Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009044.1 Hibiscus syriacus cultivar Beakdansim tig00112454_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: 88927
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:283 original size:16 final size:16
Alignment explanation
Indices: 262--295 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
252 TTACTATTCA
*
262 CGTGAATAGTGAATTT
1 CGTGAATAGTGAAATT
278 CGTGAATAGTGAAATT
1 CGTGAATAGTGAAATT
294 CG
1 CG
296 GTCGGCGATA
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:0.32, C:0.09, G:0.26, T:0.32
Consensus pattern (16 bp):
CGTGAATAGTGAAATT
Found at i:1062 original size:15 final size:16
Alignment explanation
Indices: 1042--1073 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
1032 TGGCAGATCC
1042 AAATCCAG-ACGGGAA
1 AAATCCAGAACGGGAA
1057 AAATCCAGAACGGGAA
1 AAATCCAGAACGGGAA
1073 A
1 A
1074 GAAATTTTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.50, C:0.19, G:0.25, T:0.06
Consensus pattern (16 bp):
AAATCCAGAACGGGAA
Found at i:6481 original size:28 final size:28
Alignment explanation
Indices: 6441--6496 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
6431 CGTTCGTGAA
*
6441 CGTTCGGTTATGTTCGTTCGGTTATGTT
1 CGTTCGGTTATGTTCGTTCAGTTATGTT
*
6469 CGTTCGGTTATGTTCGTTCATTTATGTT
1 CGTTCGGTTATGTTCGTTCAGTTATGTT
6497 TAACTCAATC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.09, C:0.14, G:0.25, T:0.52
Consensus pattern (28 bp):
CGTTCGGTTATGTTCGTTCAGTTATGTT
Found at i:6496 original size:14 final size:14
Alignment explanation
Indices: 6441--6487 Score: 94
Period size: 14 Copynumber: 3.4 Consensus size: 14
6431 CGTTCGTGAA
6441 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
6455 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
6469 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
6483 CGTTC
1 CGTTC
6488 ATTTATGTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 33 1.00
ACGTcount: A:0.06, C:0.17, G:0.28, T:0.49
Consensus pattern (14 bp):
CGTTCGGTTATGTT
Found at i:6863 original size:16 final size:16
Alignment explanation
Indices: 6840--6900 Score: 95
Period size: 16 Copynumber: 3.8 Consensus size: 16
6830 TAGGGTCTAA
6840 CGTTTATGTTCGTGTT
1 CGTTTATGTTCGTGTT
**
6856 TATTTATGTTCGTGTT
1 CGTTTATGTTCGTGTT
*
6872 CGTTTATGTTCTTGTT
1 CGTTTATGTTCGTGTT
6888 CGTTTATGTTCGT
1 CGTTTATGTTCGT
6901 TATTTATTAA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 39 1.00
ACGTcount: A:0.08, C:0.11, G:0.21, T:0.59
Consensus pattern (16 bp):
CGTTTATGTTCGTGTT
Found at i:11401 original size:23 final size:23
Alignment explanation
Indices: 11385--11430 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
11375 CGAAGGACCG
11385 CGTAGAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* *
11408 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
11431 TATAATATGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.30, C:0.26, G:0.26, T:0.17
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:17404 original size:23 final size:23
Alignment explanation
Indices: 17388--17433 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
17378 CGAAGGACCG
17388 CGTAGAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* *
17411 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
17434 TATAATATGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.30, C:0.26, G:0.26, T:0.17
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:22089 original size:20 final size:20
Alignment explanation
Indices: 22064--22101 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
22054 AAAACCTTTT
*
22064 ATGAAGTTTTAGAACATTCC
1 ATGAAGTTCTAGAACATTCC
22084 ATGAAGTTCTAGAACATT
1 ATGAAGTTCTAGAACATT
22102 TTAGAGTAAT
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:0.37, C:0.13, G:0.16, T:0.34
Consensus pattern (20 bp):
ATGAAGTTCTAGAACATTCC
Found at i:22186 original size:20 final size:21
Alignment explanation
Indices: 22130--22186 Score: 57
Period size: 20 Copynumber: 2.8 Consensus size: 21
22120 TTCCAAAATA
*
22130 TTCTAGAACTTTCCA-TGATG
1 TTCTAGAACTTTCTATTGATG
*
22150 TTCTAG-ACATTTTTATTG-TG
1 TTCTAGAAC-TTTCTATTGATG
*
22170 TTTTAGAACTTTCTATT
1 TTCTAGAACTTTCTATT
22187 ATATTGTAGA
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
19 2 0.07
20 24 0.80
21 4 0.13
ACGTcount: A:0.23, C:0.14, G:0.12, T:0.51
Consensus pattern (21 bp):
TTCTAGAACTTTCTATTGATG
Found at i:29079 original size:42 final size:42
Alignment explanation
Indices: 29020--29102 Score: 141
Period size: 42 Copynumber: 2.0 Consensus size: 42
29010 AGTAACTGTA
*
29020 ACAACCTTTTGTTTCCAAACTTAAC-AGGTCACTGATGCAATT
1 ACAACCTTTTGTTTCCAAACGTAACGA-GTCACTGATGCAATT
29062 ACAACCTTTTGTTTCCAAACGTAACGAGTCACTGATGCAAT
1 ACAACCTTTTGTTTCCAAACGTAACGAGTCACTGATGCAAT
29103 GTTGATGAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
42 38 0.97
43 1 0.03
ACGTcount: A:0.31, C:0.24, G:0.13, T:0.31
Consensus pattern (42 bp):
ACAACCTTTTGTTTCCAAACGTAACGAGTCACTGATGCAATT
Found at i:34890 original size:25 final size:25
Alignment explanation
Indices: 34856--34904 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
34846 TATTGGTCTC
* * *
34856 CCGTCCCCGTCTCCGTTTAAAAAAT
1 CCGTACCCGTCCCCGCTTAAAAAAT
34881 CCGTACCCGTCCCCGCTTAAAAAA
1 CCGTACCCGTCCCCGCTTAAAAAA
34905 CTATGGGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.27, C:0.39, G:0.12, T:0.22
Consensus pattern (25 bp):
CCGTACCCGTCCCCGCTTAAAAAAT
Found at i:35199 original size:36 final size:35
Alignment explanation
Indices: 35151--35232 Score: 128
Period size: 36 Copynumber: 2.3 Consensus size: 35
35141 GATTACTAAA
35151 CCCGTCCCGTCCCCGTTTAACATAAACGATTTTTC
1 CCCGTCCCGTCCCCGTTTAACATAAACGATTTTTC
* *
35186 CCCGTCCCCGTCCCCGTTTAGCATAAACGGTTTTTC
1 CCCGT-CCCGTCCCCGTTTAACATAAACGATTTTTC
35222 CCCGTTCCCGT
1 CCCG-TCCCGT
35233 TTAATTCGAT
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
35 5 0.12
36 37 0.86
37 1 0.02
ACGTcount: A:0.15, C:0.40, G:0.15, T:0.30
Consensus pattern (35 bp):
CCCGTCCCGTCCCCGTTTAACATAAACGATTTTTC
Found at i:44335 original size:20 final size:20
Alignment explanation
Indices: 44298--44335 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
44288 TCTCAGTCAT
*
44298 TCCTTCCTCCAAGGTCTGTA
1 TCCTTCCTCCAAGCTCTGTA
44318 TCCTTCCCTCC-AGCTCTG
1 TCCTT-CCTCCAAGCTCTG
44336 CTTTCTGCCC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.11, C:0.42, G:0.13, T:0.34
Consensus pattern (20 bp):
TCCTTCCTCCAAGCTCTGTA
Found at i:46423 original size:55 final size:55
Alignment explanation
Indices: 46363--46471 Score: 200
Period size: 55 Copynumber: 2.0 Consensus size: 55
46353 CTAGATGTAA
*
46363 TTAATTTAATGTTAAAACATAAATGTAAAAAGGAGATAACAATGTAACTTTCATC
1 TTAATTTAATGTTAAAACATAAATGTAAAAAGGAGATAACAATATAACTTTCATC
*
46418 TTAATTTAATTTTAAAACATAAATGTAAAAAGGAGATAACAATATAACTTTCAT
1 TTAATTTAATGTTAAAACATAAATGTAAAAAGGAGATAACAATATAACTTTCAT
46472 TTCATTTTAG
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 52 1.00
ACGTcount: A:0.49, C:0.08, G:0.09, T:0.34
Consensus pattern (55 bp):
TTAATTTAATGTTAAAACATAAATGTAAAAAGGAGATAACAATATAACTTTCATC
Found at i:47023 original size:41 final size:39
Alignment explanation
Indices: 46963--47421 Score: 287
Period size: 41 Copynumber: 11.2 Consensus size: 39
46953 TAATATTAAC
* * *
46963 GGCGTTTTTCAATAAACGCCTCTAAAACTCGTACTTTAGT
1 GGCGTTTTTAAACAAACGCCGCTAAAA-TCGTACTTTAGT
** *
47003 GGCGTTTATTCGACAAACGCCGCTAAAGATAAGTACTTTAGT
1 GGCGTTT-TTAAACAAACGCCGCTAAA-AT-CGTACTTTAGT
* * *
47045 GGCGTTTTTAAACAAACGCCGCCATAGAATCATTCTTTAGT
1 GGCGTTTTTAAACAAACGCCG-C-TAAAATCGTACTTTAGT
* ** *
47086 GGCGTTTTTAAACAAACGCCGC-AATAGGGTACATATATTGT
1 GGCGTTTTTAAACAAACGCCGCTAAAATCGTAC-T-T-TAGT
* * * *
47127 GGCGTTTTTAGATAAACGCCGCTAAAACCTAGTACTTTAGA
1 GGCGTTTTTAAACAAACGCCGCTAAAA--TCGTACTTTAGT
** *
47168 GGCGCTTTATGCAA-AAACGCCGCTAAAACTCATACTTTAGT
1 GGCG-TTT-TTAAACAAACGCCGCTAAAA-TCGTACTTTAGT
* * ** *
47209 GGCGTTTGTAAACAAACACCGCCATAGGATCGTTCTTTAGT
1 GGCGTTTTTAAACAAACGCCG-C-TAAAATCGTACTTTAGT
* ** *
47250 GGCGTTTTTAAACAAACGCCG-TAATAGGGTACATATACCGT
1 GGCGTTTTTAAACAAACGCCGCTAAAATCGTAC-TTTA--GT
* * **
47291 TGCGTTTTTAAATAAACGCCGCTAAAACCTAATACTTTAGT
1 GGCGTTTTTAAACAAACGCCGCTAAAA--TCGTACTTTAGT
* *
47332 GGCGTTTTATTCAA-AAACGCCGCTAAATACTCATACTTTAGT
1 GGCG-TTT-TTAAACAAACGCCGCTAAA-A-TCGTACTTTAGT
* * * * *
47374 GACGATTTTAGACAAACGCCGCTAAAACCTAGTACTTTATT
1 GGCGTTTTTAAACAAACGCCGCTAAAA--TCGTACTTTAGT
47415 GGCGTTT
1 GGCGTTT
47422 AACCATTAAC
Statistics
Matches: 327, Mismatches: 65, Indels: 53
0.73 0.15 0.12
Matches are distributed among these distances:
38 10 0.03
39 6 0.02
40 23 0.07
41 187 0.57
42 80 0.24
43 14 0.04
44 7 0.02
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.31
Consensus pattern (39 bp):
GGCGTTTTTAAACAAACGCCGCTAAAATCGTACTTTAGT
Found at i:47206 original size:164 final size:163
Alignment explanation
Indices: 46963--47395 Score: 611
Period size: 164 Copynumber: 2.6 Consensus size: 163
46953 TAATATTAAC
* * *
46963 GGCGTTTTTCAATAAACGCCTCTAAAA-CTCGTACTTTAGTGGCGTTTATTCGACAAACGCCGCT
1 GGCGTTTTT-AATAAACGCCGCTAAAACCTAGTACTTTAGTGGCGTTTATTC-AAAAACGCCGCT
*
47027 AAAGA-TAAGTACTTTAGTGGCGTTTTTAAACAAACGCCGCCATAGAATCATTCTTTAGTGGCGT
64 AAAGACTCA-TACTTTAGTGGCGTTTTTAAACAAACGCCGCCATAGAATCATTCTTTAGTGGCGT
**
47091 TTTTAAACAAACGCCGCAATAGGGTACATATATTGT
128 TTTTAAACAAACGCCGCAATAGGGTACATATACCGT
* *
47127 GGCGTTTTTAGATAAACGCCGCTAAAACCTAGTACTTTAGAGGCGCTTTATGCAAAAACGCCGCT
1 GGCGTTTTTA-ATAAACGCCGCTAAAACCTAGTACTTTAGTGGCG-TTTATTCAAAAACGCCGCT
* * * *
47192 AAA-ACTCATACTTTAGTGGCGTTTGTAAACAAACACCGCCATAGGATCGTTCTTTAGTGGCGTT
64 AAAGACTCATACTTTAGTGGCGTTTTTAAACAAACGCCGCCATAGAATCATTCTTTAGTGGCGTT
*
47256 TTTAAACAAACGCCGTAATAGGGTACATATACCGT
129 TTTAAACAAACGCCGCAATAGGGTACATATACCGT
* *
47291 TGCGTTTTTAAATAAACGCCGCTAAAACCTAATACTTTAGTGGCGTTTTATTCAAAAACGCCGCT
1 GGCGTTTTT-AATAAACGCCGCTAAAACCTAGTACTTTAGTGGCG-TTTATTCAAAAACGCCGCT
* * * *
47356 AAATACTCATACTTTAGTGACGATTTTAGACAAACGCCGC
64 AAAGACTCATACTTTAGTGGCGTTTTTAAACAAACGCCGC
47396 TAAAACCTAG
Statistics
Matches: 240, Mismatches: 23, Indels: 11
0.88 0.08 0.04
Matches are distributed among these distances:
163 1 0.00
164 170 0.71
165 63 0.26
166 6 0.03
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.30
Consensus pattern (163 bp):
GGCGTTTTTAATAAACGCCGCTAAAACCTAGTACTTTAGTGGCGTTTATTCAAAAACGCCGCTAA
AGACTCATACTTTAGTGGCGTTTTTAAACAAACGCCGCCATAGAATCATTCTTTAGTGGCGTTTT
TAAACAAACGCCGCAATAGGGTACATATACCGT
Found at i:53346 original size:21 final size:21
Alignment explanation
Indices: 53287--53347 Score: 104
Period size: 21 Copynumber: 2.9 Consensus size: 21
53277 TGATTTATTA
* *
53287 TTATGGATTTTAAGTTTCTTG
1 TTATGGATTTCAAGTTTGTTG
53308 TTATGGATTTCAAGTTTGTTG
1 TTATGGATTTCAAGTTTGTTG
53329 TTATGGATTTCAAGTTTGT
1 TTATGGATTTCAAGTTTGT
53348 GTCTTAATTA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.20, C:0.05, G:0.21, T:0.54
Consensus pattern (21 bp):
TTATGGATTTCAAGTTTGTTG
Found at i:53533 original size:43 final size:43
Alignment explanation
Indices: 53482--53815 Score: 483
Period size: 43 Copynumber: 7.8 Consensus size: 43
53472 GTTTGTATAG
* * *
53482 AAAAACGCCGCTATAAATCTCAACCTTTTGCGGCGTTTATTCC
1 AAAAACGCCGCTATAGATCTCGACCTTTTGCGGCGTTTGTTCC
*
53525 AAAAACGCCGCTATAGATCT-GACCTTTTGCGGCATTTGTTCC
1 AAAAACGCCGCTATAGATCTCGACCTTTTGCGGCGTTTGTTCC
* * *
53567 AAAAACGCCACTATAAATCTCGACCTTTAGCGGGCGTTTGTTCC
1 AAAAACGCCGCTATAGATCTCGACCTTTTGC-GGCGTTTGTTCC
* * *
53611 AAAAACGCCGTTATAGATCTCTACCTTTTGTGGCGTTTGTTCC
1 AAAAACGCCGCTATAGATCTCGACCTTTTGCGGCGTTTGTTCC
*
53654 AAAAACGCCGCTATAGATCTCGACCTTTTGCGACGTTTGTTCC
1 AAAAACGCCGCTATAGATCTCGACCTTTTGCGGCGTTTGTTCC
* * * *
53697 AAAAACGCTGCTATA-AACTTGACCTTTTGCGGCGTCTGTTCC
1 AAAAACGCCGCTATAGATCTCGACCTTTTGCGGCGTTTGTTCC
*
53739 AAAAACGCCGCTATAGATCTCGACCTTTTGCGGCGTTTATTCC
1 AAAAACGCCGCTATAGATCTCGACCTTTTGCGGCGTTTGTTCC
* *
53782 AAAAATGCCGCTATATATCTCGACCTTTTGCGGC
1 AAAAACGCCGCTATAGATCTCGACCTTTTGCGGC
53816 ATTTTTTGTT
Statistics
Matches: 258, Mismatches: 30, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
42 74 0.29
43 148 0.57
44 36 0.14
ACGTcount: A:0.25, C:0.27, G:0.18, T:0.31
Consensus pattern (43 bp):
AAAAACGCCGCTATAGATCTCGACCTTTTGCGGCGTTTGTTCC
Found at i:53749 original size:85 final size:87
Alignment explanation
Indices: 53482--53815 Score: 464
Period size: 85 Copynumber: 3.9 Consensus size: 87
53472 GTTTGTATAG
*
53482 AAAAACGCCGCTATAAATCTCAACCTTTTGCGGCGTTTATTCCAAAAACGCCGCTATAG-A-TCT
1 AAAAACGCCGCTATAAATCTCGACCTTTTGCGGCGTTTATTCCAAAAACGCCGCTATAGAACTCT
*
53545 GACCTTTTGCGGCATTTGTTCC
66 GACCTTTTGCGGCGTTTGTTCC
* * * * *
53567 AAAAACGCCACTATAAATCTCGACCTTTAGCGGGCGTTTGTTCCAAAAACGCCGTTATAGATCTC
1 AAAAACGCCGCTATAAATCTCGACCTTTTGC-GGCGTTTATTCCAAAAACGCCGCTATAGAACTC
*
53632 T-ACCTTTTGTGGCGTTTGTTCC
65 TGACCTTTTGCGGCGTTTGTTCC
* * * *
53654 AAAAACGCCGCTATAGATCTCGACCTTTTGCGACGTTTGTTCCAAAAACGCTGCTATA-AACT-T
1 AAAAACGCCGCTATAAATCTCGACCTTTTGCGGCGTTTATTCCAAAAACGCCGCTATAGAACTCT
*
53717 GACCTTTTGCGGCGTCTGTTCC
66 GACCTTTTGCGGCGTTTGTTCC
* * * *
53739 AAAAACGCCGCTATAGATCTCGACCTTTTGCGGCGTTTATTCCAAAAATGCCGCTATATATCTC-
1 AAAAACGCCGCTATAAATCTCGACCTTTTGCGGCGTTTATTCCAAAAACGCCGCTATAGAACTCT
53803 GACCTTTTGCGGC
66 GACCTTTTGCGGC
53816 ATTTTTTGTT
Statistics
Matches: 221, Mismatches: 22, Indels: 11
0.87 0.09 0.04
Matches are distributed among these distances:
84 1 0.00
85 104 0.47
86 66 0.30
87 47 0.21
88 3 0.01
ACGTcount: A:0.25, C:0.27, G:0.18, T:0.31
Consensus pattern (87 bp):
AAAAACGCCGCTATAAATCTCGACCTTTTGCGGCGTTTATTCCAAAAACGCCGCTATAGAACTCT
GACCTTTTGCGGCGTTTGTTCC
Found at i:58781 original size:3 final size:3
Alignment explanation
Indices: 58773--58823 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
58763 ATGCTTTTAC
58773 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
58821 ATA
1 ATA
58824 TGACAATTAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:61472 original size:14 final size:15
Alignment explanation
Indices: 61453--61486 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
61443 ATAAAAATTT
61453 AATATAATAT-ATAA
1 AATATAATATGATAA
*
61467 AATATAATTTGATAA
1 AATATAATATGATAA
61482 AATAT
1 AATAT
61487 TTAGCAAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (15 bp):
AATATAATATGATAA
Found at i:65651 original size:30 final size:31
Alignment explanation
Indices: 65606--65678 Score: 87
Period size: 30 Copynumber: 2.4 Consensus size: 31
65596 AAAAAAAAAC
*
65606 ATAT-TTAAATAAAATAATAATAAAAAATTAA
1 ATATATTAAAT-AAATAATAACAAAAAATTAA
* *
65637 ATA-ATTAAATAAATACTAACAAAATATTAA
1 ATATATTAAATAAATAATAACAAAAAATTAA
*
65667 ATATAATAAATA
1 ATATATTAAATA
65679 TACATTATAA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
30 20 0.56
31 16 0.44
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (31 bp):
ATATATTAAATAAATAATAACAAAAAATTAA
Found at i:65727 original size:10 final size:10
Alignment explanation
Indices: 65712--65745 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
65702 AGGTTTGGTT
65712 TTTGAGAGGA
1 TTTGAGAGGA
*
65722 TTTGAGAGAA
1 TTTGAGAGGA
65732 TTTGAGAGGA
1 TTTGAGAGGA
65742 TTTG
1 TTTG
65746 GTGTGGTGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.29, C:0.00, G:0.35, T:0.35
Consensus pattern (10 bp):
TTTGAGAGGA
Found at i:71991 original size:3 final size:3
Alignment explanation
Indices: 71983--72062 Score: 124
Period size: 3 Copynumber: 26.7 Consensus size: 3
71973 TTTTTATCCA
* *
71983 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT TAT TAA TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
72031 TAT TAA TAT TAT TAT TAT TAT TTT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
72063 AATATATTAA
Statistics
Matches: 69, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 69 1.00
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:72833 original size:13 final size:13
Alignment explanation
Indices: 72815--72843 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
72805 ACCACCGTTA
72815 CGGTGGCCGGCGG
1 CGGTGGCCGGCGG
72828 CGGTGGCCGGCGG
1 CGGTGGCCGGCGG
72841 CGG
1 CGG
72844 AGTACGGTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.00, C:0.31, G:0.62, T:0.07
Consensus pattern (13 bp):
CGGTGGCCGGCGG
Found at i:73441 original size:19 final size:19
Alignment explanation
Indices: 73403--73438 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
73393 CAATTTAGTC
73403 ATTTATTTTATATGTTTTA
1 ATTTATTTTATATGTTTTA
73422 ATTTATTTTAT-TGTTTT
1 ATTTATTTTATATGTTTT
73439 TAAATATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.22, C:0.00, G:0.06, T:0.72
Consensus pattern (19 bp):
ATTTATTTTATATGTTTTA
Found at i:84815 original size:1 final size:1
Alignment explanation
Indices: 84809--84855 Score: 67
Period size: 1 Copynumber: 47.0 Consensus size: 1
84799 ATTATGCTTG
* * *
84809 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAAGAAGAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
84856 GGGGTCAAGG
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
1 40 1.00
ACGTcount: A:0.94, C:0.00, G:0.06, T:0.00
Consensus pattern (1 bp):
A
Found at i:85914 original size:52 final size:52
Alignment explanation
Indices: 85792--86495 Score: 1241
Period size: 52 Copynumber: 13.7 Consensus size: 52
85782 TATGTGCTCA
*
85792 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATT-GACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
*
85843 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGAACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
85895 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT-GTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
*
85946 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGAACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
85998 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
86050 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
86102 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT-GACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
86153 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
* *
86205 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCT-CTCTGATTGGACAG-A-
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
*
86254 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGAACA-AAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGACAGAAC
86306 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT-GACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
86357 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT-GTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
* *
86408 ATAGCATCTTCTGGAAGTG-TCTTTAAGTTATCTGATCT-GATGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
*
86458 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATTTGATC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
86496 CGAAGAAGTG
Statistics
Matches: 628, Mismatches: 15, Indels: 20
0.95 0.02 0.03
Matches are distributed among these distances:
49 34 0.05
50 59 0.09
51 249 0.40
52 286 0.46
ACGTcount: A:0.24, C:0.15, G:0.23, T:0.37
Consensus pattern (52 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
Found at i:85971 original size:103 final size:103
Alignment explanation
Indices: 85792--86495 Score: 1228
Period size: 103 Copynumber: 6.9 Consensus size: 103
85782 TATGTGCTCA
85792 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATT-GACAGAACATAGCATCTTCTG
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG-TTGGACAGAACATAGCATCTTCTG
85856 GAAGTGTTCTTTGAGTTATCTGATCTGGTTGAACAGAAC
65 GAAGTGTTCTTTGAGTTATCTGATCTGGTTGAACAGAAC
85895 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGTTGGACAGAACATAGCATCTTCTGG
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGTTGGACAGAACATAGCATCTTCTGG
85960 AAGTGTTCTTTGAGTTATCTGATCTGGTTGAACAGAAC
66 AAGTGTTCTTTGAGTTATCTGATCTGGTTGAACAGAAC
85998 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAGCATCTTCTG
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT-GTTGGACAGAACATAGCATCTTCTG
*
86063 GAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
65 GAAGTGTTCTTTGAGTTATCTGATCTGGTTGAACAGAAC
86102 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT-GACAGAACATAGCATCTTCTG
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT-GTTGGACAGAACATAGCATCTTCTG
*
86166 GAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
65 GAAGTGTTCTTTGAGTTATCTGATCTGGTTGAACAGAAC
*
86205 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCT-CTCTGATTGGACAG-A-ATAGCATCTTCTG
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG-TTGGACAGAACATAGCATCTTCTG
86267 GAAGTGTTCTTTGAGTTATCTGATCTGGTTTGAACA-AAC
65 GAAGTGTTCTTTGAGTTATCTGATCTGG-TTGAACAGAAC
86306 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT-GACAGAACATAGCATCTTCTG
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT-GTTGGACAGAACATAGCATCTTCTG
*
86370 GAAGTGTTCTTTGAGTTATCTGATCT-GTTGGACAGAAC
65 GAAGTGTTCTTTGAGTTATCTGATCTGGTTGAACAGAAC
* *
86408 ATAGCATCTTCTGGAAGTG-TCTTTAAGTTATCTGATCTGATGGACAGAACATAGCATCTTCTGG
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGTTGGACAGAACATAGCATCTTCTGG
*
86472 AAGTGTTCTTTGAGTTATTTGATC
66 AAGTGTTCTTTGAGTTATCTGATC
86496 CGAAGAAGTG
Statistics
Matches: 582, Mismatches: 8, Indels: 24
0.95 0.01 0.04
Matches are distributed among these distances:
100 2 0.00
101 153 0.26
102 43 0.07
103 278 0.48
104 106 0.18
ACGTcount: A:0.24, C:0.15, G:0.23, T:0.37
Consensus pattern (103 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGTTGGACAGAACATAGCATCTTCTGG
AAGTGTTCTTTGAGTTATCTGATCTGGTTGAACAGAAC
Found at i:87501 original size:110 final size:112
Alignment explanation
Indices: 87049--87814 Score: 1123
Period size: 110 Copynumber: 6.9 Consensus size: 112
87039 AAATTCAATT
* *
87049 CATCATTTGATGGATCATCATTACCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCATTTGGTGGATCATCATTTCCAGAGAAAGTTCATAAT-AGAAGAACTCATCTGAAGAAGGA
* *
87114 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAAT-
65 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTACCTGAATC
87161 CATCA-TT--TGGATCATC-TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCATTTGGTGGATCATCATTTCCAGAGAAAGTTCATAAT-AGAAGAACTCATCTGAAGAAGGA
*
87222 AGAAGAAGTTCATAATGAGAAGAA-TTGTTCAACCTTTTACCTG-ACC
65 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTACCTGAATC
*
87268 CATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCATTTGGTGGATCATCATTTCCAGAGAAAGTTCATAAT-AGAAGAACTCATCTGAAGAAGGA
* *
87333 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATC
65 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTACCTGAATC
*
87381 CATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAAT-GAAGAACTCATCTGAAGAAGGAA
1 CATCATTTGGTGGATCATCATTTCCAGAGAAAGTTCATAATAGAAGAACTCATCTGAAGAAGGAA
* *
87445 GAAG-AGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAACC
66 GAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTACCTGAATC
*
87491 CATCATTTGGTGGATCATCTTTTCCAGA-AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCATTTGGTGGATCATCATTTCCAGAGAAAGTTCATAAT-AGAAGAACTCATCTGAAGAAGGA
*
87555 AAAAGAAGTTCATAATGAGAAGAA-TTGTTC-ACCTTTTACCTGAATC
65 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTACCTGAATC
87601 CATCATTTGGTGGATCAT-ATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCATTTGGTGGATCATCATTTCCAGAGAAAGTTCATAAT-AGAAGAACTCATCTGAAGAAGGA
* *** * *
87665 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTTGTTTAAATT
65 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAAC-CTTTTACCTGAATC
* * ** *
87714 CATCATTTGATGGATCAACATGGCCAAAGAAAGTTCATGAATGAGAAGAACTCATCTGAAGAAGG
1 CATCATTTGGTGGATCATCATTTCCAGAGAAAGTTCAT-AAT-AGAAGAACTCATCTGAAGAAGG
*
87779 AAG-AG-AGTTC-TAATGAGAAGAGCTTGTTCAACCTTT
64 AAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTT
87815 GTTTGATATC
Statistics
Matches: 610, Mismatches: 28, Indels: 33
0.91 0.04 0.05
Matches are distributed among these distances:
106 1 0.00
107 22 0.04
108 70 0.11
109 29 0.05
110 167 0.27
111 139 0.23
112 63 0.10
113 72 0.12
114 18 0.03
115 29 0.05
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.28
Consensus pattern (112 bp):
CATCATTTGGTGGATCATCATTTCCAGAGAAAGTTCATAATAGAAGAACTCATCTGAAGAAGGAA
GAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTACCTGAATC
Found at i:87529 original size:222 final size:223
Alignment explanation
Indices: 87049--87814 Score: 1189
Period size: 222 Copynumber: 3.5 Consensus size: 223
87039 AAATTCAATT
*
87049 CATCATTTGATGGATCATCATTACCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCATTTGATGGATCATCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
87114 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAAT-CATCA-TT--TGGATCA
66 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATCCATCATTTGGTGGATCA
87175 TCTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
131 TCTTTCCAGAGAAAGTTCATAAT-AGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
87240 GAAGAATTGTTCAACCTTTTACCTG-ACC
195 GAAGAATTGTTCAACCTTTTACCTGAACC
* *
87268 CATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCATTTGATGGATCATCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
87333 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATCCATCATTTGGTGGATCA
66 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATCCATCATTTGGTGGATCA
87398 TCTTTTCCAGAGAAAGTTCATAAT-GAAGAACTCATCTGAAGAAGGAAGAAG-AGTTCATAATGA
131 TC-TTTCCAGAGAAAGTTCATAATAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
87461 GAAGAATTTGTTCAACCTTTTACCTGAACC
195 GAAGAA-TTGTTCAACCTTTTACCTGAACC
* *
87491 CATCATTTGGTGGATCATCTTTTCCAGA-AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCATTTGATGGATCATCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* * *
87555 AAAAGAAGTTCATAATGAGAAGAA-TTGTTC-ACCTTTTACCTGAATCCATCATTTGGTGGATCA
66 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATCCATCATTTGGTGGATCA
*
87618 TATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
131 TCTTTCCAGAGAAAGTTCATAAT-AGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
* *** * **
87683 GAAGAACTTGTTCAACTTTTTTGTTTAAATT
195 GAAGAA-TTGTTCAAC-CTTTTACCTGAACC
* ** *
87714 CATCATTTGATGGATCAACATGGCCAAAGAAAGTTCATGAATGAGAAGAACTCATCTGAAGAAGG
1 CATCATTTGATGGATCATCATTTCCAGAGAAAGTTCAT-AATGAGAAGAACTCATCTGAAGAAGG
*
87779 AAG-AG-AGTTC-TAATGAGAAGAGCTTGTTCAACCTTT
65 AAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTT
87815 GTTTGATATC
Statistics
Matches: 509, Mismatches: 23, Indels: 25
0.91 0.04 0.04
Matches are distributed among these distances:
219 130 0.26
220 37 0.07
221 53 0.10
222 143 0.28
223 80 0.16
224 38 0.07
225 28 0.06
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.28
Consensus pattern (223 bp):
CATCATTTGATGGATCATCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATCCATCATTTGGTGGATCA
TCTTTCCAGAGAAAGTTCATAATAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG
AAGAATTGTTCAACCTTTTACCTGAACC
Found at i:88111 original size:3 final size:3
Alignment explanation
Indices: 88103--88177 Score: 109
Period size: 3 Copynumber: 25.7 Consensus size: 3
88093 TTTTTATCCA
* *
88103 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT TAT TAA TAT TA- TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
88150 TAA TAT TAT TAT TAT TAT T-T TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
88178 AATATATTAA
Statistics
Matches: 64, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
2 4 0.06
3 60 0.94
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:88909 original size:13 final size:13
Alignment explanation
Indices: 88891--88919 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
88881 ACCACCGTTA
88891 CGGTGGCCGGCGG
1 CGGTGGCCGGCGG
88904 CGGTGGCCGGCGG
1 CGGTGGCCGGCGG
88917 CGG
1 CGG
88920 AGTACGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.00, C:0.31, G:0.62, T:0.07
Consensus pattern (13 bp):
CGGTGGCCGGCGG
Done.