Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006580.1 Hibiscus syriacus cultivar Beakdansim tig00016129_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: 96299
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.31
Found at i:2904 original size:20 final size:21
Alignment explanation
Indices: 2866--2906 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
2856 CAGATTGTGC
2866 AGGGGGTACAGATTCCCCCTG
1 AGGGGGTACAGATTCCCCCTG
2887 AGGGGGTATC-GATTCCCCCT
1 AGGGGGTA-CAGATTCCCCCT
2907 AAATGAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 18 0.95
22 1 0.05
ACGTcount: A:0.17, C:0.29, G:0.32, T:0.22
Consensus pattern (21 bp):
AGGGGGTACAGATTCCCCCTG
Found at i:3766 original size:21 final size:23
Alignment explanation
Indices: 3736--3780 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
3726 GTAGCAATAA
*
3736 TGTAGCA-GGGTATCGA-TTCCC
1 TGTAGCAGGGGAATCGATTTCCC
*
3757 TGTAGTAGGGGAATCGATTTCCC
1 TGTAGCAGGGGAATCGATTTCCC
3780 T
1 T
3781 CTTTGAATCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 6 0.30
22 8 0.40
23 6 0.30
ACGTcount: A:0.20, C:0.20, G:0.29, T:0.31
Consensus pattern (23 bp):
TGTAGCAGGGGAATCGATTTCCC
Found at i:7456 original size:16 final size:16
Alignment explanation
Indices: 7423--7479 Score: 51
Period size: 16 Copynumber: 3.3 Consensus size: 16
7413 AAAAGTTAGT
* **
7423 GGAAAAACTAAAGGAA
1 GGAAAAATTAAATAAA
7439 GGAAAAATTAAATAAAGGAA
1 GGAAAAATTAAAT--A--AA
7459 GGAAAAATTAAATAAA
1 GGAAAAATTAAATAAA
7475 GGAAA
1 GGAAA
7480 CAACATGAGA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
16 18 0.53
18 1 0.03
20 15 0.44
ACGTcount: A:0.65, C:0.02, G:0.21, T:0.12
Consensus pattern (16 bp):
GGAAAAATTAAATAAA
Found at i:7456 original size:20 final size:20
Alignment explanation
Indices: 7431--7478 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
7421 GTGGAAAAAC
7431 TAAAGGAAGGAAAAATTAAA
1 TAAAGGAAGGAAAAATTAAA
7451 TAAAGGAAGGAAAAATTAAA
1 TAAAGGAAGGAAAAATTAAA
7471 TAAAGGAA
1 TAAAGGAA
7479 ACAACATGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.65, C:0.00, G:0.21, T:0.15
Consensus pattern (20 bp):
TAAAGGAAGGAAAAATTAAA
Found at i:8260 original size:21 final size:22
Alignment explanation
Indices: 8230--8272 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
8220 AAGTTGATAT
8230 AGTGAATTTTC-GGGCATGAAC
1 AGTGAATTTTCTGGGCATGAAC
* *
8251 AGTGATTTTTCTGGGCTTGAAC
1 AGTGAATTTTCTGGGCATGAAC
8273 GAAATTTCAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.23, C:0.14, G:0.28, T:0.35
Consensus pattern (22 bp):
AGTGAATTTTCTGGGCATGAAC
Found at i:9102 original size:13 final size:14
Alignment explanation
Indices: 9084--9112 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
9074 TTTTAAACGT
9084 ATAAATGTA-AATG
1 ATAAATGTATAATG
9097 ATAAATGTATAATG
1 ATAAATGTATAATG
9111 AT
1 AT
9113 GAACGTTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.52, C:0.00, G:0.14, T:0.34
Consensus pattern (14 bp):
ATAAATGTATAATG
Found at i:31055 original size:20 final size:20
Alignment explanation
Indices: 31030--31069 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
31020 AGCAACAGAA
*
31030 TAAAAATGATTCTATCTAAT
1 TAAAAATGATCCTATCTAAT
31050 TAAAAATGATCCTATCTAAT
1 TAAAAATGATCCTATCTAAT
31070 AACTAATAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.45, C:0.12, G:0.05, T:0.38
Consensus pattern (20 bp):
TAAAAATGATCCTATCTAAT
Found at i:31098 original size:53 final size:51
Alignment explanation
Indices: 31026--31154 Score: 231
Period size: 53 Copynumber: 2.5 Consensus size: 51
31016 AATTAGCAAC
31026 AGAATAAAAATGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
1 AGAATAAAAATGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
31077 AGAATAAAAAATTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
1 AGAAT-AAAAA-TGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
31130 AGAATAAAAACTGATTCTATCTAAT
1 AGAATAAAAA-TGATTCTATCTAAT
31155 ATTTAATTTA
Statistics
Matches: 75, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
51 5 0.07
52 24 0.32
53 46 0.61
ACGTcount: A:0.49, C:0.12, G:0.06, T:0.33
Consensus pattern (51 bp):
AGAATAAAAATGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
Found at i:31112 original size:20 final size:21
Alignment explanation
Indices: 31083--31122 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
31073 TAATAGAATA
*
31083 AAAAATTGATTCTATCTAATT
1 AAAAATTGATCCTATCTAATT
31104 AAAAA-TGATCCTATCTAAT
1 AAAAATTGATCCTATCTAAT
31123 AACTAATAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.45, C:0.12, G:0.05, T:0.38
Consensus pattern (21 bp):
AAAAATTGATCCTATCTAATT
Found at i:35737 original size:20 final size:20
Alignment explanation
Indices: 35712--35751 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
35702 AGCAAGAGAA
*
35712 TAAAAATGATTCTATCTAAT
1 TAAAAATGATCCTATCTAAT
35732 TAAAAATGATCCTATCTAAT
1 TAAAAATGATCCTATCTAAT
35752 AACTAATAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.45, C:0.12, G:0.05, T:0.38
Consensus pattern (20 bp):
TAAAAATGATCCTATCTAAT
Found at i:35780 original size:53 final size:52
Alignment explanation
Indices: 35708--35836 Score: 242
Period size: 53 Copynumber: 2.5 Consensus size: 52
35698 AATTAGCAAG
35708 AGAATAAAAA-TGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
1 AGAATAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
35759 AGAATAAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
1 AGAAT-AAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
35812 AGAATAAAAACTGATTCTATCTAAT
1 AGAATAAAAACTGATTCTATCTAAT
35837 ATTTAATTTA
Statistics
Matches: 76, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
51 5 0.07
52 25 0.33
53 46 0.61
ACGTcount: A:0.49, C:0.12, G:0.06, T:0.33
Consensus pattern (52 bp):
AGAATAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
Found at i:35794 original size:20 final size:21
Alignment explanation
Indices: 35765--35804 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
35755 TAATAGAATA
*
35765 AAAAACTGATTCTATCTAATT
1 AAAAACTGATCCTATCTAATT
35786 AAAAA-TGATCCTATCTAAT
1 AAAAACTGATCCTATCTAAT
35805 AACTAATAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.45, C:0.15, G:0.05, T:0.35
Consensus pattern (21 bp):
AAAAACTGATCCTATCTAATT
Found at i:44617 original size:8 final size:8
Alignment explanation
Indices: 44604--44633 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
44594 TCGCTAAAAG
44604 CGTCGCCT
1 CGTCGCCT
44612 CGTCGCCT
1 CGTCGCCT
44620 CGTCGCCT
1 CGTCGCCT
44628 C-TCGCC
1 CGTCGCC
44634 GCCTCCGACG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 5 0.23
8 17 0.77
ACGTcount: A:0.00, C:0.53, G:0.23, T:0.23
Consensus pattern (8 bp):
CGTCGCCT
Found at i:49893 original size:21 final size:23
Alignment explanation
Indices: 49869--49918 Score: 54
Period size: 21 Copynumber: 2.3 Consensus size: 23
49859 TTTTGTATTA
*
49869 ATATTATTATATTA-TAC-AATT
1 ATATTATTATATAATTACTAATT
49890 ATA-TA-TATATAATTACTAATT
1 ATATTATTATATAATTACTAATT
*
49911 TTATTATT
1 ATATTATT
49919 TAAATGGTAC
Statistics
Matches: 23, Mismatches: 2, Indels: 6
0.74 0.06 0.19
Matches are distributed among these distances:
19 6 0.26
20 5 0.22
21 9 0.39
22 2 0.09
23 1 0.04
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (23 bp):
ATATTATTATATAATTACTAATT
Found at i:51139 original size:2 final size:2
Alignment explanation
Indices: 51134--51173 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
51124 TTTTTTCTAC
51134 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
51174 TATTATTTTC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:51350 original size:23 final size:23
Alignment explanation
Indices: 51323--51368 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
51313 CCATTTATAT
*
51323 TTTA-TTATATTTTCTTCTTTTTC
1 TTTATTTATATTTTCGT-TTTTTC
*
51346 TTTATTTGTATTTTCGTTTTTTC
1 TTTATTTATATTTTCGTTTTTTC
51369 CTCTTCTGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.11, C:0.11, G:0.04, T:0.74
Consensus pattern (23 bp):
TTTATTTATATTTTCGTTTTTTC
Found at i:62461 original size:23 final size:23
Alignment explanation
Indices: 62431--62476 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
62421 CAAGGCTCAT
62431 GCACATGCTTGAGATGGTTGAGG
1 GCACATGCTTGAGATGGTTGAGG
62454 GCACATGCTTGAGATGGTTGAGG
1 GCACATGCTTGAGATGGTTGAGG
62477 AGCATCTTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.22, C:0.13, G:0.39, T:0.26
Consensus pattern (23 bp):
GCACATGCTTGAGATGGTTGAGG
Found at i:62871 original size:105 final size:105
Alignment explanation
Indices: 62689--63241 Score: 1016
Period size: 105 Copynumber: 5.3 Consensus size: 105
62679 AGGTTTTACC
* *
62689 CAGAGCCAATTTCAACTTCACAATGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
*
62754 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACGAACATTTCTCAATTT
62794 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
62859 ACGAAGGGACCGCTGGTTGTCAACGAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACGAACATTTCTCAATTT
62899 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
*
62964 ACGAAGGGACCGCTGGTTGTCAACGAACATTTATCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACGAACATTTCTCAATTT
63004 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
63069 ACGAAGGGACCGCTGGTTGTCAACGAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACGAACATTTCTCAATTT
* **
63109 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGGCTCCAGACAACACAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
* *
63174 ACGAAGGGACCGTTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACGAACATTTCTCAATTT
*
63214 CAGAGCCAATTTCAACTTCGCAACGAAG
1 CAGAGCCAATTTCAACTTCACAACGAAG
63242 ACAACGCAAG
Statistics
Matches: 437, Mismatches: 11, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
105 437 1.00
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.24
Consensus pattern (105 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACGAACATTTCTCAATTT
Found at i:62946 original size:210 final size:210
Alignment explanation
Indices: 62689--63343 Score: 1115
Period size: 210 Copynumber: 3.2 Consensus size: 210
62679 AGGTTTTACC
*
62689 CAGAGCCAATTTCAACTTCACAATGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
62754 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACG
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACG
62819 AAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACG
131 AAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACG
62884 AACATTTCTCAATTT
196 AACATTTCTCAATTT
*
62899 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
62964 ACGAAGGGACCGCTGGTTGTCAACGAACATTTATCAATTTCAGAGCCAATTTCAACTTCACAACG
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACG
63029 AAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACG
131 AAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACG
63094 AACATTTCTCAATTT
196 AACATTTCTCAATTT
* *
63109 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGGCTCCAGACAACACAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
63174 ACGAAGGGACCGTTGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTCAACTTCGCAAC-
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACG
* *
63238 ----------GA----AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACA
131 AAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACG
63289 AACATTTCTCAATTT
196 AACATTTCTCAATTT
63304 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
63344 GGAACAATAC
Statistics
Matches: 431, Mismatches: 14, Indels: 15
0.94 0.03 0.03
Matches are distributed among these distances:
195 101 0.23
199 2 0.00
210 328 0.76
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.24
Consensus pattern (210 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACG
AAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACG
AACATTTCTCAATTT
Found at i:63303 original size:90 final size:90
Alignment explanation
Indices: 63150--63331 Score: 337
Period size: 90 Copynumber: 2.0 Consensus size: 90
63140 ATTGGGCTCC
*
63150 AGACAACACAAGTTCAACTTCACGACGAAGGGACCGTTGGTTGTCAACAAACATTTCTCAATTTC
1 AGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTC
*
63215 AGAGCCAATTTCAACTTCGCAACGA
66 AGAGCCAATTTCAACTTCACAACGA
*
63240 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTC
1 AGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTC
63305 AGAGCCAATTTCAACTTCACAACGA
66 AGAGCCAATTTCAACTTCACAACGA
63330 AG
1 AG
63332 GATATTGGAC
Statistics
Matches: 89, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
90 89 1.00
ACGTcount: A:0.35, C:0.26, G:0.17, T:0.23
Consensus pattern (90 bp):
AGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTC
AGAGCCAATTTCAACTTCACAACGA
Found at i:63778 original size:21 final size:23
Alignment explanation
Indices: 63754--63803 Score: 54
Period size: 21 Copynumber: 2.3 Consensus size: 23
63744 TTTTGTATTA
*
63754 ATATTATTATATTA-TAC-AATT
1 ATATTATTATATAATTACTAATT
63775 ATA-TA-TATATAATTACTAATT
1 ATATTATTATATAATTACTAATT
*
63796 TTATTATT
1 ATATTATT
63804 TAAATGGTAC
Statistics
Matches: 23, Mismatches: 2, Indels: 6
0.74 0.06 0.19
Matches are distributed among these distances:
19 6 0.26
20 5 0.22
21 9 0.39
22 2 0.09
23 1 0.04
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (23 bp):
ATATTATTATATAATTACTAATT
Found at i:64883 original size:3 final size:3
Alignment explanation
Indices: 64865--64903 Score: 51
Period size: 3 Copynumber: 12.3 Consensus size: 3
64855 ATATTACGTT
*
64865 TTA TTA TATA TATA TTA TTA TTG TTA TTA TTA TTA TTA T
1 TTA TTA T-TA T-TA TTA TTA TTA TTA TTA TTA TTA TTA T
64904 ATGTATATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
3 26 0.79
4 7 0.21
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:65029 original size:2 final size:2
Alignment explanation
Indices: 65024--65063 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
65014 TTTTTTCTAC
65024 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
65064 TATTTATTAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:65241 original size:23 final size:23
Alignment explanation
Indices: 65214--65259 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
65204 CCATTTATAT
*
65214 TTTA-TTATATTTTCTTCTTTTTC
1 TTTATTTATATTTTCGT-TTTTTC
*
65237 TTTATTTGTATTTTCGTTTTTTC
1 TTTATTTATATTTTCGTTTTTTC
65260 CTCTTCTGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.11, C:0.11, G:0.04, T:0.74
Consensus pattern (23 bp):
TTTATTTATATTTTCGTTTTTTC
Found at i:73568 original size:2 final size:2
Alignment explanation
Indices: 73561--73592 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
73551 TATTAAAATA
73561 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
73593 GAGTAAATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:76332 original size:18 final size:19
Alignment explanation
Indices: 76309--76351 Score: 70
Period size: 20 Copynumber: 2.3 Consensus size: 19
76299 CAGTAATCAT
76309 ATTCC-CTGGTAATCTTAC
1 ATTCCACTGGTAATCTTAC
76327 ATTCCCACTGGTAATCTTAC
1 ATT-CCACTGGTAATCTTAC
76347 ATTCC
1 ATTCC
76352 GTGAACCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 3 0.13
19 4 0.17
20 16 0.70
ACGTcount: A:0.23, C:0.30, G:0.09, T:0.37
Consensus pattern (19 bp):
ATTCCACTGGTAATCTTAC
Found at i:76339 original size:20 final size:20
Alignment explanation
Indices: 76314--76351 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
76304 ATCATATTCC
76314 CTGGTAATCTTACATTCCCA
1 CTGGTAATCTTACATTCCCA
76334 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
76352 GTGAACCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.24, C:0.29, G:0.11, T:0.37
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:76851 original size:7 final size:7
Alignment explanation
Indices: 76839--76885 Score: 57
Period size: 7 Copynumber: 7.3 Consensus size: 7
76829 AATATTAATG
76839 TATATGT
1 TATATGT
76846 TATATGT
1 TATATGT
76853 TAT-TG-
1 TATATGT
76858 TATATGT
1 TATATGT
*
76865 TACATGT
1 TATATGT
76872 TAT-TG-
1 TATATGT
76877 TATATGT
1 TATATGT
76884 TA
1 TA
76886 CATGATCCAT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
5 6 0.18
6 8 0.24
7 20 0.59
ACGTcount: A:0.28, C:0.02, G:0.15, T:0.55
Consensus pattern (7 bp):
TATATGT
Found at i:76861 original size:19 final size:19
Alignment explanation
Indices: 76837--76889 Score: 97
Period size: 19 Copynumber: 2.8 Consensus size: 19
76827 TGAATATTAA
*
76837 TGTATATGTTATATGTTAT
1 TGTATATGTTACATGTTAT
76856 TGTATATGTTACATGTTAT
1 TGTATATGTTACATGTTAT
76875 TGTATATGTTACATG
1 TGTATATGTTACATG
76890 ATCCATGTGA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.26, C:0.04, G:0.17, T:0.53
Consensus pattern (19 bp):
TGTATATGTTACATGTTAT
Found at i:81563 original size:21 final size:20
Alignment explanation
Indices: 81537--81631 Score: 73
Period size: 21 Copynumber: 4.6 Consensus size: 20
81527 TCGAGGGTTC
*
81537 TATGTAGTCCTTCGGGACATA
1 TATGTAGTCCTT-GGAACATA
* *
81558 TATGTAATCCTTTGAACATA
1 TATGTAGTCCTTGGAACATA
* * * *
81578 TATGTTGTACTTCGGGACACA
1 TATGTAGTCCTT-GGAACATA
* * *
81599 TATTTGGTCCATTGGAATATA
1 TATGTAGTCC-TTGGAACATA
81620 TATGTAGTCCTT
1 TATGTAGTCCTT
81632 AAGGAGAATT
Statistics
Matches: 55, Mismatches: 17, Indels: 5
0.71 0.22 0.06
Matches are distributed among these distances:
20 17 0.31
21 36 0.65
22 2 0.04
ACGTcount: A:0.26, C:0.16, G:0.19, T:0.39
Consensus pattern (20 bp):
TATGTAGTCCTTGGAACATA
Found at i:89258 original size:20 final size:21
Alignment explanation
Indices: 89233--89279 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
89223 GGTTGTGCTC
89233 ATTTCTAGCC-GTTGGGGATG
1 ATTTCTAGCCTGTTGGGGATG
*
89253 ATTTCTAGCCTTTTGGGGATG
1 ATTTCTAGCCTGTTGGGGATG
*
89274 TTTTCT
1 ATTTCT
89280 TTGCAAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 10 0.42
21 14 0.58
ACGTcount: A:0.13, C:0.15, G:0.28, T:0.45
Consensus pattern (21 bp):
ATTTCTAGCCTGTTGGGGATG
Found at i:93587 original size:21 final size:22
Alignment explanation
Indices: 93488--93588 Score: 61
Period size: 21 Copynumber: 4.8 Consensus size: 22
93478 TAAACCTGAC
* *
93488 AGGGGGTATCGGTACCCA-TCT
1 AGGGGGTATCGGTACCTATTCA
*
93509 A--GGGTATCGATACAC-ATTCA
1 AGGGGGTATCGGTAC-CTATTCA
*
93529 AGGAGGGTATCGGTACCTATTGA
1 AGG-GGGTATCGGTACCTATTCA
*** * *
93552 A-TCAGTATTGATACCTA-TCA
1 AGGGGGTATCGGTACCTATTCA
93572 AGGGGGTATCGGTACCT
1 AGGGGGTATCGGTACCT
93589 GGGTGACAAG
Statistics
Matches: 58, Mismatches: 15, Indels: 14
0.67 0.17 0.16
Matches are distributed among these distances:
19 12 0.21
20 7 0.12
21 22 0.38
22 1 0.02
23 16 0.28
ACGTcount: A:0.27, C:0.19, G:0.28, T:0.27
Consensus pattern (22 bp):
AGGGGGTATCGGTACCTATTCA
Done.