Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002192.1 Hibiscus syriacus cultivar Beakdansim tig00004468_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: 69220
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:415 original size:22 final size:22
Alignment explanation
Indices: 363--415 Score: 52
Period size: 22 Copynumber: 2.4 Consensus size: 22
353 ACAGGAGTTA
** *
363 CAAGAGTTATTTGATTTAATTC
1 CAAGAGTTACATGATATAATTC
* * *
385 CAGGGGTTACATGATATAATTT
1 CAAGAGTTACATGATATAATTC
407 CAAGAGTTA
1 CAAGAGTTA
416 TAACAGCTGA
Statistics
Matches: 23, Mismatches: 8, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.34, C:0.09, G:0.19, T:0.38
Consensus pattern (22 bp):
CAAGAGTTACATGATATAATTC
Found at i:19903 original size:67 final size:67
Alignment explanation
Indices: 19795--19925 Score: 235
Period size: 67 Copynumber: 2.0 Consensus size: 67
19785 CTGCGAGGAA
* * *
19795 TGTAAGTATTGTTGATTCTCCTTACTTGAAAATTGTTGTTGGCTATTCTATAGATATTTCTTTAA
1 TGTAAGTACTGTTGATTCTCCTTACTTGAAAAGTGTTGTTGGCTATTCTATAAATATTTCTTTAA
19860 AT
66 AT
19862 TGTAAGTACTGTTGATTCTCCTTACTTGAAAAGTGTTGTTGGCTATTCTATAAATATTTCTTTA
1 TGTAAGTACTGTTGATTCTCCTTACTTGAAAAGTGTTGTTGGCTATTCTATAAATATTTCTTTA
19926 TTTAGCTTTG
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
67 61 1.00
ACGTcount: A:0.25, C:0.11, G:0.15, T:0.48
Consensus pattern (67 bp):
TGTAAGTACTGTTGATTCTCCTTACTTGAAAAGTGTTGTTGGCTATTCTATAAATATTTCTTTAA
AT
Found at i:21264 original size:13 final size:13
Alignment explanation
Indices: 21245--21322 Score: 66
Period size: 13 Copynumber: 5.4 Consensus size: 13
21235 AACCCGACCC
21245 GACCCGACCCGTT
1 GACCCGACCCGTT
* *
21258 TACCCGACCAGTT
1 GACCCGACCCGTT
21271 GACCCGACCCGACCCGTT
1 G-----ACCCGACCCGTT
21289 GACCCGACCCGTT
1 GACCCGACCCGTT
21302 GACCCGTTGACCCGTT
1 GACCC---GACCCGTT
21318 GACCC
1 GACCC
21323 ACGTTGACCA
Statistics
Matches: 53, Mismatches: 4, Indels: 13
0.76 0.06 0.19
Matches are distributed among these distances:
13 28 0.53
16 13 0.25
18 12 0.23
ACGTcount: A:0.17, C:0.45, G:0.22, T:0.17
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:21264 original size:18 final size:18
Alignment explanation
Indices: 21240--21315 Score: 81
Period size: 18 Copynumber: 4.3 Consensus size: 18
21230 GTCATAACCC
21240 GACCCGACCCGACCCGTT
1 GACCCGACCCGACCCGTT
*
21258 TACCCGA-CC-A---GTT
1 GACCCGACCCGACCCGTT
21271 GACCCGACCCGACCCGTT
1 GACCCGACCCGACCCGTT
21289 GACCCGACCCGTTGACCCGTT
1 GACCCGACCC---GACCCGTT
21310 GACCCG
1 GACCCG
21316 TTGACCCACG
Statistics
Matches: 48, Mismatches: 2, Indels: 13
0.76 0.03 0.21
Matches are distributed among these distances:
13 9 0.19
14 2 0.04
15 1 0.02
16 1 0.02
17 2 0.04
18 19 0.40
21 14 0.29
ACGTcount: A:0.17, C:0.46, G:0.22, T:0.14
Consensus pattern (18 bp):
GACCCGACCCGACCCGTT
Found at i:21275 original size:31 final size:31
Alignment explanation
Indices: 21240--21307 Score: 118
Period size: 31 Copynumber: 2.2 Consensus size: 31
21230 GTCATAACCC
*
21240 GACCCGACCCGACCCGTTTACCCGACCAGTT
1 GACCCGACCCGACCCGTTGACCCGACCAGTT
*
21271 GACCCGACCCGACCCGTTGACCCGACCCGTT
1 GACCCGACCCGACCCGTTGACCCGACCAGTT
21302 GACCCG
1 GACCCG
21308 TTGACCCGTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.18, C:0.47, G:0.22, T:0.13
Consensus pattern (31 bp):
GACCCGACCCGACCCGTTGACCCGACCAGTT
Found at i:21329 original size:10 final size:8
Alignment explanation
Indices: 21281--21341 Score: 65
Period size: 8 Copynumber: 7.5 Consensus size: 8
21271 GACCCGACCC
21281 GACCCGTT
1 GACCCGTT
21289 GACCC---
1 GACCCGTT
21294 GACCCGTT
1 GACCCGTT
21302 GACCCGTT
1 GACCCGTT
21310 GACCCGTT
1 GACCCGTT
21318 GACCCACGTT
1 GA-CC-CGTT
21328 GACCACTGTT
1 GACC-C-GTT
21338 GACC
1 GACC
21342 AAAACTTTGA
Statistics
Matches: 47, Mismatches: 0, Indels: 10
0.82 0.00 0.18
Matches are distributed among these distances:
5 5 0.11
8 23 0.49
9 6 0.13
10 13 0.28
ACGTcount: A:0.16, C:0.39, G:0.23, T:0.21
Consensus pattern (8 bp):
GACCCGTT
Found at i:22638 original size:18 final size:18
Alignment explanation
Indices: 22612--22652 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
22602 ATTGTTCGAA
* *
22612 AAGACTGAAGTAAATGAT
1 AAGATTGAAGTAAATAAT
*
22630 AAGATTGAATTAAATAAT
1 AAGATTGAAGTAAATAAT
22648 AAGAT
1 AAGAT
22653 CGGATGGAAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.54, C:0.02, G:0.17, T:0.27
Consensus pattern (18 bp):
AAGATTGAAGTAAATAAT
Found at i:23638 original size:47 final size:47
Alignment explanation
Indices: 23579--23677 Score: 189
Period size: 47 Copynumber: 2.1 Consensus size: 47
23569 ATAACTGATG
*
23579 ATTCTGTTAGTTATTGAACTCTTTCAATAGTGATTCTGAATTCCGAT
1 ATTCTGTCAGTTATTGAACTCTTTCAATAGTGATTCTGAATTCCGAT
23626 ATTCTGTCAGTTATTGAACTCTTTCAATAGTGATTCTGAATTCCGAT
1 ATTCTGTCAGTTATTGAACTCTTTCAATAGTGATTCTGAATTCCGAT
23673 ATTCT
1 ATTCT
23678 ATCGGTATAC
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 51 1.00
ACGTcount: A:0.25, C:0.16, G:0.14, T:0.44
Consensus pattern (47 bp):
ATTCTGTCAGTTATTGAACTCTTTCAATAGTGATTCTGAATTCCGAT
Found at i:23836 original size:48 final size:48
Alignment explanation
Indices: 23784--23915 Score: 137
Period size: 48 Copynumber: 2.8 Consensus size: 48
23774 AATATTTTAC
*
23784 CTGATTTTCGATTTGATTTCTGATCTGATACTTGACATGGATTCTGAT
1 CTGATTTTCGAATTGATTTCTGATCTGATACTTGACATGGATTCTGAT
* * *
23832 CTGA-TATCTGACATGGA-TTCTGATCTGATACTTGACTTGGATTCTGAT
1 CTGATTTTC-GA-ATTGATTTCTGATCTGATACTTGACATGGATTCTGAT
** *
23880 CTG-TTACTT-GACCTGATTTCTGATATGATACTTGAC
1 CTGATT--TTCGAATTGATTTCTGATCTGATACTTGAC
23916 CTGATTTATG
Statistics
Matches: 69, Mismatches: 9, Indels: 12
0.77 0.10 0.13
Matches are distributed among these distances:
47 5 0.07
48 60 0.87
49 3 0.04
50 1 0.01
ACGTcount: A:0.22, C:0.17, G:0.19, T:0.42
Consensus pattern (48 bp):
CTGATTTTCGAATTGATTTCTGATCTGATACTTGACATGGATTCTGAT
Found at i:23922 original size:24 final size:24
Alignment explanation
Indices: 23801--23915 Score: 162
Period size: 24 Copynumber: 4.8 Consensus size: 24
23791 TCGATTTGAT
23801 TTCTGATCTGATACTTGACATGGA
1 TTCTGATCTGATACTTGACATGGA
23825 TTCTGATCTGATA-TCTGACATGGA
1 TTCTGATCTGATACT-TGACATGGA
*
23849 TTCTGATCTGATACTTGACTTGGA
1 TTCTGATCTGATACTTGACATGGA
* *
23873 TTCTGATCTGTTACTTGACCT-GA
1 TTCTGATCTGATACTTGACATGGA
*
23896 TTTCTGATATGATACTTGAC
1 -TTCTGATCTGATACTTGAC
23916 CTGATTTATG
Statistics
Matches: 83, Mismatches: 5, Indels: 6
0.88 0.05 0.06
Matches are distributed among these distances:
23 3 0.04
24 79 0.95
25 1 0.01
ACGTcount: A:0.23, C:0.17, G:0.19, T:0.41
Consensus pattern (24 bp):
TTCTGATCTGATACTTGACATGGA
Found at i:26122 original size:13 final size:13
Alignment explanation
Indices: 26103--26180 Score: 66
Period size: 13 Copynumber: 5.4 Consensus size: 13
26093 AACCCGACCC
26103 GACCCGACCCGTT
1 GACCCGACCCGTT
* *
26116 TACCCGACCAGTT
1 GACCCGACCCGTT
26129 GACCCGACCCGACCCGTT
1 G-----ACCCGACCCGTT
26147 GACCCGACCCGTT
1 GACCCGACCCGTT
26160 GACCCGTTGACCCGTT
1 GACCC---GACCCGTT
26176 GACCC
1 GACCC
26181 ACGTTGACCA
Statistics
Matches: 53, Mismatches: 4, Indels: 13
0.76 0.06 0.19
Matches are distributed among these distances:
13 28 0.53
16 13 0.25
18 12 0.23
ACGTcount: A:0.17, C:0.45, G:0.22, T:0.17
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:26122 original size:18 final size:18
Alignment explanation
Indices: 26098--26173 Score: 81
Period size: 18 Copynumber: 4.3 Consensus size: 18
26088 GTCATAACCC
26098 GACCCGACCCGACCCGTT
1 GACCCGACCCGACCCGTT
*
26116 TACCCGA-CC-A---GTT
1 GACCCGACCCGACCCGTT
26129 GACCCGACCCGACCCGTT
1 GACCCGACCCGACCCGTT
26147 GACCCGACCCGTTGACCCGTT
1 GACCCGACCC---GACCCGTT
26168 GACCCG
1 GACCCG
26174 TTGACCCACG
Statistics
Matches: 48, Mismatches: 2, Indels: 13
0.76 0.03 0.21
Matches are distributed among these distances:
13 9 0.19
14 2 0.04
15 1 0.02
16 1 0.02
17 2 0.04
18 19 0.40
21 14 0.29
ACGTcount: A:0.17, C:0.46, G:0.22, T:0.14
Consensus pattern (18 bp):
GACCCGACCCGACCCGTT
Found at i:26133 original size:31 final size:31
Alignment explanation
Indices: 26098--26165 Score: 118
Period size: 31 Copynumber: 2.2 Consensus size: 31
26088 GTCATAACCC
*
26098 GACCCGACCCGACCCGTTTACCCGACCAGTT
1 GACCCGACCCGACCCGTTGACCCGACCAGTT
*
26129 GACCCGACCCGACCCGTTGACCCGACCCGTT
1 GACCCGACCCGACCCGTTGACCCGACCAGTT
26160 GACCCG
1 GACCCG
26166 TTGACCCGTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.18, C:0.47, G:0.22, T:0.13
Consensus pattern (31 bp):
GACCCGACCCGACCCGTTGACCCGACCAGTT
Found at i:26187 original size:10 final size:8
Alignment explanation
Indices: 26139--26199 Score: 65
Period size: 8 Copynumber: 7.5 Consensus size: 8
26129 GACCCGACCC
26139 GACCCGTT
1 GACCCGTT
26147 GACCC---
1 GACCCGTT
26152 GACCCGTT
1 GACCCGTT
26160 GACCCGTT
1 GACCCGTT
26168 GACCCGTT
1 GACCCGTT
26176 GACCCACGTT
1 GA-CC-CGTT
26186 GACCACTGTT
1 GACC-C-GTT
26196 GACC
1 GACC
26200 AAAACTTTGA
Statistics
Matches: 47, Mismatches: 0, Indels: 10
0.82 0.00 0.18
Matches are distributed among these distances:
5 5 0.11
8 23 0.49
9 6 0.13
10 13 0.28
ACGTcount: A:0.16, C:0.39, G:0.23, T:0.21
Consensus pattern (8 bp):
GACCCGTT
Found at i:27496 original size:18 final size:18
Alignment explanation
Indices: 27470--27510 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
27460 ATTGTTCGAA
* *
27470 AAGACTGAAGTAAATGAT
1 AAGATTGAAGTAAATAAT
*
27488 AAGATTGAATTAAATAAT
1 AAGATTGAAGTAAATAAT
27506 AAGAT
1 AAGAT
27511 CGGATGGAAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.54, C:0.02, G:0.17, T:0.27
Consensus pattern (18 bp):
AAGATTGAAGTAAATAAT
Found at i:28496 original size:47 final size:47
Alignment explanation
Indices: 28437--28535 Score: 189
Period size: 47 Copynumber: 2.1 Consensus size: 47
28427 ATAACTGATG
*
28437 ATTCTGTTAGTTATTGAACTCTTTCAATAGTGATTCTGAATTCCGAT
1 ATTCTGTCAGTTATTGAACTCTTTCAATAGTGATTCTGAATTCCGAT
28484 ATTCTGTCAGTTATTGAACTCTTTCAATAGTGATTCTGAATTCCGAT
1 ATTCTGTCAGTTATTGAACTCTTTCAATAGTGATTCTGAATTCCGAT
28531 ATTCT
1 ATTCT
28536 ATCGGTATAC
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 51 1.00
ACGTcount: A:0.25, C:0.16, G:0.14, T:0.44
Consensus pattern (47 bp):
ATTCTGTCAGTTATTGAACTCTTTCAATAGTGATTCTGAATTCCGAT
Found at i:28694 original size:48 final size:48
Alignment explanation
Indices: 28642--28773 Score: 137
Period size: 48 Copynumber: 2.8 Consensus size: 48
28632 AATATTTTAC
*
28642 CTGATTTTCGATTTGATTTCTGATCTGATACTTGACATGGATTCTGAT
1 CTGATTTTCGAATTGATTTCTGATCTGATACTTGACATGGATTCTGAT
* * *
28690 CTGA-TATCTGACATGGA-TTCTGATCTGATACTTGACTTGGATTCTGAT
1 CTGATTTTC-GA-ATTGATTTCTGATCTGATACTTGACATGGATTCTGAT
** *
28738 CTG-TTACTT-GACCTGATTTCTGATATGATACTTGAC
1 CTGATT--TTCGAATTGATTTCTGATCTGATACTTGAC
28774 CTGATTTATG
Statistics
Matches: 69, Mismatches: 9, Indels: 12
0.77 0.10 0.13
Matches are distributed among these distances:
47 5 0.07
48 60 0.87
49 3 0.04
50 1 0.01
ACGTcount: A:0.22, C:0.17, G:0.19, T:0.42
Consensus pattern (48 bp):
CTGATTTTCGAATTGATTTCTGATCTGATACTTGACATGGATTCTGAT
Found at i:28780 original size:24 final size:24
Alignment explanation
Indices: 28659--28773 Score: 162
Period size: 24 Copynumber: 4.8 Consensus size: 24
28649 TCGATTTGAT
28659 TTCTGATCTGATACTTGACATGGA
1 TTCTGATCTGATACTTGACATGGA
28683 TTCTGATCTGATA-TCTGACATGGA
1 TTCTGATCTGATACT-TGACATGGA
*
28707 TTCTGATCTGATACTTGACTTGGA
1 TTCTGATCTGATACTTGACATGGA
* *
28731 TTCTGATCTGTTACTTGACCT-GA
1 TTCTGATCTGATACTTGACATGGA
*
28754 TTTCTGATATGATACTTGAC
1 -TTCTGATCTGATACTTGAC
28774 CTGATTTATG
Statistics
Matches: 83, Mismatches: 5, Indels: 6
0.88 0.05 0.06
Matches are distributed among these distances:
23 3 0.04
24 79 0.95
25 1 0.01
ACGTcount: A:0.23, C:0.17, G:0.19, T:0.41
Consensus pattern (24 bp):
TTCTGATCTGATACTTGACATGGA
Found at i:39375 original size:95 final size:93
Alignment explanation
Indices: 39276--39469 Score: 214
Period size: 93 Copynumber: 2.1 Consensus size: 93
39266 TTTTATTAAA
* * *
39276 ATTATTTAT-TTTGATTAATTAAAACTGAAAGAATTTAAATATAATTCTATAATAAATCTGATAA
1 ATTATTTATATCTGATTAATGAAAACTGAAAGAATTT-AATATAATTCTATAATAAA--TAATAA
*
39340 AACTTAAAGCATATATCAAC-CACTTTTAGTT
63 AAC-TAAAGCATATATCAACACACTTTTAGAT
* ** * * * *
39371 ATTA-TTATCATCTGGTTAATGAAAGTTTAAAGAATTTGATATAATTCTGTAATGAATAATAAAA
1 ATTATTTAT-ATCTGATTAATGAAAACTGAAAGAATTTAATATAATTCTATAATAAATAATAAAA
*
39435 CTAAGGCATATATCAACACACTTTTAGAT
65 CTAAAGCATATATCAACACACTTTTAGAT
39464 ATTATT
1 ATTATT
39470 ATCAATATAA
Statistics
Matches: 83, Mismatches: 12, Indels: 9
0.80 0.12 0.09
Matches are distributed among these distances:
92 15 0.18
93 22 0.27
94 5 0.06
95 20 0.24
96 21 0.25
ACGTcount: A:0.43, C:0.09, G:0.09, T:0.39
Consensus pattern (93 bp):
ATTATTTATATCTGATTAATGAAAACTGAAAGAATTTAATATAATTCTATAATAAATAATAAAAC
TAAAGCATATATCAACACACTTTTAGAT
Found at i:50937 original size:35 final size:36
Alignment explanation
Indices: 50870--50938 Score: 122
Period size: 36 Copynumber: 1.9 Consensus size: 36
50860 CTTTGATATC
50870 TTCTTCAATCACTATAGATATTAATGATTTTTTTTG
1 TTCTTCAATCACTATAGATATTAATGATTTTTTTTG
*
50906 TTCTTCAATCGCTATAGATA-TAATGATTTTTTT
1 TTCTTCAATCACTATAGATATTAATGATTTTTTT
50939 CTCTATCGGT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 13 0.41
36 19 0.59
ACGTcount: A:0.28, C:0.12, G:0.09, T:0.52
Consensus pattern (36 bp):
TTCTTCAATCACTATAGATATTAATGATTTTTTTTG
Found at i:56815 original size:187 final size:186
Alignment explanation
Indices: 56491--56858 Score: 673
Period size: 187 Copynumber: 2.0 Consensus size: 186
56481 AATATCCCAT
56491 ACCTACTTGTTTTTTAATTTAAATGGTCAAATTGCATGCAAACTCAAACACTTTTCCATATTTAG
1 ACCTACTTGTTTTTTAATTTAAATGGTCAAATTGCATGCAAACTCAAACACTTTTCCATATTTAG
56556 ATTTTAGACTTCTAAATTTTAAATCTTCTATAATTTTTACTTTATTTTTATTTTGATAATTAATT
66 ATTTTAGACTTCTAAATTTTAAATCTTCTATAATTTTTACTTTATTTTTATTTTGATAATTAATT
56621 TTGAATTTACTCTTTGATTTTAATTAACAATAATATTAATACTTTATTTTACCCCC
131 TTGAATTTACTCTTTGATTTTAATTAACAATAATATTAATACTTTATTTTACCCCC
* *
56677 ACCTACTTGTTTTTTTAATTTAAATGGTCAAATTGCATGCAAACTCTAACACTTTTCCCTATTTA
1 ACCTACTTG-TTTTTTAATTTAAATGGTCAAATTGCATGCAAACTCAAACACTTTTCCATATTTA
* *
56742 GATTTTAGACTTCTAGATTTTAAATCTTCTATAGTTTTTACTTTATTTTTATTTTGATAATTAAT
65 GATTTTAGACTTCTAAATTTTAAATCTTCTATAATTTTTACTTTATTTTTATTTTGATAATTAAT
* *
56807 TTTGAATTTACTTTTTGATTTTAATTAACAATAATATTAATAGTTTATTTTA
130 TTTGAATTTACTCTTTGATTTTAATTAACAATAATATTAATACTTTATTTTA
56859 TTCATTAATT
Statistics
Matches: 175, Mismatches: 6, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
186 9 0.05
187 166 0.95
ACGTcount: A:0.31, C:0.12, G:0.06, T:0.50
Consensus pattern (186 bp):
ACCTACTTGTTTTTTAATTTAAATGGTCAAATTGCATGCAAACTCAAACACTTTTCCATATTTAG
ATTTTAGACTTCTAAATTTTAAATCTTCTATAATTTTTACTTTATTTTTATTTTGATAATTAATT
TTGAATTTACTCTTTGATTTTAATTAACAATAATATTAATACTTTATTTTACCCCC
Found at i:57038 original size:18 final size:18
Alignment explanation
Indices: 57011--57054 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
57001 AATATCATTA
*
57011 ATTTTAATTTTGATGCTT
1 ATTTTTATTTTGATGCTT
*
57029 ATTTTTATTTTGATGTTT
1 ATTTTTATTTTGATGCTT
57047 ATTTTTAT
1 ATTTTTAT
57055 CATTGCTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.20, C:0.02, G:0.09, T:0.68
Consensus pattern (18 bp):
ATTTTTATTTTGATGCTT
Found at i:57664 original size:22 final size:21
Alignment explanation
Indices: 57613--57672 Score: 61
Period size: 22 Copynumber: 2.9 Consensus size: 21
57603 TTACTTAGAT
*
57613 TAATTATATTTT-TT-AAATA
1 TAATTAAATTTTATTAAAATA
*
57632 AAATTATAATTTTATTAAAATTA
1 TAATTA-AATTTTATTAAAA-TA
*
57655 TAATTAAATTTTAATAAA
1 TAATTAAATTTTATTAAA
57673 TGATTAATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
19 5 0.15
20 5 0.15
21 2 0.06
22 14 0.42
23 7 0.21
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
TAATTAAATTTTATTAAAATA
Found at i:57680 original size:22 final size:23
Alignment explanation
Indices: 57633--57681 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
57623 TTTTAAATAA
* *
57633 AATTATAATTTTATTAAAATTAT
1 AATTATAATTTTAATAAAATGAT
57656 AATTA-AATTTTAAT-AAATGATT
1 AATTATAATTTTAATAAAATGA-T
57678 AATT
1 AATT
57682 TTAAAAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 5 0.22
22 13 0.57
23 5 0.22
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (23 bp):
AATTATAATTTTAATAAAATGAT
Found at i:57799 original size:17 final size:18
Alignment explanation
Indices: 57777--57810 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
57767 TAAAATTATA
57777 ATTAATTTT-AATAAATG
1 ATTAATTTTAAATAAATG
57794 ATTAATTTTAAATAAAT
1 ATTAATTTTAAATAAAT
57811 CCTAATACTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (18 bp):
ATTAATTTTAAATAAATG
Found at i:58483 original size:32 final size:31
Alignment explanation
Indices: 58422--58484 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 31
58412 GTTTTTTAAG
* *
58422 TTTTTAAAATAATAATAATAATAATAATAAT
1 TTTTTAAAAAAATAATAATAATAAAAATAAT
58453 TTTTTAAAAAAATACACTAA-AATAAAAATAAT
1 TTTTTAAAAAAATA-A-TAATAATAAAAATAAT
58485 ATAATATAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 13 0.46
32 12 0.43
33 3 0.11
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (31 bp):
TTTTTAAAAAAATAATAATAATAAAAATAAT
Found at i:59061 original size:32 final size:32
Alignment explanation
Indices: 59025--59101 Score: 127
Period size: 32 Copynumber: 2.4 Consensus size: 32
59015 TTAACTGGAT
*
59025 CCGAAAGTAATCCGAATCAAAACTAATCTAAA
1 CCGAAAGCAATCCGAATCAAAACTAATCTAAA
*
59057 CCGAAAGCAATCCGAATCGAAACTAATCTAAA
1 CCGAAAGCAATCCGAATCAAAACTAATCTAAA
59089 CCGGAAAGCAATC
1 CC-GAAAGCAATC
59102 TGAACTGAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
32 32 0.76
33 10 0.24
ACGTcount: A:0.47, C:0.25, G:0.13, T:0.16
Consensus pattern (32 bp):
CCGAAAGCAATCCGAATCAAAACTAATCTAAA
Found at i:59068 original size:16 final size:16
Alignment explanation
Indices: 59049--59102 Score: 56
Period size: 16 Copynumber: 3.3 Consensus size: 16
59039 AATCAAAACT
59049 AATCTAAACCGAAAGC
1 AATCTAAACCGAAAGC
** *
59065 AATCCGAATCGAAA-C
1 AATCTAAACCGAAAGC
59080 TAATCTAAACCGGAAAGC
1 -AATCTAAACC-GAAAGC
59098 AATCT
1 AATCT
59103 GAACTGAAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
15 1 0.03
16 18 0.62
17 9 0.31
18 1 0.03
ACGTcount: A:0.46, C:0.24, G:0.13, T:0.17
Consensus pattern (16 bp):
AATCTAAACCGAAAGC
Found at i:59638 original size:20 final size:20
Alignment explanation
Indices: 59601--59639 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
59591 TTAACATGAA
**
59601 AACATATATCTTAAATAAAG
1 AACATATATAATAAATAAAG
*
59621 AACATATATAATATATAAA
1 AACATATATAATAAATAAA
59640 AAAATCACTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.59, C:0.08, G:0.03, T:0.31
Consensus pattern (20 bp):
AACATATATAATAAATAAAG
Found at i:59700 original size:22 final size:23
Alignment explanation
Indices: 59675--59717 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
59665 AAATTATTTT
*
59675 AAATAATAAA-TTAATTTAAAGA
1 AAATAATAAATTTAATATAAAGA
*
59697 AAATTATAAATTTAATATAAA
1 AAATAATAAATTTAATATAAA
59718 TATTAAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 9 0.50
23 9 0.50
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (23 bp):
AAATAATAAATTTAATATAAAGA
Found at i:62202 original size:22 final size:21
Alignment explanation
Indices: 62148--62202 Score: 51
Period size: 20 Copynumber: 2.6 Consensus size: 21
62138 TAATTATGAG
62148 TTTAT-TTTATAATTATAAATA
1 TTTATATTT-TAATTATAAATA
* * *
62169 TTT-TATTGTAATTTTAGATA
1 TTTATATTTTAATTATAAATA
62189 TTTTATATTTTAAT
1 -TTTATATTTTAAT
62203 AAGAATAATT
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
20 11 0.41
21 8 0.30
22 8 0.30
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.62
Consensus pattern (21 bp):
TTTATATTTTAATTATAAATA
Found at i:62357 original size:2 final size:2
Alignment explanation
Indices: 62350--62422 Score: 146
Period size: 2 Copynumber: 36.5 Consensus size: 2
62340 ACTAATTTGG
62350 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
62392 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 A
62423 GAGAGAGAGA
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 71 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:62427 original size:2 final size:2
Alignment explanation
Indices: 62422--62450 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
62412 ATATATATAT
62422 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
62451 TAAAGAAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:62572 original size:16 final size:17
Alignment explanation
Indices: 62523--62574 Score: 54
Period size: 16 Copynumber: 3.0 Consensus size: 17
62513 GGAATGTTTA
*
62523 TAAGAGAATTAGAATATG
1 TAAG-GAATTAGAATCTG
62541 TGAAGGAATT-GAAATCTG
1 T-AAGGAATTAG-AATCTG
62559 T-AGGAATTAGAATCTG
1 TAAGGAATTAGAATCTG
62575 AATCTGAAAC
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
16 13 0.43
17 2 0.07
18 12 0.40
19 3 0.10
ACGTcount: A:0.42, C:0.04, G:0.25, T:0.29
Consensus pattern (17 bp):
TAAGGAATTAGAATCTG
Found at i:63930 original size:2 final size:2
Alignment explanation
Indices: 63923--63962 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
63913 ACTAATTTGG
* *
63923 AT AT AT AT AC AT AT AT TT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
63963 CTAGAGAAAG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:67154 original size:2 final size:2
Alignment explanation
Indices: 67147--67174 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
67137 GTTGTAGCAA
67147 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
67175 GATTAATATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.