Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001598.1 Hibiscus syriacus cultivar Beakdansim tig00003181_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: 62102
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Found at i:11279 original size:20 final size:21
Alignment explanation
Indices: 11249--11315 Score: 59
Period size: 20 Copynumber: 3.1 Consensus size: 21
11239 AATGTTACAA
11249 ATATATTTATTAAAAAATTATT
1 ATAT-TTTATTAAAAAATTATT
11271 AT-TTTTATTCAATAAAA-TA-T
1 ATATTTTATT-AA-AAAATTATT
* *
11291 ATATTTAATTGAAAAATTATAT
1 ATATTTTATTAAAAAATTAT-T
11313 ATA
1 ATA
11316 GAGATATATT
Statistics
Matches: 37, Mismatches: 2, Indels: 12
0.73 0.04 0.24
Matches are distributed among these distances:
19 4 0.11
20 12 0.32
21 11 0.30
22 10 0.27
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (21 bp):
ATATTTTATTAAAAAATTATT
Found at i:12193 original size:35 final size:35
Alignment explanation
Indices: 12141--12510 Score: 425
Period size: 35 Copynumber: 10.5 Consensus size: 35
12131 CGCATTGACG
* *
12141 GTGGATAAGCTCAATTATGTAGGCATGCATGGATA
1 GTGGATAAGCTCAATTATGTATGCATGAATGGATA
** * * * *
12176 AAGGATAAGCTCGATTATGTAAGAATGCATGGATA
1 GTGGATAAGCTCAATTATGTATGCATGAATGGATA
* * * * *
12211 GAGGATAAGCTCGATTATATAGGCAAGAATGGATA
1 GTGGATAAGCTCAATTATGTATGCATGAATGGATA
* * *
12246 GTGAATAAGCTCGATTATGTAGGCATGAATGGATA
1 GTGGATAAGCTCAATTATGTATGCATGAATGGATA
* * *
12281 GTGGATAAGCTCGATTATGTAGGCATGCATGGATA
1 GTGGATAAGCTCAATTATGTATGCATGAATGGATA
* * * *
12316 GAGGATAAGCTCGATTATGTATACATGCATGGATA
1 GTGGATAAGCTCAATTATGTATGCATGAATGGATA
* *
12351 CTGGATATGCTCAATTATGTAATGCATGAATGGATA
1 GTGGATAAGCTCAATTATGT-ATGCATGAATGGATA
*
12387 GTGGATAAGATCAATTATGTAATGCATGAATGGATA
1 GTGGATAAGCTCAATTATGT-ATGCATGAATGGATA
** *
12423 CCGGATTAGCTCAATTATGTAATGCATGAATGGATA
1 GTGGATAAGCTCAATTATGT-ATGCATGAATGGATA
* * *
12459 CTGGATTAGCTCAATTATGTATGCATGCATGGATA
1 GTGGATAAGCTCAATTATGTATGCATGAATGGATA
12494 GTGGATAAGCTCAATTA
1 GTGGATAAGCTCAATTA
12511 CTCTTATCCA
Statistics
Matches: 297, Mismatches: 37, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
35 200 0.67
36 97 0.33
ACGTcount: A:0.34, C:0.11, G:0.26, T:0.29
Consensus pattern (35 bp):
GTGGATAAGCTCAATTATGTATGCATGAATGGATA
Found at i:12317 original size:105 final size:105
Alignment explanation
Indices: 12142--12510 Score: 477
Period size: 105 Copynumber: 3.5 Consensus size: 105
12132 GCATTGACGG
* ** * *
12142 TGGATAAGCTCAATTATGTAGGCATGCATGGATAAAGGATAAGCTCGATTATGTAAGAATGCATG
1 TGGATAAGCTCAATTATGTAGGCATGAATGGATAGTGGATAAGCTCAATTATGTAAGCATGCATG
* * * *
12207 GATAGAGGATAAGCTCGATTATATAGGCAAGAATGGATAG
66 GATAGAGGATAAGCTCGATTATGTATGCATGAATGGATAC
* * * *
12247 TGAATAAGCTCGATTATGTAGGCATGAATGGATAGTGGATAAGCTCGATTATGTAGGCATGCATG
1 TGGATAAGCTCAATTATGTAGGCATGAATGGATAGTGGATAAGCTCAATTATGTAAGCATGCATG
* *
12312 GATAGAGGATAAGCTCGATTATGTATACATGCATGGATAC
66 GATAGAGGATAAGCTCGATTATGTATGCATGAATGGATAC
* * * *
12352 TGGATATGCTCAATTATGTAATGCATGAATGGATAGTGGATAAGATCAATTATGTAATGCATGAA
1 TGGATAAGCTCAATTATGT-AGGCATGAATGGATAGTGGATAAGCTCAATTATGTAA-GCATGCA
** * *
12417 TGGATACCGGATTAGCTCAATTATGTAATGCATGAATGGATAC
64 TGGATAGAGGATAAGCTCGATTATGT-ATGCATGAATGGATAC
* * *
12460 TGGATTAGCTCAATTATGTATGCATGCATGGATAGTGGATAAGCTCAATTA
1 TGGATAAGCTCAATTATGTAGGCATGAATGGATAGTGGATAAGCTCAATTA
12511 CTCTTATCCA
Statistics
Matches: 230, Mismatches: 31, Indels: 4
0.87 0.12 0.02
Matches are distributed among these distances:
105 108 0.47
106 33 0.14
107 58 0.25
108 31 0.13
ACGTcount: A:0.34, C:0.11, G:0.26, T:0.29
Consensus pattern (105 bp):
TGGATAAGCTCAATTATGTAGGCATGAATGGATAGTGGATAAGCTCAATTATGTAAGCATGCATG
GATAGAGGATAAGCTCGATTATGTATGCATGAATGGATAC
Found at i:12863 original size:59 final size:60
Alignment explanation
Indices: 12762--12886 Score: 189
Period size: 59 Copynumber: 2.1 Consensus size: 60
12752 GATAGGATCT
* * *
12762 CCTAAATTATGACCCACATTCTAAATTGATCCTTAAAATTTAAAATATTCTACATCAATC
1 CCTAAACTATGACCCACATTCTAAATGGATCCATAAAATTTAAAATATTCTACATCAATC
* *
12822 CCTAAACTATGACCCA-ATTCTAAATGGATCCATAAATTTTAAAATATTCTATATCAATC
1 CCTAAACTATGACCCACATTCTAAATGGATCCATAAAATTTAAAATATTCTACATCAATC
*
12881 CTTAAA
1 CCTAAA
12887 TTATCAATAT
Statistics
Matches: 59, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
59 44 0.75
60 15 0.25
ACGTcount: A:0.41, C:0.21, G:0.04, T:0.34
Consensus pattern (60 bp):
CCTAAACTATGACCCACATTCTAAATGGATCCATAAAATTTAAAATATTCTACATCAATC
Found at i:12887 original size:29 final size:29
Alignment explanation
Indices: 12779--12888 Score: 78
Period size: 29 Copynumber: 3.8 Consensus size: 29
12769 TATGACCCAC
** *
12779 ATTCTAAATTGATCCTTAAAATTTAAAAT
1 ATTCTAAATCAATCCTTAAATTTTAAAAT
* * * * **
12808 ATTCTACATCAATCCCTAAACTATGACCCA-
1 ATTCTAAATCAATCCTTAAA-TTTTA-AAAT
** *
12838 ATTCTAAATGGATCCATAAATTTTAAAAT
1 ATTCTAAATCAATCCTTAAATTTTAAAAT
*
12867 ATTCTATATCAATCCTTAAATT
1 ATTCTAAATCAATCCTTAAATT
12889 ATCAATATAT
Statistics
Matches: 57, Mismatches: 21, Indels: 6
0.68 0.25 0.07
Matches are distributed among these distances:
28 1 0.02
29 37 0.65
30 18 0.32
31 1 0.02
ACGTcount: A:0.41, C:0.18, G:0.04, T:0.37
Consensus pattern (29 bp):
ATTCTAAATCAATCCTTAAATTTTAAAAT
Found at i:15947 original size:9 final size:8
Alignment explanation
Indices: 15933--15965 Score: 57
Period size: 8 Copynumber: 4.0 Consensus size: 8
15923 AAAATTAAAA
15933 TTTTAATTT
1 TTTTAA-TT
15942 TTTTAATT
1 TTTTAATT
15950 TTTTAATT
1 TTTTAATT
15958 TTTTAATT
1 TTTTAATT
15966 AACCCTTCTC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 18 0.75
9 6 0.25
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
TTTTAATT
Found at i:21281 original size:23 final size:23
Alignment explanation
Indices: 21249--21372 Score: 117
Period size: 23 Copynumber: 5.3 Consensus size: 23
21239 GAGTTAAGGG
*
21249 TTCTACGTGGTCATTCGGGACAA
1 TTCTACGTGGTCCTTCGGGACAA
* * *
21272 TTCTATGTGGTCCTTTGGGATAAA
1 TTCTACGTGGTCCTTCGGGA-CAA
* ** *
21296 TTCTATGTGGTCCTTCATGACAT
1 TTCTACGTGGTCCTTCGGGACAA
*
21319 TTCTACGTGGTCCTTCGGGACAT
1 TTCTACGTGGTCCTTCGGGACAA
21342 TTCTACGTGG-CACTTCGGTGA-ATA
1 TTCTACGTGGTC-CTTCGG-GACA-A
21366 TTCTACG
1 TTCTACG
21373 CGGCACTTTG
Statistics
Matches: 84, Mismatches: 13, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
22 1 0.01
23 55 0.65
24 28 0.33
ACGTcount: A:0.19, C:0.21, G:0.23, T:0.37
Consensus pattern (23 bp):
TTCTACGTGGTCCTTCGGGACAA
Found at i:21323 original size:47 final size:47
Alignment explanation
Indices: 21249--21351 Score: 118
Period size: 47 Copynumber: 2.2 Consensus size: 47
21239 GAGTTAAGGG
* * *
21249 TTCTACGTGGTCATTCGGGACAATTCTATGTGGTCCTTTGGGATAAA
1 TTCTACGTGGTCATTCAGGACAATTCTACGTGGTCCTTCGGGATAAA
* * * * * *
21296 TTCTATGTGGTCCTTCATGACATTTCTACGTGGTCCTTCGGGA-CAT
1 TTCTACGTGGTCATTCAGGACAATTCTACGTGGTCCTTCGGGATAAA
21342 TTCTACGTGG
1 TTCTACGTGG
21352 CACTTCGGTG
Statistics
Matches: 46, Mismatches: 10, Indels: 1
0.81 0.18 0.02
Matches are distributed among these distances:
46 10 0.22
47 36 0.78
ACGTcount: A:0.17, C:0.20, G:0.24, T:0.38
Consensus pattern (47 bp):
TTCTACGTGGTCATTCAGGACAATTCTACGTGGTCCTTCGGGATAAA
Found at i:21377 original size:24 final size:23
Alignment explanation
Indices: 21342--21393 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 23
21332 TTCGGGACAT
*
21342 TTCTACGTGGCACTTCGGTGAATA
1 TTCTACGCGGCACTTCGGTGAA-A
* *
21366 TTCTACGCGGCACTTTGGTGCAA
1 TTCTACGCGGCACTTCGGTGAAA
21389 TTCTA
1 TTCTA
21394 TGTGGCAGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
23 6 0.24
24 19 0.76
ACGTcount: A:0.19, C:0.23, G:0.23, T:0.35
Consensus pattern (23 bp):
TTCTACGCGGCACTTCGGTGAAA
Found at i:21400 original size:23 final size:24
Alignment explanation
Indices: 21319--21400 Score: 82
Period size: 23 Copynumber: 3.5 Consensus size: 24
21309 TTCATGACAT
21319 TTCTACGTGGTC-CTTCGG-GACAT-
1 TTCTACGTGG-CACTTCGGTGA-ATA
21342 TTCTACGTGGCACTTCGGTGAATA
1 TTCTACGTGGCACTTCGGTGAATA
* * *
21366 TTCTACGCGGCACTTTGGTGCA-A
1 TTCTACGTGGCACTTCGGTGAATA
*
21389 TTCTATGTGGCA
1 TTCTACGTGGCA
21401 GTTTCGACTG
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
22 1 0.02
23 29 0.57
24 21 0.41
ACGTcount: A:0.17, C:0.23, G:0.26, T:0.34
Consensus pattern (24 bp):
TTCTACGTGGCACTTCGGTGAATA
Found at i:25236 original size:38 final size:36
Alignment explanation
Indices: 25185--25423 Score: 200
Period size: 38 Copynumber: 6.4 Consensus size: 36
25175 TGAAAATATG
*
25185 TTTTCAAAACATATAATATATAGTTTTTAGAAAACGT
1 TTTTGAAAACATATAATATATAGTTTTTA-AAAACGT
* *
25222 TTTTTAAAAGCATATAATATATAGTTTTTAAAAAAATTGGT
1 TTTTGAAAA-CATATAATATATAGTTTTT--AAAAA--CGT
* * * *
25263 TTTTGAAAATATAT-A-ATATGGTTTTGAAAATAAGT
1 TTTTGAAAACATATAATATATAGTTTTTAAAA-ACGT
* * * *
25298 TTTTAAAAACATATATTATATAGTTTTGAAAACACAT
1 TTTTGAAAACATATAATATATAGTTTTTAAAA-ACGT
* *
25335 TTTTGAAAACGTATAATATATA-TCATTTTAAAAAGGAT
1 TTTTGAAAACATATAATATATAGT--TTTTAAAAACG-T
*
25373 TTTTGAAAACATAT-ATAATATAG-TTTTAAAAACAT
1 TTTTGAAAACATATAAT-ATATAGTTTTTAAAAACGT
25408 ATTTTGAAAACATATA
1 -TTTTGAAAACATATA
25424 TAGTTTTTTA
Statistics
Matches: 164, Mismatches: 23, Indels: 30
0.76 0.11 0.14
Matches are distributed among these distances:
35 15 0.09
36 28 0.17
37 47 0.29
38 54 0.33
39 5 0.03
40 5 0.03
41 10 0.06
ACGTcount: A:0.45, C:0.05, G:0.09, T:0.41
Consensus pattern (36 bp):
TTTTGAAAACATATAATATATAGTTTTTAAAAACGT
Found at i:25324 original size:37 final size:36
Alignment explanation
Indices: 25172--25424 Score: 180
Period size: 37 Copynumber: 6.8 Consensus size: 36
25162 ATAATGCAGT
* * *
25172 TTTTGAAAATA-TGTTTTCAAAACATATAATATATAG
1 TTTTGAAAAAAGT-TTTTGAAAACATATATTATATAG
* * * *
25208 TTTTTAGAAAACGTTTTTTAAAAGCATATAATATATAG
1 TTTTGA-AAAAAGTTTTTGAAAA-CATATATTATATAG
* * *
25246 TTTTTAAAAAAATTGGTTTTTG-AAA-ATATATAATATGG
1 -TTTTGAAAAAA---GTTTTTGAAAACATATATTATATAG
*
25284 TTTTGAAAATAAGTTTTTAAAAACATATATTATATAG
1 TTTTGAAAA-AAGTTTTTGAAAACATATATTATATAG
*
25321 TTTTGAAAACACA-TTTTTGAAAACGTATAATATATATCA-
1 TTTTGAAAA-A-AGTTTTTGAAAACATAT-AT-TATAT-AG
* *
25360 TTTT-AAAAAGGATTTTTGAAAACATATATAATATAG
1 TTTTGAAAAAAG-TTTTTGAAAACATATATTATATAG
25396 TTTT-AAAAACA-TATTTTGAAAACATATAT
1 TTTTGAAAAA-AGT-TTTTGAAAACATATAT
25425 AGTTTTTTAA
Statistics
Matches: 177, Mismatches: 21, Indels: 38
0.75 0.09 0.16
Matches are distributed among these distances:
35 8 0.05
36 37 0.21
37 56 0.32
38 52 0.29
39 14 0.08
40 4 0.02
41 6 0.03
ACGTcount: A:0.45, C:0.05, G:0.09, T:0.42
Consensus pattern (36 bp):
TTTTGAAAAAAGTTTTTGAAAACATATATTATATAG
Found at i:25551 original size:5 final size:5
Alignment explanation
Indices: 25521--25605 Score: 58
Period size: 5 Copynumber: 17.4 Consensus size: 5
25511 GTTTTTATTA
25521 TATAT TAT-T TATAT CTATAT CATATAT TATA- -ATAT TATAT T-T-T
1 TATAT TATAT TATAT -TATAT --TATAT TATAT TATAT TATAT TATAT
* *
25564 TATAT TCAT-T ATGTAT TAT-T TTTAT TATAT TATAT TATAT TA
1 TATAT T-ATAT -TATAT TATAT TATAT TATAT TATAT TATAT TA
25606 ATTTTATTTT
Statistics
Matches: 64, Mismatches: 5, Indels: 22
0.70 0.05 0.24
Matches are distributed among these distances:
3 5 0.08
4 9 0.14
5 36 0.56
6 9 0.14
7 5 0.08
ACGTcount: A:0.35, C:0.04, G:0.01, T:0.60
Consensus pattern (5 bp):
TATAT
Found at i:25555 original size:51 final size:51
Alignment explanation
Indices: 25500--25602 Score: 122
Period size: 51 Copynumber: 2.0 Consensus size: 51
25490 TCGAAAATAA
25500 AATATTATATAGTT-T-TT-ATTATATATTATTTATATCTATATCATATATTAT
1 AATATTATATAGTTATATTCATTATATATTATTTATAT-TATAT--TATATTAT
** * *
25551 AATATTATATTTTTATATTCATTATGTATTATTTTTATTATATTATATTAT
1 AATATTATATAGTTATATTCATTATATATTATTTATATTATATTATATTAT
25602 A
1 A
25603 TTAATTTTAT
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
51 21 0.47
52 1 0.02
53 7 0.16
54 16 0.36
ACGTcount: A:0.36, C:0.03, G:0.02, T:0.59
Consensus pattern (51 bp):
AATATTATATAGTTATATTCATTATATATTATTTATATTATATTATATTAT
Found at i:25567 original size:21 final size:20
Alignment explanation
Indices: 25543--25604 Score: 56
Period size: 22 Copynumber: 2.9 Consensus size: 20
25533 ATCTATATCA
25543 TATATTATAATATTATATTTT
1 TATATTAT-ATATTATATTTT
25564 TATATTCAT-TATGTATTATTTT
1 TATATT-ATATAT-TA-TATTTT
25586 TAT-TATATTATATTATATT
1 TATAT-TA-TATATTATATT
25605 AATTTTATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 12
0.74 0.00 0.26
Matches are distributed among these distances:
20 3 0.09
21 14 0.40
22 15 0.43
23 3 0.09
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.63
Consensus pattern (20 bp):
TATATTATATATTATATTTT
Found at i:25582 original size:54 final size:51
Alignment explanation
Indices: 25517--25620 Score: 129
Period size: 54 Copynumber: 2.0 Consensus size: 51
25507 TATAGTTTTT
25517 ATTATATATTATTTATATCTATATCATATATTATAAT-ATTATATTTTTATATTC
1 ATTATATATTATTTATAT-TATAT--TATATTATAATAATTATATTTTT-TATTC
* * * *
25571 ATTATGTATTATTTTTATTATATTATATTATATTAATTTTATTTTTTATT
1 ATTATATATTATTTATATTATATTATATTATAATAATTATATTTTTTATT
25621 TGGTCTAGGT
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
51 14 0.31
52 10 0.22
53 5 0.11
54 16 0.36
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.62
Consensus pattern (51 bp):
ATTATATATTATTTATATTATATTATATTATAATAATTATATTTTTTATTC
Found at i:25613 original size:19 final size:19
Alignment explanation
Indices: 25521--25613 Score: 50
Period size: 19 Copynumber: 4.8 Consensus size: 19
25511 GTTTTTATTA
*
25521 TATATTATTTATATCTATAT
1 TATATTAATTATAT-TATAT
*
25541 CATATATT-ATAATATTATAT
1 --TATATTAATTATATTATAT
*
25561 T-T-TTATATTCAT-TATGTAT
1 TATATTA-ATT-ATAT-TATAT
* *
25580 TATTTTTATTATATTATAT
1 TATATTAATTATATTATAT
*
25599 TATATTAATTTTATT
1 TATATTAATTATATT
25614 TTTTATTTGG
Statistics
Matches: 55, Mismatches: 9, Indels: 17
0.68 0.11 0.21
Matches are distributed among these distances:
16 2 0.04
17 1 0.02
18 4 0.07
19 25 0.45
20 10 0.18
21 7 0.13
22 6 0.11
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.61
Consensus pattern (19 bp):
TATATTAATTATATTATAT
Found at i:25725 original size:32 final size:32
Alignment explanation
Indices: 25689--25762 Score: 130
Period size: 32 Copynumber: 2.3 Consensus size: 32
25679 GGCCATACCA
*
25689 GCCTGACCCAGCAAAGCATGCTCGGTTAGGGG
1 GCCTGACCCAGCAAAGCATGCCCGGTTAGGGG
25721 GCCTGACCCAGCAAAGCATGCCCGGTTAGGGG
1 GCCTGACCCAGCAAAGCATGCCCGGTTAGGGG
*
25753 GCCTAACCCA
1 GCCTGACCCA
25763 ACCCGAATTA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.23, C:0.32, G:0.31, T:0.14
Consensus pattern (32 bp):
GCCTGACCCAGCAAAGCATGCCCGGTTAGGGG
Found at i:27426 original size:39 final size:39
Alignment explanation
Indices: 27383--27462 Score: 99
Period size: 39 Copynumber: 2.1 Consensus size: 39
27373 AAATAGGCGC
* ** *
27383 AACTTAAAATG-TAAAATTTTTCATAATATTTTTAATTAT
1 AACTTAAAATGTTAAAAATAAT-ATAATATTTTAAATTAT
*
27422 AACTTAAGATGTTAAAAATAATATAATATTTTAAATTAT
1 AACTTAAAATGTTAAAAATAATATAATATTTTAAATTAT
27461 AA
1 AA
27463 TCAGTAATAT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
39 28 0.80
40 7 0.20
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.44
Consensus pattern (39 bp):
AACTTAAAATGTTAAAAATAATATAATATTTTAAATTAT
Found at i:28688 original size:23 final size:23
Alignment explanation
Indices: 28662--28706 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
28652 CACCACAGCT
*
28662 CGTATAAATGCACCGAAGTGCCC
1 CGTAGAAATGCACCGAAGTGCCC
* *
28685 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
28707 ATATAATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.29, G:0.24, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCC
Found at i:28944 original size:149 final size:149
Alignment explanation
Indices: 28685--28988 Score: 563
Period size: 149 Copynumber: 2.0 Consensus size: 149
28675 CGAAGTGCCC
*
28685 CGTAGAATTGCACCGTAGTGCCATATAATGATGTACATAAGGACCACATAGAATTCTTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTACATAAGGACCACATAGAATTCTTTAAGAAT
28750 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
66 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
28815 CATATGTCCCGAAGAACCG
131 CATATGTCCCGAAGAACCG
*
28834 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTACATAAGGACCACATAGAATTCTTTAAGAAT
* * *
28899 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCTATACTTCACACATGTTCCAAAGCATATA
66 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
28964 CATATGTCCCGAAGAACCG
131 CATATGTCCCGAAGAACCG
28983 CGTAGA
1 CGTAGA
28989 CCCTCGACTC
Statistics
Matches: 150, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
149 150 1.00
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (149 bp):
CGTAGAATTGCACCGTAGTGCCATATAATAATGTACATAAGGACCACATAGAATTCTTTAAGAAT
CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
CATATGTCCCGAAGAACCG
Found at i:30623 original size:21 final size:21
Alignment explanation
Indices: 30593--30633 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
30583 ATTCTGTCGT
* *
30593 TTGAAGGGGTATCGGTTCCCA
1 TTGAAGGGGTACCGATTCCCA
*
30614 TTGAATGGGTACCGATTCCC
1 TTGAAGGGGTACCGATTCCC
30634 CTTGCCCAGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.20, C:0.22, G:0.29, T:0.29
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCA
Found at i:33662 original size:23 final size:23
Alignment explanation
Indices: 33636--33680 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
33626 CACCACAGCT
*
33636 CGTATAAATGCACCGAAGTGCCC
1 CGTAGAAATGCACCGAAGTGCCC
* *
33659 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
33681 ATATAATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.29, G:0.24, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCC
Found at i:33918 original size:149 final size:149
Alignment explanation
Indices: 33659--33962 Score: 581
Period size: 149 Copynumber: 2.0 Consensus size: 149
33649 CGAAGTGCCC
*
33659 CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
33724 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
66 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
33789 CATATGTCCCGAAGAACCG
131 CATATGTCCCGAAGAACCG
33808 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
* *
33873 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCTAGACTTCACACATGTTCCAAAGCATATA
66 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
33938 CATATGTCCCGAAGAACCG
131 CATATGTCCCGAAGAACCG
33957 CGTAGA
1 CGTAGA
33963 CCCTCGACTC
Statistics
Matches: 152, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
149 152 1.00
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (149 bp):
CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
CATATGTCCCGAAGAACCG
Found at i:34982 original size:18 final size:18
Alignment explanation
Indices: 34959--34993 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
34949 TCCCATCTAG
34959 CTTATC-TTATATGTTCAT
1 CTTATCATT-TATGTTCAT
34977 CTTATCATTTATGTTCA
1 CTTATCATTTATGTTCA
34994 AATCTCCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.54
Consensus pattern (18 bp):
CTTATCATTTATGTTCAT
Found at i:35601 original size:21 final size:21
Alignment explanation
Indices: 35571--35615 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
35561 ATTCTGTCGT
* *
35571 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
35592 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
35613 TTG
1 TTG
35616 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:42713 original size:30 final size:30
Alignment explanation
Indices: 42677--42735 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
42667 CTTCAGAAGG
*
42677 TTCAAGTGCCCCACAGAGAAAATGCATCAA
1 TTCAAGTGCCCCAAAGAGAAAATGCATCAA
* *
42707 TTCAAGTGCTCCAAAGAGAAAATGTATCA
1 TTCAAGTGCCCCAAAGAGAAAATGCATCA
42736 GTTTGAACCC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.41, C:0.22, G:0.17, T:0.20
Consensus pattern (30 bp):
TTCAAGTGCCCCAAAGAGAAAATGCATCAA
Found at i:44079 original size:16 final size:18
Alignment explanation
Indices: 44046--44080 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
44036 AATTAACCCG
44046 CCTTCTGAACTATGTTTT
1 CCTTCTGAACTATGTTTT
44064 CCTTCTG-ACT-TGTTTT
1 CCTTCTGAACTATGTTTT
44080 C
1 C
44081 TGTCCTTTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
17 3 0.18
18 7 0.41
ACGTcount: A:0.11, C:0.26, G:0.11, T:0.51
Consensus pattern (18 bp):
CCTTCTGAACTATGTTTT
Found at i:47255 original size:159 final size:160
Alignment explanation
Indices: 46720--47361 Score: 877
Period size: 160 Copynumber: 4.0 Consensus size: 160
46710 AAATTAATTT
* * ** * * * * *
46720 AGTTTTACATAAATTTAAGATTGTTGGATGAGTGAAAATAAAT-TACTGAGATTAATAGTAAGAA
1 AGTTTTAAACAAATTTAAGACCGTTAGATGAGTGAAAATAGATGT-CTGATATTAACAGTAGGAA
* *
46784 ATGAGAAGATATTCACTGGGAAAAGAATATAATGAGTCAATCTCAGCCATCTATTTTCACTCATC
65 ATGAGAAGATATTCACTGGAAAAAGAATATAATGAGTCAATCTCAACCATCTATTTTCACTCATC
*
46849 TAACAGTCCTAAATTTATGTAAAACTAAAAG
130 TAACGGTCCTAAATTTATGTAAAACTAAAAG
* * * * *
46880 AGTTTTAAACACATTTAGGACCGTTAGATGAGTGAAAATAGATATTTGATATTAACAGTATGAAA
1 AGTTTTAAACAAATTTAAGACCGTTAGATGAGTGAAAATAGATGTCTGATATTAACAGTAGGAAA
**
46945 TGAGAAGATATTCACTGGAAAAAGAATATAATGAGTCAATCTCAGTCATCTATTTTCACTCATCT
66 TGAGAAGATATTCACTGGAAAAAGAATATAATGAGTCAATCTCAACCATCTATTTTCACTCATCT
*
47010 AACGGTCCTAAATTTATGAAAAACTAAAAG
131 AACGGTCCTAAATTTATGTAAAACTAAAAG
* * * *
47040 AGCTTTAAACAAATTTAGGACAGTTAGATGAGTGAAAATAGATGTCTGATATTAACAATAGGAAA
1 AGTTTTAAACAAATTTAAGACCGTTAGATGAGTGAAAATAGATGTCTGATATTAACAGTAGGAAA
* * *
47105 TGAGAATATATTCACTGGAAAAAGAATATAATGAGTCAATCTCAATCATCTATTTTCACTCATTT
66 TGAGAAGATATTCACTGGAAAAAGAATATAATGAGTCAATCTCAACCATCTATTTTCACTCATCT
47170 AA-GGTCCTAAATTTATGTAAAACTAAAAG
131 AACGGTCCTAAATTTATGTAAAACTAAAAG
*
47199 AGTTTTAAACAGATTTAAGACCGTTAGATGAGTGAAAATAGATGTCTGATATTAACAGTAGGAAA
1 AGTTTTAAACAAATTTAAGACCGTTAGATGAGTGAAAATAGATGTCTGATATTAACAGTAGGAAA
* * * *
47264 TGAGAAGATATTCACT-GAGAAA-AA-AT-A-GAGTTAATTTCAACCATCTATTTTCACTCATAT
66 TGAGAAGATATTCACTGGAAAAAGAATATAATGAGTCAATCTCAACCATCTATTTTCACTCATCT
* * * *
47324 AATGATCCTATAAATCTGTGTAAAACTAAAA-
131 AACGGTCC--TAAATTTATGTAAAACTAAAAG
47355 AGTTTTA
1 AGTTTTA
47362 CTGTATAAGT
Statistics
Matches: 437, Mismatches: 41, Indels: 12
0.89 0.08 0.02
Matches are distributed among these distances:
154 31 0.07
155 5 0.01
156 9 0.02
157 21 0.05
158 5 0.01
159 101 0.23
160 264 0.60
161 1 0.00
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.31
Consensus pattern (160 bp):
AGTTTTAAACAAATTTAAGACCGTTAGATGAGTGAAAATAGATGTCTGATATTAACAGTAGGAAA
TGAGAAGATATTCACTGGAAAAAGAATATAATGAGTCAATCTCAACCATCTATTTTCACTCATCT
AACGGTCCTAAATTTATGTAAAACTAAAAG
Found at i:49549 original size:14 final size:14
Alignment explanation
Indices: 49530--49558 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
49520 AGGAGCGGTG
49530 GATGAGTTAAAATA
1 GATGAGTTAAAATA
49544 GATGAGTTAAAATA
1 GATGAGTTAAAATA
49558 G
1 G
49559 GTGGCTGAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.24, T:0.28
Consensus pattern (14 bp):
GATGAGTTAAAATA
Found at i:49834 original size:25 final size:24
Alignment explanation
Indices: 49804--49867 Score: 67
Period size: 24 Copynumber: 2.6 Consensus size: 24
49794 TCTTTTGTAG
49804 ATTTAAATATTTAATAAATTA-TT
1 ATTTAAATATTTAATAAATTAGTT
* * **
49827 ATTTTTAATGTAAAATAAATTAGTT
1 A-TTTAAATATTTAATAAATTAGTT
49852 ATTTACAATATTTAAT
1 ATTTA-AATATTTAAT
49868 CCTAGTTCCG
Statistics
Matches: 30, Mismatches: 8, Indels: 4
0.71 0.19 0.10
Matches are distributed among these distances:
23 1 0.03
24 19 0.63
25 10 0.33
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.50
Consensus pattern (24 bp):
ATTTAAATATTTAATAAATTAGTT
Found at i:55279 original size:17 final size:18
Alignment explanation
Indices: 55257--55290 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
55247 TCAGCCGATC
55257 CGGTTC-GAACGGTTCAA
1 CGGTTCTGAACGGTTCAA
*
55274 CGGTTCTGACCGGTTCA
1 CGGTTCTGAACGGTTCA
55291 CTAATAACGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.18, C:0.26, G:0.29, T:0.26
Consensus pattern (18 bp):
CGGTTCTGAACGGTTCAA
Found at i:55531 original size:20 final size:19
Alignment explanation
Indices: 55508--55551 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
55498 AAAATTTTAA
*
55508 ATTTTTTATAAATTAATTTT
1 ATTTTATATAAATT-ATTTT
* *
55528 ATTTTATATGAGTTATTTT
1 ATTTTATATAAATTATTTT
55547 ATTTT
1 ATTTT
55552 GTACCCTCAG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 10 0.48
20 11 0.52
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.66
Consensus pattern (19 bp):
ATTTTATATAAATTATTTT
Found at i:56701 original size:21 final size:20
Alignment explanation
Indices: 56670--56714 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 20
56660 TTTGAATCTT
56670 TAATTTTATTT-ACTAAATC
1 TAATTTTATTTAACTAAATC
56689 TAATGTTTCATTTAACTAAATC
1 TAAT-TTT-ATTTAACTAAATC
56711 -AATT
1 TAATT
56715 GATTATTAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
19 4 0.17
20 4 0.17
21 7 0.30
22 8 0.35
ACGTcount: A:0.38, C:0.11, G:0.02, T:0.49
Consensus pattern (20 bp):
TAATTTTATTTAACTAAATC
Found at i:56820 original size:2 final size:2
Alignment explanation
Indices: 56813--56845 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
56803 GTAAGAGAAT
56813 TA 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 TA T
56846 GAATTCAATG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:57431 original size:16 final size:16
Alignment explanation
Indices: 57412--57442 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
57402 GAATACAAAC
57412 GAACACGAACATAAAT
1 GAACACGAACATAAAT
57428 GAACACGAACATAAA
1 GAACACGAACATAAA
57443 CGTTGGAGAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.58, C:0.19, G:0.13, T:0.10
Consensus pattern (16 bp):
GAACACGAACATAAAT
Found at i:58563 original size:14 final size:14
Alignment explanation
Indices: 58546--58589 Score: 88
Period size: 14 Copynumber: 3.1 Consensus size: 14
58536 TGAACATAAG
58546 CGAACATAACCGAA
1 CGAACATAACCGAA
58560 CGAACATAACCGAA
1 CGAACATAACCGAA
58574 CGAACATAACCGAA
1 CGAACATAACCGAA
58588 CG
1 CG
58590 TTCACGAACG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.48, C:0.30, G:0.16, T:0.07
Consensus pattern (14 bp):
CGAACATAACCGAA
Found at i:59049 original size:2 final size:2
Alignment explanation
Indices: 59042--59099 Score: 75
Period size: 2 Copynumber: 30.0 Consensus size: 2
59032 ATTATAAAAG
* * *
59042 TA TA TA TA -A TT TT TA TA TA TA GA -A 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
59082 TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA
59100 GTAAATTTTA
Statistics
Matches: 51, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
1 2 0.04
2 49 0.96
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:59955 original size:2 final size:2
Alignment explanation
Indices: 59948--59984 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
59938 GAATACAACC
59948 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
59985 GCTGAAATTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.