Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005985.1 Hibiscus syriacus cultivar Beakdansim tig00014073_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: 84406
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:3417 original size:29 final size:28
Alignment explanation
Indices: 3384--3578 Score: 157
Period size: 29 Copynumber: 6.8 Consensus size: 28
3374 AATGTCTCCT
* *
3384 TTTATTATAATTTATAAAAGGTTTTATCC
1 TTTATTGTAATTTATAAAA-GTTTTATAC
* * *
3413 TTTATTGTAATTTATAAATAATTTTGTAT
1 TTTATTGTAATTTATAAA-AGTTTTATAC
* *
3442 TTTATTGTAATTTATAAATTGTTTT-TAA
1 TTTATTGTAATTTATAAA-AGTTTTATAC
* *
3470 TTTATTGTTATTTATAAATAGTTTTGTAC
1 TTTATTGTAATTTATAAA-AGTTTTATAC
* * * *
3499 TTTATTGTAGTTTATAACAAATTTTGTCC
1 TTTATTGTAATTTATAA-AAGTTTTATAC
3528 TTTATTGTAATTTATAAAA-TAATTT-T-C
1 TTTATTGTAATTTATAAAAGT--TTTATAC
3555 TTTATTGTAAATTCTA-AAAAGTTT
1 TTTATTGT-AATT-TATAAAAGTTT
3579 AAACTTTTAT
Statistics
Matches: 142, Mismatches: 16, Indels: 18
0.81 0.09 0.10
Matches are distributed among these distances:
27 12 0.08
28 36 0.25
29 92 0.65
30 2 0.01
ACGTcount: A:0.33, C:0.04, G:0.08, T:0.55
Consensus pattern (28 bp):
TTTATTGTAATTTATAAAAGTTTTATAC
Found at i:3474 original size:57 final size:57
Alignment explanation
Indices: 3383--3553 Score: 209
Period size: 58 Copynumber: 2.9 Consensus size: 57
3373 AAATGTCTCC
* *
3383 TTTTATTATAATTTATAAAAGGTTTTATCCTTTATTGTAATTTATAAATAATTTTGTA
1 TTTTATTGTAATTTATAAAATGTTTT-TCCTTTATTGTAATTTATAAATAATTTTGTA
* ** * *
3441 TTTTATTGTAATTTATAAATTGTTTTTAATTTATTGTTATTTATAAATAGTTTTGTA
1 TTTTATTGTAATTTATAAAATGTTTTTCCTTTATTGTAATTTATAAATAATTTTGTA
* * *
3498 CTTTATTGTAGTTTATAACAAAT-TTTGTCCTTTATTGTAATTTATAAAATAATTTT
1 TTTTATTGTAATTTAT-A-AAATGTTTTTCCTTTATTGTAATTTAT-AAATAATTTT
3554 CTTTATTGTA
Statistics
Matches: 95, Mismatches: 15, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
57 41 0.43
58 42 0.44
59 12 0.13
ACGTcount: A:0.32, C:0.04, G:0.08, T:0.57
Consensus pattern (57 bp):
TTTTATTGTAATTTATAAAATGTTTTTCCTTTATTGTAATTTATAAATAATTTTGTA
Found at i:3482 original size:28 final size:29
Alignment explanation
Indices: 3384--3545 Score: 168
Period size: 29 Copynumber: 5.6 Consensus size: 29
3374 AATGTCTCCT
* * **
3384 TTTATTATAATTTATAAA-AGGTTTTATCC
1 TTTATTGTAATTTATAAATA-GTTTTGTAA
* *
3413 TTTATTGTAATTTATAAATAATTTTGTAT
1 TTTATTGTAATTTATAAATAGTTTTGTAA
*
3442 TTTATTGTAATTTATAAATTGTTTT-TAA
1 TTTATTGTAATTTATAAATAGTTTTGTAA
* *
3470 TTTATTGTTATTTATAAATAGTTTTGTAC
1 TTTATTGTAATTTATAAATAGTTTTGTAA
* * **
3499 TTTATTGTAGTTTATAACA-AATTTTGTCC
1 TTTATTGTAATTTATAA-ATAGTTTTGTAA
3528 TTTATTGTAATTTATAAA
1 TTTATTGTAATTTATAAA
3546 ATAATTTTCT
Statistics
Matches: 114, Mismatches: 16, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
28 26 0.23
29 86 0.75
30 2 0.02
ACGTcount: A:0.32, C:0.04, G:0.08, T:0.56
Consensus pattern (29 bp):
TTTATTGTAATTTATAAATAGTTTTGTAA
Found at i:3502 original size:86 final size:86
Alignment explanation
Indices: 3384--3545 Score: 229
Period size: 86 Copynumber: 1.9 Consensus size: 86
3374 AATGTCTCCT
* *
3384 TTTATTATAATTTATAAAAGGTTTTATCCTTTATTGTAATTTATAA-ATAATTTTGTATTTTATT
1 TTTATTATAATTTATAAAAGGTTTTATACTTTATTGTAATTTATAACA-AATTTTGTACTTTATT
3448 GTAATTTATAAATTGTTTTTAA
65 GTAATTTATAAATTGTTTTTAA
* * * * *
3470 TTTATTGTTATTTATAAATA-GTTTTGTACTTTATTGTAGTTTATAACAAATTTTGTCCTTTATT
1 TTTATTATAATTTATAAA-AGGTTTTATACTTTATTGTAATTTATAACAAATTTTGTACTTTATT
3534 GTAATTTATAAA
65 GTAATTTATAAA
3546 ATAATTTTCT
Statistics
Matches: 67, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
86 65 0.97
87 2 0.03
ACGTcount: A:0.32, C:0.04, G:0.08, T:0.56
Consensus pattern (86 bp):
TTTATTATAATTTATAAAAGGTTTTATACTTTATTGTAATTTATAACAAATTTTGTACTTTATTG
TAATTTATAAATTGTTTTTAA
Found at i:3614 original size:29 final size:28
Alignment explanation
Indices: 3413--3622 Score: 108
Period size: 29 Copynumber: 7.4 Consensus size: 28
3403 GGTTTTATCC
* * *
3413 TTTATTGTAATTTATAAATAATTTTGTAT
1 TTTATTGTAAATTCTAAA-AATTTTGTCT
* *
3442 TTTATTGT-AATT-TATAAATTGTT-TTT
1 TTTATTGTAAATTCTAAAAATT-TTGTCT
* * * *
3468 AATTTATTGTTATTTATAAATAGTTTTGTAC-
1 --TTTATTGTAAATTCTAAA-AATTTTGT-CT
** * *
3499 TTTATTGTAGTTTATAACAAATTTTGTCC
1 TTTATTGTAAATTCTAA-AAATTTTGTCT
* * *
3528 TTTATTGTAATTTATAAAATAATTT-TC-
1 TTTATTGTAAATTCTAAAA-ATTTTGTCT
***
3555 TTTATTGTAAATTCTAAAAAGTTTAAACT
1 TTTATTGTAAATTCTAAAAA-TTTTGTCT
*
3584 TTTATTATAAATTCTAAAACATTTTGTCT
1 TTTATTGTAAATTCTAAAA-ATTTTGTCT
3613 TTTATTGTAA
1 TTTATTGTAA
3623 TTTGATGATT
Statistics
Matches: 144, Mismatches: 22, Indels: 30
0.73 0.11 0.15
Matches are distributed among these distances:
26 7 0.05
27 24 0.17
28 17 0.12
29 85 0.59
30 7 0.05
31 4 0.03
ACGTcount: A:0.33, C:0.05, G:0.07, T:0.55
Consensus pattern (28 bp):
TTTATTGTAAATTCTAAAAATTTTGTCT
Found at i:22918 original size:17 final size:17
Alignment explanation
Indices: 22896--22930 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
22886 TGCTAGGCAA
22896 GCCTCGAGATCCGACTT
1 GCCTCGAGATCCGACTT
* *
22913 GCCTCGGGATCCGTCTT
1 GCCTCGAGATCCGACTT
22930 G
1 G
22931 TCTTGGAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.11, C:0.34, G:0.29, T:0.26
Consensus pattern (17 bp):
GCCTCGAGATCCGACTT
Found at i:34965 original size:12 final size:12
Alignment explanation
Indices: 34948--34979 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
34938 TTACTACCCT
*
34948 GCCTCCACGTGA
1 GCCTCCACGTAA
34960 GCCTCCACGTAA
1 GCCTCCACGTAA
34972 GCCTCCAC
1 GCCTCCAC
34980 CTCCTCTTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.19, C:0.47, G:0.19, T:0.16
Consensus pattern (12 bp):
GCCTCCACGTAA
Found at i:41052 original size:14 final size:14
Alignment explanation
Indices: 41033--41062 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
41023 CATTTTTTAA
41033 AGGAGATCTAGATG
1 AGGAGATCTAGATG
*
41047 AGGAGATCTATATG
1 AGGAGATCTAGATG
41061 AG
1 AG
41063 AACAATGGTA
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:0.37, C:0.07, G:0.33, T:0.23
Consensus pattern (14 bp):
AGGAGATCTAGATG
Found at i:44145 original size:21 final size:21
Alignment explanation
Indices: 44119--44176 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 21
44109 ATTTACCGTG
* *
44119 ATTGCGGCCGTCGCGGGCACT
1 ATTGCGGCCATCGCGGACACT
*
44140 ATTGCGGCCATCGCGGACGCT
1 ATTGCGGCCATCGCGGACACT
* *
44161 ATTGTGGCCAACGCGG
1 ATTGCGGCCATCGCGG
44177 GTAACTCGGA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.14, C:0.31, G:0.36, T:0.19
Consensus pattern (21 bp):
ATTGCGGCCATCGCGGACACT
Found at i:48051 original size:40 final size:39
Alignment explanation
Indices: 48007--48087 Score: 108
Period size: 39 Copynumber: 2.1 Consensus size: 39
47997 ATGACTATTT
*
48007 GTGAACCATCCAAAAATGGTTTCGACAGAATCTATGAAAG
1 GTGAACCA-CCAAAAATGGTTTCGACAGAAGCTATGAAAG
* ** *
48047 GTGAATCACTGAAAATGGTTTCGACATAAGCTATGAAAG
1 GTGAACCACCAAAAATGGTTTCGACAGAAGCTATGAAAG
48086 GT
1 GT
48088 AAATCACTGA
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
39 29 0.81
40 7 0.19
ACGTcount: A:0.38, C:0.15, G:0.22, T:0.25
Consensus pattern (39 bp):
GTGAACCACCAAAAATGGTTTCGACAGAAGCTATGAAAG
Found at i:48062 original size:39 final size:39
Alignment explanation
Indices: 48019--48097 Score: 131
Period size: 39 Copynumber: 2.0 Consensus size: 39
48009 GAACCATCCA
* *
48019 AAAATGGTTTCGACAGAATCTATGAAAGGTGAATCACTG
1 AAAATGGTTTCGACAGAAGCTATGAAAGGTAAATCACTG
*
48058 AAAATGGTTTCGACATAAGCTATGAAAGGTAAATCACTG
1 AAAATGGTTTCGACAGAAGCTATGAAAGGTAAATCACTG
48097 A
1 A
48098 TTTTGAATAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.41, C:0.13, G:0.22, T:0.25
Consensus pattern (39 bp):
AAAATGGTTTCGACAGAAGCTATGAAAGGTAAATCACTG
Found at i:49001 original size:19 final size:19
Alignment explanation
Indices: 48977--49013 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
48967 AATCCTAATC
*
48977 ATTAGGCTATAATTTAGGA
1 ATTAGGCTATAACTTAGGA
48996 ATTAGGCTATAACTTAGG
1 ATTAGGCTATAACTTAGG
49014 CAACTAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.35, C:0.08, G:0.22, T:0.35
Consensus pattern (19 bp):
ATTAGGCTATAACTTAGGA
Found at i:49074 original size:74 final size:74
Alignment explanation
Indices: 48990--49138 Score: 298
Period size: 74 Copynumber: 2.0 Consensus size: 74
48980 AGGCTATAAT
48990 TTAGGAATTAGGCTATAACTTAGGCAACTAAATATACAATAGTAAATACAAAATATTTGGAGAAT
1 TTAGGAATTAGGCTATAACTTAGGCAACTAAATATACAATAGTAAATACAAAATATTTGGAGAAT
49055 ATTTTGTAA
66 ATTTTGTAA
49064 TTAGGAATTAGGCTATAACTTAGGCAACTAAATATACAATAGTAAATACAAAATATTTGGAGAAT
1 TTAGGAATTAGGCTATAACTTAGGCAACTAAATATACAATAGTAAATACAAAATATTTGGAGAAT
49129 ATTTTGTAA
66 ATTTTGTAA
49138 T
1 T
49139 CTATCACTCT
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
74 75 1.00
ACGTcount: A:0.44, C:0.08, G:0.15, T:0.33
Consensus pattern (74 bp):
TTAGGAATTAGGCTATAACTTAGGCAACTAAATATACAATAGTAAATACAAAATATTTGGAGAAT
ATTTTGTAA
Found at i:53582 original size:74 final size:74
Alignment explanation
Indices: 53498--53646 Score: 298
Period size: 74 Copynumber: 2.0 Consensus size: 74
53488 AGGCTATAAT
53498 TTAGGAATTAGGCTATAACTTAGGCAACTAAATATACAATAGTAAATACAAAATATTTGGAGAAT
1 TTAGGAATTAGGCTATAACTTAGGCAACTAAATATACAATAGTAAATACAAAATATTTGGAGAAT
53563 ATTTTGTAA
66 ATTTTGTAA
53572 TTAGGAATTAGGCTATAACTTAGGCAACTAAATATACAATAGTAAATACAAAATATTTGGAGAAT
1 TTAGGAATTAGGCTATAACTTAGGCAACTAAATATACAATAGTAAATACAAAATATTTGGAGAAT
53637 ATTTTGTAA
66 ATTTTGTAA
53646 T
1 T
53647 CTATCAAGCC
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
74 75 1.00
ACGTcount: A:0.44, C:0.08, G:0.15, T:0.33
Consensus pattern (74 bp):
TTAGGAATTAGGCTATAACTTAGGCAACTAAATATACAATAGTAAATACAAAATATTTGGAGAAT
ATTTTGTAA
Found at i:57714 original size:22 final size:23
Alignment explanation
Indices: 57688--57730 Score: 79
Period size: 22 Copynumber: 1.9 Consensus size: 23
57678 ATAGTCATGT
57688 CTTTATAACATG-TTTTCTCTAA
1 CTTTATAACATGTTTTTCTCTAA
57710 CTTTATAACATGTTTTTCTCT
1 CTTTATAACATGTTTTTCTCT
57731 GCCTTTATGG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.23, C:0.19, G:0.05, T:0.53
Consensus pattern (23 bp):
CTTTATAACATGTTTTTCTCTAA
Found at i:60461 original size:18 final size:18
Alignment explanation
Indices: 60438--60481 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
60428 CATAAATTTC
60438 TTCTTCTTACTTAATCCA
1 TTCTTCTTACTTAATCCA
*
60456 TTCTTCTTACTTGATCCA
1 TTCTTCTTACTTAATCCA
60474 TTCTTCTT
1 TTCTTCTT
60482 TAGGAGGGGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.16, C:0.27, G:0.02, T:0.55
Consensus pattern (18 bp):
TTCTTCTTACTTAATCCA
Found at i:62948 original size:45 final size:45
Alignment explanation
Indices: 62897--62984 Score: 160
Period size: 45 Copynumber: 2.0 Consensus size: 45
62887 TAGAGTAAAA
62897 TTCTAGCAGCTTACTACTAGGTAAGGTG-TTCATGGTAGGTTAACC
1 TTCTAGCAGCTTACTACTAGGTAAGGTGCTT-ATGGTAGGTTAACC
62942 TTCTAGCAGCTTACTACTAGGTAAGGTGCTTATGGTAGGTTAA
1 TTCTAGCAGCTTACTACTAGGTAAGGTGCTTATGGTAGGTTAA
62985 TCGTACCGTT
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
45 40 0.95
46 2 0.05
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.34
Consensus pattern (45 bp):
TTCTAGCAGCTTACTACTAGGTAAGGTGCTTATGGTAGGTTAACC
Found at i:64510 original size:21 final size:22
Alignment explanation
Indices: 64456--64521 Score: 73
Period size: 23 Copynumber: 3.0 Consensus size: 22
64446 ATTTATGAAA
64456 AAAAAAGTTAAATCTTTTCATG
1 AAAAAAGTTAAATCTTTTCATG
64478 AAAAATAGTTAAAT-TATTTCAT-
1 AAAAA-AGTTAAATCT-TTTCATG
** *
64500 CCAAAAGTTAACTCTTTTCATG
1 AAAAAAGTTAAATCTTTTCATG
64522 TTAAGTCTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
21 13 0.35
22 10 0.27
23 14 0.38
ACGTcount: A:0.42, C:0.12, G:0.08, T:0.38
Consensus pattern (22 bp):
AAAAAAGTTAAATCTTTTCATG
Found at i:64530 original size:15 final size:15
Alignment explanation
Indices: 64506--64535 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
64496 TCATCCAAAA
64506 GTTAACTCTTTTCAT
1 GTTAACTCTTTTCAT
*
64521 GTTAAGTCTTTTCAT
1 GTTAACTCTTTTCAT
64536 CAAAATGTTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.17, G:0.10, T:0.53
Consensus pattern (15 bp):
GTTAACTCTTTTCAT
Found at i:65534 original size:84 final size:84
Alignment explanation
Indices: 65393--65559 Score: 316
Period size: 84 Copynumber: 2.0 Consensus size: 84
65383 GATGAGGTGA
*
65393 ATGCTGCTATCATATTTAACATTACCGAAACATGAAAGCAATCTGATTTCCTATGTCGTAACTAC
1 ATGCTGCTATCACATTTAACATTACCGAAACATGAAAGCAATCTGATTTCCTATGTCGTAACTAC
65458 ATCTTGAACGGTTTACATG
66 ATCTTGAACGGTTTACATG
*
65477 ATGCTGCTATCACATTTAACATTACCGAAACATGAAAGCACTCTGATTTCCTATGTCGTAACTAC
1 ATGCTGCTATCACATTTAACATTACCGAAACATGAAAGCAATCTGATTTCCTATGTCGTAACTAC
65542 ATCTTGAACGGTTTACAT
66 ATCTTGAACGGTTTACAT
65560 AGATTAATTA
Statistics
Matches: 81, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
84 81 1.00
ACGTcount: A:0.32, C:0.22, G:0.14, T:0.33
Consensus pattern (84 bp):
ATGCTGCTATCACATTTAACATTACCGAAACATGAAAGCAATCTGATTTCCTATGTCGTAACTAC
ATCTTGAACGGTTTACATG
Found at i:67692 original size:35 final size:34
Alignment explanation
Indices: 67624--67729 Score: 178
Period size: 35 Copynumber: 3.1 Consensus size: 34
67614 TGAAACTATT
67624 TAACTAACAAACTAATTAAATA-TTTTTTATATA
1 TAACTAACAAACTAATTAAATATTTTTTTATATA
*
67657 TAACCAACAAACTAATTAAATAATTTTTTTATATA
1 TAACTAACAAACTAATTAAAT-ATTTTTTTATATA
*
67692 TAACTAACAAACTAATTAAATATTTTTTTATTTA
1 TAACTAACAAACTAATTAAATATTTTTTTATATA
67726 TAAC
1 TAAC
67730 ATCACTTAAA
Statistics
Matches: 68, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
33 20 0.29
34 17 0.25
35 31 0.46
ACGTcount: A:0.47, C:0.10, G:0.00, T:0.42
Consensus pattern (34 bp):
TAACTAACAAACTAATTAAATATTTTTTTATATA
Found at i:67767 original size:23 final size:22
Alignment explanation
Indices: 67733--67780 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 22
67723 TTATAACATC
*
67733 ACTTAAATTAACAAACTAATATA
1 ACTTAAACTAACAAACTAAT-TA
67756 ACTTAAACTAACAAACTAATTA
1 ACTTAAACTAACAAACTAATTA
67778 ACT
1 ACT
67781 AAATCTTTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 5 0.21
23 19 0.79
ACGTcount: A:0.54, C:0.17, G:0.00, T:0.29
Consensus pattern (22 bp):
ACTTAAACTAACAAACTAATTA
Found at i:68593 original size:21 final size:20
Alignment explanation
Indices: 68532--68651 Score: 62
Period size: 15 Copynumber: 6.2 Consensus size: 20
68522 TCATGAAAAA
* *
68532 AAAAGTTAAGTTTTTTCATG
1 AAAAGTTAAGTCTTTTCATC
**
68552 AAAAGTTGTTAAGTCACTTCATCC
1 AAAA---GTTAAGTCTTTTCAT-C
68576 AAAAGTTAAGTCTTTTCAT-
1 AAAAGTTAAGTCTTTTCATC
68595 ----GTTAAGTCTTTTCAT-
1 AAAAGTTAAGTCTTTTCATC
68610 ----GTTAAGTCTTTTCATC
1 AAAAGTTAAGTCTTTTCATC
* * *
68626 AAAAGGTTATGTTTTTTAATC
1 AAAA-GTTAAGTCTTTTCATC
68647 AAAAG
1 AAAAG
68652 GTCTTAACAT
Statistics
Matches: 81, Mismatches: 9, Indels: 20
0.74 0.08 0.18
Matches are distributed among these distances:
15 30 0.37
20 5 0.06
21 30 0.37
23 12 0.15
24 4 0.05
ACGTcount: A:0.33, C:0.12, G:0.13, T:0.42
Consensus pattern (20 bp):
AAAAGTTAAGTCTTTTCATC
Found at i:68600 original size:15 final size:15
Alignment explanation
Indices: 68580--68624 Score: 90
Period size: 15 Copynumber: 3.0 Consensus size: 15
68570 TCATCCAAAA
68580 GTTAAGTCTTTTCAT
1 GTTAAGTCTTTTCAT
68595 GTTAAGTCTTTTCAT
1 GTTAAGTCTTTTCAT
68610 GTTAAGTCTTTTCAT
1 GTTAAGTCTTTTCAT
68625 CAAAAGGTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.20, C:0.13, G:0.13, T:0.53
Consensus pattern (15 bp):
GTTAAGTCTTTTCAT
Found at i:69031 original size:28 final size:27
Alignment explanation
Indices: 68971--69031 Score: 63
Period size: 27 Copynumber: 2.2 Consensus size: 27
68961 CAAAACTCTT
*
68971 CTTTTTATTCAATTTTATCCTATTACA
1 CTTTCTATTCAATTTTATCCTATTACA
*
68998 -TGTTCTATTCTAATTTTA-CCTTTTACAA
1 CT-TTCTATTC-AATTTTATCCTATTAC-A
69026 CTTTCT
1 CTTTCT
69032 TATTGTAACG
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
26 1 0.04
27 14 0.50
28 12 0.43
29 1 0.04
ACGTcount: A:0.23, C:0.20, G:0.02, T:0.56
Consensus pattern (27 bp):
CTTTCTATTCAATTTTATCCTATTACA
Found at i:74758 original size:28 final size:28
Alignment explanation
Indices: 74725--74780 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
74715 AGGTAAAAGT
74725 TCAGTTGAAGACTACTACAAGGAGATGC
1 TCAGTTGAAGACTACTACAAGGAGATGC
74753 TCAGTTGAAGACTACTACAAGGAGATGC
1 TCAGTTGAAGACTACTACAAGGAGATGC
74781 AATCCTTACT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.36, C:0.18, G:0.25, T:0.21
Consensus pattern (28 bp):
TCAGTTGAAGACTACTACAAGGAGATGC
Found at i:83375 original size:40 final size:40
Alignment explanation
Indices: 83331--83406 Score: 116
Period size: 40 Copynumber: 1.9 Consensus size: 40
83321 TCGACTAGAG
* *
83331 CTAGACAGGCATCTCTAGCAATTTATTCATTTGTTATACA
1 CTAGACAGGCACCTCTAGCAATTTATTCACTTGTTATACA
**
83371 CTAGATTGGCACCTCTAGCAATTTATTCACTTGTTA
1 CTAGACAGGCACCTCTAGCAATTTATTCACTTGTTA
83407 AGCTAACATC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 32 1.00
ACGTcount: A:0.28, C:0.21, G:0.13, T:0.38
Consensus pattern (40 bp):
CTAGACAGGCACCTCTAGCAATTTATTCACTTGTTATACA
Found at i:83472 original size:43 final size:41
Alignment explanation
Indices: 83343--83480 Score: 131
Period size: 43 Copynumber: 3.3 Consensus size: 41
83333 AGACAGGCAT
* *
83343 CTCTAGCAATTTATTCATTTGTT-A--TACACTAGATTGGCAC
1 CTCTAGCAA-TTATTCACTTGTTAAGCTA-ACTAGATTGACAC
* *
83383 CTCTAGCAATTTATTCACTTGTTAAGCTAACATCATATT-AGTAC
1 CTCTAGCAA-TTATTCACTTGTTAAGCTAAC-T-AGATTGA-CAC
*
83427 CTCTAGTAATTATTCACTTGTTAAGCTATAGCTAGATTGACAC
1 CTCTAGCAATTATTCACTTGTTAAGCTA-A-CTAGATTGACAC
83470 CTCTAGCAATT
1 CTCTAGCAATT
83481 TTTCTAGGAA
Statistics
Matches: 81, Mismatches: 8, Indels: 15
0.78 0.08 0.14
Matches are distributed among these distances:
40 22 0.27
41 1 0.01
42 2 0.02
43 38 0.47
44 17 0.21
45 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.12, T:0.38
Consensus pattern (41 bp):
CTCTAGCAATTATTCACTTGTTAAGCTAACTAGATTGACAC
Done.