Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002219.1 Hibiscus syriacus cultivar Beakdansim tig00004516_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: 88567
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:3245 original size:100 final size:98
Alignment explanation
Indices: 2918--3468 Score: 376
Period size: 98 Copynumber: 5.6 Consensus size: 98
2908 AAATCTCATC
* * *
2918 TACTCTTTCCAGAAGTGAGGAGAA-TTCATATAGGAGAGGTTTTTCAACTTCAAAATTGATTT-A
1 TACTCTTTCCAGAAGTGAGAAGAAGTTCATATATGAGAGATTTTTCAACTTCAAAATTGATTTGA
* *
2981 GTGG-GAAATTAAGAAG-TCATATAGGAGAATTCATA
66 TTGGAG-AA-TAAG-AGTTCATATAGGAGAATT-GTA
* ** * * * *
3016 TATTCTTTGTAGAAG-GCA-AGGAAGTTTATATAAGAGAGATTTTTTAACTTCAAAATTGACTTT
1 TACTCTTTCCAGAAGTG-AGAAGAAGTTCATATATGAGAGATTTTTCAACTTCAAAATTGA-TTT
* * * * *
3079 -ATGGGAGGATGAGGAATTCATATAGGAG-TTTGTA
64 GATTGGAGAAT-AAGAGTTCATATAGGAGAATTGTA
* * * * * * *
3113 TACTCTTTCTATAAATGCA-AAGAATTTCATATATGGGAGCTTTTTCAATTTCAAAATTGATTTG
1 TACTCTTTCCAGAAGTG-AGAAGAAGTTCATATATGAGAGATTTTTCAACTTCAAAATTGATTTG
* *
3177 ATTGGAGAATGAAGAGTTCATACAGGAGAGATTGTG
65 ATTGGAGAAT-AAGAGTTCATATAGGAGA-ATTGTA
* * * * *
3213 TACTCTTTCCAGAAGTAAGAAGAAGTTCATATA-GAAGAGGTTTTTCATCTTCATAATTGACTTG
1 TACTCTTTCCAGAAGTGAGAAGAAGTTCATATATG-AGAGATTTTTCAACTTCAAAATTGATTTG
* ** *
3277 A-TGGAAGAATAATAAGTTCATATAGGAGATATCATC
65 ATTGG-AGAATAA-GAGTTCATATAGGAGA-ATTGTA
* * * * * *
3313 CACTCTTTCCA-AAGTGAGAATAAGTTC--ATATGAGA-AATTTTCAGCTTCAAAATTAACTTGA
1 TACTCTTTCCAGAAGTGAGAAGAAGTTCATATATGAGAGATTTTTCAACTTCAAAATTGATTTGA
*** * *
3374 TAAAAGACTAAGGAGTTCATATAGGAGAACTTGTC
66 TTGGAGAATAA-GAGTTCATATAGGAGAA-TTGTA
* * * * * * *
3409 TATTTTTTCTAGAAGTGAGAAGAAGTTCATATATGAGAGCTTTTTTAGCTTCATAATTGA
1 TACTCTTTCCAGAAGTGAGAAGAAGTTCATATATGAGAGATTTTTCAACTTCAAAATTGA
3469 CCTTTTGGAA
Statistics
Matches: 354, Mismatches: 78, Indels: 40
0.75 0.17 0.08
Matches are distributed among these distances:
95 1 0.00
96 52 0.15
97 41 0.12
98 108 0.31
99 49 0.14
100 103 0.29
ACGTcount: A:0.36, C:0.10, G:0.20, T:0.34
Consensus pattern (98 bp):
TACTCTTTCCAGAAGTGAGAAGAAGTTCATATATGAGAGATTTTTCAACTTCAAAATTGATTTGA
TTGGAGAATAAGAGTTCATATAGGAGAATTGTA
Found at i:3392 original size:96 final size:98
Alignment explanation
Indices: 3214--3441 Score: 239
Period size: 96 Copynumber: 2.3 Consensus size: 98
3204 GAGATTGTGT
* * *
3214 ACTCTTTCCAGAAGTAAGAAGAAGTTCATATAGAAGAGGTTTTTCATCTTCATAATTGACTTGAT
1 ACTCTTTCCAGAAGTAAGAAGAAGTTCATATAGAAGA-G-TTTTCAGCTTCAAAATTAACTTGAT
** *
3279 GGAAGAATAATAAGTTCATATAGGAGATATCATCC
64 AAAAGAATAAGAAGTTCATATAGGAGATATCATCC
* *
3314 ACTCTTTCCA-AAGTGAGAATAAGTTCATATGAGAA-A-TTTTCAGCTTCAAAATTAACTTGATA
1 ACTCTTTCCAGAAGTAAGAAGAAGTTCATAT-AGAAGAGTTTTCAGCTTCAAAATTAACTTGATA
* * ** *
3376 AAAGACTAAGGAGTTCATATAGGAGA-ACTTGTCT
65 AAAGAATAAGAAGTTCATATAGGAGATA-TCATCC
* * * *
3410 ATTTTTTCTAGAAGTGAGAAGAAGTTCATATA
1 ACTCTTTCCAGAAGTAAGAAGAAGTTCATATA
3442 TGAGAGCTTT
Statistics
Matches: 108, Mismatches: 17, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
95 1 0.01
96 55 0.51
97 19 0.18
99 19 0.18
100 14 0.13
ACGTcount: A:0.38, C:0.12, G:0.18, T:0.32
Consensus pattern (98 bp):
ACTCTTTCCAGAAGTAAGAAGAAGTTCATATAGAAGAGTTTTCAGCTTCAAAATTAACTTGATAA
AAGAATAAGAAGTTCATATAGGAGATATCATCC
Found at i:3499 original size:100 final size:100
Alignment explanation
Indices: 2895--3652 Score: 416
Period size: 100 Copynumber: 7.7 Consensus size: 100
2885 TTTCACTGAT
* * * * *
2895 GAGTACATATAGGA-AATCTCATCTACTCTTTCCAGAAGTGAGGAGAA-TTCATATAGGAGAGGT
1 GAGTTCATATAGGAGAA-CTCGTCTACTCTTTCCAGAAGTGAGAAGAAGTTCATATATGAGAGCT
* * * * * *
2958 TTTTCAACTTCAAAATTGATTTAGTGGGAA-ATTAAG
65 TTTTTAGCTTCAAAATTGACTT-GTTGGAAGAATGAG
* * * * * ** * * * *
2994 AAG-TCATATAGGAGAATTCATATATTCTTTGTAGAAG-GCA-AGGAAGTTTATATAAGAGAGAT
1 GAGTTCATATAGGAGAACTCGTCTACTCTTTCCAGAAGTG-AGAAGAAGTTCATATATGAGAGCT
* * *
3056 TTTTTAACTTCAAAATTGACTT-TATGGGAGGATGAG
65 TTTTTAGCTTCAAAATTGACTTGT-TGGAAGAATGAG
* * * * * * * * *
3092 GAATTCATATAGGAG--TTTGTATACTCTTTCTATAAATGCA-AAGAATTTCATATATGGGAGCT
1 GAGTTCATATAGGAGAACTCGTCTACTCTTTCCAGAAGTG-AGAAGAAGTTCATATATGAGAGCT
* ** * *
3154 TTTTCAATTTCAAAATTGATTTGATTGG-AGAATGAA
65 TTTTTAGCTTCAAAATTGACTTG-TTGGAAGAATGAG
* * * * *
3190 GAGTTCATACAGGAGAGA-TTGTGTACTCTTTCCAGAAGTAAGAAGAAGTTCATATA-GAAGAGG
1 GAGTTCATATAGGAGA-ACTCGTCTACTCTTTCCAGAAGTGAGAAGAAGTTCATATATG-AGAGC
* * * * * *
3253 TTTTTCATCTTCATAATTGACTTGATGGAAGAATAAT
64 TTTTTTAGCTTCAAAATTGACTTGTTGGAAGAATGAG
* * * * **
3290 AAGTTCATATAGGAGATA-TCATCCACTCTTTCCA-AAGTGAGAATAAGTTC--ATATGAGA-AA
1 GAGTTCATATAGGAGA-ACTCGTCTACTCTTTCCAGAAGTGAGAAGAAGTTCATATATGAGAGCT
* * * ** * *
3350 TTTTCAGCTTCAAAATTAACTTGATAAAAGACTAAG
65 TTTTTAGCTTCAAAATTGACTTGTTGGAAGAATGAG
* * * *
3386 GAGTTCATATAGGAGAACTTGTCTATTTTTTCTAGAAGTGAGAAGAAGTTCATATATGAGAGCTT
1 GAGTTCATATAGGAGAACTCGTCTACTCTTTCCAGAAGTGAGAAGAAGTTCATATATGAGAGCTT
*
3451 TTTTAGCTTCATAATTGACCTT-TTGGAAGAATGAG
66 TTTTAGCTTCAAAATTGA-CTTGTTGGAAGAATGAG
* ** * ** * * *
3486 GCGTTCATATAGGAGTGCTCATCTTGTCTTGCCCA-AATTGAGAAGAAGTTCATATATGAGAGGT
1 GAGTTCATATAGGAGAACTCGTCTACTCTT-TCCAGAAGTGAGAAGAAGTTCATATATGAGA-GC
* * * *
3550 TTTTTTAGCTTTATATTTGACTTTTTGGAAGGAAT---
64 TTTTTTAGCTTCAAAATTGACTTGTTGGAA-GAATGAG
*** * * * *
3585 -AGTTCATATAATTGAGCTCGTCTAGTCTTTCAAG-AG-GAGAAAAAGTTCATATATGAGAGCTT
1 GAGTTCATATAGGAGAACTCGTCTACTCTTTCCAGAAGTGAGAAGAAGTTCATATATGAGAGCTT
3647 GTTTTA
66 -TTTTA
3653 CTTTGATAAT
Statistics
Matches: 514, Mismatches: 117, Indels: 59
0.74 0.17 0.09
Matches are distributed among these distances:
95 4 0.01
96 81 0.16
97 46 0.09
98 143 0.28
99 45 0.09
100 161 0.31
101 30 0.06
102 4 0.01
ACGTcount: A:0.34, C:0.11, G:0.20, T:0.35
Consensus pattern (100 bp):
GAGTTCATATAGGAGAACTCGTCTACTCTTTCCAGAAGTGAGAAGAAGTTCATATATGAGAGCTT
TTTTAGCTTCAAAATTGACTTGTTGGAAGAATGAG
Found at i:8868 original size:20 final size:20
Alignment explanation
Indices: 8822--8870 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
8812 GAATTGAATC
*
8822 AAAACCGAGCAAAATCATGA
1 AAAACCTAGCAAAATCATGA
8842 AAAACCTAGCAAAATCATGA
1 AAAACCTAGCAAAATCATGA
8862 AAAACCTAG
1 AAAACCTAG
8871 TTTTGGAACT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.55, C:0.20, G:0.12, T:0.12
Consensus pattern (20 bp):
AAAACCTAGCAAAATCATGA
Found at i:9372 original size:25 final size:25
Alignment explanation
Indices: 9338--9389 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
9328 GTTCCAAAGT
9338 ATGCCTATGTTAGTAAGATTCTAAC
1 ATGCCTATGTTAGTAAGATTCTAAC
9363 ATGCCTATGTTAGTAAGATTCTAAC
1 ATGCCTATGTTAGTAAGATTCTAAC
9388 AT
1 AT
9390 TTGGTTTGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (25 bp):
ATGCCTATGTTAGTAAGATTCTAAC
Found at i:22232 original size:16 final size:16
Alignment explanation
Indices: 22211--22241 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
22201 CAGTTACATA
*
22211 TCAGGTTTATAATAGG
1 TCAGGTTGATAATAGG
22227 TCAGGTTGATAATAG
1 TCAGGTTGATAATAG
22242 ATCGGGTAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.06, G:0.26, T:0.35
Consensus pattern (16 bp):
TCAGGTTGATAATAGG
Found at i:27537 original size:27 final size:27
Alignment explanation
Indices: 27500--27551 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
27490 AAGAGCGGCA
*
27500 GTTGGAACTTCAACGACAGCAGCAGTG
1 GTTGGAACTTCAAAGACAGCAGCAGTG
*
27527 GTTGGAACTTCAAAGATAGCAGCAG
1 GTTGGAACTTCAAAGACAGCAGCAG
27552 CAGCAGCTGG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.33, C:0.19, G:0.29, T:0.19
Consensus pattern (27 bp):
GTTGGAACTTCAAAGACAGCAGCAGTG
Found at i:27552 original size:30 final size:27
Alignment explanation
Indices: 27497--27568 Score: 81
Period size: 30 Copynumber: 2.6 Consensus size: 27
27487 AACAAGAGCG
*
27497 GCAGTTGGAACTTCAACGACAGCAGCA
1 GCAGTTGGAACTTCAAAGACAGCAGCA
**
27524 GTGGTTGGAACTTCAAAGATAGCAGCAGCA
1 GCAGTTGGAACTTCAAAG--A-CAGCAGCA
*
27554 GCAGCTGGAACTTCA
1 GCAGTTGGAACTTCA
27569 GCGGCAGCTG
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
27 15 0.42
29 1 0.03
30 20 0.56
ACGTcount: A:0.32, C:0.22, G:0.28, T:0.18
Consensus pattern (27 bp):
GCAGTTGGAACTTCAAAGACAGCAGCA
Found at i:27575 original size:18 final size:18
Alignment explanation
Indices: 27549--27588 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
27539 AAGATAGCAG
*
27549 CAGCAGCAGCTGGAACTT
1 CAGCAGCAGCTGGAACTA
*
27567 CAGCGGCAGCTGGAACTA
1 CAGCAGCAGCTGGAACTA
27585 CAGC
1 CAGC
27589 TTTGCCACCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.28, C:0.30, G:0.30, T:0.12
Consensus pattern (18 bp):
CAGCAGCAGCTGGAACTA
Found at i:34611 original size:20 final size:20
Alignment explanation
Indices: 34552--34618 Score: 89
Period size: 20 Copynumber: 3.4 Consensus size: 20
34542 GTTTTGAATT
*
34552 TCGCAACGCGAATATGGAAA
1 TCGCAACGCGAATATGTAAA
*
34572 TCGCAACGCGAATATATAAA
1 TCGCAACGCGAATATGTAAA
* *
34592 TCGCAACGCAAATTTGTAAA
1 TCGCAACGCGAATATGTAAA
*
34612 TTGCAAC
1 TCGCAAC
34619 ACAGAAGTCA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.40, C:0.21, G:0.18, T:0.21
Consensus pattern (20 bp):
TCGCAACGCGAATATGTAAA
Found at i:35174 original size:20 final size:20
Alignment explanation
Indices: 35149--35206 Score: 116
Period size: 20 Copynumber: 2.9 Consensus size: 20
35139 TTTAAAACTT
35149 AAATTCGCAACACGAAAATG
1 AAATTCGCAACACGAAAATG
35169 AAATTCGCAACACGAAAATG
1 AAATTCGCAACACGAAAATG
35189 AAATTCGCAACACGAAAA
1 AAATTCGCAACACGAAAA
35207 CCGCAACACG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.52, C:0.21, G:0.14, T:0.14
Consensus pattern (20 bp):
AAATTCGCAACACGAAAATG
Found at i:35211 original size:14 final size:14
Alignment explanation
Indices: 35194--35220 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
35184 AAATGAAATT
35194 CGCAACACGAAAAC
1 CGCAACACGAAAAC
35208 CGCAACACGAAAA
1 CGCAACACGAAAA
35221 TGAAAATCGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.33, G:0.15, T:0.00
Consensus pattern (14 bp):
CGCAACACGAAAAC
Found at i:35225 original size:20 final size:20
Alignment explanation
Indices: 35153--35233 Score: 93
Period size: 20 Copynumber: 4.3 Consensus size: 20
35143 AAACTTAAAT
*
35153 TCGCAACACGAAAATGAAAT
1 TCGCAACACGAAAATGAAAA
*
35173 TCGCAACACGAAAATGAAAT
1 TCGCAACACGAAAATGAAAA
35193 TCGCAACAC------GAAAA
1 TCGCAACACGAAAATGAAAA
*
35207 CCGCAACACGAAAATGAAAA
1 TCGCAACACGAAAATGAAAA
35227 TCGCAAC
1 TCGCAAC
35234 GCGATTTTAG
Statistics
Matches: 52, Mismatches: 3, Indels: 12
0.78 0.04 0.18
Matches are distributed among these distances:
14 12 0.23
20 40 0.77
ACGTcount: A:0.49, C:0.25, G:0.15, T:0.11
Consensus pattern (20 bp):
TCGCAACACGAAAATGAAAA
Found at i:35287 original size:20 final size:20
Alignment explanation
Indices: 35237--35287 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
35227 TCGCAACGCG
* *
35237 ATTTTAGTTTCGCGTTGTGA
1 ATTTAAGTTTCGCGTTGCGA
* * *
35257 TTTTCATTTTCGCGTTGCGA
1 ATTTAAGTTTCGCGTTGCGA
35277 ATTTAAGTTTC
1 ATTTAAGTTTC
35288 AAAAACTACT
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.16, C:0.14, G:0.20, T:0.51
Consensus pattern (20 bp):
ATTTAAGTTTCGCGTTGCGA
Found at i:36828 original size:21 final size:21
Alignment explanation
Indices: 36804--36853 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
36794 GTTAGGGGAG
*
36804 TTACGTGATGAGGTCAGTGCT
1 TTACGTGATGAGGTCAGTACT
*
36825 TTACGTGATGAGGTCGGTACT
1 TTACGTGATGAGGTCAGTACT
36846 TTACGTGA
1 TTACGTGA
36854 CGACAATGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.20, C:0.14, G:0.32, T:0.34
Consensus pattern (21 bp):
TTACGTGATGAGGTCAGTACT
Found at i:36942 original size:63 final size:63
Alignment explanation
Indices: 36845--36966 Score: 147
Period size: 63 Copynumber: 1.9 Consensus size: 63
36835 AGGTCGGTAC
* **
36845 TTTACGTGACGACAATGGTGCATGAAGTGATGAGGTA-CGATCTTTACGTGGTGAGGTAGATGT
1 TTTACGCGACGACAATGGTGCATGAAGTGATGAGGTATCGA-CTTTACGTAATGAGGTAGATGT
* * * * * *
36908 TTTACGCGATGACAATGGTGCTTTACGTGGTGAGGTATCTACTTTACGTAATGAGGTAG
1 TTTACGCGACGACAATGGTGCATGAAGTGATGAGGTATCGACTTTACGTAATGAGGTAG
36967 CCGCTCTACG
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
63 47 0.96
64 2 0.04
ACGTcount: A:0.25, C:0.12, G:0.31, T:0.32
Consensus pattern (63 bp):
TTTACGCGACGACAATGGTGCATGAAGTGATGAGGTATCGACTTTACGTAATGAGGTAGATGT
Found at i:38605 original size:20 final size:20
Alignment explanation
Indices: 38582--38620 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
38572 GATTTTTGAG
* *
38582 TTGCGAATTTGATTTTCGCA
1 TTGCAAATTTGACTTTCGCA
38602 TTGCAAATTTGACTTTCGC
1 TTGCAAATTTGACTTTCGC
38621 GACAACCGCA
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:0.21, C:0.18, G:0.18, T:0.44
Consensus pattern (20 bp):
TTGCAAATTTGACTTTCGCA
Found at i:46596 original size:21 final size:23
Alignment explanation
Indices: 46570--46620 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
46560 AGGGAATCAA
46570 TCCCCCCCTG-A-GGGAACCGAT
1 TCCCCCCCTGAAGGGGAACCGAT
**
46591 TCCCCCTTTGAAGGGGAACCGAT
1 TCCCCCCCTGAAGGGGAACCGAT
46614 TCCCCCC
1 TCCCCCC
46621 ACAGGGGAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 8 0.32
22 1 0.04
23 16 0.64
ACGTcount: A:0.18, C:0.43, G:0.22, T:0.18
Consensus pattern (23 bp):
TCCCCCCCTGAAGGGGAACCGAT
Found at i:46628 original size:21 final size:21
Alignment explanation
Indices: 46602--46641 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
46592 CCCCCTTTGA
*
46602 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
46623 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
46642 TGGGGGTTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:50974 original size:12 final size:12
Alignment explanation
Indices: 50953--50986 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
50943 GGTTGTGGGT
*
50953 TTTGAGATTGTG
1 TTTGATATTGTG
50965 TTTGATATTGTG
1 TTTGATATTGTG
*
50977 TTTGGTATTG
1 TTTGATATTG
50987 AAAATGTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:51583 original size:16 final size:15
Alignment explanation
Indices: 51561--51599 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
51551 GAAATCATTG
51561 AAAAATTATATAGAAA
1 AAAAATTATATA-AAA
* *
51577 TAAAATTATGTAAAA
1 AAAAATTATATAAAA
51592 AAAAATTA
1 AAAAATTA
51600 GAGATGGGGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (15 bp):
AAAAATTATATAAAA
Found at i:51833 original size:60 final size:60
Alignment explanation
Indices: 51768--51916 Score: 142
Period size: 60 Copynumber: 2.5 Consensus size: 60
51758 TTAAAATTCA
* *
51768 TGTTGCGAATTCGAAAATCGAGTTGCGAAAACA-AAATTAGTGTTGC-AATTTAGAAAATCT
1 TGTTGCGAATTCGAAAATCGAGTTGCGAAAA-AGAAATTAGCGTTGCGAATTT-GAAAATCG
*** * * * *
51828 TGTTGCGAAAAGGAAACTTGTGTTGCGAAAAAGAAATTCGCGTTGCGAATTTGAAAATCG
1 TGTTGCGAATTCGAAAATCGAGTTGCGAAAAAGAAATTAGCGTTGCGAATTTGAAAATCG
* * *
51888 CGTTACGAATTTGAAAATCGCA-TTGCGAA
1 TGTTGCGAATTCGAAAATCG-AGTTGCGAA
51917 TTTGGAAAAT
Statistics
Matches: 69, Mismatches: 17, Indels: 6
0.75 0.18 0.07
Matches are distributed among these distances:
59 1 0.01
60 63 0.91
61 5 0.07
ACGTcount: A:0.36, C:0.13, G:0.23, T:0.28
Consensus pattern (60 bp):
TGTTGCGAATTCGAAAATCGAGTTGCGAAAAAGAAATTAGCGTTGCGAATTTGAAAATCG
Found at i:51843 original size:20 final size:20
Alignment explanation
Indices: 51727--51876 Score: 62
Period size: 20 Copynumber: 7.6 Consensus size: 20
51717 CCCAAAACAT
*
51727 TTGTGTTGC-AAAAATAAAA
1 TTGTGTTGCGAAAAAGAAAA
* **
51746 TT-TGTTGAG-AAATTAAAA
1 TTGTGTTGCGAAAAAGAAAA
* ***
51764 TTCATGTTGCGAATTCGAAAA
1 TT-GTGTTGCGAAAAAGAAAA
* * *
51785 TCGAGTTGCG-AAAACAAAA
1 TTGTGTTGCGAAAAAGAAAA
**
51804 TTAGTGTTGC-AATTTAGAAAA
1 TT-GTGTTGCGAA-AAAGAAAA
* *
51825 TCT-TGTTGCGAAAAGGAAAC
1 T-TGTGTTGCGAAAAAGAAAA
51845 TTGTGTTGCGAAAAAG-AAA
1 TTGTGTTGCGAAAAAGAAAA
*
51864 TTCGCGTTGCGAA
1 TT-GTGTTGCGAA
51877 TTTGAAAATC
Statistics
Matches: 94, Mismatches: 26, Indels: 21
0.67 0.18 0.15
Matches are distributed among these distances:
18 15 0.16
19 13 0.14
20 51 0.54
21 14 0.15
22 1 0.01
ACGTcount: A:0.39, C:0.10, G:0.21, T:0.30
Consensus pattern (20 bp):
TTGTGTTGCGAAAAAGAAAA
Found at i:51926 original size:21 final size:20
Alignment explanation
Indices: 51860--51932 Score: 110
Period size: 20 Copynumber: 3.6 Consensus size: 20
51850 TTGCGAAAAA
*
51860 GAAATTCGCGTTGCGAATTT
1 GAAAATCGCGTTGCGAATTT
*
51880 GAAAATCGCGTTACGAATTT
1 GAAAATCGCGTTGCGAATTT
*
51900 GAAAATCGCATTGCGAATTT
1 GAAAATCGCGTTGCGAATTT
51920 GGAAAATCGCGTT
1 -GAAAATCGCGTT
51933 TCGAGAAAGT
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
20 36 0.77
21 11 0.23
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.30
Consensus pattern (20 bp):
GAAAATCGCGTTGCGAATTT
Found at i:52002 original size:20 final size:20
Alignment explanation
Indices: 51963--52003 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
51953 ACGATTGCAA
* *
51963 AAACTGGGTTGCGAATTTGG
1 AAACTGGGTTGCAAAATTGG
*
51983 AAACTGTGTTGCAAAATTGG
1 AAACTGGGTTGCAAAATTGG
52003 A
1 A
52004 GTTCGCGTTG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.32, C:0.10, G:0.29, T:0.29
Consensus pattern (20 bp):
AAACTGGGTTGCAAAATTGG
Found at i:52028 original size:19 final size:19
Alignment explanation
Indices: 51990--52039 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
51980 TGGAAACTGT
* *
51990 GTTGCAAAATTGGAGTTCGC
1 GTTGC-AAATTTGAGATCGC
52010 GTTGCAAATTTGAGATCGC
1 GTTGCAAATTTGAGATCGC
* *
52029 ATTGCGAATTT
1 GTTGCAAATTT
52040 ATTGGTTATT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 21 0.81
20 5 0.19
ACGTcount: A:0.26, C:0.14, G:0.26, T:0.34
Consensus pattern (19 bp):
GTTGCAAATTTGAGATCGC
Found at i:62570 original size:3 final size:3
Alignment explanation
Indices: 62562--62675 Score: 84
Period size: 3 Copynumber: 35.7 Consensus size: 3
62552 CAATTTTGCA
* * * * *
62562 TAT TAT TAT TAAT AAA TAT TAAT TGT TAT TAG TAT TAAT TAT TAT GAT
1 TAT TAT TAT T-AT TAT TAT T-AT TAT TAT TAT TAT T-AT TAT TAT TAT
* * *
62610 TAT TAAT TAT TAT TAT TAA TATT TAT TGT TAT TAAT AAT TAT TAT TAT
1 TAT T-AT TAT TAT TAT TAT TA-T TAT TAT TAT T-AT TAT TAT TAT TAT
*
62658 TAT TGT TCAT TAT TAT TA
1 TAT TAT T-AT TAT TAT TA
62676 AATATTAAGT
Statistics
Matches: 86, Mismatches: 18, Indels: 14
0.73 0.15 0.12
Matches are distributed among these distances:
3 69 0.80
4 17 0.20
ACGTcount: A:0.37, C:0.01, G:0.04, T:0.58
Consensus pattern (3 bp):
TAT
Found at i:62582 original size:16 final size:16
Alignment explanation
Indices: 62581--62659 Score: 95
Period size: 16 Copynumber: 4.9 Consensus size: 16
62571 TAATAAATAT
* * *
62581 TAATTGTTATTAGTAT
1 TAATTATTATTATTAA
* *
62597 TAATTATTATGATTAT
1 TAATTATTATTATTAA
62613 TAATTATTATTATTAA
1 TAATTATTATTATTAA
* *
62629 TATTTATTGTTATTAA
1 TAATTATTATTATTAA
62645 TAATTATTATTATTA
1 TAATTATTATTATTA
62660 TTGTTCATTA
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 54 1.00
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (16 bp):
TAATTATTATTATTAA
Found at i:62605 original size:13 final size:13
Alignment explanation
Indices: 62587--62629 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 13
62577 ATATTAATTG
62587 TTATTAGTATTAA
1 TTATTAGTATTAA
62600 TTATTATGATTATTAA
1 TTATTA-G--TATTAA
*
62616 TTATTATTATTAA
1 TTATTAGTATTAA
62629 T
1 T
62630 ATTTATTGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
13 13 0.50
14 1 0.04
16 12 0.46
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (13 bp):
TTATTAGTATTAA
Found at i:62621 original size:19 final size:18
Alignment explanation
Indices: 62562--62675 Score: 76
Period size: 19 Copynumber: 6.3 Consensus size: 18
62552 CAATTTTGCA
*
62562 TATTATTATTAATAAATAT
1 TATTATTATT-ATAATTAT
*
62581 TAATTGTTATTAGT-ATTAAT
1 T-ATTATTATTA-TAATT-AT
*
62601 TATTATGATTATTAATTAT
1 TATTATTATTA-TAATTAT
*
62620 TATTATTA--ATATTTAT
1 TATTATTATTATAATTAT
*
62636 TGTTATTA--ATAATTAT
1 TATTATTATTATAATTAT
* *
62652 TATTATTATTGTTCATTAT
1 TATTATTATT-ATAATTAT
62671 TATTA
1 TATTA
62676 AATATTAAGT
Statistics
Matches: 76, Mismatches: 12, Indels: 14
0.75 0.12 0.14
Matches are distributed among these distances:
16 27 0.36
17 1 0.01
19 33 0.43
20 15 0.20
ACGTcount: A:0.37, C:0.01, G:0.04, T:0.58
Consensus pattern (18 bp):
TATTATTATTATAATTAT
Found at i:62635 original size:29 final size:29
Alignment explanation
Indices: 62587--62661 Score: 91
Period size: 29 Copynumber: 2.6 Consensus size: 29
62577 ATATTAATTG
*
62587 TTATTAGTATTAAT-TATTA-TGATTATTAA
1 TTATTATTATTAATAT-TTATTG-TTATTAA
62616 TTATTATTATTAATATTTATTGTTATTAA
1 TTATTATTATTAATATTTATTGTTATTAA
* *
62645 TAATTATTATTATTATT
1 TTATTATTATTAATATT
62662 GTTCATTATT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
29 38 0.93
30 3 0.07
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (29 bp):
TTATTATTATTAATATTTATTGTTATTAA
Found at i:64023 original size:76 final size:76
Alignment explanation
Indices: 63888--64036 Score: 264
Period size: 76 Copynumber: 2.0 Consensus size: 76
63878 TTATAGATTA
*
63888 TACCATGTTTGCTCATATTTGAATCTGACCCTACGGTTTACGAATCTTTTGTTTTGGTCACTATT
1 TACCATGTTTGCTCATATTTGAATCTGACCCTAAGGTTTACGAATCTTTTGTTTTGGTCACTATT
63953 TTGTATGAATG
66 TTGTATGAATG
*
63964 TACCATGTTTGCTCATATTTGAATCTGACCCTAAGGTTTACGAATCTTTT-TTTTGGGTCATTAT
1 TACCATGTTTGCTCATATTTGAATCTGACCCTAAGGTTTACGAATCTTTTGTTTT-GGTCACTAT
64028 TTTGTATGA
65 TTTGTATGA
64037 TTGCCTTTAG
Statistics
Matches: 70, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
75 4 0.06
76 66 0.94
ACGTcount: A:0.21, C:0.16, G:0.17, T:0.46
Consensus pattern (76 bp):
TACCATGTTTGCTCATATTTGAATCTGACCCTAAGGTTTACGAATCTTTTGTTTTGGTCACTATT
TTGTATGAATG
Found at i:64773 original size:28 final size:28
Alignment explanation
Indices: 64737--64789 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
64727 AAAATGATAC
64737 TAATATTTTTA-TTTTATTTTATATTTA
1 TAATATTTTTATTTTTATTTTATATTTA
*
64764 TAATATTTTTATTTTTATTTTTTATT
1 TAATATTTTTATTTTTATTTTATATT
64790 ATGTTTTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
27 11 0.46
28 13 0.54
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (28 bp):
TAATATTTTTATTTTTATTTTATATTTA
Found at i:64796 original size:23 final size:23
Alignment explanation
Indices: 64748--64800 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
64738 AATATTTTTA
64748 TTTTA-TTTTATATTTATAATAT
1 TTTTATTTTTATATTTATAATAT
* *
64770 TTTTATTTTTAT-TTTTTATTAT
1 TTTTATTTTTATATTTATAATAT
64792 GTTTTATTT
1 -TTTTATTT
64801 AATTTTGGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
22 13 0.48
23 14 0.52
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.75
Consensus pattern (23 bp):
TTTTATTTTTATATTTATAATAT
Found at i:66649 original size:22 final size:22
Alignment explanation
Indices: 66618--66668 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
66608 GACCAGAGTT
*
66618 GATGCTCGATGGAGAGCAAGAA
1 GATGCCCGATGGAGAGCAAGAA
66640 GATGCCCGATGGAGAGCAAGAA
1 GATGCCCGATGGAGAGCAAGAA
66662 GATGCCC
1 GATGCCC
66669 AAAGAATTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.33, C:0.20, G:0.35, T:0.12
Consensus pattern (22 bp):
GATGCCCGATGGAGAGCAAGAA
Done.