Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006023.1 Hibiscus syriacus cultivar Beakdansim tig00014213_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: 1315283
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 8
Found at i:1200281 original size:2 final size:2
Alignment explanation
Indices: 1200274--1200302 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1200264 CCCTAAATAC
1200274 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 A
1200303 GGTGTACATA
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:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1203533 original size:25 final size:26
Alignment explanation
Indices: 1203473--1203535 Score: 78
Period size: 26 Copynumber: 2.4 Consensus size: 26
1203463 TTTTTCTGTT
1203473 ACATGCCCAAAACCGAAAACCTAATTA
1 ACAT-CCCAAAACCGAAAACCTAATTA
1203500 ACATCCCAAAACC-AGAAACC-AATTA
1 ACATCCCAAAACCGA-AAACCTAATTA
1203525 ACAAT-CCAAAA
1 AC-ATCCCAAAA
1203536 TAGGAGGCCC
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
25 14 0.41
26 16 0.47
27 4 0.12
ACGTcount: A:0.52, C:0.30, G:0.05, T:0.13
Consensus pattern (26 bp):
ACATCCCAAAACCGAAAACCTAATTA
Found at i:1204845 original size:15 final size:17
Alignment explanation
Indices: 1204805--1204845 Score: 50
Period size: 19 Copynumber: 2.4 Consensus size: 17
1204795 TTTTTATGCT
1204805 TATTTTATATTGAGTGTCC
1 TATTTTA-A-TGAGTGTCC
1204824 TATTTTAATGAGT-TCC
1 TATTTTAATGAGTGTCC
1204840 -ATTTTA
1 TATTTTA
1204846 GTCCTGAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 6 0.27
16 3 0.14
17 5 0.23
18 1 0.05
19 7 0.32
ACGTcount: A:0.24, C:0.10, G:0.12, T:0.54
Consensus pattern (17 bp):
TATTTTAATGAGTGTCC
Found at i:1221013 original size:21 final size:21
Alignment explanation
Indices: 1220989--1221028 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
1220979 TTATGCAATC
1220989 AAAGAGTTTGGTTTCATCAGA
1 AAAGAGTTTGGTTTCATCAGA
1221010 AAAGAGTTTGGTTTCATCA
1 AAAGAGTTTGGTTTCATCA
1221029 TAAATGAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.10, G:0.23, T:0.35
Consensus pattern (21 bp):
AAAGAGTTTGGTTTCATCAGA
Found at i:1226262 original size:12 final size:12
Alignment explanation
Indices: 1226245--1226270 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1226235 AGCTTCTTCC
1226245 TCTAATACTAAT
1 TCTAATACTAAT
1226257 TCTAATACTAAT
1 TCTAATACTAAT
1226269 TC
1 TC
1226271 CTTGGAGTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.19, G:0.00, T:0.42
Consensus pattern (12 bp):
TCTAATACTAAT
Found at i:1236668 original size:6 final size:6
Alignment explanation
Indices: 1236657--1236685 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
1236647 TATTCTCCTA
1236657 TATATG TATATG TATATG TATATG TATAT
1 TATATG TATATG TATATG TATATG TATAT
1236686 ATATCTTCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.52
Consensus pattern (6 bp):
TATATG
Found at i:1238703 original size:23 final size:23
Alignment explanation
Indices: 1238625--1238693 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
1238615 CACCACAGCT
* *
1238625 CATATAAATGCACCGAAGTGCCA
1 CATAGAAATGCACCGTAGTGCCA
* *
1238648 CATAGAATTGCACCGTAGTGCCG
1 CATAGAAATGCACCGTAGTGCCA
*
1238671 CGTAGAAATGCACCGTAGTGCCA
1 CATAGAAATGCACCGTAGTGCCA
1238694 TATAATAATG
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.32, C:0.26, G:0.23, T:0.19
Consensus pattern (23 bp):
CATAGAAATGCACCGTAGTGCCA
Found at i:1240116 original size:18 final size:18
Alignment explanation
Indices: 1240093--1240127 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1240083 GTTCTTAAGG
1240093 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
*
1240111 AGTGGTCCTTCTGGACA
1 AGTGGTCCTTCGGGACA
1240128 AATTCTAAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.23, G:0.31, T:0.29
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:1242733 original size:23 final size:23
Alignment explanation
Indices: 1242700--1242798 Score: 103
Period size: 23 Copynumber: 4.3 Consensus size: 23
1242690 ATTGAGAGTT
*
1242700 CTATGTGGTCCTTTGGGACAAAC
1 CTATGTGGTCCTTCGGGACAAAC
* * * *
1242723 CTATGTAGTCCTTCAGGATAATC
1 CTATGTGGTCCTTCGGGACAAAC
*
1242746 TTATGTGGTCCTTCGGGACAACAC
1 CTATGTGGTCCTTCGGGACAA-AC
* *
1242770 CTATGTTGTCCTTCGGAACAAA-
1 CTATGTGGTCCTTCGGGACAAAC
1242792 -TATGTGG
1 CTATGTGG
1242799 CACCTTGGTG
Statistics
Matches: 61, Mismatches: 14, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
21 6 0.10
23 36 0.59
24 19 0.31
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.32
Consensus pattern (23 bp):
CTATGTGGTCCTTCGGGACAAAC
Found at i:1243261 original size:24 final size:26
Alignment explanation
Indices: 1243222--1243276 Score: 73
Period size: 25 Copynumber: 2.2 Consensus size: 26
1243212 TGCTTTGATC
1243222 TATTT-TGTAAAGTTA-T-ATTTTTT
1 TATTTATGTAAAGTTATTAATTTTTT
1243245 GTATTTATGTAAA-TTATTAATTTTTT
1 -TATTTATGTAAAGTTATTAATTTTTT
1243271 TATTTA
1 TATTTA
1243277 AATGTGAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
24 8 0.29
25 13 0.46
26 7 0.25
ACGTcount: A:0.29, C:0.00, G:0.07, T:0.64
Consensus pattern (26 bp):
TATTTATGTAAAGTTATTAATTTTTT
Found at i:1244824 original size:20 final size:19
Alignment explanation
Indices: 1244755--1244984 Score: 142
Period size: 20 Copynumber: 11.6 Consensus size: 19
1244745 AAATGACCAA
* * *
1244755 CAAATTCGCAACGCGATCT
1 CAAATTCGCAACACAATTT
* *
1244774 CAAATTCGCAACACAAACTC
1 CAAATTCGCAACAC-AATTT
* * * *
1244794 CTATTTTGCAACCCAATTT
1 CAAATTCGCAACACAATTT
*
1244813 CCAAATTCGCAACGCGAATTT
1 -CAAATTCGCAACAC-AATTT
* **
1244834 GTAAA-TCGCAACACAGAAGT
1 -CAAATTCGCAACACA-ATTT
* **
1244854 CAAATTCGCAACAGAGAAGT
1 CAAATTCGCAACACA-ATTT
**
1244874 CAAATTCGCAACACAAAAGT
1 CAAATTCGCAACAC-AATTT
**
1244894 CAAATTCGCAACACAGAAGT
1 CAAATTCGCAACACA-ATTT
*
1244914 CAAATTTGCAACACTGAATTT
1 CAAATTCGCAACAC--AATTT
1244935 CAAATTCGCAACTA-AATTT
1 CAAATTCGCAAC-ACAATTT
1244954 CAAATTCGCAACTA-AATTT
1 CAAATTCGCAAC-ACAATTT
1244973 CAAATTCGCAAC
1 CAAATTCGCAAC
1244985 TCGATTTTCG
Statistics
Matches: 174, Mismatches: 27, Indels: 20
0.79 0.12 0.09
Matches are distributed among these distances:
19 57 0.33
20 93 0.53
21 22 0.13
22 2 0.01
ACGTcount: A:0.40, C:0.25, G:0.11, T:0.23
Consensus pattern (19 bp):
CAAATTCGCAACACAATTT
Found at i:1244878 original size:60 final size:61
Alignment explanation
Indices: 1244839--1244965 Score: 177
Period size: 60 Copynumber: 2.1 Consensus size: 61
1244829 AATTTGTAAA
*
1244839 TCGCAACACAGAAGTCAAATTCGCAACAGAGAA-GTCAAATTCGCAACACAAAAGTCAAAT
1 TCGCAACACAGAAGTCAAATTCGCAACACAGAATGTCAAATTCGCAACACAAAAGTCAAAT
* * * * **
1244899 TCGCAACACAGAAGTCAAATTTGCAACACTGAATTTCAAATTCGCAAC-TAAATTTCAAAT
1 TCGCAACACAGAAGTCAAATTCGCAACACAGAATGTCAAATTCGCAACACAAAAGTCAAAT
1244959 TCGCAAC
1 TCGCAAC
1244966 TAAATTTCAA
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
60 46 0.78
61 13 0.22
ACGTcount: A:0.43, C:0.24, G:0.13, T:0.20
Consensus pattern (61 bp):
TCGCAACACAGAAGTCAAATTCGCAACACAGAATGTCAAATTCGCAACACAAAAGTCAAAT
Found at i:1244954 original size:19 final size:19
Alignment explanation
Indices: 1244930--1244985 Score: 112
Period size: 19 Copynumber: 2.9 Consensus size: 19
1244920 TGCAACACTG
1244930 AATTTCAAATTCGCAACTA
1 AATTTCAAATTCGCAACTA
1244949 AATTTCAAATTCGCAACTA
1 AATTTCAAATTCGCAACTA
1244968 AATTTCAAATTCGCAACT
1 AATTTCAAATTCGCAACT
1244986 CGATTTTCGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 37 1.00
ACGTcount: A:0.41, C:0.21, G:0.05, T:0.32
Consensus pattern (19 bp):
AATTTCAAATTCGCAACTA
Found at i:1244991 original size:19 final size:19
Alignment explanation
Indices: 1244893--1244991 Score: 90
Period size: 19 Copynumber: 5.1 Consensus size: 19
1244883 AACACAAAAG
* **
1244893 TCAAATTCGCAACACAGAAG
1 TCAAATTCGCAACTC-GATT
* *
1244913 TCAAATTTGCAACACTGAATT
1 TCAAATTCGCAACTC-G-ATT
**
1244934 TCAAATTCGCAACTAAATT
1 TCAAATTCGCAACTCGATT
**
1244953 TCAAATTCGCAACTAAATT
1 TCAAATTCGCAACTCGATT
1244972 TCAAATTCGCAACTCGATT
1 TCAAATTCGCAACTCGATT
1244991 T
1 T
1244992 TCGAATATTC
Statistics
Matches: 68, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
19 40 0.59
20 15 0.22
21 13 0.19
ACGTcount: A:0.39, C:0.22, G:0.09, T:0.29
Consensus pattern (19 bp):
TCAAATTCGCAACTCGATT
Found at i:1246283 original size:23 final size:23
Alignment explanation
Indices: 1246257--1246301 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1246247 CACCACAGCT
*
1246257 CGTATAAATGCACCGAAGTGCCC
1 CGTAGAAATGCACCGAAGTGCCC
* *
1246280 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
1246302 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:1246782 original size:29 final size:29
Alignment explanation
Indices: 1246749--1246833 Score: 129
Period size: 29 Copynumber: 3.0 Consensus size: 29
1246739 TTTTCTGCAT
1246749 ATTCATGTCATGTAATACATATAATATGA
1 ATTCATGTCATGTAATACATATAATATGA
* *
1246778 ATTCATGTCATGTAATACATTTAATATAA
1 ATTCATGTCATGTAATACATATAATATGA
1246807 ATTCATGTCATGT-AT-CATCATAATATG
1 ATTCATGTCATGTAATACAT-ATAATATG
1246834 GAATGTGATC
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
27 3 0.06
28 8 0.16
29 40 0.78
ACGTcount: A:0.39, C:0.12, G:0.09, T:0.40
Consensus pattern (29 bp):
ATTCATGTCATGTAATACATATAATATGA
Found at i:1247158 original size:19 final size:20
Alignment explanation
Indices: 1247121--1247158 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1247111 TTTTTTCTCA
*
1247121 TGGGGGAATCGGTTCCCCCC
1 TGGGGGAATCGATTCCCCCC
*
1247141 TGGGGGTATCGATTCCCC
1 TGGGGGAATCGATTCCCC
1247159 TCAAGCATTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.11, C:0.32, G:0.34, T:0.24
Consensus pattern (20 bp):
TGGGGGAATCGATTCCCCCC
Found at i:1247244 original size:65 final size:66
Alignment explanation
Indices: 1247123--1247269 Score: 217
Period size: 65 Copynumber: 2.2 Consensus size: 66
1247113 TTTTCTCATG
* *
1247123 GGGGAATCGGTTCCCCCCTGGGGGTATCGATTCCCCTCAAGCATTCTGGAATTTCATATACGATG
1 GGGGTATCGGTTCCCCCCTGGGGGTATCGATTCCCCTCAAGCATTCTGGAAATTCAT-TACGATG
1247188 -A
65 AA
* * * *
1247189 TGGGTATCGGTTCCCCCCTGGGGGTATCGATT-CCCTCTAGCATTCTGGAAATTCATTTCGTTGA
1 GGGGTATCGGTTCCCCCCTGGGGGTATCGATTCCCCTCAAGCATTCTGGAAATTCATTACGATGA
1247253 A
66 A
1247254 GGGGTATCGGTTCCCC
1 GGGGTATCGGTTCCCC
1247270 TTGAATGGGT
Statistics
Matches: 73, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
64 5 0.07
65 38 0.52
66 30 0.41
ACGTcount: A:0.18, C:0.26, G:0.27, T:0.30
Consensus pattern (66 bp):
GGGGTATCGGTTCCCCCCTGGGGGTATCGATTCCCCTCAAGCATTCTGGAAATTCATTACGATGA
A
Found at i:1247279 original size:21 final size:21
Alignment explanation
Indices: 1247249--1247291 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1247239 ATTCATTTCG
* *
1247249 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
1247270 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
1247291 T
1 T
1247292 AACCCAGAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:1253352 original size:23 final size:23
Alignment explanation
Indices: 1253326--1253370 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1253316 CACCACAGCT
*
1253326 CGTATAAATGCACCGAAGTGCCC
1 CGTAGAAATGCACCGAAGTGCCC
* *
1253349 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
1253371 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:1253621 original size:149 final size:149
Alignment explanation
Indices: 1253351--1253652 Score: 577
Period size: 149 Copynumber: 2.0 Consensus size: 149
1253341 AAGTGCCCCG
*
1253351 TAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAATCA
1 TAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGAATCA
*
1253416 TATACATATACTATGGATCAAGTATGTGTCTTTCAAGACTTCACACAGGTTCCAAAGAATATACA
66 TATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACAGGTTCCAAAGAATATACA
1253481 TATGTCCTAAAGAACCGAA
131 TATGTCCTAAAGAACCGAA
*
1253500 TAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCGCATAGAATTCCTTAAGAATCA
1 TAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGAATCA
1253565 TATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACAGGTTCCAAAGAATATACA
66 TATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACAGGTTCCAAAGAATATACA
1253630 TATGTCCTAAAGAACCGAA
131 TATGTCCTAAAGAACCGAA
1253649 TAGA
1 TAGA
1253653 CCCTCTACTC
Statistics
Matches: 150, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
149 150 1.00
ACGTcount: A:0.38, C:0.19, G:0.16, T:0.27
Consensus pattern (149 bp):
TAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGAATCA
TATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACAGGTTCCAAAGAATATACA
TATGTCCTAAAGAACCGAA
Found at i:1253854 original size:29 final size:29
Alignment explanation
Indices: 1253821--1253905 Score: 129
Period size: 29 Copynumber: 3.0 Consensus size: 29
1253811 TTTTCTGCAT
1253821 ATTCATGTCATGTAATACATATAATATGA
1 ATTCATGTCATGTAATACATATAATATGA
* *
1253850 ATTCATGTCATGTAATACATTTAATATAA
1 ATTCATGTCATGTAATACATATAATATGA
1253879 ATTCATGTCATGT-AT-CATCATAATATG
1 ATTCATGTCATGTAATACAT-ATAATATG
1253906 GAATGTGATC
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
27 3 0.06
28 8 0.16
29 40 0.78
ACGTcount: A:0.39, C:0.12, G:0.09, T:0.40
Consensus pattern (29 bp):
ATTCATGTCATGTAATACATATAATATGA
Found at i:1254354 original size:21 final size:21
Alignment explanation
Indices: 1254324--1254366 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1254314 ATTCATTTCG
* *
1254324 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
1254345 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
1254366 T
1 T
1254367 AACCCAGAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:1254366 original size:67 final size:67
Alignment explanation
Indices: 1254195--1254344 Score: 230
Period size: 67 Copynumber: 2.2 Consensus size: 67
1254185 TTTTCTCATG
* *
1254195 GGGGAATCGGTTCCCCCCCTGGGGGTATCGATTCCCCTCAAGCATTCTGGAATTTCATATACGAT
1 GGGGTATCGGTT-CCCCCCTGGGGGTATCGATTCCCCTCAAGCATTCTGGAAATTCATATACGAT
*
1254260 GAT
65 GAA
* * *
1254263 GGGGTATCGGTTCCCCCCTGGGGGTATCGATTCCCCTCTAGCATTCTGGAAATTCAT-TTCGTTG
1 GGGGTATCGGTTCCCCCCTGGGGGTATCGATTCCCCTCAAGCATTCTGGAAATTCATATACGATG
1254327 AA
66 AA
1254329 GGGGTATCGGTTCCCC
1 GGGGTATCGGTTCCCC
1254345 TTGAATGGGT
Statistics
Matches: 76, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
66 22 0.29
67 43 0.57
68 11 0.14
ACGTcount: A:0.17, C:0.27, G:0.27, T:0.29
Consensus pattern (67 bp):
GGGGTATCGGTTCCCCCCTGGGGGTATCGATTCCCCTCAAGCATTCTGGAAATTCATATACGATG
AA
Found at i:1257375 original size:18 final size:18
Alignment explanation
Indices: 1257352--1257387 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1257342 AAGCAAAAGG
*
1257352 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
1257370 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
1257388 CAACCGGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.25, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:1257645 original size:20 final size:20
Alignment explanation
Indices: 1257620--1257693 Score: 130
Period size: 20 Copynumber: 3.7 Consensus size: 20
1257610 TGCGAATGTT
*
1257620 GCGAAAGTTAAATTCGCAAC
1 GCGAAAGTCAAATTCGCAAC
*
1257640 GCGAAAGTCAAATTCACAAC
1 GCGAAAGTCAAATTCGCAAC
1257660 GCGAAAGTCAAATTCGCAAC
1 GCGAAAGTCAAATTCGCAAC
1257680 GCGAAAGTCAAATT
1 GCGAAAGTCAAATT
1257694 GCGAAAATCA
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 51 1.00
ACGTcount: A:0.42, C:0.22, G:0.19, T:0.18
Consensus pattern (20 bp):
GCGAAAGTCAAATTCGCAAC
Found at i:1257705 original size:34 final size:34
Alignment explanation
Indices: 1257618--1257718 Score: 112
Period size: 40 Copynumber: 2.8 Consensus size: 34
1257608 GTTGCGAATG
*
1257618 TTGCGAAAGTTAAATTCGCAACGCGAAAGTCAAA
1 TTGCGAAAGTCAAATTCGCAACGCGAAAGTCAAA
1257652 TTCACAACGCGAAAGTCAAATTCGCAACGCGAAAGTCAAA
1 TT------GCGAAAGTCAAATTCGCAACGCGAAAGTCAAA
* * *
1257692 TTGCGAAAATCAAAATCACAACGCGAA
1 TTGCGAAAGTCAAATTCGCAACGCGAA
1257719 TTTGACTTTC
Statistics
Matches: 57, Mismatches: 4, Indels: 12
0.78 0.05 0.16
Matches are distributed among these distances:
34 24 0.42
40 33 0.58
ACGTcount: A:0.44, C:0.22, G:0.18, T:0.17
Consensus pattern (34 bp):
TTGCGAAAGTCAAATTCGCAACGCGAAAGTCAAA
Found at i:1257737 original size:20 final size:20
Alignment explanation
Indices: 1257714--1257751 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1257704 AAATCACAAC
*
1257714 GCGAATTTGACTTTCGCATT
1 GCGAATTTGACTATCGCATT
1257734 GCGAATTTGACTATCGCA
1 GCGAATTTGACTATCGCA
1257752 ACGCAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.34
Consensus pattern (20 bp):
GCGAATTTGACTATCGCATT
Found at i:1257761 original size:54 final size:54
Alignment explanation
Indices: 1257703--1257845 Score: 209
Period size: 54 Copynumber: 2.7 Consensus size: 54
1257693 TGCGAAAATC
* *
1257703 AAAATCACAACGCGAATTTGACTTTCGCATTGCGAATTTGACTATCGCAACGCA-
1 AAAATCGCAACGCGAATTTGACTTTCGCGTTGCGAATTTGACTATCGCAACG-AG
* * * *
1257757 AAAATCGCAATGCAAATTTAACTTTCGCGTTACGAATTTGACTATCGCAACGAG
1 AAAATCGCAACGCGAATTTGACTTTCGCGTTGCGAATTTGACTATCGCAACGAG
1257811 AAAATCGCAACGCGAATTTG-CTTTCGCGTTGCGAA
1 AAAATCGCAACGCGAATTTGACTTTCGCGTTGCGAA
1257846 AGTGTACCTT
Statistics
Matches: 78, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
53 15 0.19
54 63 0.81
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.27
Consensus pattern (54 bp):
AAAATCGCAACGCGAATTTGACTTTCGCGTTGCGAATTTGACTATCGCAACGAG
Found at i:1257965 original size:14 final size:14
Alignment explanation
Indices: 1257946--1257972 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1257936 ATAATTCTTA
1257946 TTTACAAATCAACT
1 TTTACAAATCAACT
1257960 TTTACAAATCAAC
1 TTTACAAATCAAC
1257973 AAGCAAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.22, G:0.00, T:0.33
Consensus pattern (14 bp):
TTTACAAATCAACT
Found at i:1258008 original size:51 final size:48
Alignment explanation
Indices: 1257892--1257994 Score: 129
Period size: 46 Copynumber: 2.1 Consensus size: 48
1257882 TGCATATTGA
* *
1257892 ATTTAAACAAATCAACTTTTACAAATCAATGAAATAAGTAAAAAATAATTCTT
1 ATTT-AACAAATCAACTTTTACAAATC----AAACAAGCAAAAAATAATTCTT
1257945 ATTT-ACAAATCAACTTTTACAAATC-AACAAGCAAAAAATAATTCTT
1 ATTTAACAAATCAACTTTTACAAATCAAACAAGCAAAAAATAATTCTT
1257991 ATTT
1 ATTT
1257995 CCTCAACAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
46 23 0.48
51 21 0.44
53 4 0.08
ACGTcount: A:0.50, C:0.14, G:0.03, T:0.33
Consensus pattern (48 bp):
ATTTAACAAATCAACTTTTACAAATCAAACAAGCAAAAAATAATTCTT
Found at i:1259412 original size:21 final size:21
Alignment explanation
Indices: 1259388--1259486 Score: 103
Period size: 21 Copynumber: 4.7 Consensus size: 21
1259378 GCGGGCGGGA
*
1259388 CCTCTTGAACGATGACAGGGG
1 CCTCTTGAACGATGAGAGGGG
* * *
1259409 CCTCTTGAACGGTGGGAGTGG
1 CCTCTTGAACGATGAGAGGGG
*
1259430 CCTCTTCG-ATGATGAGAGGGG
1 CCTCTT-GAACGATGAGAGGGG
**
1259451 CCTCTTGAACGAT-AGGAGGCA
1 CCTCTTGAACGATGA-GAGGGG
1259472 CCTCTTGAACGATGA
1 CCTCTTGAACGATGA
1259487 TAGGTGCATC
Statistics
Matches: 63, Mismatches: 11, Indels: 7
0.78 0.14 0.09
Matches are distributed among these distances:
20 2 0.03
21 59 0.94
22 2 0.03
ACGTcount: A:0.22, C:0.22, G:0.33, T:0.22
Consensus pattern (21 bp):
CCTCTTGAACGATGAGAGGGG
Found at i:1259434 original size:42 final size:42
Alignment explanation
Indices: 1259387--1259486 Score: 123
Period size: 42 Copynumber: 2.4 Consensus size: 42
1259377 GGCGGGCGGG
* *
1259387 ACCTCTTGAACGATGACAGGGGCCTCTTGAACGGTGGGAGTG-
1 ACCTCTTGAACGATGACAGGGGCCTCTTGAACGATAGGAG-GC
* * *
1259429 GCCTCTTCG-ATGATGAGAGGGGCCTCTTGAACGATAGGAGGC
1 ACCTCTT-GAACGATGACAGGGGCCTCTTGAACGATAGGAGGC
1259471 ACCTCTTGAACGATGA
1 ACCTCTTGAACGATGA
1259487 TAGGTGCATC
Statistics
Matches: 48, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
41 2 0.04
42 45 0.94
43 1 0.02
ACGTcount: A:0.23, C:0.22, G:0.33, T:0.22
Consensus pattern (42 bp):
ACCTCTTGAACGATGACAGGGGCCTCTTGAACGATAGGAGGC
Found at i:1259807 original size:21 final size:21
Alignment explanation
Indices: 1259783--1259837 Score: 101
Period size: 21 Copynumber: 2.6 Consensus size: 21
1259773 TAGAGTGGCA
*
1259783 ACCTCATCACGTAAAGTAGAT
1 ACCTCACCACGTAAAGTAGAT
1259804 ACCTCACCACGTAAAGTAGAT
1 ACCTCACCACGTAAAGTAGAT
1259825 ACCTCACCACGTA
1 ACCTCACCACGTA
1259838 GCGCGCCATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.36, C:0.31, G:0.13, T:0.20
Consensus pattern (21 bp):
ACCTCACCACGTAAAGTAGAT
Found at i:1261677 original size:20 final size:20
Alignment explanation
Indices: 1261654--1261794 Score: 170
Period size: 20 Copynumber: 7.4 Consensus size: 20
1261644 TCTGAAACTT
*
1261654 AAAATTGCAACGCGAAAATG
1 AAAATCGCAACGCGAAAATG
1261674 AAAATCGCAACGCGAAAATG
1 AAAATCGCAACGCGAAAATG
* *
1261694 AAAATCGCAACTCGAACATG
1 AAAATCGCAACGCGAAAATG
*
1261714 AAAATCGCAACAC--AAAT-
1 AAAATCGCAACGCGAAAATG
*
1261731 ---ATCGCAACGCGAACATG
1 AAAATCGCAACGCGAAAATG
*
1261748 AAAATCGCAACGCGAAAATA
1 AAAATCGCAACGCGAAAATG
*
1261768 AAAATCGCAACGCGAAACT-
1 AAAATCGCAACGCGAAAATG
1261787 AAAATCGC
1 AAAATCGC
1261795 GTTGCGATTT
Statistics
Matches: 105, Mismatches: 10, Indels: 13
0.82 0.08 0.10
Matches are distributed among these distances:
14 9 0.09
16 3 0.03
18 3 0.03
19 8 0.08
20 82 0.78
ACGTcount: A:0.49, C:0.23, G:0.16, T:0.12
Consensus pattern (20 bp):
AAAATCGCAACGCGAAAATG
Found at i:1261692 original size:34 final size:34
Alignment explanation
Indices: 1261654--1261766 Score: 120
Period size: 34 Copynumber: 3.1 Consensus size: 34
1261644 TCTGAAACTT
*
1261654 AAAATTGCAACGCGAAAATGAAAATCGCAACGCG
1 AAAATTGCAACGCGAACATGAAAATCGCAACGCG
* *
1261688 AAAATGAAAATCGCAACTCGAACATGAAAATCGCAACAC-
1 AAAAT-----T-GCAACGCGAACATGAAAATCGCAACGCG
*
1261727 AAATATCGCAACGCGAACATGAAAATCGCAACGCG
1 AAA-ATTGCAACGCGAACATGAAAATCGCAACGCG
1261762 AAAAT
1 AAAAT
1261767 AAAAATCGCA
Statistics
Matches: 65, Mismatches: 6, Indels: 16
0.75 0.07 0.18
Matches are distributed among these distances:
34 32 0.49
35 3 0.05
39 4 0.06
40 26 0.40
ACGTcount: A:0.49, C:0.22, G:0.17, T:0.12
Consensus pattern (34 bp):
AAAATTGCAACGCGAACATGAAAATCGCAACGCG
Found at i:1271706 original size:14 final size:14
Alignment explanation
Indices: 1271687--1271716 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1271677 TATTACTTTG
1271687 TAATCACCTTAAAC
1 TAATCACCTTAAAC
*
1271701 TAATCACTTTAAAC
1 TAATCACCTTAAAC
1271715 TA
1 TA
1271717 TTAAAAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.43, C:0.23, G:0.00, T:0.33
Consensus pattern (14 bp):
TAATCACCTTAAAC
Found at i:1273492 original size:31 final size:30
Alignment explanation
Indices: 1273457--1273541 Score: 91
Period size: 31 Copynumber: 2.7 Consensus size: 30
1273447 TCAATAAAGT
1273457 TTAAAAAATTATAAAATACTTATTAAATTTA
1 TTAAAAAATTATAAAATA-TTATTAAATTTA
* *
1273488 TTAAAAGATTATAAAATTATTAATAAATTTA
1 TTAAAAAATTATAAAA-TATTATTAAATTTA
* *
1273519 TCT-AAATACTATAAAATAATTAT
1 T-TAAAAAATTATAAAAT-ATTAT
1273542 ATATATATTA
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
30 1 0.02
31 42 0.91
32 3 0.07
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.41
Consensus pattern (30 bp):
TTAAAAAATTATAAAATATTATTAAATTTA
Found at i:1273519 original size:20 final size:20
Alignment explanation
Indices: 1273452--1273519 Score: 54
Period size: 19 Copynumber: 3.5 Consensus size: 20
1273442 TTTCGTCAAT
*
1273452 AAAG-TTTAAAAAATTA-TA
1 AAAGATTTATAAAATTATTA
* * *
1273470 AAATACTTATTAAATTTATTA
1 AAAGATTTA-TAAAATTATTA
1273491 AAAGA-TTATAAAATTATTA
1 AAAGATTTATAAAATTATTA
1273510 ATAA-ATTTAT
1 A-AAGATTTAT
1273520 CTAAATACTA
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
18 3 0.08
19 15 0.38
20 15 0.38
21 6 0.15
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.41
Consensus pattern (20 bp):
AAAGATTTATAAAATTATTA
Found at i:1275746 original size:27 final size:28
Alignment explanation
Indices: 1275699--1275752 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 28
1275689 CGGGTTAGTG
1275699 CGAACAATAAAAACTAAAAGAGTTAGCT
1 CGAACAATAAAAACTAAAAGAGTTAGCT
1275727 CGAACAATAAAAA-TAAAAGAGTTAGC
1 CGAACAATAAAAACTAAAAGAGTTAGC
1275753 GGGTTAGTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
27 13 0.50
28 13 0.50
ACGTcount: A:0.56, C:0.13, G:0.15, T:0.17
Consensus pattern (28 bp):
CGAACAATAAAAACTAAAAGAGTTAGCT
Found at i:1276461 original size:29 final size:29
Alignment explanation
Indices: 1276424--1276482 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
1276414 TTAGAGACTA
1276424 ATTTATAAATTCTAAATTATATAAGATAT
1 ATTTATAAATTCTAAATTATATAAGATAT
1276453 ATTTATAAATTCTAAATTATATAAGATAT
1 ATTTATAAATTCTAAATTATATAAGATAT
1276482 A
1 A
1276483 ACATATAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.44
Consensus pattern (29 bp):
ATTTATAAATTCTAAATTATATAAGATAT
Found at i:1276492 original size:29 final size:29
Alignment explanation
Indices: 1276427--1276490 Score: 101
Period size: 29 Copynumber: 2.2 Consensus size: 29
1276417 GAGACTAATT
**
1276427 TATAAATTCTAAATTATATAAGATATATT
1 TATAAATTCTAAATTATATAAGATATACA
1276456 TATAAATTCTAAATTATATAAGATATAACA
1 TATAAATTCTAAATTATATAAGATAT-ACA
1276486 TATAA
1 TATAA
1276491 TTTAACCAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 26 0.81
30 6 0.19
ACGTcount: A:0.52, C:0.05, G:0.03, T:0.41
Consensus pattern (29 bp):
TATAAATTCTAAATTATATAAGATATACA
Found at i:1277539 original size:21 final size:21
Alignment explanation
Indices: 1277497--1277539 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
1277487 ATTTTCGGGT
* * *
1277497 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
1277518 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
1277539 A
1 A
1277540 CGAATATGAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:1278268 original size:147 final size:146
Alignment explanation
Indices: 1278067--1278377 Score: 493
Period size: 147 Copynumber: 2.1 Consensus size: 146
1278057 GGGTAGAGGG
* * *
1278067 TCTACGCGGTCCTTCAGGACATATGTATATTCTTTGGAACATGTGTGAGGTCTT-GAAAGACACA
1 TCTACGCGGTCCTTC-GGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
* * *
1278131 TACTTGATCCTTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATT
65 TAC-TGATCCCTAGTATATGTATATGA-TCTTAAGGAATTATATGTGGTCCTTAGGGACAT-ATT
1278196 ATATGGCACTACGGTGCAAT
127 ATATGGCACTACGGTGCAAT
*
1278216 TCTACGCGGTCCTTCGG-GATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACAT
1 TCTACGCGGTCCTTCGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACAT
1278280 ACTGATCCCTAGTATATGTATATGATCTTAAGGAATTATATGTGGTCCTTAGGGACATATTATAT
66 ACTGATCCCTAGTATATGTATATGATCTTAAGGAATTATATGTGGTCCTTAGGGACATATTATAT
1278345 GGCACTACGGTGCAAT
131 GGCACTACGGTGCAAT
1278361 TCTACGCGG-CACTTCGG
1 TCTACGCGGTC-CTTCGG
1278378 TGCATTTATA
Statistics
Matches: 153, Mismatches: 7, Indels: 8
0.91 0.04 0.05
Matches are distributed among these distances:
144 1 0.01
145 38 0.25
146 31 0.20
147 53 0.35
148 15 0.10
149 15 0.10
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.34
Consensus pattern (146 bp):
TCTACGCGGTCCTTCGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACAT
ACTGATCCCTAGTATATGTATATGATCTTAAGGAATTATATGTGGTCCTTAGGGACATATTATAT
GGCACTACGGTGCAAT
Found at i:1278389 original size:23 final size:23
Alignment explanation
Indices: 1278345--1278389 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1278335 CATATTATAT
*
1278345 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
* *
1278368 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
1278390 AGCTGTGGTG
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:0.20, C:0.27, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:1284096 original size:21 final size:21
Alignment explanation
Indices: 1284054--1284096 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
1284044 TTTTTGGGCT
* * *
1284054 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
1284075 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
1284096 A
1 A
1284097 CGAATATGAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:1284827 original size:149 final size:150
Alignment explanation
Indices: 1284638--1284942 Score: 540
Period size: 150 Copynumber: 2.0 Consensus size: 150
1284628 AGGTAGAGGG
* * *
1284638 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAGGTCTT-GAAAGACACA
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
* * *
1284702 TACTTGATCCTTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATT
66 TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTATATGTGGTCCTTAGGGACATCATT
1284767 ATATGGCACTACGGTGCAAT
131 ATATGGCACTACGGTGCAAT
*
1284787 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
1284852 TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTATATGTGGTCCTTAGGGACATCATT
66 TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTATATGTGGTCCTTAGGGACATCATT
1284917 ATATGGCACTACGGTGCAAT
131 ATATGGCACTACGGTGCAAT
1284937 TCTACG
1 TCTACG
1284943 AGGCACTTCG
Statistics
Matches: 148, Mismatches: 7, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
149 50 0.34
150 98 0.66
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.35
Consensus pattern (150 bp):
TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTATATGTGGTCCTTAGGGACATCATT
ATATGGCACTACGGTGCAAT
Found at i:1284954 original size:23 final size:23
Alignment explanation
Indices: 1284921--1284967 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
1284911 ATCATTATAT
*
1284921 GGCACTACGGTGCAATTCTACGA
1 GGCACTACGGTGCAATTATACGA
* *
1284944 GGCACTTCGGTGCATTTATACGA
1 GGCACTACGGTGCAATTATACGA
1284967 G
1 G
1284968 CTGTGGTGAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.26
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGA
Found at i:1288381 original size:18 final size:18
Alignment explanation
Indices: 1288358--1288393 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
1288348 TCACTGTATC
1288358 CAACTATTGACCGACTAA
1 CAACTATTGACCGACTAA
1288376 CAACTATTGACCGACTAA
1 CAACTATTGACCGACTAA
1288394 TCCCAGATCG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.28, G:0.11, T:0.22
Consensus pattern (18 bp):
CAACTATTGACCGACTAA
Found at i:1288652 original size:12 final size:12
Alignment explanation
Indices: 1288618--1288655 Score: 51
Period size: 13 Copynumber: 3.2 Consensus size: 12
1288608 AGTACTTACT
1288618 AAAAAATT-ATA
1 AAAAAATTAATA
*
1288629 AAAATATATAATA
1 AAAAAAT-TAATA
1288642 AAAAAATTAATA
1 AAAAAATTAATA
1288654 AA
1 AA
1288656 CTACTCGCGA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
11 6 0.26
12 8 0.35
13 9 0.39
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (12 bp):
AAAAAATTAATA
Found at i:1295815 original size:20 final size:20
Alignment explanation
Indices: 1295790--1295834 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
1295780 AAAAAAAGAA
1295790 GAAAAAAAGAGGACCAAAAG
1 GAAAAAAAGAGGACCAAAAG
1295810 GAAAAAAAGAGGACCAAAAG
1 GAAAAAAAGAGGACCAAAAG
1295830 GAAAA
1 GAAAA
1295835 TATTTTAACC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.67, C:0.09, G:0.24, T:0.00
Consensus pattern (20 bp):
GAAAAAAAGAGGACCAAAAG
Found at i:1298349 original size:31 final size:30
Alignment explanation
Indices: 1298275--1298353 Score: 88
Period size: 30 Copynumber: 2.6 Consensus size: 30
1298265 TTTGGTATTC
1298275 GGGTCGGATGTTTTTAAAAAAAATCGGGATT
1 GGGTCGGAT-TTTTTAAAAAAAATCGGGATT
** * *
1298306 GGGTTAGATTTTTTAAAAAAATTTCGGGGTT
1 GGGTCGGATTTTTTAAAAAAA-ATCGGGATT
*
1298337 GGGTCGG-GTTTTTAAAA
1 GGGTCGGATTTTTTAAAA
1298354 GTTTGATATT
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
30 21 0.52
31 19 0.47
ACGTcount: A:0.29, C:0.05, G:0.29, T:0.37
Consensus pattern (30 bp):
GGGTCGGATTTTTTAAAAAAAATCGGGATT
Found at i:1298383 original size:34 final size:34
Alignment explanation
Indices: 1298332--1298415 Score: 107
Period size: 34 Copynumber: 2.5 Consensus size: 34
1298322 AAAAATTTCG
* *
1298332 GGGTTGGGTCGGG-TTTTTAAAAGTTTGATATTC
1 GGGTCGGGTCGGGTTTTTTAAAAGTGTGATATTC
** *
1298365 GGGTCGGGTCGGGTTTTTTTTAAGTGTGATATTT
1 GGGTCGGGTCGGGTTTTTTAAAAGTGTGATATTC
1298399 GGGTCGGGTTCGGGTTT
1 GGGTCGGG-TCGGGTTT
1298416 AGGGTGAAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
33 12 0.27
34 24 0.55
35 8 0.18
ACGTcount: A:0.12, C:0.07, G:0.38, T:0.43
Consensus pattern (34 bp):
GGGTCGGGTCGGGTTTTTTAAAAGTGTGATATTC
Found at i:1303339 original size:167 final size:166
Alignment explanation
Indices: 1303042--1303391 Score: 474
Period size: 167 Copynumber: 2.1 Consensus size: 166
1303032 ATTTGTTATT
* * *
1303042 AACTGTATCAAGTTTTTAAATCCATCAAGTGATTTCGATGGTAAAAAGATATTATTCTCCTTAGA
1 AACTATATCAAGTTTTTAAACCCATCAAGTGATTTCGATGATAAAAAGATATTATTCTCCTTAGA
* * * * *
1303107 GGTTCTGAGTTTGATAAACTACGTTTGTGGTGTGTGTTGTTAATAAGTCAAGCAAGTTCTGAACA
66 GGTTCTGAGTTCGATAAACTACGTTTATGGTGTGTGTTGTTAATAAGTCAAGAAAATTATGAACA
* * * *
1303172 TATACTACCTTGA-AATCATTCAAGAGTATTAAAA-A
131 TATACTACCTT-ATAATAACTCAACACTATTAAAATA
* * *
1303207 AACTATATCAAGTTTTTAAACCCATCAAGTGGTTTCGATGATAAAAAAGAATATTGTTCTTCTTA
1 AACTATATCAAGTTTTTAAACCCATCAAGTGATTTCGATGAT-AAAAAG-ATATTATTCTCCTTA
* *
1303272 GAGGTAT-TGAGTTCGAGT-AACTACGTTTATGGTGTGTGTTGTTAATAGGTTAAGAAAATTATG
64 GAGGT-TCTGAGTTCGA-TAAACTACGTTTATGGTGTGTGTTGTTAATAAGTCAAGAAAATTATG
1303335 AACATATACTACCTTATAATAACTCAACACTATTAAAATA
127 AACATATACTACCTTATAATAACTCAACACTATTAAAATA
1303375 AACTATATCAAGTTTTT
1 AACTATATCAAGTTTTT
1303392 TCTTTTATAT
Statistics
Matches: 162, Mismatches: 17, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
165 38 0.23
166 7 0.04
167 97 0.60
168 20 0.12
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.36
Consensus pattern (166 bp):
AACTATATCAAGTTTTTAAACCCATCAAGTGATTTCGATGATAAAAAGATATTATTCTCCTTAGA
GGTTCTGAGTTCGATAAACTACGTTTATGGTGTGTGTTGTTAATAAGTCAAGAAAATTATGAACA
TATACTACCTTATAATAACTCAACACTATTAAAATA
Found at i:1306447 original size:4 final size:4
Alignment explanation
Indices: 1306438--1306534 Score: 51
Period size: 4 Copynumber: 25.0 Consensus size: 4
1306428 GACAATATAC
** * * * *
1306438 ATAA ATAA ATGG ATAA ATAA ATAA ACAA ATATGA GTAA ATAA ATCA A-AG
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATA--A ATAA ATAA ATAA ATAA
* * * *
1306487 ATAA A-GA A-AA ATAA A-GA A-AA ATAA ATAA ATAG ATAA CTAA ATAA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA
1306531 ATAA
1 ATAA
1306535 GATGAGGAAA
Statistics
Matches: 68, Mismatches: 20, Indels: 10
0.69 0.20 0.10
Matches are distributed among these distances:
3 9 0.13
4 56 0.82
6 3 0.04
ACGTcount: A:0.68, C:0.03, G:0.08, T:0.21
Consensus pattern (4 bp):
ATAA
Found at i:1306502 original size:10 final size:10
Alignment explanation
Indices: 1306487--1306511 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1306477 TAAATCAAAG
1306487 ATAAAGAAAA
1 ATAAAGAAAA
1306497 ATAAAGAAAA
1 ATAAAGAAAA
1306507 ATAAA
1 ATAAA
1306512 TAAATAGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.80, C:0.00, G:0.08, T:0.12
Consensus pattern (10 bp):
ATAAAGAAAA
Found at i:1308845 original size:100 final size:104
Alignment explanation
Indices: 1308521--1308969 Score: 738
Period size: 104 Copynumber: 4.4 Consensus size: 104
1308511 GTGTTGTTTC
1308521 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
*
1308586 CAGCGGTCCC-CGTTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTCG-TCGTGAAGTTGAACTTACGTTGTCTG
** *
1308625 GAGTCCAA-ATCC-TCGTTGTGAAGCAGAAATTGGCTCTGAAATTGAGAAATGTTCGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
* *
1308688 CAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCC-TCGTCGTGAAGTTGAACTTACGTTGTCTG
*
1308728 GAGTCCAATATCCTTCGTTATGAAGTTGAAA-TGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
1308792 CAGCGGT-CC-C-TCGTGAAGTTGAACTTACGTTGTCTG
66 CAGCGGTCCCTCGTCGTGAAGTTGAACTTACGTTGTCTG
1308828 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGAC-AC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
1308892 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
66 CAGCGGTCCC-TCGTCGTGAAGTTGAACTTACGTTGTCTG
1308932 GAGTCCAATATCCTTCG-TGTGAAGTTGAAATT-GCTCTG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
1308970 GGTAAAACGT
Statistics
Matches: 325, Mismatches: 11, Indels: 20
0.91 0.03 0.06
Matches are distributed among these distances:
100 64 0.20
101 33 0.10
102 63 0.19
103 56 0.17
104 95 0.29
105 14 0.04
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.32
Consensus pattern (104 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
CAGCGGTCCCTCGTCGTGAAGTTGAACTTACGTTGTCTG
Found at i:1309028 original size:156 final size:160
Alignment explanation
Indices: 1308818--1309135 Score: 592
Period size: 156 Copynumber: 2.0 Consensus size: 160
1308808 AGTTGAACTT
1308818 ACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTT
1 ACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAG-AATGTT
1308883 TGTTGAC-ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTT
65 TGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTT
1308947 CG-TGTGAAGTTGAAATT-GCTCTGGGTAAA
130 CGTTGTGAAGTTGAAATTGGCTCTGGGTAAA
1308976 ACGTTGTCTGGAGTCC-A-ATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAATGTTT
1 ACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAATGTTT
1309039 GTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTC
66 GTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTC
1309104 GTTGTGAAGTTGAAATTGGCTCTGGGTAAA
131 GTTGTGAAGTTGAAATTGGCTCTGGGTAAA
1309134 AC
1 AC
1309136 CTGCAAAGAT
Statistics
Matches: 157, Mismatches: 0, Indels: 6
0.96 0.00 0.04
Matches are distributed among these distances:
155 13 0.08
156 98 0.62
157 16 0.10
158 30 0.19
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.33
Consensus pattern (160 bp):
ACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAATGTTT
GTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTC
GTTGTGAAGTTGAAATTGGCTCTGGGTAAA
Found at i:1309907 original size:1 final size:1
Alignment explanation
Indices: 1309901--1309930 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
1309891 TTTTCACCCG
1309901 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1309931 AACTTAGGAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Done.