Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005648.1 Hibiscus syriacus cultivar Beakdansim tig00013188_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: 48651
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:1617 original size:17 final size:18
Alignment explanation
Indices: 1595--1629 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
1585 CGAATGTAAT
1595 TAGTG-TACCGATACACC
1 TAGTGTTACCGATACACC
1612 TAGTGTTTACCGATACAC
1 TAGTG-TTACCGATACAC
1630 TCAGTTATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
19 11 0.69
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.29
Consensus pattern (18 bp):
TAGTGTTACCGATACACC
Found at i:5787 original size:19 final size:19
Alignment explanation
Indices: 5763--5808 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
5753 TAGTGAGGAA
*
5763 CAAGGCTAGACTTATTTCT
1 CAAGGCTAGACTTATTGCT
*
5782 CAAGGCTAGACTTGTTGCT
1 CAAGGCTAGACTTATTGCT
5801 CAAGGCTA
1 CAAGGCTA
5809 TACTCAAGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.30
Consensus pattern (19 bp):
CAAGGCTAGACTTATTGCT
Found at i:14678 original size:43 final size:43
Alignment explanation
Indices: 14617--14703 Score: 165
Period size: 43 Copynumber: 2.0 Consensus size: 43
14607 TATGCCATGG
*
14617 CATAATTCTAACAAGTGAATGCCATCTTCATCCAACACAAGTT
1 CATAATTCTAACAAGTGAATGACATCTTCATCCAACACAAGTT
14660 CATAATTCTAACAAGTGAATGACATCTTCATCCAACACAAGTT
1 CATAATTCTAACAAGTGAATGACATCTTCATCCAACACAAGTT
14703 C
1 C
14704 TTTGGAGGCC
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.38, C:0.25, G:0.09, T:0.28
Consensus pattern (43 bp):
CATAATTCTAACAAGTGAATGACATCTTCATCCAACACAAGTT
Found at i:24173 original size:28 final size:29
Alignment explanation
Indices: 24133--24199 Score: 93
Period size: 28 Copynumber: 2.4 Consensus size: 29
24123 CCTTTATTTA
*
24133 TTCTCTTTTTTTTC-TTTCTTTTTCTATT
1 TTCTCATTTTTTTCTTTTCTTTTTCTATT
*
24161 TTCTCATTTTTTTCTTTTCTTTTTTTATT
1 TTCTCATTTTTTTCTTTTCTTTTTCTATT
*
24190 TT-TTATTTTT
1 TTCTCATTTTT
24200 CATTTTTCCT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
28 20 0.57
29 15 0.43
ACGTcount: A:0.06, C:0.13, G:0.00, T:0.81
Consensus pattern (29 bp):
TTCTCATTTTTTTCTTTTCTTTTTCTATT
Found at i:24212 original size:21 final size:20
Alignment explanation
Indices: 24151--24215 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 20
24141 TTTTTCTTTC
24151 TTTTTCTATTTTCTCATTTTTT
1 TTTTTC-ATTTT-TCATTTTTT
* *
24173 TCTTTTCTTTTTTTATTTTTT
1 T-TTTTCATTTTTCATTTTTT
*
24194 ATTTTTCATTTTTCCTTTTTT
1 -TTTTTCATTTTTCATTTTTT
24215 T
1 T
24216 CTTCATTCAG
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
20 1 0.03
21 24 0.67
22 6 0.17
23 5 0.14
ACGTcount: A:0.08, C:0.12, G:0.00, T:0.80
Consensus pattern (20 bp):
TTTTTCATTTTTCATTTTTT
Found at i:27705 original size:6 final size:6
Alignment explanation
Indices: 27694--27729 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
27684 GAACAAAAAG
27694 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
27730 GAGAAACTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (6 bp):
ATACAT
Found at i:30134 original size:8 final size:8
Alignment explanation
Indices: 30123--30157 Score: 61
Period size: 8 Copynumber: 4.2 Consensus size: 8
30113 ATTAACAAAT
30123 TAAAAAAA
1 TAAAAAAA
30131 TAAAAAAA
1 TAAAAAAA
30139 TAAAAATAA
1 TAAAAA-AA
30148 TAAAAAAA
1 TAAAAAAA
30156 TA
1 TA
30158 TGAAATGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
8 18 0.69
9 8 0.31
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (8 bp):
TAAAAAAA
Found at i:30157 original size:17 final size:17
Alignment explanation
Indices: 30108--30157 Score: 66
Period size: 17 Copynumber: 3.0 Consensus size: 17
30098 AAATTCGAAG
* * *
30108 AAAATATTAACAAATTA
1 AAAATAATAAAAAAATA
30125 AAAA-AATAAAAAAATA
1 AAAATAATAAAAAAATA
30141 AAAATAATAAAAAAATA
1 AAAATAATAAAAAAATA
30158 TGAAATGAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
16 13 0.45
17 16 0.55
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (17 bp):
AAAATAATAAAAAAATA
Found at i:32019 original size:139 final size:138
Alignment explanation
Indices: 31764--32189 Score: 559
Period size: 139 Copynumber: 3.1 Consensus size: 138
31754 TCAATTTGAA
* * *
31764 GATAATTTAGTGACAACACGGTTCCTACGTGATGAGGAAGTCTGATTGTCTAAGGATGACACTGC
1 GATAATTTGGAGACAACACGGTTCCTACGTGATGAGGAAGTCTG-TTATCTAAGGATGACACTGC
* * * *
31829 TCCTATGTGATGAGAATATCTTA-TCAGTGGAAGACATTGTTCCTACGTGATGAGGACGTCTAGC
65 TCCTATGTGATGAGAAGATC-TAGTCGGTGGACGACATTGTTCCTACATGATGAGGACGTCTAGC
*
31893 CATCTTTAGG
129 TATCTTTAGG
*
31903 GATAATTTGGAGACAACACGGTTCCTACGTGATGAGGAAGTCTAGTTATCTGAGGATGACACTGC
1 GATAATTTGGAGACAACACGGTTCCTACGTGATGAGGAAGTCT-GTTATCTAAGGATGACACTGC
* * * *
31968 TCCTACGTGATGAGGAGATCTAGTTGGTGGACGACAATGTTCCTACATGATGAGGACGTCTAGCT
65 TCCTATGTGATGAGAAGATCTAGTCGGTGGACGACATTGTTCCTACATGATGAGGACGTCTAGCT
32033 ATCTTTAGG
130 ATCTTTAGG
* * ** * ** *
32042 GATAATTTGAAGATAACACGGTTCCTATATGATGAGGAAGTCTGGTTATATAAGGATG-CTGTTA
1 GATAATTTGGAGACAACACGGTTCCTACGTGATGAGGAAGTCT-GTTATCTAAGGATGAC-ACTG
* * * *
32106 CTCCTATGTGATGAGAAGATCTGGTCGGTTGACGACATTGTTCCTACTTGATGAGGACATCTAGC
64 CTCCTATGTGATGAGAAGATCTAGTCGGTGGACGACATTGTTCCTACATGATGAGGACGTCTAGC
*
32171 TGTCTTTAGG
129 TATCTTTAGG
32181 GATAATTTG
1 GATAATTTG
32190 TTTCAAGAGA
Statistics
Matches: 252, Mismatches: 32, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
138 3 0.01
139 248 0.98
140 1 0.00
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.31
Consensus pattern (138 bp):
GATAATTTGGAGACAACACGGTTCCTACGTGATGAGGAAGTCTGTTATCTAAGGATGACACTGCT
CCTATGTGATGAGAAGATCTAGTCGGTGGACGACATTGTTCCTACATGATGAGGACGTCTAGCTA
TCTTTAGG
Found at i:32030 original size:40 final size:42
Alignment explanation
Indices: 31923--32035 Score: 115
Period size: 40 Copynumber: 2.7 Consensus size: 42
31913 AGACAACACG
* * *
31923 GTTCCTACGTGATGAGGAAGTCTAGTTATCTGAGGATGACACT
1 GTTCCTACGTGATGAGG-AGTCTAGTTATCGGAGGACGACAAT
* *
31966 GCTCCTACGTGATGAGGAGATCTAG-T-T-GGTGGACGACAAT
1 GTTCCTACGTGATGAGGAG-TCTAGTTATCGGAGGACGACAAT
* *
32006 GTTCCTACATGATGAGGACGTCTAGCTATC
1 GTTCCTACGTGATGAGGA-GTCTAGTTATC
32036 TTTAGGGATA
Statistics
Matches: 58, Mismatches: 7, Indels: 10
0.77 0.09 0.13
Matches are distributed among these distances:
40 30 0.52
41 3 0.05
42 4 0.07
43 21 0.36
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.28
Consensus pattern (42 bp):
GTTCCTACGTGATGAGGAGTCTAGTTATCGGAGGACGACAAT
Found at i:32230 original size:36 final size:36
Alignment explanation
Indices: 32184--32487 Score: 329
Period size: 36 Copynumber: 8.5 Consensus size: 36
32174 CTTTAGGGAT
*
32184 AATTTGTTTCAAGAGAAACTATCTCAAGAGAGACAA
1 AATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAA
*
32220 ATTTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAA
1 AATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAA
*
32256 AACTTTGTTTCAATAGAAACTGTCTCAAGAGAGACAA
1 AA-TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAA
* * *
32293 AACTTTGTTTCAAAATAAATTGTCTCAAGCA-AGACAA
1 AA-TTTGTTTCAAGAGAAACTGTCTCAAG-AGAGACAA
* * *
32330 AATTTATTTCAAGAGAAACTATCTTAAGAGAGACAA
1 AATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAA
* *
32366 AACTTGTTTCGAA-AGAAACTGTCTCAAGCGAGACAA
1 AATTTGTTTC-AAGAGAAACTGTCTCAAGAGAGACAA
* **
32402 AATTTGTTTCAAGGGAAACAATCTCAA-AG-G----
1 AATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAA
* *
32432 -TTTATGTTTCAAGAGAAACTGTCTCAAGCGAGACAA
1 AATT-TGTTTCAAGAGAAACTGTCTCAAGAGAGACAA
* *
32468 AACGTTGTTTCGAGAGAAAC
1 AA-TTTGTTTCAAGAGAAAC
32488 AATCTCAAAG
Statistics
Matches: 223, Mismatches: 31, Indels: 27
0.79 0.11 0.10
Matches are distributed among these distances:
29 2 0.01
30 20 0.09
31 1 0.00
32 1 0.00
34 1 0.00
35 4 0.02
36 109 0.49
37 83 0.37
38 2 0.01
ACGTcount: A:0.41, C:0.15, G:0.17, T:0.27
Consensus pattern (36 bp):
AATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAA
Found at i:32340 original size:73 final size:73
Alignment explanation
Indices: 32184--32495 Score: 349
Period size: 73 Copynumber: 4.4 Consensus size: 73
32174 CTTTAGGGAT
* *
32184 AATTTGTTTCAAGAGAAACTATCTCAAGAGAGAC-AAATTTTGTTTCAAGAGAAACTGTCTCAAG
1 AATTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTTGTTTCAAAAGAAACTGTCTCAAG
32248 -AGAGACAA
66 CA-AGACAA
* * * *
32256 AACTTTGTTTCAATAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAAATAAATTGTCTCAA
1 AA-TTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTTGTTTCAAAAGAAACTGTCTCAA
32321 GCAAGACAA
65 GCAAGACAA
* * *
32330 AATTTATTTCAAGAGAAACTATCTTAAGAGAGACAAAAC-TTGTTTCGAAAGAAACTGTCTCAAG
1 AATTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTTGTTTCAAAAGAAACTGTCTCAAG
*
32394 CGAGACAA
66 CAAGACAA
* * * *
32402 AATTTGTTTCAAGGGAAACAATCTCAA-AG-G------TTTATGTTTCAAGAGAAACTGTCTCAA
1 AATTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTT-TGTTTCAAAAGAAACTGTCTCAA
*
32459 GCGAGACAA
65 GCAAGACAA
* * *
32468 AACGTTGTTTCGAGAGAAACAATCTCAA
1 AA-TTTGTTTCAAGAGAAACTATCTCAA
32496 AGGTTTATGT
Statistics
Matches: 210, Mismatches: 24, Indels: 17
0.84 0.10 0.07
Matches are distributed among these distances:
65 1 0.00
66 32 0.15
67 22 0.10
70 1 0.00
71 2 0.01
72 54 0.26
73 63 0.30
74 34 0.16
75 1 0.00
ACGTcount: A:0.41, C:0.15, G:0.17, T:0.27
Consensus pattern (73 bp):
AATTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTTGTTTCAAAAGAAACTGTCTCAAG
CAAGACAA
Found at i:32506 original size:67 final size:67
Alignment explanation
Indices: 32370--32637 Score: 416
Period size: 67 Copynumber: 4.0 Consensus size: 67
32360 AGACAAAACT
* *
32370 TGTTTCGAA-AGAAACTGTCTCAAGCGAGACAAAA-TTTGTTTCAAGGGAAACAATCTCAAAGGT
1 TGTTTC-AAGAGAAACTGTCTCAAGCGAGACAAAACTTTGTTTCGAGAGAAACAATCTCAAAGGT
32433 TTA
65 TTA
*
32436 TGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAACGTTGTTTCGAGAGAAACAATCTCAAAGGTT
1 TGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAACTTTGTTTCGAGAGAAACAATCTCAAAGGTT
32501 TA
66 TA
* * *
32503 TGTTTCAAGAGAAATTGTCTCAA-CTGAGATAAAACTTTGTTTCGAGAGAAACAATCCCAAAGGT
1 TGTTTCAAGAGAAACTGTCTCAAGC-GAGACAAAACTTTGTTTCGAGAGAAACAATCTCAAAGGT
32567 TTA
65 TTA
* * *
32570 AGTTTCAAGAGAAACTGTCTCAGGCGAGACAAAACTTTGTTTCGAGAGAATCAATCTCAAAGGTT
1 TGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAACTTTGTTTCGAGAGAAACAATCTCAAAGGTT
32635 TA
66 TA
32637 T
1 T
32638 CAATTTTGTT
Statistics
Matches: 184, Mismatches: 14, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
65 2 0.01
66 32 0.17
67 149 0.81
68 1 0.01
ACGTcount: A:0.37, C:0.16, G:0.20, T:0.28
Consensus pattern (67 bp):
TGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAACTTTGTTTCGAGAGAAACAATCTCAAAGGTT
TA
Found at i:32733 original size:103 final size:102
Alignment explanation
Indices: 32581--32932 Score: 328
Period size: 103 Copynumber: 3.5 Consensus size: 102
32571 GTTTCAAGAG
* ** * *
32581 AAACTGTCTCAGGCGAGACAAAACTTTGTTTCGAGAGAATCAATCTCAAAGGTTTATCAATTTTG
1 AAACTGTCTCAAGCGAGACAAAA-TTTGTTTTAAGAAAAACAATCTCAAA-GTTTATCAATTTTG
* *
32646 TTTCGAGTGAAATAATTTTCAAATTT-TTTTTTGAGGGA
64 TTTCAAGTGAAACAATTTTCAAATTTATTTTTTGAGGGA
*
32684 AAACTGTCTCAAGCGAGACAAAATTTGTTTTTAAGAAAAACAATATCAAA-TTTAATCAATTTTG
1 AAACTGTCTCAAGCGAGACAAAATTTG-TTTTAAGAAAAACAATCTCAAAGTTT-ATCAATTTTG
* * * * *
32748 TTTCAAGTGAAACAATTTT-AGAATTTGTGTTTCGAAGAA
64 TTTCAAGTGAAACAATTTTCA-AATTTATTTTTTGAGGGA
** * * ** * *
32787 AAACTGTCTCAAGTAAAACAAAATTTGTTTT--G-AGAACAATCTC-AAGTAAGATAAATTTTAT
1 AAACTGTCTCAAGCGAGACAAAATTTGTTTTAAGAAAAACAATCTCAAAGT-TTATCAATTTTGT
*
32848 TTCAAGTGAAACAA-TTTCAAAATTTATTTTTCT-AGATG-
65 TTCAAGTGAAACAATTTTC-AAATTTATTTTT-TGAG-GGA
* *
32886 AAACTGTCTCAAGTGAGACGAAATTTGTTTTTAAGAAAAACAATCTC
1 AAACTGTCTCAAGCGAGACAAAATTTG-TTTTAAGAAAAACAATCTC
32933 GAATGTGTGT
Statistics
Matches: 204, Mismatches: 31, Indels: 28
0.78 0.12 0.11
Matches are distributed among these distances:
98 5 0.02
99 67 0.33
100 6 0.03
101 4 0.02
102 41 0.20
103 81 0.40
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.35
Consensus pattern (102 bp):
AAACTGTCTCAAGCGAGACAAAATTTGTTTTAAGAAAAACAATCTCAAAGTTTATCAATTTTGTT
TCAAGTGAAACAATTTTCAAATTTATTTTTTGAGGGA
Found at i:32998 original size:37 final size:37
Alignment explanation
Indices: 32957--33027 Score: 106
Period size: 37 Copynumber: 1.9 Consensus size: 37
32947 TAAGGAAGAC
* * *
32957 TGTCTTAAGTGTGGCGAAATTTATTTTTAAGAAAAAT
1 TGTCTTAAGTGAGACAAAATTTATTTTTAAGAAAAAT
*
32994 TGTCTTAAGTGAGACAAAATTTGTTTTTAAGAAA
1 TGTCTTAAGTGAGACAAAATTTATTTTTAAGAAA
33028 GTAATCTCAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 30 1.00
ACGTcount: A:0.37, C:0.06, G:0.18, T:0.39
Consensus pattern (37 bp):
TGTCTTAAGTGAGACAAAATTTATTTTTAAGAAAAAT
Found at i:40245 original size:82 final size:82
Alignment explanation
Indices: 40150--40314 Score: 251
Period size: 82 Copynumber: 2.0 Consensus size: 82
40140 ATTGAGAATA
*
40150 AATGACCTATCATGCCTTAAAGTAGTCATTTATTACTCTAACCAAAATGAAGAGATATCA-CTAT
1 AATGACCTATCATGCCTTAAAGTAGTCATTTATTACTCCAACCAAAATGAAGAGATAT-ATCTAT
40214 TTCGTCTTAAAAATCAAT
65 TTCGTCTTAAAAATCAAT
* * ***
40232 AATGACCTCTCATGCCTTAAAGTAGTCTTTTATTACTCCAATTGAAATGAAGAGATATATCTATT
1 AATGACCTATCATGCCTTAAAGTAGTCATTTATTACTCCAACCAAAATGAAGAGATATATCTATT
*
40297 TCGTCTTAAAAATTAAT
66 TCGTCTTAAAAATCAAT
40314 A
1 A
40315 TTGATTCAAG
Statistics
Matches: 75, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
81 1 0.01
82 74 0.99
ACGTcount: A:0.38, C:0.17, G:0.10, T:0.35
Consensus pattern (82 bp):
AATGACCTATCATGCCTTAAAGTAGTCATTTATTACTCCAACCAAAATGAAGAGATATATCTATT
TCGTCTTAAAAATCAAT
Found at i:40924 original size:24 final size:23
Alignment explanation
Indices: 40859--40918 Score: 66
Period size: 24 Copynumber: 2.4 Consensus size: 23
40849 CTAATTAATG
40859 ACTAAAATGAAAAAAACATGCAAAA
1 ACTAAAAT--AAAAAACATGCAAAA
*
40884 ATTAAAATAAAACAACATGCAAATA
1 ACTAAAATAAAA-AACATGCAAA-A
40909 GACTAAAATA
1 -ACTAAAATA
40919 TAAACAAACA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
23 4 0.13
24 10 0.33
25 8 0.27
26 8 0.27
ACGTcount: A:0.65, C:0.12, G:0.07, T:0.17
Consensus pattern (23 bp):
ACTAAAATAAAAAACATGCAAAA
Found at i:42386 original size:13 final size:13
Alignment explanation
Indices: 42368--42393 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
42358 GCATGCACAA
42368 AATAATAATAAAT
1 AATAATAATAAAT
42381 AATAATAATAAAT
1 AATAATAATAAAT
42394 TGGGACGAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
AATAATAATAAAT
Found at i:43911 original size:29 final size:29
Alignment explanation
Indices: 43881--43944 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
43871 TTTGAAATTA
* *
43881 AAATT-TTTGAAATTGAACTCTGAAAAAT
1 AAATTATTGGAAATTGAACTATGAAAAAT
*
43909 AAATTATTGGAAATTGAATTATGAAAAAT
1 AAATTATTGGAAATTGAACTATGAAAAAT
*
43938 GAATTAT
1 AAATTAT
43945 ATTTCTGGAA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
28 5 0.16
29 26 0.84
ACGTcount: A:0.48, C:0.03, G:0.12, T:0.36
Consensus pattern (29 bp):
AAATTATTGGAAATTGAACTATGAAAAAT
Found at i:43930 original size:15 final size:15
Alignment explanation
Indices: 43901--43944 Score: 54
Period size: 14 Copynumber: 3.0 Consensus size: 15
43891 AATTGAACTC
*
43901 TGAAAAATAAATTAT
1 TGAAAAATGAATTAT
* *
43916 TGGAAATTGAATTA-
1 TGAAAAATGAATTAT
43930 TGAAAAATGAATTAT
1 TGAAAAATGAATTAT
43945 ATTTCTGGAA
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.52, C:0.00, G:0.14, T:0.34
Consensus pattern (15 bp):
TGAAAAATGAATTAT
Found at i:44091 original size:23 final size:22
Alignment explanation
Indices: 44047--44119 Score: 74
Period size: 23 Copynumber: 3.1 Consensus size: 22
44037 AATGTTATAT
* * *
44047 TATATTTTAAAAATATTAATTAG
1 TATATTTTAAATAT-TTTATTAA
44070 TATATTTTAAATATCTTTATTAA
1 TATATTTTAAATAT-TTTATTAA
*
44093 AATATTATTAAATTATTTTATTAA
1 TATATT-TTAAA-TATTTTATTAA
44117 TAT
1 TAT
44120 TAAATATATA
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
23 24 0.57
24 15 0.36
25 3 0.07
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.53
Consensus pattern (22 bp):
TATATTTTAAATATTTTATTAA
Found at i:48358 original size:23 final size:23
Alignment explanation
Indices: 48323--48372 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
48313 TATTTATATT
48323 TAATA-TTAATAAA-ATAATTTAA
1 TAATATTTAATAAAGAT-ATTTAA
48345 TAATATTTAATAAAGATATTTAA
1 TAATATTTAATAAAGATATTTAA
48368 -AATAT
1 TAATAT
48373 ACTAATTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
22 10 0.38
23 14 0.54
24 2 0.08
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATATTTAATAAAGATATTTAA
Found at i:48378 original size:23 final size:22
Alignment explanation
Indices: 48329--48396 Score: 66
Period size: 23 Copynumber: 3.0 Consensus size: 22
48319 TATTTAATAT
*
48329 TAATAAAATAATTTAATAATAT-T
1 TAATAAAAT-ATTTAA-AATATAC
48352 TAATAAAGATATTTAAAATATAC
1 TAATAAA-ATATTTAAAATATAC
* *
48375 TAATTAATATTTTTAAAATATA
1 TAA-TAAAATATTTAAAATATA
48397 ATATAACATT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
22 5 0.13
23 29 0.74
24 5 0.13
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (22 bp):
TAATAAAATATTTAAAATATAC
Found at i:48516 original size:14 final size:14
Alignment explanation
Indices: 48499--48542 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
48489 TTCCAGAAAT
48499 ATAATTCATTTTTC
1 ATAATTCATTTTTC
* *
48513 ATAATTCAATTTCC
1 ATAATTCATTTTTC
*
48527 AATAATTTATTTTTC
1 -ATAATTCATTTTTC
48542 A
1 A
48543 GAGTTCAATT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
14 13 0.54
15 11 0.46
ACGTcount: A:0.34, C:0.14, G:0.00, T:0.52
Consensus pattern (14 bp):
ATAATTCATTTTTC
Found at i:48531 original size:29 final size:29
Alignment explanation
Indices: 48499--48554 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
48489 TTCCAGAAAT
*
48499 ATAATTCATTTTTCATAATTCAATTTCCA
1 ATAATTCATTTTTCAGAATTCAATTTCCA
* *
48528 ATAATTTATTTTTCAGAGTTCAATTTC
1 ATAATTCATTTTTCAGAATTCAATTTC
48555 AAAAATTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.32, C:0.14, G:0.04, T:0.50
Consensus pattern (29 bp):
ATAATTCATTTTTCAGAATTCAATTTCCA
Found at i:48564 original size:29 final size:29
Alignment explanation
Indices: 48501--48562 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 29
48491 CCAGAAATAT
* * *
48501 AATTCATTTTTCATAATTCAATTTCCAAT
1 AATTTATTTTTCAGAATTCAATTTCCAAA
*
48530 AATTTATTTTTCAGAGTTCAATTT-CAAA
1 AATTTATTTTTCAGAATTCAATTTCCAAA
48558 AATTT
1 AATTT
48563 TAATTTCAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 8 0.28
29 21 0.72
ACGTcount: A:0.35, C:0.13, G:0.03, T:0.48
Consensus pattern (29 bp):
AATTTATTTTTCAGAATTCAATTTCCAAA
Done.