Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003355.1 Hibiscus syriacus cultivar Beakdansim tig00007061_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: 54980
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:6352 original size:3 final size:3
Alignment explanation
Indices: 6344--6522 Score: 250
Period size: 3 Copynumber: 58.7 Consensus size: 3
6334 TTATTTATTA
*
6344 AAT AAT AAT AAT ATAT AAT AAT ATAT AAT ATT AAT AAT AAT AAT AAAT
1 AAT AAT AAT AAT A-AT AAT AAT A-AT AAT AAT AAT AAT AAT AAT -AAT
* **
6392 ACT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT GCT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * *
6440 AAT AAT AAT ACT AAT AAT AAT AAT ATT AAT AAT AAT AAT AAT ATT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
6488 AAT GAT AAT AAT AAT ATT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
6523 AATGGATAAA
Statistics
Matches: 155, Mismatches: 18, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
3 146 0.94
4 9 0.06
ACGTcount: A:0.61, C:0.02, G:0.01, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:7050 original size:113 final size:113
Alignment explanation
Indices: 6820--7720 Score: 1451
Period size: 113 Copynumber: 7.9 Consensus size: 113
6810 GATATCAAAC
* * *
6820 AAAGGTTGAACAAGCTCTTCTTATTATGAACTTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAAC-TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* ** * * *
6885 TCATGAACTTTCTTTGGCCATGTTGATCCATCAAATGATGAATTTAAACA
65 T-ATGAACTTTCTCTGGAAATGATGATCCATCAAATGATGAATTCAAGCA
*
6935 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * * *
7000 ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAGGCA
66 ATGAACTTTCTCTGGAAATGATGATCCATCAAATGATGAATTCAAGCA
7048 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* ** * * *
7113 CATGAACTTTCTTTGGCCATGTTGATCCATCAAATGATGAATTTAAACA
66 -ATGAACTTTCTCTGGAAATGATGATCCATCAAATGATGAATTCAAGCA
*
7162 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * * *
7227 ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAGGCA
66 ATGAACTTTCTCTGGAAATGATGATCCATCAAATGATGAATTCAAGCA
*
7275 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* *
7340 ATGAACTTTCTCTGGAAATGTTGATCCATCAAGTGATGAATTCAAGCA
66 ATGAACTTTCTCTGGAAATGATGATCCATCAAATGATGAATTCAAGCA
7388 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * * *
7453 ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAGGCA
66 ATGAACTTTCTCTGGAAATGATGATCCATCAAATGATGAATTCAAGCA
*
7501 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* *
7566 ATGAACTTTCTCTGGAAATGTTGATCCATCAAGTGATGAATTCAAGCA
66 ATGAACTTTCTCTGGAAATGATGATCCATCAAATGATGAATTCAAGCA
7614 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
*
7679 ATGAACTTTCTCTGGTAATGATGATCCATCAAATGATGAATT
66 ATGAACTTTCTCTGGAAATGATGATCCATCAAATGATGAATT
7721 TGAATCTTTG
Statistics
Matches: 723, Mismatches: 62, Indels: 4
0.92 0.08 0.01
Matches are distributed among these distances:
113 560 0.77
114 135 0.19
115 28 0.04
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.38
Consensus pattern (113 bp):
AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
ATGAACTTTCTCTGGAAATGATGATCCATCAAATGATGAATTCAAGCA
Found at i:8356 original size:52 final size:52
Alignment explanation
Indices: 8278--9048 Score: 1355
Period size: 52 Copynumber: 14.7 Consensus size: 52
8268 CACTTCTTCG
*
8278 GATCAAATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCTC-ATCA
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTC-CAATCA
*
8330 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAATCA
8382 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAATCA
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAATCA
* * *
8434 GATCAGATAACTCAAAGAACACTTCCAGAAGATACTATGTTCTGTTCAACCA
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAATCA
8486 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAATCA
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAATCA
8538 GATCAGATAACTCAAAGAAACACTTCCAGAAGATGCTATGTTCTGTCCAATCA
1 GATCAGATAACTCAAAG-AACACTTCCAGAAGATGCTATGTTCTGTCCAATCA
8591 GATCAGATAACTCAAAGAAACACTTCCAGAAGATGCTATGTTCTGTCCAATCA
1 GATCAGATAACTCAAAG-AACACTTCCAGAAGATGCTATGTTCTGTCCAATCA
*
8644 GATCAGATAACTCAAAGAACACTTCCAGAAGGTGCTATGTTCTGTCCAATCA
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAATCA
* *
8696 GATCAGATAACTCAAAGAAACACTTCCAGAAGATGCTATGTTCTGTTCAACCA
1 GATCAGATAACTCAAAG-AACACTTCCAGAAGATGCTATGTTCTGTCCAATCA
* *
8749 GATCAGATAACTCAAAGAAACACTTCCAGAAGATGCTATGTTCTGTTCAACCA
1 GATCAGATAACTCAAAG-AACACTTCCAGAAGATGCTATGTTCTGTCCAATCA
*
8802 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTTTCTGTCCAATCA
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAATCA
* *
8854 GATCAGATAACTCAAAGAAACACTTCCAGAAGATGCTATGTTCTGTTCAACCA
1 GATCAGATAACTCAAAG-AACACTTCCAGAAGATGCTATGTTCTGTCCAATCA
8907 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAATCA
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAATCA
8959 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAATCA
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAATCA
*
9011 GATCAGATAACTCAAAGAAAACTTCCAGAAGATGCTAT
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
9049 TGAGCACATA
Statistics
Matches: 693, Mismatches: 22, Indels: 8
0.96 0.03 0.01
Matches are distributed among these distances:
51 1 0.00
52 436 0.63
53 256 0.37
ACGTcount: A:0.37, C:0.23, G:0.15, T:0.25
Consensus pattern (52 bp):
GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAATCA
Found at i:8665 original size:105 final size:104
Alignment explanation
Indices: 8278--9048 Score: 1364
Period size: 105 Copynumber: 7.4 Consensus size: 104
8268 CACTTCTTCG
*
8278 GATCAAATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCTC-ATCAGATCAGATAACT
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTC-CAATCAGATCAGATAACT
8342 CAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
65 CAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
8382 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAATCAGATCAGATAACTC
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAATCAGATCAGATAACTC
* *
8447 AAAGAACACTTCCAGAAGATACTATGTTCTGTTCAACCA
66 AAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
8486 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAATCAGATCAGATAACTC
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAATCAGATCAGATAACTC
*
8551 AAAGAAACACTTCCAGAAGATGCTATGTTCTGTCCAATCA
66 AAAG-AACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
8591 GATCAGATAACTCAAAGAAACACTTCCAGAAGATGCTATGTTCTGTCCAATCAGATCAGATAACT
1 GATCAGATAACTCAAAG-AACACTTCCAGAAGATGCTATGTTCTGTCCAATCAGATCAGATAACT
* *
8656 CAAAGAACACTTCCAGAAGGTGCTATGTTCTGTCCAATCA
65 CAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
* *
8696 GATCAGATAACTCAAAGAAACACTTCCAGAAGATGCTATGTTCTGTTCAACCAGATCAGATAACT
1 GATCAGATAACTCAAAG-AACACTTCCAGAAGATGCTATGTTCTGTCCAATCAGATCAGATAACT
*
8761 CAAAGAAACACTTCCAGAAGATGCTATGTTCTGTTCAACCA
65 CAAAG-AACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
*
8802 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTTTCTGTCCAATCAGATCAGATAACTC
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAATCAGATCAGATAACTC
*
8867 AAAGAAACACTTCCAGAAGATGCTATGTTCTGTTCAACCA
66 AAAG-AACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
8907 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAATCAGATCAGATAACTC
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAATCAGATCAGATAACTC
*
8972 AAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAATCA
66 AAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
*
9011 GATCAGATAACTCAAAGAAAACTTCCAGAAGATGCTAT
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
9049 TGAGCACATA
Statistics
Matches: 644, Mismatches: 19, Indels: 8
0.96 0.03 0.01
Matches are distributed among these distances:
103 1 0.00
104 238 0.37
105 304 0.47
106 101 0.16
ACGTcount: A:0.37, C:0.23, G:0.15, T:0.25
Consensus pattern (104 bp):
GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAATCAGATCAGATAACTC
AAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
Found at i:8687 original size:158 final size:157
Alignment explanation
Indices: 8278--9048 Score: 1377
Period size: 158 Copynumber: 4.9 Consensus size: 157
8268 CACTTCTTCG
*
8278 GATCAAATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCTC-ATCAGATCAGATAACT
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTC-CAATCAGATCAGATAACT
*
8342 CAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCAGATCAGATAACTCAAAG-AACACTT
65 CAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAATCAGATCAGATAACTCAAAGAAACACTT
*
8406 CCAGAAGATGCTATGTTCTGTCCAATCA
130 CCAGAAGATGCTATGTTCTGTCCAACCA
* * *
8434 GATCAGATAACTCAAAGAACACTTCCAGAAGATACTATGTTCTGTTCAACCAGATCAGATAACTC
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAATCAGATCAGATAACTC
8499 AAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAATCAGATCAGATAACTCAAAGAAACACTTC
66 AAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAATCAGATCAGATAACTCAAAGAAACACTTC
*
8564 CAGAAGATGCTATGTTCTGTCCAATCA
131 CAGAAGATGCTATGTTCTGTCCAACCA
8591 GATCAGATAACTCAAAGAAACACTTCCAGAAGATGCTATGTTCTGTCCAATCAGATCAGATAACT
1 GATCAGATAACTCAAAG-AACACTTCCAGAAGATGCTATGTTCTGTCCAATCAGATCAGATAACT
*
8656 CAAAGAACACTTCCAGAAGGTGCTATGTTCTGTCCAATCAGATCAGATAACTCAAAGAAACACTT
65 CAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAATCAGATCAGATAACTCAAAGAAACACTT
*
8721 CCAGAAGATGCTATGTTCTGTTCAACCA
130 CCAGAAGATGCTATGTTCTGTCCAACCA
* *
8749 GATCAGATAACTCAAAGAAACACTTCCAGAAGATGCTATGTTCTGTTCAACCAGATCAGATAACT
1 GATCAGATAACTCAAAG-AACACTTCCAGAAGATGCTATGTTCTGTCCAATCAGATCAGATAACT
*
8814 CAAAGAACACTTCCAGAAGATGCTATTTTCTGTCCAATCAGATCAGATAACTCAAAGAAACACTT
65 CAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAATCAGATCAGATAACTCAAAGAAACACTT
*
8879 CCAGAAGATGCTATGTTCTGTTCAACCA
130 CCAGAAGATGCTATGTTCTGTCCAACCA
8907 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAATCAGATCAGATAACTC
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAATCAGATCAGATAACTC
8972 AAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAATCAGATCAGATAACTCAAAGAAA-ACTTC
66 AAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAATCAGATCAGATAACTCAAAGAAACACTTC
9036 CAGAAGATGCTAT
131 CAGAAGATGCTAT
9049 TGAGCACATA
Statistics
Matches: 594, Mismatches: 18, Indels: 6
0.96 0.03 0.01
Matches are distributed among these distances:
155 1 0.00
156 132 0.22
157 156 0.26
158 305 0.51
ACGTcount: A:0.37, C:0.23, G:0.15, T:0.25
Consensus pattern (157 bp):
GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAATCAGATCAGATAACTC
AAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAATCAGATCAGATAACTCAAAGAAACACTTC
CAGAAGATGCTATGTTCTGTCCAACCA
Found at i:9640 original size:18 final size:16
Alignment explanation
Indices: 9617--9661 Score: 54
Period size: 18 Copynumber: 2.7 Consensus size: 16
9607 AATAGAAAAG
*
9617 AATAAATTGAATTTCCAA
1 AATAAATTGAATCT-C-A
*
9635 AATAAATTAAATCTCA
1 AATAAATTGAATCTCA
9651 AATAAATTGAA
1 AATAAATTGAA
9662 CTTGAAATAG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 11 0.46
17 1 0.04
18 12 0.50
ACGTcount: A:0.56, C:0.09, G:0.04, T:0.31
Consensus pattern (16 bp):
AATAAATTGAATCTCA
Found at i:9995 original size:1 final size:1
Alignment explanation
Indices: 9989--10031 Score: 59
Period size: 1 Copynumber: 43.0 Consensus size: 1
9979 CCTTGACCCC
* * *
9989 TTTTTTTTCTTTTTCTTCTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
10032 CAAGCATAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
1 36 1.00
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (1 bp):
T
Found at i:10002 original size:9 final size:9
Alignment explanation
Indices: 9988--10032 Score: 65
Period size: 9 Copynumber: 5.1 Consensus size: 9
9978 ACCTTGACCC
9988 CTTTTTTTT
1 CTTTTTTTT
*
9997 CTTTTTCTT
1 CTTTTTTTT
10006 CTTTTTTTT
1 CTTTTTTTT
10015 -TTTTTTTT
1 CTTTTTTTT
*
10023 TTTTTTTTT
1 CTTTTTTTT
10032 C
1 C
10033 AAGCATAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
8 8 0.25
9 24 0.75
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (9 bp):
CTTTTTTTT
Found at i:22685 original size:3 final size:3
Alignment explanation
Indices: 22677--22858 Score: 256
Period size: 3 Copynumber: 59.7 Consensus size: 3
22667 TTATTTATTA
*
22677 AAT AAT AAT AAT ATAT AAT AAT AAT ATAT AAT ATT AAT AAT AAT AAT
1 AAT AAT AAT AAT A-AT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT
* **
22724 AAAT ACT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT GCT
1 -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
22770 AAT AAT AAT AAT AAT ACT AAT AAT AAT AAT ATT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * *
22818 ATT AAT AAT GAT AAT AAT AAT ATT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
22859 AATGGATAAA
Statistics
Matches: 158, Mismatches: 18, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
3 149 0.94
4 9 0.06
ACGTcount: A:0.62, C:0.02, G:0.01, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:31880 original size:3 final size:3
Alignment explanation
Indices: 31872--31908 Score: 53
Period size: 3 Copynumber: 13.3 Consensus size: 3
31862 GCTTTAGATC
31872 TCT TCT TCT TCT T-T TCT TCT T-T TCT TCT T-T TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
31909 GCCTTTCTGA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
2 6 0.19
3 25 0.81
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (3 bp):
TCT
Found at i:31890 original size:8 final size:8
Alignment explanation
Indices: 31872--31908 Score: 65
Period size: 8 Copynumber: 4.5 Consensus size: 8
31862 GCTTTAGATC
31872 TCTTCTTCT
1 TCTT-TTCT
31881 TCTTTTCT
1 TCTTTTCT
31889 TCTTTTCT
1 TCTTTTCT
31897 TCTTTTCT
1 TCTTTTCT
31905 TCTT
1 TCTT
31909 GCCTTTCTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
8 24 0.86
9 4 0.14
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (8 bp):
TCTTTTCT
Found at i:31890 original size:11 final size:12
Alignment explanation
Indices: 31872--31908 Score: 53
Period size: 11 Copynumber: 3.3 Consensus size: 12
31862 GCTTTAGATC
31872 TCTTCTTCTTCT
1 TCTTCTTCTTCT
31884 T-TTCTTCTT-T
1 TCTTCTTCTTCT
31894 TCTTCTT-TTCT
1 TCTTCTTCTTCT
31905 TCTT
1 TCTT
31909 GCCTTTCTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
10 4 0.17
11 18 0.78
12 1 0.04
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (12 bp):
TCTTCTTCTTCT
Found at i:32812 original size:17 final size:18
Alignment explanation
Indices: 32790--32830 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
32780 AAAAAATATT
32790 AGTAAAAT-ATTAAATAA
1 AGTAAAATGATTAAATAA
*
32807 AGTAAAATGTTTAAATAA
1 AGTAAAATGATTAAATAA
*
32825 ATTAAA
1 AGTAAA
32831 TAAAAATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.61, C:0.00, G:0.07, T:0.32
Consensus pattern (18 bp):
AGTAAAATGATTAAATAA
Found at i:38454 original size:2 final size:2
Alignment explanation
Indices: 38447--38481 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
38437 TGTAACAAAC
38447 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
38482 AAAGAATAAA
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:39276 original size:24 final size:23
Alignment explanation
Indices: 39247--39294 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
39237 TTTTGGTTCG
* *
39247 TTTTAATACCTAAACTTTCAATTT
1 TTTTAA-AACTAAACTTTAAATTT
*
39271 TTTTAAAACTTAACTTTAAATTT
1 TTTTAAAACTAAACTTTAAATTT
39294 T
1 T
39295 GAACATGGTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 15 0.71
24 6 0.29
ACGTcount: A:0.35, C:0.12, G:0.00, T:0.52
Consensus pattern (23 bp):
TTTTAAAACTAAACTTTAAATTT
Found at i:39870 original size:23 final size:23
Alignment explanation
Indices: 39851--39908 Score: 89
Period size: 23 Copynumber: 2.5 Consensus size: 23
39841 ACATGTCTTC
*
39851 TAGATTTACGACCGTCTGTCTCT
1 TAGATTTACAACCGTCTGTCTCT
*
39874 TAGATTTCCAACCGTCTGTCTCT
1 TAGATTTACAACCGTCTGTCTCT
*
39897 TAGATTTCCAAC
1 TAGATTTACAAC
39909 GGTTCTTGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.21, C:0.28, G:0.14, T:0.38
Consensus pattern (23 bp):
TAGATTTACAACCGTCTGTCTCT
Found at i:42080 original size:30 final size:30
Alignment explanation
Indices: 42044--42105 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
42034 GCTAAAGATG
42044 TATTTTTTCAATCAATTTATTCTATCTAAT
1 TATTTTTTCAATCAATTTATTCTATCTAAT
42074 TATTTTTTCAATCAATTTATTCTATCTAAT
1 TATTTTTTCAATCAATTTATTCTATCTAAT
42104 TA
1 TA
42106 GAAATGACCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.31, C:0.13, G:0.00, T:0.56
Consensus pattern (30 bp):
TATTTTTTCAATCAATTTATTCTATCTAAT
Found at i:43696 original size:21 final size:23
Alignment explanation
Indices: 43649--43696 Score: 55
Period size: 25 Copynumber: 2.1 Consensus size: 23
43639 TTATATATAT
43649 TTAAAAAAATCAAAAGCCTTTGAAC
1 TTAAAAAAATCAAAA--CTTTGAAC
*
43674 TTAAAAAAAT-AAAA-TTTGGAC
1 TTAAAAAAATCAAAACTTTGAAC
43695 TT
1 TT
43697 TGAACTTGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
21 8 0.36
24 4 0.18
25 10 0.45
ACGTcount: A:0.52, C:0.10, G:0.08, T:0.29
Consensus pattern (23 bp):
TTAAAAAAATCAAAACTTTGAAC
Found at i:44297 original size:25 final size:26
Alignment explanation
Indices: 44258--44307 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 26
44248 TGGTATTTAA
44258 TCAAAAAATAATTTGATATAAATATT
1 TCAAAAAATAATTTGATATAAATATT
*
44284 TCAAAAAA-ATTTTGATATAAATAT
1 TCAAAAAATAATTTGATATAAATAT
44308 GAAATTTAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 15 0.65
26 8 0.35
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.38
Consensus pattern (26 bp):
TCAAAAAATAATTTGATATAAATATT
Found at i:45561 original size:21 final size:21
Alignment explanation
Indices: 45535--45584 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
45525 GGAGCGTGGG
45535 GGGAATCGGTACCCCCTCATA
1 GGGAATCGGTACCCCCTCATA
45556 GGGAATCGGTACCCCCTCATA
1 GGGAATCGGTACCCCCTCATA
45577 GGGAATCG
1 GGGAATCG
45585 ATTCCCTAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.24, C:0.30, G:0.28, T:0.18
Consensus pattern (21 bp):
GGGAATCGGTACCCCCTCATA
Found at i:45996 original size:13 final size:13
Alignment explanation
Indices: 45978--46004 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
45968 TAACACTTCT
45978 CCCCTTTAAAACA
1 CCCCTTTAAAACA
45991 CCCCTTTAAAACA
1 CCCCTTTAAAACA
46004 C
1 C
46005 TTTAACATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.41, G:0.00, T:0.22
Consensus pattern (13 bp):
CCCCTTTAAAACA
Found at i:47509 original size:10 final size:10
Alignment explanation
Indices: 47491--47527 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
47481 CATCATCCAT
47491 AAATCCAAAC
1 AAATCCAAAC
*
47501 AAATTCAAAC
1 AAATCCAAAC
47511 --ATCCAAAC
1 AAATCCAAAC
47519 AAATCCAAA
1 AAATCCAAA
47528 GTCACAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
8 7 0.30
10 16 0.70
ACGTcount: A:0.59, C:0.27, G:0.00, T:0.14
Consensus pattern (10 bp):
AAATCCAAAC
Found at i:47535 original size:18 final size:18
Alignment explanation
Indices: 47493--47527 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
47483 TCATCCATAA
*
47493 ATCCAAACAAATTCAAAC
1 ATCCAAACAAATCCAAAC
47511 ATCCAAACAAATCCAAA
1 ATCCAAACAAATCCAAA
47528 GTCACAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.57, C:0.29, G:0.00, T:0.14
Consensus pattern (18 bp):
ATCCAAACAAATCCAAAC
Done.