Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000225.1 Hibiscus syriacus cultivar Beakdansim tig00000395_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: 64154
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:4961 original size:12 final size:12
Alignment explanation
Indices: 4906--5006 Score: 52
Period size: 12 Copynumber: 8.2 Consensus size: 12
4896 ACAATATATG
4906 TGATATAT-ATA
1 TGATATATGATA
4917 T-ATATAT-ATA
1 TGATATATGATA
*
4927 T-ATATTGTGATA
1 TGATA-TATGATA
4939 TGAATTATATGATA
1 TG-A-TATATGATA
*
4953 TGATATATGTGTA
1 TGATATATG-ATA
*
4966 TGTTA-ATGATTA
1 TGATATATGA-TA
4978 TTG-TATATGTTATA
1 -TGATATATG--ATA
*
4992 AGATATATGATA
1 TGATATATGATA
5004 TGA
1 TGA
5007 ACATAATAGA
Statistics
Matches: 71, Mismatches: 7, Indels: 23
0.70 0.07 0.23
Matches are distributed among these distances:
10 13 0.18
11 3 0.04
12 22 0.31
13 13 0.18
14 17 0.24
15 3 0.04
ACGTcount: A:0.39, C:0.00, G:0.15, T:0.47
Consensus pattern (12 bp):
TGATATATGATA
Found at i:4974 original size:19 final size:20
Alignment explanation
Indices: 4950--5005 Score: 64
Period size: 19 Copynumber: 2.9 Consensus size: 20
4940 GAATTATATG
*
4950 ATATGATATATGTGTATGTT
1 ATATGATATATGTATATGTT
4970 A-ATGAT-TATTGTATATGTT
1 ATATGATATA-TGTATATGTT
*
4989 ATAAGATATATG-ATATG
1 ATATGATATATGTATATG
5006 AACATAATAG
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
18 2 0.06
19 20 0.65
20 7 0.23
21 2 0.06
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (20 bp):
ATATGATATATGTATATGTT
Found at i:7777 original size:17 final size:18
Alignment explanation
Indices: 7755--7798 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
7745 AAAGAAGAAA
**
7755 CATCGATG-TAATTAGTG
1 CATCGATGATAAGGAGTG
7772 CATCGATGCATAAGGAGTG
1 CATCGATG-ATAAGGAGTG
7791 CATCGATG
1 CATCGATG
7799 CACCCCCTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 8 0.35
19 15 0.65
ACGTcount: A:0.30, C:0.16, G:0.27, T:0.27
Consensus pattern (18 bp):
CATCGATGATAAGGAGTG
Found at i:7889 original size:20 final size:22
Alignment explanation
Indices: 7844--7901 Score: 75
Period size: 20 Copynumber: 2.6 Consensus size: 22
7834 GCATGGGTAG
7844 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TGTT-AAGAA
7868 TGCATCGATGCACTG-T-AGAA
1 TGCATCGATGCACTGTTAAGAA
*
7888 TGTATCGATGCACT
1 TGCATCGATGCACT
7902 TCAAGGGGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 17 0.52
22 1 0.03
23 2 0.06
24 13 0.39
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (22 bp):
TGCATCGATGCACTGTTAAGAA
Found at i:8880 original size:32 final size:34
Alignment explanation
Indices: 8805--8885 Score: 82
Period size: 32 Copynumber: 2.5 Consensus size: 34
8795 ATATGTGATA
* *
8805 TATATATATAT-ATATATGTTTTGTGATATGAAT
1 TATATGTATATGATATATGTTGTGTGATATGAAT
*
8838 TATATG-ATATGATATATG-TGTGTGTTAATG-AT
1 TATATGTATATGATATATGTTGTGTGAT-ATGAAT
*
8870 TAT-TGTATATGTTATA
1 TATATGTATATGATATA
8886 AGATATATGA
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
31 2 0.05
32 24 0.59
33 15 0.37
ACGTcount: A:0.33, C:0.00, G:0.16, T:0.51
Consensus pattern (34 bp):
TATATGTATATGATATATGTTGTGTGATATGAAT
Found at i:16811 original size:23 final size:23
Alignment explanation
Indices: 16775--16824 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
16765 GAAATCGATA
16775 CCCC-TTGAAGGGGAACCGATTC
1 CCCCTTTGAAGGGGAACCGATTC
* *
16797 CCCCTTTGAATGGGAACTGATTC
1 CCCCTTTGAAGGGGAACCGATTC
16820 CCCCT
1 CCCCT
16825 AGGGGAATTG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 4 0.16
23 21 0.84
ACGTcount: A:0.20, C:0.34, G:0.22, T:0.24
Consensus pattern (23 bp):
CCCCTTTGAAGGGGAACCGATTC
Found at i:16836 original size:19 final size:19
Alignment explanation
Indices: 16808--16866 Score: 84
Period size: 19 Copynumber: 3.2 Consensus size: 19
16798 CCCTTTGAAT
* *
16808 GGGAACTGATTCCCCCTAG
1 GGGAATTGATACCCCCTAG
16827 GGGAATTGATACCCCCTAG
1 GGGAATTGATACCCCCTAG
*
16846 GGGAATCGATACCCCCT-G
1 GGGAATTGATACCCCCTAG
16864 GGG
1 GGG
16867 TTCTGGTTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
18 4 0.11
19 33 0.89
ACGTcount: A:0.22, C:0.29, G:0.31, T:0.19
Consensus pattern (19 bp):
GGGAATTGATACCCCCTAG
Found at i:22422 original size:5 final size:5
Alignment explanation
Indices: 22409--22453 Score: 51
Period size: 5 Copynumber: 9.6 Consensus size: 5
22399 GAAAATAAAG
* *
22409 AAATG AAATA AAATA AAATA AAATT AAA-A AAAT- AAAT- AAATA AAA
1 AAATA AAATA AAATA AAATA AAATA AAATA AAATA AAATA AAATA AAA
22454 CAGGACGAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
4 11 0.31
5 24 0.69
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (5 bp):
AAATA
Found at i:22574 original size:26 final size:29
Alignment explanation
Indices: 22535--22593 Score: 79
Period size: 26 Copynumber: 2.1 Consensus size: 29
22525 AACATAAAAC
* *
22535 AAAATAAAACAGT-AATA-AAAA-ATAAA
1 AAAATAAAAAAGTAAATAGAAAAGAGAAA
22561 AAAATAAAAAAGTAAATAGAAAAGAGAAA
1 AAAATAAAAAAGTAAATAGAAAAGAGAAA
22590 AAAA
1 AAAA
22594 ACACATACAG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 12 0.43
27 4 0.14
28 4 0.14
29 8 0.29
ACGTcount: A:0.78, C:0.02, G:0.08, T:0.12
Consensus pattern (29 bp):
AAAATAAAAAAGTAAATAGAAAAGAGAAA
Found at i:22809 original size:2 final size:2
Alignment explanation
Indices: 22802--22851 Score: 59
Period size: 2 Copynumber: 25.5 Consensus size: 2
22792 GAATGAAATA
*
22802 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT GAT AT A- AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT
*
22843 AT AC AT AT A
1 AT AT AT AT A
22852 ATGGAATATA
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
1 2 0.05
2 38 0.90
3 2 0.05
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (2 bp):
AT
Found at i:22864 original size:23 final size:23
Alignment explanation
Indices: 22808--22865 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 23
22798 AATAATATAT
*
22808 ATATATATATATATATATATAATG
1 ATATATA-ATATATACATATAATG
*
22832 ATATAAAATATATACATATAATGG
1 ATATATAATATATACATATAAT-G
22856 A-ATATAATAT
1 ATATATAATAT
22866 TAAATAATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
23 22 0.73
24 8 0.27
ACGTcount: A:0.53, C:0.02, G:0.05, T:0.40
Consensus pattern (23 bp):
ATATATAATATATACATATAATG
Found at i:26129 original size:16 final size:15
Alignment explanation
Indices: 26102--26131 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
26092 AAATGAAAGA
26102 TTTTATTTTTTAGTT
1 TTTTATTTTTTAGTT
26117 TTTTATGTTTTTAGT
1 TTTTAT-TTTTTAGT
26132 AAAACATATG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.13, C:0.00, G:0.10, T:0.77
Consensus pattern (15 bp):
TTTTATTTTTTAGTT
Found at i:26192 original size:21 final size:21
Alignment explanation
Indices: 26168--26207 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
26158 AACTTTTTTC
26168 TTTTT-TTAATTAAAAATAATA
1 TTTTTATT-ATTAAAAATAATA
26189 TTTTTATTATTAAAAATAA
1 TTTTTATTATTAAAAATAA
26208 AAATTAAACG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
TTTTTATTATTAAAAATAATA
Found at i:27239 original size:27 final size:27
Alignment explanation
Indices: 27201--27264 Score: 128
Period size: 27 Copynumber: 2.4 Consensus size: 27
27191 TGACATCAGA
27201 TTCAGTTCGGGTTCAGGTCAAATTAAC
1 TTCAGTTCGGGTTCAGGTCAAATTAAC
27228 TTCAGTTCGGGTTCAGGTCAAATTAAC
1 TTCAGTTCGGGTTCAGGTCAAATTAAC
27255 TTCAGTTCGG
1 TTCAGTTCGG
27265 AATGATGTCA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.34
Consensus pattern (27 bp):
TTCAGTTCGGGTTCAGGTCAAATTAAC
Found at i:27695 original size:260 final size:260
Alignment explanation
Indices: 27228--27699 Score: 739
Period size: 260 Copynumber: 1.8 Consensus size: 260
27218 TCAAATTAAC
* * *
27228 TTCAGTTCGGGTTCAGGTCAAATTAACTTCAGTTCGGAATGATGTCAGTTCATGTCATAACAGTT
1 TTCAATTCGGGTTCAGGTCAAATTAACTTCAGTTCGGAATGATGTCAGTTCATATCAAAACAGTT
* * *
27293 AAGGTCTGAAGTAGCTAAATACCAGGTTAATTCAAGTTTAGATGGACTTCAGTCGGATTTCATTC
66 AAGGTCTGAAGCAGCTAAATACCAGGTTAATTCAAGTTTAGATGGACTTCAATCGAATTTCATTC
* * * * * *
27358 AGATTAGGTTACATTATTGACATACAAAATTCAGGTAAGATCTTACCGGATACGGATTGACTTTA
131 AGATCAGGTCACATCATTGACATACAAAATTCAGGTAAGATCTTACAGGATACAGATTGACTTCA
27423 GGTTGCGTCATTTTGGGTTCAAGTCAAATCAATTCGGGTCATTTTCAGGTTGATTTGACATCAGA
196 GGTTGCGTCATTTTGGGTTCAAGTCAAATCAATTCGGGTCATTTTCAGGTTGATTTGACATCAGA
* * *
27488 TTCAATTCGGGTTTAGGTCAAGTTAACTTCAGTTCGG-ATCGATTTCAGTTCATATCAAAACAGT
1 TTCAATTCGGGTTCAGGTCAAATTAACTTCAGTTCGGAAT-GATGTCAGTTCATATCAAAACAGT
* * *
27552 TAAGGTGTGAAGCAGCTAAATACCAGGTTAATTCAAGTTTAGATGGACTTCAATTGAATTTCGTT
65 TAAGGTCTGAAGCAGCTAAATACCAGGTTAATTCAAGTTTAGATGGACTTCAATCGAATTTCATT
**
27617 CAGATCAGGTCACATCATTGACATACAAAATTCAGGTCGGATCTTACAGGATACAGATTGACTTC
130 CAGATCAGGTCACATCATTGACATACAAAATTCAGGTAAGATCTTACAGGATACAGATTGACTTC
*
27682 AGGTTGTGTCATTTTGGG
195 AGGTTGCGTCATTTTGGG
27700 GTTAATTATT
Statistics
Matches: 190, Mismatches: 21, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
259 2 0.01
260 188 0.99
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.34
Consensus pattern (260 bp):
TTCAATTCGGGTTCAGGTCAAATTAACTTCAGTTCGGAATGATGTCAGTTCATATCAAAACAGTT
AAGGTCTGAAGCAGCTAAATACCAGGTTAATTCAAGTTTAGATGGACTTCAATCGAATTTCATTC
AGATCAGGTCACATCATTGACATACAAAATTCAGGTAAGATCTTACAGGATACAGATTGACTTCA
GGTTGCGTCATTTTGGGTTCAAGTCAAATCAATTCGGGTCATTTTCAGGTTGATTTGACATCAGA
Found at i:27925 original size:24 final size:24
Alignment explanation
Indices: 27898--27944 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
27888 ACAGATCAAA
*
27898 TTGAAA-TAATTATAAAATATGAAG
1 TTGAAATTAA-TATAAAAAATGAAG
27922 TTGAAATTAATATAAAAAATGAA
1 TTGAAATTAATATAAAAAATGAA
27945 CTAGATTGCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 18 0.86
25 3 0.14
ACGTcount: A:0.57, C:0.00, G:0.11, T:0.32
Consensus pattern (24 bp):
TTGAAATTAATATAAAAAATGAAG
Found at i:28326 original size:16 final size:13
Alignment explanation
Indices: 28305--28343 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 13
28295 ATGCATACTC
28305 TATAAGTATATACTTA
1 TATAAGTATATA---A
28321 TATAAGTATATAA
1 TATAAGTATATAA
28334 TATAAGTATA
1 TATAAGTATA
28344 CATTATACTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 11 0.48
16 12 0.52
ACGTcount: A:0.49, C:0.03, G:0.08, T:0.41
Consensus pattern (13 bp):
TATAAGTATATAA
Found at i:28350 original size:13 final size:12
Alignment explanation
Indices: 28320--28478 Score: 62
Period size: 13 Copynumber: 14.2 Consensus size: 12
28310 GTATATACTT
*
28320 ATATAAGTATATA
1 ATATAAGTATA-C
28333 ATATAAGTATAC
1 ATATAAGTATAC
**
28345 ATTATACTTATA-
1 A-TATAAGTATAC
28357 ATAT-A--ATAC
1 ATATAAGTATAC
28366 ATATAAGTATAC
1 ATATAAGTATAC
***
28378 ATTATTCTTATA-
1 A-TATAAGTATAC
28390 ATAT-A--ATAC
1 ATATAAGTATAC
28399 ATATAAGTATAC
1 ATATAAGTATAC
**
28411 ATTATACTTATA-
1 A-TATAAGTATAC
28423 ATAT-A--ATAC
1 ATATAAGTATAC
28432 ATATAAGTATAC
1 ATATAAGTATAC
***
28444 ATTATTCTTATA-
1 A-TATAAGTATAC
28456 ATAT-A--ATAC
1 ATATAAGTATAC
28465 ATATAAGTATAC
1 ATATAAGTATAC
28477 AT
1 AT
28479 TATACTTATA
Statistics
Matches: 111, Mismatches: 15, Indels: 41
0.66 0.09 0.25
Matches are distributed among these distances:
8 12 0.11
9 16 0.14
10 4 0.04
11 12 0.11
12 26 0.23
13 41 0.37
ACGTcount: A:0.48, C:0.08, G:0.04, T:0.40
Consensus pattern (12 bp):
ATATAAGTATAC
Found at i:28355 original size:6 final size:7
Alignment explanation
Indices: 28340--28488 Score: 53
Period size: 6 Copynumber: 22.6 Consensus size: 7
28330 ATAATATAAG
28340 TATACAT
1 TATACAT
28347 TATAC-T
1 TATACAT
28353 TATA-AT
1 TATACAT
28359 ATAATACA-
1 -T-ATACAT
*
28367 TATA-AG
1 TATACAT
28373 TATACAT
1 TATACAT
*
28380 TATTC-T
1 TATACAT
28386 TATA-AT
1 TATACAT
28392 ATAATACA-
1 -T-ATACAT
*
28400 TATA-AG
1 TATACAT
28406 TATACAT
1 TATACAT
28413 TATAC-T
1 TATACAT
28419 TATA-AT
1 TATACAT
28425 ATAATACA-
1 -T-ATACAT
*
28433 TATA-AG
1 TATACAT
28439 TATACAT
1 TATACAT
*
28446 TATTC-T
1 TATACAT
28452 TATA-AT
1 TATACAT
28458 ATAATACA-
1 -T-ATACAT
*
28466 TATA-AG
1 TATACAT
28472 TATACAT
1 TATACAT
28479 TATAC-T
1 TATACAT
28485 TATA
1 TATA
28489 AAATGTACTT
Statistics
Matches: 110, Mismatches: 8, Indels: 49
0.66 0.05 0.29
Matches are distributed among these distances:
5 4 0.04
6 55 0.50
7 35 0.32
8 12 0.11
9 4 0.04
ACGTcount: A:0.46, C:0.09, G:0.03, T:0.42
Consensus pattern (7 bp):
TATACAT
Found at i:28367 original size:21 final size:22
Alignment explanation
Indices: 28341--28488 Score: 73
Period size: 21 Copynumber: 6.7 Consensus size: 22
28331 TAATATAAGT
*
28341 ATACATTATACTTATA-ATATA
1 ATACATTATAATTATACATATA
*
28362 ATACA-TATAAGTATACAT-T-
1 ATACATTATAATTATACATATA
*
28381 ATTC-TTATAATATAATACATATAA
1 ATACATTATAAT-T-ATACATAT-A
*
28405 GTATACATTATACTTATA-ATATA
1 --ATACATTATAATTATACATATA
*
28428 ATACA-TATAAGTATACAT-T-
1 ATACATTATAATTATACATATA
*
28447 ATTC-TTATAATATAATACATATAA
1 ATACATTATAAT-T-ATACATAT-A
*
28471 GTATACATTATACTTATA
1 --ATACATTATAATTATA
28489 AAATGTACTT
Statistics
Matches: 95, Mismatches: 12, Indels: 36
0.66 0.08 0.25
Matches are distributed among these distances:
19 16 0.17
20 20 0.21
21 26 0.27
22 2 0.02
23 1 0.01
24 4 0.04
25 6 0.06
26 8 0.08
27 12 0.13
ACGTcount: A:0.47, C:0.09, G:0.03, T:0.41
Consensus pattern (22 bp):
ATACATTATAATTATACATATA
Found at i:28375 original size:33 final size:33
Alignment explanation
Indices: 28321--28489 Score: 297
Period size: 33 Copynumber: 5.2 Consensus size: 33
28311 TATATACTTA
28321 TATAAGTAT-ATA-ATATAAGTATACATTATACT
1 TATAA-TATAATACATATAAGTATACATTATACT
*
28353 TATAATATAATACATATAAGTATACATTATTCT
1 TATAATATAATACATATAAGTATACATTATACT
28386 TATAATATAATACATATAAGTATACATTATACT
1 TATAATATAATACATATAAGTATACATTATACT
*
28419 TATAATATAATACATATAAGTATACATTATTCT
1 TATAATATAATACATATAAGTATACATTATACT
28452 TATAATATAATACATATAAGTATACATTATACT
1 TATAATATAATACATATAAGTATACATTATACT
28485 TATAA
1 TATAA
28490 AATGTACTTT
Statistics
Matches: 131, Mismatches: 4, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
31 3 0.02
32 8 0.06
33 120 0.92
ACGTcount: A:0.47, C:0.08, G:0.04, T:0.41
Consensus pattern (33 bp):
TATAATATAATACATATAAGTATACATTATACT
Found at i:29020 original size:30 final size:30
Alignment explanation
Indices: 28984--29049 Score: 105
Period size: 30 Copynumber: 2.2 Consensus size: 30
28974 TATTAAATTG
*
28984 TCATTTGCCGCTCAATCCTCCCTCTTTTTC
1 TCATTTGCCGCCCAATCCTCCCTCTTTTTC
* *
29014 TCATTTGCCGCCCAATTCTCTCTCTTTTTC
1 TCATTTGCCGCCCAATCCTCCCTCTTTTTC
29044 TCATTT
1 TCATTT
29050 CCATTGTGCG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.11, C:0.36, G:0.06, T:0.47
Consensus pattern (30 bp):
TCATTTGCCGCCCAATCCTCCCTCTTTTTC
Found at i:29226 original size:20 final size:20
Alignment explanation
Indices: 29203--29254 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
29193 AACGCGATCC
29203 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
29223 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
29243 CCAAAATCGCAA
1 CCAGAATCGCAA
29255 CGCGATTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:29404 original size:20 final size:20
Alignment explanation
Indices: 29310--29658 Score: 418
Period size: 20 Copynumber: 17.4 Consensus size: 20
29300 GATTTTCCAT
* ** *
29310 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
29330 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
29350 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
29370 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
29390 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
29410 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
29430 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
29450 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
29470 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
29490 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
29510 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
29530 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
29550 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
29570 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
29590 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
29610 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
29630 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
29650 AATCACAAC
1 AATCGCAAC
29659 ACTGAAATTT
Statistics
Matches: 285, Mismatches: 36, Indels: 16
0.85 0.11 0.05
Matches are distributed among these distances:
19 3 0.01
20 279 0.98
21 3 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:30380 original size:24 final size:24
Alignment explanation
Indices: 30341--30387 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
30331 AAATTTGGTC
30341 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
30365 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
30388 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:30579 original size:12 final size:12
Alignment explanation
Indices: 30562--30586 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
30552 ATATAATCCT
30562 GAAGAAGAAAAA
1 GAAGAAGAAAAA
30574 GAAGAAGAAAAA
1 GAAGAAGAAAAA
30586 G
1 G
30587 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:32163 original size:14 final size:14
Alignment explanation
Indices: 32144--32233 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
32134 TTGAAATGAA
32144 AATCGCAACGAGAG
1 AATCGCAACGAGAG
32158 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
32175 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
32191 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
32210 AATCGCAACGAGAG
1 AATCGCAACGAGAG
32224 AATCGCAACG
1 AATCGCAACG
32234 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:32181 original size:33 final size:33
Alignment explanation
Indices: 32136--32250 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
32126 TCTTTTGGTT
32136 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
32169 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
32202 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
32235 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
32251 TGCGATTTTG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:32182 original size:19 final size:18
Alignment explanation
Indices: 32143--32255 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
32133 GTTGAAATGA
32143 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
32158 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
32175 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
32191 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
32208 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
32224 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
32241 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
32256 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
14 24 0.30
16 15 0.19
17 12 0.15
19 28 0.35
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:32451 original size:33 final size:33
Alignment explanation
Indices: 32409--32479 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
32399 AATACTAACT
*
32409 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
32442 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
32475 TGAAA
1 TGAAA
32480 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:32886 original size:20 final size:20
Alignment explanation
Indices: 32861--33054 Score: 212
Period size: 20 Copynumber: 9.6 Consensus size: 20
32851 CTTTAAATAT
32861 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
32881 CGCGTTGCGATTTTTATGTATTA
1 CGCGTTGCGA--TTTACGGA-TA
*
32904 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
32923 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
32943 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
32963 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
32983 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
33003 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
33023 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
33043 CGCGTTGCGATT
1 CGCGTTGCGATT
33055 ATGGAAAATC
Statistics
Matches: 146, Mismatches: 22, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
19 2 0.01
20 127 0.87
21 1 0.01
22 14 0.10
23 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:33049 original size:60 final size:60
Alignment explanation
Indices: 32861--33054 Score: 244
Period size: 60 Copynumber: 3.2 Consensus size: 60
32851 CTTTAAATAT
**
32861 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA--TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
32923 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
32983 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
33043 CGCGTTGCGATT
1 CGCGTTGCGATT
33055 ATGGAAAATC
Statistics
Matches: 111, Mismatches: 21, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
60 83 0.75
62 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:33135 original size:20 final size:20
Alignment explanation
Indices: 33110--33161 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
33100 AAGAATCGCG
*
33110 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
33130 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
33150 TTGCGATTCTGG
1 TTGCGATTCTGG
33162 GGATCGCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:33422 original size:18 final size:18
Alignment explanation
Indices: 33376--33423 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
33366 TAGATAGATC
33376 ATTTAATAA-AATTAATTT
1 ATTT-ATAATAATTAATTT
* *
33394 ATTTGTTATAATTAATTT
1 ATTTATAATAATTAATTT
*
33412 TTTTATAATAAT
1 ATTTATAATAAT
33424 CATAATTAGT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
17 2 0.08
18 22 0.92
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (18 bp):
ATTTATAATAATTAATTT
Found at i:40300 original size:121 final size:121
Alignment explanation
Indices: 40081--40322 Score: 394
Period size: 121 Copynumber: 2.0 Consensus size: 121
40071 ATAAGCTTAC
* * * * * *
40081 CCTCGAATAAATTTTACGTTGAGTCCTTTAAATTTCTTTGAATATTTGTGAAACCGAAACTTAAA
1 CCTCAAATAAATTATACGTCGAATCATTTAAATTTCTTTAAATATTTGTGAAACCGAAACTTAAA
* * *
40146 TTATGTACACTCTAAGTGCTAACTATCCATTTATATCATTCATCTTTAAATACAAA
66 CTATGCACACTCTAAGTGCTAACTATCAATTTATATCATTCATCTTTAAATACAAA
*
40202 CCTCAAATAAATTATACGTCGAATCATTTAAATTTCTTTAAATATTTGTGAAACCGAATCTTAAA
1 CCTCAAATAAATTATACGTCGAATCATTTAAATTTCTTTAAATATTTGTGAAACCGAAACTTAAA
40267 CTATGCACACTCTAAGTGCTAACTATCAATTTATATCATTCATCTTTAAATACAAA
66 CTATGCACACTCTAAGTGCTAACTATCAATTTATATCATTCATCTTTAAATACAAA
40323 ACTTGAAAAT
Statistics
Matches: 111, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
121 111 1.00
ACGTcount: A:0.37, C:0.18, G:0.08, T:0.38
Consensus pattern (121 bp):
CCTCAAATAAATTATACGTCGAATCATTTAAATTTCTTTAAATATTTGTGAAACCGAAACTTAAA
CTATGCACACTCTAAGTGCTAACTATCAATTTATATCATTCATCTTTAAATACAAA
Found at i:42210 original size:2 final size:2
Alignment explanation
Indices: 42203--42227 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
42193 TATTTTAATA
42203 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 A
42228 CACACACACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:47013 original size:26 final size:24
Alignment explanation
Indices: 46984--47031 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 24
46974 ATTATTATCA
46984 CAAGATTCGAAGGCCCAATTACAAAG
1 CAAGA-TC-AAGGCCCAATTACAAAG
* *
47010 CAAGATCCAGGCCCGATTACAA
1 CAAGATCAAGGCCCAATTACAA
47032 CAACCAGAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 13 0.65
25 2 0.10
26 5 0.25
ACGTcount: A:0.40, C:0.27, G:0.19, T:0.15
Consensus pattern (24 bp):
CAAGATCAAGGCCCAATTACAAAG
Found at i:61099 original size:12 final size:13
Alignment explanation
Indices: 61084--61117 Score: 61
Period size: 12 Copynumber: 2.7 Consensus size: 13
61074 AAAACCCACT
61084 AAAAATGAATG-A
1 AAAAATGAATGAA
61096 AAAAATGAATGAA
1 AAAAATGAATGAA
61109 AAAAATGAA
1 AAAAATGAA
61118 GTTGTGAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 11 0.52
13 10 0.48
ACGTcount: A:0.71, C:0.00, G:0.15, T:0.15
Consensus pattern (13 bp):
AAAAATGAATGAA
Done.