Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006309.1 Hibiscus syriacus cultivar Beakdansim tig00015073_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: 59260
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:192 original size:22 final size:22
Alignment explanation
Indices: 163--216 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
153 AATTTGGAAA
163 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
* *
185 TTCGCAACAACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
207 ATCGCAACGA
1 ATCGCAACGA
217 ATTTGGAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.37, C:0.28, G:0.17, T:0.19
Consensus pattern (22 bp):
ATCGCAACGACAACTGTAGACT
Found at i:229 original size:19 final size:18
Alignment explanation
Indices: 207--332 Score: 90
Period size: 20 Copynumber: 6.5 Consensus size: 18
197 ACTGTAGACT
*
207 ATCGCAACGAATTTGGAAA
1 ATCGCAACGAA-ATGGAAA
* **
226 ATCGCAACGACATTGGACT
1 ATCGCAACGA-AATGGAAA
*
245 ATCGCAACGCGAAATGAAAA
1 ATCGCAA--CGAAATGGAAA
265 ATCGCAACGCGAAATGGAAA
1 ATCGCAA--CGAAATGGAAA
*
285 ATCGCAACGAGAATGAAAA
1 ATCGCAACGA-AATGGAAA
* *
304 ATCGAAACGCGAACTGGAAA
1 ATCGCAA--CGAAATGGAAA
*
324 ATCGAAACG
1 ATCGCAACG
333 CGATTTCAAC
Statistics
Matches: 90, Mismatches: 11, Indels: 13
0.79 0.10 0.11
Matches are distributed among these distances:
18 5 0.06
19 35 0.39
20 44 0.49
21 6 0.07
ACGTcount: A:0.44, C:0.20, G:0.22, T:0.13
Consensus pattern (18 bp):
ATCGCAACGAAATGGAAA
Found at i:270 original size:20 final size:20
Alignment explanation
Indices: 245--359 Score: 124
Period size: 20 Copynumber: 5.8 Consensus size: 20
235 ACATTGGACT
245 ATCGCAACGCGAAATGAAAA
1 ATCGCAACGCGAAATGAAAA
*
265 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGAAAA
*
285 ATCGCAACGAG-AATGAAAA
1 ATCGCAACGCGAAATGAAAA
* * *
304 ATCGAAACGCGAACTGGAAA
1 ATCGCAACGCGAAATGAAAA
* ** * **
324 ATCGAAACGCGATTTCAACT
1 ATCGCAACGCGAAATGAAAA
344 ATCGCAACGCGAAATG
1 ATCGCAACGCGAAATG
360 CAACGCGAAT
Statistics
Matches: 77, Mismatches: 17, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
19 16 0.21
20 61 0.79
ACGTcount: A:0.44, C:0.21, G:0.22, T:0.13
Consensus pattern (20 bp):
ATCGCAACGCGAAATGAAAA
Found at i:300 original size:39 final size:39
Alignment explanation
Indices: 245--359 Score: 140
Period size: 39 Copynumber: 2.9 Consensus size: 39
235 ACATTGGACT
245 ATCGCAACGCGAAATGAAAAATCGCAACGCGAAATGGAAA
1 ATCGCAACGCG-AATGAAAAATCGCAACGCGAAATGGAAA
* * *
285 ATCGCAACGAGAATGAAAAATCGAAACGCGAACTGGAAA
1 ATCGCAACGCGAATGAAAAATCGCAACGCGAAATGGAAA
* * * **
324 ATCGAAACGCGATTTCAACTATCGCAACGCGAAATG
1 ATCGCAACGCGA-ATGAAAAATCGCAACGCGAAATG
360 CAACGCGAAT
Statistics
Matches: 63, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
39 36 0.57
40 27 0.43
ACGTcount: A:0.44, C:0.21, G:0.22, T:0.13
Consensus pattern (39 bp):
ATCGCAACGCGAATGAAAAATCGCAACGCGAAATGGAAA
Found at i:313 original size:59 final size:59
Alignment explanation
Indices: 220--335 Score: 151
Period size: 59 Copynumber: 2.0 Consensus size: 59
210 GCAACGAATT
* * ** * *
220 TGGAAAATCGCAACGACATTGGACTATCGCAACGCGAAATGAAAAATCGCAACGCGAAA
1 TGGAAAATCGCAACGACAATGAAAAATCGAAACGCGAAATGAAAAATCGAAACGCGAAA
* * *
279 TGGAAAATCGCAACGAGAATGAAAAATCGAAACGCGAACTGGAAAATCGAAACGCGA
1 TGGAAAATCGCAACGACAATGAAAAATCGAAACGCGAAATGAAAAATCGAAACGCGA
336 TTTCAACTAT
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
59 48 1.00
ACGTcount: A:0.45, C:0.20, G:0.23, T:0.12
Consensus pattern (59 bp):
TGGAAAATCGCAACGACAATGAAAAATCGAAACGCGAAATGAAAAATCGAAACGCGAAA
Found at i:1062 original size:2 final size:2
Alignment explanation
Indices: 1055--1081 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1045 CAGATCGGTC
1055 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1082 CAATGTATGA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:16016 original size:15 final size:16
Alignment explanation
Indices: 15987--16033 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 16
15977 TATAAGGTAA
*
15987 TTTTGTTATAA-TATT
1 TTTTATTATAATTATT
*
16002 TTTTA-TATACTTATT
1 TTTTATTATAATTATT
*
16017 GTTTATTATAATTATT
1 TTTTATTATAATTATT
16033 T
1 T
16034 GAAAAAATAT
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
14 4 0.16
15 12 0.48
16 9 0.36
ACGTcount: A:0.28, C:0.02, G:0.04, T:0.66
Consensus pattern (16 bp):
TTTTATTATAATTATT
Found at i:16031 original size:16 final size:16
Alignment explanation
Indices: 15992--16032 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
15982 GGTAATTTTG
*
15992 TTATAA-TATTTTTTA
1 TTATAATTATTGTTTA
*
16007 -TATACTTATTGTTTA
1 TTATAATTATTGTTTA
16022 TTATAATTATT
1 TTATAATTATT
16033 TGAAAAAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
14 4 0.19
15 8 0.38
16 9 0.43
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.63
Consensus pattern (16 bp):
TTATAATTATTGTTTA
Found at i:16269 original size:24 final size:24
Alignment explanation
Indices: 16242--16298 Score: 96
Period size: 24 Copynumber: 2.3 Consensus size: 24
16232 ATAATATTGT
16242 CGCACTTTTAAACTCTAAGAATGA
1 CGCACTTTTAAACTCTAAGAATGA
*
16266 CGCACTTTTAAACTCTAAGAATGG
1 CGCACTTTTAAACTCTAAGAATGA
16290 CGCGACTTT
1 CGC-ACTTT
16299 CAGCTATTGT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
24 26 0.84
25 5 0.16
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.30
Consensus pattern (24 bp):
CGCACTTTTAAACTCTAAGAATGA
Found at i:19507 original size:35 final size:34
Alignment explanation
Indices: 19468--19556 Score: 99
Period size: 34 Copynumber: 2.6 Consensus size: 34
19458 AATGGTAATA
* *
19468 AACAAAATTAACCAAAATACATTAACAAA-AAGTCC
1 AACAAAATTAA-CAAAATAAATTAA-AAATAAATCC
*
19503 AACAAATTTAACAAAATAAATTAAAAATAAATCC
1 AACAAAATTAACAAAATAAATTAAAAATAAATCC
* **
19537 AACCAAATTAATGAAATAAA
1 AACAAAATTAACAAAATAAA
19557 GTAAGTATTA
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
33 3 0.07
34 33 0.72
35 10 0.22
ACGTcount: A:0.63, C:0.15, G:0.02, T:0.20
Consensus pattern (34 bp):
AACAAAATTAACAAAATAAATTAAAAATAAATCC
Found at i:23207 original size:22 final size:22
Alignment explanation
Indices: 23182--23226 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
23172 TGATCATATG
23182 TACGTTGCTGTTTAGCCTGAAT
1 TACGTTGCTGTTTAGCCTGAAT
23204 TACGTTGCTGTTTAGCCTGAAT
1 TACGTTGCTGTTTAGCCTGAAT
23226 T
1 T
23227 GTTCCATACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.18, C:0.18, G:0.22, T:0.42
Consensus pattern (22 bp):
TACGTTGCTGTTTAGCCTGAAT
Found at i:25439 original size:20 final size:20
Alignment explanation
Indices: 25416--25460 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
25406 CTCCAATTTT
*
25416 GCAATGCGAATCTATAAATC
1 GCAACGCGAATCTATAAATC
*
25436 GCAACGCGAATCTGTAAATC
1 GCAACGCGAATCTATAAATC
25456 GCAAC
1 GCAAC
25461 ACAAAGTCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.20
Consensus pattern (20 bp):
GCAACGCGAATCTATAAATC
Found at i:25490 original size:20 final size:20
Alignment explanation
Indices: 25454--25592 Score: 131
Period size: 20 Copynumber: 7.0 Consensus size: 20
25444 AATCTGTAAA
*
25454 TCGCAACAC-AAAGTCAAAT
1 TCGCAACGCGAAAGTCAAAT
* *
25473 TCGCAACGTGATAGTCAAAT
1 TCGCAACGCGAAAGTCAAAT
* *
25493 TCGCAACACAAAAGTCAAAT
1 TCGCAACGCGAAAGTCAAAT
*
25513 TCGCAACGCGAATTTGT-AAA-
1 TCGCAACGCGAA--AGTCAAAT
* *
25533 TCGCAACACAAAAGTCAAAT
1 TCGCAACGCGAAAGTCAAAT
** * *
25553 TTACAATGCGATAGTCAAAT
1 TCGCAACGCGAAAGTCAAAT
25573 TCGCAACGCGAAAGTCAAAT
1 TCGCAACGCGAAAGTCAAAT
25593 GTTTTTACGC
Statistics
Matches: 92, Mismatches: 23, Indels: 9
0.74 0.19 0.07
Matches are distributed among these distances:
18 2 0.02
19 10 0.11
20 75 0.82
21 3 0.03
22 2 0.02
ACGTcount: A:0.42, C:0.22, G:0.15, T:0.20
Consensus pattern (20 bp):
TCGCAACGCGAAAGTCAAAT
Found at i:25518 original size:40 final size:40
Alignment explanation
Indices: 25454--25592 Score: 176
Period size: 40 Copynumber: 3.5 Consensus size: 40
25444 AATCTGTAAA
*
25454 TCGCAACAC-AAAGTCAAATTCGCAACGTGATAGTCAAAT
1 TCGCAACACAAAAGTCAAATTCGCAACGCGATAGTCAAAT
*
25493 TCGCAACACAAAAGTCAAATTCGCAACGCGAATTTGT-AAA-
1 TCGCAACACAAAAGTCAAATTCGCAACGCG-A-TAGTCAAAT
** *
25533 TCGCAACACAAAAGTCAAATTTACAATGCGATAGTCAAAT
1 TCGCAACACAAAAGTCAAATTCGCAACGCGATAGTCAAAT
* *
25573 TCGCAACGCGAAAGTCAAAT
1 TCGCAACACAAAAGTCAAAT
25593 GTTTTTACGC
Statistics
Matches: 87, Mismatches: 8, Indels: 9
0.84 0.08 0.09
Matches are distributed among these distances:
38 3 0.03
39 13 0.15
40 64 0.74
41 4 0.05
42 3 0.03
ACGTcount: A:0.42, C:0.22, G:0.15, T:0.20
Consensus pattern (40 bp):
TCGCAACACAAAAGTCAAATTCGCAACGCGATAGTCAAAT
Found at i:25587 original size:80 final size:79
Alignment explanation
Indices: 25434--25592 Score: 246
Period size: 80 Copynumber: 2.0 Consensus size: 79
25424 AATCTATAAA
* *
25434 TCGCAACGCGAATCTGTAAATCGCAACACAAAGTCAAATTCGCAACGTGATAGTCAAATTCGCAA
1 TCGCAACGCGAATCTGTAAATCGCAACACAAAGTCAAATTCACAACGCGATAGTCAAATTCGCAA
25499 CACAAAAGTCAAAT
66 CACAAAAGTCAAAT
* * *
25513 TCGCAACGCGAATTTGTAAATCGCAACACAAAAGTCAAATTTACAATGCGATAGTCAAATTCGCA
1 TCGCAACGCGAATCTGTAAATCGCAACAC-AAAGTCAAATTCACAACGCGATAGTCAAATTCGCA
* *
25578 ACGCGAAAGTCAAAT
65 ACACAAAAGTCAAAT
25593 GTTTTTACGC
Statistics
Matches: 72, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
79 28 0.39
80 44 0.61
ACGTcount: A:0.42, C:0.23, G:0.16, T:0.20
Consensus pattern (79 bp):
TCGCAACGCGAATCTGTAAATCGCAACACAAAGTCAAATTCACAACGCGATAGTCAAATTCGCAA
CACAAAAGTCAAAT
Found at i:26103 original size:20 final size:20
Alignment explanation
Indices: 26068--26150 Score: 132
Period size: 20 Copynumber: 4.2 Consensus size: 20
26058 AAATCGCAAC
*
26068 GCGATTTT-AGTTTCGCGTT
1 GCGATTTTCATTTTCGCGTT
26087 GCGATTTTCATTTTCGCGTT
1 GCGATTTTCATTTTCGCGTT
*
26107 GCGATTTTCATTTTTGCGTT
1 GCGATTTTCATTTTCGCGTT
*
26127 GCGATTTTCATTTTTGCGTT
1 GCGATTTTCATTTTCGCGTT
26147 GCGA
1 GCGA
26151 ATTTAAGTTT
Statistics
Matches: 61, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
19 8 0.13
20 53 0.87
ACGTcount: A:0.11, C:0.17, G:0.23, T:0.49
Consensus pattern (20 bp):
GCGATTTTCATTTTCGCGTT
Found at i:26129 original size:40 final size:39
Alignment explanation
Indices: 26068--26161 Score: 134
Period size: 40 Copynumber: 2.4 Consensus size: 39
26058 AAATCGCAAC
26068 GCGATTTTAGTTTCGCGTTGCGATTTTCATTTTCGCGTT
1 GCGATTTTAGTTTCGCGTTGCGATTTTCATTTTCGCGTT
* * *
26107 GCGATTTTCATTTTTGCGTTGCGATTTTCATTTTTGCGTT
1 GCGATTTT-AGTTTCGCGTTGCGATTTTCATTTTCGCGTT
*
26147 GCGAATTTAAGTTTC
1 GCG-ATTTTAGTTTC
26162 AGAAACTTCT
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
39 8 0.17
40 35 0.74
41 4 0.09
ACGTcount: A:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (39 bp):
GCGATTTTAGTTTCGCGTTGCGATTTTCATTTTCGCGTT
Found at i:29861 original size:62 final size:63
Alignment explanation
Indices: 29760--29900 Score: 205
Period size: 66 Copynumber: 2.2 Consensus size: 63
29750 TTTTACATTG
*
29760 AAAGTTGATTTGTTTAATTGATGAGGAAATAAGATTTA-TTTTT-TTGATTAATTGATTTGTA
1 AAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTCTTGATTAATTGATTTGTA
* * *
29821 AAAGTTGATTTGTTTAATTTGATGTGTAAATAAGAATTATTTTTTTGCTTGTTTAATTGATTTGT
1 AAAGTTGATTTGTTTAA-TTGATGAGGAAATAAGAATTA-TTTTTT-CTTGATTAATTGATTTGT
29886 A
63 A
29887 AAAGTTGATTTGTT
1 AAAGTTGATTTGTT
29901 GTTTCTAAAA
Statistics
Matches: 71, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
61 17 0.24
62 18 0.25
64 5 0.07
66 31 0.44
ACGTcount: A:0.30, C:0.01, G:0.18, T:0.51
Consensus pattern (63 bp):
AAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTCTTGATTAATTGATTTGTA
Found at i:30054 original size:34 final size:34
Alignment explanation
Indices: 30016--30109 Score: 170
Period size: 34 Copynumber: 2.8 Consensus size: 34
30006 TGAATTTGAC
30016 TTTCGCGTTGCGAATTTGACTATCGCAACGCTTA
1 TTTCGCGTTGCGAATTTGACTATCGCAACGCTTA
30050 TTTCGCGTTGCGAATTTGACTATCGCAACGCTTA
1 TTTCGCGTTGCGAATTTGACTATCGCAACGCTTA
* *
30084 TTTCGCGTTGCAAATTTGACTTTCGC
1 TTTCGCGTTGCGAATTTGACTATCGC
30110 GTTGATCGCA
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 58 1.00
ACGTcount: A:0.19, C:0.23, G:0.20, T:0.37
Consensus pattern (34 bp):
TTTCGCGTTGCGAATTTGACTATCGCAACGCTTA
Found at i:30343 original size:39 final size:39
Alignment explanation
Indices: 30289--30375 Score: 147
Period size: 39 Copynumber: 2.2 Consensus size: 39
30279 TCAAGTTGTA
30289 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
* *
30328 GATTTTGATTTCCTTTTGTTTGGCACCATATGAGCTTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
*
30367 GATTCTGAT
1 GATTTTGAT
30376 GAGCATCGGA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 45 1.00
ACGTcount: A:0.17, C:0.15, G:0.21, T:0.47
Consensus pattern (39 bp):
GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
Found at i:31193 original size:20 final size:20
Alignment explanation
Indices: 31144--31207 Score: 67
Period size: 20 Copynumber: 3.2 Consensus size: 20
31134 AAATAATGTA
* *
31144 CAACTTGAAAGTTAAATTCG
1 CAACATGAAAGTCAAATTCG
*
31164 CAACACGAAAGTCAAATTCG
1 CAACATGAAAGTCAAATTCG
**
31184 CAATGTGAAA-TCCAAATTCG
1 CAACATGAAAGT-CAAATTCG
31204 CAAC
1 CAAC
31208 GCGATTTTCG
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
19 1 0.03
20 35 0.97
ACGTcount: A:0.42, C:0.22, G:0.14, T:0.22
Consensus pattern (20 bp):
CAACATGAAAGTCAAATTCG
Found at i:31292 original size:20 final size:20
Alignment explanation
Indices: 31267--31336 Score: 122
Period size: 20 Copynumber: 3.5 Consensus size: 20
31257 GTAATGCTTA
31267 TTTCGCGTTGCGAATTTGAC
1 TTTCGCGTTGCGAATTTGAC
31287 TTTCGCGTTGCGAATTTGAC
1 TTTCGCGTTGCGAATTTGAC
*
31307 TTTCGCGTTGCGAATTTAAC
1 TTTCGCGTTGCGAATTTGAC
*
31327 TTTCACGTTG
1 TTTCGCGTTG
31337 ATCGCAACAT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.16, C:0.20, G:0.23, T:0.41
Consensus pattern (20 bp):
TTTCGCGTTGCGAATTTGAC
Found at i:31645 original size:18 final size:18
Alignment explanation
Indices: 31622--31657 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
31612 AAGCCGTTTG
* *
31622 TGATTGGGATTTTGATTT
1 TGATTGCGAGTTTGATTT
31640 TGATTGCGAGTTTGATTT
1 TGATTGCGAGTTTGATTT
31658 CCTTTTGCTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.03, G:0.28, T:0.53
Consensus pattern (18 bp):
TGATTGCGAGTTTGATTT
Found at i:33946 original size:24 final size:24
Alignment explanation
Indices: 33919--33972 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
33909 CCATCACATC
* * *
33919 ATCAAAATCCGAGTGTTCCCCAAG
1 ATCAAAATACGAGTATTCACCAAG
* *
33943 ATCAAAGTACGAGTATTGACCAAG
1 ATCAAAATACGAGTATTCACCAAG
33967 ATCAAA
1 ATCAAA
33973 TTTTGAATAC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.41, C:0.22, G:0.17, T:0.20
Consensus pattern (24 bp):
ATCAAAATACGAGTATTCACCAAG
Found at i:34119 original size:12 final size:12
Alignment explanation
Indices: 34098--34131 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
34088 GGTTGTGGGT
*
34098 TTTGAGATTGTG
1 TTTGATATTGTG
34110 TTTGATATTGTG
1 TTTGATATTGTG
*
34122 TTTGGTATTG
1 TTTGATATTG
34132 GAAATGTGGC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:40643 original size:21 final size:22
Alignment explanation
Indices: 40597--40655 Score: 68
Period size: 21 Copynumber: 2.7 Consensus size: 22
40587 ACCCTCATGA
*
40597 GGGAACCGATT-CCCCTTTGAAG
1 GGGAACCGATTCCCCCCTT-AAG
40619 GGGAACCGATTCCCCCCTT-AG
1 GGGAACCGATTCCCCCCTTAAG
* *
40640 GGGAATCGATACCCCC
1 GGGAACCGATTCCCCC
40656 TGGGGTTCTG
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
21 16 0.48
22 11 0.33
23 6 0.18
ACGTcount: A:0.22, C:0.34, G:0.25, T:0.19
Consensus pattern (22 bp):
GGGAACCGATTCCCCCCTTAAG
Found at i:44492 original size:19 final size:19
Alignment explanation
Indices: 44468--44539 Score: 117
Period size: 19 Copynumber: 3.7 Consensus size: 19
44458 ACTAAAACAT
44468 GTTGCGAATTTGAAATTCA
1 GTTGCGAATTTGAAATTCA
44487 GTTGCGAATTTGAAATTCA
1 GTTGCGAATTTGAAATTCA
*
44506 GTTGCGAATTTGAAATTCCGT
1 GTTGCGAATTTGAAATT-C-A
44527 GTTGCGAATTTGA
1 GTTGCGAATTTGA
44540 CTATCGTGTT
Statistics
Matches: 50, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
19 36 0.72
20 1 0.02
21 13 0.26
ACGTcount: A:0.28, C:0.11, G:0.24, T:0.38
Consensus pattern (19 bp):
GTTGCGAATTTGAAATTCA
Found at i:44549 original size:20 final size:20
Alignment explanation
Indices: 44527--44622 Score: 138
Period size: 20 Copynumber: 4.8 Consensus size: 20
44517 GAAATTCCGT
*
44527 GTTGCGAATTTGACTATCGT
1 GTTGCGAATTTGACTATCGC
*
44547 GTTGCGTATTTGACTATCGC
1 GTTGCGAATTTGACTATCGC
* *
44567 GTTACGAATTTTGATTATCGC
1 GTTGCGAA-TTTGACTATCGC
*
44588 GTTGCGAATTTGGCTATCGC
1 GTTGCGAATTTGACTATCGC
44608 GTTGCGAATTTGACT
1 GTTGCGAATTTGACT
44623 TCTGTATTTC
Statistics
Matches: 66, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
20 48 0.73
21 18 0.27
ACGTcount: A:0.19, C:0.17, G:0.25, T:0.40
Consensus pattern (20 bp):
GTTGCGAATTTGACTATCGC
Found at i:44580 original size:41 final size:40
Alignment explanation
Indices: 44531--44622 Score: 130
Period size: 41 Copynumber: 2.3 Consensus size: 40
44521 TTCCGTGTTG
* *
44531 CGAATTTGACTATCGTGTTGCGTATTTGACTATCGCGTTA
1 CGAATTTGACTATCGCGTTGCGAATTTGACTATCGCGTTA
* * *
44571 CGAATTTTGATTATCGCGTTGCGAATTTGGCTATCGCGTTG
1 CGAA-TTTGACTATCGCGTTGCGAATTTGACTATCGCGTTA
44612 CGAATTTGACT
1 CGAATTTGACT
44623 TCTGTATTTC
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
40 10 0.22
41 35 0.78
ACGTcount: A:0.20, C:0.17, G:0.24, T:0.39
Consensus pattern (40 bp):
CGAATTTGACTATCGCGTTGCGAATTTGACTATCGCGTTA
Found at i:44691 original size:20 final size:19
Alignment explanation
Indices: 44642--44695 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
44632 CGATTTACAA
44642 ATTCGCGTTGCGAAATTGG
1 ATTCGCGTTGCGAAATTGG
** *
44661 AAACTGGGTTGCGAAATTGG
1 ATTC-GCGTTGCGAAATTGG
44681 AGTTCGCGTTGCGAA
1 A-TTCGCGTTGCGAA
44696 TTTGTTGGTC
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 2 0.07
20 24 0.89
21 1 0.04
ACGTcount: A:0.24, C:0.15, G:0.33, T:0.28
Consensus pattern (19 bp):
ATTCGCGTTGCGAAATTGG
Found at i:48549 original size:49 final size:49
Alignment explanation
Indices: 48493--48591 Score: 180
Period size: 49 Copynumber: 2.0 Consensus size: 49
48483 GATTACCAGG
*
48493 GAATAGGATTACTGGGAATGTTACATTACTGTGTTTGGTTGGTTTGGCA
1 GAATAGGATTACTAGGAATGTTACATTACTGTGTTTGGTTGGTTTGGCA
*
48542 GAATAGGATTACTAGGAATGTTATATTACTGTGTTTGGTTGGTTTGGCA
1 GAATAGGATTACTAGGAATGTTACATTACTGTGTTTGGTTGGTTTGGCA
48591 G
1 G
48592 GAATGTAAGA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.23, C:0.07, G:0.30, T:0.39
Consensus pattern (49 bp):
GAATAGGATTACTAGGAATGTTACATTACTGTGTTTGGTTGGTTTGGCA
Found at i:56433 original size:18 final size:17
Alignment explanation
Indices: 56401--56447 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 17
56391 TAAAAGTTAG
56401 ATATTATTTTA-AATAATT
1 ATATT-TTTTACAATAA-T
56419 ATATTTTTTACAATAAT
1 ATATTTTTTACAATAAT
56436 ATCATTTTTTAC
1 AT-ATTTTTTAC
56448 CTCATAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
17 8 0.30
18 19 0.70
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.55
Consensus pattern (17 bp):
ATATTTTTTACAATAAT
Found at i:57363 original size:3 final size:3
Alignment explanation
Indices: 57351--57433 Score: 143
Period size: 3 Copynumber: 28.0 Consensus size: 3
57341 ACTAGTAACT
57351 TAA T-A TAA TAA TAA TAA TAA TAA TAA -AA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
57397 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TATA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA
57434 ACAAGTTTAT
Statistics
Matches: 77, Mismatches: 0, Indels: 6
0.93 0.00 0.07
Matches are distributed among these distances:
2 4 0.05
3 70 0.91
4 3 0.04
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:58169 original size:21 final size:22
Alignment explanation
Indices: 58123--58170 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
58113 TGATAATTTT
*
58123 AAAAAAATATATAAAATTAATC
1 AAAAAAATATATAAAATTAATA
* *
58145 AAAAAAAT-TATAAATTTTATA
1 AAAAAAATATATAAAATTAATA
58166 AAAAA
1 AAAAA
58171 GAAAACACAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 15 0.65
22 8 0.35
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (22 bp):
AAAAAAATATATAAAATTAATA
Done.