Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008566.1 Hibiscus syriacus cultivar Beakdansim tig00111481_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: 191434
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
File 2 of 2
Found at i:132015 original size:14 final size:14
Alignment explanation
Indices: 131996--132026 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
131986 TTTCGATGAT
131996 TTTTTATATAAATA
1 TTTTTATATAAATA
*
132010 TTTTTATTTAAATA
1 TTTTTATATAAATA
132024 TTT
1 TTT
132027 AGAATTTCAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (14 bp):
TTTTTATATAAATA
Found at i:136797 original size:32 final size:30
Alignment explanation
Indices: 136721--136808 Score: 90
Period size: 32 Copynumber: 2.9 Consensus size: 30
136711 TCAAGTTAAA
*
136721 AAATCGAATTATTTTAA-TTTTGAGTTATTT
1 AAATCG-ATTAATTTAATTTTTGAGTTATTT
*
136751 AAATCGATTTATTTAATTTATTTGAGTTAATTT
1 AAATCGATTAATTTAA-TT-TTTGAGTT-ATTT
* *
136784 CAAT-TATTAATTTAATTTTTGAGTT
1 AAATCGATTAATTTAATTTTTGAGTT
136809 TAAGTCGAGT
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
29 8 0.16
30 14 0.29
31 3 0.06
32 17 0.35
33 7 0.14
ACGTcount: A:0.33, C:0.03, G:0.09, T:0.55
Consensus pattern (30 bp):
AAATCGATTAATTTAATTTTTGAGTTATTT
Found at i:137694 original size:6 final size:6
Alignment explanation
Indices: 137679--137712 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
137669 AAAACAAATT
137679 TATTAA -ATTAA TATTAA TATTAA TATTAA TATTA
1 TATTAA TATTAA TATTAA TATTAA TATTAA TATTA
137713 GTGTTAACTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.19
6 22 0.81
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
TATTAA
Found at i:139083 original size:3 final size:3
Alignment explanation
Indices: 139075--139106 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
139065 GAGTTATTTA
*
139075 ATT ATT ATT ATT ATT ATT ATT ACT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
139107 ATTTTTAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:139398 original size:44 final size:44
Alignment explanation
Indices: 139345--139463 Score: 175
Period size: 44 Copynumber: 2.7 Consensus size: 44
139335 TCGAGCGAGA
*
139345 TGATGTTGATTCAACTCCTTATGTGATGGAATCAAGCGAAGTGG
1 TGATGTTGATCCAACTCCTTATGTGATGGAATCAAGCGAAGTGG
** ** *
139389 TGATGTTGATCCAACTTTTTATGTGATAAAATCGAGCGAAGTGG
1 TGATGTTGATCCAACTCCTTATGTGATGGAATCAAGCGAAGTGG
*
139433 TGATGCTGATCCAACTCCTTATGTGATGGAA
1 TGATGTTGATCCAACTCCTTATGTGATGGAA
139464 GAGTCGAGAT
Statistics
Matches: 64, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
44 64 1.00
ACGTcount: A:0.28, C:0.14, G:0.25, T:0.33
Consensus pattern (44 bp):
TGATGTTGATCCAACTCCTTATGTGATGGAATCAAGCGAAGTGG
Found at i:139653 original size:22 final size:21
Alignment explanation
Indices: 139608--139654 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
139598 GTTAAGCAAG
* *
139608 TTCT-TCTCATTAGAAACTTC
1 TTCTCTCTCATCAGAAAATTC
139628 TTCTCTCTCATCAGACAAATTC
1 TTCTCTCTCATCAGA-AAATTC
139650 TTCTC
1 TTCTC
139655 ATTATGAACT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 4 0.17
21 9 0.39
22 10 0.43
ACGTcount: A:0.23, C:0.30, G:0.04, T:0.43
Consensus pattern (21 bp):
TTCTCTCTCATCAGAAAATTC
Found at i:145057 original size:6 final size:6
Alignment explanation
Indices: 145040--145097 Score: 91
Period size: 6 Copynumber: 9.8 Consensus size: 6
145030 ATAAAAAATT
* *
145040 TATTAA -ATTAA TATTAA TATTAA TATTAA TATGAA TATTAA TATGAA
1 TATTAA TATTAA TATTAA TATTAA TATTAA TATTAA TATTAA TATTAA
145087 TATTAA TATTA
1 TATTAA TATTA
145098 GGGTTAACTA
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
5 5 0.11
6 42 0.89
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (6 bp):
TATTAA
Found at i:145577 original size:2 final size:2
Alignment explanation
Indices: 145570--145599 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
145560 TATTTCGACG
145570 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
145600 CAAAACCAAG
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:145583 original size:92 final size:92
Alignment explanation
Indices: 145396--145581 Score: 250
Period size: 92 Copynumber: 2.0 Consensus size: 92
145386 AAAGTGAACT
* * *
145396 TATACAAAGTATGGATGGTCGCGGAAATGATTAACCCAAATGCCTAAAACGTAGAAACCCCTTCA
1 TATACAAAGTATGGATGGTCGCGGAAATGATTAACCCAAACGCCTAAAACGTAGAAAACCCTTAA
* *
145461 AAACTGCGTTGTTTCGACGTATATATA
66 AAACGGCGTTATTTCGACGTATATATA
* * * * * * *
145488 TATACAAAGTTTGGATGGTCGCGTAAATGATTCACGCGAACGCCT-ATATGTAGAAAACCC-TAA
1 TATACAAAGTATGGATGGTCGCGGAAATGATTAACCCAAACGCCTAAAACGTAGAAAACCCTTAA
145551 AAACGGCGTTATTTCGACGTATATATA
66 AAACGGCGTTATTTCGACGTATATATA
145578 TATA
1 TATA
145582 TATATATATA
Statistics
Matches: 82, Mismatches: 12, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
90 31 0.38
91 12 0.15
92 39 0.48
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.27
Consensus pattern (92 bp):
TATACAAAGTATGGATGGTCGCGGAAATGATTAACCCAAACGCCTAAAACGTAGAAAACCCTTAA
AAACGGCGTTATTTCGACGTATATATA
Found at i:146665 original size:31 final size:33
Alignment explanation
Indices: 146617--146695 Score: 90
Period size: 34 Copynumber: 2.4 Consensus size: 33
146607 TTTAAATAGT
* *
146617 TATTATATTTTATATT-AAT-ATATTTATGTAAA
1 TATTAT-TTTTTTATTAAATAATATTTATATAAA
*
146649 TATTATTTTTTTATTAAAATAATATTTATATAAT
1 TATTATTTTTTTATT-AAATAATATTTATATAAA
*
146683 TATTATTTATTTA
1 TATTATTTTTTTA
146696 GAATTATTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
31 8 0.20
32 6 0.15
33 3 0.08
34 23 0.57
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.59
Consensus pattern (33 bp):
TATTATTTTTTTATTAAATAATATTTATATAAA
Found at i:146687 original size:34 final size:31
Alignment explanation
Indices: 146607--146695 Score: 88
Period size: 34 Copynumber: 2.7 Consensus size: 31
146597 TTAGTATTTT
* * *
146607 TTTAAATAGTTATTATATTTTATATTAATATA
1 TTTATATAATTATTAT-TTTTTTATTAATATA
* *
146639 TTTATGTAAATATTATTTTTTTATTAAAATAATA
1 TTTATATAATTATTATTTTTTTATT--AAT-ATA
*
146673 TTTATATAATTATTATTTATTTA
1 TTTATATAATTATTATTTTTTTA
146696 GAATTATTAA
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
31 8 0.17
32 12 0.26
33 3 0.07
34 23 0.50
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.58
Consensus pattern (31 bp):
TTTATATAATTATTATTTTTTTATTAATATA
Found at i:146859 original size:17 final size:17
Alignment explanation
Indices: 146837--146890 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
146827 AATGTTAATA
146837 TTTAAATTTATTTTTAT
1 TTTAAATTTATTTTTAT
* * * *
146854 TTTAAAGTTATTATGAA
1 TTTAAATTTATTTTTAT
* *
146871 TTTATATTAATTTTTAT
1 TTTAAATTTATTTTTAT
146888 TTT
1 TTT
146891 TTATAATGTA
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (17 bp):
TTTAAATTTATTTTTAT
Found at i:148454 original size:21 final size:21
Alignment explanation
Indices: 148424--148471 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
148414 GCAGGGGTAC
* *
148424 ATGCCCAGCCCTCCACTTCAT
1 ATGCCAAGCCCACCACTTCAT
* *
148445 ATGCCAAGCCCACCAGTTTAT
1 ATGCCAAGCCCACCACTTCAT
148466 ATGCCA
1 ATGCCA
148472 TCTTCGCAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.40, G:0.12, T:0.23
Consensus pattern (21 bp):
ATGCCAAGCCCACCACTTCAT
Found at i:148502 original size:21 final size:21
Alignment explanation
Indices: 148476--148568 Score: 143
Period size: 21 Copynumber: 4.4 Consensus size: 21
148466 ATGCCATCTT
*
148476 CGCAGGGTTACATTCCGAGCA
1 CGCAGGGTTACATTCCGAGCC
148497 CGCAGGGTTACATTCCGAGCC
1 CGCAGGGTTACATTCCGAGCC
148518 CGCAGGGTTACATTCCGAGCC
1 CGCAGGGTTACATTCCGAGCC
* *
148539 CGCCA-GGTTACATGCCTAGCC
1 CG-CAGGGTTACATTCCGAGCC
148560 CGCAGGGTT
1 CGCAGGGTT
148569 TTATACCATA
Statistics
Matches: 67, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
20 2 0.03
21 63 0.94
22 2 0.03
ACGTcount: A:0.19, C:0.32, G:0.29, T:0.19
Consensus pattern (21 bp):
CGCAGGGTTACATTCCGAGCC
Found at i:149194 original size:34 final size:34
Alignment explanation
Indices: 149088--149186 Score: 153
Period size: 34 Copynumber: 2.9 Consensus size: 34
149078 ATAAATGTTT
*
149088 TTAAAATACAAATTATATTATTCGAAATTTAAAA
1 TTAAAATAAAAATTATATTATTCGAAATTTAAAA
* *
149122 TAAAAATAAAAATAATATTATTCGAAATTTAAAA
1 TTAAAATAAAAATTATATTATTCGAAATTTAAAA
* *
149156 TTAAAATATAAATTATAGTATTCGAAATTTA
1 TTAAAATAAAAATTATATTATTCGAAATTTA
149187 GCATTAAATT
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 58 1.00
ACGTcount: A:0.55, C:0.04, G:0.04, T:0.37
Consensus pattern (34 bp):
TTAAAATAAAAATTATATTATTCGAAATTTAAAA
Found at i:150106 original size:128 final size:128
Alignment explanation
Indices: 149878--150506 Score: 1116
Period size: 128 Copynumber: 4.9 Consensus size: 128
149868 TTACCTGATT
149878 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* * *** *
149943 TAACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCT-GAGAAATAATAGG
66 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGT-GAATAGTGAAATAATAGG
150006 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*
150071 TGACAAAATAATGGAAGGTGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
* *
150134 TACTGATATATCTAGTGTCCCCGAGGGACATAAGTGACATAATAGGGAAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*
150199 TGCCAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
*
150262 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGCCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
** *
150327 TGACAAAATAATGGAAGGAACGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATATG
66 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
150390 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
150455 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGT
66 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGT
150507 ACTCCGATTA
Statistics
Matches: 479, Mismatches: 21, Indels: 2
0.95 0.04 0.00
Matches are distributed among these distances:
127 1 0.00
128 478 1.00
ACGTcount: A:0.33, C:0.20, G:0.24, T:0.23
Consensus pattern (128 bp):
TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
Found at i:150590 original size:8 final size:8
Alignment explanation
Indices: 150577--150617 Score: 50
Period size: 8 Copynumber: 5.2 Consensus size: 8
150567 TCACAAGCTT
150577 TCAAATTC
1 TCAAATTC
150585 TCAAATTAC
1 TCAAATT-C
*
150594 -CAAACTC
1 TCAAATTC
150601 T-AAATTC
1 TCAAATTC
150608 TCAAATTC
1 TCAAATTC
150616 TC
1 TC
150618 TGAAAATGAG
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
7 7 0.25
8 20 0.71
9 1 0.04
ACGTcount: A:0.39, C:0.27, G:0.00, T:0.34
Consensus pattern (8 bp):
TCAAATTC
Found at i:154595 original size:3 final size:3
Alignment explanation
Indices: 154589--154633 Score: 81
Period size: 3 Copynumber: 15.0 Consensus size: 3
154579 TTGAGTTATT
*
154589 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAT TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
154634 AAAATGGTGA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:155065 original size:19 final size:20
Alignment explanation
Indices: 155027--155065 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
155017 ATATTGTGAG
* *
155027 TATATTTTATAATTTTAAAT
1 TATATTTGATAATATTAAAT
155047 TATATTTGAT-ATATTAAAT
1 TATATTTGATAATATTAAAT
155066 AACATTATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (20 bp):
TATATTTGATAATATTAAAT
Found at i:158096 original size:17 final size:18
Alignment explanation
Indices: 158063--158101 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
158053 AGAGAATTGA
*
158063 AATCTGTGAAGGAATTAG
1 AATCTGTCAAGGAATTAG
158081 AATCTGTCAA-GAATTAG
1 AATCTGTCAAGGAATTAG
158098 AATC
1 AATC
158102 CAATTCCATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.41, C:0.10, G:0.21, T:0.28
Consensus pattern (18 bp):
AATCTGTCAAGGAATTAG
Found at i:158926 original size:254 final size:258
Alignment explanation
Indices: 158492--158997 Score: 799
Period size: 254 Copynumber: 2.0 Consensus size: 258
158482 ATAAAGTTTC
* * * *
158492 ACCCGACCCGACCCGAAATAATAAAAAAATATTTTTATTCAATACAAACAGTGACTTAATTGAAA
1 ACCCGACCCAACCCAAAATAATAAAAAAATA--TTTATTCAATAAAAACAATGACTTAATTGAAA
158557 AAATATATATAGAGAGAGGGGTATTATTGTAATTATTCATAAATATATAAGATAAAATTATATAT
64 AAATATATATA-AGAGAGGGGTATTATTGTAATTATTCATAAATATATAAGATAAAATTATATAT
* *
158622 TTTTTGGGTCGGGTCGGGTATTTTTCACCTTAAACCCGAACCCGACCCGACCCGAATATCACACT
128 ATTTT--GTCGGGTCGGGTATTTTTCACCCTAAACCCGAACCCGACCCGACCCGAATATCACAC-
158687 TTAAAAAAACCGACCCGACCCGACCAAAATAAAGTTTCACCCGACCCG-AATATATAAATTAGAA
190 TTAAAAAAACCGACCCGACCCGACCAAAATAAAGTTTCACCCGACCCGAAATA-ATAAATTAGAA
158751 ATCCG
254 ATCCG
158756 ACCCGACCCAACCCAAAATAATAAAAAAA-A-TTATTCAATAAAAACAATGACTTAATTGAAAAA
1 ACCCGACCCAACCCAAAATAATAAAAAAATATTTATTCAATAAAAACAATGACTTAATTGAAAAA
* * *
158819 AT-TATAT-ATAGAGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATATT
66 ATATATATAAGAGAGGGGTATTATTGTAATTATTCATAAATATATAAGATAAAATTATATATATT
* *
158882 TT-TCGGGTCGTGTATTTTTCACCCTAAACCCGAACTCGACCCGACCCGAATATCACACTTAAAA
131 TTGTCGGGTCGGGTATTTTTCACCCTAAACCCGAACCCGACCCGACCCGAATATCACACTTAAAA
*
158946 AGACCGACCCGACCCGACCAAAATAAAGTTTCACCCGACCCGAAATAATAAA
196 AAACCGACCCGACCCGACCAAAATAAAGTTTCACCCGACCCGAAATAATAAA
158998 AAAATTATTT
Statistics
Matches: 229, Mismatches: 12, Indels: 13
0.90 0.05 0.05
Matches are distributed among these distances:
253 52 0.23
254 57 0.25
257 54 0.24
259 5 0.02
260 33 0.14
263 1 0.00
264 27 0.12
ACGTcount: A:0.41, C:0.21, G:0.12, T:0.26
Consensus pattern (258 bp):
ACCCGACCCAACCCAAAATAATAAAAAAATATTTATTCAATAAAAACAATGACTTAATTGAAAAA
ATATATATAAGAGAGGGGTATTATTGTAATTATTCATAAATATATAAGATAAAATTATATATATT
TTGTCGGGTCGGGTATTTTTCACCCTAAACCCGAACCCGACCCGACCCGAATATCACACTTAAAA
AAACCGACCCGACCCGACCAAAATAAAGTTTCACCCGACCCGAAATAATAAATTAGAAATCCG
Found at i:161420 original size:32 final size:32
Alignment explanation
Indices: 161383--161479 Score: 194
Period size: 32 Copynumber: 3.0 Consensus size: 32
161373 AATGTATAAG
161383 TTTTAAGAATGAAATTTGTTATTATACCAAGC
1 TTTTAAGAATGAAATTTGTTATTATACCAAGC
161415 TTTTAAGAATGAAATTTGTTATTATACCAAGC
1 TTTTAAGAATGAAATTTGTTATTATACCAAGC
161447 TTTTAAGAATGAAATTTGTTATTATACCAAGC
1 TTTTAAGAATGAAATTTGTTATTATACCAAGC
161479 T
1 T
161480 ATACCATTAT
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 65 1.00
ACGTcount: A:0.37, C:0.09, G:0.12, T:0.41
Consensus pattern (32 bp):
TTTTAAGAATGAAATTTGTTATTATACCAAGC
Found at i:169511 original size:23 final size:23
Alignment explanation
Indices: 169477--169565 Score: 124
Period size: 23 Copynumber: 3.9 Consensus size: 23
169467 TGCCACATAC
169477 TTGTCCCGAAGGACCACATAAGT
1 TTGTCCCGAAGGACCACATAAGT
* *
169500 TTGTCCCAAAGGACCACATAGGT
1 TTGTCCCGAAGGACCACATAAGT
* *
169523 TTGTCTCGAAGGACCACATAATT
1 TTGTCCCGAAGGACCACATAAGT
* *
169546 TTGTCCCGAATGACTACATA
1 TTGTCCCGAAGGACCACATA
169566 GAACCCTTGA
Statistics
Matches: 57, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 57 1.00
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.26
Consensus pattern (23 bp):
TTGTCCCGAAGGACCACATAAGT
Found at i:173450 original size:23 final size:23
Alignment explanation
Indices: 173415--173460 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
173405 CATTATTATA
*
173415 TGGCACTCTGGTGCAATTCTACG
1 TGGCACTCTGGTGCAATTATACG
173438 TGGCACT-TCGGTGCAATTATACG
1 TGGCACTCT-GGTGCAATTATACG
173461 ATCTGTGGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 1 0.05
23 20 0.95
ACGTcount: A:0.20, C:0.24, G:0.26, T:0.30
Consensus pattern (23 bp):
TGGCACTCTGGTGCAATTATACG
Found at i:179545 original size:21 final size:21
Alignment explanation
Indices: 179503--179545 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
179493 TTTCTGGGCT
* *
179503 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
* *
179524 AGGGGAATCGATTCCCCCTCA
1 AGGGGAATCGATACCCACTCA
179545 A
1 A
179546 ACGAATATGA
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:0.28, C:0.28, G:0.26, T:0.19
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:180219 original size:22 final size:23
Alignment explanation
Indices: 180181--180225 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
180171 GACATTATTA
* *
180181 TGGCACTCTGGTGCAATTCTACG
1 TGGCACTCTCGTGCAATTATACG
180204 TGGCACT-TCGTGCAATTATACG
1 TGGCACTCTCGTGCAATTATACG
180226 ATCTGTGTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.20, C:0.24, G:0.24, T:0.31
Consensus pattern (23 bp):
TGGCACTCTCGTGCAATTATACG
Found at i:182667 original size:14 final size:14
Alignment explanation
Indices: 182648--182686 Score: 78
Period size: 14 Copynumber: 2.8 Consensus size: 14
182638 AAAATCGAAC
182648 AACAGATTCTGCAA
1 AACAGATTCTGCAA
182662 AACAGATTCTGCAA
1 AACAGATTCTGCAA
182676 AACAGATTCTG
1 AACAGATTCTG
182687 TTGATCAACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.41, C:0.21, G:0.15, T:0.23
Consensus pattern (14 bp):
AACAGATTCTGCAA
Found at i:186988 original size:19 final size:19
Alignment explanation
Indices: 186972--187010 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
186962 TGCTAAAATT
186972 CAGAGTAGTGAACAAAACA
1 CAGAGTAGTGAACAAAACA
*
186991 GAGAGTAGTGAACAAAACA
1 CAGAGTAGTGAACAAAACA
187010 C
1 C
187011 TAAAGACAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.51, C:0.15, G:0.23, T:0.10
Consensus pattern (19 bp):
CAGAGTAGTGAACAAAACA
Done.