Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009087.1 Hibiscus syriacus cultivar Beakdansim tig00112531_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: 96376
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:3317 original size:34 final size:34
Alignment explanation
Indices: 3279--3351 Score: 146
Period size: 34 Copynumber: 2.1 Consensus size: 34
3269 CACCATATTT
3279 TAAATTTAAATTATATAATGATATCACCATAAAA
1 TAAATTTAAATTATATAATGATATCACCATAAAA
3313 TAAATTTAAATTATATAATGATATCACCATAAAA
1 TAAATTTAAATTATATAATGATATCACCATAAAA
3347 TAAAT
1 TAAAT
3352 ATTTAAAACT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 39 1.00
ACGTcount: A:0.53, C:0.08, G:0.03, T:0.36
Consensus pattern (34 bp):
TAAATTTAAATTATATAATGATATCACCATAAAA
Found at i:5442 original size:15 final size:17
Alignment explanation
Indices: 5411--5442 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
5401 TAATAAAATA
5411 TTATCTAAAATATTTTT
1 TTATCTAAAATATTTTT
5428 TTATC-AAAA-ATTTTT
1 TTATCTAAAATATTTTT
5443 ATCGAGTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 4 0.27
17 5 0.33
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (17 bp):
TTATCTAAAATATTTTT
Found at i:15410 original size:48 final size:48
Alignment explanation
Indices: 15339--15435 Score: 194
Period size: 48 Copynumber: 2.0 Consensus size: 48
15329 CCAAGGAGGA
15339 ACCACTGTACGAACATGAGGCATCATGCGATAAACCTCGTGTGCAACG
1 ACCACTGTACGAACATGAGGCATCATGCGATAAACCTCGTGTGCAACG
15387 ACCACTGTACGAACATGAGGCATCATGCGATAAACCTCGTGTGCAACG
1 ACCACTGTACGAACATGAGGCATCATGCGATAAACCTCGTGTGCAACG
15435 A
1 A
15436 GTTTCACTTG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.32, C:0.27, G:0.23, T:0.19
Consensus pattern (48 bp):
ACCACTGTACGAACATGAGGCATCATGCGATAAACCTCGTGTGCAACG
Found at i:23030 original size:28 final size:28
Alignment explanation
Indices: 22998--23054 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
22988 CGACAATTTC
22998 CGCACAAAAATTCACACTCACATTAAGA
1 CGCACAAAAATTCACACTCACATTAAGA
23026 CGCACAAAAATTCACACTCACATTAAGA
1 CGCACAAAAATTCACACTCACATTAAGA
23054 C
1 C
23055 ATGTATCAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.46, C:0.30, G:0.07, T:0.18
Consensus pattern (28 bp):
CGCACAAAAATTCACACTCACATTAAGA
Found at i:29343 original size:21 final size:22
Alignment explanation
Indices: 29275--29349 Score: 73
Period size: 21 Copynumber: 3.3 Consensus size: 22
29265 ATGTCTAACT
* *
29275 ATAATAAAATGGGTAGAAAA-A
1 ATAATAAAATCGATAGAAAATA
29296 ATAATAAAATCGATAGCATCTACAATA
1 ATAATAAAATCGATAG-A---A-AATA
29323 ATAATAAAATCGATA-AAAATA
1 ATAATAAAATCGATAGAAAATA
29344 ATAATA
1 ATAATA
29350 TTTTTTATAA
Statistics
Matches: 46, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
21 24 0.52
22 2 0.04
25 2 0.04
26 2 0.04
27 16 0.35
ACGTcount: A:0.60, C:0.07, G:0.09, T:0.24
Consensus pattern (22 bp):
ATAATAAAATCGATAGAAAATA
Found at i:29738 original size:62 final size:60
Alignment explanation
Indices: 29641--29762 Score: 199
Period size: 62 Copynumber: 2.0 Consensus size: 60
29631 TGAAATAAAC
*
29641 TAGAAGACAATAACCCCCAACACTATATATAGTTTCATCCCTAAACAGACTCTATTAAAAAT
1 TAGAAGACAATAACCCCCAACACTATACATAGTTTCATCCCTAAACAGA--CTATTAAAAAT
* *
29703 TAGAAGACAATAACCCCCAACGCTATACATAGTTTCTTCCCTAAACAGACTATTAAAAAT
1 TAGAAGACAATAACCCCCAACACTATACATAGTTTCATCCCTAAACAGACTATTAAAAAT
29763 AGATTTTACG
Statistics
Matches: 57, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
60 11 0.19
62 46 0.81
ACGTcount: A:0.43, C:0.25, G:0.07, T:0.25
Consensus pattern (60 bp):
TAGAAGACAATAACCCCCAACACTATACATAGTTTCATCCCTAAACAGACTATTAAAAAT
Found at i:35720 original size:23 final size:22
Alignment explanation
Indices: 35678--35720 Score: 52
Period size: 23 Copynumber: 1.9 Consensus size: 22
35668 TAAATTTATA
*
35678 TATTTTTATCTTTATTTCTTCT
1 TATTTTTATCTTTATATCTTCT
35700 TATTTTGTATCATTTA-ATCTT
1 TATTTT-TATC-TTTATATCTT
35721 TATTATCTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 6 0.33
23 8 0.44
24 4 0.22
ACGTcount: A:0.19, C:0.12, G:0.02, T:0.67
Consensus pattern (22 bp):
TATTTTTATCTTTATATCTTCT
Found at i:38555 original size:29 final size:30
Alignment explanation
Indices: 38514--38583 Score: 99
Period size: 29 Copynumber: 2.4 Consensus size: 30
38504 TTAAATTTTA
*
38514 AAAT-TATCTTTATTTTTGTTTTAACTTATT
1 AAATATAT-TTTATTTTTGTCTTAACTTATT
*
38544 AAATAT-TTTTATTTTTGTCTTAATTTATT
1 AAATATATTTTATTTTTGTCTTAACTTATT
38573 AAATATATTTT
1 AAATATATTTT
38584 GTTTGTATTC
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
29 26 0.72
30 9 0.25
31 1 0.03
ACGTcount: A:0.30, C:0.04, G:0.03, T:0.63
Consensus pattern (30 bp):
AAATATATTTTATTTTTGTCTTAACTTATT
Found at i:38694 original size:2 final size:2
Alignment explanation
Indices: 38687--38716 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
38677 TTTACTATTA
38687 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
38717 TACTCTTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:47493 original size:14 final size:15
Alignment explanation
Indices: 47466--47494 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
47456 TCAAAATCCT
47466 TTTTAATATATAATA
1 TTTTAATATATAATA
47481 TTTTAAT-TATAATA
1 TTTTAATATATAATA
47495 GATATCTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TTTTAATATATAATA
Found at i:51342 original size:97 final size:96
Alignment explanation
Indices: 51159--51347 Score: 258
Period size: 97 Copynumber: 2.0 Consensus size: 96
51149 TTATGTAGCT
* ** *
51159 TTCAGGATTTGCAAATAATTCACTTTTTTTGGTCCATTGTATATTGGGAACTATTAGAGAATTTA
1 TTCAAGATTTGCAAATAATTCACCGTTTTTGGTCCATTATATATTGGGAACTATTAGAGAATTTA
* *
51224 CATGGGTTAGCACTCTATTTTCTTGACTACCG
66 AATGGGTTAACACTCTATTTTC-TGACTACCG
*
51256 TTCAAGATTTGCAATTAATTCACCGTTTTTGGTCCATTATATATTGGGAACTATTAGAGAA-TTA
1 TTCAAGATTTGCAAATAATTCACCGTTTTTGGTCCATTATATATTGGGAACTATTAGAGAATTTA
51320 AAT-GGTTCAACACT-TAATTTTTCTGACT
66 AATGGGTT-AACACTCT-A-TTTTCTGACT
51348 GATAGTAAAT
Statistics
Matches: 82, Mismatches: 7, Indels: 7
0.85 0.07 0.07
Matches are distributed among these distances:
95 5 0.06
96 16 0.20
97 61 0.74
ACGTcount: A:0.28, C:0.15, G:0.16, T:0.41
Consensus pattern (96 bp):
TTCAAGATTTGCAAATAATTCACCGTTTTTGGTCCATTATATATTGGGAACTATTAGAGAATTTA
AATGGGTTAACACTCTATTTTCTGACTACCG
Found at i:55372 original size:14 final size:14
Alignment explanation
Indices: 55353--55379 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
55343 GAATTAGCCG
55353 CCCATTTGCCATTC
1 CCCATTTGCCATTC
55367 CCCATTTGCCATT
1 CCCATTTGCCATT
55380 TTTGACCAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.41, G:0.07, T:0.37
Consensus pattern (14 bp):
CCCATTTGCCATTC
Found at i:61696 original size:20 final size:20
Alignment explanation
Indices: 61639--61704 Score: 80
Period size: 20 Copynumber: 3.3 Consensus size: 20
61629 AATATGTAAA
*
61639 TCGCAACACAGAAGTCAAAT
1 TCGCAACACAAAAGTCAAAT
* * *
61659 TCACAACGCGATAA-TCAAAT
1 TCGCAACAC-AAAAGTCAAAT
61679 TCGCAACACAAAAGTCAAAT
1 TCGCAACACAAAAGTCAAAT
61699 TCGCAA
1 TCGCAA
61705 TTGAATTTCA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
19 3 0.08
20 32 0.84
21 3 0.08
ACGTcount: A:0.45, C:0.26, G:0.12, T:0.17
Consensus pattern (20 bp):
TCGCAACACAAAAGTCAAAT
Found at i:65230 original size:24 final size:24
Alignment explanation
Indices: 65203--65258 Score: 78
Period size: 24 Copynumber: 2.3 Consensus size: 24
65193 TTTCAAATTC
65203 ATTTCATATGT-AATTGGAGTTTGA
1 ATTTCA-ATGTCAATTGGAGTTTGA
* *
65227 ATTTCAATTTCAATTTGAGTTTGA
1 ATTTCAATGTCAATTGGAGTTTGA
65251 ATTTCAAT
1 ATTTCAAT
65259 ATAAATTTCG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 3 0.10
24 26 0.90
ACGTcount: A:0.30, C:0.07, G:0.14, T:0.48
Consensus pattern (24 bp):
ATTTCAATGTCAATTGGAGTTTGA
Found at i:65243 original size:18 final size:18
Alignment explanation
Indices: 65222--65258 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
65212 GTAATTGGAG
65222 TTTGAATTTCAATTTCAA
1 TTTGAATTTCAATTTCAA
* *
65240 TTTGAGTTTGAATTTCAA
1 TTTGAATTTCAATTTCAA
65258 T
1 T
65259 ATAAATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.30, C:0.08, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTCAATTTCAA
Found at i:65265 original size:24 final size:24
Alignment explanation
Indices: 65214--65266 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
65204 TTTCATATGT
* * *
65214 AATTGGAGTTTGAATTTCAATTTC
1 AATTTGAGTTTGAATTTCAATATA
65238 AATTTGAGTTTGAATTTCAATATA
1 AATTTGAGTTTGAATTTCAATATA
65262 AATTT
1 AATTT
65267 CGGCTCCACT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.34, C:0.06, G:0.13, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTCAATATA
Found at i:66472 original size:19 final size:20
Alignment explanation
Indices: 66423--66476 Score: 67
Period size: 19 Copynumber: 2.7 Consensus size: 20
66413 AGTAGTTTCT
*
66423 AAAACTTAAATTCGCAACGCG
1 AAAAC-TAAAATCGCAACGCG
66444 AAAA-TGAAAATCGCAACGC-
1 AAAACT-AAAATCGCAACGCG
66463 AAAACTAAAATCGC
1 AAAACTAAAATCGC
66477 GTTGCGATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
19 13 0.43
20 13 0.43
21 4 0.13
ACGTcount: A:0.50, C:0.22, G:0.13, T:0.15
Consensus pattern (20 bp):
AAAACTAAAATCGCAACGCG
Found at i:66876 original size:22 final size:22
Alignment explanation
Indices: 66849--66899 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
66839 GATGGAGATA
66849 GACAGATTTCACCGGAGATGGG
1 GACAGATTTCACCGGAGATGGG
*
66871 GACAGATTTCATCGGAGATGGG
1 GACAGATTTCACCGGAGATGGG
66893 GACAGAT
1 GACAGAT
66900 GTCGCCGTAG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.29, C:0.16, G:0.35, T:0.20
Consensus pattern (22 bp):
GACAGATTTCACCGGAGATGGG
Found at i:67087 original size:40 final size:40
Alignment explanation
Indices: 67016--67329 Score: 287
Period size: 40 Copynumber: 7.8 Consensus size: 40
67006 TGTGTTTCGC
* *
67016 GTTGCGAATTTGA-AATTCTGCGTTGCGAATTTTACTTTTGT
1 GTTGCGAATTTGACTA-TC-GCGTTGCGAATTTGACTTTTGT
* * *
67057 GTTGCGAATTTGGCTATCGCGTTGCAAATTTTGACTTCTGT
1 GTTGCGAATTTGACTATCGCGTTGCGAA-TTTGACTTTTGT
*
67098 GTTACGAATTTGACTATCGCGTTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTTTGT
* * ** * * *
67138 GTTGCGAATTTGACTTTTGTATTGCGAATTTGACTATCGC
1 GTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTTTGT
* * * ** * *
67178 GTTGTGAATTTAACT-TCTGCGTTGCG-ATTTATAAATTCGC
1 GTTGCGAATTTGACTATC-GCGTTGCGAATTT-GACTTTTGT
* *
67218 GTTGCGAATCTGACTATCGCGTTGCGAATTTGGCTTTTGT
1 GTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTTTGT
* * *
67258 GTTGTGAATTTGACTATCGCGTTGCGAATTTGACTTCTAT
1 GTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTTTGT
* *
67298 GTTGCG-ATTT-ACAGATTCGCGTTGCAAATTTG
1 GTTGCGAATTTGAC-TA-TCGCGTTGCGAATTTG
67330 GAAAATCATA
Statistics
Matches: 222, Mismatches: 43, Indels: 17
0.79 0.15 0.06
Matches are distributed among these distances:
38 2 0.01
39 10 0.05
40 154 0.69
41 55 0.25
42 1 0.00
ACGTcount: A:0.19, C:0.15, G:0.23, T:0.42
Consensus pattern (40 bp):
GTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTTTGT
Found at i:67304 original size:20 final size:20
Alignment explanation
Indices: 67014--67295 Score: 243
Period size: 20 Copynumber: 14.0 Consensus size: 20
67004 ATTGTGTTTC
*
67014 GCGTTGCGAATTTGAAATTCT
1 GCGTTGCGAATTTG-ACTTCT
* *
67035 GCGTTGCGAATTTTACTTTT
1 GCGTTGCGAATTTGACTTCT
* *
67055 GTGTTGCGAATTTGGCTATC-
1 GCGTTGCGAATTTGACT-TCT
*
67075 GCGTTGCAAATTTTGACTTCT
1 GCGTTGCGAA-TTTGACTTCT
* *
67096 GTGTTACGAATTTGACTATC-
1 GCGTTGCGAATTTGACT-TCT
*
67116 GCGTTGCGAATTTGACTTTT
1 GCGTTGCGAATTTGACTTCT
* *
67136 GTGTTGCGAATTTGACTTTT
1 GCGTTGCGAATTTGACTTCT
**
67156 GTATTGCGAATTTGACTATC-
1 GCGTTGCGAATTTGACT-TCT
* *
67176 GCGTTGTGAATTTAACTTCT
1 GCGTTGCGAATTTGACTTCT
* * *
67196 GCGTTGCGATTTATAAATTC-
1 GCGTTGCGAATT-TGACTTCT
*
67216 GCGTTGCGAATCTGACTATC-
1 GCGTTGCGAATTTGACT-TCT
* *
67236 GCGTTGCGAATTTGGCTTTT
1 GCGTTGCGAATTTGACTTCT
* *
67256 GTGTTGTGAATTTGACTATC-
1 GCGTTGCGAATTTGACT-TCT
67276 GCGTTGCGAATTTGACTTCT
1 GCGTTGCGAATTTGACTTCT
67296 ATGTTGCGAT
Statistics
Matches: 210, Mismatches: 39, Indels: 25
0.77 0.14 0.09
Matches are distributed among these distances:
19 9 0.04
20 164 0.78
21 37 0.18
ACGTcount: A:0.19, C:0.16, G:0.23, T:0.42
Consensus pattern (20 bp):
GCGTTGCGAATTTGACTTCT
Found at i:67304 original size:60 final size:59
Alignment explanation
Indices: 67014--67292 Score: 270
Period size: 60 Copynumber: 4.6 Consensus size: 59
67004 ATTGTGTTTC
* * * * * * * *
67014 GCGTTGCGAATTTGAAATTCTGCGTTGCGAATTTTACTTTTGTGTTGCGAATTTGGCTATC
1 GCGTTGCGAATTTG-ACTTC-GCGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTTT
* * *
67075 GCGTTGCAAATTTTGACTTCTGTGTTACGAATTTGACTATCGCGTTGCGAATTTGACTTTT
1 GCGTTGCGAA-TTTGACTTC-GCGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTTT
* * ** * * *
67136 GTGTTGCGAATTTGACTTTTGTATTGCGAATTTGACTATCGCGTTGTGAATTTAACTTCT
1 GCGTTGCGAATTTGAC-TTCGCGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTTT
* * * * *
67196 GCGTTGCGATTTATAAATTCGCGTTGCGAATCTGACTATCGCGTTGCGAATTTGGCTTTT
1 GCGTTGCGAATT-TGACTTCGCGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTTT
* *
67256 GTGTTGTGAATTTGACTATCGCGTTGCGAATTTGACT
1 GCGTTGCGAATTTGACT-TCGCGTTGCGAATTTGACT
67293 TCTATGTTGC
Statistics
Matches: 177, Mismatches: 37, Indels: 9
0.79 0.17 0.04
Matches are distributed among these distances:
59 3 0.02
60 113 0.64
61 57 0.32
62 4 0.02
ACGTcount: A:0.19, C:0.15, G:0.24, T:0.42
Consensus pattern (59 bp):
GCGTTGCGAATTTGACTTCGCGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTTT
Found at i:67366 original size:21 final size:21
Alignment explanation
Indices: 67324--67366 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
67314 TCGCGTTGCA
*
67324 AATTTGGAAAATCATAACGCG
1 AATTTGGAAAATCACAACGCG
* *
67345 AATTTGGAAAATCGCAATGCG
1 AATTTGGAAAATCACAACGCG
67366 A
1 A
67367 TTTACATATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.42, C:0.14, G:0.21, T:0.23
Consensus pattern (21 bp):
AATTTGGAAAATCACAACGCG
Found at i:67427 original size:20 final size:19
Alignment explanation
Indices: 67374--67427 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
67364 CGATTTACAT
67374 ATTCGCGTTGCGAAATTGG
1 ATTCGCGTTGCGAAATTGG
** * *
67393 AAACTGGGTTTCGAAATTGG
1 ATTC-GCGTTGCGAAATTGG
67413 AGTTCGCGTTGCGAA
1 A-TTCGCGTTGCGAA
67428 TTTGTTGGTC
Statistics
Matches: 25, Mismatches: 8, Indels: 3
0.69 0.22 0.08
Matches are distributed among these distances:
19 2 0.08
20 22 0.88
21 1 0.04
ACGTcount: A:0.24, C:0.15, G:0.31, T:0.30
Consensus pattern (19 bp):
ATTCGCGTTGCGAAATTGG
Found at i:67797 original size:16 final size:16
Alignment explanation
Indices: 67772--67804 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
67762 ATTCATACAG
67772 AGCATCTGAATCATTC
1 AGCATCTGAATCATTC
*
67788 AGCATTTGAATCATTC
1 AGCATCTGAATCATTC
67804 A
1 A
67805 ACGCTTAATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.21, G:0.12, T:0.33
Consensus pattern (16 bp):
AGCATCTGAATCATTC
Found at i:67960 original size:2 final size:2
Alignment explanation
Indices: 67955--67985 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
67945 TCTATCGATC
67955 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
67986 TTGTAAAGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:69114 original size:2 final size:2
Alignment explanation
Indices: 69107--69149 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
69097 CGTCTATAAG
69107 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
69149 A
1 A
69150 ATTATTAAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:70784 original size:2 final size:2
Alignment explanation
Indices: 70777--70801 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
70767 CATATACATT
70777 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
70802 GAGAAAACTA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:72551 original size:15 final size:15
Alignment explanation
Indices: 72531--72560 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
72521 TATCACAATC
72531 GCGCAGGATTCCGGG
1 GCGCAGGATTCCGGG
*
72546 GCGCAGGATTTCGGG
1 GCGCAGGATTCCGGG
72561 AGCACCGTGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.23, G:0.47, T:0.17
Consensus pattern (15 bp):
GCGCAGGATTCCGGG
Found at i:77988 original size:38 final size:38
Alignment explanation
Indices: 77932--78007 Score: 134
Period size: 38 Copynumber: 2.0 Consensus size: 38
77922 CTGCGTGTGC
*
77932 AATAGCCTGATCAAATGTAATAGATCCTTAAATGAAAT
1 AATAACCTGATCAAATGTAATAGATCCTTAAATGAAAT
*
77970 AATAACCTGATCAAATGTAATAGATCCTTGAATGAAAT
1 AATAACCTGATCAAATGTAATAGATCCTTAAATGAAAT
78008 GATATTACCA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.45, C:0.13, G:0.13, T:0.29
Consensus pattern (38 bp):
AATAACCTGATCAAATGTAATAGATCCTTAAATGAAAT
Found at i:78007 original size:22 final size:22
Alignment explanation
Indices: 77944--78008 Score: 70
Period size: 22 Copynumber: 3.2 Consensus size: 22
77934 TAGCCTGATC
*
77944 AAATGTAATAGATCCTTAAATG
1 AAATGTAATAGATCCTTGAATG
*
77966 AAA--TAATA-A-CC-TG-ATC
1 AAATGTAATAGATCCTTGAATG
77982 AAATGTAATAGATCCTTGAATG
1 AAATGTAATAGATCCTTGAATG
78004 AAATG
1 AAATG
78009 ATATTACCAA
Statistics
Matches: 34, Mismatches: 3, Indels: 12
0.69 0.06 0.24
Matches are distributed among these distances:
16 5 0.15
17 1 0.03
18 7 0.21
19 2 0.06
20 7 0.21
21 2 0.06
22 10 0.29
ACGTcount: A:0.46, C:0.11, G:0.14, T:0.29
Consensus pattern (22 bp):
AAATGTAATAGATCCTTGAATG
Found at i:79504 original size:39 final size:37
Alignment explanation
Indices: 79432--79754 Score: 268
Period size: 39 Copynumber: 8.9 Consensus size: 37
79422 ATATATATAT
* *
79432 ATATATTATATAG-TTTAAAAACATTTTTAAAAACATA
1 ATATATTATATAGTTTTTAAAACA-TTTTGAAAACATA
* * *
79469 CATATAATATATAGTTTTGAAAACATGTTTGAAAACATTT
1 -ATATATTATATAGTTTTTAAAACAT-TTTGAAAACA-TA
* *
79509 ATATATTATATAGTTTTTAAAATATTTTGAAAATA-A
1 ATATATTATATAGTTTTTAAAACATTTTGAAAACATA
* *
79545 ATATAATATATAGTTTTTAAAACATTTTTAAAA-ATA
1 ATATATTATATAGTTTTTAAAACATTTTGAAAACATA
*
79581 TATATATTATATAATTTTTAAAACATTTTTG-AAA-AT-
1 -ATATATTATATAGTTTTTAAAACA-TTTTGAAAACATA
*
79617 ATATATTATATAATTTTT-AAACATTTTG-----A-A
1 ATATATTATATAGTTTTTAAAACATTTTGAAAACATA
*
79647 A-ATA-TATATAGTTTTTAAAAAATATTTTGAAAAACATA
1 ATATATTATATAGTTTTT--AAAACATTTTG-AAAACATA
* *
79685 TATATATTATATAGTTTTGAAATCATTTTGAAAAC-T-
1 -ATATATTATATAGTTTTTAAAACATTTTGAAAACATA
* * *
79721 -TACAATATATAGTTTTAAAAACATTTTTGAAAAC
1 ATATATTATATAGTTTTTAAAACA-TTTTGAAAAC
79755 TATATAATTT
Statistics
Matches: 240, Mismatches: 24, Indels: 45
0.78 0.08 0.15
Matches are distributed among these distances:
28 11 0.05
29 3 0.01
30 2 0.01
31 9 0.04
33 5 0.02
34 24 0.10
35 29 0.12
36 31 0.13
37 29 0.12
38 32 0.13
39 50 0.21
40 4 0.02
41 11 0.05
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.44
Consensus pattern (37 bp):
ATATATTATATAGTTTTTAAAACATTTTGAAAACATA
Found at i:79775 original size:27 final size:27
Alignment explanation
Indices: 79692--79803 Score: 98
Period size: 27 Copynumber: 3.8 Consensus size: 27
79682 ATATATATAT
*
79692 TATATAGTTTTGAAATCATTTTGAAAAC
1 TATATAATTTTGAAA-CATTTTGAAAAC
*
79720 TTACAATATATAGTTTTAAAAACATTTTTGAAAAC
1 -T---ATATA-A-TTTT-GAAACA-TTTTGAAAAC
* *
79755 TATATAATTTTGAAACATTTTTAAAAT
1 TATATAATTTTGAAACATTTTGAAAAC
79782 TATATAATTTTGAAAACATTTT
1 TATATAATTTTG-AAACATTTT
79804 TTAAAATAAA
Statistics
Matches: 70, Mismatches: 5, Indels: 17
0.76 0.05 0.18
Matches are distributed among these distances:
27 20 0.29
28 14 0.20
29 5 0.07
30 1 0.01
31 5 0.07
32 5 0.07
34 7 0.10
35 13 0.19
ACGTcount: A:0.43, C:0.06, G:0.06, T:0.45
Consensus pattern (27 bp):
TATATAATTTTGAAACATTTTGAAAAC
Found at i:79776 original size:28 final size:27
Alignment explanation
Indices: 79724--79817 Score: 118
Period size: 28 Copynumber: 3.4 Consensus size: 27
79714 GAAAACTTAC
* *
79724 AATATATAGTTTTAAAAACATTTTTGAA
1 AATATATAATTTTGAAAACATTTTT-AA
79752 AACTATATAATTTTG-AAACATTTTTAA
1 AA-TATATAATTTTGAAAACATTTTTAA
79779 AATTATATAATTTTGAAAACATTTTTTAA
1 AA-TATATAATTTTGAAAACA-TTTTTAA
*
79808 AATAAATAAT
1 AATATATAAT
79818 ATAATTTTAA
Statistics
Matches: 59, Mismatches: 4, Indels: 6
0.86 0.06 0.09
Matches are distributed among these distances:
27 16 0.27
28 24 0.41
29 19 0.32
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.44
Consensus pattern (27 bp):
AATATATAATTTTGAAAACATTTTTAA
Found at i:79842 original size:28 final size:28
Alignment explanation
Indices: 79727--79843 Score: 85
Period size: 27 Copynumber: 4.0 Consensus size: 28
79717 AACTTACAAT
* *
79727 ATATAGTTTTAAAAACATTTTTGAAAACT-
1 ATATAATTTT-AAAACACTTTTGAAAA-TA
* * *
79756 ATATAATTTTGAAACA-TTTTTAAAATT
1 ATATAATTTTAAAACACTTTTGAAAATA
* *
79783 ATATAATTTTGAAAACATTTTTTAAAATAAATA
1 ATATAATTTT-AAAACA-CTTTT--GA-AAATA
*
79816 ATATAATTTTAAAATACTTTTGAAAATA
1 ATATAATTTTAAAACACTTTTGAAAATA
79844 TATTATATAG
Statistics
Matches: 72, Mismatches: 9, Indels: 15
0.75 0.09 0.16
Matches are distributed among these distances:
26 1 0.01
27 18 0.25
28 15 0.21
29 10 0.14
30 4 0.06
31 4 0.06
32 6 0.08
33 14 0.19
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.44
Consensus pattern (28 bp):
ATATAATTTTAAAACACTTTTGAAAATA
Found at i:79852 original size:32 final size:33
Alignment explanation
Indices: 79690--79863 Score: 104
Period size: 32 Copynumber: 5.5 Consensus size: 33
79680 ACATATATAT
* *
79690 ATTATATAGTTTTGAAATCA-TTTTGAAAACTTACA
1 ATTATATAATTTTGAAAACACTTTTGAAAA--TA-A
* * *
79725 A-TATATAGTTTTAAAAACATTTTTG---A-AA
1 ATTATATAATTTTGAAAACACTTTTGAAAATAA
* *
79753 ACTATATAATTTTG-AAACA-TTTT---TA-AA
1 ATTATATAATTTTGAAAACACTTTTGAAAATAA
* *
79780 ATTATATAATTTTGAAAACATTTTTTAAAATAA
1 ATTATATAATTTTGAAAACACTTTTGAAAATAA
* * *
79813 ATAATATAATTTT-AAAATACTTTTGAAAATAT
1 ATTATATAATTTTGAAAACACTTTTGAAAATAA
*
79845 ATTATATAGTTTTGGAAAA
1 ATTATATAATTTT-GAAAA
79864 TATTTATATA
Statistics
Matches: 115, Mismatches: 13, Indels: 23
0.76 0.09 0.15
Matches are distributed among these distances:
27 20 0.17
28 12 0.10
29 15 0.13
32 28 0.24
33 14 0.12
34 20 0.17
35 6 0.05
ACGTcount: A:0.45, C:0.05, G:0.06, T:0.44
Consensus pattern (33 bp):
ATTATATAATTTTGAAAACACTTTTGAAAATAA
Found at i:79870 original size:21 final size:21
Alignment explanation
Indices: 79833--79873 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
79823 TTTAAAATAC
79833 TTTTGAAAATATATTATATAG
1 TTTTGAAAATATATTATATAG
79854 TTTTGGAAAATAT-TTATATA
1 TTTT-GAAAATATATTATATA
79874 TAGCAATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (21 bp):
TTTTGAAAATATATTATATAG
Found at i:81121 original size:4 final size:4
Alignment explanation
Indices: 81112--81210 Score: 57
Period size: 4 Copynumber: 25.8 Consensus size: 4
81102 TCTTCCCTTT
* * * *
81112 TTTA TTTA TTTA TTTA TTTA -TTA TTT- TCTC TTAA TTTA -TCA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
* * * * *
81157 TTTA TTT- TATTC CTTA -TTC CTTA TTTA TTTA TTTA TTTA TTGT- TTTT
1 TTTA TTTA T-TTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT-TA TTTA
81204 TTTA TTT
1 TTTA TTT
81211 TTTTTACTTT
Statistics
Matches: 74, Mismatches: 13, Indels: 16
0.72 0.13 0.16
Matches are distributed among these distances:
3 11 0.15
4 62 0.84
5 1 0.01
ACGTcount: A:0.20, C:0.07, G:0.01, T:0.72
Consensus pattern (4 bp):
TTTA
Found at i:83481 original size:11 final size:11
Alignment explanation
Indices: 83465--83506 Score: 75
Period size: 11 Copynumber: 3.8 Consensus size: 11
83455 AGTAACTAAC
83465 ATAACAAACTA
1 ATAACAAACTA
83476 ATAACAAACTA
1 ATAACAAACTA
*
83487 ATAACAAGCTA
1 ATAACAAACTA
83498 ATAACAAAC
1 ATAACAAAC
83507 CATAACACTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.62, C:0.19, G:0.02, T:0.17
Consensus pattern (11 bp):
ATAACAAACTA
Found at i:85468 original size:11 final size:11
Alignment explanation
Indices: 85452--85499 Score: 64
Period size: 11 Copynumber: 4.5 Consensus size: 11
85442 AGTAACCAAC
85452 ATAACAAACTA
1 ATAACAAACTA
*
85463 ATAACAAGCTA
1 ATAACAAACTA
*
85474 ATAACAAA-TT
1 ATAACAAACTA
85484 ATAAC-AACTA
1 ATAACAAACTA
85494 ATAACA
1 ATAACA
85500 CTCTTAACAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
9 2 0.06
10 12 0.39
11 17 0.55
ACGTcount: A:0.60, C:0.17, G:0.02, T:0.21
Consensus pattern (11 bp):
ATAACAAACTA
Found at i:85497 original size:10 final size:10
Alignment explanation
Indices: 85452--85499 Score: 60
Period size: 10 Copynumber: 4.6 Consensus size: 10
85442 AGTAACCAAC
85452 ATAACAAACTA
1 ATAAC-AACTA
85463 ATAACAAGCTA
1 ATAACAA-CTA
* *
85474 ATAACAAATT
1 ATAACAACTA
85484 ATAACAACTA
1 ATAACAACTA
85494 ATAACA
1 ATAACA
85500 CTCTTAACAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
10 17 0.53
11 15 0.47
ACGTcount: A:0.60, C:0.17, G:0.02, T:0.21
Consensus pattern (10 bp):
ATAACAACTA
Found at i:86535 original size:15 final size:17
Alignment explanation
Indices: 86515--86548 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
86505 CTTAAGCAAT
86515 TAATAAAT-AAA-ATAA
1 TAATAAATCAAAGATAA
86530 TAATAAATCAAAGATAA
1 TAATAAATCAAAGATAA
86547 TA
1 TA
86549 TTTTGACTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.47
16 3 0.18
17 6 0.35
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.26
Consensus pattern (17 bp):
TAATAAATCAAAGATAA
Found at i:94311 original size:60 final size:59
Alignment explanation
Indices: 94193--94346 Score: 182
Period size: 60 Copynumber: 2.6 Consensus size: 59
94183 TTTGGATGAA
* ** * *
94193 TTTGTGATGAAATTTGAATGTTCAAAAAGTTTGGGGAATAATTTAGAAAGAGGGTCATAG
1 TTTGTGATGAAATTAGAATGTTC-AAAAGTTTAAGGAATAATTCAGAAAGAGAGTCATAG
* * * *
94253 TTTAGTGATGAAATTAAAATGTTCAAAAGTTTAAGGATTAATTCAGAATGATAGTCATAG
1 TTT-GTGATGAAATTAGAATGTTCAAAAGTTTAAGGAATAATTCAGAAAGAGAGTCATAG
* *
94313 TTTGGGATGAAAATTAGAATATTCAAAAGTTTAA
1 TTTGTGATG-AAATTAGAATGTTCAAAAGTTTAA
94347 TGACAATTTA
Statistics
Matches: 80, Mismatches: 12, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
59 5 0.06
60 57 0.71
61 18 0.22
ACGTcount: A:0.40, C:0.04, G:0.21, T:0.34
Consensus pattern (59 bp):
TTTGTGATGAAATTAGAATGTTCAAAAGTTTAAGGAATAATTCAGAAAGAGAGTCATAG
Done.