Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004035.1 Hibiscus syriacus cultivar Beakdansim tig00008814_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: 97839
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:3728 original size:70 final size:72
Alignment explanation
Indices: 3597--3731 Score: 195
Period size: 70 Copynumber: 1.9 Consensus size: 72
3587 AGATACTTAT
*
3597 TAGTTACAAAGCAAAAAAAGCATGAGAATAGTACAAAACGAATAAAAAAACAAATTAGTTAAAAC
1 TAGTTACAAAGCAAAAAAAGCATGAGAATAGAACAAAACGAATAAAAAAACAAATTAGTTAAAAC
3662 GATATAC
66 GATATAC
* * * *
3669 TAGTTACAAAGC-AAAAAAGGATGAGAATAGAATGAAGA-GAA-CAAAAAACAAATTAGTTAAAA
1 TAGTTACAAAGCAAAAAAAGCATGAGAATAGAA-CAAAACGAATAAAAAAACAAATTAGTTAAAA
3731 C
65 C
3732 ACATACACGA
Statistics
Matches: 57, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
70 21 0.37
71 21 0.37
72 15 0.26
ACGTcount: A:0.59, C:0.10, G:0.15, T:0.17
Consensus pattern (72 bp):
TAGTTACAAAGCAAAAAAAGCATGAGAATAGAACAAAACGAATAAAAAAACAAATTAGTTAAAAC
GATATAC
Found at i:11569 original size:10 final size:10
Alignment explanation
Indices: 11554--11583 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
11544 ATTTAAATGG
11554 TAATATATTA
1 TAATATATTA
11564 TAATATATTA
1 TAATATATTA
*
11574 TAATAAATTA
1 TAATATATTA
11584 ATATTTTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (10 bp):
TAATATATTA
Found at i:11593 original size:16 final size:16
Alignment explanation
Indices: 11563--11610 Score: 69
Period size: 16 Copynumber: 2.9 Consensus size: 16
11553 GTAATATATT
*
11563 ATAATATATTATAATAA
1 ATAA-ATATTTTAATAA
*
11580 ATTAATATTTTAATAA
1 ATAAATATTTTAATAA
11596 ATAAATATTTTAATA
1 ATAAATATTTTAATA
11611 TTTTATTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
16 25 0.89
17 3 0.11
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
ATAAATATTTTAATAA
Found at i:11791 original size:27 final size:27
Alignment explanation
Indices: 11761--11818 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
11751 TAATTATTGG
* * * * *
11761 TATTATTTTATTTATTTATTTGTTTAA
1 TATTAGTTTATATATTAATTTCTATAA
11788 TATTAGTTTATATATTAATTTCTATAA
1 TATTAGTTTATATATTAATTTCTATAA
11815 TATT
1 TATT
11819 TATTAAATTA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.31, C:0.02, G:0.03, T:0.64
Consensus pattern (27 bp):
TATTAGTTTATATATTAATTTCTATAA
Found at i:12157 original size:38 final size:38
Alignment explanation
Indices: 12114--12195 Score: 128
Period size: 38 Copynumber: 2.2 Consensus size: 38
12104 ATGACTTAAT
* *
12114 TTATTTTGTATATTACTTAATTCAAGCGAATGATTTTA
1 TTATTTTGTATATTACTTAATTCAAGCGAACGAGTTTA
* *
12152 TTATTTTGTTTATTACTTAATTGAAGCGAACGAGTTTA
1 TTATTTTGTATATTACTTAATTCAAGCGAACGAGTTTA
12190 TTATTT
1 TTATTT
12196 AGTGAATTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.29, C:0.07, G:0.12, T:0.51
Consensus pattern (38 bp):
TTATTTTGTATATTACTTAATTCAAGCGAACGAGTTTA
Found at i:20019 original size:54 final size:53
Alignment explanation
Indices: 19864--20029 Score: 174
Period size: 54 Copynumber: 3.1 Consensus size: 53
19854 TTGATCAGAA
** *
19864 ATCTGTGT-AGAAACCACAGAAAATGATGAATGTGTTGTCAAATACTTTACGAAC
1 ATCTG-GTCAGAAACCACAG-AAATGATGAATGTGTTGTCAAATGTTTTATGAAC
* * *
19918 ATCTGGTCAGAAGCCACAAGAAAGGATGAATGTGTTATCAAATGTTTTATGAAC
1 ATCTGGTCAGAAACCAC-AGAAATGATGAATGTGTTGTCAAATGTTTTATGAAC
* * * * *
19972 ATCT-ATGCATAAACCACGAGAAATGATGAATGTATTGTCACACGTTTTATGAAC
1 ATCTGGT-CAGAAACCAC-AGAAATGATGAATGTGTTGTCAAATGTTTTATGAAC
20026 ATCT
1 ATCT
20030 CTTTCCACAT
Statistics
Matches: 94, Mismatches: 15, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
53 3 0.03
54 89 0.95
55 2 0.02
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.29
Consensus pattern (53 bp):
ATCTGGTCAGAAACCACAGAAATGATGAATGTGTTGTCAAATGTTTTATGAAC
Found at i:20704 original size:3 final size:3
Alignment explanation
Indices: 20691--20745 Score: 96
Period size: 3 Copynumber: 19.0 Consensus size: 3
20681 GTAATTATAT
20691 ATA ATA A-A ATA ATA ATA ATA ATA AT- ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
20737 ATA ATA ATA
1 ATA ATA ATA
20746 GGATGAAAAA
Statistics
Matches: 50, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
2 4 0.08
3 46 0.92
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:23287 original size:24 final size:24
Alignment explanation
Indices: 23260--23309 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
23250 TATAGTTCTA
*
23260 TTTGCATTTTG-TTTTATTTTAATT
1 TTTGCATGTTGCTTTTATTTT-ATT
23284 TTTGCATGTTGCTTTTATTTTATT
1 TTTGCATGTTGCTTTTATTTTATT
23308 TT
1 TT
23310 AGTCACTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 15 0.62
25 9 0.38
ACGTcount: A:0.14, C:0.06, G:0.10, T:0.70
Consensus pattern (24 bp):
TTTGCATGTTGCTTTTATTTTATT
Found at i:23987 original size:131 final size:131
Alignment explanation
Indices: 23753--24135 Score: 491
Period size: 131 Copynumber: 2.9 Consensus size: 131
23743 AATAGTAACA
* * * * *
23753 CTCGAATTAATATTGAATTTTAGGATGAAATAGTAATATCTTTTCATTTCGGTTAGAGTAATAAA
1 CTCGAATTAATATTGAATTTTAGGACGAAATAGTAATATCTCTTCATTTCGATTGGAGTAGTAAA
* * *
23818 TGACTGCTTTAAGGCATAACATGTTATTTATTCTCGATTGGAAATAATTAGATATTATCGTTTTC
66 TGACTGCTTTAAGGCATGAGATGTTATTTATTCTCGATTGGAAATAATTAAATATTATCGTTTTC
23883 T
131 T
* *
23884 CTCGAATCAATATTGAATTTTAGGACGAAATAGTAACATCTCTTCATTTCGATTGGAGTAGTAAA
1 CTCGAATTAATATTGAATTTTAGGACGAAATAGTAATATCTCTTCATTTCGATTGGAGTAGTAAA
* *
23949 TGACTGCTTTAAGGCATGAGAGGTCATTTATTCTCGATTGGAAATAATTAAATATTATCGTTTTC
66 TGACTGCTTTAAGGCATGAGATGTTATTTATTCTCGATTGGAAATAATTAAATATTATCGTTTTC
24014 T
131 T
* * * * * * * * * * *
24015 CTTGACTTAATATTAAATTTTAGAAGGAAATAGTGATATTTCTTTATTTTGCTTGGAGTAAG-AG
1 CTCGAATTAATATTGAATTTTAGGACGAAATAGTAATATCTCTTCATTTCGATTGGAGT-AGTAA
* * * *
24079 ATGATTGCTTTAAGGCATGAGATGTTGTTTCTTCTCGA-TAGAAGATAATTAAATATT
65 ATGACTGCTTTAAGGCATGAGATGTTATTTATTCTCGATTGGAA-ATAATTAAATATT
24136 TCCTTTTTCC
Statistics
Matches: 219, Mismatches: 31, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
130 4 0.02
131 213 0.97
132 2 0.01
ACGTcount: A:0.32, C:0.10, G:0.17, T:0.40
Consensus pattern (131 bp):
CTCGAATTAATATTGAATTTTAGGACGAAATAGTAATATCTCTTCATTTCGATTGGAGTAGTAAA
TGACTGCTTTAAGGCATGAGATGTTATTTATTCTCGATTGGAAATAATTAAATATTATCGTTTTC
T
Found at i:27848 original size:20 final size:20
Alignment explanation
Indices: 27823--27860 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
27813 TTTAGTTCAC
27823 GGAATGTAAGATTACCAGTG
1 GGAATGTAAGATTACCAGTG
27843 GGAATGTAAGATTACCAG
1 GGAATGTAAGATTACCAG
27861 AGAATAAGAT
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:0.37, C:0.11, G:0.29, T:0.24
Consensus pattern (20 bp):
GGAATGTAAGATTACCAGTG
Found at i:29503 original size:26 final size:26
Alignment explanation
Indices: 29470--29536 Score: 125
Period size: 26 Copynumber: 2.6 Consensus size: 26
29460 CGGACTAAGT
29470 CTTCTAGAAACTGCCGCTGACTGGAC
1 CTTCTAGAAACTGCCGCTGACTGGAC
*
29496 CTTTTAGAAACTGCCGCTGACTGGAC
1 CTTCTAGAAACTGCCGCTGACTGGAC
29522 CTTCTAGAAACTGCC
1 CTTCTAGAAACTGCC
29537 ACGTCAGACC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 39 1.00
ACGTcount: A:0.24, C:0.30, G:0.21, T:0.25
Consensus pattern (26 bp):
CTTCTAGAAACTGCCGCTGACTGGAC
Found at i:30382 original size:23 final size:24
Alignment explanation
Indices: 30356--30409 Score: 83
Period size: 23 Copynumber: 2.3 Consensus size: 24
30346 CGAACTACTG
30356 TTTTTTTCTTCGCATTCAA-CCCT
1 TTTTTTTCTTCGCATTCAACCCCT
* *
30379 TTTTTTCCTTCGCTTTCAACCCCT
1 TTTTTTTCTTCGCATTCAACCCCT
30403 TTTTTTT
1 TTTTTTT
30410 GATGGAGCAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 17 0.63
24 10 0.37
ACGTcount: A:0.09, C:0.30, G:0.04, T:0.57
Consensus pattern (24 bp):
TTTTTTTCTTCGCATTCAACCCCT
Found at i:45476 original size:59 final size:59
Alignment explanation
Indices: 45402--45518 Score: 153
Period size: 59 Copynumber: 2.0 Consensus size: 59
45392 ATCATGTATT
* * * * * * *
45402 CTCAAATTATGACTCTCAATCTAAATTAGTTTTTAGATTTTTAACATTTTAATTTCATC
1 CTCAAATAATAACTCTCAATCTAAATTAGTCTTAAAATTTTAAACATTTGAATTTCATC
* *
45461 CTCAAATAATAACTCTCATTCTAAATTAGTCTTAAAATTTTAAACGTTTGAATTTCAT
1 CTCAAATAATAACTCTCAATCTAAATTAGTCTTAAAATTTTAAACATTTGAATTTCAT
45519 TCCCAAACAA
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
59 49 1.00
ACGTcount: A:0.35, C:0.15, G:0.05, T:0.44
Consensus pattern (59 bp):
CTCAAATAATAACTCTCAATCTAAATTAGTCTTAAAATTTTAAACATTTGAATTTCATC
Found at i:56324 original size:35 final size:35
Alignment explanation
Indices: 56268--56342 Score: 114
Period size: 35 Copynumber: 2.1 Consensus size: 35
56258 TTCATGTTCA
* * *
56268 AAATTCCAAAATATTTTAATTACATTCTAAACCCT
1 AAATTCCAAAAAACTTCAATTACATTCTAAACCCT
*
56303 AAATTCCAAAAAACTTCAATTATATTCTAAACCCT
1 AAATTCCAAAAAACTTCAATTACATTCTAAACCCT
56338 AAATT
1 AAATT
56343 AAAGTATTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.45, C:0.20, G:0.00, T:0.35
Consensus pattern (35 bp):
AAATTCCAAAAAACTTCAATTACATTCTAAACCCT
Found at i:56393 original size:35 final size:35
Alignment explanation
Indices: 56338--56414 Score: 102
Period size: 35 Copynumber: 2.2 Consensus size: 35
56328 TCTAAACCCT
* *
56338 AAATTAAAGTATTTTAGAATTTAGGGTTTAAAAT-
1 AAATTGAATTATTTTAGAATTTAGGGTTTAAAATG
* *
56372 ATAATTGAATTATTTTGGAATTTGGGGTTTAAAATG
1 A-AATTGAATTATTTTAGAATTTAGGGTTTAAAATG
56408 AAATTGA
1 AAATTGA
56415 GGAATGTGTT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
34 1 0.03
35 35 0.95
36 1 0.03
ACGTcount: A:0.40, C:0.00, G:0.18, T:0.42
Consensus pattern (35 bp):
AAATTGAATTATTTTAGAATTTAGGGTTTAAAATG
Found at i:56557 original size:21 final size:21
Alignment explanation
Indices: 56528--56573 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
56518 ATTTTCTTCT
* *
56528 AACGACACTGTAACGGCGTCA
1 AACGACACTCTAACGACGTCA
*
56549 AACGTCACTCTAACGACGTCA
1 AACGACACTCTAACGACGTCA
56570 AACG
1 AACG
56574 GTCGGTTACG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.35, C:0.30, G:0.20, T:0.15
Consensus pattern (21 bp):
AACGACACTCTAACGACGTCA
Found at i:59283 original size:14 final size:14
Alignment explanation
Indices: 59260--59290 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
59250 ATTATTTAAA
59260 TTATTAGAATTTAT
1 TTATTAGAATTTAT
*
59274 TTATTTGAATTTAT
1 TTATTAGAATTTAT
59288 TTA
1 TTA
59291 AATAATTTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.61
Consensus pattern (14 bp):
TTATTAGAATTTAT
Found at i:64788 original size:19 final size:20
Alignment explanation
Indices: 64766--64809 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
64756 GAGAAAAGGT
64766 AAAAGTTAA-AATGAAAGAG
1 AAAAGTTAATAATGAAAGAG
* *
64785 AAAAATTAATAATGAAAGAT
1 AAAAGTTAATAATGAAAGAG
64805 AAAAG
1 AAAAG
64810 AAAAAGTTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.66, C:0.00, G:0.16, T:0.18
Consensus pattern (20 bp):
AAAAGTTAATAATGAAAGAG
Found at i:73805 original size:32 final size:33
Alignment explanation
Indices: 73764--73838 Score: 116
Period size: 32 Copynumber: 2.3 Consensus size: 33
73754 AAGAAACGTT
73764 TGTTTTAGGTGTATGTGTATG-CTTTTATTTAC
1 TGTTTTAGGTGTATGTGTATGTCTTTTATTTAC
* *
73796 TGTTTTAGGTGTATGTGTATGTTTTTTATTTAG
1 TGTTTTAGGTGTATGTGTATGTCTTTTATTTAC
*
73829 TGTTTAAGGT
1 TGTTTTAGGT
73839 CTGTGAAAGA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
32 21 0.54
33 18 0.46
ACGTcount: A:0.16, C:0.03, G:0.24, T:0.57
Consensus pattern (33 bp):
TGTTTTAGGTGTATGTGTATGTCTTTTATTTAC
Found at i:74970 original size:83 final size:83
Alignment explanation
Indices: 74816--75344 Score: 551
Period size: 83 Copynumber: 6.4 Consensus size: 83
74806 TGTCATAGTG
* * * * *
74816 TTTTCCATTATTATTCAGAGAATCTCTACCATGTCATAGTATTCCATCCCATCCAAAATAAAAGG
1 TTTTCCATTATTATTCAGAGAATCTCTGCCATGTCATAGTGTTCCATCCTATCCGAAATGAAAGG
* **
74881 CACGTTCCAAAGGAAGCA
66 CGCGTTCCAGGGGAAGCA
* *
74899 TTTTCCATTATTATTCAGAGAATCTATGCCATGTCATAGTGTTCCATCCTATCCGAAATGATAGG
1 TTTTCCATTATTATTCAGAGAATCTCTGCCATGTCATAGTGTTCCATCCTATCCGAAATGAAAGG
*
74964 CGCGTTCCAGGGGAAACA
66 CGCGTTCCAGGGGAAGCA
* * * * * ** *
74982 TTTTCTATTATTATTTAGATAATCTCTTG-CATGTCATAATGTTCCATCCGATATGAAATGAAAA
1 TTTTCCATTATTATTCAGAGAATCTC-TGCCATGTCATAGTGTTCCATCCTATCCGAAATGAAAG
* *
75046 GCGCGTTCCAGGGGAAACG
65 GCGCGTTCCAGGGGAAGCA
* * * *
75065 TTTTCCATTATTATTCAGAGAATCTCTGCCATGTCATAGTGTTCAATTCTATCAGAAATGAAAGA
1 TTTTCCATTATTATTCAGAGAATCTCTGCCATGTCATAGTGTTCCATCCTATCCGAAATGAAAGG
* * * * **
75130 AGAGTTTCAGGGGACGTG
66 CGCGTTCCAGGGGAAGCA
* * * * ** ** * * *
75148 TTTTCTATTATTATTTAGAGAATATATGCCACAAT-ATAGTGTTTAATCCCATCTGAAATGAAAA
1 TTTTCCATTATTATTCAGAGAATCTCTGCCA-TGTCATAGTGTTCCATCCTATCCGAAATGAAAG
* *
75212 GCGTGTTCCAGGAGAAGCA
65 GCGCGTTCCAGGGGAAGCA
* * * * *
75231 -TTTCCATCATTATTTAGAGAATCTCTGTCATGTCATAGTGTTCTATCCTATCCGAAATGAAAGA
1 TTTTCCATTATTATTCAGAGAATCTCTGCCATGTCATAGTGTTCCATCCTATCCGAAATGAAAGG
** *
75295 CATGTTCCAGGGGAAGCG
66 CGCGTTCCAGGGGAAGCA
75313 TTTTCCATTATTATTCAGAGAATCTCTGCCAT
1 TTTTCCATTATTATTCAGAGAATCTCTGCCAT
75345 TTCACATAAC
Statistics
Matches: 364, Mismatches: 77, Indels: 10
0.81 0.17 0.02
Matches are distributed among these distances:
81 1 0.00
82 66 0.18
83 294 0.81
84 3 0.01
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Consensus pattern (83 bp):
TTTTCCATTATTATTCAGAGAATCTCTGCCATGTCATAGTGTTCCATCCTATCCGAAATGAAAGG
CGCGTTCCAGGGGAAGCA
Found at i:75436 original size:8 final size:8
Alignment explanation
Indices: 75418--75479 Score: 67
Period size: 8 Copynumber: 7.9 Consensus size: 8
75408 TCTATATCTT
75418 TCAAA-TC
1 TCAAACTC
75425 TCAAACTC
1 TCAAACTC
75433 TCAAACGT-
1 TCAAAC-TC
*
75441 TCAAACTT
1 TCAAACTC
75449 TCAAACT-
1 TCAAACTC
*
75456 TTAAATCTC
1 TCAAA-CTC
75465 TCAAACTC
1 TCAAACTC
75473 TCAAACT
1 TCAAACT
75480 AAGAAAATGA
Statistics
Matches: 48, Mismatches: 2, Indels: 9
0.81 0.03 0.15
Matches are distributed among these distances:
7 10 0.21
8 33 0.69
9 5 0.10
ACGTcount: A:0.39, C:0.29, G:0.02, T:0.31
Consensus pattern (8 bp):
TCAAACTC
Found at i:83339 original size:95 final size:95
Alignment explanation
Indices: 83174--83354 Score: 283
Period size: 95 Copynumber: 1.9 Consensus size: 95
83164 CAATACCGTT
* **
83174 GTAAGGGTATCGATACCATGCAAACATCGAATCTAATTTTGCTATCGATACCTTAAGGGGGTATC
1 GTAAGGGTATCGATACCATGCAAACATCGAAGCTAATTTTGCTATCGATACCAGAAGGGGGTATC
* *
83239 GGTACCATAATATAGTAGTATCGATATCGTG
66 AGTACCAT-ATATAGAAGTATCGATATCGTG
*
83270 GTAAGGGTATCGATACCATG-AAACATCGAAGCTAATTTTGGTATCGATACCAGAAGGGGGTATC
1 GTAAGGGTATCGATACCATGCAAACATCGAAGCTAATTTTGCTATCGATACCAGAAGGGGGTATC
*
83334 AGTACCATGTATAGAAGTATC
66 AGTACCATATATAGAAGTATC
83355 AGTACTAGGA
Statistics
Matches: 78, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
94 11 0.14
95 47 0.60
96 20 0.26
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.28
Consensus pattern (95 bp):
GTAAGGGTATCGATACCATGCAAACATCGAAGCTAATTTTGCTATCGATACCAGAAGGGGGTATC
AGTACCATATATAGAAGTATCGATATCGTG
Found at i:83807 original size:20 final size:20
Alignment explanation
Indices: 83782--83908 Score: 101
Period size: 20 Copynumber: 5.7 Consensus size: 20
83772 AATTGAAAAT
*
83782 GCATGAAAGGATGCATTAAG
1 GCATGAACGGATGCATTAAG
83802 GCATGAACGGATGCCATAATTGAAAAG
1 GCATGAACGGATG-C---ATT---AAG
83829 GCATGAACGGATGCATTAAG
1 GCATGAACGGATGCATTAAG
*
83849 GCATGAACGGATGCCATAATTGAAAAT
1 GCATGAACGGATG-C---ATT---AAG
*
83876 GCATGAAAGGATGCATTAAG
1 GCATGAACGGATGCATTAAG
83896 GCATGAACGGATG
1 GCATGAACGGATG
83909 TCATAATTGA
Statistics
Matches: 88, Mismatches: 5, Indels: 28
0.73 0.04 0.23
Matches are distributed among these distances:
20 42 0.48
21 2 0.02
23 6 0.07
24 6 0.07
26 2 0.02
27 30 0.34
ACGTcount: A:0.39, C:0.13, G:0.28, T:0.20
Consensus pattern (20 bp):
GCATGAACGGATGCATTAAG
Found at i:83837 original size:27 final size:26
Alignment explanation
Indices: 83799--83935 Score: 118
Period size: 27 Copynumber: 5.6 Consensus size: 26
83789 AGGATGCATT
83799 AAGGCATGAACGGATGCCATAATTGAA
1 AAGGCATGAACGGATG-CATAATTGAA
83826 AAGGCATGAACGGATGC---ATT---
1 AAGGCATGAACGGATGCATAATTGAA
83846 AAGGCATGAACGGATGCCATAATTGAA
1 AAGGCATGAACGGATG-CATAATTGAA
* *
83873 AATGCATGAAAGGATGC---ATT---
1 AAGGCATGAACGGATGCATAATTGAA
83893 AAGGCATGAACGGATGTCATAATTGAA
1 AAGGCATGAACGGATG-CATAATTGAA
** *
83920 AATACATGAAAGGATG
1 AAGGCATGAACGGATG
83936 TAAGGCATGA
Statistics
Matches: 89, Mismatches: 7, Indels: 28
0.72 0.06 0.23
Matches are distributed among these distances:
20 30 0.34
21 2 0.02
23 6 0.07
24 6 0.07
26 2 0.02
27 43 0.48
ACGTcount: A:0.41, C:0.12, G:0.26, T:0.20
Consensus pattern (26 bp):
AAGGCATGAACGGATGCATAATTGAA
Found at i:83841 original size:47 final size:47
Alignment explanation
Indices: 83772--84123 Score: 541
Period size: 47 Copynumber: 7.5 Consensus size: 47
83762 TCAAATTCAA
83772 AATTGAAAATGCATGAAAGGATGCATTAAGGCATGAACGGATGCCAT
1 AATTGAAAATGCATGAAAGGATGCATTAAGGCATGAACGGATGCCAT
* *
83819 AATTGAAAAGGCATGAACGGATGCATTAAGGCATGAACGGATGCCAT
1 AATTGAAAATGCATGAAAGGATGCATTAAGGCATGAACGGATGCCAT
*
83866 AATTGAAAATGCATGAAAGGATGCATTAAGGCATGAACGGATGTCAT
1 AATTGAAAATGCATGAAAGGATGCATTAAGGCATGAACGGATGCCAT
*
83913 AATTGAAAATACATGAAAGGATG---TAAGGCATGAACGGATGCCAT
1 AATTGAAAATGCATGAAAGGATGCATTAAGGCATGAACGGATGCCAT
* *
83957 AATTGAAAATGCAGGAAATGATGCATTAAGGCATGAACGGATGCCAT
1 AATTGAAAATGCATGAAAGGATGCATTAAGGCATGAACGGATGCCAT
** *
84004 AATTGAAAATATAGGAAAGGATGCATTAAGGCATGAACGGATGCCAT
1 AATTGAAAATGCATGAAAGGATGCATTAAGGCATGAACGGATGCCAT
*
84051 AATTGAAAATGCATGAAAAGGATGCATTAAGGCATGAAAGGATGCCAT
1 AATTGAAAATGCATG-AAAGGATGCATTAAGGCATGAACGGATGCCAT
*
84099 ACATATTAAAATGCAT-AAATGGATG
1 A-AT-TGAAAATGCATGAAA-GGATG
84124 AGTTAATACG
Statistics
Matches: 280, Mismatches: 18, Indels: 12
0.90 0.06 0.04
Matches are distributed among these distances:
44 40 0.14
47 188 0.67
48 35 0.12
49 7 0.03
50 10 0.04
ACGTcount: A:0.42, C:0.12, G:0.25, T:0.22
Consensus pattern (47 bp):
AATTGAAAATGCATGAAAGGATGCATTAAGGCATGAACGGATGCCAT
Found at i:84023 original size:138 final size:139
Alignment explanation
Indices: 83772--84113 Score: 515
Period size: 138 Copynumber: 2.4 Consensus size: 139
83762 TCAAATTCAA
* * *
83772 AATTGAAAATGCATGAAAGGATGCATTAAGGCATGAACGGATGCCATAATTGAAAAGGCATGAAC
1 AATTGAAAATGCATGAAAGGATG-A-TAAGGCATGAACGGATGCCATAATTGAAAATGCAGGAAA
* *
83837 GGATGCATTAAGGCATGAACGGATGCCATAATTGAAAATGCATGAAAGGATGCATTAAGGCATGA
64 GGATGCATTAAGGCATGAACGGATGCCATAATTGAAAATACAGGAAAGGATGCATTAAGGCATGA
*
83902 ACGGATGTCAT
129 ACGGATGCCAT
* *
83913 AATTGAAAATACATGAAAGGATG-TAAGGCATGAACGGATGCCATAATTGAAAATGCAGGAAATG
1 AATTGAAAATGCATGAAAGGATGATAAGGCATGAACGGATGCCATAATTGAAAATGCAGGAAAGG
*
83977 ATGCATTAAGGCATGAACGGATGCCATAATTGAAAATATAGGAAAGGATGCATTAAGGCATGAAC
66 ATGCATTAAGGCATGAACGGATGCCATAATTGAAAATACAGGAAAGGATGCATTAAGGCATGAAC
84042 GGATGCCAT
131 GGATGCCAT
* *
84051 AATTGAAAATGCATGAAAAGGATGCATTAAGGCATGAAAGGATGCCATACATATTAAAATGCA
1 AATTGAAAATGCATG-AAAGGATG-A-TAAGGCATGAACGGATGCCATA-AT-TGAAAATGCA
84114 TAAATGGATG
Statistics
Matches: 183, Mismatches: 12, Indels: 9
0.90 0.06 0.04
Matches are distributed among these distances:
138 121 0.66
139 8 0.04
141 22 0.12
142 21 0.11
143 2 0.01
144 9 0.05
ACGTcount: A:0.42, C:0.12, G:0.25, T:0.21
Consensus pattern (139 bp):
AATTGAAAATGCATGAAAGGATGATAAGGCATGAACGGATGCCATAATTGAAAATGCAGGAAAGG
ATGCATTAAGGCATGAACGGATGCCATAATTGAAAATACAGGAAAGGATGCATTAAGGCATGAAC
GGATGCCAT
Found at i:84092 original size:20 final size:20
Alignment explanation
Indices: 84018--84095 Score: 66
Period size: 20 Copynumber: 3.5 Consensus size: 20
84008 GAAAATATAG
84018 GAAAGGATGCATTAAGGCAT
1 GAAAGGATGCATTAAGGCAT
* *
84038 GAACGGATGCCATAATTGAAAATGCAT
1 GAAAGGATG-C---ATT---AAGGCAT
84065 GAAAAGGATGCATTAAGGCAT
1 G-AAAGGATGCATTAAGGCAT
84086 GAAAGGATGC
1 GAAAGGATGC
84096 CATACATATT
Statistics
Matches: 46, Mismatches: 4, Indels: 16
0.70 0.06 0.24
Matches are distributed among these distances:
20 17 0.37
21 8 0.17
24 6 0.13
27 8 0.17
28 7 0.15
ACGTcount: A:0.41, C:0.12, G:0.28, T:0.19
Consensus pattern (20 bp):
GAAAGGATGCATTAAGGCAT
Found at i:85531 original size:14 final size:14
Alignment explanation
Indices: 85512--85540 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
85502 GAATCAGTAT
85512 AAATAATTCATGTG
1 AAATAATTCATGTG
85526 AAATAATTCATGTG
1 AAATAATTCATGTG
85540 A
1 A
85541 TTATATAAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.45, C:0.07, G:0.14, T:0.34
Consensus pattern (14 bp):
AAATAATTCATGTG
Found at i:89193 original size:82 final size:82
Alignment explanation
Indices: 89058--89211 Score: 299
Period size: 82 Copynumber: 1.9 Consensus size: 82
89048 TTGATATACT
89058 CTTTCACTTGTTCACGTGGTTACATCTGATTAGTGCTATTAATTTATTAAAATTAATTATTTATA
1 CTTTCACTTGTTCACGTGGTTACATCTGATTAGTGCTATTAATTTATTAAAATTAATTATTTATA
89123 ATTAATTTGGAAAAACA
66 ATTAATTTGGAAAAACA
*
89140 CTTTCACTTGTTCACGTGGTTACATCTGATTAGTGCTATTAATTTATTAAAATTAATTGTTTATA
1 CTTTCACTTGTTCACGTGGTTACATCTGATTAGTGCTATTAATTTATTAAAATTAATTATTTATA
89205 ATTAATT
66 ATTAATT
89212 AGAAAAAAAT
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
82 71 1.00
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.46
Consensus pattern (82 bp):
CTTTCACTTGTTCACGTGGTTACATCTGATTAGTGCTATTAATTTATTAAAATTAATTATTTATA
ATTAATTTGGAAAAACA
Found at i:90342 original size:23 final size:23
Alignment explanation
Indices: 90303--90367 Score: 87
Period size: 23 Copynumber: 2.8 Consensus size: 23
90293 CAGCTCGTAT
*
90303 AAATGCACCAAAGTGCCATGTAG
1 AAATGCACCGAAGTGCCATGTAG
* *
90326 AATTGCACCGTAA-TGCCACGTAG
1 AAATGCACCG-AAGTGCCATGTAG
90349 AAATGCACCGAAGTGCCAT
1 AAATGCACCGAAGTGCCAT
90368 ATAAGATTGT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
22 2 0.06
23 31 0.89
24 2 0.06
ACGTcount: A:0.35, C:0.25, G:0.22, T:0.18
Consensus pattern (23 bp):
AAATGCACCGAAGTGCCATGTAG
Found at i:90391 original size:46 final size:46
Alignment explanation
Indices: 90298--90397 Score: 116
Period size: 46 Copynumber: 2.2 Consensus size: 46
90288 CACCACAGCT
* * *
90298 CGTATAAATGCACCAAAGTGCCATGTAGAATTGCACCGTAATGCCA
1 CGTAGAAATGCACCAAAGTGCCATATAGAATTGCACCGTAAAGCCA
*
90344 CGTAGAAATGCACCGAAGTGCCATATA-AGATTGTC-CC-TAAAGACCA
1 CGTAGAAATGCACCAAAGTGCCATATAGA-ATTG-CACCGTAAAG-CCA
90390 CGTAGAAA
1 CGTAGAAA
90398 ATTCCTTAAG
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
45 5 0.11
46 41 0.87
47 1 0.02
ACGTcount: A:0.37, C:0.23, G:0.20, T:0.20
Consensus pattern (46 bp):
CGTAGAAATGCACCAAAGTGCCATATAGAATTGCACCGTAAAGCCA
Found at i:92271 original size:71 final size:70
Alignment explanation
Indices: 92146--92278 Score: 171
Period size: 71 Copynumber: 1.9 Consensus size: 70
92136 TTTTTCCTTT
* * *
92146 AGGGGGTATCGATACCCCACTGGGGTATCGATACCCTCATGACATTCTGTAATTTT-TCGTTCAA
1 AGGGGGTATCGATACCCAACTGGGGTATCGATACCCTCATGACATTATGAAATTTTCTCGTTCAA
92210 GGGGG
66 GGGGG
* * *
92215 AGGGGGTATTGGTACCCAACTGGGGGGTATCGGTAACCCT-ATGACATTATGAAATTTTCTCGTT
1 AGGGGGTATCGATACCCAACT--GGGGTATCGAT-ACCCTCATGACATTATGAAATTTTCTCGTT
92279 TGAGAGGGTA
Statistics
Matches: 54, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
69 18 0.33
71 26 0.48
72 10 0.19
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.30
Consensus pattern (70 bp):
AGGGGGTATCGATACCCAACTGGGGTATCGATACCCTCATGACATTATGAAATTTTCTCGTTCAA
GGGGG
Found at i:95594 original size:3 final size:3
Alignment explanation
Indices: 95586--95648 Score: 117
Period size: 3 Copynumber: 20.7 Consensus size: 3
95576 CAGGCTTTGT
95586 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA
95632 TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TA
95649 TCTAAAATTT
Statistics
Matches: 59, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
3 56 0.95
4 3 0.05
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Done.