Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001878.1 Hibiscus syriacus cultivar Beakdansim tig00003814_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: 79457
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:676 original size:105 final size:105
Alignment explanation
Indices: 495--1481 Score: 1262
Period size: 105 Copynumber: 9.5 Consensus size: 105
485 GCAGTGTTCC
* * * * **
495 GAGTCCAATATCCTCCG-TCATGAAGTTGAAATTAGCTCTGGAATCAGGAAATTGTTTGTTGACA
1 GAGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAA-TGTTTGTTGACA
* * *
559 ACCAGC-GTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
64 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * ** *
600 GAGTCCAATATCCTTTGTTTGTGAAG-TGAAATTGGCTCCAAAATTGAGAAATGTTTGTTGACAA
1 GAGTCCAATATCCTTCG-CTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATGTTTGTTGACAA
*
664 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTC
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
705 GAGTCCAATATCCTTCACTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTG-TGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAA-TGTTTGTTGACAA
*
769 ACAGCGGTCCCTTCGTCGTGAAG-TGAACTTGCG-TGTCTG
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * * *
808 GAGTCCAGTATCATTCGTTGTGAAGTTGAAATTGGCT-GGAAATTGAG-AA-G-TTGTTGATAAC
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATGTTTGTTGACAAC
* *
869 CAACGGTCCCTTCGTCGTGAAGTTGAA-TTGCGTTGTATG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
908 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTTACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAA-TGTTTGTTGACAA
973 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
1014 GAGTCCAATATCTTTCGAC-GTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACA
1 GAGTCCAATATCCTTCG-CTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAA-TGTTTGTTGACA
* *
1078 ACCAGC-GTCCCTTCGTCGTGAAGTTGAACTTGCGTTATCTC
64 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
1119 GAGTTCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGT-TGTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATGT-TTGTTGACAA
* *
1183 CCAGCGGTCCCTTCGTCGTGAAGTTGAGC-TGTGTTGTCTG
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
1223 GAGT-CATATATCCTTCGTTGTGAA-TTGAAATTGGCTCTGAAATTGAGAAGTTATTTGTTGACA
1 GAGTCCA-ATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAA-ATGTTTGTTGACA
1286 A-CAGCGGTCCC-TCGTCGTGAAGTTGAACTTGCGTTGTCTG
64 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
1326 GAGTTCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTT-TTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAA-ATGTTTGTTGACAA
* * * *
1390 CCAGTGGT-CATTCGTCATGAAGTTGAACTTGCGTGGTTGTCTT
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGC---GTTGTCTG
* *
1433 GAGTCCAA-ATCCTTCGCTCTGAAGTTGAAATTGGCTCTGAATTTGGGAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAA
1482 GTTGGCATAT
Statistics
Matches: 787, Mismatches: 66, Indels: 57
0.86 0.07 0.06
Matches are distributed among these distances:
98 3 0.00
99 32 0.04
100 44 0.06
101 10 0.01
102 26 0.03
103 113 0.14
104 150 0.19
105 267 0.34
106 127 0.16
107 15 0.02
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.33
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATGTTTGTTGACAAC
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:2292 original size:23 final size:22
Alignment explanation
Indices: 2256--2305 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 22
2246 AATATAATGT
*
2256 TAATAAATAAATATAAATAAAA
1 TAATAAAAAAATATAAATAAAA
*
2278 TAATAAAAAATATATATATAAAA
1 TAATAAAAAA-ATATAAATAAAA
*
2301 AAATA
1 TAATA
2306 TATGTATAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
22 9 0.38
23 15 0.62
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (22 bp):
TAATAAAAAAATATAAATAAAA
Found at i:2321 original size:16 final size:16
Alignment explanation
Indices: 2282--2314 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
2272 ATAAAATAAT
2282 AAAAAATATATATATA
1 AAAAAATATATATATA
*
2298 AAAAAATATATGTATA
1 AAAAAATATATATATA
2314 A
1 A
2315 TATAATAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (16 bp):
AAAAAATATATATATA
Found at i:2360 original size:58 final size:56
Alignment explanation
Indices: 2243--2360 Score: 134
Period size: 58 Copynumber: 2.1 Consensus size: 56
2233 CAAAGAAACT
* *
2243 AAAAATATAATGTTAATAAATAAATATAAATAAAATAATAAAAAATATATATATAA
1 AAAAATATAATGTTAATAAATAAATATAAATAAAATAATAAAAAATAAATAAATAA
* *
2299 AAAAATAT-ATGTATAATATAATAAAATACTAAAT--AGTAATAAAAAAATAAATAAATGA
1 AAAAATATAATGT-TAATA-AAT-AAATA-TAAATAAAATAAT-AAAAAATAAATAAATAA
2357 AAAA
1 AAAA
2361 TAAATATACA
Statistics
Matches: 53, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
55 4 0.08
56 13 0.25
57 8 0.15
58 23 0.43
59 5 0.09
ACGTcount: A:0.68, C:0.01, G:0.03, T:0.28
Consensus pattern (56 bp):
AAAAATATAATGTTAATAAATAAATATAAATAAAATAATAAAAAATAAATAAATAA
Found at i:2578 original size:2 final size:2
Alignment explanation
Indices: 2566--2606 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
2556 AAATAAATAA
2566 AT AT A- AT AT AT AT AT A- 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
2606 A
1 A
2607 CAATAATAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.05
2 35 0.95
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:3105 original size:36 final size:37
Alignment explanation
Indices: 3065--3147 Score: 105
Period size: 37 Copynumber: 2.3 Consensus size: 37
3055 GGATCCTATC
**
3065 TTAGGAGTTTAAATAAT-AGTAAACTCTATCATATTT
1 TTAGGAGTTTAAATAATAACAAAACTCTATCATATTT
* ** *
3101 TTAGGAGTTTGAATCCTAACAAAATTCTATCATATTT
1 TTAGGAGTTTAAATAATAACAAAACTCTATCATATTT
3138 TTAGGAGTTT
1 TTAGGAGTTT
3148 GAATCCTAGT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
36 14 0.35
37 26 0.65
ACGTcount: A:0.35, C:0.10, G:0.13, T:0.42
Consensus pattern (37 bp):
TTAGGAGTTTAAATAATAACAAAACTCTATCATATTT
Found at i:15781 original size:85 final size:85
Alignment explanation
Indices: 15638--15812 Score: 341
Period size: 85 Copynumber: 2.1 Consensus size: 85
15628 GGTTACTGTT
15638 CTTACCTCATCCTAACCTAAGTTTTAAGGGATTACTCCTTTTAACACTGAGAGTTACCTTTCATA
1 CTTACCTCATCCTAACCTAAGTTTTAAGGGATTACTCCTTTTAACACTGAGAGTTACCTTTCATA
15703 TCCATGTTTCTAGTTATGGG
66 TCCATGTTTCTAGTTATGGG
*
15723 CTTACCTCATCCTAACCTAAGTTTTAAGGGATTACTCCTTTTAACACTGAGAGTTACCTTTCGTA
1 CTTACCTCATCCTAACCTAAGTTTTAAGGGATTACTCCTTTTAACACTGAGAGTTACCTTTCATA
15788 TCCATGTTTCTAGTTATGGG
66 TCCATGTTTCTAGTTATGGG
15808 CTTAC
1 CTTAC
15813 ATGGCAGCAC
Statistics
Matches: 89, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
85 89 1.00
ACGTcount: A:0.24, C:0.23, G:0.14, T:0.39
Consensus pattern (85 bp):
CTTACCTCATCCTAACCTAAGTTTTAAGGGATTACTCCTTTTAACACTGAGAGTTACCTTTCATA
TCCATGTTTCTAGTTATGGG
Found at i:18495 original size:20 final size:20
Alignment explanation
Indices: 18466--18528 Score: 90
Period size: 20 Copynumber: 3.1 Consensus size: 20
18456 CTTAGGCCTA
* *
18466 AAGGGCGTAGGAGTCAACTT
1 AAGGGCGTAGGAGCCAACCT
*
18486 AAGGGAGTAGGAGCCAACCT
1 AAGGGCGTAGGAGCCAACCT
*
18506 AAGGGCGTAGGAGCTAACCT
1 AAGGGCGTAGGAGCCAACCT
18526 AAG
1 AAG
18529 TGAGCACCTT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.33, C:0.17, G:0.35, T:0.14
Consensus pattern (20 bp):
AAGGGCGTAGGAGCCAACCT
Found at i:22374 original size:43 final size:43
Alignment explanation
Indices: 22323--22406 Score: 168
Period size: 43 Copynumber: 2.0 Consensus size: 43
22313 TGCAAAATGA
22323 CCGCCACCATGAGAACCGTGGGCCAAGTGGTGAGCCCCCATGG
1 CCGCCACCATGAGAACCGTGGGCCAAGTGGTGAGCCCCCATGG
22366 CCGCCACCATGAGAACCGTGGGCCAAGTGGTGAGCCCCCAT
1 CCGCCACCATGAGAACCGTGGGCCAAGTGGTGAGCCCCCAT
22407 TGCAGCTGAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.21, C:0.36, G:0.31, T:0.12
Consensus pattern (43 bp):
CCGCCACCATGAGAACCGTGGGCCAAGTGGTGAGCCCCCATGG
Found at i:23637 original size:30 final size:30
Alignment explanation
Indices: 23601--23657 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
23591 ACAAAAATTA
23601 TAATTTGAACATTTATCTTTCAATTAAGTC
1 TAATTTGAACATTTATCTTTCAATTAAGTC
* * *
23631 TAATTTGAATATTTATTTTTTAATTAA
1 TAATTTGAACATTTATCTTTCAATTAA
23658 ACTTTTTATT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.35, C:0.07, G:0.05, T:0.53
Consensus pattern (30 bp):
TAATTTGAACATTTATCTTTCAATTAAGTC
Found at i:23703 original size:18 final size:17
Alignment explanation
Indices: 23682--23721 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
23672 GTTTAGTGAG
*
23682 AAATATTAATTTAATTTT
1 AAATAATAA-TTAATTTT
23700 AAATTAATAATTAATTTT
1 AAA-TAATAATTAATTTT
23718 AAAT
1 AAAT
23722 TTGGCATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 1 0.05
18 14 0.70
19 5 0.25
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
AAATAATAATTAATTTT
Found at i:23980 original size:3 final size:3
Alignment explanation
Indices: 23972--24186 Score: 54
Period size: 3 Copynumber: 72.0 Consensus size: 3
23962 AGTTAGTATG
* * * * * * *
23972 GTT GTT GTT ATT GTT GAT GCT ATT GTT ATT GAT GTT GTT GTT CTT GTT
1 GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT
** * * ** * * * ** *
24020 ACT ATT GTT GCT ACT ATT GTT GTT GAT GTT GTT GTT CTT GTT ACT ATT
1 GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT
** * * ** * * * **
24068 -TT GTT ACT ATT GTT GTT GTT GTT GTT CTT GTT ACT ATT GCT GCT ACT
1 GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT
* ** * * * ** *
24115 GTT GTT GTT GTT GTT GTT CTT GTT ACT ATT GCT GCT ACT ATT GTT GTT
1 GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT
* *
24163 GTT GTT GTT CTT GTT GTT CTT GTT
1 GTT GTT GTT GTT GTT GTT GTT GTT
24187 ACTATTGCTG
Statistics
Matches: 155, Mismatches: 56, Indels: 2
0.73 0.26 0.01
Matches are distributed among these distances:
2 2 0.01
3 153 0.99
ACGTcount: A:0.10, C:0.09, G:0.22, T:0.59
Consensus pattern (3 bp):
GTT
Found at i:24032 original size:39 final size:39
Alignment explanation
Indices: 23989--24223 Score: 265
Period size: 39 Copynumber: 5.7 Consensus size: 39
23979 TTATTGTTGA
* * * *
23989 TGCTATTGTTATTGATGTTGTTGTTCTTGTTACTATTGT
1 TGCTACTGTTGTTGTTGTTGTTGTTCTTGTTACTATTGC
* *
24028 TGCTACTATTGTTGTTGATGTTGTTGTTCTTGTTACTATT-T
1 TGCTAC---TGTTGTTGTTGTTGTTGTTCTTGTTACTATTGC
* *
24069 TGTTACTATTGTTGTTGTTGTTGTTCTTGTTACTATTGC
1 TGCTACTGTTGTTGTTGTTGTTGTTCTTGTTACTATTGC
24108 TGCTACTGTTGTTGTTGTTGTTGTTCTTGTTACTATTGC
1 TGCTACTGTTGTTGTTGTTGTTGTTCTTGTTACTATTGC
24147 TGCTACTATTGTTGTTGTTGTTGTTCTTGTTGTTCTTGTTACTATTGC
1 TGCTAC------TGTTGTTGTTG---TTGTTGTTCTTGTTACTATTGC
*
24195 TGCTACTATTGTTGTTGTTGTTGTCTCTT
1 TGCTACTGTTGTTGTTGTTGTTGT-TCTT
24224 AAATTATAAT
Statistics
Matches: 173, Mismatches: 9, Indels: 27
0.83 0.04 0.13
Matches are distributed among these distances:
38 29 0.17
39 55 0.32
40 4 0.02
41 6 0.03
42 40 0.23
45 11 0.06
48 28 0.16
ACGTcount: A:0.10, C:0.11, G:0.21, T:0.58
Consensus pattern (39 bp):
TGCTACTGTTGTTGTTGTTGTTGTTCTTGTTACTATTGC
Found at i:24073 original size:11 final size:12
Alignment explanation
Indices: 24057--24210 Score: 58
Period size: 12 Copynumber: 12.4 Consensus size: 12
24047 GTTGTTGTTC
24057 TTGTTACTATT-
1 TTGTTACTATTG
24068 TTGTTACTATTG
1 TTGTTACTATTG
** *
24080 TTGTTGTTGTTG
1 TTGTTACTATTG
24092 TTCTTGTTACTATTG
1 ---TTGTTACTATTG
* * *
24107 CTGCTACTGTTG
1 TTGTTACTATTG
** *
24119 TTGTTGTTGTTG
1 TTGTTACTATTG
24131 TTCTTGTTACTATTG
1 ---TTGTTACTATTG
* *
24146 CTGCTACTATTG
1 TTGTTACTATTG
** *
24158 TTGTTGTTGTTG
1 TTGTTACTATTG
* ** * *
24170 TTCTTGTTGTTC
1 TTGTTACTATTG
24182 TTGTTACTATTG
1 TTGTTACTATTG
* *
24194 CTGCTACTATTG
1 TTGTTACTATTG
24206 TTGTT
1 TTGTT
24211 GTTGTTGTCT
Statistics
Matches: 102, Mismatches: 34, Indels: 13
0.68 0.23 0.09
Matches are distributed among these distances:
11 11 0.11
12 73 0.72
15 18 0.18
ACGTcount: A:0.10, C:0.12, G:0.20, T:0.58
Consensus pattern (12 bp):
TTGTTACTATTG
Found at i:24138 original size:48 final size:48
Alignment explanation
Indices: 24077--24223 Score: 213
Period size: 48 Copynumber: 3.2 Consensus size: 48
24067 TTTGTTACTA
*
24077 TTGTTGTTGTTGTTGTTCTTGTTACTATTGCTGCTAC------TGTTG
1 TTGTTGTTCTTGTTGTTCTTGTTACTATTGCTGCTACTATTGTTGTTG
24119 TTGTTG---TTGTTGTTCTTGTTACTATTGCTGCTACTATTGTTGTTG
1 TTGTTGTTCTTGTTGTTCTTGTTACTATTGCTGCTACTATTGTTGTTG
24164 TTGTTGTTCTTGTTGTTCTTGTTACTATTGCTGCTACTATTGTTGTTG
1 TTGTTGTTCTTGTTGTTCTTGTTACTATTGCTGCTACTATTGTTGTTG
24212 TTGTTGTCTCTT
1 TTGTTGT-TCTT
24224 AAATTATAAT
Statistics
Matches: 95, Mismatches: 0, Indels: 13
0.88 0.00 0.12
Matches are distributed among these distances:
39 28 0.29
42 6 0.06
45 11 0.12
48 46 0.48
49 4 0.04
ACGTcount: A:0.07, C:0.12, G:0.22, T:0.59
Consensus pattern (48 bp):
TTGTTGTTCTTGTTGTTCTTGTTACTATTGCTGCTACTATTGTTGTTG
Found at i:26498 original size:21 final size:20
Alignment explanation
Indices: 26474--26576 Score: 98
Period size: 21 Copynumber: 5.0 Consensus size: 20
26464 GCAAATTCGC
26474 GTTGCATTTCGCGTTGCGAT
1 GTTGCATTTCGCGTTGCGAT
* **
26494 AGTTGAAAATCGCGTTGCGAT
1 -GTTGCATTTCGCGTTGCGAT
* *
26515 TTTCCATTTCGCGTTGCGAT
1 GTTGCATTTCGCGTTGCGAT
* **
26535 AGTTGAAAATCGCGTTGCGAT
1 -GTTGCATTTCGCGTTGCGAT
* *
26556 TTTCCATTTCGCGTTGCGAT
1 GTTGCATTTCGCGTTGCGAT
26576 G
1 G
26577 GTCTACAGTT
Statistics
Matches: 62, Mismatches: 19, Indels: 3
0.74 0.23 0.04
Matches are distributed among these distances:
20 30 0.48
21 32 0.52
ACGTcount: A:0.17, C:0.19, G:0.26, T:0.37
Consensus pattern (20 bp):
GTTGCATTTCGCGTTGCGAT
Found at i:26506 original size:41 final size:39
Alignment explanation
Indices: 26478--26575 Score: 142
Period size: 41 Copynumber: 2.4 Consensus size: 39
26468 ATTCGCGTTG
*
26478 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCATTGCG--TTTC
*
26519 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCATTGCG--TTTC
26560 CATTTCGCGTTGCGAT
1 CATTTCGCGTTGCGAT
26576 GGTCTACAGT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 57 1.00
ACGTcount: A:0.18, C:0.20, G:0.24, T:0.37
Consensus pattern (39 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGCATTGCGTTTC
Found at i:26528 original size:20 final size:20
Alignment explanation
Indices: 26503--26628 Score: 96
Period size: 20 Copynumber: 6.2 Consensus size: 20
26493 TAGTTGAAAA
*
26503 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCAAT
* ** *
26523 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGAT-TTTCCAAT
*
26544 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCAAT
* * *
26564 TCGCGTTGCGATGGTCTACAGT
1 TCGCGTTGCGAT--TTTCCAAT
26586 T-GTCGTTGCGATTTTCCAAAT
1 TCG-CGTTGCGATTTTCC-AAT
26607 T--CGTTGCGATTTTCCAAAT
1 TCGCGTTGCGATTTTCC-AAT
26626 TCG
1 TCG
26629 TGCGAATACT
Statistics
Matches: 83, Mismatches: 16, Indels: 13
0.74 0.14 0.12
Matches are distributed among these distances:
19 19 0.23
20 30 0.36
21 19 0.23
22 15 0.18
ACGTcount: A:0.17, C:0.21, G:0.23, T:0.39
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCAAT
Found at i:26612 original size:19 final size:19
Alignment explanation
Indices: 26588--26633 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
26578 TCTACAGTTG
26588 TCGTTGCGATTTTCCAAAT
1 TCGTTGCGATTTTCCAAAT
26607 TCGTTGCGATTTTCCAAAT
1 TCGTTGCGATTTTCCAAAT
26626 TCG-TGCGA
1 TCGTTGCGA
26634 ATACTATCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 5 0.19
19 22 0.81
ACGTcount: A:0.20, C:0.22, G:0.20, T:0.39
Consensus pattern (19 bp):
TCGTTGCGATTTTCCAAAT
Found at i:26725 original size:19 final size:19
Alignment explanation
Indices: 26701--26788 Score: 104
Period size: 19 Copynumber: 4.5 Consensus size: 19
26691 CAACGAATTT
26701 TCGCAACGAATTTGGAAAA
1 TCGCAACGAATTTGGAAAA
* * **
26720 TCGCAACGACAACTGTAGACTA
1 TCGCAACG--AA-TTTGGAAAA
*
26742 TCGCAACTAATTTGGAAAA
1 TCGCAACGAATTTGGAAAA
26761 TCGCAACGAATTTGGAAAA
1 TCGCAACGAATTTGGAAAA
26780 TCGCAACGA
1 TCGCAACGA
26789 CAACTGTAGA
Statistics
Matches: 56, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
19 40 0.71
20 2 0.04
21 2 0.04
22 12 0.21
ACGTcount: A:0.40, C:0.20, G:0.19, T:0.20
Consensus pattern (19 bp):
TCGCAACGAATTTGGAAAA
Found at i:26826 original size:20 final size:20
Alignment explanation
Indices: 26754--26876 Score: 90
Period size: 20 Copynumber: 6.0 Consensus size: 20
26744 GCAACTAATT
*
26754 TGGAAAATCGCAA--CGAATT
1 TGGAAAATCGCAACGCGAA-A
*
26773 TGGAAAATCGCAACGAC-AAC
1 TGGAAAATCGCAACG-CGAAA
**
26793 TGTAGACCATCGCAACGCGAAA
1 TG--GAAAATCGCAACGCGAAA
* **
26815 AGGAAAATCGCAACGCGATT
1 TGGAAAATCGCAACGCGAAA
** *
26835 TTCAACTATCGCAACGCGAAA
1 TGGAA-AATCGCAACGCGAAA
26856 TGGAAAATCGCAACGCGAAA
1 TGGAAAATCGCAACGCGAAA
26876 T
1 T
26877 ACAACACGAA
Statistics
Matches: 79, Mismatches: 18, Indels: 13
0.72 0.16 0.12
Matches are distributed among these distances:
19 13 0.16
20 33 0.42
21 18 0.23
22 15 0.19
ACGTcount: A:0.41, C:0.23, G:0.21, T:0.15
Consensus pattern (20 bp):
TGGAAAATCGCAACGCGAAA
Found at i:30290 original size:3 final size:3
Alignment explanation
Indices: 30282--30329 Score: 57
Period size: 3 Copynumber: 17.0 Consensus size: 3
30272 TATTTGTTAG
* *
30282 TAT TAT TAT T-T TAT TAC TAT TAT CAT TAT TA- TAT TAT TAT TAT T-T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
30327 TAT
1 TAT
30330 AGTACGCATT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
2 6 0.16
3 32 0.84
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:30302 original size:11 final size:11
Alignment explanation
Indices: 30282--30329 Score: 60
Period size: 11 Copynumber: 4.3 Consensus size: 11
30272 TATTTGTTAG
30282 TATTATTATTT
1 TATTATTATTT
*
30293 TATTACTATTAT
1 TATTATTATT-T
* *
30305 CATTATTATAT
1 TATTATTATTT
30316 TATTATTATTT
1 TATTATTATTT
30327 TAT
1 TAT
30330 AGTACGCATT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
11 22 0.73
12 8 0.27
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (11 bp):
TATTATTATTT
Found at i:30311 original size:20 final size:20
Alignment explanation
Indices: 30286--30324 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
30276 TGTTAGTATT
*
30286 ATTATTTTATTACTATTATC
1 ATTATTATATTACTATTATC
*
30306 ATTATTATATTATTATTAT
1 ATTATTATATTACTATTAT
30325 TTTATAGTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (20 bp):
ATTATTATATTACTATTATC
Found at i:30322 original size:6 final size:6
Alignment explanation
Indices: 30213--30329 Score: 59
Period size: 6 Copynumber: 20.2 Consensus size: 6
30203 ATTTAATTTT
* * * *
30213 TTATT- TTATTA TTTTTA TTTTTA TT-TTCA TT-TCA TT-TTA TAATTA
1 TTATTA TTATTA TTATTA TTATTA TTATT-A TTATTA TTATTA TTATTA
* * * * * * *
30258 TTAGTA CTTGTCA TTATTTG TTAGTA TTATTA TT-TTA TTACTA TTATCA
1 TTATTA -TTATTA TTA-TTA TTATTA TTATTA TTATTA TTATTA TTATTA
30307 TTATTA -TATTA TTATTA TT-TTA T
1 TTATTA TTATTA TTATTA TTATTA T
30330 AGTACGCATT
Statistics
Matches: 86, Mismatches: 19, Indels: 14
0.72 0.16 0.12
Matches are distributed among these distances:
5 27 0.31
6 52 0.60
7 7 0.08
ACGTcount: A:0.26, C:0.05, G:0.03, T:0.65
Consensus pattern (6 bp):
TTATTA
Found at i:42774 original size:15 final size:15
Alignment explanation
Indices: 42756--42811 Score: 67
Period size: 15 Copynumber: 3.6 Consensus size: 15
42746 TAACCGGTTT
42756 CGGTTTTAAAAAAAC
1 CGGTTTTAAAAAAAC
*
42771 CGGTTTTTTTAAAAAAC
1 CGG--TTTTAAAAAAAC
*
42788 CGGTTATAAAAAAAC
1 CGGTTTTAAAAAAAC
*
42803 CGATTTTAA
1 CGGTTTTAA
42812 TATTCCAGAT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
15 20 0.59
17 14 0.41
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.32
Consensus pattern (15 bp):
CGGTTTTAAAAAAAC
Found at i:42784 original size:17 final size:17
Alignment explanation
Indices: 42759--42809 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
42749 CCGGTTTCGG
42759 TTTTAAAAAAACCGGTT
1 TTTTAAAAAAACCGGTT
*
42776 TTTTTAAAAAACCGG--
1 TTTTAAAAAAACCGGTT
* *
42791 TTATAAAAAAACCGATT
1 TTTTAAAAAAACCGGTT
42808 TT
1 TT
42810 AATATTCCAG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 12 0.43
17 16 0.57
ACGTcount: A:0.43, C:0.12, G:0.10, T:0.35
Consensus pattern (17 bp):
TTTTAAAAAAACCGGTT
Found at i:43208 original size:13 final size:13
Alignment explanation
Indices: 43187--43241 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
43177 AAGTTCGATA
*
43187 AATTTAAATACTT
1 AATTGAAATACTT
43200 AATTGAAATACTT
1 AATTGAAATACTT
* *
43213 AATT-AACTCAACAT
1 AATTGAAAT--ACTT
43227 AATTGAAATACTT
1 AATTGAAATACTT
43240 AA
1 AA
43242 ATACTTCCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.49, C:0.11, G:0.04, T:0.36
Consensus pattern (13 bp):
AATTGAAATACTT
Found at i:43323 original size:32 final size:33
Alignment explanation
Indices: 43227--43325 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
43217 AACTCAACAT
* * *
43227 AATTGAAATACTTAAATACTTCCAAGTTTGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
43260 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
43293 AATTCAAATACTTAAAAACTT-CAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
43325 A
1 A
43326 TTGAAACAAA
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 12 0.19
33 51 0.81
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.32
Consensus pattern (33 bp):
AATTCAAATACTTAAAAACTTCCAAGTTCGATA
Found at i:43344 original size:21 final size:21
Alignment explanation
Indices: 43320--43359 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
43310 ACTTCAAGTT
43320 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
43341 CGATAATTGAAATAAAGTT
1 CGATAATTGAAACAAAGTT
43360 ATAAAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.47, C:0.07, G:0.15, T:0.30
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:45676 original size:12 final size:12
Alignment explanation
Indices: 45659--45704 Score: 56
Period size: 12 Copynumber: 3.6 Consensus size: 12
45649 TTCGGATAAA
45659 AACCGGTTTTTT
1 AACCGGTTTTTT
45671 AACCGGTTTTTTT
1 AACCGG-TTTTTT
45684 CAAACCGGTTTTTT
1 --AACCGGTTTTTT
*
45698 ATCCGGT
1 AACCGGT
45705 AAAAAAACCG
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
12 12 0.40
13 6 0.20
14 6 0.20
15 6 0.20
ACGTcount: A:0.17, C:0.20, G:0.17, T:0.46
Consensus pattern (12 bp):
AACCGGTTTTTT
Found at i:45689 original size:15 final size:14
Alignment explanation
Indices: 45658--45697 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
45648 TTTCGGATAA
45658 AAACCGG-TTTTTT
1 AAACCGGTTTTTTT
45671 -AACCGGTTTTTTT
1 AAACCGGTTTTTTT
45684 CAAACCGGTTTTTT
1 -AAACCGGTTTTTT
45698 ATCCGGTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 6 0.25
13 6 0.25
15 12 0.50
ACGTcount: A:0.20, C:0.17, G:0.15, T:0.47
Consensus pattern (14 bp):
AAACCGGTTTTTTT
Found at i:46904 original size:46 final size:46
Alignment explanation
Indices: 46836--46940 Score: 165
Period size: 46 Copynumber: 2.3 Consensus size: 46
46826 ATACTTCTGA
* * *
46836 ATCAACTAGGATAGGCCATTTTTGGACTAAGATACATCGTTATTAG
1 ATCAACTAAGATAGGACATTTTTGGACTAAGATACATCGTAATTAG
*
46882 ATCAACTAAGATAGGACGTTTTTGGACTAAGATACATCGTAATTAG
1 ATCAACTAAGATAGGACATTTTTGGACTAAGATACATCGTAATTAG
*
46928 ATCAAGTAAGATA
1 ATCAACTAAGATA
46941 TGATGCTATC
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 54 1.00
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.30
Consensus pattern (46 bp):
ATCAACTAAGATAGGACATTTTTGGACTAAGATACATCGTAATTAG
Found at i:54070 original size:214 final size:218
Alignment explanation
Indices: 53774--54213 Score: 708
Period size: 214 Copynumber: 2.0 Consensus size: 218
53764 CAACAAGAGT
53774 TTATTCAATTGAAAATGGAATCGAATCCACATGGGAAAGAAGAAGAAATTAATAAATAAACATTA
1 TTATTCAATTGAAAATGGAATCGAATCCACATGGG-AAGAAGAAGAAATTAATAAATAAACATTA
* * * *
53839 GAGATAAAATTAAATAAATTTAATAATTGCATCGGCTTGGAACCTTCCTTTCTTCAATAGATTAA
65 GAAATAAAATGAAATAAATTTAATAATTGCATCGGCTTAGAACCTTCCTTTCTTCAATAAATTAA
* *
53904 TGAGTTAGAACACATTTTC-AATAATAATAATAATGAATTAGAACACAATCGAAGACCATTGGAA
130 TGAATTAGAACACATTTTCAAATAATAATAATAATGAATTAGAACACAATCGAAGACCACTGGAA
53968 ATAAATGTCCAAAATTGGGCAAAA
195 ATAAATGTCCAAAATTGGGCAAAA
53992 TTATTCAATTGAAAATGGAATCGAATCCACATGGG-A-AAGAA-AAATTAATAAATAAACATTAG
1 TTATTCAATTGAAAATGGAATCGAATCCACATGGGAAGAAGAAGAAATTAATAAATAAACATTAG
54054 AAATAAAATGAAATAAATTTAATAATTGCATCGGCTTAGAACCTTCCTTTCTTCAATAAATTAAT
66 AAATAAAATGAAATAAATTTAATAATTGCATCGGCTTAGAACCTTCCTTTCTTCAATAAATTAAT
*
54119 GAATTAGAGCACATTTTCAATAATAATAATAATAATAATAATGAATTAGAACACAATCGAAGACC
131 GAATTAGAACACATTTTC-------A-AATAATAATAATAATGAATTAGAACACAATCGAAGACC
54184 ACTGGAAATAAATGTCCAAAATTGGGCAAA
188 ACTGGAAATAAATGTCCAAAATTGGGCAAA
54214 CTATTTCGTC
Statistics
Matches: 206, Mismatches: 7, Indels: 13
0.91 0.03 0.06
Matches are distributed among these distances:
214 98 0.48
215 5 0.02
216 1 0.00
218 35 0.17
223 67 0.33
ACGTcount: A:0.47, C:0.12, G:0.13, T:0.28
Consensus pattern (218 bp):
TTATTCAATTGAAAATGGAATCGAATCCACATGGGAAGAAGAAGAAATTAATAAATAAACATTAG
AAATAAAATGAAATAAATTTAATAATTGCATCGGCTTAGAACCTTCCTTTCTTCAATAAATTAAT
GAATTAGAACACATTTTCAAATAATAATAATAATGAATTAGAACACAATCGAAGACCACTGGAAA
TAAATGTCCAAAATTGGGCAAAA
Found at i:59485 original size:37 final size:36
Alignment explanation
Indices: 59410--59485 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
59400 TTTTTATATT
*
59410 TTTAATTTTATAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTATAAAAAAATTATATAAATATTATCAA
* *
59446 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTATAAA-AAAATTATATAAATATTAT-CAA
59483 TTT
1 TTT
59486 GTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
36 26 0.74
37 9 0.26
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.47
Consensus pattern (36 bp):
TTTAATTTTATAAAAAAATTATATAAATATTATCAA
Found at i:69429 original size:14 final size:14
Alignment explanation
Indices: 69410--69438 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
69400 CGTTCGTGAA
69410 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
69424 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
69438 C
1 C
69439 ATTTATGTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.07, C:0.17, G:0.28, T:0.48
Consensus pattern (14 bp):
CGTTCGGTTATGTT
Found at i:70538 original size:15 final size:15
Alignment explanation
Indices: 70518--70558 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
70508 GTCTCCAACG
70518 TTTATGTTCGTG-TC
1 TTTATGTTCGTGTTC
70532 ATTTATGTTCGTGTTC
1 -TTTATGTTCGTGTTC
*
70548 GTTATGTTCGT
1 TTTATGTTCGT
70559 TATTTATTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 22 0.92
16 2 0.08
ACGTcount: A:0.10, C:0.12, G:0.22, T:0.56
Consensus pattern (15 bp):
TTTATGTTCGTGTTC
Found at i:70844 original size:24 final size:24
Alignment explanation
Indices: 70816--70882 Score: 89
Period size: 24 Copynumber: 2.8 Consensus size: 24
70806 GTTAAAATGA
*
70816 TAAACGAACACAAATTAATGAACG
1 TAAACGAACACAAATGAATGAACG
* *
70840 TAAACAAACACAAATGAATGAGCG
1 TAAACGAACACAAATGAATGAACG
* *
70864 TAAACGAACATAAACGAAT
1 TAAACGAACACAAATGAAT
70883 ATATAAATTA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.55, C:0.16, G:0.13, T:0.15
Consensus pattern (24 bp):
TAAACGAACACAAATGAATGAACG
Done.