Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006567.1 Hibiscus syriacus cultivar Beakdansim tig00016068_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: 56094
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Found at i:1083 original size:16 final size:15
Alignment explanation
Indices: 1064--1093 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
1054 TATTATTTAT
1064 TTATTTTGAATATATA
1 TTATTTTG-ATATATA
1080 TTATTTTGATATAT
1 TTATTTTGATATAT
1094 CTACATTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (15 bp):
TTATTTTGATATATA
Found at i:3166 original size:2 final size:2
Alignment explanation
Indices: 3152--3193 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
3142 TTTTTTGTTA
3152 AT AT A- AT AT -T 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
3192 AT
1 AT
3194 TAAGTATATT
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.05
2 36 0.95
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:7378 original size:95 final size:95
Alignment explanation
Indices: 7214--7395 Score: 265
Period size: 95 Copynumber: 1.9 Consensus size: 95
7204 ATATTAATTA
* * * * *
7214 TATACAATAAAACTTGAGTTGTCCCTTTAGAGCAATTGATTAAACGCCCCGGCTTTATGGATAAT
1 TATACAATAAAACTTGAGCTGTCCCTCTAAAGCAATTGATTAAACGCCCCGACTTTATGGATAAG
**
7279 ATTCAGCTAGTCTGATAAAGGTGAGTATAC
66 ATTCAGCTAACCTGATAAAGGTGAGTATAC
* * * *
7309 TATACAATAAAGCTTTAGCTGTCCCTCTAAAGCAATTGGTTAAATGCCCCGACTTTATGGATAAG
1 TATACAATAAAACTTGAGCTGTCCCTCTAAAGCAATTGATTAAACGCCCCGACTTTATGGATAAG
7374 ATTCAGCTAACCTGATAAAGGT
66 ATTCAGCTAACCTGATAAAGGT
7396 ATTTATATAT
Statistics
Matches: 76, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
95 76 1.00
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (95 bp):
TATACAATAAAACTTGAGCTGTCCCTCTAAAGCAATTGATTAAACGCCCCGACTTTATGGATAAG
ATTCAGCTAACCTGATAAAGGTGAGTATAC
Found at i:9387 original size:36 final size:36
Alignment explanation
Indices: 9336--9417 Score: 139
Period size: 36 Copynumber: 2.3 Consensus size: 36
9326 ATTGACCCAA
9336 CTTGAAACAATTTTTGTCTCTCTTGAGA-AGGTTTCC
1 CTTGAAACAATTTTTGTCTCTCTTGAGACA-GTTTCC
*
9372 CTTTAAACAATTTTTGTCTCTCTTGAGACAGTTTCC
1 CTTGAAACAATTTTTGTCTCTCTTGAGACAGTTTCC
9408 CTTGAAACAA
1 CTTGAAACAA
9418 AATTTTTTAA
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
36 42 0.98
37 1 0.02
ACGTcount: A:0.26, C:0.21, G:0.13, T:0.40
Consensus pattern (36 bp):
CTTGAAACAATTTTTGTCTCTCTTGAGACAGTTTCC
Found at i:9654 original size:65 final size:66
Alignment explanation
Indices: 9366--9677 Score: 291
Period size: 65 Copynumber: 4.7 Consensus size: 66
9356 TCTTGAGAAG
* * * *
9366 GTTTCCCTTTAAACAATTTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC-AAAATTTTTTAATT
1 GTTTTCCTTTAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAAATCTTTTAATA
9430 T
66 T
* * * ** *
9431 G-TTTCCTTGAAGCAAA-TTTGTCTCCCTTGAGACAGTTT-TTTTAAAACAAATTATATCTCTTT
1 GTTTTCCTTTAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA--A-A--TCTTT
*
9493 TGAGACAT
61 T-A-ATAT
* * *** *
9501 ATTCT-C-TTAAA-TTTTTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAAATCTTTGAATA
1 GTTTTCCTTTAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAAATCTTTTAATA
9563 T
66 T
*
9564 -ATTTCCTTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC-AAAATCTTTTAAT
1 GTTTTCCTTT-AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAAATCTTTTAAT
9627 AT
65 AT
* * * *
9629 GTTTTCCTTTAAACAAATTTCGTCTCTCTCGAGACAATTTCTCTTGAAA
1 GTTTTCCTTTAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAA
9678 AATTTTGTCT
Statistics
Matches: 196, Mismatches: 35, Indels: 32
0.75 0.13 0.12
Matches are distributed among these distances:
62 8 0.04
63 27 0.14
64 14 0.07
65 59 0.30
66 42 0.21
67 1 0.01
68 6 0.03
69 25 0.13
70 12 0.06
71 2 0.01
ACGTcount: A:0.28, C:0.19, G:0.10, T:0.43
Consensus pattern (66 bp):
GTTTTCCTTTAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAAATCTTTTAATA
T
Found at i:9688 original size:34 final size:34
Alignment explanation
Indices: 9643--9711 Score: 84
Period size: 34 Copynumber: 2.0 Consensus size: 34
9633 TCCTTTAAAC
*
9643 AAATTTCGTCTCTCTCGAGACAATTTCTCTTGAA
1 AAATTTCGTCTCCCTCGAGACAATTTCTCTTGAA
* * ** *
9677 AAATTTTGTCTCCCTTGAGACGGTTTCTTTTGAA
1 AAATTTCGTCTCCCTCGAGACAATTTCTCTTGAA
9711 A
1 A
9712 CACAAAATCT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.25, C:0.20, G:0.14, T:0.41
Consensus pattern (34 bp):
AAATTTCGTCTCCCTCGAGACAATTTCTCTTGAA
Found at i:10298 original size:2 final size:2
Alignment explanation
Indices: 10276--10336 Score: 60
Period size: 2 Copynumber: 33.0 Consensus size: 2
10266 ATTATAATAC
* * *
10276 AT AT AC AT AT AT A- AT AT -T AT AT A- AT GT -T AT AA AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
10313 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
10337 GGTTTATTTA
Statistics
Matches: 49, Mismatches: 5, Indels: 10
0.77 0.08 0.16
Matches are distributed among these distances:
1 5 0.10
2 44 0.90
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:11933 original size:2 final size:2
Alignment explanation
Indices: 11928--11958 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
11918 AAAAAAATTA
11928 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 A
11959 AGTATTATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:16566 original size:26 final size:26
Alignment explanation
Indices: 16535--16589 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
16525 AGTTTATTAA
16535 CTTAGAATGATTTAACTGAATACAAT
1 CTTAGAATGATTTAACTGAATACAAT
16561 CTTAGAATGATTTAACTGAATACAAT
1 CTTAGAATGATTTAACTGAATACAAT
16587 CTT
1 CTT
16590 GCTTGAACAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.40, C:0.13, G:0.11, T:0.36
Consensus pattern (26 bp):
CTTAGAATGATTTAACTGAATACAAT
Found at i:27708 original size:91 final size:92
Alignment explanation
Indices: 27544--27721 Score: 238
Period size: 91 Copynumber: 1.9 Consensus size: 92
27534 AAGTTGTGAT
* ** * *
27544 GGGTTTTAACCTAAAAATGTTATTTTGTCTATTCTAAAAAGTTATACATTTAGTAATAATTGTTG
1 GGGTTTTAACCTAAAAATGTTATCTTGTCTACCCTAAAAAGTTATAAATTGAGTAATAATTGTTG
*
27609 TTAGAATCGATAATGTTACATTGCATC
66 TTAGAATCGAGAATGTTACATTGCATC
*
27636 GGGTTTTAACCT-AAAATGTTATCTTGTCTACCCTAAAAGGTTATATAATTGA-TAATAATT-TT
1 GGGTTTTAACCTAAAAATGTTATCTTGTCTACCCTAAAAAGTTATA-AATTGAGTAATAATTGTT
27698 GGTT-GCAATCGAGAATGTTACATT
65 -GTTAG-AATCGAGAATGTTACATT
27722 AGTTTCATGA
Statistics
Matches: 76, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
90 3 0.04
91 57 0.75
92 16 0.21
ACGTcount: A:0.33, C:0.11, G:0.15, T:0.41
Consensus pattern (92 bp):
GGGTTTTAACCTAAAAATGTTATCTTGTCTACCCTAAAAAGTTATAAATTGAGTAATAATTGTTG
TTAGAATCGAGAATGTTACATTGCATC
Found at i:29119 original size:2 final size:2
Alignment explanation
Indices: 29114--29144 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
29104 AAACACACAC
*
29114 AT AT AT AT AT AT AT AT AT AT AT AT AG AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
29145 CACAATGAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (2 bp):
AT
Found at i:29712 original size:20 final size:20
Alignment explanation
Indices: 29689--29781 Score: 80
Period size: 20 Copynumber: 4.6 Consensus size: 20
29679 GTTTCCAGAT
*
29689 TCGCAACGCGATTTTGACTA
1 TCGCAACGCGATTTTGACAA
** *
29709 TCGCATTGCGATTTTAGAAAA
1 TCGCAACGCGATTTT-GACAA
* *
29730 TCGCAACGCGAATATGTA-AA
1 TCGCAACGCGATTTTG-ACAA
* * *
29750 TCGTAACGCGATTCTGACTA
1 TCGCAACGCGATTTTGACAA
29770 TCGCAACGCGAT
1 TCGCAACGCGAT
29782 AATACAAAAT
Statistics
Matches: 57, Mismatches: 13, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
19 1 0.02
20 41 0.72
21 15 0.26
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.27
Consensus pattern (20 bp):
TCGCAACGCGATTTTGACAA
Found at i:30469 original size:20 final size:20
Alignment explanation
Indices: 30366--30471 Score: 108
Period size: 20 Copynumber: 5.4 Consensus size: 20
30356 AAATCGCAAC
*
30366 GCGATTTT-AGTTTCGCGTT
1 GCGATTTTCATTTTCGCGTT
30385 GCGATTTTCATTTT-GCGTT
1 GCGATTTTCATTTTCGCGTT
** ** *
30404 GCGATAGTCAAATTCGCATT
1 GCGATTTTCATTTTCGCGTT
** *
30424 GCGATAGTCATTTTCGTGTT
1 GCGATTTTCATTTTCGCGTT
*
30444 GCGATTTTCATTTTCGTGTT
1 GCGATTTTCATTTTCGCGTT
30464 GCGATTTT
1 GCGATTTT
30472 AAGTTTCAGA
Statistics
Matches: 73, Mismatches: 12, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
19 23 0.32
20 50 0.68
ACGTcount: A:0.15, C:0.16, G:0.23, T:0.46
Consensus pattern (20 bp):
GCGATTTTCATTTTCGCGTT
Found at i:30478 original size:20 final size:20
Alignment explanation
Indices: 30435--30478 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
30425 CGATAGTCAT
* *
30435 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTTAAG
30455 TTTCGTGTTGCGATTTTAAG
1 TTTCGTGTTGCGATTTTAAG
30475 TTTC
1 TTTC
30479 AGAAACTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.11, C:0.14, G:0.20, T:0.55
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTTAAG
Found at i:32025 original size:23 final size:22
Alignment explanation
Indices: 31981--32025 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
31971 AATGCCAGAG
*
31981 GGGAACCGATACCCCCACAGGA
1 GGGAACCGATACCCCCAAAGGA
*
32003 GGGAACCGATTCCCCCTAAAGGA
1 GGGAACCGATACCCCC-AAAGGA
32026 AAAATGTGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.31, C:0.33, G:0.27, T:0.09
Consensus pattern (22 bp):
GGGAACCGATACCCCCAAAGGA
Found at i:33540 original size:21 final size:21
Alignment explanation
Indices: 33515--33554 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
33505 ATGTATATGA
33515 TTCTTAAGGA-ATGATATGTGG
1 TTCTTAAGGACAT-ATATGTGG
*
33536 TTCTTCAGGACATATATGT
1 TTCTTAAGGACATATATGT
33555 ATTCTTTGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 15 0.88
22 2 0.12
ACGTcount: A:0.28, C:0.10, G:0.23, T:0.40
Consensus pattern (21 bp):
TTCTTAAGGACATATATGTGG
Found at i:33605 original size:103 final size:103
Alignment explanation
Indices: 33426--33746 Score: 606
Period size: 103 Copynumber: 3.1 Consensus size: 103
33416 GTCGAGGGTC
33426 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
33491 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
* * *
33529 TATGTGGTTCTTCAGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTTAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
33594 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
*
33632 TATGTGGTCCTTCGGGATATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
33697 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
33735 TATGTGGTCCTT
1 TATGTGGTCCTT
33747 ATGGACATTA
Statistics
Matches: 211, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 211 1.00
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
Found at i:33830 original size:23 final size:23
Alignment explanation
Indices: 33756--33830 Score: 64
Period size: 23 Copynumber: 3.3 Consensus size: 23
33746 TATGGACATT
33756 ATTATATG--GCACTACGGTGCA
1 ATTATATGTTGCACTACGGTGCA
* * * **
33777 ACTCTACGCGGCACTACGGTGCA
1 ATTATATGTTGCACTACGGTGCA
* *
33800 ATTCTATGTTGCACTTCGGTGCA
1 ATTATATGTTGCACTACGGTGCA
*
33823 TTTATATG
1 ATTATATG
33831 AGCTGTGGTG
Statistics
Matches: 42, Mismatches: 10, Indels: 2
0.78 0.19 0.04
Matches are distributed among these distances:
21 5 0.12
23 37 0.88
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.32
Consensus pattern (23 bp):
ATTATATGTTGCACTACGGTGCA
Found at i:35750 original size:20 final size:20
Alignment explanation
Indices: 35727--35775 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
35717 GAAACTTAAA
*
35727 ATCGCAACGTGAAAATGACT
1 ATCGCAACGCGAAAATGACT
**
35747 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
35767 ATCGCAACG
1 ATCGCAACG
35776 GGATAATCGC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.20
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:36490 original size:21 final size:21
Alignment explanation
Indices: 36392--36492 Score: 87
Period size: 21 Copynumber: 4.8 Consensus size: 21
36382 CCGACTCACT
*
36392 TGTCATCGTTCAAGAGGCCTC
1 TGTCATCGTTCAAGAGGCCCC
*
36413 T-CCTATCGTTCAAGAGGCCCC
1 TGTC-ATCGTTCAAGAGGCCCC
* ** * *
36434 TATCATCCCTCAAGAGTCACC
1 TGTCATCGTTCAAGAGGCCCC
** *
36455 TCCCATTGTTCAAGAGGCCCC
1 TGTCATCGTTCAAGAGGCCCC
*
36476 TGTCATCGTTGAAGAGG
1 TGTCATCGTTCAAGAGG
36493 TCCATCCCAC
Statistics
Matches: 60, Mismatches: 18, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
20 1 0.02
21 58 0.97
22 1 0.02
ACGTcount: A:0.22, C:0.32, G:0.21, T:0.26
Consensus pattern (21 bp):
TGTCATCGTTCAAGAGGCCCC
Found at i:36491 original size:42 final size:42
Alignment explanation
Indices: 36392--36492 Score: 123
Period size: 42 Copynumber: 2.4 Consensus size: 42
36382 CCGACTCACT
*
36392 TGTCATCGTTCAAGAGGCCTCTCCTATCGTTCAAGAGGCCCC
1 TGTCATCGTTCAAGAGGCCTCTCCCATCGTTCAAGAGGCCCC
* ** * *
36434 TATCATCCCTCAAGAGTCAC-CTCCCATTGTTCAAGAGGCCCC
1 TGTCATCGTTCAAGAGGC-CTCTCCCATCGTTCAAGAGGCCCC
*
36476 TGTCATCGTTGAAGAGG
1 TGTCATCGTTCAAGAGG
36493 TCCATCCCAC
Statistics
Matches: 47, Mismatches: 11, Indels: 2
0.78 0.18 0.03
Matches are distributed among these distances:
42 46 0.98
43 1 0.02
ACGTcount: A:0.22, C:0.32, G:0.21, T:0.26
Consensus pattern (42 bp):
TGTCATCGTTCAAGAGGCCTCTCCCATCGTTCAAGAGGCCCC
Found at i:36501 original size:42 final size:41
Alignment explanation
Indices: 36392--36512 Score: 120
Period size: 42 Copynumber: 2.9 Consensus size: 41
36382 CCGACTCACT
36392 TGTCATCGTTCAAGAGG-CCTCTCCTATCGTTCAAGAGGCCCC
1 TGTCATCGTTCAAGAGGTCCTC-CC-ATCGTTCAAGAGGCCCC
* ** *
36434 TATCATCCCTCAAGA-GTCACCTCCCATTGTTCAAGAGGCCCC
1 TGTCATCGTTCAAGAGGT--CCTCCCATCGTTCAAGAGGCCCC
* * *
36476 TGTCATCGTTGAAGAGGTCCATCCCACCATTCAAGAG
1 TGTCATCGTTCAAGAGGTCC-TCCCATCGTTCAAGAG
36513 CCCGATTCAC
Statistics
Matches: 63, Mismatches: 11, Indels: 10
0.75 0.13 0.12
Matches are distributed among these distances:
41 3 0.05
42 52 0.83
43 4 0.06
44 4 0.06
ACGTcount: A:0.23, C:0.33, G:0.19, T:0.25
Consensus pattern (41 bp):
TGTCATCGTTCAAGAGGTCCTCCCATCGTTCAAGAGGCCCC
Found at i:38075 original size:20 final size:20
Alignment explanation
Indices: 38050--38113 Score: 101
Period size: 20 Copynumber: 3.2 Consensus size: 20
38040 AACGCTAAAC
38050 TCAAAATCGTAATGCGAAAG
1 TCAAAATCGTAATGCGAAAG
*
38070 TCAAAATCGCAATGCGAAAG
1 TCAAAATCGTAATGCGAAAG
* *
38090 CCAAAATCGTAACGCGAAAG
1 TCAAAATCGTAATGCGAAAG
38110 TCAA
1 TCAA
38114 TTCGCGTTGC
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.45, C:0.20, G:0.19, T:0.16
Consensus pattern (20 bp):
TCAAAATCGTAATGCGAAAG
Found at i:38080 original size:40 final size:40
Alignment explanation
Indices: 38036--38113 Score: 113
Period size: 40 Copynumber: 1.9 Consensus size: 40
38026 AGGTACACTT
* *
38036 TCGCAACGCTAAA-CTCAAAATCGTAATGCGAAAGTCAAAA
1 TCGCAACGCGAAAGC-CAAAATCGTAACGCGAAAGTCAAAA
*
38076 TCGCAATGCGAAAGCCAAAATCGTAACGCGAAAGTCAA
1 TCGCAACGCGAAAGCCAAAATCGTAACGCGAAAGTCAA
38114 TTCGCGTTGC
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
40 33 0.97
41 1 0.03
ACGTcount: A:0.44, C:0.23, G:0.18, T:0.15
Consensus pattern (40 bp):
TCGCAACGCGAAAGCCAAAATCGTAACGCGAAAGTCAAAA
Found at i:38177 original size:20 final size:20
Alignment explanation
Indices: 38103--38268 Score: 157
Period size: 20 Copynumber: 8.7 Consensus size: 20
38093 AAATCGTAAC
*
38103 GCGAAAGTC-AATTCGCGTT
1 GCGATAGTCAAATTCGCGTT
* * *
38122 GCGATAGTCTAATACGCTTT
1 GCGATAGTCAAATTCGCGTT
*
38142 GCGAT--T----TTCTCGTT
1 GCGATAGTCAAATTCGCGTT
*
38156 GCGATAGTCAAATTCCCGTT
1 GCGATAGTCAAATTCGCGTT
*
38176 GCGATAATCAAATTCGCGTT
1 GCGATAGTCAAATTCGCGTT
* **
38196 ACGATAGTCAAATTCGATTT
1 GCGATAGTCAAATTCGCGTT
*
38216 ACGATAGTCAAATTCGCGTT
1 GCGATAGTCAAATTCGCGTT
* *
38236 GCAATAGTCAAATTCACGTT
1 GCGATAGTCAAATTCGCGTT
*
38256 GCGATATTCAAAT
1 GCGATAGTCAAAT
38269 GAAAGTGTAA
Statistics
Matches: 120, Mismatches: 20, Indels: 13
0.78 0.13 0.08
Matches are distributed among these distances:
14 10 0.08
16 1 0.01
18 1 0.01
19 8 0.07
20 100 0.83
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.33
Consensus pattern (20 bp):
GCGATAGTCAAATTCGCGTT
Found at i:40530 original size:14 final size:14
Alignment explanation
Indices: 40511--40547 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
40501 TCCCGTGGCA
40511 TTTTCTTCGGGGAC
1 TTTTCTTCGGGGAC
*
40525 TTTTCTTCGGGGAT
1 TTTTCTTCGGGGAC
40539 TTCTTCTTC
1 TT-TTCTTC
40548 TTCTTTTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.05, C:0.22, G:0.22, T:0.51
Consensus pattern (14 bp):
TTTTCTTCGGGGAC
Found at i:40765 original size:24 final size:24
Alignment explanation
Indices: 40738--40791 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
40728 TTGAAACATC
*
40738 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
* *
40762 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
40786 ATCAAA
1 ATCAAA
40792 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:41467 original size:17 final size:17
Alignment explanation
Indices: 41445--41482 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
41435 CGGATGGGGA
41445 AGGATGTCGTTGGATAT
1 AGGATGTCGTTGGATAT
41462 AGGATGTCGTTGGATAT
1 AGGATGTCGTTGGATAT
41479 AGGA
1 AGGA
41483 ACGGATGTCG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.26, C:0.05, G:0.37, T:0.32
Consensus pattern (17 bp):
AGGATGTCGTTGGATAT
Found at i:41491 original size:22 final size:20
Alignment explanation
Indices: 41442--41492 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 20
41432 TGCCGGATGG
41442 GGAAGGATGTCGTTGGATAT
1 GGAAGGATGTCGTTGGATAT
41462 ---AGGATGTCGTTGGATAT
1 GGAAGGATGTCGTTGGATAT
41479 AGGAACGGATGTCG
1 -GGAA-GGATGTCG
41493 CCGGAGAGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
17 17 0.65
21 1 0.04
22 8 0.31
ACGTcount: A:0.25, C:0.08, G:0.39, T:0.27
Consensus pattern (20 bp):
GGAAGGATGTCGTTGGATAT
Found at i:41654 original size:20 final size:20
Alignment explanation
Indices: 41629--41695 Score: 64
Period size: 20 Copynumber: 3.4 Consensus size: 20
41619 GAAATTCAGT
*
41629 GTTGCGATAGTCAGAATCGC
1 GTTGCGATAGTCAAAATCGC
* * *
41649 GTTGCGAT-TTACATATTCGC
1 GTTGCGATAGT-CAAAATCGC
* *
41669 ATTGCGATAGTTAAAATCGC
1 GTTGCGATAGTCAAAATCGC
41689 GTTGCGA
1 GTTGCGA
41696 ATATGGAAAC
Statistics
Matches: 36, Mismatches: 9, Indels: 4
0.73 0.18 0.08
Matches are distributed among these distances:
19 1 0.03
20 34 0.94
21 1 0.03
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.31
Consensus pattern (20 bp):
GTTGCGATAGTCAAAATCGC
Found at i:53344 original size:18 final size:17
Alignment explanation
Indices: 53311--53345 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
53301 CATATTATTA
*
53311 GAATTATTCTTTGTGTT
1 GAATTATTCATTGTGTT
53328 GAATTATTCAATTGTGTT
1 GAATTATTC-ATTGTGTT
53346 AGCATTTAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.23, C:0.06, G:0.17, T:0.54
Consensus pattern (17 bp):
GAATTATTCATTGTGTT
Found at i:54071 original size:11 final size:11
Alignment explanation
Indices: 54057--54110 Score: 56
Period size: 11 Copynumber: 4.9 Consensus size: 11
54047 AAAATTGAAA
54057 AAAAATAAAAG
1 AAAAATAAAAG
*
54068 AAAAATCAAAG
1 AAAAATAAAAG
* **
54079 ATATAATGTAAG
1 A-AAAATAAAAG
54091 -AAAATAAAAG
1 AAAAATAAAAG
54101 AAAAATAAAA
1 AAAAATAAAA
54111 AATATTGAAC
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
10 7 0.21
11 20 0.59
12 7 0.21
ACGTcount: A:0.74, C:0.02, G:0.09, T:0.15
Consensus pattern (11 bp):
AAAAATAAAAG
Done.