Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005609.1 Hibiscus syriacus cultivar Beakdansim tig00013043_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: 87283
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Found at i:1499 original size:31 final size:32
Alignment explanation
Indices: 1459--1540 Score: 89
Period size: 31 Copynumber: 2.5 Consensus size: 32
1449 ATTTCAAAAT
* *
1459 AATGTTAAATACAACAACTTACAATA-T-ATTA
1 AATGGTAAATA-AACAAATTACAATACTAATTA
1490 AATGGTAAATGATAACCAAATTACAATACTAATTA
1 AATGGTAAAT-A-AA-CAAATTACAATACTAATTA
1525 AATGGT-AATAAACAAA
1 AATGGTAAATAAACAAA
1541 ATTAACTGAA
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
31 13 0.30
32 5 0.11
33 12 0.27
34 4 0.09
35 10 0.23
ACGTcount: A:0.54, C:0.11, G:0.07, T:0.28
Consensus pattern (32 bp):
AATGGTAAATAAACAAATTACAATACTAATTA
Found at i:3810 original size:16 final size:17
Alignment explanation
Indices: 3783--3814 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
3773 AAAAAAATTA
3783 ATTAAATAAAATTAAAC
1 ATTAAATAAAATTAAAC
3800 ATTAAAT-AAATTAAA
1 ATTAAATAAAATTAAA
3815 TAAATTTCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (17 bp):
ATTAAATAAAATTAAAC
Found at i:4396 original size:19 final size:18
Alignment explanation
Indices: 4372--4409 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
4362 GGGTGCTAAC
4372 TTAAAAATAA-TATTGTTTT
1 TTAAAAA-AATTATT-TTTT
4391 TTAAAAAAATTATTTTTT
1 TTAAAAAAATTATTTTTT
4409 T
1 T
4410 ATTAATGCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (18 bp):
TTAAAAAAATTATTTTTT
Found at i:6371 original size:19 final size:19
Alignment explanation
Indices: 6321--6371 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 19
6311 AAATACAGTA
* * *
6321 TGATCTATGATTTATGTTC
1 TGATCTCTGATATATGCTC
*
6340 TGATCTCTAATATATGCTC
1 TGATCTCTGATATATGCTC
*
6359 TGATTTCTGATAT
1 TGATCTCTGATAT
6372 CTCTATTTAT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (19 bp):
TGATCTCTGATATATGCTC
Found at i:8747 original size:3 final size:3
Alignment explanation
Indices: 8739--8765 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
8729 AACATGACAT
8739 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
8766 TACATTATTT
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:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:26307 original size:26 final size:27
Alignment explanation
Indices: 26277--26327 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
26267 AACCCTGCTA
*
26277 TTGTTGAAG-CCTGTAACTGATGGCTG
1 TTGTTGAAGCCCTCTAACTGATGGCTG
*
26303 TTGTTGAAGCCCTCTCACTGATGGC
1 TTGTTGAAGCCCTCTAACTGATGGC
26328 ATTCGTCTAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 9 0.41
27 13 0.59
ACGTcount: A:0.18, C:0.22, G:0.27, T:0.33
Consensus pattern (27 bp):
TTGTTGAAGCCCTCTAACTGATGGCTG
Found at i:30255 original size:28 final size:26
Alignment explanation
Indices: 30224--30283 Score: 68
Period size: 28 Copynumber: 2.2 Consensus size: 26
30214 ATTTTATAAA
30224 TAAAAAC-ATTAAGATTATTATATTTTAT
1 TAAAAACAATT-AGATTATT-TA-TTTAT
* *
30252 TAAAATCAATTATATTATTTATTTAT
1 TAAAAACAATTAGATTATTTATTTAT
30278 TAAAAA
1 TAAAAA
30284 AATAATATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
26 10 0.36
27 2 0.07
28 13 0.46
29 3 0.11
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.47
Consensus pattern (26 bp):
TAAAAACAATTAGATTATTTATTTAT
Found at i:30274 original size:27 final size:27
Alignment explanation
Indices: 30237--30308 Score: 76
Period size: 28 Copynumber: 2.6 Consensus size: 27
30227 AAACATTAAG
*
30237 ATTATTATATTTTATTAAAATCAAT-TAT
1 ATTATT-TATTTTATTAAAA-AAATATAT
30265 ATTATTTA-TTTATTAAAAAAATAATAT
1 ATTATTTATTTTATTAAAAAAAT-ATAT
* *
30292 ATTATTAATTATATTAA
1 ATTATTTATTTTATTAA
30309 TTACTTATTA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
25 3 0.08
26 10 0.26
27 12 0.32
28 13 0.34
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.51
Consensus pattern (27 bp):
ATTATTTATTTTATTAAAAAAATATAT
Found at i:30291 original size:25 final size:28
Alignment explanation
Indices: 30237--30296 Score: 74
Period size: 26 Copynumber: 2.3 Consensus size: 28
30227 AAACATTAAG
* *
30237 ATTATTATATTTTATTAAAATCAATTAT
1 ATTATTATATTTTATTAAAATAAATAAT
30265 ATTATT-TA-TTTATTAAAA-AAATAAT
1 ATTATTATATTTTATTAAAATAAATAAT
30290 A-TATTAT
1 ATTATTAT
30297 TAATTATATT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
24 4 0.14
25 7 0.24
26 10 0.34
27 2 0.07
28 6 0.21
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (28 bp):
ATTATTATATTTTATTAAAATAAATAAT
Found at i:30303 original size:39 final size:40
Alignment explanation
Indices: 30259--30335 Score: 120
Period size: 39 Copynumber: 1.9 Consensus size: 40
30249 TATTAAAATC
* *
30259 AATTATATTATTTATTTATTAAAAAAATAATA-TATTATT
1 AATTATATTAATTACTTATTAAAAAAATAATACTATTATT
*
30298 AATTATATTAATTACTTATTAAAATAATAATACTATTA
1 AATTATATTAATTACTTATTAAAAAAATAATACTATTA
30336 AAATATTAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
39 29 0.85
40 5 0.15
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (40 bp):
AATTATATTAATTACTTATTAAAAAAATAATACTATTATT
Found at i:30336 original size:17 final size:17
Alignment explanation
Indices: 30282--30340 Score: 57
Period size: 17 Copynumber: 3.4 Consensus size: 17
30272 ATTTATTAAA
*
30282 AAAATAAT-ATATTATT
1 AAAATAATAATACTATT
* *
30298 AATTATATTAATTACTTATT
1 AA-AATAATAA-TAC-TATT
30318 AAAATAATAATACTATT
1 AAAATAATAATACTATT
30335 AAAATA
1 AAAATA
30341 TTAAAAATTA
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
16 2 0.06
17 14 0.41
18 4 0.12
19 8 0.24
20 6 0.18
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.42
Consensus pattern (17 bp):
AAAATAATAATACTATT
Found at i:30342 original size:36 final size:37
Alignment explanation
Indices: 30262--30381 Score: 98
Period size: 39 Copynumber: 3.0 Consensus size: 37
30252 TAAAATCAAT
* *
30262 TATATTATTTATTTATTAAAAAAATAATATATTATTAA
1 TATATTAATTACTTATTAAAAAAATAATATATTA-TAA
* *
30300 TTATATTAATTACTTATTAAAATAATAATACTATTAAAA
1 -TATATTAATTACTTATTAAAAAAATAATA-TATTATAA
**
30339 TATTAAAAATTA-TAATATTAAAATAAATATATTATATTATAA
1 TA-TATTAATTACT--TATTAAAA-AAATA-A-TATATTATAA
30381 T
1 T
30382 TTAAGGAGTG
Statistics
Matches: 66, Mismatches: 8, Indels: 11
0.78 0.09 0.13
Matches are distributed among these distances:
38 3 0.05
39 35 0.53
40 13 0.20
41 4 0.06
42 9 0.14
43 2 0.03
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.46
Consensus pattern (37 bp):
TATATTAATTACTTATTAAAAAAATAATATATTATAA
Found at i:30344 original size:8 final size:8
Alignment explanation
Indices: 30314--30363 Score: 57
Period size: 8 Copynumber: 6.2 Consensus size: 8
30304 ATTAATTACT
30314 TATTAAAA
1 TATTAAAA
* *
30322 TAATAATAC
1 TATTAA-AA
30331 TATTAAAA
1 TATTAAAA
30339 TATTAAAA
1 TATTAAAA
*
30347 -ATTATAA
1 TATTAAAA
30354 TATTAAAA
1 TATTAAAA
30362 TA
1 TA
30364 AATATATTAT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
7 6 0.18
8 22 0.65
9 6 0.18
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (8 bp):
TATTAAAA
Found at i:30355 original size:15 final size:15
Alignment explanation
Indices: 30332--30361 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
30322 TAATAATACT
30332 ATTAAAATATTAAAA
1 ATTAAAATATTAAAA
*
30347 ATTATAATATTAAAA
1 ATTAAAATATTAAAA
30362 TAAATATATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
ATTAAAATATTAAAA
Found at i:30520 original size:34 final size:33
Alignment explanation
Indices: 30469--30535 Score: 98
Period size: 34 Copynumber: 2.0 Consensus size: 33
30459 AATAATCTAT
*
30469 TATATATTATTAAAATAAAAATATAATATTATA
1 TATATATTAGTAAAATAAAAATATAATATTATA
* *
30502 TATATAGTTAGTACAATAAAAATATTATATTATA
1 TATATA-TTAGTAAAATAAAAATATAATATTATA
30536 AAAGTTATAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 6 0.20
34 24 0.80
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.42
Consensus pattern (33 bp):
TATATATTAGTAAAATAAAAATATAATATTATA
Found at i:30548 original size:29 final size:33
Alignment explanation
Indices: 30466--30550 Score: 96
Period size: 34 Copynumber: 2.8 Consensus size: 33
30456 ATTAATAATC
30466 TATTATATAT-TA-TTA--AAATAAAAATATAA
1 TATTATATATATAGTTAGTAAATAAAAATATAA
*
30495 TATTATATATATAGTTAGTACAATAAAAATATTA
1 TATTATATATATAGTTAGTA-AATAAAAATATAA
30529 TATTATA-A-A-AGTTA-TAAATAAA
1 TATTATATATATAGTTAGTAAATAAA
30551 TATAATTTAC
Statistics
Matches: 50, Mismatches: 1, Indels: 10
0.82 0.02 0.16
Matches are distributed among these distances:
29 16 0.32
30 4 0.08
31 8 0.16
32 1 0.02
33 2 0.04
34 19 0.38
ACGTcount: A:0.55, C:0.01, G:0.04, T:0.40
Consensus pattern (33 bp):
TATTATATATATAGTTAGTAAATAAAAATATAA
Found at i:33007 original size:3 final size:3
Alignment explanation
Indices: 32999--33028 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
32989 TTAAAGACTT
32999 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
33029 GAACTATGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:35670 original size:2 final size:2
Alignment explanation
Indices: 35663--35695 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
35653 ATTGAAGGGA
35663 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
35696 AACCTCAAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:35717 original size:16 final size:16
Alignment explanation
Indices: 35696--35729 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
35686 TATATATATA
*
35696 AACCTCAAAGTGTATT
1 AACCTCAAAGTGCATT
35712 AACCTCAAAGTGCATT
1 AACCTCAAAGTGCATT
35728 AA
1 AA
35730 AATAAATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.41, C:0.21, G:0.12, T:0.26
Consensus pattern (16 bp):
AACCTCAAAGTGCATT
Found at i:39014 original size:2 final size:2
Alignment explanation
Indices: 39007--39087 Score: 162
Period size: 2 Copynumber: 40.5 Consensus size: 2
38997 GGATATTTGT
39007 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
39049 TA TA TA TA TA TA 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 TA TA TA TA TA TA T
39088 TCTATTTATT
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 79 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:41897 original size:22 final size:22
Alignment explanation
Indices: 41850--41897 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
41840 AAAAATTATT
* *
41850 TTTTATTAAATATTTTTGATAT
1 TTTTATTAAATATTTTTAATAA
*
41872 TTTTATTTAAT-TTTTTAAATAA
1 TTTTATTAAATATTTTT-AATAA
41894 TTTT
1 TTTT
41898 GACGTCATCC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 5 0.23
22 17 0.77
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (22 bp):
TTTTATTAAATATTTTTAATAA
Found at i:50323 original size:72 final size:72
Alignment explanation
Indices: 50206--50339 Score: 223
Period size: 72 Copynumber: 1.9 Consensus size: 72
50196 GAGTTAGACA
* * *
50206 ATGCTCGACTCGTGTTCGTTAAAAAAATTTGATGTTCAACTCGACTCGTTGCTCGTTAAGCTTGT
1 ATGCTCGACTCGTGTTCGTTAAAAAAAATTGATGCTCAACTCGACTCGTTACTCGTTAAGCTTGT
50271 TAAAATT
66 TAAAATT
* *
50278 ATGCTCGACTCGTGTTCGTTAAAAAAAATTGTTGCTCAATTCGACTCGTTACTCGTTAAGCT
1 ATGCTCGACTCGTGTTCGTTAAAAAAAATTGATGCTCAACTCGACTCGTTACTCGTTAAGCT
50340 CAATGAAAAA
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
72 57 1.00
ACGTcount: A:0.26, C:0.19, G:0.18, T:0.37
Consensus pattern (72 bp):
ATGCTCGACTCGTGTTCGTTAAAAAAAATTGATGCTCAACTCGACTCGTTACTCGTTAAGCTTGT
TAAAATT
Found at i:50892 original size:2 final size:2
Alignment explanation
Indices: 50885--50937 Score: 97
Period size: 2 Copynumber: 26.0 Consensus size: 2
50875 AGATCATGAA
50885 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
50927 AT AT AT GAT AT
1 AT AT AT -AT AT
50938 TTTATGTATC
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 48 0.96
3 2 0.04
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:52209 original size:21 final size:21
Alignment explanation
Indices: 52183--52227 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
52173 GATTTCTGGG
* *
52183 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
52204 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
52225 CAA
1 CAA
52228 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:53976 original size:23 final size:22
Alignment explanation
Indices: 53917--53983 Score: 116
Period size: 22 Copynumber: 3.0 Consensus size: 22
53907 TATGGACATC
*
53917 ATTCTACGGGCACTACGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
53939 ATTCTACGGGCACTTCGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
53961 ATTCTACGGGGCACTTCGGTGCA
1 ATTCTAC-GGGCACTTCGGTGCA
53984 TTTATACGAG
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
22 28 0.65
23 15 0.35
ACGTcount: A:0.19, C:0.27, G:0.28, T:0.25
Consensus pattern (22 bp):
ATTCTACGGGCACTTCGGTGCA
Found at i:57143 original size:21 final size:21
Alignment explanation
Indices: 57117--57161 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
57107 GATTTCTGGG
* *
57117 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
57138 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
57159 CAA
1 CAA
57162 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:58916 original size:23 final size:22
Alignment explanation
Indices: 58857--58923 Score: 116
Period size: 22 Copynumber: 3.0 Consensus size: 22
58847 TATGGACATC
*
58857 ATTCTACGGGCACTACGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
58879 ATTCTACGGGCACTTCGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
58901 ATTCTACGGGGCACTTCGGTGCA
1 ATTCTAC-GGGCACTTCGGTGCA
58924 TTTATACGAG
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
22 28 0.65
23 15 0.35
ACGTcount: A:0.19, C:0.27, G:0.28, T:0.25
Consensus pattern (22 bp):
ATTCTACGGGCACTTCGGTGCA
Found at i:62081 original size:21 final size:21
Alignment explanation
Indices: 62055--62099 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
62045 GATTTCTGGG
* *
62055 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
62076 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
62097 CAA
1 CAA
62100 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:63855 original size:23 final size:22
Alignment explanation
Indices: 63796--63862 Score: 116
Period size: 22 Copynumber: 3.0 Consensus size: 22
63786 TATGGACATC
*
63796 ATTCTACGGGCACTACGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
63818 ATTCTACGGGCACTTCGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
63840 ATTCTACGGGGCACTTCGGTGCA
1 ATTCTAC-GGGCACTTCGGTGCA
63863 TTTATACGAG
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
22 28 0.65
23 15 0.35
ACGTcount: A:0.19, C:0.27, G:0.28, T:0.25
Consensus pattern (22 bp):
ATTCTACGGGCACTTCGGTGCA
Found at i:65011 original size:23 final size:21
Alignment explanation
Indices: 64960--65005 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 21
64950 ATCTCCGACC
64960 ACTTAAATTATAATTAAATTTA
1 ACTT-AATTATAATTAAATTTA
64982 ACTTAATTATAAATTTAAATTTA
1 ACTTAATTAT-AA-TTAAATTTA
65005 A
1 A
65006 GCTAATATCT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 6 0.27
22 6 0.27
23 10 0.45
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (21 bp):
ACTTAATTATAATTAAATTTA
Found at i:65538 original size:221 final size:221
Alignment explanation
Indices: 65137--65551 Score: 571
Period size: 221 Copynumber: 1.9 Consensus size: 221
65127 ATTTAAAGTG
* * * *
65137 TAGCTTCCTAAATCTCTGTTTGGAATTAACATGCATTCTAAAAAAAAAAATCTCTCATATTTAAT
1 TAGCTTCCTAAATATCTGTTTAGAATTAACATACACTCT---AAAAAAAATCTCTCATATTTAAT
* * *
65202 GATGTATTTAAAAAAATTCTTTCAAACTTTAAGGTTTGTGTTGTTTCTATAAATCATATCAATTT
63 GATGTATTTAAAAAAAATCTTTCAAACTTTAAGGTTTGTGTCGTTTCCATAAATCATATCAATTT
**
65267 TTTTATTTTGTTTACTCGATGGTAACACTAATTTTAATATTAATTATCGATCACCGGTTCTCTTT
128 TTTTATTTTGTTTACTCGACAGTAACACTAATTTTAATATTAATTATCGATCACCGGTTCTCTTT
65332 TTTCAATACTAATTTAAAGTGTAGCTTCA
193 TTTCAATACTAATTTAAAGTGTAGCTTCA
* * *
65361 TAGCTTCCTAAATATCTGTTTAGAATTAACATACACTCT-AGAAAATTCTCTCATATTTATTGAT
1 TAGCTTCCTAAATATCTGTTTAGAATTAACATACACTCTAAAAAAAATCTCTCATATTTAATGAT
* * * * *
65425 GTATTTAAAAAAAATCTTTTAAATTTTAGGGTTTGTGTCGTTTTCCATAGATCATATCATTTTTT
66 GTATTTAAAAAAAATCTTTCAAACTTTAAGGTTTGTGTCG-TTTCCATAAATCATATCAATTTTT
* * * * * **
65490 TTATTTTGTTTACTCGACAGTAGCACTGATTTTGATGTTAGTTATCGATCATTGGTTCTCTT
130 TTATTTTGTTTACTCGACAGTAACACTAATTTTAATATTAATTATCGATCACCGGTTCTCTT
65552 GTTACTTTTT
Statistics
Matches: 166, Mismatches: 24, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
220 57 0.34
221 74 0.45
224 35 0.21
ACGTcount: A:0.30, C:0.14, G:0.11, T:0.45
Consensus pattern (221 bp):
TAGCTTCCTAAATATCTGTTTAGAATTAACATACACTCTAAAAAAAATCTCTCATATTTAATGAT
GTATTTAAAAAAAATCTTTCAAACTTTAAGGTTTGTGTCGTTTCCATAAATCATATCAATTTTTT
TATTTTGTTTACTCGACAGTAACACTAATTTTAATATTAATTATCGATCACCGGTTCTCTTTTTT
CAATACTAATTTAAAGTGTAGCTTCA
Found at i:70537 original size:14 final size:15
Alignment explanation
Indices: 70518--70548 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
70508 AACTAATTAA
70518 ATTAATATATT-TTT
1 ATTAATATATTATTT
70532 ATTAATATATTATTT
1 ATTAATATATTATTT
70547 AT
1 AT
70549 CAGAATTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.69
15 5 0.31
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
ATTAATATATTATTT
Found at i:74471 original size:19 final size:20
Alignment explanation
Indices: 74439--74479 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
74429 TCAAAATTTC
*
74439 ATTTTGATTTTCAAAATCAA
1 ATTTTGATTTTCAAAACCAA
74459 ATTTTGA-TTTCAAAACCAA
1 ATTTTGATTTTCAAAACCAA
74478 AT
1 AT
74480 CATTTTCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.41, C:0.12, G:0.05, T:0.41
Consensus pattern (20 bp):
ATTTTGATTTTCAAAACCAA
Found at i:76369 original size:20 final size:21
Alignment explanation
Indices: 76339--76378 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
76329 AGCCGTTGGG
76339 GCCTGATGGTATCGATACTAT
1 GCCTGATGGTATCGATACTAT
76360 GCCT-ATGGTATCGATACTA
1 GCCTGATGGTATCGATACTA
76379 CTATACAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.33
Consensus pattern (21 bp):
GCCTGATGGTATCGATACTAT
Found at i:77315 original size:25 final size:26
Alignment explanation
Indices: 77263--77322 Score: 113
Period size: 25 Copynumber: 2.3 Consensus size: 26
77253 AAATTATAAG
77263 ATATGTGGATACATCATAAAAAAAAC
1 ATATGTGGATACATCATAAAAAAAAC
77289 ATATGTGGATACATCAT-AAAAAAAC
1 ATATGTGGATACATCATAAAAAAAAC
77314 ATATGTGGA
1 ATATGTGGA
77323 AAAGATATAA
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
25 17 0.50
26 17 0.50
ACGTcount: A:0.50, C:0.10, G:0.15, T:0.25
Consensus pattern (26 bp):
ATATGTGGATACATCATAAAAAAAAC
Found at i:79321 original size:22 final size:22
Alignment explanation
Indices: 79291--79343 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
79281 CCGAAATAAT
* *
79291 AAAAAAATATTCTTTTTATTCA
1 AAAAAAATATTATTTTAATTCA
* *
79313 ATAAAAATATTATTTTAATTGA
1 AAAAAAATATTATTTTAATTCA
79335 AAAAAAATA
1 AAAAAAATA
79344 ATATATAGAG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.40
Consensus pattern (22 bp):
AAAAAAATATTATTTTAATTCA
Found at i:83364 original size:31 final size:31
Alignment explanation
Indices: 83302--83366 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 31
83292 CAACTATATG
* * * *
83302 CATGAAACTTTGATTTTGGTTCGATTTTACA
1 CATGAAACTTTGATATTGATTCAATTCTACA
* *
83333 CATGAAATTTTGGTATTGATTCAATTCTACA
1 CATGAAACTTTGATATTGATTCAATTCTACA
83364 CAT
1 CAT
83367 TTTATAAATA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.43
Consensus pattern (31 bp):
CATGAAACTTTGATATTGATTCAATTCTACA
Done.