Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001768.1 Hibiscus syriacus cultivar Beakdansim tig00003567_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: 72170
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:8672 original size:54 final size:54
Alignment explanation
Indices: 8591--9021 Score: 575
Period size: 54 Copynumber: 8.1 Consensus size: 54
8581 CTATGTGTAT
*
8591 TATAGGCACTAA--GTGCAACCCACAGAATTCATCATATGTTGATGAACGATCG
1 TATAGGCACTAAGTGTGCAACCCACAGAATTCATCATATGTTGATGAACGACCG
*
8643 TATAGGCACTAAGTGTGCAAGCCACAGAATTCATCATATGTTGATGAACGACCG
1 TATAGGCACTAAGTGTGCAACCCACAGAATTCATCATATGTTGATGAACGACCG
** *
8697 TATAAACACTAAGTGTGCAACCCACAGAATTCATCATATGTTGATGAAAGACCG
1 TATAGGCACTAAGTGTGCAACCCACAGAATTCATCATATGTTGATGAACGACCG
*
8751 TATAGGCACTAAGTGTGCAACCCACTGAATTCATCATA--TTGATGAACGACCG
1 TATAGGCACTAAGTGTGCAACCCACAGAATTCATCATATGTTGATGAACGACCG
* * * **
8803 TATTGGCACTAAGTGTGCAACCCACATAATTCATCATATATTGATGAACGACTA
1 TATAGGCACTAAGTGTGCAACCCACAGAATTCATCATATGTTGATGAACGACCG
* ** *
8857 TATAGGTACTAAGTGTGCAACCCATGGAATTCATCATATGTTGATGAACGACAG
1 TATAGGCACTAAGTGTGCAACCCACAGAATTCATCATATGTTGATGAACGACCG
* * * * * * *
8911 TATAGGCACTAAGTGTACAACACACATAATTTATCATATGTTGTTCAACTACCG
1 TATAGGCACTAAGTGTGCAACCCACAGAATTCATCATATGTTGATGAACGACCG
* * * * *
8965 TATAGGCACTAAGTGTACAAACCAC-GAAATTCATAATATGTTTACGAACGACCG
1 TATAGGCACTAAGTGTGCAACCCACAG-AATTCATCATATGTTGATGAACGACCG
9019 TAT
1 TAT
9022 CGATACTACG
Statistics
Matches: 330, Mismatches: 44, Indels: 8
0.86 0.12 0.02
Matches are distributed among these distances:
52 60 0.18
54 270 0.82
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (54 bp):
TATAGGCACTAAGTGTGCAACCCACAGAATTCATCATATGTTGATGAACGACCG
Found at i:8870 original size:160 final size:160
Alignment explanation
Indices: 8591--9017 Score: 538
Period size: 160 Copynumber: 2.7 Consensus size: 160
8581 CTATGTGTAT
* *
8591 TATAGGCACTAA--GTGCAACCCACAGAATTCATCATATGTTGATGAACGATCGTATAGGCACTA
1 TATAGGCACTAAGTGTGCAACCCACTGAATTCATCATA-GTTGATGAACGACCGTATAGGCACTA
* * *
8654 AGTGTGCAAGCCACAGAATTCATCATATGTTGATGAACGACCGTATAAACACTAAGTGTGCAACC
65 AGTGTGCAAACCACA-AATTCATCATATATTGATGAACGACCATATAAACACTAAGTGTGCAACC
*
8719 CACAGAATTCATCATATGTTGATGAAAGACCG
129 CACAGAATTCATCATATGTTGATGAAAGACAG
*
8751 TATAGGCACTAAGTGTGCAACCCACTGAATTCATCATA-TTGATGAACGACCGTATTGGCACTAA
1 TATAGGCACTAAGTGTGCAACCCACTGAATTCATCATAGTTGATGAACGACCGTATAGGCACTAA
* * ***
8815 GTGTGCAACCCACATAATTCATCATATATTGATGAACGACTATATAGGTACTAAGTGTGCAACCC
66 GTGTGCAAACCACA-AATTCATCATATATTGATGAACGACCATATAAACACTAAGTGTGCAACCC
** *
8880 ATGGAATTCATCATATGTTGATGAACGACAG
130 ACAGAATTCATCATATGTTGATGAAAGACAG
* * * * * *
8911 TATAGGCACTAAGTGTACAACACACAT-AATTTATCATATGTTGTTCAACTACCGTATAGGCACT
1 TATAGGCACTAAGTGTGCAACCCAC-TGAATTCATCATA-GTTGATGAACGACCGTATAGGCACT
* * * * *
8975 AAGTGTACAAACCACGAAATTCATAATATGTTTACGAACGACC
64 AAGTGTGCAAACCAC-AAATTCATCATATATTGATGAACGACC
9018 GTATCGATAC
Statistics
Matches: 232, Mismatches: 29, Indels: 10
0.86 0.11 0.04
Matches are distributed among these distances:
160 153 0.66
161 1 0.00
162 77 0.33
163 1 0.00
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.26
Consensus pattern (160 bp):
TATAGGCACTAAGTGTGCAACCCACTGAATTCATCATAGTTGATGAACGACCGTATAGGCACTAA
GTGTGCAAACCACAAATTCATCATATATTGATGAACGACCATATAAACACTAAGTGTGCAACCCA
CAGAATTCATCATATGTTGATGAAAGACAG
Found at i:8972 original size:214 final size:213
Alignment explanation
Indices: 8595--9021 Score: 581
Period size: 214 Copynumber: 2.0 Consensus size: 213
8585 GTGTATTATA
* *
8595 GGCACTAAGTGCAACCCACAGAATTCATCATATGTTGATGAACGATCGTATAGGCACTAAGTGTG
1 GGCACTAAGTGCAACCCACAGAATTCATCATATATTGATGAACGATCATATAGGCACTAAGTGTG
* * * *
8660 CAAGCCACAGAATTCATCATATGTTGATGAACGACCGTATAAACACTAAGTGTGCAACCCACAGA
66 CAACCCACAGAATTCATCATATGTTGATGAACGACAGTATAAACACTAAGTGTACAACACACAGA
* * * *
8725 ATTCATCATATGTTGATGAAAGACCGTATAGGCACTAAGTGTGCAACCCACTG-AATTCATCATA
131 ATTCATCATATGTTGATCAAAGACCGTATAGGCACTAAGTGTACAAACCAC-GAAATTCATAATA
*
8789 -TTGATGAACGACCGTATT
195 GTTGACGAACGACCGTATT
* *
8807 GGCACTAAGTGTGCAACCCACATAATTCATCATATATTGATGAACGA-CTATATAGGTACTAAGT
1 GGCACTAA--GTGCAACCCACAGAATTCATCATATATTGATGAACGATC-ATATAGGCACTAAGT
** **
8871 GTGCAACCCATGGAATTCATCATATGTTGATGAACGACAGTATAGGCACTAAGTGTACAACACAC
63 GTGCAACCCACAGAATTCATCATATGTTGATGAACGACAGTATAAACACTAAGTGTACAACACAC
* * * **
8936 ATAATTTATCATATGTTGTTCAACTACCGTATAGGCACTAAGTGTACAAACCACGAAATTCATAA
128 AGAATTCATCATATGTTGATCAAAGACCGTATAGGCACTAAGTGTACAAACCACGAAATTCATAA
*
9001 TATGTTTACGAACGACCGTAT
193 TA-GTTGACGAACGACCGTAT
9022 CGATACTACG
Statistics
Matches: 186, Mismatches: 23, Indels: 8
0.86 0.11 0.04
Matches are distributed among these distances:
212 8 0.04
213 2 0.01
214 161 0.87
216 15 0.08
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.26
Consensus pattern (213 bp):
GGCACTAAGTGCAACCCACAGAATTCATCATATATTGATGAACGATCATATAGGCACTAAGTGTG
CAACCCACAGAATTCATCATATGTTGATGAACGACAGTATAAACACTAAGTGTACAACACACAGA
ATTCATCATATGTTGATCAAAGACCGTATAGGCACTAAGTGTACAAACCACGAAATTCATAATAG
TTGACGAACGACCGTATT
Found at i:11715 original size:15 final size:15
Alignment explanation
Indices: 11691--11727 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
11681 TGAAATTTCA
11691 GAAC-TACTACATTG
1 GAACATACTACATTG
11705 GAACATACTACATTG
1 GAACATACTACATTG
11720 GAACATAC
1 GAACATAC
11728 GCCATGCTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 4 0.18
15 18 0.82
ACGTcount: A:0.41, C:0.22, G:0.14, T:0.24
Consensus pattern (15 bp):
GAACATACTACATTG
Found at i:14399 original size:31 final size:31
Alignment explanation
Indices: 14339--14429 Score: 110
Period size: 31 Copynumber: 2.9 Consensus size: 31
14329 ACTGACACTC
14339 ATGTGCATTATTTGAATAGAAACCTGACTGTA
1 ATGTGCATTATTTGAAT-GAAACCTGACTGTA
* * *
14371 ATGTGCATTATATGAATGCAGCCTGACTGTA
1 ATGTGCATTATTTGAATGAAACCTGACTGTA
* * * *
14402 TTGTGAATTATTTGAATGTATCCTGACT
1 ATGTGCATTATTTGAATGAAACCTGACT
14430 AGTATTTGAT
Statistics
Matches: 51, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
31 35 0.69
32 16 0.31
ACGTcount: A:0.30, C:0.13, G:0.20, T:0.37
Consensus pattern (31 bp):
ATGTGCATTATTTGAATGAAACCTGACTGTA
Found at i:19875 original size:18 final size:17
Alignment explanation
Indices: 19844--19877 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
19834 ACCTGAAATA
*
19844 AATCCCTTTGCTTGGTT
1 AATCCCTTTCCTTGGTT
19861 AATCTCCTTTCCTTGGT
1 AATC-CCTTTCCTTGGT
19878 ATTTTGGTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.12, C:0.26, G:0.15, T:0.47
Consensus pattern (17 bp):
AATCCCTTTCCTTGGTT
Found at i:23191 original size:21 final size:21
Alignment explanation
Indices: 23167--23211 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
23157 TAATGCTCAA
*
23167 CTCGACTCATTGCTCGTTAAG
1 CTCGACTCATTACTCGTTAAG
*
23188 CTCGACTCGTTACTCGTTAAG
1 CTCGACTCATTACTCGTTAAG
23209 CTC
1 CTC
23212 ACTAAAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.18, C:0.31, G:0.18, T:0.33
Consensus pattern (21 bp):
CTCGACTCATTACTCGTTAAG
Found at i:23334 original size:39 final size:42
Alignment explanation
Indices: 23291--23378 Score: 110
Period size: 43 Copynumber: 2.1 Consensus size: 42
23281 GGATTTTTTG
*
23291 TATTAAAAT-A-ATATTA-TTAATTAATAATATTTTGTTATT
1 TATTAAAATAATATATTAGTTAATTAATAATATTTTATTATT
* * *
23330 TATTAAAAATAATATATTAGTTAATTTATTATTTTTTATTATT
1 TATT-AAAATAATATATTAGTTAATTAATAATATTTTATTATT
23373 TATTAA
1 TATTAA
23379 TAAATTAATC
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
39 4 0.10
40 5 0.12
41 1 0.02
42 8 0.20
43 23 0.56
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (42 bp):
TATTAAAATAATATATTAGTTAATTAATAATATTTTATTATT
Found at i:23356 original size:26 final size:26
Alignment explanation
Indices: 23299--23360 Score: 74
Period size: 25 Copynumber: 2.4 Consensus size: 26
23289 TGTATTAAAA
* *
23299 TAATATTATTAATTAATAATATTTTGT
1 TAAT-TTATTAATAAATAATATTTAGT
23326 T-ATTTATTAA-AAATAATATATTAGT
1 TAATTTATTAATAAATAATAT-TTAGT
23351 TAATTTATTA
1 TAATTTATTA
23361 TTTTTTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
24 8 0.26
25 12 0.39
26 10 0.32
27 1 0.03
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (26 bp):
TAATTTATTAATAAATAATATTTAGT
Found at i:23372 original size:43 final size:45
Alignment explanation
Indices: 23301--23411 Score: 122
Period size: 43 Copynumber: 2.5 Consensus size: 45
23291 TATTAAAATA
* * * *
23301 ATATTATTAATTAATAATATTTTGTTATTTATTAA-AAA-TAAT-
1 ATATTATTAATTTATTATTTTTTATTATTTATTAATAAATTAATC
23343 ATATTAGTTAATTTATTATTTTTTATTATTTATTAATAAATTAATC
1 ATATTA-TTAATTTATTATTTTTTATTATTTATTAATAAATTAATC
23389 ATTATTATTTAGATTTATT-TTTT
1 A-TATTA-TTA-ATTTATTATTTT
23412 GCATGAAATA
Statistics
Matches: 58, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
42 6 0.10
43 25 0.43
44 3 0.05
45 4 0.07
46 1 0.02
47 12 0.21
48 7 0.12
ACGTcount: A:0.38, C:0.01, G:0.03, T:0.59
Consensus pattern (45 bp):
ATATTATTAATTTATTATTTTTTATTATTTATTAATAAATTAATC
Found at i:25420 original size:159 final size:159
Alignment explanation
Indices: 25161--25516 Score: 493
Period size: 159 Copynumber: 2.2 Consensus size: 159
25151 CAATTTCTCC
* *
25161 ATTTTAAGTCCATTTGTTTTACCAAATTTGAATCACATGCTCGTAAACCATCATAGAATACATAT
1 ATTTCAAGTCCATTT-TTTTACCAAATTTGAATCACATGCTCCTAAACCATCATAGAATACATAT
* * *
25226 GTACTTTCAATTCCTCTTTTTTATAACAAAGTTTCTATTTT-TCAATTTAGA-CCCTCAATTTTT
65 GTACTTTCAATTCCTCTTTTTGATAAAAAAGTTTCTATTTTCT-AATTCA-ATCCCTCAATTTTT
25289 CATAATTTCCGTATTTCTTCAATTCATCCTTT
128 CATAATTTCCGTATTTCTTCAATTCATCCTTT
* * * * ** * * * *
25321 ATTTCAATTCCATTTTTTTACCAATTTTGAACCACATTCTCCTAAGTCATCGTATACTACATATT
1 ATTTCAAGTCCATTTTTTTACCAAATTTGAATCACATGCTCCTAAACCATCATAGAATACATATG
* *
25386 TACTTTCAATTCCTCTTTTTGATAAAAAATTTTCTATTTTCTGATTCAATCCCTCAATTTTTCAT
66 TACTTTCAATTCCTCTTTTTGATAAAAAAGTTTCTATTTTCTAATTCAATCCCTCAATTTTTCAT
* *
25451 AATTTCTGTATTTCTTCACTTCATCCTTT
131 AATTTCCGTATTTCTTCAATTCATCCTTT
25480 ATTTCAAGTCCA-TTTTTTACCAAATTTGAATCACATG
1 ATTTCAAGTCCATTTTTTTACCAAATTTGAATCACATG
25517 TGTAGGAATG
Statistics
Matches: 171, Mismatches: 23, Indels: 6
0.86 0.12 0.03
Matches are distributed among these distances:
158 23 0.13
159 134 0.78
160 14 0.08
ACGTcount: A:0.28, C:0.21, G:0.05, T:0.46
Consensus pattern (159 bp):
ATTTCAAGTCCATTTTTTTACCAAATTTGAATCACATGCTCCTAAACCATCATAGAATACATATG
TACTTTCAATTCCTCTTTTTGATAAAAAAGTTTCTATTTTCTAATTCAATCCCTCAATTTTTCAT
AATTTCCGTATTTCTTCAATTCATCCTTT
Found at i:28696 original size:20 final size:20
Alignment explanation
Indices: 28671--28716 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
28661 GATTGTAGGG
*
28671 CTTCTATTCATCTTTCTGAA
1 CTTCTATTCATCTTTATGAA
28691 CTTCTATTCATCTTTATGAA
1 CTTCTATTCATCTTTATGAA
28711 CTTCTA
1 CTTCTA
28717 CAGTTGCCAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.22, C:0.24, G:0.04, T:0.50
Consensus pattern (20 bp):
CTTCTATTCATCTTTATGAA
Found at i:32522 original size:41 final size:41
Alignment explanation
Indices: 32477--32557 Score: 135
Period size: 41 Copynumber: 2.0 Consensus size: 41
32467 AGACCCATTG
*
32477 TTTACATATTTTCTCTATATCCCCTCAAAAAGGCCCCCTTT
1 TTTACATAGTTTCTCTATATCCCCTCAAAAAGGCCCCCTTT
* *
32518 TTTACATGGTTTCTCTATATCCCCTCAAAAAGGGCCCCTT
1 TTTACATAGTTTCTCTATATCCCCTCAAAAAGGCCCCCTT
32558 CCTGTACATT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.23, C:0.31, G:0.09, T:0.37
Consensus pattern (41 bp):
TTTACATAGTTTCTCTATATCCCCTCAAAAAGGCCCCCTTT
Found at i:33101 original size:3 final size:3
Alignment explanation
Indices: 33093--33147 Score: 94
Period size: 3 Copynumber: 18.7 Consensus size: 3
33083 TCTGAAAATA
33093 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
33140 AAT GAT AA
1 AAT AAT AA
33148 ATTAGAACCT
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
2 2 0.04
3 47 0.96
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:35010 original size:21 final size:21
Alignment explanation
Indices: 34963--35007 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 21
34953 TAACTTAGGG
34963 TTTATAATTTAGATTCTAAGA
1 TTTATAATTTAGATTCTAAGA
34984 TTTATAATTTTAGACTT-TAAGA
1 TTTATAA-TTTAGA-TTCTAAGA
35006 TT
1 TT
35008 ATATTAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 7 0.32
22 13 0.59
23 2 0.09
ACGTcount: A:0.36, C:0.04, G:0.09, T:0.51
Consensus pattern (21 bp):
TTTATAATTTAGATTCTAAGA
Found at i:35928 original size:18 final size:18
Alignment explanation
Indices: 35905--35940 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
35895 GAATAAACTT
35905 TATCGTTTTATTATTTAC
1 TATCGTTTTATTATTTAC
35923 TATCGTTTTATTATTTAC
1 TATCGTTTTATTATTTAC
35941 GTGTGTACAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.11, G:0.06, T:0.61
Consensus pattern (18 bp):
TATCGTTTTATTATTTAC
Found at i:48624 original size:13 final size:13
Alignment explanation
Indices: 48608--48635 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
48598 ATATTTCTGT
48608 GATATTTTTCAGA
1 GATATTTTTCAGA
48621 GATATTTTTCAGA
1 GATATTTTTCAGA
48634 GA
1 GA
48636 GACATATCGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.32, C:0.07, G:0.18, T:0.43
Consensus pattern (13 bp):
GATATTTTTCAGA
Found at i:49665 original size:3 final size:3
Alignment explanation
Indices: 49659--49697 Score: 55
Period size: 3 Copynumber: 13.7 Consensus size: 3
49649 TATTTGCTTA
*
49659 TAT TAT TAT TAT TAT TAT TA- TGT TA- TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
49698 AATAATTAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 3 0.09
3 29 0.91
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:49676 original size:25 final size:25
Alignment explanation
Indices: 49648--49697 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
49638 AGTTTTTTTC
49648 TTATT-TGCTTATATTATTATTATTA
1 TTATTATG-TTATATTATTATTATTA
49673 TTATTATGTTATATTATTATTATTA
1 TTATTATGTTATATTATTATTATTA
49698 AATAATTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 22 0.92
26 2 0.08
ACGTcount: A:0.30, C:0.02, G:0.04, T:0.64
Consensus pattern (25 bp):
TTATTATGTTATATTATTATTATTA
Found at i:51050 original size:9 final size:9
Alignment explanation
Indices: 51029--51075 Score: 51
Period size: 9 Copynumber: 5.0 Consensus size: 9
51019 TAACTTTAAA
51029 TTATTAGTTT
1 TTATTA-TTT
51039 TTATTATTT
1 TTATTATTT
51048 TTACTT-TTAT
1 TTA-TTATT-T
*
51058 TTATTATAT
1 TTATTATTT
51067 TTATTATTT
1 TTATTATTT
51076 AAACTTTATA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
9 19 0.59
10 13 0.41
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.72
Consensus pattern (9 bp):
TTATTATTT
Found at i:51081 original size:28 final size:28
Alignment explanation
Indices: 51020--51095 Score: 75
Period size: 28 Copynumber: 2.8 Consensus size: 28
51010 TTTAGCCATT
* * * *
51020 AACTTTAAATTATTAGTTTTTATTATTTT
1 AACTTTTATTTATTA-TATTTATTATTTA
*
51049 TACTTTTATTTATTATATTTATTATTTA
1 AACTTTTATTTATTATATTTATTATTTA
*
51077 AAC-TTTATATA-TATATTTA
1 AACTTTTATTTATTATATTTA
51096 AAATATTATT
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
26 8 0.20
27 7 0.17
28 13 0.32
29 12 0.30
ACGTcount: A:0.33, C:0.04, G:0.01, T:0.62
Consensus pattern (28 bp):
AACTTTTATTTATTATATTTATTATTTA
Found at i:51104 original size:20 final size:21
Alignment explanation
Indices: 51059--51104 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
51049 TACTTTTATT
* *
51059 TATTATATTTATTATTTAAAC
1 TATTATATATATTATTTAAAA
51080 T-TTATATATA-TATTTAAAA
1 TATTATATATATTATTTAAAA
51099 TATTAT
1 TATTAT
51105 TATTATAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
19 9 0.41
20 12 0.55
21 1 0.05
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (21 bp):
TATTATATATATTATTTAAAA
Found at i:51108 original size:15 final size:16
Alignment explanation
Indices: 51062--51118 Score: 53
Period size: 17 Copynumber: 3.3 Consensus size: 16
51052 TTTTATTTAT
51062 TATATTTATTATTTAAA
1 TATA-TTATTATTTAAA
*
51079 CTTTATATATATATTTAAA
1 -TATAT-TAT-TATTTAAA
51098 -ATATTATTATTATAAA
1 TATATTATTATT-TAAA
51114 TATAT
1 TATAT
51119 ATATAAATAA
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
15 4 0.12
16 7 0.21
17 8 0.24
18 6 0.18
19 8 0.24
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (16 bp):
TATATTATTATTTAAA
Found at i:51136 original size:28 final size:26
Alignment explanation
Indices: 51081--51132 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
51071 TATTTAAACT
* * *
51081 TTATATATATATTTAAAATATTATTA
1 TTATAAATATATATAAAATAATATTA
51107 TTATAAATATATATATAAATAATATT
1 TTATAAATATATATA-AAATAATATT
51133 TATTTATTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 13 0.59
27 9 0.41
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (26 bp):
TTATAAATATATATAAAATAATATTA
Found at i:51145 original size:5 final size:5
Alignment explanation
Indices: 51131--51163 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
51121 ATAAATAATA
51131 TTTA- TTTAT TTTAT TTTAT TTTAT TATTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT T-TTAT TTT
51164 TAAATCCTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 4 0.15
5 18 0.67
6 5 0.19
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTAT
Found at i:51393 original size:23 final size:23
Alignment explanation
Indices: 51358--51401 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
51348 CCTTTTCTGA
*
51358 TATTTCTAAATAAATAAATATCT
1 TATTTATAAATAAATAAATATCT
* *
51381 TATTTATATATAAATTAATAT
1 TATTTATAAATAAATAAATAT
51402 ATTTTCTTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (23 bp):
TATTTATAAATAAATAAATATCT
Found at i:55154 original size:15 final size:15
Alignment explanation
Indices: 55134--55165 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
55124 GATCAATACC
55134 TTTTGCATACATGCA
1 TTTTGCATACATGCA
*
55149 TTTTGCATACATTCA
1 TTTTGCATACATGCA
55164 TT
1 TT
55166 ATTCATTGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (15 bp):
TTTTGCATACATGCA
Found at i:58961 original size:9 final size:9
Alignment explanation
Indices: 58947--58978 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
58937 AAATGGTAAT
58947 CATTCTTTA
1 CATTCTTTA
58956 CATTCTTTA
1 CATTCTTTA
*
58965 CATTTTTTA
1 CATTCTTTA
58974 CATTC
1 CATTC
58979 ATTATTTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.22, C:0.22, G:0.00, T:0.56
Consensus pattern (9 bp):
CATTCTTTA
Found at i:62509 original size:12 final size:11
Alignment explanation
Indices: 62488--62544 Score: 59
Period size: 10 Copynumber: 5.4 Consensus size: 11
62478 TATTATGCTT
62488 GAAAGAAAAAA
1 GAAAGAAAAAA
62499 TGAAATGAAAAAA
1 -GAAA-GAAAAAA
62512 GAAAG-AAAAA
1 GAAAGAAAAAA
62522 -AAAG-AAAAA
1 GAAAGAAAAAA
*
62531 GAAA-AAAGAA
1 GAAAGAAAAAA
62541 GAAA
1 GAAA
62545 ATAAAAAAAG
Statistics
Matches: 41, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
9 9 0.22
10 16 0.39
11 1 0.02
12 8 0.20
13 7 0.17
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.04
Consensus pattern (11 bp):
GAAAGAAAAAA
Found at i:62510 original size:13 final size:12
Alignment explanation
Indices: 62487--62522 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
62477 ATATTATGCT
62487 TGAAAGAAAAAA
1 TGAAAGAAAAAA
62499 TGAAATGAAAAAA
1 TGAAA-GAAAAAA
62512 -GAAAGAAAAAA
1 TGAAAGAAAAAA
62523 AAGAAAAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 7 0.30
12 9 0.39
13 7 0.30
ACGTcount: A:0.75, C:0.00, G:0.17, T:0.08
Consensus pattern (12 bp):
TGAAAGAAAAAA
Found at i:62523 original size:13 final size:13
Alignment explanation
Indices: 62506--62555 Score: 61
Period size: 13 Copynumber: 3.9 Consensus size: 13
62496 AAATGAAATG
62506 AAAAAAGAAAGAA
1 AAAAAAGAAAGAA
62519 AAAAAAGAAA-AA
1 AAAAAAGAAAGAA
62531 GAAAAAAG-AAGAA
1 -AAAAAAGAAAGAA
62544 AATAAAA-AAAGA
1 AA-AAAAGAAAGA
62556 GGGTCAAGAT
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
12 6 0.18
13 27 0.82
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.02
Consensus pattern (13 bp):
AAAAAAGAAAGAA
Found at i:62528 original size:25 final size:26
Alignment explanation
Indices: 62488--62550 Score: 78
Period size: 26 Copynumber: 2.5 Consensus size: 26
62478 TATTATGCTT
* *
62488 GAAAG-AAAAAATG-AAATGAAAAAA
1 GAAAGAAAAAAAAGAAAAAGAAAAAA
62512 GAAAGAAAAAAAAGAAAAAGAAAAAA
1 GAAAGAAAAAAAAGAAAAAGAAAAAA
62538 G-AAGAAAATAAAA
1 GAAAGAAAA-AAAA
62551 AAAGAGGGTC
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
24 5 0.15
25 14 0.41
26 15 0.44
ACGTcount: A:0.79, C:0.00, G:0.16, T:0.05
Consensus pattern (26 bp):
GAAAGAAAAAAAAGAAAAAGAAAAAA
Found at i:62536 original size:16 final size:15
Alignment explanation
Indices: 62513--62545 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 15
62503 ATGAAAAAAG
62513 AAAGAAAAAAAAGAA
1 AAAGAAAAAAAAGAA
62528 AAAGAAAAAAGAAGAA
1 AAAGAAAAAA-AAGAA
62544 AA
1 AA
62546 TAAAAAAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (15 bp):
AAAGAAAAAAAAGAA
Found at i:62551 original size:16 final size:16
Alignment explanation
Indices: 62513--62555 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
62503 ATGAAAAAAG
62513 AAAGAAAAAA-AAGAA
1 AAAGAAAAAAGAAGAA
62528 AAAGAAAAAAGAAGAA
1 AAAGAAAAAAGAAGAA
62544 AATA-AAAAAAGA
1 AA-AGAAAAAAGA
62556 GGGTCAAGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
15 10 0.38
16 15 0.58
17 1 0.04
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.02
Consensus pattern (16 bp):
AAAGAAAAAAGAAGAA
Found at i:62907 original size:20 final size:18
Alignment explanation
Indices: 62871--62951 Score: 72
Period size: 20 Copynumber: 4.1 Consensus size: 18
62861 TATTTATTAA
62871 TAAATTCTAAGTTTATTTTCT
1 TAAATTC-AA-TTTATTTT-T
62892 CTAAATTCAATTTATTATTT
1 -TAAATTCAATTTATT-TTT
* *
62912 TGAGATTTAATTTATTTTT
1 T-AAATTCAATTTATTTTT
*
62931 GAAATTCAATTTATTCTTT
1 TAAATTCAATTTATT-TTT
62950 TA
1 TA
62952 TTTTGTAAAT
Statistics
Matches: 50, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
18 12 0.24
19 8 0.16
20 19 0.38
21 4 0.08
22 7 0.14
ACGTcount: A:0.31, C:0.07, G:0.05, T:0.57
Consensus pattern (18 bp):
TAAATTCAATTTATTTTT
Found at i:62932 original size:18 final size:18
Alignment explanation
Indices: 62894--62945 Score: 68
Period size: 18 Copynumber: 2.8 Consensus size: 18
62884 TATTTTCTCT
62894 AAATTCAATTTATTATTTTG
1 AAATTCAATTTA-T-TTTTG
* *
62914 AGATTTAATTTATTTTTG
1 AAATTCAATTTATTTTTG
62932 AAATTCAATTTATT
1 AAATTCAATTTATT
62946 CTTTTATTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
18 17 0.61
19 1 0.04
20 10 0.36
ACGTcount: A:0.35, C:0.04, G:0.06, T:0.56
Consensus pattern (18 bp):
AAATTCAATTTATTTTTG
Found at i:63679 original size:20 final size:20
Alignment explanation
Indices: 63617--63680 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
63607 TTTTCAGAAG
63617 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAACTT
* ***
63637 -ATC-TGAA-GAGGAAGAAGAA
1 GTTCAT-AATGA-GAAGAACTT
63656 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAACTT
63676 GTTCA
1 GTTCA
63681 ACTTTTTGTA
Statistics
Matches: 31, Mismatches: 8, Indels: 10
0.63 0.16 0.20
Matches are distributed among these distances:
18 3 0.10
19 10 0.32
20 15 0.48
21 3 0.10
ACGTcount: A:0.42, C:0.09, G:0.23, T:0.25
Consensus pattern (20 bp):
GTTCATAATGAGAAGAACTT
Found at i:63696 original size:121 final size:121
Alignment explanation
Indices: 63479--63775 Score: 418
Period size: 121 Copynumber: 2.4 Consensus size: 121
63469 CACTCGATGG
* *
63479 ATCAAC-TTTTCCAGAAAGTTCATAATGAGATGAACTTATCTGAAGAGGAAGAAGAAGTTCATAA
1 ATCAACATTTT-CAGAAGGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAA
* * *
63543 TGAGAAGAATTTGTTCAACCTTTTGCTCGATTCTATCACAAAAGGAGATATATCATC
65 TGAGAAGAACTTGTTCAACCTTTTGCTCGATTCTATCACAAAAGGAGATAGATCAGC
63600 ATCAACATTTTCAGAAGGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAAT
1 ATCAACATTTTCAGAAGGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAAT
* * *
63665 GAGAAGAACTTGTTCAACTTTTTG-TATGATTCTATCACATAAGGAGATAGATCAGC
66 GAGAAGAACTTGTTCAACCTTTTGCT-CGATTCTATCACAAAAGGAGATAGATCAGC
* * * * * *
63721 ACCAGCATTTCCAGAAGAAGTTCATAATGATAAGAACTCATCTGAAGAGAAAGAA
1 ATCAACATTTTCAGAAG--GTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAA
63776 CTTGTTCAAC
Statistics
Matches: 158, Mismatches: 14, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
120 1 0.01
121 120 0.76
122 4 0.03
123 33 0.21
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.28
Consensus pattern (121 bp):
ATCAACATTTTCAGAAGGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAAT
GAGAAGAACTTGTTCAACCTTTTGCTCGATTCTATCACAAAAGGAGATAGATCAGC
Found at i:64156 original size:3 final size:3
Alignment explanation
Indices: 64150--64188 Score: 55
Period size: 3 Copynumber: 13.7 Consensus size: 3
64140 TATTTGCTTA
*
64150 TAT TAT TAT TAT TAT TAT TA- TGT TA- TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
64189 AATAATTAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 3 0.09
3 29 0.91
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:64175 original size:25 final size:25
Alignment explanation
Indices: 64139--64188 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
64129 AGTTTTTTTC
64139 TTATTTGCTTATATTATTATTATTA
1 TTATTTGCTTATATTATTATTATTA
64164 TTATTATG-TTATATTATTATTATTA
1 TTATT-TGCTTATATTATTATTATTA
64189 AATAATTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 22 0.92
26 2 0.08
ACGTcount: A:0.30, C:0.02, G:0.04, T:0.64
Consensus pattern (25 bp):
TTATTTGCTTATATTATTATTATTA
Found at i:65617 original size:12 final size:11
Alignment explanation
Indices: 65588--65635 Score: 53
Period size: 12 Copynumber: 4.2 Consensus size: 11
65578 TATTTAAACT
*
65588 TTATATATATA
1 TTATAAATATA
65599 TTA-AAATATTA
1 TTATAAATA-TA
65610 TTATAAATATA
1 TTATAAATATA
65621 TATATAAATAATA
1 T-TATAAAT-ATA
65634 TT
1 TT
65636 TATTTATTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
10 4 0.12
11 11 0.34
12 13 0.41
13 4 0.12
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (11 bp):
TTATAAATATA
Found at i:65892 original size:23 final size:23
Alignment explanation
Indices: 65857--65900 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
65847 CCTTTTCTGA
*
65857 TATTTCTAAATAAATAAATATCT
1 TATTTATAAATAAATAAATATCT
* *
65880 TATTTATATATAAATTAATAT
1 TATTTATAAATAAATAAATAT
65901 ATTTTCTTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (23 bp):
TATTTATAAATAAATAAATATCT
Found at i:70388 original size:18 final size:17
Alignment explanation
Indices: 70365--70427 Score: 83
Period size: 16 Copynumber: 3.7 Consensus size: 17
70355 TGTTTATGAG
* *
70365 GGAATTGAAATATGTGAA
1 GGAATTGAAATCTGT-TA
70383 GGAATTGAAATCTGTTA
1 GGAATTGAAATCTGTTA
70400 GGAA-TGAAATCTGTTA
1 GGAATTGAAATCTGTTA
*
70416 GGAATTGGAATC
1 GGAATTGAAATC
70428 CAATTCCATA
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
16 16 0.39
17 11 0.27
18 14 0.34
ACGTcount: A:0.38, C:0.05, G:0.27, T:0.30
Consensus pattern (17 bp):
GGAATTGAAATCTGTTA
Found at i:71063 original size:27 final size:28
Alignment explanation
Indices: 71009--71067 Score: 111
Period size: 27 Copynumber: 2.1 Consensus size: 28
70999 CCGAATCGAA
71009 CCGAATATCACACTTAAAAAAACCCGAC
1 CCGAATATCACACTTAAAAAAACCCGAC
71037 CCGAATATCACACTT-AAAAAACCCGAC
1 CCGAATATCACACTTAAAAAAACCCGAC
71064 CCGA
1 CCGA
71068 CCCGACCCGA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 16 0.52
28 15 0.48
ACGTcount: A:0.44, C:0.34, G:0.08, T:0.14
Consensus pattern (28 bp):
CCGAATATCACACTTAAAAAAACCCGAC
Done.