Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004373.1 Hibiscus syriacus cultivar Beakdansim tig00009581_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: 62459
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:2110 original size:17 final size:18
Alignment explanation
Indices: 2077--2110 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2067 CTGCTATTAG
2077 TGAACCGGTCAGAACCGC
1 TGAACCGGTCAGAACCGC
*
2095 TGAACCGTTC-GAACCG
1 TGAACCGGTCAGAACCG
2111 GACCGGCTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.26, C:0.32, G:0.26, T:0.15
Consensus pattern (18 bp):
TGAACCGGTCAGAACCGC
Found at i:5831 original size:6 final size:6
Alignment explanation
Indices: 5814--5845 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
5804 GCTCCAGCGA
*
5814 ACCTTC ATCTTC ACCTTC ACCTTC ACCTTC AC
1 ACCTTC ACCTTC ACCTTC ACCTTC ACCTTC AC
5846 GTTGCATGCT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.19, C:0.47, G:0.00, T:0.34
Consensus pattern (6 bp):
ACCTTC
Found at i:11937 original size:28 final size:29
Alignment explanation
Indices: 11879--11945 Score: 93
Period size: 28 Copynumber: 2.3 Consensus size: 29
11869 TATTGACCAC
11879 TTAATTATTTTCATTTTAACCATCATTTTT
1 TTAATT-TTTTCATTTTAACCATCATTTTT
*
11909 TTAATTTTTTTATTTTAACCA-C-TATTTT
1 TTAATTTTTTCATTTTAACCATCAT-TTTT
11937 TTAATTTTT
1 TTAATTTTT
11946 GTTAATCAGA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
27 1 0.03
28 14 0.40
29 14 0.40
30 6 0.17
ACGTcount: A:0.25, C:0.10, G:0.00, T:0.64
Consensus pattern (29 bp):
TTAATTTTTTCATTTTAACCATCATTTTT
Found at i:11938 original size:30 final size:28
Alignment explanation
Indices: 11879--11945 Score: 91
Period size: 29 Copynumber: 2.3 Consensus size: 28
11869 TATTGACCAC
11879 TTAATTATTTTCATTTTAACCATCATTTTT
1 TTAATT-TTTTCATTTTAACCATCA-TTTT
*
11909 TTAATTTTTTTATTTTAACCA-CTATTTT
1 TTAATTTTTTCATTTTAACCATC-ATTTT
11937 TTAATTTTT
1 TTAATTTTT
11946 GTTAATCAGA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
28 14 0.40
29 15 0.43
30 6 0.17
ACGTcount: A:0.25, C:0.10, G:0.00, T:0.64
Consensus pattern (28 bp):
TTAATTTTTTCATTTTAACCATCATTTT
Found at i:13324 original size:29 final size:30
Alignment explanation
Indices: 13274--13330 Score: 82
Period size: 29 Copynumber: 1.9 Consensus size: 30
13264 GATGAACTCA
*
13274 TCAAGTGGTTAAAAAACGTTATGTACATTG
1 TCAAGTGGTTAAAAAACGTTATGAACATTG
13304 TCAA-TGGTTAAAAAA-GATTATGAACAT
1 TCAAGTGGTTAAAAAACG-TTATGAACAT
13331 ATATTATCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 1 0.04
29 20 0.80
30 4 0.16
ACGTcount: A:0.42, C:0.09, G:0.18, T:0.32
Consensus pattern (30 bp):
TCAAGTGGTTAAAAAACGTTATGAACATTG
Found at i:14428 original size:35 final size:35
Alignment explanation
Indices: 14388--14467 Score: 151
Period size: 35 Copynumber: 2.3 Consensus size: 35
14378 GTTGTATTTT
14388 GTGTTTGGTTGGTTTAGCAGGAATGTAAGATTACC
1 GTGTTTGGTTGGTTTAGCAGGAATGTAAGATTACC
*
14423 GTGTTTGGTTGGTTTAGCAGGAATGTAAGATTATC
1 GTGTTTGGTTGGTTTAGCAGGAATGTAAGATTACC
14458 GTGTTTGGTT
1 GTGTTTGGTT
14468 AAAGGAATAA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
35 44 1.00
ACGTcount: A:0.20, C:0.06, G:0.33, T:0.41
Consensus pattern (35 bp):
GTGTTTGGTTGGTTTAGCAGGAATGTAAGATTACC
Found at i:15455 original size:41 final size:41
Alignment explanation
Indices: 15404--15558 Score: 179
Period size: 41 Copynumber: 3.8 Consensus size: 41
15394 ATAAAAACGA
* **
15404 CGCTATAGACTCGTAATTTAGTGAC-TTTTTCATACAAACGG
1 CGCTATAGACTCGTACTTTAGTGACATTTTT-ATACAAACAC
** *
15445 CGCTATAGACTCGTACTTTAGTGGTA-TTTTATACAAATAC
1 CGCTATAGACTCGTACTTTAGTGACATTTTTATACAAACAC
* * *
15485 CGCTATAGATTCATTCTTTAGTGACATTTTTATACAAACAC
1 CGCTATAGACTCGTACTTTAGTGACATTTTTATACAAACAC
* * *
15526 CGCAAAAAACTCGTACTTTAGTGACATTTTTAT
1 CGCTATAGACTCGTACTTTAGTGACATTTTTAT
15559 TTACAACGCC
Statistics
Matches: 94, Mismatches: 18, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
40 28 0.30
41 66 0.70
ACGTcount: A:0.31, C:0.19, G:0.14, T:0.37
Consensus pattern (41 bp):
CGCTATAGACTCGTACTTTAGTGACATTTTTATACAAACAC
Found at i:15629 original size:23 final size:22
Alignment explanation
Indices: 15602--15645 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
15592 CGTGCCCCTT
* *
15602 TAACCTTTTTTATTTTTTTCCCA
1 TAACCTATTTT-TTTTATTCCCA
15625 TAACCTATTTTTTTTATTCCC
1 TAACCTATTTTTTTTATTCCC
15646 GCTCCCTCCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.18, C:0.23, G:0.00, T:0.59
Consensus pattern (22 bp):
TAACCTATTTTTTTTATTCCCA
Found at i:19698 original size:21 final size:21
Alignment explanation
Indices: 19674--19732 Score: 100
Period size: 21 Copynumber: 2.8 Consensus size: 21
19664 TAATTTATTA
19674 TTATGGATTTCAAGTTTCTTG
1 TTATGGATTTCAAGTTTCTTG
*
19695 TTATGGATTTCAAGTTTGTTG
1 TTATGGATTTCAAGTTTCTTG
*
19716 TTATGGATGTCAAGTTT
1 TTATGGATTTCAAGTTT
19733 ATTAGATAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.20, C:0.07, G:0.22, T:0.51
Consensus pattern (21 bp):
TTATGGATTTCAAGTTTCTTG
Found at i:19994 original size:14 final size:13
Alignment explanation
Indices: 19975--20019 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
19965 CGTTCGATTA
19975 TATGTTCTTTCATT
1 TATGTTC-TTCATT
19989 TATG---TTCATT
1 TATGTTCTTCATT
19999 TATGTTCGTTCATT
1 TATGTTC-TTCATT
20013 TATGTTC
1 TATGTTC
20020 GAACAAAGGG
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
10 10 0.37
14 17 0.63
ACGTcount: A:0.16, C:0.13, G:0.11, T:0.60
Consensus pattern (13 bp):
TATGTTCTTCATT
Found at i:20010 original size:24 final size:26
Alignment explanation
Indices: 19966--20021 Score: 89
Period size: 24 Copynumber: 2.2 Consensus size: 26
19956 GTTCGTGAAC
*
19966 GTTCGATTATATGTTCTTTCATTTAT
1 GTTCGATTATATGTTCGTTCATTTAT
19992 GTTC-ATT-TATGTTCGTTCATTTAT
1 GTTCGATTATATGTTCGTTCATTTAT
20016 GTTCGA
1 GTTCGA
20022 ACAAAGGGCA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
24 20 0.71
25 4 0.14
26 4 0.14
ACGTcount: A:0.18, C:0.12, G:0.14, T:0.55
Consensus pattern (26 bp):
GTTCGATTATATGTTCGTTCATTTAT
Found at i:20020 original size:14 final size:14
Alignment explanation
Indices: 19992--20020 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
19982 TTTCATTTAT
19992 GTTCATTTATGTTC
1 GTTCATTTATGTTC
20006 GTTCATTTATGTTC
1 GTTCATTTATGTTC
20020 G
1 G
20021 AACAAAGGGC
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:0.14, C:0.14, G:0.17, T:0.55
Consensus pattern (14 bp):
GTTCATTTATGTTC
Found at i:20302 original size:23 final size:23
Alignment explanation
Indices: 20276--20338 Score: 74
Period size: 23 Copynumber: 2.7 Consensus size: 23
20266 TTTTTTTTGT
*
20276 ATTTGTGTTGTTCGTTTATGTTC
1 ATTTATGTTGTTCGTTTATGTTC
*
20299 ATTTAT-TGTGTTCGTTTGTGTTC
1 ATTTATGT-TGTTCGTTTATGTTC
*
20322 GTTTATGTTCGTTCGTT
1 ATTTATGTT-GTTCGTT
20339 CGTGTTCGTT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
22 1 0.03
23 25 0.74
24 8 0.24
ACGTcount: A:0.08, C:0.10, G:0.22, T:0.60
Consensus pattern (23 bp):
ATTTATGTTGTTCGTTTATGTTC
Found at i:20324 original size:33 final size:34
Alignment explanation
Indices: 20284--20349 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 34
20274 GTATTTGTGT
*
20284 TGTTCGTTTATGTTCATTTATT-GTGTTCGTTTG
1 TGTTCGTTTATGTTCATTCATTCGTGTTCGTTTG
* *
20317 TGTTCGTTTATGTTCGTTCGTTCGTGTTCGTTT
1 TGTTCGTTTATGTTCATTCATTCGTGTTCGTTT
20350 ATTTATTAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 19 0.66
34 10 0.34
ACGTcount: A:0.06, C:0.12, G:0.23, T:0.59
Consensus pattern (34 bp):
TGTTCGTTTATGTTCATTCATTCGTGTTCGTTTG
Found at i:20348 original size:10 final size:10
Alignment explanation
Indices: 20304--20334 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
20294 TGTTCATTTA
20304 TTGTGTTCGT
1 TTGTGTTCGT
20314 TTGTGTTCGT
1 TTGTGTTCGT
*
20324 TTATGTTCGT
1 TTGTGTTCGT
20334 T
1 T
20335 CGTTCGTGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.03, C:0.10, G:0.26, T:0.61
Consensus pattern (10 bp):
TTGTGTTCGT
Found at i:20438 original size:16 final size:16
Alignment explanation
Indices: 20417--20449 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
20407 AAAAAAATTT
20417 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
20433 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
20449 T
1 T
20450 TTATTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.12, G:0.24, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:22423 original size:20 final size:20
Alignment explanation
Indices: 22395--22432 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
22385 TTGATTCTAC
22395 TGTAGCAGTATCAATACTAT
1 TGTAGCAGTATCAATACTAT
* *
22415 TGTATCAGTATCGATACT
1 TGTAGCAGTATCAATACT
22433 CATTTTGCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.37
Consensus pattern (20 bp):
TGTAGCAGTATCAATACTAT
Found at i:22535 original size:19 final size:20
Alignment explanation
Indices: 22472--22560 Score: 110
Period size: 19 Copynumber: 4.5 Consensus size: 20
22462 TATTGTTCAT
* *
22472 TACTGTTCACACAGTATCGG
1 TACTATTCATACAGTATCGG
* **
22492 TACTATGCATACAGTATATG
1 TACTATTCATACAGTATCGG
22512 TACTATTCATACAGTA-CGG
1 TACTATTCATACAGTATCGG
*
22531 TACTATTCATACAATA-CGG
1 TACTATTCATACAGTATCGG
22550 TACTATTCATA
1 TACTATTCATA
22561 AAAAAATTTA
Statistics
Matches: 60, Mismatches: 9, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
19 30 0.50
20 30 0.50
ACGTcount: A:0.33, C:0.20, G:0.13, T:0.34
Consensus pattern (20 bp):
TACTATTCATACAGTATCGG
Found at i:22542 original size:39 final size:39
Alignment explanation
Indices: 22472--22560 Score: 110
Period size: 39 Copynumber: 2.3 Consensus size: 39
22462 TATTGTTCAT
* * *
22472 TACTGTTCACACAGTATCGGTACTATGCATACAGTATA-TG
1 TACTATTCATACAGTATCGGTACTATGCATACA--ATACGG
*
22512 TACTATTCATACAGTA-CGGTACTATTCATACAATACGG
1 TACTATTCATACAGTATCGGTACTATGCATACAATACGG
22550 TACTATTCATA
1 TACTATTCATA
22561 AAAAAATTTA
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
37 3 0.07
38 12 0.27
39 15 0.34
40 14 0.32
ACGTcount: A:0.33, C:0.20, G:0.13, T:0.34
Consensus pattern (39 bp):
TACTATTCATACAGTATCGGTACTATGCATACAATACGG
Found at i:24583 original size:24 final size:22
Alignment explanation
Indices: 24543--24619 Score: 67
Period size: 24 Copynumber: 3.6 Consensus size: 22
24533 ATGCAATTAA
24543 TGCATCGATGCA---TAAGGAG
1 TGCATCGATGCACTGTAAGGAG
24562 TGCATCGATGCACATGTTAAGG-G
1 TGCATCGATGCAC-TG-TAAGGAG
* *
24585 ATGCATCGATACACTGT-A-GAA
1 -TGCATCGATGCACTGTAAGGAG
24606 TGCATCGATGCACT
1 TGCATCGATGCACT
24620 TCAAGGGAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 13
0.75 0.05 0.20
Matches are distributed among these distances:
19 12 0.25
20 14 0.29
21 1 0.02
22 1 0.02
23 3 0.06
24 17 0.35
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.25
Consensus pattern (22 bp):
TGCATCGATGCACTGTAAGGAG
Found at i:26172 original size:23 final size:23
Alignment explanation
Indices: 26145--26190 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
26135 ACATTTTATA
*
26145 TGGCACTTCGGTGCAATTATACG
1 TGGCACTACGGTGCAATTATACG
*
26168 TGGCACTACGGTGCATTTATACG
1 TGGCACTACGGTGCAATTATACG
26191 AGCTGTGGTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.22, C:0.22, G:0.26, T:0.30
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTATACG
Found at i:31724 original size:23 final size:23
Alignment explanation
Indices: 31697--31742 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
31687 ATATTTTATA
*
31697 TGGCACTTCGGTGCAATTATACG
1 TGGCACTACGGTGCAATTATACG
*
31720 TGGCACTACGGTGCATTTATACG
1 TGGCACTACGGTGCAATTATACG
31743 AGCTGTGGTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.22, C:0.22, G:0.26, T:0.30
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTATACG
Found at i:33354 original size:20 final size:17
Alignment explanation
Indices: 33309--33352 Score: 88
Period size: 17 Copynumber: 2.6 Consensus size: 17
33299 CTTTTTCTTG
33309 TTTTTCTTCTCTTCATA
1 TTTTTCTTCTCTTCATA
33326 TTTTTCTTCTCTTCATA
1 TTTTTCTTCTCTTCATA
33343 TTTTTCTTCT
1 TTTTTCTTCT
33353 TCCTTCAACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.09, C:0.23, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTTTCTTCTCTTCATA
Found at i:34840 original size:20 final size:20
Alignment explanation
Indices: 34817--34889 Score: 121
Period size: 20 Copynumber: 3.7 Consensus size: 20
34807 TTTCACACAA
*
34817 TATCAGTACTATTCATACAG
1 TATCGGTACTATTCATACAG
*
34837 TATCGATACTATTCATACAG
1 TATCGGTACTATTCATACAG
34857 TATCGGTACTATTCATACAG
1 TATCGGTACTATTCATACAG
34877 TAT-GGTACTATTC
1 TATCGGTACTATTC
34890 GTAAAAAAAT
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
19 10 0.20
20 40 0.80
ACGTcount: A:0.32, C:0.19, G:0.12, T:0.37
Consensus pattern (20 bp):
TATCGGTACTATTCATACAG
Found at i:34877 original size:40 final size:39
Alignment explanation
Indices: 34808--34889 Score: 119
Period size: 40 Copynumber: 2.1 Consensus size: 39
34798 TTCATTATTT
34808 TTCACACAATATCAGTACTATTCATACAGTATCGATACTA
1 TTCACACAATATCAGTACTATTCATACAGTAT-GATACTA
* * * *
34848 TTCATACAGTATCGGTACTATTCATACAGTATGGTACTA
1 TTCACACAATATCAGTACTATTCATACAGTATGATACTA
34887 TTC
1 TTC
34890 GTAAAAAAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
39 9 0.24
40 29 0.76
ACGTcount: A:0.33, C:0.21, G:0.11, T:0.35
Consensus pattern (39 bp):
TTCACACAATATCAGTACTATTCATACAGTATGATACTA
Found at i:35810 original size:21 final size:21
Alignment explanation
Indices: 35785--35825 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
35775 CCGTGAACAG
*
35785 TGCTACAGTGCATCGATGCAT
1 TGCTACAGTGCACCGATGCAT
35806 TGCTACAGTGCACCGATGCA
1 TGCTACAGTGCACCGATGCA
35826 CTAAAATTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.24
Consensus pattern (21 bp):
TGCTACAGTGCACCGATGCAT
Found at i:36727 original size:31 final size:31
Alignment explanation
Indices: 36673--36864 Score: 113
Period size: 32 Copynumber: 6.1 Consensus size: 31
36663 GAACCTTGGC
* *
36673 AACTGTCCATAGGTCCCAAAGAACCTAGGTA
1 AACTGTCCATATGTCCCAAAGAACATAGGTA
* ** *
36704 AACTGTCCATATGTTCCTTAGAACATAGTTA
1 AACTGTCCATATGTCCCAAAGAACATAGGTA
* * *
36735 TACTGTCCATATATCTCAAA-AGACATAGGTA
1 AACTGTCCATATGTCCCAAAGA-ACATAGGTA
* * * **
36766 ATTCTATCCATATATTCTGAAAG-ACATAGGTA
1 A-ACTGTCCATAT-GTCCCAAAGAACATAGGTA
* *
36798 ATTCTGTCCATATGTCCCTAAA-TACATAGGTA
1 A-ACTGTCCATATGTCCC-AAAGAACATAGGTA
* ** *
36830 ATTA-TGTCCATATGTTCCGTACAACATAGGTA
1 A--ACTGTCCATATGTCCCAAAGAACATAGGTA
36862 AAC
1 AAC
36865 CCTCGACTCT
Statistics
Matches: 125, Mismatches: 27, Indels: 18
0.74 0.16 0.11
Matches are distributed among these distances:
30 2 0.02
31 50 0.40
32 66 0.53
33 7 0.06
ACGTcount: A:0.35, C:0.20, G:0.14, T:0.31
Consensus pattern (31 bp):
AACTGTCCATATGTCCCAAAGAACATAGGTA
Found at i:36857 original size:32 final size:33
Alignment explanation
Indices: 36698--36862 Score: 139
Period size: 32 Copynumber: 5.2 Consensus size: 33
36688 CCAAAGAACC
* * *
36698 TAGGTAA-ACTGTCCATATGTTCCTTAGA-ACA
1 TAGGTAATTCTGTCCATATGTTCCGTAAAGACA
* * * *
36729 TA-GTTATACTGTCCATAT-ATCTC-AAAAGACA
1 TAGGTAATTCTGTCCATATGTTC-CGTAAAGACA
* * *
36760 TAGGTAATTCTATCCATATATTCTG-AAAGACA
1 TAGGTAATTCTGTCCATATGTTCCGTAAAGACA
* *
36792 TAGGTAATTCTGTCCATATG-TCCCTAAATACA
1 TAGGTAATTCTGTCCATATGTTCCGTAAAGACA
* *
36824 TAGGTAATTATGTCCATATGTTCCGTACA-ACA
1 TAGGTAATTCTGTCCATATGTTCCGTAAAGACA
36856 TAGGTAA
1 TAGGTAA
36863 ACCCTCGACT
Statistics
Matches: 109, Mismatches: 17, Indels: 15
0.77 0.12 0.11
Matches are distributed among these distances:
30 7 0.06
31 21 0.19
32 73 0.67
33 8 0.07
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.33
Consensus pattern (33 bp):
TAGGTAATTCTGTCCATATGTTCCGTAAAGACA
Found at i:36857 original size:64 final size:64
Alignment explanation
Indices: 36674--36862 Score: 172
Period size: 64 Copynumber: 3.0 Consensus size: 64
36664 AACCTTGGCA
** * * * *
36674 ACTGTCCATAGGTCCC-AAAGAACCTAGGTAA--ACTGTCCATATGTTCCTTAGAACATA-GTTA
1 ACTGTCCATATATCCCAAAAG-ACATAGGTAATTA-TGTCCATATGTTCCGTAAAACATAGGTAA
36735 T
64 T
* * * * *
36736 ACTGTCCATATATCTCAAAAGACATAGGTAATTCTATCCATATATTCTG-AAAGACATAGGTAAT
1 ACTGTCCATATATCCCAAAAGACATAGGTAATTATGTCCATATGTTCCGTAAA-ACATAGGTAAT
* * * * *
36800 TCTGTCCATATGTCCCTAAATACATAGGTAATTATGTCCATATGTTCCGTACAACATAGGTAA
1 ACTGTCCATATATCCCAAAAGACATAGGTAATTATGTCCATATGTTCCGTAAAACATAGGTAA
36863 ACCCTCGACT
Statistics
Matches: 100, Mismatches: 21, Indels: 10
0.76 0.16 0.08
Matches are distributed among these distances:
62 24 0.24
63 20 0.20
64 54 0.54
65 2 0.02
ACGTcount: A:0.34, C:0.20, G:0.14, T:0.31
Consensus pattern (64 bp):
ACTGTCCATATATCCCAAAAGACATAGGTAATTATGTCCATATGTTCCGTAAAACATAGGTAAT
Found at i:39981 original size:45 final size:45
Alignment explanation
Indices: 39925--40232 Score: 303
Period size: 45 Copynumber: 6.8 Consensus size: 45
39915 GTATAACATA
* * * *
39925 TTTTCTGTTGATAATGCACTCATATGCATTTCAACTATTGTATAC
1 TTTTCTGTTGATAATGTACCCATATACATTTCAACTATAGTATAC
* * * * * * *
39970 TTTTATATTGATGACGTACCTATATACATCTCAACCATAGTATAC
1 TTTTCTGTTGATAATGTACCCATATACATTTCAACTATAGTATAC
* * *
40015 TTTTTCTGTTGAGAATGTACCCATATACATTTCAACTCTAGCATAC
1 -TTTTCTGTTGATAATGTACCCATATACATTTCAACTATAGTATAC
* * *
40061 TTTTCTGTTGATAATGCACCCATATGCATTTCAACTCTAGTATAC
1 TTTTCTGTTGATAATGTACCCATATACATTTCAACTATAGTATAC
* * * * * *
40106 TTTTATGTTGATGATATACCCATATACATCTCAACCATAATATAC
1 TTTTCTGTTGATAATGTACCCATATACATTTCAACTATAGTATAC
* * * * *
40151 TTTTTATGTT-ACGAATGTACCCATATACATTTTAACCATATTATAC
1 -TTTTCTGTTGA-TAATGTACCCATATACATTTCAACTATAGTATAC
* * *
40197 TTTTCTGTTGATAACGCACCCATATGCATTTCAACT
1 TTTTCTGTTGATAATGTACCCATATACATTTCAACT
40233 CTGGCATCCT
Statistics
Matches: 212, Mismatches: 47, Indels: 8
0.79 0.18 0.03
Matches are distributed among these distances:
45 139 0.66
46 73 0.34
ACGTcount: A:0.30, C:0.20, G:0.09, T:0.40
Consensus pattern (45 bp):
TTTTCTGTTGATAATGTACCCATATACATTTCAACTATAGTATAC
Found at i:40046 original size:91 final size:89
Alignment explanation
Indices: 39925--40232 Score: 298
Period size: 91 Copynumber: 3.4 Consensus size: 89
39915 GTATAACATA
* * * * *
39925 TTTTCTGTTGATAATGCACTCATATGCATTTCAACTATTGTATACTTTTATATTGATGACGTACC
1 TTTTCTGTTGAGAATGCACCCATATACATTTCAACTATAGTATACTTTT-TATTGATGATGTACC
* *
39990 TATATACATCTCAACCATAGTATAC
65 CATATACATTTCAACCATAGTATAC
* * * * * *
40015 TTTTTCTGTTGAGAATGTACCCATATACATTTCAACTCTAGCATACTTTTCTGTTGATAATGCAC
1 -TTTTCTGTTGAGAATGCACCCATATACATTTCAACTATAGTATACTTTT-TATTGATGATGTAC
*
40080 CCATATGCATTTCAACTC-TAGTATAC
64 CCATATACATTTCAAC-CATAGTATAC
* * * * * *
40106 TTTTATGTTGATGATAT--ACCCATATACATCTCAACCATAATATACTTTTTATGTTACGAATGT
1 TTTTCTGTTGA-GA-ATGCACCCATATACATTTCAACTATAGTATACTTTTTAT-TGATG-ATGT
* *
40169 ACCCATATACATTTTAACCATATTATAC
62 ACCCATATACATTTCAACCATAGTATAC
* * *
40197 TTTTCTGTTGATAACGCACCCATATGCATTTCAACT
1 TTTTCTGTTGAGAATGCACCCATATACATTTCAACT
40233 CTGGCATCCT
Statistics
Matches: 174, Mismatches: 35, Indels: 16
0.77 0.16 0.07
Matches are distributed among these distances:
89 3 0.02
90 41 0.24
91 127 0.73
92 3 0.02
ACGTcount: A:0.30, C:0.20, G:0.09, T:0.40
Consensus pattern (89 bp):
TTTTCTGTTGAGAATGCACCCATATACATTTCAACTATAGTATACTTTTTATTGATGATGTACCC
ATATACATTTCAACCATAGTATAC
Found at i:40266 original size:136 final size:136
Alignment explanation
Indices: 39921--40234 Score: 472
Period size: 136 Copynumber: 2.3 Consensus size: 136
39911 TAAAGTATAA
* * * * *
39921 CATA-TTTTCTGTTGATAATGCACTCATATGCATTTCAACTATTGTATACTTTTATATTGATGAC
1 CATACTTTTCTGTTGATAATGCACCCATATGCATTTCAACTCTAGTATACTTTTATGTTGATGAT
* * *
39985 GTACCTATATACATCTCAACCATAGTATACTTTTTCTGTTGAGAATGTACCCATATACATTTCAA
66 GTACCCATATACATCTCAACCATAATATACTTTTTATGTTGAGAATGTACCCATATACATTTCAA
40050 CTCTAG
131 CTCTAG
40056 CATACTTTTCTGTTGATAATGCACCCATATGCATTTCAACTCTAGTATACTTTTATGTTGATGAT
1 CATACTTTTCTGTTGATAATGCACCCATATGCATTTCAACTCTAGTATACTTTTATGTTGATGAT
* *
40121 ATACCCATATACATCTCAACCATAATATACTTTTTATGTT-ACGAATGTACCCATATACATTTTA
66 GTACCCATATACATCTCAACCATAATATACTTTTTATGTTGA-GAATGTACCCATATACATTTCA
*
40185 AC-CATAT
130 ACTC-TAG
* *
40192 TATACTTTTCTGTTGATAACGCACCCATATGCATTTCAACTCT
1 CATACTTTTCTGTTGATAATGCACCCATATGCATTTCAACTCT
40235 GGCATCCTTT
Statistics
Matches: 163, Mismatches: 13, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
135 6 0.04
136 157 0.96
ACGTcount: A:0.30, C:0.21, G:0.09, T:0.40
Consensus pattern (136 bp):
CATACTTTTCTGTTGATAATGCACCCATATGCATTTCAACTCTAGTATACTTTTATGTTGATGAT
GTACCCATATACATCTCAACCATAATATACTTTTTATGTTGAGAATGTACCCATATACATTTCAA
CTCTAG
Found at i:40806 original size:20 final size:22
Alignment explanation
Indices: 40781--40835 Score: 78
Period size: 22 Copynumber: 2.6 Consensus size: 22
40771 CGATATAGAC
40781 TGGTATCGATACCC-T-CACCA
1 TGGTATCGATACCCTTACACCA
* *
40801 TGGTATCGATACCCTTATACTA
1 TGGTATCGATACCCTTACACCA
40823 TGGTATCGATACC
1 TGGTATCGATACC
40836 TCCTCTAGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 14 0.45
21 1 0.03
22 16 0.52
ACGTcount: A:0.25, C:0.27, G:0.16, T:0.31
Consensus pattern (22 bp):
TGGTATCGATACCCTTACACCA
Found at i:40863 original size:19 final size:19
Alignment explanation
Indices: 40826--40864 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
40816 TATACTATGG
**
40826 TATCGATACCTCCTCTAGA
1 TATCGATACCTAATCTAGA
*
40845 TATCGATACCTAATTTAGA
1 TATCGATACCTAATCTAGA
40864 T
1 T
40865 TTGATATTTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.31, C:0.23, G:0.10, T:0.36
Consensus pattern (19 bp):
TATCGATACCTAATCTAGA
Found at i:41399 original size:23 final size:23
Alignment explanation
Indices: 41373--41419 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
41363 ATCCTCTCTA
*
41373 AACCTTTATTAAGCTTCCCTCAT
1 AACCTTTATTAAGATTCCCTCAT
41396 AACCTTTATTAAGATTCCCTCAT
1 AACCTTTATTAAGATTCCCTCAT
41419 A
1 A
41420 GGCAAAGATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.30, C:0.28, G:0.04, T:0.38
Consensus pattern (23 bp):
AACCTTTATTAAGATTCCCTCAT
Found at i:47109 original size:45 final size:45
Alignment explanation
Indices: 47053--47360 Score: 339
Period size: 45 Copynumber: 6.8 Consensus size: 45
47043 GTATAACATT
* * * * *
47053 TTTTCTATTGATATTGCACTCATATGCATTTCAACTATTGTATAC
1 TTTTCTGTTGATAATGCACCCATATACATTTCAACTATAGTATAC
* * * * *
47098 TTTTATGTTGATGATGTACCCATATACATCTCAACCATAGTATAC
1 TTTTCTGTTGATAATGCACCCATATACATTTCAACTATAGTATAC
* ** * * *
47143 GTTTTCTGTTGAGAATATACCTATATACATTTCAACTCTAGCATAC
1 -TTTTCTGTTGATAATGCACCCATATACATTTCAACTATAGTATAC
* * *
47189 TTTTCTGTTGATAATGCACCCATATGCATTTTAACTCTAGTATAC
1 TTTTCTGTTGATAATGCACCCATATACATTTCAACTATAGTATAC
* * * * *
47234 TTTTATGTTGATGATGTACCCATATACATCTCAACCATAGTATAC
1 TTTTCTGTTGATAATGCACCCATATACATTTCAACTATAGTATAC
* *
47279 TTTTTCTGTTG-TGAATGTACCCATATACATTTCAACCATAGTATAC
1 -TTTTCTGTTGAT-AATGCACCCATATACATTTCAACTATAGTATAC
*
47325 TTTTCTGTTGATAATACACCCATATACATTTCAACT
1 TTTTCTGTTGATAATGCACCCATATACATTTCAACT
47361 CTGGCATCAT
Statistics
Matches: 219, Mismatches: 40, Indels: 8
0.82 0.15 0.03
Matches are distributed among these distances:
45 142 0.65
46 77 0.35
ACGTcount: A:0.29, C:0.20, G:0.10, T:0.41
Consensus pattern (45 bp):
TTTTCTGTTGATAATGCACCCATATACATTTCAACTATAGTATAC
Found at i:47176 original size:91 final size:90
Alignment explanation
Indices: 47073--47360 Score: 357
Period size: 91 Copynumber: 3.2 Consensus size: 90
47063 ATATTGCACT
* * * *
47073 CATATGCATTTCAACTATTGTATACTTTTATGTTGATGATGTACCCATATACATCTCAACCATAG
1 CATATACATTTCAACTATAGTATACTTTTCTGTTGATGATGTACCCATATACATTTCAACCATAG
47138 TATACGTTTTCTGTTGAGAATATACC
66 TATAC-TTTTCTGTTGAGAATATACC
* * * * * * *
47164 TATATACATTTCAACTCTAGCATACTTTTCTGTTGATAATGCACCCATATGCATTTTAACTC-TA
1 CATATACATTTCAACTATAGTATACTTTTCTGTTGATGATGTACCCATATACATTTCAAC-CATA
* *
47228 GTATACTTTTATGTTGATG-ATGTACC
65 GTATACTTTTCTGTTGA-GAATATACC
* *
47254 CATATACATCTCAACCATAGTATACTTTTTCTGTTG-TGAATGTACCCATATACATTTCAACCAT
1 CATATACATTTCAACTATAGTATAC-TTTTCTGTTGATG-ATGTACCCATATACATTTCAACCAT
* *
47318 AGTATACTTTTCTGTTGATAATACACC
64 AGTATACTTTTCTGTTGAGAATATACC
47345 CATATACATTTCAACT
1 CATATACATTTCAACT
47361 CTGGCATCAT
Statistics
Matches: 163, Mismatches: 28, Indels: 12
0.80 0.14 0.06
Matches are distributed among these distances:
90 38 0.23
91 124 0.76
92 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.10, T:0.40
Consensus pattern (90 bp):
CATATACATTTCAACTATAGTATACTTTTCTGTTGATGATGTACCCATATACATTTCAACCATAG
TATACTTTTCTGTTGAGAATATACC
Found at i:47274 original size:136 final size:136
Alignment explanation
Indices: 47053--47362 Score: 487
Period size: 136 Copynumber: 2.3 Consensus size: 136
47043 GTATAACATT
* * * * *
47053 TTTTCTATTGATATTGCACTCATATGCATTTCAACTATTGTATACTTTTATGTTGATGATGTACC
1 TTTTCTGTTGATAATGCACCCATATGCATTTCAACTCTAGTATACTTTTATGTTGATGATGTACC
*
47118 CATATACATCTCAACCATAGTATACGTTTTCTGTTGAGAATATACCTATATACATTTCAACTC-T
66 CATATACATCTCAACCATAGTATACGTTTTCTGTTGAGAATATACCCATATACATTTCAAC-CAT
47182 AGCATAC
130 AGCATAC
*
47189 TTTTCTGTTGATAATGCACCCATATGCATTTTAACTCTAGTATACTTTTATGTTGATGATGTACC
1 TTTTCTGTTGATAATGCACCCATATGCATTTCAACTCTAGTATACTTTTATGTTGATGATGTACC
* * *
47254 CATATACATCTCAACCATAGTATACTTTTTCTGTTGTGAATGTACCCATATACATTTCAACCATA
66 CATATACATCTCAACCATAGTATACGTTTTCTGTTGAGAATATACCCATATACATTTCAACCATA
*
47319 GTATAC
131 GCATAC
* *
47325 TTTTCTGTTGATAATACACCCATATACATTTCAACTCT
1 TTTTCTGTTGATAATGCACCCATATGCATTTCAACTCT
47363 GGCATCATTT
Statistics
Matches: 159, Mismatches: 14, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
135 1 0.01
136 158 0.99
ACGTcount: A:0.29, C:0.20, G:0.10, T:0.41
Consensus pattern (136 bp):
TTTTCTGTTGATAATGCACCCATATGCATTTCAACTCTAGTATACTTTTATGTTGATGATGTACC
CATATACATCTCAACCATAGTATACGTTTTCTGTTGAGAATATACCCATATACATTTCAACCATA
GCATAC
Found at i:47391 original size:136 final size:136
Alignment explanation
Indices: 47115--47394 Score: 384
Period size: 136 Copynumber: 2.1 Consensus size: 136
47105 TTGATGATGT
*
47115 ACCCATATACATCTCAACCATAGTATACGTTTTCTGTTGAGAATATACCTATATACATTTCAACT
1 ACCCATATACATCTCAACCATAGTATACGTTTTCTGTTGAGAATATACCCATATACATTTCAACT
* * * * * **
47180 CTAGCATACTTTTCTGTTGATAATGCACCCATATGCATTTTAACTCTAGTATACTTTTATGTTGA
66 CTAGCATACTTTTCTGTTGATAATACACCCATATACATTTCAACTCTAGCATACTTTCATGCCGA
* * *
47245 TGATGT
131 TAACGC
* * *
47251 ACCCATATACATCTCAACCATAGTATACTTTTTCTGTTGTGAATGTACCCATATACATTTCAAC-
1 ACCCATATACATCTCAACCATAGTATACGTTTTCTGTTGAGAATATACCCATATACATTTCAACT
* *
47315 CATAGTATACTTTTCTGTTGATAATACACCCATATACATTTCAACTCTGGCAT-CATTTCATGCC
66 C-TAGCATACTTTTCTGTTGATAATACACCCATATACATTTCAACTCTAGCATAC-TTTCATGCC
47379 GATAACGC
129 GATAACGC
47387 ACCCATAT
1 ACCCATAT
47395 GCATTTTTTC
Statistics
Matches: 126, Mismatches: 16, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
135 2 0.02
136 124 0.98
ACGTcount: A:0.30, C:0.23, G:0.10, T:0.37
Consensus pattern (136 bp):
ACCCATATACATCTCAACCATAGTATACGTTTTCTGTTGAGAATATACCCATATACATTTCAACT
CTAGCATACTTTTCTGTTGATAATACACCCATATACATTTCAACTCTAGCATACTTTCATGCCGA
TAACGC
Found at i:47984 original size:19 final size:21
Alignment explanation
Indices: 47933--47988 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 21
47923 TATCCTCACC
47933 ATGGTATCGATACCCCTATACT
1 ATGGTATCGATACCCC-ATACT
*
47955 ATGGTACCGATACCTCC-T-CT
1 ATGGTATCGATACC-CCATACT
47975 A-GGTATCGATACCC
1 ATGGTATCGATACCC
47989 AATTTAGATT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
18 1 0.03
19 11 0.35
20 3 0.10
21 1 0.03
22 13 0.42
23 2 0.06
ACGTcount: A:0.25, C:0.30, G:0.16, T:0.29
Consensus pattern (21 bp):
ATGGTATCGATACCCCATACT
Found at i:57088 original size:88 final size:89
Alignment explanation
Indices: 56948--57109 Score: 272
Period size: 88 Copynumber: 1.8 Consensus size: 89
56938 TTATAGCCAA
* *
56948 GTTACCCTAATCATATTAGGGTTTTTATTATTTCAAATTAATTAAATCTATATTTAATTAATTGA
1 GTTACCCAAATCATATTAGGGTATTTATTATTTCAAATTAATTAAATCTATATTTAATTAATTGA
*
57013 AATTTAATAATCCTTTATATCTAT
66 AATTAAATAATCCTTTATATCTAT
* *
57037 GTTACCCAAATCATATTAGGG-ATTTATTATTTCAAATTAATTAAATTTATATTTGATTAATTGA
1 GTTACCCAAATCATATTAGGGTATTTATTATTTCAAATTAATTAAATCTATATTTAATTAATTGA
57101 AATTAAATA
66 AATTAAATA
57110 TTTGGGATTA
Statistics
Matches: 68, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
88 48 0.71
89 20 0.29
ACGTcount: A:0.38, C:0.09, G:0.07, T:0.46
Consensus pattern (89 bp):
GTTACCCAAATCATATTAGGGTATTTATTATTTCAAATTAATTAAATCTATATTTAATTAATTGA
AATTAAATAATCCTTTATATCTAT
Found at i:57119 original size:24 final size:20
Alignment explanation
Indices: 57072--57113 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
57062 ATTATTTCAA
*
57072 ATTAATTAAATTTATATTTG
1 ATTAATTAAATTAATATTTG
57092 ATTAATTGAAATTAAATATTTG
1 ATTAATT-AAATT-AATATTTG
57114 GGATTATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 7 0.37
21 5 0.26
22 7 0.37
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (20 bp):
ATTAATTAAATTAATATTTG
Done.