Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002184.1 Hibiscus syriacus cultivar Beakdansim tig00004451_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: 68559
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Found at i:3014 original size:47 final size:47
Alignment explanation
Indices: 2958--3207 Score: 227
Period size: 47 Copynumber: 5.2 Consensus size: 47
2948 TCATGTCGAT
* * *
2958 AATGCACCGTTCTATCTAACTTGTATTAGAGACACCTTTTTGCCAAA
1 AATGCACCGTTCTATCTAACTTGCATTAGTGACACCTTTCTGCCAAA
* * * *
3005 AATGCACCGTTAGGC-ATTTACCTTGAATTAGTGACACCTTTCTGCCAAG
1 AATGCACCGTT---CTATCTAACTTGCATTAGTGACACCTTTCTGCCAAA
* * * * *
3054 AATGCATCATT-TCATCTAACTTGCATTAGTGGCACATTTCTGCAAAA
1 AATGCACCGTTCT-ATCTAACTTGCATTAGTGACACCTTTCTGCCAAA
* * * * *
3101 AATGCACCGTTAGGTATTTAACTTGCATTAGTGGCACCTTTCTACCAAG
1 AATGCACCGTT--CTATCTAACTTGCATTAGTGACACCTTTCTGCCAAA
* * * *
3150 AATGCATCATTTTCATCTAACTT-CATTAGTGACACCTTTATGCCAAA
1 AATGCACCGTTCT-ATCTAACTTGCATTAGTGACACCTTTCTGCCAAA
3197 AATGCACCGTT
1 AATGCACCGTT
3208 AGGTATTTAA
Statistics
Matches: 162, Mismatches: 32, Indels: 18
0.76 0.15 0.08
Matches are distributed among these distances:
47 77 0.48
48 8 0.05
49 75 0.46
50 2 0.01
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.33
Consensus pattern (47 bp):
AATGCACCGTTCTATCTAACTTGCATTAGTGACACCTTTCTGCCAAA
Found at i:3042 original size:49 final size:49
Alignment explanation
Indices: 2974--3217 Score: 244
Period size: 49 Copynumber: 5.1 Consensus size: 49
2964 CCGTTCTATC
* * *
2974 TAACTTGTATTAGAGACACCTTTTTGCCAAAAATGCACCGTTAGGCATT
1 TAACTTGCATTAGTGACACCTTTCTGCCAAAAATGCACCGTTAGGCATT
* * * * * * *
3023 TACCTTGAATTAGTGACACCTTTCTGCCAAGAATGCATCATT--TCATC
1 TAACTTGCATTAGTGACACCTTTCTGCCAAAAATGCACCGTTAGGCATT
* * * *
3070 TAACTTGCATTAGTGGCACATTTCTGCAAAAAATGCACCGTTAGGTATT
1 TAACTTGCATTAGTGACACCTTTCTGCCAAAAATGCACCGTTAGGCATT
* * * * * ** *
3119 TAACTTGCATTAGTGGCACCTTTCTACCAAGAATGCATCATT-TTCATC
1 TAACTTGCATTAGTGACACCTTTCTGCCAAAAATGCACCGTTAGGCATT
* *
3167 TAACTT-CATTAGTGACACCTTTATGCCAAAAATGCACCGTTAGGTATT
1 TAACTTGCATTAGTGACACCTTTCTGCCAAAAATGCACCGTTAGGCATT
3215 TAA
1 TAA
3218 AAGAGGTTGC
Statistics
Matches: 152, Mismatches: 40, Indels: 7
0.76 0.20 0.04
Matches are distributed among these distances:
47 66 0.43
48 13 0.09
49 73 0.48
ACGTcount: A:0.30, C:0.22, G:0.15, T:0.34
Consensus pattern (49 bp):
TAACTTGCATTAGTGACACCTTTCTGCCAAAAATGCACCGTTAGGCATT
Found at i:3131 original size:96 final size:97
Alignment explanation
Indices: 2971--3217 Score: 372
Period size: 96 Copynumber: 2.6 Consensus size: 97
2961 GCACCGTTCT
* * * * *
2971 ATCTAACTTGTATTAGAGACACCTTTTTGCCAAAAATGCACCGTTAGGCATTTACCTTGAATTAG
1 ATCTAACTTGCATTAGTGACACCTTTATGCCAAAAATGCACCGTTAGGTATTTAACTTGAATTAG
*
3036 TGACACCTTTCTGCCAAGAATGCATCA-TTTC
66 TGACACCTTTCTACCAAGAATGCATCATTTTC
* * * * *
3067 ATCTAACTTGCATTAGTGGCACATTTCTGCAAAAAATGCACCGTTAGGTATTTAACTTGCATTAG
1 ATCTAACTTGCATTAGTGACACCTTTATGCCAAAAATGCACCGTTAGGTATTTAACTTGAATTAG
*
3132 TGGCACCTTTCTACCAAGAATGCATCATTTTC
66 TGACACCTTTCTACCAAGAATGCATCATTTTC
3164 ATCTAACTT-CATTAGTGACACCTTTATGCCAAAAATGCACCGTTAGGTATTTAA
1 ATCTAACTTGCATTAGTGACACCTTTATGCCAAAAATGCACCGTTAGGTATTTAA
3218 AAGAGGTTGC
Statistics
Matches: 135, Mismatches: 15, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
96 122 0.90
97 13 0.10
ACGTcount: A:0.30, C:0.22, G:0.15, T:0.34
Consensus pattern (97 bp):
ATCTAACTTGCATTAGTGACACCTTTATGCCAAAAATGCACCGTTAGGTATTTAACTTGAATTAG
TGACACCTTTCTACCAAGAATGCATCATTTTC
Found at i:3350 original size:54 final size:54
Alignment explanation
Indices: 3222--3512 Score: 431
Period size: 54 Copynumber: 5.4 Consensus size: 54
3212 ATTTAAAAGA
* * * **
3222 GGTTGCACACTTAGTGCCTATACAGTTGTTCATCAACATATGATG-ATTTTGTG
1 GGTTGCACACATAGTGCCTATACGGTCGTTCATCAACATATGATGAATTCCGTG
* * *
3275 AGTTGCACACATAGTGCCTATACGATCGTTCATCAACATATGATGAATTTCGTG
1 GGTTGCACACATAGTGCCTATACGGTCGTTCATCAACATATGATGAATTCCGTG
* *
3329 GGTTGCACAAATAGTGCCTATACGGTCGTTCATCAACATATGGTGAATTCCGTG
1 GGTTGCACACATAGTGCCTATACGGTCGTTCATCAACATATGATGAATTCCGTG
* *
3383 GGTTGCACACATAGTGCCTATACGGTCATTCATCAACATATGATGAATTCCGTC
1 GGTTGCACACATAGTGCCTATACGGTCGTTCATCAACATATGATGAATTCCGTG
* * *
3437 GGTTGCACATATAGTGCCTACACGGTCGTTCATCAACATATGATGAATTCCATG
1 GGTTGCACACATAGTGCCTATACGGTCGTTCATCAACATATGATGAATTCCGTG
*
3491 GGTTGTACACATAGTGCCTATA
1 GGTTGCACACATAGTGCCTATA
3513 GTACATTTAA
Statistics
Matches: 214, Mismatches: 23, Indels: 1
0.90 0.10 0.00
Matches are distributed among these distances:
53 40 0.19
54 174 0.81
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.32
Consensus pattern (54 bp):
GGTTGCACACATAGTGCCTATACGGTCGTTCATCAACATATGATGAATTCCGTG
Found at i:9290 original size:21 final size:20
Alignment explanation
Indices: 9266--9305 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
9256 TGCTTTATGT
*
9266 TGAAATTGAATGTTGGAATGA
1 TGAAATTG-ATGTTAGAATGA
*
9287 TGAATTTGATGTTAGAATG
1 TGAAATTGATGTTAGAATG
9306 TTGACTTAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.35, C:0.00, G:0.28, T:0.38
Consensus pattern (20 bp):
TGAAATTGATGTTAGAATGA
Found at i:10014 original size:14 final size:14
Alignment explanation
Indices: 9976--10016 Score: 73
Period size: 14 Copynumber: 2.9 Consensus size: 14
9966 AAATATTGAT
*
9976 TTAATTTTGGACTG
1 TTAATTTTGGGCTG
9990 TTAATTTTGGGCTG
1 TTAATTTTGGGCTG
10004 TTAATTTTGGGCT
1 TTAATTTTGGGCT
10017 AGTTTGTAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.17, C:0.07, G:0.24, T:0.51
Consensus pattern (14 bp):
TTAATTTTGGGCTG
Found at i:11015 original size:17 final size:17
Alignment explanation
Indices: 10993--11027 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
10983 AATATAATAT
*
10993 AATAAATGAAATAGTAC
1 AATAAAAGAAATAGTAC
*
11010 AATAAAAGATATAGTAC
1 AATAAAAGAAATAGTAC
11027 A
1 A
11028 TCACAAAAAA
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:0.60, C:0.06, G:0.11, T:0.23
Consensus pattern (17 bp):
AATAAAAGAAATAGTAC
Found at i:13508 original size:14 final size:15
Alignment explanation
Indices: 13480--13516 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
13470 ACACTAACAT
13480 AATATAATTCCATAA
1 AATATAATTCCATAA
*
13495 AATA-AATTCTATAA
1 AATATAATTCCATAA
13509 AATATAAT
1 AATATAAT
13517 CGATGCTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 13 0.65
15 7 0.35
ACGTcount: A:0.57, C:0.08, G:0.00, T:0.35
Consensus pattern (15 bp):
AATATAATTCCATAA
Found at i:15294 original size:29 final size:30
Alignment explanation
Indices: 15252--15321 Score: 72
Period size: 30 Copynumber: 2.4 Consensus size: 30
15242 CAAAATATTT
* *
15252 AACTTTTAAAAA-TTATATTTTGGTCC-CTA
1 AACTTTTAAAAATTTATACTTTAG-CCACTA
**
15281 AACTTTTTCAAATTTATACTTTAGCCACTA
1 AACTTTTAAAAATTTATACTTTAGCCACTA
*
15311 AACTTTCAAAA
1 AACTTTTAAAA
15322 CTTACATTTT
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
29 12 0.38
30 20 0.62
ACGTcount: A:0.37, C:0.17, G:0.04, T:0.41
Consensus pattern (30 bp):
AACTTTTAAAAATTTATACTTTAGCCACTA
Found at i:19445 original size:119 final size:119
Alignment explanation
Indices: 19305--19542 Score: 467
Period size: 119 Copynumber: 2.0 Consensus size: 119
19295 TTGTAAAATT
*
19305 CCAATTCGATCGGAATTACCGATTCCGTATCGGACTTTAACCTTTTCTAATTTTTCTTTACTAAA
1 CCAATTCGATCGGAATTACCGATTCCGTATCGGACTTTAACCCTTTCTAATTTTTCTTTACTAAA
19370 ATTCAAATTCCAAAAATATGATTTCCATAAAACTCCACTCACAAGAGTAAACCA
66 ATTCAAATTCCAAAAATATGATTTCCATAAAACTCCACTCACAAGAGTAAACCA
19424 CCAATTCGATCGGAATTACCGATTCCGTATCGGACTTTAACCCTTTCTAATTTTTCTTTACTAAA
1 CCAATTCGATCGGAATTACCGATTCCGTATCGGACTTTAACCCTTTCTAATTTTTCTTTACTAAA
19489 ATTCAAATTCCAAAAATATGATTTCCATAAAACTCCACTCACAAGAGTAAACCA
66 ATTCAAATTCCAAAAATATGATTTCCATAAAACTCCACTCACAAGAGTAAACCA
19543 TCTATTTATT
Statistics
Matches: 118, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
119 118 1.00
ACGTcount: A:0.35, C:0.24, G:0.08, T:0.32
Consensus pattern (119 bp):
CCAATTCGATCGGAATTACCGATTCCGTATCGGACTTTAACCCTTTCTAATTTTTCTTTACTAAA
ATTCAAATTCCAAAAATATGATTTCCATAAAACTCCACTCACAAGAGTAAACCA
Found at i:25103 original size:28 final size:28
Alignment explanation
Indices: 25069--25131 Score: 117
Period size: 28 Copynumber: 2.2 Consensus size: 28
25059 TCATCTCATG
25069 AGTGATAAGGAAGCCAATAAGTTCATCA
1 AGTGATAAGGAAGCCAATAAGTTCATCA
*
25097 AGTGATAAGGGAGCCAATAAGTTCATCA
1 AGTGATAAGGAAGCCAATAAGTTCATCA
25125 AGTGATA
1 AGTGATA
25132 GAGTTTTTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.41, C:0.13, G:0.24, T:0.22
Consensus pattern (28 bp):
AGTGATAAGGAAGCCAATAAGTTCATCA
Found at i:27708 original size:17 final size:17
Alignment explanation
Indices: 27686--27722 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
27676 AACCAAACCA
27686 ACCCGACCCGACCGTTG
1 ACCCGACCCGACCGTTG
27703 ACCCGACCCGACCGTTG
1 ACCCGACCCGACCGTTG
27720 ACC
1 ACC
27723 GTTGACCGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.19, C:0.49, G:0.22, T:0.11
Consensus pattern (17 bp):
ACCCGACCCGACCGTTG
Found at i:27792 original size:29 final size:29
Alignment explanation
Indices: 27730--27824 Score: 93
Period size: 29 Copynumber: 3.3 Consensus size: 29
27720 ACCGTTGACC
* ** *
27730 GGTGATATTCTGGGAATTAATTCAATTTT
1 GGTGCTATTCTGGGAATTAATTCAAAATG
*
27759 AGTGCTATTCTGGGAATTAATTCAAAATG
1 GGTGCTATTCTGGGAATTAATTCAAAATG
* * * * *
27788 GGTGCTATTTTGGTAATT-TTTTAAAAAG
1 GGTGCTATTCTGGGAATTAATTCAAAATG
27816 GGTGCTATT
1 GGTGCTATT
27825 TATGTAAAAT
Statistics
Matches: 55, Mismatches: 11, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
28 16 0.29
29 39 0.71
ACGTcount: A:0.28, C:0.07, G:0.22, T:0.42
Consensus pattern (29 bp):
GGTGCTATTCTGGGAATTAATTCAAAATG
Found at i:29268 original size:17 final size:18
Alignment explanation
Indices: 29246--29280 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
29236 CTGTATTATT
29246 AATATTT-TGTTCTATAC
1 AATATTTATGTTCTATAC
29263 AATATTTAATGTTCTATA
1 AATATTT-ATGTTCTATA
29281 AGTTATATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
19 9 0.56
ACGTcount: A:0.34, C:0.09, G:0.06, T:0.51
Consensus pattern (18 bp):
AATATTTATGTTCTATAC
Found at i:35040 original size:22 final size:22
Alignment explanation
Indices: 35015--35059 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
35005 CTGAACCGGT
35015 CCGACCCGACCCGACCGTTGAC
1 CCGACCCGACCCGACCGTTGAC
*
35037 CCGACCCGACCCGATCGTTGAC
1 CCGACCCGACCCGACCGTTGAC
35059 C
1 C
35060 GTTAACCGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.18, C:0.49, G:0.22, T:0.11
Consensus pattern (22 bp):
CCGACCCGACCCGACCGTTGAC
Found at i:36115 original size:117 final size:117
Alignment explanation
Indices: 35905--36191 Score: 425
Period size: 117 Copynumber: 2.5 Consensus size: 117
35895 GTATTTCAGG
* * * *
35905 CTCCTTTGCTGTGTGCTCAGGGTAAGTCCTTACTGGTATACAGGTGGGTGTATGGTTCTGGGGAA
1 CTCCTTTGCTGTGTGCTTAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATGGTTCTGAGGAA
* * *
35970 CCTACACATTGTAGTGAGTGGAGTGACTGGATGGGGAAGTTATTACTGCAGA
66 CCTACACATTGTAGTGAGTGAAGCGACTGGATGGAGAAGTTATTACTGCAGA
* *
36022 CTCCTTTGCTGTGTGCTTAGGGTAAGTCTTTACTGGTGTGCAAGTGGGTGTATGGTTCTGAGGAA
1 CTCCTTTGCTGTGTGCTTAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATGGTTCTGAGGAA
* *
36087 CCTACACATTGTAGTGA-TGAAAGCGACTGGATGGAGACGTTATTACTGCAGG
66 CCTACACATTGTAGTGAGTG-AAGCGACTGGATGGAGAAGTTATTACTGCAGA
**
36139 CTCCTCAGCT-TCGTGCTTAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTAT
1 CTCCTTTGCTGT-GTGCTTAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTAT
36192 TTTTCGAGAA
Statistics
Matches: 153, Mismatches: 15, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
116 3 0.02
117 150 0.98
ACGTcount: A:0.20, C:0.16, G:0.32, T:0.32
Consensus pattern (117 bp):
CTCCTTTGCTGTGTGCTTAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATGGTTCTGAGGAA
CCTACACATTGTAGTGAGTGAAGCGACTGGATGGAGAAGTTATTACTGCAGA
Found at i:37105 original size:20 final size:19
Alignment explanation
Indices: 37080--37134 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 19
37070 ATTGGAATAG
37080 GGGGTTTAGAAACCAAGAAA
1 GGGGTTTAGAAACCAAG-AA
*
37100 GGGGTTTAGAAACCAAGCA
1 GGGGTTTAGAAACCAAGAA
*
37119 GGTGGTTTTGAAACCA
1 GG-GGTTTAGAAACCA
37135 TAAGGAAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 3 0.09
20 29 0.91
ACGTcount: A:0.36, C:0.13, G:0.31, T:0.20
Consensus pattern (19 bp):
GGGGTTTAGAAACCAAGAA
Found at i:39045 original size:24 final size:24
Alignment explanation
Indices: 39032--39125 Score: 136
Period size: 24 Copynumber: 4.0 Consensus size: 24
39022 AAACATAATT
39032 CAGGTCAAGTATCAGATCAGAATC
1 CAGGTCAAGTATCAGATCAGAATC
*
39056 CAGGTCATGTATCAGATCAGAATC
1 CAGGTCAAGTATCAGATCAGAATC
*
39080 CATGTC-AGTATCAGATCAGAATC
1 CAGGTCAAGTATCAGATCAGAATC
* * *
39103 CATGTCAAGTATCATAACAGAAT
1 CAGGTCAAGTATCAGATCAGAAT
39126 TCAAATCAGA
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
23 22 0.34
24 42 0.66
ACGTcount: A:0.37, C:0.20, G:0.18, T:0.24
Consensus pattern (24 bp):
CAGGTCAAGTATCAGATCAGAATC
Found at i:44296 original size:37 final size:36
Alignment explanation
Indices: 44221--44296 Score: 91
Period size: 36 Copynumber: 2.1 Consensus size: 36
44211 TTTTTATATT
*
44221 TTTAATTTTGTAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
* * *
44257 TTTAATTTTTTAAAGAAAA-TATGTAAATATTTTACAA
1 TTTAATTTTGTAAA-AAAATTATATAAATATTAT-CAA
44294 TTT
1 TTT
44297 GTAATATTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
36 25 0.74
37 9 0.26
ACGTcount: A:0.46, C:0.01, G:0.05, T:0.47
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
Found at i:44478 original size:20 final size:20
Alignment explanation
Indices: 44442--44479 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
44432 ATCCTATTCC
**
44442 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
44462 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
44480 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:51530 original size:34 final size:32
Alignment explanation
Indices: 51440--51531 Score: 80
Period size: 34 Copynumber: 2.8 Consensus size: 32
51430 TGTAATGCCC
*
51440 ATTC-TTC-CTGTATTGTTTCTTATTATTGTACT
1 ATTCTTTCACTGTATTG-TTCTT-TTAATGTACT
** * *
51472 ATTCTTTTTCTGTACTGTTCCTTTTAATGTATT
1 ATTCTTTCACTGTATTGTT-CTTTTAATGTACT
51505 ATTCATTTCACTGTATTGTATCTTTTA
1 ATTC-TTTCACTGTATTGT-TCTTTTA
51532 CTATACAATA
Statistics
Matches: 48, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
32 4 0.08
33 16 0.33
34 27 0.56
35 1 0.02
ACGTcount: A:0.17, C:0.15, G:0.09, T:0.59
Consensus pattern (32 bp):
ATTCTTTCACTGTATTGTTCTTTTAATGTACT
Found at i:54013 original size:20 final size:22
Alignment explanation
Indices: 53964--54014 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
53954 CCATAAACCC
*
53964 TAACCTTTACCAATTTCATCTT
1 TAACCATTACCAATTTCATCTT
* *
53986 TAAACATTACCAA-TTGAT-TT
1 TAACCATTACCAATTTCATCTT
54006 TAACCATTA
1 TAACCATTA
54015 TTCAAGCTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
20 10 0.40
21 4 0.16
22 11 0.44
ACGTcount: A:0.35, C:0.22, G:0.02, T:0.41
Consensus pattern (22 bp):
TAACCATTACCAATTTCATCTT
Found at i:55362 original size:43 final size:43
Alignment explanation
Indices: 55309--55393 Score: 116
Period size: 43 Copynumber: 2.0 Consensus size: 43
55299 GCAGCATTTT
* ** * *
55309 TGAGGAAAAATGCCACTATATGCATTATTATTAGTGGCGTTTG
1 TGAGGAAAAATGACACTATATAAATAATTATTAGTGACGTTTG
*
55352 TGAGGGAAAATGACACTATATAAATAATTATTAGTGACGTTT
1 TGAGGAAAAATGACACTATATAAATAATTATTAGTGACGTTT
55394 CTATCAAAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 36 1.00
ACGTcount: A:0.35, C:0.09, G:0.21, T:0.34
Consensus pattern (43 bp):
TGAGGAAAAATGACACTATATAAATAATTATTAGTGACGTTTG
Found at i:59558 original size:3 final size:3
Alignment explanation
Indices: 59537--59574 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
59527 GTTAACCATA
* *
59537 TTC TTC TTT TTC TTA TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
59575 TTTTACATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.03, C:0.26, G:0.00, T:0.71
Consensus pattern (3 bp):
TTC
Found at i:59651 original size:15 final size:16
Alignment explanation
Indices: 59626--59657 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
59616 TCATTAACTC
59626 TATTCTTTCTTCTTCT
1 TATTCTTTCTTCTTCT
59642 TATT-TTTCTTCTTCT
1 TATTCTTTCTTCTTCT
59657 T
1 T
59658 TTTCACATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.06, C:0.22, G:0.00, T:0.72
Consensus pattern (16 bp):
TATTCTTTCTTCTTCT
Found at i:61793 original size:13 final size:14
Alignment explanation
Indices: 61765--61797 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
61755 TTCATAAATA
61765 ATAATATTTATAAT
1 ATAATATTTATAAT
*
61779 ATAATA-TTATTAT
1 ATAATATTTATAAT
61792 ATAATA
1 ATAATA
61798 ATCATCACTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
ATAATATTTATAAT
Found at i:62273 original size:44 final size:43
Alignment explanation
Indices: 62206--62306 Score: 116
Period size: 44 Copynumber: 2.3 Consensus size: 43
62196 AATCTAATTT
* * * *
62206 CACTACTCTTCCGT-GAATATCAAATTCAAAGTTGAATTTGCTTC
1 CACTACTCTTTCGTGGAATATCAAACTCAAACTTGAA-TTAC-TC
* *
62250 CACTACT-TTTCGTGGAATTTCAAACTCAAACTTGGATTACTC
1 CACTACTCTTTCGTGGAATATCAAACTCAAACTTGAATTACTC
62292 CACTACTCTTTCGTG
1 CACTACTCTTTCGTG
62307 AAGTTCTCAT
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
42 9 0.18
43 15 0.31
44 25 0.51
ACGTcount: A:0.27, C:0.25, G:0.12, T:0.37
Consensus pattern (43 bp):
CACTACTCTTTCGTGGAATATCAAACTCAAACTTGAATTACTC
Found at i:62342 original size:46 final size:43
Alignment explanation
Indices: 62290--62440 Score: 136
Period size: 46 Copynumber: 3.5 Consensus size: 43
62280 CTTGGATTAC
62290 TCCACTACTCTTTCGTGAAGTTCTCATACTTTGCTGAAAACTCTGT
1 TCCACTACTCTTTCGTGAAGTT-TCATACTTTGCTGAAAA-TC-GT
* * ***
62336 TCCACTACTCTTTCATGGAG-TTCATA-TTTGCT-TTTA-C-T
1 TCCACTACTCTTTCGTGAAGTTTCATACTTTGCTGAAAATCGT
62374 T-CACTACTCTTAT-GTGAAGATTTCATACTTTGCTGAAAAATCCGT
1 TCCACTACTCTT-TCGTGAAG-TTTCATACTTTGCTG-AAAAT-CGT
*
62419 TCCACTACTCTTTCGTGGAGTT
1 TCCACTACTCTTTCGTGAAGTT
62441 CAAATTTTTA
Statistics
Matches: 83, Mismatches: 11, Indels: 23
0.71 0.09 0.20
Matches are distributed among these distances:
37 14 0.17
38 3 0.04
39 6 0.07
40 7 0.08
42 2 0.02
43 6 0.07
44 6 0.07
45 6 0.07
46 33 0.40
ACGTcount: A:0.22, C:0.24, G:0.13, T:0.41
Consensus pattern (43 bp):
TCCACTACTCTTTCGTGAAGTTTCATACTTTGCTGAAAATCGT
Found at i:62391 original size:83 final size:83
Alignment explanation
Indices: 62286--62447 Score: 247
Period size: 83 Copynumber: 2.0 Consensus size: 83
62276 CAAACTTGGA
* *
62286 TTACTCCACTACTCTTTCGTGAAG-TTCTCATACTTTGCTGAAAACTCTGTTCCACTACTCTTTC
1 TTACTCCACTACTCTTTCGTGAAGATT-TCATACTTTGCTGAAAAATCCGTTCCACTACTCTTTC
*
62350 ATGGAGTTCATATTTGCTT
65 ATGGAGTTCAAATTTGCTT
*
62369 TTACTTCACTACTCTTAT-GTGAAGATTTCATACTTTGCTGAAAAATCCGTTCCACTACTCTTTC
1 TTACTCCACTACTCTT-TCGTGAAGATTTCATACTTTGCTGAAAAATCCGTTCCACTACTCTTTC
*
62433 GTGGAGTTCAAATTT
65 ATGGAGTTCAAATTT
62448 TTATTTTGCT
Statistics
Matches: 72, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
83 69 0.96
84 3 0.04
ACGTcount: A:0.23, C:0.23, G:0.12, T:0.41
Consensus pattern (83 bp):
TTACTCCACTACTCTTTCGTGAAGATTTCATACTTTGCTGAAAAATCCGTTCCACTACTCTTTCA
TGGAGTTCAAATTTGCTT
Found at i:63006 original size:22 final size:22
Alignment explanation
Indices: 62981--63029 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
62971 AATAAAGCTT
*
62981 TCATCTTTGAAAAGAGAATCTA
1 TCATCGTTGAAAAGAGAATCTA
63003 TCATCGTTGAAAAGAGAATCTA
1 TCATCGTTGAAAAGAGAATCTA
63025 TCATC
1 TCATC
63030 CTTGCAGAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.39, C:0.16, G:0.14, T:0.31
Consensus pattern (22 bp):
TCATCGTTGAAAAGAGAATCTA
Done.