Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005768.1 Hibiscus syriacus cultivar Beakdansim tig00013502_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: 76417
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:2103 original size:21 final size:22
Alignment explanation
Indices: 2071--2111 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
2061 AAAACAATAA
*
2071 AAAAATGTAAAGTAAAGAAAGC
1 AAAAATGTAAAGAAAAGAAAGC
2093 AAAAATG-AAAGAAAAGAAA
1 AAAAATGTAAAGAAAAGAAA
2112 AAACTTTGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.71, C:0.02, G:0.17, T:0.10
Consensus pattern (22 bp):
AAAAATGTAAAGAAAAGAAAGC
Found at i:8350 original size:27 final size:27
Alignment explanation
Indices: 8293--8344 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
8283 TCTTGTTAAA
* *
8293 CTTAGAATGGAAATAGGGTCTTGGTGT
1 CTTAGAATAGAAATAGGGTCTCGGTGT
8320 CTTAGAATAGAAATAGGGTCTCGGT
1 CTTAGAATAGAAATAGGGTCTCGGT
8345 TCCTTAATCA
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:0.29, C:0.10, G:0.31, T:0.31
Consensus pattern (27 bp):
CTTAGAATAGAAATAGGGTCTCGGTGT
Found at i:14212 original size:14 final size:14
Alignment explanation
Indices: 14195--14237 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
14185 ATTAAATTAT
14195 AAATATTTTAATGA
1 AAATATTTTAATGA
14209 AAATA---T-AT-A
1 AAATATTTTAATGA
14218 AAATATTTTAATGA
1 AAATATTTTAATGA
14232 AAATAT
1 AAATAT
14238 ATAAAATATT
Statistics
Matches: 24, Mismatches: 0, Indels: 10
0.71 0.00 0.29
Matches are distributed among these distances:
9 6 0.25
10 2 0.08
11 1 0.04
12 1 0.04
13 2 0.08
14 12 0.50
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.40
Consensus pattern (14 bp):
AAATATTTTAATGA
Found at i:14225 original size:23 final size:23
Alignment explanation
Indices: 14188--14251 Score: 114
Period size: 23 Copynumber: 2.9 Consensus size: 23
14178 CTTTAATATT
14188 AAAT-TAT-AAATATTTTAATGA
1 AAATATATAAAATATTTTAATGA
14209 AAATATATAAAATATTTTAATGA
1 AAATATATAAAATATTTTAATGA
14232 AAATATATAAAATATTTTAA
1 AAATATATAAAATATTTTAA
14252 GCGTTACACT
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
21 4 0.10
22 3 0.07
23 34 0.83
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (23 bp):
AAATATATAAAATATTTTAATGA
Found at i:14382 original size:5 final size:5
Alignment explanation
Indices: 14374--14425 Score: 95
Period size: 5 Copynumber: 10.4 Consensus size: 5
14364 AACAGAACAG
*
14374 AACGT AACGT AACGT AACGT AACGT AACTT AACGT AACGT AACGT AACGT
1 AACGT AACGT AACGT AACGT AACGT AACGT AACGT AACGT AACGT AACGT
14424 AA
1 AA
14426 TAATATAAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 45 1.00
ACGTcount: A:0.42, C:0.19, G:0.17, T:0.21
Consensus pattern (5 bp):
AACGT
Found at i:15965 original size:18 final size:18
Alignment explanation
Indices: 15944--15994 Score: 54
Period size: 16 Copynumber: 3.0 Consensus size: 18
15934 AAAAGAAAGC
*
15944 GGAAGAAGAGAAGCCAAA
1 GGAAGAAGAGAAACCAAA
* *
15962 GGAAG-A-AGCACCCAAA
1 GGAAGAAGAGAAACCAAA
15978 -GAAGAAGAGAAACCAAA
1 GGAAGAAGAGAAACCAAA
15995 TCCACCCCTA
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
15 4 0.15
16 9 0.33
17 9 0.33
18 5 0.19
ACGTcount: A:0.57, C:0.16, G:0.27, T:0.00
Consensus pattern (18 bp):
GGAAGAAGAGAAACCAAA
Found at i:16474 original size:15 final size:16
Alignment explanation
Indices: 16454--16486 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
16444 CTGGGCTGAA
*
16454 GAAGAGCAGAA-GAAG
1 GAAGAGAAGAAGGAAG
16469 GAAGAGAAGAAGGAAG
1 GAAGAGAAGAAGGAAG
16485 GA
1 GA
16487 TACGCCGCAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.55, C:0.03, G:0.42, T:0.00
Consensus pattern (16 bp):
GAAGAGAAGAAGGAAG
Found at i:23738 original size:21 final size:21
Alignment explanation
Indices: 23679--23739 Score: 95
Period size: 21 Copynumber: 2.9 Consensus size: 21
23669 GAGAACCGGC
* * *
23679 AAAATCGGGGTGAACCGACTG
1 AAAACCGGTGTGAACCGTCTG
23700 AAAACCGGTGTGAACCGTCTG
1 AAAACCGGTGTGAACCGTCTG
23721 AAAACCGGTGTGAACCGTC
1 AAAACCGGTGTGAACCGTC
23740 AATTCTCTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.31, C:0.23, G:0.30, T:0.16
Consensus pattern (21 bp):
AAAACCGGTGTGAACCGTCTG
Found at i:25199 original size:3 final size:3
Alignment explanation
Indices: 25180--25216 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
25170 ACGTTTTTTA
*
25180 TAT TAT AAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
25217 AAAATAATAC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 2 0.06
3 29 0.94
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:25323 original size:16 final size:15
Alignment explanation
Indices: 25302--25340 Score: 53
Period size: 14 Copynumber: 2.6 Consensus size: 15
25292 TTACAAGTTC
25302 AACCCGAGTAGGTCCA
1 AACCCGAG-AGGTCCA
25318 AACCCG-GAGGTCCA
1 AACCCGAGAGGTCCA
*
25332 GACCCGAGA
1 AACCCGAGA
25341 AGACAAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 12 0.57
15 3 0.14
16 6 0.29
ACGTcount: A:0.31, C:0.33, G:0.28, T:0.08
Consensus pattern (15 bp):
AACCCGAGAGGTCCA
Found at i:28534 original size:12 final size:12
Alignment explanation
Indices: 28513--28583 Score: 54
Period size: 12 Copynumber: 5.9 Consensus size: 12
28503 TGATACATTA
*
28513 TCTGAATTCTGT
1 TCTGATTTCTGT
*
28525 TCTGATTTCTGA
1 TCTGATTTCTGT
28537 TCTGGA-TTCTGT
1 TCT-GATTTCTGT
* **
28549 TCTGATATCTAA
1 TCTGATTTCTGT
* *
28561 TATGAATTCTGT
1 TCTGATTTCTGT
*
28573 TTTGATTTCTG
1 TCTGATTTCTG
28584 ATATCTCCGT
Statistics
Matches: 44, Mismatches: 13, Indels: 4
0.72 0.21 0.07
Matches are distributed among these distances:
11 2 0.05
12 40 0.91
13 2 0.05
ACGTcount: A:0.18, C:0.14, G:0.17, T:0.51
Consensus pattern (12 bp):
TCTGATTTCTGT
Found at i:28539 original size:24 final size:24
Alignment explanation
Indices: 28512--28585 Score: 103
Period size: 24 Copynumber: 3.1 Consensus size: 24
28502 ATGATACATT
28512 ATCTGAATTCTGTTCTGATTTCTG
1 ATCTGAATTCTGTTCTGATTTCTG
* * *
28536 ATCTGGATTCTGTTCTGATATCTA
1 ATCTGAATTCTGTTCTGATTTCTG
* *
28560 ATATGAATTCTGTTTTGATTTCTG
1 ATCTGAATTCTGTTCTGATTTCTG
28584 AT
1 AT
28586 ATCTCCGTTT
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.20, C:0.14, G:0.16, T:0.50
Consensus pattern (24 bp):
ATCTGAATTCTGTTCTGATTTCTG
Found at i:29353 original size:21 final size:21
Alignment explanation
Indices: 29325--29368 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
29315 AGAAAGAGGG
*
29325 GACAACGAGAGATACAC-AGA
1 GACAACGAGAGAAACACGAGA
29345 GACAGACGAGAGAAACACGAGA
1 GACA-ACGAGAGAAACACGAGA
29367 GA
1 GA
29369 ACGAGGAGGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 4 0.19
21 12 0.57
22 5 0.24
ACGTcount: A:0.50, C:0.18, G:0.30, T:0.02
Consensus pattern (21 bp):
GACAACGAGAGAAACACGAGA
Found at i:31396 original size:2 final size:2
Alignment explanation
Indices: 31389--31417 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
31379 AACAAATCTA
31389 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 A
31418 ATTGCATTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:31603 original size:3 final size:3
Alignment explanation
Indices: 31595--31641 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
31585 AACTTAACAG
31595 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
31642 GGCATAGATA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:31765 original size:23 final size:24
Alignment explanation
Indices: 31717--31776 Score: 86
Period size: 23 Copynumber: 2.5 Consensus size: 24
31707 GACCAAATTG
*
31717 AAATAAAATAAAACCAAAAGGAAA
1 AAATCAAATAAAACCAAAAGGAAA
* *
31741 AAATCAAATAAAA-TAAAAGGTAA
1 AAATCAAATAAAACCAAAAGGAAA
31764 AAATCAAATAAAA
1 AAATCAAATAAAA
31777 ATTAAAGACA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
23 21 0.64
24 12 0.36
ACGTcount: A:0.73, C:0.07, G:0.07, T:0.13
Consensus pattern (24 bp):
AAATCAAATAAAACCAAAAGGAAA
Found at i:31777 original size:24 final size:24
Alignment explanation
Indices: 31717--31783 Score: 82
Period size: 23 Copynumber: 2.8 Consensus size: 24
31707 GACCAAATTG
* **
31717 AAATAAAATAAAACCAAAAGGAAA
1 AAATCAAATAAAAATAAAAGGAAA
*
31741 AAATCAAAT-AAAATAAAAGGTAA
1 AAATCAAATAAAAATAAAAGGAAA
*
31764 AAATCAAATAAAAATTAAAG
1 AAATCAAATAAAAATAAAAG
31784 ACATTAGAGT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
23 20 0.54
24 17 0.46
ACGTcount: A:0.72, C:0.06, G:0.07, T:0.15
Consensus pattern (24 bp):
AAATCAAATAAAAATAAAAGGAAA
Found at i:33108 original size:94 final size:95
Alignment explanation
Indices: 32957--33138 Score: 242
Period size: 94 Copynumber: 1.9 Consensus size: 95
32947 CGATACCAAA
* * *
32957 AAGGAAAGTATCAATACCATGGATTTCAGAATGCCAAAATGGTATCGATACTAAAAGGGAGTATC
1 AAGGAAAGTATAAATACCATGGATTCCAAAATGCCAAAATGGTATCGATACTAAAAGGGAGTATC
* * *
33022 AGTACCATAGTATAAAAGTATCGGTACTAG
66 AATACCACAATATAAAAGTATCGGTACTAG
* * * *
33052 AAGGAAAGTATAAATGCCATGGA-TCCAAAATG-TAGAAATGGTATCGATATTGAAAGGGAGTAT
1 AAGGAAAGTATAAATACCATGGATTCCAAAATGCCA-AAATGGTATCGATACTAAAAGGGAGTAT
*
33115 CAATACCACAATATAGAAGTATCG
65 CAATACCACAATATAAAAGTATCG
33139 ATACCATTGT
Statistics
Matches: 75, Mismatches: 11, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
93 1 0.01
94 53 0.71
95 21 0.28
ACGTcount: A:0.42, C:0.13, G:0.21, T:0.24
Consensus pattern (95 bp):
AAGGAAAGTATAAATACCATGGATTCCAAAATGCCAAAATGGTATCGATACTAAAAGGGAGTATC
AATACCACAATATAAAAGTATCGGTACTAG
Found at i:33683 original size:81 final size:81
Alignment explanation
Indices: 33544--33961 Score: 626
Period size: 81 Copynumber: 5.2 Consensus size: 81
33534 CTGTCTTAAA
*
33544 TAAAAGATTAATTGCCTAGATGTGCATTTGACAGAAAGGTGTCAATTATG-ACACTTAGATGAAA
1 TAAAAGATTAATTGCCTAGATGTGCATTTGACAGAAAGGTGTCAATTATGCA-AGTTAGATGAAA
*
33608 GGTTAAATACCTTTGAC
65 GGTTAAATACCTTTGAG
* * * *
33625 TAAAAGATTAATTGCCTAGTTGTGCATTTGACATAAATGTGTCAATTATGCAAGTTAGATTAAAG
1 TAAAAGATTAATTGCCTAGATGTGCATTTGACAGAAAGGTGTCAATTATGCAAGTTAGATGAAAG
*
33690 GTTAAATAGCTTTGAG
66 GTTAAATACCTTTGAG
* *
33706 TAAAAGATTAATTGCTTAGATGTGCATTTGACAGAAAGGTGTCACTTATGCCAA-TTAGATGAAA
1 TAAAAGATTAATTGCCTAGATGTGCATTTGACAGAAAGGTGTCAATTATG-CAAGTTAGATGAAA
* *
33770 GTTTAAATTCCTTTGAG
65 GGTTAAATACCTTTGAG
* * *
33787 TAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAT
1 TAAAAGATTAATTGCCTAGATGTGCATTTGACAGAAAGGTGTCAATTATGCAAGTTAGATGAAAG
*
33852 GTTAAATTCCTTTGAG
66 GTTAAATACCTTTGAG
* * *
33868 TAAAATATTAATTGCCTAGATGTGCATTTGACAGAAAGGTATCAATTATAC-AGTTAGATGAAAG
1 TAAAAGATTAATTGCCTAGATGTGCATTTGACAGAAAGGTGTCAATTATGCAAGTTAGATGAAAG
*
33932 ATTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
33948 TAAAAGATTAATTG
1 TAAAAGATTAATTG
33962 TTATTATGAC
Statistics
Matches: 304, Mismatches: 30, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
80 41 0.13
81 259 0.85
82 4 0.01
ACGTcount: A:0.37, C:0.11, G:0.19, T:0.33
Consensus pattern (81 bp):
TAAAAGATTAATTGCCTAGATGTGCATTTGACAGAAAGGTGTCAATTATGCAAGTTAGATGAAAG
GTTAAATACCTTTGAG
Found at i:33975 original size:53 final size:52
Alignment explanation
Indices: 33912--34011 Score: 139
Period size: 53 Copynumber: 1.9 Consensus size: 52
33902 AAAGGTATCA
*
33912 ATTATACAGTTAGATGAAA-GATTAAATACCTTTGAGTAAAAGATTAATTGTT
1 ATTATACAGTTAAATGAAAGGA-TAAATACCTTTGAGTAAAAGATTAATTGTT
* * *
33964 ATTATGACAGTTAAATGAAAGGATAAATGCCTTTGAGTTAAATATTAA
1 ATTAT-ACAGTTAAATGAAAGGATAAATACCTTTGAGTAAAAGATTAA
34012 ATGCCCAGAT
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
52 5 0.12
53 35 0.83
54 2 0.05
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (52 bp):
ATTATACAGTTAAATGAAAGGATAAATACCTTTGAGTAAAAGATTAATTGTT
Found at i:40099 original size:94 final size:95
Alignment explanation
Indices: 39936--40115 Score: 229
Period size: 94 Copynumber: 1.9 Consensus size: 95
39926 CGATACCAAA
* * *
39936 AAGGAAAGTATCGATACCATGGATTCCAAAATGCCAAAATGGTACCGATACTGAAAGGGAGTATT
1 AAGGAAAATATCGATACCATGGATTCCAAAATGCCAAAATGATACCGATACTGAAAGGGAGTATC
* * *
40001 GGTACCATAGTATAGAAGTATTAGTACTAG
66 GGTACCACAATATACAAGTATTAGTACTAG
* * * * * *
40031 AAGGAAAATATTGATACCATGGA-TCCAGAATG-TAGAAATGATATCTATATTGAAAGGGAGTAT
1 AAGGAAAATATCGATACCATGGATTCCAAAATGCCA-AAATGATACCGATACTGAAAGGGAGTAT
40094 CGGTACCACAATATACAAGTAT
65 CGGTACCACAATATACAAGTAT
40116 CGATACCATG
Statistics
Matches: 72, Mismatches: 12, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
93 1 0.01
94 50 0.69
95 21 0.29
ACGTcount: A:0.41, C:0.13, G:0.22, T:0.25
Consensus pattern (95 bp):
AAGGAAAATATCGATACCATGGATTCCAAAATGCCAAAATGATACCGATACTGAAAGGGAGTATC
GGTACCACAATATACAAGTATTAGTACTAG
Found at i:40676 original size:81 final size:81
Alignment explanation
Indices: 40524--41139 Score: 813
Period size: 81 Copynumber: 7.6 Consensus size: 81
40514 CTGTTTTAAA
* * * *
40524 TAAAAGATTAATTGCCTAG-TGTGCATTTGATAAAAAGGTGTCAA-TATGTCAGTTAGATGAAAT
1 TAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
40587 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* * * *
40603 TAAAAGATTAATTGCCTAGCTGTGCTTTTGACAGAAAGGAGTCAATTACGCTAGTTAGATGAAAG
1 TAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
40668 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* * * **
40684 TAAAATATTAATTGCCTAGCGGTGCATTTGATAGAAATATGTCAATTATGCCAGTTAGATGAAAG
1 TAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
40749 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* * *
40765 TAAAATATTAATTGCCTAGATGTACATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
1 TAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
*
40830 GTTAAATTCCTTTGAG
66 GTTAAATACCTTTGAG
* * * * *
40846 TAAAAGATTAATTTCCCAGCTGTGCATTTGATAGAAAGGTGTCAGTTATGCCAGTTAGATAAAAG
1 TAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
40911 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* *
40927 TAAAAGATTAATTGCCTAGCTGTGCATTTGAAAAAAAGGTGTCAATTATGCCAGTTAGATGAAAG
1 TAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
*
40992 GCTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* * * * * * * * *
41008 TTAAAGATTAAATGCTTAGCTGTGTATTTGGCATAAAGGTGTCAATCATGCAAGTTAGATGAAAT
1 TAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
* * *
41073 GCTAAATTCCTTTGGG
66 GTTAAATACCTTTGAG
* * * * * *
41089 TAAAAGACTAAATGCTTAGCAGTGCATTTTGACATAAACGGTGTCATTTAT
1 TAAAAGATTAATTGCCTAGCTGTGCA-TTTGACAGAAA-GGTGTCAATTAT
41140 TGATTTGATT
Statistics
Matches: 474, Mismatches: 59, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
79 19 0.04
80 21 0.04
81 414 0.87
82 10 0.02
83 10 0.02
ACGTcount: A:0.35, C:0.12, G:0.21, T:0.33
Consensus pattern (81 bp):
TAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
GTTAAATACCTTTGAG
Found at i:43310 original size:15 final size:17
Alignment explanation
Indices: 43279--43310 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
43269 ATTTATGAGC
43279 TAAAATATATAACTTTT
1 TAAAATATATAACTTTT
43296 TAAAAT-TAT-ACTTTT
1 TAAAATATATAACTTTT
43311 GGTCCCTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 3 0.20
17 6 0.40
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (17 bp):
TAAAATATATAACTTTT
Found at i:44364 original size:29 final size:28
Alignment explanation
Indices: 44305--44366 Score: 79
Period size: 29 Copynumber: 2.2 Consensus size: 28
44295 GATAGTGACC
* *
44305 AAAATAAAATTTTGAAAGTTAAGTGACT
1 AAAATAAAATTTGGAAAGTTAAGGGACT
* *
44333 AAAATAAAATTTGGAAAAGTTTAGGGATT
1 AAAATAAAATTTGG-AAAGTTAAGGGACT
44362 AAAAT
1 AAAAT
44367 GGTAATTTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 13 0.45
29 16 0.55
ACGTcount: A:0.52, C:0.02, G:0.16, T:0.31
Consensus pattern (28 bp):
AAAATAAAATTTGGAAAGTTAAGGGACT
Found at i:51035 original size:19 final size:19
Alignment explanation
Indices: 50999--51035 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
50989 TGAAAATGAT
*
50999 TTGATTTTGAAAGCCAAAG
1 TTGATTTTGAAAACCAAAG
*
51018 TTGATTTTGAAAATCAAA
1 TTGATTTTGAAAACCAAA
51036 ATGAAATTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.41, C:0.08, G:0.16, T:0.35
Consensus pattern (19 bp):
TTGATTTTGAAAACCAAAG
Found at i:55819 original size:27 final size:26
Alignment explanation
Indices: 55779--55840 Score: 88
Period size: 27 Copynumber: 2.3 Consensus size: 26
55769 ACTCTCAGTG
* *
55779 GTGGAGGTGGAGGTGAAGGAGGGAGA
1 GTGGAGGTGAAGGTGAAAGAGGGAGA
55805 TGTGGAGGTGAAGGTGAAAGAGGGAGA
1 -GTGGAGGTGAAGGTGAAAGAGGGAGA
55832 GATGGAGGT
1 G-TGGAGGT
55841 AGAGGAGAGA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
26 1 0.03
27 31 0.97
ACGTcount: A:0.29, C:0.00, G:0.56, T:0.15
Consensus pattern (26 bp):
GTGGAGGTGAAGGTGAAAGAGGGAGA
Found at i:55853 original size:27 final size:25
Alignment explanation
Indices: 55779--55854 Score: 73
Period size: 27 Copynumber: 2.8 Consensus size: 25
55769 ACTCTCAGTG
55779 GTGGAGGTGGAGGTGAAGGAGGGAGAT
1 GTGGAGGT-GAGGTGAA-GAGGGAGAT
55806 GTGGAGGTGAAGGTGAAAGAGGGAGA-
1 GTGGAGGTG-AGGTG-AAGAGGGAGAT
*
55832 GATGGAGGTAGAGGAGAGAGAGG
1 G-TGGAGGT-GAGGTGA-AGAGG
55855 CGTTGCTACT
Statistics
Matches: 43, Mismatches: 1, Indels: 10
0.80 0.02 0.19
Matches are distributed among these distances:
26 3 0.07
27 37 0.86
28 3 0.07
ACGTcount: A:0.32, C:0.00, G:0.57, T:0.12
Consensus pattern (25 bp):
GTGGAGGTGAGGTGAAGAGGGAGAT
Found at i:56957 original size:40 final size:40
Alignment explanation
Indices: 56897--56982 Score: 129
Period size: 40 Copynumber: 2.2 Consensus size: 40
56887 ATTTTCAAAC
*
56897 CAACTATTCAAGCCAGTTTCTTCATTGTAAACTTGAAAAT
1 CAACTATTCAAGCCAATTTCTTCATTGTAAACTTGAAAAT
* * *
56937 CAACTTTTCAAGCCAATTTCTTTATTGTAAGCTTGAAAAT
1 CAACTATTCAAGCCAATTTCTTCATTGTAAACTTGAAAAT
56977 C-ACTAT
1 CAACTAT
56983 CATCTCATGA
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
39 4 0.10
40 37 0.90
ACGTcount: A:0.34, C:0.20, G:0.09, T:0.37
Consensus pattern (40 bp):
CAACTATTCAAGCCAATTTCTTCATTGTAAACTTGAAAAT
Found at i:67919 original size:18 final size:18
Alignment explanation
Indices: 67893--67931 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
67883 ATTTGTCGTG
* *
67893 TAATTTTTCTTATTTTTT
1 TAATCTTTCTGATTTTTT
67911 TAATCTTTCTGATTTTTT
1 TAATCTTTCTGATTTTTT
67929 TAA
1 TAA
67932 ATTCAAGTAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.21, C:0.08, G:0.03, T:0.69
Consensus pattern (18 bp):
TAATCTTTCTGATTTTTT
Found at i:68128 original size:18 final size:18
Alignment explanation
Indices: 68101--68140 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
68091 AATACTATTG
* *
68101 TTTTGTAATTTTTCTGAT
1 TTTTGAAATTTGTCTGAT
68119 TTTTGAAATTTGTCTGAT
1 TTTTGAAATTTGTCTGAT
68137 TTTT
1 TTTT
68141 TAAAAATTCA
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:0.17, C:0.05, G:0.12, T:0.65
Consensus pattern (18 bp):
TTTTGAAATTTGTCTGAT
Found at i:68154 original size:112 final size:107
Alignment explanation
Indices: 67796--68216 Score: 552
Period size: 102 Copynumber: 3.9 Consensus size: 107
67786 CTACAATTTT
* * * *
67796 TTTTGTAATTTT-TTATTTTTTAAATTTAAGTAGATTAAATTGCAATATATATAAAAATACATTG
1 TTTT-TAATTTTCTGATTTTTTAAATTCAAGTAGATTAAATTGCAAGATAGATAAAAATACATTG
* *
67860 AAATTAGATAAATAAACATACTAATTTGTCGTGTAATTTTTCTTA
65 AAATTAGATAAATAAACATACTAATTT-T-TTGTAATTTTTCTGA
* *
67905 TTTTTTTAATCTTTCTGATTTTTTTAAATTCAAGTAGATTAATTTGCAAGATAGATAAAAATAAA
1 --TTTTTAAT-TTTCTGA-TTTTTTAAATTCAAGTAGATTAAATTGCAAGATAGATAAAAATACA
* * *
67970 TTGAAATTAGATAAATAAACATACTAATTATTTGTGATTTTTTTGA
62 TTGAAATTAGATAAATAAACATACTAATTTTTTGTAATTTTTCTGA
*
68016 --TTT--TTTTCT-ATTTTTTTAATTCAAGTAGATTAAATTGCAAGATAGATAAAAATACATTGA
1 TTTTTAATTTTCTGATTTTTTAAATTCAAGTAGATTAAATTGCAAGATAGATAAAAATACATTGA
*
68076 AATTAGATAAATAAAAATACT-ATTGTTTTGTAATTTTTCTGA
66 AATTAGATAAATAAACATACTAATT-TTTTGTAATTTTTCTGA
68118 TTTTTGAAATTTGTCTGATTTTTTAAAAATTCAAGTAGATTAAATTGCAAGATAGAT-AAAATAC
1 TTTTT--AATTT-TCTGATTTTTT--AAATTCAAGTAGATTAAATTGCAAGATAGATAAAAATAC
68182 ATTGAAATTAGATAAATAAACATACTAATTTTTTG
61 ATTGAAATTAGATAAATAAACATACTAATTTTTTG
68217 AAAAATAAAA
Statistics
Matches: 275, Mismatches: 20, Indels: 30
0.85 0.06 0.09
Matches are distributed among these distances:
101 3 0.01
102 81 0.29
103 1 0.00
104 8 0.03
105 1 0.00
107 3 0.01
108 3 0.01
109 3 0.01
110 11 0.04
111 55 0.20
112 36 0.13
113 70 0.25
ACGTcount: A:0.40, C:0.06, G:0.10, T:0.45
Consensus pattern (107 bp):
TTTTTAATTTTCTGATTTTTTAAATTCAAGTAGATTAAATTGCAAGATAGATAAAAATACATTGA
AATTAGATAAATAAACATACTAATTTTTTGTAATTTTTCTGA
Found at i:68928 original size:3 final size:3
Alignment explanation
Indices: 68922--68951 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
68912 TGAATTATGA
*
68922 TTC TTC TTC TTC TTC TTC TTC TTC TCC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
68952 AAATCACCCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (3 bp):
TTC
Found at i:72257 original size:19 final size:20
Alignment explanation
Indices: 72233--72270 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
72223 ATTAAACTAT
72233 ATTATGGAC-TGTAATTTTA
1 ATTATGGACTTGTAATTTTA
72252 ATTATGGACTTGTAATTTT
1 ATTATGGACTTGTAATTTT
72271 TTAATTATCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.29, C:0.05, G:0.16, T:0.50
Consensus pattern (20 bp):
ATTATGGACTTGTAATTTTA
Done.