Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001416.1 Hibiscus syriacus cultivar Beakdansim tig00002753_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: 77225
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:4250 original size:31 final size:31
Alignment explanation
Indices: 4215--4293 Score: 108
Period size: 31 Copynumber: 2.5 Consensus size: 31
4205 CTTAGGTAAT
* *
4215 AAGGTTAAGGAATCAAATGTACCTAAAATA-A
1 AAGGTTAA-GAATTAAATGTACCAAAAATATA
4246 AAGGTTAAAGAATTAAATGTACCAAAAATATA
1 AAGGTT-AAGAATTAAATGTACCAAAAATATA
4278 AA-GTTAAGAATTAAAT
1 AAGGTTAAGAATTAAAT
4294 ATCAGCAAGT
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
30 11 0.25
31 28 0.64
32 5 0.11
ACGTcount: A:0.54, C:0.06, G:0.14, T:0.25
Consensus pattern (31 bp):
AAGGTTAAGAATTAAATGTACCAAAAATATA
Found at i:19673 original size:217 final size:211
Alignment explanation
Indices: 19302--19753 Score: 562
Period size: 206 Copynumber: 2.1 Consensus size: 211
19292 TATTTTGGTT
*
19302 GGGTCGGGTTCGAGTTTAGGGTGAAAAAACCGACCCGACCCGACCTGAAAATATATATAATTCAG
1 GGGTCGGGTTCGGGTTTAGGGTGAAAAAA-C-ACCCGA-CCGACCTGAAAATATATATAATTCAG
* *
19367 GTCGTGTCGGATTAAGTCATTGTTTTTATTAAATAAAAACAATTTTTATTATTTCGGGTCGGGTC
63 G-CGTGTCGGATTAAGTCACTATTTTTATTAAATAAAAACAATTTTTATTATTTCGGGTCGGGTC
19432 GGGTTGGATTTCTAATTCATATATTCGGGTCGGGTCGGATGAAACTTTATTTTGTTCGGGACGAG
127 --G--GGATTTCTAATTCATATA-T----TCGGGTCGGATGAAACTTTATTTTGTTC--G--G-G
19497 TCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTC
178 TCGGGTCGGG-TTTTTTAAGTGTGATATTCGGGTC
*
19532 GGGTCGGGTTCGGGTTTAGGGTGAAAAAA-ACCGGA-CGA-CTCGAAAATATATATAATTC-GG-
1 GGGTCGGGTTCGGGTTTAGGGTGAAAAAACACCCGACCGACCT-GAAAATATATATAATTCAGGC
* *
19592 GT-T-GGATTAAGTCACTATTTTTATTAAATAAAAATATTTTTTTTATTATTTCGGGTCGGGTC-
65 GTGTCGGATTAAGTCACTATTTTTATTAAATAAAAACA--ATTTTTATTATTTCGGGTCGGGTCG
*
19654 GGATTTCTAATTTATATATTCGGGTCGGATGAAACTTTATTTTGTTCGGGTCGGGTCGGGTTTTT
128 GGATTTCTAATTCATATATTCGGGTCGGATGAAACTTTATTTTGTTCGGGTCGGGTCGGGTTTTT
*
19719 TAAGTGTGATGTTCGGGTC
193 TAAGTGTGATATTCGGGTC
*
19738 GAGTCGGG-TCGGGTTT
1 GGGTCGGGTTCGGGTTT
19754 TTTTAAGTGT
Statistics
Matches: 210, Mismatches: 9, Indels: 31
0.84 0.04 0.12
Matches are distributed among these distances:
205 8 0.04
206 30 0.14
207 11 0.05
208 1 0.00
210 1 0.00
212 28 0.13
216 1 0.00
217 17 0.08
220 30 0.14
221 1 0.00
222 25 0.12
224 4 0.02
225 20 0.10
227 5 0.02
230 28 0.13
ACGTcount: A:0.23, C:0.12, G:0.27, T:0.37
Consensus pattern (211 bp):
GGGTCGGGTTCGGGTTTAGGGTGAAAAAACACCCGACCGACCTGAAAATATATATAATTCAGGCG
TGTCGGATTAAGTCACTATTTTTATTAAATAAAAACAATTTTTATTATTTCGGGTCGGGTCGGGA
TTTCTAATTCATATATTCGGGTCGGATGAAACTTTATTTTGTTCGGGTCGGGTCGGGTTTTTTAA
GTGTGATATTCGGGTC
Found at i:19745 original size:37 final size:38
Alignment explanation
Indices: 19703--19789 Score: 149
Period size: 38 Copynumber: 2.3 Consensus size: 38
19693 TTTTGTTCGG
19703 GTCGGGTCGGG-TTTTTTAAGTGTGATGTTCGGGTCGA
1 GTCGGGTCGGGTTTTTTTAAGTGTGATGTTCGGGTCGA
*
19740 GTCGGGTCGGGTTTTTTTAAGTGTGATGTTCGGGTCGG
1 GTCGGGTCGGGTTTTTTTAAGTGTGATGTTCGGGTCGA
19778 GTCGGGTTCGGG
1 GTCGGG-TCGGG
19790 GTTAGGGTGA
Statistics
Matches: 47, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
37 11 0.23
38 31 0.66
39 5 0.11
ACGTcount: A:0.08, C:0.11, G:0.44, T:0.37
Consensus pattern (38 bp):
GTCGGGTCGGGTTTTTTTAAGTGTGATGTTCGGGTCGA
Found at i:23320 original size:12 final size:12
Alignment explanation
Indices: 23303--23334 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
23293 GGTTAACTAA
23303 CCAAGGCCAGGG
1 CCAAGGCCAGGG
23315 CCAAGGCCAGGG
1 CCAAGGCCAGGG
23327 CCAAGGCC
1 CCAAGGCC
23335 CAGGAACCGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.25, C:0.38, G:0.38, T:0.00
Consensus pattern (12 bp):
CCAAGGCCAGGG
Found at i:26717 original size:28 final size:29
Alignment explanation
Indices: 26642--26718 Score: 70
Period size: 28 Copynumber: 2.6 Consensus size: 29
26632 AAATATAACA
*
26642 AATATAATAAATAAAACATTTTATAAAAATT
1 AATATAA-AAATAAAA-ATTCTATAAAAATT
* *
26673 AATCCTAAAAAT-TAAATTCTAT-AAAA-T
1 AAT-ATAAAAATAAAAATTCTATAAAAATT
26700 ACATATAAAAATAAAAATT
1 A-ATATAAAAATAAAAATT
26719 TAATCGAGCA
Statistics
Matches: 38, Mismatches: 5, Indels: 9
0.73 0.10 0.17
Matches are distributed among these distances:
27 9 0.24
28 11 0.29
29 6 0.16
30 2 0.05
31 7 0.18
32 3 0.08
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.32
Consensus pattern (29 bp):
AATATAAAAATAAAAATTCTATAAAAATT
Found at i:27419 original size:21 final size:21
Alignment explanation
Indices: 27395--27606 Score: 143
Period size: 21 Copynumber: 9.9 Consensus size: 21
27385 ACTTCGACTA
*
27395 TCGCATTGCGATAGTCCAAGT
1 TCGCGTTGCGATAGTCCAAGT
** *
27416 TCGCGTTGCGATTTTCCAAAT
1 TCGCGTTGCGATAGTCCAAGT
*
27437 T--CGTTGCGATAGTCGAAGT
1 TCGCGTTGCGATAGTCCAAGT
27456 TCGCGTTGCGATTTATTCCGTCCAAGT
1 TCGCGTTGCGA--TA----GTCCAAGT
*
27483 TCGCGTTGCGATTTATTCCAAGT
1 TCGCGTTGCGA--TAGTCCAAGT
*
27506 T--CGTTGCGATAGTCGAAGT
1 TCGCGTTGCGATAGTCCAAGT
*
27525 TCGCGTTGCGATTTATTCCAAGT
1 TCGCGTTGCGA--TAGTCCAAGT
*
27548 T--CGTTGCGATAGTCGAAGT
1 TCGCGTTGCGATAGTCCAAGT
* * * *
27567 TCACGTTACGATTTATTCCAAAT
1 TCGCGTTGCGA--TAGTCCAAGT
27590 T--CGTTGCGATAGTCCAA
1 TCGCGTTGCGATAGTCCAA
27607 AATCGTAACG
Statistics
Matches: 153, Mismatches: 22, Indels: 34
0.73 0.11 0.16
Matches are distributed among these distances:
19 40 0.26
21 64 0.42
23 27 0.18
27 22 0.14
ACGTcount: A:0.21, C:0.21, G:0.23, T:0.35
Consensus pattern (21 bp):
TCGCGTTGCGATAGTCCAAGT
Found at i:27520 original size:69 final size:67
Alignment explanation
Indices: 27408--27543 Score: 245
Period size: 69 Copynumber: 2.0 Consensus size: 67
27398 CATTGCGATA
27408 GTCCAAGTTCGCGTTGCGATTTTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATT
1 GTCCAAGTTCGCGTTGCGATTTTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATT
27473 CC
66 CC
*
27475 GTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTA
1 GTCCAAGTTCGCGTTGCGA-TT-TTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTA
27540 TTCC
64 TTCC
27544 AAGTTCGTTG
Statistics
Matches: 66, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
67 19 0.29
68 2 0.03
69 45 0.68
ACGTcount: A:0.18, C:0.22, G:0.24, T:0.36
Consensus pattern (67 bp):
GTCCAAGTTCGCGTTGCGATTTTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATT
CC
Found at i:27538 original size:42 final size:42
Alignment explanation
Indices: 27479--27603 Score: 223
Period size: 42 Copynumber: 3.0 Consensus size: 42
27469 TATTCCGTCC
27479 AAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCG
1 AAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCG
27521 AAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCG
1 AAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCG
* * *
27563 AAGTTCACGTTACGATTTATTCCAAATTCGTTGCGATAGTC
1 AAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTC
27604 CAAAATCGTA
Statistics
Matches: 80, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 80 1.00
ACGTcount: A:0.22, C:0.19, G:0.23, T:0.36
Consensus pattern (42 bp):
AAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCG
Found at i:27707 original size:6 final size:6
Alignment explanation
Indices: 27696--27752 Score: 87
Period size: 6 Copynumber: 9.5 Consensus size: 6
27686 GACACATATT
* * *
27696 ACCAAG ACCAAG ACCAAG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
27744 ACCACG ACC
1 ACCACG ACC
27753 CAAGACGAGA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 50 1.00
ACGTcount: A:0.39, C:0.46, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:28262 original size:6 final size:6
Alignment explanation
Indices: 28251--28283 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
28241 TCTCGTCTCG
*
28251 GGTCGT GGTCGT GGTCGT GGTCGT TGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
28284 AATACGTGTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.00, C:0.15, G:0.48, T:0.36
Consensus pattern (6 bp):
GGTCGT
Found at i:28400 original size:23 final size:23
Alignment explanation
Indices: 28374--28567 Score: 91
Period size: 21 Copynumber: 9.2 Consensus size: 23
28364 GTTGTCGCAA
*
28374 CGAATTTGGAATAAATCGTAACG
1 CGAATTTGGAATAAATCGCAACG
* * *
28397 CGAACTTGGACT--ACCGCAA--
1 CGAATTTGGAATAAATCGCAACG
28416 CGAATTTGGAATAAATCGCAACG
1 CGAATTTGGAATAAATCGCAACG
* * *
28439 CGAACTTCGACT--ATCGCAA--
1 CGAATTTGGAATAAATCGCAACG
*
28458 CGAATTTGG-A-AAATCGTAACG
1 CGAATTTGGAATAAATCGCAACG
** * * *
28479 TAAACTTCGACT--ATCGCAA--
1 CGAATTTGGAATAAATCGCAACG
28498 CGAATTTGGAATAAATCGCAACG
1 CGAATTTGGAATAAATCGCAACG
* * *
28521 CGAACTTCGACT--ATCGCAACG
1 CGAATTTGGAATAAATCGCAACG
* * *
28542 CGAACTTGGACT--ATCGCAATG
1 CGAATTTGGAATAAATCGCAACG
28563 CGAAT
1 CGAAT
28568 ATGTAAATCG
Statistics
Matches: 126, Mismatches: 31, Indels: 30
0.67 0.17 0.16
Matches are distributed among these distances:
19 30 0.24
21 68 0.54
23 28 0.22
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.22
Consensus pattern (23 bp):
CGAATTTGGAATAAATCGCAACG
Found at i:28424 original size:19 final size:19
Alignment explanation
Indices: 28397--28560 Score: 112
Period size: 21 Copynumber: 8.0 Consensus size: 19
28387 AATCGTAACG
*
28397 CGAACTTGGACTACCGCAA
1 CGAACTTGGACTATCGCAA
* *
28416 CGAATTTGGAATAAATCGCAA
1 CGAACTTGGACT--ATCGCAA
*
28437 CGCGAACTTCGACTATCGCAA
1 --CGAACTTGGACTATCGCAA
* ** *
28458 CGAATTTGGAAAATCGTAA
1 CGAACTTGGACTATCGCAA
*
28477 CGTAAACTTCGACTATCGCAA
1 CG--AACTTGGACTATCGCAA
* *
28498 CGAATTTGGAATAAATCGCAA
1 CGAACTTGGACT--ATCGCAA
*
28519 CGCGAACTTCGACTATCGCAA
1 --CGAACTTGGACTATCGCAA
28540 CGCGAACTTGGACTATCGCAA
1 --CGAACTTGGACTATCGCAA
28561 TGCGAATATG
Statistics
Matches: 112, Mismatches: 23, Indels: 18
0.73 0.15 0.12
Matches are distributed among these distances:
19 33 0.29
21 61 0.54
23 18 0.16
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.21
Consensus pattern (19 bp):
CGAACTTGGACTATCGCAA
Found at i:28428 original size:42 final size:42
Alignment explanation
Indices: 28368--28541 Score: 280
Period size: 42 Copynumber: 4.2 Consensus size: 42
28358 CCAGTCGTTG
* *
28368 TCGCAACGAATTTGGAATAAATCGTAACGCGAACTTGGACTA
1 TCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTA
*
28410 CCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTA
1 TCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTA
* **
28452 TCGCAACGAATTTGG-A-AAATCGTAACGTAAACTTCGACTA
1 TCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTA
28492 TCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTA
1 TCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTA
28534 TCGCAACG
1 TCGCAACG
28542 CGAACTTGGA
Statistics
Matches: 120, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
40 36 0.30
41 2 0.02
42 82 0.68
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.22
Consensus pattern (42 bp):
TCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTA
Found at i:28435 original size:21 final size:21
Alignment explanation
Indices: 28368--28520 Score: 97
Period size: 21 Copynumber: 7.4 Consensus size: 21
28358 CCAGTCGTTG
28368 TCGCAACGAATTTGGAATAAA
1 TCGCAACGAATTTGGAATAAA
* * *
28389 TCGTAACGCGAACTTGGACT--A
1 TCGCAA--CGAATTTGGAATAAA
*
28410 CCGCAACGAATTTGGAATAAA
1 TCGCAACGAATTTGGAATAAA
* * *
28431 TCGCAACGCGAACTTCGACT--A
1 TCGCAA--CGAATTTGGAATAAA
28452 TCGCAACGAATTTGG-A-AAA
1 TCGCAACGAATTTGGAATAAA
* * * *
28471 TCGTAACGTAAACTTCGACT--A
1 TCGCAACG--AATTTGGAATAAA
28492 TCGCAACGAATTTGGAATAAA
1 TCGCAACGAATTTGGAATAAA
28513 TCGCAACG
1 TCGCAACG
28521 CGAACTTCGA
Statistics
Matches: 96, Mismatches: 22, Indels: 28
0.66 0.15 0.19
Matches are distributed among these distances:
19 32 0.33
21 45 0.47
23 19 0.20
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.22
Consensus pattern (21 bp):
TCGCAACGAATTTGGAATAAA
Found at i:28507 original size:82 final size:84
Alignment explanation
Indices: 28368--28541 Score: 298
Period size: 82 Copynumber: 2.1 Consensus size: 84
28358 CCAGTCGTTG
* *
28368 TCGCAACGAATTTGGAATAAATCGTAACGCGAACTTGGACTACCGCAACGAATTTGGAATAAATC
1 TCGCAACGAATTTGGAATAAATCGTAACGCAAACTTCGACTACCGCAACGAATTTGGAATAAATC
28433 GCAACGCGAACTTCGACTA
66 GCAACGCGAACTTCGACTA
* *
28452 TCGCAACGAATTTGG-A-AAATCGTAACGTAAACTTCGACTATCGCAACGAATTTGGAATAAATC
1 TCGCAACGAATTTGGAATAAATCGTAACGCAAACTTCGACTACCGCAACGAATTTGGAATAAATC
28515 GCAACGCGAACTTCGACTA
66 GCAACGCGAACTTCGACTA
28534 TCGCAACG
1 TCGCAACG
28542 CGAACTTGGA
Statistics
Matches: 86, Mismatches: 4, Indels: 2
0.93 0.04 0.02
Matches are distributed among these distances:
82 70 0.81
83 1 0.01
84 15 0.17
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.22
Consensus pattern (84 bp):
TCGCAACGAATTTGGAATAAATCGTAACGCAAACTTCGACTACCGCAACGAATTTGGAATAAATC
GCAACGCGAACTTCGACTA
Found at i:28536 original size:21 final size:21
Alignment explanation
Indices: 28430--28566 Score: 120
Period size: 21 Copynumber: 6.6 Consensus size: 21
28420 TTTGGAATAA
28430 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
* * **
28451 ATCGCAA--CGAATTTGGAAA
1 ATCGCAACGCGAACTTCGACT
* **
28470 ATCGTAACGTAAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
* * *
28491 ATCGCAA--CGAATTTGGAAT
1 ATCGCAACGCGAACTTCGACT
28510 AAATCGCAACGCGAACTTCGACT
1 --ATCGCAACGCGAACTTCGACT
*
28533 ATCGCAACGCGAACTTGGACT
1 ATCGCAACGCGAACTTCGACT
*
28554 ATCGCAATGCGAA
1 ATCGCAACGCGAA
28567 TATGTAAATC
Statistics
Matches: 88, Mismatches: 22, Indels: 12
0.72 0.18 0.10
Matches are distributed among these distances:
19 21 0.24
21 58 0.66
23 9 0.10
ACGTcount: A:0.34, C:0.25, G:0.20, T:0.21
Consensus pattern (21 bp):
ATCGCAACGCGAACTTCGACT
Found at i:28604 original size:21 final size:21
Alignment explanation
Indices: 28575--28627 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
28565 AATATGTAAA
*
28575 TCGCATTGCGATAGTCCAAGT
1 TCGCGTTGCGATAGTCCAAGT
*
28596 TCGCGTTGCGATAGTCGAAGT
1 TCGCGTTGCGATAGTCCAAGT
28617 TCGCGTTGCGA
1 TCGCGTTGCGA
28628 ATCTGGAAAC
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:0.19, C:0.23, G:0.30, T:0.28
Consensus pattern (21 bp):
TCGCGTTGCGATAGTCCAAGT
Found at i:28943 original size:42 final size:41
Alignment explanation
Indices: 28893--29008 Score: 180
Period size: 42 Copynumber: 2.8 Consensus size: 41
28883 TTTCCCTGAA
* *
28893 TTTT-CGTGTTTGTTTCACGTAATTCGTTTTTCGGAAAATAT
1 TTTTCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAAT-G
28934 TTTTCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATG
1 TTTTCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATG
*
28975 TTTTCCAGTGTTTGTTTCACGTAATTGGTTTTCC
1 TTTTCC-GTGTTTGTTTCACGTAATTCGTTTTCC
29009 TGAACGTAAT
Statistics
Matches: 70, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
41 10 0.14
42 60 0.86
ACGTcount: A:0.16, C:0.16, G:0.18, T:0.50
Consensus pattern (41 bp):
TTTTCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATG
Found at i:29230 original size:31 final size:31
Alignment explanation
Indices: 29195--29330 Score: 92
Period size: 31 Copynumber: 4.5 Consensus size: 31
29185 AAATATTATT
29195 TATTA-ATTTATTAATATT-TATAATAATATAA
1 TATTATATTT-TTAATATTATATAA-AATATAA
*
29226 TATTATATTTTTAATATTATATAAAATAATCA
1 TATTATATTTTTAATATTATATAAAAT-ATAA
* * *
29258 -ATTATA-TTATAATA--ATATAAGATATTA
1 TATTATATTTTTAATATTATATAAAATATAA
* * *
29285 TATT-TTTATTTTAATAATATATAATAA-AAAA
1 TATTATAT-TTTTAATATTATATAA-AATATAA
*
29316 T-TTATATATTTAATA
1 TATTATATTTTTAATA
29331 ATGAATAATA
Statistics
Matches: 84, Mismatches: 11, Indels: 21
0.72 0.09 0.18
Matches are distributed among these distances:
27 4 0.05
28 11 0.13
29 7 0.08
30 16 0.19
31 33 0.39
32 13 0.15
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.50
Consensus pattern (31 bp):
TATTATATTTTTAATATTATATAAAATATAA
Found at i:29233 original size:22 final size:23
Alignment explanation
Indices: 29203--29246 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
29193 TTTATTAATT
29203 TATTAATATTTATAATAATATAA
1 TATTAATATTTATAATAATATAA
* *
29226 TATT-ATATTTTTAATATTATA
1 TATTAATATTTATAATAATATA
29247 TAAAATAATC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
TATTAATATTTATAATAATATAA
Found at i:29533 original size:19 final size:19
Alignment explanation
Indices: 29511--29573 Score: 60
Period size: 21 Copynumber: 3.3 Consensus size: 19
29501 ATAAAAATAC
29511 TATTTAATAATAAATAAAT
1 TATTTAATAATAAATAAAT
*
29530 TATTTTTAATAATAAA-AAAG
1 TA--TTTAATAATAAATAAAT
*
29550 T-TTT-ATGATAAATAATAT
1 TATTTAATAATAAATAA-AT
29568 TATTTA
1 TATTTA
29574 TTGTATTTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 11
0.71 0.06 0.22
Matches are distributed among these distances:
16 7 0.20
17 5 0.14
18 2 0.06
19 5 0.14
20 4 0.11
21 12 0.34
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (19 bp):
TATTTAATAATAAATAAAT
Found at i:29946 original size:26 final size:26
Alignment explanation
Indices: 29904--29977 Score: 73
Period size: 25 Copynumber: 2.9 Consensus size: 26
29894 TTTAAGTTCT
*
29904 TTAATTTT--TTAATAATAAAAAATA
1 TTAATTTTAATTAAAAATAAAAAATA
* *
29928 TTATTTTTAATTAAAAAT-AAAAATT
1 TTAATTTTAATTAAAAATAAAAAATA
* *
29953 TTAATTTTAATGAAATTATAAAAAA
1 TTAATTTTAATTAAA-AATAAAAAA
29978 AAACCTAAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
24 7 0.17
25 19 0.47
26 9 0.22
27 5 0.12
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (26 bp):
TTAATTTTAATTAAAAATAAAAAATA
Found at i:30863 original size:24 final size:24
Alignment explanation
Indices: 30836--30887 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
30826 CGTTCATTTA
* *
30836 CGTTCGTGAACGTTCGGTTATGTT
1 CGTTCATGAACGTTCGATTATGTT
* **
30860 CGTTTATGTTCGTTCGATTATGTT
1 CGTTCATGAACGTTCGATTATGTT
30884 CGTT
1 CGTT
30888 TATGTTCTTT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.12, C:0.15, G:0.25, T:0.48
Consensus pattern (24 bp):
CGTTCATGAACGTTCGATTATGTT
Found at i:30874 original size:14 final size:14
Alignment explanation
Indices: 30857--30887 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
30847 GTTCGGTTAT
*
30857 GTTCGTTTATGTTC
1 GTTCGATTATGTTC
30871 GTTCGATTATGTTC
1 GTTCGATTATGTTC
30885 GTT
1 GTT
30888 TATGTTCTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.10, C:0.13, G:0.23, T:0.55
Consensus pattern (14 bp):
GTTCGATTATGTTC
Found at i:30888 original size:24 final size:24
Alignment explanation
Indices: 30846--30907 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
30836 CGTTCGTGAA
*
30846 CGTTCGGTTATGTTCGTTTATGTT
1 CGTTCGATTATGTTCGTTTATGTT
30870 CGTTCGATTATGTTCGTTTATGTT
1 CGTTCGATTATGTTCGTTTATGTT
*
30894 CTTTC-ATTTATGTT
1 CGTTCGA-TTATGTT
30908 TAACCCAATC
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
23 1 0.03
24 34 0.97
ACGTcount: A:0.11, C:0.13, G:0.19, T:0.56
Consensus pattern (24 bp):
CGTTCGATTATGTTCGTTTATGTT
Found at i:31914 original size:16 final size:16
Alignment explanation
Indices: 31893--31981 Score: 128
Period size: 16 Copynumber: 5.7 Consensus size: 16
31883 CCAACGTTGA
31893 TGTTCATTTATGTTCG
1 TGTTCATTTATGTTCG
*
31909 TGTTCATTTATGTTCA
1 TGTTCATTTATGTTCG
*
31925 TGTTCGTTTATGTTCG
1 TGTTCATTTATGTTCG
*
31941 TGTTCGTTTATGTTCG
1 TGTTCATTTATGTTCG
*
31957 TGTTCGTTTATGTTCG
1 TGTTCATTTATGTTCG
31973 T-TT-ATTTAT
1 TGTTCATTTAT
31982 TAAATGAACG
Statistics
Matches: 69, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
14 5 0.07
15 2 0.03
16 62 0.90
ACGTcount: A:0.11, C:0.11, G:0.19, T:0.58
Consensus pattern (16 bp):
TGTTCATTTATGTTCG
Found at i:31937 original size:10 final size:10
Alignment explanation
Indices: 31887--31977 Score: 56
Period size: 10 Copynumber: 9.7 Consensus size: 10
31877 GGGTCTCCAA
*
31887 CGTTGATGTT
1 CGTTTATGTT
*
31897 CATTTATGTT
1 CGTTTATGTT
31907 CGTGTTCAT-TT
1 CGT-TT-ATGTT
* *
31918 ATGTTCATGTT
1 -CGTTTATGTT
31929 CGTTTATGTT
1 CGTTTATGTT
31939 CG----TGTT
1 CGTTTATGTT
31945 CGTTTATGTT
1 CGTTTATGTT
31955 CG----TGTT
1 CGTTTATGTT
31961 CGTTTATGTT
1 CGTTTATGTT
31971 CGTTTAT
1 CGTTTAT
31978 TTATTAAATG
Statistics
Matches: 62, Mismatches: 7, Indels: 24
0.67 0.08 0.26
Matches are distributed among these distances:
6 12 0.19
10 39 0.63
11 7 0.11
12 4 0.06
ACGTcount: A:0.11, C:0.12, G:0.21, T:0.56
Consensus pattern (10 bp):
CGTTTATGTT
Found at i:39578 original size:2 final size:2
Alignment explanation
Indices: 39571--39601 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
39561 AGTATTACTT
39571 TA TA 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 TA TA T
39602 TGAGTTTATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:57213 original size:39 final size:39
Alignment explanation
Indices: 57090--57221 Score: 114
Period size: 39 Copynumber: 3.4 Consensus size: 39
57080 AAAGTTAAAT
* *
57090 TACAAATTTATACTTAAATTATTTTACAATTTGTAATATTA
1 TACAAATATATA-ATAAA-TATTTTACAATTTGTAATATTA
* * *
57131 TAC-AA-ATAT-ATAAATATTAT-GAA-TT-TAATTTTTTA
1 TACAAATATATAATAAATATTTTACAATTTGTAA--TATTA
* *
57166 AAGAAAATATATAATAAATATTTTACAATTTGTAATATTA
1 TA-CAAATATATAATAAATATTTTACAATTTGTAATATTA
57206 TACAAATATATAATAA
1 TACAAATATATAATAA
57222 GGACAATTTG
Statistics
Matches: 70, Mismatches: 12, Indels: 20
0.69 0.12 0.20
Matches are distributed among these distances:
33 3 0.04
34 2 0.03
35 7 0.10
36 5 0.07
37 6 0.09
38 4 0.06
39 26 0.37
40 9 0.13
41 5 0.07
42 3 0.04
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.44
Consensus pattern (39 bp):
TACAAATATATAATAAATATTTTACAATTTGTAATATTA
Found at i:57360 original size:18 final size:18
Alignment explanation
Indices: 57337--57382 Score: 65
Period size: 20 Copynumber: 2.4 Consensus size: 18
57327 CAGTAATCCT
*
57337 ATTCCCTGTTAATCTTAC
1 ATTCCCTGGTAATCTTAC
57355 ATTCCCACTGGTAATCTTAC
1 ATT-CC-CTGGTAATCTTAC
57375 ATTCCCTG
1 ATTCCCTG
57383 AACCAAACGC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
18 6 0.24
19 4 0.16
20 15 0.60
ACGTcount: A:0.22, C:0.30, G:0.09, T:0.39
Consensus pattern (18 bp):
ATTCCCTGGTAATCTTAC
Found at i:63496 original size:176 final size:175
Alignment explanation
Indices: 63148--63493 Score: 499
Period size: 177 Copynumber: 2.0 Consensus size: 175
63138 TATATATAAC
* *
63148 ATATGGGCTCAGCCCAAACCATTTAAAACTCAATTAATAATTAAGATCCAATAACTTTTAAACCT
1 ATATGGGCTAAGCCCAAACCATTTAAAACCCAATTAATAATTAAGATCCAATAACTTTTAAACCT
63213 AAATCAATATTAATTAATTAAAAAAATATATAAAATTTTTATTTTATAATTATATATTATTTAAA
66 AAATCAATATTAATTAA-TAAAAAAATATATAAAATTTTTATTTTATAATTATATATTATTTAAA
* *
63278 TTAATTGTAAACTATTTTTTAATTAAAAAATATTAAATATTTATAT
130 TTAATTATAAACTATTTTTTAATTAAAAAACATTAAATATTTATAT
*
63324 ATATGGGCTAAGCCTAAACCATTTAAAACCCAATTAATAATTTAAGATCCAATAACTTTTAAACC
1 ATATGGGCTAAGCCCAAACCATTTAAAACCCAATTAATAA-TTAAGATCCAATAACTTTTAAACC
*** * *
63389 TAAATCAATATTAATT-A-AAAATTTTATCTGAAA-TTTTATTTTATAA-T-TATATTATTTAAA
65 TAAATCAATATTAATTAATAAAAAAATATATAAAATTTTTATTTTATAATTATATATTATTTAAA
* * *
63449 TTAATTATATA-T-TTTTTTGAATTAAAAAACATTTAATTTTTATAT
130 TTAATTATAAACTATTTTTT-AATTAAAAAACATTAAATATTTATAT
63494 TTAGAAAATT
Statistics
Matches: 155, Mismatches: 13, Indels: 10
0.87 0.07 0.06
Matches are distributed among these distances:
169 6 0.04
170 24 0.15
171 22 0.14
172 1 0.01
173 13 0.08
174 11 0.07
176 38 0.25
177 40 0.26
ACGTcount: A:0.45, C:0.09, G:0.04, T:0.42
Consensus pattern (175 bp):
ATATGGGCTAAGCCCAAACCATTTAAAACCCAATTAATAATTAAGATCCAATAACTTTTAAACCT
AAATCAATATTAATTAATAAAAAAATATATAAAATTTTTATTTTATAATTATATATTATTTAAAT
TAATTATAAACTATTTTTTAATTAAAAAACATTAAATATTTATAT
Found at i:64922 original size:45 final size:45
Alignment explanation
Indices: 64872--64957 Score: 145
Period size: 45 Copynumber: 1.9 Consensus size: 45
64862 TACATCCAAC
* *
64872 TAGATGGTGACATGTGTCACCACCTTATTTGATAAGAAAAAAGCT
1 TAGATGGTGACACGTATCACCACCTTATTTGATAAGAAAAAAGCT
*
64917 TAGATGGTGACACGTATCACCACCTTATTTGATAATAAAAA
1 TAGATGGTGACACGTATCACCACCTTATTTGATAAGAAAAA
64958 GGCATGAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.29
Consensus pattern (45 bp):
TAGATGGTGACACGTATCACCACCTTATTTGATAAGAAAAAAGCT
Found at i:65237 original size:21 final size:21
Alignment explanation
Indices: 65181--65231 Score: 59
Period size: 24 Copynumber: 2.3 Consensus size: 21
65171 AACTATATAT
65181 TTTTTATATAATCGTTAAATTAAC
1 TTTTTATATAA---TTAAATTAAC
*
65205 TTTTTATATAATTAAATTTA-
1 TTTTTATATAATTAAATTAAC
65225 TTTTTAT
1 TTTTTAT
65232 TTTAATCTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 7 0.27
21 8 0.31
24 11 0.42
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.59
Consensus pattern (21 bp):
TTTTTATATAATTAAATTAAC
Found at i:65757 original size:2 final size:2
Alignment explanation
Indices: 65750--65804 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
65740 AAATTAACAT
65750 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
65792 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
65805 TGTAAAATTT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:66445 original size:23 final size:23
Alignment explanation
Indices: 66385--66446 Score: 88
Period size: 23 Copynumber: 2.7 Consensus size: 23
66375 AGAGCTTTGC
* * *
66385 AGAGAGTTTTACCATGAGATTGG
1 AGAGAGCTTTACCGTGAGACTGG
66408 AGAGAGCTTTACCGTGAGACTGG
1 AGAGAGCTTTACCGTGAGACTGG
*
66431 AGAGAGCTTTGCCGTG
1 AGAGAGCTTTACCGTG
66447 GGAGGGGGAG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.26, C:0.15, G:0.34, T:0.26
Consensus pattern (23 bp):
AGAGAGCTTTACCGTGAGACTGG
Found at i:66871 original size:15 final size:15
Alignment explanation
Indices: 66853--66890 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
66843 TCAATTTTAC
*
66853 ATATTTATTTTAATT
1 ATATTTAATTTAATT
*
66868 ATATTTAATTTAGTT
1 ATATTTAATTTAATT
66883 AT-TTTAAT
1 ATATTTAAT
66891 CTTTAAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 6 0.29
15 15 0.71
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (15 bp):
ATATTTAATTTAATT
Found at i:73267 original size:21 final size:21
Alignment explanation
Indices: 73241--73280 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
73231 TCTGCTGAAA
*
73241 CTCCACCTGTTTTGGAGTATG
1 CTCCACCTGTTATGGAGTATG
73262 CTCCACCTGTTATGGAGTA
1 CTCCACCTGTTATGGAGTA
73281 CTACTTGTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.17, C:0.25, G:0.23, T:0.35
Consensus pattern (21 bp):
CTCCACCTGTTATGGAGTATG
Found at i:75538 original size:21 final size:21
Alignment explanation
Indices: 75514--75558 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
75504 GAACCACCAG
75514 GATAACCTCAACTGAAGCTCT
1 GATAACCTCAACTGAAGCTCT
75535 GATAACCTCAACTGAAGCTCT
1 GATAACCTCAACTGAAGCTCT
75556 GAT
1 GAT
75559 GCCAAAGGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.33, C:0.27, G:0.16, T:0.24
Consensus pattern (21 bp):
GATAACCTCAACTGAAGCTCT
Done.