Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009576.1 Hibiscus syriacus cultivar Beakdansim tig00116944_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: 1684752
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 10
Found at i:1627759 original size:33 final size:33
Alignment explanation
Indices: 1627711--1627791 Score: 117
Period size: 33 Copynumber: 2.5 Consensus size: 33
1627701 AAAATCGCAA
**
1627711 TGCGATTTTGGTTTCGCGTTACGATTATCTCGT
1 TGCGATTTTCATTTCGCGTTACGATTATCTCGT
* *
1627744 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTACGATTATCTCGT
*
1627777 TGCAATTTTCATTTC
1 TGCGATTTTCATTTC
1627792 TCTCGTTGCG
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.12, C:0.21, G:0.20, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTACGATTATCTCGT
Found at i:1627794 original size:21 final size:21
Alignment explanation
Indices: 1627768--1627831 Score: 78
Period size: 21 Copynumber: 3.1 Consensus size: 21
1627758 CGCGTTGCGA
*
1627768 TTCTCTCGTTGCAATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
**
1627789 TTCTCTCGTTGCGATAGTCAT
1 TTCTCTCGTTGCGATTTTCAT
1627810 TT-TCGT-GTTGCGATTTTCAT
1 TTCTC-TCGTTGCGATTTTCAT
1627830 TT
1 TT
1627832 TCATGTTACA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
20 16 0.43
21 21 0.57
ACGTcount: A:0.12, C:0.20, G:0.16, T:0.52
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:1627821 original size:20 final size:20
Alignment explanation
Indices: 1627796--1627838 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1627786 CATTTCTCTC
*
1627796 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCAT
**
1627816 GTTGCGATTTTCATTTTCAT
1 GTTGCGATAGTCATTTTCAT
1627836 GTT
1 GTT
1627839 ACAATTTTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.14, C:0.14, G:0.21, T:0.51
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCAT
Found at i:1627845 original size:20 final size:20
Alignment explanation
Indices: 1627806--1627846 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1627796 GTTGCGATAG
* * *
1627806 TCATTTTCGTGTTGCGATTT
1 TCATTTTCATGTTACAATTT
1627826 TCATTTTCATGTTACAATTT
1 TCATTTTCATGTTACAATTT
1627846 T
1 T
1627847 AAGTTTAGAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.17, C:0.15, G:0.12, T:0.56
Consensus pattern (20 bp):
TCATTTTCATGTTACAATTT
Found at i:1628350 original size:20 final size:20
Alignment explanation
Indices: 1628325--1628538 Score: 234
Period size: 20 Copynumber: 10.6 Consensus size: 20
1628315 CTTTAAAAAT
1628325 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1628345 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
* *
1628365 TGTCGTTACGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
* * *
1628386 CGCATTGCGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
* *
1628406 CTCGTTGCGATTTACAGATA
1 CGCGTTGCGATTTACGGATA
* *
1628426 CGCGTTGCGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
* *
1628446 CTCGTTGCGATTTACTGATA
1 CGCGTTGCGATTTACGGATA
*
1628466 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
1628486 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
1628507 CGCGTTGCGATTTTACGGATA
1 CGCGTTGCGA-TTTACGGATA
*
1628528 CTCGTTGCGAT
1 CGCGTTGCGAT
1628539 AGTCAGAATC
Statistics
Matches: 158, Mismatches: 29, Indels: 14
0.79 0.14 0.07
Matches are distributed among these distances:
20 107 0.68
21 51 0.32
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.37
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:1628533 original size:41 final size:41
Alignment explanation
Indices: 1628327--1628538 Score: 338
Period size: 41 Copynumber: 5.2 Consensus size: 41
1628317 TTAAAAATCG
*
1628327 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* *
1628368 CGTTACGATTTACGGATACGCATTGCGA-TTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
*
1628408 CGTTGCGATTTACAGATACGCGTTGCGA-TTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* *
1628448 CGTTGCGATTTACTGATACGCGTTGCGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* *
1628489 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGGATACT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
1628530 CGTTGCGAT
1 CGTTGCGAT
1628539 AGTCAGAATC
Statistics
Matches: 158, Mismatches: 12, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
40 75 0.47
41 83 0.53
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.38
Consensus pattern (41 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
Found at i:1628580 original size:20 final size:20
Alignment explanation
Indices: 1628555--1628599 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
1628545 AATCGAGTTA
* * *
1628555 CGATTTTTATGTTCGCGTTG
1 CGATTTTCATATTCGCATTG
1628575 CGATTTTCATATTCGCATTG
1 CGATTTTCATATTCGCATTG
1628595 CGATT
1 CGATT
1628600 CTGATAAAGC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.16, C:0.18, G:0.20, T:0.47
Consensus pattern (20 bp):
CGATTTTCATATTCGCATTG
Found at i:1628617 original size:21 final size:21
Alignment explanation
Indices: 1628588--1628637 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
1628578 TTTTCATATT
*
1628588 CGCATTGCGATTCT-GATAAAG
1 CGCAATGCGATTCTGGA-AAAG
1628609 CGCAATGCGATTCTGGAAAAG
1 CGCAATGCGATTCTGGAAAAG
1628630 CGCAATGC
1 CGCAATGC
1628638 AAATTTGTAC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 25 0.93
22 2 0.07
ACGTcount: A:0.30, C:0.22, G:0.26, T:0.22
Consensus pattern (21 bp):
CGCAATGCGATTCTGGAAAAG
Found at i:1628698 original size:20 final size:19
Alignment explanation
Indices: 1628649--1628702 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 19
1628639 AATTTGTACT
*
1628649 ATCGCATTGCGATTCTGGG
1 ATCGCGTTGCGATTCTGGG
*
1628668 AACTG-GTTTGCGATTCTGGAG
1 ATC-GCG-TTGCGATTCTGG-G
1628689 ATCGCGTTGCGATT
1 ATCGCGTTGCGATT
1628703 TTTATTTCGC
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
19 2 0.07
20 22 0.79
21 4 0.14
ACGTcount: A:0.17, C:0.19, G:0.31, T:0.33
Consensus pattern (19 bp):
ATCGCGTTGCGATTCTGGG
Found at i:1630528 original size:20 final size:20
Alignment explanation
Indices: 1630503--1630542 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1630493 AGCAACAAAA
* *
1630503 TAAAAATGATTCTATCTAAT
1 TAAAAATAATCCTATCTAAT
1630523 TAAAAATAATCCTATCTAAT
1 TAAAAATAATCCTATCTAAT
1630543 AACTAATAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.47, C:0.12, G:0.03, T:0.38
Consensus pattern (20 bp):
TAAAAATAATCCTATCTAAT
Found at i:1630585 original size:20 final size:21
Alignment explanation
Indices: 1630556--1630595 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
1630546 TAATAGAATA
1630556 AAAAATTGAT-TCTATCTAATT
1 AAAAATTGATCT-TATCTAATT
1630577 AAAAA-TGATCTTATCTAAT
1 AAAAATTGATCTTATCTAAT
1630596 AACTAATAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.45, C:0.10, G:0.05, T:0.40
Consensus pattern (21 bp):
AAAAATTGATCTTATCTAATT
Found at i:1630637 original size:20 final size:21
Alignment explanation
Indices: 1630607--1630647 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
1630597 ACTAATAGAA
*
1630607 TAAAGACTGATTCTATCTAAT
1 TAAAGACTGATCCTATCTAAT
1630628 TAAA-ACTGATCCTATCTAAT
1 TAAAGACTGATCCTATCTAAT
1630648 ATTTAATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.39, C:0.17, G:0.07, T:0.37
Consensus pattern (21 bp):
TAAAGACTGATCCTATCTAAT
Found at i:1630638 original size:52 final size:51
Alignment explanation
Indices: 1630501--1630648 Score: 233
Period size: 53 Copynumber: 2.8 Consensus size: 51
1630491 TTAGCAACAA
*
1630501 AATAAAAATGATTCTATCTAATTAAAAATAATCCTATCTAATAACTAATAG
1 AATAAAAATGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAATAG
*
1630552 AATAAAAAATTGATTCTATCTAATTAAAAATGATCTTATCTAATAACTAATAG
1 AAT-AAAAA-TGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAATAG
* *
1630605 AATAAAGACTGATTCTATCTAATTAAAACTGATCCTATCTAATA
1 AATAAA-AATGATTCTATCTAATTAAAAATGATCCTATCTAATA
1630649 TTTAATTTAG
Statistics
Matches: 89, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
51 3 0.03
52 41 0.46
53 45 0.51
ACGTcount: A:0.48, C:0.12, G:0.05, T:0.34
Consensus pattern (51 bp):
AATAAAAATGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAATAG
Found at i:1634984 original size:20 final size:20
Alignment explanation
Indices: 1634959--1634998 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
1634949 AGCAACAGAA
1634959 TAAAAATGATTC-TATCTAAT
1 TAAAAATGA-TCATATCTAAT
1634979 TAAAAATGATCATATCTAAT
1 TAAAAATGATCATATCTAAT
1634999 AACTAATAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.11
20 17 0.89
ACGTcount: A:0.47, C:0.10, G:0.05, T:0.38
Consensus pattern (20 bp):
TAAAAATGATCATATCTAAT
Found at i:1635027 original size:53 final size:52
Alignment explanation
Indices: 1634955--1635104 Score: 257
Period size: 53 Copynumber: 2.9 Consensus size: 52
1634945 AATTAGCAAC
*
1634955 AGAATAAAAA-TGATTCTATCTAATTAAAAATGATCATATCTAATAACTAAT
1 AGAATAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
1635006 AGAATAAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
1 AGAAT-AAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
* *
1635059 AGAATAAAGACTGATTCTATCTAATTAAAACTGATCCTATCTAATA
1 AGAATAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATA
1635105 TTTAATTTAG
Statistics
Matches: 94, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
51 5 0.05
52 44 0.47
53 45 0.48
ACGTcount: A:0.48, C:0.13, G:0.07, T:0.33
Consensus pattern (52 bp):
AGAATAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
Found at i:1635041 original size:20 final size:21
Alignment explanation
Indices: 1635012--1635051 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
1635002 TAATAGAATA
*
1635012 AAAAACTGATTCTATCTAATT
1 AAAAACTGATCCTATCTAATT
1635033 AAAAA-TGATCCTATCTAAT
1 AAAAACTGATCCTATCTAAT
1635052 AACTAATAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.45, C:0.15, G:0.05, T:0.35
Consensus pattern (21 bp):
AAAAACTGATCCTATCTAATT
Found at i:1635093 original size:20 final size:21
Alignment explanation
Indices: 1635063--1635103 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
1635053 ACTAATAGAA
*
1635063 TAAAGACTGATTCTATCTAAT
1 TAAAGACTGATCCTATCTAAT
1635084 TAAA-ACTGATCCTATCTAAT
1 TAAAGACTGATCCTATCTAAT
1635104 ATTTAATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.39, C:0.17, G:0.07, T:0.37
Consensus pattern (21 bp):
TAAAGACTGATCCTATCTAAT
Found at i:1635809 original size:46 final size:46
Alignment explanation
Indices: 1635742--1635834 Score: 186
Period size: 46 Copynumber: 2.0 Consensus size: 46
1635732 TCAATGTCGG
1635742 ATTCGTTTCGGATGATTAGTAGAATAGCCAAATGGCTTTAGCAGCT
1 ATTCGTTTCGGATGATTAGTAGAATAGCCAAATGGCTTTAGCAGCT
1635788 ATTCGTTTCGGATGATTAGTAGAATAGCCAAATGGCTTTAGCAGCT
1 ATTCGTTTCGGATGATTAGTAGAATAGCCAAATGGCTTTAGCAGCT
1635834 A
1 A
1635835 AAGACTAAAG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.29, C:0.15, G:0.24, T:0.32
Consensus pattern (46 bp):
ATTCGTTTCGGATGATTAGTAGAATAGCCAAATGGCTTTAGCAGCT
Found at i:1639020 original size:16 final size:17
Alignment explanation
Indices: 1638988--1639020 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1638978 ACAAGAAAGC
*
1638988 CAAATGTCCGGTTTTTT
1 CAAATGTCCGATTTTTT
1639005 CAAATGTCC-ATTTTTT
1 CAAATGTCCGATTTTTT
1639021 ATCGTCACAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.21, C:0.18, G:0.12, T:0.48
Consensus pattern (17 bp):
CAAATGTCCGATTTTTT
Found at i:1640196 original size:24 final size:23
Alignment explanation
Indices: 1640168--1640213 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
1640158 TATTATAATT
1640168 TAAAA-TTTATTATTAATAAAAATA
1 TAAAACTTT-TTATT-ATAAAAATA
*
1640192 TAAAACTTTTTATTTTAAAAAT
1 TAAAACTTTTTATTATAAAAAT
1640214 CTTCAATCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 7 0.35
24 10 0.50
25 3 0.15
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (23 bp):
TAAAACTTTTTATTATAAAAATA
Found at i:1651993 original size:99 final size:99
Alignment explanation
Indices: 1651809--1651997 Score: 281
Period size: 99 Copynumber: 1.9 Consensus size: 99
1651799 CGTCTTGTAT
*
1651809 TTATACACATATCTAATTATATATCAAATGGTTGAACTTGAGTGAGTGTCATATTTAGACATGTG
1 TTATACACATATCTAATTATATATCAAATGGTTGAACTTGAGTGAGTGTCAGATTTAGACATGTG
* *
1651874 TCCTGCATGATATGCACAATTTTTTGGATGTTTG
66 TCCTACATGACATGCACAATTTTTTGGATGTTTG
* * * *
1651908 TTATACACCTATCTAATTATATATCATATGGTTGAACTTGGGTGAGTGTCAGATTTAGACATGTT
1 TTATACACATATCTAATTATATATCAAATGGTTGAACTTGAGTGAGTGTCAGATTTAGACATGTG
* *
1651973 TCCTATAT-AGCATGCTCAATTTTTT
66 TCCTACATGA-CATGCACAATTTTTT
1651998 TTTATGTTTG
Statistics
Matches: 80, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
98 1 0.01
99 79 0.99
ACGTcount: A:0.29, C:0.13, G:0.17, T:0.41
Consensus pattern (99 bp):
TTATACACATATCTAATTATATATCAAATGGTTGAACTTGAGTGAGTGTCAGATTTAGACATGTG
TCCTACATGACATGCACAATTTTTTGGATGTTTG
Found at i:1652029 original size:108 final size:105
Alignment explanation
Indices: 1651908--1652191 Score: 284
Period size: 103 Copynumber: 2.7 Consensus size: 105
1651898 TGGATGTTTG
* * *
1651908 TTATACACCTATCTAATTATATATCATATGGTTGAACTTGGGTGAGTGTCAGATTTAGACATGTT
1 TTATACACATATCTAAATATATATCATATGGTTGAACTTGGGTGAGTGTCAGATTT-GACAAG-T
* * ** ** *
1651973 TCCTATATAGCATGCTCAATTTTTTTTTATGTTTGTCTTGTAT
64 TCCTACATAACATGCTCAA-TTTTTTCGAAATTTGTCTTGCAT
* * * * * *
1652016 TTATACACATATCTAAATATATATCATATGATTGAATTTGCGTGCGTGTCGGATTTGA-ACG-TC
1 TTATACACATATCTAAATATATATCATATGGTTGAACTTGGGTGAGTGTCAGATTTGACAAGTTC
* *
1652079 CTACATAATATGTTCAATTTTTTCGAAATTTGTCTTGCAT
66 CTACATAACATGCTCAATTTTTTCGAAATTTGTCTTGCAT
* * * * * * *
1652119 TTATGCACATATCTAACTATATGTCAAATAGTTAAACTCGGGTGAGTGTCAGATTTGGACAAGTG
1 TTATACACATATCTAAATATATATCATATGGTTGAACTTGGGTGAGTGTCAGATTT-GACAAGT-
1652184 TCCTACAT
64 TCCTACAT
1652192 GTTATGCGTG
Statistics
Matches: 142, Mismatches: 30, Indels: 9
0.78 0.17 0.05
Matches are distributed among these distances:
103 62 0.44
104 17 0.12
105 2 0.01
106 2 0.01
107 10 0.07
108 49 0.35
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.41
Consensus pattern (105 bp):
TTATACACATATCTAAATATATATCATATGGTTGAACTTGGGTGAGTGTCAGATTTGACAAGTTC
CTACATAACATGCTCAATTTTTTCGAAATTTGTCTTGCAT
Found at i:1653824 original size:3 final size:3
Alignment explanation
Indices: 1653818--1653869 Score: 61
Period size: 3 Copynumber: 17.0 Consensus size: 3
1653808 AATATTATAT
* *
1653818 TTA TTA TTTA TTA GTA TTA TTA TTA ATA TTA TTA TTA TTA TTA GTT-
1 TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA
1653864 TTA TTA
1 TTA TTA
1653870 ATGATAATTT
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
2 2 0.05
3 35 0.83
4 5 0.12
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:1657199 original size:2 final size:2
Alignment explanation
Indices: 1657192--1657216 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1657182 CCTGAAAATA
1657192 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
1657217 TATATATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1659114 original size:72 final size:72
Alignment explanation
Indices: 1658997--1659137 Score: 248
Period size: 72 Copynumber: 2.0 Consensus size: 72
1658987 TTAGTCTTAA
*
1658997 CTTCAAATGAATTCCAGTCAAAGCAGCTTGTGATAATTTCATAACTCAAATAACGAATAAACCAT
1 CTTCAAATGAATTCCACTCAAAGCAGCTTGTGATAATTTCATAACTCAAATAACGAATAAACCAT
1659062 CAAATCT
66 CAAATCT
*
1659069 CTTCAAATGAA-TCCAACTCAAAGCAGGTTGTGATAATTTCATAACTCAAATAACGAATAAACCA
1 CTTCAAATGAATTCC-ACTCAAAGCAGCTTGTGATAATTTCATAACTCAAATAACGAATAAACCA
1659133 TCAAA
65 TCAAA
1659138 ACTCCATCTA
Statistics
Matches: 66, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
71 3 0.05
72 63 0.95
ACGTcount: A:0.43, C:0.21, G:0.10, T:0.26
Consensus pattern (72 bp):
CTTCAAATGAATTCCACTCAAAGCAGCTTGTGATAATTTCATAACTCAAATAACGAATAAACCAT
CAAATCT
Found at i:1660227 original size:23 final size:23
Alignment explanation
Indices: 1660181--1660227 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
1660171 TTTCGAATTG
* ***
1660181 AAAATTTAAAAAATCTATCGATA
1 AAAAATTAAAAAATCTAAAAATA
1660204 AAAAATTAAAAAATCTAAAAATA
1 AAAAATTAAAAAATCTAAAAATA
1660227 A
1 A
1660228 CGATAATTAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.66, C:0.06, G:0.02, T:0.26
Consensus pattern (23 bp):
AAAAATTAAAAAATCTAAAAATA
Found at i:1673541 original size:243 final size:243
Alignment explanation
Indices: 1673114--1673605 Score: 941
Period size: 243 Copynumber: 2.0 Consensus size: 243
1673104 GTTAACTAAT
*
1673114 CACTTGCAATGTTATCCAAGTTGAGGTCAGCCTAATTTCAAATTGTAGCGTATCTCAAGCGTACA
1 CACTTGCAATGTTATCCAAGTTGAGGTCAGCCTAATTTCAAATTCTAGCGTATCTCAAGCGTACA
1673179 TACACATTTCTCAAGAAGATGAAAGTAATATGAGTACATAATTTCTATAGCAATTAACAGAGGAC
66 TACACATTTCTCAAGAAGATGAAAGTAATATGAGTACATAATTTCTATAGCAATTAACAGAGGAC
1673244 AAAGAAACAAGAAAATCAAACCCCCGGAAGCTGAAGTTATGGGAATCGGTCGCAAAGTTATCTAG
131 AAAGAAACAAGAAAATCAAACCCCCGGAAGCTGAAGTTATGGGAATCGGTCGCAAAGTTATCTAG
1673309 CATGAATCGGCTCGATTACAAATGCCGATGTGTCTGGAAGAATAAGC-
196 CATGAATCGGCTCGATTACAAATGCCGATGTGTCTGGAAGAATAAGCA
1673356 CACTTGCAATGTTATCCAAGTTGAGGTCAGCCTAATTTCAAATTCTAGCGTATCTCAAAGCGTAC
1 CACTTGCAATGTTATCCAAGTTGAGGTCAGCCTAATTTCAAATTCTAGCGTATCTC-AAGCGTAC
1673421 ATACACATTTCTCAAGAAGATGAAAGTAATATGAGTACATAATTTCTATAGCAATTAACAGAGGA
65 ATACACATTTCTCAAGAAGATGAAAGTAATATGAGTACATAATTTCTATAGCAATTAACAGAGGA
*
1673486 CAAAGAAACAAGAAGATCAAACCCCCGGAAGCTGAAGTTATGGGAATCGGTCGCAAAGTTATCTA
130 CAAAGAAACAAGAAAATCAAACCCCCGGAAGCTGAAGTTATGGGAATCGGTCGCAAAGTTATCTA
*
1673551 GCATGAATCGGCTCGATTACAAATGCCGATGTGTCTGGAAGCATAAGCA
195 GCATGAATCGGCTCGATTACAAATGCCGATGTGTCTGGAAGAATAAGCA
1673600 CACTTG
1 CACTTG
1673606 AATCATTTCT
Statistics
Matches: 245, Mismatches: 3, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
242 55 0.22
243 184 0.75
244 6 0.02
ACGTcount: A:0.36, C:0.19, G:0.20, T:0.25
Consensus pattern (243 bp):
CACTTGCAATGTTATCCAAGTTGAGGTCAGCCTAATTTCAAATTCTAGCGTATCTCAAGCGTACA
TACACATTTCTCAAGAAGATGAAAGTAATATGAGTACATAATTTCTATAGCAATTAACAGAGGAC
AAAGAAACAAGAAAATCAAACCCCCGGAAGCTGAAGTTATGGGAATCGGTCGCAAAGTTATCTAG
CATGAATCGGCTCGATTACAAATGCCGATGTGTCTGGAAGAATAAGCA
Found at i:1675129 original size:15 final size:15
Alignment explanation
Indices: 1675109--1675139 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1675099 AAATTTTGAT
*
1675109 AGTCTAGGTAATTAA
1 AGTCTAAGTAATTAA
1675124 AGTCTAAGTAATTAA
1 AGTCTAAGTAATTAA
1675139 A
1 A
1675140 TTATATAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.32
Consensus pattern (15 bp):
AGTCTAAGTAATTAA
Done.