Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005149.1 Hibiscus syriacus cultivar Beakdansim tig00011602_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: 63444
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:1184 original size:58 final size:61
Alignment explanation
Indices: 1064--1189 Score: 213
Period size: 58 Copynumber: 2.1 Consensus size: 61
1054 GTTACGTGAT
1064 GAGGTCAATGCCTTGCGTGAGGAGATCGGTACTCTACGCGATAACGATGGTGCATGGCGTGTG
1 GAGGTCAATGCCTTGCGTGAGGAGATC-G-ACTCTACGCGATAACGATGGTGCATGGCGTGTG
1127 GAGGTC-ATGCCTTGCGTGAGGAGATC-ACTCTACGCGAT-ACGATGGTGCATGGCGTGTG
1 GAGGTCAATGCCTTGCGTGAGGAGATCGACTCTACGCGATAACGATGGTGCATGGCGTGTG
1185 GAGGT
1 GAGGT
1190 GTCTACTTTA
Statistics
Matches: 63, Mismatches: 0, Indels: 5
0.93 0.00 0.07
Matches are distributed among these distances:
58 25 0.40
59 12 0.19
62 20 0.32
63 6 0.10
ACGTcount: A:0.20, C:0.19, G:0.37, T:0.24
Consensus pattern (61 bp):
GAGGTCAATGCCTTGCGTGAGGAGATCGACTCTACGCGATAACGATGGTGCATGGCGTGTG
Found at i:1534 original size:93 final size:89
Alignment explanation
Indices: 1353--1537 Score: 273
Period size: 93 Copynumber: 2.0 Consensus size: 89
1343 TAGATTGCTT
*
1353 AGTAAATTTATTCGGTTGCTTCCAATACTGCTAAACTGTTTATTAACAATGTGAAGTTAGTATTT
1 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAACTGTTTATTAACAATGTGAAGTTAGTATTT
*
1418 GTCTTTTTGTTTGTCTTTGGTTGA
66 GTCTTTGTGTTTGTCTTTGGTTGA
* * *
1442 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAAC--TGT-TT-ATTAACAATGTGAAGTTAGT
1507 ATTTGTCTTTGT-TTTGTCTTTTGGTTGA
62 ATTTGTCTTTGTGTTTGTC-TTTGGTTGA
1535 AGT
1 AGT
1538 TTTGAAATAT
Statistics
Matches: 86, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
89 34 0.40
91 3 0.03
92 8 0.09
93 41 0.48
ACGTcount: A:0.22, C:0.12, G:0.19, T:0.47
Consensus pattern (89 bp):
AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAACTGTTTATTAACAATGTGAAGTTAGTATTT
GTCTTTGTGTTTGTCTTTGGTTGA
Found at i:1833 original size:21 final size:21
Alignment explanation
Indices: 1809--1875 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1799 TCATTCCTCG
1809 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
1830 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
1851 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
1872 AGAG
1 AGAG
1876 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:1833 original size:42 final size:42
Alignment explanation
Indices: 1757--1875 Score: 102
Period size: 42 Copynumber: 2.8 Consensus size: 42
1747 GATTCGCCTG
* * * *
1757 TCATCCCTC-AAGA-GTCCACTCCTATCATTGAAGAGGCCCCTA
1 TCAT-CCTCGAAGAGGTCC-CTCCCACCATTCAAGAGGCCACTA
* *
1799 TCATTCCTCG-AGA-GTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCA-TCCTCGAAGAGGT-CCCTCCCACCATTCAAGAGGCCACTA
* *
1841 TCATCGTTGAAGAGGTCCCTCCCACCATTCAAGAG
1 TCATCCTCGAAGAGGTCCCTCCCACCATTCAAGAG
1876 CCCGATTCAC
Statistics
Matches: 63, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
41 4 0.06
42 54 0.86
43 5 0.08
ACGTcount: A:0.24, C:0.36, G:0.18, T:0.23
Consensus pattern (42 bp):
TCATCCTCGAAGAGGTCCCTCCCACCATTCAAGAGGCCACTA
Found at i:3237 original size:14 final size:14
Alignment explanation
Indices: 3218--3253 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
3208 ATTGTTTAAT
3218 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
3232 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
3246 TGATTTGT
1 TGATTTGT
3254 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:3395 original size:14 final size:14
Alignment explanation
Indices: 3376--3432 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
3366 GCGAAATGAA
3376 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
3390 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
3409 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
3423 AAACGCAACG
1 AATCGCAACG
3433 CGAAATTAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 19 0.54
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.46, C:0.23, G:0.25, T:0.07
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:3403 original size:33 final size:33
Alignment explanation
Indices: 3358--3447 Score: 144
Period size: 33 Copynumber: 2.7 Consensus size: 33
3348 CAAAAGTACT
*
3358 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
3391 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
* * *
3424 AACGCAACGCGAAATTAAATTCGC
1 ATCGCAACGCGAAATGAAAATCGC
3448 GTTGCGATTT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 53 1.00
ACGTcount: A:0.44, C:0.21, G:0.22, T:0.12
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
Found at i:3417 original size:19 final size:19
Alignment explanation
Indices: 3358--3418 Score: 69
Period size: 19 Copynumber: 3.5 Consensus size: 19
3348 CAAAAGTACT
*
3358 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
3377 ATCGCAA--CG--A-GAGA
1 ATCGCAACGCGAAATGAAA
3391 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
3410 ATCGCAACG
1 ATCGCAACG
3419 AGAGAAACGC
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 10 0.29
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 19 0.54
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.11
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:3489 original size:33 final size:32
Alignment explanation
Indices: 3447--3573 Score: 184
Period size: 33 Copynumber: 3.9 Consensus size: 32
3437 ATTAAATTCG
3447 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
**
3480 CGTTGCGATTTTCATTTCGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
3513 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
*
3546 CGTTGTGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
3574 AGTAATTTTC
Statistics
Matches: 85, Mismatches: 5, Indels: 8
0.87 0.05 0.08
Matches are distributed among these distances:
31 3 0.04
33 79 0.93
35 3 0.04
ACGTcount: A:0.15, C:0.22, G:0.20, T:0.43
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:3520 original size:66 final size:66
Alignment explanation
Indices: 3440--3572 Score: 239
Period size: 66 Copynumber: 2.0 Consensus size: 66
3430 ACGCGAAATT
*
3440 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
3505 G
66 G
* *
3506 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGTGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
3571 G
66 G
3572 A
1 A
3573 TAGTAATTTT
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.17, C:0.22, G:0.20, T:0.42
Consensus pattern (66 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
G
Found at i:6086 original size:24 final size:24
Alignment explanation
Indices: 6052--6105 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
6042 CTGAAACATC
* *
6052 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAG
*
6076 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGGGTATTGACCAAG
6100 ATCAAA
1 ATCAAA
6106 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGACCAAG
Found at i:7176 original size:20 final size:20
Alignment explanation
Indices: 7151--7188 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
7141 ATTCATTTGA
*
7151 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGAGAAAATGG
7171 CTATCGCAACGAGAAAAT
1 CTATCGCAACGAGAAAAT
7189 CACAATGCGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.39, C:0.24, G:0.21, T:0.16
Consensus pattern (20 bp):
CTATCGCAACGAGAAAATGG
Found at i:7231 original size:14 final size:16
Alignment explanation
Indices: 7211--7284 Score: 66
Period size: 19 Copynumber: 4.5 Consensus size: 16
7201 TGAAAATCGC
7211 ATTGCGATTTTC-TCG
1 ATTGCGATTTTCTTCG
7226 -TTGCGATTTTCATTTCG
1 ATTGCGATTTTC--TTCG
7243 CATTGCGATTTTCATTTCG
1 -ATTGCGATTTTC--TTCG
7262 CATTGCGATTTTC-TCG
1 -ATTGCGATTTTCTTCG
7278 -TTGCGAT
1 ATTGCGAT
7285 AGCCATTTCG
Statistics
Matches: 54, Mismatches: 0, Indels: 11
0.83 0.00 0.17
Matches are distributed among these distances:
14 18 0.33
16 3 0.06
17 3 0.06
19 30 0.56
ACGTcount: A:0.14, C:0.20, G:0.19, T:0.47
Consensus pattern (16 bp):
ATTGCGATTTTCTTCG
Found at i:7248 original size:19 final size:19
Alignment explanation
Indices: 7207--7274 Score: 101
Period size: 19 Copynumber: 3.8 Consensus size: 19
7197 GAAATGAAAA
7207 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
7223 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
7240 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
7259 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
7275 TCGTTGCGAT
Statistics
Matches: 47, Mismatches: 0, Indels: 7
0.87 0.00 0.13
Matches are distributed among these distances:
14 11 0.23
16 3 0.06
17 3 0.06
19 30 0.64
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.47
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:7408 original size:14 final size:14
Alignment explanation
Indices: 7389--7425 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
7379 ACATCAATTA
7389 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
7403 ACAAATCATCTTTT
1 ACAAATCAACATTT
7417 ACAAATCAA
1 ACAAATCAA
7426 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:9303 original size:20 final size:19
Alignment explanation
Indices: 9268--9323 Score: 85
Period size: 20 Copynumber: 2.9 Consensus size: 19
9258 AAAACTTAAA
9268 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
9287 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
*
9307 ATCGCAATGCGAAATGA
1 ATCGCAACGCGAAATGA
9324 AAATTGCAAC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 16 0.48
20 17 0.52
ACGTcount: A:0.36, C:0.23, G:0.25, T:0.16
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:9346 original size:14 final size:14
Alignment explanation
Indices: 9323--9417 Score: 84
Period size: 14 Copynumber: 6.3 Consensus size: 14
9313 ATGCGAAATG
*
9323 AAAATTGCAACGAC
1 AAAATCGCAACGAC
*
9337 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
9353 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
*
9369 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
9385 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
9401 AAAATCGCAACG-C
1 AAAATCGCAACGAC
9414 AAAA
1 AAAA
9418 CACAAATCGC
Statistics
Matches: 68, Mismatches: 5, Indels: 17
0.76 0.06 0.19
Matches are distributed among these distances:
13 5 0.07
14 29 0.43
16 16 0.24
18 18 0.26
ACGTcount: A:0.49, C:0.24, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:9370 original size:32 final size:32
Alignment explanation
Indices: 9307--9413 Score: 187
Period size: 32 Copynumber: 3.3 Consensus size: 32
9297 GGAAATGGCT
* *
9307 ATCGCAATGCGAAATGAAAATTGCAACGACAAA
1 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
9340 ATCGCAACGCGAAATGAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAATCGCAACGACAAA
9372 ATCGCAACGCGAAATGAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAATCGCAACGACAAA
9404 ATCGCAACGC
1 ATCGCAACGC
9414 AAAACACAAA
Statistics
Matches: 72, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
32 57 0.79
33 15 0.21
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (32 bp):
ATCGCAACGCGAAATGAAATCGCAACGACAAA
Found at i:9446 original size:19 final size:17
Alignment explanation
Indices: 9424--9519 Score: 69
Period size: 19 Copynumber: 5.6 Consensus size: 17
9414 AAAACACAAA
9424 TCGCATTGCGATTTTCATT
1 TCGC-TTGCGA-TTTCATT
*
9443 TCGCGTTGCGATTT--TG
1 TCGC-TTGCGATTTCATT
9459 TCG-TTGCGATTTCATT
1 TCGCTTGCGATTTCATT
*
9475 TCGCGTTGCGATTT--TG
1 TCGC-TTGCGATTTCATT
*
9491 TCG-TTGCGCTTTTCATT
1 TCGCTTGCG-ATTTCATT
9508 TCGCATTGCGAT
1 TCGC-TTGCGAT
9520 AGCCATTTCC
Statistics
Matches: 61, Mismatches: 7, Indels: 19
0.70 0.08 0.22
Matches are distributed among these distances:
14 14 0.23
15 3 0.05
16 12 0.20
17 4 0.07
18 13 0.21
19 15 0.25
ACGTcount: A:0.10, C:0.21, G:0.23, T:0.46
Consensus pattern (17 bp):
TCGCTTGCGATTTCATT
Found at i:9465 original size:14 final size:14
Alignment explanation
Indices: 9446--9503 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
9436 TTTCATTTCG
9446 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
9460 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
9476 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
*
9492 CGTTGCGCTTTT
1 CGTTGCGATTTT
9504 CATTTCGCAT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 22 0.59
16 4 0.11
18 11 0.30
ACGTcount: A:0.07, C:0.19, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:9510 original size:33 final size:32
Alignment explanation
Indices: 9429--9519 Score: 146
Period size: 32 Copynumber: 2.8 Consensus size: 32
9419 ACAAATCGCA
9429 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCG-TTTTCATTTCGCGTTGCGATTTTGTCG
*
9462 TTGCGATTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGTTTTCATTTCGCGTTGCGATTTTGTCG
*
9494 TTGCGCTTTTCATTTCGCATTGCGAT
1 TTGCG-TTTTCATTTCGCGTTGCGAT
9520 AGCCATTTCC
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
32 31 0.57
33 23 0.43
ACGTcount: A:0.10, C:0.20, G:0.23, T:0.47
Consensus pattern (32 bp):
TTGCGTTTTCATTTCGCGTTGCGATTTTGTCG
Found at i:9526 original size:19 final size:19
Alignment explanation
Indices: 9504--9547 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
9494 TTGCGCTTTT
9504 CATTTCGCA-TTGCGATAGC
1 CATTTC-CACTTGCGATAGC
*
9523 CATTTCCACGTTGCGATAGT
1 CATTTCCAC-TTGCGATAGC
9543 CATTT
1 CATTT
9548 TCGTGTTGCG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 2 0.09
19 6 0.27
20 14 0.64
ACGTcount: A:0.20, C:0.25, G:0.18, T:0.36
Consensus pattern (19 bp):
CATTTCCACTTGCGATAGC
Found at i:10066 original size:18 final size:18
Alignment explanation
Indices: 10040--10084 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
10030 GTCGATCAGA
*
10040 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
10058 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
10076 TGATGGCTC
1 TGATGGCTC
10085 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:10898 original size:20 final size:20
Alignment explanation
Indices: 10873--10922 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
10863 GTAATGTGTC
10873 TAGTGTACCGACCTACATCA
1 TAGTGTACCGACCTACATCA
10893 TAGTGTACCGACCTACATCA
1 TAGTGTACCGACCTACATCA
*
10913 TCGTGT-CCGA
1 TAGTGTACCGA
10923 AGCGTAGACC
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 4 0.14
20 25 0.86
ACGTcount: A:0.26, C:0.30, G:0.18, T:0.26
Consensus pattern (20 bp):
TAGTGTACCGACCTACATCA
Found at i:11462 original size:20 final size:20
Alignment explanation
Indices: 11414--11472 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 20
11404 AATAGTTTCT
** *
11414 GAAAATGAAAATCGCAACAC
1 GAAAATGACCATCGCAACGC
11434 GAAAATGACCATCGCAACGC
1 GAAAATGACCATCGCAACGC
** *
11454 GAATTTGACTATCGCAACG
1 GAAAATGACCATCGCAACG
11473 AGAGAATCGC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.42, C:0.24, G:0.19, T:0.15
Consensus pattern (20 bp):
GAAAATGACCATCGCAACGC
Found at i:11761 original size:22 final size:22
Alignment explanation
Indices: 11734--11777 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
11724 GATGGAGATA
11734 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
11756 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
11778 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:11989 original size:20 final size:20
Alignment explanation
Indices: 11963--12076 Score: 122
Period size: 20 Copynumber: 5.7 Consensus size: 20
11953 GATTATGTAT
11963 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
11983 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
12003 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
* ** *
12023 TATCTCGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--AAGTCAG
* *
12044 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
12064 TATCGCATTGCGA
1 TATCGCGTTGCGA
12077 TTTTCCCAAT
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
19 3 0.04
20 63 0.79
21 12 0.15
22 2 0.03
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.31
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:12080 original size:41 final size:41
Alignment explanation
Indices: 11943--12078 Score: 159
Period size: 41 Copynumber: 3.3 Consensus size: 41
11933 CGCTTTGAAA
*
11943 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGT
* * * *
11984 ATCGCGTTGCGA--AAGTCAGTATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATTATGT-ATTATCGCGTTGCGAAAGTCAGT
* * * * *
12024 ATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGT
12065 ATCGCATTGCGATT
1 ATCGCATTGCGATT
12079 TTCCCAATTC
Statistics
Matches: 78, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
39 3 0.04
40 31 0.40
41 42 0.54
42 2 0.03
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (41 bp):
ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGT
Found at i:12096 original size:41 final size:41
Alignment explanation
Indices: 11943--12098 Score: 109
Period size: 41 Copynumber: 3.8 Consensus size: 41
11933 CGCTTTGAAA
* ** * * * *
11943 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTAAGT
* *** * *
11984 ATCGCGTTGCGAAAGT-CAGTATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTAAGT
* * ** * * *
12024 ATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTAAGT
12065 ATCGCATTGCGATTTTCCCAAT-TCGCGTTGCGAT
1 ATCGCATTGCGATTTT-CCAATATCGCGTTGCGAT
12099 TTACTTATTC
Statistics
Matches: 90, Mismatches: 23, Indels: 4
0.77 0.20 0.03
Matches are distributed among these distances:
40 32 0.36
41 56 0.62
42 2 0.02
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.33
Consensus pattern (41 bp):
ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTAAGT
Found at i:16525 original size:187 final size:187
Alignment explanation
Indices: 16210--16589 Score: 715
Period size: 187 Copynumber: 2.0 Consensus size: 187
16200 TTTTCAAGTC
*
16210 AAATTTCACCACCAGTTTGTGTACTATACGTACTGGGACAGAGCTAAGATTGAACTATGAGGGAT
1 AAATTTCACCACCAGTTTGTGTACTATACGTACTGGGACAGAGCTAAGATTGAACTATGAGAGAT
16275 AAGTTGTTAACTTCAAAATAAATATAATCATACAAAGTAATTAAACCATAAAAATTAAGAGATTA
66 AAGTTGTTAACTTCAAAATAAATATAATCATACAAAGTAATTAAACCATAAAAATTAAGAGATTA
* * *
16340 TGGGTTTGATTTCATTATTTTAAAATTCCAAGGTCTTAACATGTAATTAAACCAGAG
131 TGGGTTTAATTTCATTAATTTAAAAGTCCAAGGTCTTAACATGTAATTAAACCAGAG
16397 AAATTTCACCACCAGTTTGTGTACTATACGTACTGGGACAGAGCTAAGATTGAACTATGAGAGAT
1 AAATTTCACCACCAGTTTGTGTACTATACGTACTGGGACAGAGCTAAGATTGAACTATGAGAGAT
*
16462 AAGTTGTTAACTTCAAAATAAATATAATCATACAAAGTAATTAAACCATACAAATTAAGAGATTA
66 AAGTTGTTAACTTCAAAATAAATATAATCATACAAAGTAATTAAACCATAAAAATTAAGAGATTA
16527 TGGGTTTAATTTCATTAATTTAAAAGTCCAAGGTCTTAACATGTAATTAAACCAGAG
131 TGGGTTTAATTTCATTAATTTAAAAGTCCAAGGTCTTAACATGTAATTAAACCAGAG
16584 AAATTT
1 AAATTT
16590 GAGATTTAAG
Statistics
Matches: 188, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
187 188 1.00
ACGTcount: A:0.41, C:0.13, G:0.15, T:0.31
Consensus pattern (187 bp):
AAATTTCACCACCAGTTTGTGTACTATACGTACTGGGACAGAGCTAAGATTGAACTATGAGAGAT
AAGTTGTTAACTTCAAAATAAATATAATCATACAAAGTAATTAAACCATAAAAATTAAGAGATTA
TGGGTTTAATTTCATTAATTTAAAAGTCCAAGGTCTTAACATGTAATTAAACCAGAG
Found at i:27297 original size:10 final size:10
Alignment explanation
Indices: 27284--27318 Score: 61
Period size: 10 Copynumber: 3.5 Consensus size: 10
27274 TTATAAAATA
27284 TATTTTTTTT
1 TATTTTTTTT
*
27294 TATTTTTTAT
1 TATTTTTTTT
27304 TATTTTTTTT
1 TATTTTTTTT
27314 TATTT
1 TATTT
27319 CTCTTCTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (10 bp):
TATTTTTTTT
Found at i:35824 original size:30 final size:30
Alignment explanation
Indices: 35780--35874 Score: 92
Period size: 30 Copynumber: 3.2 Consensus size: 30
35770 GTCGGGTCAG
35780 ACCGGTCA-AACCGGTTTG-AACCGGTCGAA
1 ACCGGTCAGAACCGGTTTGAAACCGGT-GAA
*
35809 ACCGGTCAGAACCGG-TTGAAAACCGGTTAA
1 ACCGGTCAGAACCGGTTTG-AAACCGGTGAA
* *
35839 ACCGGTTC-GAACCGG-TCGAAACCGGTCAGA
1 ACCGG-TCAGAACCGGTTTGAAACCGGTGA-A
35869 ACCGGT
1 ACCGGT
35875 TGAAAATCGA
Statistics
Matches: 58, Mismatches: 3, Indels: 10
0.82 0.04 0.14
Matches are distributed among these distances:
29 21 0.36
30 28 0.48
31 9 0.16
ACGTcount: A:0.28, C:0.27, G:0.28, T:0.16
Consensus pattern (30 bp):
ACCGGTCAGAACCGGTTTGAAACCGGTGAA
Found at i:35834 original size:50 final size:50
Alignment explanation
Indices: 35780--35896 Score: 198
Period size: 50 Copynumber: 2.3 Consensus size: 50
35770 GTCGGGTCAG
*
35780 ACCGGTCAAACCGGTTTGAACCGGTCGAAACCGGTCAGAACCGGTTGAAA
1 ACCGGTTAAACCGGTTTGAACCGGTCGAAACCGGTCAGAACCGGTTGAAA
*
35830 ACCGGTTAAACCGGTTCGAACCGGTCGAAACCGGTCAGAACCGGTTGAAA
1 ACCGGTTAAACCGGTTTGAACCGGTCGAAACCGGTCAGAACCGGTTGAAA
* *
35880 ATCGATTAAACCGGTTT
1 ACCGGTTAAACCGGTTT
35897 CCAGCAGCCA
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
50 62 1.00
ACGTcount: A:0.30, C:0.25, G:0.26, T:0.19
Consensus pattern (50 bp):
ACCGGTTAAACCGGTTTGAACCGGTCGAAACCGGTCAGAACCGGTTGAAA
Found at i:35861 original size:10 final size:10
Alignment explanation
Indices: 35780--35879 Score: 77
Period size: 10 Copynumber: 10.1 Consensus size: 10
35770 GTCGGGTCAG
35780 ACCGGTC-AA
1 ACCGGTCGAA
*
35789 ACCGGTTTG-A
1 ACCGG-TCGAA
35799 ACCGGTCGAA
1 ACCGGTCGAA
35809 ACCGGTC-AGA
1 ACCGGTCGA-A
*
35819 ACCGGTTGAAA
1 ACCGGTCG-AA
*
35830 ACCGGT-TAA
1 ACCGGTCGAA
35839 ACCGGTTCG-A
1 ACCGG-TCGAA
35849 ACCGGTCGAA
1 ACCGGTCGAA
35859 ACCGGTC-AGA
1 ACCGGTCGA-A
*
35869 ACCGGTTGAA
1 ACCGGTCGAA
35879 A
1 A
35880 ATCGATTAAA
Statistics
Matches: 74, Mismatches: 6, Indels: 21
0.73 0.06 0.21
Matches are distributed among these distances:
9 19 0.26
10 46 0.62
11 8 0.11
12 1 0.01
ACGTcount: A:0.30, C:0.26, G:0.28, T:0.16
Consensus pattern (10 bp):
ACCGGTCGAA
Found at i:40618 original size:15 final size:15
Alignment explanation
Indices: 40598--40642 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
40588 ATGACATGTG
*
40598 TTATGT-TAGTATTAC
1 TTATGTATA-TATGAC
40613 TTATGTATATATGAC
1 TTATGTATATATGAC
*
40628 TTATGTATTTATGAC
1 TTATGTATATATGAC
40643 ATTTGCCATG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
15 25 0.93
16 2 0.07
ACGTcount: A:0.29, C:0.07, G:0.13, T:0.51
Consensus pattern (15 bp):
TTATGTATATATGAC
Found at i:45562 original size:23 final size:22
Alignment explanation
Indices: 45532--45579 Score: 62
Period size: 24 Copynumber: 2.1 Consensus size: 22
45522 TTATAATAGT
45532 TTTCT-AAATATAATTACTTTTC
1 TTTCTAAAATATAATTAC-TTTC
*
45554 TTTCTTAAAATATATTTACTTTC
1 TTTC-TAAAATATAATTACTTTC
45577 TTT
1 TTT
45580 AAATGTTGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 4 0.17
23 8 0.35
24 11 0.48
ACGTcount: A:0.29, C:0.12, G:0.00, T:0.58
Consensus pattern (22 bp):
TTTCTAAAATATAATTACTTTC
Found at i:49142 original size:30 final size:32
Alignment explanation
Indices: 49106--49183 Score: 97
Period size: 35 Copynumber: 2.4 Consensus size: 32
49096 AAAATCGAAT
49106 TAAACGGGGACGGA-GA-AAAACCATTTATGC
1 TAAACGGGGACGGATGAGAAAACCATTTATGC
* *
49136 TAAACGGGGACGGAGATGAGGAAAACCGTTTATGT
1 TAAACGGGGAC-G-GATGA-GAAAACCATTTATGC
49171 TAAACGGGGACGG
1 TAAACGGGGACGG
49184 GGACGAGTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
30 11 0.27
31 1 0.02
32 2 0.05
33 3 0.07
34 1 0.02
35 23 0.56
ACGTcount: A:0.36, C:0.14, G:0.33, T:0.17
Consensus pattern (32 bp):
TAAACGGGGACGGATGAGAAAACCATTTATGC
Found at i:49253 original size:4 final size:4
Alignment explanation
Indices: 49244--49333 Score: 50
Period size: 4 Copynumber: 24.0 Consensus size: 4
49234 AAATAATTAT
* * * *
49244 TATA TATA TATA TATA TACTA T-TA -ATA AATT TA-A TTTA AAT- TA-A
1 TATA TATA TATA TATA TA-TA TATA TATA TATA TATA TATA TATA TATA
* * * *
49288 TATA TATA TATA TATA -ATA TTTA TATA TTTA -ATT TAAA TATA TATA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
49334 CCCGGCCCGA
Statistics
Matches: 63, Mismatches: 15, Indels: 16
0.67 0.16 0.17
Matches are distributed among these distances:
3 12 0.19
4 48 0.76
5 3 0.05
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (4 bp):
TATA
Found at i:49255 original size:6 final size:6
Alignment explanation
Indices: 49244--49333 Score: 50
Period size: 6 Copynumber: 16.0 Consensus size: 6
49234 AAATAATTAT
* * * *
49244 TATATA TATATA TATATA CTAT-TA -ATAAA TTTA-A TTTAAA T-TA-A
1 TATATA TATATA TATATA -TATATA TATATA TATATA TATATA TATATA
* * * *
49288 TATATA TATATA TATA-A TATTTA TATATT TA-ATT TAAATA TATATA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
49334 CCCGGCCCGA
Statistics
Matches: 69, Mismatches: 7, Indels: 16
0.75 0.08 0.17
Matches are distributed among these distances:
4 4 0.06
5 19 0.28
6 43 0.62
7 3 0.04
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (6 bp):
TATATA
Found at i:49318 original size:42 final size:40
Alignment explanation
Indices: 49244--49333 Score: 135
Period size: 42 Copynumber: 2.2 Consensus size: 40
49234 AAATAATTAT
*
49244 TATATATATATATATATACTATTAATAAATTTAATTTAAA
1 TATATATATATATATATAATATTAATAAATTTAATTTAAA
* *
49284 TTAATATATATATATATATAATATTTATATATTTAATTTAAA
1 -T-ATATATATATATATATAATATTAATAAATTTAATTTAAA
49326 TATATATA
1 TATATATA
49334 CCCGGCCCGA
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
40 7 0.16
41 2 0.04
42 36 0.80
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (40 bp):
TATATATATATATATATAATATTAATAAATTTAATTTAAA
Found at i:60865 original size:45 final size:45
Alignment explanation
Indices: 60797--60908 Score: 147
Period size: 45 Copynumber: 2.5 Consensus size: 45
60787 TAAAAATCGG
*
60797 TAAAAAAATAATATTTTATGTAACG-TCTAATATTAACATTT-TCGA
1 TAAAAAAATAATATTTTAGGTAACGTTC-AATATTAACATTTCT-GA
* * *
60842 TAGAAAAATAATGTTTTAGGTAACGTTCAATATTAATATTTCTGA
1 TAAAAAAATAATATTTTAGGTAACGTTCAATATTAACATTTCTGA
*
60887 TAAAAAAATAATATTTTTGGTA
1 TAAAAAAATAATATTTTAGGTA
60909 TTACTTTACC
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
45 55 0.95
46 3 0.05
ACGTcount: A:0.44, C:0.06, G:0.10, T:0.40
Consensus pattern (45 bp):
TAAAAAAATAATATTTTAGGTAACGTTCAATATTAACATTTCTGA
Found at i:61942 original size:4 final size:4
Alignment explanation
Indices: 61933--61973 Score: 73
Period size: 4 Copynumber: 10.2 Consensus size: 4
61923 TGTCACTATA
*
61933 TATG TATG TATG TATG TATG TATG TATA TATG TATG TATG T
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG T
61974 GTATTCATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.27, C:0.00, G:0.22, T:0.51
Consensus pattern (4 bp):
TATG
Done.