Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009356.1 Hibiscus syriacus cultivar Beakdansim tig00113165_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: 62186
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.32
Found at i:16336 original size:47 final size:47
Alignment explanation
Indices: 16285--16415 Score: 226
Period size: 47 Copynumber: 2.8 Consensus size: 47
16275 GGAATCTGCC
*
16285 GGAAATGCACGTGGAGGGGTTGCTATTGTTGGTTGCTGGAAGCTACT
1 GGAAATGTACGTGGAGGGGTTGCTATTGTTGGTTGCTGGAAGCTACT
16332 GGAAATGTACGTGGAGGGGTTGCTATTGTTGGTTGCTGGAAGCTACT
1 GGAAATGTACGTGGAGGGGTTGCTATTGTTGGTTGCTGGAAGCTACT
* * *
16379 GGAAATGTACGTGGAGGGGTTGTTGTCGTTGGTTGCT
1 GGAAATGTACGTGGAGGGGTTGCTATTGTTGGTTGCT
16416 AAATAAGGGA
Statistics
Matches: 80, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 80 1.00
ACGTcount: A:0.18, C:0.11, G:0.40, T:0.32
Consensus pattern (47 bp):
GGAAATGTACGTGGAGGGGTTGCTATTGTTGGTTGCTGGAAGCTACT
Found at i:16812 original size:152 final size:152
Alignment explanation
Indices: 16648--17051 Score: 655
Period size: 152 Copynumber: 2.7 Consensus size: 152
16638 TCTCTGTGAT
* *
16648 GAGTCGAACAAAAGATTGAATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTT
1 GAGTCGAGCAAAAGGTTGAATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTT
*
16713 CTTCTTATTACGAACTTCTTCTGGAAATGTTGATGATGCTCTATTTCCTTTTCTAATGTTGATGA
66 CTTCTTATTACGAACTTCTTCTGGAAATGTTGATGATGCTCTATCTCCTTTTCTAATGTTGATGA
*
16778 TGTTCTATCTCATTATGCGATA
131 TATTCTATCTCATTATGCGATA
* *
16800 GAGTCGAGCAAAAGGTTGAATAAGTTCTTCAGATTATGAACTTCTTCATCCTCTTCAGTTGAGTT
1 GAGTCGAGCAAAAGGTTGAATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTT
* *
16865 CTTCTTATTACGAACTTCTTCTAGAAATGTTGATGATGCTCTATCTCTTTTTCTAATGTTGATGA
66 CTTCTTATTACGAACTTCTTCTGGAAATGTTGATGATGCTCTATCTCCTTTTCTAATGTTGATGA
* *
16930 TATTCTATCTCCTTTTGCGATA
131 TATTCTATCTCATTATGCGATA
* ** *
16952 GAGTCGAGCAAAAGGTTGAATAAGTTCTTTAGATTATGAACTTCTTCTTATTCTTCAAATGAGTT
1 GAGTCGAGCAAAAGGTTGAATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTT
* * *
17017 CTTCTTATTACGAACTCCTTCCGAAAATGTTGATG
66 CTTCTTATTACGAACTTCTTCTGGAAATGTTGATG
17052 CAATCTTCAT
Statistics
Matches: 232, Mismatches: 20, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
152 232 1.00
ACGTcount: A:0.26, C:0.17, G:0.16, T:0.41
Consensus pattern (152 bp):
GAGTCGAGCAAAAGGTTGAATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTT
CTTCTTATTACGAACTTCTTCTGGAAATGTTGATGATGCTCTATCTCCTTTTCTAATGTTGATGA
TATTCTATCTCATTATGCGATA
Found at i:16923 original size:29 final size:29
Alignment explanation
Indices: 16890--16945 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
16880 TTCTTCTAGA
* *
16890 AATGTTGATGATGCTCTATCTCTTTTTCT
1 AATGTTGATGATACTCTATCTCCTTTTCT
*
16919 AATGTTGATGATATTCTATCTCCTTTT
1 AATGTTGATGATACTCTATCTCCTTTT
16946 GCGATAGAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.20, C:0.16, G:0.12, T:0.52
Consensus pattern (29 bp):
AATGTTGATGATACTCTATCTCCTTTTCT
Found at i:17393 original size:18 final size:18
Alignment explanation
Indices: 17372--17417 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
17362 GAATCTATCA
17372 TCTTTGAAGAAAACATCC
1 TCTTTGAAGAAAACATCC
*
17390 TCTTTGAATAAAACATCC
1 TCTTTGAAGAAAACATCC
17408 TCTTTGAAGA
1 TCTTTGAAGA
17418 GAATCTATGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.37, C:0.20, G:0.11, T:0.33
Consensus pattern (18 bp):
TCTTTGAAGAAAACATCC
Found at i:17875 original size:54 final size:53
Alignment explanation
Indices: 17782--17945 Score: 204
Period size: 54 Copynumber: 3.1 Consensus size: 53
17772 GAATAACTGG
* * *
17782 TTCGTAAAACATTTGACAACACATTCA-TCATCTCATGTGGTTTCTGCTCAGAT
1 TTCGTAAAACATTTGACAACACATTCATTC-TTTCCTGTGGCTTCTGCTCAGAT
* * *
17835 TCTCGTAAAACATTTGACAACACATTCATTCTTTCCTGTGGCTTATTCCCAGAT
1 T-TCGTAAAACATTTGACAACACATTCATTCTTTCCTGTGGCTTCTGCTCAGAT
* * * *
17889 GTTCATAAAGCATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGGTCAGAT
1 -TTCGTAAAACATTTGACAACACATTCATTCTTTCCTGTGGCTTCTGCTCAGAT
17943 TTC
1 TTC
17946 TCAATCATTG
Statistics
Matches: 95, Mismatches: 13, Indels: 6
0.83 0.11 0.05
Matches are distributed among these distances:
53 4 0.04
54 88 0.93
55 3 0.03
ACGTcount: A:0.26, C:0.24, G:0.13, T:0.37
Consensus pattern (53 bp):
TTCGTAAAACATTTGACAACACATTCATTCTTTCCTGTGGCTTCTGCTCAGAT
Found at i:19800 original size:7 final size:8
Alignment explanation
Indices: 19781--19810 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
19771 TTTGATTCAA
19781 TTTTTTCC
1 TTTTTTCC
19789 TTTTTTCC
1 TTTTTTCC
19797 TTTTTTCC
1 TTTTTTCC
19805 TTTTTT
1 TTTTTT
19811 TTTTATGAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (8 bp):
TTTTTTCC
Found at i:22288 original size:6 final size:7
Alignment explanation
Indices: 22272--22317 Score: 53
Period size: 6 Copynumber: 6.9 Consensus size: 7
22262 TAAAAGTACG
22272 AATGCAA
1 AATGCAA
22279 AATG-AA
1 AATGCAA
22285 AATGCAA
1 AATGCAA
*
22292 AGATGCGA
1 A-ATGCAA
22300 AATGC-A
1 AATGCAA
22306 AATGC-A
1 AATGCAA
22312 AATGCA
1 AATGCA
22318 TATATGAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
6 18 0.51
7 11 0.31
8 6 0.17
ACGTcount: A:0.52, C:0.13, G:0.20, T:0.15
Consensus pattern (7 bp):
AATGCAA
Found at i:22302 original size:21 final size:21
Alignment explanation
Indices: 22273--22313 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
22263 AAAAGTACGA
22273 ATGCAAAATGAAAATGCAAAG
1 ATGCAAAATGAAAATGCAAAG
* *
22294 ATGCGAAATGCAAATGCAAA
1 ATGCAAAATGAAAATGCAAA
22314 TGCATATATG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.54, C:0.12, G:0.20, T:0.15
Consensus pattern (21 bp):
ATGCAAAATGAAAATGCAAAG
Found at i:22967 original size:36 final size:36
Alignment explanation
Indices: 22901--22972 Score: 99
Period size: 36 Copynumber: 2.0 Consensus size: 36
22891 TCTTACCGTA
* * *
22901 GAATGCTTTTGGTATCAATCTAACAGGATCTTTGTG
1 GAATACTTTTGGTATCAATATAACAAGATCTTTGTG
* *
22937 GAATACTTTTGGTATTAATATAATAAGATCTTTGTG
1 GAATACTTTTGGTATCAATATAACAAGATCTTTGTG
22973 TGCATAACTC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.29, C:0.10, G:0.19, T:0.42
Consensus pattern (36 bp):
GAATACTTTTGGTATCAATATAACAAGATCTTTGTG
Found at i:26053 original size:803 final size:803
Alignment explanation
Indices: 24509--26115 Score: 3160
Period size: 803 Copynumber: 2.0 Consensus size: 803
24499 TGGTGATTAC
24509 ACCTGGTTTCATGTTTATTTCTCAGCCACTGACTGGTTTGGACAATTACATTTTTAATGGGTTTA
1 ACCTGGTTTCATGTTTATTTCTCAGCCACTGACTGGTTTGGACAATTACATTTTTAATGGGTTTA
*
24574 AATGAGTCATAGTCGGTGTTGCGAAGCTAAATTTTATTGATGCAACCATTGCCTTCAGTTATACA
66 AATGAGTCATAGTCGGCGTTGCGAAGCTAAATTTTATTGATGCAACCATTGCCTTCAGTTATACA
24639 AGCTTATTTGATGATTCTTTAAGAAGAGTCTCAACGTTCTAAACTTTCTGTTCTTGCTACTCTAG
131 AGCTTATTTGATGATTCTTTAAGAAGAGTCTCAACGTTCTAAACTTTCTGTTCTTGCTACTCTAG
24704 CTACATAGTTTTGTTCTCTAATTCTGCTGGCAATTTTGAATGTCGTCGTTTTAGTGGATCTTGTG
196 CTACATAGTTTTGTTCTCTAATTCTGCTGGCAATTTTGAATGTCGTCGTTTTAGTGGATCTTGTG
24769 ATTTTTGTAAGATCAAGGGGCATAAGAAGGACCAATGCTATCATTTAATTGGGTTCCCACCTAGT
261 ATTTTTGTAAGATCAAGGGGCATAAGAAGGACCAATGCTATCATTTAATTGGGTTCCCACCTAGT
24834 TACAAGTTCACAAAGAAGAAATGATTTGTGGCTAATTCAAGTATTTCTTTGGAATCTGAGGGTAC
326 TACAAGTTCACAAAGAAGAAATGATTTGTGGCTAATTCAAGTATTTCTTTGGAATCTGAGGGTAC
24899 CTCAAAACTCATGGTGCTTCTCATGTAGCGTCATCGTTTACCACAGAGCAATATAATCAAATTTT
391 CTCAAAACTCATGGTGCTTCTCATGTAGCGTCATCGTTTACCACAGAGCAATATAATCAAATTTT
24964 GCTCCTATTGAATAAAGCTCATTATGTTGATTCAGTTGTTAATCTTGCAGGTATTATTCATTCTA
456 GCTCCTATTGAATAAAGCTCATTATGTTGATTCAGTTGTTAATCTTGCAGGTATTATTCATTCTA
25029 ATTCATTTAAGTTTAATGGTTTGTCTTCTTGGATTATTGACATAGGTGTAATTGAACATATTTTA
521 ATTCATTTAAGTTTAATGGTTTGTCTTCTTGGATTATTGACATAGGTGTAATTGAACATATTTTA
25094 TCTGATTTCAAGAGCTTGAATCATCCGATTTCCTACTCTTTCTCCATTGGTTCATCTCCCTGATA
586 TCTGATTTCAAGAGCTTGAATCATCCGATTTCCTACTCTTTCTCCATTGGTTCATCTCCCTGATA
25159 GCAATGTTGTGTCTGTTACCCATCTTGGTTCATGTGTTTTTACTCCTTACCAAATGATTCATAAT
651 GCAATGTTGTGTCTGTTACCCATCTTGGTTCATGTGTTTTTACTCCTTACCAAATGATTCATAAT
25224 GTTCTGTTTGTGCCAAATTTTAGTCATAACTTGCTTTATGTTTCTAAAATTACACGCGATCTTAA
716 GTTCTGTTTGTGCCAAATTTTAGTCATAACTTGCTTTATGTTTCTAAAATTACACGCGATCTTAA
25289 TTGTTTTTTCACTTTCTATCATG
781 TTGTTTTTTCACTTTCTATCATG
25312 ACCTGGTTTCATGTTTATTTCTCAGCCACTGACTGGTTTGGACAATTACATTTTTAATGGGTTTA
1 ACCTGGTTTCATGTTTATTTCTCAGCCACTGACTGGTTTGGACAATTACATTTTTAATGGGTTTA
25377 AATGAGTCATAGTCGGCGTTGCGAAGCTAAATTTTATTGATGCAACCATTGCCTTCAGTTATACA
66 AATGAGTCATAGTCGGCGTTGCGAAGCTAAATTTTATTGATGCAACCATTGCCTTCAGTTATACA
25442 AGCTTATTTGATGATTCTTTAAGAAGAGTCTCAACGTTCTAAACTTTCTGTTCTTGCTACTCTAG
131 AGCTTATTTGATGATTCTTTAAGAAGAGTCTCAACGTTCTAAACTTTCTGTTCTTGCTACTCTAG
*
25507 CTACATAGTTTTGTTCTCTAATTCTGCTGGCAATTTTGAATGTCGTTGTTTTAGTGGATCTTGTG
196 CTACATAGTTTTGTTCTCTAATTCTGCTGGCAATTTTGAATGTCGTCGTTTTAGTGGATCTTGTG
25572 ATTTTTGTAAGATCAAGGGGCATAAGAAGGACCAATGCTATCATTTAATTGGGTTCCCACCTAGT
261 ATTTTTGTAAGATCAAGGGGCATAAGAAGGACCAATGCTATCATTTAATTGGGTTCCCACCTAGT
*
25637 TACAAGTTCACAAAGAAGAAATGATTTGTGGCTAATTCAAGTGTTTCTTTGGAATCTGAGGGTAC
326 TACAAGTTCACAAAGAAGAAATGATTTGTGGCTAATTCAAGTATTTCTTTGGAATCTGAGGGTAC
25702 CTCAAAACTCATGGTGCTTCTCATGTAGCGTCATCGTTTACCACAGAGCAATATAATCAAATTTT
391 CTCAAAACTCATGGTGCTTCTCATGTAGCGTCATCGTTTACCACAGAGCAATATAATCAAATTTT
*
25767 GCTCCTATTGAATAAAGCTCATTCTGTTGATTCAGTTGTTAATCTTGCAGGTATTATTCATTCTA
456 GCTCCTATTGAATAAAGCTCATTATGTTGATTCAGTTGTTAATCTTGCAGGTATTATTCATTCTA
*
25832 ATTTATTTAAGTTTAATGGTTTGTCTTCTTGGATTATTGACATAGGTGTAATTGAACATATTTTA
521 ATTCATTTAAGTTTAATGGTTTGTCTTCTTGGATTATTGACATAGGTGTAATTGAACATATTTTA
25897 TCTGATTTCAAGAGCTTGAATCATCCGATTTCCTACTCTTTCTCCATTGGTTCATCTCCCTGATA
586 TCTGATTTCAAGAGCTTGAATCATCCGATTTCCTACTCTTTCTCCATTGGTTCATCTCCCTGATA
*
25962 GCAATGTTGTGTTTGTTACCCATCTTGGTTCATGTGTTTTTACTCCTTACCAAATGATTCATAAT
651 GCAATGTTGTGTCTGTTACCCATCTTGGTTCATGTGTTTTTACTCCTTACCAAATGATTCATAAT
26027 GTTCTGTTTGTGCCAAATTTTAGTCATAACTTGCTTTATGTTTCTAAAATTACACGCGATCTTAA
716 GTTCTGTTTGTGCCAAATTTTAGTCATAACTTGCTTTATGTTTCTAAAATTACACGCGATCTTAA
26092 TTGTTTTTTCACTTTCTATCATG
781 TTGTTTTTTCACTTTCTATCATG
26115 A
1 A
26116 TTTTTGTCTT
Statistics
Matches: 798, Mismatches: 6, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
803 798 1.00
ACGTcount: A:0.25, C:0.17, G:0.17, T:0.40
Consensus pattern (803 bp):
ACCTGGTTTCATGTTTATTTCTCAGCCACTGACTGGTTTGGACAATTACATTTTTAATGGGTTTA
AATGAGTCATAGTCGGCGTTGCGAAGCTAAATTTTATTGATGCAACCATTGCCTTCAGTTATACA
AGCTTATTTGATGATTCTTTAAGAAGAGTCTCAACGTTCTAAACTTTCTGTTCTTGCTACTCTAG
CTACATAGTTTTGTTCTCTAATTCTGCTGGCAATTTTGAATGTCGTCGTTTTAGTGGATCTTGTG
ATTTTTGTAAGATCAAGGGGCATAAGAAGGACCAATGCTATCATTTAATTGGGTTCCCACCTAGT
TACAAGTTCACAAAGAAGAAATGATTTGTGGCTAATTCAAGTATTTCTTTGGAATCTGAGGGTAC
CTCAAAACTCATGGTGCTTCTCATGTAGCGTCATCGTTTACCACAGAGCAATATAATCAAATTTT
GCTCCTATTGAATAAAGCTCATTATGTTGATTCAGTTGTTAATCTTGCAGGTATTATTCATTCTA
ATTCATTTAAGTTTAATGGTTTGTCTTCTTGGATTATTGACATAGGTGTAATTGAACATATTTTA
TCTGATTTCAAGAGCTTGAATCATCCGATTTCCTACTCTTTCTCCATTGGTTCATCTCCCTGATA
GCAATGTTGTGTCTGTTACCCATCTTGGTTCATGTGTTTTTACTCCTTACCAAATGATTCATAAT
GTTCTGTTTGTGCCAAATTTTAGTCATAACTTGCTTTATGTTTCTAAAATTACACGCGATCTTAA
TTGTTTTTTCACTTTCTATCATG
Found at i:39250 original size:17 final size:17
Alignment explanation
Indices: 39219--39253 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
39209 AAGCTTCTTT
**
39219 ATATTTTAATGTTAAAA
1 ATATTTTAAAATTAAAA
39236 ATATTTTAAAATTAAAA
1 ATATTTTAAAATTAAAA
39253 A
1 A
39254 CTAATATATT
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:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (17 bp):
ATATTTTAAAATTAAAA
Found at i:40824 original size:23 final size:22
Alignment explanation
Indices: 40798--40851 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
40788 AATGTATTTC
40798 TCTATTTTT-ATATCATATTTTTA
1 TCTATTTTTGATA-CAT-TTTTTA
*
40821 TCTATCTTTTGGTACATTTTTTA
1 TCTAT-TTTTGATACATTTTTTA
*
40844 TTTATTTT
1 TCTATTTT
40852 CTATCGATCC
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
22 3 0.11
23 15 0.56
24 7 0.26
25 2 0.07
ACGTcount: A:0.20, C:0.09, G:0.04, T:0.67
Consensus pattern (22 bp):
TCTATTTTTGATACATTTTTTA
Found at i:41270 original size:35 final size:33
Alignment explanation
Indices: 41217--41281 Score: 87
Period size: 33 Copynumber: 1.9 Consensus size: 33
41207 AAAAACATCC
*
41217 TAATTTTAATAATGTAATC-ATCTTGAAAAAAAA
1 TAATTTTAACAATGTAATCAATCTT-AAAAAAAA
41250 TAATTTTAACAATGTATAATCAATCTTAAAAA
1 TAATTTTAACAATG--TAATCAATCTTAAAAA
41282 TAAGACAAGT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 13 0.46
35 10 0.36
36 5 0.18
ACGTcount: A:0.51, C:0.08, G:0.05, T:0.37
Consensus pattern (33 bp):
TAATTTTAACAATGTAATCAATCTTAAAAAAAA
Found at i:41398 original size:11 final size:11
Alignment explanation
Indices: 41382--41430 Score: 55
Period size: 11 Copynumber: 4.5 Consensus size: 11
41372 ACTCTAACTC
41382 AAATTTAAATT
1 AAATTTAAATT
*
41393 AAATTTAAATA
1 AAATTTAAATT
*
41404 AAATATT-TATT
1 AAAT-TTAAATT
*
41415 AAATTTTAATT
1 AAATTTAAATT
41426 AAATT
1 AAATT
41431 GAATTCAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
10 2 0.06
11 28 0.88
12 2 0.06
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (11 bp):
AAATTTAAATT
Found at i:41407 original size:22 final size:21
Alignment explanation
Indices: 41382--41441 Score: 57
Period size: 22 Copynumber: 2.7 Consensus size: 21
41372 ACTCTAACTC
41382 AAATTTAAATTAAATTTAAATA
1 AAATTT-AATTAAATTTAAATA
* * *
41404 AAATATTTATTAAATTTTAATT
1 AAAT-TTAATTAAATTTAAATA
*
41426 AAATTGAATTCAAATT
1 AAATTTAATT-AAATT
41442 ACTCAACTCA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
21 4 0.13
22 25 0.81
23 2 0.06
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (21 bp):
AAATTTAATTAAATTTAAATA
Found at i:44300 original size:5 final size:5
Alignment explanation
Indices: 44290--44342 Score: 52
Period size: 5 Copynumber: 9.8 Consensus size: 5
44280 AACGGTCAAC
* *
44290 GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTCG GGTCAAC GGTCG GGTCG
1 GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG
44339 GGTC
1 GGTC
44343 AGACCGGTCA
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
5 32 0.80
7 8 0.20
ACGTcount: A:0.08, C:0.23, G:0.51, T:0.19
Consensus pattern (5 bp):
GGTCG
Found at i:44305 original size:17 final size:17
Alignment explanation
Indices: 44283--44343 Score: 77
Period size: 17 Copynumber: 3.3 Consensus size: 17
44273 AACGGTCAAC
44283 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
44300 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAA----C-GGTCGGGTCG
44322 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
44339 GGTCA
1 GGTCA
44344 GACCGGTCAA
Statistics
Matches: 39, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
17 21 0.54
18 1 0.03
21 1 0.03
22 16 0.41
ACGTcount: A:0.11, C:0.23, G:0.48, T:0.18
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:44318 original size:22 final size:22
Alignment explanation
Indices: 44276--44342 Score: 107
Period size: 22 Copynumber: 3.0 Consensus size: 22
44266 GAAAGTCAAC
*
44276 GGTCAACGGTCAACGGTCGGGTCG
1 GGTCAACGGTC--GGGTCGGGTCG
44300 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
44322 GGTCAACGGTCGGGTCGGGTC
1 GGTCAACGGTCGGGTCGGGTC
44343 AGACCGGTCA
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
22 31 0.74
24 11 0.26
ACGTcount: A:0.12, C:0.24, G:0.46, T:0.18
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:44363 original size:19 final size:19
Alignment explanation
Indices: 44341--44426 Score: 113
Period size: 19 Copynumber: 4.5 Consensus size: 19
44331 TCGGGTCGGG
44341 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
*
44360 TCAGACCGGTCAAGCCGGT
1 TCAGACCGGTCAAACCGGT
44379 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
*
44398 TC-GAACCGGTTGAAACCGG-
1 TCAG-ACCGG-TCAAACCGGT
*
44417 TCAAACCGGT
1 TCAGACCGGT
44427 TGAAAACCGG
Statistics
Matches: 60, Mismatches: 4, Indels: 7
0.85 0.06 0.10
Matches are distributed among these distances:
18 2 0.03
19 50 0.83
20 8 0.13
ACGTcount: A:0.26, C:0.30, G:0.28, T:0.16
Consensus pattern (19 bp):
TCAGACCGGTCAAACCGGT
Found at i:44406 original size:29 final size:27
Alignment explanation
Indices: 44383--44446 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 27
44373 GCCGGTTCAG
*
44383 ACCGGTCAAACCGGTTCGAACCGGTTGAA
1 ACCGGTCAAACCGG-TCAAACCGGTT-AA
*
44412 ACCGGTCAAACCGGTTGAAAACCGGTTAA
1 ACCGGTCAAACCGG-T-CAAACCGGTTAA
44441 ACCGGT
1 ACCGGT
44447 TTCCAGCAGC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
29 24 0.75
30 8 0.25
ACGTcount: A:0.30, C:0.27, G:0.27, T:0.17
Consensus pattern (27 bp):
ACCGGTCAAACCGGTCAAACCGGTTAA
Found at i:44447 original size:9 final size:10
Alignment explanation
Indices: 44345--44447 Score: 108
Period size: 9 Copynumber: 10.7 Consensus size: 10
44335 GTCGGGTCAG
44345 ACCGG-TCAA
1 ACCGGTTCAA
*
44354 ACCGGTTCAG
1 ACCGGTTCAA
44364 ACCGG-TCAA
1 ACCGGTTCAA
* *
44373 GCCGGTTCAG
1 ACCGGTTCAA
44383 ACCGG-TCAA
1 ACCGGTTCAA
*
44392 ACCGGTTCGA
1 ACCGGTTCAA
*
44402 ACCGGTTGAA
1 ACCGGTTCAA
44412 ACCGG-TCAA
1 ACCGGTTCAA
*
44421 ACCGGTTGAAA
1 ACCGGTT-CAA
44432 ACCGGTT-AA
1 ACCGGTTCAA
44441 ACCGGTT
1 ACCGGTT
44448 TCCAGCAGCC
Statistics
Matches: 78, Mismatches: 11, Indels: 10
0.79 0.11 0.10
Matches are distributed among these distances:
9 37 0.47
10 32 0.41
11 9 0.12
ACGTcount: A:0.27, C:0.28, G:0.27, T:0.17
Consensus pattern (10 bp):
ACCGGTTCAA
Found at i:51648 original size:17 final size:17
Alignment explanation
Indices: 51626--51687 Score: 70
Period size: 17 Copynumber: 3.4 Consensus size: 17
51616 AACAGTCAAC
51626 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
51643 GGTCAACGGTCCGGTCGGGTCG
1 GGTCAA-----CGGTCGGGTCG
51665 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
*
51682 AGTCAA
1 GGTCAA
51688 ACCGGTTCAG
Statistics
Matches: 39, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
17 22 0.56
22 17 0.44
ACGTcount: A:0.15, C:0.24, G:0.44, T:0.18
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:51653 original size:7 final size:7
Alignment explanation
Indices: 51606--51636 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
51596 GTCAAAGAAA
51606 GTCAACG
1 GTCAACG
*
51613 GTCAACA
1 GTCAACG
51620 GTCAACG
1 GTCAACG
51627 GTCAACG
1 GTCAACG
51634 GTC
1 GTC
51637 GGGTCGGGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.29, C:0.29, G:0.26, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:51660 original size:22 final size:22
Alignment explanation
Indices: 51620--51681 Score: 97
Period size: 22 Copynumber: 2.7 Consensus size: 22
51610 ACGGTCAACA
51620 GTCAACGGTCAACGGTCGGGTCGG
1 GTCAACGGTC--CGGTCGGGTCGG
51644 GTCAACGGTCCGGTCGGGTCGG
1 GTCAACGGTCCGGTCGGGTCGG
*
51666 GTCAACGGTCGGGTCG
1 GTCAACGGTCCGGTCG
51682 AGTCAAACCG
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
22 27 0.73
24 10 0.27
ACGTcount: A:0.13, C:0.26, G:0.44, T:0.18
Consensus pattern (22 bp):
GTCAACGGTCCGGTCGGGTCGG
Found at i:51710 original size:18 final size:19
Alignment explanation
Indices: 51683--51790 Score: 105
Period size: 19 Copynumber: 5.6 Consensus size: 19
51673 GTCGGGTCGA
51683 GTCAAACCGGTTCAGACC-
1 GTCAAACCGGTTCAGACCG
*
51701 GTCAAGCCGGTTCAGACCG
1 GTCAAACCGGTTCAGACCG
51720 GTCAAACCGGTTC-GAACCG
1 GTCAAACCGGTTCAG-ACCG
* *
51739 GTTGAAACCGG-TCAAACCG
1 G-TCAAACCGGTTCAGACCG
* *
51758 GTCAGAACCGGTTGAAAACCG
1 GTCA-AACCGGTT-CAGACCG
*
51779 GTTAAACCGGTT
1 GTCAAACCGGTT
51791 TCCAGCAGCC
Statistics
Matches: 76, Mismatches: 7, Indels: 12
0.80 0.07 0.13
Matches are distributed among these distances:
18 20 0.26
19 30 0.39
20 17 0.22
21 9 0.12
ACGTcount: A:0.28, C:0.28, G:0.27, T:0.18
Consensus pattern (19 bp):
GTCAAACCGGTTCAGACCG
Found at i:51730 original size:9 final size:9
Alignment explanation
Indices: 51683--51789 Score: 81
Period size: 10 Copynumber: 11.2 Consensus size: 9
51673 GTCGGGTCGA
51683 GTCAAACCG
1 GTCAAACCG
*
51692 GTTCAGACC-
1 G-TCAAACCG
*
51701 GTCAAGCCG
1 GTCAAACCG
*
51710 GTTCAGACCG
1 G-TCAAACCG
51720 GTCAAACCG
1 GTCAAACCG
*
51729 GTTCGAACCG
1 G-TCAAACCG
*
51739 GTTGAAACCG
1 G-TCAAACCG
51749 GTCAAACCG
1 GTCAAACCG
51758 GTCAGAACCG
1 GTCA-AACCG
*
51768 GTTGAAAACCG
1 G-T-CAAACCG
*
51779 GTTAAACCG
1 GTCAAACCG
51788 GT
1 GT
51790 TTCCAGCAGC
Statistics
Matches: 79, Mismatches: 12, Indels: 14
0.75 0.11 0.13
Matches are distributed among these distances:
8 5 0.06
9 30 0.38
10 36 0.46
11 7 0.09
12 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.27, T:0.17
Consensus pattern (9 bp):
GTCAAACCG
Found at i:51741 original size:29 final size:30
Alignment explanation
Indices: 51707--51790 Score: 109
Period size: 29 Copynumber: 2.8 Consensus size: 30
51697 GACCGTCAAG
* *
51707 CCGGTTCAGACCGGTCAAACCGGTTC-GAA
1 CCGGTTAAAACCGGTCAAACCGGTTCAGAA
*
51736 CCGGTTGAAACCGGTCAAACCGG-TCAGAA
1 CCGGTTAAAACCGGTCAAACCGGTTCAGAA
*
51765 CCGGTTGAAAACCGGTTAAACCGGTT
1 CCGGTT-AAAACCGGTCAAACCGGTT
51791 TCCAGCAGCC
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
28 2 0.04
29 30 0.62
30 15 0.31
31 1 0.02
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.18
Consensus pattern (30 bp):
CCGGTTAAAACCGGTCAAACCGGTTCAGAA
Found at i:51790 original size:9 final size:9
Alignment explanation
Indices: 51716--51790 Score: 69
Period size: 9 Copynumber: 7.8 Consensus size: 9
51706 GCCGGTTCAG
*
51716 ACCGGTCAA
1 ACCGGTTAA
*
51725 ACCGGTTCGA
1 ACCGGTT-AA
51735 ACCGGTTGAA
1 ACCGGTT-AA
*
51745 ACCGGTCAA
1 ACCGGTTAA
*
51754 ACCGGTCAGA
1 ACCGGTTA-A
51764 ACCGGTTGAAA
1 ACCGGTT--AA
51775 ACCGGTTAA
1 ACCGGTTAA
51784 ACCGGTT
1 ACCGGTT
51791 TCCAGCAGCC
Statistics
Matches: 56, Mismatches: 6, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
9 25 0.45
10 22 0.39
11 8 0.14
12 1 0.02
ACGTcount: A:0.29, C:0.27, G:0.27, T:0.17
Consensus pattern (9 bp):
ACCGGTTAA
Found at i:58960 original size:21 final size:22
Alignment explanation
Indices: 58923--58980 Score: 86
Period size: 20 Copynumber: 2.7 Consensus size: 22
58913 ACGGTCAACA
58923 GTCAACGGTCACGGTCGGGTCGG
1 GTCAACGGTC-CGGTCGGGTCGG
58946 GT-AACGGTCCGGTC-GGTCGG
1 GTCAACGGTCCGGTCGGGTCGG
58966 GTCAACGGT-CGGTCG
1 GTCAACGGTCCGGTCG
58981 TCAAACCGGT
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
20 13 0.39
21 11 0.33
22 7 0.21
23 2 0.06
ACGTcount: A:0.12, C:0.26, G:0.43, T:0.19
Consensus pattern (22 bp):
GTCAACGGTCCGGTCGGGTCGG
Found at i:59008 original size:19 final size:19
Alignment explanation
Indices: 58980--59066 Score: 99
Period size: 19 Copynumber: 4.6 Consensus size: 19
58970 ACGGTCGGTC
*
58980 GTCAAACCGGTTCAGACTG
1 GTCAAACCGGTTCAGACCG
*
58999 GTCAAGCCGGTTCAGACCG
1 GTCAAACCGGTTCAGACCG
59018 GTCAAACCGGTTC-GAACCG
1 GTCAAACCGGTTCAG-ACCG
* *
59037 GTTGAAACCGG-TCAAACCG
1 G-TCAAACCGGTTCAGACCG
59056 GTCAAA-CGGTT
1 GTCAAACCGGTT
59067 GAAAACCTGT
Statistics
Matches: 58, Mismatches: 6, Indels: 9
0.79 0.08 0.12
Matches are distributed among these distances:
17 3 0.05
18 6 0.10
19 41 0.71
20 8 0.14
ACGTcount: A:0.26, C:0.28, G:0.28, T:0.18
Consensus pattern (19 bp):
GTCAAACCGGTTCAGACCG
Found at i:59035 original size:10 final size:10
Alignment explanation
Indices: 58981--59086 Score: 89
Period size: 9 Copynumber: 11.1 Consensus size: 10
58971 CGGTCGGTCG
58981 TCAAACCGGT
1 TCAAACCGGT
* *
58991 TCAGACTGG-
1 TCAAACCGGT
*
59000 TCAAGCCGGT
1 TCAAACCGGT
*
59010 TCAGACCGG-
1 TCAAACCGGT
59019 TCAAACCGGT
1 TCAAACCGGT
*
59029 TCGAACCGGT
1 TCAAACCGGT
*
59039 TGAAACCGG-
1 TCAAACCGGT
59048 TCAAACCGG-
1 TCAAACCGGT
59057 TCAAA-CGGT
1 TCAAACCGGT
* *
59066 TGAAAACCTGT
1 T-CAAACCGGT
59077 T-AAACCGGT
1 TCAAACCGGT
59086 T
1 T
59087 TCCAGCAGCC
Statistics
Matches: 76, Mismatches: 15, Indels: 11
0.75 0.15 0.11
Matches are distributed among these distances:
8 3 0.04
9 36 0.47
10 33 0.43
11 4 0.05
ACGTcount: A:0.28, C:0.26, G:0.25, T:0.20
Consensus pattern (10 bp):
TCAAACCGGT
Done.