475 AATATATATATATAT
1 AATATA-ATATATAT
7490 ATATATATAG
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
18 6 0.22
19 3 0.11
20 17 0.63
21 1 0.04
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.54
Consensus pattern (20 bp):
AATATAATATATATGTTTTT
Found at i:7481 original size:2 final size:2
Alignment explanation
Indices: 7476--7508 Score: 57
Period size: 2 Copynumber: 16.0 Consensus size: 2
7466 ATAGTTTTTA
7476 AT AT AT AT AT AT AT AT AT AT AT AGT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT
7509 TACTTTTTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 28 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:7485 original size:20 final size:20
Alignment explanation
Indices: 7436--7488 Score: 56
Period size: 18 Copynumber: 2.7 Consensus size: 20
7426 AGTGTTTGAA
**
7436 AATATAATATATATTTTTTTT
1 AATAT-ATATATATAGTTTTT
*
7457 GA-ATA-ATATATAGTTTTT
1 AATATATATATATAGTTTTT
7475 AATATATATATATA
1 AATATATATATATA
7489 TATATATATA
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
18 12 0.46
19 4 0.15
20 9 0.35
21 1 0.04
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (20 bp):
AATATATATATATAGTTTTT
Found at i:10424 original size:106 final size:102
Alignment explanation
Indices: 10205--10415 Score: 269
Period size: 105 Copynumber: 2.0 Consensus size: 102
10195 TAAGGCTCGA
*
10205 CCAGGTGATTTTAGGGATTAGGTTTTCGACTTTCGTCCCCAAAGATGCTACGTGATTAGGTGTTC
1 CCAGGTGATTTTAGGGATTAGGTTTTCGACTTTCGTCCCCAAAGATGCTACGCGATTAGGTGTTC
* * * *
10270 TTCGCTAGTTTTGGTGAGTCCGTTTCTTTCTCTCCAG
66 TCCGCTAGTTTTGGTGAGACCATTTCGTTCTCTCCAG
* * * * *
10307 CCAGGTGATTTTGGGGATTAGGTTTCATTCGGCTTTCGTCCCCAAAGCTGCTACGCGTTTTGGGT
1 CCAGGTGATTTTAGGGATTAGG-TT--TTCGACTTTCGTCCCCAAAGATGCTACGCG-ATTAGGT
*
10372 GTTCTCCTCTAGTTTTTTGGTGAGACCATTTCGTTCTCTCCAG
62 GTTCTCCGCTAG--TTTTGGTGAGACCATTTCGTTCTCTCCAG
10415 C
1 C
10416 TGTGATTTTT
Statistics
Matches: 92, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
102 21 0.23
103 2 0.02
105 27 0.29
106 15 0.16
108 27 0.29
ACGTcount: A:0.14, C:0.22, G:0.25, T:0.39
Consensus pattern (102 bp):
CCAGGTGATTTTAGGGATTAGGTTTTCGACTTTCGTCCCCAAAGATGCTACGCGATTAGGTGTTC
TCCGCTAGTTTTGGTGAGACCATTTCGTTCTCTCCAG
Found at i:15431 original size:39 final size:39
Alignment explanation
Indices: 15328--15480 Score: 155
Period size: 39 Copynumber: 3.9 Consensus size: 39
15318 CCTGTACACA
* * *
15328 CAGTAAGGACTTACCCTGTGCACAAAGCAGAGGAGCTTA
1 CAGTAAGGACTTACCCTGAGCACAAAGCAGAGGAGCATG
* * *** *
15367 CAATAAGGTCTTATTATGTGCACAAAGCAGAGGAGTC-TG
1 CAGTAAGGACTTACCCTGAGCACAAAGCAGAGGAG-CATG
* * * *
15406 CAGTAAGGGCTTACCCTGAGTACAAAGCAAATGAGCATG
1 CAGTAAGGACTTACCCTGAGCACAAAGCAGAGGAGCATG
* *
15445 CAGTAAGGATTTACCCTGAGCACAAAGCCGAGGAGC
1 CAGTAAGGACTTACCCTGAGCACAAAGCAGAGGAGC
15481 CCGCGGAAAG
Statistics
Matches: 91, Mismatches: 21, Indels: 4
0.78 0.18 0.03
Matches are distributed among these distances:
38 1 0.01
39 89 0.98
40 1 0.01
ACGTcount: A:0.34, C:0.21, G:0.26, T:0.19
Consensus pattern (39 bp):
CAGTAAGGACTTACCCTGAGCACAAAGCAGAGGAGCATG
Found at i:16978 original size:23 final size:26
Alignment explanation
Indices: 16934--16980 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
16924 GACATTACTT
*
16934 ATTTTATTTCTTGTATTCATCTTAAA
1 ATTTTATTTCATGTATTCATCTTAAA
16960 ATTTTATTT-ATGT-TT-ATCTTA
1 ATTTTATTTCATGTATTCATCTTA
16981 TATAAAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 6 0.30
24 2 0.10
25 3 0.15
26 9 0.45
ACGTcount: A:0.26, C:0.09, G:0.04, T:0.62
Consensus pattern (26 bp):
ATTTTATTTCATGTATTCATCTTAAA
Found at i:17399 original size:27 final size:27
Alignment explanation
Indices: 17369--17429 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 27
17359 TAATAATAGA
*
17369 AAATTTTCGTAAAAAGTACACACAAAT
1 AAATTTTCATAAAAAGTACACACAAAT
* * *
17396 AAA-TTTCATATAAAGTAGATACAAAT
1 AAATTTTCATAAAAAGTACACACAAAT
17422 AGAATTTT
1 A-AATTTT
17430 AAGGTAGACA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
26 20 0.71
27 5 0.18
28 3 0.11
ACGTcount: A:0.51, C:0.10, G:0.08, T:0.31
Consensus pattern (27 bp):
AAATTTTCATAAAAAGTACACACAAAT
Found at i:21514 original size:3 final size:3
Alignment explanation
Indices: 21488--21589 Score: 58
Period size: 3 Copynumber: 35.3 Consensus size: 3
21478 ATACACTATC
* * * *
21488 ATT ATT -TT ACT AAT ATT ATT -TT ATT ATT ATT AATT A-G AGT -TT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT
*
21530 ATT ATT AATT ATT -TT ATT ATT -TT GTT ATT ACTT -TT ATT -TT ATT
1 ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT
*
21573 AGTT ATT ATT ACT ATT A
1 A-TT ATT ATT ATT ATT A
21590 ATTTTGAGTT
Statistics
Matches: 78, Mismatches: 9, Indels: 24
0.70 0.08 0.22
Matches are distributed among these distances:
2 14 0.18
3 53 0.68
4 11 0.14
ACGTcount: A:0.30, C:0.03, G:0.04, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:21518 original size:14 final size:14
Alignment explanation
Indices: 21488--21582 Score: 61
Period size: 14 Copynumber: 6.4 Consensus size: 14
21478 ATACACTATC
* *
21488 ATTATTTTACTAAT
1 ATTATTTTATTATT
21502 ATTATTTTATTATT
1 ATTATTTTATTATT
**
21516 ATTAATTAGAGTTTATT
1 ATT-ATTTTA--TTATT
21533 ATTAATTATT-TTATT
1 ATT-ATT-TTATTATT
21548 ATT-TTGTTATTACTT
1 ATTATT-TTATTA-TT
21563 -TTATTTTATTAGTT
1 ATTATTTTATTA-TT
21577 ATTATT
1 ATTATT
21583 ACTATTAATT
Statistics
Matches: 65, Mismatches: 8, Indels: 15
0.74 0.09 0.17
Matches are distributed among these distances:
13 4 0.06
14 28 0.43
15 21 0.32
17 12 0.18
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.64
Consensus pattern (14 bp):
ATTATTTTATTATT
Found at i:21593 original size:25 final size:25
Alignment explanation
Indices: 21528--21594 Score: 77
Period size: 25 Copynumber: 2.8 Consensus size: 25
21518 TAATTAGAGT
*
21528 TTATTATTA--ATTATTTTATTATT
1 TTATTATTACTATTATTTTATTATG
* *
21551 TTGTTATTACTTTTATTTTATTA-G
1 TTATTATTACTATTATTTTATTATG
21575 TTATTATTACTATTAATTTT
1 TTATTATTACTATT-ATTTT
21595 GAGTTTCTAT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
23 8 0.22
24 12 0.33
25 16 0.44
ACGTcount: A:0.27, C:0.03, G:0.03, T:0.67
Consensus pattern (25 bp):
TTATTATTACTATTATTTTATTATG
Found at i:26319 original size:4 final size:4
Alignment explanation
Indices: 26312--26340 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
26302 TGTTCAACTT
26312 TTTA TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA T
26341 ACATGCATTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:26485 original size:3 final size:3
Alignment explanation
Indices: 26477--26501 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
26467 GAATAGGGTT
26477 TTG TTG TTG TTG TTG TTG TTG TTG T
1 TTG TTG TTG TTG TTG TTG TTG TTG T
26502 ATTACTATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:26523 original size:13 final size:12
Alignment explanation
Indices: 26507--26592 Score: 66
Period size: 13 Copynumber: 6.8 Consensus size: 12
26497 GTTGTATTAC
26507 TATTAATTATTTT
1 TATT-ATTATTTT
*
26520 TATT-TTATTAT
1 TATTATTATTTT
*
26531 TATTATCTTATTAT
1 TATTA--TTATTTT
*
26545 TATTAGTATTTAT
1 TATTATTATTT-T
*
26558 TATTACTATTATT
1 TATTATTATT-TT
*
26571 TATTAATATTTAT
1 TATTATTATTT-T
26584 TATTATTAT
1 TATTATTAT
26593 AATTATTTCA
Statistics
Matches: 61, Mismatches: 6, Indels: 12
0.77 0.08 0.15
Matches are distributed among these distances:
11 10 0.16
12 5 0.08
13 33 0.54
14 13 0.21
ACGTcount: A:0.31, C:0.02, G:0.01, T:0.65
Consensus pattern (12 bp):
TATTATTATTTT
Found at i:26532 original size:3 final size:3
Alignment explanation
Indices: 26501--26599 Score: 85
Period size: 3 Copynumber: 32.3 Consensus size: 3
26491 GTTGTTGTTG
* * *
26501 TAT TAC TAT TAAT TAT TTT TAT T-T TAT TAT TAT TA- TCT TAT TAT
1 TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
26545 TAT TAG TATT TAT TAT TAC TAT TATT TAT TAA TATT TAT TAT TAT TAT
1 TAT TAT TA-T TAT TAT TAT TAT TA-T TAT TAT TA-T TAT TAT TAT TAT
*
26593 AAT TAT T
1 TAT TAT T
26600 TCAAAAAAAT
Statistics
Matches: 76, Mismatches: 14, Indels: 12
0.75 0.14 0.12
Matches are distributed among these distances:
2 3 0.04
3 63 0.83
4 10 0.13
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:29240 original size:14 final size:15
Alignment explanation
Indices: 29217--29249 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
29207 AATTTGTGCC
*
29217 TTTACTTTTCAG-CA
1 TTTACATTTCAGTCA
29231 TTTACATTTCAGTCA
1 TTTACATTTCAGTCA
29246 TTTA
1 TTTA
29250 AATTCCAGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.24, C:0.18, G:0.06, T:0.52
Consensus pattern (15 bp):
TTTACATTTCAGTCA
Found at i:29778 original size:139 final size:139
Alignment explanation
Indices: 29509--29781 Score: 365
Period size: 139 Copynumber: 2.0 Consensus size: 139
29499 GTTTGTTTAA
* * * *
29509 TTTCACATTTAGTCGTTAAATTAGGAGAAATTTTAATTTGGTCCTCGCTTTTGCTCGAGGTTCCA
1 TTTCACATTTAGTCCTTAAATTAGGAGAAATCTTAATTTGGTCATCGATTTTGCTCGAGGTTCCA
* * * *
29574 AATTAATTATTCGATATGTTATAATTGATTAAAATTAATTAGGATTAATATTAGAGCCTCCATTT
66 AATTAATTATTCGATATGTCATAATTGATTAAAATTAATTAAGATTAATATTAGAACCTCAATTT
29639 TAGGCCTAT
131 TAGGCCTAT
* *
29648 TTTCATATTTAGTCCTTAAATTAGGAGAAATCTTAATTT-TTACATCGATTTTGCTCGAGGTTCC
1 TTTCACATTTAGTCCTTAAATTAGGAGAAATCTTAATTTGGT-CATCGATTTTGCTCGAGGTTCC
** *
29712 ATTTTAATTATTTGA-AT-TGCATAATTGATTAAAATTAATTTAAG-TTAATATTAGAACCTACA
65 AAATTAATTATTCGATATGT-CATAATTGATTAAAATTAA-TTAAGATTAATATTAGAACCT-CA
29774 ATTTTAGG
127 ATTTTAGG
29782 TTTAATCAAT
Statistics
Matches: 117, Mismatches: 13, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
137 1 0.01
138 35 0.30
139 81 0.69
ACGTcount: A:0.32, C:0.12, G:0.14, T:0.43
Consensus pattern (139 bp):
TTTCACATTTAGTCCTTAAATTAGGAGAAATCTTAATTTGGTCATCGATTTTGCTCGAGGTTCCA
AATTAATTATTCGATATGTCATAATTGATTAAAATTAATTAAGATTAATATTAGAACCTCAATTT
TAGGCCTAT
Found at i:30560 original size:24 final size:26
Alignment explanation
Indices: 30517--30572 Score: 80
Period size: 24 Copynumber: 2.2 Consensus size: 26
30507 GAAGCAATAT
*
30517 TCGAGAATATGGATAACCTAATTTGA
1 TCGAAAATATGGATAACCTAATTTGA
*
30543 TTGAAAATAT-GA-AACCTAATTTGA
1 TCGAAAATATGGATAACCTAATTTGA
30567 TCGAAA
1 TCGAAA
30573 GTAGTACGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
24 17 0.63
25 2 0.07
26 8 0.30
ACGTcount: A:0.43, C:0.11, G:0.16, T:0.30
Consensus pattern (26 bp):
TCGAAAATATGGATAACCTAATTTGA
Found at i:32797 original size:15 final size:15
Alignment explanation
Indices: 32777--32806 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
32767 TATCACAATC
32777 GCGCAGGATTCCGGG
1 GCGCAGGATTCCGGG
32792 GCGCAGGATTCCGGG
1 GCGCAGGATTCCGGG
32807 AGCACCGTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.27, G:0.47, T:0.13
Consensus pattern (15 bp):
GCGCAGGATTCCGGG
Found at i:37994 original size:53 final size:54
Alignment explanation
Indices: 37909--38017 Score: 175
Period size: 53 Copynumber: 2.0 Consensus size: 54
37899 GATTAGCTCA
* *
37909 ACAATAAATAATTTGTAAGCTTTTTTCATATAGACCCCAAACAAACAAGTCTAAC
1 ACAATAAATAATTTATAAGC-TTTTTCATATAGACCCAAAACAAACAAGTCTAAC
*
37964 ACAATAAATAGTTTATAAGC-TTTTCATATAGACCCAAAACAAACAAGTCTAAC
1 ACAATAAATAATTTATAAGCTTTTTCATATAGACCCAAAACAAACAAGTCTAAC
38017 A
1 A
38018 TCTTAATGAA
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
53 33 0.65
55 18 0.35
ACGTcount: A:0.46, C:0.19, G:0.07, T:0.28
Consensus pattern (54 bp):
ACAATAAATAATTTATAAGCTTTTTCATATAGACCCAAAACAAACAAGTCTAAC
Found at i:48271 original size:43 final size:42
Alignment explanation
Indices: 48213--48316 Score: 127
Period size: 43 Copynumber: 2.4 Consensus size: 42
48203 AAAAAACGCC
* * * *
48213 GCAATAGGTCAAGATCTATAGCGGCGTTTTTGGAACAAAAGCA
1 GCAAAAGGTC-AGATCTATAACGACATTTTTGGAACAAAAGCA
* *
48256 GCAAAAGGTCGAGATCTATAACGACATTTTTGGAACAAACGCC
1 GCAAAAGGTC-AGATCTATAACGACATTTTTGGAACAAAAGCA
*
48299 GCTAAAGGTCAGATCTAT
1 GCAAAAGGTCAGATCTAT
48317 CCAAAAACGC
Statistics
Matches: 53, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
42 8 0.15
43 45 0.85
ACGTcount: A:0.36, C:0.18, G:0.23, T:0.23
Consensus pattern (42 bp):
GCAAAAGGTCAGATCTATAACGACATTTTTGGAACAAAAGCA
Found at i:48348 original size:115 final size:115
Alignment explanation
Indices: 48204--48418 Score: 283
Period size: 115 Copynumber: 1.9 Consensus size: 115
48194 TTTGAGAACA
* * * * *
48204 AAAAACGCCGCAATAGGTCAAGATCTATAGCGGCGTTTTTGGAACAAA-AGCAGCAAAAGGTCGA
1 AAAAACGCCGCAAAAGGGCAAGATATATAGCGACGTTTTTGGAACAAACA-CAGAAAAAGGTC-A
*
48268 GATCTATAAC-GACATTTTTGGA-ACAAACGCCGCTAAAGGTCAGATCTATCC
64 AATCTATAACAG-CATTTTTGGATACAAACGCCGCTAAAGGTCAGATCTATCC
* * *
48319 AAAAACGCCGCAAAAGGGCGAGATATATAGTGACGTTTTTGGAACAAACACAGAAAAATGTCAAA
1 AAAAACGCCGCAAAAGGGCAAGATATATAGCGACGTTTTTGGAACAAACACAGAAAAAGGTCAAA
* *
48384 TCTATAGCAGCATTTTTGGATACAAATGCCGCTAA
66 TCTATAACAGCATTTTTGGATACAAACGCCGCTAA
48419 TTACCTTTCT
Statistics
Matches: 86, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
114 19 0.22
115 66 0.77
116 1 0.01
ACGTcount: A:0.39, C:0.19, G:0.21, T:0.21
Consensus pattern (115 bp):
AAAAACGCCGCAAAAGGGCAAGATATATAGCGACGTTTTTGGAACAAACACAGAAAAAGGTCAAA
TCTATAACAGCATTTTTGGATACAAACGCCGCTAAAGGTCAGATCTATCC
Found at i:50006 original size:21 final size:21
Alignment explanation
Indices: 49981--50024 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
49971 CCAAAATAAC
49981 CATGAATCGAATGCTCAAAAG
1 CATGAATCGAATGCTCAAAAG
50002 CATGAATCGAATGCTCAAAAG
1 CATGAATCGAATGCTCAAAAG
50023 CA
1 CA
50025 ACTACGATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.43, C:0.20, G:0.18, T:0.18
Consensus pattern (21 bp):
CATGAATCGAATGCTCAAAAG
Found at i:57601 original size:23 final size:24
Alignment explanation
Indices: 57571--57623 Score: 72
Period size: 23 Copynumber: 2.2 Consensus size: 24
57561 TCCTTCGGGA
*
57571 CATAGTGGTCATTCGGGAC-ATTT
1 CATAGTGGTCATTAGGGACAATTT
*
57594 CATAGTGGTCCTTAGGGACAAATTT
1 CATAGTGGTCATTAGGGAC-AATTT
57619 CATAG
1 CATAG
57624 CCCCTAATGG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
23 17 0.65
25 9 0.35
ACGTcount: A:0.26, C:0.17, G:0.25, T:0.32
Consensus pattern (24 bp):
CATAGTGGTCATTAGGGACAATTT
Found at i:61054 original size:31 final size:31
Alignment explanation
Indices: 60972--61057 Score: 102
Period size: 31 Copynumber: 2.8 Consensus size: 31
60962 GTATGGTTTA
* * * *
60972 AAAAATGAAAGTTTGGGTACTAAAACGGATT
1 AAAACTGACAGTTTAGGTACTAAAACGGATC
* *
61003 AAAACTGATAGTTTATGTACTAAAACGGATC
1 AAAACTGACAGTTTAGGTACTAAAACGGATC
61034 AAAACTGACAGTTCT-GGTACTAAA
1 AAAACTGACAGTT-TAGGTACTAAA
61058 TGCGCATTTT
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
31 46 0.98
32 1 0.02
ACGTcount: A:0.43, C:0.12, G:0.19, T:0.27
Consensus pattern (31 bp):
AAAACTGACAGTTTAGGTACTAAAACGGATC
Found at i:61880 original size:18 final size:18
Alignment explanation
Indices: 61857--61900 Score: 88
Period size: 18 Copynumber: 2.4 Consensus size: 18
61847 AAGAAGCTAT
61857 CCAAGCTTAGAAACCGAG
1 CCAAGCTTAGAAACCGAG
61875 CCAAGCTTAGAAACCGAG
1 CCAAGCTTAGAAACCGAG
61893 CCAAGCTT
1 CCAAGCTT
61901 TGGGTTTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.36, C:0.30, G:0.20, T:0.14
Consensus pattern (18 bp):
CCAAGCTTAGAAACCGAG
Found at i:63052 original size:2 final size:2
Alignment explanation
Indices: 63045--63098 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
63035 CAATCTGAGA
63045 AT AT AT 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 AT AT AT
63087 AT AT AT AT AT AT
1 AT AT AT AT AT AT
63099 TACATTATTT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:65231 original size:16 final size:16
Alignment explanation
Indices: 65212--65242 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
65202 TAATTTTAAA
*
65212 AATTTTGAATTAAATT
1 AATTTTGAATAAAATT
65228 AATTTTGAATAAAAT
1 AATTTTGAATAAAAT
65243 GATAAAATAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.45
Consensus pattern (16 bp):
AATTTTGAATAAAATT
Found at i:80589 original size:13 final size:13
Alignment explanation
Indices: 80571--80600 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
80561 GGTCCAACCC
80571 GACCCGACCCGTT
1 GACCCGACCCGTT
80584 GACCCGACCCGTT
1 GACCCGACCCGTT
80597 GACC
1 GACC
80601 TTTGACCATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.17, C:0.47, G:0.23, T:0.13
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:80792 original size:6 final size:6
Alignment explanation
Indices: 80781--80805 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
80771 CAGTCAAACC
80781 CTTTGA CTTTGA CTTTGA CTTTGA C
1 CTTTGA CTTTGA CTTTGA CTTTGA C
80806 CAAGAATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.20, G:0.16, T:0.48
Consensus pattern (6 bp):
CTTTGA
Found at i:85042 original size:35 final size:36
Alignment explanation
Indices: 84961--85064 Score: 174
Period size: 35 Copynumber: 2.9 Consensus size: 36
84951 CAAAATCGTC
**
84961 ATTTCTAATACTAGTGGGATGCCCTAATTTGAGCAT
1 ATTTCTAATACTAGTGGGATAACCTAATTTGAGCAT
*
84997 ATTTCTAATACTAGTGGGATAACCTAATTT-AGCGT
1 ATTTCTAATACTAGTGGGATAACCTAATTTGAGCAT
85032 ATTTCTAATACTAGTGGGATAACCTAATTTGAG
1 ATTTCTAATACTAGTGGGATAACCTAATTTGAG
85065 GATTATCAAC
Statistics
Matches: 64, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
35 34 0.53
36 30 0.47
ACGTcount: A:0.31, C:0.14, G:0.18, T:0.37
Consensus pattern (36 bp):
ATTTCTAATACTAGTGGGATAACCTAATTTGAGCAT
Found at i:89075 original size:36 final size:36
Alignment explanation
Indices: 89024--89127 Score: 151
Period size: 35 Copynumber: 3.0 Consensus size: 36
89014 AATTCGTCAT
89024 TTTC-AATACTAGTGGGATAACCTAATTTGAGCATA
1 TTTCTAATACTAGTGGGATAACCTAATTTGAGCATA
*
89059 TTTCTAATACTAGTGGGATAACCTAATTT-ATCATA
1 TTTCTAATACTAGTGGGATAACCTAATTTGAGCATA
* * *
89094 TTTCTAATATTGGTGGGATAACCT-AGTTGAGCAT
1 TTTCTAATACTAGTGGGATAACCTAATTTGAGCAT
89128 TATCAACAAG
Statistics
Matches: 62, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
34 3 0.05
35 35 0.56
36 24 0.39
ACGTcount: A:0.32, C:0.13, G:0.17, T:0.38
Consensus pattern (36 bp):
TTTCTAATACTAGTGGGATAACCTAATTTGAGCATA
Found at i:104357 original size:21 final size:21
Alignment explanation
Indices: 104320--104359 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
104310 TATGCTGAAA
**
104320 CTCCACCTGTTTTGGAGTATG
1 CTCCACCTGTTGCGGAGTATG
104341 CTCCACCTGTTGCGGAGTA
1 CTCCACCTGTTGCGGAGTA
104360 CTACTTGTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.15, C:0.28, G:0.25, T:0.33
Consensus pattern (21 bp):
CTCCACCTGTTGCGGAGTATG
Done.