Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009582.1 Hibiscus syriacus cultivar Beakdansim tig00116959_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: 4978262
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 24 of 24
Found at i:4878064 original size:13 final size:14
Alignment explanation
Indices: 4878039--4878080 Score: 50
Period size: 13 Copynumber: 3.0 Consensus size: 14
4878029 CCAGTTATGC
*
4878039 AATACAAAAGCAAA
1 AATACAAATGCAAA
*
4878053 CA-ACAAATGCAAA
1 AATACAAATGCAAA
4878066 AATACAAAATGCAAA
1 AATAC-AAATGCAAA
4878081 TGCATGTATG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
13 11 0.48
14 3 0.13
15 9 0.39
ACGTcount: A:0.67, C:0.17, G:0.07, T:0.10
Consensus pattern (14 bp):
AATACAAATGCAAA
Found at i:4878077 original size:15 final size:15
Alignment explanation
Indices: 4878039--4878080 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
4878029 CCAGTTATGC
4878039 AATACAAAA-GCAAA
1 AATACAAAATGCAAA
*
4878053 CA-AC-AAATGCAAA
1 AATACAAAATGCAAA
4878066 AATACAAAATGCAAA
1 AATACAAAATGCAAA
4878081 TGCATGTATG
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
12 3 0.13
13 8 0.35
14 3 0.13
15 9 0.39
ACGTcount: A:0.67, C:0.17, G:0.07, T:0.10
Consensus pattern (15 bp):
AATACAAAATGCAAA
Found at i:4880137 original size:2 final size:2
Alignment explanation
Indices: 4880130--4880170 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
4880120 AATTTTATTA
4880130 AT AT 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 AT AT A
4880171 AATAAGATAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4880443 original size:149 final size:145
Alignment explanation
Indices: 4880128--4880445 Score: 367
Period size: 149 Copynumber: 2.2 Consensus size: 145
4880118 ATAATTTTAT
* * * *
4880128 TAATATATATATATATATATATATATATATATATATATATATAAATAAGATATTTATTTACTTAG
1 TAATATATATATATAAAAATAAATATATATATATATATATAAAAATAAGATATTTATTTACTTAG
4880193 AAATATCAGAAAATGACTTCTAGCTGCTTTAAGACAACACATTTCTTAATATTAAAAAATAAATA
66 AAATATCAGAAAATGACTTCTAGCTGCTTTAAGACAACACATTTCTTAATATTAAAAAATAAATA
4880258 AATATTAATTAAACA
131 AATATTAATTAAACA
** * * * * *
4880273 TTTCTATAAAAATAATTAAAATAAAT-TAATATATATAATTTATAAAAAATAGGATATTTATTTA
1 -TAATATATATAT-ATAAAAATAAATAT-ATATATAT-ATATAT-AAAAATAAGATATTTATTTA
* * * *
4880337 TTTA-AGAATATCATAAAA-GAACTTCTAGGTGCTTTAAGACAACTCATTTCTTTAATATTAAAA
61 CTTAGA-AATATCAGAAAATG-ACTTCTAGCTGCTTTAAGACAACACATTTC-TTAATATTAAAA
4880400 AA-AAATAAATATTATTATTTAAACA
123 AATAAATAAATATTA--A-TTAAACA
4880425 -AATATATATATATAAAAATAA
1 TAATATATATATATAAAAATAA
4880446 TAATTAAAGT
Statistics
Matches: 142, Mismatches: 20, Indels: 17
0.79 0.11 0.09
Matches are distributed among these distances:
146 9 0.06
147 16 0.11
148 7 0.05
149 81 0.57
150 21 0.15
151 1 0.01
152 7 0.05
ACGTcount: A:0.50, C:0.07, G:0.05, T:0.38
Consensus pattern (145 bp):
TAATATATATATATAAAAATAAATATATATATATATATATAAAAATAAGATATTTATTTACTTAG
AAATATCAGAAAATGACTTCTAGCTGCTTTAAGACAACACATTTCTTAATATTAAAAAATAAATA
AATATTAATTAAACA
Found at i:4880533 original size:91 final size:91
Alignment explanation
Indices: 4880438--4880607 Score: 322
Period size: 91 Copynumber: 1.9 Consensus size: 91
4880428 ATATATATAT
4880438 AAAAATAATAATTAAAGTAAAAATTTAAACATATCAAAAACAAAAATAAAATTGTAAATAAATAA
1 AAAAATAATAATTAAAGTAAAAATTTAAACATATCAAAAACAAAAATAAAATTGTAAATAAATAA
4880503 TAATCAAAAGAAATAATAATTTAAAC
66 TAATCAAAAGAAATAATAATTTAAAC
*
4880529 AAAAATAATAATTAAAGTAATAATTTAAACATATCAAAAACAAAAATAAAATTGTAAATAAATAA
1 AAAAATAATAATTAAAGTAAAAATTTAAACATATCAAAAACAAAAATAAAATTGTAAATAAATAA
*
4880594 TAATCAAAATAAAT
66 TAATCAAAAGAAAT
4880608 TAAAAGCTAT
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
91 77 1.00
ACGTcount: A:0.66, C:0.05, G:0.03, T:0.26
Consensus pattern (91 bp):
AAAAATAATAATTAAAGTAAAAATTTAAACATATCAAAAACAAAAATAAAATTGTAAATAAATAA
TAATCAAAAGAAATAATAATTTAAAC
Found at i:4881938 original size:3 final size:3
Alignment explanation
Indices: 4881932--4881973 Score: 50
Period size: 3 Copynumber: 14.0 Consensus size: 3
4881922 AATATTTTTT
* *
4881932 TAA TAA TAA TAA TAG TAA TAA TAA TAAA TAA T-A GAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA
4881974 AAACGAATGG
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
2 1 0.03
3 29 0.88
4 3 0.09
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:4881955 original size:18 final size:18
Alignment explanation
Indices: 4881932--4881973 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 18
4881922 AATATTTTTT
4881932 TAATAAT-AATAATAGTAA
1 TAATAATAAATAATAG-AA
4881950 TAATAATAAATAATAGAA
1 TAATAATAAATAATAGAA
4881968 TAATAA
1 TAATAA
4881974 AAACGAATGG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 15 0.65
19 8 0.35
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (18 bp):
TAATAATAAATAATAGAA
Found at i:4890253 original size:17 final size:18
Alignment explanation
Indices: 4890231--4890269 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
4890221 TACGACTGGG
*
4890231 GTATCGATAGTAT-CTGA
1 GTATCGATACTATCCTGA
*
4890248 GTATCGGTACTATCCTGA
1 GTATCGATACTATCCTGA
4890266 GTAT
1 GTAT
4890270 TGGTACTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.36
Consensus pattern (18 bp):
GTATCGATACTATCCTGA
Found at i:4890267 original size:18 final size:17
Alignment explanation
Indices: 4890231--4890277 Score: 58
Period size: 18 Copynumber: 2.7 Consensus size: 17
4890221 TACGACTGGG
* *
4890231 GTATCGATAGTATCTGA
1 GTATCGGTACTATCTGA
4890248 GTATCGGTACTATCCTGA
1 GTATCGGTACTAT-CTGA
*
4890266 GTATTGGTACTA
1 GTATCGGTACTA
4890278 AAATTGGGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 11 0.42
18 15 0.58
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.36
Consensus pattern (17 bp):
GTATCGGTACTATCTGA
Found at i:4900216 original size:43 final size:43
Alignment explanation
Indices: 4900130--4900217 Score: 131
Period size: 43 Copynumber: 2.0 Consensus size: 43
4900120 ATTCGCTGGT
* *
4900130 AAACCATTGAAACCATTCGACCCTGAAGTTGAACAGTCATTCA
1 AAACCATTGAAACCATTCGACCCTGAAGTTAAACAATCATTCA
* * *
4900173 AAACCATTGGAACCATTCGACCCTGAAGTTAAATAATCGTTCA
1 AAACCATTGAAACCATTCGACCCTGAAGTTAAACAATCATTCA
4900216 AA
1 AA
4900218 CAAAGGCGAC
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.39, C:0.24, G:0.14, T:0.24
Consensus pattern (43 bp):
AAACCATTGAAACCATTCGACCCTGAAGTTAAACAATCATTCA
Found at i:4901449 original size:20 final size:20
Alignment explanation
Indices: 4901410--4901448 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
4901400 CATTGCATGA
*
4901410 ATTTATGGCCTCGACAAAAG
1 ATTTATGGCCTCAACAAAAG
4901430 ATTTCATGGCCTCAACAAA
1 ATTT-ATGGCCTCAACAAA
4901449 GTCCTTGATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.36, C:0.23, G:0.15, T:0.26
Consensus pattern (20 bp):
ATTTATGGCCTCAACAAAAG
Found at i:4912540 original size:31 final size:30
Alignment explanation
Indices: 4912502--4912605 Score: 104
Period size: 31 Copynumber: 3.4 Consensus size: 30
4912492 AACTCAAAAC
* *
4912502 TTTGTGACGGAACATGTGGACCAGTCAGAAA
1 TTTGTGACGGAATA-GTGGAACAGTCAGAAA
*
4912533 TTTGTGACGGAATAG-GTGAATATGTCAGAAA
1 TTTGTGACGGAATAGTG-GAACA-GTCAGAAA
* *
4912564 TTTGTGACAGAATAGAT-GAATCTGTCAGAAA
1 TTTGTGACGGAATAG-TGGAA-CAGTCAGAAA
4912595 TTTGTGACGGA
1 TTTGTGACGGA
4912606 CCCACATATT
Statistics
Matches: 61, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
29 1 0.02
30 4 0.07
31 56 0.92
ACGTcount: A:0.34, C:0.11, G:0.28, T:0.28
Consensus pattern (30 bp):
TTTGTGACGGAATAGTGGAACAGTCAGAAA
Found at i:4913950 original size:24 final size:24
Alignment explanation
Indices: 4913918--4913966 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
4913908 AGTCTTCCTG
4913918 ATGATGTATAAAACATCTATGTAC
1 ATGATGTATAAAACATCTATGTAC
4913942 ATGATGTATAAAACATCTATGTAC
1 ATGATGTATAAAACATCTATGTAC
4913966 A
1 A
4913967 ATGTCATGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.33
Consensus pattern (24 bp):
ATGATGTATAAAACATCTATGTAC
Found at i:4914544 original size:31 final size:29
Alignment explanation
Indices: 4914509--4914572 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 29
4914499 TATTCATAAC
* **
4914509 TTTTCCAAAATTATTGAATTGGTCCCCTAAA
1 TTTTCAAAAATTAAAGAA-TGGTCCCC-AAA
4914540 TTTTCAAAAATTAAAGAATGGTCCCCAAA
1 TTTTCAAAAATTAAAGAATGGTCCCCAAA
4914569 TTTT
1 TTTT
4914573 TATAAGGCTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 7 0.23
30 8 0.27
31 15 0.50
ACGTcount: A:0.36, C:0.17, G:0.09, T:0.38
Consensus pattern (29 bp):
TTTTCAAAAATTAAAGAATGGTCCCCAAA
Found at i:4921417 original size:41 final size:41
Alignment explanation
Indices: 4921371--4921448 Score: 120
Period size: 41 Copynumber: 1.9 Consensus size: 41
4921361 CTGGTGTGAC
* *
4921371 TGTTGGTGTGGTAGTGCAGAGAAGATTTAGAAGAGTGGTTT
1 TGTTGGCGTGGTACTGCAGAGAAGATTTAGAAGAGTGGTTT
* *
4921412 TGTTGGCGTGGTCCTGCAGAGAAGATTTGGAAGAGTG
1 TGTTGGCGTGGTACTGCAGAGAAGATTTAGAAGAGTG
4921449 AATTTCTGTT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 33 1.00
ACGTcount: A:0.23, C:0.06, G:0.40, T:0.31
Consensus pattern (41 bp):
TGTTGGCGTGGTACTGCAGAGAAGATTTAGAAGAGTGGTTT
Found at i:4922336 original size:2 final size:2
Alignment explanation
Indices: 4922324--4922363 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
4922314 TTTATTAAAC
4922324 TA TA T- TA 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 TA TA TA TA T
4922364 GTTATTTTCA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:4924261 original size:31 final size:31
Alignment explanation
Indices: 4924200--4924261 Score: 74
Period size: 31 Copynumber: 2.0 Consensus size: 31
4924190 GTACCTAGTA
*
4924200 GGGTCAAATCGAGTCGATTGGTTTTCGGTTC
1 GGGTCAAATCGAGTCGATTGGTTTTAGGTTC
*
4924231 GGGTCAATATCG-GATCGGTTGG-TTTAGGTTC
1 GGGTCAA-ATCGAG-TCGATTGGTTTTAGGTTC
4924262 TGGTAAGGCT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
31 16 0.59
32 11 0.41
ACGTcount: A:0.16, C:0.15, G:0.34, T:0.35
Consensus pattern (31 bp):
GGGTCAAATCGAGTCGATTGGTTTTAGGTTC
Found at i:4924320 original size:46 final size:46
Alignment explanation
Indices: 4924270--4924407 Score: 152
Period size: 46 Copynumber: 3.0 Consensus size: 46
4924260 TCTGGTAAGG
* * *
4924270 CTTTAGATTTTCAGGTCAATTTAGGTTGATTTCGGTTCGGATCAAC
1 CTTTAGATTTTCAAGTCAATTCAGGTTGATTTAGGTTCGGATCAAC
* * *
4924316 CTTTAAATTTTCAAGTCAATTCGGGTTGGTTTAGGTTCGGATCAAC
1 CTTTAGATTTTCAAGTCAATTCAGGTTGATTTAGGTTCGGATCAAC
** * ** * *
4924362 CTTTAGATTTTTGAGTTAATTCAAATTG-TTTCGGTTTGGATCAAC
1 CTTTAGATTTTCAAGTCAATTCAGGTTGATTTAGGTTCGGATCAAC
4924407 C
1 C
4924408 GTCGTCACCC
Statistics
Matches: 77, Mismatches: 15, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
45 16 0.21
46 61 0.79
ACGTcount: A:0.23, C:0.14, G:0.20, T:0.42
Consensus pattern (46 bp):
CTTTAGATTTTCAAGTCAATTCAGGTTGATTTAGGTTCGGATCAAC
Found at i:4924724 original size:5 final size:5
Alignment explanation
Indices: 4924714--4924739 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
4924704 AATATATATA
4924714 TTAAT TTAAT TTAAT TTAAT TTAAT T
1 TTAAT TTAAT TTAAT TTAAT TTAAT T
4924740 GTTTATATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
TTAAT
Found at i:4925172 original size:14 final size:15
Alignment explanation
Indices: 4925153--4925189 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
4925143 GTCTCGATTT
*
4925153 GGGTAAATTGG-TTC
1 GGGTAAATTGGATAC
4925167 GGGT-AATTGGATAC
1 GGGTAAATTGGATAC
4925181 GGGTAAATT
1 GGGTAAATT
4925190 TGCCAAGTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
13 6 0.30
14 10 0.50
15 4 0.20
ACGTcount: A:0.27, C:0.05, G:0.35, T:0.32
Consensus pattern (15 bp):
GGGTAAATTGGATAC
Found at i:4925302 original size:20 final size:19
Alignment explanation
Indices: 4925266--4925308 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
4925256 AATCTATTTT
* *
4925266 TTAAAAAAATATCATAAAA
1 TTAAAAAAAAATAATAAAA
*
4925285 TTAAAAAAAAAGTAATAAAC
1 TTAAAAAAAAA-TAATAAAA
4925305 TTAA
1 TTAA
4925309 GTTCTATTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.67, C:0.05, G:0.02, T:0.26
Consensus pattern (19 bp):
TTAAAAAAAAATAATAAAA
Found at i:4926133 original size:125 final size:125
Alignment explanation
Indices: 4925965--4926195 Score: 317
Period size: 125 Copynumber: 1.8 Consensus size: 125
4925955 TCTTGGTTGG
* *
4925965 TTCTTCATCAGATTGGGTAGGTGGTGGTTGCTTGTGGAGCAAGGAACCTAAA-TCGGAACGA-GG
1 TTCTTCATCAGATTGGGTAGGTGATGGTTGCTTGTAGAGCAAGGAACCTAAATTC-GAA-GATGG
* *
4926028 -TTCTCACCCAATTTTCTAGCCGAACCCGTGAAAGGTTTGAACTCAGTTTTACCGGCCATTTT
64 ATTCTCACCCAA-TTTCTAGCCAAACCAGTGAAAGGTTTGAACTCAGTTTTACCGGCCATTTT
* * *
4926090 TTCTTCATCAGATTGGGTAGTTGATGGTTGCTTGTCAG-GCAAGGAGCCTAAATTCGAATATGGA
1 TTCTTCATCAGATTGGGTAGGTGATGGTTGCTTGT-AGAGCAAGGAACCTAAATTCGAAGATGGA
* *
4926154 TTTTCACCCAATTTCTAGCTAAACCAGTGAAAGGTTTGAACT
65 TTCTCACCCAATTTCTAGCCAAACCAGTGAAAGGTTTGAACT
4926196 TGGATTTCTC
Statistics
Matches: 93, Mismatches: 9, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
124 1 0.01
125 79 0.85
126 13 0.14
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.32
Consensus pattern (125 bp):
TTCTTCATCAGATTGGGTAGGTGATGGTTGCTTGTAGAGCAAGGAACCTAAATTCGAAGATGGAT
TCTCACCCAATTTCTAGCCAAACCAGTGAAAGGTTTGAACTCAGTTTTACCGGCCATTTT
Found at i:4927323 original size:2 final size:2
Alignment explanation
Indices: 4927316--4927340 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4927306 TTAAATAATT
4927316 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 T
4927341 TGAGAAAAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4927832 original size:18 final size:19
Alignment explanation
Indices: 4927811--4927847 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
4927801 CTTTTATTAG
*
4927811 TTAAAAC-GAATTTAAATT
1 TTAAAACTGAAATTAAATT
4927829 TTAAAACTGAAATTAAATT
1 TTAAAACTGAAATTAAATT
4927848 GATATAACCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.51, C:0.05, G:0.05, T:0.38
Consensus pattern (19 bp):
TTAAAACTGAAATTAAATT
Found at i:4929037 original size:20 final size:19
Alignment explanation
Indices: 4928964--4929036 Score: 128
Period size: 19 Copynumber: 3.8 Consensus size: 19
4928954 AGTAGACTTT
4928964 AGAGTTTCAAAACTTCACA
1 AGAGTTTCAAAACTTCACA
4928983 AGAGTTTCAAAACTTCACA
1 AGAGTTTCAAAACTTCACA
*
4929002 AGAGTTTCAAAACTTTAACA
1 AGAGTTTCAAAAC-TTCACA
4929022 AGAGTTTCAAAACTT
1 AGAGTTTCAAAACTT
4929037 TCCTTGTAGT
Statistics
Matches: 52, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
19 34 0.65
20 18 0.35
ACGTcount: A:0.42, C:0.18, G:0.11, T:0.29
Consensus pattern (19 bp):
AGAGTTTCAAAACTTCACA
Found at i:4932856 original size:21 final size:21
Alignment explanation
Indices: 4932827--4932870 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
4932817 ACTCCTGGAG
* *
4932827 CTAGTTCCTCTCGAGCTGCTC
1 CTAGCTCCTCTCGAGCTCCTC
*
4932848 CTAGCTCCTCTCGTGCTCCTC
1 CTAGCTCCTCTCGAGCTCCTC
4932869 CT
1 CT
4932871 CCTCCTCCTC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.07, C:0.43, G:0.16, T:0.34
Consensus pattern (21 bp):
CTAGCTCCTCTCGAGCTCCTC
Found at i:4932871 original size:3 final size:3
Alignment explanation
Indices: 4932863--4932888 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
4932853 TCCTCTCGTG
4932863 CTC CTC CTC CTC CTC CTC CTC CTC CT
1 CTC CTC CTC CTC CTC CTC CTC CTC CT
4932889 TCGGCTCCGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.65, G:0.00, T:0.35
Consensus pattern (3 bp):
CTC
Found at i:4933594 original size:18 final size:19
Alignment explanation
Indices: 4933571--4933607 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
4933561 AAAGGGGGAG
4933571 AAATGTTAAGT-TTGAAAT
1 AAATGTTAAGTGTTGAAAT
4933589 AAATGTTAAGTGTTGAAAT
1 AAATGTTAAGTGTTGAAAT
4933608 GTTTTTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.43, C:0.00, G:0.19, T:0.38
Consensus pattern (19 bp):
AAATGTTAAGTGTTGAAAT
Found at i:4934078 original size:63 final size:64
Alignment explanation
Indices: 4934001--4934159 Score: 209
Period size: 63 Copynumber: 2.5 Consensus size: 64
4933991 GAATTAAATT
*
4934001 GAACATCGAATGCATTTCATGCATCGATGCACA-CCATGCACCGATACACT-GAGGAT-TTTATA
1 GAACATCGAATGCATTTGATGCATCGATGCACAGCCATGCACCGATACACTCG-GGATATTT-TA
4934063 A
64 A
* * * *
4934064 GAACATCGAATGCATTTGATACATCGATGCACCAGCCATGCATCGATGCACTCGGGCTATTTTAA
1 GAACATCGAATGCATTTGATGCATCGATGCA-CAGCCATGCACCGATACACTCGGGATATTTTAA
*
4934129 -AACATCGAATGCACTTGATGCATCGATGCAC
1 GAACATCGAATGCATTTGATGCATCGATGCAC
4934160 TCTTAGTGCA
Statistics
Matches: 85, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
63 30 0.35
64 30 0.35
65 21 0.25
66 4 0.05
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (64 bp):
GAACATCGAATGCATTTGATGCATCGATGCACAGCCATGCACCGATACACTCGGGATATTTTAA
Found at i:4934147 original size:64 final size:64
Alignment explanation
Indices: 4934001--4934159 Score: 209
Period size: 64 Copynumber: 2.5 Consensus size: 64
4933991 GAATTAAATT
*
4934001 GAACATCGAATGCATTTCATGCATCGATGCA-CACCATGCACCGATACACTGAGGATTTTATAA
1 GAACATCGAATGCATTTGATGCATCGATGCACCACCATGCACCGATACACTGAGGATTTTATAA
* * * *
4934064 GAACATCGAATGCATTTGATACATCGATGCACCAGCCATGCATCGATGCACTCG-GGCTATTT-T
1 GAACATCGAATGCATTTGATGCATCGATGCACCA-CCATGCACCGATACACT-GAGGAT-TTTAT
4934127 AA
63 AA
*
4934129 -AACATCGAATGCACTTGATGCATCGATGCAC
1 GAACATCGAATGCATTTGATGCATCGATGCAC
4934160 TCTTAGTGCA
Statistics
Matches: 85, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
63 29 0.34
64 31 0.36
65 21 0.25
66 4 0.05
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (64 bp):
GAACATCGAATGCATTTGATGCATCGATGCACCACCATGCACCGATACACTGAGGATTTTATAA
Found at i:4934159 original size:17 final size:19
Alignment explanation
Indices: 4934131--4934179 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
4934121 TATTTTAAAA
4934131 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
4934149 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
4934168 CACCGATGCACT
1 CATCGATGCACT
4934180 AAGGTTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:4934175 original size:64 final size:62
Alignment explanation
Indices: 4934001--4934179 Score: 186
Period size: 64 Copynumber: 2.8 Consensus size: 62
4933991 GAATTAAATT
* *
4934001 GAACATCGAATGCATTTCATGCATCGATGCACACCA-TGCACCGATACACTGAGGATTTTATAA
1 GAACATCGAATGCATTTGATGCATCGATG--CACCAGTGCACCGATGCACTGAGGATTTTATAA
* * *
4934064 GAACATCGAATGCATTTGATACATCGATGCACCAGCCATGCATCGATGCACTCG-GGCTATTT-T
1 GAACATCGAATGCATTTGATGCATCGATGCACCAG---TGCACCGATGCACT-GAGGAT-TTTAT
4934127 AA
61 AA
*
4934129 -AACATCGAATGCACTTGATGCATCGATGCACTCTTAGTGCACCGATGCACT
1 GAACATCGAATGCATTTGATGCATCGATGCAC-C--AGTGCACCGATGCACT
4934180 AAGGTTCCAA
Statistics
Matches: 99, Mismatches: 8, Indels: 17
0.80 0.06 0.14
Matches are distributed among these distances:
61 5 0.05
63 27 0.27
64 42 0.42
65 19 0.19
66 4 0.04
67 2 0.02
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.26
Consensus pattern (62 bp):
GAACATCGAATGCATTTGATGCATCGATGCACCAGTGCACCGATGCACTGAGGATTTTATAA
Found at i:4936551 original size:2 final size:2
Alignment explanation
Indices: 4936544--4936573 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
4936534 TTACAAAAAT
4936544 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
4936574 AAGAAAACCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4937255 original size:29 final size:29
Alignment explanation
Indices: 4937202--4937264 Score: 83
Period size: 29 Copynumber: 2.1 Consensus size: 29
4937192 AATTATGTTG
*
4937202 TTGCTTTCTTCGTAAAATATTATTGGGTTA
1 TTGCTTTCTTC-TAAAATACTATTGGGTTA
*
4937232 TTGCTTTCTT-TATAAATACTATTGGGTTG
1 TTGCTTTCTTCTA-AAATACTATTGGGTTA
4937261 TTGC
1 TTGC
4937265 AGCAAATAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
28 2 0.07
29 18 0.60
30 10 0.33
ACGTcount: A:0.21, C:0.11, G:0.17, T:0.51
Consensus pattern (29 bp):
TTGCTTTCTTCTAAAATACTATTGGGTTA
Found at i:4948043 original size:17 final size:18
Alignment explanation
Indices: 4948013--4948046 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
4948003 TTTCGGTTTG
*
4948013 AAAAAATCCGGTTTTTTT
1 AAAAAATCCAGTTTTTTT
4948031 AAAAAA-CCAGTTTTTT
1 AAAAAATCCAGTTTTTT
4948047 AAACCCCATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.38, C:0.12, G:0.09, T:0.41
Consensus pattern (18 bp):
AAAAAATCCAGTTTTTTT
Found at i:4957979 original size:3 final size:3
Alignment explanation
Indices: 4957973--4958043 Score: 72
Period size: 3 Copynumber: 23.7 Consensus size: 3
4957963 TTTTTTTTAA
* * * *
4957973 TAT TAT T-T ATAT TAT TAT TAT TAT TAT AAA TAT TAT TAT CAA TAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
4958018 TAT TTT TAT TAA TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
4958044 CAAACATACC
Statistics
Matches: 54, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
2 1 0.02
3 52 0.96
4 1 0.02
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:4957980 original size:15 final size:15
Alignment explanation
Indices: 4957962--4958043 Score: 80
Period size: 15 Copynumber: 5.7 Consensus size: 15
4957952 TTTTTTCTTC
*
4957962 ATTTTTTTTAATATT
1 ATTTTTATTAATATT
* *
4957977 ATTTATATTATTATT
1 ATTTTTATTAATATT
*
4957992 ATTATTA-TAA-A-T
1 ATTTTTATTAATATT
* *
4958004 ATTATTATCAATATT
1 ATTTTTATTAATATT
4958019 ATTTTTATTAATATT
1 ATTTTTATTAATATT
*
4958034 ATTATTATTA
1 ATTTTTATTA
4958044 CAAACATACC
Statistics
Matches: 54, Mismatches: 10, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
12 8 0.15
13 3 0.06
14 3 0.06
15 40 0.74
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (15 bp):
ATTTTTATTAATATT
Found at i:4959380 original size:24 final size:26
Alignment explanation
Indices: 4959353--4959400 Score: 64
Period size: 24 Copynumber: 1.9 Consensus size: 26
4959343 TTTCATTTAT
*
4959353 TATAAAGTT-TTATTTT-TTTTTAAA
1 TATAAAGTTCTAATTTTATTTTTAAA
*
4959377 TATATAGTTCTAATTTTATTTTTA
1 TATAAAGTTCTAATTTTATTTTTA
4959401 TTATTATTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 8 0.40
25 6 0.30
26 6 0.30
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.62
Consensus pattern (26 bp):
TATAAAGTTCTAATTTTATTTTTAAA
Found at i:4959420 original size:27 final size:27
Alignment explanation
Indices: 4959388--4959464 Score: 84
Period size: 27 Copynumber: 2.9 Consensus size: 27
4959378 ATATAGTTCT
*
4959388 AATTTTATTTTTATTATTATTTATTTA
1 AATTTTATTTTTATTATTATATATTTA
** * *
4959415 TGTTTTAATTTTACTTGTT-TATATTTA
1 AATTTTATTTTTA-TTATTATATATTTA
*
4959442 AATATTATTTTTATTATTATATA
1 AATTTTATTTTTATTATTATATA
4959465 GTCATATAAA
Statistics
Matches: 38, Mismatches: 10, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
26 4 0.11
27 30 0.79
28 4 0.11
ACGTcount: A:0.30, C:0.01, G:0.03, T:0.66
Consensus pattern (27 bp):
AATTTTATTTTTATTATTATATATTTA
Done.