Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003656.1 Hibiscus syriacus cultivar Beakdansim tig00007775_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: 67193
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:2999 original size:20 final size:21
Alignment explanation
Indices: 2974--3012 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2964 GAGGGCTGGA
2974 AACCGGTT-TGACCAGTTTTC
1 AACCGGTTCTGACCAGTTTTC
*
2994 AACCGGTTCTGACCGGTTT
1 AACCGGTTCTGACCAGTTT
3013 GACCGGTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.18, C:0.26, G:0.23, T:0.33
Consensus pattern (21 bp):
AACCGGTTCTGACCAGTTTTC
Found at i:3011 original size:30 final size:28
Alignment explanation
Indices: 2975--3044 Score: 95
Period size: 28 Copynumber: 2.4 Consensus size: 28
2965 AGGGCTGGAA
* *
2975 ACCGGTTTGACCAGTTTTCAACCGGTTCTG
1 ACCGGTTTGACC-GGTTTCAACCGATT-TG
3005 ACCGGTTTGACCGGTTTCAACCGATTTG
1 ACCGGTTTGACCGGTTTCAACCGATTTG
*
3033 ACCGGTCTGACC
1 ACCGGTTTGACC
3045 CGACCCGACT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
28 13 0.35
29 12 0.32
30 12 0.32
ACGTcount: A:0.17, C:0.29, G:0.24, T:0.30
Consensus pattern (28 bp):
ACCGGTTTGACCGGTTTCAACCGATTTG
Found at i:3017 original size:9 final size:9
Alignment explanation
Indices: 2975--3044 Score: 59
Period size: 9 Copynumber: 7.3 Consensus size: 9
2965 AGGGCTGGAA
2975 ACCGGTTTG
1 ACCGGTTTG
* *
2984 ACCAGTTTTCA
1 ACC-GGTTT-G
2995 ACCGGTTCTG
1 ACCGGTT-TG
3005 ACCGGTTTG
1 ACCGGTTTG
*
3014 ACCGGTTTCA
1 ACCGGTTT-G
*
3024 ACCGATTTG
1 ACCGGTTTG
*
3033 ACCGGTCTG
1 ACCGGTTTG
3042 ACC
1 ACC
3045 CGACCCGACT
Statistics
Matches: 48, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
9 23 0.48
10 21 0.44
11 4 0.08
ACGTcount: A:0.17, C:0.29, G:0.24, T:0.30
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:3019 original size:19 final size:19
Alignment explanation
Indices: 2995--3044 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
2985 CCAGTTTTCA
*
2995 ACCGGTTCTGACCGGTTTG
1 ACCGGTTCTGACCGATTTG
*
3014 ACCGGTT-TCAACCGATTTG
1 ACCGGTTCT-GACCGATTTG
3033 ACCGG-TCTGACC
1 ACCGGTTCTGACC
3045 CGACCCGACT
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
18 5 0.19
19 21 0.81
ACGTcount: A:0.16, C:0.30, G:0.26, T:0.28
Consensus pattern (19 bp):
ACCGGTTCTGACCGATTTG
Found at i:3056 original size:14 final size:14
Alignment explanation
Indices: 3039--3080 Score: 68
Period size: 14 Copynumber: 3.1 Consensus size: 14
3029 TTTGACCGGT
3039 CTGACCCGACCCGA
1 CTGACCCGACCCGA
3053 CTGACCCGACCCGA
1 CTGACCCGACCCGA
*
3067 TTGA-CCGACCCGA
1 CTGACCCGACCCGA
3080 C
1 C
3081 CGTTGACCGT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
13 9 0.35
14 17 0.65
ACGTcount: A:0.21, C:0.48, G:0.21, T:0.10
Consensus pattern (14 bp):
CTGACCCGACCCGA
Found at i:3078 original size:18 final size:16
Alignment explanation
Indices: 3055--3089 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
3045 CGACCCGACT
3055 GACCCGACCCGATTGACC
1 GACCCGA-CCG-TTGACC
3073 GACCCGACCGTTGACC
1 GACCCGACCGTTGACC
3089 G
1 G
3090 TGACCGTTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
17 3 0.18
18 7 0.41
ACGTcount: A:0.20, C:0.43, G:0.26, T:0.11
Consensus pattern (16 bp):
GACCCGACCGTTGACC
Found at i:3094 original size:18 final size:19
Alignment explanation
Indices: 3053--3094 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 19
3043 CCCGACCCGA
3053 CTGACCCGACCCGATTGAC
1 CTGACCCGACCCGATTGAC
3072 C-GACCCGA-CCG-TTGAC
1 CTGACCCGACCCGATTGAC
3088 CGTGACC
1 C-TGACC
3095 GTTGACTTCC
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 6 0.29
17 3 0.14
18 11 0.52
19 1 0.05
ACGTcount: A:0.19, C:0.43, G:0.24, T:0.14
Consensus pattern (19 bp):
CTGACCCGACCCGATTGAC
Found at i:15286 original size:59 final size:59
Alignment explanation
Indices: 15109--15287 Score: 136
Period size: 59 Copynumber: 3.0 Consensus size: 59
15099 GGATGTAAAA
*
15109 TCGGGTAATCATTCAGGTTTCAGTCGGATCCTGTCAGGTCGGGTAAAATCGGATACAAG
1 TCGGGTAATCATTCAGGTTTCAGTCGGATCCTATCAGGTCGGGTAAAATCGGATACAAG
* ** * ** * **** **
15168 TC----AAGTCAGGT-AAATTTGATGCTTTGACTCATATCAGGTCGGGTCCTGGTCAAAT-CAAG
1 TCGGGTAA-TCA-TTCAGGTTTCA-G-TCGGA-TCCTATCAGGTCGGGT-AAAATCGGATACAAG
15227 TCGGGTAATCATTCAGGTTTCAGTCGGATCCTATCAGGTCGGGTAAAATCGGATACAAG
1 TCGGGTAATCATTCAGGTTTCAGTCGGATCCTATCAGGTCGGGTAAAATCGGATACAAG
15286 TC
1 TC
15288 AAGTCAGGTA
Statistics
Matches: 81, Mismatches: 27, Indels: 24
0.61 0.20 0.18
Matches are distributed among these distances:
55 2 0.02
56 8 0.10
57 2 0.02
58 7 0.09
59 43 0.53
60 7 0.09
61 2 0.02
62 8 0.10
63 2 0.02
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.28
Consensus pattern (59 bp):
TCGGGTAATCATTCAGGTTTCAGTCGGATCCTATCAGGTCGGGTAAAATCGGATACAAG
Found at i:15317 original size:118 final size:118
Alignment explanation
Indices: 15109--15350 Score: 430
Period size: 118 Copynumber: 2.1 Consensus size: 118
15099 GGATGTAAAA
*
15109 TCGGGTAATCATTCAGGTTTCAGTCGGATCCTGTCAGGTCGGGTAAAATCGGATACAAGTCAAGT
1 TCGGGTAATCATTCAGGTTTCAGTCGGATCCTATCAGGTCGGGTAAAATCGGATACAAGTCAAGT
* * *
15174 CAGGTAAATTTGATGCTTTGACTCATATCAGGTCGGGTCCTGGTCAAATCAAG
66 CAGGTAAATTTGATGATTCGACTCATATCAGGTCGGCTCCTGGTCAAATCAAG
15227 TCGGGTAATCATTCAGGTTTCAGTCGGATCCTATCAGGTCGGGTAAAATCGGATACAAGTCAAGT
1 TCGGGTAATCATTCAGGTTTCAGTCGGATCCTATCAGGTCGGGTAAAATCGGATACAAGTCAAGT
* *
15292 CAGGTAAATTTGATGATTCGACTCATATCAGGTTGGCTCTTGGTCAAATCAAG
66 CAGGTAAATTTGATGATTCGACTCATATCAGGTCGGCTCCTGGTCAAATCAAG
15345 TCGGGT
1 TCGGGT
15351 CATTTTCAGG
Statistics
Matches: 118, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
118 118 1.00
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.29
Consensus pattern (118 bp):
TCGGGTAATCATTCAGGTTTCAGTCGGATCCTATCAGGTCGGGTAAAATCGGATACAAGTCAAGT
CAGGTAAATTTGATGATTCGACTCATATCAGGTCGGCTCCTGGTCAAATCAAG
Found at i:15321 original size:59 final size:59
Alignment explanation
Indices: 15142--15324 Score: 171
Period size: 59 Copynumber: 3.1 Consensus size: 59
15132 TCGGATCCTG
* *
15142 TCAGGTCGGGTAAAATCGGATACAAGTCAAGTCAGGTAAATTTGATGCTTTGACTCATA
1 TCAGGTCGGGTAAAATCGGATACAAGTCAAGTCAGGTAAATTTGATGATTCGACTCATA
** * * * * * * *
15201 TCAGGTCGGGT--CCT-GG-T-CAAATCAAGTCGGGT-AATCATTCAGGTTTCAGTCGGATCCTA
1 TCAGGTCGGGTAAAATCGGATACAAGTCAAGTCAGGTAAAT--TTGATGATTC-GAC---TCATA
15260 TCAGGTCGGGTAAAATCGGATACAAGTCAAGTCAGGTAAATTTGATGATTCGACTCATA
1 TCAGGTCGGGTAAAATCGGATACAAGTCAAGTCAGGTAAATTTGATGATTCGACTCATA
15319 TCAGGT
1 TCAGGT
15325 TGGCTCTTGG
Statistics
Matches: 93, Mismatches: 19, Indels: 24
0.68 0.14 0.18
Matches are distributed among these distances:
53 3 0.03
54 13 0.14
55 7 0.08
56 4 0.04
57 1 0.01
59 36 0.39
61 1 0.01
62 4 0.04
63 8 0.09
64 13 0.14
65 3 0.03
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.28
Consensus pattern (59 bp):
TCAGGTCGGGTAAAATCGGATACAAGTCAAGTCAGGTAAATTTGATGATTCGACTCATA
Found at i:16345 original size:20 final size:20
Alignment explanation
Indices: 16311--16373 Score: 91
Period size: 18 Copynumber: 3.4 Consensus size: 20
16301 AATATAAGTT
16311 TATA-TATAAACTATAT-T-
1 TATATTATAAACTATATATA
16328 TATATTATAAACTATATA-A
1 TATATTATAAACTATATATA
16347 T-TATTATAAACTATATATA
1 TATATTATAAACTATATATA
16366 TATATTAT
1 TATATTAT
16374 GTTTATATGA
Statistics
Matches: 41, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
17 4 0.10
18 28 0.68
19 3 0.07
20 6 0.15
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (20 bp):
TATATTATAAACTATATATA
Found at i:16709 original size:10 final size:11
Alignment explanation
Indices: 16696--16749 Score: 62
Period size: 10 Copynumber: 5.2 Consensus size: 11
16686 AACTATAATT
16696 TATATTA-ATA
1 TATATTATATA
16706 TATA-TATATA
1 TATATTATATA
16716 TATA-TATATA
1 TATATTATATA
*
16726 TATA-TATGTA
1 TATATTATATA
16736 TATATGTATATA
1 TATAT-TATATA
16748 TA
1 TA
16750 ATTCAAAGTG
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
9 2 0.05
10 30 0.77
12 7 0.18
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (11 bp):
TATATTATATA
Found at i:16710 original size:2 final size:2
Alignment explanation
Indices: 16703--16749 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
16693 ATTTATATTA
* *
16703 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT GT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16745 AT AT A
1 AT AT A
16750 ATTCAAAGTG
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (2 bp):
AT
Found at i:16918 original size:20 final size:21
Alignment explanation
Indices: 16872--16915 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
16862 GAAAATTGTG
*
16872 AATTTAGAGGGAAATTGAGAA
1 AATTTAGAGGGAAATAGAGAA
16893 AA-TTAGAGGG-AATAGA-AA
1 AATTTAGAGGGAAATAGAGAA
16911 AATTT
1 AATTT
16916 TAGGAAGTCG
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 4 0.19
19 7 0.33
20 8 0.38
21 2 0.10
ACGTcount: A:0.50, C:0.00, G:0.25, T:0.25
Consensus pattern (21 bp):
AATTTAGAGGGAAATAGAGAA
Found at i:17127 original size:4 final size:4
Alignment explanation
Indices: 17118--17265 Score: 260
Period size: 4 Copynumber: 37.0 Consensus size: 4
17108 TTTAATTATA
17118 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
17166 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* * * *
17214 TATG TATG TATG TATG TATG TGTG TATG TGTG TATG TGTG TATG TGTG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
17262 TATG
1 TATG
17266 CGTGTATGCG
Statistics
Matches: 136, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 136 1.00
ACGTcount: A:0.22, C:0.00, G:0.28, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:17270 original size:8 final size:8
Alignment explanation
Indices: 17228--17609 Score: 710
Period size: 8 Copynumber: 47.5 Consensus size: 8
17218 TATGTATGTA
*
17228 TGTATGTG
1 TGTATGCG
*
17236 TGTATGTG
1 TGTATGCG
*
17244 TGTATGTG
1 TGTATGCG
*
17252 TGTATGTG
1 TGTATGCG
17260 TGTATGCG
1 TGTATGCG
17268 TGTATGCG
1 TGTATGCG
17276 TGTATGCG
1 TGTATGCG
17284 TGTATGCG
1 TGTATGCG
17292 TGTATGCG
1 TGTATGCG
17300 TGTATGCGCG
1 TGTAT--GCG
17310 TGTATGCG
1 TGTATGCG
17318 TGTATGCG
1 TGTATGCG
17326 TGTATGCG
1 TGTATGCG
17334 TGTATGCG
1 TGTATGCG
17342 TGTATGCG
1 TGTATGCG
17350 TGTATGCG
1 TGTATGCG
17358 TGTATGCG
1 TGTATGCG
17366 TGTATGCG
1 TGTATGCG
17374 TGTATGCG
1 TGTATGCG
17382 TGTATGCG
1 TGTATGCG
17390 TGTATGCG
1 TGTATGCG
17398 TGTATGCG
1 TGTATGCG
17406 TGTATGCG
1 TGTATGCG
17414 TGTATGCG
1 TGTATGCG
17422 TGTATGCG
1 TGTATGCG
17430 TGTATGCG
1 TGTATGCG
17438 TGTATGCG
1 TGTATGCG
17446 TGTATGCG
1 TGTATGCG
17454 TGTATGCG
1 TGTATGCG
17462 TGTATGCG
1 TGTATGCG
17470 TGTATGCG
1 TGTATGCG
17478 TGTATGCG
1 TGTATGCG
17486 TGTATGCG
1 TGTATGCG
17494 TGTATGCG
1 TGTATGCG
17502 TGTATGCG
1 TGTATGCG
17510 TGTATGCG
1 TGTATGCG
17518 TGTATGCG
1 TGTATGCG
17526 TGTATGCG
1 TGTATGCG
17534 TGTATGCG
1 TGTATGCG
17542 TGTATGCG
1 TGTATGCG
17550 TGTATGCG
1 TGTATGCG
17558 TGTATGCG
1 TGTATGCG
17566 TGTATGCG
1 TGTATGCG
17574 TGTATGCG
1 TGTATGCG
17582 TGTATGCG
1 TGTATGCG
17590 TGTATGCG
1 TGTATGCG
17598 TGTATGCG
1 TGTATGCG
17606 TGTA
1 TGTA
17610 ATTTATATTA
Statistics
Matches: 371, Mismatches: 1, Indels: 4
0.99 0.00 0.01
Matches are distributed among these distances:
8 363 0.98
10 8 0.02
ACGTcount: A:0.13, C:0.12, G:0.37, T:0.38
Consensus pattern (8 bp):
TGTATGCG
Found at i:17845 original size:15 final size:15
Alignment explanation
Indices: 17825--17873 Score: 62
Period size: 15 Copynumber: 3.1 Consensus size: 15
17815 CCATGTATGG
17825 TATATATAAACTATA
1 TATATATAAACTATA
*
17840 TATATATATACCCTATA
1 TATATATA-A-ACTATA
*
17857 TATATATAAATTATA
1 TATATATAAACTATA
17872 TA
1 TA
17874 AAGTAATAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
15 14 0.48
16 2 0.07
17 13 0.45
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.43
Consensus pattern (15 bp):
TATATATAAACTATA
Found at i:17873 original size:17 final size:17
Alignment explanation
Indices: 17825--17864 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
17815 CCATGTATGG
17825 TATATATAAACTATATA
1 TATATATAAACTATATA
**
17842 TATATATACCCTATATA
1 TATATATAAACTATATA
17859 TATATA
1 TATATA
17865 AATTATATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.47, C:0.10, G:0.00, T:0.42
Consensus pattern (17 bp):
TATATATAAACTATATA
Found at i:17922 original size:14 final size:14
Alignment explanation
Indices: 17899--17928 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
17889 TAGTTTATAA
*
17899 AAACCTTAAACCCT
1 AAACCATAAACCCT
17913 AAACCATAAACCCT
1 AAACCATAAACCCT
17927 AA
1 AA
17929 TATAAATGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.50, C:0.33, G:0.00, T:0.17
Consensus pattern (14 bp):
AAACCATAAACCCT
Found at i:18308 original size:19 final size:20
Alignment explanation
Indices: 18269--18320 Score: 79
Period size: 19 Copynumber: 2.6 Consensus size: 20
18259 AATATGTATG
* *
18269 TATAAACCATGTATAATATA
1 TATAAACTATATATAATATA
18289 TATAAACTATATAT-ATATA
1 TATAAACTATATATAATATA
18308 TATAAACTATATA
1 TATAAACTATATA
18321 AAGTAAATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 18 0.60
20 12 0.40
ACGTcount: A:0.52, C:0.08, G:0.02, T:0.38
Consensus pattern (20 bp):
TATAAACTATATATAATATA
Found at i:18411 original size:7 final size:7
Alignment explanation
Indices: 18401--18451 Score: 57
Period size: 7 Copynumber: 7.3 Consensus size: 7
18391 ATAAAAATCA
18401 TAAACCC
1 TAAACCC
18408 TAAACCC
1 TAAACCC
*
18415 TAAACAC
1 TAAACCC
**
18422 TAAACTT
1 TAAACCC
* *
18429 TAAATCA
1 TAAACCC
18436 TAAACCC
1 TAAACCC
18443 TAAACCC
1 TAAACCC
18450 TA
1 TA
18452 GATCACAAAC
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
7 36 1.00
ACGTcount: A:0.47, C:0.31, G:0.00, T:0.22
Consensus pattern (7 bp):
TAAACCC
Found at i:19378 original size:2 final size:2
Alignment explanation
Indices: 19331--19369 Score: 69
Period size: 2 Copynumber: 19.0 Consensus size: 2
19321 ATAAACCATG
19331 TA TA GTA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
19370 AACTATATAA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 34 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:19456 original size:48 final size:49
Alignment explanation
Indices: 19367--19461 Score: 147
Period size: 48 Copynumber: 2.0 Consensus size: 49
19357 ATATATATAT
* **
19367 ATAAACTATATAAAGTAAATTACTTATATAGTTTATAGAAACACTAAGC
1 ATAAACTATATAAAGTAAATAAAGTATATAGTTTATAGAAACACTAAGC
*
19416 ATAAACTATATAAAGT-AATAAAGTATATAGTTTATAGAAACCCTAA
1 ATAAACTATATAAAGTAAATAAAGTATATAGTTTATAGAAACACTAA
19462 ACTCTAAATC
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
48 26 0.62
49 16 0.38
ACGTcount: A:0.51, C:0.09, G:0.08, T:0.32
Consensus pattern (49 bp):
ATAAACTATATAAAGTAAATAAAGTATATAGTTTATAGAAACACTAAGC
Found at i:19910 original size:2 final size:2
Alignment explanation
Indices: 19856--19901 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
19846 ATATAAACTT
19856 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
19898 TA TA
1 TA TA
19902 AACTATATAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:20027 original size:21 final size:21
Alignment explanation
Indices: 19976--20035 Score: 50
Period size: 21 Copynumber: 2.9 Consensus size: 21
19966 ATAATTTATA
* ***
19976 AAACCCTAAACCCTAAATTTT
1 AAACCCTAAACACTAAACAAT
**
19997 AAACTATAAACACTAAACAAT
1 AAACCCTAAACACTAAACAAT
20018 AAACCCTAAATCAC-AAAC
1 AAACCCTAAA-CACTAAAC
20036 CCTAATATAA
Statistics
Matches: 30, Mismatches: 8, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
21 27 0.90
22 3 0.10
ACGTcount: A:0.53, C:0.27, G:0.00, T:0.20
Consensus pattern (21 bp):
AAACCCTAAACACTAAACAAT
Found at i:20360 original size:25 final size:22
Alignment explanation
Indices: 20332--20384 Score: 70
Period size: 22 Copynumber: 2.3 Consensus size: 22
20322 ATTAATCATG
20332 TTTTATCTAATTTAAATTTAAATAA
1 TTTTAT-TAATTT-AA-TTAAATAA
*
20357 TTTTATTAATTTTATTAAATAA
1 TTTTATTAATTTAATTAAATAA
20379 TTTTAT
1 TTTTAT
20385 AATATGTCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 14 0.52
23 1 0.04
24 6 0.22
25 6 0.22
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (22 bp):
TTTTATTAATTTAATTAAATAA
Found at i:20602 original size:16 final size:16
Alignment explanation
Indices: 20581--20615 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
20571 TCATTTACAT
20581 GTCAGGTTAAAAACAG
1 GTCAGGTTAAAAACAG
*
20597 GTCAGGTTAAAAATAG
1 GTCAGGTTAAAAACAG
20613 GTC
1 GTC
20616 GGGTAATACC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.40, C:0.11, G:0.26, T:0.23
Consensus pattern (16 bp):
GTCAGGTTAAAAACAG
Found at i:22984 original size:24 final size:25
Alignment explanation
Indices: 22932--22987 Score: 73
Period size: 24 Copynumber: 2.3 Consensus size: 25
22922 CCTACCACAT
*
22932 TTTCTTTTCTTCTACTTCTTTCTTC
1 TTTCTTTTCTTCTACATCTTTCTTC
22957 -TTCTTTTCTTC-ATCAT-TTTCTTC
1 TTTCTTTTCTTCTA-CATCTTTCTTC
22980 TTTCTTTT
1 TTTCTTTT
22988 GTAGTCTCAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
23 8 0.29
24 20 0.71
ACGTcount: A:0.05, C:0.25, G:0.00, T:0.70
Consensus pattern (25 bp):
TTTCTTTTCTTCTACATCTTTCTTC
Found at i:24152 original size:19 final size:18
Alignment explanation
Indices: 24130--24175 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 18
24120 CATCCTGTTA
24130 ACTTTGA-CTCGACCCATTG
1 ACTTTGACCT-GA-CCATTG
*
24149 ACTTTGACCTGACCGTTG
1 ACTTTGACCTGACCATTG
24167 ACTTTGACC
1 ACTTTGACC
24176 AAAAATGTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 14 0.56
19 9 0.36
20 2 0.08
ACGTcount: A:0.20, C:0.30, G:0.17, T:0.33
Consensus pattern (18 bp):
ACTTTGACCTGACCATTG
Found at i:30835 original size:20 final size:20
Alignment explanation
Indices: 30806--30852 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
30796 ATTCCACCAC
*
30806 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGATCCTAA
*
30826 ATGCATCTATATGATCCTAA
1 ATGCAACTATATGATCCTAA
30846 ATG-AACT
1 ATGCAACT
30853 CTTAGACATT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 3 0.12
20 21 0.88
ACGTcount: A:0.36, C:0.21, G:0.11, T:0.32
Consensus pattern (20 bp):
ATGCAACTATATGATCCTAA
Found at i:51238 original size:6 final size:6
Alignment explanation
Indices: 51215--51252 Score: 53
Period size: 6 Copynumber: 6.5 Consensus size: 6
51205 TGTATGAGCC
51215 TTGTTT TT-TTCT TT-TTT TTGTTT TTGTTT TTGTTT TTG
1 TTGTTT TTGTT-T TTGTTT TTGTTT TTGTTT TTGTTT TTG
51253 CACGCCACAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
5 5 0.17
6 25 0.83
ACGTcount: A:0.00, C:0.03, G:0.13, T:0.84
Consensus pattern (6 bp):
TTGTTT
Found at i:57133 original size:187 final size:187
Alignment explanation
Indices: 56818--57190 Score: 701
Period size: 187 Copynumber: 2.0 Consensus size: 187
56808 GAAGGTGTAC
56818 ATGAGATGCATGTATTAAAAACGAATACTTTATACTTGTATTATACTATTATTGGCAGACACTAC
1 ATGAGATGCATGTATTAAAAACGAATACTTTATACTTGTATTATACTATTATTGGCAGACACTAC
*
56883 TCACTAGTATAAAACCAAAAAGAAACGTGGCTTAACAGTGCATGTTAGCTAAGGTGAAAAAAATA
66 TCACTAGTATAAAACCAAAAAGAAACGTGGCTTAACAGTGCATGCTAGCTAAGGTGAAAAAAATA
* *
56948 TATCTAAACAAATTCAATAGAAACTCCAAGTTCGCAAATACAGCTTCTCAATAACAT
131 TACCTAAACAAATTCAATAGAAAATCCAAGTTCGCAAATACAGCTTCTCAATAACAT
*
57005 ATGAGATGCATGTATTGAAAACGAATACTTTATACTTGTATTATACTATTATTGGCAGACACTAC
1 ATGAGATGCATGTATTAAAAACGAATACTTTATACTTGTATTATACTATTATTGGCAGACACTAC
57070 TCACTAGTATAAAACCAAAAAGAAACGTGGCTTAACAGTGCATGCTAGCTAAGGTGAAAAAAATA
66 TCACTAGTATAAAACCAAAAAGAAACGTGGCTTAACAGTGCATGCTAGCTAAGGTGAAAAAAATA
*
57135 TACCTAAACAAATTCAATAGAAAATCCAAGTTCGCAAATGCAGCTTCTCAATAACA
131 TACCTAAACAAATTCAATAGAAAATCCAAGTTCGCAAATACAGCTTCTCAATAACA
57191 ATTTCTATTA
Statistics
Matches: 181, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
187 181 1.00
ACGTcount: A:0.42, C:0.17, G:0.14, T:0.27
Consensus pattern (187 bp):
ATGAGATGCATGTATTAAAAACGAATACTTTATACTTGTATTATACTATTATTGGCAGACACTAC
TCACTAGTATAAAACCAAAAAGAAACGTGGCTTAACAGTGCATGCTAGCTAAGGTGAAAAAAATA
TACCTAAACAAATTCAATAGAAAATCCAAGTTCGCAAATACAGCTTCTCAATAACAT
Found at i:59039 original size:45 final size:45
Alignment explanation
Indices: 58975--59065 Score: 182
Period size: 45 Copynumber: 2.0 Consensus size: 45
58965 AATATCTTTA
58975 GCTTTCGAAGCTTCATGCTTTTTCTTCTTAGAACACTTATACTTC
1 GCTTTCGAAGCTTCATGCTTTTTCTTCTTAGAACACTTATACTTC
59020 GCTTTCGAAGCTTCATGCTTTTTCTTCTTAGAACACTTATACTTC
1 GCTTTCGAAGCTTCATGCTTTTTCTTCTTAGAACACTTATACTTC
59065 G
1 G
59066 AAGATGGTAC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.20, C:0.24, G:0.12, T:0.44
Consensus pattern (45 bp):
GCTTTCGAAGCTTCATGCTTTTTCTTCTTAGAACACTTATACTTC
Found at i:59790 original size:82 final size:82
Alignment explanation
Indices: 59611--59893 Score: 302
Period size: 82 Copynumber: 3.4 Consensus size: 82
59601 CTATTATAGT
* * * * * * *
59611 ATTTTTATACAAACGCCGCTAAATTACTACTTTATTGCAGCGTTTGTTGAAAAAATGACACTATT
1 ATTTGTATAAAAACGCCGCTAAAGTACTACTTTATCGCAGCATTTGTTG-GAAAATGACACTATA
* *
59676 AACGAATCCTATTACGGC
65 AACGAACCCTATTACGAC
* * * * *
59694 GTTTGTATATAAACGCTGCTAAAGTACTACTTTGTCGCAGCATTTGTTGGAAAATGCCACTATAA
1 ATTTGTATAAAAACGCCGCTAAAGTACTACTTTATCGCAGCATTTGTTGGAAAATGACACTATAA
**
59759 ACGAACCCTATTGTGAC
66 ACGAACCCTATTACGAC
*
59776 ATTTGTATAAAAACGCCGGTAAAGTACT-CTTTATTACG-A-CATTTGTTGGAAAAATGACACTA
1 ATTTGTATAAAAACGCCGCTAAAGTACTACTTTA-T-CGCAGCATTTGTTGG-AAAATGACACTA
* *
59838 TAAATGAACCCTATTACAAC
63 TAAACGAACCCTATTACGAC
*** *
59858 ATTTGTATAAAAACATTGCTAAAGTACTACTCTATC
1 ATTTGTATAAAAACGCCGCTAAAGTACTACTTTATC
59894 ATGGAGTTTG
Statistics
Matches: 166, Mismatches: 30, Indels: 10
0.81 0.15 0.05
Matches are distributed among these distances:
81 15 0.09
82 104 0.63
83 47 0.28
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.33
Consensus pattern (82 bp):
ATTTGTATAAAAACGCCGCTAAAGTACTACTTTATCGCAGCATTTGTTGGAAAATGACACTATAA
ACGAACCCTATTACGAC
Found at i:59834 original size:164 final size:165
Alignment explanation
Indices: 59585--59888 Score: 389
Period size: 164 Copynumber: 1.8 Consensus size: 165
59575 TGGAAAAACA
* * * * * *
59585 CCACTATGAACAAACCCTATTATAGTATTTTTATACAAACGCCGCTAAATTACTACTTTATTGCA
1 CCACTATAAACAAACCCTATTATAGCATTTGTATAAAAACGCCGCTAAAGTACTACTTTATTACA
* * * ** * * *
59650 GCGTTTGTTGAAAAAATGACACTATTAACGAATCCTATTACGGCGTTTGTATATAAACGCTGCTA
66 GCATTTGTTGAAAAAATGACACTATAAACGAACCCTATTACAACATTTGTATAAAAACACTGCTA
59715 AAGTACTACTTTGTCGCAGCATTTGTTGGAAAATG
131 AAGTACTACTTTGTCGCAGCATTTGTTGGAAAATG
* * *
59750 CCACTATAAACGAACCCTATTGT-GACATTTGTATAAAAACGCCGGTAAAGTACT-CTTTATTAC
1 CCACTATAAACAAACCCTATTATAG-CATTTGTATAAAAACGCCGCTAAAGTACTACTTTATTAC
* * *
59813 -GACATTTGTTGGAAAAATGACACTATAAATGAACCCTATTACAACATTTGTATAAAAACATTGC
65 AG-CATTTGTTGAAAAAATGACACTATAAACGAACCCTATTACAACATTTGTATAAAAACACTGC
59877 TAAAGTACTACT
129 TAAAGTACTACT
59889 CTATCATGGA
Statistics
Matches: 117, Mismatches: 20, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
163 1 0.01
164 72 0.62
165 44 0.38
ACGTcount: A:0.36, C:0.19, G:0.14, T:0.32
Consensus pattern (165 bp):
CCACTATAAACAAACCCTATTATAGCATTTGTATAAAAACGCCGCTAAAGTACTACTTTATTACA
GCATTTGTTGAAAAAATGACACTATAAACGAACCCTATTACAACATTTGTATAAAAACACTGCTA
AAGTACTACTTTGTCGCAGCATTTGTTGGAAAATG
Found at i:65265 original size:65 final size:64
Alignment explanation
Indices: 65143--65270 Score: 177
Period size: 65 Copynumber: 2.0 Consensus size: 64
65133 CTTAAAATTC
* * *
65143 AATGCATTTTGTGTACCGATGCACAACCATGCATCGATGCACTCCTGATTTTATTGAAACATCG
1 AATGCATTTTATGTACCGATGCACAACCATGCATCGATACACTCCTGATCTTATTGAAACATCG
** *
65207 AATGCATTTTATGTATTGATGCACATACCATGCATCGATACACTCCTGGCTCTT-TTGAAACATC
1 AATGCATTTTATGTACCGATGCACA-ACCATGCATCGATACACTCCT-GATCTTATTGAAACATC
65271 ACCCCAAGTG
Statistics
Matches: 56, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
64 22 0.39
65 30 0.54
66 4 0.07
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.33
Consensus pattern (64 bp):
AATGCATTTTATGTACCGATGCACAACCATGCATCGATACACTCCTGATCTTATTGAAACATCG
Done.