Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006753.1 Hibiscus syriacus cultivar Beakdansim tig00017008_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: 74723
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:6413 original size:3 final size:3
Alignment explanation
Indices: 6407--6462 Score: 60
Period size: 3 Copynumber: 18.7 Consensus size: 3
6397 CCATTTTTTG
** *
6407 TTA TTA TTA TTA TTA AAA TTA TTA TTA TTAA ATA TTA TTA -TA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA
*
6452 TAA TTA TTA TT
1 TTA TTA TTA TT
6463 TACAAACAGT
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
2 2 0.05
3 39 0.91
4 2 0.05
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:6429 original size:15 final size:15
Alignment explanation
Indices: 6409--6462 Score: 83
Period size: 15 Copynumber: 3.6 Consensus size: 15
6399 ATTTTTTGTT
6409 ATTATTATTATTAAA
1 ATTATTATTATTAAA
6424 ATTATTATTATTAAA
1 ATTATTATTATTAAA
*
6439 TATTATTA-TATTATA
1 -ATTATTATTATTAAA
6454 ATTATTATT
1 ATTATTATT
6463 TACAAACAGT
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
14 7 0.19
15 22 0.61
16 7 0.19
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
ATTATTATTATTAAA
Found at i:6519 original size:26 final size:26
Alignment explanation
Indices: 6469--6520 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
6459 TATTTACAAA
* * *
6469 CAGTTACAAACAAAACTGGATCGGCC
1 CAGTTACAAACAAAACAGAACCGGCC
6495 CAGTTACAAACAAAACAGAACCGGCC
1 CAGTTACAAACAAAACAGAACCGGCC
6521 TAGACCAACC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.42, C:0.29, G:0.17, T:0.12
Consensus pattern (26 bp):
CAGTTACAAACAAAACAGAACCGGCC
Found at i:14598 original size:24 final size:24
Alignment explanation
Indices: 14571--14619 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
14561 TGCCACTGAC
14571 AACAAGGTCGAATTCCACAAATCT
1 AACAAGGTCGAATTCCACAAATCT
*
14595 AACAAGGTCGAATTCGACAAATCT
1 AACAAGGTCGAATTCCACAAATCT
14619 A
1 A
14620 CTCATCAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.43, C:0.22, G:0.14, T:0.20
Consensus pattern (24 bp):
AACAAGGTCGAATTCCACAAATCT
Found at i:15432 original size:114 final size:114
Alignment explanation
Indices: 15232--15451 Score: 370
Period size: 114 Copynumber: 1.9 Consensus size: 114
15222 CACGTTCTCG
* *
15232 TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTAAGTTATCTGATCTGATTT
1 TAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTAAGTTATCTGATCTGATTC
*
15297 GGTATGAACCCCAAAACCAATCATTGGATTTGAAAGATGAATTTGCTCA
66 GGTATGAACCCCAAAACCAATCATTGGAATTGAAAGATGAATTTGCTCA
* *
15346 TAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTC
1 TAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTAAGTTATCTGATCTGATTC
*
15411 GGTA-GAAACCCCAGAACCAATCATTGGAATTGAAAGATGAA
66 GGTATG-AACCCCAAAACCAATCATTGGAATTGAAAGATGAA
15452 CTGCATGATC
Statistics
Matches: 99, Mismatches: 6, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
113 1 0.01
114 98 0.99
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.30
Consensus pattern (114 bp):
TAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTAAGTTATCTGATCTGATTC
GGTATGAACCCCAAAACCAATCATTGGAATTGAAAGATGAATTTGCTCA
Found at i:16544 original size:76 final size:76
Alignment explanation
Indices: 16396--16572 Score: 189
Period size: 76 Copynumber: 2.3 Consensus size: 76
16386 TAACAAGAAA
* * * * * *
16396 CAAATGTTGGGGCATGCTGAAA-ACCCTTGTCAATCAGAATCAGGAATTTTGATGAATCCTGAAT
1 CAAATATTAGGGCATGCTGAAAGCCCCTTGTCAATCAGAATCAAGAATATTGATGAATCCTGAAC
* *
16460 GTTTATATCAG
66 GCTCATATCAG
* * **
16471 CAAA-ATGCTAGGGCATGCTGAAAGCCCCTT-TCAATCAGAATGAAGAATATTGATGTATTTTGA
1 CAAATAT--TAGGGCATGCTGAAAGCCCCTTGTCAATCAGAATCAAGAATATTGATGAATCCTGA
16534 ACGCTCATATCAG
64 ACGCTCATATCAG
* *
16547 CAAATATTGGGGCATGCTGAAGGCCC
1 CAAATATTAGGGCATGCTGAAAGCCC
16573 ACAACATCCT
Statistics
Matches: 84, Mismatches: 14, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
74 1 0.01
75 21 0.25
76 55 0.65
77 7 0.08
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.28
Consensus pattern (76 bp):
CAAATATTAGGGCATGCTGAAAGCCCCTTGTCAATCAGAATCAAGAATATTGATGAATCCTGAAC
GCTCATATCAG
Found at i:17943 original size:22 final size:22
Alignment explanation
Indices: 17914--17968 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
17904 ATCTACACTC
*
17914 TTCAAAGATGATAAATTCTCTT
1 TTCAAAGATGATAAATTATCTT
* *
17936 TTTAAAGATGATAGATTATCTT
1 TTCAAAGATGATAAATTATCTT
17958 TTCAAAGATGA
1 TTCAAAGATGA
17969 AAGCTTTATG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.38, C:0.09, G:0.13, T:0.40
Consensus pattern (22 bp):
TTCAAAGATGATAAATTATCTT
Found at i:18824 original size:76 final size:76
Alignment explanation
Indices: 18640--18971 Score: 569
Period size: 75 Copynumber: 4.4 Consensus size: 76
18630 CTATTTCCCA
*
18640 CATCTGTAAGTCCTACAGTGAATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTT-AA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
18704 AGCCTTCGGGT
66 AGCCTTCGGGT
* * * *
18715 CATCCGTAAGCCCTGCAGTGCAGGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
18780 AGCCTTAGGGT
66 AGCCTTCGGGT
*
18791 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCATTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
18856 A-CCTTCGGGT
66 AGCCTTCGGGT
*
18866 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTGGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
18931 AGCCTTCGGGT
66 AGCCTTCGGGT
*
18942 CATCTGTAAGTCCTTCAGTGCATGATGTTT
1 CATCTGTAAGTCCTACAGTGCATGATGTTT
18972 TTAAAGCCTT
Statistics
Matches: 240, Mismatches: 15, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
75 129 0.54
76 111 0.46
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.33
Consensus pattern (76 bp):
CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTCGGGT
Found at i:18914 original size:151 final size:151
Alignment explanation
Indices: 18640--18971 Score: 567
Period size: 151 Copynumber: 2.2 Consensus size: 151
18630 CTATTTCCCA
* *
18640 CATCTGTAAGTCCTACAGTGAATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTAAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCATTTTGATGTTTTAAA
* *
18705 GCCTTCGGGTCATCCGTAAGCCCTGCAGTGCAGGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTG
66 GCCTTCGGGTCATCCGTAAGCCCTACAGTGCAGGATGTTTCCAAAAAGCCTTCGGGAGCTTTTGG
18770 ATGTTTTCAAAGCCTTAGGGT
131 ATGTTTTCAAAGCCTTAGGGT
18791 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCATTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCATTTTGATGTTTT-AA
* * *
18856 A-CCTTCGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTG
65 AGCCTTCGGGTCATCCGTAAGCCCTACAGTGCAGGATGTTTCCAAAAAGCCTTCGGGAGCTTTTG
*
18920 GATGTTTTCAAAGCCTTCGGGT
130 GATGTTTTCAAAGCCTTAGGGT
*
18942 CATCTGTAAGTCCTTCAGTGCATGATGTTT
1 CATCTGTAAGTCCTACAGTGCATGATGTTT
18972 TTAAAGCCTT
Statistics
Matches: 171, Mismatches: 9, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
151 168 0.98
152 3 0.02
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.33
Consensus pattern (151 bp):
CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCATTTTGATGTTTTAAA
GCCTTCGGGTCATCCGTAAGCCCTACAGTGCAGGATGTTTCCAAAAAGCCTTCGGGAGCTTTTGG
ATGTTTTCAAAGCCTTAGGGT
Found at i:18972 original size:45 final size:45
Alignment explanation
Indices: 18919--19032 Score: 156
Period size: 45 Copynumber: 2.5 Consensus size: 45
18909 GGGAGCTTTT
* * *
18919 GGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
1 GGATGTTTTCAAAGCCTTCGGGTCATCCGTAAGCCCTGCAGTGCA
* *
18964 TGATGTTTTTAAAGCCTTCGGGTCATCCGTAAGCCCTGCAGTGCA
1 GGATGTTTTCAAAGCCTTCGGGTCATCCGTAAGCCCTGCAGTGCA
*
19009 GGATGTTTCCAAAAAGCCTTCGGG
1 GGATGTTTTC--AAAGCCTTCGGG
19033 AGCTTTTTGA
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
45 47 0.80
47 12 0.20
ACGTcount: A:0.21, C:0.23, G:0.25, T:0.31
Consensus pattern (45 bp):
GGATGTTTTCAAAGCCTTCGGGTCATCCGTAAGCCCTGCAGTGCA
Found at i:19006 original size:121 final size:119
Alignment explanation
Indices: 18844--19096 Score: 416
Period size: 121 Copynumber: 2.1 Consensus size: 119
18834 GGGAGCATTT
* * *
18844 TGATGTTTTCAAACCTTCGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTC
1 TGATGTTTTCAAACCTTCGGGTCATCCGTAAGCCCTACAGTGCAGGATGTTTCCAAAAAGCCTTC
*
18909 GGGAGCTTTTGGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
66 GGGAGCTTTTGGATGTTTTCAAA-CCTTCGGGTCATCTGTAAGTCCTACAGTGCA
* *
18964 TGATGTTTTTAAAGCCTTCGGGTCATCCGTAAGCCCTGCAGTGCAGGATGTTTCCAAAAAGCCTT
1 TGATGTTTTCAAA-CCTTCGGGTCATCCGTAAGCCCTACAGTGCAGGATGTTTCCAAAAAGCCTT
*
19029 CGGGAGCTTTTTGATGTTTTCAAACCTTCGGGTCATCTGTAAGTCCTACAGTGCA
65 CGGGAGCTTTTGGATGTTTTCAAACCTTCGGGTCATCTGTAAGTCCTACAGTGCA
*
19084 TGATGTTTCCAAA
1 TGATGTTTTCAAA
19097 AAGCCTTCGG
Statistics
Matches: 123, Mismatches: 9, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
120 53 0.43
121 70 0.57
ACGTcount: A:0.22, C:0.22, G:0.23, T:0.34
Consensus pattern (119 bp):
TGATGTTTTCAAACCTTCGGGTCATCCGTAAGCCCTACAGTGCAGGATGTTTCCAAAAAGCCTTC
GGGAGCTTTTGGATGTTTTCAAACCTTCGGGTCATCTGTAAGTCCTACAGTGCA
Found at i:19089 original size:75 final size:75
Alignment explanation
Indices: 18964--19167 Score: 336
Period size: 75 Copynumber: 2.7 Consensus size: 75
18954 CTTCAGTGCA
* * * *
18964 TGATGTTTTTAAAGCCTTCGGGTCATCCGTAAGCCCTGCAGTGCAGGATGTTTCCAAAAAGCCTT
1 TGATGTTTTCAAA-CCTTCGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTT
19029 CGGGAGCTTTT
65 CGGGAGCTTTT
*
19040 TGATGTTTTCAAACCTTCGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTC
1 TGATGTTTTCAAACCTTCGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTC
19105 GGGAGCTTTT
66 GGGAGCTTTT
*
19115 TGATGTTTTCAAAACCTTAGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTT
1 TGATGTTTTC-AAACCTTCGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTT
19168 TTAAGACCTC
Statistics
Matches: 120, Mismatches: 7, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
75 68 0.57
76 52 0.43
ACGTcount: A:0.22, C:0.21, G:0.23, T:0.34
Consensus pattern (75 bp):
TGATGTTTTCAAACCTTCGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTC
GGGAGCTTTT
Found at i:19102 original size:196 final size:196
Alignment explanation
Indices: 18768--19171 Score: 709
Period size: 196 Copynumber: 2.1 Consensus size: 196
18758 GGGAGCTTTT
* * * *
18768 TGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTT
1 TGATGTTTTTAAAGCCTTAGGGTCATCCGTAAGCCCTACAGTGCAGGATGTTTCCAAAAAGCCTT
18833 CGGGAGCATTTTGATGTTTTCAAACCTTCGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCC
66 CGGGAGCATTTTGATGTTTTCAAACCTTCGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCC
* * *
18898 AAAAAGCCTTCGGGAGCTTTTGGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGC
131 AAAAAGCCTTCGGGAGCTTTTGGATGTTTTCAAAACCTTAGGGTCATCTGTAAGTCCTGCAGTGC
18963 A
196 A
* *
18964 TGATGTTTTTAAAGCCTTCGGGTCATCCGTAAGCCCTGCAGTGCAGGATGTTTCCAAAAAGCCTT
1 TGATGTTTTTAAAGCCTTAGGGTCATCCGTAAGCCCTACAGTGCAGGATGTTTCCAAAAAGCCTT
*
19029 CGGGAGCTTTTTGATGTTTTCAAACCTTCGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCC
66 CGGGAGCATTTTGATGTTTTCAAACCTTCGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCC
*
19094 AAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAACCTTAGGGTCATCTGTAAGTCCTGCAGTGC
131 AAAAAGCCTTCGGGAGCTTTTGGATGTTTTCAAAACCTTAGGGTCATCTGTAAGTCCTGCAGTGC
19159 A
196 A
19160 TGATGTTTTTAA
1 TGATGTTTTTAA
19172 GACCTCTGGA
Statistics
Matches: 197, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
196 197 1.00
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.34
Consensus pattern (196 bp):
TGATGTTTTTAAAGCCTTAGGGTCATCCGTAAGCCCTACAGTGCAGGATGTTTCCAAAAAGCCTT
CGGGAGCATTTTGATGTTTTCAAACCTTCGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCC
AAAAAGCCTTCGGGAGCTTTTGGATGTTTTCAAAACCTTAGGGTCATCTGTAAGTCCTGCAGTGC
A
Found at i:19334 original size:3 final size:3
Alignment explanation
Indices: 19326--19384 Score: 66
Period size: 3 Copynumber: 19.7 Consensus size: 3
19316 TTTTTTGTTT
** *
19326 TTA TTA TTA TTA TTA AAA TTA TTA TTA TTA TTAA ATA TTA TTA -TA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA
*
19371 TTA TAA TTA TTA TT
1 TTA TTA TTA TTA TT
19385 TACAAACAGT
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
2 2 0.04
3 42 0.91
4 2 0.04
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:19349 original size:18 final size:18
Alignment explanation
Indices: 19326--19384 Score: 88
Period size: 18 Copynumber: 3.4 Consensus size: 18
19316 TTTTTTGTTT
19326 TTATTATTATTATTAAAA
1 TTATTATTATTATTAAAA
19344 TTATTATTATTATT-AAA
1 TTATTATTATTATTAAAA
*
19361 -TATTATTA-TATTATAA
1 TTATTATTATTATTAAAA
19377 TTATTATT
1 TTATTATT
19385 TACAAACAGT
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
15 4 0.11
16 10 0.26
17 10 0.26
18 14 0.37
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
TTATTATTATTATTAAAA
Found at i:19427 original size:26 final size:26
Alignment explanation
Indices: 19391--19445 Score: 85
Period size: 26 Copynumber: 2.1 Consensus size: 26
19381 TATTTACAAA
*
19391 CAGTTACAAACAAAACT-GGACCGGCC
1 CAGTTACAAACAAAA-TAGAACCGGCC
19417 CAGTTACAAACAAAATAGAACCGGCC
1 CAGTTACAAACAAAATAGAACCGGCC
19443 CAG
1 CAG
19446 ACCAACTAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 1 0.04
26 26 0.96
ACGTcount: A:0.42, C:0.29, G:0.18, T:0.11
Consensus pattern (26 bp):
CAGTTACAAACAAAATAGAACCGGCC
Found at i:32708 original size:2 final size:2
Alignment explanation
Indices: 32701--32740 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
32691 AGAGTACATC
32701 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
32741 TAATACTTAG
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:33349 original size:16 final size:17
Alignment explanation
Indices: 33330--33365 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
33320 CTAATTTTTT
33330 ATATTATATTTA-AAAA
1 ATATTATATTTATAAAA
*
33346 ATATTATTTTTATAAAA
1 ATATTATATTTATAAAA
33363 ATA
1 ATA
33366 AAAGAAAGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
ATATTATATTTATAAAA
Found at i:33547 original size:50 final size:51
Alignment explanation
Indices: 33489--33615 Score: 139
Period size: 50 Copynumber: 2.5 Consensus size: 51
33479 TTAACAGTAA
* *
33489 AGCGCGCCCCCTGTACCGCGTTATATGATGATTTGGC-GCCACATGGGTAT
1 AGCGCGCCCCCTGTACCGCGTTATATGATGATCTGGCAGACACATGGGTAT
* * * * * * *
33539 AGCGCGCCCCCTATCCCGCGCTATACGGTGATCTGGCATACACGTGGGTAT
1 AGCGCGCCCCCTGTACCGCGTTATATGATGATCTGGCAGACACATGGGTAT
* * *
33590 AGCGCGACCCCTGCAGCGCGTTATAT
1 AGCGCGCCCCCTGTACCGCGTTATAT
33616 TTGGATATCT
Statistics
Matches: 60, Mismatches: 16, Indels: 1
0.78 0.21 0.01
Matches are distributed among these distances:
50 31 0.52
51 29 0.48
ACGTcount: A:0.18, C:0.31, G:0.28, T:0.23
Consensus pattern (51 bp):
AGCGCGCCCCCTGTACCGCGTTATATGATGATCTGGCAGACACATGGGTAT
Found at i:34343 original size:162 final size:160
Alignment explanation
Indices: 34026--34516 Score: 820
Period size: 162 Copynumber: 3.0 Consensus size: 160
34016 AAGCAGTTTT
*
34026 TTTTAAAATTTTAGGGTTCAGGGTGGGACGGAGCCGGGTATATACGTGTATATATATATATATAG
1 TTTTAAAATTTTAGGGATCAGGGTGGGACGGAGCCGGGTATATACGTG----TATATATATATAG
*
34091 ATAGAATAATAATTTATATCAGGTTGGGTCGGATTGATTTTTTAAAATTTAAAAAAACTACTTTT
62 ATAGAATAATAATTTATATCAGGTTGGGTCGGATTGATTTTTTAAAATTTAAAAAAACTGCTTTT
34156 GTAAGGTCGGGTCGAGATTCGTTAGATTCGAGTA
127 GTAAGGTCGGGTCGAGATTCGTTAGATTCGAGTA
*
34190 TTTTAAAATTTTAGGGATCAGGGTGGGACGGAGTCGGGTATATACGTGTATATATATATAGATAG
1 TTTTAAAATTTTAGGGATCAGGGTGGGACGGAGCCGGGTATATACGTGTATATATATATAGATAG
* **
34255 AATAATAATTTATACCAGGTTGGGTTTGATTGATTTTTTAAAATTTAAAAAAAAACTGCTTTTGT
66 AATAATAATTTATATCAGGTTGGGTCGGATTGATTTTTTAAAATTT--AAAAAAACTGCTTTTGT
*
34320 AAGGTCGGGTTGAGATTCGTTAGATTCGAGTA
129 AAGGTCGGGTCGAGATTCGTTAGATTCGAGTA
* *
34352 TTTTAAAATTTTAGGGATCAAGGTAGGACGGAGCCGGGTATATACGTGTATATATATATAGATAG
1 TTTTAAAATTTTAGGGATCAGGGTGGGACGGAGCCGGGTATATACGTGTATATATATATAGATAG
*
34417 AATAATAATTTATATCAGGTTGTGTCGGATTGATTTTTTAAAATTTTAAAAAAACTGCTTTTGTA
66 AATAATAATTTATATCAGGTTGGGTCGGATTGATTTTTTAAAA-TTTAAAAAAACTGCTTTTGTA
*
34482 AGGTCGGGTCGAAATTCGTTAGATTCGAGTA
130 AGGTCGGGTCGAGATTCGTTAGATTCGAGTA
34513 TTTT
1 TTTT
34517 GATCATCCTT
Statistics
Matches: 308, Mismatches: 16, Indels: 9
0.92 0.05 0.03
Matches are distributed among these distances:
160 60 0.19
161 51 0.17
162 148 0.48
163 3 0.01
164 46 0.15
ACGTcount: A:0.32, C:0.08, G:0.23, T:0.37
Consensus pattern (160 bp):
TTTTAAAATTTTAGGGATCAGGGTGGGACGGAGCCGGGTATATACGTGTATATATATATAGATAG
AATAATAATTTATATCAGGTTGGGTCGGATTGATTTTTTAAAATTTAAAAAAACTGCTTTTGTAA
GGTCGGGTCGAGATTCGTTAGATTCGAGTA
Found at i:35799 original size:20 final size:20
Alignment explanation
Indices: 35774--35843 Score: 59
Period size: 20 Copynumber: 3.4 Consensus size: 20
35764 TTTTTCTTTA
35774 TCTTTTTAACAATAAAGTTG
1 TCTTTTTAACAATAAAGTTG
*** ** *
35794 TCTTTTTTTTATATATATTTTAA
1 TCTTTTTAACA-ATA-AAGTT-G
35817 TCTTTTTAACAATAAAGTTG
1 TCTTTTTAACAATAAAGTTG
35837 TCTTTTT
1 TCTTTTT
35844 TTTATATATA
Statistics
Matches: 35, Mismatches: 12, Indels: 6
0.66 0.23 0.11
Matches are distributed among these distances:
20 15 0.43
21 6 0.17
22 6 0.17
23 8 0.23
ACGTcount: A:0.29, C:0.09, G:0.06, T:0.57
Consensus pattern (20 bp):
TCTTTTTAACAATAAAGTTG
Found at i:35820 original size:23 final size:23
Alignment explanation
Indices: 35794--35866 Score: 71
Period size: 23 Copynumber: 3.3 Consensus size: 23
35784 AATAAAGTTG
35794 TCTTTTTTTTATATATATTTTAA
1 TCTTTTTTTTATATATATTTTAA
*** ** *
35817 TCTTTTTAACA-ATA-AAGTT-G
1 TCTTTTTTTTATATATATTTTAA
35837 TCTTTTTTTTATATATATTTTAA
1 TCTTTTTTTTATATATATTTTAA
35860 TCTTTTT
1 TCTTTTT
35867 AACAATAAAG
Statistics
Matches: 35, Mismatches: 12, Indels: 6
0.66 0.23 0.11
Matches are distributed among these distances:
20 8 0.23
21 6 0.17
22 6 0.17
23 15 0.43
ACGTcount: A:0.26, C:0.07, G:0.03, T:0.64
Consensus pattern (23 bp):
TCTTTTTTTTATATATATTTTAA
Found at i:35821 original size:43 final size:43
Alignment explanation
Indices: 35773--35882 Score: 220
Period size: 43 Copynumber: 2.6 Consensus size: 43
35763 TTTTTTCTTT
35773 ATCTTTTTAACAATAAAGTTGTCTTTTTTTTATATATATTTTA
1 ATCTTTTTAACAATAAAGTTGTCTTTTTTTTATATATATTTTA
35816 ATCTTTTTAACAATAAAGTTGTCTTTTTTTTATATATATTTTA
1 ATCTTTTTAACAATAAAGTTGTCTTTTTTTTATATATATTTTA
35859 ATCTTTTTAACAATAAAGTTGTCT
1 ATCTTTTTAACAATAAAGTTGTCT
35883 CCTGTTTCCA
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 67 1.00
ACGTcount: A:0.31, C:0.08, G:0.05, T:0.55
Consensus pattern (43 bp):
ATCTTTTTAACAATAAAGTTGTCTTTTTTTTATATATATTTTA
Found at i:35867 original size:20 final size:20
Alignment explanation
Indices: 35799--35867 Score: 57
Period size: 20 Copynumber: 3.3 Consensus size: 20
35789 AGTTGTCTTT
35799 TTTTTATATATATTTTAATC
1 TTTTTATATATATTTTAATC
* * * ** *
35819 TTTTTAACAATAAAGTTGTCTTT
1 TTTTT-A-TATATA-TTTTAATC
35842 TTTTTATATATATTTTAATC
1 TTTTTATATATATTTTAATC
35862 TTTTTA
1 TTTTTA
35868 ACAATAAAGT
Statistics
Matches: 34, Mismatches: 12, Indels: 6
0.65 0.23 0.12
Matches are distributed among these distances:
20 15 0.44
21 5 0.15
22 5 0.15
23 9 0.26
ACGTcount: A:0.29, C:0.06, G:0.03, T:0.62
Consensus pattern (20 bp):
TTTTTATATATATTTTAATC
Found at i:39773 original size:29 final size:30
Alignment explanation
Indices: 39740--39819 Score: 90
Period size: 31 Copynumber: 2.7 Consensus size: 30
39730 GTTGTATTGT
*
39740 TTATACCAATAAACTTTTAATTT-TATCAA
1 TTATACCAATGAACTTTTAATTTGTATCAA
* * * *
39769 TTATAACATTGAACTTTTATTTTTGTTTCAA
1 TTATACCAATGAACTTTTA-ATTTGTATCAA
*
39800 TTATACCAATGAACCTTTAA
1 TTATACCAATGAACTTTTAA
39820 ATCGTTAACA
Statistics
Matches: 40, Mismatches: 9, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
29 16 0.40
30 3 0.08
31 21 0.52
ACGTcount: A:0.36, C:0.14, G:0.04, T:0.46
Consensus pattern (30 bp):
TTATACCAATGAACTTTTAATTTGTATCAA
Found at i:40606 original size:27 final size:27
Alignment explanation
Indices: 40553--40605 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 27
40543 AATTACAAAC
40553 TTTTTTAATTTAAATCAATTTTTAAAAG
1 TTTTTTAATTTAAAT-AATTTTTAAAAG
* *
40581 TTTTTTATTTTAAAT-TTTTTTAAAA
1 TTTTTTAATTTAAATAATTTTTAAAA
40606 AATTAAATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 9 0.39
28 14 0.61
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (27 bp):
TTTTTTAATTTAAATAATTTTTAAAAG
Found at i:40812 original size:17 final size:17
Alignment explanation
Indices: 40790--40822 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
40780 TTAAAATAAA
40790 TATTTTATATT-AAATAG
1 TATTTTA-ATTGAAATAG
40807 TATTTTAATTGAAATA
1 TATTTTAATTGAAATA
40823 CACTTAACTC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (17 bp):
TATTTTAATTGAAATAG
Found at i:45276 original size:3 final size:3
Alignment explanation
Indices: 45268--45299 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
45258 TAAAATTAAA
45268 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
45300 ATGATTAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:52688 original size:9 final size:9
Alignment explanation
Indices: 52667--52704 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
52657 ATGTTATGTA
52667 CCCAAAA-C
1 CCCAAAATC
52675 CCCAAAATC
1 CCCAAAATC
*
52684 CCCAAATAAC
1 CCCAAA-ATC
52694 CCCAAAATC
1 CCCAAAATC
52703 CC
1 CC
52705 TAAGTGTCGT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
8 7 0.27
9 11 0.42
10 8 0.31
ACGTcount: A:0.45, C:0.47, G:0.00, T:0.08
Consensus pattern (9 bp):
CCCAAAATC
Found at i:53285 original size:20 final size:20
Alignment explanation
Indices: 53262--53314 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
53252 AGACAACTCG
53262 AACCGGCCTGAGTCAACCCA
1 AACCGGCCTGAGTCAACCCA
*
53282 AACCGGCCTGAGTTAACCCA
1 AACCGGCCTGAGTCAACCCA
* *
53302 AATCGACCTGAGT
1 AACCGGCCTGAGT
53315 TATATTTTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.30, C:0.34, G:0.21, T:0.15
Consensus pattern (20 bp):
AACCGGCCTGAGTCAACCCA
Found at i:60283 original size:19 final size:20
Alignment explanation
Indices: 60259--60304 Score: 76
Period size: 19 Copynumber: 2.4 Consensus size: 20
60249 CCCAAACCAG
*
60259 TTTGACCGTTGACT-TTGAT
1 TTTGACCGTTGACTGTTGAC
60278 TTTGACCGTTGACTGTTGAC
1 TTTGACCGTTGACTGTTGAC
60298 TTTGACC
1 TTTGACC
60305 AAAAAGTCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
19 14 0.56
20 11 0.44
ACGTcount: A:0.15, C:0.20, G:0.22, T:0.43
Consensus pattern (20 bp):
TTTGACCGTTGACTGTTGAC
Found at i:62066 original size:31 final size:29
Alignment explanation
Indices: 61987--62067 Score: 74
Period size: 31 Copynumber: 2.6 Consensus size: 29
61977 TTGCTAACAA
* *
61987 TAGGTGTCTAATGTTTTCTTCGTTATACTTT
1 TAGGTG-CTAATGTTTT-TTCATTACACTTT
*
62018 TAGGTGCCTACA-ATTTTTTCTATTACACTTT
1 TAGGTG-CTA-ATGTTTTTTC-ATTACACTTT
62049 TAGGTGCATAATGTTTTTT
1 TAGGTGC-TAATGTTTTTT
62068 TTTAATTTTT
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
30 5 0.12
31 35 0.85
32 1 0.02
ACGTcount: A:0.20, C:0.14, G:0.15, T:0.52
Consensus pattern (29 bp):
TAGGTGCTAATGTTTTTTCATTACACTTT
Found at i:62100 original size:24 final size:22
Alignment explanation
Indices: 62067--62116 Score: 57
Period size: 24 Copynumber: 2.2 Consensus size: 22
62057 TAATGTTTTT
62067 TTTTAATTTTTCTAATAATAA-AAA
1 TTTTAATTTTT-TAA-AA-AAGAAA
*
62091 TTTTATTTTTTTAAAAAAGAAA
1 TTTTAATTTTTTAAAAAAGAAA
62113 TTTT
1 TTTT
62117 TTAAAAAACA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 2 0.08
22 9 0.38
23 3 0.12
24 10 0.42
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (22 bp):
TTTTAATTTTTTAAAAAAGAAA
Found at i:62117 original size:23 final size:25
Alignment explanation
Indices: 62066--62117 Score: 58
Period size: 23 Copynumber: 2.2 Consensus size: 25
62056 ATAATGTTTT
62066 TTTTTAATTTTTCTAATAATAAAAA
1 TTTTTAATTTTTCTAATAATAAAAA
*
62091 -TTTT-ATTTTTTTAA-AA-AAGAAA
1 TTTTTAATTTTTCTAATAATAA-AAA
62113 TTTTT
1 TTTTT
62118 TAAAAAACAA
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
21 2 0.08
22 5 0.21
23 13 0.54
24 4 0.17
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (25 bp):
TTTTTAATTTTTCTAATAATAAAAA
Found at i:67154 original size:16 final size:16
Alignment explanation
Indices: 67129--67159 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
67119 GTATACATCT
*
67129 TTTTTTTTTAAAATAC
1 TTTTTATTTAAAATAC
67145 TTTTTATTTAAAATA
1 TTTTTATTTAAAATA
67160 GGTGATTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.61
Consensus pattern (16 bp):
TTTTTATTTAAAATAC
Found at i:68536 original size:14 final size:15
Alignment explanation
Indices: 68517--68546 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
68507 GAAAAGTAAA
68517 TCATA-TAGTTTATC
1 TCATATTAGTTTATC
68531 TCATATTAGTTTATC
1 TCATATTAGTTTATC
68546 T
1 T
68547 GCTAAATGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.27, C:0.13, G:0.07, T:0.53
Consensus pattern (15 bp):
TCATATTAGTTTATC
Found at i:74000 original size:25 final size:27
Alignment explanation
Indices: 73943--74013 Score: 78
Period size: 25 Copynumber: 2.7 Consensus size: 27
73933 TTAAAAAAGA
* *
73943 TTAAAATT-ATTAAGTTCGATTTAAAT
1 TTAAAATTAATTAAATTCGATCTAAAT
73969 TTAAAATTAATTAAATTCGA-CT-AAT
1 TTAAAATTAATTAAATTCGATCTAAAT
*
73994 TTAAAA-TAATTTAAACTCGA
1 TTAAAATTAA-TTAAATTCGA
74014 AACATTCTCA
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
24 3 0.08
25 18 0.45
26 9 0.22
27 10 0.25
ACGTcount: A:0.46, C:0.07, G:0.06, T:0.41
Consensus pattern (27 bp):
TTAAAATTAATTAAATTCGATCTAAAT
Done.