Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001120.1 Hibiscus syriacus cultivar Beakdansim tig00002217_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: 94436
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:200 original size:2 final size:2
Alignment explanation
Indices: 193--227 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
183 AGGGCTAAAC
193 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
228 CATGATCGAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:950 original size:23 final size:23
Alignment explanation
Indices: 902--950 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
892 AAAATGAAAC
* *
902 AAAAACTAAAATTTAGGTATTGA
1 AAAAACTAAAATTTAAGTACTGA
*
925 AAAAATTAAAAGTTTAAGTACT-A
1 AAAAACTAAAA-TTTAAGTACTGA
948 AAA
1 AAA
951 TTGATATTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 14 0.64
24 8 0.36
ACGTcount: A:0.57, C:0.04, G:0.10, T:0.29
Consensus pattern (23 bp):
AAAAACTAAAATTTAAGTACTGA
Found at i:2725 original size:2 final size:2
Alignment explanation
Indices: 2718--2752 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
2708 TATTTATTTC
*
2718 TA TA TA TA TA TA TA TA TA CA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2753 TGCACAAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:3357 original size:44 final size:43
Alignment explanation
Indices: 3289--3534 Score: 234
Period size: 42 Copynumber: 5.8 Consensus size: 43
3279 CAAAGGTCGA
* * * * *
3289 TATAGCGACGTTTTTTGAACAAACGCAACAAAAGGTCGATATT
1 TATAGCGGCATTTTTGGAACAAACGCAGCAAAAGGTCGATATC
*
3332 TATAGCGGCATTTTTTGGAACAAACG-ATGCAAAAGGCCGATATC
1 TATAGCGGCA-TTTTTGGAACAAACGCA-GCAAAAGGTCGATATC
* ** *
3376 TATAGAGGCA-TTTTGGAACAAACGTC-GCAAAACATCGAGATC
1 TATAGCGGCATTTTTGGAACAAACG-CAGCAAAAGGTCGATATC
* * * *
3418 GATAGCGGCGTTTTTGGAACAAACGCCA-CAAAAGATC-AGATC
1 TATAGCGGCATTTTTGGAACAAACG-CAGCAAAAGGTCGATATC
* * *
3460 TATAGCGACGTTTTTGGAACAAACGCCGCAAAAGGTC-ATATC
1 TATAGCGGCATTTTTGGAACAAACGCAGCAAAAGGTCGATATC
* * *
3502 TATAGTGGCATTTTTGAAACAAACGCCGCAAAA
1 TATAGCGGCATTTTTGGAACAAACGCAGCAAAA
3535 AAAATCAAAT
Statistics
Matches: 171, Mismatches: 25, Indels: 15
0.81 0.12 0.07
Matches are distributed among these distances:
41 1 0.01
42 102 0.60
43 32 0.19
44 36 0.21
ACGTcount: A:0.36, C:0.19, G:0.21, T:0.24
Consensus pattern (43 bp):
TATAGCGGCATTTTTGGAACAAACGCAGCAAAAGGTCGATATC
Found at i:5695 original size:3 final size:3
Alignment explanation
Indices: 5687--5727 Score: 57
Period size: 3 Copynumber: 13.7 Consensus size: 3
5677 TATTTATATA
*
5687 ATG ATG ATG ATT ATG ATG ATG ATG AAT- ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG -ATG ATG ATG ATG ATG AT
5728 TGGTTTATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 2 0.06
3 30 0.88
4 2 0.06
ACGTcount: A:0.37, C:0.00, G:0.27, T:0.37
Consensus pattern (3 bp):
ATG
Found at i:5707 original size:15 final size:15
Alignment explanation
Indices: 5687--5728 Score: 75
Period size: 15 Copynumber: 2.8 Consensus size: 15
5677 TATTTATATA
5687 ATGATGATGATTATG
1 ATGATGATGATTATG
*
5702 ATGATGATGAATATG
1 ATGATGATGATTATG
5717 ATGATGATGATT
1 ATGATGATGATT
5729 GGTTTATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.26, T:0.38
Consensus pattern (15 bp):
ATGATGATGATTATG
Found at i:6142 original size:28 final size:28
Alignment explanation
Indices: 6099--6152 Score: 92
Period size: 28 Copynumber: 1.9 Consensus size: 28
6089 TCAATTCAAC
6099 GATCCTAAAAATGTGTAAAACTAAAATA
1 GATCCTAAAAATGTGTAAAACTAAAATA
6127 GATCCTAAAAGA-GTGTAAAACTAAAA
1 GATCCTAAAA-ATGTGTAAAACTAAAA
6153 GAGTTTTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 24 0.96
29 1 0.04
ACGTcount: A:0.54, C:0.11, G:0.13, T:0.22
Consensus pattern (28 bp):
GATCCTAAAAATGTGTAAAACTAAAATA
Found at i:6188 original size:2 final size:2
Alignment explanation
Indices: 6181--6226 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
6171 GTTGATCATA
6181 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
6223 AT AT
1 AT AT
6227 TGTTGTATGA
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):
AT
Found at i:11004 original size:6 final size:6
Alignment explanation
Indices: 10993--11019 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
10983 AAAAAAATAA
10993 ATTAAT ATTAAT ATTAAT ATTAAT ATT
1 ATTAAT ATTAAT ATTAAT ATTAAT ATT
11020 TATGTATTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
ATTAAT
Found at i:18949 original size:46 final size:46
Alignment explanation
Indices: 18899--18992 Score: 179
Period size: 46 Copynumber: 2.0 Consensus size: 46
18889 TTTTTTTCAT
*
18899 TAGGAATAAATTAGATATATATCACTTATATAAAAACTATTTTATA
1 TAGGAATAAATTAGATATATATCACTTATATAAAAACTATTATATA
18945 TAGGAATAAATTAGATATATATCACTTATATAAAAACTATTATATA
1 TAGGAATAAATTAGATATATATCACTTATATAAAAACTATTATATA
18991 TA
1 TA
18993 TTTTTTATTT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.49, C:0.06, G:0.06, T:0.38
Consensus pattern (46 bp):
TAGGAATAAATTAGATATATATCACTTATATAAAAACTATTATATA
Found at i:31139 original size:93 final size:93
Alignment explanation
Indices: 30980--31165 Score: 311
Period size: 93 Copynumber: 2.0 Consensus size: 93
30970 TCGTCCGAGC
*
30980 CTTTCGTGATTATTGGTGGTCGAGGCATCCATCGGAACGAGGTTGGCCTCTCTTAGCTTGGTCTA
1 CTTTCGTGATTATTGGTGCTCGAGGCATCCATCGGAACGAGGTTGGCCTCTCTTAGCTTGGTCTA
*
31045 CACTATGCACA-GAGGTTCGAGTAGGAGG
66 CACTATGCA-ATCAGGTTCGAGTAGGAGG
* *
31073 CTTTCGTGATTATTGGTGCTCGGGGCATCCATCTGAACGAGGTTGGCCTCTCTTAGCTTGGTCTA
1 CTTTCGTGATTATTGGTGCTCGAGGCATCCATCGGAACGAGGTTGGCCTCTCTTAGCTTGGTCTA
*
31138 CACTATGCAATCCGGTTCGAGTAGGAGG
66 CACTATGCAATCAGGTTCGAGTAGGAGG
31166 GCGTGGATTC
Statistics
Matches: 87, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
92 1 0.01
93 86 0.99
ACGTcount: A:0.18, C:0.22, G:0.30, T:0.30
Consensus pattern (93 bp):
CTTTCGTGATTATTGGTGCTCGAGGCATCCATCGGAACGAGGTTGGCCTCTCTTAGCTTGGTCTA
CACTATGCAATCAGGTTCGAGTAGGAGG
Found at i:31903 original size:31 final size:32
Alignment explanation
Indices: 31868--31928 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 32
31858 ATGATTTTTG
*
31868 AAAATTGAAAGGTTAGGTACTAAA-GCATACC
1 AAAATTGAAAGGTTAAGTACTAAATGCATACC
* *
31899 AAAATTGATAGTTTAAGTACTAAATGCATA
1 AAAATTGAAAGGTTAAGTACTAAATGCATA
31929 GTTAACCTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 21 0.81
32 5 0.19
ACGTcount: A:0.46, C:0.10, G:0.16, T:0.28
Consensus pattern (32 bp):
AAAATTGAAAGGTTAAGTACTAAATGCATACC
Found at i:33577 original size:47 final size:49
Alignment explanation
Indices: 33506--33606 Score: 154
Period size: 47 Copynumber: 2.1 Consensus size: 49
33496 CGAAAATATG
33506 AAAATATATAAGGTACGACAACTTAATTTAAGGTT-AATGAATGGTAGAT
1 AAAATATATAAGGTACGACAACTTAATTTAAGGTTAAAT-AATGGTAGAT
* *
33555 AAAATATA-AA-GTACTACAACTTAATTTAAGGTTAAATAATTGTAGAT
1 AAAATATATAAGGTACGACAACTTAATTTAAGGTTAAATAATGGTAGAT
33602 AAAAT
1 AAAAT
33607 GTACAATCGA
Statistics
Matches: 49, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
47 36 0.73
48 5 0.10
49 8 0.16
ACGTcount: A:0.49, C:0.06, G:0.14, T:0.32
Consensus pattern (49 bp):
AAAATATATAAGGTACGACAACTTAATTTAAGGTTAAATAATGGTAGAT
Found at i:33850 original size:14 final size:13
Alignment explanation
Indices: 33809--33850 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 13
33799 ACATTCAAAT
33809 CATAAATCATAAA
1 CATAAATCATAAA
*
33822 CCCTAAATCAT-AA
1 -CATAAATCATAAA
33835 CATAACATCATAAA
1 CATAA-ATCATAAA
33849 CA
1 CA
33851 ATAGTAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
12 4 0.17
13 7 0.29
14 13 0.54
ACGTcount: A:0.55, C:0.24, G:0.00, T:0.21
Consensus pattern (13 bp):
CATAAATCATAAA
Found at i:35842 original size:21 final size:21
Alignment explanation
Indices: 35802--35842 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
35792 TAAAATACTT
**
35802 AATAATAATATTTTCGATAAA
1 AATAATAATATTTTAAATAAA
35823 AATAATAATATTTTAAATAA
1 AATAATAATATTTTAAATAA
35843 TTTTTATCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.39
Consensus pattern (21 bp):
AATAATAATATTTTAAATAAA
Found at i:37734 original size:29 final size:29
Alignment explanation
Indices: 37692--37773 Score: 146
Period size: 29 Copynumber: 2.8 Consensus size: 29
37682 GTGTTGGCCG
37692 TAGGTCGCCATGCCTTCCGGGCGACCTAT
1 TAGGTCGCCATGCCTTCCGGGCGACCTAT
37721 TAGGTCGCCATGCCTTCCGGGCGACCTAT
1 TAGGTCGCCATGCCTTCCGGGCGACCTAT
* *
37750 TAGGTCGCCATGTCTTCCCGGCGA
1 TAGGTCGCCATGCCTTCCGGGCGA
37774 GTTACAAGAG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 51 1.00
ACGTcount: A:0.13, C:0.34, G:0.28, T:0.24
Consensus pattern (29 bp):
TAGGTCGCCATGCCTTCCGGGCGACCTAT
Found at i:37956 original size:29 final size:29
Alignment explanation
Indices: 37923--38036 Score: 174
Period size: 29 Copynumber: 3.9 Consensus size: 29
37913 GAGCGAGGGT
*
37923 AGGTCGCCCGGAGTGCATGGCGACCTACA
1 AGGTCGCCCGGAGGGCATGGCGACCTACA
*
37952 AGGTCGCTCGGAGGGCATGGCGACCTACA
1 AGGTCGCCCGGAGGGCATGGCGACCTACA
* *
37981 AGGTCTCCCGGAGGGTATGGCGACCTACA
1 AGGTCGCCCGGAGGGCATGGCGACCTACA
**
38010 AGGTCGCCCGGAGGGCATAACGACCTA
1 AGGTCGCCCGGAGGGCATGGCGACCTA
38037 TGTGTTGGGA
Statistics
Matches: 76, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 76 1.00
ACGTcount: A:0.22, C:0.29, G:0.35, T:0.14
Consensus pattern (29 bp):
AGGTCGCCCGGAGGGCATGGCGACCTACA
Found at i:38082 original size:12 final size:12
Alignment explanation
Indices: 38065--38089 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
38055 TGCCATGCAA
38065 CACGTTCATTCT
1 CACGTTCATTCT
38077 CACGTTCATTCT
1 CACGTTCATTCT
38089 C
1 C
38090 TCTGTTTGAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.36, G:0.08, T:0.40
Consensus pattern (12 bp):
CACGTTCATTCT
Found at i:44618 original size:2 final size:2
Alignment explanation
Indices: 44611--44636 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
44601 AATGTGGGTC
44611 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
44637 TATTTTTAGC
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:45512 original size:34 final size:34
Alignment explanation
Indices: 45443--45515 Score: 110
Period size: 34 Copynumber: 2.1 Consensus size: 34
45433 ATGATCGTTT
** *
45443 CCTAACACTCTTACGATCCATCTTTGATTTGAAC
1 CCTAACACTCTTACGATCCATCTTTGACCTAAAC
*
45477 CCTAACACTCTTTCGATCCATCTTTGACCTAAAC
1 CCTAACACTCTTACGATCCATCTTTGACCTAAAC
45511 CCTAA
1 CCTAA
45516 ACGAAAAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.27, C:0.33, G:0.07, T:0.33
Consensus pattern (34 bp):
CCTAACACTCTTACGATCCATCTTTGACCTAAAC
Found at i:47956 original size:20 final size:20
Alignment explanation
Indices: 47931--47987 Score: 105
Period size: 20 Copynumber: 2.9 Consensus size: 20
47921 TTCAATTCGG
47931 GTCAAACTTTAGATTTTAAA
1 GTCAAACTTTAGATTTTAAA
*
47951 GTCAAACTTTAGATTTTAGA
1 GTCAAACTTTAGATTTTAAA
47971 GTCAAACTTTAGATTTT
1 GTCAAACTTTAGATTTT
47988 TAGGCTAGTA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.35, C:0.11, G:0.12, T:0.42
Consensus pattern (20 bp):
GTCAAACTTTAGATTTTAAA
Found at i:48472 original size:16 final size:16
Alignment explanation
Indices: 48453--48488 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
48443 ATTCGGGTTA
*
48453 CTTTCGGTTCGAGTTG
1 CTTTCGGTTCGAATTG
48469 CTTTCGGTTCGAATTG
1 CTTTCGGTTCGAATTG
48485 CTTT
1 CTTT
48489 TAGTCCAACT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.08, C:0.19, G:0.25, T:0.47
Consensus pattern (16 bp):
CTTTCGGTTCGAATTG
Found at i:53520 original size:13 final size:13
Alignment explanation
Indices: 53502--53544 Score: 68
Period size: 13 Copynumber: 3.2 Consensus size: 13
53492 GTCAAAGAAA
53502 GTCAACGGTCACG
1 GTCAACGGTCACG
53515 GTCAACGGTCACG
1 GTCAACGGTCACG
*
53528 GTCAATGGTCAACG
1 GTCAACGGTC-ACG
53542 GTC
1 GTC
53545 GGGTCGGGTC
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
13 22 0.79
14 6 0.21
ACGTcount: A:0.23, C:0.28, G:0.30, T:0.19
Consensus pattern (13 bp):
GTCAACGGTCACG
Found at i:53556 original size:17 final size:17
Alignment explanation
Indices: 53534--53591 Score: 89
Period size: 17 Copynumber: 3.4 Consensus size: 17
53524 CACGGTCAAT
53534 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
*
53551 GGTCAACGGTCAGGTCG
1 GGTCAACGGTCGGGTCG
* *
53568 AGTCAACAGTCGGGTCG
1 GGTCAACGGTCGGGTCG
53585 GGTCAAC
1 GGTCAAC
53592 CCGGTTCAGA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 36 1.00
ACGTcount: A:0.19, C:0.24, G:0.40, T:0.17
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:53562 original size:7 final size:7
Alignment explanation
Indices: 53502--53544 Score: 63
Period size: 7 Copynumber: 6.4 Consensus size: 7
53492 GTCAAAGAAA
53502 GTCAACG
1 GTCAACG
53509 GTC-ACG
1 GTCAACG
53515 GTCAACG
1 GTCAACG
53522 GTC-ACG
1 GTCAACG
*
53528 GTCAATG
1 GTCAACG
53535 GTCAACG
1 GTCAACG
53542 GTC
1 GTC
53545 GGGTCGGGTC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
6 12 0.38
7 20 0.62
ACGTcount: A:0.23, C:0.28, G:0.30, T:0.19
Consensus pattern (7 bp):
GTCAACG
Found at i:53580 original size:34 final size:36
Alignment explanation
Indices: 53514--53591 Score: 115
Period size: 34 Copynumber: 2.2 Consensus size: 36
53504 CAACGGTCAC
*
53514 GGTCAACGGTCACGGTCAATGGTCAACGGTCGGGTCG
1 GGTCAACGGTCACGGTCAA-GGTCAACAGTCGGGTCG
*
53551 GGTCAACGGTCA-GGTCGA-GTCAACAGTCGGGTCG
1 GGTCAACGGTCACGGTCAAGGTCAACAGTCGGGTCG
53585 GGTCAAC
1 GGTCAAC
53592 CCGGTTCAGA
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
34 22 0.56
36 5 0.13
37 12 0.31
ACGTcount: A:0.21, C:0.24, G:0.37, T:0.18
Consensus pattern (36 bp):
GGTCAACGGTCACGGTCAAGGTCAACAGTCGGGTCG
Found at i:53609 original size:19 final size:19
Alignment explanation
Indices: 53585--53731 Score: 233
Period size: 19 Copynumber: 7.7 Consensus size: 19
53575 AGTCGGGTCG
*
53585 GGTCAACCCGGTTCAGACC
1 GGTCAAACCGGTTCAGACC
53604 GGTCAAACCGGTTCAGACC
1 GGTCAAACCGGTTCAGACC
53623 GGTCAAACCGGTTCAGACC
1 GGTCAAACCGGTTCAGACC
*
53642 GGTCAAACAGGTTCAGACC
1 GGTCAAACCGGTTCAGACC
53661 GGTCAAACCGGTTCAGACC
1 GGTCAAACCGGTTCAGACC
53680 GGTCAAACCGGTTC-GAACC
1 GGTCAAACCGGTTCAG-ACC
* *
53699 GGTCAAACCGGTTCAAAACT
1 GGTCAAACCGGTTC-AGACC
53719 GGTCAAACCGGTT
1 GGTCAAACCGGTT
53732 TTCCAGCAGC
Statistics
Matches: 120, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
18 1 0.01
19 104 0.87
20 15 0.12
ACGTcount: A:0.27, C:0.30, G:0.26, T:0.17
Consensus pattern (19 bp):
GGTCAAACCGGTTCAGACC
Found at i:60234 original size:19 final size:20
Alignment explanation
Indices: 60210--60248 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
60200 AAGAAAGTCA
60210 ACGGTCAACGGTC-ACGGTC
1 ACGGTCAACGGTCAACGGTC
60229 ACGGTCAACGGTCAACGGTC
1 ACGGTCAACGGTCAACGGTC
60249 GGGTCGGGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.23, C:0.31, G:0.31, T:0.15
Consensus pattern (20 bp):
ACGGTCAACGGTCAACGGTC
Found at i:60235 original size:26 final size:24
Alignment explanation
Indices: 60206--60265 Score: 84
Period size: 26 Copynumber: 2.4 Consensus size: 24
60196 GTCAAAGAAA
60206 GTCAACGGTCAACGGTCACGGTCACG
1 GTCAACGGTCAACGGTC-CGGTC-CG
* *
60232 GTCAACGGTCAACGGTCGGGTCGG
1 GTCAACGGTCAACGGTCCGGTCCG
60256 GTCAACGGTC
1 GTCAACGGTC
60266 GGGTCGGGTC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
24 11 0.34
25 4 0.12
26 17 0.53
ACGTcount: A:0.20, C:0.28, G:0.35, T:0.17
Consensus pattern (24 bp):
GTCAACGGTCAACGGTCCGGTCCG
Found at i:60260 original size:17 final size:17
Alignment explanation
Indices: 60238--60278 Score: 82
Period size: 17 Copynumber: 2.4 Consensus size: 17
60228 CACGGTCAAC
60238 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
60255 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
60272 GGTCAAC
1 GGTCAAC
60279 CCGGTTCAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.15, C:0.24, G:0.44, T:0.17
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:60265 original size:7 final size:7
Alignment explanation
Indices: 60206--60248 Score: 72
Period size: 7 Copynumber: 6.4 Consensus size: 7
60196 GTCAAAGAAA
60206 GTCAACG
1 GTCAACG
60213 GTCAACG
1 GTCAACG
60220 GTC-ACG
1 GTCAACG
60226 GTC-ACG
1 GTCAACG
60232 GTCAACG
1 GTCAACG
60239 GTCAACG
1 GTCAACG
60246 GTC
1 GTC
60249 GGGTCGGGTC
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
6 12 0.34
7 23 0.66
ACGTcount: A:0.23, C:0.30, G:0.30, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:60294 original size:19 final size:19
Alignment explanation
Indices: 60272--60361 Score: 128
Period size: 19 Copynumber: 4.7 Consensus size: 19
60262 GGTCGGGTCG
*
60272 GGTCAACCCGGTTCAGACC
1 GGTCAAACCGGTTCAGACC
60291 GGTCAAACCGGTTCAGACC
1 GGTCAAACCGGTTCAGACC
60310 GGTCAAACCGGTTC-GAACC
1 GGTCAAACCGGTTCAG-ACC
* *
60329 GGTCAAACCGGTTCAAAACT
1 GGTCAAACCGGTTC-AGACC
60349 GGTCAAACCGGTT
1 GGTCAAACCGGTT
60362 TTCCAGCAGC
Statistics
Matches: 65, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
18 1 0.02
19 49 0.75
20 15 0.23
ACGTcount: A:0.27, C:0.30, G:0.26, T:0.18
Consensus pattern (19 bp):
GGTCAAACCGGTTCAGACC
Found at i:60344 original size:10 final size:10
Alignment explanation
Indices: 60274--60361 Score: 94
Period size: 9 Copynumber: 9.1 Consensus size: 10
60264 TCGGGTCGGG
*
60274 TCAACCCGGT
1 TCAAACCGGT
*
60284 TCAGACCGG-
1 TCAAACCGGT
60293 TCAAACCGGT
1 TCAAACCGGT
*
60303 TCAGACCGG-
1 TCAAACCGGT
60312 TCAAACCGGT
1 TCAAACCGGT
*
60322 TCGAACCGG-
1 TCAAACCGGT
60331 TCAAACCGGT
1 TCAAACCGGT
*
60341 TCAAAACTGG-
1 TC-AAACCGGT
60351 TCAAACCGGT
1 TCAAACCGGT
60361 T
1 T
60362 TTCCAGCAGC
Statistics
Matches: 64, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
9 30 0.47
10 28 0.44
11 6 0.09
ACGTcount: A:0.27, C:0.31, G:0.24, T:0.18
Consensus pattern (10 bp):
TCAAACCGGT
Found at i:61945 original size:60 final size:60
Alignment explanation
Indices: 61881--62005 Score: 153
Period size: 60 Copynumber: 2.1 Consensus size: 60
61871 AAATTTTAAT
* ** * *
61881 TTCATCCACAAATTATGACCCTCGTTCTAAGTTAGTCTCCAAACTT-TGGGGCATTCTAAA
1 TTCATACACAAACCATGACCCTCATTCTAAATTAGTCTCCAAACTTCT-GGGCATTCTAAA
** * *
61941 TTCATATTCAAACCATGATCCTCATTCTAAATTAGTCTCCAAGCTTCTGGGCATTCTAAA
1 TTCATACACAAACCATGACCCTCATTCTAAATTAGTCTCCAAACTTCTGGGCATTCTAAA
62001 TTCAT
1 TTCAT
62006 TTCTAAACTA
Statistics
Matches: 55, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
60 54 0.98
61 1 0.02
ACGTcount: A:0.29, C:0.25, G:0.11, T:0.35
Consensus pattern (60 bp):
TTCATACACAAACCATGACCCTCATTCTAAATTAGTCTCCAAACTTCTGGGCATTCTAAA
Found at i:62027 original size:60 final size:60
Alignment explanation
Indices: 61905--62033 Score: 174
Period size: 60 Copynumber: 2.1 Consensus size: 60
61895 ATGACCCTCG
* *
61905 TTCTAAGTTAGTCTCCAAACTTTGGGGCATTCTAAATTCATATTCAAACCATGATCCTCA
1 TTCTAAATTAGTCTCCAAACTTTGGGGCATTCTAAATTCATATTCAAACCATGATCCCCA
* *
61965 TTCTAAATTAGTCTCCAAGCTTCT-GGGCATTCTAAATTCAT-TTCTAAACTATGA-CCACCA
1 TTCTAAATTAGTCTCCAAACTT-TGGGGCATTCTAAATTCATATTC-AAACCATGATCC-CCA
62025 TTCTAAATT
1 TTCTAAATT
62034 GTTCCCCAAA
Statistics
Matches: 62, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
59 5 0.08
60 56 0.90
61 1 0.02
ACGTcount: A:0.30, C:0.23, G:0.10, T:0.36
Consensus pattern (60 bp):
TTCTAAATTAGTCTCCAAACTTTGGGGCATTCTAAATTCATATTCAAACCATGATCCCCA
Found at i:66897 original size:30 final size:30
Alignment explanation
Indices: 66861--67006 Score: 211
Period size: 30 Copynumber: 4.8 Consensus size: 30
66851 ACCTCGTTCT
*
66861 CCGTTCTGACATCTGCATGGGATTAATTCC
1 CCGTTCTGACATCTGCATGAGATTAATTCC
* *
66891 CCGTTCTAACATCTGCATGAGATTAATACCC
1 CCGTTCTGACATCTGCATGAGATTAAT-TCC
* *
66922 CCGTTCTGACATCTACATGGGATTAATTCC
1 CCGTTCTGACATCTGCATGAGATTAATTCC
* *
66952 CCATTCTGACATCTGCATGAGATTAGTTCC
1 CCGTTCTGACATCTGCATGAGATTAATTCC
*
66982 CCGTTCTTACATCTGCATGAGATTA
1 CCGTTCTGACATCTGCATGAGATTA
67007 TATCTCCGTC
Statistics
Matches: 102, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
30 76 0.75
31 26 0.25
ACGTcount: A:0.24, C:0.27, G:0.16, T:0.33
Consensus pattern (30 bp):
CCGTTCTGACATCTGCATGAGATTAATTCC
Found at i:66930 original size:61 final size:60
Alignment explanation
Indices: 66861--67006 Score: 220
Period size: 61 Copynumber: 2.4 Consensus size: 60
66851 ACCTCGTTCT
*
66861 CCGTTCTGACATCTGCATGGGATTAATTCCCCGTTCTAACATCTGCATGAGATTAATACCC
1 CCGTTCTGACATCTGCATGGGATTAATTCCCCATTCTAACATCTGCATGAGATTAAT-CCC
* * * *
66922 CCGTTCTGACATCTACATGGGATTAATTCCCCATTCTGACATCTGCATGAGATTAGTTCC
1 CCGTTCTGACATCTGCATGGGATTAATTCCCCATTCTAACATCTGCATGAGATTAATCCC
* *
66982 CCGTTCTTACATCTGCATGAGATTA
1 CCGTTCTGACATCTGCATGGGATTA
67007 TATCTCCGTC
Statistics
Matches: 77, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
60 24 0.31
61 53 0.69
ACGTcount: A:0.24, C:0.27, G:0.16, T:0.33
Consensus pattern (60 bp):
CCGTTCTGACATCTGCATGGGATTAATTCCCCATTCTAACATCTGCATGAGATTAATCCC
Found at i:73931 original size:23 final size:23
Alignment explanation
Indices: 73902--73946 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
73892 GATCAGGTGT
73902 AAACGAATATAAACGAACACAAA
1 AAACGAATATAAACGAACACAAA
*
73925 AAACGAATGTAAACGAACACAA
1 AAACGAATATAAACGAACACAA
73947 TAAATGAACT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.62, C:0.18, G:0.11, T:0.09
Consensus pattern (23 bp):
AAACGAATATAAACGAACACAAA
Found at i:73994 original size:23 final size:23
Alignment explanation
Indices: 73901--73994 Score: 68
Period size: 23 Copynumber: 4.2 Consensus size: 23
73891 TGATCAGGTG
* *
73901 TAAACGAATATAAACGAACACAA
1 TAAATGAACATAAACGAACACAA
* * **
73924 AAAACGAATGTAAACGAACACAA
1 TAAATGAACATAAACGAACACAA
** *
73947 TAAATGAAC-T-TGC-AACATAA
1 TAAATGAACATAAACGAACACAA
* *
73967 CAAATGAACATAATCGAACACAA
1 TAAATGAACATAAACGAACACAA
73990 TAAAT
1 TAAAT
73995 AAATGAAAAC
Statistics
Matches: 55, Mismatches: 13, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
20 14 0.25
21 2 0.04
22 2 0.04
23 37 0.67
ACGTcount: A:0.57, C:0.17, G:0.10, T:0.16
Consensus pattern (23 bp):
TAAATGAACATAAACGAACACAA
Found at i:74241 original size:34 final size:34
Alignment explanation
Indices: 74198--74294 Score: 149
Period size: 34 Copynumber: 2.9 Consensus size: 34
74188 ATTGGGTTAA
*
74198 ATATAAACGAATGAACATAAACGAACATACACGG
1 ATATAAACGAACGAACATAAACGAACATACACGG
74232 ATATAAACGAACGAACATAAACGAACATACACGG
1 ATATAAACGAACGAACATAAACGAACATACACGG
* * * *
74266 AAATAAATGAACGAACATACACAAACATA
1 ATATAAACGAACGAACATAAACGAACATA
74295 AATGAATGAA
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 58 1.00
ACGTcount: A:0.56, C:0.19, G:0.12, T:0.13
Consensus pattern (34 bp):
ATATAAACGAACGAACATAAACGAACATACACGG
Found at i:74283 original size:24 final size:24
Alignment explanation
Indices: 74251--74305 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
74241 AACGAACATA
*
74251 AACGAACATACACGGAA-ATAAATG
1 AACGAACATACAC-AAACATAAATG
74275 AACGAACATACACAAACATAAATG
1 AACGAACATACACAAACATAAATG
*
74299 AATGAAC
1 AACGAAC
74306 GGATTACTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 2 0.07
24 26 0.93
ACGTcount: A:0.56, C:0.18, G:0.13, T:0.13
Consensus pattern (24 bp):
AACGAACATACACAAACATAAATG
Found at i:76388 original size:13 final size:14
Alignment explanation
Indices: 76364--76393 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
76354 AAAATTATTT
76364 TAATATAATAATAA
1 TAATATAATAATAA
76378 TAATA-AATAATAA
1 TAATATAATAATAA
76391 TAA
1 TAA
76394 CATATTGTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
TAATATAATAATAA
Found at i:82175 original size:12 final size:13
Alignment explanation
Indices: 82153--82185 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
82143 AAAATTTTAA
82153 AATAAATATAATT
1 AATAAATATAATT
82166 AATAAA-ATAATT
1 AATAAATATAATT
*
82178 AATTAATA
1 AATAAATA
82186 CAAAAATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
AATAAATATAATT
Found at i:82182 original size:16 final size:16
Alignment explanation
Indices: 82150--82195 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 16
82140 ATAAAAATTT
82150 TAAAATAAATATAATTAA
1 TAAAAT-AAT-TAATTAA
82168 TAAAATAATTAATTAA
1 TAAAATAATTAATTAA
82184 TACAAA-AATTAA
1 TA-AAATAATTAA
82196 ACCCCAAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
16 15 0.56
17 6 0.22
18 6 0.22
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (16 bp):
TAAAATAATTAATTAA
Done.