Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009385.1 Hibiscus syriacus cultivar Beakdansim tig00113276_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: 110496
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.34
Found at i:1638 original size:23 final size:22
Alignment explanation
Indices: 1579--1645 Score: 116
Period size: 22 Copynumber: 3.0 Consensus size: 22
1569 TATGGACATC
*
1579 ATTCTACGGGCACTACGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
1601 ATTCTACGGGCACTTCGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
1623 ATTCTACGGGGCACTTCGGTGCA
1 ATTCTAC-GGGCACTTCGGTGCA
1646 TTTATACGAG
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
22 28 0.65
23 15 0.35
ACGTcount: A:0.19, C:0.27, G:0.28, T:0.25
Consensus pattern (22 bp):
ATTCTACGGGCACTTCGGTGCA
Found at i:4855 original size:18 final size:18
Alignment explanation
Indices: 4821--4855 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
4811 TATTTTGACA
* *
4821 AAAAAAATTATACGCTTT
1 AAAAAAATTAAAAGCTTT
4839 AAAAAAATTAAAAGCTT
1 AAAAAAATTAAAAGCTT
4856 ATCTTTTAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.57, C:0.09, G:0.06, T:0.29
Consensus pattern (18 bp):
AAAAAAATTAAAAGCTTT
Found at i:5090 original size:59 final size:60
Alignment explanation
Indices: 4952--5093 Score: 155
Period size: 60 Copynumber: 2.4 Consensus size: 60
4942 CTTTAAAATG
* * **
4952 TTCCAAGTTCATCCCTAAACTATGACTATAATTCTAAATTAATCCTTAAACTTTTGAACA
1 TTCCAATTTCATCCCCAAACTATGACTATAATTCTAAATTAATCCCCAAACTTTTGAACA
* * * * **
5012 -GCTCAATGTCATCCTCAAACTATGACT-TCATTCTAAATTGGTCCCCAAACTTTTTGAACA
1 TTC-CAATTTCATCCCCAAACTATGACTATAATTCTAAATTAATCCCCAAAC-TTTTGAACA
5072 TTCCAATTTCA-CCCCAAACTAT
1 TTCCAATTTCATCCCCAAACTAT
5094 ATCTATATAC
Statistics
Matches: 66, Mismatches: 13, Indels: 7
0.77 0.15 0.08
Matches are distributed among these distances:
59 29 0.44
60 36 0.55
61 1 0.02
ACGTcount: A:0.33, C:0.26, G:0.06, T:0.35
Consensus pattern (60 bp):
TTCCAATTTCATCCCCAAACTATGACTATAATTCTAAATTAATCCCCAAACTTTTGAACA
Found at i:27202 original size:20 final size:21
Alignment explanation
Indices: 27174--27215 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
27164 CAACCAGCTG
27174 GCACATCAATTTCATCA-CCT
1 GCACATCAATTTCATCAGCCT
* *
27194 GCACCTCAATTTTATCAGCCT
1 GCACATCAATTTCATCAGCCT
27215 G
1 G
27216 TGCAGTCTCC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.26, C:0.33, G:0.10, T:0.31
Consensus pattern (21 bp):
GCACATCAATTTCATCAGCCT
Found at i:28589 original size:128 final size:128
Alignment explanation
Indices: 28282--28657 Score: 613
Period size: 121 Copynumber: 3.0 Consensus size: 128
28272 GGTTTATGCT
* *
28282 GGCCTCAGAACTTGGGAATCAAATTATTCCTTTTCTAGATTATTTCGGTTGGCCAAAGCTTCATA
1 GGCCTCAGAACTTGGGAATCAAATTATTCCTTTTCTAGATTATTTAGGTTGGTCAAAGCTTCATA
* * *
28347 ATGAATATTGGGTTAGGAGCAGTATGGCTTGAGAAGAATATACAGTATG------A-TTATCA
66 ATGAATATTGGGTTAGGAGCAGTATAGTTTGAGGAGAATATACAGTATGATTATCATTTATCA
28403 GGCCTCAGAACTTGGGAATCAAATTATTCCTTTTCTAGATTATTTAGGTTGGTCAAAGCTTCATA
1 GGCCTCAGAACTTGGGAATCAAATTATTCCTTTTCTAGATTATTTAGGTTGGTCAAAGCTTCATA
28468 ATGAATATTGGGTTAGGAGCAGTATAGTTTGAGGAGAATATACAGTATGATTATCATTTATCA
66 ATGAATATTGGGTTAGGAGCAGTATAGTTTGAGGAGAATATACAGTATGATTATCATTTATCA
*
28531 GGCCTCAGAACTTGGCAATCAAATTATTCCTTTTCTAGATTATTTAGGTTGGTCAAAGCTTCATA
1 GGCCTCAGAACTTGGGAATCAAATTATTCCTTTTCTAGATTATTTAGGTTGGTCAAAGCTTCATA
* *
28596 ATGAATATAATGGGATAGGAGCAGTACAGTTTGAGGAGAATATACAGTATGATTATCATTTA
66 ATGAATAT--TGGGTTAGGAGCAGTATAGTTTGAGGAGAATATACAGTATGATTATCATTTA
28658 CAAATTGTGT
Statistics
Matches: 238, Mismatches: 8, Indels: 9
0.93 0.03 0.04
Matches are distributed among these distances:
121 109 0.46
127 1 0.00
128 78 0.33
130 50 0.21
ACGTcount: A:0.32, C:0.13, G:0.21, T:0.34
Consensus pattern (128 bp):
GGCCTCAGAACTTGGGAATCAAATTATTCCTTTTCTAGATTATTTAGGTTGGTCAAAGCTTCATA
ATGAATATTGGGTTAGGAGCAGTATAGTTTGAGGAGAATATACAGTATGATTATCATTTATCA
Found at i:32828 original size:14 final size:14
Alignment explanation
Indices: 32783--32829 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
32773 ATTAATTTAA
32783 AATAGAATGGTATT
1 AATAGAATGGTATT
* *
32797 ACTAGAATGGTCA-A
1 AATAGAATGGT-ATT
*
32811 AATAGAATGATATT
1 AATAGAATGGTATT
32825 AATAG
1 AATAG
32830 TTTGAGGATT
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
13 1 0.04
14 24 0.92
15 1 0.04
ACGTcount: A:0.47, C:0.04, G:0.19, T:0.30
Consensus pattern (14 bp):
AATAGAATGGTATT
Found at i:39031 original size:15 final size:16
Alignment explanation
Indices: 39006--39043 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
38996 ATACATAATA
39006 AAAAATAT-AAACAAGT
1 AAAAATATAAAACAA-T
39022 AAAAAT-TAAAACAAT
1 AAAAATATAAAACAAT
39037 AAAAATA
1 AAAAATA
39044 CAACTAGAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 8 0.40
16 12 0.60
ACGTcount: A:0.74, C:0.05, G:0.03, T:0.18
Consensus pattern (16 bp):
AAAAATATAAAACAAT
Found at i:39963 original size:11 final size:10
Alignment explanation
Indices: 39944--39968 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
39934 TTTCTCTGTC
39944 TTTTCTTTTT
1 TTTTCTTTTT
39954 TTTTCTTTTT
1 TTTTCTTTTT
39964 TTTTC
1 TTTTC
39969 CGTTCTCTGC
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:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (10 bp):
TTTTCTTTTT
Found at i:40376 original size:3 final size:3
Alignment explanation
Indices: 40368--40465 Score: 124
Period size: 3 Copynumber: 31.7 Consensus size: 3
40358 TTATTTATTA
*
40368 AAT AAT AAT AAT ATAT AAT ATT AAT AAT AAT AAAT AAT AAAT AAT AAT
1 AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT -AAT AAT -AAT AAT AAT
* * **
40416 TAT AAT AAT AAT AAT AAT ACT AAT AAT AAT AAT TTT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
40464 AA
1 AA
40466 ATTTAAATGA
Statistics
Matches: 82, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
3 73 0.89
4 9 0.11
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (3 bp):
AAT
Found at i:40723 original size:76 final size:76
Alignment explanation
Indices: 40592--41156 Score: 1071
Period size: 76 Copynumber: 7.5 Consensus size: 76
40582 GATGGAAATG
*
40592 TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
40657 CCCGAAGGCTT
66 CCCGAAGGCTT
40668 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
* *
40733 CCAGAAAGCTT
66 CCCGAAGGCTT
*
40744 TTTGGAAACATCATGCGCTGAAGGACTTACAGATGACCCGAAGGCTTTG-AAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
40808 CCCGAAGGCTT
66 CCCGAAGGCTT
*
40819 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
40884 CCCGAAGGCTT
66 CCCGAAGGCTT
40895 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTG-AAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
40959 CCCGAAGGCTT
66 CCCGAAGGCTT
40970 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
41035 CCCGAAGGCTT
66 CCCGAAGGCTT
41046 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
41111 CCCGAAGGCTT
66 CCCGAAGGCTT
41122 TTTGGAAACATCATGCACTGAAGGACTTACAGATG
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATG
41157 TGGGAAATAG
Statistics
Matches: 478, Mismatches: 9, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
75 146 0.31
76 332 0.69
ACGTcount: A:0.36, C:0.22, G:0.21, T:0.22
Consensus pattern (76 bp):
TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
CCCGAAGGCTT
Found at i:40872 original size:151 final size:152
Alignment explanation
Indices: 40592--41156 Score: 1071
Period size: 151 Copynumber: 3.7 Consensus size: 152
40582 GATGGAAATG
*
40592 TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
40657 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
66 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
* *
40722 ATCAAAAAGCTCCAGAAAGCTT
131 ATCAAAAAGCTCCCGAAGGCTT
*
40744 TTTGGAAACATCATGCGCTGAAGGACTTACAGATGACCCGAAGGCTTTG-AAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
*
40808 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
66 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
40873 ATCAAAAAGCTCCCGAAGGCTT
131 ATCAAAAAGCTCCCGAAGGCTT
40895 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTG-AAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
40959 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
66 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
41024 ATCAAAAAGCTCCCGAAGGCTT
131 ATCAAAAAGCTCCCGAAGGCTT
41046 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
41111 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATG
66 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATG
41157 TGGGAAATAG
Statistics
Matches: 405, Mismatches: 7, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
151 297 0.73
152 108 0.27
ACGTcount: A:0.36, C:0.22, G:0.21, T:0.22
Consensus pattern (152 bp):
TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
ATCAAAAAGCTCCCGAAGGCTT
Found at i:41026 original size:227 final size:227
Alignment explanation
Indices: 40592--41156 Score: 1069
Period size: 227 Copynumber: 2.5 Consensus size: 227
40582 GATGGAAATG
*
40592 TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
40657 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
66 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
*
40722 ATCAAAAAGCTCCAGAAAGCTTTTTGGAAACATCATGCGCTGAAGGACTTACAGATGACCCGAAG
131 ATCAAAAAGCTCCAGAAAGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAG
40787 GCTTTGAAACATCAAAAAGCTCCCGAAGGCTT
196 GCTTTGAAACATCAAAAAGCTCCCGAAGGCTT
*
40819 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
40884 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTG-AAAC
66 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
* *
40948 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAG
131 ATCAAAAAGCTCCAGAAAGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAG
41013 GCTTTGAAAACATCAAAAAGCTCCCGAAGGCTT
196 GCTTTG-AAACATCAAAAAGCTCCCGAAGGCTT
41046 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
41111 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATG
66 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATG
41157 TGGGAAATAG
Statistics
Matches: 331, Mismatches: 6, Indels: 2
0.98 0.02 0.01
Matches are distributed among these distances:
226 72 0.22
227 259 0.78
ACGTcount: A:0.36, C:0.22, G:0.21, T:0.22
Consensus pattern (227 bp):
TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
ATCAAAAAGCTCCAGAAAGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAG
GCTTTGAAACATCAAAAAGCTCCCGAAGGCTT
Found at i:41852 original size:22 final size:22
Alignment explanation
Indices: 41827--41878 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
41817 CATAAAGCTT
* *
41827 TCATCTTTAAAAAGAGAATTTG
1 TCATCTTTAAAAAGAGAATCTA
41849 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTAAAAAGAGAATCTA
41871 TCATCTTT
1 TCATCTTT
41879 GAAGAGTGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.38, C:0.13, G:0.10, T:0.38
Consensus pattern (22 bp):
TCATCTTTAAAAAGAGAATCTA
Found at i:43310 original size:75 final size:74
Alignment explanation
Indices: 43217--43385 Score: 187
Period size: 74 Copynumber: 2.3 Consensus size: 74
43207 ATTGTGGGCC
* *
43217 TTCAGCATGCCCCAACA-TTGGCTAATACAAGTGTTCAAAATGCATCAACAGTTCTGATTCTGAT
1 TTCAGCATGCCCCAACATTTGGCTAATA-AA-TATTCAAAATACATCAACAGTTCTGATTCTGAT
*
43281 TGAAATGGGTT
64 TGAAAAGGGTT
* * * ** * * *
43292 TTCAGCATGCCCCAACATTTTGCTGATAAATATTCAGAATATTTTAACATTTCTGATTCTGTTTG
1 TTCAGCATGCCCCAACATTTGGCTAATAAATATTCAAAATACATCAACAGTTCTGATTCTGATTG
43357 AAAAGGGTT
66 AAAAGGGTT
* * *
43366 TTCAGTATGTCCCAATATTT
1 TTCAGCATGCCCCAACATTT
43386 TCTTCTTGTT
Statistics
Matches: 79, Mismatches: 14, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
74 52 0.66
75 19 0.24
76 8 0.10
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.36
Consensus pattern (74 bp):
TTCAGCATGCCCCAACATTTGGCTAATAAATATTCAAAATACATCAACAGTTCTGATTCTGATTG
AAAAGGGTT
Found at i:51454 original size:16 final size:16
Alignment explanation
Indices: 51428--51479 Score: 63
Period size: 16 Copynumber: 3.2 Consensus size: 16
51418 TTAATTCTTG
*
51428 AATAAAATAAATAAATA
1 AATATAATAAAT-AATA
51445 AA-ATAATAAATAATA
1 AATATAATAAATAATA
51460 ATATATAA-AAATAATA
1 A-ATATAATAAATAATA
51476 AATA
1 AATA
51480 AAAAATTTGA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
15 8 0.25
16 18 0.56
17 6 0.19
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (16 bp):
AATATAATAAATAATA
Found at i:51483 original size:13 final size:14
Alignment explanation
Indices: 51428--51481 Score: 71
Period size: 13 Copynumber: 4.1 Consensus size: 14
51418 TTAATTCTTG
51428 AATAA-AATAAATA
1 AATAATAATAAATA
51441 AATAA-AAT-AATA
1 AATAATAATAAATA
*
51453 AATAATAATATATA
1 AATAATAATAAATA
51467 AA-AATAATAAATA
1 AATAATAATAAATA
51480 AA
1 AA
51482 AAATTTGAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
12 9 0.24
13 23 0.62
14 5 0.14
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (14 bp):
AATAATAATAAATA
Found at i:52251 original size:15 final size:16
Alignment explanation
Indices: 52226--52263 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
52216 ATACATAATA
52226 AAAAATAT-AAACAAGT
1 AAAAATATAAAACAA-T
52242 AAAAAT-TAAAACAAT
1 AAAAATATAAAACAAT
52257 AAAAATA
1 AAAAATA
52264 CAACTAGAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 8 0.40
16 12 0.60
ACGTcount: A:0.74, C:0.05, G:0.03, T:0.18
Consensus pattern (16 bp):
AAAAATATAAAACAAT
Found at i:53597 original size:3 final size:3
Alignment explanation
Indices: 53589--53691 Score: 143
Period size: 3 Copynumber: 33.7 Consensus size: 3
53579 TTATTTATTA
*
53589 AAT AAT AAT AAT ATAT AAT ATT AAT AAT AAT AAT AAAT AAT AAT AAT
1 AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT
* * **
53636 AAT TAT AAT AAT AAT AAT ACT AAT AAT AAT AAT AAT AAT TTT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
53684 AAT AAT AA
1 AAT AAT AA
53692 ATTTAAATGA
Statistics
Matches: 88, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
3 82 0.93
4 6 0.07
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (3 bp):
AAT
Found at i:54905 original size:21 final size:21
Alignment explanation
Indices: 54881--54975 Score: 129
Period size: 21 Copynumber: 4.6 Consensus size: 21
54871 TATCGCAAAT
54881 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
54902 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
* ** **
54923 TCGCGTTGCGAT-TTTCCATT
1 TCGCGTTGCGATAGTTGAAAA
*
54943 TCGCGTTGCTATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
54964 TCGCGTTGCGAT
1 TCGCGTTGCGAT
54976 TTTCCAAATT
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
20 14 0.23
21 47 0.77
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTGAAAA
Found at i:54957 original size:41 final size:41
Alignment explanation
Indices: 54902--55003 Score: 154
Period size: 41 Copynumber: 2.5 Consensus size: 41
54892 TAGTTGAAAA
54902 TCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATT
* *
54943 TCGCGTTGCTATAGTTGAAAATCGCGTTGCGATTTTCCAAAT
1 TCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCC-ATT
*
54985 T--CGTTGCGATAGTTAAAAA
1 TCGCGTTGCGATAGTTGAAAA
55004 AAAGATTTTG
Statistics
Matches: 56, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
40 16 0.29
41 37 0.66
42 3 0.05
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.35
Consensus pattern (41 bp):
TCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATT
Found at i:56159 original size:19 final size:20
Alignment explanation
Indices: 56123--56160 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
56113 ATATAATCTA
*
56123 AAATAATCAGTTAATAAATT
1 AAATAATCAGTGAATAAATT
*
56143 AAAT-ATCAGTGATTAAAT
1 AAATAATCAGTGAATAAAT
56161 AAAAAATATA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 12 0.75
20 4 0.25
ACGTcount: A:0.53, C:0.05, G:0.08, T:0.34
Consensus pattern (20 bp):
AAATAATCAGTGAATAAATT
Found at i:56661 original size:22 final size:22
Alignment explanation
Indices: 56636--56681 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
56626 AGGGCCTGTG
56636 TAAATTCTTAAAAAGAGGCCCT
1 TAAATTCTTAAAAAGAGGCCCT
*
56658 TAAATTCTTAAAAAGATGCCCT
1 TAAATTCTTAAAAAGAGGCCCT
56680 TA
1 TA
56682 GTAAAAATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.41, C:0.17, G:0.11, T:0.30
Consensus pattern (22 bp):
TAAATTCTTAAAAAGAGGCCCT
Found at i:58997 original size:2 final size:2
Alignment explanation
Indices: 58992--59056 Score: 103
Period size: 2 Copynumber: 32.5 Consensus size: 2
58982 TCTCTCTCTC
* * *
58992 TA TA TA TA TA TA TA TG TA TA TA TG TA TA TG TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
59034 TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
59057 CCAGCACTGT
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.51
Consensus pattern (2 bp):
TA
Found at i:61771 original size:136 final size:136
Alignment explanation
Indices: 61527--61799 Score: 546
Period size: 136 Copynumber: 2.0 Consensus size: 136
61517 ATTTGCGCAC
61527 ATTTCTCTCACAGATGTGTAACAGCTCTGCTCTTTGTAGTGACAATGCGTTTAGCTTGCTTTCGA
1 ATTTCTCTCACAGATGTGTAACAGCTCTGCTCTTTGTAGTGACAATGCGTTTAGCTTGCTTTCGA
61592 CTTTTTTTTGTCAAAATAAAAGCTATAAATTTAGATCATTTATCTATTCCTGTGCGTCAATTCTA
66 CTTTTTTTTGTCAAAATAAAAGCTATAAATTTAGATCATTTATCTATTCCTGTGCGTCAATTCTA
61657 GCCGTG
131 GCCGTG
61663 ATTTCTCTCACAGATGTGTAACAGCTCTGCTCTTTGTAGTGACAATGCGTTTAGCTTGCTTTCGA
1 ATTTCTCTCACAGATGTGTAACAGCTCTGCTCTTTGTAGTGACAATGCGTTTAGCTTGCTTTCGA
61728 CTTTTTTTTGTCAAAATAAAAGCTATAAATTTAGATCATTTATCTATTCCTGTGCGTCAATTCTA
66 CTTTTTTTTGTCAAAATAAAAGCTATAAATTTAGATCATTTATCTATTCCTGTGCGTCAATTCTA
61793 GCCGTG
131 GCCGTG
61799 A
1 A
61800 ATGCTTTCAT
Statistics
Matches: 137, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
136 137 1.00
ACGTcount: A:0.25, C:0.19, G:0.16, T:0.40
Consensus pattern (136 bp):
ATTTCTCTCACAGATGTGTAACAGCTCTGCTCTTTGTAGTGACAATGCGTTTAGCTTGCTTTCGA
CTTTTTTTTGTCAAAATAAAAGCTATAAATTTAGATCATTTATCTATTCCTGTGCGTCAATTCTA
GCCGTG
Found at i:66638 original size:24 final size:23
Alignment explanation
Indices: 66611--66656 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
66601 ATGAATTCGG
*
66611 ATAT-TACATTAATGTTAGATATAA
1 ATATGTAC-TTAATATTA-ATATAA
66635 ATATGTACTTAATATTAATATA
1 ATATGTACTTAATATTAATATA
66657 TTTAAATCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 5 0.25
24 12 0.60
25 3 0.15
ACGTcount: A:0.46, C:0.04, G:0.07, T:0.43
Consensus pattern (23 bp):
ATATGTACTTAATATTAATATAA
Found at i:76410 original size:29 final size:30
Alignment explanation
Indices: 76351--76415 Score: 123
Period size: 29 Copynumber: 2.2 Consensus size: 30
76341 TTTTAAAATT
76351 GATAATGTGTGATGATGGGGTAATTTTTTA
1 GATAATGTGTGATGATGGGGTAATTTTTTA
76381 GATAATGTGTGATGAT-GGGTAATTTTTTA
1 GATAATGTGTGATGATGGGGTAATTTTTTA
76410 GATAAT
1 GATAAT
76416 ATGTTGGAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 19 0.54
30 16 0.46
ACGTcount: A:0.29, C:0.00, G:0.28, T:0.43
Consensus pattern (30 bp):
GATAATGTGTGATGATGGGGTAATTTTTTA
Found at i:85616 original size:2 final size:2
Alignment explanation
Indices: 85609--85650 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
85599 GTATTTCCAG
85609 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
85651 CTTTGGATAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:90903 original size:128 final size:128
Alignment explanation
Indices: 90675--91175 Score: 939
Period size: 128 Copynumber: 3.9 Consensus size: 128
90665 TAATCGGAGT
* *
90675 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGATAATATGTTAT
1 ACTATTCACATGAAGACGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTAT
*
90740 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACATATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
90803 ACTATTCACATGAAGACGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGACGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTAT
90868 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
*
90931 ACTATTCACATGAAGAAGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGACGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTAT
*
90996 CATTGTCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
* *
91059 ACTATTCATATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGACGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTAT
91124 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
91176 AATCAGGTAA
Statistics
Matches: 364, Mismatches: 9, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
128 364 1.00
ACGTcount: A:0.24, C:0.24, G:0.19, T:0.33
Consensus pattern (128 bp):
ACTATTCACATGAAGACGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTAT
CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
Found at i:92112 original size:34 final size:34
Alignment explanation
Indices: 92074--92180 Score: 133
Period size: 40 Copynumber: 3.0 Consensus size: 34
92064 AAATTTAATG
*
92074 TTAAATTTCGAATACTATAATTTATATTTTAAAT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
*
92108 TTAAATTTCGAATAATATGATTTTTATTTTTATTTTAAAT
1 TTAAATTTCGAATAATAT-A-----ATTTATATTTTAAAT
*
92148 TTAAATTTCGAATAATATAATTTGTATTTTAAA
1 TTAAATTTCGAATAATATAATTTATATTTTAAA
92181 AACATTTATC
Statistics
Matches: 64, Mismatches: 3, Indels: 12
0.81 0.04 0.15
Matches are distributed among these distances:
34 30 0.47
35 1 0.02
39 1 0.02
40 32 0.50
ACGTcount: A:0.39, C:0.04, G:0.05, T:0.52
Consensus pattern (34 bp):
TTAAATTTCGAATAATATAATTTATATTTTAAAT
Found at i:92142 original size:40 final size:40
Alignment explanation
Indices: 92093--92177 Score: 143
Period size: 40 Copynumber: 2.1 Consensus size: 40
92083 GAATACTATA
* * *
92093 ATTTATATTTTAAATTTAAATTTCGAATAATATGATTTTT
1 ATTTTTATTTTAAATTTAAATTTCGAATAATATAATTTGT
92133 ATTTTTATTTTAAATTTAAATTTCGAATAATATAATTTGT
1 ATTTTTATTTTAAATTTAAATTTCGAATAATATAATTTGT
92173 ATTTT
1 ATTTT
92178 AAAAACATTT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.36, C:0.02, G:0.05, T:0.56
Consensus pattern (40 bp):
ATTTTTATTTTAAATTTAAATTTCGAATAATATAATTTGT
Found at i:92787 original size:21 final size:21
Alignment explanation
Indices: 92699--92792 Score: 127
Period size: 21 Copynumber: 4.5 Consensus size: 21
92689 TATGGTATAA
*
92699 AACCCTGCGGGCTAGGCATGT
1 AACCCTGCGGGCTAGGAATGT
92720 AA-CCTGGCGGGCTAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
* * *
92741 AACCCTGCGAGCTCGAAATGT
1 AACCCTGCGGGCTAGGAATGT
*
92762 AACCCTGCGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGT
92783 AACCCTGCGG
1 AACCCTGCGG
92793 AGATGGCATA
Statistics
Matches: 65, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
20 3 0.05
21 59 0.91
22 3 0.05
ACGTcount: A:0.22, C:0.28, G:0.32, T:0.18
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:92822 original size:21 final size:21
Alignment explanation
Indices: 92796--92843 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
92786 CCTGCGGAGA
*
92796 TGGCATATAAACTGGTGGGCT
1 TGGCATATAAACTGGAGGGCT
* *
92817 TGGCATATGAAGTGGAGGGCT
1 TGGCATATAAACTGGAGGGCT
*
92838 GGGCAT
1 TGGCAT
92844 GTACCCCTGC
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:0.23, C:0.12, G:0.40, T:0.25
Consensus pattern (21 bp):
TGGCATATAAACTGGAGGGCT
Found at i:94633 original size:31 final size:33
Alignment explanation
Indices: 94568--94650 Score: 98
Period size: 34 Copynumber: 2.5 Consensus size: 33
94558 TTAATAATTC
* *
94568 TAAATAAATAATAATTATATAAATATTATTTTAA
1 TAAAAAAATAATAATTACATAAATATTA-TTTAA
*
94602 TAAAAAAATAATATTTACATAAATA-TA-TTAA
1 TAAAAAAATAATAATTACATAAATATTATTTAA
*
94633 TATAAAATATAATAATTA
1 TA-AAAAAATAATAATTA
94651 TTTAAAAAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
31 6 0.14
32 13 0.30
33 2 0.05
34 22 0.51
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (33 bp):
TAAAAAAATAATAATTACATAAATATTATTTAA
Found at i:108479 original size:23 final size:24
Alignment explanation
Indices: 108434--108480 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
108424 AAATTGGACG
*
108434 ACCGAATTTTTTACCGGATAAAAA
1 ACCGAATTTTTTACCGGAAAAAAA
108458 ACCG-ATTTTTTATCC-GAAAAAAA
1 ACCGAATTTTTTA-CCGGAAAAAAA
108481 TTCGGTCTGG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 15 0.71
24 6 0.29
ACGTcount: A:0.43, C:0.17, G:0.11, T:0.30
Consensus pattern (24 bp):
ACCGAATTTTTTACCGGAAAAAAA
Found at i:108480 original size:24 final size:24
Alignment explanation
Indices: 108434--108480 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
108424 AAATTGGACG
* *
108434 ACCGAATTTTTTACCGGATAAAAA
1 ACCGAATTTTTTACCGAAAAAAAA
108458 ACCG-ATTTTTTATCCGAAAAAAA
1 ACCGAATTTTTTA-CCGAAAAAAA
108481 TTCGGTCTGG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.43, C:0.17, G:0.11, T:0.30
Consensus pattern (24 bp):
ACCGAATTTTTTACCGAAAAAAAA
Done.