Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000661.1 Hibiscus syriacus cultivar Beakdansim tig00001290_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: 78558
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Found at i:477 original size:227 final size:226
Alignment explanation
Indices: 73--894 Score: 788
Period size: 227 Copynumber: 3.7 Consensus size: 226
63 CAGAGTTCTT
* * * * *
73 CCATCTTCAAGCTGTTTTCCTGCAAAATCAA-TCTTTGTTGATCTGGTGGGATTCC-TTCTTTGT
1 CCATCTTCAAGCTGTTTTCCAGCAAAA--AAGCCTTTGCTGATCTGGTGGGA-TCCTTTCCTAGT
* * * * * * * * *
136 CCTGAATTTTGGCTTTCACATTATCAAT-G-GTCTGAACTCTCAA-CTCCAAGG----TGTCTTT
63 CTTGGATCTTAGCCTTGACATTATCAATAGTGTCAGAGCTTTCAACCTCCAAGGTAATTGTCTTT
* * * * * *
194 CCAGTGAGAGTCTTGACAAATATTTGCATACAACCTCGAAGGCGGAGCACTAGGTGGAGGGTAGA
128 CCAGTGAGAGTCTTGACAAAGATTTGCATACCACCACGAAGACGAAGCACTAGGTGGAGGGTGGA
* * * * *
259 TTCCTTTTGAATGTTGTAATCAGCTAGGGTACGG
193 TTCCTTCTGGATGTTATAGTCAGCTAGTGTACGG
* *
293 CCATCTTCCAGCTGTTTTCCAGCAAAAAAGCCTTTGCTGATCAGGTGGGATCCTTTCCTAGTCTT
1 CCATCTTCAAGCTGTTTTCCAGCAAAAAAGCCTTTGCTGATCTGGTGGGATCCTTTCCTAGTCTT
* * * * * * * * * * * * *
358 GAATCTTTGCCTTTACGTTGTCGATGGTGTCAGAACTCTCAACCTCGAGGGTAATAGTCTTCCCA
66 GGATCTTAGCCTTGACATTATCAATAGTGTCAGAGCTTTCAACCTCCAAGGTAATTGTCTTTCCA
* * * *
423 GTCAGGGTTTTGACAAAGATTTGCATAACCACCACGAAGACGAAGCACTAGGTGGAGGGTGGACT
131 GTGAGAGTCTTGACAAAGATTTGCAT-ACCACCACGAAGACGAAGCACTAGGTGGAGGGTGGATT
* *
488 CCTTCTGGATGTTATAGTCAGCCAATGTACGG
195 CCTTCTGGATGTTATAGTCAGCTAGTGTACGG
* * * * * * ** * *
520 CCATCTTCAAGCTGCTTTCCGGCAAGATAAGCCTCTGTTGGTCTGGACGTATTCCTTAT-TTA-T
1 CCATCTTCAAGCTGTTTTCCAGCAA-AAAAGCCTTTGCTGATCTGGTGGGA-TCCTT-TCCTAGT
*
583 CTTGGATCTTAGCCTTGACATTATCAATAGTGTCCGAGCTTTCAACCTCCAAGGTAATTGTCTTT
63 CTTGGATCTTAGCCTTGACATTATCAATAGTGTCAGAGCTTTCAACCTCCAAGGTAATTGTCTTT
* * * * * * * *
648 CCGGTGAGAGTCTT-ACAAAGATTTGCATGCCACCACGAAGTCGAAGAACCAAGTGAAGAGTGGA
128 CCAGTGAGAGTCTTGACAAAGATTTGCATACCACCACGAAGACGAAGCACTAGGTGGAGGGTGGA
**
712 TTCCTTCTGGATGTTATAGTCAGCTAGTGTACTA
193 TTCCTTCTGGATGTTATAGTCAGCTAGTGTACGG
* * * * * *
746 CCATCTTCAAGTTATTTGCCAGCAAAGATGAGCCTTTGCTGATCTGGTGGGATCCCTTCCTTGTC
1 CCATCTTCAAGCTGTTTTCCAGCAAA-A-AAGCCTTTGCTGATCTGGTGGGATCCTTTCCTAGTC
*
811 TTGGATCTTAGACTTGACATTATCAATAGTGTCAGAGCTTTCAACCTCCAAGGTAATTGTCTTT-
64 TTGGATCTTAGCCTTGACATTATCAATAGTGTCAGAGCTTTCAACCTCCAAGGTAATTGTCTTTC
*
875 CAGGTGAGAGTTTTGACAAA
129 CA-GTGAGAGTCTTGACAAA
895 TATTCGTGAG
Statistics
Matches: 484, Mismatches: 99, Indels: 30
0.79 0.16 0.05
Matches are distributed among these distances:
218 5 0.01
219 43 0.09
220 26 0.05
221 13 0.03
222 6 0.01
225 2 0.00
226 114 0.24
227 183 0.38
228 84 0.17
229 7 0.01
230 1 0.00
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.32
Consensus pattern (226 bp):
CCATCTTCAAGCTGTTTTCCAGCAAAAAAGCCTTTGCTGATCTGGTGGGATCCTTTCCTAGTCTT
GGATCTTAGCCTTGACATTATCAATAGTGTCAGAGCTTTCAACCTCCAAGGTAATTGTCTTTCCA
GTGAGAGTCTTGACAAAGATTTGCATACCACCACGAAGACGAAGCACTAGGTGGAGGGTGGATTC
CTTCTGGATGTTATAGTCAGCTAGTGTACGG
Found at i:15180 original size:21 final size:21
Alignment explanation
Indices: 15128--15183 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
15118 CGAGTTACCA
*
15128 GCGACAGCCGCAATAGCGTCC
1 GCGACAGCCGCAATAGCGCCC
*
15149 GCGA-TGACCGCAATAGCGCCC
1 GCGACAG-CCGCAATAGCGCCC
15170 GCGACAGCCGCAAT
1 GCGACAGCCGCAAT
15184 CACAGTAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 1 0.03
21 28 0.93
22 1 0.03
ACGTcount: A:0.25, C:0.38, G:0.29, T:0.09
Consensus pattern (21 bp):
GCGACAGCCGCAATAGCGCCC
Found at i:23452 original size:69 final size:69
Alignment explanation
Indices: 23341--23479 Score: 260
Period size: 69 Copynumber: 2.0 Consensus size: 69
23331 ATTCCAACAT
*
23341 TCCAAAGCTTCTGTCCTCCCCTGTTCATTCTTATCTGAAACAAAATCCGACCCCTTGCCACTGCA
1 TCCAAAGCTTCTGTCCTCCCCTGTTCATTCTTATCTGAAACAAAATCCGACCCCTTACCACTGCA
23406 ACTA
66 ACTA
*
23410 TCCAAAGCTTTTGTCCTCCCCTGTTCATTCTTATCTGAAACAAAATCCGACCCCTTACCACTGCA
1 TCCAAAGCTTCTGTCCTCCCCTGTTCATTCTTATCTGAAACAAAATCCGACCCCTTACCACTGCA
23475 ACTA
66 ACTA
23479 T
1 T
23480 TAACTTCCCC
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
69 68 1.00
ACGTcount: A:0.25, C:0.35, G:0.09, T:0.30
Consensus pattern (69 bp):
TCCAAAGCTTCTGTCCTCCCCTGTTCATTCTTATCTGAAACAAAATCCGACCCCTTACCACTGCA
ACTA
Found at i:26143 original size:138 final size:138
Alignment explanation
Indices: 25893--26168 Score: 498
Period size: 138 Copynumber: 2.0 Consensus size: 138
25883 ATGTCTATGG
*
25893 AATGGTTTAGCTCTCCATTTGGAACTCTTATACGTTTTCGCAAACAATCATTCTCTCTGATTAGT
1 AATGGTTTAGCTCTCCATTTGGAACTCTTATACGTTTTCGCAAACAATCATTATCTCTGATTAGT
* * *
25958 TTGAGGCTTTTGGTTAACATTGGCATCCAAAATTTCTTTTCTATGTTTGTGTGAATTATATCTTA
66 TTGAGGCTTTTGGTTAACATTGGCATCCAAAATTTCTTTTCTATGTTTGTATAAATTATATCATA
*
26023 CATGCTAC
131 CATACTAC
26031 AATGGTTTAGCTCTCCATTTGGAACTCTTATACGTTTTCGCAAACAATCATTATCTCTGATTAGT
1 AATGGTTTAGCTCTCCATTTGGAACTCTTATACGTTTTCGCAAACAATCATTATCTCTGATTAGT
*
26096 TTGAGGCTTTTGGTTAACATTGGCATCCAAAATTTCTTTTCTGTGTTTGTATAAATTATATCATA
66 TTGAGGCTTTTGGTTAACATTGGCATCCAAAATTTCTTTTCTATGTTTGTATAAATTATATCATA
26161 CATACTAC
131 CATACTAC
26169 TAGATAAACA
Statistics
Matches: 132, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
138 132 1.00
ACGTcount: A:0.25, C:0.18, G:0.14, T:0.42
Consensus pattern (138 bp):
AATGGTTTAGCTCTCCATTTGGAACTCTTATACGTTTTCGCAAACAATCATTATCTCTGATTAGT
TTGAGGCTTTTGGTTAACATTGGCATCCAAAATTTCTTTTCTATGTTTGTATAAATTATATCATA
CATACTAC
Found at i:36169 original size:18 final size:18
Alignment explanation
Indices: 36146--36186 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
36136 CAACGGTCAA
36146 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
36164 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
36182 CGGGT
1 CGGGT
36187 AAACGGGTCG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.10, C:0.22, G:0.51, T:0.17
Consensus pattern (18 bp):
CGGGTCGGGTCAACGGGT
Found at i:36186 original size:13 final size:13
Alignment explanation
Indices: 36140--36169 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
36130 CACGGTCAAC
36140 GGTCAACGGGTCG
1 GGTCAACGGGTCG
36153 GGTCAACGGGTCG
1 GGTCAACGGGTCG
36166 GGTC
1 GGTC
36170 GGGTCAACGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.13, C:0.23, G:0.47, T:0.17
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:36191 original size:13 final size:13
Alignment explanation
Indices: 36164--36196 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
36154 GTCAACGGGT
*
36164 CGGGTCGGGTCAA
1 CGGGTCGGGTAAA
36177 CGGGTCGGGTAAA
1 CGGGTCGGGTAAA
36190 CGGGTCG
1 CGGGTCG
36197 TGACCGGTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.15, C:0.21, G:0.48, T:0.15
Consensus pattern (13 bp):
CGGGTCGGGTAAA
Found at i:36206 original size:31 final size:31
Alignment explanation
Indices: 36139--36207 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
36129 GCACGGTCAA
* *
36139 CGGTCAACGGGTCGGGTCAACGGGTCGGGTC
1 CGGTCAACGGGTCGGGTAAACGGGTCGGGAC
* *
36170 GGGTCAACGGGTCGGGTAAACGGGTCGTGAC
1 CGGTCAACGGGTCGGGTAAACGGGTCGGGAC
36201 CGGTCAA
1 CGGTCAA
36208 ACCGGTCAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.17, C:0.23, G:0.43, T:0.16
Consensus pattern (31 bp):
CGGTCAACGGGTCGGGTAAACGGGTCGGGAC
Found at i:36219 original size:10 final size:10
Alignment explanation
Indices: 36199--36253 Score: 78
Period size: 10 Copynumber: 5.6 Consensus size: 10
36189 ACGGGTCGTG
36199 ACCGGTC-AA
1 ACCGGTCAAA
36208 ACCGGTCAAA
1 ACCGGTCAAA
36218 ACCGGTTCAAA
1 ACCGG-TCAAA
*
36229 ACCGGT-TAA
1 ACCGGTCAAA
36238 ACCGGTCAAA
1 ACCGGTCAAA
36248 ACCGGT
1 ACCGGT
36254 TTCCAACGTT
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
9 15 0.37
10 16 0.39
11 10 0.24
ACGTcount: A:0.35, C:0.29, G:0.22, T:0.15
Consensus pattern (10 bp):
ACCGGTCAAA
Found at i:36254 original size:19 final size:19
Alignment explanation
Indices: 36199--36254 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
36189 ACGGGTCGTG
*
36199 ACCGGTC-AAACCGGTCAAA
1 ACCGGTCAAAACCGGT-TAA
36218 ACCGGTTCAAAACCGGTTAA
1 ACCGG-TCAAAACCGGTTAA
36238 ACCGGTCAAAACCGGTT
1 ACCGGTCAAAACCGGTT
36255 TCCAACGTTC
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
19 17 0.50
20 9 0.26
21 8 0.24
ACGTcount: A:0.34, C:0.29, G:0.21, T:0.16
Consensus pattern (19 bp):
ACCGGTCAAAACCGGTTAA
Found at i:43369 original size:13 final size:13
Alignment explanation
Indices: 43351--43387 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
43341 CACGGTCAAC
43351 GGTCAACGGGTCG
1 GGTCAACGGGTCG
43364 GGTCAACGGGTCG
1 GGTCAACGGGTCG
*
43377 GGTAAACGGGT
1 GGTCAACGGGT
43388 AAACGGGTCG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.19, C:0.19, G:0.46, T:0.16
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:43420 original size:10 final size:10
Alignment explanation
Indices: 43400--43454 Score: 78
Period size: 10 Copynumber: 5.6 Consensus size: 10
43390 ACGGGTCGTG
43400 ACCGGTC-AA
1 ACCGGTCAAA
43409 ACCGGTCAAA
1 ACCGGTCAAA
43419 ACCGGTTCAAA
1 ACCGG-TCAAA
*
43430 ACCGGT-TAA
1 ACCGGTCAAA
43439 ACCGGTCAAA
1 ACCGGTCAAA
43449 ACCGGT
1 ACCGGT
43455 TTCCAACGTT
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
9 15 0.37
10 16 0.39
11 10 0.24
ACGTcount: A:0.35, C:0.29, G:0.22, T:0.15
Consensus pattern (10 bp):
ACCGGTCAAA
Found at i:43455 original size:19 final size:19
Alignment explanation
Indices: 43400--43455 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
43390 ACGGGTCGTG
*
43400 ACCGGTC-AAACCGGTCAAA
1 ACCGGTCAAAACCGGT-TAA
43419 ACCGGTTCAAAACCGGTTAA
1 ACCGG-TCAAAACCGGTTAA
43439 ACCGGTCAAAACCGGTT
1 ACCGGTCAAAACCGGTT
43456 TCCAACGTTC
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
19 17 0.50
20 9 0.26
21 8 0.24
ACGTcount: A:0.34, C:0.29, G:0.21, T:0.16
Consensus pattern (19 bp):
ACCGGTCAAAACCGGTTAA
Found at i:47411 original size:25 final size:25
Alignment explanation
Indices: 47380--47431 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
47370 AATGACCCAT
47380 CTTCTTTGTTAAATTTCAAGCTTGC
1 CTTCTTTGTTAAATTTCAAGCTTGC
47405 CTTCTTTGTTAAATTTCAAGCTTGC
1 CTTCTTTGTTAAATTTCAAGCTTGC
47430 CT
1 CT
47432 CCATTGGTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.19, C:0.21, G:0.12, T:0.48
Consensus pattern (25 bp):
CTTCTTTGTTAAATTTCAAGCTTGC
Found at i:56691 original size:13 final size:13
Alignment explanation
Indices: 56660--56691 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
56650 GGAGAGGGTG
*
56660 AGTTTAGAGATGA
1 AGTTTCGAGATGA
56673 AGTTTCGAGATGA
1 AGTTTCGAGATGA
56686 AGTTTC
1 AGTTTC
56692 ATTGGTGGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.06, G:0.28, T:0.34
Consensus pattern (13 bp):
AGTTTCGAGATGA
Found at i:63544 original size:42 final size:43
Alignment explanation
Indices: 63493--63587 Score: 174
Period size: 42 Copynumber: 2.2 Consensus size: 43
63483 TACATATTCG
63493 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTT-
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTC
63535 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTC
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTC
63578 GCGTTGCGAT
1 -CGTTGCGAT
63588 TTATTCCAAA
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
42 42 0.82
44 9 0.18
ACGTcount: A:0.18, C:0.20, G:0.27, T:0.35
Consensus pattern (43 bp):
CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTC
Found at i:63584 original size:65 final size:65
Alignment explanation
Indices: 63489--63650 Score: 269
Period size: 65 Copynumber: 2.6 Consensus size: 65
63479 GATTTACATA
* * *
63489 TTCGCGTTGCGA--TAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATTTATTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCGAAG
63552 TTCGCGTTGCGATTTATTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATTTATTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCGAAG
63617 TTCGCGTTGCGATTTATTCCAAGTT--CGTTGCGAT
1 TTCGCGTTGCGATTTATTCCAAGTTCGCGTTGCGAT
63651 AGTCCAAAAT
Statistics
Matches: 94, Mismatches: 3, Indels: 4
0.93 0.03 0.04
Matches are distributed among these distances:
63 21 0.22
65 73 0.78
ACGTcount: A:0.19, C:0.20, G:0.25, T:0.36
Consensus pattern (65 bp):
TTCGCGTTGCGATTTATTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCGAAG
Found at i:63618 original size:42 final size:42
Alignment explanation
Indices: 63572--63654 Score: 157
Period size: 42 Copynumber: 2.0 Consensus size: 42
63562 GATTTATTCC
63572 AAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCG
1 AAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCG
*
63614 AAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTC
1 AAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTC
63655 CAAAATCGCA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.36
Consensus pattern (42 bp):
AAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCG
Found at i:64404 original size:20 final size:20
Alignment explanation
Indices: 64379--64492 Score: 126
Period size: 20 Copynumber: 5.6 Consensus size: 20
64369 ACTTGGACTA
64379 TCGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
***
64399 TCGCATTGCGATAGCCGACTA-
1 TCGCATTGCGATTTAC-A-TAT
*
64420 TCGCATTGTGATTTACATAT
1 TCGCATTGCGATTTACATAT
64440 TCGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
64460 TCGCATTGCGATATT-C-TAAGT
1 TCGCATTGCGAT-TTACAT-A-T
64481 TCGCATTGCGAT
1 TCGCATTGCGAT
64493 AGTCCAAGTT
Statistics
Matches: 80, Mismatches: 8, Indels: 11
0.81 0.08 0.11
Matches are distributed among these distances:
19 3 0.04
20 47 0.59
21 28 0.35
22 2 0.03
ACGTcount: A:0.24, C:0.21, G:0.18, T:0.37
Consensus pattern (20 bp):
TCGCATTGCGATTTACATAT
Found at i:64409 original size:41 final size:41
Alignment explanation
Indices: 64374--64451 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
64364 TGCGAACTTG
64374 GACTATCGCATTGCGATTTACATATTCGCATTGCGATAGCC
1 GACTATCGCATTGCGATTTACATATTCGCATTGCGATAGCC
*
64415 GACTATCGCATTGTGATTTACATATTCGCATTGCGAT
1 GACTATCGCATTGCGATTTACATATTCGCATTGCGAT
64452 TTACATATTC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.24, C:0.22, G:0.19, T:0.35
Consensus pattern (41 bp):
GACTATCGCATTGCGATTTACATATTCGCATTGCGATAGCC
Found at i:64425 original size:21 final size:21
Alignment explanation
Indices: 64342--64427 Score: 63
Period size: 21 Copynumber: 4.1 Consensus size: 21
64332 CCACCAGTCG
*
64342 TTGCGATAGTCGACTATCGCA
1 TTGCGATAGCCGACTATCGCA
* *
64363 ATGCGA-A-CTTGGACTATCGCA
1 TTGCGATAGC--CGACTATCGCA
***
64384 TTGCGATTTAC-A-TATTCGCA
1 TTGCGATAGCCGACTA-TCGCA
64404 TTGCGATAGCCGACTATCGCA
1 TTGCGATAGCCGACTATCGCA
64425 TTG
1 TTG
64428 TGATTTACAT
Statistics
Matches: 48, Mismatches: 10, Indels: 14
0.67 0.14 0.19
Matches are distributed among these distances:
19 2 0.04
20 15 0.31
21 29 0.60
22 2 0.04
ACGTcount: A:0.24, C:0.23, G:0.22, T:0.30
Consensus pattern (21 bp):
TTGCGATAGCCGACTATCGCA
Found at i:64485 original size:21 final size:20
Alignment explanation
Indices: 64459--64533 Score: 105
Period size: 21 Copynumber: 3.6 Consensus size: 20
64449 GATTTACATA
*
64459 TTCGCATTGCGATATTCTAAG
1 TTCGCATTGCGATAGTC-AAG
64480 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGT-CAAG
64501 TTCGCATTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTC-AAG
*
64522 TTCGCGTTGCGA
1 TTCGCATTGCGA
64534 ATCTGGAAAC
Statistics
Matches: 50, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
20 1 0.02
21 48 0.96
22 1 0.02
ACGTcount: A:0.21, C:0.21, G:0.25, T:0.32
Consensus pattern (20 bp):
TTCGCATTGCGATAGTCAAG
Found at i:69333 original size:12 final size:12
Alignment explanation
Indices: 69318--69353 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
69308 AATGTCTAAT
69318 TAAAATTTAAGA
1 TAAAATTTAAGA
69330 TAAAATTTAAGA
1 TAAAATTTAAGA
* *
69342 TTAATTTTAAGA
1 TAAAATTTAAGA
69354 ACTTCAAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.53, C:0.00, G:0.08, T:0.39
Consensus pattern (12 bp):
TAAAATTTAAGA
Found at i:75604 original size:21 final size:21
Alignment explanation
Indices: 75574--75627 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
75564 GATTTACATA
*
75574 TTCGCATTGCGATAGACCAAG
1 TTCGCGTTGCGATAGACCAAG
* * *
75595 TTCGTGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGACCAAG
75616 TTCGCGTTGCGA
1 TTCGCGTTGCGA
75628 ATCTGGAAAC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.30
Consensus pattern (21 bp):
TTCGCGTTGCGATAGACCAAG
Found at i:75668 original size:21 final size:21
Alignment explanation
Indices: 75642--75837 Score: 90
Period size: 21 Copynumber: 9.3 Consensus size: 21
75632 GGAAACTGAT
*
75642 TTGCGATAGTCGAAGTTCGCG
1 TTGCGATAGTCCAAGTTCGCG
* *
75663 TTGCGATTTATTACACA-TT--CG
1 TTGCGA--TAGTCCA-AGTTCGCG
*
75684 TTGCGATAGTCTAAGTTCGCG
1 TTGCGATAGTCCAAGTTCGCG
* *
75705 TTGCGATTTATTCCAAATT--CG
1 TTGCGA--TAGTCCAAGTTCGCG
*
75726 TTGCGATTTATTCCAAGTT--CG
1 TTGCGA--TAGTCCAAGTTCGCG
* *
75747 TTGCGATTTATTCAAAGTT--CG
1 TTGCGA--TAGTCCAAGTTCGCG
*
75768 TTGCGATAGTCGAAGTTCGCG
1 TTGCGATAGTCCAAGTTCGCG
* *
75789 TTGCGATTTATTCCAAATT--CG
1 TTGCGA--TAGTCCAAGTTCGCG
*
75810 TTGCGATAGTTCAAGTTCGCG
1 TTGCGATAGTCCAAGTTCGCG
*
75831 TTACGAT
1 TTGCGAT
75838 TTATTCCAAG
Statistics
Matches: 141, Mismatches: 20, Indels: 28
0.75 0.11 0.15
Matches are distributed among these distances:
18 1 0.01
19 23 0.16
21 94 0.67
23 22 0.16
24 1 0.01
ACGTcount: A:0.21, C:0.18, G:0.22, T:0.38
Consensus pattern (21 bp):
TTGCGATAGTCCAAGTTCGCG
Found at i:75701 original size:42 final size:42
Alignment explanation
Indices: 75600--75862 Score: 299
Period size: 42 Copynumber: 6.3 Consensus size: 42
75590 CCAAGTTCGT
** *
75600 GTTGCGATAGTCGAAGTTCGCGTTGCGA---ATCTGGAAACT-
1 GTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT-TCCAAATTC
* *
75639 GATTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTACACATTC
1 G--TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTC
*
75683 GTTGCGATAGTCTAAGTTCGCGTTGCGATTTATTCCAAATTC
1 GTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTC
* *
75725 GTTGCGATTTATTCCAAGTT--CGTTGCGATTTATT-CAAAGTTC
1 GTTGCGA--TAGTCGAAGTTCGCGTTGCGATTTATTCCAAA-TTC
75767 GTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTC
1 GTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTC
* * *
75809 GTTGCGATAGTTC-AAGTTCGCGTTACGATTTATTCCAAGTTT
1 GTTGCGATAG-TCGAAGTTCGCGTTGCGATTTATTCCAAATTC
*
75851 GTTGCTATAGTC
1 GTTGCGATAGTC
75863 CAAAATCGCA
Statistics
Matches: 196, Mismatches: 15, Indels: 24
0.83 0.06 0.10
Matches are distributed among these distances:
39 1 0.01
40 9 0.05
41 33 0.17
42 131 0.67
43 10 0.05
44 12 0.06
ACGTcount: A:0.22, C:0.18, G:0.23, T:0.37
Consensus pattern (42 bp):
GTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTC
Found at i:76742 original size:42 final size:41
Alignment explanation
Indices: 76714--76856 Score: 232
Period size: 42 Copynumber: 3.4 Consensus size: 41
76704 CTTGGAATAA
* *
76714 ATCGCAACGAATTTGGAATAAATCGCAACGTGTACTTCGACT
1 ATCGCAACGAACTTGGAATAAATCGCAACG-GAACTTCGACT
76756 ATCGCAACGAACTTGGAATAAATCGCAACGTGAACTTCGACT
1 ATCGCAACGAACTTGGAATAAATCGCAACG-GAACTTCGACT
*
76798 ATCGCAACGAACTTGGAATAAATCGCAACGTGTACTTCGACT
1 ATCGCAACGAACTTGGAATAAATCGCAACG-GAACTTCGACT
76840 ATCGCAACGAACTTGGA
1 ATCGCAACGAACTTGGA
76857 CTATCGCAAC
Statistics
Matches: 98, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 98 1.00
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.23
Consensus pattern (41 bp):
ATCGCAACGAACTTGGAATAAATCGCAACGGAACTTCGACT
Found at i:76823 original size:63 final size:61
Alignment explanation
Indices: 76693--76900 Score: 190
Period size: 63 Copynumber: 3.3 Consensus size: 61
76683 ATTTTGGACT
* * * * *
76693 ATCGCAACGAACTTGGAATAAATCGCAACGAATTTGGAATAAATCGCAACGTGTACTTCGACT--
1 ATCGCAACGAACTTGGAATAAATCGCAACGAACTTGGACT--ATCGCAAC--GAACTTGGAATAA
*
76756 ATCGCAACGAACTTGGAATAAATCGCAACGTGAACTTCGACTATCGCAACGAACTTGGAATAA
1 ATCGCAACGAACTTGGAATAAATCGCAAC--GAACTTGGACTATCGCAACGAACTTGGAATAA
* * * *
76819 ATCGCAACGTGTACTTCGACT--ATCGCAACGAACTTGGACTATCGCAACGCGAATTTGGAATAA
1 ATCGCAAC--GAACTTGGAATAAATCGCAACGAACTTGGACTATCGCAA--CGAACTTGGAATAA
76882 ATCGCAATGCGAACTTGGA
1 ATCGCAA--CGAACTTGGA
76901 CTATTGCAAC
Statistics
Matches: 122, Mismatches: 13, Indels: 20
0.79 0.08 0.13
Matches are distributed among these distances:
61 25 0.20
63 80 0.66
65 17 0.14
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.23
Consensus pattern (61 bp):
ATCGCAACGAACTTGGAATAAATCGCAACGAACTTGGACTATCGCAACGAACTTGGAATAA
Found at i:76877 original size:105 final size:103
Alignment explanation
Indices: 76689--76927 Score: 288
Period size: 105 Copynumber: 2.3 Consensus size: 103
76679 TGCGATTTTG
* * *
76689 GACTATCGCAACGAACTTGGAATAAATCGCAACGAATTTGGAATAAATCGCAACGTGTACTTCGA
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGAACTTCGAAT-AATCGCAACG-GAACTTCGA
*
76754 CTATCGCAACGAACTTGGAATAAATCGCAACGTGAACTTC
64 CTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
* * *
76794 GACTATCGCAACGAACTTGGAATAAATCGCAACGTGTACTTCGACT-ATCGCAAC-GAACTTGGA
1 GACTATCGCAACGAACTTGGAATAAATCGCAAC--GAACTTCGAATAATCGCAACGGAACTTCGA
* * *
76857 CTATCGCAACGCGAATTTGGAATAAATCGCAATGCGAACTTG
64 CTATCGCAA--CGAACTTGGAATAAATCGCAACGCGAACTTC
* *
76899 GACTATTGCAACGAATTTGG-A-AAATCGCA
1 GACTATCGCAACGAACTTGGAATAAATCGCA
76928 TTGCGATAGT
Statistics
Matches: 118, Mismatches: 12, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
103 24 0.20
104 1 0.01
105 86 0.73
107 7 0.06
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.23
Consensus pattern (103 bp):
GACTATCGCAACGAACTTGGAATAAATCGCAACGAACTTCGAATAATCGCAACGGAACTTCGACT
ATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
Found at i:76886 original size:42 final size:41
Alignment explanation
Indices: 76693--76900 Score: 197
Period size: 42 Copynumber: 4.9 Consensus size: 41
76683 ATTTTGGACT
* *
76693 ATCGCAA--CGAACTTGGAATAAATCGCAACGAATTTGGAATAA
1 ATCGCAACGCGAACTTCGAAT--ATCGCAACGAACTTGGAAT-A
* * *
76735 ATCGCAACGTGTACTTCGACTATCGCAACGAACTTGGAATAA
1 ATCGCAACGCGAACTTCGAATATCGCAACGAACTTGGAAT-A
* *
76777 ATCGCAACGTGAACTTCGACTATCGCAACGAACTTGGAATAA
1 ATCGCAACGCGAACTTCGAATATCGCAACGAACTTGGAAT-A
* * * *
76819 ATCGCAACGTGTACTTCGACTATCGCAACGAACTTGGACT-
1 ATCGCAACGCGAACTTCGAATATCGCAACGAACTTGGAATA
* *
76859 ATCGCAACGCGAATTTGGAATAAATCGCAATGCGAACTTGGA
1 ATCGCAACGCGAACTTCGAAT--ATCGCAA--CGAACTTGGA
76901 CTATTGCAAC
Statistics
Matches: 147, Mismatches: 13, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
40 16 0.11
42 113 0.77
44 18 0.12
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.23
Consensus pattern (41 bp):
ATCGCAACGCGAACTTCGAATATCGCAACGAACTTGGAATA
Found at i:76886 original size:84 final size:84
Alignment explanation
Indices: 76686--76900 Score: 312
Period size: 84 Copynumber: 2.6 Consensus size: 84
76676 CGTTGCGATT
*
76686 TTGGACTATCGCAA--CGAACTTGGAATAAATCGCAACGAATTTGGAATAAATCGCAACGTGTAC
1 TTGGACTATCGCAACGCGAACTTGGAATAAATCGCAACGAACTTGGAATAAATCGCAACGTGTAC
76749 TTCGACTATCGCAACGAAC
66 TTCGACTATCGCAACGAAC
* * * *
76768 TTGGAATAAATCGCAACGTGAACTTCGACT--ATCGCAACGAACTTGGAATAAATCGCAACGTGT
1 TTGGACT--ATCGCAACGCGAACTTGGAATAAATCGCAACGAACTTGGAATAAATCGCAACGTGT
76831 ACTTCGACTATCGCAACGAAC
64 ACTTCGACTATCGCAACGAAC
*
76852 TTGGACTATCGCAACGCGAATTTGGAATAAATCGCAATGCGAACTTGGA
1 TTGGACTATCGCAACGCGAACTTGGAATAAATCGCAA--CGAACTTGGA
76901 CTATTGCAAC
Statistics
Matches: 115, Mismatches: 10, Indels: 12
0.84 0.07 0.09
Matches are distributed among these distances:
82 23 0.20
84 73 0.63
86 19 0.17
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.23
Consensus pattern (84 bp):
TTGGACTATCGCAACGCGAACTTGGAATAAATCGCAACGAACTTGGAATAAATCGCAACGTGTAC
TTCGACTATCGCAACGAAC
Found at i:76899 original size:44 final size:40
Alignment explanation
Indices: 76840--76933 Score: 120
Period size: 44 Copynumber: 2.3 Consensus size: 40
76830 TACTTCGACT
76840 ATCGCAA--CGAACTTGGACTATCGCAACGCGAATTTGGAATAA
1 ATCGCAATGCGAACTTGGACTATCGCAA--CGAATTTGG-A-AA
*
76882 ATCGCAATGCGAACTTGGACTATTGCAACGAATTTGGAAA
1 ATCGCAATGCGAACTTGGACTATCGCAACGAATTTGGAAA
*
76922 ATCGCATTGCGA
1 ATCGCAATGCGA
76934 TAGTCGAAGT
Statistics
Matches: 48, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
40 13 0.27
41 1 0.02
42 16 0.33
44 18 0.38
ACGTcount: A:0.34, C:0.20, G:0.22, T:0.23
Consensus pattern (40 bp):
ATCGCAATGCGAACTTGGACTATCGCAACGAATTTGGAAA
Found at i:76903 original size:63 final size:60
Alignment explanation
Indices: 76756--76919 Score: 177
Period size: 63 Copynumber: 2.6 Consensus size: 60
76746 TACTTCGACT
* *
76756 ATCGCAA-CGAACTTGGAATAAATCGCAACGTGAACTTCGACTATCGCAACGAACTTGGAATAA
1 ATCGCAAGCGAACTTGGACT--ATCGCAAC--GAACTTGGACTATCGCAACGAACTTGGAATAA
* * * *
76819 ATCGCAACGTGTACTTCGACTATCGCAACGAACTTGGACTATCGCAACGCGAATTTGGAATAA
1 ATCGCAA-GCGAACTTGGACTATCGCAACGAACTTGGACTATCGCAA--CGAACTTGGAATAA
* *
76882 ATCGCAATGCGAACTTGGACTATTGCAACGAATTTGGA
1 ATCGCAA-GCGAACTTGGACTATCGCAACGAACTTGGA
76920 AAATCGCATT
Statistics
Matches: 85, Mismatches: 12, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
61 17 0.20
63 60 0.71
65 8 0.09
ACGTcount: A:0.34, C:0.22, G:0.21, T:0.23
Consensus pattern (60 bp):
ATCGCAAGCGAACTTGGACTATCGCAACGAACTTGGACTATCGCAACGAACTTGGAATAA
Found at i:76918 original size:19 final size:20
Alignment explanation
Indices: 76686--76919 Score: 138
Period size: 21 Copynumber: 11.2 Consensus size: 20
76676 CGTTGCGATT
76686 TTGGACTATCGCAA-CGAAC
1 TTGGACTATCGCAAGCGAAC
* *
76705 TTGGAATAAATCGCAA-CGAAT
1 TTGGACT--ATCGCAAGCGAAC
* * *
76726 TTGGAATAAATCGCAACGTGTAC
1 TTGGACT--ATCGCAA-GCGAAC
*
76749 TTCGACTATCGCAA-CGAAC
1 TTGGACTATCGCAAGCGAAC
* *
76768 TTGGAATAAATCGCAACGTGAAC
1 TTGGACT--ATCGCAA-GCGAAC
*
76791 TTCGACTATCGCAA-CGAAC
1 TTGGACTATCGCAAGCGAAC
* * *
76810 TTGGAATAAATCGCAACGTGTAC
1 TTGGACT--ATCGCAA-GCGAAC
*
76833 TTCGACTATCGCAA-CGAAC
1 TTGGACTATCGCAAGCGAAC
*
76852 TTGGACTATCGCAACGCGAAT
1 TTGGACTATCGCAA-GCGAAC
*
76873 TTGGAATAAATCGCAATGCGAAC
1 TTGGACT--ATCGCAA-GCGAAC
* *
76896 TTGGACTATTGCAA-CGAAT
1 TTGGACTATCGCAAGCGAAC
76915 TTGGA
1 TTGGA
76920 AAATCGCATT
Statistics
Matches: 168, Mismatches: 31, Indels: 32
0.73 0.13 0.14
Matches are distributed among these distances:
19 48 0.29
21 78 0.46
23 42 0.25
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.24
Consensus pattern (20 bp):
TTGGACTATCGCAAGCGAAC
Found at i:76952 original size:21 final size:21
Alignment explanation
Indices: 76923--76975 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
76913 ATTTGGAAAA
*
76923 TCGCATTGCGATAGTCGAAGT
1 TCGCGTTGCGATAGTCGAAGT
*
76944 TCGCGTTGCGATAGTCGATGT
1 TCGCGTTGCGATAGTCGAAGT
76965 TCGCGTTGCGA
1 TCGCGTTGCGA
76976 ATCTGGAACT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.17, C:0.21, G:0.32, T:0.30
Consensus pattern (21 bp):
TCGCGTTGCGATAGTCGAAGT
Found at i:77344 original size:15 final size:15
Alignment explanation
Indices: 77320--77361 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
77310 TATTTTTTTG
*
77320 TAAAATTAAT-ATAAA
1 TAAAAATAATAAT-AA
77335 TAAAAATAATAATAA
1 TAAAAATAATAATAA
*
77350 TAATAATAATAA
1 TAAAAATAATAA
77362 ACCGGACAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 22 0.92
16 2 0.08
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
TAAAAATAATAATAA
Done.