Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009366.1 Hibiscus syriacus cultivar Beakdansim tig00113196_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: 121597
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:3842 original size:105 final size:105
Alignment explanation
Indices: 3165--3834 Score: 1223
Period size: 105 Copynumber: 6.4 Consensus size: 105
3155 AGGTTTTACC
*
3165 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
3230 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
*
3270 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
3335 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
* *
3375 CAGAGCCAATTTCAACTTTACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
3440 ACGAAGGGACCGCTGATTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
*
3480 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGATAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
3545 ACGAAGGGACCACTGGTTGTCAACGAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
3585 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
3650 ACGAAGGGACCGCTGGTTGTCAACGAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
* ** *
3690 CAGAGCCAATTGCTGCTTCACAACGAAGGATATTGGACTCTAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
3755 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
3795 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
3835 GAAACAACAC
Statistics
Matches: 545, Mismatches: 20, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
105 545 1.00
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.23
Consensus pattern (105 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
Found at i:5399 original size:16 final size:16
Alignment explanation
Indices: 5380--5432 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
5370 GTATTATTAG
*
5380 TATATATTATTTTACT-
1 TATATATTATATTA-TA
*
5396 TATATGTTATATTATA
1 TATATATTATATTATA
5412 TATATATATATATGTATA
1 TATATAT-TATAT-TATA
5430 TAT
1 TAT
5433 GTATACATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
15 1 0.03
16 18 0.58
17 5 0.16
18 7 0.23
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.57
Consensus pattern (16 bp):
TATATATTATATTATA
Found at i:5796 original size:9 final size:9
Alignment explanation
Indices: 5762--5835 Score: 51
Period size: 9 Copynumber: 7.7 Consensus size: 9
5752 ATTATCATTA
5762 TTTATTTTT
1 TTTATTTTT
*
5771 TTTA-GTTT
1 TTTATTTTT
5779 TTTAGTTTTT
1 TTTA-TTTTT
*
5789 TTTATTTTA
1 TTTATTTTT
5798 TTTATTACTATT
1 TTTATT--T-TT
* *
5810 ATATATATCTT
1 -TTTAT-TTTT
5821 TTTATTTTT
1 TTTATTTTT
5830 TTTATT
1 TTTATT
5836 GTTTATATCT
Statistics
Matches: 50, Mismatches: 8, Indels: 14
0.69 0.11 0.19
Matches are distributed among these distances:
8 7 0.14
9 23 0.46
10 11 0.22
11 3 0.06
12 1 0.02
13 4 0.08
14 1 0.02
ACGTcount: A:0.19, C:0.03, G:0.03, T:0.76
Consensus pattern (9 bp):
TTTATTTTT
Found at i:5796 original size:17 final size:17
Alignment explanation
Indices: 5762--5803 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
5752 ATTATCATTA
5762 TTTATTTTTTTTAGTTT
1 TTTATTTTTTTTAGTTT
*
5779 TTTAGTTTTTTTTATTTT
1 TTTA-TTTTTTTTAGTTT
5797 ATTTATT
1 -TTTATT
5804 ACTATTATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 4 0.18
18 14 0.64
19 4 0.18
ACGTcount: A:0.14, C:0.00, G:0.05, T:0.81
Consensus pattern (17 bp):
TTTATTTTTTTTAGTTT
Found at i:9312 original size:18 final size:18
Alignment explanation
Indices: 9289--9327 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
9279 ACCGGTCACA
9289 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
9307 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
9325 ACC
1 ACC
9328 GTTGACCACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.18, C:0.51, G:0.21, T:0.10
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:11790 original size:24 final size:24
Alignment explanation
Indices: 11763--11878 Score: 146
Period size: 24 Copynumber: 4.8 Consensus size: 24
11753 TATGATTTGA
*
11763 ATTCTGATATGATACTTGACATGG
1 ATTCTGATCTGATACTTGACATGG
11787 ATTCTGATCTGATA-TCTGACATGG
1 ATTCTGATCTGATACT-TGACATGG
*
11811 ATTCTGATCTGATACTTGACTTGG
1 ATTCTGATCTGATACTTGACATGG
* * *
11835 ATTTTGATCTGTTACTTGACCT-G
1 ATTCTGATCTGATACTTGACATGG
*
11858 ATTTCTGATATGATACTTGAC
1 A-TTCTGATCTGATACTTGAC
11879 TTGAATTATT
Statistics
Matches: 81, Mismatches: 8, Indels: 6
0.85 0.08 0.06
Matches are distributed among these distances:
23 3 0.04
24 77 0.95
25 1 0.01
ACGTcount: A:0.24, C:0.16, G:0.19, T:0.41
Consensus pattern (24 bp):
ATTCTGATCTGATACTTGACATGG
Found at i:15709 original size:187 final size:185
Alignment explanation
Indices: 15385--15752 Score: 639
Period size: 187 Copynumber: 2.0 Consensus size: 185
15375 AAATTTTAAA
*
15385 TTTTAAATATATTATATATAACATATGGGCTCAGCCCAAACCATTTAAAACCCAATTAATAATTT
1 TTTTAAATATATTATATATAACATATGGGATCAGCCCAAACCATTTAAAACCCAATTAATAATTT
*
15450 AAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTTAAAAAATTATATAAAATTTTTA
66 AAGATCCAATAACATTTAAACCTAAATCAATATTAATTAATTTAAAAAATTATATAAAATTTTTA
* *
15515 TTTTATAATTATATATTATTTAAATTAATTTTAAACTGTGTTTTTTTGAATTAAATT
131 CTTTATAATTATATATTATTTAAATTAATTATAAA-T-TGTTTTTTTGAATTAAATT
* *
15572 TTTTAAATATATTATATATAACATATGGGATCAGCCTAAACCATTTAAAATCCAATTAATAATTT
1 TTTTAAATATATTATATATAACATATGGGATCAGCCCAAACCATTTAAAACCCAATTAATAATTT
*
15637 AAGATCCAATAACATTTAAACCTAAATCAATATTAATTAA-TTAAAAAATTTATATAAATTTTTT
66 AAGATCCAATAACATTTAAACCTAAATCAATATTAATTAATTTAAAAAA-TTATATAAAATTTTT
15701 ACTTTATAATTATATATTATTTAAATTAATTATAAATTGTTTTTTTGAATTA
130 ACTTTATAATTATATATTATTTAAATTAATTATAAATTGTTTTTTTGAATTA
15753 TAAAATATTT
Statistics
Matches: 173, Mismatches: 7, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
185 15 0.09
186 9 0.05
187 149 0.86
ACGTcount: A:0.43, C:0.09, G:0.04, T:0.43
Consensus pattern (185 bp):
TTTTAAATATATTATATATAACATATGGGATCAGCCCAAACCATTTAAAACCCAATTAATAATTT
AAGATCCAATAACATTTAAACCTAAATCAATATTAATTAATTTAAAAAATTATATAAAATTTTTA
CTTTATAATTATATATTATTTAAATTAATTATAAATTGTTTTTTTGAATTAAATT
Found at i:31211 original size:23 final size:23
Alignment explanation
Indices: 31168--31211 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
31158 TATTTAAATG
**
31168 ATAAACGAACATAAACGAATACA
1 ATAAACGAACATAAAAAAATACA
31191 ATAAACGAACA-ACAAAAAATA
1 ATAAACGAACATA-AAAAAATA
31212 AACTTATTCG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 1 0.06
23 17 0.94
ACGTcount: A:0.66, C:0.16, G:0.07, T:0.11
Consensus pattern (23 bp):
ATAAACGAACATAAAAAAATACA
Found at i:31478 original size:14 final size:14
Alignment explanation
Indices: 31459--31495 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
31449 CATTTGTTCA
31459 AACATAAATGAACG
1 AACATAAATGAACG
*
31473 AACATAAATGAATG
1 AACATAAATGAACG
31487 AACATAAAT
1 AACATAAAT
31496 AAACATATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.59, C:0.11, G:0.11, T:0.19
Consensus pattern (14 bp):
AACATAAATGAACG
Found at i:36695 original size:21 final size:21
Alignment explanation
Indices: 36670--36710 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
36660 AACATTAATA
36670 TTTCTATCGGTTTTGTTATTT
1 TTTCTATCGGTTTTGTTATTT
*
36691 TTTCTATCGTTTTTGTTATT
1 TTTCTATCGGTTTTGTTATT
36711 ATTGGGCACT
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:0.10, C:0.10, G:0.12, T:0.68
Consensus pattern (21 bp):
TTTCTATCGGTTTTGTTATTT
Found at i:37520 original size:12 final size:12
Alignment explanation
Indices: 37503--37537 Score: 70
Period size: 12 Copynumber: 2.9 Consensus size: 12
37493 ATATATTTTT
37503 TATTTTTAATAG
1 TATTTTTAATAG
37515 TATTTTTAATAG
1 TATTTTTAATAG
37527 TATTTTTAATA
1 TATTTTTAATA
37538 ATTTAAATCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (12 bp):
TATTTTTAATAG
Found at i:37738 original size:21 final size:21
Alignment explanation
Indices: 37686--37746 Score: 52
Period size: 21 Copynumber: 3.0 Consensus size: 21
37676 TGATTGATAT
* * *
37686 ATCAACATGATGAACCATCAT
1 ATCAACATTATGAATCATCAC
* * *
37707 GTTAACGTTATGAATCATCAC
1 ATCAACATTATGAATCATCAC
*
37728 ATCAACATTAT-AATGATCA
1 ATCAACATTATGAATCATCA
37747 ACATTTAATT
Statistics
Matches: 30, Mismatches: 10, Indels: 1
0.73 0.24 0.02
Matches are distributed among these distances:
20 7 0.23
21 23 0.77
ACGTcount: A:0.41, C:0.20, G:0.10, T:0.30
Consensus pattern (21 bp):
ATCAACATTATGAATCATCAC
Found at i:43908 original size:2 final size:2
Alignment explanation
Indices: 43901--43927 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
43891 AAAGAGGAAA
43901 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 A
43928 AATTTATTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:44163 original size:21 final size:19
Alignment explanation
Indices: 44117--44165 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 19
44107 AATGTATACA
44117 TATAATAAATAATTATTTT
1 TATAATAAATAATTATTTT
44136 TATTAATAAGATAA-TATTTATT
1 TA-TAATAA-ATAATTA-TT-TT
44158 TATAATAA
1 TATAATAA
44166 TTATTTAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
19 2 0.08
20 8 0.31
21 12 0.46
22 4 0.15
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (19 bp):
TATAATAAATAATTATTTT
Found at i:44164 original size:13 final size:13
Alignment explanation
Indices: 44146--44178 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
44136 TATTAATAAG
44146 ATAATATTTATTT
1 ATAATATTTATTT
*
44159 ATAATAATTATTT
1 ATAATATTTATTT
44172 A-AATATT
1 ATAATATT
44179 CTTACAAACG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
12 5 0.28
13 13 0.72
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
ATAATATTTATTT
Found at i:47334 original size:20 final size:20
Alignment explanation
Indices: 47293--47336 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
47283 TTTACTTTTA
*
47293 TTTTTATTTTAGGAATTTTCT
1 TTTTTATTTTA-GAATTATCT
47314 TTTTTATTTTA-AATGTATCT
1 TTTTTATTTTAGAAT-TATCT
47334 TTT
1 TTT
47337 AAGGTTTTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 3 0.14
20 7 0.33
21 11 0.52
ACGTcount: A:0.20, C:0.05, G:0.07, T:0.68
Consensus pattern (20 bp):
TTTTTATTTTAGAATTATCT
Found at i:47466 original size:15 final size:15
Alignment explanation
Indices: 47446--47477 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
47436 AAAGTTGTTA
47446 TTCTTTTATTTTTCT
1 TTCTTTTATTTTTCT
47461 TTCTTTTATTTTTCT
1 TTCTTTTATTTTTCT
47476 TT
1 TT
47478 AAAAGTTTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.06, C:0.12, G:0.00, T:0.81
Consensus pattern (15 bp):
TTCTTTTATTTTTCT
Found at i:52242 original size:16 final size:16
Alignment explanation
Indices: 52221--52273 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
52211 GTTCGAGCAG
52221 AAAAAAGAGAAAAAGA
1 AAAAAAGAGAAAAAGA
*
52237 AAAAAAAAGAAACATTA-A
1 AAAAAAGAGAAA-A--AGA
*
52255 AAAAAAGAAAAAAAGA
1 AAAAAAGAGAAAAAGA
52271 AAA
1 AAA
52274 GAAAAATAGA
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
15 1 0.03
16 15 0.50
17 2 0.07
18 11 0.37
19 1 0.03
ACGTcount: A:0.83, C:0.02, G:0.11, T:0.04
Consensus pattern (16 bp):
AAAAAAGAGAAAAAGA
Found at i:54873 original size:21 final size:21
Alignment explanation
Indices: 54849--54889 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
54839 TTTTTTCTTC
*
54849 AAAAATAATT-ATTTTTTAAA
1 AAAAATAATTAAATTTTTAAA
54869 AAAAATAATTAAATTTTTAAA
1 AAAAATAATTAAATTTTTAAA
54890 TTTTAAAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
AAAAATAATTAAATTTTTAAA
Found at i:58903 original size:31 final size:31
Alignment explanation
Indices: 58868--58928 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
58858 GGTGGAATAC
58868 TAAAATGAAACAAAAATGAAAGTTTAGATAG
1 TAAAATGAAACAAAAATGAAAGTTTAGATAG
* ** * *
58899 TAAAATGGATTAAAATTGATAGTTTAGATA
1 TAAAATGAAACAAAAATGAAAGTTTAGATA
58929 CCAAACGCGT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.52, C:0.02, G:0.16, T:0.30
Consensus pattern (31 bp):
TAAAATGAAACAAAAATGAAAGTTTAGATAG
Found at i:76509 original size:3 final size:3
Alignment explanation
Indices: 76501--76572 Score: 74
Period size: 3 Copynumber: 23.0 Consensus size: 3
76491 TTTTACTTAA
* *
76501 ATT ATT ATT ATT ATT ATA AAT ATT ATT ATT ATT ATT ATT ATT ATT -TAT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T
*
76549 ATTT ATAT ACAT ATT ATT ATT ATT
1 A-TT AT-T A-TT ATT ATT ATT ATT
76573 TAATAAATAT
Statistics
Matches: 58, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
2 1 0.02
3 50 0.86
4 6 0.10
5 1 0.02
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:76539 original size:27 final size:28
Alignment explanation
Indices: 76502--76584 Score: 96
Period size: 27 Copynumber: 2.9 Consensus size: 28
76492 TTTACTTAAA
76502 TTATTATTATTATTATAAATATTAT-TA
1 TTATTATTATTATTATAAATATTATATA
**
76529 TTATTATTATTATTATTTATATTTATATA
1 TTATTATTATTATTATAAATA-TTATATA
*
76558 CATATTATTATTATTTAATAAATATTA
1 -TTATTATTATTA-TT-ATAAATATTA
76585 CAAACCCAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
27 19 0.41
28 4 0.09
29 2 0.04
30 11 0.24
31 5 0.11
32 5 0.11
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (28 bp):
TTATTATTATTATTATAAATATTATATA
Found at i:78970 original size:24 final size:27
Alignment explanation
Indices: 78920--78975 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 27
78910 TAATTCTTTC
78920 TTTTCAAAATTATTATATATACTTATTA
1 TTTTCAAAATTATTATATATAC-TATTA
*
78948 TTTTCATAA-TATT-TATATA-TATTA
1 TTTTCAAAATTATTATATATACTATTA
78972 TTTT
1 TTTT
78976 TTTGTTATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
24 9 0.33
26 6 0.22
27 4 0.15
28 8 0.30
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (27 bp):
TTTTCAAAATTATTATATATACTATTA
Found at i:81323 original size:7 final size:7
Alignment explanation
Indices: 81288--81328 Score: 57
Period size: 7 Copynumber: 5.9 Consensus size: 7
81278 TTTTCATACA
81288 TGCATTT
1 TGCATTT
81295 T-CATTT
1 TGCATTT
81301 TGCATCTT
1 TGCAT-TT
81309 TGCATTT
1 TGCATTT
*
81316 TTCATTT
1 TGCATTT
81323 TGCATT
1 TGCATT
81329 CATACTTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
6 6 0.20
7 17 0.57
8 7 0.23
ACGTcount: A:0.15, C:0.17, G:0.10, T:0.59
Consensus pattern (7 bp):
TGCATTT
Found at i:89055 original size:22 final size:23
Alignment explanation
Indices: 89004--89059 Score: 87
Period size: 23 Copynumber: 2.5 Consensus size: 23
88994 ATCTACACTC
*
89004 TTCAAAGATGATAGATTCTCTTT
1 TTCAAAGATGATAGATTCTCATT
*
89027 TTTAAAGATGATAGATTCT-ATT
1 TTCAAAGATGATAGATTCTCATT
89049 TTCAAAGATGA
1 TTCAAAGATGA
89060 AAGCTTTATG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
22 12 0.40
23 18 0.60
ACGTcount: A:0.36, C:0.09, G:0.14, T:0.41
Consensus pattern (23 bp):
TTCAAAGATGATAGATTCTCATT
Found at i:89928 original size:185 final size:185
Alignment explanation
Indices: 89610--89980 Score: 706
Period size: 185 Copynumber: 2.0 Consensus size: 185
89600 CCAATCAACA
*
89610 TGTTATTTTGAAAAATAATGAGAAAACGATTTCCATAGTTTCTCATTCAATCTTTTCTAAAAATG
1 TGTTACTTTGAAAAATAATGAGAAAACGATTTCCATAGTTTCTCATTCAATCTTTTCTAAAAATG
89675 AAATTGTTGAAAAGTAAGAAAACAATTTCCTTAGTTTTTTTACTTAGTAAACTATTTCCCACATC
66 AAATTGTTGAAAAGTAAGAAAACAATTTCCTTAGTTTTTTTACTTAGTAAACTATTTCCCACATC
*
89740 TGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGT
131 TGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGT
89795 TGTTACTTTGAAAAATAATGAGAAAACGATTTCCATAGTTTCTCATTCAATCTTTTCTAAAAATG
1 TGTTACTTTGAAAAATAATGAGAAAACGATTTCCATAGTTTCTCATTCAATCTTTTCTAAAAATG
* *
89860 AAATTGTTGAAAAGTAAGAAAACGATTTCCTTAGTTTTTTTACTTAGTAAATTATTTCCCACATC
66 AAATTGTTGAAAAGTAAGAAAACAATTTCCTTAGTTTTTTTACTTAGTAAACTATTTCCCACATC
89925 TGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGT
131 TGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGT
89980 T
1 T
89981 TTCAAACCCT
Statistics
Matches: 182, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
185 182 1.00
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (185 bp):
TGTTACTTTGAAAAATAATGAGAAAACGATTTCCATAGTTTCTCATTCAATCTTTTCTAAAAATG
AAATTGTTGAAAAGTAAGAAAACAATTTCCTTAGTTTTTTTACTTAGTAAACTATTTCCCACATC
TGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGT
Found at i:90020 original size:76 final size:76
Alignment explanation
Indices: 89921--90759 Score: 1554
Period size: 76 Copynumber: 11.0 Consensus size: 76
89911 TTATTTCCCA
*
89921 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
89986 ACCCTTAGGGT
66 ACCCTCAGGGT
89997 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
90062 ACCCTCAGGGT
66 ACCCTCAGGGT
90073 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
90138 ACCCTCAGGGT
66 ACCCTCAGGGT
*
90149 CATCTGTAAGTCATGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
90214 ACCCTCAGGGT
66 ACCCTCAGGGT
* *
90225 CATATGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGACGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
90290 ACCCTCAGGGT
66 ACCCTCAGGGT
* *
90301 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTAACGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
90366 ACCCTCAGGGT
66 ACCCTCAGGGT
* *
90377 CATCTGTAAGTCCTGCAGTGCATGATGTCTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTCTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
90442 ACCCTCAGGGT
66 ACCCTCAGGGT
*
90453 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGACGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
90518 ACCCTCAGGGT
66 ACCCTCAGGGT
*
90529 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTAACT-TTTTCA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGA-TGTTTTCA
90593 AACCCTCAGGGT
65 AACCCTCAGGGT
90605 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
90670 AGCCTCAGGGT
66 ACCCTCAGGGT
90681 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
90746 ACCCTCAGGGT
66 ACCCTCAGGGT
90757 CAT
1 CAT
90760 TCATAAGACC
Statistics
Matches: 741, Mismatches: 20, Indels: 4
0.97 0.03 0.01
Matches are distributed among these distances:
75 1 0.00
76 740 1.00
ACGTcount: A:0.23, C:0.23, G:0.22, T:0.32
Consensus pattern (76 bp):
CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
ACCCTCAGGGT
Found at i:90925 original size:3 final size:3
Alignment explanation
Indices: 90917--90988 Score: 74
Period size: 3 Copynumber: 23.0 Consensus size: 3
90907 TTTTACTTAA
* *
90917 ATT ATT ATT ATT ATT ATA AAT ATT ATT ATT ATT ATT ATT ATT ATT -TAT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T
*
90965 ATTT ATAT ACAT ATT ATT ATT ATT
1 A-TT AT-T A-TT ATT ATT ATT ATT
90989 TAATAAATAT
Statistics
Matches: 58, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
2 1 0.02
3 50 0.86
4 6 0.10
5 1 0.02
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:90955 original size:27 final size:28
Alignment explanation
Indices: 90918--91000 Score: 96
Period size: 27 Copynumber: 2.9 Consensus size: 28
90908 TTTACTTAAA
90918 TTATTATTATTATTATAAATATTAT-TA
1 TTATTATTATTATTATAAATATTATATA
**
90945 TTATTATTATTATTATTTATATTTATATA
1 TTATTATTATTATTATAAATA-TTATATA
*
90974 CATATTATTATTATTTAATAAATATTA
1 -TTATTATTATTA-TT-ATAAATATTA
91001 CAAACCCAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
27 19 0.41
28 4 0.09
29 2 0.04
30 11 0.24
31 5 0.11
32 5 0.11
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (28 bp):
TTATTATTATTATTATAAATATTATATA
Found at i:100942 original size:3 final size:3
Alignment explanation
Indices: 100936--100976 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
100926 ACGACTTTGT
100936 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
100977 TTGCATTTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:119263 original size:153 final size:155
Alignment explanation
Indices: 118942--119588 Score: 917
Period size: 153 Copynumber: 4.2 Consensus size: 155
118932 TTATATTCAT
*
118942 TTTTTTTACTAAATTTGAACCACATGCTCCTAAACCTATCGTAGAATAC-TATGTACTTTCAATT
1 TTTTTTTACCAAATTTGAACCACATGCTCCTAAACCTATCGTAGAATACATATGTACTTTCAATT
* *
119006 CTTCTTTTAATAACAAATTGTCTATTTTTCAATTTAG--TCTCAATTTTTATAATTTCCTTATTT
66 CTTCTTTTGATAACAAATTGTCTA-TTTTCAATTTAGCCCCTCAATTTTTATAATTTCCTTATTT
119069 CTTAAATTCATCCTTTAGTTTAAGTC
130 CTTAAATTCATCCTTTAGTTTAAGTC
* * *
119095 GTTTTTTTACCAAATTTGAA-C-CATGCTCTTAAATC-ATCCTAGAATACATATGTACTTTCAAT
1 -TTTTTTTACCAAATTTGAACCACATGCTCCTAAACCTATCGTAGAATACATATGTACTTTCAAT
119157 TCTTCTTTTTGATAACAAATTGTCTATTTTCAATTTAGCCCCTCAATGTTTTATAATTTCCTTA-
65 TCTTC-TTTTGATAACAAATTGTCTATTTTCAATTTAGCCCCTCAAT-TTTTATAATTTCCTTAT
*
119221 TT-TTAAATTCA-CCATTTAATTTAAGTC
128 TTCTTAAATTCATCC-TTTAGTTTAAGTC
* *
119248 TATTTTTTACTAAATTTGAACCACATGCTCCTAAACC-ATCATAGAATACATATGTACTTTCAAT
1 T-TTTTTTACCAAATTTGAACCACATGCTCCTAAACCTATCGTAGAATACATATGTACTTTCAAT
119312 TCTTCTTTTTGATAACAAATTGTCTATAATTTTCAATTTAGCCCCTCAATTTTTTATAATTT-CT
65 TCTTC-TTTTGATAACAAATTGTC--T-ATTTTCAATTTAGCCCCTCAA-TTTTTATAATTTCCT
119376 TATTTCTTAAATTCATCCTTTAGTTTAAGTC
125 TATTTCTTAAATTCATCCTTTAGTTTAAGTC
* *
119407 TATTTTTACCAAATTTGAACCACATGCTCTTAAA-CTATCGTAGAATACATATGTACTTTCAATT
1 TTTTTTTACCAAATTTGAACCACATGCTCCTAAACCTATCGTAGAATACATATGTACTTTCAATT
* * * *
119471 CCTCTTTT-ATAACAAATTATCTATTTTCAATTTAGTCCCTTAATTTTTCATAATTTCCTTATTT
66 CTTCTTTTGATAACAAATTGTCTATTTTCAATTTAGCCCCTCAATTTTT-ATAATTTCCTTATTT
* *
119535 CTTCAATTCATCC-TTATTTTAAGTC
130 CTTAAATTCATCCTTTAGTTTAAGTC
* *
119560 TGTTTTTACCAAATTTAAACCACATGCTC
1 TTTTTTTACCAAATTTGAACCACATGCTC
119589 ATGTACCAAT
Statistics
Matches: 450, Mismatches: 24, Indels: 39
0.88 0.05 0.08
Matches are distributed among these distances:
151 11 0.02
152 51 0.11
153 122 0.27
154 47 0.10
155 78 0.17
156 12 0.03
157 10 0.02
158 94 0.21
159 23 0.05
160 2 0.00
ACGTcount: A:0.30, C:0.19, G:0.06, T:0.46
Consensus pattern (155 bp):
TTTTTTTACCAAATTTGAACCACATGCTCCTAAACCTATCGTAGAATACATATGTACTTTCAATT
CTTCTTTTGATAACAAATTGTCTATTTTCAATTTAGCCCCTCAATTTTTATAATTTCCTTATTTC
TTAAATTCATCCTTTAGTTTAAGTC
Found at i:119531 original size:311 final size:307
Alignment explanation
Indices: 118942--119631 Score: 974
Period size: 311 Copynumber: 2.2 Consensus size: 307
118932 TTATATTCAT
*
118942 TTTTTTTACTAAATTTGAACCACATGCTCCTAAACCTATCGTAGAATACTATGTACTTTCAATTC
1 TTTTTTTACTAAATTTGAACCACATGCTCCTAAACC-ATCATAGAATACTATGTACTTTCAATTC
*
119007 TTC-TTTTAATAACAAATTGTCTATTTTTCAATTTAGTCTCAATTTTTATAATTTCCTTATTTCT
65 TTCTTTTTAATAACAAATTGTCTATTTTTCAATTTAGCCTCAATTTTTATAATTTCCTTATTTCT
*
119071 TAAATTCATCCTTTAGTTTAAGTCGTTTTTTTACCAAATTTGAACCATGCTCTTAAATCATCCTA
130 TAAATTCATCCTTTAGTTTAAGTCGTATTTTTACCAAATTTGAACCATGCTCTTAAATCATCCTA
* *
119136 GAATACATATGTACTTTCAATTCTTCTTTTTGATAACAAATTGTCTATTTTCAATTTAGCCCCTC
195 GAATACATATGTACTTTCAATTCCTCTTTTTGATAACAAATTATCTATTTTCAATTTAGCCCCTC
119201 AATGTTTTATAATTTCCTTA-TT-TTAAATTCA-CCATTTAATTTAAGTC
260 AATGTTTTATAATTTCCTTATTTCTTAAATTCATCC--TTAATTTAAGTC
119248 TATTTTTTACTAAATTTGAACCACATGCTCCTAAACCATCATAGAATACATATGTACTTTCAATT
1 T-TTTTTTACTAAATTTGAACCACATGCTCCTAAACCATCATAGAATAC-TATGTACTTTCAATT
*
119313 CTTCTTTTTGATAACAAATTGTCTATAATTTTCAATTTAGCCCCTCAATTTTTTATAATTT-CTT
64 CTTCTTTTTAATAACAAATTGTCTAT--TTTTCAATTTAG--CCTCAA-TTTTTATAATTTCCTT
119377 ATTTCTTAAATTCATCCTTTAGTTTAAGTC-TATTTTTACCAAATTTGAACCACATGCTCTTAAA
124 ATTTCTTAAATTCATCCTTTAGTTTAAGTCGTATTTTTACCAAATTTGAA-C-CATGCTCTTAAA
*
119441 -CTATCGTAGAATACATATGTACTTTCAATTCCTC-TTTT-ATAACAAATTATCTATTTTCAATT
187 TC-ATCCTAGAATACATATGTACTTTCAATTCCTCTTTTTGATAACAAATTATCTATTTTCAATT
* * * *
119503 TAGTCCCTTAAT-TTTTCATAATTTCCTTATTTCTTCAATTCATCCTTATTTTAAGTC
251 TAGCCCCTCAATGTTTT-ATAATTTCCTTATTTCTTAAATTCATCCTTAATTTAAGTC
* * * * ** *
119560 TGTTTTTACCAAATTTAAACCACATGCTCATGTACCA--ATAGAATACCTATATAAC-TTCAATT
1 TTTTTTTACTAAATTTGAACCACATGCTCCTAAACCATCATAGAATA-CTATGT-ACTTTCAATT
119622 CTTACTTTTT
64 CTT-CTTTTT
119632 TACTAAAAAT
Statistics
Matches: 348, Mismatches: 18, Indels: 32
0.87 0.05 0.08
Matches are distributed among these distances:
306 12 0.03
307 54 0.16
308 20 0.06
309 22 0.06
310 25 0.07
311 93 0.27
312 58 0.17
313 62 0.18
314 2 0.01
ACGTcount: A:0.30, C:0.19, G:0.06, T:0.46
Consensus pattern (307 bp):
TTTTTTTACTAAATTTGAACCACATGCTCCTAAACCATCATAGAATACTATGTACTTTCAATTCT
TCTTTTTAATAACAAATTGTCTATTTTTCAATTTAGCCTCAATTTTTATAATTTCCTTATTTCTT
AAATTCATCCTTTAGTTTAAGTCGTATTTTTACCAAATTTGAACCATGCTCTTAAATCATCCTAG
AATACATATGTACTTTCAATTCCTCTTTTTGATAACAAATTATCTATTTTCAATTTAGCCCCTCA
ATGTTTTATAATTTCCTTATTTCTTAAATTCATCCTTAATTTAAGTC
Done.