Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004130.1 Hibiscus syriacus cultivar Beakdansim tig00009036_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: 105088
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:92053 original size:180 final size:184
Alignment explanation
Indices: 91847--92210 Score: 567
Period size: 180 Copynumber: 2.0 Consensus size: 184
91837 ATCTACCTCC
* * * *
91847 TTCTGTGATAGAATCGAGCAAAAAGTTAACGCTGATCCAACTCCTTCTGCGATGGATTTGAGCGA
1 TTCTGTGATAAAATCGAGCAAAAAGTTAACACTGATCCAACTCATTCTGCGATAGATTTGAGCGA
* *
91912 AAATAAAAATGTCGATCCACCTCCTTCTGTGATGGAATCGAACGAGATGTTTCTG-AT-CTACC-
66 AAATAAAAATGTCGATCCACCTCCTTCTATGATGGAATCGAACGAGATGTTGCTGAATCCT-CCT
* *
91974 TC-C-TTCTGCGATAGAATCGAACTAAAAGTTGACGCTGATCCAAGTCCTTCTCT
130 TCTCATTCTGCGATAGAATCGAACTAAAAGTTAACGCTGATCCAACTCCTTCTCT
* *
92027 TTCTGTGATAAAATCGAGCTAAAAGTTGACACTGATCCAACTCATTCTGCGATAGATTTGAGCGA
1 TTCTGTGATAAAATCGAGCAAAAAGTTAACACTGATCCAACTCATTCTGCGATAGATTTGAGCGA
92092 AAATAAAAATGTCGATCCACCTCCTTCTATGATGGAATCGAACGAGATGTTGCTGATATGCCTCC
66 AAATAAAAATGTCGATCCACCTCCTTCTATGATGGAATCGAACGAGATGTTGCTGA-AT-CCTCC
*
92157 TTCTCATTCTGCGATAGAATCGAGCTAAAAGTTAACGCTGATCCAACTCCTTCT
129 TTCTCATTCTGCGATAGAATCGAACTAAAAGTTAACGCTGATCCAACTCCTTCT
92211 GCGATGGATT
Statistics
Matches: 166, Mismatches: 11, Indels: 8
0.90 0.06 0.04
Matches are distributed among these distances:
180 112 0.67
182 2 0.01
183 2 0.01
184 4 0.02
185 1 0.01
186 45 0.27
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.29
Consensus pattern (184 bp):
TTCTGTGATAAAATCGAGCAAAAAGTTAACACTGATCCAACTCATTCTGCGATAGATTTGAGCGA
AAATAAAAATGTCGATCCACCTCCTTCTATGATGGAATCGAACGAGATGTTGCTGAATCCTCCTT
CTCATTCTGCGATAGAATCGAACTAAAAGTTAACGCTGATCCAACTCCTTCTCT
Found at i:92351 original size:140 final size:139
Alignment explanation
Indices: 92018--92435 Score: 644
Period size: 140 Copynumber: 3.0 Consensus size: 139
92008 CTGATCCAAG
* * * *
92018 TCCTTCTCTTTCTGTGATAAAATCGAGCTAAAAGTTGACACTGATCCAACTCATTCTGCGATAGA
1 TCCTTCTCATTCTGTGATAAAATCGAGCTAAAAGTTGACGCTGATCCAACTCCTTCTGCGATGGA
* *
92083 TTTGAGCGAAAATAAAAATGTCGATCCACCTCCTTCTATGATGG-AATCGAACGAGATGT--TGC
66 TTTGAGCGAAAATAAAAATGTCGATCCACCTCCTTCTGTGATGGAAATCGAACGATATGTGATGC
* *
92145 TGATATGCC
131 TGATCTACC
* * *
92154 TCCTTCTCATTCTGCGATAGAATCGAGCTAAAAGTTAACGCTGATCCAACTCCTTCTGCGATGGA
1 TCCTTCTCATTCTGTGATAAAATCGAGCTAAAAGTTGACGCTGATCCAACTCCTTCTGCGATGGA
* *
92219 TTTGAGCAAAAATAAAAATGTCGATCCACCTCCTTCTGTGATGGAAATCGAATGATATGTCGATG
66 TTTGAGCGAAAATAAAAATGTCGATCCACCTCCTTCTGTGATGGAAATCGAACGATATGT-GATG
92284 CTGATCTACC
130 CTGATCTACC
* * * *
92294 TTCTTCTCATTCTGTGATATAATCGAACTAAAAGTTGACGTTGATCCAACTCCTTCTGCGATGGA
1 TCCTTCTCATTCTGTGATAAAATCGAGCTAAAAGTTGACGCTGATCCAACTCCTTCTGCGATGGA
92359 TTTGAGCGAAAATAAAAATGTCGATCCACCTCCTTCTGTGATGGAAATCGAACGATATGTTGATG
66 TTTGAGCGAAAATAAAAATGTCGATCCACCTCCTTCTGTGATGGAAATCGAACGATATG-TGATG
92424 CTGATCTACC
130 CTGATCTACC
92434 TC
1 TC
92436 AATCTATGAT
Statistics
Matches: 255, Mismatches: 22, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
136 100 0.39
137 13 0.05
140 141 0.55
141 1 0.00
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (139 bp):
TCCTTCTCATTCTGTGATAAAATCGAGCTAAAAGTTGACGCTGATCCAACTCCTTCTGCGATGGA
TTTGAGCGAAAATAAAAATGTCGATCCACCTCCTTCTGTGATGGAAATCGAACGATATGTGATGC
TGATCTACC
Found at i:92435 original size:45 final size:45
Alignment explanation
Indices: 91398--92435 Score: 289
Period size: 45 Copynumber: 23.2 Consensus size: 45
91388 TAAAAATATC
* *
91398 GATCCACCTCCTTCTGTGATGG-AATCGAACGAGATGTCGATGCT
1 GATCCACCTCCTTCTGTGATGGAAATCGAACGAAATGTTGATGCT
* * * * * *
91442 GATCTACCTCCTTCTGTGATAG-AATCGAGCAAAAAGTTGACGCT
1 GATCCACCTCCTTCTGTGATGGAAATCGAACGAAATGTTGATGCT
* * * * * ****
91486 GATCCAACTCCTTCTGCGATGG-ATTTGAGCGAAAATAAAAATG-T
1 GATCCACCTCCTTCTGTGATGGAAATCGAACG-AAATGTTGATGCT
* *
91530 CGATCCACATCCTTCTGTGATGG-AATCGAACGAGATG-T--TGCT
1 -GATCCACCTCCTTCTGTGATGGAAATCGAACGAAATGTTGATGCT
* * * * * * *
91572 GATCTACCTCCTTCTGCGATAG-AATCAAACTAAAAGTTGACGCT
1 GATCCACCTCCTTCTGTGATGGAAATCGAACGAAATGTTGATGCT
* * * * * ****
91616 GATCCAACTCCTTCTGCGATGG-ATTTGAGCGAAAATAAAAATG-T
1 GATCCACCTCCTTCTGTGATGGAAATCGAACG-AAATGTTGATGCT
* *
91660 CGATCCACCTCTTTCTGTGATGG-AATCGAACGAGATGTT-A--CT
1 -GATCCACCTCCTTCTGTGATGGAAATCGAACGAAATGTTGATGCT
* * * * * * *
91702 GATCTACCTCCTTCTGCGATAG-AATCGAGCTAAAAGTTGACGCT
1 GATCCACCTCCTTCTGTGATGGAAATCGAACGAAATGTTGATGCT
* * * * * * ****
91746 AATCCAACTCCTTCTGCGATGG-ATTTGAGCGAAAATAAAAATG-T
1 GATCCACCTCCTTCTGTGATGGAAATCGAACG-AAATGTTGATGCT
* * *
91790 CGATCCACCTCCTTCTGTGATGGAAATCGAACGATATATCGATGCT
1 -GATCCACCTCCTTCTGTGATGGAAATCGAACGAAATGTTGATGCT
* * * * * * *
91836 GATCTACCTCCTTCTGTGATAG-AATCGAGCAAAAAGTTAACGCT
1 GATCCACCTCCTTCTGTGATGGAAATCGAACGAAATGTTGATGCT
* * * * * ****
91880 GATCCAACTCCTTCTGCGATGG-ATTTGAGCGAAAATAAAAATG-T
1 GATCCACCTCCTTCTGTGATGGAAATCGAACG-AAATGTTGATGCT
*
91924 CGATCCACCTCCTTCTGTGATGG-AATCGAACGAGATGTT--T-CT
1 -GATCCACCTCCTTCTGTGATGGAAATCGAACGAAATGTTGATGCT
* * * * * *
91966 GATCTACCTCCTTCTGCGATAG-AATCGAACTAAAAGTTGACGCT
1 GATCCACCTCCTTCTGTGATGGAAATCGAACGAAATGTTGATGCT
* * * * **
92010 GATCCAAGTCCTTCTCTTTCTGTGAT-AAAATCGAGCTAAAAGTTGACACT
1 GATCC-A--CC-TC-C-TTCTGTGATGGAAATCGAACGAAATGTTGATGCT
* * * * * * * ****
92060 GATCCAACTCATTCTGCGATAG-ATTTGAGCGAAAATAAAAATG-T
1 GATCCACCTCCTTCTGTGATGGAAATCGAACG-AAATGTTGATGCT
* * * *
92104 CGATCCACCTCCTTCTATGATGG-AATCGAACGAGATGTTGCTGAT
1 -GATCCACCTCCTTCTGTGATGGAAATCGAACGAAATGTTGATGCT
* * * * * * * *
92149 -ATGCCTCCTTCTCATTCTGCGATAG-AATCGAGCTAAAAGTTAACGCT
1 GAT-CCACC-TC-C-TTCTGTGATGGAAATCGAACGAAATGTTGATGCT
* * * * * * ****
92196 GATCCAACTCCTTCTGCGATGG-ATTTGAGCAAAAATAAAAATG-T
1 GATCCACCTCCTTCTGTGATGGAAATCGAAC-GAAATGTTGATGCT
* * *
92240 CGATCCACCTCCTTCTGTGATGGAAATCGAATGATATGTCGATGCT
1 -GATCCACCTCCTTCTGTGATGGAAATCGAACGAAATGTTGATGCT
* * * * *
92286 GATCTACCTTCTTCTCATTCTGTGAT--ATAATCGAACTAAAAGTTGACGTT
1 GATCCA-C--C-TC-C-TTCTGTGATGGA-AATCGAACGAAATGTTGATGCT
* * * * * ****
92336 GATCCAACTCCTTCTGCGATGG-ATTTGAGCGAAAATAAAAATG-T
1 GATCCACCTCCTTCTGTGATGGAAATCGAACG-AAATGTTGATGCT
*
92380 CGATCCACCTCCTTCTGTGATGGAAATCGAACGATATGTTGATGCT
1 -GATCCACCTCCTTCTGTGATGGAAATCGAACGAAATGTTGATGCT
*
92426 GATCTACCTC
1 GATCCACCTC
92436 AATCTATGAT
Statistics
Matches: 707, Mismatches: 232, Indels: 109
0.67 0.22 0.10
Matches are distributed among these distances:
41 92 0.13
42 6 0.01
43 3 0.00
44 224 0.32
45 253 0.36
46 27 0.04
47 29 0.04
48 5 0.01
49 5 0.01
50 54 0.08
51 9 0.01
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.29
Consensus pattern (45 bp):
GATCCACCTCCTTCTGTGATGGAAATCGAACGAAATGTTGATGCT
Found at i:92989 original size:15 final size:15
Alignment explanation
Indices: 92971--93025 Score: 56
Period size: 15 Copynumber: 3.5 Consensus size: 15
92961 GATCGGTGTT
92971 TCAAGGGAAACTGTC
1 TCAAGGGAAACTGTC
* * *
92986 TCAAGAGAAAATTCGTT
1 TCAAG-GGAAACT-GTC
*
93003 TAAAGGGAAACTGTC
1 TCAAGGGAAACTGTC
93018 TCAAGGGA
1 TCAAGGGA
93026 GACAAAATTT
Statistics
Matches: 30, Mismatches: 8, Indels: 4
0.71 0.19 0.10
Matches are distributed among these distances:
15 14 0.47
16 10 0.33
17 6 0.20
ACGTcount: A:0.38, C:0.15, G:0.25, T:0.22
Consensus pattern (15 bp):
TCAAGGGAAACTGTC
Found at i:93011 original size:32 final size:34
Alignment explanation
Indices: 92902--93351 Score: 148
Period size: 39 Copynumber: 13.0 Consensus size: 34
92892 AAGTTTTTGT
* *
92902 GTTTCAAGAGAAACTGTCTCCAGGGAGACAAAATTC
1 GTTTCAAGGGAAACTGTCT-CAAGGAGA-AAAATTC
****
92938 AG-TTCAAGGGAAAC-GATCTCAA--AG-ATCGGT-
1 -GTTTCAAGGGAAACTG-TCTCAAGGAGAAAAATTC
92968 GTTTCAAGGGAAACTGTCTCAA-GAG-AAAATTC
1 GTTTCAAGGGAAACTGTCTCAAGGAGAAAAATTC
* *
93000 GTTTAAAGGGAAACTGTCTCAAGGGAGACAAAATTT
1 GTTTCAAGGGAAACTGTCTCAA-GGAGA-AAAATTC
** * ****
93036 GTTTCAAGGGAAACAATCTCAA--A-TATTGGT-
1 GTTTCAAGGGAAACTGTCTCAAGGAGAAAAATTC
* *
93066 GTTTCAAGGGAAACTGTGTCAAGAGAGACAAAACTTT
1 GTTTCAAGGGAAACTGTCTCAAG-GAGA-AAAA-TTC
* ** ****
93103 ATTTCAAGGGAAACAATCTCAA--AG-ATTGGT-
1 GTTTCAAGGGAAACTGTCTCAAGGAGAAAAATTC
*
93133 GTTTCAAGGGAAACTGTCTCAAGAGAGACAAAACTTT
1 GTTTCAAGGGAAACTGTCTCAAG-GAGA-AAAA-TTC
** ****
93170 GTTTCAAGGGAAACAATCTCAA--AG-ATTGGT-
1 GTTTCAAGGGAAACTGTCTCAAGGAGAAAAATTC
* *
93200 GTTTCAAGAGAAACTATCTCAAGAGAGATAAAATCTTC
1 GTTTCAAGGGAAACTGTCTCAAG-GAGA-AAAA--TTC
* *
93238 TGTTTCGAGGGAAACTATCTCAAGCGAGATAAAATCTTC
1 -GTTTCAAGGGAAACTGTCTCAAG-GAGA-AAAA--TTC
* *
93277 TGTTTCAAGGGAAACTATCTCAAGCGAGACAAAATCTTAT
1 -GTTTCAAGGGAAACTGTCTCAAG-GAGA-AAAA--TT-C
* *
93317 GTTTCGAGGGAAACTATCTCAAGCGAGATAAAATT
1 GTTTCAAGGGAAACTGTCTCAAG-GAGA-AAAATT
93352 TTCTGTTTCG
Statistics
Matches: 317, Mismatches: 63, Indels: 66
0.71 0.14 0.15
Matches are distributed among these distances:
29 1 0.00
30 76 0.24
31 11 0.03
32 23 0.07
33 8 0.03
34 7 0.02
35 6 0.02
36 41 0.13
37 42 0.13
39 102 0.32
ACGTcount: A:0.38, C:0.15, G:0.22, T:0.26
Consensus pattern (34 bp):
GTTTCAAGGGAAACTGTCTCAAGGAGAAAAATTC
Found at i:93020 original size:62 final size:64
Alignment explanation
Indices: 92900--93021 Score: 153
Period size: 62 Copynumber: 1.9 Consensus size: 64
92890 CAAAGTTTTT
*
92900 GTGTTTCAAGAGAAACTGTCTCCAGGGAGACAAAATTCAGTTCAAGGGAAACGATCTCAAAGATC
1 GTGTTTCAAGAGAAACTGTCTCCA--GAGACAAAATTCAGTTAAAGGGAAACGATCTCAAAGATC
92965 G
64 G
* *
92966 GTGTTTCAAGGGAAACTGTCT-CA-AGAGAAAATTC-GTTTAAAGGGAAACTG-TCTCAA
1 GTGTTTCAAGAGAAACTGTCTCCAGAGACAAAATTCAG-TTAAAGGGAAAC-GATCTCAA
93022 GGGAGACAAA
Statistics
Matches: 51, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
61 1 0.02
62 27 0.53
63 1 0.02
65 2 0.04
66 20 0.39
ACGTcount: A:0.36, C:0.16, G:0.24, T:0.24
Consensus pattern (64 bp):
GTGTTTCAAGAGAAACTGTCTCCAGAGACAAAATTCAGTTAAAGGGAAACGATCTCAAAGATCG
Found at i:93042 original size:98 final size:98
Alignment explanation
Indices: 92902--93091 Score: 292
Period size: 98 Copynumber: 1.9 Consensus size: 98
92892 AAGTTTTTGT
* * *
92902 GTTTCAAGAGAAACTGTCTCCAGGGAGACAAAATTCAGTTCAAGGGAAACGATCTCAAAGATCGG
1 GTTTAAAGAGAAACTGTCTCAAGGGAGACAAAATTCAGTTCAAGGGAAACAATCTCAAAGATCGG
92967 TGTTTCAAGGGAAACTGTCTCAAGAGAAAATTC
66 TGTTTCAAGGGAAACTGTCTCAAGAGAAAATTC
* * * *
93000 GTTTAAAGGGAAACTGTCTCAAGGGAGACAAAATT-TGTTTCAAGGGAAACAATCTCAAATATTG
1 GTTTAAAGAGAAACTGTCTCAAGGGAGACAAAATTCAG-TTCAAGGGAAACAATCTCAAAGATCG
*
93064 GTGTTTCAAGGGAAACTGTGTCAAGAGA
65 GTGTTTCAAGGGAAACTGTCTCAAGAGA
93092 GACAAAACTT
Statistics
Matches: 83, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
97 1 0.01
98 82 0.99
ACGTcount: A:0.37, C:0.15, G:0.24, T:0.24
Consensus pattern (98 bp):
GTTTAAAGAGAAACTGTCTCAAGGGAGACAAAATTCAGTTCAAGGGAAACAATCTCAAAGATCGG
TGTTTCAAGGGAAACTGTCTCAAGAGAAAATTC
Found at i:93131 original size:67 final size:67
Alignment explanation
Indices: 93000--93338 Score: 410
Period size: 67 Copynumber: 4.9 Consensus size: 67
92990 GAGAAAATTC
* * *
93000 GTTTAAAGGGAAACTGTCTCAAGGGAGACAAAA-TTTGTTTCAAGGGAAACAATCTCAAATATTG
1 GTTTCAAGGGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACAATCTCAAAGATTG
93064 GT
66 GT
* *
93066 GTTTCAAGGGAAACTGTGTCAAGAGAGACAAAACTTTATTTCAAGGGAAACAATCTCAAAGATTG
1 GTTTCAAGGGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACAATCTCAAAGATTG
93131 GT
66 GT
93133 GTTTCAAGGGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACAATCTCAAAGATTG
1 GTTTCAAGGGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACAATCTCAAAGATTG
93198 GT
66 GT
* * * * *
93200 GTTTCAAGAGAAACTATCTCAAGAGAGATAAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGA
1 GTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-CTT-TGTTTCAAGGGAAACAATCTCAA---A
**
93265 GATAAAATCTTCT
61 G-----AT-TGGT
* * * *
93278 GTTTCAAGGGAAACTATCTCAAGCGAGACAAAATCTTATGTTTCGAGGGAAACTATCTCAA
1 GTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-CTT-TGTTTCAAGGGAAACAATCTCAA
93339 GCGAGATAAA
Statistics
Matches: 243, Mismatches: 18, Indels: 12
0.89 0.07 0.04
Matches are distributed among these distances:
66 30 0.12
67 126 0.52
68 3 0.01
69 21 0.09
72 2 0.01
77 2 0.01
78 59 0.24
ACGTcount: A:0.37, C:0.15, G:0.21, T:0.27
Consensus pattern (67 bp):
GTTTCAAGGGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACAATCTCAAAGATTG
GT
Found at i:93138 original size:30 final size:30
Alignment explanation
Indices: 93104--93221 Score: 105
Period size: 30 Copynumber: 3.7 Consensus size: 30
93094 CAAAACTTTA
93104 TTTCAAGGGAAACAATCTCAAAGATTGGTG
1 TTTCAAGGGAAACAATCTCAAAGATTGGTG
**
93134 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAACTT--TG
1 TTTCAAGGGAAACAATCTC-A-A-AG-----A-TTGGTG
93171 TTTCAAGGGAAACAATCTCAAAGATTGGTG
1 TTTCAAGGGAAACAATCTCAAAGATTGGTG
* *
93201 TTTCAAGAGAAACTATCTCAA
1 TTTCAAGGGAAACAATCTCAA
93222 GAGAGATAAA
Statistics
Matches: 71, Mismatches: 6, Indels: 22
0.72 0.06 0.22
Matches are distributed among these distances:
28 2 0.03
29 1 0.01
30 38 0.54
31 1 0.01
32 1 0.01
33 2 0.03
34 2 0.03
35 1 0.01
36 1 0.01
37 19 0.27
38 1 0.01
39 2 0.03
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.26
Consensus pattern (30 bp):
TTTCAAGGGAAACAATCTCAAAGATTGGTG
Found at i:93253 original size:39 final size:39
Alignment explanation
Indices: 93199--93433 Score: 321
Period size: 39 Copynumber: 6.0 Consensus size: 39
93189 CAAAGATTGG
* *
93199 TGTTTCAAGAGAAACTATCTCAAGAGAGATAAAATCTTC
1 TGTTTCGAGGGAAACTATCTCAAGAGAGATAAAATCTTC
*
93238 TGTTTCGAGGGAAACTATCTCAAGCGAGATAAAATCTTC
1 TGTTTCGAGGGAAACTATCTCAAGAGAGATAAAATCTTC
* * * *
93277 TGTTTCAAGGGAAACTATCTCAAGCGAGACAAAATCTTA
1 TGTTTCGAGGGAAACTATCTCAAGAGAGATAAAATCTTC
* *
93316 TGTTTCGAGGGAAACTATCTCAAGCGAGATAAAATTTTC
1 TGTTTCGAGGGAAACTATCTCAAGAGAGATAAAATCTTC
* * *
93355 TGTTTCGAGAGAAACTATCTCAA-ATGAGACAAACTCTTC
1 TGTTTCGAGGGAAACTATCTCAAGA-GAGATAAAATCTTC
*
93394 TGTTTCGAGGGAAATTATCTCAAGTA-AGATAAAATCTTC
1 TGTTTCGAGGGAAACTATCTCAAG-AGAGATAAAATCTTC
93433 T
1 T
93434 TTAAAAACAA
Statistics
Matches: 174, Mismatches: 19, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
39 173 0.99
41 1 0.01
ACGTcount: A:0.36, C:0.17, G:0.18, T:0.29
Consensus pattern (39 bp):
TGTTTCGAGGGAAACTATCTCAAGAGAGATAAAATCTTC
Found at i:93328 original size:78 final size:78
Alignment explanation
Indices: 93199--93433 Score: 364
Period size: 78 Copynumber: 3.0 Consensus size: 78
93189 CAAAGATTGG
*
93199 TGTTTCAAGAGAAACTATCTCAAGAGAGATAAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCG
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCG
93264 AGATAAAATCTTC
66 AGATAAAATCTTC
* * *
93277 TGTTTCAAGGGAAACTATCTCAAGCGAGACAAAATCTTATGTTTCGAGGGAAACTATCTCAAGCG
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCG
*
93342 AGATAAAATTTTC
66 AGATAAAATCTTC
* * * *
93355 TGTTTCGAGAGAAACTATCTCAA-ATGAGACAAACTCTTCTGTTTCGAGGGAAATTATCTCAAGT
1 TGTTTCAAGAGAAACTATCTCAAGA-GAGACAAAATCTTCTGTTTCGAGGGAAACTATCTCAAGC
*
93419 AAGATAAAATCTTC
65 GAGATAAAATCTTC
93433 T
1 T
93434 TTAAAAACAA
Statistics
Matches: 142, Mismatches: 14, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
78 142 1.00
ACGTcount: A:0.36, C:0.17, G:0.18, T:0.29
Consensus pattern (78 bp):
TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCG
AGATAAAATCTTC
Found at i:93533 original size:76 final size:75
Alignment explanation
Indices: 93436--93597 Score: 234
Period size: 75 Copynumber: 2.1 Consensus size: 75
93426 AATCTTCTTT
* * * * *
93436 AAAAACAATCTTGAGTGAAATGAAATGTATTCTTTCGAGTAAAAATTGTCTCAAGAAAGACAAAT
1 AAAAACAATCTTGAGTCAAATGAAATGTATTCTTTCGAAT-AAAACTATCTCAAGAAAGACAAAA
*
93501 TTTGTTTTAAG
65 TCTGTTTTAAG
* **
93512 AAAAACAATCTTGAGTCAAATGAAATGTCTTCTTTCGAATAAAACTATCTCAAGTGAGACAAAAT
1 AAAAACAATCTTGAGTCAAATGAAATGTATTCTTTCGAATAAAACTATCTCAAGAAAGACAAAAT
93577 CTGTTTTAAG
66 CTGTTTTAAG
93587 AAAAACAATCT
1 AAAAACAATCT
93598 CAAGTGAGAT
Statistics
Matches: 77, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
75 40 0.52
76 37 0.48
ACGTcount: A:0.43, C:0.12, G:0.14, T:0.31
Consensus pattern (75 bp):
AAAAACAATCTTGAGTCAAATGAAATGTATTCTTTCGAATAAAACTATCTCAAGAAAGACAAAAT
CTGTTTTAAG
Found at i:94992 original size:9 final size:9
Alignment explanation
Indices: 94960--95048 Score: 54
Period size: 9 Copynumber: 9.4 Consensus size: 9
94950 ATCGATTTTC
94960 TTTTTTCTT
1 TTTTTTCTT
* *
94969 TCTTTCGTCTC
1 T-TTT-TTCTT
94980 TTTTTTCTT
1 TTTTTTCTT
*
94989 TTTTTTATT
1 TTTTTTCTT
* *
94998 TCTTTTATT
1 TTTTTTCTT
*
95007 TCTTTT-TT
1 TTTTTTCTT
*
95015 TTTTTGCTT
1 TTTTTTCTT
*
95024 TTTTTTTTAT
1 TTTTTTCT-T
95034 TTTTATATCTT
1 TTTT-T-TCTT
95045 TTTT
1 TTTT
95049 GTTATATCCT
Statistics
Matches: 63, Mismatches: 11, Indels: 10
0.75 0.13 0.12
Matches are distributed among these distances:
8 6 0.10
9 34 0.54
10 11 0.17
11 10 0.16
12 2 0.03
ACGTcount: A:0.06, C:0.11, G:0.02, T:0.81
Consensus pattern (9 bp):
TTTTTTCTT
Found at i:94999 original size:13 final size:12
Alignment explanation
Indices: 94987--95037 Score: 57
Period size: 12 Copynumber: 4.2 Consensus size: 12
94977 CTCTTTTTTC
94987 TTTTTTTTATTT
1 TTTTTTTTATTT
* *
94999 CTTTTATTTCTTT
1 -TTTTTTTTATTT
**
95012 TTTTTTTTGCTT
1 TTTTTTTTATTT
95024 TTTTTTTTATTT
1 TTTTTTTTATTT
95036 TT
1 TT
95038 ATATCTTTTT
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
12 21 0.68
13 10 0.32
ACGTcount: A:0.06, C:0.06, G:0.02, T:0.86
Consensus pattern (12 bp):
TTTTTTTTATTT
Found at i:95000 original size:29 final size:28
Alignment explanation
Indices: 94955--95019 Score: 76
Period size: 29 Copynumber: 2.3 Consensus size: 28
94945 GATTGATCGA
* * *
94955 TTTTCTTTTTTCTTTCTTTCGTCTCTTT
1 TTTTTTTTTTTATTTCTTTCATCTCTTT
* *
94983 TTTCTTTTTTTTATTTCTTTTATTTCTTT
1 TTT-TTTTTTTTATTTCTTTCATCTCTTT
95012 TTTTTTTT
1 TTTTTTTT
95020 GCTTTTTTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
28 8 0.26
29 23 0.74
ACGTcount: A:0.03, C:0.14, G:0.02, T:0.82
Consensus pattern (28 bp):
TTTTTTTTTTTATTTCTTTCATCTCTTT
Found at i:95001 original size:20 final size:20
Alignment explanation
Indices: 94956--95048 Score: 89
Period size: 20 Copynumber: 4.5 Consensus size: 20
94946 ATTGATCGAT
* **
94956 TTTCTTTTTTCTTTCTTTCG
1 TTTCTTTTTTCTTTTTTTTA
*
94976 TCTCTTTTTTCTTTTTTTTA
1 TTTCTTTTTTCTTTTTTTTA
94996 TTTCTTTTATTTCTTTTTTTT-
1 TTTC-TTT-TTTCTTTTTTTTA
*
95017 TTTGCTTTTTTTTTTATTTTTA
1 TTT-CTTTTTTCTTT-TTTTTA
*
95039 TATCTTTTTT
1 TTTCTTTTTT
95049 GTTATATCCT
Statistics
Matches: 61, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
20 25 0.41
21 21 0.34
22 15 0.25
ACGTcount: A:0.05, C:0.12, G:0.02, T:0.81
Consensus pattern (20 bp):
TTTCTTTTTTCTTTTTTTTA
Found at i:95061 original size:36 final size:35
Alignment explanation
Indices: 94986--95064 Score: 90
Period size: 34 Copynumber: 2.2 Consensus size: 35
94976 TCTCTTTTTT
* * *
94986 CTTTTTTTTATTTCTTTTATTTCTTTTTTTTTTTG
1 CTTTTTTTTATTTCTTTTATATCTTTTTTTTTATC
95021 CTTTTTTTT-TTAT-TTTTATATCTTTTTTGTTATATC
1 CTTTTTTTTATT-TCTTTTATATCTTTTTT-TT-TATC
95057 CTTTTTTT
1 CTTTTTTT
95065 CTCTCTGTGT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
34 16 0.42
35 12 0.32
36 10 0.26
ACGTcount: A:0.09, C:0.09, G:0.03, T:0.80
Consensus pattern (35 bp):
CTTTTTTTTATTTCTTTTATATCTTTTTTTTTATC
Found at i:101112 original size:17 final size:19
Alignment explanation
Indices: 101071--101112 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
101061 AGGAGCGTAG
*
101071 GTGTATCGGTACACTATCAA
1 GTGTATCGATACAC-ATCAA
101091 GTGTATCGATACAC-TC-A
1 GTGTATCGATACACATCAA
101108 GTGTA
1 GTGTA
101113 AAATTCAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 6 0.29
18 2 0.10
20 13 0.62
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.31
Consensus pattern (19 bp):
GTGTATCGATACACATCAA
Done.