Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005087.1 Hibiscus syriacus cultivar Beakdansim tig00011431_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: 98974
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:2550 original size:3 final size:3
Alignment explanation
Indices: 2537--2567 Score: 53
Period size: 3 Copynumber: 10.0 Consensus size: 3
2527 TTAAACTCTT
2537 TTA TATA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA
2568 AATTTATAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 24 0.89
4 3 0.11
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:4968 original size:32 final size:32
Alignment explanation
Indices: 4926--5001 Score: 100
Period size: 33 Copynumber: 2.4 Consensus size: 32
4916 GTAAATTTTG
* *
4926 TTTCAATTATCGAA-TTTGAAGTTTTTAAGTA
1 TTTCAATTATCGAACTTGGAAGTATTTAAGTA
* *
4957 TTTGAATTTATCAAACTTGGAAGTATTTAAGTA
1 TTTCAA-TTATCGAACTTGGAAGTATTTAAGTA
4990 TTTCAATTATCG
1 TTTCAATTATCG
5002 TAAACTTTGT
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
31 5 0.14
32 12 0.32
33 20 0.54
ACGTcount: A:0.33, C:0.08, G:0.13, T:0.46
Consensus pattern (32 bp):
TTTCAATTATCGAACTTGGAAGTATTTAAGTA
Found at i:22071 original size:2 final size:2
Alignment explanation
Indices: 22066--22099 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
22056 ATATACTTGG
22066 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
22100 TTGCTACATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:22227 original size:28 final size:28
Alignment explanation
Indices: 22195--22252 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
22185 TTCGGGTAAA
22195 TTACATAAATGATCACCCAATTATAGGT
1 TTACATAAATGATCACCCAATTATAGGT
22223 TTACATAAATGATCACCCAATTATAGGT
1 TTACATAAATGATCACCCAATTATAGGT
22251 TT
1 TT
22253 TGTCTCTAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.38, C:0.17, G:0.10, T:0.34
Consensus pattern (28 bp):
TTACATAAATGATCACCCAATTATAGGT
Found at i:23810 original size:18 final size:17
Alignment explanation
Indices: 23756--23804 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
23746 TTGGACCCTT
* *
23756 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
23774 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
23792 AGTGCATTCGATG
1 AGTGCA-TCGATG
23805 TTTCAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:23891 original size:56 final size:55
Alignment explanation
Indices: 23785--23892 Score: 146
Period size: 56 Copynumber: 1.9 Consensus size: 55
23775 AGTGCATCGA
* *
23785 TGCATCAAGTGCATTCGATGTTTCAAAATAGCCAGAGTGCATCGATGCATGGCTG
1 TGCATCAAATGCATTCGATGTTTCAAAATAGCCACAGTGCATCGATGCATGGCTG
* * *
23840 TGCATCAAATGCATTCGATGTTTTCATAAA-ATCCTCAGTGCATCGGTGCATGG
1 TGCATCAAATGCATTCGATG-TTTCA-AAATAGCCACAGTGCATCGATGCATGG
23893 TAAGTGCATC
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
55 19 0.41
56 24 0.52
57 3 0.07
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.30
Consensus pattern (55 bp):
TGCATCAAATGCATTCGATGTTTCAAAATAGCCACAGTGCATCGATGCATGGCTG
Found at i:23908 original size:56 final size:54
Alignment explanation
Indices: 23785--23909 Score: 137
Period size: 56 Copynumber: 2.2 Consensus size: 54
23775 AGTGCATCGA
*
23785 TGCATCAAGTGCATTCGATGTTTCAAAATAGCCAGAGTGCATCGATGCATGGCTG
1 TGCATCAA-TGCATTCGATGTTTCAAAATAGCCACAGTGCATCGATGCATGGCTG
* * *
23840 TGCATCAAATGCATTCGATGTTTTCATAAA-ATCCTCAGTGCATCGGTGCATGG-TAAG
1 TGCATC-AATGCATTCGATG-TTTCA-AAATAGCCACAGTGCATCGATGCATGGCT--G
*
23897 TGCATCGATGCAT
1 TGCATCAATGCAT
23910 GAAATGCATT
Statistics
Matches: 60, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
55 18 0.30
56 32 0.53
57 10 0.17
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.30
Consensus pattern (54 bp):
TGCATCAATGCATTCGATGTTTCAAAATAGCCACAGTGCATCGATGCATGGCTG
Found at i:30801 original size:21 final size:21
Alignment explanation
Indices: 30775--30819 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
30765 GATTTCTGGG
* *
30775 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
30796 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
30817 CAA
1 CAA
30820 ATGAACAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:31280 original size:19 final size:21
Alignment explanation
Indices: 31256--31298 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
31246 ATATGTTATG
31256 ATGATA-TAAACCATATG-AT
1 ATGATAGTAAACCATATGAAT
*
31275 ATGATAGTAAACTATATGAAT
1 ATGATAGTAAACCATATGAAT
31296 ATG
1 ATG
31299 TGATTATGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 6 0.29
20 10 0.48
21 5 0.24
ACGTcount: A:0.47, C:0.07, G:0.14, T:0.33
Consensus pattern (21 bp):
ATGATAGTAAACCATATGAAT
Found at i:31826 original size:31 final size:31
Alignment explanation
Indices: 31788--31974 Score: 340
Period size: 31 Copynumber: 6.0 Consensus size: 31
31778 AGGGTCGAGG
31788 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
31819 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
31850 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
31881 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
31912 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
31943 GTTTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
31974 G
1 G
31975 GTCCTTCGGG
Statistics
Matches: 153, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
31 152 0.99
32 1 0.01
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.39
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:35313 original size:21 final size:21
Alignment explanation
Indices: 35287--35331 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
35277 GATTTCTGGG
* *
35287 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
35308 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
35329 CAA
1 CAA
35332 ACGAACAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:35793 original size:19 final size:21
Alignment explanation
Indices: 35769--35811 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
35759 ATATGTTATG
35769 ATGATA-TAAACCATATG-AT
1 ATGATAGTAAACCATATGAAT
*
35788 ATGATAGTAAACTATATGAAT
1 ATGATAGTAAACCATATGAAT
35809 ATG
1 ATG
35812 TGATTATGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 6 0.29
20 10 0.48
21 5 0.24
ACGTcount: A:0.47, C:0.07, G:0.14, T:0.33
Consensus pattern (21 bp):
ATGATAGTAAACCATATGAAT
Found at i:36339 original size:31 final size:31
Alignment explanation
Indices: 36301--36456 Score: 278
Period size: 31 Copynumber: 5.0 Consensus size: 31
36291 AGGGTCGAGG
36301 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
36332 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
36363 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
36394 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
36425 GTTTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
36456 G
1 G
36457 GTCCTTCGGG
Statistics
Matches: 122, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
31 121 0.99
32 1 0.01
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:39633 original size:65 final size:65
Alignment explanation
Indices: 39499--39659 Score: 195
Period size: 65 Copynumber: 2.5 Consensus size: 65
39489 GTGCACTAAG
* * *
39499 AGTGTATCGATGCATCAAGTGCATTCGATG-TTTCAAAATAGCCAGAGTGCATCGATGCATGGCT
1 AGTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAGCCACAGTGCATCGATGCATGGCT
* * * *
39563 GGTGCATCGATGCATCAAATGCATTTGATGTTTTCATAAA-ATCCTCAGTGCATC-AGTGCATGG
1 AGTGCATCGATGCATCAAATGCATTCGATGTTTTCA-AAATAGCCACAGTGCATCGA-TGCATGG
39626 -T
64 CT
*
39627 AAGTGCATCGATGCATGAAATGCATTCGATGTT
1 -AGTGCATCGATGCATCAAATGCATTCGATGTT
39660 CAATTTAATT
Statistics
Matches: 83, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
64 28 0.34
65 52 0.63
66 3 0.04
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.30
Consensus pattern (65 bp):
AGTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAGCCACAGTGCATCGATGCATGGCT
Found at i:39698 original size:65 final size:63
Alignment explanation
Indices: 39504--39701 Score: 172
Period size: 65 Copynumber: 3.1 Consensus size: 63
39494 CTAAGAGTGT
* * * *
39504 ATCGATGCATCAAGTGCATTCGATGTTTCA-AAATAGC-CAGAGTGCATCGATGCATGGCTGGTG
1 ATCGATGCATCAAATGCATTCGATGTTTCATAAA-ATCTC--AGTGCATTGATGCATGGTTGGTG
39567 C
63 C
* * **
39568 ATCGATGCATCAAATGCATTTGATGTTTTCATAAAATCCTCAGTGCA-TCAGTGCATGGTAAGTG
1 ATCGATGCATCAAATGCATTCGATG-TTTCATAAAAT-CTCAGTGCATTGA-TGCATGGTTGGTG
39632 C
63 C
* **
39633 ATCGATGCATGAAATGCATTCGATG-TTCAATTTAAT-TCATGGTGCATTGATGCATGGATTGGT
1 ATCGATGCATCAAATGCATTCGATGTTTC-ATAAAATCTCA--GTGCATTGATGCATGG-TTGGT
39696 GC
62 GC
39698 ATCG
1 ATCG
39702 GTGTATCACT
Statistics
Matches: 109, Mismatches: 15, Indels: 19
0.76 0.10 0.13
Matches are distributed among these distances:
62 3 0.03
63 3 0.03
64 41 0.38
65 57 0.52
66 4 0.04
67 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (63 bp):
ATCGATGCATCAAATGCATTCGATGTTTCATAAAATCTCAGTGCATTGATGCATGGTTGGTGC
Found at i:40241 original size:2 final size:2
Alignment explanation
Indices: 40232--40273 Score: 61
Period size: 2 Copynumber: 21.5 Consensus size: 2
40222 TATCATTAAC
40232 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA GTA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA
40273 T
1 T
40274 TTGATTCTTA
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
1 2 0.05
2 33 0.89
3 2 0.05
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:42980 original size:33 final size:33
Alignment explanation
Indices: 42934--43005 Score: 108
Period size: 33 Copynumber: 2.2 Consensus size: 33
42924 ATGATGCAGT
*
42934 TGATGACCCTGAGCTAGATGATTCCAACCATAA
1 TGATGACCATGAGCTAGATGATTCCAACCATAA
* * *
42967 TGATGACCATGAGCTGGATGATTCCAATCATGA
1 TGATGACCATGAGCTAGATGATTCCAACCATAA
43000 TGATGA
1 TGATGA
43006 TGAAGATGAC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.26
Consensus pattern (33 bp):
TGATGACCATGAGCTAGATGATTCCAACCATAA
Found at i:43132 original size:12 final size:12
Alignment explanation
Indices: 43115--43141 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
43105 TGATGAAGAG
43115 TCTGCATGTGAA
1 TCTGCATGTGAA
43127 TCTGCATGTGAA
1 TCTGCATGTGAA
43139 TCT
1 TCT
43142 CTTGGCCTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.37
Consensus pattern (12 bp):
TCTGCATGTGAA
Found at i:43503 original size:18 final size:18
Alignment explanation
Indices: 43480--43526 Score: 94
Period size: 18 Copynumber: 2.6 Consensus size: 18
43470 AGATTGGTGC
43480 AATTGATTTCTGTTGAGA
1 AATTGATTTCTGTTGAGA
43498 AATTGATTTCTGTTGAGA
1 AATTGATTTCTGTTGAGA
43516 AATTGATTTCT
1 AATTGATTTCT
43527 TCGATTTATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.28, C:0.06, G:0.19, T:0.47
Consensus pattern (18 bp):
AATTGATTTCTGTTGAGA
Found at i:46724 original size:2 final size:2
Alignment explanation
Indices: 46717--46742 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
46707 AGTATTTTCA
46717 TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC
46743 AAACACTCAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:47329 original size:51 final size:51
Alignment explanation
Indices: 47264--47405 Score: 212
Period size: 51 Copynumber: 2.8 Consensus size: 51
47254 TGCTCACCTC
* * *
47264 ATCAGCAAAGTGATGAGAAGAACCAATCCAGGAAAACCTCGAGTAAGACTC
1 ATCAGCAAAGTGATGAGAAGAACCAATCCAGGGAAACCTCGAATAAGACTA
* * * *
47315 CTCAGCAAAATGATGAGAAGAACCAATCCAGGGAGACCTCGAATAAGAGTA
1 ATCAGCAAAGTGATGAGAAGAACCAATCCAGGGAAACCTCGAATAAGACTA
*
47366 ATCAGCAAAGTGATGAGAAGAACCAGTCCAGGGAAACCTC
1 ATCAGCAAAGTGATGAGAAGAACCAATCCAGGGAAACCTC
47406 ATGTAAGCTT
Statistics
Matches: 80, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
51 80 1.00
ACGTcount: A:0.42, C:0.21, G:0.23, T:0.13
Consensus pattern (51 bp):
ATCAGCAAAGTGATGAGAAGAACCAATCCAGGGAAACCTCGAATAAGACTA
Found at i:50724 original size:46 final size:46
Alignment explanation
Indices: 50657--50785 Score: 231
Period size: 46 Copynumber: 2.8 Consensus size: 46
50647 AAATAAATCA
*
50657 CTAAATAATTCACCATAATTTGGCAATAAATTAATGAATCATTAAT
1 CTAAATAATTCACCATAATTTGGCAATAGATTAATGAATCATTAAT
* *
50703 CTAAATAATTCACCATAATTTGGCAATAGATTAAGGAATCATTACT
1 CTAAATAATTCACCATAATTTGGCAATAGATTAATGAATCATTAAT
50749 CTAAATAATTCACCATAATTTGGCAATAGATTAATGA
1 CTAAATAATTCACCATAATTTGGCAATAGATTAATGA
50786 TTCACTAAAT
Statistics
Matches: 79, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 79 1.00
ACGTcount: A:0.43, C:0.14, G:0.09, T:0.33
Consensus pattern (46 bp):
CTAAATAATTCACCATAATTTGGCAATAGATTAATGAATCATTAAT
Found at i:62162 original size:260 final size:260
Alignment explanation
Indices: 61701--62228 Score: 1004
Period size: 260 Copynumber: 2.0 Consensus size: 260
61691 AAGTCAGGTC
*
61701 ATACCAAAAAAGAAGTCAAAAGAACAGACCTAATCAGTGACTATGGAACTAAAGGGAAACTGATC
1 ATACCAAAAAAGAAGTCAAAAGAACAGACCTAATCAGTGACTATGGAACCAAAGGGAAACTGATC
*
61766 AAGCATACTAGTAGAAATTTGGCTTCTCAAACACTGCAATTTTACAAAGGTAGAGAAATACATAT
66 AAGCATACTAGTAGAAATTTGGATTCTCAAACACTGCAATTTTACAAAGGTAGAGAAATACATAT
61831 TCAGTAAGTTGTTGCAAAATCAACAGCAATTCAGCATTGAAAAAATATGTTGAACTTCTTCATCC
131 TCAGTAAGTTGTTGCAAAATCAACAGCAATTCAGCATTGAAAAAATATGTTGAACTTCTTCATCC
61896 TCACATTCCTCGCTCAACAAACAAAGAAACCCTTACTTTGATTCACTAAAACCGAACAATCAGCT
196 TCACATTCCTCGCTCAACAAACAAAGAAACCCTTACTTTGATTCACTAAAACCGAACAATCAGCT
61961 ATACCAAAAAAGAAGTCAAAAGAACAGACCTAATCAGTGACTATGGAACCAAAGGGAAACTGATC
1 ATACCAAAAAAGAAGTCAAAAGAACAGACCTAATCAGTGACTATGGAACCAAAGGGAAACTGATC
62026 AAGCATACTAGTAGAAATTTGGATTCTCAAACACTGCAATTTTACAAAGGTAGAGAAATACATAT
66 AAGCATACTAGTAGAAATTTGGATTCTCAAACACTGCAATTTTACAAAGGTAGAGAAATACATAT
62091 TCAGTAAGTTGTTGCAAAATCAACAGCAATTCAGCATTGAAAAAATATGTTGAACTTCTTCATCC
131 TCAGTAAGTTGTTGCAAAATCAACAGCAATTCAGCATTGAAAAAATATGTTGAACTTCTTCATCC
* *
62156 TCACATTCCTCGCTCAACAACCAAAGAAACCCTTATTTTGATTCACTAAAACCGAACAATCAGCT
196 TCACATTCCTCGCTCAACAAACAAAGAAACCCTTACTTTGATTCACTAAAACCGAACAATCAGCT
*
62221 -TAACAAAA
1 ATACCAAAA
62229 TAATCAACTT
Statistics
Matches: 263, Mismatches: 5, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
259 7 0.03
260 256 0.97
ACGTcount: A:0.42, C:0.20, G:0.14, T:0.24
Consensus pattern (260 bp):
ATACCAAAAAAGAAGTCAAAAGAACAGACCTAATCAGTGACTATGGAACCAAAGGGAAACTGATC
AAGCATACTAGTAGAAATTTGGATTCTCAAACACTGCAATTTTACAAAGGTAGAGAAATACATAT
TCAGTAAGTTGTTGCAAAATCAACAGCAATTCAGCATTGAAAAAATATGTTGAACTTCTTCATCC
TCACATTCCTCGCTCAACAAACAAAGAAACCCTTACTTTGATTCACTAAAACCGAACAATCAGCT
Found at i:64099 original size:32 final size:32
Alignment explanation
Indices: 64062--64134 Score: 94
Period size: 32 Copynumber: 2.3 Consensus size: 32
64052 AACCGGGTAT
64062 CGGGTACCCACAAAATCCAGG-TACCCGATTAC
1 CGGGTACCCACAAAATCC-GGATACCCGATTAC
* **
64094 TGGGTACCCGTAAAATCCGGATACCCGATTAC
1 CGGGTACCCACAAAATCCGGATACCCGATTAC
*
64126 CGGATACCC
1 CGGGTACCC
64135 GTAACATCCG
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
31 2 0.06
32 33 0.94
ACGTcount: A:0.29, C:0.33, G:0.21, T:0.18
Consensus pattern (32 bp):
CGGGTACCCACAAAATCCGGATACCCGATTAC
Found at i:64135 original size:32 final size:31
Alignment explanation
Indices: 64073--64145 Score: 101
Period size: 32 Copynumber: 2.3 Consensus size: 31
64063 GGGTACCCAC
* *
64073 AAAATCCAGGTACCCGATTACTGGGTACCCGT
1 AAAATCC-GGTACCCGATTACCGGATACCCGT
64105 AAAATCCGGATACCCGATTACCGGATACCCGT
1 AAAATCCGG-TACCCGATTACCGGATACCCGT
*
64137 AACATCCGG
1 AAAATCCGG
64146 GTCGAGACAC
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
31 2 0.05
32 35 0.95
ACGTcount: A:0.30, C:0.30, G:0.21, T:0.19
Consensus pattern (31 bp):
AAAATCCGGTACCCGATTACCGGATACCCGT
Found at i:64212 original size:15 final size:16
Alignment explanation
Indices: 64188--64226 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
64178 AAAGTTTCGA
*
64188 TACCCAAAAAT-CAGG
1 TACCCGAAAATCCAGG
*
64203 TACCCGAAAATCCGGG
1 TACCCGAAAATCCAGG
64219 TACCCGAA
1 TACCCGAA
64227 TTTGCACACC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 10 0.48
16 11 0.52
ACGTcount: A:0.38, C:0.31, G:0.18, T:0.13
Consensus pattern (16 bp):
TACCCGAAAATCCAGG
Found at i:77768 original size:20 final size:20
Alignment explanation
Indices: 77729--77768 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
77719 TTTAAGTAGT
* **
77729 AAAATTAATATTTTCGATAA
1 AAAAATAATATTTTAAATAA
77749 AAAAATAATATTTTAAATAA
1 AAAAATAATATTTTAAATAA
77769 TCTTTACCGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.38
Consensus pattern (20 bp):
AAAAATAATATTTTAAATAA
Found at i:84403 original size:20 final size:20
Alignment explanation
Indices: 84380--84420 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
84370 CATGTGACTA
84380 CCCCGATCACGATGCGTCTC
1 CCCCGATCACGATGCGTCTC
84400 CCCCGATCACGATGCGTCTC
1 CCCCGATCACGATGCGTCTC
84420 C
1 C
84421 ATGGCGCCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.15, C:0.46, G:0.20, T:0.20
Consensus pattern (20 bp):
CCCCGATCACGATGCGTCTC
Found at i:84814 original size:115 final size:115
Alignment explanation
Indices: 84599--84814 Score: 317
Period size: 115 Copynumber: 1.9 Consensus size: 115
84589 ATAAATTTTG
* *
84599 AAAATCAATTTTTTTCTCACAATTCTTATGTTTTCTTTATATTTTATATTTTTCTTTAGCCAATT
1 AAAATCAATTTTTTTCTCACAATTATTATGTTTTCTTTATATTTTATATTTTTCTTTAACCAATT
* ** * *
84664 AAACTTAATTTGATTGTTATCGTTATCAACGTTGCACATAAATTCTGAAA
66 AAACTTAATTCGATTGGCATCATTACCAACGTTGCACATAAATTCTGAAA
* **
84714 AAAATCAA-TTTTTTCTCCCAATTATTATGTTTTCTTTATATTTTATATTTTTCCTTTAACCTCT
1 AAAATCAATTTTTTTCTCACAATTATTATGTTTTCTTTATATTTTATATTTTT-CTTTAACCAAT
*
84778 TAAACTTAATTCGATTGGCATCATTACCAGCGTTGCA
65 TAAACTTAATTCGATTGGCATCATTACCAACGTTGCA
84815 TAAAATACGT
Statistics
Matches: 89, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
114 42 0.47
115 47 0.53
ACGTcount: A:0.29, C:0.16, G:0.07, T:0.48
Consensus pattern (115 bp):
AAAATCAATTTTTTTCTCACAATTATTATGTTTTCTTTATATTTTATATTTTTCTTTAACCAATT
AAACTTAATTCGATTGGCATCATTACCAACGTTGCACATAAATTCTGAAA
Found at i:89021 original size:22 final size:23
Alignment explanation
Indices: 88975--89029 Score: 71
Period size: 22 Copynumber: 2.5 Consensus size: 23
88965 AGTATTTTTA
88975 TTATTAAATATAAATTAAAGTTT
1 TTATTAAATATAAATTAAAGTTT
*
88998 TTATTAATTA-AAATTAAA-TATT
1 TTATTAAATATAAATTAAAGT-TT
89020 TT-TTAAATAT
1 TTATTAAATAT
89030 TAAAATATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
21 7 0.25
22 12 0.43
23 9 0.32
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (23 bp):
TTATTAAATATAAATTAAAGTTT
Found at i:89021 original size:23 final size:23
Alignment explanation
Indices: 88975--89029 Score: 62
Period size: 21 Copynumber: 2.5 Consensus size: 23
88965 AGTATTTTTA
*
88975 TTATTAAATATAAATTAAAGTTT
1 TTATTAAATATAAATTAAAATTT
*
88998 TTATTAATTA-AAATT-AAATATT
1 TTATTAAATATAAATTAAAAT-TT
89020 TT-TTAAATAT
1 TTATTAAATAT
89030 TAAAATATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
21 9 0.33
22 9 0.33
23 9 0.33
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (23 bp):
TTATTAAATATAAATTAAAATTT
Found at i:90269 original size:3 final size:3
Alignment explanation
Indices: 90261--90286 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
90251 TCAGTGATAG
90261 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
90287 GTGATGGATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:94982 original size:2 final size:2
Alignment explanation
Indices: 94975--95028 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
94965 TATTCGATCA
94975 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
95017 AT AT AT AT AT AT
1 AT AT AT AT AT AT
95029 TACTAGGACC
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.