Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007353.1 Hibiscus syriacus cultivar Beakdansim tig00019704_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: 109443
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32
Found at i:1172 original size:3 final size:3
Alignment explanation
Indices: 1152--1243 Score: 87
Period size: 3 Copynumber: 31.0 Consensus size: 3
1142 TGAAGCTGAC
* * * * * **
1152 GAT GAA GAT GAC GAT GAT GAT GAT GAT GAT GAT GAC GAT GAA GCT GGC
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
* * *
1200 G-T GAA GAT GAT GAC GAT GAT GAT GAT GAT GAT GAA GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
1244 CCAAACAAGT
Statistics
Matches: 70, Mismatches: 18, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
2 1 0.01
3 69 0.99
ACGTcount: A:0.35, C:0.05, G:0.35, T:0.25
Consensus pattern (3 bp):
GAT
Found at i:1243 original size:12 final size:12
Alignment explanation
Indices: 1140--1239 Score: 85
Period size: 12 Copynumber: 8.4 Consensus size: 12
1130 GGTCGCAGAA
*
1140 GATGAAGCTGAC
1 GATGAAGATGAC
1152 GATGAAGATGAC
1 GATGAAGATGAC
* *
1164 GATGATGATGAT
1 GATGAAGATGAC
*
1176 GATGATGATGAC
1 GATGAAGATGAC
* *
1188 GATGAAGCTGGC
1 GATGAAGATGAC
*
1200 G-TGAAGATGAT
1 GATGAAGATGAC
* * *
1211 GACGATGATGAT
1 GATGAAGATGAC
* *
1223 GATGATGATGAA
1 GATGAAGATGAC
1235 GATGA
1 GATGA
1240 TGATCCAAAC
Statistics
Matches: 73, Mismatches: 14, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
11 8 0.11
12 65 0.89
ACGTcount: A:0.35, C:0.07, G:0.35, T:0.23
Consensus pattern (12 bp):
GATGAAGATGAC
Found at i:2996 original size:179 final size:183
Alignment explanation
Indices: 2580--3060 Score: 841
Period size: 182 Copynumber: 2.7 Consensus size: 183
2570 CTTTCAAAAT
**
2580 ATTATAATAAAATAGATAATTTTGTAATATAACCGGTAT-AATATACCGGTCTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
2644 GGTCTACAACCTATATCGACAC-TTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACC-ATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
*
2708 AATGTGTCGATACGATGTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
130 AATGTGTCGATACAATGTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
2762 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
2827 GGTCTACAA-C-TATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAA
66 GGTCTACAACCATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAG-AAA
*
2890 AATGTGTCGATACAAT-TTAAAAAGTGTCGACA-TTTACACATCGGAA-CCATA
130 AATGTGTCGATACAATGTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
2941 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
*
3006 GGTCTACAACCTATATCGACACTTTATAATATTGTGTCGGTACTTTATGTCCATA
66 GGTCTACAACC-ATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATA
3061 CCATTTAAAA
Statistics
Matches: 288, Mismatches: 5, Indels: 12
0.94 0.02 0.04
Matches are distributed among these distances:
179 79 0.27
180 24 0.08
181 54 0.19
182 97 0.34
183 34 0.12
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (183 bp):
ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
GGTCTACAACCATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAA
ATGTGTCGATACAATGTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
Found at i:5638 original size:23 final size:22
Alignment explanation
Indices: 5607--5666 Score: 70
Period size: 20 Copynumber: 2.8 Consensus size: 22
5597 ATAGGTAAAC
*
5607 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTA-CCCTT
* *
5630 ATATAATGTAATA-GTATCGTT
1 ATATAATGTAATAGGTACCCTT
5651 -TATAATGTAATAGGTA
1 ATATAATGTAATAGGTA
5667 ATGGTTATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
20 12 0.36
21 6 0.18
22 3 0.09
23 12 0.36
ACGTcount: A:0.37, C:0.07, G:0.18, T:0.38
Consensus pattern (22 bp):
ATATAATGTAATAGGTACCCTT
Found at i:6064 original size:23 final size:23
Alignment explanation
Indices: 6033--6095 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
6023 ATAGGTAAAC
*
6033 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
6056 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
6079 ATATAATGTAATAGGTA
1 ATATAATGTAATAGGTA
6096 ATGGTTATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.37, C:0.06, G:0.19, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:6103 original size:23 final size:23
Alignment explanation
Indices: 6033--6105 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
6023 ATAGGTAAAC
* * **
6033 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTATCGGTT
*
6056 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTATCGGTT
6079 ATATAATGTAATAGGTAAT-GGTT
1 ATATAATGTAATAGGT-ATCGGTT
6102 ATAT
1 ATAT
6106 TGTAAGTGTC
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
23 42 0.95
24 2 0.05
ACGTcount: A:0.36, C:0.05, G:0.19, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTATCGGTT
Found at i:6489 original size:23 final size:23
Alignment explanation
Indices: 6458--6520 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
6448 ATAGGTAAAC
*
6458 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
6481 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
6504 ATATAATGTAATAGGTA
1 ATATAATGTAATAGGTA
6521 ATGGTTATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.37, C:0.06, G:0.19, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:6528 original size:23 final size:23
Alignment explanation
Indices: 6458--6530 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
6448 ATAGGTAAAC
* * **
6458 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTATCGGTT
*
6481 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTATCGGTT
6504 ATATAATGTAATAGGTAAT-GGTT
1 ATATAATGTAATAGGT-ATCGGTT
6527 ATAT
1 ATAT
6531 TGTAAAGTGT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
23 42 0.95
24 2 0.05
ACGTcount: A:0.36, C:0.05, G:0.19, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTATCGGTT
Found at i:6717 original size:29 final size:30
Alignment explanation
Indices: 6674--6740 Score: 75
Period size: 30 Copynumber: 2.2 Consensus size: 30
6664 GTTACGGTAT
* *
6674 ATATTATTATTAAAT-TAAAA-ATTCTAAATA
1 ATATT-TTATAAAATATAAAACAATC-AAATA
6704 ATATTTTATAAAATATAAAACAATCAAATA
1 ATATTTTATAAAATATAAAACAATCAAATA
*
6734 ATTTTTT
1 ATATTTT
6741 GTGCAAATGA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
29 8 0.25
30 21 0.66
31 3 0.09
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.43
Consensus pattern (30 bp):
ATATTTTATAAAATATAAAACAATCAAATA
Found at i:6775 original size:426 final size:431
Alignment explanation
Indices: 5508--6947 Score: 2766
Period size: 425 Copynumber: 3.4 Consensus size: 431
5498 AATTCGCAGT
5508 ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATA
1 ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATA
5573 AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
66 AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
5638 TAATA-GTATCG-TT-TATAATGTAATAGGTAATGGTTATATTGTAAAGTGTCTATCCTTTTTAT
131 TAATAGGTATCGTTTATATAATGTAATAGGTAATGGTTATATTGTAAAGTGTCTATCCTTTTTAT
5700 AAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTT
196 AAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTT
5765 AAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTATATATTATT
261 AAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTATATATTATT
*
5830 ATTAAATTTAAAATTCTAAATAATATTTTATAAAATATAAAAACAATCAAATAATTTTTTGTGCA
326 ATTAAATTAAAAATTCTAAATAATATTTTATAAAATATAAAAACAATCAAATAATTTTTTGTGCA
5895 AATGAAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
391 AATGAAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
5936 ACACTGTT-AAAAAATTGAAACATAAATTACATAAGTTTT-AAAAAAGTATCGATCCTTTTTATA
1 ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATA
5999 AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
66 AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
6064 TAATAGGTATCGTTTATATAATGTAATAGGTAATGGTTATATTGT-AAGTGTCTATCCTTTTTAT
131 TAATAGGTATCGTTTATATAATGTAATAGGTAATGGTTATATTGTAAAGTGTCTATCCTTTTTAT
6128 AAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTT
196 AAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTT
6193 AAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGG--TATATTATT
261 AAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTATATATTATT
6256 ATT-AATTAAAAATTCTAAATAATATTTTATAAAATATAAAAACAATCAAATAATTTTTTGTGCA
326 ATTAAATTAAAAATTCTAAATAATATTTTATAAAATATAAAAACAATCAAATAATTTTTTGTGCA
6320 AATGAAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
391 AATGAAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
6361 ACACTGTT-AAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTAT-
1 ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATA
6424 AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
66 AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
6489 TAATAGGTATCGTTTATATAATGTAATAGGTAATGGTTATATTGTAAAGTGTCTATCCTTTTTAT
131 TAATAGGTATCGTTTATATAATGTAATAGGTAATGGTTATATTGTAAAGTGTCTATCCTTTTTAT
6554 AAAAGTGTCCATACTTTTTTCACTGTGG-AAACATTAATTTAAGGTTATCTTTTGAGTGAG-TTT
196 AAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTT
6617 AAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTATATATTATT
261 AAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTATATATTATT
6682 ATTAAATTAAAAATTCTAAATAATATTTTATAAAATAT-AAAACAATCAAATAATTTTTTGTGCA
326 ATTAAATTAAAAATTCTAAATAATATTTTATAAAATATAAAAACAATCAAATAATTTTTTGTGCA
6746 AATGAAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
391 AATGAAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
6787 ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTAT-
1 ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATA
6851 AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
66 AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
6916 TAATAGGTATCGTTTATATAATGTAATAGGTA
131 TAATAGGTATCGTTTATATAATGTAATAGGTA
6948 TCTATCTCGC
Statistics
Matches: 1002, Mismatches: 1, Indels: 19
0.98 0.00 0.02
Matches are distributed among these distances:
424 57 0.06
425 282 0.28
426 263 0.26
427 223 0.22
428 148 0.15
429 29 0.03
ACGTcount: A:0.40, C:0.08, G:0.13, T:0.39
Consensus pattern (431 bp):
ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATA
AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
TAATAGGTATCGTTTATATAATGTAATAGGTAATGGTTATATTGTAAAGTGTCTATCCTTTTTAT
AAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTT
AAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTATATATTATT
ATTAAATTAAAAATTCTAAATAATATTTTATAAAATATAAAAACAATCAAATAATTTTTTGTGCA
AATGAAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
Found at i:6948 original size:23 final size:23
Alignment explanation
Indices: 6885--6949 Score: 94
Period size: 23 Copynumber: 2.8 Consensus size: 23
6875 ATAGGTAAAC
* *
6885 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTATCCCTT
**
6908 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTATCCCTT
6931 ATATAATGTAATAGGTATC
1 ATATAATGTAATAGGTATC
6950 TATCTCGCAT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.35, C:0.08, G:0.18, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTATCCCTT
Found at i:7174 original size:18 final size:18
Alignment explanation
Indices: 7153--7189 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
7143 GTAATTGGAG
7153 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
7171 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
7189 T
1 T
7190 ATATATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:7197 original size:24 final size:24
Alignment explanation
Indices: 7145--7191 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
7135 TTTCATATGT
* *
7145 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATC
*
7169 AATTTGAGTTTGAATTTCAATAT
1 AATTTGAGTTTGAATTTAAATAT
7192 ATATTTCGGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.34, C:0.04, G:0.15, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATC
Found at i:12214 original size:16 final size:16
Alignment explanation
Indices: 12184--12213 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
12174 ATATTTACAT
12184 TTTATTTTTATTTTTA
1 TTTATTTTTATTTTTA
12200 TTTA-TTTTATTTTT
1 TTTATTTTTATTTTT
12214 TGTGTCAGGC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (16 bp):
TTTATTTTTATTTTTA
Found at i:13555 original size:2 final size:2
Alignment explanation
Indices: 13550--13590 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
13540 ATATATTTTA
*
13550 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
13591 CTTATAATAG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:14766 original size:10 final size:10
Alignment explanation
Indices: 14751--14784 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
14741 TTCATTTACC
14751 ATTTATTTTT
1 ATTTATTTTT
14761 ATTTATTTTT
1 ATTTATTTTT
* *
14771 ATCTATTTCT
1 ATTTATTTTT
14781 ATTT
1 ATTT
14785 TACTAACGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.74
Consensus pattern (10 bp):
ATTTATTTTT
Found at i:24205 original size:7 final size:7
Alignment explanation
Indices: 24194--24228 Score: 61
Period size: 7 Copynumber: 5.0 Consensus size: 7
24184 CCTAAGTTGA
*
24194 AAAAAAA
1 AAAAAAC
24201 AAAAAAC
1 AAAAAAC
24208 AAAAAAC
1 AAAAAAC
24215 AAAAAAC
1 AAAAAAC
24222 AAAAAAC
1 AAAAAAC
24229 GCTTAGGGTG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (7 bp):
AAAAAAC
Found at i:25446 original size:22 final size:22
Alignment explanation
Indices: 25414--25479 Score: 125
Period size: 22 Copynumber: 3.0 Consensus size: 22
25404 CTCGTATAAA
25414 TGCA-CGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
25435 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
25457 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
25479 T
1 T
25480 ATGTCCATAA
Statistics
Matches: 44, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
21 4 0.09
22 40 0.91
ACGTcount: A:0.27, C:0.26, G:0.27, T:0.20
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:26418 original size:18 final size:18
Alignment explanation
Indices: 26395--26429 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
26385 TTTCCCCTAG
26395 CTTATC-TTATATGTTCAT
1 CTTATCATT-TATGTTCAT
26413 CTTATCATTTATGTTCA
1 CTTATCATTTATGTTCA
26430 AATCTCCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.54
Consensus pattern (18 bp):
CTTATCATTTATGTTCAT
Found at i:27058 original size:22 final size:21
Alignment explanation
Indices: 27012--27054 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
27002 TTCATATTCG
* *
27012 CTTGAAGGGGTATCGGTTCCC
1 CTTGAAGGGGTACCGATTCCC
*
27033 CTTGAATGGGTACCGATTCCC
1 CTTGAAGGGGTACCGATTCCC
27054 C
1 C
27055 CTTGCCCAGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.28, G:0.28, T:0.28
Consensus pattern (21 bp):
CTTGAAGGGGTACCGATTCCC
Found at i:30190 original size:22 final size:22
Alignment explanation
Indices: 30173--30239 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
30163 CTCGTATAAA
30173 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
30195 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
30217 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
30239 T
1 T
30240 ATGTCCATAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:31185 original size:18 final size:18
Alignment explanation
Indices: 31164--31198 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
31154 TCCCCTCTAG
31164 CTTATC-TTATATGTTCAT
1 CTTATCATT-TATGTTCAT
31182 CTTATCATTTATGTTCA
1 CTTATCATTTATGTTCA
31199 AATCTCCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.54
Consensus pattern (18 bp):
CTTATCATTTATGTTCAT
Found at i:31803 original size:20 final size:21
Alignment explanation
Indices: 31778--31819 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
31768 TTCATATTCG
* *
31778 CTTGAA-GGGTATCGGTTCCC
1 CTTGAATGGGTACCGATTCCC
31798 CTTGAATGGGTACCGATTCCC
1 CTTGAATGGGTACCGATTCCC
31819 C
1 C
31820 CTTGCCCAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.17, C:0.29, G:0.26, T:0.29
Consensus pattern (21 bp):
CTTGAATGGGTACCGATTCCC
Found at i:32949 original size:105 final size:105
Alignment explanation
Indices: 32767--33454 Score: 1073
Period size: 105 Copynumber: 6.7 Consensus size: 105
32757 AGGTTTTACC
*
32767 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCTAGACAACGTAAGTTCAACTTCACG
32832 ACGAAGGGACCGCTGGTTGTCAACGAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACGAACATTTCTCAATTT
32872 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCTAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCTAGACAACGTAAGTTCAACTTCACG
32937 ACGAAGGGACCGCTGGTTGTCAACGAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACGAACATTTCTCAATTT
32977 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCTAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCTAGACAACGTAAGTTCAACTTCACG
33042 ACGAAGGGACCGCTGGTTGTCAACGAACATTTCTC-ATTT
66 ACGAAGGGACCGCTGGTTGTCAACGAACATTTCTCAATTT
*
33081 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCTAGACAACGTAAGTTCAACTTCACG
*
33146 ACGAAGGGACCGCTGGTTGTAAACGAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACGAACATTTCTCAATTT
*
33186 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACT-TCAGACAACGCAAGTTCAACTTCAC
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCT-AGACAACGTAAGTTCAACTTCAC
* * * *
33250 GACGAAGGGACCGCTGCTTGTCAAC-AACAACTTCCCAATCT
65 GACGAAGGGACCGCTGGTTGTCAACGAAC-ATTTCTCAATTT
* *
33291 CAGAGCC-A----AACTTCACAACGAAGAATATTGGACT-TCAGACAACGCAAGTTCAACTTCAC
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCT-AGACAACGTAAGTTCAACTTCAC
* * * *
33350 GACGAAGGGACCGCTGCTTGTCAAC-AACAACTTCCCAATCT
65 GACGAAGGGACCGCTGGTTGTCAACGAAC-ATTTCTCAATTT
* * * *
33391 CAGAGCC-A----AACTTCACAACGAAGAATATGGGACTCTAGACAACGCAAGTCCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCTAGACAACGTAAGTTCAACTTCACG
33451 ACGA
66 ACGA
33455 TGGATATCCA
Statistics
Matches: 566, Mismatches: 13, Indels: 13
0.96 0.02 0.02
Matches are distributed among these distances:
100 151 0.27
101 1 0.00
104 106 0.19
105 308 0.54
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (105 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCTAGACAACGTAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACGAACATTTCTCAATTT
Found at i:33178 original size:209 final size:210
Alignment explanation
Indices: 32767--33454 Score: 1080
Period size: 209 Copynumber: 3.3 Consensus size: 210
32757 AGGTTTTACC
* *
32767 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCTAGACAACGCAAGTTCAACTTCACG
32832 ACGAAGGGACCGCTGGTTGTCAACGAACATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACG
66 ACGAAGGGACCGCTGGTTGTCAACGAACATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACG
*
32897 AAGGATATTGGACTCTAGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACG
131 AAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACG
32962 AACATTTCTCAATTT
196 AACATTTCTCAATTT
*
32977 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCTAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCTAGACAACGCAAGTTCAACTTCACG
33042 ACGAAGGGACCGCTGGTTGTCAACGAACATTTCTC-ATTTCAGAGCCAATTTCAACTTCACAACG
66 ACGAAGGGACCGCTGGTTGTCAACGAACATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACG
*
33106 AAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTAAACG
131 AAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACG
33171 AACATTTCTCAATTT
196 AACATTTCTCAATTT
33186 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACT-TCAGACAACGCAAGTTCAACTTCAC
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCT-AGACAACGCAAGTTCAACTTCAC
* * * *
33250 GACGAAGGGACCGCTGCTTGTCAAC-AACAACTTCCCAATCTCAGAGCC-A----AACTTCACAA
65 GACGAAGGGACCGCTGGTTGTCAACGAAC-ATTTCTCAATTTCAGAGCCAATTTCAACTTCACAA
* * * *
33309 CGAAGAATATTGGACTTCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAA
129 CGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA
* * *
33374 C-AACAACTTCCCAATCT
194 CGAAC-ATTTCTCAATTT
* * *
33391 CAGAGCC-A----AACTTCACAACGAAGAATATGGGACTCTAGACAACGCAAGTCCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCTAGACAACGCAAGTTCAACTTCACG
33451 ACGA
66 ACGA
33455 TGGATATCCA
Statistics
Matches: 454, Mismatches: 19, Indels: 20
0.92 0.04 0.04
Matches are distributed among these distances:
200 51 0.11
201 1 0.00
204 4 0.01
205 87 0.19
208 4 0.01
209 198 0.44
210 109 0.24
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (210 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCTAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACGAACATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACG
AAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACG
AACATTTCTCAATTT
Found at i:35326 original size:2 final size:2
Alignment explanation
Indices: 35319--35357 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
35309 TATTATTTTA
*
35319 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
35358 CTTATAATAG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:37158 original size:15 final size:15
Alignment explanation
Indices: 37138--37173 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
37128 GATTAATAAT
37138 AATATTGATTAAATC
1 AATATTGATTAAATC
37153 AATATTGATTAAATC
1 AATATTGATTAAATC
37168 AATATT
1 AATATT
37174 CAGTCTCCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.42
Consensus pattern (15 bp):
AATATTGATTAAATC
Found at i:41100 original size:15 final size:15
Alignment explanation
Indices: 41055--41100 Score: 74
Period size: 15 Copynumber: 3.1 Consensus size: 15
41045 TTAGATGGGT
*
41055 GGGCGGATGTGGGGC
1 GGGCGGATGCGGGGC
*
41070 AGGCGGATGCGGGGC
1 GGGCGGATGCGGGGC
41085 GGGCGGATGCGGGGC
1 GGGCGGATGCGGGGC
41100 G
1 G
41101 AGTAATGTCT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.09, C:0.17, G:0.65, T:0.09
Consensus pattern (15 bp):
GGGCGGATGCGGGGC
Found at i:44815 original size:31 final size:31
Alignment explanation
Indices: 44733--44816 Score: 91
Period size: 29 Copynumber: 2.8 Consensus size: 31
44723 ATGTTCCAAA
* * * * *
44733 ATTGGATATTTTGTCAAAGGACAAGTCCCAC
1 ATTGGATATTTTGTAAAAGTACAGGTACAAC
*
44764 ATTGGACA-TTT-TAAAAGTACAGGTACAAC
1 ATTGGATATTTTGTAAAAGTACAGGTACAAC
*
44793 ATTGGATATTTTGTTAAAGTACAG
1 ATTGGATATTTTGTAAAAGTACAG
44817 ATACCAAATG
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
29 20 0.47
30 6 0.14
31 17 0.40
ACGTcount: A:0.36, C:0.13, G:0.19, T:0.32
Consensus pattern (31 bp):
ATTGGATATTTTGTAAAAGTACAGGTACAAC
Found at i:55313 original size:15 final size:16
Alignment explanation
Indices: 55295--55325 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
55285 GGTGTCATTA
55295 ATTTTTTTTA-AAATT
1 ATTTTTTTTATAAATT
55310 ATTTTTTTTATAAATT
1 ATTTTTTTTATAAATT
55326 TAATATAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
ATTTTTTTTATAAATT
Found at i:55315 original size:16 final size:17
Alignment explanation
Indices: 55291--55329 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
55281 GAGGGGTGTC
55291 ATTAATTTTTTT-TAAA
1 ATTAATTTTTTTATAAA
*
55307 ATTATTTTTTTTATAAA
1 ATTAATTTTTTTATAAA
*
55324 TTTAAT
1 ATTAAT
55330 ATAAAATACT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
ATTAATTTTTTTATAAA
Found at i:55433 original size:2 final size:2
Alignment explanation
Indices: 55426--55452 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
55416 TGACACCCTA
55426 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
55453 AAATTTGACA
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:56314 original size:2 final size:2
Alignment explanation
Indices: 56307--56338 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
56297 TTAAGAGGAA
56307 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
56339 TTAAAGAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:56444 original size:16 final size:14
Alignment explanation
Indices: 56421--56466 Score: 58
Period size: 14 Copynumber: 3.2 Consensus size: 14
56411 CACAAACAAT
56421 AATTGAGAATTAAA
1 AATTGAGAATTAAA
*
56435 AACGTTGAGAA-TAAT
1 AA--TTGAGAATTAAA
56450 AATTGAGAATTAAA
1 AATTGAGAATTAAA
56464 AAT
1 AAT
56467 GTTAGGCATA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
13 7 0.26
14 8 0.30
15 5 0.19
16 7 0.26
ACGTcount: A:0.54, C:0.02, G:0.15, T:0.28
Consensus pattern (14 bp):
AATTGAGAATTAAA
Found at i:56488 original size:32 final size:32
Alignment explanation
Indices: 56415--56628 Score: 244
Period size: 32 Copynumber: 6.8 Consensus size: 32
56405 ATTATACACA
*
56415 AACAATAATTGAGAATTAAAAACGTTGAGA-AT
1 AACAATAATTGAGAATTAAAAACATTG-GACAT
**
56447 ---AATAATTGAGAATTAAAAATGTTAGG-CAT
1 AACAATAATTGAGAATTAAAAACATT-GGACAT
56476 AACAATAATTGAGAATTAAAAACATTGGACAT
1 AACAATAATTGAGAATTAAAAACATTGGACAT
* *
56508 AGCAATTATTGAGAATTAAAAACATTGGACAT
1 AACAATAATTGAGAATTAAAAACATTGGACAT
* * **
56540 AGCAATTATTGAGAATT-AAAATGTTAGG-CAT
1 AACAATAATTGAGAATTAAAAACATT-GGACAT
*
56571 AAAAATAATTGAGAATTAAAAACATTGGACAT
1 AACAATAATTGAGAATTAAAAACATTGGACAT
* *
56603 AGCAATTATTGAGAATTAAAAACATT
1 AACAATAATTGAGAATTAAAAACATT
56629 AGAGTACCAA
Statistics
Matches: 158, Mismatches: 15, Indels: 18
0.83 0.08 0.09
Matches are distributed among these distances:
29 25 0.16
30 1 0.01
31 27 0.17
32 105 0.66
ACGTcount: A:0.50, C:0.07, G:0.15, T:0.28
Consensus pattern (32 bp):
AACAATAATTGAGAATTAAAAACATTGGACAT
Found at i:56583 original size:95 final size:93
Alignment explanation
Indices: 56417--56628 Score: 338
Period size: 95 Copynumber: 2.3 Consensus size: 93
56407 TATACACAAA
* * *
56417 CAATAATTGAGAATTAAAAACGTTGAGAATAATAATTGAGAATTAAAAATGTTAGGCATAACAAT
1 CAATTATTGAGAATTAAAAACATTGAGAATAATAATTGAGAATTAAAAATGTTAGGCATAAAAAT
56482 AATTGAGAATTAAAAACATTGGACATAG
66 AATTGAGAATTAAAAACATTGGACATAG
*
56510 CAATTATTGAGAATTAAAAACATTG-GACATAGCAATTATTGAGAATT-AAAATGTTAGGCATAA
1 CAATTATTGAGAATTAAAAACATTGAGA-AT---AATAATTGAGAATTAAAAATGTTAGGCATAA
56573 AAATAATTGAGAATTAAAAACATTGGACATAG
62 AAATAATTGAGAATTAAAAACATTGGACATAG
56605 CAATTATTGAGAATTAAAAACATT
1 CAATTATTGAGAATTAAAAACATT
56629 AGAGTACCAA
Statistics
Matches: 111, Mismatches: 4, Indels: 6
0.92 0.03 0.05
Matches are distributed among these distances:
92 2 0.02
93 25 0.23
95 71 0.64
96 13 0.12
ACGTcount: A:0.50, C:0.07, G:0.15, T:0.28
Consensus pattern (93 bp):
CAATTATTGAGAATTAAAAACATTGAGAATAATAATTGAGAATTAAAAATGTTAGGCATAAAAAT
AATTGAGAATTAAAAACATTGGACATAG
Found at i:56593 original size:63 final size:63
Alignment explanation
Indices: 56447--56628 Score: 233
Period size: 63 Copynumber: 2.9 Consensus size: 63
56437 CGTTGAGAAT
** * * **
56447 AATAATTGAGAATTAAAAATGTTAGG-CATAACAATAATTGAGAATTAAAAACATTGGACATAGC
1 AATAATTGAGAATTAAAAACATT-GGACATAGCAATTATTGAGAATT-AAAACATTGGACATAAA
* **
56511 AATTATTGAGAATTAAAAACATTGGACATAGCAATTATTGAGAATTAAAATGTTAGG-CATAAA
1 AATAATTGAGAATTAAAAACATTGGACATAGCAATTATTGAGAATTAAAACATT-GGACATAAA
56574 AATAATTGAGAATTAAAAACATTGGACATAGCAATTATTGAGAATTAAAAACATT
1 AATAATTGAGAATTAAAAACATTGGACATAGCAATTATTGAGAATT-AAAACATT
56629 AGAGTACCAA
Statistics
Matches: 103, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
63 57 0.55
64 46 0.45
ACGTcount: A:0.49, C:0.07, G:0.15, T:0.29
Consensus pattern (63 bp):
AATAATTGAGAATTAAAAACATTGGACATAGCAATTATTGAGAATTAAAACATTGGACATAAA
Found at i:62355 original size:16 final size:17
Alignment explanation
Indices: 62328--62361 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
62318 TATCGCCGAC
62328 CGAAATTTCACTATTCA
1 CGAAATTTCACTATTCA
62345 CGAAA-TTCACTATTCA
1 CGAAATTTCACTATTCA
62361 C
1 C
62362 ATGAATAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.35, C:0.26, G:0.06, T:0.32
Consensus pattern (17 bp):
CGAAATTTCACTATTCA
Found at i:65618 original size:20 final size:20
Alignment explanation
Indices: 65574--65683 Score: 179
Period size: 20 Copynumber: 5.5 Consensus size: 20
65564 ATCATATTCC
65574 CTGATAATCTTTTATTCCC-
1 CTGATAATCTTTTATTCCCT
65593 CTGATAATCTTTTATTCCCT
1 CTGATAATCTTTTATTCCCT
65613 CTGATAATCTTTTATT-CCT
1 CTGATAATCTTTTATTCCCT
65632 ACTGATAATCTTTTATTCCCT
1 -CTGATAATCTTTTATTCCCT
*
65653 CTGATAATCTTTTATTCCCA
1 CTGATAATCTTTTATTCCCT
*
65673 CTAATAATCTT
1 CTGATAATCTT
65684 ACATCCCGTG
Statistics
Matches: 86, Mismatches: 2, Indels: 5
0.92 0.02 0.05
Matches are distributed among these distances:
19 22 0.26
20 61 0.71
21 3 0.03
ACGTcount: A:0.24, C:0.24, G:0.05, T:0.48
Consensus pattern (20 bp):
CTGATAATCTTTTATTCCCT
Found at i:68581 original size:14 final size:14
Alignment explanation
Indices: 68562--68588 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
68552 TAACAAAAAC
68562 AAATAATTTCTATG
1 AAATAATTTCTATG
68576 AAATAATTTCTAT
1 AAATAATTTCTAT
68589 CAAGACAGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.44
Consensus pattern (14 bp):
AAATAATTTCTATG
Found at i:74490 original size:19 final size:18
Alignment explanation
Indices: 74462--74498 Score: 65
Period size: 19 Copynumber: 2.0 Consensus size: 18
74452 GTTGGATTTT
74462 TTTCTTTAAATTAGAAAA
1 TTTCTTTAAATTAGAAAA
74480 TTTCATTTAAATTAGAAAA
1 TTTC-TTTAAATTAGAAAA
74499 CCCTAGTCGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.43
Consensus pattern (18 bp):
TTTCTTTAAATTAGAAAA
Found at i:102549 original size:16 final size:18
Alignment explanation
Indices: 102528--102572 Score: 58
Period size: 20 Copynumber: 2.5 Consensus size: 18
102518 AACATTCCCA
102528 GTAATCTTATT-CC-CTG
1 GTAATCTTATTCCCACTG
102544 GTAATCTTACATTCCCACTG
1 GTAATCTT--ATTCCCACTG
102564 GTAATCTTA
1 GTAATCTTA
102573 CATTCCGTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
16 8 0.32
18 4 0.16
19 2 0.08
20 11 0.44
ACGTcount: A:0.24, C:0.24, G:0.11, T:0.40
Consensus pattern (18 bp):
GTAATCTTATTCCCACTG
Found at i:102566 original size:20 final size:20
Alignment explanation
Indices: 102541--102578 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
102531 ATCTTATTCC
102541 CTGGTAATCTTACATTCCCA
1 CTGGTAATCTTACATTCCCA
102561 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
102579 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:108391 original size:45 final size:48
Alignment explanation
Indices: 108342--108456 Score: 112
Period size: 48 Copynumber: 2.4 Consensus size: 48
108332 TTATTTACAT
* **
108342 TATTAT-ACTAATA-TATATTTTAATATT-ATATAAAATAATCAATTA
1 TATTATAAATAATATTATATTTTAATATTAATATAAAATAAAAAATTA
* * * *
108387 TATTATAAATATTATTATATTTTTATTTTAATATATAATAAAAAATTA
1 TATTATAAATAATATTATATTTTAATATTAATATAAAATAAAAAATTA
*
108435 TATT-TAATATGAAAATTATATT
1 TATTATAA-AT-AATATTATATT
108457 ATTTATTAAA
Statistics
Matches: 56, Mismatches: 9, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
45 6 0.11
46 5 0.09
47 15 0.27
48 21 0.38
49 9 0.16
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.50
Consensus pattern (48 bp):
TATTATAAATAATATTATATTTTAATATTAATATAAAATAAAAAATTA
Found at i:108442 original size:17 final size:18
Alignment explanation
Indices: 108417--108456 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
108407 TTTTATTTTA
*
108417 ATATATAATA-AAAAATT
1 ATATTTAATATAAAAATT
*
108434 ATATTTAATATGAAAATT
1 ATATTTAATATAAAAATT
108452 ATATT
1 ATATT
108457 ATTTATTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (18 bp):
ATATTTAATATAAAAATT
Found at i:108578 original size:21 final size:20
Alignment explanation
Indices: 108554--108607 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 20
108544 ATTAAATAAC
108554 AAAATTAATATTTT-TATTTAT
1 AAAA-TAATATTTTATATTT-T
*
108575 AAAAAAATTATTTTAATATTTT
1 AAAATAA-TATTTT-ATATTTT
108597 AAAATAATATT
1 AAAATAATATT
108608 AAGTTTTATG
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
20 2 0.07
21 14 0.50
22 7 0.25
23 5 0.18
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
AAAATAATATTTTATATTTT
Found at i:108590 original size:29 final size:29
Alignment explanation
Indices: 108525--108596 Score: 81
Period size: 29 Copynumber: 2.5 Consensus size: 29
108515 TAAATCTAAT
* *
108525 AATTTTAATATTTTTATTCATTAAATAAC
1 AATTTTAATATTTTTATTCATAAAAAAAC
** * *
108554 AAAATTAATATTTTTATTTATAAAAAAAT
1 AATTTTAATATTTTTATTCATAAAAAAAC
*
108583 TATTTTAATATTTT
1 AATTTTAATATTTT
108597 AAAATAATAT
Statistics
Matches: 34, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (29 bp):
AATTTTAATATTTTTATTCATAAAAAAAC
Found at i:108764 original size:15 final size:14
Alignment explanation
Indices: 108744--108777 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
108734 AAATGTAATT
*
108744 CATTTTACGGAAAA
1 CATTTTTCGGAAAA
108758 CATTTTTCGGAAAA
1 CATTTTTCGGAAAA
*
108772 CGTTTT
1 CATTTT
108778 CCATAAATGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (14 bp):
CATTTTTCGGAAAA
Found at i:108831 original size:15 final size:15
Alignment explanation
Indices: 108786--108831 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
108776 TTCCATAAAT
108786 GTAATTCATTTTCCA
1 GTAATTCATTTTCCA
**
108801 G-AATTCAAATTCCA
1 GTAATTCATTTTCCA
*
108815 GTAATTCATTTTACA
1 GTAATTCATTTTCCA
108830 GT
1 GT
108832 TCTAGTAATT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
14 12 0.48
15 13 0.52
ACGTcount: A:0.33, C:0.17, G:0.09, T:0.41
Consensus pattern (15 bp):
GTAATTCATTTTCCA
Done.